Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr7
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 55462051
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2780933 characters in sequence are not A, C, G, or T
File 131 of 163
Found at i:42261196 original size:27 final size:27
Alignment explanation
Indices: 42261158--42261224 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
42261148 AATTACAATA
42261158 TTCATTGGCGCCTCTCTATGAGGCACC
1 TTCATTGGCGCCTCTCTATGAGGCACC
*
42261185 TTCATTGGCGCCTCTCTGTGAGGCACC
1 TTCATTGGCGCCTCTCTATGAGGCACC
42261212 TTCATTGGCGCCT
1 TTCATTGGCGCCT
42261225 ACCTGATAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.12, C:0.33, G:0.24, T:0.31
Consensus pattern (27 bp):
TTCATTGGCGCCTCTCTATGAGGCACC
Found at i:42261329 original size:16 final size:15
Alignment explanation
Indices: 42261287--42261330 Score: 54
Period size: 16 Copynumber: 2.9 Consensus size: 15
42261277 GTATTTTTTT
42261287 AAAAAA-ATTATTAA
1 AAAAAATATTATTAA
*
42261301 AAAAATATTTTATTCAA
1 AAAAA-ATATTATT-AA
42261318 AAAAAATATTATT
1 AAAAAATATTATT
42261331 TTTTTATTCA
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
14 5 0.20
15 1 0.04
16 12 0.48
17 7 0.28
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.36
Consensus pattern (15 bp):
AAAAAATATTATTAA
Found at i:42272398 original size:22 final size:23
Alignment explanation
Indices: 42272363--42272409 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
42272353 AGAAACCACC
* *
42272363 AAAAATCATGAGGAAGTACCAAA
1 AAAAATCATAAGGAAATACCAAA
*
42272386 AAAAAT-ATAAGGAAATATCAAA
1 AAAAATCATAAGGAAATACCAAA
42272408 AA
1 AA
42272410 TTAAAGGGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.64, C:0.09, G:0.13, T:0.15
Consensus pattern (23 bp):
AAAAATCATAAGGAAATACCAAA
Found at i:42272910 original size:20 final size:20
Alignment explanation
Indices: 42272719--42273003 Score: 110
Period size: 20 Copynumber: 14.4 Consensus size: 20
42272709 TTTGAAACTA
*
42272719 TACCAAAAATTATGA-TAGAG
1 TACCAAAAATTATGAGGA-AG
* * *
42272739 TACCGAGAATTATGA-TAATG
1 TACCAAAAATTATGAGGAA-G
*
42272759 TACCAACAAA-TATGATGAAG
1 TACCAA-AAATTATGAGGAAG
* *
42272779 TAGCAAAATTTATGAGGAAG
1 TACCAAAAATTATGAGGAAG
* *
42272799 TACCAAAACTTA--A--ATG
1 TACCAAAAATTATGAGGAAG
* * * *
42272815 TA-TAGAAAATCATTAGGAAA
1 TACCA-AAAATTATGAGGAAG
*
42272835 TACCAAAAATTATGAAAGAA-
1 TACCAAAAATTATG-AGGAAG
*
42272855 TACCATAAAACT-TGAGGAAG
1 TACCA-AAAATTATGAGGAAG
* ** *
42272875 TATCAAAAACAAATGAGGATG
1 TACCAAAAA-TTATGAGGAAG
42272896 TACCAAAAATTATGAGGGAA-
1 TACCAAAAATTATGA-GGAAG
* * *
42272916 TAGCAAAAACTAGGAGGAAG
1 TACCAAAAATTATGAGGAAG
* *
42272936 TGCCAAAAATTATGAAAGAA-
1 TACCAAAAATTATG-AGGAAG
** * *
42272956 TATCGTAAAACT-TGAGGAAA
1 TA-CCAAAAATTATGAGGAAG
* **
42272976 TACCAAAATTTATGAGGATT
1 TACCAAAAATTATGAGGAAG
42272996 TACCAAAA
1 TACCAAAA
42273004 CATATTCCTT
Statistics
Matches: 195, Mismatches: 49, Indels: 42
0.68 0.17 0.15
Matches are distributed among these distances:
15 1 0.01
16 9 0.05
18 2 0.01
19 24 0.12
20 117 0.60
21 42 0.22
ACGTcount: A:0.49, C:0.11, G:0.17, T:0.22
Consensus pattern (20 bp):
TACCAAAAATTATGAGGAAG
Found at i:42273523 original size:22 final size:23
Alignment explanation
Indices: 42273488--42273534 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 23
42273478 AGAAACCACC
* *
42273488 AAAAATCATGAGGAAGTACCAAA
1 AAAAATCATAAGGAAATACCAAA
*
42273511 AAAAAT-ATAAGGAAATATCAAA
1 AAAAATCATAAGGAAATACCAAA
42273533 AA
1 AA
42273535 TTAAAGGGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
22 15 0.71
23 6 0.29
ACGTcount: A:0.64, C:0.09, G:0.13, T:0.15
Consensus pattern (23 bp):
AAAAATCATAAGGAAATACCAAA
Found at i:42273897 original size:20 final size:19
Alignment explanation
Indices: 42273844--42273899 Score: 51
Period size: 20 Copynumber: 2.8 Consensus size: 19
42273834 TTTGAAACTA
42273844 TACCAAAAATTATGATAGAG
1 TACCAAAAA-TATGATAGAG
* *
42273864 TACCGAGAATTATGATA-ATG
1 TACC-AAAAATATGATAGA-G
42273884 TACCAACAAATATGAT
1 TACCAA-AAATATGAT
42273900 GAAGTAGCAA
Statistics
Matches: 29, Mismatches: 4, Indels: 6
0.74 0.10 0.15
Matches are distributed among these distances:
19 2 0.07
20 24 0.83
21 3 0.10
ACGTcount: A:0.46, C:0.12, G:0.14, T:0.27
Consensus pattern (19 bp):
TACCAAAAATATGATAGAG
Found at i:42273917 original size:20 final size:20
Alignment explanation
Indices: 42273894--42274148 Score: 71
Period size: 20 Copynumber: 12.9 Consensus size: 20
42273884 TACCAACAAA
* *
42273894 TATGATGAAGTAGCAAAATT
1 TATGAGGAAGTACCAAAATT
*
42273914 TATGAGGAAGTACCAAAACT
1 TATGAGGAAGTACCAAAATT
* * * *
42273934 TA-AATGTA-TA-GAAAA-T
1 TATGAGGAAGTACCAAAATT
* * * *
42273950 CATTAGGAAATACCAAAAAT
1 TATGAGGAAGTACCAAAATT
* **
42273970 TATGAAAGAA-TACCATAAAAC
1 TATG-AGGAAGTACCA-AAATT
* **
42273991 T-TGAGGAAGTATCAAAAACA
1 TATGAGGAAGTA-CCAAAATT
* * *
42274011 AATGAGGATGTACCAAAAAT
1 TATGAGGAAGTACCAAAATT
* **
42274031 TATGAGGGAA-TAGCAAAAAC
1 TATGA-GGAAGTACCAAAATT
* * *
42274051 TAGGAGGAAGTGCCAAAAAT
1 TATGAGGAAGTACCAAAATT
* * *
42274071 TATGAAAGAA-TATCGTAAAA-C
1 TATG-AGGAAGTA-C-CAAAATT
*
42274092 T-TGAGGAAATACCAAAATT
1 TATGAGGAAGTACCAAAATT
** **
42274111 TATGAGGATTTACCAAAACA
1 TATGAGGAAGTACCAAAATT
42274131 TATGAGGAAGTACCAAAA
1 TATGAGGAAGTACCAAAA
42274149 ATCCGAGAAA
Statistics
Matches: 171, Mismatches: 47, Indels: 34
0.68 0.19 0.13
Matches are distributed among these distances:
16 2 0.01
17 7 0.04
18 8 0.05
19 21 0.12
20 100 0.58
21 29 0.17
22 4 0.02
ACGTcount: A:0.50, C:0.11, G:0.18, T:0.22
Consensus pattern (20 bp):
TATGAGGAAGTACCAAAATT
Found at i:42274098 original size:40 final size:40
Alignment explanation
Indices: 42274003--42274150 Score: 122
Period size: 40 Copynumber: 3.7 Consensus size: 40
42273993 GAGGAAGTAT
* * **
42274003 CAAAAACAAATGAGGATGTACCAAAAATTATGAGGGAATAG
1 CAAAAAC-TATGAGGAAGTACCAAAAATTATGAAAGAATAG
* * *
42274044 CAAAAACTAGGAGGAAGTGCCAAAAATTATGAAAGAATAT
1 CAAAAACTATGAGGAAGTACCAAAAATTATGAAAGAATAG
* * * * *
42274084 CGTAAAACT-TGAGGAAATACCAAAATTTATG-AGGATTTA-
1 C-AAAAACTATGAGGAAGTACCAAAAATTATGAAAGA-ATAG
*
42274123 CCAAAACATATGAGGAAGTACCAAAAAT
1 CAAAAAC-TATGAGGAAGTACCAAAAAT
42274151 CCGAGAAAAC
Statistics
Matches: 86, Mismatches: 17, Indels: 9
0.77 0.15 0.08
Matches are distributed among these distances:
38 5 0.06
39 5 0.06
40 63 0.73
41 13 0.15
ACGTcount: A:0.50, C:0.11, G:0.19, T:0.20
Consensus pattern (40 bp):
CAAAAACTATGAGGAAGTACCAAAAATTATGAAAGAATAG
Found at i:42274647 original size:57 final size:57
Alignment explanation
Indices: 42274559--42274669 Score: 172
Period size: 57 Copynumber: 1.9 Consensus size: 57
42274549 TTCAGATTAT
42274559 CCGTCCAGGCTCAATCCATTTTCCACATATTCTTCGAGAGGGCTATATCAAGATCAC
1 CCGTCCAGGCTCAATCCATTTTCCACATATTCTTCGAGAGGGCTATATCAAGATCAC
* *
42274616 CCGTCCAGGCT-AGAT-CTTTTTCACACATATTCTTCGGGAGGGCTATATCAAGAT
1 CCGTCCAGGCTCA-ATCCATTTTC-CACATATTCTTCGAGAGGGCTATATCAAGAT
42274670 AGGATCACCC
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
56 7 0.14
57 43 0.86
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (57 bp):
CCGTCCAGGCTCAATCCATTTTCCACATATTCTTCGAGAGGGCTATATCAAGATCAC
Found at i:42282536 original size:74 final size:75
Alignment explanation
Indices: 42282442--42282596 Score: 294
Period size: 74 Copynumber: 2.1 Consensus size: 75
42282432 TTAACTATAA
42282442 AAAAATAAAAAAATTTTGAAATAAAAAAAATCAACACAAGTTCTAATAAATTATAAAAAAAATAT
1 AAAAATAAAAAAATTTTGAAATAAAAAAAATCAACACAAGTTCTAATAAATTATAAAAAAAATAT
42282507 TAATAAATAT
66 TAATAAATAT
42282517 AAAAAT-AAAAAATTTTGAAATAAAAAAAATCAACACAAGTTCTAATAAATTATAAAAAAAATAT
1 AAAAATAAAAAAATTTTGAAATAAAAAAAATCAACACAAGTTCTAATAAATTATAAAAAAAATAT
42282581 TAATAAATAT
66 TAATAAATAT
42282591 ATAAAA
1 A-AAAA
42282597 AAGTATTTAT
Statistics
Matches: 79, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
74 69 0.87
75 10 0.13
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (75 bp):
AAAAATAAAAAAATTTTGAAATAAAAAAAATCAACACAAGTTCTAATAAATTATAAAAAAAATAT
TAATAAATAT
Found at i:42282597 original size:23 final size:23
Alignment explanation
Indices: 42282485--42282598 Score: 81
Period size: 22 Copynumber: 4.8 Consensus size: 23
42282475 ACACAAGTTC
42282485 TAATAAAT-TATAAAAAAAATAT
1 TAATAAATATATAAAAAAAATAT
* *
42282507 TAATAAATATAAAAATAAAAAATTT
1 TAATAAATAT-ATAA-AAAAAATAT
* * * * *
42282532 TGAAATAAAAAAAATCAACACAAGT-T
1 T--AAT-AAATATAT-AAAAAAAATAT
42282558 CTAATAAAT-TATAAAAAAAATAT
1 -TAATAAATATATAAAAAAAATAT
42282581 TAATAAATATATAAAAAA
1 TAATAAATATATAAAAAA
42282599 GTATTTATTT
Statistics
Matches: 69, Mismatches: 13, Indels: 19
0.68 0.13 0.19
Matches are distributed among these distances:
22 22 0.32
23 13 0.19
24 6 0.09
25 12 0.17
26 1 0.01
27 9 0.13
28 6 0.09
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.28
Consensus pattern (23 bp):
TAATAAATATATAAAAAAAATAT
Found at i:42283085 original size:29 final size:28
