Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167860.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_13, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22724830
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.34
Warning! 82000 characters in sequence are not A, C, G, or T
File 20 of 109
Found at i:3384649 original size:78 final size:80
Alignment explanation
Indices: 3384541--3384686 Score: 190
Period size: 78 Copynumber: 1.9 Consensus size: 80
3384531 TTGAGTTCTC
* * *
3384541 AAATGAGAATATTTGAATTTCAAATAAGAATTTTGA-GGTGTGAAA-CCTAAAATTTATCGAATG
1 AAATGAAAATATTTGAATTTCAAATAAGAATTTTGATAGTGTGAAACCCTAAAATTTATCAAATG
3384604 TGAATCTTCGAACTT
66 TGAATCTTCGAACTT
* * * * *
3384619 AAATGAAAATCTTT-AAGTTTCGAATGAGAATTTTTATAGTGTGAAACCCTAAAATTTGTCAAAT
1 AAATGAAAATATTTGAA-TTTCAAATAAGAATTTTGATAGTGTGAAACCCTAAAATTTATCAAAT
3384683 GTGA
65 GTGA
3384687 GCCTTTAGAC
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
77 2 0.04
78 28 0.49
79 8 0.14
80 19 0.33
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.35
Consensus pattern (80 bp):
AAATGAAAATATTTGAATTTCAAATAAGAATTTTGATAGTGTGAAACCCTAAAATTTATCAAATG
TGAATCTTCGAACTT
Found at i:3385114 original size:42 final size:41
Alignment explanation
Indices: 3384987--3385234 Score: 289
Period size: 42 Copynumber: 6.0 Consensus size: 41
3384977 ATGATCGTCA
* **
3384987 AGGAGCAATTTATTTTTCAAAGTTGTGGCGCCTCTATTTAG
1 AGGAGCATTTTATTTTTCAAAGTTGTGGTACCTCTATTTAG
* * * * * *
3385028 ATGAGCAATTTATTTTTCAAAATTATGGTATCTCTGTTTAG
1 AGGAGCATTTTATTTTTCAAAGTTGTGGTACCTCTATTTAG
* * * *
3385069 AGGAGTAGTTTATTTTTCAAAAGTTGTGGTCCCTCTGTTTAG
1 AGGAGCATTTTATTTTTC-AAAGTTGTGGTACCTCTATTTAG
*
3385111 AGGAGCATTTTATTTTTCAAAGTTGTGGTTAACTCTATTTAG
1 AGGAGCATTTTATTTTTCAAAGTTGTGG-TACCTCTATTTAG
* *
3385153 AGGAGCATTTTATTTTTCAAAATTGTGGTTGCCTCTATTTAG
1 AGGAGCATTTTATTTTTCAAAGTTGTGG-TACCTCTATTTAG
** * *
3385195 AGGATAATTTTATTTTTCAAAGTTGTGGTGCCTCTGTTTA
1 AGGAGCATTTTATTTTTCAAAGTTGTGGTACCTCTATTTA
3385235 TAAGAGCTTT
Statistics
Matches: 179, Mismatches: 26, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
41 70 0.39
42 109 0.61
ACGTcount: A:0.25, C:0.11, G:0.20, T:0.44
Consensus pattern (41 bp):
AGGAGCATTTTATTTTTCAAAGTTGTGGTACCTCTATTTAG
Found at i:3385297 original size:44 final size:44
Alignment explanation
Indices: 3385206--3385381 Score: 144
Period size: 44 Copynumber: 4.0 Consensus size: 44
3385196 GGATAATTTT
* * * * * *
3385206 ATTTTTC-AAAGTTGTGGTGCCTCTGT-TTATAAGAGCTTTATTT
1 ATTTTTCAAAAGTTGTTGAGCCTCT-TATTAGAAAAGCTTTGTTC
** *
3385249 ATTTTTTTAAAGTTGTTGAGCCTCTTATTAGAAAATCTTTGTTC
1 ATTTTTCAAAAGTTGTTGAGCCTCTTATTAGAAAAGCTTTGTTC
* * * ** *
3385293 ATTTTTCAAAAGTCGTTGAG-CTTTTGTTTAGAGGAGCTTTGTTT
1 ATTTTTCAAAAGTTGTTGAGCCTCTT-ATTAGAAAAGCTTTGTTC
* *
3385337 ATTTTTCAAAAGTTGTTGAGCCTC-TATTTAGAAGAGTTTTGTTC
1 ATTTTTCAAAAGTTGTTGAGCCTCTTA-TTAGAAAAGCTTTGTTC
3385381 A
1 A
3385382 CTCTAAAAAA
Statistics
Matches: 105, Mismatches: 23, Indels: 9
0.77 0.17 0.07
Matches are distributed among these distances:
43 11 0.10
44 92 0.88
45 2 0.02
ACGTcount: A:0.23, C:0.11, G:0.18, T:0.48
Consensus pattern (44 bp):
ATTTTTCAAAAGTTGTTGAGCCTCTTATTAGAAAAGCTTTGTTC
Found at i:3385378 original size:88 final size:86
Alignment explanation
Indices: 3385059--3385381 Score: 245
Period size: 84 Copynumber: 3.8 Consensus size: 86
3385049 ATTATGGTAT
** * ** * * *
3385059 CTCTGTTTAGAGGAG-TAGTTTATTTTTCAAAAGTTGTGGTCCCTCTGTTTAGAGGAGCA-TT-T
1 CTCTGTTTAGAGGAGCTTTTTTATTTTTCAAAAGTTGTTGAGCCTCTATTTAGAAGA-TATTTGT
* *
3385121 T-ATTTTTCAAAGTTGTGGTTA-A
65 TCATTTTTCAAAGTCGTGG--AGC
* * * * * *
3385143 CTCTATTTAGAGGAGC-ATTTTATTTTTCAAAA-TTGTGGTTGCCTCTATTTAGAGGATAATT-T
1 CTCTGTTTAGAGGAGCTTTTTTATTTTTCAAAAGTTGTTG-AGCCTCTATTTAGAAGATATTTGT
* *
3385205 T-ATTTTTCAAAGTTGTGGTGC
65 TCATTTTTCAAAGTCGTGGAGC
* * ** * *
3385226 CTCTGTTTATAAGAGCTTTATTTATTTTTTTAAAGTTGTTGAGCCTCT-TATTAGAAAATCTTTG
1 CTCTGTTTAGAGGAGCTTT-TTTATTTTTCAAAAGTTGTTGAGCCTCTAT-TTAGAAGATATTTG
*
3385290 TTCATTTTTCAAAAGTCGTTGAGC
64 TTCATTTTTC-AAAGTCGTGGAGC
* *
3385314 TTTTGTTTAGAGGAGCTTTGTTTATTTTTCAAAAGTTGTTGAGCCTCTATTTAGAAGAGT-TTTG
1 CTCTGTTTAGAGGAGCTTT-TTTATTTTTCAAAAGTTGTTGAGCCTCTATTTAGAAGA-TATTTG
3385378 TTCA
64 TTCA
3385382 CTCTAAAAAA
Statistics
Matches: 196, Mismatches: 30, Indels: 22
0.79 0.12 0.09
Matches are distributed among these distances:
83 20 0.10
84 67 0.34
85 27 0.14
86 7 0.04
87 7 0.04
88 66 0.34
89 2 0.01
ACGTcount: A:0.24, C:0.11, G:0.19, T:0.46
Consensus pattern (86 bp):
CTCTGTTTAGAGGAGCTTTTTTATTTTTCAAAAGTTGTTGAGCCTCTATTTAGAAGATATTTGTT
CATTTTTCAAAGTCGTGGAGC
Found at i:3386373 original size:21 final size:23
Alignment explanation
Indices: 3386335--3386383 Score: 75
Period size: 21 Copynumber: 2.2 Consensus size: 23
3386325 ATTTTTTTGT
3386335 TTTATTTTTTATGTGTTTGTTTA
1 TTTATTTTTTATGTGTTTGTTTA
*
3386358 TTTATTTTTT-TG-GTTTTTTTA
1 TTTATTTTTTATGTGTTTGTTTA
3386379 TTTAT
1 TTTAT
3386384 GTGTTTGTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 13 0.52
22 2 0.08
23 10 0.40
ACGTcount: A:0.12, C:0.00, G:0.10, T:0.78
Consensus pattern (23 bp):
TTTATTTTTTATGTGTTTGTTTA
Found at i:3386374 original size:37 final size:36
Alignment explanation
Indices: 3386325--3386401 Score: 122
Period size: 37 Copynumber: 2.1 Consensus size: 36
3386315 GCCGTTTTCA
3386325 ATTTTTTTGTTTTATTT-TTTATGTGTTTGTTTATTT
1 ATTTTTTTGTTTT-TTTATTTATGTGTTTGTTTATTT
3386361 ATTTTTTTGGTTTTTTTATTTATGTGTTTGTTTATTT
1 ATTTTTTT-GTTTTTTTATTTATGTGTTTGTTTATTT
3386398 -TTTT
1 ATTTT
3386402 AAACAGTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
36 15 0.38
37 24 0.62
ACGTcount: A:0.10, C:0.00, G:0.12, T:0.78
Consensus pattern (36 bp):
ATTTTTTTGTTTTTTTATTTATGTGTTTGTTTATTT
Found at i:3386390 original size:21 final size:20
Alignment explanation
Indices: 3386330--3386402 Score: 75
Period size: 20 Copynumber: 3.8 Consensus size: 20
3386320 TTTCAATTTT
3386330 TTTGTTTTATTT-TTTATGTG
1 TTTGTTTT-TTTATTTATGTG
*
3386350 TTTGTTTATTTATTT-T-T-
1 TTTGTTTTTTTATTTATGTG
*
3386367 TTGGTTTTTTTATTTATGTG
1 TTTGTTTTTTTATTTATGTG
3386387 TTTGTTTATTTT-TTTA
1 TTTGTTT-TTTTATTTA
3386403 AACAGTTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 10
0.76 0.07 0.17
Matches are distributed among these distances:
17 13 0.30
18 2 0.05
19 5 0.11
20 20 0.45
21 4 0.09
ACGTcount: A:0.11, C:0.00, G:0.12, T:0.77
Consensus pattern (20 bp):
TTTGTTTTTTTATTTATGTG
Found at i:3386411 original size:37 final size:36
Alignment explanation
Indices: 3386333--3386414 Score: 94
Period size: 37 Copynumber: 2.2 Consensus size: 36
3386323 CAATTTTTTT
****
3386333 GTTTTATTTTTTATGTGTTTGTTTATTTATTTTTTTG
1 GTTTT-TTTTTTATGTGTTTGTTTATTTATTTTAACA
3386370 GTTTTTTTATTTATGTGTTTGTTTATTT-TTTTAAACA
1 GTTTTTTT-TTTATGTGTTTGTTTATTTATTTT-AACA
3386407 GTTTTTTT
1 GTTTTTTT
3386415 GCATGAATAA
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
36 7 0.18
37 32 0.82
ACGTcount: A:0.13, C:0.01, G:0.12, T:0.73
Consensus pattern (36 bp):
GTTTTTTTTTTATGTGTTTGTTTATTTATTTTAACA
Found at i:3386573 original size:72 final size:71
Alignment explanation
Indices: 3386495--3386695 Score: 190
Period size: 71 Copynumber: 2.9 Consensus size: 71
3386485 TAATTTGTTT
* *
3386495 TAAAATAAAATTATAAAAAAAATATTTTAAGGAAAAGTTAAAAGTATCAATTTTTCTTAAAAATA
1 TAAAATAAAATT-TAAAAAAAACATTTTAAGAAAAAGTTAAAAGTATCAATTTTTCTTAAAAATA
3386560 AAATTTC
65 AAATTTC
**** * * * * *
3386567 TAAAATAAAATTTTTCGAAAGCATTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAATTAA
1 TAAAATAAAATTTAAAAAAAACATTTTAAGAAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAA
3386632 AATTTC
66 AATTTC
*
3386638 ------AAAA---AAAAAAAACATTTTGAAG-AAAAGTTAGAAGTATCAATTTTT-TTAAAAAAT
1 TAAAATAAAATTTAAAAAAAACATTTT-AAGAAAAAGTTAAAAGTATCAATTTTTCTT-AAAAAT
3386692 AAAA
64 AAAA
3386696 ATTATTAAGA
Statistics
Matches: 106, Mismatches: 21, Indels: 14
0.75 0.15 0.10
Matches are distributed among these distances:
61 2 0.02
62 38 0.36
63 2 0.02
65 4 0.04
71 48 0.45
72 12 0.11
ACGTcount: A:0.53, C:0.05, G:0.08, T:0.34
Consensus pattern (71 bp):
TAAAATAAAATTTAAAAAAAACATTTTAAGAAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAA
AATTTC
Found at i:3386582 original size:16 final size:18
Alignment explanation
Indices: 3386543--3386582 Score: 52
Period size: 14 Copynumber: 2.4 Consensus size: 18
3386533 TAAAAGTATC
3386543 AATTTTTCTTAAAAATAA
1 AATTTTTCTTAAAAATAA
3386561 AA--TTTC-T-AAAATAA
1 AATTTTTCTTAAAAATAA
3386575 AATTTTTC
1 AATTTTTC
3386583 GAAAGCATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 6
0.77 0.00 0.23
Matches are distributed among these distances:
14 9 0.45
15 1 0.05
16 8 0.40
18 2 0.10
ACGTcount: A:0.47, C:0.07, G:0.00, T:0.45
Consensus pattern (18 bp):
AATTTTTCTTAAAAATAA
Found at i:3386739 original size:61 final size:62
Alignment explanation
Indices: 3386509--3386742 Score: 179
Period size: 71 Copynumber: 3.6 Consensus size: 62
3386499 ATAAAATTAT
* * * *
3386509 AAAAAAAATATTTT-AAGGAAAAGTTAAAAGTATCAATTTTTCTTAAAAATAAAATTTCTAAAA
1 AAAAAAAACATTTTGAA-AAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAAATTC-AAAA
* * * * *
3386572 TAAAATTTTTCGAAAGCATTTTGAGAAAAAGTTGAAAGTATCAATTTTTCTTGAAATTAAAATTT
1 -AAAA-------AAAACATTTTGAAAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAAATT
3386637 CAAAA
58 CAAAA
* **
3386642 AAAAAAAACATTTTGAAGAAAAGTT-AGAAGTATCAATTTTT-TTAAAAAATAAAAATT-ATTA
1 AAAAAAAACATTTTGAAAAAAAGTTGA-AAGTATCAATTTTTCTT-AAAAATAAAAATTCAAAA
* *** *
3386703 AGAAAAATTTTTTTTAAAAAAAGTTGAAAGTATCAATTTT
1 AAAAAAAACATTTTGAAAAAAAGTTGAAAGTATCAATTTT
3386743 GTTTTGTATA
Statistics
Matches: 138, Mismatches: 21, Indels: 25
0.75 0.11 0.14
Matches are distributed among these distances:
61 37 0.27
62 43 0.31
64 4 0.03
69 4 0.03
70 4 0.03
