Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014146.1 Corchorus olitorius cultivar O-4 contig14179, 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: 29361
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.35
Found at i:918 original size:65 final size:65
Alignment explanation
Indices: 810--938 Score: 172
Period size: 65 Copynumber: 2.0 Consensus size: 65
800 CGGGCGTGTC
* * *
810 AAAAAGAGATATTACGCCAAAATTCCATAATGCGCCCTGAAAGGTCTTTGAGGCTAAATCTCTTA
1 AAAAAGAAATATTACGCCAAAATTCCATAATGCACCCTGAAAGGTCTTTGAGGCCAAATCTCTTA
* * *
875 AAAAAGAAATGTTGCGCCAAAATT-CACTAGTGCACCCAT-AAAGGTCTTTGAGGCCAAATCTCT
1 AAAAAGAAATATTACGCCAAAATTCCA-TAATGCACCC-TGAAAGGTCTTTGAGGCCAAATCTCT
938 T
64 T
939 TGAGGAAAGA
Statistics
Matches: 56, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
64 2 0.04
65 53 0.95
66 1 0.02
ACGTcount: A:0.36, C:0.21, G:0.17, T:0.26
Consensus pattern (65 bp):
AAAAAGAAATATTACGCCAAAATTCCATAATGCACCCTGAAAGGTCTTTGAGGCCAAATCTCTTA
Found at i:2282 original size:97 final size:93
Alignment explanation
Indices: 2167--2345 Score: 232
Period size: 97 Copynumber: 1.9 Consensus size: 93
2157 GGACTGAATT
* * *
2167 GACTAATACAAAACTATTTGAGATTATATTTTTAGAATATTAATGAACAAAACTAAAAAAATAAA
1 GACTAATACAAAACTATTTGAGATCATATTTATAGAATATT-A--AACAAAA-TAAAAAAACAAA
2232 TATTAAGAAAGATAAAAGAAAAAAAGGTGAAA
62 TATTAAGAAAGATAAAAGAAAAAAAGGTGAAA
* * * * ***
2264 GACTAATAGAAAAGTATTTGGGATCATATTTATAGAATATTAAACAATATACTTAAACAAATATT
1 GACTAATACAAAACTATTTGAGATCATATTTATAGAATATTAAACAAAATAAAAAAACAAATATT
2329 AAGAAAGATAAAAGAAA
66 AAGAAAGATAAAAGAAA
2346 TAGGGCAAAA
Statistics
Matches: 72, Mismatches: 10, Indels: 4
0.84 0.12 0.05
Matches are distributed among these distances:
93 29 0.40
94 6 0.08
96 1 0.01
97 36 0.50
ACGTcount: A:0.56, C:0.06, G:0.12, T:0.27
Consensus pattern (93 bp):
GACTAATACAAAACTATTTGAGATCATATTTATAGAATATTAAACAAAATAAAAAAACAAATATT
AAGAAAGATAAAAGAAAAAAAGGTGAAA
Found at i:2542 original size:31 final size:30
Alignment explanation
Indices: 2487--2561 Score: 82
Period size: 31 Copynumber: 2.5 Consensus size: 30
2477 TGCTTAGGGG
*
2487 GCAAAACGTCC-AAA-ATTAAGTTCAGAGC
1 GCAAAACGTCCAAAACATCAAGTTCAGAGC
* *
2515 GCAAAACGTCCAAAACATACAAGTTCAGGGG
1 GCAAAACGTCCAAAACAT-CAAGTTCAGAGC
* *
2546 GTAAAACATCCAAAAC
1 GCAAAACGTCCAAAAC
2562 TTCGTCCGAC
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
28 11 0.28
29 3 0.08
30 2 0.05
31 23 0.59
ACGTcount: A:0.45, C:0.23, G:0.17, T:0.15
Consensus pattern (30 bp):
GCAAAACGTCCAAAACATCAAGTTCAGAGC
Found at i:17140 original size:12 final size:12
Alignment explanation
Indices: 17125--17149 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17115 CAATCTTGAA
17125 GAAAATCATGTC
1 GAAAATCATGTC
17137 GAAAATCATGTC
1 GAAAATCATGTC
17149 G
1 G
17150 GATTTTGTAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.16, G:0.20, T:0.24
Consensus pattern (12 bp):
GAAAATCATGTC
Found at i:17253 original size:10 final size:10
Alignment explanation
Indices: 17240--17323 Score: 56
Period size: 10 Copynumber: 9.0 Consensus size: 10
