Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023996.1 Corchorus olitorius cultivar O-4 contig24029, 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: 51333
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.33
Found at i:2225 original size:247 final size:248
Alignment explanation
Indices: 1778--2279 Score: 846
Period size: 247 Copynumber: 2.0 Consensus size: 248
1768 GCAGAGTCAG
1778 GTAAACTGTTTTCAATTTAGTGCAAACTAGATACTGGACAAACATGACAGACTCAACAAAAACCA
1 GTAAACTGTTTTCAATTTAGTGCAAACTAGATACTGGACAAACATGACAGACTCAACAAAAACCA
* *
1843 CTGACTCAACACTAACTCATTAAAAAAAACTAACTAAAACCTGATAGATCAACAGATCTAGGGAC
66 CTGACTCAACACTAACTCATTAAAAAAAACTAACTAAAACCCGACAGATCAACAGATCTAGGGAC
* *
1908 TCTTTATTCTAAAAGAAAAAAGAAACACAATATATATAGCTTTTAACTTAAGTTTTCTTTACCTT
131 TCTTTATTCTAAAAGAAAAAAGAAACACAATATATATAGCTTTTAACTTAACTTTTCTTCACCTT
* *
1973 ATAAGACATGCAATAATTAGGAATCTATGTATATTTGCAACTTCCGACTGATA
196 ATAAGACATGCAATAATAAGGAATCTATGTATATGTGCAACTTCCGACTGATA
* * *
2026 GTAAACTGTTTTCAATTTATTGCAAACTGGATACTGGACAAACATGCCAGACTCAACAAAAACCA
1 GTAAACTGTTTTCAATTTAGTGCAAACTAGATACTGGACAAACATGACAGACTCAACAAAAACCA
* * * *
2091 CTGACTCAACACTAACTCATT-AAAAAAACTGATTAAAACCCGACAGATCAATAGATCTAGGGAT
66 CTGACTCAACACTAACTCATTAAAAAAAACTAACTAAAACCCGACAGATCAACAGATCTAGGGAC
*
2155 TCTTTATTCTAAAAGAAAAAAGAAACACAATATATATAGCTTTTAGCTTAACTATTT-TTCACCT
131 TCTTTATTCTAAAAGAAAAAAGAAACACAATATATATAGCTTTTAACTTAACT-TTTCTTCACCT
2219 TATAAGACATGCAATAATAAGGAATCTATGTATATGTGCAACTTCCGACTGATA
195 TATAAGACATGCAATAATAAGGAATCTATGTATATGTGCAACTTCCGACTGATA
*
2273 GCAAACT
1 GTAAACT
2280 CTCCTCATAA
Statistics
Matches: 238, Mismatches: 15, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
247 152 0.64
248 86 0.36
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.28
Consensus pattern (248 bp):
GTAAACTGTTTTCAATTTAGTGCAAACTAGATACTGGACAAACATGACAGACTCAACAAAAACCA
CTGACTCAACACTAACTCATTAAAAAAAACTAACTAAAACCCGACAGATCAACAGATCTAGGGAC
TCTTTATTCTAAAAGAAAAAAGAAACACAATATATATAGCTTTTAACTTAACTTTTCTTCACCTT
ATAAGACATGCAATAATAAGGAATCTATGTATATGTGCAACTTCCGACTGATA
Found at i:9647 original size:14 final size:14
Alignment explanation
Indices: 9628--9654 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
9618 GCTATTATGG
9628 ATAAACAAGGTTGC
1 ATAAACAAGGTTGC
9642 ATAAACAAGGTTG
1 ATAAACAAGGTTG
9655 AAGCATCATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.11, G:0.22, T:0.22
Consensus pattern (14 bp):
ATAAACAAGGTTGC
Found at i:10105 original size:27 final size:28
Alignment explanation
Indices: 10026--10112 Score: 95
Period size: 28 Copynumber: 3.0 Consensus size: 28
