Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold152
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: 2945013
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
File 8 of 18
Found at i:1313601 original size:33 final size:33
Alignment explanation
Indices: 1313559--1313623 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
1313549 TTAGAAGCAA
* * *
1313559 TGTATCGATAGAAT-TCATCATGTATTGATACAT
1 TGTATCGATACAATGT-ACCATGTATCGATACAT
1313592 TGTATCGATACAATGTACCATGTATCGATACA
1 TGTATCGATACAATGTACCATGTATCGATACA
1313624 AACAGTAGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 27 0.96
34 1 0.04
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Consensus pattern (33 bp):
TGTATCGATACAATGTACCATGTATCGATACAT
Found at i:1313676 original size:20 final size:19
Alignment explanation
Indices: 1313651--1313705 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 19
1313641 TACTGCCAGT
1313651 TTCATGTATCGATACAATTG
1 TTCATGTATCGATACAA-TG
1313671 TTCATGTATCGATACAATG
1 TTCATGTATCGATACAATG
**
1313690 AACATGTATCGATACA
1 TTCATGTATCGATACA
1313706 TCTGGGTGTG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.35
Consensus pattern (19 bp):
TTCATGTATCGATACAATG
Found at i:1313697 original size:19 final size:20
Alignment explanation
Indices: 1313653--1313705 Score: 81
Period size: 19 Copynumber: 2.7 Consensus size: 20
1313643 CTGCCAGTTT
**
1313653 CATGTATCGATACAATTGTT
1 CATGTATCGATACAATTGAA
1313673 CATGTATCGATACAA-TGAA
1 CATGTATCGATACAATTGAA
1313692 CATGTATCGATACA
1 CATGTATCGATACA
1313706 TCTGGGTGTG
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (20 bp):
CATGTATCGATACAATTGAA
Found at i:1314695 original size:33 final size:33
Alignment explanation
Indices: 1314658--1314721 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
1314648 TGCACCAAAG
* *
1314658 TGCTCATCCATACGTTGTGAGAGTGAAGTGAAT
1 TGCTCACCCATACGTTGTGAAAGTGAAGTGAAT
**
1314691 TGCTCACCCATGTGTTGTGAAAGTGAAGTGA
1 TGCTCACCCATACGTTGTGAAAGTGAAGTGA
1314722 TCAACTCTCG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.30
Consensus pattern (33 bp):
TGCTCACCCATACGTTGTGAAAGTGAAGTGAAT
Found at i:1316061 original size:20 final size:21
Alignment explanation
Indices: 1316036--1316076 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
1316026 TTTTTTTAGT
*
1316036 TATTTTGATG-AAAAATGAAG
1 TATTTTGAAGTAAAAATGAAG
1316056 TATTTTGAAGTAAAAATGAAG
1 TATTTTGAAGTAAAAATGAAG
1316077 AAATTTGTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.46, C:0.00, G:0.20, T:0.34
Consensus pattern (21 bp):
TATTTTGAAGTAAAAATGAAG
Found at i:1316288 original size:20 final size:21
Alignment explanation
Indices: 1316258--1316299 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
1316248 ATCTGGGTTT
1316258 TTCAGATGTATCGATACATTC
1 TTCAGATGTATCGATACATTC
1316279 TTCA-ATGTATCGATACATTC
1 TTCAGATGTATCGATACATTC
1316299 T
1 T
1316300 GAAAAATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 17 0.81
21 4 0.19
ACGTcount: A:0.29, C:0.19, G:0.12, T:0.40
Consensus pattern (21 bp):
TTCAGATGTATCGATACATTC
Found at i:1316421 original size:20 final size:21
Alignment explanation
Indices: 1316396--1316435 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
1316386 ACATAACATA
* *
1316396 AATAAACAA-CAAATTCATCC
1 AATAAAAAAGCAAAATCATCC
1316416 AATAAAAAAGCAAAATCATC
1 AATAAAAAAGCAAAATCATC
1316436 AAAAATCACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.60, C:0.20, G:0.03, T:0.17
Consensus pattern (21 bp):
AATAAAAAAGCAAAATCATCC
Found at i:1323732 original size:13 final size:13
Alignment explanation
Indices: 1323714--1323739 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1323704 CAATTTTTTG
1323714 TGTATCGATACAT
1 TGTATCGATACAT
1323727 TGTATCGATACAT
1 TGTATCGATACAT
1323740 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1323824 original size:20 final size:20
Alignment explanation
Indices: 1323799--1323871 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1323789 CAACTTTTTT
1323799 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1323819 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1323840 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1323860 ATGTATCGATAC
1 ATGTATCGATAC
1323872 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1323837 original size:41 final size:41
Alignment explanation
Indices: 1323778--1323871 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
1323768 CTGCCAAGAA
*
1323778 ATGTATCGATACAACTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
*
1323819 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
1323860 ATGTATCGATAC
1 ATGTATCGATAC
1323872 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
Found at i:1323853 original size:21 final size:21
Alignment explanation
Indices: 1323778--1323853 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
1323768 CTGCCAAGAA
* *
1323778 ATGTATCGATACAACTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1323799 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1323819 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1323840 ATGTATCGATACAT
1 ATGTATCGATACAT
1323854 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1326318 original size:13 final size:13
Alignment explanation
Indices: 1326300--1326337 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
1326290 ATAAACACCC
1326300 TGTATCGATACAG
1 TGTATCGATACAG
*
1326313 TGTATCGATACAT
1 TGTATCGATACAG
1326326 TGTATCGATACA
1 TGTATCGATACA
1326338 AATAAAAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Consensus pattern (13 bp):
TGTATCGATACAG
Found at i:1328429 original size:15 final size:15
Alignment explanation
Indices: 1328409--1328439 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1328399 ATTTCGTTTG
*
1328409 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
1328424 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
1328439 G
1 G
1328440 GACATTTTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:1330272 original size:21 final size:21
Alignment explanation
Indices: 1330243--1330287 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1330233 AAGTTTTCAT
*
1330243 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1330263 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1330285 TTT
1 TTT
1330288 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1332520 original size:13 final size:13
Alignment explanation
Indices: 1332502--1332527 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1332492 CAATTTTTTG
1332502 TGTATCGATACAT
1 TGTATCGATACAT
1332515 TGTATCGATACAT
1 TGTATCGATACAT
1332528 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1332612 original size:20 final size:20
Alignment explanation
Indices: 1332587--1332659 Score: 101
Period size: 20 Copynumber: 3.6 Consensus size: 20
1332577 CAACTTTTTT
1332587 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
****
1332607 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACAT-TGCAAC
1332628 ATGTATCGATACATTGCAAC
1 ATGTATCGATACATTGCAAC
1332648 ATGTATCGATAC
1 ATGTATCGATAC
1332660 TTTGAATTGT
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
20 28 0.64
21 16 0.36
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.36
Consensus pattern (20 bp):
ATGTATCGATACATTGCAAC
Found at i:1332625 original size:41 final size:41
Alignment explanation
Indices: 1332566--1332659 Score: 170
Period size: 41 Copynumber: 2.3 Consensus size: 41
1332556 CTGCCAAGAA
*
1332566 ATGTATCGATACAACTTTTTTATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
*
1332607 ATGTATCGATACATCTTTTTCATGTATCGATACATTGCAAC
1 ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
1332648 ATGTATCGATAC
1 ATGTATCGATAC
1332660 TTTGAATTGT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 51 1.00
ACGTcount: A:0.31, C:0.18, G:0.13, T:0.38
Consensus pattern (41 bp):
ATGTATCGATACAACTTTTTCATGTATCGATACATTGCAAC
Found at i:1332641 original size:21 final size:21
Alignment explanation
Indices: 1332566--1332641 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
1332556 CTGCCAAGAA
* *
1332566 ATGTATCGATACAACTTTTTT
1 ATGTATCGATACATCTTTTTC
****
1332587 ATGTATCGATACAT-TGCAAC
1 ATGTATCGATACATCTTTTTC
1332607 ATGTATCGATACATCTTTTTC
1 ATGTATCGATACATCTTTTTC
1332628 ATGTATCGATACAT
1 ATGTATCGATACAT
1332642 TGCAACATGT
Statistics
Matches: 44, Mismatches: 10, Indels: 2
0.79 0.18 0.04
Matches are distributed among these distances:
20 15 0.34
21 29 0.66
ACGTcount: A:0.30, C:0.17, G:0.12, T:0.41
Consensus pattern (21 bp):
ATGTATCGATACATCTTTTTC
Found at i:1334609 original size:155 final size:156
Alignment explanation
Indices: 1334441--1334827 Score: 388
Period size: 156 Copynumber: 2.5 Consensus size: 156
1334431 GTTTTTGTAG
* * * *
1334441 AAAAATTATAAAAATGCCCCT-AGGGTATACCTTCG-GTGTAAAAGTATCTTGAAAACCCTAAAA
1 AAAAATCACAAAAATACCCCTAAGGG-ATACCTTCGACT-TAAAAGTATC-TGAAAACCCTAAAA
* *
1334504 GACTT-AAAAA-GGTTATAAATGGGATAACCTATGCTAAATACCCACCTTCAACATAAAAGCAAA
63 GACTTGAAAAATGATTATAAATGGGATAACCTATCCTAAATACCCACCTTCAACATAAAAGCAAA
1334567 CCCAGTGACAACCTAGGACTTAGCTTTAA
128 CCCAGTGACAACCTAGGACTTAGCTTTAA
* * * * * *
1334596 AAAAATCACAAAAATACCCTTAAGGGATACCTTTGACTTAAAAGTGTCTGATACCCCTAAAGGAC
1 AAAAATCACAAAAATACCCCTAAGGGATACCTTCGACTTAAAAGTATCTGAAAACCCTAAAAGAC
* * * ** * *
1334661 TTGAAAAATTATTATAGATGGGATAACCTATCCTAAATACTCACCTTCGGCATAAAAGCAGACTC
66 TTGAAAAATGATTATAAATGGGATAACCTATCCTAAATACCCACCTTCAACATAAAAGCAAACCC
* * * * *
1334726 GGTGACAACTTTGGACTT-GATTTTA
131 AGTGACAACCTAGGACTTAGCTTTAA
* * * * * * ** * * *
1334751 GAAAATTACAAAAAAAACCCTTAGGGGATACCTTTGACTTAAAAGTGCCTGATATCCCTAAAGGA
1 AAAAATCAC-AAAAATACCCCTAAGGGATACCTTCGACTTAAAAGTATCTGAAAACCCTAAAAGA
1334816 CTTGAAAAATGA
65 CTTGAAAAATGA
1334828 AAGGAATGAT
Statistics
Matches: 196, Mismatches: 31, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
154 16 0.08
155 51 0.26
156 129 0.66
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.25
Consensus pattern (156 bp):
AAAAATCACAAAAATACCCCTAAGGGATACCTTCGACTTAAAAGTATCTGAAAACCCTAAAAGAC
TTGAAAAATGATTATAAATGGGATAACCTATCCTAAATACCCACCTTCAACATAAAAGCAAACCC
AGTGACAACCTAGGACTTAGCTTTAA
Found at i:1334731 original size:156 final size:156
Alignment explanation
Indices: 1334516--1334825 Score: 442
Period size: 156 Copynumber: 2.0 Consensus size: 156
1334506 CTTAAAAAGG
*
1334516 TTATAAATGGGATAACCTATGCTAAATACCCACCTTCAACATAAAAGCAAACCCAGTGACAACCT
1 TTATAAATGGGATAACCTATCCTAAATACCCACCTTCAACATAAAAGCAAACCCAGTGACAACCT
* * *
1334581 AGGACTTAGCTTTAAAAAAATCAC-AAAAATACCCTTAAGGGATACCTTTGACTTAAAAGTGTCT
66 AGGACTT-GATTTAAAAAAATCACAAAAAAAACCCTTAAGGGATACCTTTGACTTAAAAGTGCCT
1334645 GATACCCCTAAAGGACTTGAAAAATTA
130 GATACCCCTAAAGGACTTGAAAAATTA
* * ** * * * *
1334672 TTATAGATGGGATAACCTATCCTAAATACTCACCTTCGGCATAAAAGCAGACTCGGTGACAACTT
1 TTATAAATGGGATAACCTATCCTAAATACCCACCTTCAACATAAAAGCAAACCCAGTGACAACCT
* * * * *
1334737 TGGACTTGATTTTAGAAAATTACAAAAAAAACCCTTAGGGGATACCTTTGACTTAAAAGTGCCTG
66 AGGACTTGATTTAAAAAAATCACAAAAAAAACCCTTAAGGGATACCTTTGACTTAAAAGTGCCTG
*
1334802 ATATCCCTAAAGGACTTGAAAAAT
131 ATACCCCTAAAGGACTTGAAAAAT
1334826 GAAAGGAATG
Statistics
Matches: 135, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
155 12 0.09
156 123 0.91
ACGTcount: A:0.39, C:0.20, G:0.15, T:0.26
Consensus pattern (156 bp):
TTATAAATGGGATAACCTATCCTAAATACCCACCTTCAACATAAAAGCAAACCCAGTGACAACCT
AGGACTTGATTTAAAAAAATCACAAAAAAAACCCTTAAGGGATACCTTTGACTTAAAAGTGCCTG
ATACCCCTAAAGGACTTGAAAAATTA
Found at i:1336065 original size:23 final size:22
Alignment explanation
Indices: 1336039--1336090 Score: 77
Period size: 24 Copynumber: 2.3 Consensus size: 22
1336029 TTGCTTTAAT
1336039 TTTCTTTTTTTCTCTCTTTCTTC
1 TTTCTTTTTTTCTCTCTTT-TTC
*
1336062 TTTCTTTTTTTTTTCTCTTTTTC
1 TTTC-TTTTTTTCTCTCTTTTTC
1336085 TTTCTT
1 TTTCTT
1336091 GCCAAAACTC
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
22 2 0.07
23 11 0.41
24 14 0.52
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTCTTTTTTTCTCTCTTTTTC
Found at i:1336067 original size:11 final size:11
Alignment explanation
Indices: 1336039--1336090 Score: 59
Period size: 11 Copynumber: 4.5 Consensus size: 11
1336029 TTGCTTTAAT
1336039 TTTCTTTTTTTC
1 TTTC-TTTTTTC
* *
1336051 TCTCTTTCTTC
1 TTTCTTTTTTC
*
1336062 TTTCTTTTTTT
1 TTTCTTTTTTC
1336073 TTTCTCTTTTTC
1 TTTCT-TTTTTC
1336085 TTTCTT
1 TTTCTT
1336091 GCCAAAACTC
Statistics
Matches: 33, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
