Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011291.1 Corchorus capsularis cultivar CVL-1 contig11312, 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: 15523
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.27
Found at i:1115 original size:55 final size:55
Alignment explanation
Indices: 1034--1396 Score: 568
Period size: 55 Copynumber: 6.6 Consensus size: 55
1024 TAAAAAGGGG
*
1034 CAATCAGT-AATAAGTAAAAAGAGATTAATCAGAGTCAAGGTGATGGTAATCAGT
1 CAATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGGTGATGGTAATCAGT
* *
1088 CAATCAGTAAATCAGTAGAAAGAGATTAATCAAAGTCAAGGTGATGGTAATCAGT
1 CAATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGGTGATGGTAATCAGT
* * *
1143 CAATCAGTAAATCAATAGAAAGAGATTAATCAAAGTCAAGGTGATGGTAATCAGT
1 CAATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGGTGATGGTAATCAGT
* * *
1198 AAATCAGTAAATCAGTAAAAAGAGATTAATCGGAGTCAAAGTGATGGTAATCAGT
1 CAATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGGTGATGGTAATCAGT
1253 CAATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGGTGATGGTAATCAGT
1 CAATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGGTGATGGTAATCAGT
* *
1308 CAATCAGTAAATCAGTAAAAAGAGATTAATCAAGAGTCAAGGTAATAGTAATCAGT
1 CAATCAGTAAATCAGTAAAAAGAGATTAATC-AGAGTCAAGGTGATGGTAATCAGT
* * *
1364 AAATCAGT-AATCAAGTAAAAAGATAGTAATCAG
1 CAATCAGTAAATC-AGTAAAAAGAGATTAATCAG
1397 TAAATTGATA
Statistics
Matches: 288, Mismatches: 18, Indels: 5
0.93 0.06 0.02
Matches are distributed among these distances:
54 8 0.03
55 235 0.82
56 45 0.16
ACGTcount: A:0.46, C:0.10, G:0.20, T:0.23
Consensus pattern (55 bp):
CAATCAGTAAATCAGTAAAAAGAGATTAATCAGAGTCAAGGTGATGGTAATCAGT
Found at i:1204 original size:8 final size:8
Alignment explanation
Indices: 1191--1216 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
1181 AGGTGATGGT
1191 AATCAGTA
1 AATCAGTA
1199 AATCAGTA
1 AATCAGTA
1207 AATCAGTA
1 AATCAGTA
1215 AA
1 AA
1217 AAGAGATTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.54, C:0.12, G:0.12, T:0.23
Consensus pattern (8 bp):
AATCAGTA
Found at i:1419 original size:71 final size:70
Alignment explanation
Indices: 1334--1472 Score: 174
Period size: 71 Copynumber: 2.0 Consensus size: 70
1324 AAAAAGAGAT
* * *
1334 TAATCAAGAGTCAAGGTAATAG-TAATCAGTAAATCAGTAATCAA-GTAAAAAGATAGTAATCAG
1 TAATCAAGAATCAAGGTAAGAGATAATCAGTAAATAAG-AATCAAGGT-AAAA-ATAGTAATCAG
1397 TAAATTGA
63 TAAATTGA
* * *
1405 TAATTAAGAATCAAGGTAAGAGATTAATCAGTAATTAAGAGTCAAGGTAAAAATAGTAATCAGTA
1 TAATCAAGAATCAAGGTAAGAGA-TAATCAGTAAATAAGAATCAAGGTAAAAATAGTAATCAGTA
1470 AAT
65 AAT
1473 CAGTAATTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
71 35 0.59
72 9 0.15
73 15 0.25
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.26
Consensus pattern (70 bp):
TAATCAAGAATCAAGGTAAGAGATAATCAGTAAATAAGAATCAAGGTAAAAATAGTAATCAGTAA
ATTGA
Found at i:1470 original size:32 final size:31
Alignment explanation
