Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024458.1 Corchorus olitorius cultivar O-4 contig24491, 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: 20975
ACGTcount: A:0.32, C:0.18, G:0.15, T:0.34
Found at i:3308 original size:55 final size:53
Alignment explanation
Indices: 3226--3336 Score: 186
Period size: 55 Copynumber: 2.1 Consensus size: 53
3216 ACAAATAGAA
* *
3226 AAAGGTCAATCACAATAATTAAATTCTAAATAAATTTTTAACTTAATTAGTTT
1 AAAGGTCAATCACAATAATTAAATTCTAAATAAATGTTTAACTTAATTAATTT
3279 AAAGGTCAATCACACAATAATTAAATTCTAAATAAATGTTTAACTTAATTAATTT
1 AAAGGTCAAT--CACAATAATTAAATTCTAAATAAATGTTTAACTTAATTAATTT
3334 AAA
1 AAA
3337 AAATGATTAA
Statistics
Matches: 54, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
53 10 0.19
55 44 0.81
ACGTcount: A:0.48, C:0.10, G:0.05, T:0.37
Consensus pattern (53 bp):
AAAGGTCAATCACAATAATTAAATTCTAAATAAATGTTTAACTTAATTAATTT
Found at i:3350 original size:23 final size:25
Alignment explanation
Indices: 3294--3354 Score: 72
Period size: 25 Copynumber: 2.4 Consensus size: 25
3284 TCAATCACAC
*
3294 AATAATTAAATTCTAAATAAATGTTT
1 AATAATT-AATTCTAAATAAATGATT
3320 AACTTAATTAATT-TAAA-AAATGATT
1 AA--TAATTAATTCTAAATAAATGATT
3345 AATAATTAAT
1 AATAATTAAT
3355 GATTAAGAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
23 8 0.25
25 9 0.28
26 6 0.19
27 4 0.12
28 5 0.16
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.41
Consensus pattern (25 bp):
AATAATTAATTCTAAATAAATGATT
Found at i:3773 original size:116 final size:120
Alignment explanation
Indices: 3611--3846 Score: 347
Period size: 116 Copynumber: 2.0 Consensus size: 120
3601 TTAAAAATTC
*
3611 TAATATATCTAAGTTTTTTAATTAATTAAATTAGTAAAATGGTAAAAATAAAAAAGGTATGAGGA
1 TAATATATCTAAGTTTTTTAATTAA-TAAATTAGTAAAATGGTAAAAATAAAAAAGGTATAAGGA
*
3676 TAGTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGAG-TAAAA-TATAAAAGTA
65 TAGTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTG-GCTAAAACTACAAAAGTA
* * * *
3731 TAATATATTTAAGTTTTTTAATT-A-AAA-TAGTATAATGGTAAAAATAAAATAGTTATAAGGAT
1 TAATATATCTAAGTTTTTTAATTAATAAATTAGTAAAATGGTAAAAATAAAAAAGGTATAAGGAT
* *
3793 ATTAGATTTGATTAAATAAAAATAGAGTTTTTAGTTGGCTAAAACTACAAAAGT
66 AGTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGGCTAAAACTACAAAAGT
3847 TTAAACAATG
Statistics
Matches: 106, Mismatches: 8, Indels: 7
0.88 0.07 0.06
Matches are distributed among these distances:
115 1 0.01
116 71 0.67
117 11 0.10
119 1 0.01
120 22 0.21
ACGTcount: A:0.48, C:0.02, G:0.14, T:0.37
Consensus pattern (120 bp):
TAATATATCTAAGTTTTTTAATTAATAAATTAGTAAAATGGTAAAAATAAAAAAGGTATAAGGAT
AGTAGATTTAATTAAATAAAAATAGAGTTTTTAGTTGGCTAAAACTACAAAAGTA
Found at i:5357 original size:33 final size:34
Alignment explanation
Indices: 5315--5380 Score: 98
Period size: 34 Copynumber: 2.0 Consensus size: 34
5305 CCCGGTGACC
5315 TTTCGAGTACTGG-ATGAAGACGAATTCGAGGGG
1 TTTCGAGTACTGGCATGAAGACGAATTCGAGGGG
* * *
5348 TTTCGAGTACTGGCATGAGGATGAATTTGAGGG
1 TTTCGAGTACTGGCATGAAGACGAATTCGAGGG
5381 CTTACCTCTC
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
33 13 0.45
34 16 0.55
ACGTcount: A:0.26, C:0.11, G:0.36, T:0.27
Consensus pattern (34 bp):
TTTCGAGTACTGGCATGAAGACGAATTCGAGGGG
Found at i:9580 original size:13 final size:13
Alignment explanation
