Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr7
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: 47983841
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 869652 characters in sequence are not A, C, G, or T
File 128 of 153
Found at i:40556320 original size:14 final size:15
Alignment explanation
Indices: 40556293--40556327 Score: 54
Period size: 14 Copynumber: 2.4 Consensus size: 15
40556283 ATGTTTGAAA
40556293 TGTAAAATTATATTT
1 TGTAAAATTATATTT
40556308 TGTAAAA-TATATTT
1 TGTAAAATTATATTT
*
40556322 TTTAAA
1 TGTAAA
40556328 TAATGTAAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.43, C:0.00, G:0.06, T:0.51
Consensus pattern (15 bp):
TGTAAAATTATATTT
Found at i:40561409 original size:28 final size:27
Alignment explanation
Indices: 40561368--40561427 Score: 68
Period size: 28 Copynumber: 2.2 Consensus size: 27
40561358 TTAATTTCGC
* *
40561368 TTATCGATTTATTTA-TATTATTGATAT
1 TTATTGATGTATTTATTATTATTG-TAT
*
40561395 GTTATTGATGTATTTATTATTGTTGTAT
1 -TTATTGATGTATTTATTATTATTGTAT
40561423 TTATT
1 TTATT
40561428 ATTATAGCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 5 0.18
28 16 0.57
29 7 0.25
ACGTcount: A:0.25, C:0.02, G:0.12, T:0.62
Consensus pattern (27 bp):
TTATTGATGTATTTATTATTATTGTAT
Found at i:40561416 original size:15 final size:15
Alignment explanation
Indices: 40561396--40561430 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
40561386 TATTGATATG
40561396 TTATTGATGTATTTA
1 TTATTGATGTATTTA
*
40561411 TTATTGTTGTATTTA
1 TTATTGATGTATTTA
40561426 TTATT
1 TTATT
40561431 ATAGCATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.11, T:0.66
Consensus pattern (15 bp):
TTATTGATGTATTTA
Found at i:40567077 original size:24 final size:24
Alignment explanation
Indices: 40567026--40567077 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
40567016 GCCCAATAAT
* * *
40567026 GCCCGGGCCCAAGCAAACAAATAT
1 GCCCGGGCCCAAACAAACAAACAG
* *
40567050 GCCCGGGCCCAAACCAATAAACAG
1 GCCCGGGCCCAAACAAACAAACAG
40567074 GCCC
1 GCCC
40567078 AAAACCCAAC
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.35, C:0.38, G:0.21, T:0.06
Consensus pattern (24 bp):
GCCCGGGCCCAAACAAACAAACAG
Found at i:40567462 original size:11 final size:11
Alignment explanation
Indices: 40567446--40567476 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
40567436 GTCGGTTTTT
40567446 TTTTATTTTCA
1 TTTTATTTTCA
*
40567457 TTTTATTTTCG
1 TTTTATTTTCA
40567468 TTTTATTTT
1 TTTTATTTT
40567477 TGCTTAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.13, C:0.06, G:0.03, T:0.77
Consensus pattern (11 bp):
TTTTATTTTCA
Found at i:40573187 original size:6 final size:7
Alignment explanation
Indices: 40573164--40573207 Score: 56
Period size: 7 Copynumber: 6.3 Consensus size: 7
40573154 AAAAGTGATG
40573164 TGAAAAA
1 TGAAAAA
40573171 TGAAAAGA
1 TGAAAA-A
40573179 TG-AAAA
1 TGAAAAA
40573185 TGAAAAA
1 TGAAAAA
40573192 TGAAAAA
1 TGAAAAA
40573199 -GTAAAAA
1 TG-AAAAA
40573206 TG
1 TG
40573208 GAGAGGCTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 7
0.82 0.00 0.17
Matches are distributed among these distances:
6 4 0.12
7 25 0.76
8 4 0.12
ACGTcount: A:0.66, C:0.00, G:0.18, T:0.16
Consensus pattern (7 bp):
TGAAAAA
Found at i:40573205 original size:21 final size:21
Alignment explanation
Indices: 40573164--40573207 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
40573154 AAAAGTGATG
*
40573164 TGAAAAATGAAAAGATGAAAA
1 TGAAAAATGAAAAGATAAAAA
40573185 TGAAAAATGAAAA-AGTAAAAA
1 TGAAAAATGAAAAGA-TAAAAA
40573206 TG
1 TG
40573208 GAGAGGCTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.66, C:0.00, G:0.18, T:0.16
Consensus pattern (21 bp):
TGAAAAATGAAAAGATAAAAA
Found at i:40574614 original size:100 final size:100
Alignment explanation
Indices: 40574441--40575399 Score: 1431
Period size: 100 Copynumber: 9.6 Consensus size: 100
40574431 ACCATAGATT
40574441 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGACGGATCTGGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGACGGATCTGGTTTCCCTGATAT
40574506 TGCACTTAAAAAGATTGAAGCCACAACGGCGGATC
66 TGCACTTAAAAAGATTGAAGCCACAACGGCGGATC
* *
40574541 TTACTTCCTTAGTAGTGCAGTGGAACAGATTGAAGCTACGACGATGGATCTGGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGACGGATCTGGTTTCCCTGATAT
* * *
40574606 TGTACTTAAAAAGATTGAAGCCACAACGACGAATC
66 TGCACTTAAAAAGATTGAAGCCACAACGGCGGATC
* * *
40574641 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCAGATCTAGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGACGGATCTGGTTTCCCTGATAT
*
40574706 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
66 TGCACTTAAAAAGATTGAAGCCACAACGGCGGATC
* * * *
40574741 TTACTTCCCT-GACGGTGCGGTGGAACAGATTGAAGCTACGACGATGGATCTGGTTTCCCTGATA
1 TTACTTCCTTAG-CAGTGCAGTGGAACAGATTGAAGCTACGACGACGGATCTGGTTTCCCTGATA
* * *
40574805 TTGTACTTAAAAAGATTGAAGCCACAACGACGAATC
65 TTGCACTTAAAAAGATTGAAGCCACAACGGCGGATC
* * *
40574841 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCAGATCTAGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGACGGATCTGGTTTCCCTGATAT
*
40574906 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
66 TGCACTTAAAAAGATTGAAGCCACAACGGCGGATC
* * * *
40574941 TTACTTCCCT-GACGGTGCGGTGGAACAGATTGAAGCTACGACGATGGATCTGGTTTCCCTGATA
1 TTACTTCCTTAG-CAGTGCAGTGGAACAGATTGAAGCTACGACGACGGATCTGGTTTCCCTGATA
* * *
40575005 TTGTACTTAAAAAGATTGAAGCCACAACGACGAATC
65 TTGCACTTAAAAAGATTGAAGCCACAACGGCGGATC
* * *
40575041 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCAGATCTAGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGACGGATCTGGTTTCCCTGATAT
*
40575106 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
66 TGCACTTAAAAAGATTGAAGCCACAACGGCGGATC
* * * *
40575141 TTACTTCCCT-GACGGTGCGGTGGAACAGATTGAAGCTACGACGATGGATCTGGTTTCCCTGATA
1 TTACTTCCTTAG-CAGTGCAGTGGAACAGATTGAAGCTACGACGACGGATCTGGTTTCCCTGATA
* * *
40575205 TTGTACTTAAAAAGATTGAAGCCACAACGACGAATC
65 TTGCACTTAAAAAGATTGAAGCCACAACGGCGGATC
* * *
40575241 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCAGATCTAGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGACGGATCTGGTTTCCCTGATAT
*
40575306 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATC
66 TGCACTTAAAAAGATTGAAGCCACAACGGCGGATC
* * * * *
40575341 TTACTTCCCT-GACGGTGCGGTGGAACAGATTGAAGCTACGACGATGAATCTGGTTTCCC
1 TTACTTCCTTAG-CAGTGCAGTGGAACAGATTGAAGCTACGACGACGGATCTGGTTTCCC
40575400 CGACATTACA
Statistics
Matches: 764, Mismatches: 88, Indels: 14
0.88 0.10 0.02
Matches are distributed among these distances:
99 4 0.01
100 757 0.99
101 3 0.00
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.26
Consensus pattern (100 bp):
TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGACGGATCTGGTTTCCCTGATAT
TGCACTTAAAAAGATTGAAGCCACAACGGCGGATC
Found at i:40574784 original size:200 final size:200
Alignment explanation
Indices: 40574441--40575399 Score: 1823
Period size: 200 Copynumber: 4.8 Consensus size: 200
40574431 ACCATAGATT
* * *
40574441 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGACGGATCTGGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCAGATCTAGTTTCCCTGATAT
* * *
40574506 TGCACTTAAAAAGATTGAAGCCACAACGGCGGATCTTACTT-CCTTA-GTAGTGCAGTGGAACAG
66 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGACG--GTGCGGTGGAACAG
40574569 ATTGAAGCTACGACGATGGATCTGGTTTCCCTGATATTGTACTTAAAAAGATTGAAGCCACAACG
129 ATTGAAGCTACGACGATGGATCTGGTTTCCCTGATATTGTACTTAAAAAGATTGAAGCCACAACG
40574634 ACGAATC
194 ACGAATC
40574641 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCAGATCTAGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCAGATCTAGTTTCCCTGATAT
40574706 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGACGGTGCGGTGGAACAGAT
66 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGACGGTGCGGTGGAACAGAT
40574771 TGAAGCTACGACGATGGATCTGGTTTCCCTGATATTGTACTTAAAAAGATTGAAGCCACAACGAC
131 TGAAGCTACGACGATGGATCTGGTTTCCCTGATATTGTACTTAAAAAGATTGAAGCCACAACGAC
40574836 GAATC
196 GAATC
40574841 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCAGATCTAGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCAGATCTAGTTTCCCTGATAT
40574906 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGACGGTGCGGTGGAACAGAT
66 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGACGGTGCGGTGGAACAGAT
40574971 TGAAGCTACGACGATGGATCTGGTTTCCCTGATATTGTACTTAAAAAGATTGAAGCCACAACGAC
131 TGAAGCTACGACGATGGATCTGGTTTCCCTGATATTGTACTTAAAAAGATTGAAGCCACAACGAC
40575036 GAATC
196 GAATC
40575041 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCAGATCTAGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCAGATCTAGTTTCCCTGATAT
40575106 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGACGGTGCGGTGGAACAGAT
66 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGACGGTGCGGTGGAACAGAT
40575171 TGAAGCTACGACGATGGATCTGGTTTCCCTGATATTGTACTTAAAAAGATTGAAGCCACAACGAC
131 TGAAGCTACGACGATGGATCTGGTTTCCCTGATATTGTACTTAAAAAGATTGAAGCCACAACGAC
40575236 GAATC
196 GAATC
40575241 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCAGATCTAGTTTCCCTGATAT
1 TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCAGATCTAGTTTCCCTGATAT
40575306 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGACGGTGCGGTGGAACAGAT
66 TGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGACGGTGCGGTGGAACAGAT
*
40575371 TGAAGCTACGACGATGAATCTGGTTTCCC
131 TGAAGCTACGACGATGGATCTGGTTTCCC
40575400 CGACATTACA
Statistics
Matches: 750, Mismatches: 7, Indels: 4
0.99 0.01 0.01
Matches are distributed among these distances:
200 745 0.99
201 4 0.01
202 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.26
Consensus pattern (200 bp):
TTACTTCCTTAGCAGTGCAGTGGAACAGATTGAAGCTACGACGGCAGATCTAGTTTCCCTGATAT
TGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGACGGTGCGGTGGAACAGAT
TGAAGCTACGACGATGGATCTGGTTTCCCTGATATTGTACTTAAAAAGATTGAAGCCACAACGAC
GAATC
Found at i:40575399 original size:50 final size:50
Alignment explanation
Indices: 40574453--40575404 Score: 473
Period size: 50 Copynumber: 19.0 Consensus size: 50
40574443 ACTTCCTTAG
* *
40574453 CAGTGCAGTGGAACAGATTGAAGCTACGACGACGGATCTGGTTTCCCTGA
1 CAGTGCAGTGGAACAGATTGAAGCTACGACGACGAATCTTGTTTCCCTGA
* * * ** * * * * * ** *
40574503 TATTGCACTTAAAAAGATTGAAGCCACAACGGCGGATCTTACTT-CCTTA
1 CAGTGCAGTGGAACAGATTGAAGCTACGACGACGAATCTTGTTTCCCTGA
* * * *
40574552 GTAGTGCAGTGGAACAGATTGAAGCTACGACGATGGATCTGGTTTCCCTGA
1 -CAGTGCAGTGGAACAGATTGAAGCTACGACGACGAATCTTGTTTCCCTGA
* * * * ** * * * ** *
40574603 TATTGTACTTAAAAAGATTGAAGCCACAACGACGAATCTTACTT-CCTTA
1 CAGTGCAGTGGAACAGATTGAAGCTACGACGACGAATCTTGTTTCCCTGA
* *
40574652 GCAGTGCAGTGGAACAGATTGAAGCTACGACGGC-AGATCTAGTTTCCCTGA
1 -CAGTGCAGTGGAACAGATTGAAGCTACGACGACGA-ATCTTGTTTCCCTGA
* * * ** * * * * * **
40574703 TATTGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGA
1 CAGTGCAGTGGAACAGATTGAAGCTACGACGACGAATCTTGTTTCCCTGA
* * * * *
40574753 CGGTGCGGTGGAACAGATTGAAGCTACGACGATGGATCTGGTTTCCCTGA
1 CAGTGCAGTGGAACAGATTGAAGCTACGACGACGAATCTTGTTTCCCTGA
* * * * ** * * * ** *
40574803 TATTGTACTTAAAAAGATTGAAGCCACAACGACGAATCTTACTT-CCTTA
1 CAGTGCAGTGGAACAGATTGAAGCTACGACGACGAATCTTGTTTCCCTGA
* *
40574852 GCAGTGCAGTGGAACAGATTGAAGCTACGACGGC-AGATCTAGTTTCCCTGA
1 -CAGTGCAGTGGAACAGATTGAAGCTACGACGACGA-ATCTTGTTTCCCTGA
* * * ** * * * * * **
40574903 TATTGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGA
1 CAGTGCAGTGGAACAGATTGAAGCTACGACGACGAATCTTGTTTCCCTGA
* * * * *
40574953 CGGTGCGGTGGAACAGATTGAAGCTACGACGATGGATCTGGTTTCCCTGA
1 CAGTGCAGTGGAACAGATTGAAGCTACGACGACGAATCTTGTTTCCCTGA
* * * * ** * * * ** *
40575003 TATTGTACTTAAAAAGATTGAAGCCACAACGACGAATCTTACTT-CCTTA
1 CAGTGCAGTGGAACAGATTGAAGCTACGACGACGAATCTTGTTTCCCTGA
* *
40575052 GCAGTGCAGTGGAACAGATTGAAGCTACGACGGC-AGATCTAGTTTCCCTGA
1 -CAGTGCAGTGGAACAGATTGAAGCTACGACGACGA-ATCTTGTTTCCCTGA
* * * ** * * * * * **
40575103 TATTGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGA
1 CAGTGCAGTGGAACAGATTGAAGCTACGACGACGAATCTTGTTTCCCTGA
* * * * *
40575153 CGGTGCGGTGGAACAGATTGAAGCTACGACGATGGATCTGGTTTCCCTGA
1 CAGTGCAGTGGAACAGATTGAAGCTACGACGACGAATCTTGTTTCCCTGA
* * * * ** * * * ** *
40575203 TATTGTACTTAAAAAGATTGAAGCCACAACGACGAATCTTACTT-CCTTA
1 CAGTGCAGTGGAACAGATTGAAGCTACGACGACGAATCTTGTTTCCCTGA
* *
40575252 GCAGTGCAGTGGAACAGATTGAAGCTACGACGGC-AGATCTAGTTTCCCTGA
1 -CAGTGCAGTGGAACAGATTGAAGCTACGACGACGA-ATCTTGTTTCCCTGA
* * * ** * * * * * **
40575303 TATTGCAATTAAAAAGATTGAAGCCACAACGGCGGATCTTACTTCCCTGA
1 CAGTGCAGTGGAACAGATTGAAGCTACGACGACGAATCTTGTTTCCCTGA
* * * * *
40575353 CGGTGCGGTGGAACAGATTGAAGCTACGACGATGAATCTGGTTTCCCCGA
1 CAGTGCAGTGGAACAGATTGAAGCTACGACGACGAATCTTGTTTCCCTGA
40575403 CA
1 CA
40575405 TTACAGTTGA
Statistics
Matches: 626, Mismatches: 258, Indels: 36
0.68 0.28 0.04
Matches are distributed among these distances:
49 24 0.04
50 582 0.93
51 20 0.03
ACGTcount: A:0.30, C:0.21, G:0.24, T:0.25
Consensus pattern (50 bp):
CAGTGCAGTGGAACAGATTGAAGCTACGACGACGAATCTTGTTTCCCTGA
Found at i:40575488 original size:44 final size:44
