Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014091.1 Corchorus olitorius cultivar O-4 contig14124, 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: 79444
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:863 original size:22 final size:22
Alignment explanation
Indices: 816--870 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 22
806 CGAAAAATTC
* *
816 CTCCTTGTAGTTGACTATTGCT
1 CTCCTTGAAGTTGACTATTGCA
*
838 CTCCTTGAAGTTGA-TAATTTCA
1 CTCCTTGAAGTTGACT-ATTGCA
860 CTCCTTGAAGT
1 CTCCTTGAAGT
871 CGACAATTCC
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
21 1 0.03
22 28 0.97
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42
Consensus pattern (22 bp):
CTCCTTGAAGTTGACTATTGCA
Found at i:12939 original size:2 final size:2
Alignment explanation
Indices: 12932--12956 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12922 CTCTCAAATA
12932 GT GT GT GT GT GT GT GT GT GT GT GT G
1 GT GT GT GT GT GT GT GT GT GT GT GT G
12957 ATTACCACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.52, T:0.48
Consensus pattern (2 bp):
GT
Found at i:13711 original size:16 final size:17
Alignment explanation
Indices: 13690--13722 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
13680 TATGGTCGAA
13690 ATTTTTTTAAT-TTTTT
1 ATTTTTTTAATATTTTT
13706 ATTTTTTTAATATTTTT
1 ATTTTTTTAATATTTTT
13723 TCGATATAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (17 bp):
ATTTTTTTAATATTTTT
Found at i:15515 original size:21 final size:19
Alignment explanation
Indices: 15490--15528 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 19
15480 ACTATTCTAA
15490 GTTGGTGTTGTTATGTTTTCG
1 GTTGGT-TTG-TATGTTTTCG
*
15511 GTTGGTTTGTATTTTTTC
1 GTTGGTTTGTATGTTTTC
15529 TGCTGTTGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.05, C:0.05, G:0.28, T:0.62
Consensus pattern (19 bp):
GTTGGTTTGTATGTTTTCG
Found at i:19773 original size:2 final size:2
Alignment explanation
Indices: 19768--19792 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
19758 TTTTGTTGTG
19768 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 T
19793 TTTAAATATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:25499 original size:21 final size:21
Alignment explanation
Indices: 25473--25513 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
25463 CACCACGTGA
25473 GTGTATAAAACAAAGAATAAT
1 GTGTATAAAACAAAGAATAAT
25494 GTGTATAAAACAAAGAATAA
1 GTGTATAAAACAAAGAATAA
25514 CTTCATATAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.59, C:0.05, G:0.15, T:0.22
Consensus pattern (21 bp):
GTGTATAAAACAAAGAATAAT
Found at i:28007 original size:13 final size:14
Alignment explanation
Indices: 27975--28012 Score: 60
Period size: 14 Copynumber: 2.8 Consensus size: 14
27965 AAATTGTAAA
27975 ATTTAAAAAATATC
1 ATTTAAAAAATATC
*
27989 ATTTAAGAAATAT-
1 ATTTAAAAAATATC
28002 ATTTAAAAAAT
1 ATTTAAAAAAT
28013 TCTAATATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 10 0.45
14 12 0.55
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (14 bp):
ATTTAAAAAATATC
Found at i:28735 original size:1 final size:1
Alignment explanation
Indices: 28729--28755 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
