Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NC_068761
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: 606136
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Found at i:47672 original size:28 final size:28
Alignment explanation
Indices: 47632--47689 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
47622 AACTTTTCAA
47632 TATAAAGAAAGACCTTGTACATCTGTCC
1 TATAAAGAAAGACCTTGTACATCTGTCC
47660 TATAAAGAAAGACCTTGTACATCTGTCC
1 TATAAAGAAAGACCTTGTACATCTGTCC
47688 TA
1 TA
47690 ACTTTGATAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.36, C:0.21, G:0.14, T:0.29
Consensus pattern (28 bp):
TATAAAGAAAGACCTTGTACATCTGTCC
Left flanking sequence: Indices 47132 -- 47631
AGTGGGATAGCTGAAAGCTTTTGATATGGATCTTAAGTAAGCACAAACCTGTGATAAAGGTAGTT
TCCCCCTCTTGGCATTGTAGGAGTCATTCCAGTAGTTTCATTCCAAGCATAAAAAGTACCCGCAT
TGAATTCGCCTTCGTGGCAGTCTCTTAGGCGTCAGATTTTAGGCAAGCAGAAGGATCAGATAAGA
CATAGATTTATTTTAGTGGGAGTTATCCATCTAGGTCAAGCGCTAATATATACATTGATTTCCTT
TAGAGTTGAGAGTAAAATAGCTAGAAGAAGGCTAGGAAGGTGGAAGAGAAATTACCTATAATAAG
AAAGAGAATCCAATTTTATAATATGAATTTGAATGGATTCTCCACTAACTGGAAAACCTGCCAAT
CCACTCTTCCTTTTTGGTCTGCCACTACTGTCTTACTGAAGCTGGCTTGCCTTGCGTAGATCAAA
AACTTTTCAAACTCTTTTGGTCGGCTTACTAATAGAACTTTTCAA
Right flanking sequence: Indices 47690 -- 48189
ACTTTGATAACACTGGAATACATACTTTACTTCCGCGGGTATTGGCTTTCGGGCTTGATGAGCTC
CACCTTAAAGAGAAAAAAAATGGGCCTACTGCATGGGTTAATGTTGATAGGATCTGGGAGATTGG
AAAAGACATCCCGGTAAATGTATTTCTTTTAATAAAGGAAAGCTTCCACGTCACATCCGATAGTC
TGATTGGACTTCTGCTGGAACTGGCTGGTCACACTCGGTAAGACTTTTTTTATCCTGTAAGACTG
GCTTTTAATAGAACCCCTAACATCTCTAAGAAAGCATCGACCCTCGCTGATGCTCGTACATACTT
TGATTTCCGACTAAATAAAAGAGGCTTTCTTTGCAGCATCCGTCTTGCAAGCAACCTATCCCCCT
ATATTAGATTAATCGGGTTACAAAAACTCTAACGGATATAGAGCCAACGGACGCTATGGATTTGT
TGTACCATTTTACGTGCTTGAACTCAGAACACACGCCATCCGATC
Found at i:98136 original size:25 final size:25
Alignment explanation
Indices: 98091--98138 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
98081 GAAGCGAGAC
*
98091 TCGACTGTTAAGGACCCAGAGGGGA
1 TCGACTGTTAAGGACACAGAGGGGA
* *
98116 TCGACTGTTAAGGAGAGAGAGGG
1 TCGACTGTTAAGGACACAGAGGG
98139 AAGCACAAGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.29, C:0.15, G:0.40, T:0.17
Consensus pattern (25 bp):
TCGACTGTTAAGGACACAGAGGGGA
Left flanking sequence: Indices 97591 -- 98090
CGCATTCGCTGCATCTGAAGGGACGATTTCAGATAGGTAGGTTGGGTTGCTCGTTGTGGTTGCCC
GGACCTCGATCTAGATCCAAGATAAACCAAAAGCATGGGTCGTGGTCGGCAGATATATATGATTC
TGCCGGGGCTTGGGCTTGACTTCTTTCTTCATGAATGATTTTGGAGAAGCCTGCCTCGAGAGAGA
CATATGGCATATCTGACTGCCTGATTGGCGAGCAGCTGTCCTCATTCATAAGTCCAAAGAACTAG
CAACCAAACTGGTCGCAAGCAGGAGAGTGACCAGGCCTGATACTGATTGAAACGTTTATTTAATT
GGAAGCCGTTCAGATAGCCCTAATTAGTTTTAATTAGTTTAGTCAATGTTGAGCTGTCATATCTA
GCTGCCATATATGTAAACATGCCCTAAAAGTAAAGGGATCATATTTCCTTTAGTAACCACTTTTA
CCCATCCGCTCTTCTCCTGACCGATTGGAGGAAGAGAAGCGAGAC
Right flanking sequence: Indices 98139 -- 98638
AAGCACAAGGTTGGTGACCCGGGGGAAAGCGAATGCAGATCTCACGCAAAGTGAAATCTCAAGAT
TCAGATTGGGTTTGTGTTCGGTGTGGAGTAGATAGGGCTATTCCTTAGCAAGGCTATTCAGTAAA
GGCGAGAAGGGATCTATAGCAAGGGCAGCCCGGGTCTACCCGCAGAGTTGAGGAAGATAGATCAA
ACAGCCTTAGCGCTTTAGCTTGAACTGTAACCTTACCCTCGCTACTGACCTGTCGCTTGGCCCGA
AAGACTGGAACTAGAAGTCAACTGTGCCTAGACCTCAATCAATACGCTTACTGAGAGTACCGGTA
CCAGAACAAGAACAAGGATTTCTCTTTGGTCAAAGCCGCCGCACTTGAACCGTAACCAGCTAATG
CATCGCCTTCTATCTGCATTTCTAAGACCAGTCCCTTATTCTGCTAACCAATTAGGTTGGTTCAT
CAGGTGCCAAGGCATCTCTTTCTCCCAGGTCCCATCTCGAACATT
Found at i:100000 original size:22 final size:22
Alignment explanation
Indices: 99974--100018 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
99964 TAGTGGAGCC
99974 TTCGTGTACCAATTTCAGTGGT
1 TTCGTGTACCAATTTCAGTGGT
99996 TTCGTGTACCAATTTCAGTGGT
1 TTCGTGTACCAATTTCAGTGGT
100018 T
1 T
100019 GAGTTTCGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42
Consensus pattern (22 bp):
TTCGTGTACCAATTTCAGTGGT
Left flanking sequence: Indices 99474 -- 99973
AATCACTCCGTTGGGACGGGAACATGTATCCCTCCCAACCAAAAATCTTTTTGTCTAAATCAGCT
TTCGGCCTATCGATTTAACCGGGAGCTGCTGTTGAGCACTCTCACCGGATTCCCTATGCGCTGAT
TGATGCTTCCTCTCCGACTCGATGAGACCACACTACTGAGTGAGCTTCTTTCTGGCGCTCTTCCT
AGGATTCCTAATGCCTCTTGCTTCAACACAGAATAAGGTCTTTTCTCGGCCACTTTGTCATGAAA
TGAAAGCACAGTGAGTGAGTCTTCTTTCCGAGTCGAGTACTAGGCAGTCAATGTAGAGTTCACTT
CATTTGTCAGACTCCCGGTACCGAAGCAAAGTACTCATCCGAAAAGACGGTTTGATCATGCCCTT
