Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012137.1 Corchorus capsularis cultivar CVL-1 contig12158, 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: 92270
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:6129 original size:2 final size:2
Alignment explanation
Indices: 6122--6152 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6112 AAAATTATCC
6122 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
6153 AGAAAGAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:7426 original size:10 final size:10
Alignment explanation
Indices: 7411--7435 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
7401 GAGGACTCTA
7411 GAATTTTCTG
1 GAATTTTCTG
7421 GAATTTTCTG
1 GAATTTTCTG
7431 GAATT
1 GAATT
7436 GTGCAGGAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.24, C:0.08, G:0.20, T:0.48
Consensus pattern (10 bp):
GAATTTTCTG
Found at i:13438 original size:6 final size:6
Alignment explanation
Indices: 13422--13460 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
13412 CAAAACAAAG
13422 TAAAT- TAAATC TAAATC TAAATC TAAATC TAAATC TAAA
1 TAAATC TAAATC TAAATC TAAATC TAAATC TAAATC TAAA
13461 GCAAATTAAT
Statistics
Matches: 33, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.15
6 28 0.85
ACGTcount: A:0.54, C:0.13, G:0.00, T:0.33
Consensus pattern (6 bp):
TAAATC
Found at i:20468 original size:2 final size:2
Alignment explanation
Indices: 20463--20492 Score: 51
Period size: 2 Copynumber: 14.5 Consensus size: 2
20453 TCAACCCTTC
20463 AT AT AT AT AT AT AT AT AT AT AT CAT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT -AT AT AT A
20493 ATAATGCATA
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
2 25 0.93
3 2 0.07
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:22167 original size:15 final size:17
Alignment explanation
Indices: 22141--22173 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
22131 ATCTACCTAC
22141 CAAATATACAAA-TAAA
1 CAAATATACAAACTAAA
22157 CAAAT-TACAAACTAAA
1 CAAATATACAAACTAAA
22173 C
1 C
22174 TCACATTCCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.64, C:0.18, G:0.00, T:0.18
Consensus pattern (17 bp):
CAAATATACAAACTAAA
Found at i:35671 original size:2 final size:2
Alignment explanation
Indices: 35659--35691 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
35649 TGGGTCATTA
35659 AT AT A- AT AT AT 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 AT AT
35692 CATGTAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:35874 original size:34 final size:34
Alignment explanation
Indices: 35836--35904 Score: 102
Period size: 34 Copynumber: 2.0 Consensus size: 34
35826 TAATGTATTG
* *
35836 AAATTTTTATATTAAAAATTAAATTTGATAAGAA
