Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013052.1 Corchorus capsularis cultivar CVL-1 contig13073, 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: 3209
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Found at i:89 original size:27 final size:27
Alignment explanation
Indices: 14--98 Score: 66
Period size: 27 Copynumber: 3.1 Consensus size: 27
4 ATTGGGGGTC
14 ACTTGAGTTGAAAACCCGAAAAGGGCGG
1 ACTTGAGTTGAAAACCCGAAAAGGG-GG
** * ** *
42 -CTCAAG-TGAAGGATGCTAAAAGGGGG
1 ACTTGAGTTGAA-AACCCGAAAAGGGGG
*
68 ACTTGAGTTGAAAACCCGAAAAAGGGCG
1 ACTTGAGTTGAAAACCCG-AAAAGGGGG
96 ACT
1 ACT
99 CAGGTGGAAG
Statistics
Matches: 40, Mismatches: 13, Indels: 8
0.66 0.21 0.13
Matches are distributed among these distances:
26 6 0.15
27 19 0.47
28 15 0.38
ACGTcount: A:0.36, C:0.16, G:0.32, T:0.15
Consensus pattern (27 bp):
ACTTGAGTTGAAAACCCGAAAAGGGGG
Found at i:1210 original size:38 final size:38
Alignment explanation
Indices: 1178--1500 Score: 248
Period size: 38 Copynumber: 8.6 Consensus size: 38
1168 AATTAAGGAC
* *
1178 CAAAGTAATAGTAATCAGTAAAATTGATAATTAAGAGT
1 CAAAGTAAGAATAATCAGTAAAATTGATAATTAAGAGT
*
1216 CAAAGTAAGAATAATCAGTAAAATTGATAATTACGAGT
1 CAAAGTAAGAATAATCAGTAAAATTGATAATTAAGAGT
1254 C--A--AAG--TAATCAGTAAAATTGATAATTAAGAGT
1 CAAAGTAAGAATAATCAGTAAAATTGATAATTAAGAGT
*
1286 CAAAGTAAGAATAATCAGTAAAATTGATAATCAAGAGT
1 CAAAGTAAGAATAATCAGTAAAATTGATAATTAAGAGT
* * *
1324 CAAGGTAACG-GTAATCAGT-AAA-TCAGTAATTAAGTAG-
1 CAAAGTAA-GAATAATCAGTAAAATTGA-TAATTAAG-AGT
* * * *
1361 -AAAG--GGATTAATCAGT--AATTCGGTAATCAAGAGT
1 CAAAGTAAGAATAATCAGTAAAATT-GATAATTAAGAGT
* * * * *
1395 CAAGGTAATAGATTAATCAGTGAAATCGGTAATTAAAGAGT
1 CAAAGT-A-AGAATAATCAGTAAAATTGATAATT-AAGAGT
*
1436 CAAAGTAAAAGAAGTAATCAGTAAAA-TGGTAATTAAGAGT
1 CAAAGT--AAGAA-TAATCAGTAAAATTGATAATTAAGAGT
1476 -AAGAGTAAAAGAAGTAATCAGTAAA
1 CAA-AGT--AAGAA-TAATCAGTAAA
1501 TCGGTAAAGA
Statistics
Matches: 238, Mismatches: 23, Indels: 46
0.78 0.07 0.15
Matches are distributed among these distances:
32 27 0.11
33 5 0.02
34 20 0.08
35 3 0.01
36 9 0.04
37 10 0.04
38 79 0.33
39 14 0.06
40 34 0.14
41 24 0.10
42 13 0.05
ACGTcount: A:0.49, C:0.07, G:0.19, T:0.25
Consensus pattern (38 bp):
CAAAGTAAGAATAATCAGTAAAATTGATAATTAAGAGT
Found at i:1270 original size:70 final size:70
Alignment explanation
Indices: 1187--1331 Score: 263
Period size: 70 Copynumber: 2.1 Consensus size: 70
1177 CCAAAGTAAT
* *
1187 AGTAATCAGTAAAATTGATAATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGATAATTACGA
1 AGTAATCAGTAAAATTGATAATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGATAATCAAGA
1252 GTCAA
66 GTCAA
1257 AGTAATCAGTAAAATTGATAATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGATAATCAAGA
1 AGTAATCAGTAAAATTGATAATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGATAATCAAGA
1322 GTCAA
66 GTCAA
*
1327 GGTAA
1 AGTAA
1332 CGGTAATCAG
Statistics
