Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D03
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 53248092
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1300000 characters in sequence are not A, C, G, or T
File 4 of 175
Found at i:1148574 original size:343 final size:343
Alignment explanation
Indices: 1147948--1148642 Score: 1381
Period size: 343 Copynumber: 2.0 Consensus size: 343
1147938 CAAATTAGAG
1147948 TCAAATTATGCCATTTACAATACAGGGATTAATTTCCAAGTTTGAGCATAATAGAGGTGCCAAAA
1 TCAAATTATGCCATTTACAATACAGGGATTAATTTCCAAGTTTGAGCATAATAGAGGTGCCAAAA
1148013 CCAGAATTTTACCAATAAAATCTCTTAGCCTACAAGGCAAAGGTCAACGGCGGAGTGATAGATGA
66 CCAGAATTTTACCAATAAAATCTCTTAGCCTACAAGGCAAAGGTCAACGGCGGAGTGATAGATGA
1148078 CCGAATTCGGTAGGGTGATGACCGGCCCACAGACTGCCACGTAGGAGAATCATGGAGAGATACAT
131 CCGAATTCGGTAGGGTGATGACCGGCCCACAGACTGCCACGTAGGAGAATCATGGAGAGATACAT
1148143 CGCTGTTGCACTTTACAGCCACGACGGATTGTTTTGGCTGGAAAGAAGAGCAGCCACGTTGCCTC
196 CGCTGTTGCACTTTACAGCCACGACGGATTGTTTTGGCTGGAAAGAAGAGCAGCCACGTTGCCTC
1148208 CTGTTTAAATTTTTTTAACCCCAAAAATTTTAAATTATTAGTAAGTTAAGGTAACTCAACTTCAA
261 CTGTTTAAATTTTTTTAACCCCAAAAATTTTAAATTATTAGTAAGTTAAGGTAACTCAACTTCAA
1148273 TAAATTATAAAATAGTTA
326 TAAATTATAAAATAGTTA
1148291 TCAAATTATGCCATTTACAATACAGGGATTAATTTCCAAGTTTGAGCATAATAGAGGTGCCAAAA
1 TCAAATTATGCCATTTACAATACAGGGATTAATTTCCAAGTTTGAGCATAATAGAGGTGCCAAAA
1148356 CCAGAATTTTACCAATAAAATCTCTTAGCCTACAAGGCAAAGGTCAACGGCGGAGTGATAGATGA
66 CCAGAATTTTACCAATAAAATCTCTTAGCCTACAAGGCAAAGGTCAACGGCGGAGTGATAGATGA
1148421 CCGAATTCGGTAGGGTGATGACCGGCCCACAGACTGCCACGTAGGAGAATCATGGAGAGATACAT
131 CCGAATTCGGTAGGGTGATGACCGGCCCACAGACTGCCACGTAGGAGAATCATGGAGAGATACAT
1148486 CGCTGTTGCACTTTACAGCCACGACGGATTGTTTTGGCTGGAAAGAAGAGCAGCCACGTTGCCTC
196 CGCTGTTGCACTTTACAGCCACGACGGATTGTTTTGGCTGGAAAGAAGAGCAGCCACGTTGCCTC
1148551 CTGTTTAAATTTTTTTAACCCCAAAAATTTTAAATTATTAGTAAGTTAAGGTAACTCAACTTCAA
261 CTGTTTAAATTTTTTTAACCCCAAAAATTTTAAATTATTAGTAAGTTAAGGTAACTCAACTTCAA
1148616 TAAATTATAAAATAGTTA
326 TAAATTATAAAATAGTTA
*
1148634 TTAAATTAT
1 TCAAATTAT
1148643 TTGAAAGTTT
Statistics
Matches: 351, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
343 351 1.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.27
Consensus pattern (343 bp):
TCAAATTATGCCATTTACAATACAGGGATTAATTTCCAAGTTTGAGCATAATAGAGGTGCCAAAA
CCAGAATTTTACCAATAAAATCTCTTAGCCTACAAGGCAAAGGTCAACGGCGGAGTGATAGATGA
CCGAATTCGGTAGGGTGATGACCGGCCCACAGACTGCCACGTAGGAGAATCATGGAGAGATACAT
CGCTGTTGCACTTTACAGCCACGACGGATTGTTTTGGCTGGAAAGAAGAGCAGCCACGTTGCCTC
CTGTTTAAATTTTTTTAACCCCAAAAATTTTAAATTATTAGTAAGTTAAGGTAACTCAACTTCAA
TAAATTATAAAATAGTTA
Found at i:1155248 original size:13 final size:13
Alignment explanation
Indices: 1155230--1155254 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1155220 AAATGTCACC
1155230 AAAAATTTTAACT
1 AAAAATTTTAACT
1155243 AAAAATTTTAAC
1 AAAAATTTTAAC
1155255 GGGATTAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.08, G:0.00, T:0.36
Consensus pattern (13 bp):
AAAAATTTTAACT
Found at i:1156717 original size:21 final size:21
Alignment explanation
Indices: 1156691--1156755 Score: 94
Period size: 24 Copynumber: 3.0 Consensus size: 21
1156681 TTGTTGCTTC
1156691 ACCACTATAAATTGGTCCTGA
1 ACCACTATAAATTGGTCCTGA
*
1156712 ACCACTATAAAATTGTCTTCCTGA
1 ACCACTAT-AAATTG--GTCCTGA
1156736 ACCACTATAAATTGGTCCTG
1 ACCACTATAAATTGGTCCTG
1156756 GTGGCATTGG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
21 13 0.33
22 6 0.15
23 6 0.15
24 14 0.36
ACGTcount: A:0.32, C:0.25, G:0.12, T:0.31
Consensus pattern (21 bp):
ACCACTATAAATTGGTCCTGA
Found at i:1156814 original size:45 final size:45
Alignment explanation
Indices: 1156754--1156839 Score: 163
Period size: 45 Copynumber: 1.9 Consensus size: 45
1156744 AAATTGGTCC
1156754 TGGTGGCATTGGGGATGATGAACTCCATCCATTGCCACCACTTGG
1 TGGTGGCATTGGGGATGATGAACTCCATCCATTGCCACCACTTGG
*
1156799 TGGTGGCATTGGGGATGATGAACTCCATCCATTGCCGCCAC
1 TGGTGGCATTGGGGATGATGAACTCCATCCATTGCCACCAC
1156840 CATAGCCATT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.20, C:0.26, G:0.29, T:0.26
Consensus pattern (45 bp):
TGGTGGCATTGGGGATGATGAACTCCATCCATTGCCACCACTTGG
Found at i:1157419 original size:31 final size:31
Alignment explanation
Indices: 1157349--1157419 Score: 106
Period size: 31 Copynumber: 2.3 Consensus size: 31
1157339 TTTAACAAGC
* *
1157349 AACATTGAGGGCTAGATTGACATAATATGTA
1 AACATTGAGAGCTAGATTAACATAATATGTA
*
1157380 ATCATTGAGAGCTAGATTAACATAATATGTA
1 AACATTGAGAGCTAGATTAACATAATATGTA
*
1157411 AACTTTGAG
1 AACATTGAG
1157420 GACTAAATTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.39, C:0.10, G:0.20, T:0.31
Consensus pattern (31 bp):
AACATTGAGAGCTAGATTAACATAATATGTA
Found at i:1159650 original size:24 final size:24
Alignment explanation
Indices: 1159618--1159668 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
1159608 GGTCACATTT
1159618 GGTTCGCTGGAATAGAGGTATAGA
1 GGTTCGCTGGAATAGAGGTATAGA
1159642 GGTTCGCTGGAATAGAGGTATAGA
1 GGTTCGCTGGAATAGAGGTATAGA
1159666 GGT
1 GGT
1159669 GTAATGGAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.27, C:0.08, G:0.39, T:0.25
Consensus pattern (24 bp):
GGTTCGCTGGAATAGAGGTATAGA
Found at i:1159676 original size:24 final size:24
Alignment explanation
Indices: 1159625--1159679 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
1159615 TTTGGTTCGC
**
1159625 TGGAATAGAGGTATAGAGGTTCGC
1 TGGAATAGAGGTATAGAGGTTCAA
1159649 TGGAATAGAGGTATAGAGGTGT-AA
1 TGGAATAGAGGTATAGAGGT-TCAA
1159673 TGGAATA
1 TGGAATA
1159680 AAACTGTAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 27 0.96
25 1 0.04
ACGTcount: A:0.35, C:0.04, G:0.36, T:0.25
Consensus pattern (24 bp):
TGGAATAGAGGTATAGAGGTTCAA
Found at i:1159722 original size:45 final size:44
Alignment explanation
Indices: 1159671--1159763 Score: 143
Period size: 44 Copynumber: 2.1 Consensus size: 44
1159661 ATAGAGGTGT
1159671 AATGGAATAAAACTGTAATAGTAATTCAAT-TGTTTGGTTGAATGG
1 AATGGAATAAAACTGTAATAGT-ATTC-ATGTGTTTGGTTGAATGG
* *
1159716 AATGGAATAGAACTGTAATAGTATTCTTGTGTTTGGTTGAATGG
1 AATGGAATAAAACTGTAATAGTATTCATGTGTTTGGTTGAATGG
1159760 AATG
1 AATG
1159764 ATTGTGTTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 23 0.51
45 21 0.47
ACGTcount: A:0.34, C:0.04, G:0.25, T:0.37
Consensus pattern (44 bp):
AATGGAATAAAACTGTAATAGTATTCATGTGTTTGGTTGAATGG
Found at i:1159772 original size:23 final size:23
Alignment explanation
Indices: 1159742--1159788 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1159732 AATAGTATTC
1159742 TTGTGTTTGGTTGAATGGAATGA
1 TTGTGTTTGGTTGAATGGAATGA
1159765 TTGTGTTTGGTTGAATGGAATGA
1 TTGTGTTTGGTTGAATGGAATGA
1159788 T
1 T
1159789 GTTGTAATAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.21, C:0.00, G:0.34, T:0.45
Consensus pattern (23 bp):
TTGTGTTTGGTTGAATGGAATGA
Found at i:1160010 original size:57 final size:56
Alignment explanation
Indices: 1159894--1160023 Score: 145
Period size: 57 Copynumber: 2.3 Consensus size: 56
1159884 AATAAGATTG
* *
1159894 TTAATATAAATAATAAATAATCTAATCATATTTTAACATAATTATTATTAAATATAAT
1 TTAATA-AAATAATAAATAATCTAATAAAATTTTAACATAATTATTATT-AATATAAT
* * * *
1159952 TTAATAAAATAATATATAATTTAATAAAATTCTTAATATAATTATTCTT-ATATGAAT
1 TTAATAAAATAATAAATAATCTAATAAAATT-TTAACATAATTATTATTAATAT-AAT
* *
1160009 TTACTAAAATCATAA
1 TTAATAAAATAATAA
1160024 TATGTAATAC
Statistics
Matches: 61, Mismatches: 9, Indels: 5
0.81 0.12 0.07
Matches are distributed among these distances:
56 4 0.07
57 36 0.59
58 21 0.34
ACGTcount: A:0.51, C:0.05, G:0.01, T:0.43
Consensus pattern (56 bp):
TTAATAAAATAATAAATAATCTAATAAAATTTTAACATAATTATTATTAATATAAT
Found at i:1161779 original size:24 final size:21
Alignment explanation
Indices: 1161714--1161764 Score: 70
Period size: 20 Copynumber: 2.5 Consensus size: 21
1161704 TGATAAAATG
*
1161714 GAGAA-AAGAAAAGAAATGTA
1 GAGAAGAAGAAAAGAAACGTA
*
1161734 AAG-AGAAGAAAAGAAACGTA
1 GAGAAGAAGAAAAGAAACGTA
1161754 GAGAAGAAGAA
1 GAGAAGAAGAA
1161765 GCAGAAATCG
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
19 1 0.04
20 18 0.69
21 7 0.27
ACGTcount: A:0.65, C:0.02, G:0.27, T:0.06
Consensus pattern (21 bp):
GAGAAGAAGAAAAGAAACGTA
Found at i:1162217 original size:26 final size:26
Alignment explanation
Indices: 1162187--1162244 Score: 116
Period size: 26 Copynumber: 2.2 Consensus size: 26
1162177 GATAAAAAAA
1162187 ACAAAACTGTTTAAAAAAATAAACTG
1 ACAAAACTGTTTAAAAAAATAAACTG
1162213 ACAAAACTGTTTAAAAAAATAAACTG
1 ACAAAACTGTTTAAAAAAATAAACTG
1162239 ACAAAA
1 ACAAAA
1162245 AAAAGTGATG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 32 1.00
ACGTcount: A:0.60, C:0.12, G:0.07, T:0.21
Consensus pattern (26 bp):
ACAAAACTGTTTAAAAAAATAAACTG
Found at i:1162298 original size:27 final size:27
Alignment explanation
Indices: 1162268--1162336 Score: 129
Period size: 27 Copynumber: 2.6 Consensus size: 27
1162258 GGACGGGACA
*
1162268 GCACCGGTCACGCCTGGGGAAGAGGCG
1 GCACCGGTCACGCCTGGGGAAAAGGCG
1162295 GCACCGGTCACGCCTGGGGAAAAGGCG
1 GCACCGGTCACGCCTGGGGAAAAGGCG
1162322 GCACCGGTCACGCCT
1 GCACCGGTCACGCCT
1162337 TCCTCAGAGG
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 41 1.00
ACGTcount: A:0.19, C:0.33, G:0.39, T:0.09
Consensus pattern (27 bp):
GCACCGGTCACGCCTGGGGAAAAGGCG
Found at i:1162347 original size:27 final size:27
Alignment explanation
Indices: 1162290--1162377 Score: 95
Period size: 27 Copynumber: 3.3 Consensus size: 27
1162280 CCTGGGGAAG
*****
1162290 AGGCGGCACCGGTCACGCCTGGGGAAA
1 AGGCGGCACCGGTCACGCCTTCCCCAA
* *
1162317 AGGCGGCACCGGTCACGCCTTCCTCAG
1 AGGCGGCACCGGTCACGCCTTCCCCAA
* *
1162344 AGGCGGCATCGGTCATGCCTTCCCCAA
1 AGGCGGCACCGGTCACGCCTTCCCCAA
1162371 AGGCGGC
1 AGGCGGC
1162378 TCCTGTTGCT
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 51 1.00
ACGTcount: A:0.18, C:0.35, G:0.34, T:0.12
Consensus pattern (27 bp):
AGGCGGCACCGGTCACGCCTTCCCCAA
Found at i:1162495 original size:11 final size:11
Alignment explanation
Indices: 1162479--1162516 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
1162469 GGCCAGTCGA
1162479 AAGAAAGAAAG
1 AAGAAAGAAAG
*
1162490 AAGAAAAAAAG
1 AAGAAAGAAAG
1162501 AAGAGAAG-AAG
1 AAGA-AAGAAAG
1162512 AAGAA
1 AAGAA
1162517 GAAGGAGGGA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 1 0.04
11 21 0.88
12 2 0.08
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (11 bp):
AAGAAAGAAAG
Found at i:1162800 original size:13 final size:13
Alignment explanation
Indices: 1162782--1162806 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1162772 AGTTTGGCAA
1162782 TGCTTTTGAAAAG
1 TGCTTTTGAAAAG
1162795 TGCTTTTGAAAA
1 TGCTTTTGAAAA
1162807 CGTGGAGAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (13 bp):
TGCTTTTGAAAAG
Found at i:1163059 original size:24 final size:24
Alignment explanation
Indices: 1163025--1163070 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
1163015 TATATGAAAT
* *
1163025 ATAAATTTTAAATATTTTTAAACA
1 ATAAATATTAAATATTTATAAACA
*
1163049 ATAAATATTAATTATTTATAAA
1 ATAAATATTAAATATTTATAAA
1163071 ATTTAATTAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (24 bp):
ATAAATATTAAATATTTATAAACA
Found at i:1163660 original size:23 final size:24
Alignment explanation
Indices: 1163629--1163674 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 24
1163619 CTAATTAAAT
*
1163629 TTTATAAATAATTAATATTTATTG
1 TTTATAAATAATTAAAATTTATTG
*
1163653 TTTA-AAATATTTAAAATTTATT
1 TTTATAAATAATTAAAATTTATT
1163675 TTTCATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 16 0.80
24 4 0.20
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.54
Consensus pattern (24 bp):
TTTATAAATAATTAAAATTTATTG
Found at i:1169655 original size:52 final size:52
Alignment explanation
Indices: 1169525--1169741 Score: 329
Period size: 52 Copynumber: 4.3 Consensus size: 52
1169515 GAATTTGAGT
*
1169525 ACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTAT
1 ACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTAC
* *
1169577 ACTTATCTGATCAAGAGAC------AAAGTGATAAGTGATAGTTTCGGCTAC
1 ACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTAC
1169623 ACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTAC
1 ACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTAC
* * **
1169675 ACTTATCTGATCAAGTGACAAGTGAAAAATGATAAGTGATAGCTTTAGCTAC
1 ACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTAC
1169727 ACTTATCTGATCAAG