1 AAATTTTTATATTAAAAATCAAATTTGAGAAGAA
* *
35870 AAATTTTTGTATTCAAAATCAAATTTGAGAAGAA
1 AAATTTTTATATTAAAAATCAAATTTGAGAAGAA
35904 A
1 A
35905 TTAGTAGATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
34 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.09, T:0.38
Consensus pattern (34 bp):
AAATTTTTATATTAAAAATCAAATTTGAGAAGAA
Found at i:36681 original size:12 final size:12
Alignment explanation
Indices: 36639--36687 Score: 53
Period size: 12 Copynumber: 4.0 Consensus size: 12
36629 TTTCAGATTT
36639 GGAACGAGTTTA
1 GGAACGAGTTTA
* *
36651 GGAATGACGTTTT
1 GGAACGA-GTTTA
*
36664 GGAACGAGTTCA
1 GGAACGAGTTTA
*
36676 GGAACGGGTTTA
1 GGAACGAGTTTA
36688 ACCGAAACCC
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
12 19 0.66
13 10 0.34
ACGTcount: A:0.29, C:0.10, G:0.35, T:0.27
Consensus pattern (12 bp):
GGAACGAGTTTA
Found at i:36741 original size:12 final size:13
Alignment explanation
Indices: 36710--36742 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
36700 TCCTGAACAT
36710 GTTCCAAAACGCC
1 GTTCCAAAACGCC
*
36723 ATTCCAAAAC-CC
1 GTTCCAAAACGCC
36735 GTTCCAAA
1 GTTCCAAA
36743 GTTTTTTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
12 9 0.50
13 9 0.50
ACGTcount: A:0.36, C:0.36, G:0.09, T:0.18
Consensus pattern (13 bp):
GTTCCAAAACGCC
Found at i:39121 original size:35 final size:35
Alignment explanation
Indices: 39070--39138 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 35
39060 TATAAATACA
*
39070 TTCTTAAAGCTTTTTCATATTCTTTTAGCCTTTCC
1 TTCTTAAAGCTATTTCATATTCTTTTAGCCTTTCC
* *
39105 TTCTTAAGGCTATTTCATATTCTTTTAGCTTTTC
1 TTCTTAAAGCTATTTCATATTCTTTTAGCCTTTC
39139 TTTTAACTGA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.17, C:0.20, G:0.07, T:0.55
Consensus pattern (35 bp):
TTCTTAAAGCTATTTCATATTCTTTTAGCCTTTCC
Found at i:42766 original size:18 final size:18
Alignment explanation
Indices: 42745--42793 Score: 98
Period size: 18 Copynumber: 2.7 Consensus size: 18
42735 TATTATTAAA
42745 TAAATAATAAATATATTT
1 TAAATAATAAATATATTT
42763 TAAATAATAAATATATTT
1 TAAATAATAAATATATTT
42781 TAAATAATAAATA
1 TAAATAATAAATA
42794 ATGAATTCAA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 31 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TAAATAATAAATATATTT
Found at i:44389 original size:13 final size:13
Alignment explanation
Indices: 44366--44399 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
44356 CCAATGCAGC
44366 AGAAGAACAAAGAA
1 AGAA-AACAAAGAA
44380 AGAAAACAAAGAA
1 AGAAAACAAAGAA
44393 AGAAAAC
1 AGAAAAC
44400 CAGCTATCTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.74, C:0.09, G:0.18, T:0.00
Consensus pattern (13 bp):
AGAAAACAAAGAA
Found at i:45007 original size:24 final size:24