TGTCCTCAACCCATGGTTCTCCTATATCTCCTAACTTTCGCTTTGCTTTCTCTTGAGCCCGCATT
TCGTGTTTTTTAAGATATTAAGAGGTGAACCCGCATAGTGGAGCC
Right flanking sequence: Indices 100019 -- 100518
GAGTTTCGCACTCCCGTCATCTTCCTCTTCTTTTTGGAAAATCCCAAATAGTCATCAGAAACAAG
CTAGCCGAGCATTGATTTGGGTGTGGGTGGGGTATGGTGCCCCAACGGATGGATCTCCATCAACA
TGGGATTTTTCCGAGGGGATCAATGTCTGGTCGAACCAAGCTTCCTTCTCTCTCTCTTGCTTCCC
CACCTGTGACTGAAGCTTCCACATGAACTTGACTTTCCTATCTGAGTAGACCGAAAGTTCTACTT
TTTGGGAGGGACATTAAAAAGGTAGCTTTCTCCCTGGTCGATCAGTCGTTCAATCCTTTCCTCTT
GATCAAATGCATTTCTAAAAGATTCTCACAACACAATGGACTCCAATACTGAACTGAGACGGACC
CAGACCCCCTACCGAAAGGGCTCTGTACCTATATGTTCTTTATCTCAAGCGATAGCTTTCAAGTG
CCCGACCCTCTTCCCTTGATCAATGAGTGAGAAAGCAATAGCCAG
Found at i:195742 original size:27 final size:28
Alignment explanation
Indices: 195703--195756 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 28
195693 CTAATGTCGT
*
195703 TCTCTGGCAATGC-TATGCTGGAGGGAA
1 TCTCTGGCAATGCAAATGCTGGAGGGAA
*
195730 TCTCTGGCTATGCAAATGCTGGAGGGA
1 TCTCTGGCAATGCAAATGCTGGAGGGA
195757 TTATGAAGTC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 12 0.50
28 12 0.50
ACGTcount: A:0.22, C:0.19, G:0.33, T:0.26
Consensus pattern (28 bp):
TCTCTGGCAATGCAAATGCTGGAGGGAA
Left flanking sequence: Indices 195203 -- 195702
TGAAGTCGTCAGTCACAGCAGTAACCGTAGCACCCAGCTCTTGAGGATTTGCATCTTCAGTACCA
TGAGTGTCGGAATCAACAGCATCAACAATCGCGCCACCCAGATCTTGATGTTGCTGAGCGCCGAT
CGCGAGAGCTCCTTGCAAAACTTCAACCGAAGTACGAGATCTGCACCCAGCAGCCACTCTTCTAT
CACGGACATTATGGACTCGGCATTAGCCTCTTGCAACCTACCCGCACGACCAGAGGCCATCTCCT
CACTAGAAGGATCGGATCTCTACCATTGATCGAAGCCTTAGGAGTCGTCATCCGCCGATAACAAA
CTTTCTGCTTGTTTCACTAAAACCAATTCCTTAGGTGGCAAGCCTAAGATGAAGCCCGTTTGGTT
AGCACGAAGATTAACAACACCTTATGGAGATAGCTTGCCTTCACTCTCACAGCTTGTGTGCCAAA
GTACCTATACCATTATGATCACCTTTAGAGTAAAACTAATGTCGT
Right flanking sequence: Indices 195757 -- 196256
TTATGAAGTCTTTGGGTAATGGCACTAAGCTTAATACACTTAGGAAATCCCTAGATAGAGAATGA
CCTTAAAAGGAACAAAGCTCTATTCAATCCACGGATAGAGACCTTAAAAGGAACAAAGCTCTATT
AAATGCCGGTCTCCTGCTGTATGTTTTTCTTTTTATTCTCTTACATAAAATTAAGGACATAGTGT
CCGAAAACCTCTCATAGCAGGTGTTAAGTCTAAATCAGACTGAGACTGATGGTCCAGGGTAGCGA
CACCTGAAATCTTATTGGCAATGGTCGCTTGGTATGAAGGGGATTCATGAGGGCTAAAGCAGCCT
GGGGTGAGACCCGAAAAGGAGATCCATCTGTTTCCTTTGGTATCTCATGATCCTGTCAAGTAAGT
TCTTACTAATTGACCATCTTTCTATTTGGTTTGGGGAGGAAAAGTGCGGGGGTGAGGGAGGGTTC
CCCTCGTGATAGCATAAGGAGGCTAACTCGCTGCAAGTTCATATC
Found at i:208725 original size:15 final size:16
Alignment explanation
Indices: 208695--208727 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
208685 TTCTATTCTA
*
208695 ATTATAGGATTCTATT
1 ATTATAGGATTATATT
208711 ATTATA-GATTATATT
1 ATTATAGGATTATATT
208726 AT
1 AT
208728 ATATTATATA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 10 0.62
16 6 0.38
ACGTcount: A:0.36, C:0.03, G:0.09, T:0.52
Consensus pattern (16 bp):
ATTATAGGATTATATT
Left flanking sequence: Indices 208195 -- 208694
GCAAGTTCAGTCTTTTCAGGGCGAGCTGACCGCAGAAACCGTAGACTTCCATGATGAACCCACCT
TAGCCACCTCCGATCAGACAGAAAGATGCGATCGTTAGAGATTCGACGATTCCCGGTTGGACCTA
TTCAAGCGATTGAACGAGATACTCGACAACTAGAAAGACGCACTTGAATACTGAATGCTATGAGG
AGAAAGAATGACTATCACCAACCATAAAGACGATAAAAGAAGGCACTCCCGTTCCCCCGAAATCA
TCTTCTGTGCGTGGTTATCCAATCATGATGTGGTAGGCTTAGTAGGGCTCGAACCTACAATCTAA
CCGTTATGAGCGGTACGTTTCAACCAATTAAACTATAAGCCCCTACAGATCTCTACATGCAATTC
GCTCACTTCGGGAAGAGCGGACGGAAGGCGACGGGGAGGCCTTTGCTCTATCTGCTTCTTCCTCT
TCTCAGGAATGAAGAATTAGATAAAAAAAAATGGATTCTATTCTA
Right flanking sequence: Indices 208728 -- 209227
ATATTATATATATAATATTCTATATCTATTATTAGAATGAATAATATAATTAAGCAAGCGGCCCT
TTTGCGACTCAAACTGCCGGTACGCTTTCCGGCTCGCAACGACTCAAACGGGCGGAGGCTCTCTA
TTTGCTTGCACTGCCGGCTGTTCGCCTTTAGTTAGAAGTAGAAGTCGCTCTTTGCCCCACACTTC
TAAAAAAGTATGGATTAATTCAGTAAGAAAAAAAAAACTTGGTTACGGGAACCGAAGGTTAGGCC
GACTACTTACTTTCTCCTTACCCTTAACAGGATTGTCTCCTACCGATCGAGGAAAGGCTTAGAAT
CCATGCTTTGACCGGTAATGTCCAATCTAAGAACGTCTTGTGCCTTTTCCTGGGCCCCCTTCATT
CTGACTTAGCTAATTCAATTCTTTCTATTTCTAATGGGCTTATACTTTTTTCTATATCCCCCGAG
AAAAGAAAGTCCTGCTATATCTAATGTATTTTTTCCAGGACCGCT
Found at i:231535 original size:19 final size:19
Alignment explanation
Indices: 231511--231549 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
231501 CAAAGAGCTG
231511 TTTTCTTTCTTGCTT-TGTT
1 TTTTC-TTCTTGCTTCTGTT
*
231530 TTTTCTTGTTGCTTCTGTT
1 TTTTCTTCTTGCTTCTGTT
231549 T
1 T
