Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_065235
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: 456900
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Found at i:2279 original size:42 final size:42
Alignment explanation
Indices: 2233--2313 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
2223 CGCCTCCAGG
*
2233 AACGTGGGAGAGCCCTTGAAGCGGAAAATGAGCTGCTCCGGA
1 AACGTGGGAGAGCCCTTGAAGCGGAAAATGAGCGGCTCCGGA
2275 AACGTGGGAGAGCCCTTGAAGCGGAAAATGAGCGGCTCC
1 AACGTGGGAGAGCCCTTGAAGCGGAAAATGAGCGGCTCC
2314 AGTCCCTTAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.28, C:0.22, G:0.36, T:0.14
Consensus pattern (42 bp):
AACGTGGGAGAGCCCTTGAAGCGGAAAATGAGCGGCTCCGGA
Left flanking sequence: Indices 1733 -- 2232
TTGGATTATCCGCTTTTTGAAAAAAAAGGTTTTTAGCACCATTTTTTGTTTTCTCTTCCCTTTGC
CTTTTTGCTATGAAGACTTCTTCACGTTTTTTATGAACCCTCCGGGTCCCAACGCCGGCGTAGCC
GAGGAAATAGTGGCTGAAGCCGACATGGGCTCGGTAGAAGACTCCCACGAGGAGCAAGACGGGCC
AAACCTTCCCCAGCTACGCCATGAAATTAAAATTTGCGAGGAGGAGAGCCGGAATTACGTACGTC
TTGCTCAAGATTCCCTTGAACGCGCGGAAAACCTGGTCAACGAAGTAAACTACCGGAGATCCTTG
CCCGACCAGGGACCCGCGTGGCAGGAGCGCACGGACCAACTTATTGCCGCCGCGAAAAATGAACT
AGACTTCCCCGAGGAGGACCTGGAGATGGCGCAAGAACTCGACCAAGACAAAAAGGAGGCGGTAG
AGGAGTATAAGGAAGCGCTGGACGCGGAATGTAGCCGCCTCCAGG
Right flanking sequence: Indices 2314 -- 2813
AGTCCCTTAAAAAGTCAAGATTTTAAGGGGCTTCGCTTGGACTATGCTATGTATAAATAATCTTT
ACTTTTTTTAATTGGAAAAATGACACTGGGACGAAGCCAGAATTCTATCGAAAAGTCACTCAAGG
AAACCGTGAAGTAAAAGAAGAAAAGGTAGACCACTAATACTAAGAACCTAACAGAACAAGCAATG
CCCCATGCCTTTCTTGGTTGGACCAGCCCAACCGGCGATTTCCGTCTTCCTGAATTGGGAGAGCA
AGCACAAGTCTCTCTTCTTTTTTTCCTTTGAATTACTCATATATATATCCTATGAATTTCATTTC
GCACCGGAAACTATTCTAGGAGAAGTTCGAATCCGTTCCGTTCGGATATTGATCGGTCTTGGTTT
GACATGGTTTACGCGTTACTGGTTCCCGGAAGAGTTAATATCTCCATTAGCTAAACCCTTTCTTA
CCCTTCCCTTGGACTCGTATTTTGTTTGTACACAATCAACGGAGG
Found at i:22050 original size:16 final size:16
Alignment explanation
Indices: 22029--22062 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
22019 AAGTGTGCCC
*
22029 TAAGTGTAATCCTACT
1 TAAGTGGAATCCTACT
22045 TAAGTGGAATCCTACT
1 TAAGTGGAATCCTACT
22061 TA
1 TA
22063 TACTCTTTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.35
Consensus pattern (16 bp):
TAAGTGGAATCCTACT
Left flanking sequence: Indices 21529 -- 22028
ATCTAGGCAGCTACTCTCTAGCTTCCATCTATTCTTCCTTCTCTTATGGTACTTGAAGCCAAGTA
AAGGCAGCTTTCTGTTGAGTTATATTCTTTCAGATCTGAGATTTAGTCGTAGAGCCTGAGTTAAC
CAAACTAGTAATCTAATCAGTCATCTAATCTTAGGCTTCGCTACCGTACTTATCGTCCAGCAAGT
AACCCACCTTACCCCCCCTCAATCTCAGTAAGGAGTTAGGAGGGTTTCGGGCTAGGAGTTGACCC
AAGGCGTCTATTCAGATAGTAGTTCCCAAGTATGATATGAAATAGGAGGTAATAGAGTAAAGTCC
TTGTCCTACTCTAATACAAGTAAGTAGCTAAGGTTACCTTAATCCGCTGAAGCAAGGATTGGTAA
GCTCCGGAGCAAGAGTAACTGTAGTTGCTACGTCCGGTCCCGTAACTGCGGGCAGCTCGAGTTCT
AGTTCTTTACAAGACAGATGGGAACTGTAGCTAATAAGTGTGCCC
Right flanking sequence: Indices 22063 -- 22562
TACTCTTTCTACTATATTAGCATGTCGGGTTCCAAGTTATTAGTAGCTAGGCAGCTAAGCCAGTA
GTAGTTCAGTTCAGGTCGGGGCATGAAGCTACAGGTTCTATTTTCGGTTGTGAGACAGAGGTCAG
AGGCCCCCTGTTATATAGGTAGCCATGCGCGTTAATAGATCTTCTTCTATACTAGTAGTAGGAGT
AATGAGTGAATCGGTTTCTTAGGCAAGTTTTTGTTTCTTTATTAGAAGGATAAGCACGGTTATTG
CTCTTTGTCCCAACATGGAGCCGAGGTAGCTACACCGTTTGAAGTAGTTAACGAAGGGAAATAAG
TCCATTTGAGTGAAGATTGGATAGTTGCCCGCTCCTTAGGTCTGCTTTCATACGTGCTGGTGTTC
GTGTTCTGTTGGTTTTTCTGTTCTGTTGTGGGAAGGGGGGATTTTCGCATCTACAAGTTGAGAGT
GTGCTGGGGCAAGTGGGCTAACCCGAACTCCCTGTAAGGGGCTTT
Found at i:74628 original size:25 final size:25
Alignment explanation
Indices: 74590--74639 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
74580 TTCCCTACTT
** *
74590 CTGTACTTGGTTGCCTGTCTCTAAG
1 CTGTACTTCCTTGCCTGTATCTAAG
74615 CTGTACTTCCTTGCCTGTATCTAAG
1 CTGTACTTCCTTGCCTGTATCTAAG
74640 TAGGTACGTC
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.14, C:0.26, G:0.20, T:0.40
Consensus pattern (25 bp):
CTGTACTTCCTTGCCTGTATCTAAG
Left flanking sequence: Indices 74090 -- 74589
GCTCGTTCGCTAAAGTCCTGTCTGCCTGCCCGTTGATTCAGTACGTTCCTATCCCCTTGGGAAGT
TTGATCAATCTTCCTCTCCCTCTCCCTTTGGTCGAGCAAGTAACCTCCCTTCTCCCCAAAGGTCG
AGTGAGTCCCTACCTTCGATGCCCATTTGTTGATTAATCTGGGGCGGTATTCATCCCCGGCTTTG
GTGCCTTTCCTCGCCCTCTTTCATTTGGTAATACCCTTTGATTGACTGCATTTGCTTATCCTGGT
ATATAGGTAGTGAACTTCTGTCCTGTCGTATTGTCCTTATTGAGTTATCCTAGCAAGAATCCCCC
ATCGACTAAGAAAGCTATGTATTGATTACTATAAGAAGGAAGCCCCGCTATCTATCTCTGCTTTC
