Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010273.1 Corchorus capsularis cultivar CVL-1 contig10294, 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: 14577
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Found at i:1347 original size:22 final size:21
Alignment explanation
Indices: 1299--1357 Score: 84
Period size: 22 Copynumber: 2.8 Consensus size: 21
1289 AGAAAGATGC
*
1299 AATCAGTAAA-AGGTAAATGGT
1 AATCAGTAAAGA-GTAAATGAT
1320 AATCAGTAAAGAGTAAAGTGAT
1 AATCAGTAAAGAGTAAA-TGAT
1342 AATCAGTAAAGAGTAA
1 AATCAGTAAAGAGTAA
1358 TAGAAGTCAG
Statistics
Matches: 35, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
21 15 0.43
22 20 0.57
ACGTcount: A:0.51, C:0.05, G:0.22, T:0.22
Consensus pattern (21 bp):
AATCAGTAAAGAGTAAATGAT
Found at i:1423 original size:55 final size:55
Alignment explanation
Indices: 1350--1553 Score: 277
Period size: 55 Copynumber: 3.7 Consensus size: 55
1340 ATAATCAGTA
*
1350 AAGAGTAATAG-AAGTCAGTAAATCAGTAATTAAGTAAAAAGAAATTAATCAGAGTT
1 AAGA-TAATAGTAA-TCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTT
* * * *
1406 AAGATAATAGTGATCAGTAAATCAGTAATTAAGTAAAAAGAGGTAAATCAGAGTC
1 AAGATAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTT
**
1461 AA-AGTAGCAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTT
1 AAGA-TAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTT
* * *
1516 AAGGTAATAGTAATCAGTAAATCAGTAATCAGGTAAAA
1 AAGATAATAGTAATCAGTAAATCAGTAATTAAGTAAAA
1554 GATAGTAATC
Statistics
Matches: 129, Mismatches: 16, Indels: 7
0.85 0.11 0.05
Matches are distributed among these distances:
54 1 0.01
55 123 0.95
56 5 0.04
ACGTcount: A:0.50, C:0.07, G:0.19, T:0.25
Consensus pattern (55 bp):
AAGATAATAGTAATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTT
Found at i:1453 original size:26 final size:26
Alignment explanation
Indices: 1366--1501 Score: 87
Period size: 26 Copynumber: 5.0 Consensus size: 26
1356 AATAGAAGTC
1366 AGTAAATCAGTAATTAAGTAAAAAGA
1 AGTAAATCAGTAATTAAGTAAAAAGA
* * * **
1392 AATTAATCAG-AGTTAAGATAATAGTGA
1 AGTAAATCAGTAATTAAG-TAA-AAAGA
1419 TCAGTAAATCAGTAATTAAGTAAAAAGA
1 --AGTAAATCAGTAATTAAGTAAAAAGA
* * * * **
1447 GGTAAATCAG-AGTCAAAGTAGCAGTAATC
1 AGTAAATCAGTAAT-TAAGTA--A-AAAGA
1476 AGTAAATCAGTAATTAAGTAAAAAGA
1 AGTAAATCAGTAATTAAGTAAAAAGA
1502 GATTAATCAG
Statistics
Matches: 78, Mismatches: 22, Indels: 20
0.65 0.18 0.17
Matches are distributed among these distances:
25 8 0.10
26 27 0.35
27 4 0.05
28 4 0.05
29 27 0.35
30 8 0.10
ACGTcount: A:0.51, C:0.07, G:0.18, T:0.24
Consensus pattern (26 bp):
AGTAAATCAGTAATTAAGTAAAAAGA
