Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr2
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: 61750188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1877335 characters in sequence are not A, C, G, or T
File 11 of 186
Found at i:3335431 original size:263 final size:263
Alignment explanation
Indices: 3334979--3335464 Score: 607
Period size: 263 Copynumber: 1.8 Consensus size: 263
3334969 ACAACGAAAG
* * * * * * * * *
3334979 AAAATTGATTCCTTTATCCTCATTATTTCAAGGTCAGTTTTGAGTTCTTTCTCCACACGCCTATA
1 AAAATTAATTCCTCTATCCTCATTATTTAAAGGTCAATTTTAAGTTCCTCCTCAACACGCCTAAA
* * * *
3335044 TTCATGATCTCTAGCATCTAGCTTACTCTAAAGGGCAAAGAGGTCAAAATTAGCTAGTTGAAAAT
66 TTCATCATCACTAGCATCTAACTTACTCTAAAGGGCAAAGAGGCCAAAATTAGCTAGTTGAAAAT
* * *
3335109 TATATCTAGCCACGCTTAGTACTAGTTCAGCAAATTTAAATTCCTTGTGATCTAAGAAGTGTTCA
131 TATATCTAGCCACGCTTAGAACTAGTTCAACAAATTTAAATTCCTTGTGAACTAAGAAGTGTTCA
* *
3335174 TGATAATAAATCAATTAACTGAAGTCGTGATGAAAACAGTAACTTTAACCTTACAAAGACAATGT
196 GGATAACAAATCAATTAACTGAAGTCGTGATGAAAACAGTAACTTTAACCTTACAAAGACAATGT
3335239 TAC
261 TAC
* * * *
3335242 AAAATTAATTCCTCTATCCTCCTTCTTTAAAGGTCAATTTTAAGTTCCTCCTCAATACGTCTAAA
1 AAAATTAATTCCTCTATCCTCATTATTTAAAGGTCAATTTTAAGTTCCTCCTCAACACGCCTAAA
* * * * * *
3335307 TTTATCATCACTAGCATCTAACTTGCTCTGAAA-TGCAGAGAGGCCAGAATTAGCTTGTTGAAAA
66 TTCATCATCACTAGCATCTAACTTACTCT-AAAGGGCAAAGAGGCCAAAATTAGCTAGTTGAAAA
* * * * * * *
3335371 TTGTCTCTAGCCATGCTTGGAATTAGTTCAACAAATTTAAATTCCTTTTGAAAC-AAGAAGTTTT
130 TTATATCTAGCCACGCTTAGAACTAGTTCAACAAATTTAAATTCCTTGTG-AACTAAGAAGTGTT
**
3335435 CAGGATCGCAAATCAATTAACTGAAGTCGT
194 CAGGATAACAAATCAATTAACTGAAGTCGT
3335465 CATTTTAAAT
Statistics
Matches: 184, Mismatches: 37, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
263 179 0.97
264 5 0.03
ACGTcount: A:0.33, C:0.19, G:0.14, T:0.34
Consensus pattern (263 bp):
AAAATTAATTCCTCTATCCTCATTATTTAAAGGTCAATTTTAAGTTCCTCCTCAACACGCCTAAA
TTCATCATCACTAGCATCTAACTTACTCTAAAGGGCAAAGAGGCCAAAATTAGCTAGTTGAAAAT
TATATCTAGCCACGCTTAGAACTAGTTCAACAAATTTAAATTCCTTGTGAACTAAGAAGTGTTCA
GGATAACAAATCAATTAACTGAAGTCGTGATGAAAACAGTAACTTTAACCTTACAAAGACAATGT
TAC
Found at i:3336017 original size:830 final size:828
Alignment explanation
Indices: 3334414--3336031 Score: 1889
Period size: 829 Copynumber: 2.0 Consensus size: 828
3334404 ACAATAAAAC
* * * * *
3334414 AAATTGATTCCTCTACGCTCCATCTTTCAAGCTCAGTTTTAAGTTCGGTCTCAACACGCCTATAT
1 AAATTAATTCCTCTACGCTCCATCTTTAAAGCTCAATTTTAAGTTCGCTCTCAACACGCCTAAAT
* * * * *
3334479 TCATCATCTCTGGCATTTAACTTGCTCAAAAGGACAGAGAGGTCAGACTTAGCTAGTTGAAAATC
66 TCATCATCACTAGCATCTAACTTGCTCAAAAGGACAGAGAGGCCAGAATTAGCTAGTTGAAAATC
* * * * * * *
3334544 ATCTCTGGCTACGCTTGGAAATAGGCCAGCAAAAGTACATTTCTTGTGAGAAAAGAAGTTTTTAT
131 ATCTCTAGCCACGCTTGGAAATAGGCCAACAAAAGTAAATTCCTTGTGAGAAAAGAAGTTTTCAG
* * * *
3334609 GATAGTAAATCAATTAACTGAAGACGTGATTGTAAATAAACGAGCTTTAAAAATGACAGTTATGG
196 GATAGCAAATCAATTAACTGAAGACGTCATTGTAAATAAACGAGCTTTAAAAATGACAATTATGA
* * * ** ** *
3334674 TCGTAAATCTACAAACTGTTTAAGTAGAGTTGTGATCTTAAATCGGTGAACTCTTAATGAAGTGT
261 TCGTAAATCAAAAAACTGTTTAAGTAGAGTAGCAATCTTAAATCGACGAACTCTTAATGAAGGGT
* * * * *
3334739 TCATTATCGTAAATCAATGAATTGAAACAGTGACTGTAAATTAGCGAGTTTTAAAAATGATAGTT
326 ACATGATCGTAAATCAATGAACTGAAACAGTGACTGTAAAGTAGCGAGCTTTAAAAATGATAGTT
* ** *
3334804 GTGATCATAAATCAGCGGATCTGAGATTCGTAAAATCTTATAACTAGGTCGTGATTGTAAATGAG
391 GTGATCATAAATCAGCGAATCTGAGATTCGTAAAATCTTATAACTAGGTCGTGATCATAAATCAG
* ** ** *
3334869 CTGAATCTCTTCAGTAAGTTCTTTGTTTTTTTTAAGATCGATCCATTTCAAGCCTCGTTTCAAAC
456 CTGAAGCTCTTCAAAAAGTTC-TTGTTTTTTAGAAGATCGATCCATTTCAAGCCTCATTTCAAAC
* *
3334934 ATATAGTGAAAAGAAATAGCTTCAGCCTCACAAAGACAACGAAAGAAAATTGATTCCTTTATCCT
520 ATATAGTGAAAAGAAATAGCTTCAGCCTCACAAAGACAACGAAACAAAATTGATTCCTCTATCCT
* * * * * * * *
3334999 CATTATTTCAAGGTCAGTTTTGAGTTCTTTCTCCACACGCCTATATTCATGATCTCTAGCATCTA
585 CATTATTTAAAGGTCAATTTTAAGTTCTTCCTCAACACACCTAAATTCATCATCTCTAGCATCTA
* * * * *
3335064 GCTTACTCTAAAGGGCAAAGAGGTCAAAATTAGCTAGTTGAAAATTATATCTAGCCACGCTTAGT
650 ACTTACTCTAAAAGGCAAAGAGGTCAAAATTAGCAAGTTGAAAATCATATCTAGCCACGCTTAGA
*
3335129 ACTAGTTCAGCAAATTTAAATTCCTTGTGATCTAAGAAGTGTTCATGATAATAAATCAATTAACT
715 ACTAGTTCAGCAAATTTAAATTCCTTGTGAACTAAGAAGTGTTCATGATAATAAATCAATTAACT
3335194 GAAGTCGTGATGAAAACAGTAACTTTAACCTTACAAAGACAATGTTACA
780 GAAGTCGTGATGAAAACAGTAACTTTAACCTTACAAAGACAATGTTACA
* * * *
3335243 AAATTAATTCCTCTATC-CTCCTTCTTTAAAGGTCAATTTTAAGTTC-CTCCTCAATACGTCTAA
1 AAATTAATTCCTCTA-CGCTCCATCTTTAAAGCTCAATTTTAAGTTCGCT-CTCAACACGCCTAA
* * * *
3335306 ATTTATCATCACTAGCATCTAACTTGCTCTGAAATG-CAGAGAGGCCAGAATTAGCTTGTTGAAA
64 ATTCATCATCACTAGCATCTAACTTGCTC-AAAAGGACAGAGAGGCCAGAATTAGCTAGTTGAAA
** * * ** ** *
3335370 ATTGTCTCTAGCCATGCTTGGAATTAGTTCAACAAATTTAAATTCCTTTTGA-AACAAGAAGTTT
128 ATCATCTCTAGCCACGCTTGGAAATAGGCCAACAAAAGTAAATTCCTTGTGAGAA-AAGAAGTTT
* * * * * *
3335434 TCAGGATCGCAAATCAATTAACTGAAGTCGTCATTTTAAATCAGCGGGCTTTAAAAATGACAATT
192 TCAGGATAGCAAATCAATTAACTGAAGACGTCATTGTAAATAAACGAGCTTTAAAAATGACAATT
* *
3335499 GTGATCGTAAAT-AAAAGAATTGTTTAAGT-GAAGTAGCAAT-TGTAAATCGACGAACTCTTAAT
257 ATGATCGTAAATCAAAA-AACTGTTTAAGTAG-AGTAGCAATCT-TAAATCGACGAACTCTTAAT
* * *
3335561 TAAGGGTACATGATCGTAAATCAATGAACTGAAGATA-TG-GTAGTAAAGTAGCGAGCTTTAAAA
319 GAAGGGTACATGATCGTAAATCAATGAACTGAA-ACAGTGACT-GTAAAGTAGCGAGCTTTAAAA
* * * * * *
3335624 ATTATAGTTGTGATCGTAAATTAGTGAATCGTGAGATTCGTAAAATCTTGTAAGTAGAAAGTCGT
382 ATGATAGTTGTGATCATAAATCAGCGAATC-TGAGATTCGTAAAATCTTATAACTAG---GTCGT
* * * *
3335689 GATCATAAATCAGCTTAAGCTTTTCAAAAAGTTC-T-TTTTTTAGCAGATTGATCCATTTCAAGC
443 GATCATAAATCAGCTGAAGCTCTTCAAAAAGTTCTTGTTTTTTAGAAGATCGATCCATTTCAAGC
* * * * * * *
3335752 CTCATTTCAAACATGTAGTTAAGAGAAGTAGCTTCAGCCTTACAAAGACAATGCAACAAAATTGA
508 CTCATTTCAAACATATAGTGAAAAGAAATAGCTTCAGCCTCACAAAGACAACGAAACAAAATTGA
* * *
3335817 TTCCTCTATCCTCCTTCTTTAAAGGTCAATTTTAAGTTCTTCCTCAACACATCTAAATTCATCAT
573 TTCCTCTATCCTCATTATTTAAAGGTCAATTTTAAGTTCTTCCTCAACACACCTAAATTCATCAT
* * * *
3335882 CTCTAGCATCTAACTTGCTCTAAAAGGCAGAA-AGG-CTAGAATTAGCAAGTTGAAAATCGTCTC
638 CTCTAGCATCTAACTTACTCTAAAAGGCA-AAGAGGTC-AAAATTAGCAAGTTGAAAATCATATC
* * * * * *
3335945 TAGCCATGCTTGGAATTAGTTCAGCAAATTTACATTCCTTTTGAAAC-AAGAAGTTTTCA-GAAT
701 TAGCCACGCTTAGAACTAGTTCAGCAAATTTAAATTCCTTGTG-AACTAAGAAGTGTTCATG-AT
**
3336008 GGTAAATCAATTAACTGAAGTCGT
764 AATAAATCAATTAACTGAAGTCGT
3336032 CGTTTTATAT
Statistics
Matches: 652, Mismatches: 120, Indels: 33
0.81 0.15 0.04
Matches are distributed among these distances:
828 8 0.01
829 322 0.49
830 286 0.44
831 5 0.01
833 31 0.05
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (828 bp):
AAATTAATTCCTCTACGCTCCATCTTTAAAGCTCAATTTTAAGTTCGCTCTCAACACGCCTAAAT
TCATCATCACTAGCATCTAACTTGCTCAAAAGGACAGAGAGGCCAGAATTAGCTAGTTGAAAATC
ATCTCTAGCCACGCTTGGAAATAGGCCAACAAAAGTAAATTCCTTGTGAGAAAAGAAGTTTTCAG
GATAGCAAATCAATTAACTGAAGACGTCATTGTAAATAAACGAGCTTTAAAAATGACAATTATGA
TCGTAAATCAAAAAACTGTTTAAGTAGAGTAGCAATCTTAAATCGACGAACTCTTAATGAAGGGT
ACATGATCGTAAATCAATGAACTGAAACAGTGACTGTAAAGTAGCGAGCTTTAAAAATGATAGTT
GTGATCATAAATCAGCGAATCTGAGATTCGTAAAATCTTATAACTAGGTCGTGATCATAAATCAG
CTGAAGCTCTTCAAAAAGTTCTTGTTTTTTAGAAGATCGATCCATTTCAAGCCTCATTTCAAACA
TATAGTGAAAAGAAATAGCTTCAGCCTCACAAAGACAACGAAACAAAATTGATTCCTCTATCCTC
ATTATTTAAAGGTCAATTTTAAGTTCTTCCTCAACACACCTAAATTCATCATCTCTAGCATCTAA
CTTACTCTAAAAGGCAAAGAGGTCAAAATTAGCAAGTTGAAAATCATATCTAGCCACGCTTAGAA
CTAGTTCAGCAAATTTAAATTCCTTGTGAACTAAGAAGTGTTCATGATAATAAATCAATTAACTG
AAGTCGTGATGAAAACAGTAACTTTAACCTTACAAAGACAATGTTACA
Found at i:3336514 original size:543 final size:540
Alignment explanation
Indices: 3335603--3336690 Score: 1612
Period size: 543 Copynumber: 2.0 Consensus size: 540
3335593 AGATATGGTA
* * * *
3335603 GTAAAGTAGCGAGCTTTAAAAATTATAGTTGTGATCGTAAATTAGTGAATCGTGAGATTCGTAAA
1 GTAAAGCAGCAAGCTTTAAAAATTATAGTTGTGATCGTAAATTAGGGAACCGTGAGATTCGTAAA
* *
3335668 ATCTTGTAAGTAGAAAGTCGTGATCATAAATCAGCTTAAGCTTTTCAAAAAGTTCTTTTTTTAGC
66 ATCTTGTAAGTAGAAAGTCGTAATCATAAATCAACTTAAGCTTTTCAAAAAGTTCTTTTTTTAGC
* *
3335733 AGATTGATCCATTTCAAGCCTCATTTCAAACATGTAGTTAAGAGAAGTAGCTTCAGCCTTACAAA
131 AGATTCATCCATTTCAAGCCTCATTTCAAACATGCAGTTAAGAGAAGTAGCTTCAGCCTTACAAA
3335798 GACAATGCAACAAAATTGATTCCTCTATCCTCCTTCTTTAAAGGTCAATTTTAAGTTCTTCCTCA
196 GACAATGCAACAAAATTGATTCCTCTATCCTCCTTCTTTAAAGGTCAATTTTAAGTTCTTCCTCA
* *
3335863 ACACATCTAAATTCATCATCTCTAGCATCTAACTTGCTCTAAAAGGCAGAAAGGCTAGAATTAGC
261 ACACATCTAAATTCATCATCTCTAGCATCTAACTTGCTCTAAAAGGCAAAAAGGCCAGAATTAGC
* * *
3335928 AAGTTGAAAATCGTCTCTAGCCATGCTTGGAATTAGTTCAGCAAATTTACATTCCTTTTGAAACA
326 AAGTTGAAAAGCATCTCTAGCCATGCTTGGAATTAGTTCAGCAAATTTACATTCCTTGTGAAACA
* * * * *
3335993 AGAAGT-TTTCA-GAATGGTAAATCAATTAACTGAAGTCGTCG-TTTTATATCAGC-AGGCTTTA
391 AGAAATGTTT-ATG-ATCGTAAATCAATTAACCGAAGTCGT-GATTGTAAATCAGCGA-GCTTTA
* * * ** * *
3336054 AAAATGACAGTTGTGAT-AGTAAATCAATGAATTGTTTAAGTGAAGTAGCGATCGTAAATTGGCG
452 AAAATGACAATTCTAATCA-TAAATCAACAAATTGTTTAAGTGAAGTAGCGATCATAAATTGACG
* * *
3336118 AACTTTTACTTAAGGGTTCATGATC
516 AACTCTTAATGAAGGGTTCATGATC
*
3336143 GTAAAGCAGCAAGCTTTAAAAATTATAGTTGTGATCGTAAATTAGGGGACCGTGAGATTCGTAAA
1 GTAAAGCAGCAAGCTTTAAAAATTATAGTTGTGATCGTAAATTAGGGAACCGTGAGATTCGTAAA
* *
3336208 ATCTTGTAAGTAGAAGGTCGTAATCATAAATCAACTTAAGCTTTTCAAAAATTTCCTTTTTTTTA
66 ATCTTGTAAGTAGAAAGTCGTAATCATAAATCAACTTAAGCTTTTCAAAAAGTT-C-TTTTTTTA
* *
3336273 GCAGA-TCACTCCATTTCAAGCCTCATTTCAAAGATGCAGTTAAGAGAAGTAGCTTTAGCCTTAC
129 GCAGATTCA-TCCATTTCAAGCCTCATTTCAAACATGCAGTTAAGAGAAGTAGCTTCAGCCTTAC
* *
3336337 AAAGACAATGTAACAAAATTGATTCCTCTATCCTCCTTTTTTAAAGGTCAAATTTTAAGTTCTTC
193 AAAGACAATGCAACAAAATTGATTCCTCTATCCTCCTTCTTTAAAGGTC-AATTTTAAGTTCTTC
* * *
3336402 CTCAACACGTCTAAATTCATCATCTCTAGCATCTCACTTGCTCTGAAAGGCAAAAAGGCCAGAAT
257 CTCAACACATCTAAATTCATCATCTCTAGCATCTAACTTGCTCTAAAAGGCAAAAAGGCCAGAAT
** *
3336467 TAGCTTGTTGAAAAGCATCTCTAGCCATGCTTGGAATTAGTTCAGCAAATTTACATTGCTTGTGA
322 TAGCAAGTTGAAAAGCATCTCTAGCCATGCTTGGAATTAGTTCAGCAAATTTACATTCCTTGTGA
*
3336532 ACCAAGAAATGTTTATGATCGTAAATCAATTAACCGAAGTCGTGATTGTAAATCAGCGAGCTTTA
387 AACAAGAAATGTTTATGATCGTAAATCAATTAACCGAAGTCGTGATTGTAAATCAGCGAGCTTTA
* * * * *
3336597 AAAATGACAATTCTAATCATAAATCAGCAAATTGTTTAAGTGCAGTTGTGATCATAAATTGATGA
452 AAAATGACAATTCTAATCATAAATCAACAAATTGTTTAAGTGAAGTAGCGATCATAAATTGACGA
*
3336662 ACTCTTAATGAAGTGTTCATGATC
517 ACTCTTAATGAAGGGTTCATGATC
*
3336686 CTAAA
1 GTAAA
3336691 TCAATGAACT
Statistics
Matches: 490, Mismatches: 49, Indels: 15
0.88 0.09 0.03
Matches are distributed among these distances:
540 110 0.22
541 3 0.01
542 113 0.23
543 258 0.53
544 6 0.01
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Consensus pattern (540 bp):
GTAAAGCAGCAAGCTTTAAAAATTATAGTTGTGATCGTAAATTAGGGAACCGTGAGATTCGTAAA
ATCTTGTAAGTAGAAAGTCGTAATCATAAATCAACTTAAGCTTTTCAAAAAGTTCTTTTTTTAGC
AGATTCATCCATTTCAAGCCTCATTTCAAACATGCAGTTAAGAGAAGTAGCTTCAGCCTTACAAA
GACAATGCAACAAAATTGATTCCTCTATCCTCCTTCTTTAAAGGTCAATTTTAAGTTCTTCCTCA
ACACATCTAAATTCATCATCTCTAGCATCTAACTTGCTCTAAAAGGCAAAAAGGCCAGAATTAGC
AAGTTGAAAAGCATCTCTAGCCATGCTTGGAATTAGTTCAGCAAATTTACATTCCTTGTGAAACA
AGAAATGTTTATGATCGTAAATCAATTAACCGAAGTCGTGATTGTAAATCAGCGAGCTTTAAAAA
TGACAATTCTAATCATAAATCAACAAATTGTTTAAGTGAAGTAGCGATCATAAATTGACGAACTC
TTAATGAAGGGTTCATGATC
Found at i:3336821 original size:47 final size:47
Alignment explanation
Indices: 3336767--3336860 Score: 152
Period size: 47 Copynumber: 2.0 Consensus size: 47
3336757 GCAGATTGTG
* *
3336767 AGATTCGTAAAATCCTATAAGTAAAAGGTCATGATCGTAAATTAGCT
1 AGATTCGTAAAATCCTATAAGTAAAAGGTCATAATCATAAATTAGCT
* *
3336814 AGATTCGTAAAATCCTGTAAGTAAAATGTCATAATCATAAATTAGCT
1 AGATTCGTAAAATCCTATAAGTAAAAGGTCATAATCATAAATTAGCT
3336861 GACACTTTTC
Statistics
Matches: 43, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.41, C:0.13, G:0.15, T:0.31
Consensus pattern (47 bp):
AGATTCGTAAAATCCTATAAGTAAAAGGTCATAATCATAAATTAGCT
Found at i:3337372 original size:618 final size:617
Alignment explanation
Indices: 3336197--3337379 Score: 1445
Period size: 618 Copynumber: 1.9 Consensus size: 617
3336187 GGGGACCGTG
* * * * *
3336197 AGATTCGTAAAATCTTGTAAGTAGAAGGTCGTAATCATAAATCAACTTAAGCTTTTCAAAAATTT
1 AGATTCGTAAAATCCTGTAAGTAAAAGGTCATAATCATAAATCAACTGAAGCTTTTCAAAAAGTT
* *
3336262 CCTTTTTTTTAGCAGATCACTCCATTTCAAGCCTCATTTCAAAGATGCAGTTAAGAGAAGTAGCT
66 CCTTTTTTTTAGCAAATCAATCCATTTCAAGCCTCATTTCAAAGATGCAGTTAAGAGAAGTAGCT
* * * * * *
3336327 TTAGCCTTACAAAGACAATGTAACAAAATTGATTCCTCTATCCTCCTTTTTTAAAGGTCAAATTT
131 TCAACCTCACAAAGACAATATAACAAAATTGATCCCTCTATCCTCCTTTTTTAAAGATCAAATTT
* *
3336392 TAAGTTCTTCCTCAACACGTCTAAATTCATCATCTCTAGCATCTCACTTGCTCTGAAAGGCAAAA
196 TAAGTTCTTCCTCAACACATCTAAATTCATCATCTCTAGCATATCACTTGCTCTGAAAGGCAAAA
* * * * *
3336457 AGGCCAGAATTAGCTTGTTGAAAAGCATCTCTAGCCATGCTTGGAATTAGTTCAGCAAATTTACA
261 AGGCCAAAATTAACTTGTTGAAAAGCAACTCTAGCCATGCTTAGAACTAGTTCAGCAAATTTACA
* * * * *
3336522 TTGCTTGTGAACCAAGAAATGTTTATGATCGTAAATCAATTAACCGAAGTCGTGATTGTAAATCA
326 TTGCTTGTGAACAAAGAAATGTTCATGATCGTAAATCAATTAACCGAAGCCATGATTGTAAAACA
** * * * **
3336587 GCGAGCTTTAAAAATGACAATTCTAATCATAAATCAGCAAATTGTTTAAGTGCAGTTGTGATCAT
391 AAGAACTTTAAAAATGACAATTCTAATCATAAATCAGCAAACTATTTAAGTGCAGTTACGATCAT
* * *
3336652 AAATTGATGAACTCTTAATGAAGTGTTCATGATCCTAAATCAATGAACTGAAGCTATGATCGTAA
456 AAACTGATGAACTCTTAATGAAGTGTTCATGATCATAAATCAATGAACTGAAGCTATGATCCTAA
*
3336717 ATCAATGAGTTTTAAAAAAGACAGTTATGATCGTAAATCAGCAGATTGTGAGATTCGTAAAATCC
521 ATCAATGAGCTTTAAAAAAGACAGTTATGATCGTAAATCAGCAGATTGTGAGATTCGTAAAATCC
3336782 TATAAGTAAAAGGTCATGATCGTAAATTAGCT
586 TATAAGTAAAAGGTCATGATCGTAAATTAGCT
* * * *
3336814 AGATTCGTAAAATCCTGTAAGTAAAATGTCATAATCATAAATTAGCTGACA-CTTTTCAGAAAGT
1 AGATTCGTAAAATCCTGTAAGTAAAAGGTCATAATCATAAATCAACTGA-AGCTTTTCAAAAAGT
* * *
3336878 TCCTTTCTTTTTTTGGCAAATCAATCCGTTTCAAGCCTCATTTCTAATG-TGCAGTTAAGAGAAG
65 TCC--T-TTTTTTTAGCAAATCAATCCATTTCAAGCCTCATTTC-AAAGATGCAGTTAAGAGAAG
* *
3336942 TAGCTTCAACCTCACAGAGACAATATAACAAAATTGATCCCTCTATCCTTCTTCTTTT-AAGAT-
126 TAGCTTCAACCTCACAAAGACAATATAACAAAATTGATCCCTCTATCCTCCTT-TTTTAAAGATC
* * * * * *
3337005 TAGTTTTGAGTTCTTCCTCAACACATCTATATTCATCATCTGT-G-ATATCAAACTTGTTCTG-A
190 AAATTTTAAGTTCTTCCTCAACACATCTAAATTCATCATCTCTAGCATATC--ACTTGCTCTGAA
* * * * * * *
3337067 AGTGCAGATAGGTCAAAATTAACTAT-TTGAAAA-CAACTTTAGCTATGCTTAGAACTGGTTTAG
253 AG-GCAAAAAGGCCAAAATTAACT-TGTTGAAAAGCAACTCTAGCCATGCTTAGAACTAGTTCAG
* * ** *
3337130 GAAATTTACATTGCTTGTGAACAAAG-AATCGTTCATGATCTTAAATCAATTTTCTGAAGCCATG
316 CAAATTTACATTGCTTGTGAACAAAGAAAT-GTTCATGATCGTAAATCAATTAACCGAAGCCATG
* * * * * ** *
3337194 ATTGTAAAACAAAGAACTTTAAAAATGACAGTTGTGATCGTAAATTAGTGAACTATTTAAGTGGA
380 ATTGTAAAACAAAGAACTTTAAAAATGACAATTCTAATCATAAATCAGCAAACTATTTAAGTGCA
** * *
3337259 GTTACGATTGTAAACCTG-TGAACTCTTAATGAAGTGTTCATGATCATAAATTAATGAACTGAAT
445 GTTACGATCATAAA-CTGATGAACTCTTAATGAAGTGTTCATGATCATAAATCAATGAACTGAAG
* * * * *
3337323 CTGTGATCCTAAATCAGTGTGCTTTAAAAATA-ACAGTTGTGATCGTAAATTAGCAGA
509 CTATGATCCTAAATCAATGAGCTTTAAAAA-AGACAGTTATGATCGTAAATCAGCAGA
3337380 CCGTGATATT
Statistics
Matches: 473, Mismatches: 80, Indels: 25
0.82 0.14 0.04
Matches are distributed among these distances:
617 63 0.13
618 231 0.49
619 73 0.15
620 99 0.21
621 7 0.01
ACGTcount: A:0.35, C:0.16, G:0.16, T:0.33
Consensus pattern (617 bp):
AGATTCGTAAAATCCTGTAAGTAAAAGGTCATAATCATAAATCAACTGAAGCTTTTCAAAAAGTT
CCTTTTTTTTAGCAAATCAATCCATTTCAAGCCTCATTTCAAAGATGCAGTTAAGAGAAGTAGCT
TCAACCTCACAAAGACAATATAACAAAATTGATCCCTCTATCCTCCTTTTTTAAAGATCAAATTT
TAAGTTCTTCCTCAACACATCTAAATTCATCATCTCTAGCATATCACTTGCTCTGAAAGGCAAAA
