Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007203.1 Corchorus capsularis cultivar CVL-1 contig07224, 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: 51764
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:1385 original size:114 final size:114
Alignment explanation
Indices: 1242--1610 Score: 456
Period size: 114 Copynumber: 3.2 Consensus size: 114
1232 AAATATACAA
* ** ** * *
1242 ATGGCGGCGTCTTTAAATTCAGACGCCTCCATTTAGCGGCGTCCT-GGACCAAGGCGTCGCTATA
1 ATGGCGGCGTCTTGAGGTTCAGACGCCTCCATTTAGCGGCGT-CTGGGGTCAAGACGCCGCTATA
** *
1306 TTTTAGCCTTCAGCTTTACCCAATTTGACTTTCTCGGAGAAAAATTAAAG
65 TTTTAGCCTTCATTTTTACCCAATTTGACTTCCTCGGAGAAAAATTAAAG
* * * *
1356 ATGGCGGCGTCTTGAGGTTCAGAAGCCTCCATTTAGCGGCGTCTGAGGGTC-AGACACCACTATT
1 ATGGCGGCGTCTTGAGGTTCAGACGCCTCCATTTAGCGGCGTCTG-GGGTCAAGACGCCGCTATA
* * * *
1420 TTTTAGGCTTCAATTTTTATCCAATTTGTCTTCCTCAGAGAAAAATTAAAG
65 TTTTAGCCTTC-ATTTTTACCCAATTTGACTTCCTCGGAGAAAAATTAAAG
* * *
1471 ATGGCGGCGTCTTGAGGATAAGACGCCTCCATTTAGCGGCGTCTGGGGTCAAGACGCCGCTATCT
1 ATGGCGGCGTCTTGAGGTTCAGACGCCTCCATTTAGCGGCGTCTGGGGTCAAGACGCCGCTATAT
* *
1536 TTTAGCCTTCATTTTTACCCAATTTGCCTTCCTTGGAGAAAAATTAAAG
66 TTTAGCCTTCATTTTTACCCAATTTGACTTCCTCGGAGAAAAATTAAAG
** *
1585 ATCACGGCGT-TTGTGGTTCAGACGCC
1 ATGGCGGCGTCTTGAGGTTCAGACGCC
1611 GCTATCTTTT
Statistics
Matches: 217, Mismatches: 34, Indels: 9
0.83 0.13 0.03
Matches are distributed among these distances:
113 15 0.07
114 104 0.48
115 98 0.45
ACGTcount: A:0.24, C:0.23, G:0.23, T:0.30
Consensus pattern (114 bp):
ATGGCGGCGTCTTGAGGTTCAGACGCCTCCATTTAGCGGCGTCTGGGGTCAAGACGCCGCTATAT
TTTAGCCTTCATTTTTACCCAATTTGACTTCCTCGGAGAAAAATTAAAG
Found at i:1644 original size:82 final size:82
Alignment explanation
Indices: 1507--1692 Score: 268
Period size: 82 Copynumber: 2.3 Consensus size: 82
1497 CTCCATTTAG
* *
1507 CGGCGTC-TGGGGTCAAGACGCCGCTATCTTTTAGCCTTCATTTTTACCCAATTTGCCTTCCTTG
1 CGGCGTCTTGAGGTTAAGACGCCGCTATCTTTTAGCCTTCATTTTTACCCAATTTGCCTTCCTTG
*
1571 GAGAAAAATTAAAGATCA
66 AAG-AAAATTAAAGATCA
* * * *
1589 CGGCGT-TTGTGGTTCAGACGCCGCTATCTTTTAGCCTTCTTTTTTACCCAATTTGCCTTCCTTT
1 CGGCGTCTTGAGGTTAAGACGCCGCTATCTTTTAGCCTTCATTTTTACCCAATTTGCCTTCCTTG
**
1653 AAGAAAATTAAAGATGG
66 AAGAAAATTAAAGATCA
1670 CGGCGTCTTGAGGTTAAGACGCC
1 CGGCGTCTTGAGGTTAAGACGCC
1693 TCCATTTAGC
Statistics
Matches: 92, Mismatches: 10, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
81 18 0.20
82 74 0.80
ACGTcount: A:0.22, C:0.24, G:0.21, T:0.33
Consensus pattern (82 bp):
CGGCGTCTTGAGGTTAAGACGCCGCTATCTTTTAGCCTTCATTTTTACCCAATTTGCCTTCCTTG
AAGAAAATTAAAGATCA
Found at i:3794 original size:22 final size:21
Alignment explanation
Indices: 3764--3822 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 21
3754 AATTCTTGCT
* *
3764 TCTTGAAATAATTCTTCAATTG
1 TCTTCAAATAA-TCTTCAATTA
3786 TCTTC--A-AATCTTCAAATTA
1 TCTTCAAATAATCTTC-AATTA
3805 TCTTCAAATAATCTTCAA
1 TCTTCAAATAATCTTCAA
3823 ACACGAACTT
Statistics
Matches: 31, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
18 5 0.16
19 11 0.35
20 1 0.03
21 3 0.10
22 11 0.35
ACGTcount: A:0.36, C:0.19, G:0.03, T:0.42
Consensus pattern (21 bp):
TCTTCAAATAATCTTCAATTA
Found at i:3809 original size:11 final size:11
Alignment explanation
Indices: 3792--3823 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
3782 ATTGTCTTCA
3792 AATCTTCAAAT
1 AATCTTCAAAT
*
3803 TATCTTCAAAT
1 AATCTTCAAAT
3814 AATCTTCAAA
1 AATCTTCAAA
