Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021141.1 Corchorus olitorius cultivar O-4 contig21174, 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: 71608
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:4241 original size:29 final size:29
Alignment explanation
Indices: 4189--4244 Score: 78
Period size: 29 Copynumber: 1.9 Consensus size: 29
4179 ACTTTGCCAT
*
4189 AAATCTCAAATAAGGGCACGAACTTTTAA
1 AAATCTCAAATAAGGGCACCAACTTTTAA
*
4218 AAATGTCAAATAAGGGTC-CCAACTTTT
1 AAATCTCAAATAAGGG-CACCAACTTTT
4245 CGGGAAGACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 23 0.96
30 1 0.04
ACGTcount: A:0.41, C:0.18, G:0.14, T:0.27
Consensus pattern (29 bp):
AAATCTCAAATAAGGGCACCAACTTTTAA
Found at i:10235 original size:652 final size:646
Alignment explanation
Indices: 8137--11702 Score: 2848
Period size: 652 Copynumber: 5.4 Consensus size: 646
8127 CCCGAAATTT
* ** * * * *
8137 TTTTCCTCACTTTTTGGAAAAAATACTCATAAA-ATATATATAATACAATGCCAAAAAGATTAGA
1 TTTTCCTCAATTTTTGG-CTAAATACTCA-AAAGATATATATAATTCAACG-CAAAAAAATTGGA
*
8201 GGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAAATAAATCGAA
63 GGACTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTCTGAATTAATTTCTAATTAAATCGAA
* *
8266 ACAAGATTCAGATGCACAT-AAAACAAATCCTTAAA-TCTAATGTGGCTGAGATTTGATTAGATG
127 ACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTC-AATGTGGCTGAGATTTGATTAGATG
* * *
8329 AATAAAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACAGAGCC-GTGACCCTGAAA
191 AATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGCCAG-GGCCC-GAAA
* * * * * *
8393 CGCATTTTTAGCCAAAAACCG--T-GATG-GTTAGTAC-AAAATTACAGTTA-AAAAATTGACTC
254 CGCGTTTTTAGCCAAAAACCGTTTACACGATTTCG-ACTAAAATT----TTACAAAAAATGACTC
* * * * *** *
8452 GAAAGATATTTCCTCAAATTTTGGCTAAAATACTCATAAAAAATATATAATTCAACATTAAAAAA
314 AAAAAAT-TTTCCTCAATTTTTAGCTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAG
* ** * * *
8517 ATTGAAGGGTTTTTAACGCTTCTAATATTGTTTTTCCTTTTTTTCCGAATTAATTTCTAATTAAA
378 ATTGGAGGACTTTTCACGCTTCTAATATCGTTTTTCATTTTTTTCCGAATTAATTTCTAATTAAA
* * * *
8582 TAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATTTGGCTG-GAATTTGGTT
443 TCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATATGGCTGAG-ATTTGATT
* *
8646 AGATGAATATAGATATTTCAA-GACGTCTTGGCACCAAAAATCATGCAAAATTGAACCA--GGCT
507 AGATGAATATAGATA-CTCAAGGA-GTCTTGGCACCAAAAATCATGCAAAACT-AACCAGGGGC-
*
8708 CCGGAACGTGTTTTTAGCCGAAAAGTGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATT
568 CCGGAACGCGTTTTTAGCC----A---AAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATT
* *
8773 TTGAAAAAATTGACCCGAAAGAT
626 TTGTAAAAATTGACCC-AAA-AA
* * * * * * *
8796 TTTTCCTCGATTTCTAGCAAAAATACTCATAAAGA-ATATATAATTCAATGCCAAGAAAATTGAA
1 TTTTCCTCAATTTTTGGC-TAAATACTCA-AAAGATATATATAATTCAACG-CAAAAAAATTGGA
* * * * * ** * *
8860 AGCCTTTTTCACGCTTATAA-ATCGTTTTCCTATTTTATTTCCAAATTATTTTCTGATTAAATCG
63 GGAC-TTTTCACGCTTTTAATATCGTTTTTC-ATATT-TTTCTGAATTAATTTCTAATTAAATCG
* * ** * * * *
8924 AAACAAGATTTAAAAACTCTTAAAAACAAATCCTTGAATACAATGTGGCTAAGATTT-AGTTAGA
125 AAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGGCTGAGATTTGA-TTAGA