71 45 0.33
72 1 0.01
ACGTcount: A:0.51, C:0.05, G:0.09, T:0.35
Consensus pattern (62 bp):
AAAAAAAACATTTTGAAAAAAAGTTGAAAGTATCAATTTTTCTTAAAAATAAAAATTCAAAA
Found at i:3387356 original size:18 final size:18
Alignment explanation
Indices: 3387333--3387372 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
3387323 GAAAAGAGAA
*
3387333 AGGAATGAGAGAGTTGTG
1 AGGAATGAGAGAGTTGAG
*
3387351 AGGAATGATAGAGTTGAG
1 AGGAATGAGAGAGTTGAG
3387369 AGGA
1 AGGA
3387373 CTAATGCCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.00, G:0.42, T:0.20
Consensus pattern (18 bp):
AGGAATGAGAGAGTTGAG
Found at i:3388158 original size:13 final size:13
Alignment explanation
Indices: 3388140--3388165 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3388130 TTAGTTAAAG
3388140 AAAAATCAAAATA
1 AAAAATCAAAATA
3388153 AAAAATCAAAATA
1 AAAAATCAAAATA
3388166 GAAAGGAATG
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:0.77, C:0.08, G:0.00, T:0.15
Consensus pattern (13 bp):
AAAAATCAAAATA
Found at i:3388354 original size:59 final size:61
Alignment explanation
Indices: 3388190--3388492 Score: 374
Period size: 58 Copynumber: 5.1 Consensus size: 61
3388180 AATGATTTTT
* * * * * *
3388190 TTTTTAGGGAAAATTGATACTTTCAAC-TTTCCCCACAAACATTTTTTTTTGAAAATTT-A
1 TTTTTAAGGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTTGGAAATTTTGA
* *
3388249 -TTTTAAGAAAAATTGATACTTTCAACTTTTTCTCAAAAATA-TTTTTTTGGAAA-TTT-A
1 TTTTTAAGGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTTGGAAATTTTGA
* *
3388306 TTTTTAAGGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTT-GAAACTTTGA
1 TTTTTAAGGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTTGGAAATTTTGA
** * * *
3388366 TTTCCAAGGAAAATTGATACTTTCAACTTTTTCCTAAAAATA--TTTTTCGAAAATTTTGA
1 TTTTTAAGGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTTGGAAATTTTGA
*
3388425 TTTTCAAGGAAAATTGATACTTTCAA-TTTTTCCCTAAAAATATTTTTTTTTGGAAATTTTGA
1 TTTTTAAGGAAAATTGATACTTTCAACTTTTTCCC-AAAAATA-TTTTTTTTGGAAATTTTGA
3388487 TTTTTA
1 TTTTTA
3388493 TTTAAAGAAA
Statistics
Matches: 214, Mismatches: 20, Indels: 17
0.85 0.08 0.07
Matches are distributed among these distances:
57 4 0.02
58 91 0.43
59 60 0.28
60 39 0.18
62 20 0.09
ACGTcount: A:0.34, C:0.11, G:0.08, T:0.47
Consensus pattern (61 bp):
TTTTTAAGGAAAATTGATACTTTCAACTTTTTCCCAAAAATATTTTTTTTGGAAATTTTGA
Found at i:3388520 original size:22 final size:21
Alignment explanation
Indices: 3388495--3388581 Score: 65
Period size: 22 Copynumber: 4.2 Consensus size: 21
3388485 GATTTTTATT
3388495 TAAAGAAAATAGAATAATAAAA
1 TAAAGAAAATAGAA-AATAAAA
* *
3388517 TAAAAAAAAT-GAAAGTTAAAA
1 TAAAGAAAATAGAAA-ATAAAA
*
3388538 -ATA-AAAATA-AAAATAAAA
1 TAAAGAAAATAGAAAATAAAA
* * *
3388556 TAAAGATAAAAAGAATATTAAA
1 TAAAGA-AAATAGAAAATAAAA
3388578 TAAA
1 TAAA
3388582 CCTAATCTAA
Statistics
Matches: 51, Mismatches: 8, Indels: 12
0.72 0.11 0.17
Matches are distributed among these distances:
18 5 0.10
19 10 0.20
20 4 0.08
21 12 0.24
22 20 0.39
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.20
Consensus pattern (21 bp):
TAAAGAAAATAGAAAATAAAA
Found at i:3388544 original size:6 final size:6
Alignment explanation
Indices: 3388533--3388567 Score: 54
Period size: 6 Copynumber: 6.0 Consensus size: 6
3388523 AAATGAAAGT
*
3388533 TAAAAA TAAAAA TAAAAA T-AAAA TAAAGA TAAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
3388568 GAATATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.80, C:0.00, G:0.03, T:0.17
Consensus pattern (6 bp):
TAAAAA
Found at i:3388555 original size:11 final size:11
Alignment explanation
Indices: 3388533--3388566 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
3388523 AAATGAAAGT
3388533 TAAAAATAAAAA
1 TAAAAAT-AAAA
3388545 TAAAAATAAAA
1 TAAAAATAAAA
*
3388556 TAAAGATAAAA
1 TAAAAATAAAA
3388567 AGAATATTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 14 0.67
12 7 0.33
ACGTcount: A:0.79, C:0.00, G:0.03, T:0.18
Consensus pattern (11 bp):
TAAAAATAAAA
Found at i:3388555 original size:17 final size:17
Alignment explanation
Indices: 3388535--3388567 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3388525 ATGAAAGTTA
3388535 AAAATAAAAATAAAAAT
1 AAAATAAAAATAAAAAT
*
3388552 AAAATAAAGATAAAAA
1 AAAATAAAAATAAAAA
3388568 GAATATTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.82, C:0.00, G:0.03, T:0.15
Consensus pattern (17 bp):
AAAATAAAAATAAAAAT
Found at i:3388565 original size:29 final size:28
Alignment explanation
Indices: 3388513--3388567 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 28
3388503 ATAGAATAAT
*
3388513 AAAATAAAAAAAATGAAAGTTAAAAATA
1 AAAATAAAAAAAATGAAAGATAAAAATA
3388541 AAAATAAAAATAAAAT-AAAGATAAAAA
1 AAAAT-AAAA-AAAATGAAAGATAAAAA
3388568 GAATATTAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
28 5 0.21
29 14 0.58
30 5 0.21
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.16
Consensus pattern (28 bp):
AAAATAAAAAAAATGAAAGATAAAAATA
Found at i:3388624 original size:24 final size:24
Alignment explanation
Indices: 3388590--3388635 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
3388580 AACCTAATCT
*
3388590 AATAAATAAATAAAAT-AAAAAACA
1 AATAAACAAAT-AAATGAAAAAACA
3388614 AATAAACAAATAAATGAAAAAA
1 AATAAACAAATAAATGAAAAAA
3388636 AAAAACCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 16 0.80
ACGTcount: A:0.78, C:0.04, G:0.02, T:0.15
Consensus pattern (24 bp):
AATAAACAAATAAATGAAAAAACA
Found at i:3389570 original size:25 final size:25
Alignment explanation
Indices: 3389542--3389669 Score: 74
Period size: 25 Copynumber: 5.2 Consensus size: 25
3389532 AAAAAAGAAA
*
3389542 ATAATTATA-ATATAATAATAAATAT
1 ATAATTATATAAAT-ATAATAAATAT
*
3389567 ATAATTATATAAATATAATACATAT
1 ATAATTATATAAATATAATAAATAT
* * *
3389592 A-AA-TAT-TAACAGAGAAATAAATAA
1 ATAATTATATAA-ATA-TAATAAATAT
* * *
3389616 ATAAATAAATAAATA-AATAAAGAT
1 ATAATTATATAAATATAATAAATAT
3389640 ATACA-TATATTAATATATAAT-AATA-
1 ATA-ATTATA-TAA-ATATAATAAATAT
3389665 ATAAT
1 ATAAT
3389670 GAATAATAAA
Statistics
Matches: 80, Mismatches: 12, Indels: 22
0.70 0.11 0.19
Matches are distributed among these distances:
22 3 0.04
23 5 0.06
24 24 0.30
25 29 0.36
26 13 0.16
27 6 0.08
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.34
Consensus pattern (25 bp):
ATAATTATATAAATATAATAAATAT
Found at i:3389580 original size:16 final size:14
Alignment explanation
Indices: 3389551--3389683 Score: 73
Period size: 16 Copynumber: 9.3 Consensus size: 14
3389541 AATAATTATA
3389551 ATATAATAATAAAT
1 ATATAATAATAAAT
3389565 ATATAATTATATAAAT
1 ATATAA-TA-ATAAAT
3389581 ATAATACAT-ATAAAT
1 AT-ATA-ATAATAAAT
* *
3389596 AT-TAACAGAGAAAT
1 ATATAATA-ATAAAT
*
3389610 AAAT-A-AATAAAT
1 ATATAATAATAAAT
* *
3389622 AAATAAATAAATAAAG
1 ATAT-AAT-AATAAAT
*
3389638 ATATACATATATTAAT
1 ATATA-ATA-ATAAAT
3389654 ATATAATAAT-AAT
1 ATATAATAATAAAT
3389667 A-ATGAATAATAAA-
1 ATAT-AATAATAAAT
3389680 ATAT
1 ATAT
3389684 GTAAAATACA
Statistics
Matches: 95, Mismatches: 8, Indels: 32
0.70 0.06 0.24
Matches are distributed among these distances:
12 12 0.13
13 14 0.15
14 20 0.21
15 16 0.17
16 28 0.29
17 4 0.04
18 1 0.01
ACGTcount: A:0.62, C:0.02, G:0.03, T:0.32
Consensus pattern (14 bp):
ATATAATAATAAAT
Found at i:3389582 original size:14 final size:14
Alignment explanation
Indices: 3389541--3389669 Score: 78
Period size: 14 Copynumber: 9.4 Consensus size: 14
3389531 AAAAAAAGAA
3389541 AATAAT-TATAATAT
1 AATAATATA-AATAT
3389555 AATAATA-AATATAT
1 AATAATATAA-ATAT
*
3389569 AATTATATAAATAT
1 AATAATATAAATAT
3389583 AATACATATAAATATT
1 AATA-ATATAAATA-T
* * *
3389599 AA-CAGAGAAATA-
1 AATAATATAAATAT
3389611 AATAA-ATAAATA-
1 AATAATATAAATAT
3389623 AATAA-ATAAATA-
1 AATAATATAAATAT
* *
3389635 AA-GATATACATAT
1 AATAATATAAATAT
*
3389648 ATTAATATATAATAAT
1 AATAATATA-AAT-AT
3389664 AATAAT
1 AATAAT
3389670 GAATAATAAA
Statistics
Matches: 91, Mismatches: 13, Indels: 20
0.73 0.10 0.16
Matches are distributed among these distances:
11 1 0.01
12 28 0.31
13 3 0.03
14 36 0.40
15 13 0.14
16 10 0.11
ACGTcount: A:0.62, C:0.02, G:0.02, T:0.33
Consensus pattern (14 bp):
AATAATATAAATAT
Found at i:3389615 original size:4 final size:4
Alignment explanation
Indices: 3389606--3389636 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
3389596 ATTAACAGAG
3389606 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAA
3389637 GATATACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (4 bp):
AAAT
Found at i:3389882 original size:1 final size:1
Alignment explanation
Indices: 3389872--3389972 Score: 67
Period size: 1 Copynumber: 101.0 Consensus size: 1
3389862 AACATTGTCA
* * ** * ** * ** * *
3389872 TTTTTGTTTTTTTTTGTTTTTTCGTGTTTTTTTTTGGTTTTTTTTGTTTTGCTTTTTGTTCTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
* * *
3389937 TTTTGTTTTTTTTTTATTTTTTTGTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
3389973 ACCAAAGCTC
Statistics
Matches: 74, Mismatches: 26, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
1 74 1.00
ACGTcount: A:0.01, C:0.03, G:0.11, T:0.85
Consensus pattern (1 bp):
T
Found at i:3389887 original size:10 final size:10
Alignment explanation
Indices: 3389872--3389969 Score: 117
Period size: 10 Copynumber: 9.5 Consensus size: 10
3389862 AACATTGTCA
3389872 TTTTTGTTTT
1 TTTTTGTTTT
3389882 TTTTTGTTTT
1 TTTTTGTTTT
**
3389892 TTCGTGTTTT
1 TTTTTGTTTT
*
3389902 TTTTTGGTTT
1 TTTTTGTTTT
3389912 TTTTTGTTTT
1 TTTTTGTTTT
3389922 GCTTTTTGTTCTTT
1 --TTTTTG-T-TTT
3389936 TTTTTGTTTT
1 TTTTTGTTTT
*
3389946 TTTTT-TATT
1 TTTTTGTTTT
3389955 TTTTTGTTTT
1 TTTTTGTTTT
3389965 TTTTT
1 TTTTT
3389970 TTTACCAAAG
Statistics
Matches: 75, Mismatches: 8, Indels: 10
0.81 0.09 0.11
Matches are distributed among these distances:
9 8 0.11
10 50 0.67
11 1 0.01