CTGTCTTCCTATCTTTCTGCCTATCTGTCTTTCCTCTTTCTGCTTTGTCTTTCTCGCTGTCGGTA
GAGATTAGTATTTCCTAAGTTGTCTGAGGCTGAGCTTCCCTACTT
Right flanking sequence: Indices 74640 -- 75139
TAGGTACGTCTCGCTTCGCTCCTCATTTCCTTGCCGTCTTTCAATTCTGACTATTGAGAAATATC
CATGAGTCTGTCCCCCCGCGAGTAAATAAGCTAACCTTGGCTTCCCCTTCGACTGAGGCGGACTT
GAGCCTAGTTATTGACTTCCTGAACCTTAAACAAGTTATCAAAGAAGTGGATTTGCTCACAGCTT
CTCCTTCGTTCCTAGACCAACAGCTTAGCTTACCTTAGCCCAGCCGTACGTCCTACTGCTTACCT
TAGCCCAACCATAGGTCCTACAGCTTCGATGGCAGAATGATTGACCGGGCCGCTTGGCCCACTTG
AACTAGCAGCCCTACCTGCTGCCGTACCTGTCTGTGAATGAACTTCTGGATATTCACCTACCAAC
ACAACCCGGGCCACGCCGGGACTTTCTTTATCCATTCAATCAAACTAGGGAAGTGGTTAGAGAAG
CAGTAGCTGCTATGCGAGTTAGATCGGTCAAGTTTTGATGTAGAT
Found at i:74898 original size:30 final size:30
Alignment explanation
Indices: 74861--74925 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
74851 CCAACAGCTT
* *
74861 AGCTTACCTTAGCCCAGCCGTACGTCCTAC
1 AGCTTACCTTAGCCCAACCATACGTCCTAC
* *
74891 TGCTTACCTTAGCCCAACCATAGGTCCTAC
1 AGCTTACCTTAGCCCAACCATACGTCCTAC
74921 AGCTT
1 AGCTT
74926 CGATGGCAGA
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.22, C:0.37, G:0.15, T:0.26
Consensus pattern (30 bp):
AGCTTACCTTAGCCCAACCATACGTCCTAC
Left flanking sequence: Indices 74361 -- 74860
GAACTTCTGTCCTGTCGTATTGTCCTTATTGAGTTATCCTAGCAAGAATCCCCCATCGACTAAGA
AAGCTATGTATTGATTACTATAAGAAGGAAGCCCCGCTATCTATCTCTGCTTTCCTGTCTTCCTA
TCTTTCTGCCTATCTGTCTTTCCTCTTTCTGCTTTGTCTTTCTCGCTGTCGGTAGAGATTAGTAT
TTCCTAAGTTGTCTGAGGCTGAGCTTCCCTACTTCTGTACTTGGTTGCCTGTCTCTAAGCTGTAC
TTCCTTGCCTGTATCTAAGTAGGTACGTCTCGCTTCGCTCCTCATTTCCTTGCCGTCTTTCAATT
CTGACTATTGAGAAATATCCATGAGTCTGTCCCCCCGCGAGTAAATAAGCTAACCTTGGCTTCCC
CTTCGACTGAGGCGGACTTGAGCCTAGTTATTGACTTCCTGAACCTTAAACAAGTTATCAAAGAA
GTGGATTTGCTCACAGCTTCTCCTTCGTTCCTAGACCAACAGCTT
Right flanking sequence: Indices 74926 -- 75425
CGATGGCAGAATGATTGACCGGGCCGCTTGGCCCACTTGAACTAGCAGCCCTACCTGCTGCCGTA
CCTGTCTGTGAATGAACTTCTGGATATTCACCTACCAACACAACCCGGGCCACGCCGGGACTTTC
TTTATCCATTCAATCAAACTAGGGAAGTGGTTAGAGAAGCAGTAGCTGCTATGCGAGTTAGATCG
GTCAAGTTTTGATGTAGATATAGTCGCCCTCTTCTCTATGTCATAAAGTCGCTTATAATTAATGG
TTGTTCACTTCAGATGTGATACGTTGTTCACTTCGGATGTGGTGGATGAACCCTGATCGATGCGG
TTCAGGCCGTTTGATTGAACTACGCTAAGCTGAGACTTTCTCTTGTGCTTCGGGCGATCATAGTG
GATTTGATAATAGAAATAGCGAGCGGTCCGCCTTCCTTCTTCGCCTTTTCAATTTCAAGTAATGA
TAGGACTCATGGGCCAAAAGGATATTGTCTTGAATTTGTCTTTCA
Found at i:81491 original size:22 final size:23
Alignment explanation
Indices: 81452--81497 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
81442 CTTTGAGACT
**
81452 TTCTTCTCTTTGCTAGAAT-CGC
1 TTCTTCTCTTTGAAAGAATGCGC
81474 TTCTTCTCTTTGAAAGAATGCGC
1 TTCTTCTCTTTGAAAGAATGCGC
81497 T
1 T
81498 GTGATCTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 17 0.81
23 4 0.19
ACGTcount: A:0.17, C:0.24, G:0.15, T:0.43
Consensus pattern (23 bp):
TTCTTCTCTTTGAAAGAATGCGC
Left flanking sequence: Indices 80952 -- 81451
CGGAAAGGAATGGAATTTCTTTAAGCTTCACTCCGCTATCAGACTAGTTGCGAAGCGTTGGGATA
ACTAAAGTGGAATATGCCTCAACTAGTTGCCCAGGATGAGGCCATTGCAGCCACTAGCACGGCCA
AGTCACCAACCTATGGCTCCGGGGAAGCCGGCAGGGAGGAAGGATGATAATCCAACCAAAGGAAT
TAGCCACTCGTTCTATCAATAGGCGCCGTGGGCCTATGAGCTTCTGGGCCTGTACGATTTCCTGT
CCTCAACAGTTCAAAACGCTTGACACTGAGAGCTTTGGTGAATATTTTGCCTTTTGGTTATGGAG
TCTTTCCTTCCTTCCAAGCCGCTTTCAAAGCAGTAGGCAGTCTCTTCTTTCTTCTTATACGGTAG
CCAGTCTTTTTTAGAATGGTTGAATAGAGCCTCCCTTCTGTCTCCCAGTCTGTCTTATAAGAAGA
TAGTAGTAAGTCAGTTGTAGGTTTACGAATGGCTTCTTTGAGACT
Right flanking sequence: Indices 81498 -- 81997
GTGATCTTTTCAAGTTCATCCTAGCTATCATCTCAATCATTCTTCATTCACTTCGAGCCCTCGGG
TAGTTTTCTCATCCAGGAGAGTCGTCTTAGAGGCGGTCTCCTCCCTGTCCTTCTTAGATGGTATC
CTCTCTGTCCTTCCCCTTTCCCGGACTCGAGAACCCCTGAAGCGCACTGGAAGCATCTCAAGGAA
AAGAGAGAAGTCAAATATCGTAGGCTTTAGATAAGATTCCCTAGTAGATAGCTAAGCTAAGAGAG
TGCTCCGGAAGAGCTAATATTAAAAATTCTTTCCCTTTCTTTCACCGAGGAGGCTAACTAGATAG
ATGGTGGGTCTAAGGAAGAGAAGAATATGAGCTATATTTTCATCCCCTTTCAGTTCCTTTCCTTA
TCCTTAGAACAGTAGGGTTTGAAGCTGGCAAAGTCAATCAATCCAGCAGTCAAAGGGGCAAGTGC
AGTCACTCAACCAACGCCTTTCAAGCAATATCTTAAGTAGGGGTA
Found at i:100253 original size:14 final size:14
Alignment explanation
Indices: 100234--100261 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
100224 GAAATAAGAG
100234 TACATATTCGAGAA
1 TACATATTCGAGAA
100248 TACATATTCGAGAA
1 TACATATTCGAGAA
100262 GAAGGGATGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (14 bp):
TACATATTCGAGAA
Left flanking sequence: Indices 99734 -- 100233
