Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009732.1 Corchorus capsularis cultivar CVL-1 contig09753, 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: 76031
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2435 original size:17 final size:18
Alignment explanation
Indices: 2415--2451 Score: 67
Period size: 17 Copynumber: 2.1 Consensus size: 18
2405 GCAACCTATC
2415 ACCTCATACTACCT-GGT
1 ACCTCATACTACCTAGGT
2432 ACCTCATACTACCTAGGT
1 ACCTCATACTACCTAGGT
2450 AC
1 AC
2452 TTTGAGGAGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 14 0.74
18 5 0.26
ACGTcount: A:0.27, C:0.35, G:0.11, T:0.27
Consensus pattern (18 bp):
ACCTCATACTACCTAGGT
Found at i:12236 original size:2 final size:2
Alignment explanation
Indices: 12224--12260 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
12214 GATTTTCATA
12224 AT AT AT A- 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 AT AT AT AT
12261 TGCTTGCCTG
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:12627 original size:22 final size:21
Alignment explanation
Indices: 12602--13115 Score: 238
Period size: 22 Copynumber: 23.7 Consensus size: 21
12592 ATGATCCCAT
12602 TATGAAATTTTGATAACCTTCC
1 TATGAAATTTTGATAACC-TCC
* * *
12624 TATGAAATTTTAATAACAATAC
1 TATGAAATTTTGATAAC-CTCC
* * * * **
12646 TATGGAATTTCGAGAATCTTTT
1 TATGAAATTTTGATAA-CCTCC
** **
12668 TAT-AAATTTTTTTAACCTTTT
1 TATGAAATTTTGATAACC-TCC
*
12689 TATGAAATTTTGTTAACCTCTC
1 TATGAAATTTTGATAACCTC-C
* * * *
12711 TAAGGAATTTCGATAACCAACAC
1 TATGAAATTTTGATAACC-TC-C
* *
12734 TATGAGATGTTGATAACCTCC
1 TATGAAATTTTGATAACCTCC
* * * *
12755 ATATGATATATTGATAACCACGT
1 -TATGAAATTTTGATAACCTC-C
* * *
12778 TATGAAAATTTAAAAACCTCC
1 TATGAAATTTTGATAACCTCC
* *
12799 ATATG-AATTGTT-AGTAATCACAC
1 -TATGAAATT-TTGA-TAACCTC-C
* * * *
12822 TCTGAAATTTTGATAATCACAA
1 TATGAAATTTTGATAACCTC-C
*
12844 TATGAAATTGTGATAACCTCGC
1 TATGAAATTTTGATAACCTC-C
*
12866 TATGAAATTTTGATAAATCTTCC
1 TATGAAATTTTGAT-AA-CCTCC
*
12889 TATAAAATTTTGATAAACCTCCC
1 TATGAAATTTTGAT-AACCT-CC
* * *
12912 TATAAAATTTTGATAACTTTCT
1 TATGAAATTTTGATAAC-CTCC
*
12934 TATGAAATCTTGATAA----C
1 TATGAAATTTTGATAACCTCC
* *
12951 TA-CAAATTTTGATAAGCTCCC
1 TATGAAATTTTGATAACCT-CC
** *
12972 TATGATTTTTTGATAACCTCAT
1 TATGAAATTTTGATAACCTC-C
* *
12994 TATGAAATTTTGTTAATCTCCC
1 TATGAAATTTTGATAACCT-CC
*
13016 TATGAAATTTTGATAACCCTCT
1 TATGAAATTTTGATAA-CCTCC
* * *
13038 TACGAAATTTTGA-AAACTAAAC
1 TATGAAATTTTGATAACCT--CC
*
13060 TATGAAATTTTGATAACCTTCA
1 TATGAAATTTTGATAACC-TCC
*
13082 TATGAAATTTTGATATCCTCC
1 TATGAAATTTTGATAACCTCC
13103 T-TGAAATTTTGAT
1 TATGAAATTTTGAT
13116 TACTCCATAA
Statistics
Matches: 373, Mismatches: 88, Indels: 64
0.71 0.17 0.12
Matches are distributed among these distances:
16 11 0.03
17 2 0.01
20 15 0.04
21 28 0.08
22 249 0.67
23 64 0.17
24 4 0.01
ACGTcount: A:0.36, C:0.15, G:0.10, T:0.39
Consensus pattern (21 bp):
TATGAAATTTTGATAACCTCC
Found at i:12896 original size:23 final size:23
Alignment explanation
Indices: 12865--12949 Score: 100
Period size: 23 Copynumber: 3.7 Consensus size: 23
12855 GATAACCTCG
*
12865 CTATGAAATTTTGATAAATCTTC
1 CTATAAAATTTTGATAAATCTTC
* *
12888 CTATAAAATTTTGATAAACCTCC
