Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011844.1 Corchorus olitorius cultivar O-4 contig11877, 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: 72586
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:168 original size:15 final size:15
Alignment explanation
Indices: 142--194 Score: 97
Period size: 15 Copynumber: 3.5 Consensus size: 15
132 TTTGCTTTGT
142 TTTCTAGTTTAATTGC
1 TTTCT-GTTTAATTGC
158 TTTCTGTTTAATTGC
1 TTTCTGTTTAATTGC
173 TTTCTGTTTAATTGC
1 TTTCTGTTTAATTGC
188 TTTCTGT
1 TTTCTGT
195 CAATCTCTGT
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
15 32 0.86
16 5 0.14
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.60
Consensus pattern (15 bp):
TTTCTGTTTAATTGC
Found at i:4888 original size:18 final size:18
Alignment explanation
Indices: 4861--4895 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
4851 ACAAAAATTG
*
4861 AAATTGTTCATAAACAAA
1 AAATTATTCATAAACAAA
*
4879 AAATTATTCATGAACAA
1 AAATTATTCATAAACAA
4896 TGTAATAATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.11, G:0.06, T:0.29
Consensus pattern (18 bp):
AAATTATTCATAAACAAA
Found at i:5137 original size:35 final size:35
Alignment explanation
Indices: 5098--5172 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
5088 TTATATAAAC
*
5098 GAACACTTAAATGAACAATAAACGAGCTTGTTCGT
1 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
5133 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
1 GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
5168 GAACA
1 GAACA
5173 TAAACGAACT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.41, C:0.19, G:0.17, T:0.23
Consensus pattern (35 bp):
GAACACTTAAATGAACAATAAACGAGCCTGTTCGT
Found at i:9855 original size:327 final size:327
Alignment explanation
Indices: 9261--9915 Score: 1193
Period size: 327 Copynumber: 2.0 Consensus size: 327
9251 GAGCAGAGTC
9261 GTAAGGTTAACTAAAACAAAATAAAATGTATCTCTTATACTTTCAAAAGCACATAATACGAAGCA
1 GTAAGGTTAACTAAAACAAAATAAAATGTATCTCTTATACTTTCAAAAGCACATAATACGAAGCA
* *
9326 AAAGTTTCATACTTTCTATTCATAACAAAAAAACATTTTAACATTGATTTTAATGCCATATTATG
66 AAAGTTTCATACTTTATATTCATAACAAAAAAACATTTTAACATTGATTTTAATGCCATATCATG
* * *
9391 CTAGTCAAAACTTAATCAAAACTAATTTCAAAGCATAATATCATATTGTAGACACCCATTTTTTA
131 CTAGTCAAAACTCAATCAAAACCAATTTCAAAGCATAATATCATATTGTAGACACCCATTTTTGA
*
9456 CCTATATCCTTTAATTTATTTCCATTTGCGCTTAGGGGACATTTAGGTCAATTCCTAATTTTCTA
196 CATATATCCTTTAATTTATTTCCATTTGCGCTTAGGGGACATTTAGGTCAATTCCTAATTTTCTA
9521 AGACATTGTGATAGATTAGCACGTTAACATTCATATTATATTTGCTTGTAAGTTTAAATTTAAAG
261 AGACATTGTGATAGATTAGCACGTTAACATTCATATTATATTTGCTTGTAAGTTTAAATTTAAAG
9586 TT
326 TT
*
9588 GTAAGGTTGACTAAAACAAAATAAAATGTATCTCTTATACTTTCAAAAGCACATAATACGAAGCA
1 GTAAGGTTAACTAAAACAAAATAAAATGTATCTCTTATACTTTCAAAAGCACATAATACGAAGCA
* *
9653 AAAGTTTCATACTTTATATTCATAGCAAAATAACATTTTAACATTGATTTTAATGCCATATCATG
66 AAAGTTTCATACTTTATATTCATAACAAAAAAACATTTTAACATTGATTTTAATGCCATATCATG
9718 CTAGTCAAAACTCAATCAAAACCAATTTCAAAGCATAATATCATATTGTAGACACCCATTTTTGA
131 CTAGTCAAAACTCAATCAAAACCAATTTCAAAGCATAATATCATATTGTAGACACCCATTTTTGA
*
9783 CATATATCCTTTAATTTATTTCCATTTGCGCTTAGGGGACATTTAGGTCGATTCCTAATTTTCTA
196 CATATATCCTTTAATTTATTTCCATTTGCGCTTAGGGGACATTTAGGTCAATTCCTAATTTTCTA
