Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021077.1 Corchorus olitorius cultivar O-4 contig21110, 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: 23046
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Found at i:11801 original size:22 final size:22
Alignment explanation
Indices: 11776--11819 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
11766 ATATAAAGCT
11776 GGCATCCTTCAGATATTGTTGC
1 GGCATCCTTCAGATATTGTTGC
11798 GGCATCCTTCAGATATTGTTGC
1 GGCATCCTTCAGATATTGTTGC
11820 TTTATGAATA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (22 bp):
GGCATCCTTCAGATATTGTTGC
Found at i:19349 original size:34 final size:34
Alignment explanation
Indices: 19306--19411 Score: 212
Period size: 34 Copynumber: 3.1 Consensus size: 34
19296 GATGCTTATA
19306 CAGTTATACTCCAATGACACAATTCTGAGTTACT
1 CAGTTATACTCCAATGACACAATTCTGAGTTACT
19340 CAGTTATACTCCAATGACACAATTCTGAGTTACT
1 CAGTTATACTCCAATGACACAATTCTGAGTTACT
19374 CAGTTATACTCCAATGACACAATTCTGAGTTACT
1 CAGTTATACTCCAATGACACAATTCTGAGTTACT
19408 CAGT
1 CAGT
19412 ATTGTTTTCT
Statistics
Matches: 72, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 72 1.00
ACGTcount: A:0.32, C:0.24, G:0.12, T:0.32
Consensus pattern (34 bp):
CAGTTATACTCCAATGACACAATTCTGAGTTACT
Found at i:21632 original size:658 final size:639
Alignment explanation
Indices: 20301--22127 Score: 1839
Period size: 658 Copynumber: 2.8 Consensus size: 639
20291 ATCTGAGCTT
* * * *
20301 TGTTTCGATTTAATTAGAAATTAATT--TAGAAAAATATGAAAAATGATATTAAAAGCGTGAAAA
1 TGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACGATATT-AAAGCGTGAAAA
** * * * * * * ** * * *
20364 GTTCTCCAATCTTTTTGACATTAAATTATATATATTTTACGAGTATTTTATCCAAAAATAGGGGA
65 GCCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTATGGCTAAAAATTGAGGA
* * * * **
20429 AAAATTTTTCGGGTCATTTTTTGCAAAGTTTTTAGCCAAAATCGTGTACTAACCATC-ACGGTTT
130 AATATTTTTC-GGTCATTTTTTGCAAA-ATTTTAGCCGAAATCGTGTAATAACCATCAACATTTT
* * * * * * * *
20493 TAGGCTTAAAACGCGTTTCGGGGCCCCAGCTCAGTTTTGCATGATTTTTGGTGGCGACACTTTTT
193 TTGGCTAAAAACGCGTTTC-GGGCCCCGGCTCAGTTTTGCATGATTTTTTGCGTCGAAACTTCTT
* * *
20558 GAAATATCTATACTCAACTTATAAAATCTTAGCCACATTGCATTTAAGGATTTGTTTTTACGAGC
257 GGAATATC-ATA-TC-A-TT-TAAAATCTCAGACACATTGCATTTAAGGATTTGTTTTTACGAGC
* * * *
20623 ATCTAAATCTTGTTTCGATTTACTAAG-AATTAATTCAGTTTGAAAAACGATAAGTGAAAAATGA
317 ATCTGAATCTTGTTTCGATTTAATCAGAAATTAA-T---TTAG-AAAA--AT-A-TGAAAAATGA
* * * *