1 ACTTATCTGATCAAG
1169742 AAACAAAGTG
Statistics
Matches: 150, Mismatches: 9, Indels: 12
0.88 0.05 0.07
Matches are distributed among these distances:
46 43 0.29
52 107 0.71
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.29
Consensus pattern (52 bp):
ACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTAC
Found at i:1169655 original size:98 final size:99
Alignment explanation
Indices: 1169525--1169741 Score: 330
Period size: 98 Copynumber: 2.2 Consensus size: 99
1169515 GAATTTGAGT
*
1169525 ACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCA
1 ACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCA
* *
1169590 AGAGAC-AAAGTGATAAGTGATAG-TTTCGGCTAC
66 AGAGACAAAAATGATAAGTGATAGCTTT-AGCTAC
1169623 ACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCA
1 ACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCA
*
1169688 AGTGACAAGTGAAAAATGATAAGTGATAGCTTTAGCTAC
66 AGAGAC-----AAAAATGATAAGTGATAGCTTTAGCTAC
1169727 ACTTATCTGATCAAG
1 ACTTATCTGATCAAG
1169742 AAACAAAGTG
Statistics
Matches: 108, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
98 69 0.64
104 36 0.33
105 3 0.03
ACGTcount: A:0.35, C:0.15, G:0.22, T:0.29
Consensus pattern (99 bp):
ACTTATCTGATCAAGTGACAAGTGGAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCA
AGAGACAAAAATGATAAGTGATAGCTTTAGCTAC
Found at i:1169793 original size:35 final size:37
Alignment explanation
Indices: 1169722--1169793 Score: 112
Period size: 37 Copynumber: 2.0 Consensus size: 37
1169712 GATAGCTTTA
1169722 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
1169759 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1169794 ATCATACGTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
35 12 0.36
36 4 0.12
37 17 0.52
ACGTcount: A:0.36, C:0.17, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:1173353 original size:27 final size:27
Alignment explanation
Indices: 1173265--1173355 Score: 119
Period size: 27 Copynumber: 3.4 Consensus size: 27
1173255 GGGGGGAGTG
* * *
1173265 GATGCCGCCTATGGGGATGGCATCACC
1 GATGCCGCCTATGGGGAAGGCGTGACC
1173292 GATGCCGCCTATGGGGAAGGCGTGACC
1 GATGCCGCCTATGGGGAAGGCGTGACC
* * *
1173319 GATACCGCCTATGGGAAAGGCGTGACT
1 GATGCCGCCTATGGGGAAGGCGTGACC
*
1173346 GGTGCCGCCT
1 GATGCCGCCT
1173356 CTTCCATAGG
Statistics
Matches: 56, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 56 1.00
ACGTcount: A:0.19, C:0.27, G:0.36, T:0.18
Consensus pattern (27 bp):
GATGCCGCCTATGGGGAAGGCGTGACC
Found at i:1176115 original size:14 final size:13
Alignment explanation
Indices: 1176084--1176123 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
1176074 AAAATAAGTC
*
1176084 TAAAAAATCAAAA
1 TAAAAAATTAAAA
*
1176097 TAAAAAATTAATA
1 TAAAAAATTAAAA
1176110 TAAAAAAATTAAAA
1 T-AAAAAATTAAAA
1176124 AACTGAACTG
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
13 12 0.52
14 11 0.48
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.23
Consensus pattern (13 bp):
TAAAAAATTAAAA
Found at i:1178786 original size:12 final size:12
Alignment explanation
Indices: 1178769--1178818 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
1178759 TACCTCTTCT
1178769 TCCTCATCATCC
1 TCCTCATCATCC
*
1178781 TCCTCATCATCA
1 TCCTCATCATCC
* *
1178793 TCTTCGTCATCC
1 TCCTCATCATCC
* *
1178805 TCATCCTCATCC
1 TCCTCATCATCC
1178817 TC
1 TC
1178819 TACCCCATCT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.16, C:0.46, G:0.02, T:0.36
Consensus pattern (12 bp):
TCCTCATCATCC
Found at i:1178792 original size:15 final size:15
Alignment explanation
Indices: 1178772--1178812 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
1178762 CTCTTCTTCC
1178772 TCATCATCCTCCTCA
1 TCATCATCCTCCTCA
* *
1178787 TCATCATCTTCGTCA
1 TCATCATCCTCCTCA
*
1178802 TCCTCATCCTC
1 TCATCATCCTC
1178813 ATCCTCTACC
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.17, C:0.44, G:0.02, T:0.37
Consensus pattern (15 bp):
TCATCATCCTCCTCA
Found at i:1179184 original size:15 final size:15
Alignment explanation
Indices: 1179164--1179200 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
1179154 CTGGATCATA
1179164 TTCATCATCATCCTC
1 TTCATCATCATCCTC
* *
1179179 TTCATCTTCCTCCTC
1 TTCATCATCATCCTC
1179194 TTCATCA
1 TTCATCA
1179201 GACTCCGGCC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.16, C:0.41, G:0.00, T:0.43
Consensus pattern (15 bp):
TTCATCATCATCCTC
Found at i:1180777 original size:19 final size:20
Alignment explanation
Indices: 1180743--1180802 Score: 70
Period size: 19 Copynumber: 3.0 Consensus size: 20
1180733 AGGAAGGAAG
1180743 GAGAGGAAAGAGAGAA-AAAAA
1 GAGA-GAAAGA-AGAAGAAAAA
*
1180764 GAGAGAAAGAAGAAGAAGAA
1 GAGAGAAAGAAGAAGAAAAA
*
1180784 GAG-GAAAGGAGAAGAAAAA
1 GAGAGAAAGAAGAAGAAAAA
1180803 AAAAGAAGGA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
19 18 0.51
20 13 0.37
21 4 0.11
ACGTcount: A:0.65, C:0.00, G:0.35, T:0.00
Consensus pattern (20 bp):
GAGAGAAAGAAGAAGAAAAA
Found at i:1180817 original size:24 final size:24
Alignment explanation
Indices: 1180785--1180834 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
1180775 GAAGAAGAAG
1180785 AGGAAAGGAGAAGAAAAAAAAAGA
1 AGGAAAGGAGAAGAAAAAAAAAGA
* *
1180809 AGGAAAGGAGAAGAGAAAAAACGA
1 AGGAAAGGAGAAGAAAAAAAAAGA
1180833 AG
1 AG
1180835 AAGAGAAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.66, C:0.02, G:0.32, T:0.00
Consensus pattern (24 bp):
AGGAAAGGAGAAGAAAAAAAAAGA
Found at i:1181592 original size:63 final size:64
Alignment explanation
Indices: 1181472--1181603 Score: 171
Period size: 66 Copynumber: 2.1 Consensus size: 64
1181462 AGGAAAAGAG
1181472 TTTTTTAGGGTTTTTTACCAAAATATTACAAAAAAAATAAAAAAAATACCAAAATATTATAAACT
1 TTTTTTAGGGTTTTTTACCAAAATATTACAAAAAAAATAAAAAAAATACCAAAATATTAT-AA-T
1181537 T
64 T
* * * * * *
1181538 TTTTTTCGGGTTTTTTACTAAATTATTA-TAAAAAAAT-AAAAATA-ACCACAATATTATAATT
1 TTTTTTAGGGTTTTTTACCAAAATATTACAAAAAAAATAAAAAAAATACCAAAATATTATAATT
1181599 TTTTT
1 TTTTT
1181604 ATTTATCAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
61 7 0.12
62 2 0.03
63 12 0.20
64 6 0.10
65 8 0.13
66 25 0.42
ACGTcount: A:0.46, C:0.08, G:0.05, T:0.41
Consensus pattern (64 bp):
TTTTTTAGGGTTTTTTACCAAAATATTACAAAAAAAATAAAAAAAATACCAAAATATTATAATT
Found at i:1181644 original size:28 final size:26
Alignment explanation
Indices: 1181582--1181640 Score: 100
Period size: 26 Copynumber: 2.3 Consensus size: 26
1181572 AATAAAAATA
*
1181582 ACCACAATATTATAATTTTTTTATTT
1 ACCAAAATATTATAATTTTTTTATTT
*
1181608 ATCAAAATATTATAATTTTTTTATTT
1 ACCAAAATATTATAATTTTTTTATTT
1181634 ACCAAAA
1 ACCAAAA
1181641 AATAAAAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (26 bp):
ACCAAAATATTATAATTTTTTTATTT
Found at i:1182093 original size:16 final size:15
Alignment explanation
Indices: 1182067--1182096 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1182057 ATACTGAAAT
1182067 AATATAAAATAATAA
1 AATATAAAATAATAA
1182082 AATATGAAAATAATA
1 AATAT-AAAATAATA
1182097 TATTTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (15 bp):
AATATAAAATAATAA
Found at i:1184933 original size:15 final size:16
Alignment explanation
Indices: 1184907--1184936 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1184897 AATAAAAATA
1184907 TATTATTTTTATATTT
1 TATTATTTTTATATTT
1184923 TATTA-TTTTATATT
1 TATTATTTTTATATT
1184937 ATTTCAGTAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TATTATTTTTATATTT
Found at i:1185453 original size:64 final size:64
Alignment explanation
Indices: 1185385--1185516 Score: 187
Period size: 64 Copynumber: 2.1 Consensus size: 64
1185375 TTTGGTAAAT
*
1185385 AAAAAAG-TTATAATATTTTAGTTATTTTTATTT-TTATTTATAATAATTTAGTAAAAAACCCGA
1 AAAAAAGTTTATAATATTTT-GGTATTTTT-TTTATTATTTATAATAATTTAGTAAAAAACCCGA
1185448 A
64 A
* * * *
1185449 AAAAAAGTTTATAATATTTTGGTATTTTTTTTATTTTTTGTAATATTTTGGTAAAAAACCCGAA
1 AAAAAAGTTTATAATATTTTGGTATTTTTTTTATTATTTATAATAATTTAGTAAAAAACCCGAA
1185513 AAAA
1 AAAA
1185517 CCCTTTCCTT
Statistics
Matches: 61, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
63 3 0.05
64 46 0.75
65 12 0.20
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (64 bp):
AAAAAAGTTTATAATATTTTGGTATTTTTTTTATTATTTATAATAATTTAGTAAAAAACCCGAA
Found at i:1186203 original size:10 final size:10
Alignment explanation
Indices: 1186180--1186291 Score: 56
Period size: 10 Copynumber: 11.1 Consensus size: 10
1186170 TCTTTTCTCA
1186180 TTTCCTT-TT
1 TTTCCTTCTT
1186189 CTTTCCTTCTT
1 -TTTCCTTCTT
*
1186200 TTTCTTTCTT
1 TTTCCTTCTT
* *
1186210 TTTTCTTCTCC
1 TTTCCTTCT-T
1186221 TTTCC-TCTT
1 TTTCCTTCTT
*
1186230 CTT-CTTCTT
1 TTTCCTTCTT
1186239 CGTTT--TT-TT
1 --TTTCCTTCTT
*
1186248 TTTCTCTTCTCC
1 TTTC-CTTCT-T
*
1186260 TTTCCTTTTT
1 TTTCCTTCTT
1186270 CTTTCCTTCTT
1 -TTTCCTTCTT
*
1186281 TTTCTTTCTT
1 TTTCCTTCTT
1186291 T
1 T
1186292 CCTCTCCTTC
Statistics
Matches: 78, Mismatches: 13, Indels: 22
0.69 0.12 0.19
Matches are distributed among these distances:
7 3 0.04
8 1 0.01
9 8 0.10
10 40 0.51
11 22 0.28
12 4 0.05
ACGTcount: A:0.00, C:0.29, G:0.01, T:0.71
Consensus pattern (10 bp):
TTTCCTTCTT
Found at i:1186208 original size:36 final size:35
Alignment explanation
Indices: 1186157--1186296 Score: 118
Period size: 36 Copynumber: 3.6 Consensus size: 35
1186147 CTTCCCTCTT
*
1186157 CTTCTTCTTTTTTTCTTTTCTCATTTCCTTTTCTTTC
1 CTTCTT-TTTCTTTCTTTTCTC-TTTCCTTTTCTTTC
*
1186194 CTTCTTTTTCTTTCTTTTTTCTTCTCCTTTCCTCTTCTTC
1 CTTCTTTTTCTTTCTTTTCTCTT-TCCTTT--TC-T-TTC
* *
1186234 TTCTTCGTTTTTTTTTTCTCTTCTCCTTTCCTTTTTCTTTC
1 --CTTC--TTTTTCTTTCTTTTCT-CTTTCC-TTTTCTTTC
*
1186275 CTTCTTTTTCTTTCTTTCCTCT
1 CTTCTTTTTCTTTCTTTTCTCT
1186297 CCTTCCTTCC
Statistics
Matches: 84, Mismatches: 8, Indels: 23
0.73 0.07 0.20
Matches are distributed among these distances:
35 2 0.02
36 21 0.25
37 19 0.23
38 2 0.02
39 5 0.06
40 3 0.04
41 3 0.04
42 5 0.06
43 2 0.02
44 16 0.19
45 6 0.07
ACGTcount: A:0.01, C:0.29, G:0.01, T:0.69
Consensus pattern (35 bp):
CTTCTTTTTCTTTCTTTTCTCTTTCCTTTTCTTTC
Found at i:1186298 original size:39 final size:39
Alignment explanation
Indices: 1186154--1186304 Score: 143
Period size: 39 Copynumber: 3.8 Consensus size: 39
1186144 TTACTTCCCT
* * *
1186154 CTTCTTCTTCTTTTTTTCTTTTCTCATTTCC-TTTTCTTTC
1 CTTCTTTTTCTTTCTTTC--TTCTCCTTTCCTTTTTCTTTC
1186194 CTTCTTTTTCTTTCTTTTTTCTTCTCCTTTCCTCTTCTTC-TT-
1 CTTCTTTTTCTTTC---TTTCTTCTCCTTTCCT-TT-TTCTTTC
1186236 CTTCGTTTTT-TTT-TTCTCTTCTCCTTTCCTTTTTCTTTC
1 CTTC-TTTTTCTTTCTT-TCTTCTCCTTTCCTTTTTCTTTC
*
1186275 CTTCTTTTTCTTTCTTTCCTCTCC-TTCCTT
1 CTTCTTTTTCTTTCTTTCTTCTCCTTTCCTT
1186305 CCTTCCTTTC
Statistics
Matches: 95, Mismatches: 4, Indels: 26
0.76 0.03 0.21
Matches are distributed among these distances:
37 3 0.03
38 17 0.18
39 28 0.29
40 14 0.15
41 10 0.11
42 7 0.07
43 13 0.14
44 3 0.03
ACGTcount: A:0.01, C:0.30, G:0.01, T:0.68
Consensus pattern (39 bp):
CTTCTTTTTCTTTCTTTCTTCTCCTTTCCTTTTTCTTTC
Found at i:1186307 original size:81 final size:79
Alignment explanation
Indices: 1186153--1186304 Score: 223
Period size: 81 Copynumber: 1.9 Consensus size: 79
1186143 CTTACTTCCC
* ** *
1186153 TCTTCTTCTTCTTTTTTTCTTTTCTCATTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTTTTCTTC
1 TCTTCTTCTTCTTTTTTTCTCTTCTCATTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTCC
1186218 TCCTTTCCTCTTCT
66 TCCTTTCCTCTTCT
* *
1186232 TCTTCTTCGTTTTTTTTTTCTCTTCTCCTTTCCTTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCT
1 TCTTCTTC-TTCTTTTTTTCTCTTCTCATTTCC-TTTTCTTTCCTTCTTTTTCTTTCTTTCCTCT
1186297 CCTTCCTT
64 CC-TCCTT
1186305 CCTTCCTTTC
Statistics
Matches: 64, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
79 8 0.12
80 21 0.33
81 30 0.47
82 5 0.08
ACGTcount: A:0.01, C:0.30, G:0.01, T:0.68
Consensus pattern (79 bp):
TCTTCTTCTTCTTTTTTTCTCTTCTCATTTCCTTTTCTTTCCTTCTTTTTCTTTCTTTCCTCTCC
TCCTTTCCTCTTCT
Found at i:1186319 original size:13 final size:14
Alignment explanation
Indices: 1186284--1186327 Score: 56
Period size: 13 Copynumber: 3.2 Consensus size: 14
1186274 CCTTCTTTTT
1186284 CTTTCTTTCCTCTC
1 CTTTCTTTCCTCTC
*
1186298 C-TTCCTTCCT-TC
1 CTTTCTTTCCTCTC
1186310 CTTTCTTTCCCTCTC
1 CTTTCTTT-CCTCTC
1186325 CTT
1 CTT
1186328 CTCCCCCCAA
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
12 3 0.12
13 13 0.52
14 4 0.16
15 5 0.20
ACGTcount: A:0.00, C:0.45, G:0.00, T:0.55
Consensus pattern (14 bp):
CTTTCTTTCCTCTC