CCAGAGATTCTTCTTCCTTGACTTGTGATCAATTAGACAAGAGGTGCATATAGCTCCTTGTAGGT
GCGGAGGAAAGATATCGGCTACAAAGAAAATTGAAGATGGCGACTCATAGTTAAGAGGATAAGTT
CGGGTCTGGTGAAGTCCCTACATTAAAAGATTCGGCCTTGCGATCATGCCCCTTGAGTCACGGTA
CTTTGGTTTAGTCAGGATCACCCTGTAAAACTAGCTTAATAGAGGTCGAAATAAAAGAGTTTTGA
GGTTCAATCTTCAAGTAAGGAGGAGTAAAGAAGAGGAATCGCGAACATACTCAATAGATATCTTT
CTTCGACGAGGCGGTGCCTATTAAAGAGTTATTATTTCAGGGACGCCACCCTACCACCGATGAAT
GCTACCCGAGGATGAGGCCTTGCTTGCTTATTATGTGGTAATTGTCTACCTTCCTGACGAACCGG
GCAGCGTAGAGAAAGGCGAGATGGTTCATTTCTATGAAATAAGAG
Right flanking sequence: Indices 100262 -- 100761
GAAGGGATGGTTATTTTCTGTAGAGTAGATACAGAAGGGTCCAATCTAGTATAGTCGGGCTTGGA
AGCCCTACGATTGCTTATGGGCTCATCTAGCAGAAGAATGACATGATGAAGAAGCTAAAGCTCCC
CTTGCTATGCTTCGGTTGCTTTCATTGATCTAGGATTGTTCCCGGGTATCATCCTCAAATAGGAA
GGAGGTTAAGGGCTTTTGATCGAGGCAGTCACTAGAGCTTGTTGGCCGCGAGATGCACTTCAAAA
GCACTAAAATCCGCAGGTAAGAGATGAAGCTTCATTTTCAATATTAGAAGCAAAAGTCTTATAGT
TTACTACTAATATAATCTATTTCTTGTACAGCAGCTATAATCGTTATAGTTTTGAATAAGGCGAC
TGCTCCGGGACATAAAAAGAAAACGCTAGTGAAGACAATAAGGGGATGCTATCCACTACAAAAGG
AAATCCGAATCGGAACAGGATCGAGATCACAGCAAATAAAAGGTT
Found at i:213216 original size:16 final size:17
Alignment explanation
Indices: 213195--213228 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
213185 ACCAAGCACT
213195 AGGCGCTAACA-GACAA
1 AGGCGCTAACAGGACAA
213211 AGGCGCTAACAGGACAA
1 AGGCGCTAACAGGACAA
213228 A
1 A
213229 AAACAAGCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.44, C:0.24, G:0.26, T:0.06
Consensus pattern (17 bp):
AGGCGCTAACAGGACAA
Left flanking sequence: Indices 212695 -- 213194
CTTAACACATGCAAGTCGAACGTGATTTTCGGGGAAAATCTAAGCTTTGTAAAGAGCTGCTCGTT
AGCTAGCAAATCCGCTATGGTCTATGGTCTCCTAATAAGCGTACTACCTAGAAAGCTCAGTAATT
GGAAAAGAAACAGAACTAGAACAAGAAAGCGGTGGGTTTCGGGCTTGCGAGTGCCTATCTATTCT
AACTTCCTACTAGCTAGTGGAGCGAGTATTACATAACCTTGACTGATAAGGAGAGGAGTACTGAA
CATTAAGCTAAAGAGGAGTCTATGCATGTCGAGCAGAGATAAGACCAGTGCGAGATATGAGATCG
AGAGCATACTAGCACAGTTATAGAACATAACCGCGAGGTGCAACCTCTATTCCAAGAAAAGACTT
AAGAGGTCCAAGATCCTTCATATCTTAAAGGCCAGCTGATCCTTAAGAAAAGAAACGAAATGGCA
TCAGCCCCATCTCCAGAGATAATAAATCGACATATACCAAGCACT
Right flanking sequence: Indices 213229 -- 213728
AAACAAGCTTCGAACGAGAATGAAAAGATCGAGAGTACGTTCAGTGGTTGTTGAGTTGTCTTGGC
CTACTGAATAGAGAGTTGAATTGACTAAGCGCCCCGTTTGCTGGGCCTACAGAGAGAGAGTTACG
TGTAGTCAACTCGGTGGGGTATTCTCAATCGGCGAAGCCTCGCTACAGTCACAGCTACAACAGCT
AACAACAGAGCGGATATCACGCAGCGGATATATCGGTTGTTAACATCGGGTGCTAAAAGAAAGCA
ACACGAATTCTCTTATATAACGAGATCCTATTATCTTACATAACCAGCGACAGGGGTCTCTGGCT
TGAAAGATGGCTTTATCCGGAGGTCTCTTCATCGGCCCCAACCGAGGGAGGGAAAACGCAGGTGC
ATTAGATGCTTCATTTGTTTATGTTTGCTCGCCCACAGATGAATGACATATTGGATGTTGGATGT
TAAAGTGAGAACTTTTTGGGAAAAGCAACCAACCTCTAGGAACCT
Found at i:219511 original size:19 final size:19
Alignment explanation
Indices: 219475--219529 Score: 62
Period size: 17 Copynumber: 3.0 Consensus size: 19
219465 ACTAAAGGGG
*
219475 TTATGAGTTAGAAG-AGTTA
1 TTATGAGTTA-TAGCAGTTA
219494 TTATGAGTTATAGCAG-T-
1 TTATGAGTTATAGCAGTTA
*
219511 TTAAGAGTTATAGCAGTTA
1 TTATGAGTTATAGCAGTTA
219530 GGGAGTTATG
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
17 15 0.48
18 4 0.13
19 12 0.39
ACGTcount: A:0.35, C:0.04, G:0.24, T:0.38
Consensus pattern (19 bp):
TTATGAGTTATAGCAGTTA
Left flanking sequence: Indices 218975 -- 219474
AAAGTTAGGGGAGCAGTGTAACTGCCATCAACTCCTATAACTCTTTTCCTTAAGTTTAGGTTAGT
TCCCTCTTAATTAGGTATTCTGCAGAGTTCCGACCTAGAACTCCCTTATAAACTAGAAAGCTAAC
TCGAACTCGTAACTCAATTAATTTAAGTTACAGGTATGATAAATATAAGTTACTGTTATTAGGCA
CATCCTTCTTTCTTGTCCTTGTTGGGGAATCCTATATCTTTTAAGAAAAAAGAAGTTTTTAGTCC
TCTCCTTTGCAGTCGAGTTACTTTATTCCTCATAGCTTCACTCTTTTCTTTTAGTTCCCTACGGG
GTTAAGTTAAAGTCTTATTATTATTGATATTCCCCCTACGGGGAGGTTACCGTTATTATTATTAA
TAGAATTCTAATTAGTTACCAGTAAAGTATTATTAGGTATTAAAAGTATTTTTAGTTAGGGGTGT
AACTGGGGGGTCTGGGGGCACTCCCCCGGAACTAAACTAAAGGGG
Right flanking sequence: Indices 219530 -- 220029
GGGAGTTATGAGTTGCTAATTGTCATTCTCTTTAGTTCCCTACGGGGTAGTTACAGGTATGATAA
ATATAAATCTTAGTTACCGGTATTAGAAATATAAGTAATATAAATATATTGGTAGTTACAGATAT
TCTTAATTTGGTGGAACTGGGGGGTCTGGCGCAGTGTAACTGCCCCCGGAACTGGTTTAAAGAAG
AGTTAATTGTCTTAATCTTTAGAAACTAATAGCTAGAAAAACAGGCTATTCCATCTAAGGCATAA
CATGAACCGAGGAATCCAACCAAATAGGAATGAATAGGCATGTGGGAACAGCATTGCTTGCATTG
ATTCAATTGATTTGAAGCGGCGGTTATACTATACATACAGACATAGTTTTCACTAGGGGTTTTTA
CCGAGTTGGTCACAAGCCCGTCAGAAGCAACCTCAGCAGAAAGCCACTCTGGAAGAGTCTCGTCC