20687 TATTAAAAGCGTGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATAT-TTTTATGAGTATTA
373 TATTAAAAGCGTGAAAAGTCCTCCAATCTTTTTGGAGTTGAATTATATATATTTTATGAGTATTT
* *
20751 T-GACTAAAAATTGAGGAACATATCTTTCGGGTCAATTTTTTTGCAAAATTTTAGCCGAAATCGT
438 TAGAC-AAAAATTGAGGAA-AAATCTTTCAGGTCAA--TTTTTGCAAAATTTTAGCCGAAATCGT
* **
20815 -GTAATAATCATCACGATTTTTGACTAAAACGCGTTCTAGGGAGCGGTTCAATTTTGAATGATTT
499 AGTAATAA-CATCACGATTTTTGACTAAAACGCGTTCTAGGGAGCGGTACAACGTTGAATGATTT
* * *
20879 TTGGCACTGAGACTCCTTGAAATATCTATATTCATCTAACCAAATCCCAACCATTGTTTTTACAA
563 TTGGCACCGAGACTCCTTGAAATATCTACATTCATCTAACCAAATCCCAACCATTGTTTTAACAA
*
20944 GCATTTGAATCA
628 GCATCTGAATCA
*
20956 TGTTTCGTTTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACGATATTGAAAGCGTGAAAA
1 TGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACGATATT-AAAGCGTGAAAA
* *
21021 GCCCTTCAATTTTTTTTTGGCATTGAATTATATATTTTTTATGAGTATTGTGGCTAAAAATTGA-
65 GCCCTTCAA--TCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTATGGCTAAAAATTGAG
* **
21085 GAGAATATTTTTCTGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTATTAACCATCAATTTT
128 GA-AATATTTTTC-GGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCAACATT
* * * *
21150 TTTTTGCTAAAAACGCGTTTC-GGTCCCGGCTCAGTATTGCATGATTTTTTGCGTCGAAACTTCC
191 TTTTGGCTAAAAACGCGTTTCGGGCCCCGGCTCAGTTTTGCATGATTTTTTGCGTCGAAACTTCT
* * *
21214 CGGAATATC-TAT-A-TT-AAATCTCAGTCATATTGCATTTAAGGATTTGTTTTTACGAGCATCT
256 TGGAATATCATATCATTTAAAATCTCAGACACATTGCATTTAAGGATTTGTTTTTACGAGCATCT
* * *
21275 GAATCTTGTTTCGATTTAATCAGAAATTAATTTAGAAAAATATGAAAAACGATATTAAAAGTGAG
321 GAATCTTGTTTCGATTTAATCAGAAATTAATTTAGAAAAATATGAAAAATGATATTAAAAGCGTG
* * *
21340 AAAAGTGCTCCAATCTTTTTGGAGTTGAATTATATATATTTTATAAGTATTTTAGACAAAAATTT
386 AAAAGTCCTCCAATCTTTTTGGAGTTGAATTATATATATTTTATGAGTATTTTAGACAAAAATTG
* * * * *
21405 AGGAAAAATATTCCTGGTCAATTTTTGCAAAATATTAGCCGAAATCGTACGTTAGTCGAA-ATCA
451 AGGAAAAATCTTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTA-G-TAAT--AACATCA
* * * * * * *
21469 CGGTTTTTGGCTGAAAATGCGTT-TCGGG-GCCTCGGTACAGCGTTGCAAT-ATTTTTTGCGCCG
512 CGATTTTTGACT-AAAACGCGTTCTAGGGAG---CGGTACAACGTTG-AATGATTTTTGGCACCG
**
21531 AGACTCCTTGAAATATCTACATTCATCTAACCAAATTTCAGCCACATTGGATTGAAGGATTTGTA
572 AGACTCCTTGAAATATCTACATTCATCTAACCAAA--TC--CCA-A--CCATT----G-TTT-T-
21596 AAACAAGCATCTGAATCA
623 -AACAAGCATCTGAATCA
* *
21614 TGTTTCGATTTAATTAGAAATTAATTCGGAAAATAATAGGAAAAACGATATTAGAAGCATGAAAA
1 TGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACGATATTA-AAGCGTGAAAA
