Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017547.1 Corchorus olitorius cultivar O-4 contig17580, 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: 89417
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:94 original size:2 final size:2
Alignment explanation
Indices: 87--112 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
77 GTAAATGAAG
87 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
113 TGATATACAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1840 original size:2 final size:2
Alignment explanation
Indices: 1822--1875 Score: 83
Period size: 2 Copynumber: 26.5 Consensus size: 2
1812 GCTAGTGATC
1822 TA TA TA TCA CTA T- TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA T-A -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1865 TA TA TA TA TA T
1 TA TA TA TA TA T
1876 GGAGATTTCG
Statistics
Matches: 49, Mismatches: 0, Indels: 6
0.89 0.00 0.11
Matches are distributed among these distances:
1 1 0.02
2 45 0.92
3 2 0.04
4 1 0.02
ACGTcount: A:0.46, C:0.04, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15873 original size:40 final size:39
Alignment explanation
Indices: 15825--15946 Score: 174
Period size: 40 Copynumber: 3.1 Consensus size: 39
15815 CAAATTGTCC
15825 ATCCAATTT-GCCGCTCCTAATAATTAAGGTAATAAATTAA
1 ATCCAATTTAGCC-CT-CTAATAATTAAGGTAATAAATTAA
*
15865 ATCCAATTTAATCCCTCTAATAATTAAGGTAATAAATTAA
1 ATCCAATTT-AGCCCTCTAATAATTAAGGTAATAAATTAA
* *
15905 ATCCAGTTTAGCCCCTATAATAATTAAGGTAATAAATTAA
1 ATCCAATTTAG-CCCTCTAATAATTAAGGTAATAAATTAA
15945 AT
1 AT
15947 ACAGGTTTAA
Statistics
Matches: 75, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
39 1 0.01
40 70 0.93
41 2 0.03
42 2 0.03
ACGTcount: A:0.43, C:0.16, G:0.08, T:0.34
Consensus pattern (39 bp):
ATCCAATTTAGCCCTCTAATAATTAAGGTAATAAATTAA
Found at i:15984 original size:24 final size:25
Alignment explanation
Indices: 15942--15996 Score: 76
Period size: 24 Copynumber: 2.2 Consensus size: 25
15932 GGTAATAAAT
15942 TAAATACAGGTTTAACCCCTAATTA
1 TAAATACAGGTTTAACCCCTAATTA
* * *
15967 TGAATA-AGGTTTAGCCCCTAGTTA
1 TAAATACAGGTTTAACCCCTAATTA
15991 TAAATA
1 TAAATA
15997 GGGAGAGTCT
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
24 21 0.81
25 5 0.19
ACGTcount: A:0.38, C:0.16, G:0.13, T:0.33
Consensus pattern (25 bp):
TAAATACAGGTTTAACCCCTAATTA
Found at i:30457 original size:47 final size:47
Alignment explanation
Indices: 30403--30529 Score: 222
Period size: 45 Copynumber: 2.7 Consensus size: 47
30393 CATTTTCGTT
30403 GAATCGTTCTTCGATTTTTTTTTTGTTTGGTAATCAAGTTAAAAGTC
1 GAATCGTTCTTCGATTTTTTTTTTGTTTGGTAATCAAGTTAAAAGTC
30450 GAATCGTTCTTCGA--TTTTTTTTGTTTGGTAATCAAGTTAAAAGTC
1 GAATCGTTCTTCGATTTTTTTTTTGTTTGGTAATCAAGTTAAAAGTC
* *
30495 GAATCGTTCTTTGATTTTTTTTTTGTTTGGCAATC
1 GAATCGTTCTTCGATTTTTTTTTTGTTTGGTAATC
30530 TTTGGACAGC
Statistics
Matches: 76, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
45 44 0.58
47 32 0.42
ACGTcount: A:0.21, C:0.11, G:0.17, T:0.50
Consensus pattern (47 bp):
GAATCGTTCTTCGATTTTTTTTTTGTTTGGTAATCAAGTTAAAAGTC
