Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019243.1 Corchorus olitorius cultivar O-4 contig19276, 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: 21394
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:533 original size:17 final size:16
Alignment explanation
Indices: 511--550 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 16
501 AACATCATTT
*
511 TTATTTAATTTGTTATA
1 TTATTTAATTAGTT-TA
*
528 TTATTTTATTAGTTTA
1 TTATTTAATTAGTTTA
544 TTATTTA
1 TTATTTA
551 TATTGTTGCT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
16 8 0.40
17 12 0.60
ACGTcount: A:0.28, C:0.00, G:0.05, T:0.68
Consensus pattern (16 bp):
TTATTTAATTAGTTTA
Found at i:2939 original size:666 final size:663
Alignment explanation
Indices: 1439--4778 Score: 2862
Period size: 666 Copynumber: 5.0 Consensus size: 663
1429 ATATTTGTGT
* * * * * *
1439 AAAAAGTCAT-CAAAACTGAGTCGGGGCCTCGGAATGCG-TTTTAGCCAAATATCGTGATATGAT
1 AAAAA-TCATGCAAAACTGAG-CCGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGCG--ATGAT
* * * * * * * *
1502 TAATAT-ACGATTTCAGAT-AAATTTTTCAAAGATTGGGCCT-AAATATTTTTCCTCAATTTTT-
62 TGATTTCACGATTTCAGCTAAAATTTTGCAAAAACT-GACCTGAAA-GTTTTT-CTCAATTTTTA
** * * * * * * *
1563 CCCAAAATACTCAT-AAAAATATAAAATTCAATG-GAAAAAGATTGAAAGG-TTTTCACGCTTCT
124 GTCACAATAATCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTAACGCTTCT
* * * * **
1625 AATATCGTTTTCCCTA-TTTTTTCTAAATTAATTTCTAATTCAATCGAAAC-CGATTTTTGATGC
189 AATATCGTTTTTCCTATTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGA-TTCAGATGC
*** ** * ** * *
1688 TTGGAAAAACAAAT-CCTTAAATCCAATGTTTCTAAGATTTCCTTAGATGAATATAGATACTTCT
253 TCATAAAAAC--ATCCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCA
* *** * * * * *
1752 ATGAGTCTTGGCGCCAAAAATCATGTAAAACTGA-CCCGAGGCACC-AGATCGCGTTTTAAGTCA
316 AGGAGTCTCAACGCCAAAAATCATGCAAAACTGAGCCAG-GGC-CCGA-AACGCGTTTTTAGGCA
* * * * * **
1815 AAAACCGCGATGGGTTAGTACTTAGTATACACGATTTTGGCTAAAATTTTGCAAAAA-TAACTTG
378 AAAA---C--TGTGAT-G-A-TTA--CTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCG
* * * * * * ** *
1879 AAA-GTTTTTTC-CACAATTTTTAGCCACTATAA-TCATAGAGAATATATAATTCAACGCCACAA
433 AAATTTTTTTTCTCA-AATTTATGGCCAC-AAAACTCATAAAAAATATATAATTCAATTCCAAAA
* * **
1941 AGTTTGAAGG--------GCTT-T-TTATC-TTTTTCCTTATTTTTTTTCCGAATTAATTAGTAA
496 AGATTGAAGGCTTTTCACGCTTCTAATATCGTTTTTCC-TATTTTTTTTCCGAATTAATTTCTAA
* * * *
1995 TTGAATTGAAACTAGTTTCCGATGCTCGAAAAAACAAATCCTTATATCCAATGTGGATGAGATAT
560 TTAAATCGAAACTAGTTTCTGATGCTCGAAAAAACAAATCCTTATATCCAATGTGGATGAGATTT
* * * *
2060 GGTTAGTTGAATATAGATATTTCAAGGAGACTCGACACC
625 GGTTAGTTGAATATAGATATTTCAAGGAGTCTTGGCGCC
* ** ** * * ** **
2099 AAAAATTATGCAAAACTGAGATGGGGCCATGGAATGCGTATTTAG-CAAAAA--GTAAAAAACTT
1 AAAAATCATGCAAAACTGAG-CCGGGCCCCGGAACGCGTTTTTAGCCAAAAACCG-CGATGA--T
** * * * * * * *
2161 GTGAACTAACAATTTCGGTTAAAATTTTGCAAAAAATTGACCCGAATGATTTTTCTCAATTTTTA
62 -TGATTTCACGATTTCAGCTAAAATTTTGC-AAAAACTGACCTGAAAG-TTTTTCTCAATTTTTA
* * * * *
2226 GGCAAAATACTCATAAAAAATATATAATTCAACGCC-AAAATATTGAAGGGCTTTTCACGCTTCT
124 GTCACAATAATCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTAACGCTTCT
** *
2290 AATATCGTTTTTCCTATTTTTTTCCAAATTAATTTCGGATTAAATTGAAACAAGATTCAGATGCT
189 AATATCGTTTTTCCTATTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCT
* * *
2355 CATAAAAACATGCCCTTAAATCCAATTTGGTTGAGATTTGATTAGATAAATATAGATATTTCAAG
254 CATAAAAACAT-CCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAG
2420 GAGTCTCAACGCCAAAAATCATGCAAAACTGAGCCAGGGCACCGAAACGCGTTTTTAGGCAAAAA
318 GAGTCTCAACGCCAAAAATCATGCAAAACTGAGCCAGGGC-CCGAAACGCGTTTTTAGGCAAAAA
*
2485 CTGTGATGATTTACTACACGATTTCTGCTAAAATTTTTGCAAAAACTGACCCGAAA-TTTTTTTC
382 CTGTGATGA-TTACTACACGATTTCGGCTAAAA-TTTTGCAAAAACTGACCCGAAATTTTTTTTC
* * * *
2549 TCAAATTT-TGGCTACAAAACTCATAAAAACTATATAATTCTATTCCAAAAATATTGAAAGGCTT
445 TCAAATTTATGGCCACAAAACTCATAAAAAATATATAATTCAATTCCAAAAAGATTG-AAGGCTT
* * * *
2613 TTCACGCTTCTAATATTGTTTTTCCTATTTTTTTTCCGAATTAGTTTTTAATT-AATCGAAACTG