Indices: 1405--1470 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 31
1395 AGTAAATTGA
*
1405 TAATTAAGAATCAAGGTAAGAGATTAATCAG
1 TAATTAAGAATCAAGGTAAGAAATTAATCAG
*
1436 TAATTAAGAGTCAAGGTAA-AAATAGTAATCAG
1 TAATTAAGAATCAAGGTAAGAAAT--TAATCAG
1468 TAA
1 TAA
1471 ATCAGTAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
30 3 0.10
31 18 0.58
32 10 0.32
ACGTcount: A:0.50, C:0.06, G:0.18, T:0.26
Consensus pattern (31 bp):
TAATTAAGAATCAAGGTAAGAAATTAATCAG
Found at i:1646 original size:14 final size:14
Alignment explanation
Indices: 1609--1648 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
1599 GATGGTAAAG
*
1609 AGTAAAGAATAATC
1 AGTAAAGAGTAATC
* *
1623 AGTAAGGAGTAATT
1 AGTAAAGAGTAATC
1637 AGTAAAGAGTAA
1 AGTAAAGAGTAA
1649 AATGATAAAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.53, C:0.03, G:0.23, T:0.23
Consensus pattern (14 bp):
AGTAAAGAGTAATC
Found at i:1701 original size:35 final size:35
Alignment explanation
Indices: 1656--1750 Score: 145
Period size: 35 Copynumber: 2.7 Consensus size: 35
1646 TAAAATGATA
1656 AAAAAGTAAAGGGTAATCAGTAAAAGAAGAATGGT
1 AAAAAGTAAAGGGTAATCAGTAAAAGAAGAATGGT
* *
1691 AAAAAGTAAAGAGTAATCAGTAAAGGAAGAATGGT
1 AAAAAGTAAAGGGTAATCAGTAAAAGAAGAATGGT
* * *
1726 AAAGAGAAAAGGGTAATCGGTAAAA
1 AAAAAGTAAAGGGTAATCAGTAAAA
1751 AGTAAAAAGA
Statistics
Matches: 53, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 53 1.00
ACGTcount: A:0.55, C:0.03, G:0.26, T:0.16
Consensus pattern (35 bp):
AAAAAGTAAAGGGTAATCAGTAAAAGAAGAATGGT
Found at i:1785 original size:121 final size:120
Alignment explanation
Indices: 1579--1809 Score: 270
Period size: 121 Copynumber: 1.9 Consensus size: 120
1569 TAAATTCAAG
* ** ** *
1579 AGAGTAATCAGTAAAGGAAAGATGGTAAAGAGTAAAGAATAATCAGTAAGGAGTAATTAGTAAAG
1 AGAGTAATCAGTAAAGGAAAGATGGTAAAGAGAAAAGAATAATCAGTAAAAAGTAAAAAGTAAAC
*
1644 AGTAAAATGATAAAAAAGTAAAGGGTAATCAGTAAAAGAAG-AATGGTAAAAAGTAA
66 AGTAAAA-GATAAAAAAGTAAAAGGTAATCAGTAAAA-AAGTAATGGTAAAAAGTAA
** *
1700 AGAGTAATCAGTAAAGG-AAGAATGGTAAAGAGAAAAGGGTAATCGGTAAAAAGTAAAAAGATAA
1 AGAGTAATCAGTAAAGGAAAG-ATGGTAAAGAGAAAAGAATAATCAGTAAAAAGTAAAAAG-TAA
* * * *
1764 TCAGT-AAAGAATGAAATAGTAAAAGGTAATCCGTAAAAAAGTAATG
64 ACAGTAAAAG-ATAAAAAAGTAAAAGGTAATCAGTAAAAAAGTAATG
1810 ATAATCAGTA
Statistics
Matches: 92, Mismatches: 14, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
120 7 0.08
121 79 0.86
122 6 0.07
ACGTcount: A:0.54, C:0.03, G:0.24, T:0.19
Consensus pattern (120 bp):
AGAGTAATCAGTAAAGGAAAGATGGTAAAGAGAAAAGAATAATCAGTAAAAAGTAAAAAGTAAAC
AGTAAAAGATAAAAAAGTAAAAGGTAATCAGTAAAAAAGTAATGGTAAAAAGTAA
Found at i:1831 original size:50 final size:51
Alignment explanation
Indices: 1732--1835 Score: 124
Period size: 50 Copynumber: 2.0 Consensus size: 51
1722 TGGTAAAGAG
* *
1732 AAAAGGGTAATCGGTAAAAAGTAAAAAGATAATCAGTAAAGAATGAAATAGT
1 AAAAGGGTAATCCGTAAAAAGT-AAAAGATAATCAGTAAAGAATAAAATAGT
* *
1784 AAAA-GGTAATCCGTAAAAAAGT-AATGATAATCAGTAAA-AGGTAAAATAGT