** *
9848 AGACATTGTGATAGATTAGTTCGTTAACATTCATATTCTATTTGCTTGTAAGTTTAAATTTAAAG
261 AGACATTGTGATAGATTAGCACGTTAACATTCATATTATATTTGCTTGTAAGTTTAAATTTAAAG
9913 TT
326 TT
9915 G
1 G
9916 CATTGGGAAA
Statistics
Matches: 315, Mismatches: 13, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
327 315 1.00
ACGTcount: A:0.37, C:0.15, G:0.11, T:0.37
Consensus pattern (327 bp):
GTAAGGTTAACTAAAACAAAATAAAATGTATCTCTTATACTTTCAAAAGCACATAATACGAAGCA
AAAGTTTCATACTTTATATTCATAACAAAAAAACATTTTAACATTGATTTTAATGCCATATCATG
CTAGTCAAAACTCAATCAAAACCAATTTCAAAGCATAATATCATATTGTAGACACCCATTTTTGA
CATATATCCTTTAATTTATTTCCATTTGCGCTTAGGGGACATTTAGGTCAATTCCTAATTTTCTA
AGACATTGTGATAGATTAGCACGTTAACATTCATATTATATTTGCTTGTAAGTTTAAATTTAAAG
TT
Found at i:11455 original size:24 final size:24
Alignment explanation
Indices: 11428--11477 Score: 100
Period size: 24 Copynumber: 2.1 Consensus size: 24
11418 ACCAACCCTT
11428 CAGACACTGGCAAACACCCACTAC
1 CAGACACTGGCAAACACCCACTAC
11452 CAGACACTGGCAAACACCCACTAC
1 CAGACACTGGCAAACACCCACTAC
11476 CA
1 CA
11478 AGCTCAAACG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.38, C:0.42, G:0.12, T:0.08
Consensus pattern (24 bp):
CAGACACTGGCAAACACCCACTAC
Found at i:15340 original size:33 final size:33
Alignment explanation
Indices: 15303--15414 Score: 172
Period size: 33 Copynumber: 3.4 Consensus size: 33
15293 GGCGGTGTTT
* *
15303 CTTGGGCGGCACTGACCATGG-CGTGCCGCCCTC
1 CTTGGGCGGCA-TGACCATGGTCATGCCTCCCTC
*
15336 CTTGGGCGGCATGACCATGGTCATACCTCCCTC
1 CTTGGGCGGCATGACCATGGTCATGCCTCCCTC
*
15369 ATTGGGCGGCATGACCATGGTCATGCCTCCCTC
1 CTTGGGCGGCATGACCATGGTCATGCCTCCCTC
15402 CTTGGGCGGCATG
1 CTTGGGCGGCATG
15415 CCGCCCTCCT
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
32 9 0.12
33 63 0.88
ACGTcount: A:0.12, C:0.35, G:0.30, T:0.22
Consensus pattern (33 bp):
CTTGGGCGGCATGACCATGGTCATGCCTCCCTC
Found at i:15416 original size:21 final size:21
Alignment explanation
Indices: 15390--15433 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
15380 TGACCATGGT
* *
15390 CATGCCTCCCTCCTTGGGCGG
1 CATGCCGCCCTCCTAGGGCGG
15411 CATGCCGCCCTCCTAGGGCGG
1 CATGCCGCCCTCCTAGGGCGG
15432 CA
1 CA
15434 CCGGTTATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.09, C:0.43, G:0.30, T:0.18
Consensus pattern (21 bp):
CATGCCGCCCTCCTAGGGCGG
Found at i:15512 original size:7 final size:7
Alignment explanation
Indices: 15454--15528 Score: 57
Period size: 7 Copynumber: 10.6 Consensus size: 7
15444 TTTTGTTTTT
*
15454 TAATTAT
1 TAATTAA
*
15461 TAATTAT
1 TAATTAA
15468 TAATT-A
1 TAATTAA
15474 TAATTAA
1 TAATTAA
15481 TAA-TAA
1 TAATTAA
*
15487 CAATTTAAA
1 TAA-TT-AA
15496 TTAA-TAA
1 -TAATTAA
15503 TAATTAA
1 TAATTAA
15510 TAATTAAA
1 TAATT-AA
*
15518 TAATTGA
1 TAATTAA
15525 TAAT
1 TAAT
15529 AATTAAAAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
6 13 0.23
7 31 0.54
8 9 0.16
9 2 0.04
10 2 0.04
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (7 bp):
TAATTAA
Found at i:15653 original size:12 final size:12
Alignment explanation
Indices: 15636--15660 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15626 CTACAAAATC
15636 CGACATGATTTT
1 CGACATGATTTT
15648 CGACATGATTTT
1 CGACATGATTTT
15660 C
1 C