ATCGTCTGCTTAGGCGACTATTTAATAGCCTTTAGATCTGCCTGT
Found at i:224433 original size:26 final size:26
Alignment explanation
Indices: 224397--224470 Score: 148
Period size: 26 Copynumber: 2.8 Consensus size: 26
224387 CTCGCTCGAC
224397 TGAAAGGAACGAAGTAGCTTGATTGA
1 TGAAAGGAACGAAGTAGCTTGATTGA
224423 TGAAAGGAACGAAGTAGCTTGATTGA
1 TGAAAGGAACGAAGTAGCTTGATTGA
224449 TGAAAGGAACGAAGTAGCTTGA
1 TGAAAGGAACGAAGTAGCTTGA
224471 CCGCGGGCGC
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 48 1.00
ACGTcount: A:0.39, C:0.08, G:0.31, T:0.22
Consensus pattern (26 bp):
TGAAAGGAACGAAGTAGCTTGATTGA
Left flanking sequence: Indices 223897 -- 224396
GGATGCCCAACATGAGCAGTTCCACCTGAAGCACCGGCTAAGTGAATGGAAAAAAGATAACCAGT
TGACGAGGCACAAGGGCGGGTGTAGCTGATTGTACTTCCTCTCTGCCAGACCCAACCCTAAAACT
AATAAAAAGAAAAGAAAGGGGAATCAGAATACATTTCCTCGAGCAAGCAAATCAAGAAAAGACTC
ACCCTTGCCATGGGCGATAGCGGCTATGTCTAAGCAGCTGCTTTCCCATTCATTCCATAGGTAAG
TCTTATTTTTTGCTGTAAACGAAGAAGGAATGATTCAATATCATATCATAAAAGACCTAGATGCT
CTAGCTCCAAGAAAAGACTAAGAAAACTCCTTAAAAAGAGAAGAGTCAATCCTCAGCGTCGGATT
CTTCTTATGCTGATTGACCTAGCCGTGCGTTTCCAACTGTTATGACTGGGAGCTAGGCGCTATTT
AGCCCTCCATTTCTAAAGCAAGCAGGGGAGCTAGACTCGCTCGAC
Right flanking sequence: Indices 224471 -- 224970
CCGCGGGCGCAGGGAAAGGAGAGGGAGTCACCGAAGAGAAAAAATAAAGGTTCAAGACAATGAAA
AATATAAACGCAGGAAGGAACAAAAGTCAAGTATGTAATCTAGCAGTCATGAGAGCAGGTTAGAG
GCAAGCCGACCTAACCAACCTACGATATATAGTAACCGACCTACGAATATAACTTTGGGTTAGGT
TGAAAAGTCTAGTTGGAAAAACAGATCAATCGCATCCCAAAGGGTCAAGGGCTGAGTTGCACATT
CTATTTTGGCCTCTTTTCTTAAGTAGAATGAAATGTTCGGCCTAATCTATGATATTGTGATTATG
TTACTGTTATTTGGTCTTTTTCAAGCTTCCCAGAGTTGTCCTTCAGCAAGCAATTATAGGGGTTG
AAGGGGTACCCTTCTAGGTCGTCGCTTTAGTGGTCTAATTTCGGTCTTTTTACGTTATGGAGTTT
ACTCACTTCTTTTTTATATTATTAGAGTTGAGTCTGGTATCGATA
Found at i:224642 original size:21 final size:20
Alignment explanation
Indices: 224612--224651 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 20
224602 CAAGCCGACC
224612 TAACCAACCTACGATATATAG
1 TAACCAACCTACGA-ATATAG
*
224633 TAACCGACCTACGAATATA
1 TAACCAACCTACGAATATA
224652 ACTTTGGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.42, C:0.25, G:0.10, T:0.23
Consensus pattern (20 bp):
TAACCAACCTACGAATATAG
Left flanking sequence: Indices 224112 -- 224611
CGGCTATGTCTAAGCAGCTGCTTTCCCATTCATTCCATAGGTAAGTCTTATTTTTTGCTGTAAAC
GAAGAAGGAATGATTCAATATCATATCATAAAAGACCTAGATGCTCTAGCTCCAAGAAAAGACTA
AGAAAACTCCTTAAAAAGAGAAGAGTCAATCCTCAGCGTCGGATTCTTCTTATGCTGATTGACCT
AGCCGTGCGTTTCCAACTGTTATGACTGGGAGCTAGGCGCTATTTAGCCCTCCATTTCTAAAGCA
AGCAGGGGAGCTAGACTCGCTCGACTGAAAGGAACGAAGTAGCTTGATTGATGAAAGGAACGAAG
TAGCTTGATTGATGAAAGGAACGAAGTAGCTTGACCGCGGGCGCAGGGAAAGGAGAGGGAGTCAC
CGAAGAGAAAAAATAAAGGTTCAAGACAATGAAAAATATAAACGCAGGAAGGAACAAAAGTCAAG
TATGTAATCTAGCAGTCATGAGAGCAGGTTAGAGGCAAGCCGACC
Right flanking sequence: Indices 224652 -- 225151
ACTTTGGGTTAGGTTGAAAAGTCTAGTTGGAAAAACAGATCAATCGCATCCCAAAGGGTCAAGGG
CTGAGTTGCACATTCTATTTTGGCCTCTTTTCTTAAGTAGAATGAAATGTTCGGCCTAATCTATG
ATATTGTGATTATGTTACTGTTATTTGGTCTTTTTCAAGCTTCCCAGAGTTGTCCTTCAGCAAGC
AATTATAGGGGTTGAAGGGGTACCCTTCTAGGTCGTCGCTTTAGTGGTCTAATTTCGGTCTTTTT
ACGTTATGGAGTTTACTCACTTCTTTTTTATATTATTAGAGTTGAGTCTGGTATCGATAGATTGG
CAACCTCTAGGGTACAAGCCCCTCCAGGTACACATATATGGGCTCTAATCCCAGGTTAAACTATC
CAGTCGAACTACGTAATCAAATAATCCATGGAAGACAGGGGTTGATCGAGTTTATTACCCTTTCT
CGTTTTTGGGTATAGGCTGATAGTTAGGCGGTGACTCACGTATCC
Found at i:261195 original size:21 final size:21
Alignment explanation
Indices: 261171--261212 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
261161 CTTCTTCCAC
261171 TTCTCTTTCTTGTGGTAGTCG
1 TTCTCTTTCTTGTGGTAGTCG
261192 TTCTCTTTCTTGTGGTAGTCG
1 TTCTCTTTCTTGTGGTAGTCG
261213 AATGAGGAAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.05, C:0.19, G:0.24, T:0.52
Consensus pattern (21 bp):
TTCTCTTTCTTGTGGTAGTCG
Left flanking sequence: Indices 260671 -- 261170
ATCACCTATATAACACGAAAGGAAGAAAAAAGCAGGGAATACAAGCATTACGGGGAGTTTAAAAA
AAGAATATGAATATGACTCTTCTCAACTCAAGTCAAGCGAAGCGTAGTGAGGGGAAGAACTACTA
GAGAAAGGCTACGCGAAGTTCTTCTCCAAATAGGTAAAACTCTTGGTAAACCTATTAAAATTGAT
ACCGGTTAAGTACATTAACAAGTAAGCAAGTAAACTACCTTCAATCCACTAGTATAAGAAAGACG
GTGACGAAAGTTGTCACAAATAAAACCTACTTCAACTGAAGGGTGATAAATCAGCCGTACTCTTT
CCCAATCCATGCTATCTATGGCGTGTAGAAATACACCAGCTGTAACCGACCAATACCTACAAATG
CATCTCAAGTAATTTGAGTTATTTTATTAGGCGGGGACAGGATTCGAACCTGCAGTCTTCAGGTC