* * * *
8988 TGAATATAGATATATTTTAAGGAGTCTTGCCGCCAAAAATCATGCAAAACTGA-CTCAGGGCCCA
189 TGAATATAG--ATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGC-CAGGGCCCG
* * * * *
9052 AGAATGTGTTTTTAGCCAAAAAAAAACCATGATGATACACGATTTCGTCTAAAATTTTGCAAAAA
251 A-AACGCGTTTTTAGCC----AAAAACC--G-T-TTACACGATTTCGACTAAAATTTTACAAAAA
* * * * * * *
9117 TTGAC-CATAAATATTTTTCTCAATTTTTAGCCACAATACTCATAAAAAAAATATAATTCAATGC
307 ATGACTCA-AAAAATTTTCCTCAATTTTTAGCTAAAATACTCATAAAAAATATATAATTCAACGC
* * * * *
9181 CAAAAAGATTGAAAGG-CTTCTCACGCTTCTAATATCGTTTTTCCTTTTATTTTTCAAATTAATT
371 CAAAAAGATTG-GAGGACTTTTCACGCTTCTAATATCGTTTTT-CATTT-TTTTCCGAATTAATT
* * * * *
9245 TTTAATTAAATCGAAACATGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAA
433 TCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATATGGCTGA
* * ** * * * *
9310 GATTTGTTTAGATGAATATAGATATTTCAAATAGTTTTGCCACCAAAAATCATACAAAACTGACC
498 GATTTGATTAGATGAATATAGATA-CTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTAACC
* * * * *
9375 CGGGGCCCCGGAACGTGTTTTTAGCTAAAAAACCGTGATGG-TA-T--ACGATTTTGACTAAAAT
562 AGGGG-CCCGGAACGCGTTTTTAGC-CAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAT
* * *
9436 TTTGTAAAAATTGATCCGAGATAT
625 TTTGTAAAAATTGA-CCCA-AAAA
** * * * *
9460 TTTTGTTCAATTTTTAGCCACAATACAT-ATAAA-ATATCA-ATAATTCAATGC--CAAAATTGG
1 TTTTCCTCAATTTTTGGCTA-AATAC-TCA-AAAGATAT-ATATAATTCAACGCAAAAAAATTGG
*
9520 AGGACTTTTC-CTGCTTTTAATATCGTTTTTCATATTTCTCTGAATTAAATTT-TAATTAAATCG
62 AGGACTTTTCAC-GCTTTTAATATCGTTTTTCATATTTTTCTGAATT-AATTTCTAATTAAATCG
* * * * *
9583 AAACAAGATTCAGATACTCGTAAAAACAAATACTT-AATTAAATGTGG-TAGAAATTTTATTAGA
125 AAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGGCT-GAGATTTGATTAGA
* * * *
9646 TGAATATAGATATTTCATGGATTCTCGGCGCCAAAAATCAAGCAAAACTAAGCCAGGGTCCCGAA
189 TGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGCCAGGG-CCCGAA
* *
9711 ACACGTTTTTAGCCAAAAACCG-TTACACGATTTCGGCTAAAATTTTACAAAAAATGACTCAAAA
253 ACGCGTTTTTAGCCAAAAACCGTTTACACGATTTCGACTAAAATTTTACAAAAAATGACTCAAAA
* * * * * * * *
9775 AATTTTCCCGTAAATTTTTGGCTAAAATAGTCATAAAATACATATAATTTAACGTCAAAACGATT
318 AATTTT-CC-TCAATTTTTAGCTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATT
* * *
9840 GGAGAACTTTTCACGCTTTCT-ATATCGTTTTTCATATTTTTT-GGAATTAAATTTCTAATTCAA
381 GGAGGACTTTTCACGC-TTCTAATATCGTTTTTCAT-TTTTTTCCGAATT-AATTTCTAATTAAA
* ** *
9903 TCGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTTAATATGGCTGATATTTGATTA
443 TCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATATGGCTGAGATTTGATTA
* * * * ** ** **
9968 GACGAATATCGATACT-ATGGAGTATTGGTGCCAAAAATCATGCAAAACTAAGGAGGGGCCCAAA
508 GATGAATATAGATACTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTAACCAGGGGCCCGGA
* ** * * * *
10032 ATGCCATTTTAACCAAAAACCGTGATGGTTAGTACACGATTTCGACTAAAATTTTGCAAAAAATG
573 ACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAATTG
10097 ACCCAATAAA
638 ACCCAA-AAA
* * *
10107 TTTTCCGTC-ACTTTTGGCTAAATACTCAAAATATATATATAATTTAACGTCAAAAAAAGATTGG
1 TTTTCC-TCAATTTTTGGCTAAATACTCAAAAGATATATATAATTCAACG-C-AAAAAA-ATTGG
*
10171 AGTACTTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGA
62 AGGAC-TTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGA
** * * * *
10236 AACAAGATTCAGATGCTCGTAAAAACAAATTATTAAATCCAATGTAGCTAAGATTTGATTAGATA
126 AACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGGCTGAGATTTGATTAGATG
* * * * * * * * * * * *
10301 AATATGGATATCTCAAAGAGACTTGACGCCAAAAATCATGCGAAACTTAGTCGGGGCCCCGGAAT
191 AATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGCCAGGG-CCCGAAAC
* * ** * *
10366 GCGTTTTTAGTCAAAAACTGTGATGATTATTACACGATTTCGGTTAGAATTTTGC-AAAAATCGA
255 GCGTTTTTAGCCAAAAAC-----CG--T-TTACACGATTTCGACTAAAATTTTACAAAAAAT-GA
** * * * * * * *
10430 CTCAAAAGTTATTTACTCAATTTTTATCCACAATACTCATAAAAAATATATGATTCAATGCAAAA
311 CTCAAAAAAT-TTTCCTCAATTTTTAGCTAAAATACTCATAAAAAATATATAATTCAACGCCAAA
* * * * *
10495 AAGATTGAAGGGCTTTTCATGCTTCTAATATCGTTTTTCCTATTATTTTCCGAATTAATTTTTAA
375 AAGATTGGAGGACTTTTCACGCTTCTAATATCGTTTTT-C-ATTTTTTTCCGAATTAATTTCTAA
* * *** *
10560 TTAAATCGAAACATGATTCAGATGCTTGT-TTTACAAATCCTTAAATCCAATATGGTTGAGATTT
438 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATATGGCTGAGATTT
* * ** * * ** *
10624 GGTTATATGAATATAGAATTTTCAAGAAGTCTCT-GCGACAAAAAAAAATGCAACACTGAACC-G
503 GATTAGATGAATATAG-ATACTCAAGGAGTCT-TGGC-ACCAAAAATCATGCAAAACT-AACCAG
* * * * *
10687 GGGTCCTGGAAC-CTTTTTTTAGCCAAAAACCGTGACTTCGACTAACGTACACGATTAT-GGTTA
564 GGG-CCCGGAACGC-GTTTTTAGCCAAAAACCGTGA--T-G-GTTA-GTACACGATT-TCGGCTA
* *
10750 ATATTTTGTAAAAATTGA-CCAGAGATAC
621 AAATTTTGTAAAAATTGACCCA-A-A-AA
** * * * * *
10778 TTTTCCTCGGTTTTTGTCTAAAATACTCATAACATATATATACTTCAACTCCAAAAAAATTGGAG
1 TTTTCCTCAATTTTTGGCT-AAATACTCAAAAGATATATATAATTCAAC-GCAAAAAAATTGGAG
*
10843 GACTTTTCACGCTTTTAAAATCGTTTTTCATA-TTTTCTGAATTAATTTCTAATTAAATCGAAAC
64 GACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAAC
* * * *
10907 AAGATTTAGATGCTCGTAAAAGCAAATGCTTAAATGCAATGTGGCTGAGATTTGATTAGATGAAT
129 AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAAT
* * * * *
10972 ATAGATATTTCAAGGAGACTCGACGCCAAAAATCATGCAAAACTGAGCCCGGGCCTCAAAAGGCG
194 ATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGCCAGGGCC-CGAAACGCG
* * ** *
11037 TTTTTAG-CAAAAATCGTGATGGTTTGTACACGATATCGACTAAAATTTTTTAAAAAATGACCTG
258 TTTTTAGCCAAAAA-C-----CG-TT-TACACGATTTCGACTAAAATTTTACAAAAAATGA-CTC
* * *
11101 AAAAATTTTTCCTCAATTTTTAGCTAAAATACTC-T------T-GA-AA-T----GCCCAAAAGA
314 AAAAAATTTTCCTCAATTTTTAGCTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGA
* * * * *
11152 TTAGAGGACTTTTCACGTTTTTCATATCGTTTTTTCATTTTTTTCTGAATTAATTTCTAATTAAA
379 TTGGAGGACTTTTCACGCTTCTAATATCG-TTTTTCATTTTTTTCCGAATTAATTTCTAATTAAA
* * * ** *
11217 TCGAAA-AAGGATTCAGATTCTCATAAAAACAAATCCTTAAATGCAATGCGACTGAGATTTGATT
443 TCGAAACAA-GATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATATGGCTGAGATTTGATT
* * * ** * * * * *
11281 AGATGAATACAAATATCTCAAGGAGTCTTAGCGGCAAAAGTAATGCAAAACTGACCCGGGGTCCT
507 AGATGAATATAGATA-CTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTAACCAGGGG-CCC
* * * * * * * *
11346 GTAATGCGTTTTTATTCAAAAAACCGTGATGATTATTAAATGATTTCGGCTAAAATTTTGTAAAA
570 GGAACGCGTTTTTA-GCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGTAAAA
* ** *
11411 TTTGACCTGGAAGA
