Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015208.1 Corchorus olitorius cultivar O-4 contig15241, 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: 44903
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Found at i:4333 original size:5 final size:5
Alignment explanation
Indices: 4323--4365 Score: 58
Period size: 5 Copynumber: 9.4 Consensus size: 5
4313 TATATAGTAC
4323 TAAGA TAAGA TAAGA T-AG- TAAGA T-AG- TAAGA TAAGA TAAGA TA
1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TA
4366 TTTAGGCTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 8
0.81 0.00 0.19
Matches are distributed among these distances:
3 2 0.06
4 8 0.24
5 24 0.71
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.23
Consensus pattern (5 bp):
TAAGA
Found at i:4346 original size:8 final size:9
Alignment explanation
Indices: 4323--4365 Score: 54
Period size: 8 Copynumber: 4.8 Consensus size: 9
4313 TATATAGTAC
4323 TAAGATAAGA
1 TAAGAT-AGA
4333 TAAGATAG-
1 TAAGATAGA
4341 TAAGATAG-
1 TAAGATAGA
4349 TAAGATAAGA
1 TAAGAT-AGA
4359 TAAGATA
1 TAAGATA
4366 TTTAGGCTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
8 14 0.45
9 5 0.16
10 12 0.39
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.23
Consensus pattern (9 bp):
TAAGATAGA
Found at i:10550 original size:16 final size:16
Alignment explanation
Indices: 10478--10561 Score: 80
Period size: 16 Copynumber: 5.3 Consensus size: 16
10468 AATCCGCCCG
10478 AACCCGAACCC-AAAA
1 AACCCGAACCCGAAAA
* *
10493 AACCTGAACCTGAAAA
1 AACCCGAACCCGAAAA
* * *
10509 AGCTCAAACCCGAAAA
1 AACCCGAACCCGAAAA
* **
10525 AAACAAAACCCGAAAA
1 AACCCGAACCCGAAAA
*
10541 AACCCGAACCTGAAAA
1 AACCCGAACCCGAAAA
10557 AACCC
1 AACCC
10562 AAATTCAATA
Statistics
Matches: 53, Mismatches: 15, Indels: 1
0.77 0.22 0.01
Matches are distributed among these distances:
15 9 0.17
16 44 0.83
ACGTcount: A:0.54, C:0.32, G:0.10, T:0.05
Consensus pattern (16 bp):
AACCCGAACCCGAAAA
Found at i:10938 original size:32 final size:32
Alignment explanation
Indices: 10895--11091 Score: 130
Period size: 32 Copynumber: 6.1 Consensus size: 32
10885 ATTTTCCTAT
* * *
10895 AAAAAAACCCTAATTT-GGGGCGTCTATAGAAG
1 AAAAAACCCCT-ATTTAGAGGCGTCTATTGAAG
* *
10927 AAAAAACCCCTAATTATGAGTCGTCTATTGAA-
1 AAAAAACCCCTATTTA-GAGGCGTCTATTGAAG
** *
10959 AAAAACACCAGTATTTAGTGGCGTCTATTGAAG
1 AAAAA-ACCCCTATTTAGAGGCGTCTATTGAAG
**
10992 AAAACGCCCCTATTTA-ACGGCGTCTATTGAAG
1 AAAAAACCCCTATTTAGA-GGCGTCTATTGAAG
** * * * * * *
11024 AAAACGCCGCTACTTAGCGACGTCTACTAAAG
1 AAAAAACCCCTATTTAGAGGCGTCTATTGAAG
** * * *
11056 AAAATGCCCCTATTTAGCGGTGTTTATTGAAG
1 AAAAAACCCCTATTTAGAGGCGTCTATTGAAG
11088 AAAA
1 AAAA
11092 CGACTTAAAA
Statistics
Matches: 130, Mismatches: 29, Indels: 12
0.76 0.17 0.07
Matches are distributed among these distances:
31 3 0.02
32 103 0.79
33 24 0.18
ACGTcount: A:0.37, C:0.19, G:0.19, T:0.25
Consensus pattern (32 bp):
AAAAAACCCCTATTTAGAGGCGTCTATTGAAG
Found at i:11049 original size:64 final size:64
Alignment explanation
Indices: 10948--11093 Score: 177
Period size: 64 Copynumber: 2.3 Consensus size: 64
10938 AATTATGAGT
* * * * * * *
10948 CGTCTATTGAAAAAAACACCAGTATTTAGTGGCGTCTATTGAAGAAAACGCCCCTATTTAACGG
1 CGTCTATTGAAGAAAACGCCAGTACTTAGCGACGTCTACTAAAGAAAACGCCCCTATTTAACGG
* *
11012 CGTCTATTGAAGAAAACGCC-GCTACTTAGCGACGTCTACTAAAGAAAATGCCCCTATTTAGCGG
1 CGTCTATTGAAGAAAACGCCAG-TACTTAGCGACGTCTACTAAAGAAAACGCCCCTATTTAACGG
* *
11076 TGTTTATTGAAGAAAACG
1 CGTCTATTGAAGAAAACG
11094 ACTTAAAATA
Statistics
Matches: 70, Mismatches: 11, Indels: 2