Found at i:1575 original size:18 final size:17
Alignment explanation
Indices: 1522--1576 Score: 60
Period size: 18 Copynumber: 3.2 Consensus size: 17
1512 AGTTAAGGTA
1522 ATAGTAATCAGTAAAT-
1 ATAGTAATCAGTAAATG
* *
1538 -CAGTAATCAGGTAAAAG
1 ATAGTAATCA-GTAAATG
1555 ATAGTAATCAGTAAATTG
1 ATAGTAATCAGTAAA-TG
1573 ATAG
1 ATAG
1577 GCAACGTAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
15 8 0.26
16 5 0.16
17 5 0.16
18 13 0.42
ACGTcount: A:0.47, C:0.07, G:0.18, T:0.27
Consensus pattern (17 bp):
ATAGTAATCAGTAAATG
Found at i:2039 original size:22 final size:22
Alignment explanation
Indices: 1830--2197 Score: 225
Period size: 22 Copynumber: 16.8 Consensus size: 22
1820 AATAGCATGC
*
1830 AATCAGTAAAAAGTAAAAA-GT
1 AATCAGTAAAGAGTAAAAAGGT
* * *
1851 -ATCTG-AAAGGGTAAAATGGT
1 AATCAGTAAAGAGTAAAAAGGT
* *
1871 AGTTAGT-AAGAGT-AAAAGGT
1 AATCAGTAAAGAGTAAAAAGGT
* * *
1891 AATCATTAAAAAGTAAGAAGGT
1 AATCAGTAAAGAGTAAAAAGGT
1913 AATCA--ACAAGAGTGAAATAA--T
1 AATCAGTA-AAGAGT-AAA-AAGGT
* *
1934 AGTCAGTAAAAAAAGTAAAATA-GT
1 AATCAGT--AAAGAGTAAAA-AGGT
*
1958 AATCAGT-AAGAGTAAAAAAGT
1 AATCAGTAAAGAGTAAAAAGGT
*
1979 AA-CAAGT-AAGAAGT-AAAAGGA
1 AATC-AGTAAAG-AGTAAAAAGGT
*
2000 AATCAGT-AAGAGTGAAAAGGT
1 AATCAGTAAAGAGTAAAAAGGT
* *
2021 GATCAGTAAAGAGTAAAAAGCT
1 AATCAGTAAAGAGTAAAAAGGT
*
2043 AATCAGTATGAA-A-TAAAGAGGT
1 AATCAGTA--AAGAGTAAAAAGGT
* * *
2065 AATCAGTAAAAAG-CAAAAGGC
1 AATCAGTAAAGAGTAAAAAGGT
*
2086 AATCAGTAAAAAGT-AAAAGAGT
1 AATCAGTAAAGAGTAAAAAG-GT
*
2108 AATCAGTAAAAAAGGAGCAGAAAATGGT
1 AATCAGT---AAA-GAGTA-AAAA-GGT
*
2136 AATCAGTAAAAAGTAAAAAGGT
1 AATCAGTAAAGAGTAAAAAGGT
* *
2158 AATCAGTAAAAAGTAAGAAGGT
1 AATCAGTAAAGAGTAAAAAGGT
2180 AATCAGTAAAGAGTAAAA
1 AATCAGTAAAGAGTAAAA
2198 TCCGTAAAGA
Statistics
Matches: 274, Mismatches: 40, Indels: 65
0.72 0.11 0.17
Matches are distributed among these distances:
19 9 0.03
20 24 0.09
21 90 0.33
22 100 0.36
23 11 0.04
24 17 0.06
25 7 0.03
26 2 0.01
28 13 0.05
29 1 0.00
ACGTcount: A:0.55, C:0.06, G:0.21, T:0.18
Consensus pattern (22 bp):
AATCAGTAAAGAGTAAAAAGGT
Found at i:2084 original size:65 final size:64
Alignment explanation
Indices: 1830--2188 Score: 218
Period size: 65 Copynumber: 5.5 Consensus size: 64
1820 AATAGCATGC
* * ** * * *
1830 AATCAGTAAAAAGTAAAAAGT-ATCTGAAAG-GGTAAAATGGTAGTTAGT-AAGAGT-AAAAGGT
1 AATCAGTAAAAAGTAAAAAGTAATCAGTAAGAAATAAAA-GGTAATCAGTAAAAAGTAAAAAGGT
* * ** * * *
1891 AATCATTAAAAAGTAAGAAGGTAATCAACAAG-AGTGAAATA-ATAGTCAGTAAAAAAAGTAAAA
1 AATCAGTAAAAAGTAA-AAAGTAATCAGTAAGAAAT-AAA-AGGTAATCAGT--AAAAAGTAAAA
1954 TA-GT
61 -AGGT
* * * * *
