Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016592.1 Corchorus olitorius cultivar O-4 contig16625, 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: 73105
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Found at i:689 original size:334 final size:330
Alignment explanation
Indices: 1--1169 Score: 1156
Period size: 334 Copynumber: 3.5 Consensus size: 330
* * * * **
1 CAATTTCTGGCCA-AATACTCAT--AAAAATCATATAATTCAATGCCAAAATGATTGAAGGGCTT
1 CAATTTTTGGCCACAGTACTCATAAAAAAAT-ATATAATTCAACGCCAAAATAATTGAAGGATTT
* *
63 TCCACGT-TTCTAATATCAATTTTT-TAATTTTTTTT-GAATTAATTTCT-ATTTAAATCGAAAC
65 TTCACGTATT-TAATATC-ATTTTTCT--TTTTTTTTCAAATT-ATTTCTCA-TTAAATCGAAAC
* * * * * * * * *
124 AAGATTCAGATACTCG-TAAAATCAAATACTTGAATCAAATTTGGATGGGATTGGGCTGGATGAA
124 AAGATTCAGATGCTCGTTAAAA-CAAATCCTTAAATCCAATGTGGATGCGATTTGGATGAATGAA
* * ** * * * *
188 TATAAATATTTCAAGGTGTCTGGGTGACAAAAATCATGTGAAACTGAGCCGGGGACCCGGAACGC
188 TATAGATATTCCAAGAAGTCTGAGCGACAAAAATCATGCGAAACTGAGTCGGGG-CCCGGAACGC
* * * * *
253 ATTTTTTGCCAAAAAAACGTGATGGTTACTACACGATTTCGTCTAAAACTTT-ACAAAAACTGAT
252 GTTTTTAGCC-AAAAAACGTGATGGTTAGTACACGATTTCGGCTAAAACTTTGA-AAAAATTGA-
*
317 CTC-AAAAAATTTTCCT
314 CCCGAAAAAATTTTCCT
* * * *
333 CAATTTTTGGCCATAGTACTCATAAAAAAATATTTAATTTAACGCCAAAATAATGGAAGGATTTT
1 CAATTTTTGGCCACAGTACTCATAAAAAAATATATAATTCAACGCCAAAATAATTGAAGGATTTT
* *
398 TCATGTATTTAATATCATTTTTCTTTTTATTTTCAAATCTATTTCTCATTAAATCAAAACAAGAT
66 TCACGTATTTAATATCATTTTTCTTTTT-TTTTCAAAT-TATTTCTCATTAAATCGAAACAAGAT
* * * *
463 TCAGATGCTCGTTAAAAAAAATCCTTAAATCCAATGTGGCTGCTATTT-GATTAATTGAATATAG
129 TCAGATGCTCGTTAAAACAAATCCTTAAATCCAATGTGGATGCGATTTGGATGAA-TGAATATAG
* * *
527 ATATTCCAAGAAGTCTTAGC-ATCAAAAATCATGCAAAACTGAGTCGGGGCCTTGGAACGCGTTT
193 ATATTCCAAGAAGTCTGAGCGA-CAAAAATCATGCGAAACTGAGTCGGGGCC-CGGAACGCGTTT
* *
591 TTAGCCAAAAAACGGTGATGTTTTAGTACACGATTTCGGCTAAAATTTTGAAAAAATTGACCCGA
256 TTAGCCAAAAAAC-GTGATG-GTTAGTACACGATTTCGGCTAAAACTTTGAAAAAATTGACCCGA
***
656 AAGTTTTTTCCT
319 AAAAATTTTCCT
* * * * **
668 CAATTTCTGGCCA-AATACTCAT-AAAAATTATATAATTCAATGCCAAAA-AGATTGAAGGGCTT
1 CAATTTTTGGCCACAGTACTCATAAAAAAATATATAATTCAACGCCAAAATA-ATTGAAGGATTT
* * **
730 TCCACGCT-TCTAATATCATTTTT-TTAATATTTTTTTGAATTAATTTCT-ATTTAAATCGAAAC
65 TTCACG-TATTTAATATCATTTTTCTT--T-TTTTTTCAAATT-ATTTCTCA-TTAAATCGAAAC
* * * * * * *
792 AAGATTTAGATACTCG-TAAAATCAAATACTTGAATCCAATGTGGATGGGATTTGGCTGGATGAA
124 AAGATTCAGATGCTCGTTAAAA-CAAATCCTTAAATCCAATGTGGATGCGATTTGGATGAATGAA
* * * *
856 TATAGATATTTCAAGGAGTCTGGGCGACAAAAATCATGCGAAACTGAGTCTGGGTCCCCGGAACG
188 TATAGATATTCCAAGAAGTCTGAGCGACAAAAATCATGCGAAACTGAGTC-GGG-GCCCGGAACG
* * * * *
921 CGTTTTTAGCCCAAAACCGTGATGGTTAGTACACGATTTCTGCTAAAACTTTGCAAAAACTT-AT
251 CGTTTTTAGCCAAAAAACGTGATGGTTAGTACACGATTTCGGCTAAAACTTTG-AAAAAATTGAC
*
985 CTGAAAAAATTTTCCT
315 CCGAAAAAATTTTCCT
* * *
1001 CAATTTTTGGCTACAGTACTCATAAAAATATATATAATCCAACGCCAAAATAATTGAAGGATTTT
1 CAATTTTTGGCCACAGTACTCATAAAAAAATATATAATTCAACGCCAAAATAATTGAAGGATTTT
* * *
1066 TCACGTATTTAATATCGTTTTTC-TTTTTTTTCACATTTATTTCTCATTAAATGGAAACAAGATT
66 TCACGTATTTAATATCATTTTTCTTTTTTTTTCA-AATTATTTCTCATTAAATCGAAACAAGATT
* *
1130 CAGTTGCTCGTTAAAACAAATCTTTAAATCCAATGTGGAT
130 CAGATGCTCGTTAAAACAAATCCTTAAATCCAATGTGGAT
1170 TCAGATACTC
Statistics
