Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01008830.1 Corchorus capsularis cultivar CVL-1 contig08851, 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: 3241
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Found at i:1250 original size:30 final size:30
Alignment explanation
Indices: 1208--1276 Score: 104
Period size: 30 Copynumber: 2.3 Consensus size: 30
1198 AAAAAAGGGC
1208 AATCAGCTATTAAGTTCAATAAGAAA-AAGT
1 AATCAG-TATTAAGTTCAATAAGAAAGAAGT
*
1238 AATCAGTGATTAAGTTCAATAAGAAAGATGT
1 AATCAGT-ATTAAGTTCAATAAGAAAGAAGT
1269 AATCAGTA
1 AATCAGTA
1277 AAAGGTAAAG
Statistics
Matches: 36, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
29 1 0.03
30 25 0.69
31 10 0.28
ACGTcount: A:0.48, C:0.09, G:0.16, T:0.28
Consensus pattern (30 bp):
AATCAGTATTAAGTTCAATAAGAAAGAAGT
Found at i:1294 original size:22 final size:23
Alignment explanation
Indices: 1269--1328 Score: 72
Period size: 22 Copynumber: 2.7 Consensus size: 23
1259 AGAAAGATGT
1269 AATCAGTAAAAG-GTAAAGCGAC
1 AATCAGTAAAAGAGTAAAGCGAC
* *
1291 AATCAGT-AAAGAGTAAAGTGAT
1 AATCAGTAAAAGAGTAAAGCGAC
*
1313 AGTCAGT-AAAGAGTAA
1 AATCAGTAAAAGAGTAA
1329 TAGAAATCAG
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 4 0.12
22 30 0.88
ACGTcount: A:0.50, C:0.08, G:0.23, T:0.18
Consensus pattern (23 bp):
AATCAGTAAAAGAGTAAAGCGAC
Found at i:1435 original size:107 final size:109
Alignment explanation
Indices: 1315--1516 Score: 354
Period size: 107 Copynumber: 1.9 Consensus size: 109
1305 AAAGTGATAG
*
1315 TCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAA-A-AATAATCAGAGTCAAG
1 TCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAGAGAATAATCAGAGTCAAA
1378 GTAATAGAAATCAGTAAATCAATAATTAAGTGAAAAGAAATTAA
66 GTAATAGAAATCAGTAAATCAATAATTAAGTGAAAAGAAATTAA
*
1422 TCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAA
1 TCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAGAGAATAATCAGAGTCAAA
* *
1487 GTAATAGTAATCAGTAAATCGATAATTAAG
66 GTAATAGAAATCAGTAAATCAATAATTAAG
1517 AGTTAAAATG
Statistics
Matches: 89, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
107 46 0.52
108 1 0.01
109 42 0.47
ACGTcount: A:0.53, C:0.07, G:0.16, T:0.24
Consensus pattern (109 bp):
TCAGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAGAGAATAATCAGAGTCAAA
GTAATAGAAATCAGTAAATCAATAATTAAGTGAAAAGAAATTAA
Found at i:1451 original size:54 final size:54
Alignment explanation
Indices: 1317--1516 Score: 264
Period size: 54 Copynumber: 3.7 Consensus size: 54
