Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023828.1 Corchorus olitorius cultivar O-4 contig23861, 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: 45862
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:4155 original size:29 final size:29
Alignment explanation
Indices: 4114--4172 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
4104 TATCTCAAGG
*
4114 ATTTTCTGTTATTTTTGCGTTAA-AAAAA
1 ATTTTCTCTTATTTTTGCGTTAACAAAAA
4142 ATTTCTCTCTTATTTTTGCGTTAACAAAAA
1 ATTT-TCTCTTATTTTTGCGTTAACAAAAA
4172 A
1 A
4173 AAATCTTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 4 0.14
29 18 0.64
30 6 0.21
ACGTcount: A:0.32, C:0.12, G:0.08, T:0.47
Consensus pattern (29 bp):
ATTTTCTCTTATTTTTGCGTTAACAAAAA
Found at i:7287 original size:16 final size:16
Alignment explanation
Indices: 7268--7360 Score: 91
Period size: 16 Copynumber: 5.8 Consensus size: 16
7258 CTCGGGCGGG
7268 TTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
* *
7284 TTCGGGCTCGGGT-TAA
1 TTCGGGTTCGGGTAT-T
*
7300 GTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
** *
7316 TTCATGCTCGGGT-TAT
1 TTCGGGTTCGGGTAT-T
*
7332 GTCGGGTTCGGGTATT
1 TTCGGGTTCGGGTATT
7348 TTCGGGTTCGGGT
1 TTCGGGTTCGGGT
7361 TCGGGCTCGG
Statistics
Matches: 59, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
15 2 0.03
16 55 0.93
17 2 0.03
ACGTcount: A:0.08, C:0.15, G:0.39, T:0.39
Consensus pattern (16 bp):
TTCGGGTTCGGGTATT
Found at i:7295 original size:32 final size:33
Alignment explanation
Indices: 7254--7377 Score: 121
Period size: 32 Copynumber: 3.8 Consensus size: 33
7244 GGCAATTGGG
7254 CGGGCTCGGG-CGGGTTCGGGTTCGGGTATTTT
1 CGGGCTCGGGTCGGGTTCGGGTTCGGGTATTTT
***
7286 CGGGCTCGGGTTAAG-TCGGGTTCGGGTATTTT
1 CGGGCTCGGGTCGGGTTCGGGTTCGGGTATTTT
** ***
7318 CATGCTCGGGTTATG-TCGGGTTCGGGTATTTT
1 CGGGCTCGGGTCGGGTTCGGGTTCGGGTATTTT
* *
7350 CGGGTTCGGGTTCGGGCTCGGG-TCGGGT
1 CGGGCTCGGG-TCGGGTTCGGGTTCGGGT
7378 TCAGGCTCGG
Statistics
Matches: 77, Mismatches: 12, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
32 63 0.82
33 9 0.12
34 5 0.06
ACGTcount: A:0.06, C:0.18, G:0.44, T:0.33
Consensus pattern (33 bp):
CGGGCTCGGGTCGGGTTCGGGTTCGGGTATTTT
Found at i:7377 original size:5 final size:6
Alignment explanation
Indices: 7348--7390 Score: 52
Period size: 6 Copynumber: 7.3 Consensus size: 6
7338 TTCGGGTATT
* * *
7348 TTCGGG TTCGGG TTCGGG CTCGGG -TCGGG TTCAGG CTCGGG TT
1 TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TTCGGG TT
7391 TGATTTTGAT
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
5 5 0.16
6 26 0.84
ACGTcount: A:0.02, C:0.21, G:0.47, T:0.30
Consensus pattern (6 bp):
TTCGGG
Found at i:7377 original size:17 final size:17
Alignment explanation
Indices: 7349--7389 Score: 64
Period size: 17 Copynumber: 2.4 Consensus size: 17
