Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022793.1 Corchorus olitorius cultivar O-4 contig22826, 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: 22224
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Found at i:691 original size:278 final size:281
Alignment explanation
Indices: 131--695 Score: 974
Period size: 278 Copynumber: 2.0 Consensus size: 281
121 ATAAAAACTA
131 CCCATTTTAAATAAAACTACTCATTAGAGGATAAATATAAGTATTTAAATTTTATTTATACCATT
1 CCCATTTTAAATAAAACTACTCATTAGAGGATAAATATAAGTATTTAAATTTTATTTATACCATT
*
196 TTAAAAAAATTACCCATTTAAAAAAGAACTGTCAAAAACTACTCACGTAGTGAGTGCCCTGTGTT
66 TTAAAAAAACTACCCATTTAAAAAAGAACTGTCAAAAACTACTCACGTAGTGAGTGCCCTGTG--
* * * *
261 TTGTATGTATATATATATATATATGATGCGTTAAAATGATTGTAAACCAATGTTTTTGTAACCGG
129 TTCTATG-ATATATATATATATATGATGCATTAAAATGATTGTAAACCAATATTTTTGTAACCGA
326 CCCGTTACACAAACCGCCCCAGCTCCCAGTTGAGCCGTCCGGGCGGTTCAATAACGTCAGCCAAG
193 CCCGTTACACAAACCGCCCCAGCTCCCAGTTGAGCCGTCCGGGCGGTTCAATAACGTCAGCCAAG
391 ATTTTAGATGCTGTTGAAATATTC
258 ATTTTAGATGCTGTTGAAATATTC
* *
415 CCCATTTTAAATAAAGCTACTCATTAGAGGATAAATATAAGTATTTAAATTTTATTTATATCATT
1 CCCATTTTAAATAAAACTACTCATTAGAGGATAAATATAAGTATTTAAATTTTATTTATACCATT
*
480 TTAAAAAAACTACCCATTTAAAAAAGAACTGTCAAAAACTACTCACGTAGTGATTGCCCTGTG-T
66 TTAAAAAAACTACCCATTTAAAAAAGAACTGTCAAAAACTACTCACGTAGTGAGTGCCCTGTGTT
*
544 CT-TG-TATATATATATATATGATGCATTAAAATGATTGTAAACCAATATTTTTGTAACTGACCC
131 CTATGATATATATATATATATGATGCATTAAAATGATTGTAAACCAATATTTTTGTAACCGACCC
* * *
607 GTTACACAAGCCGCCCCAGCTCCCAGTTGAGCCGTCCGGGCGGTTTAATAACGTCAGCTAAGATT
196 GTTACACAAACCGCCCCAGCTCCCAGTTGAGCCGTCCGGGCGGTTCAATAACGTCAGCCAAGATT
672 TTAGATGCTGTTGAAATATTC
261 TTAGATGCTGTTGAAATATTC
693 CCC
1 CCC
696 TAATCTGAAA
Statistics
Matches: 269, Mismatches: 12, Indels: 6
0.94 0.04 0.02
Matches are distributed among these distances:
278 141 0.52
280 2 0.01
281 2 0.01
284 124 0.46
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.33
Consensus pattern (281 bp):
CCCATTTTAAATAAAACTACTCATTAGAGGATAAATATAAGTATTTAAATTTTATTTATACCATT
TTAAAAAAACTACCCATTTAAAAAAGAACTGTCAAAAACTACTCACGTAGTGAGTGCCCTGTGTT
CTATGATATATATATATATATGATGCATTAAAATGATTGTAAACCAATATTTTTGTAACCGACCC
GTTACACAAACCGCCCCAGCTCCCAGTTGAGCCGTCCGGGCGGTTCAATAACGTCAGCCAAGATT
TTAGATGCTGTTGAAATATTC
Found at i:3484 original size:19 final size:19
Alignment explanation
Indices: 3456--3499 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
3446 TTCCCTTTCT
3456 TTGGGCCACTTATCTTAAA
1 TTGGGCCACTTATCTTAAA
* *
3475 TTGGGTCACTTATCTTAAT
1 TTGGGCCACTTATCTTAAA
3494 TTGGGC
1 TTGGGC
3500 TTTGGCCTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.20, C:0.18, G:0.20, T:0.41
Consensus pattern (19 bp):
TTGGGCCACTTATCTTAAA
Found at i:4954 original size:17 final size:18
Alignment explanation