634 ATTGACC-CAAAAA
*
11425 TATTTCCTCAAGTTTTGGCTAAAATACTCATAAAAGATATATATAATTCAACGCAAAAAATATTG
1 T-TTTCCTCAATTTTTGGCT-AAATACTC--AAAAGATATATATAATTCAACGCAAAAAA-ATTG
* * * * * * *
11490 AAGGATTTTTTACGCTTCTAATATCGTTTTTCCTACTTTTT-TCGAATTAATTTATAACTAAATC
61 GAGGACTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTTCT-GAATTAATTTCTAATTAAATC
* * *
11554 GAAACAAGATTTAGATGCTCATAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGA
124 GAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGGCTGAGATTTGATTAGA
* * * * * *
11619 TGAATATAGATATTTTAAGGAGTATTGGCGCCAAAAATCATGCAAAACTGACCCGGGGTCCCGGA
189 TGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGCCAGGG-CCCGAA
* *
11684 ACGTGTTTTTAGCAAAAAA
253 ACGCGTTTTTAGCCAAAAA
11703 ATAAAAACGT
Statistics
Matches: 2341, Mismatches: 432, Indels: 274
0.77 0.14 0.09
Matches are distributed among these distances:
644 14 0.01
645 19 0.01
646 51 0.02
647 64 0.03
648 172 0.07
649 78 0.03
650 60 0.03
651 20 0.01
652 313 0.13
653 189 0.08
654 6 0.00
656 52 0.02
657 7 0.00
658 31 0.01
659 114 0.05
660 80 0.03
661 172 0.07
662 79 0.03
663 75 0.03
664 90 0.04
665 29 0.01
666 3 0.00
667 64 0.03
668 177 0.08
669 34 0.01
670 41 0.02
671 97 0.04
672 52 0.02
673 123 0.05
674 25 0.01
675 10 0.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (646 bp):
TTTTCCTCAATTTTTGGCTAAATACTCAAAAGATATATATAATTCAACGCAAAAAAATTGGAGGA
CTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATCGAAACAA
GATTCAGATGCTCGTAAAAACAAATCCTTAAATTCAATGTGGCTGAGATTTGATTAGATGAATAT
AGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGCCAGGGCCCGAAACGCGTTT
TTAGCCAAAAACCGTTTACACGATTTCGACTAAAATTTTACAAAAAATGACTCAAAAAATTTTCC
TCAATTTTTAGCTAAAATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGGAGGACTTT
TCACGCTTCTAATATCGTTTTTCATTTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATT
CAGATGCTCGTAAAAACAAATCCTTAAATCCAATATGGCTGAGATTTGATTAGATGAATATAGAT
ACTCAAGGAGTCTTGGCACCAAAAATCATGCAAAACTAACCAGGGGCCCGGAACGCGTTTTTAGC
CAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAATTGACCCAAAAA
Found at i:11043 original size:335 final size:330
Alignment explanation
Indices: 8137--11675 Score: 2633
Period size: 335 Copynumber: 10.8 Consensus size: 330
8127 CCCGAAATTT
* ** * *
8137 TTTTCCTCACTTTTTGGAAAAAATACTCATAAAATATATATAATACAA-TGCC-AAAAAGATTAG
1 TTTTCCTCAATTTTTGGCTAAAATACTCATAAAATATATATAATTCAACT-CCAAAAAAGATTGG
*
8200 AGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTTTCTGAATTAATTTCTAAATAAATCGA
65 AGGACTTTTCACGCTTTTAATATCGTTTTTCATA--TTTTCTGAATTAATTTCTAATTAAATCGA
* * *
8265 AACAAGATTCAGATGCACAT-AAAACAAATCCTTAAATCTAATGTGGCTGAGATTTGATTAGATG
128 AACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATG
* * * * * * *
8329 AATAAAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACAGAG-CCGTGACC-CTGAA
193 AATATAGATATCTCAAGGAGACTTGACGCCAAAAATCATGCAAAACTGAGCCCG-GGCCTC-GAA
* * * ** * * * ** * *
8392 ACGCATTTTTAGCCAAAAACCGTGATGGTTAGTACAAAATTACAGTTAAAAAATTG----ACTCG
256 ATGCGTTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGTAAAAATTG
8453 A--A-AGATA
321 ACCAGAGATA
* * * *
