Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01016330.1 Corchorus capsularis cultivar CVL-1 contig16351, whole genome shotgun sequence
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: 58821
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:4019 original size:10 final size:10
Alignment explanation
Indices: 4004--4032 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
3994 ATCCCATCAT
4004 CTCCATGCTC
1 CTCCATGCTC
4014 CTCCATGCTC
1 CTCCATGCTC
4024 CTCCATGCT
1 CTCCATGCT
4033 TCCTTTCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.10, C:0.48, G:0.10, T:0.31
Consensus pattern (10 bp):
CTCCATGCTC
Found at i:11033 original size:26 final size:27
Alignment explanation
Indices: 10995--11050 Score: 87
Period size: 26 Copynumber: 2.1 Consensus size: 27
10985 TTGCACGCAG
10995 AGTCCATTAATCAAGAGC-TAACACAT
1 AGTCCATTAATCAAGAGCTTAACACAT
* *
11021 AGTCCATTCATCAAGAGCTTAACACGT
1 AGTCCATTAATCAAGAGCTTAACACAT
11048 AGT
1 AGT
11051 TAACAAAGCA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
26 17 0.63
27 10 0.37
ACGTcount: A:0.38, C:0.23, G:0.14, T:0.25
Consensus pattern (27 bp):
AGTCCATTAATCAAGAGCTTAACACAT
Found at i:11883 original size:50 final size:51
Alignment explanation
Indices: 11793--12214 Score: 331
Period size: 51 Copynumber: 8.3 Consensus size: 51
11783 TGAGTTGATG
* * ** *
11793 ATAAAAATGAAAT-TCTTAAAGTAAAAAGATTGAGTTTTTGATTAATTTGT-G
1 ATAAAAATGAAATCT-TTGAACT-AAAAGATTGAACTTTTGATTAATTTGTAA
* * *
11844 ATAAAAATTATATCTTTGAACTAAAAGATTGAACTTTTGATTAATCTGTAA
1 ATAAAAATGAAATCTTTGAACTAAAAGATTGAACTTTTGATTAATTTGTAA
* * * *
11895 ATAAAAATGATATCTTTGAACCAAATGATGGAACTTTTGATTAATTTGTAA
1 ATAAAAATGAAATCTTTGAACTAAAAGATTGAACTTTTGATTAATTTGTAA
* * ** ** * * *
11946 ATAAAAGTGAGATCTTT-AGGTTGAAGATTGACCTTTTAAGTAATTTGT-A
1 ATAAAAATGAAATCTTTGAACTAAAAGATTGAACTTTTGATTAATTTGTAA
* * * * * * *
11995 ATAGAAATGAGACCTTTAAACTAAGAGATTAAACTTTTGATCAATTTGTAA
1 ATAAAAATGAAATCTTTGAACTAAAAGATTGAACTTTTGATTAATTTGTAA
** * * *
12046 ATAAAGGTGAAACCTTTGGACTAAAAGATT-AAATTTTAGATTAATTTGTAA
1 ATAAAAATGAAATCTTTGAACTAAAAGATTGAACTTTT-GATTAATTTGTAA
* *
12097 ATAAAAATGAAATCTTTGAACTAAAAGATTTAA-TTTTGATTGATTTGTAA
1 ATAAAAATGAAATCTTTGAACTAAAAGATTGAACTTTTGATTAATTTGTAA
* * * ** ** * *
12147 TTAAAAAGTGAGACCTTCCAA-TGAAAAGATTGAAAATTTG-TTAAAATTGGAA
1 ATAAAAA-TGAAATCTTTGAACT-AAAAGATTGAACTTTTGATT-AATTTGTAA
12199 AT-AAAATGAAATCTTT
1 ATAAAAATGAAATCTTT
12215 AAGTCAAGGG
Statistics
Matches: 295, Mismatches: 66, Indels: 21
0.77 0.17 0.05
Matches are distributed among these distances:
49 15 0.05
50 98 0.33
51 168 0.57
52 14 0.05
ACGTcount: A:0.43, C:0.06, G:0.14, T:0.36
Consensus pattern (51 bp):
ATAAAAATGAAATCTTTGAACTAAAAGATTGAACTTTTGATTAATTTGTAA
Found at i:12143 original size:151 final size:151
Alignment explanation
Indices: 11793--12163 Score: 377
Period size: 151 Copynumber: 2.4 Consensus size: 151
11783 TGAGTTGATG
* ** * * * *
11793 ATAAAAATGAAATTCTTAAAGTAAAAAGATTGAGTTTTTGATTAATTTGTGATAAAAATTATATC
1 ATAAAAATGAAA-TCTTTAAGT-AAAAGATTGACATTTTGATTAATTTGTAATAAAAATGAGACC
* * * * * *
11858 TTTGAACTAAAAGATTGAACTTTTGATTAATCTGTAAATAAAAATGATATCTTTGAACCAAATGA
64 TTTAAACTAAAAGATTAAACTTTTGATCAATCTGTAAATAAAAATGAAACCTTTGAACCAAAAGA
*
11923 TGGAACTTTTGATTAATTTGTAA
129 TGGAAATTTTGATTAATTTGTAA
* * * ** * * * *
11946 ATAAAAGTGAGATCTTTAGGTTGAAGATTGACCTTTTAAGTAATTTGTAATAGAAATGAGACCTT
1 ATAAAAATGAAATCTTTAAGTAAAAGATTGACATTTTGATTAATTTGTAATAAAAATGAGACCTT
* * ** * *
12011 TAAACTAAGAGATTAAACTTTTGATCAATTTGTAAATAAAGGTGAAACCTTTGGACTAAAAGAT-
66 TAAACTAAAAGATTAAACTTTTGATCAATCTGTAAATAAAAATGAAACCTTTGAACCAAAAGATG
*
12075 TAAATTTTAGATTAATTTGTAA
131 GAAATTTT-GATTAATTTGTAA
* * *
12097 ATAAAAATGAAATCTTTGAACTAAAAGATTTA-ATTTTGATTGATTTGTAATTAAAAAGTGAGAC
1 ATAAAAATGAAATCTTT-AAGTAAAAGATTGACATTTTGATTAATTTGTAA-TAAAAA-TGAGAC
12161 CTT
63 CTT
12164 CCAATGAAAA
Statistics
Matches: 173, Mismatches: 41, Indels: 8
0.78 0.18 0.04
Matches are distributed among these distances:
150 6 0.03
151 127 0.73
152 21 0.12
153 19 0.11
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.37
Consensus pattern (151 bp):
ATAAAAATGAAATCTTTAAGTAAAAGATTGACATTTTGATTAATTTGTAATAAAAATGAGACCTT
TAAACTAAAAGATTAAACTTTTGATCAATCTGTAAATAAAAATGAAACCTTTGAACCAAAAGATG
GAAATTTTGATTAATTTGTAA
Found at i:12788 original size:15 final size:15
Alignment explanation
Indices: 12768--12799 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
12758 AGACACCCAT
*
12768 TTTTAACTCGTATCC
1 TTTTAACTCGTACCC
12783 TTTTAACTCGTACCC
1 TTTTAACTCGTACCC
12798 TT
1 TT
12800 CTACACCTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.28, G:0.06, T:0.47
Consensus pattern (15 bp):
TTTTAACTCGTACCC
Found at i:15645 original size:18 final size:18
Alignment explanation
Indices: 15622--15658 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
15612 CATTTCGACC
15622 GATTAATCCATCATCGGA
1 GATTAATCCATCATCGGA
15640 GATTAATCCATCATCGGA
1 GATTAATCCATCATCGGA
15658 G
1 G
15659 TCCATTTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.22, G:0.19, T:0.27
Consensus pattern (18 bp):
GATTAATCCATCATCGGA
Found at i:18215 original size:15 final size:16
Alignment explanation