0.84 0.13 0.02
Matches are distributed among these distances:
63 1 0.01
64 69 0.99
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.26
Consensus pattern (64 bp):
CGTCTATTGAAGAAAACGCCAGTACTTAGCGACGTCTACTAAAGAAAACGCCCCTATTTAACGG
Found at i:11196 original size:23 final size:24
Alignment explanation
Indices: 11168--11235 Score: 93
Period size: 23 Copynumber: 2.9 Consensus size: 24
11158 TAAATATAGG
11168 GGCGTTTAAATGCCCCTATATGA-
1 GGCGTTTAAATGCCCCTATATGAC
* * *
11191 GGCGTTTAAACGCCTCTAGATGAC
1 GGCGTTTAAATGCCCCTATATGAC
*
11215 GGCGTTTAAATGCCGCTATAT
1 GGCGTTTAAATGCCCCTATAT
11236 AAAATTTAAA
Statistics
Matches: 38, Mismatches: 6, Indels: 1
0.84 0.13 0.02
Matches are distributed among these distances:
23 20 0.53
24 18 0.47
ACGTcount: A:0.25, C:0.22, G:0.24, T:0.29
Consensus pattern (24 bp):
GGCGTTTAAATGCCCCTATATGAC
Found at i:12749 original size:15 final size:16
Alignment explanation
Indices: 12724--12753 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
12714 AATAATTATT
12724 TTTAGATTATAATATA
1 TTTAGATTATAATATA
12740 TTTA-ATTATAATAT
1 TTTAGATTATAATAT
12754 TATTATTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.53
Consensus pattern (16 bp):
TTTAGATTATAATATA
Found at i:14345 original size:668 final size:667
Alignment explanation
Indices: 13084--16340 Score: 1831
Period size: 668 Copynumber: 5.0 Consensus size: 667
13074 ATACTTTACA
*
13084 TCATCTAACCAAATCTCAACCACATTGCATTTAAGAATTTGCTTTTACGAGCATCTGAATCTTGT
1 TCATCTAACCAAATCTCAACTACATTGCATTTAAGAATTTGCTTTTACGAGCATCTGAATCTTGT
* * *
13149 TTCGATTTAATTAGAAATTAATTTAGAAAAAATAAGAAATATGATATTAAAAGCGTGAAAGGCCC
66 TTCGATTTAATTAAAAATTAATTCAGAAAAAATAAGAAATATGATATTAAAAGCGTGAAAAGCCC
** * * *
13214 CCCAATCTTTTTTGACGTTGAATTATATATTTTTATGAGTTTTTTAGCCAAAAATTGAGGAGAAA
131 CCCAATCTTTTTTGACGTCAAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGAAAAAA
* *
13279 TCTTTCGTGTCAATTTTTGCAAAAATTTAGCCGAAATAGTGTACTTACTAACCATAACAGTTTTT
196 TCTTTCGGGTCAATTTTTGCAAAAATTTAGCCAAAATAGTGTACTTACTAACCATAACAGTTTTT
*
13344 GGCTAAAAATGCGTTCTGGGGACCCACCTCAATTTTGCATGATTTTTGACTCCGAGACTGCTTGA
261 GGCTAAAAACGCGTTCTGGGGACCCACCTCAATTTTGCATGATTTTTGACTCCGAGACTGCTTGA
* * ** *
13409 AATATATATATTTATCTAATCAAATCTCAACAACATAGGTTTTAAGGATTTGTTTTTACGAGCAT
326 AAAATATATATTTATCTAATAAAATCTCAACAACATAGCATTTAAGAATTTGTTTTTACGAGCAT
* * *
13474 CTTAATCTTGTTTCGATTTAATTATAAATTAATTCGGAAAAAAATAGAAAAACGATATTAGAAAT
391 CTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGAAAAACGATATTAGAAAC
* * *
13539 GTCAAAAGCCCTTCAATCTTTTTGGCGTTGAAATATATATTTTTATGAGTATTTTAGCCAAAAAT
456 GTCAAAAGCCCTACAATCTTTTTGGCGTAGAAATATATATTTTTATGAGTATTGTAGCCAAAAAT
* ** * *
13604 TGAGGAAATATCTTTCGGGCCCTTTTTTTGCAAAATTTTAGCCGAAATTGTGTAATAACCATCAC
521 TGAGAAAATATCTTTCGGGCCCAATTTTTGCAAAATTTTAGCCGAAATCGTATAATAACCATCAC
* * * *
13669 TATTTTTGGCTAAAAAAGCGTTCCGGGGCCCCGGCTT-AGTTTTGCATGATTTTTTGCGCC-ATG
586 TATTTTTGGCTAAAAAAGCATTCCGGGG-CCCGG-TTCAGTTCTGCATGATTTTTGGCCCCGA-G
*
13732 ACTCCTTGAGATATAC-ATAT
648 ACTCCTTGAAATAT-CTATAT
* * * * *
13752 TCATTTAATCAAATCTCAACTACATTGGATTTAAGAATTT-TTTTTACGAGCATCTTAATCTTGT
1 TCATCTAACCAAATCTCAACTACATTGCATTTAAGAATTTGCTTTTACGAGCATCTGAATCTTGT
*
13816 TTCGATTTAATTAAAAATTAATTCA-AACAAATATAA-AAA-ATGATATTAAAAGCGTGAAAAGT
66 TTCGATTTAATTAAAAATTAATTCAGAA-AAA-ATAAGAAATATGATATTAAAAGCGTGAAAAGC
* * *
13878 CCTCCAATC-TTTTTGATGTCAAATTATATATATTTTATGAGTATTTTATCCAAAAATTGAGAAA
129 CCCCCAATCTTTTTTGACGTCAAATTATATAT-TTTTATGAGTATTTTAGCCAAAAATTGAGAAA
* * * * * * * *
13942 AAATTTTTCGGGTCATTTTTTTTTTCAAAATTTTAGTCAAAATCGTGTAC-TA-TAACCATCACG
