Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01007180.1 Corchorus olitorius cultivar O-4 contig07205, 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: 10021
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.35
Found at i:8158 original size:719 final size:710
Alignment explanation
Indices: 6286--8604 Score: 2902
Period size: 727 Copynumber: 3.3 Consensus size: 710
6276 TTCTAATTGT
* * * *
6286 GCTCGATCAGCATCTGATACAGTAAATTATGGATCTTTTACCCGTAACTTATTTGGCCAACAGAT
1 GCTCGATAAGCATCTGATACAGTACATTATGAATCTTTTACCCGTAACTTATTTGGCCAACGGAT
* * * * *
6351 TATTTTATTTTATCCAATAAATTCGACCCAAAGATCTGAGAAAGGGATCGTCGGTGCAGAAATT-
66 TATTTTATCTTATCCAATTAATTCGACCCAAAGATCAGAGAAAGAGATCGTCGATGCAGAAATTA
* *
6415 -T-TTT-TTTTAAAGGCACTAGCCTATATATGTATATTGTTTTGTGTATTTATGTGTTCATAGTG
131 ATATTTGTTTT-AATGCACTAGCCTATATATGTATCTTG-TTT-TG------TGTG-T--TAGT-
* * * ** * * *
6477 AATACTTCTTGCTATCATTATGTCCATTCTTTCCATGTTTTGAATAACGGGAGCGTCTATTTACC
183 -A-A-TT-TTGCTATCATTATCTCCATACTTTCAACCTTTGGAATAGCGAGAGCGTCTATTTACC
** * *
6542 CGTCGTTTCTTCGTTTTGTCAATCTCAAGTTGCCATTTATGTCAAAGATATTTTGCAATTAAATG
244 TATCGTTTCTTCGTTTTGTCAATCTCAAGTTGCCATTTATGTCAAAGATATCTTGCAATTGAATG
* * *
6607 ATTAAATTTAATTGGGAGGAGACACATACATAGTGCATGATGTGACAATATTAGATATAGATCTC
309 ATTAAATTCAATTGGGAGGAGACACATACATAGTGCGTGATGTGACAATATTAGATACAGATCTC
* * * * * * *
6672 GTTAGATCTGATGGAGATATATGCATGTATCAACTACAAAATATGATCGATTCTACTTTTAGTGA
374 GTTAGAACTGATGGAGATATATGTATGTATCAATTGCAAAATATGATAGTTTCTAGTTTTAGTGA
* *
6737 CATGAATTTGCTTTGTTGAAGCTTATATATAATTTAAGCATTGAAAAATATGATTGTTTCTAGTT
439 CTTGAATTTGCTTTGTTGAAGCTTATGTATAATTTAAGCATTGAAAAATATGATTGTTTCTAGTT
* * *
6802 TTACTGACTTTAATAT-ATTTTTTTGAATTTTATTA-CAAGGAACAGCTATTGTTCTTGTACAAC
504 TTACTGACTTGAATTTGA-TTTTTTGAATTTTATTATC-AGGAACAGCTATGGTTCTTGTACAAC
*
6865 CATTATGGATACGTGTAATACCCTCACTAATTGGGATATTTGTCTCAATTTTCCTTAATCAACTG
567 CATTATGGATACGTGTAATACCCTCACTAAATGGGATATTTGTCTCAATTTTCCTTAATCAACTG
* * *
6930 TGGCGATCAGAATTGGATCATATTGATATGGCGAAAGTTGGCCAACTCTGACATATCATATCTTC
632 TGGCGATCAGAATTTGATCATATTGATATGGAGAAAGTTGGCCAACTATGACATATCATATCTTC
*
6995 CAATCGAAAATTAG
697 CAATCGAAAATTAA
* * * *