AGGCCAAAATTAACTTGTTGAAAAGCAACTCTAGCCATGCTTAGAACTAGTTCAGCAAATTTACA
TTGCTTGTGAACAAAGAAATGTTCATGATCGTAAATCAATTAACCGAAGCCATGATTGTAAAACA
AAGAACTTTAAAAATGACAATTCTAATCATAAATCAGCAAACTATTTAAGTGCAGTTACGATCAT
AAACTGATGAACTCTTAATGAAGTGTTCATGATCATAAATCAATGAACTGAAGCTATGATCCTAA
ATCAATGAGCTTTAAAAAAGACAGTTATGATCGTAAATCAGCAGATTGTGAGATTCGTAAAATCC
TATAAGTAAAAGGTCATGATCGTAAATTAGCT
Found at i:3337989 original size:550 final size:547
Alignment explanation
Indices: 3336934--3338015 Score: 1187
Period size: 550 Copynumber: 2.0 Consensus size: 547
3336924 ATGTGCAGTT
3336934 AAGAGAAGTAGCTTCAACCTCACAGAGACAATATAACAAAATTGATCCCTCTATCCTTCTTCTTT
1 AAGAGAAGTAGCTTCAACCTCACAGAGACAATATAACAAAATTGATCCCTCTATCCTTCTTCTTT
* * * * *
3336999 TAAGATTAGTTTTGAGTTCTTCCTCAACACATCTATATTCATCATCTGTGATATCAAACTTGTTC
66 TAAGATCAGTTTTGAGTTCTTCCTCAACACACCTATATTCATCATCTCTGACATCAAACTTGCTC
* ** * * * * * * *
3337064 TGAAGTGCAGATAGGTCAAAATTAACTATTTGAAAACAACTTTAGCTATGCTTAGAACTGGTTTA
131 TAAACAGCAAAGAGGTCAAAATTAACTAGTCGAAAACAACTCTAGCCATGCTTAGAACTAGTTTA
* ** ** * **
3337129 GGAAATTTACATTGCTTGTGAACAAAGAATCGTTCATGATCTTAAATCAATTTTCTGAAGCCATG
196 GCAAATAAACATACCTTGTGAACAAAGAATCGTTCATGATCGTAAATCAATAATCTGAAGCCATG
* * * *
3337194 ATTGTAAAACAAAGAACTTTAAAAATGACAGTTGTGATCGTAAATTAGTGAACTATTTAAGTGGA
261 ATTATAAAACAAAG-ACTTTAAAAATGACAATTGTGATCGTAAATAAGTCAACTATTTAAGTGGA
* * * * *
3337259 GTTACGATTGTAAACCTGTGAACTCTTAATGAAGTGTTCATGATCATAAATTAATGAACTGAATC
325 GTCACGATTGTAAACCGGTGAAATCTTAATGAAGTGTTAATGATCATAAATCAATGAACTGAATC
* * * * ** ** * *
3337324 TGTGATCCTAAATCAGTGTGCTTTAAAAATAACAGTTGTGATCGTAAATTAGCAGACCGTGATAT
390 TGTGATCATAAATCAATGAGCTTTAAAAATAACAGTTGGGATAATAAATTAGCAGAAAGTAAGAT
* * *
3337389 TCAAAAAATCGTGTGAGTAGCAAGTCAATATCATTAATTAGATAAAGCTTTTTAAAAAGT-TCCT
455 TCAAAAAATCGTGTAAGTAGCAAGTCAATATCATAAATTAGATAAAGCTTTTCAAAAA-TATCCT
*
3337453 TGTTTTTTTTAGCAAGTCAAATGTACGGTG
519 T-ATTTTTTTAGCAAGTCAAATGTACGGTG
* * *
3337483 AAGAGAAGTAGCTTCAGCCTCACAGAGACAATGTAACAAAATTGATTCCTCTATCC-TCTTTCTT
1 AAGAGAAGTAGCTTCAACCTCACAGAGACAATATAACAAAATTGATCCCTCTATCCTTC-TTCTT
* * * * * *
3337547 TTAAGGTCAGTTTTGAGTTCTTTCTCAACACGCCTATATTTATCATTTCT-AGCATCTAACTTGC
65 TTAAGATCAGTTTTGAGTTCTTCCTCAACACACCTATATTCATCATCTCTGA-CATCAAACTTGC
* * * * * *
3337611 TCTAAACAGTAAAGAGGTCAGAATTAGCTAGTCGAAAATCATCTCTGGCCATGCTTGGAACTAGT
129 TCTAAACAGCAAAGAGGTCAAAATTAACTAGTCGAAAA-CAACTCTAGCCATGCTTAGAACTAGT
* * *
3337676 TTAGCAAATAAACATACCTTGTGAACCAAG-TTGTGTTCATGATCGTAAATCAATCAAT-TGAAG
193 TTAGCAAATAAACATACCTTGTGAACAAAGAAT-CGTTCATGATCGTAAATCAAT-AATCTGAAG
* * * *
3337739 CCATGATTATAATTTAGC-AAG-CTTTAAAAATGACAATTTTGATCGTAAATAATTCAACTGTTT
256 CCATGATTATAA---AACAAAGACTTTAAAAATGACAATTGTGATCGTAAATAAGTCAACTATTT
* *
3337802 AAGTGGAGTCACGATTGTAAATCGGTGAAATCTTAATGAAGTGTTAATGATCATAAATCAATGCA
318 AAGTGGAGTCACGATTGTAAACCGGTGAAATCTTAATGAAGTGTTAATGATCATAAATCAATGAA
* * * * ***
3337867 CTTAATTTGTGATCATAAATCAATGAGGTTTAGAAATGGTAGTTGGGATAATAAAATTAGCAGAA
383 CTGAATCTGTGATCATAAATCAATGAGCTTTAAAAATAACAGTTGGGATAAT-AAATTAGCAGAA
* * * * * * *
3337932 AGTAAGGTTCATAAGATCTTGTAAGTAG-AAGGTC-GTGCTGCA-AAATTAGCT-AAGCTTTTCA
447 AGTAAGATTCAAAAAATCGTGTAAGTAGCAA-GTCAAT-AT-CATAAATTAGATAAAGCTTTTCA
*
3337993 GAAATATCCTTATTTTTTTAGCA
509 AAAATATCCTTATTTTTTTAGCA
3338016 GATCAATCCA
Statistics
Matches: 435, Mismatches: 85, Indels: 26
0.80 0.16 0.05
Matches are distributed among these distances:
548 3 0.01
549 150 0.34
550 232 0.53
551 43 0.10
552 5 0.01
553 2 0.00
ACGTcount: A:0.35, C:0.15, G:0.17, T:0.33
Consensus pattern (547 bp):
AAGAGAAGTAGCTTCAACCTCACAGAGACAATATAACAAAATTGATCCCTCTATCCTTCTTCTTT
TAAGATCAGTTTTGAGTTCTTCCTCAACACACCTATATTCATCATCTCTGACATCAAACTTGCTC
TAAACAGCAAAGAGGTCAAAATTAACTAGTCGAAAACAACTCTAGCCATGCTTAGAACTAGTTTA
GCAAATAAACATACCTTGTGAACAAAGAATCGTTCATGATCGTAAATCAATAATCTGAAGCCATG
ATTATAAAACAAAGACTTTAAAAATGACAATTGTGATCGTAAATAAGTCAACTATTTAAGTGGAG
TCACGATTGTAAACCGGTGAAATCTTAATGAAGTGTTAATGATCATAAATCAATGAACTGAATCT
GTGATCATAAATCAATGAGCTTTAAAAATAACAGTTGGGATAATAAATTAGCAGAAAGTAAGATT
CAAAAAATCGTGTAAGTAGCAAGTCAATATCATAAATTAGATAAAGCTTTTCAAAAATATCCTTA
TTTTTTTAGCAAGTCAAATGTACGGTG
Found at i:3338820 original size:134 final size:134
Alignment explanation
Indices: 3338580--3338919 Score: 403
Period size: 134 Copynumber: 2.5 Consensus size: 134
3338570 ACTATTCATA
* * * * *
3338580 ATCGTAATTCAATTAATTGAAGCCGTGATTGTAATTCAGCCAGCTTTAAAAATGATAGTTGTGAT
1 ATCGTAAATCAATCAATTGAAGCTGTGATTGTAATTCAGCAAGCTTTAAAAATGACAGTTGTGAT
* ** * * *
3338645 CATAAATCAGTAAATTGTTTAAGTAGAGTTGCGATTGTAAATCGATGAACTCTTAATGAAGTGTT
66 CATAAATAAGTAAATTGTTTAAGTAGAGTCACAACTGTAAATCAATGAACTCTTAATGAAGTGTT
3338710 CAAG
131 CAAG
* **
3338714 ATCGTAAATCAATCAATTGAAGCTATGATTGTAATTCAGTGAGCTTTAAAAATGACAGTTGTGAT
1 ATCGTAAATCAATCAATTGAAGCTGTGATTGTAATTCAGCAAGCTTTAAAAATGACAGTTGTGAT
** * * *
3338779 TGTAAATAATTGAATTGTTTAAGTGGAGTCACAACTGTAAATCAATGAACTCTTAATGAAGTGTT
66 CATAAATAAGTAAATTGTTTAAGTAGAGTCACAACTGTAAATCAATGAACTCTTAATGAAGTGTT
*
3338844 CATG
131 CAAG
* * * * ** * *
3338848 ATCATAAATGAATGAACTT-AAGTTGTGATCATAAATCAGCAACCTTTAAAAATGACAGTTGTGA
1 ATCGTAAATCAATCAA-TTGAAGCTGTGATTGTAATTCAGCAAGCTTTAAAAATGACAGTTGTGA
*
3338912 TAATAAAT
65 TCATAAAT
3338920 TAGCAGATAG
Statistics
Matches: 173, Mismatches: 32, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
134 171 0.99
135 2 0.01
ACGTcount: A:0.38, C:0.11, G:0.18, T:0.34
Consensus pattern (134 bp):
ATCGTAAATCAATCAATTGAAGCTGTGATTGTAATTCAGCAAGCTTTAAAAATGACAGTTGTGAT
CATAAATAAGTAAATTGTTTAAGTAGAGTCACAACTGTAAATCAATGAACTCTTAATGAAGTGTT
CAAG
Found at i:3341785 original size:24 final size:25
Alignment explanation
Indices: 3341758--3341885 Score: 59
Period size: 25 Copynumber: 5.2 Consensus size: 25
3341748 AAGCTCATGC
*
3341758 GAGCCAATAA-CGGGTAGCTCCAAA
1 GAGCCAATAATCGGGAAGCTCCAAA
* * *
3341782 GAGCTATTAATCGGGAAGCTTCAAA
1 GAGCCAATAATCGGGAAGCTCCAAA
* * * * *
3341807 TAGCC-ATATATCAGGAA-ATTCAAGT
1 GAGCCAATA-ATCGGGAAGCTCCAA-A
* * *
3341832 GAG-CAAT-ATCAGAAAGCTCCGAA
1 GAGCCAATAATCGGGAAGCTCCAAA
* * *
3341855 GAGACATTAATCAGGAAGCTCGCAAA
1 GAGCCAATAATCGGGAAGCTC-CAAA
3341881 GAGCC
1 GAGCC
3341886 TTTAATTGGG
Statistics
Matches: 76, Mismatches: 20, Indels: 14
0.69 0.18 0.13
Matches are distributed among these distances:
23 10 0.13
24 22 0.29
25 37 0.49
26 7 0.09
ACGTcount: A:0.39, C:0.20, G:0.23, T:0.18
Consensus pattern (25 bp):
GAGCCAATAATCGGGAAGCTCCAAA
Found at i:3352227 original size:573 final size:569
Alignment explanation
Indices: 3350232--3355477 Score: 4571
Period size: 570 Copynumber: 9.2 Consensus size: 569
3350222 GGTTGTTACA
* * ** * * *
3350232 GTAAATTAGCTGAAACTTTT-AGAAAAGTTTATTTTTTTTTAGTAGATCGATCCATTTCAAGCCT
1 GTAAATCAGCTGAAGCTTTTCA-AAAAGTTCCTTTTTTTTGAGCAAATCGATCCATTTCAAGCCT
* * * * * *
3350296 TGTTT-AAACGGATGGTGAAGAGAAGTAGCTTCAGCCTAATAAAGATAATTTTAACAAAATTGAT
65 CGTTTCAGACGTATGGTGAAGAGAA-TAGCTTCAGCCTCATAAAGACAA-TGTAACAAAATTGAT
* * *** *
3350360 TCCTCTATCCTCCTTTTTTCAAGGTCAATTTTGAGTTCTTCCTCAACACATATTTATTTATCATT
128 TCCTCTATCCTCCTTCTTTCAAGGTCAGTTTTGAGTTCTTCCTCAACACGCCTTTATTTATCATC
* * * * * *
3350425 TCTAGAATCTAACTTG-----AAGGGCAAAAAGTTCAGAATTAGCTAGTTGAAAATCATCTCTAA
193 TCTAGCATCTAACTTGCTCTAAAGGGCAGAGAGGTCAAAATTAGCTAGTTGAAAATCATCTCTGA
* * * * * *
3350485 CAACGCTTGGAACTAGTTCAGCAAATTTACATTCCTAGTGAACCAACAAGTGCTCAAGATCATAA
258 CCACGCTTGGAACTAGTTCAGCAAATTTACATTCCTTGTGAACCAAGAAGTGTTCATGATCGTAA
* ** * * *
3350550 ATCAATGAACTGAA-AC-TAGATTGTAAATCAGTAAGCTTTGAATATGACAGTTGTGATCGTAAA
323 ATCAATGAACTGAAGCCGT-GATTGTAAATCAGCGAGCTTTAAAAATGATAGTTGTGATCGTAAA
* * * * ** *
3350613 TCAACGAATTGTTTAAGTGGACTTGCGATCGTAAATCGAAGAACTCTTAATTAAGTGTTCATG-T
387 TCAACGAACTATTTAAGTGAAGTTGCGATCGTAAATCGGCGAACTCTTAATGAAGTGTTCATGAT
* * * * * *
3350677 TCGTAAATAAATGAACTAAAGTTGTATAA-GTAAATCAGTGAGCTTTACAAATGACAGATATGAT
452 T-GTAAATCAATGAACTAAAGTTGTA-AATGTAAATCAGCGAGCTGTAAAAAAGACAGTTATGAT
* * ** * * * * *
3350741 CATAAATTTGTGGATCGTAAGATTCT-TAAAATCCTATAAGTAGAAGGTTGTGATC
515 CGTAAATCTGCAGACCGTGAGATT-TGTAAAATCCTGTAAGTACAAGGTCGTGATC
* * * *
3350796 GTAAATGAGTTGAAGCTTTTCAAATAGTTCCTCATTTTTTTGAG-AAGATCGATCCATTT-AATC
1 GTAAATCAGCTGAAGCTTTTCAAAAAGTTCCT--TTTTTTTGAGCAA-ATCGATCCATTTCAAGC
* * * * *
3350859 CTC-ATTCTAGTCGTATGGTGAAGAGAAGTAGCTTCAACCTAATAAAGACAATTTAACAAAATTG
63 CTCGTTTC-AGACGTATGGTGAAGAGAA-TAGCTTCAGCCTCATAAAGACAATGTAACAAAATTG
* * *
3350923 ATCCCTCTATCCTCCTTCTTTCAAGGTCAGTTTTAAGTTCTTCCTCAACACGTCTTTATTTATCA
126 ATTCCTCTATCCTCCTTCTTTCAAGGTCAGTTTTGAGTTCTTCCTCAACACGCCTTTATTTATCA
* * ** * *
3350988 TCTCTAGAATCTAACTTGCTATGGAGGGCAAAGAGGTCAAAATTAGCTACTTGAAAATCATCTCT
191 TCTCTAGCATCTAACTTGCTCTAAAGGGCAGAGAGGTCAAAATTAGCTAGTTGAAAATCATCTCT
* * * * * * * *
3351053 GGCCACGCTTGAAACTAGTTCAGTAAATTTAAATTTCTTGTGAACCAAGAAGAGTTAATGATCAT
256 GACCACGCTTGGAACTAGTTCAGCAAATTTACATTCCTTGTGAACCAAGAAGTGTTCATGATCGT
* * * * *
3351118 AAATAAATAAACTGAAGTCATGATTGTAAATCAGCGAGCTTTAAAAATGACAGTTGTGATCGTAA
321 AAATCAATGAACTGAAGCCGTGATTGTAAATCAGCGAGCTTTAAAAATGATAGTTGTGATCGTAA
* * * * * ** * * * *
3351183 ACCAACGAAATGTTTAAGTCG-AGTTGCAATCATAAATCAACAAACTCTTAATGGAGTTTTTATG
386 ATCAACGAACTATTTAAGT-GAAGTTGCGATCGTAAATCGGCGAACTCTTAATGAAGTGTTCATG
* ** *
3351247 ATTGTAAATCAATGAACTAAAGTTGTGAACATAAATCAGC-ATGTTGTAAAAAAGACAGTGT-TG
450 ATTGTAAATCAATGAACTAAAGTTGTAAATGTAAATCAGCGA-GCTGTAAAAAAGACAGT-TATG
* * * * *
3351310 ATCG-AAAACTCGCAGACCGTGAGATTCT-TAAAACCCTATAAGTACAAGGTCGTAATT
513 ATCGTAAATCT-GCAGACCGTGAGATT-TGTAAAATCCTGTAAGTACAAGGTCGTGATC
* * * ** * * * ** *
3351367 ATAAGTCAGCTAAATTTTTTTAGAAACTTCCTTGTTTTTTGAGCAAATCGATTAATTTCGAGCCT
1 GTAAATCAGCTGAAGCTTTTCAAAAAGTTCCTT-TTTTTTGAGCAAATCGATCCATTTCAAGCCT
* * * * * *
3351432 CGTTT-AGACGTATGGTTCAAAAAAATAGCTTTAGCCTCACAAAGACAATGTAACAAAATTAATT
65 CGTTTCAGACGTATGG-TGAAGAGAATAGCTTCAGCCTCATAAAGACAATGTAACAAAATTGATT
*
3351496 CCTCTATCCTCCTTCTTTTAAGG-CTAGTTTTGAGTTCTTCCTCAACACGCCTTTATTTATCATC
129 CCTCTATCCTCCTTCTTTCAAGGTC-AGTTTTGAGTTCTTCCTCAACACGCCTTTATTTATCATC
* * * * * *
3351560 TCTAGCATCTAATTTACTTTGAAA-GGCAGAGAAGTCAGAGTTAGCTAGTTGAAAATCATCTCTG
193 TCTAGCATCTAACTTGCTCT-AAAGGGCAGAGAGGTCAAAATTAGCTAGTTGAAAATCATCTCTG
* * * ** *
3351624 GCCACACTTTGAACTAGTTCAGCAAATTTACATTCCTTGCAAAACAA-AGAGTGTTCATGATCGT
257 ACCACGCTTGGAACTAGTTCAGCAAATTTACATTCCTTGTGAACCAAGA-AGTGTTCATGATCGT
* * *
3351688 AAATCAATGAACTGAAGCCGTGATTGTGAATCAGTGAGCTTTAAAAATAATAGTTGTGATCGTAA
321 AAATCAATGAACTGAAGCCGTGATTGTAAATCAGCGAGCTTTAAAAATGATAGTTGTGATCGTAA
* * ** * * * * *
3351753 CTCAACAAACTATTTAAGTGAAGTCACAATTGTAAATTGGCGGACTTTTAATGAAGTGTTCAT-A
386 ATCAACGAACTATTTAAGTGAAGTTGCGATCGTAAATCGGCGAACTCTTAATGAAGTGTTCATGA
* * *
3351817 GTTGTAAATCAATGAACTAAAGTTGTAAATGTAAATAAACAAGCTGTAAAAAAGACAGTTATGAT
451 -TTGTAAATCAATGAACTAAAGTTGTAAATGTAAATCAGCGAGCTGTAAAAAAGACAGTTATGAT
* * * * *
3351882 CGTAAATCTGCGGACCATTAGATTTGTATAATCCTGTAAGTATAAGGTCGTGATC
515 CGTAAATCTGCAGACCGTGAGATTTGTAAAATCCTGTAAGTACAAGGTCGTGATC
* * * * *
3351937 ATAAATCAGCTGAAGCTTTTCAAAAAGTTCCTTGTCTTTTTGAGCAAATCAATTCATTTTAAACC
1 GTAAATCAGCTGAAGCTTTTCAAAAAGTTCCTT-T-TTTTTGAGCAAATCGATCCATTTCAAGCC
* * * *
3352002 TCATTTCAGACGGACGGTGAAAAGATATAGC-TCTAGCCTCATAAAGACAATGTAACAAAAATTG
64 TCGTTTCAGACGTATGGTGAAGAGA-ATAGCTTC-AGCCTCATAAAGACAATGTAAC-AAAATTG
* * *
3352066 ATCCCTCTATCCTCCTTCTTTCAAGGTCAGTTTTGAGTTCTTCCTAAACATGCCTTTATTTATCA
126 ATTCCTCTATCCTCCTTCTTTCAAGGTCAGTTTTGAGTTCTTCCTCAACACGCCTTTATTTATCA
* * * *
3352131 TGTCTAGCATCTAACTTGCTCTAAAGGGTAGAGAGGGCAAAACTAGCTAGTTGAAAATCATCTCT
191 TCTCTAGCATCTAACTTGCTCTAAAGGGCAGAGAGGTCAAAATTAGCTAGTTGAAAATCATCTCT
* * * *
3352196 GACCACGCTTGAAACTAGTTCAGCAAATTTACATTCCTTGTGACCCAATAAGTTTTCATGATCGT
256 GACCACGCTTGGAACTAGTTCAGCAAATTTACATTCCTTGTGAACCAAGAAGTGTTCATGATCGT
* * * * *
3352261 AAATAAATGAATTGAAGCTGTGATTGTAAATCAGAGAGCTTTAAAAATGATAGTTGTGATCATAA
321 AAATCAATGAACTGAAGCCGTGATTGTAAATCAGCGAGCTTTAAAAATGATAGTTGTGATCGTAA
* * * **
3352326 ATCAACGAACTGTTT-A-T---G-T--G-TAGT---T--GCG-ACTCTTAATTAAGTACTCATGA
386 ATCAACGAACTATTTAAGTGAAGTTGCGATCGTAAATCGGCGAACTCTTAATGAAGTGTTCATGA
** * * * * * ** * * *
3352376 TCATAAATAAATGAATTGAAGTTGTATATGTAAATTAGAAAACTTTAAAAATGACAGTTATGATC
451 TTGTAAATCAATGAACTAAAGTTGTAAATGTAAATCAGCGAGCTGTAAAAAAGACAGTTATGATC
** * *
3352441 GTAAAT-TCGCAGACCGTGAGATTCATAAAATCCTGTAAGTAAAAGGTCATGATC
516 GTAAATCT-GCAGACCGTGAGATTTGTAAAATCCTGTAAGTACAAGGTCGTGATC
* ** * * * * * * *
3352495 GTAAATTAATTGAAGCTTTTTAGATAGTT-CTTTTTTTTTAG-AAGACCGATCCACTTCAAACCT
1 GTAAATCAGCTGAAGCTTTTCAAAAAGTTCCTTTTTTTTGAGCAA-ATCGATCCATTTCAAGCCT
* * * ** * *
3352558 CATTTTAGACGTATGGTGAAGAGATGTAGCTTCAGTATCACAAAGACAATTTAACAAAATTGATT
65 CGTTTCAGACGTATGGTGAAGAGA-ATAGCTTCAGCCTCATAAAGACAATGTAACAAAATTGATT
* * ** * * * *
3352623 CCTCTATCCTCCTTCTTTCAAGGTTAGTTTTGAGTTCTT-TTCTAGTACGTCTATATTCATTATC
129 CCTCTATCCTCCTTCTTTCAAGGTCAGTTTTGAGTTCTTCCTC-AACACGCCTTTATTTATCATC
* * * * * *
3352687 TCTAGCATCTAACTTACTCTGAAGGGTAAATAGG-CTAAAATTAGCTAGTTGAAAATCATCT-TC
193 TCTAGCATCTAACTTGCTCTAAAGGGCAGAGAGGTC-AAAATTAGCTAGTTGAAAATCATCTCTG
* * * * * *
3352750 AGCAATGCTT-GAACTAGTTTAG-ATAATTTATATTCCTTGTAAACCAAGAAGTGTTC-TAATCG
257 A-CCACGCTTGGAACTAGTTCAGCA-AATTTACATTCCTTGTGAACCAAGAAGTGTTCATGATCG
* ** * * * ** *
3352812 TAAATCAATGAATTGAAGTTGTCATTGTAAATCAGCGAGCTTTAAAAATAACAGTTGTGATATTT
320 TAAATCAATGAACTGAAGCCGTGATTGTAAATCAGCGAGCTTTAAAAATGATAGTTGTGATCGTA
* * * ** * * *
3352877 AATCAATGAATTATTTAAGTGGAGTTATGATTGTAAATCGGTGAACTCTTAATGAACG-ATTCAT
385 AATCAACGAACTATTTAAGTGAAGTTGCGATCGTAAATCGGCGAACTCTTAATGAA-GTGTTCAT
* * ** * * * * *
3352941 CATTGTAAATCAATGAATTGAAA-TCAT-GATCGTAAATTAGCGAGCTTTAAAAATGACAGTTTT
449 GATTGTAAATCAATGAACT-AAAGTTGTAAAT-GTAAATCAGCGAGCTGTAAAAAAGACAGTTAT
** * * * * * * *
3353004 GATCGTAAATCAACGGACCATGAGATTTATAAAAT-CTGGTAAGTAGAAGGCCATGATT
512 GATCGTAAATCTGCAGACCGTGAGATTTGTAAAATCCT-GTAAGTACAAGGTCGTGATC
* * * * *
3353062 GTAAA-CTAACTAAAGCTTTTCAGAAAGTTCCTTTTTTTTTAGCAGATCGATCCATTTTC-AGCC
1 GTAAATC-AGCTGAAGCTTTTCAAAAAGTTCCTTTTTTTTGAGCAAATCGATCCA-TTTCAAGCC
*
3353125 TCTTTTCAGACGTATGGTGAAGAGAAGTAGCTTCAGCATCTCA-AAA-ACAATGTAACAAAATTG
64 TCGTTTCAGACGTATGGTGAAGAGAA-TAGCTTCAGC--CTCATAAAGACAATGTAACAAAATTG
** * ** * * * *
3353188 ATTTATCTATCTTCCTTCTTTCAAAATCAGTTTTAAGTTCTTTCTCAACACGTCTATATTTATCA
126 ATTCCTCTATCCTCCTTCTTTCAAGGTCAGTTTTGAGTTCTTCCTCAACACGCCTTTATTTATCA
* *
3353253 TCTCTAGAATCTAACTTGCTTTGAAA-GGCAGAGAGGTCAAAATTAGCTAGTTGAAAATCATCTC
191 TCTCTAGCATCTAACTTGCTCT-AAAGGGCAGAGAGGTCAAAATTAGCTAGTTGAAAATCATCTC
* * * * * ** *
3353317 TAACCACGCTTGGAACTAGTTCACCAAATTTAAATTTCTTATGAACCCGGAAGTGTTCATGATCA
255 TGACCACGCTTGGAACTAGTTCAGCAAATTTACATTCCTTGTGAACCAAGAAGTGTTCATGATCG
* * * * *
3353382 TAAATCAATGAACTAAAGCTGTGATTGT-AATCAACGAGCTTTAAAAAT-CTCAGTTGCGATCGT
320 TAAATCAATGAACTGAAGCCGTGATTGTAAATCAGCGAGCTTTAAAAATGAT-AGTTGTGATCGT
* * * *
3353445 AAATCAATGAACTATTTAAGTAAAGTTGTGATCGTAAATCGGTGAACTCTTAATGAAGTGTTCAT
384 AAATCAACGAACTATTTAAGTGAAGTTGCGATCGTAAATCGGCGAACTCTTAATGAAGTGTTCAT
** * * *
3353510 GATTGTAAATCAATGAACTGGAGCTATAAATGTAAATCAGCGAGCTGTAAAAAAGATAGTTAAT-
449 GATTGTAAATCAATGAACTAAAGTTGTAAATGTAAATCAGCGAGCTGTAAAAAAGACAGTT-ATG
* * ** * * * *
3353574 ATAGTAAATCCGCAGATCC-ACAAATTTGTAAAATCTTGCAAGTACAAGGTCATGATC
513 ATCGTAAATCTGCAGA-CCGTGAGATTTGTAAAATCCTGTAAGTACAAGGTCGTGATC
* * * *
3353631 ATAAATCAGCTAAAACTTTTCAAGAAGTTCCTTTTTTTT-AGCAAATCGATCCATTTCAAGCCTC
1 GTAAATCAGCTGAAGCTTTTCAAAAAGTTCCTTTTTTTTGAGCAAATCGATCCATTTCAAGCCTC
** * * * * * *
3353695 GTTTCAGACAAATGGTGAA-A-AGTAGCTTCAGCTTCATAAAGACAACGTAATAAAATTTATTAC
