Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr1
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: 37323695
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.32
Warning! 1370832 characters in sequence are not A, C, G, or T
File 24 of 93
Found at i:10439195 original size:22 final size:22
Alignment explanation
Indices: 10439171--10439244 Score: 77
Period size: 22 Copynumber: 3.5 Consensus size: 22
10439161 CTGAATTCAG
**
10439171 CTGCAGCGAGAATGGATTCTTG
1 CTGCAGCGAGAATGGATTCTCA
10439193 CTGCAGC---AA-GGAATT-TCA
1 CTGCAGCGAGAATGG-ATTCTCA
*
10439211 CTGCAGCGAAAATGGATTCTCA
1 CTGCAGCGAGAATGGATTCTCA
10439233 CTGCAGCGAGAA
1 CTGCAGCGAGAA
10439245 ATTCTCAAGT
Statistics
Matches: 43, Mismatches: 3, Indels: 12
0.74 0.05 0.21
Matches are distributed among these distances:
18 10 0.23
19 5 0.12
21 5 0.12
22 23 0.53
ACGTcount: A:0.30, C:0.22, G:0.27, T:0.22
Consensus pattern (22 bp):
CTGCAGCGAGAATGGATTCTCA
Found at i:10439250 original size:19 final size:19
Alignment explanation
Indices: 10439193--10439251 Score: 57
Period size: 22 Copynumber: 3.0 Consensus size: 19
10439183 TGGATTCTTG
* *
10439193 CTGCAGCAAGGAATT-TCA
1 CTGCAGCGAGAAATTCTCA
*
10439211 CTGCAGCGAAAATGGATTCTCA
1 CTGCAGCGAGAA---ATTCTCA
10439233 CTGCAGCGAGAAATTCTCA
1 CTGCAGCGAGAAATTCTCA
10439252 AGTGGTTCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
18 9 0.27
19 7 0.21
21 3 0.09
22 14 0.42
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (19 bp):
CTGCAGCGAGAAATTCTCA
Found at i:10440796 original size:14 final size:14
Alignment explanation
Indices: 10440779--10440809 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
10440769 TAAATTTGAT
10440779 TTTTTTTTAAAAAA
1 TTTTTTTTAAAAAA
*
10440793 TTTTTTTTAAAGAA
1 TTTTTTTTAAAAAA
10440807 TTT
1 TTT
10440810 CTTAAAATCT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.61
Consensus pattern (14 bp):
TTTTTTTTAAAAAA
Found at i:10443992 original size:15 final size:15
Alignment explanation
Indices: 10443972--10444002 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
10443962 ACTACCCAAA
*
10443972 AGAATAAATATTTAT
1 AGAATAAATATATAT
10443987 AGAATAAATATATAT
1 AGAATAAATATATAT
10444002 A
1 A
10444003 TTAAAAGGTT
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:0.58, C:0.00, G:0.06, T:0.35
Consensus pattern (15 bp):
AGAATAAATATATAT
Found at i:10447318 original size:16 final size:16
Alignment explanation
Indices: 10447297--10447328 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
10447287 CTATTCTGTG
10447297 GGAATAGAATAAAATA
1 GGAATAGAATAAAATA
*
10447313 GGAATAGAATAGAATA
1 GGAATAGAATAAAATA
10447329 ATTATTACTT
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:0.59, C:0.00, G:0.22, T:0.19
Consensus pattern (16 bp):
GGAATAGAATAAAATA
Found at i:10447741 original size:22 final size:20
Alignment explanation
Indices: 10447698--10447739 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
10447688 AAGCTAATTC
10447698 TTCATATATTATGAATCATT
1 TTCATATATTATGAATCATT
10447718 TTCATATATTATGAATCATT
1 TTCATATATTATGAATCATT
10447738 TT
1 TT
10447740 TTTCTAAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.33, C:0.10, G:0.05, T:0.52
Consensus pattern (20 bp):
TTCATATATTATGAATCATT
Found at i:10453961 original size:24 final size:24
Alignment explanation
Indices: 10453922--10453970 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
10453912 CCCAAACAGT
*
10453922 GGAAGAGTGGCGGAGAGAAAGAGG
1 GGAAGAGCGGCGGAGAGAAAGAGG
*
10453946 GGAAGAGCGGCTGAGAGAAAGAGG
1 GGAAGAGCGGCGGAGAGAAAGAGG
10453970 G
1 G
10453971 AAAGGAGGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.37, C:0.06, G:0.53, T:0.04
Consensus pattern (24 bp):
GGAAGAGCGGCGGAGAGAAAGAGG
Found at i:10453984 original size:23 final size:24
Alignment explanation
Indices: 10453934--10453986 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
10453924 AAGAGTGGCG
* * **
10453934 GAGAGAAAGAGGGGAAGAGCGGCT
1 GAGAGAAAGAGGGAAAGAGAGGAA
10453958 GAGAGAAAGAGGGAAAG-GAGGAA
1 GAGAGAAAGAGGGAAAGAGAGGAA
10453981 GAGAGA
1 GAGAGA
10453987 GAGAAAAAAA
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
23 9 0.36
24 16 0.64
ACGTcount: A:0.45, C:0.04, G:0.49, T:0.02
Consensus pattern (24 bp):
GAGAGAAAGAGGGAAAGAGAGGAA
Found at i:10460393 original size:47 final size:47
Alignment explanation
Indices: 10460342--10460432 Score: 137
Period size: 47 Copynumber: 1.9 Consensus size: 47
10460332 CAACATGGTA
*
10460342 GGAATGTGTGACACGGCAAGGTTCAGAGTTTGTAACACGCCATGGAG
1 GGAATCTGTGACACGGCAAGGTTCAGAGTTTGTAACACGCCATGGAG
* * * *
10460389 GGAATCTGTGATATGGCAGGGTTCAGAGTTTGTGACACGCCATG
1 GGAATCTGTGACACGGCAAGGTTCAGAGTTTGTAACACGCCATG
10460433 CAAAGAATCG
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
47 39 1.00
ACGTcount: A:0.25, C:0.16, G:0.34, T:0.24
Consensus pattern (47 bp):
GGAATCTGTGACACGGCAAGGTTCAGAGTTTGTAACACGCCATGGAG
Found at i:10460441 original size:47 final size:47
Alignment explanation
Indices: 10460356--10460460 Score: 147
Period size: 47 Copynumber: 2.2 Consensus size: 47
10460346 TGTGTGACAC
* * ** *
10460356 GGCAAGGTTCAGAGTTTGTAACACGCCATGGAGGGAATCTGTGATAT
1 GGCAGGGTTCAGAGTTTGTAACACGCCATGCAAAGAATCGGTGATAT
*
10460403 GGCAGGGTTCAGAGTTTGTGACACGCCATGCAAAGAATCGGTGATAT
1 GGCAGGGTTCAGAGTTTGTAACACGCCATGCAAAGAATCGGTGATAT
*
10460450 GGTAGGGTTCA
1 GGCAGGGTTCA
10460461 CTATGACATG
Statistics
Matches: 51, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
47 51 1.00
ACGTcount: A:0.27, C:0.15, G:0.33, T:0.25
Consensus pattern (47 bp):
GGCAGGGTTCAGAGTTTGTAACACGCCATGCAAAGAATCGGTGATAT
Found at i:10460494 original size:114 final size:114
Alignment explanation
Indices: 10460350--10460560 Score: 296
Period size: 114 Copynumber: 1.9 Consensus size: 114
10460340 TAGGAATGTG
* * * * * * *
10460350 TGACACGGCAAGGTTCAGAGTTTGTAACACGCCATGGAGGGAATCTGTGATATGGCAGGGTTCAG
1 TGACACGGCAAGGTTCAGAGTTTATAACACGCCATAGAGGGAATCTATGATACGACAGCGTTCAA
*
10460415 AGTTTGTGACACGCCATGCAAAGAATCGGTGATATGGTAGGGTTCACTA
66 AGTTTGTGACACACCATGCAAAGAATCGGTGATATGGTAGGGTTCACTA
* * *
10460464 TGACATGGCAGGGTTCAGAGTTTATGACACGCCATAGAGGGAATCTATGATACGACAGCGTTCAA
1 TGACACGGCAAGGTTCAGAGTTTATAACACGCCATAGAGGGAATCTATGATACGACAGCGTTCAA
* * *
10460529 AGTTTGTGACACACCATGGAAGGAATCTGTGA
66 AGTTTGTGACACACCATGCAAAGAATCGGTGA
10460561 CACTACAGGA
Statistics
Matches: 83, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
114 83 1.00
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (114 bp):
TGACACGGCAAGGTTCAGAGTTTATAACACGCCATAGAGGGAATCTATGATACGACAGCGTTCAA
AGTTTGTGACACACCATGCAAAGAATCGGTGATATGGTAGGGTTCACTA
Found at i:10460527 original size:67 final size:67
Alignment explanation
Indices: 10460401--10460527 Score: 157
Period size: 67 Copynumber: 1.9 Consensus size: 67
10460391 AATCTGTGAT
* * * ** *
10460401 ATGGCAGGGTTCAGAGTTTGTGACACGCCATGCAAAGAATCGGTGATATGGTAGGGTTCACTATG
1 ATGGCAGGGTTCAGAGTTTATGACACGCCATGCAAAGAATCGATGATACGACAGCGTTCACTATG
10460466 AC
66 AC
** *
10460468 ATGGCAGGGTTCAGAGTTTATGACACGCCATAG-AGGGAATCTATGATACGACAGCGTTCA
1 ATGGCAGGGTTCAGAGTTTATGACACGCCAT-GCAAAGAATCGATGATACGACAGCGTTCA
10460528 AAGTTTGTGA
Statistics
Matches: 50, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
67 49 0.98
68 1 0.02
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.24
Consensus pattern (67 bp):
ATGGCAGGGTTCAGAGTTTATGACACGCCATGCAAAGAATCGATGATACGACAGCGTTCACTATG
AC
Found at i:10460533 original size:47 final size:46
Alignment explanation
Indices: 10460461--10460688 Score: 197
Period size: 47 Copynumber: 4.8 Consensus size: 46
10460451 GTAGGGTTCA
* * * *
10460461 CTATGACATGGCAGGGTTCAGAGTTTATGACACGCCATAGAGGGAAT
1 CTATGACACGACA-GGTTCAGAGTTTGTGACACGCCATGGAGGGAAT
* * * *
10460508 CTATGATACGACAGCGTTCAAAGTTTGTGACACACCATGGAAGGAAT
1 CTATGACACGACAG-GTTCAGAGTTTGTGACACGCCATGGAGGGAAT
* *
10460555 CTGTGACACTACAGGATTCAGAGTTTGTGACACGCCATGGAGGGAAT
1 CTATGACACGACAGG-TTCAGAGTTTGTGACACGCCATGGAGGGAAT
* * * * **
10460602 CTGTGACAATG-CAGGGTTCAGAGTTTGTCAGAATCCATGGAGGGAAT
1 CTATGAC-ACGACA-GGTTCAGAGTTTGTGACACGCCATGGAGGGAAT
* * * * * *
10460649 CTGTGACATGGCAAGGTTTAGAGTGTGTGACACGGCATGG
1 CTATGACACGAC-AGGTTCAGAGTTTGTGACACGCCATGG
10460689 CTTGAACATG
Statistics
Matches: 148, Mismatches: 27, Indels: 12
0.79 0.14 0.06
Matches are distributed among these distances:
46 5 0.03
47 139 0.94
48 4 0.03
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (46 bp):
CTATGACACGACAGGTTCAGAGTTTGTGACACGCCATGGAGGGAAT
Found at i:10460672 original size:94 final size:94
Alignment explanation
Indices: 10460464--10460688 Score: 251
Period size: 94 Copynumber: 2.4 Consensus size: 94
10460454 GGGTTCACTA
* * * *
10460464 TGACATGGCAGGGTTCAGAGTTTATGACACGCCATAGAGGGAATCTATGATACGACAGCGTTCAA
1 TGACATGGCAAGGTTCAGAGTTTGTGACACGCCATGGAGGGAATCTATGAAACGACAGCGTTCAA
*
10460529 AGTTTGTGACACACCATGGAAGGAATCTG
66 AGTTTGTCACACACCATGGAAGGAATCTG
* * * *
10460558 TGACACT-AC-AGGATTCAGAGTTTGTGACACGCCATGGAGGGAATCTGTGACAATG-CAGGGTT
1 TGACA-TGGCAAGG-TTCAGAGTTTGTGACACGCCATGGAGGGAATCTATGA-AACGACAGCGTT
* * *
10460620 CAGAGTTTGTCAGA-ATCCATGGAGGGAATCTG
63 CAAAGTTTGTCACACA-CCATGGAAGGAATCTG
* * *
10460652 TGACATGGCAAGGTTTAGAGTGTGTGACACGGCATGG
1 TGACATGGCAAGGTTCAGAGTTTGTGACACGCCATGG
10460689 CTTGAACATG
Statistics
Matches: 109, Mismatches: 16, Indels: 12
0.80 0.12 0.09
Matches are distributed among these distances:
93 4 0.04
94 99 0.91
95 6 0.06
ACGTcount: A:0.28, C:0.17, G:0.31, T:0.24
Consensus pattern (94 bp):
TGACATGGCAAGGTTCAGAGTTTGTGACACGCCATGGAGGGAATCTATGAAACGACAGCGTTCAA
AGTTTGTCACACACCATGGAAGGAATCTG
Found at i:10460704 original size:23 final size:23
Alignment explanation
Indices: 10460674--10460717 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
10460664 GTTTAGAGTG
*
10460674 TGTGACACGGCATGGCTTGAACA
1 TGTGACACGACATGGCTTGAACA
*
10460697 TGTGACACGACATGGTTTGAA
1 TGTGACACGACATGGCTTGAA
10460718 AAAGGAAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.25
Consensus pattern (23 bp):
TGTGACACGACATGGCTTGAACA
Found at i:10461487 original size:31 final size:31
Alignment explanation
Indices: 10461316--10461486 Score: 290
Period size: 31 Copynumber: 5.5 Consensus size: 31
10461306 GTTAGCGTTA
*
10461316 GCGTGTAACAACATTTGACTTGATATGCATG
1 GCGTGTAACAACATTTGACTTGATACGCATG
10461347 GCGTGTAACAACATTTGACTTGATACGCATG
1 GCGTGTAACAACATTTGACTTGATACGCATG
10461378 GCGTGTAACAACATTTGACTTGATACGCATG
