Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010101.1 Corchorus capsularis cultivar CVL-1 contig10122, 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: 73818
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Found at i:1398 original size:19 final size:19
Alignment explanation
Indices: 1366--1419 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
1356 TTTTTTCTTA
1366 TTTTCTTATT-TTCTCTT-CC
1 TTTTCTT-TTCTTCT-TTCCC
1385 TTTTCTTTTCTTCTTTCCC
1 TTTTCTTTTCTTCTTTCCC
*
1404 TTTTATTTTCTT-TTTC
1 TTTTCTTTTCTTCTTTC
1420 TTTTTCCTTC
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
18 8 0.25
19 24 0.75
ACGTcount: A:0.04, C:0.24, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTCTTTTCTTCTTTCCC
Found at i:3483 original size:15 final size:15
Alignment explanation
Indices: 3459--3488 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3449 TTTATGTTTA
*
3459 AAAAAGAAAAAATTT
1 AAAAACAAAAAATTT
3474 AAAAACAAAAAATTT
1 AAAAACAAAAAATTT
3489 GGTGCACGCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.73, C:0.03, G:0.03, T:0.20
Consensus pattern (15 bp):
AAAAACAAAAAATTT
Found at i:14407 original size:14 final size:14
Alignment explanation
Indices: 14388--14416 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
14378 TTCTTTGCCG
14388 GACTACTGCTCAAC
1 GACTACTGCTCAAC
14402 GACTACTGCTCAAC
1 GACTACTGCTCAAC
14416 G
1 G
14417 GAAAGAAAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.34, G:0.17, T:0.21
Consensus pattern (14 bp):
GACTACTGCTCAAC
Found at i:20421 original size:9 final size:9
Alignment explanation
Indices: 20409--20442 Score: 59
Period size: 9 Copynumber: 3.7 Consensus size: 9
20399 ATTTTCTTTT
20409 TTTTTTAAA
1 TTTTTTAAA
20418 TTTTTTAAA
1 TTTTTTAAA
20427 TTTTTTTAAA
1 -TTTTTTAAA
20437 TTTTTT
1 TTTTTT
20443 TTAATATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 15 0.62
10 9 0.38
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (9 bp):
TTTTTTAAA
Found at i:20421 original size:10 final size:10
Alignment explanation
Indices: 20408--20443 Score: 65
Period size: 10 Copynumber: 3.7 Consensus size: 10
20398 CATTTTCTTT
20408 TTTTTTTAAA
1 TTTTTTTAAA
20418 -TTTTTTAAA
1 TTTTTTTAAA
20427 TTTTTTTAAA
1 TTTTTTTAAA
20437 TTTTTTT
1 TTTTTTT
20444 TAATATTAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
9 9 0.36
10 16 0.64
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (10 bp):
TTTTTTTAAA
Found at i:20528 original size:26 final size:26
Alignment explanation
Indices: 20499--20566 Score: 102
Period size: 26 Copynumber: 2.6 Consensus size: 26
20489 TATTTAGTTT
20499 ATTAGTTTA-TATTTAATTAGTATCTA
1 ATTAGTTTATTA-TTAATTAGTATCTA
*
20525 ATTAGTTTATTATTAATTAGTATTTA
1 ATTAGTTTATTATTAATTAGTATCTA
*
20551 ATTAGTTTATGATTAA
1 ATTAGTTTATTATTAA
20567 AATGAAGGAA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