231550 GGGCTTGCTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 8 0.44
19 10 0.56
ACGTcount: A:0.00, C:0.15, G:0.13, T:0.72
Consensus pattern (19 bp):
TTTTCTTCTTGCTTCTGTT
Left flanking sequence: Indices 231011 -- 231510
TTCTCCATCCGCCCGCCAGCAGCAGGGGGGTTCGATTCCCGTTATACGCGATGTGGCGAAGAAAA
GCGCTTGTTATTTGCGGAAAGGAAGAAGTCATCCCTCTTGCTGGAGGAAACTACCTTTCTATCCT
TCTCCTGCCCCTCTCAGTTGGAAAAAGGGCTTTCGACTTTCCCTAATCTCCTTTGCTCCCTAATC
CATTCCCGGTGCCATTCAACTATCTGACAATAGAGTATCTAAGTCAAAGCTGTTCCCGGGTTCAG
GTGAAGAATGTTAGAAAGACTCTCATGAAAAAAACCTCTAACTTGGTTCGAGTGGCTGATAGCTG
CTTATCGCTCCTGTCCAGTCATCTTAGTCCATGGCTTCTGTTTCATGCTTGGTTGATGGAAGACA
GCTTTGAGTGCCGTTACTTTCCCCCTCCATGCTTGAAGTTCATTCCTCCGTTGTGCTTTGTCTGT
CATCTTCTTTCTTCCCTTCCTCGGGCACAGTAAGACAAAGAGCTG
Right flanking sequence: Indices 231550 -- 232049
GGGCTTGCTCCTCTGTTATCCCTGACTCCCTAAACTTAATGAATGAAGGAAGGGTCTCCGCTCCT
TACCCTATCGGGCAAGTGGCTTACACTCCTTGCTTGCTTTCATCCTGCTTTTAGTGCCGCTTGCT
TGCTCGAAGGAGGGGCTACCGCTCTTTAACCTCGTCGGTAAAGCGGCTTGAATAGGACTTTCCCT
ATTTTCATTGGCCTTTTCTTCGATGTCAATGTGCTCAGGTCCTTTCTTTGCCCCTTCCCTTGGGT
TGGGCTCTCCCTCAAATGCCCTTTCCCTTCGTTATCTCTACATGAGTGAAACTCAAGCACTCGAA
TATCAGTAGATTAGCGTCACGCCAACGCAACTCTCAAACCATCGGCGAGAGGAGAGTAGGTCCGG
CTATGACTTTCATAGGAACCGTTGGGCCACTATGTCATAGTGAGAGTAGGGACCCATCCCATATG
ACTCAGAGTCAAAGAAAGCTCTTAGCCTCCGACCAGTGAAGATCA
Found at i:277831 original size:15 final size:15
Alignment explanation
Indices: 277811--277840 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
277801 AGGTTATAGC
277811 CTTTTATTTTACTTA
1 CTTTTATTTTACTTA
277826 CTTTTATTTTACTTA
1 CTTTTATTTTACTTA
277841 TTCAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.20, C:0.13, G:0.00, T:0.67
Consensus pattern (15 bp):
CTTTTATTTTACTTA
Left flanking sequence: Indices 277311 -- 277810
CTCATAAACCCAATAAAAAAAGTTTCACCCAGGTATACATATCCTTAGCTTGCGCCCTATTTGAG
ACTAAGGCAGGGAACCCTGTCCTATCACCTTTATCAAATCCCTAGCTCTATTCCTTAGTGCAACT
GTCCTATTCCTACCATGGAAATATCTATATTTCTTTTGTTCTATAGTTTCGGATAGAAAAGCGGA
CGGTATCATATATGAAGAAAGAGATTTAAAAGCCATAAGTCGTGCTAGCAACAGTCTTACTGTCT
TGGCTCCTTTGCCCCGGTCTTTTCTTTTTATAAAGTAGCACGTTCCTCTACGAAGGTGCGTTTTA
GGCCACGGTAGCAAGTGTTCTGTAAGGAGCTGTGGGACTAAAAGGCTTATGCTTATCGAGCCCTT
AATTAAGAGGAAGATGTGATTTAGTTTTCCCTGTTTTTCGCAAGTTAATCAGAATCGGCAAGATC
CCCTCTTGTTCTTGCTGCTTGGGAAGAGCAGGAAGAGGTTATAGC
Right flanking sequence: Indices 277841 -- 278340
TTCAATTTAAATCGCAAAAAGATGGATGGGCCAAATTGAACAAATCAATTTGCCTGTGCTATCGG
GCTACTCAGCTTCAAATCCTTCACGCTCCTTGGGATGCCTTACAGTCAGGGAATCACGAAGATGA
AACTAGACTCCTTTTTTGCAGTACCTTCGGTTGAGGTGCATTTATGATTTAATCCAAAGCCTGAG
CCTCTGAACAACCTGATGAATCGCGTTAAATGTGCTTTTCTGGCGTCTTTGAGTTTATGTTATGA
GTTGATCCTAGTTCATAGTAAGTAGAAGGTGTTACGGGTCGGCCTCGGGAATTCGAGGAGCTACT
GACGTTAAGCGTTAAGATTGGACTGCTCTTGGGGGAACAGCTTAGTCCATCTTCAACTCCTAGCA
TGAAAGTGAAAGTCTCAATCCCAGTTCCATATTAAGAAAGTAGACGGACAGAACTCCCCGACCTT
GTTAGGACCCCTTCGGATTGGTCCTCTTCTAGTCGAGTAAGGTGC
Found at i:279454 original size:20 final size:20
Alignment explanation
Indices: 279429--279467 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
279419 AGGTAACTCG
279429 AGAGTA-GAAAGAACTAGAAT
1 AGAGTATGAAAGAAC-AGAAT
*
279449 AGAGTATGACAGAACAGAA
1 AGAGTATGAAAGAACAGAA
279468 CCAGTAGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.54, C:0.08, G:0.26, T:0.13
Consensus pattern (20 bp):
AGAGTATGAAAGAACAGAAT
Left flanking sequence: Indices 278929 -- 279428
TCTTCTTTCCCCGTTGTGAAAGGAGTTGGTTCCGTAGTTTTAGAATTCGGCTGATCCCAAGTACT
CCATCTCCATCATTGCATATTTTTATATAGAAAGTAAAGAAGAAAAGGCATAACCAGAAGAATTG
TGTAAAATAAGTGAATTTATCCAGTTGAGGCATGATTGATTTTTTAAAAAGGATTCCCTCCAGAC
AGCTTAACTCCGTCAAGCCTGTACGAGTAAACAATAGATAAGGTTTGCTTGTTGGTTGTTGACCA
ACAGAAAGCATGGGATGCCCCACAACAAATAGATGGGAGCAGGAAATCTTTATCATTCGGCGTAG
TGCAGCTTATATAGAATAGAAGGGGCAAAGCGCTGTTCGTGGCACAGCTTTCTTATATTACGATA
TTTTCATTGATCGTAGCTAATTAGGTGGCAACAACCGAAGAAGCAGAAGAAGTAGCTGCTACCGC
TTCGTGGGCTTCTTCTTTTTCTGAGTCTGCTCGAAAGGTAACTCG
Right flanking sequence: Indices 279468 -- 279967
CCAGTAGCTTTGAGCTTTCACGTGCTCTTGTTCACAATCCAGTTGCTATTGAATCAGCGTAAGGA
GATGCCGATGAGGGTACAAGAAAAGAATGAGCTTTTGTTCAGAGCTTGAATCAGAATATCCTTCA
GTAACTCCAGGATTCCCCTGGTAGGGCATACAGGACATACCAGGTGAGAAGTTCGGGCGGAAAGA
TAGATCGAGTTTACTTTACCCTCTTGATTGACTTTCACTTTAGGACTGAAAGATAGCAAAGGAAA
TGGCAGCAGTGCTTTATATATTAGGTCTTCGTTGATCACTTCTGCTTAATTTAAGCACTTCTCTT