1 CTATAAAATTTTGATAAATCTTC
*
12911 CTATAAAATTTTGATAACT-TTC
1 CTATAAAATTTTGATAAATCTTC
* * *
12933 TTATGAAATCTTGATAA
1 CTATAAAATTTTGATAA
12950 CTACAAATTT
Statistics
Matches: 53, Mismatches: 9, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
22 16 0.30
23 37 0.70
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.41
Consensus pattern (23 bp):
CTATAAAATTTTGATAAATCTTC
Found at i:12948 original size:45 final size:45
Alignment explanation
Indices: 12844--12949 Score: 126
Period size: 45 Copynumber: 2.3 Consensus size: 45
12834 ATAATCACAA
* *
12844 TATGAAATTGTGAT-AACCTCGCTATGAAATTTTGATAAATCTTCC
1 TATGAAATT-TGATAAACCTCCCTATAAAATTTTGATAAATCTTCC
* * *
12889 TATAAAATTTTGATAAACCTCCCTATAAAATTTTGATAACT-TTCT
1 TATGAAA-TTTGATAAACCTCCCTATAAAATTTTGATAAATCTTCC
12934 TATGAAATCTTGATAA
1 TATGAAAT-TTGATAA
12950 CTACAAATTT
Statistics
Matches: 52, Mismatches: 6, Indels: 6
0.81 0.09 0.09
Matches are distributed among these distances:
44 1 0.02
45 26 0.50
46 25 0.48
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.40
Consensus pattern (45 bp):
TATGAAATTTGATAAACCTCCCTATAAAATTTTGATAAATCTTCC
Found at i:13272 original size:22 final size:22
Alignment explanation
Indices: 13222--13300 Score: 79
Period size: 22 Copynumber: 3.6 Consensus size: 22
13212 TCACATTTTG
*
13222 AAAA-TTTGATAAACTCTTTAT
1 AAAATTTTGATAACCTCTTTAT
*
13243 GAAATTTTGATAACCTCTTTAT
1 AAAATTTTGATAACCTCTTTAT
* * * *
13265 AAAATTTTGTTGACCCCTCTAT
1 AAAATTTTGATAACCTCTTTAT
* *
13287 GAAATTATGATAAC
1 AAAATTTTGATAAC
13301 AACACTATGA
Statistics
Matches: 46, Mismatches: 11, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
21 3 0.07
22 43 0.93
ACGTcount: A:0.37, C:0.14, G:0.09, T:0.41
Consensus pattern (22 bp):
AAAATTTTGATAACCTCTTTAT
Found at i:13488 original size:22 final size:22
Alignment explanation
Indices: 13240--13490 Score: 97
Period size: 22 Copynumber: 11.3 Consensus size: 22
13230 ATAAACTCTT
* **
13240 TATGAAATTTTGATAACCTCTT
1 TATGAAATTTTGATAACCACAC
* * * * *
13262 TATAAAATTTTGTTGACCCCTC
1 TATGAAATTTTGATAACCACAC
* *
13284 TATGAAATTATGATAACAACAC
1 TATGAAATTTTGATAACCACAC
* *
13306 TATGAAATTTCGAT-ACTCACTC
1 TATGAAATTTTGATAAC-CACAC
* **
13328 TATGAGA-TTTGATAACC-TTC
1 TATGAAATTTTGATAACCACAC
* *
13348 TATCAAATTTTGAT-ACTC-C-T
1 TATGAAATTTTGATAAC-CACAC
* *
13368 TATGAAATTGAGACTTTTATAACCTTCA-
1 TATGAAA-T-----TTTGATAACC-ACAC
*
13396 TATGAAATTTTGATAACCACAT
1 TATGAAATTTTGATAACCACAC
* * *
13418 TATAAAATTTTGATAACCTCCC
1 TATGAAATTTTGATAACCACAC
* * *
13440 CATGAAATGTT-AGTAACCTC-C
1 TATGAAATTTTGA-TAACCACAC
*
13461 TAATGAAATTTTGTTAACCACAC
1 T-ATGAAATTTTGATAACCACAC
13484 TATGAAA
1 TATGAAA
13491 AGATGATGTA
Statistics
Matches: 172, Mismatches: 38, Indels: 38
0.69 0.15 0.15
Matches are distributed among these distances:
20 15 0.09
21 20 0.12
22 118 0.69
23 2 0.01
26 6 0.03
27 3 0.02
28 8 0.05
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.37
Consensus pattern (22 bp):
TATGAAATTTTGATAACCACAC
Found at i:14452 original size:31 final size:32
Alignment explanation
Indices: 14416--14483 Score: 86
Period size: 30 Copynumber: 2.2 Consensus size: 32
14406 TTTAGTAATG
*
14416 ACAATTTAGAAATATATTTTTAAAA-AAAGGT