26 37 0.95
27 2 0.05
ACGTcount: A:0.35, C:0.01, G:0.09, T:0.54
Consensus pattern (26 bp):
ATTAGTTTATTATTAATTAGTATCTA
Found at i:20551 original size:11 final size:11
Alignment explanation
Indices: 20508--20556 Score: 53
Period size: 11 Copynumber: 4.1 Consensus size: 11
20498 TATTAGTTTA
20508 TATTTAATTAG
1 TATTTAATTAG
*
20519 TATCTAATTAG
1 TATTTAATTAG
20530 TTTATTATTAATTAG
1 --TA-T-TTAATTAG
20545 TATTTAATTAG
1 TATTTAATTAG
20556 T
1 T
20557 TTATGATTAA
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
11 19 0.59
12 1 0.03
13 4 0.12
14 1 0.03
15 7 0.22
ACGTcount: A:0.35, C:0.02, G:0.08, T:0.55
Consensus pattern (11 bp):
TATTTAATTAG
Found at i:20566 original size:15 final size:14
Alignment explanation
Indices: 20499--20566 Score: 58
Period size: 15 Copynumber: 5.1 Consensus size: 14
20489 TATTTAGTTT
20499 ATTAGTTTATATTTA
1 ATTAGTTTATA-TTA
*
20514 ATTAG--TAT-CTA
1 ATTAGTTTATATTA
20525 ATTAGTTTATTATTA
1 ATTAGTTTA-TATTA
20540 ATTAG--TAT-TTA
1 ATTAGTTTATATTA
20551 ATTAGTTTATGATTA
1 ATTAGTTTAT-ATTA
20566 A
1 A
20567 AATGAAGGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 16
0.70 0.03 0.26
Matches are distributed among these distances:
11 15 0.35
12 1 0.02
13 10 0.23
14 1 0.02
15 16 0.37
ACGTcount: A:0.35, C:0.01, G:0.09, T:0.54
Consensus pattern (14 bp):
ATTAGTTTATATTA
Found at i:20610 original size:24 final size:25
Alignment explanation
Indices: 20576--20634 Score: 95
Period size: 25 Copynumber: 2.4 Consensus size: 25
20566 AAATGAAGGA
*
20576 AAATGAA-TTTGAAG-ATTTGTTAG
1 AAATGAAGTTTGAAGAAGTTGTTAG
20599 AAATGAAGTTTGAAGAAGTTGTTAG
1 AAATGAAGTTTGAAGAAGTTGTTAG
20624 AAATGAAGTTT
1 AAATGAAGTTT
20635 AGGGTTTGAA
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
23 7 0.21
24 7 0.21
25 19 0.58
ACGTcount: A:0.41, C:0.00, G:0.24, T:0.36
Consensus pattern (25 bp):
AAATGAAGTTTGAAGAAGTTGTTAG
Found at i:20733 original size:20 final size:20
Alignment explanation
Indices: 20705--20746 Score: 66
Period size: 20 Copynumber: 2.1 Consensus size: 20
20695 CAAAAGTGTA
20705 AAAAAGGGACGGTATTTAGC
1 AAAAAGGGACGGTATTTAGC
* *
20725 AAAAGGGGACGGTGTTTAGC
1 AAAAAGGGACGGTATTTAGC
20745 AA
1 AA
20747 TCCAGTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.38, C:0.10, G:0.33, T:0.19
Consensus pattern (20 bp):
AAAAAGGGACGGTATTTAGC
Found at i:24210 original size:64 final size:64
Alignment explanation
Indices: 24094--24232 Score: 170
Period size: 64 Copynumber: 2.2 Consensus size: 64
24084 GACATTGTCT
* * * * ** *
24094 TGTAATTTTGACTAATTAGCTATGGACAATACGACTCGCAGGGGTATGGATTATCCGTAGGAAG
1 TGTAATTTTGACTAAGTAGCTAAGGACAATACGACTCACAGGGCTACAGATTATACGTAGGAAG
* * * *
24158 TGTAATTTTGACTAAGTAGCTAAGGACAGTGCGACTCATAGGGCTACAGATTATACGTAGGAGG
1 TGTAATTTTGACTAAGTAGCTAAGGACAATACGACTCACAGGGCTACAGATTATACGTAGGAAG
*
24222 CGTAATTTTGA