11 20 0.61
12 13 0.39
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (11 bp):
TTTCTTTTTTC
Found at i:1336410 original size:5 final size:5
Alignment explanation
Indices: 1336400--1336424 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1336390 TTGATAGTAC
1336400 AAATT AAATT AAATT AAATT AAATT
1 AAATT AAATT AAATT AAATT AAATT
1336425 TTCAAAAATC
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:1336858 original size:165 final size:166
Alignment explanation
Indices: 1336573--1337158 Score: 705
Period size: 166 Copynumber: 3.5 Consensus size: 166
1336563 ATATATACTA
* * * * * *
1336573 AAAAAATTCAAAACTCAT--AAATAAATTGAATTTCTCAAAACTAATTTAAT-GTAAATTTAATT
1 AAAAAATTCAAAACTCATGAAAATGAA-TGAATTTTTAAAAACTAATTTAATAG-GAATTAAATA
* * * * * *
1336635 ACAATATTTAACGAATTTTAAAAATTAAAAACTAAAAAAAATCCCCCCAAAAACATTTATGGAGT
64 ATAATATTTGATGAATTTTAAAAATTAAAAACTAAGAAAAATTCCCCCGAAAACATTTATGGAGT
* *
1336700 AGAAAACTCCATATTTTAGAAACAAGAAAATTTCTAAG
129 AGAAAACTCCATATTTTAGAAACAAGGAAATTTCCAAG
* * *
1336738 AAAAAATTCAAAACTCACGAAAATGAATGAATTTTTTAAATCTAATTTAATAGGAATTAAATAAT
1 AAAAAATTCAAAACTCATGAAAATGAATGAATTTTTAAAAACTAATTTAATAGGAATTAAATAAT
* *
1336803 AACATTTTATGAATTTTAAAAATT-AAAACTAAGAAAAATTCCCCCGAAAACATTTATGGAGTAG
66 AATATTTGATGAATTTTAAAAATTAAAAACTAAGAAAAATTCCCCCGAAAACATTTATGGAGTAG
* * * *
1336867 AAAA-TTCAGTATTTCAAAAATAAGGGAAATTTCCAAG
131 AAAACTCCA-TATTTTAGAAACAA-GGAAATTTCCAAG
* * * * * *
1336904 AAAGAATTCCAAACTCATGAAAATGAATGAATTTTTAAAAATTGATTTAGTATGAATTAAATAAT
1 AAAAAATTCAAAACTCATGAAAATGAATGAATTTTTAAAAACTAATTTAATAGGAATTAAATAAT
* * * *
1336969 AATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATTTCCTCGAAAACATTTATGGAATAG
66 AATATTTGATGAATTTTAAAAATTAAAAACTAAGAAAAATTCCCCCGAAAACATTTATGGAGTAG
** * * * *
1337034 AAAACTCTGTATTTTGGAAACAGGGTAATTTCCAAT
131 AAAACTCCATATTTTAGAAACAAGGAAATTTCCAAG
* * *
1337070 AAAAAATTCCAAACTCATGAAAATGAATGAATTTTTAAAAACTAACTTAATATGAATTAAATAAT
1 AAAAAATTCAAAACTCATGAAAATGAATGAATTTTTAAAAACTAATTTAATAGGAATTAAATAAT
* *
1337135 AATATTTGATAAATTTAAAAAATT
66 AATATTTGATGAATTTTAAAAATT
1337159 TTGGATCAAT
Statistics
Matches: 361, Mismatches: 53, Indels: 13
0.85 0.12 0.03
Matches are distributed among these distances:
164 3 0.01
165 69 0.19
166 232 0.64
167 56 0.16
168 1 0.00
ACGTcount: A:0.50, C:0.10, G:0.09, T:0.31
Consensus pattern (166 bp):
AAAAAATTCAAAACTCATGAAAATGAATGAATTTTTAAAAACTAATTTAATAGGAATTAAATAAT
AATATTTGATGAATTTTAAAAATTAAAAACTAAGAAAAATTCCCCCGAAAACATTTATGGAGTAG
AAAACTCCATATTTTAGAAACAAGGAAATTTCCAAG
Found at i:1337270 original size:332 final size:332
Alignment explanation
Indices: 1336637--1337327 Score: 756
Period size: 332 Copynumber: 2.1 Consensus size: 332
1336627 ATTTAATTAC
* *
1336637 AATATTTAACGAATTTTAAAAATTAAAAACTAAAAAAAATCCCCCCAAAAACATTTATGGAGTAG
1 AATATTTAACGAATTTTAAAAATTAAAAACCAAAAAAAATCCCCCCAAAAACATTTATGGAATAG
*
1336702 AAAACTCCATATTTTAGAAACAAGAAAATTTCTAAGAAAAAATTCAAAACTCACGAAAATGAATG
66 AAAACTCCATATTTTAGAAACAAGAAAATTTCCAAGAAAAAATTCAAAACTCACGAAAATGAATG
* * * * * *
1336767 AATTTTTTAAATCTAATTTAATAGGAATTAAATAATAACATTTTATGAATTTTAAAAATTAAAAC
131 AATTTTTAAAAACTAACTTAATAGGAATTAAATAATAACATTTGATAAATTTAAAAAATTAAAAC
* * * * *
1336832 TAAGAAAAATTCCCCCGAAAACATTTATGGAGTAGAAAATTCAGTATTTCAAAAATAAGGGAAAT
196 TAAGAAAAATTCCCCCAAAAAAATTTACGAAGTAGAAAACTCAGTATTTCAAAAATAAGGGAAAT
** * * * *
1336897 TTCCAAGAAAGAATTCCAAACTCATGAAAATGAATGAATTTTTAAAAATTGATTTAGTAT-G-AA
261 TTAAAAGAAAGAATTACAAACTCATGAAAATAAAAGAATTTTTAAAAACTGATTT--TATGGTAA
1336960 TTAAATAAT
324 TTAAATAAT
* * * ** * *
1336969 AATATTTGATGAATTTTAAAAATTAAAAACCAAGAAAAATTTCCTCGAAAACATTTATGGAATAG
1 AATATTTAACGAATTTTAAAAATTAAAAACCAAAAAAAATCCCCCCAAAAACATTTATGGAATAG
** * * ** * * *
1337034 AAAACTCTGTATTTTGGAAACAGGGTAATTTCCAATAAAAAATTCCAAACTCATGAAAATGAATG
66 AAAACTCCATATTTTAGAAACAAGAAAATTTCCAAGAAAAAATTCAAAACTCACGAAAATGAATG
* * ***
1337099 AATTTTTAAAAACTAACTTAATATGAATTAAATAATAATATTTGATAAATTTAAAAAATTTTGGA
131 AATTTTTAAAAACTAACTTAATAGGAATTAAATAATAACATTTGATAAATTTAAAAAA-TTAAAA
* * * *
1337164 -TCAATG-AAAA-TCGTCTCAAAAAAATTTACGAAGTAGAAAACTCCGTATTTTAAAAATAAGAG
195 CT-AA-GAAAAATTC-CCCCAAAAAAATTTACGAAGTAGAAAACTCAGTATTTCAAAAATAAG-G
* *
1337226 G-AATTATAAAAG-AA-AATTA-ACAAGTCAT-AAAATAAAAAGAATTTTTCAAAACTGATTTTA
256 GAAATT-TAAAAGAAAGAATTACA-AACTCATGAAAAT-AAAAGAATTTTTAAAAACTGATTTTA
* *
1337286 TGGTGATTAAATGAT
318 TGGTAATTAAATAAT
* *
1337301 AATATTTAAGGAATTTT-AGAATTAAAA
1 AATATTTAACGAATTTTAAAAATTAAAA
1337328 GCTCGAGAAA
Statistics
Matches: 297, Mismatches: 52, Indels: 21
0.80 0.14 0.06
Matches are distributed among these distances:
330 3 0.01
331 16 0.05
332 218 0.73
333 53 0.18
334 7 0.02
ACGTcount: A:0.49, C:0.09, G:0.10, T:0.31
Consensus pattern (332 bp):
AATATTTAACGAATTTTAAAAATTAAAAACCAAAAAAAATCCCCCCAAAAACATTTATGGAATAG
AAAACTCCATATTTTAGAAACAAGAAAATTTCCAAGAAAAAATTCAAAACTCACGAAAATGAATG
AATTTTTAAAAACTAACTTAATAGGAATTAAATAATAACATTTGATAAATTTAAAAAATTAAAAC
TAAGAAAAATTCCCCCAAAAAAATTTACGAAGTAGAAAACTCAGTATTTCAAAAATAAGGGAAAT
TTAAAAGAAAGAATTACAAACTCATGAAAATAAAAGAATTTTTAAAAACTGATTTTATGGTAATT
AAATAAT
Found at i:1337494 original size:24 final size:23
Alignment explanation
Indices: 1337441--1337507 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 23
1337431 AAAACCTCTT
* *
1337441 TTTAAATAAAATATTAATTTTCAAA
1 TTTAAA-AAAATA-AAATTATCAAA
*
1337466 -ATAAAGAAAATAAAATTATCAAA
1 TTTAAA-AAAATAAAATTATCAAA
1337489 TTTAAAAGAAATAAAATTA
1 TTTAAAA-AAATAAAATTA
1337508 AAAAATATAG
Statistics
Matches: 35, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
23 10 0.29
24 25 0.71
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (23 bp):
TTTAAAAAAATAAAATTATCAAA
Found at i:1337495 original size:29 final size:29
Alignment explanation
Indices: 1337444--1337510 Score: 73
Period size: 29 Copynumber: 2.3 Consensus size: 29
1337434 ACCTCTTTTT
* * *
1337444 AAATAAAATATTAATTTTCAAAATAAAGA
1 AAATAAAATATCAAATTTCAAAAGAAAGA
*
1337473 AAATAAAATTATCAAATTT-AAAAGAAATA
1 AAATAAAA-TATCAAATTTCAAAAGAAAGA
1337502 AAATTAAAA
1 AAA-TAAAA
1337511 AATATAGTGT
Statistics
Matches: 32, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
29 19 0.59
30 13 0.41
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (29 bp):
AAATAAAATATCAAATTTCAAAAGAAAGA
Found at i:1338374 original size:83 final size:84
Alignment explanation
Indices: 1338206--1338443 Score: 247
Period size: 83 Copynumber: 2.8 Consensus size: 84
1338196 TAAAATTGAC
* * * * * *
1338206 AAGTCAACAAAGGAT-AAAGAAATTTACCCCA-AACTAAGTCGACAGGTAAACAAGGGATGAAAG
1 AAGTCAACAAAGGATAAAAG-AGTTCA-CCAAGAACTAAGCCGACAAGTAAACAAGGGATGAAAA
1338269 GTTGACCACAGCTAAATCGAT
64 GTTGACCACAGCTAAATCGAT
* ** * * *
1338290 AAGTCAACAAAGGGTAAGGGAGTTTACCAAGAACTGAGCCGATC-AGTAAAC-AGAGATGAAAAG
1 AAGTCAACAAAGGATAAAAGAGTTCACCAAGAACTAAGCCGA-CAAGTAAACAAGGGATGAAAAG
1338353 TTGACCA-AGGCTAAA-CTGAT
65 TTGACCACA-GCTAAATC-GAT
* *
1338373 AAGTCAACAAAGGATAAAAGAGTTCACCAGGGACTAAGCCGACAAGTAAACAAGGGAT-AAAAGG
1 AAGTCAACAAAGGATAAAAGAGTTCACCAAGAACTAAGCCGACAAGTAAACAAGGGATGAAAA-G
1338437 TTGACCA
65 TTGACCA
1338444 GGGCAGCAAC
Statistics
Matches: 128, Mismatches: 18, Indels: 16
0.79 0.11 0.10
Matches are distributed among these distances:
82 3 0.02
83 75 0.59
84 47 0.37
85 3 0.02
ACGTcount: A:0.45, C:0.17, G:0.23, T:0.16
Consensus pattern (84 bp):
AAGTCAACAAAGGATAAAAGAGTTCACCAAGAACTAAGCCGACAAGTAAACAAGGGATGAAAAGT
TGACCACAGCTAAATCGAT
Found at i:1338803 original size:44 final size:44
Alignment explanation
Indices: 1338700--1339318 Score: 241
Period size: 44 Copynumber: 14.1 Consensus size: 44
1338690 AAGAGGTAAA
* * * * * * *
1338700 TTTGACTAGGGTGGTAACCATGCGTCAAATTAGAATAAAAAGA-
1 TTTGACTAGGGTGGTAACCATACGTTAGACTAAAATGAGAAGAG
* * *
1338743 TTCTGACCAAGGTGGTAACCATACGTTTGACTAAAATGAGAAGAG
1 TT-TGACTAGGGTGGTAACCATACGTTAGACTAAAATGAGAAGAG
** *
1338788 TTTGACTAGACTGGTAACCATACGTCA-A-TAAGAA-GAAGATAGA-
1 TTTGACTAGGGTGGTAACCATACGTTAGACTAA-AATG-AGA-AGAG
* * * * * *
1338831 TTTAACTAGGGTGGTAACCATAC-ATAAACTCAGAATGAAAAGAA
1 TTTGACTAGGGTGGTAACCATACGTTAGACT-AAAATGAGAAGAG
* * * *
1338875 TCTGACCAGGGTGGTAACCATACGTCAGACCAAAATGAGAAGAG
1 TTTGACTAGGGTGGTAACCATACGTTAGACTAAAATGAGAAGAG
* * *
1338919 TTTGACTAGGGTGGTAACCATACG-TAAAATGAGAATG-GAAAGAG
1 TTTGACTAGGGTGGTAACCATACGTTAGACT-AAAATGAG-AAGAG
* * * * * * *
1338963 CTTGACCAGGGTGGCAACCATACATCA-AGC-AAGAAAGAGGTAGA-
1 TTTGACTAGGGTGGTAACCATACGTTAGA-CTAA-AATGA-GAAGAG
* * * * * ** *
1339007 TTTGACCAGGGTGGT-ACCATGCATCA-AATCAACTTGAAAAGAG
1 TTTGACTAGGGTGGTAACCATACGTTAGACT-AAAATGAGAAGAG
* * * * * *
1339050 TTTGACTAGGGTGGTAACTATACGTCAAAC-AGGAAGGAGGCAGA-
1 TTTGACTAGGGTGGTAACCATACGTTAGACTA-AAATGA-GAAGAG
* * * * * * * * * *
1339094 TTTGACCAAGGTGGTAACCATGCATCAAATTAGAATGAAAAGAA
1 TTTGACTAGGGTGGTAACCATACGTTAGACTAAAATGAGAAGAG
* * * * * * *
1339138 TCTAACCAGGGTGTTAGCCATACATTAGACTAAAATGAAAAGAG
1 TTTGACTAGGGTGGTAACCATACGTTAGACTAAAATGAGAAGAG
* * * * * *
1339182 TTTAACTAGGGTGGTAGCCATACGTCAAAC-AAGAAAGAGGTAGA-
1 TTTGACTAGGGTGGTAACCATACGTTAGACTAA-AATGA-GAAGAG
* * * *
1339226 TTTGA-TGAGGGTGGTAACCATACATTA-AATCAAAATGAAAAGAA
1 TTTGACT-AGGGTGGTAACCATACGTTAGACT-AAAATGAGAAGAG
* * * * *
1339270 TCTGACTAGGGTGGTAACCATGCATTAGACTGAAATAAGAAGAG
1 TTTGACTAGGGTGGTAACCATACGTTAGACTAAAATGAGAAGAG
1339314 TTTGA
1 TTTGA
1339319 TCAGATATAG
Statistics
Matches: 427, Mismatches: 114, Indels: 69
0.70 0.19 0.11
Matches are distributed among these distances:
42 8 0.02
43 74 0.17
44 320 0.75
45 24 0.06
46 1 0.00
ACGTcount: A:0.39, C:0.14, G:0.24, T:0.22
Consensus pattern (44 bp):
TTTGACTAGGGTGGTAACCATACGTTAGACTAAAATGAGAAGAG
Found at i:1338954 original size:88 final size:86
Alignment explanation
Indices: 1338828--1339290 Score: 335
Period size: 88 Copynumber: 5.3 Consensus size: 86
1338818 AGAAGAAGAT
*
1338828 AGATTTAACTAGGGTGGTAACCATACAT-AAACTCAGAATGAAAAGAATCTGACCAGGGTGGTAA
1 AGATTTGACTAGGGTGGTAACCATACATCAAA-TCAGAATGAAAAGAATCTGACCAGGGTGGTAA
*
1338892 CCATACGTCAGACCAAAATGAGA
65 CCATACATCA-ACCAAAATGAGA
* * * * * *
1338915 AGAGTTTGACTAGGGTGGTAACCATACGTAAAATGAGAATGGAAAG-AGCTTGACCAGGGTGGCA
1 AGA-TTTGACTAGGGTGGTAACCATACATCAAATCAGAATGAAAAGAATC-TGACCAGGGTGGTA
* * *
1338979 ACCATACATCAAGCAAGAAAGAGGT
64 ACCATACATCAACCAA-AATGA-GA
* * * * * *
1339004 AGATTTGACCAGGGTGGT-ACCATGCATCAAATCA-ACTTGAAAAGAGTTTGACTAGGGTGGTAA
1 AGATTTGACTAGGGTGGTAACCATACATCAAATCAGA-ATGAAAAGAATCTGACCAGGGTGGTAA
* * * * * *
1339067 CTATACGTCAAACAGGAAGGAGGC
65 CCATACATCAACCA-AAATGA-GA
* * * * * * *
1339091 AGATTTGACCAAGGTGGTAACCATGCATCAAATTAGAATGAAAAGAATCTAACCAGGGTGTTAGC
1 AGATTTGACTAGGGTGGTAACCATACATCAAATCAGAATGAAAAGAATCTGACCAGGGTGGTAAC
* * *
1339156 CATACATTAGACTAAAATGAAA
66 CATACATCA-ACCAAAATGAGA
* * * * ** * **
1339178 AGAGTTTAACTAGGGTGGTAGCCATACGTCAAA-CAAGAAAGAGGTAG-ATTTGATGAGGGTGGT
1 AGA-TTTGACTAGGGTGGTAACCATACATCAAATC-AGAATGA-AAAGAATCTGACCAGGGTGGT
* * *
1339241 AACCATACATTAAATCAAAATGAAA
63 AACCATACA-TCAACCAAAATGAGA
*
1339266 AGAATCTGACTAGGGTGGTAACCAT
1 AG-ATTTGACTAGGGTGGTAACCAT
1339291 GCATTAGACT
Statistics
Matches: 292, Mismatches: 68, Indels: 31
0.75 0.17 0.08
Matches are distributed among these distances:
86 1 0.00
87 77 0.26
88 199 0.68
89 15 0.05
ACGTcount: A:0.39, C:0.15, G:0.25, T:0.21
Consensus pattern (86 bp):
AGATTTGACTAGGGTGGTAACCATACATCAAATCAGAATGAAAAGAATCTGACCAGGGTGGTAAC
CATACATCAACCAAAATGAGA
Found at i:1339109 original size:175 final size:174
Alignment explanation
Indices: 1338739--1339114 Score: 379
Period size: 175 Copynumber: 2.1 Consensus size: 174
1338729 TTAGAATAAA
** * * * *
1338739 AAGATTCTGACCAAGGTGGTAACCATACGTTTGACTAAAATGAGAAGAGTTTGACTAGACTGGTA
1 AAGATT-TGACCAAGGTGGTAACCATACGTTAAAATAAAATGAGAAGAGCTTGACCAGACTGGCA
* * *
1338804 ACCATACGTCAATAAGAAGAAGATAGATTTAACTAGGGTGGTAACCATACATAAACTCAGAATGA
65 ACCATACATCAACAAGAAGAAGATAGATTTAACCAGGGTGGTAACCATACATAAACTCAGAATGA
* *
1338869 AAAGAATCTGACCAGGGTGGTAACCATACGTCAGACCAAAATGAG
130 AAAGAATCTGACCAGGGTGGTAACCATACGTCAGAACAAAAGGAG
* * * **
1338914 AAGAGTTTGACTAGGGTGGTAACCATACG-TAAAATGAGAATG-GAAAGAGCTTGACCAGGGTGG
1 AAGA-TTTGACCAAGGTGGTAACCATACGTTAAAAT-AAAATGAG-AAGAGCTTGACCAGACTGG
* * *
1338977 CAACCATACATCAAGCAAGAA-AGAGGTAGATTTGACCAGGGTGGT-ACCATGCATCAAA-TCA-
63 CAACCATACATCAA-CAAGAAGA-AGATAGATTTAACCAGGGTGGTAACCATACAT-AAACTCAG
* * * * * *
1339038 ACTTGAAAAGAGTTTGACTAGGGTGGTAACTATACGTCA-AACAGGAAGGAGG
125 A-ATGAAAAGAATCTGACCAGGGTGGTAACCATACGTCAGAACA-AAAGGA-G
*
1339090 CAGATTTGACCAAGGTGGTAACCAT
1 AAGATTTGACCAAGGTGGTAACCAT
1339115 GCATCAAATT
Statistics
