Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D02
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: 70731513
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1900000 characters in sequence are not A, C, G, or T
File 195 of 222
Found at i:62293060 original size:82 final size:82
Alignment explanation
Indices: 62292923--62293096 Score: 312
Period size: 82 Copynumber: 2.1 Consensus size: 82
62292913 TTTGAGTACT
*
62292923 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
*
62292988 GATAAGTGTTACACTTA
66 GATAAGTGCTACACTTA
*
62293005 TCTGATCAATAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
*
62293070 GATAAGTGCTATACTTA
66 GATAAGTGCTACACTTA
62293087 TCTGATCAAG
1 TCTGATCAAG
62293097 TGATAACTAT
Statistics
Matches: 87, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 87 1.00
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.30
Consensus pattern (82 bp):
TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
GATAAGTGCTACACTTA
Found at i:62298926 original size:46 final size:45
Alignment explanation
Indices: 62298859--62299184 Score: 359
Period size: 46 Copynumber: 7.6 Consensus size: 45
62298849 TTTGAGTACT
* *
62298859 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
62298905 TCTGATCAAGTGAAAAAGTGAT-A-----AG--T-GCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* * *
62298941 TCTGTTCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTA
62298987 TCTGATCAAGTGAAAAAGTGATAA---GT-GC-TA--T--ACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* * *
62299023 TCTTATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
*
62299069 TCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAG-CTTAGCTACACTTA
* *
62299115 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
* *
62299160 TCTGATC-AG-GGACAAGTGATAAGTG
1 TCTGATCAAGTGAAAAAGTGATAAGTG
62299185 ATCATACATA
Statistics
Matches: 241, Mismatches: 19, Indels: 43
0.80 0.06 0.14
Matches are distributed among these distances:
36 56 0.23
37 2 0.01
38 1 0.00
39 1 0.00
40 5 0.02
41 1 0.00
42 6 0.02
43 15 0.06
44 3 0.01
45 22 0.09
46 129 0.54
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTA
Found at i:62298936 original size:36 final size:36
Alignment explanation
Indices: 62298895--62299049 Score: 166
Period size: 36 Copynumber: 4.0 Consensus size: 36
62298885 GGTAGCTTTA
62298895 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* * *
62298931 GCTACACTTATCTGTTCAAGAGACAAAGTGATAAGTGGTAGCTTT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGAT-A-----AG---T
62298976 AGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 -GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* * *
62299013 GCTATACTTATCTTATCAAGTGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
62299049 G
1 G
62299050 TTAGCCTTAG
Statistics
Matches: 100, Mismatches: 9, Indels: 20
0.78 0.07 0.16
Matches are distributed among these distances:
36 63 0.63
37 2 0.02
40 2 0.02
42 2 0.02
45 2 0.02
46 29 0.29
ACGTcount: A:0.36, C:0.14, G:0.20, T:0.30
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:62299001 original size:82 final size:82
Alignment explanation
Indices: 62298859--62299184 Score: 433
Period size: 82 Copynumber: 3.9 Consensus size: 82
62298849 TTTGAGTACT
*
62298859 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
62298924 GATAAGTGCTACACTTA
66 GATAAGTGCTACACTTA
*
62298941 TCTGTTCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
*
62299006 GATAAGTGCTATACTTA
66 GATAAGTGCTACACTTA
* * * * *
62299023 TCTTATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTATCTGATCAAGTGAGAAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
62299088 GATAAGTGGTAGCCTTAGCTACACTTA
66 GAT-A-----AG---T-GCTACACTTA
* * * *
62299115 TCTGATCAAGTGACAAAGTGATAAGTGGTAGC-CTAGCTACACTTATCTGATC-AG-GGACAAGT
1 TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
62299177 GATAAGTG
66 GATAAGTG
62299185 ATCATACATA
Statistics
Matches: 218, Mismatches: 16, Indels: 23
0.85 0.06 0.09
Matches are distributed among these distances:
79 1 0.00
80 1 0.00
82 141 0.65
83 3 0.01
88 3 0.01
89 8 0.04
90 2 0.01
91 20 0.09
92 39 0.18
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (82 bp):
TCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
GATAAGTGCTACACTTA
Found at i:62299011 original size:128 final size:126
Alignment explanation
Indices: 62298859--62299184 Score: 374
Period size: 128 Copynumber: 2.6 Consensus size: 126
62298849 TTTGAGTACT
* *
62298859 TCTGATCAAGAGATAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGT
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAAGTG-AAAAGT
* *
62298924 GATAAGTGCTACACTTATCTGTTCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTA
64 GATAAGTGCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
* * * * * ** *
62298987 TCTGATCAAGTGAAAAAGTGATAAGTGCTATACTTATCT-TA-TCAAGTGA-CAAAGTGATAAGT
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTA-GCTTAGCTACACTTATCTGATC-AAGTGAAAAGT
* * *
62299049 G-TTAGCCTTAGCTACACTTATCTGATCAAGTGAGAAAGTGATAAGTGGTAGCCTTAGCTACACT
64 GATAAG---T-GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACT
62299113 TA
125 TA
* * * *
62299115 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGATC-AGGGACAAGTGA
1 TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGTGAAAAGTGA
62299179 TAAGTG
66 TAAGTG
62299185 ATCATACATA
Statistics
Matches: 161, Mismatches: 27, Indels: 23
0.76 0.13 0.11
Matches are distributed among these distances:
124 3 0.02
125 8 0.05
126 11 0.07
127 7 0.04
128 122 0.76
129 9 0.06
130 1 0.01
ACGTcount: A:0.34, C:0.15, G:0.22, T:0.29
Consensus pattern (126 bp):
TCTGATCAAGTGAAAAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAAGTGAAAAGTGA
TAAGTGCTACACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTA
Found at i:62301122 original size:13 final size:14
Alignment explanation
Indices: 62301096--62301124 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
62301086 TAAAATCAAT
62301096 ATTTAACAAAAATC
1 ATTTAACAAAAATC
62301110 ATTTAAC-AAAATC
1 ATTTAACAAAAATC
62301123 AT
1 AT
62301125 CACACAACAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (14 bp):
ATTTAACAAAAATC
Found at i:62309917 original size:93 final size:92
Alignment explanation
Indices: 62309740--62309957 Score: 256
Period size: 93 Copynumber: 2.3 Consensus size: 92
62309730 TATGATCACG
* * *
62309740 ACCTTTTACTCACAGGATTTTATGAATCTCGCAGTCCGCTGATTTACGATAACAACCTTTGGCTT
1 ACCTTTTACTTAC-GGATTTTATGAATCTCGCAGTCCGCTGATTTACGATAACAACATTTGACTT
*
62309805 TTTTACAATCCGCTAATTTACGATCATA
65 TCTTACAATCCGCTAATTTACGATCATA
* ** * * **
62309833 ATCTTTTACTTACGGTATTTTATGAATCTCGTGGTCCGTTGATTTACGATTATGACATTTGACTT
1 ACCTTTTACTTACGG-ATTTTATGAATCTCGCAGTCCGCTGATTTACGATAACAACATTTGACTT
** * * * *
62309898 TCTTACGGTCCGTTGATTTATGATCATT
65 TCTTACAATCCGCTAATTTACGATCATA
62309926 ACCTTTTACTTACGAGATTTTATGAATCTCGC
1 ACCTTTTACTTACG-GATTTTATGAATCTCGC
62309958 GGTATGATCA
Statistics
Matches: 104, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
92 2 0.02
93 101 0.97
94 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.15, T:0.41
Consensus pattern (92 bp):
ACCTTTTACTTACGGATTTTATGAATCTCGCAGTCCGCTGATTTACGATAACAACATTTGACTTT
CTTACAATCCGCTAATTTACGATCATA
Found at i:62310050 original size:38 final size:39
Alignment explanation
Indices: 62310002--62310106 Score: 140
Period size: 38 Copynumber: 2.7 Consensus size: 39
62309992 AGAATCTTGT
* *
62310002 GGTCCACTGATTTATGATCACAACTTTTGGCTTTCT-AC
1 GGTCCGCTGATTTACGATCACAACTTTTGGCTTTCTCAC
* * *
62310040 GGTCTGCTGATTTACGATCACGACCTTTGGCTTTCTCAC
1 GGTCCGCTGATTTACGATCACAACTTTTGGCTTTCTCAC
* *
62310079 GGTCCGTTGATTTACGATCGCAACTTTT
1 GGTCCGCTGATTTACGATCACAACTTTT
62310107 TACTTACAAG
Statistics
Matches: 56, Mismatches: 10, Indels: 1
0.84 0.15 0.01
Matches are distributed among these distances:
38 31 0.55
39 25 0.45
ACGTcount: A:0.18, C:0.25, G:0.19, T:0.38
Consensus pattern (39 bp):
GGTCCGCTGATTTACGATCACAACTTTTGGCTTTCTCAC
Found at i:62310944 original size:42 final size:42
Alignment explanation
Indices: 62310887--62311005 Score: 177
Period size: 42 Copynumber: 2.8 Consensus size: 42
62310877 GTTTACAAAC
* *
62310887 AAAAACGCCGCTAAAGACCATGTTCTTTAGTGGCGCTT-AGAA
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAAG-A
* *
62310929 AAAAACGCCACTAAAGAACATGTTCTTTAGCGGCGCTTAAGG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAAGA
*
62310971 AAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCG
1 AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCG
62311006 TTTTTTTCTA
Statistics
Matches: 70, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
42 68 0.97
43 2 0.03
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.23
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGCTTAAGA
Found at i:62311028 original size:84 final size:83
Alignment explanation
Indices: 62310886--62311185 Score: 240
Period size: 84 Copynumber: 3.6 Consensus size: 83
62310876 CGTTTACAAA
* * **** * *
62310886 CAAAAACGCCGCTAAAGACCATGTTCTTTAGTGGCGCTTAGAAAAAAACGCCACTAAAGAACATG
1 CAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCG-TTTTTTACAAGCGCCACTAAAGAACATG
62310951 TTCTTTAGCGGCGCTTAAG
