Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012744.1 Corchorus capsularis cultivar CVL-1 contig12765, 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: 24243
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Found at i:607 original size:32 final size:31
Alignment explanation
Indices: 570--655 Score: 82
Period size: 32 Copynumber: 2.7 Consensus size: 31
560 CTAAGAGAGG
*
570 AAGTAAAAGTAGTAATCAGTAAGTAAGGGTCA
1 AAGTAAAAG-AGTAATCAGTAAGTAAGAGTCA
* * *
602 AAGTAAAAGGGCAAGTCAGTAATTAAGAGTCA
1 AAGTAAAAGAGTAA-TCAGTAAGTAAGAGTCA
* * *
634 AGGTAGAAGGATTAATCAGTAA
1 AAGTA-AAAGAGTAATCAGTAA
656 ATTGATAATT
Statistics
Matches: 43, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
31 3 0.07
32 35 0.81
33 5 0.12
ACGTcount: A:0.47, C:0.07, G:0.26, T:0.21
Consensus pattern (31 bp):
AAGTAAAAGAGTAATCAGTAAGTAAGAGTCA
Found at i:849 original size:33 final size:32
Alignment explanation
Indices: 811--889 Score: 88
Period size: 32 Copynumber: 2.4 Consensus size: 32
801 ATCAGTAAAG
*
811 AGTAAAATGGTAAAATGGTAATTAAATTCAAAA
1 AGTAAAAT-GTAAAATGGCAATTAAATTCAAAA
* *
844 AGTAAAATG-ACAAATGGCGATTAAATTCAAAG
1 AGTAAAATGTA-AAATGGCAATTAAATTCAAAA
876 AGTGAAAATAGTAA
1 AGT-AAAAT-GTAA
890 TTAAATTCAA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
31 1 0.03
32 22 0.56
33 13 0.33
34 2 0.05
35 1 0.03
ACGTcount: A:0.53, C:0.05, G:0.18, T:0.24
Consensus pattern (32 bp):
AGTAAAATGTAAAATGGCAATTAAATTCAAAA
Found at i:892 original size:26 final size:26
Alignment explanation
Indices: 863--916 Score: 92
Period size: 26 Copynumber: 2.1 Consensus size: 26
853 ACAAATGGCG
863 ATTAAATTCAA-AGAGTGAAAATAGTA
1 ATTAAATTCAAGAGAGT-AAAATAGTA
889 ATTAAATTCAAGAGAGTAAAATAGTA
1 ATTAAATTCAAGAGAGTAAAATAGTA
915 AT
1 AT
917 CAGTAAAGAG
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 22 0.81
27 5 0.19
ACGTcount: A:0.54, C:0.04, G:0.15, T:0.28
Consensus pattern (26 bp):
ATTAAATTCAAGAGAGTAAAATAGTA
Found at i:953 original size:28 final size:30
Alignment explanation
Indices: 901--965 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 30
891 TAAATTCAAG
901 AGAGTAAAATAGTAATCAGTAAAGAG-AAA
1 AGAGTAAAATAGTAATCAGTAAAGAGTAAA
*
930 AGAGTAAAA-AGTAATCAGTGAAGAGTAAA
1 AGAGTAAAATAGTAATCAGTAAAGAGTAAA
*
959 AAAGTAA
1 AGAGTAA
966 TCAGTAAAGA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
28 15 0.45
29 18 0.55
ACGTcount: A:0.58, C:0.03, G:0.22, T:0.17
Consensus pattern (30 bp):
AGAGTAAAATAGTAATCAGTAAAGAGTAAA
Found at i:956 original size:14 final size:14
Alignment explanation
Indices: 911--1056 Score: 87
Period size: 14 Copynumber: 11.0 Consensus size: 14
901 AGAGTAAAAT
911 AGTAATCAGTAAAG
1 AGTAATCAGTAAAG
* ** *