Indices: 9538--9587 Score: 52
Period size: 13 Copynumber: 4.1 Consensus size: 13
9528 TAGCCTATAG
*
9538 CCTTTCTAATTA-
1 CCTTTGTAATTAT
*
9550 CC-TTGTTATTAT
1 CCTTTGTAATTAT
9562 -CTTTGTAATTAT
1 CCTTTGTAATTAT
*
9574 CCTTTGTATTTAT
1 CCTTTGTAATTAT
9587 C
1 C
9588 ACTTACCTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
11 8 0.26
12 11 0.35
13 12 0.39
ACGTcount: A:0.20, C:0.18, G:0.06, T:0.56
Consensus pattern (13 bp):
CCTTTGTAATTAT
Found at i:9796 original size:23 final size:22
Alignment explanation
Indices: 9770--9820 Score: 79
Period size: 20 Copynumber: 2.4 Consensus size: 22
9760 CTTCATCAAC
9770 CTCAGAAACACCTGTTCTTTCTT
1 CTCA-AAACACCTGTTCTTTCTT
9793 CTC-AAA-ACCTGTTCTTTCTT
1 CTCAAAACACCTGTTCTTTCTT
9813 CTCAAAAC
1 CTCAAAAC
9821 TCTACCTCTG
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
20 17 0.65
21 6 0.23
23 3 0.12
ACGTcount: A:0.25, C:0.31, G:0.06, T:0.37
Consensus pattern (22 bp):
CTCAAAACACCTGTTCTTTCTT
Found at i:9804 original size:20 final size:20
Alignment explanation
Indices: 9779--9820 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
9769 CCTCAGAAAC
9779 ACCTGTTCTTTCTTCTCAAA
1 ACCTGTTCTTTCTTCTCAAA
9799 ACCTGTTCTTTCTTCTCAAA
1 ACCTGTTCTTTCTTCTCAAA
9819 AC
1 AC
9821 TCTACCTCTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.21, C:0.31, G:0.05, T:0.43
Consensus pattern (20 bp):
ACCTGTTCTTTCTTCTCAAA
Found at i:10728 original size:20 final size:20
Alignment explanation
Indices: 10697--10743 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
10687 GCAAACAATG
10697 CAACAA-TAACTCCCAGAAA
1 CAACAACTAACTCCCAGAAA
10716 CAACAACTAACTCCCAGAAA
1 CAACAACTAACTCCCAGAAA
10736 CAACAACT
1 CAACAACT
10744 GGATTGCTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 6 0.22
20 21 0.78
ACGTcount: A:0.51, C:0.34, G:0.04, T:0.11
Consensus pattern (20 bp):
CAACAACTAACTCCCAGAAA
Found at i:13898 original size:12 final size:12
Alignment explanation
Indices: 13869--13911 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 12
13859 TAGCCTATAG
*
13869 CCTTTCTAATTA
1 CCTTTGTAATTA
*
13881 CC-TTGTTATTA
1 CCTTTGTAATTA
*
13892 TCTTTGTAATTA
1 CCTTTGTAATTA
13904 CCTTTGTA
1 CCTTTGTA
13912 TTTATCGAGA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
11 8 0.32
12 17 0.68
ACGTcount: A:0.21, C:0.19, G:0.07, T:0.53
Consensus pattern (12 bp):
CCTTTGTAATTA
Found at i:14430 original size:40 final size:40
Alignment explanation
Indices: 14375--14450 Score: 143
Period size: 40 Copynumber: 1.9 Consensus size: 40
14365 CAGCTTCACT
*
14375 ACTTGCATTGTAATCTGCACTAACATATGAAATTAGGATA
1 ACTTGCATTGTAATCTGAACTAACATATGAAATTAGGATA
14415 ACTTGCATTGTAATCTGAACTAACATATGAAATTAG
1 ACTTGCATTGTAATCTGAACTAACATATGAAATTAG
14451 TATCCTATCT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
40 35 1.00
ACGTcount: A:0.38, C:0.14, G:0.14, T:0.33
Consensus pattern (40 bp):
ACTTGCATTGTAATCTGAACTAACATATGAAATTAGGATA
Found at i:19313 original size:54 final size:52
Alignment explanation
Indices: 19257--19655 Score: 451
Period size: 54 Copynumber: 7.7 Consensus size: 52
19247 TATTTCTGCT
* ** *
19257 TTTTACTTTTTAGTTTAATTATTCAGAATT-AACTAATTACCGTTTACTCTTTC
1 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAA-TACTGTTTACT-TTTC
* * *