Found at i:40654 original size:21 final size:20
Alignment explanation
Indices: 40616--40654 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
40606 CTTGAAAGAG
**
40616 GTCCATGTGTGGTTAAGAAT
1 GTCCATGTGTGGGGAAGAAT
40636 GTCCATGTCGTGGGGAAGA
1 GTCCATGT-GTGGGGAAGA
40655 CTTTCGCTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 8 0.50
21 8 0.50
ACGTcount: A:0.23, C:0.13, G:0.36, T:0.28
Consensus pattern (20 bp):
GTCCATGTGTGGGGAAGAAT
Found at i:50372 original size:25 final size:26
Alignment explanation
Indices: 50321--50371 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
50311 ACTGTATTTT
50321 TTTGCACTGTTTAAATAAAAAAAAAA
1 TTTGCACTGTTTAAATAAAAAAAAAA
* *
50347 TTTGCACTGTTTACAGAAAAAAAAA
1 TTTGCACTGTTTAAATAAAAAAAAA
50372 TATATACTGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.51, C:0.10, G:0.10, T:0.29
Consensus pattern (26 bp):
TTTGCACTGTTTAAATAAAAAAAAAA
Found at i:51339 original size:3 final size:3
Alignment explanation
Indices: 51333--51359 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
51323 AGAAGTAGAA
51333 GAG GAG GAG GAG GAG GAG GAG GAG GAG
1 GAG GAG GAG GAG GAG GAG GAG GAG GAG
51360 AGAGACTGTG
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:0.33, C:0.00, G:0.67, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:56444 original size:137 final size:139
Alignment explanation
Indices: 56280--56544 Score: 444
Period size: 139 Copynumber: 1.9 Consensus size: 139
56270 TTATTATTGT
*
56280 CAAATTGAGTTAAATGTAATTAATGTCTT-AAGT-AAAGTCTCGAATTCAAATCTTATTATTTAT
1 CAAATTGAGTTAAATGAAATTAATGTCTTAAAGTAAAAGTCTCGAATTCAAATCTTATTATTTAT
* *
56343 TAATATAGATAATGGGTATTTGGAGAACTTTCCACCTTATATTGCCTAATTCCAAATTAGTTTTT
66 TAATATAGATAATGAGTATTTGGAGAACTTCCCACCTTATATTGCCTAATTCCAAATTAGTTTTT
56408 TTTTCTTGG
131 TTTTCTTGG
* *
56417 CAAATTGAGTTAAATGAAATTAATGTCTTAAATTAAAAGTCTCGGATTCAAATCTTATTATTTAT
1 CAAATTGAGTTAAATGAAATTAATGTCTTAAAGTAAAAGTCTCGAATTCAAATCTTATTATTTAT
* * *
56482 TAATGTAGATAATGAGTATTTGGAGAACTTCCCACCTTATATTGCTTAATTCCGAATTAGTTT
66 TAATATAGATAATGAGTATTTGGAGAACTTCCCACCTTATATTGCCTAATTCCAAATTAGTTT
56545 AAGGTTACCA
Statistics
Matches: 118, Mismatches: 8, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
137 28 0.24
138 3 0.03
139 87 0.74
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.42
Consensus pattern (139 bp):
CAAATTGAGTTAAATGAAATTAATGTCTTAAAGTAAAAGTCTCGAATTCAAATCTTATTATTTAT
TAATATAGATAATGAGTATTTGGAGAACTTCCCACCTTATATTGCCTAATTCCAAATTAGTTTTT
TTTTCTTGG
Found at i:57030 original size:30 final size:30
Alignment explanation
Indices: 56973--57031 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
56963 ACTCCATAAC
* * *
56973 AATACTAAATAGATTTTTGTTCAAAAAATG
1 AATACTAAATAAATTTATGATCAAAAAATG
57003 AATACTAAATAAATTTATGCATCAAAAAA
1 AATACTAAATAAATTTATG-ATCAAAAAA
57032 CAATTACAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 17 0.68
31 8 0.32
ACGTcount: A:0.53, C:0.08, G:0.07, T:0.32
Consensus pattern (30 bp):
AATACTAAATAAATTTATGATCAAAAAATG
Found at i:78721 original size:36 final size:36
