Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007893.1 Corchorus capsularis cultivar CVL-1 contig07914, 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: 20288
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Found at i:742 original size:47 final size:46
Alignment explanation
Indices: 672--840 Score: 158
Period size: 47 Copynumber: 3.4 Consensus size: 46
662 AGTAAAAAGG
* * * * *
672 GGTAATCAGTACTCAGTAGAAAGAGATTAATCAAAGCCAAGGTGAT
1 GGTAATCAGTAATCAGTAAAAAGAAATCAATCAAAGCCAAGGTAAT
* *
718 GGTAATCAGTAAATCAGTAAAAAGAAATCAATCAGAGTCAAGGTAAT
1 GGTAATCAGT-AATCAGTAAAAAGAAATCAATCAAAGCCAAGGTAAT
* *
765 GGTAATCAGTCAATCAGTAAATCAGTAAAAAGAAATCAATCAGAGTCAAGGTAAT
1 -G------GT-AATCAGT-AATCAGTAAAAAGAAATCAATCAAAGCCAAGGTAAT
820 GGTAATCAGTCAATCAGTAAA
1 GGTAATCAGT-AATCAGTAAA
841 TCAGTAAAAA
Statistics
Matches: 106, Mismatches: 8, Indels: 17
0.81 0.06 0.13
Matches are distributed among these distances:
46 10 0.09
47 46 0.43
48 3 0.03
54 3 0.03
55 44 0.42
ACGTcount: A:0.46, C:0.12, G:0.20, T:0.22
Consensus pattern (46 bp):
GGTAATCAGTAATCAGTAAAAAGAAATCAATCAAAGCCAAGGTAAT
Found at i:778 original size:29 final size:29
Alignment explanation
Indices: 745--836 Score: 88
Period size: 29 Copynumber: 3.3 Consensus size: 29
735 TAAAAAGAAA
745 TCAATCAGAGTCAAGGTAATGGTAATCAG
1 TCAATCAGAGTCAAGGTAATGGTAATCAG
* **
774 TCAATCAGTAAATC-A-GTAAAAAG-AA--A-
1 TCAATCAG--AGTCAAGGT-AATGGTAATCAG
800 TCAATCAGAGTCAAGGTAATGGTAATCAG
1 TCAATCAGAGTCAAGGTAATGGTAATCAG
829 TCAATCAG
1 TCAATCAG
837 TAAATCAGTA
Statistics
Matches: 48, Mismatches: 6, Indels: 18
0.67 0.08 0.25
Matches are distributed among these distances:
24 3 0.06
25 4 0.08
26 12 0.25
27 1 0.02
28 1 0.02
29 20 0.42
30 4 0.08
31 3 0.06
ACGTcount: A:0.43, C:0.14, G:0.20, T:0.23
Consensus pattern (29 bp):
TCAATCAGAGTCAAGGTAATGGTAATCAG
Found at i:783 original size:55 final size:55
Alignment explanation
Indices: 721--906 Score: 275
Period size: 55 Copynumber: 3.4 Consensus size: 55
711 AGGTGATGGT
721 AATCAGTAAATCAGTAAAAAGAAATCAATCAGAGTCAAGGTAATGGTAATCAGTC
1 AATCAGTAAATCAGTAAAAAGAAATCAATCAGAGTCAAGGTAATGGTAATCAGTC
776 AATCAGTAAATCAGTAAAAAGAAATCAATCAGAGTCAAGGTAATGGTAATCAGTC
1 AATCAGTAAATCAGTAAAAAGAAATCAATCAGAGTCAAGGTAATGGTAATCAGTC
* * * * * * * *
831 AATCAGTAAATCAGTAAAAAGAGATTAATTAAAAGTTAAGGTAATAGCAATCAGTA
1 AATCAGTAAATCAGTAAAAAGAAATCAA-TCAGAGTCAAGGTAATGGTAATCAGTC
887 AATCAGT-AATCAAGTAAAAA
1 AATCAGTAAATC-AGTAAAAA
907 TATAGTAATC
Statistics
Matches: 121, Mismatches: 8, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
55 85 0.70
56 36 0.30