Found at i:1186473 original size:26 final size:28
Alignment explanation
Indices: 1186444--1186505 Score: 110
Period size: 26 Copynumber: 2.3 Consensus size: 28
1186434 TTTTTTTTGT
1186444 ATATTTTGGTAAAT-AAAAAAA-TTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
1186470 ATATTTTGGTAAATAAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
1186498 ATATTTTG
1 ATATTTTG
1186506 ATTATTTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
26 14 0.41
27 7 0.21
28 13 0.38
ACGTcount: A:0.50, C:0.00, G:0.10, T:0.40
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTATA
Found at i:1192809 original size:18 final size:20
Alignment explanation
Indices: 1192768--1192811 Score: 65
Period size: 20 Copynumber: 2.3 Consensus size: 20
1192758 AATATAATCA
*
1192768 TATCATATTTATAAATACAT
1 TATCATAATTATAAATACAT
1192788 TATCATAATT-TAAATA-AT
1 TATCATAATTATAAATACAT
1192806 TATCAT
1 TATCAT
1192812 TTATTGATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 8 0.35
19 6 0.26
20 9 0.39
ACGTcount: A:0.45, C:0.09, G:0.00, T:0.45
Consensus pattern (20 bp):
TATCATAATTATAAATACAT
Found at i:1197838 original size:18 final size:18
Alignment explanation
Indices: 1197817--1197970 Score: 85
Period size: 18 Copynumber: 8.9 Consensus size: 18
1197807 ATATTAAGAA
1197817 TTTTATTAAATTATATAT
1 TTTTATTAAATTATATAT
1197835 TTTTATTAAA-T-TATA-
1 TTTTATTAAATTATATAT
* *
1197850 -TTTAAT-AATAAT-TAT
1 TTTTATTAAATTATATAT
* *
1197865 TTTAAATTATATTATATAT
1 TTT-TATTAAATTATATAT
* * *
1197884 TATTA-TATATTAT-GA-
1 TTTTATTAAATTATATAT
*
1197899 TTTTATTAAATTCATATAA
1 TTTTATTAAATT-ATATAT
*** * *
1197918 GAATATTTAATATTA-AAAA
1 TTTTA-TTAA-ATTATATAT
1197937 TTTTATTAAATTATATAT
1 TTTTATTAAATTATATAT
1197955 TTTTATTAAATTATAT
1 TTTTATTAAATTATAT
1197971 TTAATAATAA
Statistics
Matches: 101, Mismatches: 21, Indels: 28
0.67 0.14 0.19
Matches are distributed among these distances:
13 2 0.02
14 7 0.07
15 5 0.05
16 12 0.12
17 17 0.17
18 38 0.38
19 12 0.12
20 5 0.05
21 3 0.03
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (18 bp):
TTTTATTAAATTATATAT
Found at i:1197888 original size:120 final size:120
Alignment explanation
Indices: 1197752--1198231 Score: 791
Period size: 120 Copynumber: 4.0 Consensus size: 120
1197742 ATTATTAATC
*
1197752 TATATTATATAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAA
1 TATATTATATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
*
1197817 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAAT
66 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAT
* * *
1197872 TATATTATATATTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAAAA
1 TATATTATATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
1197937 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAT
66 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAT
* *
1197992 TATATTTTATAGTATTATATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAA
1 TATATTATATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
*
1198057 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAA
66 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAT
* * * * * * *
1198112 TATATTTTATAGTATCATATATTATTATTTTAGTAAATTCAGATAAAAATATTGATTATTAAGAA
1 TATATTATATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
* *
1198177 TTTTATTAAATTATATA-TTTAATTAAAATATATTTAATAATAATTATGTTTAAAT
66 TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATG-TTAAAT
1198232 ATGATTAAAT
Statistics
Matches: 340, Mismatches: 19, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
119 29 0.09
120 311 0.91
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (120 bp):
TATATTATATAGTATTATATATTATGATTTTAGTAAATTCATATAAGAATATTTAATATTAAGAA
TTTTATTAAATTATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAAT
Found at i:1198196 original size:17 final size:17
Alignment explanation
Indices: 1198176--1198209 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1198166 ATTATTAAGA
* *
1198176 ATTTTATTAAATTATAT
1 ATTTAATTAAAATATAT
1198193 ATTTAATTAAAATATAT
1 ATTTAATTAAAATATAT
1198210 TTAATAATAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
ATTTAATTAAAATATAT
Found at i:1198400 original size:39 final size:40
Alignment explanation
Indices: 1198357--1198461 Score: 104
Period size: 44 Copynumber: 2.5 Consensus size: 40
1198347 TTCCATTATG
1198357 CTATTACACCTCTATTCCATTCAACCAAACACAAGA-TTA
1 CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
** *** *
1198396 CTATTACGTCTCTATTCCATTACATTCAACCAAACAGTTGATTTG
1 CTATTACACCTCTATT-C----CATTCAACCAAACACAAGATTTA
1198441 CTATTACACCTCTATTCCATT
1 CTATTACACCTCTATTCCATT
1198462 ACACCTCTAT
Statistics
Matches: 52, Mismatches: 8, Indels: 11
0.73 0.11 0.15
Matches are distributed among these distances:
39 14 0.27
40 5 0.10
44 17 0.33
45 16 0.31
ACGTcount: A:0.31, C:0.29, G:0.05, T:0.35
Consensus pattern (40 bp):
CTATTACACCTCTATTCCATTCAACCAAACACAAGATTTA
Found at i:1198456 original size:45 final size:44
Alignment explanation
Indices: 1198355--1198464 Score: 122
Period size: 45 Copynumber: 2.6 Consensus size: 44
1198345 TTTTCCATTA
1198355 TGCTATTACACCTCTATT-C----CATTCAACCAAACACAAGAT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
* ** ***
1198394 TACTATTACGTCTCTATTCCATTACATTCAACCAAACAGTTGATT
1 TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGA-T
1198439 TGCTATTACACCTCTATTCCATTACA
1 TGCTATTACACCTCTATTCCATTACA
1198465 CCTCTATTCC
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
39 15 0.27
40 1 0.02
44 16 0.29
45 24 0.43
ACGTcount: A:0.32, C:0.28, G:0.05, T:0.35
Consensus pattern (44 bp):
TGCTATTACACCTCTATTCCATTACATTCAACCAAACACAAGAT
Found at i:1198464 original size:16 final size:16
Alignment explanation
Indices: 1198443--1198512 Score: 95
Period size: 16 Copynumber: 4.4 Consensus size: 16
1198433 TTGATTTGCT
*
1198443 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
*
1198459 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
*
1198475 ATTATACCTCTAATCC
1 ATTACACCTCTAATCC
*
1198491 AATACACCTCTAATCC
1 ATTACACCTCTAATCC
*
1198507 AATACA
1 ATTACA
1198513 GCGAACCAAA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 50 1.00
ACGTcount: A:0.33, C:0.34, G:0.00, T:0.33
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:1204407 original size:26 final size:26
Alignment explanation
Indices: 1204359--1204408 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
1204349 TGGTAATGTA
*
1204359 TTAAATATTTTTTTCCATTAAATTTG
1 TTAAATATTTTTTTCCATAAAATTTG
*
1204385 TTAAATTTTTTTTTCTCA-AAAATT
1 TTAAATATTTTTTTC-CATAAAATT
1204409 GTTGGATTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 19 0.90
27 2 0.10
ACGTcount: A:0.32, C:0.08, G:0.02, T:0.58
Consensus pattern (26 bp):
TTAAATATTTTTTTCCATAAAATTTG
Found at i:1206054 original size:31 final size:31
Alignment explanation
Indices: 1206019--1206084 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
1206009 ATTTACTTAA
*
1206019 ATGTATACAAT-TGAATTAAAAGT-AAAGTTTC
1 ATGTATA-AATCTGAATCAAAA-TAAAAGTTTC
*
1206050 ATGTATAAATCTGAATCACAATAAAAGTTTC
1 ATGTATAAATCTGAATCAAAATAAAAGTTTC
1206081 ATGT
1 ATGT
1206085 GTATAATTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
30 4 0.13
31 27 0.87
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (31 bp):
ATGTATAAATCTGAATCAAAATAAAAGTTTC
Found at i:1219575 original size:58 final size:56
Alignment explanation
Indices: 1219433--1219583 Score: 142
Period size: 58 Copynumber: 2.6 Consensus size: 56
1219423 AGTCGTTTTT
* * ** * *
1219433 TTGGGGCTTGTACTTTTTTGGTCCAAAATAGTTTCTAAACTTGGCAATTTTTCCACA
1 TTGGGGCTTGAATTTTTTTGGTCCAAGTTAG-TCCTAAACTTGGCAATTGTTCCACA
* * * *
1219490 TTGGGGCTTGAGCTTTCTTTTTGTCCAAGTTAGTCCTTAACTTGGCAATTGTT-CATGTA
1 TTGGGGCTTGA-ATTT-TTTTGGTCCAAGTTAGTCCTAAACTTGGCAATTGTTCCA--CA
*
1219549 TTGGGGCTTGAATTATTTTTGGTCCAAGTTGGTCC
1 TTGGGGCTTGAATT-TTTTTGGTCCAAGTTAGTCC
1219584 AAGTTAGTTC
Statistics
Matches: 76, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
57 12 0.16
58 38 0.50
59 26 0.34
ACGTcount: A:0.19, C:0.17, G:0.22, T:0.43
Consensus pattern (56 bp):
TTGGGGCTTGAATTTTTTTGGTCCAAGTTAGTCCTAAACTTGGCAATTGTTCCACA
Found at i:1220567 original size:88 final size:87
Alignment explanation
Indices: 1220364--1220605 Score: 253
Period size: 89 Copynumber: 2.8 Consensus size: 87
1220354 CCTGTATTTC
*
1220364 TTTTTACACTCAATTCGATACTTGAACTTTTAAAATGCATCAAAAAAACCTTCAAACTTTTTCAA
1 TTTTTGCACTCAATT-GATACTTGAACTTTTAAAATGCATCAAAAAAACCTTCAAACTTTTTCAA
* *
1220429 AAAAAGTAATTAAGCCCCGCCCTT
65 AAAAAGCAATTAA-CACCGCCCTT
* * * * **
1220453 TTTTTGTACTTAATTGGGTACTTGAACTTTTAAAATGTAT-AAAAAAGACCTTCAATTTTTTTTT
1 TTTTTGCACTCAATT-GATACTTGAACTTTTAAAATGCATCAAAAAA-ACCTTCAA--ACTTTTT
**
1220517 CAAAAAAAGCAATTAA-ACC-CTTTT
62 CAAAAAAAGCAATTAACACCGCCCTT
**
1220541 TTTTTGCACTCAATTGAATACTTGAACCGTTAAAATGCATCAAAAAAA--TTCTAAA-TTTTTCA
1 TTTTTGCACTCAATTG-ATACTTGAACTTTTAAAATGCATCAAAAAAACCTTC-AAACTTTTTCA
1220603 AAA
64 AAA
1220606 TTTAATCCTC
Statistics
Matches: 128, Mismatches: 19, Indels: 17
0.78 0.12 0.10
Matches are distributed among these distances:
84 10 0.08
86 3 0.02
87 3 0.02
88 42 0.33
89 50 0.39
91 20 0.16
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (87 bp):
TTTTTGCACTCAATTGATACTTGAACTTTTAAAATGCATCAAAAAAACCTTCAAACTTTTTCAAA
AAAAGCAATTAACACCGCCCTT
Found at i:1223631 original size:156 final size:153
Alignment explanation
Indices: 1223320--1223625 Score: 404
Period size: 156 Copynumber: 2.0 Consensus size: 153
1223310 GGTTAAAGCA
* * * * *
1223320 GGAGGTTGAGGAGGTCGTATGCTTGCAGATACAGTTGAGGAGGCAAATAAGCTTGCAAATACACC
1 GGAGGTTGAGGAGGTCGAATGCTTGCAGATACAGTCGAGGACGCAAATAAGCTCGAAAATACACC
* * **
1223385 ACTGCTGCTGCTATTGCTAGCACCACTGCTAACCAGGCTGATGCTACCGCTACAACTTCCATTTA
66 ACCGCTGCTGCTA-T-CTA-CACCACTGCTAACCAAGCTGACACTACCGCTACAACTTCCATTTA
1223450 AGCCAGCCGATGGTGGAGCTGGTGCC
128 AGCCAGCCGATGGTGGAGCTGGTGCC
*
1223476 GGAGGTTGAGGAGGTCGAATGCTTGCAGATACAGTCGAGGACGTAAATAAGCTCGAAAATACACC
1 GGAGGTTGAGGAGGTCGAATGCTTGCAGATACAGTCGAGGACGCAAATAAGCTCGAAAATACACC
* * **
1223541 GCCGCTGCTGCTA-C-A-ACCACTGCTAATCAAGCTGACACTAGTGCTACAACTTCCATTTAAGC
66 ACCGCTGCTGCTATCTACACCACTGCTAACCAAGCTGACACTACCGCTACAACTTCCATTTAAGC
* *
1223603 TAGCCGGA-GGTGGAGCCGGTGCC
131 CAGCC-GATGGTGGAGCTGGTGCC
1223626 AGTGCCATAG
Statistics
Matches: 133, Mismatches: 16, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
150 59 0.44
151 2 0.02
152 1 0.01
153 1 0.01
156 70 0.53
ACGTcount: A:0.26, C:0.25, G:0.27, T:0.22
Consensus pattern (153 bp):
GGAGGTTGAGGAGGTCGAATGCTTGCAGATACAGTCGAGGACGCAAATAAGCTCGAAAATACACC
ACCGCTGCTGCTATCTACACCACTGCTAACCAAGCTGACACTACCGCTACAACTTCCATTTAAGC
CAGCCGATGGTGGAGCTGGTGCC
Found at i:1223650 original size:12 final size:12
Alignment explanation
Indices: 1223634--1223663 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
1223624 CCAGTGCCAT
1223634 AGCTGGTGCTGG
1 AGCTGGTGCTGG
*
1223646 TGCTGGTGCTGG
1 AGCTGGTGCTGG
1223658 AGCTGG
1 AGCTGG
1223664 AGCTTTTTCC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.07, C:0.17, G:0.50, T:0.27
Consensus pattern (12 bp):
AGCTGGTGCTGG
Found at i:1225763 original size:16 final size:17
Alignment explanation
Indices: 1225723--1225772 Score: 57
Period size: 16 Copynumber: 2.8 Consensus size: 17
1225713 TAGAATATTA
1225723 ATTCTATTATATATTTATCT
1 ATTCTATTATATA--TA-CT
1225743 ATTCTATTATATATA-T
1 ATTCTATTATATATACT
*
1225759 ATTCTAATATATAT
1 ATTCTATTATATAT
1225773 TAGTACTAGA
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
16 14 0.48
18 2 0.07
20 13 0.45
ACGTcount: A:0.36, C:0.08, G:0.00, T:0.56
Consensus pattern (17 bp):
ATTCTATTATATATACT
Found at i:1225803 original size:21 final size:21
Alignment explanation
Indices: 1225779--1225818 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1225769 ATATTAGTAC
*
1225779 TAGAAT-TTATTTATAATATAT
1 TAGAATATTATAT-TAATATAT
1225800 TAGAATATTATATTAATAT
1 TAGAATATTATATTAATAT
1225819 TATTTTTATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (21 bp):
TAGAATATTATATTAATATAT
Found at i:1233055 original size:79 final size:72
Alignment explanation
Indices: 1232896--1233080 Score: 217
Period size: 75 Copynumber: 2.4 Consensus size: 72
1232886 CATGCATAGT
* * *
1232896 GCACTAAAGATTGATAAAAATTGATCATTGGACACACCCACATAAATACATGCATGCATACATAT
1 GCACTAAAGATTGAT-AAAATTGACCATTGGACACACACACACAAATACATGCATGCATACATAT