193 AAATCTTTCGGGTCA---ATTTTTGCAAAAATTTAGCCAAAATAGTGTACTTACTAACCATAACA
* ** * *
14005 GTCTTTTGGCTAAAAACGCGTT-TCGGGGCCCCGGCTCAGTTTTGCATGATTTTTGGCGT-CGAG
255 GT-TTTTGGCTAAAAACGCGTTCT-GGGGACCCACCTCAATTTTGCATGATTTTTGAC-TCCGAG
* * * * * *
14068 ACTTCTTGAAAAATCTATATTTATCTAATAAAATCTTAGCCACATTGCATTTAAGAATTTGTTTT
317 ACTGCTTGAAAAATATATATTTATCTAATAAAATCTCAACAACATAGCATTTAAGAATTTGTTTT
* * *
14133 TACGAGCATCTGAATCTTGTTTTGATTTAATTAGAAATTAATTCTG-AAAAAATATGAAAAAGGA
382 TACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATA-GAAAAACGA
* * *
14197 TATTA-AAAGCGTGAAAAGCCCTACAATCTTTTTGGTGTAGAATTATATAATTTTTATGAGTATT
446 TATTAGAAA-CGTCAAAAGCCCTACAATCTTTTTGGCGTAGAAATATAT-ATTTTTATGAGTATT
* * * * *
14261 GTGGCTAAAATTTGA-AATAATATCTTT-GTG-TCAATTTTTGCAAAATTTTAGCCGAAAATCGT
509 GTAGCCAAAAATTGAGAA-AATATCTTTCGGGCCCAATTTTTGCAAAATTTTAGCCG-AAATCGT
** * *
14323 ATAATAATTATCAC-AGTTTTTGGCTAAAAATGCATTCCGGGGCCTGGTTCAGTTCTGCATGATT
572 ATAATAACCATCACTA-TTTTTGGCTAAAAAAGCATTCCGGGGCCCGGTTCAGTTCTGCATGATT
14387 TTTGGCCCCGAGACTCCTTGAAATATCTATAT
636 TTTGGCCCCGAGACTCCTTGAAATATCTATAT
* * * * * *
14419 TTATCTAACCAAATCGC-A--AC--T--A-TT--G----T--TTTTACAAGCATTTAAATCATGT
1 TCATCTAACCAAATCTCAACTACATTGCATTTAAGAATTTGCTTTTACGAGCATCTGAATCTTGT
* * * * * * * * * *
14468 TTTGATTTAATTAGAAATTAGTTCGGAAAAAATAGGAAAAACGATTTTTACAAGCATCTTCGATC
66 TTCGATTTAATTAAAAATTAATTCAGAAAAAATAAGAAATATGA-TATTA-AA--AGCGT-GA--
*** * **** * * * * * * ** * * *
14533 TTTTTGGCGTTGAATTATAAATTTTCTTATG-AAAATTGTGGCTAAACATTGAGGAAAAATATTT
124 --AAAGCCCCCCAA-TCT---TTTT-TGACGTCAAA-T-T--ATATATTTTTATG---AGTATTT
* * * * * *** *
14597 CA-CCAAAAATTGAGGAGAAATTTTTTGGGTC-ATTTTCTGC-AAAATTTAAGCTGGAATCGTGT
175 TAGCCAAAAATTGAGAAAAAATCTTTCGGGTCAATTTT-TGCAAAAATTT-AGCCAAAATAGTGT
* * * * ** * *
14659 ACGT--T-ACCATCACAGTTTTTGGCTAAAAACACGTT-TCGGGGCCCCGGCTTAGTTTTGCATG
238 ACTTACTAACCATAACAGTTTTTGGCTAAAAACGCGTTCT-GGGGACCCACCTCAATTTTGCATG
* * * * * * * * * *
14720 ATTTTTGGCGCCGAGACTCCTTGAAATATCTATATTCATCTAATCAAATCTCAGCCACATTTG-A
302 ATTTTTGACTCCGAGACTGCTTGAAAAATATATATTTATCTAATAAAATCTCAACAACA-TAGCA
* * * * *
14784 ATTAAAAGATTTGTTTTTACGAGCATCTGAATGTTGTTTTGATTTAATTAGAAATTAATTCAGAA
366 TTTAAGA-ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAA
* * * * * * *
14849 AAATAT-GAAAAACGATA-T-GAAAAGCTCAAAAAGTCCTTCAACCTTTTTGGTGTTA-AATTAT
430 AAAAATAGAAAAACGATATTAGAAACG-TC-AAAAGCCCTACAATCTTTTTGGCG-TAGAAATAT
* * * * * *
14910 ATATATTTCATGAGTATAT-TAGCAAAAAATTAAGAAAA-AT-TTTCCGAG-TCGATTTTTGCAA
492 ATAT-TTTTATGAGTAT-TGTAGCCAAAAATTGAGAAAATATCTTT-CGGGCCCAATTTTTGCAA
* ** * * * * *
14971 AATTTTAGTCGAAATCG-----T---CA-CGGT-TTTTTTGCTAAAAACGCGTTTCGGAGCTCCG
554 AATTTTAGCCGAAATCGTATAATAACCATCACTATTTTTGGCTAAAAAAGCATTCCGGGGC-CCG
* * **** *
15026 GCTCAGTTTTGCATGATTTTTGGTGTTGAGACGCCTTGAAATATCTATAT
618 GTTCAGTTCTGCATGATTTTTGGCCCCGAGACTCCTTGAAATATCTATAT
* ** * * * *
15076 TCATTTAATAAAATCTCAGC-ACATTGTATTTAAGGATTTG-TTTGTACGAGCATTTGAATCTTG
1 TCATCTAACCAAATCTCAACTACATTGCATTTAAGAATTTGCTTT-TACGAGCATCTGAATCTTG
* *
15139 TTTCGATTTAATTAGAAATTAATTTAG-------AA-AAATATG--A--AAAA-C-------G--
65 TTTCGATTTAATTAAAAATTAATTCAGAAAAAATAAGAAATATGATATTAAAAGCGTGAAAAGCC
* * * * * *
15182 -----A----TATTGA----ATA-TATATA-TTTTATGACTATTTTAGCCAAAAATTAAGGAGAA
130 CCCCAATCTTTTTTGACGTCAAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGAAAAA
* * * ** * * * *** * * * *
15232 ATTTTTCGGGCCATTTTCCGCAAGATTTAAGCTGGAATCGTGTACT----AATCATCACGGTTTT
195 ATCTTTCGGGTCAATTTTTGCAAAAATTTAGCCAAAATAGTGTACTTACTAACCATAACAGTTTT
* ** * * *