10016 CCCCATCCCT
* *
10026 TTTTTTTTATTTATTTACTTTTCTAATTTTGA
1 TTTTTTTTATTT-CTT--TTTTCTGA-TTTGA
*
10058 TTTTTTTTATTTCTTTCTTCTGATTTGA
1 TTTTTTTTATTTCTTTTTTCTGATTTGA
*
10086 TTTTTTTTCTTT-TTTTTTCTGATTTGA
1 TTTTTTTTATTTCTTTTTTCTGATTTGA
10113 CTTTCCTCCC
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
27 14 0.28
28 16 0.32
29 6 0.12
31 2 0.04
32 12 0.24
ACGTcount: A:0.13, C:0.08, G:0.06, T:0.74
Consensus pattern (28 bp):
TTTTTTTTATTTCTTTTTTCTGATTTGA
Found at i:14873 original size:43 final size:43
Alignment explanation
Indices: 14812--14898 Score: 156
Period size: 43 Copynumber: 2.0 Consensus size: 43
14802 ACTCCATCTC
* *
14812 CACGACTCCACATATCCTATCTTCAACCTTGAGGGCAAGGTTG
1 CACGACTCCACATATCCTACCTTCAACCTTGAGGGCAAGATTG
14855 CACGACTCCACATATCCTACCTTCAACCTTGAGGGCAAGATTG
1 CACGACTCCACATATCCTACCTTCAACCTTGAGGGCAAGATTG
14898 C
1 C
14899 CATAGACGAG
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.26, C:0.32, G:0.17, T:0.24
Consensus pattern (43 bp):
CACGACTCCACATATCCTACCTTCAACCTTGAGGGCAAGATTG
Found at i:17402 original size:36 final size:36
Alignment explanation
Indices: 17341--17412 Score: 92
Period size: 36 Copynumber: 2.0 Consensus size: 36
17331 GTCAATCCCA
* *
17341 GGGAACTAACTTTGAATTGGCAACTGCCTTTGAATG
1 GGGAACTAACTTTGAATTGGCAACTGACTTGGAATG
* *
17377 GGGAACTAGCTTTGAA-TGGAGAACTGACTTGGAATG
1 GGGAACTAACTTTGAATTGG-CAACTGACTTGGAATG
17413 AGAGACTGAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 3 0.10
36 28 0.90
ACGTcount: A:0.29, C:0.14, G:0.29, T:0.28
Consensus pattern (36 bp):
GGGAACTAACTTTGAATTGGCAACTGACTTGGAATG
Found at i:17411 original size:18 final size:18
Alignment explanation
Indices: 17343--17428 Score: 79
Period size: 18 Copynumber: 4.8 Consensus size: 18
17333 CAATCCCAGG
*
17343 GAACTAACTTTGAATTGG-
1 GAACTGACTTTGAA-TGGA
* * *
17361 CAACTGCCTTTGAATGGG
1 GAACTGACTTTGAATGGA
17379 GAACT-AGCTTTGAATGGA
1 GAACTGA-CTTTGAATGGA
*
17397 GAACTGACTTGGAAT-GA
1 GAACTGACTTTGAATGGA
17414 GAGACTGACTTTGAA
1 GA-ACTGACTTTGAA
17429 AGATCCTTAA
Statistics
Matches: 56, Mismatches: 8, Indels: 8
0.78 0.11 0.11
Matches are distributed among these distances:
17 7 0.12
18 48 0.86
19 1 0.02
ACGTcount: A:0.31, C:0.14, G:0.27, T:0.28
Consensus pattern (18 bp):
GAACTGACTTTGAATGGA
Found at i:17749 original size:17 final size:17
Alignment explanation
Indices: 17716--17761 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
17706 CCAAAATTAG
*
17716 TAATAATTATTGGATAA
1 TAATAATTATTTGATAA
*
17733 TAATAATTATTTTATAA
1 TAATAATTATTTGATAA
* *
17750 TTATTATTATTT
1 TAATAATTATTT
