Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014114.1 Corchorus capsularis cultivar CVL-1 contig14135, 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: 16973
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:682 original size:13 final size:13
Alignment explanation
Indices: 660--704 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
650 AATTATTGTT
660 TGCTTTATTAATC
1 TGCTTTATTAATC
* *
673 TGCTTGATTAATT
1 TGCTTTATTAATC
686 TGCTTTA-TAATC
1 TGCTTTATTAATC
*
698 TGTTTTA
1 TGCTTTA
705 GATTTAGATT
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
12 10 0.37
13 17 0.63
ACGTcount: A:0.22, C:0.11, G:0.11, T:0.56
Consensus pattern (13 bp):
TGCTTTATTAATC
Found at i:1065 original size:36 final size:36
Alignment explanation
Indices: 931--1536 Score: 658
Period size: 36 Copynumber: 16.6 Consensus size: 36
921 ACTATCAACT
*
931 GACTGACTTAATTTCAAGGAAATTAGGTAAA-AAGAA
1 GACTGGCTTAATTTCAAGGAAATTAGGTAAAGAA-AA
* *
967 GACTGATTGCTTTAATTTTAAGGAAATTAGGTAAAAGAAGACT
1 GACTG---GC-TTAATTTCAAGGAAATTAGGT-AAAGAA-A-A
* *
1010 GACTGGCTTAATTTCAAGGAAATTAAGTACAGAAAA
1 GACTGGCTTAATTTCAAGGAAATTAGGTAAAGAAAA
* * *
1046 GACTGGCTTAGTTTTAAGGAAACTAGGTAAAGAAAA
1 GACTGGCTTAATTTCAAGGAAATTAGGTAAAGAAAA
* * *
1082 GATTAGCTTAATTTCAAGGAAATTAAGTAAAGAAAA
1 GACTGGCTTAATTTCAAGGAAATTAGGTAAAGAAAA
* *
1118 GACTGGCTTAGTTTCAAGGAAACTAGGTAAAGAAAA
1 GACTGGCTTAATTTCAAGGAAATTAGGTAAAGAAAA
*
1154 GACT-GCTTAATTTCAAGGAAATTAAGTAAAAGAAGACTA
1 GACTGGCTTAATTTCAAGGAAATTAGGT-AAAGAA-A--A
* * * *
1193 -ATTGACTTACTTTCAAGGAAATTAGGTAAA-AGAA
1 GACTGGCTTAATTTCAAGGAAATTAGGTAAAGAAAA
*
1227 GACTGACTGCTTTAATTTCAAGGAAATTAGGTAAAAGAAGACT
1 GACTG---GC-TTAATTTCAAGGAAATTAGGT-AAAGAA-A-A
*
1270 GACTGGCTTAATTTCAAGGAAATTAAGTAAAGAAAA
1 GACTGGCTTAATTTCAAGGAAATTAGGTAAAGAAAA
* * *
1306 TATTGGCTTAGTTTCAAGGAAATTAGGTAAAGAAAA
1 GACTGGCTTAATTTCAAGGAAATTAGGTAAAGAAAA
* * *
1342 AACTGGTTTAATTTCAAGGAAATTAAGTAAAGAAAA
1 GACTGGCTTAATTTCAAGGAAATTAGGTAAAGAAAA
*
1378 GACTGGCTTAGTTTCAAGGAAATTAGGTAAAGAAAA
1 GACTGGCTTAATTTCAAGGAAATTAGGTAAAGAAAA
* *
1414 GACT-GCTTAATTTCAAGGAAGTTAGGTAAAG-ATA
1 GACTGGCTTAATTTCAAGGAAATTAGGTAAAGAAAA
* * *
1448 GACTGGC-TAGTTTGAAGGAAACTAGGTAAAG-AAA
1 GACTGGCTTAATTTCAAGGAAATTAGGTAAAGAAAA
*
1482 GACTGGCTTAATTTCAAGGAAATTAAGT--AG-AAA
1 GACTGGCTTAATTTCAAGGAAATTAGGTAAAGAAAA
*
1515 GACAGGCTTAATTTCAAGGAAA
1 GACTGGCTTAATTTCAAGGAAA
1537 GAAATTAAGT
Statistics
Matches: 483, Mismatches: 64, Indels: 49
0.81 0.11 0.08
Matches are distributed among these distances:
33 26 0.05
34 36 0.07
35 66 0.14
36 207 0.43
37 4 0.01
38 17 0.04
39 81 0.17
40 27 0.06
41 4 0.01
42 5 0.01
43 10 0.02
ACGTcount: A:0.43, C:0.09, G:0.21, T:0.27
Consensus pattern (36 bp):
GACTGGCTTAATTTCAAGGAAATTAGGTAAAGAAAA
Found at i:1396 original size:260 final size:261
Alignment explanation
Indices: 934--1451 Score: 878
Period size: 260 Copynumber: 2.0 Consensus size: 261
924 ATCAACTGAC
* *
934 TGACTTAATTTCAAGGAAATTAGGTAAAAAGAAGACTGATTGCTTTAATTTTAAGGAAATTAGGT
1 TGACTTAATTTCAAGGAAATTAGGTAAAAAGAAGACTGACTGCTTTAATTTCAAGGAAATTAGGT
* *
999 AAAAGAAGACTGACTGGCTTAATTTCAAGGAAATTAAGTACAGAAAAGACTGGCTTAGTTTTAAG