12 12 0.16
13 1 0.01
14 3 0.04
ACGTcount: A:0.01, C:0.03, G:0.11, T:0.85
Consensus pattern (10 bp):
TTTTTGTTTT
Found at i:3389901 original size:20 final size:20
Alignment explanation
Indices: 3389872--3389969 Score: 103
Period size: 19 Copynumber: 4.8 Consensus size: 20
3389862 AACATTGTCA
3389872 TTTTTGTTTTTTTTTGT-TT
1 TTTTTGTTTTTTTTTGTATT
*
3389891 TTTCGTGTTTTTTTTTGGT-TT
1 TTT-TTGTTTTTTTTT-GTATT
*
3389912 TTTTTGTTTTGCTTTTTGTTCTTT
1 TTTTTGTTTT--TTTTTG-T-ATT
3389936 TTTTTGTTTTTTTTT-TATT
1 TTTTTGTTTTTTTTTGTATT
3389955 TTTTTGTTTTTTTTT
1 TTTTTGTTTTTTTTT
3389970 TTTACCAAAG
Statistics
Matches: 69, Mismatches: 3, Indels: 14
0.80 0.03 0.16
Matches are distributed among these distances:
19 20 0.29
20 18 0.26
21 8 0.12
22 11 0.16
24 12 0.17
ACGTcount: A:0.01, C:0.03, G:0.11, T:0.85
Consensus pattern (20 bp):
TTTTTGTTTTTTTTTGTATT
Found at i:3389972 original size:24 final size:24
Alignment explanation
Indices: 3389872--3389972 Score: 82
Period size: 27 Copynumber: 4.0 Consensus size: 24
3389862 AACATTGTCA
* *
3389872 TTTTTGTTTT-TTTTTGTTTTTTC
1 TTTTTTTTTTGTTTTTTTTTTTTC
3389895 GTGTTTTTTTTTGGTTTTTTTTGTTTTGC
1 -T-TTTTTTTTT-GTTTTTTTT-TTTT-C
3389924 TTTTTGTTCTTT-TTTTTGTTTTTTT-
1 TTTTT-TT-TTTGTTTTT-TTTTTTTC
3389949 TTTATTTTTTTGTTTTTTTTTTTT
1 TTT-TTTTTTTGTTTTTTTTTTTT
3389973 ACCAAAGCTC
Statistics
Matches: 65, Mismatches: 2, Indels: 20
0.75 0.02 0.23
Matches are distributed among these distances:
24 11 0.17
25 18 0.28
26 2 0.03
27 20 0.31
28 10 0.15
29 4 0.06
ACGTcount: A:0.01, C:0.03, G:0.11, T:0.85
Consensus pattern (24 bp):
TTTTTTTTTTGTTTTTTTTTTTTC
Found at i:3390072 original size:41 final size:41
Alignment explanation
Indices: 3389979--3390528 Score: 777
Period size: 41 Copynumber: 13.1 Consensus size: 41
3389969 TTTTACCAAA
* * *
3389979 GCTCCTCTAAACAGAGGCTCAACGACTTTGAGAAACATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAA-GTAAATT
* *
3390022 GCTCCTCTAAATAGAGGCACCACGAC-TTGAAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTG-AAAAGTAAATT
3390063 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
3390104 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAATTAAATTGCTCTGT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAA------T-T
*
3390152 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAATTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
3390193 GCTCCTCTAAACAGAGGCACCACGACTTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATT
*
3390235 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
3390276 GCTCCTCTAAACAGAGGCA--ACGGAACTTTGAAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCAC-G-ACTTTG-AAAAGTAAATT
3390318 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
*
3390359 GCTCCTCTAAACAGAGGCA--ACGAAACTTTGAAAAAATAAATT
1 GCTCCTCTAAACAGAGGCACCACG--ACTTTG-AAAAGTAAATT
*
3390401 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
* *
3390442 ACTCCTCTAAACAGAGGCATCACGACTTTTGAAAAGTAAATT
1 GCTCCTCTAAACAGAGGCACCACGAC-TTTGAAAAGTAAATT
*
3390484 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAACT
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
3390525 GCTC
1 GCTC
3390529 TTTGACAATC
Statistics
Matches: 466, Mismatches: 20, Indels: 44
0.88 0.04 0.08
Matches are distributed among these distances:
39 5 0.01
40 1 0.00
41 232 0.50
42 157 0.34
43 25 0.05
44 5 0.01
47 1 0.00
48 40 0.09
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (41 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATT
Found at i:3390274 original size:83 final size:83
Alignment explanation
Indices: 3389979--3390528 Score: 792
Period size: 83 Copynumber: 6.5 Consensus size: 83
3389969 TTTTACCAAA
* * * *
3389979 GCTCCTCTAAACAGAGGCTCAACGACTTTGAGAAACATAAATTGCTCCTCTAAATAGAGGCACCA
1 GCTCCTCTAAACAGAGGCACCACGACTTTGA-AAA-GTAAATTGCTCCTCTAAACAGAGGCACCA
3390044 CGAC-TTGAAAAAATAAATT
64 CGACTTTGAAAAAATAAATT
3390063 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
*
3390128 ACTTTG-AAAATTAAATTGCTCTGT
66 ACTTTGAAAAAATAAA------T-T
*
3390152 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAATTAAATTGCTCCTCTAAACAGAGGCACCACG
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
*
3390217 ACTTTTG-AAAAGTAAATT
66 AC-TTTGAAAAAATAAATT
*
3390235 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTGCTCCTCTAAACAGAGGCA--ACG
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCAC-
3390298 GAACTTTGAAAAAATAAATT
65 G-ACTTTGAAAAAATAAATT
3390318 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCA--ACG
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
3390381 AAACTTTGAAAAAATAAATT
66 --ACTTTGAAAAAATAAATT
* * *
3390401 GCTCCTCTAAACAGAGGCACCACGACTTTGGAAAGTAAATTACTCCTCTAAACAGAGGCATCACG
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
*
3390466 ACTTTTG-AAAAGTAAATT
66 AC-TTTGAAAAAATAAATT
*
3390484 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAACTGCTC
1 GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTC
3390529 TTTGACAATC
Statistics
Matches: 433, Mismatches: 17, Indels: 33
0.90 0.04 0.07
Matches are distributed among these distances:
81 2 0.00
82 45 0.10
83 269 0.62
84 34 0.08
85 3 0.01
88 1 0.00
89 67 0.15
90 12 0.03
ACGTcount: A:0.37, C:0.23, G:0.17, T:0.23
Consensus pattern (83 bp):
GCTCCTCTAAACAGAGGCACCACGACTTTGAAAAGTAAATTGCTCCTCTAAACAGAGGCACCACG
ACTTTGAAAAAATAAATT
Found at i:3391747 original size:10 final size:10
Alignment explanation
Indices: 3391732--3391773 Score: 59
Period size: 10 Copynumber: 4.3 Consensus size: 10
3391722 TATTTTTTCA
3391732 TTTTCTCATT
1 TTTTCTCATT
3391742 TTTTCTCATT
1 TTTTCTCATT
* *
3391752 TTTTTTC-TC
1 TTTTCTCATT
3391761 TTTTCTCATT
1 TTTTCTCATT
3391771 TTT
1 TTT
3391774 CATCCATTGT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
9 7 0.26
10 20 0.74
ACGTcount: A:0.07, C:0.19, G:0.00, T:0.74
Consensus pattern (10 bp):
TTTTCTCATT
Found at i:3394465 original size:15 final size:15
Alignment explanation
Indices: 3394445--3394491 Score: 76
Period size: 15 Copynumber: 3.1 Consensus size: 15
3394435 TTGTAAGTGT
3394445 AATGAATGAGAATGC
1 AATGAATGAGAATGC
*
3394460 AATGAATGAGAATGT
1 AATGAATGAGAATGC
3394475 AATGAATGAGAAATGC
1 AATGAATGAG-AATGC
3394491 A
1 A
3394492 TGTATGCAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
15 24 0.83
16 5 0.17
ACGTcount: A:0.49, C:0.04, G:0.26, T:0.21
Consensus pattern (15 bp):
AATGAATGAGAATGC
Found at i:3397519 original size:60 final size:59
Alignment explanation
Indices: 3397451--3397807 Score: 393
Period size: 60 Copynumber: 6.0 Consensus size: 59
3397441 TTTTGTGTAG
3397451 GGAAAATTGATACTTTCAACTTTTCCCCACAAACATTTTTTTTTTGAAAATTT-ATTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCA-AAA-ATTTTTTTTTTGAAAATTTGATTTTAA
* * * *
3397511 GGAAAATTGATACTTTCAACTTTTCCTCAAAAA-TATGTTTTTGGAAATTT-ATTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATTTTTTTTTTGAAAATTTGA-TTTTAA
* * * *
3397569 GGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTTTGAAACTTTGATTTCCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAAT-TTTTTTTTTGAAAATTTGATTT-TAA
* * **
3397630 GAAAAATTGATACTTTCAACTTTTCCCCAAAAATCTTTTTTTTT-AAATTTATTTTTTTAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAAT-TTTTTTTTTGAAAATT-TGATTTTAA
* * * * *
3397690 GAAAAATTGATACTTTCAACTTTTTCCTAAAAA--TATTTTTCGAAAATTTTGATTTTCAA
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAATTTTTTTTTTGAAAA-TTTGATTTT-AA
* * *
3397749 AGAAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAAATTTTGATTTT
1 GGAAAATTGATACTTTCAACTTTTCCCCAAAAAT-TTTTTTTTT-GAAAATTTGATTTT
3397808 TATTTAAAGA
Statistics
Matches: 253, Mismatches: 31, Indels: 24
0.82 0.10 0.08
Matches are distributed among these distances:
57 21 0.08
58 47 0.19
59 37 0.15
60 82 0.32
61 47 0.19
62 15 0.06
63 4 0.02
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.46
Consensus pattern (59 bp):
GGAAAATTGATACTTTCAACTTTTCCCCAAAAATTTTTTTTTTGAAAATTTGATTTTAA
Found at i:3397661 original size:119 final size:117
Alignment explanation
Indices: 3397451--3397809 Score: 433
Period size: 119 Copynumber: 3.0 Consensus size: 117
3397441 TTTTGTGTAG
* * *
3397451 GGAAAATTGATACTTTCAACTTTTCCCCACAAACAT-TTTTTTTTTGAAAATTT-ATTTTAAGGA
1 GGAAAATTGATACTTTCAACTTTT-TCCA-AAA-ATATTTTTTTTTGAAAATTTGATTTCAAGAA
* *
3397514 AAATTGATACTTTCAACTTTTCCTCAAAAATATGTTTTTGGAAATTTATTTTTAA
63 AAATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTATTTTTAA
*
3397569 GGAAAATTGATACTTTCAACTTTTTCTCAAAAATATTTTTTTTTGAAACTTTGATTTCCAAGAAA
1 GGAAAATTGATACTTTCAACTTTTTC-CAAAAATATTTTTTTTTGAAAATTTGATTT-CAAGAAA
* **
3397634 AATTGATACTTTCAACTTTTCCCCAAAAATCTTTTTTTTTAAATTTATTTTTTTAA
64 AATTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTA--TTTTTAA
* *
3397690 GAAAAATTGATACTTTCAACTTTTTCCTAAAAATA---TTTTTCGAAAATTTTGATTTTCAA-AG
1 GGAAAATTGATACTTTCAACTTTTTCC-AAAAATATTTTTTTTTGAAAA-TTTGA-TTTCAAGA-
*
3397751 AAAATTGATACTTTCAACTTTTCCCTAAAAATATTTTTTTTTGGAAATTTTGATTTTTA
62 AAAATTGATACTTTCAACTTTTCCCCAAAAATA--TTTTTTTGGAAA-TTT-ATTTTTA
3397810 TTTAAAGAAA
Statistics
Matches: 211, Mismatches: 16, Indels: 25
0.84 0.06 0.10
Matches are distributed among these distances:
116 2 0.01
117 20 0.09
118 40 0.19
119 86 0.41
120 4 0.02
121 55 0.26
122 3 0.01
123 1 0.00
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.47
Consensus pattern (117 bp):
GGAAAATTGATACTTTCAACTTTTTCCAAAAATATTTTTTTTTGAAAATTTGATTTCAAGAAAAA
TTGATACTTTCAACTTTTCCCCAAAAATATTTTTTTGGAAATTTATTTTTAA
Found at i:3397790 original size:179 final size:180
Alignment explanation
Indices: 3397453--3397806 Score: 517
Period size: 179 Copynumber: 2.0 Consensus size: 180
3397443 TTGTGTAGGG
*
3397453 AAAATTGATACTTTCAACTTTTCCCCACAAACATTTTTTTTTTGAAAATTTATTTTAAGGAAAAT
1 AAAATTGATACTTTCAACTTTTCCCCACAAACATTTTTTTTTTGAAAATTTATTTTAAGAAAAAT