17230 TTTTTATTTT
17240 TTAATTATTA
1 TTAATTATTA
17250 TTAATTA-T-
1 TTAATTATTA
17258 TT-A--ATTA
1 TTAATTATTA
17265 TTAATTATTA
1 TTAATTATTA
*
17275 TTAATT-TAAA
1 TTAATTAT-TA
*
17285 TT-GTTATTA
1 TTAATTATTA
*
17294 TTAATTATAA
1 TTAATTATTA
*
17304 TTAATAATTA
1 TTAATTATTA
* *
17314 ATAATAATTA
1 TTAATTATTA
17324 AAAAACAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 16
0.71 0.10 0.20
Matches are distributed among these distances:
5 1 0.02
6 1 0.02
7 3 0.05
8 3 0.05
9 7 0.12
10 43 0.74
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (10 bp):
TTAATTATTA
Found at i:17256 original size:7 final size:7
Alignment explanation
Indices: 17246--17324 Score: 65
Period size: 7 Copynumber: 11.1 Consensus size: 7
17236 TTTTTTAATT
17246 ATTATTA
1 ATTATTA
17253 ATTATTTA
1 ATTA-TTA
17261 ATTATTA
1 ATTATTA
17268 ATTATT-
1 ATTATTA
17274 ATTAATTTAA
1 ATT-A-TT-A
*
17284 ATTGTT-
1 ATTATTA
17290 ATTATTA
1 ATTATTA
17297 ATTA-TA
1 ATTATTA
*
17303 ATTAATA
1 ATTATTA
*
17310 ATTAATA
1 ATTATTA
*
17317 ATAATTA
1 ATTATTA
17324 A
1 A
17325 AAAACAAAAA
Statistics
Matches: 61, Mismatches: 4, Indels: 14
0.77 0.05 0.18
Matches are distributed among these distances:
6 14 0.23
7 33 0.54
8 11 0.18
10 3 0.05
ACGTcount: A:0.46, C:0.00, G:0.01, T:0.53
Consensus pattern (7 bp):
ATTATTA
Found at i:17268 original size:25 final size:27
Alignment explanation
Indices: 17240--17312 Score: 89
Period size: 29 Copynumber: 2.7 Consensus size: 27
17230 TTTTTATTTT
17240 TTAATTATTATTAATT-ATT-TAATTA
1 TTAATTATTATTAATTAATTGTAATTA
*
17265 TTAATTATTATTAATTTAAATTGTTATTA
1 TTAATTATTATTAA-TT-AATTGTAATTA
*
17294 TTAATTATAATTAA-TAATT
1 TTAATTATTATTAATTAATT
17313 AATAATAATT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
25 14 0.33
26 6 0.14
27 1 0.02
28 3 0.07
29 18 0.43
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (27 bp):
TTAATTATTATTAATTAATTGTAATTA
Found at i:19702 original size:7 final size:7
Alignment explanation
Indices: 19690--19718 Score: 51
Period size: 7 Copynumber: 4.3 Consensus size: 7
19680 AATTCCATCA
19690 AATCTTC
1 AATCTTC
19697 AATCTTC
1 AATCTTC
19704 AA-CTTC
1 AATCTTC
19710 AATCTTC
1 AATCTTC
19717 AA
1 AA
19719 GGACATGCAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
6 6 0.29
7 15 0.71
ACGTcount: A:0.34, C:0.28, G:0.00, T:0.38
Consensus pattern (7 bp):
AATCTTC
Found at i:19711 original size:13 final size:13
Alignment explanation
Indices: 19693--19718 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
19683 TCCATCAAAT
19693 CTTCAATCTTCAA
1 CTTCAATCTTCAA
19706 CTTCAATCTTCAA
1 CTTCAATCTTCAA
19719 GGACATGCAT
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:0.31, C:0.31, G:0.00, T:0.38
Consensus pattern (13 bp):
CTTCAATCTTCAA
Found at i:20249 original size:25 final size:25
Alignment explanation
Indices: 20215--20263 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
20205 CCAAACAATC
*
20215 TTGAGCACTCTCGCTCGGTCTCTAT
1 TTGAGCACTCTCGCTCGATCTCTAT
*
20240 TTGAGCACTCTCGTTCGATCTCTA
