Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010464.1 Corchorus capsularis cultivar CVL-1 contig10485, 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: 25658
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1947 original size:769 final size:769
Alignment explanation
Indices: 877--2333 Score: 2001
Period size: 769 Copynumber: 1.9 Consensus size: 769
867 ACTTTTTTGC
877 TATTTTAGATCACATTGATAATTCATTAATTTGGTAGAGTAATAGCGAGATATCAATTTTAATTT
1 TATTTTAGATCACATTGATAATTCATTAATTTGGTAGAGTAATAGCGAGATATCAATTTTAATTT
*
942 TACTTCAACTTGCTAAAGATATGCATATATAGCATATAAATTTAATTTCTCTATCACCAAAAAAA
66 TACTTCAACTTGCCAAAGATATGCA-ATATA--ATATAAATTTAATTTCTCTATCACCAAAAAAA
* *
1007 GGAAGGACATATGAATTAGTAATTAGGAATCATTTTGTACATCTAATTTTATACTTCCTCAGGTT
128 GGAAGGACATATGAATTAGTAATTAGGAACCATTTTGTACACCTAATTTTATACTTCCTCAGGTT
** * * *
1072 GCATTAAGTTTAGTTATAACCTTGTAAAAACTTGACTTCCAGGTCCGGTATGATTGGTTGAATTG
193 GCATTAAGTTTAGAAATAACCTTATAAAAACTTGACTTACAGGTCCGGTATGATTAGTTGAATTG
* * * *
1137 TGAGATTTGTTTTGTAGAGATTGAAATGGTGAAATTAGGTATTATAG-TGTG-A-C-ATCAGAAT
258 TGAGATTTGTTTTGTAGAGATTGAAATAGTAAAATTAGGTATT-GAGTTGTGAATCAATAAGAAT
* * * * *
1198 AAC-AATAATGA-GA-AA-AAAATTTGTTGAAAATATTTATGAAATACTAAGATTGATTAACATA
322 AACAAATAATAATAATAATAAAATTTGTTGAAAATATTCATAAAACACTAAGATTGATTAACATA
* * *
1259 TACACATAGAATAAGATAATAAAATTAAACTCCTAATTCTATATACAAGGACTTTAACTGACCAT
387 TACAC--AGAATAAAATAATAAAATTAAACTCCTAATTCTATATACAAGAACTTTAACTAACCAT
*
1324 CAATCTATATATCAATAAATTAAACTCACTA-TTTTTTAACCCTATATATCTCTTAAATTATCCA
450 CAATCTATATATCAATAAATTAAACTCACTATTTTTTTAACCCTAAATATCTC-T---TTATCCA
* *
1388 CTACAACTTTTTTAGTAATCTTAAATTAAAAA-TTAATAAC-ATTCACCATTGATAATGTTACTA
511 CTACAAC-TTTTTAGTAATCTTAAATCAAAAAGTTAATAACAATTCACCATTGATAAAGTTACTA
* *
1451 AGCATGTAAGGTTGCTAAATTTCTTGATAATTCTATAGTTTAGCTTTCTAATTAGAAACCATAAA
575 AGCATGTAAGGTTGCTAAATTTCTTGATAA-TATAGAGTTTAGCTTTCTAATTAGAAACCATAAA
1516 TGAGAAATTTGATAACCAAAATTACTAAGAATGTAAAGTTATTAAATTAGTTCATAGTAGTATTA
639 TGAGAAATTTGATAACCAAAATTACTAAGAATGTAAAGTTATTAAATTAGTTCATAGTAGTATTA
1581 TGCCTTTTTTTATCATTATAGATTTTTTTTGTAACCTTAAATAAAATTATTACCTTTTTGCTATG
704 TGCCTTTTTTTATCATTATAGATTTTTTTTGTAACCTTAAATAAAATTATTACCTTTTTGCTATG
1646 T
769 T
* * * *
1647 TATTTTAGATCATATTGATCATTCATTATTGGTTTGGTAGAGTAATAGCTAGATATCAATTTTAA
1 TATTTTAGATCACATTGATAATTCATTA---ATTTGGTAGAGTAATAGCGAGATATCAATTTTAA
* *
1712 TTTTGCTTCAACTTGCCAAAGGTATGC-ATAT-ATATAAATTTAATTTCTCTATCACC-AAAAAA
63 TTTTACTTCAACTTGCCAAAGATATGCAATATAATATAAATTTAATTTCTCTATCACCAAAAAAA
*
1774 GGAAAGGACATATGAATTAGTAATTAGGAACCAATTTTGTACACCTAATTTTATACTTCCTCATG
128 GG-AAGGACATATGAATTAGTAATTAGGAACC-ATTTTGTACACCTAATTTTATACTTCCTCAGG
* * * *
1839 TTGCATTAAGTTTA-AAATAACCTTATACAAATTTGACTTACAGGTCCGGATGTGTTTAGTTGAA