* * * *
3397518 TGATACTTTCAACTTTTCCTCAAAAATATGTTTTTGGAAATTTATTTTTAAGGAAAATTGATACT
66 TGATACTTTCAACTTTTCCTCAAAAATATGTTTTCGAAAATTTATTTTCAAAGAAAATTGATACT
*
3397583 TTCAACTTTTTCTCAAAAATATTTTTTTTT-GAAACTTTGATTTCCAAGA
131 TTCAACTTTTCCTCAAAAATATTTTTTTTTGGAAACTTTGATTTCCAAGA
3397632 AAAATTGATACTTTCAACTTTTCCCCA-AAA-ATCTTTTTTTTT--AAATTTATTTTTTTAAGAA
1 AAAATTGATACTTTCAACTTTTCCCCACAAACAT-TTTTTTTTTGAAAATTTA---TTTTAAGAA
3397693 AAATTGATACTTTCAACTTTTTCCT-AAAAATAT-TTTTCGAAAATTTTGATTTTCAAAGAAAAT
62 AAATTGATACTTTCAAC-TTTTCCTCAAAAATATGTTTTCGAAAA-TTT-ATTTTCAAAGAAAAT
*
3397756 TGATACTTTCAACTTTTCC-CTAAAAATATTTTTTTTTGGAAATTTTGATTT
124 TGATACTTTCAACTTTTCCTC-AAAAATATTTTTTTTTGGAAACTTTGATTT
3397807 TTATTTAAAG
Statistics
Matches: 159, Mismatches: 7, Indels: 16
0.87 0.04 0.09
Matches are distributed among these distances:
176 7 0.04
177 2 0.01
178 20 0.13
179 64 0.40
180 54 0.34
181 12 0.08
ACGTcount: A:0.34, C:0.12, G:0.07, T:0.47
Consensus pattern (180 bp):
AAAATTGATACTTTCAACTTTTCCCCACAAACATTTTTTTTTTGAAAATTTATTTTAAGAAAAAT
TGATACTTTCAACTTTTCCTCAAAAATATGTTTTCGAAAATTTATTTTCAAAGAAAATTGATACT
TTCAACTTTTCCTCAAAAATATTTTTTTTTGGAAACTTTGATTTCCAAGA
Found at i:3397835 original size:5 final size:5
Alignment explanation
Indices: 3397827--3397883 Score: 57
Period size: 5 Copynumber: 11.4 Consensus size: 5
3397817 AAAATAGAAT
*
3397827 AATAA AATAA AA-AA AAT-A AA-AA AACAA AATAAA AATAAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AATAA AATAA AAT-AA AAT-AA AATAA AATAA
3397876 AGATAA AA
1 A-ATAA AA
3397884 AGAATATTAA
Statistics
Matches: 46, Mismatches: 1, Indels: 10
0.81 0.02 0.18
Matches are distributed among these distances:
4 10 0.22
5 20 0.43
6 16 0.35
ACGTcount: A:0.82, C:0.02, G:0.02, T:0.14
Consensus pattern (5 bp):
AATAA
Found at i:3397847 original size:6 final size:6
Alignment explanation
Indices: 3397838--3397884 Score: 60
Period size: 6 Copynumber: 7.8 Consensus size: 6
3397828 ATAAAATAAA
* *
3397838 AAAAAT AAAAAA ACAAAAT AAAAAT AAAAAT -AAAAT AAAGAT AAAAA
1 AAAAAT AAAAAT A-AAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAA
3397885 GAATATTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
5 5 0.14
6 25 0.71
7 5 0.14
ACGTcount: A:0.83, C:0.02, G:0.02, T:0.13
Consensus pattern (6 bp):
AAAAAT
Found at i:3397873 original size:17 final size:17
Alignment explanation
Indices: 3397817--3397884 Score: 68
Period size: 17 Copynumber: 3.9 Consensus size: 17
3397807 TTATTTAAAG
3397817 AAAATAGAATAAT-AAAAT
1 AAAATA-AA-AATAAAAAT
* *
3397835 AAAA-AAAATAAAAAAAC
1 AAAATAAAA-ATAAAAAT
3397852 AAAATAAAAATAAAAAT
1 AAAATAAAAATAAAAAT
*
3397869 AAAATAAAGATAAAAA
1 AAAATAAAAATAAAAA
3397885 GAATATTAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 7
0.78 0.09 0.13
Matches are distributed among these distances:
15 1 0.02
16 3 0.07
17 30 0.71
18 8 0.19
ACGTcount: A:0.81, C:0.01, G:0.03, T:0.15
Consensus pattern (17 bp):
AAAATAAAAATAAAAAT
Found at i:3397914 original size:4 final size:4
Alignment explanation
Indices: 3397907--3397946 Score: 53
Period size: 4 Copynumber: 9.8 Consensus size: 4
3397897 AACATAATCT
* *
3397907 AATA AATA AATAA AATA AACA AATA AATA AACA AATA AAT
1 AATA AATA AAT-A AATA AATA AATA AATA AATA AATA AAT
3397947 GAAAAAAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
4 27 0.87
5 4 0.13
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (4 bp):
AATA
Found at i:3397924 original size:21 final size:22
Alignment explanation
Indices: 3397818--3397937 Score: 72
Period size: 22 Copynumber: 5.5 Consensus size: 22
3397808 TATTTAAAGA
*
3397818 AAATAGAAT-AATAAA-ATAAAAA
1 AAATA-AATAAATAAACAT-AAAC
* *
3397840 AAATAAAAAAACAAA-ATAAA-
1 AAATAAATAAATAAACATAAAC
* * *
3397860 AATAAAAATAAAATAAAGATAAAA
1 AA-ATAAAT-AAATAAACATAAAC
* *
3397884 AGAAT-ATTAAATAAACATAATC
1 A-AATAAATAAATAAACATAAAC
*
3397906 TAATAAATAAATAAA-ATAAAC
1 AAATAAATAAATAAACATAAAC
3397927 AAATAAATAAA
1 AAATAAATAAA
3397938 CAAATAAATG
Statistics
Matches: 77, Mismatches: 14, Indels: 15
0.73 0.13 0.14
Matches are distributed among these distances:
20 2 0.03
21 27 0.35
22 38 0.49
23 7 0.09
24 2 0.03
25 1 0.01
ACGTcount: A:0.75, C:0.03, G:0.03, T:0.19
Consensus pattern (22 bp):
AAATAAATAAATAAACATAAAC
Found at i:3397934 original size:12 final size:12
Alignment explanation
Indices: 3397891--3397946 Score: 67
Period size: 12 Copynumber: 4.4 Consensus size: 12
3397881 AAAAGAATAT
3397891 TAAATAAACATAA
1 TAAATAAACA-AA
* *
3397904 TCTAATAAATAAA
1 T-AAATAAACAAA
3397917 TAAAATAAACAAA
1 T-AAATAAACAAA
3397930 TAAATAAACAAA
1 TAAATAAACAAA
3397942 TAAAT
1 TAAAT
3397947 GAAAAAAAAA
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
12 16 0.43
13 14 0.38
14 7 0.19
ACGTcount: A:0.70, C:0.07, G:0.00, T:0.23
Consensus pattern (12 bp):
TAAATAAACAAA
Found at i:3398958 original size:25 final size:25
Alignment explanation
Indices: 3398929--3398979 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
3398919 AGAAAAGAAA
*
3398929 ATAATTATA-ATATAATAATAAATAT
1 ATAATTATATAAAT-ATAATAAATAT
*
3398954 ATAATTATATAAATATAATACATAT
1 ATAATTATATAAATATAATAAATAT
3398979 A
1 A
3398980 AATATTAACA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 20 0.87
26 3 0.13
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (25 bp):
ATAATTATATAAATATAATAAATAT
Found at i:3398969 original size:14 final size:14
Alignment explanation
Indices: 3398928--3399049 Score: 67
Period size: 14 Copynumber: 8.4 Consensus size: 14
3398918 AAGAAAAGAA
3398928 AATAAT-TATAATAT
1 AATAATATA-AATAT
3398942 AATAATA-AATATAT
1 AATAATATAA-ATAT
*
3398956 AATTATATAAATAT
1 AATAATATAAATAT
3398970 AATACATATAAATATT
1 AATA-ATATAAATA-T
* *
3398986 AACAGAGA-AAATA-
1 AATA-ATATAAATAT
3398999 AATAA-ATAAATA-
1 AATAATATAAATAT
*
3399011 AATAAAGATATACATAT
1 AAT--A-ATATAAATAT
*
3399028 ATTAATATATAATAAT
1 AATAATATA-AAT-AT
3399044 AATAAT
1 AATAAT
3399050 GGATAATAAA
Statistics
Matches: 85, Mismatches: 10, Indels: 24
0.71 0.08 0.20
Matches are distributed among these distances:
11 1 0.01
12 9 0.11
13 4 0.05
14 30 0.35
15 20 0.24
16 19 0.22
17 2 0.02
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.34
Consensus pattern (14 bp):
AATAATATAAATAT
Found at i:3400220 original size:21 final size:21
Alignment explanation
Indices: 3400194--3400234 Score: 82
Period size: 21 Copynumber: 2.0 Consensus size: 21
3400184 CTTTTTGAAT
3400194 TAAAATATCATGCAATTAATA
1 TAAAATATCATGCAATTAATA
3400215 TAAAATATCATGCAATTAAT
1 TAAAATATCATGCAATTAAT
3400235 TATATTAAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.51, C:0.10, G:0.05, T:0.34
Consensus pattern (21 bp):
TAAAATATCATGCAATTAATA
Found at i:3401292 original size:18 final size:18
Alignment explanation
Indices: 3401258--3401291 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
3401248 AAATTCCACG
*
3401258 TTTTCTTTCCTTTTTTTA
1 TTTTCTCTCCTTTTTTTA
3401276 TTTTCTCT-CTTTTTTT
1 TTTTCTCTCCTTTTTTT
3401292 TTACTTTTAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.03, C:0.18, G:0.00, T:0.79
Consensus pattern (18 bp):
TTTTCTCTCCTTTTTTTA
Found at i:3401306 original size:19 final size:19
Alignment explanation
Indices: 3401284--3401337 Score: 74
Period size: 18 Copynumber: 2.8 Consensus size: 19
3401274 TATTTTCTCT
3401284 CTTTTTTTTTACTTTTAAC
1 CTTTTTTTTTACTTTTAAC
*
3401303 C-TTTTTTTTACTTTTTAC
1 CTTTTTTTTTACTTTTAAC
*
3401321 TTTTATTTTTTACTTTT
1 CTTT-TTTTTTACTTTT
3401338 GACCAAACTA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
18 16 0.52
19 3 0.10
20 12 0.39
ACGTcount: A:0.13, C:0.13, G:0.00, T:0.74
Consensus pattern (19 bp):
CTTTTTTTTTACTTTTAAC
Found at i:3401307 original size:18 final size:19
Alignment explanation
Indices: 3401268--3401337 Score: 72
Period size: 20 Copynumber: 3.7 Consensus size: 19
3401258 TTTTCTTTCC
**
3401268 TTTTTTTA-TTTTCTCTCTT
1 TTTTTTTACTTTTAACTC-T
3401287 TTTTTTTACTTTTAAC-CT
1 TTTTTTTACTTTTAACTCT
* *
3401305 TTTTTTTACTTTTTACTTT
1 TTTTTTTACTTTTAACTCT
3401324 TATTTTTTACTTTT
1 T-TTTTTTACTTTT
3401338 GACCAAACTA
Statistics
Matches: 44, Mismatches: 4, Indels: 5
0.83 0.08 0.09
Matches are distributed among these distances:
18 16 0.36
19 11 0.25
20 17 0.39
ACGTcount: A:0.11, C:0.13, G:0.00, T:0.76
Consensus pattern (19 bp):
TTTTTTTACTTTTAACTCT
Found at i:3402917 original size:18 final size:18
Alignment explanation
Indices: 3402894--3402937 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
3402884 ATTTGATTAA
*
3402894 TCTTAATTCTTACATTGT
1 TCTTAATTCTTACATTGG
** *
3402912 TCTTAAGACTTACTTTGG
1 TCTTAATTCTTACATTGG
3402930 TCTTAATT
1 TCTTAATT
3402938 TTTCTAAATT
Statistics
Matches: 20, Mismatches: 6, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.23, C:0.16, G:0.09, T:0.52
Consensus pattern (18 bp):
TCTTAATTCTTACATTGG
Found at i:3404513 original size:17 final size:17
Alignment explanation
Indices: 3404487--3404528 Score: 52
Period size: 17 Copynumber: 2.5 Consensus size: 17
3404477 AGCTAAAAAA
*
3404487 TTATTA-TTATATTATAT
1 TTATTATTTATAATAT-T
3404504 TTA-TATTTATAATATT
1 TTATTATTTATAATATT
3404520 TTATTATTT
1 TTATTATTT
3404529 TATGTATACA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 6 0.27
17 16 0.73
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTATTATTTATAATATT
Found at i:3405020 original size:17 final size:17
Alignment explanation
Indices: 3404986--3405023 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
3404976 AACATGCTAA
*
3404986 ATAATAAATTAGTTAAT
1 ATAATAAATTAGTAAAT
3405003 ATAATAAATATA-TAAAT
1 ATAATAAAT-TAGTAAAT
3405020 ATAA
1 ATAA
3405024 AATGAATTAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (17 bp):
ATAATAAATTAGTAAAT
Found at i:3410692 original size:230 final size:231
Alignment explanation
