Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_056991
Parameters: 2 7 7 80 10 50 500
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 500
Length: 267334
ACGTcount: A:0.28, C:0.23, G:0.22, T:0.28
Found at i:6182 original size:11 final size:11
Alignment explanation
Indices: 6166--6199 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
6156 AAGCCCCTCT
6166 TTTCTCGCCTA
1 TTTCTCGCCTA
6177 TTTCTCGCCTA
1 TTTCTCGCCTA
6188 TTTCTCGCCTA
1 TTTCTCGCCTA
6199 T
1 T
6200 AAGTAAGAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.09, C:0.35, G:0.09, T:0.47
Consensus pattern (11 bp):
TTTCTCGCCTA
Left flanking sequence: Indices 5666 -- 6165
TTTGAGGCTGACCGGCAACAGAAAGAGAGGCTCTTTTAATAGTGGGAAGGCCACTAGGACCTTCT
ACGTCATTTCTTTGAGAAAGAACGCAGAAAAGAGGCCGAAAAGGACGTCTATAGACAAGGATTTT
AGTCGATAGAGCCGTTCCTCCGCTGGAAGAATCGGGATCTCTCGCAGAGAAGAGACGATGGTATT
ATTCGAATATTTCTTCTTGTATTTCAAAGGGTCTGCGTAACAGAAGTAGTTTGGTAGAATACCAT
ATATGCTCTAAAAAGCAATCCGTATGATGAACGCCCAAGGTTGGTAAGTAAAAGAAGGATGAAAG
CTGCAAATAGGCTGGATAACTTATGCTACCAAATCTGTTTCTGTTGCTGAAAGACCGTCTGCTAC
CACTTCACTTATTAAGATGCTCTTGCTATTAAGAGAAGAGGACATCTCCTAACCGTGGTAATTGC
CGATGTGTTGATAATAGAGTAGTTGATGTAGCCCCAAGCCCCTCT
Right flanking sequence: Indices 6200 -- 6699
AAGTAAGAAATTAGGGGTGATAAAGAAAGAAAGGAAAGTGCACTCTCCTAGGAAGCCATTTGAGA
AAGTCCTACAGTCTCCTCTCCTTGAAGTCGAGGGAGTTGTCTCCTCTCTGCGTGAATCCCATTTC
TGATAAAGCGTGTACTGACGGAGTCGGCGAGCAGCACAAGAGGTTCTTTCTAAGTCGGAGTATCG
GGACTCGCACTCATTGAACTTCTTGCGCACAGGACAAGCATTCTCGCGCATACCCCCTATTCTTT
TAGTCAAGCTTGGAAGCCTATACTCTTTTCAAAAAGGAAAGCAGTAGACCTATATGAACTGAAGA
AAGATAGGGATGTCGCTAATCGCCTACTCGATTGACAGGCATAGCTTTTATAGCTGCTTTATCTG
CCTGAAGTCGGTTATTACTGGTTCCATGCTTGCTGCTCTGATTTAACATGCTCAAGGGTTCGAAC
AAGCCCCCCATCTCAAGTCAATTTCATACATGATGTCATTCGCTC
Found at i:83089 original size:30 final size:30
Alignment explanation
Indices: 83055--83123 Score: 120
Period size: 30 Copynumber: 2.3 Consensus size: 30
83045 CAGAATGGTT
83055 CCTACTACTAAAAACTAAGAAGGAATGCCG
1 CCTACTACTAAAAACTAAGAAGGAATGCCG
*
83085 CCTACTACTAAAAACTAAGAAGGGATGCCG
1 CCTACTACTAAAAACTAAGAAGGAATGCCG
*
83115 CTTACTACT
1 CCTACTACT
83124 CAAATCCCCG
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.39, C:0.25, G:0.16, T:0.20
Consensus pattern (30 bp):
CCTACTACTAAAAACTAAGAAGGAATGCCG
Left flanking sequence: Indices 82555 -- 83054
AGAGAACTTACAATAATACAACGTCGCATTCTCCGAAAATTGAGAAAGAAGAAAAGCTATATTAA
GAAAAAGATTTCTCCGAGAAAAAATCGTAACAGTTACATCCAATTACAAACTACACGAAAGTTGC
CCCTTTTTCATGGGAATTTACCCATCACAAAGATGCACAGAGGAACAAAACGAACTTCATATATC
CCTTTTCTACTCAATCCAGAAACAAGATTGGACGTTATTCCGGTTCGTCTCCATTTTTGTGAAAC
TATTCCTCAAGCAAGGCAGCCGATAAGTCATCGAAAAGTGTGTGTGAATAATGGAATAGTAAACA
TTACTCATTTTAAAGTTTCCCACGGTGATATAATATCTTTTCAAGAAAATTACGCGAGAACCCGC
GGTGAAGAAATAAGGAAATCTTTCTATATCAAAAAATCAGTTGAAAAAATAATAGGCAAATTCCT
GGGTCACCGGGTAAGAAGGGGGAGAAGAAGAAAAACAGAATGGTT
Right flanking sequence: Indices 83124 -- 83623
CAAATCCCCGTTTTTGCAAAAGTTACGTTCTTCTATGCAAGAAGAAGACTTAGAAAGAACAAAGA
AGTTTGGATCCGAAAAAGTATGCTTAGGCGGTTCCTTCGCGGAGCACAATAGAATGAAGAGGAAT
TTGTATCATTTCAAATCCTTATTCTTATCGAAGAAGAGAAGGAACGAGAAAAACCGAAATCTTCC
TACTCGAACAAGAAGTTCTATAGTTTACAACTCTTCTTTACCTACATATAGTAATTTGATCTATT
GCTCTGCATCCTCCCATCAGTTTAGTATTCAGAGAAGAATCAAAAGGATCGAACTACCTACTCAT
TATTCGGAGGTCAATCATAGAACACTAAAAGCTGTGGTATCTTATGGACCTAACATAGATCACAT
CCCTCACGACATAAGATTGAAAGATTCAAACCTTCCTCTTCGGAGCGGAAACGGACGTGGCCAAA
ACATATAAAGATCGGCGTAGTCGCTCATAGGGACATCTCTATCCG
Found at i:87251 original size:12 final size:12
Alignment explanation
Indices: 87234--87258 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
87224 CCTCTTTTCG
87234 TTAAATCATATA
1 TTAAATCATATA
87246 TTAAATCATATA
1 TTAAATCATATA
87258 T
1 T
87259 ATAGTAAGAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.48, C:0.08, G:0.00, T:0.44
Consensus pattern (12 bp):
TTAAATCATATA
Left flanking sequence: Indices 86734 -- 87233
AGTCTTCGATTCACCGAGTCGGAAGAGACCGGCAACGGGTATATATTATTATATAGAGTAAACCA
ACCACAGCAACGTACGAGTTACTATACGTATAACTAGACTAGGGTACTAGCTCTTGTACAACAGA
TATCATGGGACCAGACCTGCTTCTTTATATCCCTTCGTCCATTTTCCTGGTCAGGAAGACCTTTT
TCTACTCTTCCCGTGAGGAGGTAGATAGTTCTTCTTATCTAATCATGTGAGTTATAGCAGTCCTA
GGTAATTTATTTGTTGTCTCGGACAGAGAATCACCCTATTACAGGATCCTTCTTCGCGTACGCAC
TACCTTTTTAGCACTTCGCTTTCATGCACTAATGTGCTCCGGAGCCGTCTTGGAAGTTGGAAGTT
CCCGGATGACTAACTAGGTCCATTTCCCTCTCTCCCATTGAGTTGGGAGCATCTAAGATGTCAAG
TTGGACCAAAGCACTCGCAGCACACTGACTATAAACCTCTTTTCG
Right flanking sequence: Indices 87259 -- 87758
ATAGTAAGAAAGATGTCTTATTTAAGATTATCATGAACGGAAGAAGTTTCACCCTCTTTCATAGT
CTCTGGTAGCTCTAAAGGATAGGTTATTACCGTACTGCCTCAATCAGAACTTTAAGAATTACTTA
TTCTAGGCTTTCCCGAAAGCACATGAAACTGACTCAACGGGGAGTTAGCAGGAGTAACTGTTTAG
TAATATAGCTGTCATTGAGACCGCTCAAGAATCGGTTATTTTAAAATAGAAGGGCTTTTGTATGA
GGAAGGGGAAAGGTTGCTTCAATTAGCCTTTCGATTATAGTGAAATACCAACCCCCCGTTGCCTG
