Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010192.1 Corchorus capsularis cultivar CVL-1 contig10213, 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: 83215
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.32
Found at i:152 original size:12 final size:12
Alignment explanation
Indices: 99--140 Score: 66
Period size: 12 Copynumber: 3.4 Consensus size: 12
89 TTTAAAATTA
99 ATTTTTTTATTG
1 ATTTTTTTATTG
111 ATTTTTTTATTTG
1 ATTTTTTTA-TTG
*
124 ATTTTTTGATTG
1 ATTTTTTTATTG
136 ATTTT
1 ATTTT
141 GATTTTTTTT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
12 17 0.61
13 11 0.39
ACGTcount: A:0.17, C:0.00, G:0.10, T:0.74
Consensus pattern (12 bp):
ATTTTTTTATTG
Found at i:464 original size:13 final size:13
Alignment explanation
Indices: 426--463 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
416 AACGAATTTC
*
426 GAAAACCATTTTT
1 GAAAAACATTTTT
*
439 GAAAAACACTTTT
1 GAAAAACATTTTT
452 GAAAAAC-TTTTT
1 GAAAAACATTTTT
464 TTTATTTAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
12 4 0.18
13 18 0.82
ACGTcount: A:0.42, C:0.13, G:0.08, T:0.37
Consensus pattern (13 bp):
GAAAAACATTTTT
Found at i:512 original size:20 final size:21
Alignment explanation
Indices: 473--520 Score: 80
Period size: 20 Copynumber: 2.3 Consensus size: 21
463 TTTTATTTAA
473 AAAACCATGACTCTTTTTTTG
1 AAAACCATGACTCTTTTTTTG
*
494 AAAATCATGACTC-TTTTTTG
1 AAAACCATGACTCTTTTTTTG
514 AAAACCA
1 AAAACCA
521 CTTTATTGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 13 0.52
21 12 0.48
ACGTcount: A:0.35, C:0.19, G:0.08, T:0.38
Consensus pattern (21 bp):
AAAACCATGACTCTTTTTTTG
Found at i:8995 original size:13 final size:13
Alignment explanation
Indices: 8977--9019 Score: 52
Period size: 13 Copynumber: 3.3 Consensus size: 13
8967 ATCTGACTGT
8977 TTTGGTTTATTA-
1 TTTGGTTTATTAC
*
8989 TTCTGGTTTAATAC
1 TT-TGGTTTATTAC
*
9003 TTTGGTTTATGAC
1 TTTGGTTTATTAC
9016 TTTG
1 TTTG
9020 ATTATGATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
12 2 0.08
13 22 0.85
14 2 0.08
ACGTcount: A:0.16, C:0.07, G:0.19, T:0.58
Consensus pattern (13 bp):
TTTGGTTTATTAC
Found at i:11879 original size:24 final size:24
Alignment explanation
Indices: 11852--11897 Score: 83
Period size: 24 Copynumber: 1.9 Consensus size: 24
11842 TTCTTTTTCC
*
11852 TGTTGCTCATTCTTTTTCTTCTGT
1 TGTTGCTCACTCTTTTTCTTCTGT
11876 TGTTGCTCACTCTTTTTCTTCT
1 TGTTGCTCACTCTTTTTCTTCT
11898 TCTACTGCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.04, C:0.24, G:0.11, T:0.61
Consensus pattern (24 bp):
TGTTGCTCACTCTTTTTCTTCTGT
Found at i:11906 original size:24 final size:24
Alignment explanation
Indices: 11855--11907 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
11845 TTTTTCCTGT
* **
11855 TGCTCATTCTTTTTCTTCTGTTGT
1 TGCTCACTCTTTTTCTTCTGTTAC
11879 TGCTCACTCTTTTTCTTCT-TCTAC
1 TGCTCACTCTTTTTCTTCTGT-TAC
11903 TGCTC
1 TGCTC
11908 TTTTTCTCTC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 1 0.04
24 24 0.96
ACGTcount: A:0.06, C:0.28, G:0.09, T:0.57
Consensus pattern (24 bp):
TGCTCACTCTTTTTCTTCTGTTAC
Found at i:50500 original size:32 final size:33
Alignment explanation
Indices: 50464--50531 Score: 95
Period size: 33 Copynumber: 2.1 Consensus size: 33
50454 CGCCACCATT
*
50464 TAGCGGCGCCTA-ACGAAG-AAAACGCCGCTATA
1 TAGCGGCGCCTATAAG-AGCAAAACGCCGCTATA
*
50496 TAGCGGCGTCTATAAGAGCAAAACGCCGCTATA