1 ACAATTTAGAAATATATTTTAAAAATAAAGGT
* * *
14447 ACAA-TTGGAAATATGTTTTAAAAATAAAGTT
1 ACAATTTAGAAATATATTTTAAAAATAAAGGT
14478 ACAATT
1 ACAATT
14484 GGAAAATATA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
30 17 0.55
31 13 0.42
32 1 0.03
ACGTcount: A:0.50, C:0.04, G:0.10, T:0.35
Consensus pattern (32 bp):
ACAATTTAGAAATATATTTTAAAAATAAAGGT
Found at i:14459 original size:30 final size:31
Alignment explanation
Indices: 14424--14493 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 31
14414 TGACAATTTA
*
14424 GAAATATATTTTTAAAA-AAAGGTACAATTG
1 GAAATATATTTTAAAAATAAAGGTACAATTG
* *
14454 GAAATATGTTTTAAAAATAAAGTTACAATTG
1 GAAATATATTTTAAAAATAAAGGTACAATTG
14485 GAAAATATA
1 G-AAATATA
14494 AAGTTTCACC
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
30 15 0.44
31 13 0.38
32 6 0.18
ACGTcount: A:0.51, C:0.03, G:0.13, T:0.33
Consensus pattern (31 bp):
GAAATATATTTTAAAAATAAAGGTACAATTG
Found at i:15297 original size:228 final size:228
Alignment explanation
Indices: 14894--15351 Score: 810
Period size: 228 Copynumber: 2.0 Consensus size: 228
14884 AGGTTTTTCA
14894 TCTCTAAAATAATTTAGGGTCTCTTTGAAGTTTTTAGATTTAAAAATTGTCTACTAATAAAAGTT
1 TCTCTAAAATAATTTAGGGTCTCTTTGAAGTTTTTAGATTTAAAAATTGTCTACTAATAAAAGTT
* *
14959 TTTATGGAGATTCAAATTCGAGTGTCTTTCATCACAAGTCTAAATCCTTATCGCTTAAACCGCAT
66 TTTATGGAGATTCAAATTCGAGTATCTTCCATCACAAGTCTAAATCCTTATCGCTTAAACCGCAT
* *
15024 TAGCAAGATATATATACCTGCCTAGTTTCAATATTTCAGTATCTAGTTAATAGTAATAGTACTCT
131 TAGCAAGATATATATACCCGCCTAGTTTCAATATTTCAGTATCTAGTTAATAGTAATAGTACCCT
*
15089 AAATTAGGTGCTGATAATCAATTCTCCAATAAAT
196 AAATTAGGTGCT-ACAATCAATTCTCCAATAAAT
* *
15123 TCTCTAAGATAATTTAGGGTCTCTTTGAAGTTTTTAGATTTAGAAATTGTCTACT-ATAAAAGTT
1 TCTCTAAAATAATTTAGGGTCTCTTTGAAGTTTTTAGATTTAAAAATTGTCTACTAATAAAAGTT
* *
15187 TTTATGGAGATTTAAATTCGAGTATCTTCCATCACAAGTCTAAATTCTTATCGCTTAAACCGCAT
66 TTTATGGAGATTCAAATTCGAGTATCTTCCATCACAAGTCTAAATCCTTATCGCTTAAACCGCAT
*
15252 TAGCAAGATATATATACCCGCCTAGTTTCAATATTTCATTATCTAGTTAATAGTAATAGTACCCT
131 TAGCAAGATATATATACCCGCCTAGTTTCAATATTTCAGTATCTAGTTAATAGTAATAGTACCCT
15317 AAATTAGGTGCTACAATCAATTCTCCAATAAAT
196 AAATTAGGTGCTACAATCAATTCTCCAATAAAT
15350 TC
1 TC
15352 CCAATCCAAA
Statistics
Matches: 219, Mismatches: 10, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
227 22 0.10
228 144 0.66
229 53 0.24
ACGTcount: A:0.34, C:0.16, G:0.12, T:0.38
Consensus pattern (228 bp):
TCTCTAAAATAATTTAGGGTCTCTTTGAAGTTTTTAGATTTAAAAATTGTCTACTAATAAAAGTT
TTTATGGAGATTCAAATTCGAGTATCTTCCATCACAAGTCTAAATCCTTATCGCTTAAACCGCAT
TAGCAAGATATATATACCCGCCTAGTTTCAATATTTCAGTATCTAGTTAATAGTAATAGTACCCT
AAATTAGGTGCTACAATCAATTCTCCAATAAAT
Found at i:17586 original size:7 final size:6
Alignment explanation
Indices: 17584--17625 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
17574 GTTTTTCTGT
* *
17584 TTTTTG TTTTTG TTTTTG -TTTCG TTTTTG -TTTTA TTTTTG TT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TT
17626 GCGTTGTCAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
5 8 0.27
6 22 0.73
ACGTcount: A:0.02, C:0.02, G:0.14, T:0.81
Consensus pattern (6 bp):
TTTTTG
Found at i:17610 original size:22 final size:22
Alignment explanation
