Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 ID=Chr05-JGI_221_v2.0
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: 64140413
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 820884 characters in sequence are not A, C, G, or T
File 54 of 208
Found at i:15269711 original size:16 final size:16
Alignment explanation
Indices: 15269692--15269725 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
15269682 TTCAATAAAT
15269692 AATGAAAGCAAACACA
1 AATGAAAGCAAACACA
* *
15269708 AATGAAATCATACACA
1 AATGAAAGCAAACACA
15269724 AA
1 AA
15269726 CTAATCCTAT
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:0.62, C:0.18, G:0.09, T:0.12
Consensus pattern (16 bp):
AATGAAAGCAAACACA
Found at i:15275603 original size:51 final size:50
Alignment explanation
Indices: 15275499--15275664 Score: 190
Period size: 51 Copynumber: 3.3 Consensus size: 50
15275489 TTAGGCTTCG
* * * * * *
15275499 CATAGTACTACACACGTGATCAAACTTTCCGGTTCACGTAGTAGCCTGTA
1 CATAGTACTACACATGTGACCAAACCTTCCAGTACACGTAGTAGCCTGCA
* *
15275549 CATAGTACTACACATTTGACCAAAGCCTTCCAGTACACATAGTAGCCTGCA
1 CATAGTACTACACATGTGACCAAA-CCTTCCAGTACACGTAGTAGCCTGCA
* * *
15275600 CATAGTACTACACATGTGACCATTATCTATCGA-TACACGTAGTAGCCTGCA
1 CATAGTACTACACATGTGACCA-AACCT-TCCAGTACACGTAGTAGCCTGCA
*
15275651 CTTAGTACTACACA
1 CATAGTACTACACA
15275665 CGTGTTTATA
Statistics
Matches: 99, Mismatches: 14, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
50 21 0.21
51 74 0.75
52 4 0.04
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.27
Consensus pattern (50 bp):
CATAGTACTACACATGTGACCAAACCTTCCAGTACACGTAGTAGCCTGCA
Found at i:15282709 original size:17 final size:18
Alignment explanation
Indices: 15282680--15282727 Score: 62
Period size: 17 Copynumber: 2.7 Consensus size: 18
15282670 GATTATTATA
*
15282680 TTATTATTATATTCTATT
1 TTATTATTTTATTCTATT
*
15282698 TT-TTATTTTATTTTATT
1 TTATTATTTTATTCTATT
*
15282715 TTATTATCTTATT
1 TTATTATTTTATT
15282728 ACATTTGAAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 15 0.58
18 11 0.42
ACGTcount: A:0.23, C:0.04, G:0.00, T:0.73
Consensus pattern (18 bp):
TTATTATTTTATTCTATT
Found at i:15282810 original size:15 final size:16
Alignment explanation
Indices: 15282792--15282825 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
15282782 GTTTTTATTA
15282792 TTACTATT-TATTAGT
1 TTACTATTATATTAGT
15282807 TTACTATTAGTATTAGT
1 TTACTATTA-TATTAGT
15282824 TT
1 TT
15282826 GGACATTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 8 0.47
17 9 0.53
ACGTcount: A:0.26, C:0.06, G:0.09, T:0.59
Consensus pattern (16 bp):
TTACTATTATATTAGT
Found at i:15289473 original size:35 final size:35
Alignment explanation
Indices: 15289339--15289503 Score: 131
Period size: 35 Copynumber: 4.7 Consensus size: 35
15289329 AACTTATTTT
* * *
15289339 ATCAATCATCCCACCACAATGCCAAAACTTCA-TC-
1 ATCAA-CATCCCGCCACAACGCCAATACTTCATTCA
* * * *
15289373 ATCAATCATCCCGCCATAAGGCCAATACCTCTTTCA
1 ATCAA-CATCCCGCCACAACGCCAATACTTCATTCA
* * *
15289409 ATTAACATTCCGCCACAACACCAATACTTCATTCA
1 ATCAACATCCCGCCACAACGCCAATACTTCATTCA
* **
15289444 ACCAACATCCCGCCACAACGCCAGA-ACTTC-TTTT
1 ATCAACATCCCGCCACAACGCCA-ATACTTCATTCA
* * *
15289478 ATCAATATCCCACCACAATGCCAATA
1 ATCAACATCCCGCCACAACGCCAATA
15289504 TGTCATAACA
Statistics
Matches: 104, Mismatches: 23, Indels: 8
0.77 0.17 0.06
Matches are distributed among these distances:
33 1 0.01
34 48 0.46
35 50 0.48
36 5 0.05
ACGTcount: A:0.35, C:0.37, G:0.05, T:0.22
Consensus pattern (35 bp):
ATCAACATCCCGCCACAACGCCAATACTTCATTCA
Found at i:15289502 original size:69 final size:67
Alignment explanation
Indices: 15289328--15289503 Score: 174
Period size: 69 Copynumber: 2.6 Consensus size: 67
15289318 CATCCGACCA
* * * * *
15289328 AAACTTATTTTATCAATCATCCCACCACAATGCCAAAACTTCATCATCAATCATCCCGCCATAAG
1 AAACTTCTTTTATCAAT-ATCCCACCACAATGCCAATACTTCATCACCAATCATCCCGCCACAAC
15289393 GCC
65 GCC
* * * * * * **
15289396 AATACCTCTTTCAATTAACATTCCGCCACAACACCAATACTTCATTCAACCAA-CATCCCGCCAC
1 AA-ACTTCTTT-TATCAATATCCCACCACAATGCCAATACTTCA-TC-ACCAATCATCCCGCCAC
15289460 AACGCC
62 AACGCC
15289466 AGAACTTCTTTTATCAATATCCCACCACAATGCCAATA
1 A-AACTTCTTTTATCAATATCCCACCACAATGCCAATA
15289504 TGTCATAACA
Statistics
Matches: 82, Mismatches: 21, Indels: 9
0.73 0.19 0.08
Matches are distributed among these distances:
68 2 0.02
69 46 0.56
70 29 0.35
71 5 0.06
ACGTcount: A:0.35, C:0.35, G:0.05, T:0.24
Consensus pattern (67 bp):
AAACTTCTTTTATCAATATCCCACCACAATGCCAATACTTCATCACCAATCATCCCGCCACAACG
CC
Found at i:15292627 original size:23 final size:23
Alignment explanation
Indices: 15292601--15292644 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
15292591 AGTATTATTA
* * *
15292601 ATGATTAGTTAATTTAATTAAAT
1 ATGATTAATTAAGTAAATTAAAT
15292624 ATGATTAATTAAGTAAATTAA
1 ATGATTAATTAAGTAAATTAA
15292645 GGTTTAATTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.09, T:0.43
Consensus pattern (23 bp):
ATGATTAATTAAGTAAATTAAAT
Found at i:15294298 original size:19 final size:19
Alignment explanation
Indices: 15294271--15294310 Score: 71
Period size: 19 Copynumber: 2.1 Consensus size: 19
15294261 AACTTGATAT
15294271 AATGACAGCTTATGTGAGC
1 AATGACAGCTTATGTGAGC
*
15294290 AATGTCAGCTTATGTGAGC
1 AATGACAGCTTATGTGAGC
15294309 AA
1 AA
15294311 CTTTATTCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.33, C:0.15, G:0.25, T:0.28
Consensus pattern (19 bp):
AATGACAGCTTATGTGAGC
Found at i:15302875 original size:43 final size:43
Alignment explanation
Indices: 15302814--15302925 Score: 179
Period size: 43 Copynumber: 2.6 Consensus size: 43
15302804 TACTATCGTA
*
15302814 AACATATATCCATGCCTAATTAACATTAACCTTTTAGTTTTTT
1 AACATATATCCATGCCTAATTAACATTAACCTTTTAGTTTCTT
*
15302857 AACATATATCCATGCCTAATTAACATTAATCTTTTAGTTTCTT
1 AACATATATCCATGCCTAATTAACATTAACCTTTTAGTTTCTT
* * *
15302900 AACTTATTTCCATGCCAAATTAACAT
1 AACATATATCCATGCCTAATTAACAT
15302926 CAAGATCACC
Statistics
Matches: 64, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
43 64 1.00
ACGTcount: A:0.34, C:0.20, G:0.04, T:0.42
Consensus pattern (43 bp):
AACATATATCCATGCCTAATTAACATTAACCTTTTAGTTTCTT
Found at i:15317771 original size:29 final size:29
Alignment explanation
Indices: 15317695--15317959 Score: 251
Period size: 29 Copynumber: 9.1 Consensus size: 29
15317685 TTGCTATTTC
* *
15317695 TAAACGGATGCCTTTGTGGCTATCTCTAT
1 TAAAAGGAAGCCTTTGTGGCTATCTCTAT
* * * * * *
15317724 GAAAAAGAAGCATTCGTGGTTACCTCTAT
1 TAAAAGGAAGCCTTTGTGGCTATCTCTAT
* * **
15317753 CAAAAGGAATCCTTTGTGGAAATCTCTAT
1 TAAAAGGAAGCCTTTGTGGCTATCTCTAT
15317782 TAAAAGGAAGCCTTTGTGGCTATCTCTAT
1 TAAAAGGAAGCCTTTGTGGCTATCTCTAT
* * *
15317811 TAAAAGGATGCATTTATGGCTATCTCTAT
1 TAAAAGGAAGCCTTTGTGGCTATCTCTAT
* * * * **
15317840 TAAACGGATGCTTTTATGGCTATCTCCGT
1 TAAAAGGAAGCCTTTGTGGCTATCTCTAT
* * *
15317869 TAAAAGGATGCATTTGTGGCTATCTCTAC
1 TAAAAGGAAGCCTTTGTGGCTATCTCTAT
* * *
15317898 TAGAAGGATGCCTTTGTGGCTATCTCTGT
1 TAAAAGGAAGCCTTTGTGGCTATCTCTAT
* * * *
15317927 TAATAGGATGCCTTTTTGGCTATCTCGAT
1 TAAAAGGAAGCCTTTGTGGCTATCTCTAT
15317956 TAAA
1 TAAA
15317960 GGTATGCCTT
Statistics
Matches: 193, Mismatches: 43, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
29 193 1.00
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.35
Consensus pattern (29 bp):
TAAAAGGAAGCCTTTGTGGCTATCTCTAT
Found at i:15317836 original size:58 final size:58
Alignment explanation
Indices: 15317695--15317959 Score: 280
Period size: 58 Copynumber: 4.6 Consensus size: 58
15317685 TTGCTATTTC
* * * * * * *
15317695 TAAACGGATGCCTTTGTGGCTATCTCTATGAAAAAGAAGCATTCGTGGTTACCTCTAT
1 TAAAAGGATGCCTTTGTGGCTATCTCTATTAAAAGGAAGCCTTTGTGGCTATCTCTAT
* **
15317753 CAAAAGGAAT-CCTTTGTGGAAATCTCTATTAAAAGGAAGCCTTTGTGGCTATCTCTAT
1 TAAAAGG-ATGCCTTTGTGGCTATCTCTATTAAAAGGAAGCCTTTGTGGCTATCTCTAT
* * * * * * **
15317811 TAAAAGGATGCATTTATGGCTATCTCTATTAAACGGATGCTTTTATGGCTATCTCCGT
1 TAAAAGGATGCCTTTGTGGCTATCTCTATTAAAAGGAAGCCTTTGTGGCTATCTCTAT
* * * * *
15317869 TAAAAGGATGCATTTGTGGCTATCTCTACTAGAAGGATGCCTTTGTGGCTATCTCTGT
1 TAAAAGGATGCCTTTGTGGCTATCTCTATTAAAAGGAAGCCTTTGTGGCTATCTCTAT
* * *
15317927 TAATAGGATGCCTTTTTGGCTATCTCGATTAAA
1 TAAAAGGATGCCTTTGTGGCTATCTCTATTAAA
15317960 GGTATGCCTT
Statistics
Matches: 171, Mismatches: 34, Indels: 4
0.82 0.16 0.02
Matches are distributed among these distances:
57 2 0.01
58 167 0.98
59 2 0.01
ACGTcount: A:0.27, C:0.17, G:0.20, T:0.35
Consensus pattern (58 bp):
TAAAAGGATGCCTTTGTGGCTATCTCTATTAAAAGGAAGCCTTTGTGGCTATCTCTAT
Found at i:15317865 original size:87 final size:85
Alignment explanation
Indices: 15317695--15317969 Score: 282
Period size: 87 Copynumber: 3.2 Consensus size: 85
15317685 TTGCTATTTC
* * * * * * * *
15317695 TAAACGGATGCCTTTGTGGCTATCTCTATGAAAAAGAAGCATTCGTGGTTACCTCTATCAAAAGG
1 TAAAAGGATGCCTTTGTGGCTATCTCTATTAAAAGGATGCATTTGTGGCTATCTCTAT-TAAAGG
* * ** *
15317760 AATCCTTTGTGGAAATCTCTAT
65 -ATGCTTTTTGGCTATCTCCAT
* *
15317782 TAAAAGGAAGCCTTTGTGGCTATCTCTATTAAAAGGATGCATTTATGGCTATCTCTATTAAACGG
1 TAAAAGGATGCCTTTGTGGCTATCTCTATTAAAAGGATGCATTTGTGGCTATCTCTATTAAA-GG
*
15317847 ATGCTTTTATGGCTATCTCCGT
65 ATGCTTTT-TGGCTATCTCCAT
* * * * *
15317869 TAAAAGGATGCATTTGTGGCTATCTCTACTAGAAGGATGCCTTTGTGGCTATCTCTGTTAATAGG
1 TAAAAGGATGCCTTTGTGGCTATCTCTATTAAAAGGATGCATTTGTGGCTATCTCTATTAA-AGG
*
15317934 ATGCCTTTTTGGCTATCTCGAT
65 ATG-CTTTTTGGCTATCTCCAT
15317956 T-AAAGGTATGCCTT
1 TAAAAGG-ATGCCTT
15317970 GCGACAAACT
Statistics
Matches: 157, Mismatches: 26, Indels: 10
0.81 0.13 0.05
Matches are distributed among these distances:
86 14 0.09
87 137 0.87
88 6 0.04
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (85 bp):
TAAAAGGATGCCTTTGTGGCTATCTCTATTAAAAGGATGCATTTGTGGCTATCTCTATTAAAGGA
TGCTTTTTGGCTATCTCCAT
Found at i:15321116 original size:5 final size:5
Alignment explanation
Indices: 15321106--15321131 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
15321096 TTAAGGATTT
15321106 AACTA AACTA AACTA AACTA AACTA A
1 AACTA AACTA AACTA AACTA AACTA A
15321132 GAATACAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.62, C:0.19, G:0.00, T:0.19
Consensus pattern (5 bp):
AACTA
Found at i:15323436 original size:16 final size:15
Alignment explanation
Indices: 15323394--15323446 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 15
15323384 TTGTTTAACT
*
15323394 AAAACACTAAAAATAA
1 AAAA-ACTAAAAATAG
*
15323410 AATAAAATAAAAATAGG
1 AA-AAACTAAAAATA-G
15323427 AAAAACTAAAAA-AG
1 AAAAACTAAAAATAG
15323441 AAAAAC
1 AAAAAC
15323447 GAACCCGGGC
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
14 7 0.22
15 1 0.03
16 20 0.62
17 4 0.12
ACGTcount: A:0.75, C:0.08, G:0.06, T:0.11
Consensus pattern (15 bp):
AAAAACTAAAAATAG
Found at i:15330421 original size:15 final size:15
Alignment explanation
Indices: 15330401--15330430 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