Alignment explanation
Indices: 42283053--42283132 Score: 74
Period size: 28 Copynumber: 2.8 Consensus size: 28
42283043 TTTTTTTAAA
*
42283053 TTTCTAATTTTTATATAATTTATTAGATT
1 TTTCTAATTTTTATATAATTT-TTACATT
*
42283082 TTTC--ATTTTTTTATATATGTTTTACATT
1 TTTCTAATTTTTATATA-AT-TTTTACATT
* *
42283110 TTTATGAATTTTTATAAAATTTT
1 TTTCT-AATTTTTATATAATTTT
42283133 AAATATGTTT
Statistics
Matches: 41, Mismatches: 5, Indels: 10
0.73 0.09 0.18
Matches are distributed among these distances:
27 10 0.24
28 11 0.27
29 9 0.22
30 2 0.05
31 9 0.22
ACGTcount: A:0.29, C:0.04, G:0.04, T:0.64
Consensus pattern (28 bp):
TTTCTAATTTTTATATAATTTTTACATT
Found at i:42294904 original size:2 final size:2
Alignment explanation
Indices: 42294892--42294927 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
42294882 NNNNNTGATT
*
42294892 TA TA GA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42294928 GATTTGCAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (2 bp):
TA
Found at i:42302828 original size:232 final size:233
Alignment explanation
Indices: 42302411--42302875 Score: 923
Period size: 232 Copynumber: 2.0 Consensus size: 233
42302401 TATTTATGTT
42302411 TATTATCAATGTATATTATTAATATGCAATGTAGTATATTATCAATTTTTATGTACAACTAAAAT
1 TATTATCAATGTATATTATTAATATGCAATGTAGTATATTATCAATTTTTATGTACAACTAAAAT
42302476 CTCAAAGAAAGTCCAATATGGAATAAGCAAAAATGAAATTTTAGTTCCATTTTTTCCAGATTATT
66 CTCAAAGAAAGTCCAATATGGAATAAGCAAAAATGAAATTTTAGTTCCATTTTTTCCAGATTATT
42302541 TTAAATTTAAATTTAATCATATTCGTGATATATTATTTATGATTTGTACTTAAATCCGGGATTTT
131 TTAAATTTAAATTTAATCATATTCGTGATATATTATTTATGATTTGTACTTAAATCCGGGATTTT
42302606 ACTTACAAATTCCATAAAAGGAAAAAAAAATACTGAAA
196 ACTTACAAATTCCATAAAAGGAAAAAAAAATACTGAAA
42302644 TATTATCAAT-TATATTATTAATATGCAATGTAGTATATTATCAATTTTTATGTACAACTAAAAT
1 TATTATCAATGTATATTATTAATATGCAATGTAGTATATTATCAATTTTTATGTACAACTAAAAT
42302708 CTCAAAGAAAGTCCAATATGGAATAAGCAAAAATGAAATTTTAGTTCCATTTTTTCCAGATTATT
66 CTCAAAGAAAGTCCAATATGGAATAAGCAAAAATGAAATTTTAGTTCCATTTTTTCCAGATTATT
42302773 TTAAATTTAAATTTAATCATATTCGTGATATATTATTTATGATTTGTACTTAAATCCGGGATTTT
131 TTAAATTTAAATTTAATCATATTCGTGATATATTATTTATGATTTGTACTTAAATCCGGGATTTT
42302838 ACTTACAAATTCCATAAAAGGAAAAAAAAATACTGAAA
196 ACTTACAAATTCCATAAAAGGAAAAAAAAATACTGAAA
42302876 AAGGTATTTG
Statistics
Matches: 232, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
232 222 0.96
233 10 0.04
ACGTcount: A:0.41, C:0.10, G:0.10, T:0.39
Consensus pattern (233 bp):
TATTATCAATGTATATTATTAATATGCAATGTAGTATATTATCAATTTTTATGTACAACTAAAAT
CTCAAAGAAAGTCCAATATGGAATAAGCAAAAATGAAATTTTAGTTCCATTTTTTCCAGATTATT
TTAAATTTAAATTTAATCATATTCGTGATATATTATTTATGATTTGTACTTAAATCCGGGATTTT
ACTTACAAATTCCATAAAAGGAAAAAAAAATACTGAAA
Found at i:42309930 original size:2 final size:2
Alignment explanation
Indices: 42309925--42309949 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
42309915 TATAATTTTA
42309925 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
42309950 ATACATCAAA
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:42315796 original size:2 final size:2
Alignment explanation
Indices: 42315789--42315820 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
42315779 TGAATGAATC
42315789 AT AT AT 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 AT AT AT
42315821 TTGATTCAGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42325993 original size:21 final size:21
Alignment explanation
Indices: 42325967--42326027 Score: 65
Period size: 21 Copynumber: 2.9 Consensus size: 21
42325957 GTGGTTGTTG
*
42325967 GGAGAGAGAAATGG-AGAGAAA
1 GGAGAGAGAAAAGGAAG-GAAA
42325988 GGAGAG-GAAAAGGAAGGAAA
1 GGAGAGAGAAAAGGAAGGAAA
42326008 GTGAGAGTAG-AAAGGAAGGA
1 G-GAGAG-AGAAAAGGAAGGA
42326028 GTAGACATGG
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
20 11 0.31
21 13 0.37
22 10 0.29
23 1 0.03
ACGTcount: A:0.51, C:0.00, G:0.44, T:0.05
Consensus pattern (21 bp):
GGAGAGAGAAAAGGAAGGAAA
Found at i:42327861 original size:31 final size:31
Alignment explanation
Indices: 42327822--42327911 Score: 119
Period size: 31 Copynumber: 2.9 Consensus size: 31
42327812 AACAAATAGC
*
42327822 TCAATGACTTAAATAAAAACTTTCGAATAATT
1 TCAATGACTTAAATAAAAACTTTCAAAT-ATT
*
42327854 T-AATGACTTAAATAAAAAATTTCAAATATT
1 TCAATGACTTAAATAAAAACTTTCAAATATT
* **
42327884 TCAATAACTTAAATTTAAACTTTCAAAT
1 TCAATGACTTAAATAAAAACTTTCAAAT
42327912 CATTGGCTCC
Statistics
Matches: 51, Mismatches: 6, Indels: 3
0.85 0.10 0.05
Matches are distributed among these distances:
30 4 0.08
31 46 0.90
32 1 0.02
ACGTcount: A:0.49, C:0.11, G:0.03, T:0.37
Consensus pattern (31 bp):
TCAATGACTTAAATAAAAACTTTCAAATATT
Found at i:42328125 original size:19 final size:19
Alignment explanation
Indices: 42328103--42328141 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
42328093 ATTTATTTTT
42328103 TATTTT-TAATATATATAAA
1 TATTTTCTAAT-TATATAAA
*
42328122 TATTTTCTAATTATTTAAA
1 TATTTTCTAATTATATAAA
42328141 T
1 T
42328142 TGCCACGTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.41, C:0.03, G:0.00, T:0.56
Consensus pattern (19 bp):
TATTTTCTAATTATATAAA
Found at i:42329754 original size:17 final size:17
Alignment explanation
Indices: 42329722--42329782 Score: 70
Period size: 18 Copynumber: 3.5 Consensus size: 17
42329712 TTAACTAATA
42329722 ATTTAAAAATTATAAAAT
1 ATTTAAAAATT-TAAAAT
*
42329740 ATTTAAAAACTTAAAAT
1 ATTTAAAAATTTAAAAT
* *
42329757 AATT-AGAATTTAAAAT
1 ATTTAAAAATTTAAAAT
42329773 AATTTAAAAA
1 -ATTTAAAAA
42329783 ATCATACAAT
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
16 10 0.29
17 12 0.34
18 13 0.37
ACGTcount: A:0.61, C:0.02, G:0.02, T:0.36
Consensus pattern (17 bp):
ATTTAAAAATTTAAAAT
Found at i:42335850 original size:14 final size:15
Alignment explanation
Indices: 42335824--42335855 Score: 57
Period size: 14 Copynumber: 2.2 Consensus size: 15
42335814 TATACATTGG
42335824 ATTTACATCGATTTT
1 ATTTACATCGATTTT
42335839 ATTTAC-TCGATTTT
1 ATTTACATCGATTTT
42335853 ATT
1 ATT
42335856 CTTTGTACAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.25, C:0.12, G:0.06, T:0.56
Consensus pattern (15 bp):
ATTTACATCGATTTT
Found at i:42348319 original size:38 final size:38
Alignment explanation
Indices: 42348277--42348352 Score: 152
Period size: 38 Copynumber: 2.0 Consensus size: 38
42348267 TAGATGATTT
42348277 GATACTTTAAACATTCGCTTAATGTTTGCTTTTACCGC
1 GATACTTTAAACATTCGCTTAATGTTTGCTTTTACCGC
42348315 GATACTTTAAACATTCGCTTAATGTTTGCTTTTACCGC
1 GATACTTTAAACATTCGCTTAATGTTTGCTTTTACCGC
42348353 TAATAACTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 38 1.00
ACGTcount: A:0.24, C:0.21, G:0.13, T:0.42
Consensus pattern (38 bp):
GATACTTTAAACATTCGCTTAATGTTTGCTTTTACCGC
Found at i:42350532 original size:2 final size:2
Alignment explanation
Indices: 42350525--42350552 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
42350515 AATTGGTGTA
42350525 AT 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 AT
42350553 TTTAAATTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42353163 original size:21 final size:21
Alignment explanation
Indices: 42353117--42353163 Score: 51
Period size: 21 Copynumber: 2.2 Consensus size: 21
42353107 TTTGGCCATA
*
42353117 TTAATTTTTTATTTTTAAAAT
1 TTAATTTTTTATATTTAAAAT
* *
42353138 ATAATTATTTT-TATTTAATAT
1 TTAATT-TTTTATATTTAAAAT
42353159 TTAAT
1 TTAAT
42353164 AATTATATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
21 17 0.81
22 4 0.19
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (21 bp):
TTAATTTTTTATATTTAAAAT
Found at i:42353848 original size:29 final size:30
Alignment explanation
Indices: 42353796--42353854 Score: 102
Period size: 29 Copynumber: 2.0 Consensus size: 30
42353786 GTGGCAGGGA
42353796 CTGGATTAGGGTTCTTTGAACTTAACCAAT
1 CTGGATTAGGGTTCTTTGAACTTAACCAAT
*
42353826 CTGGATTAGGG-TCTTTGAACTTAGCCAAT
1 CTGGATTAGGGTTCTTTGAACTTAACCAAT
42353855 ATGTCTTTGT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 17 0.61
30 11 0.39
ACGTcount: A:0.25, C:0.17, G:0.22, T:0.36
Consensus pattern (30 bp):
CTGGATTAGGGTTCTTTGAACTTAACCAAT
Found at i:42368389 original size:20 final size:20
Alignment explanation
Indices: 42368364--42368401 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
42368354 GTTATATATT
42368364 AATTTTATTAAAA-AAATTTC
1 AATTTT-TTAAAATAAATTTC
42368384 AATTTTTTAAAATAAATT
1 AATTTTTTAAAATAAATT
42368402 AATTATTGTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
AATTTTTTAAAATAAATTTC
Found at i:42378132 original size:131 final size:132
Alignment explanation
Indices: 42377897--42378160 Score: 521
Period size: 131 Copynumber: 2.0 Consensus size: 132
42377887 TCATTTGTAT
42377897 AATGTGAGGTGACGATTAATTTATCACAATAGAAAAATCAACTTTTTTTTTTTGCATGGTGTCAG
1 AATGTGAGGTGACGATTAATTTATCACAATAGAAAAATCAACTTTTTTTTTTTGCATGGTGTCAG
42377962 GGAGACTATCCTCCGTCTCTAAATTAGCCAAGACTGTGCAATAGACAGAAAATAACTAATGAAAT
66 GGAGACTATCCTCCGTCTCTAAATTAGCCAAGACTGTGCAATAGACAGAAAATAACTAATGAAAT
