Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023984.1 Corchorus olitorius cultivar O-4 contig24017, 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: 28163
ACGTcount: A:0.32, C:0.16, G:0.18, T:0.34
Found at i:130 original size:3 final size:3
Alignment explanation
Indices: 2--117 Score: 193
Period size: 3 Copynumber: 39.0 Consensus size: 3
1 T
2 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
50 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-A
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
97 TAA TTAA -AA TAA -ATA TAA TAA
1 TAA -TAA TAA TAA TA-A TAA TAA
118 AGAAGAATAA
Statistics
Matches: 108, Mismatches: 0, Indels: 10
0.92 0.00 0.08
Matches are distributed among these distances:
2 5 0.05
3 99 0.92
4 4 0.04
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:224 original size:27 final size:25
Alignment explanation
Indices: 194--254 Score: 59
Period size: 27 Copynumber: 2.3 Consensus size: 25
184 ACTATTATAC
*
194 CCTTGGATGGGTAAAATTACTAAATTT
1 CCTTAGAT-GGTAAAATTAC-AAATTT
* *
221 CCTTAGATTGTTAAATTACAAATTT
1 CCTTAGATGGTAAAATTACAAATTT
246 ACCCTTAGA
1 --CCTTAGA
255 AAAGAAATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
25 6 0.21
26 9 0.31
27 14 0.48
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (25 bp):
CCTTAGATGGTAAAATTACAAATTT
Found at i:1247 original size:13 final size:13
Alignment explanation
Indices: 1231--1260 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
1221 ATCTGACTGT
*
1231 TTTGGTTTATTAC
1 TTTGGTTTATGAC
1244 TTTGGTTTATGAC
1 TTTGGTTTATGAC
1257 TTTG
1 TTTG
1261 ATTATGATAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.13, C:0.07, G:0.20, T:0.60
Consensus pattern (13 bp):
TTTGGTTTATGAC
Found at i:4593 original size:4 final size:4
Alignment explanation
Indices: 4584--4615 Score: 64
Period size: 4 Copynumber: 8.0 Consensus size: 4
4574 GACTTATGAA
4584 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT
4616 TATTTAATAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 28 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (4 bp):
AAAT
Found at i:11486 original size:12 final size:12
Alignment explanation
Indices: 11455--11496 Score: 50
Period size: 12 Copynumber: 3.4 Consensus size: 12
11445 TTGAGGAACT
11455 ATTTTATATAATTG
1 ATTTTATA-AA-TG
11469 -TTTTATAAATG
1 ATTTTATAAATG
*
11480 ATTTTATAAACG
1 ATTTTATAAATG
11492 ATTTT
1 ATTTT
11497 TGGGTGCATG
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
11 2 0.08
12 17 0.65
13 7 0.27
ACGTcount: A:0.36, C:0.02, G:0.07, T:0.55
Consensus pattern (12 bp):
ATTTTATAAATG
Found at i:25537 original size:31 final size:31