65 TTCTTTAGCGGCGCTTAAG
* * * * *
62310970 GAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTTTTTCTAAGCGCCTCTAAAGAACGTG
1 CAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTAC-AAGCGCCACTAAAGAACATG
* ***
62311035 TTCTTTAGCGGCGTTTTTT
65 TTCTTTAGCGGCGCTTAAG
** * * * * *
62311054 CCTAAGCACCTCTAAAGAACGTGTTCTTTAGCGGCGTTTTTCTACAAGCGCCGCTAAAGAACATG
1 CAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTT-TACAAGCGCCACTAAAGAACATG
* ** ***
62311119 TTCTTTAGTGGCATTTTTTT
65 TTCTTTAGCGGC-GCTTAAG
* * * * *
62311139 TACAAACGCCGCAAAAGAACATGTTCTTTAGTGGCGCTTTTATACAA
1 CAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCG-TTTTTTACAA
62311186 AAACGCCACT
Statistics
Matches: 173, Mismatches: 39, Indels: 7
0.79 0.18 0.03
Matches are distributed among these distances:
83 2 0.01
84 127 0.73
85 40 0.23
86 4 0.02
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.31
Consensus pattern (83 bp):
CAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTACAAGCGCCACTAAAGAACATGT
TCTTTAGCGGCGCTTAAG
Found at i:62311038 original size:126 final size:126
Alignment explanation
Indices: 62310888--62311196 Score: 332
Period size: 126 Copynumber: 2.4 Consensus size: 126
62310878 TTTACAAACA
* * *
62310888 AAAACGCCGCTAAAGACCATGTTCTTTAGTGGCGCTTAGAAAAAAACGCCACTAAAGAACATGTT
1 AAAACGCCGCTAAAGAACATGTTCTTTAGTGGCGCTTATACAAAAACGCCACTAAAGAACATGTT
* * *
62310953 CTTTAGCGGCGCTTAAGGAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTTTTTCT
66 CTTTAGCGGCGCTTAACGAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCATTTTTTT-T
* * * * * * * ** * * * *
62311015 -AAGCGCCTCTAAAGAACGTGTTCTTTAGCGGCGTTTTTTCCTAAGCACCTCTAAAGAACGTGTT
1 AAAACGCCGCTAAAGAACATGTTCTTTAGTGGCGCTTATACAAAAACGCCACTAAAGAACATGTT
* ** * * * *
62311079 CTTTAGCGGCGTTTTTCTACAAGCGCCGCTAAAGAACATGTTCTTTAGTGGCATTTTTTTT
66 CTTTAGCGGCGCTTAACGAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCATTTTTTTT
*
62311140 ACAAACGCCGCAAAAGAACATGTTCTTTAGTGGCGCTTTTATACAAAAACGCCACTA
1 A-AAACGCCGCTAAAGAACATGTTCTTTAGTGGCGC--TTATACAAAAACGCCACTA
62311197 TTTTGGAGAT
Statistics
Matches: 139, Mismatches: 39, Indels: 6
0.76 0.21 0.03
Matches are distributed among these distances:
125 1 0.01
126 98 0.71
127 28 0.20
129 12 0.09
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.30
Consensus pattern (126 bp):
AAAACGCCGCTAAAGAACATGTTCTTTAGTGGCGCTTATACAAAAACGCCACTAAAGAACATGTT
CTTTAGCGGCGCTTAACGAAAAACGCCGCTAAAGAACATGTTCTTTAGCGGCATTTTTTTT
Found at i:62311156 original size:43 final size:43
Alignment explanation
Indices: 62310934--62311179 Score: 250
Period size: 42 Copynumber: 5.8 Consensus size: 43
62310924 TAGAAAAAAA
* * **** * *
62310934 CGCCACTAAAGAACATGTTCTTTAGCGGCGCTTAAGGA-AAAA
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTACTAAG
*
62310976 CGCCGCTAAAGATCATGTTCTTTAGCGGCGTTTTTTT-CTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTACTAAG
* * *
62311018 CGCCTCTAAAGAACGTGTTCTTTAGCGGCG-TTTTTTCCTAAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTACTAAG
* * * *
62311060 CACCTCTAAAGAACGTGTTCTTTAGCGGCGTTTTTCTAC-AAG
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTACTAAG
* * *
62311102 CGCCGCTAAAGAACATGTTCTTTAGTGGCATTTTTTTTAC-AAA
1 CGCCGCTAAAGAACATGTTCTTTAGCGGC-GTTTTTTTACTAAG
* * *
62311145 CGCCGCAAAAGAACATGTTCTTTAGTGGCGCTTTT
1 CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTT
62311180 ATACAAAAAC
Statistics
Matches: 175, Mismatches: 25, Indels: 8
0.84 0.12 0.04
Matches are distributed among these distances:
41 6 0.03
42 125 0.71
43 44 0.25
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.33
Consensus pattern (43 bp):
CGCCGCTAAAGAACATGTTCTTTAGCGGCGTTTTTTTACTAAG
Found at i:62311572 original size:21 final size:21
Alignment explanation
Indices: 62311505--62311560 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
62311495 TTTCTCTGCT
* * **
62311505 CTGCTTCTCTCGTTGCAGCTT
1 CTGCTTCCCTCGCTGCAGCCG
*
62311526 CCGCTTCCCTCGCTGCAGCCG
1 CTGCTTCCCTCGCTGCAGCCG
62311547 CTGCTTCCCTCGCT
1 CTGCTTCCCTCGCT
62311561 TCCGCCTCTG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.04, C:0.45, G:0.20, T:0.32
Consensus pattern (21 bp):
CTGCTTCCCTCGCTGCAGCCG
Found at i:62313086 original size:13 final size:13
Alignment explanation
Indices: 62313068--62313169 Score: 73
Period size: 13 Copynumber: 7.5 Consensus size: 13
62313058 AGGAAAGAAT
62313068 TAGTATTATGCAC
1 TAGTATTATGCAC
62313081 TAGTATTATGCAC
1 TAGTATTATGCAC
* *
62313094 TAGTAAGGTGATTG--T
1 TAGT-A--TTA-TGCAC
* *
62313109 TAGTAATATGTGCAG
1 TAGT-AT-TATGCAC
*
62313124 TAGTAGTATTGCAC
1 TAGTATTA-TGCAC
62313138 TAGTATTATGCAC
1 TAGTATTATGCAC
*
62313151 TAGTATTATGCAT
1 TAGTATTATGCAC
62313164 TAGTAT
1 TAGTAT
62313170 CTCTTGTCTA
Statistics
Matches: 71, Mismatches: 10, Indels: 16
0.73 0.10 0.16
Matches are distributed among these distances:
13 44 0.62
14 13 0.18
15 10 0.14
16 2 0.03
17 2 0.03
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (13 bp):
TAGTATTATGCAC
Found at i:62313375 original size:11 final size:11
Alignment explanation
Indices: 62313359--62313387 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
62313349 GATGATAATA
62313359 CATTAGTTACC
1 CATTAGTTACC
62313370 CATTAGTTACC
1 CATTAGTTACC
62313381 CA-TAGTT
1 CATTAGTT
62313388 TGAGATATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.28
11 13 0.72
ACGTcount: A:0.28, C:0.24, G:0.10, T:0.38
Consensus pattern (11 bp):
CATTAGTTACC
Found at i:62314842 original size:86 final size:84
Alignment explanation
Indices: 62314649--62314919 Score: 479
Period size: 84 Copynumber: 3.2 Consensus size: 84
62314639 CCACATTTCC
62314649 GGCGTTTTCCTAAAAACGCCACTAAATATTACAGCTGTGAACAGAAACGACACCGTTTTCGTGGT
1 GGCGTTTTCCTAAAAACGCCACTAAATATTACAGCTGTGAACAGAAACGACACCGTTTTCGTGGT
62314714 CTGGAATTGCATTATTTGT
66 CTGGAATTGCATTATTTGT
* *
62314733 GGCGTTTTCCTAAAAACGCCACTAAAGATTACAGCTGTGAACAGAAACGACACCATTTTGCGTGG
1 GGCGTTTTCCTAAAAACGCCACTAAATATTACAGCTGTGAACAGAAACGACACCGTTTT-CGTGG
** *
62314798 TCTGGAACAAGCATTGTTTGT
65 TCTGGAA-TTGCATTATTTGT
62314819 GGCGTTTTCCTAAAAACGCCACTAAATATTACAGCTGTGAACAGAAACGACACCGTTTTCGTGGT
1 GGCGTTTTCCTAAAAACGCCACTAAATATTACAGCTGTGAACAGAAACGACACCGTTTTCGTGGT
62314884 CTGGAATTGCATTATTTGT
66 CTGGAATTGCATTATTTGT
62314903 GGCGTTTTCCTAAAAAC
1 GGCGTTTTCCTAAAAAC
62314920 AAGATTGAAA
Statistics
Matches: 175, Mismatches: 10, Indels: 4
0.93 0.05 0.02
Matches are distributed among these distances:
84 84 0.48
85 24 0.14
86 67 0.38
ACGTcount: A:0.29, C:0.21, G:0.21, T:0.30
Consensus pattern (84 bp):
GGCGTTTTCCTAAAAACGCCACTAAATATTACAGCTGTGAACAGAAACGACACCGTTTTCGTGGT
CTGGAATTGCATTATTTGT
Found at i:62320838 original size:21 final size:19
Alignment explanation
Indices: 62320785--62320842 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 19
62320775 TAATAATACT
*
62320785 ATATGATAATAATGATAATA
1 ATATGATAATAAT-ATAAAA
62320805 ATAGTGA-AATAATATAAAA
1 ATA-TGATAATAATATAAAA
62320824 ATGTATGATAATAATATAA
1 A--TATGATAATAATATAA
62320843 TTACATAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 7
0.80 0.02 0.17
Matches are distributed among these distances:
19 6 0.18
20 12 0.36
21 15 0.45
ACGTcount: A:0.57, C:0.00, G:0.10, T:0.33
Consensus pattern (19 bp):
ATATGATAATAATATAAAA
Found at i:62321014 original size:23 final size:23
Alignment explanation
Indices: 62320987--62321058 Score: 101
Period size: 24 Copynumber: 3.1 Consensus size: 23
62320977 ATGTAATAGA
62320987 AAAAAATATAAATGGGCTAACTTT
1 AAAAAA-ATAAATGGGCTAACTTT
* *
62321011 AAAAAAATAAA-GGACTAAATTT
1 AAAAAAATAAATGGGCTAACTTT
62321033 AAAATAAATAAATGGGCTAACTTT
1 AAAA-AAATAAATGGGCTAACTTT
62321057 AA
1 AA
62321059 TGAATTAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
22 13 0.31
23 12 0.29
24 17 0.40
ACGTcount: A:0.56, C:0.07, G:0.11, T:0.26
Consensus pattern (23 bp):
AAAAAAATAAATGGGCTAACTTT
Found at i:62323151 original size:21 final size:21
Alignment explanation
Indices: 62323113--62323152 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
62323103 ATTAGTTTGA
*
62323113 TTAATTGATTGGCTATCGAAG
1 TTAATTGATTGGCGATCGAAG
62323134 TTAATTTGATTGG-GATCGA
1 TTAA-TTGATTGGCGATCGA
62323153 TTAAAAGTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 9 0.53
22 8 0.47
ACGTcount: A:0.28, C:0.07, G:0.25, T:0.40
Consensus pattern (21 bp):
TTAATTGATTGGCGATCGAAG
Found at i:62329614 original size:24 final size:24
Alignment explanation
Indices: 62329587--62329633 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
62329577 TGAAATGTTT
62329587 AAGGTTAAAAAAGATGAAAGGTGG
1 AAGGTTAAAAAAGATGAAAGGTGG
***
62329611 AAGGTTAAGGGAGATGAAAGGTG
1 AAGGTTAAAAAAGATGAAAGGTG
62329634 AAATGTTGAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.45, C:0.00, G:0.38, T:0.17
Consensus pattern (24 bp):
AAGGTTAAAAAAGATGAAAGGTGG
Found at i:62340571 original size:22 final size:22
Alignment explanation
Indices: 62340532--62340573 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
62340522 ATAATATAGA
*
62340532 TTTAATAAATGCAGAAAAATCT
1 TTTAATAAATGCAAAAAAATCT
62340554 TTTAATAAATAG-AAAAAAAT
1 TTTAATAAAT-GCAAAAAAAT
62340574 TTAAACTGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.31
Consensus pattern (22 bp):
TTTAATAAATGCAAAAAAATCT
