Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010624.1 Corchorus capsularis cultivar CVL-1 contig10645, 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: 51581
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:7648 original size:31 final size:32
Alignment explanation
Indices: 7613--7680 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 32
7603 TAAGTTATTG
*
7613 CAAATTAAA-ATAAAT-TAAGCATTAAATTAAA
1 CAAATTAAATA-AAATGAAAGCATTAAATTAAA
* *
7644 CAAA-TAATTAAAATGAAAGCCTTAAATTAAA
1 CAAATTAAATAAAATGAAAGCATTAAATTAAA
7675 CAAATT
1 CAAATT
7681 TAAAGCTGAT
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
30 7 0.23
31 23 0.74
32 1 0.03
ACGTcount: A:0.59, C:0.09, G:0.04, T:0.28
Consensus pattern (32 bp):
CAAATTAAATAAAATGAAAGCATTAAATTAAA
Found at i:7919 original size:2 final size:2
Alignment explanation
Indices: 7912--7938 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
7902 CACTTTAAGT
7912 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
7939 TTTGATTAAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22682 original size:2 final size:2
Alignment explanation
Indices: 22675--22707 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
22665 CCAATAAATT
22675 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
22708 TATTAATTTG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:29903 original size:130 final size:128
Alignment explanation
Indices: 29669--30067 Score: 524
Period size: 130 Copynumber: 3.1 Consensus size: 128
29659 AACAATAGTA
* * * * *
29669 ATTTTGATGGTATTTTACCCAACGACTTTTTCAATTGTTGCCAATGCTTACAGTTTTTGTAACAA
1 ATTTTGATGGTATTTTACACAAC-ACTTTTTTAGTTGTT-TCAATGCTTACAATTTTTGTAACAA
* * * *
29734 AAAAAACAAAGTCGTTGCGAAATCATAATTTATTCGTAACAATTTTATAAAATCGTTGCCTAAGT
64 CAAAAACAAAGTCGTTGCGATATCATAA-ATATTCGTAACAATTTTATAAAAACGTTGCCTAAGT
29799 G
128 G
* * * * *
29800 ATTTTGACGATATTTTACGCAACACTTTTTTAGTCGTTTACAATGCTTACAATTTTCGTAACAAC
1 ATTTTGATGGTATTTTACACAACACTTTTTTAGTTGTTT-CAATGCTTACAATTTTTGTAACAAC
* *
29865 AAAAACAAAGTCGTTGCGATATCATAAACTATTCGTAACAACTTTATAAAAACGTTGTCTAAGTG
65 AAAAACAAAGTCGTTGCGATATCATAAA-TATTCGTAACAATTTTATAAAAACGTTGCCTAAGTG
*
29930 ATTTTGATGGTATTTTACACAACACTTTTTTAGTTGTTGTCAATGCTTATAATTTTTGTAACAAC
1 ATTTTGATGGTATTTTACACAACACTTTTTTAGTTGTT-TCAATGCTTACAATTTTTGTAACAAC
**
29995 AAAAACAAAGTCGTTATGATATCAT-AA-A-----AACAATTTTATAAAAACGTTGCCTAAGTG
65 AAAAACAAAGTCGTTGCGATATCATAAATATTCGTAACAATTTTATAAAAACGTTGCCTAAGTG
30052 ATTTTGATGGTATTTT
1 ATTTTGATGGTATTTT
30068 TTTTTGCAGT
Statistics
Matches: 240, Mismatches: 25, Indels: 15
0.86 0.09 0.05
Matches are distributed among these distances:
122 43 0.18
127 1 0.00
129 2 0.01
130 173 0.72
131 21 0.09
ACGTcount: A:0.35, C:0.14, G:0.13, T:0.38
Consensus pattern (128 bp):
ATTTTGATGGTATTTTACACAACACTTTTTTAGTTGTTTCAATGCTTACAATTTTTGTAACAACA
AAAACAAAGTCGTTGCGATATCATAAATATTCGTAACAATTTTATAAAAACGTTGCCTAAGTG
Found at i:39447 original size:53 final size:53
Alignment explanation
Indices: 39359--39461 Score: 134
Period size: 53 Copynumber: 1.9 Consensus size: 53
39349 GACGTGGCAC
* ** *
39359 GCCACGTGTACCAAAAAGTGACATGTGGCACGCCACATATATCAAAAAGTCGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATATACCAAAAAGTCGT
* * * *
39412 GCCACATGTACCAAAAAGTGACACATGTCATGCCACGTGTACCAAAAAGT
1 GCCACATGTACCAAAAAGTGACACATGGCACGCCACATATACCAAAAAGT
39462 GACACGTGAC
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
53 42 1.00
ACGTcount: A:0.37, C:0.25, G:0.19, T:0.18
Consensus pattern (53 bp):
