Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015615.1 Corchorus capsularis cultivar CVL-1 contig15636, 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: 31684
ACGTcount: A:0.32, C:0.18, G:0.21, T:0.29
Found at i:434 original size:52 final size:54
Alignment explanation
Indices: 371--613 Score: 262
Period size: 53 Copynumber: 4.5 Consensus size: 54
361 TAGTAGATTA
* *
371 GTTTAATTCAGAGTAATTAACCTAAGCAGTAAAAAAGAG-AAGTCAGTAAATAG
1 GTTTAATTCAGAGTAATTAACCTAAACAGTAAAAAAGAGAAAATCAGTAAATAG
* * * *
424 GTTT-ATTCAGAGTAATTAACCTAAGCGGTAAAAAGGAGAAAATTAGTAAATAG
1 GTTTAATTCAGAGTAATTAACCTAAACAGTAAAAAAGAGAAAATCAGTAAATAG
* * *
477 ATTT-ATTCAGAGTAATTAACCTAAACAGT-AAAAGGGGAAAATCAGTAAATAG
1 GTTTAATTCAGAGTAATTAACCTAAACAGTAAAAAAGAGAAAATCAGTAAATAG
* * * *
529 GTTTAATTCAGAGTTATTAGCCTAAACATTAAAAGA-AGAAAATCAGTAAGCAGTAATCG
1 GTTTAATTCAGAGTAATTAACCTAAACAGTAAAAAAGAGAAAATCAGTAA--A-T-A--G
* *
588 GTTTAATACAGAGTAATTAAGCTAAA
1 GTTTAATTCAGAGTAATTAACCTAAA
614 AAGAGTGAAA
Statistics
Matches: 161, Mismatches: 20, Indels: 12
0.83 0.10 0.06
Matches are distributed among these distances:
52 56 0.35
53 76 0.47
54 3 0.02
55 1 0.01
56 1 0.01
57 1 0.01
59 23 0.14
ACGTcount: A:0.46, C:0.09, G:0.18, T:0.26
Consensus pattern (54 bp):
GTTTAATTCAGAGTAATTAACCTAAACAGTAAAAAAGAGAAAATCAGTAAATAG
Found at i:563 original size:105 final size:105
Alignment explanation
Indices: 376--577 Score: 273
Period size: 105 Copynumber: 1.9 Consensus size: 105
366 GATTAGTTTA
* *
376 ATTCAGAGTAATTAACCTAAGCAGTAAAAAAGAGAAGTCAGTAAATAGGTTTATTCAGAGTAATT
1 ATTCAGAGTAATTAACCTAAACAGTAAAAAAGAGAAATCAGTAAATAGGTTTATTCAGAGTAATT
* * * *
441 AACCTAAGCGGTAAAAAGGAGAAAATTAGTAAATAGATTT
66 AACCTAAACGATAAAAAGAAGAAAATCAGTAAATAGATTT
* * *
481 ATTCAGAGTAATTAACCTAAACAGT-AAAAGGGGAAAATCAGTAAATAGGTTTAATTCAGAGTTA
1 ATTCAGAGTAATTAACCTAAACAGTAAAAAAGAG-AAATCAGTAAATAGGTTT-ATTCAGAGTAA
* *
545 TTAGCCTAAAC-ATTAAAAGAAGAAAATCAGTAA
64 TTAACCTAAACGATAAAAAGAAGAAAATCAGTAA
578 GCAGTAATCG
Statistics
Matches: 84, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
104 6 0.07
105 59 0.70
106 19 0.23
ACGTcount: A:0.48, C:0.09, G:0.18, T:0.25
Consensus pattern (105 bp):
ATTCAGAGTAATTAACCTAAACAGTAAAAAAGAGAAATCAGTAAATAGGTTTATTCAGAGTAATT
AACCTAAACGATAAAAAGAAGAAAATCAGTAAATAGATTT
Found at i:643 original size:22 final size:21
Alignment explanation
Indices: 617--692 Score: 76
Period size: 22 Copynumber: 3.9 Consensus size: 21
607 AGCTAAAAAG
617 AGTGAAAGTAAAAGGAGTAATT
1 AGTGAAAGTAAAA-GAGTAATT
639 AGTGAAAGTAAAAGAG----T
1 AGTGAAAGTAAAAGAGTAATT
*
656 A---AAAGTAAAAGAAGTAATC
1 AGTGAAAGTAAAAG-AGTAATT
675 AGTGAAAGTAAAAGAGTA