1232961 ATATACGC
65 ATATACGC
* * * *
1232969 GCGCTAAAGATCGATAAAAGTTGACCATTGGATGCACACACACACAAATGCATGGATGCATACAT
1 GCACTAAAGATTGATAAAA-TTGACCATTGGA--CACACACACACAAATACATGCATGCATACAT
1233034 ATATATACCCACGC
63 ATATAT----ACGC
*
1233048 GCACTAAAGATTGATAGAAATTGAGCATTGGAC
1 GCACTAAAGATTGATA-AAATTGACCATTGGAC
1233081 CTCATTTGGC
Statistics
Matches: 94, Mismatches: 10, Indels: 12
0.81 0.09 0.10
Matches are distributed among these distances:
72 4 0.04
73 24 0.26
75 33 0.35
77 1 0.01
79 29 0.31
80 3 0.03
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.23
Consensus pattern (72 bp):
GCACTAAAGATTGATAAAATTGACCATTGGACACACACACACAAATACATGCATGCATACATATA
TATACGC
Found at i:1241080 original size:14 final size:16
Alignment explanation
Indices: 1241045--1241078 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
1241035 AATATCAAAA
*
1241045 TTTTCGAACATTTATT
1 TTTTAGAACATTTATT
1241061 TTTTAGAACATTT-TT
1 TTTTAGAACATTTATT
1241076 TTT
1 TTT
1241079 AGGAAAATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 5 0.29
16 12 0.71
ACGTcount: A:0.24, C:0.09, G:0.06, T:0.62
Consensus pattern (16 bp):
TTTTAGAACATTTATT
Found at i:1259018 original size:29 final size:28
Alignment explanation
Indices: 1258976--1259085 Score: 87
Period size: 30 Copynumber: 3.8 Consensus size: 28
1258966 TTAAAACCTT
* *
1258976 CAAAACTTTT-AAAATTTTAATCAAACTC
1 CAAAATTTTTGAAAATTTTAAT-AAACCC
* * * *
1259004 CACAATTTTTGAAAAATCTCATTAAACCC
1 CAAAATTTTTG-AAAATTTTAATAAACCC
* * *
1259033 CTAAAAGTTTTAAAAATTTGAAGTAAACCC
1 C-AAAATTTTTGAAAATTTTAA-TAAACCC
1259063 TCAAAATTTTTGAAAATTTTAAT
1 -CAAAATTTTTGAAAATTTTAAT
1259086 TAGATCAGCC
Statistics
Matches: 62, Mismatches: 15, Indels: 9
0.72 0.17 0.10
Matches are distributed among these distances:
28 8 0.13
29 14 0.23
30 39 0.63
31 1 0.02
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (28 bp):
CAAAATTTTTGAAAATTTTAATAAACCC
Found at i:1259028 original size:59 final size:60
Alignment explanation
Indices: 1258951--1259078 Score: 138
Period size: 59 Copynumber: 2.2 Consensus size: 60
1258941 TCTCTAAGCT
* * * * * *
1258951 TTTTTG-AAATTCTTATTAAAACCTTCAAAACTTTT-AAAATTTTAA-TCAAACTC-CACAA
1 TTTTTGAAAAATCTCATTAAAACCCT-AAAACTTTTAAAAATTTGAAGT-AAACCCTCAAAA
* *
1259009 TTTTTGAAAAATCTCATTAAACCCCTAAAAGTTTTAAAAATTTGAAGTAAACCCTCAAAA
1 TTTTTGAAAAATCTCATTAAAACCCTAAAACTTTTAAAAATTTGAAGTAAACCCTCAAAA
1259069 TTTTTGAAAA
1 TTTTTGAAAA
1259079 TTTTAATTAG
Statistics
Matches: 58, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
58 14 0.24
59 29 0.50
60 15 0.26
ACGTcount: A:0.43, C:0.16, G:0.05, T:0.37
Consensus pattern (60 bp):
TTTTTGAAAAATCTCATTAAAACCCTAAAACTTTTAAAAATTTGAAGTAAACCCTCAAAA
Found at i:1267242 original size:27 final size:28
Alignment explanation
Indices: 1267203--1267257 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 28
1267193 TAAAGGTAGC
*
1267203 TAAAAAACATTTACTAATAGTTAAGTGA
1 TAAAAAACATTTACTAATAATTAAGTGA
*
1267231 TAAAAAA-ATTTACTAATAATTGAGTGA
1 TAAAAAACATTTACTAATAATTAAGTGA
1267258 CTATGAATAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
27 18 0.72
28 7 0.28
ACGTcount: A:0.51, C:0.05, G:0.11, T:0.33
Consensus pattern (28 bp):
TAAAAAACATTTACTAATAATTAAGTGA
Found at i:1273335 original size:21 final size:21
Alignment explanation
Indices: 1273311--1273358 Score: 96
Period size: 21 Copynumber: 2.3 Consensus size: 21
1273301 TTTAAAATTA
1273311 ATTTTTCATTTTTGGTCCTTG
1 ATTTTTCATTTTTGGTCCTTG
1273332 ATTTTTCATTTTTGGTCCTTG
1 ATTTTTCATTTTTGGTCCTTG
1273353 ATTTTT
1 ATTTTT
1273359 AGAATTTTAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.10, C:0.12, G:0.12, T:0.65
Consensus pattern (21 bp):
ATTTTTCATTTTTGGTCCTTG
Found at i:1274668 original size:24 final size:22
Alignment explanation
Indices: 1274621--1274682 Score: 65
Period size: 24 Copynumber: 2.8 Consensus size: 22
1274611 TGTATATTTA
1274621 ATTTT-ATTTTTTAATTTGTTG
1 ATTTTAATTTTTTAATTTGTTG
1274642 ATTTTAATTTTTTATATTT-TTCGG
1 ATTTTAATTTTTTA-ATTTGTT--G
**
1274666 ATTTTAAAATTTTAATT
1 ATTTTAATTTTTTAATT
1274683 CTGACTCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
21 5 0.14
22 10 0.29
23 7 0.20
24 13 0.37
ACGTcount: A:0.26, C:0.02, G:0.06, T:0.66
Consensus pattern (22 bp):
ATTTTAATTTTTTAATTTGTTG
Found at i:1279725 original size:42 final size:42
Alignment explanation
Indices: 1279662--1279757 Score: 99
Period size: 42 Copynumber: 2.3 Consensus size: 42
1279652 GCTATTGCTT
1279662 CCTAACTTTTTGCGCCATTTAT-AATAAAAACAG-AGCTATAGC
1 CCTAACTTTTTGCGCCATTTATGAA-AAAAA-AGCAGCTATAGC
** * *
1279704 CCTAACTTTTTGCAG-TGTTTATGAAAAAAATGCCGCTATAGC
1 CCTAACTTTTTGC-GCCATTTATGAAAAAAAAGCAGCTATAGC
*
1279746 TCTAACTTTTTG
1 CCTAACTTTTTG
1279758 TGGTGTTTTC
Statistics
Matches: 46, Mismatches: 5, Indels: 6
0.81 0.09 0.11
Matches are distributed among these distances:
41 1 0.02
42 42 0.91
43 3 0.07
ACGTcount: A:0.31, C:0.20, G:0.14, T:0.35
Consensus pattern (42 bp):
CCTAACTTTTTGCGCCATTTATGAAAAAAAAGCAGCTATAGC
Found at i:1286904 original size:265 final size:264
Alignment explanation
Indices: 1286059--1287008 Score: 1507
Period size: 265 Copynumber: 3.6 Consensus size: 264
1286049 ATTGAATCAT
*
1286059 TTGTTTCCCAGCAGGTGGTGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCC
1 TTGTTTCCTAGCAGGTGGTGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCC
* * *
1286124 GGTTTTCTTTGGACTGATTTCGACAATGAATTGGAATTCTTTGTTACCTTGAAAATAAATATTAT
66 GGTTTTCTTTGGACCGATTTCGACAATGAATCGGAACTCTTTGTTACCTTGAAAA-AAATATTAT
*
1286189 TACATTGACAAATGCTTTAAATTGGATATGTAGATTCAGCTGTGAGAATGCATACATTTATTTTT
130 TACATTGACAAATGCTTTAAATTGGATATGTAGATTCAGCTGTGAGAATGCATACATTTATTTAT
1286254 ATATGTGTGTGTGATGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCGATCTC
195 ATATGTGTGTGTGATGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCGATCTC
*
1286319 CAGGC
260 CATGC
* *
1286324 TTATTTCCTAGCAGGTGTTGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCC
1 TTGTTTCCTAGCAGGTGGTGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCC
* * ** * *
1286389 GGTTTTCTTTGGACTGATTTCGGCGGTAAACCGGAACTCTTTGTTACCTTGAAAAAAAATATTAT
66 GGTTTTCTTTGGACCGATTTCGACAATGAATCGGAACTCTTTGTTACCTTG-AAAAAAATATTAT
* * * *
1286454 TACATTGACAAATGTTTTAAACTGGATATGTAGACTCAGCTGTGAGAATGCATACGTTTATTTAT
130 TACATTGACAAATGCTTTAAATTGGATATGTAGATTCAGCTGTGAGAATGCATACATTTATTTAT
1286519 ATA--TGTGTGTGATGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCGATCTC
195 ATATGTGTGTGTGATGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCGATCTC
1286582 CATGC
260 CATGC
* * * *
1286587 TTGTTTCCTAGCAGGTGTTGTTGTACTTTAGTTTCTTAAAGTGCTATCCCTATTCTCCCTAATCC
1 TTGTTTCCTAGCAGGTGGTGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCC
* *
1286652 TGTTTTCTTTGGACCGATTTC-AGCGATGAATCGGAACTCTTTGTTACCTTGAAAAAGAATATTA
66 GGTTTTCTTTGGACCGATTTCGA-CAATGAATCGGAACTCTTTGTTACCTTGAAAAA-AATATTA
* *
1286716 TTACATTGACAAATGCTTTACATTGGATATATACG-TTCAGCTGTGAGAATGCATACATTTATTT
129 TTACATTGACAAATGCTTTAAATTGGATATGTA-GATTCAGCTGTGAGAATGCATACATTTATTT
* * * *
1286780 ATATATGTGTGTGTGATGCAATGTTGCTATGTTATTAGTGTTGACTGAATCATTAGCCCCCCATC
193 ATATATGTGTGTGTGATGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCGATC
1286845 TCCATGC
258 TCCATGC
*
1286852 TTGTTTCCTAGCAGGTGGTGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTACCCCGAATCC
1 TTGTTTCCTAGCAGGTGGTGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCC
** *
1286917 GGTTTTCTTTGGACCGATTTCGACAATGAATTAGAATTCTTTGTTACCTT--AAAAAATATTATT
66 GGTTTTCTTTGGACCGATTTCGACAATGAATCGGAACTCTTTGTTACCTTGAAAAAAATATTATT
1286980 ACATTGACAAATGCTTTAAATTGGATATG
131 ACATTGACAAATGCTTTAAATTGGATATG
1287009 CTTTTTTTTT
Statistics
Matches: 630, Mismatches: 48, Indels: 17
0.91 0.07 0.02
Matches are distributed among these distances:
262 41 0.07
263 241 0.38
264 1 0.00
265 342 0.54
266 5 0.01
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (264 bp):
TTGTTTCCTAGCAGGTGGTGTTGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCC
GGTTTTCTTTGGACCGATTTCGACAATGAATCGGAACTCTTTGTTACCTTGAAAAAAATATTATT
ACATTGACAAATGCTTTAAATTGGATATGTAGATTCAGCTGTGAGAATGCATACATTTATTTATA
TATGTGTGTGTGATGCAATGCTGCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCGATCTCC
ATGC
Found at i:1287176 original size:27 final size:27
Alignment explanation
Indices: 1287146--1287202 Score: 96
Period size: 27 Copynumber: 2.1 Consensus size: 27
1287136 GCCTGATCAG
1287146 GCCAATGTGATTGGCAGCACCAAAGGT
1 GCCAATGTGATTGGCAGCACCAAAGGT
* *
1287173 GCCAATGTGATTGGCGGCACCAATGGT
1 GCCAATGTGATTGGCAGCACCAAAGGT
1287200 GCC
1 GCC
1287203 GAAGGACTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.25, C:0.25, G:0.32, T:0.19
Consensus pattern (27 bp):
GCCAATGTGATTGGCAGCACCAAAGGT
Found at i:1287537 original size:19 final size:19
Alignment explanation
Indices: 1287513--1287576 Score: 85
Period size: 19 Copynumber: 3.4 Consensus size: 19
1287503 ATTAAAACAA
1287513 TTTAATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
* *
1287532 TTTAATGTAATAA-ACTAT
1 TTTAATTTAATAACTCTAT
* *
1287550 TCTCATTTAATAACTCTAT
1 TTTAATTTAATAACTCTAT
1287569 TTTAATTT
1 TTTAATTT
1287577 TAAAAATAAA
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
18 14 0.39
19 22 0.61
ACGTcount: A:0.36, C:0.11, G:0.02, T:0.52
Consensus pattern (19 bp):
TTTAATTTAATAACTCTAT
Found at i:1287849 original size:37 final size:37
Alignment explanation
Indices: 1287807--1287894 Score: 167
Period size: 37 Copynumber: 2.4 Consensus size: 37
1287797 ATTTTAAATG
*
1287807 AAATAGAGTTATTAAATGAGAATAGTTTATTAAATTA
1 AAATAGAGTTATTAAATAAGAATAGTTTATTAAATTA
1287844 AAATAGAGTTATTAAATAAGAATAGTTTATTAAATTA
1 AAATAGAGTTATTAAATAAGAATAGTTTATTAAATTA
1287881 AAATAGAGTTATTA
1 AAATAGAGTTATTA
1287895 CTTAATTAGA
Statistics
Matches: 50, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 50 1.00
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (37 bp):
AAATAGAGTTATTAAATAAGAATAGTTTATTAAATTA
Found at i:1287857 original size:19 final size:19
Alignment explanation
Indices: 1287807--1287894 Score: 110
Period size: 18 Copynumber: 4.7 Consensus size: 19
1287797 ATTTTAAATG
*
1287807 AAATAGAGTTATTAAATGA
1 AAATAGAGTTATTAAATTA
* *
1287826 GAATAG-TTTATTAAATTA
1 AAATAGAGTTATTAAATTA
1287844 AAATAGAGTTATTAAA-TA
1 AAATAGAGTTATTAAATTA
*
1287862 AGAATAG-TTTATTAAATTA
1 A-AATAGAGTTATTAAATTA
1287881 AAATAGAGTTATTA
1 AAATAGAGTTATTA
1287895 CTTAATTAGA
Statistics
Matches: 58, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
18 31 0.53
19 27 0.47
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (19 bp):
AAATAGAGTTATTAAATTA
Found at i:1288576 original size:26 final size:28
Alignment explanation
Indices: 1288524--1288584 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
1288514 TTATTTTAGT
1288524 ATATTTTGATAAATAAAAAAAATTTATA
1 ATATTTTGATAAATAAAAAAAATTTATA
*
1288552 ATATTTTGGTAAAT-AAAAAAA-TTATA
1 ATATTTTGATAAATAAAAAAAATTTATA
1288578 ATATTTT
1 ATATTTT
1288585 AATTATTTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
26 12 0.38
27 7 0.22
28 13 0.41
ACGTcount: A:0.52, C:0.00, G:0.05, T:0.43
Consensus pattern (28 bp):
ATATTTTGATAAATAAAAAAAATTTATA
Found at i:1293900 original size:262 final size:262
Alignment explanation
Indices: 1293099--1294004 Score: 1405
Period size: 256 Copynumber: 3.5 Consensus size: 262
1293089 CATGTGGTGT
*
1293099 TGTACATTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCTGGTTTTCTTTGGACCGATTTC
1 TGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCTGGTTTTCTTTGGACCGATTTC
* *
1293164 GGTGATGAATTGGAACTCTTTGTTACCTTGAAAATAAATATTATTACATTGACAAATGCTTTAAA
66 GGCGATGAATCGGAACTCTTTGTTACCTTGAAAA-AAATATTATTACATTGACAAATGCTTTAAA
*
1293229 TTGGATATGTAGATTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTGTGATGCAATGGT
130 TTGGATATGTAGATTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTGTGATGCAATGCT
*
1293294 GCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCTGATCTCCATGCTTGTTTCCTAGCAGGTGG
195 GCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCTGATCTCCATGCTTGTTTCCTAGCAGGTGT
1293359 TGG
260 TGG
* * * * *
1293362 TGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCTAATCCGGTTTT-TTTGAACTGATTTT
1 TGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCTGGTTTTCTTTGGACCGATTTC
* * *
1293426 GGCGATGAATCGAAACTCTTTGTTACCTTGAAAAAAGTATTATTACATTGACAAATGCTTTAAAA