ACGTcount: A:0.50, C:0.11, G:0.17, T:0.23
Consensus pattern (55 bp):
AATCAGTAAATCAGTAAAAAGAAATCAATCAGAGTCAAGGTAATGGTAATCAGTC
Found at i:818 original size:26 final size:26
Alignment explanation
Indices: 734--818 Score: 68
Period size: 26 Copynumber: 3.2 Consensus size: 26
724 CAGTAAATCA
734 GTAAAAAGAAATCAATCAGAGTCAAG
1 GTAAAAAGAAATCAATCAGAGTCAAG
** *
760 GT-AATGGTAATCAGTCAATCAGTAAATC-A-
1 GTAAAAAG-AA--A-TCAATCAG--AGTCAAG
789 GTAAAAAGAAATCAATCAGAGTCAAG
1 GTAAAAAGAAATCAATCAGAGTCAAG
815 GTAA
1 GTAA
819 TGGTAATCAG
Statistics
Matches: 44, Mismatches: 6, Indels: 18
0.65 0.09 0.26
Matches are distributed among these distances:
24 3 0.07
25 4 0.09
26 16 0.36
27 1 0.02
28 1 0.02
29 12 0.27
30 4 0.09
31 3 0.07
ACGTcount: A:0.49, C:0.12, G:0.19, T:0.20
Consensus pattern (26 bp):
GTAAAAAGAAATCAATCAGAGTCAAG
Found at i:1167 original size:14 final size:14
Alignment explanation
Indices: 1130--1168 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 14
1120 AATGGTAAAG
*
1130 AGTAAAGAATAATC
1 AGTAAAGAGTAATC
* *
1144 AGTAAGGAGTAATT
1 AGTAAAGAGTAATC
1158 AGTAAAGAGTA
1 AGTAAAGAGTA
1169 TAATGATAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.51, C:0.03, G:0.23, T:0.23
Consensus pattern (14 bp):
AGTAAAGAGTAATC
Found at i:1223 original size:35 final size:35
Alignment explanation
Indices: 1144--1271 Score: 157
Period size: 35 Copynumber: 3.6 Consensus size: 35
1134 AAGAATAATC
* * * * *
1144 AGTAAGGAGTAATTAGTAAAGAGTATAATGATAAAAA
1 AGTAAAGAGTAATCAGTAAA-AGAAGAATGGT-AAAA
1181 AGTAAAGAGTAATCAGTAAAAGAAGAATGGTAAAA
1 AGTAAAGAGTAATCAGTAAAAGAAGAATGGTAAAA
* *
1216 AGTAAAGAGTAATCAGTAAAGGAAGAATGGTAAAG
1 AGTAAAGAGTAATCAGTAAAAGAAGAATGGTAAAA
* *
1251 AGAAAAGGGTAATCAGTAAAA
1 AGTAAAGAGTAATCAGTAAAA
1272 AGTAAAAGGA
Statistics
Matches: 81, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
35 55 0.68
36 8 0.10
37 18 0.22
ACGTcount: A:0.55, C:0.02, G:0.24, T:0.19
Consensus pattern (35 bp):
AGTAAAGAGTAATCAGTAAAAGAAGAATGGTAAAA
Found at i:1269 original size:21 final size:21
Alignment explanation
Indices: 1245--1293 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
1235 AGGAAGAATG
*
1245 GTAAAGAG-AAAAGGGTAATCA
1 GTAAAGAGTAAAAGGATAAT-A
*
1266 GTAAAAAGTAAAAGGATAATA
1 GTAAAGAGTAAAAGGATAATA
1287 GTAAAGA
1 GTAAAGA
1294 AGGAAATAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.57, C:0.02, G:0.24, T:0.16
Consensus pattern (21 bp):
GTAAAGAGTAAAAGGATAATA
Found at i:1308 original size:16 final size:16
Alignment explanation
Indices: 1277--1306 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1267 TAAAAAGTAA