17762 CAGTAAATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.54
Consensus pattern (17 bp):
TAATAATTATTTGATAA
Found at i:25091 original size:15 final size:15
Alignment explanation
Indices: 25068--25105 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
25058 CATGAATGAA
*
25068 GAGAAAATCGAATAC-
1 GAGACAATCGAAT-CT
25083 GAGACAATCGAATCT
1 GAGACAATCGAATCT
25098 GAGACAAT
1 GAGACAAT
25106 GGAAGAAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 1 0.05
15 20 0.95
ACGTcount: A:0.47, C:0.16, G:0.21, T:0.16
Consensus pattern (15 bp):
GAGACAATCGAATCT
Found at i:29054 original size:18 final size:18
Alignment explanation
Indices: 29027--29103 Score: 86
Period size: 18 Copynumber: 4.3 Consensus size: 18
29017 TTGGGTACCT
*
29027 TTTATGATTTGGGCTTTTA
1 TTTATAATTTGGGC-TTTA
*
29046 TTT-TAATTT-GGCATTA
1 TTTATAATTTGGGCTTTA
29062 TTTATAATTTGGGCTTTA
1 TTTATAATTTGGGCTTTA
* *
29080 TTTATTACTTGGGCTTTTA
1 TTTATAATTTGGGC-TTTA
29099 TTTAT
1 TTTAT
29104 GGATTTGGAT
Statistics
Matches: 50, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
16 6 0.12
17 9 0.18
18 23 0.46
19 12 0.24
ACGTcount: A:0.19, C:0.06, G:0.16, T:0.58
Consensus pattern (18 bp):
TTTATAATTTGGGCTTTA
Found at i:29952 original size:39 final size:39
Alignment explanation
Indices: 29838--30057 Score: 238
Period size: 39 Copynumber: 5.6 Consensus size: 39
29828 TTTTCGAATT
29838 GGGAAAGATCCCATCAAGTTTTT---T-TTTTCAATTTA
1 GGGAAAGATCCCATCAAGTTTTTCAATGTTTTCAATTTA
* * *
29873 GAGAAAGATCCCATCCAGTTTTTCAAAGTTTTCATTTTCAATTTA
1 GGGAAAGATCCCATCAAGTTTTTC-AA----T-GTTTTCAATTTA
*
29918 GGGAAAGATTCCATCAAGTTTTTCAATGTTTTCAATTTA
1 GGGAAAGATCCCATCAAGTTTTTCAATGTTTTCAATTTA
* *
29957 GGGAAAGATTCCATCAAGTTTTTCAAGGTTTTCAATTTA
1 GGGAAAGATCCCATCAAGTTTTTCAATGTTTTCAATTTA
*
29996 GGGAAAGATCCCATTC-AG-TTTTCAAAGTTTTCAA-TTA
1 GGGAAAGATCCCA-TCAAGTTTTTCAATGTTTTCAATTTA
*
30033 GGGGAAAGACCCCATCAAAGTTTTT
1 -GGGAAAGATCCCATC-AAGTTTTT
30058 TTTTTATAAA
Statistics
Matches: 160, Mismatches: 10, Indels: 25
0.82 0.05 0.13
Matches are distributed among these distances:
35 21 0.13
37 5 0.03
38 27 0.17
39 65 0.41
40 7 0.04
43 1 0.01
44 2 0.01
45 32 0.20
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (39 bp):
GGGAAAGATCCCATCAAGTTTTTCAATGTTTTCAATTTA
Found at i:32264 original size:30 final size:30
Alignment explanation
Indices: 32228--32286 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
32218 AATTTTTGCC
*
32228 TCTTGAAATAATTCTTCAAT-AGTCTTCAAA
1 TCTTGAAATAA-TCTTCAATAAATCTTCAAA
*
32258 TCTTGAAATTATCTTCAATAAATCTTCAA
1 TCTTGAAATAATCTTCAATAAATCTTCAA
32287 TCACGAACTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