Alignment explanation
Indices: 44979--45025 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
44969 GAGGTAGTTG
*
44979 ATGTCGAAAATCCGGTACAACCTA
1 ATGTCGAAAATCCGGCACAACCTA
*
45003 ATGTCGTAAATCCGGCACAACCT
1 ATGTCGAAAATCCGGCACAACCT
45026 CTGAAAGCTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.17, T:0.21
Consensus pattern (24 bp):
ATGTCGAAAATCCGGCACAACCTA
Found at i:45133 original size:51 final size:52
Alignment explanation
Indices: 45074--45206 Score: 168
Period size: 51 Copynumber: 2.7 Consensus size: 52
45064 AGCTAATGTC
* *
45074 GAAGATGAGTTTCTTGATGGTTTGGATGAACTTT-CTCAAGAAGGTGATGAA
1 GAAGATGAGTTTCTTGATGGTTTGGATGAACTTTGCTCAACAAGCTGATGAA
* * *
45125 GAATATGAGTTTCTTGATGGTTTGGATGAA-TTTGTTCAACAAGCTGATGAC
1 GAAGATGAGTTTCTTGATGGTTTGGATGAACTTTGCTCAACAAGCTGATGAA
* *
45176 GAAGATCAG--T-TTGATGGTTTGGCTGAACTTT
1 GAAGATGAGTTTCTTGATGGTTTGGATGAACTTT
45207 TTTTCACGAA
Statistics
Matches: 72, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
48 16 0.22
49 4 0.06
50 3 0.04
51 49 0.68
ACGTcount: A:0.27, C:0.09, G:0.28, T:0.36
Consensus pattern (52 bp):
GAAGATGAGTTTCTTGATGGTTTGGATGAACTTTGCTCAACAAGCTGATGAA
Found at i:54577 original size:16 final size:17
Alignment explanation
Indices: 54551--54592 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 17
54541 CGATGCTGAG
*
54551 GAAGA-AAAAG-AAGAA
1 GAAGAGAAAAGAAAAAA
54566 GAAGAGAAAAGAAAAAA
1 GAAGAGAAAAGAAAAAA
54583 GAA-AGAAAAG
1 GAAGAGAAAAG
54593 TGAGGAGGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
15 5 0.21
16 12 0.50
17 7 0.29
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (17 bp):
GAAGAGAAAAGAAAAAA
Found at i:54604 original size:23 final size:24
Alignment explanation
Indices: 54547--54609 Score: 67
Period size: 23 Copynumber: 2.7 Consensus size: 24
54537 GGTTCGATGC
*
54547 TGAGGAAGAAAAAG-AAGAAGAAG
1 TGAGGAGGAAAAAGAAAGAAGAAG
* ** *
54570 AGAAAAGAAAAAAGAAAGAA-AAG
1 TGAGGAGGAAAAAGAAAGAAGAAG
54593 TGAGGAGGAAAAAGAAA
1 TGAGGAGGAAAAAGAAA
54610 ATAATAATGG
Statistics
Matches: 30, Mismatches: 9, Indels: 2
0.73 0.22 0.05
Matches are distributed among these distances:
23 25 0.83
24 5 0.17
ACGTcount: A:0.67, C:0.00, G:0.30, T:0.03
Consensus pattern (24 bp):
TGAGGAGGAAAAAGAAAGAAGAAG
Found at i:55187 original size:7 final size:7
Alignment explanation
Indices: 55175--55201 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
55165 ATAAACAAAC
55175 CAGTAAT
1 CAGTAAT
55182 CAGTAAT
1 CAGTAAT
55189 CAGTAAT
1 CAGTAAT
55196 CAGTAA
1 CAGTAA
55202 AAGAGTAAGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.26
Consensus pattern (7 bp):
CAGTAAT
Found at i:55261 original size:53 final size:52
Alignment explanation
