Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009568.1 Corchorus capsularis cultivar CVL-1 contig09589, 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: 31902
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:413 original size:55 final size:55
Alignment explanation
Indices: 353--809 Score: 689
Period size: 55 Copynumber: 8.3 Consensus size: 55
343 AGAAAAGGGC
353 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGT
1 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGT
* *
408 CATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATGGT
1 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGT
* * *
463 CATCAGTAAATCAGTAATTAGGTAAAAAGAGATTAATCAGAGTCAAGGTAATAAT
1 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGT
* * *
518 AATCAGCAAATCAGTAATTAAGTAAAAAGGGATTAATCAAAGTCAAGGTAATAGT
1 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGT
* * * * *
573 AATCGGTAAATCAGTAATTAAGTAAAAAGGGATTAATCAGAGTTAAGGAAATAGC
1 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGT
* * * *
628 AATCAGTAAATCAGTAATTAAGTAAAAAGGGATTAATCAGAGTTAAGGAAATAGC
1 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGT
* * *
683 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAACCAGAGTTAAGGAAATAGT
1 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGT
* * *
738 AATCAGTAAATCAGTAATTAAGTGAAAAGAGATTAATCAGAATCAAGGTAATGGT
1 AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGT
* *
793 AATGAGTAAATCGGTAA
1 AATCAGTAAATCAGTAA
810 AAAGAGATTG
Statistics
Matches: 373, Mismatches: 29, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
55 373 1.00
ACGTcount: A:0.48, C:0.08, G:0.19, T:0.25
Consensus pattern (55 bp):
AATCAGTAAATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGT
Found at i:420 original size:29 final size:29
Alignment explanation
Indices: 387--476 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 29
377 AAAAGAGATT
387 AATCAGAGTCAAGGTAATAGTCATCAGTA
1 AATCAGAGTCAAGGTAATAGTCATCAGTA
* * ** *
416 AATCAGTAATTAA-GTAA-A---AAGAGATT
1 AATCAG-AGTCAAGGTAATAGTCATCAG-TA
*
442 AATCAGAGTCAAGGTAATGGTCATCAGTA
1 AATCAGAGTCAAGGTAATAGTCATCAGTA
471 AATCAG
1 AATCAG
477 TAATTAGGTA
Statistics
Matches: 43, Mismatches: 11, Indels: 14
0.63 0.16 0.21
Matches are distributed among these distances:
25 7 0.16
26 11 0.26
28 1 0.02
29 17 0.40
30 7 0.16
ACGTcount: A:0.44, C:0.11, G:0.20, T:0.24
Consensus pattern (29 bp):
AATCAGAGTCAAGGTAATAGTCATCAGTA
Found at i:458 original size:26 final size:26
Alignment explanation
Indices: 374--458 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
364 CAGTAATTAA
374 GTAAAAAGAGATTAATCAGAGTCAAG
1 GTAAAAAGAGATTAATCAGAGTCAAG
* * * * *
400 GT-AATAGTCATCAGTAAATCAGTAATTAA-
1 GTAAAAAG--A-GA-TTAATCAG-AGTCAAG
429 GTAAAAAGAGATTAATCAGAGTCAAG
1 GTAAAAAGAGATTAATCAGAGTCAAG
455 GTAA
1 GTAA
459 TGGTCATCAG