1 TGTAATTTTGA
24233 TTAATTAGTT
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
64 63 1.00
ACGTcount: A:0.30, C:0.14, G:0.27, T:0.29
Consensus pattern (64 bp):
TGTAATTTTGACTAAGTAGCTAAGGACAATACGACTCACAGGGCTACAGATTATACGTAGGAAG
Found at i:24864 original size:107 final size:106
Alignment explanation
Indices: 24678--24941 Score: 404
Period size: 107 Copynumber: 2.5 Consensus size: 106
24668 AGTTTAGCCT
* *
24678 TAATTTCACTATGTTTAGTCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTTCAAAATT
1 TAATTTCACTAAGTTTAG-CCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
24743 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
65 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
* * *
24785 TAATTTCACTAAGTTTAGCCCCAGATTAAAATTTTATTTTTATTTTAAGTGTAAATTCCATAATT
1 TAATTTCACTAAGTTTAG-CCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATT
* * *
24850 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATATATAAT
65 AATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
** *
24892 TAA-TTCACTAAGTTTAGCCCAAATTAAAATTAAAATTTTATTTTAAGGGT
1 TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGT
24942 TAGAAAAATT
Statistics
Matches: 143, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
105 28 0.20
106 14 0.10
107 101 0.71
ACGTcount: A:0.39, C:0.08, G:0.09, T:0.43
Consensus pattern (106 bp):
TAATTTCACTAAGTTTAGCCCAAATTAAAATTTTATTTTTATTTTAAGGGTAAATTCCAAAATTA
ATAATTTATTGTTATAGGGTTTTAGAAATAAAATACAAAAC
Found at i:27035 original size:31 final size:27
Alignment explanation
Indices: 26968--27036 Score: 68
Period size: 26 Copynumber: 2.4 Consensus size: 27
26958 CAAAAACTTA
26968 CCTATTGAATTTCTAATTTCAAGACAG
1 CCTATTGAATTTCTAATTTCAAGACAG
* **
26995 -TTAACGAATTTCTAATTTACAGAGAGCTAG
1 CCTATTGAATTTCTAATTT-CA-AGA-C-AG
27025 CCTATTGAATTT
1 CCTATTGAATTT
27037 TAAATTATGG
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
26 15 0.48
27 2 0.06
28 3 0.10
29 1 0.03
30 2 0.06
31 8 0.26
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (27 bp):
CCTATTGAATTTCTAATTTCAAGACAG
Found at i:36014 original size:132 final size:131
Alignment explanation
Indices: 35728--36095 Score: 490
Period size: 132 Copynumber: 2.8 Consensus size: 131
35718 ATATTGTCGT
* * * * * * ** * * *
35728 GGAAATTTTGTGCCGCTTACCAGTCAATGATCTGCTGAGATTCAAGTGCGTTTCAAAGGGTTATC
1 GGAAATTTTGTGTCGCTTATCGGTGAAAGATCTGATTCGATTCAGGTGCGTGTCAAAGGGTTTTC
* * * *
35793 GTGATTTAATCGACAGTCCTGATTTCGTGAAAAC-TA--ATAATATCATGAAAACTAATATCTTG
66 GTCATTTAATCGACAGCCCTGATTTCGTG-AAGCTTATCATCATATCATGAAAACTAATATCTTG
*
35855 AT
130 AC
*
35857 GGAAATTTTGTGTCGCTTATCGGTGAAAGATGTGATTCGATTCAGGTGCGTGTCAAAGGGTTTTC
1 GGAAATTTTGTGTCGCTTATCGGTGAAAGATCTGATTCGATTCAGGTGCGTGTCAAAGGGTTTTC
* *
35922 GTTATTTAATCGACAGCCCTGATTTCGTGAAGCTTGATCATCATATCATGAAGACTAATATCTTG
