Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011310.1 Corchorus capsularis cultivar CVL-1 contig11331, 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: 44709
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Found at i:1011 original size:79 final size:78
Alignment explanation
Indices: 819--1066 Score: 381
Period size: 78 Copynumber: 3.2 Consensus size: 78
809 TTGTTTAGGT
* * * * *
819 TTTTA-TAGTTTTAGTCAACTAAAAACTCTATTTTTATTTAATTAAATATAACATCTTTATAACT
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACT
*
883 ATTTTATTTTACCA
65 ATTATATTTTACCA
*
897 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAAGCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
**
962 AAATATTTTAACCA
66 TTATATTTT-ACCA
*
976 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATTCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
1041 TTATATTTTACCA
66 TTATATTTTACCA
1054 TTTTACTATTTTA
1 TTTTACTATTTTA
1067 ATTAAAAACT
Statistics
Matches: 155, Mismatches: 13, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
78 79 0.51
79 76 0.49
ACGTcount: A:0.37, C:0.13, G:0.01, T:0.48
Consensus pattern (78 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATCTAATATCCTTATAACTA
TTATATTTTACCA
Found at i:1849 original size:70 final size:70
Alignment explanation
Indices: 1767--1999 Score: 279
Period size: 70 Copynumber: 3.2 Consensus size: 70
1757 TCATTTAGGT
* *
1767 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATATATTTATAATT
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCTTTATAATT
1831 ATTTTA
65 ATTTTA
*
1837 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATTTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATAT-CTT-T-A-TA
*
1902 TTATATTTTACCA
62 AT-TATTTT---A
* * * * *
1915 TTTTACTATTTTACCCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCTTTATAATTA
*
1980 TTATA
66 TTTTA
*
1985 TTTTACAATTTTACT
1 TTTTACTATTTTACT
2000 ATTTTAGTTA
Statistics
Matches: 141, Mismatches: 13, Indels: 18
0.82 0.08 0.10
Matches are distributed among these distances:
70 63 0.45
71 4 0.03
72 1 0.01
73 6 0.04
74 5 0.04
75 7 0.05
76 1 0.01
77 2 0.01
78 52 0.37
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.49
Consensus pattern (70 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCTTTATAATTA
TTTTA
Found at i:1849 original size:78 final size:77
Alignment explanation
Indices: 1767--2005 Score: 332
Period size: 78 Copynumber: 3.2 Consensus size: 77
1757 TCATTTAGGT
* *
1767 TTTTA-TAGTTTTACTCAACTAAAAACTCTATTTTTATTTAATTAAATATAATAT-ATT-T-A-T
1 TTTTACTA-TTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACT
*
1827 AAT-TATTTT--A
65 ATTATATTTTACA
*
1837 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATTTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTA
1902 TTATATTTTACCA
66 TTATATTTTA-CA
* * *
1915 TTTTACTATTTTACCCAACTAAAAACTCAATTTTTATATAATTAAATCTAATATCCTTATAACTA
1 TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTA
1980 TTATATTTTACAA
66 TTATATTTTAC-A
1993 TTTTACTATTTTA
1 TTTTACTATTTTA
2006 GTTAAAAAAA
Statistics
Matches: 152, Mismatches: 7, Indels: 12
0.89 0.04 0.07
Matches are distributed among these distances:
70 49 0.32
71 4 0.03
72 1 0.01
73 1 0.01
74 3 0.02
75 6 0.04
77 1 0.01
78 87 0.57
ACGTcount: A:0.38, C:0.12, G:0.00, T:0.50
Consensus pattern (77 bp):
TTTTACTATTTTACTCAACTAAAAACTCTATTTTTATATAATTAAATATAATATCCTTATAACTA
TTATATTTTACA
Found at i:2840 original size:87 final size:88
Alignment explanation
Indices: 2733--2899 Score: 282