Statistics
Matches: 42, Mismatches: 10, Indels: 14
0.64 0.15 0.21
Matches are distributed among these distances:
25 8 0.19
26 13 0.31
27 2 0.05
28 2 0.05
29 9 0.21
30 8 0.19
ACGTcount: A:0.48, C:0.08, G:0.20, T:0.24
Consensus pattern (26 bp):
GTAAAAAGAGATTAATCAGAGTCAAG
Found at i:862 original size:165 final size:160
Alignment explanation
Indices: 361--873 Score: 465
Period size: 165 Copynumber: 3.1 Consensus size: 160
351 GCAATCAGTA
*
361 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTCATCAGTAAATCAGTAAT
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAAT
* * **
426 TAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATGGTCATCAGTAAATCAGTAATTAGG--TA--
66 TAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATGGTAATCAGTAAATCGGTAAAAAGGATTATC
*
487 A-AAAGAGATTAATCAGAGTCAAGGTAATAATAAT
131 AGAAA-AGA-TAATCAGAATCAAGGTAAT-AT--T
* * *
521 CAGCAAATCAGTAATTAAGTAAAAAGGGATTAATCAAAGTCAAGGTAATAGTAATCGGTAAATCA
1 -----AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTAAATCA
* * * * * * *
586 GTAATTAAGTAAAAAGGGATTAATCAGAGTTAAGGAAATAGCAATCAGTAAATCAGTAATTAA-G
61 GTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATGGTAATCAGTAAATCGGTAA-AAAGG
* * * *
650 --TA--A-AAAGGGATTAATCAGAGTTAAGGAAATAGCAATCAGTA
125 ATTATCAGAAA-AGA-TAATCAGAATCAAGG---T---AAT-A-TT
* * *
691 AATCAGTAATTAAGTAAAAAGAGATTAACCAGAGTTAAGGAAATAGTAATCAGTAAATCAGTAAT
1 AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAAT
* * *
756 TAAGTGAAAAGAGATTAATCAGAATCAAGGTAATGGTAATGAGTAAATCGGTAAAAAGAGATTGA
66 TAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATGGTAATCAGTAAATCGGTAAAAAG-GATT-A
821 TCAGTAAAATGATAATCAAGAATCAAGGTAATATT
129 TCAG-AAAA-GATAATC-AGAATCAAGGTAATATT
856 AATCAGTAAATT-AGTAAA
1 AATCAGT-AATTAAGTAAA
874 GCAGTAAAAA
Statistics
Matches: 293, Mismatches: 35, Indels: 40
0.80 0.10 0.11
Matches are distributed among these distances:
164 2 0.01
165 252 0.86
166 8 0.03
167 3 0.01
168 2 0.01
169 1 0.00
170 1 0.00
171 5 0.02
172 6 0.02
173 13 0.04
ACGTcount: A:0.49, C:0.08, G:0.19, T:0.25
Consensus pattern (160 bp):
AATCAGTAATTAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATAGTAATCAGTAAATCAGTAAT
TAAGTAAAAAGAGATTAATCAGAGTCAAGGTAATGGTAATCAGTAAATCGGTAAAAAGGATTATC
AGAAAAGATAATCAGAATCAAGGTAATATT
Found at i:944 original size:15 final size:14
Alignment explanation
Indices: 917--951 Score: 61
Period size: 15 Copynumber: 2.4 Consensus size: 14
907 TTAAGAACCA
917 AGGTAATAGTAATT
1 AGGTAATAGTAATT
931 AGGTAATCAGTAATT
1 AGGTAAT-AGTAATT
946 AGGTAA
1 AGGTAA
952 AAGAGACTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 7 0.35
15 13 0.65
ACGTcount: A:0.43, C:0.03, G:0.23, T:0.31
Consensus pattern (14 bp):
AGGTAATAGTAATT
Found at i:952 original size:71 final size:70
Alignment explanation
Indices: 790--992 Score: 189
Period size: 71 Copynumber: 2.9 Consensus size: 70
