Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007967.1 Corchorus capsularis cultivar CVL-1 contig07988, 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: 10584
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:503 original size:38 final size:38
Alignment explanation
Indices: 461--658 Score: 183
Period size: 39 Copynumber: 5.2 Consensus size: 38
451 GTGAATTAAG
* *
461 TAATTAAGAGTCAAAGTAAGGATATTCAGTAAAATTGA
1 TAATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGA
* * *
499 TAATTAAGAGTCAAATTAATAGTAATCAGTAAAAATTGA
1 TAATTAAGAGTCAAAGTAAGAATAATCAGT-AAAATTGA
*
538 TAATTAAGAAGTCAAAGTAAGAACAATCAGTAAAATTGA
1 TAATTAAG-AGTCAAAGTAAGAATAATCAGTAAAATTGA
* * * *
577 TAATCAAGAGTCAAGGTAAAAATAGTAATCAGT-AAA-TCA
1 TAATTAAGAGTCAAAGT-AAGA-A-TAATCAGTAAAATTGA
* *
616 GTAATTAAGAGTC-AAG--GGATTAATCAGT-AAATTGA
1 -TAATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGA
*
651 TACTTAAG
1 TAATTAAG
659 GGAGAGAGTA
Statistics
Matches: 132, Mismatches: 21, Indels: 18
0.77 0.12 0.11
Matches are distributed among these distances:
34 18 0.14
35 2 0.02
36 1 0.01
38 33 0.25
39 38 0.29
40 33 0.25
41 7 0.05
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.27
Consensus pattern (38 bp):
TAATTAAGAGTCAAAGTAAGAATAATCAGTAAAATTGA
Found at i:545 original size:39 final size:38
Alignment explanation
Indices: 424--658 Score: 191
Period size: 38 Copynumber: 6.2 Consensus size: 38
414 TACCCCAATA
* * *
424 AATTAAGAGTC-AAGATAATAGTAACCAGT-GAATTAAGT
1 AATTAAGAGTCAAAG-TAATAGTAATCAGTAAAATTGA-T
* *
462 AATTAAGAGTCAAAGTAA-GGATATTCAGTAAAATTGAT
1 AATTAAGAGTCAAAGTAATAG-TAATCAGTAAAATTGAT
*
500 AATTAAGAGTCAAATTAATAGTAATCAGTAAAAATTGAT
1 AATTAAGAGTCAAAGTAATAGTAATCAGT-AAAATTGAT
* **
539 AATTAAGAAGTCAAAGTAAGAACAATCAGTAAAATTGAT
1 AATTAAG-AGTCAAAGTAATAGTAATCAGTAAAATTGAT
* * *
578 AATCAAGAGTCAAGGTAAAAATAGTAATCAGT-AAA-TCAGT
1 AATTAAGAGTCAAAGT---AATAGTAATCAGTAAAATTGA-T
**
618 AATTAAGAGTC-AAGGGAT--TAATCAGT-AAATTGAT
1 AATTAAGAGTCAAAGTAATAGTAATCAGTAAAATTGAT
*
652 ACTTAAG
1 AATTAAG
659 GGAGAGAGTA
Statistics
Matches: 162, Mismatches: 24, Indels: 26
0.76 0.11 0.12
Matches are distributed among these distances:
34 18 0.11
35 2 0.01
36 2 0.01
37 1 0.01
38 53 0.33
39 44 0.27
40 32 0.20
41 10 0.06
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.27
Consensus pattern (38 bp):
AATTAAGAGTCAAAGTAATAGTAATCAGTAAAATTGAT
Found at i:573 original size:78 final size:76
Alignment explanation
Indices: 424--630 Score: 240
Period size: 78 Copynumber: 2.7 Consensus size: 76
414 TACCCCAATA
* * * *
424 AATTAAGAGTCAAGATAATAGTAACCAGTGAATTAAGTAATTAAGAGTCAAAGTAAGGATATTCA
1 AATTAAGAGTCAAGATAATAGTAACCAGTAAATTAAGTAATTAAGAGTCAAAGTAAGAACAATCA
489 GTAAAATTGAT
66 GTAAAATTGAT
* *
500 AATTAAGAGTCAA-ATTAATAGTAATCAGTAAAAATTGA-TAATTAAGAAGTCAAAGTAAGAACA