66 AAAAGAAGACTGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAAAAGACTGGCTTAGTTTCAAG
* *
1064 GAAACTAGGTAAAGAAAAGATTAGCTTAATTTCAAGGAAATTAAGTAAAGAAAAGACTGGCTTAG
131 GAAACTAGGTAAAGAAAAAACTAGCTTAATTTCAAGGAAATTAAGTAAAGAAAAGACTGGCTTAG
1129 TTTCAAGGAAACTAGGTAAAGAAAAGACTGCTTAATTTCAAGGAAATTAAGTAAAAGA-AGACTA
196 TTTCAAGGAAACTAGGTAAAGAAAAGACTGCTTAATTTCAAGGAAATTAAGT-AAAGATAGACTA
1193 AT
260 AT
*
1195 TGACTTACTTTCAAGGAAATTAGGT-AAAAGAAGACTGACTGCTTTAATTTCAAGGAAATTAGGT
1 TGACTTAATTTCAAGGAAATTAGGTAAAAAGAAGACTGACTGCTTTAATTTCAAGGAAATTAGGT
* *
1259 AAAAGAAGACTGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAAAATATTGGCTTAGTTTCAAG
66 AAAAGAAGACTGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAAAAGACTGGCTTAGTTTCAAG
* * *
1324 GAAATTAGGTAAAGAAAAAACTGGTTTAATTTCAAGGAAATTAAGTAAAGAAAAGACTGGCTTAG
131 GAAACTAGGTAAAGAAAAAACTAGCTTAATTTCAAGGAAATTAAGTAAAGAAAAGACTGGCTTAG
* * *
1389 TTTCAAGGAAATTAGGTAAAGAAAAGACTGCTTAATTTCAAGGAAGTTAGGTAAAGATAGACT
196 TTTCAAGGAAACTAGGTAAAGAAAAGACTGCTTAATTTCAAGGAAATTAAGTAAAGATAGACT
1452 GGCTAGTTTG
Statistics
Matches: 241, Mismatches: 15, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
259 5 0.02
260 212 0.88
261 24 0.10
ACGTcount: A:0.44, C:0.08, G:0.21, T:0.27
Consensus pattern (261 bp):
TGACTTAATTTCAAGGAAATTAGGTAAAAAGAAGACTGACTGCTTTAATTTCAAGGAAATTAGGT
AAAAGAAGACTGACTGGCTTAATTTCAAGGAAATTAAGTAAAGAAAAGACTGGCTTAGTTTCAAG
GAAACTAGGTAAAGAAAAAACTAGCTTAATTTCAAGGAAATTAAGTAAAGAAAAGACTGGCTTAG
TTTCAAGGAAACTAGGTAAAGAAAAGACTGCTTAATTTCAAGGAAATTAAGTAAAGATAGACTAA
T
Found at i:1634 original size:19 final size:19
Alignment explanation
Indices: 1573--1634 Score: 56
Period size: 19 Copynumber: 3.2 Consensus size: 19
1563 TTCAGGGTAA
*
1573 TTAAGTGGAATAAAAGAAC
1 TTAAGTAGAATAAAAGAAC
* *
1592 TTAATTA-ATCTAAAAAGAGA-
1 TTAAGTAGA-AT-AAAAGA-AC
1612 TTAAGTAGAATAAAAGAAC
1 TTAAGTAGAATAAAAGAAC
1631 TTAA
1 TTAA
1635 TCTAAAAAGA
Statistics
Matches: 33, Mismatches: 5, Indels: 10
0.69 0.10 0.21
Matches are distributed among these distances:
18 2 0.06
19 16 0.48
20 13 0.39
21 2 0.06
ACGTcount: A:0.55, C:0.05, G:0.15, T:0.26
Consensus pattern (19 bp):
TTAAGTAGAATAAAAGAAC
Found at i:1642 original size:35 final size:36
Alignment explanation
Indices: 1572--1653 Score: 121
Period size: 35 Copynumber: 2.2 Consensus size: 36
1562 ATTCAGGGTA
*
1572 ATTAAGTGGAATAAAAGAACTTAATTAATCTAAAAAGAG
1 ATTAAGTAGAATAAAAGAAC---ATTAATCTAAAAAGAG
1611 ATTAAGTAGAATAAAAGAAC-TTAATCTAAAAAGAG
1 ATTAAGTAGAATAAAAGAACATTAATCTAAAAAGAG
1646 ATTAAGTA
1 ATTAAGTA
1654 AAACAATAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
35 23 0.55
39 19 0.45
ACGTcount: A:0.55, C:0.05, G:0.15, T:0.26
Consensus pattern (36 bp):
ATTAAGTAGAATAAAAGAACATTAATCTAAAAAGAG
Found at i:1650 original size:16 final size:16
Alignment explanation
Indices: 1595--1650 Score: 51
Period size: 16 Copynumber: 3.3 Consensus size: 16
1585 AAAGAACTTA
1595 ATTAATCTAAAAAGAG
1 ATTAATCTAAAAAGAG
* *
1611 ATTAA-GTAGAATAAAAG
1 ATTAATCTA-AA-AAGAG
1628 AACTTAATCTAAAAAGAG
1 -A-TTAATCTAAAAAGAG
1646 ATTAA
1 ATTAA