Indices: 18195--18224 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
18185 CTCTATCCAT
18195 ATTTATTT-TATTTTC
1 ATTTATTTATATTTTC
18210 ATTTATTTATATTTT
1 ATTTATTTATATTTT
18225 TTGTAAACTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.73
Consensus pattern (16 bp):
ATTTATTTATATTTTC
Found at i:20300 original size:41 final size:42
Alignment explanation
Indices: 20169--20309 Score: 214
Period size: 42 Copynumber: 3.4 Consensus size: 42
20159 ATGCATAGTT
*
20169 AAAGTCAACCATAGTTAAAGTTCTAATCCAGGGTGATTAAGA
1 AAAGTCAAACATAGTTAAAGTTCTAATCCAGGGTGATTAAGA
* *
20211 AAAGTCAACCATAGTTAAAGTTCTAATCTAGGGTGATTAAGA
1 AAAGTCAAACATAGTTAAAGTTCTAATCCAGGGTGATTAAGA
*
20253 AAAGTCAAACATAGTTAAAGTT-TAAATCCA-GGTGATCAAGA
1 AAAGTCAAACATAGTTAAAGTTCT-AATCCAGGGTGATTAAGA
*
20294 AGAGTCAAACATAGTT
1 AAAGTCAAACATAGTT
20310 CAAGGTCCTA
Statistics
Matches: 93, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
41 26 0.28
42 67 0.72
ACGTcount: A:0.43, C:0.13, G:0.18, T:0.26
Consensus pattern (42 bp):
AAAGTCAAACATAGTTAAAGTTCTAATCCAGGGTGATTAAGA
Found at i:20435 original size:61 final size:61
Alignment explanation
Indices: 20339--20454 Score: 187
Period size: 61 Copynumber: 1.9 Consensus size: 61
20329 ATTAAGGAGA
* *
20339 ATATGGTCTTAATTCAGGGTAATTAAGAAAAGAAAGTACAGTCAAGATCCTAATTTGGAAG
1 ATATGGTCTTAATTCAGGGCAATTAAGAAAAGAAAGTACAGTCAAGATCCAAATTTGGAAG
* * *
20400 ATATGGTCTTAATTCAGGGCAATTAAGAAAGGAAAGTACATTCAAGGTCCAAATT
1 ATATGGTCTTAATTCAGGGCAATTAAGAAAAGAAAGTACAGTCAAGATCCAAATT
20455 GGGATAATTA
Statistics
Matches: 50, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
61 50 1.00
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.28
Consensus pattern (61 bp):
ATATGGTCTTAATTCAGGGCAATTAAGAAAAGAAAGTACAGTCAAGATCCAAATTTGGAAG
Found at i:20541 original size:45 final size:45
Alignment explanation
Indices: 20477--21175 Score: 1057
Period size: 45 Copynumber: 15.6 Consensus size: 45
20467 AAGAGTGAAG
* *
20477 TCTTAATTCGGGGTAATTAAGAAAAGTAAACACAGCCAGTCAAAA
1 TCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGTCAGTCAAAA
* * *
20522 TCTTAATTCAGGGTAATTAAGAAAAGTAAACACATTCAGTTAAAG
1 TCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGTCAGTCAAAA
* * * * * *
20567 CCTTAATTCAAGGTAATTAAGAAAAGCAACCATAGTCTGTCAAAA
1 TCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGTCAGTCAAAA
*
20612 TCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGCCAGTCAAAA
1 TCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGTCAGTCAAAA
*
20657 TCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGCCAGTCAAAA
1 TCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGTCAGTCAAAA
* * *
20702 TCTTATTTCAGGGTAATTAAGAAAAGTAAACATAGTCAGTCAAAG
1 TCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGTCAGTCAAAA
*
20747 TCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGTCAGTTAAAA
1 TCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGTCAGTCAAAA
*
20792 TCTTAATTCAGGGTAATTAAGAAAAGCAAACACAGTCAGTCAAAA
1 TCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGTCAGTCAAAA
*
20837 TCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGCCAGTCAAAA
1 TCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGTCAGTCAAAA
*
20882 TCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGCCAGTCAAAA
1 TCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGTCAGTCAAAA
20927 TCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGTCAGTCAAAA
1 TCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGTCAGTCAAAA
* *
20972 TCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGTCAGTTAAAG
1 TCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGTCAGTCAAAA
* * * *
21017 TCTTAATTCAGGGTAATTAAGAAAAGCAACCATAGTCAGTCGAAA
1 TCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGTCAGTCAAAA
*
21062 TCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGTCAGTCAAAG
1 TCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGTCAGTCAAAA
* * * *
21107 TCTTAAATCCGGGTAATTAAGAAAAAG-AAA-ATA--CAGTTAAAGA
1 TCTTAATTCAGGGTAATTAAG-AAAAGTAAACACAGTCAGTCAAA-A
21150 -CTTAATTCAGGGTAATTAAGTAAAAG
1 TCTTAATTCAGGGTAATTAAG-AAAAG
21176 AAGGTAAAGA
Statistics
Matches: 597, Mismatches: 55, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
42 30 0.05
44 2 0.00
45 560 0.94
46 5 0.01
ACGTcount: A:0.45, C:0.14, G:0.16, T:0.25
Consensus pattern (45 bp):
TCTTAATTCAGGGTAATTAAGAAAAGTAAACACAGTCAGTCAAAA
Found at i:21379 original size:32 final size:34
Alignment explanation
Indices: 21335--21419 Score: 102
Period size: 37 Copynumber: 2.5 Consensus size: 34
21325 TAAGTAAGAT
*
21335 CAGTTAAAAACTTAA-CC-CAAGGGGATTAAGTA
1 CAGTTAAGAACTTAATCCACAAGGGGATTAAGTA
* *
21367 GAGTTAAGAACTTAATTCCAAGGAAGGGGATTAAGTA
1 CAGTTAAGAACTTAA-TCC-A-CAAGGGGATTAAGTA
21404 CAGTTAAGAACTTAAT
1 CAGTTAAGAACTTAAT
21420 TCCAAGGAAG
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
32 13 0.30
34 2 0.05
36 1 0.02
37 28 0.64
ACGTcount: A:0.42, C:0.12, G:0.21, T:0.25
Consensus pattern (34 bp):
CAGTTAAGAACTTAATCCACAAGGGGATTAAGTA
Found at i:21398 original size:37 final size:37
Alignment explanation
Indices: 21353--21444 Score: 157
Period size: 37 Copynumber: 2.5 Consensus size: 37