1 GCGTGTAACAACATTTGACTTGATACGCATG
10461409 GCGTGTAACAACATTTGACTTGATACGCATG
1 GCGTGTAACAACATTTGACTTGATACGCATG
* **
10461440 GCGTGTAACAACATTTTACGTT-ATATACATG
1 GCGTGTAACAACATTTGAC-TTGATACGCATG
10461471 GCGTGTAACAACATTT
1 GCGTGTAACAACATTT
10461487 TTTTTCTTCA
Statistics
Matches: 135, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
31 133 0.99
32 2 0.01
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (31 bp):
GCGTGTAACAACATTTGACTTGATACGCATG
Found at i:10463235 original size:144 final size:145
Alignment explanation
Indices: 10462901--10463245 Score: 389
Period size: 144 Copynumber: 2.4 Consensus size: 145
10462891 AGAGCCGATA
* * * * *
10462901 AAGA-CAGTTTTAAC-GGTTTCTGTTCAACAATTCTATATGTGATTATCAAATAACATATCTGTG
1 AAGATCAGTTCTAACTGGTTTGTGTTCAACAATTCCATATGTGATTATCGAATAACATATCTATG
* * *
10462964 TTTACAGTTGGACCATGTGACAACAACTCCACAACCACCGAGAGGTTCTTCTCAAACTCATAATG
66 TTTACAGTTAGACCATGTGACAACAACTCCACAACCACCGAGACGTTCTTCTCAAACGCATAATG
* *
10463029 CTACGAGCCGTCGGT
131 CTACGACCCATCGGT
** * *
10463044 AAGATGGGTTCTAACT-ATTTGTGTTCAACAATTCCATACGTGATTATCGAATAACATATCTATG
1 AAGATCAGTTCTAACTGGTTTGTGTTCAACAATTCCATATGTGATTATCGAATAACATATCTATG
** * * *
10463108 TTTACAGTTAGACCATGTGATGACAGCTCCTCAACCACCGAGACGTCCTCTT-T-AGACGCATAA
66 TTTACAGTTAGACCATGTGACAACAACTCCACAACCACCGAGACGT--TCTTCTCAAACGCATAA
*
10463171 TGCTAATGACCCATCGGT
129 TGCT-ACGACCCATCGGT
* * * * *
10463189 AAGATCAG-TCTAA-TGGTTTGTGTTCAACATTTCCACATATGTTTATCGAGTAACATA
1 AAGATCAGTTCTAACTGGTTTGTGTTCAACAATTCCATATGTGATTATCGAATAACATA
10463246 GTAATTTCTG
Statistics
Matches: 167, Mismatches: 29, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
143 5 0.03
144 141 0.84
145 17 0.10
146 4 0.02
ACGTcount: A:0.30, C:0.21, G:0.17, T:0.31
Consensus pattern (145 bp):
AAGATCAGTTCTAACTGGTTTGTGTTCAACAATTCCATATGTGATTATCGAATAACATATCTATG
TTTACAGTTAGACCATGTGACAACAACTCCACAACCACCGAGACGTTCTTCTCAAACGCATAATG
CTACGACCCATCGGT
Found at i:10463938 original size:75 final size:75
Alignment explanation
Indices: 10463859--10464012 Score: 236
Period size: 75 Copynumber: 2.1 Consensus size: 75
10463849 TTTGAGGCTG
* * * * *
10463859 ATTCAAATGATGCTGTGGTAGGGGATGTGACCCTTTAATCAGATGATACTGAAGGAGACCCTGTT
1 ATTCAAATGATGCTGTGGCAGGGAATGTGACCCTTCAATCAAATGATACTAAAGGAGACCCTGTT
10463924 CCTGAGGCCA
66 CCTGAGGCCA
*
10463934 ATTCAAATGATGCTGTGGCAGGGAATGTGACCCTTCAATTAAATGATACTAAAGGAGACCCTGTT
1 ATTCAAATGATGCTGTGGCAGGGAATGTGACCCTTCAATCAAATGATACTAAAGGAGACCCTGTT
* *
10463999 CTTGAGGTCA
66 CCTGAGGCCA
10464009 ATTC
1 ATTC
10464013 GGTTATCGAT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
75 71 1.00
ACGTcount: A:0.29, C:0.18, G:0.25, T:0.28
Consensus pattern (75 bp):
ATTCAAATGATGCTGTGGCAGGGAATGTGACCCTTCAATCAAATGATACTAAAGGAGACCCTGTT
CCTGAGGCCA
Found at i:10465559 original size:62 final size:62
Alignment explanation
Indices: 10465474--10465592 Score: 175
Period size: 62 Copynumber: 1.9 Consensus size: 62
10465464 GTCACCTTAG
* ** * *
10465474 ATACTGTAACAAGTCAGCGTGTCATGCCACGTATTTGTTTCCACTCAGCATGTCACCCCACA
1 ATACTGCAACAAGTCAGCGTGTCATGCCACAAATCTATTTCCACTCAGCATGTCACCCCACA
* *
10465536 ATACTGCAACAAGTCAGCGTGTCATGCCATAAATCTATTTCCACTCAGCGTGTCACC
1 ATACTGCAACAAGTCAGCGTGTCATGCCACAAATCTATTTCCACTCAGCATGTCACC
10465593 ACAATTGGGG
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
62 50 1.00
ACGTcount: A:0.27, C:0.30, G:0.16, T:0.27
Consensus pattern (62 bp):
ATACTGCAACAAGTCAGCGTGTCATGCCACAAATCTATTTCCACTCAGCATGTCACCCCACA
Found at i:10465634 original size:86 final size:86
Alignment explanation
Indices: 10465524--10465765 Score: 331
Period size: 86 Copynumber: 2.8 Consensus size: 86
10465514 CCACTCAGCA
* *
10465524 TGTCACCCCACAATACTGCAACAAGTCAGCGTGTCATGCCATAAATCTATTTCCACTCAGCGTGT
1 TGTCACCCCACAATACTGCAACAAGTCAGCGTGTCATGCCATAAATCTGTTTCCACTCAACGTGT
* *
10465589 CACCACAATTGGGGCATGGTG
66 CACCACAATTGGGGCATAGCG
* * *** *
10465610 TGTCACCCCACAATAATGCAACAAGTCAACGTGTCATGCCACGTATCTGCTTCCACTCAACGTGT
1 TGTCACCCCACAATACTGCAACAAGTCAGCGTGTCATGCCATAAATCTGTTTCCACTCAACGTGT
* *
10465675 CACCATAATTGGGGCGTAGCG
66 CACCACAATTGGGGCATAGCG
* * * *
10465696 TGTCACCCCACAATACTGCAACAAGTCAGCGTGTCACGCCATAAATTTGTTACCACTCATCGTGT
1 TGTCACCCCACAATACTGCAACAAGTCAGCGTGTCATGCCATAAATCTGTTTCCACTCAACGTGT
*
10465761 TACCA
66 CACCA
10465766 TAAGATGACA
Statistics
Matches: 133, Mismatches: 23, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
86 133 1.00
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.24
Consensus pattern (86 bp):
TGTCACCCCACAATACTGCAACAAGTCAGCGTGTCATGCCATAAATCTGTTTCCACTCAACGTGT
CACCACAATTGGGGCATAGCG
Found at i:10465897 original size:106 final size:107
Alignment explanation
Indices: 10465681--10465878 Score: 285
Period size: 106 Copynumber: 1.9 Consensus size: 107
10465671 GTGTCACCAT
10465681 AATTGGGGCGTAGCGTGTCACCCCACAATACTGCAACAAGTCAGCGTGTCACGCCATAAATTTGT
1 AATTGGGGCGTAGCGTGTCACCCCACAATACTGCAACAAGTCAGCGTGTCACGCCATAAATTTGT
* * *
10465746 TACCACTCATCGTGTTACCATAAGATGACATCCACATATGAC
66 TACCACTCAGCGTGTGACCACAAGATGACATCCACATATGAC
* * * * *
10465788 AATTGGGGCGTGGCGTGTCACCCTACAATACTG-GAGAAGTCAGCGTGTCATGCCAT-AATTCTG
1 AATTGGGGCGTAGCGTGTCACCCCACAATACTGCAACAAGTCAGCGTGTCACGCCATAAATT-TG
10465851 CTT-CCACTCAGCGTGTGACCACAAGATG
65 -TTACCACTCAGCGTGTGACCACAAGATG
10465879 TCATTGACAT
Statistics
Matches: 81, Mismatches: 8, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
105 4 0.05
106 44 0.54
107 33 0.41
ACGTcount: A:0.27, C:0.26, G:0.22, T:0.24
Consensus pattern (107 bp):
AATTGGGGCGTAGCGTGTCACCCCACAATACTGCAACAAGTCAGCGTGTCACGCCATAAATTTGT
TACCACTCAGCGTGTGACCACAAGATGACATCCACATATGAC
Found at i:10466197 original size:22 final size:23
Alignment explanation
Indices: 10466166--10466209 Score: 81
Period size: 22 Copynumber: 2.0 Consensus size: 23
10466156 TAATATTATT
10466166 TTTGTAAAAATGATAAATTAATA
1 TTTGTAAAAATGATAAATTAATA
10466189 TTTGT-AAAATGATAAATTAAT
1 TTTGTAAAAATGATAAATTAAT
10466210 TTATTAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (23 bp):
TTTGTAAAAATGATAAATTAATA
Found at i:10467115 original size:28 final size:28
Alignment explanation
Indices: 10467083--10467137 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
10467073 GTCAATTAGG
*
10467083 GTTCAAATAAGAAATATAGATATTCTTT
1 GTTCAAATAAGAAATAAAGATATTCTTT
10467111 GTTCAAATAAGAAATAAAGATATTCTT
1 GTTCAAATAAGAAATAAAGATATTCTT
10467138 ACCTTATTGC
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.45, C:0.07, G:0.11, T:0.36
Consensus pattern (28 bp):
GTTCAAATAAGAAATAAAGATATTCTTT
Found at i:10469938 original size:35 final size:34
Alignment explanation
Indices: 10469825--10469938 Score: 90
Period size: 35 Copynumber: 3.4 Consensus size: 34
10469815 TTTCGCAGGT
* *
10469825 TCAACCACAACCTTAACAATGGTTTTTTC-CGGGA
1 TCAACCAAAACCTTAACAATGG-TTTTTCAAGGGA
* * * * * *
10469859 TTAGCCAAAACC-CAA-AATGGCTTTTCAAAGGC
1 TCAACCAAAACCTTAACAATGGTTTTTCAAGGGA
** *
10469891 TCAACCGCAACCTTTAACAATGGTTTTTCATGGGA
1 TCAACCAAAACC-TTAACAATGGTTTTTCAAGGGA
10469926 TCAACCAAAACCT
1 TCAACCAAAACCT
10469939 AAACTAACTT
Statistics
Matches: 57, Mismatches: 19, Indels: 8
0.68 0.23 0.10
Matches are distributed among these distances:
31 5 0.09
32 15 0.26
33 2 0.04
34 12 0.21
35 23 0.40
ACGTcount: A:0.33, C:0.26, G:0.14, T:0.26
Consensus pattern (34 bp):
TCAACCAAAACCTTAACAATGGTTTTTCAAGGGA
Found at i:10469950 original size:67 final size:66
Alignment explanation
Indices: 10469825--10469950 Score: 155
Period size: 67 Copynumber: 1.9 Consensus size: 66
10469815 TTTCGCAGGT
* * **
10469825 TCAACCACAACCTTAACAATGGTTTTTTCCGGGATTAGCCAAAACCCAAAATGGCTTTTCAAAGG
1 TCAACCACAACCTTAACAATGGTTTTTTCCGGGATCAACCAAAACCCAAAATAACTTTTCAAAGG
10469890 C
66 C
* * * *
10469891 TCAACCGCAACCTTTAACAATGG-TTTTTCATGGGATCAACCAAAACCTAAACTAACTTTT
1 TCAACCACAACC-TTAACAATGGTTTTTTC-CGGGATCAACCAAAACCCAAAATAACTTTT
10469951 ACTAGGATGA
Statistics
Matches: 50, Mismatches: 8, Indels: 3
0.82 0.13 0.05
Matches are distributed among these distances:
66 17 0.34
67 33 0.66
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (66 bp):
TCAACCACAACCTTAACAATGGTTTTTTCCGGGATCAACCAAAACCCAAAATAACTTTTCAAAGG
C
Found at i:10479330 original size:31 final size:31
Alignment explanation
Indices: 10479292--10479431 Score: 210
Period size: 31 Copynumber: 4.5 Consensus size: 31
10479282 TTTGTCAGTC
*
10479292 ATGTTGTTACACGTCATGCATAT-AACGTAAA
1 ATGTTGTTACACGCCATGCATATCAA-GTAAA
* * *
10479323 ATGTTGTTACATGCCATGCGTATCAAGTCAA
1 ATGTTGTTACACGCCATGCATATCAAGTAAA
10479354 ATGTTGTTACACGCCATGCATATCAAGTAAA
1 ATGTTGTTACACGCCATGCATATCAAGTAAA
* *
10479385 ATGTTGTTACACGCCGTGCATATCAAGTCAA
1 ATGTTGTTACACGCCATGCATATCAAGTAAA
10479416 ATGTTGTTACACGCCA
1 ATGTTGTTACACGCCA
10479432 ACGTTGACAT
Statistics
Matches: 98, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
31 96 0.98
32 2 0.02
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Consensus pattern (31 bp):
ATGTTGTTACACGCCATGCATATCAAGTAAA
Found at i:10487318 original size:776 final size:777
Alignment explanation
Indices: 10486265--10487688 Score: 2295
Period size: 775 Copynumber: 1.8 Consensus size: 777
10486255 GGACTTGAAA
* * *
10486265 AGAATGAAGAAAACACCAGATTAATAGTTGAGAGTCAAGCTACAGAGTTATTAAAAGAATTTGAA
1 AGAACGAAGAAAACACCAGATTAACAGTTGAGAGTCAAGCTACAAAGTTATTAAAAGAATTTGAA
*
10486330 GAATTCAAGGAGATTTGAAGATCAAGAATACATTCTTTGGTTTTTTCTATCTTTTTGTTATTCTT
66 GAATTCAAGGAGATTTGAAGATCAAGAATACATTCCTTGGTTTTTTCTATCTTTTTGTTATTCTT
10486395 TTATTCCCTTGATTATAATGTGTAAATTTTATTCAATGATGATGTATGACTTGATGGGGAACTAA
131 TTATTCCCTTGATTATAATGTGTAAATTTTATTCAATGATGATGTATGACTTGATGGGGAACTAA
10486460 ATTTTTTATCTAAGATTATGATTGAACTCAATATATAGTCTGAATTATTTATCTCTCTTTTACTT
196 ATTTTTTATCTAAGATTATGATTGAACTCAATATATAGTCTGAATTATTTATCTCTCTTTTACTT
*
10486525 ATGTTTGATAGATTTAAGTTATTTATTTTATTCTGTTCTTAATACTGCTAATTGCC-TGATCACC
261 ATGTTTGATAGATTTAAG-TATTTATTTTATTCTGTTCTTAATACTGCTAATTGCCTTG-CCACC
* * * * * *
10486589 AATTAGATTGAATTGGAAACGTAGGTTAAACTTTGACAGAGGAGATTTAGGTAGACCTTGAATAG
324 AATTAGATTAAATTGGAAACCTAAGTTAAACATTGACAAAGGAGATTTAGGTAGACCTTGAATAA
* *
10486654 AATACCGTATGATCGAATACACTTAGTTGATTAGGTGGATTGATTTGCATATAGGGCAGACATAC
389 AATACCGTATGATCAAATACACTTAGTTGATTAGGTAGATTGATTTGCATATAGGGCAGACATAC
*
10486719 ACTTATAAG-C-CAAA-ATTAGAGCACAAACTTAGA-GAATCTTTCTTCAATTTAATTTGCATAG
454 ACCTATAAGACGCAAAGATTAGAGCACAAACTTA-ATGAATCTTTCTTCAATTTAATTTGCATAG
* * *