Found at i:62340576 original size:19 final size:21
Alignment explanation
Indices: 62340531--62340577 Score: 53
Period size: 22 Copynumber: 2.3 Consensus size: 21
62340521 AATAATATAG
*
62340531 ATTTAATAAATGCAGAAAAATC
1 ATTTAATAAAT-CAGAAAAATA
*
62340553 TTTTAATAAAT-AGAAAAA-A
1 ATTTAATAAATCAGAAAAATA
62340572 ATTTAA
1 ATTTAA
62340578 ACTGTTATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
19 5 0.23
20 7 0.32
22 10 0.45
ACGTcount: A:0.57, C:0.04, G:0.06, T:0.32
Consensus pattern (21 bp):
ATTTAATAAATCAGAAAAATA
Found at i:62351280 original size:40 final size:40
Alignment explanation
Indices: 62351133--62351385 Score: 416
Period size: 40 Copynumber: 6.2 Consensus size: 40
62351123 AGTAAATATA
*
62351133 TGCAAACACTCGTCTCACCAATGTCAATATGCATATCTGAT
1 TGCAAACACTCATCTCACCAATGTCAATATGCATATCTG-T
*
62351174 TGCAAACACTCATCTCACCAATGTCAATATGCACATCTGAT
1 TGCAAACACTCATCTCACCAATGTCAATATGCATATCTG-T
*
62351215 TGCAAATACTCATCTCACCAATGTCAATATGCATATCTGT
1 TGCAAACACTCATCTCACCAATGTCAATATGCATATCTGT
* *
62351255 TACAAACACTCATCTCACCAGTGTCAATATGCATATCTGT
1 TGCAAACACTCATCTCACCAATGTCAATATGCATATCTGT
62351295 TGCAAACACTCATCTCACCAATGTCAATATGCATATCTGT
1 TGCAAACACTCATCTCACCAATGTCAATATGCATATCTGT
*
62351335 TGCAAACACTCGTCTCACCAATGTCAATATGCATATCTGAT
1 TGCAAACACTCATCTCACCAATGTCAATATGCATATCTG-T
*
62351376 AGCAAACACT
1 TGCAAACACT
62351386 AGAGTTATGT
Statistics
Matches: 200, Mismatches: 11, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
40 114 0.57
41 86 0.43
ACGTcount: A:0.33, C:0.27, G:0.11, T:0.29
Consensus pattern (40 bp):
TGCAAACACTCATCTCACCAATGTCAATATGCATATCTGT
Found at i:62355785 original size:16 final size:16
Alignment explanation
Indices: 62355761--62355791 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
62355751 TTTGTTGAGT
*
62355761 ATTGTCAAGACAAGAC
1 ATTGACAAGACAAGAC
62355777 ATTGACAAGACAAGA
1 ATTGACAAGACAAGA
62355792 GACTAGTACA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.48, C:0.16, G:0.19, T:0.16
Consensus pattern (16 bp):
ATTGACAAGACAAGAC
Found at i:62362682 original size:9 final size:8
Alignment explanation
Indices: 62362624--62362681 Score: 64
Period size: 8 Copynumber: 7.0 Consensus size: 8
62362614 ATATATATAC
62362624 TAAAAAAA
1 TAAAAAAA
*
62362632 TATAAAAA
1 TAAAAAAA
62362640 TAACAATATAA
1 TAA-AA-A-AA
*
62362651 TATAAAAA
1 TAAAAAAA
62362659 T-AAAAAA
1 TAAAAAAA
62362666 TAAAAAAA
1 TAAAAAAA
62362674 TAAAAAAA
1 TAAAAAAA
62362682 AAATATTTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
7 6 0.14
8 26 0.62
9 3 0.07
10 3 0.07
11 4 0.10
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (8 bp):
TAAAAAAA
Found at i:62362684 original size:19 final size:19
Alignment explanation
Indices: 62362624--62362686 Score: 56
Period size: 19 Copynumber: 3.1 Consensus size: 19
62362614 ATATATATAC
62362624 TAAAAAAATATAAAAATAACAA
1 TAAAAAAATA-AAAAA-AA-AA
* *
62362646 TATAATATAA-AAATAAAAAA
1 TA-AA-AAAATAAAAAAAAAA
62362666 TAAAAAAATAAAAAAAAAA
1 TAAAAAAATAAAAAAAAAA
62362685 TA
1 TA
62362687 TTTTTTTTAC
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
18 3 0.09
19 13 0.38
20 4 0.12
21 2 0.06
22 6 0.18
23 3 0.09
24 3 0.09
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (19 bp):
TAAAAAAATAAAAAAAAAA
Found at i:62363315 original size:3 final size:3
Alignment explanation
Indices: 62363291--62363358 Score: 57
Period size: 3 Copynumber: 22.3 Consensus size: 3
62363281 AATATCCTTG
* * * *
62363291 TTA TTT TTA -TA TTA TTA GTA TTA TTA GTA TTA GTA TTA TTA TTA TGTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA
* *
62363339 TTA GTA TATA TTT TTA TTA T
1 TTA TTA T-TA TTA TTA TTA T
62363359 GTACGTGTAT
Statistics
Matches: 50, Mismatches: 12, Indels: 6
0.74 0.18 0.09
Matches are distributed among these distances:
2 2 0.04
3 42 0.84
4 6 0.12
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:62363368 original size:23 final size:23
Alignment explanation
Indices: 62363298--62363369 Score: 67
Period size: 23 Copynumber: 3.1 Consensus size: 23
62363288 TTGTTATTTT
* *
62363298 TATATTATTAGTAT-TATTAGTA
1 TATATTATTATTATGTAGTAGTA
*
62363320 TTAGTATTATTATTATGTATTAGTA
1 -TA-TATTATTATTATGTAGTAGTA
*
62363345 TATATTTTTATTATGTACGT-GTA
1 TATATTATTATTATGTA-GTAGTA
62363368 TA
1 TA
62363370 CATATATATA
Statistics
Matches: 43, Mismatches: 3, Indels: 6
0.83 0.06 0.12
Matches are distributed among these distances:
23 21 0.49
24 14 0.33
25 8 0.19
ACGTcount: A:0.32, C:0.01, G:0.11, T:0.56
Consensus pattern (23 bp):
TATATTATTATTATGTAGTAGTA
Found at i:62363478 original size:3 final size:3
Alignment explanation
Indices: 62363465--62363503 Score: 51
Period size: 3 Copynumber: 13.0 Consensus size: 3
62363455 TATTCCAATG
* * *
62363465 TTA TCA TTA TTA TTA TTA TTA TTA TTT TTA TTT TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
62363504 GTTTATGTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:62363815 original size:19 final size:18
Alignment explanation
Indices: 62363771--62363830 Score: 57
Period size: 20 Copynumber: 3.0 Consensus size: 18
62363761 ATTATCATTG
62363771 TATATATTTTAATATTAT
1 TATATATTTTAATATTAT
62363789 TAGTTATATTTTACACTATTAT
1 TA--TATATTTTA-A-TATTAT
*
62363811 ATATATTTTTCTAATATTAT
1 -TATATATTT-TAATATTAT
62363831 ATTGTATATA
Statistics
Matches: 35, Mismatches: 1, Indels: 10
0.76 0.02 0.22
Matches are distributed among these distances:
18 2 0.06
20 15 0.43
21 8 0.23
22 8 0.23
23 2 0.06
ACGTcount: A:0.35, C:0.05, G:0.02, T:0.58
Consensus pattern (18 bp):
TATATATTTTAATATTAT
Found at i:62363835 original size:64 final size:64
Alignment explanation
Indices: 62363709--62363840 Score: 164
Period size: 64 Copynumber: 2.1 Consensus size: 64
62363699 GTCGTATTAT
*
62363709 TATATTTTAATATTATATTATATAATTATATATACATATATCTTTTATATATATTATCATTGTA
1 TATATTTTAATATTATATTATATAATTACATATACATATATCTTTTATATATATTATCATTGTA
* * *
62363773 TATATTTTAATATTATTAGTTATAT-TTTACACTATTATATATAT-TTTTCTA-ATATTAT-ATT
1 TATATTTTAATATTA-TA-TTATATAATTACA-TA-TACATATATCTTTTATATATATTATCATT
62363834 GTA
62 GTA
62363837 TATA
1 TATA
62363841 CTGTTGTTTA
Statistics
Matches: 60, Mismatches: 4, Indels: 8
0.83 0.06 0.11
Matches are distributed among these distances:
64 25 0.42
65 13 0.22
66 14 0.23
67 8 0.13
ACGTcount: A:0.37, C:0.05, G:0.02, T:0.56
Consensus pattern (64 bp):
TATATTTTAATATTATATTATATAATTACATATACATATATCTTTTATATATATTATCATTGTA
Found at i:62364273 original size:38 final size:37
Alignment explanation
Indices: 62364189--62364283 Score: 97
Period size: 38 Copynumber: 2.5 Consensus size: 37
62364179 TATACGTACT
*
62364189 TATACATACTTAAATATATTTTTCATATTTCATAATTC
1 TATACATACTTAAATATATTTTGCATATTT-ATAATTC
* *
62364227 T-TATATACTTACATATATTTATGCATATTT-TACA-TC
1 TATACATACTTAAATATATTT-TGCATATTTATA-ATTC
*
62364263 ATATACATACTTATATATATT
1 -TATACATACTTAAATATATT
62364284 CTTTATATTC
Statistics
Matches: 48, Mismatches: 5, Indels: 8
0.79 0.08 0.13
Matches are distributed among these distances:
36 4 0.08
37 19 0.40
38 25 0.52
ACGTcount: A:0.37, C:0.13, G:0.01, T:0.49
Consensus pattern (37 bp):
TATACATACTTAAATATATTTTGCATATTTATAATTC
Found at i:62370292 original size:78 final size:79
Alignment explanation
Indices: 62370159--62370310 Score: 177
Period size: 78 Copynumber: 1.9 Consensus size: 79
62370149 ACACACTAGT
* * ** * *
62370159 TTGGCACCCAGTGCCTCATCGGATAATTCGAAGTAATAATTTGACACATAGTGTCTCATCGACT-
1 TTGGCACCCAATACCTCATCAAATAATCCGAAGTAATAATTTGACACATAATGTCTCATCGACTC
62370223 AAA-TCGAAGTAAA
66 AAAGTCGAAGTAAA
* *
62370236 TTGGCACCCAATACCTCATCAAATTAATCCGAAGTAGTGAA-TTGACAC-TCAATGTCTTATCGA
1 TTGGCACCCAATACCTCATCAAA-TAATCCGAAGTAAT-AATTTGACACAT-AATGTCTCATCGA
62370299 CTCAAAGTCGAA
63 CTCAAAGTCGAA
62370311 AAAATATCTG
Statistics
Matches: 62, Mismatches: 8, Indels: 7
0.81 0.10 0.09
Matches are distributed among these distances:
77 20 0.32
78 32 0.52
79 5 0.08
80 5 0.08
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.27
Consensus pattern (79 bp):
TTGGCACCCAATACCTCATCAAATAATCCGAAGTAATAATTTGACACATAATGTCTCATCGACTC
AAAGTCGAAGTAAA
Found at i:62371214 original size:13 final size:13
Alignment explanation
Indices: 62371198--62371239 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
62371188 TTTGTTTTAT
62371198 TATATTAATATAA
1 TATATTAATATAA
62371211 TATATT-AT-T-A
1 TATATTAATATAA
*
62371221 TATAATAATATAA
1 TATATTAATATAA
62371234 TATATT
1 TATATT
62371240 TACTTAACAT
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
10 6 0.25
11 3 0.12
12 3 0.12
13 12 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (13 bp):
TATATTAATATAA
Found at i:62371229 original size:23 final size:21
Alignment explanation
Indices: 62371194--62371239 Score: 74
Period size: 23 Copynumber: 2.1 Consensus size: 21
62371184 TTTATTTGTT
62371194 TTATTATATTAATATAATATA
1 TTATTATATTAATATAATATA
62371215 TTATTATATAATAATATAATATA
1 TTATTATAT--TAATATAATATA
62371238 TT
1 TT
62371240 TACTTAACAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
21 9 0.39
23 14 0.61
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TTATTATATTAATATAATATA
Found at i:62381197 original size:21 final size:21
Alignment explanation
Indices: 62381171--62381210 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