509 TTCACGCTTCTAATATCGTTTTTCCTATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACTA
* * *
2677 GTTTCTGATGATCGAAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTTGTTGAATAT
574 GTTTCTGATGCTCGAAAAAACAAATCCTTATATCCAATGTGGATGAGATTTGGTTAGTTGAATAT
*
2742 AGATATTTCAAGGAGTCTTGGTGCC
639 AGATATTTCAAGGAGTCTTGGCGCC
*
2767 AAAAATCATGCAAAAATGAGCCGGGTCCCCGGAACGC-TTTTTAGCCAAAAACCGCGATGATT-A
1 AAAAATCATGCAAAACTGAGCCGGG-CCCCGGAACGCGTTTTTAGCCAAAAACCGCGATGATTGA
* * *
2830 TTTCACGATTTCAGCTAAAATTTTGCAAAAATTGATCC-GAGAGTTTTTTCCTTAATTTTTAGTC
65 TTTCACGATTTCAGCTAAAATTTTGCAAAAACTGA-CCTGAAAG-TTTTT-CTCAATTTTTAGTC
* * *** *
2894 ACAATAATCATAGAGAATATATAATTCAATAACAAAAAGATTGAAGGGCTTTTAATGCTTCTAAT
127 ACAATAATCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTAACGCTTCTAAT
* * * * ** * *
2959 ACCGTTTTTCCTATTTTTTTTCCGAAGTAATTTCAAATTAAATCGAAACTGGTTTCTGATGCT--
192 ATCGTTTTTCCTA-TTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCA
* * * * *
3022 TGAAAAAGCAAAT-CCTTATATCCAATGTGGCTGAGATTTGGTTAGTTGAATATGGATAATTCAA
256 T-AAAAA-C--ATCCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAA
* * * * * * * * * *
3086 GGAGTCTCAGCGCCAAAAATCATGCAAAACTGAGTCGGGGTCTCGGAATGTGATTTTAGCCAAAT
317 GGAGTCTCAACGCCAAAAATCATGCAAAACTGAGCCAGGG-CCCGAAACGCGTTTTTAGGCAAAA
* * ** * * * * *
3151 ACTGTGATTATTAGTATTCGATTTCGGCTAAAATTTTGCAAAAATTGATCTGAAAGTTTTTTGCT
381 ACTGTGATGATTACTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAATTTTTTTTCT
* * * * * * ** *
3216 -TAATTTGTAGCCACATTAA-TCATAGAGAATATATAATTCAACACTAAAAAGATTGAAGGACTT
446 CAAATTTATGGCCACA-AAACTCATAAAAAATATATAATTCAATTCCAAAAAGATTGAAGG-CTT
** * * * *
3279 TTCAAACTTCTAATATCATTTTTCCTA-TTTCTTTCCGAATTAATTTCTAATTAAATCGAAATTG
509 TTCACGCTTCTAATATCGTTTTTCCTATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACTA
*
3343 GTTTCTGATGCTCGAAAAAACAAATCCTTATATCCAATGTGGATGAGATTAGGTTAGTTGAATAT
574 GTTTCTGATGCTCGAAAAAACAAATCCTTATATCCAATGTGGATGAGATTTGGTTAGTTGAATAT
* * *
3408 AGATATTTCGAA-GAGTCCTGACACC
639 AGATATTTC-AAGGAGTCTTGGCGCC
* * * * * * * *
3433 AAAAATCATGTAAAACTTAGTCGGGCCCCGGAACGCGTTTTTAGGCAAAAACTGTGATGGTT-AC
1 AAAAATCATGCAAAACTGAGCCGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGCGATGATTGAT
* * *
3497 TACAC-ATTTCAGCTAAAATTTTGCAAAAACTGACCTGAAAAAGTTTTTCTCAATTTTTGGTGAC
66 TTCACGATTTCAGCTAAAATTTTGCAAAAACTGACCTG--AAAGTTTTTCTCAATTTTTAGTCAC
* *
3561 AATACTCATAAAAAAATATATAATTCAACGCCAAAAATATTGAAGGGCTTTTAACGCTTCTAATA
129 AATAATCAT-AAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTAACGCTTCTAATA
* *
3626 TCGTTTTTCTTA-TTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA
193 TCGTTTTTCCTATTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATA
* * * * * *
3690 AAAACATATCCTTAATAAATCCAATATAGTTGAAATTTGATTAGATGAATATAGATATTTTAAGG
258 AAAAC--ATCCCT--TAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGG
* * * * *
3755 AGTCTCAATGCCAAAAATCATGCAAAACTAAGCCAGGGCCTCGGAACGTGTTTTTA-GC-CAAA-
319 AGTCTCAACGCCAAAAATCATGCAAAACTGAGCCAGGGCC-CGAAACGCGTTTTTAGGCAAAAAC
* * * * * * * * *
3817 --T-ACG-TTAGTACACGATTTCGGTTTAAATTTTGCAAAGATTGACCCAAAATATTTTTCCTC-
383 TGTGATGATTACTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAATTTTTTTTCTCA
* * * *
3877 AATTTTTGGCCA-AAATAGTTATAAAAAATATATAATTTAATTCCAAAAAGATTTG-AGAGCTTT
448 AATTTATGGCCACAAA-ACTCATAAAAAATATATAATTCAATTCCAAAAAGA-TTGAAG-GCTTT
* * * * * *
3940 TCACGCTTGTAATATCGTTTTTCCTATTTTTTCT-AG-A-TAATTTCAAATTCAATCGAAACCAG
510 TCACGCTTCTAATATCGTTTTTCCTATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACTAG
* * * * * * *
4002 TGTCTGATGCTCTAAAAAAC----CCTTAAATCCAATATGAATGATATTTGGTTAGATGAATATA
575 TTTCTGATGCTCGAAAAAACAAATCCTTATATCCAATGTGGATGAGATTTGGTTAGTTGAATATA
*
4063 GATATTTCAAAGAGTCTTGGCGCC
640 GATATTTCAAGGAGTCTTGGCGCC
* * * * * * *
4087 AAAAATCACGCAAAACTAAGCCGTGCCCCGGAATGCGTTTTTAGCGAAAAACCACGATGGTTAGA
1 AAAAATCATGCAAAACTGAGCCGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGCGATGATT-GA
* *