1 TTGAGCACTCTCGCTCGATCTCTA
20264 CAAACTAACA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.14, C:0.31, G:0.18, T:0.37
Consensus pattern (25 bp):
TTGAGCACTCTCGCTCGATCTCTAT
Found at i:21474 original size:32 final size:32
Alignment explanation
Indices: 21421--21541 Score: 109
Period size: 32 Copynumber: 3.8 Consensus size: 32
21411 TCAGGTGGGT
* * * ***
21421 TCGGGTTCGGGTACTTT-GGGTTCGGGTTTTT
1 TCGGATTCGGATAATTTCGGGTTCGGGTTAAG
*
21452 TCGGATTTGGATAATTTCGGGTTCGGGTTAAG
1 TCGGATTCGGATAATTTCGGGTTCGGGTTAAG
* * *
21484 TCGGGTTCGGATATTTTCGGGTTCGGGTTATG
1 TCGGATTCGGATAATTTCGGGTTCGGGTTAAG
* * *
21516 TCGGGTTCGGGTATTTTTCGGGTTCG
1 TCGGATTCGGATA-ATTTCGGGTTCG
21542 ATCTCGGGTA
Statistics
Matches: 76, Mismatches: 12, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
31 13 0.17
32 51 0.67
33 12 0.16
ACGTcount: A:0.09, C:0.12, G:0.37, T:0.41
Consensus pattern (32 bp):
TCGGATTCGGATAATTTCGGGTTCGGGTTAAG
Found at i:21487 original size:16 final size:16
Alignment explanation
Indices: 21468--21541 Score: 78
Period size: 16 Copynumber: 4.6 Consensus size: 16
21458 TTGGATAATT
*
21468 TCGGGTTCGGGTTAAG
1 TCGGGTTCGGGTTATG
* *
21484 TCGGGTTC-GGATATTT
1 TCGGGTTCGGGTTA-TG
21500 TCGGGTTCGGGTTATG
1 TCGGGTTCGGGTTATG
* *
21516 TCGGGTTCGGGTATTTT
1 TCGGGTTCGGGT-TATG
21533 TCGGGTTCG
1 TCGGGTTCG
21542 ATCTCGGGTA
Statistics
Matches: 48, Mismatches: 7, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
15 4 0.08
16 29 0.60
17 15 0.31
ACGTcount: A:0.08, C:0.14, G:0.39, T:0.39
Consensus pattern (16 bp):
TCGGGTTCGGGTTATG
Found at i:21578 original size:23 final size:23
Alignment explanation
Indices: 21532--21589 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 23
21522 TCGGGTATTT
* *
21532 TTCGGGTTCGATCTCGGGTAGGG
1 TTCGGGTTCGAGCTCGGATAGGG
* *
21555 TTCGGGTTCGGGCTCGGATCGGG
1 TTCGGGTTCGAGCTCGGATAGGG
* *
21578 TTTGGGCTCGAG
1 TTCGGGTTCGAG
21590 TCTGATTTTG
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.07, C:0.19, G:0.45, T:0.29
Consensus pattern (23 bp):
TTCGGGTTCGAGCTCGGATAGGG
Found at i:22056 original size:31 final size:31
Alignment explanation
Indices: 22021--22092 Score: 78
Period size: 31 Copynumber: 2.3 Consensus size: 31
22011 TAAATTATTG
*
22021 CAAATTAAAACAAAT-TAAG-CATTAAATTAAA
1 CAAATTAAAA-AAATGAAAGTC-TTAAATTAAA
*
22052 CAAA-TAATTAAAATGAAAGTCTTAAATTAAA
1 CAAATTAA-AAAAATGAAAGTCTTAAATTAAA
22083 CAAATTAAAA
1 CAAATTAAAA
22093 GCTGATAGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 8
0.76 0.07 0.18
Matches are distributed among these distances:
30 7 0.21
31 23 0.68
32 4 0.12
ACGTcount: A:0.61, C:0.08, G:0.04, T:0.26
Consensus pattern (31 bp):
CAAATTAAAAAAATGAAAGTCTTAAATTAAA
Found at i:22682 original size:22 final size:23
Alignment explanation
Indices: 22657--22722 Score: 80
Period size: 23 Copynumber: 2.9 Consensus size: 23
22647 TTTCTGGTCA
*
22657 ACTCGGG-TAATTTCGGGTTCGG
1 ACTCGGGCGAATTTCGGGTTCGG
**
22679 ACTCGGGCGGGTTTCGGGTTCGG
1 ACTCGGGCGAATTTCGGGTTCGG
**
22702 ACTCGGGCGGGTTTCGGGTTC
1 ACTCGGGCGAATTTCGGGTTC