Indices: 3410365--3410867 Score: 600
Period size: 230 Copynumber: 2.2 Consensus size: 231
3410355 CTATTGAATG
* * * **
3410365 GGATTATTGAAGGCGTTTCTAGTTAAAATATT--TTGAATAATTCGTAAATTATTTAAGGTATTT
1 GGATTATTGAAGGCGTTTCTAGCTAAAA-ATTCCTTGAATAATTCATAAATTATTCAAGACATTT
* * * * * * **
3410428 TTAGCCAAAAACACCTTTTATAATCTACGAATTATTCATTC-AAAGAGGATTATTGATGGTGTTT
65 TTAGCCAAAAACACATTCTATAACCCACGAATTATTCATTCAAAAG-GGATTATTAAAGGCATTT
* * * * * *
3410492 TCTATCAAAAATACCTTCAATAATTCAAGC-TTTTTTTTTGGAATATTTAAAGCGTTTTTGCCTA
129 TCTATCAAAAATACCTTCAATAATTCAAGCATTTTTTTATAGAATATTCAAAGCATTTTTACCCA
*
3410556 AAAAACGCATTAAATAATTTCCTTCAATTTTTATGATA
194 AAAAACGCATTAAATAATCTCCTTCAATTTTTATGATA
*
3410594 GGATTATTGAAGGCGTTTCTAGCTAAAAATTCCTTGAATAATTCATAGATTATTCAAGACATTTT
1 GGATTATTGAAGGCGTTTCTAGCTAAAAATTCCTTGAATAATTCATAAATTATTCAAGACATTTT
* ** *
3410659 TGGCCAAAAATGCATTCTATAACCCATGAATTATTCATTCAAAAGGGATTATTAAAGGCATTTTC
66 TAGCCAAAAACACATTCTATAACCCACGAATTATTCATTCAAAAGGGATTATTAAAGGCATTTTC
* * ** * *
3410724 TGTCAAAAATACCTTTAATAATTTTAGCATTTTTTTATAGAATATTCAAGGCATTTTTACCCAGA
131 TATCAAAAATACCTTCAATAATTCAAGCATTTTTTTATAGAATATTCAAAGCATTTTTACCCAAA
* * * *
3410789 AAATGCCTTGAATAATCTCCTTCAATTTTTATGATG
196 AAACGCATTAAATAATCTCCTTCAATTTTTATGATA
* * * *
3410825 GGATTATTAAAGGCATTTTTAGCTAGAAAATACCTTGAATAAT
1 GGATTATTGAAGGCGTTTCTAGCTA-AAAATTCCTTGAATAAT
3410868 CTATTACAAA
Statistics
Matches: 230, Mismatches: 39, Indels: 7
0.83 0.14 0.03
Matches are distributed among these distances:
228 3 0.01
229 27 0.12
230 99 0.43
231 85 0.37
232 16 0.07
ACGTcount: A:0.35, C:0.13, G:0.13, T:0.39
Consensus pattern (231 bp):
GGATTATTGAAGGCGTTTCTAGCTAAAAATTCCTTGAATAATTCATAAATTATTCAAGACATTTT
TAGCCAAAAACACATTCTATAACCCACGAATTATTCATTCAAAAGGGATTATTAAAGGCATTTTC
TATCAAAAATACCTTCAATAATTCAAGCATTTTTTTATAGAATATTCAAAGCATTTTTACCCAAA
AAACGCATTAAATAATCTCCTTCAATTTTTATGATA
Found at i:3410853 original size:63 final size:63
Alignment explanation
Indices: 3410766--3410929 Score: 183
Period size: 63 Copynumber: 2.6 Consensus size: 63
3410756 TTTTATAGAA
* * * * * * *
3410766 TATTCAAGGCATTTTTACCCAGAAAATGCCTTGAATAATCTCCTT-C-AATTTTTATGATGGGAT
1 TATTAAAGGCATTTTTAGCTAGAAAATGCCTTGAATAATCT-ATTACAAAATATTA-AATGGGAT
* *
3410829 TATTAAAGGCATTTTTAGCTAGAAAATACCTTGAATAATCTATTACAAAATATTAAATGGGGT
1 TATTAAAGGCATTTTTAGCTAGAAAATGCCTTGAATAATCTATTACAAAATATTAAATGGGAT
*
3410892 TATTAAAGGTATTTTT-GACTA-AAAATGCCTTGAATAAT
1 TATTAAAGGCATTTTTAG-CTAGAAAATGCCTTGAATAAT
3410930 TCGTGGATTA
Statistics
Matches: 87, Mismatches: 11, Indels: 7
0.83 0.10 0.07
Matches are distributed among these distances:
62 19 0.22
63 62 0.71
64 6 0.07
ACGTcount: A:0.37, C:0.12, G:0.14, T:0.37
Consensus pattern (63 bp):
TATTAAAGGCATTTTTAGCTAGAAAATGCCTTGAATAATCTATTACAAAATATTAAATGGGAT
Found at i:3410986 original size:46 final size:46
Alignment explanation
Indices: 3410891--3410989 Score: 108
Period size: 46 Copynumber: 2.2 Consensus size: 46
3410881 TTAAATGGGG
* * * * * ** ** *
3410891 TTATTAAAGGTATTTTTGACTAAAAATGCCTTGAATAATTCGTGGA
1 TTATTCAAGGCATTTTTCACCAAAAATGCCTTCAATAACCCACGAA
3410937 TTATTCAAGGCATTTTTCACCAAAAATGCCTTCAATAACCCACGAA
1 TTATTCAAGGCATTTTTCACCAAAAATGCCTTCAATAACCCACGAA
3410983 TTATTCA
1 TTATTCA
3410990 TTTAAGGGGG
Statistics
Matches: 43, Mismatches: 10, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
46 43 1.00
ACGTcount: A:0.35, C:0.17, G:0.12, T:0.35
Consensus pattern (46 bp):
TTATTCAAGGCATTTTTCACCAAAAATGCCTTCAATAACCCACGAA
Found at i:3412821 original size:14 final size:15
Alignment explanation
Indices: 3412793--3412826 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
3412783 TTTATTTTTA
*
3412793 TATTTAATTTAAAAT
1 TATTAAATTTAAAAT
3412808 TATTAAATTT-AAAT
1 TATTAAATTTAAAAT
3412822 TATTA
1 TATTA
3412827 GTTTAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 9 0.50
15 9 0.50
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TATTAAATTTAAAAT
Found at i:3414417 original size:21 final size:22
Alignment explanation
Indices: 3414393--3414433 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 22
3414383 ATTTTAAAGA
3414393 TTTTTTTTT-G-AATTTTTGGT
1 TTTTTTTTTAGAAATTTTTGGT
3414413 TTTTTTTTTAGAAATTTTTGG
1 TTTTTTTTTAGAAATTTTTGG
3414434 AAATTCTAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 9 0.47
21 1 0.05
22 9 0.47
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.71
Consensus pattern (22 bp):
TTTTTTTTTAGAAATTTTTGGT
Found at i:3423129 original size:7 final size:6
Alignment explanation
Indices: 3423087--3423137 Score: 66
Period size: 6 Copynumber: 8.0 Consensus size: 6
3423077 TCTAAGTTAA
*
3423087 GGATTT GGATTT GGATTT GGATTT GGAGTTT GGGATTT AGGATTT TGATTT
1 GGATTT GGATTT GGATTT GGATTT GGA-TTT -GGATTT -GGATTT GGATTT
3423138 AACGTTTGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
6 26 0.63
7 12 0.29
8 3 0.07
ACGTcount: A:0.18, C:0.00, G:0.33, T:0.49
Consensus pattern (6 bp):
GGATTT
Found at i:3423131 original size:27 final size:27
Alignment explanation
Indices: 3423093--3423154 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 27
3423083 TTAAGGATTT
*
3423093 GGATTT-GGATTTGGATTTGGA-GTTTG
1 GGATTTAGGATTTGGATTT-AACGTTTG
*
3423119 GGATTTAGGATTTTGATTTAACGTTTG
1 GGATTTAGGATTTGGATTTAACGTTTG
*
3423146 GGGTTTAGG
1 GGATTTAGG
3423155 GGTTGGTTTT
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 7 0.23
27 24 0.77
ACGTcount: A:0.18, C:0.02, G:0.35, T:0.45
Consensus pattern (27 bp):
GGATTTAGGATTTGGATTTAACGTTTG
Found at i:3423225 original size:34 final size:33
Alignment explanation
Indices: 3423182--3423272 Score: 83
Period size: 41 Copynumber: 2.5 Consensus size: 33
3423172 GGTGATTAAA
*
3423182 GTTTTGATTTAGGGTTTAGGGTTTAGATCTGGG
1 GTTTGGATTTAGGGTTTAGGGTTTAGATCTGGG
* *
3423215 GTTTGGGATTTAGAGTTTCATGTTTAGGGTTTGGATTTGGG
1 GTTT-GGATTTAG-G------GTTTAGGGTTTAGATCTGGG
3423256 GTTTGGATTTAGGGTTT
1 GTTTGGATTTAGGGTTT
3423273 CAAGTTTAAG
Statistics
Matches: 47, Mismatches: 3, Indels: 16
0.71 0.05 0.24
Matches are distributed among these distances:
33 8 0.17
34 7 0.15
35 1 0.02
39 1 0.02
40 8 0.17
41 22 0.47
ACGTcount: A:0.14, C:0.02, G:0.36, T:0.47
Consensus pattern (33 bp):
GTTTGGATTTAGGGTTTAGGGTTTAGATCTGGG
Found at i:3423259 original size:13 final size:13
Alignment explanation
Indices: 3423196--3423272 Score: 66
Period size: 13 Copynumber: 5.8 Consensus size: 13
3423186 TGATTTAGGG
*
3423196 TTTAGGGTTTAGA
1 TTTAGGGTTTGGA
* *
3423209 TCTGGGGTTTGGGA
1 TTTAGGGTTT-GGA
* *
3423223 TTTAGAGTTT-CA
1 TTTAGGGTTTGGA
3423235 TGTTTAGGGTTTGGA
1 --TTTAGGGTTTGGA
*
3423250 TTTGGGGTTTGGA
1 TTTAGGGTTTGGA
3423263 TTTAGGGTTT
1 TTTAGGGTTT
3423273 CAAGTTTAAG
Statistics
Matches: 49, Mismatches: 11, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
12 1 0.02
13 29 0.59
14 18 0.37
15 1 0.02
ACGTcount: A:0.14, C:0.03, G:0.36, T:0.47
Consensus pattern (13 bp):
TTTAGGGTTTGGA
Found at i:3423280 original size:40 final size:41
Alignment explanation
Indices: 3423195--3423286 Score: 132
Period size: 40 Copynumber: 2.3 Consensus size: 41
3423185 TTGATTTAGG
*
3423195 GTTTAGGGTTTAGATCTGGGGTTTGGGATTTAGAGTTTCAT
1 GTTTAGGGTTTAGATCTGGGGTTTGGGATTTAGAGTTTCAA
* * *
3423236 GTTTAGGGTTTGGATTTGGGGTTT-GGATTTAGGGTTTCAA
1 GTTTAGGGTTTAGATCTGGGGTTTGGGATTTAGAGTTTCAA
*
3423276 GTTTAAGGTTT
1 GTTTAGGGTTT
3423287 TAGGGATTTC
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
40 24 0.52
41 22 0.48
ACGTcount: A:0.16, C:0.03, G:0.35, T:0.46
Consensus pattern (41 bp):
GTTTAGGGTTTAGATCTGGGGTTTGGGATTTAGAGTTTCAA
Found at i:3424337 original size:24 final size:22
Alignment explanation
Indices: 3424285--3424338 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 22
3424275 AAACAATAAA
3424285 ATTTTTTCTTTTTTTTTTCCTC
1 ATTTTTTCTTTTTTTTTTCCTC
3424307 ATGTTTTTCCTTTCTTTTTTT-CTC
1 AT-TTTTT-CTTT-TTTTTTTCCTC
3424331 TATTTTTT
1 -ATTTTTT
3424339 GCGTTTCCTC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
22 2 0.07
23 5 0.18
24 12 0.43
25 9 0.32
ACGTcount: A:0.06, C:0.17, G:0.02, T:0.76
Consensus pattern (22 bp):
ATTTTTTCTTTTTTTTTTCCTC
Found at i:3427239 original size:16 final size:17
Alignment explanation
Indices: 3427218--3427249 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
3427208 AATAATATAA
3427218 TTTTTT-CATTTTTTTT
1 TTTTTTACATTTTTTTT
3427234 TTTTTTACATTTTTTT
1 TTTTTTACATTTTTTT
3427250 CTAAAATCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.09, C:0.06, G:0.00, T:0.84
Consensus pattern (17 bp):
TTTTTTACATTTTTTTT
Found at i:3427404 original size:29 final size:29
Alignment explanation
Indices: 3427348--3427405 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
3427338 ATGAAAACGA
* * *
3427348 AATAAAAAAATAAAAATTTGATTGATTAT
1 AATAAAAAAATAAAAATTTAAGTAATTAT
* *
3427377 AATAAAATATTAAAAATTTAAGTAATTAT
1 AATAAAAAAATAAAAATTTAAGTAATTAT
3427406 TAAATTATAA
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.36
Consensus pattern (29 bp):
AATAAAAAAATAAAAATTTAAGTAATTAT
Found at i:3438203 original size:19 final size:20
Alignment explanation
Indices: 3438176--3438213 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
3438166 TTGTGAGTAT
3438176 ATAAATAATAAAA-TATAAA
1 ATAAATAATAAAATTATAAA
*
3438195 ATAATTAATAAAATTATAA
1 ATAAATAATAAAATTATAA
3438214 TTAAAAATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 12 0.71
20 5 0.29
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (20 bp):
ATAAATAATAAAATTATAAA
Found at i:3438213 original size:15 final size:15
Alignment explanation
Indices: 3438195--3438238 Score: 56
Period size: 14 Copynumber: 3.1 Consensus size: 15
3438185 AAAATATAAA
3438195 ATAATTAATAAAATT
1 ATAATTAATAAAATT
*
3438210 ATAATTAA-AAATTT
1 ATAATTAATAAAATT
*
3438224 AT-TTTAATAAAATT
1 ATAATTAATAAAATT
3438238 A
1 A