Indices: 55195--55342 Score: 218
Period size: 53 Copynumber: 2.9 Consensus size: 52
55185 TAATCAGTAA
*
55195 TCAGTAAAAGAGTAAGAAAAGAGTCATAAGTAAAAAGAGTAGAGAACAACAT
1 TCAGTAAAAGAGTAAGAAAAGAGTCATAAGTAAAAAGAGTAGAAAACAACAT
55247 TCAGTAAAAAGAGTAAGAAAAGAGTCATAAGTAAAAAAGAGTAGAAAACAACAT
1 TCAGT-AAAAGAGTAAGAAAAGAGTCATAAGT-AAAAAGAGTAGAAAACAACAT
*
55301 TC------AGAGTAAGAAAAGAGTCATAAGTAAAAAGAGTAGGAAACA
1 TCAGTAAAAGAGTAAGAAAAGAGTCATAAGTAAAAAGAGTAGAAAACA
55343 TTATTTAGCA
Statistics
Matches: 92, Mismatches: 2, Indels: 10
0.88 0.02 0.10
Matches are distributed among these distances:
46 16 0.17
47 23 0.25
52 5 0.05
53 26 0.28
54 22 0.24
ACGTcount: A:0.57, C:0.07, G:0.21, T:0.15
Consensus pattern (52 bp):
TCAGTAAAAGAGTAAGAAAAGAGTCATAAGTAAAAAGAGTAGAAAACAACAT
Found at i:55402 original size:20 final size:20
Alignment explanation
Indices: 55389--55460 Score: 67
Period size: 23 Copynumber: 3.4 Consensus size: 20
55379 AGTAATAGTG
55389 ATCAGTAAGAAGTAAAGGTA
1 ATCAGTAAGAAGTAAAGGTA
55409 ATCAGTAA-AAGAATAAAATGGTA
1 ATCAGTAAGAAG--T-AAA-GGTA
*
55432 ATCAGTAA-AGAGTAAAAGGCA
1 ATCAGTAAGA-AGT-AAAGGTA
55453 ATCAGTAA
1 ATCAGTAA
55461 AGAGTAAAAT
Statistics
Matches: 46, Mismatches: 1, Indels: 9
0.82 0.02 0.16
Matches are distributed among these distances:
19 3 0.07
20 8 0.17
21 12 0.26
22 8 0.17
23 13 0.28
24 2 0.04
ACGTcount: A:0.53, C:0.07, G:0.21, T:0.19
Consensus pattern (20 bp):
ATCAGTAAGAAGTAAAGGTA
Found at i:55441 original size:22 final size:22
Alignment explanation
Indices: 55389--55858 Score: 307
Period size: 22 Copynumber: 21.7 Consensus size: 22
55379 AGTAATAGTG
55389 ATCAGT-AAGAAGT-AAA-GGTA
1 ATCAGTAAAGAA-TAAAATGGTA
55409 ATCAGTAAAAGAATAAAATGGTA
1 ATCAGT-AAAGAATAAAATGGTA
* *
55432 ATCAGTAAAGAGTAAAA-GGCA
1 ATCAGTAAAGAATAAAATGGTA
* *
55453 ATCAGTAAAGAGTAAAATGGCA
1 ATCAGTAAAGAATAAAATGGTA
* ** ** **
55475 ATCAATAAAGCGTCGAATAATA
1 ATCAGTAAAGAATAAAATGGTA
* * * *
55497 ATTAGCAAA-AAGTAAAAAGAT-
1 ATCAGTAAAGAA-TAAAATGGTA
55518 ATCAGTAAAAGAATAAAATGGTA
1 ATCAGT-AAAGAATAAAATGGTA
* * *
55541 ATCATTAAAGAGTAAAAAGGTA
1 ATCAGTAAAGAATAAAATGGTA
55563 ATCAGT-AAGAAGTAAAATGGTA
1 ATCAGTAAAGAA-TAAAATGGTA
* * *
55585 ATGAGTAAAGAGTAAAATAGTA
1 ATCAGTAAAGAATAAAATGGTA
*
55607 ATCAGTAAA-AAGTAAAAAGGTA
1 ATCAGTAAAGAA-TAAAATGGTA
** *
55629 ATCAGTAAAAGGGTAAAATGATA
1 ATCAGT-AAAGAATAAAATGGTA
* * *
55652 ATTAGAAAAGAGTAAAATGGTA
1 ATCAGTAAAGAATAAAATGGTA
* *
55674 ATC-GTTAAAGAGT--AATAGTA
1 ATCAG-TAAAGAATAAAATGGTA
55694 ATCAGT-AAGAAGT--AATGGTA
1 ATCAGTAAAGAA-TAAAATGGTA
*
55714 ATCAGTAAA-AAGTAAAAAGGTA
1 ATCAGTAAAGAA-TAAAATGGTA
*
55736 ACCAGTAAA-AAGTAAAATGGTA
1 ATCAGTAAAGAA-TAAAATGGTA
* * *
55758 ATTAGTAAAGAGTAAAATAGTA
1 ATCAGTAAAGAATAAAATGGTA
* *
