Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024787.1 Corchorus olitorius cultivar O-4 contig24820, 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: 42143
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:4091 original size:2 final size:2
Alignment explanation
Indices: 4084--4110 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
4074 ACTTTTATGT
4084 TA 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 T
4111 TATTATTATT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7507 original size:21 final size:21
Alignment explanation
Indices: 7466--7522 Score: 62
Period size: 21 Copynumber: 2.7 Consensus size: 21
7456 AGGGAGATTA
* **
7466 ACAAAATCTCACAGGGTGGTT
1 ACAAAATCTCATAGGCAGGTT
7487 ATCAAAA-CTCATAGGCAGGTT
1 A-CAAAATCTCATAGGCAGGTT
*
7508 ACAAAATTTCATAGG
1 ACAAAATCTCATAGG
7523 AAGATTTATT
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
20 5 0.17
21 20 0.67
22 5 0.17
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.25
Consensus pattern (21 bp):
ACAAAATCTCATAGGCAGGTT
Found at i:7619 original size:22 final size:22
Alignment explanation
Indices: 7592--7649 Score: 71
Period size: 22 Copynumber: 2.6 Consensus size: 22
7582 TTCATAGGTA
*
7592 AATTATCAAAATTTAAGAGCAT
1 AATTATCAAAATTTAAGAGAAT
* * *
7614 ATTTATCAAAATTAAATAGAAT
1 AATTATCAAAATTTAAGAGAAT
*
7636 AATTATAAAAATTT
1 AATTATCAAAATTT
7650 TATAAAAATA
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.53, C:0.05, G:0.05, T:0.36
Consensus pattern (22 bp):
AATTATCAAAATTTAAGAGAAT
Found at i:12958 original size:17 final size:16
Alignment explanation
Indices: 12931--12963 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
12921 ACAACAACTT
12931 TATAGGTGAATACATA
1 TATAGGTGAATACATA
12947 TATAGTGTGAATACATA
1 TATAG-GTGAATACATA
12964 GCTAATTTAC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.42, C:0.06, G:0.18, T:0.33
Consensus pattern (16 bp):
TATAGGTGAATACATA
Found at i:13432 original size:13 final size:13
Alignment explanation
Indices: 13414--13440 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
13404 ATCTTAACTT
13414 TATTACATTTGCA
1 TATTACATTTGCA
13427 TATTACATTTGCA
1 TATTACATTTGCA
13440 T
1 T
13441 TATAGTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.15, G:0.07, T:0.48
Consensus pattern (13 bp):
TATTACATTTGCA
Found at i:15804 original size:25 final size:23
Alignment explanation
Indices: 15770--15824 Score: 74
Period size: 24 Copynumber: 2.3 Consensus size: 23
15760 GTTTACGGAT
15770 TTGGGTTCTAATTTTCATTTATGC
1 TTGGGTTCTAATTTT-ATTTATGC
* *
15794 TTGGGCTTCTAATTTTGTTTATGT
1 TTGGG-TTCTAATTTTATTTATGC
15818 TTGGGTT
1 TTGGGTT
15825 GTAGCCTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 2 0.07
24 16 0.57