42378027 AA
131 AA
42378029 AATGTGAGGT-ACGATTAATTTATCACAATAGAAAAATCAACTTTTTTTTTTTGCATGGTGTCAG
1 AATGTGAGGTGACGATTAATTTATCACAATAGAAAAATCAACTTTTTTTTTTTGCATGGTGTCAG
42378093 GGAGACTATCCTCCGTCTCTAAATTAGCCAAGACTGTGCAATAGACAGAAAATAACTAATGAAAT
66 GGAGACTATCCTCCGTCTCTAAATTAGCCAAGACTGTGCAATAGACAGAAAATAACTAATGAAAT
42378158 AA
131 AA
42378160 A
1 A
42378161 CATTTCTGAA
Statistics
Matches: 132, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
131 122 0.92
132 10 0.08
ACGTcount: A:0.38, C:0.15, G:0.17, T:0.30
Consensus pattern (132 bp):
AATGTGAGGTGACGATTAATTTATCACAATAGAAAAATCAACTTTTTTTTTTTGCATGGTGTCAG
GGAGACTATCCTCCGTCTCTAAATTAGCCAAGACTGTGCAATAGACAGAAAATAACTAATGAAAT
AA
Found at i:42383727 original size:21 final size:22
Alignment explanation
Indices: 42383702--42383753 Score: 54
Period size: 21 Copynumber: 2.5 Consensus size: 22
42383692 GATTAATGAT
* *
42383702 TAAATTTTAATTAA-AAAAATA
1 TAAATTTTAAATAACAAAAAAA
*
42383723 TAAA-TATAAATAACAAAAAAA
1 TAAATTTTAAATAACAAAAAAA
*
42383744 TAAATATTAA
1 TAAATTTTAA
42383754 GGACTAAATT
Statistics
Matches: 24, Mismatches: 5, Indels: 3
0.75 0.16 0.09
Matches are distributed among these distances:
20 7 0.29
21 14 0.58
22 3 0.12
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (22 bp):
TAAATTTTAAATAACAAAAAAA
Found at i:42388909 original size:3 final size:3
Alignment explanation
Indices: 42388901--42388962 Score: 115
Period size: 3 Copynumber: 20.7 Consensus size: 3
42388891 ATAGTTAAAC
*
42388901 TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
42388949 TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TA
42388963 ATGTCTTATT
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:42399976 original size:11 final size:11
Alignment explanation
Indices: 42399959--42399992 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
42399949 CTATTTTTAC
42399959 ATCATAAAATA
1 ATCATAAAATA
* *
42399970 TTCATAAATTA
1 ATCATAAAATA
42399981 ATCATAAAATA
1 ATCATAAAATA
42399992 A
1 A
42399993 AAATTTATAC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (11 bp):
ATCATAAAATA
Found at i:42407645 original size:11 final size:11
Alignment explanation
Indices: 42407625--42407655 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
42407615 CTCTCAATAT
*
42407625 ATTATTCACAC
1 ATTATACACAC
42407636 ATTATACACAC
1 ATTATACACAC
42407647 ATTATACAC
1 ATTATACAC
42407656 TCTACTGGGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.42, C:0.26, G:0.00, T:0.32
Consensus pattern (11 bp):
ATTATACACAC
Found at i:42407781 original size:2 final size:2
Alignment explanation
Indices: 42407774--42407799 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
42407764 CCTCTCGTAA
42407774 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
42407800 TCCTCTAAAA
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:42420099 original size:15 final size:15
Alignment explanation
Indices: 42420079--42420111 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
42420069 CTTTGCCCTG
*
42420079 CTTGTTTTTCTTCTT
1 CTTGTTTCTCTTCTT
42420094 CTTGTTTCTCTTCTT
1 CTTGTTTCTCTTCTT
42420109 CTT
1 CTT
42420112 CTTCTCCTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.00, C:0.24, G:0.06, T:0.70
Consensus pattern (15 bp):
CTTGTTTCTCTTCTT
Found at i:42421811 original size:16 final size:16
Alignment explanation
Indices: 42421790--42421821 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
42421780 GTTTTTCTAT
*
42421790 ATTTTTTATTTCTTTA
1 ATTTTTCATTTCTTTA
42421806 ATTTTTCATTTCTTTA
1 ATTTTTCATTTCTTTA
42421822 GCAAATGAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.19, C:0.09, G:0.00, T:0.72
Consensus pattern (16 bp):
ATTTTTCATTTCTTTA
Found at i:42421903 original size:9 final size:8
Alignment explanation
Indices: 42421885--42421942 Score: 53
Period size: 9 Copynumber: 6.5 Consensus size: 8
42421875 ATAGAGAGAG
42421885 AAATAAAA
1 AAATAAAA
42421893 AAATGAAAA
1 AAAT-AAAA
42421902 AAATAAAAA
1 AAAT-AAAA
42421911 AAATAAATA
1 AAATAAA-A
*
42421920 AAGTTAAAA
1 AA-ATAAAA
42421929 GAACATAAAA
1 -AA-ATAAAA
42421939 AAAT
1 AAAT
42421943 TGCTCAATGA
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
8 9 0.21
9 22 0.52
10 11 0.26
ACGTcount: A:0.78, C:0.02, G:0.05, T:0.16
Consensus pattern (8 bp):
AAATAAAA
Found at i:42438448 original size:2 final size:2
Alignment explanation
Indices: 42438441--42438485 Score: 72
Period size: 2 Copynumber: 22.5 Consensus size: 2
42438431 ATCTATTATA
* *
42438441 TG TG TG TG TG TA TG TG TG TG TG TG TG TG TG TA TG TG TG TG TG
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG
42438483 TG T
1 TG T
42438486 ATTCTTTGCT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.04, C:0.00, G:0.44, T:0.51
Consensus pattern (2 bp):
TG
Found at i:42440658 original size:21 final size:21
Alignment explanation
Indices: 42440624--42440692 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 21
42440614 GAAGCTGGAA
* * *
42440624 AGCTGAATAGAAGCTTATAAG
1 AGCTGAACAAAAGCTCATAAG
* *
42440645 AGTTGAACAAAAGCTCGTAAG
1 AGCTGAACAAAAGCTCATAAG
*
42440666 AGCTGAACAAAAGCTCGTAAG
1 AGCTGAACAAAAGCTCATAAG
42440687 AGCTGA
1 AGCTGA
42440693 TCCACCCAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.42, C:0.14, G:0.25, T:0.19
Consensus pattern (21 bp):
AGCTGAACAAAAGCTCATAAG
Found at i:42440892 original size:21 final size:21
Alignment explanation
Indices: 42440858--42440926 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 21
42440848 GAAGCTGGAA
* * *
42440858 AGCTGAATAGAAGCTTATAAG
1 AGCTGAACAAAAGCTCATAAG
* *
42440879 AGTTGAACAAAAGCTCGTAAG
1 AGCTGAACAAAAGCTCATAAG
*
42440900 AGCTGAACAAAAGCTCGTAAG
1 AGCTGAACAAAAGCTCATAAG
42440921 AGCTGA
1 AGCTGA
42440927 TCCACCCAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.42, C:0.14, G:0.25, T:0.19
Consensus pattern (21 bp):
AGCTGAACAAAAGCTCATAAG
Found at i:42440909 original size:234 final size:234
Alignment explanation
Indices: 42440500--42440958 Score: 918
Period size: 234 Copynumber: 2.0 Consensus size: 234
42440490 ATGTCTTTCA
42440500 AATTCATTAAATAAATCACTTGACCAAGATTTTTCCATTTGAAGAACGACTTACGGATAAGAGTA
1 AATTCATTAAATAAATCACTTGACCAAGATTTTTCCATTTGAAGAACGACTTACGGATAAGAGTA
42440565 TATCGTCAACAGAAGCTCATAAGAGCTGGTCCTCCCAAATACGCCAATAGAAGCTGGAAAGCTGA
66 TATCGTCAACAGAAGCTCATAAGAGCTGGTCCTCCCAAATACGCCAATAGAAGCTGGAAAGCTGA
42440630 ATAGAAGCTTATAAGAGTTGAACAAAAGCTCGTAAGAGCTGAACAAAAGCTCGTAAGAGCTGATC
131 ATAGAAGCTTATAAGAGTTGAACAAAAGCTCGTAAGAGCTGAACAAAAGCTCGTAAGAGCTGATC
42440695 CACCCAATTACGCCAACAAAAAGTAAAACATAACATGTC
196 CACCCAATTACGCCAACAAAAAGTAAAACATAACATGTC
42440734 AATTCATTAAATAAATCACTTGACCAAGATTTTTCCATTTGAAGAACGACTTACGGATAAGAGTA
1 AATTCATTAAATAAATCACTTGACCAAGATTTTTCCATTTGAAGAACGACTTACGGATAAGAGTA
42440799 TATCGTCAACAGAAGCTCATAAGAGCTGGTCCTCCCAAATACGCCAATAGAAGCTGGAAAGCTGA
66 TATCGTCAACAGAAGCTCATAAGAGCTGGTCCTCCCAAATACGCCAATAGAAGCTGGAAAGCTGA
42440864 ATAGAAGCTTATAAGAGTTGAACAAAAGCTCGTAAGAGCTGAACAAAAGCTCGTAAGAGCTGATC
131 ATAGAAGCTTATAAGAGTTGAACAAAAGCTCGTAAGAGCTGAACAAAAGCTCGTAAGAGCTGATC
42440929 CACCCAATTACGCCAACAAAAAGTAAAACA
196 CACCCAATTACGCCAACAAAAAGTAAAACA
42440959 CGAGAGTTCG
Statistics
Matches: 225, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
234 225 1.00
ACGTcount: A:0.41, C:0.20, G:0.18, T:0.22
Consensus pattern (234 bp):
AATTCATTAAATAAATCACTTGACCAAGATTTTTCCATTTGAAGAACGACTTACGGATAAGAGTA
TATCGTCAACAGAAGCTCATAAGAGCTGGTCCTCCCAAATACGCCAATAGAAGCTGGAAAGCTGA
ATAGAAGCTTATAAGAGTTGAACAAAAGCTCGTAAGAGCTGAACAAAAGCTCGTAAGAGCTGATC
CACCCAATTACGCCAACAAAAAGTAAAACATAACATGTC
Found at i:42443281 original size:21 final size:21
Alignment explanation
Indices: 42443247--42443315 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 21
42443237 GAAGCTGGAA
* * *
42443247 AGCTGAATAGAAGCTTATAAG
1 AGCTGAACAAAAGCTCATAAG
* *
42443268 AGTTGAACAAAAGCTCGTAAG
1 AGCTGAACAAAAGCTCATAAG
*
42443289 AGCTGAACAAAAGCTCGTAAG
1 AGCTGAACAAAAGCTCATAAG
42443310 AGCTGA
1 AGCTGA
42443316 TCCACCCAAT
Statistics
Matches: 42, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 42 1.00
ACGTcount: A:0.42, C:0.14, G:0.25, T:0.19
Consensus pattern (21 bp):
AGCTGAACAAAAGCTCATAAG
Found at i:42445921 original size:29 final size:27
Alignment explanation
Indices: 42445863--42445927 Score: 67
Period size: 29 Copynumber: 2.3 Consensus size: 27
42445853 GGACTTGATT
* *
42445863 AAATTAGTTTCTCTACTATTAAATGGATC
1 AAATTAG--TCTCTACTATTAAAAGAATC
*
42445892 AATTTAGTCTCGTACTATTACAAAGAATC
1 AAATTAGTCTC-TACTATTA-AAAGAATC
42445921 AAATTAG
1 AAATTAG
42445928 GCCAAGTTAG
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
27 4 0.13
28 8 0.27
29 18 0.60
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (27 bp):
AAATTAGTCTCTACTATTAAAAGAATC
Found at i:42447832 original size:16 final size:15
Alignment explanation
Indices: 42447795--42447834 Score: 53
Period size: 16 Copynumber: 2.6 Consensus size: 15