28719 TATATGTTAT
28729 AAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAA
28756 CTATCCATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:30424 original size:4 final size:4
Alignment explanation
Indices: 30415--30595 Score: 127
Period size: 4 Copynumber: 45.8 Consensus size: 4
30405 CAATTTTAAT
* * * * *
30415 TATA TATA TATA TATG TATG TATG TATG TATA AATA TATA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * * *
30463 -AGTA TGTA TATA TATA TATA TGTA TGTA TGTA TAAA TATA TATA TA-A
1 TA-TA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * * * * *
30510 GA-A TGTA TGTA TATA TATA TATA TGTA TGTA TGTA TAAA TATA TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * *
30557 TATA TATT TATA TA-A GTATG TATG TATG TATA TATA TAT
1 TATA TATA TATA TATA -TATA TATA TATA TATA TATA TAT
30596 GTGTGTGTAT
Statistics
Matches: 150, Mismatches: 22, Indels: 10
0.82 0.12 0.05
Matches are distributed among these distances:
3 5 0.03
4 145 0.97
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.47
Consensus pattern (4 bp):
TATA
Found at i:30485 original size:46 final size:46
Alignment explanation
Indices: 30423--30595 Score: 181
Period size: 46 Copynumber: 3.7 Consensus size: 46
30413 ATTATATATA
* *
30423 TATATATGTATGTATGTATGTATAAATATATATATATATAAGTATG
1 TATATATATATATATGTATGTATAAATATATATATATATAAGTATG
*
30469 TATATATATATATATGTATGTATGTATAA-ATATATATATAAGAATGTATG
1 TATATATATATATATGTATGTA--TA-AATATATATATAT-ATAA-GTATG
** * *
30519 TATATATATATATATGTATGTATGTATAAATATATATATATA-TATT
1 TATATATATATATATGTATGTATAAATATATATATATATA-AGTATG
* *
30565 TATATA-AGTATGTATGTATGTATATATATAT
1 TATATATA-TATATATGTATGTATAAATATAT
30596 GTGTGTGTAT
Statistics
Matches: 108, Mismatches: 11, Indels: 16
0.80 0.08 0.12
Matches are distributed among these distances:
45 1 0.01
46 49 0.45
47 3 0.03
48 23 0.21
49 5 0.05
50 27 0.25
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (46 bp):
TATATATATATATATGTATGTATAAATATATATATATATAAGTATG
Found at i:30494 original size:50 final size:51
Alignment explanation
Indices: 30411--30562 Score: 256
Period size: 50 Copynumber: 3.0 Consensus size: 51
30401 GCATCAATTT
* *
30411 TAAT-TATATATATATATATGTATGTATGTATGTATAAATATATATATATA
1 TAATGTATGTATATATATATATATGTATGTATGTATAAATATATATATATA
30461 TAA-GTATGTATATATATATATATGTATGTATGTATAAATATATATATA-A
1 TAATGTATGTATATATATATATATGTATGTATGTATAAATATATATATATA
*
30510 GAATGTATGTATATATATATATATGTATGTATGTATAAATATATATATATA
1 TAATGTATGTATATATATATATATGTATGTATGTATAAATATATATATATA
30561 TA
1 TA
30563 TTTATATAAG
Statistics
Matches: 95, Mismatches: 4, Indels: 5
0.91 0.04 0.05
Matches are distributed among these distances:
49 3 0.03
50 90 0.95
51 2 0.02
ACGTcount: A:0.44, C:0.00, G:0.10, T:0.46
Consensus pattern (51 bp):
TAATGTATGTATATATATATATATGTATGTATGTATAAATATATATATATA
Found at i:30556 original size:26 final size:26
Alignment explanation
Indices: 30417--30559 Score: 204
Period size: 26 Copynumber: 5.7 Consensus size: 26
30407 ATTTTAATTA
* *
30417 TATATATATATATGTATGTATGTATG
1 TATAAATATATATATATGTATGTATG
* *
30443 TATAAATATATATATATATAAGTATG
1 TATAAATATATATATATGTATGTATG