8460 -TTTCCTCAAATTTTGGCTAAAATACTCATAAAAAATATATAATTCAACAT-TAAAAAA-ATTGA
1 TTTTCCTCAATTTTTGGCTAAAATACTCATAAAATATATATAATTCAAC-TCCAAAAAAGATTGG
** * * * * * * *
8522 AGGGTTTTTAACGCTTCTAATATTGTTTTTCCTTTTTTTCCGAATTAATTTCTAATTAAATAGAA
65 AGGACTTTTCACGCTTTTAATATCGTTTTT-CATATTTTCTGAATTAATTTCTAATTAAATCGAA
* * *
8587 ACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCTAATTTGGCTG-GAATTTGGTTAGATG
129 ACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAG-ATTTGATTAGATG
* * * * * * * *
8651 AATATAGATATTTCAA-GACGTCTTGGCACCAAAAATCATGCAAAATTGA-ACCAGG-CTCCGGA
193 AATATAGATATCTCAAGGA-GACTTGACGCCAAAAATCATGCAAAACTGAGCCCGGGCCT-CGAA
* * * *
8713 ACGTGTTTTTAGCCGAAAAGTGAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGAA
256 ATGCGTTTTTAGCC----A---AAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGTA
*
8778 AAAATTGACCCGAAAGAT-
314 AAAATTGA-CC-AGAGATA
* * * * *
8796 TTTTCCTCGATTTCTAGCAAAAATACTCATAAAGA-ATATATAATTCAA-TGCCAAGAAA-ATTG
1 TTTTCCTCAATTTTTGGCTAAAATACTCATAAA-ATATATATAATTCAACT-CCAAAAAAGATTG
* * * * * * ** * *
8858 AAAGCCTTTTTCACGCTTATAA-ATCGTTTTCCTATTTTATTTCCAAATTATTTTCTGATTAAAT
64 GAGGAC-TTTTCACGCTTTTAATATCGTTTTTC-A-TAT-TTTCTGAATTAATTTCTAATTAAAT
* * ** * * * *
8922 CGAAACAAGATTTAAAAACTCTTAAAAACAAATCCTTGAATACAATGTGGCTAAGATTT-AGTTA
125 CGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGA-TTA
* * * * *
8986 GATGAATATAGATATATTTTAAGGAGTCTTGCCGCCAAAAATCATGCAAAACTGA-CTCAGGGCC
189 GATGAATATAG--ATATCTCAAGGAGACTTGACGCCAAAAATCATGCAAAACTGAGC-CCGGGCC
* * ***** * * *
9050 -CAAGAATGTGTTTTTAGCCAAAAAAAAACCATGATGA-TACACGATTTCGTCTAAAATTTTGCA
251 TCGA-AATGCGTTTTTAGCC-AAAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGTA
* *
9113 AAAATTGACCATAAATA
314 AAAATTGACCAGAGATA
* * * * * *
9130 TTTTTCTCAATTTTTAGCCACAATACTCATAAAAAAAATATAATTCAA-TGCC-AAAAAGATTGA
1 TTTTCCTCAATTTTTGGCTAAAATACTCATAAAATATATATAATTCAACT-CCAAAAAAGATTG-
* * * * * *
9193 AAGG-CTTCTCACGCTTCTAATATCGTTTTTCCTTTTATTTT-TCAAATTAATTTTTAATTAAAT
64 GAGGACTTTTCACGCTTTTAATATCGTTTTT-C--ATATTTTCT-GAATTAATTTCTAATTAAAT
* * * *
9256 CGAAACATGATTCAAATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGTTTAG
125 CGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAG
* ** ** * * * *
9321 ATGAATATAGATATTTCAAATAGTTTTGCCACCAAAAATCATACAAAACTGA-CCCGGGGCCCCG
190 ATGAATATAGATATCTCAAGGAGACTTGACGCCAAAAATCATGCAAAACTGAGCCC-GGGCCTCG
* * * * * * *
9385 GAACGTGTTTTTAGCTAAAAAACCGTGATG----GTATACGATTTTGACTAAAATTTTGTAAAAA
254 AAATGCGTTTTTAGC-CAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGTAAAAA
9446 TTGATCC-GAGATA
318 TTGA-CCAGAGATA
** * * *
9459 TTTTTGTTCAATTTTTAGCCACAATACAT-ATAAAATATCA-ATAATTCAA-TGCC---AAA-AT
1 -TTTTCCTCAATTTTTGGCTAAAATAC-TCATAAAATAT-ATATAATTCAACT-CCAAAAAAGAT
9517 TGGAGGACTTTTC-CTGCTTTTAATATCGTTTTTCATATTTCTCTGAATTAAATTT-TAATTAAA
62 TGGAGGACTTTTCAC-GCTTTTAATATCGTTTTTCATATTT-TCTGAATT-AATTTCTAATTAAA
* * ** * *
9580 TCGAAACAAGATTCAGATACTCGTAAAAACAAATACTT-AATTAAATGTGG-TAGAAATTTTATT
124 TCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCT-GAGATTTGATT
* * ** * * * * *
9643 AGATGAATATAGATATTTCATGGATTCTCGGCGCCAAAAATCAAGCAAAACTAAGCCAGGGTCC-