TTATGAATAGAACCAGGCTATGTCTGATTCCTTAATGAATCTGAGATGAGCTTGAGAAAGGCTTT
TCATAAATCTCTCATTAAAGAATGGGGTTCCCATACAAGAAAACAAGGGACGAGTCTGGTGAGAG
AGGTGAGTCTTCTCCTTTTTTCTTTTTCCATGCCTGCTGGAGAAA
Found at i:119315 original size:81 final size:81
Alignment explanation
Indices: 119216--119410 Score: 354
Period size: 81 Copynumber: 2.4 Consensus size: 81
119206 TCATTTCCTC
* *
119216 TCCTCTCCTTTCAGTCGAGTTACTGCGTGCCTCTAGCAAAGCTAGAGCGACTACGTCCCTCTCCT
1 TCCTCTCCTTTCAGTCGAGTGACTGCGTACCTCTAGCAAAGCTAGAGCGACTACGTCCCTCTCCT
119281 TATCAGTCGACACGAA
66 TATCAGTCGACACGAA
*
119297 TCCTCTCCTTTCAGTCGAGTGACTTCGTACCTCTAGCAAAGCTAGAGCGACTACGTCCCTCTCCT
1 TCCTCTCCTTTCAGTCGAGTGACTGCGTACCTCTAGCAAAGCTAGAGCGACTACGTCCCTCTCCT
119362 TATCAGTCGACACGAA
66 TATCAGTCGACACGAA
*
119378 TCCTCTCCTTTCAGTCGAGTGACTTCGTACCTC
1 TCCTCTCCTTTCAGTCGAGTGACTGCGTACCTC
119411 ACTCTCGTAT
Statistics
Matches: 111, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
81 111 1.00
ACGTcount: A:0.20, C:0.34, G:0.17, T:0.29
Consensus pattern (81 bp):
TCCTCTCCTTTCAGTCGAGTGACTGCGTACCTCTAGCAAAGCTAGAGCGACTACGTCCCTCTCCT
TATCAGTCGACACGAA
Left flanking sequence: Indices 118716 -- 119215
TCAATGTAGCAATGGCAATAGCATTATTTATAAAAAAAAATGTAAAACTTGAGACAAAAGCTTCC
TTGCAGCAACAGGAAATCCAGTAATGCACGAAGACTAAAAAAAGAAAAGATGATTAAAGCTTATT
GGCTAGAGCACCAGCTATTCGTCGAAGAAGGAATTTGCTTCTCCCTTTCTTGCAAAGAGCTCCAA
GCAGTAGCTAGCATGTTCACTTCGTGAACTCCAAGGCAAATAAGATAATAGATTCTCATTTTGCC
ACTCCTGGACATGGTCAAAGAGGGCTTTCGGTTGAGACTATTGATCTGATATGGCAAAGCCCTTT
CCAAAAGGGCAGGTAGGGTCCCAGTCACTCGACTTGGAAGAATAATTATCCTAAGAAGAAAGCAA
CTTCGGGACTTTCTGTCTCAAGCACAGGCATACGATTTCAAGAAGGTTTCTCAGTAACTATTAGC
AAAAAAATTCCAAAACCCTCTCCTTTTACTGAATTTCATTTCCTC
Right flanking sequence: Indices 119411 -- 119910
ACTCTCGTATAGGTGAACTTGGTTCTTAGGGAGAAGAAGGATCCACTGGGAATGAATGGGCAGAC
GGAAGTAGTATCTTCATTAGCCGGAAGGAATTCGTCTCCACTAGCGTCATTCGAAGAATGAACAA
GAAAAGGCTTACTGTTTAGGTAGGATAGATGGATATGGTCCAATGGCAGGGCTAAAGCTCTGCCA
GCTTCTTGTAGACTGAACTTTCTTTAGGCTCCGAGTTGTTTTTGGGTAAGATGGTTGAATTTTTC
TTCGCCACTAGTGGCAACGAAGTTCAAGGAAGGAAGATCTCCACTCATTTCATTCAGTGCCTGCG
GTAAGGCAAGGCGCGACCCACAACAAAGGAAGGGGGAAAGCTTGCTTGCTGTAGCCCTATTTTAG
TAGACTAGGCTTAGTAAGCGTAAGCTATTTATTTAAGTAGGCTCGCAGCTTCGCCAGAAGCGACG
AAGGGGGGGCTGGGGAAGAAGGCCGACGACTACATAAGAGGGAGT
Found at i:125942 original size:65 final size:65
Alignment explanation
Indices: 125861--126033 Score: 346
Period size: 65 Copynumber: 2.7 Consensus size: 65
125851 TAACTTATTA
125861 AGGTACGAAGTAACTCGACTGAAAGGAGAGGAGAGGGCAAGACGTAGTCGCTCTAGCAAAGCTAG
1 AGGTACGAAGTAACTCGACTGAAAGGAGAGGAGAGGGCAAGACGTAGTCGCTCTAGCAAAGCTAG
125926 AGGTACGAAGTAACTCGACTGAAAGGAGAGGAGAGGGCAAGACGTAGTCGCTCTAGCAAAGCTAG
1 AGGTACGAAGTAACTCGACTGAAAGGAGAGGAGAGGGCAAGACGTAGTCGCTCTAGCAAAGCTAG
125991 AGGTACGAAGTAACTCGACTGAAAGGAGAGGAGAGGGCAAGAC
1 AGGTACGAAGTAACTCGACTGAAAGGAGAGGAGAGGGCAAGAC
126034 AATGAAATGA
Statistics
Matches: 108, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
65 108 1.00
ACGTcount: A:0.36, C:0.16, G:0.35, T:0.13
Consensus pattern (65 bp):
AGGTACGAAGTAACTCGACTGAAAGGAGAGGAGAGGGCAAGACGTAGTCGCTCTAGCAAAGCTAG
Left flanking sequence: Indices 125361 -- 125860
CAGCTGTTAGTTAGTACCCTCTTGGTTTCGGAGTGGACCCTTTCACTCTATTTTATTATATACGT
TTAGTGAAAAGAATGTTTTTTGATACACCTAGGACATGGATTCTATATGAACCAATGGATCGTGA
CAAGTCGTTACTACTAGCAATGACTTCCTCTTTCATTACTTCATCCTTTCCATATCCTTCTCCCT
TGTTCTCAGTTACTCATCAAATGGCACTCAGTTTATATCTTTAAGTTCGATCATTGACAAGGTTC
AAAGAAAGGGTGGGCCATTGATAAAGAATCGATTCCAAACCACAATGCTAGCAGATGGTGGGCCT
CCGCTTTTCTTTTCATTAATGAAACCTGCCATGCCAGTTATTATGGACTCAAATCATAAGGACAA
AAAATGAGCTGTTCAAAAGAAAAAAAAGACGTGGATGGCATTATGACTGGGGTGTCAGTTAGAAA
GATTCTTACAATGTTCGTTCAATCAAGCAACATCTTAACTTATTA
Right flanking sequence: Indices 126034 -- 126533
AATGAAATGAAATAAAGTCATTGATAAATAAAGCGTTGATAAATGAAGGAGAGATTTTCTATTTT
TTGGGAACGAAAGGAAGTTTAGGGCCCTTCTGAATAAGGAGGCTGAGTCCTATCGAATTTCCTGC
ATTACCCGGCCTTCTTGGACCACCATAGCAGTGGCAACGGGATGGATCGTTTCCGTTAGAGTTAG
GTACTCTTGAGTCTAGTAAGTCCGGTTGTGAGCGGTGTGAACCATAGAAGTCCACCCTAGGTGTT
TAAGAACAGCTTACCTGTTAGCAGCCGCCCTATTGATTGAGAGAACACAGATTTAAGACATTTGA
TTAAAGATTCAACCTAATTAAAAGCCTACGATCTTGGTTTTCGTGCAGATGAAGGTTTCTTTCTG
GTTGGAGAGTGGAGAAGACCCACAAGAGTTCGATCAAGAGCAAGAAGCCAGGAATTGTACGACCA
AACAATCAACGTCATTGGAGACGAGGTTTGGAACCCTACTCAATA
Found at i:126074 original size:15 final size:16
Alignment explanation
Indices: 126043--126077 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
126033 CAATGAAATG
126043 AAATAAAGTCATTGAT
1 AAATAAAGTCATTGAT
*
126059 AAATAAAG-CGTTGAT
1 AAATAAAGTCATTGAT
126074 AAAT
1 AAAT
126078 GAAGGAGAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 10 0.56
16 8 0.44
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.29
Consensus pattern (16 bp):
AAATAAAGTCATTGAT
Left flanking sequence: Indices 125543 -- 126042