3824 CACGAACTTC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.44, C:0.19, G:0.00, T:0.38
Consensus pattern (11 bp):
AATCTTCAAAT
Found at i:3823 original size:22 final size:22
Alignment explanation
Indices: 3764--3823 Score: 65
Period size: 22 Copynumber: 2.9 Consensus size: 22
3754 AATTCTTGCT
* *
3764 TCTTGAAATAATTCTTC-AATTG
1 TCTTCAAATAA-TCTTCAAATTA
3786 TCTTC--A-AATCTTCAAATTA
1 TCTTCAAATAATCTTCAAATTA
3805 TCTTCAAATAATCTTCAAA
1 TCTTCAAATAATCTTCAAA
3824 CACGAACTTC
Statistics
Matches: 32, Mismatches: 2, Indels: 8
0.76 0.05 0.19
Matches are distributed among these distances:
18 5 0.16
19 11 0.34
20 1 0.03
21 1 0.03
22 14 0.44
ACGTcount: A:0.37, C:0.18, G:0.03, T:0.42
Consensus pattern (22 bp):
TCTTCAAATAATCTTCAAATTA
Found at i:8436 original size:10 final size:12
Alignment explanation
Indices: 8409--8442 Score: 54
Period size: 10 Copynumber: 3.0 Consensus size: 12
8399 TCCCATGCAA
8409 TGGCCGGTCATG
1 TGGCCGGTCATG
8421 TGGCCGGTC-T-
1 TGGCCGGTCATG
8431 TGGCCGGTCATG
1 TGGCCGGTCATG
8443 GTCCCATGCG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.45
11 2 0.10
12 9 0.45
ACGTcount: A:0.06, C:0.26, G:0.41, T:0.26
Consensus pattern (12 bp):
TGGCCGGTCATG
Found at i:15003 original size:10 final size:12
Alignment explanation
Indices: 14976--15009 Score: 54
Period size: 10 Copynumber: 3.0 Consensus size: 12
14966 TCCCATGCAA
14976 TGGCCGGTCATG
1 TGGCCGGTCATG
14988 TGGCCGGTC-T-
1 TGGCCGGTCATG
14998 TGGCCGGTCATG
1 TGGCCGGTCATG
15010 GTCCCATGCG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
10 9 0.45
11 2 0.10
12 9 0.45
ACGTcount: A:0.06, C:0.26, G:0.41, T:0.26
Consensus pattern (12 bp):
TGGCCGGTCATG
Found at i:16828 original size:18 final size:18
Alignment explanation
Indices: 16805--16842 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
16795 ATCAAGGAGT
*
16805 GCAAGGAAGCATGGATAA
1 GCAAGGAAGCATGGACAA
*
16823 GCAAGGAAGCTTGGACAA
1 GCAAGGAAGCATGGACAA
16841 GC
1 GC
16843 TTAAAGGAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.16, G:0.34, T:0.11
Consensus pattern (18 bp):
GCAAGGAAGCATGGACAA
Found at i:19432 original size:17 final size:17
Alignment explanation
Indices: 19406--19455 Score: 91
Period size: 17 Copynumber: 2.9 Consensus size: 17
19396 TCCCCCTCAT
19406 GGTACCAGGTAGCATGA
1 GGTACCAGGTAGCATGA
*
19423 GGTACTAGGTAGCATGA
1 GGTACCAGGTAGCATGA
19440 GGTACCAGGTAGCATG
1 GGTACCAGGTAGCATG
19456 TGTTGTATCT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 31 1.00
ACGTcount: A:0.28, C:0.16, G:0.36, T:0.20
Consensus pattern (17 bp):
GGTACCAGGTAGCATGA
Found at i:22435 original size:6 final size:6
Alignment explanation
Indices: 22424--22455 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
22414 TATATTCTGT
22424 TTTAGA TTTAGA TTTAGA TTTAGA TTTA-A TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTTAGA TTT
22456 TCTTTGCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.15
6 22 0.85
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:22798 original size:34 final size:34
Alignment explanation
Indices: 22729--22797 Score: 111
Period size: 35 Copynumber: 2.0 Consensus size: 34
22719 TCCAAGAATT
* *
22729 AGTTTTTGTTTTTCCGTTTTTTCTAAAAAAAAAA
1 AGTTTTTCTTTTTCCGATTTTTCTAAAAAAAAAA
22763 AGTTTTTCCTTTTTCCGATTTTTCTAAAAAAAAAA
1 AGTTTTT-CTTTTTCCGATTTTTCTAAAAAAAAAA
22798 GACTTGCGAT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 7 0.22
35 25 0.78