TCGAAACCTAGAAAGCGAGAAAGAGAAGAGTCAGTTCTTGTGAACGACTCCGATGCTCTTTCTAT
TTAAGAAGATGGAGGAATAAGCGATGCTGCTAAGATCCGCAGTCGATTTAGCTCTTGAGGGAAGG
GAAAGGCGGACTTTAATTTGATGGGCTTTTAGGACTGGCCCGGAG
Found at i:285060 original size:13 final size:13
Alignment explanation
Indices: 285042--285070 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
285032 GGATGAGTAT
285042 AAGAATGAATTAC
1 AAGAATGAATTAC
285055 AAGAATGAATTAC
1 AAGAATGAATTAC
285068 AAG
1 AAG
285071 GGGTATAGAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.55, C:0.07, G:0.17, T:0.21
Consensus pattern (13 bp):
AAGAATGAATTAC
Left flanking sequence: Indices 284542 -- 285041
CGCCTGACCCACTTTCCACTGTGAACCTGCGCCGACACAAGACACAACCGCAGCAGTTCGACGGA
GAGCATGGTTCCTCCTCCTCACGAAATGGATTTTCAGTTCTTTGCCTCGGGTCAGCGGATGGTCA
GGGGACAGGTAATTACATTAACTAACAAAGCGAAATGGATAGGGATAGCTCGCTTACTACCTTCT
GGTCTCATCCAGCGTCTACAAGCGGAGAATTAGTTATAGCGTAGGGGTGGAAAAGAGGAAGAGTG
CCCGCTAGAATCTTCTTTCACATCCATCTTTCTGCGTCAAAGCTTTATGTTTGCCGCCCATTCTT
ATTCATCATACGACACGAGAAAGACAAAACGAATATCACAAGTAGAGTGAAAAGCATAATCTAAC
CTAGATGGGAATCCGAAGACAAAAGTTGGAATCTAAATCCGTTGAAGACAAAGAATACTGCGTGG
AAGCCATTGGATTTTCAAGATGTAGATGCGAAACCGGATGAGTAT
Right flanking sequence: Indices 285071 -- 285570
GGGTATAGACGTATGACTAGACTATGTTTTATAAATTGATACAACTTCTGAATTGAAGGCTCTGG
CAAGAGTTCGTGAATAGTCGACGTAAACAGATAAGAAAGAAGGATTCTAATTCTAGGCCAACCGG
CCCTAACTGATAGGGGTATTGGTCTTCTTTACCAATGTTTGGTAAAAAAGTTATATTGTACCCGA
CCTGTTCGGATATGTGTTAGAGTCGATAGGAGGTTCCCTCCCGAACTCGATCAAAATAAGGACGG
ACGAATATGTTTTGTAAATCTCTCACTGGAGCATCCTCAGGAAAAGGTGTAAGTGAAGGAGTTGC
CCGATCCCGAAGAAATTCACATACTCTCTTTATCCTCAGAGTTCTTAATGGCTTTAGTAAGGAAA
GTCTTAAAACCAGCCTGCCGTTTGGTCTTGTTCTTCCCTCTATGCCAAGATAAATCGAAAGGAGA
AATCTTGAGATCCCCGGTAGCGGGAGGACCCATTAGAGCTGCAAG
Found at i:299115 original size:24 final size:24
Alignment explanation
Indices: 299088--299135 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
299078 AACTTGCAAA
*
299088 CATAACCAGGCAGTGAGGTATCTT
1 CATAACCAGGCAGTGAGGAATCTT
* *
299112 CATACCCAGGCGGTGAGGAATCTT
1 CATAACCAGGCAGTGAGGAATCTT
299136 AAGGGGAGGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.27, C:0.23, G:0.27, T:0.23
Consensus pattern (24 bp):
CATAACCAGGCAGTGAGGAATCTT
Left flanking sequence: Indices 298588 -- 299087
GGCCAAATCAGGTCTTGTAATATACTGCAGGGCTCCAACGATGCTTCTGTACAGAGATGGATTAT
GAAATGGAGTAGAAGAGACTGCAGCAGAGGACTGATTTTAAAGTTAATTGGAGAAGAGCAGGGCT
TACAATTCAGCATAGCAGCTCTCTGGAGGAGATCCAACGCATATTTTTGCTGTGTTAAAAAAAGT
CCACGATCATTCTTGTCTTGAGTACCTCAATGCCAAGAAAATAGTTCAAGTTCCCGAGGTTCTTT
ATAGCGGAGCACTTAATTCAGTGATTAGAGTGGAGATATAAGAGGTATCACTGCCAGTTATAATA
ATATCATCCACATAAACCGCAAGAATTGTAGTTCGCAAACTGTTAGTTTGAATAAATAACGAGGA
ATCACTACGGCTCATAAGAAAGCCTTTACTGATTAAAAAGCTATAAAACTTATCATACCAAGCGC
GTGATGCCTGTTTAAGACCATACAATGCTTTCTGCAACTTGCAAA
Right flanking sequence: Indices 299136 -- 299635
AAGGGGAGGGGTTGGTAGTGAAGGGAAGTCCAGGGCTGTGTCTGATCAGCTTACTGGGAGAATTC
CAGGCGAGGGAGTATTGGTAAGGTTATGGAGGAAAGAGGAAATAGGATTTTGGGCATCTCTCGTT
GCTTCGGATGTTTATGAGAAAGAAGCTTCTCACAGATATTGACTTTTAGATAGATACCAGCATCG
TATCTTAATTAGCAGTTTCTTGAACTTGGTTGCACTCGTAAAGCAGCTTAAGAGAGCAACGAAAG
ACGGAGCGGTGATATTTCATGACTAGCAAGTGGAGGATCATTCCAGGCTCTAATTCAGTCTCTGA
TGGCGTAGCTGATGTGTCATGCTAGGAAGCTGAGCTAGGGCATTTCTTCTTTCGGTTTAAGTGTT
GTGAAAACCCTCCTCTCCGCTTCTGGCAGCATAGAAGGAAGCTTGGGGGAAAGGTCTAAGTGCAA
GCATTGAGTCAAACTGATTCAGGTATAGCAATGTAGTTCTTGTCT
Found at i:324285 original size:14 final size:14
Alignment explanation
Indices: 324266--324293 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
324256 TCTCTATTTT
324266 TTTAAGAATACCGA
1 TTTAAGAATACCGA
324280 TTTAAGAATACCGA
1 TTTAAGAATACCGA
324294 GTCGGGGTCT
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):
TTTAAGAATACCGA
Left flanking sequence: Indices 323766 -- 324265
GTCTCTGTGGACCGAGGAGAAAGGGGCTCGGCGAGAAGAGGATTGTACCATGAGAGAAGCAAGGA
GGTCAGCCTCTTTCAAATATACAACATGGATTCTGGCAATTCAATGGAGTTGGACTCTCATGTCG
ATCCGATCCAAATGAATCATCCTTTCCACGGAGGTAAATCTTTGCCTGCTAGGCAAGAGGATAGC
AAGTTACAAATTCTGTCTCGGTAGGATATACATGTATTTTCTTTCTATTACTATGAATAAATGAA
GTAGTTAATAAATGAAATAAAATAGTTAAGGGCCATTATCCTTTTTGTAGTGATGAATCTTGTAT
GTGTTCCTAAGAAAAGGAATTTGTCCATTTTTCGGGGGCGTGGAAACACATAAGAACTCTTGAAT
GGAAATGGAAAAGAGATGTAACTCCAGTTCCTTCGAAATGGTAAGATCTTTGGCGCAAGAAGAAG
GGGTTGATCCGTATCATCTTGACTTGGTTCTGATTTCTCTATTTT