15330391 GCATTTATCA
15330401 ACATCTCAAGCTAAG
1 ACATCTCAAGCTAAG
15330416 ACATCTCAAGCTAAG
1 ACATCTCAAGCTAAG
15330431 TCATTTTATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.27, G:0.13, T:0.20
Consensus pattern (15 bp):
ACATCTCAAGCTAAG
Found at i:15334447 original size:9 final size:9
Alignment explanation
Indices: 15334430--15334463 Score: 50
Period size: 9 Copynumber: 3.8 Consensus size: 9
15334420 TGAGTTTTCG
15334430 AATTCGAAT
1 AATTCGAAT
*
15334439 AACTCGAAT
1 AATTCGAAT
*
15334448 AATTCAAAT
1 AATTCGAAT
15334457 AATTCGA
1 AATTCGA
15334464 CTATCAAACT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.47, C:0.15, G:0.09, T:0.29
Consensus pattern (9 bp):
AATTCGAAT
Found at i:15349611 original size:26 final size:26
Alignment explanation
Indices: 15349581--15349630 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
15349571 AAATGATAGA
* *
15349581 ATTAATTA-TATAAATATTTTAAAATT
1 ATTAAATATTATAAA-ATTTAAAAATT
15349607 ATTAAATATTATAAAATTTAAAAA
1 ATTAAATATTATAAAATTTAAAAA
15349631 CACTACTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
26 15 0.71
27 6 0.29
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (26 bp):
ATTAAATATTATAAAATTTAAAAATT
Found at i:15349614 original size:18 final size:19
Alignment explanation
Indices: 15349584--15349624 Score: 66
Period size: 18 Copynumber: 2.2 Consensus size: 19
15349574 TGATAGAATT
*
15349584 AATTATATAAATATTTTAA
1 AATTATATAAATATTATAA
15349603 AATTAT-TAAATATTATAA
1 AATTATATAAATATTATAA
15349621 AATT
1 AATT
15349625 TAAAAACACT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
18 15 0.71
19 6 0.29
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (19 bp):
AATTATATAAATATTATAA
Found at i:15366272 original size:37 final size:37
Alignment explanation
Indices: 15366224--15366297 Score: 139
Period size: 37 Copynumber: 2.0 Consensus size: 37
15366214 TTAGACAAAG
*
15366224 AAAGATTTTGGACACATAGAGGAGAATTAGGTATTAC
1 AAAGATTTTGGACACATAGAGGAGAATTAGATATTAC
15366261 AAAGATTTTGGACACATAGAGGAGAATTAGATATTAC
1 AAAGATTTTGGACACATAGAGGAGAATTAGATATTAC
15366298 TACATTGTCT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 36 1.00
ACGTcount: A:0.42, C:0.08, G:0.23, T:0.27
Consensus pattern (37 bp):
AAAGATTTTGGACACATAGAGGAGAATTAGATATTAC
Found at i:15368274 original size:30 final size:29
Alignment explanation
Indices: 15368238--15368294 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 29
15368228 CAAGTTTCAA
*
15368238 GAGCCACACGGGCTATACACACGGCCATAT
1 GAGCCACACGGGCTA-ACACACGACCATAT
*
15368268 GAGCCACATGGGCTAACACACGACCAT
1 GAGCCACACGGGCTAACACACGACCAT
15368295 GTGCCAGACC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
29 11 0.44
30 14 0.56
ACGTcount: A:0.32, C:0.33, G:0.23, T:0.12
Consensus pattern (29 bp):
GAGCCACACGGGCTAACACACGACCATAT
Found at i:15377336 original size:12 final size:12
Alignment explanation
Indices: 15377319--15377349 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
15377309 TTTCTTTATT
*
15377319 TTATTATTTTTA
1 TTATTATCTTTA
15377331 TTATTATCTTTA
1 TTATTATCTTTA
15377343 TTATTAT
1 TTATTAT
15377350 GTACTCTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (12 bp):
TTATTATCTTTA
Found at i:15377604 original size:22 final size:22
Alignment explanation
Indices: 15377576--15377619 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
15377566 CCAATTTCAT
15377576 CATGAGATGGGTTGGTTGTTGA
1 CATGAGATGGGTTGGTTGTTGA
15377598 CATGAGATGGGTTGGTTGTTGA
1 CATGAGATGGGTTGGTTGTTGA
15377620 TGTGTCTTAC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.18, C:0.05, G:0.41, T:0.36
Consensus pattern (22 bp):
CATGAGATGGGTTGGTTGTTGA
Found at i:15382361 original size:9 final size:9
Alignment explanation
Indices: 15382347--15382377 Score: 62
Period size: 9 Copynumber: 3.4 Consensus size: 9
15382337 ATGCTAACCA
15382347 TATGCAAAT
1 TATGCAAAT
15382356 TATGCAAAT
1 TATGCAAAT
15382365 TATGCAAAT
1 TATGCAAAT
15382374 TATG
1 TATG
15382378 TGACCATTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.42, C:0.10, G:0.13, T:0.35
Consensus pattern (9 bp):
TATGCAAAT
Found at i:15393380 original size:17 final size:16
Alignment explanation
Indices: 15393339--15393383 Score: 56
Period size: 17 Copynumber: 2.8 Consensus size: 16
15393329 AAAAATGAAC
*
15393339 TTTTAAATCATTTTTAA
1 TTTTAAAT-TTTTTTAA
15393356 TTTT-AATTTTTTTAAA
1 TTTTAAATTTTTTT-AA
15393372 TTTTAAATTTTT
1 TTTTAAATTTTT
15393384 AAAAATCAAG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
15 5 0.20
16 9 0.36
17 11 0.44
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (16 bp):
TTTTAAATTTTTTTAA
Found at i:15393384 original size:15 final size:16
Alignment explanation
Indices: 15393348--15393386 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
15393338 CTTTTAAATC
15393348 ATTTTT-AATTTTAAT
1 ATTTTTAAATTTTAAT
*
15393363 TTTTTTAAATTTTAA-
1 ATTTTTAAATTTTAAT
15393378 ATTTTTAAA
1 ATTTTTAAA
15393387 AATCAAGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
ATTTTTAAATTTTAAT
Found at i:15410992 original size:21 final size:20
Alignment explanation
Indices: 15410953--15410991 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
15410943 GTAGACAACT
15410953 TTTTTTTTTGCAGTTTTTTC
1 TTTTTTTTTGCAGTTTTTTC
*
15410973 TTTTTTTTTGCTGTTTTTT
1 TTTTTTTTTGCAGTTTTTT
15410992 TAAAGAATAA
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:0.03, C:0.08, G:0.10, T:0.79
Consensus pattern (20 bp):
TTTTTTTTTGCAGTTTTTTC
Found at i:15426494 original size:56 final size:56
Alignment explanation
Indices: 15426426--15426578 Score: 209
Period size: 56 Copynumber: 2.7 Consensus size: 56
15426416 GTTATTTAAG
*
15426426 AATCAAATTGCTAAAAGATAATATCCCATAATAACATCCTATAATATCCCA-TTCAA
1 AATCAAATTGCTAAAAGATAATATCCCATAATAACATCCTATAATATCCCACTAC-A
* * * * *
15426482 AATCAAATTGCTAAGAGATAATATCTCATAATAATATCTTATAATATCCCACTACG
1 AATCAAATTGCTAAAAGATAATATCCCATAATAACATCCTATAATATCCCACTACA
* * *
15426538 AATCAAATTGTTAAAAAATAATATCCCATAATTACATCCTA
1 AATCAAATTGCTAAAAGATAATATCCCATAATAACATCCTA
15426579 ACATCCCCTC
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
56 81 0.98
57 2 0.02
ACGTcount: A:0.46, C:0.19, G:0.05, T:0.31
Consensus pattern (56 bp):
AATCAAATTGCTAAAAGATAATATCCCATAATAACATCCTATAATATCCCACTACA
Found at i:15430147 original size:56 final size:56
Alignment explanation
Indices: 15430065--15430221 Score: 253
Period size: 56 Copynumber: 2.8 Consensus size: 56
15430055 AGTAGTTACG
* *
15430065 TAGGAATCAAATTGCTAAAAGATAATACCCCATAATAATATCCTATAGTATC-CAT
1 TAGGAATCAAATTGCTAAAAGATAATATCCCATAATAATATCCTATAATATCTCAT
*
15430120 TAGGAATCAAATTGTCTAAGAGATAATATCCCATAATAATATCCTATAATATCTCAT
1 TAGGAATCAAATTG-CTAAAAGATAATATCCCATAATAATATCCTATAATATCTCAT
* *
15430177 TAGGAATCAAATTACTAAAAGGTAATATCCCATAATAATATCCTA
1 TAGGAATCAAATTGCTAAAAGATAATATCCCATAATAATATCCTA
15430222 ACATTTACTT
Statistics
Matches: 94, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
55 14 0.15
56 64 0.68
57 16 0.17
ACGTcount: A:0.44, C:0.17, G:0.09, T:0.31
Consensus pattern (56 bp):
TAGGAATCAAATTGCTAAAAGATAATATCCCATAATAATATCCTATAATATCTCAT
Found at i:15432860 original size:163 final size:163
Alignment explanation
Indices: 15432590--15432916 Score: 645
Period size: 163 Copynumber: 2.0 Consensus size: 163
15432580 TTGGCTTTGA
*
15432590 AAGTGCGCATCTGTGAGCCCACATTGATTCACCATATCTCTAAAACTCTTCGTTTTCCTCTCTGT
1 AAGTGCGCATCTGTGAGCCCACATTGATTCACCATATCACTAAAACTCTTCGTTTTCCTCTCTGT
15432655 ACAATTATTTCCCCCTTATTTTCATATTGAAATAAGATATATTTAAAGTCTCCTAAACATATCCA
66 ACAATTATTTCCCCCTTATTTTCATATTGAAATAAGATATATTTAAAGTCTCCTAAACATATCCA
15432720 TCTACATATATTCCTTTTGCTCTTGTTTTCCAC
131 TCTACATATATTCCTTTTGCTCTTGTTTTCCAC
15432753 AAGTGCGCATCTGTGAGCCCACATTGATTCACCATATCACTAAAACTCTTCGTTTTCCTCTCTGT
1 AAGTGCGCATCTGTGAGCCCACATTGATTCACCATATCACTAAAACTCTTCGTTTTCCTCTCTGT
15432818 ACAATTATTTCCCCCTTATTTTCATATTGAAATAAGATATATTTAAAGTCTCCTAAACATATCCA
66 ACAATTATTTCCCCCTTATTTTCATATTGAAATAAGATATATTTAAAGTCTCCTAAACATATCCA
15432883 TCTACATATATTCCTTTTGCTCTTGTTTTCCAC
131 TCTACATATATTCCTTTTGCTCTTGTTTTCCAC
15432916 A
1 A
15432917 CCTCAAATTT
Statistics
Matches: 163, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
163 163 1.00
ACGTcount: A:0.27, C:0.25, G:0.09, T:0.39
Consensus pattern (163 bp):
AAGTGCGCATCTGTGAGCCCACATTGATTCACCATATCACTAAAACTCTTCGTTTTCCTCTCTGT
ACAATTATTTCCCCCTTATTTTCATATTGAAATAAGATATATTTAAAGTCTCCTAAACATATCCA
TCTACATATATTCCTTTTGCTCTTGTTTTCCAC
Found at i:15437594 original size:29 final size:29
Alignment explanation
Indices: 15437479--15437614 Score: 89
Period size: 29 Copynumber: 4.6 Consensus size: 29
15437469 TCAACACCGG
* **
15437479 TACATAGTACTTGATAA-ATATAACACTGGA
1 TACATAGTACCTGATAATATA-AACA-TCAA
* * *
15437509 -ACATAGTGCCTGATACAACATGAACATCAA
1 TACATAGTACCTGAT--AATATAAACATCAA
* **
15437539 TACA-AGGTACCTGATAATGTAGTCATCAA
1 TACATA-GTACCTGATAATATAAACATCAA
*
15437568 TACATAGTACCTGATAATATAAACATCGA
1 TACATAGTACCTGATAATATAAACATCAA
* * *
15437597 CACATAGTGCCTGTTAAT
1 TACATAGTACCTGATAAT
15437615 CCCAAATGAC
Statistics
Matches: 82, Mismatches: 18, Indels: 13
0.73 0.16 0.12
Matches are distributed among these distances:
29 59 0.72
30 4 0.05
31 17 0.21
32 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.14, T:0.27
Consensus pattern (29 bp):
TACATAGTACCTGATAATATAAACATCAA
Found at i:15441107 original size:25 final size:24
Alignment explanation
Indices: 15441079--15441134 Score: 69
Period size: 24 Copynumber: 2.3 Consensus size: 24
15441069 TTTGTAGTTA
15441079 CACTAGCT-GTTTTAGTTGCTCCTAT
1 CACTA-CTAGTTTTA-TTGCTCCTAT
*
15441104 CACTACTAGTTTTATTGCTCCTTT
1 CACTACTAGTTTTATTGCTCCTAT
*
15441128 AACTACT
1 CACTACT
15441135 TGCAAAATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
24 17 0.61
25 11 0.39
ACGTcount: A:0.20, C:0.25, G:0.11, T:0.45
Consensus pattern (24 bp):
CACTACTAGTTTTATTGCTCCTAT
Found at i:15441132 original size:24 final size:25
Alignment explanation
Indices: 15441087--15441134 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 25
15441077 TACACTAGCT
*
15441087 GTTTTAGTTGCTCCTATCACTACTA
1 GTTTTAGTTGCTCCTATAACTACTA
*
15441112 GTTTTA-TTGCTCCTTTAACTACT
1 GTTTTAGTTGCTCCTATAACTACT
15441135 TGCAAAATCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 15 0.71
25 6 0.29
ACGTcount: A:0.19, C:0.23, G:0.10, T:0.48
Consensus pattern (25 bp):
GTTTTAGTTGCTCCTATAACTACTA
Found at i:15445278 original size:29 final size:29
Alignment explanation
Indices: 15445236--15445571 Score: 327
Period size: 29 Copynumber: 11.6 Consensus size: 29
15445226 GATTGTTAAA
15445236 ACCATCCCTTTTCATATTCGATGGTCGTC
1 ACCATCCCTTTTCATATTCGATGGTCGTC
* * **
15445265 ACCATCCCTTTTCATAGTCGATGGTTGAA
1 ACCATCCCTTTTCATATTCGATGGTCGTC
* *
15445294 ACCATCCCTTTTCAATAATGGATGGTCGTC
1 ACCATCCCTTTTC-ATATTCGATGGTCGTC
*
15445324 ACCATCCTTTTTCATAGTT-GATGGTCGTC
1 ACCATCCCTTTTCATA-TTCGATGGTCGTC