Alignment explanation
Indices: 40575416--40575753 Score: 189
Period size: 44 Copynumber: 7.7 Consensus size: 44
40575406 TACAGTTGAA
* * * *
40575416 TAGATTAAAGATAACAGATCTTATCTCCCTAAGCAGTAGTGGAG
1 TAGATTAAAGATAGCAGATTTTATCTCCCTAGGCAGCAGTGGAG
* * * * **
40575460 CAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTGCAGTGGAG
1 TAGATTAAAGATAGCAGATTTTATCTCCCT-AGGCAGCAGTGGAG
* * ** * * * * * *
40575505 TACATTGAAGCCAGTA-AATCTGTCTCCCTGGGCAGCAGTGGAA
1 TAGATTAAAGATAGCAGATTTTATCTCCCTAGGCAGCAGTGGAG
* * * * *
40575548 TAGATTAAAGATAACAGATCTTATCTCTCTAAGCAGTAGTGGAG
1 TAGATTAAAGATAGCAGATTTTATCTCCCTAGGCAGCAGTGGAG
* * * * **
40575592 CAGATCAAAGATGGCAGATTTTACCTCCCTGAGGTTGCAGTGGAG
1 TAGATTAAAGATAGCAGATTTTATCTCCCT-AGGCAGCAGTGGAG
* * ** * * * * *
40575637 TACATTGAAGCCAGTA-ACTCTATCTCCCTGGGCAGCAGTGGAA
1 TAGATTAAAGATAGCAGATTTTATCTCCCTAGGCAGCAGTGGAG
* * *
40575680 TAGATTAAAGATTA-CAGATCTTATCTCCCTAAGCAGTAGTGGAG
1 TAGATTAAAGA-TAGCAGATTTTATCTCCCTAGGCAGCAGTGGAG
* * * *
40575724 CATATCAAAGAT-GACAGATTTTACCTCCCT
1 TAGATTAAAGATAG-CAGATTTTATCTCCCT
40575754 GAAGTTGCAG
Statistics
Matches: 203, Mismatches: 84, Indels: 14
0.67 0.28 0.05
Matches are distributed among these distances:
43 40 0.20
44 127 0.63
45 36 0.18
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.26
Consensus pattern (44 bp):
TAGATTAAAGATAGCAGATTTTATCTCCCTAGGCAGCAGTGGAG
Found at i:40575590 original size:132 final size:132
Alignment explanation
Indices: 40575408--40575832 Score: 692
Period size: 132 Copynumber: 3.2 Consensus size: 132
40575398 CCCGACATTA
*
40575408 CAGTTGAATAGATTAAAGATAACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATG
1 CAGTGGAATAGATTAAAGATAACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATG
*
40575473 GCAGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAAATCTGTCTCCCTGGGC
66 GCAGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAAATCTATCTCCCTGGGC
40575538 AG
131 AG
*
40575540 CAGTGGAATAGATTAAAGATAACAGATCTTATCTCTCTAAGCAGTAGTGGAGCAGATCAAAGATG
1 CAGTGGAATAGATTAAAGATAACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATG
*
40575605 GCAGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAACTCTATCTCCCTGGGC
66 GCAGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAAATCTATCTCCCTGGGC
40575670 AG
131 AG
* *
40575672 CAGTGGAATAGATTAAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCATATCAAAGATG
1 CAGTGGAATAGATTAAAGATAACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATG
* * * * *
40575737 ACAGATTTTACCTCCCTGAAGTTGCAGTGGAGTACATTGAAGCCAGTAATTCTATC-CCCCGGTC
66 GCAGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAAATCTATCTCCCTGGGC
*
40575801 GG
131 AG
* * *
40575803 CAGTCGAATTGATTGAAGA-AAGCAGATCTT
1 CAGTGGAATAGATTAAAGATAA-CAGATCTT
40575833 GTCTTCATGT
Statistics
Matches: 275, Mismatches: 17, Indels: 3
0.93 0.06 0.01
Matches are distributed among these distances:
130 1 0.00
131 31 0.11
132 243 0.88
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.26
Consensus pattern (132 bp):
CAGTGGAATAGATTAAAGATAACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAAAGATG
GCAGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAAATCTATCTCCCTGGGC
AG
Found at i:40575880 original size:44 final size:45
Alignment explanation
Indices: 40575817--40575909 Score: 125
Period size: 44 Copynumber: 2.1 Consensus size: 45
40575807 CGAATTGATT
** *
40575817 GAAGAAAGCAGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATC
1 GAAGAAAGCAGATCTTGTCTTCACATACTGGTCGTGAAGTAGATC
* * *
40575861 GAAGAAAGTAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATC
1 GAAGAAAGCAGATCTTGTCTTCACATACTGGTCGTGAAGTAGATC
40575906 GAAG
1 GAAG
40575910 TTACAAGTCT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
44 26 0.62
45 16 0.38
ACGTcount: A:0.30, C:0.14, G:0.28, T:0.28
Consensus pattern (45 bp):
GAAGAAAGCAGATCTTGTCTTCACATACTGGTCGTGAAGTAGATC
Found at i:40576569 original size:13 final size:14
Alignment explanation
Indices: 40576535--40576561 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
40576525 CGCCCACACG
40576535 CCGCACTCGTCGCT
1 CCGCACTCGTCGCT
40576549 CCGCACTCGTCGC
1 CCGCACTCGTCGC
40576562 GCGCACTCCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.07, C:0.52, G:0.22, T:0.19
Consensus pattern (14 bp):
CCGCACTCGTCGCT
Found at i:40576796 original size:11 final size:11
Alignment explanation
Indices: 40576780--40576810 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
40576770 AGAGTCGGTT
40576780 TTTTATTTTCA
1 TTTTATTTTCA
*
40576791 TTTTATTTTCG
1 TTTTATTTTCA
40576802 TTTTATTTT
1 TTTTATTTT
40576811 TGCTTAATAC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.13, C:0.06, G:0.03, T:0.77
Consensus pattern (11 bp):
TTTTATTTTCA
Found at i:40579484 original size:22 final size:22
Alignment explanation
Indices: 40579430--40579477 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
40579420 ATAAAAGGGA
40579430 AAATAA-AACTAATAATGATAAT
1 AAATAATAA-TAATAATGATAAT
*
40579452 AATTAATAATAATAATGATAAT
1 AAATAATAATAATAATGATAAT
40579474 AAAT
1 AAAT
40579478 GCTAATACAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
22 21 0.91
23 2 0.09
ACGTcount: A:0.62, C:0.02, G:0.04, T:0.31
Consensus pattern (22 bp):
AAATAATAATAATAATGATAAT
Found at i:40581797 original size:13 final size:14
Alignment explanation
Indices: 40581779--40581807 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
40581769 TTCTGGAGAC
40581779 AAATTTC-ATTTAA
1 AAATTTCAATTTAA
40581792 AAATTTCAATTTAA
1 AAATTTCAATTTAA
40581806 AA
1 AA
40581808 GTTTGAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (14 bp):
AAATTTCAATTTAA
Found at i:40588841 original size:39 final size:38
Alignment explanation
Indices: 40588790--40588916 Score: 114
Period size: 39 Copynumber: 3.3 Consensus size: 38
40588780 TCGAATTTAA
*
40588790 ACATACTTAAAACA-TGTATTAAAGATGTCCTAAACTATG
1 ACATAATTAAAACACT-TATTAAAGATGTCC-AAACTATG
* * * * *
40588829 ACATAATTAAAACACTTATTAATGTTGTTCAGATTATG
1 ACATAATTAAAACACTTATTAAAGATGTCCAAACTATG
* * * *
40588867 ACATAATTAAAA-ACTCATATTAATGATGTTCAAATTATA
1 ACATAATTAAAACACT--TATTAAAGATGTCCAAACTATG
40588906 ACATAATTAAA
1 ACATAATTAAA
40588917 GACTCAAACT
Statistics
Matches: 76, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
37 3 0.04
38 18 0.24
39 54 0.71
40 1 0.01
ACGTcount: A:0.46, C:0.12, G:0.08, T:0.35
Consensus pattern (38 bp):
ACATAATTAAAACACTTATTAAAGATGTCCAAACTATG
Found at i:40588922 original size:39 final size:38
Alignment explanation
Indices: 40588806--40588922 Score: 135
Period size: 39 Copynumber: 3.0 Consensus size: 38
40588796 TTAAAACATG
* * * * *
40588806 TATTAAAGATGTCCTAAACTATGACATAATTAAAACACT
1 TATTAATGATGTTC-AAATTATGACATAATTAAAACTCA
* *
40588845 TATTAATGTTGTTCAGATTATGACATAATTAAAAACTCA
1 TATTAATGATGTTCAAATTATGACATAATT-AAAACTCA
*
40588884 TATTAATGATGTTCAAATTATAACATAATTAAAGACTCA
1 TATTAATGATGTTCAAATTATGACATAATTAAA-ACTCA
40588923 AACTAAATTA
Statistics
Matches: 66, Mismatches: 10, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
38 17 0.26
39 49 0.74
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (38 bp):
TATTAATGATGTTCAAATTATGACATAATTAAAACTCA
Found at i:40591209 original size:22 final size:24
Alignment explanation
Indices: 40591184--40591230 Score: 71
Period size: 22 Copynumber: 2.0 Consensus size: 24
40591174 CATATTTGCG
*
40591184 TATAATAACTA-TTTAACA-AAAA
1 TATAATAACCATTTTAACATAAAA
40591206 TATAATAACCATTTTAACATAAAA
1 TATAATAACCATTTTAACATAAAA
40591230 T
1 T
40591231 TTTAATGTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 10 0.45
23 7 0.32
24 5 0.23
ACGTcount: A:0.55, C:0.11, G:0.00, T:0.34
Consensus pattern (24 bp):
TATAATAACCATTTTAACATAAAA
Found at i:40591950 original size:12 final size:11
Alignment explanation
Indices: 40591928--40591953 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
40591918 AATTTCCCAC
40591928 TTTCCTTTTTT
1 TTTCCTTTTTT
40591939 TTTCCTTTTTT
1 TTTCCTTTTTT
40591950 TTTC
1 TTTC
40591954 TAAACTTTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTCCTTTTTT
Found at i:40592594 original size:17 final size:17
Alignment explanation
Indices: 40592572--40592621 Score: 84
Period size: 17 Copynumber: 2.9 Consensus size: 17
40592562 ATGGAAAGTC
40592572 AAAGATATGAGTATCAG
1 AAAGATATGAGTATCAG
40592589 AAAGATAT-AGGTATCAG
1 AAAGATATGA-GTATCAG
40592606 AAAGATATGAGTATCA
1 AAAGATATGAGTATCA
40592622 AAATCTGAGA
Statistics
Matches: 31, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 1 0.03
17 29 0.94
18 1 0.03
ACGTcount: A:0.48, C:0.06, G:0.22, T:0.24
Consensus pattern (17 bp):
AAAGATATGAGTATCAG
Found at i:40593659 original size:28 final size:30
Alignment explanation
Indices: 40593627--40593706 Score: 101
Period size: 31 Copynumber: 2.7 Consensus size: 30
40593617 ATTTTATAGA
* *
40593627 TTTAGTCCATATACTTTT-ATTTGATC-AT
1 TTTAGTCCCTATACTTTTGAATTGATCAAT
* *
40593655 TTTAGTCCCTGTACTTTTTGAATTGTTCAAT
1 TTTAGTCCCTATAC-TTTTGAATTGATCAAT
40593686 TTTAGTCCCTATACTTTTGAA
1 TTTAGTCCCTATACTTTTGAA
40593707 AATTTAAAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 4
0.83 0.09 0.08
Matches are distributed among these distances:
28 12 0.27
29 4 0.09
30 13 0.30
31 15 0.34
ACGTcount: A:0.23, C:0.16, G:0.10, T:0.51
Consensus pattern (30 bp):
TTTAGTCCCTATACTTTTGAATTGATCAAT
Found at i:40593718 original size:31 final size:31
Alignment explanation
Indices: 40593653--40593721 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 31
40593643 TTATTTGATC
* **
40593653 ATTTTAGTCCCTGTACTTTTTGAATTGTTCA
1 ATTTTAGTCCCTATACTTTTTGAATTGTAAA
40593684 ATTTTAGTCCCTATAC-TTTTGAAAATT-TAAA
1 ATTTTAGTCCCTATACTTTTTG--AATTGTAAA
40593715 ATTTTAG
1 ATTTTAG
40593722 ACCTGATCAA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 5 0.15
31 24 0.73
32 4 0.12
ACGTcount: A:0.28, C:0.13, G:0.10, T:0.49
Consensus pattern (31 bp):
ATTTTAGTCCCTATACTTTTTGAATTGTAAA
Found at i:40605424 original size:8 final size:8
Alignment explanation
Indices: 40605411--40605437 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
40605401 TTCATTTATT
40605411 TTATAAAA
1 TTATAAAA
40605419 TTATAAAA
1 TTATAAAA
40605427 TTATAAAA
1 TTATAAAA
40605435 TTA
1 TTA
40605438 CACAAAAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (8 bp):
TTATAAAA
Found at i:40623375 original size:24 final size:24
Alignment explanation
Indices: 40623312--40623368 Score: 87
Period size: 24 Copynumber: 2.4 Consensus size: 24
40623302 AAACCTAATT
* * *
40623312 CTAATCAATGTTAAATATATTATG
1 CTAATAAATGCTAAATATATTATA
40623336 CTAATAAATGCTAAATATATTATA
1 CTAATAAATGCTAAATATATTATA
40623360 CTAATAAAT
1 CTAATAAAT
40623369 AGTAAATCTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.47, C:0.09, G:0.05, T:0.39
Consensus pattern (24 bp):
CTAATAAATGCTAAATATATTATA
Found at i:40628371 original size:25 final size:27
Alignment explanation
Indices: 40628318--40628371 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
40628308 TTTCTTATCC
* * *
40628318 TTTCATTTTTTGATTAAATTTTTTCTT
1 TTTCATTTTTAGAATAAATTTTATCTT
40628345 TTTC-TTTTTAGAATAAATTTTAT-TT
1 TTTCATTTTTAGAATAAATTTTATCTT
40628370 TT
1 TT
40628372 GTTGATTTGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 4 0.17
26 16 0.67
27 4 0.17
ACGTcount: A:0.22, C:0.06, G:0.04, T:0.69
Consensus pattern (27 bp):
TTTCATTTTTAGAATAAATTTTATCTT
Found at i:40630494 original size:32 final size:32
Alignment explanation
Indices: 40630305--40630514 Score: 174
Period size: 32 Copynumber: 6.6 Consensus size: 32
40630295 TAATATCATT
* **
40630305 GGCACAAAGCCATCAGTAGCAGTGATACAATC
1 GGCACAAAGCCATCAGTAACAGTGATATGATC
* ** * *
40630337 GGCACACAGCCATCAGTAATGGTAACATGATC
1 GGCACAAAGCCATCAGTAACAGTGATATGATC
* * *
40630369 AGTACAAAGCCATCAGTAACAATGATATGATC
1 GGCACAAAGCCATCAGTAACAGTGATATGATC
* *
40630401 GGTACACAA-CCATCAGTAACGGTGATATGATC
1 GGCACA-AAGCCATCAGTAACAGTGATATGATC
* * * *
40630433 AGCACACAGCCATC-GATAACGGTAATATGATC
1 GGCACAAAGCCATCAG-TAACAGTGATATGATC
* ** *
40630465 GGTACAAAGCCATCAGTAGTAGT-ACTATGATT
1 GGCACAAAGCCATCAGTAACAGTGA-TATGATC
*
40630497 GACACAAAGCCATCAGTA
1 GGCACAAAGCCATCAGTA
40630515 GCATCACAGC
Statistics
Matches: 141, Mismatches: 32, Indels: 10
0.77 0.17 0.05
Matches are distributed among these distances:
31 3 0.02
32 135 0.96
33 3 0.02
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (32 bp):
GGCACAAAGCCATCAGTAACAGTGATATGATC
Found at i:40630494 original size:64 final size:65
Alignment explanation
Indices: 40630306--40630514 Score: 196
Period size: 64 Copynumber: 3.3 Consensus size: 65
40630296 AATATCATTG
* * * ** * *
40630306 GCACAAAGCCATCAGTAGCAGTGATACAATCGGCACACAGCCATCAGTAATGGTAAC-ATGATCA
1 GCACAAAGCCATCAGTAACAATAATATGATCGGTACAAAGCCATCAGTAATGGTAACTATGATCA
* * * *
40630370 GTACAAAGCCATCAGTAACAATGATATGATCGGTACACAA-CCATCAGTAACGGTGA-TATGATC
1 GCACAAAGCCATCAGTAACAATAATATGATCGGTACA-AAGCCATCAGTAATGGTAACTATGATC
40630433 A
65 A
* ** * *