Alignment explanation
Indices: 25499--25560 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
25489 GTCAGATCTG
*
25499 ATGGAGATATATGCATGTATTTATTGCAAAA
1 ATGGAGATATATGCATGTATTTAATGCAAAA
25530 ATGGAGATATATGCATGTATTTAATGCAAAA
1 ATGGAGATATATGCATGTATTTAATGCAAAA
25561 TATGATCGTT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.40, C:0.06, G:0.19, T:0.34
Consensus pattern (31 bp):
ATGGAGATATATGCATGTATTTAATGCAAAA
Found at i:27017 original size:733 final size:731
Alignment explanation
Indices: 25530--27904 Score: 3527
Period size: 733 Copynumber: 3.2 Consensus size: 731
25520 TATTGCAAAA
* *
25530 ATGGAGATATATGCATGTATTTAA-TGCAAAATATGATCGTTTATAGTTTTAGTGACTTAAATTT
1 ATGGAGATATATGCATGTA-TCAATTGCAAAATATGATCGTTTATAGTTTTAGTGACTTGAATTT
** *
25594 GCTTTGTTGAAGCCTT-TATATAATGCAAGAATTGCAAAATATGATTGTTTCTAGTTGTACTGAC
65 GCTTTGTTGAAG-CTTATATATAATTTAAGCATTGCAAAATATGATTGTTTCTAGTTGTACTGAC
*
25658 TTGAATTTGTTTTTTTGAATTTTAATAGCAGCAACAACTATGGTTCATGTACAACCGTTACT-AA
129 TTGAATTTGCTTTTTTGAATTTTAATA-CAGCAACAACTATGGTTCATGTACAACCGTTACTGAA
*
25722 TACGTGTAATACTCTCAATAATTGGGATGTTTGTCTCAATTTTTCTTAATCATCTGTGACGATCG
193 TACGTGTAATACTCTCAATAATTGGGATGTTTGTCTCAATTTTTCTTAATCATCTGTGGCGATCG
25787 GAATTGGATCATATTGATATGGCGAAAGTTGGGAAGGATGACAGACTCGGACATATTATATCTTT
258 GAATTGGATCATATTGATATGGCGAAAGTTGGGAAGGATGACAGACTCGGACATATTATATCTTT
**
25852 CAATCGAAAATTAAGCTCGATTTGCATCTGATATAGTAGATTACAGATCATTTACCCGTAACTTA
323 CAATCGAAAATTGTGCTCGATTTGCATCTGATATAGTAGATTACAGATCATTTACCCGTAACTTA
*
25917 TTTGGCCACCCGGTTAATTTATCTTATCCTACTAATTCGACCCACAGATCAGAGAAAAGTATTGT
388 TTTGGCCA-CCGATTAATTTATCTTATCCTACTAATTCGACCCACAGATCAGAGAAAAGTATTGT
*
25982 CGGTGCAGGAAATGAATTTTTTTTAAAGCATTAGCTTATATAAGTATCTTGTTTTGTGTGTTAGT
452 CGGTGCAGGAAATGAATTTTTTTTAATGCATTAGC-TATATAAGTATCTTGTTTTGTGTGTTAGT
*
26047 AATTTCATGGTGGATACTTCTTACTATCGTTATCACCATACTTTCAATGTTTGGAATAGAAGAAA
516 AATTTCATGGTGGATACTTCTTACTATCGTTATCACCATACTTTCAATGTTTGGAATAGCAGAAA
26112 CGTCTATTCACCGAACGTTTCTTCGTTTTGTCAATCTCAAGTTGCCATTTATGTCAAAGATATCT
581 CGTCTATTCACCGAACGTTTCTTCGTTTTGTCAATCTCAAGTTGCCATTTATGTCAAAGATATCT
*
26177 TGCATTTAATTGATTAAATTCAATTGGGAGAAGACACATACATAGTGCGTGATGTGACAATATTG
646 TGCATTTAAATGATTAAATTCAATTGGGAGAAGACACATACATAGTGCGTGATGTGACAATATTG
*
26242 GATATAGATCTCGTCAGATCT
711 GATACAGATCTCGTCAGATCT
** *
26263 GATGTCGATATATGCATGTATCAATTGCAAAATATGATCGTTTCTAGTTTTAGTGACTTGAATTT
1 -ATGGAGATATATGCATGTATCAATTGCAAAATATGATCGTTTATAGTTTTAGTGACTTGAATTT
* * * * *
26328 GCTTTGTTGAAACTTATATATAATTTAAGCATTGCAAAATATGATCGTTTCTTGTTTTACTGACA
65 GCTTTGTTGAAGCTTATATATAATTTAAGCATTGCAAAATATGATTGTTTCTAGTTGTACTGACT
* * * *