3438239 ACCTCAATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
13 4 0.16
14 13 0.52
15 8 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (15 bp):
ATAATTAATAAAATT
Found at i:3439561 original size:67 final size:67
Alignment explanation
Indices: 3439484--3439611 Score: 202
Period size: 67 Copynumber: 1.9 Consensus size: 67
3439474 AACAATCTTA
* *
3439484 TGATTAAATTAAAGTAACTAATAATTTCTTACCTTAAAATATGCCTAGAATCTATTGTTTTATGT
1 TGATTAAATTAAAGTAACTAATAATTTCTTACCTTAAAATATGCCTAGAATATATTATTTTATGT
3439549 TT
66 TT
* * **
3439551 TGATTAAATTAAAGTAACTAATGATTTCTTACTTTAAAATATGGGTAGAATATATTATTTT
1 TGATTAAATTAAAGTAACTAATAATTTCTTACCTTAAAATATGCCTAGAATATATTATTTT
3439612 CAAGTATCTC
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
67 55 1.00
ACGTcount: A:0.38, C:0.08, G:0.10, T:0.45
Consensus pattern (67 bp):
TGATTAAATTAAAGTAACTAATAATTTCTTACCTTAAAATATGCCTAGAATATATTATTTTATGT
TT
Found at i:3440169 original size:2 final size:2
Alignment explanation
Indices: 3440162--3440186 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3440152 CTTAGACTTG
3440162 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
3440187 TCTTGTATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3442325 original size:21 final size:20
Alignment explanation
Indices: 3442285--3442325 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
3442275 ATAAAATGTT
* *
3442285 AAAATTTTAATTTTATTAAC
1 AAAAATTTAATTTTAATAAC
3442305 AAAAATTTAATTTCTAATAAC
1 AAAAATTTAATTT-TAATAAC
3442326 CTCAAGCACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.49, C:0.07, G:0.00, T:0.44
Consensus pattern (20 bp):
AAAAATTTAATTTTAATAAC
Found at i:3444531 original size:13 final size:13
Alignment explanation
Indices: 3444507--3444541 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
3444497 TTAGGTATTG
3444507 GATGAGTTATAAAT
1 GATGA-TTATAAAT
3444521 GATGATTATAAAT
1 GATGATTATAAAT
*
3444534 GATAATTA
1 GATGATTA
3444542 GCTAATGGAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 15 0.75
14 5 0.25
ACGTcount: A:0.46, C:0.00, G:0.17, T:0.37
Consensus pattern (13 bp):
GATGATTATAAAT
Found at i:3445336 original size:16 final size:16
Alignment explanation
Indices: 3445315--3445347 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
3445305 AAAATCATAT
3445315 TTAAATCTCTTTAAGG
1 TTAAATCTCTTTAAGG
3445331 TTAAATCTCTTTAAGG
1 TTAAATCTCTTTAAGG
3445347 T
1 T
3445348 AAGGAAATGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (16 bp):
TTAAATCTCTTTAAGG
Found at i:3451271 original size:61 final size:61
Alignment explanation
Indices: 3451185--3451314 Score: 170
Period size: 61 Copynumber: 2.1 Consensus size: 61
3451175 TATTATTTTC
* * * * *
3451185 TTTCCAAAATAAAAAAAAAAAAGAATTTTTAAATTGACCCAAATTGTGAAAAATTTAGAAA
1 TTTCAAAAATAAAAAAAAAAAAGAATTTCTAAATAGACCCAAATGGTAAAAAATTTAGAAA
* * * * *
3451246 TTTCAAAAATAATAAATAAAGAGAATTTCTAAATAGGCCTAAATGGTAAAAAATTTAGAAA
1 TTTCAAAAATAAAAAAAAAAAAGAATTTCTAAATAGACCCAAATGGTAAAAAATTTAGAAA
3451307 TTTCAAAA
1 TTTCAAAA
3451315 GGGAAAATAT
Statistics
Matches: 59, Mismatches: 10, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
61 59 1.00
ACGTcount: A:0.55, C:0.08, G:0.09, T:0.28
Consensus pattern (61 bp):
TTTCAAAAATAAAAAAAAAAAAGAATTTCTAAATAGACCCAAATGGTAAAAAATTTAGAAA
Found at i:3455336 original size:23 final size:23
Alignment explanation
Indices: 3455306--3455352 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
3455296 TCACTAATGG
*
3455306 ATGAAAAATGAGAAGAGAAAAAA
1 ATGAAAAATGAGAAAAGAAAAAA
3455329 ATGAAAAATGAGAAAAGAAAAAA
1 ATGAAAAATGAGAAAAGAAAAAA
3455352 A
1 A
3455353 AATAAGAAGA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.72, C:0.00, G:0.19, T:0.09
Consensus pattern (23 bp):
ATGAAAAATGAGAAAAGAAAAAA
Found at i:3455353 original size:18 final size:18
Alignment explanation
Indices: 3455332--3455370 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
3455322 GAAAAAAATG
*
3455332 AAAAATGAGAAAAGAAAA
1 AAAAATAAGAAAAGAAAA
*
3455350 AAAAATAAGAAGAGAAAA
1 AAAAATAAGAAAAGAAAA
3455368 AAA
1 AAA
3455371 TAAAAAAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.15, T:0.05
Consensus pattern (18 bp):
AAAAATAAGAAAAGAAAA
Found at i:3455392 original size:15 final size:15
Alignment explanation
Indices: 3455374--3455415 Score: 50
Period size: 14 Copynumber: 2.8 Consensus size: 15
3455364 AAAAAAATAA
3455374 AAAAAATAAAAAGGG
1 AAAAAATAAAAAGGG
* *
3455389 -AAAAATGAAAAGTG
1 AAAAAATAAAAAGGG
3455403 AAAAAATGAAAAA
1 AAAAAAT-AAAAA
3455416 ATAAAAAAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
14 12 0.55
15 6 0.27
16 4 0.18
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.10
Consensus pattern (15 bp):
AAAAAATAAAAAGGG
Found at i:3455393 original size:23 final size:23
Alignment explanation
Indices: 3455323--3455425 Score: 68
Period size: 25 Copynumber: 4.3 Consensus size: 23
3455313 ATGAGAAGAG
*
3455323 AAAAAAATGAAAAATGAGAAAAGA-A
1 AAAAAAAT-AAAAA-GA-AAAAAATA
3455348 AAAAAAATAAGAAGAGAAAAAAATA
1 AAAAAAATAA-AA-AGAAAAAAATA
**
3455373 AAAAAAATAAAAAGGGAAAAATGA
1 AAAAAAATAAAAAGAAAAAAAT-A
** *
3455397 AAAGTGAA-AAAATG-AAAAAATA
1 AAA-AAAATAAAAAGAAAAAAATA
3455419 AAAAAAA
1 AAAAAAA
3455426 ATGAGGAAAA
Statistics
Matches: 64, Mismatches: 9, Indels: 14
0.74 0.10 0.16
Matches are distributed among these distances:
21 2 0.03
22 4 0.06
23 14 0.22
24 18 0.28
25 25 0.39
26 1 0.02
ACGTcount: A:0.78, C:0.00, G:0.14, T:0.09
Consensus pattern (23 bp):
AAAAAAATAAAAAGAAAAAAATA
Found at i:3455423 original size:15 final size:15
Alignment explanation
Indices: 3455374--3455415 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
3455364 AAAAAAATAA
*
3455374 AAAAAAT-AAAAAGG
1 AAAAAATGAAAAATG
* *
3455388 GAAAAATGAAAAGTG
1 AAAAAATGAAAAATG
3455403 AAAAAATGAAAAA
1 AAAAAATGAAAAA
3455416 ATAAAAAAAA
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
14 6 0.27
15 16 0.73
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.10
Consensus pattern (15 bp):
AAAAAATGAAAAATG
Found at i:3456687 original size:21 final size:21
Alignment explanation
Indices: 3456658--3456741 Score: 105
Period size: 21 Copynumber: 4.0 Consensus size: 21
3456648 TCTTTGGATG
*
3456658 AAGTTTTAAATGAGAATCTTT
1 AAGTTTTAAATAAGAATCTTT
* *
3456679 AAGTCTTAAATAAAAATCTTT
1 AAGTTTTAAATAAGAATCTTT
* * * *
3456700 GAGTTTCAAATGAGAATTTTT
1 AAGTTTTAAATAAGAATCTTT
3456721 AAGTTTTAAATAAGAATCTTT
1 AAGTTTTAAATAAGAATCTTT
3456742 GAGATGTGAA
Statistics
Matches: 50, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.40, C:0.06, G:0.12, T:0.42
Consensus pattern (21 bp):
AAGTTTTAAATAAGAATCTTT
Found at i:3456711 original size:42 final size:42
Alignment explanation
Indices: 3456659--3456744 Score: 136
Period size: 42 Copynumber: 2.0 Consensus size: 42
3456649 CTTTGGATGA
*
3456659 AGTTTTAAATGAGAATCTTTAAGTCTTAAATAAAAATCTTTG
1 AGTTTCAAATGAGAATCTTTAAGTCTTAAATAAAAATCTTTG
* * *
3456701 AGTTTCAAATGAGAATTTTTAAGTTTTAAATAAGAATCTTTG
1 AGTTTCAAATGAGAATCTTTAAGTCTTAAATAAAAATCTTTG
3456743 AG
1 AG
3456745 ATGTGAAACC
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.40, C:0.06, G:0.14, T:0.41
Consensus pattern (42 bp):
AGTTTCAAATGAGAATCTTTAAGTCTTAAATAAAAATCTTTG
Found at i:3457341 original size:41 final size:41
Alignment explanation
Indices: 3457183--3457949 Score: 806
Period size: 41 Copynumber: 18.6 Consensus size: 41
3457173 GATTGTCGAA
* *
3457183 GAGCTTTTTATTTTTTCAAAAGTTGTTGTGCCTCTGTTTAGAA
1 GAGCCTTTTA-TTTTT-AAAAGTTGTTGTGCCTCTGTTTAGAG
* *
3457226 GAGCCTTTTATTTTTCAAAAGTTATTATGCCTCTGTTTAGAG
1 GAGCCTTTTATTTTT-AAAAGTTGTTGTGCCTCTGTTTAGAG
* * *
3457268 GAGCCTTTTATTTTTCAAAAGTTATTGTACCTCTATTTAGAG
1 GAGCCTTTTATTTTT-AAAAGTTGTTGTGCCTCTGTTTAGAG
** * * *
3457310 GAGTTTTTTATTTTTAAAAGTTATTGTACCTCTATTTAGAG
1 GAGCCTTTTATTTTTAAAAGTTGTTGTGCCTCTGTTTAGAG
*
3457351 GAGCCTTTTATTTTTAAAAGTTGTTATGCCTCTGTTTAGAG
1 GAGCCTTTTATTTTTAAAAGTTGTTGTGCCTCTGTTTAGAG
* * *
3457392 GAGCCTTTTATTTTTCAAAGTTGTTGTGCCTTTGTTTAGAT
1 GAGCCTTTTATTTTTAAAAGTTGTTGTGCCTCTGTTTAGAG
* * *
3457433 GAGCCTTTTATTTTTCAAAA-TTGTTATACCTCTGTTTAGAT
1 GAGCCTTTTATTTTT-AAAAGTTGTTGTGCCTCTGTTTAGAG
* * **
3457474 GAGCTTTTTATTTTTTAAAGTTGTTGTGCCTCTACTTAGAG
1 GAGCCTTTTATTTTTAAAAGTTGTTGTGCCTCTGTTTAGAG
* **
3457515 GAGCCTTTTATTTTTCAAAGTCATTGTGCCTCTGTTTAGAG
1 GAGCCTTTTATTTTTAAAAGTTGTTGTGCCTCTGTTTAGAG
* ** ** * * *
3457556 GAGCCTTTTATTTTTCAAAGTCATTAAGTCTCTGTATAGAA
1 GAGCCTTTTATTTTTAAAAGTTGTTGTGCCTCTGTTTAGAG
* * * *
3457597 GAGCCTTTTATTTTTTAAAGTCGTTGAGCCTCTGTATAGAG
1 GAGCCTTTTATTTTTAAAAGTTGTTGTGCCTCTGTTTAGAG
* * * * * *
3457638 GAACCTTTTATTTTTCAAAGTTGCTATGCCTCTATTTAGAT
1 GAGCCTTTTATTTTTAAAAGTTGTTGTGCCTCTGTTTAGAG
* * *
3457679 GAG-CTTTTATTTTTTAAAGTTGTTGAGCCTCTATTTAGAG
1 GAGCCTTTTATTTTTAAAAGTTGTTGTGCCTCTGTTTAGAG
* * *
3457719 AAGCCTTTTATTTTTCAAAGTTGTTGTGCCTCTGTTTAGAT
1 GAGCCTTTTATTTTTAAAAGTTGTTGTGCCTCTGTTTAGAG
* * * *
3457760 GAGCCTTTTATTTTTCAAAA-TCGTTGAGCCTCTATTTAGAT
1 GAGCCTTTTATTTTT-AAAAGTTGTTGTGCCTCTGTTTAGAG
* ** * * *
3457801 AAGCCTTTTATTTTTTCAAGTTATTGTGCATCTGCTTAGAG
1 GAGCCTTTTATTTTTAAAAGTTGTTGTGCCTCTGTTTAGAG
* * *
3457842 GAGCCTTTTATTTTTCAAAGTTGTTGTGCCTCTATTTAGAT
1 GAGCCTTTTATTTTTAAAAGTTGTTGTGCCTCTGTTTAGAG
* * * *
3457883 GAGCCTTTTATTTTCTAAAA-TTGTTATGCTTCTATTTAAAG
1 GAGCCTTTTATTTT-TAAAAGTTGTTGTGCCTCTGTTTAGAG
* *
3457924 GAACTTTTTATTTTTCAAAA-TTGTTG
1 GAGCCTTTTATTTTT-AAAAGTTGTTG
3457950 AGTCTTCATT
Statistics
Matches: 620, Mismatches: 97, Indels: 16
0.85 0.13 0.02
Matches are distributed among these distances:
40 40 0.06
41 480 0.77
42 91 0.15
43 9 0.01
ACGTcount: A:0.23, C:0.13, G:0.17, T:0.47
Consensus pattern (41 bp):
GAGCCTTTTATTTTTAAAAGTTGTTGTGCCTCTGTTTAGAG
Found at i:3458072 original size:44 final size:43
Alignment explanation
Indices: 3457969--3458072 Score: 111
