Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013076.1 Corchorus olitorius cultivar O-4 contig13109, 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: 2646
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.30
Found at i:374 original size:43 final size:42
Alignment explanation
Indices: 327--420 Score: 136
Period size: 43 Copynumber: 2.2 Consensus size: 42
317 CAGACCTCTA
*
327 AAAATTGACAAGAAGACAATTC-GGAAATCAACATAGATCTCCG
1 AAAATTGACAAGAAGACAATTCAAG-AATCAACATAGAT-TCCG
* *
370 AAAATTAACAAGAAGACAATTCAAGAATCAACATAGATTCCT
1 AAAATTGACAAGAAGACAATTCAAGAATCAACATAGATTCCG
412 AAAATTGAC
1 AAAATTGAC
421 TGAAAGGCCA
Statistics
Matches: 46, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
42 11 0.24
43 34 0.74
44 1 0.02
ACGTcount: A:0.50, C:0.17, G:0.13, T:0.20
Consensus pattern (42 bp):
AAAATTGACAAGAAGACAATTCAAGAATCAACATAGATTCCG
Found at i:813 original size:70 final size:70
Alignment explanation
Indices: 710--851 Score: 173
Period size: 70 Copynumber: 2.0 Consensus size: 70
700 AAACCTCATT
* * * * *
710 GAACTTTGCTTATGGAAAAGCCCTCTTGTGCTTGGGTGGAACC-AAGACTTAAAGTGACTCATAT
1 GAACTTTGCTTATGGAAAAGCCCTCTAGTGCTTGGATGAAACCGAAG-CTTAAACTAACTCATAT
774 GGAAAC
65 GGAAAC
* *
780 GAACTTTGGCTTATGGAGAAG-CCTC-AGATGCTTGGATGAAACCGAAGCTTAAACTAACTCGTA
1 GAACTTT-GCTTATGGAAAAGCCCTCTAG-TGCTTGGATGAAACCGAAGCTTAAACTAACTCATA
843 TGGAAAC
64 TGGAAAC
850 GA
1 GA
852 GTTTGCTCTT
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
69 1 0.02
70 46 0.74
71 15 0.24
ACGTcount: A:0.32, C:0.18, G:0.25, T:0.25
Consensus pattern (70 bp):
GAACTTTGCTTATGGAAAAGCCCTCTAGTGCTTGGATGAAACCGAAGCTTAAACTAACTCATATG
GAAAC
Found at i:1038 original size:128 final size:128
Alignment explanation
Indices: 772--1234 Score: 732
Period size: 128 Copynumber: 3.6 Consensus size: 128
762 AGTGACTCAT
* * * * * *
772 ATGGAAACGAACTTTGGCTTATGGAGAAGCCTCAGATGCTTGGATGAAACCGAAGCTTAAACTAA
1 ATGGAAGCGAAC-TTGGCTTATGGAAAAGCCCCAAATGCTTGGATGGAACCAAAGCTTAAACTAA
837 CTCGTATGGAAACGAGTTTGCTCTTG-AAGACTGAACTATCTTCAAATCAAATTGTATACTCGC
65 CTCGTATGGAAACGAGTTTGCTCTTGAAAGACTGAACTATCTTCAAATCAAATTGTATACTCGC
900 ATGGAAGCGAACTTGGCTTATGGAAAAGCCCCAAATGCTTGGATGGAACCAAAGCTTAAACTAAC
1 ATGGAAGCGAACTTGGCTTATGGAAAAGCCCCAAATGCTTGGATGGAACCAAAGCTTAAACTAAC
*
965 TCGTATGGAAACGAGTTTGCTCTTGAAAGACTGAACTATCATCAAATCAAATTGTATACTCGC
66 TCGTATGGAAACGAGTTTGCTCTTGAAAGACTGAACTATCTTCAAATCAAATTGTATACTCGC
* *
1028 ATTGAAGCGAACTTGGCTTATGAAAAAGCCCCAAATGCTTGGATGGAACCAAAGCTTAAACTAAC
1 ATGGAAGCGAACTTGGCTTATGGAAAAGCCCCAAATGCTTGGATGGAACCAAAGCTTAAACTAAC
* * *
1093 TCGTATGGGAACGAGTTTGGTCTTGAAGGACTGAACTATCTTCAAATCAAATTGTATACTCGC
66 TCGTATGGAAACGAGTTTGCTCTTGAAAGACTGAACTATCTTCAAATCAAATTGTATACTCGC
* * * **
1156 ATGGAAGCGAACTTGGCTTATGGAAAAGCCCC-AATAGCTTAGATGGAACCAAAGGTTAAATTGG
1 ATGGAAGCGAACTTGGCTTATGGAAAAGCCCCAAAT-GCTTGGATGGAACCAAAGCTTAAACTAA
*
1220 CCCGTATGGAAACGA
65 CTCGTATGGAAACGA
1235 ACTTTGGCTT
Statistics
Matches: 311, Mismatches: 22, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
127 76 0.24
128 235 0.76
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (128 bp):
ATGGAAGCGAACTTGGCTTATGGAAAAGCCCCAAATGCTTGGATGGAACCAAAGCTTAAACTAAC
TCGTATGGAAACGAGTTTGCTCTTGAAAGACTGAACTATCTTCAAATCAAATTGTATACTCGC
Found at i:1256 original size:70 final size:69
Alignment explanation
Indices: 1156--1304 Score: 185
Period size: 70 Copynumber: 2.1 Consensus size: 69
1146 GTATACTCGC
* *
1156 ATGGAAGCGAACTTGGCTTATGGAAAAGCCCCA-ATAGCTTAGATGGAACCAAAGG-TTAAATTG