TATCCTTCTCCCTTGTTCTCAGTTACTCATCAAATGGCACTCAGTTTATATCTTTAAGTTCGATC
ATTGACAAGGTTCAAAGAAAGGGTGGGCCATTGATAAAGAATCGATTCCAAACCACAATGCTAGC
AGATGGTGGGCCTCCGCTTTTCTTTTCATTAATGAAACCTGCCATGCCAGTTATTATGGACTCAA
ATCATAAGGACAAAAAATGAGCTGTTCAAAAGAAAAAAAAGACGTGGATGGCATTATGACTGGGG
TGTCAGTTAGAAAGATTCTTACAATGTTCGTTCAATCAAGCAACATCTTAACTTATTAAGGTACG
AAGTAACTCGACTGAAAGGAGAGGAGAGGGCAAGACGTAGTCGCTCTAGCAAAGCTAGAGGTACG
AAGTAACTCGACTGAAAGGAGAGGAGAGGGCAAGACGTAGTCGCTCTAGCAAAGCTAGAGGTACG
AAGTAACTCGACTGAAAGGAGAGGAGAGGGCAAGACAATGAAATG
Right flanking sequence: Indices 126078 -- 126577
GAAGGAGAGATTTTCTATTTTTTGGGAACGAAAGGAAGTTTAGGGCCCTTCTGAATAAGGAGGCT
GAGTCCTATCGAATTTCCTGCATTACCCGGCCTTCTTGGACCACCATAGCAGTGGCAACGGGATG
GATCGTTTCCGTTAGAGTTAGGTACTCTTGAGTCTAGTAAGTCCGGTTGTGAGCGGTGTGAACCA
TAGAAGTCCACCCTAGGTGTTTAAGAACAGCTTACCTGTTAGCAGCCGCCCTATTGATTGAGAGA
ACACAGATTTAAGACATTTGATTAAAGATTCAACCTAATTAAAAGCCTACGATCTTGGTTTTCGT
GCAGATGAAGGTTTCTTTCTGGTTGGAGAGTGGAGAAGACCCACAAGAGTTCGATCAAGAGCAAG
AAGCCAGGAATTGTACGACCAAACAATCAACGTCATTGGAGACGAGGTTTGGAACCCTACTCAAT
ACTCACCCGGTGTCTTTAGAGCACCCGAATGAAAGAGTAGATGAG
Found at i:159323 original size:18 final size:18
Alignment explanation
Indices: 159300--159342 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
159290 CGCCCTTGTT
159300 GACTATGACAACAG-TCGC
1 GACTATGA-AACAGATCGC
159318 GACTAT-AAACAGACTCGC
1 GACTATGAAACAGA-TCGC
159336 GACTATG
1 GACTATG
159343 GTAGGTTCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.23
17 1 0.05
18 16 0.73
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.19
Consensus pattern (18 bp):
GACTATGAAACAGATCGC
Left flanking sequence: Indices 158800 -- 159299
CGTCTAGCCGTTGGTACTCCGCATCTTCACGGAGAATTCAATTTCACCGGGTCCATGTCGGAGAC
AGCGGGGCAGTCGTTACACCATTCGTGCAGGTCGCTACTTATGCGACAAGGAATTTCGCTACCTT
AGGACAGTTAGAGTTACTGCCGCCGTTTACTGGGGCTTCCATTCAAAGCTTATAACACTTTTCCT
TCCGACCTTCCAGCACCGGGCAGGTGTCAGACTCTATACATCGTGTTACCACTTAGCAGAGTCCT
GTGTTTTTAATAAACAGTCGCTACCCCCTGGTATGTGCCGCTTTCCTAATCAAAAGATAGGAGAG
CACCCCTTCTCCCGAAGTTACGGGGTCATTTTGCCGAGTTCCTTCGACATGGTTCTCTCAAGCGC
CCTAGTATACTCTACTTGTTCACCTGTGTCGGTTTGGGGTACGGTCAGTTCACCGGGAGGATCGC
CCTCCCAATTCGAAGTTTTTTCCTGGAAGCCTAAACGCCCTTGTT
Right flanking sequence: Indices 159343 -- 159842
GTAGGTTCTGCAAGGCTTTGATGACTCAAGGTTCATATTAGGGAAAGGAGAGTGAGGGGAAGAGG
CGACGAGAGTCGGCCCGATCATCCAATTCGCTCCAACAGACAGGCATGGTTCTGTAGTCAAAGCA
ACTTCGTCACTTTCGTGTACCCATCGGACGGCAGCCCTTTCGGGGGTTCCTTAGGGACCGATTCA
CTCTGCGTAGATTGACTGAACGCAGAAAGCCTTCCACTGGCAGGCGATCGTGTTTTTCACAGGAT
TTATCGTTACTCATGTCAGCATTCTCACTTCTGATATCTCCAGGTCTTGTCACCAAAAACCTTCC
CCGATTGACAGAACGTCCCGCTACTGACACTTGAAAAAGCAGCTTTCAAGGTCTCGTCGCTTCGG
TGAATCACTTGAGCCCTGATACATTTTCGGTGCCATGGAGCTAGACCAGTGAGCTATTACGCTTT
CTTCAAAGGATGGCTGCTTCCAAGCCCACCTCCTGGTTGTCATCG
Found at i:160820 original size:23 final size:23
Alignment explanation
Indices: 160791--160867 Score: 68
Period size: 23 Copynumber: 3.1 Consensus size: 23
160781 CACTTTGCTG
160791 AGGTACGAAGTGACTCGACTGAA
1 AGGTACGAAGTGACTCGACTGAA
160814 AGGTACGAAGTCG-CTTTAGCGAAGCT-AA
1 AGGTACGAAGT-GAC--T--CG-A-CTGAA
*
160842 AGGTACGAAGTAACTCGACTGAA
1 AGGTACGAAGTGACTCGACTGAA
160865 AGG
1 AGG
160868 AGAGGAGAGG
Statistics
Matches: 44, Mismatches: 1, Indels: 18
0.70 0.02 0.29
Matches are distributed among these distances:
22 2 0.05
23 18 0.41
24 3 0.07
25 1 0.02
26 1 0.02
27 2 0.05
28 15 0.34
29 2 0.05
ACGTcount: A:0.35, C:0.17, G:0.30, T:0.18
Consensus pattern (23 bp):
AGGTACGAAGTGACTCGACTGAA
Left flanking sequence: Indices 160291 -- 160790
CCATTTCCTCGCTGACCCATCATGCAAAAGGTACGCCGTTAGAGTGAGTGCGCTTTACTAATAGA
ATTCAAAGTAAAGGCTCTAAGCTCCGCTCCTTCGACTGATTGTTCGCATCGGATCTCAGGTTCTC
TATTGCACTCCCTAAATAGGGTTCTTTTCACCTTTCCCTCACGGTACTTGTACGCTATCGGTCAT
TGAGGAATACTTAGGCTTAGAGGGTGGTCCCCCTTTCTCGCGTAAAAGCGATCAGAATTCGAACA
CGCCGCGTTTTACTGGGAAGGATCGAACCATGGGAACGAATCTACAGGGCTATCACCTTCTTTGG
CCAGATCTTCCAACCTTTTCACAATTACAGTCCCCTGCGCCCTGGAGCCTAAGAAATAGGCGTAA
GTGGCTTGAAAGCTTACTAAGCTTTTCCGCCGTAGCTTGCTGGTTTTTCCATCATCCAATCCACA
ACAAATCGAATGAAACCTGGCGAAAAAGAAGTGAACACTTTGCTG
Right flanking sequence: Indices 160868 -- 161367
AGAGGAGAGGAAATGAAATGAAATTCAGTCATTGATAAATAATATGTATTCGTGTTTGTTTTTCT
TCAAACCCCCAATCCGCTCTCGCTCGCCGCTACTAACGGGGTCTCGGTTGATTTCCCTTCCTTTA
GCTACTCAGATGTTTCAGTTCGCTAAGTTTGAAAAGTCCAAAGAGCGCAGACTAGCCACGGAGCT
TGGATACGGTTTCCCGATCGGAGATCCATGGATCACAGACGGTATCTCCCCATGGCCTTTCGCCT
CTGAAAGCGTCCTTCCTTCTCAATGCCCGGGCATCCATCCAATGCATTCTTTTCGATCTTGTACG
AAAGTACACTGAACACCAACCCAATCTCGACGAAAAAAAGAAAAGCGTTATCGGAGCAAGAAAAC
GGCTTAAGTGACTAACGCACAACGGCTTTCGCGCTAGCGCGCTTACCCGTTGCTTGTTGACTTAA
GCCAAAAAAAAAGAGAATCGGACACAAAAACAAAAAAAAGGAAAT
Found at i:162154 original size:28 final size:28
Alignment explanation
Indices: 162114--162179 Score: 123
Period size: 28 Copynumber: 2.4 Consensus size: 28
162104 TTTTCGTGTA
*