19310 TTTTACTCTTTAGTTTAATTACTCAAAATTAAACTAATTACTGTTTATTTCTTC
1 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAA-TACTGTTTACTT-TTC
* *
19364 CTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAATTATTGTTTACTTCTTC
1 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAA-TACTGTTTACTT-TTC
* *
19418 TTTTACTCTTTAGTTTAATTACCCAGAATCAAACTAACA-T-TTT-C--TTC
1 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAATACTGTTTACTTTTC
* * *
19465 TTTTACTATTCAGTTTAATTACCCAGAATTAAACTAAAATCTGTTTACTTCTTC
1 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAATA-CTGTTTACTT-TTC
*
19519 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAACATCTGTTTACTTCTTC
1 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAATA-CTGTTTACTT-TTC
* *
19573 TTTTACTCTTTAGTTTAATTTCCCAGAATTAAACT-A-AC-CTTT--TTTTC
1 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAATACTGTTTACTTTTC
* * *
19620 TTTTACTATTTAGTTTAATTATCCAGAATAAAACTA
1 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTA
19656 GGTGTAAACT
Statistics
Matches: 310, Mismatches: 26, Indels: 25
0.86 0.07 0.07
Matches are distributed among these distances:
47 72 0.23
48 2 0.01
49 1 0.00
50 7 0.02
51 5 0.02
52 2 0.01
53 30 0.10
54 191 0.62
ACGTcount: A:0.29, C:0.18, G:0.05, T:0.48
Consensus pattern (52 bp):
TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAATACTGTTTACTTTTC
Found at i:19509 original size:155 final size:156
Alignment explanation
Indices: 19307--19655 Score: 542
Period size: 155 Copynumber: 2.2 Consensus size: 156
19297 CGTTTACTCT
* * * * *
19307 TTCTTTTACTCTTTAGTTTAATTACTCAAAATTAAACT-AATTACTGTTTATTTCTTCCTTTACT
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAAAATACTGTTTACTTCTTCCTTTACT
*
19371 CTTTAGTTTAATTACCCAGAATTAAACTAATTAT-TGTTTACTTCTTCTTTTACTCTTTAGTTTA
66 CTTTAGTTTAATTACCCAGAATTAAACTAA-CATCTGTTTACTTCTTCTTTTACTCTTTAGTTTA
19435 ATTACCCAGAATCAAACTAACATTTTC
130 ATTACCCAGAATCAAACTAACATTTTC
* *
19462 TTCTTTTACTATTCAGTTTAATTACCCAGAATTAAACTAAAAT-CTGTTTACTTCTTCTTTTACT
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAAAATACTGTTTACTTCTTCCTTTACT
19526 CTTTAGTTTAATTACCCAGAATTAAACTAACATCTGTTTACTTCTTCTTTTACTCTTTAGTTTAA
66 CTTTAGTTTAATTACCCAGAATTAAACTAACATCTGTTTACTTCTTCTTTTACTCTTTAGTTTAA
* * * *
19591 TTTCCCAGAATTAAACTAACCTTTTT
131 TTACCCAGAATCAAACTAACATTTTC
* *
19617 TTCTTTTACTATTTAGTTTAATTATCCAGAATAAAACTA
1 TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTA
19656 GGTGTAAACT
Statistics
Matches: 177, Mismatches: 15, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
154 2 0.01
155 172 0.97
156 3 0.02
ACGTcount: A:0.30, C:0.18, G:0.05, T:0.48
Consensus pattern (156 bp):
TTCTTTTACTATTTAGTTTAATTACCCAGAATTAAACTAAAATACTGTTTACTTCTTCCTTTACT
CTTTAGTTTAATTACCCAGAATTAAACTAACATCTGTTTACTTCTTCTTTTACTCTTTAGTTTAA
TTACCCAGAATCAAACTAACATTTTC
Found at i:19511 original size:101 final size:100
Alignment explanation
Indices: 19257--19655 Score: 411
Period size: 101 Copynumber: 3.9 Consensus size: 100
19247 TATTTCTGCT
* ** * *
19257 TTTTACTTTTTAGTTTAATTATTCAGAATT-AACTAATTACCGTTTAC-TCTTTCTTTTACTCTT
1 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAAAT-CTGTTTACTTC-TTCTTTTACTCTT
* * *
19320 TAGTTTAATTACTCAAAATTAAACTAATTACTGTTTATTTCTTC
64 TAGTTTAATTACCCAGAATTAAACT-A--AC---AT-TTTCTTC
*