Matches: 164, Mismatches: 28, Indels: 18
0.78 0.13 0.09
Matches are distributed among these distances:
174 8 0.05
175 123 0.75
176 33 0.20
ACGTcount: A:0.38, C:0.16, G:0.25, T:0.21
Consensus pattern (174 bp):
AAGATTTGACCAAGGTGGTAACCATACGTTAAAATAAAATGAGAAGAGCTTGACCAGACTGGCAA
CCATACATCAACAAGAAGAAGATAGATTTAACCAGGGTGGTAACCATACATAAACTCAGAATGAA
AAGAATCTGACCAGGGTGGTAACCATACGTCAGAACAAAAGGAG
Found at i:1339162 original size:175 final size:176
Alignment explanation
Indices: 1338827--1339150 Score: 372
Period size: 175 Copynumber: 1.8 Consensus size: 176
1338817 AAGAAGAAGA
*
1338827 TAGATTTAACTAGGGTGGTAACCATACATAAACTCAGAATGAAAAGAATCTGACCAGGGTGGTAA
1 TAGATTTAACCAGGGTGGTAACCATACATAAACTCAGAATGAAAAGAATCTGACCAGGGTGGTAA
* * * * * *
1338892 CCATACGTCAGACCAAAATGAGAAGAGTTTGACTAGGGTGGTAACCATACGTAAAATGAGAATGG
66 CCATACGTCAGAACAAAAGGAGAAGAGTTTGACCAAGGTGGTAACCATACATAAAATGAGAATGA
*
1338957 AAAGAGCTTGACCAGGGTGGCAACCATACATCAAGCAAGAAAGAGG
131 AAAGAGCTTAACCAGGGTGGCAACCATACATCAAGCAAGAAAGAGG
* * * * * *
1339003 TAGATTTGACCAGGGTGGT-ACCATGCATCAAA-TCA-ACTTGAAAAGAGTTTGACTAGGGTGGT
1 TAGATTTAACCAGGGTGGTAACCATACAT-AAACTCAGA-ATGAAAAGAATCTGACCAGGGTGGT
* * * * * *
1339065 AACTATACGTCA-AACAGGAAGGAGGCAGA-TTTGACCAAGGTGGTAACCATGCATCAAATTAGA
64 AACCATACGTCAGAACA-AAAGGA-GAAGAGTTTGACCAAGGTGGTAACCATACATAAAATGAGA
*
1339128 ATGAAAAGA-ATCTAACCAGGGTG
127 ATGAAAAGAGCT-TAACCAGGGTG
1339151 TTAGCCATAC
Statistics
Matches: 122, Mismatches: 21, Indels: 11
0.79 0.14 0.07
Matches are distributed among these distances:
174 5 0.04
175 93 0.76
176 24 0.20
ACGTcount: A:0.38, C:0.16, G:0.26, T:0.20
Consensus pattern (176 bp):
TAGATTTAACCAGGGTGGTAACCATACATAAACTCAGAATGAAAAGAATCTGACCAGGGTGGTAA
CCATACGTCAGAACAAAAGGAGAAGAGTTTGACCAAGGTGGTAACCATACATAAAATGAGAATGA
AAAGAGCTTAACCAGGGTGGCAACCATACATCAAGCAAGAAAGAGG
Found at i:1344012 original size:149 final size:149
Alignment explanation
Indices: 1343742--1344041 Score: 600
Period size: 149 Copynumber: 2.0 Consensus size: 149
1343732 TAATCAATAT
1343742 TTCCATAAATATTCATGATAAGTTAAGATATAATTTTTATAAAAAAATAATAAATACATTTTAAA
1 TTCCATAAATATTCATGATAAGTTAAGATATAATTTTTATAAAAAAATAATAAATACATTTTAAA
1343807 AGTTTAATTTGATTAAGAACAAAATAAGCAAGTGACAGGAAGAAATCAAATATTATTACAACTTG
66 AGTTTAATTTGATTAAGAACAAAATAAGCAAGTGACAGGAAGAAATCAAATATTATTACAACTTG
1343872 TACATTGTCGCTAATCCCA
131 TACATTGTCGCTAATCCCA
1343891 TTCCATAAATATTCATGATAAGTTAAGATATAATTTTTATAAAAAAATAATAAATACATTTTAAA
1 TTCCATAAATATTCATGATAAGTTAAGATATAATTTTTATAAAAAAATAATAAATACATTTTAAA
1343956 AGTTTAATTTGATTAAGAACAAAATAAGCAAGTGACAGGAAGAAATCAAATATTATTACAACTTG
66 AGTTTAATTTGATTAAGAACAAAATAAGCAAGTGACAGGAAGAAATCAAATATTATTACAACTTG
1344021 TACATTGTCGCTAATCCCA
131 TACATTGTCGCTAATCCCA
1344040 TT
1 TT
1344042 GACCCTATTT
Statistics
Matches: 151, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
149 151 1.00
ACGTcount: A:0.46, C:0.11, G:0.10, T:0.33
Consensus pattern (149 bp):
TTCCATAAATATTCATGATAAGTTAAGATATAATTTTTATAAAAAAATAATAAATACATTTTAAA
AGTTTAATTTGATTAAGAACAAAATAAGCAAGTGACAGGAAGAAATCAAATATTATTACAACTTG
TACATTGTCGCTAATCCCA
Found at i:1353363 original size:20 final size:19
Alignment explanation
Indices: 1353317--1353368 Score: 72
Period size: 18 Copynumber: 2.7 Consensus size: 19
1353307 CTGCCAATTT
1353317 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
1353336 CA-GTATCGATACAATGCATA
1 CATGTATCGATACAATG-A-A
1353356 -ATGTATCGATACA
1 CATGTATCGATACA
1353369 TCTAGATGTG
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
18 14 0.47
19 4 0.13
20 12 0.40
ACGTcount: A:0.40, C:0.17, G:0.15, T:0.27
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1355933 original size:13 final size:13
Alignment explanation
Indices: 1355915--1355957 Score: 61
Period size: 13 Copynumber: 3.4 Consensus size: 13
1355905 TAGTAACCCT
1355915 TATATTGATACAA
1 TATATTGATACAA
1355928 TATATTGATACAA
1 TATATTGATACAA
* *
1355941 TGTATCGATACAA
1 TATATTGATACAA
1355954 -ATAT
1 TATAT
1355958 CCTTGTATCG
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
12 3 0.11
13 24 0.89
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.37
Consensus pattern (13 bp):
TATATTGATACAA
Found at i:1359828 original size:14 final size:14
Alignment explanation
Indices: 1359793--1359831 Score: 53
Period size: 14 Copynumber: 2.8 Consensus size: 14
1359783 AACATGAATA
*
1359793 ATATATAAAAAAAT
1 ATATATAATAAAAT
1359807 ATATATAATAAAAT
1 ATATATAATAAAAT
1359821 AGTA-ATAATAA
1 A-TATATAATAA
1359832 TTAATTAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 21 0.91
15 2 0.09
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (14 bp):
ATATATAATAAAAT
Found at i:1360063 original size:17 final size:17
Alignment explanation
Indices: 1360037--1360081 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
1360027 TACGGGTCAT
*
1360037 TGCATGCTTTTACTTCA
1 TGCATGCTTTCACTTCA
* *
1360054 TGCATACTTTCATTTCA
1 TGCATGCTTTCACTTCA
1360071 TGCATGCTTTC
1 TGCATGCTTTC
1360082 TTTCATGTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.18, C:0.24, G:0.11, T:0.47
Consensus pattern (17 bp):
TGCATGCTTTCACTTCA
Found at i:1360137 original size:29 final size:29
Alignment explanation
Indices: 1360101--1360224 Score: 116
Period size: 29 Copynumber: 4.4 Consensus size: 29
1360091 TCACTCATGA
1360101 GTTCATTTCATGCATGCATTTCACGTAAT
1 GTTCATTTCATGCATGCATTTCACGTAAT
* *
1360130 GTTCATTTCATGCATTGCATTTCATG-CAT
1 GTTCATTTCATGCA-TGCATTTCACGTAAT
* * ***
1360159 G--C-TTTCTTTCATG--TTTCACACCAT
1 GTTCATTTCATGCATGCATTTCACGTAAT
1360183 GAGTTCATTTCATGCATGCATTTCACGTAAT
1 --GTTCATTTCATGCATGCATTTCACGTAAT
1360214 GTTCATTTCAT
1 GTTCATTTCAT
1360225 TACATTGCTT
Statistics
Matches: 75, Mismatches: 11, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
23 5 0.07
24 3 0.04
25 2 0.03
26 8 0.11
27 1 0.01
28 1 0.01
29 37 0.49
30 10 0.13
31 8 0.11
ACGTcount: A:0.22, C:0.22, G:0.13, T:0.44
Consensus pattern (29 bp):
GTTCATTTCATGCATGCATTTCACGTAAT
Found at i:1360152 original size:14 final size:14
Alignment explanation
Indices: 1360104--1360158 Score: 58
Period size: 14 Copynumber: 3.9 Consensus size: 14
1360094 CTCATGAGTT
1360104 CATTTCATGCA-TG
1 CATTTCATGCATTG
* * *
1360117 CATTTCACGTAATGTT
1 CATTTCATG-CAT-TG
1360133 CATTTCATGCATTG
1 CATTTCATGCATTG
1360147 CATTTCATGCAT
1 CATTTCATGCAT
1360159 GCTTTCTTTC
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
13 8 0.24
14 14 0.42
15 2 0.06
16 9 0.27
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.42
Consensus pattern (14 bp):
CATTTCATGCATTG
Found at i:1360210 original size:84 final size:84
Alignment explanation
Indices: 1360064--1360242 Score: 308
Period size: 84 Copynumber: 2.1 Consensus size: 84
1360054 TGCATACTTT
*
1360064 CATTTCATGCATGCTTTCTTTCATGTTTCACTCATGAGTTCATTTCATGCATGCATTTCACGTAA
1 CATTTCATGCATGCTTTCTTTCATGTTTCACCCATGAGTTCATTTCATGCATGCATTTCACGTAA
*
1360129 TGTTCATTTCA-TGCATTG
66 TGTTCATTTCATTACATTG
1360147 CATTTCATGCATGCTTTCTTTCATGTTTCACACCATGAGTTCATTTCATGCATGCATTTCACGTA
1 CATTTCATGCATGCTTTCTTTCATGTTTCAC-CCATGAGTTCATTTCATGCATGCATTTCACGTA
1360212 ATGTTCATTTCATTACATTG
65 ATGTTCATTTCATTACATTG
*
1360232 C-TTTCTTGCAT
1 CATTTCATGCAT
1360243 TCATAATGAA
Statistics
Matches: 91, Mismatches: 3, Indels: 3
0.94 0.03 0.03
Matches are distributed among these distances:
83 31 0.34
84 53 0.58
85 7 0.08
ACGTcount: A:0.21, C:0.22, G:0.12, T:0.45
Consensus pattern (84 bp):
CATTTCATGCATGCTTTCTTTCATGTTTCACCCATGAGTTCATTTCATGCATGCATTTCACGTAA
TGTTCATTTCATTACATTG
Found at i:1360474 original size:33 final size:33
Alignment explanation
Indices: 1360428--1360496 Score: 102
Period size: 33 Copynumber: 2.1 Consensus size: 33
1360418 AAAAAGCAAT
* * *
1360428 AATGGAATTGTTGCTAAAATGAATGAGATAAGA
1 AATGAAATAGTTGCTAAAATGAATGAGATAAAA
*
1360461 AATGAAATAGTTGCTGAAATGAATGAGATAAAA
1 AATGAAATAGTTGCTAAAATGAATGAGATAAAA
1360494 AAT
1 AAT
1360497 AGTAGTTGAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.49, C:0.03, G:0.22, T:0.26
Consensus pattern (33 bp):
AATGAAATAGTTGCTAAAATGAATGAGATAAAA
Found at i:1360926 original size:24 final size:24
Alignment explanation
Indices: 1360881--1360933 Score: 56
Period size: 24 Copynumber: 2.2 Consensus size: 24
1360871 GAACAGCAAT
* *
1360881 CAAAAAACAAGACAAACCGAAACAG
1 CAAAAAACAAAACAAACAGAAA-AG
*
1360906 CAAAAAA-AAAACAAATAGAAAAG
1 CAAAAAACAAAACAAACAGAAAAG
1360929 -AAAAA
1 CAAAAA
1360934 GGTATAGAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 5 0.20
23 2 0.08
24 11 0.44
25 7 0.28
ACGTcount: A:0.74, C:0.15, G:0.09, T:0.02
Consensus pattern (24 bp):
CAAAAAACAAAACAAACAGAAAAG
Found at i:1361980 original size:20 final size:22
Alignment explanation
Indices: 1361941--1361986 Score: 69
Period size: 20 Copynumber: 2.2 Consensus size: 22
1361931 CGTCGGGTAC
*
1361941 GAAATGTAACTTTCAAAATTTA
1 GAAATGTAAATTTCAAAATTTA
1361963 GAAAT-TAAATTT-AAAATTTA
1 GAAATGTAAATTTCAAAATTTA
1361983 GAAA
1 GAAA
1361987 AATTTAGCTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 12 0.52
21 6 0.26
22 5 0.22
ACGTcount: A:0.52, C:0.04, G:0.09, T:0.35
Consensus pattern (22 bp):
GAAATGTAAATTTCAAAATTTA
Found at i:1365455 original size:17 final size:17
Alignment explanation
Indices: 1365435--1365469 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1365425 TAGATAGCAA
1365435 AAAAAAAAAAAAAGAAG
1 AAAAAAAAAAAAAGAAG
* *
1365452 AAAAAGAAAAAGAGAAG
1 AAAAAAAAAAAAAGAAG
1365469 A
1 A
1365470 GGAAATAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAAGAAG
Found at i:1366840 original size:17 final size:17
Alignment explanation
Indices: 1366820--1366854 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1366810 GTAGATAGCA
1366820 AAAAAAAAAAAAAGAAG
1 AAAAAAAAAAAAAGAAG
* *
1366837 AAAAAGAAAAAGAGAAG
1 AAAAAAAAAAAAAGAAG
1366854 A
1 A
1366855 GGAAATAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAAGAAG
Found at i:1366854 original size:20 final size:18
Alignment explanation
Indices: 1366819--1366867 Score: 53
Period size: 20 Copynumber: 2.6 Consensus size: 18
1366809 TGTAGATAGC
1366819 AAAAAAAAAAAAAAGAAG
1 AAAAAAAAAAAAAAGAAG
* *
1366837 AAAAAGAAAAAGAGAAGAGG
1 AAAAA-AAAAA-AAAAGAAG
1366857 AAATAAAAAAA
1 AAA-AAAAAAA
1366868 CACTACATCC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 5 0.19
19 5 0.19
20 14 0.54
21 2 0.08
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (18 bp):
AAAAAAAAAAAAAAGAAG
Found at i:1368229 original size:17 final size:17
Alignment explanation
Indices: 1368209--1368243 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
1368199 TAGATAGCAA
1368209 AAAAAAAAAAAAAGAAG
1 AAAAAAAAAAAAAGAAG
* *
1368226 AAAAAGAAAAAGAGAAG
1 AAAAAAAAAAAAAGAAG
1368243 A
1 A
1368244 GGAAATAAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (17 bp):
AAAAAAAAAAAAAGAAG
Found at i:1370087 original size:91 final size:91
Alignment explanation
Indices: 1369976--1370175 Score: 276
Period size: 91 Copynumber: 2.2 Consensus size: 91
1369966 ACTCAGCCCT
* * * * *
1369976 TAGACGGTATTGATGCATCACAAAGCCCGATATCCTTGGGGCAAGGAGAACCAACCATTTATTTC
1 TAGATGGTACTGATACATCACAAAGCCCGATATCCTTGGGGCAAGGAGAACCAACAACTTATTTC
*
1370041 TAATCATATCCT-TCCTCTTCAACCAC
66 TAATCAT-GCCTCTCCTCTTCAACCAC
* *
1370067 TAGATGGTACTGATACATCACAAAGCCCGATATCCTTGGGGCAAGGAGAATCGACAACTTATTTC
1 TAGATGGTACTGATACATCACAAAGCCCGATATCCTTGGGGCAAGGAGAACCAACAACTTATTTC
* *
1370132 TAATCATGCCTCTCCTCTTTAATCAC
66 TAATCATGCCTCTCCTCTTCAACCAC
* *
1370158 TAAATGGTACTAATACAT
1 TAGATGGTACTGATACAT
1370176 TGAAACTCAC
Statistics
Matches: 96, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
90 3 0.03
91 93 0.97
ACGTcount: A:0.31, C:0.25, G:0.15, T:0.28
Consensus pattern (91 bp):
TAGATGGTACTGATACATCACAAAGCCCGATATCCTTGGGGCAAGGAGAACCAACAACTTATTTC
TAATCATGCCTCTCCTCTTCAACCAC
Found at i:1370984 original size:44 final size:44
Alignment explanation
Indices: 1370919--1371016 Score: 133
Period size: 44 Copynumber: 2.2 Consensus size: 44
1370909 CTGACGTATG
**
1370919 GTTACCACCTTAGTCAGATTTTTCTCATTCTAATTCGACATCTA
1 GTTACCACCCCAGTCAGATTTTTCTCATTCTAATTCGACATCTA
* * * * *
1370963 GTTACCACCCCAGTCATATTTTTCTCATTTTGATTCGACATTTG
1 GTTACCACCCCAGTCAGATTTTTCTCATTCTAATTCGACATCTA
1371007 GTTACCACCC
1 GTTACCACCC
1371017 TGGTCAAATC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
44 47 1.00
ACGTcount: A:0.22, C:0.28, G:0.10, T:0.40
Consensus pattern (44 bp):
GTTACCACCCCAGTCAGATTTTTCTCATTCTAATTCGACATCTA
Found at i:1371233 original size:84 final size:84
Alignment explanation