* * ***
15445353 ACCATCCCTTTTCATAGTCGATAGTCAAA
1 ACCATCCCTTTTCATATTCGATGGTCGTC
* * * ***
15445382 ACTATCTCTTTTCATATTCGATAGTCAAA
1 ACCATCCCTTTTCATATTCGATGGTCGTC
* * * *
15445411 ACTATCTCTTTTCATATTCGATGGTTGCC
1 ACCATCCCTTTTCATATTCGATGGTCGTC
* ** * **
15445440 ACCATCCCTTTTCATAGTCGATAATTGAA
1 ACCATCCCTTTTCATATTCGATGGTCGTC
* *
15445469 ACTATCCCTTTTCATATTCGATGGTCATC
1 ACCATCCCTTTTCATATTCGATGGTCGTC
*
15445498 ACCATCCTTTTTCATAGTT-GATGGTCGTC
1 ACCATCCCTTTTCATA-TTCGATGGTCGTC
*
15445527 ACCATCCTTTTTCATAGTT-GATGGTCGTC
1 ACCATCCCTTTTCATA-TTCGATGGTCGTC
15445556 ACCATCCCTTTTCATA
1 ACCATCCCTTTTCATA
15445572 GTTGATAGTT
Statistics
Matches: 259, Mismatches: 44, Indels: 8
0.83 0.14 0.03
Matches are distributed among these distances:
28 1 0.00
29 232 0.90
30 26 0.10
ACGTcount: A:0.23, C:0.26, G:0.13, T:0.38
Consensus pattern (29 bp):
ACCATCCCTTTTCATATTCGATGGTCGTC
Found at i:15445303 original size:58 final size:58
Alignment explanation
Indices: 15445234--15445599 Score: 392
Period size: 58 Copynumber: 6.3 Consensus size: 58
15445224 CTGATTGTTA
* *
15445234 AAACCATCCCTTTTCATATTCGATGGTCGTCACCATCCCTTTTCATAGTCGATGGTTG
1 AAACCATCCCTTTTCATATTCGATGGTCGTCACCATCCCTTTTCATAGTCGATAGTCG
* * * * *
15445292 AAACCATCCCTTTTCAATAATGGATGGTCGTCACCATCCTTTTTCATAGTTGATGGTCG
1 AAACCATCCCTTTTC-ATATTCGATGGTCGTCACCATCCCTTTTCATAGTCGATAGTCG
** * * *** * * * *
15445351 TCACCATCCCTTTTCATAGTCGATAGTCAAAACTATCTCTTTTCATATTCGATAGTCA
1 AAACCATCCCTTTTCATATTCGATGGTCGTCACCATCCCTTTTCATAGTCGATAGTCG
* * * * * *
15445409 AAACTATCTCTTTTCATATTCGATGGTTGCCACCATCCCTTTTCATAGTCGATAATTG
1 AAACCATCCCTTTTCATATTCGATGGTCGTCACCATCCCTTTTCATAGTCGATAGTCG
* * * * *
15445467 AAACTATCCCTTTTCATATTCGATGGTCATCACCATCCTTTTTCATAGTTGATGGTCG
1 AAACCATCCCTTTTCATATTCGATGGTCGTCACCATCCCTTTTCATAGTCGATAGTCG
** * * *
15445525 TCACCATCCTTTTTCATAGTT-GATGGTCGTCACCATCCCTTTTCATAGTTGATAGTTG
1 AAACCATCCCTTTTCATA-TTCGATGGTCGTCACCATCCCTTTTCATAGTCGATAGTCG
*
15445583 AAACTATCCCTTTTCAT
1 AAACCATCCCTTTTCAT
15445600 TTTTTTGATA
Statistics
Matches: 249, Mismatches: 57, Indels: 4
0.80 0.18 0.01
Matches are distributed among these distances:
58 196 0.79
59 53 0.21
ACGTcount: A:0.23, C:0.25, G:0.13, T:0.39
Consensus pattern (58 bp):
AAACCATCCCTTTTCATATTCGATGGTCGTCACCATCCCTTTTCATAGTCGATAGTCG
Found at i:15445462 original size:87 final size:86
Alignment explanation
Indices: 15445233--15445599 Score: 380
Period size: 87 Copynumber: 4.2 Consensus size: 86
15445223 ACTGATTGTT
* *
15445233 AAAACCATCCCTTTTCATA-TTCGATGGTCGTCACCATCCCTTTTCATAGTCGATGGTTGAAACC
1 AAAACCAT-CCTTTTCATAGTT-GATGGTCGTCACCATCCCTTTTCATAGTCGATAGTCGAAACC
* * *
15445297 ATCCCTTTTCAATAATGGATGGTC
64 ATCCCTTTTC-ATATTCGATAGTC
*** * *
15445321 GTCACCATCCTTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGTCGATAGTCAAAACTA
1 AAAACCATCC-TTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGTCGATAGTCGAAACCA
*
15445386 TCTCTTTTCATATTCGATAGTC
65 TCCCTTTTCATATTCGATAGTC
* * * * * *
15445408 AAAACTATCTCTTTTCATA-TTCGATGGTTGCCACCATCCCTTTTCATAGTCGATAATTGAAACT
1 AAAACCATC-CTTTTCATAGTT-GATGGTCGTCACCATCCCTTTTCATAGTCGATAGTCGAAACC
*
15445472 ATCCCTTTTCATATTCGATGGTC
64 ATCCCTTTTCATATTCGATAGTC
** * * * **
15445495 ATCACCATCCTTTTTCATAGTTGATGGTCGTCACCATCCTTTTTCATAGTTGATGGTCGTCACCA
1 AAAACCATCC-TTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGTCGATAGTCGAAACCA
*
15445560 TCCCTTTTCATAGTT-GATAGTT
65 TCCCTTTTCATA-TTCGATAGTC
* *
15445582 GAAACTATCCCTTTTCAT
1 AAAACCAT-CCTTTTCAT
15445600 TTTTTTGATA
Statistics
Matches: 230, Mismatches: 41, Indels: 17
0.80 0.14 0.06
Matches are distributed among these distances:
86 3 0.01
87 158 0.69
88 67 0.29
89 2 0.01
ACGTcount: A:0.23, C:0.25, G:0.13, T:0.38
Consensus pattern (86 bp):
AAAACCATCCTTTTCATAGTTGATGGTCGTCACCATCCCTTTTCATAGTCGATAGTCGAAACCAT
CCCTTTTCATATTCGATAGTC
Found at i:15447094 original size:73 final size:74
Alignment explanation
Indices: 15446975--15447130 Score: 251
Period size: 73 Copynumber: 2.1 Consensus size: 74
15446965 ATTGTCCAAA
* *
15446975 TAGAGCAAAAGATTTCAAGGATATCAAAGATTCCATAAGGGAAAAGGGAAAGGTGTGGCTATTGA
1 TAGAGCAAAAGATTTCAAGGATATCAAAGATTCAATAAGGGAAAAGGGAAAGGTGTGGCCATTGA
15447040 TGAGAA-CC
66 TGAGAACCC
* * * *
15447048 TAGAGCAAAAGATTTCAAGGATATCAAAGATTTAATGAGGGAAAAGGTAAATGTGTGGCCATTGA
1 TAGAGCAAAAGATTTCAAGGATATCAAAGATTCAATAAGGGAAAAGGGAAAGGTGTGGCCATTGA
15447113 TGAGAACCC
66 TGAGAACCC
15447122 TAGAGCAAA
1 TAGAGCAAA
15447131 GAAGAGATGC
Statistics
Matches: 76, Mismatches: 6, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
73 65 0.86
74 11 0.14
ACGTcount: A:0.42, C:0.11, G:0.26, T:0.21
Consensus pattern (74 bp):
TAGAGCAAAAGATTTCAAGGATATCAAAGATTCAATAAGGGAAAAGGGAAAGGTGTGGCCATTGA
TGAGAACCC
Found at i:15449840 original size:97 final size:97
Alignment explanation
Indices: 15449674--15449855 Score: 319
Period size: 97 Copynumber: 1.9 Consensus size: 97
15449664 TTTCATATGT
15449674 CTTTCCATTAACCTTCACTTACCCGTTGAACCATATAGAATTACATCAGATACTCAGGAATACTC
1 CTTTCCATTAACCTTCACTTACCCGTTGAACCATATAGAATTACATCAGATACTCAGGAATACTC
*
15449739 ACACAAAGTGTACCTTTTCATATAATCGTTAC
66 ACACAAAGTGTAACTTTTCATATAATCGTTAC
* * * *
15449771 CTTTCCATTAACCTTTACTTACCCGTTGAACTATATAGAATTACATCGGATACTGAGGAATACTC
1 CTTTCCATTAACCTTCACTTACCCGTTGAACCATATAGAATTACATCAGATACTCAGGAATACTC
15449836 ACACAAAGTGTAACTTTTCA
66 ACACAAAGTGTAACTTTTCA
15449856 AATGGGCCTG
Statistics
Matches: 80, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
97 80 1.00
ACGTcount: A:0.33, C:0.24, G:0.10, T:0.32
Consensus pattern (97 bp):
CTTTCCATTAACCTTCACTTACCCGTTGAACCATATAGAATTACATCAGATACTCAGGAATACTC
ACACAAAGTGTAACTTTTCATATAATCGTTAC
Found at i:15455624 original size:20 final size:20
Alignment explanation
Indices: 15455595--15455642 Score: 60
Period size: 21 Copynumber: 2.4 Consensus size: 20
15455585 TGCTAGTTTA
* *
15455595 TTTGACTTTTGTTTTGTTGT
1 TTTGATTTTTGTTTCGTTGT
15455615 TTTGATTTTTTGTTTCGTTGT
1 TTTGA-TTTTTGTTTCGTTGT
*
15455636 TTGGATT
1 TTTGATT
15455643 GGTGTAGCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 7 0.29
21 17 0.71
ACGTcount: A:0.06, C:0.04, G:0.21, T:0.69
Consensus pattern (20 bp):
TTTGATTTTTGTTTCGTTGT
Found at i:15455627 original size:21 final size:21
Alignment explanation
Indices: 15455601--15455642 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
15455591 TTTATTTGAC
* *
15455601 TTTTGTTTTGTTGTTTTGATT
1 TTTTGTTTCGTTGTTTGGATT
15455622 TTTTGTTTCGTTGTTTGGATT
1 TTTTGTTTCGTTGTTTGGATT
15455643 GGTGTAGCTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.05, C:0.02, G:0.21, T:0.71
Consensus pattern (21 bp):
TTTTGTTTCGTTGTTTGGATT
Found at i:15463376 original size:126 final size:126
Alignment explanation
Indices: 15463151--15463528 Score: 648
Period size: 126 Copynumber: 3.0 Consensus size: 126
15463141 TGTAAAGAAG
* * *
15463151 CTATTTGGTTGAAGGGACTCTCTAGTAAACTCAATGAAGACCTTCAAATCAATAGAGTATTTTGT
1 CTATTTGGTTGAAGGGACTCTTTAGTGAACTCAATGAAGACCTTCAAATCAATACAGTATTTTGT
* *
15463216 GACAGACAGAGTGTCATCTTCCTTACAAAAGATCAAATGTTTCATGAGAGAACAAAACACA
66 GAAAGTCAGAGTGTCATCTTCCTTACAAAAGATCAAATGTTTCATGAGAGAACAAAACACA
*
15463277 CTATTTGGTTGAAGGGACTCTTTAGTGAATTCAATGAAGACCTTCAAATCAATACAGTATTTTGT
1 CTATTTGGTTGAAGGGACTCTTTAGTGAACTCAATGAAGACCTTCAAATCAATACAGTATTTTGT
* * *
15463342 GATAGTCAGAGTGCCATCTTCCTTACAAAAGATCAAATGTTTCATGAGAGAAAAAAACACA
66 GAAAGTCAGAGTGTCATCTTCCTTACAAAAGATCAAATGTTTCATGAGAGAACAAAACACA
*
15463403 CTATTTGGTTGAAGGGACTCTTTAGTGAACTCAATGAAGACCTTCAAATCAATACAATATTTTGT
1 CTATTTGGTTGAAGGGACTCTTTAGTGAACTCAATGAAGACCTTCAAATCAATACAGTATTTTGT
* *
15463468 GAAAGTTAGAGTGTCATCTTTCTTACAAAAGATCAAATGTTTCATGAGAGAACAAAACACA
66 GAAAGTCAGAGTGTCATCTTCCTTACAAAAGATCAAATGTTTCATGAGAGAACAAAACACA
15463529 TTGATGTTCG
Statistics
Matches: 237, Mismatches: 15, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
126 237 1.00
ACGTcount: A:0.37, C:0.16, G:0.17, T:0.30
Consensus pattern (126 bp):
CTATTTGGTTGAAGGGACTCTTTAGTGAACTCAATGAAGACCTTCAAATCAATACAGTATTTTGT
GAAAGTCAGAGTGTCATCTTCCTTACAAAAGATCAAATGTTTCATGAGAGAACAAAACACA
Found at i:15473742 original size:35 final size:35
Alignment explanation
Indices: 15473692--15473762 Score: 124
Period size: 35 Copynumber: 2.0 Consensus size: 35
15473682 TTAAACTTTA
*
15473692 ACTTTCCAACTACATGCAAAAGTTACTTTCTCACC
1 ACTTTCCAACGACATGCAAAAGTTACTTTCTCACC
*
15473727 ACTTTCCAACGACATGCAAAAGTTATTTTCTCACC
1 ACTTTCCAACGACATGCAAAAGTTACTTTCTCACC
15473762 A
1 A
15473763 TTATACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.32, C:0.30, G:0.07, T:0.31
Consensus pattern (35 bp):
ACTTTCCAACGACATGCAAAAGTTACTTTCTCACC
Found at i:15474074 original size:8 final size:9
Alignment explanation
Indices: 15474054--15474081 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
15474044 ATTTGGGGAG
15474054 TTTTGACAT
1 TTTTGACAT
15474063 TTTTGACAT
1 TTTTGACAT
15474072 TTTTGACAT
1 TTTTGACAT
15474081 T
1 T
15474082 CTGGTTCCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.21, C:0.11, G:0.11, T:0.57
Consensus pattern (9 bp):
TTTTGACAT
Found at i:15476555 original size:20 final size:20
Alignment explanation
Indices: 15476500--15476560 Score: 61
Period size: 20 Copynumber: 3.1 Consensus size: 20
15476490 TCCAATAAAA
*
15476500 TGCCAGT-TTGTGGACAAGC
1 TGCCAGTATTGTGGACAAGT
** **
15476519 CACCAGTATTGCAGACAAGT
1 TGCCAGTATTGTGGACAAGT
*
15476539 TGCCAGTATTGTGGACATGT
1 TGCCAGTATTGTGGACAAGT
15476559 TG
1 TG
15476561 GATATGGTGC
Statistics
Matches: 31, Mismatches: 10, Indels: 1
0.74 0.24 0.02
Matches are distributed among these distances:
19 5 0.16
20 26 0.84
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.28
Consensus pattern (20 bp):
TGCCAGTATTGTGGACAAGT
Found at i:15477406 original size:30 final size:30
Alignment explanation
Indices: 15477370--15477430 Score: 95
Period size: 30 Copynumber: 2.0 Consensus size: 30
15477360 TTGAGTTAAG
15477370 TGTTTAAGATAGGTAAAAAAGAAAACATCT
1 TGTTTAAGATAGGTAAAAAAGAAAACATCT
* * *
15477400 TGTTTAAGATAGGTTAAGAAGAAAATATCT
1 TGTTTAAGATAGGTAAAAAAGAAAACATCT
15477430 T
1 T
15477431 ATCTCTTTCT
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:0.46, C:0.05, G:0.18, T:0.31
Consensus pattern (30 bp):
TGTTTAAGATAGGTAAAAAAGAAAACATCT
Found at i:15478881 original size:26 final size:26
Alignment explanation
Indices: 15478847--15478897 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 26
15478837 CAATTTCTAA
* *
15478847 AAAAAGATGCCTTTGTGGTTATCTCT
1 AAAAAGATGCCTTTATGGCTATCTCT
*
15478873 AAAAGGATGCCTTTATGGCTATCTC
1 AAAAAGATGCCTTTATGGCTATCTC
15478898 AATCAAAAGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (26 bp):
AAAAAGATGCCTTTATGGCTATCTCT
Found at i:15479004 original size:29 final size:29
Alignment explanation
Indices: 15478958--15479015 Score: 89
Period size: 29 Copynumber: 2.0 Consensus size: 29
15478948 GCAGTTTCAG
*