Matches: 72, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
70 72 1.00
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.26
Consensus pattern (70 bp):
AGTAATCAGTAAAATTGATAATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGATAATCAAGA
GTCAA
Found at i:1483 original size:40 final size:42
Alignment explanation
Indices: 1369--1507 Score: 175
Period size: 40 Copynumber: 3.5 Consensus size: 42
1359 AGAAAGGGAT
* * * *
1369 TAATCAGT-AATTCGGTAATCAAGAGTCAAG-GTAATAG-AT
1 TAATCAGTAAAATCGGTAATTAAGAGTCAAGAGTAAAAGAAG
*
1408 TAATCAGTGAAATCGGTAATTAAAGAGTCAA-AGTAAAAGAAG
1 TAATCAGTAAAATCGGTAATT-AAGAGTCAAGAGTAAAAGAAG
1450 TAATCAGTAAAAT-GGTAATTAAGAGT-AAGAGTAAAAGAAG
1 TAATCAGTAAAATCGGTAATTAAGAGTCAAGAGTAAAAGAAG
1490 TAATCAGT-AAATCGGTAA
1 TAATCAGTAAAATCGGTAA
1508 AGAGTAAAAA
Statistics
Matches: 89, Mismatches: 5, Indels: 11
0.85 0.05 0.10
Matches are distributed among these distances:
39 14 0.16
40 40 0.45
41 22 0.25
42 13 0.15
ACGTcount: A:0.47, C:0.07, G:0.21, T:0.24
Consensus pattern (42 bp):
TAATCAGTAAAATCGGTAATTAAGAGTCAAGAGTAAAAGAAG
Found at i:1524 original size:16 final size:17
Alignment explanation
Indices: 1498--1532 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
1488 AGTAATCAGT
*
1498 AAATCGGTAAAGAGTAA
1 AAATCGGTAAAAAGTAA
1515 AAAT-GGTAAAAAGTAA
1 AAATCGGTAAAAAGTAA
1531 AA
1 AA
1533 GGGTAATCGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.60, C:0.03, G:0.20, T:0.17
Consensus pattern (17 bp):
AAATCGGTAAAAAGTAA
Found at i:1573 original size:43 final size:43
Alignment explanation
Indices: 1520--1920 Score: 339
Period size: 43 Copynumber: 9.4 Consensus size: 43
1510 AGTAAAAATG
* ** * * *
1520 GTAAAAAGTAAAAGGGTAATCGGTAAGAGCAAAATGGTAACCA
1 GTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGTAATCA
* *
1563 GTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGGAACCA
1 GTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGTAATCA
1606 GTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGTAAAAT-A
1 GTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGT--AATCA
* * * *
1650 GTAAAAAGT--GAT-GATAATCCGTAAAAGGTAAAATGGTAATCA
1 GTAAAGAGTAAAATAG-TAATCAGTAAAA-GCAAAATGGTAATCA
* *
1692 GT-AAGAGCAAAATAGTAATCAGTAAAAAGTAAGAA-GGTAATCA
1 GTAAAGAGTAAAATAGTAATCAGT-AAAAGCAA-AATGGTAATCA
** ** *
1735 GTAAAGAGTAAAATAGTAA--A--AAAAG--TGATGACAACCA
1 GTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGTAATCA
* * * *
1772 GTAAA-AGGTAAAATGGTAATCAGTAAGAGCGAAATAGTAATCA
1 GTAAAGA-GTAAAATAGTAATCAGTAAAAGCAAAATGGTAATCA
*
1815 GTAAAGAGCAAAA-AGGTAATCAGTAAGAA-CAAAATGGTAATCA
1 GTAAAGAGTAAAATA-GTAATCAGTAA-AAGCAAAATGGTAATCA
* * * *
1858 ATAAAGAGTAAAATAGTAATCAGTAAAAAGTAAGAA-GATGATCA
1 GTAAAGAGTAAAATAGTAATCAGT-AAAAGCAA-AATGGTAATCA
1902 GTAAAGAGTAAAATAGTAA
1 GTAAAGAGTAAAATAGTAA
1921 AAAGTAATTA
Statistics
Matches: 291, Mismatches: 41, Indels: 51
0.76 0.11 0.13