1 AATTAAGAGTCAAGA-TAATAGTAACCAGT--AAATTAAGTAATTAAG-AGTCAAAGTAAGAACA
563 ATCAGTAAAATTGAT
62 ATCAGTAAAATTGAT
* * * *
578 AATCAAGAGTCAAGGTAAAAATAGTAATCAGTAAA-TCAGTAATTAAGAGTCAA
1 AATTAAGAGTCAA-G--ATAATAGTAACCAGTAAATTAAGTAATTAAGAGTCAA
631 GGGATTAATC
Statistics
Matches: 113, Mismatches: 9, Indels: 16
0.82 0.07 0.12
Matches are distributed among these distances:
75 1 0.01
76 26 0.23
77 8 0.07
78 53 0.47
79 11 0.10
81 13 0.12
82 1 0.01
ACGTcount: A:0.50, C:0.07, G:0.16, T:0.26
Consensus pattern (76 bp):
AATTAAGAGTCAAGATAATAGTAACCAGTAAATTAAGTAATTAAGAGTCAAAGTAAGAACAATCA
GTAAAATTGAT
Found at i:700 original size:33 final size:33
Alignment explanation
Indices: 663--738 Score: 136
Period size: 33 Copynumber: 2.3 Consensus size: 33
653 CTTAAGGGAG
663 AGAGTAAAAGAA-ATAATCAGTAAAAATGGAGTA
1 AGAGTAAAAGAAGA-AATCAGTAAAAATGGAGTA
696 AGAGTAAAAGAAGAAATCAGTAAAAATGGAGTA
1 AGAGTAAAAGAAGAAATCAGTAAAAATGGAGTA
729 AGAGTAAAAG
1 AGAGTAAAAG
739 TAAAAAAAGT
Statistics
Matches: 42, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
33 41 0.98
34 1 0.02
ACGTcount: A:0.58, C:0.03, G:0.24, T:0.16
Consensus pattern (33 bp):
AGAGTAAAAGAAGAAATCAGTAAAAATGGAGTA
Found at i:701 original size:17 final size:17
Alignment explanation
Indices: 681--737 Score: 64
Period size: 17 Copynumber: 3.4 Consensus size: 17
671 AGAAATAATC
681 AGTAAAAATGGAGTAAG
1 AGTAAAAATGGAGTAAG
* * *
698 AGT-AAAA-GAAGAAATC
1 AGTAAAAATGGAGTAA-G
714 AGTAAAAATGGAGTAAG
1 AGTAAAAATGGAGTAAG
731 AGTAAAA
1 AGTAAAA
738 GTAAAAAAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
15 5 0.16
16 7 0.23
17 14 0.45
18 5 0.16
ACGTcount: A:0.58, C:0.02, G:0.25, T:0.16
Consensus pattern (17 bp):
AGTAAAAATGGAGTAAG
Found at i:704 original size:16 final size:16
Alignment explanation
Indices: 685--737 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
675 ATAATCAGTA
685 AAAATGGAGTAAGAGT
1 AAAATGGAGTAAGAGT
* * *
701 AAAA-GAAGAAATCAGT
1 AAAATGGAGTAA-GAGT
717 AAAAATGGAGTAAGAGT
1 -AAAATGGAGTAAGAGT
734 AAAA
1 AAAA
738 GTAAAAAAAG
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
15 5 0.18
16 11 0.39
17 7 0.25
18 5 0.18
ACGTcount: A:0.58, C:0.02, G:0.25, T:0.15
Consensus pattern (16 bp):
AAAATGGAGTAAGAGT
Found at i:743 original size:22 final size:22
Alignment explanation
Indices: 725--765 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
715 GTAAAAATGG
725 AGTAA-GAGTAAAAGTAAAAAA
1 AGTAATGAGTAAAAGTAAAAAA
*
746 AGTAATTAGTAAAAGTAAAA
1 AGTAATGAGTAAAAGTAAAA
766 GAGCAAAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.63, C:0.00, G:0.17, T:0.20
Consensus pattern (22 bp):
AGTAATGAGTAAAAGTAAAAAA
Found at i:816 original size:13 final size:15
Alignment explanation
Indices: 776--834 Score: 63
Period size: 15 Copynumber: 4.0 Consensus size: 15
766 GAGCAAAAGT
776 AGAAGAAGTAATCAG
1 AGAAGAAGTAATCAG