15293 TGGCTAAAAACGCGTT-TCGGGGCCCCGGCTTAGTTTTGCATGATTTTTTG--TGCCGAGACTCC
260 TGGCTAAAAACGCGTTCT-GGGGACCCACCTCAATTTTGCATGA-TTTTTGACT-CCGAGACTGC
* * * * * * * *
15355 TTGAAATATCTATACTCATCTAATCAAATCTCAGGC-ACATTTGAATTTAATG-ATTTGTTTTTA
322 TTGAAAAATATATATTTATCTAATAAAATCTCA-ACAACA-TAGCATTTAA-GAATTTGTTTTTA
* * * * *
15418 TGAGCATCCTGAATCTTGTTTTGATTTAATTAGAAATTAATTCAGAAAAATAT-GAAAAGCGATA
384 CGAGCAT-CTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGAAAAACGATA
* * * * *
15482 TTA-AAA-GCTCGAAAAGTCCTTCAACCTTTTTGGCGTTA-AATTATATATATTTCATGAGTATT
448 TTAGAAACG-TC-AAAAGCCCTACAATCTTTTTGGCG-TAGAAATATATAT-TTTTATGAGTATT
* ** *
15544 TTAGCCAAAAATTGAAGAAAA-AT-TTTC-GGATCATTTTTTGCAAAATTTTAGCCGAAATCGTA
509 GTAGCCAAAAATTG-AGAAAATATCTTTCGGGCCCAATTTTTGCAAAATTTTAGCCGAAATCGTA
* * ** * * * * * * ** * *
15606 TACTAACTATCACGGTTTTTTGCTACAAACGCGTTTCAGGGCTCCGACTCAGTTTTGTATGATTT
573 TAATAACCATCACTATTTTTGGCTAAAAAAGCATTCCGGGGC-CCGGTTCAGTTCTGCATGATTT
*** *
15671 TTGGTGTCGAGACTCCTTGTAATATCTATAT
637 TTGGCCCCGAGACTCCTTGAAATATCTATAT
* * * * * * *
15702 TCATCTAATCAAATCTCAGCTACATTGCGTTTAAGGATTTG-TTTATACAAGCATTTGAATCTTA
1 TCATCTAACCAAATCTCAACTACATTGCATTTAAGAATTTGCTTT-TACGAGCATCTGAATCTTG
* * *
15766 TTTCGATTTAATTAGAAATTAATTCAGAAAAATATAA-AAA-AGCGATATTAAAAGCGTGAAAAA
65 TTTCGATTTAATTAAAAATTAATTCAGAAAAA-ATAAGAAATA-TGATATTAAAAGCGTGAAAAG
* * * * *
15829 TCCTCCAATC-TTTTTGGCGTTAAATTATATATATATATATCTATTATGAGTATTTTAGCTAAAA
128 CCCCCCAATCTTTTTTGACG-T-CA--A-AT-TATATAT-T-T-TTATGAGTATTTTAGCCAAAA
* * *** *
15893 ATTGAGAAAAAAT-TTGACGGGTC-ATTTTCTGC-AAAATTTAATCTGGAATCGTG----TACTA
184 ATTGAGAAAAAATCTT-TCGGGTCAATTTT-TGCAAAAATTT-AGCCAAAATAGTGTACTTACTA
* * ** * * * ** * ** *
15951 ACCATCACGGTTTTTCACTAAAACCGTGTT-TCGAGG-CCCGGCTTAGGTTTGCATGATTTTTGG
246 ACCATAACAGTTTTTGGCTAAAAACGCGTTCT-GGGGACCCACCTCAATTTTGCATGATTTTTGA
* * * * * * * * * * *
16014 CACCGAGACTCCTTGAAATATCTATACTCATCTAATCAAATCTCAACCATATTTGAATTTAATG-
310 CTCCGAGACTGCTTGAAAAATATATATTTATCTAATAAAATCTCAACAACA-TAGCATTTAA-GA
* * * * * *
16078 ATTTGTTTTTACGAGCATCAGAATCTTGTTTTGATTTAATTAGAATTTGATTCAGAAAAATAT-G
373 ATTTGTTTTTACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAG
* * *** *** * * * * *
16142 GAAAACGATATTA-AAAGCGTGAAAATTTCTTTTATCTTTTTGGAGTTGTATTGTATATATTTTA
438 AAAAACGATATTAGAAA-CGTCAAAAGCCCTACAATCTTTTTGGCGTAGAAATATATAT-TTTTA
* * * * * *
16206 TGAGTATTGTGGCTAAAAATTGAGGAAAA-ATATTTCGGG-TCTATTTTTGTAAAATTTTAGCCG
501 TGAGTATTGTAGCCAAAAATTGA-GAAAATATCTTTCGGGCCCAATTTTTGCAAAATTTTAGCCG
* * * * * * *
16269 AATTCG--T-GT-ACCATCACGATTTTTTGGCTAAAAACGCGTTCCGGGGTCCCGGGTCAGTTTT
565 AAATCGTATAATAACCATCACTA-TTTTTGGCTAAAAAAGCATTCCGGGG-CCCGGTTCAGTTCT
16330 GCATGATTTTT
628 GCATGATTTTT
16341 TTTTGTGGCA
Statistics
Matches: 2120, Mismatches: 303, Indels: 332
0.77 0.11 0.12
Matches are distributed among these distances:
615 129 0.06
616 203 0.10
617 22 0.01
618 4 0.00
619 3 0.00
621 2 0.00
624 3 0.00
625 1 0.00
626 91 0.04
627 66 0.03
628 2 0.00
634 1 0.00
635 6 0.00
636 1 0.00
637 1 0.00
639 4 0.00
640 1 0.00
643 1 0.00
651 3 0.00
652 46 0.02
653 6 0.00
654 5 0.00
655 3 0.00
656 23 0.01
657 66 0.03
658 5 0.00
659 5 0.00
660 1 0.00
661 2 0.00
662 6 0.00
663 3 0.00
664 9 0.00
665 24 0.01
666 93 0.04
667 353 0.17
668 415 0.20
669 88 0.04
670 128 0.06
671 141 0.07
672 147 0.07
673 7 0.00
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (667 bp):
TCATCTAACCAAATCTCAACTACATTGCATTTAAGAATTTGCTTTTACGAGCATCTGAATCTTGT
TTCGATTTAATTAAAAATTAATTCAGAAAAAATAAGAAATATGATATTAAAAGCGTGAAAAGCCC
CCCAATCTTTTTTGACGTCAAATTATATATTTTTATGAGTATTTTAGCCAAAAATTGAGAAAAAA