1958 AATCAGT-AAGAGTAAAAAAGTAA-CAAGTAAGAAGTAAAAGGAAATCAGT-AAGAGTGAAAAGG
1 AATCAGTAAAAAGT-AAAAAGTAATC-AGTAAGAAATAAAAGGTAATCAGTAAAAAGTAAAAAGG
2020 T
64 T
* * * *
2021 GATCAGTAAAGAGTAAAAAGCTAATCAGTATGAAATAAAGAGGTAATCAGTAAAAAG-CAAAAGG
1 AATCAGTAAAAAGTAAAAAG-TAATCAGTAAGAAATAAA-AGGTAATCAGTAAAAAGTAAAAAGG
*
2085 C
64 T
* *
2086 AATCAGTAAAAAGTAAAAGAGTAATCAGTAAAAAAGGAGCAGAAAATGGTAATCAGTAAAAAGTA
1 AATCAGTAAAAAGTAAAA-AGTAATCAGT----AA-GA-AATAAAA-GGTAATCAGTAAAAAGTA
2151 AAAAGGT
58 AAAAGGT
*
2158 AATCAGTAAAAAGTAAGAAGGTAATCAGTAA
1 AATCAGTAAAAAGTAA-AAAGTAATCAGTAA
2189 AGAGTAAAAT
Statistics
Matches: 235, Mismatches: 34, Indels: 51
0.73 0.11 0.16
Matches are distributed among these distances:
61 15 0.06
62 5 0.02
63 37 0.16
64 23 0.10
65 44 0.19
66 35 0.15
67 16 0.07
68 3 0.01
69 1 0.00
70 3 0.01
71 20 0.09
72 31 0.13
73 2 0.01
ACGTcount: A:0.54, C:0.06, G:0.21, T:0.19
Consensus pattern (64 bp):
AATCAGTAAAAAGTAAAAAGTAATCAGTAAGAAATAAAAGGTAATCAGTAAAAAGTAAAAAGGT
Found at i:2199 original size:16 final size:16
Alignment explanation
Indices: 2180--2219 Score: 64
Period size: 16 Copynumber: 2.6 Consensus size: 16
2170 GTAAGAAGGT
2180 AATCAGTAAAGAGTAA
1 AATCAGTAAAGAGTAA
*
2196 AATCCGTAAAGAGTAA
1 AATCAGTAAAGAGTAA
2212 AAT-AGTAA
1 AATCAGTAA
2220 TCAGTAAAAG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 4 0.18
16 18 0.82
ACGTcount: A:0.55, C:0.07, G:0.17, T:0.20
Consensus pattern (16 bp):
AATCAGTAAAGAGTAA
Found at i:2255 original size:21 final size:21
Alignment explanation
Indices: 2222--2311 Score: 94
Period size: 21 Copynumber: 4.3 Consensus size: 21
2212 AATAGTAATC
*
2222 AGTAAAAGA-TAACCAGTAAG
1 AGTAAAATAGTAACCAGTAAG
2242 AGTAAAATAGTAACCAGTAAG
1 AGTAAAATAGTAACCAGTAAG
* * *
2263 AGCAAAGT-GATAACTAGTAAG
1 AGTAAAATAG-TAACCAGTAAG
* *
2284 AGTCAAATAGTAATCAGTAAAG
1 AGTAAAATAGTAACCAGT-AAG
2306 AGTAAA
1 AGTAAA
2312 GGGTGATCAG
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
20 9 0.16
21 38 0.68
22 9 0.16
ACGTcount: A:0.52, C:0.09, G:0.20, T:0.19
Consensus pattern (21 bp):
AGTAAAATAGTAACCAGTAAG
Found at i:2275 original size:42 final size:43
Alignment explanation
Indices: 2229--2312 Score: 125
Period size: 42 Copynumber: 2.0 Consensus size: 43
2219 ATCAGTAAAA
2229 GATAACCAGTAAGAGTAAAATAGTAACCAGT-AAGAGCAAAGT
1 GATAACCAGTAAGAGTAAAATAGTAACCAGTAAAGAGCAAAGT
* * * *
2271 GATAACTAGTAAGAGTCAAATAGTAATCAGTAAAGAGTAAAG
1 GATAACCAGTAAGAGTAAAATAGTAACCAGTAAAGAGCAAAG
2313 GGTGATCAGT
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
42 28 0.76
43 9 0.24
ACGTcount: A:0.50, C:0.10, G:0.21, T:0.19
Consensus pattern (43 bp):