40630434 GCACACAGCCATC-GATAACGGTAATATGATCGGTACAAAGCCATCAGTAGTAGT-ACTATGAT-
1 GCACAAAGCCATCAG-TAACAATAATATGATCGGTACAAAGCCATCAGTAATGGTAACTATGATC
*
40630496 T
65 A
40630497 GACACAAAGCCATCAGTA
1 G-CACAAAGCCATCAGTA
40630515 GCATCACAGC
Statistics
Matches: 119, Mismatches: 19, Indels: 14
0.78 0.12 0.09
Matches are distributed among these distances:
63 5 0.04
64 112 0.94
65 2 0.02
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.20
Consensus pattern (65 bp):
GCACAAAGCCATCAGTAACAATAATATGATCGGTACAAAGCCATCAGTAATGGTAACTATGATCA
Found at i:40630510 original size:96 final size:96
Alignment explanation
Indices: 40630292--40630514 Score: 247
Period size: 96 Copynumber: 2.3 Consensus size: 96
40630282 GCCATAAGTT
* * * * * *
40630292 CAATAATATCATTGGCACAAAGCCATCAGTAGCAGTGATACAATCGGCACACAGCCATCAGTAAT
1 CAATGATATGATTGACACAAAGCCATCAGTAACAGTGATACAATCAGCACACAGCCATCAGTAAC
40630357 GGTAACATGATCAGTACAAAGCCATCAGTAA
66 GGTAACATGATCAGTACAAAGCCATCAGTAA
* * **
40630388 CAATGATATGATCGGTACAC-AA-CCATCAGTAACGGTGATATGATCAGCACACAGCCATC-GAT
1 CAATGATATGAT-TG-ACACAAAGCCATCAGTAACAGTGATACAATCAGCACACAGCCATCAG-T
* * *
40630450 AACGGTAATATGATCGGTACAAAGCCATCAGTAG
63 AACGGTAACATGATCAGTACAAAGCCATCAGTAA
* *
40630484 TAGT-ACTATGATTGACACAAAGCCATCAGTA
1 CAATGA-TATGATTGACACAAAGCCATCAGTA
40630515 GCATCACAGC
Statistics
Matches: 105, Mismatches: 16, Indels: 12
0.79 0.12 0.09
Matches are distributed among these distances:
94 4 0.04
95 5 0.05
96 90 0.86
97 3 0.03
98 3 0.03
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (96 bp):
CAATGATATGATTGACACAAAGCCATCAGTAACAGTGATACAATCAGCACACAGCCATCAGTAAC
GGTAACATGATCAGTACAAAGCCATCAGTAA
Found at i:40630612 original size:27 final size:27
Alignment explanation
Indices: 40630558--40630617 Score: 70
Period size: 27 Copynumber: 2.2 Consensus size: 27
40630548 AGCAAAGCTG
*
40630558 CCAGTAACAGTATATGTGGCCAAGCCA
1 CCAGTAACAGTATATGTGGCCAAACCA
*
40630585 CTAGTAACAGTGAT-TGTGG-CAGAACCA
1 CCAGTAACAGT-ATATGTGGCCA-AACCA
40630612 CCAGTA
1 CCAGTA
40630618 TAGTACTTAC
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
26 2 0.07
27 24 0.86
28 2 0.07
ACGTcount: A:0.33, C:0.23, G:0.23, T:0.20
Consensus pattern (27 bp):
CCAGTAACAGTATATGTGGCCAAACCA
Found at i:40630719 original size:24 final size:24
Alignment explanation
Indices: 40630686--40630791 Score: 113
Period size: 24 Copynumber: 4.4 Consensus size: 24
40630676 CCATGCTCAG
*
40630686 AATCAGTCATACAAATCACACACA
1 AATCAGTCATACAAATCACAGACA
* *
40630710 AATCAATCATACCAATCACAGACA
1 AATCAGTCATACAAATCACAGACA
** *
40630734 AATCAGTCATTTAAATCACAGATA
1 AATCAGTCATACAAATCACAGACA
* ** *
40630758 AATTAGTCATTTACATCACAGACA
1 AATCAGTCATACAAATCACAGACA
*
40630782 AATCAATCAT
1 AATCAGTCAT
40630792 TTACACTCGA
Statistics
Matches: 69, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 69 1.00
ACGTcount: A:0.47, C:0.24, G:0.06, T:0.24
Consensus pattern (24 bp):
AATCAGTCATACAAATCACAGACA
Found at i:40630868 original size:27 final size:27
Alignment explanation
Indices: 40630817--40630982 Score: 147
Period size: 27 Copynumber: 6.1 Consensus size: 27
40630807 AAAATAGTTA
* ** *
40630817 TTTACCCTCTAGGGACATTATGGTCAT
1 TTTACCCTATAGGGGTATTACGGTCAT
* *
40630844 TTTACCTTATAGGGGTATTTCGGTCAT
1 TTTACCCTATAGGGGTATTACGGTCAT
* **
40630871 TTAACCCTAT-GAGGGTATTACAATCAT
1 TTTACCCTATAG-GGGTATTACGGTCAT
* * *
40630898 TTTACCCTACAGGGGCATTACGATCAT
1 TTTACCCTATAGGGGTATTACGGTCAT
* * **
40630925 TTTACCCTAT-GAAGGTTTTTTGGTCAT
1 TTTACCCTATAG-GGGTATTACGGTCAT
*
40630952 TTTACCCTACAGGGGTATTACGGTCAT
1 TTTACCCTATAGGGGTATTACGGTCAT
40630979 TTTA
1 TTTA
40630983 TAAATATTAG
Statistics
Matches: 108, Mismatches: 27, Indels: 8
0.76 0.19 0.06
Matches are distributed among these distances:
26 2 0.02
27 104 0.96
28 2 0.02
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (27 bp):
TTTACCCTATAGGGGTATTACGGTCAT
Found at i:40630917 original size:81 final size:81
Alignment explanation
Indices: 40630817--40630982 Score: 185
Period size: 81 Copynumber: 2.0 Consensus size: 81
40630807 AAAATAGTTA
* * * *
40630817 TTTACCCTCTAGGGACATTATGGTCATTTTACCTTAT-AGGGGTATTTCGGTCATTTAACCCTA-
1 TTTACCCTCTAGGGACATTACGATCATTTTACCCTATGA-AGGTATTTCGGTCATTTAACCCTAC
*
40630880 TGAGGGTATTACAATCAT
65 AG-GGGTATTACAATCAT
* * * *
40630898 TTTACCCTAC-AGGGGCATTACGATCATTTTACCCTATGAAGGTTTTTTGGTCATTTTACCCTAC
1 TTTACCCT-CTAGGGACATTACGATCATTTTACCCTATGAAGGTATTTCGGTCATTTAACCCTAC
**
40630962 AGGGGTATTACGGTCAT
65 AGGGGTATTACAATCAT
40630979 TTTA
1 TTTA
40630983 TAAATATTAG
Statistics
Matches: 71, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
81 68 0.96
82 3 0.04
ACGTcount: A:0.23, C:0.19, G:0.19, T:0.39
Consensus pattern (81 bp):
TTTACCCTCTAGGGACATTACGATCATTTTACCCTATGAAGGTATTTCGGTCATTTAACCCTACA
GGGGTATTACAATCAT
Found at i:40630981 original size:54 final size:54
Alignment explanation
Indices: 40630833--40630982 Score: 192
Period size: 54 Copynumber: 2.8 Consensus size: 54
40630823 CTCTAGGGAC
* * * * *
40630833 ATTATGGTCATTTTACCTTATAGGGGTATTTCGGTCATTTAACCCTATGAGGGT
1 ATTATGGTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTATGAAGGT
*** * *
40630887 ATTACAATCATTTTACCCTACAGGGGCATTACGATCATTTTACCCTATGAAGGT
1 ATTATGGTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTATGAAGGT
* *
40630941 TTTTTGGTCATTTTACCCTACAGGGGTATTACGGTCATTTTA
1 ATTATGGTCATTTTACCCTACAGGGGTATTACGGTCATTTTA
40630983 TAAATATTAG
Statistics
Matches: 79, Mismatches: 17, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
54 79 1.00
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Consensus pattern (54 bp):
ATTATGGTCATTTTACCCTACAGGGGTATTACGGTCATTTTACCCTATGAAGGT
Found at i:40633944 original size:45 final size:45
Alignment explanation
Indices: 40633893--40633982 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
40633883 AAATTTTGGC
*
40633893 ATGTAGCATAGTTTTATTGGTCAGATTGATAAAAATAAACTGTAT
1 ATGTAGCATAGATTTATTGGTCAGATTGATAAAAATAAACTGTAT
40633938 ATGTAGCATAGATTTATTGGTCAGATTGATAAAAATAAACTGTAT
1 ATGTAGCATAGATTTATTGGTCAGATTGATAAAAATAAACTGTAT
40633983 TAACGAGGTA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.39, C:0.07, G:0.18, T:0.37
Consensus pattern (45 bp):
ATGTAGCATAGATTTATTGGTCAGATTGATAAAAATAAACTGTAT
Found at i:40637693 original size:18 final size:19
Alignment explanation
Indices: 40637640--40637696 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
40637630 AATTACAAAA
*
40637640 AAAAAATCAAAATAATTT-T
1 AAAAATTCAAAAT-ATTTAT
*
40637659 TAAAATTCAAAATATTTAT
1 AAAAATTCAAAATATTTAT
*
40637678 AAAAATTCTAAA-ATTTAT
1 AAAAATTCAAAATATTTAT
40637696 A
1 A
40637697 TTTTTAAAGA
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 11 0.33
19 22 0.67
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (19 bp):
AAAAATTCAAAATATTTAT
Found at i:40637718 original size:26 final size:24
Alignment explanation
Indices: 40637670--40637719 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 24
40637660 AAAATTCAAA
*
40637670 ATATTTATAAAAATTCTAAAATTT
1 ATATTTATAAAAATTATAAAATTT
*
40637694 ATATTTTTAAAGAATTATAATAATTT
1 ATATTTATAAA-AATTATAA-AATTT
40637720 TAAAAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 10 0.45
25 7 0.32
26 5 0.23
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (24 bp):
ATATTTATAAAAATTATAAAATTT
Found at i:40637882 original size:16 final size:16
Alignment explanation
Indices: 40637863--40637893 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40637853 TTAAAAAAGT
40637863 TTTCAAATATATATGG
1 TTTCAAATATATATGG
*
40637879 TTTCAAATTTATATG
1 TTTCAAATATATATG
40637894 CTCCAACATG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.35, C:0.06, G:0.10, T:0.48
Consensus pattern (16 bp):
TTTCAAATATATATGG
Found at i:40639690 original size:23 final size:22
Alignment explanation
Indices: 40639664--40639708 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
40639654 ATATATATAG
*
40639664 ATTACAAGATATAAATAATAATA
1 ATTACAAGATAT-AATAAAAATA
*
40639687 ATTACAATATATAATAAAAATA
1 ATTACAAGATATAATAAAAATA
40639709 TATGAGTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.31
Consensus pattern (22 bp):
ATTACAAGATATAATAAAAATA
Found at i:40639835 original size:12 final size:12
Alignment explanation
Indices: 40639818--40639851 Score: 59
Period size: 12 Copynumber: 2.8 Consensus size: 12
40639808 ATAAATTAAA
40639818 ATATGTATGTAT
1 ATATGTATGTAT
*
40639830 ATATGTATATAT
1 ATATGTATGTAT
40639842 ATATGTATGT
1 ATATGTATGT
40639852 GAAAATTATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.15, T:0.50
Consensus pattern (12 bp):
ATATGTATGTAT
Found at i:40640027 original size:20 final size:20
Alignment explanation
Indices: 40640004--40640056 Score: 52
Period size: 20 Copynumber: 2.6 Consensus size: 20
40639994 AAAACAATTG
40640004 AATATATAAAATAACAAAAA
1 AATATATAAAATAACAAAAA
* * ***
40640024 AATATTTATAATAATTTAAA
1 AATATATAAAATAACAAAAA
*
40640044 AATATAAAAAATA
1 AATATATAAAATA
40640057 CTCCACTGTT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (20 bp):
AATATATAAAATAACAAAAA
Found at i:40640201 original size:40 final size:42
Alignment explanation
Indices: 40640145--40640253 Score: 132
Period size: 40 Copynumber: 2.6 Consensus size: 42
40640135 CTTTGATCTG
* *
40640145 CTCCACTACTGCTTAGGGAGATAAGATCTGTAAT-TT-CCTA
1 CTCCACTGCTGCTTAGGGAGATAAGATCTATAATCTTACCTA
* * *
40640185 CTCCACTGCTGTTTAGGGATATAAGGTCTATAATCTTCAACCTA
1 CTCCACTGCTGCTTAGGGAGATAAGATCTATAATCTT--ACCTA
*
40640229 CTCCACTGCTGCTCAGGGAGATAAG
1 CTCCACTGCTGCTTAGGGAGATAAG
40640254 GCTAGTGGCT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
40 29 0.51
41 2 0.04
44 26 0.46
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.30
Consensus pattern (42 bp):
CTCCACTGCTGCTTAGGGAGATAAGATCTATAATCTTACCTA
Found at i:40640322 original size:88 final size:88
Alignment explanation
Indices: 40640057--40640341 Score: 237
Period size: 88 Copynumber: 3.3 Consensus size: 88
40640047 ATAAAAAATA
** * * *
40640057 CTCCACTGTTGCTCAGGGAGATAAGGCTAGTGGCTTTAATCTGCTTCCCTACTACCTTAGGAAGA
1 CTCCACTACTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTACTTCCCTACTACCTTGGGAAGA
** **
40640122 TAAGATTCGCTGTCTTTGATCTG
66 TAAGATTTACAATCTTTGATCTG
* * * **
40640145 CTCCACTACTGCTTAGGGAGATAA-G--A-T--CTGTAATTTCCTAC-TCCACTGCT-GTTTAGG
1 CTCCACTACTGCTCAGGGAGATAAGGCTAGTGGCT-TAA-AT-CTACTTCC-CTACTACCTT-GG
* * * * ** * *
40640202 G-ATATAAGGTCTATAATCTTCAACCTA
61 GAAGATAAGATTTACAATCTTTGATCTG
*
40640229 CTCCACTGCTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTACTTCCCTACTACCTTGGGAAGA
1 CTCCACTACTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTACTTCCCTACTACCTTGGGAAGA
*
40640294 TAAGATTTACCATCTTTGATCTG
66 TAAGATTTACAATCTTTGATCTG
*
40640317 CTCCACTACTGCTTAGGGAGATAAG
1 CTCCACTACTGCTCAGGGAGATAAG
40640342 ATTTGTAATT
Statistics
Matches: 144, Mismatches: 39, Indels: 28
0.68 0.18 0.13
Matches are distributed among these distances:
82 2 0.01
83 2 0.01
84 43 0.30
85 11 0.08
87 13 0.09
88 68 0.47
89 3 0.02
90 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.20, T:0.32
Consensus pattern (88 bp):
CTCCACTACTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTACTTCCCTACTACCTTGGGAAGA
TAAGATTTACAATCTTTGATCTG
Found at i:40640341 original size:172 final size:174
Alignment explanation
Indices: 40640055--40640427 Score: 522
Period size: 172 Copynumber: 2.1 Consensus size: 174
40640045 ATATAAAAAA
* * *
40640055 TACTCCACTGTTGCTCAGGGAGATAAGGCTAGTGGCTTTAATCTGCTTCCCTACTACCTTAGGAA
1 TACTCCACTGCTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTACTTCCCTACTACCTTAGGAA
* **
40640120 GATAAGATTCGCTGTCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAA-TTT-CC
66 GATAAGATTCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTACC
*** * *
40640183 TACTCCACTGCTGTTTAGGGATATAAGG--TCTATAATCTTCAACC
131 TACTCCACTGCTGACCAGGGAGAT-AGGATTC-ACAATCTTCAACC
*
40640227 TACTCCACTGCTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTACTTCCCTACTACCTTGGGAA
1 TACTCCACTGCTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTACTTCCCTACTACCTTAGGAA
* *
40640292 GATAAGATTTACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATTTGTAATTTTCAA
66 GATAAGATTCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTT--A
40640357 CCTACTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCAACC
129 CCTACTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCAACC
* *
40640403 TATTCCACTACTGAC-CAGGGAGATA
1 TACTCCACTGCTG-CTCAGGGAGATA
40640428 GGATTCACAA
Statistics
Matches: 178, Mismatches: 16, Indels: 10
0.87 0.08 0.05
Matches are distributed among these distances:
172 114 0.64
173 3 0.02
175 3 0.02
176 55 0.31
177 3 0.02
ACGTcount: A:0.26, C:0.24, G:0.19, T:0.31
Consensus pattern (174 bp):
TACTCCACTGCTGCTCAGGGAGATAAGGCTAGTGGCTTAAATCTACTTCCCTACTACCTTAGGAA
GATAAGATTCACCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAAGATCTGTAATTTTACC
TACTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTCAACC
Found at i:40640365 original size:44 final size:44