25 10 0.36
ACGTcount: A:0.13, C:0.09, G:0.22, T:0.56
Consensus pattern (23 bp):
TTGGGTTCTAATTTTATTTATGC
Found at i:16469 original size:7 final size:7
Alignment explanation
Indices: 16457--16500 Score: 52
Period size: 7 Copynumber: 6.0 Consensus size: 7
16447 CAAAAAGGTT
16457 TTCAAAA
1 TTCAAAA
*
16464 TCCAAAAGA
1 TTC-AAA-A
16473 TTCAAAA
1 TTCAAAA
16480 TTCAAAA
1 TTCAAAA
16487 TTCAAAA
1 TTCAAAA
*
16494 ATCAAAA
1 TTCAAAA
16501 AGAATTTCCC
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
7 23 0.72
8 6 0.19
9 3 0.09
ACGTcount: A:0.59, C:0.16, G:0.02, T:0.23
Consensus pattern (7 bp):
TTCAAAA
Found at i:16478 original size:16 final size:16
Alignment explanation
Indices: 16457--16503 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
16447 CAAAAAGGTT
16457 TTCAAAATCCAAAAGA
1 TTCAAAATCCAAAAGA
*
16473 TTCAAAATTC-AAA-A
1 TTCAAAATCCAAAAGA
*
16487 TTCAAAAATCAAAAAGA
1 TTC-AAAATCCAAAAGA
16504 ATTTCCCATC
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
14 4 0.16
15 8 0.32
16 12 0.48
17 1 0.04
ACGTcount: A:0.60, C:0.15, G:0.04, T:0.21
Consensus pattern (16 bp):
TTCAAAATCCAAAAGA
Found at i:16535 original size:28 final size:28
Alignment explanation
Indices: 16503--16585 Score: 70
Period size: 28 Copynumber: 3.2 Consensus size: 28
16493 AATCAAAAAG
16503 AATTTCCCATCAAGTTTTCAAAGTATTC
1 AATTTCCCATCAAGTTTTCAAAGTATTC
* ****
16531 AA-TT----T-AAGTTTTGAAAGTGGGA
1 AATTTCCCATCAAGTTTTCAAAGTATTC
*
16553 AAGTTCCCATCAAGTTTTCAAAGTATTC
1 AATTTCCCATCAAGTTTTCAAAGTATTC
16581 AATTT
1 AATTT
16586 AGGTCTTTTC
Statistics
Matches: 38, Mismatches: 11, Indels: 12
0.62 0.18 0.20
Matches are distributed among these distances:
22 14 0.37
23 3 0.08
27 3 0.08
28 18 0.47
ACGTcount: A:0.34, C:0.14, G:0.13, T:0.39
Consensus pattern (28 bp):
AATTTCCCATCAAGTTTTCAAAGTATTC
Found at i:16561 original size:50 final size:51
Alignment explanation
Indices: 16506--16728 Score: 317
Period size: 52 Copynumber: 4.4 Consensus size: 51
16496 CAAAAAGAAT
*
16506 TTCCCATCAAGTTTTCAAAGTATTCAATTTAAG-TTTTGAAAGTGGGAAAG
1 TTCCCATCAAGTTTTCAAAGTATTCAATTTAAGCTTTTCAAAGTGGGAAAG
*
16556 TTCCCATCAAGTTTTCAAAGTATTCAATTTAGGTCTTTTCAAAGTGGGAAAG
1 TTCCCATCAAGTTTTCAAAGTATTCAATTTAAG-CTTTTCAAAGTGGGAAAG
* *
16608 TTCCAATCAAGTTTTCAAAGTATTCAATTTAAG-TTTTCAAAGAGGGAAAG
1 TTCCCATCAAGTTTTCAAAGTATTCAATTTAAGCTTTTCAAAGTGGGAAAG
* * * *
16658 TTCCCAACATA-TTTCCAAAGTGTTCAATTTAGGTCTTTTCAAAGTGGGAAAG
1 TTCCCATCA-AGTTTTCAAAGTATTCAATTTAAG-CTTTTCAAAGTGGGAAAG
*
16710 TTCCCATCAGGTTTTCAAA
1 TTCCCATCAAGTTTTCAAA
16729 ACGTTCAATT
Statistics
Matches: 153, Mismatches: 14, Indels: 10
0.86 0.08 0.06
Matches are distributed among these distances:
50 74 0.48
51 1 0.01
52 78 0.51