Right flanking sequence: Indices 324294 -- 324793
GTCGGGGTCTTCTCCTACCTGTATCGAATAGAACATGCTGAGCCAAATCTTCTTCATGTAAAACC
TGCTTTATTTAGATCGGGAAAATCATATGCTTTTTTGAAACCATGTGCTATGGCTCGAATCCGTA
GTCAATCCTATTTTCGATAGGAGCAGTTGACAATTGAATCCAATTTTCCCATTATTTTCGTATCC
GTAATAGTTCGAAAAGAGGGCCCGACTCCAAGTTGTTCAAGAATAGTGGCGTTGAGTTTCTCGAC
CCTTTGACTTAGGATTAGTCAGTTCTCTTTCTCGATGGGGGCAAGGGAAGGGATATAACTCAGCG
GTAGAGTGTCACCTTGACGTGGTGGAAGTCATCAGTTCGAGCCTGATTATCCCTAAACCCAATGT
GAGTTTTTCTATTTTGACTTGCTCCCCCTCCGCCGTGATCGAATGAGAATGGATAAGAGGCTCGT
GGGATTGACGTGAGGGGGTAGGGATGGCTATATTTCTTGGAGCGA
Found at i:330006 original size:13 final size:13
Alignment explanation
Indices: 329988--330013 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
329978 TCCTGCGAGC
329988 TTAGTTTATGAAT
1 TTAGTTTATGAAT
330001 TTAGTTTATGAAT
1 TTAGTTTATGAAT
330014 AATGCAGCAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.15, T:0.54
Consensus pattern (13 bp):
TTAGTTTATGAAT
Left flanking sequence: Indices 329488 -- 329987
AAGAATAGACGGAGACGAGACGTACGATTGAAATCACGTTTATGAAAGCAATGGCTCTTAGCCGA
CTAAGATGACCACATAGTGGTATACTACTTCACGTAATTCACGTAATTTTCCACTTTACCACTAT
CAGACTAGACCGGAGCTTTTGAATAGGGCTTTGAGGATAAAAAGACTAGCCGGAAAGCCATTCCC
CTGCTTGCGACCGCTGGACCACTTGGAATGATGGAAAAGAGAGTACAGAGAGCATTCCATATGGG
GCTTCCCATCGGGGCTACCATTTTCTCAGGCCCGATCGAGGTTCTCTTCTTTCCCGTTCATATGA
AAAAGACCTGCAATGCTAATCTCGTTAGGCCACCCGAACCCATCGAACCGGAGTTAGATAGGTGA
AAAGATAACAAGACAACACCTGCCTATATCGCTCCTGTCTAAGCGAGCGAGACTTTTTCCATTGA
TATTTCCATATCATGTAGCGAGACTCCACTTTAGATCCTGCGAGC
Right flanking sequence: Indices 330014 -- 330513
AATGCAGCAATCGTAGGGTCGACAGTACCGGTGGGCTTTGAGCTACCAGAGCAAGGAGATAGAGC
TTGAGCTTTTCCTTCATGGACCAAGGCGACTCTCGTTAGCTCTACTTGGGCTTAGTGCGATTCGA
AACTGGGATTTTTTCTAGCCCGAAGAACGAACAAAGACAACAAGGAGCGACTGATAAGGAGCGGT
TCAAGCTTTCTGGCCATTCCAACTGCCTCCATTATTCTACTTTTTAAGCGCCATAAGCAGCCAAG
CATAGTGGTTCGCTCAAGCAATGGAGTTTGCGAAACTTCCGTTCCGGTAGTCCTTAACGCAAGGA
AATAGTAAGATCAGACCCTCGAATTCGATTACACACAAGCTGCCAAGTAAGCTCTCGAAAGAGCT
ACCTCAGAATGAAAGCTACATCAATCCAAAGGAATTCAATCCGTTATATCTCCACCTCGTAAAGC
CGTAACAGCATCGACTCATTAATGCGCCCTCAAGGGGCAGCCTAT
Found at i:488373 original size:18 final size:18
Alignment explanation
Indices: 488350--488386 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
488340 TATCTATTAA
488350 TATCTTTTCTTATAATGT
1 TATCTTTTCTTATAATGT
488368 TATCTTTTCTTATAATGT
1 TATCTTTTCTTATAATGT
488386 T
1 T
488387 GTTGTTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.22, C:0.11, G:0.05, T:0.62
Consensus pattern (18 bp):
TATCTTTTCTTATAATGT
Left flanking sequence: Indices 487850 -- 488349
TCCGAAGAAGTTATCACGGACGAGCCACATGCAGGGAAACTTGCACGTGTGGTTCTGGCCGGGCT
TTCCTGAGGTATCTAATAACCTTGCTTCTGCTCGCCGCTGGCGCACCTCTCCTAACTATTGCCCA
TTTATTCTGGAATAATTTTTTTAGGAGGGACAATTTTACATATTTCTGCCAAATCCTTCTATTAT
TAAGTACGGCTGGTACCATTTCGATGTGTTTCGATTCTTCCGAACAAGAGAGGTTTGATGCTTTT
GAATTCATTGTATTAATTCTACTTCCTACTCGCAGTATGCTCTTTATGATCTCGGCTCATGATTC
AATTGCCATGTATTTAGCTATTGAGCCTCAAAGTTTATGTTTTTATGTGATCGCAGCATCAAAAA
GAAAGTCTGAATTTTCCACGGAAGCCGGCTCGAAATATTTGATCTTAGGTGCATTTCCCTCTGGA
ATCTTATTGTTTGGGTACGACCGGACAACTACCGATATCTATTAA
Right flanking sequence: Indices 488387 -- 488886
GTTGTTAAATATCTATATCGTAAACTACCGGATCGGGTATTACTTAGATGTGAAACTTGCAGACC
TCATTGGTTGTGATATTGATCGTCACGGGGGGAACGAAATCTAAGAATATATAGACTTGTAGAGA
CCCTCTATGTAGTTGTCTATCTAGGGCGATCGATCTACATCTTTCCCCATAGCCCTGGGGCTGTG
TCTCGATCTCCTACGTGCGAAATCTGAGGGACTAGTTCCTATGGAGATTCCCCTTGGTCTAATTC
CACGCCTTATGACGTTTCGAAAAGGGAGTCGGTGTGGCGTAAAGTGAAGATCACGGGAAGTAGAG
AAGAATTCCCTTTCTGGGGTATTCCGAAGGTGTAACCTAGACAACGAAAAAGGGGCCCGATACTT
CAACTAGAAGAGCGACCAGTTGGTTCACCAAACCCCGACCCAGCGTTACACGTTTTCCAGGTCCG
AAGGGATCCAGTGCCCAATTACCGACTCCTCCCGGAATTGCGTTA
Found at i:493749 original size:7 final size:7
Alignment explanation
Indices: 493739--493773 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
493729 TATATCCTAT
493739 ATATAAG
1 ATATAAG
493746 ATATAAG
1 ATATAAG
493753 ATATAAG
1 ATATAAG
493760 ATATAAG
1 ATATAAG
493767 ATATAAG
1 ATATAAG
493774 TGTCCTCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.57, C:0.00, G:0.14, T:0.29
Consensus pattern (7 bp):
ATATAAG
Left flanking sequence: Indices 493239 -- 493738
CAGCATTCCGACTCACTCCTCAACCTGAGAAAGCAGGAGCCGCGGTATTTCACTCAAGATTGGCT
CTCTCTACCCGTAGCTTCAGGGGTATTCACCTTTGGCATATGCCCGCTCTGACCGAGATTCTTCC