162114 AAAGGAAAGGTACGAAGTGACTCGACTG
1 AAAGGAGAGGTACGAAGTGACTCGACTG
162142 AAAGGAGAGGTACGAAGTGACTCGACTG
1 AAAGGAGAGGTACGAAGTGACTCGACTG
162170 AAAGGAGAGG
1 AAAGGAGAGG
162180 AGAGAAATTG
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.39, C:0.12, G:0.36, T:0.12
Consensus pattern (28 bp):
AAAGGAGAGGTACGAAGTGACTCGACTG
Left flanking sequence: Indices 161614 -- 162113
GGATCAGGTCCCCCCTGAGACGATGCATCTCTTCTTCCTGGCGACGAAGAAATTCTTCGTCTTCC
TGGTCTCGGCCCTCCTCTGACCCATCCGCATCGGGCTGGTTCAGATCGGCTGGCGCATCGCCGGA
AGCGTAGGACGGATCGGCCATAGAAATAATAAGGGACGAAAAAAGTGGAGGTAAGCCCCAGCCTA
GGCGCCTAAAGAAGACGCTTATTCCGGAGCCCACTATCATAAATAGGAGTCGTCGGAAAATGCGA
GAAAAATCCAACTGATAGTGGGCACATACCCAATAAGAAATGGTAAGAATGAAAACGAAAATAAA
AAGCAGGACCAAGATTCTGTTCGCGCGGTCGCCCTCACTGAACCGACTTGAATCTGAACTACGAT
TCAGACCAAGCCTTACCGAAATCGGATTTCCTTTTCGCACCATATACGCTTAGACTTGACTTTGT
CCCCCTTTTTCTTCCCTGTCCAATATTTTTCTTCGTTTTCGTGTA
Right flanking sequence: Indices 162180 -- 162679
AGAGAAATTGTTGACCAACTTGTCCTCTTTCCATCTTTTCTTTCCCCAAAAGGTCCATACTATAG
AAAATAAGGCTCGGCAAAGACGAGACCTAGGGACATAAAGTTCCTTACCACTCCGTGGGCTTAGG
CTCGGGGGTCAGGTAAATTGGGATTCGGCCACTGATCGAAGCAGATGTACCACTGAAGCTTCGAA
CAATCTAGATAATATACGATTATATTAGCGAGCTGATTGAAAGGAAGATAGGACGAATTCTATCC
AGGGAATCAAAAGACTAAGGCGACCTTCACATGAGAAAAAGACACTCACGATTAGGATTGGATTT
GGTGACTGCTCTATCTATAGTTAGGGATGAGCTGACGACCATGCTACACACGTAGGTCTGCTTTG
AGAATGACCTACTGAGCCCGCCTTGAGTCTAATTCCCCTTCAGGTTGGAGAAAGTACGACGTGTG
TCTCGATCTTGACAACTGAATCACAGCCGGACGCTATATTCATCC
Found at i:172532 original size:23 final size:23
Alignment explanation
Indices: 172459--172535 Score: 68
Period size: 23 Copynumber: 3.1 Consensus size: 23
172449 CCTCTCCTCT
*
172459 CCTTTCAGTCGAGTTACTTCGTA
1 CCTTTCAGTCGAGTCACTTCGTA
172482 CCTTT-AGCTTCGCTAAAG-CGACTTCGTA
1 CCTTTCAG--TCG----AGTC-ACTTCGTA
172510 CCTTTCAGTCGAGTCACTTCGTA
1 CCTTTCAGTCGAGTCACTTCGTA
172533 CCT
1 CCT
172536 CTACTTCAAT
Statistics
Matches: 44, Mismatches: 1, Indels: 18
0.70 0.02 0.29
Matches are distributed among these distances:
22 2 0.05
23 18 0.41
24 4 0.09
27 3 0.07
28 15 0.34
29 2 0.05
ACGTcount: A:0.18, C:0.30, G:0.17, T:0.35
Consensus pattern (23 bp):
CCTTTCAGTCGAGTCACTTCGTA
Left flanking sequence: Indices 171959 -- 172458
AGCAAGACGAGGTCGCTCTGCTTTGTAGACAAGGCTCGTTCCGTACTTGACTTACGAGCTCGTCT
AGTACTCGCCTCTATCTCTAAAGGAAGGGGCTTATGCACTCTACTTGCTGTCTACTAAACGAGCG
TTAGAGCGAAGCCTTCTTAGTGGCTTCTCTTCTTTTTCCTCACCCTATTCTTTCATTTCCGCTTA
AGCTTCTCCGGTTTGGGGGATTAATTGATTAGATACCCGAGAACCATAATCTTTCCTAGAAACAG
CTTCTACGACGATAGATAGGGGTCAGGTTTGTTTGGCATCTATGCCTCCTGCCCTCCAAACAGTA
TGGGAGCCTTTCAGCTCGTACTGCTCACACTCCTAGATCTTCACGGCACCTCCCCCACCCTGTGA
AACAAAAGTGTATATACATCCAGAAGGCTGGTTATGACCTTTATTTATCTTTCTCTCCTAAAGCT
TCGCTAAAGCGACTACGTCACTTTCTTTCACGAATCCTCTCCTCT
Right flanking sequence: Indices 172536 -- 173035
CTACTTCAATGAAAGCTAGCTCCTACTCCTTCTCCTCCTGAATCCTCGTTGGTCTTTCGTTCGTA
GTGCGAATTCTATAGTGAGAAAGCTCACCCCTGCCTTTAGACGAGAAAGCCCTCTTTTACATCCT
CTAGACAAATCAATAGAAAATGCTACAACCCATTGTTGTTCTTTTGACGATGAACCACTCCAGTA
CAACAGGCTAAAGTAAGCTCTATGCTTCGTCCCCGGTGCGTAGGGCCGATCCCCGTGTGCTGGAG
GGACGACCAGAAAGTGTGTGTTAAGCATATTCAAACAAAAGAAGCAAAAAAGGGAGATATTTATA
CGAAAGAGGCAAGGGCTTTCGCCTTCGAATTGAGTAGTTTTTTTTCTTTCTACTCGAAAGAAACT
TTAATCGAAAGTAGACTCAAGCCTTACCCCCTTATTATATATATATGTGTATGTGATTTAGTTCG
AAATAATGGACTGATCTTTCTCCGCTTTAAATTAAAGAAGGTCTA
Found at i:180255 original size:28 final size:28
Alignment explanation
Indices: 180215--180362 Score: 227
Period size: 28 Copynumber: 5.5 Consensus size: 28
180205 GACTCGACTG
180215 AAAGGTACGAAGTCGCTTTAGCGAAGCT
1 AAAGGTACGAAGTCGCTTTAGCGAAGCT
180243 AAAGGTACGAAGTCGCTTTAGCGAAGCT
1 AAAGGTACGAAGTCGCTTTAGCGAAGCT
180271 AAAGGTACGAAGTCGCTTTAGCGAAGCT
1 AAAGGTACGAAGTCGCTTTAGCGAAGCT
**
180299 AAAGGTACGAAGTAAC--T--CG-A-CT
1 AAAGGTACGAAGTCGCTTTAGCGAAGCT
180321 GAAAGGTACGAAGTCGCTTTAGCGAAGCT
1 -AAAGGTACGAAGTCGCTTTAGCGAAGCT
180350 AAAGGTACGAAGT
1 AAAGGTACGAAGT
180363 AACTCGACTG
Statistics
Matches: 109, Mismatches: 4, Indels: 14
0.86 0.03 0.11
Matches are distributed among these distances:
22 2 0.02
23 15 0.14
24 2 0.02
25 1 0.01
26 1 0.01
27 2 0.02
28 84 0.77
29 2 0.02
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.20
Consensus pattern (28 bp):
AAAGGTACGAAGTCGCTTTAGCGAAGCT
Left flanking sequence: Indices 179715 -- 180214
TCTTTGCTCCGGGAAATCAAATTCCTTGCTTCTTGAGCTGGTACAAGAACTAAAGCAAAAAGGAG
TTCACCTGATTAAGACGATAGGGCTATGCTGGAAATGAACCCCCTCGCTCTCAGTTACTCCCTCT
GCTCCGTCCCTTTCACCGAAGGAAGGTGCTTTTCTAGCGTGAAGTGAGACAGCAATGCCCGGTAA
AAGCATGAATAGAAGAATAGCAAGAGCAATTCGTACTCTTACAGTTTACCCGGAGCACTTGCTAA
CACACTAGTATGGAATGGAAAGAGCGGATTCAAGCTTTGAGAAGAAGAATCAATCACCAATGCTT
CTAGACCCCACACTCGAGATAGGACTTCTCCGACCTCCATGGTTACCGGCTTCGGGGAAGACAAG
TCAACTCAAGAATACACTGCTTTGACATCCTCAAGTGACAAATAAAGGGGAGGAACTGAACTACC
TTTAGAGAGGAAAAAGAAAGAATGAGGTACGAAGTGACTCGACTG