42447785 TTCAATTCTG
*
42447795 AATTAACTCAATCCA
1 AATTAACTCAATCAA
*
42447810 TATTAACTCAATTCAA
1 AATTAACTCAA-TCAA
42447826 AATTAACTC
1 AATTAACTC
42447835 TCTCCACTCG
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 10 0.48
16 11 0.52
ACGTcount: A:0.45, C:0.23, G:0.00, T:0.33
Consensus pattern (15 bp):
AATTAACTCAATCAA
Found at i:42450597 original size:3 final size:3
Alignment explanation
Indices: 42450589--42450622 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
42450579 AGTTTATGTG
42450589 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
42450623 TTCAGTCGGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:42451182 original size:59 final size:58
Alignment explanation
Indices: 42451090--42451211 Score: 199
Period size: 59 Copynumber: 2.1 Consensus size: 58
42451080 CTTTTTGCCG
*
42451090 CTGTTTTGTCACTATTTAGCGCCGTTTCACTATTATATTACTACTACTTTGTTGTTAT
1 CTGTTTTGTCAATATTTAGCGCCGTTTCACTATTATATTACTACTACTTTGTTGTTAT
* * *
42451148 CTGTTTTGTCAATATTTTAGTGCCGTTTCGCTATTATATTACTGCTACTTTGTTGTTAT
1 CTGTTTTGTCAATA-TTTAGCGCCGTTTCACTATTATATTACTACTACTTTGTTGTTAT
42451207 CTGTT
1 CTGTT
42451212 AAATATTGTA
Statistics
Matches: 59, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
58 13 0.22
59 46 0.78
ACGTcount: A:0.17, C:0.17, G:0.14, T:0.52
Consensus pattern (58 bp):
CTGTTTTGTCAATATTTAGCGCCGTTTCACTATTATATTACTACTACTTTGTTGTTAT
Found at i:42452137 original size:18 final size:18
Alignment explanation
Indices: 42452096--42452138 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 18
42452086 AAAATGCCAG
*
42452096 ACATGAATACTTCAAGAA
1 ACATGAAAACTTCAAGAA
* * *
42452114 AAATGAAAAGTTCAAGTA
1 ACATGAAAACTTCAAGAA
42452132 ACATGAA
1 ACATGAA
42452139 GGACCATGAA
Statistics
Matches: 20, Mismatches: 5, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.53, C:0.12, G:0.14, T:0.21
Consensus pattern (18 bp):
ACATGAAAACTTCAAGAA
Found at i:42467161 original size:13 final size:13
Alignment explanation
Indices: 42467139--42467175 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
42467129 TATCACATAT
42467139 GAAA-TACAGTTA
1 GAAAGTACAGTTA
42467151 GAAAGTACAGTTA
1 GAAAGTACAGTTA
42467164 GAAAGTACAGTT
1 GAAAGTACAGTT
42467176 TCTATTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
12 4 0.17
13 20 0.83
ACGTcount: A:0.46, C:0.08, G:0.22, T:0.24
Consensus pattern (13 bp):
GAAAGTACAGTTA
Found at i:42491664 original size:12 final size:12
Alignment explanation
Indices: 42491647--42491671 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
42491637 ACTAAAAAAT
42491647 ACGAAAAATTAA
1 ACGAAAAATTAA
42491659 ACGAAAAATTAA
1 ACGAAAAATTAA
42491671 A
1 A
42491672 ATATTTTTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.68, C:0.08, G:0.08, T:0.16
Consensus pattern (12 bp):
ACGAAAAATTAA
Found at i:42492883 original size:12 final size:13
Alignment explanation
Indices: 42492858--42492889 Score: 57
Period size: 12 Copynumber: 2.5 Consensus size: 13
42492848 TTGACTGTGT
42492858 TTTTTTAAATAAA
1 TTTTTTAAATAAA
42492871 TTTTTTAAA-AAA
1 TTTTTTAAATAAA
42492883 TTTTTTA
1 TTTTTTA
42492890 TTTCGGCCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 10 0.53
13 9 0.47
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTTTTAAATAAA
Found at i:42494176 original size:23 final size:22
Alignment explanation
Indices: 42494134--42494176 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
42494124 ATATTTATAC
*
42494134 TAAAAAATATTACCATTAATAA
1 TAAAAAATATTACAATTAATAA
42494156 TAAAACAATATTA-AATATAAT
1 TAAAA-AATATTACAAT-TAAT
42494177 TTTTAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAAAATATTACAATTAATAA
Found at i:42494312 original size:23 final size:22
Alignment explanation
Indices: 42494270--42494312 Score: 52
Period size: 23 Copynumber: 1.9 Consensus size: 22
42494260 NNNNNNNNAC
*
42494270 TAAAAAATATTACCATTAATAA
1 TAAAAAATATTACAATTAATAA
42494292 TAAAACAATATTA-AATATAAT
1 TAAAA-AATATTACAAT-TAAT
42494313 TTTTAAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 7 0.39
23 11 0.61
ACGTcount: A:0.60, C:0.07, G:0.00, T:0.33
Consensus pattern (22 bp):
TAAAAAATATTACAATTAATAA
Found at i:42498186 original size:2 final size:2
Alignment explanation
Indices: 42498179--42498208 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
42498169 TTTACTGATT
42498179 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42498209 ATAATGTTGT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:42500748 original size:3 final size:3
Alignment explanation
Indices: 42500740--42500769 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
42500730 ACAAAATTAT
42500740 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA GAA
42500770 TATTCAGATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:42504037 original size:27 final size:27
Alignment explanation
Indices: 42503998--42504049 Score: 95
Period size: 27 Copynumber: 1.9 Consensus size: 27
42503988 TAAGTCAAAT
*
42503998 ATCAACAAGCATTGTAACTAGTGAATC
1 ATCAACAAACATTGTAACTAGTGAATC
42504025 ATCAACAAACATTGTAACTAGTGAA
1 ATCAACAAACATTGTAACTAGTGAA
42504050 ACAAGTACAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.44, C:0.17, G:0.13, T:0.25
Consensus pattern (27 bp):
ATCAACAAACATTGTAACTAGTGAATC
Found at i:42504702 original size:17 final size:17
Alignment explanation
Indices: 42504668--42504722 Score: 58
Period size: 20 Copynumber: 3.1 Consensus size: 17
42504658 GATCACCAAT
*
42504668 AAATCTTATTC-ATTAAG
1 AAATCTTATTCTA-CAAG
42504685 AAATCTTATTCTACAAG
1 AAATCTTATTCTACAAG
42504702 ATTTAATCTTATTCTACAAG
1 A---AATCTTATTCTACAAG
42504722 A
1 A
42504723 TTTCCTACCC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
17 15 0.45
18 1 0.03
20 17 0.52
ACGTcount: A:0.40, C:0.15, G:0.05, T:0.40
Consensus pattern (17 bp):
AAATCTTATTCTACAAG
Found at i:42504711 original size:20 final size:20
Alignment explanation
Indices: 42504686--42504725 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
42504676 TTCATTAAGA
42504686 AATCTTATTCTACAAGATTT
1 AATCTTATTCTACAAGATTT
42504706 AATCTTATTCTACAAGATTT
1 AATCTTATTCTACAAGATTT
42504726 CCTACCCATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (20 bp):
AATCTTATTCTACAAGATTT
Found at i:42509390 original size:20 final size:19
Alignment explanation
Indices: 42509349--42509384 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
42509339 ATCTAACATC
42509349 AATTTTTTTTTACATATTT
1 AATTTTTTTTTACATATTT
42509368 AATTTTTTTTTA-ATATT
1 AATTTTTTTTTACATATT
42509385 CATAATCTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (19 bp):
AATTTTTTTTTACATATTT
Found at i:42509787 original size:15 final size:17
Alignment explanation
Indices: 42509766--42509806 Score: 59
Period size: 15 Copynumber: 2.5 Consensus size: 17
42509756 TAATCGTCTA
42509766 AAAATTATAAAAAT-AT
1 AAAATTATAAAAATAAT
*
42509782 -AAATTATTAAAATAAT
1 AAAATTATAAAAATAAT
42509798 AAAATTATA
1 AAAATTATA
42509807 TTTTTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 12 0.57
16 2 0.10
17 7 0.33
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (17 bp):
AAAATTATAAAAATAAT
Found at i:42510128 original size:6 final size:6
Alignment explanation
Indices: 42510117--42510142 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
42510107 GGTTGATCCC
42510117 CCAATG CCAATG CCAATG CCAATG CC
1 CCAATG CCAATG CCAATG CCAATG CC
42510143 TCAATCCATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.38, G:0.15, T:0.15
Consensus pattern (6 bp):
CCAATG
Found at i:42520834 original size:22 final size:22
Alignment explanation
Indices: 42520808--42520849 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
42520798 ATTCAAACAC
42520808 TAAGAACAAAATAATAGCAATA
1 TAAGAACAAAATAATAGCAATA
* *
42520830 TAAGAGCGAAATAATAGCAA
1 TAAGAACAAAATAATAGCAA
42520850 AACAATAAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.10, G:0.14, T:0.17
Consensus pattern (22 bp):
TAAGAACAAAATAATAGCAATA
Found at i:42520856 original size:11 final size:11
Alignment explanation
Indices: 42520814--42520856 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
42520804 ACACTAAGAA
42520814 CAAAATAATAG
1 CAAAATAATAG
* *
42520825 CAATATAAGAG
1 CAAAATAATAG
*
42520836 CGAAATAATAG
1 CAAAATAATAG
*
42520847 CAAAACAATA
1 CAAAATAATA
42520857 AAAAAATAAC
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.60, C:0.12, G:0.12, T:0.16
Consensus pattern (11 bp):
CAAAATAATAG
Found at i:42524960 original size:52 final size:52
Alignment explanation
Indices: 42524904--42525004 Score: 132
Period size: 52 Copynumber: 1.9 Consensus size: 52
42524894 ACAAGATGCG
* * * *
42524904 CTTTCAAATAACATTTTGCCAGC-TCAGTTGAAAACGCGTCCTGCAAGGCGCA
1 CTTTCAAAGAACATTCTGCC-GCATCAGCTGAAAACGCATCCTGCAAGGCGCA
* *
42524956 CTTTCAGAGAACATTCTGCCGCATCAGCTGAAAATGCATCCTGCAAGGC
1 CTTTCAAAGAACATTCTGCCGCATCAGCTGAAAACGCATCCTGCAAGGC
42525005 ATGTTTTCTT
Statistics