10486780 ACATATAGTAAATTAATTAGGAGAGGTATTTTTATGAGAAACTCGACAGAGACTTGTAAATAATT
518 ACATATAGTAAATTAATTAGGAAAGGTATTTTTATAAGAAACTCGACAAAGACTTGTAAATAATT
* * *
10486845 TAGGACTTTAGATTAGCAACT-TAATCCACTAAACTGAGTTAAGAGAGAGAGAGACAATAATTAG
583 TAGGACTCTAGATTAGCAA-TATAATCCACTAAACTAAGTTAACAGAGA-A-AGACAATAATTAG
10486909 ATGAAGACCATTCTTAACTACAGCTAGAGCAATTAGTGGTGTGCAGAATGACAAAATAACTTTCA
645 ATGAAGACCATTCTTAACTACAGCTAGAGCAATTAGTGGTGTGCAGAATGACAAAATAACTTTCA
10486974 GAGTTGGAGAGGAGAAAGTGGAGTTTAATTTGATAATGAAGATTAACAAAAGATTATCTTCATTA
710 GAGTTGGAGAGGAGAAAGTGGAGTTTAATTTGATAATGAAGATTAACAAAAGATTATCTTCATTA
10487039 AAG
775 AAG
* * * * *
10487042 AGAACGAAGAAAATATCAGATTAACAGTTGAGAGTCAAGGTACAAAGTTATTGAAGGAATTTGAA
1 AGAACGAAGAAAACACCAGATTAACAGTTGAGAGTCAAGCTACAAAGTTATTAAAAGAATTTGAA
*
10487107 GAATTCAAGGAGATTTGGAGATCAAGAATACATTCCTTGGTTTTTTCTATC-TTTTGTTATTCTT
66 GAATTCAAGGAGATTTGAAGATCAAGAATACATTCCTTGGTTTTTTCTATCTTTTTGTTATTCTT
* *
10487171 TTATTCCCTTGGTTTTAATGTGTAAATTTTATTCAATGATGATGTATGACTTGATGGGGAACTAA
131 TTATTCCCTTGATTATAATGTGTAAATTTTATTCAATGATGATGTATGACTTGATGGGGAACTAA
10487236 ATTTTTTATCTAAGATTATGATTGAACTCAATATATAGTCTGAATTATTTATCTCTCTTTTACTT
196 ATTTTTTATCTAAGATTATGATTGAACTCAATATATAGTCTGAATTATTTATCTCTCTTTTACTT
* * * * *
10487301 ATGTTTGATGGATTTAAGTGTTTATTTTATTTTGTTCTTAATGCTTCTAATTGCCTTGCCACCAA
261 ATGTTTGATAGATTTAAGTATTTATTTTATTCTGTTCTTAATACTGCTAATTGCCTTGCCACCAA
*
10487366 TTAGATTAAATTGGAAACCTAAGTTAAACATTGAGAAAGGAGATTTAGGTAGACCTTGAATAAAA
326 TTAGATTAAATTGGAAACCTAAGTTAAACATTGACAAAGGAGATTTAGGTAGACCTTGAATAAAA
* ** *
10487431 TAGCGTATGATCAAATATTCTTAGTTGATTAGGTAGATTGATTTGCATATAGGGTAGACATACAC
391 TACCGTATGATCAAATACACTTAGTTGATTAGGTAGATTGATTTGCATATAGGGCAGACATACAC
10487496 CTATAAGCCATACGTAGCAAAGATTAGAGCACAAACTTAATGAATCTTTCTTCAATTTAATTTGC
456 CTATAAG----AC---GCAAAGATTAGAGCACAAACTTAATGAATCTTTCTTCAATTTAATTTGC
* *
10487561 ATAGACATATAGTAAATTAATTGGGAAATGTATTTTTATAAGAAACTCGACAAAGACTTGTAAAT
514 ATAGACATATAGTAAATTAATTAGGAAAGGTATTTTTATAAGAAACTCGACAAAGACTTGTAAAT
* * *
10487626 AATTTAGGACTCTAGGTTAGCAATATGATCCATTAAACTAAGTTAACAGAGAAAGACAATAAT
579 AATTTAGGACTCTAGATTAGCAATATAATCCACTAAACTAAGTTAACAGAGAAAGACAATAAT
10487689 CAAATAAAGG
Statistics
Matches: 591, Mismatches: 43, Indels: 20
0.90 0.07 0.03
Matches are distributed among these distances:
775 162 0.27
776 160 0.27
777 106 0.18
780 1 0.00
783 10 0.02
784 7 0.01
785 145 0.25
ACGTcount: A:0.36, C:0.11, G:0.18, T:0.36
Consensus pattern (777 bp):
AGAACGAAGAAAACACCAGATTAACAGTTGAGAGTCAAGCTACAAAGTTATTAAAAGAATTTGAA
GAATTCAAGGAGATTTGAAGATCAAGAATACATTCCTTGGTTTTTTCTATCTTTTTGTTATTCTT
TTATTCCCTTGATTATAATGTGTAAATTTTATTCAATGATGATGTATGACTTGATGGGGAACTAA
ATTTTTTATCTAAGATTATGATTGAACTCAATATATAGTCTGAATTATTTATCTCTCTTTTACTT
ATGTTTGATAGATTTAAGTATTTATTTTATTCTGTTCTTAATACTGCTAATTGCCTTGCCACCAA
TTAGATTAAATTGGAAACCTAAGTTAAACATTGACAAAGGAGATTTAGGTAGACCTTGAATAAAA
TACCGTATGATCAAATACACTTAGTTGATTAGGTAGATTGATTTGCATATAGGGCAGACATACAC
CTATAAGACGCAAAGATTAGAGCACAAACTTAATGAATCTTTCTTCAATTTAATTTGCATAGACA
TATAGTAAATTAATTAGGAAAGGTATTTTTATAAGAAACTCGACAAAGACTTGTAAATAATTTAG
GACTCTAGATTAGCAATATAATCCACTAAACTAAGTTAACAGAGAAAGACAATAATTAGATGAAG
ACCATTCTTAACTACAGCTAGAGCAATTAGTGGTGTGCAGAATGACAAAATAACTTTCAGAGTTG
GAGAGGAGAAAGTGGAGTTTAATTTGATAATGAAGATTAACAAAAGATTATCTTCATTAAAG
Found at i:10490658 original size:22 final size:21
Alignment explanation
Indices: 10490633--10490679 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
10490623 GGATATGTTC
10490633 ATGCAATTCATGACAAAGACTG
1 ATGC-ATTCATGACAAAGACTG
* * *
10490655 ATGCATTTATGATAAGGACTG
1 ATGCATTCATGACAAAGACTG
10490676 ATGC
1 ATGC
10490680 CTCCATTCAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 18 0.82
22 4 0.18
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (21 bp):
ATGCATTCATGACAAAGACTG
Found at i:10490927 original size:12 final size:12
Alignment explanation
Indices: 10490910--10490944 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
10490900 CAAAATGATG
10490910 AAAAGAAATTGA
1 AAAAGAAATTGA
**
10490922 AAAAGATGTTGA
1 AAAAGAAATTGA
10490934 AAAAGAAATTG
1 AAAAGAAATTG
10490945 TAGTTGAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.60, C:0.00, G:0.20, T:0.20
Consensus pattern (12 bp):
AAAAGAAATTGA
Found at i:10491850 original size:49 final size:49
Alignment explanation
Indices: 10491788--10491885 Score: 187
Period size: 49 Copynumber: 2.0 Consensus size: 49
10491778 GAATATGCTA
10491788 ACCATCTTGATGCCCATTCACGTCTTCCAAGATCTCAATTTGAATCTTT
1 ACCATCTTGATGCCCATTCACGTCTTCCAAGATCTCAATTTGAATCTTT
*
10491837 ACCATCTTGATGCCCATTGACGTCTTCCAAGATCTCAATTTGAATCTTT
1 ACCATCTTGATGCCCATTCACGTCTTCCAAGATCTCAATTTGAATCTTT
10491886 GGAATTATCA
Statistics
Matches: 48, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 48 1.00
ACGTcount: A:0.24, C:0.28, G:0.11, T:0.37
Consensus pattern (49 bp):
ACCATCTTGATGCCCATTCACGTCTTCCAAGATCTCAATTTGAATCTTT
Found at i:10497621 original size:19 final size:19
Alignment explanation
Indices: 10497605--10497649 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
10497595 ACTTACTTTC
*
10497605 TTTTATTTTTTTTACTTAT
1 TTTTATTTATTTTACTTAT
10497624 TTTTATTTATTTTA-TTAT
1 TTTTATTTATTTTACTTAT
10497642 TATTTATT
1 T-TTTATT
10497650 AATATTTTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 5 0.21
19 19 0.79
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (19 bp):
TTTTATTTATTTTACTTAT
Found at i:10497644 original size:15 final size:15
Alignment explanation
Indices: 10497620--10497649 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
10497610 TTTTTTTTAC
*
10497620 TTATTTTTATTTATT
1 TTATTATTATTTATT
10497635 TTATTATTATTTATT
1 TTATTATTATTTATT
10497650 AATATTTTTT
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:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (15 bp):
TTATTATTATTTATT
Found at i:10498297 original size:19 final size:19
Alignment explanation
Indices: 10498273--10498310 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
10498263 CCATTTGACT
10498273 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
10498292 TATTGGAGTATGATTTGAG
1 TATTGGAGTATGATTTGAG
10498311 GTTTAGAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.00, G:0.32, T:0.42
Consensus pattern (19 bp):
TATTGGAGTATGATTTGAG
Found at i:10499506 original size:427 final size:422
Alignment explanation
Indices: 10498714--10499564 Score: 1445
Period size: 427 Copynumber: 2.0 Consensus size: 422
10498704 AAAGGTAAAA
10498714 TTTCTTTATTTTAGTTTATGAACTATTTTTCCTATGCATTTTCCCTTAATTTTCATTGTTGAAAA
1 TTTCTTTATTTTAGTTTATGAACTATTTTTCCTATGCATTTTCCCTTAATTTTCATTGTTGAAAA
*
10498779 GCATGCTTTTATGGTGAATTCATGGCTGGTCCAAATGGGTAAGGAGAGAGAATCTTGGATTGGTT
66 GCATGCTTTTATGGTGAATTCATGGCTGGTCAAAATGGGTAAGGAGAGAGAATCTTGGATTGGTT
* *
10498844 TGTTTTTTAGGTATGTTAGTGTTTTTTAGGTGATTAATGATGTGAAGCATGAAAACAAGTGAAGA
131 TGATTTTTAGGTATGTTAGTGTTTTTTAGGTGATTAATGATATGAAGCATGAAAACAAGTGAAGA
*
10498909 AACCACCAAAGGTTTGGTGCCATCAATAGCTGAATTCTCTAAGTGAATAATGACGAAGAACGAGA
196 AACCACCAAAAGTTTGGTGCCATCAATAGCTGAATTCTCTAAGTGAATAATGACGAAGAACGAGA
*
10498974 TGTTATTCTAGGTGATTTTATTAAGAAATAATAGTTTTTAGTGAATTGAGGAATTGGAAAAGAAA
261 TGTTATTCTAGGTGATTTGATTAAGAAATAATAGTTTTTAGTGAATTGAGGAATTGGAAAAGAAA
* * * *
10499039 TGGAGTAAGTTGGAGTGAAATTGGATGCGTTGGTCAATTTATCGGATG-AAAATCCGACTTAGGC
326 TGGAGCAAGTTGGAGTGAAATTGGACGCATTGGCCAATTTATCGGATGAAAAAT-CGACTTAGGC
*
10499103 CAATACCGAGTCTATATGGCTACCCGTGCATTT
390 CAATACCGAGTCTAGATGGCTACCCGTGCATTT
10499136 NTTTCTTTATTTTAGTTTATGAACTATTTTTCCTATGCATTTTCCCTTAATTTTCATTGTTGAAA
1 -TTTCTTTATTTTAGTTTATGAACTATTTTTCCTATGCATTTTCCCTTAATTTTCATTGTTGAAA
*
10499201 AGCATGCTTTTATGGTGAATTCATGGCTGGTCAAAATGGGTATGGAGAGAGAATGATCTTGGATT
65 AGCATGCTTTTATGGTGAATTCATGGCTGGTCAAAATGGGTAAGGAGAGAG-A--ATCTTGGATT
*
10499266 GGTTTGATTTTTAGGTATGTTAGTG-TTTTTAGGTGATTAATGATATGTAGCATGAAAACAAGTG
127 GGTTTGATTTTTAGGTATGTTAGTGTTTTTTAGGTGATTAATGATATGAAGCATGAAAACAAGTG
* *
10499330 AAGAAAACTACCAAAAGTTTGGTGCCCATCAATAGCTGAATTCTCTAAGTGAATAATGAGGAAGA
192 AAG-AAACCACCAAAAGTTTGGTG-CCATCAATAGCTGAATTCTCTAAGTGAATAATGACGAAGA
* *
10499395 ATGGGATGTTATTCTAGGTGATTTGATTAAGAAATAATAGTTTTTAGTGAATTGAGGAATTGGAA
255 ACGAGATGTTATTCTAGGTGATTTGATTAAGAAATAATAGTTTTTAGTGAATTGAGGAATTGGAA
*
10499460 AAGAAATGGAGCAAGTTGGAGTGAAATTGGACGCATTGGCCAATTTATTGGATGAAAAATCGACT
320 AAGAAATGGAGCAAGTTGGAGTGAAATTGGACGCATTGGCCAATTTATCGGATGAAAAATCGACT
* * *
10499525 TAGGCCAATACCGGGTCTAGATGGCTATCCGTGTATTT
385 TAGGCCAATACCGAGTCTAGATGGCTACCCGTGCATTT
10499563 TT
1 TT
10499565 CATTTCATAT
Statistics
Matches: 402, Mismatches: 20, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
423 113 0.28
424 1 0.00
425 40 0.10
426 54 0.13
427 189 0.47
428 5 0.01
ACGTcount: A:0.30, C:0.11, G:0.23, T:0.36
Consensus pattern (422 bp):
TTTCTTTATTTTAGTTTATGAACTATTTTTCCTATGCATTTTCCCTTAATTTTCATTGTTGAAAA
GCATGCTTTTATGGTGAATTCATGGCTGGTCAAAATGGGTAAGGAGAGAGAATCTTGGATTGGTT
TGATTTTTAGGTATGTTAGTGTTTTTTAGGTGATTAATGATATGAAGCATGAAAACAAGTGAAGA
AACCACCAAAAGTTTGGTGCCATCAATAGCTGAATTCTCTAAGTGAATAATGACGAAGAACGAGA
TGTTATTCTAGGTGATTTGATTAAGAAATAATAGTTTTTAGTGAATTGAGGAATTGGAAAAGAAA
TGGAGCAAGTTGGAGTGAAATTGGACGCATTGGCCAATTTATCGGATGAAAAATCGACTTAGGCC
AATACCGAGTCTAGATGGCTACCCGTGCATTT
Found at i:10508143 original size:19 final size:20
Alignment explanation
Indices: 10508116--10508161 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
10508106 AAGAGACAAG
*
10508116 ATAAAATTTTTA-GAATAAA
1 ATAATATTTTTATGAATAAA
*
10508135 ATAATA-TTTTATTAATAAA
1 ATAATATTTTTATGAATAAA
10508154 ATAATATT
1 ATAATATT
10508162 AAAATATTAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
18 5 0.22
19 17 0.74
20 1 0.04
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.43
Consensus pattern (20 bp):
ATAATATTTTTATGAATAAA
Found at i:10508630 original size:20 final size:20
Alignment explanation
Indices: 10508565--10508622 Score: 116
Period size: 20 Copynumber: 2.9 Consensus size: 20
10508555 TTTTGGCCCC
10508565 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
10508585 ATTTGACTTATTGGAGTATA
1 ATTTGACTTATTGGAGTATA
10508605 ATTTGACTTATTGGAGTA
1 ATTTGACTTATTGGAGTA
10508623 GGATTTGAGG
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (20 bp):
ATTTGACTTATTGGAGTATA
Found at i:10512873 original size:13 final size:13
Alignment explanation
Indices: 10512855--10512879 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10512845 AGAGAAATTG
