Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold370
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: 805812
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.33
Warning! 29760 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:412213 original size:108 final size:108
Alignment explanation
Indices: 412024--412235 Score: 379
Period size: 108 Copynumber: 2.0 Consensus size: 108
412014 GGGGAATTAT
** * *
412024 GGGAAGGTGTAGGAGAAGGGGGTTGTATTGTGGACTGGGCAGGTAAAGAATTAGTTGACATAGGG
1 GGGAAGGCATAGGAGAAGGGGGTTGTATTATGGACTGGACAGGTAAAGAATTAGTTGACATAGGG
412089 GAAGGTGTGAGAGTAGGTAACGTGGACCTAGCAGGTGACATAG
66 GAAGGTGTGAGAGTAGGTAACGTGGACCTAGCAGGTGACATAG
412132 GGGAAGGCATAGGAGAAGGGGGTTGTATTATGGACTGGACAGGTAAAGAATTAGTTGACATAGGG
1 GGGAAGGCATAGGAGAAGGGGGTTGTATTATGGACTGGACAGGTAAAGAATTAGTTGACATAGGG
*
412197 GAAGGTGTGAGAGTAGGTAATGTGGACCTAGCAGGTGAC
66 GAAGGTGTGAGAGTAGGTAACGTGGACCTAGCAGGTGAC
412236 GGAGAGAGAG
Statistics
Matches: 99, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
108 99 1.00
ACGTcount: A:0.30, C:0.08, G:0.42, T:0.21
Consensus pattern (108 bp):
GGGAAGGCATAGGAGAAGGGGGTTGTATTATGGACTGGACAGGTAAAGAATTAGTTGACATAGGG
GAAGGTGTGAGAGTAGGTAACGTGGACCTAGCAGGTGACATAG
Found at i:415262 original size:2 final size:2
Alignment explanation
Indices: 415255--415297 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
415245 GTCAAGCCAA
415255 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
415297 T
1 T
415298 ATATATATAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:421700 original size:3 final size:3
Alignment explanation
Indices: 421692--421719 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
421682 TGTATAAAGT
421692 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
421720 AGGAACCGTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:422896 original size:81 final size:82
Alignment explanation
Indices: 422803--422965 Score: 319
Period size: 81 Copynumber: 2.0 Consensus size: 82
422793 TTTTATTCGT
422803 GAAATTTAGAAAATGTTATTGTGAAATAATTTATTATACAGGTTGACTCAAGTCGTCGAATTATG
1 GAAATTTAGAAAATGTTATTGTGAAATAATTTATTATACAGGTTGACTCAAGTCGTCGAATTATG
422868 AGCC-AAAACAAGTTTA
66 AGCCAAAAACAAGTTTA
422884 GAAATTTAGAAAATGTTATTGTGAAATAATTTATTATACAGGTTGACTCAAGTCGTCGAATTATG
1 GAAATTTAGAAAATGTTATTGTGAAATAATTTATTATACAGGTTGACTCAAGTCGTCGAATTATG
422949 AGCCAAAAACAAGTTTA
66 AGCCAAAAACAAGTTTA
422966 AATGACAAAA
Statistics
Matches: 81, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
81 69 0.85
82 12 0.15
ACGTcount: A:0.40, C:0.10, G:0.17, T:0.33
Consensus pattern (82 bp):
GAAATTTAGAAAATGTTATTGTGAAATAATTTATTATACAGGTTGACTCAAGTCGTCGAATTATG
AGCCAAAAACAAGTTTA
Found at i:422991 original size:81 final size:80
Alignment explanation
Indices: 422825--422991 Score: 201
Period size: 81 Copynumber: 2.1 Consensus size: 80
422815 ATGTTATTGT
*
422825 GAAATAATTTATTATACAGGTTGACTCAAGTCGTCGAATTATGAGCCAAAACAAGTTTAGAAATT
1 GAAATAATTTATTATACAGGTTGACTCAAGTCGTCGAATTATGAGCCAAAACAAGTTTA-AAATA
* * **** ****
422890 TAGAAAATGTTATTGT
65 CAAAAAAAAAAAAAAA
422906 GAAATAATTTATTATACAGGTTGACTCAAGTCGTCGAATTATGAGCCAAAAACAAGTTT-AAATG
1 GAAATAATTTATTATACAGGTTGACTCAAGTCGTCGAATTATGAGCC-AAAACAAGTTTAAAAT-
422970 ACAAAAAAAAAAAAAAA
64 ACAAAAAAAAAAAAAAA
422987 GAAAT
1 GAAAT
422992 TTTAGGCTGT
Statistics
Matches: 73, Mismatches: 11, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
80 4 0.05
81 58 0.79
82 11 0.15
ACGTcount: A:0.46, C:0.10, G:0.16, T:0.28
Consensus pattern (80 bp):
GAAATAATTTATTATACAGGTTGACTCAAGTCGTCGAATTATGAGCCAAAACAAGTTTAAAATAC
AAAAAAAAAAAAAAA
Found at i:425694 original size:22 final size:22
Alignment explanation
Indices: 425652--425694 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
425642 GGCCAGGCCT
*
425652 ATTTTTTTAATAAACACAAAAA
1 ATTTTTTTAATAAACAAAAAAA
*
425674 ATTTATTTTAA-AAATAAAAAA
1 ATTT-TTTTAATAAACAAAAAA
425695 TAAAAAAAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 12 0.67
23 6 0.33
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (22 bp):
ATTTTTTTAATAAACAAAAAAA
Found at i:425742 original size:17 final size:17
Alignment explanation
Indices: 425709--425741 Score: 59
Period size: 16 Copynumber: 2.0 Consensus size: 17
425699 AAAAAGTATT
425709 TTAAAAATATTTTAAAA
1 TTAAAAATATTTTAAAA
425726 TTAAAAA-ATTTTAAAA
1 TTAAAAATATTTTAAAA
425742 AATAAATTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.56
17 7 0.44
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
TTAAAAATATTTTAAAA
Found at i:425747 original size:17 final size:17
Alignment explanation
Indices: 425710--425747 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
425700 AAAAGTATTT
*
425710 TAAAAATATTTTAAAAT
1 TAAAAATATTTTAAAAA
425727 TAAAAA-ATTTTAAAAAA
1 TAAAAATATTTT-AAAAA
425744 TAAA
1 TAAA
425748 TTTATTATAT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 5 0.26
17 14 0.74
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
TAAAAATATTTTAAAAA
Found at i:429257 original size:27 final size:28
Alignment explanation
Indices: 429209--429262 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
429199 CTCTTTTGAG
* *
429209 TTAATAAATTCTTTCTGGGTTTCTTTTT
1 TTAATAAATTCTCTCTGAGTTTCTTTTT
*
429237 TTAATAATTTCTCT-TGAGTTTCTTTT
1 TTAATAAATTCTCTCTGAGTTTCTTTT
429263 GGAAGAGTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.19, C:0.11, G:0.09, T:0.61
Consensus pattern (28 bp):
TTAATAAATTCTCTCTGAGTTTCTTTTT
Found at i:435662 original size:394 final size:384
Alignment explanation
Indices: 434911--435684 Score: 989
Period size: 394 Copynumber: 2.0 Consensus size: 384
434901 CCATAAAGTC
* *
434911 TTTGGACTTTAGAAAAAAAAGGAACATAACTTGACCTTACAACATTATAACATTAAATGTGGTCC
1 TTTGAACTTTAGAAAAAAAAGGAACATAACTTGACCTTACAACATTATAACATAAAATGTGGTCC
* *
434976 AAACTATGACCATAACATCATTACCTTAGCTTGAAAAAAAAACCCCCAAATCTCCAAATGGCATG
66 AAACAATGACCATAACATCATTACCTTAGCTTGAAAAAAAAACACCCAAATCTCCAAATGGCATG
** *
435041 ATCAATTGGGAATGATTTATTTTGGATCTCTAATGGACAACACCTACACATTTGGTTAACGAACA
131 ATCAACCGGGAATGATTTATTTTGGATCTCTAATGGACAACACCTACACACTTGGTTAACGAACA
* * * * *
435106 CAAATTGTCCTAAGGGACTTGTGACAATTATTGTCATGCTTGATAATACACATTTCAATTTTCTT
196 CAAATTGTCCTAAAGGACTTGTGACAACTATTGTCATGCTTGACAATACACATTTCAAATTTCTC
* * *
435171 GATTTCATAAAGCTAGAATTAACATATGGATACATAGAACCAAGGTCAATTAAAGCATGAACGGG
261 AATTTCATAAAGCTAGAATTAACATATGAATACATAGAACCAAGGTCAATTAAAGCATGAACGAG
* * * *
435236 TGCAAAATATAAAAAAATTATACCTGCTACAACATCGGTAGCATCACCCTCATCTTTGA
326 TGCAAAACATAAAAAAATTATACCTCCTACAACATCGATAACATCACCCTCATCTTTGA
* * *
435295 TTTGAACTTTAG-GAAAAAAGGAACATAACTTGACTTTACAACGTTATAACAACATAAAATGTGG
1 TTTGAACTTTAGAAAAAAAAGGAACATAACTTGACCTTACAACATTAT---AACATAAAATGTGG
* * *
435359 TCCAGAGAATGACCATAACATTATTACCTTAGCTTGAAAAAAAACAATACAAAAACCCAAATCTC
63 TCCAAACAATGACCATAACATCATTACCTTAGCTTG--AAAAAA-AA-AC----ACCCAAATCTC
* *** *
435424 CAAATGGCATGATCAACCGGGAATGATTTTTTTTTGGATCTCTAATGGACAGTGCCTACAGACTT
120 CAAATGGCATGATCAACCGGGAATGA-TTTATTTTGGATCTCTAATGGACAACACCTACACACTT
* * * ** *
435489 GGTTAACGAGCGCAGATTGTCCTAAAGGACTTGTGACAACTATTG-CGATGCTTGACAATTTAGA
184 GGTTAACGAACACAAATTGTCCTAAAGGACTTGTGACAACTATTGTC-ATGCTTGACAATACACA
* * *** * *
435553 TTTCAAATTTCTCAATTTCATAAAGTTAG-ATTAACATATGAATACGTAGATTTAGGGTTAATTA
248 TTTCAAATTTCTCAATTTCATAAAGCTAGAATTAACATATGAATACATAGAACCAAGGTCAATTA
* *
435617 AAGCATGAACGAGTGCAGAACATAAAAGAAA-TATACCTCCTACAACATCGATAACATCACCTTC
313 AAGCATGAACGAGTGCAAAACATAAAA-AAATTATACCTCCTACAACATCGATAACATCACCCTC
435681 ATCT
377 ATCT
435685 CTGGTTTTAA
Statistics
Matches: 331, Mismatches: 45, Indels: 18
0.84 0.11 0.05
Matches are distributed among these distances:
383 32 0.10
384 11 0.03
386 45 0.14
388 6 0.02
389 2 0.01
390 2 0.01
394 120 0.36
395 113 0.34
ACGTcount: A:0.38, C:0.18, G:0.15, T:0.29
Consensus pattern (384 bp):
TTTGAACTTTAGAAAAAAAAGGAACATAACTTGACCTTACAACATTATAACATAAAATGTGGTCC
AAACAATGACCATAACATCATTACCTTAGCTTGAAAAAAAAACACCCAAATCTCCAAATGGCATG
ATCAACCGGGAATGATTTATTTTGGATCTCTAATGGACAACACCTACACACTTGGTTAACGAACA
CAAATTGTCCTAAAGGACTTGTGACAACTATTGTCATGCTTGACAATACACATTTCAAATTTCTC
AATTTCATAAAGCTAGAATTAACATATGAATACATAGAACCAAGGTCAATTAAAGCATGAACGAG
TGCAAAACATAAAAAAATTATACCTCCTACAACATCGATAACATCACCCTCATCTTTGA
Found at i:442439 original size:16 final size:17
Alignment explanation
Indices: 442399--442439 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
442389 TAATTATATA
442399 ATATTTT-T-AATTTTC
1 ATATTTTATAAATTTTC
*
442414 ATATTATATAAATTTT-
1 ATATTTTATAAATTTTC
442430 ATATTTTATA
1 ATATTTTATA
442440 CGAGTCTACT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
15 6 0.27
16 10 0.45
17 6 0.27
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.61
Consensus pattern (17 bp):
ATATTTTATAAATTTTC
Found at i:449579 original size:60 final size:60
Alignment explanation
Indices: 449495--449683 Score: 204
Period size: 60 Copynumber: 3.1 Consensus size: 60
449485 TTAATATAAC
* * * * * * *
449495 ATTTGGTATTTGAATTTGACATTTTTTTTTAATTTGGTACTTCAACTTTTTTTTGGCCAA
1 ATTTGGTATCTGAACTTGATATTTTTTTTTAATTTGGTACCTAAACTTTTTTTAGCCCAA
*
449555 ATTTGGTATCTGAACTTGATATTTTTTTCTAATTTGGTACCTAAACTTTTTTTAGCCCAA
1 ATTTGGTATCTGAACTTGATATTTTTTTTTAATTTGGTACCTAAACTTTTTTTAGCCCAA
* * * * *
449615 A-TTAGTA-CATGAACTTGACTCTTTTTTTTCTAATTTGGTACCTAAGCCTTTTTTAGGTCC-A
1 ATTTGGTATC-TGAACTTGA-TATTTTTTTT-TAATTTGGTACCTAAACTTTTTTTA-GCCCAA
449676 ATTTGGTA
1 ATTTGGTA
449684 CCTAAATTTA
Statistics
Matches: 109, Mismatches: 15, Indels: 8
0.83 0.11 0.06
Matches are distributed among these distances:
58 1 0.01
59 14 0.13
60 61 0.56
61 25 0.23
62 8 0.07
ACGTcount: A:0.23, C:0.14, G:0.13, T:0.50
Consensus pattern (60 bp):
ATTTGGTATCTGAACTTGATATTTTTTTTTAATTTGGTACCTAAACTTTTTTTAGCCCAA
Found at i:449591 original size:31 final size:31
Alignment explanation
Indices: 449495--449602 Score: 80
Period size: 31 Copynumber: 3.5 Consensus size: 31
449485 TTAATATAAC
* * * *
449495 ATTTGGTATTTGAATTTGACATTTTTTTTTA
1 ATTTGGTATCTGAACTTGATATTTTTTTCTA
* ** *
449526 ATTTGGTA-CTTCAACTT--T-TTTTTGGCCAA
1 ATTTGGTATC-TGAACTTGATATTTTT-TTCTA
449555 ATTTGGTATCTGAACTTGATATTTTTTTCTA
1 ATTTGGTATCTGAACTTGATATTTTTTTCTA
* *
449586 ATTTGGTACCTAAACTT
1 ATTTGGTATCTGAACTT
449603 TTTTTAGCCC
Statistics
Matches: 57, Mismatches: 14, Indels: 12
0.69 0.17 0.14
Matches are distributed among these distances:
28 5 0.09
29 15 0.26
30 1 0.02
31 31 0.54
32 5 0.09
ACGTcount: A:0.23, C:0.11, G:0.13, T:0.53
Consensus pattern (31 bp):
ATTTGGTATCTGAACTTGATATTTTTTTCTA
Found at i:449650 original size:61 final size:60
Alignment explanation
Indices: 449516--449670 Score: 190
Period size: 61 Copynumber: 2.6 Consensus size: 60
449506 GAATTTGACA
* * * * *
449516 TTTTTTTT-TAATTTGGTACTTCAACTTTTTTTTGGCCAAATTTGGTATCTGAACTTGAT
1 TTTTTTTTCTAATTTGGTACCTAAACTTTTTTTAGCCCAAATTTAGTATCTGAACTTGAT
*
449575 ATTTTTTTCTAATTTGGTACCTAAACTTTTTTTAGCCCAAA-TTAGTA-CATGAACTTGACT
1 TTTTTTTTCTAATTTGGTACCTAAACTTTTTTTAGCCCAAATTTAGTATC-TGAACTTGA-T
* *
449635 CTTTTTTTTCTAATTTGGTACCTAAGCCTTTTTTAG
1 -TTTTTTTTCTAATTTGGTACCTAAACTTTTTTTAG
449671 GTCCAATTTG
Statistics
Matches: 83, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
58 1 0.01
59 21 0.25
60 29 0.35
61 32 0.39
ACGTcount: A:0.23, C:0.15, G:0.12, T:0.51
Consensus pattern (60 bp):
TTTTTTTTCTAATTTGGTACCTAAACTTTTTTTAGCCCAAATTTAGTATCTGAACTTGAT