780 TCAAGGTAAT
* * * ** * * *
790 GGTAATGAGTAAATCGGTAAAAAGAGATTGATCAGTAAAATGATAATCAAGAATCAAGGTAATAT
1 GGTAATCAGT-AATAGGTAAAAAGAGGTCAATCAGTAAATTGATAATTAAGAATCAAGGTAATAG
855 TAATCA
65 TAATCA
* *
861 -GTAAATTAGTAA-AGCAGTAAAAAGAGGTCAATCAGTAAATTGATAATTAAGAACCAAGGTAAT
1 GGT-AATCAGTAATAG--GTAAAAAGAGGTCAATCAGTAAATTGATAATTAAGAATCAAGGTAAT
*
924 AGTAATTA
63 AGTAATCA
* * * *
932 GGTAATCAGTAATTAGGT-AAAAGA-GACTAATCAGTAGATCGATAATTAAGAGTCAAGGTAA
1 GGTAATCAGTAA-TAGGTAAAAAGAGGTC-AATCAGTAAATTGATAATTAAGAATCAAGGTAA
993 GAAATTAATC
Statistics
Matches: 109, Mismatches: 16, Indels: 15
0.78 0.11 0.11
Matches are distributed among these distances:
69 3 0.03
70 39 0.36
71 63 0.58
72 2 0.02
73 2 0.02
ACGTcount: A:0.47, C:0.07, G:0.20, T:0.25
Consensus pattern (70 bp):
GGTAATCAGTAATAGGTAAAAAGAGGTCAATCAGTAAATTGATAATTAAGAATCAAGGTAATAGT
AATCA
Found at i:1017 original size:32 final size:31
Alignment explanation
Indices: 974--1040 Score: 100
Period size: 32 Copynumber: 2.1 Consensus size: 31
964 AGTAGATCGA
974 TAATTAAGAGTCAAGGTAAGAAAT-TAATCAG
1 TAATTAAGAGTCAAGGTAA-AAATATAATCAG
1005 TAATTAAAGAGTCAAGGTAAAAATAGTAATCAG
1 TAATT-AAGAGTCAAGGTAAAAATA-TAATCAG
1038 TAA
1 TAA
1041 ATCGATAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
31 9 0.27
32 14 0.42
33 10 0.30
ACGTcount: A:0.51, C:0.06, G:0.18, T:0.25
Consensus pattern (31 bp):
TAATTAAGAGTCAAGGTAAAAATATAATCAG
Found at i:1214 original size:24 final size:24
Alignment explanation
Indices: 1186--1232 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
1176 GAGATTGGTA
*
1186 ATTAAAGTAGTAATTTAGATTCAT
1 ATTAAAGTAGTAATTGAGATTCAT
*
1210 ATTAAAGTGGTAATTGAGATTCA
1 ATTAAAGTAGTAATTGAGATTCA
1233 AAGTAAGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.40, C:0.04, G:0.17, T:0.38
Consensus pattern (24 bp):
ATTAAAGTAGTAATTGAGATTCAT
Found at i:1509 original size:27 final size:26
Alignment explanation
Indices: 1479--1543 Score: 87
Period size: 26 Copynumber: 2.5 Consensus size: 26
1469 GAGAGAGTAA
1479 AAAAAATGGTAATTAAAGTA-AAAGAGT
1 AAAAAATGGTAA-T-AAGTACAAAGAGT
* *
1506 AAAATATGGTAATCAGTACAAAGAGT
1 AAAAAATGGTAATAAGTACAAAGAGT
1532 AAAAAATGGTAA
1 AAAAAATGGTAA
1544 CAAGCAATCA
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 4 0.12
26 19 0.56
27 11 0.32
ACGTcount: A:0.57, C:0.03, G:0.18, T:0.22
Consensus pattern (26 bp):
AAAAAATGGTAATAAGTACAAAGAGT
Found at i:2051 original size:22 final size:22
Alignment explanation
Indices: 1999--2138 Score: 113
Period size: 22 Copynumber: 6.2 Consensus size: 22
1989 GGAAAAATAC
* *
1999 CCTATGAAATTTTACTAACCAATC
1 CCTATGAAATTTTAGTAACC--TT
*
2023 CCTATGAAATTTTGGTAACCTT
1 CCTATGAAATTTTAGTAACCTT
* * *
2045 CCTATG-AATTTCTGGTAATCGT
1 CCTATGAAATTT-TAGTAACCTT
* * * *
2067 CCAATGAAATTATAGTAATCTC
1 CCTATGAAATTTTAGTAACCTT
*
2089 CCTATGAAATTTTTTGATAA-CTT
1 CCTATGAAA-TTTTAG-TAACCTT
