Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01018800.1 Corchorus olitorius cultivar O-4 contig18833, 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: 45319
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:6113 original size:21 final size:22
Alignment explanation
Indices: 6084--6124 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
6074 TGTAGTACCG
6084 GGCATGGCCGGGCAATTGGCTC
1 GGCATGGCCGGGCAATTGGCTC
*
6106 GGCA-GGCCGGGCACTTGGC
1 GGCATGGCCGGGCAATTGGC
6125 GCGGAGGAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 14 0.78
22 4 0.22
ACGTcount: A:0.12, C:0.29, G:0.44, T:0.15
Consensus pattern (22 bp):
GGCATGGCCGGGCAATTGGCTC
Found at i:6284 original size:75 final size:75
Alignment explanation
Indices: 6191--6361 Score: 252
Period size: 75 Copynumber: 2.3 Consensus size: 75
6181 AGATGGCTCG
** ** * *
6191 GATGGCCAAGCCATGGCCGGGCACGTGTCTCGGTGCGGCTCGGGCATGGCCGATCCTGTTCGGGC
1 GATGGCCGGGCCATGGCCGGGCACGTGTCTCGGCACGGCTCGGACATGGCCGATCCTGTCCGGGC
6256 CATGTGTGAC
66 CATGTGTGAC
* *
6266 GATGGCCGGGCCATGGCCGGGCACGTGTCTCGGCACGGCTCGGATATGGCCGGTCCTGTCCGGGC
1 GATGGCCGGGCCATGGCCGGGCACGTGTCTCGGCACGGCTCGGACATGGCCGATCCTGTCCGGGC
6331 CATGTGTGAC
66 CATGTGTGAC
* *
6341 GATGGCCGGGCTACGGCCGGG
1 GATGGCCGGGCCATGGCCGGG
6362 TAATGGCTGG
Statistics
Matches: 86, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
75 86 1.00
ACGTcount: A:0.11, C:0.30, G:0.41, T:0.18
Consensus pattern (75 bp):
GATGGCCGGGCCATGGCCGGGCACGTGTCTCGGCACGGCTCGGACATGGCCGATCCTGTCCGGGC
CATGTGTGAC
Found at i:11321 original size:11 final size:10
Alignment explanation
Indices: 11274--11321 Score: 55
Period size: 11 Copynumber: 4.8 Consensus size: 10
11264 TTGAAATATT
*
11274 TCTTCAATGA
1 TCTTCAATTA
11284 TCTTC-A-TA
1 TCTTCAATTA
11292 TCTTCAAATTA
1 TCTTC-AATTA
11303 TCTTCAATTAA
1 TCTTCAATT-A
11314 TCTTCAAT
1 TCTTCAAT
11322 CACGAACTTC
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
8 6 0.18
9 1 0.03
10 10 0.30
11 16 0.48
ACGTcount: A:0.31, C:0.21, G:0.02, T:0.46
Consensus pattern (10 bp):
TCTTCAATTA
Found at i:22104 original size:36 final size:36
Alignment explanation
Indices: 22057--22129 Score: 119
Period size: 36 Copynumber: 2.0 Consensus size: 36
22047 ACAACTCCCC
* *
22057 ACTTTAGGTTATGCCATCCTAAGGCGCTGCTAAATT
1 ACTTTAGGTTATACCATCCTAAGGCGCTACTAAATT
*
22093 ACTTTAGGTTATATCATCCTAAGGCGCTACTAAATT
1 ACTTTAGGTTATACCATCCTAAGGCGCTACTAAATT
22129 A
1 A