Right flanking sequence: Indices 180363 -- 180862
AACTCGACTGAAAGGAGAGGATTCGTGTCGACTGATAAGGAGAGGGACGTAGTCGCTCTAGCTTT
GCTAGAGGCACGCAGTAACTCGACTGAAAGGAGAGGAGAGGAAATGAAATAAAGTCATTGATAAA
TAAAGCATTGATAATGTACATGTAAAAACGATTTCTCCTTTCTTTTCTACGCTATGATCTTTCTT
CTCTTATTCCATTTCTAGTTTGATCGAGGACAGTACACTTCTCCCCAATACAATATGAGATAGGT
TGCAGCTATAGGAAGAACTCCAAACTAGTAATCCAGCATCTATTAAATATCTTTAAATTATGGAA
TGGATTAAAGTAAGAGTTACCACAAATATTTCATCTTTCATAGTCAACTCTCTAGTAGCGTTAAG
AAGTCACTCTTCCGATACGAATACTGGTATATATAAATCAACGCTCTTTTCCTTTAGCTCTTACA
CTAAACTAAGTAGAGTCTATATCACCGTAGATGCTGAGATAGAAA
Found at i:180281 original size:56 final size:51
Alignment explanation
Indices: 180194--180377 Score: 280
Period size: 51 Copynumber: 3.5 Consensus size: 51
180184 AGAAAGAATG
*
180194 AGGTACGAAGTGACTCGACTGAAAGGTACGAAGTCGCTTTAGCGAAGCTAA
1 AGGTACGAAGTAACTCGACTGAAAGGTACGAAGTCGCTTTAGCGAAGCTAA
**
180245 AGGTACGAAGTCGCTTTAGCGAAGCT-AAAGGTACGAAGTCGCTTTAGCGAAGCTAA
1 AGGTACGAAGTAAC--T--CG-A-CTGAAAGGTACGAAGTCGCTTTAGCGAAGCTAA
180301 AGGTACGAAGTAACTCGACTGAAAGGTACGAAGTCGCTTTAGCGAAGCTAA
1 AGGTACGAAGTAACTCGACTGAAAGGTACGAAGTCGCTTTAGCGAAGCTAA
180352 AGGTACGAAGTAACTCGACTGAAAGG
1 AGGTACGAAGTAACTCGACTGAAAGG
180378 AGAGGATTCG
Statistics
Matches: 122, Mismatches: 4, Indels: 14
0.87 0.03 0.10
Matches are distributed among these distances:
50 2 0.02
51 69 0.57
52 2 0.02
53 1 0.01
54 1 0.01
55 2 0.02
56 43 0.35
57 2 0.02
ACGTcount: A:0.34, C:0.17, G:0.29, T:0.20
Consensus pattern (51 bp):
AGGTACGAAGTAACTCGACTGAAAGGTACGAAGTCGCTTTAGCGAAGCTAA
Left flanking sequence: Indices 179694 -- 180193
CAAGCAAGAAAGCAAAATCAGTCTTTGCTCCGGGAAATCAAATTCCTTGCTTCTTGAGCTGGTAC
AAGAACTAAAGCAAAAAGGAGTTCACCTGATTAAGACGATAGGGCTATGCTGGAAATGAACCCCC
TCGCTCTCAGTTACTCCCTCTGCTCCGTCCCTTTCACCGAAGGAAGGTGCTTTTCTAGCGTGAAG
TGAGACAGCAATGCCCGGTAAAAGCATGAATAGAAGAATAGCAAGAGCAATTCGTACTCTTACAG
TTTACCCGGAGCACTTGCTAACACACTAGTATGGAATGGAAAGAGCGGATTCAAGCTTTGAGAAG
AAGAATCAATCACCAATGCTTCTAGACCCCACACTCGAGATAGGACTTCTCCGACCTCCATGGTT
ACCGGCTTCGGGGAAGACAAGTCAACTCAAGAATACACTGCTTTGACATCCTCAAGTGACAAATA
AAGGGGAGGAACTGAACTACCTTTAGAGAGGAAAAAGAAAGAATG
Right flanking sequence: Indices 180378 -- 180877
AGAGGATTCGTGTCGACTGATAAGGAGAGGGACGTAGTCGCTCTAGCTTTGCTAGAGGCACGCAG
TAACTCGACTGAAAGGAGAGGAGAGGAAATGAAATAAAGTCATTGATAAATAAAGCATTGATAAT
GTACATGTAAAAACGATTTCTCCTTTCTTTTCTACGCTATGATCTTTCTTCTCTTATTCCATTTC
TAGTTTGATCGAGGACAGTACACTTCTCCCCAATACAATATGAGATAGGTTGCAGCTATAGGAAG
AACTCCAAACTAGTAATCCAGCATCTATTAAATATCTTTAAATTATGGAATGGATTAAAGTAAGA
GTTACCACAAATATTTCATCTTTCATAGTCAACTCTCTAGTAGCGTTAAGAAGTCACTCTTCCGA
TACGAATACTGGTATATATAAATCAACGCTCTTTTCCTTTAGCTCTTACACTAAACTAAGTAGAG
TCTATATCACCGTAGATGCTGAGATAGAAAGCTTTCACTTAGCCC
Found at i:180329 original size:23 final size:23
Alignment explanation
Indices: 180299--180377 Score: 79
Period size: 23 Copynumber: 3.2 Consensus size: 23
180289 TAGCGAAGCT
180299 AAAGGTACGAAGTAACTCGACTG
1 AAAGGTACGAAGTAACTCGACTG
**
180322 AAAGGTACGAAGTCGCTTTAGCGAAGCT-
1 AAAGGTACGAAGTAAC--T--CG-A-CTG
180350 AAAGGTACGAAGTAACTCGACTG
1 AAAGGTACGAAGTAACTCGACTG
180373 AAAGG
1 AAAGG
180378 AGAGGATTCG
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
22 2 0.04
23 20 0.44
24 2 0.04
25 1 0.02
26 1 0.02
27 2 0.04
28 15 0.33
29 2 0.04
ACGTcount: A:0.38, C:0.16, G:0.28, T:0.18
Consensus pattern (23 bp):
AAAGGTACGAAGTAACTCGACTG
Left flanking sequence: Indices 179799 -- 180298
AGGGCTATGCTGGAAATGAACCCCCTCGCTCTCAGTTACTCCCTCTGCTCCGTCCCTTTCACCGA
AGGAAGGTGCTTTTCTAGCGTGAAGTGAGACAGCAATGCCCGGTAAAAGCATGAATAGAAGAATA
GCAAGAGCAATTCGTACTCTTACAGTTTACCCGGAGCACTTGCTAACACACTAGTATGGAATGGA
AAGAGCGGATTCAAGCTTTGAGAAGAAGAATCAATCACCAATGCTTCTAGACCCCACACTCGAGA
TAGGACTTCTCCGACCTCCATGGTTACCGGCTTCGGGGAAGACAAGTCAACTCAAGAATACACTG
CTTTGACATCCTCAAGTGACAAATAAAGGGGAGGAACTGAACTACCTTTAGAGAGGAAAAAGAAA
GAATGAGGTACGAAGTGACTCGACTGAAAGGTACGAAGTCGCTTTAGCGAAGCTAAAGGTACGAA
GTCGCTTTAGCGAAGCTAAAGGTACGAAGTCGCTTTAGCGAAGCT
Right flanking sequence: Indices 180378 -- 180877
AGAGGATTCGTGTCGACTGATAAGGAGAGGGACGTAGTCGCTCTAGCTTTGCTAGAGGCACGCAG
TAACTCGACTGAAAGGAGAGGAGAGGAAATGAAATAAAGTCATTGATAAATAAAGCATTGATAAT
GTACATGTAAAAACGATTTCTCCTTTCTTTTCTACGCTATGATCTTTCTTCTCTTATTCCATTTC
TAGTTTGATCGAGGACAGTACACTTCTCCCCAATACAATATGAGATAGGTTGCAGCTATAGGAAG
AACTCCAAACTAGTAATCCAGCATCTATTAAATATCTTTAAATTATGGAATGGATTAAAGTAAGA
GTTACCACAAATATTTCATCTTTCATAGTCAACTCTCTAGTAGCGTTAAGAAGTCACTCTTCCGA
TACGAATACTGGTATATATAAATCAACGCTCTTTTCCTTTAGCTCTTACACTAAACTAAGTAGAG
TCTATATCACCGTAGATGCTGAGATAGAAAGCTTTCACTTAGCCC
Found at i:180503 original size:15 final size:16
Alignment explanation
Indices: 180474--180506 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
180464 AGAGGAAATG
180474 AAATAAAGTCATTGAT
1 AAATAAAGTCATTGAT
180490 AAATAAAG-CATTGAT
1 AAATAAAGTCATTGAT
180505 AA
1 AA