4152 TTTCACGATTTCGGCTTAAATTTTGCAAAAACTGACCTGAAAGCTTTTTCCTCAATTTTTAG-CG
65 TTTCACGATTTCAGCTAAAATTTTGCAAAAACTGACCTGAAAG-TTTTT-CTCAATTTTTAGTC-
* * * * *
4216 ACAATAATCATATAGAATATATAATTTAACGCCAAAAAGATTGAGGGGCTTTTCACGCTTCTAAT
127 ACAATAATCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTAACGCTTCTAAT
* * * * *
4281 ATCGTTTTTCCTATTTTTTTCCGAATTAATTTTTAATTAAATCGAAACTAGTTTCTGATGCTCGA
192 ATCGTTTTTCCTATTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTC-A
* * * * * * **
4346 AAAAATAAAT-CCTTATATCCAACGTGGCGGAGATTTGGTTATTTGAATATAGATATTTCAAGGA
256 TAAAA-ACATCCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGA
* **** * * * * *
4410 GTGTTGGTGCCAAAATTCATGCAAAACTGAGCCAAGACCCTAGAACGCGTTTTTAGTCAAAAACT
320 GTCTCAACGCCAAAAATCATGCAAAACTGAGCCAGGGCCCGA-AACGCGTTTTTAGGCAAAAACT
* *
4475 GTGATGATTTTTACAACACGATTTCGGCTAAAATTTTGCAAATACTGACCC-AAATTTTTTTTTT
384 GTGATGA---TTACTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAA---TTTTTTT
* * **
4539 TCTC-AATTTATGACCACAATACTCATAAAAAATATATAATTCAATGGCAAAAAGATTGAAGTGC
443 TCTCAAATTTATGGCCACAAAACTCATAAAAAATATATAATTCAATTCCAAAAAGATTGAAG-GC
* * ** *
4603 TTTTCACGCTTCTAATATCGTTTTTCATA-TTTGTTTAAGAATTAATTTTTAATTAAATCGAAAC
507 TTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAAC
* * * * ** *
4667 AAGATTCAGATGCTCGAATAAACATGTCCTTATATCCAATGTGGATGAGATTTGATTAGTTGAAT
572 TAGTTTCTGATGCTCGAAAAAACAAATCCTTATATCCAATGTGGATGAGATTTGGTTAGTTGAAT
* * *
4732 ATAGATATTTTAAGGAGTCTCGGCGGC
637 ATAGATATTTCAAGGAGTCTTGGCGCC
*
4759 AAAAATCATCCAAAACTGAG
1 AAAAATCATGCAAAACTGAG
4779 ACAAAGTCAT
Statistics
Matches: 2173, Mismatches: 401, Indels: 200
0.78 0.14 0.07
Matches are distributed among these distances:
653 3 0.00
654 186 0.09
655 5 0.00
656 75 0.03
657 119 0.05
658 87 0.04
659 36 0.02
660 151 0.07
661 28 0.01
662 22 0.01
663 29 0.01
664 130 0.06
665 217 0.10
666 552 0.25
667 262 0.12
668 159 0.07
669 32 0.01
670 8 0.00
672 72 0.03
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (663 bp):
AAAAATCATGCAAAACTGAGCCGGGCCCCGGAACGCGTTTTTAGCCAAAAACCGCGATGATTGAT
TTCACGATTTCAGCTAAAATTTTGCAAAAACTGACCTGAAAGTTTTTCTCAATTTTTAGTCACAA
TAATCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAGGGCTTTTAACGCTTCTAATATCG
TTTTTCCTATTTTTTTCCAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCATAAAA
ACATCCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCA
ACGCCAAAAATCATGCAAAACTGAGCCAGGGCCCGAAACGCGTTTTTAGGCAAAAACTGTGATGA
TTACTACACGATTTCGGCTAAAATTTTGCAAAAACTGACCCGAAATTTTTTTTCTCAAATTTATG
GCCACAAAACTCATAAAAAATATATAATTCAATTCCAAAAAGATTGAAGGCTTTTCACGCTTCTA
ATATCGTTTTTCCTATTTTTTTTCCGAATTAATTTCTAATTAAATCGAAACTAGTTTCTGATGCT
CGAAAAAACAAATCCTTATATCCAATGTGGATGAGATTTGGTTAGTTGAATATAGATATTTCAAG
GAGTCTTGGCGCC
Found at i:3037 original size:333 final size:330
Alignment explanation
Indices: 1547--4778 Score: 2840
Period size: 334 Copynumber: 9.7 Consensus size: 330
1537 GGCCTAAATA
* * * * *
1547 TTTTTCCTCAATTTTT-CCCAAAATACTCAT-AAAAATATAAAATTCAATG-GAAAAAGATTGAA
1 TTTTTCCTCAATTTTTAGCCACAATAATCATAAAAAATATATAATTCAATGCCAAAAAGATTGAA
* * ** *
1609 AGG-TTTTCACGCTTCTAATATCGTTTTCCCTA-TTTTTTCTAAATTAATTTCTAATTCAATCGA
66 GGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCCGAATTAATTTCTAATTAAATCGA
* * * * *** * ** *
1672 AAC-CGATTTTTGATGCTTGGAAAAACAAATCCTTAAATCCAATGTTTCTAAGATTTCCTTAGAT
131 AACTAG-TTTCTGATGC-TCGAAAAACAAATCCTTATATCCAATGTGGATGAGATTTGGTTAGTT
* * * * * * * * *
1736 GAATATAGATACTTCTATGAGTCTTGGCGCCAAAAATCATGTAAAACTGACCCGAGGCACCAGAT
194 GAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGCCG-GGCCCCGGAA
* * * * *
1801 CGCGTTTTAAGTCAAAAACCGCGATGGGTTAGTACTTAGTATACACGATTTTGGCTAAAATTTTG
258 CGCGTTTTTAGCCAAAAACTGCGA-----T-G-A-TTA-T-TTCACGATTTCGGCTAAAATTTTG
* *
1866 CAAAAA-TAACTTGAAAGT
313 CAAAAACTGAC-CGAAAGT
* * * * * * *
1884 TTTTTCCACAATTTTTAGCCACTATAATCATAGAGAATATATAATTCAACGCCACAAAGTTTGAA
1 TTTTTCCTCAATTTTTAGCCACAATAATCATAAAAAATATATAATTCAATGCCAAAAAGATTGAA
