Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010378.1 Corchorus capsularis cultivar CVL-1 contig10399, 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: 24131
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--36 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
37 ACAAAACTAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:15569 original size:638 final size:635
Alignment explanation
Indices: 13785--16909 Score: 3543
Period size: 638 Copynumber: 4.9 Consensus size: 635
13775 TTTTCCTCAA
* * * ** *
13785 TTTTTTGTCACAATATTCAGAAAAAATATATAATTCAACGCCAAAAGAA-TGAAGGGTTTTTCAT
1 TTTTTTG-CAAAATATTCATAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGCATTTCAC
* * *
13849 GCTTCTAATATCGTTTTTCCATTTTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATT
65 GCTTCTAATATCGGTTTTCCA--TTTTTTTT--GAATTAATTTCTAATTAAATCGAAATAAGATT
* * * * * * * *
13914 CAAATGCTCGTAAAAAGAAATCCTTAAATCCATTGTAGCTGAGATTTAGTT-AGATGAATATAGA
126 CAGATACTCGTAAAAACAAATCCTTATATCCAATCTGGCTGAGATTTGGTTCA-ATGAATATAGA
* * * * * *
13978 TATTTCAAGGAGTCTTTCTGC-C-AAAAATTATGTAAAACTGAGCCTGGAC-CCTGGTACGCGTT
190 TATTTCAAGGAGT-TTT-TGCACAAAAAATCATGCAAAATTGAGCCGGGTCTCC-GGAACGCGTT
* * * * * * * *
14040 TTTATCCAAAAACCGTGATGATTAGTACACGATTTAGCCTAAAAACTAACACGAAAAGTTTTTAC
252 TTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAATTGACCCGAAAAG-TTTTCC
* * * * * * *
14105 ATAATTTTTTTTG-TAAAATATTCATAAAAAATATATAATTCAACGCCAAAAAGATTGACA-GGC
316 TTAA--TTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAA-AATGA-AGGGG
* * ** * * * *
14168 ATTTCACGCTTATAATATCGTTTTTCCAATTTCTGAATTAATTTCTAATTAAATAGAAATAAGAT
377 TTTTCACGCTTCTAATATCGTTTTT--TTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGAT
* * * * * * * *
14233 TCAGATACTCATAAAAATAAATCCTTAAATCCAATCTGCCAGAAATTTGGTTCA-ATGAATATAG
440 TCAGATGCTCGTAAAAAGAAATCCTTAAAT-CATTGTGGCTGAGATTTGGTT-AGATGAATATAG
* * * * * * * * **
14297 AAATTTCAAGGAGT-TTTTTGCACAAAAAATCATGCAAAATTGAGCCGGGTCTCCGGAATGCGTT
503 ATATTTCAAGGAGTCTTTCT--ACCAAAAATCATGCAAAACTGAGCCTGGACCCCGGCACACGTT
* * * * * * * *
14361 TTTAGCCAAAAACCGTGATGGTTAGCACATGATTTCGGCTAAAAATTGACCCGAAAGGTTTTTCC
566 TTTAACCAAAAACCGTGATGATTAGTACACGATTTAGGCTAAAAACTGA-CCGAAAAGTTTTTAC
*
14426 TCA--T
630 ACATTT
* * * * * * **
14430 TTTTTCGCCACAATACTGAGAAAAAA-ATATAATTCAACACCAAAAAAA-TGAAGGGGTTTTCAC
1 TTTTTTG-CAAAATATTCATAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGCATTTCAC
* * * * * *
14493 GCTTCTAATATC-GTTTTTCATTTTTTTT--CTGAA----TAA-AAAATTGAAATAAGATT-AAA
65 GCTTCTAATATCGGTTTTCCATTTTTTTTGAATTAATTTCTAATTAAATCGAAATAAGATTCAGA
* ** *
14549 TACTTGTAAAAACAAATCCTTATATCCAATCTGGCTGAGATTTGGTTTGATGAATATAGAAATTT
130 TACTCGTAAAAACAAATCCTTATATCCAATCTGGCTGAGATTTGGTTCAATGAATATAGATATTT
* * *
14614 CAAGGAATTTTTGCACAAAAAATCATGCAAAATTGAGCCGGGTCTCTGGAACGCGTTTTTAGCGA
195 CAAGGAGTTTTTGCACAAAAAATCATGCAAAATTGAGCCGGGTCTCCGGAACGCGTTTTTAGCCA
* * * *
14679 AAAACCGTGAATGGTTAGAACACGATTTTGGCTAAAAATTGACCTGAAAAGTTTTTCCTCAATTT
260 AAAACCGTG-ATGGTTAGTACACGATTTCGGCTAAAAATTGACCCGAAAAG-TTTTCCTTAATTT
* * *
14744 TTTGCCACAATGCTAAGAAAAAATATATAATTCAACGCCAAAAAAATGAAGGGTTTTTCACGCTT
323 TTTGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATGAAGGGGTTTTCACGCTT
*
14809 CTAATATCCTCTTTCCAATTTTTTTTCCTGAATTTATTTCTAATTAAATCGAAACAAGATAT-AG
388 CTAATA---TCGTT----TTTTTTTTCC-GAATTTATTTCTAATTAAATCGAAACAAGAT-TCAG
* * *
14873 ATGCTCGTAAAAAGAAATCCTTAAATTCATTGTGACTGAGACTTGGTTAAATGAATATAGATATT
444 ATGCTCGTAAAAAGAAATCCTTAAA-TCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATT
* * *
14938 TCAAGGAGTCTTTCTATCAAAAATCATTCAAAACTGAGCCTGGACCCCGGCACACGTTTTTAACA
508 TCAAGGAGTCTTTCTACCAAAAATCATGCAAAACTGAGCCTGGACCCCGGCACACGTTTTTAACC
* * *
15003 AAAAACCGTGATAATTAGTACACGATTTAGGCTAAAAAAATGACTTGAAAAGTTTTTACACATTT
573 AAAAACCGTGATGATTAGTACACGATTTAGGCT-AAAAACTGAC-CGAAAAGTTTTTACACATTT
* *
15068 TTTTTTGCAAAATATTCATAAAAAATATATAATTCAACGCTAAAAAAATTGACGGGCATTTCACG
1 TTTTTTGCAAAATATTCATAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGCATTTCACG
* * *
15133 CTTATAATATCGGTTTACCATTTTTTTTGAATTAATTTCTAATTAAATCAAAATAAGATTCAGAT
66 CTTCTAATATCGGTTTTCCATTTTTTTTGAATTAATTTCTAATTAAATCGAAATAAGATTCAGAT
* * * * *
15198 ACTCGTAAAAACAAATCCTTATATCCAATCTGCCTAAGATTTGATTCAATGAATATATATATTCC
131 ACTCGTAAAAACAAATCCTTATATCCAATCTGGCTGAGATTTGGTTCAATGAATATAGATATTTC
* * * * *
15263 AATGAGTTTTTGCACAAAAAATCATGCAAAATTGAGCCGGCTCTCCGGAACACGTTTTTGGCTAA
196 AAGGAGTTTTTGCACAAAAAATCATGCAAAATTGAGCCGGGTCTCCGGAACGCGTTTTTAGCCAA
*
15328 AAACCGTGATGGTCAGTACACGATTTCGGCTAAAAATTGACCCGAAAAGTTTTCCTTAATTTTTT
261 AAACCGTGATGGTTAGTACACGATTTCGGCTAAAAATTGACCCGAAAAGTTTTCCTTAATTTTTT
*
15393 GCCACAATACTCAG-AAAAATATATAATTCAACGCCAAAAAAATGAAGGGTTTTTTCACGCTTCT