62381161 CTTTCACACA
*
62381171 AGATTT-TTTCTTTCACAAGGG
1 AGATTTGTTT-TTTAACAAGGG
62381192 AGATTTGTTTTTTAACAAG
1 AGATTTGTTTTTTAACAAG
62381211 CATCATAGAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.28, C:0.10, G:0.17, T:0.45
Consensus pattern (21 bp):
AGATTTGTTTTTTAACAAGGG
Found at i:62383136 original size:22 final size:22
Alignment explanation
Indices: 62383089--62383133 Score: 65
Period size: 22 Copynumber: 2.1 Consensus size: 22
62383079 AATTTAATCC
62383089 TTAAATTTCTATTTTTAGAAAT
1 TTAAATTTCTATTTTTAGAAAT
* *
62383111 TTAATTTTTTATTTTTA-AAAT
1 TTAAATTTCTATTTTTAGAAAT
62383132 TT
1 TT
62383134 TAAAATTCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (22 bp):
TTAAATTTCTATTTTTAGAAAT
Found at i:62387560 original size:28 final size:28
Alignment explanation
Indices: 62387528--62387582 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
62387518 TTTAGTATGA
62387528 ATAAAGACTTAAGTTTCACTACCCTTCT
1 ATAAAGACTTAAGTTTCACTACCCTTCT
*
62387556 ATAAAGACTTAAGTTTTACTACCCTTC
1 ATAAAGACTTAAGTTTCACTACCCTTC
62387583 CTTTTATGCT
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:0.33, C:0.24, G:0.07, T:0.36
Consensus pattern (28 bp):
ATAAAGACTTAAGTTTCACTACCCTTCT
Found at i:62395862 original size:37 final size:37
Alignment explanation
Indices: 62395831--62395906 Score: 134
Period size: 37 Copynumber: 2.1 Consensus size: 37
62395821 TCATAAACAT
*
62395831 TTCTAAATATATTAAGGTTAAAATATGTCATAAGTCC
1 TTCTAAATATATTAAGGTTAAAATATGTCATAAGACC
*
62395868 TTCTAAATATATTAAGGTTAAAATATGTCATAAGTCC
1 TTCTAAATATATTAAGGTTAAAATATGTCATAAGACC
62395905 TT
1 TT
62395907 ATACTCTTCG
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.39, C:0.11, G:0.11, T:0.39
Consensus pattern (37 bp):
TTCTAAATATATTAAGGTTAAAATATGTCATAAGACC
Found at i:62397901 original size:21 final size:23
Alignment explanation
Indices: 62397876--62397932 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
62397866 TTAATAATTT
62397876 TATATTTATAT-TGTAAAT-AAA
1 TATATTTATATATGTAAATAAAA
*
62397897 TATATTTATATATATGTAATTAAAA
1 TATA-TT-TATATATGTAAATAAAA
62397922 TATATTTATAT
1 TATATTTATAT
62397933 CTATAAAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
21 4 0.13
22 2 0.06
23 10 0.32
24 8 0.26
25 7 0.23
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.51
Consensus pattern (23 bp):
TATATTTATATATGTAAATAAAA
Found at i:62397908 original size:23 final size:25
Alignment explanation
Indices: 62397882--62397932 Score: 79
Period size: 25 Copynumber: 2.1 Consensus size: 25
62397872 ATTTTATATT
62397882 TATAT-TGTAAAT-AAATATATTTA
1 TATATATGTAAATAAAATATATTTA
*
62397905 TATATATGTAATTAAAATATATTTA
1 TATATATGTAAATAAAATATATTTA
62397930 TAT
1 TAT
62397933 CTATAAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
23 5 0.20
24 6 0.24
25 14 0.56
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (25 bp):
TATATATGTAAATAAAATATATTTA
Found at i:62397945 original size:21 final size:20
Alignment explanation
Indices: 62397876--62397948 Score: 65
Period size: 21 Copynumber: 3.3 Consensus size: 20
62397866 TTAATAATTT
*
62397876 TATATTTATATTGTAAATAAA
1 TATATTTATATTATAAA-AAA
62397897 TATATTTATATATATGTAATTAAAA
1 TATATTTATAT-TA--TAA--AAAA
*
62397922 TATATTTATATCTATAAAATA
1 TATATTTATAT-TATAAAAAA
62397943 TATATT
1 TATATT
62397949 ATTAAGAAAT
Statistics
Matches: 44, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
21 20 0.45
22 1 0.02
23 3 0.07
24 3 0.07
25 16 0.36
26 1 0.02
ACGTcount: A:0.47, C:0.01, G:0.03, T:0.49
Consensus pattern (20 bp):
TATATTTATATTATAAAAAA
Found at i:62398942 original size:22 final size:22
Alignment explanation
Indices: 62398914--62398958 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
62398904 AGTGATCACA
62398914 AATTATGCATAAGATTAAATGG
1 AATTATGCATAAGATTAAATGG
62398936 AATTATGCATAAGATTAAATGG
1 AATTATGCATAAGATTAAATGG
62398958 A
1 A
62398959 TTGAATACAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.47, C:0.04, G:0.18, T:0.31
Consensus pattern (22 bp):
AATTATGCATAAGATTAAATGG
Found at i:62401952 original size:3 final size:3
Alignment explanation
Indices: 62401944--62401987 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
62401934 ATTATGTTTG
62401944 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA A-A AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA
62401988 GGGAAGAATT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:62406185 original size:15 final size:16
Alignment explanation
Indices: 62406167--62406206 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
62406157 ATGAGGATGA
62406167 GAGAGATGA-AAGGAT
1 GAGAGATGAGAAGGAT
*
62406182 GAGAGATGAGAGGGAT
1 GAGAGATGAGAAGGAT
*
62406198 GAGGGATGA
1 GAGAGATGA
62406207 TTGAAAAAGT
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 9 0.41
16 13 0.59
ACGTcount: A:0.40, C:0.00, G:0.47, T:0.12
Consensus pattern (16 bp):
GAGAGATGAGAAGGAT
Found at i:62406189 original size:24 final size:23
Alignment explanation
Indices: 62406155--62406199 Score: 72
Period size: 24 Copynumber: 1.9 Consensus size: 23
62406145 GAGAGCTGAG
62406155 GGATGAGGATGAGAGAGATGAAA
1 GGATGAGGATGAGAGAGATGAAA
*
62406178 GGATGAGAGATGAGAGGGATGA
1 GGATGAG-GATGAGAGAGATGA
62406200 GGGATGATTG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.40, C:0.00, G:0.47, T:0.13
Consensus pattern (23 bp):
GGATGAGGATGAGAGAGATGAAA
Found at i:62406752 original size:17 final size:18
Alignment explanation
Indices: 62406730--62406765 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
62406720 CCACTTTATA
62406730 GCTTAAA-AATATAAAAT
1 GCTTAAATAATATAAAAT
62406747 GCTTAAATTAATATAAAAT
1 GCTTAAA-TAATATAAAAT
62406766 AAGCCATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
19 10 0.59
ACGTcount: A:0.56, C:0.06, G:0.06, T:0.33
Consensus pattern (18 bp):
GCTTAAATAATATAAAAT
Found at i:62410229 original size:20 final size:20
Alignment explanation
Indices: 62410204--62410241 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
62410194 ACCCCCTTTA
62410204 TTAACATAAA-AATTTAAAAT
1 TTAACA-AAATAATTTAAAAT
62410224 TTAACAAAATAATTTAAA
1 TTAACAAAATAATTTAAA
62410242 CTAGAAAAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 3 0.18
20 14 0.82
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (20 bp):
TTAACAAAATAATTTAAAAT
Found at i:62415782 original size:24 final size:23
Alignment explanation
Indices: 62415755--62415830 Score: 73
Period size: 24 Copynumber: 3.2 Consensus size: 23
62415745 AGATATTTAT
*
62415755 ATTATTTATTTATATAATATATAA
1 ATTAATTATTTATATAATAT-TAA
** *
62415779 ATTAATTATAAAGTATATTATTAA
1 ATTAATTATTTA-TATAATATTAA
*
62415803 ATTAATTATATTATA-AATATTAT
1 ATTAATTAT-TTATATAATATTAA
62415826 ATTAA
1 ATTAA
62415831 GAAATAAATT
Statistics
Matches: 42, Mismatches: 8, Indels: 5
0.76 0.15 0.09
Matches are distributed among these distances:
23 11 0.26
24 23 0.55
25 8 0.19
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.50
Consensus pattern (23 bp):
ATTAATTATTTATATAATATTAA
Found at i:62415798 original size:12 final size:11
Alignment explanation
Indices: 62415769--62415812 Score: 52
Period size: 12 Copynumber: 3.7 Consensus size: 11
62415759 TTTATTTATA
62415769 TAATATATAAAT
1 TAAT-TATAAAT
*
62415781 TAATTATAAAG
1 TAATTATAAAT
62415792 TATATTATTAAAT
1 TA-ATTA-TAAAT
62415805 TAATTATA
1 TAATTATA
62415813 TTATAAATAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
11 10 0.36
12 12 0.43
13 6 0.21
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (11 bp):
TAATTATAAAT
Found at i:62415824 original size:14 final size:17
Alignment explanation
Indices: 62415792--62415829 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
62415782 AATTATAAAG
62415792 TATATTATTAAATTAAT
1 TATATTATTAAATTAAT
62415809 TATATTA-TAAA-T-AT
1 TATATTATTAAATTAAT
62415823 TATATTA
1 TATATTA
62415830 AGAAATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.43
15 1 0.05
16 4 0.19
17 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATTATTAAATTAAT
Found at i:62416614 original size:12 final size:12
Alignment explanation
Indices: 62416599--62416651 Score: 88
Period size: 12 Copynumber: 4.4 Consensus size: 12
62416589 GTGAGGTAAG
* *
62416599 TATTAATATTAG
1 TATTAGTATTAT
62416611 TATTAGTATTAT
1 TATTAGTATTAT
62416623 TATTAGTATTAT
1 TATTAGTATTAT
62416635 TATTAGTATTAT
1 TATTAGTATTAT
62416647 TATTA
1 TATTA
62416652 TTAAGATGAG
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 39 1.00
ACGTcount: A:0.36, C:0.00, G:0.08, T:0.57
Consensus pattern (12 bp):
TATTAGTATTAT
Found at i:62416654 original size:6 final size:6
Alignment explanation
Indices: 62416597--62416651 Score: 74
Period size: 6 Copynumber: 9.2 Consensus size: 6
62416587 ATGTGAGGTA
* * *
62416597 AGTATT AATATT AGTATT AGTATT ATTATT AGTATT ATTATT AGTATT
1 AGTATT AGTATT AGTATT AGTATT AGTATT AGTATT AGTATT AGTATT
*
62416645 ATTATT A
1 AGTATT A
62416652 TTAAGATGAG
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 42 1.00
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (6 bp):
AGTATT
Found at i:62416842 original size:24 final size:27
Alignment explanation
Indices: 62416805--62416868 Score: 73
Period size: 27 Copynumber: 2.5 Consensus size: 27