Indices: 17584--17630 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
17574 GTTTTTCTGT
* *
17584 TTTTTGTTTTTGTTTTTGTTTCG
1 TTTTTG-TTTTATTTTTGTTGCG
17607 TTTTTGTTTTATTTTTGTTGCG
1 TTTTTGTTTTATTTTTGTTGCG
17629 TT
1 TT
17631 GTCAATTTTT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.73
23 6 0.27
ACGTcount: A:0.02, C:0.04, G:0.17, T:0.77
Consensus pattern (22 bp):
TTTTTGTTTTATTTTTGTTGCG
Found at i:31262 original size:20 final size:21
Alignment explanation
Indices: 31234--31275 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
31224 ACAGGAATTG
* *
31234 TAAACAAAATAACTTTT-TTT
1 TAAAAAAAAAAACTTTTCTTT
31254 TAAAAAAAAAAACTTTTCTTT
1 TAAAAAAAAAAACTTTTCTTT
31275 T
1 T
31276 CCCTTTTCAG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.48, C:0.10, G:0.00, T:0.43
Consensus pattern (21 bp):
TAAAAAAAAAAACTTTTCTTT
Found at i:31671 original size:41 final size:42
Alignment explanation
Indices: 31570--31679 Score: 102
Period size: 43 Copynumber: 2.6 Consensus size: 42
31560 TCTCTCCCCC
* * * * *
31570 CAAAATCCCCAAACACAATTATAACACAGGGGCAACTCTCTCT
1 CAAAGTCCCTAAACAC-ATTATAACACAGAGGCAACTCTATAT
*
31613 CAAAGT-CCTCAAGCACATTCATAACACAGAGGC-A-TCTATAT
1 CAAAGTCCCT-AAACACATT-ATAACACAGAGGCAACTCTATAT
*
31654 CAAAGTCCCTAAACACA-TGTAACACA
1 CAAAGTCCCTAAACACATTATAACACA
31680 AGGGCAATTT
Statistics
Matches: 56, Mismatches: 8, Indels: 10
0.76 0.11 0.14
Matches are distributed among these distances:
39 7 0.12
40 1 0.02
41 17 0.30
42 9 0.16
43 22 0.39
ACGTcount: A:0.41, C:0.30, G:0.10, T:0.19
Consensus pattern (42 bp):
CAAAGTCCCTAAACACATTATAACACAGAGGCAACTCTATAT
Found at i:31783 original size:2 final size:2
Alignment explanation
Indices: 31776--31817 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
31766 AAACCCATAT
31776 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
31818 TATATATATA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:31822 original size:2 final size:2
Alignment explanation
Indices: 31817--31843 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31807 ACACACACAC
31817 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 A
31844 CGTTGGGCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:41259 original size:12 final size:12
Alignment explanation
Indices: 41242--41272 Score: 55
Period size: 11 Copynumber: 2.7 Consensus size: 12
41232 CGGTCTGTTT
41242 TCGGTTTTTTAG
1 TCGGTTTTTTAG
41254 TCGG-TTTTTAG
1 TCGGTTTTTTAG
41265 TCGGTTTT
1 TCGGTTTT
41273 AATTTTGAGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.06, C:0.10, G:0.26, T:0.58
Consensus pattern (12 bp):
TCGGTTTTTTAG
Found at i:41373 original size:9 final size:9
Alignment explanation
Indices: 41349--41384 Score: 54
Period size: 9 Copynumber: 3.9 Consensus size: 9
41339 TGGTGGCGGT
*
41349 CGGTTTCGG
1 CGGTTTTGG
41358 TCGGTTTTGG
1 -CGGTTTTGG
41368 CGGTTTTGG
1 CGGTTTTGG
41377 CGGTTTTG
1 CGGTTTTG
41385 ATTTATATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.00, C:0.14, G:0.42, T:0.44
Consensus pattern (9 bp):
CGGTTTTGG
Found at i:42453 original size:21 final size:21
Alignment explanation
Indices: 42428--42488 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 21
42418 TGGAATTCTT