10512855 TGATTTTATAAAA
1 TGATTTTATAAAA
10512868 TGATTTTATAAA
1 TGATTTTATAAA
10512880 TTTTCTGAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (13 bp):
TGATTTTATAAAA
Found at i:10516591 original size:12 final size:12
Alignment explanation
Indices: 10516574--10516600 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
10516564 AAAGCATGCT
10516574 AATCCTAAATTA
1 AATCCTAAATTA
10516586 AATCCTAAATTA
1 AATCCTAAATTA
10516598 AAT
1 AAT
10516601 GAGATTTCCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (12 bp):
AATCCTAAATTA
Found at i:10522503 original size:12 final size:12
Alignment explanation
Indices: 10522488--10522513 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
10522478 AAGGAAGCAA
10522488 ATAATTCAATTG
1 ATAATTCAATTG
10522500 ATAATTCAATTG
1 ATAATTCAATTG
10522512 AT
1 AT
10522514 TGGAAGTTTC
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:0.42, C:0.08, G:0.08, T:0.42
Consensus pattern (12 bp):
ATAATTCAATTG
Found at i:10524049 original size:50 final size:50
Alignment explanation
Indices: 10523995--10524100 Score: 194
Period size: 50 Copynumber: 2.1 Consensus size: 50
10523985 CACAAAAAAA
*
10523995 TAAAACAACTTTCAAACTTGTACAGTAATAATAATATTAGATTTTTTGAT
1 TAAAAAAACTTTCAAACTTGTACAGTAATAATAATATTAGATTTTTTGAT
*
10524045 TAAAAANACTTTCAAACTTGTACAGTAATAATAATATTAGATTTTTTGAT
1 TAAAAAAACTTTCAAACTTGTACAGTAATAATAATATTAGATTTTTTGAT
10524095 TAAAAA
1 TAAAAA
10524101 GAGAGAAAAC
Statistics
Matches: 54, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 54 1.00
ACGTcount: A:0.44, C:0.08, G:0.08, T:0.39
Consensus pattern (50 bp):
TAAAAAAACTTTCAAACTTGTACAGTAATAATAATATTAGATTTTTTGAT
Found at i:10525781 original size:23 final size:23
Alignment explanation
Indices: 10525755--10525800 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
10525745 TAGAATAATA
*
10525755 ATTCCTAATTCTATTAGGATAAG
1 ATTCCTAATTATATTAGGATAAG
10525778 ATTCCTAATTATATTAGGATAAG
1 ATTCCTAATTATATTAGGATAAG
10525801 GTTATTGTAT
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:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (23 bp):
ATTCCTAATTATATTAGGATAAG
Found at i:10529284 original size:23 final size:23
Alignment explanation
Indices: 10529258--10529303 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
10529248 TAGAATAACA
*
10529258 ATTCCTAATTCTATTAGGATAAG
1 ATTCCTAATTATATTAGGATAAG
10529281 ATTCCTAATTATATTAGGATAAG
1 ATTCCTAATTATATTAGGATAAG
10529304 GTTATTGTAT
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:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (23 bp):
ATTCCTAATTATATTAGGATAAG
Found at i:10530210 original size:21 final size:21
Alignment explanation
Indices: 10530184--10530257 Score: 69
Period size: 21 Copynumber: 3.3 Consensus size: 21
10530174 ATAACAATAA
*
10530184 AATAATAATAGAAATTAAAAC
1 AATAATAATACAAATTAAAAC
* *
10530205 AATAATACAACAACACAATTAAATAA
1 AATAAT--AA-TACA-AATTAAA-AC
10530231 AAT-ATAATACAAATTAAAAC
1 AATAATAATACAAATTAAAAC
10530251 AATAATA
1 AATAATA
10530258 CCACAACAAC
Statistics
Matches: 42, Mismatches: 5, Indels: 12
0.71 0.08 0.20
Matches are distributed among these distances:
20 4 0.10
21 16 0.38
22 3 0.07
23 4 0.10
24 2 0.05
25 9 0.21
26 4 0.10
ACGTcount: A:0.66, C:0.09, G:0.01, T:0.23
Consensus pattern (21 bp):
AATAATAATACAAATTAAAAC
Found at i:10530257 original size:18 final size:17
Alignment explanation
Indices: 10530179--10530258 Score: 55
Period size: 18 Copynumber: 4.9 Consensus size: 17
10530169 GCACAATAAC
* *
10530179 AATAAAATAATAATAGA
1 AATAAAACAATAATACA
10530196 AATTAAAACAATAATAC-
1 AA-TAAAACAATAATACA
* *
10530213 AACAACACAAT--T--A
1 AATAAAACAATAATACA
*
10530226 AATAAAA-TATAATACA
1 AATAAAACAATAATACA
10530242 AATTAAAACAATAATAC
1 AA-TAAAACAATAATAC
10530259 CACAACAACA
Statistics
Matches: 47, Mismatches: 8, Indels: 15
0.67 0.11 0.21
Matches are distributed among these distances:
12 2 0.04
13 5 0.11
14 2 0.04
16 10 0.21
17 9 0.19
18 19 0.40
ACGTcount: A:0.66, C:0.10, G:0.01, T:0.23
Consensus pattern (17 bp):
AATAAAACAATAATACA
Found at i:10530268 original size:49 final size:48
Alignment explanation
Indices: 10530145--10530265 Score: 162
Period size: 46 Copynumber: 2.6 Consensus size: 48
10530135 CAACAACAAG
* *
10530145 AATACAAATTAAAACAA-AA-A-TACAGCACAATAACAATAAAATAAT
1 AATACAAATTAAAACAATAATACAACAACACAATAACAATAAAATAAT
* *
10530190 AATAGAAATTAAAACAATAATACAACAACACAATTA-AATAAAAT-AT
1 AATACAAATTAAAACAATAATACAACAACACAATAACAATAAAATAAT
*
10530236 AATACAAATTAAAACAATAATACCACAACA
1 AATACAAATTAAAACAATAATACAACAACA
10530266 ACAACGATAA
Statistics
Matches: 67, Mismatches: 6, Indels: 5
0.86 0.08 0.06
Matches are distributed among these distances:
45 16 0.24
46 32 0.48
47 9 0.13
48 10 0.15
ACGTcount: A:0.65, C:0.14, G:0.02, T:0.19
Consensus pattern (48 bp):
AATACAAATTAAAACAATAATACAACAACACAATAACAATAAAATAAT
Found at i:10530299 original size:15 final size:15
Alignment explanation
Indices: 10530279--10530316 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
10530269 ACGATAACTC
10530279 AACAACATATA-CAAT
1 AACAACA-ATAGCAAT
10530294 AACAACAATAGCAAT
1 AACAACAATAGCAAT
10530309 AA-AACAAT
1 AACAACAAT
10530317 TATACAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.41
15 13 0.59
ACGTcount: A:0.63, C:0.18, G:0.03, T:0.16
Consensus pattern (15 bp):
AACAACAATAGCAAT
Found at i:10534182 original size:6 final size:6
Alignment explanation
Indices: 10534171--10534195 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
10534161 CTTTAACCAT
10534171 TTCAAA TTCAAA TTCAAA TTCAAA T
1 TTCAAA TTCAAA TTCAAA TTCAAA T
10534196 CAACTATCCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (6 bp):
TTCAAA
Found at i:10543874 original size:56 final size:56
Alignment explanation
Indices: 10543786--10543897 Score: 197
Period size: 56 Copynumber: 2.0 Consensus size: 56
10543776 TTTATACAAC
*
10543786 TTTAGATCACTAAATCAACCTGACTATGAAAAAAAAAATAAAACACTTACATGCAT
1 TTTAGATCACTAAATCAACCTGACTATGAAAAAAAAAAGAAAACACTTACATGCAT
* *
10543842 TTTAGATCACTAAATCAACTTGACTATTAAAAAAAAAAGAAAACACTTACATGCAT
1 TTTAGATCACTAAATCAACCTGACTATGAAAAAAAAAAGAAAACACTTACATGCAT
10543898 GTGGGCGCTC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
56 53 1.00
ACGTcount: A:0.50, C:0.17, G:0.07, T:0.26
Consensus pattern (56 bp):
TTTAGATCACTAAATCAACCTGACTATGAAAAAAAAAAGAAAACACTTACATGCAT
Found at i:10546863 original size:280 final size:280
Alignment explanation
Indices: 10546362--10546924 Score: 1047
Period size: 280 Copynumber: 2.0 Consensus size: 280
10546352 AGTTATTTCA
* *
10546362 TATAATGAAAAGTTATCTTAGCTCAAAGTTTAAATCGTAAAGAGTGACATAATGTGACTATTAGA
1 TATAATGAAAAGTTATCCTAGCTCAAAGGTTAAATCGTAAAGAGTGACATAATGTGACTATTAGA
10546427 TTTTAGGTAAGTTTTTCATGTGAATAATTATGTCTCTTGGTAAAGTGACATATTGAAAAAATACC
66 TTTTAGGTAAGTTTTTCATGTGAATAATTATGTCTCTTGGTAAAGTGACATATTGAAAAAATACC
*
10546492 TTTAAATCCAAAAGTTACTAGACAATTGAAAAACACCACAACTGAAAAGTTTAGATATGAAATAT
131 TTTAAATCCAAAAGATACTAGACAATTGAAAAACACCACAACTGAAAAGTTTAGATATGAAATAT
10546557 TATCTTTTCATATGGTAGCTCAAAAGTTATATTTTATGGTATGAATGGTTGTCTTTTTATAAGGT
196 TATCTTTTCATATGGTAGCTCAAAAGTTATATTTTATGGTATGAATGGTTGTCTTTTTATAAGGT
10546622 GATTATTAAAACAATACATT
261 GATTATTAAAACAATACATT
* *
10546642 TATAATGAAAAGTTATCCTATCTCAAAGGTTATATCGTAAAGAGTGACATAATGTGACTATTAGA
1 TATAATGAAAAGTTATCCTAGCTCAAAGGTTAAATCGTAAAGAGTGACATAATGTGACTATTAGA
10546707 TTTTAGGTAAGTTTTTCATGTGAATAATTATGTCTCTTGGTAAAGTGACATATTGAAAAAATACC
66 TTTTAGGTAAGTTTTTCATGTGAATAATTATGTCTCTTGGTAAAGTGACATATTGAAAAAATACC
*
10546772 TTTAAATCCAAAAGATA-TGAGATAATTGAAAAACACCACAACTGAAAAGTTTAGATATGAAATA
131 TTTAAATCCAAAAGATACT-AGACAATTGAAAAACACCACAACTGAAAAGTTTAGATATGAAATA
10546836 TTATCTTTTCATATGGTAGCTCAAAAGTTATATTTTATGGTATGAATGGTTGTCTTTTTATAAGG
195 TTATCTTTTCATATGGTAGCTCAAAAGTTATATTTTATGGTATGAATGGTTGTCTTTTTATAAGG
*
10546901 TGATTATTAAAACAATGCATT
260 TGATTATTAAAACAATACATT
10546922 TAT
1 TAT
10546925 TCAAGAATTG
Statistics
Matches: 275, Mismatches: 7, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
279 1 0.00
280 274 1.00
ACGTcount: A:0.38, C:0.10, G:0.15, T:0.37
Consensus pattern (280 bp):
TATAATGAAAAGTTATCCTAGCTCAAAGGTTAAATCGTAAAGAGTGACATAATGTGACTATTAGA
TTTTAGGTAAGTTTTTCATGTGAATAATTATGTCTCTTGGTAAAGTGACATATTGAAAAAATACC
TTTAAATCCAAAAGATACTAGACAATTGAAAAACACCACAACTGAAAAGTTTAGATATGAAATAT
TATCTTTTCATATGGTAGCTCAAAAGTTATATTTTATGGTATGAATGGTTGTCTTTTTATAAGGT
GATTATTAAAACAATACATT
Found at i:10548544 original size:13 final size:13
Alignment explanation
Indices: 10548526--10548550 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10548516 GGAAAATGAG
10548526 ATTTTATAAAATA
1 ATTTTATAAAATA
10548539 ATTTTATAAAAT
1 ATTTTATAAAAT
10548551 TTTTGAAAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (13 bp):
ATTTTATAAAATA
Found at i:10558430 original size:17 final size:17
Alignment explanation
Indices: 10558383--10558431 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
10558373 ATAAAAATAA
10558383 AATAAAAAA-ATA-TTT
1 AATAAAAAATATATTTT
*
10558398 AATAAAATAATCTATTTT
1 AATAAAA-AATATATTTT
*
10558416 AATGAAAAATATATTT
1 AATAAAAAATATATTT
10558432 ATATATATAT
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
15 7 0.25
16 2 0.07
17 10 0.36
18 9 0.32
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (17 bp):
AATAAAAAATATATTTT
Found at i:10559442 original size:13 final size:13
Alignment explanation
Indices: 10559424--10559448 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
10559414 ATTTTCAAAA
10559424 ATTTTATAAAATT
1 ATTTTATAAAATT
10559437 ATTTTATAAAAT
1 ATTTTATAAAAT
10559449 CTCATTTTCC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
ATTTTATAAAATT
Found at i:10560657 original size:28 final size:29
Alignment explanation
Indices: 10560599--10560664 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 29
10560589 GCAAATTTTT
* *
10560599 AAAAATTACACTTTTACCCCCATAAAGTG
1 AAAAATTACACTTTTACCCCCAAAAACTG
** *
10560628 AAAAATTACA-TTTTTGCCTCAAAAACTG
1 AAAAATTACACTTTTACCCCCAAAAACTG
10560656 AAAAATTAC
1 AAAAATTAC
10560665 CCCATAGACA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
28 22 0.69
29 10 0.31
ACGTcount: A:0.45, C:0.20, G:0.06, T:0.29
Consensus pattern (29 bp):
AAAAATTACACTTTTACCCCCAAAAACTG
Found at i:10563629 original size:51 final size:52
Alignment explanation
Indices: 10563525--10563665 Score: 178
Period size: 51 Copynumber: 2.6 Consensus size: 52