Period size: 44 Copynumber: 2.4 Consensus size: 43
3457959 TTAGAGGAGC
* * * *
3457969 ATTTATGTTTCAAAGTCATTGAGCTTCTTATTAGAGGAGCATT
1 ATTTATTTTTCAAAGTCATTGACCCTCTTATTAGAAGAGCATT
* *
3458012 ATTTATTTTCTAAAAGTCATTGACCCTC-TAGTTAGAAGAGCTTT
1 ATTTATTTT-TCAAAGTCATTGACCCTCTTA-TTAGAAGAGCATT
*
3458056 GTTTACTTTTTCAAAGT
1 ATTTA-TTTTTCAAAGT
3458073 AATGGAGTCT
Statistics
Matches: 50, Mismatches: 8, Indels: 5
0.79 0.13 0.08
Matches are distributed among these distances:
43 10 0.20
44 36 0.72
45 4 0.08
ACGTcount: A:0.28, C:0.13, G:0.15, T:0.43
Consensus pattern (43 bp):
ATTTATTTTTCAAAGTCATTGACCCTCTTATTAGAAGAGCATT
Found at i:3459053 original size:15 final size:16
Alignment explanation
Indices: 3459025--3459058 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
3459015 TTCAAAACAA
3459025 AAAAAAGAAGAAAAAT
1 AAAAAAGAAGAAAAAT
*
3459041 AAAAAATAA-AAAAAT
1 AAAAAAGAAGAAAAAT
3459056 AAA
1 AAA
3459059 CATTTTGATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.85, C:0.00, G:0.06, T:0.09
Consensus pattern (16 bp):
AAAAAAGAAGAAAAAT
Found at i:3459156 original size:24 final size:25
Alignment explanation
Indices: 3459103--3459160 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
3459093 TACCCAAGGA
*
3459103 TGAAATTTTTAGAAATTTCAAATGG
1 TGAAATTTTTAGAAATCTCAAATGG
*
3459128 T-AAATTTTTAAGAAATCTC-TA-GG
1 TGAAATTTTT-AGAAATCTCAAATGG
3459151 TGAAATTTTT
1 TGAAATTTTT
3459161 TTTCTAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 5
0.81 0.06 0.14
Matches are distributed among these distances:
23 3 0.10
24 17 0.59
25 9 0.31
ACGTcount: A:0.38, C:0.05, G:0.14, T:0.43
Consensus pattern (25 bp):
TGAAATTTTTAGAAATCTCAAATGG
Found at i:3460264 original size:19 final size:19
Alignment explanation
Indices: 3460242--3460279 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
3460232 CATAACTTAC
3460242 AAAAAAAAAAAGAGAAAGG
1 AAAAAAAAAAAGAGAAAGG
* *
3460261 AAAAAAGAATAGAGAAAGG
1 AAAAAAAAAAAGAGAAAGG
3460280 GAAATGGCAG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.03
Consensus pattern (19 bp):
AAAAAAAAAAAGAGAAAGG
Found at i:3461339 original size:24 final size:24
Alignment explanation
Indices: 3461310--3461359 Score: 91
Period size: 24 Copynumber: 2.1 Consensus size: 24
3461300 GATCCTAAAG
*
3461310 AAGTTCAAGTAGTAATTTTTTAGA
1 AAGTTCAAGTAGTAATTCTTTAGA
3461334 AAGTTCAAGTAGTAATTCTTTAGA
1 AAGTTCAAGTAGTAATTCTTTAGA
3461358 AA
1 AA
3461360 TCTCTAAGTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.40, C:0.06, G:0.16, T:0.38
Consensus pattern (24 bp):
AAGTTCAAGTAGTAATTCTTTAGA
Found at i:3461553 original size:22 final size:23
Alignment explanation
Indices: 3461528--3461571 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
3461518 AACTGGCAAT
*
3461528 AATA-AGATTTTTTAGAATTCTG
1 AATAGAGATTTTTAAGAATTCTG
3461550 AATAGAGATTTTTAAGAATTCT
1 AATAGAGATTTTTAAGAATTCT
3461572 TTAGGTGAGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
22 4 0.20
23 16 0.80
ACGTcount: A:0.39, C:0.05, G:0.14, T:0.43
Consensus pattern (23 bp):
AATAGAGATTTTTAAGAATTCTG
Found at i:3461697 original size:21 final size:20
Alignment explanation
Indices: 3461658--3461697 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
3461648 TAATTTTTCA
**
3461658 AAAATAAAAAATACTAAAAG
1 AAAATAAAAAATAAAAAAAG
3461678 AAAATGAAAAAATAAAAAAA
1 AAAAT-AAAAAATAAAAAAA
3461698 AATTTTACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.80, C:0.03, G:0.05, T:0.12
Consensus pattern (20 bp):
AAAATAAAAAATAAAAAAAG
Found at i:3468952 original size:13 final size:13
Alignment explanation
Indices: 3468934--3468958 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3468924 AATCTCCTCT
3468934 TTATTATTAAATA
1 TTATTATTAAATA
3468947 TTATTATTAAAT
1 TTATTATTAAAT
3468959 CTCTAAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
TTATTATTAAATA
Found at i:3469272 original size:52 final size:51
Alignment explanation
Indices: 3469176--3469273 Score: 135
Period size: 52 Copynumber: 1.9 Consensus size: 51
3469166 TTATTTAAGT
* * *
3469176 ATATATTAAAAATTAAAATTTTATTTAAATATAAATTAAAAATTTATTTTG
1 ATATAATAAAAATTAAAAATTTATTTAAATATAAATGAAAAATTTATTTTG
*
3469227 ATATAATAAAAATATAAAAATTTATTTAAATA-AAATGATAGAATTTA
1 ATATAATAAAAAT-TAAAAATTTATTTAAATATAAATGA-AAAATTTA
3469274 AAATTTTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 3
0.85 0.08 0.06
Matches are distributed among these distances:
51 17 0.41
52 24 0.59
ACGTcount: A:0.55, C:0.00, G:0.03, T:0.42
Consensus pattern (51 bp):
ATATAATAAAAATTAAAAATTTATTTAAATATAAATGAAAAATTTATTTTG
Found at i:3470965 original size:2 final size:2
Alignment explanation
Indices: 3470958--3470987 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
3470948 GCGAGAAGGG
3470958 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
3470988 ACACACACAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:3475090 original size:3 final size:3
Alignment explanation
Indices: 3475084--3475111 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
3475074 TAATAATATA
3475084 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
3475112 TAACAAAGTG
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:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:3477706 original size:14 final size:14
Alignment explanation
Indices: 3477687--3477714 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3477677 CCCTTTCAAA
3477687 AGATAGAGCTATTG
1 AGATAGAGCTATTG
3477701 AGATAGAGCTATTG
1 AGATAGAGCTATTG
3477715 GCTTCATTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.36, C:0.07, G:0.29, T:0.29
Consensus pattern (14 bp):
AGATAGAGCTATTG
Found at i:3478367 original size:21 final size:20
Alignment explanation
Indices: 3478343--3478390 Score: 69
Period size: 21 Copynumber: 2.4 Consensus size: 20
3478333 TATTTTTATA
3478343 TAATATATTAATATAAAATTT
1 TAATATATTAATAT-AAATTT
* *
3478364 TAATATATTTATATAGATTT
1 TAATATATTAATATAAATTT
3478384 TAATATA
1 TAATATA
3478391 AATTTATTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
20 12 0.48
21 13 0.52
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
TAATATATTAATATAAATTT
Found at i:3478402 original size:25 final size:24
Alignment explanation
Indices: 3478372--3478420 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 24
3478362 TTTAATATAT
*
3478372 TTATATAGATTTTAATATAAATTTA
1 TTATATAGATTTT-ATAAAAATTTA
**
3478397 TTATATTTATTTTATAAAAATTTA
1 TTATATAGATTTTATAAAAATTTA
3478421 AAAATAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 10 0.48
25 11 0.52
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (24 bp):
TTATATAGATTTTATAAAAATTTA
Found at i:3478405 original size:31 final size:33
Alignment explanation
Indices: 3478328--3478406 Score: 94
Period size: 34 Copynumber: 2.4 Consensus size: 33
3478318 AAATTTTATT
*
3478328 TTTTATATTTTTATATAATATATTAATATAAAA
1 TTTTATATATTTATATAATATATTAATATAAAA
3478361 TTTTAATATATTTATATAGAT-T-TTAATAT-AAA
1 TTTT-ATATATTTATATA-ATATATTAATATAAAA
3478393 -TTTATTATATTTAT
1 TTTTA-TATATTTAT
3478407 TTTATAAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
30 1 0.02
31 12 0.29
32 3 0.07
33 11 0.26
34 13 0.31
35 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (33 bp):
TTTTATATATTTATATAATATATTAATATAAAA
Found at i:3489282 original size:17 final size:17
Alignment explanation
Indices: 3489260--3489302 Score: 86
Period size: 17 Copynumber: 2.5 Consensus size: 17
3489250 ACAGATGCAT
3489260 GTCATTTGTCATGATGG
1 GTCATTTGTCATGATGG
3489277 GTCATTTGTCATGATGG
1 GTCATTTGTCATGATGG
3489294 GTCATTTGT
1 GTCATTTGT
3489303 TTGTATTTGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 26 1.00
ACGTcount: A:0.16, C:0.12, G:0.28, T:0.44
Consensus pattern (17 bp):
GTCATTTGTCATGATGG
Found at i:3492255 original size:16 final size:16
Alignment explanation
Indices: 3492234--3492267 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3492224 TATCGTATTA
*
3492234 TTTCATGCTATTTTTG
1 TTTCATACTATTTTTG
*
3492250 TTTCATACTGTTTTTG
1 TTTCATACTATTTTTG
3492266 TT
1 TT
3492268 GATCTCATTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.12, C:0.12, G:0.12, T:0.65
Consensus pattern (16 bp):
TTTCATACTATTTTTG
Found at i:3492291 original size:28 final size:27
Alignment explanation
Indices: 3492260--3492315 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 27
3492250 TTTCATACTG
* *
3492260 TTTTTGTTGATCTCATTGTATCAGATTA
1 TTTTTGTTGATCTAATTATATCA-ATTA
*
3492288 TTTTTGTTTATCTAATTATATCAATTA
1 TTTTTGTTGATCTAATTATATCAATTA
3492315 T
1 T
3492316 AATTTTTAAG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
27 5 0.20
28 20 0.80
ACGTcount: A:0.25, C:0.09, G:0.09, T:0.57
Consensus pattern (27 bp):
TTTTTGTTGATCTAATTATATCAATTA
Found at i:3493707 original size:6 final size:6
Alignment explanation
Indices: 3493696--3493720 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
3493686 TTTTTTGTTG
3493696 AAACTA AAACTA AAACTA AAACTA A
1 AAACTA AAACTA AAACTA AAACTA A
3493721 TTCTTCAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.68, C:0.16, G:0.00, T:0.16
Consensus pattern (6 bp):
AAACTA
Found at i:3501294 original size:16 final size:16
Alignment explanation
Indices: 3501270--3501345 Score: 61
Period size: 16 Copynumber: 4.9 Consensus size: 16
3501260 TTAAGGATAT
*
3501270 TATATTAAAATTTATA
1 TATAATAAAATTTATA
3501286 TATAATAAAATTTATA
1 TATAATAAAATTTATA
*
3501302 -AT-AT-ATATTTA-A
1 TATAATAAAATTTATA
* *
3501314 TATTCATAAAATTAATA
1 TA-TAATAAAATTTATA
*
3501331 AATAATTAAAATTTA
1 TATAA-TAAAATTTA
3501346 ATAAATTTAT
Statistics
Matches: 47, Mismatches: 7, Indels: 11
0.72 0.11 0.17
Matches are distributed among these distances:
12 1 0.02
13 7 0.15
14 3 0.06
15 4 0.09
16 22 0.47
17 10 0.21
ACGTcount: A:0.54, C:0.01, G:0.00, T:0.45
Consensus pattern (16 bp):
