Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014229.1 Corchorus capsularis cultivar CVL-1 contig14250, 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: 28019
ACGTcount: A:0.34, C:0.16, G:0.18, T:0.33
Found at i:891 original size:15 final size:15
Alignment explanation
Indices: 837--893 Score: 53
Period size: 15 Copynumber: 3.6 Consensus size: 15
827 TCCGAACCGT
*
837 ATGACCCGAAACCGAAA
1 ATGACCCG-AACC-CAA
*
854 ACGACCC-AACCCAGA
1 ATGACCCGAACCCA-A
869 ATTGACCCGAACCCAA
1 A-TGACCCGAACCCAA
885 ATGACCCGA
1 ATGACCCGA
894 CATTTGAACG
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
14 1 0.03
15 14 0.41
16 7 0.21
17 12 0.35
ACGTcount: A:0.40, C:0.37, G:0.16, T:0.07
Consensus pattern (15 bp):
ATGACCCGAACCCAA
Found at i:3794 original size:44 final size:46
Alignment explanation
Indices: 3744--3829 Score: 131
Period size: 46 Copynumber: 1.9 Consensus size: 46
3734 AGAGTAATGT
*
3744 AATTACTAAAA-ATCCCTATCCC-GAATTAATGATGAGCTGGGTGG
1 AATTACTAAAAGATCCCTACCCCAGAATTAATGATGAGCTGGGTGG
* *
3788 AATTACTAAAAGATTCCTACCCCAGTATTAATGATGAGCTGG
1 AATTACTAAAAGATCCCTACCCCAGAATTAATGATGAGCTGG
3830 AGAAGTAATC
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
44 11 0.30
45 9 0.24
46 17 0.46
ACGTcount: A:0.35, C:0.19, G:0.19, T:0.28
Consensus pattern (46 bp):
AATTACTAAAAGATCCCTACCCCAGAATTAATGATGAGCTGGGTGG
Found at i:4312 original size:16 final size:17
Alignment explanation
Indices: 4291--4332 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
4281 CTCTCTAAAA
4291 TGAGAGTTTCTCT-CTT
1 TGAGAGTTTCTCTCCTT
**
4307 TGAGAGCATCTCTCCTT
1 TGAGAGTTTCTCTCCTT
*
4324 TGTGAGTTT
1 TGAGAGTTT
4333 TACTCATTTT
Statistics
Matches: 20, Mismatches: 5, Indels: 1
0.77 0.19 0.04
Matches are distributed among these distances:
16 11 0.55
17 9 0.45
ACGTcount: A:0.14, C:0.19, G:0.21, T:0.45
Consensus pattern (17 bp):
TGAGAGTTTCTCTCCTT
Found at i:8552 original size:35 final size:35
Alignment explanation
Indices: 8513--9066 Score: 795
Period size: 35 Copynumber: 15.9 Consensus size: 35
8503 AGTAATAAGA
*
8513 AACTTAATTCAGGGTAATTAAGTAAGTCAATAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
8548 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
*
8583 AACTTAATTCAGGGCAATTAAGTAAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
*
8618 AACTTAATTCAGGGTAATTAAGTAACTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
8653 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
*
8688 AACTTAATTCAGGGTAATTAAGTAAGTCAGTTATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
* *
8723 AACTTAATTCAGGGTAATTAAATAAGTCGGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
*
8758 AACTTAATTCGGGGTAATTAAGTAAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
*
8793 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAACC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
8828 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
*
8863 AACTTAATTCAGGGTAATTAAGTATGTCAGTGAAT-
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGT-AATC