2112 ACCTATGAAATTTTAGTAACCTT
1 -CCTATGAAATTTTAGTAACCTT
2135 CCTA
1 CCTA
2139 GCTATATGAC
Statistics
Matches: 95, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
21 5 0.05
22 42 0.44
23 18 0.19
24 30 0.32
ACGTcount: A:0.32, C:0.19, G:0.10, T:0.39
Consensus pattern (22 bp):
CCTATGAAATTTTAGTAACCTT
Found at i:4877 original size:13 final size:13
Alignment explanation
Indices: 4859--4885 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4849 TTTATTTATT
4859 TATTGTAGTAGGA
1 TATTGTAGTAGGA
4872 TATTGTAGTAGGA
1 TATTGTAGTAGGA
4885 T
1 T
4886 CTTAACCTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.30, T:0.41
Consensus pattern (13 bp):
TATTGTAGTAGGA
Found at i:9111 original size:8 final size:8
Alignment explanation
Indices: 9100--9133 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
9090 GGTGAGAGAG
9100 AAAAACAA
1 AAAAACAA
9108 AAAAACAA
1 AAAAACAA
*
9116 AAAAA-AC
1 AAAAACAA
9123 AAAAACAA
1 AAAAACAA
9131 AAA
1 AAA
9134 CAAAAACAGC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
7 6 0.26
8 17 0.74
ACGTcount: A:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (8 bp):
AAAAACAA
Found at i:9117 original size:6 final size:6
Alignment explanation
Indices: 9100--9141 Score: 61
Period size: 6 Copynumber: 7.2 Consensus size: 6
9090 GGTGAGAGAG
9100 AAAAAC AAAAA- AACAAA- AAAAAC AAAAAC AAAAAC AAAAAC A
1 AAAAAC AAAAAC AA-AAAC AAAAAC AAAAAC AAAAAC AAAAAC A
9142 GCAACAGGCA
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
5 5 0.15
6 29 0.85
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (6 bp):
AAAAAC
Found at i:18438 original size:10 final size:10
Alignment explanation
Indices: 18420--18454 Score: 54
Period size: 10 Copynumber: 3.6 Consensus size: 10
18410 AAAGAAAGAA
*
18420 GTTTATTTTT
1 GTTTTTTTTT
18430 GTTTTTTTTT
1 GTTTTTTTTT
18440 -TTTTTTTTT
1 GTTTTTTTTT
18449 GTTTTT
1 GTTTTT
18455 GGACGGGCCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
9 9 0.39
10 14 0.61
ACGTcount: A:0.03, C:0.00, G:0.09, T:0.89
Consensus pattern (10 bp):
GTTTTTTTTT
Found at i:20152 original size:31 final size:31
Alignment explanation
Indices: 20114--20182 Score: 93
Period size: 31 Copynumber: 2.2 Consensus size: 31
20104 AGTTTTAAGA
*
20114 AACTTTTGAAACATCTATTATACCCTTATTT
1 AACTTTTGAAACACCTATTATACCCTTATTT
* * **
20145 AATTTTTGAAATACCTATTATATTCTTATTT
1 AACTTTTGAAACACCTATTATACCCTTATTT
20176 AACTTTT
1 AACTTTT
20183 ACAGTTTTTT
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.14, G:0.03, T:0.51
Consensus pattern (31 bp):
AACTTTTGAAACACCTATTATACCCTTATTT
Found at i:28371 original size:22 final size:23
Alignment explanation
Indices: 28334--28377 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
28324 AAAAGAATAT
**
28334 ATGAATATTATGCCAAA-AAAGG
1 ATGAATATTACACCAAATAAAGG
28356 ATGAATATTACACCAAATAAAG
1 ATGAATATTACACCAAATAAAG