191 TTGCATTAAGTTTAGAAATAACCTTATAAAAACTTGACTTACAGGTCCGG-TATGATTAGTTGAA
*
1903 TTGTGAGATTTGTTTTAG-AGAGATTGAAATAGTAAAATTAGGTATTGCGTTGTGATATCAAAAT
255 TTGTGAGATTTGTTTT-GTAGAGATTGAAATAGTAAAATTAGGTATTGAGTTGTGA-ATC-----
*
1967 ATAATAATAATAATAATAATAACAATAATAATAATAATAATAAAATTTGTTGAAAATATTCATAA
313 -----------AATAAGAATAAC-A-AATAATAATAATAATAAAATTTGTTGAAAATATTCATAA
* *
2032 AACACTAAGATTGATTAACATATACACAGTATAAAATAATAAAATTAAACTCGTAATTCTATATA
365 AACACTAAGATTGATTAACATATACACAGAATAAAATAATAAAATTAAACTCCTAATTCTATATA
* * ** *
2097 TAAGAACTTTAACTAACCATCAATCTATATATCGATAAATTACCCTCTCTATTTTTTTAACCCTA
430 CAAGAACTTTAACTAACCATCAATCTATATATCAATAAATTAAACTCACTATTTTTTTAACCCTA
* * **
2162 AATATCTCTTTATTCACTACAACTTTTTAGTACTCTTTGATCAAAAAGTTAATAACAATTCACCA
495 AATATCTCTTTATCCACTACAACTTTTTAGTAATCTTAAATCAAAAAGTTAATAACAATTCACCA
*
2227 TTGATAAAGTTACTAAGCATGTAAGGTTGTTAAATTTCTTGATAATATAGAGTTTAGCTTTCTAA
560 TTGATAAAGTTACTAAGCATGTAAGGTTGCTAAATTTCTTGATAATATAGAGTTTAGCTTTCTAA
*
2292 TTAGAAACCATAAATGAGAAATTTGATAACGAAAATTACTAA
625 TTAGAAACCATAAATGAGAAATTTGATAACCAAAATTACTAA
2334 TATTATAAGG
Statistics
Matches: 599, Mismatches: 51, Indels: 54
0.85 0.07 0.08
Matches are distributed among these distances:
767 8 0.01
768 83 0.14
769 101 0.17
770 27 0.05
771 5 0.01
772 1 0.00
773 56 0.09
789 29 0.05
790 80 0.13
791 51 0.09
792 7 0.01
793 81 0.14
794 22 0.04
795 48 0.08
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.38
Consensus pattern (769 bp):
TATTTTAGATCACATTGATAATTCATTAATTTGGTAGAGTAATAGCGAGATATCAATTTTAATTT
TACTTCAACTTGCCAAAGATATGCAATATAATATAAATTTAATTTCTCTATCACCAAAAAAAGGA
AGGACATATGAATTAGTAATTAGGAACCATTTTGTACACCTAATTTTATACTTCCTCAGGTTGCA
TTAAGTTTAGAAATAACCTTATAAAAACTTGACTTACAGGTCCGGTATGATTAGTTGAATTGTGA
GATTTGTTTTGTAGAGATTGAAATAGTAAAATTAGGTATTGAGTTGTGAATCAATAAGAATAACA
AATAATAATAATAATAAAATTTGTTGAAAATATTCATAAAACACTAAGATTGATTAACATATACA
CAGAATAAAATAATAAAATTAAACTCCTAATTCTATATACAAGAACTTTAACTAACCATCAATCT
ATATATCAATAAATTAAACTCACTATTTTTTTAACCCTAAATATCTCTTTATCCACTACAACTTT
TTAGTAATCTTAAATCAAAAAGTTAATAACAATTCACCATTGATAAAGTTACTAAGCATGTAAGG
TTGCTAAATTTCTTGATAATATAGAGTTTAGCTTTCTAATTAGAAACCATAAATGAGAAATTTGA
TAACCAAAATTACTAAGAATGTAAAGTTATTAAATTAGTTCATAGTAGTATTATGCCTTTTTTTA
TCATTATAGATTTTTTTTGTAACCTTAAATAAAATTATTACCTTTTTGCTATGT
Found at i:1975 original size:3 final size:3
Alignment explanation
Indices: 1967--2009 Score: 77
Period size: 3 Copynumber: 14.3 Consensus size: 3
1957 ATATCAAAAT
*
1967 ATA ATA ATA ATA ATA ATA ATA ACA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2010 AATTTGTTGA
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:3117 original size:332 final size:333
Alignment explanation
Indices: 2494--3149 Score: 820
Period size: 332 Copynumber: 1.9 Consensus size: 333