1651 GTAAAACAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 10
0.69 0.09 0.22
Matches are distributed among these distances:
15 2 0.06
16 11 0.35
17 5 0.16
18 5 0.16
19 6 0.19
20 2 0.06
ACGTcount: A:0.57, C:0.05, G:0.12, T:0.25
Consensus pattern (16 bp):
ATTAATCTAAAAAGAG
Found at i:7092 original size:15 final size:15
Alignment explanation
Indices: 7072--7101 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
7062 AATTACCTTC
*
7072 TCCTGCTATAATTAG
1 TCCTGCCATAATTAG
7087 TCCTGCCATAATTAG
1 TCCTGCCATAATTAG
7102 CTGCACTAAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.27, C:0.23, G:0.13, T:0.37
Consensus pattern (15 bp):
TCCTGCCATAATTAG
Found at i:9760 original size:24 final size:24
Alignment explanation
Indices: 9733--9785 Score: 88
Period size: 24 Copynumber: 2.2 Consensus size: 24
9723 TCTGGCAACA
* *
9733 AAAATTGATCAAACTTAGTGGGCC
1 AAAACTGATCAAACTTAGTGAGCC
9757 AAAACTGATCAAACTTAGTGAGCC
1 AAAACTGATCAAACTTAGTGAGCC
9781 AAAAC
1 AAAAC
9786 GAAATAACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.43, C:0.19, G:0.17, T:0.21
Consensus pattern (24 bp):
AAAACTGATCAAACTTAGTGAGCC
Found at i:15830 original size:25 final size:25
Alignment explanation
Indices: 15796--15963 Score: 273
Period size: 25 Copynumber: 6.7 Consensus size: 25
15786 AATTTGCATA
15796 TAGCGGCGTCCAGACGCCACTATTT
1 TAGCGGCGTCCAGACGCCACTATTT
15821 TAGCGGCGTCCAGACGCCACTATTT
1 TAGCGGCGTCCAGACGCCACTATTT
15846 TAGCGGCGTCCAGACGCCACTATTT
1 TAGCGGCGTCCAGACGCCACTATTT
* *
15871 TAGCGGCGTCAAGACGCCACTACTT
1 TAGCGGCGTCCAGACGCCACTATTT
*
15896 TAGCGGCGTCTAGACGCCACTATTTT
1 TAGCGGCGTCCAGACGCCACTA-TTT
* *
15922 TAGAGGCGTCTAGACGCCACTATTT
1 TAGCGGCGTCCAGACGCCACTATTT
*
15947 TAGCGGCGTCTAGACGC
1 TAGCGGCGTCCAGACGC
15964 TGCTACTTAT
Statistics
Matches: 136, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
25 113 0.83
26 23 0.17
ACGTcount: A:0.21, C:0.30, G:0.25, T:0.24
Consensus pattern (25 bp):
TAGCGGCGTCCAGACGCCACTATTT
Found at i:16074 original size:32 final size:31
Alignment explanation
Indices: 16038--16108 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 31
16028 ACTATGGCGC
16038 GGCGTTTGGATATTTAGACGCCACTAAATA-AG
1 GGCGTTT-GATATTTAGACGCCACTAAA-AGAG
* * *
16070 GGCGTCTTGTTCTTTAGACGCCGCTAAAAGAG
1 GGCGT-TTGATATTTAGACGCCACTAAAAGAG
16102 GGCGTTT
1 GGCGTTT
16109 TCTTTTCATG
Statistics
Matches: 34, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
31 3 0.09
32 29 0.85
33 2 0.06
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (31 bp):
GGCGTTTGATATTTAGACGCCACTAAAAGAG
Found at i:16895 original size:32 final size:33
Alignment explanation
Indices: 16833--16895 Score: 76
Period size: 32 Copynumber: 1.9 Consensus size: 33
16823 TTGAAAAATT
*
16833 ATTTTTGAACTAAAAAACAGATTTCGTTTTTTA
1 ATTTTTGAACTAAAAAACAGATTTCATTTTTTA
* *
16866 ATTTTT-AATTAAAAAACCA-ATTTTATTTTT
1 ATTTTTGAACTAAAAAA-CAGATTTCATTTTT
16896 GAAAATATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
32 18 0.69
33 8 0.31
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.49
Consensus pattern (33 bp):
ATTTTTGAACTAAAAAACAGATTTCATTTTTTA
Done.