Found at i:450195 original size:30 final size:31
Alignment explanation
Indices: 450115--450206 Score: 114
Period size: 31 Copynumber: 3.0 Consensus size: 31
450105 AAATCCCAAA
* * *
450115 AAGAAAAGGTGTCAAGCTTAGGTACTAACTT
1 AAGAAAAGGTGTCAAGTTTAGGTATTAAATT
*
450146 AAGAAAATGTGTCAAGTTTAGGTATTAAATT
1 AAGAAAAGGTGTCAAGTTTAGGTATTAAATT
* * *
450177 AGGAAAA-GTGTTAAGTTTAAGTATTAAATT
1 AAGAAAAGGTGTCAAGTTTAGGTATTAAATT
450207 GGACAAAAAA
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
30 21 0.39
31 33 0.61
ACGTcount: A:0.41, C:0.05, G:0.21, T:0.33
Consensus pattern (31 bp):
AAGAAAAGGTGTCAAGTTTAGGTATTAAATT
Found at i:452104 original size:54 final size:54
Alignment explanation
Indices: 452045--452147 Score: 154
Period size: 54 Copynumber: 1.9 Consensus size: 54
452035 CACTTCTAAT
*
452045 ATAATATA-AAGACTAATTGAAACTAAATGAAAGTGATTGCTAGTTTGATGTAAG
1 ATAATATATAA-ACTAATTGAAACTAAATGAAAGTGATTCCTAGTTTGATGTAAG
** *
452099 ATAATATATAAACTAATTGCCACTAAATTAAAGTGATTCCTAGTTTGAT
1 ATAATATATAAACTAATTGAAACTAAATGAAAGTGATTCCTAGTTTGAT
452148 CATGTGCATG
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
54 42 0.95
55 2 0.05
ACGTcount: A:0.43, C:0.09, G:0.15, T:0.34
Consensus pattern (54 bp):
ATAATATATAAACTAATTGAAACTAAATGAAAGTGATTCCTAGTTTGATGTAAG
Found at i:452589 original size:26 final size:27
Alignment explanation
Indices: 452527--452590 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
452517 AGTTCTTTTT
*
452527 TGCTTTT-AAAATGTGCTTTTGAAAAG
1 TGCTTTTGAAAATGTGATTTTGAAAAG
* *
452553 TG-TTGTGGAAAA-GTGATTTTGAGAAG
1 TGCTT-TTGAAAATGTGATTTTGAAAAG
452579 TGCTTTTGAAAA
1 TGCTTTTGAAAA
452591 ATTTGAGTGT
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
25 2 0.06
26 23 0.74
27 6 0.19
ACGTcount: A:0.31, C:0.05, G:0.25, T:0.39
Consensus pattern (27 bp):
TGCTTTTGAAAATGTGATTTTGAAAAG
Found at i:460547 original size:39 final size:42
Alignment explanation
Indices: 460503--460585 Score: 136
Period size: 39 Copynumber: 2.0 Consensus size: 42
460493 TCAAACTGTA
460503 AAATCAAAGTCTAAC-TTGGAT-AAAAAAAA-TTTAAGTTCC
1 AAATCAAAGTCTAACTTTGGATAAAAAAAAATTTTAAGTTCC
*
460542 AAATCAAGGTCTAACTTTGGATAAAAAAAAATTTTAAGTTCC
1 AAATCAAAGTCTAACTTTGGATAAAAAAAAATTTTAAGTTCC
460584 AA
1 AA
460586 TATGAAAATA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
39 14 0.35
40 6 0.15
41 8 0.20
42 12 0.30
ACGTcount: A:0.48, C:0.12, G:0.11, T:0.29
Consensus pattern (42 bp):
AAATCAAAGTCTAACTTTGGATAAAAAAAAATTTTAAGTTCC
Found at i:473436 original size:30 final size:31
Alignment explanation
Indices: 473402--473465 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 31
473392 TTACAAAATG
*
473402 GTCACTAAACTATTCTAAAGTTTTCA-TTAA
1 GTCACTAAACTATTCGAAAGTTTTCATTTAA
* * *
473432 GTCACTGAACTATTCGGAAGTTTTTATTTAA
1 GTCACTAAACTATTCGAAAGTTTTCATTTAA
473463 GTC
1 GTC
473466 GGGTTGTTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
30 22 0.76
31 7 0.24
ACGTcount: A:0.31, C:0.16, G:0.12, T:0.41
Consensus pattern (31 bp):
GTCACTAAACTATTCGAAAGTTTTCATTTAA
Found at i:476129 original size:30 final size:31
Alignment explanation
Indices: 476090--476149 Score: 104
Period size: 30 Copynumber: 2.0 Consensus size: 31
476080 TACTCATTAA
476090 TTTTCTTAAAATTTTAATTAGAT-CCTCAAT
1 TTTTCTTAAAATTTTAATTAGATCCCTCAAT
*
476120 TTTTTTTAAAATTTTAATTAGATCCCTCAA
1 TTTTCTTAAAATTTTAATTAGATCCCTCAA
476150 AATTTAATGT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
30 22 0.79
31 6 0.21
ACGTcount: A:0.33, C:0.13, G:0.03, T:0.50
Consensus pattern (31 bp):
TTTTCTTAAAATTTTAATTAGATCCCTCAAT
Found at i:479781 original size:21 final size:21
Alignment explanation
Indices: 479755--479794 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
479745 GGTAATATCT
479755 TTCGTCACTAAATCATTTTTA
1 TTCGTCACTAAATCATTTTTA
479776 TTCGTCACTAAATCATTTT
1 TTCGTCACTAAATCATTTT
479795 CTCCGTCGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.28, C:0.20, G:0.05, T:0.47
Consensus pattern (21 bp):
TTCGTCACTAAATCATTTTTA
Found at i:482240 original size:3 final size:3
Alignment explanation
Indices: 482232--482282 Score: 102
Period size: 3 Copynumber: 17.0 Consensus size: 3
482222 TAAGTTTCTT
482232 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
482280 TTA
1 TTA
482283 CGGTTGCGGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:483360 original size:6 final size:6
Alignment explanation
Indices: 483351--483385 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
483341 TACATATATT
483351 ATATAG ATATAG ATATAG ATATAG ATATAG ATATA
1 ATATAG ATATAG ATATAG ATATAG ATATAG ATATA
483386 TACATCAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.00, G:0.14, T:0.34
Consensus pattern (6 bp):
ATATAG
Found at i:491241 original size:26 final size:27
Alignment explanation
Indices: 491187--491243 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
491177 AATTTTAAAA
** * *
491187 TATTTTTAAAATACTTTTTTATTTTTT
1 TATTTTTAAAATAAGTTTTTATGTGTT
491214 TATTTTTAAAATAAGTTTTTA-GTGTT
1 TATTTTTAAAATAAGTTTTTATGTGTT
491240 TATT
1 TATT
491244 AAAAATGGAC
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
26 7 0.27
27 19 0.73
ACGTcount: A:0.28, C:0.02, G:0.05, T:0.65
Consensus pattern (27 bp):
TATTTTTAAAATAAGTTTTTATGTGTT
Found at i:494783 original size:147 final size:146
Alignment explanation
Indices: 494624--495016 Score: 416
Period size: 138 Copynumber: 2.8 Consensus size: 146
494614 TTTTAATGTA
* * *
494624 TTTTATATTTTGATTAAAATGAATTAATATAATTATTTATATTAATAAATTCGATAAAACATATA
1 TTTTATATTTTGATCAATATTAATTAATATAA-TATTTATATTAATAAATTCGATAAAACATATA
* *
494689 TAGTTAATATTTTGTAATATTTTGTATGAATCAAATTCATATATTAA-TATATTCTTTTCAAACA
65 TA-TTAATATTTTGTAATATTTTGTATGAATCAAATTCATATATTAATTATATTATTTCCAAA-A
*
494753 -AATAATATTTTTCATATC
128 TAATAATAATTTTCATATC
* *
494771 TTTTATATTTTGATCGATATTAATTAATATAACTGTTTATATTAATAAATTC-AGTAAAAC--AT
1 TTTTATATTTTGATCAATATTAATTAATATAA-TATTTATATTAATAAATTCGA-TAAAACATAT
* *
494833 ATA--CA-A---T-TAATATTTTGTATGAATCAAATTTATATATTAATTATATTATTTCCAAAAT
64 ATATTAATATTTTGTAATATTTTGTATGAATCAAATTCATATATTAATTATATTATTTCCAAAAT
* *
494891 AATATTAATTTTCATTTC
129 AATAATAATTTTCATATC
* * * * *
494909 TTTTATATTCTGAGCAGTATTAATTAATATAACAGTTTATATTAATAAATTCGGT--AA-A-ATA
1 TTTTATATTTTGATCAATATTAATTAATATAATA-TTTATATTAATAAATTCGATAAAACATATA
494970 T-TTACA-A---T-TAATATTTTGTATGAATCAAATTCATATATTAATTATAT
65 TATTA-ATATTTTGTAATATTTTGTATGAATCAAATTCATATATTAATTATAT
495017 ATGTGTCCTC
Statistics
Matches: 215, Mismatches: 22, Indels: 27
0.81 0.08 0.10
Matches are distributed among these distances:
136 6 0.03
137 33 0.15
138 116 0.54
141 1 0.00
142 1 0.00
145 5 0.02
146 1 0.00
147 52 0.24
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (146 bp):
TTTTATATTTTGATCAATATTAATTAATATAATATTTATATTAATAAATTCGATAAAACATATAT
ATTAATATTTTGTAATATTTTGTATGAATCAAATTCATATATTAATTATATTATTTCCAAAATAA
TAATAATTTTCATATC
Found at i:494915 original size:138 final size:138
Alignment explanation
Indices: 494703--495016 Score: 481
Period size: 138 Copynumber: 2.3 Consensus size: 138
494693 TAATATTTTG
* * *
494703 TAATATTTTGTATGAATCAAATTCATATATTAA-TATATTCTTTTCAAACAAATAATATTTTTCA
1 TAATATTTTGTATGAATCAAATTCATATATTAATTATATTATTTCCAAACAAATAATAATTTTCA
* * *
494767 TATCTTTTATATTTTGATC-GATATTAATTAATATAACTGTTTATATTAATAAATTCAGTAAAAC
66 TATCTTTTATATTCTGAGCAG-TATTAATTAATATAACAGTTTATATTAATAAATTCAGTAAAAC
494831 ATATACAAT
130 ATATACAAT
* *
494840 TAATATTTTGTATGAATCAAATTTATATATTAATTATATTATTTCCAAA-ATAATATTAATTTTC
1 TAATATTTTGTATGAATCAAATTCATATATTAATTATATTATTTCCAAACA-AATAATAATTTTC
* * *
494904 ATTTCTTTTATATTCTGAGCAGTATTAATTAATATAACAGTTTATATTAATAAATTCGGTAAAAT
65 ATATCTTTTATATTCTGAGCAGTATTAATTAATATAACAGTTTATATTAATAAATTCAGTAAAAC
*
494969 ATTTACAAT
130 ATATACAAT
494978 TAATATTTTGTATGAATCAAATTCATATATTAATTATAT
1 TAATATTTTGTATGAATCAAATTCATATATTAATTATAT
495017 ATGTGTCCTC
Statistics
Matches: 161, Mismatches: 13, Indels: 5
0.90 0.07 0.03
Matches are distributed among these distances:
137 33 0.20
138 127 0.79
139 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.05, T:0.47
Consensus pattern (138 bp):
TAATATTTTGTATGAATCAAATTCATATATTAATTATATTATTTCCAAACAAATAATAATTTTCA
TATCTTTTATATTCTGAGCAGTATTAATTAATATAACAGTTTATATTAATAAATTCAGTAAAACA
TATACAAT
Found at i:499621 original size:19 final size:18
Alignment explanation
Indices: 499573--499626 Score: 58
Period size: 19 Copynumber: 3.1 Consensus size: 18
499563 CAATTTGGTC
499573 TTTA-ATTTTTTTTTG-T
1 TTTACATTTTTTTTTGAT
** *
499589 TTTACATTAATTTTAGAT
1 TTTACATTTTTTTTTGAT
499607 TTTAACATTTTTTTTTGAT
1 TTT-ACATTTTTTTTTGAT
499626 T
1 T
499627 CTTCAATGTA
Statistics
Matches: 29, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
16 4 0.14
17 8 0.28
18 4 0.14
19 13 0.45
ACGTcount: A:0.22, C:0.04, G:0.06, T:0.69
Consensus pattern (18 bp):
TTTACATTTTTTTTTGAT
Found at i:505933 original size:27 final size:30
Alignment explanation
Indices: 505873--505933 Score: 74
Period size: 29 Copynumber: 2.1 Consensus size: 30
505863 NNNNNNNTAA
* * *
505873 TTAAAATATTAAAAATATATTATTTTAAAT
1 TTAAAATATTAAAAATATATTAGTTCAAAC
505903 TTAAAA-ATTAAAAATAT-TT-GTTCAAAC
1 TTAAAATATTAAAAATATATTAGTTCAAAC
505930 TTAA
1 TTAA
505934 CCCAAATTCG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 9 0.32
28 2 0.07
29 11 0.39
30 6 0.21
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (30 bp):
TTAAAATATTAAAAATATATTAGTTCAAAC
Found at i:507189 original size:24 final size:24
Alignment explanation
Indices: 507162--507208 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
507152 AATAAAATTT
507162 AAAAATAGAATATTAAAAA-TTAAG
1 AAAAAT-GAATATTAAAAAGTTAAG
* *
507186 AAAAATGATTTTTAAAAAGTTAA
1 AAAAATGAATATTAAAAAGTTAA
507209 AGACAAAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.62, C:0.00, G:0.09, T:0.30
Consensus pattern (24 bp):
AAAAATGAATATTAAAAAGTTAAG
Found at i:507506 original size:23 final size:23
Alignment explanation
Indices: 507476--507529 Score: 83
Period size: 23 Copynumber: 2.3 Consensus size: 23
507466 ATTCTAACAC
507476 ATATTAAAAATTATATTATTTT-T
1 ATATTAAAAATTATA-TATTTTCT
507499 ATATTAAAAATTATATATTTTCT
1 ATATTAAAAATTATATATTTTCT
507522 ATAATTAA
1 AT-ATTAA
507530 TGAATAGTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.21
23 18 0.62
24 5 0.17
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
ATATTAAAAATTATATATTTTCT
Found at i:507949 original size:125 final size:126
Alignment explanation
Indices: 507801--508062 Score: 499
Period size: 125 Copynumber: 2.1 Consensus size: 126
507791 TATTTTACCC
* *
507801 TTTATATATATATGCTATTACAATGGTAAAATTGTAACCCATATATTTTATGATTAAACATTTCA
1 TTTATGTATTTATGCTATTACAATGGTAAAATTGTAACCCATATATTTTATGATTAAACATTTCA
507866 AATTATTTATTATATTAACATTAATATAAATTTTAAATTTATTATTATATTTTTGAAAATA
66 AATTATTTATTATATTAACATTAATATAAATTTTAAATTTATTATTATATTTTTGAAAATA
507927 -TTATGTATTTATGCTATTACAATGGTAAAATTGTAACCCATATATTTTATGATTAAACATTTCA
1 TTTATGTATTTATGCTATTACAATGGTAAAATTGTAACCCATATATTTTATGATTAAACATTTCA
507991 AATTATTTATTATATTAACATTAATATAAATTTTAAATTTATTATTATATTTTTGAAAATA
66 AATTATTTATTATATTAACATTAATATAAATTTTAAATTTATTATTATATTTTTGAAAATA
508052 TTTATGTATTT
1 TTTATGTATTT
508063 TTATATTTTT
Statistics
Matches: 133, Mismatches: 2, Indels: 2
0.97 0.01 0.01
Matches are distributed among these distances:
125 123 0.92
126 10 0.08
ACGTcount: A:0.40, C:0.06, G:0.05, T:0.49
Consensus pattern (126 bp):