30469 TAT--ATATATATATATGTATGTATG
1 TATAAATATATATATATGTATGTATG
* *
30493 TATAAATATATATATAAGAATGTATG
1 TATAAATATATATATATGTATGTATG
30519 TAT--ATATATATATATGTATGTATG
1 TATAAATATATATATATGTATGTATG
30543 TATAAATATATATATAT
1 TATAAATATATATATAT
30560 ATATTTATAT
Statistics
Matches: 103, Mismatches: 10, Indels: 8
0.85 0.08 0.07
Matches are distributed among these distances:
24 44 0.43
26 59 0.57
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.46
Consensus pattern (26 bp):
TATAAATATATATATATGTATGTATG
Found at i:30585 original size:50 final size:50
Alignment explanation
Indices: 30415--30587 Score: 242
Period size: 50 Copynumber: 3.5 Consensus size: 50
30405 CAATTTTAAT
* *
30415 TATATATATATATATGTATGTATGTATGTATAAATATATATATATATAAG
1 TATATATATATATATATATGTATGTATGTATAAATATATATATATATATG
* *
30465 TATGTATATATATATATATGTATGTATGTATAAATATATATATA-AGAATG
1 TATATATATATATATATATGTATGTATGTATAAATATATATATATA-TATG
* *
30515 TATGTATATATATATATATGTATGTATGTATAAATATATATATATATATT
1 TATATATATATATATATATGTATGTATGTATAAATATATATATATATATG
* *
30565 TATATA-AGTATGTATGTATGTAT
1 TATATATA-TATATATATATGTAT
30588 ATATATATGT
Statistics
Matches: 111, Mismatches: 9, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
49 2 0.02
50 108 0.97
51 1 0.01
ACGTcount: A:0.42, C:0.00, G:0.11, T:0.47
Consensus pattern (50 bp):
TATATATATATATATATATGTATGTATGTATAAATATATATATATATATG
Found at i:31477 original size:27 final size:27
Alignment explanation
Indices: 31447--31513 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
31437 GTTAATCATC
*
31447 AACGATTTCCTTTTTAAATAAATGATG
1 AACGATTTTCTTTTTAAATAAATGATG
31474 AACGATTTTCTTTTTAAATAAATGATG
1 AACGATTTTCTTTTTAAATAAATGATG
31501 AACGATTTTCTTT
1 AACGATTTTCTTT
31514 AAACGTTTCC
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.45
Consensus pattern (27 bp):
AACGATTTTCTTTTTAAATAAATGATG
Found at i:39270 original size:15 final size:14
Alignment explanation
Indices: 39250--39310 Score: 65
Period size: 14 Copynumber: 4.4 Consensus size: 14
39240 TCCACACAAA
39250 AAAAACACAATAAAC
1 AAAAACACAA-AAAC
39265 -AAAA-ACAAAAAC
1 AAAAACACAAAAAC
*
39277 AATAAACAAAAAAAC
1 AA-AAACACAAAAAC
*
39292 AAAAAAACAAAAA-
1 AAAAACACAAAAAC
39305 AAAAAC
1 AAAAAC
39311 TCCACTCTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
12 4 0.10
13 10 0.26
14 16 0.41
15 9 0.23
ACGTcount: A:0.82, C:0.15, G:0.00, T:0.03
Consensus pattern (14 bp):
AAAAACACAAAAAC
Found at i:39272 original size:13 final size:12
Alignment explanation
Indices: 39245--39310 Score: 68
Period size: 11 Copynumber: 5.7 Consensus size: 12
39235 ACCCGTCCAC
*
39245 ACAAAAA-AAAC
1 ACAAAAACAAAA
39256 ACAATAAACAAAA
1 ACAA-AAACAAAA
39269 ACAAAAACAATAA
1 ACAAAAACAA-AA
*
39282 ACAAAAA-AACA
1 ACAAAAACAAAA
39293 A-AAAAACAAAA
1 ACAAAAACAAAA
39304 A-AAAAAC
1 ACAAAAAC
39311 TCCACTCTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
10 5 0.10
11 16 0.33
12 11 0.23
13 16 0.33
ACGTcount: A:0.82, C:0.15, G:0.00, T:0.03
Consensus pattern (12 bp):
ACAAAAACAAAA
Found at i:39278 original size:19 final size:18
Alignment explanation
Indices: 39245--39310 Score: 91
Period size: 19 Copynumber: 3.7 Consensus size: 18
39235 ACCCGTCCAC
*