Matches are distributed among these distances:
36 2 0.01
37 21 0.07
39 6 0.02
41 12 0.04
42 17 0.06
43 167 0.57
44 62 0.21
45 4 0.01
ACGTcount: A:0.53, C:0.07, G:0.21, T:0.19
Consensus pattern (43 bp):
GTAAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGTAATCA
Found at i:1575 original size:22 final size:22
Alignment explanation
Indices: 1520--1920 Score: 284
Period size: 22 Copynumber: 18.9 Consensus size: 22
1510 AGTAAAAATG
* * *
1520 GTAAAAAGTAAAAGGGTAATCG
1 GTAAAGAGTAAAATGGTAATCA
* *
1542 GT-AAGAGCAAAATGGTAACCA
1 GTAAAGAGTAAAATGGTAATCA
*
1563 GTAAAGAGTAAAATAGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
* * *
1585 GTAAA-AGCAAAATGGGAACCA
1 GTAAAGAGTAAAATGGTAATCA
*
1606 GTAAAGAGTAAAATAGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
*
1628 GTAAA-AGCAAAATGGTAAAAT-A
1 GTAAAGAGTAAAATGGT--AATCA
* * * *
1650 GTAAAAAGT--GATGATAATCC
1 GTAAAGAGTAAAATGGTAATCA
1670 GTAAA-AGGTAAAATGGTAATCA
1 GTAAAGA-GTAAAATGGTAATCA
* *
1692 GT-AAGAGCAAAATAGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
*
1713 GTAAAAAGTAAGAA-GGTAATCA
1 GTAAAGAGTAA-AATGGTAATCA
*
1735 GTAAAGAGTAAAATAGTAA--A
1 GTAAAGAGTAAAATGGTAATCA
* ** *
1755 --AAA-AGT--GATGACAACCA
1 GTAAAGAGTAAAATGGTAATCA
1772 GTAAA-AGGTAAAATGGTAATCA
1 GTAAAGA-GTAAAATGGTAATCA
** *
1794 GT-AAGAGCGAAATAGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
* *
1815 GTAAAGAGCAAAAAGGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
**
1837 GT-AAGAACAAAATGGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
* *
1858 ATAAAGAGTAAAATAGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
* * *
1880 GTAAAAAGTAAGAA-GATGATCA
1 GTAAAGAGTAA-AATGGTAATCA
*
1902 GTAAAGAGTAAAATAGTAA
1 GTAAAGAGTAAAATGGTAA
1921 AAAGTAATTA
Statistics
Matches: 293, Mismatches: 61, Indels: 50
0.73 0.15 0.12
Matches are distributed among these distances:
15 4 0.01
17 4 0.01
18 3 0.01
19 8 0.03
20 10 0.03
21 101 0.34
22 154 0.53
23 9 0.03
ACGTcount: A:0.53, C:0.07, G:0.21, T:0.19
Consensus pattern (22 bp):
GTAAAGAGTAAAATGGTAATCA
Found at i:1807 original size:102 final size:101
Alignment explanation
Indices: 1558--1840 Score: 340
Period size: 102 Copynumber: 2.7 Consensus size: 101
1548 GCAAAATGGT
* * * * * *
1558 AACCAGT-AAAGAGTAAAATAGTAATCAGTAAAAGCAAAATGGGAACCAGTAAAGAGTAAAATAG
1 AACCAGTAAAAG-GTAAAATGGTAATCAGTAAGAGCAAAATAGTAATCAGTAAAGAGTAAAA-GG
*
1622 TAATCAGTAAAAGCAAAATGGTAAAATAGTAAAAAGTGATGAT
64 TAATCAGT-AAAG---AA-GGTAAAATAGTAAAAAGTGATGAC
*
1665 AATCC-GTAAAAGGTAAAATGGTAATCAGTAAGAGCAAAATAGTAATCAGTAAAAAGTAAGAAGG
1 AA-CCAGTAAAAGGTAAAATGGTAATCAGTAAGAGCAAAATAGTAATCAGTAAAGAGTAA-AAGG
1729 TAATCAGTAAAG-A-GTAAAATAGTAAAAAAAGTGATGAC
64 TAATCAGTAAAGAAGGTAAAATAGT--AAAAAGTGATGAC
* *
1767 AACCAGTAAAAGGTAAAATGGTAATCAGTAAGAGCGAAATAGTAATCAGTAAAGAGCAAAAAGGT
1 AACCAGTAAAAGGTAAAATGGTAATCAGTAAGAGCAAAATAGTAATCAGTAAAGAG-TAAAAGGT
1832 AATCAGTAA
65 AATCAGTAA
1841 GAACAAAATG