26393 AGAATTTGCTTTTTTGAATTTTAGTA-A-CAACAACTATGGTTCATGTATAACCATTA-TGAATA
130 TGAATTTGCTTTTTTGAATTTTAATACAGCAACAACTATGGTTCATGTACAACCGTTACTGAATA
* * * *
26455 TGTGTAATACTCTCAAGAATTGGGATGTTTGTCTCAATTTTTCTTAATCATATGTGGCAATCGGA
195 CGTGTAATACTCTCAATAATTGGGATGTTTGTCTCAATTTTTCTTAATCATCTGTGGCGATCGGA
* * * *** * ** * * *
26520 ATAGGATCATATTGGTGTGGCGAAAGTTGGGAAGGATAGGTTGATTTTGAAATATCATAGCTTTC
260 ATTGGATCATATTGATATGGCGAAAGTTGGGAAGGAT-GACAGACTCGGACATATTATATCTTTC
* * * * *
26585 AATCGAAAATTGTGCTTGATCTGCATCTGATACAGTAGATTACTGATCTTTTACCCGTAACTTAT
324 AATCGAAAATTGTGCTCGATTTGCATCTGATATAGTAGATTACAGATCATTTACCCGTAACTTAT
** * * * * * * *
26650 TTGGCCTACAAATTATTTTATCCTATCCTATTAATTCGACCTACAGATCAGA-AAATGGGATCGT
389 TTGGCC-ACCGATTAATTTATCTTATCCTACTAATTCGACCCACAGATCAGAGAAA-AGTATTGT
* * *
26714 CGGTGCAGGAAATAAATATTTTTTTAATGCACTAGCATATATATGTATCTTGTTTTGTGTGTTAG
452 CGGTGCAGGAAATGAAT-TTTTTTTAATGCATTAGC-TATATAAGTATCTTGTTTTGTGTGTTAG
* * * * * *
26779 TAATTTCATGGTGGATACTTCTTGCCATCATTATCTCCATACTTTCAATGTTTGGAATAGCGGGA
515 TAATTTCATGGTGGATACTTCTTACTATCGTTATCACCATACTTTCAATGTTTGGAATAGCAGAA
** * * * * *
26844 GTGTCTATTCACCCAACGGTTCTTCATTTTGTCAATCTCAAGTTGCTATTTATGTCAAACATATC
580 ACGTCTATTCACCGAACGTTTCTTCGTTTTGTCAATCTCAAGTTGCCATTTATGTCAAAGATATC
* * * * **
26909 TTGCATTTGAGTAACTAAATTCAATTGGGATGAGGAGACACATACATAGTAAGTGATGTGACAAT
645 TTGCATTTAAATGATTAAATTCAATTGGGA-GA--AGACACATACATAGTGCGTGATGTGACAAT
* *
26974 ATTGGAGACAGATCTCATCAGAT-T
707 ATTGGATACAGATCTCGTCAGATCT
* *
26998 -TGGAGATGTATGAATGTATCAATTGCAAAATATGATCGTTTATAGTTTTAGTGACTTGAATTTG
1 ATGGAGATATATGCATGTATCAATTGCAAAATATGATCGTTTATAGTTTTAGTGACTTGAATTTG
*
27062 CTTTGTTGAAGCCTATATATAATTTAAGCATTGCAAAATATGATTGTTTCTAGTTGTACTGACTT
66 CTTTGTTGAAGCTTATATATAATTTAAGCATTGCAAAATATGATTGTTTCTAGTTGTACTGACTT
* *
27127 GAATTTGTTTTTTTGAATTTTAATAGCAGCAACAACTATGG-T--T-TACAACTGTTACTG-ATA
131 GAATTTGCTTTTTTGAATTTTAATA-CAGCAACAACTATGGTTCATGTACAACCGTTACTGAATA
*
27187 CGTGTAATACTCTCAATAATTGGGATGTTTGTCTGAATTTTTCTTAATCATCTGTGGCGATCGGA
195 CGTGTAATACTCTCAATAATTGGGATGTTTGTCTCAATTTTTCTTAATCATCTGTGGCGATCGGA
* *
27252 ATTGGATCATATTGATATGGCGAATGTTGGGAAGGATGACCGACTCGGACATATTATATCTTTCA
260 ATTGGATCATATTGATATGGCGAAAGTTGGGAAGGATGACAGACTCGGACATATTATATCTTTCA
27317 ATCGAAAATTGTGCTCGATTTGCATCTGATATAGTAGATTACAGATCATTTACCCGTAACTTATT
325 ATCGAAAATTGTGCTCGATTTGCATCTGATATAGTAGATTACAGATCATTTACCCGTAACTTATT
* *
27382 TGGCCACTCGATTAATTTATCTTGTCCTACTAATTTGACCCACAGATCAGAGAAAAGTATTGTCG
390 TGGCCAC-CGATTAATTTATCTTATCCTACTAATTCGACCCACAGATCAGAGAAAAGTATTGTCG
* *
27447 GTGCAGGAAATGAATTTTTTTTAATGCATTAGCTATATAAGTATCTTGTTTTGTGTATTAATAAT
454 GTGCAGGAAATGAATTTTTTTTAATGCATTAGCTATATAAGTATCTTGTTTTGTGTGTTAGTAAT