TCTTTCGGGTCAATTTTTGCAAAAATTTAGCCAAAATAGTGTACTTACTAACCATAACAGTTTTT
GGCTAAAAACGCGTTCTGGGGACCCACCTCAATTTTGCATGATTTTTGACTCCGAGACTGCTTGA
AAAATATATATTTATCTAATAAAATCTCAACAACATAGCATTTAAGAATTTGTTTTTACGAGCAT
CTGAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAATAGAAAAACGATATTAGAAAC
GTCAAAAGCCCTACAATCTTTTTGGCGTAGAAATATATATTTTTATGAGTATTGTAGCCAAAAAT
TGAGAAAATATCTTTCGGGCCCAATTTTTGCAAAATTTTAGCCGAAATCGTATAATAACCATCAC
TATTTTTGGCTAAAAAAGCATTCCGGGGCCCGGTTCAGTTCTGCATGATTTTTGGCCCCGAGACT
CCTTGAAATATCTATAT
Found at i:16414 original size:331 final size:324
Alignment explanation
Indices: 15190--16424 Score: 1276
Period size: 332 Copynumber: 3.7 Consensus size: 324
15180 CGATATTGAA
* * * * * * *
15190 TATATATATTTTATGACTATTTTAGCCAAAAATTAAGGAGAAATTTTTCGGGCCATTTTCCGCAA
1 TATATATATTTTATGAGTATTTTAGCTAAAAATTGA-GAAAAATATTTCGGGTCATTTT-TGCAA
* * *
15255 GATTTAAGCTGGAATCGTGTACTAATCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCG
64 AATTTTAGC-CGAATCGTGTAC----CATCACGGTTTTTGGCTAAAAACGCGTTTCGGGG-CCCG
* *
15320 GCTTAGTTTTGCATGATTTTTTGTGCCGAGACTCCTTGAAATATCTATACTCATCTAATCAAATC
123 GCTCAGTTTTGCATGATTTTTGGTGCCGAGACTCCTTGAAATATCTATACTCATCTAATCAAATC
* * *
15385 TCAGGCACATTTGAATTTAATGATTTGTTTTTATGAGCATCCTGAATCTTGTTTTGATTTAATTA
188 TCAGCCACATTTGAATTTAAGGATTTGTTTTTACGAGCAT-CTGAATCTTGTTTTGATTTAATTA
* *
15450 GAAATTAATTCAGAAAAATATGAAAAGCGATATTAAAAGC-TCGAAAAGTCCTTCAACCTTTTTG
252 GAAATTAATTCAGAAAAATATGAAAAGCGATATTAAAAGCGT-GAAAAATCCTTCAATCTTTTTG
* *
15514 GCGTTAAAT
316 GAGTTATAT
* * *
15523 TATATATATTTCATGAGTATTTTAGCCAAAAATTGAAGAAAAAT-TTTCGGATCATTTTTTGCAA
1 TATATATATTTTATGAGTATTTTAGCTAAAAATTG-AGAAAAATATTTCGGGTCA-TTTTTGCAA
* * * *
15587 AATTTTAGCCGAAATCGTATACTAACTATCACGGTTTTTTGCTACAAACGCGTTTCAGGGCTCCG
64 AATTTTAGCCG-AATCGTGTAC---C-ATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGC-CCG
* * * * *
15652 ACTCAGTTTTGTATGATTTTTGGTGTCGAGACTCCTTGTAATATCTATATTCATCTAATCAAATC
123 GCTCAGTTTTGCATGATTTTTGGTGCCGAGACTCCTTGAAATATCTATACTCATCTAATCAAATC
* ** * * * * *
15717 TCAGCTACA-TTGCGTTTAAGGATTTGTTTATACAAGCATTTGAATCTTATTTCGATTTAATTAG
188 TCAGCCACATTTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTTGATTTAATTAG
* *
15781 AAATTAATTCAGAAAAATATAAAAAAGCGATATTAAAAGCGTGAAAAATCCTCCAATCTTTTTGG
253 AAATTAATTCAGAAAAATAT-GAAAAGCGATATTAAAAGCGTGAAAAATCCTTCAATCTTTTT-G
*
15846 CGTTAAATTATAT
316 -G---AGTTATAT
15859 ATATATATATCTATTATGAGTATTTTAGCTAAAAATTGAGAAAAA-ATTTGACGGGTCATTTTCT
1 -TATATATAT-T-TTATGAGTATTTTAGCTAAAAATTGAGAAAAATATTT--CGGGTCATTTT-T
* * * ** * * *
15923 GCAAAATTTAATCTGGAATCGTGTACTAACCATCACGGTTTTTCACTAAAACCGTGTTTCGAGGC
60 GCAAAATTTTAGC-CGAATCGTG---T-ACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGC
* * **
15988 CCGGCTTAGGTTTGCATGATTTTTGGCACCGAGACTCCTTGAAATATCTATACTCATCTAATCAA
120 CCGGCTCAGTTTTGCATGATTTTTGGTGCCGAGACTCCTTGAAATATCTATACTCATCTAATCAA
* * * *
16053 ATCTCAACCATATTTGAATTTAATGATTTGTTTTTACGAGCATCAGAATCTTGTTTTGATTTAAT
185 ATCTCAGCCACATTTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTTGATTTAAT
* * * * **
16118 TAGAATTTGATTCAGAAAAATATGGAAAA-CGATATTAAAAGCGTGAAAATTTCTTTTATCTTTT
250 TAGAAATTAATTCAGAAAAATAT-GAAAAGCGATATTAAAAGCGTGAAAAATCCTTCAATCTTTT
*
16182 TGGAGTTGTAT
314 TGGAGTTATAT
* * * *
16193 TGTATATATTTTATGAGTATTGTGGCTAAAAATTGAGGAAAAATATTTCGGGTCTATTTTTGTAA
1 TATATATATTTTATGAGTATTTTAGCTAAAAATTGA-GAAAAATATTTCGGGTC-ATTTTTGCAA
* * *
16258 AATTTTAGCCGAATTCGTGTACCATCACGATTTTTTGGCTAAAAACGCGTTCCGGGGTCCCGGGT
64 AATTTTAGCCGAA-TCGTGTACCATCACG-GTTTTTGGCTAAAAACGCGTTTCGGGG-CCCGGCT