22130 AATTGAAGGA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Consensus pattern (36 bp):
ACTTTAGGTTATACCATCCTAAGGCGCTACTAAATT
Found at i:40679 original size:2 final size:2
Alignment explanation
Indices: 40674--40699 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
40664 CTTTCACCAA
40674 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
40700 CAATGTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:41619 original size:9 final size:11
Alignment explanation
Indices: 41593--41626 Score: 68
Period size: 11 Copynumber: 3.1 Consensus size: 11
41583 ATTTGAAATG
41593 AATATATAATA
1 AATATATAATA
41604 AATATATAATA
1 AATATATAATA
41615 AATATATAATA
1 AATATATAATA
41626 A
1 A
41627 CGACTAATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (11 bp):
AATATATAATA
Found at i:41969 original size:666 final size:649
Alignment explanation
Indices: 40698--42558 Score: 2743
Period size: 666 Copynumber: 2.8 Consensus size: 649
40688 ATATATATAT
40698 ATCAATGTAAAAATATTATAT-ATGTCTATATGGCATAGCCACATATTGGGATCAATTGACCCAC
1 ATCAATGTAAAAATATTATATAATGTCTATATGGCATAGCCACATATTGGGATCAATTGACCCAC
* * * * * * * *
40762 TAAAATTATATTATCTCCCTTATATTTATAATATATATATATATATAGTATAGATTAATTTGAGC
66 TAAAATTTTATCATCTCCCTTGTA-ATA-AATA-ATATA-ATATATAGAATATAATATTTTGAGC
*
40827 TAATATTATAAATTTACTGTATAATATAGAAAATTTGAAGATTTTGATCCATTAAAAATTGAATT
127 TAATATTATAAATTTACTGTATAATATAGAAAATTTGAAGATTTTGATCCATTAAAAATTCAATT
40892 TTACAATATTTACCCACTGAAATTAAGAATCGAGATATA-CATAAAACAATTTGAAATGAATATG
192 TTACAATATTTACCCACTGAAATTAAGAATCGAGATATACCATAAAACAATTTGAAATGAATATG
* *
40956 TAATAACGACTAATTTGGTGTTGTTATTGTAATTGGAAACTTGGTCTTACACAAACAAAACTTGT
257 TAATAACGACTAATTTGGTATTGTTATTGTAATTGAAAACTTGGTCTTACACAAACAAAACTTGT
* *
41021 TTGAAACTA--TTTGAGTGAAAAAAAAACAACATTTTTATCTCTCAACACCCAGCTAAATAAATA
322 TTGAAACTATTTTTGAGTG-GAAAAAAACAACATTTTTATCTCTCAACACCCAGCTAAATAGATA
*
41084 TAGTTAACCCTAAATATCACGCTAAACGAGCTAAATAGATATAGTGGTAGAAATTCACAGACGAC
386 TAGTTAACCCTAAATACCACGCTAAACGAGCTAAATAGATATAGTGGTAGAAATTCACAGACGAC
*
41149 TTGACCCCACTGGAGGAAAGTCCTGGCTACTCTAATATGAGAACATGTACGTAATAAGAGAGTAG
451 TTGACCCCACT-GAGGAAAG-CCTGGCTACACTAATATGAGAACATGTACGTAATAAGAGAGTAG
41214 TCATGTTTTCATCTCATAGATCTCAATTCATCTACACCGTCAGTATATCAAATAATTAACATTTT
514 TCATGTTTTCATCTCATAGATCTCAATTCATCTACA-C--CAGTATATCAAATAATTAACATTTT
*
41279 TGTTAAAGTGATTTATGGATATATATATATATATATATATTTTGGTGAAAGAGTATATATAAATT
576 TGTTAAAGCGATTTATGGATATATATATATATATA-AT-TTTTGGTGAAAGAGTATATATAAATT
41344 TTTTCATCTTA