55780 ATCAGTTAAA-AGTAAAAGGGTA
1 ATCAG-TAAAGAATAAAATGGTA
55802 ATCAGTAAA-AAGTAAAA-GAGTA
1 ATCAGTAAAGAA-TAAAATG-GTA
*
55824 ATCATTAAAG-A-AAAATGGTA
1 ATCAGTAAAGAATAAAATGGTA
**
55844 AAGAGTAAAGAATAA
1 ATCAGTAAAGAATAA
55859 TCAGTAAAGA
Statistics
Matches: 359, Mismatches: 63, Indels: 54
0.75 0.13 0.11
Matches are distributed among these distances:
19 4 0.01
20 47 0.13
21 42 0.12
22 225 0.63
23 41 0.11
ACGTcount: A:0.54, C:0.05, G:0.20, T:0.21
Consensus pattern (22 bp):
ATCAGTAAAGAATAAAATGGTA
Found at i:55460 original size:44 final size:45
Alignment explanation
Indices: 55389--55844 Score: 400
Period size: 44 Copynumber: 10.5 Consensus size: 45
55379 AGTAATAGTG
*
55389 ATCAGT-AAGAAGT-AAA-GGTAATCAGTAAAAGAATAAAATGGTA
1 ATCAGTAAAG-AGTAAAATGGTAATCAGTAAAAGAGTAAAATGGTA
* *
55432 ATCAGTAAAGAGTAAAA-GGCAATCAGT-AAAGAGTAAAATGGCA
1 ATCAGTAAAGAGTAAAATGGTAATCAGTAAAAGAGTAAAATGGTA
* * ** ** * * * *
55475 ATCAATAAAGCGTCGAATAATAATTAGCAAAA-AGTAAAAAGAT-
1 ATCAGTAAAGAGTAAAATGGTAATCAGTAAAAGAGTAAAATGGTA
* * *
55518 ATCAGTAAAAGAATAAAATGGTAATCA-TTAAAGAGTAAAAAGGTA
1 ATCAGT-AAAGAGTAAAATGGTAATCAGTAAAAGAGTAAAATGGTA
* *
55563 ATCAGT-AAGAAGTAAAATGGTAATGAGT-AAAGAGTAAAATAGTA
1 ATCAGTAAAG-AGTAAAATGGTAATCAGTAAAAGAGTAAAATGGTA
* * * *
55607 ATCAGTAAAAAGTAAAAAGGTAATCAGTAAAAGGGTAAAATGATA
1 ATCAGTAAAGAGTAAAATGGTAATCAGTAAAAGAGTAAAATGGTA
* * * *
55652 ATTAGAAAAGAGTAAAATGGTAATC-GTTAAAGAGT--AATAGTA
1 ATCAGTAAAGAGTAAAATGGTAATCAGTAAAAGAGTAAAATGGTA
*
55694 ATCAGT-AAGAAGT--AATGGTAATCAGTAAAA-AGTAAAAAGGTA
1 ATCAGTAAAG-AGTAAAATGGTAATCAGTAAAAGAGTAAAATGGTA
* * * *
55736 ACCAGTAAAAAGTAAAATGGTAATTAGT-AAAGAGTAAAATAGTA
1 ATCAGTAAAGAGTAAAATGGTAATCAGTAAAAGAGTAAAATGGTA
*
55780 ATCAGTTAAA-AGTAAAAGGGTAATCAGTAAAA-AGTAAAA-GAGTA
1 ATCAG-TAAAGAGTAAAATGGTAATCAGTAAAAGAGTAAAATG-GTA
*
55824 ATCATTAAAGA--AAAATGGTAA
1 ATCAGTAAAGAGTAAAATGGTAA
55845 AGAGTAAAGA
Statistics
Matches: 330, Mismatches: 60, Indels: 47
0.76 0.14 0.11
Matches are distributed among these distances:
40 13 0.04
41 8 0.02
42 34 0.10
43 56 0.17
44 166 0.50
45 53 0.16
ACGTcount: A:0.54, C:0.05, G:0.20, T:0.21
Consensus pattern (45 bp):
ATCAGTAAAGAGTAAAATGGTAATCAGTAAAAGAGTAAAATGGTA
Found at i:55576 original size:66 final size:66
Alignment explanation
Indices: 55389--55840 Score: 368
Period size: 66 Copynumber: 7.0 Consensus size: 66
55379 AGTAATAGTG
* * *
55389 ATCAGTAAGA-AGT-AAA-GGTAATCAGTAAAAGAATAAAATGGTAATCAGTAAAGAGTAAAA-G
1 ATCAGTAAAAGAGTAAAATGGTAATCAGT-AAAGAGTAAAAAGGTAATCAGTAAA-AGTAAAATG
**
55450 GCA
64 ATA
* * * * * * *
55453 ATCAGT-AAAGAGTAAAATGGCAATCAATAAAGCGTCGAATAA--TAATTAGCAAAAAGTAAAAA
1 ATCAGTAAAAGAGTAAAATGGTAATCAGTAAAGAGT--AAAAAGGTAATCAG-TAAAAGTAAAAT
55515 GAT-
63 GATA