* * * * * * * * *
16323 CAGTTTTGCATGATTTTTTTTTGTGGCAAAACTCCTTCAAATATCTATAGTCATTTAACCTAATC
126 CAGTTTTGCATGA---TTTTTGGTGCCGAGACTCCTTGAAATATCTATACTCATCTAATCAAATC
* * *
16388 TTAGCCAAATTAG-ATTTAAGGATTTGTTTTTACGAGC
188 TCAGCCACATTTGAATTTAAGGATTTGTTTTTACGAGC
16425 TGTAGAGCAA
Statistics
Matches: 748, Mismatches: 120, Indels: 70
0.80 0.13 0.07
Matches are distributed among these distances:
327 9 0.01
328 21 0.03
329 17 0.02
330 45 0.06
331 133 0.18
332 187 0.25
333 55 0.07
334 7 0.01
336 5 0.01
337 10 0.01
338 12 0.02
339 123 0.16
340 119 0.16
341 2 0.00
343 1 0.00
344 2 0.00
ACGTcount: A:0.31, C:0.15, G:0.16, T:0.38
Consensus pattern (324 bp):
TATATATATTTTATGAGTATTTTAGCTAAAAATTGAGAAAAATATTTCGGGTCATTTTTGCAAAA
TTTTAGCCGAATCGTGTACCATCACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCGGCTCAGTT
TTGCATGATTTTTGGTGCCGAGACTCCTTGAAATATCTATACTCATCTAATCAAATCTCAGCCAC
ATTTGAATTTAAGGATTTGTTTTTACGAGCATCTGAATCTTGTTTTGATTTAATTAGAAATTAAT
TCAGAAAAATATGAAAAGCGATATTAAAAGCGTGAAAAATCCTTCAATCTTTTTGGAGTTATAT
Found at i:17969 original size:334 final size:331
Alignment explanation
Indices: 17354--18058 Score: 875
Period size: 334 Copynumber: 2.1 Consensus size: 331
17344 TGTGTGTTAC
* * * *
17354 ACGAGCATTTGAATCATGTTTCGATTTAATTAGAAATT-AATTTGAAAAAAAAAAGAAAAAACGA
1 ACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAAAATAGAAAAAAAAAAGAAAAAACGA
*
17418 TATTGAAGCATGAGAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGT
66 TATTGAAGCATGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGT
* *
17483 GGCTAAAAATTGAGATAAATATTTAGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACCA
131 CGCTAAAAATTGAGAAAAATATTTAGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACCA
** * * ** * *
17548 TCATGGTTTTTTTGGCTAAAAACGTGTTTTGGGGCCCCAAGTCAGTTTTGCATGATTTTTTACGC
196 TCACAG-TTTTTTGACTAAAAACGCGTTCCGGGGCCACAAGTCAGTTTTGCATGATTTTTTACAC
* * * *
17613 TAAGACTCCTTAAAATATATCTTTATTCATGTAACCAAATCTCAGCCACATTGTATTTAAGAATT
260 CAAGACTCCTTAAAATATATCTTTATTCATCTAACCAAATCTCAGCCACATTGGATATAAGAATT
17678 TGTTTTT
325 TGTTTTT
* * *
17685 ACGAGCATCT-ACATCTTGTTTCGATTTAATCAGAAATTAAAATAGAAATAAAATAGAAAAAACG
1 ACGAGCATCTGA-ATCTTGTTTCGATTTAATTAGAAATTAAAATAGAAAAAAAAAAGAAAAAACG
* * * * * *
17749 ATATTAGAAGCGTGAAAAAGGCTTTCAATTTTTTTGGTGTTGATTTATATA-TTTTTATGAGTAT
65 ATATT-GAAGCATG-AAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTAT
* * * *
17813 TTTCGCTAGAAATTGAGGAAAAATCTTTTGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGT
128 TGTCGCTAAAAATTGA-GAAAAATATTTAGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTG-
* **
17878 ACTAACCATCACAG-TTTTTGACTAAAAACGCGTTCCGGGGCCAC-GGCTTTGTTTTGCATGATT
191 --T-ACCATCACAGTTTTTTGACTAAAAACGCGTTCCGGGGCCACAAG-TCAGTTTTGCATGATT
* * **
17941 TTTTGCACCAAGACTCCTT-GAA-ATATCTTTATTCATCTAATTAAATCTCAGCCACATTGGATA
252 TTTTACACCAAGACTCCTTAAAATATATCTTTATTCATCTAACCAAATCTCAGCCACATTGGATA
*
18004 TAAGGATTTGTTTTT
317 TAAGAATTTGTTTTT
* * * *
18019 ACGTGCATTTGAATCTTGTTTTGATTTAATTAAAAATTAA
1 ACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAA
18059 TTCAGAAAAA
Statistics
Matches: 318, Mismatches: 45, Indels: 19
0.83 0.12 0.05
Matches are distributed among these distances:
330 1 0.00
331 33 0.10
332 26 0.08
333 33 0.10
334 157 0.49
335 4 0.01
336 55 0.17
337 1 0.00
338 8 0.03
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.38
Consensus pattern (331 bp):
ACGAGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAAAATAGAAAAAAAAAAGAAAAAACGA
TATTGAAGCATGAAAAGCCCTTCAATCTTTTTGGCGTTGAATTATATATTTTTTATGAGTATTGT