15478958 TAAGGAAGCCTTTATGGTGATCTCTGTTA
1 TAAGAAAGCCTTTATGGTGATCTCTGTTA
* *
15478987 TAAGAAAGCCTTTGTGGTTATCTCTGTTA
1 TAAGAAAGCCTTTATGGTGATCTCTGTTA
15479016 AAGGAATGCT
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.24, C:0.14, G:0.22, T:0.40
Consensus pattern (29 bp):
TAAGAAAGCCTTTATGGTGATCTCTGTTA
Found at i:15481155 original size:25 final size:26
Alignment explanation
Indices: 15481099--15481156 Score: 64
Period size: 25 Copynumber: 2.3 Consensus size: 26
15481089 TAATTTCTCG
* *
15481099 AAATTTTATTAGGGGCAAAATCGCCA
1 AAATTTTACTAGGGGCAAAATCACCA
* * *
15481125 ATATTTTACTA-GGGTAAAATCATCA
1 AAATTTTACTAGGGGCAAAATCACCA
15481150 AAATTTT
1 AAATTTT
15481157 GTTGAGGTAT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
25 17 0.65
26 9 0.35
ACGTcount: A:0.40, C:0.12, G:0.14, T:0.34
Consensus pattern (26 bp):
AAATTTTACTAGGGGCAAAATCACCA
Found at i:15502088 original size:30 final size:31
Alignment explanation
Indices: 15502046--15502124 Score: 99
Period size: 30 Copynumber: 2.5 Consensus size: 31
15502036 AATGAGTAAC
*
15502046 AAAGAATAGTTTAGGTACC-ACTTGTGACAAAA
1 AAAG-ATAGTTTAGGTACCAACTTGAGA-AAAA
15502078 AAAGA-AGTTTAGGTACCAACTTGAGAAAAA
1 AAAGATAGTTTAGGTACCAACTTGAGAAAAA
* *
15502108 AAATATTGTTTAGGTAC
1 AAAGATAGTTTAGGTAC
15502125 TAATTTGTGA
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
30 20 0.48
31 18 0.43
32 4 0.10
ACGTcount: A:0.44, C:0.10, G:0.19, T:0.27
Consensus pattern (31 bp):
AAAGATAGTTTAGGTACCAACTTGAGAAAAA
Found at i:15502109 original size:31 final size:30
Alignment explanation
Indices: 15502053--15502110 Score: 89
Period size: 31 Copynumber: 1.9 Consensus size: 30
15502043 AACAAAGAAT
* *
15502053 AGTTTAGGTACCACTTGTGACAAAAAAAGA
1 AGTTTAGGTACCACTTGAGAAAAAAAAAGA
15502083 AGTTTAGGTACCAACTTGAGAAAAAAAA
1 AGTTTAGGTACC-ACTTGAGAAAAAAAA
15502111 TATTGTTTAG
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
30 12 0.48
31 13 0.52
ACGTcount: A:0.47, C:0.12, G:0.19, T:0.22
Consensus pattern (30 bp):
AGTTTAGGTACCACTTGAGAAAAAAAAAGA
Found at i:15503900 original size:20 final size:21
Alignment explanation
Indices: 15503877--15503917 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
15503867 TTATGAATTA
*
15503877 GGGAT-TATGGTTTAAGGGTT
1 GGGATGTAAGGTTTAAGGGTT
*
15503897 GGGATGTAAGGTTTAGGGGTT
1 GGGATGTAAGGTTTAAGGGTT
15503918 AGGGGTTTAG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.20, C:0.00, G:0.44, T:0.37
Consensus pattern (21 bp):
GGGATGTAAGGTTTAAGGGTT
Found at i:15503921 original size:7 final size:7
Alignment explanation
Indices: 15503909--15503957 Score: 53
Period size: 7 Copynumber: 6.9 Consensus size: 7
15503899 GATGTAAGGT
15503909 TTAGGGG
1 TTAGGGG
15503916 TTAGGGG
1 TTAGGGG
15503923 TTTAGGGG
1 -TTAGGGG
**
15503931 TTAGATG
1 TTAGGGG
15503938 TTAGGGG
1 TTAGGGG
* *
15503945 TTAAGAG
1 TTAGGGG
15503952 TTAGGG
1 TTAGGG
15503958 ATTTAAGGTT
Statistics
Matches: 33, Mismatches: 8, Indels: 2
0.77 0.19 0.05
Matches are distributed among these distances:
7 26 0.79
8 7 0.21
ACGTcount: A:0.20, C:0.00, G:0.47, T:0.33
Consensus pattern (7 bp):
TTAGGGG
Found at i:15503926 original size:15 final size:15
Alignment explanation
Indices: 15503905--15503972 Score: 63
Period size: 15 Copynumber: 4.7 Consensus size: 15
15503895 TTGGGATGTA
15503905 AGGTTTAGGGGTTAG
1 AGGTTTAGGGGTTAG
*
15503920 GGGTTTAGGGGTTAG
1 AGGTTTAGGGGTTAG
*
15503935 ATG-TTAGGGGTTA-
1 AGGTTTAGGGGTTAG
*
15503948 AGAG-TTAGGGATTTA-
1 AG-GTTTAGGG-GTTAG
15503963 AGGTTTAGGG
1 AGGTTTAGGG
15503973 ATTCAGGGGT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
13 1 0.02
14 18 0.40
15 26 0.58
ACGTcount: A:0.22, C:0.00, G:0.44, T:0.34
Consensus pattern (15 bp):
AGGTTTAGGGGTTAG
Found at i:15509070 original size:43 final size:41
Alignment explanation
Indices: 15509004--15509158 Score: 175
Period size: 43 Copynumber: 3.6 Consensus size: 41
15508994 TCTTTATCGG
* * *
15509004 AAAGATCATGTTCTTTAGTGGCGTTTGTGATAAAAGCGCTGCT
1 AAAGAACATGTTCTTTAGCGGCGTTT-TGAT-AAAGCGCCGCT
* *
15509047 AAAGATCATGTTCTTTAGCGGCGTTTATGGGTAAAGCGCCGCT
1 AAAGAACATGTTCTTTAGCGGCGTTT-T-GATAAAGCGCCGCT
* *
15509090 AAAGAACATGTTCTTTAGCGGCGTTTTGTTTTTAAGCGCCGCT
1 AAAGAACATGTTCTTTAGCGGCGTTTTG--ATAAAGCGCCGCT
**
15509133 AAAGAACATGACCTTTAGCGGCGTTT
1 AAAGAACATGTTCTTTAGCGGCGTTT
15509159 ATTTCTGTAA
Statistics
Matches: 100, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
41 1 0.01
42 1 0.01
43 96 0.96
44 2 0.02
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (41 bp):
AAAGAACATGTTCTTTAGCGGCGTTTTGATAAAGCGCCGCT
Found at i:15509280 original size:22 final size:22
Alignment explanation
Indices: 15509252--15509294 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
15509242 TAGTGGCGCT
* *
15509252 AAAAAGCGCTGCTAAAGGCCTA
1 AAAAAGCGCCGCTAAAAGCCTA
15509274 AAAAAGCGCCGCTAAAAGCCT
1 AAAAAGCGCCGCTAAAAGCCT
15509295 GTTTTGGTGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.42, C:0.26, G:0.21, T:0.12
Consensus pattern (22 bp):
AAAAAGCGCCGCTAAAAGCCTA
Found at i:15511571 original size:26 final size:26
Alignment explanation
Indices: 15511519--15511571 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
15511509 AGAAACAAAT
* * *
15511519 TAAGAAGCCAACGAAGGATTACTCAC
1 TAAGAAGCCAACAAAGGATCACCCAC
*
15511545 TAAGAAGCCAACAAAGGGTCACCCAC
1 TAAGAAGCCAACAAAGGATCACCCAC
15511571 T
1 T
15511572 TTCCAAGAGA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.42, C:0.26, G:0.19, T:0.13
Consensus pattern (26 bp):
TAAGAAGCCAACAAAGGATCACCCAC
Found at i:15522095 original size:31 final size:31
Alignment explanation
Indices: 15522060--15522124 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
15522050 AGTTGGGAAG
* *
15522060 AAACTGTGTTCGATTCAAAAAGTTTATTCAA
1 AAACTGCGTTCGATTCAAAAAATTTATTCAA
*
15522091 AAACTGCGTTCGATTCAAAAAATTTATTCGA
1 AAACTGCGTTCGATTCAAAAAATTTATTCAA
15522122 AAA
1 AAA
15522125 GTGTTGTGTT
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (31 bp):
AAACTGCGTTCGATTCAAAAAATTTATTCAA
Found at i:15524206 original size:15 final size:15
Alignment explanation
Indices: 15524170--15524211 Score: 68
Period size: 16 Copynumber: 2.8 Consensus size: 15
15524160 TATATATATT
15524170 TTAAACATAAAAAAC
1 TTAAACATAAAAAAC
15524185 TTAAAACATAAAAAAC
1 TT-AAACATAAAAAAC
15524201 TTAAAC-TAAAA
1 TTAAACATAAAA
15524212 CTAAAAACTT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.19
15 6 0.23
16 15 0.58
ACGTcount: A:0.67, C:0.12, G:0.00, T:0.21
Consensus pattern (15 bp):
TTAAACATAAAAAAC
Found at i:15524219 original size:19 final size:21
Alignment explanation
Indices: 15524181--15524227 Score: 71
Period size: 19 Copynumber: 2.3 Consensus size: 21
15524171 TAAACATAAA
15524181 AAACTTAAAACATAAAAAACTT
1 AAAC-TAAAACATAAAAAACTT
15524203 AAACTAAAAC-T-AAAAACTT
1 AAACTAAAACATAAAAAACTT
15524222 AAACTA
1 AAACTA
15524228 GTATATTTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
19 14 0.56
20 1 0.04
21 6 0.24
22 4 0.16
ACGTcount: A:0.64, C:0.15, G:0.00, T:0.21
Consensus pattern (21 bp):
AAACTAAAACATAAAAAACTT
Found at i:15525168 original size:2 final size:2
Alignment explanation
Indices: 15525163--15525197 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
15525153 TAATATATGC
15525163 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
15525198 GATTACCTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:15525448 original size:30 final size:30
Alignment explanation
Indices: 15525412--15525483 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
15525402 GTCACCACTA
*
15525412 ACCATTTTTCATTACAGACGTAACGAAGCT
1 ACCATTTTCCATTACAGACGTAACGAAGCT
* * * *
15525442 ACCATTTTCCGTTATAGACTTAACGGAGCT
1 ACCATTTTCCATTACAGACGTAACGAAGCT
15525472 ACCATTTTCCAT
1 ACCATTTTCCAT
15525484 CCCCCTATCA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.29, C:0.25, G:0.12, T:0.33
Consensus pattern (30 bp):
ACCATTTTCCATTACAGACGTAACGAAGCT
Found at i:15525595 original size:49 final size:49
Alignment explanation
Indices: 15525514--15525622 Score: 125
Period size: 49 Copynumber: 2.2 Consensus size: 49
15525504 ATCCCTTTCT
15525514 CTCTTCCCCACCATCCCTCCCCCTCCCTTGATTCTCT-CT-CCCTCTCCCC
1 CTCTTCCCCACCATCCCTCCCCCTCCCTTGATTCTCTGCTACCCTCT--CC
* * * *
15525563 CTCTTCCCCACCATCCTTCCTCCT-ACTCTGATTCTTTGCTAACCCTCTCC
1 CTCTTCCCCACCATCCCTCCCCCTCCCT-TGATTCTCTGCT-ACCCTCTCC
15525613 CTCTTCCCCA
1 CTCTTCCCCA
15525623 TCGTCCCTTT
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
48 2 0.04
49 30 0.58
50 14 0.27
52 6 0.12
ACGTcount: A:0.09, C:0.55, G:0.03, T:0.33
Consensus pattern (49 bp):
CTCTTCCCCACCATCCCTCCCCCTCCCTTGATTCTCTGCTACCCTCTCC
Found at i:15527473 original size:110 final size:111
Alignment explanation
Indices: 15527275--15527474 Score: 321
Period size: 110 Copynumber: 1.8 Consensus size: 111
15527265 ACATCTTTTT
*
15527275 TTTTGCTTAAGAATATATTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAACACCTCACCCCG
1 TTTTGCTTAAGAATATATTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAACACCCCACCCCG
* *
15527340 GTTACTTAGCCCAACATACTCCTAATTTATTATATTTATATATATA
66 GTTACTCAGCCCAACACACTCCTAATTTATTATATTTATATATATA
* * **
15527386 TTTT-CTTAAGAATATATTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAGCACCCCATCTTG
1 TTTTGCTTAAGAATATATTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAACACCCCACCCCG
*
15527450 GTTACTCAGCCCAACACATTCCTAA
66 GTTACTCAGCCCAACACACTCCTAA
15527475 AAAATTTTTG
Statistics
Matches: 81, Mismatches: 8, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
110 77 0.95
111 4 0.05
ACGTcount: A:0.33, C:0.23, G:0.14, T:0.30
Consensus pattern (111 bp):
TTTTGCTTAAGAATATATTGAACCTTTTGACGCGAAGAGAGATGACAGCCAAACACCCCACCCCG
GTTACTCAGCCCAACACACTCCTAATTTATTATATTTATATATATA
Found at i:15528637 original size:8 final size:7
Alignment explanation
Indices: 15528624--15528727 Score: 56
Period size: 8 Copynumber: 14.0 Consensus size: 7
15528614 ATCTAAACAA
15528624 AATAAAGT
1 AATAAA-T
15528632 AATAAAT
1 AATAAAT
15528639 AAT-AA-
1 AATAAAT
15528644 AATAAAGT
1 AATAAA-T
15528652 GAAATAAAGT
1 --AATAAA-T
15528662 AATAAAT
1 AATAAAT
*
15528669 AAATAATAA
1 -AATAA-AT
15528678 AATAAAAT
1 AAT-AAAT
15528686 AATAAAT
1 AATAAAT
15528693 AATAAAAT
1 AAT-AAAT
15528701 AAAATAAA-
1 --AATAAAT
*
15528709 AATAAAG
1 AATAAAT
15528716 AA-AAAT
1 AATAAAT
15528722 AA-AAAT
1 AATAAAT
15528728 TGGGTTGCCT
Statistics
Matches: 81, Mismatches: 3, Indels: 26
0.74 0.03 0.24
Matches are distributed among these distances:
5 3 0.04
6 19 0.23
7 14 0.17
8 28 0.35
9 6 0.07
10 11 0.14
ACGTcount: A:0.73, C:0.00, G:0.05, T:0.22
Consensus pattern (7 bp):
AATAAAT
Found at i:15528647 original size:20 final size:19
Alignment explanation
Indices: 15528622--15528714 Score: 88
Period size: 20 Copynumber: 4.8 Consensus size: 19
15528612 ATATCTAAAC
15528622 AAAATAAAGTAATAAATAAT
1 AAAATAAA-TAATAAATAAT
