Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019999.1 Corchorus olitorius cultivar O-4 contig20032, 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: 15433
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.31
Found at i:93 original size:47 final size:46
Alignment explanation
Indices: 65--472 Score: 372
Period size: 47 Copynumber: 8.4 Consensus size: 46
55 AAACAGAGGT
65 TAGTTTAATTCTGGGTAATTAAACTAAAAGTAAGAGAAGAAGGAA-A
1 TAGTTTAATTCTGGGTAATTAAACTAAAAGTAAGAGAAGAA-GAAGA
* * * *
111 GAGTTTAATTCTGGGTAATTAAACTAAAGAGCATGAGAAGAAGAAAA
1 TAGTTTAATTCTGGGTAATTAAACTAAA-AGTAAGAGAAGAAGAAGA
* * * *
158 CAATTTAATTATGGGTAATTAAACTAAAAAGTAAAAGAAGAAGTAAACAGA
1 TAGTTTAATTCTGGGTAATTAAACT-AAAAGTAAGAGAAGAAG---A-AGA
* *
209 GGCTAGTTTAATTCTGGATAATTAAACTAAAAAGTAAGAGAAGAAGAAAA
1 ---TAGTTTAATTCTGGGTAATTAAACT-AAAAGTAAGAGAAGAAGAAGA
* * *
259 GAGTTTAATTC-GAGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAA
1 TAGTTTAATTCTG-GGTAATTAAACTAAA-AGTAAGAGAAGAAGAAGA
* * * *
306 CAGTTTAATTCTTGGTGATTAAACTAAAGAGTAAAAGAAGAAGTACACAGA
1 TAGTTTAATTCTGGGTAATTAAACTAAA-AGTAAGAGAAGAAG---A-AGA
*
357 GGCTAGTTTAATTCTGGGTAATTAAACTAAAAAGTTAA-AGAAGAAGAAAA
1 ---TAGTTTAATTCTGGGTAATTAAACT-AAAAG-TAAGAGAAGAAGAAGA
* * *
407 GAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAA
1 TAGTTTAATTCTGGGTAATTAAACTAAA-AGTAAGAGAAGAAGAAGA
* *
454 CAGTTTGATTCTGGGTAAT
1 TAGTTTAATTCTGGGTAAT
473 CAAGCTAAGC
Statistics
Matches: 305, Mismatches: 33, Indels: 47
0.79 0.09 0.12
Matches are distributed among these distances:
46 39 0.13
47 175 0.57
48 3 0.01
50 6 0.02
51 6 0.02
54 70 0.23
55 6 0.02
ACGTcount: A:0.48, C:0.07, G:0.21, T:0.25
Consensus pattern (46 bp):
TAGTTTAATTCTGGGTAATTAAACTAAAAGTAAGAGAAGAAGAAGA
Found at i:250 original size:101 final size:94
Alignment explanation
Indices: 2--492 Score: 529
Period size: 101 Copynumber: 5.0 Consensus size: 94
1 A
* * *
2 AAGAAG-AAACAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGTT
1 AAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAGAGAAGAAG--AA-A-A---C
*
66 AGTTTAATTCTGGGTAATTAAACT-AAAAGTAAGAG
59 AGTTTAATTCTGGGTAATTAAACTAAAAAGTAAAAG
* * * *
101 AAGAAGGAAAGAGTTTAATTCTGGGTAATTAAACTAAAGAGCATGAGAAGAAGAAAACAATTTAA
1 AAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAGAGAAGAAGAAAACAGTTTAA
*
166 TTATGGGTAATTAAACTAAAAAGTAAAAG
66 TTCTGGGTAATTAAACTAAAAAGTAAAAG
* * *
195 AAGAAGTAAACAGAGGCTAGTTTAATTCTGGATAATTAAACTAAAAAGTAAGAGAAGAAGAAAAG
1 AAGAAG--AA-A-A-G--AGTTTAATTCTGGGTAATTAAACTAAAGAGTAAGAGAAGAAGAAAAC
* * *
260 AGTTTAATTC-GAGGTAATTAAACTAAAGAGCAAGAG
59 AGTTTAATTCTG-GGTAATTAAACTAAAAAGTAAAAG
* * * *
296 AAGAAGAAAACAGTTTAATTCTTGGTGATTAAACTAAAGAGTAAAAGAAGAAGTACACAGAGGCT