15661 TTCAAGATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (12 bp):
CGACATGATTTT
Found at i:21482 original size:33 final size:36
Alignment explanation
Indices: 21407--21520 Score: 130
Period size: 36 Copynumber: 3.2 Consensus size: 36
21397 CTACTGACCC
** *
21407 ACTTAATTACCCTGAATTAAGTTTTTTCTGATTTTT
1 ACTTAATTACCCTGAATTAAGTTTGATCTGATCTTT
21443 ACTTAATTACCCTGAATTAA-TTTGAT-TGA-CTTT
1 ACTTAATTACCCTGAATTAAGTTTGATCTGATCTTT
*
21476 ACTTAATTACCCTTAATTAAGTCTTCGA-CTGAT-TTT
1 ACTTAATTACCCTGAATTAAGT-TT-GATCTGATCTTT
*
21512 ACTCAATTA
1 ACTTAATTA
21521 TTTGAGCTTA
Statistics
Matches: 68, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
33 22 0.32
34 4 0.06
35 6 0.09
36 36 0.53
ACGTcount: A:0.29, C:0.17, G:0.08, T:0.46
Consensus pattern (36 bp):
ACTTAATTACCCTGAATTAAGTTTGATCTGATCTTT
Found at i:23870 original size:156 final size:156
Alignment explanation
Indices: 23586--23898 Score: 590
Period size: 156 Copynumber: 2.0 Consensus size: 156
23576 ATTTGACAGC
* *
23586 TCAATGTAAGCTCCTTTTCCTTTTGCTTTGTTCATCTTTCTGCATGAATTTCCTGCTGAGATGGC
1 TCAATGTAAGCTCCTTTTCCTTTTGCTCTGTACATCTTTCTGCATGAATTTCCTGCTGAGATGGC
*
23651 ATCTTCATTGGTGAATGCATGAGAGTGTCTATATGCTGACTAAGTTCTAATTGTGTGACCATGTA
66 ATCTTCATTGGTGAATGCATGAGAGTGTCTATATGCTGACTAAGTTCTAAATGTGTGACCATGTA
23716 ACTTGTGAATTTGTGTGCAAAGTGGA
131 ACTTGTGAATTTGTGTGCAAAGTGGA
23742 TCAATGTAAGCTCCTTTTCCTTTTGCTCTGTACATCTTTCTGCATGAATTTCCTGCTGAGATGGC
1 TCAATGTAAGCTCCTTTTCCTTTTGCTCTGTACATCTTTCTGCATGAATTTCCTGCTGAGATGGC
23807 ATCTTCATTGGTGAATGCATGAGAGTGTCTATATGCTGACTAAGTTCTAAATGTGTGACCATGTA
66 ATCTTCATTGGTGAATGCATGAGAGTGTCTATATGCTGACTAAGTTCTAAATGTGTGACCATGTA
*
23872 ACTTGTGAATTTTTGTGCAAAGTGGA
131 ACTTGTGAATTTGTGTGCAAAGTGGA
23898 T
1 T
23899 GTAATGTATA
Statistics
Matches: 153, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
156 153 1.00
ACGTcount: A:0.22, C:0.17, G:0.21, T:0.39
Consensus pattern (156 bp):
TCAATGTAAGCTCCTTTTCCTTTTGCTCTGTACATCTTTCTGCATGAATTTCCTGCTGAGATGGC
ATCTTCATTGGTGAATGCATGAGAGTGTCTATATGCTGACTAAGTTCTAAATGTGTGACCATGTA
ACTTGTGAATTTGTGTGCAAAGTGGA
Found at i:26477 original size:21 final size:22
Alignment explanation
Indices: 26449--26495 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
26439 TTCTACACAT
*
26449 GTTG-GTTC-AACCTTATTCAG
1 GTTGAGTTCGAACCTTATGCAG
* *
26469 GTTGAGTTCGACCCTTCTGCAG
1 GTTGAGTTCGAACCTTATGCAG
26491 GTTGA
1 GTTGA
26496 AAACAGAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
20 4 0.18
21 4 0.18
22 14 0.64
ACGTcount: A:0.17, C:0.21, G:0.26, T:0.36
Consensus pattern (22 bp):
GTTGAGTTCGAACCTTATGCAG
Found at i:26510 original size:73 final size:72
Alignment explanation
Indices: 26367--26515 Score: 219
Period size: 72 Copynumber: 2.1 Consensus size: 72
26357 GATTTGAAGT
* * *
26367 TTCTATACAAGTTAGTTCGACCCTATTCAGGTTGAGTTCGACCTTCTGCATGTTGAAACAGAAAA
1 TTCTACACAAGTTAGTTCAACCCTATTCAGGTTGAGTTCGACCTTCTGCAGGTTGAAACAGAAAA
26432 ATTTTTG
66 ATTTTTG
* * *
26439 TTCTACACATGTTGGTTCAACCTTATTCAGGTTGAGTTCGACCCTTCTGCAGGTTGAAAACAG-A
1 TTCTACACAAGTTAGTTCAACCCTATTCAGGTTGAGTTCGA-CCTTCTGCAGGTTG-AAACAGAA
26503 AAATTTTTG
64 AAATTTTTG
26512 TTCT
1 TTCT
26516 CAATTAAGCA
Statistics
Matches: 69, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