Indices: 4920--4963 Score: 63
Period size: 17 Copynumber: 2.5 Consensus size: 18
4910 TACCAAAGAA
4920 ACAGATCCCAAAACACAT
1 ACAGATCCCAAAACACAT
*
4938 ACAGATCCC-ATACACAT
1 ACAGATCCCAAAACACAT
*
4955 ATAGATCCC
1 ACAGATCCC
4964 TAGAACAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
17 15 0.62
18 9 0.38
ACGTcount: A:0.43, C:0.34, G:0.07, T:0.16
Consensus pattern (18 bp):
ACAGATCCCAAAACACAT
Found at i:9798 original size:332 final size:333
Alignment explanation
Indices: 9205--10332 Score: 1329
Period size: 332 Copynumber: 3.4 Consensus size: 333
9195 GAAAAGCAAG
* * * * * * *
9205 ATTAGAAGCATGAAAAACCCTTCAGTCTTTTTGGCATTGAGTTATATATTTTTTATTAGTATTGT
1 ATTAGAAGCATGAAAAACCTTTCAATCTTTTTGGCGTTGAATTATATATTTCTTATGAGTATCGT
* * ** * * *
9270 GGCCCAAAATTGAGGAGAAATT-TCTCGGGTCAATTTTGGCAACATTTTAGCTGAAATCGTGTAT
66 GGCCAAAAATTGAGGAGAAATTCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAC
* * * *
9334 TAACCATCACGGTTTTTAACTAAAAACGC-ATTCCGGAGGCTCGCCTCAGTTTTGCACGATTTTT
131 TAACCATCACGGTTTTTGACTAAAAACGCGTTTCGGGA-GCTCGCCTCAGTTTTGCATGATTTTT
* * * *
9398 GGCGCCAAGTCTCATTAAAATATCTATATCCATTTAACCAAATCTTACCCACATTGGATTTAAGG
195 GGCGCCAAGTCTCATTGAAATATCTATATCCATCTAACCAAATCTCAACCACATTGGATTTAAGG
* * ** *
9463 ATTTGTTTTTACGAGCATATGAATCATGTTTCGATTCAATTAG-GTTTAAATACGGAAAAAATAG
260 ATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATTAGAAATT-AATTCGGAAAAAATAG
*
9527 GAAAAACGAC
324 GAAAAACGAT
* * * * *
9537 ATTAGAAGCATGAATAGCCTTTCAATCTTTTTAGTGTTGAATTATATATTTCTTATGAGTATCAT
1 ATTAGAAGCATGAAAAACCTTTCAATCTTTTTGGCGTTGAATTATATATTTCTTATGAGTATCGT
*
9602 GGCCAAAAATTGAGGA-AAATTCTTTCGGGTCAATTTTTACAAAATTTTAGTCGAAATCGTGTAC
66 GGCCAAAAATTGAGGAGAAATTCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAC
* * * * * *
9666 TAACGATCACGGTGTTTGGCTAAAAACGCGTTTTGGGAGCCCGGCTCAGTTTTGCATGATTTTTG
131 TAACCATCACGGTTTTTGACTAAAAACGCGTTTCGGGAGCTCGCCTCAGTTTTGCATGATTTTTG
* * * ** *
9731 GCGCCAAGACTCTTTGGAATATCTATATTTATCTAACGAAATCTCAACCACATTGGATTTAAGGA
196 GCGCCAAGTCTCATTGAAATATCTATATCCATCTAACCAAATCTCAACCACATTGGATTTAAGGA
* * *
9796 TTTGTTTCTACGAGCATCTCAATCCA-GTTTCAATTTAATTAGAAATTAATTC-G--AAAA-A--
261 TTTGTTTTTACGAGCATCTGAAT-CATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGG
*
9854 AAAAACAAT
325 AAAAACGAT
* * * * * *
9863 ATTAGAAGCGTGAGAAGCCTTTCAATCTTTTTGGCGTTGAGTTATATAATTT-TTATGAATATGG
1 ATTAGAAGCATGAAAAACCTTTCAATCTTTTTGGCGTTGAATTATAT-ATTTCTTATGAGTATCG
* * * * *
9927 TGG-CAGGAAATTGAGGAGAAA-TGTTTCGTGTCAATTTTTACAAAATTTTAGCCGAAATTGTAT
65 TGGCCA-AAAATTGAGGAGAAATTCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGT
* ** * * * **
9990 ACGTTA-CATCATAGTTTTTGACTAAAAACGTGTTTCGGG-TCTCGTCTTTGTTTTGCATGATTT
129 AC-TAACCATCACGGTTTTTGACTAAAAACGCGTTTCGGGAGCTCGCCTCAGTTTTGCATGATTT
*
10053 TTGGAGCCAAGTCTCATTGAAATATCTATATCCATCTAACCAAATCTCAACCACATTGGATTTAA