1 TAGCGGCGCCTATAAGAGCAAAACGCCGCTATA
50529 TAG
1 TAG
50532 TGGAGTCCAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
32 13 0.41
33 19 0.59
ACGTcount: A:0.34, C:0.25, G:0.25, T:0.16
Consensus pattern (33 bp):
TAGCGGCGCCTATAAGAGCAAAACGCCGCTATA
Found at i:51094 original size:29 final size:29
Alignment explanation
Indices: 51062--51119 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
51052 ACACTCCTCC
51062 ATTTTCTTTCATCTTCTCCCTTCTCCCTT
1 ATTTTCTTTCATCTTCTCCCTTCTCCCTT
51091 ATTTTCTTTCATCTTCTCCCTTCTCCCTT
1 ATTTTCTTTCATCTTCTCCCTTCTCCCTT
51120 CTCCTCTCCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.07, C:0.38, G:0.00, T:0.55
Consensus pattern (29 bp):
ATTTTCTTTCATCTTCTCCCTTCTCCCTT
Found at i:51258 original size:13 final size:13
Alignment explanation
Indices: 51240--51265 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
51230 AATTTTATGG
51240 TTCTCCTTTCCTT
1 TTCTCCTTTCCTT
51253 TTCTCCTTTCCTT
1 TTCTCCTTTCCTT
51266 ACGTTCTCCT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.38, G:0.00, T:0.62
Consensus pattern (13 bp):
TTCTCCTTTCCTT
Found at i:51367 original size:84 final size:84
Alignment explanation
Indices: 51243--51436 Score: 347
Period size: 84 Copynumber: 2.3 Consensus size: 84
51233 TTTATGGTTC
*
51243 TCCTTTCCTTTTCTCCTTTCCTTACGTTCTCCTTGAATCATTCCCAAATTTCTAAAACCCTAAAT
1 TCCTTTCCTTTTCTCCTTTCCTTACGTTCTCCTAGAATCATTCCCAAATTTCTAAAACCCTAAAT
51308 TCATTTTCTTCGGTTCATT
66 TCATTTTCTTCGGTTCATT
*
51327 TCCTTTCCTTTTCTCCTTTCCTTACGTTCTCCTAGAATCATTCCCAAATTTTTAAAACCCTAAAT
1 TCCTTTCCTTTTCTCCTTTCCTTACGTTCTCCTAGAATCATTCCCAAATTTCTAAAACCCTAAAT
51392 TCATTTTCTTCGGTTCATT
66 TCATTTTCTTCGGTTCATT
*
51411 TCCTTTCC--TTCTCCTTTCCTTCCGTT
1 TCCTTTCCTTTTCTCCTTTCCTTACGTT
51437 TGATTGATTT
Statistics
Matches: 107, Mismatches: 3, Indels: 2
0.96 0.03 0.02
Matches are distributed among these distances:
82 17 0.16
84 90 0.84
ACGTcount: A:0.17, C:0.31, G:0.05, T:0.47
Consensus pattern (84 bp):
TCCTTTCCTTTTCTCCTTTCCTTACGTTCTCCTAGAATCATTCCCAAATTTCTAAAACCCTAAAT
TCATTTTCTTCGGTTCATT
Found at i:53206 original size:27 final size:27
Alignment explanation
Indices: 53169--53285 Score: 180
Period size: 27 Copynumber: 4.3 Consensus size: 27
53159 TCCGGCTGTC
53169 CCCACTTCGACCCCAGAAGTGGATCCT
1 CCCACTTCGACCCCAGAAGTGGATCCT
*
53196 CCCACTTCGACCCCAGAAGTCGATCCT
1 CCCACTTCGACCCCAGAAGTGGATCCT
* * *
53223 CCCACTTCGACCCAAGTAGTGAATCCT
1 CCCACTTCGACCCCAGAAGTGGATCCT
* *
53250 CCCACTTCGACCCTAGCAGTGGATCCT
1 CCCACTTCGACCCCAGAAGTGGATCCT
53277 CCCACTTCG
1 CCCACTTCG
53286 GGTCCAGTTG
Statistics
Matches: 82, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
27 82 1.00
ACGTcount: A:0.21, C:0.42, G:0.16, T:0.21
Consensus pattern (27 bp):
CCCACTTCGACCCCAGAAGTGGATCCT
Found at i:55494 original size:2 final size:2
Alignment explanation
Indices: 55487--55516 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
55477 AACAATTTTC
55487 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
55517 GCTACTTTGA
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):
AT
Found at i:55754 original size:32 final size:32
Alignment explanation
Indices: 55702--55764 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
55692 GGATATACCT
* *
55702 TTATATAGCGGCGTCTAAAGAACAAAACGCCC
1 TTATATAGCGGCATCCAAAGAACAAAACGCCC
*
55734 TTATCTAGCGGCATCCAAAGAACAAAACGCC
1 TTATATAGCGGCATCCAAAGAACAAAACGCC