Matches: 42, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
51 2 0.05
52 40 0.95
ACGTcount: A:0.29, C:0.28, G:0.20, T:0.24
Consensus pattern (52 bp):
CTTTCAAAGAACATTCTGCCGCATCAGCTGAAAACGCATCCTGCAAGGCGCA
Found at i:42528174 original size:21 final size:21
Alignment explanation
Indices: 42528150--42528211 Score: 70
Period size: 23 Copynumber: 2.9 Consensus size: 21
42528140 TGGGAAACTT
42528150 ATTAAAATTAATAAAAAAATA
1 ATTAAAATTAATAAAAAAATA
* * * *
42528171 ATTATAATAAATTATAAAAACTT
1 ATTAAAATTAA-TA-AAAAAATA
42528194 ATTAAAATTAATAAAAAA
1 ATTAAAATTAATAAAAAA
42528212 TGGTTAAAAT
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
21 14 0.42
22 4 0.12
23 15 0.45
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (21 bp):
ATTAAAATTAATAAAAAAATA
Found at i:42528391 original size:11 final size:10
Alignment explanation
Indices: 42528316--42528395 Score: 54
Period size: 10 Copynumber: 7.6 Consensus size: 10
42528306 TCCAAGCATG
*
42528316 ATTTTTAATC
1 ATTTTTAATA
42528326 ATTTTTAA-A
1 ATTTTTAATA
*
42528335 TATTTTAAAAATA
1 -ATTTT--TAATA
*
42528348 TATATTTAATA
1 -ATTTTTAATA
* *
42528359 ATTTCTCATA
1 ATTTTTAATA
*
42528369 ATTGTTAATA
1 ATTTTTAATA
42528379 ATTTTTAAATA
1 ATTTTT-AATA
42528390 ATTTTT
1 ATTTTT
42528396 TACCAAAAAA
Statistics
Matches: 54, Mismatches: 11, Indels: 9
0.73 0.15 0.12
Matches are distributed among these distances:
10 32 0.59
11 14 0.26
12 2 0.04
13 6 0.11
ACGTcount: A:0.40, C:0.04, G:0.01, T:0.55
Consensus pattern (10 bp):
ATTTTTAATA
Found at i:42528793 original size:26 final size:26
Alignment explanation
Indices: 42528744--42528793 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
42528734 AATTGTATTG
** *
42528744 AAGGCTTAATTGATTTTTTTTTCACT
1 AAGGCTTAATTGATTAATTCTTCACT
42528770 AAGGCTTAATTGATTAATTCTTCA
1 AAGGCTTAATTGATTAATTCTTCA
42528794 TTATTTAAGG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.28, C:0.12, G:0.12, T:0.48
Consensus pattern (26 bp):
AAGGCTTAATTGATTAATTCTTCACT
Found at i:42538905 original size:58 final size:59
Alignment explanation
Indices: 42538811--42538955 Score: 177
Period size: 58 Copynumber: 2.5 Consensus size: 59
42538801 ATTTGAACAA
* * ** * *
42538811 AAAAAAGATTAGGTACCAAATT-AGAAAAAAGAGTCAAGTTCAAGTGTCAAATTGGACT
1 AAAAAAGTTTAGGTACCAAATTAAGAAAAAAGAGTCAAGTTCAAATACCAAATTAGACC
* *
42538869 AAAAAAGTTTAAGTACCAAATTAAGAAAAAA-TGTCAAGTTCAAATACCAAATTAGACC
1 AAAAAAGTTTAGGTACCAAATTAAGAAAAAAGAGTCAAGTTCAAATACCAAATTAGACC
*
42538927 AAAAAAGAATTTAGGTATCAAATTAAGAA
1 AAAAAAG--TTTAGGTACCAAATTAAGAA
42538956 TCACTCCATT
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
58 48 0.65
59 8 0.11
60 18 0.24
ACGTcount: A:0.52, C:0.10, G:0.14, T:0.23
Consensus pattern (59 bp):
AAAAAAGTTTAGGTACCAAATTAAGAAAAAAGAGTCAAGTTCAAATACCAAATTAGACC
Found at i:42539182 original size:8 final size:8
Alignment explanation
Indices: 42539166--42539239 Score: 51
Period size: 8 Copynumber: 8.5 Consensus size: 8
42539156 TCATGATTCT
*
42539166 AAATTTAA
1 AAATATAA
42539174 AAATATAAA
1 AAATAT-AA
42539183 AATATTATAA
1 AA-A-TATAA
42539193 AAATCCATAA
1 AAAT--ATAA
*
42539203 AATTATAA
1 AAATATAA
*
42539211 AAATATTTTA
1 AAATA--TAA
42539221 AAATATAA
1 AAATATAA
42539229 AAAT-TAA
1 AAATATAA
42539236 AAAT
1 AAAT
42539240 TTTCAAAAGG
Statistics
Matches: 54, Mismatches: 5, Indels: 15
0.73 0.07 0.20
Matches are distributed among these distances:
7 7 0.13
8 20 0.37
9 5 0.09
10 19 0.35
11 3 0.06
ACGTcount: A:0.65, C:0.03, G:0.00, T:0.32
Consensus pattern (8 bp):
AAATATAA
Found at i:42540112 original size:16 final size:16
Alignment explanation
Indices: 42540091--42540147 Score: 87
Period size: 16 Copynumber: 3.6 Consensus size: 16
42540081 TTTGGTTCGC
*
42540091 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
42540107 TGTATTGGATTAGAGG
1 TGTAATGGATTAGAGG
*
42540123 TGTAATGGAATAGAGG
1 TGTAATGGATTAGAGG
42540139 TGTAATGGA
1 TGTAATGGA
42540148 AAAGCTGTGT
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 39 1.00
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (16 bp):
TGTAATGGATTAGAGG
Found at i:42540414 original size:18 final size:17
Alignment explanation
Indices: 42540393--42540427 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
42540383 TTATTATTAA
*
42540393 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
42540411 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
42540428 TCTTAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:42541991 original size:12 final size:12
Alignment explanation
Indices: 42541974--42542004 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
42541964 GCCAATTTAT
42541974 TTCACTTCAATA
1 TTCACTTCAATA
42541986 TTCACTTCAATA
1 TTCACTTCAATA
42541998 TTCACTT
1 TTCACTT
42542005 AAGGCTAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.29, C:0.26, G:0.00, T:0.45
Consensus pattern (12 bp):
TTCACTTCAATA
Found at i:42567536 original size:14 final size:14
Alignment explanation
Indices: 42567510--42567547 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
42567500 ATATAAAACA
42567510 AATACATAA-ACAAT
1 AATA-ATAATACAAT
42567524 AATAATAATACAAT
1 AATAATAATACAAT
*
42567538 AATAAAAATA
1 AATAATAATA
42567548 AGTATGATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
13 4 0.18
14 18 0.82
ACGTcount: A:0.68, C:0.08, G:0.00, T:0.24
Consensus pattern (14 bp):
AATAATAATACAAT
Found at i:42569703 original size:30 final size:31
Alignment explanation
Indices: 42569667--42569728 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
42569657 ACTTGGATCA
* * *
42569667 ACTTAAAT-AAAATTTTTGAATAGTTCAGTG
1 ACTTAAATGAAAACTTTCGAATAATTCAGTG
*
42569697 ACTTAAATGTAAACTTTCGAATAATTCAGTG
1 ACTTAAATGAAAACTTTCGAATAATTCAGTG
42569728 A
1 A
42569729 TCATTTTGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 8 0.30
31 19 0.70
ACGTcount: A:0.40, C:0.10, G:0.13, T:0.37
Consensus pattern (31 bp):
ACTTAAATGAAAACTTTCGAATAATTCAGTG
Found at i:42573445 original size:123 final size:123
Alignment explanation
Indices: 42573221--42573467 Score: 433
Period size: 123 Copynumber: 2.0 Consensus size: 123
42573211 ATTAGCCTAA
* *
42573221 GTTGTCATATCTTCATTATCGGGCCAACCAGGCTTCAATTTGACAGGCTTCTCCAACAGCTTCTT
1 GTTGCCATATCTTCATTATCGGGCCAACCAGGCTTCAATCTGACAGGCTTCTCCAACAGCTTCTT
42573286 GAATCAGGCCAGTTCTTGCGGGCCAAATGATTCCCATCTAAACAATAGACCTCCATTG
66 GAATCAGGCCAGTTCTTGCGGGCCAAATGATTCCCATCTAAACAATAGACCTCCATTG
*
42573344 GTTGCCATATCTTCATTATCGGGCCAACCAGGCTTCAATCTGACAGGCTTCTCTAACAGCTTCTT
1 GTTGCCATATCTTCATTATCGGGCCAACCAGGCTTCAATCTGACAGGCTTCTCCAACAGCTTCTT
* *
42573409 GAATC-GAGCCAGTTCTTGCGGGCCAAATGATTCCCATCTAAATAATAGACCTCTATTG
66 GAATCAG-GCCAGTTCTTGCGGGCCAAATGATTCCCATCTAAACAATAGACCTCCATTG
42573467 G
1 G
42573468 ATGCATTTGG
Statistics
Matches: 118, Mismatches: 5, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
122 1 0.01
123 117 0.99
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.30
Consensus pattern (123 bp):
GTTGCCATATCTTCATTATCGGGCCAACCAGGCTTCAATCTGACAGGCTTCTCCAACAGCTTCTT
GAATCAGGCCAGTTCTTGCGGGCCAAATGATTCCCATCTAAACAATAGACCTCCATTG
Found at i:42582489 original size:12 final size:12
Alignment explanation
Indices: 42582474--42582499 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
42582464 CACAAGCATT
42582474 TTAACAAACACC
1 TTAACAAACACC
42582486 TTAACAAACACC
1 TTAACAAACACC
42582498 TT
1 TT
42582500 GGAGTCATAG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.31, G:0.00, T:0.23
Consensus pattern (12 bp):
TTAACAAACACC
Found at i:42584735 original size:79 final size:80
Alignment explanation
Indices: 42584600--42584758 Score: 248
Period size: 79 Copynumber: 2.0 Consensus size: 80
42584590 TTATTTTATT
* * *
42584600 ATTATTTGACATATAAATTTAGTCTATAAATAGGCTTTTTTACAACTTTAGAAAATACACCCATT
1 ATTATTTGACATATAAATTTAGCCTATAAATAGGCTATTTTACAACATTAGAAAATACACCCATT
* *
42584665 AGATATTAGAACTCA
66 AGAGACTAGAACTCA
* *
42584680 ATTATTTGACATATGAATTTAGCCTAT-AATAGGCTATTTTACAACATTAGAAAATACACTCATT
1 ATTATTTGACATATAAATTTAGCCTATAAATAGGCTATTTTACAACATTAGAAAATACACCCATT
42584744 AGAGACTAGAACTCA
66 AGAGACTAGAACTCA
42584759 TAACACATTT
Statistics
Matches: 72, Mismatches: 7, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
79 47 0.65
80 25 0.35
ACGTcount: A:0.40, C:0.14, G:0.10, T:0.35
Consensus pattern (80 bp):
ATTATTTGACATATAAATTTAGCCTATAAATAGGCTATTTTACAACATTAGAAAATACACCCATT
AGAGACTAGAACTCA
Found at i:42590030 original size:25 final size:25
Alignment explanation
Indices: 42589997--42590047 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
42589987 GGCGGTTCTG
42589997 ATGTGTGAAAAAGCTTCAGCAACAT
1 ATGTGTGAAAAAGCTTCAGCAACAT
42590022 ATGTGTGAAAAAGCTTCAGCAACAT
1 ATGTGTGAAAAAGCTTCAGCAACAT
42590047 A
1 A
42590048 ATGATGATGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.24
Consensus pattern (25 bp):
ATGTGTGAAAAAGCTTCAGCAACAT
Found at i:42591948 original size:15 final size:15
Alignment explanation
