Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01012563.1 Corchorus capsularis cultivar CVL-1 contig12584, 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: 20862
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 2 characters in sequence are not A, C, G, or T
Found at i:2280 original size:90 final size:89
Alignment explanation
Indices: 2090--2459 Score: 594
Period size: 86 Copynumber: 4.2 Consensus size: 89
2080 TACAATATAC
2090 ATATATATATATATATATTATTGATTTTAAAACTTACTAATTTACATATCGTTTAGTCCTATATA
1 ATATATATATATATATATTATTGATTTTAAAACTTACTAATTTACATATCGTTTAGTCCTATATA
2155 TTACTGTACCCAATTAACTAAC--
66 TTACTGTACCCAATTAACTAACTA
2177 -TATATATATATATATATTATTGATTTTAAAACTTACTAATTTACATATCGTTTAGTCCTATATA
1 ATATATATATATATATATTATTGATTTTAAAACTTACTAATTTACATATCGTTTAGTCCTATATA
2241 TTACTGTACCCAATTAACTAACTA
66 TTACTGTACCCAATTAACTAACTA
2265 TATATATATATATATATATTATTGATTTTAAAACTTACTAATTTACATATCGTTTAGTCCTATAT
1 -ATATATATATATATATATTATTGATTTTAAAACTTACTAATTTACATATCGTTTAGTCCTATAT
* * *
2330 ATTACTNT--NC-ATCAA-TAACTA
65 ATTACTGTACCCAATTAACTAACTA
*
2351 TATATATATATATATATATTATTGATTTTTAAAACTTACTAATTTACATACCGTTTAGTCCTATA
1 -ATATATATATATATATATTATTGA-TTTTAAAACTTACTAATTTACATATCGTTTAGTCCTATA
*
2416 TATTACTGTACCTAATTAACTAACTA
64 TATTACTGTACCCAATTAACTAACTA
2442 ACTA-ACTATATATATATA
1 A-TATA-TATATATATATA
2460 GGCTAAAATG
Statistics
Matches: 264, Mismatches: 8, Indels: 18
0.91 0.03 0.06
Matches are distributed among these distances:
86 117 0.44
87 50 0.19
88 1 0.00
90 76 0.29
91 20 0.08
ACGTcount: A:0.38, C:0.13, G:0.04, T:0.44
Consensus pattern (89 bp):
ATATATATATATATATATTATTGATTTTAAAACTTACTAATTTACATATCGTTTAGTCCTATATA
TTACTGTACCCAATTAACTAACTA
Found at i:2597 original size:2 final size:2
Alignment explanation
Indices: 2590--2626 Score: 56
Period size: 2 Copynumber: 18.0 Consensus size: 2
2580 TCACCATAAT
*
2590 TA TA TA TA TA TA CTA TA TA TA TA TA TG TA TA TA TA TA
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
2627 GCATATAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
2 30 0.94
3 2 0.06
ACGTcount: A:0.46, C:0.03, G:0.03, T:0.49
Consensus pattern (2 bp):
TA
Found at i:2829 original size:25 final size:26
Alignment explanation
Indices: 2786--2839 Score: 65
Period size: 25 Copynumber: 2.1 Consensus size: 26
2776 TTCTCTTACC
*
2786 TAGGGTTTATATTACATG-TTATATA
1 TAGGGTTTAGATTACATGCTTATATA
**
2811 TAGGGTTTAGATTTTATGTCTTATATA
1 TAGGGTTTAGATTACATG-CTTATATA
2838 TA
1 TA
2840 TTTTATACAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 15 0.62
27 9 0.38
ACGTcount: A:0.30, C:0.04, G:0.17, T:0.50
Consensus pattern (26 bp):
TAGGGTTTAGATTACATGCTTATATA
Found at i:3738 original size:82 final size:83
Alignment explanation
Indices: 3648--3803 Score: 244