791 A-AA-AATGGTAATCA-
1 AGAAGAA--GTAATCAG
805 AG-AGAAGTAATCAG
1 AGAAGAAGTAATCAG
819 TAGAAGAAGTAATCAG
1 -AGAAGAAGTAATCAG
835 TAAAATGAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 13
0.74 0.00 0.26
Matches are distributed among these distances:
13 9 0.24
14 4 0.11
15 12 0.32
16 12 0.32
ACGTcount: A:0.53, C:0.07, G:0.24, T:0.17
Consensus pattern (15 bp):
AGAAGAAGTAATCAG
Found at i:828 original size:16 final size:16
Alignment explanation
Indices: 773--869 Score: 73
Period size: 16 Copynumber: 6.2 Consensus size: 16
763 AAAGAGCAAA
773 AGTAGAAGAAGTAATC
1 AGTAGAAGAAGTAATC
789 AG-A-AA-AATGGTAATC
1 AGTAGAAGAA--GTAATC
804 A--AG-AGAAGTAATC
1 AGTAGAAGAAGTAATC
817 AGTAGAAGAAGTAATC
1 AGTAGAAGAAGTAATC
* **
833 AGTAAAATGAAG-AAAG
1 AGTAGAA-GAAGTAATC
*
849 AGTAAAAGAAGTAAATC
1 AGTAGAAGAAGT-AATC
866 AGTA
1 AGTA
870 AAAAATGGAG
Statistics
Matches: 66, Mismatches: 5, Indels: 19
0.73 0.06 0.21
Matches are distributed among these distances:
13 9 0.14
14 4 0.06
15 16 0.24
16 27 0.41
17 10 0.15
ACGTcount: A:0.55, C:0.05, G:0.23, T:0.18
Consensus pattern (16 bp):
AGTAGAAGAAGTAATC
Found at i:875 original size:35 final size:32
Alignment explanation
Indices: 808--891 Score: 89
Period size: 35 Copynumber: 2.5 Consensus size: 32
798 GTAATCAAGA
* *
808 GAAGTAATCAGTAGAAGAAGTAATCAGTAAAAT
1 GAAGTAA-AAGTAAAAGAAGTAATCAGTAAAAT
841 GAAG-AAAGAGTAAAAGAAGTAAATCAGTAAAAAAT
1 GAAGTAAA-AGTAAAAGAAGT-AATCAGT--AAAAT
*
876 GGAGTAAAAGTAAAAG
1 GAAGTAAAAGTAAAAG
892 GAGTGTTTAG
Statistics
Matches: 43, Mismatches: 3, Indels: 8
0.80 0.06 0.15
Matches are distributed among these distances:
32 13 0.30
33 11 0.26
35 16 0.37
36 3 0.07
ACGTcount: A:0.57, C:0.04, G:0.23, T:0.17
Consensus pattern (32 bp):
GAAGTAAAAGTAAAAGAAGTAATCAGTAAAAT
Found at i:1030 original size:32 final size:32
Alignment explanation
Indices: 969--1033 Score: 87
Period size: 32 Copynumber: 2.0 Consensus size: 32
959 TAAAAAGTAT
* * *
969 TGGTAATTAGTAATTAAGTTCAGTAAGTAAAA
1 TGGTAATCAGTAATCAAGTTCAGAAAGTAAAA
1001 TGGTAATCAGTAATCAAGTTCA-AAGAGTAAAA
1 TGGTAATCAGTAATCAAGTTCAGAA-AGTAAAA
1033 T
1 T
1034 AGTTTGGTAA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 1 0.03
32 28 0.97
ACGTcount: A:0.45, C:0.06, G:0.18, T:0.31
Consensus pattern (32 bp):
TGGTAATCAGTAATCAAGTTCAGAAAGTAAAA
Found at i:1203 original size:15 final size:13
Alignment explanation
Indices: 1140--1226 Score: 61
Period size: 14 Copynumber: 6.3 Consensus size: 13
1130 TCAGTAAAAG
*
1140 GTAAAAGTAATCA
1 GTAAAAGTAATAA
*
1153 GTAAAGAGTAAAAA
1 GTAAA-AGTAATAA
*
1167 TGTCAAAGAGTAGTAA
1 -GT-AAA-AGTAATAA
1183 --AAAAGTAATACA
1 GTAAAAGTAATA-A
1195 GGTAAAAGTAATAA
1 -GTAAAAGTAATAA
*
1209 GTAAGAAGTAATGA
1 GTAA-AAGTAATAA
1223 GTAA
1 GTAA
1227 GAAGGTCAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 15
0.74 0.07 0.19