7339 TCGGGTATTT
*
7349 TCGGGTTCGGGTTCGGGC
1 TCGGG-TCGGGTTCAGGC
7367 TCGGGTCGGGTTCAGGC
1 TCGGGTCGGGTTCAGGC
7384 TCGGGT
1 TCGGGT
7390 TTGATTTTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.02, C:0.22, G:0.49, T:0.27
Consensus pattern (17 bp):
TCGGGTCGGGTTCAGGC
Found at i:12966 original size:22 final size:21
Alignment explanation
Indices: 12914--12967 Score: 60
Period size: 19 Copynumber: 2.6 Consensus size: 21
12904 TGCTTCTTGA
12914 AATAATTCTTC-AATGATCTTC
1 AATAA-TCTTCAAATGATCTTC
*
12935 -A-AATCTTCAAATTATCTTC
1 AATAATCTTCAAATGATCTTC
12954 AATAAGTCTTCAAA
1 AATAA-TCTTCAAA
12968 CACGAACTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
18 5 0.18
19 11 0.39
20 2 0.07
21 2 0.07
22 8 0.29
ACGTcount: A:0.39, C:0.19, G:0.04, T:0.39
Consensus pattern (21 bp):
AATAATCTTCAAATGATCTTC
Found at i:17062 original size:737 final size:722
Alignment explanation
Indices: 15659--17121 Score: 2367
Period size: 737 Copynumber: 2.0 Consensus size: 722
15649 CATAGTCTCA
*
15659 AGGAAACTCCCTGAGGGAGTAAGCAAGGCCGTGAAGAATAAGATAGTTAATGATTCAAGACATTA
1 AGGAAACTCCCTGAGGGAGTAAGCAAGGCCGTGAAGAATAAGATAATTAATGATTCAAGACATTA
*
15724 CTTCTGGGATGATCCTTATCTTTCGAAGTTTTGTCTTGATAAGGTCATTAGGAGATGCATTCCTC
66 CTTCTGGGATGATCCTTATCTTTCGAAGTTTTGTCCTGATAAGGTCATTAGGAGATGCATTCCTC
*
15789 AAGATGAATTTCAATCCACATTAAAATTCTGCCACTCTTTAGAGTGTGGTGGACATTTTAGTTAT
131 AAGATGAATTTCAATACACATTAAAATTCTGCCACTCTTTAGAGTGTGGTGGACATTTTAGTTAT
* * *
15854 AAGAAAACAGCAATGAAAGTGCTAGATGTTGGCCTTTATTGGCCGACTATATTCAAAGATGCTGA
196 AAGAAAACAACAATGAAAGTGCTAGATGCTAGCCTTTATTGGCCGACTATATTCAAAGATGCTGA
*
15919 AGAGTATATATTGCAAGTATTGTCCTGAATGCCAAAAGTTGGGAGCTATTACTATACAAACACCA
261 AGAG---ATATTGCAAGTATTGTCCTGAATGCCAAAAGATGGGAGCTATTACTATACAAACACCA
*
15984 ATATTGATTGTTGAGATATTTGATGTTTGGGGTATAGATTTCATGGGACCATTTCCACCATCTTT
323 ATATTGATTGTTGAGATATTTGATATTTGGGGTATAGATTTCATGGGACCATTTCCACCATCTTT
*
16049 TCACTGTGAGTATATACTCTTAGCTGTTGATTATGTTTCTAAATGGATTGAAGCAATACGAACAC
388 TCACTGTGAGTATATACTCTTAGCTGTTGATTATGTTTCTAAATGGACTGAAGCAATACGAACAC
*
16114 AAAAAAATGATGCTGCCACTGTTTCGAAATTTCTAAAGAGCAACATTCTAAGTAGATTTGGAGTT
453 AAAAAAATGATGCTGCCACTGTTTCAAAATTTCTAAAGAGCAACATTCTAAGTAGATTTGGAGTT
*
16179 CCAAGATACTTGATAAGTGATCAAGGTTCACATTTCTGCAATAAAGTGATTGAAGCATTAGTAGC
518 CCAAGATACTTGATAAGTGATCAAGGTTCACATTTCTGCAATAAAGTGATTGAAGCATTAGTAAC
* *
16244 TAAATATGGGCTTATACACAAGGTAGCAACCGCATATCATCCTTAAACAAGTGACCAAGCAGAAG
583 TAAAAATGGGCTTATACACAAGGTAGCAACCGCATATCATCCTCAAACAAGTGACCAAGCAGAAG
*
16309 TTTCTAATAGACAAATTAAGCAAATCCTGGAAAAGACAATTAATCCTTCAAGAAAAGATTGGAGT
648 TTTCTAATAAACAAATTAAGCAAATCCTGGAAAAGACAATTAATCCTTCAAGAAAAGATTGGAGT
16374 TTACGTTTGG
713 TTACGTTTGG
* * *
16384 AGGAAACTCCTTGAGTGAGTATGCAAGGCCGTGAAGAATAAGATAATTAATGATTCAAGACATTA