639 TTTTCATCTTA
41355 ATCAATGTAAAAATATTATAT-ATGTCTATATGGCATAGCCACATATTGGGATCAATTGACCCAC
1 ATCAATGTAAAAATATTATATAATGTCTATATGGCATAGCCACATATTGGGATCAATTGACCCAC
41419 TAAAATTTTATCATCTCCC-T-T-ATAAAT-ATAT-ATATATAG-AT-T-A-A-TTTGAGCTAAT
66 TAAAATTTTATCATCTCCCTTGTAATAAATAATATAATATATAGAATATAATATTTTGAGCTAAT
41474 ATTATAAATTTACTGTATAATATAGAAAATTTGAAGATTTTGATCCATTAAAAATTCAATTTTAC
131 ATTATAAATTTACTGTATAATATAGAAAATTTGAAGATTTTGATCCATTAAAAATTCAATTTTAC
*
41539 AATATTTACCCACTGAAATTAAGAATCGAGATATA-CATAAAATAATTTGAAATGAATATATAAT
196 AATATTTACCCACTGAAATTAAGAATCGAGATATACCATAAAACAATTTGAAATG----------
*
41603 AAATATATAATAAATATATAATAACGACTAATTTGGTATTGTTATTGTAATTGAAAACTTGGTCT
251 ------------AATATGTAATAACGACTAATTTGGTATTGTTATTGTAATTGAAAACTTGGTCT
*
41668 TACACAAACCAAACTTGTTTGAAACTATTTTTGAGTGGAAAAAAACAACATTTTTATCTCTCAAC
304 TACACAAACAAAACTTGTTTGAAACTATTTTTGAGTGGAAAAAAACAACATTTTTATCTCTCAAC
41733 ACCCAGCTAAATAGATATAGTTAACCCTAAATACCACGCTAAACGAGCTAAATAGATATAGTGGT
369 ACCCAGCTAAATAGATATAGTTAACCCTAAATACCACGCTAAACGAGCTAAATAGATATAGTGGT
* *
41798 AGAAATTCACAGACGACTTGACCCCATTGAAGGAAAGACCTGGCTACACCAATATGAGAACATGT
434 AGAAATTCACAGACGACTTGACCCCACTG-AGGAAAG-CCTGGCTACACTAATATGAGAACATGT
*
41863 ACGTAATAAGAGAGTAGTCATGTTTTCATCTCATAGATCTCAATTCATTTACA-CAGTATATCAA
497 ACGTAATAAGAGAGTAGTCATGTTTTCATCTCATAGATCTCAATTCATCTACACCAGTATATCAA
*
41927 ATAATTAACCTTTTTGTTAAAGCGATTTATGGATATATATATATATATATAATTTTTGGTGAAAG
562 ATAATTAACATTTTTGTTAAAGCGATTTATGG--ATATATATATATATATAATTTTTGGTGAAAG
41992 AGTATATATAAATTTTTTCATCTTA
625 AGTATATATAAATTTTTTCATCTTA
* *
42017 ATCAATGTAAGAATATTATATAATGTCTATATGGCATAGCCACATATTGGGATCAATTGACGCAC
1 ATCAATGTAAAAATATTATATAATGTCTATATGGCATAGCCACATATTGGGATCAATTGACCCAC
*
42082 TAAAATTTTATTATCTCCCTTGTAAATAAATAAATATAGATATATAGATATATAGATTATTTTGA
66 TAAAATTTTATCATCTCCCTTGT-AATAAAT-AATATA-ATATATAGA-ATATA-A-TATTTTGA
* *
42147 GCTAATATTATAAATTTACTGTATGATATAGAAAATTTGAAGATTTTGATCCATTAAAAATTCTA
125 GCTAATATTATAAATTTACTGTATAATATAGAAAATTTGAAGATTTTGATCCATTAAAAATTCAA
*
42212 TTTTACAATATTTACCCATTGAAATTAAGAATCGAGATATACCATAAAACAATTTGAAATGAATA
190 TTTTACAATATTTACCCACTGAAATTAAGAATCGAGATATACCATAAAACAATTTGAAATGAATA
* **
42277 TGTAATAAGGACTAATTTGGTATTACTATTGTAATTGAAAACTTGGTCTTACACAAACAAAACTT
255 TGTAATAACGACTAATTTGGTATTGTTATTGTAATTGAAAACTTGGTCTTACACAAACAAAACTT
* * *
42342 GTTTGAAACTATTTTTGAGT-GAAAAAAACATCATTTTTATCTCTCAACACCCAACTAACTAGAT
320 GTTTGAAACTATTTTTGAGTGGAAAAAAACAACATTTTTATCTCTCAACACCCAGCTAAATAGAT
* * * * *