1 AGTGAAAGTAAAAGAGTA
693 GAAGTAAAAG
Statistics
Matches: 45, Mismatches: 1, Indels: 17
0.71 0.02 0.27
Matches are distributed among these distances:
14 10 0.22
15 2 0.04
17 2 0.04
19 1 0.02
21 7 0.16
22 23 0.51
ACGTcount: A:0.55, C:0.01, G:0.25, T:0.18
Consensus pattern (21 bp):
AGTGAAAGTAAAAGAGTAATT
Found at i:659 original size:30 final size:32
Alignment explanation
Indices: 623--745 Score: 83
Period size: 36 Copynumber: 3.7 Consensus size: 32
613 AAAGAGTGAA
*
623 AGTAAAAG-G-AGTAATTAGTGAAAGTAAAAG
1 AGTAAAAGAGAAGTAATCAGTGAAAGTAAAAG
653 AGTAAAAGTAAAAGAAGTAATCAGTGAAAGTAAAAG
1 AGTAAAAG----AGAAGTAATCAGTGAAAGTAAAAG
* * * *
689 AGTAGAAGTAAAAGAAGTAATCAGTAAAAGGGAGTAAG
1 AGT--AA--AAGAGAAGTAATCAGTGAAA-GTA-AAAG
727 AGTAAAAG-G-AGTAATCAGT
1 AGTAAAAGAGAAGTAATCAGT
746 AAATAGGTAA
Statistics
Matches: 75, Mismatches: 6, Indels: 22
0.73 0.06 0.21
Matches are distributed among these distances:
30 8 0.11
32 10 0.13
33 1 0.01
34 2 0.03
35 1 0.01
36 41 0.55
37 2 0.03
38 8 0.11
40 2 0.03
ACGTcount: A:0.54, C:0.02, G:0.26, T:0.18
Consensus pattern (32 bp):
AGTAAAAGAGAAGTAATCAGTGAAAGTAAAAG
Found at i:661 original size:36 final size:36
Alignment explanation
Indices: 612--718 Score: 169
Period size: 36 Copynumber: 3.0 Consensus size: 36
602 AATTAAGCTA
* * *
612 AAAAGAGTGAAAGTAAAAGGAGTAATTAGTGAAAGT
1 AAAAGAGTAAAAGTAAAAGAAGTAATCAGTGAAAGT
648 AAAAGAGTAAAAGTAAAAGAAGTAATCAGTGAAAGT
1 AAAAGAGTAAAAGTAAAAGAAGTAATCAGTGAAAGT
* *
684 AAAAGAGTAGAAGTAAAAGAAGTAATCAGTAAAAG
1 AAAAGAGTAAAAGTAAAAGAAGTAATCAGTGAAAG
719 GGAGTAAGAG
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
36 66 1.00
ACGTcount: A:0.57, C:0.02, G:0.24, T:0.17
Consensus pattern (36 bp):
AAAAGAGTAAAAGTAAAAGAAGTAATCAGTGAAAGT
Found at i:688 original size:72 final size:70
Alignment explanation
Indices: 612--773 Score: 168
Period size: 72 Copynumber: 2.3 Consensus size: 70
602 AATTAAGCTA
* *
612 AAAAGAGTGAAAGTAAAAGGAGTAATTAGTGAAAGTAAAAGAGTAAAAGTAAAAGAAGTAATCAG
1 AAAAGAGTGAAAGTAAAAGAAGTAATCAGT--AA--AAAAGAGTAAAAGTAAAAGAAGTAATCAG
*
677 TGAA-A-GT
62 TAAATAGGT
** * *
684 AAAAGAGT-AGAAGTAAAAGAAGTAATCAGTAAAAGGGAGTAAGAGTAAAAGGAGTAATCAGTAA
1 AAAAGAGTGA-AAGTAAAAGAAGTAATCAGTAAAAAAGAGTAAAAGTAAAAGAAGTAATCAGTAA
748 ATAGGT
65 ATAGGT
*
754 AATTAAGAGTGAAATTAAAA
1 AA--AAGAGTGAAAGTAAAA
774 AAAAAAGCAA
Statistics
Matches: 76, Mismatches: 8, Indels: 12
0.79 0.08 0.12
Matches are distributed among these distances:
68 28 0.37
69 1 0.01
70 6 0.08
71 1 0.01
72 39 0.51
73 1 0.01
ACGTcount: A:0.55, C:0.02, G:0.25, T:0.19
Consensus pattern (70 bp):
AAAAGAGTGAAAGTAAAAGAAGTAATCAGTAAAAAAGAGTAAAAGTAAAAGAAGTAATCAGTAAA