Indices: 42591928--42591958 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
42591918 TTGAATTTTG
42591928 AGTTAATTAAATTAA
1 AGTTAATTAAATTAA
42591943 AGTTAATTAAATTAA
1 AGTTAATTAAATTAA
42591958 A
1 A
42591959 TTATTTGAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (15 bp):
AGTTAATTAAATTAA
Found at i:42592170 original size:22 final size:20
Alignment explanation
Indices: 42592130--42592176 Score: 51
Period size: 19 Copynumber: 2.2 Consensus size: 20
42592120 AAAGATTAAA
42592130 AAAAATTAAAATAATTTTC-
1 AAAAATTAAAATAATTTTCT
*
42592149 AAAAATTCAAAATTTATATTTCT
1 AAAAATT-AAAA-TAAT-TTTCT
42592172 AAAAA
1 AAAAA
42592177 AATTATTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
19 7 0.30
20 4 0.17
21 3 0.13
22 4 0.17
23 5 0.22
ACGTcount: A:0.57, C:0.06, G:0.00, T:0.36
Consensus pattern (20 bp):
AAAAATTAAAATAATTTTCT
Found at i:42604854 original size:19 final size:19
Alignment explanation
Indices: 42604830--42604883 Score: 67
Period size: 18 Copynumber: 2.9 Consensus size: 19
42604820 CATTTTTTTT
42604830 TAATTTTATAAACTATTTA
1 TAATTTTATAAACTATTTA
* *
42604849 TAATTTTA-AAAGTTTTTA
1 TAATTTTATAAACTATTTA
*
42604867 TAATATT-TAAACTATTT
1 TAATTTTATAAACTATTT
42604884 GTTAACATGA
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
18 21 0.72
19 8 0.28
ACGTcount: A:0.41, C:0.04, G:0.02, T:0.54
Consensus pattern (19 bp):
TAATTTTATAAACTATTTA
Found at i:42604868 original size:18 final size:18
Alignment explanation
Indices: 42604824--42604877 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
42604814 GTAATTCATT
*
42604824 TTTTTTTAATTTTATAAAC
1 TTTTTATAATTTTA-AAAC
* *
42604843 TATTTATAATTTTAAAAG
1 TTTTTATAATTTTAAAAC
42604861 TTTTTATAATATTTAAA
1 TTTTTATAAT-TTTAAA
42604878 CTATTTGTTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
18 12 0.40
19 18 0.60
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (18 bp):
TTTTTATAATTTTAAAAC
Found at i:42605970 original size:23 final size:23
Alignment explanation
Indices: 42605940--42605990 Score: 93
Period size: 23 Copynumber: 2.2 Consensus size: 23
42605930 ACAAGCAATA
42605940 TGTAATATCCCGAAAATTACTAC
1 TGTAATATCCCGAAAATTACTAC
42605963 TGTAATATCCCGAAAATTACTAC
1 TGTAATATCCCGAAAATTACTAC
*
42605986 AGTAA
1 TGTAA
42605991 GAAAGTAGGT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.41, C:0.20, G:0.10, T:0.29
Consensus pattern (23 bp):
TGTAATATCCCGAAAATTACTAC
Found at i:42614073 original size:91 final size:86
Alignment explanation
Indices: 42613966--42614192 Score: 208
Period size: 91 Copynumber: 2.6 Consensus size: 86
42613956 AATAATTAAG
* * * * * * * *
42613966 TTTTTTTTTCATTTAATTGGGTACATGAATTTTTAAAATATATAAAAATACCCTAAAAATCTTTT
1 TTTTTTTTTCACTTAATTGAGTACATAAACTTTCAAAATACATAAAAAGACCAT-AAAA-C-TTT
*
42614031 TAGAAAAAGCAATTAAGCCCCTTCT
63 TAAAAAAAGCAATTAAGCCCCTT-T
** * *
42614056 TTTTTTGTTTCACTTAATTGAGTATTTAAACTTTCAAAATACATCAAAAGACCATTAAACTTTTA
1 TTTTTT-TTTCACTTAATTGAGTACATAAACTTTCAAAATACATAAAAAGACCATAAAACTTTTA
42614121 AAAAAAGCAATTAAGCCCC--T
65 AAAAAAGCAATTAAGCCCCTTT
* * ** * *
42614141 TTTTTTTGT-ACTAAATTGAGTATTTGAACTGTCAAAATACATAAAAATGACC
1 TTTTTTTTTCACTTAATTGAGTACATAAACTTTCAAAATACATAAAAA-GACC
42614193 CTTTGACCAT
Statistics
Matches: 117, Mismatches: 18, Indels: 10
0.81 0.12 0.07
Matches are distributed among these distances:
83 34 0.29
84 6 0.05
85 7 0.06
88 23 0.20
89 1 0.01
90 9 0.08
91 37 0.32
ACGTcount: A:0.39, C:0.14, G:0.08, T:0.39
Consensus pattern (86 bp):
TTTTTTTTTCACTTAATTGAGTACATAAACTTTCAAAATACATAAAAAGACCATAAAACTTTTAA
AAAAAGCAATTAAGCCCCTTT
Found at i:42614132 original size:88 final size:84
Alignment explanation
Indices: 42614028--42614192 Score: 233
Period size: 83 Copynumber: 1.9 Consensus size: 84
42614018 CTAAAAATCT
* * *
42614028 TTTTAGAAAAAGCAATTAAGCCCCTTCTTTTTTTGTTTCACTTAATTGAGTATTTAAACTTTCAA
1 TTTTAAAAAAAGCAATTAAGCCCC-T-TTTTTTTG--T-ACTAAATTGAGTATTTAAACTGTCAA
*
42614093 AATACATCAAAA-GACCATTAAAC
61 AATACATAAAAATGACCATTAAAC
*
42614116 TTTTAAAAAAAGCAATTAAGCCCCTTTTTTTTGTACTAAATTGAGTATTTGAACTGTCAAAATAC
1 TTTTAAAAAAAGCAATTAAGCCCCTTTTTTTTGTACTAAATTGAGTATTTAAACTGTCAAAATAC
42614181 ATAAAAATGACC
66 ATAAAAATGACC
42614193 CTTTGACCAT
Statistics
Matches: 71, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
83 34 0.48
84 5 0.07
86 8 0.11
87 1 0.01
88 23 0.32
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (84 bp):
TTTTAAAAAAAGCAATTAAGCCCCTTTTTTTTGTACTAAATTGAGTATTTAAACTGTCAAAATAC
ATAAAAATGACCATTAAAC
Found at i:42614360 original size:28 final size:28
Alignment explanation
Indices: 42614294--42614382 Score: 78
Period size: 28 Copynumber: 3.2 Consensus size: 28
42614284 CATGCGATAA
*
42614294 AAAAATT-AT-AAAAAT-AAAAATTATT
1 AAAAATTAATAAAAAATAAAAAAATATT
**
42614319 AAAGTTTAATAAAAAATAAAAAAATATT
1 AAAAATTAATAAAAAATAAAAAAATATT
*
42614347 AAAAATTAGA-AAAAAATTTATAAAAAACATT
1 AAAAATTA-ATAAAAAA--TA-AAAAAATATT
42614378 AAAAA
1 AAAAA
42614383 GACCCTTTAA
Statistics
Matches: 51, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
25 5 0.10
26 2 0.04
27 6 0.12
28 21 0.41
29 1 0.02
30 2 0.04
31 14 0.27
ACGTcount: A:0.70, C:0.01, G:0.02, T:0.27
Consensus pattern (28 bp):
AAAAATTAATAAAAAATAAAAAAATATT
Found at i:42614792 original size:12 final size:11
Alignment explanation
Indices: 42614754--42614795 Score: 50
Period size: 11 Copynumber: 3.7 Consensus size: 11
42614744 GAATTTTATA
42614754 TTTCTT-TACAT
1 TTTCTTATA-AT
*
42614765 TTTTTTATAAT
1 TTTCTTATAAT
42614776 TTTCTTATAACT
1 TTTCTTATAA-T
42614788 TTTCTTAT
1 TTTCTTAT
42614796 GACTATAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
11 16 0.59
12 11 0.41
ACGTcount: A:0.21, C:0.12, G:0.00, T:0.67
Consensus pattern (11 bp):
TTTCTTATAAT
Found at i:42614849 original size:19 final size:19
Alignment explanation
Indices: 42614827--42614868 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
42614817 TTTCTATATA
* *
42614827 TTTTATAAATTTTTACAAT
1 TTTTATAAAATTTTAAAAT
42614846 TTTTATAAAATTTTAAAAT
1 TTTTATAAAATTTTAAAAT
42614865 TTTT
1 TTTT
42614869 TTTACGATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTATAAAATTTTAAAAT
Found at i:42614868 original size:9 final size:10
Alignment explanation
Indices: 42614804--42614890 Score: 63
Period size: 10 Copynumber: 8.8 Consensus size: 10
42614794 ATGACTATAA
*
42614804 AAATTTTTCT
1 AAATTTTTAT
* *
42614814 ATATTTCTAT
1 AAATTTTTAT
*
42614824 ATA-TTTTAT
1 AAATTTTTAT
42614833 AAATTTTTA-
1 AAATTTTTAT
*
42614842 CAATTTTTAT
1 AAATTTTTAT
*
42614852 AAAATTTTA-
1 AAATTTTTAT
*
42614861 AAATTTTTTTT
1 AAA-TTTTTAT
*
42614872 ACGATTTTTAT
1 A-AATTTTTAT
42614883 AAATTTTT
1 AAATTTTT
42614891 GTTTCTAATT
Statistics
Matches: 59, Mismatches: 13, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
9 18 0.31
10 32 0.54
11 8 0.14
12 1 0.02
ACGTcount: A:0.34, C:0.05, G:0.01, T:0.60
Consensus pattern (10 bp):
AAATTTTTAT
Found at i:42614956 original size:28 final size:30
Alignment explanation
Indices: 42614908--42614965 Score: 102
Period size: 28 Copynumber: 2.0 Consensus size: 30
42614898 ATTTATAATA
42614908 AAATTTAAGTAATTTTTTATATTTTTATTT
1 AAATTTAAGTAATTTTTTATATTTTTATTT
42614938 AAATTTAA-TAA-TTTTTATATTTTTATTT
1 AAATTTAAGTAATTTTTTATATTTTTATTT
42614966 TTTACCATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
28 17 0.61
29 3 0.11
30 8 0.29
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (30 bp):
AAATTTAAGTAATTTTTTATATTTTTATTT
Found at i:42621548 original size:19 final size:18
Alignment explanation
Indices: 42621524--42621558 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
42621514 AAATACAAAT
42621524 TTAAAAACTAAAAAAAAA
1 TTAAAAACTAAAAAAAAA
42621542 TTAAAAACTAAAAAAAA
1 TTAAAAACTAAAAAAAA
42621559 TAAAAGGTCA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.77, C:0.06, G:0.00, T:0.17
Consensus pattern (18 bp):
TTAAAAACTAAAAAAAAA
Found at i:42621848 original size:15 final size:15
Alignment explanation
Indices: 42621828--42621860 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
42621818 TTAGGGTTAG
42621828 AGAAAAAGAAGAAGA
1 AGAAAAAGAAGAAGA
*
42621843 AGAAAAAGAAGGAGA
1 AGAAAAAGAAGAAGA
42621858 AGA
1 AGA
42621861 GGAAAAATGG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (15 bp):
AGAAAAAGAAGAAGA
Found at i:42622261 original size:36 final size:36
Alignment explanation
Indices: 42622221--42622289 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
42622211 GTAATATTAT
*
42622221 TGCTGGTATATTGTTGCTTATGTTGTTATACATGGC
1 TGCTGGTATATTATTGCTTATGTTGTTATACATGGC
42622257 TGCTGGTATATTATTGCTTATGTTGTTATACAT
1 TGCTGGTATATTATTGCTTATGTTGTTATACAT
42622290 TATTGCTTAT
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.19, C:0.10, G:0.22, T:0.49
Consensus pattern (36 bp):
TGCTGGTATATTATTGCTTATGTTGTTATACATGGC
Found at i:42622291 original size:22 final size:22
Alignment explanation
Indices: 42622266--42622311 Score: 92