* * *
55518 ATCAGTAAAAGAATAAAATGGTAATCATTAAAGAGTAAAAAGGTAATCAGTAAGAAGTAAAATGG
1 ATCAGTAAAAGAGTAAAATGGTAATCAGTAAAGAGTAAAAAGGTAATCAGTAA-AAGTAAAATGA
55583 TA
65 TA
* * *
55585 ATGAGT-AAAGAGTAAAATAGTAATCAGTAAAAAGTAAAAAGGTAATCAGTAAAAGGGTAAAATG
1 ATCAGTAAAAGAGTAAAATGGTAATCAGTAAAGAGTAAAAAGGTAATCAGTAAAA--GTAAAATG
55649 ATA
64 ATA
* *
55652 ATTAG-AAAAGAGTAAAATGGTAATC-GTTAAAGAGT-AATA-GTAATCAGTAAGAAGT--AATG
1 ATCAGTAAAAGAGTAAAATGGTAATCAG-TAAAGAGTAAAAAGGTAATCAGTAA-AAGTAAAATG
*
55711 GTA
64 ATA
* * * * *
55714 ATCAGTAAAA-AGTAAAAAGGTAACCAGTAAAAAGTAAAATGGTAATTAGTAAAGAGTAAAAT-A
1 ATCAGTAAAAGAGTAAAATGGTAATCAGTAAAGAGTAAAAAGGTAATCAGTAAA-AGTAAAATGA
55777 GTA
65 -TA
* * * * *
55780 ATCAGTTAAA-AGTAAAAGGGTAATCAGTAAAAAGT-AAAAGAGTAATCA-TTAAAGAAAAATG
1 ATCAGTAAAAGAGTAAAATGGTAATCAGTAAAGAGTAAAAAG-GTAATCAGTAAAAGTAAAATG
55841 GTAAAGAGTA
Statistics
Matches: 315, Mismatches: 46, Indels: 53
0.76 0.11 0.13
Matches are distributed among these distances:
62 30 0.10
63 10 0.03
64 35 0.11
65 49 0.16
66 144 0.46
67 47 0.15
ACGTcount: A:0.54, C:0.05, G:0.20, T:0.21
Consensus pattern (66 bp):
ATCAGTAAAAGAGTAAAATGGTAATCAGTAAAGAGTAAAAAGGTAATCAGTAAAAGTAAAATGAT
A
Found at i:55727 original size:7 final size:7
Alignment explanation
Indices: 55717--55824 Score: 63
Period size: 7 Copynumber: 14.7 Consensus size: 7
55707 AATGGTAATC
55717 AGTAAAA
1 AGTAAAA
55724 AGTAAAA
1 AGTAAAA
**
55731 AGGTAACC
1 A-GTAAAA
55739 AGTAAAA
1 AGTAAAA
55746 AGTAAAA
1 AGTAAAA
* **
55753 TGGTAATT
1 -AGTAAAA
*
55761 AGTAAAG
1 AGTAAAA
55768 AGTAAAA
1 AGTAAAA
**
55775 TAGTAATC
1 -AGTAAAA
*
55783 AGTTAAA
1 AGTAAAA
55790 AGTAAAA
1 AGTAAAA
* **
55797 GGGTAATC
1 -AGTAAAA
55805 AGTAAAA
1 AGTAAAA
55812 AGTAAAA
1 AGTAAAA
55819 GAGTAA
1 -AGTAA
55825 TCATTAAAGA
Statistics
Matches: 73, Mismatches: 23, Indels: 9
0.70 0.22 0.09
Matches are distributed among these distances:
7 50 0.68
8 23 0.32
ACGTcount: A:0.56, C:0.04, G:0.19, T:0.20
Consensus pattern (7 bp):
AGTAAAA
Found at i:55886 original size:173 final size:173
Alignment explanation
Indices: 55526--55901 Score: 474
Period size: 173 Copynumber: 2.2 Consensus size: 173
55516 ATATCAGTAA
* * * *
55526 AAGAATAAAATGGTAATCATTAAAGAGTAAAAAGGTAATCAGTAAGAAGTAAAATGGTAATGAGT
1 AAGAAGAAAATGGTAATCAGTAAAGAGTAAAAAGGTAACCAGTAAAAAGTAAAATGGTAATGAGT
* *
55591 AAAGAGTAAAATAGTAATCAGTAAAAAGTAAAAAGGTAATCAGTAAAAGGGTAAAATGATAATTA
66 AAAGAGTAAAATAGTAATCAGTAAAAAGTAAAAAGGTAATCAGTAAAAGAGTAAAATGATAATCA
* * * *
55656 GAAAAGAGTAAAATGGTAATCGTTAAAGAGTAATAGTAATCAGT
131 GAAAAGAG-AAAATGGTAATAGGTAAAGAATAATAGTAAACAGT
* * *
55700 AAGAAG-TAATGGTAATCAGTAAAAAGTAAAAAGGTAACCAGTAAAAAGTAAAATGGTAATTAGT
1 AAGAAGAAAATGGTAATCAGTAAAGAGTAAAAAGGTAACCAGTAAAAAGTAAAATGGTAATGAGT