TTTATGTATTTATGCTATTACAATGGTAAAATTGTAACCCATATATTTTATGATTAAACATTTCA
AATTATTTATTATATTAACATTAATATAAATTTTAAATTTATTATTATATTTTTGAAAATA
Found at i:519938 original size:20 final size:20
Alignment explanation
Indices: 519913--519951 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
519903 GAGGTACATT
519913 TTTTTAA-TCACTTCAATTTG
1 TTTTTAATTCACTT-AATTTG
519933 TTTTTAATTCACTTAATTT
1 TTTTTAATTCACTTAATTT
519952 TTATTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.26, C:0.13, G:0.03, T:0.59
Consensus pattern (20 bp):
TTTTTAATTCACTTAATTTG
Found at i:521316 original size:22 final size:22
Alignment explanation
Indices: 521291--521333 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
521281 GCAAAAAAAA
*
521291 TTGTAATTTTTTTACTGTTTTG
1 TTGTAATTTTCTTACTGTTTTG
* *
521313 TTGTTATTTTCTTATTGTTTT
1 TTGTAATTTTCTTACTGTTTT
521334 TTTTTCACTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.12, C:0.05, G:0.12, T:0.72
Consensus pattern (22 bp):
TTGTAATTTTCTTACTGTTTTG
Found at i:524933 original size:3 final size:3
Alignment explanation
Indices: 524925--524961 Score: 74
Period size: 3 Copynumber: 12.3 Consensus size: 3
524915 TAATTAGTTC
524925 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
524962 TTAGGGCAAA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 34 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:525167 original size:29 final size:29
Alignment explanation
Indices: 525107--525167 Score: 70
Period size: 29 Copynumber: 2.1 Consensus size: 29
525097 AACTTGGCTC
* * *
525107 AAATTTAATTTAAATAATAAAATTTTTTA
1 AAATTTAATTTAAATAATAAAATATATGA
*
525136 AAATTTAAATTT-AATTATAAAATATATGA
1 AAATTT-AATTTAAATAATAAAATATATGA
525165 AAA
1 AAA
525168 ATCAACTAAA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
29 22 0.81
30 5 0.19
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.43
Consensus pattern (29 bp):
AAATTTAATTTAAATAATAAAATATATGA
Found at i:525921 original size:3 final size:3
Alignment explanation
Indices: 525913--525958 Score: 92
Period size: 3 Copynumber: 15.3 Consensus size: 3
525903 AGTAAGTAGT
525913 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
525959 ATATAAAGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 43 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:526798 original size:14 final size:14
Alignment explanation
Indices: 526779--526811 Score: 66
Period size: 14 Copynumber: 2.4 Consensus size: 14
526769 AGAGGTTTAT
526779 TTTTTAATTTTGGC
1 TTTTTAATTTTGGC
526793 TTTTTAATTTTGGC
1 TTTTTAATTTTGGC
526807 TTTTT
1 TTTTT
526812 CTTTATGTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.12, C:0.06, G:0.12, T:0.70
Consensus pattern (14 bp):
TTTTTAATTTTGGC
Found at i:537826 original size:18 final size:18
Alignment explanation
Indices: 537789--537827 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
537779 TAACCGGTTC
*
537789 AATTAAAAAATTATTAAA
1 AATTAAAAAATTATAAAA
537807 AATTCAAAAAATT-TAAAA
1 AATT-AAAAAATTATAAAA
537825 AAT
1 AAT
537828 ATATTCAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (18 bp):
AATTAAAAAATTATAAAA
Found at i:538259 original size:6 final size:6
Alignment explanation
Indices: 538248--538293 Score: 92
Period size: 6 Copynumber: 7.7 Consensus size: 6
538238 AGACATGGCG
538248 CAGGCA CAGGCA CAGGCA CAGGCA CAGGCA CAGGCA CAGGCA CAGG
1 CAGGCA CAGGCA CAGGCA CAGGCA CAGGCA CAGGCA CAGGCA CAGG
538294 GTACTCAGCT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.33, C:0.33, G:0.35, T:0.00
Consensus pattern (6 bp):
CAGGCA
Found at i:542382 original size:24 final size:24
Alignment explanation
Indices: 542332--542382 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
542322 AAACCCTAAT
* *
542332 TTTTTTTTCTCCTTTTTCATTCTC
1 TTTTTCTTCTCCTATTTCATTCTC
*
542356 TTTTTCTTCT-CTATTTCGTTCTAC
1 TTTTTCTTCTCCTATTTCATTCT-C
542380 TTT
1 TTT
542383 GATCTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.06, C:0.24, G:0.02, T:0.69
Consensus pattern (24 bp):
TTTTTCTTCTCCTATTTCATTCTC
Found at i:542394 original size:263 final size:263
Alignment explanation
Indices: 541892--542421 Score: 924
Period size: 263 Copynumber: 2.0 Consensus size: 263
541882 AATCTATCAA
* * *
541892 TTTAATCCCAAATACTTAAATTATTCAACATGAGCAACATCTAAAAATTCAGTATTTTCTAAAAT
1 TTTATTCCCAAATACTTAAATTATTCAACATGAACAACATCTAAAAATTCAATATTTTCTAAAAT
541957 TTCAACATAGGTTAAGTAGTATTTAATACTAGGATTCTAAAAACATAAAAATTACAAGAAAAAGG
66 TTCAACATAGGTTAAGTAGTATTTAATACTAGGATTCTAAAAACATAAAAATTACAAGAAAAAGG
*
542022 ACTAAATTGACTTACCAATTAAGCTTTGAACCCTTGAAAACCCTAATTTTTTTCCTCCTTTTTCT
131 ACTAAATTGACTTACCAATTAAGCTTTAAACCCTTGAAAACCCTAATTTTTTTCCTCCTTTTTCT
* *
542087 TTCTCTCTTTTTCTTCTCTATTTCGTTCTACTTTGTTCTTTTTTTTTCTATT-TTTTTCTTTCAT
196 ATCTCTCTTTTTCTTCTCTATTTCGTTCTACTTTGATC-TTTTTTTTCTATTCTTTTTCTTTCAT
542151 TTAT
260 TTAT
*
542155 TTTATTCCCAAATACTTAAATTATTCAACATGAACAACATCTAAAAATTCAATATTTTCTTAAAT
1 TTTATTCCCAAATACTTAAATTATTCAACATGAACAACATCTAAAAATTCAATATTTTCTAAAAT
542220 TTCAACATAGGTTAAGTAGTATTTAATACTAGGATTCTAAAAACATAAAAATTACAAGAAAATA-
66 TTCAACATAGGTTAAGTAGTATTTAATACTAGGATTCTAAAAACATAAAAATTACAAGAAAA-AG
* *
542284 GACTAAATTGACTTACCAATTAAGTTTTAAACCCTTGAAAACCCTAATTTTTTTTTCTCCTTTTT
130 GACTAAATTGACTTACCAATTAAGCTTTAAACCCTTGAAAACCCTAA-TTTTTTTCCTCCTTTTT
542349 C-AT-TCTCTTTTTCTTCTCTATTTCGTTCTACTTTGATCTTTTTTTTCTATTCTTTTTCTTTCA
194 CTATCTCTCTTTTTCTTCTCTATTTCGTTCTACTTTGATCTTTTTTTTCTATTCTTTTTCTTTCA
542412 TTTAT
259 TTTAT
542417 TTTAT
1 TTTAT
542422 GTTTTAATTA
Statistics
Matches: 255, Mismatches: 9, Indels: 7
0.94 0.03 0.03
Matches are distributed among these distances:
261 13 0.05
262 55 0.22
263 169 0.66
264 18 0.07
ACGTcount: A:0.32, C:0.17, G:0.06, T:0.45
Consensus pattern (263 bp):
TTTATTCCCAAATACTTAAATTATTCAACATGAACAACATCTAAAAATTCAATATTTTCTAAAAT
TTCAACATAGGTTAAGTAGTATTTAATACTAGGATTCTAAAAACATAAAAATTACAAGAAAAAGG
ACTAAATTGACTTACCAATTAAGCTTTAAACCCTTGAAAACCCTAATTTTTTTCCTCCTTTTTCT
ATCTCTCTTTTTCTTCTCTATTTCGTTCTACTTTGATCTTTTTTTTCTATTCTTTTTCTTTCATT
TAT
Found at i:549146 original size:23 final size:23
Alignment explanation
Indices: 549076--549160 Score: 108
Period size: 21 Copynumber: 3.9 Consensus size: 23
549066 CCTGATCAGT
549076 ATACGACACAT-AAGTGCCTGA-
1 ATACGACACATAAAGTGCCTGAG
** *
549097 A-ACGACACACGAGGTGCCT--G
1 ATACGACACATAAAGTGCCTGAG
549117 ATACGACACATAAAGTGCCTGAG
1 ATACGACACATAAAGTGCCTGAG
549140 ATACGACACATAAAGTGCCTG
1 ATACGACACATAAAGTGCCTG
549161 GTCGGCAAAG
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
20 9 0.17
21 23 0.43
23 22 0.41
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.16
Consensus pattern (23 bp):
ATACGACACATAAAGTGCCTGAG
Found at i:549158 original size:44 final size:41
Alignment explanation
Indices: 549076--549160 Score: 116
Period size: 44 Copynumber: 2.0 Consensus size: 41
549066 CCTGATCAGT
* *
549076 ATACGACACATAAGTGCCTGAAACGACACACGAGGTGCCTG
1 ATACGACACATAAGTGCCTGAAACGACACACAAAGTGCCTG
*
549117 ATACGACACATAAAGTGCCTGAGATACGACACATAAAGTGCCTG
1 ATACGACACAT-AAGTGCCTGA-A-ACGACACACAAAGTGCCTG
549161 GTCGGCAAAG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
41 11 0.29
42 10 0.26
43 1 0.03
44 16 0.42
ACGTcount: A:0.36, C:0.25, G:0.22, T:0.16
Consensus pattern (41 bp):
ATACGACACATAAGTGCCTGAAACGACACACAAAGTGCCTG
Found at i:549462 original size:3 final size:3
Alignment explanation
Indices: 549454--549488 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
549444 TAATTCACCC
*
549454 TAA TAA TAA TAA TAA TAA TAA TAA TAA TGA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
549489 CTACTTACCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:550192 original size:19 final size:18
Alignment explanation
Indices: 550159--550205 Score: 51
Period size: 19 Copynumber: 2.6 Consensus size: 18
550149 CTGTTTCTTC
* *
550159 TCTGTTTCGTCTCTTCTAT
1 TCTGTTTCTTTTCTTC-AT
*
550178 TCTGTTTCTTTTCTTCCT
1 TCTGTTTCTTTTCTTCAT
550196 T-TGTTTCTTT
1 TCTGTTTCTTT
550206 CTTTTATTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 9 0.36
18 2 0.08
19 14 0.56
ACGTcount: A:0.02, C:0.23, G:0.09, T:0.66
Consensus pattern (18 bp):
TCTGTTTCTTTTCTTCAT
Found at i:554920 original size:20 final size:20
Alignment explanation
Indices: 554883--554934 Score: 50
Period size: 20 Copynumber: 2.6 Consensus size: 20
554873 TTTTATCTTG
* * *
554883 AACCTCAAACCCTGAACTCA
1 AACCTCGAACTCTAAACTCA
**
554903 AACCTCGAACTCTAAACTTG
1 AACCTCGAACTCTAAACTCA
*
554923 AGCCTCGAACTC
1 AACCTCGAACTC
554935 CGAACCCTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.35, C:0.37, G:0.10, T:0.19
Consensus pattern (20 bp):
AACCTCGAACTCTAAACTCA
Found at i:555837 original size:19 final size:19
Alignment explanation
Indices: 555786--555839 Score: 58
Period size: 19 Copynumber: 2.9 Consensus size: 19
555776 TTTATTTATG
* *
555786 AAATAGAAAACTGAAA-TT
1 AAATTGAAAACTTAAATTT
*
555804 AAATT-AAACAATTAAATTT
1 AAATTGAAA-ACTTAAATTT
555823 AAATTGAAAACTTAAAT
1 AAATTGAAAACTTAAAT
555840 GGAAAAAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 5
0.76 0.11 0.13
Matches are distributed among these distances:
17 3 0.10
18 9 0.31
19 14 0.48
20 3 0.10
ACGTcount: A:0.59, C:0.06, G:0.06, T:0.30
Consensus pattern (19 bp):
AAATTGAAAACTTAAATTT
Found at i:562384 original size:62 final size:62
Alignment explanation
Indices: 562287--562412 Score: 227
Period size: 62 Copynumber: 2.0 Consensus size: 62
562277 AATTTAGAAC
562287 TACCAGGATATTAATGGCATGCCATTAAGGAACTTTAGCGCGCTCTCTGA-TTATTAGCACGT
1 TACCAGGATATTAATGGCATGCCATTAAGGAACTTTAGCGCGCTCTCTGAGTT-TTAGCACGT
*
562349 TACCAGGATATTAGTGGCATGCCATTAAGGAACTTTAGCGCGCTCTCTGAGTTTTAGCACGT
1 TACCAGGATATTAATGGCATGCCATTAAGGAACTTTAGCGCGCTCTCTGAGTTTTAGCACGT
562411 TA
1 TA
562413 GTGCTCTCTG
Statistics
Matches: 62, Mismatches: 1, Indels: 2
0.95 0.02 0.03
Matches are distributed among these distances:
62 60 0.97
63 2 0.03
ACGTcount: A:0.26, C:0.21, G:0.22, T:0.31
Consensus pattern (62 bp):
TACCAGGATATTAATGGCATGCCATTAAGGAACTTTAGCGCGCTCTCTGAGTTTTAGCACGT
Found at i:562421 original size:27 final size:25
Alignment explanation
Indices: 562390--562460 Score: 99
Period size: 25 Copynumber: 2.8 Consensus size: 25
562380 ACTTTAGCGC
* *
562390 GCTCTCTGAGTTTTAGCACGTTAGT
1 GCTCTCTGACTATTAGCACGTTAGT
*
562415 GCTCTCTGACTATTAGCACGTTGGT
1 GCTCTCTGACTATTAGCACGTTAGT
562440 GCTCTCTGA-TATTTAGCACGT
1 GCTCTCTGACTA-TTAGCACGT
562461 AATAATGCAC
Statistics
Matches: 42, Mismatches: 3, Indels: 2
0.89 0.06 0.04
Matches are distributed among these distances:
24 2 0.05
25 40 0.95
ACGTcount: A:0.17, C:0.23, G:0.23, T:0.38
Consensus pattern (25 bp):
GCTCTCTGACTATTAGCACGTTAGT
Found at i:563830 original size:30 final size:30
Alignment explanation
Indices: 563795--563855 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
563785 TTCAACTCTC
* *
563795 TAATTTCACTCAAATACTTAAATTTTTAAT
1 TAATTTCACTCAAATACCTAAATTTTGAAT
*
563825 TAATTTCACTCAAATCCCTAAATTTTGAAT
1 TAATTTCACTCAAATACCTAAATTTTGAAT
563855 T
1 T
563856 TTTTACAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.38, C:0.16, G:0.02, T:0.44
Consensus pattern (30 bp):
TAATTTCACTCAAATACCTAAATTTTGAAT
Found at i:564170 original size:24 final size:24
Alignment explanation
Indices: 564120--564170 Score: 59
Period size: 24 Copynumber: 2.1 Consensus size: 24
564110 AAACCCTAAT
* *
564120 TTTTTTTTCTCCTTTTTCATTCTC