1 AGGAAACTCCCTGAGGGAGTAAGCAAGGCCGTGAAGAATAAGATAATTAATGATTCAAGACATTA
*
16449 CTTCTGGGATGATCCTTATCTTTGGAAGTTTTGTCCTGATAAGGTCATTAGGAGATGCATTCCTC
66 CTTCTGGGATGATCCTTATCTTTCGAAGTTTTGTCCTGATAAGGTCATTAGGAGATGCATTCCTC
*** *
16514 AAGATGAATTTCAATATGGATTGAAATTCTGCCACTCTTTAGAGTGTGGTGGACATTTTAGTTAT
131 AAGATGAATTTCAATACACATTAAAATTCTGCCACTCTTTAGAGTGTGGTGGACATTTTAGTTAT
16579 AAGAAAACAACAATGAAAGTGCTAGATGCTAGCCTTTATTGGCCGACTATATTCAAAGATGCTGA
196 AAGAAAACAACAATGAAAGTGCTAGATGCTAGCCTTTATTGGCCGACTATATTCAAAGATGCTGA
16644 AGAG-TATTGCAAGTATCAAT-TCCTGAATGCCAAAAGAT-GGAGCTATTACTAAGAGAGGTTAA
261 AGAGATATTGCAAGTAT---TGTCCTGAATGCCAAAAGATGGGAGCTATTAC----------T--
16706 ATGCTACAAACACCAATATTGATTGTTGAGATATTTGATATTTGGGGTATAGATTTCATGGGACC
311 A---TACAAACACCAATATTGATTGTTGAGATATTTGATATTTGGGGTATAGATTTCATGGGACC
*
16771 ATTTCCACCATCTTTTCACTGTGAGTATATACTCTTAGTTGTTGATTATGTTTCTAAATGGACTG
373 ATTTCCACCATCTTTTCACTGTGAGTATATACTCTTAGCTGTTGATTATGTTTCTAAATGGACTG
* *
16836 AAGCAATACGAACACAAAAGAATGATGCTGCCACTGTTTCAAAATTTCTGAAGAGCAACATTCTA
438 AAGCAATACGAACACAAAAAAATGATGCTGCCACTGTTTCAAAATTTCTAAAGAGCAACATTCTA
*
16901 AGTAGATTTGGAGTTCCAAGATACTTGATAAGTGATCAAGGTTCACATTTTTGCAATAGAA-TGA
503 AGTAGATTTGGAGTTCCAAGATACTTGATAAGTGATCAAGGTTCACATTTCTGCAATA-AAGTGA
* ** * *
16965 TTGAAGCATTAGTAACTAAAAATGGGGTTATATGCAAGGTTGCAACCGCATTTCATCCTCAAACA
567 TTGAAGCATTAGTAACTAAAAATGGGCTTATACACAAGGTAGCAACCGCATATCATCCTCAAACA
* * * * *
17030 AGTGGCCAAGCAGAAGTTTTTAATAAACAAATTAAGCAAATCTTGGAAAAGACTATTAATCCTTT
632 AGTGACCAAGCAGAAGTTTCTAATAAACAAATTAAGCAAATCCTGGAAAAGACAATTAATCCTTC
*
17095 AAGAAAAGATTGGAGTTTATGTTTGG
697 AAGAAAAGATTGGAGTTTACGTTTGG
17121 A
1 A
17122 TGATGCACTA
Statistics
Matches: 682, Mismatches: 37, Indels: 26
0.92 0.05 0.03
Matches are distributed among these distances:
721 12 0.02
722 11 0.02
723 17 0.02
724 1 0.00
725 250 0.37
732 1 0.00
734 1 0.00
737 387 0.57
738 2 0.00
ACGTcount: A:0.34, C:0.15, G:0.20, T:0.31
Consensus pattern (722 bp):
AGGAAACTCCCTGAGGGAGTAAGCAAGGCCGTGAAGAATAAGATAATTAATGATTCAAGACATTA
CTTCTGGGATGATCCTTATCTTTCGAAGTTTTGTCCTGATAAGGTCATTAGGAGATGCATTCCTC
AAGATGAATTTCAATACACATTAAAATTCTGCCACTCTTTAGAGTGTGGTGGACATTTTAGTTAT
AAGAAAACAACAATGAAAGTGCTAGATGCTAGCCTTTATTGGCCGACTATATTCAAAGATGCTGA
AGAGATATTGCAAGTATTGTCCTGAATGCCAAAAGATGGGAGCTATTACTATACAAACACCAATA
TTGATTGTTGAGATATTTGATATTTGGGGTATAGATTTCATGGGACCATTTCCACCATCTTTTCA
CTGTGAGTATATACTCTTAGCTGTTGATTATGTTTCTAAATGGACTGAAGCAATACGAACACAAA
AAAATGATGCTGCCACTGTTTCAAAATTTCTAAAGAGCAACATTCTAAGTAGATTTGGAGTTCCA
AGATACTTGATAAGTGATCAAGGTTCACATTTCTGCAATAAAGTGATTGAAGCATTAGTAACTAA
AAATGGGCTTATACACAAGGTAGCAACCGCATATCATCCTCAAACAAGTGACCAAGCAGAAGTTT
CTAATAAACAAATTAAGCAAATCCTGGAAAAGACAATTAATCCTTCAAGAAAAGATTGGAGTTTA
CGTTTGG
Found at i:22252 original size:24 final size:24
Alignment explanation