180507 TGTACATGTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.55, C:0.06, G:0.12, T:0.27
Consensus pattern (16 bp):
AAATAAAGTCATTGAT
Left flanking sequence: Indices 179974 -- 180473
ACACACTAGTATGGAATGGAAAGAGCGGATTCAAGCTTTGAGAAGAAGAATCAATCACCAATGCT
TCTAGACCCCACACTCGAGATAGGACTTCTCCGACCTCCATGGTTACCGGCTTCGGGGAAGACAA
GTCAACTCAAGAATACACTGCTTTGACATCCTCAAGTGACAAATAAAGGGGAGGAACTGAACTAC
CTTTAGAGAGGAAAAAGAAAGAATGAGGTACGAAGTGACTCGACTGAAAGGTACGAAGTCGCTTT
AGCGAAGCTAAAGGTACGAAGTCGCTTTAGCGAAGCTAAAGGTACGAAGTCGCTTTAGCGAAGCT
AAAGGTACGAAGTAACTCGACTGAAAGGTACGAAGTCGCTTTAGCGAAGCTAAAGGTACGAAGTA
ACTCGACTGAAAGGAGAGGATTCGTGTCGACTGATAAGGAGAGGGACGTAGTCGCTCTAGCTTTG
CTAGAGGCACGCAGTAACTCGACTGAAAGGAGAGGAGAGGAAATG
Right flanking sequence: Indices 180507 -- 181006
TGTACATGTAAAAACGATTTCTCCTTTCTTTTCTACGCTATGATCTTTCTTCTCTTATTCCATTT
CTAGTTTGATCGAGGACAGTACACTTCTCCCCAATACAATATGAGATAGGTTGCAGCTATAGGAA
GAACTCCAAACTAGTAATCCAGCATCTATTAAATATCTTTAAATTATGGAATGGATTAAAGTAAG
AGTTACCACAAATATTTCATCTTTCATAGTCAACTCTCTAGTAGCGTTAAGAAGTCACTCTTCCG
ATACGAATACTGGTATATATAAATCAACGCTCTTTTCCTTTAGCTCTTACACTAAACTAAGTAGA
GTCTATATCACCGTAGATGCTGAGATAGAAAGCTTTCACTTAGCCCTCGGGCTGTGAACCATTGT
CACTTGTATGGATGTATGTACCTCCGCGCCTAGAAGAGAGCTTTCACTGGGGATTAAAACAAGAG
GGGGGTACCAGGGGGTGATATTGGCATTTATTCCCCAAGGAGAAA
Found at i:199903 original size:18 final size:18
Alignment explanation
Indices: 199880--199922 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
199870 CGCCCTTGTT
199880 GACTATGACAACAG-TCGC
1 GACTATGA-AACAGATCGC
199898 GACTAT-AAACAGACTCGC
1 GACTATGAAACAGA-TCGC
199916 GACTATG
1 GACTATG
199923 GTAGGTTCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
16 5 0.23
17 1 0.05
18 16 0.73
ACGTcount: A:0.35, C:0.26, G:0.21, T:0.19
Consensus pattern (18 bp):
GACTATGAAACAGATCGC
Left flanking sequence: Indices 199380 -- 199879
CGTCTAGCCGTTGGTACTCCGCATCTTCACGGAGAATTCAATTTCACCGGGTCCATGTCGGAGAC
AGCGGGGCAGTCGTTACACCATTCGTGCAGGTCGCTACTTATGCGACAAGGAATTTCGCTACCTT
AGGACAGTTAGAGTTACTGCCGCCGTTTACTGGGGCTTCCATTCAAAGCTTATAACACTTTTCCT
TCCGACCTTCCAGCACCGGGCAGGTGTCAGACTCTATACATCGTGTTACCACTTAGCAGAGTCCT
GTGTTTTTAATAAACAGTCGCTACCCCCTGGTATGTGCCGCTTTCCTAATCAAAAGATAGGAGAG
CACCCCTTCTCCCGAAGTTACGGGGTCATTTTGCCGAGTTCCTTCGACATGGTTCTCTCAAGCGC
CCTAGTATACTCTACTTGTTCACCTGTGTCGGTTTGGGGTACGGTCAGTTCACCGGGAGGATCGC
CCTCCCAATTCGAAGTTTTTTCCTGGAAGCCTAAACGCCCTTGTT
Right flanking sequence: Indices 199923 -- 200422
GTAGGTTCTGCAAGGCTTTGATGACTCAAGGTTCATATTAGGGAAAGGAGAGTGAGGGGAAGAGG
CGACGAGAGTCGGCCCGATCATCCAATTCGCTCCAACAGACAGGCATGGTTCTGTAGTCAAAGCA
ACTTCGTCACTTTCGTGTACCCATCGGACGGCAGCCCTTTCGGGGGTTCCTTAGGGACCGATTCA
CTCTGCGTAGATTGACTGAACGCAGAAAGCCTTCCACTGGCAGGCGATCGTGTTTTTCACAGGAT
TTATCGTTACTCATGTCAGCATTCTCACTTCTGATATCTCCAGGTCTTGTCACCAAAAACCTTCC
CCGATTGACAGAACGTCCCGCTACTGACACTTGAAAAAGCAGCTTTCAAGGTCTCGTCGCTTCGG
TGAATCACTTGAGCCCTGATACATTTTCGGTGCCATGGAGCTAGACCAGTGAGCTATTACGCTTT
CTTCAAAGGATGGCTGCTTCCAAGCCCACCTCCTGGTTGTCATCG
Found at i:201400 original size:23 final size:23
Alignment explanation
Indices: 201371--201447 Score: 68
Period size: 23 Copynumber: 3.1 Consensus size: 23
201361 CACTTTGCTG
201371 AGGTACGAAGTGACTCGACTGAA
1 AGGTACGAAGTGACTCGACTGAA
201394 AGGTACGAAGTCG-CTTTAGCGAAGCT-AA
1 AGGTACGAAGT-GAC--T--CG-A-CTGAA
*
201422 AGGTACGAAGTAACTCGACTGAA
1 AGGTACGAAGTGACTCGACTGAA
201445 AGG
1 AGG
201448 AGAGGAGAGT
Statistics
Matches: 44, Mismatches: 1, Indels: 18
0.70 0.02 0.29
Matches are distributed among these distances:
22 2 0.05
23 18 0.41
24 3 0.07
25 1 0.02
26 1 0.02
27 2 0.05
28 15 0.34
29 2 0.05
ACGTcount: A:0.35, C:0.17, G:0.30, T:0.18
Consensus pattern (23 bp):
AGGTACGAAGTGACTCGACTGAA
Left flanking sequence: Indices 200871 -- 201370
CCATTTCCTCGCTGACCCATCATGCAAAAGGTACGCCGTTAGAGTGAGTGCGCTTTACTAATAGA
ATTCAAAGTAAAGGCTCTAAGCTCCGCTCCTTCGACTGATTGTTCGCATCGGATCTCAGGTTCTC
TATTGCACTCCCTAAATAGGGTTCTTTTCACCTTTCCCTCACGGTACTTGTACGCTATCGGTCAT
TGAGGAATACTTAGGCTTAGAGGGTGGTCCCCCTTTCTCGCGTAAAAGCGATCAGAATTCGAACA
CGCCGCGTTTTACTGGGAAGGATCGAACCATGGGAACGAATCTACAGGGCTATCACCTTCTTTGG
CCAGATCTTCCAACCTTTTCACAATTACAGTCCCCTGCGCCCTGGAGCCTAAGAAATAGGCGTAA
GTGGCTTGAAAGCTTACTAAGCTTTTCCGCCGTAGCTTGCTGGTTTTTCCATCATCCAATCCACA
ACAAATCGAATGAAACCTGGCGAAAAAGAAGTGAACACTTTGCTG
Right flanking sequence: Indices 201448 -- 201947
AGAGGAGAGTGCATTGATCAATTTGGAAGTAGCGAAGAAATTATCATAAAAGAAAGGGAAAAGTG
TGAAGAACTCAAATTGAAAATCGTTTCTATCCCACGAATCCAAAACGAATTTAGGAAAGCCGAGG
TTTTTTTAACCACGCCACTGATTTCTCCAACGAAAGCAATCGACATGATGATTCGTAGCGAAAAC
TCGCGAAAAGGAATCAAGCCGGAAGCTTCGATTGAAGAGATTCGATCTTGCATCATCTTCCACTT
TTCTCGAGATCCGGAGTTTTTCGAGAAAAGGTCCCATCCTTCAATATCATGATTGGGTCAACCAG
GCCAGATCATGAGTCAAATATCATGATCGGGTCGACCAGGCCAGATCATGAGTGAATAGAAAATC
GAAAACGTACATAGCTGTTCCAGCTGAAATACTTGGAATAATTCTACCACTTCTACTAGGAGTAG
CCTTTTTAGTGCTAGCTGAACGTAAAGTAATGGCTTTTGTGCAAC