Indices: 1371078--1372010 Score: 795
Period size: 84 Copynumber: 11.0 Consensus size: 84
1371068 CCATATGAAT
* * * * *
1371078 TTTCCTACCCTCAGTCTACCTGTC-GACTTTGACCTTGGAGACTGCCTCATATAAAGTCTACCTG
1 TTTCCTACCTTCAGTCTGCCTGTCAG-CTTTGACCCTGGAGACTGCCTCATCTAAAGTCTGCCTG
* * *
1371142 TCAGCTTTGACCCTAGAGAC
65 TCGGCTTTGACCTTGGAGAC
* * * * * * *
1371162 TTTCCTACCTTTAGTCTGCTTATCGGCTTTGACCCTAGAGACTGCCTCATCTAATGTCTGCCTAT
1 TTTCCTACCTTCAGTCTGCCTGTCAGCTTTGACCCTGGAGACTGCCTCATCTAAAGTCTGCCTGT
* *
1371227 CGGCTTTAACCTTAGAGAC
66 CGGCTTTGACCTTGGAGAC
* * * * * *
1371246 TTTCTTACTCCTTCAGTTTGTCTGTCAGCTTTGACCTTGGAGACTGCTTCATCTAAAGTTTGCCT
1 TTTCCTA--CCTTCAGTCTGCCTGTCAGCTTTGACCCTGGAGACTGCCTCATCTAAAGTCTGCCT
*
1371311 GTTGGCTTTGACCTTGGAGAC
64 GTCGGCTTTGACCTTGGAGAC
* * * *
1371332 TTTCCTACCTTTAGTATGCCTGTCAGCTTTCACCCTGGAGACTGCCTCATCTAAAGTCTGCTTGT
1 TTTCCTACCTTCAGTCTGCCTGTCAGCTTTGACCCTGGAGACTGCCTCATCTAAAGTCTGCCTGT
*
1371397 CGGTTTTGACCTTGGAGAC
66 CGGCTTTGACCTTGGAGAC
* * * * *
1371416 TTTCCAACCCTCAGTCTGCCTGTCGGCTTTGACCTTGGAGAATGCCTCATCTAAAGTCTGCCTGT
1 TTTCCTACCTTCAGTCTGCCTGTCAGCTTTGACCCTGGAGACTGCCTCATCTAAAGTCTGCCTGT
* *
1371481 TGGCTTTGATCC-TAGAGAC
66 CGGCTTTGA-CCTTGGAGAC
* * * * * * *
1371500 TTTCCTTCCCTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCACCTAAAGTTTGCCCGT
1 TTTCCTACCTTCAGTCTGCCTGTCAGCTTTGACCCTGGAGACTGCCTCATCTAAAGTCTGCCTGT
*
1371565 CGGCTTTGACCCTGGAGAC
66 CGGCTTTGACCTTGGAGAC
* * * * * *
1371584 TTTCCTACCCTT-AGACTGCTTGTCAGCTTTGACACTGGAGACTGCCTCATTTAAAGTCTACTTG
1 TTTCCTA-CCTTCAGTCTGCCTGTCAGCTTTGACCCTGGAGACTGCCTCATCTAAAGTCTGCCTG
**
1371648 TTAGCTTTGACCTTGGAGAC
65 TCGGCTTTGACCTTGGAGAC
** * * * * *
1371668 TTTTTTACCCTTCAGTCTGCCCGTCGGCTTTGACCCAGGAGACTGTCTCATCTAAAGTCTGTCTG
1 TTTCCTA-CCTTCAGTCTGCCTGTCAGCTTTGACCCTGGAGACTGCCTCATCTAAAGTCTGCCTG
*
1371733 TCGACTTTGA-CTATGGAGAC
65 TCGGCTTTGACCT-TGGAGAC
* * ** * * ** *
1371753 TTTCCTACCCTTCAGTCTGCCTATCAGCTTTGACCCTAGAGACTATCTTACCCTTCAGTCTGCTT
1 TTTCCTA-CCTTCAGTCTGCCTGTCAGCTTTGACCCTGGAGACTGCCTCA-TCTAAAGTCTGCCT
* * * *
1371818 GTTGGCTTTAACCCTAGAGA-
64 GTCGGCTTTGACCTTGGAGAC
* * ** * * ** * * *
1371838 TTGCCTCATCTAAAGTCTGCGTGTC-GACTTTGACCCTAGAGACT-TTTCTACCCT-GAGTCTGA
1 TTTCCT-ACCTTCAGTCTGCCTGTCAG-CTTTGACCCTGGAGACTGCCTC-A-TCTAAAGTCTGC
* *
1371900 CTGTCGGCTTTGACCCTAGAGAAC
62 CTGTCGGCTTTGACCTTGGAG-AC
** * * * * * * * *
1371924 TTTTTTACCCTCAATCTACCGGTCAGCTTTGACCCTGGAGACTGTCTCACCTCAAGTATGCCTGT
1 TTTCCTACCTTCAGTCTGCCTGTCAGCTTTGACCCTGGAGACTGCCTCATCTAAAGTCTGCCTGT
*
1371989 TGGCTTTGA-CTCTGGAGAC
66 CGGCTTTGACCT-TGGAGAC
1372008 TTT
1 TTT
1372011 TTCACCTTTT
Statistics
Matches: 686, Mismatches: 144, Indels: 38
0.79 0.17 0.04
Matches are distributed among these distances:
83 2 0.00
84 395 0.58
85 190 0.28
86 98 0.14
87 1 0.00
ACGTcount: A:0.18, C:0.28, G:0.20, T:0.34
Consensus pattern (84 bp):
TTTCCTACCTTCAGTCTGCCTGTCAGCTTTGACCCTGGAGACTGCCTCATCTAAAGTCTGCCTGT
CGGCTTTGACCTTGGAGAC
Found at i:1371501 original size:168 final size:168
Alignment explanation
Indices: 1371078--1371998 Score: 857
Period size: 170 Copynumber: 5.4 Consensus size: 168
1371068 CCATATGAAT
* *
1371078 TTTCCTACCCTCAGTCTACCTGTC-GACTTTGACCTTGGAGACTGCCTCATATAAAGTCTACCTG
1 TTTCCTACCCTCAGTCTGCCTGTCAG-CTTTGACCTTGGAGACTGCCTCATCTAAAGTCTACCTG
* * * * * *
1371142 TCAGCTTTGACCCTAGAGACTTTCCTACCTTTAGTCTGCTTATCGGCTTTGACCCTAGAGACTGC
65 TTAGCTTTGACCTTAGAGACTTTCCTACCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTGC
* * * *
1371207 CTCATCTAATGTCTGCCTATCGGCTTTAACCTTAGAGAC
130 CTCATCTAAAGTCTGCCTGTCGGCTTTGACCTTGGAGAC
* * * * * *
1371246 TTTCTTACTCCTTCAGTTTGTCTGTCAGCTTTGACCTTGGAGACTGCTTCATCTAAAGTTTGCCT
1 TTTCCTAC-CC-TCAGTCTGCCTGTCAGCTTTGACCTTGGAGACTGCCTCATCTAAAGTCTACCT
* * * * * *
1371311 GTTGGCTTTGACCTTGGAGACTTTCCTACCTTTAGTATGCCTGTCAGCTTTCACCCTGGAGACTG
64 GTTAGCTTTGACCTTAGAGACTTTCCTACCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTG
* *
1371376 CCTCATCTAAAGTCTGCTTGTCGGTTTTGACCTTGGAGAC
129 CCTCATCTAAAGTCTGCCTGTCGGCTTTGACCTTGGAGAC
* * * *
1371416 TTTCCAACCCTCAGTCTGCCTGTCGGCTTTGACCTTGGAGAATGCCTCATCTAAAGTCTGCCTGT
1 TTTCCTACCCTCAGTCTGCCTGTCAGCTTTGACCTTGGAGACTGCCTCATCTAAAGTCTACCTGT
* * * *
1371481 TGGCTTTGATCC-TAGAGACTTTCCTTCCCTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTGC
66 TAGCTTTGA-CCTTAGAGACTTTCCTACCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTGC
* * * *
1371545 CTCACCTAAAGTTTGCCCGTCGGCTTTGACCCTGGAGAC
130 CTCATCTAAAGTCTGCCTGTCGGCTTTGACCTTGGAGAC
* * * * *
1371584 TTTCCTACCCTTAGACTGCTTGTCAGCTTTGACAC-TGGAGACTGCCTCATTTAAAGTCTACTTG
1 TTTCCTACCCTCAGTCTGCCTGTCAGCTTTGAC-CTTGGAGACTGCCTCATCTAAAGTCTACCTG
* ** * *
1371648 TTAGCTTTGACCTTGGAGACTTTTTTACCCTTCAGTCTGCCCGTCGGCTTTGACCCAGGAGACTG
65 TTAGCTTTGACCTTAGAGACTTTCCTA-CCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTG
* * *
1371713 TCTCATCTAAAGTCTGTCTGTCGACTTTGA-CTATGGAGAC
129 CCTCATCTAAAGTCTGCCTGTCGGCTTTGACCT-TGGAGAC
* * * ** * * ** * *
1371753 TTTCCTACCCTTCAGTCTGCCTATCAGCTTTGACCCTAGAGACTATCTTACCCTTCAGTCTGCTT
1 TTTCCTACCC-TCAGTCTGCCTGTCAGCTTTGACCTTGGAGACTGCCTCA-TCTAAAGTCTACCT
* * * * * ** * * *
1371818 GTTGGCTTTAACCCTAGAGA-TTGCCTCATCTAAAGTCTGCGTGTCGACTTTGACCCTAGAGACT
64 GTTAGCTTTGACCTTAGAGACTTTCCT-ACCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACT
** * * * * *
1371882 -TTTCTACCCT-GAGTCTGACTGTCGGCTTTGACCCTAGAGAAC
128 GCCTC-A-TCTAAAGTCTGCCTGTCGGCTTTGACCTTGGAG-AC
** * * * * * * * * *
1371924 TTTTTTACCCTCAATCTACCGGTCAGCTTTGACCCTGGAGACTGTCTCACCTCAAGTATGCCTGT
1 TTTCCTACCCTCAGTCTGCCTGTCAGCTTTGACCTTGGAGACTGCCTCATCTAAAGTCTACCTGT
*
1371989 TGGCTTTGAC
66 TAGCTTTGAC
1371999 TCTGGAGACT
Statistics
Matches: 617, Mismatches: 120, Indels: 31
0.80 0.16 0.04
Matches are distributed among these distances:
167 2 0.00
168 215 0.35
169 106 0.17
170 254 0.41
171 40 0.06
ACGTcount: A:0.18, C:0.28, G:0.19, T:0.34
Consensus pattern (168 bp):
TTTCCTACCCTCAGTCTGCCTGTCAGCTTTGACCTTGGAGACTGCCTCATCTAAAGTCTACCTGT
TAGCTTTGACCTTAGAGACTTTCCTACCTTCAGTCTGCCTGTCGGCTTTGACCCTGGAGACTGCC
TCATCTAAAGTCTGCCTGTCGGCTTTGACCTTGGAGAC
Found at i:1371825 original size:128 final size:126
Alignment explanation
Indices: 1371422--1372010 Score: 417
Period size: 127 Copynumber: 4.6 Consensus size: 126
1371412 AGACTTTCCA
* ** * * * *
1371422 ACCC-TCAGTCTGCCTGTCGGCTTTGACCTTGGAGAATGCCTCATCTAAAGTCTGCCTGTTGGCT
1 ACCCTTCAGTCTGCCCGTCGGCTTTGACCCAGGAGACTGTCTCATCTAAAGTCTG-CTGTCGACT
* * * * * * * *** *
1371486 TTGA-TCCTAGAGACTTTCCTTCCCTCAGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTC
65 TTGACT-CTGGAGACTTTCCTACCCTCAGTCTGACTATCAGCTTTGACCCTAGAGACTTTTTT
** * * * * * *
1371548 A-CCTAAAGTTTGCCCGTCGGCTTTGACCCTGGAGACTTTC-CTACCCT-TAGACTGCTTGTC-A
1 ACCCTTCAGTCTGCCCGTCGGCTTTGACCCAGGAGACTGTCTC-A-TCTAAAGTCTGC-TGTCGA
* * ** * * * * *
1371609 GCTTTGACACTGGAGAC-TGCCT-CATTTAAAGTCT-ACTTGTTAGCTTTGACCTTGGAGACTTT
63 -CTTTGACTCTGGAGACTTTCCTAC-CCT-CAGTCTGAC-TATCAGCTTTGACCCTAGAGACTTT
1371671 TTT
124 TTT
1371674 ACCCTTCAGTCTGCCCGTCGGCTTTGACCCAGGAGACTGTCTCATCTAAAGTCTGTCTGTCGACT
1 ACCCTTCAGTCTGCCCGTCGGCTTTGACCCAGGAGACTGTCTCATCTAAAGTCTG-CTGTCGACT
* * * *
1371739 TTGACTATGGAGACTTTCCTACCCTTCAGTCTGCCTATCAGCTTTGACCCTAGAGACTATCTT
65 TTGACTCTGGAGACTTTCCTACCC-TCAGTCTGACTATCAGCTTTGACCCTAGAGACTTTTTT
** * * * *
1371802 ACCCTTCAGTCTGCTTGTTGGCTTTAACCCTA-GAGATTGCCTCATCTAAAGTCTGCGTGTCGAC
1 ACCCTTCAGTCTGCCCGTCGGCTTTGACCC-AGGAGACTGTCTCATCTAAAGTCTGC-TGTCGAC
* * * * * *
1371866 TTTGACCCTAGAGACTTTTCTACCCTGAGTCTGACTGTCGGCTTTGACCCTAGAGAACTTTTTT
64 TTTGACTCTGGAGACTTTCCTACCCTCAGTCTGACTATCAGCTTTGACCCTAGAG-ACTTTTTT
* * * * * * * * * *
1371930 ACCC-TCAATCTACCGGTCAGCTTTGACCCTGGAGACTGTCTCACCTCAAGTATGCCTGTTGGCT
1 ACCCTTCAGTCTGCCCGTCGGCTTTGACCCAGGAGACTGTCTCATCTAAAGTCTG-CTGTCGACT
1371994 TTGACTCTGGAGACTTT
65 TTGACTCTGGAGACTTT
1372011 TTCACCTTTT
Statistics
Matches: 360, Mismatches: 80, Indels: 45
0.74 0.16 0.09
Matches are distributed among these distances:
124 1 0.00
125 10 0.03
126 81 0.22
127 144 0.40
128 120 0.33
129 4 0.01
ACGTcount: A:0.18, C:0.29, G:0.20, T:0.33
Consensus pattern (126 bp):
ACCCTTCAGTCTGCCCGTCGGCTTTGACCCAGGAGACTGTCTCATCTAAAGTCTGCTGTCGACTT
TGACTCTGGAGACTTTCCTACCCTCAGTCTGACTATCAGCTTTGACCCTAGAGACTTTTTT
Found at i:1371855 original size:85 final size:84
Alignment explanation
Indices: 1371766--1371921 Score: 201
Period size: 85 Copynumber: 1.8 Consensus size: 84
1371756 CCTACCCTTC
*
1371766 AGTCTGCCTATC-AGCTTTGACCCTAGAGACTATCT-TACCCTTCAGTCTG-CTTGTTGGCTTTA
1 AGTCTGCCTATCGA-CTTTGACCCTAGAGACT-TCTCTACCC-TCAGTCTGAC-TGTCGGCTTTA
1371828 ACCCTAGAGATTGCCTCATCTAA
62 ACCCTAGAGATTGCCTCATCTAA
* * * * *
1371851 AGTCTGCGTGTCGACTTTGACCCTAGAGACTTTTCTACCCTGAGTCTGACTGTCGGCTTTGACCC
1 AGTCTGCCTATCGACTTTGACCCTAGAGACTTCTCTACCCTCAGTCTGACTGTCGGCTTTAACCC
1371916 TAGAGA
66 TAGAGA
1371922 ACTTTTTTAC
Statistics
Matches: 62, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
84 28 0.45
85 33 0.53
86 1 0.02
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.33
Consensus pattern (84 bp):
AGTCTGCCTATCGACTTTGACCCTAGAGACTTCTCTACCCTCAGTCTGACTGTCGGCTTTAACCC
TAGAGATTGCCTCATCTAA
Found at i:1371897 original size:42 final size:41
Alignment explanation
Indices: 1371652--1371936 Score: 152
Period size: 43 Copynumber: 6.7 Consensus size: 41
1371642 TACTTGTTAG
* * * * *
1371652 CTTTGACCTTGGAGACTTTTTTACCCTTCAGTCTGCCCGTCGG
1 CTTTGACCCTAGAGACTTTTCTACCC-TCAGTCTG-CTGTCGA
* * *
1371695 CTTTGACCC-AGGAGAC-TGTCT-CATCTAAAGTCTGTCTGTCGA
1 CTTTGACCCTA-GAGACTTTTCTAC-CCT-CAGTCTG-CTGTCGA
** * * *
1371737 CTTTGACTATGGAGACTTTCCTACCCTTCAGTCTGCCTATC-A
1 CTTTGACCCTAGAGACTTTTCTACCC-TCAGTCTG-CTGTCGA
* * *
1371779 GCTTTGACCCTAGAGAC-TATCTTACCCTTCAGTCTGCTTGTTGG
1 -CTTTGACCCTAGAGACTTTTC-TACCC-TCAGTCTGC-TGTCGA
* ** * *
1371823 CTTTAACCCTAGAGA-TTGCCT-CATCTAAAGTCTGCGTGTCGA
1 CTTTGACCCTAGAGACTTTTCTAC-CCT-CAGTCTGC-TGTCGA
* *
1371865 CTTTGACCCTAGAGACTTTTCTACCCTGAGTCTGACTGTCGG
1 CTTTGACCCTAGAGACTTTTCTACCCTCAGTCTG-CTGTCGA
*
1371907 CTTTGACCCTAGAGAACTTTTTTACCCTCA
1 CTTTGACCCTAGAG-ACTTTTCTACCCTCA
1371937 ATCTACCGGT
Statistics
Matches: 182, Mismatches: 42, Indels: 36
0.70 0.16 0.14
Matches are distributed among these distances:
41 4 0.02
42 83 0.46
43 92 0.51
44 3 0.02
ACGTcount: A:0.19, C:0.28, G:0.19, T:0.34
Consensus pattern (41 bp):
CTTTGACCCTAGAGACTTTTCTACCCTCAGTCTGCTGTCGA
Found at i:1372004 original size:42 final size:42
Alignment explanation
Indices: 1371086--1372017 Score: 453
Period size: 42 Copynumber: 22.1 Consensus size: 42
1371076 ATTTTCCTAC
* * * *
1371086 CCTC-AGTCTACCTGTCGACTTTGACCTTGGAGACTGCCTCA
1 CCTCAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTGTCTCA
** * * * * *
1371127 TATAAAGTCTACCTGTCAGCTTTGACCCTAGAGACTTTC-CTA
1 CCTCAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTGTCTC-A
** * * * *
1371169 CCTTTAGTCTGCTTATCGGCTTTGACCCTAGAGACTGCCTCA
1 CCTCAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTGTCTCA
* * * * * * *
1371211 TCT-AATGTCTGCCTATCGGCTTTAACCTTAGAGACTTTCTTACT
1 CCTCAA-GTCTGCCTGTCGGCTTTGACCCTGGAGACTGTC-T-CA
* * * *
1371255 CCTTC-AGTTTGTCTGTCAGCTTTGACCTTGGAGACTG-CTTCA
1 CC-TCAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTGTC-TCA
* * * * * *
1371297 TCTAAAGTTTGCCTGTTGGCTTTGACCTTGGAGACTTTC-CTA
1 CCTCAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTGTCTC-A
** * * * *
1371339 CCTTTAGTATGCCTGTCAGCTTTCACCCTGGAGACTGCCTCA
1 CCTCAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTGTCTCA
* * * * * *
1371381 TCTAAAGTCTGCTTGTCGGTTTTGACCTTGGAGACTTTC-CAA
1 CCTCAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTGTCTC-A
* * *
1371423 CCCTC-AGTCTGCCTGTCGGCTTTGACCTTGGAGAATGCCTCA
1 -CCTCAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTGTCTCA
* * * * * *
1371465 TCTAAAGTCTGCCTGTTGGCTTTGATCCTAGAGACTTTCCTTC-
1 CCTCAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTGT-C-TCA
* *
1371508 CCTC-AGTCTGCCTGTCGGCTTTGACCTTGGAGACTGCCTCA
1 CCTCAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTGTCTCA
* * * *
1371549 CCTAAAGTTTGCCCGTCGGCTTTGACCCTGGAGACTTTC-CTA
1 CCTCAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTGTCTC-A
* * * * * *
1371591 CC-CTTAGACTGCTTGTCAGCTTTGACACTGGAGACTGCCTCA
1 CCTC-AAGTCTGCCTGTCGGCTTTGACCCTGGAGACTGTCTCA
** * * * ** * * * *
1371633 TTTAAAGTCTACTTGTTAGCTTTGACCTTGGAGACTTTTTTA
1 CCTCAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTGTCTCA
* *
1371675 CCCTTC-AGTCTGCCCGTCGGCTTTGACCCAGGAGACTGTCTCA
1 -CC-TCAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTGTCTCA
* * * * ** *
1371718 TCTAAAGTCTGTCTGTCGACTTTGACTATGGAGACTTTC-CTA
1 CCTCAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTGTCTC-A
* * * * *
1371760 CCCTTC-AGTCTGCCTATCAGCTTTGACCCTAGAGACTATCTTA
1 -CC-TCAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTGTCTCA
* * * * * *
1371803 CCCTTC-AGTCTGCTTGTTGGCTTTAACCCTAGAGATTGCCTCA
1 -CC-TCAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTGTCTCA
* * * * * *
1371846 TCTAAAGTCTGCGTGTCGACTTTGACCCTAGAGACT-TTTCTA
1 CCTCAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTGTCTC-A
* * * * * *
1371888 CC-CTGAGTCTGACTGTCGGCTTTGACCCTAGAGAACTTTTTTA
1 CCTC-AAGTCTGCCTGTCGGCTTTGACCCTGGAG-ACTGTCTCA
* * *
1371931 CCCTCAA-TCTACCGGTCAGCTTTGACCCTGGAGACTGTCTCA
1 -CCTCAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTGTCTCA
* * * * *
1371973 CCTCAAGTATGCCTGTTGGCTTTGACTCTGGAGACTTTTTCA
1 CCTCAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTGTCTCA
1372015 CCT
1 CCT
1372018 TTTATCTACC
Statistics
Matches: 661, Mismatches: 191, Indels: 77
0.71 0.21 0.08
Matches are distributed among these distances:
40 2 0.00
41 24 0.04
42 468 0.71
43 128 0.19
44 36 0.05
45 3 0.00
ACGTcount: A:0.18, C:0.28, G:0.20, T:0.34
Consensus pattern (42 bp):
CCTCAAGTCTGCCTGTCGGCTTTGACCCTGGAGACTGTCTCA
Found at i:1372558 original size:13 final size:14
Alignment explanation
Indices: 1372540--1372580 Score: 59
Period size: 13 Copynumber: 3.0 Consensus size: 14
1372530 TAACATGAAT
1372540 AATATATAAAA-AA
1 AATATATAAAATAA
1372553 AATATATAAAATAA
1 AATATATAAAATAA
1372567 AATA-ATAATAATAA
1 AATATATAA-AATAA
1372581 TTAATTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
13 15 0.58
14 11 0.42
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (14 bp):
AATATATAAAATAA
Found at i:1372610 original size:27 final size:27
Alignment explanation
Indices: 1372579--1372639 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
1372569 TAATAATAAT
**
1372579 AATTAATTAA-TTAATTAAAAAAATTAA
1 AATTAATTAATTTAAAGAAAAAAATT-A
*
1372606 AATTAATTAATTTAAAGAAAAAAATTG
1 AATTAATTAATTTAAAGAAAAAAATTA
1372633 AATTAAT
1 AATTAAT
1372640 GGAATTGTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 17 0.57
28 13 0.43
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (27 bp):
AATTAATTAATTTAAAGAAAAAAATTA
Found at i:1372613 original size:23 final size:21
Alignment explanation
Indices: 1372583--1372639 Score: 69
Period size: 23 Copynumber: 2.5 Consensus size: 21
1372573 AATAATAATT
1372583 AATTAATTAATTAAAAAAATTAA
1 AATTAATTAATTAAAAAAA--AA
*
1372606 AATTAATTAATTTAAAGAAAAA
1 AATTAATTAA-TTAAAAAAAAA
1372628 AATTGAATTAAT
1 AATT-AATTAAT
1372640 GGAATTGTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
22 7 0.23
23 16 0.52
24 8 0.26
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (21 bp):
AATTAATTAATTAAAAAAAAA
Found at i:1372817 original size:17 final size:17
Alignment explanation
Indices: 1372795--1372840 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
1372785 ATACGTGTCA
*
1372795 ATGCATGCTTTTACTTC
1 ATGCATGCTTTCACTTC
* *
1372812 ATGCATACTTTCATTTC
1 ATGCATGCTTTCACTTC
*
1372829 ACGCATGCTTTC
1 ATGCATGCTTTC
1372841 TTTCATGGTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.20, C:0.26, G:0.11, T:0.43
Consensus pattern (17 bp):
ATGCATGCTTTCACTTC
Found at i:1372896 original size:29 final size:29
Alignment explanation
Indices: 1372860--1372983 Score: 107
Period size: 29 Copynumber: 4.4 Consensus size: 29
1372850 TCACTCATGA
*
1372860 GTTCATTTCATGCATGCATTTCACTTAAT
1 GTTCATTTCATGCATGCATTTCACGTAAT
* * *
1372889 GTTCATTTCATGCATTACATTTCATG-CAT
1 GTTCATTTCATGCA-TGCATTTCACGTAAT
* * **
1372918 G--C-TTTCTTTCATG--TTTCACGCCAT
1 GTTCATTTCATGCATGCATTTCACGTAAT
1372942 CAGTTCATTTCATGCATGCATTTCACGTAAT
1 --GTTCATTTCATGCATGCATTTCACGTAAT
1372973 GTTCATTTCAT
1 GTTCATTTCAT
1372984 TACATTGTTT
Statistics
Matches: 74, Mismatches: 12, Indels: 18
0.71 0.12 0.17
Matches are distributed among these distances:
23 6 0.08
24 3 0.04
25 1 0.01
26 8 0.11
27 1 0.01
28 1 0.01
29 37 0.50
30 8 0.11
31 9 0.12
ACGTcount: A:0.22, C:0.23, G:0.11, T:0.44
Consensus pattern (29 bp):
GTTCATTTCATGCATGCATTTCACGTAAT
Found at i:1372973 original size:84 final size:83
Alignment explanation
Indices: 1372823--1372983 Score: 268
Period size: 84 Copynumber: 1.9 Consensus size: 83
1372813 TGCATACTTT
* * *
1372823 CATTTCACGCATGCTTTCTTTCATGGTTCACTCATGAGTTCATTTCATGCATGCATTTCACTTAA
1 CATTTCACGCATGCTTTCTTTCATGGTTCACCCATCAGTTCATTTCATGCATGCATTTCACGTAA
1372888 TGTTCATTTCATGCATTA
66 TGTTCATTTCATGCATTA
* *
1372906 CATTTCATGCATGCTTTCTTTCATGTTTCACGCCATCAGTTCATTTCATGCATGCATTTCACGTA
1 CATTTCACGCATGCTTTCTTTCATGGTTCAC-CCATCAGTTCATTTCATGCATGCATTTCACGTA
1372971 ATGTTCATTTCAT
65 ATGTTCATTTCAT
1372984 TACATTGTTT
Statistics
Matches: 72, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
83 29 0.40
84 43 0.60
ACGTcount: A:0.21, C:0.24, G:0.12, T:0.43
Consensus pattern (83 bp):
CATTTCACGCATGCTTTCTTTCATGGTTCACCCATCAGTTCATTTCATGCATGCATTTCACGTAA
TGTTCATTTCATGCATTA
Found at i:1373222 original size:16 final size:16
Alignment explanation
Indices: 1373203--1373256 Score: 65
Period size: 16 Copynumber: 3.3 Consensus size: 16
1373193 AATTGTTGCT
1373203 GAAATGAATGAGATAA
1 GAAATGAATGAGATAA
* *
1373219 GAAATGAAAT-AGCTATT
1 GAAATG-AATGAGATA-A
1373236 GAAATGAATGAGATAA
1 GAAATGAATGAGATAA
1373252 GAAAT
1 GAAAT
1373257 AGTAGTTGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
16 18 0.58
17 13 0.42
ACGTcount: A:0.54, C:0.02, G:0.22, T:0.22
Consensus pattern (16 bp):
GAAATGAATGAGATAA
Found at i:1374039 original size:20 final size:19
Alignment explanation
Indices: 1373992--1374048 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1373982 TTGTATCAAT
*
1373992 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
* *
1374011 TCCTTGTATCGATACATGG
1 ACATTGTATCGATACATGG
1374030 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
1374049 AAACTGGCAG
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:1374102 original size:20 final size:20
Alignment explanation
Indices: 1374077--1374130 Score: 74
Period size: 20 Copynumber: 2.7 Consensus size: 20
1374067 CTACCACTGT
*
1374077 TTGTATCGATACATGGT-ACA
1 TTGTATCGATACATGATGA-A
1374097 TTGTATCGATACATGATGAA
1 TTGTATCGATACATGATGAA
*
1374117 TTGTATCAATACAT
1 TTGTATCGATACAT
1374131 TGCTTCTAAC
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
20 30 0.97
21 1 0.03
ACGTcount: A:0.33, C:0.13, G:0.17, T:0.37
Consensus pattern (20 bp):
TTGTATCGATACATGATGAA
Found at i:1382673 original size:13 final size:13
Alignment explanation
Indices: 1382655--1382681 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
1382645 ACATTATGCT
1382655 TTGTATCGATACA
1 TTGTATCGATACA
1382668 TTGTATCGATACA
1 TTGTATCGATACA
1382681 T
1 T
1382682 GTTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1382711 original size:20 final size:19
Alignment explanation
Indices: 1382665--1382721 Score: 78
Period size: 19 Copynumber: 2.9 Consensus size: 19
1382655 TTGTATCGAT
*
1382665 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGG
* *
1382684 TCATTGTATCCATACATGG
1 ACATTGTATCGATACATGG
1382703 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
1382722 AACTAACAGT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 17 0.53
20 15 0.47
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGG
Found at i:1385464 original size:13 final size:13
Alignment explanation
Indices: 1385446--1385471 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1385436 TACAGCAAGT
1385446 ATGTATCGATACA
1 ATGTATCGATACA
1385459 ATGTATCGATACA
1 ATGTATCGATACA
1385472 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1387646 original size:19 final size:19
Alignment explanation
Indices: 1387622--1387659 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
1387612 ATTAGTATGT
1387622 TTAGAAAATAATGCGCTAA
1 TTAGAAAATAATGCGCTAA
1387641 TTAGAAAATAATGCGCTAA
1 TTAGAAAATAATGCGCTAA
1387660 AGAAAGATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.11, G:0.16, T:0.26
Consensus pattern (19 bp):
TTAGAAAATAATGCGCTAA
Found at i:1387741 original size:21 final size:21
Alignment explanation
Indices: 1387708--1387752 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1387698 TTGCAAGTTG
*
1387708 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1387730 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1387750 AAA
1 AAA
1387753 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1389576 original size:15 final size:15
Alignment explanation
Indices: 1389556--1389586 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1389546 TAAAAATGTC
*
1389556 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1389571 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1389586 C
1 C
1389587 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1391679 original size:20 final size:20
Alignment explanation
Indices: 1391600--1391679 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
1391590 AATGTCCAAA
*
1391600 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
1391620 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
1391645 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
1391665 TTGTATCGATACATT
1 ATGTATCGATACATT
1391680 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:1391683 original size:13 final size:13
Alignment explanation
Indices: 1391665--1391703 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1391655 ACATTTTTCT
1391665 TTGTATCGATACA
1 TTGTATCGATACA
1391678 TTGTATCGATACA
1 TTGTATCGATACA
*
1391691 CTGTATCGATACA
1 TTGTATCGATACA
1391704 GGGTGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1394263 original size:13 final size:13
Alignment explanation
Indices: 1394245--1394270 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1394235 TACAGCAAGT
1394245 ATGTATCGATACA
1 ATGTATCGATACA
1394258 ATGTATCGATACA
1 ATGTATCGATACA
1394271 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1398735 original size:20 final size:20
Alignment explanation
Indices: 1398676--1398735 Score: 59
Period size: 20 Copynumber: 3.0 Consensus size: 20
1398666 CTTGGAACAT
1398676 GCATTGTATCAATACAA-GG
1 GCATTGTATCAATACAATGG
* * *
1398695 CCATATTGTATCTATAAAATGG
1 GC--ATTGTATCAATACAATGG
*
1398717 GCATTGTATCGATACAATG
1 GCATTGTATCAATACAATG
1398736 TTATGTTTTC
Statistics
Matches: 32, Mismatches: 6, Indels: 5
0.74 0.14 0.12
Matches are distributed among these distances:
19 1 0.03
20 15 0.47
21 13 0.41
22 3 0.09
ACGTcount: A:0.35, C:0.15, G:0.18, T:0.32
Consensus pattern (20 bp):
GCATTGTATCAATACAATGG
Found at i:1399423 original size:12 final size:12
Alignment explanation
Indices: 1399414--1399442 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
1399404 AGAGAAAAGG
1399414 AGAAAGAAAAAA
1 AGAAAGAAAAAA
1399426 AGAAAGAAAAAA
1 AGAAAGAAAAAA
1399438 AGAAA
1 AGAAA
1399443 AATATAGGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (12 bp):
AGAAAGAAAAAA
Found at i:1400344 original size:58 final size:57
Alignment explanation
Indices: 1400281--1400468 Score: 195
Period size: 58 Copynumber: 3.2 Consensus size: 57
1400271 TTTATTTACA
*
1400281 TTCATGCATTTTAATGTCATTTTAGTAAATTTTCATGATTTAGGACCATTTATGCAT
1 TTCATGCATTTTAAGGTCATTTTAGTAAATTTTCATGATTTAGGACCATTTATGCAT
* * * * *
1400338 TCTCATGTATTTT-AGGATCATTATAGT-AGTTTGCCAT-ATTTTAGGACCATTTATGTAAT
1 T-TCATGCATTTTAAGG-TCATTTTAGTAAATTT-TCATGA-TTTAGGACCATTTATG-CAT
* **
1400397 TTCATGCATTTTAAGGTCATTTTAGTAATTTTTTCATGATTTAAGGATTA-TTATGCAAT
1 TTCATGCATTTTAAGGTCATTTTAGTAA-ATTTTCATGATTT-AGGACCATTTATGC-AT
1400456 TTCATGCATTTTA
1 TTCATGCATTTTA
1400469 CAACCATTTT
Statistics
Matches: 107, Mismatches: 13, Indels: 20
0.76 0.09 0.14
Matches are distributed among these distances:
57 8 0.07
58 57 0.53
59 33 0.31
60 9 0.08
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.48
Consensus pattern (57 bp):
TTCATGCATTTTAAGGTCATTTTAGTAAATTTTCATGATTTAGGACCATTTATGCAT
Found at i:1400417 original size:29 final size:30
Alignment explanation
Indices: 1400281--1400468 Score: 93
Period size: 29 Copynumber: 6.4 Consensus size: 30
1400271 TTTATTTACA
*
1400281 TTCATGCATTTTAATG-TCATTT-TAGTAAATT
1 TTCATGCATTTTAAGGATCATTTAT-GT-AA-T
* *
1400312 TTCATG-A-TTT-AGGACCATTTATG-CAT
1 TTCATGCATTTTAAGGATCATTTATGTAAT
* *
1400338 TCTCATGTATTTT-AGGATCA-TTATAGTAGT
1 T-TCATGCATTTTAAGGATCATTTAT-GTAAT
*
1400368 TTGCCAT--ATTTT-AGGACCATTTATGTAAT