TAGGT
Found at i:716 original size:16 final size:16
Alignment explanation
Indices: 695--748 Score: 74
Period size: 16 Copynumber: 3.4 Consensus size: 16
685 AAAGAGTAGA
*
695 AGTAAAAGAAGTAATC
1 AGTAAAAGGAGTAATC
*
711 AGTAAAAGGGAGTAA-G
1 AGTAAAA-GGAGTAATC
727 AGTAAAAGGAGTAATC
1 AGTAAAAGGAGTAATC
743 AGTAAA
1 AGTAAA
749 TAGGTAATTA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
15 7 0.21
16 20 0.61
17 6 0.18
ACGTcount: A:0.54, C:0.04, G:0.26, T:0.17
Consensus pattern (16 bp):
AGTAAAAGGAGTAATC
Found at i:731 original size:32 final size:30
Alignment explanation
Indices: 645--748 Score: 102
Period size: 36 Copynumber: 3.2 Consensus size: 30
635 AATTAGTGAA
*
645 AGTAAAAGAGTAAAAGTAAAAGAAGTAATC
1 AGTAAAAGAGTAAGAGTAAAAGAAGTAATC
675 AGTGAAAGTAAAAGAGT-AGAAGTAAAAGAAGTAATC
1 ------AGTAAAAGAGTAAG-AGTAAAAGAAGTAATC
*
711 AGTAAAAGGGAGTAAGAGTAAAAGGAGTAATC
1 AGTAAAA--GAGTAAGAGTAAAAGAAGTAATC
743 AGTAAA
1 AGTAAA
749 TAGGTAATTA
Statistics
Matches: 62, Mismatches: 2, Indels: 12
0.82 0.03 0.16
Matches are distributed among these distances:
30 7 0.11
32 25 0.40
33 2 0.03
35 1 0.02
36 27 0.44
ACGTcount: A:0.56, C:0.03, G:0.25, T:0.16
Consensus pattern (30 bp):
AGTAAAAGAGTAAGAGTAAAAGAAGTAATC
Found at i:739 original size:15 final size:15
Alignment explanation
Indices: 681--740 Score: 61
Period size: 16 Copynumber: 3.9 Consensus size: 15
671 AATCAGTGAA
681 AGTAAAA-GAGT-AG
1 AGTAAAAGGAGTAAG
* *
694 AAGTAAAAGAAGTAATC
1 -AGTAAAAGGAGTAA-G
711 AGTAAAAGGGAGTAAG
1 AGTAAAA-GGAGTAAG
727 AGTAAAAGGAGTAA
1 AGTAAAAGGAGTAA
741 TCAGTAAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
14 7 0.18
15 10 0.26
16 15 0.39
17 6 0.16
ACGTcount: A:0.55, C:0.02, G:0.28, T:0.15
Consensus pattern (15 bp):
AGTAAAAGGAGTAAG
Found at i:916 original size:9 final size:9
Alignment explanation
Indices: 902--942 Score: 57
Period size: 9 Copynumber: 4.6 Consensus size: 9
892 TTAATCAATA
902 AGTAAAAGG
1 AGTAAAAGG
911 AGT-AAAGG
1 AGTAAAAGG
*
919 AAGTAAAAAG
1 -AGTAAAAGG
929 AGTAAAAGG
1 AGTAAAAGG
938 AGTAA
1 AGTAA
943 GCAATAGTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
8 5 0.18
9 19 0.68
10 4 0.14
ACGTcount: A:0.59, C:0.00, G:0.29, T:0.12
Consensus pattern (9 bp):
AGTAAAAGG
Found at i:1079 original size:76 final size:76
Alignment explanation
Indices: 914--1094 Score: 188
Period size: 76 Copynumber: 2.4 Consensus size: 76
904 TAAAAGGAGT
* * * *
914 AAAGGAAGTAAAAAGAGTAAAAGGAGTAAGCAATAGTAATTAACTTAATTCATAGTAATTATGTT
1 AAAGG-AGTAAAAGGAGTAAAAGGAGTAAACAATAGTAATTAACTTAATTCAGAGTAATTAAGTT
**
979 AATTAAGAAGCA
65 AAGAAAGAAGCA
* ** *