1277 AAGGATAATAGTAAAG
1 AAGGATAATAGTAAAG
1293 AAGGA-AATAGTAAA
1 AAGGATAATAGTAAA
1307 AGGTAATCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.60, C:0.00, G:0.23, T:0.17
Consensus pattern (16 bp):
AAGGATAATAGTAAAG
Found at i:1355 original size:21 final size:22
Alignment explanation
Indices: 1330--1479 Score: 119
Period size: 22 Copynumber: 6.6 Consensus size: 22
1320 AAAAGTAATG
* *
1330 ATAGTAATTAGTAAG-AGTCAA
1 ATAGTAATCAGTAAGAAGTAAA
1351 ATAGTAATCAGTAAGAAGTAAA
1 ATAGTAATCAGTAAGAAGTAAA
*
1373 AGAGTAATCAGTAAAAAAGGAGCAG-AAA
1 ATAGTAATCAGT----AA-GA--AGTAAA
*
1401 ATAGTAATCAGTAAAAGAGTAAA
1 ATAGTAATCAGTAAGA-AGTAAA
* *
1424 ATGGTAATCAGTAAAAAGTAAA
1 ATAGTAATCAGTAAGAAGTAAA
**
1446 A-AGGTAATCAACAAG-AGTAAA
1 ATA-GTAATCAGTAAGAAGTAAA
1467 ATAGTAATCAGTA
1 ATAGTAATCAGTA
1480 CAAGATAAAG
Statistics
Matches: 105, Mismatches: 13, Indels: 22
0.75 0.09 0.16
Matches are distributed among these distances:
21 29 0.28
22 35 0.33
23 19 0.18
24 2 0.02
26 2 0.02
27 2 0.02
28 14 0.13
29 2 0.02
ACGTcount: A:0.54, C:0.06, G:0.19, T:0.21
Consensus pattern (22 bp):
ATAGTAATCAGTAAGAAGTAAA
Found at i:1385 original size:15 final size:15
Alignment explanation
Indices: 1367--1422 Score: 62
Period size: 15 Copynumber: 3.9 Consensus size: 15
1357 ATCAGTAAGA
1367 AGTAAAAGAGTAATC
1 AGTAAAAGAGTAATC
* * *
1382 AGTAAAAAAG-GAGC
1 AGTAAAAGAGTAATC
*
1396 AG-AAAATAGTAATC
1 AGTAAAAGAGTAATC
1410 AGTAAAAGAGTAA
1 AGTAAAAGAGTAA
1423 AATGGTAATC
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
Found at i:1408 original size:95 final size:96
Alignment explanation
Indices: 1245--1479 Score: 218
Period size: 95 Copynumber: 2.5 Consensus size: 96
1235 AGGAAGAATG
* * * * *
1245 GTAAAGAG-AAAAGGGTAATCAGTAAAAAGTAAAAG-GATAAT-AGTAAAGAAGGAAATAGTAAA
1 GTAAAAAGTAAAAAGGTAATCAGTAAGAAGTAAAAGAG-TAATCAGTAAAAAAGGAAACAGTAAA
* * *
1307 AGGTAATCCA-TAAAAAAGTAATGATAGTAATTA
65 AAGTAAT-CAGTAAAAAAGTAA-AATAGTAATCA
* * *
1340 GT-AAGAGTCAAATA-GTAATCAGTAAGAAGTAAAAGAGTAATCAGTAAAAAAGG-AGCAG-AAA
1 GTAAAAAGT-AAAAAGGTAATCAGTAAGAAGTAAAAGAGTAATCAGTAAAAAAGGAAACAGTAAA
* *
1401 ATAGTAATCAGTAAAAGAGTAAAATGGTAATCA
65 A-AGTAATCAGTAAAAAAGTAAAATAGTAATCA
** *
1434 GTAAAAAGTAAAAAGGTAATCAACAAG-AGTAAAATAGTAATCAGTA
1 GTAAAAAGTAAAAAGGTAATCAGTAAGAAGTAAAAGAGTAATCAGTA
1480 CAAGATAAAG
Statistics
Matches: 116, Mismatches: 16, Indels: 17
0.78 0.11 0.11
Matches are distributed among these distances:
94 43 0.37
95 59 0.51
96 14 0.12
ACGTcount: A:0.55, C:0.05, G:0.20, T:0.20
Consensus pattern (96 bp):