1 TT--CATGCATTTTAAGGATCATTTATGTAAT
1400397 TTCATGCATTTTAAGG-TCATTT-TAGTAATTTT
1 TTCATGCATTTTAAGGATCATTTAT-GTAA---T
* *
1400429 TTCATG-A-TTTAAGGATTA-TTATGCAAT
1 TTCATGCATTTTAAGGATCATTTATGTAAT
1400456 TTCATGCATTTTA
1 TTCATGCATTTTA
1400469 CAACCATTTT
Statistics
Matches: 125, Mismatches: 11, Indels: 44
0.69 0.06 0.24
Matches are distributed among these distances:
26 2 0.02
27 16 0.13
28 9 0.07
29 55 0.44
30 23 0.18
31 13 0.10
32 7 0.06
ACGTcount: A:0.28, C:0.11, G:0.13, T:0.48
Consensus pattern (30 bp):
TTCATGCATTTTAAGGATCATTTATGTAAT
Found at i:1400534 original size:53 final size:54
Alignment explanation
Indices: 1400427--1400571 Score: 159
Period size: 53 Copynumber: 2.6 Consensus size: 54
1400417 TTTAGTAATT
* * ** *
1400427 TTTTCATGATTTAAGGATTATTATGCAATTTCATGCATTTTACAACCATTTTAG
1 TTTTCATGATTTAAGGGTTATTATGTAATTTCACACATTTTACAACCATCTTAG
*
1400481 -TTTCATGATTTAAGGGTTATTATGTAATTTCACACATTTTAGC-ACCGTCTTAG
1 TTTTCATGATTTAAGGGTTATTATGTAATTTCACACATTTTA-CAACCATCTTAG
* *
1400534 TCATTTTTCATGATTTAGGGGTTATTATGTATTTTCAC
1 ----TTTTCATGATTTAAGGGTTATTATGTAATTTCAC
1400572 GCGTTTTTGT
Statistics
Matches: 77, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
53 45 0.58
54 1 0.01
58 31 0.40
ACGTcount: A:0.26, C:0.13, G:0.14, T:0.47
Consensus pattern (54 bp):
TTTTCATGATTTAAGGGTTATTATGTAATTTCACACATTTTACAACCATCTTAG
Found at i:1400592 original size:58 final size:58
Alignment explanation
Indices: 1400426--1400610 Score: 175
Period size: 58 Copynumber: 3.3 Consensus size: 58
1400416 TTTTAGTAAT
* * **
1400426 TTTTTCATGATTTAAGGATTATTATGCAATTTCATGCATTTTA-CAACCAT-TT--T-A
1 TTTTTCATGATTTAAGGGTTATTATGTAATTTCACACATTTTAGC-ACCATCTTAGTCA
* *
1400480 -GTTTCATGATTTAAGGGTTATTATGTAATTTCACACATTTTAGCACCGTCTTAGTCA
1 TTTTTCATGATTTAAGGGTTATTATGTAATTTCACACATTTTAGCACCATCTTAGTCA
* * * * * *** *
1400537 TTTTTCATGATTTAGGGGTTATTATGTATTTTCACGCGTTTTTGTGTCATTTTAGTCA
1 TTTTTCATGATTTAAGGGTTATTATGTAATTTCACACATTTTAGCACCATCTTAGTCA
*
1400595 TTTTCCATGATTTAAG
1 TTTTTCATGATTTAAG
1400611 ACCATTGATG
Statistics
Matches: 106, Mismatches: 19, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
53 41 0.39
54 3 0.03
56 1 0.01
57 1 0.01
58 60 0.57
ACGTcount: A:0.24, C:0.13, G:0.15, T:0.48
Consensus pattern (58 bp):
TTTTTCATGATTTAAGGGTTATTATGTAATTTCACACATTTTAGCACCATCTTAGTCA
Found at i:1404908 original size:21 final size:20
Alignment explanation
Indices: 1404882--1404920 Score: 60
Period size: 21 Copynumber: 1.9 Consensus size: 20
1404872 TTATTAATTT
*
1404882 TAATTTTCTTTTAATTTTAGA
1 TAATTTTATTTT-ATTTTAGA
1404903 TAATTTTATTTTATTTTA
1 TAATTTTATTTTATTTTA
1404921 TTTTTAGACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 6 0.35
21 11 0.65
ACGTcount: A:0.28, C:0.03, G:0.03, T:0.67
Consensus pattern (20 bp):
TAATTTTATTTTATTTTAGA
Found at i:1404913 original size:26 final size:27
Alignment explanation
Indices: 1404876--1404928 Score: 81
Period size: 26 Copynumber: 2.0 Consensus size: 27
1404866 TTATGATTAT
*
1404876 TAATTTTAATTTTCTTTTAATTTTAGA
1 TAATTTTAATTTTATTTTAATTTTAGA
*
1404903 TAATTTT-ATTTTATTTTATTTTTAGA
1 TAATTTTAATTTTATTTTAATTTTAGA
1404929 CTAGTTTCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 17 0.71
27 7 0.29
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.66
Consensus pattern (27 bp):
TAATTTTAATTTTATTTTAATTTTAGA
Found at i:1406828 original size:156 final size:155
Alignment explanation
Indices: 1406533--1406957 Score: 427
Period size: 156 Copynumber: 2.7 Consensus size: 155
1406523 TTACCAAGAC
* * ** * *
1406533 ACTTTCATGTCTAAA-GTGTACCACAAAAGCATTTTGGTAA-TTTTCTTAAAACCAAGT-CGAAT
1 ACTTTCATGTC-AAAGGTATACCCCAAGTGCATTTTGGTAATTTTTCTTAGAACCATGTCCG-AT
* * * ** *
1406595 GTAGGCATTGGGATGCTTTTATGCCAAATATGTGCATTTAGGATAGGTTCACCTTTTGGTGAGTA
64 GTA-GTAATAGGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCACCTTTTGATGAGTA
1406660 TTTTAGAATCTTTTA-AGGAAACAAGAAT
128 TTTTAGAATCTTTTAGA-GAAACAAGAAT
** ** * *
1406688 ACTTTCATGTCAAAGGTATACCTTGAAG-GCATTTTGGTCTTTTTTTCTTAGAATCGA-GTCTGA
1 ACTTTCATGTCAAAGGTATACC-CCAAGTGCATTTTGGT-AATTTTTCTTAGAA-CCATGTCCGA
1406751 TGTAGTAACTAGGATGCTTTTATGCCAAA-GTGTGCATTTAGGATAGGTTCACCCTTTT-ATGAG
63 TGTAGTAA-TAGGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCA-CCTTTTGATGAG
* ** ** *
1406814 TATTTTA-ATGTCTTTTAGAGTTATTAGGAT
126 TATTTTAGA-ATCTTTTAGAGAAACAAGAAT
* *
1406844 ACTTTCATGTTAAAGGTATACCCCAAGTGCATTTTGGTAATTTTTCTTAGAACCATTTCCGATGT
1 ACTTTCATGTCAAAGGTATACCCCAAGTGCATTTTGGTAATTTTTCTTAGAACCATGTCCGATGT
* * *
1406909 AGTCATCGAGATGCTTTTATGCCAAAGGTGTGCTTTTAGGATAGGTTCA
66 AGTAATAG-GATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCA
1406958 TCCTCAAAAC
Statistics
Matches: 225, Mismatches: 31, Indels: 27
0.80 0.11 0.10
Matches are distributed among these distances:
154 7 0.03
155 71 0.32
156 101 0.45
157 43 0.19
158 3 0.01
ACGTcount: A:0.28, C:0.14, G:0.20, T:0.38
Consensus pattern (155 bp):
ACTTTCATGTCAAAGGTATACCCCAAGTGCATTTTGGTAATTTTTCTTAGAACCATGTCCGATGT
AGTAATAGGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCACCTTTTGATGAGTATTT
TAGAATCTTTTAGAGAAACAAGAAT
Found at i:1408153 original size:21 final size:20
Alignment explanation
Indices: 1408127--1408179 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
1408117 TTTTACAAGT
*
1408127 TGTATCGATATAAATAGTAAA
1 TGTATCGATACAAA-AGTAAA
*
1408148 TGTATCGATACAAAAGTGAA
1 TGTATCGATACAAAAGTAAA
*
1408168 TGTATCAATACA
1 TGTATCGATACA
1408180 TGCGTGAGAT
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.45, C:0.09, G:0.15, T:0.30
Consensus pattern (20 bp):
TGTATCGATACAAAAGTAAA
Found at i:1408171 original size:20 final size:20
Alignment explanation
Indices: 1408127--1408202 Score: 73
Period size: 21 Copynumber: 3.8 Consensus size: 20
1408117 TTTTACAAGT
* *
1408127 TGTATCGATATAAATAGTAAA
1 TGTATCGATACAAA-AGTGAA
1408148 TGTATCGATACAAAAGTGAA
1 TGTATCGATACAAAAGTGAA
* ***
1408168 TGTATCAATACATGCGTGAGA
1 TGTATCGATACAAAAGTGA-A
1408189 TGTATCGATA-AAAA
1 TGTATCGATACAAAA
1408203 CCACCCTGCA
Statistics
Matches: 44, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
20 21 0.48
21 23 0.52
ACGTcount: A:0.43, C:0.09, G:0.18, T:0.29
Consensus pattern (20 bp):
TGTATCGATACAAAAGTGAA
Found at i:1408292 original size:20 final size:21
Alignment explanation
Indices: 1408247--1408301 Score: 78
Period size: 20 Copynumber: 2.7 Consensus size: 21
1408237 AATAAGTAAA
1408247 TGTATCGATACATTTACTATT
1 TGTATCGATACATTTACTATT
*
1408268 TGTATCGATACA-TTATTCA-T
1 TGTATCGATACATTTACT-ATT
1408288 TGTATCGATACATT
1 TGTATCGATACATT
1408302 CTGGGTTTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
20 17 0.55
21 14 0.45
ACGTcount: A:0.29, C:0.15, G:0.11, T:0.45
Consensus pattern (21 bp):
TGTATCGATACATTTACTATT
Found at i:1412004 original size:20 final size:19
Alignment explanation
Indices: 1411958--1412014 Score: 87
Period size: 19 Copynumber: 2.9 Consensus size: 19
1411948 TTGTATTGAT
*
1411958 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGC
*
1411977 TCATTGTATCGATACATGC
1 ACATTGTATCGATACATGC
1411996 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
1412015 AAACTGGCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.53
20 16 0.47
ACGTcount: A:0.32, C:0.18, G:0.16, T:0.35
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:1412082 original size:13 final size:13
Alignment explanation
Indices: 1412064--1412088 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1412054 CATGGGACAT
1412064 TGTATCGATACAA
1 TGTATCGATACAA
1412077 TGTATCGATACA
1 TGTATCGATACA
1412089 TGATGAATTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1412107 original size:33 final size:33
Alignment explanation
Indices: 1412044--1412108 Score: 87
Period size: 33 Copynumber: 2.0 Consensus size: 33
1412034 TACCACTATT
**
1412044 TGTATCGATACATGGGACATTGTATCGATACAA
1 TGTATCGATACATGGGACATTGTAAAGATACAA
*
1412077 TGTATCGATACATGATGA-ATTGTAAAGATACA
1 TGTATCGATACATG-GGACATTGTAAAGATACA
1412109 TTGCTTCAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
33 26 0.93
34 2 0.07
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (33 bp):
TGTATCGATACATGGGACATTGTAAAGATACAA
Found at i:1418269 original size:13 final size:13
Alignment explanation
Indices: 1418251--1418288 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
1418241 ATAATATTCT
1418251 TTGTATTGATACA
1 TTGTATTGATACA
*
1418264 TTGTATCGATACA
1 TTGTATTGATACA
*
1418277 ATGTATTGATAC
1 TTGTATTGATAC
1418289 GTGGGTTACT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.32, C:0.11, G:0.16, T:0.42
Consensus pattern (13 bp):
TTGTATTGATACA
Found at i:1418455 original size:20 final size:20
Alignment explanation
Indices: 1418417--1418456 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
1418407 TTTCAAATTT
1418417 CTTCATTTTCACTTCAAAATA
1 CTTCATTTTCAC-TCAAAATA
1418438 CTTCATTTTTCA-TCAAAAT
1 CTTCA-TTTTCACTCAAAAT
1418457 TATCATCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 7 0.39
21 5 0.28
22 6 0.33
ACGTcount: A:0.33, C:0.23, G:0.00, T:0.45
Consensus pattern (20 bp):
CTTCATTTTCACTCAAAATA
Found at i:1419796 original size:33 final size:33
Alignment explanation
Indices: 1419759--1419822 Score: 92
Period size: 33 Copynumber: 1.9 Consensus size: 33
1419749 CAAGAGTTGA
*
1419759 TCACTTCACTTTCACAACACATGAATGAGCATT
1 TCACTTCACTCTCACAACACATGAATGAGCATT
** *
1419792 TCACTTCACTCTCACAATGCATGGATGAGCA
1 TCACTTCACTCTCACAACACATGAATGAGCA
1419823 CTTTGGTGCA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.28
Consensus pattern (33 bp):
TCACTTCACTCTCACAACACATGAATGAGCATT
Found at i:1420185 original size:30 final size:30
Alignment explanation
Indices: 1420149--1420235 Score: 97
Period size: 31 Copynumber: 2.8 Consensus size: 30
1420139 AAATAAATTT
*
1420149 TTTATCAAGAGGGAGAGAATTTTTTAAA-CA
1 TTTATCAAG-GGGAGAAAATTTTTTAAATCA
*
1420179 TTTATCAAGGGAGAGAAAATCTTTTTAAATGA
1 TTTATCAAGGG-GAGAAAAT-TTTTTAAATCA
*
1420211 -CTATCAAGTGGGAGAAAATTTTTTA
1 TTTATCAAG-GGGAGAAAATTTTTTA
1420236 TCAAAAGGGA
Statistics
Matches: 50, Mismatches: 3, Indels: 8
0.82 0.05 0.13
Matches are distributed among these distances:
29 2 0.04
30 22 0.44
31 23 0.46
32 3 0.06
ACGTcount: A:0.39, C:0.07, G:0.20, T:0.34
Consensus pattern (30 bp):
TTTATCAAGGGGAGAAAATTTTTTAAATCA
Found at i:1420853 original size:13 final size:13
Alignment explanation
Indices: 1420835--1420859 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1420825 ATTATGCTTC
1420835 GTATCGATACATT
1 GTATCGATACATT
1420848 GTATCGATACAT
1 GTATCGATACAT
1420860 GTTCATTGTA
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:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1420868 original size:19 final size:19
Alignment explanation
Indices: 1420843--1420897 Score: 69
Period size: 19 Copynumber: 2.9 Consensus size: 19
1420833 TCGTATCGAT
*
1420843 ACATTGTATCGATACATGT
1 ACATTGTATCGATACATGC
*
1420862 TCATTGTATCGAT--ATGC
1 ACATTGTATCGATACATGC
1420879 ACAATTGTATCGATACATG
1 AC-ATTGTATCGATACATG
1420898 AAACTGGCAG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
17 4 0.13
18 11 0.37
19 12 0.40
20 3 0.10
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.36
Consensus pattern (19 bp):
ACATTGTATCGATACATGC
Found at i:1422720 original size:13 final size:13
Alignment explanation
Indices: 1422702--1422726 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1422692 AAGAGAGAAG
1422702 AAGAAAAAGAAAA
1 AAGAAAAAGAAAA
1422715 AAGAAAAAGAAA
1 AAGAAAAAGAAA
1422727 TTTTAGATGC
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:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAGAAAAAGAAAA
Found at i:1428828 original size:5 final size:5
Alignment explanation
Indices: 1428818--1428858 Score: 59
Period size: 5 Copynumber: 8.6 Consensus size: 5
1428808 AAAAATAAAC
*
1428818 ACAAA ACAAA ACAAA ACAAA ATAAA ACAAA A-AAA A-AAA ACA
1 ACAAA ACAAA ACAAA ACAAA ACAAA ACAAA ACAAA ACAAA ACA
1428859 CAGAAAAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
4 8 0.24
5 25 0.76
ACGTcount: A:0.83, C:0.15, G:0.00, T:0.02
Consensus pattern (5 bp):
ACAAA
Found at i:1428838 original size:15 final size:14
Alignment explanation
Indices: 1428808--1428858 Score: 59
Period size: 15 Copynumber: 3.5 Consensus size: 14
1428798 TGAAAAAGTC
*
1428808 AAAAATAAACACAAA
1 AAAAACAAA-ACAAA
1428823 ACAAAACAAAACAAA
1 A-AAAACAAAACAAA
1428838 ATAAAACAAAA-AAA
1 A-AAAACAAAACAAA
1428852 AAAAACA
1 AAAAACA
1428859 CAGAAAAAAG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