39245 ACAAAAAAAACACAATAA
1 ACAAAAAAAAAACAATAA
39263 ACAAAAACAAAAACAATAA
1 ACAAAAA-AAAAACAATAA
*
39282 ACAAAAAAACAA-AA-AA
1 ACAAAAAAAAAACAATAA
39298 ACAAAAAAAAAAC
1 ACAAAAAAAAAAC
39311 TCCACTCTTT
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
16 13 0.30
17 2 0.05
18 11 0.26
19 17 0.40
ACGTcount: A:0.82, C:0.15, G:0.00, T:0.03
Consensus pattern (18 bp):
ACAAAAAAAAAACAATAA
Found at i:39293 original size:8 final size:8
Alignment explanation
Indices: 39248--39306 Score: 64
Period size: 8 Copynumber: 6.9 Consensus size: 8
39238 CGTCCACACA
39248 AAAAAAAC
1 AAAAAAAC
*
39256 ACAATAAAC
1 A-AAAAAAC
*
39265 AAAAACAAA
1 AAAAA-AAC
39274 AACAATAAAC
1 AA-AA-AAAC
39284 AAAAAAAC
1 AAAAAAAC
39292 AAAAAAAC
1 AAAAAAAC
39300 AAAAAAA
1 AAAAAAA
39307 AAACTCCACT
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
8 23 0.53
9 13 0.30
10 6 0.14
11 1 0.02
ACGTcount: A:0.83, C:0.14, G:0.00, T:0.03
Consensus pattern (8 bp):
AAAAAAAC
Found at i:41524 original size:2 final size:2
Alignment explanation
Indices: 41517--41546 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
41507 TATTACAATA
41517 AT 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
41547 TTCTCTTGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:57309 original size:55 final size:53
Alignment explanation
Indices: 57226--57332 Score: 144
Period size: 55 Copynumber: 2.0 Consensus size: 53
57216 AATCTGTAAA
* * *
57226 TAGTATCTAGGAGGAAGCAACTTCTACATTTATAAAGGTGATAGAATTA-ATAAT
1 TAGTATCTAAGAGGAAGCAACTTCTACATTCAT-AAGGTAATA-AATTATATAAT
*
57280 TAGTACTCTAAGAGGAAGCAGCTTCTACATTCATAAGGTAATAAATTATATAA
1 TAGTA-TCTAAGAGGAAGCAACTTCTACATTCATAAGGTAATAAATTATATAA
57333 AGAGGACTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
53 5 0.11
54 17 0.36
55 25 0.53
ACGTcount: A:0.41, C:0.11, G:0.17, T:0.31
Consensus pattern (53 bp):
TAGTATCTAAGAGGAAGCAACTTCTACATTCATAAGGTAATAAATTATATAAT
Found at i:57984 original size:1 final size:1
Alignment explanation
Indices: 57978--58005 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
57968 GAAGAGTAAG
57978 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAA
58006 GAAACAACCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:60012 original size:17 final size:18
Alignment explanation
Indices: 59992--60038 Score: 71
Period size: 17 Copynumber: 2.7 Consensus size: 18
59982 TTCAGATCAT
59992 TTTTGGGTTTAGT-TTTG
1 TTTTGGGTTTAGTGTTTG
60009 TTTTGGGTTTA-TGTTTG
1 TTTTGGGTTTAGTGTTTG
*
60026 CTTTGGGTTTAGT
1 TTTTGGGTTTAGT
60039 ATATTTGGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 1 0.04
17 25 0.93
18 1 0.04
ACGTcount: A:0.06, C:0.02, G:0.30, T:0.62
Consensus pattern (18 bp):
TTTTGGGTTTAGTGTTTG
Found at i:60126 original size:32 final size:32
Alignment explanation
Indices: 60063--60143 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 32
60053 TTTTTTCAGG
*
60063 TTCAAGTCAGATTAATTCGGGCTCAGATCAAT
1 TTCAAGTCAGATTAATTCGAGCTCAGATCAAT
** * * *
60095 TTCAAGTCAGATTTTTTCGAGTTCGGGTCAAT
1 TTCAAGTCAGATTAATTCGAGCTCAGATCAAT
*
60127 TTC-AGATCAGGTTAATT
1 TTCAAG-TCAGATTAATT
60144 TGGATTCGGA
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
31 2 0.05
32 37 0.95