1 AAAAGGGTAATCCGT-AAAAAGTAAAAGATAATCAGTAAAGA-ATAAAATAGT
1834 AA
1 AA
1836 TCAGTAAGAG
Statistics
Matches: 46, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
49 1 0.02
50 25 0.54
51 9 0.20
52 11 0.24
ACGTcount: A:0.56, C:0.05, G:0.19, T:0.20
Consensus pattern (51 bp):
AAAAGGGTAATCCGTAAAAAGTAAAAGATAATCAGTAAAGAATAAAATAGT
Found at i:1856 original size:21 final size:21
Alignment explanation
Indices: 1806--2244 Score: 154
Period size: 21 Copynumber: 21.0 Consensus size: 21
1796 GTAAAAAAGT
* *
1806 AATGATAATCAGTAAAAGGTAA
1 AATGGTAATCAGTAAGA-GTAA
* *
1828 AATAGTAATCAGTAAGAGCAA
1 AATGGTAATCAGTAAGAGTAA
* * *
1849 AATGGTAATCAATGAGAGCAA
1 AATGGTAATCAGTAAGAGTAA
* * *
1870 AATGGTAATCAATGAGAGCAA
1 AATGGTAATCAGTAAGAGTAA
1891 AATGGTAATCAGTAAAGAGTAA
1 AATGGTAATCAGT-AAGAGTAA
* * *
1913 AATAGTAATCATTAAAAAGTAA
1 AATGGTAATCAGT-AAGAGTAA
1935 GAA-GGTAATCAGTAAAGAGTAA
1 -AATGGTAATCAGT-AAGAGTAA
* *
1957 AATAGTAATC------AGCAA
1 AATGGTAATCAGTAAGAGTAA
*
1972 AA-GGCAATCAGTAAGAGTAA
1 AATGGTAATCAGTAAGAGTAA
*
1992 AATAGTAATCAGT-AGAAGGT--
1 AATGGTAATCAGTAAG-A-GTAA
* *
2012 AAT--CAGT-A--AAGAGTAA
1 AATGGTAATCAGTAAGAGTAA
*
2028 AATAGTAATCAGT---AG---
1 AATGGTAATCAGTAAGAGTAA
*
2043 AA-GATAATCAGTAAGAGTAA
1 AATGGTAATCAGTAAGAGTAA
** * * * *
2063 AACAGTAACCACTGAGAGCAA
1 AATGGTAATCAGTAAGAGTAA
* * *
2084 AGTGGTAATTAGTAAGAGTCA
1 AATGGTAATCAGTAAGAGTAA
*
2105 AATAGTAATCAGTAAGAAGTAA
1 AATGGTAATCAGTAAG-AGTAA
*
2127 AA-GAGTAATCAGTAAAAAAGGAGCAGAA
1 AATG-GTAATCAGT----AA-GAG--TAA
*
2155 AATAGTAATCAGTAAAAGAGTAA
1 AATGGTAATCAGT--AAGAGTAA
* *
2178 AATAGTAATCAGTAAAAAGTAA
1 AATGGTAATCAGT-AAGAGTAA
**
2200 GAA-GGTAAATCAACAAGAGTAA
1 -AATGGT-AATCAGTAAGAGTAA
* *
2222 AATAGTAATCAGTATAAAGTAA
1 AATGGTAATCAGTA-AGAGTAA
2244 A
1 A
2245 GAATAATCAG
Statistics
Matches: 315, Mismatches: 61, Indels: 82
0.69 0.13 0.18
Matches are distributed among these distances:
14 15 0.05
15 9 0.03
16 5 0.02
17 3 0.01
18 6 0.02
19 1 0.00
20 13 0.04
21 110 0.35
22 104 0.33
23 24 0.08
25 3 0.01
26 8 0.03
27 1 0.00
28 13 0.04
ACGTcount: A:0.52, C:0.07, G:0.20, T:0.20
Consensus pattern (21 bp):
AATGGTAATCAGTAAGAGTAA
Found at i:1914 original size:22 final size:22
Alignment explanation
Indices: 1781--1968 Score: 158
Period size: 21 Copynumber: 8.8 Consensus size: 22
1771 AGAATGAAAT
* *
1781 AGTAAAA-GGTAATCCGTAAAAA
1 AGTAAAATGGTAATCAGT-AAAG
*
1803 AGT--AATGATAATCAGTAAA-
1 AGTAAAATGGTAATCAGTAAAG
*
1822 AGGTAAAATAGTAATCAGT-AAG
1 A-GTAAAATGGTAATCAGTAAAG
* * *
1844 AGCAAAATGGTAATCAAT-GAG
1 AGTAAAATGGTAATCAGTAAAG
* * *
1865 AGCAAAATGGTAATCAAT-GAG
1 AGTAAAATGGTAATCAGTAAAG
*
1886 AGCAAAATGGTAATCAGTAAAG
1 AGTAAAATGGTAATCAGTAAAG
* * *
1908 AGTAAAATAGTAATCATTAAAA
1 AGTAAAATGGTAATCAGTAAAG
1930 AGTAAGAA-GGTAATCAGTAAAG
1 AGTAA-AATGGTAATCAGTAAAG
*
1952 AGTAAAATAGTAATCAG
1 AGTAAAATGGTAATCAG
1969 CAAAAGGCAA
Statistics
Matches: 140, Mismatches: 18, Indels: 16