326 GCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATGAAGGG-GTTTTCACGCTTCT
* * *
15457 AATATCGTTTTTTTTTTCCGAAATTATTTCTGATTAAATCGAAACAAGATTCATATGCTCGTAAA
390 AATATCGTTTTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAA
* ** *
15522 AAGAAATCCTTAAATCAAATGTGGCTGATTTTTGGTTAGATGAATATAGATATTTCAAGGAGTAT
455 AAGAAATCCTTAAATC-ATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCT
* * * * * ** *
15587 TTCTGCAAAAAATCATGCACAACTAAGCCTGGACCCAGGCACGTGTTTTTGACCAAAAACCGTGA
519 TTCTACCAAAAATCATGCAAAACTGAGCCTGGACCCCGGCACACGTTTTTAACCAAAAACCGTGA
* *
15652 TGATTACTACACGATTTAGGCTAAAAACTGAACC-ACAAAGTTTTTACGCACTTT
584 TGATTAGTACACGATTTAGGCTAAAAACTG-ACCGA-AAAGTTTTTACACA-TTT
* * * *
15706 TTTTGTGCAAAATATTCATAAAAAATATATAATTCAATGCCAAAAAAATTGACGGGAATTTCACG
1 TTTTTTGCAAAATATTCATAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGCATTTCACG
* * * *
15771 CTTGTAATATCGATTTTCCATTTTTTCTGAATTAATTTTTAATTAAATCGAAATAAGATTCAGAT
66 CTTCTAATATCGGTTTTCCATTTTTTTTGAATTAATTTCTAATTAAATCGAAATAAGATTCAGAT
15836 ACTCGTAAAAACAAATCCTTATATCCAATCTGGCTGAGATTTGGTTCAATGAATATAGATATTTC
131 ACTCGTAAAAACAAATCCTTATATCCAATCTGGCTGAGATTTGGTTCAATGAATATAGATATTTC
* *
15901 AAGGAGTTTTTGCACAAAAAAATCATGCAAAATTGAGCTGGGTCTCCGGAACGCG--TTTAACCA
196 AAGGAGTTTTTGCAC-AAAAAATCATGCAAAATTGAGCCGGGTCTCCGGAACGCGTTTTTAGCCA
* *
15964 AAAATCGTGATGGTTAGTACACGATTTC-GCTAAAAATTGACCCGAAAAGTTTTCCTCAATTTTT
260 AAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAATTGACCCGAAAAGTTTTCCTTAATTTTT
* * *
16028 TGCCATAATACTCAGAAAAAATACATAATTCAACGCCAAAAAAATGAAGGGGTTTTCATGCTTCT
325 TGCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATGAAGGGGTTTTCACGCTTCT
* * * *
16093 AATAACGTTTTTTCATTTTTTTTCCCGATTTTACTTATAATTAAATCGAAACAAGATTCAGATGC
390 AATATCG----TT--TTTTTTTT-CCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGC
* * * * *
16158 TCAT-AAAAGAAATCCTTAAATTCATTGTGGCTGAGATTTGGTTAGATTAATAAAGACATTTCGA
448 TCGTAAAAAGAAATCCTTAAA-TCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAA
* * * * * * *
16222 GGAGTCTTTCTGCCAAAAATTATGCAAAACTGAGCTTGAAACCTGG--CACGTTTTTATCCAAAA
512 GGAGTCTTTCTACCAAAAATCATGCAAAACTGAGCCTGGACCCCGGCACACGTTTTTAACCAAAA
* * * * *
16285 ACCGTTATGATAAGTACACGATTTAGGTTAAAAACTAACACGAAAAGTTTTTGCACAATTT
577 ACCGTGATGATTAGTACACGATTTAGGCTAAAAACTGAC-CGAAAAGTTTTTACAC-ATTT
* * * *
16346 TGTTTTTGCAAAATATTCATAAAAAATTTATAATTCAACGCTAGAAAGATTGAAGGGCATTTCAC
1 T-TTTTTGCAAAATATTCATAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGCATTTCAC
* *
16411 GCTTTTAATATC-GTTTTCCATTTTTTCTGAATTAATTTCTAATTAAATCG----AAGATTCAGA
65 GCTTCTAATATCGGTTTTCCATTTTTTTTGAATTAATTTCTAATTAAATCGAAATAAGATTCAGA
* * * *
16471 TACTTGTAAAAACAAATCCTTATATCCAATCTGGCTGAGACTCGGTTCGATGAATATAGATATTT
130 TACTCGTAAAAACAAATCCTTATATCCAATCTGGCTGAGATTTGGTTCAATGAATATAGATATTT
* *
16536 CAAGGAGTTTTTGCACAAAAAATCATGCAAATTTGAGCCGGGTCTCCGAAACGCGTTTTTAGCCA
195 CAAGGAGTTTTTGCACAAAAAATCATGCAAAATTGAGCCGGGTCTCCGGAACGCGTTTTTAGCCA
* * * * *
16601 AAAACCGTGATGGTTAGTACACGATTTTGCCTAAAAATTGATCCGAAAATATTTTCATTAATTTT
260 AAAACCGTGATGGTTAGTACACGATTTCGGCTAAAAATTGACCCGAAAA-GTTTTCCTTAATTTT
* *
16666 TTGCCACAATACTAAGAAAAAAATATATAATTCAACACCAAAAAAAATGAAGGGGTTTTCACGCT
324 TTGCCACAATACTCAG-AAAAAATATATAATTCAACGCC-AAAAAAATGAAGGGGTTTTCACGCT
* *
16731 TCTAATATCGATTTTTTCATTTTTTTCTGAATTTATTTCTAATTAAATCGAAACAAGATTTAGAT
387 TCTAATATCG----TTT--TTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGAT
* *
16796 GCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGACTTGGTTAGATGAATATA-AGTATTT
446 GCTCGTAAAAAGAAATCCTTAAAT-CATTGTGGCTGAGATTTGGTTAGATGAATATAGA-TATTT
* * * *
16860 CAAGGAGTCTTTCTGCCAAAAATCATACAAAACTGAGCCCGGAACCCGGC
509 CAAGGAGTCTTTCTACCAAAAATCATGCAAAACTGAGCCTGGACCCCGGC
16910 CTCAACGCCA
Statistics
Matches: 2133, Mismatches: 281, Indels: 135
0.84 0.11 0.05
Matches are distributed among these distances:
629 4 0.00
630 32 0.02
631 143 0.07
632 56 0.03
633 7 0.00
635 108 0.05
636 266 0.12
637 146 0.07
638 414 0.19
639 98 0.05
640 174 0.08
641 211 0.10
642 98 0.05
643 50 0.02
644 45 0.02
645 57 0.03
646 48 0.02
647 51 0.02
648 125 0.06
ACGTcount: A:0.36, C:0.16, G:0.14, T:0.33
Consensus pattern (635 bp):
TTTTTTGCAAAATATTCATAAAAAATATATAATTCAACGCCAAAAAAATTGAAGGGCATTTCACG
CTTCTAATATCGGTTTTCCATTTTTTTTGAATTAATTTCTAATTAAATCGAAATAAGATTCAGAT
ACTCGTAAAAACAAATCCTTATATCCAATCTGGCTGAGATTTGGTTCAATGAATATAGATATTTC
AAGGAGTTTTTGCACAAAAAATCATGCAAAATTGAGCCGGGTCTCCGGAACGCGTTTTTAGCCAA
AAACCGTGATGGTTAGTACACGATTTCGGCTAAAAATTGACCCGAAAAGTTTTCCTTAATTTTTT
GCCACAATACTCAGAAAAAATATATAATTCAACGCCAAAAAAATGAAGGGGTTTTCACGCTTCTA
ATATCGTTTTTTTTTTCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
AGAAATCCTTAAATCATTGTGGCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTTT
CTACCAAAAATCATGCAAAACTGAGCCTGGACCCCGGCACACGTTTTTAACCAAAAACCGTGATG
ATTAGTACACGATTTAGGCTAAAAACTGACCGAAAAGTTTTTACACATTT
Found at i:17095 original size:212 final size:214
Alignment explanation
Indices: 16697--17102 Score: 545
Period size: 212 Copynumber: 1.9 Consensus size: 214
16687 AATATATAAT
* * * *
16697 TCAACACCAAAAAAAATGAAGGGGTTTTCACGCTTCTAATATCGATTTTTTCATTTTTTTCTGAA
1 TCAACACCAAAAAAAATGAACGGGTTTTCACGCTTATAATATCGAGTTTTCCATTTTTTTCTGAA
* * * * * *
16762 TTTATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCATTGT
66 TTAATTTCTAATTAAATCGAAACAAGATTCAAATACTCGTAAAAACAAATCCTTAAATCCAATCT
* * *
16827 GGCTGAGACTTGGTTAGATGAATATAAGTATTTCAAGGAGTCTTTCTGCCAAAAATCATACAAAA
131 CGCTGAGACTTGGTTAGATAAATATAAGTATTTCAAGGAGTCTTTCTGCAAAAAATCATACAAAA
16892 CTGAGCCCGGAACCCGGCC
196 CTGAGCCCGGAACCCGGCC
* *
16911 TCAACGCC-AAAAAAATTAACGGGTATTTCACGCTTATAATATCG-GTTTTCCATTTTTTT-TGA
1 TCAACACCAAAAAAAATGAACGGGT-TTTCACGCTTATAATATCGAGTTTTCCATTTTTTTCTGA
* *
16973 ATTAATTTCTAATTAAATCGAAATAAGATTCAAATACTCGTAAAAACAAATCCTTATATCCAATC
65 ATTAATTTCTAATTAAATCGAAACAAGATTCAAATACTCGTAAAAACAAATCCTTAAATCCAATC
* ** *
17038 TCGCTGAGATTTGGTTCTATAAATAT-AGATATTTCAAGGAGT-TTT-TGCATAAAAAATCATGC
130 TCGCTGAGACTTGGTTAGATAAATATAAG-TATTTCAAGGAGTCTTTCTGC--AAAAAATCATAC
17100 AAA
192 AAA
17103 TTTGAGCGGG
Statistics
Matches: 167, Mismatches: 21, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
210 3 0.02
211 5 0.03
212 107 0.64
213 27 0.16
214 25 0.15
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (214 bp):
TCAACACCAAAAAAAATGAACGGGTTTTCACGCTTATAATATCGAGTTTTCCATTTTTTTCTGAA
TTAATTTCTAATTAAATCGAAACAAGATTCAAATACTCGTAAAAACAAATCCTTAAATCCAATCT
CGCTGAGACTTGGTTAGATAAATATAAGTATTTCAAGGAGTCTTTCTGCAAAAAATCATACAAAA
CTGAGCCCGGAACCCGGCC
Found at i:17706 original size:323 final size:321
Alignment explanation
Indices: 16911--18646 Score: 2088
Period size: 323 Copynumber: 5.4 Consensus size: 321
16901 GAACCCGGCC
* * * * * *
16911 TCAACGCC-AAAAAAATTAACGGGTATTTCACGCTTATAATATCGGTTTTCCATTTTTTT-TGAA
1 TCAACACCAAAAAAAATGAAGGGGT-TTTCACGCTTCTAATATCGTTTTTTCATTTTTTTCTGAA
* * * * *
16974 TTAATTTCTAATTAAATCGAAATAAGATTCAAATACTCGTAAAAACAAATCCTTATATCCAATCT
65 TTTATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCATTCT
* * ** * *
17039 CGCTGAGATTTGGTTCTATAAATATAGATATTTCAAGGAGTTTTTGCATAAAAAATCATGCAAAT
130 GGCTGAGACTTGGTTAGATGAATATAGATATTTCAAGGAGTTTTTGCACAAAAAATCATGCAAAT
* * * * *
17104 TTGAGCGGGGTCTCCGAAATGCGTTTTTAGCCAAAAACCGTTATCGTTTGTAAACGATTTCGGCT
195 TTGAGCCGGGTCTCCGAAACGCGTTTTTAGCCAAAAACCGTGAT-GTTAGTACACGATTTCGGCT
* *
17169 AAAAATTGACACGAAAAGTTTTTCGTCAATTTTTTGCCACAATACTAAG-AAAAAATATATAATT
259 AAAAATTGAC-CGAAAAGTTTTTCGTTAATTTTTTGCCAAAATACTAAGAAAAAAATATATAA-T
* * * * *
17233 TC-ACACCAAATAAAATGAAGGGGTTTTCACGCTTCAAATATCGTTTTCTCATATTTTTCAGAAT
1 TCAACACCAAAAAAAATGAAGGGGTTTTCACGCTTCTAATATCGTTTTTTCATTTTTTTCTGAAT
*
17297 TTATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCATTATG
66 TTATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCATTCTG
*
17362 GCTGAGACGTGGTTAGATGAATATAGATATTTCAAGGAGTTTTTGCACAAAAAATCATGCAAATT
131 GCTGAGACTTGGTTAGATGAATATAGATATTTCAAGGAGTTTTTGCACAAAAAATCATGCAAATT
* *
17427 TGAGCCGGGTCTCCGAAACGCGTTTTTAGCCAAAAGCCGTGATAGTTAGTACACGATTTCGCCTA
196 TGAGCCGGGTCTCCGAAACGCGTTTTTAGCCAAAAACCGTGAT-GTTAGTACACGATTTCGGCTA
*
17492 AAAATTGATCCGAAAAGTTTTTCGTTAATTTTTTGCCACAATACTAAGAAAAAAATATATAAT
260 AAAATTGA-CCGAAAAGTTTTTCGTTAATTTTTTGCCAAAATACTAAGAAAAAAATATATAAT
17555 TCAACACCAAAAAAAATGAAGGGGTTTTCACGCTTCTAATATCGTTTTTTCATTTTTTTCTGAAT
1 TCAACACCAAAAAAAATGAAGGGGTTTTCACGCTTCTAATATCGTTTTTTCATTTTTTTCTGAAT
* * *
17620 TTATTTCTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTG
66 TTATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCATTCTG
17685 GCTGAGACTTGGTTAGATGAATATA-AGTATTTCAAGGAGTCTTTCTGC-C-AAAAATCATGCAA
131 GCTGAGACTTGGTTAGATGAATATAGA-TATTTCAAGGAGT-TTT-TGCACAAAAAATCATGCAA
** ** * * * * *
17747 ATTTGAGCCTGGAAC-CCGGCACGCGTTTTTAACCAAATACCGTAATGATTAGTACACAATTTAG
193 ATTTGAGCC-GGGTCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATG-TTAGTACACGATTTCG
* * * ** * * *
17811 GCTAAAAACTGACCTGAAAATTTTTTACACACTTTTTTTTTTG-CAAAATATTCA-TAAAAAATA
256 GCTAAAAATTGACC-GAAAAGTTTTT---C-GTTAATTTTTTGCCAAAATACTAAGAAAAAAATA
17874 TATAAT
316 TATAAT
*
17880 TCAACACC-AAAAAAATGAAGGGGTTTTCACGCTTCTAATATCGTTTATTCATTTTTTTTTCTGA
1 TCAACACCAAAAAAAATGAAGGGGTTTTCACGCTTCTAATATCGTTTTTTCA--TTTTTTTCTGA
* * *
17944 ATTTATTTCTAATTAAATCGAAACAAGATTTAGATACTCGTAAAAACAAATCTTTAAATCCATTG
64 ATTTATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCATTC
18009 TGGCTGAGACTTGGTTAGATGAATATA-AGTATTTCAAGGAGTCTTTCTGC-C-AAAAATCATGC
129 TGGCTGAGACTTGGTTAGATGAATATAGA-TATTTCAAGGAGT-TTT-TGCACAAAAAATCATGC
** * * * * *
18071 AAAACTGAGCCTGGAATCT-TG-CACGCGTTTTTAACCAAAAACCATGATGATTAGTACACGATT
191 AAATTTGAGCC-GG-GTCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATG-TTAGTACACGATT
** * * * * *
18134 TAAGCTAAAAA-TGACCTGAAAATTTTTTACACACTT-TTTTTTTTCGCAAAATA-T-TGATAAA
253 TCGGCTAAAAATTGACC-GAAAAGTTTTT---C-GTTAATTTTTTGC-CAAAATACTAAGA-AAA
18195 AAATATATAAT
311 AAATATATAAT
* * * * * * *
18206 TCAACAACAAAAAAAATTG-ACGGGTATTTCACACTTATAATATCGGTTTTCCA--ATTTT-TGA
1 TCAACACCAAAAAAAA-TGAAGGGGT-TTTCACGCTTCTAATATCGTTTTTTCATTTTTTTCTGA
* * * ** * * *
18267 ATTAATTTCTAATTAAATGGAAATAAGATTCAGATTTTTGTAAAAACAAATCCTTATATCCAATC
64 ATTTATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCATTC
* *
18332 TGGCTGAGA-TTCGGTTCGATGAATATAGATATTTCAAGGAGATTTTGCACAAAAAATCATGCAA
129 TGGCTGAGACTT-GGTTAGATGAATATAGATATTTCAAGGAGTTTTTGCACAAAAAATCATGCAA
*
18396 ATTTGAGCCGGGTCTCCGAAATGCGTTTTTAGCCAAAAACCGTGATG---GTACACGATTTCGGC
193 ATTTGAGCCGGGTCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGTTAGTACACGATTTCGGC
**
18458 TAAAAATTGACCCGAAAAGTTTTTCGGCAATTTTTTGCCAAAATACTAAGAAAAAAATATATAAT
258 TAAAAATTGA-CCGAAAAGTTTTTCGTTAATTTTTTGCCAAAATACTAAGAAAAAAATATATAAT
*
18523 TCAATACCAAAAAAAATGAAGGGGTTTTCACGCTTCTAATATCGTTTTTTCATTTTTTTCTGAAT
1 TCAACACCAAAAAAAATGAAGGGGTTTTCACGCTTCTAATATCGTTTTTTCATTTTTTTCTGAAT
* * * *
18588 ATATTTTTAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCC
66 TTATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCC
18647 TTAAACAAGA
Statistics
Matches: 1240, Mismatches: 133, Indels: 85
0.85 0.09 0.06
Matches are distributed among these distances:
316 32 0.03
317 42 0.03
318 6 0.00
319 73 0.06
320 13 0.01
321 40 0.03
322 254 0.20
323 387 0.31
324 61 0.05
325 51 0.04
326 233 0.19
327 24 0.02
328 24 0.02
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.34
Consensus pattern (321 bp):
TCAACACCAAAAAAAATGAAGGGGTTTTCACGCTTCTAATATCGTTTTTTCATTTTTTTCTGAAT
TTATTTCTAATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCATTCTG
GCTGAGACTTGGTTAGATGAATATAGATATTTCAAGGAGTTTTTGCACAAAAAATCATGCAAATT
TGAGCCGGGTCTCCGAAACGCGTTTTTAGCCAAAAACCGTGATGTTAGTACACGATTTCGGCTAA
AAATTGACCGAAAAGTTTTTCGTTAATTTTTTGCCAAAATACTAAGAAAAAAATATATAAT
Found at i:18277 original size:649 final size:638
Alignment explanation
Indices: 16919--18646 Score: 2183
Period size: 649 Copynumber: 2.7 Consensus size: 638
16909 CCTCAACGCC
*
16919 AAAAAAATTAACGGGTATTTCACGCTTATAATATCGGTTTTCCATTTTTTTTGAATTAATTTCTA
1 AAAAAAATTGACGGGTATTTCACGCTTATAATATCGGTTTTCCA-TTTTTTTGAATTAATTTCTA
* *
16984 ATTAAATCGAAATAAGATTCAAATACTCGTAAAAACAAATCCTTATATCCAATCTCGCTGAGATT
65 ATTAAATCGAAATAAGATTCAGATACTCGTAAAAACAAATCCTTATATCCAATCTGGCTGAGA-T
* * * *
17049 TGGTTCTATAAATATAGATATTTCAAGGAGTTTTTGCATAAAAAATCATGCAAATTTGAGCGGGG
129 TGGTTCGATGAATATAGATATTTCAAGGAGTTTTTGCA-CAAAAATCATGCAAATTTGAGCCGGG
* *
17114 TCTCCGAAATGCGTTTTTAGCCAAAAACCGTTATCG-TTTGTAAACGATTTCGGCTAAAAATTGA
193 TCTCCGAAATGCGTTTTTAGCCAAAAACCG-TAT-GATTAGTACACGATTTCGGCTAAAAATTGA
* * *
17178 CACGAAAAGTTTTTCGTCAATTTTTTGCCACAATACTAAGAAAAAATATATAATTTC-ACACCAA
256 C-CGAAAAGTTTTTCGACAATTTTTTGCCAAAATACTAAAAAAAAATATATAA-TTCAACACCAA
* * *
17242 ATAAAATGAAGGGGTTTTCACGCTTCAAATATCGTTTTCTCATATTTTTCAGAATTTATTTCTAA
319 A-AAAATGAAGGGGTTTTCACGCTTCTAATATCGTTTT-TCATTTTTTTCTGAATTTATTTCTAA
*
17307 TTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCATTATGGCTGAGACGT
382 TTAAATCGAAACAAGATTTAGATACTCGTAAAAACAAATCCTTAAATCCATTATGGCTGAGACGT
** *
17372 GGTTAGATGAATATAGATATTTCAAGGAGTTTTTGCACAAAAAATCATGCAAATTTGAGCCGGGT
447 GGTTAGATGAATATAGATATTTCAAGGAGTTTTTGCACAAAAAATCATGCAAAACTGAGCCGGAT
* * * *
17437 CTCCGAAACGCGTTTTTAGCCAAAAGCCGTGATAGTTAGTACACGATTTCGCCTAAAAATTGATC
512 CTCCGAAACGCGTTTTTAACCAAAAACCATGATAGTTAGTACACGATTTAGCCTAAAAATTGATC
* * *
17502 CGAAAAGTTTTTCGTTAATTTTTTGCCACAATACTAAGAAAAAAATATATAATTCAACACCA
577 CGAAAAGTTTTTCCTTAATTTTTTGCCAAAATACTAAGAAAAAAATATATAATTCAACAACA
* * * * *
17564 AAAAAAA-TGAAGGGGT-TTTCACGCTTCTAATATCGTTTTTTCATTTTTTTCTGAATTTATTTC
1 AAAAAAATTG-ACGGGTATTTCACGCTTATAATATCGGTTTTCCA-TTTTTT-TGAATTAATTTC
* * * * * *
17627 TAATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGA
63 TAATTAAATCGAAATAAGATTCAGATACTCGTAAAAACAAATCCTTATATCCAATCTGGCTGAGA
*
17692 CTTGGTTAGATGAATATA-AGTATTTCAAGGAGTCTTTCTGC-CAAAAATCATGCAAATTTGAGC
128 -TTGGTTCGATGAATATAGA-TATTTCAAGGAGT-TTT-TGCACAAAAATCATGCAAATTTGAGC
** ** * * * * *
17755 CTGGAAC-CCGGCACGCGTTTTTAACCAAATACCGTAATGATTAGTACACAATTTAGGCTAAAAA
189 C-GGGTCTCCGAAATGCGTTTTTAGCCAAAAACCGT-ATGATTAGTACACGATTTCGGCTAAAAA
* * * * * *