GTACTAGAATTCGGTGGAGGAAGTTTAGGGCACCCGGTTCCGTCGCTAATCGAGTAGCTCCAGAA
GCTCGTAATGAGGGATGTGAGGCTAGCAAATAGAGTCCTTTTCTAGCGGCTGCTTGTGAAGTATG
GAAGGAGATTCAATTGAAATTCCCAGCAATGGAGACAAAGTAATCCATTAATGTTCGTTCTCGTA
ATTGAAACTTGCCCTTTCGTTTTCTTCTTTTATATTATTAGTGAGCACCCTCATCCCACACTCAC
TTGTCAAAGCATGGGAGAAAAGTAAGTAATGCTATTTTTCCTTCTCTCATTCTATGCTAAAACCT
TTCTTCTTCTCTTCTGTTAGCGAAGGCAGAAAGCCTATATCCTAT
Right flanking sequence: Indices 493774 -- 494273
TGTCCTCATTCAGCCTTGCTTGACCGAAGGAGATAGAAGGCTCATCAATCAGTCATAGCCTAAAC
TGAGGCATTGGAGGGGCATGAGAGAAGGTGCGCATTCCGATTTGGTCAATCTCATCTCTTTCTTC
TCTGCAACTCGGGTAAAAGCCTAGAAGTTAAAAGGAAGTCAAGATTGAATTGGATTTGCTTTCCG
GCATTCTGCTTTTGTTTGGATCGAACTCCAAGGGTTGCCATTCTACTAAGTAAGAAGAAATCGAA
CTCGCAGGAAAATCTAAGTAGCAAAGGGTACGACATTCAGTCAGCTTGGTGAAAGACTTTGTCTA
ATTCCACAGTGCTTTCAAGAGGAATAGTAAATAGAAAGTACCAGGGATCAAACGAGAAGGAAGGT
ACGACATTGTCAAAATGATTGGAAATCTTCCACGTTTGCCCTTCCTTAGTCGGTAATGATAGATC
TATGTCTAAAAGGAGGGCATGTTGGCAAGAAAGCATTCACCGACG
Found at i:505959 original size:14 final size:14
Alignment explanation
Indices: 505942--505970 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
505932 GACTACATCC
505942 ATCTATCCTACCTA
1 ATCTATCCTACCTA
505956 ATCTATCCTACCTA
1 ATCTATCCTACCTA
505970 A
1 A
505971 ACAGTAAGCC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.31, C:0.34, G:0.00, T:0.34
Consensus pattern (14 bp):
ATCTATCCTACCTA
Left flanking sequence: Indices 505442 -- 505941
GAACAAATACTATTTATTAGCTTAGCCGGGAGAATCTAGTCATTTAGTCAGTTCATAACAATCTC
TGTAAAGCAAGGGGCAAAGCTTCTACGACAGCTTCTCCCTCATGTCATGTAGTCGTCGGCCTTCC
CGACGCCCCCCCTTCGTCGCTTCTGGCTAAGCATCTTTCGGCGGAGGAAAGGAGGCGACTAGTCG
CTTCTGGCGAAGCTGCGAGCCTACCCTGCCTACTTAAATAGCTTACGCTTACTCAGCCTAGTCTA
CTAAAAGAGGGCTACAGCAAGCAACGAAGTTGCCTTTGTTTGTTGTGGGTCGCGCCTCGCCGTAG
GCACTGAATGAATGAAATGAGTGGAGATCTTCCTTCCTCCTTTCAAATAACCAAGAACTTCGTTG
GTACTAGTGGCGAAGAAAAATCTTACCCCAAAAAAAGCAACTCGGAACCTAAAGAGAAGAGAGTT
CAGTCTACAAGAAGCTGGCAGAGCTTTAGCCATTGGACTACATCC
Right flanking sequence: Indices 505971 -- 506470
ACAGTAAGCCTTTTCTTGTTCGTTCTTCGAGCTAGTGGAGTCCTTCCGGCTAATGAAGATACTAC
TCCAGTCTTCCCATTCATTCACAGTGGATCCTTCCTTTTCCCTAAGAATTGAACGAACCAAGTTC
ACCTATACGAGAGTGAAGAATAAAACCCTACAATCAACTTCCCACTTTTGATGTCCCACGATTCT
GCTAGTTTAGAAACTAAAGAGAAAAACAGGCGTCAGAAAAGCGATAACTCAAAATTCTCCCCAAG
TAGGATTTGAACCTACGACCAGTCAGTTAACAGCCGACCGCTCTACCACTGAGCTACTGAGGAAG
AACTCCCTTAAGGAAGCCGACTCTCGTTCTTTGGACCAACCTATGACCGGGTTCGTCACTCTTTT
TTTTTCCCTTGATTGAAAGAGGCTAAGCGCGGTACATTGAGTAAAGGGAGGATTTGCTACATCGC
TACATCGGGCGGTGGGTGGCCCCTTCGAGAGTTGCGGGTCCTTGC
Found at i:524219 original size:19 final size:19
Alignment explanation
Indices: 524168--524220 Score: 51
Period size: 19 Copynumber: 2.9 Consensus size: 19
524158 CATGGATGCG
524168 AACTTTAACAAAGAAC-TT
1 AACTTTAACAAAGAACTTT
* *
524186 -A-GTTAATTAAA-AACTTT
1 AACTTTAA-CAAAGAACTTT
524203 AACTTTAACAAAGAACTT
1 AACTTTAACAAAGAACTT
524221 AGTTAATTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 9
0.67 0.10 0.23
Matches are distributed among these distances:
16 7 0.27
17 6 0.23
18 4 0.15
19 9 0.35
ACGTcount: A:0.49, C:0.13, G:0.06, T:0.32
Consensus pattern (19 bp):
AACTTTAACAAAGAACTTT
Left flanking sequence: Indices 523668 -- 524167
ATCCTTCTCGTTCGATCCGTGCTTTTAACGAATTACCACTTATTCTGTGGCCTCTAGCCTTCTAC
CCCTCTCCTGACGTCGAGCCGCTTCGCCCCTTAGTCCAGAGCAGGAGCAGCGGATTCGCCTACTT
CAAAGTCTAAAGTCAATAATCCGGATTTCCCCTCTTTCCTTCAAGCAAGGCTGACTTCATTAGCT
ATAGGTAGACTTCACACAAATCCAATCGTACAAGCAAGTAGATCAACATCAACGTTGAATAGTTT
CATTCCATCTAGGGTTCCCTGCAAACTTCTTATATCTACCGGGGCAACAACCTCTTCCTTGAAGA
CCCTGTATTGCTTGTCTTTCTTCTCCTAGTTACTTCTTGGATTCGCCGCAAACAGATGACTAAAA
GCGCTTACTAAGCATAGTCCCGGAAATTCCAATGCAATTAGCAGCGAATCTTGCACTTGAGGAGC
AGATCTCTATCTGTAAGAGCAGATTAGGCGCATGCCATGGATGCG
Right flanking sequence: Indices 524221 -- 524720
AGTTAATTAAAAGGCTCTGCGCAGCAATTTTCCTCGTAGGCAGAGGTTGGACAGAGACTCAAACA
TATAAGGCAAAGGTGTGCAGGAAAGGCACCCGGACTTATTTCCAATCGCATATAGAGTGAGCGAA
GCACGGGTAGATCCCATTACAGATTGAGTAGGGGGAACCCCAACTAAAGTAGCAAAGAGAAAGTC
AGCAGCAATTGCTAATCTCTTGATCTATGCACTTTCAATAGCACGCAGAGGTGAGGATCGACTAA
GCATTTCCAGTAGGAGAACTCGCCCAAAGGGAACATTTAGAGTTGTTCCAGAAAGGTCCGCAGGT
GAAAGAAAAGAGACTGGCTCTCTCTATCTATTATACTTATACGCAATATCTTGAAAGGCGAAGAG
TGACTACTTCTTTCTGCTTGTATTGTACTTCCTGTTCCTGTAGTGATACAGGACTCGTGCAAGAG