66 GTTTCAGACGTATGGTGAAGAGAATAGCTTCAGCCTCATAAAGACAATGTAACAAAATTGATTCC
* * * * * * *
3353758 TTTATCTTCCTTTTTTCAAGGTCAGTTTTGAGTTCTTCCTCAATACGCCTTTATTAATCATGTTT
131 TCTATCCTCCTTCTTTCAAGGTCAGTTTTGAGTTCTTCCTCAACACGCCTTTATTTATCATCTCT
* * * * *
3353823 AGCATCTAACTTGCTCTAAACGGTAGAGAGGTCAAAATTAGCTAGTTGAAAACCATCCCTGGCCA
196 AGCATCTAACTTGCTCTAAAGGGCAGAGAGGTCAAAATTAGCTAGTTGAAAATCATCTCTGACCA
* * * * * *
3353888 CGCTTGGAACTAGTTCAACAAATTTACTTTCTTTGTGAACCAAGACGTATTCATGATCGTAAATG
261 CGCTTGGAACTAGTTCAGCAAATTTACATTCCTTGTGAACCAAGAAGTGTTCATGATCGTAAATC
* * * * * * * *
3353953 AATGAATTAAAGCCGTGATTGTAAATCAACAAGCTTTAAAGATGATAGTTTTGATCATAAATAAA
326 AATGAACTGAAGCCGTGATTGTAAATCAGCGAGCTTTAAAAATGATAGTTGTGATCGTAAATCAA
* * * * * * * ***
3354018 TGGACTATTTAAGTGGAGTTGCGATCATAAATCAGCGAACTCTTAATTAAGTGTTCATTATCACA
391 CGAACTATTTAAGTGAAGTTGCGATCGTAAATCGGCGAACTCTTAATGAAGTGTTCATGATTGTA
* * * * * * * ** * *
3354083 AATAAAT-AACCTGAAGTTGTATACGTAAATCAACGAGCTCTACAATTGACTGTTATGATTGTAA
456 AATCAATGAA-CTAAAGTTGTAAATGTAAATCAGCGAGCTGTAAAAAAGACAGTTATGATCGTAA
* ** * * *
3354147 ATTTGTGGACCGTGAGATTCGTAAAATCCTGTAAGTAGAAGGTAGTGATC
520 ATCTGCAGACCGTGAGATTTGTAAAATCCTGTAAGTACAAGGTCGTGATC
* * *
3354197 GTAAATCAGC-GAAAGCTTTTCAAATAGTTCCTTATTTTTTCAG-AAGATCGATCCATTACAAGC
1 GTAAATCAGCTG-AAGCTTTTCAAAAAGTTCCTT-TTTTTTGAGCAA-ATCGATCCATTTCAAGC
* * * * * * * * *
3354260 TTTGTTTCAAACATATTGTGAAGAG-ATGCAGCTTCAGCATTACAAAGACAATTTAACAAAATTG
63 CTCGTTTCAGACGTATGGTGAAGAGAAT--AGCTTCAGCCTCATAAAGACAATGTAACAAAATTG
* * * ** *
3354324 ATTCCTCTATCCT-C--CTTTCAAGGTTAGTTTTAAGTTCTTCCTCAACACGTCTAAATTCATCA
126 ATTCCTCTATCCTCCTTCTTTCAAGGTCAGTTTTGAGTTCTTCCTCAACACGCCTTTATTTATCA
* * * *
3354386 TCTCTAGCATCGAACTTTCTTTAAAGGGTAGAGAGGTCAAAATTAGCTAGTTGAAAATCATCTCT
191 TCTCTAGCATCTAACTTGCTCTAAAGGGCAGAGAGGTCAAAATTAGCTAGTTGAAAATCATCTCT
* * * * * *
3354451 GGCCACACTTGGAACTAGTTCAGCAAATTTACTTTCCTTATGAACCAAGAAGTGTTCGTGATCAT
256 GACCACGCTTGGAACTAGTTCAGCAAATTTACATTCCTTGTGAACCAAGAAGTGTTCATGATCGT
* * * * * * *
3354516 AAATAAATGAAATGAAGTCATGATTGTAAATAAGTGAGCTTTAAAAATGATAGTTGTGATCATAA
321 AAATCAATGAACTGAAGCCGTGATTGTAAATCAGCGAGCTTTAAAAATGATAGTTGTGATCGTAA
* * ** **
3354581 ATTAACGAACTATTTAAGTGAAGTAGCGATCGTAAA-CTGGTAAACTCTTAACAAAGTGTTCATG
386 ATCAACGAACTATTTAAGTGAAGTTGCGATCGTAAATC-GGCGAACTCTTAATGAAGTGTTCATG
* * * * * * * ** *
3354645 ATTGTAAATTAATGAACTGAAGCTATAAACGTTAATTAGCGAGAAGTAAAAAAGACAGTTTTGAT
450 ATTGTAAATCAATGAACTAAAGTTGTAAATGTAAATCAGCGAGCTGTAAAAAAGACAGTTATGAT
* ** * *
3354710 CGTGTAATTCCACAGACCGTGAGATTTTTAAAATCCTGTAAGTACAAGGTTGTGATC
515 C--GTAAATCTGCAGACCGTGAGATTTGTAAAATCCTGTAAGTACAAGGTCGTGATC
* * * * * *
3354767 GTAAATCAGTTGAAGCTTTTCAGAAAGTTCTTTGTTTTTTGAGAAAATCAATCCATTTCGAGCCT
1 GTAAATCAGCTGAAGCTTTTCAAAAAGTTCCTT-TTTTTTGAGCAAATCGATCCATTTCAAGCCT
* * ** * ** *
3354832 CGTTTCAAACGT-TCAGTTCAGAAAAGTAATTTCGGCCTCATAAAGACAATGTAACAAAATTGAT
65 CGTTTCAGACGTAT-GGTGAAGAGAA-TAGCTTCAGCCTCATAAAGACAATGTAACAAAATTGAT
* * * * * * * *
3354896 TCCTCTATCCCCCTTCTTTCAAGGTTAGTTTTTAGTTCTTCCTTAATACACATTTATTTATCATG
128 TCCTCTATCCTCCTTCTTTCAAGGTCAGTTTTGAGTTCTTCCTCAACACGCCTTTATTTATCATC
* * * * *
3354961 TCTAGCATCTAACTTGCTCTGAAGGGCAAAGAGGACAGAATTAGCTAGTTGAAAATCATCTCAAG
193 TCTAGCATCTAACTTGCTCTAAAGGGCAGAGAGGTCAAAATTAGCTAGTTGAAAATCATCTC-TG
* * * * * * *
3355026 A-GAGAGTTTGGAACTAGTTTAGCAAATTTATATTTCTTGTGAACCAAGAAGTGGTCATGATCGT
257 ACCA-CGCTTGGAACTAGTTCAGCAAATTTACATTCCTTGTGAACCAAGAAGTGTTCATGATCGT
* * *** * * *
3355090 AAATTATTGAACTGAAATAGTGATTGTAAATCAGCGAGCTTTAAAAATGAAAATTGTAATCGTAA
321 AAATCAATGAACTGAAGCCGTGATTGTAAATCAGCGAGCTTTAAAAATGATAGTTGTGATCGTAA
** * * * * *
3355155 ATCAGTGAACTGTTTAAATGGAGTTGCGATCGTAAATCGGCGAATTCTTAATGAAGTGTTCTTGA
386 ATCAACGAACTATTTAAGTGAAGTTGCGATCGTAAATCGGCGAACTCTTAATGAAGTGTTCATGA
** * * * * * * * * * * * *
3355220 TCATAAATAAATAAACTGAAGCTAT-GATCATAAATCAGCAAGCTTTAAAAATGATAGTTGTGAT
451 TTGTAAATCAATGAACTAAAGTTGTAAAT-GTAAATCAGCGAGCTGTAAAAAAGACAGTTATGAT
** * * * ** *
3355284 CGTAAATCAACGGATCGTGAGATTTGTAAAATCTTGTAAGTAGGAGGTTGTGATC
515 CGTAAATCTGCAGACCGTGAGATTTGTAAAATCCTGTAAGTACAAGGTCGTGATC
* * * * * * * * *
3355339 GTAAATTAGCTAAAGCTTTTTAGATAGTTCCTTGTTTTTTTTTAGTAGATCTATCCATTTCAAGC
1 GTAAATCAGCTGAAGCTTTTCAAAAAGTTCC---TTTTTTTTGAGCAAATCGATCCATTTCAAGC
* * * *
3355404 CTCGTTTCAGACATATGATGAAGAGAAATAGCTTCAGCATCACAAAGACAATGTAACAAAATTGA
63 CTCGTTTCAGACGTATGGTGAAGAG-AATAGCTTCAGCCTCATAAAGACAATGTAACAAAATTGA
*
3355469 TTTCTCTAT
127 TTCCTCTAT
3355478 TGTAACTTGT
Statistics
Matches: 3800, Mismatches: 753, Indels: 248
0.79 0.16 0.05
Matches are distributed among these distances:
552 75 0.02
553 42 0.01
554 123 0.03
555 64 0.02
556 3 0.00
557 5 0.00
558 136 0.04
559 4 0.00
560 1 0.00
561 4 0.00
563 3 0.00
564 36 0.01
565 309 0.08
566 257 0.07
567 145 0.04
568 556 0.15
569 262 0.07
570 738 0.19
571 296 0.08
572 117 0.03
573 336 0.09
574 282 0.07
575 6 0.00
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.33
Consensus pattern (569 bp):
GTAAATCAGCTGAAGCTTTTCAAAAAGTTCCTTTTTTTTGAGCAAATCGATCCATTTCAAGCCTC
GTTTCAGACGTATGGTGAAGAGAATAGCTTCAGCCTCATAAAGACAATGTAACAAAATTGATTCC
TCTATCCTCCTTCTTTCAAGGTCAGTTTTGAGTTCTTCCTCAACACGCCTTTATTTATCATCTCT
AGCATCTAACTTGCTCTAAAGGGCAGAGAGGTCAAAATTAGCTAGTTGAAAATCATCTCTGACCA
CGCTTGGAACTAGTTCAGCAAATTTACATTCCTTGTGAACCAAGAAGTGTTCATGATCGTAAATC
AATGAACTGAAGCCGTGATTGTAAATCAGCGAGCTTTAAAAATGATAGTTGTGATCGTAAATCAA
CGAACTATTTAAGTGAAGTTGCGATCGTAAATCGGCGAACTCTTAATGAAGTGTTCATGATTGTA
AATCAATGAACTAAAGTTGTAAATGTAAATCAGCGAGCTGTAAAAAAGACAGTTATGATCGTAAA
TCTGCAGACCGTGAGATTTGTAAAATCCTGTAAGTACAAGGTCGTGATC
Found at i:3355997 original size:80 final size:80
Alignment explanation
Indices: 3355858--3356019 Score: 281
Period size: 80 Copynumber: 2.0 Consensus size: 80
3355848 GGATATCTCC
*
3355858 CTGTACAGGGCTTCAATACTGATGCCGTTTGTTTCTATAGAAACTAGACTCAAATAGGAATCTAT
1 CTGTACAGGGCTTCAATACTGATGCCGTTTGTTTCTAAAGAAACTAGACTCAAATAGGAATCTAT
3355923 ACATATATGGCATGA
66 ACATATATGGCATGA
* *
3355938 CTGTACCGGGCTTCAATACTTATGCCGTTTGTTTCTAAAGAAACTAGACTCGAAA-AGGAATCTA
1 CTGTACAGGGCTTCAATACTGATGCCGTTTGTTTCTAAAGAAACTAGACTC-AAATAGGAATCTA
3356002 TACATATATGGCATGA
65 TACATATATGGCATGA
3356018 CT
1 CT
3356020 TCTAACTATC
Statistics
Matches: 78, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
80 75 0.96
81 3 0.04
ACGTcount: A:0.32, C:0.19, G:0.19, T:0.31
Consensus pattern (80 bp):
CTGTACAGGGCTTCAATACTGATGCCGTTTGTTTCTAAAGAAACTAGACTCAAATAGGAATCTAT
ACATATATGGCATGA
Found at i:3359019 original size:56 final size:56
Alignment explanation
Indices: 3358952--3359183 Score: 437
Period size: 56 Copynumber: 4.1 Consensus size: 56
3358942 TATTAGTTTA
*
3358952 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTGATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
3359008 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
3359064 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
*
3359120 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
3359176 TTGCCCAT
1 TTGCCCAT
3359184 CATCCCTTGT
Statistics
Matches: 172, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 172 1.00
ACGTcount: A:0.23, C:0.22, G:0.09, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:3362503 original size:20 final size:20
Alignment explanation
Indices: 3362480--3362519 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
3362470 TTTTAGGAAT
* *
3362480 TAAAAATCATTAAAATTATA
1 TAAAAAGCATAAAAATTATA
*
3362500 TAAAAAGGATAAAAATTATA
1 TAAAAAGCATAAAAATTATA
3362520 ACGAAAACAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (20 bp):
TAAAAAGCATAAAAATTATA
Found at i:3369380 original size:19 final size:19
Alignment explanation
Indices: 3369358--3369450 Score: 64
Period size: 19 Copynumber: 4.7 Consensus size: 19
3369348 ATTTTATATC
*
3369358 TTTTAATAATTTTTACAAT
1 TTTTAATAATTTTTAAAAT
* *
3369377 TTTTTATACTTTATTAAAAT
1 TTTTAATAATTT-TTAAAAT
*
3369397 TTTT-AT-ATTATTTATAAGT
1 TTTTAATAATT-TTTA-AAAT
*
3369416 TTTTATTAATTTTTATAGAAT
1 TTTTAATAATTTTTA-A-AAT
*
3369437 TTTAAATATATTTT
1 TTTTAATA-ATTTT
3369451 ATTAATTTTA
Statistics
Matches: 58, Mismatches: 9, Indels: 11
0.74 0.12 0.14
Matches are distributed among these distances:
18 5 0.09
19 20 0.34
20 17 0.29
21 11 0.19
22 5 0.09
ACGTcount: A:0.34, C:0.02, G:0.02, T:0.61
Consensus pattern (19 bp):
TTTTAATAATTTTTAAAAT
Found at i:3369430 original size:20 final size:19
Alignment explanation
Indices: 3369365--3369733 Score: 102
Period size: 20 Copynumber: 18.9 Consensus size: 19
3369355 ATCTTTTAAT
*
3369365 AATTTTTACAATTTTT-TA
1 AATTTTTATAATTTTTATA
* *
3369383 TACTTTATTAAAATTTTTAT-
1 -AATTT-TTATAATTTTTATA
*
3369403 -ATTATTTATAAGTTTTTATT
1 AATT-TTTATAA-TTTTTATA
*
3369423 AATTTTTATAGAATTTTA-A
1 AATTTTTATA-ATTTTTATA
3369442 ATATATTTTATTAA-TTTTAT-
1 A-AT-TTTTA-TAATTTTTATA
* *
3369462 -TTTTTTATAATTATT-T-
1 AATTTTTATAATTTTTATA
* * *
3369478 GATTTTTGTAATTTTTAAA
1 AATTTTTATAATTTTTATA
*** * *
3369497 AAAAATTATGATTTTTTTA
1 AATTTTTATAATTTTTATA
* * *
3369516 TACTTTTTATAAGTTTATATC
1 -AATTTTTATAA-TTTTTATA
* *
3369537 AATTTTAAT-ATTTTTAAA
1 AATTTTTATAATTTTTATA
** *
3369555 AAAATTTA-AATGTTTATA
1 AATTTTTATAATTTTTATA
* * *
3369573 ATTTTTTAAGAATTCTTATA
1 AATTTTT-ATAATTTTTATA
*
3369593 CATTTTTATAAAATTTTTAATA
1 AATTTTTAT--AATTTTT-ATA
3369615 AA-TTTTATTAATTTTTATA
1 AATTTTTA-TAATTTTTATA
* * *
3369634 AAATTTTATAACTTATTA-G
1 AATTTTTATAA-TTTTTATA
*
3369653 AA-TTTTATAATATTTATA
1 AATTTTTATAATTTTTATA
*
3369671 AGTTATTTTTTTATAACTTTTATA
1 A---A--TTTTTATAATTTTTATA
*
3369695 AATTTATATCAATTTTT-TAA
1 AATTTTTAT-AATTTTTAT-A
*
3369715 TAATTTTTAGTGATTTTTA
1 -AATTTTTA-TAATTTTTA
3369734 ATCATTTATT
Statistics
Matches: 253, Mismatches: 59, Indels: 73
0.66 0.15 0.19
Matches are distributed among these distances:
16 4 0.02
17 24 0.09
18 38 0.15
19 44 0.17
20 78 0.31
21 42 0.17
22 8 0.03
24 15 0.06
ACGTcount: A:0.36, C:0.02, G:0.03, T:0.58
Consensus pattern (19 bp):
AATTTTTATAATTTTTATA
Found at i:3369599 original size:21 final size:19
Alignment explanation
Indices: 3369568--3369607 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 19
3369558 ATTTAAATGT
3369568 TTATAATTTTTTAAGAATTC
1 TTATAATTTTTTAA-AATTC
3369588 TTATACATTTTTATAAAATT
1 TTATA-ATTTTT-TAAAATT
3369608 TTTAATAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 5 0.28
21 10 0.56
22 3 0.17
ACGTcount: A:0.38, C:0.05, G:0.03, T:0.55
Consensus pattern (19 bp):
TTATAATTTTTTAAAATTC
Found at i:3369721 original size:42 final size:42
Alignment explanation
Indices: 3369637--3369722 Score: 97
Period size: 42 Copynumber: 2.0 Consensus size: 42
3369627 TTTTATAAAA
* *
3369637 TTTTATAACTTATTAGAATTTTATAATATTTATAAGTTATTT
1 TTTTATAACTTATTAAAATTTTATAATATTTATAAGTAATTT
*
3369679 TTTTATAACTT-TTATAAATTTATATCAAT-TTTTTAA-TAATTT
1 TTTTATAACTTATTA-AAATTT-TAT-AATATTTATAAGTAATTT
3369721 TT
1 TT
3369723 AGTGATTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
41 3 0.08
42 23 0.61
43 9 0.24
44 3 0.08
ACGTcount: A:0.35, C:0.03, G:0.02, T:0.59
Consensus pattern (42 bp):
TTTTATAACTTATTAAAATTTTATAATATTTATAAGTAATTT
Found at i:3369723 original size:10 final size:10
Alignment explanation
Indices: 3369570--3369740 Score: 50
Period size: 10 Copynumber: 16.7 Consensus size: 10
3369560 TTAAATGTTT
3369570 ATAATTTTTTA
1 ATAA-TTTTTA
* *
3369581 AGAATTCTT-
1 ATAATTTTTA
3369590 ATACATTTTTA
1 ATA-ATTTTTA
*
3369601 TAAAATTTTTA
1 -ATAATTTTTA
*
3369612 ATAAATTTTA
1 ATAATTTTTA
*
3369622 TTAATTTTT-
1 ATAATTTTTA
*
3369631 ATAAAATTTT-
1 AT-AATTTTTA
*
3369641 ATAACTTATT-
1 ATAA-TTTTTA
*
3369651 AGAATTTTATA
1 ATAATTTT-TA
*
3369662 AT-ATTTATA
1 ATAATTTTTA
* *
3369671 AGTTATTTTTTT
1 A--TAATTTTTA
*
3369683 ATAACTTTT-
1 ATAATTTTTA
*
3369692 ATAA-ATTTA
1 ATAATTTTTA
3369701 TATCAATTTTTTA
1 -AT-AA-TTTTTA
3369714 ATAATTTTTA
1 ATAATTTTTA
* *
3369724 GTGATTTTTA
1 ATAATTTTTA
*
3369734 ATCATTT
1 ATAATTT
3369741 ATTATGAGAA
Statistics
Matches: 117, Mismatches: 28, Indels: 31
0.66 0.16 0.18
Matches are distributed among these distances:
8 3 0.03
9 15 0.13
10 70 0.60
11 16 0.14
12 9 0.08
13 4 0.03
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.57
Consensus pattern (10 bp):
ATAATTTTTA
Found at i:3376241 original size:40 final size:39
Alignment explanation
Indices: 3376197--3376286 Score: 128
Period size: 40 Copynumber: 2.3 Consensus size: 39
3376187 AAAAAAATAT
*
3376197 TTATATT-AAAAACACTACCATAAATATAATAAATATTTTA
1 TTATATTAAAAAACAC-A-AATAAATATAATAAATATTTTA
3376237 TTATATTTAAAAAACACAAATAAATATAATAAATATTTTA
1 TTATA-TTAAAAAACACAAATAAATATAATAAATATTTTA
*
3376277 TTGTATTAAA
1 TTATATTAAA
3376287 TATATTTTTA
Statistics
Matches: 46, Mismatches: 2, Indels: 5
0.87 0.04 0.09
Matches are distributed among these distances:
39 5 0.11
40 30 0.65
41 3 0.07
42 8 0.17
ACGTcount: A:0.53, C:0.07, G:0.01, T:0.39
Consensus pattern (39 bp):
TTATATTAAAAAACACAAATAAATATAATAAATATTTTA
Found at i:3377176 original size:20 final size:21
Alignment explanation
Indices: 3377145--3377191 Score: 71
Period size: 20 Copynumber: 2.3 Consensus size: 21
3377135 AAATCGTAGC
3377145 AAAATAGTGAAAAAATAA-TAA
1 AAAATAGTGAAAAAA-AAGTAA
3377166 AAAATAG-GAAAAAAAAGTAA
1 AAAATAGTGAAAAAAAAGTAA
3377186 AAAATA
1 AAAATA
3377192 AAATAAAAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 2 0.08
20 16 0.64
21 7 0.28
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.15
Consensus pattern (21 bp):
AAAATAGTGAAAAAAAAGTAA
Found at i:3381064 original size:43 final size:43
Alignment explanation
Indices: 3380996--3381309 Score: 330
Period size: 43 Copynumber: 7.3 Consensus size: 43
3380986 TATTTTAAAA
* * * * *
3380996 AAACGCCGCTAAAGGTCATGGCCTTTAGCGGTGCTTTTCCCAC
1 AAACGCCGCTAAAAGCCATGACCTTTAACGGCGCTTTTCCCAC
* * *
3381039 AAACGCCGCTAAAGGCCATGACCTTTAACGGCACTTTTCTCAC
1 AAACGCCGCTAAAAGCCATGACCTTTAACGGCGCTTTTCCCAC
*****
3381082 AAACGCCGCTAAAAATTGCGACCTTTAACGGCGCTTTTCCCAC
1 AAACGCCGCTAAAAGCCATGACCTTTAACGGCGCTTTTCCCAC
*
3381125 AAACGCCGCT-AAAGCCCATGACCTTTAACGGCGCTTTTCTCAC
1 AAACGCCGCTAAAAG-CCATGACCTTTAACGGCGCTTTTCCCAC
* * * *
3381168 AAACGCCGCTAAAAATCGCA--ACTTTTAGC-ACGCTTTTCCCAC
1 AAACGCCGCT-AAAAGC-CATGACCTTTAACGGCGCTTTTCCCAC
* * * ** *
3381210 AAATGCCACTAAAAAGTCGCGACCTTTAACGACGCTTTTCCCAC
1 AAACGCCGCT-AAAAGCCATGACCTTTAACGGCGCTTTTCCCAC
* *
3381254 AAACGTCGCTAAAAGCCGTGACCTTTAACGGCGCTTTTCCCAC
1 AAACGCCGCTAAAAGCCATGACCTTTAACGGCGCTTTTCCCAC
3381297 AAACGCCGCTAAA
1 AAACGCCGCTAAA
3381310 GGTCATGAAA
Statistics
Matches: 225, Mismatches: 39, Indels: 14
0.81 0.14 0.05
Matches are distributed among these distances:
41 1 0.00
42 27 0.12
43 171 0.76
44 21 0.09
45 5 0.02
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.23
Consensus pattern (43 bp):
AAACGCCGCTAAAAGCCATGACCTTTAACGGCGCTTTTCCCAC
Found at i:3381144 original size:86 final size:86
Alignment explanation
Indices: 3381017--3381310 Score: 378
Period size: 86 Copynumber: 3.4 Consensus size: 86
3381007 AAGGTCATGG
* * * *
3381017 CCTTTAGCGGTGCTTTTCCCACAAACGCCGCTAAAGGCCATGACCTTTAACGGCACTTTTCTCAC
1 CCTTTAACGGCGCTTTTCCCACAAACGCCGCTAAAGCCCATGACCTTTAACGGCGCTTTTCTCAC
*
3381082 AAACGCCGCTAAAAATTGCGA
66 AAACGCCGCTAAAAATCGCGA
3381103 CCTTTAACGGCGCTTTTCCCACAAACGCCGCTAAAGCCCATGACCTTTAACGGCGCTTTTCTCAC
1 CCTTTAACGGCGCTTTTCCCACAAACGCCGCTAAAGCCCATGACCTTTAACGGCGCTTTTCTCAC
*
3381168 AAACGCCGCTAAAAATCGCAA
66 AAACGCCGCTAAAAATCGCGA
* * * * * * * *
3381189 CTTTTAGC-ACGCTTTTCCCACAAATGCCACTAAAAAGTCGC--GACCTTTAACGACGCTTTTCC