TATAATAAAATTTATA
Found at i:3502095 original size:7 final size:7
Alignment explanation
Indices: 3502083--3502117 Score: 70
Period size: 7 Copynumber: 5.0 Consensus size: 7
3502073 TAAGAAATTA
3502083 AAATTTT
1 AAATTTT
3502090 AAATTTT
1 AAATTTT
3502097 AAATTTT
1 AAATTTT
3502104 AAATTTT
1 AAATTTT
3502111 AAATTTT
1 AAATTTT
3502118 TTTGATGCTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 28 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (7 bp):
AAATTTT
Found at i:3504971 original size:21 final size:20
Alignment explanation
Indices: 3504947--3504996 Score: 68
Period size: 19 Copynumber: 2.5 Consensus size: 20
3504937 TATTTCAATC
3504947 TTTTTTAATTCTCTCTTTTGA
1 TTTTTT-ATTCTCTCTTTTGA
*
3504968 -TTTTTCTTCTCTCTTTTGA
1 TTTTTTATTCTCTCTTTTGA
3504987 TTTTTT-TTCT
1 TTTTTTATTCT
3504997 TGCATAAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
19 17 0.63
20 10 0.37
ACGTcount: A:0.08, C:0.16, G:0.04, T:0.72
Consensus pattern (20 bp):
TTTTTTATTCTCTCTTTTGA
Found at i:3504977 original size:19 final size:19
Alignment explanation
Indices: 3504955--3504996 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
3504945 TCTTTTTTAA
3504955 TTCTCTCTTTTGATTTTTC
1 TTCTCTCTTTTGATTTTTC
*
3504974 TTCTCTCTTTTGATTTTTT
1 TTCTCTCTTTTGATTTTTC
3504993 TTCT
1 TTCT
3504997 TGCATAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.05, C:0.19, G:0.05, T:0.71
Consensus pattern (19 bp):
TTCTCTCTTTTGATTTTTC
Found at i:3507035 original size:16 final size:15
Alignment explanation
Indices: 3506998--3507046 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
3506988 GGATACAATG
*
3506998 AATTCATGAATGATT
1 AATTCATGAATAATT
3507013 AAGTTCATGAATAATT
1 AA-TTCATGAATAATT
*
3507029 AGATTCATAAATAATT
1 A-ATTCATGAATAATT
3507045 AA
1 AA
3507047 ATTTATATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
15 3 0.10
16 26 0.87
17 1 0.03
ACGTcount: A:0.47, C:0.06, G:0.10, T:0.37
Consensus pattern (15 bp):
AATTCATGAATAATT
Found at i:3508137 original size:13 final size:14
Alignment explanation
Indices: 3508105--3508137 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
3508095 TTTGTTGTTT
3508105 TTGGGTTGTTGTGA
1 TTGGGTTGTTGTGA
3508119 TT-GGTTGTT-TGA
1 TTGGGTTGTTGTGA
3508131 TTGGGTT
1 TTGGGTT
3508138 TTTTTCACTC
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 5 0.28
13 11 0.61
14 2 0.11
ACGTcount: A:0.06, C:0.00, G:0.39, T:0.55
Consensus pattern (14 bp):
TTGGGTTGTTGTGA
Found at i:3513380 original size:18 final size:18
Alignment explanation
Indices: 3513357--3513401 Score: 81
Period size: 18 Copynumber: 2.5 Consensus size: 18
3513347 TAATATATAG
3513357 GTGATTGATGTTCATCTT
1 GTGATTGATGTTCATCTT
3513375 GTGATTGATGTTCATCTT
1 GTGATTGATGTTCATCTT
*
3513393 GTGGTTGAT
1 GTGATTGAT
3513402 CCGTGGACGA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.16, C:0.09, G:0.27, T:0.49
Consensus pattern (18 bp):
GTGATTGATGTTCATCTT
Found at i:3514047 original size:13 final size:13
Alignment explanation
Indices: 3514012--3514049 Score: 51
Period size: 12 Copynumber: 3.0 Consensus size: 13
3514002 TTTGGTTCAA
* *
3514012 ATTAAGTTTAGAT
1 ATTAAATTTATAT
3514025 ATTAAA-TTATAT
1 ATTAAATTTATAT
3514037 ATTAAATTTATAT
1 ATTAAATTTATAT
3514050 CAAATTTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.45, C:0.00, G:0.05, T:0.50
Consensus pattern (13 bp):
ATTAAATTTATAT
Found at i:3514054 original size:11 final size:11
Alignment explanation
Indices: 3514023--3514056 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
3514013 TTAAGTTTAG
3514023 ATATTAAATTAT
1 ATATTAAATT-T
3514035 ATATTAAATTT
1 ATATTAAATTT
*
3514046 ATATCAAATTT
1 ATATTAAATTT
3514057 TGAATTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 11 0.52
12 10 0.48
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (11 bp):
ATATTAAATTT
Found at i:3514174 original size:20 final size:21
Alignment explanation
Indices: 3514149--3514189 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
3514139 ATAATTATTT
* *
3514149 TATATTTAAATTTAT-TTAAA
1 TATATTAAAAATTATATTAAA
3514169 TATATTAAAAATTATATTAAA
1 TATATTAAAAATTATATTAAA
3514190 ATAATATACA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (21 bp):
TATATTAAAAATTATATTAAA
Found at i:3523995 original size:13 final size:13
Alignment explanation
Indices: 3523977--3524001 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3523967 TTTTGTTTTA
3523977 AAAAAAAAAAAAC
1 AAAAAAAAAAAAC
3523990 AAAAAAAAAAAA
1 AAAAAAAAAAAA
3524002 AACCATAATA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.96, C:0.04, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAAAAC
Found at i:3523995 original size:14 final size:14
Alignment explanation
Indices: 3523976--3524002 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
3523966 GTTTTGTTTT
3523976 AAAAAAAAAAAAAC
1 AAAAAAAAAAAAAC
3523990 AAAAAAAAAAAAA
1 AAAAAAAAAAAAA
3524003 ACCATAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.96, C:0.04, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAAAC
Found at i:3523996 original size:15 final size:15
Alignment explanation
Indices: 3523976--3524004 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
3523966 GTTTTGTTTT
3523976 AAAAAAAAAAAAACA
1 AAAAAAAAAAAAACA
3523991 AAAAAAAAAAAAAC
1 AAAAAAAAAAAAAC
3524005 CATAATATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.93, C:0.07, G:0.00, T:0.00
Consensus pattern (15 bp):
AAAAAAAAAAAAACA
Found at i:3524990 original size:2 final size:2
Alignment explanation
Indices: 3524985--3525015 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3524975 TGTGTGTGTC
3524985 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3525016 TAAGCATCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3527864 original size:31 final size:31
Alignment explanation
Indices: 3527815--3527874 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
3527805 GGATTTTGTG
*
3527815 GGTTTTAAAGTTTCAAGATTTTAAGGTTTAC
1 GGTTTTAAAGTTTCAAGATTTTAAAGTTTAC
* * *
3527846 GGTTTTTAGGTTTTAAGATTTTAAAGTTT
1 GGTTTTAAAGTTTCAAGATTTTAAAGTTT
3527875 TAATGTTTTA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.27, C:0.03, G:0.20, T:0.50
Consensus pattern (31 bp):
GGTTTTAAAGTTTCAAGATTTTAAAGTTTAC
Found at i:3527875 original size:16 final size:16
Alignment explanation
Indices: 3527817--3527877 Score: 61
Period size: 16 Copynumber: 3.9 Consensus size: 16
3527807 ATTTTGTGGG
*
3527817 TTTTAAAGTTTCAAGA
1 TTTTAAAGTTTTAAGA
* * *
3527833 TTTT-AAGGTTTACGG
1 TTTTAAAGTTTTAAGA
* *
3527848 TTTTTAGGTTTTAAGA
1 TTTTAAAGTTTTAAGA
3527864 TTTTAAAGTTTTAA
1 TTTTAAAGTTTTAA
3527878 TGTTTTACGG
Statistics
Matches: 34, Mismatches: 10, Indels: 2
0.74 0.22 0.04
Matches are distributed among these distances:
15 11 0.32
16 23 0.68
ACGTcount: A:0.30, C:0.03, G:0.16, T:0.51
Consensus pattern (16 bp):
TTTTAAAGTTTTAAGA
Found at i:3527883 original size:16 final size:15
Alignment explanation
Indices: 3527816--3527884 Score: 50
Period size: 16 Copynumber: 4.4 Consensus size: 15
3527806 GATTTTGTGG
*
3527816 GTTTTAAAGTTTCAA
1 GTTTTAAAGTTTTAA
* *
3527831 GATTTT-AAGGTTTACG
1 G-TTTTAAAGTTTTA-A
* *
3527847 GTTTTTAGGTTTTAA
1 GTTTTAAAGTTTTAA
3527862 GATTTTAAAGTTTTAA
1 G-TTTTAAAGTTTTAA
3527878 TGTTTTA
1 -GTTTTA
3527885 CGGTATTTCT
Statistics
Matches: 41, Mismatches: 8, Indels: 9
0.71 0.14 0.16
Matches are distributed among these distances:
15 12 0.29
16 28 0.68
17 1 0.02
ACGTcount: A:0.28, C:0.03, G:0.17, T:0.52
Consensus pattern (15 bp):
GTTTTAAAGTTTTAA
Found at i:3529289 original size:5 final size:5
Alignment explanation
Indices: 3529279--3529306 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
3529269 CCTCACTGTG
3529279 GTTTT GTTTT GTTTT GTTTT GTTTT GTT
1 GTTTT GTTTT GTTTT GTTTT GTTTT GTT
3529307 GTGATTTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.21, T:0.79
Consensus pattern (5 bp):
GTTTT
Found at i:3531266 original size:12 final size:12
Alignment explanation
Indices: 3531249--3531278 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
3531239 ACCCTTTCAA
*
3531249 AACCAGATTCCT
1 AACCAGATTCCC
3531261 AACCAGATTCCC
1 AACCAGATTCCC
3531273 AACCAG
1 AACCAG
3531279 CCCTTTCATA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.37, C:0.37, G:0.10, T:0.17
Consensus pattern (12 bp):
AACCAGATTCCC
Found at i:3532958 original size:17 final size:17
Alignment explanation
Indices: 3532936--3532971 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
3532926 TTTTACTATT
3532936 AAAAATTAAAATATTAA
1 AAAAATTAAAATATTAA
* *
3532953 AAAAATTTATATATTAA
1 AAAAATTAAAATATTAA
3532970 AA
1 AA
3532972 TTTTAATATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAAATTAAAATATTAA
Found at i:3535217 original size:20 final size:20
Alignment explanation
Indices: 3535189--3535228 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3535179 TTTAAAATAA
*
3535189 AAATTAAATAAAAATTTGAT
1 AAATAAAATAAAAATTTGAT
*
3535209 AAATAAAATAATAATTTGAT
1 AAATAAAATAAAAATTTGAT
3535229 CAGGTTGAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (20 bp):
AAATAAAATAAAAATTTGAT
Found at i:3537142 original size:33 final size:32
Alignment explanation
Indices: 3537105--3537182 Score: 77
Period size: 33 Copynumber: 2.4 Consensus size: 32
3537095 TGATTTATCG
* *
3537105 ATTTTTATTTTTTATA-TATTATTTTAATATTAA
1 ATTTTTATTTTTTA-AGTA-GATTTTAATATAAA
* *
3537138 ATTTTAATATATTTAAGTAGATTTTAATATAAA
1 ATTTTTAT-TTTTTAAGTAGATTTTAATATAAA
*
3537171 ATTATTATTTTT
1 ATTTTTATTTTT
3537183 ATTTTATAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 5
0.75 0.15 0.10
Matches are distributed among these distances:
32 3 0.08
33 26 0.72
34 7 0.19
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (32 bp):
ATTTTTATTTTTTAAGTAGATTTTAATATAAA
Done.