Period size: 87 Copynumber: 1.9 Consensus size: 88
2723 ATATTTAATA
2733 TTTTAATTATGTTATATAATCTTTTTATTTTAGACAAACTCTTAACCATTTTTAATCTCAACCAA
1 TTTTAATTATGTTATATAATCTTTTTATTTTAGACAAACTCTTAACCATTTTTAATCTCAACCAA
*
2798 ATTCCAAATTATAATTTTAATTC
66 ACTCCAAATTATAATTTTAATTC
* *
2821 TTTTAA-TATGTTATATAATCTTTTTATTTTAGACAAATTCTTAACCATTTTTAATCTCAATCAA
1 TTTTAATTATGTTATATAATCTTTTTATTTTAGACAAACTCTTAACCATTTTTAATCTCAACCAA
* *
2885 ACTCCCAATTTTAAT
66 ACTCCAAATTATAAT
2900 CTCAATTAAT
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
87 68 0.92
88 6 0.08
ACGTcount: A:0.35, C:0.15, G:0.02, T:0.48
Consensus pattern (88 bp):
TTTTAATTATGTTATATAATCTTTTTATTTTAGACAAACTCTTAACCATTTTTAATCTCAACCAA
ACTCCAAATTATAATTTTAATTC
Found at i:3118 original size:23 final size:24
Alignment explanation
Indices: 3092--3139 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
3082 TCACCGTAAG
*
3092 TTAACT-CTTTTTCTCTCTTTTTT
1 TTAACTCCGTTTTCTCTCTTTTTT
*
3115 TTAATTCCGTTTTCTCTCTTTTTT
1 TTAACTCCGTTTTCTCTCTTTTTT
3139 T
1 T
3140 GCAATTAAAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 5 0.23
24 17 0.77
ACGTcount: A:0.08, C:0.21, G:0.02, T:0.69
Consensus pattern (24 bp):
TTAACTCCGTTTTCTCTCTTTTTT
Found at i:5261 original size:2 final size:2
Alignment explanation
Indices: 5254--5286 Score: 50
Period size: 2 Copynumber: 17.0 Consensus size: 2
5244 TCTATAAAGG
*
5254 TA TA TA TA TA TA TG TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5287 CATTTTATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6224 original size:67 final size:68
Alignment explanation
Indices: 6146--6281 Score: 215
Period size: 68 Copynumber: 2.0 Consensus size: 68
6136 TGTGAACCCT
**
6146 CCATCCAATCCATAGA-AGGAAGTAAACCGATAATATTTGTT-CTAGATAAAATTCTA-TATTTA
1 CCATCCAATCCATAGAGAAAAAGTAAACCGATAATATTTGTTCCTA-ATAAAATTCTACT-TTTA
6208 CTAGA
64 CTAGA
6213 CCATCCAATCCATAGAGAAAAAGTAAACCGATAATATTTGTTCCTAATAAAATTCTACTTTTACT
1 CCATCCAATCCATAGAGAAAAAGTAAACCGATAATATTTGTTCCTAATAAAATTCTACTTTTACT
6278 AGA
66 AGA
6281 C
1 C
6282 ATCTATTAAG
Statistics
Matches: 64, Mismatches: 2, Indels: 5
0.90 0.03 0.07
Matches are distributed among these distances:
67 16 0.25
68 44 0.69
69 4 0.06
ACGTcount: A:0.40, C:0.18, G:0.10, T:0.31
Consensus pattern (68 bp):
CCATCCAATCCATAGAGAAAAAGTAAACCGATAATATTTGTTCCTAATAAAATTCTACTTTTACT
AGA
Found at i:7329 original size:18 final size:19
Alignment explanation
Indices: 7303--7338 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
7293 ATGAATAAAG
*
7303 ATAGTATTTGG-TTCCAAT
1 ATAGAATTTGGTTTCCAAT
7321 ATAGAATTTGGTTTCCAA
1 ATAGAATTTGGTTTCCAA
7339 CAGTACTCTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.42
Consensus pattern (19 bp):
ATAGAATTTGGTTTCCAAT
Found at i:10392 original size:57 final size:57
Alignment explanation
Indices: 10299--10407 Score: 155
Period size: 57 Copynumber: 1.9 Consensus size: 57
10289 CGAAACATAT
* * * * *
10299 GATACACGGACCTTGTGGAGAAGTAAATCCTAATAATTCCTGCATGATCAAGCAGAA
1 GATACAAGAACCTTGTGGAGAAGCAAATACTAATAATTCCTCCATGATCAAGCAGAA
* *
10356 GATACAAGAACCTTGTGGAGATGCAAATACTGATAATTCCTCCATGATCAAG
1 GATACAAGAACCTTGTGGAGAAGCAAATACTAATAATTCCTCCATGATCAAG
10408 GACAAATGTA
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
57 45 1.00
ACGTcount: A:0.37, C:0.19, G:0.20, T:0.24
Consensus pattern (57 bp):
GATACAAGAACCTTGTGGAGAAGCAAATACTAATAATTCCTCCATGATCAAGCAGAA
Found at i:24799 original size:173 final size:175
Alignment explanation
Indices: 24489--24829 Score: 399