21343 AACTTAACCC
21353 AAGGGGATTAAGTAGAGTTAAGAACTTAATTCCAAGG
1 AAGGGGATTAAGTAGAGTTAAGAACTTAATTCCAAGG
*
21390 AAGGGGATTAAGTACAGTTAAGAACTTAATTCCAAGG
1 AAGGGGATTAAGTAGAGTTAAGAACTTAATTCCAAGG
*
21427 AAGGGAATTAAGTTAGAG
1 AAGGGGATTAAG-TAGAG
21445 ACTTGATTCC
Statistics
Matches: 51, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
37 47 0.92
38 4 0.08
ACGTcount: A:0.41, C:0.08, G:0.27, T:0.24
Consensus pattern (37 bp):
AAGGGGATTAAGTAGAGTTAAGAACTTAATTCCAAGG
Found at i:21454 original size:32 final size:33
Alignment explanation
Indices: 21368--21471 Score: 122
Period size: 37 Copynumber: 3.1 Consensus size: 33
21358 GATTAAGTAG
*
21368 AGTTA-AGAACTTAATTCCAAGGAAGGGGATTA
1 AGTTAGAGAACTTAATTCCAAGGAAGGGAATTA
*
21400 AGTACAGTTAAGAACTTAATTCCAAGGAAGGGAATTA
1 AGT-TAG---AGAACTTAATTCCAAGGAAGGGAATTA
* *
21437 AGTTAGAG-ACTTGATTCCAAGGAAGGGAATCA
1 AGTTAGAGAACTTAATTCCAAGGAAGGGAATTA
21469 AGT
1 AGT
21472 CAAGTTAGAG
Statistics
Matches: 62, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
32 28 0.45
33 3 0.05
36 2 0.03
37 29 0.47
ACGTcount: A:0.40, C:0.11, G:0.25, T:0.24
Consensus pattern (33 bp):
AGTTAGAGAACTTAATTCCAAGGAAGGGAATTA
Found at i:21522 original size:36 final size:36
Alignment explanation
Indices: 21482--21667 Score: 232
Period size: 36 Copynumber: 5.1 Consensus size: 36
21472 CAAGTTAGAG
* *
21482 ACTTAATTCAAGGTAATTAAGTAGCGTCAATAAAGA
1 ACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAGA
* * **
21518 ACTTAATTCACGGTAATTAAGTCGAGTCAAGT-TCGA
1 ACTTAATTCAGGGTAATTAAGTAGAGTCAA-TAAAGA
*
21554 GACTTAATTCAGGGTAATTAAGTAGCGTCAATAAAGA
1 -ACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAGA
* *
21591 ATTTAATTCAGGGTAATTAAGTCGAGTCAATAAAGA
1 ACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAGA
* *
21627 ATTTAATTCAGGGTAATCAAGT-GAAGTCAATAAAGA
1 ACTTAATTCAGGGTAATTAAGTAG-AGTCAATAAAGA
21663 ACTTA
1 ACTTA
21668 CTCTAAAAAG
Statistics
Matches: 131, Mismatches: 15, Indels: 8
0.85 0.10 0.05
Matches are distributed among these distances:
35 1 0.01
36 100 0.76
37 30 0.23
ACGTcount: A:0.41, C:0.11, G:0.19, T:0.29
Consensus pattern (36 bp):
ACTTAATTCAGGGTAATTAAGTAGAGTCAATAAAGA
Found at i:21556 original size:73 final size:73
Alignment explanation
Indices: 21469--21667 Score: 287
Period size: 73 Copynumber: 2.7 Consensus size: 73
21459 AAGGGAATCA
*
21469 AGTCAAGTTAGAGACTTAATTCAAGGTAATTAAGTAGCGTCAATAAAGAACTTAATTCACGGTAA
1 AGTCAAGTTAGAGACTTAATTCAGGGTAATTAAGTAGCGTCAATAAAGAACTTAATTCACGGTAA
21534 TTAAGTCG
66 TTAAGTCG
* * *
21542 AGTCAAGTTCGAGACTTAATTCAGGGTAATTAAGTAGCGTCAATAAAGAATTTAATTCAGGGTAA
1 AGTCAAGTTAGAGACTTAATTCAGGGTAATTAAGTAGCGTCAATAAAGAACTTAATTCACGGTAA
21607 TTAAGTCG
66 TTAAGTCG
* * * *
21615 AGTCAA--TAAAGAATTTAATTCAGGGTAATCAAGT-GAAGTCAATAAAGAACTTA
1 AGTCAAGTTAGAG-ACTTAATTCAGGGTAATTAAGTAG-CGTCAATAAAGAACTTA
21668 CTCTAAAAAG
Statistics
Matches: 114, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
71 4 0.04
72 35 0.31
73 75 0.66
ACGTcount: A:0.41, C:0.11, G:0.20, T:0.29
Consensus pattern (73 bp):
AGTCAAGTTAGAGACTTAATTCAGGGTAATTAAGTAGCGTCAATAAAGAACTTAATTCACGGTAA
TTAAGTCG
Found at i:22271 original size:41 final size:41
Alignment explanation
Indices: 22192--23302 Score: 848
Period size: 41 Copynumber: 26.3 Consensus size: 41
22182 GACACCACCA
* * * *
22192 GAAGGTGTTG-TTCAGTTTCCCGGTCTG-CCTTCCCCATCG
1 GAAGGTGTTGTTTAAATTTCCCAGTTTGCCCTTCCCCATCG
* *
22231 GAAGATGTTGTTTAAATTCCCCAGTTTGCCCTTCCCCATCG
1 GAAGGTGTTGTTTAAATTTCCCAGTTTGCCCTTCCCCATCG
* * * *
22272 GAAGATGTTGTTTAAGTTTCCCAGTTTTCCCTTCCCCACCG
1 GAAGGTGTTGTTTAAATTTCCCAGTTTGCCCTTCCCCATCG
* *
22313 GAAGGTGTTGTTT-AGTTTCCCAGTTTGCCCTTCCCCATCA
1 GAAGGTGTTGTTTAAATTTCCCAGTTTGCCCTTCCCCATCG
* * **
22353 GAAGGTGTTGTTT-AGTTTCCCAGTTTGCCCTGCCCGGTCG
1 GAAGGTGTTGTTTAAATTTCCCAGTTTGCCCTTCCCCATCG
* *
22393 GAAGGTGTTG-TT-AAGTTCCCAGTTTGCTCATT-CCCATCG
1 GAAGGTGTTGTTTAAATTTCCCAGTTTGC-CCTTCCCCATCG
** * **
22432 GAAGGTGTTGTTTAGCTTTCCCAGTTTGCTCTTCCCGGTCG
1 GAAGGTGTTGTTTAAATTTCCCAGTTTGCCCTTCCCCATCG
* * **
22473 GAAGGTGTTGTTTACA-TTCCTAGTTTGCCCTTCCCCGGCG
1 GAAGGTGTTGTTTAAATTTCCCAGTTTGCCCTTCCCCATCG
** * **
22513 GAAGGTGTTGTTTAGCTTTCCCAGTTTGCTCTTCCCCGCCG
1 GAAGGTGTTGTTTAAATTTCCCAGTTTGCCCTTCCCCATCG
* *
22554 GAAGGTGTT-TTCTAAGTCTACATTTCCCATTTTGCCCTTCCCCACCG
1 GAAGGTGTTGTT-T-A----A-ATTTCCCAGTTTGCCCTTCCCCATCG
** *
22601 GAAGGTGTTGTTTAGCTTTCCCAGTTTGCCCTTCCCCGTCG
1 GAAGGTGTTGTTTAAATTTCCCAGTTTGCCCTTCCCCATCG
**
22642 GAAGGTGTTGTTTAAGTCTATATTTCCCAGTTTGCCCTTCCCCATTA
1 GAAGGTGTTGTTT-A----A-ATTTCCCAGTTTGCCCTTCCCCATCG
* ** *
22689 GAAGGTGTTGTTT-AGTTTCATAGTTTGCCCTTCCCCACCG
1 GAAGGTGTTGTTTAAATTTCCCAGTTTGCCCTTCCCCATCG
* *
22729 AAAGGTGTTGTTTAAGTCTATATTTCCCAGTTTGCCTTTCCCCATCG
1 GAAGGTGTTGTTT-A----A-ATTTCCCAGTTTGCCCTTCCCCATCG
* *** * *
22776 GAAGGTGTTGTTTACA-TTCCTTTTTTGCCCTTTCCCACCG
1 GAAGGTGTTGTTTAAATTTCCCAGTTTGCCCTTCCCCATCG
* * * * * *
22816 AAAGATGTTGTTTATATTTCCTAATTTGCCCTTCCCCACCG
1 GAAGGTGTTGTTTAAATTTCCCAGTTTGCCCTTCCCCATCG
** * *
22857 GAAGGTGTTGTTTAGCTTTCCCAGTTTGCCTTTCCCCGTCG
1 GAAGGTGTTGTTTAAATTTCCCAGTTTGCCCTTCCCCATCG
* * *
22898 GAAGGTGTTGTCTAAACCTACTTTTCCCATTTTGCCCTTCCCCACCG