* *
27512 TTCATGGTGGATACTTCTTACTATCGTTATCACCATACTTTCAATGCTTGGAATAGCAGAAACAT
519 TTCATGGTGGATACTTCTTACTATCGTTATCACCATACTTTCAATGTTTGGAATAGCAGAAACGT
*
27577 CTATTCACCGAACGTTTCTTCGTTTTGTCAATCTCAAGTTGCCATTTATGTCAAAGATATCTTGT
584 CTATTCACCGAACGTTTCTTCGTTTTGTCAATCTCAAGTTGCCATTTATGTCAAAGATATCTTGC
*
27642 ATTTTAATGATTAAATTCAATTGGGAGAAGACACATACATAGTGCGTGATGTGACAATATTGGAT
649 ATTTAAATGATTAAATTCAATTGGGAGAAGACACATACATAGTGCGTGATGTGACAATATTGGAT
*
27707 ACCGATCTCGTCAGATCT
714 ACAGATCTCGTCAGATCT
*
27725 GATGGAGATTTATGCATGTATCAATTGCAAAATATGATCGTTTATAGTTTTAGTGACTTGAATTT
1 -ATGGAGATATATGCATGTATCAATTGCAAAATATGATCGTTTATAGTTTTAGTGACTTGAATTT
* * * * * *
27790 GCTTTGTTTAAGCTTCTATATAATTTAAGCATTGCAAAATATGATTGTTTTTAATTTTACTGACC
65 GCTTTGTTGAAGCTTATATATAATTTAAGCATTGCAAAATATGATTGTTTCTAGTTGTACTGACT
* **
27855 TGAATTTGCTTTTTTGTATTTTCTTAGCAGCAACAACTATGGTTCATGTA
130 TGAATTTGCTTTTTTGAATTTTAATA-CAGCAACAACTATGGTTCATGTA
27905 TAACAACTAT
Statistics
Matches: 1444, Mismatches: 174, Indels: 47
0.87 0.10 0.03
Matches are distributed among these distances:
726 48 0.03
727 1 0.00
728 2 0.00
729 322 0.22
730 21 0.01
731 268 0.19
732 249 0.17
733 337 0.23
734 133 0.09
735 3 0.00
736 60 0.04
ACGTcount: A:0.30, C:0.14, G:0.18, T:0.38
Consensus pattern (731 bp):
ATGGAGATATATGCATGTATCAATTGCAAAATATGATCGTTTATAGTTTTAGTGACTTGAATTTG
CTTTGTTGAAGCTTATATATAATTTAAGCATTGCAAAATATGATTGTTTCTAGTTGTACTGACTT
GAATTTGCTTTTTTGAATTTTAATACAGCAACAACTATGGTTCATGTACAACCGTTACTGAATAC
GTGTAATACTCTCAATAATTGGGATGTTTGTCTCAATTTTTCTTAATCATCTGTGGCGATCGGAA
TTGGATCATATTGATATGGCGAAAGTTGGGAAGGATGACAGACTCGGACATATTATATCTTTCAA
TCGAAAATTGTGCTCGATTTGCATCTGATATAGTAGATTACAGATCATTTACCCGTAACTTATTT
GGCCACCGATTAATTTATCTTATCCTACTAATTCGACCCACAGATCAGAGAAAAGTATTGTCGGT
GCAGGAAATGAATTTTTTTTAATGCATTAGCTATATAAGTATCTTGTTTTGTGTGTTAGTAATTT
CATGGTGGATACTTCTTACTATCGTTATCACCATACTTTCAATGTTTGGAATAGCAGAAACGTCT
ATTCACCGAACGTTTCTTCGTTTTGTCAATCTCAAGTTGCCATTTATGTCAAAGATATCTTGCAT
TTAAATGATTAAATTCAATTGGGAGAAGACACATACATAGTGCGTGATGTGACAATATTGGATAC
AGATCTCGTCAGATCT
Found at i:28014 original size:29 final size:29
Alignment explanation
Indices: 27959--28028 Score: 68
Period size: 29 Copynumber: 2.3 Consensus size: 29
27949 TCTCGACCTA
* **
27959 ATTTGGGGTATAACCTTTTAATTTGGTCG
1 ATTTGGGGTAAAACCTTTTAAAATGGTCG
* * *
27988 ATTTTGGGTAAAACGTTTTAAAATGGTGTCA
1 ATTTGGGGTAAAACCTTTTAAAAT-G-GTCG
28019 ATTTGGGGTA
1 ATTTGGGGTA
28029 TGATGTCAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
29 19 0.59
30 1 0.03
31 12 0.38
ACGTcount: A:0.26, C:0.07, G:0.26, T:0.41
Consensus pattern (29 bp):
ATTTGGGGTAAAACCTTTTAAAATGGTCG
Done.