* *
8898 AACTTAATTCAGGGTAATTAAGTAAGT-AATAGGT-
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTA-ATC
8932 AACTTAATTCAGGGTAA-T---TAAGTCAGTAAGT-
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAA-TC
* * *
8963 AGCTTAATTCAAGGTAATTAAGTAAGTCAGCTAGT-
1 AACTTAATTCAGGGTAATTAAGTAAGTCAG-TAATC
* * * * *
8998 AATTTGATTCTGGGTAATTAAGTAAAGTAAGTCAGT-
1 AACTTAATTCAGGGTAATTAAGT-AAGTCAGT-AATC
* *
9034 AACTTAATTAAGGGTAATTAAGTAAGTAAGTAA
1 AACTTAATTCAGGGTAATTAAGTAAGTCAGTAA
9067 GTCAGTCAGT
Statistics
Matches: 473, Mismatches: 35, Indels: 23
0.89 0.07 0.04
Matches are distributed among these distances:
30 5 0.01
31 19 0.04
32 1 0.00
33 2 0.00
34 21 0.04
35 392 0.83
36 33 0.07
ACGTcount: A:0.40, C:0.10, G:0.18, T:0.32
Consensus pattern (35 bp):
AACTTAATTCAGGGTAATTAAGTAAGTCAGTAATC
Found at i:12672 original size:14 final size:14
Alignment explanation
Indices: 12653--12682 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
12643 AAATCAAATC
12653 ACATGTAAAATATT
1 ACATGTAAAATATT
*
12667 ACATGTAAAGTATT
1 ACATGTAAAATATT
12681 AC
1 AC
12683 TAGTGACAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (14 bp):
ACATGTAAAATATT
Found at i:12877 original size:62 final size:62
Alignment explanation
Indices: 12780--12916 Score: 247
Period size: 62 Copynumber: 2.2 Consensus size: 62
12770 TTTTCCCCCT
* *
12780 TTTTATCTTTCAAACCAATGGCAGTTATCTCTCTTGACTTCATTTCTCCCGGTCCTTTGTTA
1 TTTTATCTTTTAAACCAATGGCAGTTATCTCTCTTGACTTCATTTCTCCCGGACCTTTGTTA
12842 TTTTATCTTTTAAACCAATGGCAGTTATCTCTCTTGACTTCATTTCTCCCGGACCTTTGTTA
1 TTTTATCTTTTAAACCAATGGCAGTTATCTCTCTTGACTTCATTTCTCCCGGACCTTTGTTA
12904 TTTTATCATTTTA
1 TTTTATC-TTTTA
12917 TGCATGGAAT
Statistics
Matches: 72, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
62 67 0.93
63 5 0.07
ACGTcount: A:0.19, C:0.23, G:0.10, T:0.47
Consensus pattern (62 bp):
TTTTATCTTTTAAACCAATGGCAGTTATCTCTCTTGACTTCATTTCTCCCGGACCTTTGTTA
Found at i:15295 original size:2 final size:2
Alignment explanation
Indices: 15288--15312 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15278 CATCTTTTAA
15288 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 A
15313 AGATATTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18953 original size:18 final size:19
Alignment explanation
Indices: 18923--18973 Score: 68
Period size: 18 Copynumber: 2.6 Consensus size: 19
18913 CCTATGCTTA
18923 TATTATATATATATATATATT
1 TATTAT-TATATATATATA-T
18944 TATTATTATAT-TATATAT
1 TATTATTATATATATATAT
*
18962 TATTATAATATA
1 TATTATTATATA
18974 ATACTAGTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
18 11 0.39
19 6 0.21
20 5 0.18
21 6 0.21
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATTATTATATATATATAT
Found at i:18964 original size:15 final size:15
Alignment explanation
Indices: 18920--18973 Score: 67
Period size: 15 Copynumber: 3.7 Consensus size: 15
18910 TAGCCTATGC
18920 TTATATTATATA-TA
1 TTATATTATATATTA
*
18934 -TATATATATTTATTA
1 TTATAT-TATATATTA
18949 TTATATTATATATTA
1 TTATATTATATATTA
*