7009 GCTCGATAAGCATATGATAAAGTACATTATGTATCTTTTACCCGTAACTTATTTGGTCAACGGAT
1 GCTCGATAAGCATCTGATACAGTACATTATGAATCTTTTACCCGTAACTTATTTGGCCAACGGAT
* * * * * *
7074 TATTTTATCTTATCCAATTAATTCGATCCATAGATCAGCGAAAGAGATCGT-TAGGGCAAAAATT
66 TATTTTATCTTATCCAATTAATTCGACCCAAAGATCAGAGAAAGAGATCGTCGA-TGCAGAAA-T
7138 TAATATTTGTTTTAATGCACTAGCCTATATATGTATCTTGTTTTGTGTGTTAGTAATTTCATGGC
129 TAATATTTGTTTTAATGCACTAGCCTATATATGTATCTTGTTTTGTGTGTTAGTAATTT--T-GC
7203 GGATACTTCTTGATATCGTTATCTCCATACTTTCAACCTTTGGAATAGCGAGAGCGTCTATTTAC
191 ---TA--TC-----A---TTATCTCCATACTTTCAACCTTTGGAATAGCGAGAGCGTCTATTTAC
* *
7268 CTATCGTTTCTTCGTTTTGTAAATCTCAAGTTGCCATTTATGTCAAATATATCTTGCAATTGAAT
243 CTATCGTTTCTTCGTTTTGTCAATCTCAAGTTGCCATTTATGTCAAAGATATCTTGCAATTGAAT
*
7333 GATTAAATTCAATTGGGAGGAGACACATACATAGTGCGTGATGTGACAATATTGGATACAGATCT
308 GATTAAATTCAATTGGGAGGAGACACATACATAGTGCGTGATGTGACAATATTAGATACAGATCT
*
7398 CGTTAGATA-TGATGGAGATATATGTATGTATCAATTGCAAAAT-TAGATAGTTTTTAGTTTTAG
373 CGTTAGA-ACTGATGGAGATATATGTATGTATCAATTGCAAAATAT-GATAGTTTCTAGTTTTAG
* * *
7461 TGACTTGAATTTCCTTTGTTGAAGCTTATGTATACTTTAAGCATTGCAAAATATGATTGTTTCTA
436 TGACTTGAATTTGCTTTGTTGAAGCTTATGTATAATTTAAGCATTGAAAAATATGATTGTTTCTA
* * * * *
7526 GTTTTACTGACTTGAATTTGCTTTTTTAAATTTTATTATCAGTAACAGCTATGGTTCATGGACAA
501 GTTTTACTGACTTGAATTTGATTTTTTGAATTTTATTATCAGGAACAGCTATGGTTCTTGTACAA
*
7591 CCATTATGGATACGTGTAATACCCTCACTAAATGGGATATTTATCTCAATTTTCCTTAATCAACT
566 CCATTATGGATACGTGTAATACCCTCACTAAATGGGATATTTGTCTCAATTTTCCTTAATCAACT
* *
7656 GTGGCGATCAAAATTTGATCATATTGATATGGAGAAAGTTGAGAAGGATGGGCCAACTATTACAT
631 GTGGCGATCAGAATTTGATCATATTGATATGGAGAAAG-T--------T-GGCCAACTATGACAT
* *
7721 ATCATATCTTTCAATCGATAATTAA
686 ATCATATCTTCCAATCGAAAATTAA
*
7746 GCTCGATAAGCATCTGATACGGTACATTATGAATCTTTTACCCGTAACTTATTTGGCCAACGGAT
1 GCTCGATAAGCATCTGATACAGTACATTATGAATCTTTTACCCGTAACTTATTTGGCCAACGGAT
* *
7811 GATTTTATCTTATCCAATTAATTCGACCCACAGATCAGAGAAAGAGATCGTCGATGCAGAAATTG
66 TATTTTATCTTATCCAATTAATTCGACCCAAAGATCAGAGAAAGAGATCGTCGATGCAGAAATT-
7876 AATATTTGTTTTAATGCACTAGCCTATATATGTATCTTGTTTTGTGTGTTAGTAA-TTT-CTATC
130 AATATTTGTTTTAATGCACTAGCCTATATATGTATCTTGTTTTGTGTGTTAGTAATTTTGCTATC
*