42428 TGAATTATCAGAATTTGATAA
1 TGAATTATCAGAATTTGATAA
* * *
42449 TGAATTATCA-AAATTCATGA
1 TGAATTATCAGAATTTGATAA
*
42469 TGAATTATCAGAATTCGATA
1 TGAATTATCAGAATTTGATA
42489 TTTTAGTTGT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
20 17 0.53
21 15 0.47
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.36
Consensus pattern (21 bp):
TGAATTATCAGAATTTGATAA
Found at i:42962 original size:17 final size:16
Alignment explanation
Indices: 42935--42977 Score: 50
Period size: 17 Copynumber: 2.6 Consensus size: 16
42925 GAAGGAGAAG
*
42935 GAAAAAGAAAAAAAAA
1 GAAAGAGAAAAAAAAA
*
42951 GAAATGAGAAAATAAAA
1 GAAA-GAGAAAAAAAAA
*
42968 GGAAGAGAAA
1 GAAAGAGAAA
42978 TGTAAAAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 10 0.43
17 13 0.57
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (16 bp):
GAAAGAGAAAAAAAAA
Found at i:42975 original size:16 final size:17
Alignment explanation
Indices: 42940--42977 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
42930 AGAAGGAAAA
42940 AGAAAAAAAAAGAAATG
1 AGAAAAAAAAAGAAATG
* *
42957 AGAAAATAAAAGGAA-G
1 AGAAAAAAAAAGAAATG
42973 AGAAA
1 AGAAA
42978 TGTAAAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 6 0.32
17 13 0.68
ACGTcount: A:0.74, C:0.00, G:0.21, T:0.05
Consensus pattern (17 bp):
AGAAAAAAAAAGAAATG
Found at i:49607 original size:18 final size:17
Alignment explanation
Indices: 49573--49612 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
49563 TTCTAACCCT
*
49573 TCTTTTTTTTTATTCTC
1 TCTTTTTTATTATTCTC
*
49590 TCTTTTTTATTCTCTCTC
1 TCTTTTTTATTAT-TCTC
49608 TCTTT
1 TCTTT
49613 CTTTCTTTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 11 0.55
18 9 0.45
ACGTcount: A:0.05, C:0.23, G:0.00, T:0.72
Consensus pattern (17 bp):
TCTTTTTTATTATTCTC
Found at i:49608 original size:16 final size:14
Alignment explanation
Indices: 49578--49606 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
49568 ACCCTTCTTT
49578 TTTTTTATTCTCTC
1 TTTTTTATTCTCTC
49592 TTTTTTATTCTCTC
1 TTTTTTATTCTCTC
49606 T
1 T
49607 CTCTTTCTTT
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:0.07, C:0.21, G:0.00, T:0.72
Consensus pattern (14 bp):
TTTTTTATTCTCTC
Found at i:52321 original size:17 final size:17
Alignment explanation
Indices: 52301--52333 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
52291 CCAGATTACT
52301 AGTGATCCAAGATCACC
1 AGTGATCCAAGATCACC
*
52318 AGTGATGCAAGATCAC
1 AGTGATCCAAGATCAC
52334 TGGTAATCTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.36, C:0.24, G:0.21, T:0.18
Consensus pattern (17 bp):
AGTGATCCAAGATCACC
Found at i:58894 original size:13 final size:12
Alignment explanation
Indices: 58871--58938 Score: 118
Period size: 12 Copynumber: 5.5 Consensus size: 12
58861 TTAATACAGG
58871 TATCGACGGATA
1 TATCGACGGATA
58883 TATCGAACGGATA
1 TATCG-ACGGATA
58896 TATCGACGGATA
1 TATCGACGGATA
58908 TATCGAACGGATA
1 TATCG-ACGGATA
58921 TATCGACGGATA
1 TATCGACGGATA
58933 TATCGA
1 TATCGA
58939 GGTATCGATG
Statistics
Matches: 54, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
12 30 0.56
13 24 0.44
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (12 bp):
TATCGACGGATA
Found at i:58905 original size:25 final size:25