13 6 0.18
14 4 0.12
15 16 0.48
16 7 0.21
ACGTcount: A:0.82, C:0.14, G:0.00, T:0.04
Consensus pattern (14 bp):
AAAAACAAAACAAA
Found at i:1429130 original size:17 final size:16
Alignment explanation
Indices: 1429108--1429165 Score: 55
Period size: 17 Copynumber: 3.4 Consensus size: 16
1429098 TCTTTTCCAA
1429108 AAAAGAAACAAAACAAG
1 AAAAGAAACAAAA-AAG
1429125 AAAAGAAA-AAAAAAG
1 AAAAGAAACAAAAAAG
* *
1429140 AAGAAACAAACAAACAAAA
1 -A-AAAGAAACAAA-AAAG
1429159 AAAAGAA
1 AAAAGAA
1429166 GAAAGGAAAA
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
15 3 0.09
16 5 0.15
17 19 0.56
18 4 0.12
19 3 0.09
ACGTcount: A:0.81, C:0.09, G:0.10, T:0.00
Consensus pattern (16 bp):
AAAAGAAACAAAAAAG
Found at i:1430157 original size:31 final size:31
Alignment explanation
Indices: 1430117--1430294 Score: 218
Period size: 32 Copynumber: 5.7 Consensus size: 31
1430107 ATACCTTCTT
*
1430117 AAAGTCCACGACTCAGTGGCAATCTCT-TCTC
1 AAAGTCCACGACTCAGTGGC-ATCTTTGTCTC
* *
1430148 AACGCCCACGACTCAGTGGCAT-TTTGTCTC
1 AAAGTCCACGACTCAGTGGCATCTTTGTCTC
1430178 AAAGTCCACGACTCAGTGGCATCCTTT-TCTTC
1 AAAGTCCACGACTCAGTGGCAT-CTTTGTC-TC
1430210 AAAGTCCACGACTCAGTGGCATCTTTTGTCTC
1 AAAGTCCACGACTCAGTGGCATC-TTTGTCTC
* * *
1430242 AAAGTCCACGACTTAGTGGCATCCTTATCTGC
1 AAAGTCCACGACTCAGTGGCATCTTTGTCT-C
* *
1430274 AAAGTCCACAACTCCGTGGCA
1 AAAGTCCACGACTCAGTGGCA
1430295 CCCTTTTAAG
Statistics
Matches: 129, Mismatches: 11, Indels: 13
0.84 0.07 0.08
Matches are distributed among these distances:
29 2 0.02
30 26 0.20
31 26 0.20
32 73 0.57
33 2 0.02
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (31 bp):
AAAGTCCACGACTCAGTGGCATCTTTGTCTC
Found at i:1430248 original size:64 final size:62
Alignment explanation
Indices: 1430117--1430294 Score: 243
Period size: 64 Copynumber: 2.9 Consensus size: 62
1430107 ATACCTTCTT
* * *
1430117 AAAGTCCACGACTCAGTGGCAAT-CTCTTC-TCAACGCCCACGACTCAGTGGCATTTTGTCTC
1 AAAGTCCACGACTCAGTGGC-ATCCTTTTCTTCAAAGTCCACGACTCAGTGGCATTTTGTCTC
1430178 AAAGTCCACGACTCAGTGGCATCCTTTTCTTCAAAGTCCACGACTCAGTGGCATCTTTTGTCTC
1 AAAGTCCACGACTCAGTGGCATCCTTTTCTTCAAAGTCCACGACTCAGTGGCA--TTTTGTCTC
* * * * *
1430242 AAAGTCCACGACTTAGTGGCATCCTTATCTGCAAAGTCCACAACTCCGTGGCA
1 AAAGTCCACGACTCAGTGGCATCCTTTTCTTCAAAGTCCACGACTCAGTGGCA
1430295 CCCTTTTAAG
Statistics
Matches: 105, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
60 2 0.02
61 25 0.24
62 21 0.20
64 57 0.54
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (62 bp):
AAAGTCCACGACTCAGTGGCATCCTTTTCTTCAAAGTCCACGACTCAGTGGCATTTTGTCTC
Found at i:1430346 original size:61 final size:60
Alignment explanation
Indices: 1430275--1430491 Score: 256
Period size: 61 Copynumber: 3.5 Consensus size: 60
1430265 CTTATCTGCA
1430275 AAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCA-TCTTTTTCCTTCT
* * * *
1430336 AAGTCCACAACTCCATGGCACCTTTTTCTTTTTAAAGCCCACAAC-CTTGTGGCATCCTGTTCCT
1 AAGTCCACAACTCCGTGGCACC-----C-TTTT-AAGCCCACAACTC-CGTGGCATCTTTTTCCT
*
1430400 TTT
58 TCT
* *
1430403 AAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCATGGCATTCTTTTTCCTTCA
1 AAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCA-TCTTTTTCCTTCT
* *
1430464 AAGCCCACAACTCCGTGGCACTCTTTTA
1 AAGTCCACAACTCCGTGGCACCCTTTTA
1430492 CCCTCTCTAA
Statistics
Matches: 132, Mismatches: 14, Indels: 20
0.80 0.08 0.12
Matches are distributed among these distances:
60 16 0.12
61 61 0.46
62 1 0.01
66 1 0.01
67 36 0.27
68 17 0.13
ACGTcount: A:0.22, C:0.35, G:0.12, T:0.31
Consensus pattern (60 bp):
AAGTCCACAACTCCGTGGCACCCTTTTAAGCCCACAACTCCGTGGCATCTTTTTCCTTCT
Found at i:1430349 original size:34 final size:34
Alignment explanation
Indices: 1430296--1430490 Score: 194
Period size: 34 Copynumber: 6.0 Consensus size: 34
1430286 TCCGTGGCAC
1430296 CCTTTTAAGCCCACAACTCCGTGGCACTCTTTTT
1 CCTTTTAAGCCCACAACTCCGTGGCACTCTTTTT
* * *
1430330 CCTTCTAAGTCCACAACTCCATGGCAC-CTTTTT
1 CCTTTTAAGCCCACAACTCCGTGGCACTCTTTTT
* * * *
1430363 CTTTTTAAAGCCCACAAC-CTTGTGGCA-TCCTGTT
1 CCTTTT-AAGCCCACAACTC-CGTGGCACTCTTTTT
*
1430397 CCTTTTAAGTCCACAACTCCGTGGCA--C-----
1 CCTTTTAAGCCCACAACTCCGTGGCACTCTTTTT
* *
1430424 CCTTTTAAGCCCACAACTCCATGGCATTCTTTTT
1 CCTTTTAAGCCCACAACTCCGTGGCACTCTTTTT
**
1430458 CCTTCAAAGCCCACAACTCCGTGGCACTCTTTT
1 CCTTTTAAGCCCACAACTCCGTGGCACTCTTTT
1430491 ACCCTCTCTA
Statistics
Matches: 131, Mismatches: 19, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
27 24 0.18
29 1 0.01
32 1 0.01
33 27 0.21
34 78 0.60
ACGTcount: A:0.21, C:0.35, G:0.12, T:0.33
Consensus pattern (34 bp):
CCTTTTAAGCCCACAACTCCGTGGCACTCTTTTT
Found at i:1430406 original size:67 final size:67
Alignment explanation
Indices: 1430298--1430490 Score: 186
Period size: 67 Copynumber: 3.0 Consensus size: 67
1430288 CGTGGCACCC
* * *
1430298 TTTTAAGCCCACAACTCCGTGGCACTCTTTTTCCTTCTAAGTCCACAACTCCATGGCACCTTTTT
1 TTTTAAGCCCACAACTCCGTGGCACTCCTGTTCCTTCTAAGTCCACAACTCCATGGCACCCTTTT
1430363 CT
66 CT
* * *
1430365 TTTTAAAGCCCACAAC-CTTGTGGCA-TCCTGTTCCTTTTAAGTCCACAACTCCGTGGCA-CC--
1 TTTT-AAGCCCACAACTC-CGTGGCACTCCTGTTCCTTCTAAGTCCACAACTCCATGGCACCCTT
1430425 --C-
64 TTCT
* * * * * * * *
1430426 TTTTAAGCCCACAACTCCATGGCATTCTTTTTCCTTCAAAGCCCACAACTCCGTGGCACTCTTTT
1 TTTTAAGCCCACAACTCCGTGGCACTCCTGTTCCTTCTAAGTCCACAACTCCATGGCACCCTTTT
1430491 ACCCTCTCTA
Statistics
Matches: 103, Mismatches: 14, Indels: 19
0.76 0.10 0.14
Matches are distributed among these distances:
60 16 0.16
61 33 0.32
62 2 0.02
66 1 0.01
67 34 0.33
68 17 0.17
ACGTcount: A:0.21, C:0.34, G:0.12, T:0.33
Consensus pattern (67 bp):
TTTTAAGCCCACAACTCCGTGGCACTCCTGTTCCTTCTAAGTCCACAACTCCATGGCACCCTTTT
CT
Found at i:1430456 original size:27 final size:27
Alignment explanation
Indices: 1430397--1430449 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
1430387 GCATCCTGTT
* *
1430397 CCTTTTAAGTCCACAACTCCGTGGCAC
1 CCTTTTAAGCCCACAACTCCATGGCAC
1430424 CCTTTTAAGCCCACAACTCCATGGCA
1 CCTTTTAAGCCCACAACTCCATGGCA
1430450 TTCTTTTTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.25, C:0.38, G:0.13, T:0.25
Consensus pattern (27 bp):
CCTTTTAAGCCCACAACTCCATGGCAC
Found at i:1430536 original size:32 final size:32
Alignment explanation
Indices: 1430500--1430657 Score: 223
Period size: 32 Copynumber: 4.9 Consensus size: 32
1430490 TACCCTCTCT
*
1430500 AAAGCCCACACAAGTCGATGGCAACCCTTCCC
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCCC
*
1430532 AAAGCCCACACAAGTCGGTGGCAA-CCTTCTTCT
1 AAAGCCCACACAAGTCGGTGGCAACCCTTC--CC
* *
1430565 AAAGCCCACACAAGTTGGTGGCAATCCCCTT--T
1 AAAGCCCACACAAGTCGGTGGCAA--CCCTTCCC
1430597 AAAGCCCACACAAGTCGGTGGCAACCCTTCCC
1 AAAGCCCACACAAGTCGGTGGCAACCCTTCCC
1430629 AAAGCCCACACAAGTCGGTGGCAACCCTT
1 AAAGCCCACACAAGTCGGTGGCAACCCTT
1430658 TTAAGCCCAA
Statistics
Matches: 114, Mismatches: 5, Indels: 14
0.86 0.04 0.11
Matches are distributed among these distances:
30 5 0.04
31 5 0.04
32 76 0.67
33 24 0.21
36 4 0.04
ACGTcount: A:0.29, C:0.36, G:0.18, T:0.16
Consensus pattern (32 bp):
AAAGCCCACACAAGTCGGTGGCAACCCTTCCC
Found at i:1430572 original size:65 final size:61
Alignment explanation
Indices: 1430491--1430666 Score: 226
Period size: 65 Copynumber: 2.8 Consensus size: 61
1430481 GCACTCTTTT
*
1430491 ACCCTCTCTAAAGCCCACACAAGTCGATGGCAACCCTTCCCAAAGCCCACACAAGTCGGTGGCA
1 ACCCT-TCTAAAGCCCACACAAGTCGGTGGCAACCCTT--CAAAGCCCACACAAGTCGGTGGCA
* *
1430555 ACCTTCTTCTAAAGCCCACACAAGTTGGTGGCAATCCCCTTTAAAGCCCACACAAGTCGGTGGCA
1 ACC--CTTCTAAAGCCCACACAAGTCGGTGGCAA--CCCTTCAAAGCCCACACAAGTCGGTGGCA
* **
1430620 ACCCTTCCCAAAGCCCACACAAGTCGGTGGCAACCCTTTTAAGCCCA
1 ACCCTT-CTAAAGCCCACACAAGTCGGTGGCAACCCTTCAAAGCCCA
1430667 ATATCGCTGG
Statistics
Matches: 101, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
62 13 0.13
63 3 0.03
64 27 0.27
65 51 0.50
66 2 0.02
67 5 0.05
ACGTcount: A:0.28, C:0.37, G:0.17, T:0.18
Consensus pattern (61 bp):
ACCCTTCTAAAGCCCACACAAGTCGGTGGCAACCCTTCAAAGCCCACACAAGTCGGTGGCA
Found at i:1430750 original size:21 final size:21
Alignment explanation
Indices: 1430726--1430836 Score: 52
Period size: 21 Copynumber: 5.2 Consensus size: 21
1430716 ATGTAGCTGG
1430726 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
* ** * *
1430747 CCTTTAAGTCCAATATAGATGGC-
1 CCTTGAA-T-CAGCACA-TTGGCA
1430770 -CTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
* * *
1430790 CCTTTAAGTC--CA-ATATAGCTGG
1 CCTTGAA-TCAGCACAT-TGGC--A
1430812 CCTTGAATCAGCACATTGGCA
1 CCTTGAATCAGCACATTGGCA
1430833 CCTT
1 CCTT
1430837 TAAGTCCAAT
Statistics
Matches: 62, Mismatches: 16, Indels: 24
0.61 0.16 0.24
Matches are distributed among these distances:
19 6 0.10
20 9 0.15
21 18 0.29
22 14 0.23
23 9 0.15
24 6 0.10
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.28
Consensus pattern (21 bp):
CCTTGAATCAGCACATTGGCA
Found at i:1430934 original size:92 final size:92
Alignment explanation
Indices: 1430657--1431737 Score: 1467
Period size: 92 Copynumber: 11.6 Consensus size: 92
1430647 TGGCAACCCT
* *
1430657 TTTAAGCCCAATATCGCTGGCCTTGAATTAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
1430722 CTGGCCTTGAATCAGCACATTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
* * * *
1430749 TTTAAGTCCAATATAGATGGCCTTGAATCAGCACATTGGCA----C--CTTTAAGTCCAATATAG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
1430808 CTGGCCTTGAATCAGCACATTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
* *
1430835 TTTAAGTCCAATATCTCTGGCCTTGAATCAGCATATTGGCATCTTCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
1430900 CTGGCCTTGAATCAGCACATTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
* * ** *
1430927 CTTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAATTTCTTCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
1430992 CTGGCCTTGAATCAGCACATTGGCACC
66 CTGGCCTTGAATCAGCACATTGGCACC
*
1431019 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCATCATCTTTAAGTCCAATGTAG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
*
1431084 CTGGCCTTGAATCAGCACATTGGCAAC
66 CTGGCCTTGAATCAGCACATTGGCACC
** * * * *
1431111 TCCAAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCCTCATCTTTTAAGCCCAATGTC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC-TTTAAGTCCAATGTA
*
1431176 GCTGGCCTTGAATAAGCACATTGGCACC
65 GCTGGCCTTGAATCAGCACATTGGCACC
*
1431204 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTTCAATG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCATCTTTAAGTCCAATG
*
1431269 TAGCTGGCCTTGAATCAGCACATTGGCAAC
63 TAGCTGGCCTTGAATCAGCACATTGGCACC
** *
1431299 TCCAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CTCTCATCTTTTAAGCCCAATGT
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCT-TCATC-TTTAAGTCCAATGT
*
1431363 CGCTGGCCTTGAATCAGCACATTGGCACC
64 AGCTGGCCTTGAATCAGCACATTGGCACC
* * **
1431392 TTTAAGTCCAATATCGTTGGCCTTGAATCAGTATATTGGTGCCTTTGTCATCTTTAAGTCCAATG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC--T-TCATCTTTAAGTCCAATG
* *
1431457 TAGCTGGCCTTGAATCAGCATATTGGCAAC
63 TAGCTGGCCTTGAATCAGCACATTGGCACC
** * * *
1431487 TCCAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCCTCATCTTTTAAGCCCAATGTC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATC-TTTAAGTCCAATGTA
1431552 GCTGGCCTTGAATCAGCACATTGGCACC
65 GCTGGCCTTGAATCAGCACATTGGCACC
* *
1431580 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTTGTGC-CTTTGTCATTTTTAAGTCCAAT
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATA-TTG-GCAC-CT-TCATCTTTAAGTCCAAT
* * * * *
1431644 ATCGCTAGCCTTGAATCAGCATATTGGCGTCTTTGTCATC
62 GTAGCTGGCCTTGAATCAGCACATT---G-----G-CACC
**
1431684 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACGTTGGCACCTTCATCTTTAA
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAA
1431738 CATTCCTAAG
Statistics
Matches: 876, Mismatches: 84, Indels: 49
0.87 0.08 0.05
Matches are distributed among these distances:
86 80 0.09
88 1 0.00
90 1 0.00
92 306 0.35
93 225 0.26
94 6 0.01
95 188 0.21
96 15 0.02
98 1 0.00
101 9 0.01
102 3 0.00
103 5 0.01
104 36 0.04
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (92 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTCATCTTTAAGTCCAATGTAG
CTGGCCTTGAATCAGCACATTGGCACC
Found at i:1431281 original size:52 final size:48
Alignment explanation
Indices: 1430657--1431737 Score: 1014
Period size: 43 Copynumber: 23.1 Consensus size: 48
1430647 TGGCAACCCT
* *
1430657 TTTAAGCCCAATATCGCTGGCCTTGAATTAGCATATTGGCACCTTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TCATC
* * *