62416795 AATTGCGGAT
*
62416805 TAATTATTG-ATTGAAAG-GTG-GAAA
1 TAATGATTGAATTGAAAGTGTGAGAAA
62416829 -AATGATTGAATTGAAAGTGTGAGAAA
1 TAATGATTGAATTGAAAGTGTGAGAAA
**
62416855 TTGTGATTGAATTG
1 TAATGATTGAATTG
62416869 GGAATATATG
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
23 7 0.21
24 8 0.24
25 3 0.09
26 4 0.12
27 11 0.33
ACGTcount: A:0.39, C:0.00, G:0.27, T:0.34
Consensus pattern (27 bp):
TAATGATTGAATTGAAAGTGTGAGAAA
Found at i:62420139 original size:17 final size:18
Alignment explanation
Indices: 62420117--62420152 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
62420107 CACTTCATAG
62420117 CTTAAA-AATATAAAATA
1 CTTAAATAATATAAAATA
62420134 CTTAAATTAATATAAAATA
1 CTTAAA-TAATATAAAATA
62420153 AGCCATTTTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.35
19 11 0.65
ACGTcount: A:0.61, C:0.06, G:0.00, T:0.33
Consensus pattern (18 bp):
CTTAAATAATATAAAATA
Found at i:62425069 original size:7 final size:7
Alignment explanation
Indices: 62425057--62425087 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
62425047 GAGAGCATGT
62425057 ATATGAG
1 ATATGAG
62425064 ATATGAG
1 ATATGAG
62425071 ATATGAG
1 ATATGAG
62425078 ATATGAG
1 ATATGAG
62425085 ATA
1 ATA
62425088 GTAGTGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.45, C:0.00, G:0.26, T:0.29
Consensus pattern (7 bp):
ATATGAG
Found at i:62428773 original size:3 final size:3
Alignment explanation
Indices: 62428767--62428850 Score: 64
Period size: 3 Copynumber: 27.7 Consensus size: 3
62428757 TTTAGCATTT
* * * * *
62428767 TTA TTA TT- TTC TTCA TTA TTT TTA ATA -TA TTA TCA TCTT TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
* *
62428812 TTA TTT TTG TTA TTA TTA GTTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TT
62428851 TCTTCATCTA
Statistics
Matches: 65, Mismatches: 11, Indels: 10
0.76 0.13 0.12
Matches are distributed among these distances:
2 4 0.06
3 55 0.85
4 6 0.09
ACGTcount: A:0.26, C:0.05, G:0.02, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:62428837 original size:22 final size:22
Alignment explanation
Indices: 62428809--62428850 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
62428799 TCATCTTTTA
* *
62428809 TTATTATTTTTGTTATTATTAG
1 TTATTATTATTATTATTATTAG
62428831 TTATTATTATTATTATTATT
1 TTATTATTATTATTATTATT
62428851 TCTTCATCTA
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:0.26, C:0.00, G:0.05, T:0.69
Consensus pattern (22 bp):
TTATTATTATTATTATTATTAG
Found at i:62429197 original size:22 final size:22
Alignment explanation
Indices: 62429156--62429220 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 22
62429146 CTTTATTGTT
* *
62429156 TTTATGTTCATTTATGTATTTA-
1 TTTA-GTTTATTTATTTATTTAC
*
62429178 TTTATGTGTTCTTT-TTTATTTAC
1 TTTA-GT-TTATTTATTTATTTAC
62429201 TTTAGTTTATTTATTTATTT
1 TTTAGTTTATTTATTTATTT
62429221 GCTATGATTG
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
21 5 0.14
22 23 0.64
23 8 0.22
ACGTcount: A:0.18, C:0.05, G:0.08, T:0.69
Consensus pattern (22 bp):
TTTAGTTTATTTATTTATTTAC
Found at i:62429518 original size:109 final size:110
Alignment explanation
Indices: 62429339--62429738 Score: 560
Period size: 109 Copynumber: 3.6 Consensus size: 110
62429329 AAAAATTTCT
* * * * * *
62429339 AAATGAGGCAATATTTAGCCTTTGGAAATTCGAGAAAACATGCCCTAATGTACTGGGTTTCGATT
1 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAG-GAACGTGCCCTAAGGTACTGGGTTTCGATT
62429404 TCTCGTTCGACCAAATAGCTAAATATTCTTTT-AAAAACTTTTCAA
65 TCTCGTTCGACCAAATAGCTAAATATTCTTTTAAAAAACTTTTCAA
*
62429449 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
1 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
* * * * *
62429514 CTCGTTCCACTAAAT-GACTTAATATCCTTTTTCAAAAA-TTTTC-A
66 CTCGTTCGACCAAATAG-CTAAATATTC-TTTTAAAAAACTTTTCAA
62429558 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACT-GGTTTCGATTT
1 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
*
62429622 CTTGTTCGACCAAATAGCTAAATA-TCTTTTAAGAAAAACTTTTCAA
66 CTCGTTCGACCAAATAGCTAAATATTCTTTT-A-AAAAACTTTTCAA
* * * *
62429668 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTACCCTAAGGTGCTGGGTTTTGATTT
1 AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
62429733 CTCGTT
66 CTCGTT
62429739 TAACCAAACT
Statistics
Matches: 258, Mismatches: 23, Indels: 17
0.87 0.08 0.06
Matches are distributed among these distances:
106 4 0.02
107 1 0.00
108 35 0.14
109 108 0.42
110 90 0.35
111 20 0.08
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.34
Consensus pattern (110 bp):
AAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTT
CTCGTTCGACCAAATAGCTAAATATTCTTTTAAAAAACTTTTCAA
Found at i:62429707 original size:219 final size:219
Alignment explanation
Indices: 62429328--62429738 Score: 666
Period size: 219 Copynumber: 1.9 Consensus size: 219
62429318 CAAAAAAGCA
* * *
62429328 AAAAAATTTCTAAATGAGGCAATATTTAGCCTTTGGAAATTCGAGAAAACATGCCCTAATGTACT
1 AAAAAATTTCAAAATAAGGCAATATTTAGCCTTTGGAAATTCGAGAAAACATGCCCTAAGGTACT
62429393 GGGTTTCGATTTCTCGTTCGACCAAATAGCTAAATATTCTTTTAAAAACTTTTCAAAAATAAGGC
66 GGGTTTCGATTTCTCGTTCGACCAAATAGCTAAATATTCTTTTAAAAACTTTTCAAAAATAAGGC
*
62429458 AATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTTCGATTTCTCGTTCCA
131 AATGTTTTGCGTTTGGAAATTCGAGGAACGTACCCTAAGGTACTGGGTTTCGATTTCTCGTTCCA
62429523 CTAAATGACTTAATATCCTTTTTC
196 CTAAATGACTTAATATCCTTTTTC
* * * * *
62429547 AAAAATTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAG-GAACGTGCCCTAAGGTACT
1 AAAAAATTTCAAAATAAGGCAATATTTAGCCTTTGGAAATTCGAGAAAACATGCCCTAAGGTACT
*
62429611 -GGTTTCGATTTCTTGTTCGACCAAATAGCTAAATA-TCTTTTAAGAAAAACTTTTCAAAAATAA
66 GGGTTTCGATTTCTCGTTCGACCAAATAGCTAAATATTCTTTT---AAAAACTTTTCAAAAATAA
* *
62429674 GGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTACCCTAAGGTGCTGGGTTTTGATTTCTCGTT
128 GGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTACCCTAAGGTACTGGGTTTCGATTTCTCGTT
62429739 TAACCAAACT
Statistics
Matches: 177, Mismatches: 12, Indels: 6
0.91 0.06 0.03
Matches are distributed among these distances:
216 6 0.03
217 34 0.19
218 16 0.09
219 121 0.68
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.35
Consensus pattern (219 bp):
AAAAAATTTCAAAATAAGGCAATATTTAGCCTTTGGAAATTCGAGAAAACATGCCCTAAGGTACT
GGGTTTCGATTTCTCGTTCGACCAAATAGCTAAATATTCTTTTAAAAACTTTTCAAAAATAAGGC
AATGTTTTGCGTTTGGAAATTCGAGGAACGTACCCTAAGGTACTGGGTTTCGATTTCTCGTTCCA
CTAAATGACTTAATATCCTTTTTC
Found at i:62433084 original size:17 final size:18
Alignment explanation
Indices: 62433062--62433098 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
62433052 TTATTCTTTT
62433062 ATTCTTTCATCCA-AATC
1 ATTCTTTCATCCATAATC
*
62433079 ATTCTTTCATTCATAATC
1 ATTCTTTCATCCATAATC
62433097 AT
1 AT
62433099 ACTGTGCAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.67
18 6 0.33
ACGTcount: A:0.30, C:0.24, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTCTTTCATCCATAATC
Found at i:62433842 original size:7 final size:7
Alignment explanation
Indices: 62433827--62433881 Score: 67
Period size: 7 Copynumber: 7.6 Consensus size: 7
62433817 AAAATAGGAG
62433827 AAAAAGA
1 AAAAAGA
*
62433834 AAGAAGA
1 AAAAAGA
62433841 AAAAAGAA
1 AAAAAG-A
62433849 AAAAAGA
1 AAAAAGA
62433856 AAAAAGA
1 AAAAAGA
62433863 AAAAA-A
1 AAAAAGA
62433869 AGAAAATGA
1 A-AAAA-GA
62433878 AAAA
1 AAAA
62433882 GGAGAGGTCA
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
6 2 0.05
7 28 0.67
8 10 0.24
9 2 0.05
ACGTcount: A:0.84, C:0.00, G:0.15, T:0.02
Consensus pattern (7 bp):
AAAAAGA
Found at i:62433855 original size:15 final size:15
Alignment explanation
Indices: 62433827--62433874 Score: 71
Period size: 15 Copynumber: 3.2 Consensus size: 15
62433817 AAAATAGGAG
*
62433827 AAAAAG-AAAGAAGA
1 AAAAAGAAAAAAAGA
62433841 AAAAAGAAAAAAAGA
1 AAAAAGAAAAAAAGA
62433856 AAAAAGAAAAAAAAGA
1 AAAAAG-AAAAAAAGA
62433872 AAA
1 AAA
62433875 TGAAAAAGGA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
14 6 0.19
15 13 0.42
16 12 0.39
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAAAGAAAAAAAGA
Found at i:62433874 original size:22 final size:23
Alignment explanation
Indices: 62433816--62433881 Score: 82
Period size: 22 Copynumber: 2.9 Consensus size: 23
62433806 AATCAAAGTC
* *
62433816 AAAAATAGGAGAAAAAGAAAGAAG
1 AAAAA-AGAAGAAAAAGAAAAAAG
62433840 AAAAAAGAA-AAAAAGAAAAAAG
1 AAAAAAGAAGAAAAAGAAAAAAG
*
62433862 AAAAAA-AAGAAAATGAAAAA
1 AAAAAAGAAGAAAAAGAAAAA
62433882 GGAGAGGTCA
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
21 2 0.05
22 28 0.74
23 3 0.08
24 5 0.13
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (23 bp):
AAAAAAGAAGAAAAAGAAAAAAG
Found at i:62433881 original size:16 final size:16
Alignment explanation
Indices: 62433837--62433874 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
62433827 AAAAAGAAAG
62433837 AAGAAAAAAG-AAAAA
1 AAGAAAAAAGAAAAAA
62433852 AAGAAAAAAGAAAAAA
1 AAGAAAAAAGAAAAAA
62433868 AAGAAAA
1 AAGAAAA
62433875 TGAAAAAGGA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
15 10 0.45
16 12 0.55
ACGTcount: A:0.87, C:0.00, G:0.13, T:0.00
Consensus pattern (16 bp):
AAGAAAAAAGAAAAAA
Found at i:62436009 original size:44 final size:44
Alignment explanation
Indices: 62435959--62436273 Score: 150