10563515 CAACAACAAC
* *
10563525 AATACAAATTAAAACAAAAATAGAACAACACAATAACAATAATAACAATAAAATAAT
1 AATACAAATTAAAACAATAAT---ACAACACAA-CACAAT-ATAACAATAAAATAAT
10563582 AATACAAATTAAAACAATAATACAACGACAACACAAT-T-ACAATAAAATAAT
1 AATACAAATTAAAACAATAATACAAC-ACAACACAATATAACAATAAAATAAT
*
10563633 AATACAAATTAAAACAATAATACCACAACAACA
1 AATACAAATTAAAACAATAATACAAC-ACAACA
10563666 AAAAAAAAGG
Statistics
Matches: 79, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
51 44 0.56
52 1 0.01
54 10 0.13
55 4 0.05
57 20 0.25
ACGTcount: A:0.65, C:0.16, G:0.01, T:0.18
Consensus pattern (52 bp):
AATACAAATTAAAACAATAATACAACACAACACAATATAACAATAAAATAAT
Found at i:10563709 original size:14 final size:14
Alignment explanation
Indices: 10563687--10563795 Score: 100
Period size: 14 Copynumber: 8.1 Consensus size: 14
10563677 AACAACAGAC
*
10563687 ACAATAACAATAAT
1 ACAACAACAATAAT
10563701 ACAACAACAATAAT
1 ACAACAACAATAAT
* * *
10563715 GCAACAAC-GT-AC
1 ACAACAACAATAAT
*
10563727 ACAATAACAATAAT
1 ACAACAACAATAAT
10563741 ACAACAACAATAAT
1 ACAACAACAATAAT
* * *
10563755 GCAACAAC-GT-AC
1 ACAACAACAATAAT
*
10563767 ACAATAACAATAAT
1 ACAACAACAATAAT
*
10563781 ACAACAACAACAAT
1 ACAACAACAATAAT
10563795 A
1 A
10563796 ATGAAACGTA
Statistics
Matches: 73, Mismatches: 18, Indels: 8
0.74 0.18 0.08
Matches are distributed among these distances:
12 14 0.19
13 4 0.05
14 55 0.75
ACGTcount: A:0.60, C:0.22, G:0.04, T:0.15
Consensus pattern (14 bp):
ACAACAACAATAAT
Found at i:10563730 original size:40 final size:40
Alignment explanation
Indices: 10563675--10563824 Score: 218
Period size: 40 Copynumber: 3.8 Consensus size: 40
10563665 AAAAAAAAAG
10563675 GCAACAACAG-ACACAATAACAATAATACAACAACAATAAT
1 GCAACAAC-GTACACAATAACAATAATACAACAACAATAAT
10563715 GCAACAACGTACACAATAACAATAATACAACAACAATAAT
1 GCAACAACGTACACAATAACAATAATACAACAACAATAAT
10563755 GCAACAACGTACACAATAACAATAATACAACAACAACAATAAT
1 GCAACAACGTACACAATAACAATAAT---ACAACAACAATAAT
* *
10563798 G--A-AACGTACACAATAACGATAAAACAA
1 GCAACAACGTACACAATAACAATAATACAA
10563825 TTATACAAAT
Statistics
Matches: 104, Mismatches: 2, Indels: 11
0.89 0.02 0.09
Matches are distributed among these distances:
37 4 0.04
39 1 0.01
40 83 0.80
41 1 0.01
43 15 0.14
ACGTcount: A:0.59, C:0.22, G:0.06, T:0.13
Consensus pattern (40 bp):
GCAACAACGTACACAATAACAATAATACAACAACAATAAT
Found at i:10571695 original size:50 final size:50
Alignment explanation
Indices: 10571590--10571715 Score: 134
Period size: 50 Copynumber: 2.5 Consensus size: 50
10571580 GGCGTGCTGG
* * *
10571590 AGAAGAAGAAAGAAGAAAGAAGAGAGAGGGAGAACAGCGACGTGTCGGAGC
1 AGAAGAAGAAAGAAG-AAGAAGAAAGAGGGAGAACAGCGACGTGTCGAAGA
** *
10571641 AGAAGAA-AAAGAAGAAGGAAGAAAGAGGGAGAGTAGCGAGGTG-CTGAAGA
1 AGAAGAAGAAAGAAGAA-GAAGAAAGAGGGAGAACAGCGACGTGTC-GAAGA
10571691 AGAAGGAAGAAAG-AGAAGAA-AAAGA
1 AGAA-GAAGAAAGAAGAAGAAGAAAGA
10571716 AGAAGGAAGA
Statistics
Matches: 65, Mismatches: 6, Indels: 10
0.80 0.07 0.12
Matches are distributed among these distances:
49 8 0.12
50 39 0.60
51 14 0.22
52 4 0.06
ACGTcount: A:0.52, C:0.06, G:0.38, T:0.04
Consensus pattern (50 bp):
AGAAGAAGAAAGAAGAAGAAGAAAGAGGGAGAACAGCGACGTGTCGAAGA
Found at i:10571747 original size:63 final size:63
Alignment explanation
Indices: 10571641--10571790 Score: 173
Period size: 63 Copynumber: 2.4 Consensus size: 63
10571631 GTGTCGGAGC
* * *
10571641 AGAAGAAAAAGAAGAAGGAAGAAAGAGGGAGAGTAGCGAGGTG-CTGAAGAAGAAGGAAGAAAG
1 AGAAGAAAAAGAAGAAGGAAGAAAGAGAGAGAGTAGCAAGGTGCCAG-AGAAGAAGGAAGAAAG
* * * **
10571704 AGAAGAAAAAGAAGAAGGAAGAGAGAGAGAGAG-AGCAACGGTGCCAGAGGATAAGGAAGAGGG
1 AGAAGAAAAAGAAGAAGGAAGAAAGAGAGAGAGTAGCAA-GGTGCCAGAGAAGAAGGAAGAAAG
*
10571767 AGAAGAAAAAAAAGAA-GAA-AAAGA
1 AGAAGAAAAAGAAGAAGGAAGAAAGA
10571791 AAGAAGGAAG
Statistics
Matches: 75, Mismatches: 10, Indels: 6
0.82 0.11 0.07
Matches are distributed among these distances:
61 4 0.05
62 7 0.09
63 62 0.83
64 2 0.03
ACGTcount: A:0.55, C:0.04, G:0.37, T:0.03
Consensus pattern (63 bp):
AGAAGAAAAAGAAGAAGGAAGAAAGAGAGAGAGTAGCAAGGTGCCAGAGAAGAAGGAAGAAAG
Found at i:10571782 original size:12 final size:13
Alignment explanation
Indices: 10571767--10571820 Score: 60
Period size: 12 Copynumber: 4.3 Consensus size: 13
10571757 AGGAAGAGGG
10571767 AGAAGAAAAA-AA
1 AGAAGAAAAAGAA
10571779 AGAAGAAAAAGAA
1 AGAAGAAAAAGAA
* *
10571792 AGAAG-GAAGGAA
1 AGAAGAAAAAGAA
10571804 TA-AAGAAAAAGAA
1 -AGAAGAAAAAGAA
10571817 AGAA
1 AGAA
10571821 AAGTATAAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
12 19 0.56
13 15 0.44
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (13 bp):
AGAAGAAAAAGAA
Found at i:10571796 original size:25 final size:25
Alignment explanation
Indices: 10571767--10571820 Score: 65
Period size: 25 Copynumber: 2.2 Consensus size: 25
10571757 AGGAAGAGGG
10571767 AGAA-GAAAAAAAAGAAGAAAAAGAA
1 AGAAGGAAAAAAAA-AAGAAAAAGAA
** *
10571792 AGAAGGAAGGAATAAAGAAAAAGAA
1 AGAAGGAAAAAAAAAAGAAAAAGAA
10571817 AGAA
1 AGAA
10571821 AAGTATAAGA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 19 0.76
26 6 0.24
ACGTcount: A:0.74, C:0.00, G:0.24, T:0.02
Consensus pattern (25 bp):
AGAAGGAAAAAAAAAAGAAAAAGAA
Found at i:10571919 original size:2 final size:2
Alignment explanation
Indices: 10571914--10571947 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
10571904 GCAGCATAAA
10571914 AT 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 AT
10571948 NNNNNNNNNN
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:10573452 original size:63 final size:60
Alignment explanation
Indices: 10573336--10573490 Score: 170
Period size: 61 Copynumber: 2.5 Consensus size: 60
10573326 CTCTCTTTTT
* * * *
10573336 TTCTTCTTCTTTTTCTTCTCCCTCTTCCTTATCCTCCGGGACCACTACTCTCCCTCTCTA
1 TTCTTCTTCTTTTTCTTCTCTCTCTTTCTTCTCCTCCGGCACCACTACTCTCCCTCTCTA
* * * *
10573396 TTCTTACTTCTTTTTTTTCTCTCTCTTTCTTCTCCTCCGGCACGCCATTGCTCTCCCTCTCTC
1 TTCTT-CTTCTTTTTCTTCTCTCTCTTTCTTCTCCTCCGGCA--CCACTACTCTCCCTCTCTA
* *
10573459 TTCCTT-TT-TTTTTCTTCTCTCTTTTTTTTCTC
1 TT-CTTCTTCTTTTTCTTCTCTCTCTTTCTTCTC
10573491 TCTTTTCCTT
Statistics
Matches: 80, Mismatches: 11, Indels: 7
0.82 0.11 0.07
Matches are distributed among these distances:
60 5 0.06
61 52 0.65
62 2 0.03
63 18 0.22
64 3 0.04
ACGTcount: A:0.05, C:0.37, G:0.05, T:0.53
Consensus pattern (60 bp):
TTCTTCTTCTTTTTCTTCTCTCTCTTTCTTCTCCTCCGGCACCACTACTCTCCCTCTCTA
Found at i:10573473 original size:134 final size:134
Alignment explanation
Indices: 10573329--10573628 Score: 329
Period size: 134 Copynumber: 2.2 Consensus size: 134
10573319 TCCTTCCCTC
* *
10573329 TCTTTTTTTCTTCT-TCTTTTTCTTCTCCCTCTTCCTTATCCTCCGGGAC-CACTACTCTCCCTC
1 TCTTTTTTTCTTCTCTCTTTTTCTTCTCCCTCTTCCTTATCCTCCGGCACGCACTACTCTCCCCC
** *
10573392 TCTATTCTTACTTCTTTTTT-TTCTCTCTCTTTCTTCTCCTCCGGCACGCCATTGCTCTCCCTCT
66 TCT-TT-TT--TTCTTTTTTCTTCTCTCTCTTTCTTCTCCTCCAACACGCCACTGCTCTCCCTCT
10573456 CTCTTCCT
127 CTCTTCCT
* * * * * * *
10573464 T-TTTTTTTCTTCTCTCTTTTTTTTCTCTCTTTTCCTTCTCCTTCGGCACGTCGCTGCTCTCCCC
1 TCTTTTTTTCTTCTCTCTTTTTCTTCTCCCTCTTCCTTATCCTCCGGCACG-CACTACTCTCCCC
* * * * * * *
10573528 CTCTTTTTTTTTTTTTTCTTCTCTCTTTTTTTTCTCCTCCAACATGTCACTGTTCTCCTTCTCTC
65 CTCTTTTTTTCTTTTTTCTTCTCTCTCTTTCTTCTCCTCCAACACGCCACTGCTCTCCCTCTCTC
10573593 TTCCT
130 TTCCT
*
10573598 TCTTCTTTCTTCTTCTCTCTCTTTCTTCTCC
1 TCTT-TTT-TTCTTCTCTCTTTTTCTTCTCC
10573629 TCCAGCACGC
Statistics
Matches: 136, Mismatches: 22, Indels: 12
0.80 0.13 0.07
Matches are distributed among these distances:
133 8 0.06
134 56 0.41
135 34 0.25
136 5 0.04
137 33 0.24
ACGTcount: A:0.04, C:0.37, G:0.05, T:0.54
Consensus pattern (134 bp):
TCTTTTTTTCTTCTCTCTTTTTCTTCTCCCTCTTCCTTATCCTCCGGCACGCACTACTCTCCCCC
TCTTTTTTTCTTTTTTCTTCTCTCTCTTTCTTCTCCTCCAACACGCCACTGCTCTCCCTCTCTCT
TCCT
Found at i:10573485 original size:15 final size:14
Alignment explanation
Indices: 10573462--10573496 Score: 52
Period size: 16 Copynumber: 2.4 Consensus size: 14
10573452 CTCTCTCTTC
10573462 CTTTTTTTTTCTTCT
1 CTTTTTTTTTC-TCT
10573477 CTCTTTTTTTTCTCT
1 CT-TTTTTTTTCTCT
10573492 CTTTT
1 CTTTT
10573497 CCTTCTCCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 3 0.16
15 7 0.37
16 9 0.47
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (14 bp):
CTTTTTTTTTCTCT
Found at i:10573502 original size:13 final size:13
Alignment explanation
Indices: 10573467--10573503 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
10573457 TCTTCCTTTT
10573467 TTTTTCTTCTCTC
1 TTTTTCTTCTCTC
*
10573480 TTTTTTTTCTCTC
1 TTTTTCTTCTCTC
*
10573493 TTTTCCTTCTC
1 TTTTTCTTCTC
10573504 CTTCGGCACG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (13 bp):
TTTTTCTTCTCTC
Found at i:10573553 original size:73 final size:74
Alignment explanation
Indices: 10573396--10573563 Score: 234
Period size: 74 Copynumber: 2.3 Consensus size: 74
10573386 TCCCTCTCTA
* *
10573396 TTCTTACT-TCTTTTTTTTCTCTCTCTTTCTTCTCCTCCGGCACGCCATTGCTCTCCCTCTCTCT
1 TTCTT-CTCTCTTTTTTTTCTCTCTCTTTCTTCTCCTCCGGCACGCCACTGCTCTCCCCCTCTCT
10573460 TCCTTTTTTT
65 TCCTTTTTTT
* * *
10573470 TTCTTCTCTCTTTTTTTTCTCTCT-TTTCCTTCTCCTTCGGCACGTCGCTGCTCTCCCCCTCT-T
1 TTCTTCTCTCTTTTTTTTCTCTCTCTTT-CTTCTCCTCCGGCACGCCACTGCTCTCCCCCTCTCT
**
10573533 TTTTTTTTTT
65 TCCTTTTTTT
10573543 TTCTTCTCTCTTTTTTTTCTC
1 TTCTTCTCTCTTTTTTTTCTC
10573564 CTCCAACATG
Statistics
Matches: 85, Mismatches: 7, Indels: 5
0.88 0.07 0.05
Matches are distributed among these distances:
73 35 0.41
74 50 0.59
ACGTcount: A:0.02, C:0.35, G:0.05, T:0.58
Consensus pattern (74 bp):
TTCTTCTCTCTTTTTTTTCTCTCTCTTTCTTCTCCTCCGGCACGCCACTGCTCTCCCCCTCTCTT
CCTTTTTTT
Found at i:10573585 original size:60 final size:62
Alignment explanation
Indices: 10573470--10573637 Score: 162
Period size: 60 Copynumber: 2.7 Consensus size: 62
10573460 TCCTTTTTTT
* * ** *
10573470 TTCTTCTCTCTTTTTT-TTCTCTCTTTTCCTTCTCCTTCGGCACGTCGCTGCTCTCC-CCCTC
1 TTCTTCT-TCTTTTTTCTTCTCTCTTTTTCTTCTCCTCCAACACGTCACTGCTCTCCTCCCTC
* * * * * *
10573531 TT-TTTTTTTTTTTTCTTCTCTCTTTTTTTTCTCCTCCAACATGTCACTGTTCTCCTTCTCTC
1 TTCTTCTTCTTTTTTCTTCTCTCTTTTTCTTCTCCTCCAACACGTCACTGCTCTCC-TCCCTC
* * *
10573593 TTCCTTCTTCTTTCTTCTTCTCTCTCTTTCTTCTCCTCCAGCACG
1 TT-CTTCTTCTTTTTTCTTCTCTCTTTTTCTTCTCCTCCAACACG
10573638 CTGCTCTCCC
Statistics
Matches: 84, Mismatches: 18, Indels: 7
0.77 0.17 0.06
Matches are distributed among these distances:
59 7 0.08
60 35 0.42
61 2 0.02
62 6 0.07