18964 TTATAATATA
1 TTATATTATA
18974 ATACTAGTAA
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
13 5 0.15
14 5 0.15
15 19 0.56
16 5 0.15
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (15 bp):
TTATATTATATATTA
Found at i:23930 original size:221 final size:221
Alignment explanation
Indices: 23487--23928 Score: 721
Period size: 221 Copynumber: 2.0 Consensus size: 221
23477 AGCAATTAAT
*
23487 TAAAAACCTTAAACATTAATTAAAAACAATCAAGGAAGAGAAATGTGTAATTACAAAAAGGGTAG
1 TAAAAACCTTAAACATTAATTAAAAACAATCAAGGAAGAGAAATGTGTAATTACAAAAAGGATAG
* * * * *
23552 AAGGAAAAGGAATGGGGGGAAAGTCATAGATGTGCTTTTTAGTCATCCGAAAAGTGAGAAAAGAC
66 AAGGAAAAGGAATGGGGGGAAACTCATAAAGGGGCTTTTTAGTCATCCAAAAAGTGAGAAAAGAC
* * * *
23617 CAAAAATAGTCAAAAGGTGGCACCATATTAATCCTCAATTTGGTCATTTAGTAATTTTCATAGTA
131 CAAAAATAATCAAAAGGTAGCACCACATTAATCCTCAATTTGGTCATTTAATAATTTTCATAGTA
23682 GTTAAAAATAATATATAGTATATATA
196 GTTAAAAATAATATATAGTATATATA
* *
23708 TAAAAACCTTAAACATTAATTAAAAACAATCAAGGAAGGGAAATGTGTAATTACAAAAAATGATA
1 TAAAAACCTTAAACATTAATTAAAAACAATCAAGGAAGAGAAATGTGTAATTAC-AAAAAGGATA
*
23773 GAAGGAAAAGGAAT-GGGGGAAACTCATAAAGGGGCTTTTTAGTCATCCAAAAAGTGAGAAAATA
65 GAAGGAAAAGGAATGGGGGGAAACTCATAAAGGGGCTTTTTAGTCATCCAAAAAGTGAGAAAAGA
23837 CCAAAAATAATCAAAAGGTAGCACCACATTAATCCTCAATTTGGT-ATTTAATAA-TTTCATAGT
130 CCAAAAATAATCAAAAGGTAGCACCACATTAATCCTCAATTTGGTCATTTAATAATTTTCATAGT
23900 AGTTAAAAA-AATATAATAGTATATATA
195 AGTTAAAAATAATAT-ATAGTATATATA
23927 TA
1 TA
23929 TATATATATA
Statistics
Matches: 206, Mismatches: 13, Indels: 6
0.92 0.06 0.03
Matches are distributed among these distances:
218 5 0.02
219 32 0.16
220 8 0.04
221 139 0.67
222 22 0.11
ACGTcount: A:0.47, C:0.10, G:0.17, T:0.26
Consensus pattern (221 bp):
TAAAAACCTTAAACATTAATTAAAAACAATCAAGGAAGAGAAATGTGTAATTACAAAAAGGATAG
AAGGAAAAGGAATGGGGGGAAACTCATAAAGGGGCTTTTTAGTCATCCAAAAAGTGAGAAAAGAC
CAAAAATAATCAAAAGGTAGCACCACATTAATCCTCAATTTGGTCATTTAATAATTTTCATAGTA
GTTAAAAATAATATATAGTATATATA
Found at i:26522 original size:91 final size:91
Alignment explanation
Indices: 26367--26590 Score: 344
Period size: 91 Copynumber: 2.5 Consensus size: 91
26357 GCTTAAGAAG
* * *
26367 ATTGAAAGAAGATCCACGTCTGTGGAAAATTCTTCTTTCAAAGAAGACTCAATTATTGGAGAATT
1 ATTGAAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAAGAAGACTCAATTATTGAAGAATT
* *
26432 ACTGAAGACCCAGTTATTTGGG-AGTT
66 ACGGAAGACCCAGTTA-TTGGGAAATT
* *
26458 ATTGAAAGAAGATCCATGTATGTGGAGTATTCTTCTTTCAAAGAAGA-TACAATTATTGAAGAAT
1 ATTGAAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAAGAAGACT-CAATTATTGAAGAAT
26522 TACGGAAGACCCAGTTATTGGGAAATT
65 TACGGAAGACCCAGTTATTGGGAAATT
*
26549 ATTGAAAGAAGATCCACGTATGTGGAGGATTCTTCTTTCAAA
1 ATTGAAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAA
26591 TTATCAAAGA
Statistics
Matches: 122, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
90 6 0.05
91 116 0.95
ACGTcount: A:0.35, C:0.13, G:0.21, T:0.31
Consensus pattern (91 bp):
ATTGAAAGAAGATCCACGTATGTGGAGAATTCTTCTTTCAAAGAAGACTCAATTATTGAAGAATT
ACGGAAGACCCAGTTATTGGGAAATT
Done.