1 CCTTTAACGGCGCTTTTCCCACAAACGCCGCT--AAAG-CCCATGACCTTTAACGGCGCTTTTCT
* ** *
3381251 CACAAACGTCGCTAAAAGCCGTGA
63 CACAAACGCCGCTAAAAATCGCGA
3381275 CCTTTAACGGCGCTTTTCCCACAAACGCCGCTAAAG
1 CCTTTAACGGCGCTTTTCCCACAAACGCCGCTAAAG
3381311 GTCATGAAAT
Statistics
Matches: 180, Mismatches: 24, Indels: 9
0.85 0.11 0.04
Matches are distributed among these distances:
85 24 0.13
86 130 0.72
87 24 0.13
88 2 0.01
ACGTcount: A:0.28, C:0.33, G:0.16, T:0.23
Consensus pattern (86 bp):
CCTTTAACGGCGCTTTTCCCACAAACGCCGCTAAAGCCCATGACCTTTAACGGCGCTTTTCTCAC
AAACGCCGCTAAAAATCGCGA
Found at i:3381232 original size:129 final size:128
Alignment explanation
Indices: 3380996--3381309 Score: 391
Period size: 129 Copynumber: 2.4 Consensus size: 128
3380986 TATTTTAAAA
* * * * *
3380996 AAACGCCGCTAAAGGTCATGGCCTTTAGCGGTGCTTTTCCCACAAACGCCGCT-AAAGGCCATGA
1 AAACGCCGCTAAA-GCCATGACCTTTAACGGCGCTTTTCCCACAAACGCCGCTAAAAAGCCA-GA
* * * * *
3381060 CCTTTAACGGCACTTTTCTCACAAACGCCGCTAAAAATTGCGACCTTTAACGGCGCTTTTCCCAC
64 CCTTTAACGACACTTTTCCCACAAACGCCACTAAAAATCGCGACCTTTAACGACGCTTTTCCCAC
* *
3381125 AAACGCCGCTAAAGCCCATGACCTTTAACGGCGCTTTTCTCACAAACGCCGCTAAAAATCGCA-A
1 AAACGCCGCTAAAG-CCATGACCTTTAACGGCGCTTTTCCCACAAACGCCGCTAAAAAGC-CAGA
* * * *
3381189 CTTTTAGC-ACGCTTTTCCCACAAATGCCACTAAAAAGTCGCGACCTTTAACGACGCTTTTCCCA
64 CCTTTAACGACACTTTTCCCACAAACGCCACTAAAAA-TCGCGACCTTTAACGACGCTTTTCCCA
3381253 C
128 C
* *
3381254 AAACGTCGCTAAAAGCCGTGACCTTTAACGGCGCTTTTCCCACAAACGCCGCTAAA
1 AAACGCCGCT-AAAGCCATGACCTTTAACGGCGCTTTTCCCACAAACGCCGCTAAA
3381310 GGTCATGAAA
Statistics
Matches: 161, Mismatches: 19, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
128 24 0.15
129 127 0.79
130 8 0.05
131 2 0.01
ACGTcount: A:0.28, C:0.32, G:0.17, T:0.23
Consensus pattern (128 bp):
AAACGCCGCTAAAGCCATGACCTTTAACGGCGCTTTTCCCACAAACGCCGCTAAAAAGCCAGACC
TTTAACGACACTTTTCCCACAAACGCCACTAAAAATCGCGACCTTTAACGACGCTTTTCCCAC
Found at i:3381622 original size:19 final size:19
Alignment explanation
Indices: 3381577--3381623 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
3381567 TAAATATTAA
*
3381577 AATAAAAATAAAAATATAG
1 AATAAAAATAAAAATAAAG
* *
3381596 AATCAAAACT-AAAATAAAT
1 AAT-AAAAATAAAAATAAAG
3381615 AATAAAAAT
1 AATAAAAAT
3381624 TAGATTAAAT
Statistics
Matches: 23, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
18 5 0.22
19 13 0.57
20 5 0.22
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.21
Consensus pattern (19 bp):
AATAAAAATAAAAATAAAG
Found at i:3385779 original size:21 final size:21
Alignment explanation
Indices: 3385753--3385837 Score: 71
Period size: 21 Copynumber: 3.7 Consensus size: 21
3385743 ACTCCTAAAC
*
3385753 CTTAAACCCTAAACCATATAT
1 CTTAAACCATAAACCATATAT
*
3385774 CTTAAACCATAGTTAACTCATAAACCT
1 CTTAAACCATA---AAC-CATATA--T
* *
3385801 GCTTAAACCCTAAATCATATAT
1 -CTTAAACCATAAACCATATAT
3385823 CTTAAACCATAAACC
1 CTTAAACCATAAACC
3385838 TTAAACTATA
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
21 23 0.46
22 1 0.02
24 8 0.16
25 7 0.14
27 1 0.02
28 10 0.20
ACGTcount: A:0.42, C:0.27, G:0.02, T:0.28
Consensus pattern (21 bp):
CTTAAACCATAAACCATATAT
Found at i:3385820 original size:49 final size:46
Alignment explanation
Indices: 3385737--3385833 Score: 149
Period size: 49 Copynumber: 2.0 Consensus size: 46
3385727 CTTCAAATAC
*
3385737 TAGTTAACTCCTAAACCTTAAACCCTAAACCATATATCTTAAACCA
1 TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAACCA
*
3385783 TAGTTAACTCATAAACCTGCTTAAACCCTAAATCATATATCTTAAACCA
1 TAGTTAACTCATAAA-C--CTTAAACCCTAAACCATATATCTTAAACCA
3385832 TA
1 TA
3385834 AACCTTAAAC
Statistics
Matches: 46, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
46 14 0.30
47 1 0.02
49 31 0.67
ACGTcount: A:0.41, C:0.26, G:0.03, T:0.30
Consensus pattern (46 bp):
TAGTTAACTCATAAACCTTAAACCCTAAACCATATATCTTAAACCA
Found at i:3386054 original size:41 final size:41
Alignment explanation
Indices: 3386009--3386206 Score: 251
Period size: 41 Copynumber: 4.9 Consensus size: 41
3385999 ATATGACTTT
* **
3386009 AAGCGCTGCTAATGCTCAAGTTTTTAGCGGCGTTTTACCAA
1 AAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTACCAA
*
3386050 AAGCGCCGCTAATGCTCTGGTTTTTAGCTGCGTTTTACCAA
1 AAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTACCAA
* *
3386091 AAGCGCCGCTAATACTCTGGTTTTTAGCGGCATTTTACCAA
1 AAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTACCAA
* * *
3386132 AAGCACCGCTAATGCTCT-GTTTTTAGTGGCGTTTTTTACTAA
1 AAGCGCCGCTAATGCTCTGGTTTTTAGCGGCG--TTTTACCAA
**
3386174 AA-CGCCGCTGTTGCTCT--TTTTTAGCGGCGTTTT
1 AAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTT
3386207 TTGATAAAAC
Statistics
Matches: 139, Mismatches: 16, Indels: 7
0.86 0.10 0.04
Matches are distributed among these distances:
38 4 0.03
40 22 0.16
41 103 0.74
42 10 0.07
ACGTcount: A:0.20, C:0.23, G:0.21, T:0.36
Consensus pattern (41 bp):
AAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTACCAA
Found at i:3386195 original size:40 final size:41
Alignment explanation
Indices: 3386144--3386222 Score: 117
Period size: 40 Copynumber: 2.0 Consensus size: 41
3386134 GCACCGCTAA
*
3386144 TGCTCTGTTTTTAGTGGCGTTTTTT-ACTAAAACGCCGCTGT
1 TGCTCTGTTTTTAGCGGCGTTTTTTGA-TAAAACGCCGCTGT
*
3386185 TGCTCT-TTTTTAGCGGCGTTTTTTGATAAAACGTCGCT
1 TGCTCTGTTTTTAGCGGCGTTTTTTGATAAAACGCCGCT
3386223 AAAAACGCCA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
40 28 0.80
41 7 0.20
ACGTcount: A:0.15, C:0.19, G:0.22, T:0.44
Consensus pattern (41 bp):
TGCTCTGTTTTTAGCGGCGTTTTTTGATAAAACGCCGCTGT
Found at i:3393799 original size:62 final size:60
Alignment explanation
Indices: 3393720--3393845 Score: 146
Period size: 60 Copynumber: 2.1 Consensus size: 60
3393710 TTTTTTCTAA
* * ***
3393720 TTTTAGAGTTAAGACTAAATTGACAACTTTTGTAAATGCTGAGGGCTAAATTTATTGACTTT
1 TTTTAGAATTAAGACTAAAATGAC-A-TTTTGTAAACAATGAGGGCTAAATTTATTGACTTT
* * *
3393782 TTTTAGAATT-AGAACTAAAATGACATTTTGTAAACAATGGGGGCTAAATTTGTTGATTTT
1 TTTTAGAATTAAG-ACTAAAATGACATTTTGTAAACAATGAGGGCTAAATTTATTGACTTT
3393842 TTTT
1 TTTT
3393846 TATGTTTAGG
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
60 33 0.60
61 3 0.05
62 19 0.35
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (60 bp):
TTTTAGAATTAAGACTAAAATGACATTTTGTAAACAATGAGGGCTAAATTTATTGACTTT
Found at i:3394478 original size:25 final size:26
Alignment explanation
Indices: 3394436--3394484 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
3394426 ATTATTATTA
*
3394436 AAAGTAAAGTAAATAG-AAAGAAAAT
1 AAAGTAAAGTAAAAAGAAAAGAAAAT
3394461 AAAGTAAAG-AACAAAGAAAAGAAA
1 AAAGTAAAGTAA-AAAGAAAAGAAA
3394485 CAGAATAGGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 2 0.10
25 12 0.57
26 7 0.33
ACGTcount: A:0.71, C:0.02, G:0.16, T:0.10
Consensus pattern (26 bp):
AAAGTAAAGTAAAAAGAAAAGAAAAT
Found at i:3396029 original size:23 final size:21
Alignment explanation
Indices: 3396003--3396047 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 21
3395993 AGGCACTTTA
3396003 TGTGTCGTATTTCAGGCACCTCG
1 TGTGTCGTA--TCAGGCACCTCG
*
3396026 TGTGTTGTATCAGGCACCTCG
1 TGTGTCGTATCAGGCACCTCG
3396047 T
1 T
3396048 TTTCTTTCTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.62
23 8 0.38
ACGTcount: A:0.13, C:0.24, G:0.27, T:0.36
Consensus pattern (21 bp):
TGTGTCGTATCAGGCACCTCG
Found at i:3398908 original size:23 final size:23
Alignment explanation
Indices: 3398876--3398919 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
3398866 GAAATGTTAG
*
3398876 TTTAAAAATTTTTTAGGTTTAAT
1 TTTAAAAATTTTTTAGATTTAAT
*
3398899 TTTAAGAATTTTTTAGATTTA
1 TTTAAAAATTTTTTAGATTTA
3398920 TACATATTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.34, C:0.00, G:0.09, T:0.57
Consensus pattern (23 bp):
TTTAAAAATTTTTTAGATTTAAT
Found at i:3400416 original size:21 final size:21
Alignment explanation
Indices: 3400391--3400437 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3400381 GTGTTTTATG
3400391 GTTTAAGGCTTAGGGCTTAGA
1 GTTTAAGGCTTAGGGCTTAGA
* * *
3400412 GTTTATGGTTTATGGCTTAGA
1 GTTTAAGGCTTAGGGCTTAGA
3400433 GTTTA
1 GTTTA
3400438 TATTTTAGGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.21, C:0.06, G:0.30, T:0.43
Consensus pattern (21 bp):
GTTTAAGGCTTAGGGCTTAGA
Found at i:3400444 original size:21 final size:21
Alignment explanation
Indices: 3400404--3400444 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3400394 TAAGGCTTAG
*
3400404 GGCTTAGAGTTTATGGTTTAT
1 GGCTTAGAGTTTATAGTTTAT
*
3400425 GGCTTAGAGTTTATATTTTA
1 GGCTTAGAGTTTATAGTTTA
3400445 GGGTTCGGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.22, C:0.05, G:0.24, T:0.49
Consensus pattern (21 bp):
GGCTTAGAGTTTATAGTTTAT
Found at i:3400444 original size:28 final size:28
Alignment explanation
Indices: 3400384--3400449 Score: 78
Period size: 28 Copynumber: 2.4 Consensus size: 28
3400374 GGGTCTAGTG
*
3400384 TTTTATGGTTTAAGGCTTAGGGCTTAGA
1 TTTTATGGTTTAAGGCTTAGAGCTTAGA
* * * *
3400412 GTTTATGGTTTATGGCTTAGAGTTTATA
1 TTTTATGGTTTAAGGCTTAGAGCTTAGA
*
3400440 TTTTAGGGTT
1 TTTTATGGTT
3400450 CGGGAGTTAT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.20, C:0.05, G:0.27, T:0.48
Consensus pattern (28 bp):
TTTTATGGTTTAAGGCTTAGAGCTTAGA
Found at i:3410310 original size:42 final size:42
Alignment explanation
Indices: 3410262--3410354 Score: 109
Period size: 42 Copynumber: 2.2 Consensus size: 42
3410252 TGATATTAGG
*
3410262 GTTATGAG-TTTACATGTAAGAACATATT-TGAGATATGGCATC
1 GTTATGAGATTT-CATGTAAGAACAT-TTCTGAGACATGGCATC
* * *
3410304 GTTATGAGATTTCGTGTAAGACCATTTCTGGGACATGGCATC
1 GTTATGAGATTTCATGTAAGAACATTTCTGAGACATGGCATC
*
3410346 GATATGAGA
1 GTTATGAGA
3410355 ATCGTGTAAG
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
41 2 0.05
42 39 0.89
43 3 0.07
ACGTcount: A:0.30, C:0.12, G:0.25, T:0.33
Consensus pattern (42 bp):
GTTATGAGATTTCATGTAAGAACATTTCTGAGACATGGCATC
Found at i:3410385 original size:42 final size:41
Alignment explanation
Indices: 3410296--3410413 Score: 121
Period size: 42 Copynumber: 2.8 Consensus size: 41
3410286 TATTTGAGAT
* ** *
3410296 ATGGCATCGTTATGAGATTTCGTGTAAGACCATTTCTGGGAC
1 ATGGCATCGATATGAGA-TTCGTGTAAGACCATAGCTAGGAC
*
3410338 ATGGCATCGATATGAGAATCGTGTAAGACCATAGCTAGG-C
1 ATGGCATCGATATGAGATTCGTGTAAGACCATAGCTAGGAC
* * *
3410378 TATTGGCATCAATATAAGATTCCATGTAAGACCATA
1 -A-TGGCATCGATATGAGATT-CGTGTAAGACCATA
3410414 TCTGGGATAT
Statistics
Matches: 64, Mismatches: 9, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
40 1 0.02
41 19 0.30
42 31 0.48
43 13 0.20
ACGTcount: A:0.31, C:0.17, G:0.23, T:0.29
Consensus pattern (41 bp):
ATGGCATCGATATGAGATTCGTGTAAGACCATAGCTAGGAC
Found at i:3412083 original size:32 final size:32
Alignment explanation
Indices: 3412025--3412089 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
3412015 TTTGGATCTG
* *
3412025 GTGTTTAAAGCTGTTAAAGACATAAGTTAAGT
1 GTGTTTAAAGCTGCTAAAGACATAAGTCAAGT
* **
3412057 GTGTTTAGAGCTGCTAAAGATGTAAGTCAAGT
1 GTGTTTAAAGCTGCTAAAGACATAAGTCAAGT
3412089 G
1 G
3412090 AGTCCCTAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.34, C:0.08, G:0.26, T:0.32
Consensus pattern (32 bp):
GTGTTTAAAGCTGCTAAAGACATAAGTCAAGT
Found at i:3412577 original size:29 final size:28
Alignment explanation
Indices: 3412484--3412863 Score: 324
Period size: 29 Copynumber: 13.3 Consensus size: 28
3412474 AAAAGCACAC
* *
3412484 CTTTATGGCTATCTCTGTTAAAAAGATG
1 CTTTGTGGCTATCTCTGTTAAAAGGATG
* ** *
3412512 TCTATGTGGAGATATCTG--AAAAGGATG
1 -CTTTGTGGCTATCTCTGTTAAAAGGATG
* **
3412539 TCTTTATGGCTATCTCTGTTAAAAATATG
1 -CTTTGTGGCTATCTCTGTTAAAAGGATG
*
3412568 CGTTTGTGGCTATCTCAGTTAAAAGGATG
1 C-TTTGTGGCTATCTCTGTTAAAAGGATG
* *
3412597 ACTTTGTGGCTATCTC-ATTAAAGGGATG
1 -CTTTGTGGCTATCTCTGTTAAAAGGATG
*
3412625 TCTTTGTGGCTATCTCTGTTAAAAGGAAG
1 -CTTTGTGGCTATCTCTGTTAAAAGGATG
* * *
3412654 TCTTTGTGACGATCTCTGTTAAAAGGAAG
1 -CTTTGTGGCTATCTCTGTTAAAAGGATG
* * *
3412683 TCTTTATGG-TGATATCTG-AAAAAGGATG
1 -CTTTGTGGCT-ATCTCTGTTAAAAGGATG
* *
3412711 CCTTTATGGCTATCTCTATTAAAAGGATG
1 -CTTTGTGGCTATCTCTGTTAAAAGGATG
*
3412740 CCTTTGTGGCTATCTCTGTTAAGAGGATG
1 -CTTTGTGGCTATCTCTGTTAAAAGGATG
* * *
3412769 CCTTTGTGGTTATCTCTATTAAGAGGATG
1 -CTTTGTGGCTATCTCTGTTAAAAGGATG
3412798 CCTTTGTGGCTATCT-TAGTT-AAAGGAATG
1 -CTTTGTGGCTATCTCT-GTTAAAAGG-ATG
* * *
3412827 CCTTGTGACTATCTCTATTAAAAGGATG
1 CTTTGTGGCTATCTCTGTTAAAAGGATG
3412855 TCTTTGTGG
1 -CTTTGTGG
3412864 TGAGACTCTG
Statistics
Matches: 290, Mismatches: 48, Indels: 26
0.80 0.13 0.07
Matches are distributed among these distances:
27 21 0.07
28 69 0.24
29 199 0.69
30 1 0.00
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.38
Consensus pattern (28 bp):
CTTTGTGGCTATCTCTGTTAAAAGGATG
Found at i:3412642 original size:86 final size:83
Alignment explanation
Indices: 3412484--3412864 Score: 354
Period size: 86 Copynumber: 4.5 Consensus size: 83
3412474 AAAAGCACAC
* * * * * *
3412484 CTTTATGGCTATCTCTGTTAAAAAGATGTCTATGTGGAGATATCTGAAAAGGATGTCTTTATGGC
1 CTTTGTGGCTATCTCTGTTAAAAGGATGTCTTTGTGG-TATATCTTAAAAGGATGCCTTTATGGC
*
3412549 TATCTCTGTTAAAAATATG
65 TATCTCTGTTAAAAAGATG
* * * * * *
3412568 CGTTTGTGGCTATCTCAGTTAAAAGGATGACTTTGTGGCTATCTCATTAAAGGGATGTCTTTGTG
1 C-TTTGTGGCTATCTCTGTTAAAAGGATGTCTTTGTGG-TATATC-TTAAAAGGATGCCTTTATG
* *
3412633 GCTATCTCTGTTAAAAGGAAG
63 GCTATCTCTGTTAAAAAGATG
* * * * *
3412654 TCTTTGTGACGATCTCTGTTAAAAGGAAGTCTTTATGGTGATATCTGAAAAAGGATGCCTTTATG
1 -CTTTGTGGCTATCTCTGTTAAAAGGATGTCTTTGTGGT-ATATCT-TAAAAGGATGCCTTTATG
* *
3412719 GCTATCTCTATTAAAAGGATG
63 GCTATCTCTGTTAAAAAGATG
* * *
3412740 CCTTTGTGGCTATCTCTGTTAAGAGGATGCCTTTGTGGT-TATCTCTATTAAGAGGATGCCTTTG
1 -CTTTGTGGCTATCTCTGTTAAAAGGATGTCTTTGTGGTATATCT-TA--AA-AGGATGCCTTTA
*
3412804 TGGCTATCT-TAGTT-AAAGGAATG
61 TGGCTATCTCT-GTTAAAAAG-ATG
* * *
3412827 CCTTGTGACTATCTCTATTAAAAGGATGTCTTTGTGGT
1 CTTTGTGGCTATCTCTGTTAAAAGGATGTCTTTGTGGT
3412865 GAGACTCTGA
Statistics
Matches: 244, Mismatches: 43, Indels: 18
0.80 0.14 0.06
Matches are distributed among these distances:
84 7 0.03
85 37 0.15
86 174 0.71
87 26 0.11
ACGTcount: A:0.25, C:0.14, G:0.23, T:0.38
Consensus pattern (83 bp):
CTTTGTGGCTATCTCTGTTAAAAGGATGTCTTTGTGGTATATCTTAAAAGGATGCCTTTATGGCT
ATCTCTGTTAAAAAGATG
Found at i:3412676 original size:115 final size:114
Alignment explanation
Indices: 3412484--3412863 Score: 394
Period size: 115 Copynumber: 3.3 Consensus size: 114
3412474 AAAAGCACAC
* * * * ** * *
3412484 CTTTATGGCTATCTCTGTTAAAAAGATGTCTATGTGGAGATATCTG--AAAAGGATGTCTTTATG
1 CTTTGTGGCTATCTCTATTAAAAGGATGTCTTTGTGGCTATCTCTGTTAAAAGGATGTCTTTGTG
**
3412547 GCTATCTCTGTTAAAAATATGCGTTTGTGGCTATCTCAGTTAAAAGGATG
66 GCTATCTCTGTTAAAAGGATGC-TTTGTGGCTATCTCAGTTAAAAGGATG
* *
3412597 ACTTTGTGGCTATCTC-ATTAAAGGGATGTCTTTGTGGCTATCTCTGTTAAAAGGAAGTCTTTGT
1 -CTTTGTGGCTATCTCTATTAAAAGGATGTCTTTGTGGCTATCTCTGTTAAAAGGATGTCTTTGT
* * * * * * *
3412661 GACGATCTCTGTTAAAAGGAAGTCTTTATGG-TGATATCTG-AAAAAGGATG
65 GGCTATCTCTGTTAAAAGGATG-CTTTGTGGCT-ATCTCAGTTAAAAGGATG
* * * *
3412711 CCTTTATGGCTATCTCTATTAAAAGGATGCCTTTGTGGCTATCTCTGTTAAGAGGATGCCTTTGT
1 -CTTTGTGGCTATCTCTATTAAAAGGATGTCTTTGTGGCTATCTCTGTTAAAAGGATGTCTTTGT
* * * *
3412776 GGTTATCTCTATTAAGAGGATGCCTTTGTGGCTATCTTAGTT-AAAGGAATG
65 GGCTATCTCTGTTAAAAGGATG-CTTTGTGGCTATCTCAGTTAAAAGG-ATG
* *
3412827 CCTTGTGACTATCTCTATTAAAAGGATGTCTTTGTGG
1 CTTTGTGGCTATCTCTATTAAAAGGATGTCTTTGTGG
3412864 TGAGACTCTG
Statistics
Matches: 216, Mismatches: 42, Indels: 15
0.79 0.15 0.05
Matches are distributed among these distances:
113 23 0.11
114 38 0.18
115 150 0.69