Period size: 84 Copynumber: 1.9 Consensus size: 83
3638 AATATCCAAA
*
3648 GTCCCCAAACACAATCCTAACACAGGGGCAACTC-TT-TCAAAGTCCTCAAGCACATTCATAACA
1 GTCCCCAAACACAATCATAACACAGGGGCAA-TCATTCTCAAAGTCCTCAAGCACATTCATAACA
3711 CAGAAGCATTAACATCAGT
65 CAGAAGCATTAACATCAGT
* *
3730 GTCCCCAAACACAATTATAACACAGGGTCAATCATTTCTCAAAGTCCTCAAGCACATTCATAACA
1 GTCCCCAAACACAATCATAACACAGGGGCAATCA-TTCTCAAAGTCCTCAAGCACATTCATAACA
*
3795 CAGAGGCAT
65 CAGAAGCAT
3804 CTATCAATGT
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
81 2 0.03
82 28 0.42
83 2 0.03
84 35 0.52
ACGTcount: A:0.38, C:0.29, G:0.12, T:0.21
Consensus pattern (83 bp):
GTCCCCAAACACAATCATAACACAGGGGCAATCATTCTCAAAGTCCTCAAGCACATTCATAACAC
AGAAGCATTAACATCAGT
Found at i:3815 original size:82 final size:80
Alignment explanation
Indices: 3648--3824 Score: 232
Period size: 82 Copynumber: 2.2 Consensus size: 80
3638 AATATCCAAA
*
3648 GTCCCCAAACACAATCCTAACACAGGGGCAACTCTTTCAAAGTCCTCAAGCACATTCATAACACA
1 GTCCCCAAACACAATCATAACACAGGGGCAACTCTTTCAAAGTCCTCAAGCACATTCATAACACA
*
3713 GAAGCATTAACATCAGT
66 GAAGCATT-A-ATCAAT
* *
3730 GTCCCCAAACACAATTATAACACAGGGTCAA-TCATTTCTCAAAGTCCTCAAGCACATTCATAAC
1 GTCCCCAAACACAATCATAACACAGGGGCAACTC--TT-TCAAAGTCCTCAAGCACATTCATAAC
*
3794 ACAGAGGCATCT-ATCAAT
63 ACAGAAGCAT-TAATCAAT
*
3812 GTCCCTAAACACA
1 GTCCCCAAACACA
3825 TGTAACATAA
Statistics
Matches: 85, Mismatches: 6, Indels: 8
0.86 0.06 0.08
Matches are distributed among these distances:
81 2 0.02
82 45 0.53
83 2 0.02
84 35 0.41
85 1 0.01
ACGTcount: A:0.38, C:0.30, G:0.11, T:0.21
Consensus pattern (80 bp):
GTCCCCAAACACAATCATAACACAGGGGCAACTCTTTCAAAGTCCTCAAGCACATTCATAACACA
GAAGCATTAATCAAT
Found at i:6806 original size:19 final size:19
Alignment explanation
Indices: 6782--6820 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
6772 TTGGCAGAAA
*
6782 CTTCATCTTCTTTAACCTT
1 CTTCATCTTCTTCAACCTT
6801 CTTCATCTTCTTCAACCTT
1 CTTCATCTTCTTCAACCTT
6820 C
1 C
6821 AAACCCTCTC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.15, C:0.36, G:0.00, T:0.49
Consensus pattern (19 bp):
CTTCATCTTCTTCAACCTT
Found at i:7186 original size:103 final size:103
Alignment explanation
Indices: 7000--7207 Score: 344
Period size: 103 Copynumber: 2.0 Consensus size: 103
6990 CCACTTTGCC
*
7000 CCCTGAAATTGTAAAATCATGTCAATCCCTCCCTTCACTTCACGGATTCCATTAAGTCCCACAAA
1 CCCTGAAATTGTAAAATCAAGTCAATCCCTCCCTTCACTTCACGGATTCCATTAAGTCCCACAAA
* *
7065 ATTTGCTGACGTGACAAACTTTTGCTAACGTGGCACTT
66 ATTTGCTGACCTGACAAACTTATGCTAACGTGGCACTT
* *
7103 CCCTGAAATTGTAAAATCAAGTTAATCCCTTCCTTCACTTCACGGATTCCATTAAGTCCCACAAA
1 CCCTGAAATTGTAAAATCAAGTCAATCCCTCCCTTCACTTCACGGATTCCATTAAGTCCCACAAA
* * *
7168 ATTTGCTGACCTGGCAAACTTATGTTGACGTGGCACTT
66 ATTTGCTGACCTGACAAACTTATGCTAACGTGGCACTT
7206 CC
1 CC
7208 ATGTCAGCAC