1 TTTTTCTTCTCCTATTTCATTCTC
*
564144 TTTTTCTTCT-CTATTTCGTTCTAC
1 TTTTTCTTCTCCTATTTCATTCT-C
564168 TTT
1 TTT
564171 GATCTTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 10 0.43
24 13 0.57
ACGTcount: A:0.06, C:0.24, G:0.02, T:0.69
Consensus pattern (24 bp):
TTTTTCTTCTCCTATTTCATTCTC
Found at i:570585 original size:20 final size:21
Alignment explanation
Indices: 570562--570604 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
570552 TTGAACCCCA
570562 AACCCAT-AACCCAAACCTCG
1 AACCCATGAACCCAAACCTCG
* *
570582 AA-CCTTGAACCCAAATCTCG
1 AACCCATGAACCCAAACCTCG
570602 AAC
1 AAC
570605 TCTAAACCTA
Statistics
Matches: 19, Mismatches: 2, Indels: 3
0.79 0.08 0.12
Matches are distributed among these distances:
19 3 0.16
20 16 0.84
ACGTcount: A:0.40, C:0.40, G:0.07, T:0.14
Consensus pattern (21 bp):
AACCCATGAACCCAAACCTCG
Found at i:570612 original size:20 final size:19
Alignment explanation
Indices: 570569--570647 Score: 68
Period size: 20 Copynumber: 3.9 Consensus size: 19
570559 CCAAACCCAT
*
570569 AACCCAAACCTCGAACCTTG
1 AACCCAAATCTCGAACC-TG
*
570589 AACCCAAATCTCGAACTCTA
1 AACCCAAATCTCGAAC-CTG
* * * *
570609 AACCTAAGTCTCAAACCCCG
1 AACCCAAATCTCGAA-CCTG
570629 AACCCTAAATCTCGAACCT
1 AACCC-AAATCTCGAACCT
570648 CATAGTTAAT
Statistics
Matches: 45, Mismatches: 11, Indels: 6
0.73 0.18 0.10
Matches are distributed among these distances:
20 35 0.78
21 10 0.22
ACGTcount: A:0.37, C:0.38, G:0.08, T:0.18
Consensus pattern (19 bp):
AACCCAAATCTCGAACCTG
Found at i:572516 original size:19 final size:19
Alignment explanation
Indices: 572492--572529 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
572482 AAAACTGAAA
572492 TTAAATT-AAACAATTAAAT
1 TTAAATTGAAA-AATTAAAT
572511 TTAAATTGAAAAATTAAAT
1 TTAAATTGAAAAATTAAAT
572530 GGAAAAAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 15 0.83
20 3 0.17
ACGTcount: A:0.58, C:0.03, G:0.03, T:0.37
Consensus pattern (19 bp):
TTAAATTGAAAAATTAAAT
Found at i:578002 original size:43 final size:44
Alignment explanation
Indices: 577941--578027 Score: 167
Period size: 43 Copynumber: 2.0 Consensus size: 44
577931 ACGAGTAGGT
577941 GTCGAAACCGTTTTTTTGAAAAAAC-AAAAATTTAGTTGTCGAC
1 GTCGAAACCGTTTTTTTGAAAAAACAAAAAATTTAGTTGTCGAC
577984 GTCGAAACCGTTTTTTTGAAAAAACAAAAAATTTAGTTGTCGAC
1 GTCGAAACCGTTTTTTTGAAAAAACAAAAAATTTAGTTGTCGAC
578028 TTTTAGAAAA
Statistics
Matches: 43, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
43 25 0.58
44 18 0.42
ACGTcount: A:0.38, C:0.14, G:0.16, T:0.32
Consensus pattern (44 bp):
GTCGAAACCGTTTTTTTGAAAAAACAAAAAATTTAGTTGTCGAC
Found at i:582299 original size:24 final size:24
Alignment explanation
Indices: 582271--582317 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
582261 CTATTAAAAC
*
582271 GTGATTGATAATTTATCATTAATG
1 GTGATTGATAATTAATCATTAATG
* *
582295 GTGATTGGTTATTAATCATTAAT
1 GTGATTGATAATTAATCATTAAT
582318 TTTTCATGGA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.32, C:0.04, G:0.17, T:0.47
Consensus pattern (24 bp):
GTGATTGATAATTAATCATTAATG
Found at i:589724 original size:15 final size:14
Alignment explanation
Indices: 589700--589729 Score: 51
Period size: 15 Copynumber: 2.1 Consensus size: 14
589690 GCTTTGAGTC
589700 AAAAAAAAAAAGAA
1 AAAAAAAAAAAGAA
589714 AAAAGAAAAAAAGAA
1 AAAA-AAAAAAAGAA
589729 A
1 A
589730 GTGGAGAGGC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.27
15 11 0.73
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGAA
Found at i:591161 original size:89 final size:89
Alignment explanation
Indices: 590993--591467 Score: 684
Period size: 89 Copynumber: 5.3 Consensus size: 89
590983 AAAAGAAAAT
* * *
590993 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATAAAAAATAAGCAGATATTGTCTTCCCATATT
1 AGATCTTGTCTTCATGTATTGGCGTAAAGTAGATAAAAAA-AAGCAGATCTTGTCTTCCCATACT
*
591058 GGTGGCGAAGTAGATCGAATAAAGC
65 GGTGGCGAAGTAGATCGAAGAAAGC
*
591083 AGATCTTGTCTTCATGTATTGGCGTAAAGTACATAAAAAAAAGCAGATCTTGTCTTCCCATACTG
1 AGATCTTGTCTTCATGTATTGGCGTAAAGTAGATAAAAAAAAGCAGATCTTGTCTTCCCATACTG
* *
591148 GCGGCGAAGTAGATCGAAGAAAAC
66 GTGGCGAAGTAGATCGAAGAAAGC
* * *
591172 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAAACAGCAGATCTTGTCTTCCCATACTG
1 AGATCTTGTCTTCATGTATTGGCGTAAAGTAGATAAAAAAAAGCAGATCTTGTCTTCCCATACTG
*
591237 GTGGCGAAGTAGATCGAAGAAAAC
66 GTGGCGAAGTAGATCGAAGAAAGC
* *
591261 AGATCTTGTCTTCATGTATTGGCGTGAAGTAGATAAAAAACAAGCAGATCTTGTCTTCCCATATT
1 AGATCTTGTCTTCATGTATTGGCGTAAAGTAGATAAAAAA-AAGCAGATCTTGTCTTCCCATACT
* *
591326 GGTGGTGAAGTAGATCAAAGAAAGC
65 GGTGGCGAAGTAGATCGAAGAAAGC
* ** * *
591351 AGATCTTGTCTTCATGTATTGGCGTGAAA-TAGATCAAAATTAGTAGATCTTGTGTTCCCATACT
1 AGATCTTGTCTTCATGTATTGGCGT-AAAGTAGATAAAAAAAAGCAGATCTTGTCTTCCCATACT
* ** *
591415 AGTGGC-AGAGTAGATAAAAGATAGC
65 GGTGGCGA-AGTAGATCGAAGAAAGC
591440 AGATCTTGTCTTCATGTATTGGCGTAAA
1 AGATCTTGTCTTCATGTATTGGCGTAAA
591468 ATCAAAGATC
Statistics
Matches: 353, Mismatches: 29, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
88 4 0.01
89 231 0.65
90 116 0.33
91 2 0.01
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (89 bp):
AGATCTTGTCTTCATGTATTGGCGTAAAGTAGATAAAAAAAAGCAGATCTTGTCTTCCCATACTG
GTGGCGAAGTAGATCGAAGAAAGC
Found at i:591310 original size:179 final size:178
Alignment explanation
Indices: 590984--591467 Score: 727
Period size: 179 Copynumber: 2.7 Consensus size: 178
590974 AGCAGGTTGA
* * *
590984 AAAGAAAATAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATAAAAAATAAGCAGATATTGTCT
1 AAAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAAA-AAGCAGATCTTGTCT
* *
591049 TCCCATATTGGTGGCGAAGTAGATCGAATAAAGCAGATCTTGTCTTCATGTATTGGCGTAAAGTA
65 TCCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTAAAGTA
591114 CATAAAAAAAAGCAGATCTTGTCTTCCCATACTGGCGGCGAAGTAGATC
130 CATAAAAAAAAGCAGATCTTGTCTTCCCATACTGGCGGCGAAGTAGATC
* *
591163 GAAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAAACAGCAGATCTTGTCTT
1 AAAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAAAAAGCAGATCTTGTCTT
* * *
591228 CCCATACTGGTGGCGAAGTAGATCGAAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAG
66 CCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTAAAGTAC
* * *
591293 ATAAAAAACAAGCAGATCTTGTCTTCCCATATTGGTGGTGAAGTAGATC
131 ATAAAAAA-AAGCAGATCTTGTCTTCCCATACTGGCGGCGAAGTAGATC
* * ** * *
591342 AAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTGAAATAGATCAAAATTAGTAGATCTTGTGTT
1 AAAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAAAAAGCAGATCTTGTCTT
* ** *
591407 CCCATACTAGTGGC-AGAGTAGATAAAAGATAGCAGATCTTGTCTTCATGTATTGGCGTAAA
66 CCCATACTGGTGGCGA-AGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTAAA
591468 ATCAAAGATC
Statistics
Matches: 277, Mismatches: 26, Indels: 4
0.90 0.08 0.01
Matches are distributed among these distances:
178 83 0.30
179 194 0.70
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (178 bp):
AAAGAAAACAGATCTTGTCTTCATGTATTGGCGTGAAGTAGATCAAAAAAAGCAGATCTTGTCTT
CCCATACTGGTGGCGAAGTAGATCGAAGAAAGCAGATCTTGTCTTCATGTATTGGCGTAAAGTAC
ATAAAAAAAAGCAGATCTTGTCTTCCCATACTGGCGGCGAAGTAGATC
Found at i:592368 original size:23 final size:23
Alignment explanation
Indices: 592325--592371 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
592315 TGGACAGTGT
* *
592325 AAAAGAGATGAAAATAGAAGGGG
1 AAAAGAGAAGAAAATAAAAGGGG
592348 AAAAGAGAAG-AAATACAAAGGGG
1 AAAAGAGAAGAAAATA-AAAGGGG
592371 A
1 A
592372 TTTGTTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 5 0.24
23 16 0.76
ACGTcount: A:0.60, C:0.02, G:0.32, T:0.06
Consensus pattern (23 bp):
AAAAGAGAAGAAAATAAAAGGGG
Found at i:592450 original size:25 final size:24
Alignment explanation
Indices: 592422--592468 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
592412 ACTTTTTTTG
592422 TTTATATATTT-ATTTTTTATTTTCT
1 TTTAT-TATTTCA-TTTTTATTTTCT
*
592447 TTTATTTTTTCATTTTTATTTT
1 TTTATTATTTCATTTTTATTTT
592469 ACCTAAAATA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.17, C:0.04, G:0.00, T:0.79
Consensus pattern (24 bp):
TTTATTATTTCATTTTTATTTTCT
Found at i:598915 original size:103 final size:100
Alignment explanation
Indices: 598775--598961 Score: 243
Period size: 103 Copynumber: 1.8 Consensus size: 100
598765 TACGTTATAT
* * * *
598775 AAAAATTACATTAAAAAAATCACAAAACACATAACTAAGCACTAACAATTTATATAACTTAA-TC
1 AAAAAATACATTAAAAAAAGCACAAAACACATAACTAAACACTAACAA-TT-TATAACCTAACTC
598839 ATAAATTACTAACAAAATAACTATAGAATTATTTTTG
64 ATAAATTACTAACAAAATAACTATAGAATTATTTTTG
* * *
598876 AAAAAATACATTACTAAAAAAGCACAAAACTC-TATACTAAACACTAACTATTTGTAACCTAATC
1 AAAAAATACATTA--AAAAAAGCACAAAACACATA-ACTAAACACTAACAATTTATAACCTAA-C
598940 TCATAAATTACTAACAAAATAA
62 TCATAAATTACTAACAAAATAA
598962 ATAACTATAA
Statistics
Matches: 74, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
101 20 0.27
102 4 0.05
103 50 0.68
ACGTcount: A:0.53, C:0.16, G:0.03, T:0.28
Consensus pattern (100 bp):
AAAAAATACATTAAAAAAAGCACAAAACACATAACTAAACACTAACAATTTATAACCTAACTCAT
AAATTACTAACAAAATAACTATAGAATTATTTTTG
Found at i:600748 original size:21 final size:21
Alignment explanation
Indices: 600723--600765 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
600713 CTGGTTGTTA
* *
600723 AAGTACAAGTTTAGAATAGTT
1 AAGTAAAAGTTCAGAATAGTT
*
600744 AAGTAAAAGTTCGGAATAGTT
1 AAGTAAAAGTTCAGAATAGTT
600765 A
1 A
600766 GGTATCTATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.44, C:0.05, G:0.21, T:0.30
Consensus pattern (21 bp):
AAGTAAAAGTTCAGAATAGTT
Found at i:600885 original size:31 final size:31
Alignment explanation
Indices: 600850--600910 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
600840 ATAAAAGCAT
* *
600850 ATTGCTCATATGGGTGTATTGTCATTTAAGG
1 ATTGCTCAAATGGGTGTAATGTCATTTAAGG
600881 ATTGCTCAAATGGGTGTAATGTCATTTAAG
1 ATTGCTCAAATGGGTGTAATGTCATTTAAG
600911 AATATTTAGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.26, C:0.10, G:0.25, T:0.39
Consensus pattern (31 bp):
ATTGCTCAAATGGGTGTAATGTCATTTAAGG
Found at i:610359 original size:17 final size:17
Alignment explanation
Indices: 610334--610369 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
610324 ATTTTTGAAC
*
610334 TAGTGAATTTTGTGATT
1 TAGTAAATTTTGTGATT
610351 TAGTAAATTTTGTGATT
1 TAGTAAATTTTGTGATT
610368 TA
1 TA
610370 AAAAAAGAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.28, C:0.00, G:0.19, T:0.53
Consensus pattern (17 bp):
TAGTAAATTTTGTGATT
Found at i:611671 original size:46 final size:46
Alignment explanation
Indices: 611592--611822 Score: 374
Period size: 46 Copynumber: 5.0 Consensus size: 46
611582 CATGGCAAAA
* *
611592 TGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAATGAAGAAAACCATACTGAGT
* *
611638 TGTGAAAAGTAGGTGTGGTATTTCGAT-ATAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAATGA-AGAAAACCATACTGAGT
* *
611684 TGTGAAAAGTAGGTATGATTTTTCAATGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAATGAAGAAAACCATACTGAGT
* *
611730 TGTGAAAAGTAGGTATGATTTTTCAATGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAATGAAGAAAACCATACTGAGT
611776 TGTGAAAAGTAGGTATGGTATTTCAATGAAGAAAACCATACTGAGT
1 TGTGAAAAGTAGGTATGGTATTTCAATGAAGAAAACCATACTGAGT
611822 T
1 T
611823 ATAGCAATGT
Statistics
Matches: 173, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
45 1 0.01
46 171 0.99
47 1 0.01
ACGTcount: A:0.37, C:0.09, G:0.24, T:0.30
Consensus pattern (46 bp):
TGTGAAAAGTAGGTATGGTATTTCAATGAAGAAAACCATACTGAGT