Period size: 44 Copynumber: 7.2 Consensus size: 44
62435949 AGTTATAGAG
* *
62435959 CTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGATACAAAC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGAAACAAAC
* * * * *
62436003 CTTGCC-TCTCT-CGATTG-TAGCGGAGCTGGTTC-AAGACAACAGAT
1 CTTGCCTTC-CTGC-ATTGACAGCGAAGCAGG-TCGAAGA-AACAAAC
* *
62436047 CTTGCCTTCCTGCATTGACAGCAAAGCAGGTCGAAGACACAAAC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGAAACAAAC
** * * * * *
62436091 CTTGCC-TCTCTCGGTTGTGA-TG-G-AGCTGGTTGAAGACAACATAT
1 CTTGCCTTC-CT-GCAT-TGACAGCGAAGCAGGTCGAAGA-AACAAAC
* * * *
62436135 CTTGCCTTCCTGCATTGACAGCAAAGTAGATCGAAGACACAAAC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGAAACAAAC
* ** * * * * *
62436179 CTTGCC-TCTCT-CGGTTG-TGGTGGAGCTGGTTGAAGACAA-AAGAT
1 CTTGCCTTC-CTGC-ATTGACAGCGAAGCAGGTCGAAGA-AACAA-AC
* * * *
62436223 CTTGCCTTCCTTCATTGACAACGAAGCAGATCGAAGACACAAAC
1 CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGAAACAAAC
62436267 CTTGCCT
1 CTTGCCT
62436274 CCCTCGGTTG
Statistics
Matches: 190, Mismatches: 57, Indels: 48
0.64 0.19 0.16
Matches are distributed among these distances:
42 3 0.02
43 46 0.24
44 93 0.49
45 45 0.24
46 3 0.02
ACGTcount: A:0.27, C:0.25, G:0.23, T:0.25
Consensus pattern (44 bp):
CTTGCCTTCCTGCATTGACAGCGAAGCAGGTCGAAGAAACAAAC
Found at i:62436116 original size:88 final size:88
Alignment explanation
Indices: 62435959--62436292 Score: 508
Period size: 88 Copynumber: 3.8 Consensus size: 88
62435949 AGTTATAGAG
* * * * * *
62435959 CTTGCCTTCCTGTATTGACAGCGAAGCAGGTCGAAGATACAAACCTTGCCTCTCTCGATTGTAGC
1 CTTGCCTTCCTGCATTGACAGCAAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGTTGTAGT
*
62436024 GGAGCTGGTTCAAGACAACAGAT
66 GGAGCTGGTTGAAGACAACAGAT
*
62436047 CTTGCCTTCCTGCATTGACAGCAAAGCAGGTCGAAGACACAAACCTTGCCTCTCTCGGTTGT-GA
1 CTTGCCTTCCTGCATTGACAGCAAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGTTGTAG-
*
62436111 TGGAGCTGGTTGAAGACAACATAT
65 TGGAGCTGGTTGAAGACAACAGAT
* *
62436135 CTTGCCTTCCTGCATTGACAGCAAAGTAGATCGAAGACACAAACCTTGCCTCTCTCGGTTGTGGT
1 CTTGCCTTCCTGCATTGACAGCAAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGTTGTAGT
*
62436200 GGAGCTGGTTGAAGACAAAAGAT
66 GGAGCTGGTTGAAGACAACAGAT
* * * *
62436223 CTTGCCTTCCTTCATTGACAACGAAGCAGATCGAAGACACAAACCTTGCCTCCCTCGGTTGTAGT
1 CTTGCCTTCCTGCATTGACAGCAAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGTTGTAGT
62436288 GGAGC
66 GGAGC
62436293 AGATCAAAGA
Statistics
Matches: 227, Mismatches: 17, Indels: 4
0.92 0.07 0.02
Matches are distributed among these distances:
87 1 0.00
88 225 0.99
89 1 0.00
ACGTcount: A:0.26, C:0.25, G:0.24, T:0.25
Consensus pattern (88 bp):
CTTGCCTTCCTGCATTGACAGCAAAGCAGATCGAAGACACAAACCTTGCCTCTCTCGGTTGTAGT
GGAGCTGGTTGAAGACAACAGAT
Found at i:62437141 original size:18 final size:18
Alignment explanation
Indices: 62437120--62437166 Score: 67
Period size: 18 Copynumber: 2.6 Consensus size: 18
62437110 GTATAAGTTA
*
62437120 TATTTTTCTTTTTCTTTT
1 TATTTTTCTTTTTCTCTT
* *
62437138 TATTCTTATTTTTCTCTT
1 TATTTTTCTTTTTCTCTT
62437156 TATTTTTCTTT
1 TATTTTTCTTT
62437167 CTTTCGAAAC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.09, C:0.13, G:0.00, T:0.79
Consensus pattern (18 bp):
TATTTTTCTTTTTCTCTT
Found at i:62437803 original size:3 final size:3
Alignment explanation
Indices: 62437797--62437874 Score: 52
Period size: 3 Copynumber: 25.7 Consensus size: 3
62437787 TTTAGCATTT
* * * * *
62437797 TTA TTA TT- TTC TTCA TTA TTT TTA ATA -TA TTA TCA TCTT TTA TTA
1 TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA
* *
62437842 TTA TTG TTG TTA TTA TTA GTTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TT
62437875 TCTTCATCTA
Statistics
Matches: 60, Mismatches: 10, Indels: 10
0.75 0.12 0.12
Matches are distributed among these distances:
2 4 0.07
3 50 0.83
4 6 0.10
ACGTcount: A:0.26, C:0.05, G:0.04, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:62438209 original size:22 final size:22
Alignment explanation
Indices: 62438173--62438250 Score: 72
Period size: 22 Copynumber: 3.5 Consensus size: 22
62438163 TCTATTTTTC
*
62438173 TTTATTGTTTTTATGTTCATTTA
1 TTTATT-TATTTATGTTCATTTA
*
62438196 TGTATTTATTTATGTGTTC-TTT-
1 TTTATTTATTTA--TGTTCATTTA
*
62438218 TTTATTTACTTTA-GTTTATTTA
1 TTTATTTA-TTTATGTTCATTTA
62438240 TTTATTTATTT
1 TTTATTTATTT
62438251 GCTATGATTG
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
20 3 0.07
21 6 0.13
22 20 0.43
23 12 0.26
24 5 0.11
ACGTcount: A:0.18, C:0.04, G:0.08, T:0.71
Consensus pattern (22 bp):
TTTATTTATTTATGTTCATTTA
Found at i:62438268 original size:4 final size:4
Alignment explanation
Indices: 62438191--62438250 Score: 52
Period size: 4 Copynumber: 15.0 Consensus size: 4
62438181 TTTTATGTTC
* * * *
62438191 ATTT ATGT ATTT ATTT ATGT -GTT CTTT -TTT ATTT ACTTT AGTTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT A-TTT A-TTT ATTT
62438239 ATTT ATTT ATTT
1 ATTT ATTT ATTT
62438251 GCTATGATTG
Statistics
Matches: 46, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
3 4 0.09
4 34 0.74
5 8 0.17
ACGTcount: A:0.20, C:0.03, G:0.07, T:0.70
Consensus pattern (4 bp):
ATTT
Found at i:62438598 original size:109 final size:108
Alignment explanation
Indices: 62438362--62438776 Score: 566
Period size: 109 Copynumber: 3.8 Consensus size: 108
62438352 AAAGAAAATT
* * * * * *
62438362 TTTTCTAAATGAGGCAATATTTAGCCTTTGGAAATTCGAGAAAACATGCCCTAAGGTACTGGGTT
1 TTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAG-GAACGTGCCCTAAGGTACTGGGTT
*
62438427 TCGATTTCTCGTTCGACCAAATAGCTAAATATTC-TTTTAAAAA
65 TCGATTTCTCGTTCGACCAAATAGCTAAATATCCTTTTTAAAAA
* *
62438470 CTTTTCAAAAAAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCACTAAGGTACTGGGTT
1 -TTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTT
* *
62438535 TCGATTTCTCGTTCCACCAAAT-GACTTAATATCCTTTTTCAAAAA
65 TCGATTTCTCGTTCGACCAAATAG-CTAAATATCCTTTTT-AAAAA
62438580 TTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACT-GGTTT
1 TTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTT
* * *
62438644 CGATTTCTCGTTCGACCAAATAGCTAAATATCTTTTTTTTTTAAAC
66 CGATTTCTCGTTCGACCAAATAGCTAAATATC---CTTTTTAAAAA
* *
62438690 TTTTCAAAAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTGCTGGGTT
1 TTTTC-AAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTT
* **
62438755 TTGATTTCTCGTTTAACCAAAT
65 TCGATTTCTCGTTCGACCAAAT
62438777 TGCCAAATGT
Statistics
Matches: 274, Mismatches: 23, Indels: 15
0.88 0.07 0.05
Matches are distributed among these distances:
107 1 0.00
108 83 0.30
109 97 0.35
110 13 0.05
111 57 0.21
112 23 0.08
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (108 bp):
TTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTACTGGGTTT
CGATTTCTCGTTCGACCAAATAGCTAAATATCCTTTTTAAAAA
Found at i:62438738 original size:220 final size:218
Alignment explanation
Indices: 62438362--62438776 Score: 645
Period size: 220 Copynumber: 1.9 Consensus size: 218
62438352 AAAGAAAATT
* *
62438362 TTTTCTAAATGAGGCAATATTTAGCCTTTGGAAATTCGAGAAAACATGCCCTAAGGTACTGGGTT
1 TTTTCAAAATAAGGCAATATTTAGCCTTTGGAAATTCGAGAAAACATGCCCTAAGGTACTGGGTT
62438427 TCGATTTCTCGTTCGACCAAATAGCTAAATATTCTTTTAAAAACTTTTCAAAAAAAGGCAATATT
66 TCGATTTCTCGTTCGACCAAATAGCTAAATATTCTTTTAAAAACTTTTCAAAAAAAGGCAATATT
*
62438492 TTGCGTTTGGAAATTCGAGGAACGTGCACTAAGGTACTGGGTTTCGATTTCTCGTTCCACCAAAT
131 TTGCGTTTGGAAATTCGAGGAACGTGCACTAAGGTACTGGGTTTCGATTTCTCGTTCAACCAAAT
62438557 GACTTAATATCCTTTTTCAAAAA
196 GACTTAATATCCTTTTTCAAAAA
* * * *
62438580 TTTTCAAAATAAGGCAATATTTTGCGTTTGGAAATTCGAG-GAACGTGCCCTAAGGTACT-GGTT
1 TTTTCAAAATAAGGCAATATTTAGCCTTTGGAAATTCGAGAAAACATGCCCTAAGGTACTGGGTT
* **
62438643 TCGATTTCTCGTTCGACCAAATAGCTAAATATCTTTTTTTTTTAAACTTTTCAAAAATAAGGCAA
66 TCGATTTCTCGTTCGACCAAATAGCTAAATA---TTCTTTTAAAAACTTTTCAAAAA-AAGGCAA
* * * * *
62438708 TGTTTTGCGTTTGGAAATTCGAGGAACGTGCCCTAAGGTGCTGGGTTTTGATTTCTCGTTTAACC
127 TATTTTGCGTTTGGAAATTCGAGGAACGTGCACTAAGGTACTGGGTTTCGATTTCTCGTTCAACC
62438773 AAAT
192 AAAT
62438777 TGCCAAATGT
Statistics
Matches: 178, Mismatches: 15, Indels: 6
0.89 0.08 0.03
Matches are distributed among these distances:
216 35 0.20
217 17 0.10
218 36 0.20
219 20 0.11
220 70 0.39
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (218 bp):
TTTTCAAAATAAGGCAATATTTAGCCTTTGGAAATTCGAGAAAACATGCCCTAAGGTACTGGGTT
TCGATTTCTCGTTCGACCAAATAGCTAAATATTCTTTTAAAAACTTTTCAAAAAAAGGCAATATT
TTGCGTTTGGAAATTCGAGGAACGTGCACTAAGGTACTGGGTTTCGATTTCTCGTTCAACCAAAT
GACTTAATATCCTTTTTCAAAAA
Found at i:62445513 original size:16 final size:16
Alignment explanation
Indices: 62445492--62445524 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
62445482 CTTTCTAAGT
62445492 GGGAGTACATTTTTAA
1 GGGAGTACATTTTTAA
62445508 GGGAGTACATTTTTAA
1 GGGAGTACATTTTTAA
62445524 G
1 G
62445525 ATATTAGAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.30, C:0.06, G:0.27, T:0.36
Consensus pattern (16 bp):
GGGAGTACATTTTTAA
Found at i:62455460 original size:15 final size:15
Alignment explanation
Indices: 62455442--62455471 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
62455432 AATAATGACA
62455442 ATAATAATAAATAAT
1 ATAATAATAAATAAT
*
62455457 ATAATAATACATAAT
1 ATAATAATAAATAAT
62455472 GATTTAATTT