66 GGCGATGAATCGGAACTCTTTGTTACCTTGAAAAAAATATTATTACATTGACAAATGCTTTAAAT
* * * * *
1293491 TGGATATGTACATTCAGCTGTTAGAATGCATATATTTATTTTTATAAGTGTGTG-TG--ATGC--
131 TGGATATGTAGATTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTGTGATGCAATGCTG
* * * *
1293551 ATATGTCCTTAGTGTTGATTGAATCATTAGCCCCTGATCTCCATGCTTGTTTACTAGCAGATGTT
196 CTATGTTCTTAGTGTTGATTGAATCATTAGCCCCTGATCTCCATGCTTGTTTCCTAGCAGGTGTT
*
1293616 GT
261 GG
* *
1293618 TGTACTTTAGTCTCTTAAAGTGCTATCACTATTCCCCC-AATCTGGTTTTCTTCGGACCGATTTC
1 TGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCTGGTTTTCTTTGGACCGATTTC
* *
1293682 GGGGATGAATCAGAACTCTTTGTTACCTTGAAAATAAATATTATTACATTGACAAATGCTTTAAA
66 GGCGATGAATCGGAACTCTTTGTTACCTTGAAAA-AAATATTATTACATTGACAAATGCTTTAAA
*
1293747 TTGGATATGTAGATTCAGCTGTGAGAATGCATACGTTTATTTATATATGTGTGTGATGCAATGCT
130 TTGGATATGTAGATTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTGTGATGCAATGCT
*
1293812 GCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCCGATCTCCATGCTTGTTTCCTAGCAGGTGT
195 GCTATGTTCTTAGTGTTGATTGAATCATTAGCCCCTGATCTCCATGCTTGTTTCCTAGCAGGTGT
1293877 TGG
260 TGG
* * ** * *
1293880 TGTACTTTAGTTTCTTAAAGTGCTATCCCCATTCGTCCTAATCCT-GTTTCCTTTGGACCGATTT
1 TGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAAT-CTGGTTTTCTTTGGACCGATTT
1293944 CGGCGATGAATCGGAACTCTTTGTTACCTTGAAAAAGAATATTATTACATTGACAAATGCT
65 CGGCGATGAATCGGAACTCTTTGTTACCTTGAAAAA-AATATTATTACATTGACAAATGCT
1294005 ATCCCTATTC
Statistics
Matches: 578, Mismatches: 55, Indels: 20
0.89 0.08 0.03
Matches are distributed among these distances:
255 10 0.02
256 139 0.24
257 77 0.13
258 5 0.01
260 6 0.01
261 78 0.13
262 137 0.24
263 124 0.21
264 2 0.00
ACGTcount: A:0.25, C:0.17, G:0.19, T:0.39
Consensus pattern (262 bp):
TGTACTTTAGTCTCTTAAAGTGCTATCCCTATTCCCCCGAATCTGGTTTTCTTTGGACCGATTTC
GGCGATGAATCGGAACTCTTTGTTACCTTGAAAAAAATATTATTACATTGACAAATGCTTTAAAT
TGGATATGTAGATTCAGCTGTGAGAATGCATACATTTATTTATATATGTGTGTGATGCAATGCTG
CTATGTTCTTAGTGTTGATTGAATCATTAGCCCCTGATCTCCATGCTTGTTTCCTAGCAGGTGTT
GG
Found at i:1294074 original size:100 final size:100
Alignment explanation
Indices: 1293900--1294103 Score: 320
Period size: 100 Copynumber: 2.0 Consensus size: 100
1293890 TTTCTTAAAG
** * *
1293900 TGCTATCCCCATTCGTCCTAATCCTGTTTCCTTTGGACCGATTTCGGCGATGAATCGGAACTCTT
1 TGCTATCCCCATTCCCCCTAATCCGGTTTCCTTTGGACCGATTTCGGCGATGAATCGAAACTCTT
1293965 TGTTACCTTGAAAAAGAATATTATTACATTGACAAA
66 TGTTACCTTGAAAAA-AATATTATTACATTGACAAA
* * *
1294001 TGCTATCCCTATTCCCCCTAATCCGGTTT-TTTTGGACCGATTTTGGCGATGAATCGAAACTCTT
1 TGCTATCCCCATTCCCCCTAATCCGGTTTCCTTTGGACCGATTTCGGCGATGAATCGAAACTCTT
*
1294065 TGTTACCTTGAAAAAAGTATTATTACATTGACAAA
66 TGTTACCTTGAAAAAAATATTATTACATTGACAAA
1294100 TGCT
1 TGCT
1294104 TTAAAATGGA
Statistics
Matches: 95, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
99 23 0.24
100 47 0.49
101 25 0.26
ACGTcount: A:0.26, C:0.22, G:0.16, T:0.36
Consensus pattern (100 bp):
TGCTATCCCCATTCCCCCTAATCCGGTTTCCTTTGGACCGATTTCGGCGATGAATCGAAACTCTT
TGTTACCTTGAAAAAAATATTATTACATTGACAAA
Found at i:1294823 original size:883 final size:879
Alignment explanation
Indices: 1293119--1294887 Score: 2958
Period size: 883 Copynumber: 2.0 Consensus size: 879
1293109 TCTCTTAAAG
* * * *
1293119 TGCTATCCCTATTCCCCCGAATCTGGTTTTCTTTGGACCGATTTCGGTGATGAATTGGAACTCTT
1 TGCTATCCCTATTCCCCCGAATCCGGTTTTCTTTGGACCGATTTCGGCGATGAATCGAAACTCTT
* *
1293184 TGTTACCTTGAAAATAAATATTATTACATTGACAAATGCTTTAAATTGGATATGTAGATTCAGCT
66 TGTTACCTTGAAAATAAATATTATTACATTGACAAATGCTTTAAAATGGATATGTACATTCAGCT
* *
1293249 GTGAGAATGCATACATTTATTTATATATGTGTGTGATGCAATGGTGCTATGTTCTTAGTGTTGAT
131 GTGAGAATGCATACATTTATTTATATAAGTGTGTGATG-AA--GTGCTATGTCCTTAGTGTTGAT
* *
1293314 TGAATCATTAGCCCCTGATCTCCATGCTTGTTTCCTAGCAGGTGGTGGTGTACTTTAGTCTCTTA
193 TGAATCATTAGCCCCTGATCTCCATGCTTGTTTACTAGCAGATGGTGGTGTACTTTAGTCTCTTA
*
1293379 AAGTGCTATCCCTATTCCCCCTAATCCGGTTTTTTTGAACTGATTTTGGCGATGAATCGAAACTC
258 AAGTGCTATCCCTATTCCCCCTAATCCGGTTTTTTTGAACCGATTTTGGCGATGAATCGAAACTC
1293444 TTTGTTACCTTGAAAAAAGTATTATTACATTGACAAATGCTTTAAAATGGATATGTACATTCAGC
323 TTTGTTACCTTGAAAAAAGTATTATTACATTGACAAATGCTTTAAAATGGATATGTACATTCAGC
* *
1293509 TGTTAGAATGCATATATTTATTTTTATAAGTGTGTGTGATGCATATGTCCTTAGTGTTGATTGAA
388 TGTGAGAATGCATACATTTATTTTTATAAGTGTGTGTGATGCATATGTCCTTAGTGTTGATTGAA
* * *
1293574 TCATTAGCCCCTGATCTCCATGCTTGTTTACTAGCAGATGTTGTTGTACTTTAGTCTCTTAAAGT
453 TCATTAGCCCCCGATCTCCAGGCTTATTTACTAGCAGATGTTGTTGTACTTTAGTCTCTTAAAGT
* *
1293639 GCTATCACTATTCCCCCAATCTGGTTTTCTTCGGACCGATTTCGGGGATGAATCAGAACTCTTTG
518 GCTATCACTATTCCCCCAATCCGGTTTTCTTCGGACCGATTTCGGGGATAAATCAGAACTCTTTG
*
1293704 TTACCTTGAAAATAAATATTATTACATTGACAAATGCTTTAAATTGGATATGTAGATTCAGCTGT
583 TTACCTTGAAAAAAAATATTATTACATTGACAAATGCTTTAAATTGGATATGTAGATTCAGCTGT
1293769 GAGAATGCATACGTTTATTTATATATGTGTGTGATGCAATGCTGCTATGTTCTTAGTGTTGATTG
648 GAGAATGCATACGTTTATTTATATATGTGTGTGATGCAATGCTGCTATGTTCTTAGTGTTGATTG
1293834 AATCATTAGCCCCCGATCTCCATGCTTGTTTCCTAGCAGGTGTTGGTGTACTTTAGTTTCTTAAA
713 AATCATTAGCCCCCGATCTCCATGCTTGTTTCCTAGCAGGTGTTGGTGTACTTTAGTTTCTTAAA
*
1293899 GTGCTATCCCCATTCGTCCTAATCCTGTTTCCTTTGGACCGATTTCGGCGATGAATCGGAACTCT
778 GTGCTATCCCCATTCGTCCTAATCCTGTTTCCTTTGGACCGATTTCAGCGATGAATCGGAACTCT
1293964 TTGTTACCTTGAAAAAGAATATTATTACATTGACAAA
843 TTGTTACCTTGAAAAAGAATATTATTACATTGACAAA
* *
1294001 TGCTATCCCTATTCCCCCTAATCCGGTTTT-TTTGGACCGATTTTGGCGATGAATCGAAACTCTT
1 TGCTATCCCTATTCCCCCGAATCCGGTTTTCTTTGGACCGATTTCGGCGATGAATCGAAACTCTT
*
1294065 TGTTACCTTGAAAA-AAGTATTATTACATTGACAAATGCTTTAAAATGGATATGTACATTCAGCT
66 TGTTACCTTGAAAATAAATATTATTACATTGACAAATGCTTTAAAATGGATATGTACATTCAGCT
* * *
1294129 GTTAGAATGCATATATTTATTTTTATAAGTGTGTG-TG-A-TGCATATGTCCTTAGTGTTGATTG
131 GTGAGAATGCATACATTTATTTATATAAGTGTGTGATGAAGTGC-TATGTCCTTAGTGTTGATTG
* *
1294191 AATCATTAGCCCCTGATCTCCATGCTTGTTTACTAGCAGATGTTGTTGTACTTTAGTCTCTTAAA
195 AATCATTAGCCCCTGATCTCCATGCTTGTTTACTAGCAGATGGTGGTGTACTTTAGTCTCTTAAA
*
1294256 GTGCTATCCCTATTCCCCCTAATCCGGTTTTTTTGGACCGATTTTGGCGATGAATCGAAACTCTT
260 GTGCTATCCCTATTCCCCCTAATCCGGTTTTTTTGAACCGATTTTGGCGATGAATCGAAACTCTT
* *
1294321 TGTTACCTTGAAAAAAGTATTATTACATTGACAAATGCTTTAAATTGGATATGTAGATTCAGCTG
325 TGTTACCTTGAAAAAAGTATTATTACATTGACAAATGCTTTAAAATGGATATGTACATTCAGCTG
* * *
1294386 TGAGAATGCATACATTTATTTATATATATGTGTGTGATGCAATGCTGCTATGTTCTTAGTGTTGA
390 TGAGAATGCATACATTTATTT-T-TATAAGTGTGTG-TG--ATGC--ATATGTCCTTAGTGTTGA
* *
1294451 TTGAATCATTAGCCCCCGATCTCCAGGCTTATTTCCTAGCAGGTGTTGTTGTACTTTAGTCTCTT
448 TTGAATCATTAGCCCCCGATCTCCAGGCTTATTTACTAGCAGATGTTGTTGTACTTTAGTCTCTT
* * * * *
1294516 AAAGTGCTATCCCTATTCCCCTGAATCCGGTTTTCTTTGGACTGATTTCGGCGG-TAAATCGGAA
513 AAAGTGCTATCACTATTCCCC-CAATCCGGTTTTCTTCGGACCGATTTCGG-GGATAAATCAGAA
*
1294580 CTCTTTGTTACCTTGAAAAAAAATATTATTACATTGACAAATGTTTTAAATTGGATATGTAGATT
576 CTCTTTGTTACCTTGAAAAAAAATATTATTACATTGACAAATGCTTTAAATTGGATATGTAGATT
1294645 CAGCTGTGAGAATGCATACGTTTATTTATATATGTGTGTGATGCAATGCTGCTATGTTCTTAGTG
641 CAGCTGTGAGAATGCATACGTTTATTTATATATGTGTGTGATGCAATGCTGCTATGTTCTTAGTG
*
1294710 TTGATTGAATCATTAGCCCCCGATCTCCATGCTTGTTTCCTAGCAGGTGTTGTTGTACTTTAGTT
706 TTGATTGAATCATTAGCCCCCGATCTCCATGCTTGTTTCCTAGCAGGTGTTGGTGTACTTTAGTT
* *
1294775 TCTTAAAGTGCTATCCCTATTC-TCCCTAATCCTGTTTTCTTTGGACCGATTTCAGCGATGAATC
771 TCTTAAAGTGCTATCCCCATTCGT-CCTAATCCTGTTTCCTTTGGACCGATTTCAGCGATGAATC
1294839 GGAACTCTTTGTTACCTTGAAAAAGAATATTATTACATTGACAAA
835 GGAACTCTTTGTTACCTTGAAAAAGAATATTATTACATTGACAAA
1294884 TGCT
1 TGCT
1294888 TTACATTGGA
Statistics
Matches: 831, Mismatches: 45, Indels: 21
0.93 0.05 0.02
Matches are distributed among these distances:
874 3 0.00
875 225 0.27
876 1 0.00
877 12 0.01
878 2 0.00
879 2 0.00
880 82 0.10
881 44 0.05
882 125 0.15
883 333 0.40
884 2 0.00
ACGTcount: A:0.25, C:0.17, G:0.18, T:0.39
Consensus pattern (879 bp):
TGCTATCCCTATTCCCCCGAATCCGGTTTTCTTTGGACCGATTTCGGCGATGAATCGAAACTCTT
TGTTACCTTGAAAATAAATATTATTACATTGACAAATGCTTTAAAATGGATATGTACATTCAGCT
GTGAGAATGCATACATTTATTTATATAAGTGTGTGATGAAGTGCTATGTCCTTAGTGTTGATTGA
ATCATTAGCCCCTGATCTCCATGCTTGTTTACTAGCAGATGGTGGTGTACTTTAGTCTCTTAAAG
TGCTATCCCTATTCCCCCTAATCCGGTTTTTTTGAACCGATTTTGGCGATGAATCGAAACTCTTT
GTTACCTTGAAAAAAGTATTATTACATTGACAAATGCTTTAAAATGGATATGTACATTCAGCTGT
GAGAATGCATACATTTATTTTTATAAGTGTGTGTGATGCATATGTCCTTAGTGTTGATTGAATCA
TTAGCCCCCGATCTCCAGGCTTATTTACTAGCAGATGTTGTTGTACTTTAGTCTCTTAAAGTGCT
ATCACTATTCCCCCAATCCGGTTTTCTTCGGACCGATTTCGGGGATAAATCAGAACTCTTTGTTA
CCTTGAAAAAAAATATTATTACATTGACAAATGCTTTAAATTGGATATGTAGATTCAGCTGTGAG
AATGCATACGTTTATTTATATATGTGTGTGATGCAATGCTGCTATGTTCTTAGTGTTGATTGAAT
CATTAGCCCCCGATCTCCATGCTTGTTTCCTAGCAGGTGTTGGTGTACTTTAGTTTCTTAAAGTG
CTATCCCCATTCGTCCTAATCCTGTTTCCTTTGGACCGATTTCAGCGATGAATCGGAACTCTTTG
TTACCTTGAAAAAGAATATTATTACATTGACAAA
Found at i:1294988 original size:528 final size:520
Alignment explanation
Indices: 1294001--1295164 Score: 1841
Period size: 528 Copynumber: 2.2 Consensus size: 520
1293991 CATTGACAAA
* *
1294001 TGCTATCCCTATTCCCCCT-AATCCGGTTTT-TTTGGACCGATTTTGGCGATGAATCGAAACTCT
1 TGCTATCCCTATT-CCCCTGAATCCGGTTTTCTTTGGACCGATTTCGGCGATGAATCGGAACTCT
* *
1294064 TTGTTACCTTGAAAAAAGTATTATTACATTGACAAATGCTTTAAAATGGATATGTACATTCAGCT
65 TTGTTACCTTGAAAAAAATATTATTACATTGACAAATGCTTTAAATTGGATATGTACATTCAGCT
* * *
1294129 GTTAGAATGCATATATTTATTTTTATAAGTGTGTGTGATGCATATGTCCTTAGTGTTGATTGAAT
130 GTGAGAATGCATACATTTATTTATATAAGTGTGTGTGATGCATATGTCCTTAGTGTTGATTGAAT
*
1294194 CATTAGCCCCTGATCTCCATGCTTGTTTACTAGCAGATGTTGTTGTACTTTAGTCTCTTAAAGTG
195 CATTAGCCCCCGATCTCCATGCTTGTTTACTAGCAGATGTTGTTGTACTTTAGTCTCTTAAAGTG
**
1294259 CTATCCCTATTCCCCCTAATCCGGTTTTTTTGGACCGATTTTGGCGATGAATCGAAACTCTTTGT
260 CTATCCCTATTCCCCCTAATCCGGTTTTTTTGGACCGATTTCAGCGATGAATCGAAACTCTTTGT
* *
1294324 TACCTTGAAAAAAGTATTATTACATTGACAAATGCTTTAAATTGGATATGTAGATTCAGCTGTGA
325 TACCTTGAAAAAAATATTATTACATTGACAAATGCTTTAAATTGGATATATAGATTCAGCTGTGA
*
1294389 GAATGCATACATTTATTTATATATATGTGTGTGATGCAATGCTGCTATGTTCTTAGTGTTGATTG
390 GAATGCATACATTTATTTATATATATGTGTGTGATGCAATGCTGCTATGTTCTTAGTGTTGACTG
* *
1294454 AATCATTAGCCCCCGATCTCCAGGCTTATTTCCTAGCAGGTGTTGTTGTACTTTAGTCTCTTAAA
455 AATCATTAGCCCCCCATCTCCAGGCTTATTTCCTAGCAGGTGGTGTTGTACTTTAGTCTCTTAAA
1294519 G
520 G
* * *
1294520 TGCTATCCCTATTCCCCTGAATCCGGTTTTCTTTGGACTGATTTCGGCGGTAAATCGGAACTCTT
1 TGCTATCCCTATTCCCCTGAATCCGGTTTTCTTTGGACCGATTTCGGCGATGAATCGGAACTCTT
* *
1294585 TGTTACCTTGAAAAAAAATATTATTACATTGACAAATGTTTTAAATTGGATATGTAGATTCAGCT
66 TGTTACCTTG-AAAAAAATATTATTACATTGACAAATGCTTTAAATTGGATATGTACATTCAGCT
* * * *
1294650 GTGAGAATGCATACGTTTATTTATATATGTGTGTGATGCAATGCTGCTATGTTCTTAGTGTTGAT
130 GTGAGAATGCATACATTTATTTATATAAGTGTGTG-TG--ATGC--ATATGTCCTTAGTGTTGAT
* * *
1294715 TGAATCATTAGCCCCCGATCTCCATGCTTGTTTCCTAGCAGGTGTTGTTGTACTTTAGTTTCTTA
190 TGAATCATTAGCCCCCGATCTCCATGCTTGTTTACTAGCAGATGTTGTTGTACTTTAGTCTCTTA
* * *
1294780 AAGTGCTATCCCTATTCTCCCTAATCCTGTTTTCTTTGGACCGATTTCAGCGATGAATCGGAACT
255 AAGTGCTATCCCTATTCCCCCTAATCCGGTTTT-TTTGGACCGATTTCAGCGATGAATCGAAACT
*
1294845 CTTTGTTACCTTGAAAAAGAATATTATTACATTGACAAATGCTTTACATTGGATATATACG-TTC
319 CTTTGTTACCTTGAAAAA-AATATTATTACATTGACAAATGCTTTAAATTGGATATATA-GATTC
*
1294909 AGCTGTGAGAATGCATACATTTATTTATATATATGTGTGTGATGCAATGTTGCTATGTTCTTAGT
382 AGCTGTGAGAATGCATACATTTATTTATATATATGTGTGTGATGCAATGCTGCTATGTTCTTAGT
* *
1294974 GTTGACTGAATCATTAGCCCCCCATCTCCATGCTTGTTTCCTAGCAGGTGGTGTTGTACTTTAGT
447 GTTGACTGAATCATTAGCCCCCCATCTCCAGGCTTATTTCCTAGCAGGTGGTGTTGTACTTTAGT
1295039 CTCTTAAAG
512 CTCTTAAAG
* * * ** *
1295048 TGCTATCCCTATTCCCCCGAATCCGGTTTTCTTTGGACCGATTTCGACAATGAATTAGAATTCTT
1 TGCTATCCCTATTCCCCTGAATCCGGTTTTCTTTGGACCGATTTCGGCGATGAATCGGAACTCTT
*
1295113 TGTTACCTT-AAAAAAATATTATTACATTGAGAAATGCTTTAAATTGGATATG
66 TGTTACCTTGAAAAAAATATTATTACATTGACAAATGCTTTAAATTGGATATG
1295165 CTTGTTTTTT
Statistics
Matches: 589, Mismatches: 45, Indels: 15
0.91 0.07 0.02
Matches are distributed among these distances:
518 5 0.01
519 24 0.04
520 39 0.07
521 80 0.14
522 2 0.00
524 4 0.01
526 150 0.25
527 46 0.08
528 238 0.40
529 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (520 bp):
TGCTATCCCTATTCCCCTGAATCCGGTTTTCTTTGGACCGATTTCGGCGATGAATCGGAACTCTT
TGTTACCTTGAAAAAAATATTATTACATTGACAAATGCTTTAAATTGGATATGTACATTCAGCTG
TGAGAATGCATACATTTATTTATATAAGTGTGTGTGATGCATATGTCCTTAGTGTTGATTGAATC
ATTAGCCCCCGATCTCCATGCTTGTTTACTAGCAGATGTTGTTGTACTTTAGTCTCTTAAAGTGC
TATCCCTATTCCCCCTAATCCGGTTTTTTTGGACCGATTTCAGCGATGAATCGAAACTCTTTGTT