Alignment explanation
Indices: 58871--58938 Score: 136
Period size: 25 Copynumber: 2.7 Consensus size: 25
58861 TTAATACAGG
58871 TATCGACGGATATATCGAACGGATA
1 TATCGACGGATATATCGAACGGATA
58896 TATCGACGGATATATCGAACGGATA
1 TATCGACGGATATATCGAACGGATA
58921 TATCGACGGATATATCGA
1 TATCGACGGATATATCGA
58939 GGTATCGATG
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.35, C:0.16, G:0.24, T:0.25
Consensus pattern (25 bp):
TATCGACGGATATATCGAACGGATA
Found at i:61224 original size:6 final size:6
Alignment explanation
Indices: 61213--61245 Score: 59
Period size: 6 Copynumber: 5.7 Consensus size: 6
61203 ATTAATTTGC
61213 TTTAGA TTTAGA TTTAGA TTTAGA TTTA-A TTTA
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTTA
61246 CTTTGCTTTA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 5 0.19
6 22 0.81
ACGTcount: A:0.33, C:0.00, G:0.12, T:0.55
Consensus pattern (6 bp):
TTTAGA
Found at i:61863 original size:3 final size:3
Alignment explanation
Indices: 61855--61896 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
61845 TCATTTCCCC
61855 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CA- CAT C
1 CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT CAT C
61897 TTCCATGAGC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 36 0.95
ACGTcount: A:0.33, C:0.36, G:0.00, T:0.31
Consensus pattern (3 bp):
CAT
Found at i:62851 original size:10 final size:10
Alignment explanation
Indices: 62839--62874 Score: 63
Period size: 10 Copynumber: 3.6 Consensus size: 10
62829 AATTTAATAT
*
62839 GGATATTTAT
1 GGATATTTAC
62849 GGATATTTAC
1 GGATATTTAC
62859 GGATATTTAC
1 GGATATTTAC
62869 GGATAT
1 GGATAT
62875 ATCGAGATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
10 25 1.00
ACGTcount: A:0.31, C:0.06, G:0.22, T:0.42
Consensus pattern (10 bp):
GGATATTTAC
Found at i:63002 original size:12 final size:12
Alignment explanation
Indices: 62985--63023 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
62975 GTACAGATAT
62985 CGGATATATCGA
1 CGGATATATCGA
62997 CGGATATATCGA
1 CGGATATATCGA
63009 -GG---TATCGA
1 CGGATATATCGA
63017 CGGATAT
1 CGGATAT
63024 TTAATTCCAT
Statistics
Matches: 23, Mismatches: 0, Indels: 8
0.74 0.00 0.26
Matches are distributed among these distances:
8 6 0.26
9 2 0.09
11 2 0.09
12 13 0.57
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (12 bp):
CGGATATATCGA
Found at i:63369 original size:2 final size:2
Alignment explanation
Indices: 63362--63387 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
63352 TTATTGCCAA
63362 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
63388 TTAGAGGAGC
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:70226 original size:28 final size:26
Alignment explanation
Indices: 70173--70227 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 26
70163 TTTAACCTTT
*
70173 AGAACACTATAAAAAAAATTGAGATA
1 AGAACACTATAAAAAAAATTAAGATA
70199 AGAACACTATAAAAAAAATTTAATGATA
1 AGAACACTATAAAAAAAA-TTAA-GATA
70227 A
1 A
70228 TAGTATGAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 18 0.69
27 3 0.12
28 5 0.19
ACGTcount: A:0.62, C:0.07, G:0.09, T:0.22
Consensus pattern (26 bp):
AGAACACTATAAAAAAAATTAAGATA
Done.