66 GTCATTTAATCGACAGCCCTGATTTCGTGAAGCTT-ATCATCATATCATGAAAACTAATATCTTG
35987 AC
130 AC
* *
35989 GGAAATTTTGTGTCGCTTATCGGTGAGAGATCTGGTTCGATTCAGGTGCGTGTCAAAGGGTTTTC
1 GGAAATTTTGTGTCGCTTATCGGTGAAAGATCTGATTCGATTCAGGTGCGTGTCAAAGGGTTTTC
*
36054 GTCATATAATCGACAGCCCTGATTTCGTGAAGCTTCATCATC
66 GTCATTTAATCGACAGCCCTGATTTCGTGAAGCTT-ATCATC
36096 TCTCCTACGC
Statistics
Matches: 211, Mismatches: 24, Indels: 5
0.88 0.10 0.02
Matches are distributed among these distances:
128 3 0.01
129 81 0.38
130 1 0.00
132 126 0.60
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (131 bp):
GGAAATTTTGTGTCGCTTATCGGTGAAAGATCTGATTCGATTCAGGTGCGTGTCAAAGGGTTTTC
GTCATTTAATCGACAGCCCTGATTTCGTGAAGCTTATCATCATATCATGAAAACTAATATCTTGA
C
Found at i:36259 original size:3 final size:3
Alignment explanation
Indices: 36251--36284 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
36241 TTTTTTATAT
36251 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG A
36285 ATGACATAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.35, C:0.00, G:0.32, T:0.32
Consensus pattern (3 bp):
ATG
Found at i:37750 original size:16 final size:16
Alignment explanation
Indices: 37725--37760 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
37715 TGAATTTATA
* *
37725 TAATATTAATTAATAT
1 TAATAATAATCAATAT
37741 TAATAATAATCAATAT
1 TAATAATAATCAATAT
37757 TAAT
1 TAAT
37761 TTTGCCATAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.44
Consensus pattern (16 bp):
TAATAATAATCAATAT
Found at i:39490 original size:24 final size:25
Alignment explanation
Indices: 39445--39492 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
39435 TTTAATAGGT
* *
39445 TTTAGTTTAATTATTTCTGTCTTTA
1 TTTAGTTTAATTATATCAGTCTTTA
*
39470 TTTA-TTTAATTATATGAGTCTTT
1 TTTAGTTTAATTATATCAGTCTTT
39493 TAGTTTTTTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 16 0.80
25 4 0.20
ACGTcount: A:0.23, C:0.06, G:0.08, T:0.62
Consensus pattern (25 bp):
TTTAGTTTAATTATATCAGTCTTTA
Found at i:40178 original size:95 final size:95
Alignment explanation
Indices: 40047--40242 Score: 347
Period size: 95 Copynumber: 2.1 Consensus size: 95
40037 TTTGTAAAAC
* * *
40047 TTTTGAATCGACCATTATATCCTCATTTTTTTAATATATTTCTTAAATGCCCTTGCTTAAACTAT
1 TTTTTAATCGACCATTATATCCTCATTTTTTAAATATATTTCTTAAATGCCATTGCTTAAACTAT
40112 TGTAGTTTTATTCTATTGATGAAAACTCTA
66 TGTAGTTTTATTCTATTGATGAAAACTCTA
* *
40142 TTTTTAATTGACCATTATATCCTCATTTTTTAAATATATTTCTTAAATGTCATTGCTTAAACTAT
1 TTTTTAATCGACCATTATATCCTCATTTTTTAAATATATTTCTTAAATGCCATTGCTTAAACTAT
40207 TGTAGTTTTATTCTATTGATGAAAACTCTA
66 TGTAGTTTTATTCTATTGATGAAAACTCTA
40237 TTTTTA
1 TTTTTA
40243 TTTAATTATT
Statistics
Matches: 96, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
95 96 1.00
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.49
Consensus pattern (95 bp):
TTTTTAATCGACCATTATATCCTCATTTTTTAAATATATTTCTTAAATGCCATTGCTTAAACTAT