1 GAAGGTGTTGT-TTAA---A--TTTCCCAGTTTGCCCTTCCCCATCG
** * * **
22945 GAAGGTGTTGTTTAGCTTTCCCAATTTGCTCTTCCCCGCCG
1 GAAGGTGTTGTTTAAATTTCCCAGTTTGCCCTTCCCCATCG
* * *
22986 GAAGGTGTTGTCTAAATCTACTTTTCCCATTTTGCCCATCCCCATCG
1 GAAGGTGTTGT-TTAA---A--TTTCCCAGTTTGCCCTTCCCCATCG
* *
23033 GAAGGTGTTGTTTAAGTTTATTTTTCCCAGTTTGCCCTTCCTCATCA
1 GAAGGTGTTGTTTAA----A--TTTCCCAGTTTGCCCTTCCCCATCG
* **
23080 AAAGGTGTTGTTTAGTTTTCCCAGTTTTGCCCTTCCCCATCG
1 GAAGGTGTTGTTTAAATTTCCCAG-TTTGCCCTTCCCCATCG
*
23122 GAAGGTGTTGTCTAAGTCTATATTTCCCA-TCTTGCCCTT-CCCAGTCG
1 GAAGGTGTTG--T---T-TAAATTTCCCAGT-TTGCCCTTCCCCA-TCG
** * * **
23169 GAAGGTGTTGTTTAGCTTTACTAGTTTGCCCTTCCCCGCCG
1 GAAGGTGTTGTTTAAATTTCCCAGTTTGCCCTTCCCCATCG
* * *
23210 GAAGGTGTTGTTTAGATTTCCCATTTTACCCTTCCCCATCG
1 GAAGGTGTTGTTTAAATTTCCCAGTTTGCCCTTCCCCATCG
* * * * *
23251 GAAGGTGTTGTTTACA-TT-CCTGTCTTGCGCTTCCTCACCG
1 GAAGGTGTTGTTTAAATTTCCCAGT-TTGCCCTTCCCCATCG
23291 GAAGGTGTTGTT
1 GAAGGTGTTGTT
23303 CTCTCTTCTA
Statistics
Matches: 870, Mismatches: 148, Indels: 107
0.77 0.13 0.10
Matches are distributed among these distances:
39 42 0.05
40 213 0.24
41 331 0.38
42 35 0.04
44 1 0.00
45 1 0.00
46 13 0.01
47 223 0.26
48 11 0.01
ACGTcount: A:0.15, C:0.27, G:0.20, T:0.38
Consensus pattern (41 bp):
GAAGGTGTTGTTTAAATTTCCCAGTTTGCCCTTCCCCATCG
Found at i:22645 original size:88 final size:88
Alignment explanation
Indices: 22408--23264 Score: 802
Period size: 88 Copynumber: 9.9 Consensus size: 88
22398 TGTTGTTAAG
* * *
22408 TTCCCAGTTTGCTCATT-CCCATCGGAAGGTGTTGTTTAGCTTTCCCAGTTTGCTCTTCCCGGTC
1 TTCCCAGTTTGC-CCTTCCCCATCGGAAGGTGTTGTTTAGCTTTCCCAGTTTGCCCTTCCCCGTC
22472 GGAAGGTGTTG--T---T-TACA-
65 GGAAGGTGTTGTTTAAGTCTACAT
* ** * *
22489 TTCCTAGTTTGCCCTTCCCCGGCGGAAGGTGTTGTTTAGCTTTCCCAGTTTGCTCTTCCCCGCCG
1 TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGCTTTCCCAGTTTGCCCTTCCCCGTCG
22554 GAAGGTGTT-TTCTAAGTCTACAT
66 GAAGGTGTTGTT-TAAGTCTACAT
* *
22577 TTCCCATTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGCTTTCCCAGTTTGCCCTTCCCCGTCG
1 TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGCTTTCCCAGTTTGCCCTTCCCCGTCG
*
22642 GAAGGTGTTGTTTAAGTCTATAT
66 GAAGGTGTTGTTTAAGTCTACAT
** ** **
22665 TTCCCAGTTTGCCCTTCCCCATTAGAAGGTGTTGTTTAG-TTTCATAGTTTGCCCTTCCCCACCG
1 TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGCTTTCCCAGTTTGCCCTTCCCCGTCG
* *
22729 AAAGGTGTTGTTTAAGTCTATAT
66 GAAGGTGTTGTTTAAGTCTACAT
* * *** * **
22752 TTCCCAGTTTGCCTTTCCCCATCGGAAGGTGTTGTTTA-CATTCCTTTTTTGCCCTTTCCCACCG
1 TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGCTTTCCCAGTTTGCCCTTCCCCGTCG
* *
22816 AAAGATGTTGTTT-A---T--AT
66 GAAGGTGTTGTTTAAGTCTACAT
* * * *
22833 TTCCTAATTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGCTTTCCCAGTTTGCCTTTCCCCGTCG
1 TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGCTTTCCCAGTTTGCCCTTCCCCGTCG
* ** *
22898 GAAGGTGTTGTCTAAACCTACTT
66 GAAGGTGTTGTTTAAGTCTACAT
* * * * *
22921 TTCCCATTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGCTTTCCCAATTTGCTCTTCCCCGCCG
1 TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGCTTTCCCAGTTTGCCCTTCCCCGTCG
* * *
22986 GAAGGTGTTGTCTAAATCTACTT
66 GAAGGTGTTGTTTAAGTCTACAT
* * *
23009 TTCCCATTTTGCCCATCCCCATCGGAAGGTGTTGTTTAAGTTTATTTTTCCCAGTTTGCCCTTCC
1 TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTT-AG-----CTTTCCCAGTTTGCCCTTCC
* * **
23074 TCATCAAAAGGTGTTGTTT-AG--T---T
60 CCGTCGGAAGGTGTTGTTTAAGTCTACAT
*
23097 TTCCCAGTTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAAGTCTATATTTCCCA-TCTTGCCCTT
1 TTCCCAG-TTTGCCCTTCCCCATCGGAAGGTGTTGT-TTAG-C----TTTCCCAGT-TTGCCCTT
*
23161 CCCAGTCGGAAGGTGTTGTTT-AG----C-T
58 CCCCGTCGGAAGGTGTTGTTTAAGTCTACAT
* * ** * * * *
23186 TTACTAGTTTGCCCTTCCCCGCCGGAAGGTGTTGTTTAGATTTCCCATTTTACCCTTCCCCATCG
1 TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGCTTTCCCAGTTTGCCCTTCCCCGTCG
23251 GAAGGTGTTGTTTA
66 GAAGGTGTTGTTTA
23265 CATTCCTGTC
Statistics
Matches: 658, Mismatches: 84, Indels: 66
0.81 0.10 0.08
Matches are distributed among these distances:
80 3 0.00
81 100 0.15
82 61 0.09
83 4 0.01
85 1 0.00
86 3 0.00
87 117 0.18
88 264 0.40
89 72 0.11
90 1 0.00
91 1 0.00
93 1 0.00
94 30 0.05
ACGTcount: A:0.15, C:0.27, G:0.20, T:0.38
Consensus pattern (88 bp):
TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTAGCTTTCCCAGTTTGCCCTTCCCCGTCG
GAAGGTGTTGTTTAAGTCTACAT
Found at i:22874 original size:344 final size:336
Alignment explanation
Indices: 22192--23261 Score: 1176
Period size: 344 Copynumber: 3.2 Consensus size: 336
22182 GACACCACCA
* * * * * * *
22192 GAAGGTGTTGTTCAG-TTTCCCGGTCTGCCTTCCCCATCGGAAGATGTTGT-T-----TAAATTC
1 GAAGGTGTTGTTTAGCTTTCCCAGTTTGCCTTCCCCGTCGGAAGGTGTTGTCTAAACCTACATTT
* * * * *
22250 CCCAGTTTGCCCTTCCCCATCGGAAGATGTTGTTTAAG-TTTCCCAGTTTTCCCTTCCCCACCGG
66 CCCATTTTGCCCTTCCCCACCGGAAGGTGTTGTTT-AGCTTTCCCAGTTTGCCCTTCCCCGCCGG
*
22314 AAGGTGTTGTTT-AG-----TTTCCCAGTTTGCCCTTCCCCATCAGAAGGTGTTGTTTAGTTTCC
130 AAGGTGTTGTTTAAGTCTATTTTCCCAGTTTGCCCTTCCCCATCAGAAGGTGTTGTTTAGTTTCA
* * ** *
22373 CAGTTTGCCCTGCCCGGTCGGAAGGTGTTG-TTAAG--TTCCCAGTTTGCTCATT-CCCATCGGA
195 TAGTTTGCCCTTCCCCATCGAAAGGTGTTGTTTAAGTTTTCCCAGTTTGC-CATTCCCCATCGGA
* * * *