1 ATGGAAACGAACTTGGCTTATGGAAAAG-CCCATATAGCTTAGATGGAACC-AAGGCTTAAACTG
*
1219 GCCCGT
64 ACCCGT
* * *
1225 ATGGAAACGAACTTTGGCTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGA
1 ATGGAAACGAAC-TTGGCTTATGGAAAAGCCCATATAGCTTAGATGGAACCAAGGCTTAAACTGA
*
1290 CTCGT
65 CCCGT
*
1295 ATGAAAACGA
1 ATGGAAACGA
1305 GTTTAGTCTT
Statistics
Matches: 69, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
69 19 0.28
70 50 0.72
ACGTcount: A:0.34, C:0.18, G:0.26, T:0.23
Consensus pattern (69 bp):
ATGGAAACGAACTTGGCTTATGGAAAAGCCCATATAGCTTAGATGGAACCAAGGCTTAAACTGAC
CCGT
Found at i:1414 original size:102 final size:102
Alignment explanation
Indices: 1238--1510 Score: 519
Period size: 102 Copynumber: 2.7 Consensus size: 102
1228 GAAACGAACT
*
1238 TTGGCTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGAAAAC
1 TTGGCTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
*
1303 GAGTTTAGTCTTGGAAGACTGAATTCATGTGGAAAAC
66 GAGTATAGTCTTGGAAGACTGAATTCATGTGGAAAAC
*
1340 TTGGCTTATGGAAAAGCCCATGTTGCTTGGATAGAACCAAGGCTTAAACTGACTCGTATGGAAAC
1 TTGGCTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
1405 GAGTATAGTCTTGGAAGACTGAATTCATGTGGAAAAC
66 GAGTATAGTCTTGGAAGACTGAATTCATGTGGAAAAC
1442 TTGGCTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
1 TTGGCTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
1507 GAGT
66 GAGT
1511 TTGACTTATG
Statistics
Matches: 167, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
102 167 1.00
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (102 bp):
TTGGCTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAAC
GAGTATAGTCTTGGAAGACTGAATTCATGTGGAAAAC
Found at i:1471 original size:53 final size:53
Alignment explanation
Indices: 1312--1472 Score: 142
Period size: 53 Copynumber: 3.1 Consensus size: 53
1302 CGAGTTTAGT
1312 CTTGGAAGACTGAATTCATGTGGAAAACTTGGCTTATGGAAAAGCCCATGTTG
1 CTTGGAAGACTGAATTCATGTGGAAAACTTGGCTTATGGAAAAGCCCATGTTG
* ** * * ***
1365 CTTGGATAGAAC-CAAGGC-T-T---AAAC-TGACTCGTATGGAAACGAGTATAG-T-
1 CTTGGA-AG-ACTGAATTCATGTGGAAAACTTGGCT--TATGGAAAAGCCCAT-GTTG
1414 CTTGGAAGACTGAATTCATGTGGAAAACTTGGCTTATGGAAAAGCCCATGTTG
1 CTTGGAAGACTGAATTCATGTGGAAAACTTGGCTTATGGAAAAGCCCATGTTG
1467 CTTGGA
1 CTTGGA
1473 TGGAACCAAG
Statistics
Matches: 78, Mismatches: 16, Indels: 28
0.64 0.13 0.23
Matches are distributed among these distances:
47 2 0.03
48 9 0.12
49 11 0.14
50 13 0.17
51 2 0.03
52 13 0.17
53 17 0.22
54 9 0.12
55 2 0.03
ACGTcount: A:0.31, C:0.16, G:0.26, T:0.27
Consensus pattern (53 bp):
CTTGGAAGACTGAATTCATGTGGAAAACTTGGCTTATGGAAAAGCCCATGTTG
Found at i:1536 original size:68 final size:69
Alignment explanation
Indices: 1446--1578 Score: 259
Period size: 68 Copynumber: 1.9 Consensus size: 69
1436 GAAAACTTGG
1446 CTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGT
1 CTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGT
1511 TTGA
66 TTGA
1515 CTTATGGAAAA-CCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGT
1 CTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGT
1579 ATAATCTTGG
Statistics
Matches: 64, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
68 53 0.83
69 11 0.17
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.26
Consensus pattern (69 bp):
CTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGT
TTGA
Found at i:1549 original size:170 final size:171
Alignment explanation
Indices: 1344--1696 Score: 672