Alignment explanation
Indices: 78674--78761 Score: 167
Period size: 36 Copynumber: 2.4 Consensus size: 36
78664 AGTATAATCT
*
78674 AAAATTTGACTTGTTAGTATTATTTTTTTTAAAAGA
1 AAAATTTGACTTGTTAATATTATTTTTTTTAAAAGA
78710 AAAATTTGACTTGTTAATATTATTTTTTTTAAAAGA
1 AAAATTTGACTTGTTAATATTATTTTTTTTAAAAGA
78746 AAAATTTGACTTGTTA
1 AAAATTTGACTTGTTA
78762 TTAGTAGATG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.38, C:0.03, G:0.10, T:0.49
Consensus pattern (36 bp):
AAAATTTGACTTGTTAATATTATTTTTTTTAAAAGA
Found at i:84447 original size:2 final size:2
Alignment explanation
Indices: 84442--84468 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
84432 AAGTCGAGAG
84442 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
84469 AATCTGTGGA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:87598 original size:45 final size:45
Alignment explanation
Indices: 87512--87601 Score: 108
Period size: 45 Copynumber: 2.0 Consensus size: 45
87502 AAAAACTTGT
* **
87512 AGCATTCGGCAATTATGGAGCCAAAGCTCTCATTGTTCTCCTTCA
1 AGCATTCGGCAATCATGGAGCCAAAGCTCTCATTGAGCTCCTTCA
* ** * *
87557 AGCATTCTGCAATCATGGAGCTGAAGCTTTCCTTGAGCTCCTTCA
1 AGCATTCGGCAATCATGGAGCCAAAGCTCTCATTGAGCTCCTTCA
87602 TGGTTTCACT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
45 37 1.00
ACGTcount: A:0.23, C:0.27, G:0.19, T:0.31
Consensus pattern (45 bp):
AGCATTCGGCAATCATGGAGCCAAAGCTCTCATTGAGCTCCTTCA
Found at i:89325 original size:20 final size:20
Alignment explanation
Indices: 89280--89410 Score: 145
Period size: 20 Copynumber: 6.5 Consensus size: 20
89270 CATTGAGGGC
*
89280 CAATGTGAATTAAGGCAAGTT
1 CAATGTGAATT-AGGAAAGTT
*
89301 CAATGTGAATTGGGAAAGTT
1 CAATGTGAATTAGGAAAGTT
* * *
89321 GAATGTGAATAAGGCAAGTT
1 CAATGTGAATTAGGAAAGTT
*
89341 CAATGTGAATTGGGAAAGTT
1 CAATGTGAATTAGGAAAGTT
* * * *
89361 GAATGTGAGTAAGGCAAGTT
1 CAATGTGAATTAGGAAAGTT
*
89381 CAATGTGAATTGGGAAAGTT
1 CAATGTGAATTAGGAAAGTT
*
89401 GAATGTGAAT
1 CAATGTGAAT
89411 CAAGGCA
Statistics
Matches: 89, Mismatches: 21, Indels: 1
0.80 0.19 0.01
Matches are distributed among these distances:
20 78 0.88
21 11 0.12
ACGTcount: A:0.37, C:0.05, G:0.30, T:0.28
Consensus pattern (20 bp):
CAATGTGAATTAGGAAAGTT
Found at i:89338 original size:40 final size:40
Alignment explanation
Indices: 89281--89417 Score: 247
Period size: 40 Copynumber: 3.4 Consensus size: 40
89271 ATTGAGGGCC
89281 AATGTGAATTAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
1 AATGTGAA-TAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
89322 AATGTGAATAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
1 AATGTGAATAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
*
89362 AATGTGAGTAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
1 AATGTGAATAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
89402 AATGTGAATCAAGGCA
1 AATGTGAAT-AAGGCA
Statistics
Matches: 93, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
40 79 0.85
41 14 0.15
ACGTcount: A:0.37, C:0.06, G:0.30, T:0.27
Consensus pattern (40 bp):
AATGTGAATAAGGCAAGTTCAATGTGAATTGGGAAAGTTG
Done.