Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005131.1 Corchorus capsularis cultivar CVL-1 contig05149, 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: 6121
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Found at i:1675 original size:37 final size:37
Alignment explanation
Indices: 1596--1676 Score: 117
Period size: 37 Copynumber: 2.2 Consensus size: 37
1586 TACTCCAATA
* * *
1596 AATTAAGAGTCAAAGTAATGGTAATCGGTAATTAAGT
1 AATTAAGAGTCAAAGTAATAGTAATCAGTAAATAAGT
* *
1633 GATTAAGAGTCAAAGTAATAGTAATCAGTAAATCAGT
1 AATTAAGAGTCAAAGTAATAGTAATCAGTAAATAAGT
1670 AATTAAG
1 AATTAAG
1677 TAAAAAGTGA
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.46, C:0.06, G:0.20, T:0.28
Consensus pattern (37 bp):
AATTAAGAGTCAAAGTAATAGTAATCAGTAAATAAGT
Found at i:1686 original size:52 final size:51
Alignment explanation
Indices: 1629--1769 Score: 192
Period size: 52 Copynumber: 2.7 Consensus size: 51
1619 ATCGGTAATT
1629 AAGTGATTAAGAGTCAAAGTAATAGTAATCAGTAAATCAGTAATTAAGTAAA
1 AAGTGATTAAGAGTCAAAGTAATAGTAATCAGTAAATCAGTAA-TAAGTAAA
*
1681 AAGTGATTAAGAGTCAAAGTAATAGTAATCAGTAAATCAGTAATCAGTAAA
1 AAGTGATTAAGAGTCAAAGTAATAGTAATCAGTAAATCAGTAATAAGTAAA
** * * *
1732 TTGATAATTAAGAGTCAAGGTAAGAGATTAATCAGTAA
1 AAG-TGATTAAGAGTCAAAGTAATAG--TAATCAGTAA
1770 TTAAAGAGTC
Statistics
Matches: 80, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
51 8 0.10
52 62 0.77
54 10 0.12
ACGTcount: A:0.48, C:0.06, G:0.18, T:0.27
Consensus pattern (51 bp):
AAGTGATTAAGAGTCAAAGTAATAGTAATCAGTAAATCAGTAATAAGTAAA
Found at i:1725 original size:7 final size:7
Alignment explanation
Indices: 1698--1730 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
1688 TAAGAGTCAA
1698 AGTAAT-
1 AGTAATC
1704 AGTAATC
1 AGTAATC
1711 AGTAAATC
1 AGT-AATC
1719 AGTAATC
1 AGTAATC
1726 AGTAA
1 AGTAA
1731 ATTGATAATT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 6 0.24
7 12 0.48
8 7 0.28
ACGTcount: A:0.48, C:0.09, G:0.15, T:0.27
Consensus pattern (7 bp):
AGTAATC
Found at i:1739 original size:15 final size:15
Alignment explanation
Indices: 1704--1732 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1694 TCAAAGTAAT
1704 AGTAATCAGTAAATC
1 AGTAATCAGTAAATC
1719 AGTAATCAGTAAAT
1 AGTAATCAGTAAAT
1733 TGATAATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.48, C:0.10, G:0.14, T:0.28
Consensus pattern (15 bp):
AGTAATCAGTAAATC
Found at i:1802 original size:33 final size:31
Alignment explanation
Indices: 1736--1802 Score: 91
Period size: 32 Copynumber: 2.1 Consensus size: 31
1726 AGTAAATTGA
*
1736 TAATTAAGAGTCAAGGTAAGAGATTAATCAG
1 TAATTAAGAGTCAAGGTAAGAAATTAATCAG
1767 TAATTAAAGAGTCAAGGTAA-AAATAGTAATCAG
1 TAATT-AAGAGTCAAGGTAAGAAAT--TAATCAG
1800 TAA
1 TAA
1803 ATCGATAATT
Statistics
Matches: 32, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
31 8 0.25
32 14 0.44
33 10 0.31
ACGTcount: A:0.49, C:0.06, G:0.19, T:0.25
Consensus pattern (31 bp):
TAATTAAGAGTCAAGGTAAGAAATTAATCAG
Found at i:2063 original size:31 final size:31
Alignment explanation
Indices: 2028--2097 Score: 113
Period size: 31 Copynumber: 2.3 Consensus size: 31
2018 AATCAGTAGA
2028 AGTAAAAGGAGTAAAAACAAAAGAAGTAATC
1 AGTAAAAGGAGTAAAAACAAAAGAAGTAATC
***
2059 AGTAAAAGGAGTAAACGTAAAAGAAGTAATC
1 AGTAAAAGGAGTAAAAACAAAAGAAGTAATC
2090 AGTAAAAG
1 AGTAAAAG
2098 CCAAAGAGCA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 36 1.00
ACGTcount: A:0.59, C:0.06, G:0.21, T:0.14
Consensus pattern (31 bp):
AGTAAAAGGAGTAAAAACAAAAGAAGTAATC
Found at i:2071 original size:16 final size:16
Alignment explanation
Indices: 2046--2097 Score: 79
Period size: 16 Copynumber: 3.3 Consensus size: 16
2036 GAGTAAAAAC
2046 AAAAGAAGTAATCAGT
1 AAAAGAAGTAATCAGT
* *