19364 CTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAATTAT-TGTTTACTTCTTCTTTTACTCTT
1 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAA--ATCTGTTTACTTCTTCTTTTACTCTT
*
19428 TAGTTTAATTACCCAGAATCAAACTAACATTTTCTTC
64 TAGTTTAATTACCCAGAATTAAACTAACATTTTCTTC
* *
19465 TTTTACTATTCAGTTTAATTACCCAGAATTAAACTAAAATCTGTTTACTTCTTCTTTTACTCTTT
1 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACT-AAATCTGTTTACTTCTTCTTTTACTCTTT
19530 AGTTTAATTACCCAGAATTAAACTAACATCTGTTTACTTCTTC
65 AGTTTAATTACCCAGAATTAAACTAACA-----TT--TTCTTC
* * *
19573 TTTTACTCTTTAGTTTAATTTCCCAGAATTAAACT-AA-C-CTTT--TT-TTCTTTTACTATTTA
1 TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAAATCTGTTTACTTCTTCTTTTACTCTTTA
* *
19632 GTTTAATTATCCAGAATAAAACTA
66 GTTTAATTACCCAGAATTAAACTA
19656 GGTGTAAACT
Statistics
Matches: 258, Mismatches: 21, Indels: 32
0.83 0.07 0.10
Matches are distributed among these distances:
100 2 0.01
101 126 0.49
102 5 0.02
104 3 0.01
105 3 0.01
106 4 0.02
107 27 0.10
108 85 0.33
109 2 0.01
110 1 0.00
ACGTcount: A:0.29, C:0.18, G:0.05, T:0.48
Consensus pattern (100 bp):
TTTTACTCTTTAGTTTAATTACCCAGAATTAAACTAAATCTGTTTACTTCTTCTTTTACTCTTTA
GTTTAATTACCCAGAATTAAACTAACATTTTCTTC
Found at i:20401 original size:6 final size:6
Alignment explanation
Indices: 20392--20440 Score: 80
Period size: 6 Copynumber: 7.8 Consensus size: 6
20382 CCACCACATA
20392 TATATC TATATAC TATATC TATATC TATATC TATATC TATATAC TATAT
1 TATATC TATAT-C TATATC TATATC TATATC TATATC TATAT-C TATAT
20441 AAGTCTAAAC
Statistics
Matches: 41, Mismatches: 0, Indels: 3
0.93 0.00 0.07
Matches are distributed among these distances:
6 29 0.71
7 12 0.29
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (6 bp):
TATATC
Found at i:20421 original size:25 final size:25
Alignment explanation
Indices: 20392--20440 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
20382 CCACCACATA
20392 TATATCTATATACTATATCTATATC
1 TATATCTATATACTATATCTATATC
20417 TATATCTATAT-CTATATACTATAT
1 TATATCTATATACTATAT-CTATAT
20441 AAGTCTAAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 6 0.26
25 17 0.74
ACGTcount: A:0.37, C:0.14, G:0.00, T:0.49
Consensus pattern (25 bp):
TATATCTATATACTATATCTATATC
Found at i:20713 original size:39 final size:40
Alignment explanation
Indices: 20657--20737 Score: 119
Period size: 39 Copynumber: 2.0 Consensus size: 40
20647 TTTAATTCCT
20657 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
* * * *
20697 ATGTAATA-CTATAATAACTGAAATCCTTATATTAATTAA
1 ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
20736 AT
1 AT
20738 TCTTAGATAT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
39 29 0.78
40 8 0.22
ACGTcount: A:0.49, C:0.09, G:0.04, T:0.38
Consensus pattern (40 bp):
ATGTAATATATATAATAACTAAAATACTTACATTAATTAA
Found at i:20763 original size:24 final size:23
Alignment explanation
Indices: 20728--20773 Score: 74
Period size: 24 Copynumber: 2.0 Consensus size: 23
20718 AATCCTTATA
20728 TTAATTAAATTCTTAGATATTTT
1 TTAATTAAATTCTTAGATATTTT
*
20751 TTAATTCAAATTCTTAGGTATTT
1 TTAATT-AAATTCTTAGATATTT
20774 GTGCAAACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
23 6 0.29
24 15 0.71
ACGTcount: A:0.33, C:0.07, G:0.07, T:0.54
Consensus pattern (23 bp):
TTAATTAAATTCTTAGATATTTT
Done.