193 TTGGCGCCAAGTCTCATTGAAATATCTATATCCATCTAACCAAATCTCAACCACATTGGATTTAA
* *
10118 GGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAACTAGAAATTAATTCGGAAATAATA
258 GGATTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATA
*
10183 GGAAAACCGAT
323 GGAAAAACGAT
* * *
10194 GTTAGAAGCGTGAAAAACCTTTCAATCTTTTTGCCGTTGAATTATATATTTCTTATGAGTATCGT
1 ATTAGAAGCATGAAAAACCTTTCAATCTTTTTGGCGTTGAATTATATATTTCTTATGAGTATCGT
* * * * *
10259 GGCAAAAAATTTAGGA-AAATTCTTTTGGGTAAATTTTTGCAAAATCTTTA-CCGAAATCGTGTA
66 GGCCAAAAATTGAGGAGAAATTCTTTCGGGTCAATTTTTACAAAAT-TTTAGCCGAAATCGTGTA
*
10322 TTAACCATCAC
130 CTAACCATCAC
10333 ATTTTTTTGG
Statistics
Matches: 664, Mismatches: 112, Indels: 41
0.81 0.14 0.05
Matches are distributed among these distances:
324 2 0.00
325 127 0.19
326 136 0.20
327 9 0.01
328 4 0.01
329 5 0.01
330 9 0.01
331 113 0.17
332 250 0.38
333 9 0.01
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.36
Consensus pattern (333 bp):
ATTAGAAGCATGAAAAACCTTTCAATCTTTTTGGCGTTGAATTATATATTTCTTATGAGTATCGT
GGCCAAAAATTGAGGAGAAATTCTTTCGGGTCAATTTTTACAAAATTTTAGCCGAAATCGTGTAC
TAACCATCACGGTTTTTGACTAAAAACGCGTTTCGGGAGCTCGCCTCAGTTTTGCATGATTTTTG
GCGCCAAGTCTCATTGAAATATCTATATCCATCTAACCAAATCTCAACCACATTGGATTTAAGGA
TTTGTTTTTACGAGCATCTGAATCATGTTTCGATTTAATTAGAAATTAATTCGGAAAAAATAGGA
AAAACGAT
Found at i:15639 original size:2 final size:2
Alignment explanation
Indices: 15632--15665 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
15622 TAATTACAAC
15632 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
15666 AGAATTTAGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:16650 original size:136 final size:136
Alignment explanation
Indices: 16420--16693 Score: 521
Period size: 136 Copynumber: 2.0 Consensus size: 136
16410 TAGATGAACA
*
16420 CTTGTTTGTTTCCTATGCAAATCACCAATTTCAAGGTATTGTTAGATTTAAATGTGTTAAAATGA
1 CTTGTTTGTTTCCTATGCAAATCACCAATTCCAAGGTATTGTTAGATTTAAATGTGTTAAAATGA
*
16485 TTGTAATCATGATGATAATTCCCAATCCACTGATTAGTTATTTGAAACGGGTGGCACAATTTTAG
66 TTGTAATCATGATGATAATTCCCAATCCACTGATTAGGTATTTGAAACGGGTGGCACAATTTTAG
16550 CCACCT
131 CCACCT
16556 CTTGTTTGTTTCCTATGCAAATCACCAATTCCAAGGTATTGTTAGATTTAAATGTGTTAAAATGA
1 CTTGTTTGTTTCCTATGCAAATCACCAATTCCAAGGTATTGTTAGATTTAAATGTGTTAAAATGA
16621 TTGTAATCATGATGATAATTCCCAATCCACTGATTAGGTATTTGAAACGGGTGGCACAATTTTAG
66 TTGTAATCATGATGATAATTCCCAATCCACTGATTAGGTATTTGAAACGGGTGGCACAATTTTAG
*
16686 CCGCCT
131 CCACCT
16692 CT
1 CT
16694 CCCTTTCCGT
Statistics
Matches: 135, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
136 135 1.00
ACGTcount: A:0.30, C:0.17, G:0.17, T:0.37
Consensus pattern (136 bp):
CTTGTTTGTTTCCTATGCAAATCACCAATTCCAAGGTATTGTTAGATTTAAATGTGTTAAAATGA
TTGTAATCATGATGATAATTCCCAATCCACTGATTAGGTATTTGAAACGGGTGGCACAATTTTAG
CCACCT
Done.