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (51 bp):
TTCCCATCAAGTTTTCAAAGTATTCAATTTAAGCTTTTCAAAGTGGGAAAG
Found at i:16740 original size:102 final size:102
Alignment explanation
Indices: 16506--16728 Score: 367
Period size: 102 Copynumber: 2.2 Consensus size: 102
16496 CAAAAAGAAT
* * * *
16506 TTCCCATCAAGTTTTCAAAGTATTCAATTTAAGTTTTGAAAGTGGGAAAGTTCCCATCAAGTTTT
1 TTCCCATCAAGTTTTCAAAGTATTCAATTTAAGTTTTCAAAGAGGGAAAGTTCCCAACAAGTTTC
16571 CAAAGTATTCAATTTAGGTCTTTTCAAAGTGGGAAAG
66 CAAAGTATTCAATTTAGGTCTTTTCAAAGTGGGAAAG
*
16608 TTCCAATCAAGTTTTCAAAGTATTCAATTTAAGTTTTCAAAGAGGGAAAGTTCCCAACATA-TTT
1 TTCCCATCAAGTTTTCAAAGTATTCAATTTAAGTTTTCAAAGAGGGAAAGTTCCCAACA-AGTTT
*
16672 CCAAAGTGTTCAATTTAGGTCTTTTCAAAGTGGGAAAG
65 CCAAAGTATTCAATTTAGGTCTTTTCAAAGTGGGAAAG
*
16710 TTCCCATCAGGTTTTCAAA
1 TTCCCATCAAGTTTTCAAA
16729 ACGTTCAATT
Statistics
Matches: 112, Mismatches: 8, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
102 111 0.99
103 1 0.01
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.35
Consensus pattern (102 bp):
TTCCCATCAAGTTTTCAAAGTATTCAATTTAAGTTTTCAAAGAGGGAAAGTTCCCAACAAGTTTC
CAAAGTATTCAATTTAGGTCTTTTCAAAGTGGGAAAG
Found at i:22303 original size:2 final size:2
Alignment explanation
Indices: 22296--22327 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
22286 AGGAAAGGGA
22296 AT 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
22328 TAGTAGTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:23190 original size:106 final size:106
Alignment explanation
Indices: 23068--23281 Score: 419
Period size: 106 Copynumber: 2.0 Consensus size: 106
23058 TTTAGATTTC
23068 ACAAACGGGTAAAAAGTTGACGCATACCATATCTTCTAATTAATTATATATATTTAATGTTCAAA
1 ACAAACGGGTAAAAAGTTGACGCATACCATATCTTCTAATTAATTATATATATTTAATGTTCAAA
*
23133 AATCAAAACTATTCCCTAAGGAGACACATGTCGACCCTTTA
66 AATCAAAACTATTCCCTAAGGACACACATGTCGACCCTTTA
23174 ACAAACGGGTAAAAAGTTGACGCATACCATATCTTCTAATTAATTATATATATTTAATGTTCAAA
1 ACAAACGGGTAAAAAGTTGACGCATACCATATCTTCTAATTAATTATATATATTTAATGTTCAAA
23239 AATCAAAACTATTCCCTAAGGACACACATGTCGACCCTTTA
66 AATCAAAACTATTCCCTAAGGACACACATGTCGACCCTTTA
23280 AC
1 AC
23282 CCTAACCCTG
Statistics
Matches: 107, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
106 107 1.00
ACGTcount: A:0.40, C:0.20, G:0.11, T:0.30
Consensus pattern (106 bp):
ACAAACGGGTAAAAAGTTGACGCATACCATATCTTCTAATTAATTATATATATTTAATGTTCAAA
AATCAAAACTATTCCCTAAGGACACACATGTCGACCCTTTA
Found at i:30210 original size:108 final size:108
Alignment explanation
Indices: 29990--30203 Score: 385
Period size: 107 Copynumber: 2.0 Consensus size: 108
29980 ATTTTAGACT
29990 TTTTTTAATATGGAAATAAAATCTGACTGGATAGATTACATATTAACCTTTAAAAATATAATTAA
1 TTTTTTAATATGGAAATAAAATCTGACTGGATAGATTACATATTAACCTTTAAAAATATAATTAA
*