Found at i:613587 original size:30 final size:30
Alignment explanation
Indices: 613551--613608 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
613541 CTGGCTATTT
* *
613551 CCACACGGGTTGGCCACACGCCCCTGTGAG
1 CCACACGGGCTGGCCACACGCCCATGTGAG
613581 CCACACGGGCTGGCCACACGCCCATGTG
1 CCACACGGGCTGGCCACACGCCCATGTG
613609 CCTGCCCGTG
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.17, C:0.41, G:0.29, T:0.12
Consensus pattern (30 bp):
CCACACGGGCTGGCCACACGCCCATGTGAG
Found at i:619335 original size:6 final size:6
Alignment explanation
Indices: 619324--619368 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
619314 AAAGCCACCT
619324 GATTCA GATTCA GATTCA GATTCA GATTCA GATTCA GATTCA GAT
1 GATTCA GATTCA GATTCA GATTCA GATTCA GATTCA GATTCA GAT
619369 GGAGAGTGCA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Consensus pattern (6 bp):
GATTCA
Found at i:619387 original size:12 final size:12
Alignment explanation
Indices: 619372--619397 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
619362 TTCAGATGGA
619372 GAGTGCATTTGC
1 GAGTGCATTTGC
619384 GAGTGCATTTGC
1 GAGTGCATTTGC
619396 GA
1 GA
619398 TTTCTGTGAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.19, C:0.15, G:0.35, T:0.31
Consensus pattern (12 bp):
GAGTGCATTTGC
Found at i:625809 original size:6 final size:6
Alignment explanation
Indices: 625798--625824 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
625788 AAAGCCACCT
625798 GATTCA GATTCA GATTCA GATTCA GAT
1 GATTCA GATTCA GATTCA GATTCA GAT
625825 GGAGAGTGCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (6 bp):
GATTCA
Found at i:630557 original size:20 final size:20
Alignment explanation
Indices: 630528--630568 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
630518 TTCAATTTAA
630528 GAAAAAATCAAGTGGGTGTC
1 GAAAAAATCAAGTGGGTGTC
*
630548 GAAAATATCAAGTGGGTGTC
1 GAAAAAATCAAGTGGGTGTC
630568 G
1 G
630569 CGACATTGAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.37, C:0.10, G:0.32, T:0.22
Consensus pattern (20 bp):
GAAAAAATCAAGTGGGTGTC
Found at i:652870 original size:29 final size:30
Alignment explanation
Indices: 652813--652884 Score: 78
Period size: 29 Copynumber: 2.5 Consensus size: 30
652803 GTATTATTCA
652813 TAAA-TTTAAAATTTAATCTTTATA-CTTT
1 TAAATTTTAAAATTTAATCTTTATATCTTT
** * *
652841 TATTTTTTAAAATTTAAT-TTATCTATTTTT
1 TAAATTTTAAAATTTAATCTT-TATATCTTT
652871 TAAATTTTAAAATT
1 TAAATTTTAAAATT
652885 GAAGTAAAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
28 4 0.11
29 16 0.46
30 15 0.43
ACGTcount: A:0.38, C:0.04, G:0.00, T:0.58
Consensus pattern (30 bp):
TAAATTTTAAAATTTAATCTTTATATCTTT
Found at i:656474 original size:90 final size:91
Alignment explanation
Indices: 656342--656539 Score: 274
Period size: 90 Copynumber: 2.2 Consensus size: 91
656332 AAAAAAAAAG
* * *
656342 TTAAGTCCCTACTTTTTTTTTTGCACTCATTTGAGTATTTGAACTTTCAAAATGCATTAAAAAAG
1 TTAAGCCCCTACTTTTTTTTTTGCACTCAATTGAGTACTTGAACTTTCAAAATG-ATTAAAAAAG
* * *
656407 -CCCTCAAATTTTTTCGAAAAAAGTAA
65 ACCCTCAAACTTTTTCAAAAAAAGCAA
* *
656433 TTAAGCCCCTA-TTTTTTTTTTGCACTCAATTGAGTACTTGAACTTTCAAAATGGTTCAAAAAGA
1 TTAAGCCCCTACTTTTTTTTTTGCACTCAATTGAGTACTTGAACTTTCAAAATGATTAAAAAAGA
*
656497 CCCTCAAGCTTTTTCAAAAAAAGCAA
66 CCCTCAAACTTTTTCAAAAAAAGCAA
* *
656523 TTAAGCCCATGCTTTTT
1 TTAAGCCCCTACTTTTT
656540 ATTAAAAATT
Statistics
Matches: 94, Mismatches: 11, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
89 8 0.09
90 71 0.76
91 15 0.16
ACGTcount: A:0.33, C:0.19, G:0.11, T:0.38
Consensus pattern (91 bp):
TTAAGCCCCTACTTTTTTTTTTGCACTCAATTGAGTACTTGAACTTTCAAAATGATTAAAAAAGA
CCCTCAAACTTTTTCAAAAAAAGCAA
Found at i:656621 original size:19 final size:20
Alignment explanation
Indices: 656589--656628 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
656579 AATAAAAGCT
* *
656589 ATAAATATTATTAAATTTTA
1 ATAAAAATTATTAAATATTA
656609 ATAAAAATT-TTAAATATTA
1 ATAAAAATTATTAAATATTA
656628 A
1 A
656629 AAATTAGAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 10 0.56
20 8 0.44
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
ATAAAAATTATTAAATATTA
Found at i:656649 original size:10 final size:9
Alignment explanation
Indices: 656620--656667 Score: 53
Period size: 9 Copynumber: 5.2 Consensus size: 9
656610 TAAAAATTTT
656620 AAATATTAAA
1 AAATA-TAAA
* *
656630 AATTAGAAA
1 AAATATAAA
656639 AAATAT-AA
1 AAATATAAA
656647 AAATCATAAA
1 AAAT-ATAAA
656657 AAATATAAA
1 AAATATAAA
656666 AA
1 AA
656668 TTGTAAAATT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
8 6 0.19
9 16 0.50
10 10 0.31
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (9 bp):
AAATATAAA
Found at i:656649 original size:18 final size:18
Alignment explanation
Indices: 656620--656669 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
656610 TAAAAATTTT
656620 AAATATTAAAAATTAGAAA
1 AAATA-TAAAAATTAGAAA
* *
656639 AAATATAAAAATCATAAA
1 AAATATAAAAATTAGAAA
656657 AAATATAAAAATT
1 AAATATAAAAATT
656670 GTAAAATTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 23 0.82
19 5 0.18
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (18 bp):
AAATATAAAAATTAGAAA
Found at i:656674 original size:18 final size:18
Alignment explanation
Indices: 656636--656696 Score: 77
Period size: 18 Copynumber: 3.3 Consensus size: 18
656626 TAAAAATTAG
*
656636 AAAAAATATAAAAATCAT
1 AAAAAATATAAAAATCGT
*
656654 AAAAAATATAAAAATTGT
1 AAAAAATATAAAAATCGT
**
656672 AAAATTTTATAAAAATCGT
1 AAAA-AATATAAAAATCGT
656691 AAAAAA
1 AAAAAA
656697 ATTATAAAAT
Statistics
Matches: 35, Mismatches: 7, Indels: 2
0.80 0.16 0.05
Matches are distributed among these distances:
18 20 0.57
19 15 0.43
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.26
Consensus pattern (18 bp):
AAAAAATATAAAAATCGT
Found at i:656674 original size:27 final size:25
Alignment explanation
Indices: 656609--656675 Score: 62
Period size: 27 Copynumber: 2.6 Consensus size: 25
656599 TTAAATTTTA
* * *
656609 ATAAAAATTTTAAATATTAAAAATT
1 ATAAAAATTATAAAAATTAAAAAAT
* *
656634 AGAAAAAATATAAAAATCATAAAAAAT
1 ATAAAAATTATAAAAAT--TAAAAAAT
*
656661 ATAAAAATTGTAAAA
1 ATAAAAATTATAAAA
656676 TTTTATAAAA
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
25 13 0.41
27 19 0.59
ACGTcount: A:0.67, C:0.01, G:0.03, T:0.28
Consensus pattern (25 bp):
ATAAAAATTATAAAAATTAAAAAAT
Found at i:656675 original size:16 final size:16
Alignment explanation
Indices: 656620--656676 Score: 51
Period size: 18 Copynumber: 3.2 Consensus size: 16
656610 TAAAAATTTT
656620 AAATATTAAAAATTAGAAA
1 AAATA-TAAAAATT-G-AA
*
656639 AAATATAAAAATCATAAA
1 AAATATAAAAAT--TGAA
*
656657 AAATATAAAAATTGTA
1 AAATATAAAAATTGAA
656673 AAAT
1 AAAT
656677 TTTATAAAAA
Statistics
Matches: 33, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
16 6 0.18
18 21 0.64
19 5 0.15
20 1 0.03
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.26
Consensus pattern (16 bp):
AAATATAAAAATTGAA
Found at i:656699 original size:30 final size:30
Alignment explanation
Indices: 656663--656785 Score: 121
Period size: 30 Copynumber: 4.1 Consensus size: 30
656653 TAAAAAATAT
*
656663 AAAAATTGTAAAATTTTATAAAAATCGTAA
1 AAAAATTATAAAATTTTATAAAAATCGTAA
* *
656693 AAAAATTATAAAA-TATATAGAAATATTG-AA
1 AAAAATTATAAAATTTTATA-AAA-ATCGTAA
*
656723 AAAAATTATAAAATTTTAT-AAAGTCGTAA
1 AAAAATTATAAAATTTTATAAAAATCGTAA
* *
656752 GAAAATTATAAAAAATGTT-TAAAAAT-GTAA
1 AAAAATTAT--AAAATTTTATAAAAATCGTAA
656782 AAAA
1 AAAA
656786 TGTAAAGAAA
Statistics
Matches: 76, Mismatches: 10, Indels: 14
0.76 0.10 0.14
Matches are distributed among these distances:
28 2 0.03
29 18 0.24
30 38 0.50
31 18 0.24
ACGTcount: A:0.60, C:0.02, G:0.07, T:0.31
Consensus pattern (30 bp):
AAAAATTATAAAATTTTATAAAAATCGTAA
Found at i:656705 original size:10 final size:10
Alignment explanation
Indices: 656627--656735 Score: 63
Period size: 10 Copynumber: 11.3 Consensus size: 10
656617 TTTAAATATT
*
656627 AAAAATTAGA
1 AAAAATTATA
656637 AAAAA-TAT-
1 AAAAATTATA
*
656645 AAAAATCATA
1 AAAAATTATA
656655 AAAAA-TAT-
1 AAAAATTATA
*
656663 AAAAATTGTA
1 AAAAATTATA
**
656673 AAATTTTAT-
1 AAAAATTATA
656682 AAAAATCGTA-A
1 AAAAAT--TATA
656693 AAAAATTATA
1 AAAAATTATA
*
656703 AAATA-TATA
1 AAAAATTATA
*
656712 GAAATATTGA-A
1 -AAAAATT-ATA
656723 AAAAATTATA
1 AAAAATTATA
656733 AAA
1 AAA
656736 TTTTATAAAG
Statistics
Matches: 76, Mismatches: 11, Indels: 24
0.68 0.10 0.22
Matches are distributed among these distances:
8 10 0.13
9 19 0.25
10 36 0.47
11 10 0.13
12 1 0.01
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.28
Consensus pattern (10 bp):
AAAAATTATA
Found at i:656785 original size:59 final size:60
Alignment explanation
Indices: 656636--656767 Score: 159
Period size: 59 Copynumber: 2.3 Consensus size: 60
656626 TAAAAATTAG
* *
656636 AAAAAA-TAT-AAAAATCATA-AAAAA-T-ATAAAAATTGTAAAATTTTATAAAAATCGTA
1 AAAAAATTATAAAAAAT-ATAGAAAAATTGAAAAAAATTATAAAATTTTATAAAAATCGTA
* * *
656692 AAAAAATTATAAAATATATAGAAATATTGAAAAAAATTATAAAATTTTAT-AAAGTCGTA
1 AAAAAATTATAAAAAATATAGAAAAATTGAAAAAAATTATAAAATTTTATAAAAATCGTA
*
656751 AGAAAATTATAAAAAAT
1 AAAAAATTATAAAAAAT
656768 GTTTAAAAAT
Statistics
Matches: 64, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
56 6 0.09
57 6 0.09
58 9 0.14
59 24 0.38
60 19 0.30
ACGTcount: A:0.63, C:0.02, G:0.05, T:0.30
Consensus pattern (60 bp):
AAAAAATTATAAAAAATATAGAAAAATTGAAAAAAATTATAAAATTTTATAAAAATCGTA
Found at i:656828 original size:29 final size:28
Alignment explanation
Indices: 656689--656828 Score: 74
Period size: 29 Copynumber: 4.8 Consensus size: 28
656679 TATAAAAATC
*
656689 GTAAAAAAATTATAAAATATATAGAAATATT
1 GTAAAAAAATTATAAAAT-TAT-CAAAT-TT
* *
656720 G-AAAAAAATTATAAAATTTTAT-AAAGTC
1 GTAAAAAAATTATAAAA--TTATCAAATTT
* * **
656748 GTAAGAAAATTATAAAAAATGT-TTAAAAAT
1 GTAAAAAAATTAT--AAAAT-TATCAAATTT
*
656778 GT-AAAAAATGTA-AAGAAATATCAAATTT
1 GTAAAAAAAT-TATAA-AATTATCAAATTT
656806 GTAAAAAAATTATAGAAATTATC
1 GTAAAAAAATTATA-AAATTATC
656829 GTACCAAAAG
Statistics
Matches: 84, Mismatches: 12, Indels: 28
0.68 0.10 0.23
Matches are distributed among these distances:
27 3 0.04
28 13 0.15
29 35 0.42
30 24 0.29
31 8 0.10
32 1 0.01
ACGTcount: A:0.59, C:0.02, G:0.09, T:0.31
Consensus pattern (28 bp):
GTAAAAAAATTATAAAATTATCAAATTT
Found at i:657010 original size:86 final size:88
Alignment explanation
Indices: 656911--657079 Score: 211
Period size: 87 Copynumber: 1.9 Consensus size: 88
656901 AAAGAGTAGC
* * ** *
656911 GGCTTAATTGCTTTT-TTTGAA-AAATTTTGAAAATCTTTTTGATGTATTTTGAAAGTTCAAGTA
1 GGCTTAATCGCTTTTGTTTGAAGAAA-TTTGAAAACCTTTTTGATACATTTTAAAAGTTCAAGTA
*
656974 C-CTAATTGAGTG-AAAAAAGCAGG
65 CTC-AATTAAGTGCAAAAAAGCAGG
** *
656997 GGCTTAATCGCTTTTGTTTGAAGAAATTTGAGGACCTTTTTGATACATTTTAAAAGTTTAAGTAC
1 GGCTTAATCGCTTTTGTTTGAAGAAATTTGAAAACCTTTTTGATACATTTTAAAAGTTCAAGTAC
657062 TCAATTAAGTGCAAAAAA
66 TCAATTAAGTGCAAAAAA
657080 AATAGACTTA
Statistics
Matches: 70, Mismatches: 9, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
86 14 0.20
87 46 0.66
88 10 0.14
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.38
Consensus pattern (88 bp):
GGCTTAATCGCTTTTGTTTGAAGAAATTTGAAAACCTTTTTGATACATTTTAAAAGTTCAAGTAC
TCAATTAAGTGCAAAAAAGCAGG
Found at i:660406 original size:40 final size:40
Alignment explanation
Indices: 660332--660408 Score: 102
Period size: 40 Copynumber: 1.9 Consensus size: 40