* *
55764 AAAGAGTAAAATAGTAATCAGTTAAAAGTAAAAGGGTAATCAGTAAAA-AGTAAAA-GAGTAATC
66 AAAGAGTAAAATAGTAATCAGTAAAAAGTAAAAAGGTAATCAGTAAAAGAGTAAAATGA-TAATC
** *
55827 ATTAAAGA-AAAATGGTAA-AGAGTAAAGAATAATCAGTAAAGAGT
130 AGAAAAGAGAAAATGGTAATAG-GTAAAGAATAAT-AGTAAACAGT
** **
55871 AATCAGCAAAATGGTAAAGAGTAAAGAGTAA
1 AAGAAG-AAAATGGTAATCAGTAAAGAGTAA
55902 TCAGTAAGGA
Statistics
Matches: 173, Mismatches: 24, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
169 1 0.01
170 20 0.12
171 14 0.08
172 16 0.09
173 117 0.68
174 5 0.03
ACGTcount: A:0.54, C:0.04, G:0.20, T:0.22
Consensus pattern (173 bp):
AAGAAGAAAATGGTAATCAGTAAAGAGTAAAAAGGTAACCAGTAAAAAGTAAAATGGTAATGAGT
AAAGAGTAAAATAGTAATCAGTAAAAAGTAAAAAGGTAATCAGTAAAAGAGTAAAATGATAATCA
GAAAAGAGAAAATGGTAATAGGTAAAGAATAATAGTAAACAGT
Found at i:55907 original size:14 final size:14
Alignment explanation
Indices: 55847--55908 Score: 63
Period size: 14 Copynumber: 4.4 Consensus size: 14
55837 AATGGTAAAG
*
55847 AGTAAAGAATAATC
1 AGTAAAGAGTAATC
55861 AGTAAAGAGTAATC
1 AGTAAAGAGTAATC
* **
55875 AGCAAA-ATGGTAAAG
1 AGTAAAGA--GTAATC
55890 AGTAAAGAGTAATC
1 AGTAAAGAGTAATC
55904 AGTAA
1 AGTAA
55909 GGAAAAAATG
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
13 1 0.03
14 27 0.71
15 9 0.24
16 1 0.03
ACGTcount: A:0.53, C:0.06, G:0.21, T:0.19
Consensus pattern (14 bp):
AGTAAAGAGTAATC
Found at i:55954 original size:35 final size:34
Alignment explanation
Indices: 55878--55944 Score: 98
Period size: 35 Copynumber: 1.9 Consensus size: 34
55868 AGTAATCAGC
55878 AAAATGGTAAAGAGTAAAGAGTAATCAGTAAGGAA
1 AAAATGGTAAAGAGTAAAGAGTAATCAGTAA-GAA
* *
55913 AAAATGGTAAAGAGTAAAATATTAATCAGTAA
1 AAAATGGTAAAGAGT-AAAGAGTAATCAGTAA
55945 AAAGTAATGG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
35 15 0.52
36 14 0.48
ACGTcount: A:0.55, C:0.03, G:0.21, T:0.21
Consensus pattern (34 bp):
AAAATGGTAAAGAGTAAAGAGTAATCAGTAAGAA
Found at i:55986 original size:78 final size:76
Alignment explanation
Indices: 55762--55973 Score: 225
Period size: 78 Copynumber: 2.7 Consensus size: 76
55752 ATGGTAATTA
* * *
55762 GTAAAGAGTAAAATAGTAATCAGTTAAAAGTAAAAGGGTAATCAGTAAA-AAGTAAAAGAGTAAT
1 GTAAAGAGTAAAATA-TAATCAGTAAAAAGT--AATGGCAATCAGTAAAGAA-TAAAAGAGTAAT
*
55826 CATTAAAGAAAAATG
62 CAGTAAAGAAAAATG
* * * *
55841 GTAAAGAGTAAAGA-ATAATCAGTAAAGAGTAATCAGCAAAAT-GGTAAAGAGT-AAAGAGTAAT
1 GTAAAGAGTAAA-ATATAATCAGTAAAAAGTAAT-GGC--AATCAGTAAAGAATAAAAGAGTAAT
*
55903 CAGTAAGGAAAAAATG
62 CAGTAAAG-AAAAATG
55919 GTAAAGAGTAAAATATTAATCAGTAAAAAGTAATGGCAATCAGTAAAGAATAAAA
1 GTAAAGAGTAAAATA-TAATCAGTAAAAAGTAATGGCAATCAGTAAAGAATAAAA
55974 TGGTAACTAG
Statistics
Matches: 110, Mismatches: 13, Indels: 21
0.76 0.09 0.15