2062 AAAAGGAGTAAAC-GT
1 AAAAGAAGTAATCAGT
2077 AAAAGAAGTAATCAGT
1 AAAAGAAGTAATCAGT
2093 AAAAG
1 AAAAG
2098 CCAAAGAGCA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
15 13 0.42
16 18 0.58
ACGTcount: A:0.58, C:0.06, G:0.21, T:0.15
Consensus pattern (16 bp):
AAAAGAAGTAATCAGT
Found at i:2080 original size:15 final size:16
Alignment explanation
Indices: 2028--2097 Score: 72
Period size: 15 Copynumber: 4.5 Consensus size: 16
2018 AATCAGTAGA
*
2028 AGTAAAAGGAGTAAA-
1 AGTAAAAGAAGTAAAC
** *
2043 AACAAAAGAAGTAATC
1 AGTAAAAGAAGTAAAC
*
2059 AGTAAAAGGAGTAAAC
1 AGTAAAAGAAGTAAAC
*
2075 -GTAAAAGAAGTAATC
1 AGTAAAAGAAGTAAAC
2090 AGTAAAAG
1 AGTAAAAG
2098 CCAAAGAGCA
Statistics
Matches: 43, Mismatches: 10, Indels: 3
0.77 0.18 0.05
Matches are distributed among these distances:
15 24 0.56
16 19 0.44
ACGTcount: A:0.59, C:0.06, G:0.21, T:0.14
Consensus pattern (16 bp):
AGTAAAAGAAGTAAAC
Found at i:2160 original size:28 final size:28
Alignment explanation
Indices: 2107--2180 Score: 78
Period size: 28 Copynumber: 2.5 Consensus size: 28
2097 GCCAAAGAGC
*
2107 AAAAGTAAAAGAAGTAATCAGAAAAATGGTA
1 AAAAGT-AAAG-AGTAATCAGAAAAA-AGTA
*
2138 AAAAGTAAAGAG-AATCAGTAAAAAGTA
1 AAAAGTAAAGAGTAATCAGAAAAAAGTA
*
2165 AAATGGTAAAGAGTAA
1 AAA-AGTAAAGAGTAA
2181 AGGGTGATCA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
27 6 0.16
28 18 0.47
29 4 0.11
30 4 0.11
31 6 0.16
ACGTcount: A:0.61, C:0.03, G:0.20, T:0.16
Consensus pattern (28 bp):
AAAAGTAAAGAGTAATCAGAAAAAAGTA
Found at i:2168 original size:35 final size:36
Alignment explanation
Indices: 2129--2203 Score: 116
Period size: 35 Copynumber: 2.1 Consensus size: 36
2119 AGTAATCAGA
2129 AAAATGGTAAAAAGTAAAGAG-AATCAGTAAAAAGT
1 AAAATGGTAAAAAGTAAAGAGTAATCAGTAAAAAGT
* * *
2164 AAAATGGTAAAGAGTAAAGGGTGATCAGTAAAAAGT
1 AAAATGGTAAAAAGTAAAGAGTAATCAGTAAAAAGT
2200 AAAA
1 AAAA
2204 AGATAATCAG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
35 19 0.53
36 17 0.47
ACGTcount: A:0.57, C:0.03, G:0.23, T:0.17
Consensus pattern (36 bp):
AAAATGGTAAAAAGTAAAGAGTAATCAGTAAAAAGT
Found at i:2217 original size:15 final size:15
Alignment explanation
Indices: 2197--2253 Score: 50
Period size: 15 Copynumber: 3.9 Consensus size: 15
2187 ATCAGTAAAA
2197 AGTAAAAAGATAATC
1 AGTAAAAAGATAATC
2212 AGTAAAGAATGA-AAT-
1 AGTAAA-AA-GATAATC
*
2227 AGT-AAAAGGTAATC
1 AGTAAAAAGATAATC
*
2241 AATAAAAAG-TAAT
1 AGTAAAAAGATAAT
2254 ATCTGATTTA
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
12 1 0.03
13 5 0.14
14 8 0.23
15 14 0.40
16 5 0.14
17 2 0.06
ACGTcount: A:0.60, C:0.04, G:0.16, T:0.21
Consensus pattern (15 bp):
AGTAAAAAGATAATC
Found at i:2305 original size:2 final size:2
Alignment explanation
Indices: 2298--2367 Score: 58
Period size: 2 Copynumber: 36.5 Consensus size: 2
2288 TTTATATTAC
* * *
2298 TA TA TA TA TA TA TG TG TA -A TA TC TGA TA TA TA TA T- TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA TA TA TA TA
* *
2338 TA TA TA AA TA TA TA -A TT TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2368 TAATCGGTCG
Statistics
Matches: 55, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
1 4 0.07
2 50 0.91
3 1 0.02
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.49
Consensus pattern (2 bp):
TA
Found at i:3107 original size:18 final size:19
Alignment explanation
Indices: 3084--3122 Score: 55
Period size: 18 Copynumber: 2.1 Consensus size: 19
3074 CTCCTAATTT
3084 AATTATGGA-AATT-AAGGA
1 AATTAT-GATAATTAAAGGA
3102 AATTATGATAATTAAAGGA
1 AATTATGATAATTAAAGGA
3121 AA
1 AA
3123 ATTAAGTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 2 0.11
18 10 0.53
19 7 0.37
ACGTcount: A:0.54, C:0.00, G:0.18, T:0.28
Consensus pattern (19 bp):
AATTATGATAATTAAAGGA
Done.