ACGTcount: A:0.27, C:0.16, G:0.20, T:0.37
Consensus pattern (32 bp):
TTCAAGTCAGATTAATTCGAGCTCAGATCAAT
Found at i:60660 original size:14 final size:15
Alignment explanation
Indices: 60641--60669 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
60631 TGACATATAA
60641 AAGGAAAATT-AATT
1 AAGGAAAATTCAATT
60655 AAGGAAAATTCAATT
1 AAGGAAAATTCAATT
60670 CAATTAAATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.55, C:0.03, G:0.14, T:0.28
Consensus pattern (15 bp):
AAGGAAAATTCAATT
Found at i:60863 original size:13 final size:13
Alignment explanation
Indices: 60847--60871 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
60837 TCGGGTTCGG
60847 TTTTCTTTCGGGT
1 TTTTCTTTCGGGT
60860 TTTTCTTTCGGG
1 TTTTCTTTCGGG
60872 CTCGAGTTCT
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:0.00, C:0.16, G:0.24, T:0.60
Consensus pattern (13 bp):
TTTTCTTTCGGGT
Found at i:66452 original size:12 final size:12
Alignment explanation
Indices: 66421--66456 Score: 58
Period size: 11 Copynumber: 3.2 Consensus size: 12
66411 ATACAATTTC
66421 TTTTCTTCTA-T
1 TTTTCTTCTAGT
66432 TTTTC-TCTAGT
1 TTTTCTTCTAGT
66443 TTTTCTTCTAGT
1 TTTTCTTCTAGT
66455 TT
1 TT
66457 CAAGAGGGAG
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 4 0.17
11 11 0.48
12 8 0.35
ACGTcount: A:0.08, C:0.17, G:0.06, T:0.69
Consensus pattern (12 bp):
TTTTCTTCTAGT
Found at i:67224 original size:16 final size:17
Alignment explanation
Indices: 67203--67241 Score: 55
Period size: 16 Copynumber: 2.4 Consensus size: 17
67193 TAATTGCCAA
67203 TAGTTTAGATTTA-ATT
1 TAGTTTAGATTTATATT
*
67219 TAGTTT-GATTTATTTT
1 TAGTTTAGATTTATATT
67235 TAGTTTA
1 TAGTTTA
67242 ACTGCTTCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 6 0.30
16 14 0.70
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.62
Consensus pattern (17 bp):
TAGTTTAGATTTATATT
Found at i:69744 original size:23 final size:21
Alignment explanation
Indices: 69714--69763 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
69704 GAAAATCTGG
69714 AAAATTTTAATACAAATTTCTT
1 AAAATTTTAAT-CAAATTTCTT
* **
69736 AAAACTTTTGATCAGTTTTCTT
1 AAAA-TTTTAATCAAATTTCTT
69758 AAAATT
1 AAAATT
69764 GATCCAAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
21 2 0.08
22 16 0.67
23 6 0.25
ACGTcount: A:0.40, C:0.10, G:0.04, T:0.46
Consensus pattern (21 bp):
AAAATTTTAATCAAATTTCTT
Found at i:73796 original size:21 final size:21
Alignment explanation
Indices: 73772--73902 Score: 210
Period size: 21 Copynumber: 6.2 Consensus size: 21
73762 CTTAGGCAAT
*
73772 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
73793 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
* *
73814 TCCGATGAGCTCGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
73835 TCCAATGAGCTTGGAATCTTC
1 TCCAATGAGCTTGGAACCTTC
73856 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
73877 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
73898 TCCAA
1 TCCAA
73903 GCCTCCTTGC
Statistics
Matches: 102, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
20 3 0.03
21 99 0.97
ACGTcount: A:0.24, C:0.28, G:0.19, T:0.28
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Done.