660322 CGTAAATAAC
** **
660332 AATCATAAAATATAAAAATATATATGTAGGTATATATATG
1 AATCATAAAATATAAAAATATATATCAAAATATATATATG
660372 AATCATAAAATATAAAGAATATATA-CAAAATATATAT
1 AATCATAAAATATAAA-AATATATATCAAAATATATAT
660409 TTTGAAAGTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
40 24 0.75
41 8 0.25
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.32
Consensus pattern (40 bp):
AATCATAAAATATAAAAATATATATCAAAATATATATATG
Found at i:660560 original size:24 final size:24
Alignment explanation
Indices: 660510--660561 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
660500 ATATTATAAA
* * *
660510 ATATAAAAATATATATAGGTACGT
1 ATATAAAAATATACACAGGTACAT
* *
660534 ATATAAAAATATACACATGTATAT
1 ATATAAAAATATACACAGGTACAT
660558 ATAT
1 ATAT
660562 TATAAAAAAA
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:0.52, C:0.06, G:0.08, T:0.35
Consensus pattern (24 bp):
ATATAAAAATATACACAGGTACAT
Found at i:660784 original size:3 final size:3
Alignment explanation
Indices: 660776--660810 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
660766 GATAGGAGTA
*
660776 AAT AAT AAT AAT AATT AAT AAT AAT AAT GAT AAT A
1 AAT AAT AAT AAT AA-T AAT AAT AAT AAT AAT AAT A
660811 GTATTAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
3 26 0.90
4 3 0.10
ACGTcount: A:0.63, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:660796 original size:13 final size:13
Alignment explanation
Indices: 660778--660803 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
660768 TAGGAGTAAA
660778 TAATAATAATAAT
1 TAATAATAATAAT
660791 TAATAATAATAAT
1 TAATAATAATAAT
660804 GATAATAGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TAATAATAATAAT
Found at i:663908 original size:27 final size:27
Alignment explanation
Indices: 663867--663922 Score: 103
Period size: 27 Copynumber: 2.1 Consensus size: 27
663857 TGATTTCCAC
663867 TGAAAATGGTCATGAAGAACTTGAAGA
1 TGAAAATGGTCATGAAGAACTTGAAGA
*
663894 TGAAAATGGTGATGAAGAACTTGAAGA
1 TGAAAATGGTCATGAAGAACTTGAAGA
663921 TG
1 TG
663923 TTAGAGAGTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.43, C:0.05, G:0.29, T:0.23
Consensus pattern (27 bp):
TGAAAATGGTCATGAAGAACTTGAAGA
Found at i:670093 original size:33 final size:33
Alignment explanation
Indices: 670051--670121 Score: 83
Period size: 33 Copynumber: 2.2 Consensus size: 33
670041 GTTGTCCAAC
*
670051 TTGGTCATATGCG-TTAGCACCAGGCTGTG-CAGG
1 TTGGCCATATG-GATTAGCACCAGGCTGTGTC-GG
**
670084 TTGGCCATATGGATTAGCACTTGGCTGTGTCGG
1 TTGGCCATATGGATTAGCACCAGGCTGTGTCGG
670117 TTGGC
1 TTGGC
670122 TGTACATATT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
32 1 0.03
33 31 0.94
34 1 0.03
ACGTcount: A:0.15, C:0.20, G:0.34, T:0.31
Consensus pattern (33 bp):
TTGGCCATATGGATTAGCACCAGGCTGTGTCGG
Found at i:672310 original size:6 final size:6
Alignment explanation
Indices: 672295--672325 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
672285 AGGTCCACCA
*
672295 CCCATT CCCATG CCCATG CCCATG CCCATG C
1 CCCATG CCCATG CCCATG CCCATG CCCATG C
672326 TACCCATACT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.16, C:0.52, G:0.13, T:0.19
Consensus pattern (6 bp):
CCCATG
Found at i:673058 original size:33 final size:33
Alignment explanation
Indices: 673012--673087 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 33
673002 GTCATATGCG
** **
673012 TTAGCACCAGGCTGTG-CAGGTTGGCCGTATGGA
1 TTAGCACTTGGCTGTGTC-GGTTGGCCGTACAGA
* *
673045 TTAGCACTTGGCTGTGTCGGTTGGCTGTACATA
1 TTAGCACTTGGCTGTGTCGGTTGGCCGTACAGA
673078 TTAGCACTTG
1 TTAGCACTTG
673088 ATTGTGCCTG
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
33 35 0.97
34 1 0.03
ACGTcount: A:0.17, C:0.20, G:0.32, T:0.32
Consensus pattern (33 bp):
TTAGCACTTGGCTGTGTCGGTTGGCCGTACAGA
Found at i:688734 original size:2 final size:2
Alignment explanation
Indices: 688727--688764 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
688717 ACACTCCTTT
*
688727 TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA T- TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
688765 GGGGAGGAAT
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:692224 original size:48 final size:48
Alignment explanation
Indices: 692176--693716 Score: 1031
Period size: 48 Copynumber: 32.1 Consensus size: 48
692166 TGAGTGGTAG
* * * * * *
692176 TAGTATGGAGGAGGTGGTGAGGGAGATGGAGGAGGTGGAGATTTGTAG
1 TAGTATGGTGGAGGTGGTGAAGGAGATGGTGGTGGTGGAGACTTGTAA
* * * *
692224 TAGTATGGTGGTGG-GG-GAGAGTG-GACTGGTGGTGGGGGAGATTTGTAG
1 TAGTATGGTGGAGGTGGTGA-AG-GAGA-TGGTGGTGGTGGAGACTTGTAA
* * * * * * * * *
692272 TAGTATGGGGGAGGAGGAGATGGTGATGGTGGAGGAGGGGAGTTGTAA
1 TAGTATGGTGGAGGTGGTGAAGGAGATGGTGGTGGTGGAGACTTGTAA
* * * *** * * * * *
692320 TGGTA-GGT--AGGTGCTGGAGCCTTCACTGGAGGTGGGGGTGATTTGTAG
1 TAGTATGGTGGAGGTGGTGAAG--GAGA-TGGTGGTGGTGGAGACTTGTAA
* * *
692368 TAGTATGGTGGAGGTGGTGAAGGAGATGGTGGTGGTGGGGATTTGTAG
1 TAGTATGGTGGAGGTGGTGAAGGAGATGGTGGTGGTGGAGACTTGTAA
* * * * *
692416 TAGTATGGTGGGGGTGGAG-AGTGA-ACTGGTGGTGGTGGGGATTTGTAG
1 TAGTATGGTGGAGGTGGTGAAG-GAGA-TGGTGGTGGTGGAGACTTGTAA
* * * * *
692464 TAGTATGGTGGGGGTGGAG-AGTG-GACTGGTGGTGGTGGGGATTTGTAG
1 TAGTATGGTGGAGGTGGTGAAG-GAGA-TGGTGGTGGTGGAGACTTGTAA
* * * * * * * * *
692512 TAGTATGGTGGAGGAGGAGATGGCGATGGCGGAGGAGGGGATTTGTAA
1 TAGTATGGTGGAGGTGGTGAAGGAGATGGTGGTGGTGGAGACTTGTAA
* * *
692560 TAGTATGGTGGTGGTGGAG-AGTG-GACTGGTGGTGGTGGGGACTTGTAA
1 TAGTATGGTGGAGGTGGTGAAG-GAGA-TGGTGGTGGTGGAGACTTGTAA
* * * * * * *
692608 TAATATGGTGGAGGAGGAGATGGTGATGGTGGTGGAGGAGATTTGTAA
1 TAGTATGGTGGAGGTGGTGAAGGAGATGGTGGTGGTGGAGACTTGTAA
* ** * * *** *
692656 -ATGTATGG-GG-GCTCCTCTACGTGTTTTGGTGGTGGTGGGGACTTGTAA
1 TA-GTATGGTGGAGGTGGT-GAAG-GAGATGGTGGTGGTGGAGACTTGTAA
*
692704 TAGTATGGTGGAGGTGGTGAAGGAGAAGGTGGTGGTGGAGACTTGTAA
1 TAGTATGGTGGAGGTGGTGAAGGAGATGGTGGTGGTGGAGACTTGTAA
* * *
692752 TAGTATGGTGGGGGTGG-GGAGTG-GACTGGTGGTGGTGGAGACTTGTAG
1 TAGTATGGTGGAGGTGGTGAAG-GAGA-TGGTGGTGGTGGAGACTTGTAA
* * * * *
692800 TAGTATGGTGGTGGTGGGGAATGGA-CTAGTGGTGGTGGGGACTTGTAA
1 TAGTATGGTGGAGGTGGTGAA-GGAGATGGTGGTGGTGGAGACTTGTAA
* * * * * * *
692848 TAGTATGGTGGTGGAGGAGATGGCGATGGTGGTGGAGGAGATTTGTAGA
1 TAGTATGGTGGAGGTGGTGAAGGAGATGGTGGTGGTGGAGACTTGTA-A
* ** * * ** * *
692897 T-GTATGG-GG-GCTCCTCTACATG-CTTCGGTGGTGGGGGGGACTTGTAA
1 TAGTATGGTGGAGGTGGT-GA-AGGAGAT-GGTGGTGGTGGAGACTTGTAA
*
692944 TAGTATGGTGGAGGTGGTGAAGGAGAAGGTGGTGGTGGAGACTTGTAA
1 TAGTATGGTGGAGGTGGTGAAGGAGATGGTGGTGGTGGAGACTTGTAA
*
692992 TAGTATGGTGGAGGTGGTGAAGGAGAAGGTGGTGGTGGAGACTTGTAA
1 TAGTATGGTGGAGGTGGTGAAGGAGATGGTGGTGGTGGAGACTTGTAA
*
693040 TAGTATGGTGGAGGTGGTGAAGGAGAAGGTGGTGGTGGAGACTTGTAA
1 TAGTATGGTGGAGGTGGTGAAGGAGATGGTGGTGGTGGAGACTTGTAA
*
693088 TAGTATGGTGGAGGTGGTGAAGGAGAAGGTGGTGGTGGAGACTTGTAA
1 TAGTATGGTGGAGGTGGTGAAGGAGATGGTGGTGGTGGAGACTTGTAA
*
693136 TAGTATGGTGGAGGTGGTGAAGGAGAAGGTGGTGGTGGAGACTTGTAA
1 TAGTATGGTGGAGGTGGTGAAGGAGATGGTGGTGGTGGAGACTTGTAA
*
693184 TAGTATGGTGGAGGTGGTGAAGGAGAAGGTGGTGGTGGAGACTTGTAA
1 TAGTATGGTGGAGGTGGTGAAGGAGATGGTGGTGGTGGAGACTTGTAA
*
693232 TAGTATGGTGGAGGTGGTGAAGGAGAAGGTGGTGGTGGAGACTTGTAA
1 TAGTATGGTGGAGGTGGTGAAGGAGATGGTGGTGGTGGAGACTTGTAA
* * * * * *
693280 TAGTATGGTGGAGGAGGAGATGGCGATGGTGGTGGGGGAGACTTGTAG
1 TAGTATGGTGGAGGTGGTGAAGGAGATGGTGGTGGTGGAGACTTGTAA
* * * * * * * *
693328 TAGTATGGTGGAGGAGGAGATGGCGATGGTGGTGGGGGTGATTTGTAG
1 TAGTATGGTGGAGGTGGTGAAGGAGATGGTGGTGGTGGAGACTTGTAA
* * * *** * * *
693376 TAGTA---TGGAGGTTGCTCCACATGTTTTGGCGGTGGTGGGGACTTGTAG
1 TAGTATGGTGGAGG-TGGT-GA-AGGAGATGGTGGTGGTGGAGACTTGTAA
* * * * * * *
693424 TAGTATGGTGGAGGAGGAGATGGTGATGGTGGTGGAGGAGATTTGTAG
1 TAGTATGGTGGAGGTGGTGAAGGAGATGGTGGTGGTGGAGACTTGTAA
* ** * * *** * * *
693472 TAGTATGG-GG-GCTCTTCTACATGTTTTGGTGGTGGTGGGGATTTGTAG
1 TAGTATGGTGGAGGTGGT-GA-AGGAGATGGTGGTGGTGGAGACTTGTAA
* * * * * * * * *
693520 TAGTATGGTGGTGGAGGAGATGGCGATGGTGGAGGAGGAGATTTGTAG
1 TAGTATGGTGGAGGTGGTGAAGGAGATGGTGGTGGTGGAGACTTGTAA
* * * *** * *
693568 TAGTA---TGGAGGTTGCTCCACATGTTTTGGTGGTGGTGGGGACTTGTAG
1 TAGTATGGTGGAGG-TGGT-GA-AGGAGATGGTGGTGGTGGAGACTTGTAA
* * *
693616 TAGTATGGTGGTGGTGGAG-AGTGA-ACTGGTGGTGGTGGGGACTTGTAA
1 TAGTATGGTGGAGGTGGTGAAG-GAGA-TGGTGGTGGTGGAGACTTGTAA
* * * * * * *
693664 TAGTATGGTGGAGGAGGAGATGGCGATGGTGGTGGAGGAGATTTGTAG
1 TAGTATGGTGGAGGTGGTGAAGGAGATGGTGGTGGTGGAGACTTGTAA
693712 TAGTA
1 TAGTA
693717 CGGGGGCTGC
Statistics
Matches: 1216, Mismatches: 216, Indels: 122
0.78 0.14 0.08
Matches are distributed among these distances:
45 17 0.01
46 7 0.01
47 39 0.03
48 1086 0.89
49 34 0.03
50 13 0.01
51 20 0.02
ACGTcount: A:0.20, C:0.04, G:0.48, T:0.27
Consensus pattern (48 bp):
TAGTATGGTGGAGGTGGTGAAGGAGATGGTGGTGGTGGAGACTTGTAA
Found at i:693308 original size:21 final size:21
Alignment explanation
Indices: 693284--693359 Score: 71
Period size: 21 Copynumber: 3.3 Consensus size: 21
693274 TTGTAATAGT
693284 ATGGTGGAGGAGGAGATGGCG
1 ATGGTGGAGGAGGAGATGGCG
* * *
693305 ATGGTGGTGGGGGAGACTTGTAGTAG
1 ATGGTGGAGGAGGAGA--TG--G-CG
693331 TATGGTGGAGGAGGAGATGGCG
1 -ATGGTGGAGGAGGAGATGGCG
693353 ATGGTGG
1 ATGGTGG
693360 TGGGGGTGAT
Statistics
Matches: 43, Mismatches: 6, Indels: 12
0.70 0.10 0.20
Matches are distributed among these distances:
21 21 0.49
22 1 0.02
23 3 0.07
25 3 0.07
26 1 0.02
27 14 0.33
ACGTcount: A:0.21, C:0.04, G:0.54, T:0.21
Consensus pattern (21 bp):
ATGGTGGAGGAGGAGATGGCG
Found at i:693728 original size:144 final size:144
Alignment explanation
Indices: 693498--693759 Score: 434
Period size: 144 Copynumber: 1.8 Consensus size: 144
693488 CTACATGTTT
* * *
693498 TGGTGGTGGTGGGGATTTGTAGTAGTATGGTGGTGGAGGAGATGGCGATGGTGGAGGAGGAGATT
1 TGGTGGTGGTGGGGACTTGTAATAGTATGGTGGAGGAGGAGATGGCGATGGTGGAGGAGGAGATT
* * * *
693563 TGTAGTAGTATGGAGGTTGCTCCACATGTTTTGGTGGTGGTGGGGACTTGTAGTAGTATGGTGGT
66 TGTAGTAGTACGGAGGCTGCTCCACATGCTTTGGTGGTGGTGGAGACTTGTAGTAGTATGGTGGT
693628 GGTGGAGAGTGAAC
131 GGTGGAGAGTGAAC
*
693642 TGGTGGTGGTGGGGACTTGTAATAGTATGGTGGAGGAGGAGATGGCGATGGTGGTGGAGGAGATT
1 TGGTGGTGGTGGGGACTTGTAATAGTATGGTGGAGGAGGAGATGGCGATGGTGGAGGAGGAGATT
* *
693707 TGTAGTAGTACGGGGGCTGCTCTACATGCTTTGGTGGTGGTGGAGACTTGTAG
66 TGTAGTAGTACGGAGGCTGCTCCACATGCTTTGGTGGTGGTGGAGACTTGTAG
693760 ACATAAGTGG
Statistics
Matches: 108, Mismatches: 10, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
144 108 1.00
ACGTcount: A:0.18, C:0.06, G:0.46, T:0.30
Consensus pattern (144 bp):
TGGTGGTGGTGGGGACTTGTAATAGTATGGTGGAGGAGGAGATGGCGATGGTGGAGGAGGAGATT
TGTAGTAGTACGGAGGCTGCTCCACATGCTTTGGTGGTGGTGGAGACTTGTAGTAGTATGGTGGT
GGTGGAGAGTGAAC
Found at i:693875 original size:36 final size:36
Alignment explanation
Indices: 693799--693887 Score: 115
Period size: 36 Copynumber: 2.5 Consensus size: 36
693789 GTAGTACACA
* * * *
693799 GGTGGTGGAGGTGACTTGTAAACATAAGTCGGCGAT
1 GGTGGAGGTGGTGACTTGTAAACATAAGTCGGAGAC
* *
693835 GGTGGAGGTGGTGACTTGTAAACATAAGTGGGAGCC
1 GGTGGAGGTGGTGACTTGTAAACATAAGTCGGAGAC
*
693871 GGTGGAGGTGGAGACTT
1 GGTGGAGGTGGTGACTT
693888 ATAGTAGTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
36 46 1.00
ACGTcount: A:0.24, C:0.10, G:0.43, T:0.24
Consensus pattern (36 bp):
GGTGGAGGTGGTGACTTGTAAACATAAGTCGGAGAC
Found at i:693929 original size:150 final size:150
Alignment explanation
Indices: 693775--694046 Score: 490
Period size: 150 Copynumber: 1.8 Consensus size: 150
693765 AGTGGGAGGA
* * *
693775 GGTGGTGATTTGTAGTAGTACACAGGTGGTGGAGGTGACTTGTAAACATAAGTCGGCGATGGTGG