15528642 AAAATAAAGTGAAATAAAGTAAT
1 AAAATAAA-T--AATAAA-TAAT
15528665 -AAATAAATAATAAAATAA-
1 AAAATAAATAAT-AAATAAT
15528683 AATAATAAATAAT-AA-AAT
1 AA-AATAAATAATAAATAAT
15528701 AAAATAAA-AATAAA
1 AAAATAAATAATAAA
15528715 GAAAAATAAA
Statistics
Matches: 65, Mismatches: 0, Indels: 19
0.77 0.00 0.23
Matches are distributed among these distances:
16 3 0.05
17 10 0.15
18 4 0.06
19 7 0.11
20 23 0.35
21 1 0.02
22 13 0.20
23 4 0.06
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (19 bp):
AAAATAAATAATAAATAAT
Found at i:15528649 original size:5 final size:5
Alignment explanation
Indices: 15528639--15528725 Score: 61
Period size: 5 Copynumber: 16.4 Consensus size: 5
15528629 AGTAATAAAT
* * *
15528639 AATAA AATAA AGTGA AATAA AGTAATA AATAAA TAATAA AATAA AATAA
1 AATAA AATAA AATAA AATAA AAT-A-A AAT-AA -AATAA AATAA AATAA
*
15528688 TAA-AT AATAA AATAA AATAAA AATAA AGA-AA AATAA AA
1 -AATAA AATAA AATAA AAT-AA AATAA A-ATAA AATAA AA
15528726 ATTGGGTTGC
Statistics
Matches: 66, Mismatches: 8, Indels: 16
0.73 0.09 0.18
Matches are distributed among these distances:
4 3 0.05
5 43 0.65
6 12 0.18
7 8 0.12
ACGTcount: A:0.75, C:0.00, G:0.05, T:0.21
Consensus pattern (5 bp):
AATAA
Found at i:15528689 original size:54 final size:53
Alignment explanation
Indices: 15528622--15528724 Score: 154
Period size: 54 Copynumber: 1.9 Consensus size: 53
15528612 ATATCTAAAC
* * *
15528622 AAAATAAAGTAATAAATAATAAAATAAAGT-GAAATAAAGTAATAAATAAATAAT
1 AAAATAAAATAATAAATAATAAAATAAAATAAAAATAAAG-AA-AAATAAATAAT
15528676 AAAATAAAATAATAAATAATAAAATAAAATAAAAATAAAGAAAAATAAA
1 AAAATAAAATAATAAATAATAAAATAAAATAAAAATAAAGAAAAATAAA
15528725 AATTGGGTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
53 7 0.16
54 30 0.67
55 8 0.18
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.21
Consensus pattern (53 bp):
AAAATAAAATAATAAATAATAAAATAAAATAAAAATAAAGAAAAATAAATAAT
Found at i:15528714 original size:16 final size:17
Alignment explanation
Indices: 15528632--15528724 Score: 86
Period size: 16 Copynumber: 5.4 Consensus size: 17
15528622 AAAATAAAGT
15528632 AATAAATAATAAAATAA
1 AATAAATAATAAAATAA
* *
15528649 AGTGAAATAA-AGTAAT-A
1 AAT-AAATAATA-AAATAA
15528666 AATAAATAATAAAATAAAA
1 AATAAATAATAAAAT--AA
15528685 TAATAAATAATAAAATAA
1 -AATAAATAATAAAATAA
15528703 AATAAA-AATAAAGA-AA
1 AATAAATAATAAA-ATAA
15528719 AATAAA
1 AATAAA
15528725 AATTGGGTTG
Statistics
Matches: 64, Mismatches: 4, Indels: 17
0.75 0.05 0.20
Matches are distributed among these distances:
16 23 0.36
17 14 0.22
18 11 0.17
19 1 0.02
20 15 0.23
ACGTcount: A:0.74, C:0.00, G:0.04, T:0.22
Consensus pattern (17 bp):
AATAAATAATAAAATAA
Found at i:15528725 original size:16 final size:16
Alignment explanation
Indices: 15528622--15528727 Score: 67
Period size: 16 Copynumber: 6.3 Consensus size: 16
15528612 ATATCTAAAC
15528622 AAAATAAAGTAATAAATAA
1 AAAATAAAG-AA-AAAT-A
**
15528641 TAAAATAAAGTGAAATA
1 -AAAATAAAGAAAAATA
*
15528658 AAGTAATAAATAAATAAT-
1 AA--AATAAAGAAA-AATA
*
15528676 AAAAT-AA-AATAATA
1 AAAATAAAGAAAAATA
15528690 AATAATAAA-ATAAAATA
1 AA-AATAAAGA-AAAATA
15528707 AAAATAAAGAAAAATA
1 AAAATAAAGAAAAATA
15528723 AAAAT
1 AAAAT
15528728 TGGGTTGCCT
Statistics
Matches: 71, Mismatches: 7, Indels: 20
0.72 0.07 0.20
Matches are distributed among these distances:
13 3 0.04
14 4 0.06
15 5 0.07
16 25 0.35
17 9 0.13
18 13 0.18
19 3 0.04
20 9 0.13
ACGTcount: A:0.74, C:0.00, G:0.05, T:0.22
Consensus pattern (16 bp):
AAAATAAAGAAAAATA
Found at i:15532464 original size:10 final size:10
Alignment explanation
Indices: 15532449--15532477 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
15532439 CTAAAATTTA
15532449 AAAGATAAAT
1 AAAGATAAAT
15532459 AAAGATAAAT
1 AAAGATAAAT
15532469 AAAGATAAA
1 AAAGATAAA
15532478 AGCTAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.17
Consensus pattern (10 bp):
AAAGATAAAT
Found at i:15533551 original size:30 final size:30
Alignment explanation
Indices: 15533517--15533573 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
15533507 TAGGGGATGG
15533517 AAAATGGTAGCTCCGTTAAGTCTGTAATGA
1 AAAATGGTAGCTCCGTTAAGTCTGTAATGA
* * *
15533547 AAAATGGTAGCTCTGTTACGTTTGTAA
1 AAAATGGTAGCTCCGTTAAGTCTGTAA
15533574 CAGATTATGG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.33
Consensus pattern (30 bp):
AAAATGGTAGCTCCGTTAAGTCTGTAATGA
Found at i:15534268 original size:2 final size:2
Alignment explanation
Indices: 15534261--15534286 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
15534251 CCTTTTGATA
15534261 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
15534287 TTCCATGAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:15535352 original size:14 final size:15
Alignment explanation
Indices: 15535327--15535359 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
15535317 CGAATTTATC
*
15535327 TATTTTTAAATATTT
1 TATTTTTAAATAATT
15535342 TATTTTT-AATAATT
1 TATTTTTAAATAATT
15535356 TATT
1 TATT
15535360 CAATCGAACT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 10 0.59
15 7 0.41
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (15 bp):
TATTTTTAAATAATT
Found at i:15544593 original size:375 final size:375
Alignment explanation
Indices: 15543900--15544599 Score: 1114
Period size: 375 Copynumber: 1.9 Consensus size: 375
15543890 AATGTTAATG
* * *
15543900 CCTCATTTTTCTTATGATTGAAATCTAATGGACCAATTAGCTTATTGCTGAGGGTGTCTAATTGT
1 CCTCATTTTTCTTATGACTGAAAGCTAATGGACCAATTAGCTTATTGCTGAGGGTGTCTAATTAT
** * *
15543965 TTCAATAGGGGTTGAATGTTTAAGAGCATCTTTTGAAGCTTAACCAATTGTGGTGTTTGTTAATT
66 TTCAATAGGGGCCGAATGTATAAGAGCATCTTTTGAAGCTTAACCAATTGTGGTGTGTGTTAATT
* *
15544030 GTGATGCTTGCCGGTTGTGTTGGAAGTGTAAATGAAATGGGTAAATGAATGTAAGTTGTCCTTTA
131 GTAATGCTTGCCGATTGTGTTGGAAGTGTAAATGAAATGGGTAAATGAATGTAAGTTGTCCTTTA
*
15544095 TATGATCGAATGTGTTATGTGATAACTTGGGATGTTTGCCAAAAGTGCCATGCCAATTCTATACT
196 TATGACCGAATGTGTTATGTGATAACTTGGGATGTTTGCCAAAAGTGCCATGCCAATTCTATACT
** * * *
15544160 ATGTGTTTACTTAAGTTGATTGAATGTGTCTATTGGTTTGCTTGCTATAAACGAATATGCATAAT
261 ATGTGTTTACTTAAGTTGACCGAATGTGTCTATTGGCTTACTTGATATAAACGAATATGCATAAT
15544225 CTGCTAATGTATGCTACTGTATTGCTGTCACATTTTCACTGAATGCTCAT
326 CTGCTAATGTATGCTACTGTATTGCTGTCACATTTTCACTGAATGCTCAT
* * * *
15544275 CCTCATTTTTCTTATGACTGAAAGCTAATTGACTAGTTAGCTTATTGCTGAGGGTGTTTAATTAT
1 CCTCATTTTTCTTATGACTGAAAGCTAATGGACCAATTAGCTTATTGCTGAGGGTGTCTAATTAT
* *
15544340 TTCAATAGGGGCCGAATGTATAAGAGCATCTTTTGAAGCTTAATCGATTGTGGTGTGTGTTAATT
66 TTCAATAGGGGCCGAATGTATAAGAGCATCTTTTGAAGCTTAACCAATTGTGGTGTGTGTTAATT
* * *
15544405 GTAATGCTTGTCGATTGTGTTGGAAGTGTAAATGAAAT-GGTCGAATGAATGTAAGTTGTCTTTT
131 GTAATGCTTGCCGATTGTGTTGGAAGTGTAAATGAAATGGGT-AAATGAATGTAAGTTGTCCTTT
* * * *
15544469 ATATGGCCGAATGTGTTATGTGATAAGTTGGGATGTTTGCCAAAAGTGCGATGCCTATTCTATAC
195 ATATGACCGAATGTGTTATGTGATAACTTGGGATGTTTGCCAAAAGTGCCATGCCAATTCTATAC
* *
15544534 TATGTGTTTACTTAAGTTGACCGAATGTGTCTATTGGCTTACTTGATATAAATGAATATGCGTAA
260 TATGTGTTTACTTAAGTTGACCGAATGTGTCTATTGGCTTACTTGATATAAACGAATATGCATAA
15544599 T
325 T
15544600 ATATTGCATT
Statistics
Matches: 294, Mismatches: 30, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
374 3 0.01
375 291 0.99
ACGTcount: A:0.26, C:0.12, G:0.23, T:0.39
Consensus pattern (375 bp):
CCTCATTTTTCTTATGACTGAAAGCTAATGGACCAATTAGCTTATTGCTGAGGGTGTCTAATTAT
TTCAATAGGGGCCGAATGTATAAGAGCATCTTTTGAAGCTTAACCAATTGTGGTGTGTGTTAATT
GTAATGCTTGCCGATTGTGTTGGAAGTGTAAATGAAATGGGTAAATGAATGTAAGTTGTCCTTTA
TATGACCGAATGTGTTATGTGATAACTTGGGATGTTTGCCAAAAGTGCCATGCCAATTCTATACT
ATGTGTTTACTTAAGTTGACCGAATGTGTCTATTGGCTTACTTGATATAAACGAATATGCATAAT
CTGCTAATGTATGCTACTGTATTGCTGTCACATTTTCACTGAATGCTCAT
Found at i:15555063 original size:22 final size:22
Alignment explanation
Indices: 15555038--15555104 Score: 107
Period size: 22 Copynumber: 3.0 Consensus size: 22
15555028 GAACTAAACC
15555038 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
15555060 CTCATGGCTAACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
** *
15555082 CTCATGTTTCACGTACTAAGCT
1 CTCATGGCTAACGTACTAAGCT
15555104 C
1 C
15555105 AGAATGGTGA
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.25, C:0.28, G:0.16, T:0.30
Consensus pattern (22 bp):
CTCATGGCTAACGTACTAAGCT
Found at i:15560714 original size:25 final size:25
Alignment explanation
Indices: 15560660--15560707 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
15560650 GTTGTAATTG
15560660 GTAAGCTCCTCCGAGCTGAATAACA
1 GTAAGCTCCTCCGAGCTGAATAACA
15560685 GTAAGCTCCTCCGAGCTGAATAA
1 GTAAGCTCCTCCGAGCTGAATAA
15560708 TGATAAGTTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.31, C:0.27, G:0.21, T:0.21
Consensus pattern (25 bp):
GTAAGCTCCTCCGAGCTGAATAACA
Found at i:15560724 original size:25 final size:25
Alignment explanation
Indices: 15560696--15560744 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
15560686 TAAGCTCCTC
15560696 CGAGCTGAATAATGATAAGTTCATG
1 CGAGCTGAATAATGATAAGTTCATG
* * *
15560721 CGAGCTGAGTATTGGTAAGTTCAT
1 CGAGCTGAATAATGATAAGTTCAT
15560745 ACAAGCTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.31, C:0.12, G:0.27, T:0.31
Consensus pattern (25 bp):
CGAGCTGAATAATGATAAGTTCATG
Found at i:15562505 original size:23 final size:23
Alignment explanation
Indices: 15562479--15562524 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
15562469 TGAATGTTGT
15562479 GTATGAGATGATAAAGATTAAAG
1 GTATGAGATGATAAAGATTAAAG
*
15562502 GTATGAGATGATAGAGATTAAAG
1 GTATGAGATGATAAAGATTAAAG
15562525 ATTCCATGAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.46, C:0.00, G:0.28, T:0.26
Consensus pattern (23 bp):
GTATGAGATGATAAAGATTAAAG
Found at i:15577704 original size:51 final size:51
Alignment explanation
Indices: 15577636--15577794 Score: 203
Period size: 51 Copynumber: 3.1 Consensus size: 51
15577626 AAAAGATTCA
*
15577636 TTCAATCAACAACATAGTTTCCTACATCATCAACCTATATATATATCACAT
1 TTCAACCAACAACATAGTTTCCTACATCATCAACCTATATATATATCACAT
* * * * *
15577687 TTCAACCCACGATATAGTTTCCT-CTATCACCAACCAATATATATATCACAT
1 TTCAACCAACAACATAGTTTCCTAC-ATCATCAACCTATATATATATCACAT
* * *
15577738 TTCAACCAACAACATAGTTTTCTACATCATCAACGAATACATATATATCACAT
1 TTCAACCAACAACATAGTTTCCTACATCATCAAC--CTATATATATATCACAT
15577791 TTCA
1 TTCA
15577795 TACATGTTGA
Statistics
Matches: 90, Mismatches: 14, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
50 1 0.01
51 70 0.78
52 1 0.01
53 18 0.20
ACGTcount: A:0.38, C:0.26, G:0.03, T:0.32
Consensus pattern (51 bp):
TTCAACCAACAACATAGTTTCCTACATCATCAACCTATATATATATCACAT
Found at i:15583440 original size:18 final size:18
Alignment explanation
Indices: 15583412--15583447 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
15583402 AAAAGGTTAT
15583412 TAAAGTAAATT-AGTAAA
1 TAAAGTAAATTAAGTAAA
15583429 TAAAGATAAATTAAGTAAA
1 TAAAG-TAAATTAAGTAAA
15583448 ACAAAACATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 5 0.29