ATGAGCCTGATGAGTCGACCAATTCCTCTACCCCGCTTCTTCCAC
Right flanking sequence: Indices 261213 -- 261712
AATGAGGAAGTATGTTGCGGCAACTAAAGAGTTATCGAGACTGACCGCAATTGCAGTAAGAGTTT
GACTTTCTTTCAGTTATGTAAAGTTGTTTAGTACGAGATCGCTTCACACCTCGCGGTGCTTACAC
CTCTCGCCTATCGAAGTTCTGTTCTAAAACCTCTTCCGAGAACTTGTATAGAGAAGGATTTCCCG
CAGAGCTGCAGTTCTTCCATACCAACTTAGCTGCCCGGCGCTGCTATTGGCATAACAACCGGTAC
ACCATAGGTTGGCCCAACCCAGTCCTCTCGTACTAGGGTTGGCTCCTCGCAGTTCTCCCTTTAAC
ACCAACGGTAGATAGGAACCGAACTGTCTCACGACGTTCTAAACCCAACTCACGTACCACTTGAA
TCGGCGAACAACCGAACCCTTGGGACCTTCTTCAACCCCAGGATGTGATGAGTCGACATCGAGGT
GCCAAACGACTCCGTCGATAAGAGCTCTTGGGAGTCATCAGCCTG
Found at i:262613 original size:18 final size:18
Alignment explanation
Indices: 262592--262634 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
262582 CAACCTTGTT
262592 GACTATGACAACAG-TCGC
1 GACTATGA-AACAGATCGC
262610 GACTAT-AAACAGACTCGC
1 GACTATGAAACAGA-TCGC
262628 GACTATG
1 GACTATG
262635 GCAGGGCGGT
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 262092 -- 262591
TACCGTCTAGCCGTTGGTACTCCGCATCTTCACGGAGAATTCAATTTCACCGGGTCCATGTCGGA
GACAGCGGGGCAGTCGTTACACCATTCGTGCAGGTCGCTACTTATGCGACAAGGAATTTCGCTAC
CTTAGGACAGTTAGAGTTACTGCCGCCGTTTACCGGGGCTTCCATTCAAAGCTTATAACACTTCT
CCTTCCGACCTTCCAGCACCGGGCAGGTGTCAGACTCTATACATCGTGTTACCACTTAGCAGAGT
CCTGTGTTTTTAATAAACAGTCGCTACCCCCTGGTATGTGCCGCTTTCCTAATCAAAAGATAGGA
GAGCACCCCTTCTCCCGAAGTTACGGGGTCATTTTGCCGAGTTCCTTCGACATGGTTCTCTCAAG
CGCCCTAGTATACTCTACTTGTTCACCTGTGTCGGTTTGGGGTACGGTCAGTTCACCGGGAGGAT
CGCCCTCCCAATTCGAAGTTTTTTCCTGGAAGTTTCAACCTTGTT
Right flanking sequence: Indices 262635 -- 263134
GCAGGGCGGTACGCTCTGCTCTCTCGCGACCCCTACTCTAATCAAAAGACTAAGGGCCCCTTAGG
TCGCCAAACTACGACGAGAGTTTCGCCTTTTGAAGCGCCAGTCGCGTAGGGCGACCGGGCCAGGC
CGAGTCAGAAAGGCTTTGATGACTCAAGGTTCATATTAGGGAAAGGAGAGTGAGGGGAAGAGGGG
GCAGCCCTCGGCCCGATCATCCAATTCGCTCCAACAGATAGGCATGGTTCTGTAGTCAAAGCAAC
TTCGTCACTTTCGTGTACCCATCGGACGGCAGCCCTTTCGGGGGTTCCTTAGGGACCGATTCACT
CTGCGTAGATTGACTGAACGCAGAAAGCCTTCCACTGGCAGGCGATCGTGTTTTTCACAGGATTT
ATCGTTACTCATGTCAGCATTCTCACTTCTGATATCTCCAGGTGTTGTCACCAAAAACCTTCCCC
GATTGACAGAACGTTCCGCTACTGACACTTGAAAAAGAAGCTTTC
Found at i:273448 original size:39 final size:39
Alignment explanation
Indices: 273405--273483 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
273395 CGATTTTCTA
* *
273405 TTCACTCATGATCTGGCCTGGTCGACTCGATCATGATAT
1 TTCACTCATGATCTGGCCTGGTCGACCCAATCATGATAT
273444 TTCACTCATGATCTGGCCTGGTCGACCCAATCATGATAT
1 TTCACTCATGATCTGGCCTGGTCGACCCAATCATGATAT
273483 T
1 T
273484 GAAGGATGGG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.22, C:0.27, G:0.19, T:0.33
Consensus pattern (39 bp):
TTCACTCATGATCTGGCCTGGTCGACCCAATCATGATAT
Left flanking sequence: Indices 272905 -- 273404
GCCCACACCTGTGTAGAGTGGATCGTTCAACACCTGCGGCACAAACCCATTTTTGACCTATTGGT
CCTAGTATCATAGGCGACCGAACGGCCGCCCCCTAATTACTAGACCAACCTGCTATAATAATTCC
ATAAACACCTAGCGAAGATATGGCAAACAAATAAAGTAGCCCTATGTTCGAATCTGACAATACCA
TACCATAATCAAAAGGTACAACGGCCCGAGCAACCAGACTTAACATAAATGTAGTCACTGGAGCC
ATTCTAAAAAGGGAGAAATTAGCACTACTTGGTGAAATAGGTTCTTTTAGAATCAATTTCAAACC
ATCTGCTAGAGGTTGTAACAATCCGAACGATCCCACTACATCAGGACCCTTTCGACGTTGCACAA
AAGCCATTACTTTACGTTCAGCTAGCACTAAAAAGGCTACTCCTAGTAGAAGTGGTAGAATTATT
CCAAGTATTTCGGCTGGAACAGCTATGTACGTTTTCGATTTTCTA
Right flanking sequence: Indices 273484 -- 273983
GAAGGATGGGACCTTTTCTCGAAAAACTCCGGATCCAGAGAAGAGTTGAAGATGGTGCAACATCG
AATCCTGTTACCTTACTTCGAATGGAATCTTAGCCCGCCTCACTTGCTTTCTGTACTGCATAAGG
GCCATAAGGGCATAAGCGAAGTCAAGGGATTTCCTTCTAACTAGTGGCTGAGAGTAAGCAAGCTA
CCTTCATTCAACAGATTTGTGGTTGAGTCAATAACATGCTCTGGGTCGGGAATCTTTGCTCTTCT
CTTTTGCATTTCCGCTGCCTGCGTTCTTCTTCGTGTCCGTCCGTATCGCAAAGCTGGTCGACGCC
AGCTGTAATGGTTGAAAATAGGGGGCCAACCAAGACCCCTACCCTAATCAAGCTTTGTTCGATAA
AGCAAACGAGTCGTTCCGACAACTTCGGACCAGATTAACCCTTTTGAATTAGCCGATCTTACAAA
ATCGATCGGGCGGGGGTGATTAGCGGAGAAAAGAATCGCTGAGAG
Found at i:288270 original size:17 final size:17
Alignment explanation
Indices: 288248--288284 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
288238 GCACAGATTC
*
288248 CCTATAAATAAAAATTT
1 CCTATAAAGAAAAATTT
*
288265 CCTATAAAGAAAGATTT
1 CCTATAAAGAAAAATTT
288282 CCT
1 CCT
288285 CTCTTCCCCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.46, C:0.16, G:0.05, T:0.32
Consensus pattern (17 bp):
CCTATAAAGAAAAATTT
Left flanking sequence: Indices 287748 -- 288247
TTTCATCTCTTATTGCTCCAGCTCCTAAGGAATGAGATTAGCTTGATTACGCACCAGATTTACTT