* * *
21679 ACCCTTCAATCTTTTTGGCATTGAATTATATAATTTTTATGAGTATTATGGATAAAAATTGAGGA
65 GCCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTATGGCTAAAAATTGAGGA
** * * ** *
21744 AATAACTTTCGAGTCAATTTTTGCAAAATTCTAGCCGAAATCGTGTAATATTCATC-ACGATTGT
130 AATATTTTTCG-GTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCAAC-ATTTT
* *
21808 TTGGCTAAAAACGCGTTCCAGGGCCCCGGCTAAGTTTTGCATGA-TTTTTGACGTC-AAGAC-TC
193 TTGGCTAAAAACGCGTTTC-GGGCCCCGGCTCAGTTTTGCATGATTTTTTG-CGTCGAA-ACTTC
* * * *
21870 TTTGAGATATCCATAATCATTTAATCTAATCTCA-ACAACATTGGATTGAAGAATTTGTTTTTAC
255 TTGGA-ATAT-CAT-ATCATTTAA---AATCTCAGAC-ACATTGCATTTAAGGATTTGTTTTTAC
* * *
21934 GAGCATCCGAATCTTGTTTCGATTTAA-CTAGAAATTAATTCAGAAAAATATGAAAAATAATATT
313 GAGCATCTGAATCTTGTTTCGATTTAATC-AGAAATTAATTTAGAAAAATATGAAAAATGATATT
* *
21998 AAAAACGTGAAAAGTCCTCCAATCTTTTT-GACGTTAAATTATATATATATATATTTTATGAGTA
377 AAAAGCGTGAAAAGTCCTCCAATCTTTTTGGA-G-T---TGA-AT-TATATATATTTTATGAGTA
* *
22062 TTTTAGACAACAATTGATGGAAAAATCTTTCAGGTCAATTTTTGCAAACTTTTAGCCGAAATCGT
435 TTTTAGACAAAAATTGA-GGAAAAATCTTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCGT
22127 A
499 A
22128 TACTAACCAT
Statistics
Matches: 981, Mismatches: 129, Indels: 105
0.81 0.11 0.09
Matches are distributed among these distances:
638 26 0.03
640 67 0.07
641 47 0.05
642 14 0.01
643 55 0.06
644 7 0.01
645 5 0.01
647 3 0.00
648 65 0.07
649 7 0.01
650 4 0.00
652 1 0.00
654 2 0.00
655 32 0.03
656 117 0.12
657 94 0.10
658 141 0.14
659 88 0.09
660 1 0.00
661 2 0.00
662 1 0.00
663 2 0.00
664 1 0.00
666 4 0.00
667 114 0.12
668 1 0.00
671 2 0.00
672 2 0.00
673 33 0.03
674 43 0.04
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Consensus pattern (639 bp):
TGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGGAAAAACGATATTAAAGCGTGAAAAG
CCCTTCAATCTTTTTGGCATTGAATTATATATTTTTTATGAGTATTATGGCTAAAAATTGAGGAA
ATATTTTTCGGTCATTTTTTGCAAAATTTTAGCCGAAATCGTGTAATAACCATCAACATTTTTTG
GCTAAAAACGCGTTTCGGGCCCCGGCTCAGTTTTGCATGATTTTTTGCGTCGAAACTTCTTGGAA
TATCATATCATTTAAAATCTCAGACACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATC
TTGTTTCGATTTAATCAGAAATTAATTTAGAAAAATATGAAAAATGATATTAAAAGCGTGAAAAG
TCCTCCAATCTTTTTGGAGTTGAATTATATATATTTTATGAGTATTTTAGACAAAAATTGAGGAA
AAATCTTTCAGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTAGTAATAACATCACGATTTTTG
ACTAAAACGCGTTCTAGGGAGCGGTACAACGTTGAATGATTTTTGGCACCGAGACTCCTTGAAAT
ATCTACATTCATCTAACCAAATCCCAACCATTGTTTTAACAAGCATCTGAATCA
Done.