Period size: 22 Copynumber: 2.1 Consensus size: 22
42622256 CTGCTGGTAT
42622266 ATTATTGCTTATGTTGTTATAC
1 ATTATTGCTTATGTTGTTATAC
42622288 ATTATTGCTTATGTTGTTATAC
1 ATTATTGCTTATGTTGTTATAC
42622310 AT
1 AT
42622312 GGCTGCTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.24, C:0.09, G:0.13, T:0.54
Consensus pattern (22 bp):
ATTATTGCTTATGTTGTTATAC
Found at i:42622299 original size:58 final size:58
Alignment explanation
Indices: 42622234--42622347 Score: 228
Period size: 58 Copynumber: 2.0 Consensus size: 58
42622224 TGGTATATTG
42622234 TTGCTTATGTTGTTATACATGGCTGCTGGTATATTATTGCTTATGTTGTTATACATTA
1 TTGCTTATGTTGTTATACATGGCTGCTGGTATATTATTGCTTATGTTGTTATACATTA
42622292 TTGCTTATGTTGTTATACATGGCTGCTGGTATATTATTGCTTATGTTGTTATACAT
1 TTGCTTATGTTGTTATACATGGCTGCTGGTATATTATTGCTTATGTTGTTATACAT
42622348 GGCATGGCTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.20, C:0.11, G:0.19, T:0.50
Consensus pattern (58 bp):
TTGCTTATGTTGTTATACATGGCTGCTGGTATATTATTGCTTATGTTGTTATACATTA
Found at i:42622318 original size:22 final size:22
Alignment explanation
Indices: 42622271--42622318 Score: 69
Period size: 22 Copynumber: 2.2 Consensus size: 22
42622261 GGTATATTAT
* *
42622271 TGCTTATGTTGTTATACATTAT
1 TGCTTATGTTGTTATACATGAC
*
42622293 TGCTTATGTTGTTATACATGGC
1 TGCTTATGTTGTTATACATGAC
42622315 TGCT
1 TGCT
42622319 GGTATATTAT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.19, C:0.12, G:0.19, T:0.50
Consensus pattern (22 bp):
TGCTTATGTTGTTATACATGAC
Found at i:42623941 original size:95 final size:92
Alignment explanation
Indices: 42623849--42624075 Score: 278
Period size: 95 Copynumber: 2.4 Consensus size: 92
42623839 ACATGCATAT
**
42623849 TATTAAAAAAATACTCGTTGCATGCATATT-AAAAAATAGCCAACAACATGTATATTAAAAAAAA
1 TATTAAAAAAATACTCACTGCATGCATATTAAAAAAATAGCCAACAACATGTATATT----AAAA
*
42623913 ACAGTCATACACACCAACAATCATTGCATGCA
62 ACAGTCATACACACCAACAATCACTGCAT-CA
* *
42623945 TATTATTAAAAAATACTCACTGCATGCATATTAAAAAAATAGTCAACAACATGTATATTAAAATC
1 TATTA--AAAAAATACTCACTGCATGCATATTAAAAAAATAGCCAACAACATGTATATTAAAAAC
42624010 AGTCATACACACCAACAATCACTGCATGCA
64 AGTCATACACACCAACAATCACTGCAT-CA
* ** *
42624040 TATT-AAAAAATAGTCAACAACATGTATATTAAAAAA
1 TATTAAAAAAATACTC-ACTGCATGCATATTAAAAAA
42624076 CATTCATACA
Statistics
Matches: 118, Mismatches: 9, Indels: 11
0.86 0.07 0.08
Matches are distributed among these distances:
92 10 0.08
93 17 0.14
95 38 0.32
96 5 0.04
98 23 0.19
99 25 0.21
ACGTcount: A:0.49, C:0.18, G:0.07, T:0.26
Consensus pattern (92 bp):
TATTAAAAAAATACTCACTGCATGCATATTAAAAAAATAGCCAACAACATGTATATTAAAAACAG
TCATACACACCAACAATCACTGCATCA
Found at i:42623949 original size:99 final size:95
Alignment explanation
Indices: 42623829--42624044 Score: 317
Period size: 99 Copynumber: 2.2 Consensus size: 95
42623819 ACCCTTAAAA
* * **
42623829 AACAACCATTACATGCATATTATTAAAAAAATACTCGTTGCATGCATATT-AAAAAATAGCCAAC
1 AACAATCATTGCATGCATATTATT-AAAAAATACTCACTGCATGCATATTAAAAAAATAGCCAAC
42623893 AACATGTATATTAAAAAAAAACAGTCATACACACC
65 AACATGTATATT----AAAAACAGTCATACACACC
*
42623928 AACAATCATTGCATGCATATTATTAAAAAATACTCACTGCATGCATATTAAAAAAATAGTCAACA
1 AACAATCATTGCATGCATATTATTAAAAAATACTCACTGCATGCATATTAAAAAAATAGCCAACA
*
42623993 ACATGTATATTAAAATCAGTCATACACACC
66 ACATGTATATTAAAAACAGTCATACACACC
*
42624023 AACAATCACTGCATGCATATTA
1 AACAATCATTGCATGCATATTA
42624045 AAAAATAGTC
Statistics
Matches: 109, Mismatches: 7, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
95 39 0.36
98 23 0.21
99 47 0.43
ACGTcount: A:0.47, C:0.19, G:0.07, T:0.26
Consensus pattern (95 bp):
AACAATCATTGCATGCATATTATTAAAAAATACTCACTGCATGCATATTAAAAAAATAGCCAACA
ACATGTATATTAAAAACAGTCATACACACC
Found at i:42623997 original size:27 final size:26
Alignment explanation
Indices: 42623939--42624007 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 26
42623929 ACAATCATTG
**
42623939 CATGCATATTATTAAAAAATACTCACTG
1 CATGCATATTA--AAAAAATACTCACAA
*
42623967 CATGCATATTAAAAAAATAGTCAACAA
1 CATGCATATTAAAAAAATACTC-ACAA
*
42623994 CATGTATATTAAAA
1 CATGCATATTAAAA
42624008 TCAGTCATAC
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
26 10 0.28
27 15 0.42
28 11 0.31
ACGTcount: A:0.49, C:0.14, G:0.07, T:0.29
Consensus pattern (26 bp):
CATGCATATTAAAAAAATACTCACAA
Found at i:42624007 original size:26 final size:25
Alignment explanation
Indices: 42623948--42624007 Score: 66
Period size: 26 Copynumber: 2.3 Consensus size: 25
42623938 GCATGCATAT
**
42623948 TATTAAAAAATACTCACTGCATGCA
1 TATTAAAAAATACTCACAACATGCA
* *
42623973 TATTAAAAAAATAGTCAACAACATGTA
1 TATT-AAAAAATACTC-ACAACATGCA
42624000 TATTAAAA
1 TATTAAAA
42624008 TCAGTCATAC
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
25 4 0.14
26 14 0.48
27 11 0.38
ACGTcount: A:0.52, C:0.13, G:0.07, T:0.28
Consensus pattern (25 bp):
TATTAAAAAATACTCACAACATGCA
Found at i:42624039 original size:67 final size:68
Alignment explanation
Indices: 42623961--42624116 Score: 226
Period size: 67 Copynumber: 2.3 Consensus size: 68
42623951 TAAAAAATAC
* **
42623961 TCACTGCATGCATATTAAAAAAATAGTCAACAACATGTATATT-AAAATCAGTCATACACACCAA
1 TCACTGCATGCATATTAAAAAAATAGTCAACAACATGTATATTAAAAAACAGTCATACACAAAAA
42624025 CAA
66 CAA
*
42624028 TCACTGCATGCATATT-AAAAAATAGTCAACAACATGTATATTAAAAAACATTCATACACAAAAA
1 TCACTGCATGCATATTAAAAAAATAGTCAACAACATGTATATTAAAAAACAGTCATACACAAAAA
* *
42624092 TAG
66 CAA
* *
42624095 TCACTACATGCAAATTAAAAAA
1 TCACTGCATGCATATTAAAAAA
42624117 CACTCACTAA
Statistics
Matches: 79, Mismatches: 8, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
66 26 0.33
67 48 0.61
68 5 0.06
ACGTcount: A:0.50, C:0.19, G:0.07, T:0.24
Consensus pattern (68 bp):
TCACTGCATGCATATTAAAAAAATAGTCAACAACATGTATATTAAAAAACAGTCATACACAAAAA
CAA
Found at i:42625814 original size:15 final size:15
Alignment explanation
Indices: 42625796--42625825 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
42625786 CTTTCAAATG
*
42625796 CATCATTACCAGACA
1 CATCACTACCAGACA
42625811 CATCACTACCAGACA
1 CATCACTACCAGACA
42625826 TTTATTATTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.40, C:0.37, G:0.07, T:0.17
Consensus pattern (15 bp):
CATCACTACCAGACA
Found at i:42626004 original size:61 final size:62
Alignment explanation
Indices: 42625929--42626062 Score: 218
Period size: 62 Copynumber: 2.2 Consensus size: 62
42625919 CCATTTCTGT
42625929 CAGACAATAACCAATAC-AAAATAA-TTTGATACAAAAACAACCATTTCTGTCATGCACATGA
1 CAGACAATAACCAATACAAAAATAATTTTG-TACAAAAACAACCATTTCTGTCATGCACATGA
* * *
42625990 CAGACAATAACCAATACAAAAATAATTTTGTACAAACACAACCATTTTTGTCATGCACATGG
1 CAGACAATAACCAATACAAAAATAATTTTGTACAAAAACAACCATTTCTGTCATGCACATGA
42626052 CAGACAATAAC
1 CAGACAATAAC
42626063 AGACAATAAC
Statistics
Matches: 68, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
61 17 0.25
62 47 0.69
63 4 0.06
ACGTcount: A:0.46, C:0.22, G:0.09, T:0.23
Consensus pattern (62 bp):
CAGACAATAACCAATACAAAAATAATTTTGTACAAAAACAACCATTTCTGTCATGCACATGA
Found at i:42626330 original size:6 final size:6
Alignment explanation
Indices: 42626321--42626390 Score: 77
Period size: 6 Copynumber: 11.7 Consensus size: 6
42626311 AAATAACCCT
* ** *
42626321 AAATCG AAATCA AAATCA AAATCA AAATCA AAATCA AAATTG AAATCG
1 AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA AAATCA
* **
42626369 AAATTA AAATTG AAATCA AAAT
1 AAATCA AAATCA AAATCA AAAT
42626391 TGAAATCAGT
Statistics
Matches: 55, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 55 1.00
ACGTcount: A:0.61, C:0.11, G:0.06, T:0.21
Consensus pattern (6 bp):
AAATCA
Found at i:42626391 original size:12 final size:12
Alignment explanation
Indices: 42626299--42626398 Score: 78
Period size: 12 Copynumber: 8.5 Consensus size: 12
42626289 ATAGCAAATA
42626299 AAATCAAAATCG
1 AAATCAAAATCG
** *
42626311 AAAT--AACCCT
1 AAATCAAAATCG
* *
42626321 AAATCGAAATCA
1 AAATCAAAATCG
*
42626333 AAATCAAAATCA
1 AAATCAAAATCG
*
42626345 AAATCAAAATCA
1 AAATCAAAATCG
**
42626357 AAATTGAAATCG
1 AAATCAAAATCG
* *
42626369 AAATTAAAATTG
1 AAATCAAAATCG
*
42626381 AAATCAAAATTG
1 AAATCAAAATCG
42626393 AAATCA
1 AAATCA
42626399 GTGAGTGTTT
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
10 7 0.10
12 66 0.90
ACGTcount: A:0.59, C:0.14, G:0.06, T:0.21
Consensus pattern (12 bp):
AAATCAAAATCG
Found at i:42626396 original size:18 final size:18
Alignment explanation
Indices: 42626294--42626390 Score: 101
Period size: 18 Copynumber: 5.6 Consensus size: 18
42626284 CATTAATAGC
42626294 AAAT-AAAATCAAAATCG
1 AAATCAAAATCAAAATCG
** *
42626311 AAAT--AACCCTAAATCG
1 AAATCAAAATCAAAATCG
*
42626327 AAATCAAAATCAAAATCA
1 AAATCAAAATCAAAATCG
*
42626345 AAATCAAAATCAAAATTG
1 AAATCAAAATCAAAATCG
* * *
42626363 AAATCGAAATTAAAATTG
1 AAATCAAAATCAAAATCG
42626381 AAATCAAAAT
1 AAATCAAAAT
42626391 TGAAATCAGT
Statistics
Matches: 66, Mismatches: 12, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
16 13 0.20
17 4 0.06
18 49 0.74
ACGTcount: A:0.61, C:0.13, G:0.05, T:0.21