72 36 0.52
73 27 0.39
74 6 0.09
ACGTcount: A:0.26, C:0.19, G:0.18, T:0.37
Consensus pattern (72 bp):
TTCTACACAAGTTAGTTCAACCCTATTCAGGTTGAGTTCGACCTTCTGCAGGTTGAAACAGAAAA
ATTTTTG
Found at i:32191 original size:28 final size:28
Alignment explanation
Indices: 32143--32267 Score: 137
Period size: 28 Copynumber: 4.5 Consensus size: 28
32133 ATTTACTTTT
**
32143 CATTTTGGTCATTTTTTATG-TCTAGGGG
1 CATTTTGGTCATTTTGCATGTTC-AGGGG
* *
32171 CATTTTGGTCATCTTGCATGTCCAGGGG
1 CATTTTGGTCATTTTGCATGTTCAGGGG
* * *
32199 CATTTTGGTCATTTTGCATATTCATGGA
1 CATTTTGGTCATTTTGCATGTTCAGGGG
*
32227 CATTTTGGTCA-TTTGCACGTTCAGGGG
1 CATTTTGGTCATTTTGCATGTTCAGGGG
**
32254 CGCTTTGGTCATTT
1 CATTTTGGTCATTT
32268 AAAGTCTACT
Statistics
Matches: 80, Mismatches: 15, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
27 21 0.26
28 58 0.73
29 1 0.01
ACGTcount: A:0.15, C:0.17, G:0.25, T:0.43
Consensus pattern (28 bp):
CATTTTGGTCATTTTGCATGTTCAGGGG
Found at i:59903 original size:16 final size:16
Alignment explanation
Indices: 59882--59912 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
59872 GATAAGAAGA
59882 AAAAATAAAAATAAAG
1 AAAAATAAAAATAAAG
59898 AAAAATAAAAATAAA
1 AAAAATAAAAATAAA
59913 ATTTTAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.03, T:0.13
Consensus pattern (16 bp):
AAAAATAAAAATAAAG
Found at i:63361 original size:19 final size:18
Alignment explanation
Indices: 63328--63363 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
63318 TTGAAATTAT
63328 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
63346 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
63364 TAAATCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:65920 original size:18 final size:19
Alignment explanation
Indices: 65893--65937 Score: 51
Period size: 18 Copynumber: 2.5 Consensus size: 19
65883 AAATTCAAAG
*
65893 AAAAATTAAT-GTAAAAATT
1 AAAAATTAATAAT-AAAATT
65912 AAAAA-TAATAATAAAATT
1 AAAAATTAATAATAAAATT
65930 -AAAATTAA
1 AAAAATTAA
65938 AATTAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 4 0.17
18 13 0.57
19 6 0.26
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (19 bp):
AAAAATTAATAATAAAATT
Found at i:65932 original size:6 final size:6
Alignment explanation
Indices: 65906--65945 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
65896 AATTAATGTA
*
65906 AAAATT AAAAAT AATAA-T AAAATT AAAATT AAAATT AAAA
1 AAAATT AAAATT AA-AATT AAAATT AAAATT AAAATT AAAA
65946 ATGCAAAGAA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
5 2 0.06
6 27 0.87
7 2 0.06
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (6 bp):
AAAATT
Found at i:72374 original size:29 final size:31
Alignment explanation
Indices: 72310--72374 Score: 80
Period size: 31 Copynumber: 2.2 Consensus size: 31
72300 GCTTAATGCC
* *
72310 CAAATTGGCCCTTTAACTATTTATTTTGGGA
1 CAAATCGGCCCCTTAACTATTTATTTTGGGA
* *
72341 TAAATCGGCCCCTTATCTA-TT-TTTTGGGA
1 CAAATCGGCCCCTTAACTATTTATTTTGGGA
72370 CAAAT
1 CAAAT
72375 AAGCCCCACA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
29 12 0.41
30 2 0.07
31 15 0.52
ACGTcount: A:0.26, C:0.18, G:0.15, T:0.40
Consensus pattern (31 bp):
CAAATCGGCCCCTTAACTATTTATTTTGGGA
Done.