Matches are distributed among these distances:
11 6 0.10
12 4 0.07
13 9 0.15
14 19 0.32
15 12 0.20
16 10 0.17
ACGTcount: A:0.55, C:0.03, G:0.21, T:0.21
Consensus pattern (13 bp):
GTAAAAGTAATAA
Found at i:1367 original size:15 final size:15
Alignment explanation
Indices: 1347--1376 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1337 AAAGAGTAAG
*
1347 AAAATGGTAAAAGTA
1 AAAATGATAAAAGTA
1362 AAAATGATAAAAGTA
1 AAAATGATAAAAGTA
1377 GCAAAAGTAA
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:0.63, C:0.00, G:0.17, T:0.20
Consensus pattern (15 bp):
AAAATGATAAAAGTA
Found at i:2660 original size:6 final size:7
Alignment explanation
Indices: 2639--2673 Score: 52
Period size: 7 Copynumber: 4.9 Consensus size: 7
2629 CACATAAGAT
2639 AAATAAA
1 AAATAAA
2646 AAATAAA
1 AAATAAA
2653 AAATAAA
1 AAATAAA
*
2660 AAATTAAG
1 AAA-TAAA
2668 AAATAA
1 AAATAA
2674 TTTATTTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
7 20 0.77
8 6 0.23
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (7 bp):
AAATAAA
Found at i:3370 original size:14 final size:14
Alignment explanation
Indices: 3351--3387 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
3341 TTCTTATTGC
3351 TTCTTTTTCTCTTT
1 TTCTTTTTCTCTTT
*
3365 TTCTTTTTCTTTTT
1 TTCTTTTTCTCTTT
3379 TTCTATTTT
1 TTCT-TTTT
3388 TAAAAAAATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 17 0.81
15 4 0.19
ACGTcount: A:0.03, C:0.16, G:0.00, T:0.81
Consensus pattern (14 bp):
TTCTTTTTCTCTTT
Found at i:7801 original size:11 final size:11
Alignment explanation
Indices: 7777--7811 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
7767 TTGATAGTGC
7777 AACAAAAACAA
1 AACAAAAACAA
* *
7788 AACGAAAACGA
1 AACAAAAACAA
7799 AACAAAAACAA
1 AACAAAAACAA
7810 AA
1 AA
7812 AACAGAAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.77, C:0.17, G:0.06, T:0.00
Consensus pattern (11 bp):
AACAAAAACAA
Found at i:10386 original size:21 final size:21
Alignment explanation
Indices: 10362--10404 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
10352 ATATAGGGGA
10362 TTACTAAATACCGCCCCCCTT
1 TTACTAAATACCGCCCCCCTT
*
10383 TTACTAGATACCGCCCCCCTT
1 TTACTAAATACCGCCCCCCTT
10404 T
1 T
10405 GGACTATTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.21, C:0.42, G:0.07, T:0.30
Consensus pattern (21 bp):
TTACTAAATACCGCCCCCCTT
Found at i:10410 original size:22 final size:21
Alignment explanation
Indices: 10364--10410 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
10354 ATAGGGGATT
*
10364 ACTAAATACCGCCCCCCTTTT
1 ACTAAATACCGCCCCCCTTTG
*
10385 ACTAGATACCGCCCCCCTTTGG
1 ACTAAATACCGCCCCCCTTT-G
10407 ACTA
1 ACTA
10411 TTTTGTCATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 19 0.83
22 4 0.17
ACGTcount: A:0.23, C:0.40, G:0.11, T:0.26
Consensus pattern (21 bp):
ACTAAATACCGCCCCCCTTTG
Done.