Alignment explanation
Indices: 40640145--40640455 Score: 174
Period size: 44 Copynumber: 7.2 Consensus size: 44
40640135 CTTTGATCTG
* *
40640145 CTCCACTACTGCTTAGGGAGATAAGATCTGTAAT-TT---CCTA
1 CTCCACTACTGCTTAGGGAGATAAGATTTATAATCTTCAACCTA
* * * * *
40640185 CTCCACTGCTGTTTAGGGATATAAGGTCTATAATCTTCAACCTA
1 CTCCACTACTGCTTAGGGAGATAAGATTTATAATCTTCAACCTA
* * ** ** * *
40640229 CTCCACTGCTGCTCAGGGAGATAAG-GCTAGT-GGCTTAAATCTA
1 CTCCACTACTGCTTAGGGAGATAAGATTTA-TAATCTTCAACCTA
* ** ** * *
40640272 CTTCC-CTACTACCTT-GGGAAGATAAGATTTACCATCTTTGATCTG
1 C-TCCACTACT-GCTTAGGG-AGATAAGATTTATAATCTTCAACCTA
* *
40640317 CTCCACTACTGCTTAGGGAGATAAGATTTGTAATTTTCAACCTA
1 CTCCACTACTGCTTAGGGAGATAAGATTTATAATCTTCAACCTA
* * * * *
40640361 CTCCACTGCTGAC-CAGGGAGATAGGATTCACAATCTTCAACCTA
1 CTCCACTACTG-CTTAGGGAGATAAGATTTATAATCTTCAACCTA
* * * * * *
40640405 TTCCACTACTGAC-CAGGGAGATAGGATTCACAATCTTCAACTTA
1 CTCCACTACTG-CTTAGGGAGATAAGATTTATAATCTTCAACCTA
*
40640449 TTCCACT
1 CTCCACT
40640456 GCTGACCAGG
Statistics
Matches: 215, Mismatches: 43, Indels: 22
0.77 0.15 0.08
Matches are distributed among these distances:
40 29 0.13
41 2 0.01
43 19 0.09
44 146 0.68
45 19 0.09
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (44 bp):
CTCCACTACTGCTTAGGGAGATAAGATTTATAATCTTCAACCTA
Found at i:40640383 original size:88 final size:88
Alignment explanation
Indices: 40640145--40640476 Score: 248
Period size: 88 Copynumber: 3.8 Consensus size: 88
40640135 CTTTGATCTG
* * *** *
40640145 CTCCACTACTGCTTAGGGAGATAAGATCTGTAAT-TT---CCTACTCCACTGCTGTTTAGGGATA
1 CTCCACTACTGCTCAGGGAGATAAGATTTGTAATCTTCAACCTACTCCACTGCTGACCAGGGAGA
* * *
40640206 TAAGGTCTATAATCTTCAACCTA
66 TAAGATTTACAATCTTCAACCTA
* ** * ** * * * *
40640229 CTCCACTGCTGCTCAGGGAGATAAGGCTAGT-GGCTTAAATCTACTTCC-CTACT-ACCTTGGGA
1 CTCCACTACTGCTCAGGGAGATAAGATTTGTAATCTTCAACCTAC-TCCACTGCTGACC-AGGG-
* ** * *
40640291 AGATAAGATTTACCATCTTTGATCTG
63 AGATAAGATTTACAATCTTCAACCTA
* *
40640317 CTCCACTACTGCTTAGGGAGATAAGATTTGTAATTTTCAACCTACTCCACTGCTGACCAGGGAGA
1 CTCCACTACTGCTCAGGGAGATAAGATTTGTAATCTTCAACCTACTCCACTGCTGACCAGGGAGA
* *
40640382 TAGGATTCACAATCTTCAACCTA
66 TAAGATTTACAATCTTCAACCTA
* * *** * *
40640405 TTCCACTACTGAC-CAGGGAGATAGGATTCACAATCTTCAACTTATTCCACTGCTGACCAGGGAG
1 CTCCACTACTG-CTCAGGGAGATAAGATTTGTAATCTTCAACCTACTCCACTGCTGACCAGGGAG
*
40640469 ATATGATT
65 ATAAGATT
40640477 CACCTATTCC
Statistics
Matches: 185, Mismatches: 52, Indels: 18
0.73 0.20 0.07
Matches are distributed among these distances:
84 27 0.15
87 11 0.06
88 128 0.69
89 16 0.09
90 3 0.02
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (88 bp):
CTCCACTACTGCTCAGGGAGATAAGATTTGTAATCTTCAACCTACTCCACTGCTGACCAGGGAGA
TAAGATTTACAATCTTCAACCTA
Found at i:40640461 original size:44 final size:44
Alignment explanation
Indices: 40640352--40640644 Score: 324
Period size: 44 Copynumber: 7.1 Consensus size: 44
40640342 ATTTGTAATT
*
40640352 TTCAACCTACTCCACTGCTGACCAGGGAGATAGGATTCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
*
40640396 TTCAACCTATTCCACTACTGACCAGGGAGATAGGATTCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
* *
40640440 TTCAACTTATTCCACTGCTGACCAGGGAGAT---A-T---GA--
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
40640475 TTC-ACCTATTCCACTGCTGACCAGGGAGATAGGACTT-ACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGA-TTCACAATC
* *
40640518 TTCAACCAATTCCACCGCTGACCAGGGAGATAGGATTCAC---C
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
*
40640559 -T--A--T-TT-CATTGCTGACCAGGGAGATAGGACTT-ACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGA-TTCACAATC
* * *
40640596 TTTAACCTATTTCACTGCTGACCAGGGAGATAGGACTCACAATC
1 TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
40640640 TTCAA
1 TTCAA
40640645 TCTGCTTCGC
Statistics
Matches: 211, Mismatches: 15, Indels: 46
0.78 0.06 0.17
Matches are distributed among these distances:
34 49 0.23
35 7 0.03
37 3 0.01
38 2 0.01
39 1 0.00
40 3 0.01
41 3 0.01
42 1 0.00
43 8 0.04
44 134 0.64
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (44 bp):
TTCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATC
Found at i:40640490 original size:34 final size:34
Alignment explanation
Indices: 40640447--40640583 Score: 130
Period size: 34 Copynumber: 3.7 Consensus size: 34
40640437 ATCTTCAACT
40640447 TATTCCACTGCTGACCAGGGAGATATGATTCACC
1 TATTCCACTGCTGACCAGGGAGATATGATTCACC
*
40640481 TATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCAACC
1 TATTCCACTGCTGACCAGGGAGAT---A--T--GA--TTC-ACC
* * *
40640525 AATTCCACCGCTGACCAGGGAGATAGGATTCACC
1 TATTCCACTGCTGACCAGGGAGATATGATTCACC
* *
40640559 TATTTCATTGCTGACCAGGGAGATA
1 TATTCCACTGCTGACCAGGGAGATA
40640584 GGACTTACAA
Statistics
Matches: 84, Mismatches: 9, Indels: 20
0.74 0.08 0.18
Matches are distributed among these distances:
34 48 0.57
35 3 0.04
37 2 0.02
39 1 0.01
41 2 0.02
43 3 0.04
44 25 0.30
ACGTcount: A:0.28, C:0.26, G:0.21, T:0.25
Consensus pattern (34 bp):
TATTCCACTGCTGACCAGGGAGATATGATTCACC
Found at i:40640530 original size:78 final size:78
Alignment explanation
Indices: 40640400--40640635 Score: 366
Period size: 78 Copynumber: 3.0 Consensus size: 78
40640390 ACAATCTTCA
* *
40640400 ACCTATTCCACTACTGACCAGGGAGATAGGA-TTCACAATCTTCAACTTATTCCACTGCTGACCA
1 ACCTATTCCACTGCTGACCAGGGAGATAGGACTT-ACAATCTTCAACCTATTCCACTGCTGACCA
*
40640464 GGGAGATATGATTC
65 GGGAGATAGGATTC
* *
40640478 ACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCAACCAATTCCACCGCTGACCAG
1 ACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGACCAG
40640543 GGAGATAGGATTC
66 GGAGATAGGATTC
* * * *
40640556 ACCTATTTCATTGCTGACCAGGGAGATAGGACTTACAATCTTTAACCTATTTCACTGCTGACCAG
1 ACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGACCAG
*
40640621 GGAGATAGGACTC
66 GGAGATAGGATTC
40640634 AC
1 AC
40640636 AATCTTCAAT
Statistics
Matches: 145, Mismatches: 12, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
78 143 0.99
79 2 0.01
ACGTcount: A:0.29, C:0.26, G:0.19, T:0.25
Consensus pattern (78 bp):
ACCTATTCCACTGCTGACCAGGGAGATAGGACTTACAATCTTCAACCTATTCCACTGCTGACCAG
GGAGATAGGATTC
Found at i:40646553 original size:3 final size:3
Alignment explanation
Indices: 40646545--40646569 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
40646535 GTACATGGTT
40646545 ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
40646570 GAGTATTAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:40648198 original size:31 final size:29
Alignment explanation
Indices: 40648147--40648213 Score: 75
Period size: 31 Copynumber: 2.3 Consensus size: 29
40648137 CAATTTGAAC
*
40648147 CTAAATT-TTAAAATCTAAAAAATAAAGAAA
1 CTAAATTCTTAAAATCAAAAAAATAAAG--A
*
40648177 CTAAATTCTTAAAAAT-AAAAAAATACAGA
1 CTAAATTCTT-AAAATCAAAAAAATAAAGA
40648206 CTAAATTC
1 CTAAATTC
40648214 CAAATTCATA
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
29 9 0.27
30 7 0.21
31 12 0.36
32 5 0.15
ACGTcount: A:0.60, C:0.10, G:0.03, T:0.27
Consensus pattern (29 bp):
CTAAATTCTTAAAATCAAAAAAATAAAGA
Found at i:40650686 original size:6 final size:6
Alignment explanation
Indices: 40650675--40650714 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
40650665 CAATTCAAAA
* * *
40650675 AAAATC AAAATC AAAATC AAAGTC AAAATG AAAATG AAAA
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAATC AAAA
40650715 AAGAGAGAAG
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.68, C:0.10, G:0.07, T:0.15
Consensus pattern (6 bp):
AAAATC
Found at i:40651575 original size:6 final size:7
Alignment explanation
Indices: 40651554--40651604 Score: 68
Period size: 7 Copynumber: 7.0 Consensus size: 7
40651544 ACAAAAAATG
40651554 TGAAAAA
1 TGAAAAA
40651561 TGAAAAAAA
1 TG--AAAAA
40651570 TG-AAAA
1 TGAAAAA
40651576 TGAAAAA
1 TGAAAAA
40651583 TGAAAAA
1 TGAAAAA
40651590 TGAAAAAA
1 TG-AAAAA
40651598 TGAAAAA
1 TGAAAAA
40651605 GTAAAAATAG
Statistics
Matches: 40, Mismatches: 0, Indels: 8
0.83 0.00 0.17
Matches are distributed among these distances:
6 6 0.15
7 20 0.50
8 7 0.17
9 7 0.17
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (7 bp):
TGAAAAA
Found at i:40651589 original size:29 final size:29
Alignment explanation
Indices: 40651554--40651612 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
40651544 ACAAAAAATG
*
40651554 TGAAAAATGAAAAAAATGAAAATG-AAAAA
1 TGAAAAATG-AAAAAATGAAAAAGTAAAAA
40651583 TGAAAAATGAAAAAATGAAAAAGTAAAAA
1 TGAAAAATGAAAAAATGAAAAAGTAAAAA
40651612 T
1 T
40651613 AGAGAGGCTA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
28 13 0.46
29 15 0.54
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.15
Consensus pattern (29 bp):
TGAAAAATGAAAAAATGAAAAAGTAAAAA
Found at i:40651597 original size:22 final size:21
Alignment explanation
Indices: 40651554--40651612 Score: 68
Period size: 22 Copynumber: 2.7 Consensus size: 21
40651544 ACAAAAAATG
40651554 TGAAAAATGAAAAAAATG-AAAA
1 TGAAAAATG--AAAAATGAAAAA
40651576 TGAAAAATGAAAAATGAAAAAA
1 TGAAAAATGAAAAATG-AAAAA
40651598 TGAAAAA-GTAAAAAT
1 TGAAAAATG-AAAAAT
40651613 AGAGAGGCTA
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.21
21 1 0.03
22 26 0.76
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.15
Consensus pattern (21 bp):
TGAAAAATGAAAAATGAAAAA
Found at i:40651604 original size:15 final size:15
Alignment explanation
Indices: 40651554--40651604 Score: 79
Period size: 15 Copynumber: 3.5 Consensus size: 15
40651544 ACAAAAAATG
40651554 TGAAAAATGAAAAAAA
1 TGAAAAATG-AAAAAA
40651570 TG-AAAATG-AAAAA
1 TGAAAAATGAAAAAA
40651583 TGAAAAATGAAAAAA
1 TGAAAAATGAAAAAA
40651598 TGAAAAA
1 TGAAAAA
40651605 GTAAAAATAG
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
13 7 0.21
14 6 0.18
15 18 0.55
16 2 0.06
ACGTcount: A:0.73, C:0.00, G:0.14, T:0.14
Consensus pattern (15 bp):
TGAAAAATGAAAAAA
Found at i:40651610 original size:15 final size:14
Alignment explanation
Indices: 40651554--40651611 Score: 64
Period size: 15 Copynumber: 3.9 Consensus size: 14
40651544 ACAAAAAATG
40651554 TGAAAAATGAAAAAAA
1 TGAAAAAT--AAAAAA
*
40651570 TG-AAAATGAAAAA
1 TGAAAAATAAAAAA
40651583 TGAAAAATGAAAAAA
1 TGAAAAAT-AAAAAA
40651598 TGAAAAAGTAAAAA
1 TGAAAAA-TAAAAA
40651612 TAGAGAGGCT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
13 7 0.19
14 5 0.14
15 22 0.59
16 3 0.08
ACGTcount: A:0.72, C:0.00, G:0.14, T:0.14
Consensus pattern (14 bp):
TGAAAAATAAAAAA
Found at i:40653140 original size:128 final size:128
Alignment explanation
Indices: 40652809--40653632 Score: 1132
Period size: 128 Copynumber: 6.4 Consensus size: 128
40652799 AACAGATCAG
* * * * * *
40652809 GGAACTTATAGATCTTGTATCCCTAAGCAATAGCGGAGCAGATCGAAGACGGTGAATCTTATCTG
1 GGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTT
* * * * * *
40652874 CAAGTGTAAGGAAGCAAATTTAAGCCAAAAGTCCTATCTCCCTGGCCAGTAGTGGAATAAGTT
66 CAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
* **
40652937 GGGAAATTACAGATCTTGTCTCCCTAAGCACTAGCGGAGCAGATTAAAGACGGCGAATCTTATCT
1 -GGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCT
* * *
40653002 TCAAGTGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTAGTCAGTAGTGGAATAGGTT
65 TCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
* ** * * *
40653066 GGAAATTGCAGAAATTGTCTCCCTAAGCAGTAGCGGAGCAGATTGAAGACGACAAATCTTATCTT
1 GGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTT
* * * *
40653131 CAAGAGTAAGAAAACA-ATTTAAGCCACAAGACCTATATCCCTGGTCAGCAGTGGAATAGGTT
66 CAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
* *
40653193 GGGAAATTACAGATCTTATCTCCAC-AAGCAGTAGCGGAGCAGATCGAAGACGGCAAATCTTATC
1 -GGAAATTACAGATCTTGTCTCC-CTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATC
* * *
40653257 TTCAAGAGTAAGGAAGCAAATTTAAGCCACAAGTCCTATATTCCTGGTCAGCAGTGGAATAGGTT
64 TTCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
* * * *
40653322 GAGAAATTACAGATCTTGTCTCCATAAGCAGTAGTGGAGCAGATCGAAGACGGTGAATCATATCT
1 G-GAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCT
* **
40653387 TCAAGAGTAAGGAAGTAGATTTAAGCCACAAGTCCTATCTCATTGGTCAGCAGTGGAATAGGTT
65 TCAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
*
40653451 GAAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTT
1 GGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTT
*
40653516 CAAGAGTAAGGAAGCAGATTTAACCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
66 CAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
** * * * * * *
40653579 GGAAA-TATCAGATCTCATCTCCTTACGCAATAGTGGAGCAGATCAAAGATGGCG
1 GGAAATTA-CAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCG
40653633 GATTTTACCT
Statistics
Matches: 622, Mismatches: 67, Indels: 13
0.89 0.10 0.02
Matches are distributed among these distances:
127 44 0.07
128 303 0.49
129 275 0.44
ACGTcount: A:0.33, C:0.19, G:0.23, T:0.24
Consensus pattern (128 bp):
GGAAATTACAGATCTTGTCTCCCTAAGCAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTT
CAAGAGTAAGGAAGCAGATTTAAGCCACAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTT
Found at i:40653593 original size:385 final size:385
Alignment explanation
Indices: 40652833--40653627 Score: 1171
Period size: 385 Copynumber: 2.1 Consensus size: 385
40652823 TTGTATCCCT
** *
40652833 AAGCAATAGCGGAGCAGATCGAAGACGGTGAATCTTATCTGCAAGTGTAAGGAAGCAAATTTAAG
1 AAGCAATAGCGGAGCAGATCGAAGACGGCAAATCTTATCTGCAAGAGTAAGGAAGCAAATTTAAG
* * * *
40652898 CCAAAAGTCCTATCTCCCTGGCCAGTAGTGGAATAAGTTGGGAAATTACAGATCTTGTCTCCCTA
66 CCAAAAGTCCTATATCCCTGGCCAGCAGTGGAATAAGTTGAGAAATTACAGATCTTGTCTCCATA
* * *
40652963 AGCACTAGCGGAGCAGATTAAAGACGGCGAATCTTATCTTCAAGTGTAAGGAAGCAGATTTAAGC
131 AGCACTAGCGGAGCAGATCAAAGACGGCGAATCATATCTTCAAGAGTAAGGAAGCAGATTTAAGC
* * * *
40653028 CACAAGTCCTATCTCCCTAGTCAGTAGTGGAATAGGTTGGAAATTGCAGAAATTGTCTCCCTAAG
196 CACAAGTCCTATCTCACTAGTCAGCAGTGGAATAGGTTGAAAATTACAGAAATTGTCTCCCTAAG
* *
40653093 CAGTAGCGGAGCAGATTGAAGACGACAAATCTTATCTTCAAGAGTAAGAAAACAATTTAAGCCAC
261 CAGTAGCGGAGCAGATCGAAGACGACAAATCTTATCTTCAAGAGTAAGAAAACAATTTAACCCAC
*
40653158 AAGACCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTACAGATCTTATCTCCAC
326 AAGACCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTACAGATCTCATCTCCAC
* *
40653218 AAGCAGTAGCGGAGCAGATCGAAGACGGCAAATCTTATCTTCAAGAGTAAGGAAGCAAATTTAAG
1 AAGCAATAGCGGAGCAGATCGAAGACGGCAAATCTTATCTGCAAGAGTAAGGAAGCAAATTTAAG
* * * *
40653283 CCACAAGTCCTATATTCCTGGTCAGCAGTGGAATAGGTTGAGAAATTACAGATCTTGTCTCCATA
66 CCAAAAGTCCTATATCCCTGGCCAGCAGTGGAATAAGTTGAGAAATTACAGATCTTGTCTCCATA
* * * * *
40653348 AGCAGTAGTGGAGCAGATCGAAGACGGTGAATCATATCTTCAAGAGTAAGGAAGTAGATTTAAGC
131 AGCACTAGCGGAGCAGATCAAAGACGGCGAATCATATCTTCAAGAGTAAGGAAGCAGATTTAAGC
* * **
40653413 CACAAGTCCTATCTCATTGGTCAGCAGTGGAATAGGTTGAAAATTACAGATCTTGTCTCCCTAAG
196 CACAAGTCCTATCTCACTAGTCAGCAGTGGAATAGGTTGAAAATTACAGAAATTGTCTCCCTAAG
* * * *
40653478 CAGTAGCGGAGCAGATCGAAGACGGCGAATCTTATCTTCAAGAGTAAGGAAGCAGATTTAACCCA
261 CAGTAGCGGAGCAGATCGAAGACGACAAATCTTATCTTCAAGAGTAAGAAAACA-ATTTAACCCA
* * **
40653543 CAAGTCCTATCTCCCTGGTCAGCAGTGGAATAGGTT-GGAAA-TATCAGATCTCATCTCCTT
325 CAAGACCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTA-CAGATCTCATCTCCAC
* * *
40653603 ACGCAATAGTGGAGCAGATCAAAGA
1 AAGCAATAGCGGAGCAGATCGAAGA
40653628 TGGCGGATTT
Statistics
Matches: 364, Mismatches: 44, Indels: 4
0.88 0.11 0.01
Matches are distributed among these distances:
384 2 0.01
385 319 0.88
386 43 0.12
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (385 bp):
AAGCAATAGCGGAGCAGATCGAAGACGGCAAATCTTATCTGCAAGAGTAAGGAAGCAAATTTAAG
CCAAAAGTCCTATATCCCTGGCCAGCAGTGGAATAAGTTGAGAAATTACAGATCTTGTCTCCATA
AGCACTAGCGGAGCAGATCAAAGACGGCGAATCATATCTTCAAGAGTAAGGAAGCAGATTTAAGC
CACAAGTCCTATCTCACTAGTCAGCAGTGGAATAGGTTGAAAATTACAGAAATTGTCTCCCTAAG
CAGTAGCGGAGCAGATCGAAGACGACAAATCTTATCTTCAAGAGTAAGAAAACAATTTAACCCAC
AAGACCTATATCCCTGGTCAGCAGTGGAATAGGTTGGGAAATTACAGATCTCATCTCCAC
Found at i:40653727 original size:132 final size:132
Alignment explanation
Indices: 40653549--40653818 Score: 371
Period size: 132 Copynumber: 2.0 Consensus size: 132
40653539 CCCACAAGTC
* * * * * *
40653549 CTATCTCCCTGGTCAGCAGTGGAATAGGTTGGAAATATCAGATCTCATCTCCTTACGCAATAGTG
1 CTATCTCCCTGGGCAGCAGCGGAATAGATTGGAAATATCAGATCTCATCTCCCTAAGCAATAGTC
* * * *
40653614 GAGCAGATCAAAGATGGCGGATTTTACCTCCTTGTGATTACAGTGGAATACATTGAAACCAGTAA
66 GAACAAATCAAAGATGGCGAATTTTACCTCCCTGTGATTACAGTGGAATACATTGAAACCAGTAA
40653679 TT
131 TT
* *
40653681 CTATCTCCCTGGGCAGCAGCGGAATAGATT-GAAGATTTCAGATCTCATCTCCCTAAGTAATAGT
1 CTATCTCCCTGGGCAGCAGCGGAATAGATTGGAA-ATATCAGATCTCATCTCCCTAAGCAATAGT
* * * *
40653745 CGAACAAATCAAAGATGGTGAATTTTACCTCCCTGTGATTACAGTGGAGTACATTGAAGCCTGTA
65 CGAACAAATCAAAGATGGCGAATTTTACCTCCCTGTGATTACAGTGGAATACATTGAAACCAGTA
40653810 ATT
130 ATT
*
40653813 TTATCT
1 CTATCT
40653819 GCTCGAGGTT
Statistics
Matches: 120, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
131 3 0.03
132 117 0.98
ACGTcount: A:0.30, C:0.20, G:0.21, T:0.30
Consensus pattern (132 bp):
CTATCTCCCTGGGCAGCAGCGGAATAGATTGGAAATATCAGATCTCATCTCCCTAAGCAATAGTC
GAACAAATCAAAGATGGCGAATTTTACCTCCCTGTGATTACAGTGGAATACATTGAAACCAGTAA
TT
Found at i:40653855 original size:132 final size:132
Alignment explanation
Indices: 40653549--40653876 Score: 338
Period size: 132 Copynumber: 2.5 Consensus size: 132
40653539 CCCACAAGTC
* * * ** * * *
40653549 CTATCTCCCTGGTCAGCAGTGGAATAGGTTGGAA-ATATCAGATCTCATCTCCTTACGCAATAGT
1 CTATCTCCCTGGGCAGCAGCGGAACAGACT-GAAGATAACAGATCTCATCTCCCTAAGCAATAGT
* * * * *
40653613 GGAGCAGATCAAAGATGGCGGATTTTACCTCCTTGTGATTACAGTGGAATACATTGAAACCAGTA
65 CGAACAAATCAAAGATGGCGAATTTTACCTCCCTGTGATTACAGTGGAATACATTGAAACCAGTA
40653678 ATT
130 ATT
* * ** *
40653681 CTATCTCCCTGGGCAGCAGCGGAATAGATTGAAGATTTCAGATCTCATCTCCCTAAGTAATAGTC
1 CTATCTCCCTGGGCAGCAGCGGAACAGACTGAAGATAACAGATCTCATCTCCCTAAGCAATAGTC
* * * *
40653746 GAACAAATCAAAGATGGTGAATTTTACCTCCCTGTGATTACAGTGGAGTACATTGAAGCCTGTAA
66 GAACAAATCAAAGATGGCGAATTTTACCTCCCTGTGATTACAGTGGAATACATTGAAACCAGTAA
40653811 TT
131 TT
* * ** * * * *
40653813 TTATCT-GCTCGAGGTTGCAGCGGAGCAGACTGAAGA-AACAGATCTTATCTCCCAAAGCAGTAG
1 CTATCTCCCT-G-GGCAGCAGCGGAACAGACTGAAGATAACAGATCTCATCTCCCTAAGCAATAG
40653876 T
64 T
40653877 GGGGCAGATC
Statistics
Matches: 164, Mismatches: 29, Indels: 6
0.82 0.15 0.03
Matches are distributed among these distances:
131 5 0.03
132 140 0.85
133 19 0.12
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (132 bp):
CTATCTCCCTGGGCAGCAGCGGAACAGACTGAAGATAACAGATCTCATCTCCCTAAGCAATAGTC
GAACAAATCAAAGATGGCGAATTTTACCTCCCTGTGATTACAGTGGAATACATTGAAACCAGTAA
TT
Found at i:40655841 original size:26 final size:26
Alignment explanation
Indices: 40655812--40655872 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
40655802 ATAAGGCTAA
* *
40655812 TTATTTTAAGTT-CTTTATATATTATT
1 TTATTTTAAGTTACTTTACATATTA-C
* *
40655838 TTATTTAAAGTTATTTTACATATTAC
1 TTATTTTAAGTTACTTTACATATTAC
40655864 TTATTTTAA
1 TTATTTTAA
40655873 AATTAACCTA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
26 19 0.66
27 10 0.34
ACGTcount: A:0.31, C:0.05, G:0.03, T:0.61
Consensus pattern (26 bp):
TTATTTTAAGTTACTTTACATATTAC
Found at i:40655871 original size:27 final size:25
Alignment explanation
Indices: 40655811--40655873 Score: 65
Period size: 27 Copynumber: 2.4 Consensus size: 25
40655801 TATAAGGCTA
*
40655811 ATTATTTT-AAGTTCTTTATATATT
1 ATTATTTTAAAGTTCTTTACATATT
* *
40655835 ATTTTATTTAAAGTTATTTTACATATT
1 ATTAT-TTTAAAGTT-CTTTACATATT
40655862 ACTTATTTTAAA
1 A-TTATTTTAAA
40655874 ATTAACCTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 5
0.77 0.10 0.12
Matches are distributed among these distances:
24 4 0.13
25 3 0.10
26 5 0.16
27 16 0.52
28 3 0.10
ACGTcount: A:0.33, C:0.05, G:0.03, T:0.59
Consensus pattern (25 bp):
ATTATTTTAAAGTTCTTTACATATT
Found at i:40668860 original size:115 final size:112
Alignment explanation
Indices: 40668499--40669052 Score: 468
Period size: 114 Copynumber: 4.9 Consensus size: 112
40668489 TAATCATTCC
* * * * *
40668499 CGGCGTTTTTGAGAAAGCGCCGC-AAAAAACCTAGCGCAACGACGCCGTTTCCCCAGCATTC-GG
1 CGGCGTTTTTGTGAAAGCGCCGCTAAAAAA-CTAGCGCAACGATGTCGTTTCCCGAGCTTTCAGG
* * * *
40668562 TGATTTAGCGGCGTTTTTCAGTAAGCGCCGCTAATTCTCAAGGCTTTAG
65 -GATTTAGCGGCGCTTTTCAGAAAGCGCCGCTAATGCTCAAGTCTTTAG
* * * *
40668611 CGACGTTTATATGAAAGCGCCG-TAAAAATAACTAAGCCCAACGATGTCGTTTCCCGAGCTTTCA
1 CGGCGTTTTTGTGAAAGCGCCGCT-AAAA-AACT-AGCGCAACGATGTCGTTTCCCGAGCTTTCA
* * * * *
40668675 TGGATTTAGCGGCGC-TTTCTATAAAGCGCCGCTAATGGTTAGGTCTTTAG
63 GGGATTTAGCGGCGCTTTTC-AGAAAGCGCCGCTAATGCTCAAGTCTTTAG
* * * *
40668725 CAGCGTTTCTG-GAAAAGCGCCGCTACTTAAAACTAGCGCAACGATGTCGTCTCCCGAGCTTTCA
1 CGGCGTTTTTGTG-AAAGCGCCGCTA--AAAAACTAGCGCAACGATGTCGTTTCCCGAGCTTTCA
* *
40668789 GGGATTTAGCGGCGCTTTTACAGAAAGCGCCACTAATGCTGAAGTCTTTAG
63 GGGATTTAGCGGCGCTTTT-CAGAAAGCGCCGCTAATGCTCAAGTCTTTAG
* * * * * * *
40668840 CGGCGTTTTTGTTAAAGCGCCGC-AAAAAACCTAAGCCCAACGACGCCGTTTTCTG-GCTTTCGG
1 CGGCGTTTTTGTGAAAGCGCCGCTAAAAAA-CT-AGCGCAACGATGTCGTTTCCCGAGCTTTCAG
* * *
40668903 GGATTTTAGCGGCG-TTTT-TGTAAAGCGCCGTTAATGTTC-AGTCTTTAG
64 GGA-TTTAGCGGCGCTTTTCAG-AAAGCGCCGCTAATGCTCAAGTCTTTAG
* * * * *
40668951 TGGCGTTTTT-TAGAAAGCGCCGCAAAAAAAACTAAGCGCAACG-TCGTCGTTTTCTGTGCTTTT
1 CGGCGTTTTTGT-GAAAGCGCCGC-TAAAAAACT-AGCGCAACGAT-GTCGTTTCCCGAGC-TTT
* *
40669014 GAGGGATTTAGCGGCG-TTTTTAGAAAAGCGCCGCTAATG
61 CAGGGATTTAGCGGCGCTTTTCAG-AAAGCGCCGCTAATG
40669053 ATCAGAGATT
Statistics
Matches: 361, Mismatches: 57, Indels: 46
0.78 0.12 0.10
Matches are distributed among these distances:
110 1 0.00
111 29 0.08
112 57 0.16
113 49 0.14
114 169 0.47
115 53 0.15
116 3 0.01
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.28
Consensus pattern (112 bp):
CGGCGTTTTTGTGAAAGCGCCGCTAAAAAACTAGCGCAACGATGTCGTTTCCCGAGCTTTCAGGG
ATTTAGCGGCGCTTTTCAGAAAGCGCCGCTAATGCTCAAGTCTTTAG
Found at i:40668876 original size:228 final size:225
Alignment explanation
Indices: 40668501--40669052 Score: 580
Period size: 226 Copynumber: 2.4 Consensus size: 225
40668491 ATCATTCCCG
* * * * * *
40668501 GCGTTTTTGAGAAAGCGCCGC-AAAAAACCTAGCGCAACGACGCCGTTTCCCCAGCATTC-GGTG
1 GCGTTTTGGAGAAAGCGCCGCAAAAAAAACTAGCGCAACGATGTCGTTTCCCGAGCTTTCAGG-G
* * *
40668564 ATTTAGCGGCGTTTTTCAGTAAGCGCCGCTAATTCTCAAGGCTTTAGCGACGTTTATATGAAAGC
65 ATTTAGCGGCGTTTTACAGAAAGCGCCGCTAATGCTCAAGGCTTTAGCGACGTTTATATGAAAGC
* * * *
40668629 GCCGTAAAAATAACTAAGCCCAACGATGTCGTTTCCCGAGCTTTCATGGA-TTTAGCGGCGCTTT
130 GCCGCAAAAATAACTAAGCCCAACGACGCCGTTTCCCG-GCTTTCAGGGATTTTAGCGGCG-TTT
40668693 CTATAAAGCGCCGCTAATGGTT-AGGTCTTTAGCA
193 CTATAAAGCGCCGCTAAT-GTTCA-GTCTTTAGCA
*** *
40668727 GCGTTTCTGGA-AAAGCGCCGCTACTTAAAACTAGCGCAACGATGTCGTCTCCCGAGCTTTCAGG
1 GCGTTT-TGGAGAAAGCGCCGC-AAAAAAAACTAGCGCAACGATGTCGTTTCCCGAGCTTTCAGG
* * * * * * *
40668791 GATTTAGCGGCGCTTTTACAGAAAGCGCCACTAATGCTGAAGTCTTTAGCGGCGTTTTTGTTAAA
64 GATTTAGCGGCG-TTTTACAGAAAGCGCCGCTAATGCTCAAGGCTTTAGCGACGTTTATATGAAA
* * * *
40668856 GCGCCGCAAAAA-ACCTAAGCCCAACGACGCCGTTTTCTGGCTTTCGGGGATTTTAGCGGCGTTT
128 GCGCCGCAAAAATAACTAAGCCCAACGACGCCGTTTCCCGGCTTTCAGGGATTTTAGCGGCGTTT
* * * **
40668920 TTGTAAAGCGCCGTTAATGTTCAGTCTTTAGTG
193 CTATAAAGCGCCGCTAATGTTCAGTCTTTAGCA
** * * * *
40668953 GCGTTTTTTAGAAAGCGCCGCAAAAAAAACTAAGCGCAACG-TCGTCGTTTTCTGTGCTTTTGAG
1 GCGTTTTGGAGAAAGCGCCGCAAAAAAAACT-AGCGCAACGAT-GTCGTTTCCCGAGC-TTTCAG
*
40669017 GGATTTAGCGGCGTTTT-TAGAAAAGCGCCGCTAATG
63 GGATTTAGCGGCGTTTTACAG-AAAGCGCCGCTAATG
40669053 ATCAGAGATT
Statistics
Matches: 269, Mismatches: 45, Indels: 24
0.80 0.13 0.07
Matches are distributed among these distances:
225 12 0.04
226 80 0.30
227 49 0.18
228 73 0.27
229 55 0.20
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.28
Consensus pattern (225 bp):
GCGTTTTGGAGAAAGCGCCGCAAAAAAAACTAGCGCAACGATGTCGTTTCCCGAGCTTTCAGGGA
TTTAGCGGCGTTTTACAGAAAGCGCCGCTAATGCTCAAGGCTTTAGCGACGTTTATATGAAAGCG
CCGCAAAAATAACTAAGCCCAACGACGCCGTTTCCCGGCTTTCAGGGATTTTAGCGGCGTTTCTA
TAAAGCGCCGCTAATGTTCAGTCTTTAGCA
Found at i:40669044 original size:226 final size:227
Alignment explanation
Indices: 40668499--40669052 Score: 579
Period size: 228 Copynumber: 2.4 Consensus size: 227
40668489 TAATCATTCC
* * * * * *
40668499 CGGCGTTTTTGAGAAAGCGCCGC-AAAAAACCTAGCGCAACGACGCCGTTTCCCCAGCATTCG-G
1 CGGCGTTTTTTAGAAAGCGCCGCAAAAAAAACTAGCGCAACGTCGTCGTTTCCCGAGC-TTTGAG
* * *
40668562 TGATTTAGCGGCGTTTTTCAG-TAAGCGCCGCTAATTCTCAAGGCTTTAGCGACGTTTATATGAA
65 GGATTTAGCGGCGTTTTT-AGAAAAGCGCCGCTAATGCTCAAGGCTTTAGCGACGTTTATATGAA
* * * *
40668626 AGCGCCGTAAAAATAACTAAGCCCAACGATGTCGTTTCCCGAGCTTTCATGGATTTAGCGGCGCT
129 AGCGCCGCAAAAATAACTAAGCCCAACGACGCCGTTTCCCGAGCTTTCAGGGATTTAGCGGCGCT
40668691 TTCTATAAAGCGCCGCTAATGGTTAGGTCTTTAG
194 TTCTATAAAGCGCCGCTAATGGTTAGGTCTTTAG
* * * *** * *
40668725 CAGCG-TTTCTGGAAAAGCGCCGCTACTTAAAACTAGCGCAACGAT-GTCGTCTCCCGAGCTTTC
1 CGGCGTTTTTTAG-AAAGCGCCGC-AAAAAAAACTAGCGCAACG-TCGTCGTTTCCCGAGCTTTG
* * * * * * * * *
40668788 AGGGATTTAGCGGCGCTTTTACAGAAAGCGCCACTAATGCTGAAGTCTTTAGCGGCGTTTTTGTT
63 AGGGATTTAGCGGCGTTTTTAGA-AAAGCGCCGCTAATGCTCAAGGCTTTAGCGACGTTTATATG
* * * *
40668853 AAAGCGCCGCAAAAA-ACCTAAGCCCAACGACGCCGTTTTCTG-GCTTTCGGGGATTTTAGCGGC
127 AAAGCGCCGCAAAAATAACTAAGCCCAACGACGCCGTTTCCCGAGCTTTCAGGGA-TTTAGCGGC
* * *
40668916 G-TTTTTGTAAAGCGCCGTTAAT-GTTCA-GTCTTTAG
191 GCTTTCTATAAAGCGCCGCTAATGGTT-AGGTCTTTAG
* * * *
40668951 TGGCGTTTTTTAGAAAGCGCCGCAAAAAAAACTAAGCGCAACGTCGTCGTTTTCTGTGCTTTTGA
1 CGGCGTTTTTTAGAAAGCGCCGCAAAAAAAACT-AGCGCAACGTCGTCGTTTCCCGAGC-TTTGA
40669016 GGGATTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATG
64 GGGATTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATG
40669053 ATCAGAGATT
Statistics
Matches: 263, Mismatches: 52, Indels: 26
0.77 0.15 0.08
Matches are distributed among these distances:
225 12 0.05
226 71 0.27
227 60 0.23
228 74 0.28
229 46 0.17
ACGTcount: A:0.24, C:0.23, G:0.25, T:0.28
Consensus pattern (227 bp):
CGGCGTTTTTTAGAAAGCGCCGCAAAAAAAACTAGCGCAACGTCGTCGTTTCCCGAGCTTTGAGG
GATTTAGCGGCGTTTTTAGAAAAGCGCCGCTAATGCTCAAGGCTTTAGCGACGTTTATATGAAAG
CGCCGCAAAAATAACTAAGCCCAACGACGCCGTTTCCCGAGCTTTCAGGGATTTAGCGGCGCTTT