116 5 0.02
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.38
Consensus pattern (114 bp):
CTTTGTGGCTATCTCTATTAAAAGGATGTCTTTGTGGCTATCTCTGTTAAAAGGATGTCTTTGTG
GCTATCTCTGTTAAAAGGATGCTTTGTGGCTATCTCAGTTAAAAGGATG
Found at i:3413018 original size:163 final size:163
Alignment explanation
Indices: 3412839--3413152 Score: 425
Period size: 163 Copynumber: 1.9 Consensus size: 163
3412829 TTGTGACTAT
* ** *
3412839 CTCTATTAAAAGGATGTCTTTGTGGTGAGACTCTGAAAGAAAAACT-TTTGTAGCTATCTTTGGA
1 CTCTATTAAAAGGATGTCTTCGTGGCAAGACTCTAAAAG-AAAACTCTTTGTAGCTATCTTT-GA
* *
3412903 AAA-GAATGCCTTCGTGGCAGAATCTGAAGAACGGATCTCATGATGACCAACTGAAGACAACGCC
64 AAAGGAATGCCTTCGTGGCAGAATCTAAAGAACGGATCTCATGATGACCAACTAAAGACAACGCC
*
3412967 TTTAGGCGGACACCAAATGAATGCCTTATGGCAAA
129 TTTAGGCAGACACCAAATGAATGCCTTATGGCAAA
* * *
3413002 CTCTGTTAAAAGGATGTCTTCGTGGCAAGACTCTAAAAGGAAAGTCTTTGTAGCTATCTTTGAAA
1 CTCTATTAAAAGGATGTCTTCGTGGCAAGACTCTAAAAGAAAACTCTTTGTAGCTATCTTTGAAA
** * * * **
3413067 AGGAATGCCTTCGTGGTGGAATCTAAAGAACTGATCTCATGATGACCATCTAAAGACAATGTTTT
66 AGGAATGCCTTCGTGGCAGAATCTAAAGAACGGATCTCATGATGACCAACTAAAGACAACGCCTT
* *
3413132 TGGGCAGACACTAAATGAATG
131 TAGGCAGACACCAAATGAATG
3413153 ACAAACATCA
Statistics
Matches: 130, Mismatches: 19, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
162 9 0.07
163 121 0.93
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (163 bp):
CTCTATTAAAAGGATGTCTTCGTGGCAAGACTCTAAAAGAAAACTCTTTGTAGCTATCTTTGAAA
AGGAATGCCTTCGTGGCAGAATCTAAAGAACGGATCTCATGATGACCAACTAAAGACAACGCCTT
TAGGCAGACACCAAATGAATGCCTTATGGCAAA
Found at i:3413874 original size:6 final size:6
Alignment explanation
Indices: 3413844--3413931 Score: 65
Period size: 6 Copynumber: 14.3 Consensus size: 6
3413834 AAGAAACATT
* * * *
3413844 ATCAGA A-CTAGA ATCAAA ATAAGA ATCAGA ATTAGA ATCA-A GTGACAGA
1 ATCAGA ATC-AGA ATCAGA ATCAGA ATCAGA ATCAGA ATCAGA AT--CAGA
*
3413893 ATCAGA ATCAGT ATCAGGTA A-CAGA ATCAGA ATCAGA AT
1 ATCAGA ATCAGA ATCA-G-A ATCAGA ATCAGA ATCAGA AT
3413932 GTGAATGCAA
Statistics
Matches: 64, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
5 5 0.08
6 50 0.78
7 6 0.09
8 3 0.05
ACGTcount: A:0.50, C:0.14, G:0.17, T:0.19
Consensus pattern (6 bp):
ATCAGA
Found at i:3413898 original size:25 final size:24
Alignment explanation
Indices: 3413844--3413931 Score: 90
Period size: 25 Copynumber: 3.6 Consensus size: 24
3413834 AAGAAACATT
*
3413844 ATCAGAA-CTAGAATCAAAATA-AGA
1 ATCAGAATC-AGAATC-AAGTACAGA
*
3413868 ATCAGAATTAGAATCAAGTGACAGA
1 ATCAGAATCAGAATCAAGT-ACAGA
* *
3413893 ATCAGAATCAGTATCAGGTAACAGA
1 ATCAGAATCAGAATCAAGT-ACAGA
3413918 ATCAGAATCAGAAT
1 ATCAGAATCAGAAT
3413932 GTGAATGCAA
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
23 3 0.06
24 14 0.26
25 37 0.69
ACGTcount: A:0.50, C:0.14, G:0.17, T:0.19
Consensus pattern (24 bp):
ATCAGAATCAGAATCAAGTACAGA
Found at i:3414160 original size:71 final size:67
Alignment explanation
Indices: 3414083--3414224 Score: 185
Period size: 67 Copynumber: 2.1 Consensus size: 67
3414073 TCACCAGATA
* * *
3414083 CAGATATTGTGGCTAGGCCACCAGAACAGATATATATATATGGCGAAGCCACCAGATTGCAGCGA
1 CAGATATTGTGACGAAGCCACCAGAAC--A-A-ATATATATGGCGAAGCCACCAGATTGCAGCGA
3414148 GGCTGC
62 GGCTGC
* * * *
3414154 CAGATATTGTGACGAAGTCACCAGAACAAATATATGTGGCGAGGCCACCAGATTGTAGCGAGGCT
1 CAGATATTGTGACGAAGCCACCAGAACAAATATATATGGCGAAGCCACCAGATTGCAGCGAGGCT
3414219 GC
66 GC
3414221 CAGA
1 CAGA
3414225 ACGCTTCCTC
Statistics
Matches: 64, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
67 39 0.61
68 1 0.02
69 1 0.02
71 23 0.36
ACGTcount: A:0.32, C:0.22, G:0.27, T:0.19
Consensus pattern (67 bp):
CAGATATTGTGACGAAGCCACCAGAACAAATATATATGGCGAAGCCACCAGATTGCAGCGAGGCT
GC
Found at i:3414482 original size:27 final size:27
Alignment explanation
Indices: 3414452--3414558 Score: 133
Period size: 27 Copynumber: 4.0 Consensus size: 27
3414442 GGGATAAAAT
* * *
3414452 GGTAATTTTACCCTACAAGGGTGTCTC
1 GGTAATTCTACCCTACAAGGGTATTTC
*
3414479 GGTAATTCTACCCTACAGGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* *
3414506 AGTATTTCTACCCTACAAGGGTATTTC
1 GGTAATTCTACCCTACAAGGGTATTTC
* * *
3414533 GGTGATTCTACCCTATAGGGGTATTT
1 GGTAATTCTACCCTACAAGGGTATTT
3414559 TACTAAATCG
Statistics
Matches: 68, Mismatches: 12, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 68 1.00
ACGTcount: A:0.22, C:0.21, G:0.21, T:0.36
Consensus pattern (27 bp):
GGTAATTCTACCCTACAAGGGTATTTC
Found at i:3414518 original size:54 final size:53
Alignment explanation
Indices: 3414456--3414558 Score: 161
Period size: 54 Copynumber: 1.9 Consensus size: 53
3414446 TAAAATGGTA
*
3414456 ATTTTACCCTACAAGGGTGTCTCGGTAATTCTACCCTACAGGGGTATTTCAGT
1 ATTTTACCCTACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCAGT
* * *
3414509 ATTTCTACCCTACAAGGGTATTTCGGTGATTCTACCCTATAGGGGTATTT
1 ATTT-TACCCTACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTT
3414559 TACTAAATCG
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
53 4 0.09
54 41 0.91
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.36
Consensus pattern (53 bp):
ATTTTACCCTACAAGGGTATCTCGGTAATTCTACCCTACAGGGGTATTTCAGT
Found at i:3414600 original size:27 final size:27
Alignment explanation
Indices: 3414562--3414709 Score: 206
Period size: 27 Copynumber: 5.5 Consensus size: 27
3414552 GGTATTTTAC
* *
3414562 TAAATCGAGGGTAAAACAGTAATTCTA
1 TAAATTGAGGGTAAAACAGTAATTCTG
*
3414589 TAAATTGAGGGTAAAACGGTAATTCTG
1 TAAATTGAGGGTAAAACAGTAATTCTG
** * *
3414616 TAAATCAAGGGTAAAACAATAATTCTA
1 TAAATTGAGGGTAAAACAGTAATTCTG
* *
3414643 TAAATTAAGGGTAAAATAGTAATTCTG
1 TAAATTGAGGGTAAAACAGTAATTCTG
*
3414670 TAAATTGAGGGTAAAACGGTAATTCTG
1 TAAATTGAGGGTAAAACAGTAATTCTG
3414697 TAAATTGAGGGTA
1 TAAATTGAGGGTA
3414710 CTTTGGTAAT
Statistics
Matches: 106, Mismatches: 15, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
27 106 1.00
ACGTcount: A:0.43, C:0.07, G:0.21, T:0.29
Consensus pattern (27 bp):
TAAATTGAGGGTAAAACAGTAATTCTG
Found at i:3414719 original size:54 final size:54
Alignment explanation
Indices: 3414562--3414736 Score: 224
Period size: 54 Copynumber: 3.2 Consensus size: 54
3414552 GGTATTTTAC
*
3414562 TAAATCGAGGGTAAAACAGTAATTCTATAAATTGAGGGTAAAACGGTAATTCTG
1 TAAATCGAGGGTAAAACAGTAATTCTATAAATTGAGGGTAAAATGGTAATTCTG
* * * *
3414616 TAAATCAAGGGTAAAACAATAATTCTATAAATTAAGGGTAAAATAGTAATTCTG
1 TAAATCGAGGGTAAAACAGTAATTCTATAAATTGAGGGTAAAATGGTAATTCTG
* * * *** *
3414670 TAAATTGAGGGTAAAACGGTAATTCTGTAAATTGAGGGTACTTTGGTAATTCTA
1 TAAATCGAGGGTAAAACAGTAATTCTATAAATTGAGGGTAAAATGGTAATTCTG
* *
3414724 CAAGTCGAGGGTA
1 TAAATCGAGGGTA
3414737 TTTTAGTAAT
Statistics
Matches: 102, Mismatches: 19, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 102 1.00
ACGTcount: A:0.40, C:0.09, G:0.22, T:0.30
Consensus pattern (54 bp):
TAAATCGAGGGTAAAACAGTAATTCTATAAATTGAGGGTAAAATGGTAATTCTG
Found at i:3417089 original size:41 final size:41
Alignment explanation
Indices: 3417034--3417366 Score: 181
Period size: 41 Copynumber: 8.2 Consensus size: 41
3417024 CGTTTGTCTG
*
3417034 AAACGCCACTAAAAACTAAACTATAGCGGCATTTTTGG-CA
1 AAACGCCACTAAAAACTAAACAATAGCGGCATTTTTGGCCA
* ** *
3417074 AACACGCCGCTAAAAACTAGTCAATAGCGGCGTTTTTGGCCA
1 AA-ACGCCACTAAAAACTAAACAATAGCGGCATTTTTGGCCA
*** * **
3417116 AAACGCCACTAAAAACTGGTCAAT-GCGGCGTTTTTCACC-
1 AAACGCCACTAAAAACTAAACAATAGCGGCATTTTTGGCCA
* * * * *** *
3417155 AAACGCCACTAAAAGCTTATCAATAGAGGCATTTTAATCCC
1 AAACGCCACTAAAAACTAAACAATAGCGGCATTTTTGGCCA
* * * * ** *
3417196 AAATGCCACTAAAAACTGATCAATTA-CGGCGTTTTTATCCC
1 AAACGCCACTAAAAACTAAACAA-TAGCGGCATTTTTGGCCA
* * * ** **
3417237 AAACGCCACTAAAAACTAATCAATTGTGGTGTTTTTATCCA
1 AAACGCCACTAAAAACTAAACAATAGCGGCATTTTTGGCCA
* *** * * * * **
3417278 AAACGCCACTAAACACTGCTCAATTGTGGCGTTTCTATCCA
1 AAACGCCACTAAAAACTAAACAATAGCGGCATTTTTGGCCA
* * * *
3417319 AAACGCCACTAAACACTGATCAATAGCGGCGTTTTTGGTCC-
1 AAACGCCACTAAAAACTAAACAATAGCGGCATTTTTGG-CCA
3417360 AAACGCC
1 AAACGCC
3417367 GCAAAAAGTT
Statistics
Matches: 246, Mismatches: 40, Indels: 13
0.82 0.13 0.04
Matches are distributed among these distances:
39 21 0.09
40 26 0.11
41 191 0.78
42 8 0.03
ACGTcount: A:0.34, C:0.26, G:0.16, T:0.25
Consensus pattern (41 bp):
AAACGCCACTAAAAACTAAACAATAGCGGCATTTTTGGCCA
Found at i:3417158 original size:82 final size:82
Alignment explanation
Indices: 3417034--3417354 Score: 303
Period size: 82 Copynumber: 3.9 Consensus size: 82
3417024 CGTTTGTCTG
* * * * * ** *
3417034 AAACGCCACTAAAAACTAAACTATAGCGGCATTTTT-GGCAAACACGCCGCTAAAAACTAGTCAA
1 AAACGCCACTAAAAACTGATCAATTGCGGCGTTTTTATCCAAA-ACGCCACTAAAAACTAGTCAA
*
3417098 TAGCGGCGTTTTTGGCCA
65 TAGCGGCGTTTTTAGCCA
* *
3417116 AAACGCCACTAAAAACTGGTCAA-TGCGGCGTTTTTCA-CC-AAACGCCACTAAAAGCTTA-TCA
1 AAACGCCACTAAAAACTGATCAATTGCGGCGTTTTT-ATCCAAAACGCCACTAAAAAC-TAGTCA
* * * * *
3417177 ATAGAGGCATTTTAATCCC
64 ATAGCGGCGTTTTTAGCCA
* * * *
3417196 AAATGCCACTAAAAACTGATCAATTACGGCGTTTTTATCCCAAACGCCACTAAAAACTAATCAAT
1 AAACGCCACTAAAAACTGATCAATTGCGGCGTTTTTATCCAAAACGCCACTAAAAACTAGTCAAT
* * * *
3417261 TGTGGTGTTTTTATCCA
66 AGCGGCGTTTTTAGCCA
* * * * *
3417278 AAACGCCACTAAACACTGCTCAATTGTGGCGTTTCTATCCAAAACGCCACTAAACACT-GATCAA
1 AAACGCCACTAAAAACTGATCAATTGCGGCGTTTTTATCCAAAACGCCACTAAAAACTAG-TCAA
3417342 TAGCGGCGTTTTT
65 TAGCGGCGTTTTT
3417355 GGTCCAAACG
Statistics
Matches: 194, Mismatches: 37, Indels: 16
0.79 0.15 0.06
Matches are distributed among these distances:
80 50 0.26
81 29 0.15
82 115 0.59
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.26
Consensus pattern (82 bp):
AAACGCCACTAAAAACTGATCAATTGCGGCGTTTTTATCCAAAACGCCACTAAAAACTAGTCAAT
AGCGGCGTTTTTAGCCA
Found at i:3417362 original size:123 final size:121
Alignment explanation
Indices: 3417072--3417366 Score: 325
Period size: 123 Copynumber: 2.4 Consensus size: 121
3417062 GCATTTTTGG
* **
3417072 CAAACACGCCGCTAAAAACT-AGTCAATAGCGGCGTTTTTGG-CCAAAACGCCACTAAAAACTGG
1 CAAA-ACGCCACTAAAAACTGA-TCAATAGCGGCGTTTTTGGTCC-AAACGCCACTAAAAACTAA
*
3417135 TCAATGCGGCGTTTTTCACCAAACGCCACTAAAAGCTTATCAATAGAGGCATTTTAATC
63 TCAATGCGGCGTTTTTCACCAAACGCCACTAAAAGCTGATCAATAGAGGCATTTTAATC
* * *
3417194 CCAAATGCCACTAAAAACTGATCAATTA-CGGCGTTTTT-ATCCCAAACGCCACTAAAAACTAAT
1 CAAAACGCCACTAAAAACTGATCAA-TAGCGGCGTTTTTGGT-CCAAACGCCACTAAAAACTAAT
* * * * * *
3417257 CAATTGTGGTGTTTTT-ATCCAAAACGCCACTAAACA-CTGCTCAATTGTGGCGTTTCT-ATC
64 CAA-TGCGGCGTTTTTCA-CC-AAACGCCACTAAA-AGCTGATCAATAGAGGCATTT-TAATC
*
3417317 CAAAACGCCACTAAACACTGATCAATAGCGGCGTTTTTGGTCCAAACGCC
1 CAAAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGGTCCAAACGCC
3417367 GCAAAAAGTT
Statistics
Matches: 145, Mismatches: 17, Indels: 21
0.79 0.09 0.11
Matches are distributed among these distances:
121 49 0.34
122 22 0.15
123 71 0.49
124 3 0.02
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (121 bp):
CAAAACGCCACTAAAAACTGATCAATAGCGGCGTTTTTGGTCCAAACGCCACTAAAAACTAATCA
ATGCGGCGTTTTTCACCAAACGCCACTAAAAGCTGATCAATAGAGGCATTTTAATC
Found at i:3417695 original size:14 final size:14
Alignment explanation
Indices: 3417656--3417748 Score: 51
Period size: 14 Copynumber: 6.5 Consensus size: 14
3417646 TGGCTTTTTG
*
3417656 TAAACCCTTAAATCT
1 TAAACCC-TAAACCT
**
3417671 TAAACATTAAACCT
1 TAAACCCTAAACCT
**
3417685 TAAACCCTAAATTT
1 TAAACCCTAAACCT
* * *
3417699 TAAAACATAAACCA
1 TAAACCCTAAACCT
* * *
3417713 TAAACACTAATCCA
1 TAAACCCTAAACCT
* *
3417727 TAAACTCCAAAACCC
1 TAAAC-CCTAAACCT
3417742 TAAACCC
1 TAAACCC
3417749 CCCAAAAAAA
Statistics
Matches: 57, Mismatches: 20, Indels: 3
0.71 0.25 0.04
Matches are distributed among these distances:
14 42 0.74
15 15 0.26
ACGTcount: A:0.48, C:0.28, G:0.00, T:0.24
Consensus pattern (14 bp):
TAAACCCTAAACCT
Found at i:3417695 original size:21 final size:21
Alignment explanation
Indices: 3417656--3417718 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 21
3417646 TGGCTTTTTG
* *
3417656 TAAACCCTTAAATCTTAAACAT
1 TAAA-CCTTAAACCATAAACAT
* **
3417678 TAAACCTTAAACCCTAAATTT
1 TAAACCTTAAACCATAAACAT
* *
3417699 TAAAACATAAACCATAAACA
1 TAAACCTTAAACCATAAACA
3417719 CTAATCCATA
Statistics
Matches: 32, Mismatches: 9, Indels: 1
0.76 0.21 0.02
Matches are distributed among these distances:
21 28 0.88
22 4 0.12
ACGTcount: A:0.51, C:0.22, G:0.00, T:0.27
Consensus pattern (21 bp):
TAAACCTTAAACCATAAACAT
Found at i:3417979 original size:43 final size:41
Alignment explanation
Indices: 3417903--3417988 Score: 100
Period size: 43 Copynumber: 2.0 Consensus size: 41
3417893 TATGGTTTAG
* * * *
3417903 GGTTCAATGGTAGAATATATTTTAAGTTTATGGTTTAGGCC
1 GGTTCAATGGTAGAACATATATTAAGTTAATGGTATAGGCC
* *
3417944 GGTTCAATGGTATAGTACATATATTAAGTTAATGGTATGGGCC
1 GGTTCAATGG--TAGAACATATATTAAGTTAATGGTATAGGCC
3417987 GG
1 GG
3417989 GTTTGTTATC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
41 10 0.27
43 27 0.73
ACGTcount: A:0.28, C:0.08, G:0.27, T:0.37
Consensus pattern (41 bp):
GGTTCAATGGTAGAACATATATTAAGTTAATGGTATAGGCC
Found at i:3418268 original size:13 final size:13
Alignment explanation
Indices: 3418250--3418288 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
3418240 AGATAATTTA
3418250 AAATACTTTAATT
1 AAATACTTTAATT
3418263 AAATACTTTAATT
1 AAATACTTTAATT
*
3418276 AAGTACTTTAATT
1 AAATACTTTAATT
3418289 TTAAGATGCA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.44, C:0.08, G:0.03, T:0.46
Consensus pattern (13 bp):
AAATACTTTAATT
Found at i:3418837 original size:40 final size:41
Alignment explanation
Indices: 3418793--3418886 Score: 97
Period size: 40 Copynumber: 2.4 Consensus size: 41
3418783 GCGTTTTTAC
***
3418793 AAAAACGCCACTAAAAA-TAGAGAATTAGTGGCGCTTTCATA
1 AAAAACGCCACTAAAAACT-GAGAATTAGCAACGCTTTCATA
* *
3418834 AAAAACGCCGC-AAAAACTGAGAATTAGCAACGCTTT--TG
1 AAAAACGCCACTAAAAACTGAGAATTAGCAACGCTTTCATA
*
3418872 TAAAACGCCACTAAA
1 AAAAACGCCACTAAA
3418887 TTTTTAATTG
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
38 10 0.23
39 3 0.07
40 20 0.45
41 11 0.25
ACGTcount: A:0.45, C:0.20, G:0.16, T:0.19
Consensus pattern (41 bp):
AAAAACGCCACTAAAAACTGAGAATTAGCAACGCTTTCATA
Found at i:3419486 original size:18 final size:19
Alignment explanation
Indices: 3419452--3419487 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
3419442 CTTCTTTTTG
3419452 TAGAATTGCAAAGATGAAA
1 TAGAATTGCAAAGATGAAA
*
3419471 TAGAATTG-AGAGATGAA
1 TAGAATTGCAAAGATGAA
3419488 GAATTTCAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.50, C:0.03, G:0.25, T:0.22
Consensus pattern (19 bp):
TAGAATTGCAAAGATGAAA
Found at i:3419882 original size:11 final size:11
Alignment explanation
Indices: 3419866--3419915 Score: 64
Period size: 11 Copynumber: 4.4 Consensus size: 11
3419856 CAACTTGTAT
3419866 ATTTGTCAAGA
1 ATTTGTCAAGA
3419877 ATTTGTCAAGA
1 ATTTGTCAAGA
* *
3419888 ATTTGACAAAATA
1 ATTTGTC--AAGA
3419901 ATTTGTCAAGA
1 ATTTGTCAAGA
3419912 ATTT
1 ATTT
3419916 TTAAAATATT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
11 24 0.73
13 9 0.27
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (11 bp):
ATTTGTCAAGA
Found at i:3423084 original size:9 final size:9
Alignment explanation
Indices: 3423061--3423188 Score: 112
Period size: 9 Copynumber: 13.6 Consensus size: 9
3423051 ATTGATCATT
*
3423061 ACTTAAATA
1 ACTTACATA
*
3423070 AATTACATA
1 ACTTACATA
3423079 ACTTACATA
1 ACTTACATA
* *
3423088 ACTCATATA
1 ACTTACATA
3423097 ACTTACATA
1 ACTTACATA
*
3423106 ATTTACATAACA
1 ACTTACAT---A
3423118 ACTTACATA
1 ACTTACATA
*
3423127 ACTCACATA
1 ACTTACATA
3423136 ACTTACATA
1 ACTTACATA