18 6 0.35
19 6 0.35
ACGTcount: A:0.61, C:0.00, G:0.11, T:0.28
Consensus pattern (18 bp):
TAAAGTAAATTAAGTAAA
Found at i:15588239 original size:61 final size:61
Alignment explanation
Indices: 15588168--15588357 Score: 245
Period size: 61 Copynumber: 3.1 Consensus size: 61
15588158 TACCTTGCCT
* * * *
15588168 GAGTTATTCCACAAAGGCATTCCTTAAGATTCAATACTCGCCATAAAGGCTTTCCTGTCCA
1 GAGTTTTTCCACAAAGGCATTCCTTAACATTCAGTACTCGCCACAAAGGCTTTCCTGTCCA
* ** * * * *
15588229 GAGTTTTTCCATAAAAACATTCATTAACATTTAGTAATCGCCACAAGGGCTTTCCTGTCCA
1 GAGTTTTTCCACAAAGGCATTCCTTAACATTCAGTACTCGCCACAAAGGCTTTCCTGTCCA
* * * *
15588290 GAGTTTTTCCAGAAAGGCGTTCCTTAACATTCAGTACTCGCCACAATGGCTTTCCTATCCA
1 GAGTTTTTCCACAAAGGCATTCCTTAACATTCAGTACTCGCCACAAAGGCTTTCCTGTCCA
15588351 GAGTTTT
1 GAGTTTT
15588358 GCCTCCCTCT
Statistics
Matches: 109, Mismatches: 20, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
61 109 1.00
ACGTcount: A:0.28, C:0.25, G:0.15, T:0.32
Consensus pattern (61 bp):
GAGTTTTTCCACAAAGGCATTCCTTAACATTCAGTACTCGCCACAAAGGCTTTCCTGTCCA
Found at i:15592644 original size:16 final size:16
Alignment explanation
Indices: 15592623--15592668 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
15592613 AATTAGGTTG
15592623 AGAAAATAATTTAATT
1 AGAAAATAATTTAATT
15592639 AGAAAATTAA-TTAATT
1 AGAAAA-TAATTTAATT
* *
15592655 -TAAATTAATTTAAT
1 AGAAAATAATTTAAT
15592669 AAATAATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
14 3 0.12
15 8 0.31
16 12 0.46
17 3 0.12
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (16 bp):
AGAAAATAATTTAATT
Found at i:15595136 original size:35 final size:34
Alignment explanation
Indices: 15595055--15595140 Score: 102
Period size: 35 Copynumber: 2.4 Consensus size: 34
15595045 GAATTCTATT
*
15595055 GGGACAGTAAACACAGAACAAAGATGAAGTCCTTC
1 GGGA-AGTAAACACGGAACAAAGATGAAGTCCTTC
* *
15595090 AGGACGTTAAACACGGAACAAAGATGAAG-CCTGTC
1 GGGAAG-TAAACACGGAACAAAGATGAAGTCCT-TC
15595125 GGGATAGTAAACACGG
1 GGGA-AGTAAACACGG
15595141 GTAAGCCTAC
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
34 4 0.09
35 38 0.88
36 1 0.02
ACGTcount: A:0.41, C:0.19, G:0.27, T:0.14
Consensus pattern (34 bp):
GGGAAGTAAACACGGAACAAAGATGAAGTCCTTC
Found at i:15601199 original size:63 final size:63
Alignment explanation
Indices: 15601094--15601217 Score: 212
Period size: 63 Copynumber: 2.0 Consensus size: 63
15601084 AATAAAAAAG
* * * *
15601094 AAGTAACCAACATGCAATACAAAGAGAAAAACTCTCTGAATGCACCACTTCACCATATATAAT
1 AAGTAACCAAAATGCAATACAAAGAGAAAAACCCTCTAAATGCACCACTTAACCATATATAAT
15601157 AAGTAACCAAAATGCAATACAAAGAGAAAAACCCTCTAAATGCACCACTTAACCATATATA
1 AAGTAACCAAAATGCAATACAAAGAGAAAAACCCTCTAAATGCACCACTTAACCATATATA
15601218 TATATATATT
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.48, C:0.23, G:0.09, T:0.19
Consensus pattern (63 bp):
AAGTAACCAAAATGCAATACAAAGAGAAAAACCCTCTAAATGCACCACTTAACCATATATAAT
Found at i:15602201 original size:43 final size:43
Alignment explanation
Indices: 15602079--15602202 Score: 149
Period size: 43 Copynumber: 2.9 Consensus size: 43
15602069 AACTGTGTAG
* * *
15602079 AATTCAAAAATAAGGTCACACGATTGTGTCGTCAGGCCGTGTGC
1 AATTC-AAAATAAGGTCACACGGTCGTGTCGTCAGGCCATGTGC
** *
15602123 AATTTGAAATAAGGTCACACGGTCATGTCGTCAGGCCATGTGC
1 AATTCAAAATAAGGTCACACGGTCGTGTCGTCAGGCCATGTGC
* * * *
15602166 AATTCAAAATAAGGTTAGACGGTCGTTTCGCCAGGCC
1 AATTCAAAATAAGGTCACACGGTCGTGTCGTCAGGCC
15602203 GTGTAACAAC
Statistics
Matches: 67, Mismatches: 13, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
43 63 0.94
44 4 0.06
ACGTcount: A:0.29, C:0.21, G:0.25, T:0.25
Consensus pattern (43 bp):
AATTCAAAATAAGGTCACACGGTCGTGTCGTCAGGCCATGTGC
Found at i:15602906 original size:26 final size:26
Alignment explanation
Indices: 15602846--15602896 Score: 102
Period size: 26 Copynumber: 2.0 Consensus size: 26
15602836 GCTTAGTAAG
15602846 CTCGTATATCGTAAACTTAAACTTAA
1 CTCGTATATCGTAAACTTAAACTTAA
15602872 CTCGTATATCGTAAACTTAAACTTA
1 CTCGTATATCGTAAACTTAAACTTA
15602897 CCGAATATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.37, C:0.20, G:0.08, T:0.35
Consensus pattern (26 bp):
CTCGTATATCGTAAACTTAAACTTAA
Found at i:15607194 original size:27 final size:27
Alignment explanation
Indices: 15607164--15607249 Score: 136
Period size: 27 Copynumber: 3.1 Consensus size: 27
15607154 TTAATTATAA
15607164 TATCATTCATAAAATTAAAATATATGT
1 TATCATTCATAAAATTAAAATATATGT
**
15607191 TATCATTCATAAAATTAAAATATATAAAA
1 TATCATTCATAAAATTAAAATATAT--GT
15607220 TATCATTCATAAAATTAAAATATATGT
1 TATCATTCATAAAATTAAAATATATGT
15607247 TAT
1 TAT
15607250 AATTTCTTAT
Statistics
Matches: 53, Mismatches: 4, Indels: 4
0.87 0.07 0.07
Matches are distributed among these distances:
27 28 0.53
29 25 0.47
ACGTcount: A:0.51, C:0.07, G:0.02, T:0.40
Consensus pattern (27 bp):
TATCATTCATAAAATTAAAATATATGT
Found at i:15607219 original size:15 final size:15
Alignment explanation
Indices: 15607199--15607244 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
15607189 GTTATCATTC
15607199 ATAAAATTAAAATAT
1 ATAAAATTAAAATAT
**
15607214 ATAAAA-TATCAT-T
1 ATAAAATTAAAATAT
15607227 CATAAAATTAAAATAT
1 -ATAAAATTAAAATAT
15607243 AT
1 AT
15607245 GTTATAATTT
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
13 1 0.04
14 10 0.42
15 12 0.50
16 1 0.04
ACGTcount: A:0.61, C:0.04, G:0.00, T:0.35
Consensus pattern (15 bp):
ATAAAATTAAAATAT
Found at i:15609623 original size:5 final size:5
Alignment explanation
Indices: 15609613--15609646 Score: 59
Period size: 5 Copynumber: 6.8 Consensus size: 5
15609603 GATATGTCAT
*
15609613 ATCTA ATCTA ATCTA ATCTA ATCTA ATATA ATCT
1 ATCTA ATCTA ATCTA ATCTA ATCTA ATCTA ATCT
15609647 TTACAAGATA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 27 1.00
ACGTcount: A:0.41, C:0.18, G:0.00, T:0.41
Consensus pattern (5 bp):
ATCTA
Found at i:15610155 original size:2 final size:2
Alignment explanation
Indices: 15610148--15610178 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
15610138 TATCTTATGG
15610148 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
15610179 TATGTGATAT
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:15612941 original size:14 final size:14
Alignment explanation
Indices: 15612922--15612961 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
15612912 TTGATTGCCA
15612922 GTAAAATGTTTTCC
1 GTAAAATGTTTTCC
* *
15612936 GTAAAATGATTTCT
1 GTAAAATGTTTTCC
*
15612950 GGAAAATGTTTT
1 GTAAAATGTTTT
15612962 ACTTTTCTGT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.33, C:0.07, G:0.17, T:0.42
Consensus pattern (14 bp):
GTAAAATGTTTTCC
Found at i:15612970 original size:20 final size:20
Alignment explanation
Indices: 15612945--15612984 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
15612935 CGTAAAATGA
*
15612945 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
15612965 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
15612985 GGAAAATATT
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:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:15613179 original size:22 final size:24
Alignment explanation
Indices: 15613154--15613204 Score: 56
Period size: 26 Copynumber: 2.2 Consensus size: 24
15613144 TTATTTATAA
15613154 ATAAATAA-A-TCAA-ATT-AAAT
1 ATAAATAATACTCAATATTAAAAT
15613174 ATATAATAATACTCAATTATTAAAAT
1 ATA-AATAATACTCAA-TATTAAAAT
15613200 ATAAA
1 ATAAA
15613205 AGCATTGCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
20 3 0.12
21 5 0.20
22 1 0.04
23 4 0.16
25 5 0.20
26 7 0.28
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (24 bp):
ATAAATAATACTCAATATTAAAAT
Found at i:15615627 original size:26 final size:24
Alignment explanation
Indices: 15615580--15615628 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 24
15615570 AGTTGTAAAT
15615580 AAAAAATATCTTTAGAAATTTTCG
1 AAAAAATATCTTTAGAAATTTTCG
15615604 AAAATAATAT-TTTCAGAGAATTTTC
1 AAAA-AATATCTTT-AGA-AATTTTC
15615629 TCTCTACAAC
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
24 7 0.32
25 8 0.36
26 7 0.32
ACGTcount: A:0.45, C:0.08, G:0.08, T:0.39
Consensus pattern (24 bp):
AAAAAATATCTTTAGAAATTTTCG
Found at i:15619159 original size:25 final size:28
Alignment explanation
Indices: 15619131--15619184 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 28
15619121 ATGCTGAGAG
15619131 TTATTT-T-TATAT-TAGATAAATATAA
1 TTATTTATGTATATATAGATAAATATAA
*
15619156 TTATTTATGTATATAATATATAAATATAA
1 TTATTTATGTATAT-ATAGATAAATATAA
15619185 AATGATGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
25 6 0.25
26 1 0.04
27 5 0.21
29 12 0.50
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (28 bp):
TTATTTATGTATATATAGATAAATATAA
Found at i:15621231 original size:3 final size:3
Alignment explanation
Indices: 15621223--15621267 Score: 54
Period size: 3 Copynumber: 14.7 Consensus size: 3
15621213 TGTAATACTG
* * *
15621223 TTA TTA TTA TATA ATA TCA CTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
15621268 TATGTATACT
Statistics
Matches: 35, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
3 33 0.94
4 2 0.06
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:15621367 original size:25 final size:25
Alignment explanation
Indices: 15621339--15621391 Score: 106
Period size: 25 Copynumber: 2.1 Consensus size: 25
15621329 GCACATATTT
15621339 TACAATCCGTACATATCCATACACA
1 TACAATCCGTACATATCCATACACA
15621364 TACAATCCGTACATATCCATACACA
1 TACAATCCGTACATATCCATACACA
15621389 TAC
1 TAC
15621392 TTATATGTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.40, C:0.32, G:0.04, T:0.25
Consensus pattern (25 bp):
TACAATCCGTACATATCCATACACA
Found at i:15621991 original size:19 final size:19
Alignment explanation
Indices: 15621967--15622005 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
15621957 CCCAAGAATT
15621967 AATGAAAGATCGTGTTCTA
1 AATGAAAGATCGTGTTCTA
15621986 AATGAAAGATCGTGTTCTA
1 AATGAAAGATCGTGTTCTA
15622005 A
1 A
15622006 CTTACGGGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.38, C:0.10, G:0.21, T:0.31
Consensus pattern (19 bp):
AATGAAAGATCGTGTTCTA
Found at i:15625286 original size:19 final size:20
Alignment explanation
Indices: 15625262--15625301 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
15625252 AGTGCCTCTT
15625262 TTTGCATT-CAT-ATCATGCA
1 TTTGCATTACATCA-CATGCA
15625281 TTTGCATTACATCACATGCA
1 TTTGCATTACATCACATGCA
15625301 T
1 T
15625302 CAAGTTTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 8 0.42
20 10 0.53
21 1 0.05
ACGTcount: A:0.28, C:0.23, G:0.10, T:0.40
Consensus pattern (20 bp):
TTTGCATTACATCACATGCA
Found at i:15627881 original size:16 final size:16
Alignment explanation
Indices: 15627860--15627890 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
15627850 CATCACAACC
15627860 CGTTGCAAGGGGTATA
1 CGTTGCAAGGGGTATA
*
15627876 CGTTGCCAGGGGTAT
1 CGTTGCAAGGGGTAT