2484 CAAAAAATGC
* * * * ** * *
2494 AAGGTTATTGAATTAATTGTTAGTACTATACATCTTTTATGATCATTATAGGTTTTTTAATAACT
1 AAGGTCATTGAATTAATTGATAGTACCATACATCTTTTATAAAAATTATAGATTTTTCAATAACT
*
2559 TTTGAGAAAAAAAAAAAGGTAAATATTCACCATTGATGAAAGTTTACTCATGTTATTAAGAATGT
66 TTTGAG--AAAAAAAAAGGTAAATATTCACCATTGATGAAAGTTTACTAATG-T-TT---AATGT
* * * *
2624 AAGGATTAGTAAATACAATTTTAATTTACTTTTATAGCTTTTTTAGTAAACTTAAGTAATAAAAT
124 AAGGATTAGTAAATAAAATTTTAATTAACTTTTATAGCTGTTTCAGTAAACTTAAGTAATAAAAT
* ** * ** * *
2689 TGGTAATTTTTATTAATGATGAAAAGTTACTAAACTTAATAAGAACGTGTAAGGTTATTTCAATT
189 TGGTAACTTCCATTAATGATGAAAAGTTACTAAAATTAATAAGAAC-TGTAAAATTACTTCAATG
* *
2754 TAGATAGTACTATAAAGTTTTCCATAACCTTTATAACCTTTTAAGTAATCTTAGGTAAGAAAATC
253 TAGATAGAACTATAAAGTTTTCCATAACCTTTATAA-C-TTTAAGTAATCTTAGATAAGAAAATC
2819 AGTACTTTACTATAATAT
316 AGTACTTTACTATAATAT
* * * *
2837 AAGGTCATTGAATTAGTTGATAGTACCATACCTTTTTTATAAAAATTATAGATTTTTCAGTAACT
1 AAGGTCATTGAATTAATTGATAGTACCATACATCTTTTATAAAAATTATAGATTTTTCAATAACT
* * *
2902 TTTGAG-AGAAAAAAGGTAAATATTTACTATTGATGAAAGTTTACTAATG-TT-AT-TAAGGATT
66 TTTGAGAAAAAAAAAGGTAAATATTCACCATTGATGAAAGTTTACTAATGTTTAATGTAAGGATT
* *
2963 GGTAAATAAAATTTTAA-TAACTTTTATAGGTGTTTCAGTAGATCACTTAAGTAATAAAATTGGT
131 AGTAAATAAAATTTTAATTAACTTTTATAGCTGTTTCAGTA-A--ACTTAAGTAATAAAATTGGT
* * * *
3027 AACTTCCATTATTGATTAAAAGTTACTAAAATTAATAAGGA-TGTAAAATTACTTGAATGTAGAT
193 AACTTCCATTAATGATGAAAAGTTACTAAAATTAATAAGAACTGTAAAATTACTTCAATGTAGAT
*
3091 AGAACTATAATGTTTTCCATAACCTTTATAACTTTAAGTAATCTTAGATAAGAAAATCA
258 AGAACTATAAAGTTTTCCATAACCTTTATAACTTTAAGTAATCTTAGATAAGAAAATCA
3150 ATAACCAATA
Statistics
Matches: 273, Mismatches: 37, Indels: 19
0.83 0.11 0.06
Matches are distributed among these distances:
330 26 0.10
331 20 0.07
332 71 0.26
333 2 0.01
334 54 0.20
337 2 0.01
340 39 0.14
343 59 0.22
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (333 bp):
AAGGTCATTGAATTAATTGATAGTACCATACATCTTTTATAAAAATTATAGATTTTTCAATAACT
TTTGAGAAAAAAAAAGGTAAATATTCACCATTGATGAAAGTTTACTAATGTTTAATGTAAGGATT
AGTAAATAAAATTTTAATTAACTTTTATAGCTGTTTCAGTAAACTTAAGTAATAAAATTGGTAAC
TTCCATTAATGATGAAAAGTTACTAAAATTAATAAGAACTGTAAAATTACTTCAATGTAGATAGA
ACTATAAAGTTTTCCATAACCTTTATAACTTTAAGTAATCTTAGATAAGAAAATCAGTACTTTAC
TATAATAT
Found at i:4130 original size:21 final size:20
Alignment explanation
Indices: 4105--4146 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
4095 CTAAATTACC
4105 TTATAATACTATAACATTTTT
1 TTATAATACTATAAC-TTTTT
**
4126 TTATAATTTTATAACTTTTT
1 TTATAATACTATAACTTTTT
4146 T
1 T
4147 AGCAACCTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 6 0.32
21 13 0.68
ACGTcount: A:0.33, C:0.07, G:0.00, T:0.60
Consensus pattern (20 bp):
TTATAATACTATAACTTTTT
Found at i:5780 original size:2 final size:2