GTAAAAAGTAAAAAGGTAATCAGTAAGAAGTAAAAGAGTAATCAGTAAAAAAGGAAACAGTAAAA
AGTAATCAGTAAAAAAGTAAAATAGTAATCA
Found at i:7171 original size:95 final size:95
Alignment explanation
Indices: 7008--7197 Score: 380
Period size: 95 Copynumber: 2.0 Consensus size: 95
6998 GAGAATAGTC
7008 CACGAGGATGTCTAGCCAAAGACAATAAATGAAGGCGCTAATTGGGAGGCAACCCAATACACTAA
1 CACGAGGATGTCTAGCCAAAGACAATAAATGAAGGCGCTAATTGGGAGGCAACCCAATACACTAA
7073 CATCTATCCTTTTCTTTTGAATTTTCTTTT
66 CATCTATCCTTTTCTTTTGAATTTTCTTTT
7103 CACGAGGATGTCTAGCCAAAGACAATAAATGAAGGCGCTAATTGGGAGGCAACCCAATACACTAA
1 CACGAGGATGTCTAGCCAAAGACAATAAATGAAGGCGCTAATTGGGAGGCAACCCAATACACTAA
7168 CATCTATCCTTTTCTTTTGAATTTTCTTTT
66 CATCTATCCTTTTCTTTTGAATTTTCTTTT
7198 TCTTAGTTAT
Statistics
Matches: 95, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
95 95 1.00
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.31
Consensus pattern (95 bp):
CACGAGGATGTCTAGCCAAAGACAATAAATGAAGGCGCTAATTGGGAGGCAACCCAATACACTAA
CATCTATCCTTTTCTTTTGAATTTTCTTTT
Found at i:9490 original size:6 final size:6
Alignment explanation
Indices: 9482--9511 Score: 51
Period size: 6 Copynumber: 5.0 Consensus size: 6
9472 CATTGCATGC
*
9482 ATTTGC ATTTGT ATTTGT ATTTGT ATTTGT
1 ATTTGT ATTTGT ATTTGT ATTTGT ATTTGT
9512 TCTATTTGGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.17, C:0.03, G:0.17, T:0.63
Consensus pattern (6 bp):
ATTTGT
Found at i:9775 original size:24 final size:24
Alignment explanation
Indices: 9743--9812 Score: 83
Period size: 24 Copynumber: 3.0 Consensus size: 24
9733 ACTTAAAAAT
9743 ATTAGGCTCTTTGAAATTTTTGTC
1 ATTAGGCTCTTTGAAATTTTTGTC
9767 ATTAGGCTCTTT-AAA--TTTGTC
1 ATTAGGCTCTTTGAAATTTTTGTC
* * * *
9788 ATGAGCCTATTGGAAATTTTTGTC
1 ATTAGGCTCTTTGAAATTTTTGTC
9812 A
1 A
9813 AAATGCTAGC
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
21 14 0.36
22 3 0.08
23 3 0.08
24 19 0.49
ACGTcount: A:0.24, C:0.13, G:0.17, T:0.46
Consensus pattern (24 bp):
ATTAGGCTCTTTGAAATTTTTGTC
Found at i:20281 original size:33 final size:33
Alignment explanation
Indices: 20184--20288 Score: 140
Period size: 33 Copynumber: 3.2 Consensus size: 33
20174 TTGCAAAGAG
*
20184 TGTTTT-AGATGTTGTTTGCGATGATACTAAACC
1 TGTTTTAAG-TGTTGTTTGCGATGATACTAAATC
** * *
20217 TAATTTAAGTGTTGTTTGCAATGACACTAAATC
1 TGTTTTAAGTGTTGTTTGCGATGATACTAAATC
*
20250 TGTTTTAAGTGTTGTTTGTGATGATACTAAATC
1 TGTTTTAAGTGTTGTTTGCGATGATACTAAATC
20283 TGTTTT
1 TGTTTT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
33 59 0.97
34 2 0.03
ACGTcount: A:0.26, C:0.10, G:0.19, T:0.46
Consensus pattern (33 bp):
TGTTTTAAGTGTTGTTTGCGATGATACTAAATC
Done.