GCCACATGTACCAAAAAGTGACACATGGCACGCCACATATACCAAAAAGTCGT
Found at i:39453 original size:31 final size:31
Alignment explanation
Indices: 39411--39540 Score: 170
Period size: 31 Copynumber: 4.2 Consensus size: 31
39401 CAAAAAGTCG
* *
39411 TGCCACATGTACCAAAAAGTGACACATGTCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
* *
39442 TGCCACGTGTACCAAAAAGTGACACGTGACA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
** *
39473 TGCCACATGTTTCAAAAAGTGGCACGTGGCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
** *
39504 TGCCACATGTTTCAAAAAGTGGCACGTGGCA
1 TGCCACATGTACCAAAAAGTGACACGTGGCA
39535 TGCCAC
1 TGCCAC
39541 GTGCACAAAA
Statistics
Matches: 91, Mismatches: 8, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 91 1.00
ACGTcount: A:0.32, C:0.25, G:0.22, T:0.20
Consensus pattern (31 bp):
TGCCACATGTACCAAAAAGTGACACGTGGCA
Found at i:40642 original size:99 final size:104
Alignment explanation
Indices: 40445--40653 Score: 302
Period size: 109 Copynumber: 2.0 Consensus size: 104
40435 ATTAATCGGA
* * *
40445 TATATTAATTTTTCAACAAAATAATCCGACTTTACATTATAAATTTTAAGGCTGGGATATTCGGA
1 TATATTAATTCTTCAACAAAATAATCCGACTTTACATTATAAATTATAAGGCTGAGATATTCGG-
40510 AAAAAGAAAACAAAAAAATTGATTTAAGGATATTGTTAATTAAT
65 ---AAGAAAACAAAAAAATTGA-TTAAGGATATTGTTAATTAAT
*
40554 TATATTAATTCTTGAACAAAATAATCCGACTTTACATTATAAATTATAAGGCTGAGATATTC-G-
1 TATATTAATTCTTCAACAAAATAATCCGACTTTACATTATAAATTATAAGGCTGAGATATTCGGA
40617 A-AAAA-AAAAAAATTGA-TAAGGATATTGTTAATTAAT
66 AGAAAACAAAAAAATTGATTAAGGATATTGTTAATTAAT
40653 T
1 T
40654 TTTACACTAT
Statistics
Matches: 96, Mismatches: 4, Indels: 10
0.87 0.04 0.09
Matches are distributed among these distances:
99 21 0.22
101 11 0.11
102 4 0.04
103 1 0.01
108 1 0.01
109 58 0.60
ACGTcount: A:0.45, C:0.08, G:0.11, T:0.35
Consensus pattern (104 bp):
TATATTAATTCTTCAACAAAATAATCCGACTTTACATTATAAATTATAAGGCTGAGATATTCGGA
AGAAAACAAAAAAATTGATTAAGGATATTGTTAATTAAT
Found at i:41357 original size:31 final size:31
Alignment explanation
Indices: 41322--41380 Score: 100
Period size: 31 Copynumber: 1.9 Consensus size: 31
41312 GTTAGATAAG
*
41322 TAAGGATATAATAGGCATTTCAAAAGTTAAA
1 TAAGGATACAATAGGCATTTCAAAAGTTAAA
*
41353 TAAGGGTACAATAGGCATTTCAAAAGTT
1 TAAGGATACAATAGGCATTTCAAAAGTT
41381 TCTCAAAACT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.44, C:0.08, G:0.19, T:0.29
Consensus pattern (31 bp):
TAAGGATACAATAGGCATTTCAAAAGTTAAA
Found at i:41535 original size:31 final size:31
Alignment explanation
Indices: 41491--41549 Score: 91
Period size: 31 Copynumber: 1.9 Consensus size: 31
41481 GTTAGATAAG
* *
41491 TAAGGATATAATAGGTATTTTAAAAGTTAAA
1 TAAGGATACAATAGGTATTTCAAAAGTTAAA
*
41522 TAAGGGTACAATAGGTATTTCAAAAGTT
1 TAAGGATACAATAGGTATTTCAAAAGTT
41550 TCTCAAAACT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.44, C:0.03, G:0.19, T:0.34
Consensus pattern (31 bp):
TAAGGATACAATAGGTATTTCAAAAGTTAAA
Found at i:42606 original size:21 final size:21
Alignment explanation
Indices: 42582--42623 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
42572 GGTTTAACAT
* *
42582 GGTTTGACCATGAAACTTTGG
1 GGTTTGACCATCAAAATTTGG
42603 GGTTTGACCATCAAAATTTGG
1 GGTTTGACCATCAAAATTTGG
42624 ACAAAAACAC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.26, C:0.14, G:0.26, T:0.33
Consensus pattern (21 bp):
GGTTTGACCATCAAAATTTGG
Found at i:42614 original size:100 final size:101
Alignment explanation
Indices: 42441--42702 Score: 427
Period size: 100 Copynumber: 2.6 Consensus size: 101