Matches: 685, Mismatches: 114, Indels: 76
0.78 0.13 0.09
Matches are distributed among these distances:
332 76 0.11
333 147 0.21
334 307 0.45
335 151 0.22
336 4 0.01
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (330 bp):
CAATTTTTGGCCACAGTACTCATAAAAAAATATATAATTCAACGCCAAAATAATTGAAGGATTTT
TCACGTATTTAATATCATTTTTCTTTTTTTTTCAAATTATTTCTCATTAAATCGAAACAAGATTC
AGATGCTCGTTAAAACAAATCCTTAAATCCAATGTGGATGCGATTTGGATGAATGAATATAGATA
TTCCAAGAAGTCTGAGCGACAAAAATCATGCGAAACTGAGTCGGGGCCCGGAACGCGTTTTTAGC
CAAAAAACGTGATGGTTAGTACACGATTTCGGCTAAAACTTTGAAAAAATTGACCCGAAAAAATT
TTCCT
Found at i:12449 original size:30 final size:29
Alignment explanation
Indices: 12387--12456 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
12377 ACCGAACCGT
* ****
12387 CAAATAAGCCCCTGAACTTTTATTTCGGC
1 CAAATAAGCCCCTGAACTTTAAAAAAGGC
12416 CAAATAAGCCCCTGAACTCTTAAAAAAGGC
1 CAAATAAGCCCCTGAACT-TTAAAAAAGGC
12446 CAAATAAGCCC
1 CAAATAAGCCC
12457 TGTTGCCAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 18 0.51
30 17 0.49
ACGTcount: A:0.37, C:0.29, G:0.13, T:0.21
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTTTAAAAAAGGC
Found at i:24404 original size:4 final size:4
Alignment explanation
Indices: 24395--24421 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
24385 AAAAACAAAG
24395 AGAA AGAA AGAA AGAA AGAA AGAA AGA
1 AGAA AGAA AGAA AGAA AGAA AGAA AGA
24422 GTATCCTGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:31260 original size:72 final size:72
Alignment explanation
Indices: 31174--31319 Score: 256
Period size: 72 Copynumber: 2.0 Consensus size: 72
31164 TGGATTAATA
*
31174 ATCTATTTGCAGCTAGAAACAAATATTCAAATTCTAAACCAAATTTCTAGCGAATGGTAACCAAA
1 ATCTATTTGCAGCTAGAAACAAATATTCAAATTCTAAACCAAATTTCTAGCCAATGGTAACCAAA
31239 GTAACAG
66 GTAACAG
** *
31246 ATCTATTTGCAGCTAGAAACAAATATTCTGATTCTAAACCAAATTTCTAGCCAATGGTACCCAAA
1 ATCTATTTGCAGCTAGAAACAAATATTCAAATTCTAAACCAAATTTCTAGCCAATGGTAACCAAA
31311 GTAACAG
66 GTAACAG
31318 AT
1 AT
31320 TATAAAGTAC
Statistics
Matches: 70, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
72 70 1.00
ACGTcount: A:0.41, C:0.19, G:0.12, T:0.27
Consensus pattern (72 bp):
ATCTATTTGCAGCTAGAAACAAATATTCAAATTCTAAACCAAATTTCTAGCCAATGGTAACCAAA
GTAACAG
Found at i:35922 original size:2 final size:2
Alignment explanation
Indices: 35915--36029 Score: 70
Period size: 2 Copynumber: 61.5 Consensus size: 2
35905 CGGTTTTTAT
* * * *
35915 TA TA TA TA TA TA AA TA TA TA T- TT TA T- TA TA AA TA T- TA AA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
35954 TA TA TT TA -A GA TA TA TA TA T- TA TA TA TA T- TA TA TA T- TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
35992 GTA -A TA -A GTT TT TA T- 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 TA TA TA TA TA TA T
36030 TAAAGATAAT
Statistics
Matches: 89, Mismatches: 12, Indels: 24
0.71 0.10 0.19
Matches are distributed among these distances:
1 10 0.11
2 77 0.87
3 2 0.02
ACGTcount: A:0.46, C:0.00, G:0.03, T:0.51
Consensus pattern (2 bp):
TA
Found at i:35978 original size:22 final size:21
Alignment explanation
Indices: 35846--35898 Score: 52
Period size: 23 Copynumber: 2.4 Consensus size: 21
35836 AGAACCCGAA
* * *
35846 TATATATTTTATTATAAATAT
1 TATATATTTAAATATATATAT
35867 TAAATATATTTAAGATATATATAT