*
3423145 ATTTACATA
1 ACTTACATA
*
3423154 ACTCACATA
1 ACTTACATA
* *
3423163 ACGTATATAACA
1 AC-T-TA-CATA
3423175 ACTTACATA
1 ACTTACATA
3423184 ACTTA
1 ACTTA
3423189 ACTAATACAT
Statistics
Matches: 94, Mismatches: 19, Indels: 12
0.75 0.15 0.10
Matches are distributed among these distances:
9 77 0.82
10 3 0.03
11 2 0.02
12 12 0.13
ACGTcount: A:0.47, C:0.20, G:0.01, T:0.32
Consensus pattern (9 bp):
ACTTACATA
Found at i:3423130 original size:39 final size:39
Alignment explanation
Indices: 3423078--3423155 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
3423068 TAAATTACAT
*
3423078 AACTTACATAACTCATATAACTTACATAATTTACATAAC
1 AACTTACATAACTCACATAACTTACATAATTTACATAAC
3423117 AACTTACATAACTCACATAACTTACATAATTTACATAAC
1 AACTTACATAACTCACATAACTTACATAATTTACATAAC
3423156 TCACATAACG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (39 bp):
AACTTACATAACTCACATAACTTACATAATTTACATAAC
Found at i:3423155 original size:57 final size:57
Alignment explanation
Indices: 3423074--3423186 Score: 163
Period size: 57 Copynumber: 2.0 Consensus size: 57
3423064 TAAATAAATT
* * **
3423074 ACATAACTTACATAACTCATATAACTTACATAATTTACATAACAACTTACATAACTC
1 ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACTC
* * *
3423131 ACATAACTTACATAATTTACATAACTCACATAACGTATATAACAACTTACATAACT
1 ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACT
3423187 TAACTAATAC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
57 49 1.00
ACGTcount: A:0.46, C:0.22, G:0.01, T:0.31
Consensus pattern (57 bp):
ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACTC
Found at i:3429271 original size:43 final size:43
Alignment explanation
Indices: 3429210--3429327 Score: 218
Period size: 43 Copynumber: 2.7 Consensus size: 43
3429200 TTTGTAGAAA
*
3429210 AAACGCCGCTAAAAGCCTTGACCTTTAGTGGCGCTTTTCCCAC
1 AAACGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCAC
3429253 AAACGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCAC
1 AAACGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCAC
*
3429296 AAACGCCGCTAAAAGCCTTGACTTTTAGCGGC
1 AAACGCCGCTAAAAGCCTTGACCTTTAGCGGC
3429328 ATTTTTTTCA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
43 73 1.00
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (43 bp):
AAACGCCGCTAAAAGCCTTGACCTTTAGCGGCGCTTTTCCCAC
Found at i:3434178 original size:23 final size:22
Alignment explanation
Indices: 3434152--3434196 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 22
3434142 TATATAATGC
*
3434152 AATAATAATGAAGACAAAAATAA
1 AATAAGAATGAA-ACAAAAATAA
* *
3434175 AATAAGGATGAAACAATAATAA
1 AATAAGAATGAAACAAAAATAA
3434197 TGAAATAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.67, C:0.04, G:0.11, T:0.18
Consensus pattern (22 bp):
AATAAGAATGAAACAAAAATAA
Found at i:3434197 original size:3 final size:3
Alignment explanation
Indices: 3434189--3434344 Score: 141
Period size: 3 Copynumber: 53.3 Consensus size: 3
3434179 AGGATGAAAC
* * *
3434189 AAT AAT AAT GA- AAT AA- AAT AAA AAT AAC AAT ACATT AAT AA- AACT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-A-T AAT AAT AA-T
* * *
3434234 AAT AAT -AT ATT AAT ACA- AAT AGT AAT -AT AA- AGGT AAT AAT AAT
1 AAT AAT AAT AAT AAT A-AT AAT AAT AAT AAT AAT A-AT AAT AAT AAT
3434277 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
*
3434325 AAT AAT -AT AAT -TT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT A
3434345 GCGATGATGT
Statistics
Matches: 125, Mismatches: 14, Indels: 28
0.75 0.08 0.17
Matches are distributed among these distances:
2 14 0.11
3 103 0.82
4 6 0.05
5 2 0.02
ACGTcount: A:0.63, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:3434230 original size:20 final size:20
Alignment explanation
Indices: 3434205--3434254 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
3434195 AATGAAATAA
3434205 AATAAAAATAACAATACATT
1 AATAAAAATAACAATACATT
* * *
3434225 AATAAAACTAATAATATATT
1 AATAAAAATAACAATACATT
*
3434245 AATACAAATA
1 AATAAAAATA
3434255 GTAATATAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.64, C:0.08, G:0.00, T:0.28
Consensus pattern (20 bp):
AATAAAAATAACAATACATT
Found at i:3434441 original size:25 final size:22
Alignment explanation
Indices: 3434398--3434443 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
3434388 TATAATGAAG
*
3434398 TAATAATATAAATTAATTAGCC
1 TAATAATATAAATAAATTAGCC
3434420 TAATAATATGATAATAATATTAGC
1 TAATAATAT-A-AATAA-ATTAGC
3434444 AACAATACAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
22 9 0.45
23 1 0.05
24 4 0.20
25 6 0.30
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.37
Consensus pattern (22 bp):
TAATAATATAAATAAATTAGCC
Found at i:3434501 original size:20 final size:20
Alignment explanation
Indices: 3434478--3434516 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3434468 TAGAAAAGAT
* *
3434478 AATAATAATGTATTAATAAG
1 AATAAAAATATATTAATAAG
3434498 AATAAAAATATATTAATAA
1 AATAAAAATATATTAATAA
3434517 TAATCATGGA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (20 bp):
AATAAAAATATATTAATAAG
Found at i:3435698 original size:17 final size:17
Alignment explanation
Indices: 3435669--3435711 Score: 59
Period size: 17 Copynumber: 2.5 Consensus size: 17
3435659 GGGCTGATAG
*
3435669 TTGGGTTTAGGTTTGGA
1 TTGGGTTTGGGTTTGGA
* *
3435686 TTGGTTTTGGGTTTGTA
1 TTGGGTTTGGGTTTGGA
3435703 TTGGGTTTG
1 TTGGGTTTG
3435712 TTTTAGCCCG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.07, C:0.00, G:0.40, T:0.53
Consensus pattern (17 bp):
TTGGGTTTGGGTTTGGA
Found at i:3438477 original size:3 final size:3
Alignment explanation
Indices: 3438469--3438498 Score: 51
Period size: 3 Copynumber: 9.7 Consensus size: 3
3438459 TGTCTGATGC
3438469 TAT TAT TAT TAT TAT TAT TAT TAT GTAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT -TAT TA
3438499 GTATATACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
3 23 0.88
4 3 0.12
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:3438606 original size:3 final size:3
Alignment explanation
Indices: 3438598--3438636 Score: 71
Period size: 3 Copynumber: 13.3 Consensus size: 3
3438588 AATATTATCG
3438598 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT- TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3438637 GCTTTATTCA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.06
3 33 0.94
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3440384 original size:20 final size:21
Alignment explanation
Indices: 3440359--3440406 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 21
3440349 AAAGCCAAAC
*
3440359 CTCAAACCTTAAACC-CTAAA
1 CTCAAACCTTAAACCTCGAAA
**
3440379 CTCAAATTTTAAACCTCGAAA
1 CTCAAACCTTAAACCTCGAAA
3440400 C-CAAACC
1 CTCAAACC
3440407 CCGAACCTCA
Statistics
Matches: 22, Mismatches: 5, Indels: 2
0.76 0.17 0.07
Matches are distributed among these distances:
20 17 0.77
21 5 0.23
ACGTcount: A:0.44, C:0.33, G:0.02, T:0.21
Consensus pattern (21 bp):
CTCAAACCTTAAACCTCGAAA
Found at i:3440606 original size:22 final size:22
Alignment explanation
Indices: 3440581--3440625 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
3440571 AAGGACTAAG
3440581 TTATAAGAA-CTGTAAAAATTAA
1 TTATAAGAACCT-TAAAAATTAA
3440603 TTATAAGAACCTTAAAAATTAA
1 TTATAAGAACCTTAAAAATTAA
3440625 T
1 T
3440626 CGTTATTGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 20 0.91
23 2 0.09
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (22 bp):
TTATAAGAACCTTAAAAATTAA
Found at i:3443004 original size:43 final size:43
Alignment explanation
Indices: 3442956--3443119 Score: 161
Period size: 43 Copynumber: 3.8 Consensus size: 43
3442946 TATCAAGATG
* * * *
3442956 TGATTACATGTAAGACCGTGTCTGGGACATTAGCATTGTATTA
1 TGATTACATGTAAGACCATATCTGGGACATTGGCATCGTATTA
** * *
3442999 TGATTATGTGTAAGACCATGTCTGGGACATTGGTATCGTATTA
1 TGATTACATGTAAGACCATATCTGGGACATTGGCATCGTATTA
* * * * * *
3443042 TGATTTCGTGTAAGACCCTATCTTGGACAGTGGCATCG-ATATG
1 TGATTACATGTAAGACCATATCTGGGACATTGGCATCGTAT-TA
* *
3443085 TGATAACATGTAAGACCATATCTGGGATA-TGGCAT
1 TGATTACATGTAAGACCATATCTGGGACATTGGCAT
3443120 TGTACGAGCT
Statistics
Matches: 100, Mismatches: 20, Indels: 3
0.81 0.16 0.02
Matches are distributed among these distances:
42 8 0.08
43 92 0.92
ACGTcount: A:0.27, C:0.15, G:0.24, T:0.34
Consensus pattern (43 bp):
TGATTACATGTAAGACCATATCTGGGACATTGGCATCGTATTA
Found at i:3447757 original size:27 final size:29
Alignment explanation
Indices: 3447700--3447757 Score: 84
Period size: 27 Copynumber: 2.1 Consensus size: 29
3447690 CAATAAACGT
*
3447700 TGTTGAATTTGAATGTGTATGATTTTATA
1 TGTTGAATTTGAATGTGTATGAATTTATA
*
3447729 TGTTGAATTT-AAT-TGTATGAATTTCTA
1 TGTTGAATTTGAATGTGTATGAATTTATA
3447756 TG
1 TG
3447758 GTTATAGCCG
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
27 14 0.52
28 3 0.11
29 10 0.37
ACGTcount: A:0.28, C:0.02, G:0.19, T:0.52
Consensus pattern (29 bp):
TGTTGAATTTGAATGTGTATGAATTTATA
Found at i:3447882 original size:39 final size:42
Alignment explanation
Indices: 3447839--3447962 Score: 105
Period size: 41 Copynumber: 3.0 Consensus size: 42
3447829 ATAAGATCAA
3447839 CTTTG-TAACAGTG-AT-ATATCAGGCTTATTGCCTAGCAGG
1 CTTTGATAACAGTGTATGATATCAGGCTTATTGCCTAGCAGG
** * * *
3447878 CTTTGATGCCGGTGTATGATATCAGGCTTATTTCCTAGCATG
1 CTTTGATAACAGTGTATGATATCAGGCTTATTGCCTAGCAGG
** * * * *
3447920 CTTT-ATGCCGGTGTCTTGA-ATCAGGTTTATTACCTAGCAGG
1 CTTTGATAACAGTGT-ATGATATCAGGCTTATTGCCTAGCAGG
3447961 CT
1 CT
3447963 CTGTGCCGGT
Statistics
Matches: 72, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
39 5 0.07
40 5 0.07
41 33 0.46
42 29 0.40
ACGTcount: A:0.21, C:0.19, G:0.23, T:0.36
Consensus pattern (42 bp):
CTTTGATAACAGTGTATGATATCAGGCTTATTGCCTAGCAGG
Found at i:3447901 original size:42 final size:43
Alignment explanation
Indices: 3447854--3447972 Score: 156
Period size: 41 Copynumber: 2.9 Consensus size: 43
3447844 TAACAGTGAT
*
3447854 ATATCAGGCTTATTGCCTAGCAGGCTTTGATGCCGGTGT-ATG
1 ATATCAGGCTTATTACCTAGCAGGCTTTGATGCCGGTGTCATG
* * *
3447896 ATATCAGGCTTATTTCCTAGCATGCTTT-ATGCCGGTGTCTTG
1 ATATCAGGCTTATTACCTAGCAGGCTTTGATGCCGGTGTCATG
* *
3447938 A-ATCAGGTTTATTACCTAGCAGGCTCTG-TGCCGGT
1 ATATCAGGCTTATTACCTAGCAGGCTTTGATGCCGGT
3447973 ATTTTATACG
Statistics
Matches: 68, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
41 39 0.57
42 29 0.43
ACGTcount: A:0.18, C:0.21, G:0.25, T:0.35
Consensus pattern (43 bp):
ATATCAGGCTTATTACCTAGCAGGCTTTGATGCCGGTGTCATG
Found at i:3449474 original size:26 final size:26
Alignment explanation
Indices: 3449445--3449526 Score: 155
Period size: 26 Copynumber: 3.2 Consensus size: 26
3449435 TGATACAAAT
3449445 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
3449471 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
3449497 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
3449523 TGAT
1 TGAT
3449527 GGGAATTTCA
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 54 1.00
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:3455723 original size:26 final size:26
Alignment explanation
Indices: 3455694--3455801 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
3455684 TGGTACAAAT
3455694 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
3455720 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
3455746 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
3455772 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
3455798 TGAT
1 TGAT
3455802 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:3459211 original size:14 final size:14
Alignment explanation
Indices: 3459187--3459232 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
3459177 GATTTTGAAT
3459187 TTTAA-GTTTAGGG
1 TTTAAGGTTTAGGG
* *
3459200 TTTGATGTTTAGGG
1 TTTAAGGTTTAGGG
*
3459214 TTTAAGGTTTAGGA
1 TTTAAGGTTTAGGG
3459228 TTTAA
1 TTTAA
3459233 AGTTCAAGGT
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
13 4 0.14
14 24 0.86
ACGTcount: A:0.24, C:0.00, G:0.28, T:0.48
Consensus pattern (14 bp):
TTTAAGGTTTAGGG
Found at i:3459216 original size:21 final size:21
Alignment explanation
Indices: 3459158--3459223 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
3459148 AAGGTTTAAA
*
3459158 GTTTGAGGTTT-GGGTTTAGG
1 GTTTGATGTTTAGGGTTTAGG
* *
3459178 ATTTTGAAT-TTTA-AGTTTAGG
1 -GTTTG-ATGTTTAGGGTTTAGG
*
3459199 GTTTGATGTTTAGGGTTTAAG
1 GTTTGATGTTTAGGGTTTAGG
3459220 GTTT
1 GTTT
3459224 AGGATTTAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
19 2 0.06
20 8 0.23
21 24 0.69
22 1 0.03
ACGTcount: A:0.18, C:0.00, G:0.32, T:0.50
Consensus pattern (21 bp):
GTTTGATGTTTAGGGTTTAGG
Found at i:3460900 original size:17 final size:17
Alignment explanation
Indices: 3460874--3460907 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3460864 TCTAGTAAAT
3460874 TAATCCTAGAATATTTG
1 TAATCCTAGAATATTTG
*
3460891 TAATCTTAGAATATTTG
1 TAATCCTAGAATATTTG
3460908 ATTTTGTAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.35, C:0.09, G:0.12, T:0.44
Consensus pattern (17 bp):
TAATCCTAGAATATTTG
Found at i:3468027 original size:55 final size:55
Alignment explanation
Indices: 3467886--3468029 Score: 171
Period size: 55 Copynumber: 2.6 Consensus size: 55
3467876 TGCAATATGG
* * *
3467886 CCGTGGTCGAGCCTGTCAAAACAACAGGGGTGTGAGACACGCCCGTGTGGAAGAA
1 CCGTGGTCGAGCCTGTCAAAACAACAAGGGCGTGAGACACGCCCGTGTGGAACAA
* * * * * *
3467941 CCATGGGCGAGCCTGGCAAAACAACACGGGCGTGCGACACGCCCGTGTGGAACAC
1 CCGTGGTCGAGCCTGTCAAAACAACAAGGGCGTGAGACACGCCCGTGTGGAACAA
* * **
3467996 CCGTGGTCGAACCTGTTAAATTAACAAGGGCGTG
1 CCGTGGTCGAGCCTGTCAAAACAACAAGGGCGTG
3468030 GGGCTTGCAC
Statistics
Matches: 73, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
55 73 1.00
ACGTcount: A:0.26, C:0.26, G:0.33, T:0.15
Consensus pattern (55 bp):
CCGTGGTCGAGCCTGTCAAAACAACAAGGGCGTGAGACACGCCCGTGTGGAACAA
Found at i:3473841 original size:46 final size:46
Alignment explanation
Indices: 3473771--3473863 Score: 168
Period size: 46 Copynumber: 2.0 Consensus size: 46
3473761 GTAACAACTT
*
3473771 GTTTTTAGTCAAATTGGAACAGTGGTTTCGGAACCATAAATTCGAG
1 GTTTTTAGTCAAATTGGAACAGTGGTTTCAGAACCATAAATTCGAG
*
3473817 GTTTTTAGTCAAATTGGAATAGTGGTTTCAGAACCATAAATTCGAG
1 GTTTTTAGTCAAATTGGAACAGTGGTTTCAGAACCATAAATTCGAG
3473863 G
1 G
3473864 CTAAAATATT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 45 1.00
ACGTcount: A:0.31, C:0.12, G:0.24, T:0.33
Consensus pattern (46 bp):
GTTTTTAGTCAAATTGGAACAGTGGTTTCAGAACCATAAATTCGAG
Found at i:3475127 original size:24 final size:25
Alignment explanation
Indices: 3475049--3475166 Score: 70
Period size: 24 Copynumber: 4.7 Consensus size: 25
3475039 AGACTCACCA
* *
3475049 CAGCTCG-TATGAGCTTACTGGTATAT
1 CAGCTCGATA-GAGCTTACT-GTTTCT
* *
3475075 CAACTC-ATAAGAGCTTACT-ATTCT
1 CAGCTCGAT-AGAGCTTACTGTTTCT
3475099 CAGCTCG-TCAGAGCTTACTGTTTCT
1 CAGCTCGAT-AGAGCTTACTGTTTCT
* *
3475124 -AGCTTGATAAAGCTTACTG-TTCAT
1 CAGCTCGATAGAGCTTACTGTTTC-T
3475148 CAGCTCAGA-AGGAGCTTAC
1 CAGCTC-GATA-GAGCTTAC
3475167 CGATCATAGC
Statistics
Matches: 72, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
23 3 0.04
24 34 0.47
25 10 0.14
26 24 0.33
27 1 0.01
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (25 bp):
CAGCTCGATAGAGCTTACTGTTTCT
Found at i:3475173 original size:26 final size:24
Alignment explanation
Indices: 3475134--3475186 Score: 61
Period size: 26 Copynumber: 2.1 Consensus size: 24
3475124 AGCTTGATAA
* * *
3475134 AGCTTACTGTTCATCAGCTCAGAAGG
1 AGCTTACCGATCAT-AGCTC-GAAAG