1 AAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAGAGAAGAAG-A-A-A-A--C-
*
361 AGTTTAATTCTGGGTAATTAAACTAAAAAGTTAAAG
59 AGTTTAATTCTGGGTAATTAAACTAAAAAGTAAAAG
* *
397 AAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAAAGAGCAAGAGAAGAAGAAAACAGTTTGA
1 AAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAGAGAAGAAGAAAACAGTTTAA
* * **
462 TTCTGGGTAATCAAGCTAAGCAGTAAAAG
66 TTCTGGGTAATTAAACTAAAAAGTAAAAG
491 AA
1 AA
493 AGAGTAATCA
Statistics
Matches: 333, Mismatches: 41, Indels: 41
0.80 0.10 0.10
Matches are distributed among these distances:
93 22 0.07
94 85 0.26
95 2 0.01
96 3 0.01
97 5 0.02
98 6 0.02
99 10 0.03
100 44 0.13
101 155 0.47
102 1 0.00
ACGTcount: A:0.48, C:0.07, G:0.21, T:0.23
Consensus pattern (94 bp):
AAGAAGAAAAGAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAGAGAAGAAGAAAACAGTTTAA
TTCTGGGTAATTAAACTAAAAAGTAAAAG
Found at i:314 original size:148 final size:148
Alignment explanation
Indices: 2--492 Score: 803
Period size: 148 Copynumber: 3.3 Consensus size: 148
1 A
*
2 AAGAAG-AAACAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGTT
1 AAGAAGAAAACAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGCT
*
66 AGTTTAATTCTGGGTAATTAAACT-AAAAGTAAGAGAAGAAGGAAAGAGTTTAATTCTGGGTAAT
66 AGTTTAATTCTGGGTAATTAAACTAAAAAGTAAGAGAAGAAGAAAAGAGTTTAATTCTGGGTAAT
*
130 TAAACTAAAGAGCATGAG
131 TAAACTAAAGAGCAAGAG
* * *
148 AAGAAGAAAACAATTTAATTATGGGTAATTAAACTAAAAAGTAAAAGAAGAAGTAAACAGAGGCT
1 AAGAAGAAAACAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGCT
*
213 AGTTTAATTCTGGATAATTAAACTAAAAAGTAAGAGAAGAAGAAAAGAGTTTAATTC-GAGGTAA
66 AGTTTAATTCTGGGTAATTAAACTAAAAAGTAAGAGAAGAAGAAAAGAGTTTAATTCTG-GGTAA
277 TTAAACTAAAGAGCAAGAG
130 TTAAACTAAAGAGCAAGAG
* * *
296 AAGAAGAAAACAGTTTAATTCTTGGTGATTAAACTAAAGAGTAAAAGAAGAAGTACACAGAGGCT
1 AAGAAGAAAACAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGCT
361 AGTTTAATTCTGGGTAATTAAACTAAAAAGTTAA-AGAAGAAGAAAAGAGTTTAATTCTGGGTAA
66 AGTTTAATTCTGGGTAATTAAACTAAAAAG-TAAGAGAAGAAGAAAAGAGTTTAATTCTGGGTAA
425 TTAAACTAAAGAGCAAGAG
130 TTAAACTAAAGAGCAAGAG
* * *
444 AAGAAGAAAACAGTTTGATTCTGGGTAATCAAGCT-AAGCAGTAAAAGAA
1 AAGAAGAAAACAGTTTAATTCTGGGTAATTAAACTAAAG-AGTAAAAGAA
493 AGAGTAATCA
Statistics
Matches: 320, Mismatches: 19, Indels: 10
0.92 0.05 0.03
Matches are distributed among these distances:
146 6 0.02
147 81 0.25
148 229 0.72
149 4 0.01
ACGTcount: A:0.48, C:0.07, G:0.21, T:0.23
Consensus pattern (148 bp):
AAGAAGAAAACAGTTTAATTCTGGGTAATTAAACTAAAGAGTAAAAGAAGAAGTAAACAGAGGCT
AGTTTAATTCTGGGTAATTAAACTAAAAAGTAAGAGAAGAAGAAAAGAGTTTAATTCTGGGTAAT
TAAACTAAAGAGCAAGAG
Found at i:511 original size:22 final size:22
Alignment explanation
Indices: 483--649 Score: 206