1 GGTGGAGACTTGTAGTAGTACACAGGAGGTGGAGGTGACTTGTAAACATAAGTCGGCGATGGTGG
693840 AGGTGGTGACTTGTAAACATAAGTGGGAGCCGGTGGAGGTGGAGACTTATAGTAGTATGGGGGTT
66 AGGTGGTGACTTGTAAACATAAGTGGGAGCCGGTGGAGGTGGAGACTTATAGTAGTATGGGGGTT
693905 GTTCCACATGCTTTGGTGGT
131 GTTCCACATGCTTTGGTGGT
* *
693925 GGTGGAGACTTGTAGTAGTACACAGGAGGTGGAGGTGACTTGTAAACATAAGTTGGTGATGGTGG
1 GGTGGAGACTTGTAGTAGTACACAGGAGGTGGAGGTGACTTGTAAACATAAGTCGGCGATGGTGG
*
693990 AGGTGGTGACTTGTAAACGTAAGTGGGAGCCGGTGGAGGTGGAGACTTATAGTAGTA
66 AGGTGGTGACTTGTAAACATAAGTGGGAGCCGGTGGAGGTGGAGACTTATAGTAGTA
694047 CGGTGGTGGC
Statistics
Matches: 116, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
150 116 1.00
ACGTcount: A:0.24, C:0.09, G:0.40, T:0.27
Consensus pattern (150 bp):
GGTGGAGACTTGTAGTAGTACACAGGAGGTGGAGGTGACTTGTAAACATAAGTCGGCGATGGTGG
AGGTGGTGACTTGTAAACATAAGTGGGAGCCGGTGGAGGTGGAGACTTATAGTAGTATGGGGGTT
GTTCCACATGCTTTGGTGGT
Found at i:694003 original size:36 final size:36
Alignment explanation
Indices: 693958--694037 Score: 106
Period size: 36 Copynumber: 2.2 Consensus size: 36
693948 AGGAGGTGGA
* * *
693958 GGTGACTTGTAAACATAAGTTGGTGATGGTGGAGGT
1 GGTGACTTGTAAACATAAGTGGGAGACGGTGGAGGT
* *
693994 GGTGACTTGTAAACGTAAGTGGGAGCCGGTGGAGGT
1 GGTGACTTGTAAACATAAGTGGGAGACGGTGGAGGT
*
694030 GGAGACTT
1 GGTGACTT
694038 ATAGTAGTAC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.24, C:0.09, G:0.41, T:0.26
Consensus pattern (36 bp):
GGTGACTTGTAAACATAAGTGGGAGACGGTGGAGGT
Found at i:695187 original size:24 final size:24
Alignment explanation
Indices: 695160--695282 Score: 76
Period size: 24 Copynumber: 5.1 Consensus size: 24
695150 ACTTCACTGG
695160 TGGTGGTGGAGATTTGTAGTAGTA
1 TGGTGGTGGAGATTTGTAGTAGTA
* * **
695184 TGGTGGT-GAGA--CGTAATGTGGGGG
1 TGGTGGTGGAGATTTGT-A-GT-AGTA
695208 TGGTGGTGGAGATTTGTAGTAGTA
1 TGGTGGTGGAGATTTGTAGTAGTA
* * * * *
695232 AGGTGGTGGAGGAGATGGT-GAAG-G
1 TGGTGGTGGA-GA-TTTGTAGTAGTA
*
695256 TGGTGGTGGAGACTTGTAGTAGTA
1 TGGTGGTGGAGATTTGTAGTAGTA
695280 TGG
1 TGG
695283 GGGTTGTTCT
Statistics
Matches: 71, Mismatches: 18, Indels: 20
0.65 0.17 0.18
Matches are distributed among these distances:
21 2 0.03
22 4 0.06
23 11 0.15
24 37 0.52
25 11 0.15
26 4 0.06
27 2 0.03
ACGTcount: A:0.20, C:0.02, G:0.48, T:0.30
Consensus pattern (24 bp):
TGGTGGTGGAGATTTGTAGTAGTA
Found at i:695376 original size:147 final size:147
Alignment explanation
Indices: 695157--695573 Score: 391
Period size: 147 Copynumber: 2.9 Consensus size: 147
695147 GAGACTTCAC
* * * *
695157 TGGTGGTGGTGGAGATTTGTAGTAGTATGGTGGTGAGACGTAATGTGGGGGTGGTGGTGGAGATT
1 TGGTGGTGGTGGAGATTTGTAGTAGTATGGAGGAGAGACGTAATGTGGGGGAGGTGGTGGAGACT
* *
695222 TGTAGTAGTAAGGTGGTGGAGGAGATGGTGAAGGTGGTGGTGGAGACTTGTAGTAGTATGGGGGT
66 TGTAGTAGTAAGGAGGTGGAGGAGATGGTGAAGGTGGTGGTGGAGACTTATAGTAGTATGGGGGT
695287 TGTTCTTCATGCTTTGG
131 TGTTCTTCATGCTTTGG
** * * *
695304 TGGTGGTGGTGGAGATTTGTAGTAGTATGGAGGAG-GTGGTGATG-GAGATGGAGGTGGTGGGGA
1 TGGTGGTGGTGGAGATTTGTAGTAGTATGGAGGAGAGACGTAATGTG-G-GGGAGGTGGTGGAGA
* * * *
695367 CTTGTAGTAGTAAGGAGGTGGTGGAGATGGTGAAGGTGGTGGTGGAGATTTATAGTAGTAAGGTG
64 CTTGTAGTAGTAAGGAGGTGGAGGAGATGGTGAAGGTGGTGGTGGAGACTTATAGTAGTATGGGG
* ** * ** *
695432 G-TGGTGGTGA-G-GGTGA
129 GTTGTTCTTCATGCTTTGG
* * * * * * *** *
695448 TGGAGGTGGAGGAGACTTGTAGTAGTATGG-GG-GTTG-CTCTACGTGTTTTGGTGGTGGTGGAG
1 TGGTGGTGGTGGAGATTTGTAGTAGTATGGAGGAG-AGAC-GTA-ATGTGGGGGAGGTGGTGGAG
* * * * * *
695510 ACTTGTAGTAGTATGGAGGTGGTGGTGATGGTGAAGGAGGTGGTGGGGACTTGTAGTAGTATGG
63 ACTTGTAGTAGTAAGGAGGTGGAGGAGATGGTGAAGGTGGTGGTGGAGACTTATAGTAGTATGG
695574 AGGAGGTGGT
Statistics
Matches: 223, Mismatches: 40, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
142 1 0.00
143 2 0.01
144 100 0.45
145 4 0.02
146 12 0.05
147 104 0.47
ACGTcount: A:0.19, C:0.03, G:0.48, T:0.30
Consensus pattern (147 bp):
TGGTGGTGGTGGAGATTTGTAGTAGTATGGAGGAGAGACGTAATGTGGGGGAGGTGGTGGAGACT
TGTAGTAGTAAGGAGGTGGAGGAGATGGTGAAGGTGGTGGTGGAGACTTATAGTAGTATGGGGGT
TGTTCTTCATGCTTTGG
Found at i:695574 original size:48 final size:48
Alignment explanation
Indices: 695161--695759 Score: 511
Period size: 48 Copynumber: 12.4 Consensus size: 48
695151 CTTCACTGGT
* * ** * ** *
695161 GGTGGTGGAGATTTGTAGTAGTATGGTGGTGAGACGTAAT-GTGGGGGT
1 GGTGGTGGAGACTTGTAGTAGTATGGAGGTG-GTGGTGATGGTGATGGA
* * * * * * *
695209 GGTGGTGGAGATTTGTAGTAGTAAGGTGGTGGAGGAGATGGTGAAGGT
1 GGTGGTGGAGACTTGTAGTAGTATGGAGGTGGTGGTGATGGTGATGGA
* * ** * * * *
695257 GGTGGTGGAGACTTGTAGTAGTATGGGGGTTGTTCTTCATGCTTTGGTGGT
1 GGTGGTGGAGACTTGTAGTAGTATGGAGG-TGGTGGTGATG--GTGATGGA
* * *
695308 GGTGGTGGAGATTTGTAGTAGTATGGAGGAGGTGGTGATGGAGATGGA
1 GGTGGTGGAGACTTGTAGTAGTATGGAGGTGGTGGTGATGGTGATGGA
* * * * *
695356 GGTGGTGGGGACTTGTAGTAGTAAGGAGGTGGTGGAGATGGTGAAGGT
1 GGTGGTGGAGACTTGTAGTAGTATGGAGGTGGTGGTGATGGTGATGGA
* * * * *
695404 GGTGGTGGAGATTTATAGTAGTAAGGTGGTGGTGGTGAGGGTGATGGA
1 GGTGGTGGAGACTTGTAGTAGTATGGAGGTGGTGGTGATGGTGATGGA
* * * * * ** *
695452 GGTGGAGGAGACTTGTAGTAGTATGG-GG-GTTGCTCTACGTGTTTTGGT
1 GGTGGTGGAGACTTGTAGTAGTATGGAGGTGGTGGT-GATG-GTGATGGA
*
695500 GGTGGTGGAGACTTGTAGTAGTATGGAGGTGGTGGTGATGGTGAAGGA
1 GGTGGTGGAGACTTGTAGTAGTATGGAGGTGGTGGTGATGGTGATGGA
* * *
695548 GGTGGTGGGGACTTGTAGTAGTATGGAGGAGGTGGTGATGGAGATGGA
1 GGTGGTGGAGACTTGTAGTAGTATGGAGGTGGTGGTGATGGTGATGGA
* * * * * * ** * * * *
695596 GGAGGAGGTGACTTGTAGTAATATGGTGGTTGTTCTTCATGCTTTGGTGGT
1 GGTGGTGGAGACTTGTAGTAGTATGGAGG-TGGTGGTGATG--GTGATGGA
*
695647 GGTGGTGGGGACTTGTAGTAGTATGGAGGTGGTGGTGATGGTGATGGA
1 GGTGGTGGAGACTTGTAGTAGTATGGAGGTGGTGGTGATGGTGATGGA
* * * *
695695 GGTGGTGGAGATTTATAGTAGTATGGAGGAGGTGGTGATGGAGATGGA
1 GGTGGTGGAGACTTGTAGTAGTATGGAGGTGGTGGTGATGGTGATGGA
695743 GGTGGTGGAGACTTGTA
1 GGTGGTGGAGACTTGTA
695760 TTCATAAGGC
Statistics
Matches: 438, Mismatches: 102, Indels: 22
0.78 0.18 0.04
Matches are distributed among these distances:
46 4 0.01
47 9 0.02
48 333 0.76
49 15 0.03
50 17 0.04
51 60 0.14
ACGTcount: A:0.19, C:0.03, G:0.48, T:0.30
Consensus pattern (48 bp):
GGTGGTGGAGACTTGTAGTAGTATGGAGGTGGTGGTGATGGTGATGGA
Found at i:695576 original size:27 final size:27
Alignment explanation
Indices: 695308--695759 Score: 112
Period size: 27 Copynumber: 18.6 Consensus size: 27
695298 CTTTGGTGGT
*
695308 GGTGGTGGAGATTTGTAGTAGTATGGA
1 GGTGGTGGAGACTTGTAGTAGTATGGA
* *
695335 GGAGGTGGTGA--TG--G-AG-ATGGA
1 GGTGGTGGAGACTTGTAGTAGTATGGA
* *
695356 GGTGGTGGGGACTTGTAGTAGTAAGGA
1 GGTGGTGGAGACTTGTAGTAGTATGGA
* *
695383 GGTGGTGGAGA--TG--GT-G-AAGGT
1 GGTGGTGGAGACTTGTAGTAGTATGGA
* * * *
695404 GGTGGTGGAGATTTATAGTAGTAAGGT
1 GGTGGTGGAGACTTGTAGTAGTATGGA
* *
695431 GGTGGTGGTGA---G-GGT-G-ATGGA
1 GGTGGTGGAGACTTGTAGTAGTATGGA
*
695452 GGTGGAGGAGACTTGTAGTAGTAT-G-
1 GGTGGTGGAGACTTGTAGTAGTATGGA
* * * *
695477 GG-GGT--TG-C-TCTACGT-GTTTTGGT
1 GGTGGTGGAGACTTGTA-GTAG-TATGGA
695500 GGTGGTGGAGACTTGTAGTAGTATGGA
1 GGTGGTGGAGACTTGTAGTAGTATGGA
* *
695527 GGTGGTGGTGA--TG--GT-G-AAGGA
1 GGTGGTGGAGACTTGTAGTAGTATGGA
*
695548 GGTGGTGGGGACTTGTAGTAGTATGGA
1 GGTGGTGGAGACTTGTAGTAGTATGGA
* *
695575 GGAGGTGGTGA--TG--G-AG-ATGGA
1 GGTGGTGGAGACTTGTAGTAGTATGGA
* * * * *
695596 GGAGGAGGTGACTTGTAGTAATATGGT
1 GGTGGTGGAGACTTGTAGTAGTATGGA
* **** * * * *
695623 GGTTGT-TCTTCATGCT--TTG-GTGGT
1 GGTGGTGGAGACTTG-TAGTAGTATGGA
*
695647 GGTGGTGGGGACTTGTAGTAGTATGGA
1 GGTGGTGGAGACTTGTAGTAGTATGGA
*
695674 GGTGGTGGTGA--TG--GT-G-ATGGA
1 GGTGGTGGAGACTTGTAGTAGTATGGA
* *
695695 GGTGGTGGAGATTTATAGTAGTATGGA
1 GGTGGTGGAGACTTGTAGTAGTATGGA
* *
695722 GGAGGTGGTGA--TG--G-AG-ATGGA
1 GGTGGTGGAGACTTGTAGTAGTATGGA
695743 GGTGGTGGAGACTTGTA
1 GGTGGTGGAGACTTGTA
695760 TTCATAAGGC
Statistics
Matches: 309, Mismatches: 61, Indels: 112
0.64 0.13 0.23
Matches are distributed among these distances:
20 4 0.01
21 104 0.34
22 12 0.04
23 23 0.07
24 16 0.05
25 27 0.09
26 14 0.05
27 105 0.34
28 4 0.01
ACGTcount: A:0.20, C:0.03, G:0.48, T:0.29
Consensus pattern (27 bp):
GGTGGTGGAGACTTGTAGTAGTATGGA
Found at i:695667 original size:147 final size:144
Alignment explanation
Indices: 695356--695759 Score: 592
Period size: 144 Copynumber: 2.8 Consensus size: 144
695346 TGGAGATGGA
* * *
695356 GGTGGTGGGGACTTGTAGTAGTAAGGAGGTGGTGGAGATGGTGAAGGTGGTGGTGGAGATTTATA
1 GGTGGTGGGGACTTGTAGTAGTATGGAGGTGGTGGTGATGGTGAAGGAGGTGGTGGAGATTTATA
* * * * * *
695421 GTAGTAAGGTGGTGGTGGTGAGGGTGATGGAGGTGGAGGAGACTTGTAGTAGTATGGGGGTTGCT
66 GTAGTATGGAGGAGGTGGTGATGGAGATGGAGGTGGAGGAGACTTGTAGTAATATGGGGGTTGCT
*
695486 CTACGTGTTTTGGT
131 CTACATGTTTTGGT
* * * *
695500 GGTGGTGGAGACTTGTAGTAGTATGGAGGTGGTGGTGATGGTGAAGGAGGTGGTGGGGACTTGTA
1 GGTGGTGGGGACTTGTAGTAGTATGGAGGTGGTGGTGATGGTGAAGGAGGTGGTGGAGATTTATA
* * * *
695565 GTAGTATGGAGGAGGTGGTGATGGAGATGGAGGAGGAGGTGACTTGTAGTAATATGGTGGTTGTT
66 GTAGTATGGAGGAGGTGGTGATGGAGATGGAGGTGGAGGAGACTTGTAGTAATATGGGGGTTGCT
*
695630 CTTCATGCTTTGGTGGT
131 CTACATG-TTT--TGGT
*
695647 GGTGGTGGGGACTTGTAGTAGTATGGAGGTGGTGGTGATGGTGATGGAGGTGGTGGAGATTTATA
1 GGTGGTGGGGACTTGTAGTAGTATGGAGGTGGTGGTGATGGTGAAGGAGGTGGTGGAGATTTATA
*
695712 GTAGTATGGAGGAGGTGGTGATGGAGATGGAGGTGGTGGAGACTTGTA
66 GTAGTATGGAGGAGGTGGTGATGGAGATGGAGGTGGAGGAGACTTGTA
695760 TTCATAAGGC
Statistics
Matches: 230, Mismatches: 27, Indels: 3
0.88 0.10 0.01
Matches are distributed among these distances:
144 118 0.51
145 3 0.01
147 109 0.47
ACGTcount: A:0.19, C:0.03, G:0.48, T:0.30
Consensus pattern (144 bp):
GGTGGTGGGGACTTGTAGTAGTATGGAGGTGGTGGTGATGGTGAAGGAGGTGGTGGAGATTTATA
GTAGTATGGAGGAGGTGGTGATGGAGATGGAGGTGGAGGAGACTTGTAGTAATATGGGGGTTGCT
CTACATGTTTTGGT
Found at i:695694 original size:21 final size:21
Alignment explanation
Indices: 695669--695750 Score: 74
Period size: 21 Copynumber: 3.6 Consensus size: 21
695659 TTGTAGTAGT
695669 ATGGAGGTGGTGGTGATGGTG
1 ATGGAGGTGGTGGTGATGGTG
* *
695690 ATGGAGGTGGTGGAGATTTATAGTAG
1 ATGGAGGTGGT-G-G--TGATGGT-G
* *
695716 TATGGAGGAGGTGGTGATGGAG
1 -ATGGAGGTGGTGGTGATGGTG
695738 ATGGAGGTGGTGG
1 ATGGAGGTGGTGG
695751 AGACTTGTAT
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
21 23 0.48
22 2 0.04
23 5 0.10
25 6 0.12
26 2 0.04
27 10 0.21
ACGTcount: A:0.21, C:0.00, G:0.52, T:0.27
Consensus pattern (21 bp):
ATGGAGGTGGTGGTGATGGTG
Found at i:695799 original size:42 final size:42
Alignment explanation
Indices: 695743--695997 Score: 260
Period size: 42 Copynumber: 5.8 Consensus size: 42
695733 TGGAGATGGA
695743 GGTGGTGGAGACTTGTATTCATAAGGCTTCTCCTTCGGTGGT
1 GGTGGTGGAGACTTGTATTCATAAGGCTTCTCCTTCGGTGGT
695785 GGTGGTGGAGACTTGTATTCATAAGGCTTCTCCTTCGGTGGT
1 GGTGGTGGAGACTTGTATTCATAAGGCTTCTCCTTCGGTGGT
*
695827 GGTGGTGGAGACTTGTATTCATAAGGCTTCTCCTCATGCTTTGGTGGA
1 GGTGGTGGAGACTTGTATTCATAAGGCTTCTCCT--T-C---GGTGGT
* * ** * ******* *
695875 GGTGGAGGAGACTTATACACATAAGGAGGTGGTGGAGAAGGTGATGGA
1 GGTGGTGGAGACTTGTATTCATAA-G-GCT--TCTCCTTCG-G-TGGT
*
695923 GGTGGTGGAGACTTGTATTCATAAGGCTTCTCTTTCGGTGGT
1 GGTGGTGGAGACTTGTATTCATAAGGCTTCTCCTTCGGTGGT
695965 GGTGGTGGAGACTTGTATTCA-AAGGCTTCTCCT
1 GGTGGTGGAGACTTGTATTCATAAGGCTTCTCCT
695998 CATGCTTTGG
Statistics
Matches: 174, Mismatches: 27, Indels: 25
0.77 0.12 0.11
Matches are distributed among these distances:
41 11 0.06
42 100 0.57
43 1 0.01
44 3 0.02
45 1 0.01
46 3 0.02
47 2 0.01
48 49 0.28
49 1 0.01
50 2 0.01
52 1 0.01
ACGTcount: A:0.18, C:0.15, G:0.35, T:0.33
Consensus pattern (42 bp):
GGTGGTGGAGACTTGTATTCATAAGGCTTCTCCTTCGGTGGT
Found at i:696048 original size:137 final size:138