30 18 0.69
ACGTcount: A:0.37, C:0.17, G:0.05, T:0.41
Consensus pattern (30 bp):
TCTTGAAATAATCTTCAATAAATCTTCAAA
Found at i:35979 original size:10 final size:10
Alignment explanation
Indices: 35964--35989 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
35954 TATCGGTAGG
35964 AATTTATAAA
1 AATTTATAAA
35974 AATTTATAAA
1 AATTTATAAA
35984 AATTTA
1 AATTTA
35990 CTATTTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (10 bp):
AATTTATAAA
Found at i:36554 original size:14 final size:14
Alignment explanation
Indices: 36533--36567 Score: 61
Period size: 14 Copynumber: 2.5 Consensus size: 14
36523 CATCTTATGT
36533 TAAAATAATCCAAA
1 TAAAATAATCCAAA
*
36547 TGAAATAATCCAAA
1 TAAAATAATCCAAA
36561 TAAAATA
1 TAAAATA
36568 GTCTAAGAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.63, C:0.11, G:0.03, T:0.23
Consensus pattern (14 bp):
TAAAATAATCCAAA
Found at i:39086 original size:66 final size:67
Alignment explanation
Indices: 39004--39328 Score: 408
Period size: 66 Copynumber: 4.9 Consensus size: 67
38994 CATGCATCAA
** * * * * * * * *
39004 TCAGTATACATTGAAGCGCTCGGTCTGGGCTCGAAATCTTTCA-CAATTGATTTTAGATCAATAT
1 TCAGTATACGCTGAAGCACTTGGCCTCGGCTCGAAATCTTTCAGCAAATGATTTAAGACCAACAT
*
39068 CA
66 CG
* * * * * * * *
39070 TCAGTATACACGGAAGCGCTTGGTCTGGGCTTGAAATCTTTCA-CAAATGATCTAAGACCAGCAT
1 TCAGTATACGCTGAAGCACTTGGCCTCGGCTCGAAATCTTTCAGCAAATGATTTAAGACCAACAT
39134 CG
66 CG
*
39136 TCAGTATACGCTGAAGCACTTGGCCTCGGCTCGAAATCTTT-AGTAAATGATTTAAGACCAACAT
1 TCAGTATACGCTGAAGCACTTGGCCTCGGCTCGAAATCTTTCAGCAAATGATTTAAGACCAACAT
39200 CG
66 CG
*
39202 TCAGTATACGCTGAAGCACTTGGCCTCGGCTCGAAATCTTT-AGCGAATGATTTAAGACCAACAT
1 TCAGTATACGCTGAAGCACTTGGCCTCGGCTCGAAATCTTTCAGCAAATGATTTAAGACCAACAT
39266 CG
66 CG
* *
39268 TCAGCATACGCTGAAGCACTTGGCCTCGGCTCGAAATCTTTC-GTAAATGATTTAAGACCAA
1 TCAGTATACGCTGAAGCACTTGGCCTCGGCTCGAAATCTTTCAGCAAATGATTTAAGACCAA
39329 TACTATCAGT
Statistics
Matches: 232, Mismatches: 25, Indels: 4
0.89 0.10 0.02
Matches are distributed among these distances:
65 1 0.00
66 231 1.00
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (67 bp):
TCAGTATACGCTGAAGCACTTGGCCTCGGCTCGAAATCTTTCAGCAAATGATTTAAGACCAACAT
CG
Found at i:43662 original size:21 final size:21
Alignment explanation
Indices: 43636--43677 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
43626 GCATCTTAGG
*
43636 CAACTCCGATGAGCTTGAAAC
1 CAACTCCAATGAGCTTGAAAC
43657 CAACTCCAATGAGCTTGAAAC
1 CAACTCCAATGAGCTTGAAAC
43678 TTCTTTGTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.36, C:0.29, G:0.17, T:0.19
Consensus pattern (21 bp):