0.80 0.10 0.09
Matches are distributed among these distances:
19 1 0.01
20 7 0.05
21 66 0.47
22 64 0.46
23 2 0.01
ACGTcount: A:0.52, C:0.07, G:0.20, T:0.21
Consensus pattern (22 bp):
AGTAAAATGGTAATCAGTAAAG
Found at i:1992 original size:35 final size:36
Alignment explanation
Indices: 1934--2070 Score: 215
Period size: 35 Copynumber: 3.9 Consensus size: 36
1924 TTAAAAAGTA
*
1934 AGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGC
1 AGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGT
* *
1970 AAAAGGCAATCAGT-AAGAGTAAAATAGTAATCAGT
1 AGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGT
2005 AGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGT
1 AGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGT
* *
2041 AGAAGATAATCAGT-AAGAGTAAAACAGTAA
1 AGAAGGTAATCAGTAAAGAGTAAAATAGTAA
2071 CCACTGAGAG
Statistics
Matches: 93, Mismatches: 7, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
35 47 0.51
36 46 0.49
ACGTcount: A:0.52, C:0.07, G:0.21, T:0.20
Consensus pattern (36 bp):
AGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGT
Found at i:2012 original size:71 final size:71
Alignment explanation
Indices: 1934--2070 Score: 229
Period size: 71 Copynumber: 1.9 Consensus size: 71
1924 TTAAAAAGTA
* *
1934 AGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGCAAAAGGCAATCAGTAAGAGTAAAATAGTA
1 AGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGCAAAAGACAATCAGTAAGAGTAAAACAGTA
1999 ATCAGT
66 ATCAGT
* * *
2005 AGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGTAGAAGATAATCAGTAAGAGTAAAACAGTA
1 AGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGCAAAAGACAATCAGTAAGAGTAAAACAGTA
2070 A
66 A
2071 CCACTGAGAG
Statistics
Matches: 61, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
71 61 1.00
ACGTcount: A:0.52, C:0.07, G:0.21, T:0.20
Consensus pattern (71 bp):
AGAAGGTAATCAGTAAAGAGTAAAATAGTAATCAGCAAAAGACAATCAGTAAGAGTAAAACAGTA
ATCAGT
Found at i:2027 original size:14 final size:15
Alignment explanation
Indices: 1995--2027 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
1985 AGAGTAAAAT
1995 AGTAATCAGTAGAAG
1 AGTAATCAGTAGAAG
2010 -GTAATCAGTA-AAG
1 AGTAATCAGTAGAAG
2023 AGTAA
1 AGTAA
2028 AATAGTAATC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
13 3 0.18
14 14 0.82
ACGTcount: A:0.48, C:0.06, G:0.24, T:0.21
Consensus pattern (15 bp):
AGTAATCAGTAGAAG
Found at i:2194 original size:15 final size:15
Alignment explanation
Indices: 2122--2177 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
2112 ATCAGTAAGA
2122 AGTAAAAGAGTAATC
1 AGTAAAAGAGTAATC
* * *
2137 AGTAAAAAAG-GAGC
1 AGTAAAAGAGTAATC
*
2151 AG-AAAATAGTAATC
1 AGTAAAAGAGTAATC
2165 AGTAAAAGAGTAA
1 AGTAAAAGAGTAA
2178 AATAGTAATC
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
13 6 0.19
14 8 0.25
15 18 0.56
ACGTcount: A:0.57, C:0.05, G:0.21, T:0.16
Consensus pattern (15 bp):
AGTAAAAGAGTAATC
Done.