1307 AGTGATAGTC
* *
1317 AGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAA-AAAATAATCA
1 AGTAAAGAGTAATAGAAATCAGTAAATCAATAATTAAGTAAAAGAAATTAATCA
*
1370 GAGTCAAG-GTAATAGAAATCAGTAAATCAATAATTAAGTGAAAAGAAATTAATC-
1 -AGTAAAGAGTAATAGAAATCAGTAAATCAATAATTAAGT-AAAAGAAATTAATCA
* *
1424 AGTAAAGAGTAATAGAAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCA
1 AGTAAAGAGTAATAGAAATCAGTAAATCAATAATTAAGT-AAAAGAAATTAATCA
* * *
1479 GAGTCAA-AGTAATAGTAATCAGTAAATCGATAATTAAG
1 -AGTAAAGAGTAATAGAAATCAGTAAATCAATAATTAAG
1517 AGTTAAAATG
Statistics
Matches: 130, Mismatches: 11, Indels: 9
0.87 0.07 0.06
Matches are distributed among these distances:
53 36 0.28
54 53 0.41
55 36 0.28
56 5 0.04
ACGTcount: A:0.54, C:0.07, G:0.16, T:0.24
Consensus pattern (54 bp):
AGTAAAGAGTAATAGAAATCAGTAAATCAATAATTAAGTAAAAGAAATTAATCA
Found at i:1782 original size:66 final size:63
Alignment explanation
Indices: 1702--2101 Score: 236
Period size: 65 Copynumber: 6.3 Consensus size: 63
1692 AATAGCAGGC
* * *
1702 AATCAGTAAAAAGTAAAAAGGT-ACCTGA-AAGGGTAAAAAGAGTAATCAGTAAAAGAGTAAAAT
1 AATCAGTAAAAAGTAAAAAGGTAATC-AACAAGAGT-AAAAGAGTAATCAGT-AAA-AGT-AAAT
1765 AGT
61 AGT
* * *
1768 AATCAGTAAAAAGTAAGAAGGTAATCAACAAGAGTAAAATAGTAGTCAGTAAAAGTAAATAGT
1 AATCAGTAAAAAGTAAAAAGGTAATCAACAAGAGTAAAAGAGTAATCAGTAAAAGTAAATAGT
* * * * *
1831 AATCAGT-AAGAGTAAAAAAGGTAAT-AAGTAAGAAGTAAAAG-GAAATCAGTAAGAGTAAAAAG
1 AATCAGTAAAAAGT-AAAAAGGTAATCAA-CAAG-AGTAAAAGAGTAATCAGTAAAAGTAAATA-
1893 GT
62 GT
* * * * *
1895 GATCAGTAAAGAGTAAAAAGCTAATCAGCAAGAAGTAAAA-ATGTAATCAGTAAAAAGCAAA-AG
1 AATCAGTAAAAAGTAAAAAGGTAATCAACAAG-AGTAAAAGA-GTAATCAGT-AAAAGTAAATA-
1958 GCT
62 G-T
* ** * * * **
1961 -ATCAGTAAAAAGTAAAAAAGTAATCAGTAA-A--AAAAG-GGAGT-AGAAAATAGTAAAGGGT
1 AATCAGTAAAAAGTAAAAAGGTAATCAACAAGAGTAAAAGAGTAATCAGTAAA-AGTAAATAGT
* * * ** *
2019 AATCAGTAAAAGAGTAAAATGATAATCAGTA-AAAAGTAAGAAG-GTAATCAACAAGAGTAAAAT
1 AATCAGTAAAA-AGTAAAAAGGTAATCA--ACAAGAGTAA-AAGAGTAATCAGTAAAAGT-AAAT
2082 AGT
61 AGT
*
2085 AATCAGTACAAAGTAAA
1 AATCAGTAAAAAGTAAA
2102 GAATAATCAG
Statistics
Matches: 267, Mismatches: 42, Indels: 51
0.74 0.12 0.14
Matches are distributed among these distances:
58 4 0.01
59 18 0.07
60 16 0.06
61 6 0.02
62 8 0.03
63 44 0.16
64 41 0.15
65 62 0.23
66 61 0.23
67 7 0.03
ACGTcount: A:0.55, C:0.06, G:0.20, T:0.18
Consensus pattern (63 bp):
AATCAGTAAAAAGTAAAAAGGTAATCAACAAGAGTAAAAGAGTAATCAGTAAAAGTAAATAGT
Found at i:1804 original size:43 final size:42
Alignment explanation