Alignment explanation
Indices: 695785--696085 Score: 559
Period size: 137 Copynumber: 2.2 Consensus size: 138
695775 CTTCGGTGGT
695785 GGTGGTGGAGACTTGTATTCATAAGGCTTCTCCTTCGGTGGTGGTGGTGGAGACTTGTATTCATA
1 GGTGGTGGAGACTTGTATTCATAAGGCTTCTCCTTCGGTGGTGGTGGTGGAGACTTGTATTCATA
695850 AGGCTTCTCCTCATGCTTTGGTGGAGGTGGAGGAGACTTATACACATAAGGAGGTGGTGGAGAAG
66 AGGCTTCTCCTCATGCTTTGGTGGAGGTGGAGGAGACTTATACACATAAGGAGGTGGTGGAGAAG
695915 GTGATGGA
131 GTGATGGA
*
695923 GGTGGTGGAGACTTGTATTCATAAGGCTTCTCTTTCGGTGGTGGTGGTGGAGACTTGTATTCA-A
1 GGTGGTGGAGACTTGTATTCATAAGGCTTCTCCTTCGGTGGTGGTGGTGGAGACTTGTATTCATA
*
695987 AGGCTTCTCCTCATGCTTTGGTGGAGGTGGTGGAGACTTATACACATAAGGAGGTGGTGGAGAAG
66 AGGCTTCTCCTCATGCTTTGGTGGAGGTGGAGGAGACTTATACACATAAGGAGGTGGTGGAGAAG
696052 GTGATGGA
131 GTGATGGA
* *
696060 GGTGGTGGAGATTTGTACTCATAAGG
1 GGTGGTGGAGACTTGTATTCATAAGG
696086 AGGTGGAGGA
Statistics
Matches: 159, Mismatches: 4, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
137 97 0.61
138 62 0.39
ACGTcount: A:0.21, C:0.12, G:0.37, T:0.30
Consensus pattern (138 bp):
GGTGGTGGAGACTTGTATTCATAAGGCTTCTCCTTCGGTGGTGGTGGTGGAGACTTGTATTCATA
AGGCTTCTCCTCATGCTTTGGTGGAGGTGGAGGAGACTTATACACATAAGGAGGTGGTGGAGAAG
GTGATGGA
Found at i:696088 original size:27 final size:26
Alignment explanation
Indices: 696009--696097 Score: 71
Period size: 27 Copynumber: 3.5 Consensus size: 26
695999 ATGCTTTGGT
* *
696009 GGAGGTGGTGGAGACTTATACACATAA
1 GGAGGTGGTGGAGA-TTGTACTCATAA
* * *
696036 GGAGGTGGTGGAGA-AG--GTGAT--
1 GGAGGTGGTGGAGATTGTACTCATAA
696057 GGAGGTGGTGGAGATTTGTACTCATAA
1 GGAGGTGGTGGAGA-TTGTACTCATAA
*
696084 GGAGGTGGAGGAGA
1 GGAGGTGGTGGAGA
696098 AGGTGATGGT
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
21 14 0.30
23 3 0.06
25 3 0.06
27 27 0.57
ACGTcount: A:0.28, C:0.06, G:0.45, T:0.21
Consensus pattern (26 bp):
GGAGGTGGTGGAGATTGTACTCATAA
Found at i:696224 original size:48 final size:45
Alignment explanation
Indices: 695743--696227 Score: 263
Period size: 48 Copynumber: 10.6 Consensus size: 45
695733 TGGAGATGGA
* *
695743 GGTGGTGGAGACTTGTATTCATAAGGCTTCTCCT-T--CGGTGGT
1 GGTGGTGGAGACTTGTACTCATAAGGCTTCTCCTATGGTGGTGGT
* *
695785 GGTGGTGGAGACTTGTATTCATAAGGCTTCTCCT-T--CGGTGGT
1 GGTGGTGGAGACTTGTACTCATAAGGCTTCTCCTATGGTGGTGGT
* * *
695827 GGTGGTGGAGACTTGTATTCATAAGGCTTCTCCTCATGCTTTGGTGGA
1 GGTGGTGGAGACTTGTACTCATAAGGCTTCTCCT-ATG--GTGGTGGT
* * * * ** *** * * *
695875 GGTGGAGGAGACTTATACACATAAGGAGGTGGTGGAGAAGGTGATGGA
1 GGTGGTGGAGACTTGTACTCATAA-G-GCTTCT-CCTATGGTGGTGGT
*
695923 GGTGGTGGAGACTTGTATTCATAAGGCTTCT-CT-T--TCGGTGGT
1 GGTGGTGGAGACTTGTACTCATAAGGCTTCTCCTATGGT-GGTGGT
* * *
695965 GGTGGTGGAGACTTGTATTCA-AAGGCTTCTCCTCATGCTTTGGTGGA
1 GGTGGTGGAGACTTGTACTCATAAGGCTTCTCCT-ATG--GTGGTGGT
* * * ** *** * * *
696012 GGTGGTGGAGACTTATACACATAAGGAGGTGGTGGAGAAGGTGATGGA
1 GGTGGTGGAGACTTGTACTCATAA-G-GCTTCT-CCTATGGTGGTGGT
* * ****** * *
696060 GGTGGTGGAGATTTGTACTCATAAGGAGGTGGAGGAGAAGGTGATGGT
1 GGTGGTGGAGACTTGTACTCATAA-G-GCT-TCTCCTATGGTGGTGGT
* *
696108 GGGGGTGGAGACTTGTACTCATAAGGCTTCTCCTTTGGTGGTGGT
1 GGTGGTGGAGACTTGTACTCATAAGGCTTCTCCTATGGTGGTGGT
* *
696153 GGTGGTGGAGACTTGTATTCATAAGGCTTCTCCTCATGTTTAGGTGGT
1 GGTGGTGGAGACTTGTACTCATAAGGCTTCTCCT-ATG-GT-GGTGGT
* * *
696201 GGTGGTGGAGATTTATACACATAAGGC
1 GGTGGTGGAGACTTGTACTCATAAGGC
696228 GGTGGTGGAG
Statistics
Matches: 352, Mismatches: 66, Indels: 44
0.76 0.14 0.10
Matches are distributed among these distances:
41 10 0.03
42 103 0.29
44 2 0.01
45 40 0.11
46 7 0.02
47 26 0.07
48 151 0.43
49 3 0.01
50 10 0.03
ACGTcount: A:0.20, C:0.13, G:0.36, T:0.31
Consensus pattern (45 bp):
GGTGGTGGAGACTTGTACTCATAAGGCTTCTCCTATGGTGGTGGT
Found at i:707611 original size:257 final size:261
Alignment explanation
Indices: 707120--707612 Score: 690
Period size: 263 Copynumber: 1.9 Consensus size: 261
707110 GACCGGCTTG
* * * *
707120 GATCTAAACCCTAAGGTATGTTTTTCTACTCGTCAATTGGTATTAATCTATCGTACCAATCGTCA
1 GATCTAAACCCTAAGATATATTTTTCTACTCGTCAATGGGTATTAATCCATCGTACCAATCGTCA
* * *
707185 ATTTTTCATTTGGAACTGCTAGCCGAACAATTAAAAAAAACTTAACGATTCAATGACTTAAATGA
66 ATTTATCACTTGGAACTGCTAGCCGAACAATTAAAAAAAACTTAACGAATCAATGACTTAAATGA
* * *
707250 AAACTTCCGAATAGTTCAGTAACCATTTTGTAACCTTTTGAAGTTGAGTGACTAAAACGTAAACT
131 AAACTTCCGAATAGTTCAATAACCA--TTGTAACCTTCTGAAATTGAGTGACTAAAACGTAAACT
*
707315 TACTAATAATTTAGTAACCTTAAATGTAGTTTGCCCAAAAAATTATTTTCTACTCATCAATGGGT
194 TACTAATAATTTAGTAACCTTAAATGTAGTTTACCCAAAAAATTATTTTCTACTCATCAATGGGT
707380 ATT
259 ATT
* * * *
707383 GATCTAAGCCCTAAGATATATTTTTCTACTTGTCAATGGGTATTGATCCA-CTGTACCAATTGTC
1 GATCTAAACCCTAAGATATATTTTTCTACTCGTCAATGGGTATTAATCCATC-GTACCAATCGTC
* * * * *
707447 AATTTATCGCTTGGAGCTGCTAGCTGGACAATTAAAAAATA-TTAAC-AATCAATGACTTAAATG
65 AATTTATCACTTGGAACTGCTAGCCGAACAATTAAAAAAAACTTAACGAATCAATGACTTAAATG
* * * *
707510 AAATCTTTCGAATAGTTTAATAACCA-T-TAACCTTCTGAAATTGAGTGACTAAAACGTAAGCTT
130 AAAACTTCCGAATAGTTCAATAACCATTGTAACCTTCTGAAATTGAGTGACTAAAACGTAAACTT
* *
707573 ACTAATGATTTAGTGACCTTAAATGTAGTTTACCCAAAAA
195 ACTAATAATTTAGTAACCTTAAATGTAGTTTACCCAAAAA
707613 TATTTTTGAT
Statistics
Matches: 203, Mismatches: 26, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
257 70 0.34
258 1 0.00
261 38 0.19
262 6 0.03
263 88 0.43
ACGTcount: A:0.35, C:0.17, G:0.14, T:0.34
Consensus pattern (261 bp):
GATCTAAACCCTAAGATATATTTTTCTACTCGTCAATGGGTATTAATCCATCGTACCAATCGTCA
ATTTATCACTTGGAACTGCTAGCCGAACAATTAAAAAAAACTTAACGAATCAATGACTTAAATGA
AAACTTCCGAATAGTTCAATAACCATTGTAACCTTCTGAAATTGAGTGACTAAAACGTAAACTTA
CTAATAATTTAGTAACCTTAAATGTAGTTTACCCAAAAAATTATTTTCTACTCATCAATGGGTAT
T
Found at i:711889 original size:24 final size:23
Alignment explanation
Indices: 711862--711906 Score: 54
Period size: 24 Copynumber: 1.9 Consensus size: 23
711852 ATATTATAAG
711862 ATTAACTTAATTAAATGATGTGGC
1 ATTAACTTAATT-AATGATGTGGC
** *
711886 ATTAGTTTAATTTATGATGTG
1 ATTAACTTAATTAATGATGTG
711907 AAAATTTTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
23 8 0.44
24 10 0.56
ACGTcount: A:0.33, C:0.04, G:0.18, T:0.44
Consensus pattern (23 bp):
ATTAACTTAATTAATGATGTGGC
Found at i:717199 original size:13 final size:14
Alignment explanation
Indices: 717176--717208 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
717166 TAGTATTGAA
717176 ATATATAATATTTT
1 ATATATAATATTTT
717190 ATAT-TAATATTTT
1 ATATATAATATTTT
*
717203 AAATAT
1 ATATAT
717209 TTTAAAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (14 bp):
ATATATAATATTTT
Found at i:721682 original size:31 final size:31
Alignment explanation
Indices: 721638--721698 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
721628 GGATACAAAA
*
721638 TAGTCATCTAACTATTCCAAA-TATTTTATTT
1 TAGTCATCTAACTATTCAAAAGT-TTTTATTT
721669 TAGTCAT-TGAACTATTCAAAAGTTTTTATT
1 TAGTCATCT-AACTATTCAAAAGTTTTTATT
721699 CAAATCACTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 1 0.04
31 25 0.93
32 1 0.04
ACGTcount: A:0.33, C:0.13, G:0.07, T:0.48
Consensus pattern (31 bp):
TAGTCATCTAACTATTCAAAAGTTTTTATTT
Found at i:724436 original size:20 final size:20
Alignment explanation
Indices: 724411--724449 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
724401 AAATTTTATA
*
724411 ATATATTAAAATAATATAAT
1 ATATATTAAAAAAATATAAT
724431 ATATATTAAAAAAATATAA
1 ATATATTAAAAAAATATAA
724450 AACAATGCAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (20 bp):
ATATATTAAAAAAATATAAT
Found at i:731141 original size:12 final size:12
Alignment explanation
Indices: 731124--731150 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
731114 CCAGAACCGG
731124 CCAAATCTTCTA
1 CCAAATCTTCTA
731136 CCAAATCTTCTA
1 CCAAATCTTCTA
731148 CCA
1 CCA
731151 GATCAAGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.33, C:0.37, G:0.00, T:0.30
Consensus pattern (12 bp):
CCAAATCTTCTA
Found at i:733826 original size:16 final size:16
Alignment explanation
Indices: 733805--733841 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
733795 TAGATTTTTT
733805 TTAAAAAAATTAATAA
1 TTAAAAAAATTAATAA
**
733821 TTAAAAGTATTAATAA
1 TTAAAAAAATTAATAA
733837 TTAAA
1 TTAAA
733842 TTTTAAAATC
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.35
Consensus pattern (16 bp):
TTAAAAAAATTAATAA
Found at i:751784 original size:44 final size:44
Alignment explanation
Indices: 751688--751806 Score: 120
Period size: 44 Copynumber: 2.7 Consensus size: 44
751678 ACTTGATGCG
*
751688 ATCTGCTCTACTACAACTTCAGAGAGATAAGATCTATTACTTTA
1 ATCTGCTCCACTACAACTTCAGAGAGATAAGATCTATTACTTTA
* * *
751732 ATCCGCTCCACTACAACTTCA-ATGAGATAGGAT-TAATTTCTTCT-
1 ATCTGCTCCACTACAACTTCAGA-GAGATAAGATCT-ATTACTT-TA
* * *
751776 GTCTGCTCCACTACTACTT-AGGGAGATAAGA
1 ATCTGCTCCACTACAACTTCAGAGAGATAAGA
751807 CTTGTAATTT
Statistics
Matches: 62, Mismatches: 9, Indels: 9
0.77 0.11 0.11
Matches are distributed among these distances:
43 11 0.18
44 50 0.81
45 1 0.02
ACGTcount: A:0.31, C:0.23, G:0.14, T:0.32
Consensus pattern (44 bp):
ATCTGCTCCACTACAACTTCAGAGAGATAAGATCTATTACTTTA
Found at i:752033 original size:29 final size:29
Alignment explanation
Indices: 751985--752043 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 29
751975 GTTTTCGATC
* * *
751985 TGCTTCGCTGTTGACGCAGGAAAGCAAGA
1 TGCTTCGCTATTAACACAGGAAAGCAAGA
*
752014 TGCTTCGCTATTAACACAGGAAGGCAAGA
1 TGCTTCGCTATTAACACAGGAAAGCAAGA
752043 T
1 T
752044 CTGCTATCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (29 bp):
TGCTTCGCTATTAACACAGGAAAGCAAGA
Found at i:752102 original size:116 final size:116
Alignment explanation
Indices: 751914--752130 Score: 335
Period size: 116 Copynumber: 1.9 Consensus size: 116
751904 ACTGTCGATG
* * * * *
751914 CAGGAAGGCAAGATCTATTATCTTTAACTAGCTCCACTACAACCGATGGAGGCAAGGCTTTGTTT
1 CAGGAAGGCAAGATCTACTATCTTCAACCAACTCCACTACAACCGATGGAGGCAAGGCTTCGTTT
* *
751979 TCGATCTGCTTCGCTGTTGACGCAGGAAAGCAAGATGCTTCGCTATTAACA
66 TCGATCTGCTTCGCTATTAACGCAGGAAAGCAAGATGCTTCGCTATTAACA
* *
752030 CAGGAAGGCAAGATCTGCTATCTTCAACCAACTCCACTGCAACCGATGGAGGCAAGGCTTCGTTT
1 CAGGAAGGCAAGATCTACTATCTTCAACCAACTCCACTACAACCGATGGAGGCAAGGCTTCGTTT
* *
752095 TTGATCTGCTTCGCTATTAACGCAGGAAGGCAAGAT
66 TCGATCTGCTTCGCTATTAACGCAGGAAAGCAAGAT
752131 CTGCTATCTT
Statistics
Matches: 90, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
116 90 1.00
ACGTcount: A:0.28, C:0.24, G:0.23, T:0.26
Consensus pattern (116 bp):
CAGGAAGGCAAGATCTACTATCTTCAACCAACTCCACTACAACCGATGGAGGCAAGGCTTCGTTT
TCGATCTGCTTCGCTATTAACGCAGGAAAGCAAGATGCTTCGCTATTAACA
Found at i:752160 original size:87 final size:87
Alignment explanation
Indices: 752014--752188 Score: 278
Period size: 87 Copynumber: 2.0 Consensus size: 87
752004 GAAAGCAAGA
* *
752014 TGCTTCGCTATTAACACAGGAAGGCAAGATCTGCTATCTTCAACCAACTCCACTGCAACCGATGG
1 TGCTTCGCTATTAACACAGGAAGGCAAGATCTGCTATCTTCAACCAACTCCACTACAACCGATGA
*
752079 AGGCAAGGCTTCGTTTTTGATC
66 AGGCAAGGCTTCGTTTTTCATC
* * * *
752101 TGCTTCGCTATTAACGCAGGAAGGCAAGATCTGCTATCTTTAACCAGCTTCACTACAACCGATGA
1 TGCTTCGCTATTAACACAGGAAGGCAAGATCTGCTATCTTCAACCAACTCCACTACAACCGATGA
*
752166 AGGCAAGGCTTTGTTTTTCATC
66 AGGCAAGGCTTCGTTTTTCATC
752188 T
1 T
752189 TCACTGATCT
Statistics
Matches: 80, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
87 80 1.00
ACGTcount: A:0.26, C:0.25, G:0.20, T:0.29
Consensus pattern (87 bp):
TGCTTCGCTATTAACACAGGAAGGCAAGATCTGCTATCTTCAACCAACTCCACTACAACCGATGA
AGGCAAGGCTTCGTTTTTCATC
Done.