925 AGAAAAGAGTAAAA
1 AGTAATCAGTAAAG
*
939 AGTAATCAGTGAAG
1 AGTAATCAGTAAAG
953 AGT-A--A--AAA-
1 AGTAATCAGTAAAG
961 AGTAATCAGTAAAG
1 AGTAATCAGTAAAG
*
975 AGTAATCAGTAAAA
1 AGTAATCAGTAAAG
** **
989 AGTAAAAATGGCAA-
1 AGTAATCA-GTAAAG
* *
1003 A-TAGT-AGTAAAA
1 AGTAATCAGTAAAG
1015 AGTAATCAGGTAAA-
1 AGTAATCA-GTAAAG
*
1029 AGTAATCGGTAAAG
1 AGTAATCAGTAAAG
1043 AGTAATCAGTAAAG
1 AGTAATCAGTAAAG
1057 GGAGAATGGT
Statistics
Matches: 98, Mismatches: 22, Indels: 24
0.68 0.15 0.17
Matches are distributed among these distances:
8 3 0.03
9 3 0.03
11 5 0.05
12 2 0.02
13 14 0.14
14 63 0.64
15 8 0.08
ACGTcount: A:0.54, C:0.05, G:0.21, T:0.19
Consensus pattern (14 bp):
AGTAATCAGTAAAG
Found at i:963 original size:22 final size:22
Alignment explanation
Indices: 928--979 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
918 AGTAAAGAGA
928 AAAGAGT-AAAAAGTAATCAGT
1 AAAGAGTAAAAAAGTAATCAGT
*
949 GAAGAGTAAAAAAGTAATCAGT
1 AAAGAGTAAAAAAGTAATCAGT
971 AAAGAGTAA
1 AAAGAGTAA
980 TCAGTAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
21 6 0.21
22 22 0.79
ACGTcount: A:0.58, C:0.04, G:0.21, T:0.17
Consensus pattern (22 bp):
AAAGAGTAAAAAAGTAATCAGT
Found at i:1076 original size:35 final size:35
Alignment explanation
Indices: 1037--1117 Score: 101
Period size: 35 Copynumber: 2.3 Consensus size: 35
1027 AAAGTAATCG
* *
1037 GTAAAGAGTAATCAGTAA-AGGGAGAATGGTAAAGA
1 GTAAAGAGTAATCAGTAAGA-GCAAAATGGTAAAGA
* **
1072 GTAAAGGGTAATCAGTAAGAGCAAAATGGTAATTA
1 GTAAAGAGTAATCAGTAAGAGCAAAATGGTAAAGA
1107 GTAAAGAGTAA
1 GTAAAGAGTAA
1118 AATAGTAATC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
35 38 0.97
36 1 0.03
ACGTcount: A:0.48, C:0.04, G:0.28, T:0.20
Consensus pattern (35 bp):
GTAAAGAGTAATCAGTAAGAGCAAAATGGTAAAGA
Found at i:1089 original size:21 final size:21
Alignment explanation
Indices: 1065--1274 Score: 120
Period size: 21 Copynumber: 10.2 Consensus size: 21
1055 AGGGAGAATG
1065 GTAAAGAGTAAAGGGTAATCA
1 GTAAAGAGTAAAGGGTAATCA
* * *
1086 GT-AAGAGCAAAATGGTAATTA
1 GTAAAGAG-TAAAGGGTAATCA
**
1107 GTAAAGAGTAAAATAGTAATCA
1 GTAAAGAGT-AAAGGGTAATCA
* *
1129 GTAAAAAGTAAGAAGGTAATCA
1 GTAAAGAGTAA-AGGGTAATCA
*
1151 GTAAAGAGTAAAGTAGTAATCA
1 GTAAAGAGTAAAG-GGTAATCA
1173 GT----A--AAA-GGTAATCA
1 GTAAAGAGTAAAGGGTAATCA
**
1187 GTAAGAGTA--AAACCGTAATCA
1 GTAA-AG-AGTAAAGGGTAATCA
* *
1208 GTA-AGAGCAAAGTGGTAATTA
1 GTAAAGAGTAAAG-GGTAATCA
**
1229 GT-AAGAGTAAAATAGTAATCA
1 GTAAAGAGT-AAAGGGTAATCA
* *
1250 GTAAAGAGTAAAAGGTGATCA
1 GTAAAGAGTAAAGGGTAATCA
1271 GTAA
1 GTAA
1275 TTCAAAGAGT
Statistics
Matches: 147, Mismatches: 24, Indels: 36
0.71 0.12 0.17
Matches are distributed among these distances:
14 9 0.06
16 3 0.02