Matches are distributed among these distances:
76 5 0.05
77 26 0.24
78 44 0.40
79 34 0.31
80 1 0.01
ACGTcount: A:0.55, C:0.05, G:0.20, T:0.20
Consensus pattern (76 bp):
GTAAAGAGTAAAATATAATCAGTAAAAAGTAATGGCAATCAGTAAAGAATAAAAGAGTAATCAGT
AAAGAAAAATG
Found at i:56006 original size:21 final size:21
Alignment explanation
Indices: 55976--56037 Score: 63
Period size: 21 Copynumber: 2.9 Consensus size: 21
55966 GAATAAAATG
*
55976 GTAACTAGTAATTAGTAAAGA
1 GTAACCAGTAATTAGTAAAGA
* *
55997 GTAACCAGTAAAATAGT-AATA
1 GTAACCAGT-AATTAGTAAAGA
*
56018 GTAATCAGTAATTCAGTAAA
1 GTAACCAGTAATT-AGTAAA
56038 AAGTGAGTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 5
0.77 0.12 0.12
Matches are distributed among these distances:
20 3 0.09
21 22 0.67
22 8 0.24
ACGTcount: A:0.48, C:0.08, G:0.16, T:0.27
Consensus pattern (21 bp):
GTAACCAGTAATTAGTAAAGA
Found at i:63192 original size:19 final size:19
Alignment explanation
Indices: 63168--63215 Score: 78
Period size: 19 Copynumber: 2.5 Consensus size: 19
63158 GAGAAGGAAA
63168 AAGAAAATAAAAAGAAAAG
1 AAGAAAATAAAAAGAAAAG
**
63187 AAGAAACGAAAAAGAAAAG
1 AAGAAAATAAAAAGAAAAG
63206 AAGAAAATAA
1 AAGAAAATAA
63216 GAGAATTAAT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.77, C:0.02, G:0.17, T:0.04
Consensus pattern (19 bp):
AAGAAAATAAAAAGAAAAG
Found at i:63689 original size:2 final size:2
Alignment explanation
Indices: 63682--63707 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
63672 TTGTATACAA
63682 AT AT 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
63708 CTAATTAAAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:92162 original size:132 final size:133
Alignment explanation
Indices: 92020--92270 Score: 407
Period size: 132 Copynumber: 1.9 Consensus size: 133
92010 AATTCATAGT
92020 CTTTTCGCAACGACTTCTGCTAGTCATTGT-TTAATATATTTTACAAATTGATTTTCGCAGCGAC
1 CTTTTCGCAACGACTTCTGCTAGTCATT-TCTTAATATATTTTACAAATTGATTTTCGCAGCGAC
*
92084 CTTGAAAGTCTCTAC-AAAAAACATGATTACTTTTGAAACGACATATTAAGTCGTTGCGAAATCT
65 CTTGAAAGTCGCTACAAAAAAACATGATTACTTTTGAAACGACATATTAAGTCGTTGCGAAATCT
92148 GAAA
130 GAAA
* * * *
92152 CTTTTTGCAACGACTTTTGTTAGTCGTTTCTTAATATATTTTACAAATTGATTTTCGCAGCGACC
1 CTTTTCGCAACGACTTCTGCTAGTCATTTCTTAATATATTTTACAAATTGATTTTCGCAGCGACC
*
92217 TTGAAAGTCGCTACAAAAAAAAATATGATTACTTTTGAAACGACATATTAAGTC
66 TTGAAAGTCGCTAC--AAAAAAACATGATTACTTTTGAAACGACATATTAAGTC
Statistics
Matches: 109, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
131 1 0.01
132 72 0.66
135 36 0.33
ACGTcount: A:0.33, C:0.17, G:0.14, T:0.36
Consensus pattern (133 bp):
CTTTTCGCAACGACTTCTGCTAGTCATTTCTTAATATATTTTACAAATTGATTTTCGCAGCGACC
TTGAAAGTCGCTACAAAAAAACATGATTACTTTTGAAACGACATATTAAGTCGTTGCGAAATCTG
AAA
Done.