Period size: 170 Copynumber: 2.1 Consensus size: 171
1334 GAAAACTTGG
1344 CTTATGGAAAAGCCCATGTTGCTTGGATAGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGT
1 CTTATGGAAAAGCCCATGTTGCTTGGATAGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGT
*
1409 ATAGTCTTGGAAGACTGAATTCATGTGGAAAACTTGGCTTATGGAAAAGCCCATGTTGCTTGGAT
66 ATAATCTTGGAAGACTGAATTCATGTGGAAAACTTGGCTTATGGAAAAGCCCATGTTGCTTGGAT
1474 GGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGA
131 GGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGA
*
1515 CTTATGGAAAA-CCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGT
1 CTTATGGAAAAGCCCATGTTGCTTGGATAGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGT
*
1579 ATAATCTTGGAAGACTGAATTCATGTGGAAAACTTGGCTTATGGAAAAGCCCATGTTGTTTGGAT
66 ATAATCTTGGAAGACTGAATTCATGTGGAAAACTTGGCTTATGGAAAAGCCCATGTTGCTTGGAT
1644 GGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGA
131 GGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGA
1685 CTTATGGAAAAG
1 CTTATGGAAAAG
1697 TCAAAGCATT
Statistics
Matches: 178, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
170 167 0.94
171 11 0.06
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (171 bp):
CTTATGGAAAAGCCCATGTTGCTTGGATAGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGT
ATAATCTTGGAAGACTGAATTCATGTGGAAAACTTGGCTTATGGAAAAGCCCATGTTGCTTGGAT
GGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTTTGA
Found at i:1653 original size:272 final size:274
Alignment explanation
Indices: 1165--1680 Score: 869
Period size: 272 Copynumber: 1.9 Consensus size: 274
1155 CATGGAAGCG
* *
1165 AACTTGGCTTATGGAAAAGCCCCAATAGCTTAGATGGAACCAAAGGTTAAATTGGCCCGTATGGA
1 AACTTGGCTTATGGAAAAGCCCCAATAGCTTAGATGGAACCAAAGGTTAAACTGACCCGTATGGA
*
1230 AACGAACTTTGGCTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGT
66 AACGAACTTTGACTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGT
* *
1295 ATGAAAACGAGTTTAGTCTTGGAAGACTGAATTCATGTGGAAAACTTGGCTTATGGAAAAGCCCA
131 ATGAAAACGAGTATAATCTTGGAAGACTGAATTCATGTGGAAAACTTGGCTTATGGAAAAGCCCA
1360 TGTTGCTTGGATAGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTATAGTCTTGGAAGACT
196 TGTTGCTTGGATAGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTATAGTCTTGGAAGACT
1425 GAATTCATGTGGAA
261 GAATTCATGTGGAA
* * * *
1439 AACTTGGCTTATGGAAAAG-CCCATGTTGCTTGGATGGAACC-AAGGCTTAAACTGACTCGTATG
1 AACTTGGCTTATGGAAAAGCCCCA-ATAGCTTAGATGGAACCAAAGG-TTAAACTGACCCGTATG
*
1502 GAAACG-AGTTTGACTTATGGAAAA-CCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTC
64 GAAACGAACTTTGACTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTC
*
1565 GTATGGAAACGAGTATAATCTTGGAAGACTGAATTCATGTGGAAAACTTGGCTTATGGAAAAGCC
129 GTATGAAAACGAGTATAATCTTGGAAGACTGAATTCATGTGGAAAACTTGGCTTATGGAAAAGCC
* *
1630 CATGTTGTTTGGATGGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGT
194 CATGTTGCTTGGATAGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGT
1681 TTGACTTATG
Statistics
Matches: 227, Mismatches: 13, Indels: 6
0.92 0.05 0.02
Matches are distributed among these distances:
272 150 0.66
273 24 0.11
274 53 0.23
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.26
Consensus pattern (274 bp):
AACTTGGCTTATGGAAAAGCCCCAATAGCTTAGATGGAACCAAAGGTTAAACTGACCCGTATGGA
AACGAACTTTGACTTATGGAAAAGCCCATGTTGCTTGGATGGAACCAAGGCTTAAACTGACTCGT
ATGAAAACGAGTATAATCTTGGAAGACTGAATTCATGTGGAAAACTTGGCTTATGGAAAAGCCCA
TGTTGCTTGGATAGAACCAAGGCTTAAACTGACTCGTATGGAAACGAGTATAGTCTTGGAAGACT
GAATTCATGTGGAA
Done.