Period size: 22 Copynumber: 7.9 Consensus size: 22
473 CAAGCTAAGC
483 AGTAAAAGAAAGAGTAATCAGA
1 AGTAAAAGAAAGAGTAATCAGA
505 AGTAAAAGAAAGAGTAATCATG-
1 AGTAAAAGAAAGAGTAATCA-GA
* *
527 AGTAAAAGGAAGAGTAATCAAA
1 AGTAAAAGAAAGAGTAATCAGA
* *
549 AGCAGAAGAAAGAGTAATCAG-
1 AGTAAAAGAAAGAGTAATCAGA
* *
570 AGTAAAAGGAAGAGTAATCAAA
1 AGTAAAAGAAAGAGTAATCAGA
*
592 AGCAAAAGAAAGAGTAATC---
1 AGTAAAAGAAAGAGTAATCAGA
611 AG---AAGAAAGAGTAATCAGA
1 AGTAAAAGAAAGAGTAATCAGA
630 AGTAAAAGAAAGAGTAATCA
1 AGTAAAAGAAAGAGTAATCA
650 AAAGATTAGA
Statistics
Matches: 124, Mismatches: 12, Indels: 18
0.81 0.08 0.12
Matches are distributed among these distances:
16 14 0.11
19 4 0.03
21 17 0.14
22 88 0.71
23 1 0.01
ACGTcount: A:0.57, C:0.06, G:0.23, T:0.13
Consensus pattern (22 bp):
AGTAAAAGAAAGAGTAATCAGA
Found at i:587 original size:43 final size:43
Alignment explanation
Indices: 483--649 Score: 227
Period size: 43 Copynumber: 4.0 Consensus size: 43
473 CAAGCTAAGC
* *
483 AGTAAAAGAAAGAGTAATCAGAAGTAAAAGAAAGAGTAATCATG
1 AGTAAAAGAAAGAGTAATCAAAAGCAAAAGAAAGAGTAATCA-G
* *
527 AGTAAAAGGAAGAGTAATCAAAAGCAGAAGAAAGAGTAATCAG
1 AGTAAAAGAAAGAGTAATCAAAAGCAAAAGAAAGAGTAATCAG
*
570 AGTAAAAGGAAGAGTAATCAAAAGCAAAAGAAAGAGTAATC--
1 AGTAAAAGAAAGAGTAATCAAAAGCAAAAGAAAGAGTAATCAG
* *
611 AG---AAGAAAGAGTAATCAGAAGTAAAAGAAAGAGTAATCA
1 AGTAAAAGAAAGAGTAATCAAAAGCAAAAGAAAGAGTAATCA
650 AAAGATTAGA
Statistics
Matches: 114, Mismatches: 8, Indels: 7
0.88 0.06 0.05
Matches are distributed among these distances:
38 33 0.29
41 2 0.02
43 41 0.36
44 38 0.33
ACGTcount: A:0.57, C:0.06, G:0.23, T:0.13
Consensus pattern (43 bp):
AGTAAAAGAAAGAGTAATCAAAAGCAAAAGAAAGAGTAATCAG
Found at i:618 original size:16 final size:16
Alignment explanation
Indices: 597--631 Score: 70
Period size: 16 Copynumber: 2.2 Consensus size: 16
587 TCAAAAGCAA
597 AAGAAAGAGTAATCAG
1 AAGAAAGAGTAATCAG
613 AAGAAAGAGTAATCAG
1 AAGAAAGAGTAATCAG
629 AAG
1 AAG
632 TAAAAGAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.57, C:0.06, G:0.26, T:0.11
Consensus pattern (16 bp):
AAGAAAGAGTAATCAG
Found at i:674 original size:38 final size:39
Alignment explanation
Indices: 486--677 Score: 162
Period size: 38 Copynumber: 4.8 Consensus size: 39
476 GCTAAGCAGT
486 AAAAGAAAGAGTAATCAGAAG-TAAAAGAAAGAGTAATC
1 AAAAGAAAGAGTAATCAGAAGCTAAAAGAAAGAGTAATC
* * *
524 ATGAGTAAAAGGAAGAGTAATCAAAAGC-AGAAGAAAGAGTAATC
1 ------AAAAGAAAGAGTAATCAGAAGCTAAAAGAAAGAGTAATC
* *
568 AGAGTAAAAGGAAGAGTAATCAAAAGC-AAAAGAAAGAGTAATC
1 -----AAAAGAAAGAGTAATCAGAAGCTAAAAGAAAGAGTAATC
*
611 AGAAGAAAGAGTAATCAGAAG-TAAAAGAAAGAGTAATC
1 AAAAGAAAGAGTAATCAGAAGCTAAAAGAAAGAGTAATC
* *
649 AAAAGATTAGAGTAA-C-TAAGCTAAAAGAA
1 AAAAGA-AAGAGTAATCAGAAGCTAAAAGAA
678 GTAAAAGCAA