22434 AGGTGTTGTTTAGCTTTCCCAGTTTGCTCTTCCCGGTCGGAAGGTGTTGTTTACA-TTCCTAGTT
259 AGGTGTTGTTTA-CATTCCCATTTTGCCCTTCCC-ATCGGAAGGTGTTGTTTACATTTCCTAGTT
*
22498 TGCCCTTCCCCGGCG
322 TGCCCTTCCCCGCCG
* * **
22513 GAAGGTGTTGTTTAGCTTTCCCAGTTTGCTCTTCCCCGCCGGAAGGTGTTTTCTAAGTCTACATT
1 GAAGGTGTTGTTTAGCTTTCCCAGTTTGC-CTTCCCCGTCGGAAGGTGTTGTCTAAACCTACATT
*
22578 TCCCATTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGCTTTCCCAGTTTGCCCTTCCCCGTCGG
65 TCCCATTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGCTTTCCCAGTTTGCCCTTCCCCGCCGG
*
22643 AAGGTGTTGTTTAAGTCTATATTTCCCAGTTTGCCCTTCCCCATTAGAAGGTGTTGTTTAGTTTC
130 AAGGTGTTGTTTAAGTCTAT-TTTCCCAGTTTGCCCTTCCCCATCAGAAGGTGTTGTTTAGTTTC
* *
22708 ATAGTTTGCCCTTCCCCACCGAAAGGTGTTGTTTAAGTCTATATTTCCCAGTTTGCCTTTCCCCA
194 ATAGTTTGCCCTTCCCCATCGAAAGGTGTTGTTTAAG----T-TTTCCCAGTTTGCCATTCCCCA
** * * * *
22773 TCGGAAGGTGTTGTTTACATTCCTTTTTTGCCCTTTCCCACCGAAAGATGTTGTTTATATTTCCT
254 TCGGAAGGTGTTGTTTACATTCCCATTTTGCCC-TTCCCATCGGAAGGTGTTGTTTACATTTCCT
* *
22838 AATTTGCCCTTCCCCACCG
318 AGTTTGCCCTTCCCCGCCG
*
22857 GAAGGTGTTGTTTAGCTTTCCCAGTTTGCCTTTCCCCGTCGGAAGGTGTTGTCTAAACCTACTTT
1 GAAGGTGTTGTTTAGCTTTCCCAGTTTGCC-TTCCCCGTCGGAAGGTGTTGTCTAAACCTACATT
* *
22922 TCCCATTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGCTTTCCCAATTTGCTCTTCCCCGCCGG
65 TCCCATTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGCTTTCCCAGTTTGCCCTTCCCCGCCGG
* * * * *
22987 AAGGTGTTGTCTAAATCTACTTTTCCCATTTTGCCCATCCCCATCGGAAGGTGTTGTTTAAGTTT
130 AAGGTGTTGTTTAAGTCTA-TTTTCCCAGTTTGCCCTTCCCCATCAGAAGGTGTTGTTT-AGTTT
* * *
23052 -ATTTTTCCCAGTTTGCCCTTCCTCATCAAAAGGTGTTGTTT-AGTTTTCCCAGTTTTGCCCTTC
193 CA----T---AGTTTGCCCTTCCCCATCGAAAGGTGTTGTTTAAGTTTTCCCAG-TTTGCCATTC
* *
23115 CCCATCGGAAGGTGTTGTCTAAGTCTATATTTCCCATCTTGCCCTTCCCAGTCGGAAGGTGTTGT
250 CCCATCGGAAGGTGTTG--T---T-TACA-TTCCCATTTTGCCCTTCCCA-TCGGAAGGTGTTGT
*
23180 TTAGC-TTTACTAGTTTGCCCTTCCCCGCCG
307 TTA-CATTTCCTAGTTTGCCCTTCCCCGCCG
* * * *
23210 GAAGGTGTTGTTTAGATTTCCCATTTTACCCTTCCCCATCGGAAGGTGTTGT
1 GAAGGTGTTGTTTAGCTTTCCCAGTTT-GCCTTCCCCGTCGGAAGGTGTTGT
23262 TTACATTCCT
Statistics
Matches: 631, Mismatches: 70, Indels: 64
0.82 0.09 0.08
Matches are distributed among these distances:
321 14 0.02
322 11 0.02
323 18 0.03
324 1 0.00
328 2 0.00
329 72 0.11
330 2 0.00
336 67 0.11
337 5 0.01
343 30 0.05
344 231 0.37
345 14 0.02
346 27 0.04
348 2 0.00
350 2 0.00
351 30 0.05
352 9 0.01
353 92 0.15
354 2 0.00
ACGTcount: A:0.15, C:0.27, G:0.20, T:0.38
Consensus pattern (336 bp):
GAAGGTGTTGTTTAGCTTTCCCAGTTTGCCTTCCCCGTCGGAAGGTGTTGTCTAAACCTACATTT
CCCATTTTGCCCTTCCCCACCGGAAGGTGTTGTTTAGCTTTCCCAGTTTGCCCTTCCCCGCCGGA
AGGTGTTGTTTAAGTCTATTTTCCCAGTTTGCCCTTCCCCATCAGAAGGTGTTGTTTAGTTTCAT
AGTTTGCCCTTCCCCATCGAAAGGTGTTGTTTAAGTTTTCCCAGTTTGCCATTCCCCATCGGAAG
GTGTTGTTTACATTCCCATTTTGCCCTTCCCATCGGAAGGTGTTGTTTACATTTCCTAGTTTGCC
CTTCCCCGCCG
Found at i:23138 original size:89 final size:89
Alignment explanation
Indices: 23007--23220 Score: 283
Period size: 89 Copynumber: 2.4 Consensus size: 89
22997 CTAAATCTAC
* * * *
23007 TTTTCCCA-TTTTGCCCATCCCCATCGGAAGGTGTTGTTTAAGTTTATTTTTCCCAGT-TTGCCC
1 TTTTCCCAGTTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAAGTCTATATTTCCCA-TCTTGCCC
23070 TTCCTCA-TCAAAAGGTGTTGTTTAG
65 TTCC-CAGTCAAAAGGTGTTGTTTAG
23095 TTTTCCCAGTTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAAGTCTATATTTCCCATCTTGCCCT
1 TTTTCCCAGTTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAAGTCTATATTTCCCATCTTGCCCT
**
23160 TCCCAGTCGGAAGGTGTTGTTTAG
66 TCCCAGTCAAAAGGTGTTGTTTAG
* * * **
23184 CTTTACTAG-TTTGCCCTTCCCCGCCGGAAGGTGTTGT
1 TTTTCCCAGTTTTGCCCTTCCCCATCGGAAGGTGTTGT
23221 TTAGATTTCC
Statistics
Matches: 112, Mismatches: 11, Indels: 6
0.87 0.09 0.05
Matches are distributed among these distances:
88 37 0.33
89 75 0.67
ACGTcount: A:0.15, C:0.26, G:0.20, T:0.39
Consensus pattern (89 bp):
TTTTCCCAGTTTTGCCCTTCCCCATCGGAAGGTGTTGTCTAAGTCTATATTTCCCATCTTGCCCT
TCCCAGTCAAAAGGTGTTGTTTAG
Found at i:27077 original size:32 final size:31
Alignment explanation
Indices: 27033--27250 Score: 156
Period size: 32 Copynumber: 7.5 Consensus size: 31
27023 GGGTATTCAT
27033 AAGTCC-CTAAACACAGAGGCATCTCTATCAAA
1 AAGTCCTC-AAACACAGAGGCAT-TCTATCAAA
**
27065 AAGTCCTCAAACACCTAGGCATTC-AT----
1 AAGTCCTCAAACACAGAGGCATTCTATCAAA
27091 AAGTCC-CTAAACACAGAGGCATCTCTATCAAA
1 AAGTCCTC-AAACACAGAGGCAT-TCTATCAAA
*
27123 AAGTCCTCAAACACCTG-GGCATTC-AT----
1 AAGTCCTCAAACA-CAGAGGCATTCTATCAAA
*
27149 AAGTCC-CTTAACACAGAGGCATTTCTATCAAA
1 AAGTCCTC-AAACACAGAGGCA-TTCTATCAAA
*
27181 AAGTCCTCAAACACATG-GGCATTC-AT-AAG
1 AAGTCCTCAAACACA-GAGGCATTCTATCAAA
*
27210 AA--CCT-AAACACAGAGGCATT-TCTC-AA
1 AAGTCCTCAAACACAGAGGCATTCTATCAAA
27236 AAGTCCTCAAACACA
1 AAGTCCTCAAACACA
27251 AGGGCAATTC
Statistics
Matches: 149, Mismatches: 11, Indels: 55
0.69 0.05 0.26
Matches are distributed among these distances:
25 5 0.03
26 49 0.33
27 8 0.05
28 7 0.05
29 11 0.07
30 6 0.04
31 7 0.05
32 50 0.34
33 6 0.04
ACGTcount: A:0.39, C:0.28, G:0.13, T:0.21
Consensus pattern (31 bp):
AAGTCCTCAAACACAGAGGCATTCTATCAAA
Found at i:27096 original size:58 final size:58
Alignment explanation
Indices: 27006--27280 Score: 430