64 34 0.40
ACGTcount: A:0.04, C:0.36, G:0.05, T:0.54
Consensus pattern (62 bp):
TTCTTCTTCTTTTTTCTTCTCTCTTTTTCTTCTCCTCCAACACGTCACTGCTCTCCTCCCTC
Found at i:10573667 original size:14 final size:14
Alignment explanation
Indices: 10573648--10573687 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
10573638 CTGCTCTCCC
10573648 TTTCTCTCTTTC-T
1 TTTCTCTCTTTCTT
10573661 TTT-TCTCTTTCTT
1 TTTCTCTCTTTCTT
10573674 TCTTCTC-CTTTCTT
1 T-TTCTCTCTTTCTT
10573688 CTTTTATTTC
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
12 8 0.33
13 5 0.21
14 9 0.38
15 2 0.08
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (14 bp):
TTTCTCTCTTTCTT
Found at i:10573874 original size:24 final size:23
Alignment explanation
Indices: 10573842--10573914 Score: 76
Period size: 24 Copynumber: 3.2 Consensus size: 23
10573832 GTCTCTTTTC
* *
10573842 TTTTTT-TTTAATTATATATATA
1 TTTTTTATTTTATTATATATTTA
* *
10573864 TTTTTTATTTTTTTATTATTTTTA
1 TTTTTTATTTTATTA-TATATTTA
* *
10573888 TTATTTATTTTATTATTTATTTA
1 TTTTTTATTTTATTATATATTTA
10573911 TTTT
1 TTTT
10573915 ATTCTCTTTC
Statistics
Matches: 40, Mismatches: 9, Indels: 3
0.77 0.17 0.06
Matches are distributed among these distances:
22 6 0.15
23 15 0.38
24 19 0.47
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTTTTATTTTATTATATATTTA
Found at i:10573877 original size:8 final size:8
Alignment explanation
Indices: 10573864--10573914 Score: 59
Period size: 8 Copynumber: 6.4 Consensus size: 8
10573854 TATATATATA
10573864 TTTTTTAT
1 TTTTTTAT
10573872 TTTTTTAT
1 TTTTTTAT
10573880 TATTTTTA-
1 T-TTTTTAT
*
10573888 TTATTTAT
1 TTTTTTAT
*
10573896 TTTATTAT
1 TTTTTTAT
*
10573904 TTATTTAT
1 TTTTTTAT
10573912 TTT
1 TTT
10573915 ATTCTCTTTC
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
7 5 0.14
8 24 0.69
9 6 0.17
ACGTcount: A:0.20, C:0.00, G:0.00, T:0.80
Consensus pattern (8 bp):
TTTTTTAT
Found at i:10573877 original size:29 final size:31
Alignment explanation
Indices: 10573837--10573912 Score: 84
Period size: 32 Copynumber: 2.5 Consensus size: 31
10573827 TGCGAGTCTC
*
10573837 TTTTCTTTTTTT-TTAATTATA-TATATATT
1 TTTTATTTTTTTATTAATTATATTATATATT
* * *
10573866 TTTTATTTTTTTATTATTTTTATTATTTATT
1 TTTTATTTTTTTATTAATTATATTATATATT
*
10573897 TTATTATTTATTTATT
1 TT-TTATTTTTTTATT
10573913 TTATTCTCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 11 0.28
30 7 0.18
31 9 0.23
32 12 0.31
ACGTcount: A:0.22, C:0.01, G:0.00, T:0.76
Consensus pattern (31 bp):
TTTTATTTTTTTATTAATTATATTATATATT
Found at i:10573891 original size:12 final size:12
Alignment explanation
Indices: 10573868--10573917 Score: 54
Period size: 11 Copynumber: 4.4 Consensus size: 12
10573858 TATATATTTT
10573868 TTATTTTT-TTA
1 TTATTTTTATTA
10573879 TTATTTTTATTA
1 TTATTTTTATTA
10573891 TT-TATTTTATTA
1 TTAT-TTTTATTA
*
10573903 TT-TATTTATT-
1 TTATTTTTATTA
10573913 TTATT
1 TTATT
10573918 CTCTTTCATT
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
10 2 0.06
11 16 0.47
12 16 0.47
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (12 bp):
TTATTTTTATTA
Found at i:10573915 original size:9 final size:9
Alignment explanation
Indices: 10573867--10573917 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
10573857 ATATATATTT
10573867 TTTATTTT-
1 TTTATTTTA
10573875 TTTA--TTA
1 TTTATTTTA
10573882 TTT-TTATTA
1 TTTATT-TTA
10573891 TTTATTTTA
1 TTTATTTTA
10573900 -TTA-TTTA
1 TTTATTTTA
10573907 TTTATTTTA
1 TTTATTTTA
10573916 TT
1 TT
10573918 CTCTTTCATT
Statistics
Matches: 36, Mismatches: 0, Indels: 13
0.73 0.00 0.27
Matches are distributed among these distances:
6 2 0.06
7 7 0.19
8 10 0.28
9 15 0.42
10 2 0.06
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (9 bp):
TTTATTTTA
Found at i:10581158 original size:74 final size:72
Alignment explanation
Indices: 10581043--10581193 Score: 207
Period size: 74 Copynumber: 2.1 Consensus size: 72
10581033 TCTCCCTCTC
*
10581043 TCTTC-CTTTTTCTTTTTTTTTCTCTCTCTTCTTTCTCCTCCGACATGTCGCTGCTCTCCCTCTC
1 TCTTCTCTTTTTCTTTTTTTTTCTCTCTCTTCTTTCTCCTCCGACATGTCACTGCTCTCCCTCTC
10581107 TCTTCCT
66 TCTTCCT
* * * *
10581114 TCTTCTCTTCTTTCTTTTTTTTT-TCTTTCTTTTTCTTCTCCTCCGACATGTCATTGTTCTCCCT
1 TCTTCTCTT-TTTCTTTTTTTTTCTCTCTC-TTCT-TTCTCCTCCGACATGTCACTGCTCTCCCT
10581178 CTCTCTTCCT
63 CTCTCTTCCT
*
10581188 TTTTCT
1 TCTTCT
10581194 TCCTCATTCT
Statistics
Matches: 70, Mismatches: 6, Indels: 5
0.86 0.07 0.06
Matches are distributed among these distances:
71 5 0.07
72 8 0.11
73 16 0.23
74 41 0.59
ACGTcount: A:0.03, C:0.34, G:0.05, T:0.58
Consensus pattern (72 bp):
TCTTCTCTTTTTCTTTTTTTTTCTCTCTCTTCTTTCTCCTCCGACATGTCACTGCTCTCCCTCTC
TCTTCCT
Found at i:10581213 original size:74 final size:75
Alignment explanation
Indices: 10581075--10581219 Score: 177
Period size: 74 Copynumber: 1.9 Consensus size: 75
10581065 TCTCTCTTCT
* * * *** *
10581075 TTCTCCTCCGACATGTCGCTGCTCTCCCTCTCTCTTCCTTCTTCTCTTCTTTCTTTTTTTTTTCT
1 TTCTCCTCCGACATGTCACTGCTCTCCCTCTCTCTTCCTTCTTCTCCTCATTCTTCCCTCTTTCT
10581140 T-TCTTTTTC
66 TCTCTTTTTC
* * *
10581149 TTCTCCTCCGACATGTCATTGTTCTCCCTCTCTCTTCCTTTTTCTTCCTCATTC-TCCCTCTTTC
1 TTCTCCTCCGACATGTCACTGCTCTCCCTCTCTCTTCCTTCTTC-TCCTCATTCTTCCCTCTTTC
10581213 TTCTCTT
65 TTCTCTT
10581220 CCAGCACGCT
Statistics
Matches: 59, Mismatches: 10, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
74 48 0.81
75 11 0.19
ACGTcount: A:0.04, C:0.37, G:0.05, T:0.54
Consensus pattern (75 bp):
TTCTCCTCCGACATGTCACTGCTCTCCCTCTCTCTTCCTTCTTCTCCTCATTCTTCCCTCTTTCT
TCTCTTTTTC
Found at i:10581257 original size:12 final size:12
Alignment explanation
Indices: 10581237--10581275 Score: 51
Period size: 12 Copynumber: 3.1 Consensus size: 12
10581227 GCTACCCTTC
*
10581237 CTTTCTCTCTTT
1 CTTTTTCTCTTT
10581249 CTTTTTCTCTTT
1 CTTTTTCTCTTT
10581261 CTTTCTTCTCCTTT
1 CTTT-TTCT-CTTT
10581275 C
1 C
10581276 CTCTTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 15 0.62
13 4 0.17
14 5 0.21
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (12 bp):
CTTTTTCTCTTT
Found at i:10581262 original size:20 final size:21
Alignment explanation
Indices: 10581237--10581281 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
10581227 GCTACCCTTC
* *
10581237 CTTTCTCTCTT-TCTTTTTCT
1 CTTTCTCTCTTCTCCTTTCCT
*
10581257 CTTTCTTTCTTCTCCTTTCCT
1 CTTTCTCTCTTCTCCTTTCCT
10581278 CTTT
1 CTTT
10581282 TATTTCTTTT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 10 0.48
21 11 0.52
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (21 bp):
CTTTCTCTCTTCTCCTTTCCT
Found at i:10583299 original size:22 final size:21
Alignment explanation
Indices: 10583274--10583318 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
10583264 ATATATATAT
10583274 TTATATTTATATATTT-TTTCTA
1 TTATATTTAT-TATTTATTT-TA
*
10583296 TTATTTTTATTATTTATTTTA
1 TTATATTTATTATTTATTTTA
10583317 TT
1 TT
10583319 CCCTTCCATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.73
Consensus pattern (21 bp):
TTATATTTATTATTTATTTTA
Found at i:10584423 original size:14 final size:14
Alignment explanation
Indices: 10584406--10584436 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
10584396 AATATCTATT
*
10584406 TCAATATATTTTCA
1 TCAAAATATTTTCA
10584420 TCAAAATATTTTCA
1 TCAAAATATTTTCA
10584434 TCA
1 TCA
10584437 TCCAGTGCTC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.39, C:0.16, G:0.00, T:0.45
Consensus pattern (14 bp):
TCAAAATATTTTCA
Found at i:10587296 original size:2 final size:2
Alignment explanation
Indices: 10587289--10587352 Score: 105
Period size: 2 Copynumber: 33.0 Consensus size: 2
10587279 ATTCCTGGTT
10587289 TA TA TA TA TA TA TA -A 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 TA TA TA
*
10587330 TA T- TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA
10587353 CATTATGTAC
Statistics
Matches: 58, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
1 2 0.03
2 56 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:10587352 original size:23 final size:23
Alignment explanation
Indices: 10587288--10587358 Score: 110
Period size: 23 Copynumber: 3.2 Consensus size: 23
10587278 CATTCCTGGT
10587288 TTATATATATATATA-ATATATA
1 TTATATATATATATATATATATA
10587310 -TATATATATATATATATATATA
1 TTATATATATATATATATATATA
* *
10587332 TTATATATATATATATTTATACA
1 TTATATATATATATATATATATA
10587355 TTAT
1 TTAT
10587359 GTACAAAATA
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
21 14 0.31
22 7 0.16
23 24 0.53
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (23 bp):
TTATATATATATATATATATATA
Found at i:10588592 original size:14 final size:14
Alignment explanation
Indices: 10588573--10588603 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
10588563 TTAGTCTGAA
10588573 CAAAGTGTGGCATT
1 CAAAGTGTGGCATT
10588587 CAAAGTGTGGCATT
1 CAAAGTGTGGCATT
10588601 CAA
1 CAA
10588604 GATTTGGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (14 bp):
CAAAGTGTGGCATT
Found at i:10592592 original size:17 final size:17
Alignment explanation
Indices: 10592570--10592604 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
10592560 TATATTTGAG
*
10592570 TTTTGAGTTGTTTAAAA
1 TTTTGAATTGTTTAAAA
10592587 TTTTGAATTGTTTAAAA
1 TTTTGAATTGTTTAAAA
10592604 T
1 T
10592605 CAAGTTCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.31, C:0.00, G:0.14, T:0.54
Consensus pattern (17 bp):
TTTTGAATTGTTTAAAA
Found at i:10594727 original size:27 final size:27
Alignment explanation
Indices: 10594697--10594755 Score: 93
Period size: 26 Copynumber: 2.2 Consensus size: 27
10594687 TTTTCTTTTC
* *
10594697 TTTTATTTCCTTCTTTTTTTGCCCAAA
1 TTTTAGTTCCTTCTTTCTTTGCCCAAA
10594724 TTTT-GTTCCTTCTTTCTTTGCCCAAA
1 TTTTAGTTCCTTCTTTCTTTGCCCAAA
10594750 TTTTAG
1 TTTTAG
10594756 AATTATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
26 24 0.83
27 5 0.17
ACGTcount: A:0.14, C:0.22, G:0.07, T:0.58
Consensus pattern (27 bp):
TTTTAGTTCCTTCTTTCTTTGCCCAAA
Found at i:10594827 original size:17 final size:17
Alignment explanation
Indices: 10594805--10594843 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
10594795 ATGCATGACT
10594805 TAATTGCCTAAAGAA-TA
1 TAATTGCCTAAA-AAGTA
*
10594822 TAATTGTCTAAAAAGTA
1 TAATTGCCTAAAAAGTA
10594839 TAATT
1 TAATT
10594844 TTTTACTTTG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 2 0.10
17 18 0.90
ACGTcount: A:0.46, C:0.08, G:0.10, T:0.36
Consensus pattern (17 bp):
TAATTGCCTAAAAAGTA