** * *
1949 GGGC---T-----TT-T--TATC-TTTTTCCTTATTTTTTTTCCGAATTAATTAGTAATTGAATT
66 GGGCTTTTCACGCTTCTAATATCGTTTTTCC-TA-TTTTTTTCCGAATTAATTTCTAATTAAATC
* *
2002 GAAACTAGTTTCCGATGCTCGAAAAAACAAATCCTTATATCCAATGTGGATGAGATATGGTTAGT
129 GAAACTAGTTTCTGATGCTCG-AAAAACAAATCCTTATATCCAATGTGGATGAGATTTGGTTAGT
* * * * ** **
2067 TGAATATAGATATTTCAAGGAGACTCGACACCAAAAATTATGCAAAACTGAGATGGGGCCATGGA
193 TGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAG-CCGGGCCCCGGA
* * * *** * ** * * *
2132 ATGCGTATTTAG-CAAAAAGTAAAAAACTTG-TGAACTAACAATTTCGGTTAAAATTTTGCAAAA
257 ACGCGTTTTTAGCCAAAAACT--GCGA--TGATTATTTCACGATTTCGGCTAAAATTTTGC-AAA
* * *
2195 AATTGACCCGAATGA
317 AACTGA-CCGAAAGT
* * * * *
2210 TTTTT-CTCAATTTTTAGGCAAAATACTCATAAAAAATATATAATTCAACGCC-AAAATATTGAA
1 TTTTTCCTCAATTTTTAGCCACAATAATCATAAAAAATATATAATTCAATGCCAAAAAGATTGAA
* ** *
2273 GGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCCAAATTAATTTCGGATTAAATTGA
66 GGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCCGAATTAATTTCTAATTAAATCGA
* * * * *** * * * * * *
2338 AACAAGATTCAGATGCTCATAAAAACATGCCCTTAAATCCAATTTGGTTGAGATTTGATTAGATA
131 AACTAGTTTCTGATGCTC-GAAAAACAAATCCTTATATCCAATGTGGATGAGATTTGGTTAGTTG
** * *
2403 AATATAGATATTTCAAGGAGTCTCAACGCCAAAAATCATGCAAAACTGAGCCAGGGCACCGAAAC
195 AATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGCC-GGGCCCCGGAAC
* * * * *
2468 GCGTTTTTAGGCAAAAACTGTGATGATTTACTACACGATTTCTGCTAAAATTTTTGCAAAAACTG
259 GCGTTTTTAGCCAAAAACTGCGATGA-TTATTTCACGATTTCGGCTAAAA-TTTTGCAAAAACTG
2533 ACCCGAAA-T
322 A-CCGAAAGT
* * * * * * * *
2542 TTTTTTCTCAAATTTTGGCTACAA-AACTCATAAAAACTATATAATTCTATTCCAAAAATATTGA
1 TTTTTCCTCAATTTTTAGCCACAATAA-TCATAAAAAATATATAATTCAATGCCAAAAAGATTGA
* * * *
2606 AAGGCTTTTCACGCTTCTAATATTGTTTTTCCTATTTTTTTTCCGAATTAGTTTTTAATT-AATC
65 AGGGCTTTTCACGCTTCTAATATCGTTTTTCCTA-TTTTTTTCCGAATTAATTTCTAATTAAATC
* * * *
2670 GAAACTGGTTTCTGATGATCGAAAAAACAAATCCTTATATCCAATGTGGCTGAGATTTGGTTTGT
129 GAAACTAGTTTCTGATGCTCG-AAAAACAAATCCTTATATCCAATGTGGATGAGATTTGGTTAGT
* * *
2735 TGAATATAGATATTTCAAGGAGTCTTGGTGCCAAAAATCATGCAAAAATGAGCCGGGTCCCCGGA
193 TGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGCCGGG-CCCCGGA
* * *
2800 ACGC-TTTTTAGCCAAAAACCGCGATGATTATTTCACGATTTCAGCTAAAATTTTGCAAAAATTG
257 ACGCGTTTTTAGCCAAAAACTGCGATGATTATTTCACGATTTCGGCTAAAATTTTGCAAAAACTG
*
2864 ATCCGAGAGT
322 A-CCGAAAGT
* * * * **
2874 TTTTTCCTTAATTTTTAGTCACAATAATCATAGAGAATATATAATTCAATAACAAAAAGATTGAA
1 TTTTTCCTCAATTTTTAGCCACAATAATCATAAAAAATATATAATTCAATGCCAAAAAGATTGAA
* * * * *
2939 GGGCTTTTAATGCTTCTAATACCGTTTTTCCTATTTTTTTTCCGAAGTAATTTCAAATTAAATCG
66 GGGCTTTTCACGCTTCTAATATCGTTTTTCCTA-TTTTTTTCCGAATTAATTTCTAATTAAATCG
* * *
3004 AAACTGGTTTCTGATGCTTGAAAAAGCAAATCCTTATATCCAATGTGGCTGAGATTTGGTTAGTT
130 AAACTAGTTTCTGATGCTCGAAAAA-CAAATCCTTATATCCAATGTGGATGAGATTTGGTTAGTT
* * * * * *
3069 GAATATGGATAATTCAAGGAGTCTCAGCGCCAAAAATCATGCAAAACTGAGTCGGGGTCTCGGAA
194 GAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAG-CCGGGCCCCGGAA
* * * * * * *
3134 TGTGATTTTAGCCAAATACTGTGATTATTAGTATT--CGATTTCGGCTAAAATTTTGCAAAAATT
258 CGCGTTTTTAGCCAAAAACTGCGATGATTA-T-TTCACGATTTCGGCTAAAATTTTGCAAAAACT
*
3197 GATCTGAAAGT
321 GA-CCGAAAGT
* * * * * * ** *
3208 TTTTTGCTTAATTTGTAGCCACATTAATCATAGAGAATATATAATTCAACACTAAAAAGATTGAA
1 TTTTTCCTCAATTTTTAGCCACAATAATCATAAAAAATATATAATTCAATGCCAAAAAGATTGAA
* ** * *
3273 GGACTTTTCAAACTTCTAATATCATTTTTCCTATTTCTTTCCGAATTAATTTCTAATTAAATCGA
66 GGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCCGAATTAATTTCTAATTAAATCGA
* * *
3338 AATTGGTTTCTGATGCTCGAAAAAACAAATCCTTATATCCAATGTGGATGAGATTAGGTTAGTTG
131 AACTAGTTTCTGATGCTCG-AAAAACAAATCCTTATATCCAATGTGGATGAGATTTGGTTAGTTG
* * * * *
3403 AATATAGATATTTCGAA-GAGTC-CTGACACCAAAAATCATGTAAAACTTAGTCGGGCCCCGGAA
195 AATATAGATATTTC-AAGGAGTCTC-GGCGCCAAAAATCATGCAAAACTGAGCCGGGCCCCGGAA
* * * * * *
3466 CGCGTTTTTAGGCAAAAACTGTGATGGTTACTACAC-ATTTCAGCTAAAATTTTGCAAAAACTGA
258 CGCGTTTTTAGCCAAAAACTGCGATGATTATTTCACGATTTCGGCTAAAATTTTGCAAAAACTGA
3530 CCTGAAAAAG-