Statistics
Matches: 133, Mismatches: 11, Indels: 14
0.84 0.07 0.09
Matches are distributed among these distances:
37 3 0.02
38 48 0.36
39 7 0.05
43 41 0.31
44 34 0.26
ACGTcount: A:0.58, C:0.06, G:0.22, T:0.14
Consensus pattern (39 bp):
AAAAGAAAGAGTAATCAGAAGCTAAAAGAAAGAGTAATC
Found at i:722 original size:47 final size:46
Alignment explanation
Indices: 627--727 Score: 118
Period size: 47 Copynumber: 2.2 Consensus size: 46
617 AAGAGTAATC
*
627 AGAAGTAAAAGAAAGAGTAATCAAAAGATTAGAGTAACTAAGCTAAA
1 AGAAGTAAAAGAAAGAGTAATCAAAAGA-TAAAGTAACTAAGCTAAA
* ** *
674 AGAAGTAAAAGCAAGAGTAATCAGTAG-TAAAGTTAATTAAGCT-AA
1 AGAAGTAAAAGAAAGAGTAATCAAAAGATAAAG-TAACTAAGCTAAA
719 A-AAGTAAAA
1 AGAAGTAAAA
728 AGTAATAATA
Statistics
Matches: 48, Mismatches: 5, Indels: 5
0.83 0.09 0.09
Matches are distributed among these distances:
44 8 0.17
45 7 0.15
46 9 0.19
47 24 0.50
ACGTcount: A:0.56, C:0.06, G:0.19, T:0.19
Consensus pattern (46 bp):
AGAAGTAAAAGAAAGAGTAATCAAAAGATAAAGTAACTAAGCTAAA
Found at i:1958 original size:27 final size:21
Alignment explanation
Indices: 1899--1947 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
1889 ATGCCACATA
*
1899 CATTATCATAAACACCATAAC
1 CATTATTATAAACACCATAAC
1920 CATTATTATAAACACCATAAC
1 CATTATTATAAACACCATAAC
1941 CATTATT
1 CATTATT
1948 TTATAATTAA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.45, C:0.24, G:0.00, T:0.31
Consensus pattern (21 bp):
CATTATTATAAACACCATAAC
Found at i:2175 original size:13 final size:13
Alignment explanation
Indices: 2157--2183 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2147 AAACGGAAAA
2157 TCCAGAAGTGCTT
1 TCCAGAAGTGCTT
2170 TCCAGAAGTGCTT
1 TCCAGAAGTGCTT
2183 T
1 T
2184 TTAGTTGTTT
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:0.22, C:0.22, G:0.22, T:0.33
Consensus pattern (13 bp):
TCCAGAAGTGCTT
Found at i:10167 original size:32 final size:33
Alignment explanation
Indices: 10094--10181 Score: 108
Period size: 32 Copynumber: 2.7 Consensus size: 33
10084 AAAGTTTATA
*
10094 AACGCTGGCATATAGGGGCGTTTTGTACAAGTGG
1 AACGCCGGCATATAGGGGCGTTTTG-ACAAGTGG
*
10128 AACGCCGGCATATAGGGGCGTTTATG-GAAG-GG
1 AACGCCGGCATATAGGGGCGTTT-TGACAAGTGG
* *
10160 AACGCCGGAATACAGGGGCGTT
1 AACGCCGGCATATAGGGGCGTT
10182 AGTAGATTGT
Statistics
Matches: 49, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
32 22 0.45
33 3 0.06
34 22 0.45
35 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.38, T:0.20
Consensus pattern (33 bp):
AACGCCGGCATATAGGGGCGTTTTGACAAGTGG
Found at i:12314 original size:13 final size:13
Alignment explanation
Indices: 12296--12320 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
12286 AAACTGAAAC
12296 AGAAACAGTTTGT
1 AGAAACAGTTTGT