Found at i:10598696 original size:34 final size:34
Alignment explanation
Indices: 10598653--10598726 Score: 130
Period size: 34 Copynumber: 2.2 Consensus size: 34
10598643 TCTTCTCTCG
*
10598653 TTATAATTTCAAAACTCTAAATTCTTAATTTTGA
1 TTATAATTTCAAAACTCTAAAATCTTAATTTTGA
*
10598687 TTATAATTTCAAAACTCTAAAATCTTGATTTTGA
1 TTATAATTTCAAAACTCTAAAATCTTAATTTTGA
10598721 TTATAA
1 TTATAA
10598727 ACATGGGTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
34 38 1.00
ACGTcount: A:0.39, C:0.11, G:0.04, T:0.46
Consensus pattern (34 bp):
TTATAATTTCAAAACTCTAAAATCTTAATTTTGA
Found at i:10598795 original size:136 final size:136
Alignment explanation
Indices: 10598551--10598828 Score: 430
Period size: 136 Copynumber: 2.0 Consensus size: 136
10598541 TCTTCTCCCG
* *
10598551 TTATAATTTCAAAACTCTAAATTCTTAATTTTGATTATAAACATGGGTTTTTCACCACTTATCAG
1 TTATAATTTCAAAACTCTAAAATCTTAATTTTGATTATAAACATGGGTTTTTCACCACTTATCAA
* * * * * *
10598616 ACGTATCCTTGTTAACTAATCTTTTCATCTTCTCTCGTTATAATTTCAAAACTCTAAATTCTTAA
66 ACATATCCTTCTCAACCAATCTCTTCATCTTCTCCCGTTATAATTTCAAAACTCTAAATTCTTAA
10598681 TTTTGA
131 TTTTGA
*
10598687 TTATAATTTCAAAACTCTAAAATCTTGATTTTGATTATAAACATGGGTTTTTCACCACTTATCAA
1 TTATAATTTCAAAACTCTAAAATCTTAATTTTGATTATAAACATGGGTTTTTCACCACTTATCAA
* * * *
10598752 ACATGTCTTTCTCAACCAATCTCTTCTTCTTCTCCCGTTATAATTTCAAAACTCTAAATTTTTAA
66 ACATATCCTTCTCAACCAATCTCTTCATCTTCTCCCGTTATAATTTCAAAACTCTAAATTCTTAA
10598817 TTTTGA
131 TTTTGA
*
10598823 TAATAA
1 TTATAA
10598829 ACATGGGTTT
Statistics
Matches: 128, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
136 128 1.00
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (136 bp):
TTATAATTTCAAAACTCTAAAATCTTAATTTTGATTATAAACATGGGTTTTTCACCACTTATCAA
ACATATCCTTCTCAACCAATCTCTTCATCTTCTCCCGTTATAATTTCAAAACTCTAAATTCTTAA
TTTTGA
Found at i:10599339 original size:202 final size:203
Alignment explanation
Indices: 10598985--10599388 Score: 605
Period size: 202 Copynumber: 2.0 Consensus size: 203
10598975 CTCTAAATTC
* *
10598985 TTAATTTTGATTCTTAAAGATAATATTTATTTCAATCTTCTTCTTAGTTTACCATTTTCTATATA
1 TTAATTTTGATTCTTAAAAATAATATTTATTTCAATATTCTTCTTAGTTTACCATTTTCTATATA
*
10599050 TTGTGATTGTTTATTTATCACTTTTATTTGATTAACAAAAGAGACTTTTCAAACACCTTCGAAAC
66 ---TGATTGTTTATTTATCACTTTTATTTGATTAACAAAAGAGACTTTTCAAACACCTTCAAAAC
* * * * *
10599115 TCACATGGTGAAGACATCATTCTAAAGTTTTAACGTGATAATCCTATGGGGCTCATGATGTAAAC
128 TCACATGGTGAAGACATCATTCTAAAGTTTCAACATGATAATCCTATAGGACTCACGATGTAAAC
10599180 AAGAAAATGGA
193 AAGAAAATGGA
* *
10599191 TTAATTTTGATTCTTAAAAATAATATTTATTTCAATATTCTTCTTAGTTTACCATTTTCTCTGTA
1 TTAATTTTGATTCTTAAAAATAATATTTATTTCAATATTCTTCTTAGTTTACCATTTTCTATATA
* *
10599256 -GATTGTTTATTTATCACTTTTATTTGATTAACAAAAGAGAGTTTTCAAACACCTTTAAAACTCA
66 TGATTGTTTATTTATCACTTTTATTTGATTAACAAAAGAGACTTTTCAAACACCTTCAAAACTCA
** * * *
10599320 CATGGTGAAGA-AGTCATTCTGTAGTTTCAACATGATAATCTTGTAGGACTCACGTTGTAAACAA
131 CATGGTGAAGACA-TCATTCTAAAGTTTCAACATGATAATCCTATAGGACTCACGATGTAAACAA
10599384 GAAAA
195 GAAAA
10599389 ACGGATTTTT
Statistics
Matches: 180, Mismatches: 17, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
201 1 0.01
202 118 0.66
206 61 0.34
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.41
Consensus pattern (203 bp):
TTAATTTTGATTCTTAAAAATAATATTTATTTCAATATTCTTCTTAGTTTACCATTTTCTATATA
TGATTGTTTATTTATCACTTTTATTTGATTAACAAAAGAGACTTTTCAAACACCTTCAAAACTCA
CATGGTGAAGACATCATTCTAAAGTTTCAACATGATAATCCTATAGGACTCACGATGTAAACAAG
AAAATGGA
Found at i:10599920 original size:25 final size:23
Alignment explanation
Indices: 10599866--10599908 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
10599856 CTATAAATAT
*
10599866 CATCTTCCAGCAGCTTCTTCTCA
1 CATCTTTCAGCAGCTTCTTCTCA
10599889 CAT-TTTCAGCAGCTTCTTCT
1 CATCTTTCAGCAGCTTCTTCT
10599909 TCTTCTTCTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 16 0.84
23 3 0.16
ACGTcount: A:0.16, C:0.35, G:0.09, T:0.40
Consensus pattern (23 bp):
CATCTTTCAGCAGCTTCTTCTCA
Found at i:10600776 original size:42 final size:43
Alignment explanation
Indices: 10600716--10600807 Score: 134
Period size: 42 Copynumber: 2.2 Consensus size: 43
10600706 TTTTGTGTAA
*
10600716 TGATGATGACCCAACTATGTGCGTGT-GGGAGTGCACATGAGC
1 TGATGATGACCCAACTATGTGCGAGTGGGGAGTGCACATGAGC
* * *
10600758 TGATGATGACCCAGCTATGTGTGAGTGGGGAGTGCACATGGGC
1 TGATGATGACCCAACTATGTGCGAGTGGGGAGTGCACATGAGC
10600801 TG-TGATG
1 TGATGATG
10600808 GTGGGGTGGT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 28 0.62
43 17 0.38
ACGTcount: A:0.22, C:0.16, G:0.37, T:0.25
Consensus pattern (43 bp):
TGATGATGACCCAACTATGTGCGAGTGGGGAGTGCACATGAGC
Found at i:10607942 original size:21 final size:21
Alignment explanation
Indices: 10607896--10607951 Score: 53
Period size: 21 Copynumber: 2.7 Consensus size: 21
10607886 TATTATAAAG
*
10607896 AAATATA-ATTACTATT-ATAT
1 AAATATATA-TACTTTTAATAT
* *
10607916 ATATATGTATACTTTTAATAT
1 AAATATATATACTTTTAATAT
*
10607937 AAATATATTTACTTT
1 AAATATATATACTTT
10607952 CTATTTTGTA
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
20 11 0.39
21 17 0.61
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (21 bp):
AAATATATATACTTTTAATAT
Found at i:10608317 original size:21 final size:21
Alignment explanation
Indices: 10608287--10608326 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
10608277 GTGTGTATAT
*
10608287 ATATATATATATATACTTTAA
1 ATATAAATATATATACTTTAA
*
10608308 ATATAAATATATTTACTTT
1 ATATAAATATATATACTTT
10608327 TTATTTTGTA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (21 bp):
ATATAAATATATATACTTTAA
Found at i:10624207 original size:15 final size:15
Alignment explanation
Indices: 10624187--10624230 Score: 61
Period size: 15 Copynumber: 2.9 Consensus size: 15
10624177 ATTTTTCCTC
*
10624187 CAATCATATTGCTTG
1 CAATCATATTGCATG
* *
10624202 CAATCACATTACATG
1 CAATCATATTGCATG
10624217 CAATCATATTGCAT
1 CAATCATATTGCAT
10624231 TGTAAAATAT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.34, C:0.23, G:0.09, T:0.34
Consensus pattern (15 bp):
CAATCATATTGCATG
Found at i:10627126 original size:24 final size:26
Alignment explanation
Indices: 10627083--10627139 Score: 75
Period size: 25 Copynumber: 2.3 Consensus size: 26
10627073 CTTGTCCTTT
*
10627083 TTAACTAA-TTATTTTATTATTTAAAA
1 TTAA-TAATTTATTTTATTATATAAAA
10627109 -TAATAATTTATTTT-TTATATAAAA
1 TTAATAATTTATTTTATTATATAAAA
10627133 TTAATAA
1 TTAATAA
10627140 ATCTATAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 12 0.43
25 16 0.57
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (26 bp):
TTAATAATTTATTTTATTATATAAAA
Found at i:10627593 original size:30 final size:29
Alignment explanation
Indices: 10627559--10627648 Score: 90
Period size: 30 Copynumber: 3.0 Consensus size: 29
10627549 TTAAAAATAA
10627559 TATAATATTTAAATAAAATTTTAAATTATT
1 TATAATATTTAAAT-AAATTTTAAATTATT
* * * *
10627589 TATAAAAATTTAAATAAATTTTTATTTTTT
1 TAT-AATATTTAAATAAATTTTAAATTATT
* * *
10627619 TATTATATTTAATTAAATCTTTATATTATT
1 TATAATATTTAAATAAAT-TTTAAATTATT
10627649 ATTTTAGATC
Statistics
Matches: 47, Mismatches: 11, Indels: 4
0.76 0.18 0.06
Matches are distributed among these distances:
29 12 0.26
30 25 0.53
31 10 0.21
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (29 bp):
TATAATATTTAAATAAATTTTAAATTATT
Found at i:10627641 original size:29 final size:29
Alignment explanation
Indices: 10627563--10627651 Score: 81
Period size: 29 Copynumber: 3.0 Consensus size: 29
10627553 AAATAATATA
* *
10627563 ATATTTAAATAAAAT-TTTAAATTATTTATAA
1 ATATTTAAAT-AAATCTTTATATTA-TTAT-T
* * * *
10627594 AAATTTAAATAAATTTTTATTTTTTTATT
1 ATATTTAAATAAATCTTTATATTATTATT
*
10627623 ATATTTAATTAAATCTTTATATTATTATT
1 ATATTTAAATAAATCTTTATATTATTATT
10627652 TTAGATCAAA
Statistics
Matches: 47, Mismatches: 10, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
29 24 0.51
30 8 0.17
31 15 0.32
ACGTcount: A:0.43, C:0.01, G:0.00, T:0.56
Consensus pattern (29 bp):
ATATTTAAATAAATCTTTATATTATTATT
Found at i:10629162 original size:3 final size:3
Alignment explanation
Indices: 10629156--10629190 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
10629146 CTATCATTAG
10629156 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
10629191 AAATAAATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:10659641 original size:15 final size:15
Alignment explanation
Indices: 10659621--10659669 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
10659611 AAATATTTAC
10659621 TAATAATAAATAAAA
1 TAATAATAAATAAAA
10659636 TAATAATAAATAAAA
1 TAATAATAAATAAAA
10659651 T-A-AATAAA-ATAAA
1 TAATAATAAATA-AAA
10659664 TAATAA
1 TAATAA
10659670 ATACAAAAAT
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
12 1 0.03
13 10 0.32
14 2 0.06
15 18 0.58
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (15 bp):
TAATAATAAATAAAA
Found at i:10659652 original size:9 final size:9
Alignment explanation
Indices: 10659625--10659666 Score: 63
Period size: 9 Copynumber: 5.0 Consensus size: 9
10659615 ATTTACTAAT
10659625 AATAAATAA
1 AATAAATAA
10659634 AAT-AAT--
1 AATAAATAA
10659640 AATAAATAA
1 AATAAATAA
10659649 AATAAATAA
1 AATAAATAA
10659658 AATAAATAA
1 AATAAATAA
10659667 TAAATACAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
6 3 0.10
7 3 0.10
8 3 0.10
9 21 0.70
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
AATAAATAA
Found at i:10659678 original size:28 final size:24
Alignment explanation
Indices: 10659625--10659680 Score: 87
Period size: 24 Copynumber: 2.3 Consensus size: 24
10659615 ATTTACTAAT
10659625 AATAAATAAAATAATAATAAATAA
1 AATAAATAAAATAATAATAAATAA
*
10659649 AATAAATAAAATAAATAATAAATAC
1 AATAAATAAAAT-AATAATAAATAA
10659674 AA-AAATA
1 AATAAATA
10659681 CCATGATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
24 17 0.57
25 13 0.43
ACGTcount: A:0.75, C:0.02, G:0.00, T:0.23
Consensus pattern (24 bp):
AATAAATAAAATAATAATAAATAA
Found at i:10664770 original size:26 final size:28
Alignment explanation
Indices: 10664714--10664778 Score: 80
Period size: 29 Copynumber: 2.4 Consensus size: 28
10664704 ACATGCTTTC
*
10664714 ATTATAATAATTTGAAACCTTTCAAAAAA
1 ATTATAATAATTTGAAACATTT-AAAAAA
*
10664743 ATTATAATAATTTGAAA-ATTT-AAGAA
1 ATTATAATAATTTGAAACATTTAAAAAA
*
10664769 ATTAAAATAA
1 ATTATAATAA
10664779 GAGTTTTGAT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
26 13 0.39
28 3 0.09
29 17 0.52
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.35