55765 GCTATATTTA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.38, C:0.27, G:0.17, T:0.17
Consensus pattern (32 bp):
TTATATAGCGGCATCCAAAGAACAAAACGCCC
Found at i:55850 original size:26 final size:26
Alignment explanation
Indices: 55815--55963 Score: 223
Period size: 26 Copynumber: 5.8 Consensus size: 26
55805 TAAATTGCAT
* *
55815 ATAGCGGCGTCTAGACGCCGTCAAAC
1 ATAGTGGCGTCTAGACGCCGCCAAAC
55841 ATAGTGGCGTCTAGACGCCGCCAAAC
1 ATAGTGGCGTCTAGACGCCGCCAAAC
*
55867 ATAGAGGCGTCTAGACGCCGCCAAAC
1 ATAGTGGCGTCTAGACGCCGCCAAAC
55893 ATAGTGGCGTCTAGACGCCGCCAAAC
1 ATAGTGGCGTCTAGACGCCGCCAAAC
*
55919 ATAGTGGCGTCTAGACGCCGTC-AA-
1 ATAGTGGCGTCTAGACGCCGCCAAAC
*
55943 ATAGGGGCGTC-AGGACGCCGC
1 ATAGTGGCGTCTA-GACGCCGC
55964 AATTTGATAT
Statistics
Matches: 115, Mismatches: 7, Indels: 4
0.91 0.06 0.03
Matches are distributed among these distances:
23 1 0.01
24 17 0.15
25 2 0.02
26 95 0.83
ACGTcount: A:0.26, C:0.30, G:0.30, T:0.15
Consensus pattern (26 bp):
ATAGTGGCGTCTAGACGCCGCCAAAC
Found at i:56113 original size:90 final size:88
Alignment explanation
Indices: 55919--56115 Score: 218
Period size: 88 Copynumber: 2.2 Consensus size: 88
55909 GCCGCCAAAC
** * * *
55919 ATAGTGGCGTCTAGACGCCGTCAAATAGGGGCGTCAGGACGCCGCAATTTGATATTCAAAAAGTT
1 ATAGTGGCGTCTAGACGCCCCCAAATAGGAGCGTCAGGACGCCGCAATTTAATATTAAAAAAGTT
**
55984 TTATTTTTCCATAAACGCCTTAG
66 TTATTTTTCCATAAACGCCACAG
* * *
56007 TTAGTGGCGTCTAGACGCCCCCAAATAGTAGCGTCCA-GACGCCGCAATATATAATTTTAAAAAA
1 ATAGTGGCGTCTAGACGCCCCCAAATAGGAGCGT-CAGGACGCCGCAAT-T-TAATATTAAAAAA
* * *
56071 TTTTTATTTTT-CATAAAGGTCGACAG
63 GTTTTATTTTTCCATAAACG-CCACAG
*
56097 ATAGCGGCGTCTAGACGCC
1 ATAGTGGCGTCTAGACGCC
56116 GCTATGTTTT
Statistics
Matches: 90, Mismatches: 15, Indels: 6
0.81 0.14 0.05
Matches are distributed among these distances:
88 40 0.44
89 10 0.11
90 40 0.44
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.28
Consensus pattern (88 bp):
ATAGTGGCGTCTAGACGCCCCCAAATAGGAGCGTCAGGACGCCGCAATTTAATATTAAAAAAGTT
TTATTTTTCCATAAACGCCACAG
Found at i:56193 original size:24 final size:24
Alignment explanation
Indices: 56161--56206 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
56151 TTGGAAAAAT
56161 TATACGACGGCGTCTAAACGCCTC
1 TATACGACGGCGTCTAAACGCCTC
* * *
56185 TATATGACGGCGTTTAGACGCC
1 TATACGACGGCGTCTAAACGCC
56207 GTAATAAAGA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.24, C:0.28, G:0.24, T:0.24
Consensus pattern (24 bp):
TATACGACGGCGTCTAAACGCCTC
Found at i:56533 original size:22 final size:21
Alignment explanation
Indices: 56506--56560 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 21
56496 CGAAGTTCGT
56506 ATTTGAAGACTTATTGAAGATA
1 ATTTGAAGA-TTATTGAAGATA
*
56528 ATTTGAAGA-T-TTGAAGATC
1 ATTTGAAGATTATTGAAGATA
56547 A-TTGAAGAATTATT
1 ATTTGAAG-ATTATT
56561 TTAAGAAGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 10 0.34
20 2 0.07
21 2 0.07
22 9 0.31
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.38
Consensus pattern (21 bp):
ATTTGAAGATTATTGAAGATA
Found at i:57666 original size:19 final size:18
Alignment explanation
Indices: 57642--57677 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
57632 TGAAGATTTC
57642 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
57661 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
57678 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:67235 original size:33 final size:32