CTATAAAGCGCCGCTAATGGTTAGGTCTTTAG
Found at i:40669348 original size:7 final size:7
Alignment explanation
Indices: 40669338--40669391 Score: 72
Period size: 7 Copynumber: 7.4 Consensus size: 7
40669328 AGAGTTAAGA
40669338 TTTAGGG
1 TTTAGGG
40669345 TTTAGGGG
1 TTTA-GGG
40669353 TTTAGGG
1 TTTAGGG
40669360 TTTAGGG
1 TTTAGGG
40669367 TTTAGGG
1 TTTAGGG
**
40669374 ATTTCTGG
1 -TTTAGGG
40669382 TTTAGGG
1 TTTAGGG
40669389 TTT
1 TTT
40669392 GAACGGTAAG
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
7 29 0.71
8 12 0.29
ACGTcount: A:0.13, C:0.02, G:0.39, T:0.46
Consensus pattern (7 bp):
TTTAGGG
Found at i:40669351 original size:31 final size:30
Alignment explanation
Indices: 40669277--40669352 Score: 75
Period size: 31 Copynumber: 2.6 Consensus size: 30
40669267 TCAGGGTATG
* * *
40669277 GATTTAGGGTTTA--GGGATTAGGTGTTAT
1 GATTTAGGGTTTAGGGGGATTAAGAGTTAA
* * *
40669305 GCTTTTGGGGTTAGGGGGAGTTAAGAGTTAA
1 GATTTAGGGTTTAGGGGGA-TTAAGAGTTAA
40669336 GATTTAGGGTTTAGGGG
1 GATTTAGGGTTTAGGGG
40669353 TTTAGGGTTT
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
28 10 0.28
30 4 0.11
31 22 0.61
ACGTcount: A:0.21, C:0.01, G:0.41, T:0.37
Consensus pattern (30 bp):
GATTTAGGGTTTAGGGGGATTAAGAGTTAA
Found at i:40669358 original size:15 final size:14
Alignment explanation
Indices: 40669338--40669391 Score: 72
Period size: 15 Copynumber: 3.7 Consensus size: 14
40669328 AGAGTTAAGA
40669338 TTTAGGGTTTAGGGG
1 TTTAGGGTTTA-GGG
40669353 TTTAGGGTTTAGGG
1 TTTAGGGTTTAGGG
**
40669367 TTTAGGGATTTCTGG
1 TTTAGGG-TTTAGGG
40669382 TTTAGGGTTT
1 TTTAGGGTTT
40669392 GAACGGTAAG
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
14 13 0.36
15 23 0.64
ACGTcount: A:0.13, C:0.02, G:0.39, T:0.46
Consensus pattern (14 bp):
TTTAGGGTTTAGGG
Found at i:40669365 original size:22 final size:22
Alignment explanation
Indices: 40669338--40669391 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
40669328 AGAGTTAAGA
*
40669338 TTTAGGGTTTAGGGGTTTAGGG
1 TTTAGGGTTTAGGGATTTAGGG
**
40669360 TTTAGGGTTTAGGGATTTCTGG
1 TTTAGGGTTTAGGGATTTAGGG
40669382 TTTAGGGTTT
1 TTTAGGGTTT
40669392 GAACGGTAAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.13, C:0.02, G:0.39, T:0.46
Consensus pattern (22 bp):
TTTAGGGTTTAGGGATTTAGGG
Found at i:40669706 original size:31 final size:30
Alignment explanation
Indices: 40669663--40669744 Score: 94
Period size: 31 Copynumber: 2.7 Consensus size: 30
40669653 AATAAAATTT
40669663 TTTAGGGGTTATGGTTTAGGGGTT-AGAGGA
1 TTTAGGGGTTATGGTTTAGGGGTTAAG-GGA
* * *
40669693 GTTTAGGGTTTATGCTTTAAGGGTTTAAGGGA
1 -TTTAGGGGTTATGGTTT-AGGGGTTAAGGGA
*
40669725 TTTAGGGGTTATGGGTTAGG
1 TTTAGGGGTTATGGTTTAGG
40669745 AATTTGGGAA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
30 3 0.07
31 29 0.67
32 9 0.21
33 2 0.05
ACGTcount: A:0.20, C:0.01, G:0.40, T:0.39
Consensus pattern (30 bp):
TTTAGGGGTTATGGTTTAGGGGTTAAGGGA
Found at i:40673005 original size:9 final size:9
Alignment explanation
Indices: 40672971--40673518 Score: 189
Period size: 9 Copynumber: 63.8 Consensus size: 9
40672961 AACAACTCAA
40672971 AACTTACAT
1 AACTTACAT
* *
40672980 AACCTAAAT
1 AACTTACAT
*
40672989 AACCTACAT
1 AACTTACAT
40672998 AACTTACAT
1 AACTTACAT
*
40673007 AA--TACAA
1 AACTTACAT
*
40673014 AACTCACAT
1 AACTTACAT
*
40673023 AACTTAAAT
1 AACTTACAT
** *
40673032 CTCTTACAC
1 AACTTACAT
40673041 AACTTACAT
1 AACTTACAT
40673050 AACCTT-CAT
1 AA-CTTACAT
40673059 AA--TACATTT
1 AACTTACA--T
40673068 AACTTACAT
1 AACTTACAT
40673077 AACTTACAT
1 AACTTACAT
*
40673086 AATACATA-AT
1 -A-ACTTACAT
40673096 AACTTAC--
1 AACTTACAT
40673103 AACTTACAT
1 AACTTACAT
*
40673112 AACATACAT
1 AACTTACAT
* **
40673121 TACTTTGAT
1 AACTTACAT
40673130 AACTTACAT
1 AACTTACAT
40673139 AAC-T---T
1 AACTTACAT
40673144 -ACTTACAT
1 AACTTACAT
40673152 AACTTACAT
1 AACTTACAT
40673161 AACTTACAT
1 AACTTACAT
*
40673170 AACTAACAT
1 AACTTACAT
* *
40673179 TA--TACAC
1 AACTTACAT
40673186 AACTTACAT
1 AACTTACAT
40673195 AA--TACAT
1 AACTTACAT
*
40673202 TACTTACAT
1 AACTTACAT
40673211 AACTTAAAGCAT
1 AACTT--A-CAT
40673223 AA--TA-AT
1 AACTTACAT
*
40673229 AATTTACAT
1 AACTTACAT
*
40673238 AA--TACAC
1 AACTTACAT
40673245 AACTTACAT
1 AACTTACAT
* *
40673254 AGCTTACAC
1 AACTTACAT
40673263 AA--TACAT
1 AACTTACAT
*
40673270 AACTTACCCGT
1 AACTTA--CAT
* *
40673281 GCAATTTA-TT
1 --AACTTACAT
** * *
40673291 GTC-AAGATT
1 AACTTACA-T
*
40673300 AACTTACGT
1 AACTTACAT
* *
40673309 AA-TCCATCTT
1 AACT-TA-CAT
40673319 AACTTACAT
1 AACTTACAT
*
40673328 AATACATA-AT
1 -A-ACTTACAT
40673338 AACTTAC--
1 AACTTACAT
40673345 AACTTACAT
1 AACTTACAT
*
40673354 AACATACAT
1 AACTTACAT
* **
40673363 TACTTTGAT
1 AACTTACAT
40673372 AACTTACAT
1 AACTTACAT
40673381 AAC-T---T
1 AACTTACAT
40673386 -ACTTACAT
1 AACTTACAT
40673394 AACTTACAT
1 AACTTACAT
40673403 AACTTACAT
1 AACTTACAT
*
40673412 AACTAACAT
1 AACTTACAT
* *
40673421 TA--TACAC
1 AACTTACAT
40673428 AACTTACAT
1 AACTTACAT
40673437 AA--TACAT
1 AACTTACAT
*
40673444 TACTTACAT
1 AACTTACAT
40673453 AACTTAAAGCAT
1 AACTT--A-CAT
40673465 AA--TA-AT
1 AACTTACAT
*
40673471 AATTTACAT
1 AACTTACAT
*
40673480 AA--TACAC
1 AACTTACAT
40673487 AACTTACAT
1 AACTTACAT
* *
40673496 AGCTTACAC
1 AACTTACAT
40673505 AA--TACAT
1 AACTTACAT
40673512 AACTTAC
1 AACTTAC
40673519 CCGTGCAATT
Statistics
Matches: 392, Mismatches: 81, Indels: 132
0.65 0.13 0.22
Matches are distributed among these distances:
4 4 0.01
5 4 0.01
6 9 0.02
7 67 0.17
8 19 0.05
9 239 0.61
10 18 0.05
11 17 0.04
12 10 0.03
13 5 0.01
ACGTcount: A:0.45, C:0.21, G:0.02, T:0.32
Consensus pattern (9 bp):
AACTTACAT
Found at i:40673023 original size:43 final size:43
Alignment explanation
Indices: 40672968--40673051 Score: 114
Period size: 43 Copynumber: 2.0 Consensus size: 43
40672958 CTGAACAACT
* *
40672968 CAAAACTTACATAACCTAAATAACCTACATAACTTACATAATA
1 CAAAACTCACATAACCTAAATAACCTACACAACTTACATAATA
* ** *
40673011 CAAAACTCACATAACTTAAATCTCTTACACAACTTACATAA
1 CAAAACTCACATAACCTAAATAACCTACACAACTTACATAA
40673052 CCTTCATAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 35 1.00
ACGTcount: A:0.49, C:0.25, G:0.00, T:0.26
Consensus pattern (43 bp):
CAAAACTCACATAACCTAAATAACCTACACAACTTACATAATA
Found at i:40673112 original size:62 final size:64
Alignment explanation
Indices: 40673039--40673168 Score: 160
Period size: 62 Copynumber: 2.0 Consensus size: 64
40673029 AATCTCTTAC
* *
40673039 ACAACTTACATAACCTTCATAATACATT-TAACTTACATAACTTACATA-AT-ACATA-ATAACT
1 ACAACTTACATAACATACAT--TACATTATAACTTACATAACTTACATACATAACATACATAACT
40673100 T
64 T
* * *
40673101 ACAACTTACATAACATACATTACTTTGATAACTTACATAACTTACTTACATAACTTACATAACTT
1 ACAACTTACATAACATACATTACATT-ATAACTTACATAACTTACATACATAACATACATAACTT
40673166 ACA
1 ACA
40673169 TAACTAACAT
Statistics
Matches: 58, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
60 5 0.09
62 37 0.64
63 2 0.03
64 4 0.07
65 10 0.17
ACGTcount: A:0.44, C:0.22, G:0.01, T:0.34
Consensus pattern (64 bp):
ACAACTTACATAACATACATTACATTATAACTTACATAACTTACATACATAACATACATAACTT
Found at i:40673147 original size:13 final size:13
Alignment explanation
Indices: 40673131--40673158 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
40673121 TACTTTGATA
40673131 ACTTACATAACTT
1 ACTTACATAACTT
40673144 ACTTACATAACTT
1 ACTTACATAACTT
40673157 AC
1 AC
40673159 ATAACTTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.25, G:0.00, T:0.36
Consensus pattern (13 bp):
ACTTACATAACTT
Found at i:40673189 original size:25 final size:23
Alignment explanation
Indices: 40673156--40673203 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 23
40673146 TTACATAACT
*
40673156 TACATAACTTACATAACTAACATTA
1 TACACAACTTACATAA-T-ACATTA
40673181 TACACAACTTACATAATACATTA
1 TACACAACTTACATAATACATTA
40673204 CTTACATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.27
24 1 0.05
25 15 0.68
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (23 bp):
TACACAACTTACATAATACATTA
Found at i:40673243 original size:59 final size:56
Alignment explanation
Indices: 40673130--40673254 Score: 148
Period size: 59 Copynumber: 2.2 Consensus size: 56
40673120 TTACTTTGAT
*
40673130 AACTTACAT-AACTTACTTACATAACTTACATAACTTACATAACTAACATTATACAC
1 AACTTACATAAACTTACTTACATAACTTACATAAC-TACATAACTAACATAATACAC
* *
40673186 AACTTACATAATACATTACTTACATAACTTAAAGCATAA-TA-ATAATTTACATAATACAC
1 AACTTACATAA-AC-TTACTTACATAACTT--A-CATAACTACATAACTAACATAATACAC
40673245 AACTTACATA
1 AACTTACATA
40673255 GCTTACACAA
Statistics
Matches: 60, Mismatches: 3, Indels: 9
0.83 0.04 0.12
Matches are distributed among these distances:
56 9 0.15
57 1 0.02
58 2 0.03
59 40 0.67
60 2 0.03
61 1 0.02
62 5 0.08
ACGTcount: A:0.47, C:0.20, G:0.01, T:0.32
Consensus pattern (56 bp):
AACTTACATAAACTTACTTACATAACTTACATAACTACATAACTAACATAATACAC
Found at i:40673322 original size:19 final size:19
Alignment explanation
Indices: 40673297--40673345 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
40673287 TATTGTCAAG
* *
40673297 ATTAACTTACGTAATCCAT
1 ATTAACTTACATAATACAT
*
40673316 CTTAACTTACATAATACAT
1 ATTAACTTACATAATACAT
*
40673335 AATAACTTACA
1 ATTAACTTACA
40673346 ACTTACATAA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.43, C:0.20, G:0.02, T:0.35
Consensus pattern (19 bp):
ATTAACTTACATAATACAT
Found at i:40673389 original size:13 final size:13
Alignment explanation
Indices: 40673373--40673400 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
40673363 TACTTTGATA
40673373 ACTTACATAACTT
1 ACTTACATAACTT
40673386 ACTTACATAACTT
1 ACTTACATAACTT
40673399 AC
1 AC
40673401 ATAACTTACA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.25, G:0.00, T:0.36
Consensus pattern (13 bp):
ACTTACATAACTT
Found at i:40673431 original size:25 final size:23
Alignment explanation
Indices: 40673398--40673445 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 23
40673388 TTACATAACT
*
40673398 TACATAACTTACATAACTAACATTA
1 TACACAACTTACATAA-T-ACATTA
40673423 TACACAACTTACATAATACATTA
1 TACACAACTTACATAATACATTA
40673446 CTTACATAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 6 0.27
24 1 0.05
25 15 0.68
ACGTcount: A:0.48, C:0.21, G:0.00, T:0.31
Consensus pattern (23 bp):
TACACAACTTACATAATACATTA
Found at i:40673453 original size:59 final size:56
Alignment explanation
Indices: 40673372--40673496 Score: 148
Period size: 59 Copynumber: 2.2 Consensus size: 56
40673362 TTACTTTGAT
*
40673372 AACTTACAT-AACTTACTTACATAACTT-A-CATAACTTACATAACTAACATTATACAC
1 AACTTACATAAACTTACTTACATAACTTAAGCATAA--TA-ATAACTAACATAATACAC
* *
40673428 AACTTACATAATACATTACTTACATAACTTAAAGCATAATAATAATTTACATAATACAC
1 AACTTACATAA-AC-TTACTTACATAACTT-AAGCATAATAATAACTAACATAATACAC
40673487 AACTTACATA
1 AACTTACATA
40673497 GCTTACACAA
Statistics
Matches: 60, Mismatches: 3, Indels: 9
0.83 0.04 0.12
Matches are distributed among these distances:
56 9 0.15
57 1 0.02
58 2 0.03
59 40 0.67
60 2 0.03
61 1 0.02
62 5 0.08
ACGTcount: A:0.47, C:0.20, G:0.01, T:0.32
Consensus pattern (56 bp):
AACTTACATAAACTTACTTACATAACTTAAGCATAATAATAACTAACATAATACAC
Found at i:40673478 original size:43 final size:43
Alignment explanation
Indices: 40673386--40673518 Score: 132
Period size: 43 Copynumber: 3.1 Consensus size: 43
40673376 TACATAACTT
*
40673386 ACTTACATAACTTACATAACTTACATAAC-T-AACATTATACACA
1 ACTTACATAA--TACATAACTTACATAACTTAAACATAATACACA
* *
40673429 ACTTACATAATACATTACTTACATAACTTAAAGCATAATA-ATA
1 ACTTACATAATACATAACTTACATAACTTAAA-CATAATACACA
* * * * *
40673472 ATTTACATAATACACAACTTACATAGCTT--ACACAATACATA
1 ACTTACATAATACATAACTTACATAACTTAAACATAATACACA
40673513 ACTTAC
1 ACTTAC
40673519 CCGTGCAATT
Statistics
Matches: 77, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
40 6 0.08
41 25 0.32
42 1 0.01
43 39 0.51
44 6 0.08
ACGTcount: A:0.47, C:0.21, G:0.02, T:0.31
Consensus pattern (43 bp):
ACTTACATAATACATAACTTACATAACTTAAACATAATACACA
Found at i:40673495 original size:16 final size:16
Alignment explanation
Indices: 40673318--40673496 Score: 91
Period size: 16 Copynumber: 11.7 Consensus size: 16
40673308 TAATCCATCT
40673318 TAACTTACATAATACA
1 TAACTTACATAATACA
*
40673334 TAA-TAAC-T--TAC-
1 TAACTTACATAATACA
40673345 -AACTTACATAACATACA
1 TAACTTACAT-A-ATACA
* **
40673362 TTACTTTGATAACTTACA
1 TAACTTACATAA--TACA
40673380 TAACTTAC-T--TACA
1 TAACTTACATAATACA
40673393 TAACTTACATAACTTACA
1 TAACTTACATAA--TACA
* *
40673411 TAACTAACATTATACA
1 TAACTTACATAATACA
*
40673427 CAACTTACATAATACA
1 TAACTTACATAATACA
* *
40673443 TTACTTACAT-A-ACT
1 TAACTTACATAATACA
40673457 TAA---AGCATAATA-A
1 TAACTTA-CATAATACA
*
40673470 TAATTTACATAATACA
1 TAACTTACATAATACA
*
40673486 CAACTTACATA
1 TAACTTACATA
40673497 GCTTACACAA
Statistics
Matches: 121, Mismatches: 20, Indels: 44
0.65 0.11 0.24
Matches are distributed among these distances:
10 2 0.02
11 4 0.03
12 7 0.06
13 16 0.13
14 7 0.06
15 11 0.09
16 43 0.36
17 2 0.02
18 29 0.24
ACGTcount: A:0.46, C:0.20, G:0.01, T:0.33