15627891 TAATTGATAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.16, G:0.39, T:0.26
Consensus pattern (16 bp):
CGTTGCAAGGGGTATA
Found at i:15633466 original size:43 final size:43
Alignment explanation
Indices: 15633390--15633901 Score: 221
Period size: 43 Copynumber: 11.8 Consensus size: 43
15633380 TATTGTAGAT
* * ** * *
15633390 CTTATCTCCCTAAACAGTAGTAGAGCAGATCGAAAGCACCAGC
1 CTTATCTCCCTAAGCAGCAGCGGAGTAGGTCGAAAGCACCAGC
* * * * **
15633433 CTTATCTCCCTCAGCAGCAACAGAGTAGGTCGAAGATTGTA--AAT
1 CTTATCTCCCTAAGCAGCAGCGGAGTAGGTCGAA-A--GCACCAGC
* * * * *
15633477 CTTATCCCCCTAAACAGTAGCGGAGCAGATCGAAAGCACCAGC
1 CTTATCTCCCTAAGCAGCAGCGGAGTAGGTCGAAAGCACCAGC
** *
15633520 CTTATCTCCCTAAGCAGCAGCGGAGTAGGTCG-AAG-ATTGTAGAT
1 CTTATCTCCCTAAGCAGCAGCGGAGTAGGTCGAAAGCA--CCAG-C
* * * * * *
15633564 CTGATCTCCCTAAACAGTAGTGGAGCAGATCGAAAGCACCAGC
1 CTTATCTCCCTAAGCAGCAGCGGAGTAGGTCGAAAGCACCAGC
* * ** *
15633607 CTTATCTCCCTGAGCAGCAGCGGAGTAGGTTG-AAG-ATTGTAGAT
1 CTTATCTCCCTAAGCAGCAGCGGAGTAGGTCGAAAGCA--CCAG-C
* * * * * * *
15633651 ATTATCTCCCTAAGCAGTAGTGGAGCAGATCGACAGCACCAAC
1 CTTATCTCCCTAAGCAGCAGCGGAGTAGGTCGAAAGCACCAGC
* * ** *
15633694 CTTATCTCCCTAAGCAGTAGCAGAGTAGGTCG-AAG-ATTGTAGAT
1 CTTATCTCCCTAAGCAGCAGCGGAGTAGGTCGAAAGCA--CCAG-C
* * * * * *
15633738 CTTATCTCCCTAAGCAGTAGTGGGGCAGATCAAAAGCACCAGC
1 CTTATCTCCCTAAGCAGCAGCGGAGTAGGTCGAAAGCACCAGC
* * * * * * **** *
15633781 CTTAGCTCCTTGAGCAGTAGAGGAGTAGGTCGAAGGTTGTAGAT
1 CTTATCTCCCTAAGCAGCAGCGGAGTAGGTCGAAAGCACCAG-C
* * * * * * *
15633825 CTTATCTACCTAAACAGTAGTGGAGCAGATCGAAAGCACCAAC
1 CTTATCTCCCTAAGCAGCAGCGGAGTAGGTCGAAAGCACCAGC
* * *
15633868 CTTATCTCCCTGAGCAGCAGTGGAATAGGTCGAA
1 CTTATCTCCCTAAGCAGCAGCGGAGTAGGTCGAA
15633902 GATTGTAGAT
Statistics
Matches: 332, Mismatches: 116, Indels: 42
0.68 0.24 0.09
Matches are distributed among these distances:
41 5 0.02
42 8 0.02
43 168 0.51
44 138 0.42
45 8 0.02
46 5 0.02
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (43 bp):
CTTATCTCCCTAAGCAGCAGCGGAGTAGGTCGAAAGCACCAGC
Found at i:15633527 original size:87 final size:87
Alignment explanation
Indices: 15633381--15633950 Score: 852
Period size: 87 Copynumber: 6.6 Consensus size: 87
15633371 TGAAGTCATT
* *
15633381 ATTGTAGATCTTATCTCCCTAAACAGTAGTAGAGCAGATCGAAAGCACCAGCCTTATCTCCCTCA
1 ATTGTAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAAGCACCAGCCTTATCTCCCTGA
* *
15633446 GCAGCAACAGAGTAGGTCGAAG
66 GCAGCAGCGGAGTAGGTCGAAG
* * * *
15633468 ATTGTAAATCTTATCCCCCTAAACAGTAGCGGAGCAGATCGAAAGCACCAGCCTTATCTCCCTAA
1 ATTGTAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAAGCACCAGCCTTATCTCCCTGA
15633533 GCAGCAGCGGAGTAGGTCGAAG
66 GCAGCAGCGGAGTAGGTCGAAG
*
15633555 ATTGTAGATCTGATCTCCCTAAACAGTAGTGGAGCAGATCGAAAGCACCAGCCTTATCTCCCTGA
1 ATTGTAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAAGCACCAGCCTTATCTCCCTGA
*
15633620 GCAGCAGCGGAGTAGGTTGAAG
66 GCAGCAGCGGAGTAGGTCGAAG
* * * * *
15633642 ATTGTAGATATTATCTCCCTAAGCAGTAGTGGAGCAGATCGACAGCACCAACCTTATCTCCCTAA
1 ATTGTAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAAGCACCAGCCTTATCTCCCTGA
* *
15633707 GCAGTAGCAGAGTAGGTCGAAG
66 GCAGCAGCGGAGTAGGTCGAAG
* * * * *
15633729 ATTGTAGATCTTATCTCCCTAAGCAGTAGTGGGGCAGATCAAAAGCACCAGCCTTAGCTCCTTGA
1 ATTGTAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAAGCACCAGCCTTATCTCCCTGA
* *
15633794 GCAGTAGAGGAGTAGGTCGAAG
66 GCAGCAGCGGAGTAGGTCGAAG
* * *
15633816 GTTGTAGATCTTATCTACCTAAACAGTAGTGGAGCAGATCGAAAGCACCAACCTTATCTCCCTGA
1 ATTGTAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAAGCACCAGCCTTATCTCCCTGA
* *
15633881 GCAGCAGTGGAATAGGTCGAAG
66 GCAGCAGCGGAGTAGGTCGAAG
* * *
15633903 ATTGTAGATCTTATCTCCCTAAGCAGTAGCGGAGCAAATCGAAAGCAC
1 ATTGTAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAAGCAC
15633951 AGATCTTCTC
Statistics
Matches: 435, Mismatches: 48, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
87 435 1.00
ACGTcount: A:0.31, C:0.23, G:0.24, T:0.22
Consensus pattern (87 bp):
ATTGTAGATCTTATCTCCCTAAACAGTAGTGGAGCAGATCGAAAGCACCAGCCTTATCTCCCTGA
GCAGCAGCGGAGTAGGTCGAAG
Found at i:15636837 original size:18 final size:18
Alignment explanation
Indices: 15636816--15636853 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
15636806 ATTTATTTTA
*
15636816 TTATATCGTTTTATCTAT
1 TTATATCGTTTTATATAT
*
15636834 TTATATCTTTTTATATAT
1 TTATATCGTTTTATATAT
15636852 TT
1 TT
15636854 TCAAACTCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.24, C:0.08, G:0.03, T:0.66
Consensus pattern (18 bp):
TTATATCGTTTTATATAT
Found at i:15640455 original size:62 final size:62
Alignment explanation
Indices: 15640386--15640512 Score: 236
Period size: 62 Copynumber: 2.0 Consensus size: 62
15640376 TACTTGTGTG
*
15640386 AAATTTTCATGTTTTAATTTTATCATTTAAGTGTCTGATTAAATGAAAGGATTTAATCCCTT
1 AAATTTTCATGTTTTAATTTTATCATTTAAGTGTCTGATTAAATGAAAGGATTTAATCCCGT
*
15640448 AAATTTTCATGTTTTAATTTTATCGTTTAAGTGTCTGATTAAATGAAAGGATTTAATCCCGT
1 AAATTTTCATGTTTTAATTTTATCATTTAAGTGTCTGATTAAATGAAAGGATTTAATCCCGT
15640510 AAA
1 AAA
15640513 ATGAAAATTT
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
62 63 1.00
ACGTcount: A:0.33, C:0.09, G:0.13, T:0.45
Consensus pattern (62 bp):
AAATTTTCATGTTTTAATTTTATCATTTAAGTGTCTGATTAAATGAAAGGATTTAATCCCGT
Found at i:15641621 original size:42 final size:42
Alignment explanation
Indices: 15641560--15641659 Score: 146
Period size: 42 Copynumber: 2.4 Consensus size: 42
15641550 CTATATGAAC
* * *
15641560 GGCACTAAGTGTGCAAAATTAAAATAATGATGTTGGATAATA
1 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGAATAACA
* * *
15641602 GGCACTAAGTGTGCGAAATTAAGATGATGATGTTGAATAACG
1 GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGAATAACA
15641644 GGCACTAAGTGTGCGA
1 GGCACTAAGTGTGCGA
15641660 TACCAAGAGC
Statistics
Matches: 52, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.37, C:0.10, G:0.27, T:0.26
Consensus pattern (42 bp):
GGCACTAAGTGTGCGAAATTAAAATAATGATGTTGAATAACA
Found at i:15642772 original size:2 final size:2
Alignment explanation
Indices: 15642765--15642789 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
15642755 TACATAGTAA
15642765 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
15642790 GGATCGGCTT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:15646206 original size:44 final size:43
Alignment explanation
Indices: 15646140--15646719 Score: 294
Period size: 44 Copynumber: 12.8 Consensus size: 43
15646130 CATAGCAAAC
* * *
15646140 CTTATCTCCCTGAAGTTACAGTGGAGCAGGTTGAAGATACAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACAA-T
* * *
15646184 CTTATCTCCCTAAAGTTGCAGTGGGGCAGACTAAAGATAGCAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATA-C-AAT
* * * *
15646229 TTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTGCAGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG--AT--A---CA-AT
* * * * * * *
15646280 TTTATCTCTCTGAAGTTGCAGTAGAGCAGATCATAG-CA-AAC
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACAAT
* *
15646321 CTTATCTCCCTGAAGTTGTAGTGGAGCA-AGTTAAAGTTACAAGT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAAAGATACAA-T
* * * *
15646365 CTTATCTCCCTAAAGTTGTAATGGAGCAGACTGAAA-ATAGCGAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAAAGATA-C-AAT
* * * * *
15646410 CTTATTTCCCTGAAGTTGCAATGAAACAGATTAAAGCTATAAATTACGGAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG------A-TAC-AAT
* * * * * *
15646461 CTTATCTCTCTAAAGTTGCAGTAGAGCAGA-T-CATAT-CAAA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACAAT
*
15646501 CTTTATCTCCCTGAAGTTGCAGTGGAGCA-AGTTAAAAATAAACCAAT
1 C-TTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAAAGAT--A-CAAT
* * * *
15646548 ATTATCTCCTTGAAGTTGCAGTGAAGCAGATTGAAGACAAGCTACAAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATT----A-AAGATAC-AAT
* ** *
15646597 ATTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACAAAA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATAC-AAT
* * * * * * *
15646641 CCTATCTACCTAAAGTTGCAGTAGAACAGATTAAAGCTATTAAT
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATA-CAAT
* **
15646685 CCTATCTCCCTGAAGTTGCAGTGGAGTGGATTAAA
1 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
15646720 ACGATGAACC
Statistics
Matches: 413, Mismatches: 83, Indels: 80
0.72 0.14 0.14
Matches are distributed among these distances:
40 4 0.01
41 54 0.13
42 4 0.01
43 6 0.01
44 137 0.33
45 64 0.15
46 32 0.08
47 6 0.01
48 1 0.00
49 36 0.09
50 3 0.01
51 64 0.15
52 2 0.00
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (43 bp):
CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACAAT
Found at i:15646244 original size:89 final size:88
Alignment explanation
Indices: 15646131--15646710 Score: 341
Period size: 92 Copynumber: 6.4 Consensus size: 88
15646121 ATTGAAGATC
*
15646131 ATAGCAAACCTTATCTCCCTGAAGTTACAGTGGAGCAGGTTGAAGATACAAGTCTTATCTCCCTA
1 ATAGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACAAGTCTTATCTCCCTA
*
15646196 AAGTTGCAGTGGGGCAGACTAAA
66 AAGTTGCAGTGGAGCAGACTAAA
** * * * * *
15646219 GATAGCAAATTTTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTGCAGATTTTA
1 -ATAGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAG--ATACA----AG-TCTTA
* * * *
15646284 TCTCTCTGAAGTTGCAGTAGAGCAGA-T--C
58 TCTCCCTAAAGTTGCAGTGGAGCAGACTAAA
* * * *
15646312 ATAGCAAACCTTATCTCCCTGAAGTTGTAGTGGAGCAAGTTAAAGTTACAAGTCTTATCTCCCTA
1 ATAGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACAAGTCTTATCTCCCTA
* *
15646377 AAGTTGTAATGGAGCAGACTGAAA
66 AAGTTGCAGTGGAGCAGACT-AAA
* * * * * * * * *
15646401 ATAGCGAATCTTATTTCCCTGAAGTTGCAATGAAACAGATTAAAGCTATAAATTACGGATCTTAT
1 ATAGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAG--ATACA--A--G-TCTTAT
* * *
15646466 CTCTCTAAAGTTGCAGTAGAGCAGA-T--C
59 CTCCCTAAAGTTGCAGTGGAGCAGACTAAA
* * * * * *
15646493 ATATCAAACTTTATCTCCCTGAAGTTGCAGTGGAGCAAGTTAAAAATAAACCAA-TATTATCTCC
1 ATAGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGAT--A-CAAGTCTTATCTCC
* * * *
15646557 TTGAAGTTGCAGTGAAGCAGATTGAAGA
63 CTAAAGTTGCAGTGGAGCAGACT-AA-A
** * * ** ** * *
15646585 CA-AGCTACAAATATTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCACAAAACCTATCTA
1 -ATAG---CAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACAAGTCTTATCTC
* * *
15646649 CCTAAAGTTGCAGTAGAACAGATTAAA
62 CCTAAAGTTGCAGTGGAGCAGACTAAA
* ** *
15646676 GCTATTAATCC-TATCTCCCTGAAGTTGCAGTGGAG
1 -ATAGCAAACCTTATCTCCCTGAAGTTGCAGTGGAG
15646711 TGGATTAAAA
Statistics
Matches: 370, Mismatches: 89, Indels: 65
0.71 0.17 0.12
Matches are distributed among these distances:
85 25 0.07
86 3 0.01
87 25 0.07
88 25 0.07
89 77 0.21
90 5 0.01
91 9 0.02
92 79 0.21
93 28 0.08
95 41 0.11
96 53 0.14
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.28
Consensus pattern (88 bp):
ATAGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGGTTGAAGATACAAGTCTTATCTCCCTA
AAGTTGCAGTGGAGCAGACTAAA