TGTAGTTTTATTCTATTGATGAAAACTCTA
Found at i:41491 original size:68 final size:68
Alignment explanation
Indices: 41364--41501 Score: 190
Period size: 68 Copynumber: 2.0 Consensus size: 68
41354 AGATACCTTC
* * *
41364 CACTATAAGTTCAAGTCTTTACTACTTTTGCAAATCTACATTAGACCAAACAAAATTACCATTAA
1 CACTACAAGTTCAAGCCTTTACTACTTTTGCAAATCCACATTAGACCAAACAAAATTACCATTAA
41429 TCA
66 TCA
* * *
41432 CACTACAAGTTCAAGCCTTTA-TCACTTTTGCCAA-CCCCATTAGCCCAAACAAAATTTACCATT
1 CACTACAAGTTCAAGCCTTTACT-ACTTTTGCAAATCCACATTAGACCAAACAAAA-TTACCATT
41495 AATCA
64 AATCA
41500 CA
1 CA
41502 TATAAATAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
67 18 0.29
68 44 0.71
ACGTcount: A:0.38, C:0.27, G:0.06, T:0.30
Consensus pattern (68 bp):
CACTACAAGTTCAAGCCTTTACTACTTTTGCAAATCCACATTAGACCAAACAAAATTACCATTAA
TCA
Found at i:42175 original size:16 final size:16
Alignment explanation
Indices: 42154--42188 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
42144 ATCTGAAATA
*
42154 CTTCAGAGTTTTTCTG
1 CTTCAGAGCTTTTCTG
42170 CTTCAGAGCTTTTCTG
1 CTTCAGAGCTTTTCTG
42186 CTT
1 CTT
42189 TCTGAATTGT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.11, C:0.23, G:0.17, T:0.49
Consensus pattern (16 bp):
CTTCAGAGCTTTTCTG
Found at i:45609 original size:45 final size:46
Alignment explanation
Indices: 45529--45616 Score: 117
Period size: 45 Copynumber: 1.9 Consensus size: 46
45519 ATGTATCATT
* * *
45529 TGGAGTAATGTTGAATGAATGGAGCTCAAATTGATAATATGCTATG
1 TGGAGGAATGCTGAATGAATGGAGCTCAAATTGATAACATGCTATG
*
45575 TGGAGGAATGCTGAATGGA-GGAGCTC-AATGTGATAACATGCT
1 TGGAGGAATGCTGAATGAATGGAGCTCAAAT-TGATAACATGCT
45617 CTATATACTA
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
44 3 0.08
45 18 0.49
46 16 0.43
ACGTcount: A:0.33, C:0.09, G:0.30, T:0.28
Consensus pattern (46 bp):
TGGAGGAATGCTGAATGAATGGAGCTCAAATTGATAACATGCTATG
Found at i:45873 original size:22 final size:20
Alignment explanation
Indices: 45813--45874 Score: 61
Period size: 22 Copynumber: 3.0 Consensus size: 20
45803 GTATATAATT
*
45813 TTATAGAGAGGTTATCAAAA
1 TTATAGAGAGATTATCAAAA
* * * *
45833 TTATTGGGAGATAAACAAAA
1 TTATAGAGAGATTATCAAAA
45853 TCTTATAGAGAGATTATCAAAA
1 --TTATAGAGAGATTATCAAAA
45875 ACCATAGGAA
Statistics
Matches: 31, Mismatches: 9, Indels: 2
0.74 0.21 0.05
Matches are distributed among these distances:
20 15 0.48
22 16 0.52
ACGTcount: A:0.47, C:0.06, G:0.18, T:0.29
Consensus pattern (20 bp):
TTATAGAGAGATTATCAAAA
Found at i:45978 original size:21 final size:22
Alignment explanation
Indices: 45952--46024 Score: 78
Period size: 22 Copynumber: 3.4 Consensus size: 22
45942 CTTACGGAGT
*
45952 TTATCACAATTTCATA-GATAA
1 TTATCAAAATTTCATATGATAA
* *
45973 TTATCAAAATTTCATATGGTGA
1 TTATCAAAATTTCATATGATAA
* *
45995 TTATCAAAATTTAATAATG-TAG
1 TTATCAAAATTTCAT-ATGATAA
46017 TTATCAAA
1 TTATCAAA
