Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009942.1 Corchorus capsularis cultivar CVL-1 contig09963, 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: 38268
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.33
Found at i:3541 original size:3 final size:3
Alignment explanation
Indices: 3533--3559 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
3523 AATCGCAACA
3533 AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT
3560 GTGAATTGTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:3755 original size:4 final size:4
Alignment explanation
Indices: 3748--3773 Score: 52
Period size: 4 Copynumber: 6.5 Consensus size: 4
3738 TTGCCATATC
3748 TTAT TTAT TTAT TTAT TTAT TTAT TT
1 TTAT TTAT TTAT TTAT TTAT TTAT TT
3774 CCTTCGTCCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 22 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (4 bp):
TTAT
Found at i:19460 original size:2 final size:2
Alignment explanation
Indices: 19453--19479 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
19443 GGGAGACCTA
19453 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
19480 ATGCTTGTGT
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:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Found at i:25926 original size:118 final size:117
Alignment explanation
Indices: 25703--25928 Score: 332
Period size: 118 Copynumber: 1.9 Consensus size: 117
25693 GTTGTAACTG
*
25703 TAATTTGATTTTGAGCAAATCTCTTTGGGTAGGAAAGTGGGACGTTTAAATTTTCTTGAGTTGGA
1 TAATTTGATTTTGAGCAAATCTCTTTGGGTAGGAAAATGGGACGTTTAAATTTTCTTGAGTTGGA
* *
25768 CTTAGAAGAGGAAAAGTAGGAGTTTTGTTAGTAAGAATTCAATTTGATTCCT
66 CTTAGAAGAGGAAAAGGAGGAGTTTTGTCAGTAAGAATTCAATTTGATTCCT
* * *
25820 TAATTTGCTTTTGAGCAATTCTCTTTGGGTAGGAAAATGAGG-TGTTTAAATTGGTT-TTGAGTT
1 TAATTTGATTTTGAGCAAATCTCTTTGGGTAGGAAAATG-GGACGTTTAAATT--TTCTTGAGTT
*
25883 GGACTTAGAAGAGGAAAAGGAGGAGTTTTGTCATTTAA-AATTCAAT
63 GGACTTAGAAGAGGAAAAGGAGGAGTTTTGTCA-GTAAGAATTCAAT
25929 ATAATTCATC
Statistics
Matches: 98, Mismatches: 7, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
117 45 0.46
118 48 0.49
119 5 0.05
ACGTcount: A:0.30, C:0.07, G:0.25, T:0.38
Consensus pattern (117 bp):
TAATTTGATTTTGAGCAAATCTCTTTGGGTAGGAAAATGGGACGTTTAAATTTTCTTGAGTTGGA
CTTAGAAGAGGAAAAGGAGGAGTTTTGTCAGTAAGAATTCAATTTGATTCCT
Found at i:32770 original size:156 final size:156
Alignment explanation
Indices: 32486--32796 Score: 536
Period size: 156 Copynumber: 2.0 Consensus size: 156
32476 CCTTGGAACC
* **
32486 ATAATTTGGCTCTGCTTAACTCCTTCTCACCAAGAGGTTTATACTTTATTGTTTTGTTTTAACAA
1 ATAATTTGGCTCTCCTTAACTCCTTCTCACCAAGAGGTAAATACTTTATTGTTTTGTTTTAACAA
* *
32551 ATAAAACAACAGTACTTTATAATTTTCTTTTTTATAACTCTTTGTGGGTATTTTATGTAGGGAAA
66 ATAAAACAACAGTACTTTATAATTTTCATTTTTATAACTCTTTGTGGGTATATTATGTAGGGAAA
32616 GAGAGTTACCTTTGATGGTTGCTGCA
131 GAGAGTTACCTTTGATGGTTGCTGCA
32642 ATAATTTGGCTCTCCTTAACTCCTTCTCACCAAGAGGTAAATACTTTATTGTTTT-TTCTTAACA
1 ATAATTTGGCTCTCCTTAACTCCTTCTCACCAAGAGGTAAATACTTTATTGTTTTGTT-TTAACA
*
32706 AATAAAA-AAGCAGTACTTTATATTTTTCATTTTTATAACTCTTTGTGGGTATATTATGTAGGGA
65 AATAAAACAA-CAGTACTTTATAATTTTCATTTTTATAACTCTTTGTGGGTATATTATGTAGGGA
32770 AAGAGAGTTACCTTTGATGGTTGCTGC
129 AAGAGAGTTACCTTTGATGGTTGCTGC
32797 GATATCTATT
Statistics
Matches: 147, Mismatches: 6, Indels: 4
0.94 0.04 0.03
Matches are distributed among these distances:
155 4 0.03
156 143 0.97
ACGTcount: A:0.28, C:0.14, G:0.16, T:0.42
Consensus pattern (156 bp):
ATAATTTGGCTCTCCTTAACTCCTTCTCACCAAGAGGTAAATACTTTATTGTTTTGTTTTAACAA
ATAAAACAACAGTACTTTATAATTTTCATTTTTATAACTCTTTGTGGGTATATTATGTAGGGAAA
GAGAGTTACCTTTGATGGTTGCTGCA
Found at i:33177 original size:6 final size:5
Alignment explanation
Indices: 33147--33176 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
33137 TGTTGCTCTT
33147 TTTTA TTTTTA TTTTA TTTTA TTTTA TTTT
1 TTTTA -TTTTA TTTTA TTTTA TTTTA TTTT
33177 TTGTTGCTGA
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTTA
Found at i:33424 original size:2 final size:2
Alignment explanation