ACGTcount: A:0.33, C:0.12, G:0.07, T:0.48
Consensus pattern (34 bp):
AGTTTTTCTTTTTCCGATTTTTCTAAAAAAAAAA
Found at i:25363 original size:17 final size:18
Alignment explanation
Indices: 25335--25369 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
25325 CGACACCCTC
25335 AACCTAAAACTAAAGAAA
1 AACCTAAAACTAAAGAAA
25353 AACCT-AAACTAAAGAAA
1 AACCTAAAACTAAAGAAA
25370 GGTAGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.66, C:0.17, G:0.06, T:0.11
Consensus pattern (18 bp):
AACCTAAAACTAAAGAAA
Found at i:30229 original size:17 final size:18
Alignment explanation
Indices: 30201--30235 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
30191 CGACACCCTT
30201 AACCTAAAACTAAAGAAA
1 AACCTAAAACTAAAGAAA
30219 AACCT-AAACTAAAGAAA
1 AACCTAAAACTAAAGAAA
30236 GGTAGAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.66, C:0.17, G:0.06, T:0.11
Consensus pattern (18 bp):
AACCTAAAACTAAAGAAA
Found at i:44287 original size:11 final size:11
Alignment explanation
Indices: 44271--44301 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
44261 CATTTTCGTC
44271 TCTTTTCTTTT
1 TCTTTTCTTTT
44282 TCTTTTCTTTT
1 TCTTTTCTTTT
*
44293 TCTCTTCTT
1 TCTTTTCTT
44302 CCCCTAGCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (11 bp):
TCTTTTCTTTT
Found at i:45503 original size:30 final size:30
Alignment explanation
Indices: 45469--45531 Score: 117
Period size: 30 Copynumber: 2.1 Consensus size: 30
45459 TAGCTAGCCC
45469 CTGTTACATTGCTTGTAATTGCCTTATTCT
1 CTGTTACATTGCTTGTAATTGCCTTATTCT
*
45499 CTGTTACTTTGCTTGTAATTGCCTTATTCT
1 CTGTTACATTGCTTGTAATTGCCTTATTCT
45529 CTG
1 CTG
45532 CCATGATGTG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.14, C:0.21, G:0.14, T:0.51
Consensus pattern (30 bp):
CTGTTACATTGCTTGTAATTGCCTTATTCT
Found at i:46150 original size:24 final size:25
Alignment explanation
Indices: 46102--46150 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
46092 AATAAATAAA
*
46102 AATTCTCTATTTTTTTGTGATTTTT
1 AATTCTCTATTTTTTTGTGACTTTT
* *
46127 AATT-TCTATTTTTTTTTTACTTTT
1 AATTCTCTATTTTTTTGTGACTTTT
46151 TACAGTGACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.16, C:0.08, G:0.04, T:0.71
Consensus pattern (25 bp):
AATTCTCTATTTTTTTGTGACTTTT
Found at i:46462 original size:27 final size:26
Alignment explanation
Indices: 46431--46504 Score: 85
Period size: 26 Copynumber: 2.8 Consensus size: 26
46421 AATTGAGCTT
46431 AAAATGACCAAAATGCCCCTAAATATG
1 AAAATGACCAAAATG-CCCTAAATATG
* * * * *
46458 CAAATGACCAAAATGACCTTAGTGTG
1 AAAATGACCAAAATGCCCTAAATATG
46484 AAAATGACCAAAATGTCCCTA
1 AAAATGACCAAAATG-CCCTA
46505 GGTGACCCTA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
26 21 0.55
27 17 0.45
ACGTcount: A:0.45, C:0.22, G:0.14, T:0.20
Consensus pattern (26 bp):
AAAATGACCAAAATGCCCTAAATATG
Found at i:48884 original size:43 final size:43
Alignment explanation
Indices: 48775--48865 Score: 182
Period size: 43 Copynumber: 2.1 Consensus size: 43
48765 GAAAACATTA
48775 TAGTACTATCTAGATTCAAATAATCTTACATCCTTATTAATTT
1 TAGTACTATCTAGATTCAAATAATCTTACATCCTTATTAATTT
48818 TAGTACTATCTAGATTCAAATAATCTTACATCCTTATTAATTT
1 TAGTACTATCTAGATTCAAATAATCTTACATCCTTATTAATTT
48861 TAGTA
1 TAGTA
48866 ACTTTTTATG
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 48 1.00
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.44
Consensus pattern (43 bp):
TAGTACTATCTAGATTCAAATAATCTTACATCCTTATTAATTT
Done.