Consensus pattern (16 bp):
TAACTTACATAATACA
Found at i:40673500 original size:242 final size:242
Alignment explanation
Indices: 40673076--40673542 Score: 934
Period size: 242 Copynumber: 1.9 Consensus size: 242
40673066 TTAACTTACA
40673076 TAACTTACATAATACATAATAACTTACAACTTACATAACATACATTACTTTGATAACTTACATAA
1 TAACTTACATAATACATAATAACTTACAACTTACATAACATACATTACTTTGATAACTTACATAA
40673141 CTTACTTACATAACTTACATAACTTACATAACTAACATTATACACAACTTACATAATACATTACT
66 CTTACTTACATAACTTACATAACTTACATAACTAACATTATACACAACTTACATAATACATTACT
40673206 TACATAACTTAAAGCATAATAATAATTTACATAATACACAACTTACATAGCTTACACAATACATA
131 TACATAACTTAAAGCATAATAATAATTTACATAATACACAACTTACATAGCTTACACAATACATA
40673271 ACTTACCCGTGCAATTTATTGTCAAGATTAACTTACGTAATCCATCT
196 ACTTACCCGTGCAATTTATTGTCAAGATTAACTTACGTAATCCATCT
40673318 TAACTTACATAATACATAATAACTTACAACTTACATAACATACATTACTTTGATAACTTACATAA
1 TAACTTACATAATACATAATAACTTACAACTTACATAACATACATTACTTTGATAACTTACATAA
40673383 CTTACTTACATAACTTACATAACTTACATAACTAACATTATACACAACTTACATAATACATTACT
66 CTTACTTACATAACTTACATAACTTACATAACTAACATTATACACAACTTACATAATACATTACT
40673448 TACATAACTTAAAGCATAATAATAATTTACATAATACACAACTTACATAGCTTACACAATACATA
131 TACATAACTTAAAGCATAATAATAATTTACATAATACACAACTTACATAGCTTACACAATACATA
40673513 ACTTACCCGTGCAATTTATTGTCAAGATTA
196 ACTTACCCGTGCAATTTATTGTCAAGATTA
40673543 GGCTTCAAGA
Statistics
Matches: 225, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
242 225 1.00
ACGTcount: A:0.43, C:0.20, G:0.03, T:0.33
Consensus pattern (242 bp):
TAACTTACATAATACATAATAACTTACAACTTACATAACATACATTACTTTGATAACTTACATAA
CTTACTTACATAACTTACATAACTTACATAACTAACATTATACACAACTTACATAATACATTACT
TACATAACTTAAAGCATAATAATAATTTACATAATACACAACTTACATAGCTTACACAATACATA
ACTTACCCGTGCAATTTATTGTCAAGATTAACTTACGTAATCCATCT
Found at i:40679019 original size:66 final size:66
Alignment explanation
Indices: 40678913--40679075 Score: 195
Period size: 66 Copynumber: 2.5 Consensus size: 66
40678903 GCAAATTACA
* * * * * *
40678913 CAACTTAAAGCGGAGGCAACATCAAGAGAAGCTGATGTTCAAAG-AAGATATGAAGAACTCCAGC
1 CAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAAAGAAAG-TATGAAGAACTCCAGC
40678977 TA-
65 -AG
* *
40678979 CAACTTAAAGTAGATGCAGCAGCGAGAGAAGCTGAGGTTCAACGAAAGTATGAAGAACTCCAGCA
1 CAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAAAGAAAGTATGAAGAACTCCAGCA
40679044 G
66 G
* * *
40679045 CAGCTTAGAGCAGATGCGGCAGCGAGAGAAG
1 CAACTTAAAGCAGATGCAGCAGCGAGAGAAG
40679076 TACAGGCTGC
Statistics
Matches: 83, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
65 1 0.01
66 79 0.95
67 3 0.04
ACGTcount: A:0.39, C:0.18, G:0.28, T:0.15
Consensus pattern (66 bp):
CAACTTAAAGCAGATGCAGCAGCGAGAGAAGCTGAGGTTCAAAGAAAGTATGAAGAACTCCAGCA
G
Found at i:40679135 original size:21 final size:21
Alignment explanation
Indices: 40679063--40679138 Score: 64
Period size: 21 Copynumber: 3.6 Consensus size: 21
40679053 AGCAGATGCG
* *
40679063 GCAGCGAGAGAAGTACAGGCT
1 GCAGCGAGGGAAGTAGAGGCT
* *
40679084 GCTA-AGAGGGAAGCAGAGGCT
1 GC-AGCGAGGGAAGTAGAGGCT
** * *
40679105 AAAACAAGGGAAGTAGAGGCT
1 GCAGCGAGGGAAGTAGAGGCT
40679126 GCAGCGAGGGAAG
1 GCAGCGAGGGAAG
40679139 CAAAGTAGCG
Statistics
Matches: 40, Mismatches: 13, Indels: 4
0.70 0.23 0.07
Matches are distributed among these distances:
20 1 0.03
21 38 0.95
22 1 0.03
ACGTcount: A:0.37, C:0.14, G:0.41, T:0.08
Consensus pattern (21 bp):
GCAGCGAGGGAAGTAGAGGCT
Found at i:40683010 original size:34 final size:35
Alignment explanation
Indices: 40682965--40683032 Score: 104
Period size: 34 Copynumber: 2.0 Consensus size: 35
40682955 CCAATAAAAT
40682965 ATTTTCCGTAAAATGATTT-C-GAGAAAATATTTTA
1 ATTTTCCGTAAAATGATTTACTG-GAAAATATTTTA
*
40682999 ATTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 ATTTTCCGTAAAATGATTTACTGGAAAATATTTT
40683033 TTGGTGTTTG
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
34 18 0.58
35 12 0.39
36 1 0.03
ACGTcount: A:0.37, C:0.07, G:0.12, T:0.44
Consensus pattern (35 bp):
ATTTTCCGTAAAATGATTTACTGGAAAATATTTTA
Found at i:40686010 original size:23 final size:24
Alignment explanation
Indices: 40685984--40686038 Score: 67
Period size: 23 Copynumber: 2.3 Consensus size: 24
40685974 TATAATTTTT
* *
40685984 AAAAATCAAAATTTATAAAA-TAA
1 AAAAATCAAAATTCAAAAAATTAA
*
40686007 AAAATTCAAAATTCAAAAAATTAA
1 AAAAATCAAAATTCAAAAAATTAA
*
40686031 AAATATCA
1 AAAAATCA
40686039 TTTTAAATAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
23 17 0.65
24 9 0.35
ACGTcount: A:0.67, C:0.07, G:0.00, T:0.25
Consensus pattern (24 bp):
AAAAATCAAAATTCAAAAAATTAA
Found at i:40686500 original size:21 final size:20
Alignment explanation
Indices: 40686452--40686500 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
40686442 AGATGATTAA
*
40686452 AAAATTAATATTAATTGTAT
1 AAAATTTATATTAATTGTAT
**
40686472 ATTGATTTATATTAATTGATAT
1 A-AAATTTATATTAATTG-TAT
40686494 AAAATTT
1 AAAATTT
40686501 GTGTTAATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 3
0.73 0.17 0.10
Matches are distributed among these distances:
20 1 0.05
21 17 0.77
22 4 0.18
ACGTcount: A:0.45, C:0.00, G:0.06, T:0.49
Consensus pattern (20 bp):
AAAATTTATATTAATTGTAT
Found at i:40688017 original size:27 final size:27
Alignment explanation
Indices: 40687979--40688050 Score: 94
Period size: 27 Copynumber: 2.7 Consensus size: 27
40687969 ACATCAGGAT
40687979 AGAAAAACCTTTGT-GCTGTAATATAAA
1 AGAAAAACCTTTGTGGC-GTAATATAAA
* *
40688006 AGAAACACCTTTGTGGCGTAATATCAA
1 AGAAAAACCTTTGTGGCGTAATATAAA
40688033 AGAATAAA-CTTTGTGGCG
1 AGAA-AAACCTTTGTGGCG
40688051 AACTCTGAAT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
27 36 0.90
28 4 0.10
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.28
Consensus pattern (27 bp):
AGAAAAACCTTTGTGGCGTAATATAAA
Found at i:40692824 original size:15 final size:16
Alignment explanation
Indices: 40692795--40692824 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
40692785 CAAACACGCT
40692795 TTAACACATTATCAAA
1 TTAACACATTATCAAA
40692811 TTAACACA-TATCAA
1 TTAACACATTATCAA
40692825 CAAGGCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:40696656 original size:15 final size:15
Alignment explanation
Indices: 40696636--40696665 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
40696626 AACCATGTCG
40696636 ACGCGTTAAAATCAT
1 ACGCGTTAAAATCAT
40696651 ACGCGTTAAAATCAT
1 ACGCGTTAAAATCAT
40696666 TTCCATTAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.20, G:0.13, T:0.27
Consensus pattern (15 bp):
ACGCGTTAAAATCAT
Found at i:40700025 original size:27 final size:27
Alignment explanation
Indices: 40699995--40700247 Score: 172
Period size: 27 Copynumber: 9.4 Consensus size: 27
40699985 CCTAATATTT
40699995 GTAAAATGACTGTAATACCCCTATAGG
1 GTAAAATGACTGTAATACCCCTATAGG
* * * * *
40700022 GTAAAATAACCGAAAAACCCCCATAGG
1 GTAAAATGACTGTAATACCCCTATAGG
* * **
40700049 GTAAAATGACGGTAATGCCCCCGTAGG
1 GTAAAATGACTGTAATACCCCTATAGG
* * ** *
40700076 ATAAAATAACCATAA-AGCCCCTATAAG
1 GTAAAATGACTGTAATA-CCCCTATAGG
* * *
40700103 GTAAAATGACCGTAATACCCCTGTAAG
1 GTAAAATGACTGTAATACCCCTATAGG
* * * *
40700130 GTAAAATGATTGAAAGACCTCC-ATTGG
1 GTAAAATGACTGTAATACC-CCTATAGG
* *
40700157 ATAAAATGA-TCGTAATGCCCCTATAGG
1 GTAAAATGACT-GTAATACCCCTATAGG
* *
40700184 GTAAAAT-AATCGTAATACCCCTATAGA
1 GTAAAATGACT-GTAATACCCCTATAGG
* * * * *
40700211 GTTAAATGACTGAAATACCTCTGTAAG
1 GTAAAATGACTGTAATACCCCTATAGG
40700238 GTAAAATGAC
1 GTAAAATGAC
40700248 CATAATGCCC
Statistics
Matches: 173, Mismatches: 46, Indels: 14
0.74 0.20 0.06
Matches are distributed among these distances:
26 4 0.02
27 164 0.95
28 5 0.03
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (27 bp):
GTAAAATGACTGTAATACCCCTATAGG
Found at i:40700054 original size:54 final size:54
Alignment explanation
Indices: 40699995--40700244 Score: 216
Period size: 54 Copynumber: 4.6 Consensus size: 54
40699985 CCTAATATTT
*
40699995 GTAAAATGACTGTAATACCCCTATAGGGTAAAATAACCGAAAAACCCCCATAGG
1 GTAAAATGACTGTAATACCCCTGTAGGGTAAAATAACCGAAAAACCCCCATAGG
* * * * * * *
40700049 GTAAAATGACGGTAATGCCCCCGTAGGATAAAATAACC-ATAAAGCCCCTATAAG
1 GTAAAATGACTGTAATACCCCTGTAGGGTAAAATAACCGA-AAAACCCCCATAGG
* * * ** * * *
40700103 GTAAAATGACCGTAATACCCCTGTAAGGTAAAATGATTGAAAGACCTCCATTGG
1 GTAAAATGACTGTAATACCCCTGTAGGGTAAAATAACCGAAAAACCCCCATAGG
* * * * * * * *
40700157 ATAAAATGA-TCGTAATGCCCCTATAGGGTAAAATAATCGTAATACCCCTATAGA
1 GTAAAATGACT-GTAATACCCCTGTAGGGTAAAATAACCGAAAAACCCCCATAGG
* * * *
40700211 GTTAAATGACTGAAATACCTCTGTAAGGTAAAAT
1 GTAAAATGACTGTAATACCCCTGTAGGGTAAAAT
40700245 GACCATAATG
Statistics
Matches: 150, Mismatches: 42, Indels: 8
0.75 0.21 0.04
Matches are distributed among these distances:
53 1 0.01
54 147 0.98
55 2 0.01
ACGTcount: A:0.40, C:0.19, G:0.18, T:0.23
Consensus pattern (54 bp):
GTAAAATGACTGTAATACCCCTGTAGGGTAAAATAACCGAAAAACCCCCATAGG
Found at i:40700133 original size:81 final size:81
Alignment explanation
Indices: 40700012--40700269 Score: 216
Period size: 81 Copynumber: 3.2 Consensus size: 81
40700002 GACTGTAATA
* * * * * *
40700012 CCCCTATAGGGTAAAATAACCGAAAAACCCCCATAGGGTAAAATGACGGTAATG-CCCCCGTAGG
1 CCCCTATAGGGTAAAATAACCGTAATACCCCTATAAGGTAAAATGACGG-AAAGACCCCCATAGG
40700076 ATAAAATAACCATAAAG
65 ATAAAATAACCATAAAG
* * * ** * *
40700093 CCCCTATAAGGTAAAATGACCGTAATACCCCTGTAAGGTAAAATGATTGAAAGACCTCCATTGGA
1 CCCCTATAGGGTAAAATAACCGTAATACCCCTATAAGGTAAAATGACGGAAAGACCCCCATAGGA
* * * *
40700158 TAAAATGATCGTAATG
66 TAAAATAACCATAAAG
* * * * * **
40700174 CCCCTATAGGGTAAAATAATCGTAATACCCCTAT-AGAGTTAAATGACTGAAATACCTCTGTAAG
1 CCCCTATAGGGTAAAATAACCGTAATACCCCTATAAG-GTAAAATGACGGAAAGACCCCCAT-AG
* *
40700238 G-TAAAATGACCATAATG
64 GATAAAATAACCATAAAG
* *
40700255 CCCCTAGAGGTTAAA
1 CCCCTATAGGGTAAA
40700270 TGAATATTTT
Statistics
Matches: 143, Mismatches: 31, Indels: 6
0.79 0.17 0.03
Matches are distributed among these distances:
80 5 0.03
81 136 0.95
82 2 0.01
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.22
Consensus pattern (81 bp):
CCCCTATAGGGTAAAATAACCGTAATACCCCTATAAGGTAAAATGACGGAAAGACCCCCATAGGA
TAAAATAACCATAAAG
Found at i:40700346 original size:24 final size:24
Alignment explanation
Indices: 40700319--40700376 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
40700309 CGTGAAGTAA
*
40700319 ATGACTGATTTGTCTGTGATTGGT
1 ATGACTGATTTGTCTGTAATTGGT
* *
40700343 ATGACTTATTTGTCTGTAATTTGT
1 ATGACTGATTTGTCTGTAATTGGT
40700367 ATGACTGATT
1 ATGACTGATT
40700377 CTGAGCATGG
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.21, C:0.09, G:0.22, T:0.48
Consensus pattern (24 bp):
ATGACTGATTTGTCTGTAATTGGT
Found at i:40700501 original size:27 final size:27
Alignment explanation
Indices: 40700448--40700501 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
40700438 AGTATTGTGT
*
40700448 TGGTGGCTCTGCCACAATCACTGTTAC
1 TGGTGGCTCTGCCACAATCACTATTAC
40700475 TGGTGGCT-TGGCCACATAT-ACTATTAC
1 TGGTGGCTCT-GCCACA-ATCACTATTAC
40700502 GGGCAGCTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
26 1 0.04
27 21 0.88
28 2 0.08
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.31
Consensus pattern (27 bp):
TGGTGGCTCTGCCACAATCACTATTAC
Found at i:40700592 original size:32 final size:32
Alignment explanation
Indices: 40700551--40700675 Score: 153
Period size: 32 Copynumber: 3.9 Consensus size: 32
40700541 GCGATGCTAC
* *
40700551 TGATGGCTTTGTGCTGGTCATATTACTGTTAT
1 TGATGGCTTTGTGCCGATCATATTACTGTTAT
* *
40700583 TGATGGCTTTGTGCCGATCATATTACCGTTAA
1 TGATGGCTTTGTGCCGATCATATTACTGTTAT
* * *
40700615 TGATGGCTGTGTGCCGATCATATCACTGCTACT
1 TGATGGCTTTGTGCCGATCATATTACTGTTA-T
* *
40700648 T-ATGGCTTTGTGCCAATCAAATTACTGT
1 TGATGGCTTTGTGCCGATCATATTACTGT
40700676 ACTTATGGGT
Statistics
Matches: 78, Mismatches: 14, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
32 77 0.99
33 1 0.01
ACGTcount: A:0.20, C:0.18, G:0.22, T:0.39
Consensus pattern (32 bp):
TGATGGCTTTGTGCCGATCATATTACTGTTAT
Found at i:40700703 original size:22 final size:22
Alignment explanation
Indices: 40700678--40700729 Score: 59
Period size: 22 Copynumber: 2.4 Consensus size: 22
40700668 ATTACTGTAC
* * *
40700678 TTATGGGTTGTAGCCATTCTGT
1 TTATGGCTTATAGCCATCCTGT
* *
40700700 TTATAGCTTATAGCTATCCTGT
1 TTATGGCTTATAGCCATCCTGT
40700722 TTATGGCT
1 TTATGGCT
40700730 CTTAACCATT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.17, C:0.15, G:0.21, T:0.46
Consensus pattern (22 bp):
TTATGGCTTATAGCCATCCTGT
Found at i:40703356 original size:27 final size:26
Alignment explanation
Indices: 40703325--40703550 Score: 105
Period size: 27 Copynumber: 8.3 Consensus size: 26
40703315 CCTAATATTT
*
40703325 GTAAAATGACCATAATACCCATATAGG
1 GTAAAATGACCATAATACCC-CATAGG
* ** * *
40703352 GTAAAATAATAAAAAAAACTCCCATAGG
1 GTAAAATGA-CCATAATAC-CCCATAGG
* *
40703380 GTAAAATGACCGTAATACCCCCGTAGG
1 GTAAAATGACCATAATA-CCCCATAGG
* * * ** *
40703407 GTAAAATGATCGTAATGCCTCTGTAAG
1 GTAAAATGACCATAATACC-CCATAGG
*
40703434 GTAAAATGACCGA-AATACCCCCGTAGG
1 GTAAAATGACC-ATAATA-CCCCATAGG
* ** *