Alignment explanation
Indices: 5773--5823 Score: 84
Period size: 2 Copynumber: 24.5 Consensus size: 2
5763 TGGTGGGGCA
5773 AT AT AT AT GAT AT AT AT GAT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT -AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT
5817 AT AT AT A
1 AT AT AT A
5824 GCTTTCTTCA
Statistics
Matches: 47, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
2 43 0.91
3 4 0.09
ACGTcount: A:0.49, C:0.00, G:0.04, T:0.47
Consensus pattern (2 bp):
AT
Found at i:9654 original size:16 final size:16
Alignment explanation
Indices: 9631--9705 Score: 73
Period size: 16 Copynumber: 4.8 Consensus size: 16
9621 ATTTTTGGGT
9631 ACCCGAATCCGAAATG
1 ACCCGAATCCGAAATG
* *
9647 ACCTGAATCC-AAACG
1 ACCCGAATCCGAAATG
9662 ACCCGAA-CCTGAAATG
1 ACCCGAATCC-GAAATG
* * *
9678 ACCCAAACCCAAAATG
1 ACCCGAATCCGAAATG
*
9694 ACCCGAACCCGA
1 ACCCGAATCCGA
9706 TCAACCTGAC
Statistics
Matches: 48, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
14 2 0.04
15 10 0.21
16 34 0.71
17 2 0.04
ACGTcount: A:0.40, C:0.36, G:0.15, T:0.09
Consensus pattern (16 bp):
ACCCGAATCCGAAATG
Found at i:9690 original size:31 final size:31
Alignment explanation
Indices: 9631--9702 Score: 83
Period size: 31 Copynumber: 2.3 Consensus size: 31
9621 ATTTTTGGGT
** *
9631 ACCCGAATCCGAAATGACCTGAATCC-AAACG
1 ACCCGAA-CCGAAATGACCCAAACCCAAAACG
*
9662 ACCCGAACCTGAAATGACCCAAACCCAAAATG
1 ACCCGAACC-GAAATGACCCAAACCCAAAACG
9694 ACCCGAACC
1 ACCCGAACC
9703 CGATCAACCT
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
30 2 0.06
31 20 0.57
32 13 0.37
ACGTcount: A:0.40, C:0.36, G:0.14, T:0.10
Consensus pattern (31 bp):
ACCCGAACCGAAATGACCCAAACCCAAAACG
Found at i:11427 original size:17 final size:17
Alignment explanation
Indices: 11405--11441 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
11395 AATGGGCGAT
11405 GGACAAGAAACACTCAG
1 GGACAAGAAACACTCAG
*
11422 GGACAAGAAACACTCGG
1 GGACAAGAAACACTCAG
11439 GGA
1 GGA
11442 TATTATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.43, C:0.22, G:0.30, T:0.05
Consensus pattern (17 bp):
GGACAAGAAACACTCAG
Found at i:11484 original size:19 final size:19
Alignment explanation
Indices: 11411--11485 Score: 64
Period size: 19 Copynumber: 4.0 Consensus size: 19
11401 CGATGGACAA
* *
11411 GAAACACTCAGGGACA--A
1 GAAACACTCAGGGATATTT
*
11428 GAAACACTCGGGGATATTAT
1 GAAACACTCAGGGATATT-T
* * *
11448 TAAACACTCAGTGTTATTT
1 GAAACACTCAGGGATATTT
*
11467 GAAACACTAAGGGATATTT
1 GAAACACTCAGGGATATTT
11486 TTAAAAACTC
Statistics
Matches: 44, Mismatches: 11, Indels: 4
0.75 0.19 0.07
Matches are distributed among these distances:
17 14 0.32
19 16 0.36
20 14 0.32
ACGTcount: A:0.39, C:0.16, G:0.20, T:0.25
Consensus pattern (19 bp):