7939 ATTATCTCCATACTTTCAACCTTTGGAATAGCGAGAGCGTCTATTTACCTATCGTATCTTCGTTT
195 ATTATCTCCATACTTTCAACCTTTGGAATAGCGAGAGCGTCTATTTACCTATCGTTTCTTCGTTT
* *
8004 TGTCAAGCTCAAGTTGCCATTTATGTCAAAGATATCTTGCAATTGCATGATTAAATTCAATTGGG
260 TGTCAATCTCAAGTTGCCATTTATGTCAAAGATATCTTGCAATTGAATGATTAAATTCAATTGGG
* * * * *
8069 AGGAGACATATACATAGTGCGTGATGTTACATTATTTGATACAGATCTCGTCAGAACTGATGGAG
325 AGGAGACACATACATAGTGCGTGATGTGACAATATTAGATACAGATCTCGTTAGAACTGATGGAG
* * *
8134 ATATATGTATGTATCAATTGCAAAATATGAAAGTTTCTAGTTTAAGTGACTTGAATTTGTTTTGT
390 ATATATGTATGTATCAATTGCAAAATATGATAGTTTCTAGTTTTAGTGACTTGAATTTGCTTTGT
*
8199 TGAAGCTTATGTATAATTTAAGCATTGAAAAATATGATTGTTTCTAGGTTTACTGACTTGAATTT
455 TGAAGCTTATGTATAATTTAAGCATTGAAAAATATGATTGTTTCTAGTTTTACTGACTTGAATTT
* *
8264 GATTTTTTGAATTTTATTATCAGGAACAGCTATGGTTCTTGTACAACAATTATGGATACGTATAA
520 GATTTTTTGAATTTTATTATCAGGAACAGCTATGGTTCTTGTACAACCATTATGGATACGTGTAA
* * **
8329 TACCATCACTAAATGAGATATTTGTCTCTGTTTTCCTTAATCAACTGT-G-G--C-------GAT
585 TACCCTCACTAAATGGGATATTTGTCTCAATTTTCCTTAATCAACTGTGGCGATCAGAATTTGAT
*
8383 C--A--GA-AT--------TT-G------AT--CATATC---T-TT-CAATCGAAAATTAG
650 CATATTGATATGGAGAAAGTTGGCCAACTATGACATATCATATCTTCCAATCGAAAATTAA
* * *
8417 GCTCGATAAGCATCTGATACAGTACATTATGGATCTTTTACCCGTAAGTTATTTGGCCAATGGAT
1 GCTCGATAAGCATCTGATACAGTACATTATGAATCTTTTACCCGTAACTTATTTGGCCAACGGAT
* * * * **
8482 TATGTTATCTTATCCAATTAATTCGACCCACATATCAGAGAAAGAGATCGTTGGGGCA-AATATT
66 TATTTTATCTTATCCAATTAATTCGACCCAAAGATCAGAGAAAGAGATCGTCGATGCAGAA-ATT
*
8546 GAATATTTGTTTTAATGCACTAGCCTATATATGTATTTTGTTTTGTGTGTTAGTAATTT
130 -AATATTTGTTTTAATGCACTAGCCTATATATGTATCTTGTTTTGTGTGTTAGTAATTT
8605 CATGGCGGAT
Statistics
Matches: 1430, Mismatches: 124, Indels: 135
0.85 0.07 0.08
Matches are distributed among these distances:
670 2 0.00
671 183 0.13
672 4 0.00
673 1 0.00
676 6 0.00
678 2 0.00
684 1 0.00
686 1 0.00
694 1 0.00
703 2 0.00
704 2 0.00
706 1 0.00
708 4 0.00
711 1 0.00
712 2 0.00
713 2 0.00
714 3 0.00
715 1 0.00
716 4 0.00
717 3 0.00
718 3 0.00
719 409 0.29
720 1 0.00
722 1 0.00
723 108 0.08
724 3 0.00
725 2 0.00
726 5 0.00
727 453 0.32
728 6 0.00
729 2 0.00
732 1 0.00
734 1 0.00
736 5 0.00
737 203 0.14