ACCTTGAAAAAAATATTATTACATTGACAAATGCTTTAAATTGGATATATAGATTCAGCTGTGAG
AATGCATACATTTATTTATATATATGTGTGTGATGCAATGCTGCTATGTTCTTAGTGTTGACTGA
ATCATTAGCCCCCCATCTCCAGGCTTATTTCCTAGCAGGTGGTGTTGTACTTTAGTCTCTTAAAG
Found at i:1295059 original size:265 final size:263
Alignment explanation
Indices: 1294001--1295164 Score: 1830
Period size: 263 Copynumber: 4.4 Consensus size: 263
1293991 CATTGACAAA
* *
1294001 TGCTATCCCTATTCCCCCTAATCCGGTTTT-TTTGGACCGATTTTGGCGATGAATCGAAACTCTT
1 TGCTATCCCTATTCCCCCTAATCCGGTTTTCTTTGGACCGATTTCGGCGATGAATCGGAACTCTT
* * *
1294065 TGTTACCTTGAAAAAAGTATTATTACATTGACAAATGCTTTAAAATGGATATGTACATTCAGCTG
66 TGTTACCTTGAAAAAAATATTATTACATTGACAAATGCTTTAAATTGGATATGTAGATTCAGCTG
* * * * *
1294130 TTAGAATGCATATATTTATTTT-TATAAGTGTGTG-TG--ATGC--ATATGTCCTTAGTGTTGAT
131 TGAGAATGCATACATTTATTTTATATATGTGTGTGATGCAATGCTGCTATGTTCTTAGTGTTGAT
* * *
1294189 TGAATCATTAGCCCCTGATCTCCATGCTTGTTTACTAGCAGATGTTGTTGTACTTTAGTCTCTTA
196 TGAATCATTAGCCCCCGATCTCCATGCTTGTTTCCTAGCAGGTGTTGTTGTACTTTAGTCTCTTA
1294254 AAG
261 AAG
* *
1294257 TGCTATCCCTATTCCCCCTAATCCGGTTTT-TTTGGACCGATTTTGGCGATGAATCGAAACTCTT
1 TGCTATCCCTATTCCCCCTAATCCGGTTTTCTTTGGACCGATTTCGGCGATGAATCGGAACTCTT
*
1294321 TGTTACCTTGAAAAAAGTATTATTACATTGACAAATGCTTTAAATTGGATATGTAGATTCAGCTG
66 TGTTACCTTGAAAAAAATATTATTACATTGACAAATGCTTTAAATTGGATATGTAGATTCAGCTG
1294386 TGAGAATGCATACATTTATTTATATATATGTGTGTGATGCAATGCTGCTATGTTCTTAGTGTTGA
131 TGAGAATGCATACATTTATTT-TATATATGTGTGTGATGCAATGCTGCTATGTTCTTAGTGTTGA
* *
1294451 TTGAATCATTAGCCCCCGATCTCCAGGCTTATTTCCTAGCAGGTGTTGTTGTACTTTAGTCTCTT
195 TTGAATCATTAGCCCCCGATCTCCATGCTTGTTTCCTAGCAGGTGTTGTTGTACTTTAGTCTCTT
1294516 AAAG
260 AAAG
* * *
1294520 TGCTATCCCTATT-CCCCTGAATCCGGTTTTCTTTGGACTGATTTCGGCGGTAAATCGGAACTCT
1 TGCTATCCCTATTCCCCCT-AATCCGGTTTTCTTTGGACCGATTTCGGCGATGAATCGGAACTCT
*
1294584 TTGTTACCTTGAAAAAAAATATTATTACATTGACAAATGTTTTAAATTGGATATGTAGATTCAGC
65 TTGTTACCTTG-AAAAAAATATTATTACATTGACAAATGCTTTAAATTGGATATGTAGATTCAGC
*
1294649 TGTGAGAATGCATACGTTTA-TTTATATATGTGTGTGATGCAATGCTGCTATGTTCTTAGTGTTG
129 TGTGAGAATGCATACATTTATTTTATATATGTGTGTGATGCAATGCTGCTATGTTCTTAGTGTTG
*
1294713 ATTGAATCATTAGCCCCCGATCTCCATGCTTGTTTCCTAGCAGGTGTTGTTGTACTTTAGTTTCT
194 ATTGAATCATTAGCCCCCGATCTCCATGCTTGTTTCCTAGCAGGTGTTGTTGTACTTTAGTCTCT
1294778 TAAAG
259 TAAAG
* * *
1294783 TGCTATCCCTATTCTCCCTAATCCTGTTTTCTTTGGACCGATTTCAGCGATGAATCGGAACTCTT
1 TGCTATCCCTATTCCCCCTAATCCGGTTTTCTTTGGACCGATTTCGGCGATGAATCGGAACTCTT
* *
1294848 TGTTACCTTGAAAAAGAATATTATTACATTGACAAATGCTTTACATTGGATATATACG-TTCAGC
66 TGTTACCTTGAAAAA-AATATTATTACATTGACAAATGCTTTAAATTGGATATGTA-GATTCAGC
*
1294912 TGTGAGAATGCATACATTTATTTATATATATGTGTGTGATGCAATGTTGCTATGTTCTTAGTGTT
129 TGTGAGAATGCATACATTTATTT-TATATATGTGTGTGATGCAATGCTGCTATGTTCTTAGTGTT
* * *
1294977 GACTGAATCATTAGCCCCCCATCTCCATGCTTGTTTCCTAGCAGGTGGTGTTGTACTTTAGTCTC
193 GATTGAATCATTAGCCCCCGATCTCCATGCTTGTTTCCTAGCAGGTGTTGTTGTACTTTAGTCTC
1295042 TTAAAG
258 TTAAAG
* * * ** *
1295048 TGCTATCCCTATTCCCCCGAATCCGGTTTTCTTTGGACCGATTTCGACAATGAATTAGAATTCTT
1 TGCTATCCCTATTCCCCCTAATCCGGTTTTCTTTGGACCGATTTCGGCGATGAATCGGAACTCTT
*
1295113 TGTTACCTT-AAAAAAATATTATTACATTGAGAAATGCTTTAAATTGGATATG
66 TGTTACCTTGAAAAAAATATTATTACATTGACAAATGCTTTAAATTGGATATG
1295165 CTTGTTTTTT
Statistics
Matches: 843, Mismatches: 50, Indels: 23
0.92 0.05 0.03
Matches are distributed among these distances:
256 146 0.17
257 1 0.00
258 11 0.01
259 2 0.00
261 4 0.00
262 10 0.01
263 374 0.44
264 53 0.06
265 242 0.29
ACGTcount: A:0.25, C:0.18, G:0.18, T:0.39
Consensus pattern (263 bp):
TGCTATCCCTATTCCCCCTAATCCGGTTTTCTTTGGACCGATTTCGGCGATGAATCGGAACTCTT
TGTTACCTTGAAAAAAATATTATTACATTGACAAATGCTTTAAATTGGATATGTAGATTCAGCTG
TGAGAATGCATACATTTATTTTATATATGTGTGTGATGCAATGCTGCTATGTTCTTAGTGTTGAT
TGAATCATTAGCCCCCGATCTCCATGCTTGTTTCCTAGCAGGTGTTGTTGTACTTTAGTCTCTTA
AAG
Found at i:1299387 original size:21 final size:21
Alignment explanation
Indices: 1299361--1299401 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
1299351 AGACGAGCAA
* *
1299361 TACTCCACAGCAGGTGGAGTG
1 TACTCCAAAACAGGTGGAGTG
1299382 TACTCCAAAACAGGTGGAGT
1 TACTCCAAAACAGGTGGAGT
1299402 TTGAGCAGAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (21 bp):
TACTCCAAAACAGGTGGAGTG
Found at i:1306089 original size:19 final size:20
Alignment explanation
Indices: 1306047--1306089 Score: 63
Period size: 19 Copynumber: 2.2 Consensus size: 20
1306037 ACATACTTTC
*
1306047 TATTCACATTTTCATATTCA
1 TATTCACATTTTCAAATTCA
1306067 -ATTCACATTTTCAAATT-A
1 TATTCACATTTTCAAATTCA
1306085 TATTC
1 TATTC
1306090 CACAATCACG
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
18 1 0.05
19 20 0.95
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.49
Consensus pattern (20 bp):
TATTCACATTTTCAAATTCA
Found at i:1306281 original size:18 final size:18
Alignment explanation
Indices: 1306260--1306294 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
1306250 GATCATTAAT
* *
1306260 CAGTAACGGTAGCAGTAG
1 CAGTAACAGTAACAGTAG
1306278 CAGTAACAGTAACAGTA
1 CAGTAACAGTAACAGTA
1306295 TTCAACACAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.40, C:0.17, G:0.26, T:0.17
Consensus pattern (18 bp):
CAGTAACAGTAACAGTAG
Found at i:1306342 original size:45 final size:45
Alignment explanation
Indices: 1306278--1306513 Score: 346
Period size: 45 Copynumber: 5.2 Consensus size: 45
1306268 GTAGCAGTAG
* * * *
1306278 CAGTAACAGTAACAGTATTCAACACACAAAGTGCTGATTCTGTAA
1 CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCGGTAA
** * *
1306323 CAGTAATGGTAATAGTATTCGACACACAAAGTGCCGAATTGGTAA
1 CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCGGTAA
1306368 CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCGGTAA
1 CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCGGTAA
* **
1306413 TAGTAACAGTAACAGTATTCGACACACAAAGTGTTGAATCGGTAA
1 CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCGGTAA
* **
1306458 CAGTAACAGTAACAGTATTTGACACACAAAGTATCGAATCGGTAA
1 CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCGGTAA
1306503 CAGTAACAGTA
1 CAGTAACAGTA
1306514 GTCAGCACAT
Statistics
Matches: 172, Mismatches: 19, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
45 172 1.00
ACGTcount: A:0.40, C:0.18, G:0.19, T:0.22
Consensus pattern (45 bp):
CAGTAACAGTAACAGTATTCGACACACAAAGTGCCGAATCGGTAA
Found at i:1309588 original size:73 final size:73
Alignment explanation
Indices: 1309492--1309649 Score: 221
Period size: 73 Copynumber: 2.2 Consensus size: 73
1309482 TTTTTTTATC
* * * *
1309492 TATTTATTTATTTGTTATTCTTTTACTTTTAAAACATTTAAATTTGATATTATTTAAATTTGTTT
1 TATTTATTTATTTATTATTCTTTTACTTTTAAAACACTTAAATTTAATATCATTTAAATTTGTTT
1309557 TATCTATT
66 TATCTATT
* ** *
1309565 TATTTATTTATTTATTATTCTTTTACTTTTTAAATGCTTAAATTTAATATCATTTATATTTGTTT
1 TATTTATTTATTTATTATTCTTTTACTTTTAAAACACTTAAATTTAATATCATTTAAATTTGTTT
*
1309630 TATTTATT
66 TATCTATT
1309638 TA-TTATTT-TTTA
1 TATTTATTTATTTA
1309650 CTTTTTAAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 2
0.87 0.10 0.02
Matches are distributed among these distances:
71 4 0.05
72 6 0.08
73 66 0.87
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (73 bp):
TATTTATTTATTTATTATTCTTTTACTTTTAAAACACTTAAATTTAATATCATTTAAATTTGTTT
TATCTATT
Found at i:1309667 original size:61 final size:61
Alignment explanation
Indices: 1309567--1309686 Score: 179
Period size: 61 Copynumber: 2.0 Consensus size: 61
1309557 TATCTATTTA
* *
1309567 TTTATTTATTTATTATTCTTTTACTTTTTAAATGCTTAAATTTAATATCATTTATATTTGT
1 TTTATTTATTTATTATTCTTTTACTTTTTAAATACTTAAATTTAATATCACTTATATTTGT
* * *
1309628 TTTATTTATTTATTATT-TTTTACTTTTTAAAATATTTAAATTTGATATTACTTATATTT
1 TTTATTTATTTATTATTCTTTTACTTTTT-AAATACTTAAATTTAATATCACTTATATTT
1309687 CCTTTTCATT
Statistics
Matches: 53, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
60 11 0.21
61 42 0.79
ACGTcount: A:0.29, C:0.05, G:0.03, T:0.63
Consensus pattern (61 bp):
TTTATTTATTTATTATTCTTTTACTTTTTAAATACTTAAATTTAATATCACTTATATTTGT
Found at i:1309875 original size:13 final size:12
Alignment explanation
Indices: 1309844--1309892 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
1309834 GAGTATGACA
1309844 TTTTTATTTTATC
1 TTTTTA-TTTATC
*
1309857 TTTTTATTTATT
1 TTTTTATTTATC
*
1309869 TTCTTTATTAATC
1 TT-TTTATTTATC
*
1309882 TATTTATTTAT
1 TTTTTATTTAT
1309893 TTATGTCATT
Statistics
Matches: 30, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
12 15 0.50
13 15 0.50
ACGTcount: A:0.20, C:0.06, G:0.00, T:0.73
Consensus pattern (12 bp):
TTTTTATTTATC
Found at i:1310286 original size:32 final size:32
Alignment explanation
Indices: 1310245--1310314 Score: 131
Period size: 32 Copynumber: 2.2 Consensus size: 32
1310235 CATTGTGTCC
1310245 TAACTTACGGGACATGATCCTTCATTCTCGAT
1 TAACTTACGGGACATGATCCTTCATTCTCGAT
*
1310277 TAACTTACGGGACATGATCCTTCATTCTTGAT
1 TAACTTACGGGACATGATCCTTCATTCTCGAT
1310309 TAACTT
1 TAACTT
1310315 GAAATAAACC
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 37 1.00
ACGTcount: A:0.26, C:0.23, G:0.14, T:0.37
Consensus pattern (32 bp):
TAACTTACGGGACATGATCCTTCATTCTCGAT
Found at i:1315712 original size:23 final size:23
Alignment explanation
Indices: 1315686--1315783 Score: 144
Period size: 23 Copynumber: 4.3 Consensus size: 23
1315676 ATAAGTGCCA
1315686 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
1315709 CACTGATATGTAGCC-AAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
1315731 CATTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * *
1315754 CGCTGAAATGTAGTCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
1315777 CACTGAT
1 CACTGAT
1315784 CAATAACACT
Statistics
Matches: 67, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
22 20 0.30
23 47 0.70
ACGTcount: A:0.32, C:0.24, G:0.21, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:1316988 original size:103 final size:104
Alignment explanation
Indices: 1316755--1317020 Score: 435
Period size: 103 Copynumber: 2.6 Consensus size: 104
1316745 GTTGTACATA
** *
1316755 AAGGGGTTGCTGTGTGCTGATTCCCCGATTCATTGGTGGTGCTATGTGCGATATCCACCGTATCT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
* *
1316820 TTGAAATGTAAAAGGGGGTTGCTATGTGCTGATTCCCCC
66 CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
* *
1316859 GAGGGGTTGCTAAGTGCTGATTCCCCGGTTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
1316924 CTGAAAT-AAAAAGGGGGTTGCTATGTGCTGATTCCCCC
66 CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
* * *
1316962 AAGGGGTTGCTAAGTGCTGATTCCCCGATTAAGTGGTGGTGCTAAGTGCGAGATCCACC
1 AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACC
1317021 AATAACGGTT
Statistics
Matches: 150, Mismatches: 12, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
103 84 0.56
104 66 0.44
ACGTcount: A:0.20, C:0.21, G:0.30, T:0.30
Consensus pattern (104 bp):
AAGGGGTTGCTAAGTGCTGATTCCCCGATTCATTGGTGGTGCTAAGTGCGATATCCACCGTATCT
CTGAAATGAAAAAGGGGGTTGCTATGTGCTGATTCCCCC
Found at i:1325887 original size:43 final size:44
Alignment explanation
Indices: 1325781--1326030 Score: 262
Period size: 43 Copynumber: 5.8 Consensus size: 44
1325771 GCGTCGCTAA
*
1325781 CTTTAGCGGCGTTTTTCCAACAAACGCCGCTAAAGACCATA-AC
1 CTTTAGCGGCGCTTTTCCAACAAACGCCGCTAAAGACCATAGAC
* *
1325824 CTTTTAGCGGCGCTTTTACAAAAAACGCCGCTAAAGACCA-AGAC
1 C-TTTAGCGGCGCTTTTCCAACAAACGCCGCTAAAGACCATAGAC
* * *
1325868 CTTTAGCGGCGCTTTTACAAAAAACGCTGCTAAAGACCA-AGAC
1 CTTTAGCGGCGCTTTTCCAACAAACGCCGCTAAAGACCATAGAC
* * * * * * * *
1325911 TTTTAGTGTCGCTTTTCCCACAAACGCCGCTAAATA-TATTGAG
1 CTTTAGCGGCGCTTTTCCAACAAACGCCGCTAAAGACCATAGAC
* *
1325954 CTTTAGCGGCGCTTTTTCCCACAAACGCCGCTATAGA--ATAGAC
1 CTTTAGCGGCGC-TTTTCCAACAAACGCCGCTAAAGACCATAGAC
* *
1325997 CTTTAGCGGTGCTTTTCTC-ACAAACGCCACTAAA
1 CTTTAGCGGCGCTTTTC-CAACAAACGCCGCTAAA
1326031 AATATATCTT
Statistics
Matches: 177, Mismatches: 25, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
42 19 0.11
43 98 0.55
44 60 0.34
ACGTcount: A:0.30, C:0.28, G:0.17, T:0.26
Consensus pattern (44 bp):
CTTTAGCGGCGCTTTTCCAACAAACGCCGCTAAAGACCATAGAC
Found at i:1326144 original size:32 final size:33
Alignment explanation
Indices: 1326081--1326144 Score: 96
Period size: 34 Copynumber: 1.9 Consensus size: 33
1326071 TTATTTAAAT
1326081 TAAATATTATTATGTTTTAAGGATAAATATTATA
1 TAAATATTATTATGTTTTAA-GATAAATATTATA
1326115 TAAATATTATTAT-TTTTCAA-ATAAATATTA
1 TAAATATTATTATGTTTT-AAGATAAATATTA
1326145 AATTATGTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