12309 AGAAACAGTTTG
1 AGAAACAGTTTG
12321 CAGTTTGCAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.24, T:0.28
Consensus pattern (13 bp):
AGAAACAGTTTGT
Found at i:12367 original size:24 final size:24
Alignment explanation
Indices: 12321--12419 Score: 85
Period size: 24 Copynumber: 3.9 Consensus size: 24
12311 AAACAGTTTG
**
12321 CAGTTTGCAGACAATGTAC-AAACA
1 CAGTTTGCAG-CAACATACAAAACA
*
12345 CAGTTTGCAGCAACTTACAAAACAAAA
1 CAGTTTGCAGCAACATACAAAAC---A
*
12372 CAGTTTGCAGTGTAACATA-ACAAACA
1 CAGTTTGCA--GCAACATACA-AAACA
12398 CAGTTTGCAGCAACATACAAAA
1 CAGTTTGCAGCAACATACAAAA
12420 AAAAAACAAG
Statistics
Matches: 62, Mismatches: 5, Indels: 16
0.75 0.06 0.19
Matches are distributed among these distances:
23 6 0.10
24 24 0.39
25 1 0.02
26 10 0.16
27 10 0.16
28 1 0.02
29 10 0.16
ACGTcount: A:0.44, C:0.21, G:0.14, T:0.20
Consensus pattern (24 bp):
CAGTTTGCAGCAACATACAAAACA
Found at i:12399 original size:53 final size:54
Alignment explanation
Indices: 12338--12492 Score: 188
Period size: 57 Copynumber: 2.8 Consensus size: 54
12328 CAGACAATGT
* *
12338 ACAAACACAGTTTGCAGCAACTTACAAAACAAAACAGTTTGCAG-TGTAACATA
1 ACAAACACAGTTTGCAGCAACTTACAAAACAAAACAGTTTGCAGATATAACAAA
* *
12391 ACAAACACAGTTTGCAGCAACATACAAAAAAAAAACAAGTTTGCAGATTATAACAAA
1 ACAAACACAGTTTGCAGCAACTTAC-AAAACAAAAC-AGTTTGCAGA-TATAACAAA
** *
12448 ACAAACA-TTTGTTGCAGCAACTTACAAAACAGAAATAGTTTGCAG
1 ACAAACACAGT-TTGCAGCAACTTACAAAACA-AAACAGTTTGCAG
12493 CAACTTACAA
Statistics
Matches: 87, Mismatches: 9, Indels: 9
0.83 0.09 0.09
Matches are distributed among these distances:
53 24 0.28
54 9 0.10
55 9 0.10
56 15 0.17
57 30 0.34
ACGTcount: A:0.48, C:0.19, G:0.13, T:0.21
Consensus pattern (54 bp):
ACAAACACAGTTTGCAGCAACTTACAAAACAAAACAGTTTGCAGATATAACAAA
Found at i:12407 original size:26 final size:27
Alignment explanation
Indices: 12338--12506 Score: 107
Period size: 28 Copynumber: 6.1 Consensus size: 27
12328 CAGACAATGT
*
12338 ACAAACACAGTTTGCAGCAACTTACAAA
1 ACAAACACAGTTTGCAG-AACTAACAAA
** *
12366 ACAAA-ACAGTTTGCAG-TGTAACATA
1 ACAAACACAGTTTGCAGAACTAACAAA
12391 ACAAACACAGTTTGCAGCAAC-ATACAAA
1 ACAAACACAGTTTGCAG-AACTA-ACAAA
* *
12419 AAAAAAACAAGTTTGCAGATTA-TAACAAA
1 ACAAACAC-AGTTTGCAGA--ACTAACAAA
** *
12448 ACAAACA-TTTGTTGCAGCAACTTACAAA
1 ACAAACACAGT-TTGCAG-AACTAACAAA
* *
12476 ACAGAA-ATAGTTTGCAGCAACTTACAAA
1 ACA-AACACAGTTTGCAG-AACTAACAAA
12504 ACA
1 ACA
12507 GGAACAATTT
Statistics
Matches: 112, Mismatches: 16, Indels: 26
0.73 0.10 0.17
Matches are distributed among these distances:
25 10 0.09
26 11 0.10
27 14 0.12
28 52 0.46
29 23 0.21
30 2 0.02
ACGTcount: A:0.49, C:0.20, G:0.12, T:0.20
Consensus pattern (27 bp):
ACAAACACAGTTTGCAGAACTAACAAA
Done.