CGCTAAAAATTGAGAAAAATATTTAGGGTCAATTTTTGCAAAATTTTAGCCGAAATCGTGTACCA
TCACAGTTTTTTGACTAAAAACGCGTTCCGGGGCCACAAGTCAGTTTTGCATGATTTTTTACACC
AAGACTCCTTAAAATATATCTTTATTCATCTAACCAAATCTCAGCCACATTGGATATAAGAATTT
GTTTTT
Found at i:23018 original size:351 final size:348
Alignment explanation
Indices: 22371--23032 Score: 995
Period size: 351 Copynumber: 1.9 Consensus size: 348
22361 TCCAAAACAT
* * * *
22371 TCTCCAAGTCGGTTTAGAAGAAGATCAATTATGTCTAGAAATTTCAAGGGCAAAATCGTCCACCA
1 TCTCCAAGTCGGTTTAGAAGAAGATCAATTATATCCAGAAAATTCAAGGGAAAAATCGTCCACCA
* *
22436 GAACTGCAGAATTAGGTCTCAAGGTAACATAAAATTTGTAGATCTCGGAATCCTCTTTCCAACAG
66 GAACTGCAGAATCAGGTCTCAAGGTAACATAAAATTTGTAAATCTCGGAATCCTCTTTCCAACAG
* *
22501 TACCTCATTTGCATTTTTCTGAACTCTAGTCAAAAGTTATAAATTTTCTTCCAAAACTGCTATTG
131 TACCTCATTTGCATTTTTCTGAACTCCAGTCAAAAATTATAAATTTTCTTCCAAAACTGCTATTG
* ** * *
22566 TGAAGTCCTCTTTTGAATAGGATTTAACAATGTTGCATCAGGATTGAATCATTACTGCATCATAA
196 TGAAGTCCTCCTTCAAATAGGATTTAAAAATGCTGCATCAGGATTGAATCATTACTGCATCATAA
* * *
22631 ATACTGATTGAACTTGGACTCCTTCTTTGTGCTTCCATATTAACGAATTGGGGCTAAAAATATCA
261 ATACTGATTGAACTTGGACTCCTTCTTTGGGCTTCCACAGTAACGAATTGGGGCTAAAAATATCA
22696 GATTTAGCCTTCAAGACATAAGC
326 GATTTAGCCTTCAAGACATAAGC
* * **
22719 TCTCCAAGTCGGTTTAGGAGAAGATCAATTCTATCCAGAAAATTCAAGGGAAAAATCGTCCACTG
1 TCTCCAAGTCGGTTTAGAAGAAGATCAATTATATCCAGAAAATTCAAGGGAAAAATCGTCCACCA
*
22784 GAACTGCAGAATCAGGTCTCAAGGTAAACATAAAAGTTT-TAAATCTTGGAATCCTCTTTCCAAC
66 GAACTGCAGAATCAGGTCTCAAGGT-AACATAAAA-TTTGTAAATCTCGGAATCCTCTTTCCAAC
* * * *
22848 GGTACCTCATTTGCATTTTTCTGAGCTCCGGATCAAAAATTATGAATTTTCTTTCCAAAACTGCT
129 AGTACCTCATTTGCATTTTTCTGAACTCCAG-TCAAAAATTATAAATTTTC-TTCCAAAACTGCT
* * * *
22913 CTTGTGAAGTCTTCCTTCAAATATGATTTAAAAATGCTGCATCAGGGTTGAATCATTACTGCATC
192 ATTGTGAAGTCCTCCTTCAAATAGGATTTAAAAATGCTGCATCAGGATTGAATCATTACTGCATC
*
22978 ATAATTACTGATTGGAA-TTGGACTCCTTCTTTGGGCTTCCACAGTAACGAATTGG
257 ATAAATACTGATT-GAACTTGGACTCCTTCTTTGGGCTTCCACAGTAACGAATTGG
23033 ATCTAAGAAT
Statistics
Matches: 279, Mismatches: 30, Indels: 7
0.88 0.09 0.02
Matches are distributed among these distances:
348 81 0.29
349 59 0.21
350 20 0.07
351 116 0.42
352 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.32
Consensus pattern (348 bp):
TCTCCAAGTCGGTTTAGAAGAAGATCAATTATATCCAGAAAATTCAAGGGAAAAATCGTCCACCA
GAACTGCAGAATCAGGTCTCAAGGTAACATAAAATTTGTAAATCTCGGAATCCTCTTTCCAACAG
TACCTCATTTGCATTTTTCTGAACTCCAGTCAAAAATTATAAATTTTCTTCCAAAACTGCTATTG
TGAAGTCCTCCTTCAAATAGGATTTAAAAATGCTGCATCAGGATTGAATCATTACTGCATCATAA
ATACTGATTGAACTTGGACTCCTTCTTTGGGCTTCCACAGTAACGAATTGGGGCTAAAAATATCA
GATTTAGCCTTCAAGACATAAGC
Found at i:23592 original size:26 final size:27
Alignment explanation
Indices: 23542--23593 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
23532 ATTATTAAAA
*
23542 TATTTTATTTAGATAAAATTTAATTTT
1 TATTTTATTTAGATAAAATTCAATTTT
23569 TATTTTATTTAGA-AAAATTCAATTT
1 TATTTTATTTAGATAAAATTCAATTT
23594 CTACAGTTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
26 11 0.46
27 13 0.54
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (27 bp):
TATTTTATTTAGATAAAATTCAATTTT
Found at i:25157 original size:2 final size:2
Alignment explanation
Indices: 25150--25182 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
25140 TTAAGACTAG
25150 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
25183 GATTAATGTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28803 original size:37 final size:37
Alignment explanation
Indices: 28762--28833 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
28752 CTTATAACAT