Indices: 1754--1993 Score: 229
Period size: 43 Copynumber: 5.6 Consensus size: 42
1744 TAATCAGTAA
*
1754 AAGAGTAAAATA-GTAATCAGTAAAAAGTAAGAAGGTAATCAAC
1 AAGAGTAAAA-AGGTAATCAGTAAAAAGTAA-AAGGTAATCAGC
* *
1797 AAGAGTAAAATA-GTAGTCAGT-AAAAGTAAATA-GTAATCAGT
1 AAGAGTAAAA-AGGTAATCAGTAAAAAGTAAA-AGGTAATCAGC
* * * *
1838 AAGAGTAAAAAAGGTAATAAGTAAGAAGTAAAAGGAAATCAGT
1 AAGAGT-AAAAAGGTAATCAGTAAAAAGTAAAAGGTAATCAGC
* * *
1881 AAGAGTAAAAAGGTGATCAGTAAAGAGTAAAAAGCTAATCAGC
1 AAGAGTAAAAAGGTAATCAGTAAAAAGT-AAAAGGTAATCAGC
* * *
1924 AAGAAGTAAAAATGTAATCAGTAAAAAGCAAAAGGCT-ATCAGTA
1 AAG-AGTAAAAAGGTAATCAGTAAAAAGTAAAAGG-TAATCAG-C
* *
1968 AAAAGTAAAAAAGTAATCAGTAAAAA
1 AAGAGTAAAAAGGTAATCAGTAAAAA
1994 AAGGGAGTAG
Statistics
Matches: 166, Mismatches: 22, Indels: 18
0.81 0.11 0.09
Matches are distributed among these distances:
41 15 0.09
42 39 0.23
43 88 0.53
44 24 0.14
ACGTcount: A:0.56, C:0.06, G:0.20, T:0.18
Consensus pattern (42 bp):
AAGAGTAAAAAGGTAATCAGTAAAAAGTAAAAGGTAATCAGC
Found at i:1824 original size:21 final size:20
Alignment explanation
Indices: 1737--2116 Score: 232
Period size: 22 Copynumber: 17.9 Consensus size: 20
1727 TGAAAGGGTA
1737 AAAAGAGTAATCAGTAAAAGAGT
1 AAAA-AGTAATCAGT-AAA-AGT
1760 AAAATAGTAATCAGTAAAAAGT
1 AAAA-AGTAATCAGT-AAAAGT
* ** *
1782 AAGAAGGTAATCAACAAGAGT
1 AA-AAAGTAATCAGTAAAAGT
*
1803 AAAATAGTAGTCAGTAAAAGT
1 AAAA-AGTAATCAGTAAAAGT
* *
1824 AAATAGTAATCAGTAAGAGT
1 AAAAAGTAATCAGTAAAAGT
*
1844 AAAAAAGGTAATAAGTAAGAAGT
1 -AAAAA-GTAATCAGTAA-AAGT
* * *
1867 AAAAGGAAATCAGTAAGAGT
1 AAAAAGTAATCAGTAAAAGT
*
1887 AAAAAGGTGATCAGTAAAGAGT
1 AAAAA-GTAATCAGTAAA-AGT
*
1909 AAAAAGCTAATCAGCAAGAAGT
1 AAAAAG-TAATCAGTAA-AAGT
*
1931 AAAAATGTAATCAGTAAAAAGC
1 AAAAA-GTAATCAGT-AAAAGT
*
1953 AAAAGGCT-ATCAGTAAAAAGT
1 AAAAAG-TAATCAGT-AAAAGT
1974 AAAAAAGTAATCAGT-AAA--
1 -AAAAAGTAATCAGTAAAAGT
* * * *
1992 AAAAGGGAGT-AGAAAATAGT
1 AAAAAGTAATCAGTAAA-AGT
**
2012 AAAGGGTAATCAGTAAAAGAGT
1 AAAAAGTAATCAGT-AAA-AGT
*
2034 AAAATGATAATCAGTAAAAAGT
1 AAAAAG-TAATCAGT-AAAAGT
* ** *
2056 AAGAAGGTAATCAACAAGAGT
1 AA-AAAGTAATCAGTAAAAGT
2077 AAAATAGTAATCAGTACAAAGT
1 AAAA-AGTAATCAGTA-AAAGT
2099 AAAGAA-TAATCAGTAAAA
1 AAA-AAGTAATCAGTAAAA
2117 TAGTGATGTT
Statistics
Matches: 282, Mismatches: 50, Indels: 53
0.73 0.13 0.14
Matches are distributed among these distances:
16 2 0.01
17 9 0.03
18 1 0.00
20 38 0.13
21 84 0.30
22 105 0.37
23 43 0.15
ACGTcount: A:0.56, C:0.06, G:0.20, T:0.18
Consensus pattern (20 bp):
AAAAAGTAATCAGTAAAAGT
Done.