40703461 GTAAAATAATTGA-AAAACCCCCATAGG
1 GTAAAATGA-CCATAATA-CCCCATAGG
* * *
40703488 GTAAAATGACCGTAATGCCTCTATAGG
1 GTAAAATGACCATAATACC-CCATAGG
* * *
40703515 GTAAAATGACCGTAGTACCCTCATAAG
1 GTAAAATGACCATAATACCC-CATAGG
*
40703542 GTTAAATGA
1 GTAAAATGA
40703551 TTGAAATACC
Statistics
Matches: 150, Mismatches: 39, Indels: 20
0.72 0.19 0.10
Matches are distributed among these distances:
26 5 0.03
27 122 0.81
28 21 0.14
29 2 0.01
ACGTcount: A:0.41, C:0.19, G:0.19, T:0.22
Consensus pattern (26 bp):
GTAAAATGACCATAATACCCCATAGG
Found at i:40703452 original size:54 final size:53
Alignment explanation
Indices: 40703379--40703584 Score: 187
Period size: 54 Copynumber: 3.8 Consensus size: 53
40703369 ACTCCCATAG
* * * *
40703379 GGTAAAATGACCGTAATACCCCCGTAGGGTAAAATGATCGTAATGCCTCTGTAA
1 GGTAAAATGACCGAAATACCCCCGTAGGGTAAAATAATCGTAATACC-CTATAA
* * * * *
40703433 GGTAAAATGACCGAAATACCCCCGTAGGGTAAAATAATTGAAAAACCCCCATAG
1 GGTAAAATGACCGAAATACCCCCGTAGGGTAAAATAATCGTAATA-CCCTATAA
* * * ** * * *
40703487 GGTAAAATGACCGTAATGCCTCTATAGGGTAAAATGACCGTAGTACCCTCATAA
1 GGTAAAATGACCGAAATACCCCCGTAGGGTAAAATAATCGTAATACCCT-ATAA
* ** * *
40703541 GGTTAAATGATTGAAATACCCCTGTAAGGTAAAATAATCGTAAT
1 GGTAAAATGACCGAAATACCCCCGTAGGGTAAAATAATCGTAAT
40703585 GCCCCTAGAG
Statistics
Matches: 117, Mismatches: 33, Indels: 4
0.76 0.21 0.03
Matches are distributed among these distances:
53 3 0.03
54 112 0.96
55 2 0.02
ACGTcount: A:0.38, C:0.19, G:0.20, T:0.23
Consensus pattern (53 bp):
GGTAAAATGACCGAAATACCCCCGTAGGGTAAAATAATCGTAATACCCTATAA
Found at i:40703482 original size:81 final size:81
Alignment explanation
Indices: 40703396--40703604 Score: 249
Period size: 81 Copynumber: 2.6 Consensus size: 81
40703386 TGACCGTAAT
* * *
40703396 ACCCCCGTAGGGTAAAATGATCGTAATGCCTCTGTAAGGTAAAATGACCGAAATACCCCCGTAGG
1 ACCCCCGTAGGGTAAAATGATCGTAATGCCTCTATAAGGTAAAATGACCGAAATACCCCCATAAG
40703461 GTAAAATAATTGAAAA
66 GTAAAATAATTGAAAA
* * * * * *
40703477 ACCCCCATAGGGTAAAATGACCGTAATGCCTCTATAGGGTAAAATGACCGTAGTACCCTCATAAG
1 ACCCCCGTAGGGTAAAATGATCGTAATGCCTCTATAAGGTAAAATGACCGAAATACCCCCATAAG
* * *
40703542 GTTAAATGATTGAAAT
66 GTAAAATAATTGAAAA
* * * * * *
40703558 ACCCCTGTAAGGTAAAATAATCGTAATGCCCCTAGAGGGT-AAATGAC
1 ACCCCCGTAGGGTAAAATGATCGTAATGCCTCTATAAGGTAAAATGAC
40703605 TATTTTGCCC
Statistics
Matches: 109, Mismatches: 19, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
80 7 0.06
81 102 0.94
ACGTcount: A:0.37, C:0.20, G:0.21, T:0.22
Consensus pattern (81 bp):
ACCCCCGTAGGGTAAAATGATCGTAATGCCTCTATAAGGTAAAATGACCGAAATACCCCCATAAG
GTAAAATAATTGAAAA
Found at i:40703589 original size:27 final size:27
Alignment explanation
Indices: 40703376--40703604 Score: 167
Period size: 27 Copynumber: 8.5 Consensus size: 27
40703366 AAAACTCCCA
*
40703376 TAGGGTAAAATGACCGTAATACCCCCG
1 TAGGGTAAAATGACCGTAATACCCCTG
* * *
40703403 TAGGGTAAAATGATCGTAATGCCTCTG
1 TAGGGTAAAATGACCGTAATACCCCTG
* * *
40703430 TAAGGTAAAATGACCGAAATACCCCCG
1 TAGGGTAAAATGACCGTAATACCCCTG
* ** * * **
40703457 TAGGGTAAAATAATTGAAAAACCCCCA
1 TAGGGTAAAATGACCGTAATACCCCTG
* * *
40703484 TAGGGTAAAATGACCGTAATGCCTCTA
1 TAGGGTAAAATGACCGTAATACCCCTG
* *
40703511 TAGGGTAAAATGACCGTAGTA-CCCTCA
1 TAGGGTAAAATGACCGTAATACCCCT-G
* * ** *
40703538 TAAGGTTAAATGATTGAAATACCCCTG
1 TAGGGTAAAATGACCGTAATACCCCTG
* * * *
40703565 TAAGGTAAAATAATCGTAATGCCCCTAG
1 TAGGGTAAAATGACCGTAATACCCCT-G
40703593 -AGGGT-AAATGAC
1 TAGGGTAAAATGAC
40703605 TATTTTGCCC
Statistics
Matches: 157, Mismatches: 42, Indels: 7
0.76 0.20 0.03
Matches are distributed among these distances:
26 8 0.05
27 144 0.92
28 5 0.03
ACGTcount: A:0.37, C:0.19, G:0.21, T:0.23
Consensus pattern (27 bp):
TAGGGTAAAATGACCGTAATACCCCTG
Found at i:40703653 original size:24 final size:24
Alignment explanation
Indices: 40703623--40703717 Score: 77
Period size: 24 Copynumber: 4.0 Consensus size: 24
40703613 CCCTCGAGTT
*
40703623 TAAATGATTGATATGTCCGTGATG
1 TAAATGACTGATATGTCCGTGATG
* ** *
40703647 TAAATGACTGATTTGTTTGTGATT
1 TAAATGACTGATATGTCCGTGATG
* **
40703671 TAAATGACTGATTTGTTTGTGATTGG
1 TAAATGACTGATATGTCCGTGA-T-G
*
40703697 T--ATGACTGATTTGTCCGTGAT
1 TAAATGACTGATATGTCCGTGAT
40703718 TTGTATGTCT
Statistics
Matches: 61, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
23 1 0.02
24 58 0.95
25 1 0.02
26 1 0.02
ACGTcount: A:0.24, C:0.07, G:0.24, T:0.44
Consensus pattern (24 bp):
TAAATGACTGATATGTCCGTGATG
Found at i:40703693 original size:48 final size:48
Alignment explanation
Indices: 40703621--40703719 Score: 112
Period size: 48 Copynumber: 2.1 Consensus size: 48
40703611 GCCCCTCGAG
* **
40703621 TTTAAATGATTGATATGTCCGTGA-T-GTAAATGACTGATTTGTTTGTGA
1 TTTAAATGACTGATATGTCCGTGATTGGT--ATGACTGATTTGTCCGTGA
* **
40703669 TTTAAATGACTGATTTGTTTGTGATTGGTATGACTGATTTGTCCGTGA
1 TTTAAATGACTGATATGTCCGTGATTGGTATGACTGATTTGTCCGTGA
40703717 TTT
1 TTT
40703720 GTATGTCTGA
Statistics
Matches: 43, Mismatches: 6, Indels: 4
0.81 0.11 0.08
Matches are distributed among these distances:
48 40 0.93
49 1 0.02
50 2 0.05
ACGTcount: A:0.23, C:0.07, G:0.23, T:0.46
Consensus pattern (48 bp):
TTTAAATGACTGATATGTCCGTGATTGGTATGACTGATTTGTCCGTGA
Found at i:40703718 original size:24 final size:24
Alignment explanation
Indices: 40703650--40703731 Score: 110
Period size: 24 Copynumber: 3.4 Consensus size: 24
40703640 CGTGATGTAA
**
40703650 ATGACTGATTTGTTTGTGATTTAA
1 ATGACTGATTTGTTTGTGATTTGT
*
40703674 ATGACTGATTTGTTTGTGATTGGT
1 ATGACTGATTTGTTTGTGATTTGT
**
40703698 ATGACTGATTTGTCCGTGATTTGT
1 ATGACTGATTTGTTTGTGATTTGT
*
40703722 ATGTCTGATT
1 ATGACTGATT
40703732 CTAAGCATGG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 51 1.00
ACGTcount: A:0.20, C:0.07, G:0.24, T:0.49
Consensus pattern (24 bp):
ATGACTGATTTGTTTGTGATTTGT
Found at i:40703901 original size:32 final size:32
Alignment explanation
Indices: 40703849--40704051 Score: 246
Period size: 32 Copynumber: 6.4 Consensus size: 32
40703839 GCTGCGATGC
* * *
40703849 TACTGATGGCTTTTTACCGATCATATTATCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* *
40703881 TACTAATGGCTTTGTGCCGATCATATTACCAT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* *
40703913 TACTGATGGCTTTGTACCGATCATATTATCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
40703945 TACTGATGGCTTTGTGCCGATCATATTACCGT
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* * ** * *
40703977 TACTGATGGCTGTGTGCCGGTCATACCACTGC
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
* * *
40704009 TACTGATGGATTTGTGCCAATCATATTACTG-
1 TACTGATGGCTTTGTGCCGATCATATTACCGT
*
40704040 TACTTATGGCTT
1 TACTGATGGCTT
40704052 GTAGCCATTC
Statistics
Matches: 146, Mismatches: 25, Indels: 1
0.85 0.15 0.01
Matches are distributed among these distances:
31 10 0.07
32 136 0.93
ACGTcount: A:0.21, C:0.21, G:0.20, T:0.38
Consensus pattern (32 bp):
TACTGATGGCTTTGTGCCGATCATATTACCGT
Found at i:40704073 original size:22 final size:21
Alignment explanation
Indices: 40704043--40704105 Score: 63
Period size: 22 Copynumber: 2.9 Consensus size: 21
40704033 ATTACTGTAC
40704043 TTATGGCTTGTAGCCATTCTAT
1 TTATGGCTT-TAGCCATTCTAT
* * * *
40704065 TTATAGCTTATAGCTATCCTGT
1 TTATGGCTT-TAGCCATTCTAT
40704087 TTATGGCTCTTAGCCATTC
1 TTATGGCT-TTAGCCATTC
40704106 GTGTTACTGG
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
22 31 0.97
23 1 0.03
ACGTcount: A:0.19, C:0.21, G:0.16, T:0.44
Consensus pattern (21 bp):
TTATGGCTTTAGCCATTCTAT
Found at i:40707684 original size:14 final size:13
Alignment explanation
Indices: 40707658--40707682 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
40707648 ATCGTGTATT
40707658 AAAAAAAAGAAAG
1 AAAAAAAAGAAAG
40707671 AAAAAAAAGAAA
1 AAAAAAAAGAAA
40707683 AGTGTTTCTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (13 bp):
AAAAAAAAGAAAG
Found at i:40710232 original size:20 final size:21
Alignment explanation
Indices: 40710207--40710245 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
40710197 ACCAGCTCCA
40710207 ATTCAGCTCAATA-AATTTTG
1 ATTCAGCTCAATATAATTTTG
*
40710227 ATTCAGCTCCATATAATTT
1 ATTCAGCTCAATATAATTT
40710246 AGTCATTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.33, C:0.18, G:0.08, T:0.41
Consensus pattern (21 bp):
ATTCAGCTCAATATAATTTTG
Found at i:40710491 original size:20 final size:19
Alignment explanation
Indices: 40710459--40710496 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
40710449 TCCAAACCGA
40710459 ATTAATTAGGTCTTAGTTTG
1 ATTAATTAGGTCTT-GTTTG
40710479 ATTAATT-GTGTCTTGTTT
1 ATTAATTAG-GTCTTGTTT
40710497 TAATTATGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.21, C:0.05, G:0.18, T:0.55
Consensus pattern (19 bp):
ATTAATTAGGTCTTGTTTG
Found at i:40720072 original size:10 final size:10
Alignment explanation
Indices: 40720049--40720100 Score: 56
Period size: 10 Copynumber: 5.3 Consensus size: 10
40720039 TTTTTTGAAA
*
40720049 TTTTATGAACT
1 TTTTAT-AATT
40720060 TTTTATAATT
1 TTTTATAATT
40720070 TTTTATTAA--
1 TTTTA-TAATT
40720079 TTTT-TAATT
1 TTTTATAATT
40720088 TTTTATAATT
1 TTTTATAATT
40720098 TTT
1 TTT
40720101 AAATTATTTG
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
7 3 0.08
9 8 0.22
10 16 0.44
11 9 0.25
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.69
Consensus pattern (10 bp):
TTTTATAATT
Found at i:40720088 original size:18 final size:17
Alignment explanation
Indices: 40720060--40720102 Score: 68
Period size: 17 Copynumber: 2.4 Consensus size: 17
40720050 TTTATGAACT
40720060 TTTTATAATTTTTTATTAA
1 TTTT-TAATTTTTTA-TAA
40720079 TTTTTAATTTTTTATAA
1 TTTTTAATTTTTTATAA
40720096 TTTTTAA
1 TTTTTAA
40720103 ATTATTTGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 10 0.42
18 10 0.42
19 4 0.17
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (17 bp):
TTTTTAATTTTTTATAA
Found at i:40720105 original size:18 final size:18
Alignment explanation
Indices: 40720049--40720105 Score: 71
Period size: 18 Copynumber: 3.0 Consensus size: 18
40720039 TTTTTTGAAA
40720049 TTTTATGAACTTTTTATAATT
1 TTTTAT-AA-TTTTTA-AATT
40720070 TTTTATTAATTTTT-AATT
1 TTTTA-TAATTTTTAAATT
40720088 TTTTATAATTTTTAAATT
1 TTTTATAATTTTTAAATT
40720106 ATTTGTTGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
17 8 0.24
18 13 0.38
20 5 0.15
21 7 0.21
22 1 0.03
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.67
Consensus pattern (18 bp):
TTTTATAATTTTTAAATT
Found at i:40729332 original size:16 final size:17
Alignment explanation
Indices: 40729311--40729346 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
40729301 TCAATCATCC
40729311 CTCATCCCTCATCC-CT
1 CTCATCCCTCATCCTCT
*
40729327 CTCATCTCTCATCCTCT
1 CTCATCCCTCATCCTCT
40729344 CTC
1 CTC
40729347 TCAACTCTCT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 13 0.72
17 5 0.28
ACGTcount: A:0.11, C:0.53, G:0.00, T:0.36
Consensus pattern (17 bp):
CTCATCCCTCATCCTCT
Found at i:40739554 original size:7 final size:7
Alignment explanation
Indices: 40739506--40739542 Score: 74
Period size: 7 Copynumber: 5.3 Consensus size: 7
40739496 ACTTTTTCAA
40739506 TCATCCC
1 TCATCCC
40739513 TCATCCC
1 TCATCCC
40739520 TCATCCC
1 TCATCCC
40739527 TCATCCC
1 TCATCCC
40739534 TCATCCC
1 TCATCCC
40739541 TC
1 TC
40739543 TCATCTCTCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 30 1.00
ACGTcount: A:0.14, C:0.57, G:0.00, T:0.30
Consensus pattern (7 bp):
TCATCCC
Found at i:40749472 original size:16 final size:16
Alignment explanation
Indices: 40749451--40749519 Score: 77
Period size: 16 Copynumber: 4.3 Consensus size: 16
40749441 AAAATTACTG
*
40749451 ATTATAGCTCTATTCT
1 ATTATAACTCTATTCT
*
40749467 ATTATAACTTTATTCT
1 ATTATAACTCTATTCT
40749483 ATTATAACTCTA-TCT
1 ATTATAACTCTATTCT
* **
40749498 AATTACAAGACTATTCT
1 -ATTATAACTCTATTCT
40749515 ATTAT
1 ATTAT
40749520 GGTACTCAAA
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
15 3 0.07
16 38 0.86
17 3 0.07
ACGTcount: A:0.33, C:0.16, G:0.03, T:0.48
Consensus pattern (16 bp):
ATTATAACTCTATTCT
Found at i:40752348 original size:18 final size:17
Alignment explanation
Indices: 40752312--40752351 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
40752302 AAGTAAAAAT
40752312 ATAATTTTATCATTTTA
1 ATAATTTTATCATTTTA
40752329 ATAA-TTTAT-ATCTTT-
1 ATAATTTTATCAT-TTTA
40752344 ATAATTTT
1 ATAATTTT
40752352 TAAAAGATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
15 6 0.29
16 11 0.52
17 4 0.19
ACGTcount: A:0.35, C:0.05, G:0.00, T:0.60
Consensus pattern (17 bp):
ATAATTTTATCATTTTA
Found at i:40754437 original size:17 final size:17
Alignment explanation
Indices: 40754402--40754439 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
40754392 TTTTTTAATT
*
40754402 AATTTTAATTAGTTTTA
1 AATTTTAATTAGTTATA
40754419 AATTTATAATTA-TTATA
1 AATTT-TAATTAGTTATA
40754436 AATT
1 AATT
40754440 ATATTTTATA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 13 0.68
18 6 0.32
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (17 bp):
AATTTTAATTAGTTATA
Done.