188 AGATGAATATAGATATCTCAAGGAGACTTGACGCCAAAAATCATGCAAAACTGAGCCCGGG-CCT
** **
9707 CGAAACACGTTTTTAGCCAAAAACC-----G--T--TACACGATTTCGGCTAAAATTTTACAAAA
252 CGAAATGCGTTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGTAAAA
* * *
9763 AATGACTCA-AAAAA
317 ATTGAC-CAGAGATA
* * * * *
9777 TTTTCCCGTAAATTTTTGGCTAAAATAGTCATAAAATACATATAATTTAACGT-C-AAAACGATT
1 TTTT-CC-TCAATTTTTGGCTAAAATACTCATAAAATATATATAATTCAAC-TCCAAAAAAGATT
* * *
9840 GGAGAACTTTTCACGCTTTCT-ATATCGTTTTTCATATTTTTTGGAATTAAATTTCTAATTCAAT
63 GGAGGACTTTTCACGCTTT-TAATATCGTTTTTCATATTTTCT-GAATT-AATTTCTAATTAAAT
* ** * *
9904 CGAAATAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATTTAATATGGCTGATATTTGATTAG
125 CGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAG
* * * ** * *** *
9969 ACGAATATCGATA-CT-ATGGAGTA-TTGGTGCCAAAAATCATGCAAAACTAAGGAGGGGCC-CA
190 ATGAATATAGATATCTCAAGGAG-ACTTGACGCCAAAAATCATGCAAAACTGAGCCCGGGCCTCG
** * * * * *
10030 AAATGCCATTTTAACCAAAAACCGTGATGGTTAGTACACGATTTCGACTAAAATTTTGCAAAAAA
254 AAATGCGTTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGTAAAAAT
* *
10095 TGACCCA-ATAAA
319 TGA-CCAGAGATA
* * *
10107 TTTTCCGTC-ACTTTTGGCT-AAATACTCA-AAATATATATATAATTTAACGTCAAAAAAAGATT
1 TTTTCC-TCAATTTTTGGCTAAAATACTCATAAA-ATATATATAATTCAAC-TCCAAAAAAGATT
*
10169 GGAGTACTTTTTCACGCTTTTAATATCGTTTTTCATATTTTTCTGAATTAATTTCTAATTAAATC
63 GGAGGAC-TTTTCACGCTTTTAATATCGTTTTTCATA-TTTTCTGAATTAATTTCTAATTAAATC
** * *
10234 GAAACAAGATTCAGATGCTCGTAAAAACAAATTATTAAATCCAATGTAGCTAAGATTTGATTAGA
126 GAAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGA
* * * * * * * * *
10299 TAAATATGGATATCTCAAAGAGACTTGACGCCAAAAATCATGCGAAACTTAGTCGGGGCCCCGGA
191 TGAATATAGATATCTCAAGGAGACTTGACGCCAAAAATCATGCAAAACTGAGCCCGGGCCTCGAA
* * * * * * *
10364 ATGCGTTTTTAGTCAAAAACTGTGATGATTATTACACGATTTCGGTTAGAATTTTGCAAAAATCG
256 ATGCGTTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGTAAAAATTG
* *
10429 ACTCAAAAGTTA
321 AC-C-AGAGATA
* ** * * * * * *
10441 -TTTACTCAATTTTTATCCACAATACTCATAAAAAATATATGATTCAA-TGCAAAAAAGATTGAA
1 TTTTCCTCAATTTTTGGCTAAAATACTCATAAAATATATATAATTCAACTCCAAAAAAGATTGGA
* * * * *
10504 GGGCTTTTCATGCTTCTAATATCGTTTTTCCTATTATTTTCCGAATTAATTTTTAATTAAATCGA
66 GGACTTTTCACGCTTTTAATATCGTTTTT-C-A-TATTTTCTGAATTAATTTCTAATTAAATCGA
* * *** * * * *
10569 AACATGATTCAGATGCTTGT-TTTACAAATCCTTAAATCCAATATGGTTGAGATTTGGTTATATG
128 AACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATG
* * * * ** * * *
10633 AATATAGA-ATTTTCAAGAAGTCTCTG-CGACAAAAAAAAATGCAACACTGAACCGGGGTCCT-G
193 AATATAGATA-TCTCAAGGAGACT-TGACG-CCAAAAATCATGCAAAACTGAGCCCGGG-CCTCG
* * * * * *
10695 GAA-CCTTTTTTTAGCCAAAAACCGTGACTTCGACTAACGTACACGATTAT-GGTTAATATTTTG
254 AAATGC-GTTTTTAGCCAAAAACCGTGA--T-GA-TTA-GTACACGATT-TCGGCTAAAATTTTG
10758 TAAAAATTGACCAGAGATA
312 TAAAAATTGACCAGAGATA
** * * *
10777 CTTTTCCTCGGTTTTTGTCTAAAATACTCATAACATATATATACTTCAACTCCAAAAAA-ATTGG
1 -TTTTCCTCAATTTTTGGCTAAAATACTCATAAAATATATATAATTCAACTCCAAAAAAGATTGG
*
10841 AGGACTTTTCACGCTTTTAAAATCGTTTTTCATATTTTCTGAATTAATTTCTAATTAAATCGAAA
65 AGGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTCTGAATTAATTTCTAATTAAATCGAAA
* * * *