323 CC-G--AAAGT
* ** * * *
3540 TTTTT-CTCAATTTTTGGTGACAATACTCATAAAAAAATATATAATTCAACGCCAAAAATATTGA
1 TTTTTCCTCAATTTTTAGCCACAATAATCAT-AAAAAATATATAATTCAATGCCAAAAAGATTGA
* * *
3604 AGGGCTTTTAACGCTTCTAATATCGTTTTTCTTA-TTTTTTCCAAATTAATTTCTAATTAAATCG
65 AGGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCCGAATTAATTTCTAATTAAATCG
* * * * * * * * *
3668 AAACAAGATTCAGATGCTCGTAAAAACATATCCTTAATAAATCCAATATAGTTGAAATTTGATTA
130 AAACTAGTTTCTGATGCTCG-AAAAACAAATCCTT-AT--ATCCAATGTGGATGAGATTTGGTTA
* * *** * *
3733 GATGAATATAGATATTTTAAGGAGTCTCAATGCCAAAAATCATGCAAAACTAAGCCAGGGCCTCG
191 GTTGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGCC-GGGCCCCG
* * * * * * * *
3798 GAACGTGTTTTTAGCC--AAA-T---ACG-TTAGTACACGATTTCGGTTTAAATTTTGCAAAGAT
255 GAACGCGTTTTTAGCCAAAAACTGCGATGATTATTTCACGATTTCGGCTAAAATTTTGCAAAAAC
* *
3856 TGACCCAAAAT
320 TGACCGAAAGT
* * * * * *
3867 ATTTTTCCTCAATTTTTGGCCAAAATAGTTATAAAAAATATATAATTTAATTCCAAAAAGATTTG
1 -TTTTTCCTCAATTTTTAGCCACAATAATCATAAAAAATATATAATTCAATGCCAAAAAGA-TTG
* * * * *
3932 -AGAGCTTTTCACGCTTGTAATATCGTTTTTCCTA-TTTTTT-CTAGA-TAATTTCAAATTCAAT
64 AAGGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCCGA-ATTAATTTCTAATTAAAT
* * * * * * * * *
3993 CGAAACCAGTGTCTGATGCTC--TAAA-AAACCCTTAAATCCAATATGAATGATATTTGGTTAGA
128 CGAAACTAGTTTCTGATGCTCGAAAAACAAATCCTTATATCCAATGTGGATGAGATTTGGTTAGT
* * * * *
4055 TGAATATAGATATTTCAAAGAGTCTTGGCGCCAAAAATCACGCAAAACTAAGCCGTGCCCCGGAA
193 TGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGCCGGGCCCCGGAA
* * ** * *
4120 TGCGTTTTTAGCGAAAAACCACGATGGTTAGATTTCACGATTTCGGCTTAAATTTTGCAAAAACT
258 CGCGTTTTTAGCCAAAAACTGCGATGATT--ATTTCACGATTTCGGCTAAAATTTTGCAAAAACT
*
4185 GACCTGAAAGC
321 GACC-GAAAGT
* * * * * *
4196 TTTTTCCTCAATTTTTAGCGACAATAATCATATAGAATATATAATTTAACGCCAAAAAGATTGAG
1 TTTTTCCTCAATTTTTAGCCACAATAATCATAAAAAATATATAATTCAATGCCAAAAAGATTGAA
*
4261 GGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCCGAATTAATTTTTAATTAAATCGA
66 GGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCCGAATTAATTTCTAATTAAATCGA
* * ** *
4326 AACTAGTTTCTGATGCTCGAAAAAATAAATCCTTATATCCAACGTGGCGGAGATTTGGTTATTTG
131 AACTAGTTTCTGATGCTCG-AAAAACAAATCCTTATATCCAATGTGGATGAGATTTGGTTAGTTG
* * * * * * **
4391 AATATAGATATTTCAAGGAGTGTTGGTGCCAAAATTCATGCAAAACTGAGCCAAGACCCTAGAAC
195 AATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGCC-GGGCCCCGGAAC
* * *
4456 GCGTTTTTAGTCAAAAACTGTGATGATT-TTTACAACACGATTTCGGCTAAAATTTTGCAAATAC
259 GCGTTTTTAGCCAAAAACTGCGATGATTATTT----CACGATTTCGGCTAAAATTTTGCAAAAAC
* *
4520 TGACCCAAATTTTT
320 TGACCGAAA---GT
* * * *
4534 TTTTTTCTCAATTTAT-GACCACAATACTCATAAAAAATATATAATTCAATGGCAAAAAGATTGA
1 TTTTTCCTCAATTTTTAG-CCACAATAATCATAAAAAATATATAATTCAATGCCAAAAAGATTGA
* * * ** *
4598 AGTGCTTTTCACGCTTCTAATATCGTTTTTCATATTTGTTTAAGAATTAATTTTTAATTAAATCG
65 AGGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCCGAATTAATTTCTAATTAAATCG
* * * ** *
4663 AAACAAGATTCAGATGCTCGAATAAACATGTCCTTATATCCAATGTGGATGAGATTTGATTAGTT
130 AAACTAGTTTCTGATGCTCGAA-AAACAAATCCTTATATCCAATGTGGATGAGATTTGGTTAGTT
* * *
4728 GAATATAGATATTTTAAGGAGTCTCGGCGGCAAAAATCATCCAAAACTGAG
194 GAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAG
4779 ACAAAGTCAT
Statistics
Matches: 2345, Mismatches: 454, Indels: 191
0.78 0.15 0.06
Matches are distributed among these distances:
319 19 0.01
320 69 0.03
321 3 0.00
322 1 0.00
323 6 0.00
324 34 0.01
325 47 0.02
326 18 0.01
327 38 0.02
328 190 0.08
329 67 0.03
330 44 0.02
331 130 0.06
332 360 0.15
333 343 0.15
334 585 0.25
335 87 0.04
336 41 0.02
337 18 0.01
338 218 0.09
339 15 0.01
340 12 0.01
ACGTcount: A:0.35, C:0.16, G:0.15, T:0.34
Consensus pattern (330 bp):
TTTTTCCTCAATTTTTAGCCACAATAATCATAAAAAATATATAATTCAATGCCAAAAAGATTGAA
GGGCTTTTCACGCTTCTAATATCGTTTTTCCTATTTTTTTCCGAATTAATTTCTAATTAAATCGA
AACTAGTTTCTGATGCTCGAAAAACAAATCCTTATATCCAATGTGGATGAGATTTGGTTAGTTGA
ATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAGCCGGGCCCCGGAACGC
GTTTTTAGCCAAAAACTGCGATGATTATTTCACGATTTCGGCTAAAATTTTGCAAAAACTGACCG
AAAGT
Found at i:4959 original size:22 final size:21
Alignment explanation
Indices: 4908--4969 Score: 61
Period size: 22 Copynumber: 2.8 Consensus size: 21
4898 TCATAAAAAA
* *
4908 TATGAAATTCTTGTAACCCACC
1 TATGAAATT-TTGTAACCAAAC
* *
4930 TATAAAATTTTGATAACCAAAT
1 TATGAAATTTTG-TAACCAAAC
4952 TATGAAATTTTTGTAACC
1 TATGAAA-TTTTGTAACC
4970 TGTAAATTAA
Statistics
Matches: 33, Mismatches: 5, Indels: 4
0.79 0.12 0.10
Matches are distributed among these distances:
21 3 0.09
22 25 0.76
23 5 0.15
ACGTcount: A:0.39, C:0.16, G:0.08, T:0.37
Consensus pattern (21 bp):
TATGAAATTTTGTAACCAAAC
Found at i:5350 original size:27 final size:27
Alignment explanation
Indices: 5315--5377 Score: 69
Period size: 27 Copynumber: 2.3 Consensus size: 27
5305 TTTTTTGTTC
5315 AAAAT-ATATTTCTAA-ATTGCCATTATT
1 AAAATAATATTT-TAATATT-CCATTATT
*
5342 -AAATAATATTTTAATTATTTCATTATT
1 AAAATAATATTTTAA-TATTCCATTATT
5369 AAAATAATA
1 AAAATAATA
5378 AAAATTTAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
26 7 0.23
27 13 0.42
28 11 0.35
ACGTcount: A:0.46, C:0.06, G:0.02, T:0.46
Consensus pattern (27 bp):
AAAATAATATTTTAATATTCCATTATT
Found at i:6030 original size:22 final size:23
Alignment explanation
Indices: 6005--6066 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
5995 CACAGAGAGG
*
6005 TTATCAAAA-ATCATAGGAAGGT
1 TTATTAAAATATCATAGGAAGGT
*
6027 TTATTAAAATTTCATAGGAAGGT
1 TTATTAAAATATCATAGGAAGGT
*
6050 TTATTAAAATTTCATAG
1 TTATTAAAATATCATAG
6067 TTAGGTTATC
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
22 8 0.22
23 29 0.78
ACGTcount: A:0.42, C:0.06, G:0.15, T:0.37
Consensus pattern (23 bp):
TTATTAAAATATCATAGGAAGGT
Found at i:6087 original size:22 final size:23
Alignment explanation
Indices: 6015--6066 Score: 104
Period size: 23 Copynumber: 2.3 Consensus size: 23
6005 TTATCAAAAA
6015 TCATAGGAAGGTTTATTAAAATT
1 TCATAGGAAGGTTTATTAAAATT
6038 TCATAGGAAGGTTTATTAAAATT
1 TCATAGGAAGGTTTATTAAAATT
6061 TCATAG
1 TCATAG
6067 TTAGGTTATC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.38
Consensus pattern (23 bp):
TCATAGGAAGGTTTATTAAAATT
Found at i:6127 original size:22 final size:22
Alignment explanation
Indices: 6102--6163 Score: 88
Period size: 22 Copynumber: 2.8 Consensus size: 22
6092 ATAGGTAAAG
** *
6102 TATCAAAATTTCATAACGTGGT
1 TATCAAAATTTCATAAAATAGT
*
6124 TATCAAAATTTAATAAAATAGT
1 TATCAAAATTTCATAAAATAGT
6146 TATCAAAATTTCATAAAA
1 TATCAAAATTTCATAAAA
6164 ATATTCAATC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 35 1.00
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.35
Consensus pattern (22 bp):
TATCAAAATTTCATAAAATAGT
Found at i:9077 original size:104 final size:104
Alignment explanation
Indices: 8957--9165 Score: 409
Period size: 104 Copynumber: 2.0 Consensus size: 104
8947 AAATATGAAA
8957 AAGATTTTTTTAGTTAAATGTGTGAATATTTCTTAAAGACAACACATAAAAAGAAGTTTAAGGGT
1 AAGATTTTTTTAGTTAAATGTGTGAATATTTCTTAAAGACAACACATAAAAAGAAGTTTAAGGGT
*
9022 ATAATAGTCTAATTAGACACAAACTTAACACTTTCAAGT
66 ATAATAGTCTAATTAGACACAAACTCAACACTTTCAAGT
9061 AAGATTTTTTTAGTTAAATGTGTGAATATTTCTTAAAGACAACACATAAAAAGAAGTTTAAGGGT
1 AAGATTTTTTTAGTTAAATGTGTGAATATTTCTTAAAGACAACACATAAAAAGAAGTTTAAGGGT
9126 ATAATAGTCTAATTAGACACAAACTCAACACTTTCAAGT
66 ATAATAGTCTAATTAGACACAAACTCAACACTTTCAAGT
9165 A
1 A
9166 TTATTTCAAA
Statistics
Matches: 104, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
104 104 1.00
ACGTcount: A:0.43, C:0.11, G:0.13, T:0.33
Consensus pattern (104 bp):
AAGATTTTTTTAGTTAAATGTGTGAATATTTCTTAAAGACAACACATAAAAAGAAGTTTAAGGGT
ATAATAGTCTAATTAGACACAAACTCAACACTTTCAAGT
Found at i:14973 original size:331 final size:330
Alignment explanation
Indices: 14345--15686 Score: 1457
Period size: 331 Copynumber: 4.0 Consensus size: 330
14335 ACAATGGTTG
* * * * * * *
14345 AGATTTGGTTAGATTAATATAGATATTTCAAGCAGTTTCGGCGCCAAAAATCATTCAAAATTGAA
1 AGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAG
* * * * *
14410 CC-GAGCCCCGGAACGCGTTTTTAGGCAAAAACCGTGATGATTATTACACGATTTCAGCTAAAAC
66 CCGGAGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAC
* *
14474 TTTGCAATAATTGACCCGAAAGA-TATTTCCTCAATTTTTAG-TCATAATACTCATAAAAAATAT
131 TTTGCAAAAATTGACCCGAAA-ATTATTTCC-CAATTTTTAGCT-AAAATACTCATAAAAAATAT
* *
14537 ATAATTCAACACCGAAAAAATTGAAGGCTTTTCACGCTTTTAATATCATTTTTTCATATTTTTTC
193 ATAATTCAACGCC-AAAAAATTGAAGGCTTTTCACTCTTTTAATATCATTTTTTCATATTTTTTC
* * * *
14602 TAAATTAATTTCTAAATAAATCGAAACAAGAGTT-AGATGCTCGTAAAAATAAATCCTTAAATGC
257 TAAATTAATTTCTAATTAAATCGAAACAAGA-TTCAGATGCTCGTAAAAACAAATTCTTAAATCC
*
14666 AATGTGGATA
321 AATGTGGCTA
* * * *
14676 AGATTTTATTAGATGAATATAGATATTTCAAGGAGTGTCGGCGCTAAAAACCATGCAAAACTGAG
1 AGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAG
* * * * * *
14741 CCGGAACCCTGAAACGCGTTTTTAGCC-AAAACCGTGATGGTTAGTATATGATTTTGGCGAAAAC
66 CCGGAGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAC
** * * * * * * * *
14805 AATGAAAAAAATGACCCGAAAATTTTTTTCCCCTATTTATGGATAAAATACTCATAAAATATATA
131 TTTGCAAAAATTGACCCGAAAA-TTATTT-CCCAATTTTTAGCTAAAATACTCATAAAAAATATA
* ** * * *
14870 TAATTTAACGTGAAAAAGATTGGAGAACTTTTCACTATTTTAATATCA-TTTTTCATATTTTTT-
194 TAATTCAACGCCAAAAA-ATTGAAG-GCTTTTCACTCTTTTAATATCATTTTTTCATATTTTTTC
* * * *
14933 TGAATTAATTTCTAATTAAATGGAAACATGATTCAGATGCTTGTAAAAACAAATTCTTAAATCCA
257 TAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCA
*
14998 ATGTGGCTG
322 ATGTGGCTA
* * *
15007 AGATTTGATTAGATGAATATGGATATCTCAAGGAGTCTCGGTGCCAAAAATCATGCAAAACTGAG
1 AGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAG
* * * * * *
15072 CCGGGGCCCC-AGAATGCTTTTTTAGCCAAAAACTGTTATGGTTATTACACGATTTCGGCTAAAA
66 CCGGAGCCCCGA-AACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAA
* * *** * * * *
15136 TTTTGTAAAAATTGATTAGAAAAATAATTTCTCAATTTTTAGCTAAAATGCTTATAAAAAATATA
130 CTTTGCAAAAATTGACCCG-AAAATTATTTCCCAATTTTTAGCTAAAATACTCATAAAAAATATA
* *
15201 TAATTCAA--CCAAAAAATTGAAGCGCTTTTGACGT-TTATAATATCATTTTTTTC-TATTTTTT
194 TAATTCAACGCCAAAAAATTGAAG-GCTTTTCAC-TCTTTTAATATCA-TTTTTTCATATTTTTT
* *
15262 CCAAATTAATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATTCTTAAATCC
256 CTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCC
*
15327 AATTTGGCTA
321 AATGTGGCTA
* * * **
15337 AGATTTGATTAGATGAATATAGATATTTCAAGTAGTCTTGGAGCCAAAAATCATGCAAATTTGAG
1 AGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAG
* *
15402 TCGG-GTCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTTGTTAGTACACGATTTCGGCT
66 CCGGAG-CCCCGAAACGCGTTTTTAGCCAAAAACCGTGAT-G---GTTAGTACACGATTTCGGCT
* * * *
15466 AAAATTTTGCAAAAATTGACAC-AAAA-GATTTCTCCTTAATTTTTGGCTAAAATACTCAT-AAA
126 AAAACTTTGCAAAAATTGACCCGAAAATTATTTC-CC--AATTTTTAGCTAAAATACTCATAAAA
* * *
15528 AATATATAATTCAACGCCAAAAAGATTGGAGGCTTTGT-A-TGCTTTTAATAT--TGTATTTCTT
188 AATATATAATTCAACGCCAAAAA-ATTGAAGGCTTT-TCACT-CTTTTAATATCAT-TTTTTCAT
15589 ATTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA-AAATTTC
249 ATTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAA-TTC
* *
15653 TTAAATCCAATGTTGCTG
313 TTAAATCCAATGTGGCTA
**
15671 AGATTTGCGTAGATGA
1 AGATTTGATTAGATGA
15687 TGTATAAGTA
Statistics
Matches: 842, Mismatches: 136, Indels: 63
0.81 0.13 0.06
Matches are distributed among these distances:
328 23 0.03
329 15 0.02
330 164 0.19
331 287 0.34
332 129 0.15
333 52 0.06
334 144 0.17
335 21 0.02
336 7 0.01
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (330 bp):
AGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTCGGCGCCAAAAATCATGCAAAACTGAG
CCGGAGCCCCGAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAC
TTTGCAAAAATTGACCCGAAAATTATTTCCCAATTTTTAGCTAAAATACTCATAAAAAATATATA
ATTCAACGCCAAAAAATTGAAGGCTTTTCACTCTTTTAATATCATTTTTTCATATTTTTTCTAAA
TTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATTCTTAAATCCAATGT
GGCTA
Found at i:16056 original size:15 final size:15
Alignment explanation
Indices: 16028--16070 Score: 59