991 AAAGGAG-CAAAGGAAGTAAAAGGAGTAAACTGTAGTAATTAGCTTAATTCAGAGTAATTAAGTT
1 AAAGGAGTAAAAGG-AGTAAAAGGAGTAAACAATAGTAATTAACTTAATTCAGAGTAATTAAGTT
*
1055 AAGAAAG-AGTA
65 AAGAAAGAAGCA
* *
1066 ATCA-GAGTAAAAGGAGTAAACAGTAGTAA
1 A-AAGGAGTAAAAGGAGTAAA-AGGAGTAA
1095 TTAAGTTAAT
Statistics
Matches: 86, Mismatches: 14, Indels: 9
0.79 0.13 0.08
Matches are distributed among these distances:
75 17 0.20
76 64 0.74
77 5 0.06
ACGTcount: A:0.50, C:0.06, G:0.22, T:0.23
Consensus pattern (76 bp):
AAAGGAGTAAAAGGAGTAAAAGGAGTAAACAATAGTAATTAACTTAATTCAGAGTAATTAAGTTA
AGAAAGAAGCA
Found at i:5155 original size:153 final size:152
Alignment explanation
Indices: 4931--5207 Score: 470
Period size: 153 Copynumber: 1.8 Consensus size: 152
4921 CTCTACCTTG
4931 AATGATGAATTAGTAGGTTCATGCATCATGGCATCATGGCATAAAGCCAAGAGCCATGATTATTC
1 AATGATGAATTAGTAGGTTCATGCATCATGGCATCATGGCATAAAGCCAAGAGCCATGATTATTC
*
4996 ACAGAATTGTAAATAGTCACGG-TTTTGCCTTGTGGAAGTTCCTACCA-AGATGTGGAGGGACCC
66 ACAGAATTGTAAATAGTCACGGTTTTTGACTTGTGGAAGTTCCTACCAGA-ATGTGGAGGGACCC
5059 CACACCTTTAAGAATCATGAATA
130 CACACCTTTAAGAATCATGAATA
* *
5082 AATGATGAATTGGTAGGTTCATGACATTCAT-TCATCATGTGCATAAAGCCAAGAGCCATGATTA
1 AATGATGAATTAGTAGGTTCATG-CA-TCATGGCATCATG-GCATAAAGCCAAGAGCCATGATTA
5146 TTCACAGAATTGTAAATAGTCACGGTTTTTGACTTGTGGAAGTTCCTACCAGAATGTGGAGG
63 TTCACAGAATTGTAAATAGTCACGGTTTTTGACTTGTGGAAGTTCCTACCAGAATGTGGAGG
5208 AGCCCTACAC
Statistics
Matches: 118, Mismatches: 3, Indels: 7
0.92 0.02 0.05
Matches are distributed among these distances:
151 22 0.19
152 9 0.08
153 53 0.45
154 33 0.28
155 1 0.01
ACGTcount: A:0.32, C:0.17, G:0.22, T:0.29
Consensus pattern (152 bp):
AATGATGAATTAGTAGGTTCATGCATCATGGCATCATGGCATAAAGCCAAGAGCCATGATTATTC
ACAGAATTGTAAATAGTCACGGTTTTTGACTTGTGGAAGTTCCTACCAGAATGTGGAGGGACCCC
ACACCTTTAAGAATCATGAATA
Found at i:6794 original size:11 final size:12
Alignment explanation
Indices: 6778--6809 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
6768 GAAGTTCGTG
6778 TTTGAAGATTA-
1 TTTGAAGATTAT
6789 TTTGAAGA-TAT
1 TTTGAAGATTAT
6800 TTTGAAGATT
1 TTTGAAGATT
6810 TGAAAACAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 2 0.11
11 16 0.84
12 1 0.05
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (12 bp):
TTTGAAGATTAT
Found at i:7453 original size:17 final size:17
Alignment explanation
Indices: 7427--7461 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
7417 CTTTTCTACC
*
7427 TTTCTTTAGTTTTAGGT
1 TTTCTCTAGTTTTAGGT
7444 TTTCTCTAGTTTTAGGT
1 TTTCTCTAGTTTTAGGT
7461 T
1 T
7462 AAGGGTGTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.11, C:0.09, G:0.17, T:0.63