Alignment explanation
Indices: 67138--67242 Score: 129
Period size: 33 Copynumber: 3.2 Consensus size: 32
67128 TTGAAGAGAG
*
67138 TGTTTTAGATGTTGTTTGCGATGATACTAAACC
1 TGTTTTAG-TGTTGTTTGCGATGATACTAAATC
* * * *
67171 TAATTTGAGTGTTGTTTGCAATGACACTAAATC
1 T-GTTTTAGTGTTGTTTGCGATGATACTAAATC
*
67204 TGTTTTAAGTGTTGTTTGTGATGATACTAAATC
1 TGTTTT-AGTGTTGTTTGCGATGATACTAAATC
67237 TGTTTT
1 TGTTTT
67243 GGATGCTAAT
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
32 3 0.05
33 52 0.87
34 5 0.08
ACGTcount: A:0.25, C:0.10, G:0.20, T:0.46
Consensus pattern (32 bp):
TGTTTTAGTGTTGTTTGCGATGATACTAAATC
Found at i:67305 original size:33 final size:33
Alignment explanation
Indices: 67268--67376 Score: 191
Period size: 33 Copynumber: 3.3 Consensus size: 33
67258 TGAAAACAAA
67268 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
67301 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
** *
67334 TCTGTTTTGGTTGATCATAATATTGAAAATAAT
1 TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
67367 TCTGTTTTGG
1 TCTGTTTTGG
67377 GTGAAAAGAA
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 73 1.00
ACGTcount: A:0.27, C:0.10, G:0.18, T:0.45
Consensus pattern (33 bp):
TCTGTTTTGGTTGATCATAGCATTGCAAATAAT
Found at i:67790 original size:30 final size:30
Alignment explanation
Indices: 67754--67813 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
67744 CAAGGGGGAG
67754 GGAATGATGCGCCCAAGG-CTTATCATGGAC
1 GGAATGATGCG-CCAAGGACTTATCATGGAC
*
67784 GGAATGATGCGCCAAGGACTTATTATGGAC
1 GGAATGATGCGCCAAGGACTTATCATGGAC
67814 TTGAAGACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
29 6 0.21
30 22 0.79
ACGTcount: A:0.28, C:0.20, G:0.30, T:0.22
Consensus pattern (30 bp):
GGAATGATGCGCCAAGGACTTATCATGGAC
Found at i:69059 original size:32 final size:32
Alignment explanation
Indices: 68988--69063 Score: 84
Period size: 32 Copynumber: 2.3 Consensus size: 32
68978 TGCGACAATA
*
68988 CCGGCCAGTGCTGCGCCAGCCCGTGCACCCAGC
1 CCGGCCA-TGCCGCGCCAGCCCGTGCACCCAGC
* *
69021 CAGGCCACTGCCGCGCCA-CCCGTGC-CGCATGC
1 CCGGCCA-TGCCGCGCCAGCCCGTGCACCCA-GC
69053 CCGGCCATGCC
1 CCGGCCATGCC
69064 CAGCTCGTGC
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 7 0.19
32 15 0.41
33 15 0.41
ACGTcount: A:0.12, C:0.50, G:0.29, T:0.09
Consensus pattern (32 bp):
CCGGCCATGCCGCGCCAGCCCGTGCACCCAGC
Found at i:71012 original size:22 final size:21
Alignment explanation
Indices: 70987--71041 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 21
70977 CGAAGTTCGT
70987 ATTTGAAGACTTATTGAAGATA
1 ATTTGAAGA-TTATTGAAGATA
*
71009 ATTTGAAGA-T-TTGAAGATC
1 ATTTGAAGATTATTGAAGATA
71028 A-TTGAAGAATTATT
1 ATTTGAAG-ATTATT
71042 TCAAGAAGCA
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 6 0.21
19 10 0.34
20 2 0.07
21 2 0.07
22 9 0.31
ACGTcount: A:0.40, C:0.04, G:0.18, T:0.38
Consensus pattern (21 bp):
ATTTGAAGATTATTGAAGATA
Found at i:72414 original size:20 final size:21
Alignment explanation
Indices: 72375--72422 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
72365 TAGATTTAGA
* *
72375 TTTAATTTACTTTGCTTTGTT
1 TTTAATTTACATTACTTTGTT
72396 TTTAATTTA-ATTACTTTGTT
1 TTTAATTTACATTACTTTGTT
72416 TTTAATT
1 TTTAATT
72423 GATCTGTTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 16 0.64
21 9 0.36
ACGTcount: A:0.21, C:0.06, G:0.06, T:0.67
Consensus pattern (21 bp):
TTTAATTTACATTACTTTGTT
Done.