46025 GTTTTATAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
21 15 0.34
22 26 0.59
23 3 0.07
ACGTcount: A:0.42, C:0.10, G:0.08, T:0.40
Consensus pattern (22 bp):
TTATCAAAATTTCATATGATAA
Found at i:46000 original size:22 final size:22
Alignment explanation
Indices: 45908--46006 Score: 76
Period size: 22 Copynumber: 4.5 Consensus size: 22
45898 ATAGCAAAGT
* * *
45908 TTATTAAAATTTCAT-TGTTAGG
1 TTATCAAAATTTCATATGGT-GA
* * * * *
45930 TTATCAAAGTTTCTTACGGAGT
1 TTATCAAAATTTCATATGGTGA
* * *
45952 TTATCACAATTTCATA-GATAA
1 TTATCAAAATTTCATATGGTGA
45973 TTATCAAAATTTCATATGGTGA
1 TTATCAAAATTTCATATGGTGA
45995 TTATCAAAATTT
1 TTATCAAAATTT
46007 AATAATGTAG
Statistics
Matches: 58, Mismatches: 17, Indels: 4
0.73 0.22 0.05
Matches are distributed among these distances:
21 16 0.28
22 41 0.71
23 1 0.02
ACGTcount: A:0.35, C:0.10, G:0.11, T:0.43
Consensus pattern (22 bp):
TTATCAAAATTTCATATGGTGA
Found at i:50024 original size:13 final size:13
Alignment explanation
Indices: 50006--50030 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49996 AAATCTTCTA
50006 TTGAAAATTCTGG
1 TTGAAAATTCTGG
50019 TTGAAAATTCTG
1 TTGAAAATTCTG
50031 AATTACAGAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.20, T:0.40
Consensus pattern (13 bp):
TTGAAAATTCTGG
Found at i:52651 original size:93 final size:93
Alignment explanation
Indices: 52492--52678 Score: 365
Period size: 93 Copynumber: 2.0 Consensus size: 93
52482 ATTGATAGTT
52492 GCAGAATATTTGTTCAAATTTGGGATAATGTTGTGAGGACAAATTGTAGTTTTTAATGATCATGT
1 GCAGAATATTTGTTCAAATTTGGGATAATGTTGTGAGGACAAATTGTAGTTTTTAATGATCATGT
52557 TAGATCCCATTATATAGATGGAGATAGA
66 TAGATCCCATTATATAGATGGAGATAGA
52585 GCAGAATATTTGTTCAAATTTGGGATAATGTTGTGAGGACAAATTGTAGTTTTTAATGATCATGT
1 GCAGAATATTTGTTCAAATTTGGGATAATGTTGTGAGGACAAATTGTAGTTTTTAATGATCATGT
*
52650 TAGCTCCCATTATATAGATGGAGATAGA
66 TAGATCCCATTATATAGATGGAGATAGA
52678 G
1 G
52679 TCCTGAAATC
Statistics
Matches: 93, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 93 1.00
ACGTcount: A:0.33, C:0.08, G:0.23, T:0.36
Consensus pattern (93 bp):
GCAGAATATTTGTTCAAATTTGGGATAATGTTGTGAGGACAAATTGTAGTTTTTAATGATCATGT
TAGATCCCATTATATAGATGGAGATAGA
Found at i:54963 original size:2 final size:2
Alignment explanation
Indices: 54950--54979 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
54940 ATCAACAAAC
*
54950 AT AT AT AG 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
54980 CTCACATTAG
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:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
AT
Found at i:55399 original size:17 final size:17
Alignment explanation
Indices: 55379--55413 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
55369 TGATTATTAA
55379 TTAA-ATTGAAATAAAAT
1 TTAACATTGAAA-AAAAT
55396 TTAACATTGAAAAAAAT
1 TTAACATTGAAAAAAAT
55413 T
1 T