CGCTTACGGCAGGAGATGAGGCTTAGAATCCAGATCAGATTCCAT
Found at i:556344 original size:50 final size:50
Alignment explanation
Indices: 556269--556367 Score: 171
Period size: 50 Copynumber: 2.0 Consensus size: 50
556259 TCCAGGCTGA
**
556269 GGTTGGGGTTCACGTTTGGTGCTTGGTGGTAATTCCCCGCGTGCTCCCCG
1 GGTTGGGGTTCACGTTTGGTGCTTGGTGGTAAGGCCCCGCGTGCTCCCCG
*
556319 GGTTGGGGTTCACGTTTGGTGCTTGGTGGTAAGGCCCCGGGTGCTCCCC
1 GGTTGGGGTTCACGTTTGGTGCTTGGTGGTAAGGCCCCGCGTGCTCCCC
556368 CTCCCCGGTT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 46 1.00
ACGTcount: A:0.06, C:0.25, G:0.38, T:0.30
Consensus pattern (50 bp):
GGTTGGGGTTCACGTTTGGTGCTTGGTGGTAAGGCCCCGCGTGCTCCCCG
Left flanking sequence: Indices 555769 -- 556268
ATCAAAATTTTGGCAGGGGCTTTGCTAAACTGTTCAGCCGCATTCTATTCCGACCTCTGGATTTC
CTTGAGAAAAGCATCCGTATTTTCCTTCCCTTTTCCTTTCTCTTTGTCTTTTTCTTTATTTCCAT
ATGTTTTTAGGTTGTCTGGCTTAAAACATTTGCCAGAGCGAGTCATGTTCCCAATCTCATCACAA
TCTTCCCTTTCTCTCTTCTCTGTATCTTTTCACCCAAGAGACTTTATCAAGATTGTAGACGGGGG
AGGTGGTTGGTAAGGGGTAATAGTGGTCTCTAAACCCGGTCGTCCGGCACCAGTGGCGGGTTCGC
GGATCTGAGATCCGATTCTCGAACTCCAGCAAGCGGTTATATTCCGCCTGCGAGGGCGCTTGAGC
AAGTGCCTCCTTGATCTCTCTCCAGTAGTCCCCCTTGGTTTATCAAGGAGAAACGAGCTATGTTC
GTTTTCGAGCCCGATAACCCTATTTTTGAGAGATTTCCAGGCTGA
Right flanking sequence: Indices 556368 -- 556867
CTCCCCGGTTGGGTGACTCGTGGCTTGGTGGGATGGCCCCGCTTCCTCTTGCTGGGAAGGCCCCT
GTTCCTCTTGCTGGGCTGGCCCCGGTTGATCCATGACCCCGGTTTGGTTTGGTTGACTAGTGGCT
TCCTGGTTGTAGTACCTTCCAATCCACGAGCTACTCCACGTGGATGAGATTGATTGTTCGGCGGC
GGAATCTCCTTCGTTCCCAGATGAGAAGTTTAGATATTGACTCCAATTCCCTGAGCTGGATGCGC
AGGAAGCTCCGGATGGTGTCATCATGCGCGATAGAGCGGGTGATTCAACCAGAGACAAGATTCTA
GCCAAAAATAGACCTACTTCCCTCTGTAAGAAGGAGAAGAGTCCTTCTAGCAAAATAGAGATCAG
ATTTAAACAACCAGGTACAGCATCGCATTTGACACCTAAGGAAGGGACAGCCCAACTATGAAGTA
CATCAGCAGATGTTACAAGAAGACGTAGATGACTATTTGCTGGCA
Found at i:556423 original size:24 final size:23
Alignment explanation
Indices: 556391--556456 Score: 87
Period size: 24 Copynumber: 2.8 Consensus size: 23
556381 TGACTCGTGG
*
556391 CTTGGTGGGATGGCCCCGCTTCCT
1 CTTGCTGGGATGGCCCCG-TTCCT
*
556415 CTTGCTGGGAAGGCCCCTGTTCCT
1 CTTGCTGGGATGGCCCC-GTTCCT
*
556439 CTTGCTGGGCTGGCCCCG
1 CTTGCTGGGATGGCCCCG
556457 GTTGATCCAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
23 1 0.03
24 35 0.95
25 1 0.03
ACGTcount: A:0.05, C:0.35, G:0.33, T:0.27
Consensus pattern (23 bp):
CTTGCTGGGATGGCCCCGTTCCT
Left flanking sequence: Indices 555891 -- 556390
ATTTCCATATGTTTTTAGGTTGTCTGGCTTAAAACATTTGCCAGAGCGAGTCATGTTCCCAATCT
CATCACAATCTTCCCTTTCTCTCTTCTCTGTATCTTTTCACCCAAGAGACTTTATCAAGATTGTA
GACGGGGGAGGTGGTTGGTAAGGGGTAATAGTGGTCTCTAAACCCGGTCGTCCGGCACCAGTGGC
GGGTTCGCGGATCTGAGATCCGATTCTCGAACTCCAGCAAGCGGTTATATTCCGCCTGCGAGGGC
GCTTGAGCAAGTGCCTCCTTGATCTCTCTCCAGTAGTCCCCCTTGGTTTATCAAGGAGAAACGAG
CTATGTTCGTTTTCGAGCCCGATAACCCTATTTTTGAGAGATTTCCAGGCTGAGGTTGGGGTTCA
CGTTTGGTGCTTGGTGGTAATTCCCCGCGTGCTCCCCGGGTTGGGGTTCACGTTTGGTGCTTGGT
GGTAAGGCCCCGGGTGCTCCCCCTCCCCGGTTGGGTGACTCGTGG
Right flanking sequence: Indices 556457 -- 556956
GTTGATCCATGACCCCGGTTTGGTTTGGTTGACTAGTGGCTTCCTGGTTGTAGTACCTTCCAATC
CACGAGCTACTCCACGTGGATGAGATTGATTGTTCGGCGGCGGAATCTCCTTCGTTCCCAGATGA
GAAGTTTAGATATTGACTCCAATTCCCTGAGCTGGATGCGCAGGAAGCTCCGGATGGTGTCATCA
TGCGCGATAGAGCGGGTGATTCAACCAGAGACAAGATTCTAGCCAAAAATAGACCTACTTCCCTC
TGTAAGAAGGAGAAGAGTCCTTCTAGCAAAATAGAGATCAGATTTAAACAACCAGGTACAGCATC
GCATTTGACACCTAAGGAAGGGACAGCCCAACTATGAAGTACATCAGCAGATGTTACAAGAAGAC
GTAGATGACTATTTGCTGGCACAACCAATCTATTGTCAACTTCTAATAAACGTAATTGACCCAAT
TCTAAATCAGAATCTTGAATCATATAACTGTGAAAATAAGAATCT
Found at i:556956 original size:30 final size:30
Alignment explanation
Indices: 556915--556976 Score: 106
Period size: 30 Copynumber: 2.1 Consensus size: 30
556905 ACCCAATTCT
*
556915 AAATCAGAATCTTGAATCATATAACTGTGA
1 AAATAAGAATCTTGAATCATATAACTGTGA
*
556945 AAATAAGAATCTTGATTCATATAACTGTGA
1 AAATAAGAATCTTGAATCATATAACTGTGA
556975 AA
1 AA
556977 TGCGTATAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.45, C:0.11, G:0.13, T:0.31
Consensus pattern (30 bp):
AAATAAGAATCTTGAATCATATAACTGTGA
Left flanking sequence: Indices 556415 -- 556914
CTTGCTGGGAAGGCCCCTGTTCCTCTTGCTGGGCTGGCCCCGGTTGATCCATGACCCCGGTTTGG
TTTGGTTGACTAGTGGCTTCCTGGTTGTAGTACCTTCCAATCCACGAGCTACTCCACGTGGATGA
GATTGATTGTTCGGCGGCGGAATCTCCTTCGTTCCCAGATGAGAAGTTTAGATATTGACTCCAAT