Period size: 58 Copynumber: 4.8 Consensus size: 58
26996 CCCAATAATT
*
27006 AAAGTCCTCAAACACCTGGGTATTCATAAGTCCCTAAACACAGAGGCATCTCTATCAA
1 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATCTCTATCAA
*
27064 AAAGTCCTCAAACACCTAGGCATTCATAAGTCCCTAAACACAGAGGCATCTCTATCAA
1 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATCTCTATCAA
* *
27122 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTTAACACAGAGGCATTTCTATCAA
1 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATCTCTATCAA
* ** *
27180 AAAGTCCTCAAACACATGGGCATTCATAAGAACCTAAACACAGAGGCAT-T-TCTC-A
1 AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATCTCTATCAA
**
27235 AAAGTCCTCAAACACAAGGGCAATTCATAAGTCCCTAAACACAGAG
1 AAAGTCCTCAAACACCTGGGC-ATTCATAAGTCCCTAAACACAGAG
27281 ACAATTTTTC
Statistics
Matches: 203, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
55 21 0.10
56 25 0.12
57 1 0.00
58 156 0.77
ACGTcount: A:0.38, C:0.27, G:0.14, T:0.21
Consensus pattern (58 bp):
AAAGTCCTCAAACACCTGGGCATTCATAAGTCCCTAAACACAGAGGCATCTCTATCAA
Found at i:27102 original size:26 final size:26
Alignment explanation
Indices: 27007--27280 Score: 134
Period size: 26 Copynumber: 9.7 Consensus size: 26
26997 CCAATAATTA
* *
27007 AAGTCCTCAAACACCTG-GGTATTCAT
1 AAGTCCTCAAACA-CAGAGGCATTCAT
27033 AAGTCC-CTAAACACAGAGGCATCTCTAT
1 AAGTCCTC-AAACACAGAGGCAT-TC-AT
**
27061 CAAAAAGTCCTCAAACACCTAGGCATTCAT
1 ----AAGTCCTCAAACACAGAGGCATTCAT
27091 AAGTCC-CTAAACACAGAGGCATCTCTAT
1 AAGTCCTC-AAACACAGAGGCAT-TC-AT
*
27119 CAAAAAGTCCTCAAACACCTG-GGCATTCAT
1 ----AAGTCCTCAAACA-CAGAGGCATTCAT
*
27149 AAGTCC-CTTAACACAGAGGCATTTCTAT
1 AAGTCCTC-AAACACAGAGGCA-TTC-AT
27177 CAAAAAGTCCTCAAACACATG-GGCATTCAT
1 ----AAGTCCTCAAACACA-GAGGCATTCAT
* *
27207 AAGAACCT-AAACACAGAGGCATTTCTCAA
1 AAG-TCCTCAAACACAGAGGCA--T-TCAT
27236 AAGTCCTCAAACACA-AGGGCAATTCAT
1 AAGTCCTCAAACACAGA-GGC-ATTCAT
27263 AAGTCC-CTAAACACAGAG
1 AAGTCCTC-AAACACAGAG
27281 ACAATTTTTC
Statistics
Matches: 196, Mismatches: 14, Indels: 75
0.69 0.05 0.26
Matches are distributed among these distances:
25 8 0.04
26 62 0.32
27 27 0.14
28 13 0.07
29 16 0.08
30 7 0.04
31 7 0.04
32 50 0.26
33 6 0.03
ACGTcount: A:0.38, C:0.27, G:0.14, T:0.21
Consensus pattern (26 bp):
AAGTCCTCAAACACAGAGGCATTCAT
Found at i:27274 original size:27 final size:27
Alignment explanation
Indices: 27181--27277 Score: 85
Period size: 27 Copynumber: 3.6 Consensus size: 27
27171 TTCTATCAAA
*
27181 AAGTCCTCAAACACATGGGC-ATTCAT
1 AAGTCCTCAAACACAAGGGCAATTCAT
* * *
27207 AAGAACCT-AAACAC-AGAGGCATTTCTCAA
1 AAG-TCCTCAAACACAAG-GGCA-AT-TCAT
27236 AAGTCCTCAAACACAAGGGCAATTCAT
1 AAGTCCTCAAACACAAGGGCAATTCAT
27263 AAGTCC-CTAAACACA
1 AAGTCCTC-AAACACA
27278 GAGACAATTT
Statistics
Matches: 56, Mismatches: 7, Indels: 15
0.72 0.09 0.19
Matches are distributed among these distances:
25 1 0.02
26 13 0.23
27 19 0.34
28 5 0.09
29 16 0.29
30 2 0.04
ACGTcount: A:0.41, C:0.27, G:0.13, T:0.19
Consensus pattern (27 bp):
AAGTCCTCAAACACAAGGGCAATTCAT
Found at i:27285 original size:27 final size:26
Alignment explanation
Indices: 27027--27286 Score: 104
Period size: 32 Copynumber: 9.1 Consensus size: 26
27017 ACACCTGGGT
27027 ATTCATAAGTCCCTAAACACAGAGGC-
1 ATTCATAAGT-CCTAAACACAGAGGCA
**
27053 ATCTCTATCAAAAAGTCCTCAAACACCTAGGC-
1 AT-TC-AT----AAGTCCT-AAACACAGAGGCA
27085 ATTCATAAGTCCCTAAACACAGAGGC-
1 ATTCATAAGT-CCTAAACACAGAGGCA
*
27111 ATCTCTATCAAAAAGTCCTCAAACACCTG-GGC-
1 AT-TC-AT----AAGTCCT-AAACA-CAGAGGCA
*
27143 ATTCATAAGTCCCTTAACACAGAGGCA
1 ATTCATAAGT-CCTAAACACAGAGGCA
*
27170 TTTCTATCAAAAAGTCCTCAAACACATG-GGC-
1 ATTC-AT----AAGTCCT-AAACACA-GAGGCA
*
27201 ATTCATAAGAACCTAAACACAGAGGCA
1 ATTCATAAG-TCCTAAACACAGAGGCA
* *
27228 TTTCTCAAAAGTCCTCAAACACA-AGGGCA
1 -AT-TCATAAGTCCT-AAACACAGA-GGCA
*
27257 ATTCATAAGTCCCTAAACACAGAGACA
1 ATTCATAAGT-CCTAAACACAGAGGCA
27284 ATT
1 ATT
27287 TTTCTTCTCT
Statistics
Matches: 182, Mismatches: 17, Indels: 69
0.68 0.06 0.26
Matches are distributed among these distances:
25 3 0.02
26 42 0.23
27 36 0.20
28 16 0.09
29 17 0.09
30 6 0.03
31 16 0.09
32 43 0.24
33 3 0.02
ACGTcount: A:0.39, C:0.27, G:0.13, T:0.21
Consensus pattern (26 bp):
ATTCATAAGTCCTAAACACAGAGGCA
Found at i:34933 original size:8 final size:8
Alignment explanation
Indices: 34920--34961 Score: 52
Period size: 8 Copynumber: 5.4 Consensus size: 8
34910 TACCCAAATG
34920 CCAAATAT
1 CCAAATAT
34928 CCAAATA-
1 CCAAATAT
*
34935 CCAAACAT
1 CCAAATAT
34943 CCAAATA-
1 CCAAATAT
34950 CTCAAATAT
1 C-CAAATAT
34959 CCA
1 CCA
34962 TCAGATTTCA
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
7 7 0.24
8 21 0.72
9 1 0.03
ACGTcount: A:0.50, C:0.31, G:0.00, T:0.19
Consensus pattern (8 bp):
CCAAATAT
Found at i:34933 original size:15 final size:15
Alignment explanation
Indices: 34913--34961 Score: 71
Period size: 15 Copynumber: 3.2 Consensus size: 15
34903 TCATACATAC
*
34913 CCAAATGCCAAATAT
1 CCAAATACCAAATAT
*
34928 CCAAATACCAAACAT
1 CCAAATACCAAATAT
34943 CCAAATACTCAAATAT
1 CCAAATAC-CAAATAT
34959 CCA
1 CCA
34962 TCAGATTTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
15 21 0.70
16 9 0.30
ACGTcount: A:0.49, C:0.31, G:0.02, T:0.18
Consensus pattern (15 bp):