55414 CGGGGAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 10 0.59
18 7 0.41
ACGTcount: A:0.57, C:0.03, G:0.06, T:0.34
Consensus pattern (17 bp):
TTAACATTGAAAAAAAT
Found at i:57045 original size:39 final size:39
Alignment explanation
Indices: 56991--57068 Score: 138
Period size: 39 Copynumber: 2.0 Consensus size: 39
56981 CATCACTCCC
*
56991 TCGTTGTCGCTTGTTCTTTCAAACAAAAAGCTTTGATCA
1 TCGTTGTCGCTTGTTCTTCCAAACAAAAAGCTTTGATCA
*
57030 TCGTTGTCGCTTGTTCTTCCAAACAAAAAGTTTTGATCA
1 TCGTTGTCGCTTGTTCTTCCAAACAAAAAGCTTTGATCA
57069 ACGATGATCA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.26, C:0.21, G:0.15, T:0.38
Consensus pattern (39 bp):
TCGTTGTCGCTTGTTCTTCCAAACAAAAAGCTTTGATCA
Found at i:58064 original size:16 final size:16
Alignment explanation
Indices: 58043--58073 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
58033 TTCTTCTCCA
58043 TATTCTATTGTCTTTC
1 TATTCTATTGTCTTTC
*
58059 TATTCTCTTGTCTTT
1 TATTCTATTGTCTTT
58074 TCCATATTTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.19, G:0.06, T:0.65
Consensus pattern (16 bp):
TATTCTATTGTCTTTC
Found at i:66081 original size:19 final size:19
Alignment explanation
Indices: 66040--66083 Score: 54
Period size: 19 Copynumber: 2.3 Consensus size: 19
66030 TTGTCCTTCT
*
66040 TCTCTCTCCCTCCACTAAG
1 TCTCTCTCCCTCCACTAAC
*
66059 TCTCTCT-CCTCCCACTTAC
1 TCTCTCTCCCT-CCACTAAC
66078 TCTCTC
1 TCTCTC
66084 ATAGTCAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.11, C:0.50, G:0.02, T:0.36
Consensus pattern (19 bp):
TCTCTCTCCCTCCACTAAC
Found at i:68765 original size:11 final size:11
Alignment explanation
Indices: 68751--68788 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
68741 ATTCATAACA
68751 AATTTATAATT
1 AATTTATAATT
68762 AATTTATAATT
1 AATTTATAATT
68773 -ATTTGATAATT
1 AATTT-ATAATT
*
68784 TATTT
1 AATTT
68789 TATATAGAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.16
11 17 0.68
12 4 0.16
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (11 bp):
AATTTATAATT
Found at i:69607 original size:19 final size:19
Alignment explanation
Indices: 69583--69622 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
69573 TGTAACTATC
69583 GGAAGAGAAAGATGAAAAA
1 GGAAGAGAAAGATGAAAAA
69602 GGAAGAGAAAGATGAAAAA
1 GGAAGAGAAAGATGAAAAA
69621 GG
1 GG
69623 TTTGTGTTTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.60, C:0.00, G:0.35, T:0.05
Consensus pattern (19 bp):
GGAAGAGAAAGATGAAAAA
Found at i:71218 original size:17 final size:17
Alignment explanation
Indices: 71196--71230 Score: 70
Period size: 17 Copynumber: 2.1 Consensus size: 17
71186 CAAATCGAAT
71196 ACGCTTGGTTGCAGAAC
1 ACGCTTGGTTGCAGAAC
71213 ACGCTTGGTTGCAGAAC
1 ACGCTTGGTTGCAGAAC
71230 A
1 A
71231 TAAGATCTGA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.23
Consensus pattern (17 bp):
ACGCTTGGTTGCAGAAC
Done.