17819 CTGACCTGAAAATTTTTTAC-ACACTTTTTTTTTTG-CAAAATATTCATAAAAAATATATAATTC
252 TTGACC-GAAAAGTTTTT-CGACA----ATTTTTTGCCAAAATACTAAAAAAAAATATATAATTC
17882 AACACCAAAAAAATGAAGGGGTTTTCACGCTTCTAATATCGTTTATTCATTTTTTTTTCTGAATT
311 AACACCAAAAAAATGAAGGGGTTTTCACGCTTCTAATATCGTTT-TTCA--TTTTTTTCTGAATT
* *
17947 TATTTCTAATTAAATCGAAACAAGATTTAGATACTCGTAAAAACAAATCTTTAAATCCATTGTGG
373 TATTTCTAATTAAATCGAAACAAGATTTAGATACTCGTAAAAACAAATCCTTAAATCCATTATGG
*
18012 CTGAGACTTGGTTAGATGAATATA-AGTATTTCAAGGAGTCTTTCTGC-C-AAAAATCATGCAAA
438 CTGAGACGTGGTTAGATGAATATAGA-TATTTCAAGGAGT-TTT-TGCACAAAAAATCATGCAAA
* *
18074 ACTGAGCCTGGAATCT-TG-CACGCGTTTTTAACCAAAAACCATGAT-GATTAGTACACGATTTA
500 ACTGAGCC-GG-ATCTCCGAAACGCGTTTTTAACCAAAAACCATGATAG-TTAGTACACGATTT-
* * * *
18136 AG-CTAAAAA-TGA-CCTGAAAATTTTTTACACACTT-TTTTTTTTCGCAAAATA-T-TGATAAA
561 AGCCTAAAAATTGATCC-GAAAAGTTTTT---C-CTTAATTTTTTGC-CAAAATACTAAGA-AAA
18195 AAATATATAATTCAACAACA
619 AAATATATAATTCAACAACA
* *
18215 AAAAAAATTGACGGGTATTTCACACTTATAATATCGGTTTTCCA-ATTTTTGAATTAATTTCTAA
1 AAAAAAATTGACGGGTATTTCACGCTTATAATATCGGTTTTCCATTTTTTTGAATTAATTTCTAA
* ** *
18279 TTAAATGGAAATAAGATTCAGATTTTTGTAAAAACAAATCCTTATATCCAATCTGGCTGAGATTC
66 TTAAATCGAAATAAGATTCAGATACTCGTAAAAACAAATCCTTATATCCAATCTGGCTGAGATT-
*
18344 GGTTCGATGAATATAGATATTTCAAGGAGATTTTGCACAAAAAATCATGCAAATTTGAGCCGGGT
130 GGTTCGATGAATATAGATATTTCAAGGAGTTTTTGCAC-AAAAATCATGCAAATTTGAGCCGGGT
*
18409 CTCCGAAATGCGTTTTTAGCCAAAAACCG--TGA-TGGTACACGATTTCGGCTAAAAATTGACCC
194 CTCCGAAATGCGTTTTTAGCCAAAAACCGTATGATTAGTACACGATTTCGGCTAAAAATTGA-CC
* *
18471 GAAAAGTTTTTCGGCAATTTTTTGCCAAAATACTAAGAAAAAAATATATAATTCAATACCAAAAA
258 GAAAAGTTTTTCGACAATTTTTTGCCAAAATACTAA-AAAAAAATATATAATTCAACACC-AAAA
* *
18536 AAATGAAGGGGTTTTCACGCTTCTAATATCGTTTTTTCATTTTTTTCTGAATATATTTTTAATTA
321 AAATGAAGGGGTTTTCACGCTTCTAATATCG-TTTTTCATTTTTTTCTGAATTTATTTCTAATTA
*
18601 AATCGAAACAAGATTTAGATGCTCGTAAAAACAAATCCTTAAATCC
385 AATCGAAACAAGATTTAGATACTCGTAAAAACAAATCCTTAAATCC
18647 TTAAACAAGA
Statistics
Matches: 936, Mismatches: 102, Indels: 93
0.83 0.09 0.08
Matches are distributed among these distances:
641 7 0.01
642 77 0.08
643 21 0.02
644 76 0.08
645 226 0.24
646 12 0.01
647 48 0.05
648 54 0.06
649 318 0.34
650 15 0.02
651 49 0.05
652 33 0.04
ACGTcount: A:0.37, C:0.16, G:0.14, T:0.34
Consensus pattern (638 bp):
AAAAAAATTGACGGGTATTTCACGCTTATAATATCGGTTTTCCATTTTTTTGAATTAATTTCTAA
TTAAATCGAAATAAGATTCAGATACTCGTAAAAACAAATCCTTATATCCAATCTGGCTGAGATTG
GTTCGATGAATATAGATATTTCAAGGAGTTTTTGCACAAAAATCATGCAAATTTGAGCCGGGTCT
CCGAAATGCGTTTTTAGCCAAAAACCGTATGATTAGTACACGATTTCGGCTAAAAATTGACCGAA
AAGTTTTTCGACAATTTTTTGCCAAAATACTAAAAAAAAATATATAATTCAACACCAAAAAAATG
AAGGGGTTTTCACGCTTCTAATATCGTTTTTCATTTTTTTCTGAATTTATTTCTAATTAAATCGA
AACAAGATTTAGATACTCGTAAAAACAAATCCTTAAATCCATTATGGCTGAGACGTGGTTAGATG
AATATAGATATTTCAAGGAGTTTTTGCACAAAAAATCATGCAAAACTGAGCCGGATCTCCGAAAC
GCGTTTTTAACCAAAAACCATGATAGTTAGTACACGATTTAGCCTAAAAATTGATCCGAAAAGTT
TTTCCTTAATTTTTTGCCAAAATACTAAGAAAAAAATATATAATTCAACAACA
Found at i:19192 original size:3 final size:3
Alignment explanation
Indices: 19180--19226 Score: 64
Period size: 3 Copynumber: 16.7 Consensus size: 3
19170 ACCCATATTA
*
19180 TCT T-T TCT TCT TC- TCT T-T TCT TCT TTT TCT TCT TCT TCT TCT TCT
1 TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT TCT
19225 TC
1 TC
19227 GCCACTTCAA
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
2 6 0.15
3 33 0.85
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (3 bp):
TCT
Found at i:21604 original size:325 final size:323
Alignment explanation
Indices: 20930--22740 Score: 1161
Period size: 325 Copynumber: 5.5 Consensus size: 323
20920 TTAGTCAAAT
* *
20930 AAGATTCAGATTCTCGTAAAAACAAATCCTTATATCCAATCTGGCTGAGA-TTCGGTTCA-ATGA
1 AAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATCTGGCTGAGACTT-GGTT-AGATGA
* * **
20993 ATAT-AGATATTTCAAGGAGTTTTTGCA-CAAAAAATCATGCAAATTTGAGTCGGGTCTCCGG-A
64 ATATAAGATATTTCAAGGAGTCTTTGCAGCAAAAAATCATGCAAAATTGAGTCGGAACTCCGGCA
* * * * *
21055 ACGCGTTTTTAGCCAAAAAACCGTGAAGGTTAGTACATGATTTCGGCTAAAAA-TTGA-TCCGAA
129 A-GCGTTTTTAACC-AAAAACCGTGATGATTAGTACACGATTTAGGCTAAAAACTT-ACT-CGAA
* * * *
21118 AAGTTTTT-CCTC-AA-TTTTTTGCAACAATACTCATAAAAATATATAACTCAACGCCAAAAAAA
190 AAGTTTTTACCACTAATTTTTTTGCAA-AATATTCAAAAAAATATATAATTCAACGCCAAAAAAA
* **
21180 T-AATGGGTTTTTCACGCTTCTAATTTCGTTTTTCCATTTTTTCCGAATTTATTTCTAATTAAAT
254 TGAA-GGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTTGAATTTATTTCTAATTAAAT
*
21244 TGAAAC
318 CGAAAC
* ** * * *
21250 AAGATTCAGATGCTCGTAAAATGAAATCCTTAAATCTATTTTGGCTGAGACTTGGTTAGATGAAT
1 AAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATCTGGCTGAGACTTGGTTAGATGAAT