22723 ATTTTGCCAG
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
22 7 0.17
23 33 0.82
ACGTcount: A:0.08, C:0.21, G:0.42, T:0.29
Consensus pattern (23 bp):
ACTCGGGCGAATTTCGGGTTCGG
Found at i:22696 original size:23 final size:23
Alignment explanation
Indices: 22667--22722 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
22657 ACTCGGGTAA
22667 TTTCGGGTTCGGACTCGGGCGGG
1 TTTCGGGTTCGGACTCGGGCGGG
22690 TTTCGGGTTCGGACTCGGGCGGG
1 TTTCGGGTTCGGACTCGGGCGGG
22713 TTTCGGGTTC
1 TTTCGGGTTC
22723 ATTTTGCCAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.04, C:0.21, G:0.45, T:0.30
Consensus pattern (23 bp):
TTTCGGGTTCGGACTCGGGCGGG
Found at i:23206 original size:31 final size:30
Alignment explanation
Indices: 23134--23207 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 30
23124 CACCAAATTG
* * * *
23134 TAAGTGGATGGACCAAATTGATAGTTTTTG
1 TAAGTAGAGGGACCAAATTGATACTTTTTA
* *
23164 T-AGTAGTGGGACCAAATTGATCCCTTTTTA
1 TAAGTAGAGGGACCAAATTGAT-ACTTTTTA
23194 TAAGTAGAGGGACC
1 TAAGTAGAGGGACC
23208 TGTACGATAT
Statistics
Matches: 35, Mismatches: 7, Indels: 3
0.78 0.16 0.07
Matches are distributed among these distances:
29 17 0.49
30 7 0.20
31 11 0.31
ACGTcount: A:0.30, C:0.12, G:0.26, T:0.32
Consensus pattern (30 bp):
TAAGTAGAGGGACCAAATTGATACTTTTTA
Found at i:24682 original size:29 final size:29
Alignment explanation
Indices: 24645--24715 Score: 135
Period size: 28 Copynumber: 2.5 Consensus size: 29
24635 TATAATTTAA
24645 TTCTTCTTATTTTTTTTGGCCAAAAAAAT
1 TTCTTCTTATTTTTTTTGGCCAAAAAAAT
24674 TTCTTCTTA-TTTTTTTGGCCAAAAAAAT
1 TTCTTCTTATTTTTTTTGGCCAAAAAAAT
24702 TTCTTCTTATTTTT
1 TTCTTCTTATTTTT
24716 CTTAAAAGCT
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
28 28 0.68
29 13 0.32
ACGTcount: A:0.24, C:0.14, G:0.06, T:0.56
Consensus pattern (29 bp):
TTCTTCTTATTTTTTTTGGCCAAAAAAAT
Found at i:27097 original size:31 final size:30
Alignment explanation
Indices: 27056--27122 Score: 98
Period size: 31 Copynumber: 2.2 Consensus size: 30
27046 GCCGTTGCTG
*
27056 GGGAGGGAAAACTTTCTCCTGCTTTTTGCCA
1 GGGAAGGAAAACTTTCTCCTGCTTTTT-CCA
* *
27087 GGGAAGGAAAACTTTCTCCTGGTTTTTCCG
1 GGGAAGGAAAACTTTCTCCTGCTTTTTCCA
27117 GGGAAG
1 GGGAAG
27123 TAAGGAATAG
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
30 8 0.24
31 25 0.76
ACGTcount: A:0.21, C:0.19, G:0.30, T:0.30
Consensus pattern (30 bp):
GGGAAGGAAAACTTTCTCCTGCTTTTTCCA
Found at i:27290 original size:28 final size:26
Alignment explanation
Indices: 27259--27346 Score: 86
Period size: 28 Copynumber: 3.2 Consensus size: 26
27249 AATTTTTGTG
*
27259 TTTTGCGTTTTTGAAAAAAAAAGAGAGT
1 TTTTGCGTTTTTGAAAAAAAAA-A-AAT
*
27287 TTTTACGTTTTCTGAAAAAAAAAAAAT
1 TTTTGCGTTTT-TGAAAAAAAAAAAAT
* *
27314 TTATGCGTTTTTACAAAAAGAAAAAAAT
1 TTTTGCGTTTTT-GAAAAA-AAAAAAAT
27342 ATTTT
1 -TTTT
27347 CCTTTATTTT
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
26 1 0.02
27 16 0.32
28 19 0.38
29 14 0.28
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (26 bp):
TTTTGCGTTTTTGAAAAAAAAAAAAT
Done.