42431 ATATACTTTA
* * * *
42441 GCAAAAATATGGTGAGTGCTTCAATTGATAAGGTTTAACATGGTTTAAGTATCAAACTTTGGGGT
1 GCAAAAATGTGGTGGGTGCTTCAATTGATAAGGTTTAACATGGTTTGACTATCAAACTTTGGGGT
42506 TTGACCATCAAAATTTGG-CAAAAACACAGTTTTGG
66 TTGACCATCAAAATTTGGACAAAAACACAGTTTTGG
* *
42541 GCAAAAATGTGGTGGGTGCTTCAATTGATAAGGTTTAACATGGTTTGACCATGAAACTTTGGGGT
1 GCAAAAATGTGGTGGGTGCTTCAATTGATAAGGTTTAACATGGTTTGACTATCAAACTTTGGGGT
42606 TTGACCATCAAAATTTGGACAAAAACACAGTTTTGG
66 TTGACCATCAAAATTTGGACAAAAACACAGTTTTGG
* * * *
42642 GTAAAAATGTGGTGGGTGCCTCAATTAATAAGGTTTAACATGGTTTGACTATTAAACTTTG
1 GCAAAAATGTGGTGGGTGCTTCAATTGATAAGGTTTAACATGGTTTGACTATCAAACTTTG
42703 ACATTTGGCT
Statistics
Matches: 150, Mismatches: 11, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
100 77 0.51
101 73 0.49
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.32
Consensus pattern (101 bp):
GCAAAAATGTGGTGGGTGCTTCAATTGATAAGGTTTAACATGGTTTGACTATCAAACTTTGGGGT
TTGACCATCAAAATTTGGACAAAAACACAGTTTTGG
Found at i:42709 original size:21 final size:21
Alignment explanation
Indices: 42684--42829 Score: 139
Period size: 21 Copynumber: 7.0 Consensus size: 21
42674 GTTTAACATG
*
42684 GTTTGACTATTAAACTTTGAC
1 GTTTGACTATCAAACTTTGAC
* *
42705 ATTTGGCTATCAAACTTTGAC
1 GTTTGACTATCAAACTTTGAC
* *
42726 GTTTGGCTATCAAACTTTGAG
1 GTTTGACTATCAAACTTTGAC
* **
42747 GTTTGACCATCAAACTTTGGG
1 GTTTGACTATCAAACTTTGAC
** **
42768 GTTCAACTATCAAACTTTGGG
1 GTTTGACTATCAAACTTTGAC
* **
42789 GTTTGACTATCAAATTTTGGG
1 GTTTGACTATCAAACTTTGAC
* *
42810 GTTTGACCATCAAAATTTGA
1 GTTTGACTATCAAACTTTGA
42830 GTGACTGAAA
Statistics
Matches: 108, Mismatches: 17, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 108 1.00
ACGTcount: A:0.27, C:0.16, G:0.19, T:0.38
Consensus pattern (21 bp):
GTTTGACTATCAAACTTTGAC
Found at i:43993 original size:21 final size:21
Alignment explanation
Indices: 43950--43993 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
43940 AGCCGGACGG
* * * *
43950 TTTGGTCGTAATTAAATTGGA
1 TTTGGTCCTAATAAAACTAGA
43971 TTTGGTCCTAATAAAACTAGA
1 TTTGGTCCTAATAAAACTAGA
43992 TT
1 TT
43994 CTAGAGAGTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.32, C:0.09, G:0.18, T:0.41
Consensus pattern (21 bp):
TTTGGTCCTAATAAAACTAGA
Found at i:44976 original size:20 final size:17
Alignment explanation
Indices: 44953--44996 Score: 52
Period size: 17 Copynumber: 2.4 Consensus size: 17
44943 CAATGTTTAC
44953 TGGTGAAGGACAATGCTAGA
1 TGGTGAA-GA-AATGC-AGA
*
44973 TGGTGAAGAATTGCAGA
1 TGGTGAAGAAATGCAGA
44990 TGGTGAA
1 TGGTGAA
44997 TTCTCATGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
17 10 0.43
18 4 0.17
19 2 0.09
20 7 0.30
ACGTcount: A:0.34, C:0.07, G:0.36, T:0.23
Consensus pattern (17 bp):
TGGTGAAGAAATGCAGA
Found at i:50707 original size:42 final size:40
Alignment explanation
Indices: 50661--50775 Score: 135
Period size: 39 Copynumber: 2.8 Consensus size: 40
50651 CTCTCTCGCC
* *
50661 AAAGTCCCAAAACACATATAACACAGGGGCAATTCTCCTTCT
1 AAAGTCCC-AAACACATATAACACAGGGGCAATTCT-ATACT
* *
50703 AAAGTCCTCAAACACATATAACACAGAGG-TA-TCTATACT
1 AAAGTCC-CAAACACATATAACACAGGGGCAATTCTATACT
*
50742 AAAGTCCCTAAACACATATAACACAAGGGCAATT
1 AAAGTCCC-AAACACATATAACACAGGGGCAATT
50776 TTCTTCTTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 9
0.79 0.09 0.12
Matches are distributed among these distances:
38 1 0.02
39 28 0.45
40 4 0.06
41 2 0.03
42 26 0.42
43 1 0.02
ACGTcount: A:0.43, C:0.25, G:0.11, T:0.21
Consensus pattern (40 bp):
AAAGTCCCAAACACATATAACACAGGGGCAATTCTATACT
Done.