10906 CAAGATTTAGATGCTCGTAAAAGCAAATGCTTAAATGCAATGTGGCTGAGATTTGATTAGATGAA
130 CAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAA
* * * *
10971 TATAGATATTTCAAGGAGACTCGACGCCAAAAATCATGCAAAACTGAGCCCGGGCCTCAAAAGGC
195 TATAGATATCTCAAGGAGACTTGACGCCAAAAATCATGCAAAACTGAGCCCGGGCCTCGAAATGC
* * * * * * * *
11036 GTTTTTAG-CAAAAATCGTGATGGTTTGTACACGATATCGACTAAAATTTTTTAAAAAATGACCT
260 GTTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGTAAAAATTGACCA
* *
11100 GAAAAA
325 GAGATA
* * * *
11106 TTTTTCCTCAATTTTTAGCTAAAATACTC------T-T-GA-AA-T--GC-CC--AAAAGATTAG
1 -TTTTCCTCAATTTTTGGCTAAAATACTCATAAAATATATATAATTCAACTCCAAAAAAGATTGG
* * *
11156 AGGACTTTTCACGTTTTTCATATCGTTTTTTCATTTTTTTCTGAATTAATTTCTAATTAAATCGA
65 AGGACTTTTCACGCTTTTAATATCG-TTTTTCA-TATTTTCTGAATTAATTTCTAATTAAATCGA
* * * * *
11221 AA-AAGGATTCAGATTCTCATAAAAACAAATCCTTAAATGCAATGCGACTGAGATTTGATTAGAT
128 AACAA-GATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGAT
* * * * * *
11285 GAATACAAATATCTCAAGGAGTCTT-AGCGGCAAAAGTAATGCAAAACTGA-CCCGGGGTCCT-G
192 GAATATAGATATCTCAAGGAGACTTGA-CGCCAAAAATCATGCAAAACTGAGCCC-GGG-CCTCG
* * * * * * *
11347 TAATGCGTTTTTATTCAAAAAACCGTGATGATTATTAAATGATTTCGGCTAAAATTTTGTAAAAT
254 AAATGCGTTTTTA-GCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGTAAAAA
*
11412 TTGACCTGGAAGATA
318 TTGACC-AG-AGATA
* * *
11427 -TTTCCTCAAGTTTTGGCTAAAATACTCATAAAAGATATATATAATTCAAC-GCAAAAAATATTG
1 TTTTCCTCAATTTTTGGCTAAAATACTCAT-AAA-ATATATATAATTCAACTCCAAAAAAGATTG
* * * * * * * *
11490 AAGGATTTTTTACGCTTCTAATATCGTTTTTCCTACTTTTTTCGAATTAATTTATAACTAAATCG
64 GAGGACTTTTCACGCTTTTAATATCGTTTTTCATA-TTTTCT-GAATTAATTTCTAATTAAATCG
* *
11555 AAACAAGATTTAGATGCTCATAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGAT
127 AAACAAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGAT
* * *
11620 GAATATAGATATTTTAAGGAGTA-TTGGCGCCAAAAATCATGCAAAACTGA-CCCGGG
192 GAATATAGATATCTCAAGGAG-ACTTGACGCCAAAAATCATGCAAAACTGAGCCCGGG
11676 GTCCCGGAAC
Statistics
Matches: 2586, Mismatches: 463, Indels: 323
0.77 0.14 0.10
Matches are distributed among these distances:
314 4 0.00
315 26 0.01
316 15 0.01
317 144 0.06
318 38 0.01
319 101 0.04
320 3 0.00
321 92 0.04
322 235 0.09
323 61 0.02
324 115 0.04
325 53 0.02
326 15 0.01
327 52 0.02
328 49 0.02
329 191 0.07
330 126 0.05
331 70 0.03
332 194 0.08
333 127 0.05
334 199 0.08
335 267 0.10
336 78 0.03
337 68 0.03
338 113 0.04
339 93 0.04
340 1 0.00
341 36 0.01
342 19 0.01
343 1 0.00
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.33
Consensus pattern (330 bp):
TTTTCCTCAATTTTTGGCTAAAATACTCATAAAATATATATAATTCAACTCCAAAAAAGATTGGA
GGACTTTTCACGCTTTTAATATCGTTTTTCATATTTTCTGAATTAATTTCTAATTAAATCGAAAC
AAGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAAT
ATAGATATCTCAAGGAGACTTGACGCCAAAAATCATGCAAAACTGAGCCCGGGCCTCGAAATGCG
TTTTTAGCCAAAAACCGTGATGATTAGTACACGATTTCGGCTAAAATTTTGTAAAAATTGACCAG
AGATA
Found at i:34582 original size:82 final size:82
Alignment explanation
Indices: 34486--34652 Score: 334
Period size: 82 Copynumber: 2.0 Consensus size: 82
34476 TGAAGACTTT
34486 CTTGCTTTTCGTTTCCCATTTATTTATTTTAGAAAGACGAAAGCCTCCAATCACTCACCAGCAAA