* * * *
21315 ATAAG-TATTTCAAGGAGTCTTT-CAGCCAAAAATCATGCAAAACTGAGCCTGCAAC-CCGGCAA
66 ATAAGATATTTCAAGGAGTCTTTGCAGCAAAAAATCATGCAAAATTGAGTC-GGAACTCCGGCAA
* *
21377 GCGTTTTTAACCAAAAACCGTGATGATTAGTACACGATTTAGGCTTTAAAAACTTACTTGAAAAT
130 GCGTTTTTAACCAAAAACCGTGATGATTAGTACACGATTTAGGC--TAAAAACTTACTCGAAAAG
** *
21442 TTTTTACACACTTTTTTTTTTGCAAAATATTCACAAAAATATATAATTCAACGCCAAAAAAATTG
193 TTTTTAC-CACTAATTTTTTTGCAAAATATTCAAAAAAATATATAATTCAACGCCAAAAAAA-TG
* ** * * *
21507 ACGGGAATTTCACGCTTATAATATCGGTTTTCCATTTTTTTTGAATTAATTTCTAATTAAATCGA
256 AAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTTGAATTTATTTCTAATTAAATCGA
*
21572 AAT
321 AAC
* * * * **
21575 AAGATTCAAATACTCGTAAATACAAATCCTTATATCCAATCTGGCTGAGATTTGGTTCTATGAAT
1 AAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATCTGGCTGAGACTTGGTTAGATGAAT
* * **
21640 ATAA-ATATTTCAAGGAGTTTTTGCA-CAAAAAATCATGCAAATTTGAGTCGGGTCTCCGG-AAC
66 ATAAGATATTTCAAGGAGTCTTTGCAGCAAAAAATCATGCAAAATTGAGTCGGAACTCCGGCAA-
** * * * * *
21702 GCGTTTTTAGCAAAAAAAAACCGTGATGGTTAGTACACGATTTCGGCT-AATAGTTGACCCGAAA
130 GCGTTTTT---AACCAAAAACCGTGATGATTAGTACACGATTTAGGCTAAAAACTT-ACTCGAAA
* * * * *
21766 AGTTTTT-CCTC-AA-TTTTTTGCCACAGTACTCAGAAAAAATATATAATTCAACGCCGAAAAAA
191 AGTTTTTACCACTAATTTTTTTG-CAAAATATTCA-AAAAAATATATAATTCAACGCCAAAAAAA
* * *
21828 TGAATGGTTTTTCACGCTTCTAATTTCGTTTTTCCATTTCTTTTCCGAATTTATTTCTAATTAAA
254 TGAAGGGTTTTTCACGCTTCTAATATCGTTTTTCCATTT-TTTT-TGAATTTATTTCTAATTAAA
21893 TCGAAAC
317 TCGAAAC
* * * * *
21900 AGGATTCAGATACTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGACATGGTTAGATAAAT
1 AAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATCTGGCTGAGACTTGGTTAGATGAAT
* * * * **
21965 AT-AGATATTTCAATGAGTC-TTACTGCCAAAAATCATAG-ATATTTCAA-TGAGTC-TTACTGC
66 ATAAGATATTTCAAGGAGTCTTTGCAGCAAAAAATCAT-GCA-A----AATTGAGTCGGAACT-C
*** * * **** ** ** ** * ** ** * * *
22025 CAAAAATCATGCAAAACTGAGGCTGGATCCCGACATGCGTTTTTAGCCAAAAACCGTGATGGTTA
124 CGGCAAGCGTTTTTAAC-----C-AAAAACCGTGATG-ATTAGTA--C-ACGA--TTTA-GGCTA
* * * * * * * * ** * **** *
22090 GTACACGATTTCTGCTAAAA--ATTGACC-CGAAAATTTTTTCGTCAATTTTTTTGCCACAATAC
176 -AAAAC--TTACT-CGAAAAGTTTTTACCAC--TAATTTTTTTG-CAAAATATTCAAAAAAATA-
* ** **** *** **** ****** *
22152 TCAGAA-AAAATATTTAATTCAATGCCAAAAAATGAAGGGGTTTTCACGCATCTAATATCGTTTT
233 T-ATAATTCAA-CGCCAAAAAAATG--AAGGGTTTTTCACG--CT------TCTAATATCGTTTT
22216 TCCATTTTTTTTGAATTTATTTCTAATTAAATCGAAAC
286 TCCATTTTTTTTGAATTTATTTCTAATTAAATCGAAAC
* * * *
22254 AAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCATTGTGGTTGAGACTTGGTGAGATGAAT
1 AAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATCTGGCTGAGACTTGGTTAGATGAAT
** * *
22319 ATAAG-TATTTCAAGGAGTCTTT-TTGCCAAAAATCATGCAAAACTGAG-CATGGAAC-CCGGCA
66 ATAAGATATTTCAAGGAGTCTTTGCAGCAAAAAATCATGCAAAATTGAGTC--GGAACTCCGGCA
* * * * *
22380 CGCATTTTTAACCAAAAACCGTGATCATTAGTACACGAGTTAGGCTAAAAACTGAAC-CGAAAAG
129 AGCGTTTTTAACCAAAAACCGTGATGATTAGTACACGATTTAGGCTAAAAACT-TACTCGAAAAG
* *
22444 TCTTTA-CAC-AATTTTTTATGCAAAATATTCATAAAAAATATATAATTCAACGCCAAAAAGATT
193 TTTTTACCACTAATTTTTT-TGCAAAATATTCA-AAAAAATATATAATTCAACGCCAAAAA-AAT
* ** * * *
22507 GACGGGCATTTCACGC-TCATAATATCGGTTTTCCA-TTTTTTTGAATTAATTTCTAATTAAATG
255 GAAGGGTTTTTCACGCTTC-TAATATCGTTTTTCCATTTTTTTTGAATTTATTTCTAATTAAATC
*
22570 GAAAT
319 GAAAC
* * * *
22575 AAGATTCAGATTCTCGTAAAAACAAATCCTTATATCCAATCTGGCTGAGATTTGGTTCGATGAAT
1 AAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATCTGGCTGAGACTTGGTTAGATGAAT
* * **
22640 A-AAGATATTTCAAGGAGT-TTTCCAG-AAAAAATCATGCAAAATTGAGTCGGATCTCCGAAACA
66 ATAAGATATTTCAAGGAGTCTTTGCAGCAAAAAATCATGCAAAATTGAGTCGGAACTCCGGCA-A
* *
22702 CCGTTTTTAACCAAAAACTGTGATTG-TTAGTACACGATT
130 GCGTTTTTAACCAAAAACCGTGA-TGATTAGTACACGATT
22741 CCGCTAAAAA
Statistics
Matches: 1124, Mismatches: 271, Indels: 191
0.71 0.17 0.12
Matches are distributed among these distances:
319 35 0.03
320 135 0.12
321 162 0.14
322 27 0.02
323 42 0.04
324 75 0.07
325 282 0.25
326 20 0.02
328 34 0.03
329 10 0.01
330 5 0.00
331 5 0.00
332 27 0.02
333 16 0.01
334 2 0.00
335 6 0.01
336 5 0.00
337 4 0.00
338 4 0.00
339 3 0.00
340 2 0.00
341 6 0.01
342 3 0.00
343 11 0.01
344 13 0.01
345 14 0.01
346 8 0.01
348 4 0.00
349 3 0.00
350 14 0.01
352 2 0.00
353 2 0.00
354 115 0.10
355 8 0.01
356 20 0.02
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (323 bp):
AAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCAATCTGGCTGAGACTTGGTTAGATGAAT
ATAAGATATTTCAAGGAGTCTTTGCAGCAAAAAATCATGCAAAATTGAGTCGGAACTCCGGCAAG
CGTTTTTAACCAAAAACCGTGATGATTAGTACACGATTTAGGCTAAAAACTTACTCGAAAAGTTT
TTACCACTAATTTTTTTGCAAAATATTCAAAAAAATATATAATTCAACGCCAAAAAAATGAAGGG
TTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTTTGAATTTATTTCTAATTAAATCGAAAC
Found at i:22008 original size:34 final size:34
Alignment explanation
Indices: 21961--22034 Score: 141
Period size: 34 Copynumber: 2.2 Consensus size: 34
21951 ATGGTTAGAT
21961 AAAT-ATAGATATTTCAATGAGTCTTACTGCCAA
1 AAATCATAGATATTTCAATGAGTCTTACTGCCAA
21994 AAATCATAGATATTTCAATGAGTCTTACTGCCAA
1 AAATCATAGATATTTCAATGAGTCTTACTGCCAA
22028 AAATCAT
1 AAATCAT
22035 GCAAAACTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 4 0.10
34 36 0.90
ACGTcount: A:0.41, C:0.16, G:0.11, T:0.32
Consensus pattern (34 bp):
AAATCATAGATATTTCAATGAGTCTTACTGCCAA
Found at i:22715 original size:321 final size:318
Alignment explanation
Indices: 22004--22738 Score: 874
Period size: 320 Copynumber: 2.3 Consensus size: 318
21994 AAATCATAGA
* * * * *
22004 TATTTCAATGAGTCTTACTGCCAAAAATCATGCAAAACTGAGGCTGGATCCCGACATGCGTTTTT
1 TATTTCAAGGAGTCTTTCAGCAAAAAATCATGCAAAACTGA-GCTGGATCCCGACA-CCGTTTTT
* * * ** * * * * *
22069 AGCCAAAAACCGTGATGGTTAGTACACGATTTCTGCTAAAAATTGACCCGAAAATTTTTTCGTCA
64 AACCAAAAACCGTGATCGTTAGTACACGAGTTAGGCTAAAAACTGAACCGAAAATCTTTACGACA
* * * **
22134 ATTTTTTTGCCACAATACTCAGAAAAAATATTTAATTCAATGCCAAAAAATGAAGGGGTTTTCAC
129 ATTTTTTTGCCAAAATACTCAGAAAAAATATATAATTCAACGCCAAAAAATGAAGGGCATTTCAC
* *
22199 GCATCTAATATCGTTTTTCCATTTTTTTTGAATTTATTTCTAATTAAATCGAAACAAGATTCAGA
194 GCATCTAATATCGGTTTTCCATTTTTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGA
* * *
22264 TACTCGTAAAAACAAATCCTTAAATCCATTGTGGTTGAGACTTGGTGAGATGAATATAAG
259 TACTCGTAAAAACAAATCCTTAAATCCAATCTGGCTGAGACTTGGTGAGATGAATATAAG
** * * * *
22324 TATTTCAAGGAGTCTTTTTGCCAAAAATCATGCAAAACTGAGCATGGAACCCGGCACGCATTTTT
1 TATTTCAAGGAGTCTTTCAGCAAAAAATCATGCAAAACTGAGC-TGGATCCCGACAC-CGTTTTT
*
22389 AACCAAAAACCGTGATCATTAGTACACGAGTTAGGCTAAAAACTGAACCGAAAAGTCTTTAC-AC
64 AACCAAAAACCGTGATCGTTAGTACACGAGTTAGGCTAAAAACTGAACCGAAAA-TCTTTACGAC
* * *
22453 AATTTTTTATG-CAAAATATTCATAAAAAATATATAATTCAACGCCAAAAAGATTGACGGGCATT
128 AATTTTTT-TGCCAAAATACTCAGAAAAAATATATAATTCAACGCCAAAAA-A-TGAAGGGCATT
* *
22517 TCACGC-TCATAATATCGGTTTTCCA-TTTTTTTGAATTAATTTCTAATTAAATGGAAATAAGAT
190 TCACGCATC-TAATATCGGTTTTCCATTTTTTTTGAATTAATTTCTAATTAAATCGAAACAAGAT
* * * **
22580 TCAGATTCTCGTAAAAACAAATCCTTATATCCAATCTGGCTGAGATTTGGTTCGATGAATA-AAG
254 TCAGATACTCGTAAAAACAAATCCTTAAATCCAATCTGGCTGAGACTTGGTGAGATGAATATAAG
*
22644 ATATTTCAAGGAGT-TTTCCAG-AAAAAATCATGCAAAATTGAG-TCGGATCTCCGAAACACCGT
1 -TATTTCAAGGAGTCTTT-CAGCAAAAAATCATGCAAAACTGAGCT-GGATC-CCG--ACACCGT
* *
22706 TTTTAACCAAAAACTGTGATTGTTAGTACACGA
60 TTTTAACCAAAAACCGTGATCGTTAGTACACGA
22739 TTCCGCTAAA
Statistics
Matches: 354, Mismatches: 48, Indels: 25
0.83 0.11 0.06
Matches are distributed among these distances:
318 1 0.00
319 6 0.02
320 171 0.48
321 144 0.41
322 32 0.09
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (318 bp):
TATTTCAAGGAGTCTTTCAGCAAAAAATCATGCAAAACTGAGCTGGATCCCGACACCGTTTTTAA
CCAAAAACCGTGATCGTTAGTACACGAGTTAGGCTAAAAACTGAACCGAAAATCTTTACGACAAT
TTTTTTGCCAAAATACTCAGAAAAAATATATAATTCAACGCCAAAAAATGAAGGGCATTTCACGC
ATCTAATATCGGTTTTCCATTTTTTTTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATA
CTCGTAAAAACAAATCCTTAAATCCAATCTGGCTGAGACTTGGTGAGATGAATATAAG
Found at i:22998 original size:249 final size:247
Alignment explanation
Indices: 22535--22999 Score: 614
Period size: 249 Copynumber: 1.9 Consensus size: 247
22525 ATAATATCGG
* * * * *
22535 TTTTCCATTTTTTTGAATTAATTTCTAATTAAATGGAAATAAGATTCAGATTCTCGTAAAAACAA
1 TTTTCCATTTTTTTAAATTAATTTATAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
* * * *
22600 ATCCTTATATCCAATCTGGCTGAGATTTGGTTCGATGAATAAAGATATTTCAAGGAGTTTTCCAG
66 ATCCTTAAATCCAATCTCGCTGAGATTTGGTTAGATAAATAAAGATATTTCAAGGAGTTTTCCAG
* * * * *
22665 AAAAAATCATGCAAAATTGAGTCGGATCTCCGAAACACCGTTTTTAACCAAAAACTGTGATTGTT
131 AAAAAATAATGCAAAACTGAGCCGGATCTCCG-AACACCGTTTTCAACCAAAAACCGTGATTGTT
* *
22730 AGTACACGATTCCGCTAAAAAAAATGAAGGGGTTTTCACGCTTCTAATTTCAC
195 AGCACACGATTCAGCTAAAAAAAATGAAGGGGTTTTCACGCTTCTAATTTCAC
* *
22783 TTTTCCATTTTTTCTAAATTTATTTATAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAAGA
1 TTTTCCATTTTTT-TAAATTAATTTATAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACA
* * * *
22848 AATCCTTAAATCCAGTGTCGCTGATATTTGGTTAGATAAATATAGATATTTCAAGGAGTCTTT-C
65 AATCCTTAAATCCAATCTCGCTGAGATTTGGTTAGATAAATAAAGATATTTCAAGGAGT-TTTCC
* *
22912 AGCCAAAAATAATGCAAAACTGAGCCTGGATC-CCG-GCACGCGTTTTCAACCAAAAACCGTGA-
129 AG-AAAAAATAATGCAAAACTGAGCC-GGATCTCCGAACAC-CGTTTTCAACCAAAAACCGTGAT
*
22974 TGATTAGCACACGATTTAGCTAAAAA
191 TG-TTAGCACACGATTCAGCTAAAAA
23000 CTGACCTGAA
Statistics
Matches: 186, Mismatches: 25, Indels: 11
0.84 0.11 0.05
Matches are distributed among these distances:
248 18 0.10
249 138 0.74
250 25 0.13
251 5 0.03
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (247 bp):
TTTTCCATTTTTTTAAATTAATTTATAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAA
ATCCTTAAATCCAATCTCGCTGAGATTTGGTTAGATAAATAAAGATATTTCAAGGAGTTTTCCAG
AAAAAATAATGCAAAACTGAGCCGGATCTCCGAACACCGTTTTCAACCAAAAACCGTGATTGTTA
GCACACGATTCAGCTAAAAAAAATGAAGGGGTTTTCACGCTTCTAATTTCAC
Found at i:23884 original size:319 final size:318
Alignment explanation
Indices: 22747--24131 Score: 1613
Period size: 319 Copynumber: 4.3 Consensus size: 318
22737 GATTCCGCTA
* ** *
22747 AAAAAAATGAAGGGGTTTTCACGCTTCTAATTTCACTTTTCCATTTTTTCTAAATTTATTTATAA
1 AAAAAAATGAAGGGGTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCTAAATTTATTTCTAA
* * * * * *
22812 TTAAATCGAAACAAGATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCAGTGTCGCTGATATTT
66 TTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGACTT
* * * *
22877 GGTTAGATAAATATAGATATTTCAAGGAGTCTTTCAGCCAAAAATAATGCAAAACTGAGCCTGGA
131 GGTGAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCTGGA
* * * * *
22942 TCCCGGCACGCGTTTTCAACCAAAAACCGTGATGATTAGCACACGATTTAGCTAAAAACTGACCT
196 CCCCGACACGCGTTTTTAACCAAAAACCGTGATGATTAGTACACGATTTAGCTAAAAACTGACCC
* * * * * *
23007 GAAAACTTTTTACACACTTTTATTCTTGCAAAATATTCA-TAAAAATATATTATTCGACACC
261 GAAAAGTTTTT-CTCA-ATTT-TT-TTGCAAAATATTCAGAAAAAATATATAATTCAACACC
* ** *
23068 AAAAAAATTGACGGGCATTTCACGCTTATAATATCGGTTTTT-CATTTTTTTTCT-AATTTAATT
1 AAAAAAA-TGAAGGGGTTTTCACGCTTCTAATATC-GTTTTTCCA--TTTTTTCTAAATTT-ATT
* * * * *
23131 TCTAATTAAATCGAAAAAAAGATTCAGATACTCATAAAAACAAATCCTTATATCCAATCTGGCTG
61 TCTAATTAAATCG-AAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCATTGTGGCTG
** ** * **
23196 AGA-TTCATTTCGAAGAATATAGATATTTCAAGGAGT-TTT-TGCACAAAAAATCATGCAAATTT
125 AGACTT-GGTGAGATGAATATAGATATTTCAAGGAGTCTTTCTGC-C-AAAAATCATGCAAAACT
* * * * * * * *
23258 GAGCCAGGTCTCCGAAACGCATTTTTAGCCCAAAACCGTGATGGTTAGTACACGATTTCAGCTAA
187 GAGCCTGGACCCCGACACGCGTTTTTAACCAAAAACCGTGATGATTAGTACACGATTT-AGCTAA
* * *
23323 AAATTGACCCGAAAAGTTTTTCCTCAA-TTTTTTGTCACAATAATCAAGAAAAAAATATATAATT
251 AAACTGACCCGAAAAGTTTTT-CTCAATTTTTTTG-CAAAATATTC-AG-AAAAAATATATAATT
23387 CAACACC
312 CAACACC
* *
23394 AAAAAAATGAAGGGGTTTTCACGCTTCTAATATCGTTTTTTCATTTTTTTCTGAATTTATTTCTA
1 AAAAAAATGAAGGGGTTTTCACGCTTCTAATATCGTTTTTCCA-TTTTTTCTAAATTTATTTCTA
* * *
23459 ATTAAATCGAAACCAGATTCAGATGCTCGTAAAAAGAAATCCTTAAATCCATTGTGGCTGAGACT
65 ATTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGACT
* *
23524 TGGTTAGATGAATATAGATATTTCAAGGAGTCTTACTGCCAAAAATCATGCAAAACTGAGCCTGG
130 TGGTGAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCTGG
* * * * *
23589 ACCCCGACACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTATACGATTTCAGCTAAAAATTGTC
195 ACCCCGACACGCGTTTTTAACCAAAAACCGTGATGATTAGTACACGATTT-AGCTAAAAACTGAC
* * *
23654 CCGAAAAGTTTTTCGTCAATTTTTTTGCCACAATACTCAGAAAAAATATATAATTCAACGCC
259 CCGAAAAGTTTTTC-TCAATTTTTTTG-CAAAATATTCAGAAAAAATATATAATTCAACACC
*
23716 AAAAAAATGAAGGGGTTTTCACTCTTCTAATATCGTTTTTCCATTTTTT-T-AATTTATTTCTAA
1 AAAAAAATGAAGGGGTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCTAAATTTATTTCTAA
* *
23779 TTAAATCGAAATAAGATTCAGATACTCGTAAAAACAAATCTTTAAATCCATTGTGGCTGAGACTT
66 TTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGACTT
* *
23844 GGAGAGATGAATATCAG-TATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTAAGCCTGG
131 GGTGAGATGAATAT-AGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCTGG
**** * * *
23908 AATTTGGCACGCGTTTTTAACCAAAAACCATGATGATTAGTACACGATTTAGACTAAAAACTGAA
195 ACCCCGACACGCGTTTTTAACCAAAAACCGTGATGATTAGTACACGATTTAG-CTAAAAACTGAC
* * * *
23973 CCGAAAAGTCTTTATACAATTTTTTTTGCAAAATATTCATAAAAAATATATAATTCAACGCC
259 CCGAAAAGTTTTTCT-CAA-TTTTTTTGCAAAATATTCAGAAAAAATATATAATTCAACACC
* * ** * *
24035 AAAAAGATTGACGGGCATTTCACGC-TCATAATATCGGTTTTCCATTTTTTCTAAATTAATTTCT
1 AAAAA-AATGAAGGGGTTTTCACGCTTC-TAATATCGTTTTTCCATTTTTTCTAAATTTATTTCT
* * *
24099 AATTAAATGGAAATAAGATTCAGATTCTCGTAA
64 AATTAAATCGAAACAAGATTCAGATACTCGTAA
Statistics
Matches: 919, Mismatches: 116, Indels: 57
0.84 0.11 0.05
Matches are distributed among these distances:
318 3 0.00
319 233 0.25
320 46 0.05
321 14 0.02
322 131 0.14
323 192 0.21
324 84 0.09
325 163 0.18
326 53 0.06
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (318 bp):
AAAAAAATGAAGGGGTTTTCACGCTTCTAATATCGTTTTTCCATTTTTTCTAAATTTATTTCTAA
TTAAATCGAAACAAGATTCAGATACTCGTAAAAACAAATCCTTAAATCCATTGTGGCTGAGACTT
GGTGAGATGAATATAGATATTTCAAGGAGTCTTTCTGCCAAAAATCATGCAAAACTGAGCCTGGA
CCCCGACACGCGTTTTTAACCAAAAACCGTGATGATTAGTACACGATTTAGCTAAAAACTGACCC
GAAAAGTTTTTCTCAATTTTTTTGCAAAATATTCAGAAAAAATATATAATTCAACACC
Done.