32 10 0.34
33 4 0.14
34 15 0.52
ACGTcount: A:0.45, C:0.02, G:0.05, T:0.48
Consensus pattern (33 bp):
TAAATATTATTATGTTTTAAGATAAATATTATA
Found at i:1326424 original size:43 final size:43
Alignment explanation
Indices: 1326358--1326448 Score: 121
Period size: 43 Copynumber: 2.1 Consensus size: 43
1326348 ACATATGCAA
* * * *
1326358 GGTAATAAAATATACAATTCATTTTCTTAATCAACTAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAACGAAATCTT
* *
1326401 GGTAATAAAAGATATAATACATTTACTTAATCAAGGAAATCTT
1 GGTAATAAAAGATACAATACATTTACTTAATCAACGAAATCTT
1326444 -GTAAT
1 GGTAAT
1326449 GAACTCAAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
42 5 0.12
43 37 0.88
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.36
Consensus pattern (43 bp):
GGTAATAAAAGATACAATACATTTACTTAATCAACGAAATCTT
Found at i:1330466 original size:21 final size:21
Alignment explanation
Indices: 1330442--1330493 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
1330432 CCCTAAATCA
1330442 CTAACTCTTAACCT-CTAACCC
1 CTAACTCTTAA-CTACTAACCC
* *
1330463 CTAACCCCTAACTACTAACCC
1 CTAACTCTTAACTACTAACCC
*
1330484 CTAAATCTTA
1 CTAACTCTTA
1330494 TTTAATATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
20 2 0.08
21 23 0.92
ACGTcount: A:0.33, C:0.40, G:0.00, T:0.27
Consensus pattern (21 bp):
CTAACTCTTAACTACTAACCC
Found at i:1330716 original size:14 final size:15
Alignment explanation
Indices: 1330699--1330731 Score: 59
Period size: 14 Copynumber: 2.3 Consensus size: 15
1330689 CTTAAACCAA
1330699 AATCCCTAATT-CAT
1 AATCCCTAATTCCAT
1330713 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
1330728 AATC
1 AATC
1330732 TATAAACCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.61
15 7 0.39
ACGTcount: A:0.36, C:0.30, G:0.00, T:0.33
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:1330939 original size:42 final size:42
Alignment explanation
Indices: 1330886--1331111 Score: 258
Period size: 42 Copynumber: 5.3 Consensus size: 42
1330876 TTATGTAAAA
* **
1330886 AAACGCTGCTAAAGATCATGGTCTTTAGCGGCGCTTTTAT-AC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTT-TCAC
** * *
1330928 AAACGCCGCTAAAGATCATGGTCTTTAGCGGCGCTTTTATTAA
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTT-TCAC
1330971 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTGTCAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTT-TCAC
** *
1331014 AAATACCGCTAAAAAT-ATGACCTTTAGCGGCGCTTTTTGCCAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTT--CAC
* * ** *
1331057 AAACGCCGCTAAAAAACATGACCTTTAGCAACACTTTTTCAC
1 AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTTCAC
1331099 AAACGCCGCTAAA
1 AAACGCCGCTAAA
1331112 AACATGCTTT
Statistics
Matches: 164, Mismatches: 16, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
41 1 0.01
42 76 0.46
43 68 0.41
44 19 0.12
ACGTcount: A:0.31, C:0.25, G:0.18, T:0.27
Consensus pattern (42 bp):
AAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTTCAC
Found at i:1330982 original size:85 final size:84
Alignment explanation
Indices: 1330884--1331113 Score: 266
Period size: 85 Copynumber: 2.7 Consensus size: 84
1330874 GTTTATGTAA
* ** *
1330884 AAAAACGCTGCTAAAGATCATGGTCTTTAGCGGCGCTTTTAT-ACAAACGCCGCTAAAGATCATG
1 AAAAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTT-TCACAAACGCCGCTAAAAAT-ATG
** *
1330948 GTCTTTAGCGGCGCTTTTAT-T
64 ACCTTTAGCGGCGCTTTT-TCC
**
1330969 AAAAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTGTCACAAATACCGCTAAAAATATGA
1 AAAAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTT-TCACAAACGCCGCTAAAAATATGA
1331034 CCTTTAGCGGCGCTTTTTGCC
65 CCTTTAGCGGCGCTTTTT-CC
* * * ** *
1331055 ACAAACGCCGCTAAAAAACATGACCTTTAGCAACACTTTTTCACAAACGCCGCTAAAAA
1 AAAAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTTCACAAACGCCGCTAAAAA
1331114 CATGCTTTTA
Statistics
Matches: 124, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
84 1 0.01
85 74 0.60
86 49 0.40
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (84 bp):
AAAAACGCCGCTAAAGATCATGACCTTTAGCGGCGCTTTTTCACAAACGCCGCTAAAAATATGAC
CTTTAGCGGCGCTTTTTCC
Found at i:1331113 original size:42 final size:43
Alignment explanation
Indices: 1330908--1331117 Score: 232
Period size: 43 Copynumber: 5.0 Consensus size: 43
1330898 AGATCATGGT
* * **
1330908 CTTTAGCGGCGCTTTTAT-ACAAACGCCGCTAAAGATCATGGT
1 CTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAAAACATGAC
* * * *
1330950 CTTTAGCGGCGCTTTTATTAAAAACGCCGCTAAAGATCATGAC
1 CTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAAAACATGAC
* ** *
1330993 CTTTAGCGGCGCTTTTGTCACAAATACCGCT-AAAAATATGAC
1 CTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAAAACATGAC
1331035 CTTTAGCGGCGCTTTT-TGCCACAAACGCCGCTAAAAAACATGAC
1 CTTTAGCGGCGCTTTTAT--CACAAACGCCGCTAAAAAACATGAC
** *
1331079 CTTTAGCAACACTTTT-TCACAAACGCCGCT-AAAAACATG
1 CTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAAAACATG
1331118 CTTTTAAAAA
Statistics
Matches: 147, Mismatches: 17, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
41 10 0.07
42 55 0.37
43 58 0.39
44 24 0.16
ACGTcount: A:0.30, C:0.26, G:0.17, T:0.27
Consensus pattern (43 bp):
CTTTAGCGGCGCTTTTATCACAAACGCCGCTAAAAAACATGAC
Found at i:1331232 original size:5 final size:5
Alignment explanation
Indices: 1331222--1331246 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1331212 TAAAGATAAA
1331222 AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT
1331247 TTCTATTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
AAATT
Found at i:1333639 original size:21 final size:21
Alignment explanation
Indices: 1333611--1333661 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
1333601 CAATAAGTCA
1333611 AATTTGAAAATTTAAATCGCC
1 AATTTGAAAATTTAAATCGCC
*
1333632 AGTTTGAAAATTTAAATCGCC
1 AATTTGAAAATTTAAATCGCC
1333653 AATTTGAAA
1 AATTTGAAA
1333662 GCAATAAAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.43, C:0.12, G:0.12, T:0.33
Consensus pattern (21 bp):
AATTTGAAAATTTAAATCGCC
Found at i:1335435 original size:25 final size:25
Alignment explanation
Indices: 1335407--1335463 Score: 105
Period size: 25 Copynumber: 2.3 Consensus size: 25
1335397 ACCGCAAAAA
1335407 ATTATTTCATTTTGCACAAAACGAC
1 ATTATTTCATTTTGCACAAAACGAC
*
1335432 ATTATTTCATTTTGCACAAAATGAC
1 ATTATTTCATTTTGCACAAAACGAC
1335457 ATTATTT
1 ATTATTT
1335464 TACTCTGCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 31 1.00
ACGTcount: A:0.35, C:0.16, G:0.07, T:0.42
Consensus pattern (25 bp):
ATTATTTCATTTTGCACAAAACGAC
Found at i:1336406 original size:33 final size:33
Alignment explanation
Indices: 1336362--1336437 Score: 111
Period size: 33 Copynumber: 2.3 Consensus size: 33
1336352 AATTAATCTA
*
1336362 AATCCT-AAACCCTAACCCGACCCTAAATCCCT
1 AATCCTCAAACCCTAACCCGACCCCAAATCCCT
*
1336394 AATCCTCAAACCCTAACCTGACCCCAAATCCCT
1 AATCCTCAAACCCTAACCCGACCCCAAATCCCT
1336427 AA-CCTCTAAAC
1 AATCCTC-AAAC
1336438 ATTATTTAAT
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
32 10 0.25
33 30 0.75
ACGTcount: A:0.36, C:0.43, G:0.03, T:0.18
Consensus pattern (33 bp):
AATCCTCAAACCCTAACCCGACCCCAAATCCCT
Found at i:1336428 original size:19 final size:19
Alignment explanation
Indices: 1336371--1336431 Score: 60
Period size: 19 Copynumber: 3.5 Consensus size: 19
1336361 AAATCCTAAA
* *
1336371 CCCTAACCCGACCCTAAAT
1 CCCTAACCTGACCCCAAAT
*
1336390 CCCTAA--T--CCTCAAA-
1 CCCTAACCTGACCCCAAAT
1336404 CCCTAACCTGACCCCAAAT
1 CCCTAACCTGACCCCAAAT
1336423 CCCTAACCT
1 CCCTAACCT
1336432 CTAAACATTA
Statistics
Matches: 33, Mismatches: 4, Indels: 10
0.70 0.09 0.21
Matches are distributed among these distances:
14 6 0.18
15 5 0.15
16 1 0.03
18 6 0.18
19 15 0.45
ACGTcount: A:0.31, C:0.48, G:0.03, T:0.18
Consensus pattern (19 bp):
CCCTAACCTGACCCCAAAT
Found at i:1336620 original size:14 final size:15
Alignment explanation
Indices: 1336603--1336634 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
1336593 CTTAAATCAG
1336603 AATCCCTAA-TCCAT
1 AATCCCTAATTCCAT
1336617 AATCCCTAATTCCAT
1 AATCCCTAATTCCAT
1336632 AAT
1 AAT
1336635 ATATAAACCT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.38, C:0.31, G:0.00, T:0.31
Consensus pattern (15 bp):
AATCCCTAATTCCAT
Found at i:1337446 original size:40 final size:40
Alignment explanation
Indices: 1337322--1337456 Score: 154
Period size: 40 Copynumber: 3.4 Consensus size: 40
1337312 GGGCTTAGGC
*
1337322 TTTTT-GCGGCGCTTTT-TAAAAAACGCCGCTAATGCTT-A
1 TTTTTAGCGGCGCTTTTAT-AAAAGCGCCGCTAATGCTTGA
*
1337360 TTTTTAGCGGCG-TTTTCCA-AAAAGCGCCGCTAATGCTCGA
1 TTTTTAGCGGCGCTTTT--ATAAAAGCGCCGCTAATGCTTGA
**
1337400 CCTTTAGCGGCGCTTTTATAAAAGCGCCGCTAATGCTTGA
1 TTTTTAGCGGCGCTTTTATAAAAGCGCCGCTAATGCTTGA
* *
1337440 TTTTTAGTGGCGTTTTT
1 TTTTTAGCGGCGCTTTT
1337457 TGTCCAAGCG
Statistics
Matches: 81, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
38 9 0.11
39 24 0.30
40 44 0.54
41 4 0.05
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.36
Consensus pattern (40 bp):
TTTTTAGCGGCGCTTTTATAAAAGCGCCGCTAATGCTTGA
Found at i:1337939 original size:41 final size:41
Alignment explanation
Indices: 1337875--1338114 Score: 354
Period size: 41 Copynumber: 5.9 Consensus size: 41
1337865 ACAAAAACAG
* * * *
1337875 GCATTAGCGGCGCTTTTTAAAAAACGCCTCTAAAGGCTCGA
1 GCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGA
*
1337916 GCATTAGCGGCGCTTCTTCAAAAACGCCACTAAAGGCCCGA
1 GCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGA
* * *
1337957 GCATTAGCGACGCTTCCTCAAAAATGCCGCTAAAGGCCCGA
1 GCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGA
**
1337998 GCATTAGCGGCGCTTCTTCAAAAACAACGCTAAAGGCCCGA
1 GCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGA
* * *
1338039 GCAGTAGCGGCGCTTCTTTAAAAACGCCGCTAAAGGCCTGA
1 GCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGA
*
1338080 GCATTAGCGGCGCTTCTTCAAAAATGCCGCTAAAG
1 GCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAG
1338115 ACCCCCTAAA
Statistics
Matches: 178, Mismatches: 21, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 178 1.00
ACGTcount: A:0.29, C:0.28, G:0.23, T:0.20
Consensus pattern (41 bp):
GCATTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGGCCCGA
Found at i:1338209 original size:38 final size:40
Alignment explanation
Indices: 1338155--1338229 Score: 118
Period size: 39 Copynumber: 1.9 Consensus size: 40
1338145 AGGCTTAGCC
1338155 TTTTTGCGGCGCTTTT-CAAAAAACACCGCTAATGCTTAT
1 TTTTTGCGGCGCTTTTCCAAAAAACACCGCTAATGCTTAT
* *
1338194 TTTTTGCGGCG-TTTTCCAAAAAGCGCCGCTAATGCT
1 TTTTTGCGGCGCTTTTCCAAAAAACACCGCTAATGCT
1338230 CGACCTTTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
38 4 0.12
39 29 0.88
ACGTcount: A:0.23, C:0.24, G:0.19, T:0.35
Consensus pattern (40 bp):
TTTTTGCGGCGCTTTTCCAAAAAACACCGCTAATGCTTAT
Found at i:1338279 original size:40 final size:40
Alignment explanation
Indices: 1338154--1338279 Score: 100
Period size: 40 Copynumber: 3.2 Consensus size: 40
1338144 TAGGCTTAGC
* * *
1338154 CTTTTT-GCGGCGCTTTT-CAAAAAACACCGCTAATGCTT-
1 CTTTTTAGCGGC-ATTTTCCAAAAAGCGCCGCTAATGCTTG
* * * *
1338192 ATTTTTTGCGGCGTTTTCCAAAAAGCGCCGCTAATGCTCG
1 CTTTTTAGCGGCATTTTCCAAAAAGCGCCGCTAATGCTTG
* * *
1338232 AC-CTTTAGCGGCATTTT-TATAGAAGCGCCGCTAATGCTTG
1 -CTTTTTAGCGGCATTTTCCA-AAAAGCGCCGCTAATGCTTG
1338272 CTTTTTAG
1 CTTTTTAG
1338280 TGACGTTTTT
Statistics
Matches: 69, Mismatches: 13, Indels: 10
0.75 0.14 0.11
Matches are distributed among these distances:
38 9 0.13
39 25 0.36
40 35 0.51
ACGTcount: A:0.21, C:0.24, G:0.20, T:0.35
Consensus pattern (40 bp):
CTTTTTAGCGGCATTTTCCAAAAAGCGCCGCTAATGCTTG
Found at i:1340656 original size:2 final size:2
Alignment explanation
Indices: 1340651--1340723 Score: 137
Period size: 2 Copynumber: 36.5 Consensus size: 2
1340641 TTAAGCTCCT
*
1340651 TC TC TC CC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1340693 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1340724 TTTTGGCATT
Statistics
Matches: 69, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
2 69 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:1340814 original size:13 final size:13
Alignment explanation
Indices: 1340796--1340851 Score: 103
Period size: 13 Copynumber: 4.3 Consensus size: 13
1340786 ATTTTTACGG
1340796 ACGGTTAATTTTT
1 ACGGTTAATTTTT
1340809 ACGGTTAATTTTT
1 ACGGTTAATTTTT
*
1340822 ACAGTTAATTTTT