Statistics
Matches: 97, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
103 97 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.30
Consensus pattern (103 bp):
CCCTGAAATTGTAAAATCAAGTCAATCCCTCCCTTCACTTCACGGATTCCATTAAGTCCCACAAA
ATTTGCTGACCTGACAAACTTATGCTAACGTGGCACTT
Found at i:14536 original size:9 final size:9
Alignment explanation
Indices: 14522--14547 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
14512 TGTTTTGGCC
14522 ATAATAAGT
1 ATAATAAGT
14531 ATAATAAGT
1 ATAATAAGT
14540 ATAATAAG
1 ATAATAAG
14548 CATACTTAGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.58, C:0.00, G:0.12, T:0.31
Consensus pattern (9 bp):
ATAATAAGT
Found at i:16551 original size:2 final size:2
Alignment explanation
Indices: 16544--16570 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
16534 AAACTACTAA
16544 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
16571 ACTTAAAGCA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16618 original size:15 final size:15
Alignment explanation
Indices: 16598--16628 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
16588 ATAAAGTACC
16598 AGTATAACTAATTAA
1 AGTATAACTAATTAA
*
16613 AGTATAATTAATTAA
1 AGTATAACTAATTAA
16628 A
1 A
16629 CACATGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.03, G:0.06, T:0.35
Consensus pattern (15 bp):
AGTATAACTAATTAA
Found at i:17344 original size:16 final size:16
Alignment explanation
Indices: 17325--17383 Score: 93
Period size: 16 Copynumber: 3.7 Consensus size: 16
17315 CCCGAGCCCG
17325 ACCCGAACCCGAAAAT
1 ACCCGAACCCGAAAAT
*
17341 ACCCGAATCCGACAAA-
1 ACCCGAACCCGA-AAAT
17357 ACCCGAACCCGAAAAT
1 ACCCGAACCCGAAAAT
17373 ACCCGAACCCG
1 ACCCGAACCCG
17384 CCCAATTGCC
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
15 3 0.08
16 33 0.85
17 3 0.08
ACGTcount: A:0.41, C:0.41, G:0.14, T:0.05
Consensus pattern (16 bp):
ACCCGAACCCGAAAAT
Found at i:19326 original size:17 final size:17
Alignment explanation
Indices: 19301--19340 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
19291 TTTTCATGTT
*
19301 TCTGCTCAAATTGTTTG
1 TCTGCTCAAATTATTTG
*
19318 TCTGTTCAAATTATTTG
1 TCTGCTCAAATTATTTG
*
19335 TTTGCT
1 TCTGCT
19341 GACCGCCTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.17, C:0.15, G:0.15, T:0.53
Consensus pattern (17 bp):
TCTGCTCAAATTATTTG
Found at i:19947 original size:31 final size:31
Alignment explanation
Indices: 19906--19965 Score: 102
Period size: 31 Copynumber: 1.9 Consensus size: 31
19896 AATTGATCAA
* *
19906 ATTTTGAAACGTTTAGTACCTATTTGAGCCC
1 ATTTTAAAACGTTTAGTACCAATTTGAGCCC
19937 ATTTTAAAACGTTTAGTACCAATTTGAGC
1 ATTTTAAAACGTTTAGTACCAATTTGAGC
19966 TGGTTCAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (31 bp):
ATTTTAAAACGTTTAGTACCAATTTGAGCCC
Done.