Period size: 173 Copynumber: 2.0 Consensus size: 175
24479 ATTTATTAAA
* *
24489 GACTCAAAAGCCAATTTTGAGGTTTCAGTTCTCAAAAATATTTCTGAAATTTGGTCGTCTCACTT
1 GACTCAAAAGCCAATTTTGAGGTTTCAATTCTCAAAAATATTTCTGAAATTTAGTCGTCTCACTT
* * * * *
24554 GATGGTCTATCTAATATATCATATAATTTTCGATCCACGTGTCCGATTAAAATTGTTCAAATGTC
66 AACGGTCTATCTAATATATCATATAATTTTCAATCCACGTATCCGATTAAAATTATTCAAATGTC
* *
24619 AGTTAAAAGGTTATTGCGTGATCTACGACTTTCATGAAGGTGAAG
131 AGTTAAAAGGTTATTGCATGATCTAAGACTTTCATGAAGGTGAAG
* * * * * * *
24664 GACTCGAAAGTCAATTTTTATGTTTCAATTCT-AAAAAGTGTTTCTGAAATTTAGTCGTTTTGA-
1 GACTCAAAAGCCAATTTTGAGGTTTCAATTCTCAAAAA-TATTTCTGAAATTTAGTCG-TCTCAC
* *
24727 TTAACGGTCTAT-TTA-ATATCATATAATTTTCAATCTA-GATATCC-AGTTAAAATTATTCCAA
64 TTAACGGTCTATCTAATATATCATATAATTTTCAATCCACG-TATCCGA-TTAAAATTATT-CAA
* * *
24788 GTGTC-GTTAAAAGGTTATTTCATGATCTAAGATTTTCATGAA
126 ATGTCAGTTAAAAGGTTATTGCATGATCTAAGACTTTCATGAA
24830 AGACCCGAAA
Statistics
Matches: 140, Mismatches: 21, Indels: 12
0.81 0.12 0.07
Matches are distributed among these distances:
172 2 0.01
173 67 0.48
174 14 0.10
175 54 0.39
176 3 0.02
ACGTcount: A:0.32, C:0.14, G:0.16, T:0.39
Consensus pattern (175 bp):
GACTCAAAAGCCAATTTTGAGGTTTCAATTCTCAAAAATATTTCTGAAATTTAGTCGTCTCACTT
AACGGTCTATCTAATATATCATATAATTTTCAATCCACGTATCCGATTAAAATTATTCAAATGTC
AGTTAAAAGGTTATTGCATGATCTAAGACTTTCATGAAGGTGAAG
Found at i:27631 original size:40 final size:39
Alignment explanation
Indices: 27570--27660 Score: 105
Period size: 40 Copynumber: 2.3 Consensus size: 39
27560 AAAAAAAAAA
* * * *
27570 CCTTTAATTCACTGAAAGGCCATGTGTTG-TTTTTCCCA-G
1 CCTTTAATCCACTAAAAGGCCAGGTGTTGCTCTTT--CAGG
27609 CCTTTAATCCACTAAAAAGGCCAGGTGTTGCTCTTTCAGG
1 CCTTTAATCCACT-AAAAGGCCAGGTGTTGCTCTTTCAGG
27649 CCTTTAATCCAC
1 CCTTTAATCCAC
27661 CAGGTGTTAG
Statistics
Matches: 45, Mismatches: 4, Indels: 5
0.83 0.07 0.09
Matches are distributed among these distances:
39 14 0.31
40 27 0.60
41 4 0.09
ACGTcount: A:0.23, C:0.26, G:0.16, T:0.34
Consensus pattern (39 bp):
CCTTTAATCCACTAAAAGGCCAGGTGTTGCTCTTTCAGG
Found at i:27767 original size:17 final size:16
Alignment explanation
Indices: 27747--27786 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
27737 GTCTGCGTGC
*
27747 TTTTCTTTCTTTTTTT
1 TTTTCATTCTTTTTTT
*
27763 GTTTTCATTGTTTTTTT
1 -TTTTCATTCTTTTTTT
27780 TTTTCAT
1 TTTTCAT
27787 GTGTGCTCTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 7 0.33
17 14 0.67
ACGTcount: A:0.05, C:0.10, G:0.05, T:0.80
Consensus pattern (16 bp):
TTTTCATTCTTTTTTT
Found at i:30606 original size:19 final size:19
Alignment explanation
Indices: 30559--30606 Score: 51
Period size: 20 Copynumber: 2.5 Consensus size: 19
30549 GTTTATCTTA
*
30559 GTTTCTTTTTCCTCATTTT
1 GTTTCTTTTTCCTCATTAT
* * *
30578 CTTTCTTTTTTCTTGATTAT
1 GTTTC-TTTTTCCTCATTAT
30598 GTTTCTTTT
1 GTTTCTTTT
30607 CTATTGATTC
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
19 8 0.35
20 15 0.65
ACGTcount: A:0.06, C:0.17, G:0.06, T:0.71
Consensus pattern (19 bp):
GTTTCTTTTTCCTCATTAT
Found at i:31182 original size:14 final size:14
Alignment explanation
Indices: 31163--31193 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
31153 ATAAGAATGT
31163 CATCTTAGAATTGA
1 CATCTTAGAATTGA
31177 CATCTTAGAATTGA
1 CATCTTAGAATTGA
31191 CAT
1 CAT
31194 AGGAGGATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.35, C:0.16, G:0.13, T:0.35
Consensus pattern (14 bp):
CATCTTAGAATTGA
Found at i:32424 original size:2 final size:2
Alignment explanation
Indices: 32417--32452 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