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:0.63, C:0.03, G:0.00, T:0.33
Consensus pattern (15 bp):
ATAATAATAAATAAT
Found at i:62455501 original size:23 final size:22
Alignment explanation
Indices: 62455444--62455501 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
62455434 TAATGACAAT
*
62455444 AATAATAAATAATATAATAATA
1 AATAATAATTAATATAATAATA
* * *
62455466 CATAATGATTTAATTTAATAATA
1 AATAAT-AATTAATATAATAATA
62455489 AATAAATAATTAA
1 AAT-AATAATTAA
62455502 ATAGTAAAAT
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
22 5 0.18
23 20 0.71
24 3 0.11
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (22 bp):
AATAATAATTAATATAATAATA
Found at i:62457269 original size:44 final size:44
Alignment explanation
Indices: 62457216--62457549 Score: 171
Period size: 44 Copynumber: 7.5 Consensus size: 44
62457206 CACTACTGCT
* * *
62457216 TAGGGAGATAAGATCTGTTTCCTT-GATCTACTTCGCCACCAGTA
1 TAGGAAGACAAGATCTGTAT-CTTCGATCTACTTCGCCACCAGTA
* * * * * * *
62457260 TGGGAAGATAAAATCTGTATATTCGATCCACTTTGCTACC-GATA
1 TAGGAAGACAAGATCTGTATCTTCGATCTACTTCGCCACCAG-TA
* * * * *
62457304 TAGGAAGACAGGACCTGCTATCTTTGATCTACTTC-ACGCCAGTA
1 TAGGAAGACAAGATCTG-TATCTTCGATCTACTTCGCCACCAGTA
* * * * * *
62457348 CATGAAGACAAGATCTGTTTTCTTCGATCTGCTTTGCCACTAGTA
1 TAGGAAGACAAGATCTG-TATCTTCGATCTACTTCGCCACCAGTA
* * * * *
62457393 TGGGAAGGCAAGATCTGGTATCTAT-GACCTACTTC-ACGCCAGTA
1 TAGGAAGACAAGATCT-GTATCT-TCGATCTACTTCGCCACCAGTA
* ** * * *
62457437 CATAAAGACAAGATCTACTTTCTTCGATCTGCTTCGCCACCAGTA
1 TAGGAAGACAAGATCT-GTATCTTCGATCTACTTCGCCACCAGTA
* * * *
62457482 TGGGAAGGCAAGATCTGGTATCTAT-GGTCTACTT--CAAGCCAGTA
1 TAGGAAGACAAGATCT-GTATCT-TCGATCTACTTCGCCA-CCAGTA
* *
62457526 CATGAAGACAAGATCTGTTATCTT
1 TAGGAAGACAAGATCTG-TATCTT
62457550 TCAACCTGCT
Statistics
Matches: 208, Mismatches: 70, Indels: 25
0.69 0.23 0.08
Matches are distributed among these distances:
43 8 0.04
44 125 0.60
45 72 0.35
46 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.30
Consensus pattern (44 bp):
TAGGAAGACAAGATCTGTATCTTCGATCTACTTCGCCACCAGTA
Found at i:62457399 original size:89 final size:89
Alignment explanation
Indices: 62457322--62457549 Score: 366
Period size: 89 Copynumber: 2.6 Consensus size: 89
62457312 CAGGACCTGC
* *
62457322 TATCTTTGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTGCTTTGCCA
1 TATCTATGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTGCTTCGCCA
*
62457387 CTAGTATGGGAAGGCAAGATCTGG
66 CCAGTATGGGAAGGCAAGATCTGG
* * **
62457411 TATCTATGACCTACTTCACGCCAGTACATAAAGACAAGATCTACTTTCTTCGATCTGCTTCGCCA
1 TATCTATGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTGCTTCGCCA
62457476 CCAGTATGGGAAGGCAAGATCTGG
66 CCAGTATGGGAAGGCAAGATCTGG
* * *
62457500 TATCTATGGTCTACTTCAAGCCAGTACATGAAGACAAGATCTGTTATCTT
1 TATCTATGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTT
62457550 TCAACCTGCT
Statistics
Matches: 125, Mismatches: 14, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
89 125 1.00
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.31
Consensus pattern (89 bp):
TATCTATGATCTACTTCACGCCAGTACATGAAGACAAGATCTGTTTTCTTCGATCTGCTTCGCCA
CCAGTATGGGAAGGCAAGATCTGG
Found at i:62457407 original size:45 final size:45
Alignment explanation
Indices: 62457351--62457498 Score: 124
Period size: 45 Copynumber: 3.3 Consensus size: 45
62457341 GCCAGTACAT
* *
62457351 GAAGACAAGATCTGTTTTCTTCGATCTGCTTTGCCACTAGTATGG
1 GAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACTAGTATGG
* * * * * * *
62457396 GAAGGCAAGATCTGGTATCTAT-GACCTACTTCACGCCAGTA-CAT--
1 GAAGACAAGATCTGCTTTCT-TCGATCTGCTT--CGCCACTAGTATGG
* * *
62457440 AAAGACAAGATCTACTTTCTTCGATCTGCTTCGCCACCAGTATGG
1 GAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACTAGTATGG
*
62457485 GAAGGCAAGATCTG
1 GAAGACAAGATCTG
62457499 GTATCTATGG
Statistics
Matches: 75, Mismatches: 21, Indels: 14
0.68 0.19 0.13
Matches are distributed among these distances:
42 6 0.08
43 3 0.04
44 22 0.29
45 35 0.47
46 3 0.04
47 6 0.08
ACGTcount: A:0.27, C:0.23, G:0.22, T:0.28
Consensus pattern (45 bp):
GAAGACAAGATCTGCTTTCTTCGATCTGCTTCGCCACTAGTATGG
Found at i:62469462 original size:3 final size:3
Alignment explanation
Indices: 62469447--62469504 Score: 50
Period size: 3 Copynumber: 19.7 Consensus size: 3
62469437 GTACAATTAA
* *
62469447 AAT AAT AAC AAT AAT AAT AAAT AAT -AT AAT AAT ACAT AAT GAT -AT
1 AAT AAT AAT AAT AAT AAT -AAT AAT AAT AAT AAT A-AT AAT AAT AAT
*
62469492 AAT -GT AAT AAT AA
1 AAT AAT AAT AAT AA
62469505 ATAAATAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 10
0.75 0.08 0.17
Matches are distributed among these distances:
2 5 0.11
3 34 0.76
4 6 0.13
ACGTcount: A:0.62, C:0.03, G:0.03, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:62469479 original size:8 final size:8
Alignment explanation
Indices: 62469457--62469513 Score: 52
Period size: 7 Copynumber: 7.6 Consensus size: 8
62469447 AATAATAACA
62469457 ATAATAAT
1 ATAATAAT
62469465 A-AATAAT
1 ATAATAAT
62469472 ATAATAAT
1 ATAATAAT
*
62469480 A-CATAAT
1 ATAATAAT
62469487 GAT-ATAAT
1 -ATAATAAT
*
62469495 GTAATAAT
1 ATAATAAT
62469503 A-AATAA-
1 ATAATAAT
62469509 ATAAT
1 ATAAT
62469514 TAAATAGTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 11
0.75 0.05 0.20
Matches are distributed among these distances:
6 1 0.02
7 21 0.51
8 19 0.46
ACGTcount: A:0.61, C:0.02, G:0.04, T:0.33
Consensus pattern (8 bp):
ATAATAAT
Found at i:62471752 original size:19 final size:19
Alignment explanation
Indices: 62471708--62471768 Score: 70
Period size: 20 Copynumber: 3.2 Consensus size: 19
62471698 CTTTCAACAA
* *
62471708 AAAATACAAAATAATTTTCA
1 AAAATTCAAAATAATTTT-T
62471728 AAAATTCAAAATAATTTTT
1 AAAATTCAAAATAATTTTT
* *
62471747 AAAATTTAAAAT-ATTTAT
1 AAAATTCAAAATAATTTTT
62471765 AAAA
1 AAAA
62471769 ATTCTAAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
18 9 0.24
19 11 0.30
20 17 0.46
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAATTCAAAATAATTTTT
Found at i:62471769 original size:19 final size:19
Alignment explanation
Indices: 62471727--62471788 Score: 58
Period size: 19 Copynumber: 3.3 Consensus size: 19
62471717 AATAATTTTC
*
62471727 AAAAATTCAAAATAATTT-T
1 AAAAATTTAAAAT-ATTTAT
*
62471746 TAAAATTTAAAATATTTAT
1 AAAAATTTAAAATATTTAT
62471765 AAAAATTCT-AAAT-TTTAT
1 AAAAATT-TAAAATATTTAT
62471783 ATAAAA
1 A-AAAA
62471789 AAATTTAAAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
18 10 0.27
19 26 0.70
20 1 0.03
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAAATTTAAAATATTTAT
Found at i:62471817 original size:33 final size:32
Alignment explanation
Indices: 62471754--62471820 Score: 80
Period size: 33 Copynumber: 2.1 Consensus size: 32
62471744 TTTAAAATTT
* * ***
62471754 AAAATATTTATAAAAATTCTAAATTTTATATA
1 AAAAAATTTAAAAAAATTCTAAAGAATATATA
62471786 AAAAAATTTAAAAAAAGTTCTAAAGAATATATA
1 AAAAAATTTAAAAAAA-TTCTAAAGAATATATA
62471819 AA
1 AA
62471821 GAAAGTTCAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
32 14 0.48
33 15 0.52
ACGTcount: A:0.60, C:0.03, G:0.03, T:0.34
Consensus pattern (32 bp):
AAAAAATTTAAAAAAATTCTAAAGAATATATA
Found at i:62473909 original size:31 final size:32
Alignment explanation
Indices: 62473874--62473941 Score: 111
Period size: 31 Copynumber: 2.2 Consensus size: 32
62473864 AATGAAGATT
* *
62473874 AAAATTTTAAAATATGTG-AATAGTTAAACTA
1 AAAATTTTAAAATATGAGAAATAATTAAACTA
62473905 AAAATTTTAAAATATGAGAAATAATTAAACTA
1 AAAATTTTAAAATATGAGAAATAATTAAACTA
62473937 AAAAT
1 AAAAT
62473942 AATCAAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
31 17 0.50
32 17 0.50
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.32
Consensus pattern (32 bp):
AAAATTTTAAAATATGAGAAATAATTAAACTA
Found at i:62476748 original size:50 final size:51
Alignment explanation
Indices: 62476642--62476853 Score: 329
Period size: 51 Copynumber: 4.2 Consensus size: 51
62476632 ATCACATTTA
* *
62476642 TCACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACCACTTATCACTTG
1 TCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
* * *
62476693 TCACTTGTAACCGATCAGATAAGTGTAGCT-AAGCTACCACTTATCACTTG
1 TCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
*
62476743 TCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCAGTTATCACTTG
1 TCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
*
62476794 TCACTTATCACTGATCAGATAAGTGTAACTAAA-CTACCACTTATCACTTG
1 TCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
* *
62476844 TTACTGATCA
1 TCACTTATCA
62476854 GAAGTACTCA
Statistics
Matches: 149, Mismatches: 11, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
50 71 0.48
51 78 0.52
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.32
Consensus pattern (51 bp):
TCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTTG
Found at i:62476757 original size:101 final size:101
Alignment explanation
Indices: 62476642--62476853 Score: 334
Period size: 101 Copynumber: 2.1 Consensus size: 101
62476632 ATCACATTTA
* *
62476642 TCACTTGTCACTGATCAAATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTGTAACCGA
1 TCACTTATCACTGATCAAATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTATAACCGA
* *
62476707 TCAGATAAGTGTAGCTAAGCTACCACTTATCACTTG