3475160 AGCTTACCGATCATAGCTCGAAAG
1 AGCTTACCGATCATAGCTCGAAAG
3475184 AGC
1 AGC
3475187 GAATACGATG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
24 7 0.29
25 5 0.21
26 12 0.50
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.23
Consensus pattern (24 bp):
AGCTTACCGATCATAGCTCGAAAG
Found at i:3477109 original size:27 final size:27
Alignment explanation
Indices: 3477070--3477371 Score: 182
Period size: 27 Copynumber: 11.1 Consensus size: 27
3477060 TTAGAATACT
*
3477070 TTAGTTTACTAAAATTACCGAAATACCC
1 TTAGTTT-GTAAAATTACCGAAATACCC
* *
3477098 TTAGTTTGTAAAAATACTGAAATACCC
1 TTAGTTTGTAAAATTACCGAAATACCC
* *
3477125 -TCGATTTGTAAAATTACTGAAATA-CC
1 TTAG-TTTGTAAAATTACCGAAATACCC
* * *
3477151 TTCGACTTGTAAAATTACCAAAATACCC
1 TTAG-TTTGTAAAATTACCGAAATACCC
** *
3477179 CCAGTTTGTAAAATTACCAAAATACCAC
1 TTAGTTTGTAAAATTACCGAAATACC-C
* * *
3477207 -TAGTTTGTGAAATTATCGCAATACCC
1 TTAGTTTGTAAAATTACCGAAATACCC
* * * *
3477233 TCAATTTCTAAAATTACCAAAATACCC
1 TTAGTTTGTAAAATTACCGAAATACCC
* * *
3477260 CT-GATT-TACAAAGTTACAGAAATACCC
1 TTAGTTTGTA-AAA-TTACCGAAATACCC
* * ** *
3477287 TTGACTTTCTAAAAATTATAGAAATACCA
1 TT-AGTTTGT-AAAATTACCGAAATACCC
* ** *
3477316 TTGGTTTACAAAATTACTGAAATACCC
1 TTAGTTTGTAAAATTACCGAAATACCC
* * * * *
3477343 TTGGTTTGTAGATTTACCAAAACACCC
1 TTAGTTTGTAAAATTACCGAAATACCC
3477370 TT
1 TT
3477372 GTAGGATGAA
Statistics
Matches: 214, Mismatches: 49, Indels: 23
0.75 0.17 0.08
Matches are distributed among these distances:
25 2 0.01
26 10 0.05
27 167 0.78
28 14 0.07
29 16 0.07
30 4 0.02
31 1 0.00
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.32
Consensus pattern (27 bp):
TTAGTTTGTAAAATTACCGAAATACCC
Found at i:3477147 original size:54 final size:54
Alignment explanation
Indices: 3477079--3477371 Score: 202
Period size: 54 Copynumber: 5.4 Consensus size: 54
3477069 TTTAGTTTAC
*
3477079 TAAAATTACCGAAATACCCTTAGTTTGTAAAAATACTGAAATACCCTCGATTTG
1 TAAAATTACCGAAATACCCTTAGTTTGTAAAATTACTGAAATACCCTCGATTTG
* * * ** *
3477133 TAAAATTACTGAAATA-CCTTCGACTTGTAAAATTACCAAAATACCC-CCAGTTTG
1 TAAAATTACCGAAATACCCTTAG-TTTGTAAAATTACTGAAATACCCTCGA-TTTG
* * * * *
3477187 TAAAATTACCAAAATACCAC-TAGTTTGTGAAATTA-TCGCAATACCCTCAATTTC
1 TAAAATTACCGAAATACC-CTTAGTTTGTAAAATTACT-GAAATACCCTCGATTTG
* * * * * *
3477241 TAAAATTACCAAAATACCCCT-GATT-TACAAAGTTACAGAAATACCCTTGACTTTC
1 TAAAATTACCGAAATACCCTTAGTTTGTA-AAA-TTACTGAAATACCCTCGA-TTTG
** * * ** * *
3477296 TAAAAATTATAGAAATACCATTGGTTTACAAAATTACTGAAATACCCTTGGTTTG
1 T-AAAATTACCGAAATACCCTTAGTTTGTAAAATTACTGAAATACCCTCGATTTG
* * * *
3477351 TAGATTTACCAAAACACCCTT
1 TAAAATTACCGAAATACCCTT
3477372 GTAGGATGAA
Statistics
Matches: 185, Mismatches: 40, Indels: 28
0.73 0.16 0.11
Matches are distributed among these distances:
52 1 0.01
53 14 0.08
54 117 0.63
55 14 0.08
56 32 0.17
57 6 0.03
58 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.09, T:0.31
Consensus pattern (54 bp):
TAAAATTACCGAAATACCCTTAGTTTGTAAAATTACTGAAATACCCTCGATTTG
Found at i:3477202 original size:81 final size:81
Alignment explanation
Indices: 3477078--3477260 Score: 217
Period size: 81 Copynumber: 2.3 Consensus size: 81
3477068 CTTTAGTTTA
* ** ** *
3477078 CTAAAATTACCGAAATACCCTTAGTTTGTAAAAATACTGAAATACC-CTCGATTTGTAAAATTA-
1 CTAAAATTACCAAAATACCCCCAGTTTGTAAAAATACCAAAATACCACTAG-TTTGTAAAATTAT
* *
3477141 CTGAAATACCTTCGACTT
65 C-GAAATACCCTCAACTT
* * *
3477159 GTAAAATTACCAAAATACCCCCAGTTTGTAAAATTACCAAAATACCACTAGTTTGTGAAATTATC
1 CTAAAATTACCAAAATACCCCCAGTTTGTAAAAATACCAAAATACCACTAGTTTGTAAAATTATC
* *
3477224 GCAATACCCTCAATTT
66 GAAATACCCTCAACTT
3477240 CTAAAATTACCAAAATACCCC
1 CTAAAATTACCAAAATACCCC
3477261 TGATTTACAA
Statistics
Matches: 86, Mismatches: 14, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
81 82 0.95
82 4 0.05
ACGTcount: A:0.40, C:0.22, G:0.08, T:0.30
Consensus pattern (81 bp):
CTAAAATTACCAAAATACCCCCAGTTTGTAAAAATACCAAAATACCACTAGTTTGTAAAATTATC
GAAATACCCTCAACTT
Found at i:3477433 original size:27 final size:28
Alignment explanation
Indices: 3477403--3477494 Score: 104
Period size: 27 Copynumber: 3.4 Consensus size: 28
3477393 ACCCCTATTA
*
3477403 GGTAAAAAT-ACTGTAAAGCCCCTGTAG
1 GGTAAAAATGACCGTAAAGCCCCTGTAG
*
3477430 GGT-AAAGTGACCGTAAAGCCCCTGTAG
1 GGTAAAAATGACCGTAAAGCCCCTGTAG
* *
3477457 GGT-AAAGTGACCGTAATA-CCCCTGTAT
1 GGTAAAAATGACCGTAA-AGCCCCTGTAG
3477484 GGT-AAAATGAC
1 GGTAAAAATGAC
3477495 GAATATGCCC
Statistics
Matches: 59, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
26 4 0.07
27 54 0.92
28 1 0.02
ACGTcount: A:0.34, C:0.20, G:0.25, T:0.22
Consensus pattern (28 bp):
GGTAAAAATGACCGTAAAGCCCCTGTAG
Found at i:3478277 original size:26 final size:25
Alignment explanation
Indices: 3478248--3478343 Score: 140
Period size: 25 Copynumber: 3.8 Consensus size: 25
3478238 GAGGAAGTGC
**
3478248 AAAAGGGCTTATGCCCCAGTTTATTG
1 AAAAGGGCTT-TGCCCCAGTTTACCG
*
3478274 AAAAGGGCGTATG-CCCAGTTTACCG
1 AAAAGGGC-TTTGCCCCAGTTTACCG
3478299 AAAAGGGCTTTGCCCCAGTTTACCG
1 AAAAGGGCTTTGCCCCAGTTTACCG
3478324 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
3478344 ATTAAAAGAG
Statistics
Matches: 64, Mismatches: 4, Indels: 5
0.88 0.05 0.07
Matches are distributed among these distances:
24 3 0.05
25 50 0.78
26 10 0.16
27 1 0.02
ACGTcount: A:0.26, C:0.24, G:0.25, T:0.25
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCG
Found at i:3478548 original size:42 final size:42
Alignment explanation
Indices: 3478489--3478580 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
3478479 TAGTCTCCCC
* ** *
3478489 AAATGGGCTTGCATACATTCATTGGTATTTCATATGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
*
3478531 AAATGGGCTTGCATACATCCATTGACATTACATGTGATATTG
1 AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
3478573 AAATGGGC
1 AAATGGGC
3478581 CTATGGGCCA
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.30, C:0.14, G:0.21, T:0.35
Consensus pattern (42 bp):
AAATGGGCTTGCATACATCCATTGACATTACATATGATATTG
Found at i:3478639 original size:31 final size:31
Alignment explanation
Indices: 3478604--3478682 Score: 140
Period size: 31 Copynumber: 2.5 Consensus size: 31
3478594 CGTTTACAGT
3478604 AAAGGCTTCGGCCCAGTGAAATGATTTATGA
1 AAAGGCTTCGGCCCAGTGAAATGATTTATGA
* *
3478635 AAAGGCTTCAGCCCAGTGATATGATTTATGA
1 AAAGGCTTCGGCCCAGTGAAATGATTTATGA
3478666 AAAGGCTTCGGCCCAGT
1 AAAGGCTTCGGCCCAGT
3478683 AACCGTTAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 45 1.00
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.25
Consensus pattern (31 bp):
AAAGGCTTCGGCCCAGTGAAATGATTTATGA
Found at i:3497677 original size:137 final size:137
Alignment explanation
Indices: 3497505--3498184 Score: 986
Period size: 137 Copynumber: 5.0 Consensus size: 137
3497495 CAAATGATTC
* * * * *
3497505 TATCTTTCTGAAGTTGTAGTAGAGCGGATCAAAACAAGTCTTATCTCCCTGAAGCTGCAGTGGAG
1 TATCTCTCTGAAGTTGCAGTAGAGCAGATCAAAACAAGTCTTATCTCCCTGAAGTTGCAGCGGAG
* * *
3497570 CAGGCTAGAGATAGTAAATCTTATTTCCCTAAAGTTACAGTGGAACAGATTGAAGCTATAAATTA
66 CAGGCTAGAGATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTA
3497635 CAGATCT
131 CAGATCT
* * * *
3497642 TATCTTTCTGAAGTTGCAGTAAAGCAGATCAAAACAAGTCTTATCTCCCTGAAGTTACAGCGGAA
1 TATCTCTCTGAAGTTGCAGTAGAGCAGATCAAAACAAGTCTTATCTCCCTGAAGTTGCAGCGGAG
* * *
3497707 CAGGCCAGAGATAGCAAATCTTATTTCCTTGAAGTTGCAGTGGAACAGATTAAAGCTATAAATTA
66 CAGGCTAGAGATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTA
3497772 CAGATCT
131 CAGATCT
*
3497779 TATCTATCTGAAGTTGCAGTAGAGCAGATCAAAACAAGTCTTATCTCCCTGAAGTTGCAGCGGAG
1 TATCTCTCTGAAGTTGCAGTAGAGCAGATCAAAACAAGTCTTATCTCCCTGAAGTTGCAGCGGAG
* * *
3497844 CAGGC-CGAAGATAGCAAATCTTTTTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAGTT
66 CAGGCTAG-AGATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATT
*
3497908 ATAGATCT
130 ACAGATCT
* * * *
3497916 TATCTCTCTGAATTTGCATTAGAGCAAATCAAAACAAGTCTTATCTCCCTGATGTTGCAGCGGAG
1 TATCTCTCTGAAGTTGCAGTAGAGCAGATCAAAACAAGTCTTATCTCCCTGAAGTTGCAGCGGAG
* * * * * *
3497981 TAGGTTAAAGATAGCAAATATTATTTCCCTGAAGTTGCAGTAGAACAGATTGAAGCTATAAGTTA
66 CAGGCTAGAGATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTA
3498046 CAGATCT
131 CAGATCT
*
3498053 TATCTCTCTGCAGTTGCAGTAGAGCAGATCAAAACAAGTCTTATCTCCCTGAAGTTGCAGCGGAG
1 TATCTCTCTGAAGTTGCAGTAGAGCAGATCAAAACAAGTCTTATCTCCCTGAAGTTGCAGCGGAG
* * * * ** *
3498118 CAGGTTAAAGATAGCAAATCTTATTTCCCTAAAATTTTAGTGGAATAGATT-AGAGCTATAAATT
66 CAGGCTAGAGATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGA-AGCTATAAATT
3498182 ACA
130 ACA
3498185 AAAACCTAAT
Statistics
Matches: 490, Mismatches: 50, Indels: 6
0.90 0.09 0.01
Matches are distributed among these distances:
136 2 0.00
137 488 1.00
ACGTcount: A:0.33, C:0.17, G:0.20, T:0.29
Consensus pattern (137 bp):
TATCTCTCTGAAGTTGCAGTAGAGCAGATCAAAACAAGTCTTATCTCCCTGAAGTTGCAGCGGAG
CAGGCTAGAGATAGCAAATCTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTA
CAGATCT
Found at i:3497696 original size:41 final size:41
Alignment explanation
Indices: 3497639--3497838 Score: 107
Period size: 41 Copynumber: 4.5 Consensus size: 41
3497629 AAATTACAGA
**
3497639 TCTTATCTTTCTGAAGTTGCAGTAAAGCAGATCAAAACAAG
1 TCTTATCTCCCTGAAGTTGCAGTAAAGCAGATCAAAACAAG
* * * * * *
3497680 TCTTATCTCCCTGAAGTTACAGCGGAACAGGCCAGA-GATAGCAAA
1 TCTTATCTCCCTGAAGTTGCA--GTAA-A-G-CAGATCAAAACAAG
* * * *
3497725 TCTTATTTCCTTGAAGTTGCAGTGGAA-CAGATTAAAGCTATAAATTACAG
1 TCTTATCTCCCTGAAGTTGCAGT-AAAGCAGA-T----C-A-AAA-CA-AG
** *
3497775 ATCTTATCTATCTGAAGTTGCAGTAGAGCAGATCAAAACAAG
1 -TCTTATCTCCCTGAAGTTGCAGTAAAGCAGATCAAAACAAG
3497817 TCTTATCTCCCTGAAGTTGCAG
1 TCTTATCTCCCTGAAGTTGCAG
3497839 CGGAGCAGGC
Statistics
Matches: 114, Mismatches: 27, Indels: 36
0.64 0.15 0.20
Matches are distributed among these distances:
40 4 0.04
41 38 0.33
42 2 0.02
43 6 0.05
44 5 0.04
45 25 0.22
46 5 0.04
47 1 0.01
48 1 0.01
49 1 0.01
50 3 0.03
51 23 0.20
ACGTcount: A:0.34, C:0.19, G:0.19, T:0.28
Consensus pattern (41 bp):
TCTTATCTCCCTGAAGTTGCAGTAAAGCAGATCAAAACAAG
Found at i:3497845 original size:41 final size:42
Alignment explanation
Indices: 3497776--3498112 Score: 160
Period size: 41 Copynumber: 7.5 Consensus size: 42
3497766 AAATTACAGA
**
3497776 TCTTATCTATCTGAAGTTGCAGTAGAGCAGATCAAA-ACAAG
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCAAATACAAG
** ** *
3497817 TCTTATCTCCCTGAAGTTGCAGCGGAGCAGGCCGAAGATAGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATC-AA-ATA-CAAG
* * * * * *
3497862 TCTTTTTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAGTTATAG
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGA-TCAA---AT-A--CA-AG
* * * *
3497912 ATCTTATCTCTCTGAATTTGCATTAGAGCAAATCAAA-ACAAG
1 -TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCAAATACAAG
* ** * * * *
3497954 TCTTATCTCCCTGATGTTGCAGCGGAGTAGGTTAAAGATAGCAAA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCA-GATCAA-ATA-CAAG
* * *
3497999 TATTATTTCCCTGAAGTTGCAGTAGAACAGATTGAAGCTATAAGTTAC-AG
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGA-T----C-A-AA--TACAAG
* *
3498049 ATCTTATCTCTCTGCAGTTGCAGTAGAGCAGATCAAA-ACAAG
1 -TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCAAATACAAG
3498091 TCTTATCTCCCTGAAGTTGCAG
1 TCTTATCTCCCTGAAGTTGCAG
3498113 CGGAGCAGGT
Statistics
Matches: 214, Mismatches: 56, Indels: 52
0.66 0.17 0.16
Matches are distributed among these distances:
41 71 0.33
42 9 0.04
43 3 0.01
44 5 0.02
45 59 0.28
46 1 0.00
47 3 0.01
48 1 0.00
49 1 0.00
50 8 0.04
51 51 0.24
52 2 0.01
ACGTcount: A:0.31, C:0.19, G:0.20, T:0.29
Consensus pattern (42 bp):
TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCAAATACAAG
Found at i:3508221 original size:46 final size:46
Alignment explanation
Indices: 3508171--3508343 Score: 208
Period size: 46 Copynumber: 3.7 Consensus size: 46
3508161 TGGTTGAGCA
3508171 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* * * *
3508217 TCCGAACTCGTTGAGTTGAGTCCGAGTTC-GTGA--GATGTAACTAGG
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAA--ATG
* * *
3508262 CATTCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAATG
1 --TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
* *
3508310 CCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTA
1 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTA
3508344 GGGGCGGGTT
Statistics
Matches: 106, Mismatches: 14, Indels: 14
0.79 0.10 0.10
Matches are distributed among these distances:
43 6 0.06
45 4 0.04
46 59 0.56
47 28 0.26
48 4 0.04
50 5 0.05
ACGTcount: A:0.22, C:0.20, G:0.28, T:0.31
Consensus pattern (46 bp):
TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
Found at i:3508332 original size:93 final size:93
Alignment explanation
Indices: 3508168--3508338 Score: 297
Period size: 93 Copynumber: 1.8 Consensus size: 93
3508158 GGATGGTTGA
*
3508168 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGTCCGAACTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAACTCGTTGAGT
3508233 TGAGTCCGAGTTCGTGAGATGTAACTAG
66 TGAGTCCGAGTTCGTGAGATGTAACTAG
* * * *
3508261 GCATTCGAACTCGTTGAGTTGAGTCCGAGTTCATTTATGGATGCGAATGCCCGAGCTCGTTGAGT
1 GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAACTCGTTGAGT
3508326 TGAGTCCGAGTTC
66 TGAGTCCGAGTTC
3508339 ACTTAGGGGC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
93 73 1.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.30
Consensus pattern (93 bp):
GCATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATGCCCGAACTCGTTGAGT
TGAGTCCGAGTTCGTGAGATGTAACTAG
Found at i:3508605 original size:19 final size:20
Alignment explanation
Indices: 3508568--3508605 Score: 53
Period size: 19 Copynumber: 1.9 Consensus size: 20
3508558 ATAAGGTGGT
3508568 AAGATGATGAATGATGTTTA
1 AAGATGATGAATGATGTTTA
3508588 AAGATG-TGATAT-ATGTTT
1 AAGATGATGA-ATGATGTTT
3508606 TGGTGGTACC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.00, G:0.24, T:0.39
Consensus pattern (20 bp):
AAGATGATGAATGATGTTTA
Found at i:3510227 original size:24 final size:24
Alignment explanation
Indices: 3510197--3510279 Score: 73
Period size: 24 Copynumber: 3.4 Consensus size: 24
3510187 TCAACTCATA
3510197 AGAGCTTACTATTCTCAGCTCG-T
1 AGAGCTTACTATTCTCAGCTCGAT
* *
3510220 CAGAGCTTATTGTT-TCCAGCTCGAT
1 -AGAGCTTACTATTCT-CAGCTCGAT
*
3510245 AAAGCTTACTATTCATCAGCTCAGA-
1 AGAGCTTACTATTC-TCAGCTC-GAT
3510270 AGGAGCTTAC
1 A-GAGCTTAC
3510280 CGATCATAGC
Statistics
Matches: 47, Mismatches: 6, Indels: 10
0.75 0.10 0.16
Matches are distributed among these distances:
23 1 0.02
24 28 0.60
25 8 0.17
26 10 0.21
ACGTcount: A:0.27, C:0.24, G:0.18, T:0.31
Consensus pattern (24 bp):
AGAGCTTACTATTCTCAGCTCGAT
Found at i:3514628 original size:82 final size:81
Alignment explanation
Indices: 3514521--3514840 Score: 276
Period size: 82 Copynumber: 3.9 Consensus size: 81
3514511 TTTTTGTCTA
* ** * * *
3514521 AAACGCCACTAAAAAC-ATATCAATAGAGGCGGTTTTATCTAAAACGCCACTAAAAACGGATCAA
1 AAACGCCACTAAAAACTAGAGAAATAGCGGCGTTTTTGTCTAAAACGCCACT-AAAACGGATCAA
*
3514585 TAGCGTCGTTTTCACGT
65 TAGCGGCGTTTTCACGT
* * * ** * * *
3514602 AAACGCCACTAAAAACTGGGGAAATAGCTGCGTTTTTGTCCCAAATGCCCCTAAAA-GTTATCAA
1 AAACGCCACTAAAAACTAGAGAAATAGCGGCGTTTTTGTCTAAAACGCCACTAAAACG-GATCAA
**
3514666 TAGCGGCGTTTTCATCCA
65 TAGCGGCGTTTTCA-CGT
* * *
3514684 AAACGCCACTAAAAAGC-AGAGAAATAGTGGCGTTTTTGTC-CAAACGCCAGTAAAAACTAGGA-
1 AAACGCCACTAAAAA-CTAGAGAAATAGCGGCGTTTTTGTCTAAAACGCCACT-AAAAC--GGAT
* * * *
3514746 AAATAGTGGCGTTTTTATGT
62 CAATAGCGGCGTTTTCACGT
* **