TTAGTTACTGAAAGCGCTGATGAACGATCTTCCTTATTTTAGGATGCAACTCGGATTCCTCCTTC
ACGGCTTGAAGCCGGATAGCTTGAAGCTTAAGGGCTCTCGGAATTCCCTTTCAAGCTTTCTCGAG
TCACCCTAACGTAACGGCTAAGAGAACTTGGCTAACTTCGATCAATTCCACGACTTTCCATCCTT
CTTGTGTTGTGAGAGTTTCAGATTAAGGGGATGCGAGTCATCAGTTCTTTCCTCCTAGTCTAGGC
TTTAGGCCTGATAGTTCATTCTCGAGGATCACTGAACTTGGCTTACTTCTTACTGAATGCCGTAC
TTAGAGTTATCCCACTCGGGGTGAGCTCTTAGCGATTAGTCAGTCCGGGTCCAGCTAGTCTTGCA
CTTTCAGACCGGTCCTTCAAACAAAGGCTTAGTAAGCACAGATTC
Right flanking sequence: Indices 288285 -- 288784
CTCTTCCCCAGAATTAGAATGCTTTCCTTAGCTAATACTGATTGATTCACCGCATCTTCTCGTTC
ATTACATTAGGAGATCTAACCAAGCACTCGAAATGCGACATTGACTAAAGAAGGTAGACAAAAAG
GCAAACTAGAGAAAAAGCCAAGCTGACTGAATTAAATATGTAAGCGGATTGGTGTGGAACTAGAT
CCTCTGTTAGAGTTACAGTTGTTGTGTAGCCGGGTTCACCCCCAATGATACGAAGGGCTAGCTTT
GCTACCCGAAAAGGCTACTTGCTTGCGGGACCCTTTCGTTTTCGAGTTTGCCCATACTTTTTGTT
TGAACAGATATTATGTTAGTGTTCCGTCTTAGGTCGAAAAGAAAAAAGAATTGCGTAAATAACTC
GTCAGAGTCACGATCTACTAAAAGGCAAGTAGCTTGATTGGTTCGAATCCAATTCGTGAGATGGT
TTCTTTTCTTCTTTTTTTCCGGTATGCCGCTCCGCGAACAAGGAG
Found at i:362491 original size:15 final size:16
Alignment explanation
Indices: 362471--362513 Score: 52
Period size: 18 Copynumber: 2.6 Consensus size: 16
362461 CGGATGGACA
362471 GATCGACTGT-CGCAT
1 GATCGACTGTGCGCAT
*
362486 GATCGAGTGTGAGCGCAT
1 GATCGACTGT--GCGCAT
362504 GATCGACTGT
1 GATCGACTGT
362514 TAAGGTAGGA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
15 9 0.39
18 14 0.61
ACGTcount: A:0.21, C:0.21, G:0.33, T:0.26
Consensus pattern (16 bp):
GATCGACTGTGCGCAT
Left flanking sequence: Indices 361971 -- 362470
ACCTGTATTCGATACTGGGTCATTCATAGCAAACCTATACCTTCCCTATTTACTTTACTCGACGA
ATTAAGGGGTTTGGTTATTCGTCAGCACGGGTTTAGCTTCCTCTTCCTCTTGGATTGCGTCAACC
GCTCAAGTGAAGCCAAAAAGGGAGGATTTCCGAAAGGCTCCGATCCAGTTAAAATCCGTTTAAGC
TAAAAGCACCGGTTTTCTCCCCAGGCAAAGGCCAGTCAACAGCCAGTCCACAAGAGAACCCCGAA
ACGGGAGCAAACCCCCCTTCTACCTTTCTTTCTTTCAGAACCTTTCTCGCCTGCCGTTAAATGAA
AGTTTATTTGAGTTCCCAATGGCTGGTGAAAGTTAAATAGGAGACCTCAAGCTGCCATACTTGAC
TAGAACCGAAGGAAGATCTCTCACACCGGCAATGGAAACTAGATGTCAACGAGCGGCACATAATT
GAAATTGGACAACCTCACCCCCCAGTGAATGTAGTCGGATGGACA
Right flanking sequence: Indices 362514 -- 363013
TAAGGTAGGACCTTCAACAAAGAGAGTTGATCAACAAGTTCAGACTATTTTCTGTCAATTCGGCT
GTCCTCTCATTTCTATTATAAAATCAAATGTCTTGAATCATTCGATATAAGGGCTTCACTTCAAA
GAGGCATAGGAACAATGTCCCGAAACTGAAGATGAGACTGAAAGCTGCCATACGAGATTAGAGAA
TAGAAAGTAAGGAACTGTTAGAAATGGAATATGGATCTTGCCCATATATATGTACTTTATTTTAT
CTTCTTTCTTGTCGGATTCTCTGGGGGATAAAGAAAAAGTATATGCCCCGGACTCGCGATTTGGG
GATTTCCCTGGCTAGGATGCTAAAGATCGGATGCTGCCTCCTTTAAGGAAGGTGCCTAGCCTTGC
TAAAGGACATGCTACCACCCTACCAAAGCCGACAAAGTAAAGCAGGAAAGTCATCAGGTGACGAA
GACGGAGGAAAGGCAAAAAAGGTCAATAAAAGCTTCTTATGTGGC
Found at i:367808 original size:21 final size:21
Alignment explanation
Indices: 367782--367844 Score: 117
Period size: 21 Copynumber: 3.0 Consensus size: 21
367772 AAGACCCGCT
367782 TTCTTGAGAGAGAAGCCTATG
1 TTCTTGAGAGAGAAGCCTATG
*
367803 TTCTTGAGAGAGAACCCTATG
1 TTCTTGAGAGAGAAGCCTATG
367824 TTCTTGAGAGAGAAGCCTATG
1 TTCTTGAGAGAGAAGCCTATG
367845 GACCCTTTCT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.29, C:0.16, G:0.27, T:0.29
Consensus pattern (21 bp):
TTCTTGAGAGAGAAGCCTATG
Left flanking sequence: Indices 367282 -- 367781
TAGGAGATGCACGAATATTTATTCGATGTCTAGTTCCACCTATAAGATTCTTTAATTTGAACCCT
ATAACGTCATCCCCCTTATGGGAAGAACAGCCTTCGATTTACGGGCTGAAAGCGGACATAGCAAC
ATCCTACCGAAACATCAGACACGCGCCTTCAGCCGGATTGGCATACCTAATCGAGCATCATCTGC
TATTCACCAGCAGAGCTTTGCAGCTTATTCTTCCCTCTCCAGTTGAGGAAGTTTACTAGCTCGAC
CAAAGGTAGGGAGAGGGAGAGGAAGGGTGCCGACAACCCTAGATATCTATTAAAAAAGGGCAGGC
TAGGAGGTTCTGTTACTGAACTCGAACCCACTAAGCGGGATCCCTTGCCTGGTCTTACAGCTCAA
AAAGGAGGATGAAGAATTGGGAGCCCAGTTCCTCATGCCAATAAGGGGTATTAGACCCTACCCGC
AGGGAGTACGCTTGAACGGCACTATACTACCCACTAAGACCCGCT
Right flanking sequence: Indices 367845 -- 368344
GACCCTTTCTCAATCTCAATAGGAATTGAGGGAGCTCATGGGGACTTCTAGCTACAGGACCAGTT
ACTAGTCCTCAAGAAAGATCAGATCACGCAGATCTTCCGCTTAAATCCACCTATGGAATATCTTG
CGGAAACTACTCTCTTGACACAATTTGCATCAAAAAACACGGGGTTTATGGAATTTGTGTAGTCC
GGGACAGAGACTAAATATATAGTTTCGTACCTTAGAGTTTCAATATAGGAGTCGGAAGCGAGAGA
TTAGAGAATAGAAAGTAAGGAACTGTCTGAAAGTTTGTCCCTTCAAAGCCAACTTCGTCTCTGAA
CTCAAGCCTTCCCTTTGACCCGCGTATCCTATCTGTAACCGAACCTGCGGGAAAGCCTACTGAAG
AAGGAAAAGCAACCATATCTCCTTGGCAAACAAGACGGAACCGAAGCTATGTGCATAGTCTTACC