GATAACCAGTAAGAGTAAAATAGTAACCAGTAAAGAGCAAAGT
Found at i:2401 original size:29 final size:28
Alignment explanation
Indices: 2376--2438 Score: 85
Period size: 27 Copynumber: 2.3 Consensus size: 28
2366 GTAAAAAGTG
2376 GTAATAAATAAAAGAGAGTAAGAAAAGA
1 GTAATAAATAAAAGAGAGTAAGAAAAGA
***
2404 GTAATTGGTAAAA-AGAGTAAGAAAAGA
1 GTAATAAATAAAAGAGAGTAAGAAAAGA
2431 GTAA-AAAT
1 GTAATAAAT
2439 GATAAAAGTA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
26 1 0.03
27 18 0.62
28 10 0.34
ACGTcount: A:0.60, C:0.00, G:0.22, T:0.17
Consensus pattern (28 bp):
GTAATAAATAAAAGAGAGTAAGAAAAGA
Found at i:2444 original size:29 final size:28
Alignment explanation
Indices: 2383--2446 Score: 85
Period size: 27 Copynumber: 2.2 Consensus size: 28
2373 GTGGTAATAA
*
2383 ATAAAAGAGAGTAAGAAAAGAGTAATTG
1 ATAAAAGAGAGTAAGAAAAGAGTAAATG
*
2411 GTAAAA-AGAGTAAGAAAAGAGTAAAAATG
1 ATAAAAGAGAGTAAGAAAAGAGT--AAATG
2440 ATAAAAG
1 ATAAAAG
2447 TAGCAAAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
27 16 0.53
28 5 0.17
29 9 0.30
ACGTcount: A:0.61, C:0.00, G:0.23, T:0.16
Consensus pattern (28 bp):
ATAAAAGAGAGTAAGAAAAGAGTAAATG
Found at i:7538 original size:11 final size:11
Alignment explanation
Indices: 7503--7540 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
7493 TCTGGTCGAA
*
7503 ATTTTTTTTTT
1 ATTTTTTTTAT
7514 ATTTTTTTTA-
1 ATTTTTTTTAT
*
7524 ATTTTTTTGAT
1 ATTTTTTTTAT
7535 ATTTTT
1 ATTTTT
7541 CGATATAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.16, C:0.00, G:0.03, T:0.82
Consensus pattern (11 bp):
ATTTTTTTTAT
Found at i:8621 original size:33 final size:31
Alignment explanation
Indices: 8557--8653 Score: 144
Period size: 30 Copynumber: 3.1 Consensus size: 31
8547 AAGGGTCCAT
*
8557 TGGCCAGTTGTGGCCGGT-TGCTCCATGCGA
1 TGGCCGGTTGTGGCCGGTGTGCTCCATGCGA
*
8587 TGGCCGGTTGTGGCCGGTTGATGCCCCATGCGA
1 TGGCCGGTTGTGGCCGG-TG-TGCTCCATGCGA
8620 TGGCCGGTTGTGGCCGG-GTGCTCCATGCGA
1 TGGCCGGTTGTGGCCGGTGTGCTCCATGCGA
8650 TGGC
1 TGGC
8654 GCATGCGATG
Statistics
Matches: 61, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
30 31 0.51
31 2 0.03
33 28 0.46
ACGTcount: A:0.08, C:0.27, G:0.40, T:0.25
Consensus pattern (31 bp):
TGGCCGGTTGTGGCCGGTGTGCTCCATGCGA
Found at i:9593 original size:14 final size:15
Alignment explanation
Indices: 9559--9590 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
9549 TGTTTTTTAG
*
9559 TTTAATTGCTTTCTT
1 TTTAATTGATTTCTT
9574 TTTAATTGATTTCTT
1 TTTAATTGATTTCTT
9589 TT
1 TT
9591 AATCCCCTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.09, G:0.06, T:0.69
Consensus pattern (15 bp):
TTTAATTGATTTCTT
Done.