30055 AATTTTAAAATTTAAAAGCGTATTTTAGATATTTCATGTCAAC
66 AATTTTAAAATTTAAAAGCGTATTTTAGATATTTCAGGTCAAC
**
30098 TTTTTTAATATGGAAATAAAATCTGGTTGGATAGATTACATATTAACCTTT-AAAATATAATTAA
1 TTTTTTAATATGGAAATAAAATCTGACTGGATAGATTACATATTAACCTTTAAAAATATAATTAA
*
30162 AATTTTAAAATTTAAAAGGGTATTTTAGATATTTCAGGTCAA
66 AATTTTAAAATTTAAAAGCGTATTTTAGATATTTCAGGTCAA
30204 GGTTTTTGAA
Statistics
Matches: 102, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
107 53 0.52
108 49 0.48
ACGTcount: A:0.42, C:0.07, G:0.11, T:0.40
Consensus pattern (108 bp):
TTTTTTAATATGGAAATAAAATCTGACTGGATAGATTACATATTAACCTTTAAAAATATAATTAA
AATTTTAAAATTTAAAAGCGTATTTTAGATATTTCAGGTCAAC
Found at i:35906 original size:36 final size:36
Alignment explanation
Indices: 35859--35931 Score: 146
Period size: 36 Copynumber: 2.0 Consensus size: 36
35849 TATGACAGTG
35859 TTATATCGTAGTAAAGCGGCTTTGGGTAAATCTTAT
1 TTATATCGTAGTAAAGCGGCTTTGGGTAAATCTTAT
35895 TTATATCGTAGTAAAGCGGCTTTGGGTAAATCTTAT
1 TTATATCGTAGTAAAGCGGCTTTGGGTAAATCTTAT
35931 T
1 T
35932 AAAAAATTCT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.27, C:0.11, G:0.22, T:0.40
Consensus pattern (36 bp):
TTATATCGTAGTAAAGCGGCTTTGGGTAAATCTTAT
Found at i:37166 original size:19 final size:19
Alignment explanation
Indices: 37119--37168 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 19
37109 TCTTTACCTA
37119 ATATTTTGGTTTATG-A--
1 ATATTTTGGTTTATGAATT
37135 AT-TTTT--TTT-TGAATT
1 ATATTTTGGTTTATGAATT
37150 ATATTTTGGTTTATGAATT
1 ATATTTTGGTTTATGAATT
37169 GAATGTGCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 11
0.71 0.00 0.29
Matches are distributed among these distances:
12 2 0.07
13 4 0.15
15 6 0.22
16 6 0.22
18 3 0.11
19 6 0.22
ACGTcount: A:0.24, C:0.00, G:0.14, T:0.62
Consensus pattern (19 bp):
ATATTTTGGTTTATGAATT
Found at i:37824 original size:41 final size:41
Alignment explanation
Indices: 37765--37846 Score: 121
Period size: 41 Copynumber: 2.0 Consensus size: 41
37755 TTTATAACTA
*
37765 GGGGCTAAACTCGAATTTAATTTCTTACCTTAATTATTAGG
1 GGGGCTAAACTCGAATTTAATTTATTACCTTAATTATTAGG
* *
37806 GGGGCTAAAC-CTGGATTTAATTTATTTCCTTAATTATTAGG
1 GGGGCTAAACTC-GAATTTAATTTATTACCTTAATTATTAGG
37847 AGGGTCAAGT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
40 1 0.03
41 36 0.97
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.40
Consensus pattern (41 bp):
GGGGCTAAACTCGAATTTAATTTATTACCTTAATTATTAGG
Found at i:37863 original size:13 final size:13
Alignment explanation
Indices: 37845--37881 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
37835 TTAATTATTA
*
37845 GGAGGGTCAAGTT
1 GGAGGGTCAAATT
*
37858 GGAGGGACAAATT
1 GGAGGGTCAAATT
37871 GGAGGGTCAAA
1 GGAGGGTCAAA
37882 AAGAATTATC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.32, C:0.08, G:0.43, T:0.16