CCTGCCCAATCTACTCAAAGGATTAGAGATCATGAACGAGAAAAT
Found at i:401877 original size:16 final size:16
Alignment explanation
Indices: 401856--401986 Score: 70
Period size: 16 Copynumber: 7.8 Consensus size: 16
401846 TAGTAGAGAC
401856 GGCTTGCATAAGGGTT
1 GGCTTGCATAAGGGTT
* *
401872 GGCTTGGATAAGGCTTAT
1 GGCTTGCATAAGG-GT-T
*
401890 GTG-TAGCATAAGGGTT
1 G-GCTTGCATAAGGGTT
* *
401906 GGCTTGGATAAGGCTTAT
1 GGCTTGCATAAGG-GT-T
*
401924 GTG-TAGCATAAGGGTT
1 G-GCTTGCATAAGGGTT
* *
401940 GGCTTGGATAAGGCTTAT
1 GGCTTGCATAAGG-GT-T
*
401958 GTG-TAGCATAAGGGTT
1 G-GCTTGCATAAGGGTT
*
401974 GGCTTGGATAAGG
1 GGCTTGCATAAGG
401987 CTTATGTGTA
Statistics
Matches: 84, Mismatches: 19, Indels: 24
0.66 0.15 0.19
Matches are distributed among these distances:
15 3 0.04
16 42 0.50
17 6 0.07
18 30 0.36
19 3 0.04
ACGTcount: A:0.23, C:0.09, G:0.37, T:0.31
Consensus pattern (16 bp):
GGCTTGCATAAGGGTT
Left flanking sequence: Indices 401356 -- 401855
GGATAAGCAAGAAGGTAATATCAGTAGTGAGACTCGAGGGTACCATCAGGGGGGGTTTGGGGGTC
CTCCCCCAGCCTAGCTAATAGAGAACTTAAATCTTCCCGTTAAGACTGACCAGAAATACCGGGGT
TGAAGGCTTCAGTGAGAGTTCCAGGGTTGTCAACTAGAAGGCTGATTAGAAGATAAGGTTTTTCC
AGGGTTGTCTACGATCAGAACTAGAAGGAAGATGTGATAGCAGTAGCAGAAGGCGGATGCTCTAG
TTCCAGGCTGATTATAAGAGATAGTTTACTCGGACGGTGGGATAGCTTAAACATCATCTCCTCCT
ATCCCGGTGGGAGTACTGAAAGAGGGTGTTACGGGCTTCTTCTTATAAGAAGGAGGGCTTTAGGG
CTTAACTAAGTATTAGTTAAGGGCTCGGAACTTCTAGTAAGTGAAGGTCAGCGGGAGCTGCTATC
GGTAGCGGAAAGGGCTTGACTTATCTAAGTAAAGGTAGTAGAGAC
Right flanking sequence: Indices 401987 -- 402486
CTTATGTGTAGCATAAGGGTTGGCTTTTAGTCCTTCTTTCCCAAAAAGAAGTAGACCTTATGGTA
CGTACCCTTCTTAGCCATTGGTGCGTTAAGGCTGAATGGGTAGTCTAAAAACAAAAGAGGCTTCT
CCTCAAAGGTAGTTTACTTGCTTAGTGCTTGCTTGCGCTAAGGATCGAAGAGCTTAGTGTGAAAC
GCTAAGGAAGTCATATGCTCTTTTCTTAAGTGTGGTGCCCTCAATACAACCTTCCCTAAAAGTGG
AGGTAGGAGATCCAGTTAACGAATAGGCTACGGCTGTAGCTGCAACGAGTAATGAATTCTCGGAA
GCTCTTTCTTAAGGGGTGCCCCCTTCCCTCGAATGCTGCATTGGAGCGAGTTCTTCTACTGCCGA
GTCCAGCTCAGGTAGCCATTCGTTCATGCTTCGCCCGGAAGGTTCCTGATAGCTGGTTGACAAAT
TGCTGTATACTATACTAGGATGCCGGATCTAGATAGATCCAAAGC
Found at i:401904 original size:34 final size:34
Alignment explanation
Indices: 401861--402012 Score: 304
Period size: 34 Copynumber: 4.5 Consensus size: 34
401851 GAGACGGCTT
401861 GCATAAGGGTTGGCTTGGATAAGGCTTATGTGTA
1 GCATAAGGGTTGGCTTGGATAAGGCTTATGTGTA
401895 GCATAAGGGTTGGCTTGGATAAGGCTTATGTGTA
1 GCATAAGGGTTGGCTTGGATAAGGCTTATGTGTA
401929 GCATAAGGGTTGGCTTGGATAAGGCTTATGTGTA
1 GCATAAGGGTTGGCTTGGATAAGGCTTATGTGTA
401963 GCATAAGGGTTGGCTTGGATAAGGCTTATGTGTA
1 GCATAAGGGTTGGCTTGGATAAGGCTTATGTGTA
401997 GCATAAGGGTTGGCTT
1 GCATAAGGGTTGGCTT
402013 TTAGTCCTTC
Statistics
Matches: 118, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 118 1.00
ACGTcount: A:0.23, C:0.09, G:0.36, T:0.32
Consensus pattern (34 bp):
GCATAAGGGTTGGCTTGGATAAGGCTTATGTGTA
Left flanking sequence: Indices 401361 -- 401860
AGCAAGAAGGTAATATCAGTAGTGAGACTCGAGGGTACCATCAGGGGGGGTTTGGGGGTCCTCCC
CCAGCCTAGCTAATAGAGAACTTAAATCTTCCCGTTAAGACTGACCAGAAATACCGGGGTTGAAG
GCTTCAGTGAGAGTTCCAGGGTTGTCAACTAGAAGGCTGATTAGAAGATAAGGTTTTTCCAGGGT
TGTCTACGATCAGAACTAGAAGGAAGATGTGATAGCAGTAGCAGAAGGCGGATGCTCTAGTTCCA
GGCTGATTATAAGAGATAGTTTACTCGGACGGTGGGATAGCTTAAACATCATCTCCTCCTATCCC
GGTGGGAGTACTGAAAGAGGGTGTTACGGGCTTCTTCTTATAAGAAGGAGGGCTTTAGGGCTTAA
CTAAGTATTAGTTAAGGGCTCGGAACTTCTAGTAAGTGAAGGTCAGCGGGAGCTGCTATCGGTAG
CGGAAAGGGCTTGACTTATCTAAGTAAAGGTAGTAGAGACGGCTT
Right flanking sequence: Indices 402013 -- 402512
TTAGTCCTTCTTTCCCAAAAAGAAGTAGACCTTATGGTACGTACCCTTCTTAGCCATTGGTGCGT
TAAGGCTGAATGGGTAGTCTAAAAACAAAAGAGGCTTCTCCTCAAAGGTAGTTTACTTGCTTAGT
GCTTGCTTGCGCTAAGGATCGAAGAGCTTAGTGTGAAACGCTAAGGAAGTCATATGCTCTTTTCT
TAAGTGTGGTGCCCTCAATACAACCTTCCCTAAAAGTGGAGGTAGGAGATCCAGTTAACGAATAG
GCTACGGCTGTAGCTGCAACGAGTAATGAATTCTCGGAAGCTCTTTCTTAAGGGGTGCCCCCTTC
CCTCGAATGCTGCATTGGAGCGAGTTCTTCTACTGCCGAGTCCAGCTCAGGTAGCCATTCGTTCA
TGCTTCGCCCGGAAGGTTCCTGATAGCTGGTTGACAAATTGCTGTATACTATACTAGGATGCCGG
ATCTAGATAGATCCAAAGCCTGACTACACGGAATAAATGTAATAA
Found at i:418811 original size:18 final size:17
Alignment explanation
Indices: 418780--418820 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 17
418770 ACCAATTACA
*
418780 TAAAGAGGTTAAACCCT
1 TAAAGAGGTCAAACCCT
418797 TAAACGAGGTCAAACCCT
1 TAAA-GAGGTCAAACCCT
*
418815 GAAAGA
1 TAAAGA
418821 AAGTAAAACC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
17 6 0.29