CCAAATACCAAATAT
Found at i:39701 original size:19 final size:18
Alignment explanation
Indices: 39668--39704 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
39658 TTGAAATAAT
39668 TCTTCAATGATCTTCAAG
1 TCTTCAATGATCTTCAAG
*
39686 TCTTCAAATTATCTTCAAG
1 TCTTC-AATGATCTTCAAG
39705 AAATCTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.30, C:0.22, G:0.08, T:0.41
Consensus pattern (18 bp):
TCTTCAATGATCTTCAAG
Found at i:47135 original size:2 final size:2
Alignment explanation
Indices: 47126--47155 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
47116 TATTGTTTTT
47126 TA TA -A TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
47156 TCCGTCGTCA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 26 0.96
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:47999 original size:15 final size:14
Alignment explanation
Indices: 47979--48012 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
47969 CTAACAACTT
*
47979 CTTCAAACTCTCAA
1 CTTCAAACCCTCAA
47993 CCTTCAAACCCTCAA
1 -CTTCAAACCCTCAA
48008 CTTCA
1 CTTCA
48013 TTTCTAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.28
15 13 0.72
ACGTcount: A:0.32, C:0.41, G:0.00, T:0.26
Consensus pattern (14 bp):
CTTCAAACCCTCAA
Found at i:48030 original size:32 final size:34
Alignment explanation
Indices: 47994--48057 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 34
47984 AACTCTCAAC
47994 CTTCAAAC-CCTC-AACTTCATTTCTAACAACTT
1 CTTCAAACTCCTCAAACTTCATTTCTAACAACTT
* *
48026 CTTCAAACTTCTTCAAATTTCATTTCTAACAA
1 CTTCAAAC-TCCTCAAACTTCATTTCTAACAA
48058 ATCTTCTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
32 8 0.30
34 3 0.11
35 16 0.59
ACGTcount: A:0.33, C:0.30, G:0.00, T:0.38
Consensus pattern (34 bp):
CTTCAAACTCCTCAAACTTCATTTCTAACAACTT
Found at i:48107 original size:11 final size:11
Alignment explanation
Indices: 48093--48136 Score: 52
Period size: 11 Copynumber: 3.6 Consensus size: 11
48083 TTAATCATAA
48093 ACTAATTAAAT
1 ACTAATTAAAT
48104 ACTAATTAATCAT
1 ACTAATTAA--AT
48117 AAACTAATTAAAT
1 --ACTAATTAAAT
48130 ACTAATT
1 ACTAATT
48137 GAACATAAAC
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
11 16 0.55
13 4 0.14
15 9 0.31
ACGTcount: A:0.52, C:0.11, G:0.00, T:0.36
Consensus pattern (11 bp):
ACTAATTAAAT
Found at i:48112 original size:26 final size:26
Alignment explanation
Indices: 48083--48150 Score: 120
Period size: 26 Copynumber: 2.6 Consensus size: 26
48073 TTCCTTCATT
48083 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
48109 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
48135 TTGAA-CATAAACTAAT
1 TT-AATCATAAACTAAT
48151 AAACTAAGTA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
26 39 0.95
27 2 0.05
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:48113 original size:15 final size:15
Alignment explanation
Indices: 48083--48150 Score: 64
Period size: 15 Copynumber: 5.1 Consensus size: 15
48073 TTCCTTCATT
48083 TTAATCATAAACTAA
1 TTAATCATAAACTAA
48098 TTAA--AT--ACTAA
1 TTAATCATAAACTAA
48109 TTAATCATAAACTAA
1 TTAATCATAAACTAA
48124 TTAA--AT--ACTAA
1 TTAATCATAAACTAA
48135 TTGAA-CATAAACTAA
1 TT-AATCATAAACTAA
48150 T
1 T
48151 AAACTAAGTA
Statistics
Matches: 45, Mismatches: 0, Indels: 16
0.74 0.00 0.26
Matches are distributed among these distances:
11 16 0.36
12 2 0.04
13 8 0.18
15 19 0.42
ACGTcount: A:0.53, C:0.12, G:0.01, T:0.34
Consensus pattern (15 bp):
TTAATCATAAACTAA
Found at i:48309 original size:33 final size:33
Alignment explanation
Indices: 48254--48353 Score: 130
Period size: 33 Copynumber: 3.0 Consensus size: 33
48244 GCGACTAGCC
* * *
48254 CATGGCCATTGGCTAGCCGCCC-AGCGTGGGCGG
1 CATGGACAATGGCTAGCCGCCCAAAC-TGGGCGG
* *
48287 CGTGGACAATGGTTAGCCGCCCAAACTGGGCGG
1 CATGGACAATGGCTAGCCGCCCAAACTGGGCGG
*
48320 CATGGACAATGGCTAGCCGGCCAAACTGGGCGG
1 CATGGACAATGGCTAGCCGCCCAAACTGGGCGG
48353 C
1 C
48354 TAGGCTATTT
Statistics
Matches: 58, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
33 56 0.97
34 2 0.03
ACGTcount: A:0.19, C:0.30, G:0.37, T:0.14
Consensus pattern (33 bp):
CATGGACAATGGCTAGCCGCCCAAACTGGGCGG
Found at i:48566 original size:21 final size:21
Alignment explanation
Indices: 48540--48584 Score: 81
Period size: 21 Copynumber: 2.1 Consensus size: 21
48530 AAAAATTATA
*
48540 AAAAGGGGGGCGGTGTTTAGC
1 AAAAGGGGGACGGTGTTTAGC
48561 AAAAGGGGGACGGTGTTTAGC
1 AAAAGGGGGACGGTGTTTAGC
48582 AAA
1 AAA
48585 CCCTTTACGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.31, C:0.09, G:0.42, T:0.18
Consensus pattern (21 bp):
AAAAGGGGGACGGTGTTTAGC
Found at i:49622 original size:35 final size:35
Alignment explanation
Indices: 49583--49653 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
49573 ATTATACAGG
* *
49583 TTTGTGCTCTATTTTTCCTTTTGTTCTATGCTATC
1 TTTGTGCTCTATTTTTCATTTTGTTATATGCTATC
*
49618 TTTGTGCTCTATTTTTCATTTTGTTATTTGCTATC
1 TTTGTGCTCTATTTTTCATTTTGTTATATGCTATC
49653 T
1 T
49654 ATCATATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.10, C:0.17, G:0.11, T:0.62
Consensus pattern (35 bp):
TTTGTGCTCTATTTTTCATTTTGTTATATGCTATC
Found at i:52178 original size:6 final size:6
Alignment explanation
Indices: 52167--52271 Score: 76