CAACTCCAATGAGCTTGAAAC
Found at i:46702 original size:25 final size:24
Alignment explanation
Indices: 46665--46711 Score: 69
Period size: 26 Copynumber: 1.9 Consensus size: 24
46655 CTAGAAAATT
46665 TGAAAAACTTTGATGGATGAGATGGA
1 TGAAAAACTTTGAT-GAT-AGATGGA
46691 TGAAAAAC-TTGATGATAGATG
1 TGAAAAACTTTGATGATAGATG
46712 AATAGAAGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
23 5 0.24
24 3 0.14
25 5 0.24
26 8 0.38
ACGTcount: A:0.40, C:0.04, G:0.28, T:0.28
Consensus pattern (24 bp):
TGAAAAACTTTGATGATAGATGGA
Found at i:47891 original size:45 final size:42
Alignment explanation
Indices: 47827--47920 Score: 136
Period size: 45 Copynumber: 2.2 Consensus size: 42
47817 AACAACAATC
*
47827 AATATTAGCTTTATTTTGATGAATTATCTAGAGATTGAGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGA-T--GGAGTAG
*
47872 AATATTAGTTTTATTTTGATGAATTACCTAGAGATGGAGTAG
1 AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAG
47914 AAT-TTAG
1 AATATTAG
47921 GTAATGCACT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 10 0.21
44 1 0.02
45 32 0.68
ACGTcount: A:0.34, C:0.04, G:0.21, T:0.40
Consensus pattern (42 bp):
AATATTAGCTTTATTTTGATGAATTACCTAGAGATGGAGTAG
Found at i:48578 original size:23 final size:23
Alignment explanation
Indices: 48535--48578 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
48525 TAAGTTTTTT
*
48535 AATAAAATTAGTAAAATGATAAA
1 AATAAAATTAGTAAAAGGATAAA
*
48558 AATAAAA-TAGGTATAAGGATA
1 AATAAAATTA-GTAAAAGGATA
48579 TTAGATTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 2 0.11
23 16 0.89
ACGTcount: A:0.61, C:0.00, G:0.14, T:0.25
Consensus pattern (23 bp):
AATAAAATTAGTAAAAGGATAAA
Found at i:48675 original size:97 final size:94
Alignment explanation
Indices: 48546--48723 Score: 286
Period size: 97 Copynumber: 1.9 Consensus size: 94
48536 ATAAAATTAG
* *
48546 TAAAATGATAAAAATAAAATAGGTATAAGGATATTAGATTTAATTAAATAAAAATAGAGTTTTTA
1 TAAAATGATAAAAATAAAATAGGTATAAGGATATTAGATTTAATCAAATAAAAATAGAGTTTCTA
48611 GTTGAGTAAAACTATAAAAGTATTTTAAT
66 GTTGAGTAAAACTATAAAAGTATTTTAAT
*
48640 TAAAAT-AGTAAAAATAAAATAGTATTTATAAGGATATTAGATTTAATCAAATAAAAATAGAGTT
1 TAAAATGA-TAAAAATAAAATAG---GTATAAGGATATTAGATTTAATCAAATAAAAATAGAGTT
48704 TCTAGTTGAGTAAAACTATA
62 TCTAGTTGAGTAAAACTATA
48724 CAAATTTAAG
Statistics
Matches: 77, Mismatches: 3, Indels: 5
0.91 0.04 0.06
Matches are distributed among these distances:
93 1 0.01
94 20 0.26
97 56 0.73
ACGTcount: A:0.51, C:0.02, G:0.12, T:0.34
Consensus pattern (94 bp):
TAAAATGATAAAAATAAAATAGGTATAAGGATATTAGATTTAATCAAATAAAAATAGAGTTTCTA
GTTGAGTAAAACTATAAAAGTATTTTAAT
Done.