Found at i:15646440 original size:181 final size:181
Alignment explanation
Indices: 15646126--15646536 Score: 635
Period size: 181 Copynumber: 2.3 Consensus size: 181
15646116 GATGGATTGA
* * *
15646126 AGATCATAGCAAACCTTATCTCCCTGAAGTTACAGTGGAGCAGGTTGAAGATACAAGTCTTATCT
1 AGATCATAGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAAGTTAAAGATACAAGTCTTATCT
* * * * *
15646191 CCCTAAAGTTGCAGTGGGGCAGACTAAAGATAGCAAATTTTATTTCCCTGAAGTTGCAGTGGAAC
66 CCCTAAAGTTGCAATGGAGCAGACTAAAGATAGCAAATCTTATTTCCCTGAAGTTGCAATGAAAC
* * * *
15646256 AGATTGAAGCTATAAATTGCAGATTTTATCTCTCTGAAGTTGCAGTAGAGC
131 AGATTAAAGCTATAAATTACAGATCTTATCTCTCTAAAGTTGCAGTAGAGC
* *
15646307 AGATCATAGCAAACCTTATCTCCCTGAAGTTGTAGTGGAGCAAGTTAAAGTTACAAGTCTTATCT
1 AGATCATAGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAAGTTAAAGATACAAGTCTTATCT
* *
15646372 CCCTAAAGTTGTAATGGAGCAGACTGAAA-ATAGCGAATCTTATTTCCCTGAAGTTGCAATGAAA
66 CCCTAAAGTTGCAATGGAGCAGACT-AAAGATAGCAAATCTTATTTCCCTGAAGTTGCAATGAAA
*
15646436 CAGATTAAAGCTATAAATTACGGATCTTATCTCTCTAAAGTTGCAGTAGAGC
130 CAGATTAAAGCTATAAATTACAGATCTTATCTCTCTAAAGTTGCAGTAGAGC
* *
15646488 AGATCATATCAAACTTTATCTCCCTGAAGTTGCAGTGGAGCAAGTTAAA
1 AGATCATAGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAAGTTAAA
15646537 AATAAACCAA
Statistics
Matches: 209, Mismatches: 20, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
181 206 0.99
182 3 0.01
ACGTcount: A:0.33, C:0.18, G:0.20, T:0.29
Consensus pattern (181 bp):
AGATCATAGCAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAAGTTAAAGATACAAGTCTTATCT
CCCTAAAGTTGCAATGGAGCAGACTAAAGATAGCAAATCTTATTTCCCTGAAGTTGCAATGAAAC
AGATTAAAGCTATAAATTACAGATCTTATCTCTCTAAAGTTGCAGTAGAGC
Found at i:15646570 original size:46 final size:50
Alignment explanation
Indices: 15646503--15646628 Score: 156
Period size: 49 Copynumber: 2.6 Consensus size: 50
15646493 ATATCAAACT
* *
15646503 TTATCTCCCTGAAGTTGCAGTGGAGCAAG-TT-AA-A-AATAAACCAATA
1 TTATCTCCCTGAAGTTGCAGTGGAGCAAGATTGAAGACAAGAAACAAATA
* * **
15646549 TTATCTCCTTGAAGTTGCAGTGAAGC-AGATTGAAGACAAGCTACAAATA
1 TTATCTCCCTGAAGTTGCAGTGGAGCAAGATTGAAGACAAGAAACAAATA
15646598 TTATCTCCCTGAAGTTGCAGTGGAGC-AGATT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAAGATT
15646629 AAAGCCACAA
Statistics
Matches: 68, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
45 2 0.03
46 26 0.38
47 2 0.03
48 1 0.01
49 37 0.54
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (50 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAAGATTGAAGACAAGAAACAAATA
Found at i:15646611 original size:49 final size:46
Alignment explanation
Indices: 15646141--15646631 Score: 167
Period size: 45 Copynumber: 10.7 Consensus size: 46
15646131 ATAGCAAACC
* * * * * *
15646141 TTATCTCCCTGAAGTTACAGTGGAGCAGGTT--GAAGATACAAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAAGAAACAAATA
* * * * *
15646185 TTATCTCCCTAAAGTTGCAGTGGGGCAGACT--AAAGATAGCAAATT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAAGA-AACAAATA
* * ** * * *
15646230 TTATTTCCCTGAAGTTGCAGTGGAACAGATTGAAGCTATAAATTGCAGATT
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AA-AAAGAAA---CAAATA
* * * * **
15646281 TTATCTCTCTGAAGTTGCAGTAGAGCAGA-T-CATAG---CAAACC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAAGAAACAAATA
* ** * *
15646322 TTATCTCCCTGAAGTTGTAGTGGAGCA-AGTT--AAAGTTACAAGTC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAAAAAGAAACAAATA
* * * * * * * * *
15646366 TTATCTCCCTAAAGTTGTAATGGAGCAGACTGAAAA-TAGCGAATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAAGAAACAAATA
* * * * ** *
15646411 TTATTTCCCTGAAGTTGCAATGAAACAGATTAAAGCTATA-AATTACGGATC
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA---A-AGAA--ACAAATA
* * * * * **
15646462 TTATCTCTCTAAAGTTGCAGTAGAGCAGA-TCATATCAAAC---T-
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAAGAAACAAATA
* *
15646503 TTATCTCCCTGAAGTTGCAGTGGAGCA-AGTTAAAAATAAACCAATA
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAAAAAGAAACAAATA
* * **
15646549 TTATCTCCTTGAAGTTGCAGTGAAGCAGATTGAAGACAAGCTACAAATA
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AA-A-AAGAAACAAATA
15646598 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
1 TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
15646632 GCCACAAAAC
Statistics
Matches: 336, Mismatches: 78, Indels: 63
0.70 0.16 0.13
Matches are distributed among these distances:
40 2 0.01
41 54 0.16
42 9 0.03
44 60 0.18
45 66 0.20
46 30 0.09
47 9 0.03
48 5 0.01
49 41 0.12
50 3 0.01
51 57 0.17
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.29
Consensus pattern (46 bp):
TTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAAAGAAACAAATA
Found at i:15647035 original size:17 final size:17
Alignment explanation
Indices: 15647010--15647042 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
15647000 AGACCAAATA
*
15647010 CAAATAATAAATAAAAC
1 CAAAAAATAAATAAAAC
15647027 CAAAAAATAAATAAAA
1 CAAAAAATAAATAAAA
15647043 AGTCTAAATA
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:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (17 bp):
CAAAAAATAAATAAAAC
Found at i:15647233 original size:16 final size:15
Alignment explanation
Indices: 15647192--15647234 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 15
15647182 CTCTTAGCTG
15647192 CCACCACGCACGCCA
1 CCACCACGCACGCCA
*
15647207 CCACCGCCGCACGCCAA
1 CCACC-ACGCACGCC-A
*
15647224 CCTCCACGCAC
1 CCACCACGCAC
15647235 CTAGTACCTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 5 0.22
16 13 0.57
17 5 0.22
ACGTcount: A:0.23, C:0.60, G:0.14, T:0.02
Consensus pattern (15 bp):
CCACCACGCACGCCA
Found at i:15648395 original size:18 final size:18
Alignment explanation
Indices: 15648361--15648407 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
15648351 TTAAAATACA
15648361 TTTATTTTATTATTATCGT
1 TTTA-TTTATTATTATCGT
*
15648380 TTTATTTACTTA-TATCTT
1 TTTATTTA-TTATTATCGT
*
15648398 TTTATATATT
1 TTTATTTATT
15648408 TTCAAATTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 2 0.08
18 16 0.64
19 7 0.28
ACGTcount: A:0.23, C:0.06, G:0.02, T:0.68
Consensus pattern (18 bp):
TTTATTTATTATTATCGT
Found at i:15651927 original size:10 final size:9
Alignment explanation
Indices: 15651911--15651976 Score: 71
Period size: 10 Copynumber: 6.9 Consensus size: 9
15651901 AATTTATATT
15651911 TTAAAAAAA
1 TTAAAAAAA
15651920 TATAAAAAAA
1 T-TAAAAAAA
15651930 TTCAAAAAAA
1 TT-AAAAAAA
15651940 TCTAAAAAACA
1 T-TAAAAAA-A
*
15651951 TATAAAAAAG
1 T-TAAAAAAA
15651961 TT-AAAAAA
1 TTAAAAAAA
15651969 TTAAAAAA
1 TTAAAAAA
15651977 TTTCTAAAAT
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
8 7 0.14
9 8 0.16
10 24 0.49
11 10 0.20
ACGTcount: A:0.73, C:0.05, G:0.02, T:0.21
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:15654520 original size:87 final size:87
Alignment explanation
Indices: 15654368--15654545 Score: 193
Period size: 87 Copynumber: 2.0 Consensus size: 87
15654358 TTAAGGGTGT
** * *
15654368 AAAAAAGCCTCAAACTTTTTTAAAAGAGCAATTAAGCCTCTATTTTTTTTCCACTCGATGAGGTA
1 AAAAAAGCCTCAAACTTTTTTAAAAGAAAAATTAAGCCCCTATTTTTTTTCCACTCAATGAGGTA
* *
15654433 CTTGAACTTTTAAAATATATAA
66 CTTGAACTATCAAAATATATAA
**
15654455 AAAAAAGCCCTCAAA-TTTTTTCAAAA-AAAAATTAAGCCCCT-TTTATTTTTGTACTCAATTG-
1 AAAAAAG-CCTCAAACTTTTTT-AAAAGAAAAATTAAGCCCCTATTT-TTTTTCCACTCAA-TGA
* * *
15654516 GGTACTTTAACTATCAAAATGTATCA
62 GGTACTTGAACTATCAAAATATATAA
15654542 AAAA
1 AAAA
15654546 GGCCCTTTGA
Statistics
Matches: 76, Mismatches: 11, Indels: 8
0.80 0.12 0.08
Matches are distributed among these distances:
86 3 0.04
87 60 0.79
88 13 0.17
ACGTcount: A:0.40, C:0.16, G:0.09, T:0.35
Consensus pattern (87 bp):
AAAAAAGCCTCAAACTTTTTTAAAAGAAAAATTAAGCCCCTATTTTTTTTCCACTCAATGAGGTA
CTTGAACTATCAAAATATATAA
Found at i:15654685 original size:28 final size:29
Alignment explanation
Indices: 15654653--15654716 Score: 71
Period size: 28 Copynumber: 2.2 Consensus size: 29
15654643 AATAAAATCA
15654653 ATAAAAATTATTAAAT-TTTAAT-AAAAA-T
1 ATAAAAA-TATTAAATATTT-ATCAAAAATT
* *
15654681 ATAAAGATATTTAATATTTATCAAAAATT
1 ATAAAAATATTAAATATTTATCAAAAATT
15654710 ATAAAAA
1 ATAAAAA
15654717 CCATAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
27 9 0.30
28 14 0.47
29 7 0.23
ACGTcount: A:0.59, C:0.02, G:0.02, T:0.38
Consensus pattern (29 bp):
ATAAAAATATTAAATATTTATCAAAAATT
Found at i:15654693 original size:21 final size:20
Alignment explanation
Indices: 15654652--15654696 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
15654642 AAATAAAATC
*
15654652 AATAAAAATTATTAAATTTT
1 AATAAAAATTATAAAATTTT
15654672 AATAAAAA-TATAAAGATATTT
1 AATAAAAATTATAAA-AT-TTT
15654693 AATA
1 AATA
15654697 TTTATCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 5 0.23
20 10 0.45
21 7 0.32
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (20 bp):
AATAAAAATTATAAAATTTT
Found at i:15655019 original size:9 final size:8
Alignment explanation
Indices: 15655000--15655061 Score: 52
Period size: 9 Copynumber: 6.9 Consensus size: 8
15654990 TATATAATTT
15655000 TTTTCTATA
1 TTTT-TATA
15655009 TTTATTATA
1 TTT-TTATA
15655018 TTTTTATA
1 TTTTTATA
*
15655026 TTTTTTACGA
1 -TTTTTA-TA
15655036 TTTTTATAA
1 TTTTTAT-A
15655045 TTTTTTATAA
1 -TTTTTAT-A
15655055 TTTTTAT
1 TTTTTAT
15655062 CATCTTTTGT
Statistics
Matches: 46, Mismatches: 2, Indels: 10
0.79 0.03 0.17
Matches are distributed among these distances:
8 5 0.11
9 30 0.65
10 11 0.24
ACGTcount: A:0.26, C:0.03, G:0.02, T:0.69
Consensus pattern (8 bp):
TTTTTATA
Found at i:15655049 original size:10 final size:10
Alignment explanation
Indices: 15654992--15655059 Score: 54
Period size: 10 Copynumber: 7.0 Consensus size: 10
15654982 TTTAAAATTA
15654992 TATAATTTTTT
1 TATAA-TTTTT
* *
15655003 TCTATATTTAT
1 TATA-ATTTTT
15655014 TAT-A-TTTT
1 TATAATTTTT
15655022 TAT-ATTTTT
1 TATAATTTTT
**
15655031 TACGA-TTTT
1 TATAATTTTT
15655040 TATAATTTTT
1 TATAATTTTT
15655050 TATAATTTTT
1 TATAATTTTT
15655060 ATCATCTTTT
Statistics
Matches: 46, Mismatches: 7, Indels: 9
0.74 0.11 0.15
Matches are distributed among these distances:
8 7 0.15
9 14 0.30
10 15 0.33
11 9 0.20
12 1 0.02
ACGTcount: A:0.26, C:0.03, G:0.01, T:0.69
Consensus pattern (10 bp):
TATAATTTTT
Found at i:15655069 original size:10 final size:9
Alignment explanation
Indices: 15655008--15655061 Score: 56
Period size: 9 Copynumber: 5.9 Consensus size: 9
15654998 TTTTTTCTAT
15655008 ATTTATTAT-
1 ATTT-TTATA
15655017 ATTTTTATA
1 ATTTTTATA
* **
15655026 TTTTTTACG
1 ATTTTTATA
15655035 ATTTTTATA
1 ATTTTTATA
15655044 ATTTTTTATA
1 A-TTTTTATA
15655054 ATTTTTAT
1 ATTTTTAT
15655062 CATCTTTTGT
Statistics
Matches: 37, Mismatches: 6, Indels: 4
0.79 0.13 0.09
Matches are distributed among these distances:
8 4 0.11
9 24 0.65
10 9 0.24
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (9 bp):
ATTTTTATA
Done.