3514766 AAAACGCCACTAAAAA-TAGAGAAATAGCGGCGTTTTTGT-TAAAACTCCACTAAAACTAATCAA
1 -AAACGCCACTAAAAACTAGAGAAATAGCGGCGTTTTTGTCTAAAACGCCACTAAAACGGATCAA
3514829 TAGCGGCGTTTT
65 TAGCGGCGTTTT
3514841 TAGGACCAAA
Statistics
Matches: 188, Mismatches: 39, Indels: 25
0.75 0.15 0.10
Matches are distributed among these distances:
79 1 0.01
80 14 0.07
81 51 0.27
82 90 0.48
83 30 0.16
84 1 0.01
85 1 0.01
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (81 bp):
AAACGCCACTAAAAACTAGAGAAATAGCGGCGTTTTTGTCTAAAACGCCACTAAAACGGATCAAT
AGCGGCGTTTTCACGT
Found at i:3514717 original size:42 final size:41
Alignment explanation
Indices: 3514480--3514842 Score: 229
Period size: 41 Copynumber: 8.9 Consensus size: 41
3514470 GTTTACTCAC
* * * * *
3514480 AAACGCCGC-AAAAAAATGAGAAATAGCAGCGTTTTTGTCTA
1 AAACGCCACTAAAAACA-GAGAAATAGCGGCGTTTTTATCCA
* ** * * *
3514521 AAACGCCACTAAAAACATATCAATAGAGGCGGTTTTATCTA
1 AAACGCCACTAAAAACAGAGAAATAGCGGCGTTTTTATCCA
* ** * * **
3514562 AAACGCCACTAAAAACGGATCAATAGCGTCGTTTTCA-CGT
1 AAACGCCACTAAAAACAGAGAAATAGCGGCGTTTTTATCCA
* * * * *
3514602 AAACGCCACTAAAAACTGGGGAAATAGCTGCGTTTTTGTCCC
1 AAACGCCACTAAAAAC-AGAGAAATAGCGGCGTTTTTATCCA
* * *** ** *
3514644 AAATGCCCCT-AAAAGTTATCAATAGCGGCGTTTTCATCCA
1 AAACGCCACTAAAAACAGAGAAATAGCGGCGTTTTTATCCA
* *
3514684 AAACGCCACTAAAAAGCAGAGAAATAGTGGCGTTTTTGTCC-
1 AAACGCCACTAAAAA-CAGAGAAATAGCGGCGTTTTTATCCA
* * **
3514725 AAACGCCAGTAAAAACTAG-GAAAATAGTGGCGTTTTTATGTA
1 AAACGCCACTAAAAAC-AGAG-AAATAGCGGCGTTTTTATCCA
* * *
3514767 AAACGCCACTAAAAATAGAGAAATAGCGGCGTTTTTGT-TA
1 AAACGCCACTAAAAACAGAGAAATAGCGGCGTTTTTATCCA
* **
3514807 AAACTCCACT-AAAACTA-ATCAATAGCGGCGTTTTTA
1 AAACGCCACTAAAAAC-AGAGAAATAGCGGCGTTTTTA
3514843 GGACCAAATG
Statistics
Matches: 251, Mismatches: 61, Indels: 22
0.75 0.18 0.07
Matches are distributed among these distances:
39 20 0.08
40 55 0.22
41 129 0.51
42 47 0.19
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.25
Consensus pattern (41 bp):
AAACGCCACTAAAAACAGAGAAATAGCGGCGTTTTTATCCA
Found at i:3514718 original size:123 final size:122
Alignment explanation
Indices: 3514499--3514781 Score: 295
Period size: 123 Copynumber: 2.3 Consensus size: 122
3514489 AAAAAAATGA
* * *
3514499 GAAATAGCAGCGTTTTTGTCTAAAACGCCACTAAAAACATATCAATAGAGGCGGTTTTATCTAAA
1 GAAATAGCTGCGTTTTTGTCCAAAACGCCACTAAAAACATATCAATAGAGGCGGTTTTATCCAAA
* ** * *
3514564 ACGCCACTAAAAACGGATCAATAGCGTCGTTTTCACGT-AAACGCCACTAAAAACTGGG
66 ACGCCACTAAAAACAGAGAAATAGCGGCGTTTT--CGTCAAACGCCACTAAAAACTAGG
* * * ** *
3514622 GAAATAGCTGCGTTTTTGTCCCAAATGCCCCT-AAAAGTTATCAATAGCGGC-GTTTTCATCCAA
1 GAAATAGCTGCGTTTTTGTCCAAAACGCCACTAAAAACATATCAATAGAGGCGGTTTT-ATCCAA
* * *
3514685 AACGCCACTAAAAAGCAGAGAAATAGTGGCGTTTTTGTCCAAACGCCAGTAAAAACTAGG
65 AACGCCACTAAAAA-CAGAGAAATAGCGGCGTTTTCGT-CAAACGCCACTAAAAACTAGG
* * **
3514745 AAAATAG-TGGCGTTTTTATGTAAAACGCCACTAAAAA
1 GAAATAGCT-GCGTTTTTGTCCAAAACGCCACTAAAAA
3514782 TAGAGAAATA
Statistics
Matches: 130, Mismatches: 24, Indels: 11
0.79 0.15 0.07
Matches are distributed among these distances:
121 7 0.05
122 36 0.28
123 83 0.64
124 4 0.03
ACGTcount: A:0.37, C:0.20, G:0.18, T:0.24
Consensus pattern (122 bp):
GAAATAGCTGCGTTTTTGTCCAAAACGCCACTAAAAACATATCAATAGAGGCGGTTTTATCCAAA
ACGCCACTAAAAACAGAGAAATAGCGGCGTTTTCGTCAAACGCCACTAAAAACTAGG
Found at i:3515318 original size:21 final size:21
Alignment explanation
Indices: 3515278--3515318 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3515268 GCTTATGCAT
* *
3515278 GGTTTGGGGTTTATTATTTTG
1 GGTTTGGGGTATAGTATTTTG
*
3515299 GGTTTGGGGTATAGTGTTTT
1 GGTTTGGGGTATAGTATTTT
3515319 AAATTAGTTT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.10, C:0.00, G:0.37, T:0.54
Consensus pattern (21 bp):
GGTTTGGGGTATAGTATTTTG
Found at i:3516415 original size:17 final size:17
Alignment explanation
Indices: 3516393--3516443 Score: 50
Period size: 17 Copynumber: 2.9 Consensus size: 17
3516383 AAACCCTTAT
*
3516393 TTTCCCCCAAATCAAAG
1 TTTCCCCCAAATCAAAA
* *
3516410 TTTCCCCTAAACCCTAAAA
1 TTTCCCCCAAA-TC-AAAA
3516429 TTT-CCCCAAATCAAA
1 TTTCCCCCAAATCAAA
3516444 CCCATTTGCC
Statistics
Matches: 27, Mismatches: 5, Indels: 5
0.73 0.14 0.14
Matches are distributed among these distances:
16 3 0.11
17 11 0.41
18 7 0.26
19 6 0.22
ACGTcount: A:0.37, C:0.35, G:0.02, T:0.25
Consensus pattern (17 bp):
TTTCCCCCAAATCAAAA
Found at i:3519028 original size:241 final size:241
Alignment explanation
Indices: 3518599--3519243 Score: 1218
Period size: 241 Copynumber: 2.7 Consensus size: 241
3518589 AGTTATAAGC
* *
3518599 AATTAAAACAATAGCTGACCTTCTCTCCAACCTTATTTTAAATATTTTAAAGATTCAAAGTATAG
1 AATTACAACAATAGCTGACCTTCTCTCCAACCTTATTTTAAATATTTTAAAGATTCAAAGTATAT
*
3518664 AGGCTGGAAACCAGACGGGTTGCCTTATATCGAGCTGTAAGATATAATGGATCCTCCCTAGGTGT
66 AGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCTGTAAGATATAATGGATCCTCCCTAGGTGT
3518729 AACAACGCCACGTATGATGAATCTTAAAAAATTCAAAAAGACTTGAAAAAAGTTCTATCGAGCTC
131 AACAACGCCACGTATGATGAATCTTAAAAAATTCAAAAAGACTTGAAAAAAGTTCTATCGAGCTC
*
3518794 ATTTACTATTGAATATTTATTACCATGTAGCTTGCTTGTCCATTAA
196 ATTTACTATTGAATATTTATTACCATCTAGCTTGCTTGTCCATTAA
*
3518840 AATTACAACAATAGCTGACCTTCTCTCCAACCTTATTTTAAATATTTTAAAGATTCAAAGTACAT
1 AATTACAACAATAGCTGACCTTCTCTCCAACCTTATTTTAAATATTTTAAAGATTCAAAGTATAT
3518905 AGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCTGTAAGATATAATGGATCCTCCCTAGGTGT
66 AGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCTGTAAGATATAATGGATCCTCCCTAGGTGT
* *
3518970 AACAACGCCACGTATGATGAATCTTCAAAAATTCAAAAAGACTTGAAAAAGGTTCTATCGAGCTC
131 AACAACGCCACGTATGATGAATCTTAAAAAATTCAAAAAGACTTGAAAAAAGTTCTATCGAGCTC
3519035 ATTTACTATTGAATATTTATTACCATCTAGCTTGCTTGTCCATTAA
196 ATTTACTATTGAATATTTATTACCATCTAGCTTGCTTGTCCATTAA
3519081 AATTACAACAATAGCTGACCTTCTCTCCAACCTTATTTTAAATATTTTAAAGATTCAAAGTATAT
1 AATTACAACAATAGCTGACCTTCTCTCCAACCTTATTTTAAATATTTTAAAGATTCAAAGTATAT
*
3519146 AGGCTGGAAACCTGACGGGTTGCCTTATATTGAGCTGTAAGATATAATGGATCCTCCCTAGGTGT
66 AGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCTGTAAGATATAATGGATCCTCCCTAGGTGT
3519211 AACAACGCCACGTATGATGAATCTTAAAAAATT
131 AACAACGCCACGTATGATGAATCTTAAAAAATT
3519244 ACTATTTTTT
Statistics
Matches: 394, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
241 394 1.00
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (241 bp):
AATTACAACAATAGCTGACCTTCTCTCCAACCTTATTTTAAATATTTTAAAGATTCAAAGTATAT
AGGCTGGAAACCTGACGGGTTGCCTTATATCGAGCTGTAAGATATAATGGATCCTCCCTAGGTGT
AACAACGCCACGTATGATGAATCTTAAAAAATTCAAAAAGACTTGAAAAAAGTTCTATCGAGCTC
ATTTACTATTGAATATTTATTACCATCTAGCTTGCTTGTCCATTAA
Found at i:3519371 original size:9 final size:9
Alignment explanation
Indices: 3519348--3519475 Score: 121
Period size: 9 Copynumber: 13.6 Consensus size: 9
3519338 ATCGATCATT
*
3519348 ACTTAAATA
1 ACTTACATA
*
3519357 AATTACATA
1 ACTTACATA
3519366 ACTTACATA
1 ACTTACATA
* *
3519375 ACTCATATA
1 ACTTACATA
3519384 ACTTACATA
1 ACTTACATA
*
3519393 ATTTACATAACA
1 ACTTACAT---A
3519405 ACTTACATA
1 ACTTACATA
*
3519414 ACTCACATA
1 ACTTACATA
3519423 ACTTACATA
1 ACTTACATA
*
3519432 ATTTACATA
1 ACTTACATA
*
3519441 ACTCACATA
1 ACTTACATA
*
3519450 ACGTACATAACA
1 ACTTACAT---A
3519462 ACTTACATA
1 ACTTACATA
3519471 ACTTA
1 ACTTA
3519476 ACTAATACAT
Statistics
Matches: 96, Mismatches: 17, Indels: 12
0.77 0.14 0.10
Matches are distributed among these distances:
9 80 0.83
12 16 0.17
ACGTcount: A:0.47, C:0.21, G:0.01, T:0.31
Consensus pattern (9 bp):
ACTTACATA
Found at i:3519417 original size:39 final size:39
Alignment explanation
Indices: 3519365--3519442 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
3519355 TAAATTACAT
*
3519365 AACTTACATAACTCATATAACTTACATAATTTACATAAC
1 AACTTACATAACTCACATAACTTACATAATTTACATAAC
3519404 AACTTACATAACTCACATAACTTACATAATTTACATAAC
1 AACTTACATAACTCACATAACTTACATAATTTACATAAC
3519443 TCACATAACG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (39 bp):
AACTTACATAACTCACATAACTTACATAATTTACATAAC
Found at i:3519442 original size:57 final size:57
Alignment explanation
Indices: 3519361--3519473 Score: 172
Period size: 57 Copynumber: 2.0 Consensus size: 57
3519351 TAAATAAATT
* * **
3519361 ACATAACTTACATAACTCATATAACTTACATAATTTACATAACAACTTACATAACTC
1 ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACTC
* *
3519418 ACATAACTTACATAATTTACATAACTCACATAACGTACATAACAACTTACATAACT
1 ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACT
3519474 TAACTAATAC
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
57 50 1.00
ACGTcount: A:0.46, C:0.23, G:0.01, T:0.30
Consensus pattern (57 bp):
ACATAACTTACATAACTCACATAACTCACATAACGTACATAACAACTTACATAACTC
Found at i:3525004 original size:17 final size:17
Alignment explanation
Indices: 3524982--3525015 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3524972 CGGTTCAGCA
3524982 AATTGCCGAGGTTCAAC
1 AATTGCCGAGGTTCAAC
*
3524999 AATTGCTGAGGTTCAAC
1 AATTGCCGAGGTTCAAC
3525016 GAAAATATGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.21, G:0.24, T:0.26
Consensus pattern (17 bp):
AATTGCCGAGGTTCAAC
Found at i:3525388 original size:33 final size:33
Alignment explanation
Indices: 3525338--3525419 Score: 96
Period size: 31 Copynumber: 2.5 Consensus size: 33
3525328 TAAGAATTAA
* *
3525338 TGTTTTTGGTTGTATTTTTTATGCTAAATTTGC
1 TGTTTTTGGTTGCATTTTTTATACTAAATTTGC
* * *
3525371 TGTTTTTGGCTGCA--TTTTATACTATATTTGT
1 TGTTTTTGGTTGCATTTTTTATACTAAATTTGC
*
3525402 TGTTTTTGGTTGGATTTT
1 TGTTTTTGGTTGCATTTT
3525420 AATGTAGGAA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
31 26 0.65
33 14 0.35
ACGTcount: A:0.13, C:0.06, G:0.20, T:0.61
Consensus pattern (33 bp):
TGTTTTTGGTTGCATTTTTTATACTAAATTTGC
Found at i:3530596 original size:27 final size:28
Alignment explanation
Indices: 3530566--3530671 Score: 119
Period size: 27 Copynumber: 3.9 Consensus size: 28
3530556 CTGCCATAAT
* * *
3530566 AGATA-TTGTGACAGAGTCACCAGATAC
1 AGATATTTGTGGCAAAGCCACCAGATAC
* * *
3530593 AGATA-TTGTGGCAGAGCCACTAGAAAC
1 AGATATTTGTGGCAAAGCCACCAGATAC
* *
3530620 AAATATTTGTGGTAAAGCCACCAGAT-C
1 AGATATTTGTGGCAAAGCCACCAGATAC
3530647 AGATATTTGTGGCAAAGCCACCAGA
1 AGATATTTGTGGCAAAGCCACCAGA
3530672 ACACTTCCTC
Statistics
Matches: 67, Mismatches: 11, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
27 51 0.76
28 16 0.24
ACGTcount: A:0.37, C:0.19, G:0.23, T:0.22
Consensus pattern (28 bp):
AGATATTTGTGGCAAAGCCACCAGATAC
Found at i:3531302 original size:20 final size:20
Alignment explanation
Indices: 3531269--3531318 Score: 82
Period size: 20 Copynumber: 2.5 Consensus size: 20
3531259 CGGCCATCAA
* *
3531269 TACCTATGCACTTGAGATCC
1 TACCTTTGCCCTTGAGATCC
3531289 TACCTTTGCCCTTGAGATCC
1 TACCTTTGCCCTTGAGATCC
3531309 TACCTTTGCC
1 TACCTTTGCC
3531319 AAAACTAGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.18, C:0.34, G:0.14, T:0.34
Consensus pattern (20 bp):
TACCTTTGCCCTTGAGATCC
Found at i:3537979 original size:19 final size:20
Alignment explanation
Indices: 3537951--3537988 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
3537941 AGTTGTTGTT
*
3537951 TACATGTGTA-AAAATAATG
1 TACATATGTATAAAATAATG
3537970 TACATATGTATAAAATAAT
1 TACATATGTATAAAATAAT
3537989 AAATTATATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.34
Consensus pattern (20 bp):
TACATATGTATAAAATAATG
Found at i:3538880 original size:7 final size:7
Alignment explanation
Indices: 3538868--3538908 Score: 82
Period size: 7 Copynumber: 5.9 Consensus size: 7
3538858 ATTTGTGATT
3538868 AATGTGA
1 AATGTGA
3538875 AATGTGA
1 AATGTGA
3538882 AATGTGA
1 AATGTGA
3538889 AATGTGA
1 AATGTGA
3538896 AATGTGA
1 AATGTGA
3538903 AATGTG
1 AATGTG
3538909 GATATTGGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 34 1.00
ACGTcount: A:0.41, C:0.00, G:0.29, T:0.29
Consensus pattern (7 bp):
AATGTGA
Found at i:3544089 original size:27 final size:27
Alignment explanation
Indices: 3544051--3544108 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 27
3544041 AAGGGTGTCA
*
3544051 GATAGGCGGCACTAGTTG-TGCCTATCT
1 GATAGGCGGCACT-GGTGATGCCTATCT
*
3544078 GATAGGCGGCACTGGTGATGCTTATCT
1 GATAGGCGGCACTGGTGATGCCTATCT
3544105 GATA
1 GATA
3544109 AGTGGCACAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 3 0.11
27 25 0.89
ACGTcount: A:0.21, C:0.19, G:0.31, T:0.29
Consensus pattern (27 bp):
GATAGGCGGCACTGGTGATGCCTATCT
Found at i:3544221 original size:21 final size:21
Alignment explanation
Indices: 3544197--3544246 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
3544187 GTATTTAAGG
*
3544197 TTAGGGTTTTGCTAAAATAAT
1 TTAGGGTTTTGCTAAAAGAAT
** *
3544218 TTAGATTTTTGTTAAAAGAAT
1 TTAGGGTTTTGCTAAAAGAAT
3544239 TTAGGGTT
1 TTAGGGTT
3544247 AAGGTTTTAG
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.32, C:0.02, G:0.20, T:0.46
Consensus pattern (21 bp):
TTAGGGTTTTGCTAAAAGAAT
Found at i:3544802 original size:21 final size:21
Alignment explanation
Indices: 3544756--3544795 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
3544746 AACCCTTAAT
3544756 CCTAAATTATTTTAACAAAAA
1 CCTAAATTATTTTAACAAAAA
*
3544777 CCTAAATTATTTTAGCAAA
1 CCTAAATTATTTTAACAAA
3544796 GCTCTAACCC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.47, C:0.15, G:0.03, T:0.35
Consensus pattern (21 bp):
CCTAAATTATTTTAACAAAAA
Found at i:3545383 original size:31 final size:30
Alignment explanation
Indices: 3545315--3545388 Score: 89
Period size: 31 Copynumber: 2.5 Consensus size: 30
3545305 AAAATATTAC
*
3545315 AATTTAA-TCACTGAACTATTCAGAAATTT
1 AATTTAAGTCATTGAACTATTCAGAAATTT
* *
3545344 CATTTAAGTCATTGAACTATTTA-AAAGTTTT
1 AATTTAAGTCATTGAACTATTCAGAAA--TTT
3545375 AATTTAAGTCATTG
1 AATTTAAGTCATTG
3545389 GGCTTTTAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
29 9 0.24
30 13 0.34
31 16 0.42
ACGTcount: A:0.38, C:0.11, G:0.09, T:0.42
Consensus pattern (30 bp):
AATTTAAGTCATTGAACTATTCAGAAATTT
Found at i:3552045 original size:22 final size:22
Alignment explanation
Indices: 3552014--3552067 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
3552004 TTTTTCAAAA
*
3552014 AGCGCCGCTATAGATCGAGTATT
1 AGCG-CGCTATAGATCGAGCATT
*
3552037 AGCGCGCTATAGATCGCGCATT
1 AGCGCGCTATAGATCGAGCATT
3552059 AGCTGCGCT
1 AGC-GCGCT
3552068 TTTTAAAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 19 0.68
23 9 0.32
ACGTcount: A:0.22, C:0.26, G:0.28, T:0.24
Consensus pattern (22 bp):
AGCGCGCTATAGATCGAGCATT
Found at i:3552184 original size:40 final size:40
Alignment explanation
Indices: 3552129--3552377 Score: 209
Period size: 40 Copynumber: 6.2 Consensus size: 40
3552119 AGCTTTAGTG
*
3552129 GCATTAGCGACGCTTTTAGAAAAACACCGCTATAGGTCGA
1 GCATTAGCGACGCTTTTAGAAAAACACCGCTATAGATCGA
* * * *
3552169 GCATTAGC-AGCGCTTTTAGAAAAATATCGTTACAGATCGA
1 GCATTAGCGA-CGCTTTTAGAAAAACACCGCTATAGATCGA
* * **
3552209 GCACTAGCGACGCTTTTTGAAAAACGTCGCTATAGATCGA
1 GCATTAGCGACGCTTTTAGAAAAACACCGCTATAGATCGA
* * * *
3552249 GCATTAGTGGCGCTTTTTA-AAAAACGCCGCTATAGCTCGA
1 GCATTAGCGACGC-TTTTAGAAAAACACCGCTATAGATCGA
* * ** * *
3552289 CCTTTAGCGACGCTTTTCA-AAAAATGCTGCTATAGATCCA
1 GCATTAGCGACGCTTTT-AGAAAAACACCGCTATAGATCGA
** * * * *
3552329 GCATTAAAGACGTTTTTCA-AAAAGCGCGGCTATAGATCGA
1 GCATTAGCGACGCTTTT-AGAAAAACACCGCTATAGATCGA
3552369 GCATTAGCG
1 GCATTAGCG
3552378 GCATTTTTTA
Statistics
Matches: 169, Mismatches: 36, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
39 5 0.03
40 159 0.94
41 5 0.03
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.26
Consensus pattern (40 bp):
GCATTAGCGACGCTTTTAGAAAAACACCGCTATAGATCGA
Done.