TCCCTGAGCTGGATGCGCAGGAAGCTCCGGATGGTGTCATCATGCGCGATAGAGCGGGTGATTCA
ACCAGAGACAAGATTCTAGCCAAAAATAGACCTACTTCCCTCTGTAAGAAGGAGAAGAGTCCTTC
TAGCAAAATAGAGATCAGATTTAAACAACCAGGTACAGCATCGCATTTGACACCTAAGGAAGGGA
CAGCCCAACTATGAAGTACATCAGCAGATGTTACAAGAAGACGTAGATGACTATTTGCTGGCACA
ACCAATCTATTGTCAACTTCTAATAAACGTAATTGACCCAATTCT
Right flanking sequence: Indices 556977 -- 557476
TGCGTATAAGAGAGCTAATGCTGGTATAGCAATGTATTTCAACCAACGACTGTTGATTTGAAAGG
CCTGACACTGCAGCTTGTTCATTACACTACAGAGTTTCTTGTAATCATGCGCTTGGGAAATATCA
ATATAAAAATTATTGATGTCACAGCTACTTAATAGGCGGTAACGATCATATATTTCACCTGTTGG
CCCACTTAAGTAACCCCTCTTAGATCAGACATGTTTCTAGGTGTTTCGCTTTCACTACTCCAATC
TAGAGGTTTGCATACCATAGGAAGGTTCAGCTTGATCGGTAGTAATGAGAGATCAAAGTTGCAGA
TAGCGTAGGGAAGATAATAAGCTGCTTTTTTCCCACGAGAAGGAGTAGTACCCTTCTGATCTAAC
GTGAAAGTTATCAATCCTCTTTCTTCCATGAATTGAACAAGGGCTGTCCCAAAGGGATAGAGCGT
TATCAATTTCGATTTCTTTTCCTCTCCTTATCCTTTTGTTTTAAA
Found at i:557500 original size:56 final size:57
Alignment explanation
Indices: 557434--557541 Score: 191
Period size: 57 Copynumber: 1.9 Consensus size: 57
557424 TAGAGCGTTA
*
557434 TCAATTTCGATTTC-TTTTCCTCTCCTTATCCTTTTGTTTTAAATCATCATTTGCTT
1 TCAATTTCGATTTCTTTTTCCTCTCCTTATCCTTTTGTTTAAAATCATCATTTGCTT
*
557490 TCAATTTCGATTTCTTTTTCCTCTCCTTCTCCTTTTGTTTAAAATCATCATT
1 TCAATTTCGATTTCTTTTTCCTCTCCTTATCCTTTTGTTTAAAATCATCATT
557542 CGCAATAGAT
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
56 14 0.29
57 35 0.71
ACGTcount: A:0.17, C:0.24, G:0.05, T:0.55
Consensus pattern (57 bp):
TCAATTTCGATTTCTTTTTCCTCTCCTTATCCTTTTGTTTAAAATCATCATTTGCTT
Left flanking sequence: Indices 556934 -- 557433
TATAACTGTGAAAATAAGAATCTTGATTCATATAACTGTGAAATGCGTATAAGAGAGCTAATGCT
GGTATAGCAATGTATTTCAACCAACGACTGTTGATTTGAAAGGCCTGACACTGCAGCTTGTTCAT
TACACTACAGAGTTTCTTGTAATCATGCGCTTGGGAAATATCAATATAAAAATTATTGATGTCAC
AGCTACTTAATAGGCGGTAACGATCATATATTTCACCTGTTGGCCCACTTAAGTAACCCCTCTTA
GATCAGACATGTTTCTAGGTGTTTCGCTTTCACTACTCCAATCTAGAGGTTTGCATACCATAGGA
AGGTTCAGCTTGATCGGTAGTAATGAGAGATCAAAGTTGCAGATAGCGTAGGGAAGATAATAAGC
TGCTTTTTTCCCACGAGAAGGAGTAGTACCCTTCTGATCTAACGTGAAAGTTATCAATCCTCTTT
CTTCCATGAATTGAACAAGGGCTGTCCCAAAGGGATAGAGCGTTA
Right flanking sequence: Indices 557542 -- 558041
CGCAATAGATAAGGGTATTTTACACCTGCTACATTGAAATAATAAAGCTTGTTTACGGATACTAG
ACTCGAGTTGTTCAACCAAAGAAGCAACACGAATTATTGAATCACATTTGTTATAAAACACACTT
AGGACATGAACTATTATTGCTTCAATCGTATATTGACCTAACTCTGATAGCAATTCAATATCTGC
CTTATCTGCCAAATTACACTTGAGATAATCCTTTGCACTTTCCTCTGTATTACGTATCAATATAT
TGATTATGTTGGGAGCAGTCTTAAAGATAGATTCCTCATCGAATAACATAGTCTGATCCTCAATA
TCCATTTGTATCTTACGTAATTCTTTTTCACTTAATGAAGACATATACTTACCTTGCTTTAAAAT
TTCAAATACTTGTTGCTTTGGATCTACCAAATGATAAGAATGCCTCTGAGAAAAATCATAAACGA
CTTTGCCTCGGTTTACCCTCCCCTTCACCCCCACCGGATTGCCAA
Found at i:587916 original size:15 final size:15
Alignment explanation
Indices: 587896--587926 Score: 53
Period size: 15 Copynumber: 2.0 Consensus size: 15
587886 ATAAAAAATA
587896 TAAAAAAGAAAAAGGC
1 TAAAAAA-AAAAAGGC
587912 TAAAAAAAAAAAGGC
1 TAAAAAAAAAAAGGC
587927 ACTCATCAGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.71, C:0.06, G:0.16, T:0.06
Consensus pattern (15 bp):
TAAAAAAAAAAAGGC
Left flanking sequence: Indices 587396 -- 587895
AGGCTGGGCTGCGTACTTTTCGGCGCCCACCTTTTCTTTAGGTGTTGGGGCAAGCCCCAGGAAAG
TCTAGGTTGGCTCCCAGCTCCATCTCGGTCGGCATCCTGCTCTCGAGGGAATGGAGTCCTGGAGC
GAACTACTCATTGCTGTCTTGCCCAAGGAAGGGCATTTGGAACATTCTTTTTAGGGAGGGAAAAC
GTGGTTGACAAGCCACTTCGAGGAGGCGACTGGAGTGCTTTCATCAAATAATGCATGTGGGCTGA
GCCATTCCCATCCCGACGTGGTGGCCCGATTCGGCCTGGCCTGGTCGGGAAGAGATTCACATAGA
GACAGACTACTGTTATCTGGGAATATCTTTCTATGTTAGCTAGCGGGGGCGGGCTTTGCTTTCCT
ATGGTAGTCCCGCGGCGGCCTCTGACCGTCCGTCCCGTCTCATCTTGATTTGGCTATACTTGTAT
GTAGCCAGCCATGTTAGCTTCACATGAGAGCCTTTATAAAAAATA
Right flanking sequence: Indices 587927 -- 588426
ACTCATCAGTCGGCCCCTTTCCTATTCAGCCTTGCCACCTCTCCAGTTAAGAGAATAGGTCCCGC
GGCCGCCCGCCTGAATCTATACTAGCTGCCACGCACGACCCGAACGATTTCAGCGCCCCTCTCCA
GATAAGAAGCAAAGCGTGCCATCACCTACAGCCCTTTCCTCTGCCGGGGACTTCCATGAAATGAA
AACGGGCGGCATCGTCGTATGCTCGACATTTGTTGCCCTGGTTTATACCCCGGAGTACTCCTATG
GCCGATCTGTCACCCAACCTCCTTAAACAACCTAAAGGCTTGGCCCCGTTCCGTTTGGAGTTGGA
GAATGGGCCTTATGGCACGGCTTAGTCAGTTATTCTCGCAGATAAGATTCGGACCGCCACTTCTC
TGAAAGCATGGTTTTTGCCTCCCTCCTTGGAGTTCGTCCATTCGTTGGGCGATCCCTTGCTCTCA
CGTTCGAGTGTTTGCTCGTCGTTTAGGCCGGTGAGTGAGATTTCT
Done.