Consensus pattern (13 bp):
GGAGGGTCAAATT
Found at i:38598 original size:43 final size:42
Alignment explanation
Indices: 38499--38635 Score: 195
Period size: 43 Copynumber: 3.2 Consensus size: 42
38489 AGCTTCAATT
*
38499 AATATTAGGTTTATTTTGATGAATTACCTAGAGATGGAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGAT---GGAGTAG
* *
38544 AATATTAGCTTTATTTTGATGAATTACCATTGAGATGGAGTAT
1 AATATTAGCTTTATTTTGATGAATTACC-TAGAGATGGAGTAG
*
38587 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGAAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAG
38629 AAT-TTAG
1 AATATTAG
38636 GTAATACTCT
Statistics
Matches: 85, Mismatches: 6, Indels: 6
0.88 0.06 0.06
Matches are distributed among these distances:
41 4 0.05
42 14 0.16
43 34 0.40
45 27 0.32
46 6 0.07
ACGTcount: A:0.34, C:0.06, G:0.21, T:0.39
Consensus pattern (42 bp):
AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAG
Found at i:41266 original size:22 final size:22
Alignment explanation
Indices: 41234--41381 Score: 103
Period size: 22 Copynumber: 6.8 Consensus size: 22
41224 TGAATATTTT
41234 TATGAAATTTTGATAACTATC-C
1 TATGAAATTTTGATAACTA-CGC
*
41256 TATTAAATTTTGATAACTACGC
1 TATGAAATTTTGATAACTACGC
* * *
41278 TATGAAATTTTAATAATTAC-A
1 TATGAAATTTTGATAACTACGC
*
41299 TATGAAATTATGATAAACT-C-C
1 TATGAAATTTTGAT-AACTACGC
* **
41320 ATATGAAACTTTGATAACCTA-AT
1 -TATGAAATTTTGATAA-CTACGC
* *
41343 TATGAAATTTTAATAAACCTTC-C
1 TATGAAATTTTGAT-AA-CTACGC
41366 TATGAAATTTTG-TAAC
1 TATGAAATTTTGATAAC
41382 CTTTCTATGA
Statistics
Matches: 101, Mismatches: 17, Indels: 18
0.74 0.12 0.13
Matches are distributed among these distances:
20 1 0.01
21 18 0.18
22 66 0.65
23 16 0.16
ACGTcount: A:0.41, C:0.12, G:0.08, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAACTACGC
Found at i:41397 original size:21 final size:21
Alignment explanation
Indices: 41234--41404 Score: 91
Period size: 22 Copynumber: 7.9 Consensus size: 21
41224 TGAATATTTT
41234 TATGAAATTTTGATAA-CTATCC
1 TATGAAATTTT-ATAACCT-TCC
* *
41256 TATTAAATTTTGATAA-CTACGC
1 TATGAAATTTT-ATAACCTTC-C
*
41278 TATGAAATTTTAATAA--TTACA
1 TATGAAATTTT-ATAACCTT-CC
* *
41299 TATGAAATTATGATAAAC-TCC
1 TATGAAATT-TTATAACCTTCC
* ***
41320 ATATGAAACTTTGATAACCTAAT
1 -TATGAAA-TTTTATAACCTTCC
41343 TATGAAATTTTAATAAACCTTCC
1 TATGAAATTTT-AT-AACCTTCC
* *
41366 TATGAAATTTTGTAACCTTTC
1 TATGAAATTTTATAACCTTCC
**
41387 TATGATTTTTTATAACCT
1 TATGAAATTTTATAACCT
41405 CAATGTGAGA
Statistics
Matches: 118, Mismatches: 21, Indels: 21
0.74 0.13 0.13
Matches are distributed among these distances:
21 41 0.35
22 59 0.50
23 18 0.15
ACGTcount: A:0.38, C:0.13, G:0.08, T:0.42
Consensus pattern (21 bp):
TATGAAATTTTATAACCTTCC
Done.