738 1 0.00
ACGTcount: A:0.30, C:0.15, G:0.17, T:0.38
Consensus pattern (710 bp):
GCTCGATAAGCATCTGATACAGTACATTATGAATCTTTTACCCGTAACTTATTTGGCCAACGGAT
TATTTTATCTTATCCAATTAATTCGACCCAAAGATCAGAGAAAGAGATCGTCGATGCAGAAATTA
ATATTTGTTTTAATGCACTAGCCTATATATGTATCTTGTTTTGTGTGTTAGTAATTTTGCTATCA
TTATCTCCATACTTTCAACCTTTGGAATAGCGAGAGCGTCTATTTACCTATCGTTTCTTCGTTTT
GTCAATCTCAAGTTGCCATTTATGTCAAAGATATCTTGCAATTGAATGATTAAATTCAATTGGGA
GGAGACACATACATAGTGCGTGATGTGACAATATTAGATACAGATCTCGTTAGAACTGATGGAGA
TATATGTATGTATCAATTGCAAAATATGATAGTTTCTAGTTTTAGTGACTTGAATTTGCTTTGTT
GAAGCTTATGTATAATTTAAGCATTGAAAAATATGATTGTTTCTAGTTTTACTGACTTGAATTTG
ATTTTTTGAATTTTATTATCAGGAACAGCTATGGTTCTTGTACAACCATTATGGATACGTGTAAT
ACCCTCACTAAATGGGATATTTGTCTCAATTTTCCTTAATCAACTGTGGCGATCAGAATTTGATC
ATATTGATATGGAGAAAGTTGGCCAACTATGACATATCATATCTTCCAATCGAAAATTAA
Found at i:8645 original size:24 final size:24
Alignment explanation
Indices: 8613--8666 Score: 108
Period size: 24 Copynumber: 2.2 Consensus size: 24
8603 TTCATGGCGG
8613 ATACTTCTTGATATCGTTATCTCC
1 ATACTTCTTGATATCGTTATCTCC
8637 ATACTTCTTGATATCGTTATCTCC
1 ATACTTCTTGATATCGTTATCTCC
8661 ATACTT
1 ATACTT
8667 TCATGCCAGT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.22, C:0.24, G:0.07, T:0.46
Consensus pattern (24 bp):
ATACTTCTTGATATCGTTATCTCC
Found at i:9259 original size:21 final size:21
Alignment explanation
Indices: 9233--9274 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
9223 GTTTGTCTCA
9233 CGAGTTGACTCGGAGACAAAC
1 CGAGTTGACTCGGAGACAAAC
9254 CGAGTTGACTCGGAGACAAAC
1 CGAGTTGACTCGGAGACAAAC
9275 TCAGTAACTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.33, C:0.24, G:0.29, T:0.14
Consensus pattern (21 bp):
CGAGTTGACTCGGAGACAAAC
Found at i:9628 original size:26 final size:26
Alignment explanation
Indices: 9592--9643 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
9582 ATATATATAT
9592 GCACTTTGGGAGATTGATTAGAAGAC
1 GCACTTTGGGAGATTGATTAGAAGAC
9618 GCACTTTGGGAGATTGATTAGAAGAC
1 GCACTTTGGGAGATTGATTAGAAGAC
9644 CTTGGAGCTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.31, C:0.12, G:0.31, T:0.27
Consensus pattern (26 bp):
GCACTTTGGGAGATTGATTAGAAGAC
Done.