28378 TACTAAGTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 15 0.79
23 4 0.21
ACGTcount: A:0.52, C:0.11, G:0.14, T:0.23
Consensus pattern (23 bp):
ATGAATATTACACCAAATAAAGG
Found at i:29373 original size:21 final size:21
Alignment explanation
Indices: 29347--29390 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
29337 AAGAACTAGA
29347 TTGCTAAATACCGCCCCATTT
1 TTGCTAAATACCGCCCCATTT
**
29368 TTGCTATTTACCGCCCCATTT
1 TTGCTAAATACCGCCCCATTT
29389 TT
1 TT
29391 TACGCTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.32, G:0.09, T:0.41
Consensus pattern (21 bp):
TTGCTAAATACCGCCCCATTT
Found at i:29658 original size:33 final size:33
Alignment explanation
Indices: 29616--29694 Score: 133
Period size: 33 Copynumber: 2.4 Consensus size: 33
29606 AGGCCGCCCC
*
29616 AGTGGGGAGGCTCCGCCGTGGTTGAGCC-TCCCT
1 AGTGGGGAGGCTCCGCCGTGGCTGAGCCGT-CCT
29649 AGTGGGGAGGCTCCGCCGTGGCTGAGCCGTCCT
1 AGTGGGGAGGCTCCGCCGTGGCTGAGCCGTCCT
29682 AGTGGGGAGGCTC
1 AGTGGGGAGGCTC
29695 AGTGTAAAAG
Statistics
Matches: 44, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
33 43 0.98
34 1 0.02
ACGTcount: A:0.10, C:0.28, G:0.43, T:0.19
Consensus pattern (33 bp):
AGTGGGGAGGCTCCGCCGTGGCTGAGCCGTCCT
Found at i:29669 original size:16 final size:16
Alignment explanation
Indices: 29617--29669 Score: 54
Period size: 16 Copynumber: 3.2 Consensus size: 16
29607 GGCCGCCCCA
29617 GTGGGGAGGCTCCGCC
1 GTGGGGAGGCTCCGCC
* * *
29633 GTGGTTGAGCCTCC-CTA
1 GTGG-GGAGGCTCCGC-C
29650 GTGGGGAGGCTCCGCC
1 GTGGGGAGGCTCCGCC
29666 GTGG
1 GTGG
29670 CTGAGCCGTC
Statistics
Matches: 28, Mismatches: 6, Indels: 6
0.70 0.15 0.15
Matches are distributed among these distances:
16 16 0.57
17 12 0.43
ACGTcount: A:0.08, C:0.28, G:0.45, T:0.19
Consensus pattern (16 bp):
GTGGGGAGGCTCCGCC
Found at i:30707 original size:105 final size:105
Alignment explanation
Indices: 30502--30712 Score: 354
Period size: 107 Copynumber: 2.0 Consensus size: 105
30492 TCTTTTAGAC
*
30502 AAAAAAAAAACTCGTAGCTTTTATGTTTGGATTTGAAATATCAAATAGGGTTTTAATTAGGTTAG
1 AAAAAAAAAACTCGTAGCGTTTATGTTTGGATTTGAAATATCAAATAGGGTTTTAATTAGGTTAG
30567 TATATCACCCTAAGAAGTAAAAAGTCTGTGATTATCAAAAT
66 -ATATCACCCTAAGAAGTAAAAAGTCTGTGATTATCAAAAT
* *
30608 AAAAAAAAATACTGGTAGCGTTTATGTTTGGATTTGAAATATCAAATAGGGTTTTAATTAGTTTA
1 AAAAAAAAA-ACTCGTAGCGTTTATGTTTGGATTTGAAATATCAAATAGGGTTTTAATTAGGTTA
30673 G-TATCACCCTACA-AAGTAAAAAGTCTGTGATTATCAAAAT
65 GATATCACCCTA-AGAAGTAAAAAGTCTGTGATTATCAAAAT
30713 CAAATTTTAT
Statistics
Matches: 100, Mismatches: 3, Indels: 5
0.93 0.03 0.05
Matches are distributed among these distances:
105 37 0.37
106 10 0.10
107 53 0.53
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.34
Consensus pattern (105 bp):
AAAAAAAAAACTCGTAGCGTTTATGTTTGGATTTGAAATATCAAATAGGGTTTTAATTAGGTTAG
ATATCACCCTAAGAAGTAAAAAGTCTGTGATTATCAAAAT
Done.