Found at i:201805 original size:39 final size:39
Alignment explanation
Indices: 201750--201825 Score: 134
Period size: 39 Copynumber: 1.9 Consensus size: 39
201740 CCCATCCTTC
*
201750 AATATCATGATTGGGTCAACCAGGCCAGATCATGAGTCA
1 AATATCATGATCGGGTCAACCAGGCCAGATCATGAGTCA
*
201789 AATATCATGATCGGGTCGACCAGGCCAGATCATGAGT
1 AATATCATGATCGGGTCAACCAGGCCAGATCATGAGT
201826 GAATAGAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.32, C:0.21, G:0.25, T:0.22
Consensus pattern (39 bp):
AATATCATGATCGGGTCAACCAGGCCAGATCATGAGTCA
Left flanking sequence: Indices 201250 -- 201749
AATAGGCGTAAGTGGCTTGAAAGCTTACTAAGCTTTTCCGCCGTAGCTTGCTGGTTTTTCCATCA
TCCAATCCACAACAAATCGAATGAAACCTGGCGAAAAAGAAGTGAACACTTTGCTGAGGTACGAA
GTGACTCGACTGAAAGGTACGAAGTCGCTTTAGCGAAGCTAAAGGTACGAAGTAACTCGACTGAA
AGGAGAGGAGAGTGCATTGATCAATTTGGAAGTAGCGAAGAAATTATCATAAAAGAAAGGGAAAA
GTGTGAAGAACTCAAATTGAAAATCGTTTCTATCCCACGAATCCAAAACGAATTTAGGAAAGCCG
AGGTTTTTTTAACCACGCCACTGATTTCTCCAACGAAAGCAATCGACATGATGATTCGTAGCGAA
AACTCGCGAAAAGGAATCAAGCCGGAAGCTTCGATTGAAGAGATTCGATCTTGCATCATCTTCCA
CTTTTCTCGAGATCCGGAGTTTTTCGAGAAAAGGTCCCATCCTTC
Right flanking sequence: Indices 201826 -- 202325
GAATAGAAAATCGAAAACGTACATAGCTGTTCCAGCTGAAATACTTGGAATAATTCTACCACTTC
TACTAGGAGTAGCCTTTTTAGTGCTAGCTGAACGTAAAGTAATGGCTTTTGTGCAACGTCGAAAG
GGTCCTGATGTAGTGGGATCGTTCGGATTGTTACAACCTCTAGCAGATGGTTCGAAATTGATTCT
AAAAGAACCTATTTCACCAAGTAGTGCTAATTTCTCCCTTTTTAGAATGGCTCCAGTCACTACAT
TTATGCTAAGTCTGGTTGCTCGGGCCGTTGTACCTTTTGATTATGGTATGGTATTGTCAGATCCG
AACATAGGGCTACTTTATTTGTTTGCCATATCTTCGCTAGGTGTTTATGGAATTATTATAGCAGG
TTGGTCTAGTAATTATAGGGGGCGGCCGTTCGGTCGCCTATGATACTAGGACCAATAGGTCAAAA
ATTGCTTTGTGCCGCAGGTGTTGAACGATCTACTCTACACAGGTG
Found at i:249632 original size:28 final size:28
Alignment explanation
Indices: 249592--249739 Score: 227
Period size: 28 Copynumber: 5.5 Consensus size: 28
249582 GACTCGACTG
249592 AAAGGTACGAAGTCGCTTTAGCGAAGCT
1 AAAGGTACGAAGTCGCTTTAGCGAAGCT
249620 AAAGGTACGAAGTCGCTTTAGCGAAGCT
1 AAAGGTACGAAGTCGCTTTAGCGAAGCT
249648 AAAGGTACGAAGTCGCTTTAGCGAAGCT
1 AAAGGTACGAAGTCGCTTTAGCGAAGCT
**
249676 AAAGGTACGAAGTAAC--T--CG-A-CT
1 AAAGGTACGAAGTCGCTTTAGCGAAGCT
249698 GAAAGGTACGAAGTCGCTTTAGCGAAGCT
1 -AAAGGTACGAAGTCGCTTTAGCGAAGCT
249727 AAAGGTACGAAGT
1 AAAGGTACGAAGT
249740 AACTCGACTG
Statistics
Matches: 109, Mismatches: 4, Indels: 14
0.86 0.03 0.11
Matches are distributed among these distances:
22 2 0.02
23 15 0.14
24 2 0.02
25 1 0.01
26 1 0.01
27 2 0.02
28 84 0.77
29 2 0.02
ACGTcount: A:0.34, C:0.17, G:0.28, T:0.20
Consensus pattern (28 bp):
AAAGGTACGAAGTCGCTTTAGCGAAGCT
Left flanking sequence: Indices 249092 -- 249591
TCATGCGTAAGAGTCAGACTACTACTTACTATATGATAGAAGAAGTGAAGTAAGAATCTAGAGAA
TCTTTCGGCGAATCTATTCGTAAAGCTTAAAGAAAGTCCGGTTGATAAACAAAAACTTCCGCCCC
AGAATGGATGTAATTCAGCGCAAATCCGCTCTTCTCTTTGAAAGAAGGAGTTCTTCCGGGCGCCG
CTAACAAGCGTTATGTCTTTTCTTATGCTTTATCCGCTAAAGCCTCACCCTGAATCCTCGGGCAA
GCGAACTCCTTTTCGCCTAGCCTAGTCGGAAATATGATTGCGACTACAGAAATAAGGTCAGGTCC
GCTCGAAGCTTCAAAGAAAATGGGCCAAATCGCCTGCTTGTCAAATATTCGCCCGAAAATTCTTT
GATATCCAAGGTCTTTCCTTAGAAAGCCTTTTCGGGCAACCGTTTCAATCTCTTCGCCACGATTA
GGTTCGTAAAGTTACCTACTTAAGAGGTACGAAGTGACTCGACTG
Right flanking sequence: Indices 249740 -- 250239
AACTCGACTGAAAGGAGAGGATTCGTGTCGACTGATAAGGAGAGGGACGTAGTCGCTCTAGCTTT
GCTAGAGGCACGCAGTAACTCGACTGAAAGGAGAGGAGAGGAAATGAAATAAAGTCATTGATCAA
TTCAGTCATTGATAATCGAGGATTCGTGAAAAAACTTCCCACTTGACTTTGGATGTCCCACGATT
CTGCTAGTTTAGAAACTAAGGAGAAGGACGGGGGTCGCTAGGTCAGAAAAGCGATAACTAGAAAT
TCTCCCCAAGTAGGATTTGAACCTACGACCAGTCAGTTAACAGCCGACCGCTCTACCACTGAGCT
ACTGAGGAACAACGGACTTAAGGAAGCCGACTCTCGTTCTTTGGCCTAACCTATGACCGAAATGG
GTTCGTCACTTTTTTCACATACACCGGGGAAAAGGTTACGATAGCAAGCCCCTCCCCGGCCGGAG
AGACTGCAGGACAAGGGGGCGGCAGTCAACCATCCACTCTCGAGA
Found at i:249706 original size:23 final size:23
Alignment explanation
Indices: 249676--249754 Score: 79
Period size: 23 Copynumber: 3.2 Consensus size: 23
249666 TAGCGAAGCT
249676 AAAGGTACGAAGTAACTCGACTG
1 AAAGGTACGAAGTAACTCGACTG
**
249699 AAAGGTACGAAGTCGCTTTAGCGAAGCT-
1 AAAGGTACGAAGTAAC--T--CG-A-CTG
249727 AAAGGTACGAAGTAACTCGACTG
1 AAAGGTACGAAGTAACTCGACTG
249750 AAAGG
1 AAAGG
249755 AGAGGATTCG
Statistics
Matches: 45, Mismatches: 4, Indels: 14
0.71 0.06 0.22
Matches are distributed among these distances:
22 2 0.04
23 20 0.44
24 2 0.04
25 1 0.02
26 1 0.02
27 2 0.04
28 15 0.33
29 2 0.04
ACGTcount: A:0.38, C:0.16, G:0.28, T:0.18
Consensus pattern (23 bp):
AAAGGTACGAAGTAACTCGACTG
Left flanking sequence: Indices 249176 -- 249675
GTAAAGCTTAAAGAAAGTCCGGTTGATAAACAAAAACTTCCGCCCCAGAATGGATGTAATTCAGC
GCAAATCCGCTCTTCTCTTTGAAAGAAGGAGTTCTTCCGGGCGCCGCTAACAAGCGTTATGTCTT
TTCTTATGCTTTATCCGCTAAAGCCTCACCCTGAATCCTCGGGCAAGCGAACTCCTTTTCGCCTA
GCCTAGTCGGAAATATGATTGCGACTACAGAAATAAGGTCAGGTCCGCTCGAAGCTTCAAAGAAA