Indices: 33419--33449 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
33409 ACTTGGTGTG
33419 TA TA 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 TA TA T
33450 GAATTTTAGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:35299 original size:26 final size:26
Alignment explanation
Indices: 35256--36684 Score: 1820
Period size: 26 Copynumber: 55.1 Consensus size: 26
35246 GAGTAATACA
* *
35256 TAGGGGACATATAGTTGCATATTAAG
1 TAGGGGCCATATAGTTGCATATTCAG
* *
35282 TAAGGTCCATATAGTTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
*
35308 TAGGGGACATATAGTTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
35334 TA-GGGCTCATATAGTTGCATATTCAG
1 TAGGGGC-CATATAGTTGCATATTCAG
*
35360 TAGGGGACATATAGTTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
* *
35386 TATGGGACATATAGTTGCATA-TCAG
1 TAGGGGCCATATAGTTGCATATTCAG
*
35411 TAGGGGACATATAGTTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
*
35437 TAGGGG--ACATAGTTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
** *
35461 TAGGGGAGATATAGTTGCATATTCAA
1 TAGGGGCCATATAGTTGCATATTCAG
*
35487 TAGGGGACATATAGTTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
*
35513 TAGGGCCCATATAGTTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
*
35539 TAGGGCCCATATAGTTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
*
35565 TAGGGCCCATATAGTTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
35591 TA-GGGCCAATATAGTTGCATATTCAG
1 TAGGGGCC-ATATAGTTGCATATTCAG
* * **
35617 TAAGGCCCATATAGTTGTGTATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
**
35643 TAGGGGAGATATAGTTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
**
35669 TAGGGAACATA-AGTTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
*
35694 TAGGGGACATATAGTTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
*
35720 TAGGGGACATATAGTTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
*
35746 TAGGGCCCATATAGTTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
*
35772 TAGGGCCCATATAG--GCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
*
35796 TAGGGCCCATATAGTTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
* *
35822 TAGAGGACATATAGTTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
35848 TA-GGGCCTATATAGTTGCATATTCAG
1 TAGGGGCC-ATATAGTTGCATATTCAG
*
35874 TA--GG-C-GATAGTTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
* *
35896 TAGAGGACATATAGTTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
*
35922 TAGGGCCCATATAGTTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
* *
35948 TAGAGGACATATAGTTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
35974 TA-GGGCCATATAGTTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
*
35999 TAGGGGACATATAGTTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
* **
36025 TAGGGCCCATATAGTTGTTTATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
*
36051 TAGGGGACATATAGTTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
* **
36077 TAGGGCCCATATAGTTGTTTATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
* *
36103 TAAGAGACC-TATAGTTGCATATTCAG
1 T-AGGGGCCATATAGTTGCATATTCAG
36129 TAGGGGGGCCCATATAGTTGCATATTCAG
1 TA--GGGG-CCATATAGTTGCATATTCAG
* *
36158 TAGGGGGCATATAGCTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
*
36184 TAGGGTCCATATAGTTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
* *
36210 TAGGGGGCATATAGCTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
* *
36236 TAGGGTCCATATAGCTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
* *
36262 TAGGGGACATATAGCTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
* *
36288 TAGGGG--ACATGGTTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
* *
36312 TAGGGCCCATATGGTTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
**
36338 TAGGGGAAATATAGTTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
* * *
36364 TAAGGGACATATTGTTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
36390 TA-GGGCTCATATAGTTGCATTTTCAGTACTCAG
1 TAGGGGC-CATATAGTTGCA---T-A-T--TCAG
*
36423 TAGGGCCCATATAGTTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
*
36449 TAGGGCCCATATAGTTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
*
36475 TA-GGGCTCATATAGTTGCGTATTCAG
1 TAGGGGC-CATATAGTTGCATATTCAG
*
36501 TAGGGTCCATATAGTTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
* *
36527 TA-TGACTCATATAGTTGCATATTCAG
1 TAGGGGC-CATATAGTTGCATATTCAG
*
36553 TAGGGGACATATAGTTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
* *
36579 TAGGGCCCATATAGTTGCATAATCAG
1 TAGGGGCCATATAGTTGCATATTCAG
* *
36605 TAGGTGACATATAGTTGCATATTCAG
1 TAGGGGCCATATAGTTGCATATTCAG
* *
36631 TAGGGCCCATATAGTTGCATAATCAG
1 TAGGGGCCATATAGTTGCATATTCAG
* *
36657 TA-GGGCCAATATAATTGTATATTCAG
1 TAGGGGCC-ATATAGTTGCATATTCAG
36683 TA
1 TA
36685 AGGCCCATTT
Statistics
Matches: 1248, Mismatches: 118, Indels: 74
0.87 0.08 0.05
Matches are distributed among these distances:
22 18 0.01
24 70 0.06
25 97 0.08
26 993 0.80
27 22 0.02
28 3 0.00
29 21 0.02
30 2 0.00
31 1 0.00
33 18 0.01
34 3 0.00
ACGTcount: A:0.29, C:0.15, G:0.25, T:0.31
Consensus pattern (26 bp):
TAGGGGCCATATAGTTGCATATTCAG
Found at i:36819 original size:50 final size:50
Alignment explanation
Indices: 36738--37011 Score: 395
Period size: 50 Copynumber: 5.5 Consensus size: 50
36728 CAACACGCGA
* * * *
36738 AGACATGAAGGTACACGAGAGGACAGAGGCCTCTGCAGTGAGGCGAGGTT
1 AGACACGAAGGTACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAGGTC
** * *
36788 AGTTACGAAGGTACAGGAGAAGACAGAGGCCTCCGCAGTGAGGCGAGGCC
1 AGACACGAAGGTACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAGGTC
* * *
36838 AGACACGAAGGTACACGAGAAGACAGAGGACTCCGCAGTGAGGCGATGCC
1 AGACACGAAGGTACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAGGTC
* *
36888 AAACACAAAGGTACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAGGTC
1 AGACACGAAGGTACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAGGTC
* * * *
36938 AGACACGAAAGTACATGAGAAGATAGAGACCTCCGCAGTGAGGCGAGGTC
1 AGACACGAAGGTACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAGGTC
36988 AGACACGAAGGTACACGAGAAGAC
1 AGACACGAAGGTACACGAGAAGAC
37012 GCGGTGGTGC
Statistics
Matches: 197, Mismatches: 27, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 197 1.00
ACGTcount: A:0.34, C:0.22, G:0.34, T:0.10
Consensus pattern (50 bp):
AGACACGAAGGTACACGAGAAGACAGAGGCCTCCGCAGTGAGGCGAGGTC
Found at i:37212 original size:16 final size:16
Alignment explanation
Indices: 37191--37221 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
37181 AAGGCCTGCA
37191 AACATTTTTGCATCTG
1 AACATTTTTGCATCTG
37207 AACATTTTTGCATCT
1 AACATTTTTGCATCT
37222 AAATTATATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.26, C:0.19, G:0.10, T:0.45
Consensus pattern (16 bp):
AACATTTTTGCATCTG
Found at i:37349 original size:18 final size:18
Alignment explanation
Indices: 37322--37363 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
37312 ATCTATCACA
*
37322 TTGTTGTTTTTTGTTTTT
1 TTGTTTTTTTTTGTTTTT
37340 TTGTTTTTTTTTGTTTTT
1 TTGTTTTTTTTTGTTTTT
37358 TT-TTTT
1 TTGTTTT
37364 CGCTAAAAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 4 0.17
18 19 0.83
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (18 bp):
TTGTTTTTTTTTGTTTTT
Found at i:37362 original size:11 final size:10
Alignment explanation
Indices: 37322--37361 Score: 57
Period size: 10 Copynumber: 4.2 Consensus size: 10
37312 ATCTATCACA
*
37322 TTGTTGTTTT
1 TTGTTTTTTT
37332 TTG--TTTTT
1 TTGTTTTTTT
37340 TTGTTTTTTT
1 TTGTTTTTTT
37350 TTGTTTTTTT
1 TTGTTTTTTT
37360 TT
1 TT
37362 TTCGCTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
8 7 0.26
10 20 0.74
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (10 bp):
TTGTTTTTTT
Found at i:37363 original size:15 final size:16
Alignment explanation
Indices: 37325--37363 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
37315 TATCACATTG
37325 TTGTTTTTTGTT-TTT
1 TTGTTTTTTGTTGTTT
*
37340 TTGTTTTTTTTTGTTT
1 TTGTTTTTTGTTGTTT
37356 TT-TTTTTT
1 TTGTTTTTT
37364 CGCTAAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 17 0.77
16 5 0.23
ACGTcount: A:0.00, C:0.00, G:0.10, T:0.90
Consensus pattern (16 bp):
TTGTTTTTTGTTGTTT
Done.