32407 TATCTAATTG
32417 AT AT AT AT AT AT 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
32453 GATAGGACTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33031 original size:23 final size:24
Alignment explanation
Indices: 33005--33052 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 24
32995 GCTAGGTATA
33005 CCGCTAAAGAG-AAGAGATCCCGC
1 CCGCTAAAGAGAAAGAGATCCCGC
33028 CCGCTAAAGAGAAAAGAGATCCCGC
1 CCGCTAAAGAG-AAAGAGATCCCGC
33053 AGCGTAGCGC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
23 11 0.48
25 12 0.52
ACGTcount: A:0.38, C:0.29, G:0.25, T:0.08
Consensus pattern (24 bp):
CCGCTAAAGAGAAAGAGATCCCGC
Found at i:33946 original size:2 final size:2
Alignment explanation
Indices: 33939--33965 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
33929 TGTTAAGTAT
33939 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 T
33966 TTGCGAATAT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:38335 original size:2 final size:2
Alignment explanation
Indices: 38330--38374 Score: 65
Period size: 2 Copynumber: 23.0 Consensus size: 2
38320 TATATTTTGC
* *
38330 AT AT AT AT AT AT AT AT -T AT GT AT AC 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
38371 AT AT
1 AT AT
38375 GTTAAATAAA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (2 bp):
AT
Found at i:38339 original size:21 final size:21
Alignment explanation
Indices: 38313--38366 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
38303 CGGCCCCAAA
* *
38313 ATATATATATATTTTGCATAT
1 ATATATATATATTATGCATAC
*
38334 ATATATATATATTATGTATAC
1 ATATATATATATTATGCATAC
38355 ATATATATATAT
1 ATATATATATAT
38367 ATATATATGT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.43, C:0.04, G:0.04, T:0.50
Consensus pattern (21 bp):
ATATATATATATTATGCATAC
Found at i:39230 original size:31 final size:31
Alignment explanation
Indices: 39177--39348 Score: 146
Period size: 31 Copynumber: 5.5 Consensus size: 31
39167 ACGGTGTCCG
* *
39177 ACGTGGCACGCCAAGTGCACCAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* * * *
39208 ATGTGGCATGCCATGTGTACCAAAAACTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* * *
39239 ACGTGGCACGCCACGTGAACAAAAAAGTGAT
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* * * *
39270 ATGTGACACGCCACGTATACTAAAAAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* * * * * *
39301 ACGTGACATGTCACATGTACTAAATAGTGAC
1 ACGTGGCACGCCACGTGTACCAAAAAGTGAC
* * *
39332 ACATGGCATGCGACGTG
1 ACGTGGCACGCCACGTG
39349 CACAAAAGGA
Statistics
Matches: 112, Mismatches: 29, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
31 112 1.00
ACGTcount: A:0.35, C:0.23, G:0.24, T:0.18
Consensus pattern (31 bp):
ACGTGGCACGCCACGTGTACCAAAAAGTGAC
Found at i:39247 original size:62 final size:62
Alignment explanation
Indices: 39177--39305 Score: 168
Period size: 62 Copynumber: 2.1 Consensus size: 62
39167 ACGGTGTCCG
* * * * * *
39177 ACGTGGCACGCCAAGTGCACCAAAAAGTGACATGTGGCATGCCATGTGTACCAAAAACTGAC
1 ACGTGGCACGCCAAGTGAACAAAAAAGTGACATGTGACACGCCACGTATACCAAAAACTGAC
* * * *
39239 ACGTGGCACGCCACGTGAACAAAAAAGTGATATGTGACACGCCACGTATACTAAAAAGTGAC
1 ACGTGGCACGCCAAGTGAACAAAAAAGTGACATGTGACACGCCACGTATACCAAAAACTGAC
39301 ACGTG
1 ACGTG
39306 ACATGTCACA
Statistics
Matches: 57, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
62 57 1.00
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.16
Consensus pattern (62 bp):
ACGTGGCACGCCAAGTGAACAAAAAAGTGACATGTGACACGCCACGTATACCAAAAACTGAC
Done.