ATGGGCCAAATCGCCTGCTTGTCAAATATTCGCCCGAAAATTCTTTGATATCCAAGGTCTTTCCT
TAGAAAGCCTTTTCGGGCAACCGTTTCAATCTCTTCGCCACGATTAGGTTCGTAAAGTTACCTAC
TTAAGAGGTACGAAGTGACTCGACTGAAAGGTACGAAGTCGCTTTAGCGAAGCTAAAGGTACGAA
GTCGCTTTAGCGAAGCTAAAGGTACGAAGTCGCTTTAGCGAAGCT
Right flanking sequence: Indices 249755 -- 250254
AGAGGATTCGTGTCGACTGATAAGGAGAGGGACGTAGTCGCTCTAGCTTTGCTAGAGGCACGCAG
TAACTCGACTGAAAGGAGAGGAGAGGAAATGAAATAAAGTCATTGATCAATTCAGTCATTGATAA
TCGAGGATTCGTGAAAAAACTTCCCACTTGACTTTGGATGTCCCACGATTCTGCTAGTTTAGAAA
CTAAGGAGAAGGACGGGGGTCGCTAGGTCAGAAAAGCGATAACTAGAAATTCTCCCCAAGTAGGA
TTTGAACCTACGACCAGTCAGTTAACAGCCGACCGCTCTACCACTGAGCTACTGAGGAACAACGG
ACTTAAGGAAGCCGACTCTCGTTCTTTGGCCTAACCTATGACCGAAATGGGTTCGTCACTTTTTT
CACATACACCGGGGAAAAGGTTACGATAGCAAGCCCCTCCCCGGCCGGAGAGACTGCAGGACAAG
GGGGCGGCAGTCAACCATCCACTCTCGAGATTCATATTAATCAAT
Found at i:249724 original size:51 final size:51
Alignment explanation
Indices: 249571--249754 Score: 280
Period size: 51 Copynumber: 3.5 Consensus size: 51
249561 CCTACTTAAG
*
249571 AGGTACGAAGTGACTCGACTGAAAGGTACGAAGTCGCTTTAGCGAAGCTAA
1 AGGTACGAAGTAACTCGACTGAAAGGTACGAAGTCGCTTTAGCGAAGCTAA
**
249622 AGGTACGAAGTCGCTTTAGCGAAGCT-AAAGGTACGAAGTCGCTTTAGCGAAGCTAA
1 AGGTACGAAGTAAC--T--CG-A-CTGAAAGGTACGAAGTCGCTTTAGCGAAGCTAA
249678 AGGTACGAAGTAACTCGACTGAAAGGTACGAAGTCGCTTTAGCGAAGCTAA
1 AGGTACGAAGTAACTCGACTGAAAGGTACGAAGTCGCTTTAGCGAAGCTAA
249729 AGGTACGAAGTAACTCGACTGAAAGG
1 AGGTACGAAGTAACTCGACTGAAAGG
249755 AGAGGATTCG
Statistics
Matches: 122, Mismatches: 4, Indels: 14
0.87 0.03 0.10
Matches are distributed among these distances:
50 2 0.02
51 69 0.57
52 2 0.02
53 1 0.01
54 1 0.01
55 2 0.02
56 43 0.35
57 2 0.02
ACGTcount: A:0.34, C:0.17, G:0.29, T:0.20
Consensus pattern (51 bp):
AGGTACGAAGTAACTCGACTGAAAGGTACGAAGTCGCTTTAGCGAAGCTAA
Left flanking sequence: Indices 249071 -- 249570
TGAGTTTGAGTTCATGAGATTTCATGCGTAAGAGTCAGACTACTACTTACTATATGATAGAAGAA
GTGAAGTAAGAATCTAGAGAATCTTTCGGCGAATCTATTCGTAAAGCTTAAAGAAAGTCCGGTTG
ATAAACAAAAACTTCCGCCCCAGAATGGATGTAATTCAGCGCAAATCCGCTCTTCTCTTTGAAAG
AAGGAGTTCTTCCGGGCGCCGCTAACAAGCGTTATGTCTTTTCTTATGCTTTATCCGCTAAAGCC
TCACCCTGAATCCTCGGGCAAGCGAACTCCTTTTCGCCTAGCCTAGTCGGAAATATGATTGCGAC
TACAGAAATAAGGTCAGGTCCGCTCGAAGCTTCAAAGAAAATGGGCCAAATCGCCTGCTTGTCAA
ATATTCGCCCGAAAATTCTTTGATATCCAAGGTCTTTCCTTAGAAAGCCTTTTCGGGCAACCGTT
TCAATCTCTTCGCCACGATTAGGTTCGTAAAGTTACCTACTTAAG
Right flanking sequence: Indices 249755 -- 250254
AGAGGATTCGTGTCGACTGATAAGGAGAGGGACGTAGTCGCTCTAGCTTTGCTAGAGGCACGCAG
TAACTCGACTGAAAGGAGAGGAGAGGAAATGAAATAAAGTCATTGATCAATTCAGTCATTGATAA
TCGAGGATTCGTGAAAAAACTTCCCACTTGACTTTGGATGTCCCACGATTCTGCTAGTTTAGAAA
CTAAGGAGAAGGACGGGGGTCGCTAGGTCAGAAAAGCGATAACTAGAAATTCTCCCCAAGTAGGA
TTTGAACCTACGACCAGTCAGTTAACAGCCGACCGCTCTACCACTGAGCTACTGAGGAACAACGG
ACTTAAGGAAGCCGACTCTCGTTCTTTGGCCTAACCTATGACCGAAATGGGTTCGTCACTTTTTT
CACATACACCGGGGAAAAGGTTACGATAGCAAGCCCCTCCCCGGCCGGAGAGACTGCAGGACAAG
GGGGCGGCAGTCAACCATCCACTCTCGAGATTCATATTAATCAAT
Found at i:264429 original size:23 final size:23
Alignment explanation
Indices: 264356--264435 Score: 74
Period size: 23 Copynumber: 3.3 Consensus size: 23
264346 CCTCTCCTCT
*
264356 CCTTTCAGTCGAGTTACTTCGTA
1 CCTTTCAGTCGAGTCACTTCGTA
264379 CCTTT-AGCTTCGCTAAAG-CGACTTCGTA
1 CCTTTCAG--TCG----AGTC-ACTTCGTA
264407 CCTTTCAGTCGAGTCACTTCGTA
1 CCTTTCAGTCGAGTCACTTCGTA
264430 CCTTTC
1 CCTTTC
264436 CATCTATCTT
Statistics
Matches: 47, Mismatches: 1, Indels: 18
0.71 0.02 0.27
Matches are distributed among these distances:
22 2 0.04
23 21 0.45
24 4 0.09
27 3 0.06
28 15 0.32
29 2 0.04
ACGTcount: A:0.17, C:0.30, G:0.16, T:0.36
Consensus pattern (23 bp):
CCTTTCAGTCGAGTCACTTCGTA
Left flanking sequence: Indices 263856 -- 264355
AGCAAGACGAGGTCGCTCTGCTTTGTAGACAAGGCTCGTTCCGTACTTGACTTACGAGCTCGTCT
AGTACTCGCCTCTATCTCTAAAGGAAGGGGCTTATGCACTCTACTTGCTGTCTACTAAACGAGCG
TTAGAGCGAAGCCTTCTTAGTGGCTTCTCTTCTTTTTCCTCACCCTATTCTTTCATTTCCGCTTA
AGCTTCTCCGGTTTGGGGGATTAATTGATTAGATACCCGAGAACCATAATCTTTCCTAGAAACAG
CTTCTACGACGATAGATAGGGGTCAGGTTTGTTTGGCATCTATGCCTCCTGCCCTCCAAACAGTA
TGGGAGCCTTTCAGCTCGTACTGCTCACACTCCTAGATCTTCACGGCACCTCCCCCACCCTGTGA
AACAAAAGTGTATATACATCCAGAAGGCTGGTTATGACCTTTATTTATCTTTCTCTCCTAAAGCT
TCGCTAAAGCGACTACGTCACTTTCTTTCACGAATCCTCTCCTCT
Right flanking sequence: Indices 264436 -- 264935
CATCTATCTTGACCGGGAAGAGGGGGGAGGCTCTTGCGGAAGCCCTGCCCGCCCTTTTCTATTTT
GAAAGATCCCTTCTATTGAGGATTCCAGGCTTTCCGGACTCGTAACAGACGGCTATAGGAACAAG
AAGAGGCGGCTGAAGCCGTTGCAGGTCCTTCTCCTTCCGCGGAAACGACCCTCTTTTTTTGTTTG
TTCACCACGGCACGAAATCATGAAGAAGCTGGAATAACTCAGAAAGAGAGTGGCGCCTAGCCGTT
GAGAGCGTCTGTTGTCTTTGTAGAGGAAGAGTACGATCTTGGACTGGCCCCCTTCGCATGATAAC
GAAAGAAAAAGAAGTCCGTGCTACTATAAGGCCTCTAAACTCCTCCCTCAGGACACTGTTGCGTT
GTCCATGGGGACGGGGTAGCCCCGACTTCCATAGGTCCTTGGTTCGATCTCCTAATGAGAATGGA
GGTCCTTGCGCGGGCGTCTCATCCCTAACCTAAGACTTGCTTGCT
Done.