Consensus pattern (17 bp):
TTTCTCTAGTTTTAGGT
Found at i:11767 original size:11 final size:11
Alignment explanation
Indices: 11751--11778 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
11741 CCGGACAGCG
11751 CAAGCCTTGTC
1 CAAGCCTTGTC
11762 CAAGCCTTGTC
1 CAAGCCTTGTC
11773 CAAGCC
1 CAAGCC
11779 AGTCCGCGCG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.21, C:0.39, G:0.18, T:0.21
Consensus pattern (11 bp):
CAAGCCTTGTC
Found at i:12550 original size:16 final size:16
Alignment explanation
Indices: 12512--12550 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
12502 TTTCTTGCAA
* *
12512 TGCTTTAATTGATTTT
1 TGCTTTGATTGATTGT
12528 TGCTTTGATTGATTGT
1 TGCTTTGATTGATTGT
*
12544 TGTTTTG
1 TGCTTTG
12551 CCTATATGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.13, C:0.05, G:0.21, T:0.62
Consensus pattern (16 bp):
TGCTTTGATTGATTGT
Found at i:15225 original size:8 final size:8
Alignment explanation
Indices: 15197--15230 Score: 50
Period size: 8 Copynumber: 4.1 Consensus size: 8
15187 GAATCGGCTA
15197 TGAATTTT
1 TGAATTTT
*
15205 TGAAGTTTC
1 TGAA-TTTT
15214 TGAATTTT
1 TGAATTTT
15222 TGAATTTT
1 TGAATTTT
15230 T
1 T
15231 CAAGAAGATG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 16 0.70
9 7 0.30
ACGTcount: A:0.24, C:0.03, G:0.15, T:0.59
Consensus pattern (8 bp):
TGAATTTT
Found at i:17472 original size:11 final size:12
Alignment explanation
Indices: 17458--17489 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
17448 GAAGTTCATG
17458 TTTGAAGATTA-
1 TTTGAAGATTAT
17469 TTTGAAGA-TAT
1 TTTGAAGATTAT
17480 TTTGAAGATT
1 TTTGAAGATT
17490 TGAAGACCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
10 2 0.11
11 16 0.84
12 1 0.05
ACGTcount: A:0.34, C:0.00, G:0.19, T:0.47
Consensus pattern (12 bp):
TTTGAAGATTAT
Found at i:18133 original size:17 final size:17
Alignment explanation
Indices: 18107--18141 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
18097 CTTTTCTACC
*
18107 TTTCTTTAGTTTTAGGT
1 TTTCTCTAGTTTTAGGT
18124 TTTCTCTAGTTTTAGGT
1 TTTCTCTAGTTTTAGGT
18141 T
1 T
18142 AAGGGTGTCG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.11, C:0.09, G:0.17, T:0.63
Consensus pattern (17 bp):
TTTCTCTAGTTTTAGGT
Found at i:26818 original size:5 final size:5
Alignment explanation
Indices: 26802--26832 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
26792 ATCGAAAAAT
26802 ATAAA A-AAA ATAAA ATAAA ATAAA ATAAA AT
1 ATAAA ATAAA ATAAA ATAAA ATAAA ATAAA AT
26833 TTCGACCAGA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
4 4 0.16
5 21 0.84
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
ATAAA
Done.