Period size: 15 Copynumber: 2.8 Consensus size: 15
16018 GTTTCATGAC
* *
16028 TATAAATAATAATAT
1 TATAATTAAAAATAT
16043 TATAATTAAAAATAT
1 TATAATTAAAAATAT
16058 TATAATCTAAAAA
1 TATAAT-TAAAAA
16071 AAATTAGAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
15 19 0.76
16 6 0.24
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.37
Consensus pattern (15 bp):
TATAATTAAAAATAT
Found at i:16467 original size:80 final size:81
Alignment explanation
Indices: 16333--16492 Score: 268
Period size: 80 Copynumber: 2.0 Consensus size: 81
16323 ATAAGATAAT
*
16333 GTAATGTTCGAAAGTTCAAAACTTGAGAATAGAAAAAACATGTGTTGAGTGAACTTCCCGCATTT
1 GTAATGTTCGAAAGTTCAAAACTTGAGAATAGAAAAAACATGTGTTGAATGAACTTCCCGCATTT
16398 GGACTCCAATATAACC
66 GGACTCCAATATAACC
* * * *
16414 GTAATGTTCGGAAGTTTAAAA-TTGAGAATAGAAAAAATATGTGTTGAATGAACTTCCTGCATTT
1 GTAATGTTCGAAAGTTCAAAACTTGAGAATAGAAAAAACATGTGTTGAATGAACTTCCCGCATTT
16478 GGACTCCAATATAAC
66 GGACTCCAATATAAC
16493 TCCACTGCGG
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
80 55 0.74
81 19 0.26
ACGTcount: A:0.38, C:0.14, G:0.19, T:0.29
Consensus pattern (81 bp):
GTAATGTTCGAAAGTTCAAAACTTGAGAATAGAAAAAACATGTGTTGAATGAACTTCCCGCATTT
GGACTCCAATATAACC
Found at i:18388 original size:25 final size:24
Alignment explanation
Indices: 18348--18394 Score: 76
Period size: 25 Copynumber: 1.9 Consensus size: 24
18338 AATACTTACA
*
18348 TTAATTAAATTTTTAGGTATTTTT
1 TTAATTAAATTCTTAGGTATTTTT
18372 TTAATTCAAATTCTTAGGTATTT
1 TTAATT-AAATTCTTAGGTATTT
18395 GTGCAAACGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 6 0.29
25 15 0.71
ACGTcount: A:0.30, C:0.04, G:0.09, T:0.57
Consensus pattern (24 bp):
TTAATTAAATTCTTAGGTATTTTT
Found at i:18709 original size:206 final size:201
Alignment explanation
Indices: 18466--18877 Score: 716
Period size: 206 Copynumber: 2.0 Consensus size: 201
18456 TTCCTTAATA
*
18466 ATAAATAAATCGAATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTGATCTAATTTA
1 ATAAATAAATCGAATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTCATCTAATTTA
18531 ATTTAATAAAGCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTCTATATATATATAATA
66 ATTTAATAAAGCAACCACTAATGTTCAACTAATTTTTTTTGGTATAG-T-T-T-TATATATAATA
* *
18596 GTAATGTGTTGTATTTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACA
127 ATAATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACA
18661 TTCACCATTG
192 TTCACCATTG
*
18671 ATAAATAAATCGGATCTTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTCATCTAATTT
1 ATAAATAAATCGAATC-TTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTCATCTAATTT
* * *
18736 AATTTAATAAATCAACCACTAATGTTCAGCTACTTTTTTTTGGTATAGTTTTATATATAATAATA
65 AATTTAATAAAGCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTTTATATATAATAATA
18801 ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC
130 ATGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTC
18866 ACCATTG
195 ACCATTG
18873 ATAAA
1 ATAAA
18878 GTTATTAAGC
Statistics
Matches: 199, Mismatches: 7, Indels: 5
0.94 0.03 0.02
Matches are distributed among these distances:
202 89 0.45
203 1 0.01
204 1 0.01
205 16 0.08
206 92 0.46
ACGTcount: A:0.36, C:0.11, G:0.08, T:0.44
Consensus pattern (201 bp):
ATAAATAAATCGAATCTTAATATCTTTTATAATTTTGAAATTTTGTTTGACATTCATCTAATTTA
ATTTAATAAAGCAACCACTAATGTTCAACTAATTTTTTTTGGTATAGTTTTATATATAATAATAA
TGTGTTGTATCTTATTCACTACAACTTTGTTAGTAATCTTAGACTTAAAAAATTAATAACATTCA
CCATTG
Found at i:19437 original size:36 final size:36
Alignment explanation
Indices: 19397--19466 Score: 104
Period size: 36 Copynumber: 1.9 Consensus size: 36
19387 GAGATTTTGG
** *
19397 AGAAATATGATATTCAAAATTACAAAAAATGTAATA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAATA
*
19433 AGAAATATGATAACCAAAATCACAAAAGATGTAA
1 AGAAATATGATAACCAAAATCACAAAAAATGTAA
19467 GGTTATTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 30 1.00
ACGTcount: A:0.59, C:0.09, G:0.10, T:0.23
Consensus pattern (36 bp):
AGAAATATGATAACCAAAATCACAAAAAATGTAATA
Done.