1 T--ATATATTTAA-ATATATATAT
35891 TATATATT
1 TATATATT
35899 AGTAATCGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
21 1 0.04
22 7 0.27
23 9 0.35
24 9 0.35
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (21 bp):
TATATATTTAAATATATATAT
Found at i:37832 original size:10 final size:10
Alignment explanation
Indices: 37817--37856 Score: 55
Period size: 10 Copynumber: 3.9 Consensus size: 10
37807 CTACCTCTCT
37817 TTTCTTTTTC
1 TTTCTTTTTC
37827 TTTCTTTTTC
1 TTTCTTTTTC
37837 TTTCTTTGTTTC
1 TTTC-TT-TTTC
37849 TTT-TTTTT
1 TTTCTTTTT
37857 AAAAAAAAAG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 3 0.11
10 16 0.57
11 2 0.07
12 7 0.25
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (10 bp):
TTTCTTTTTC
Found at i:39410 original size:6 final size:6
Alignment explanation
Indices: 39393--39431 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
39383 AAAGTGGTAA
* * *
39393 GGACTT GTACTT GGACTT GGACTT GTACTT GTACTT GGA
1 GGACTT GGACTT GGACTT GGACTT GGACTT GGACTT GGA
39432 AAAATCACAA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.18, C:0.15, G:0.28, T:0.38
Consensus pattern (6 bp):
GGACTT
Found at i:39410 original size:12 final size:12
Alignment explanation
Indices: 39393--39431 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
39383 AAAGTGGTAA
39393 GGACTTGTACTT
1 GGACTTGTACTT
*
39405 GGACTTGGACTT
1 GGACTTGTACTT
*
39417 GTACTTGTACTT
1 GGACTTGTACTT
39429 GGA
1 GGA
39432 AAAATCACAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.18, C:0.15, G:0.28, T:0.38
Consensus pattern (12 bp):
GGACTTGTACTT
Found at i:39416 original size:18 final size:18
Alignment explanation
Indices: 39393--39431 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
39383 AAAGTGGTAA
39393 GGACTTGTACTTGGACTT
1 GGACTTGTACTTGGACTT
*
39411 GGACTTGTACTTGTACTT
1 GGACTTGTACTTGGACTT
39429 GGA
1 GGA
39432 AAAATCACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.18, C:0.15, G:0.28, T:0.38
Consensus pattern (18 bp):
GGACTTGTACTTGGACTT
Found at i:43136 original size:7 final size:7
Alignment explanation
Indices: 43126--43157 Score: 64
Period size: 7 Copynumber: 4.6 Consensus size: 7
43116 AACCAATAAT
43126 TTGGGCA
1 TTGGGCA
43133 TTGGGCA
1 TTGGGCA
43140 TTGGGCA
1 TTGGGCA
43147 TTGGGCA
1 TTGGGCA
43154 TTGG
1 TTGG
43158 CAGAGTGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.12, C:0.12, G:0.44, T:0.31
Consensus pattern (7 bp):
TTGGGCA
Found at i:50479 original size:7 final size:7
Alignment explanation
Indices: 50467--50510 Score: 88
Period size: 7 Copynumber: 6.3 Consensus size: 7
50457 TTTTGACATC
50467 CAGAATT
1 CAGAATT
50474 CAGAATT
1 CAGAATT
50481 CAGAATT
1 CAGAATT
50488 CAGAATT
1 CAGAATT
50495 CAGAATT
1 CAGAATT
50502 CAGAATT
1 CAGAATT
50509 CA
1 CA
50511 TTCCTAGGAC
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 37 1.00
ACGTcount: A:0.43, C:0.16, G:0.14, T:0.27
Consensus pattern (7 bp):
CAGAATT
Found at i:64621 original size:6 final size:6
Alignment explanation
Indices: 64610--64634 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
64600 ACCATTTGGC
64610 TTGTGT TTGTGT TTGTGT TTGTGT T
1 TTGTGT TTGTGT TTGTGT TTGTGT T
64635 GTGCCAGCTC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (6 bp):
TTGTGT
Done.