18 15 0.71
ACGTcount: A:0.44, C:0.20, G:0.20, T:0.17
Consensus pattern (17 bp):
TAAAGAGGTCAAACCCT
Left flanking sequence: Indices 418280 -- 418779
AAAGCACGAACGGAAGCTGGGACCTCCTGATCGCGTAAGGTATCCAACGAGAGAAGCCATAAGTC
AGCACAGCTTTGTCACCTGTATCCGGATCCTGGATATAAATTTGACTACCCGGAAGAGCAGAAGA
AATGGGATTCTTGTTCACACGAAACCAAAGGGGTGCTTGAGCACGCCAACCACGGGTACGTGTAT
GGAACGGAAGCGGCATACGACTGGTCACAGGACAGACCGAGTCGGAGCCGTGAACACGAACTCGA
CCCTCGAAAGGTGGAGCGATCGAGTCGGAATAGGACGGACCTACGAAAATGGGATGATTTCGAAC
GATAGGATCGGACTGTAAGCACAACTTTCGAAATAGAGTAATCATGGATGGAACTTGTTATTAGA
ATAGAAGACCAGAAATCAGACAATAGCAGAGCAGCCAGGGAATGAGGAACAAGGTTAACCAACTG
TATTTTACCTCATTACATCCCCTTCCTTTCAATTAACCAATTACA
Right flanking sequence: Indices 418821 -- 419320
AAGTAAAACCACTTAAATGTAAGACTATGGATTCAATCCAGCCCGCTTTGCGAGCTAACTTGTAA
AGAAGATGTAGCTACTCGCCCATGGCGGACGAGGCCCAGAGAAGGGCAAAGGACTCATTTCTTTT
TGATCCCAAACGAGAAGAGAGAACAAACGGCGATTACTAATAGCCGGTGGAGATTGGAAATGTCC
CAACCAACATAGCTTGCTAGCTGAAGGAGCTGCCAGAGCAGAGGAAGCGAACCGCCTTGACTTAT
TCGATTCTCCTTCTTCACCGTTCGAAAAGAAGTGGATTGGCGCACGTCTTCCTATGAAATCGATT
ATGTTTCCCCATCAAGCCCGTTTCCTTACTCGAGATATCTGAGATAGCCCCGTCAACTAATAACT
TATAATAGACGAGCCCATTATCCTTCTGTTTTGAACTTGCTTCTTGGTACAAGGGGAGGGGCGAA
GAATTCGAGTTCTAGTTCTGCTTTTGCCTAATTTTTAGTATCGCT
Found at i:420060 original size:14 final size:14
Alignment explanation
Indices: 420041--420067 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
420031 TTGCCCGCGA
420041 GAAAGCGTTCTAAT
1 GAAAGCGTTCTAAT
420055 GAAAGCGTTCTAA
1 GAAAGCGTTCTAA
420068 CGATAAGCTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (14 bp):
GAAAGCGTTCTAAT
Left flanking sequence: Indices 419541 -- 420040
CCTATTACCGTTTCGCTGCTTGTTCTTCCCCTTCGCCTGAGAATAATAAATTACCTTCGATGGGA
GCTTACTCTTACTTAAGTAAGAGGGAAACTCGCTTGCCCACTGGAAAGACTGAAACTTGAAAACG
GAGGTAAGATTTTTCTTATTCTTCCTAAAAAAGAGGACTGTGTAACTAGGGTGAGAAGCGAGCTG
AGCTGCCACGGATTGCTCCTTCGATTGCTTGAAACCTCTTTGCTGAAAGTGAAAGTGAATACATG
AGAAAGACTAGAGACCCAGCTGGAGGATGCCCACTTTGAGAATCAATATCAGAGTCAGCAACCCT
TGAGTAGCCTAGCCCATGAATGAGTAGAAGAGGGTTCCTCGCCCAATTCCATAGGGATTCTAAAG
AAAAAGCAATCTCTATCGACCAAGCCCTTCCCACTAATCCCGTCTGCGCTTTTCTAAGATTCGGT
TGCTACCCCGAGACGAAAGCCCTGGACAGCTATCCTTGCCCGCGA
Right flanking sequence: Indices 420068 -- 420567
CGATAAGCTGAAAGTCCTTACTAAACTCTCAGGACAGAATGACAGACCGACCCTTCCCCTTCGCT
ACCGACGGTTTAGGCAAGCTGAAGGAAGTGGGTCAAATGCCATTTCTATAGTATAGGATTCAGTG
TTCAAGGGCTCAGTAGGTAAGCAGAGTCGGTTTGTTAGCGCCTTCCGGAGTTTTATAGTCTTCTC
TCCGTCCCGATTGCCGCTAGTCAGTAGCTCGCTTCCGGAGAAACTACATTCAACAGGAGAAACGA
AACTTTGAATAGAAAATAGAAGGATCAGTGCCCGTAGCAGTCCTGGAGTTAGGTTATGATGGTCG
TGATGAGCTCTACTAGAAAGAAAATCTCTTCTATTCATAGAGGAAGTGCTATCTAAGGGGCTTCT
AAGCCCAGCCCTTGAATTCCGTTCCGTAGTTCAGTCCGGAACTCCAGATGTGTAAGTAGCGGCCA
AGCGGCTCTGTCCTTTTCAAAGAGGTTATCCTTCTCTGTCCCCGC
Found at i:423810 original size:19 final size:19
Alignment explanation
Indices: 423786--423823 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
423776 CGGAATCTGA
*
423786 AACCCTTTGGTGTTACTGC
1 AACCCTTTGGGGTTACTGC
423805 AACCCTTTGGGGTTACTGC
1 AACCCTTTGGGGTTACTGC
423824 TGGAAACTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.26, G:0.24, T:0.34
Consensus pattern (19 bp):
AACCCTTTGGGGTTACTGC
Left flanking sequence: Indices 423286 -- 423785
TGTCAACCGAGTTCTTGCTTTTGGATTCAATCCTTGGTAAAGTGTTCGATCTCGTGGAGAGGTAC
GCCTCTAAAAGAAAAGAGAGTAGATATAGGCTCGAGAATAGGCTTGATGAACAAACAGCCGATAC
GGAATCTGAGCCAAAAAGCCAAGCCCTTGAACTTCACTCCTAGGCCATTCAACAAATCTGGCGCG
AAAAGTAAATCCGATTTCGGTCAGATCTTCAGGAGCTTCCGAATTTTTAGGTTAGTTAGGCGCCT
GGCCGAAGGTTGAAAGAATGATTCGGGGTCAGAGGAAGGGGGCAGCATTCAACCTTTCCTCTATC
AAAGAAGACTAACCCTTTGATTTTATTCAATGGTGGTTTCTACAAGAGATTCAACGACAAGGGGG
GCTATTAGTAGGATATGAAGCTTGAAATGGAAAGGTAAGGGTGAGAAAAAGAGGCCAAACGAGAT
ACGCTCGAATGAGCTAGCCGACTACGAGATCAGTCCGGAATCTGA
Right flanking sequence: Indices 423824 -- 424323
TGGAAACTCCTGAACATATAACTCTGCATGGTAAGAGGATATACAAGCTAAAGAAACATACGTCC
TGGTCGGAAAGAAGGGAATTTAGTGCTGGTAGAGCTGCCCGGTATAAGTAGGAATCTCTCTCCAG
GGCCATAGCAGCAACACCATGTAGTTACCAATTATGCTAAGCAACTTAACCGAGGAACTGGCCGA
AGTCATCAACATATTAGTAACAGAACACTGATCAGCCGGGTTCTTGAAACTCCTCGTATTTAAGG
AGCGACTTTCCCTCTTCTGCCTTCCGTCGCCTTAAGACAAGACTCAAAGCGGCGATCCAAGAAGT
TCCCTTAATGATAGTGAACTAAGGTTTTGAAAATACTCGTCCAAAGCGTCAAGTAGGAATGATCG
GTGAAATCCGCCTTCCTTGCCTTACCGACTTAAAGCAGTTAATAATATCTGTCTGCCTGCCTCAA
TGCTCGCTGACTTACTGGCCACGTTACTGAGTTCCTAGGAACGAG
Done.