1430706 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA---C--C
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCATC
* * *
1430749 TTTAAGTCCAATATAGATGGCCTTGAATCAGCACATTGGCA---C--C
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCATC
* *
1430792 TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCA---C--C
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCATC
* *
1430835 TTTAAGTCCAATATCTCTGGCCTTGAATCAGCATATTGGCATCTTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CCTCATC
* * *
1430884 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA-C-C--C
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCATC
* ** *
1430928 -TTAAGTCCAATATAGCTGGCCTTGAATCAGCATATTGGCAATTTCTTC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC-ACCTCATC
* * *
1430976 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCA---C--C
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCATC
1431019 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCATCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TCATC
* * * *
1431068 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCAACTC--C
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCATC
*
1431114 ---AAGTCCAATATTGCTGGCCTTGAATCAGCATATTGGCACCCTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CCTCATC
* * * *
1431160 TTTTAAGCCCAATGTCGCTGGCCTTGAATAAGCACATTGGCA---C--C
1 -TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCATC
1431204 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC----TCATC
* * * * *
1431256 TTTAAGTTCAATGTAGCTGGCCTTGAATCAGCACATTGGCAACTC--C
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCATC
1431302 ---AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACTCTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCAC-CTCATC
* * *
1431348 TTTTAAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA---C--C
1 -TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCATC
* * **
1431392 TTTAAGTCCAATATCGTTGGCCTTGAATCAGTATATTGGTGCCTTTGTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC----TCATC
* * *
1431444 TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCATATTGGCAACTC--C
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCATC
1431490 ---AAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCCTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCA-CCTCATC
* * *
1431536 TTTTAAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGCA---C--C
1 -TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCATC
* *
1431580 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTTGTGC-CTTTGTCATT
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATA-TTG-GCAC---CTCATC
* * *
1431632 TTTAAGTCCAATATCGCTAGCCTTGAATCAGCATATTGGCGTCTTTGTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGC-AC---CTCATC
**
1431684 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCACGTTGGCACCTTCATC
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC-TCATC
1431733 TTTAA
1 TTTAA
1431738 CATTCCTAAG
Statistics
Matches: 877, Mismatches: 85, Indels: 140
0.80 0.08 0.13
Matches are distributed among these distances:
43 406 0.46
44 17 0.02
45 4 0.00
46 11 0.01
47 2 0.00
48 8 0.01
49 161 0.18
50 108 0.12
51 4 0.00
52 156 0.18
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (48 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTCATC
Found at i:1431329 original size:188 final size:188
Alignment explanation
Indices: 1430657--1431735 Score: 1539
Period size: 188 Copynumber: 5.8 Consensus size: 188
1430647 TGGCAACCCT
* *
1430657 TTTAAGCCCAATATCGCTGGCCTTGAATTAGCATATTGGCACC--T-TCATCTTTAAGTCCAATG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATG
* ** * * *
1430719 TAGCTGGCCTTGAATCAGCACATTGGCACCTTTAAGTCCAATATAGATGGCCTTGAATCAGCACA
66 TAGCTGGCCTTGAATCAGCACATTGGCAACTCCAAGTCCAATATCGCTGGCCTTGAATCAGCATA
* * *
1430784 TTGGCA----C--C-TTTAAGTCCAATATAGCTGGCCTTGAATCAGCACATTGGCACC
131 TTGGCACCCTCATCTTTTAAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC
* *
1430835 TTTAAGTCCAATATCTCTGGCCTTGAATCAGCATATTGGCA--TCT-TCATCTTTAAGTCCAATG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATG
*
1430897 TAGCTGGCCTTGAATCAGCACATTGGC-AC-CCTTAAGTCCAATATAGCTGGCCTTGAATCAGCA
66 TAGCTGGCCTTGAATCAGCACATTGGCAACTCC--AAGTCCAATATCGCTGGCCTTGAATCAGCA
*** * * *
1430960 TATTGGCAATTTCTTC-TTTAAGTCCAATGTAGCTGGCCTTGAATCAGCACATTGGCACC
129 TATTGGCACCCTCATCTTTTAAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC
*
1431019 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACC---ATCATCTTTAAGTCCAATG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATG
*
1431081 TAGCTGGCCTTGAATCAGCACATTGGCAACTCCAAGTCCAATATTGCTGGCCTTGAATCAGCATA
66 TAGCTGGCCTTGAATCAGCACATTGGCAACTCCAAGTCCAATATCGCTGGCCTTGAATCAGCATA
*
1431146 TTGGCACCCTCATCTTTTAAGCCCAATGTCGCTGGCCTTGAATAAGCACATTGGCACC
131 TTGGCACCCTCATCTTTTAAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC
*
1431204 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTTCAATG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATG
1431269 TAGCTGGCCTTGAATCAGCACATTGGCAACTCCAAGTCCAATATCGCTGGCCTTGAATCAGCATA
66 TAGCTGGCCTTGAATCAGCACATTGGCAACTCCAAGTCCAATATCGCTGGCCTTGAATCAGCATA
*
1431334 TTGGCACTCTCATCTTTTAAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC
131 TTGGCACCCTCATCTTTTAAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC
* * **
1431392 TTTAAGTCCAATATCGTTGGCCTTGAATCAGTATATTGGTGCCTTTGTCATCTTTAAGTCCAATG
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATG
*
1431457 TAGCTGGCCTTGAATCAGCATATTGGCAACTCCAAGTCCAATATCGCTGGCCTTGAATCAGCATA
66 TAGCTGGCCTTGAATCAGCACATTGGCAACTCCAAGTCCAATATCGCTGGCCTTGAATCAGCATA
1431522 TTGGCACCCTCATCTTTTAAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC
131 TTGGCACCCTCATCTTTTAAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC
* ** * *
1431580 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTTGTGCCTTTGTCATTTTTAAGTCCAATA
1 TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATG
* * * **
1431645 TCGCTAGCCTTGAATCAGCATATTGGCGTCTTTGTCATCTTTAAGTCCAATATCGCTGGCCTTGA
66 TAGCTGGCCTTGAATCAGCACATTGGCAAC----TC--C---AAGTCCAATATCGCTGGCCTTGA
** *
1431710 ATCAGCACGTTGGCACCTTCATCTTT
122 ATCAGCATATTGGCACCCTCATCTTT
1431736 AACATTCCTA
Statistics
Matches: 831, Mismatches: 42, Indels: 37
0.91 0.05 0.04
Matches are distributed among these distances:
177 1 0.00
178 120 0.14
182 1 0.00
184 169 0.20
185 85 0.10
186 2 0.00
188 404 0.49
192 2 0.00
194 1 0.00
197 46 0.06
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.31
Consensus pattern (188 bp):
TTTAAGTCCAATATCGCTGGCCTTGAATCAGCATATTGGCACCTTTGTCATCTTTAAGTCCAATG
TAGCTGGCCTTGAATCAGCACATTGGCAACTCCAAGTCCAATATCGCTGGCCTTGAATCAGCATA
TTGGCACCCTCATCTTTTAAGCCCAATGTCGCTGGCCTTGAATCAGCACATTGGCACC
Found at i:1435598 original size:19 final size:19
Alignment explanation
Indices: 1435574--1435627 Score: 72
Period size: 20 Copynumber: 2.8 Consensus size: 19
1435564 ACATTATGCT
*
1435574 TTGTATCGATACATGTTCA
1 TTGTATCGATACATGTTAA
* *
1435593 TTGTATTGATACATACTTAA
1 TTGTATCGATACAT-GTTAA
1435613 TTGTATCGATACATG
1 TTGTATCGATACATG
1435628 AAACTGATAG
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 13 0.45
20 16 0.55
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.43
Consensus pattern (19 bp):
TTGTATCGATACATGTTAA
Found at i:1441059 original size:20 final size:21
Alignment explanation
Indices: 1441023--1441061 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
1441013 TTTAATTTTA
*
1441023 ATTTTCTTTTAATTTTAGATT
1 ATTTTATTTTAATTTTAGATT
1441044 ATTTTATTTT-ATTTTAGA
1 ATTTTATTTTAATTTTAGA
1441062 CTAGTTTCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.26, C:0.03, G:0.05, T:0.67
Consensus pattern (21 bp):
ATTTTATTTTAATTTTAGATT
Found at i:1441533 original size:21 final size:20
Alignment explanation
Indices: 1441509--1441547 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1441499 TAGTTGTTAT
1441509 GTTTAATTTTTCTTAATGATA
1 GTTTAA-TTTTCTTAATGATA
* *
1441530 GTTTGATTTTCTTCATGA
1 GTTTAATTTTCTTAATGA
1441548 AATATGTTAT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.23, C:0.08, G:0.13, T:0.56
Consensus pattern (20 bp):
GTTTAATTTTCTTAATGATA
Found at i:1443788 original size:20 final size:19
Alignment explanation
Indices: 1443763--1443815 Score: 63
Period size: 20 Copynumber: 2.7 Consensus size: 19
1443753 TATCACTATT
1443763 TGTATCAATACATG-GTACAA
1 TGTATCAATACATGAG-A-AA
*
1443783 TGTATCGATACATGAAGAAA
1 TGTATCAATACATG-AGAAA
1443803 TGTATCAATACAT
1 TGTATCAATACAT
1443816 AGCTTGTAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 27 0.93
21 1 0.03
22 1 0.03
ACGTcount: A:0.42, C:0.13, G:0.15, T:0.30
Consensus pattern (19 bp):
TGTATCAATACATGAGAAA
Found at i:1449980 original size:13 final size:13
Alignment explanation
Indices: 1449962--1449990 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
1449952 ATAACATTCC
1449962 TTGTATCGATACA
1 TTGTATCGATACA
1449975 TTGTATCGATACA
1 TTGTATCGATACA
1449988 TTG
1 TTG
1449991 GGTACTATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1452458 original size:19 final size:20
Alignment explanation
Indices: 1452430--1452487 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 20
1452420 TTGTATCGAT
*
1452430 ACATTATATCGATACATGT-
1 ACATTGTATCGATACATGTG
*
1452449 TCATTGTATCGATACAT-TG
1 ACATTGTATCGATACATGTG
1452468 ACAAATTGTATCGATACATG
1 AC--ATTGTATCGATACATG
1452488 AAACTGGTAG
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
18 1 0.03
19 16 0.50
21 15 0.47
ACGTcount: A:0.34, C:0.16, G:0.14, T:0.36
Consensus pattern (20 bp):
ACATTGTATCGATACATGTG
Found at i:1452553 original size:13 final size:13
Alignment explanation
Indices: 1452532--1452562 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1452522 CGATACATGG
*
1452532 TACAATGTATCGA
1 TACATTGTATCGA
1452545 TACATTGTATCGA
1 TACATTGTATCGA
1452558 TACAT
1 TACAT
1452563 GAAGAAATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (13 bp):
TACATTGTATCGA
Found at i:1452553 original size:33 final size:32
Alignment explanation
Indices: 1452516--1452582 Score: 100
Period size: 33 Copynumber: 2.0 Consensus size: 32
1452506 CTATCACTAT
1452516 TTGTATCGATACATG-GTACAATGTATCGATACA
1 TTGTATCGATACATGAG-A-AATGTATCGATACA
1452549 TTGTATCGATACATGAAGAAATGTATCGATACA
1 TTGTATCGATACATG-AGAAATGTATCGATACA
1452582 T
1 T
1452583 AGCTTGTAAC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
33 30 0.94
34 1 0.03
35 1 0.03
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (32 bp):
TTGTATCGATACATGAGAAATGTATCGATACA
Found at i:1457561 original size:44 final size:44
Alignment explanation
Indices: 1457511--1457598 Score: 142
Period size: 44 Copynumber: 2.0 Consensus size: 44
1457501 ACTTAAAGAT
1457511 GATGCCACCAACTGGTGTGGGCTTTAAAAAGA-AAAAAAGAAAGG
1 GATGCCACCAACTGGTGTGGGC-TTAAAAAGAGAAAAAAGAAAGG
* *
1457555 GATGCCACCAACTTGTGTGGGCTTAAAAAGAGAAAAAGGAAAGG
1 GATGCCACCAACTGGTGTGGGCTTAAAAAGAGAAAAAAGAAAGG
1457599 TGTCCTGCTC
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
43 9 0.22
44 32 0.78
ACGTcount: A:0.42, C:0.14, G:0.28, T:0.16
Consensus pattern (44 bp):
GATGCCACCAACTGGTGTGGGCTTAAAAAGAGAAAAAAGAAAGG
Found at i:1457660 original size:31 final size:31
Alignment explanation
Indices: 1457625--1457887 Score: 213
Period size: 31 Copynumber: 8.2 Consensus size: 31
1457615 GACTAAAAGG
*
1457625 TGCCACCAACTTGTGTGGGCTTTAGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
* * * * *
1457656 TGCCACCGACTTTTATGGGGTTTGGGAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
* *
1457687 TGCCACCGACTTGTATGGGCTTTGGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
* *
1457718 TACCACCGACTTATGTGGGCTTTAGAAAGGTAAAAGAGT
1 TGCCACCGACTTGTGTGGGCTTTAG-AA-G-----G-GT
* * *** *
1457757 TACCACCAACTTGTACAGGCTTTGGAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
* * *
1457788 TGCCATCGACTTGTGTGGGCTTTGGAAAGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
* *
1457819 TGCCACCGACTTATGTGGGCTTTAAAAGGGT
1 TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
* * *
1457850 T-CCAACCAACATGTGTGGGCTTTAGAAAGGGG
1 TGCC-ACCGACTTGTGTGGGCTTTAG-AAGGGT
1457882 TGCCAC
1 TGCCAC
1457888 AGAGTTATTG
Statistics
Matches: 185, Mismatches: 36, Indels: 21
0.76 0.15 0.09
Matches are distributed among these distances:
30 2 0.01
31 144 0.78
32 11 0.06
33 3 0.02
37 1 0.01
38 3 0.02
39 21 0.11
ACGTcount: A:0.22, C:0.19, G:0.31, T:0.28
Consensus pattern (31 bp):
TGCCACCGACTTGTGTGGGCTTTAGAAGGGT
Done.