Statistics
Matches: 158, Mismatches: 11, Indels: 19
0.84 0.06 0.10
Matches are distributed among these distances:
100 10 0.06
101 2 0.01
102 78 0.49
103 2 0.01
106 4 0.03
107 54 0.34
108 8 0.05
ACGTcount: A:0.53, C:0.08, G:0.20, T:0.19
Consensus pattern (101 bp):
AACCAGTAAAAGGTAAAATGGTAATCAGTAAGAGCAAAATAGTAATCAGTAAAGAGTAAAAGGTA
ATCAGTAAAGAAGGTAAAATAGTAAAAAGTGATGAC
Found at i:1902 original size:65 final size:64
Alignment explanation
Indices: 1781--1905 Score: 169
Period size: 65 Copynumber: 1.9 Consensus size: 64
1771 AGTAAAAGGT
* * * *
1781 AAAATGGTAATCAGTAAGAGCGAAATAGTAATCAGTAAAGAGCAAAAAGGTAATCAGTAAGAAC
1 AAAATGGTAATCAATAAGAGCAAAATAGTAATCAGTAAAAAGCAAAAAGATAATCAGTAAGAAC
* * * *
1845 AAAATGGTAATCAATAAAGAGTAAAATAGTAATCAGTAAAAAGTAAGAAGATGATCAGTAA
1 AAAATGGTAATCAAT-AAGAGCAAAATAGTAATCAGTAAAAAGCAAAAAGATAATCAGTAA
1906 AGAGTAAAAT
Statistics
Matches: 52, Mismatches: 8, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
64 14 0.27
65 38 0.73
ACGTcount: A:0.54, C:0.07, G:0.20, T:0.19
Consensus pattern (64 bp):
AAAATGGTAATCAATAAGAGCAAAATAGTAATCAGTAAAAAGCAAAAAGATAATCAGTAAGAAC
Found at i:1926 original size:22 final size:21
Alignment explanation
Indices: 1859--1949 Score: 56
Period size: 22 Copynumber: 4.1 Consensus size: 21
1849 TGGTAATCAA
**
1859 TAAAGAGTAAAATAGTAATCAG
1 TAAAGAGTAAAA-AGTAAAAAG
* * * **
1881 TAAAAAGTAAGAAGATGATCAG
1 TAAAGAGTAAAAAG-TAAAAAG
1903 TAAAGAGTAAAATAGTAAAAAG
1 TAAAGAGTAAAA-AGTAAAAAG
** *
1925 TAATTAGTAAAAGGTAAAATAG
1 TAAAGAGTAAAAAGTAAAA-AG
1947 TAA
1 TAA
1950 TCAGTAGGAG
Statistics
Matches: 55, Mismatches: 11, Indels: 6
0.76 0.15 0.08
Matches are distributed among these distances:
21 8 0.15
22 45 0.82
23 2 0.04
ACGTcount: A:0.57, C:0.02, G:0.19, T:0.22
Consensus pattern (21 bp):
TAAAGAGTAAAAAGTAAAAAG
Found at i:1933 original size:29 final size:29
Alignment explanation
Indices: 1879--1949 Score: 83
Period size: 29 Copynumber: 2.4 Consensus size: 29
1869 AATAGTAATC
* *
1879 AGTAAAA-AGTAAGAAGATGATCAGTAAA
1 AGTAAAATAGTAAAAAGATAATCAGTAAA
*
1907 GAGTAAAATAGTAAAAAG-TAATTAGTAAA
1 -AGTAAAATAGTAAAAAGATAATCAGTAAA
1936 AGGTAAAATAGTAA
1 A-GTAAAATAGTAA
1950 TCAGTAGGAG
Statistics
Matches: 37, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
28 1 0.03
29 28 0.76
30 8 0.22
ACGTcount: A:0.58, C:0.01, G:0.20, T:0.21
Consensus pattern (29 bp):
AGTAAAATAGTAAAAAGATAATCAGTAAA
Found at i:1934 original size:14 final size:14
Alignment explanation
Indices: 1901--1949 Score: 53
Period size: 15 Copynumber: 3.4 Consensus size: 14
1891 GAAGATGATC
*
1901 AGTAAAGAGTAAAAT
1 AGTAAAAAGT-AAAT
*
1916 AGTAAAAAGTAATT
1 AGTAAAAAGTAAAT
*
1930 AGTAAAAGGTAAAAT
1 AGTAAAAAGT-AAAT
1945 AGTAA
1 AGTAA
1950 TCAGTAGGAG
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 12 0.41
15 17 0.59
ACGTcount: A:0.59, C:0.00, G:0.18, T:0.22
Consensus pattern (14 bp):
AGTAAAAAGTAAAT
Done.