Consensus pattern (18 bp):
AAATCAAAATCAAAATCG
Found at i:42626502 original size:16 final size:16
Alignment explanation
Indices: 42626481--42626517 Score: 65
Period size: 16 Copynumber: 2.3 Consensus size: 16
42626471 ACCAAATTTG
*
42626481 AAATTGGAATAACCCT
1 AAATTGAAATAACCCT
42626497 AAATTGAAATAACCCT
1 AAATTGAAATAACCCT
42626513 AAATT
1 AAATT
42626518 CAAAAAATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.49, C:0.16, G:0.08, T:0.27
Consensus pattern (16 bp):
AAATTGAAATAACCCT
Found at i:42626956 original size:21 final size:20
Alignment explanation
Indices: 42626930--42626972 Score: 68
Period size: 21 Copynumber: 2.1 Consensus size: 20
42626920 AACGTGGCAT
*
42626930 GTTAACTTGCCACATCAGCTG
1 GTTAACTTGACACATCAG-TG
42626951 GTTAACTTGACACATCAGTG
1 GTTAACTTGACACATCAGTG
42626971 GT
1 GT
42626973 CCCATTAACA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.26, C:0.23, G:0.21, T:0.30
Consensus pattern (20 bp):
GTTAACTTGACACATCAGTG
Found at i:42634118 original size:19 final size:19
Alignment explanation
Indices: 42634082--42634119 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
42634072 TTTTTATAAG
*
42634082 GGTGTTTTTATTTTTTGTT
1 GGTGTTTTTATTTGTTGTT
42634101 GGTG-TTTTATGTTGTTGTT
1 GGTGTTTTTAT-TTGTTGTT
42634120 TCGATGATGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.05, C:0.00, G:0.26, T:0.68
Consensus pattern (19 bp):
GGTGTTTTTATTTGTTGTT
Found at i:42651228 original size:11 final size:11
Alignment explanation
Indices: 42651212--42651237 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
42651202 AGTAAAACTG
42651212 TTATGTTATTA
1 TTATGTTATTA
42651223 TTATGTTATTA
1 TTATGTTATTA
42651234 TTAT
1 TTAT
42651238 TTTAATGTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.27, C:0.00, G:0.08, T:0.65
Consensus pattern (11 bp):
TTATGTTATTA
Found at i:42654900 original size:25 final size:25
Alignment explanation
Indices: 42654866--42654913 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
42654856 TACAGTTATC
42654866 TGATCAAGTGACAAAGTGATAAGCG
1 TGATCAAGTGACAAAGTGATAAGCG
42654891 TGATCAAGTGACAAAGTGATAAG
1 TGATCAAGTGACAAAGTGATAAG
42654914 TGGTAGCCTA
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:0.42, C:0.10, G:0.27, T:0.21
Consensus pattern (25 bp):
TGATCAAGTGACAAAGTGATAAGCG
Found at i:42657846 original size:18 final size:18
Alignment explanation
Indices: 42657819--42657854 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
42657809 CTCGCAGTCC
42657819 CCATAAAAATCGTTTACA
1 CCATAAAAATCGTTTACA
*
42657837 CCATAGAAATCGTTTACA
1 CCATAAAAATCGTTTACA
42657855 ACTATCAGCT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.22, G:0.08, T:0.28
Consensus pattern (18 bp):
CCATAAAAATCGTTTACA
Found at i:42662988 original size:17 final size:16
Alignment explanation
Indices: 42662957--42663000 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
42662947 GATTTATTTA
42662957 ATAATATAATATCATT
1 ATAATATAATATCATT
*
42662973 ATAATTTAATTATCATT
1 ATAATATAA-TATCATT
*
42662990 AATTATATAAT
1 -ATAATATAAT
42663001 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
16 8 0.35
17 8 0.35
18 7 0.30
ACGTcount: A:0.48, C:0.05, G:0.00, T:0.48
Consensus pattern (16 bp):
ATAATATAATATCATT
Found at i:42663797 original size:29 final size:25
Alignment explanation
Indices: 42663732--42663785 Score: 101
Period size: 24 Copynumber: 2.2 Consensus size: 25
42663722 TTGGTAACTA
42663732 ATCTTAGAAGATAGAATAGAATCAT
1 ATCTTAGAAGATAGAATAGAATCAT
42663757 ATCTTAGAAGATA-AATAGAATCAT
1 ATCTTAGAAGATAGAATAGAATCAT
42663781 ATCTT
1 ATCTT
42663786 GTAAGATTAG
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 16 0.55
25 13 0.45
ACGTcount: A:0.46, C:0.09, G:0.13, T:0.31
Consensus pattern (25 bp):
ATCTTAGAAGATAGAATAGAATCAT
Found at i:42669668 original size:17 final size:17
Alignment explanation
Indices: 42669631--42669669 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
42669621 CCATATTATT
* *
42669631 TCTTTTGTTTCTTTTCC
1 TCTTTTGTTTCTTCTCA
*
42669648 TCTTTTGTTTCTTCTGA
1 TCTTTTGTTTCTTCTCA
42669665 TCTTT
1 TCTTT
42669670 GGTTACCCTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.03, C:0.21, G:0.08, T:0.69
Consensus pattern (17 bp):
TCTTTTGTTTCTTCTCA
Found at i:42670040 original size:19 final size:16
Alignment explanation
Indices: 42670018--42670071 Score: 54
Period size: 18 Copynumber: 3.0 Consensus size: 16
42670008 CTGTGATTGA
42670018 ATTTTTGTAAATTCAATAT
1 ATTTTT-TAAATT--ATAT
42670037 ATTTTATTAAATTATAT
1 ATTTT-TTAAATTATAT
42670054 ATTTTTATTAAATTATAT
1 A-TTTT-TTAAATTATAT
42670072 TTAATAATAA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
17 5 0.15
18 16 0.48
19 11 0.33
20 1 0.03
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (16 bp):
ATTTTTTAAATTATAT
Found at i:42670059 original size:18 final size:17
Alignment explanation
Indices: 42670033--42670071 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 17
42670023 TGTAAATTCA
42670033 ATATATTTTATTAAATT
1 ATATATTTTATTAAATT
42670050 ATATATTTTTATTAAATT
1 ATATA-TTTTATTAAATT
42670068 ATAT
1 ATAT
42670072 TTAATAATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATATATTTTATTAAATT
Found at i:42670261 original size:21 final size:21
Alignment explanation
Indices: 42670235--42670286 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
42670225 ACCGATGTTT
* *
42670235 CTAATCTCACTGCTACATTATC
1 CTAATCTCACAGCTACAGTA-C
42670257 C-AATCTCACAGCTACAGTAC
1 CTAATCTCACAGCTACAGTAC
42670277 CTAATCTCAC
1 CTAATCTCAC
42670287 CGCCACCGCT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 2 0.07
21 24 0.89
22 1 0.04
ACGTcount: A:0.31, C:0.35, G:0.06, T:0.29
Consensus pattern (21 bp):
CTAATCTCACAGCTACAGTAC
Found at i:42671401 original size:15 final size:15
Alignment explanation
Indices: 42671378--42671408 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
42671368 TAAATATTTT
42671378 TATAAAATTCTAAAA
1 TATAAAATTCTAAAA
*
42671393 TATATAATTCTAAAA
1 TATAAAATTCTAAAA
42671408 T
1 T
42671409 TCTAAAAAGG
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.06, G:0.00, T:0.39
Consensus pattern (15 bp):
TATAAAATTCTAAAA
Found at i:42673332 original size:84 final size:84
Alignment explanation
Indices: 42673191--42673357 Score: 325
Period size: 84 Copynumber: 2.0 Consensus size: 84
42673181 GTCAAATCAG
42673191 TACCTCTAGGAAATCTAAAGCAGCCGAGGCAGAATTGAACCCTGTTCTTGGATCTTGACTAGAAA
1 TACCTCTAGGAAATCTAAAGCAGCCGAGGCAGAATTGAACCCTGTTCTTGGATCTTGACTAGAAA
42673256 TTCTTTCATTGCCTGTTTA
66 TTCTTTCATTGCCTGTTTA
*
42673275 TACCTTTAGGAAATCTAAAGCAGCCGAGGCAGAATTGAACCCTGTTCTTGGATCTTGACTAGAAA
1 TACCTCTAGGAAATCTAAAGCAGCCGAGGCAGAATTGAACCCTGTTCTTGGATCTTGACTAGAAA
42673340 TTCTTTCATTGCCTGTTT
66 TTCTTTCATTGCCTGTTT
42673358 CTGACAACCG
Statistics
Matches: 82, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
84 82 1.00
ACGTcount: A:0.27, C:0.21, G:0.19, T:0.33
Consensus pattern (84 bp):
TACCTCTAGGAAATCTAAAGCAGCCGAGGCAGAATTGAACCCTGTTCTTGGATCTTGACTAGAAA
TTCTTTCATTGCCTGTTTA
Found at i:42676695 original size:18 final size:18
Alignment explanation
Indices: 42676672--42676712 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
42676662 CCATCACTTT
42676672 CAACAACAACACCAGCAG
1 CAACAACAACACCAGCAG
* *
42676690 CAACAACAACAGCATCAG
1 CAACAACAACACCAGCAG
42676708 CAACA
1 CAACA
42676713 GCTGTGGCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.51, C:0.37, G:0.10, T:0.02
Consensus pattern (18 bp):
CAACAACAACACCAGCAG
Found at i:42686412 original size:20 final size:18
Alignment explanation
Indices: 42686365--42686412 Score: 51
Period size: 20 Copynumber: 2.4 Consensus size: 18
42686355 AAAAAACTTG
42686365 TTATTTTTGTTGTTGTTT
1 TTATTTTTGTTGTTGTTT
*
42686383 TTATTGTTTTGTTGCTATTTTT
1 TTA-T-TTTTGTTG-T-TGTTT
42686405 TTATTTTT
1 TTATTTTT
42686413 TTCACCATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
18 3 0.12
19 1 0.04
20 12 0.48
21 2 0.08
22 7 0.28
ACGTcount: A:0.08, C:0.02, G:0.12, T:0.77
Consensus pattern (18 bp):
TTATTTTTGTTGTTGTTT
Found at i:42694816 original size:47 final size:47
Alignment explanation
Indices: 42694747--42694933 Score: 374
Period size: 47 Copynumber: 4.0 Consensus size: 47
42694737 CCCATTTGAA
42694747 CCTCAAGCCATTCAAGCTTCTCTGGACGCAAAAGAGAATAAAACTAT
1 CCTCAAGCCATTCAAGCTTCTCTGGACGCAAAAGAGAATAAAACTAT
42694794 CCTCAAGCCATTCAAGCTTCTCTGGACGCAAAAGAGAATAAAACTAT
1 CCTCAAGCCATTCAAGCTTCTCTGGACGCAAAAGAGAATAAAACTAT
42694841 CCTCAAGCCATTCAAGCTTCTCTGGACGCAAAAGAGAATAAAACTAT
1 CCTCAAGCCATTCAAGCTTCTCTGGACGCAAAAGAGAATAAAACTAT
42694888 CCTCAAGCCATTCAAGCTTCTCTGGACGCAAAAGAGAATAAAACTA
1 CCTCAAGCCATTCAAGCTTCTCTGGACGCAAAAGAGAATAAAACTA
42694934 GGCAAATGAA
Statistics
Matches: 140, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 140 1.00
ACGTcount: A:0.39, C:0.26, G:0.15, T:0.21
Consensus pattern (47 bp):
CCTCAAGCCATTCAAGCTTCTCTGGACGCAAAAGAGAATAAAACTAT
Done.