GAAACACTCAGGGATATTT
Found at i:11729 original size:31 final size:30
Alignment explanation
Indices: 11693--11792 Score: 130
Period size: 31 Copynumber: 3.3 Consensus size: 30
11683 GTATTACAAT
*
11693 GCTCAATTTGGTCATAAACCTTTGAGCGAGC
1 GCTCAATTTGGTCCTAAACCTTTGAGCG-GC
* * *
11724 GCTCAATTTCGTCCTAAACCTTTGAACCTGC
1 GCTCAATTTGGTCCTAAACCTTTG-AGCGGC
11755 -CTCAATTTGGTCCTAAACCTTTGAGCGGTC
1 GCTCAATTTGGTCCTAAACCTTTGAGCGG-C
11785 GCTCAATT
1 GCTCAATT
11793 CAGTCCTGTT
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
29 3 0.05
30 23 0.39
31 31 0.53
32 2 0.03
ACGTcount: A:0.23, C:0.27, G:0.18, T:0.32
Consensus pattern (30 bp):
GCTCAATTTGGTCCTAAACCTTTGAGCGGC
Found at i:14202 original size:29 final size:29
Alignment explanation
Indices: 14161--14301 Score: 203
Period size: 29 Copynumber: 4.8 Consensus size: 29
14151 GAGCGACCGC
14161 TCAAAGGTTTAGGACCAAATTGAGCAGGT
1 TCAAAGGTTTAGGACCAAATTGAGCAGGT
14190 TCAAAGGTTTAGGACCAAATTGAGCAGGT
1 TCAAAGGTTTAGGACCAAATTGAGCAGGT
* *
14219 TCAATGGTTTAGGACCAAATTCAGCAGGT
1 TCAAAGGTTTAGGACCAAATTGAGCAGGT
* *
14248 TCAAAGGTTTATGACCAAATTGAG-AGCTCGC
1 TCAAAGGTTTAGGACCAAATTGAGCAG---GT
*
14279 TCAAAGGTTTAGGACTAAATTGA
1 TCAAAGGTTTAGGACCAAATTGA
14302 ACATTTAGCC
Statistics
Matches: 101, Mismatches: 8, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
28 2 0.02
29 77 0.76
31 22 0.22
ACGTcount: A:0.34, C:0.15, G:0.25, T:0.26
Consensus pattern (29 bp):
TCAAAGGTTTAGGACCAAATTGAGCAGGT
Found at i:18332 original size:21 final size:21
Alignment explanation
Indices: 18308--18347 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
18298 GTTAATGCGA
*
18308 ATTTGGGCTGATAATTCTCAC
1 ATTTGGGCCGATAATTCTCAC
18329 ATTTGGGCCGATAATTCTC
1 ATTTGGGCCGATAATTCTC
18348 CAAAAACCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.23, C:0.20, G:0.20, T:0.38
Consensus pattern (21 bp):
ATTTGGGCCGATAATTCTCAC
Found at i:18381 original size:2 final size:2
Alignment explanation
Indices: 18374--18403 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
18364 TGTTCCATGT
18374 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
18404 GTTTGTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:25080 original size:44 final size:40
Alignment explanation
Indices: 25001--25078 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
24991 CCAAGTAATT
25001 TTATAAAATTGTGCTTCCTTCTTAATGATTTTATTTTATA
1 TTATAAAATTGTGCTTCCTTCTTAATGATTTTATTTTATA
* * *
25041 TTATAAAATTGTGCTTCCTTCCTGATGATTAT-TTTTAT
1 TTATAAAATTGTGCTTCCTTCTTAATGATTTTATTTTAT
25079 TTGTTCACAT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 6 0.17
40 29 0.83
ACGTcount: A:0.26, C:0.12, G:0.09, T:0.54
Consensus pattern (40 bp):
TTATAAAATTGTGCTTCCTTCTTAATGATTTTATTTTATA
Done.