28762 ATTAAAAACCCACTTAACATATCAATAATTAAAGGGA
1 ATTAAAAACCCACTTAACATATCAATAATTAAAGGGA
*
28799 ATTAAAATCCCACTTAACATATCAATAATTAAAGG
1 ATTAAAAACCCACTTAACATATCAATAATTAAAGG
28834 AACCTCAAAT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.50, C:0.17, G:0.07, T:0.26
Consensus pattern (37 bp):
ATTAAAAACCCACTTAACATATCAATAATTAAAGGGA
Found at i:29114 original size:31 final size:31
Alignment explanation
Indices: 29079--29142 Score: 110
Period size: 31 Copynumber: 2.1 Consensus size: 31
29069 TATATTAGAA
**
29079 TTAAATTAAATTTACTTACAACCAATTAACT
1 TTAAATTAAATTTACTTACAAAAAATTAACT
29110 TTAAATTAAATTTACTTACAAAAAATTAACT
1 TTAAATTAAATTTACTTACAAAAAATTAACT
29141 TT
1 TT
29143 GGATAAATGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (31 bp):
TTAAATTAAATTTACTTACAAAAAATTAACT
Found at i:31392 original size:45 final size:45
Alignment explanation
Indices: 31328--31453 Score: 243
Period size: 45 Copynumber: 2.8 Consensus size: 45
31318 AGCAACAATT
31328 AATATTAGCTTTATTTTGATGAATTATCTAGAGATGGAGAAGTAG
1 AATATTAGCTTTATTTTGATGAATTATCTAGAGATGGAGAAGTAG
31373 AATATTAGCTTTATTTTGATGAATTATCTAGAGATGGAGAAGTAG
1 AATATTAGCTTTATTTTGATGAATTATCTAGAGATGGAGAAGTAG
*
31418 AATATTAGCTTTATTTTGATGAATTACCTAGAGATG
1 AATATTAGCTTTATTTTGATGAATTATCTAGAGATG
31454 AAGTAGAATT
Statistics
Matches: 80, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
45 80 1.00
ACGTcount: A:0.35, C:0.06, G:0.21, T:0.39
Consensus pattern (45 bp):
AATATTAGCTTTATTTTGATGAATTATCTAGAGATGGAGAAGTAG
Found at i:31713 original size:25 final size:25
Alignment explanation
Indices: 31685--31733 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
31675 TTTTTAACTC
31685 ATTATTTA-TTATTTAAAATATATTT
1 ATTATTTATTTA-TTAAAATATATTT
*
31710 ATTATTTATTTATTAATATATATT
1 ATTATTTATTTATTAAAATATATT
31734 ACTTTTAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 19 0.86
26 3 0.14
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (25 bp):
ATTATTTATTTATTAAAATATATTT
Found at i:32099 original size:15 final size:15
Alignment explanation
Indices: 32079--32107 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
32069 TGACTTTGTC
32079 CATAATAATAATAAT
1 CATAATAATAATAAT
32094 CATAATAATAATAA
1 CATAATAATAATAA
32108 CGAGAGGGGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (15 bp):
CATAATAATAATAAT
Found at i:32544 original size:3 final size:3
Alignment explanation
Indices: 32538--32573 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
32528 TATAGTATAT
32538 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
32574 GTATTTAACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:32763 original size:15 final size:15
Alignment explanation
Indices: 32739--32772 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
32729 TACACGGTTA
* *
32739 ATAGTTTGCATAGTG
1 ATAGTATGCATAGTC
32754 ATAGTATGCATAGTC
1 ATAGTATGCATAGTC
32769 ATAG
1 ATAG
32773 CACGGCTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.32, C:0.09, G:0.24, T:0.35
Consensus pattern (15 bp):
ATAGTATGCATAGTC
Found at i:44127 original size:36 final size:36
Alignment explanation
Indices: 44080--44149 Score: 113
Period size: 36 Copynumber: 1.9 Consensus size: 36
44070 TTCAATAACC
* *
44080 TTACATCTTTTGTGATTTTGGTTATCATATTTCTTA
1 TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
*
44116 TTACATTTTTTGTAATTTTGATTATCATATTTCT
1 TTACATCTTTTGTAATTTTGATTATCATATTTCT
44150 CCAAAATCTC
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.21, C:0.10, G:0.09, T:0.60
Consensus pattern (36 bp):
TTACATCTTTTGTAATTTTGATTATCATATTTCTTA
Done.