Period size: 6 Copynumber: 17.2 Consensus size: 6
52157 TATCGAAAGT
* * *
52167 GAACCC GAACCC GAACCC G-ACCC G-GCCC GAACCT GAACCC G-ATCC
1 GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC GAACCC
*
52212 GAACCT GAACCC GAAAATACCC GAACCC GAAGTACCC GAACCC GAACCC
1 GAACCC GAACCC G---A-ACCC GAACCC G-A--ACCC GAACCC GAACCC
52261 G--CCC GAACCC G
1 GAACCC GAACCC G
52272 CCCAATTGCC
Statistics
Matches: 80, Mismatches: 8, Indels: 22
0.73 0.07 0.20
Matches are distributed among these distances:
4 4 0.05
5 13 0.16
6 49 0.61
7 2 0.03
8 1 0.01
9 6 0.08
10 5 0.06
ACGTcount: A:0.30, C:0.46, G:0.19, T:0.05
Consensus pattern (6 bp):
GAACCC
Found at i:52198 original size:22 final size:23
Alignment explanation
Indices: 52167--52271 Score: 83
Period size: 22 Copynumber: 4.6 Consensus size: 23
52157 TATCGAAAGT
52167 GAACCCGAACCCGAACCCGACCC
1 GAACCCGAACCCGAACCCGACCC
* * *
52190 G-GCCCGAACCTGAACCCGATCC
1 GAACCCGAACCCGAACCCGACCC
* ***
52212 GAACCTGAACCCGAA-AATACCC
1 GAACCCGAACCCGAACCCGACCC
52234 GAACCCGAAGTACCCGAACCCGAACCC
1 GAACCCG-A--ACCCGAACCCG-ACCC
52261 G--CCCGAACCCG
1 GAACCCGAACCCG
52272 CCCAATTGCC
Statistics
Matches: 62, Mismatches: 14, Indels: 13
0.70 0.16 0.15
Matches are distributed among these distances:
22 33 0.53
23 12 0.19
24 1 0.02
25 11 0.18
27 5 0.08
ACGTcount: A:0.30, C:0.46, G:0.19, T:0.05
Consensus pattern (23 bp):
GAACCCGAACCCGAACCCGACCC
Found at i:52206 original size:17 final size:17
Alignment explanation
Indices: 52166--52225 Score: 77
Period size: 17 Copynumber: 3.5 Consensus size: 17
52156 ATATCGAAAG
52166 TGAACCCGAACCCGAACC
1 TGAACCCG-ACCCGAACC
* *
52184 CG-ACCCGGCCCGAACC
1 TGAACCCGACCCGAACC
*
52200 TGAACCCGATCCGAACC
1 TGAACCCGACCCGAACC
52217 TGAACCCGA
1 TGAACCCGA
52226 AAATACCCGA
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
16 9 0.25
17 26 0.72
18 1 0.03
ACGTcount: A:0.28, C:0.45, G:0.20, T:0.07
Consensus pattern (17 bp):
TGAACCCGACCCGAACC
Found at i:52239 original size:16 final size:16
Alignment explanation
Indices: 52218--52257 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
52208 ATCCGAACCT
52218 GAACCCGAAAATACCC
1 GAACCCGAAAATACCC
*
52234 GAACCCG-AAGTACCC
1 GAACCCGAAAATACCC
52249 GAACCCGAA
1 GAACCCGAA
52258 CCCGCCCGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 14 0.64
16 8 0.36
ACGTcount: A:0.40, C:0.38, G:0.17, T:0.05
Consensus pattern (16 bp):
GAACCCGAAAATACCC
Found at i:53736 original size:13 final size:14
Alignment explanation
Indices: 53718--53747 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
53708 GTTTGTGTAG
53718 TTTTTCTCTT-TTT
1 TTTTTCTCTTCTTT
53731 TTTTTCTCTTCTTT
1 TTTTTCTCTTCTTT
53745 TTT
1 TTT
53748 AGCCCTTGCT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 10 0.62
14 6 0.38
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTTTCTCTTCTTT
Found at i:54470 original size:14 final size:14
Alignment explanation
Indices: 54451--54483 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
54441 CCTTCAGCAA
54451 TTGTTTTTTTTCTT
1 TTGTTTTTTTTCTT
54465 TTG-TTTTTTTCTT
1 TTGTTTTTTTTCTT
54478 TT-TTTT
1 TTGTTTT
54484 GCTAAAGACC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
13 15 0.83
14 3 0.17
ACGTcount: A:0.00, C:0.06, G:0.06, T:0.88
Consensus pattern (14 bp):
TTGTTTTTTTTCTT
Found at i:55031 original size:14 final size:14
Alignment explanation
Indices: 55012--55042 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
55002 TCGGATTTCG
*
55012 TTTCCGTTTGTTTA
1 TTTCCGTCTGTTTA
55026 TTTCCGTCTGTTTA
1 TTTCCGTCTGTTTA
55040 TTT
1 TTT
55043 TAGAGATATT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.06, C:0.16, G:0.13, T:0.65
Consensus pattern (14 bp):
TTTCCGTCTGTTTA
Found at i:55317 original size:2 final size:2
Alignment explanation
Indices: 55305--55334 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
55295 ACAACTTTAC
*
55305 AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
55335 TATTATTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:56503 original size:12 final size:12
Alignment explanation
Indices: 56486--56510 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
56476 GTTACTTGAG
56486 GTTGTTAGAGAT
1 GTTGTTAGAGAT
56498 GTTGTTAGAGAT
1 GTTGTTAGAGAT
56510 G
1 G
56511 AACTCTAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.00, G:0.36, T:0.40
Consensus pattern (12 bp):
GTTGTTAGAGAT
Found at i:58610 original size:2 final size:2
Alignment explanation
Indices: 58603--58640 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
58593 TTCGTTTTAC
*
58603 TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
58641 GACATAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:58645 original size:12 final size:12
Alignment explanation
Indices: 58603--58646 Score: 61
Period size: 12 Copynumber: 3.7 Consensus size: 12
58593 TTCGTTTTAC
*
58603 TATATATATATA
1 TATACATATATA
*
58615 TATATATATATA
1 TATACATATATA
58627 TATACATATATA
1 TATACATATATA
*
58639 TAGACATA
1 TATACATA
58647 ATTAATTTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 30 1.00
ACGTcount: A:0.50, C:0.05, G:0.02, T:0.43
Consensus pattern (12 bp):
TATACATATATA
Done.