1 ACGGTTAATTTTT
1340835 ACGGTTAATTTTT
1 ACGGTTAATTTTT
1340848 ACGG
1 ACGG
1340852 GGTGACTTTA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 41 1.00
ACGTcount: A:0.25, C:0.09, G:0.16, T:0.50
Consensus pattern (13 bp):
ACGGTTAATTTTT
Found at i:1340861 original size:26 final size:26
Alignment explanation
Indices: 1340782--1340849 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
1340772 CCCTTTGACC
*
1340782 GTTAATTTTTACGGACGGTTAATTTTTACG
1 GTTAATTTTTAC--A-GG-TAATCTTTACG
* *
1340812 GTTAATTTTTACAGTTAATTTTTACG
1 GTTAATTTTTACAGGTAATCTTTACG
1340838 GTTAATTTTTAC
1 GTTAATTTTTAC
1340850 GGGGTGACTT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
26 23 0.62
27 1 0.03
28 1 0.03
30 12 0.32
ACGTcount: A:0.25, C:0.09, G:0.15, T:0.51
Consensus pattern (26 bp):
GTTAATTTTTACAGGTAATCTTTACG
Found at i:1341585 original size:13 final size:13
Alignment explanation
Indices: 1341567--1341591 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1341557 CTCTTATTTT
1341567 TTTTTATTTTTAG
1 TTTTTATTTTTAG
1341580 TTTTTATTTTTA
1 TTTTTATTTTTA
1341592 AATTTTATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.16, C:0.00, G:0.04, T:0.80
Consensus pattern (13 bp):
TTTTTATTTTTAG
Found at i:1345197 original size:13 final size:13
Alignment explanation
Indices: 1345179--1345206 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1345169 ACAAAATTGG
1345179 AAAGATGATAAAT
1 AAAGATGATAAAT
1345192 AAAGATGATAAAT
1 AAAGATGATAAAT
1345205 AA
1 AA
1345207 TAAAATAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.64, C:0.00, G:0.14, T:0.21
Consensus pattern (13 bp):
AAAGATGATAAAT
Found at i:1349989 original size:20 final size:21
Alignment explanation
Indices: 1349947--1349989 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 21
1349937 TAATCACTAA
* *
1349947 ATTTTAAATGAAAACAATTAT
1 ATTTTAAATAAAAACAATAAT
*
1349968 ATTTTAAA-AAAAATAATAAT
1 ATTTTAAATAAAAACAATAAT
1349988 AT
1 AT
1349990 GAACAGACAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.37
Consensus pattern (21 bp):
ATTTTAAATAAAAACAATAAT
Found at i:1353350 original size:182 final size:181
Alignment explanation
Indices: 1353005--1353356 Score: 553
Period size: 182 Copynumber: 1.9 Consensus size: 181
1352995 CTAGAAAGTG
*
1353005 TTGTTAAATAAACTGTACAAGGAAATAGTTAGGCACATCAACTCCAATAGCCTTTAGTTAAGCCT
1 TTGTTAAATAAACTGCACAAGGAAATAGTTAGGCACATCAACTCCAATAGCCTTTAGTTAAGCCT
* * *
1353070 AATATCCTTCATTTCCATGATGACATTAAATTAGTGAACTTCATTGATGGTATTTTTCTCATTAT
66 AATATCCATCATTTCCATGATGACATTAAACTAGTGAACTTCATTGATGATATTTTTCTCATTAT
* ** * *
1353135 GGTATTATCTAGGGTTTTATCAGAAGGTTCAAATTATTCATCAATGGTGTC
131 GGTACTATCTAGAATTTCATCAGAAGATTCAAATTATTCATCAATGGTGTC
* * *
1353186 TTGTTAAATAAAGTGCACAAGGAAATAGTTAGGCACGTCAACTTCAATAGCCTTTAGTTAAGCCG
1 TTGTTAAATAAACTGCACAAGGAAATAGTTAGGCACATCAACTCCAATAGCCTTTAGTTAAGCC-
1353251 TAATATCCATCATTTCCATGATGACATTAAACTAGTGAACTTCATTGATGATATTTTTCTCATTA
65 TAATATCCATCATTTCCATGATGACATTAAACTAGTGAACTTCATTGATGATATTTTTCTCATTA
* *
1353316 TGGTGCTATCTAGAATTTCAT-ATGAAGATTCAAATTGTTCA
130 TGGTACTATCTAGAATTTCATCA-GAAGATTCAAATTATTCA
1353357 ACATTCAATA
Statistics
Matches: 155, Mismatches: 14, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
181 61 0.39
182 94 0.61
ACGTcount: A:0.32, C:0.16, G:0.15, T:0.37
Consensus pattern (181 bp):
TTGTTAAATAAACTGCACAAGGAAATAGTTAGGCACATCAACTCCAATAGCCTTTAGTTAAGCCT
AATATCCATCATTTCCATGATGACATTAAACTAGTGAACTTCATTGATGATATTTTTCTCATTAT
GGTACTATCTAGAATTTCATCAGAAGATTCAAATTATTCATCAATGGTGTC
Found at i:1353891 original size:17 final size:16
Alignment explanation
Indices: 1353854--1353904 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 16
1353844 TTAGATCAAC
1353854 AAATAATTTAAAAATAATAA
1 AAAT-ATTT-AAAA-AAT-A
1353874 AAATATTTAAAAAATA
1 AAATATTTAAAAAATA
1353890 AAATATTTTAAAAAA
1 AAATA-TTTAAAAAA
1353905 AAAGATAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.20
17 12 0.40
18 4 0.13
19 4 0.13
20 4 0.13
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATATTTAAAAAATA
Found at i:1359587 original size:77 final size:77
Alignment explanation
Indices: 1359456--1359839 Score: 644
Period size: 77 Copynumber: 5.0 Consensus size: 77
1359446 TTGGGGGAAT
* *
1359456 TGGGAATTAGGGTTTTTTATTTGAAGTTCAATTTGTGTAATTATATTGACCAAAGGAATAGCCTT
1 TGGGAATTAGGG-TTTTTAATTGGAGTTCAATTTGTGTAATTATATTGACCAAAGGAATAGCCTT
*
1359521 TGATAAGTATAAC
65 TGATAAGGATAAC
* * *
1359534 TGAGAATTAGGGTTTTTGATTGGAGTTCAATTTGTGTAGTTATATTGACCAAAGGAATAGCCTTT
1 TGGGAATTAGGGTTTTTAATTGGAGTTCAATTTGTGTAATTATATTGACCAAAGGAATAGCCTTT
**
1359599 GATAAGGATATT
66 GATAAGGATAAC
1359611 TGGGAATTAGGGTTTTTAATTGGAGTTCAATTTGTGTAATTATATTGACCAAAGGAATAGCCTTT
1 TGGGAATTAGGGTTTTTAATTGGAGTTCAATTTGTGTAATTATATTGACCAAAGGAATAGCCTTT
1359676 GATAAGGATAAC
66 GATAAGGATAAC
1359688 TGGGAATTAGGGTTTTTAATTGGAGTTCAATTTGTGTAATTATATTGACCAAAGGAATAGCCTTT
1 TGGGAATTAGGGTTTTTAATTGGAGTTCAATTTGTGTAATTATATTGACCAAAGGAATAGCCTTT
1359753 GATAAGGATAAC
66 GATAAGGATAAC
* * *
1359765 TGGGAATTAGGGTTTTTGATTTGTGTTCAATTTGTGTAATT-TAATTGACCAAAGGAATAGCCTT
1 TGGGAATTAGGGTTTTTAATTGGAGTTCAATTTGTGTAATTAT-ATTGACCAAAGGAATAGCCTT
1359829 TGATAAGGATA
65 TGATAAGGATA
1359840 GACTTTAAAG
Statistics
Matches: 289, Mismatches: 16, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
76 1 0.00
77 277 0.96
78 11 0.04
ACGTcount: A:0.31, C:0.07, G:0.23, T:0.38
Consensus pattern (77 bp):
TGGGAATTAGGGTTTTTAATTGGAGTTCAATTTGTGTAATTATATTGACCAAAGGAATAGCCTTT
GATAAGGATAAC
Found at i:1371050 original size:15 final size:14
Alignment explanation
Indices: 1370998--1371058 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 14
1370988 AATATTCGTT
*
1370998 TTTGTTTTCTTTCC
1 TTTGTTTTCTTTTC
1371012 TTTTGTTTGCTTCTGTTTC
1 -TTTG-TT--TTCT-TTTC
1371031 TTTGTTTTCTTTTC
1 TTTGTTTTCTTTTC
*
1371045 TGTTGTCTTCTTTT
1 T-TTGTTTTCTTTT
1371059 GCTTGCGTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 10
0.76 0.04 0.20
Matches are distributed among these distances:
14 5 0.13
15 19 0.49
16 2 0.05
17 2 0.05
18 8 0.21
19 3 0.08
ACGTcount: A:0.00, C:0.16, G:0.11, T:0.72
Consensus pattern (14 bp):
TTTGTTTTCTTTTC
Found at i:1378924 original size:29 final size:29
Alignment explanation
Indices: 1378892--1378953 Score: 81
Period size: 29 Copynumber: 2.1 Consensus size: 29
1378882 ACCAAAAAAA
*
1378892 GCCATTTTTTTCAA-AATTTACCGAAATGG
1 GCCACTTTTTT-AATAATTTACCGAAATGG
* *
1378921 GCCACTTTTTTAATTATTTACCGGAATGG
1 GCCACTTTTTTAATAATTTACCGAAATGG
1378950 GCCA
1 GCCA
1378954 ATTCCGCGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 2 0.07
29 27 0.93
ACGTcount: A:0.27, C:0.19, G:0.16, T:0.37
Consensus pattern (29 bp):
GCCACTTTTTTAATAATTTACCGAAATGG
Found at i:1379189 original size:22 final size:22
Alignment explanation
Indices: 1379156--1379211 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
1379146 TTTTCACAAA
*
1379156 CAAATATTCTCTCAATTTCCTTC
1 CAAA-ATTCTCTCAAATTCCTTC
1379179 CAAAATTCTCTCAAATTCCTTC
1 CAAAATTCTCTCAAATTCCTTC
1379201 CAAAATTCTCT
1 CAAAATTCTCT
1379212 TAAACTCTCA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
22 28 0.88
23 4 0.12
ACGTcount: A:0.30, C:0.30, G:0.00, T:0.39
Consensus pattern (22 bp):
CAAAATTCTCTCAAATTCCTTC
Found at i:1379204 original size:11 final size:11
Alignment explanation
Indices: 1379172--1379252 Score: 50
Period size: 11 Copynumber: 7.6 Consensus size: 11
1379162 TTCTCTCAAT
1379172 TTCCTTCCAAAA
1 TTCCTTCC-AAA
1379184 TT-C-TCTCAAA
1 TTCCTTC-CAAA
1379194 TTCCTTCCAAAA
1 TTCCTTCC-AAA
1379206 TTCTCTT--AAA
1 TTC-CTTCCAAA
*
1379216 CT-C-T-CAAA
1 TTCCTTCCAAA
1379224 TTCCTTCCAAA
1 TTCCTTCCAAA
* *
1379235 ATCCTTCCAAT
1 TTCCTTCCAAA
1379246 TTCCTTC
1 TTCCTTC
1379253 AAAAATCTCT
Statistics
Matches: 55, Mismatches: 5, Indels: 19
0.70 0.06 0.24
Matches are distributed among these distances:
7 1 0.02
8 5 0.09
9 1 0.02
10 12 0.22
11 23 0.42
12 10 0.18
13 3 0.05
ACGTcount: A:0.28, C:0.33, G:0.00, T:0.38
Consensus pattern (11 bp):
TTCCTTCCAAA
Found at i:1379250 original size:52 final size:53
Alignment explanation
Indices: 1379164--1379263 Score: 141
Period size: 52 Copynumber: 1.9 Consensus size: 53
1379154 AACAAATATT
* * *
1379164 CTCTCAATTTCCTTCCAAAATTCTCTCAAATTCCTTCCAAAAT-TCTCTTAAA
1 CTCTCAAATTCCTTCCAAAATCCTCTCAAATTCCTTCAAAAATCTCTCTTAAA
*
1379216 CTCTCAAATTCCTTCCAAAATCCT-TCCAATTTCCTTCAAAAATCTCTC
1 CTCTCAAATTCCTTCCAAAATCCTCT-CAAATTCCTTCAAAAATCTCTC
1379264 AAATCCATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
51 1 0.02
52 37 0.88
53 4 0.10
ACGTcount: A:0.30, C:0.33, G:0.00, T:0.37
Consensus pattern (53 bp):
CTCTCAAATTCCTTCCAAAATCCTCTCAAATTCCTTCAAAAATCTCTCTTAAA
Found at i:1379335 original size:30 final size:28
Alignment explanation
Indices: 1379299--1379357 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 28
1379289 ATTCAATTTC
1379299 ATTTTTTTAAAGAAAATTTTAAATATTTTT
1 ATTTTTTTAAA-AAAATTTTAAA-ATTTTT
*
1379329 ATTTTTTTAAAATAATTTTAAAATTTTT
1 ATTTTTTTAAAAAAATTTTAAAATTTTT
1379357 A
1 A
1379358 ATATTTTCAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 7 0.25
29 10 0.36
30 11 0.39
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.58
Consensus pattern (28 bp):
ATTTTTTTAAAAAAATTTTAAAATTTTT
Found at i:1379364 original size:29 final size:30
Alignment explanation
Indices: 1379302--1379364 Score: 85
Period size: 29 Copynumber: 2.1 Consensus size: 30
1379292 CAATTTCATT
*
1379302 TTTTTAAAGAAAATTTTAAATATTTTTATT
1 TTTTTAAAGAAAATTTTAAATATTTTTATA
*
1379332 TTTTTAAA-ATAATTTTAAA-ATTTTTAATA
1 TTTTTAAAGAAAATTTTAAATATTTTT-ATA
1379361 TTTT
1 TTTT
1379365 CAACAATGGC
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 6 0.20
29 16 0.53
30 8 0.27
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.59
Consensus pattern (30 bp):
TTTTTAAAGAAAATTTTAAATATTTTTATA
Found at i:1380458 original size:7 final size:7
Alignment explanation
Indices: 1380446--1380477 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
1380436 AGTGGATTGA
1380446 TATTTAG
1 TATTTAG
1380453 TATTTAG
1 TATTTAG
1380460 TATTTAG
1 TATTTAG
1380467 TATTTAG
1 TATTTAG
1380474 TATT
1 TATT
1380478 ATGTATATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.28, C:0.00, G:0.12, T:0.59
Consensus pattern (7 bp):
TATTTAG
Found at i:1381357 original size:24 final size:24
Alignment explanation
Indices: 1381330--1381385 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
1381320 ACATGGCTTT
* *
1381330 CAAACTCCGTCGCCGTTCATGATG
1 CAAACACCGTCACCGTTCATGATG
*
1381354 CAAACACTGTCACCGTTCATGATG
1 CAAACACCGTCACCGTTCATGATG
1381378 CAAACACC
1 CAAACACC
1381386 TCCACATACA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.29, C:0.34, G:0.16, T:0.21
Consensus pattern (24 bp):
CAAACACCGTCACCGTTCATGATG
Found at i:1381745 original size:29 final size:29
Alignment explanation
Indices: 1381665--1382019 Score: 478
Period size: 29 Copynumber: 12.5 Consensus size: 29
1381655 TTTTGATATT
*
1381665 ATTTGATTAAAAACCCTAA-CCTAATTTA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
*
1381693 ATTTAATTAAAAACCC-AAACCTAATTTA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
1381721 ATTTAATTAAAAACCCTAACCCTAATTTA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
1381750 ATTTAATTAAAAACCCTAACCC--A--T-
1 ATTTAATTAAAAACCCTAACCCTAATTTA
*
1381774 -TTTAATTAAAAACCCTAACCCTAGTTTA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
*
1381802 ATTTAATTAAAAACCCTAACCCTAGTTTA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
*
1381831 ATTTAATTAAAAACCCTAACCCTAGTTTA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
1381860 ATTTAATTAAAAACCCTAACCCTAATTTA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
* *
1381889 ATTTAATTAAAAACCCTAACCTTAACTT-
1 ATTTAATTAAAAACCCTAACCCTAATTTA
* **
1381917 ATATTAATT-AAAACCCTAAACCTTAACCTA
1 AT-TTAATTAAAAACCCT-AACCCTAATTTA
***
1381947 ATTTAATTAAAAACCCTAACCCTAACCCA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
* **
1381976 TTTTAATTAAAAACCCTAACCCTAAACTA
1 ATTTAATTAAAAACCCTAACCCTAATTTA
1382005 ATTTAATTAAAAACC
1 ATTTAATTAAAAACC
1382020 TATTTTAATT
Statistics
Matches: 302, Mismatches: 13, Indels: 23
0.89 0.04 0.07
Matches are distributed among these distances:
23 21 0.07
25 1 0.00
27 4 0.01
28 50 0.17
29 216 0.72
30 10 0.03
ACGTcount: A:0.45, C:0.22, G:0.01, T:0.33
Consensus pattern (29 bp):
ATTTAATTAAAAACCCTAACCCTAATTTA
Done.