42406 ATAGTTAACCCTAAACACCATGCTAAACGAGCTAAATAAATATAGTGATAGAAATTCACAGATGA
385 ATAGTTAACCCTAAATACCACGCTAAACGAGCTAAATAGATATAGTGGTAGAAATTCACAGACGA
* * *
42471 CTTGACCCCACT--------CCTGGTTATACTAATATGAGAACATGTAAGTAAT-A-AGAGTAGT
450 CTTGACCCCACTGAGGAAAGCCTGGCTACACTAATATGAGAACATGTACGTAATAAGAGAGTAGT
42526 CATGTTTTCATCTCATAGATCTCAATTCATCTA
515 CATGTTTTCATCTCATAGATCTCAATTCATCTA
42559 TATTAGAATT
Statistics
Matches: 1112, Mismatches: 47, Indels: 102
0.88 0.04 0.08
Matches are distributed among these distances:
643 128 0.12
644 1 0.00
645 40 0.04
646 1 0.00
647 32 0.03
648 8 0.01
650 4 0.00
652 3 0.00
653 2 0.00
655 1 0.00
656 1 0.00
657 193 0.17
658 84 0.08
662 98 0.09
663 62 0.06
664 18 0.02
665 78 0.07
666 201 0.18
667 14 0.01
669 4 0.00
671 8 0.01
673 2 0.00
674 1 0.00
676 1 0.00
678 1 0.00
679 108 0.10
680 18 0.02
ACGTcount: A:0.40, C:0.13, G:0.12, T:0.35
Consensus pattern (649 bp):
ATCAATGTAAAAATATTATATAATGTCTATATGGCATAGCCACATATTGGGATCAATTGACCCAC
TAAAATTTTATCATCTCCCTTGTAATAAATAATATAATATATAGAATATAATATTTTGAGCTAAT
ATTATAAATTTACTGTATAATATAGAAAATTTGAAGATTTTGATCCATTAAAAATTCAATTTTAC
AATATTTACCCACTGAAATTAAGAATCGAGATATACCATAAAACAATTTGAAATGAATATGTAAT
AACGACTAATTTGGTATTGTTATTGTAATTGAAAACTTGGTCTTACACAAACAAAACTTGTTTGA
AACTATTTTTGAGTGGAAAAAAACAACATTTTTATCTCTCAACACCCAGCTAAATAGATATAGTT
AACCCTAAATACCACGCTAAACGAGCTAAATAGATATAGTGGTAGAAATTCACAGACGACTTGAC
CCCACTGAGGAAAGCCTGGCTACACTAATATGAGAACATGTACGTAATAAGAGAGTAGTCATGTT
TTCATCTCATAGATCTCAATTCATCTACACCAGTATATCAAATAATTAACATTTTTGTTAAAGCG
ATTTATGGATATATATATATATATAATTTTTGGTGAAAGAGTATATATAAATTTTTTCATCTTA
Found at i:44546 original size:22 final size:22
Alignment explanation
Indices: 44398--44546 Score: 90
Period size: 22 Copynumber: 6.8 Consensus size: 22
44388 TTGATGACCT
44398 TATGAAA-TTTGATAACCTT-C
1 TATGAAATTTTGATAACCTTAC
* **
44418 TTATGAAATTTTAATAACGATAC
1 -TATGAAATTTTGATAACCTTAC
* * * * **
44441 TATAAAATTTCGAGAATCTTTT
1 TATGAAATTTTGATAACCTTAC
** *
44463 TAT-AAATTTATTTTAA-CTTTC
1 TATGAAATTT-TGATAACCTTAC
* *
44484 TTATGAAATTTTGTTAACCTTCC
1 -TATGAAATTTTGATAACCTTAC
* * *
44507 TAAGGAATTTTGAAAACCTTAC
1 TATGAAATTTTGATAACCTTAC
44529 TATGAAATTTTGATAACC
1 TATGAAATTTTGATAACC
44547 AACACTATGA
Statistics
Matches: 95, Mismatches: 27, Indels: 11
0.71 0.20 0.08
Matches are distributed among these distances:
21 17 0.18
22 67 0.71
23 11 0.12
ACGTcount: A:0.36, C:0.12, G:0.09, T:0.43
Consensus pattern (22 bp):
TATGAAATTTTGATAACCTTAC
Done.