Consensus pattern (28 bp):
ATTATAATAATTTGAAACATTTAAAAAA
Found at i:10674096 original size:3 final size:3
Alignment explanation
Indices: 10674088--10674116 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
10674078 TATTCCCATA
10674088 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
10674117 AAAGCAGCAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:10682188 original size:45 final size:45
Alignment explanation
Indices: 10682126--10682219 Score: 109
Period size: 45 Copynumber: 2.1 Consensus size: 45
10682116 ATTAAATTTA
* * * *
10682126 AATAATACTAAATAATATTCTTTATTACATTTATTATATTCAAAT
1 AATAATACTAAATAATATGCCTTATAACATTTATTATAGTCAAAT
* * *
10682171 AATAATATTAAGA-AATATGCCTTATAATATTTATTATAGTGAAAT
1 AATAATACTAA-ATAATATGCCTTATAACATTTATTATAGTCAAAT
10682216 AATA
1 AATA
10682220 TTAGTATATT
Statistics
Matches: 41, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
45 40 0.98
46 1 0.02
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (45 bp):
AATAATACTAAATAATATGCCTTATAACATTTATTATAGTCAAAT
Found at i:10690710 original size:2 final size:2
Alignment explanation
Indices: 10690703--10690741 Score: 50
Period size: 2 Copynumber: 21.5 Consensus size: 2
10690693 AAAGGTTATT
10690703 TA TA TA TA -A T- TA TA TA -A TA TA TA TA TA TA TA TA TA -A TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10690741 T
1 T
10690742 GAATGCTTAT
Statistics
Matches: 33, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
1 4 0.12
2 29 0.88
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:10690718 original size:8 final size:9
Alignment explanation
Indices: 10690703--10690741 Score: 62
Period size: 9 Copynumber: 4.3 Consensus size: 9
10690693 AAAGGTTATT
10690703 TATATATAA
1 TATATATAA
10690712 T-TATATAA
1 TATATATAA
10690720 TATATATATA
1 TATATATA-A
10690730 TATATATAA
1 TATATATAA
10690739 TAT
1 TAT
10690742 GAATGCTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
8 8 0.29
9 11 0.39
10 9 0.32
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (9 bp):
TATATATAA
Found at i:10690725 original size:19 final size:19
Alignment explanation
Indices: 10690703--10690741 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
10690693 AAAGGTTATT
10690703 TATATATA-AT-TATATAA
1 TATATATATATATATATAA
10690720 TATATATATATATATATAA
1 TATATATATATATATATAA
10690739 TAT
1 TAT
10690742 GAATGCTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 8 0.40
18 2 0.10
19 10 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (19 bp):
TATATATATATATATATAA
Found at i:10690978 original size:19 final size:21
Alignment explanation
Indices: 10690954--10690994 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
10690944 AGCAAATGAG
10690954 AAGAATA-A-AAAAAAAAGAA
1 AAGAATAGAGAAAAAAAAGAA
10690973 AAGAATAGAGAAAAAAAAGAA
1 AAGAATAGAGAAAAAAAAGAA
10690994 A
1 A
10690995 TATTTATATT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
19 7 0.35
20 1 0.05
21 12 0.60
ACGTcount: A:0.80, C:0.00, G:0.15, T:0.05
Consensus pattern (21 bp):
AAGAATAGAGAAAAAAAAGAA
Found at i:10699768 original size:20 final size:20
Alignment explanation
Indices: 10699743--10699797 Score: 92
Period size: 20 Copynumber: 2.8 Consensus size: 20
10699733 CCAGGAGCAG
10699743 TGGTTTAAGGTATAAAAATA
1 TGGTTTAAGGTATAAAAATA
10699763 TGGTTTAAGGTATAAAAATA
1 TGGTTTAAGGTATAAAAATA
* *
10699783 AGGTTTAAGGAATAA
1 TGGTTTAAGGTATAA
10699798 GGAATATATG
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 33 1.00
ACGTcount: A:0.45, C:0.00, G:0.22, T:0.33
Consensus pattern (20 bp):
TGGTTTAAGGTATAAAAATA
Found at i:10701242 original size:2 final size:2
Alignment explanation
Indices: 10701235--10701272 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
10701225 TTATAATAAT
10701235 TA TA TA TA 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 TA
10701273 ATAATCTGAC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10704991 original size:2 final size:2
Alignment explanation
Indices: 10704986--10705033 Score: 87
Period size: 2 Copynumber: 24.0 Consensus size: 2
10704976 TGTGTTTGTG
*
10704986 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
10705028 TA TA TA
1 TA TA TA
10705034 CACCGTCGAG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10712274 original size:16 final size:16
Alignment explanation
Indices: 10712249--10712300 Score: 63
Period size: 16 Copynumber: 3.3 Consensus size: 16
10712239 CATGAAAATT
*
10712249 TATTAATTAATTAATA
1 TATTATTTAATTAATA
10712265 TATTATTTAATTAATA
1 TATTATTTAATTAATA
*
10712281 -ATT-TATTAATTGATA
1 TATTAT-TTAATTAATA
10712296 TATTA
1 TATTA
10712301 ATAAAAAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
14 1 0.03
15 12 0.39
16 18 0.58
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (16 bp):
TATTATTTAATTAATA
Found at i:10713095 original size:2 final size:2
Alignment explanation
Indices: 10713047--10713082 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
10713037 TTGAGTCATG
10713047 TA TA TA 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
10713083 ATTTTGATAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:10713250 original size:15 final size:15
Alignment explanation
Indices: 10713230--10713259 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
10713220 TAATCAAGAT
*
10713230 TATTAATTTTTCAAG
1 TATTAATTTATCAAG
10713245 TATTAATTTATCAAG
1 TATTAATTTATCAAG
10713260 ATTTTCTTGT
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:0.37, C:0.07, G:0.07, T:0.50
Consensus pattern (15 bp):
TATTAATTTATCAAG
Found at i:10717164 original size:15 final size:15
Alignment explanation
Indices: 10717117--10717169 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
10717107 AATAGTTATA
*
10717117 TATATATATATAATT
1 TATATATATTTAATT
* * *
10717132 GATATNTA-TAAATAT
1 TATATATATTTAAT-T
10717147 TATATATATTTAATT
1 TATATATATTTAATT
10717162 TATATATA
1 TATATATA
10717170 AGTATTACTA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
14 3 0.10
15 22 0.76
16 4 0.14
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.51
Consensus pattern (15 bp):
TATATATATTTAATT
Found at i:10717425 original size:215 final size:215
Alignment explanation
Indices: 10717147--10717604 Score: 561
Period size: 215 Copynumber: 2.1 Consensus size: 215
10717137 NTATAAATAT
* * * *
10717147 TATATATATTTAATTTATATATAAGTATTACTATAACTTATAATAAATTTTATTTATATGATTAC
1 TATACATATTTAATTTATACATAAGCATTACTATAACTTATAATAAAATTTATTTATATGATTAC
* *
10717212 ATTTAATAACCTTATTAATTATCACT-TTAGTTTTTATAACATATTGTTTATAATTAGTTATTAT
66 ACTTAATAACCTTATTAATTATC-CTCTTAATTTTTATAACATATTGTTTATAATTAGTTATTAT
* *
10717276 GTATACAAA-TTCT-TAT-A-TAAAACATTATAACACATAAGTTGTGTCATTAATTTTATATATA
130 GTATACAAACTT-TATATAATTAAAACATTATAACACATAAGTTGTATCATTAATTTCATATATA
* *
10717337 CCTAATAAAGTAACATATTATATA
194 --TAATAAAGTAACATAGTATACA
*
10717361 TATACGAATATTTAATTTATACATAAGCATTA-TGTAACTTATAATAAACATTT-TTTATATGAT
1 TATAC--ATATTTAATTTATACATAAGCATTACTATAACTTATAATAAA-ATTTATTTATATGAT
** * * *
10717424 TACACTTAATAATTTTATTAGTTATCTTCTTAATTTTTATAATATATTGTTTATAATTAGTTATT
63 TACACTTAATAACCTTATTAATTATCCTCTTAATTTTTATAACATATTGTTTATAATTAGTTATT
* * *
10717489 ATTTATACAAACTTTGATATAAAAATTAAAATATTATAACATATAAGTTGTATCATTAATTTCAT
128 ATGTATACAAACTTT-ATAT---AATTAAAACATTATAACACATAAGTTGTATCATTAATTTCAT
**
10717554 ATATATAATAAAGTAATGTAGTATACA
189 ATATATAATAAAGTAACATAGTATACA
* *
10717581 TATACATATATAATTTTTACATAA
1 TATACATATTTAATTTATACATAA
10717605 TTAATATATT
Statistics
Matches: 209, Mismatches: 23, Indels: 20
0.83 0.09 0.08
Matches are distributed among these distances:
214 5 0.02
215 92 0.44
216 28 0.13
217 3 0.01
218 17 0.08
220 23 0.11
221 1 0.00
222 40 0.19
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.46
Consensus pattern (215 bp):
TATACATATTTAATTTATACATAAGCATTACTATAACTTATAATAAAATTTATTTATATGATTAC
ACTTAATAACCTTATTAATTATCCTCTTAATTTTTATAACATATTGTTTATAATTAGTTATTATG
TATACAAACTTTATATAATTAAAACATTATAACACATAAGTTGTATCATTAATTTCATATATATA
ATAAAGTAACATAGTATACA
Found at i:10725119 original size:17 final size:17
Alignment explanation
Indices: 10725099--10725131 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
10725089 TTATAAATTT
*
10725099 ATTCATTTTTTTGCATC
1 ATTCATTATTTTGCATC
10725116 ATTCATTATTTTGCAT
1 ATTCATTATTTTGCAT
10725132 TGCACATGAC
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:0.21, C:0.15, G:0.06, T:0.58
Consensus pattern (17 bp):
ATTCATTATTTTGCATC
Found at i:10729194 original size:6 final size:6
Alignment explanation
Indices: 10729183--10729209 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
10729173 NNNNNNNNNN
10729183 CCCCCG CCCCCG CCCCCG CCCCCG CCC
1 CCCCCG CCCCCG CCCCCG CCCCCG CCC
10729210 TGGGGCTGCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.00, C:0.85, G:0.15, T:0.00
Consensus pattern (6 bp):
CCCCCG
Found at i:10732272 original size:48 final size:48
Alignment explanation
Indices: 10732217--10732308 Score: 175
Period size: 48 Copynumber: 1.9 Consensus size: 48
10732207 AAAATGGAGA
*
10732217 ATCTCCCAAGAATTGAACGTGTTGTTGAAAGAGACATATTTCATGGGC
1 ATCTCCCAAGAATTGAACGTGTTGTTGAAAAAGACATATTTCATGGGC
10732265 ATCTCCCAAGAATTGAACGTGTTGTTGAAAAAGACATATTTCAT
1 ATCTCCCAAGAATTGAACGTGTTGTTGAAAAAGACATATTTCAT
10732309 TGGCTTTCTT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 43 1.00
ACGTcount: A:0.34, C:0.16, G:0.20, T:0.30
Consensus pattern (48 bp):
ATCTCCCAAGAATTGAACGTGTTGTTGAAAAAGACATATTTCATGGGC
Found at i:10732456 original size:2 final size:2
Alignment explanation
Indices: 10732451--10732481 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
10732441 TAATGCAGTC
10732451 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
10732482 ATTGGTACAC
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:10735490 original size:34 final size:34
Alignment explanation
Indices: 10735450--10735536 Score: 156
Period size: 34 Copynumber: 2.6 Consensus size: 34
10735440 AGGCAATGCT
10735450 CATCTCTAATAATTTATTGTAGGTATATTTGAGC
1 CATCTCTAATAATTTATTGTAGGTATATTTGAGC
*
10735484 CATCTCTAATAATTTATTGTAGGTATATTTGAGT
1 CATCTCTAATAATTTATTGTAGGTATATTTGAGC
*
10735518 GATCTCTAATAATTTATTG
1 CATCTCTAATAATTTATTG
10735537 GAAACTTAAA
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 51 1.00
ACGTcount: A:0.30, C:0.10, G:0.14, T:0.46
Consensus pattern (34 bp):
CATCTCTAATAATTTATTGTAGGTATATTTGAGC
Done.