1 CTTGCTTTTCGTTTCCCATTTATTTATTTTAGAAAGACGAAAGCCTCCAATCACTCACCAGCAAA
34551 ATATCTGTTTCTTTTGG
66 ATATCTGTTTCTTTTGG
34568 CTTGCTTTTCGTTTCCCATTTATTTATTTTAGAAAGACGAAAGCCTCCAATCACTCACCAGCAAA
1 CTTGCTTTTCGTTTCCCATTTATTTATTTTAGAAAGACGAAAGCCTCCAATCACTCACCAGCAAA
34633 ATATCTGTTTCTTTTGG
66 ATATCTGTTTCTTTTGG
34650 CTT
1 CTT
34653 AAAATCTGTC
Statistics
Matches: 85, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
82 85 1.00
ACGTcount: A:0.25, C:0.23, G:0.12, T:0.40
Consensus pattern (82 bp):
CTTGCTTTTCGTTTCCCATTTATTTATTTTAGAAAGACGAAAGCCTCCAATCACTCACCAGCAAA
ATATCTGTTTCTTTTGG
Found at i:44594 original size:17 final size:17
Alignment explanation
Indices: 44572--44618 Score: 58
Period size: 17 Copynumber: 2.8 Consensus size: 17
44562 AAGATTTGAG
44572 AAACATTACTAGTAATA
1 AAACATTACTAGTAATA
* **
44589 AAACATGACTAGTTCTA
1 AAACATTACTAGTAATA
*
44606 AACCATTACTAGT
1 AAACATTACTAGT
44619 CATGTGATAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.45, C:0.17, G:0.09, T:0.30
Consensus pattern (17 bp):
AAACATTACTAGTAATA
Found at i:45979 original size:15 final size:15
Alignment explanation
Indices: 45959--45991 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
45949 GGTTGTGTCC
45959 TATCAGTGGTTTATA
1 TATCAGTGGTTTATA
45974 TATCAGTGGTTTATA
1 TATCAGTGGTTTATA
45989 TAT
1 TAT
45992 ACTTCCTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.06, G:0.18, T:0.48
Consensus pattern (15 bp):
TATCAGTGGTTTATA
Found at i:46316 original size:31 final size:31
Alignment explanation
Indices: 46279--46345 Score: 125
Period size: 31 Copynumber: 2.2 Consensus size: 31
46269 GGTTCAATCC
46279 ATTATTATGTTATACTGTAATTACCTCTTTT
1 ATTATTATGTTATACTGTAATTACCTCTTTT
*
46310 ATTATTATGTTATACTGTAATTACTTCTTTT
1 ATTATTATGTTATACTGTAATTACCTCTTTT
46341 ATTAT
1 ATTAT
46346 CCTAAATTTT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.27, C:0.10, G:0.06, T:0.57
Consensus pattern (31 bp):
ATTATTATGTTATACTGTAATTACCTCTTTT
Found at i:47694 original size:39 final size:38
Alignment explanation
Indices: 47642--47787 Score: 204
Period size: 39 Copynumber: 3.7 Consensus size: 38
47632 AAGTGAGAAG
* *
47642 TTTGAGTCAAAACCCAATATCTTAAACTATCAAAAAGTT
1 TTTGAG-CCAAACCCAATATCTTAAACTATCAAAAAGAT
* *
47681 TTTGAGACCAAACCCAATATCCTAAACTATCAAATAGAT
1 TTTGAG-CCAAACCCAATATCTTAAACTATCAAAAAGAT
47720 TTTGAGCCCAAACCCAATATCCTT-AACTATCAAAAAGAT
1 TTTGAG-CCAAACCCAATAT-CTTAAACTATCAAAAAGAT
47759 TTTGAGCCTAAACCCAATATCTTAAACTA
1 TTTGAGCC-AAACCCAATATCTTAAACTA
47788 CCAATTCCAA
Statistics
Matches: 96, Mismatches: 8, Indels: 6
0.87 0.07 0.05
Matches are distributed among these distances:
38 5 0.05
39 89 0.93
40 2 0.02
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.28
Consensus pattern (38 bp):
TTTGAGCCAAACCCAATATCTTAAACTATCAAAAAGAT
Found at i:62392 original size:5 final size:5
Alignment explanation
Indices: 62384--62409 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
62374 TTTGGCTTAT
62384 ATTAA ATTAA ATTAA ATTAA ATTAA A
1 ATTAA ATTAA ATTAA ATTAA ATTAA A
62410 CAACTGTAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (5 bp):
ATTAA
Done.