18 2 0.01
19 2 0.01
20 12 0.08
21 60 0.41
22 59 0.40
ACGTcount: A:0.50, C:0.06, G:0.23, T:0.21
Consensus pattern (21 bp):
GTAAAGAGTAAAGGGTAATCA
Found at i:1119 original size:22 final size:22
Alignment explanation
Indices: 1065--1177 Score: 133
Period size: 22 Copynumber: 5.2 Consensus size: 22
1055 AGGGAGAATG
*
1065 GTAAAGAGT-AAAGGGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
* *
1086 GT-AAGAGCAAAATGGTAATTA
1 GTAAAGAGTAAAATGGTAATCA
*
1107 GTAAAGAGTAAAATAGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
*
1129 GTAAAAAGTAAGAA-GGTAATCA
1 GTAAAGAGTAA-AATGGTAATCA
* *
1151 GTAAAGAGTAAAGTAGTAATCA
1 GTAAAGAGTAAAATGGTAATCA
1173 GTAAA
1 GTAAA
1178 AGGTAATCAG
Statistics
Matches: 77, Mismatches: 11, Indels: 7
0.81 0.12 0.07
Matches are distributed among these distances:
20 5 0.06
21 15 0.19
22 55 0.71
23 2 0.03
ACGTcount: A:0.51, C:0.04, G:0.23, T:0.21
Consensus pattern (22 bp):
GTAAAGAGTAAAATGGTAATCA
Found at i:1274 original size:42 final size:41
Alignment explanation
Indices: 1172--1274 Score: 134
Period size: 42 Copynumber: 2.5 Consensus size: 41
1162 AGTAGTAATC
*
1172 AGTAAAAGGTAATCAGTAAGAGTAAAACCGTAATCAGTAAG
1 AGTAAAAGGTAATCAGTAAGAGTAAAACAGTAATCAGTAAG
* * * *
1213 AGCAAAGTGGTAATTAGTAAGAGTAAAATAGTAATCAGTAAAG
1 AGTAAA-AGGTAATCAGTAAGAGTAAAACAGTAATCAGT-AAG
*
1256 AGTAAAAGGTGATCAGTAA
1 AGTAAAAGGTAATCAGTAA
1275 TTCAAAGAGT
Statistics
Matches: 51, Mismatches: 9, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
41 5 0.10
42 38 0.75
43 8 0.16
ACGTcount: A:0.49, C:0.07, G:0.23, T:0.21
Consensus pattern (41 bp):
AGTAAAAGGTAATCAGTAAGAGTAAAACAGTAATCAGTAAG
Found at i:1394 original size:29 final size:29
Alignment explanation
Indices: 1333--1396 Score: 96
Period size: 27 Copynumber: 2.2 Consensus size: 29
1323 GTGGTAATCA
*
1333 ATAAAAGAGAGTAAGAAAAGAGTAAATAG
1 ATAAAAGAGAGTAAGAAAAGAGTAAAAAG
1362 -TAAAA-AGAGTAAGAAAAGAGTAAAAATG
1 ATAAAAGAGAGTAAGAAAAGAGTAAAAA-G
1390 ATAAAAG
1 ATAAAAG
1397 TAGCAAAAGT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
27 20 0.65
28 6 0.19
29 5 0.16
ACGTcount: A:0.64, C:0.00, G:0.22, T:0.14
Consensus pattern (29 bp):
ATAAAAGAGAGTAAGAAAAGAGTAAAAAG
Found at i:7281 original size:29 final size:29
Alignment explanation
Indices: 7248--7303 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
7238 ATAAATAATT
*
7248 GCAATTC-AATCAATCAATAGCAAGATATG
1 GCAATTCAAATCAA-CAATAGAAAGATATG
*
7277 GCAATTCAAATCAACAATTGAAAGATA
1 GCAATTCAAATCAACAATAGAAAGATA
7304 GAATAAACAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 18 0.75
30 6 0.25
ACGTcount: A:0.48, C:0.16, G:0.12, T:0.23
Consensus pattern (29 bp):
GCAATTCAAATCAACAATAGAAAGATATG
Done.