Indices: 22220--22270 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
22210 TCACATTGCA
22220 TCATATTAGTTTAAATAAACTGCT
1 TCATATTAGTTTAAATAAACTGCT
22244 TCATATTAGTTTAAATAAACTGCT
1 TCATATTAGTTTAAATAAACTGCT
22268 TCA
1 TCA
22271 CATTGCATAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.37, C:0.14, G:0.08, T:0.41
Consensus pattern (24 bp):
TCATATTAGTTTAAATAAACTGCT
Found at i:28063 original size:11 final size:12
Alignment explanation
Indices: 28034--28065 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
28024 GGATTCTACA
28034 AAAGA-TTCATC
1 AAAGATTTCATC
28045 AAAGATTTC-TC
1 AAAGATTTCATC
28056 AAAGATTTCA
1 AAAGATTTCA
28066 GCACCAATGT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
11 16 0.84
12 3 0.16
ACGTcount: A:0.44, C:0.16, G:0.09, T:0.31
Consensus pattern (12 bp):
AAAGATTTCATC
Found at i:31703 original size:16 final size:17
Alignment explanation
Indices: 31679--31715 Score: 58
Period size: 16 Copynumber: 2.2 Consensus size: 17
31669 TCTATCTAGT
*
31679 TTTATTTTTCTATCA-C
1 TTTAATTTTCTATCATC
31695 TTTAATTTTCTATCATC
1 TTTAATTTTCTATCATC
31712 TTTA
1 TTTA
31716 TGTTTGAGTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.74
17 5 0.26
ACGTcount: A:0.22, C:0.16, G:0.00, T:0.62
Consensus pattern (17 bp):
TTTAATTTTCTATCATC
Found at i:34808 original size:27 final size:27
Alignment explanation
Indices: 34752--34823 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 27
34742 TAGGGGTCAC
* *
34752 TCAGGGGAATTTTGGTCATTCGAATGT
1 TCAGGGGCATTTTGGTCATTCGAATAT
* *
34779 TCAGGGGCATTTTGGTCATTTGCATAT
1 TCAGGGGCATTTTGGTCATTCGAATAT
* **
34806 TCAAGGGCACGTTGGTCA
1 TCAGGGGCATTTTGGTCA
34824 CTTTAAGTCC
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.21, C:0.15, G:0.29, T:0.35
Consensus pattern (27 bp):
TCAGGGGCATTTTGGTCATTCGAATAT
Found at i:37754 original size:21 final size:22
Alignment explanation
Indices: 37730--37776 Score: 60
Period size: 22 Copynumber: 2.2 Consensus size: 22
37720 AAAATGAAGG
* *
37730 TTTTCAAAGCA-AAGTAAAAGA
1 TTTTAAAAGCAGAAATAAAAGA
*
37751 TTTTAAAAGCAGAAATAAAAGG
1 TTTTAAAAGCAGAAATAAAAGA
37773 TTTT
1 TTTT
37777 GACACAGCAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 10 0.45
22 12 0.55
ACGTcount: A:0.49, C:0.06, G:0.15, T:0.30
Consensus pattern (22 bp):
TTTTAAAAGCAGAAATAAAAGA
Found at i:37776 original size:22 final size:21
Alignment explanation
Indices: 37726--37776 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
37716 GACTAAAATG
* *
37726 AAGGTTTTCAAAGCAAAGTAA
1 AAGGTTTTAAAAGCAAAATAA
*
37747 AAGATTTTAAAAGCAGAAATAA
1 AAGGTTTTAAAAGCA-AAATAA
37769 AAGGTTTT
1 AAGGTTTT
37777 GACACAGCAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
21 13 0.52
22 12 0.48
ACGTcount: A:0.49, C:0.06, G:0.18, T:0.27
Consensus pattern (21 bp):
AAGGTTTTAAAAGCAAAATAA
Done.