66 TCAGATAAGTGTAACTAAACTACCACTTATCACTTG
* * * *
62476743 TCACTTATCACTGATCAGATAAGTGTAGCTAAAGCTACCAGTTATCACTTGTCACTTATCACTGA
1 TCACTTATCACTGATCAAATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTATAACCGA
62476808 TCAGATAAGTGTAACTAAACTACCACTTATCACTTG
66 TCAGATAAGTGTAACTAAACTACCACTTATCACTTG
* *
62476844 TTACTGATCA
1 TCACTTATCA
62476854 GAAGTACTCA
Statistics
Matches: 101, Mismatches: 10, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
101 101 1.00
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.32
Consensus pattern (101 bp):
TCACTTATCACTGATCAAATAAGTGTAGCTAAAGCTACCACTTATCACTTGTCACTTATAACCGA
TCAGATAAGTGTAACTAAACTACCACTTATCACTTG
Found at i:62476949 original size:17 final size:17
Alignment explanation
Indices: 62476927--62476959 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
62476917 TATTCTCAAT
62476927 TCATCA-ACAAATATATC
1 TCATCATAC-AATATATC
62476944 TCATCATACAATATAT
1 TCATCATACAATATAT
62476960 AATTCATGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 13 0.87
18 2 0.13
ACGTcount: A:0.45, C:0.21, G:0.00, T:0.33
Consensus pattern (17 bp):
TCATCATACAATATATC
Found at i:62488682 original size:22 final size:23
Alignment explanation
Indices: 62488650--62488698 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
62488640 ACATAAATAT
*
62488650 TTTAAATAATATATAATAATAAA
1 TTTAAATAATATATAAAAATAAA
*
62488673 TTTAAA-AATATATAAAAATAAT
1 TTTAAATAATATATAAAAATAAA
62488695 TTTA
1 TTTA
62488699 TTAATATTGA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 18 0.75
23 6 0.25
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (23 bp):
TTTAAATAATATATAAAAATAAA
Found at i:62488688 original size:10 final size:10
Alignment explanation
Indices: 62488626--62488692 Score: 55
Period size: 10 Copynumber: 6.5 Consensus size: 10
62488616 AATTTCAAAG
62488626 AAATATATAA
1 AAATATATAA
*
62488636 AAATACATAA
1 AAATATATAA
* *
62488646 ATAT-TTTAA
1 AAATATATAA
62488655 ATAATATATAA
1 A-AATATATAA
* *
62488666 TAATAAATTTAA
1 -AA-ATATATAA
62488678 AAATATATAA
1 AAATATATAA
62488688 AAATA
1 AAATA
62488693 ATTTTATTAA
Statistics
Matches: 43, Mismatches: 10, Indels: 8
0.70 0.16 0.13
Matches are distributed among these distances:
9 4 0.09
10 25 0.58
11 7 0.16
12 7 0.16
ACGTcount: A:0.64, C:0.01, G:0.00, T:0.34
Consensus pattern (10 bp):
AAATATATAA
Found at i:62488704 original size:22 final size:22
Alignment explanation
Indices: 62488654--62488705 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
62488644 AAATATTTTA
*
62488654 AATAATATATAATAATAAATTT
1 AATAATATATAAAAATAAATTT
* *
62488676 AAAAATATATAAAAATAATTTT
1 AATAATATATAAAAATAAATTT
*
62488698 ATTAATAT
1 AATAATAT
62488706 TGAATAAAAT
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (22 bp):
AATAATATATAAAAATAAATTT
Found at i:62490984 original size:16 final size:17
Alignment explanation
Indices: 62490963--62491006 Score: 65
Period size: 16 Copynumber: 2.7 Consensus size: 17
62490953 ATTAGGGGTT
62490963 AAATTGTGAAATATG-A
1 AAATTGTGAAATATGTA
*
62490979 AAATTGT-AAATGTGTA
1 AAATTGTGAAATATGTA
62490995 AAATTGTGAAAT
1 AAATTGTGAAAT
62491007 GTATGGACTG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
15 6 0.24
16 15 0.60
17 4 0.16
ACGTcount: A:0.48, C:0.00, G:0.18, T:0.34
Consensus pattern (17 bp):
AAATTGTGAAATATGTA
Found at i:62502790 original size:28 final size:28
Alignment explanation
Indices: 62502758--62502819 Score: 81
Period size: 28 Copynumber: 2.2 Consensus size: 28
62502748 TATTTTTCTC
*
62502758 ATAAAATGATTAAAAATCAGAAAAA-ATT
1 ATAAAATGA-TAAAAATCAGAAAAATAAT
*
62502786 ATAAAAATTATAAAAATCAGAAAAATAAT
1 AT-AAAATGATAAAAATCAGAAAAATAAT
62502815 ATAAA
1 ATAAA
62502820 TAATATTAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
28 20 0.67
29 10 0.33
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.24
Consensus pattern (28 bp):
ATAAAATGATAAAAATCAGAAAAATAAT
Found at i:62502791 original size:8 final size:9
Alignment explanation
Indices: 62502779--62503032 Score: 83
Period size: 9 Copynumber: 27.6 Consensus size: 9
62502769 AAAAATCAGA
62502779 AAAAATTAT
1 AAAAATTAT
62502788 AAAAATTAT
1 AAAAATTAT
* *
62502797 AAAAATCAG
1 AAAAATTAT
*
62502806 AAAAATAAT
1 AAAAATTAT
* *
62502815 ATAAATAAT
1 AAAAATTAT
*
62502824 ATTAAA-TAT
1 A-AAAATTAT
* **
62502833 TAAAACCATT
1 AAAAATTA-T
*
62502843 AAAATTTAT
1 AAAAATTAT
* *
62502852 ATGAACTTAT
1 A-AAAATTAT
*
62502862 TAAAATTAT
1 AAAAATTAT
*
62502871 AAAAAAATAT
1 -AAAAATTAT
62502881 AAAAACTTAT
1 AAAAA-TTAT
*
62502891 AAATATTAT
1 AAAAATTAT
62502900 AAAAA-TAT
1 AAAAATTAT
62502908 AATAAATCTA-
1 AA-AAAT-TAT
*
62502918 ATAAATTAT
1 AAAAATTAT
**
62502927 AAAAAAAAT
1 AAAAATTAT
**
62502936 AATTATTATTT
1 AAAAATTA--T
62502947 AAAATATT-T
1 AAAA-ATTAT
*
62502956 AAAATTTA-
1 AAAAATTAT
*
62502964 AAAAAGTATT
1 AAAAATTA-T
* *
62502974 AGAATTATTAA
1 A-AA-AATTAT
62502985 AAAAATTA-
1 AAAAATTAT
62502993 AAAAA-T-T
1 AAAAATTAT
*
62503000 AAAATTTAT
1 AAAAATTAT
* *
62503009 ATAGACTTAT
1 A-AAAATTAT
62503019 AAAAATTAT
1 AAAAATTAT
62503028 AAAAA
1 AAAAA
62503033 AAATCAAAAA
Statistics
Matches: 178, Mismatches: 45, Indels: 44
0.67 0.17 0.16
Matches are distributed among these distances:
7 5 0.03
8 24 0.13
9 95 0.53
10 40 0.22
11 8 0.04
12 6 0.03
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (9 bp):
AAAAATTAT
Found at i:62502875 original size:29 final size:29
Alignment explanation
Indices: 62502855--62502913 Score: 84
Period size: 29 Copynumber: 2.0 Consensus size: 29
62502845 AATTTATATG
*
62502855 AACTTATTAAA-ATTATAAAAAAATATAAA
1 AACTTA-TAAATATTATAAAAATATATAAA
62502884 AACTTATAAATATTATAAAAATATAATAAA
1 AACTTATAAATATTATAAAAATAT-ATAAA
62502914 TCTAATAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
28 4 0.15
29 18 0.67
30 5 0.19
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.32
Consensus pattern (29 bp):
AACTTATAAATATTATAAAAATATATAAA
Found at i:62502932 original size:29 final size:28
Alignment explanation
Indices: 62502864--62502938 Score: 93
Period size: 27 Copynumber: 2.7 Consensus size: 28
62502854 GAACTTATTA
*
62502864 AAATTATAAAAAAATATAA-AAACTTAT
1 AAATTATAAAAAAATATAATAAACTAAT
*
62502891 AAA-TATTATAAAAATATAATAAATCTAAT
1 AAATTA-TAAAAAAATATAATAAA-CTAAT
62502920 AAATTATAAAAAAA-ATAAT
1 AAATTATAAAAAAATATAAT
62502939 TATTATTTAA
Statistics
Matches: 41, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
26 2 0.05
27 15 0.37
28 8 0.20
29 14 0.34
30 2 0.05
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (28 bp):
AAATTATAAAAAAATATAATAAACTAAT
Found at i:62504087 original size:16 final size:17
Alignment explanation
Indices: 62504061--62504093 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
62504051 TATTATAATC
62504061 TATATTATAATAATAGT
1 TATATTATAATAATAGT
*
62504078 TATA-TATAATAGTAGT
1 TATATTATAATAATAGT
62504094 GCATTATATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.45, C:0.00, G:0.09, T:0.45
Consensus pattern (17 bp):
TATATTATAATAATAGT
Found at i:62504377 original size:28 final size:28
Alignment explanation
Indices: 62504311--62504383 Score: 69
Period size: 30 Copynumber: 2.6 Consensus size: 28
62504301 TTATATCTTT
* * *
62504311 TATTATAATTTATATTATAATAGTTGTA
1 TATTATAATATATATTATAATAGCTATA
*
62504339 TATGTATTAATATGT-TTAGTAATAGCTATA
1 TAT-TA-TAATATATATTA-TAATAGCTATA
62504369 TATTATAATAT-TATT
1 TATTATAATATATATT
62504384 TTATGTACTA
Statistics
Matches: 37, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
27 1 0.03
28 11 0.30
29 7 0.19
30 18 0.49
ACGTcount: A:0.38, C:0.01, G:0.08, T:0.52
Consensus pattern (28 bp):
TATTATAATATATATTATAATAGCTATA
Found at i:62504513 original size:16 final size:17
Alignment explanation
Indices: 62504465--62504526 Score: 51
Period size: 17 Copynumber: 3.8 Consensus size: 17
62504455 TAATATATTA
* *
62504465 TTATATTATCATTAATT
1 TTATATAATTATTAATT
*
62504482 TT-TA-ATTTA-TAGATT
1 TTATATAATTATTA-ATT
62504497 TTA-ATAATTATTAATT
1 TTATATAATTATTAATT
*
62504513 TTATATATTTATTA
1 TTATATAATTATTA
62504527 TACATGTATA
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
14 2 0.06
15 8 0.23
16 12 0.34
17 13 0.37
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (17 bp):
TTATATAATTATTAATT
Found at i:62504524 original size:17 final size:17
Alignment explanation
Indices: 62504475--62504526 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
62504465 TTATATTATC
62504475 ATTAATTTT-TA-ATTT
1 ATTAATTTTATATATTT
*
62504490 A-TAGATTTTA-ATAATT
1 ATTA-ATTTTATATATTT
62504506 ATTAATTTTATATATTT
1 ATTAATTTTATATATTT
62504523 ATTA
1 ATTA
62504527 TACATGTATA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
14 2 0.07
15 7 0.23
16 10 0.33
17 11 0.37
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
ATTAATTTTATATATTT
Found at i:62505095 original size:16 final size:16
Alignment explanation
Indices: 62505070--62505103 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
62505060 AAAAAAAATC
62505070 TTTTTTTTTTATT-TT
1 TTTTTTTTTTATTGTT
62505085 TTTTATTTTTTATTGTT
1 TTTT-TTTTTTATTGTT
62505102 TT
1 TT
62505104 CTCCTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 9 0.53
17 4 0.24
ACGTcount: A:0.09, C:0.00, G:0.03, T:0.88
Consensus pattern (16 bp):
TTTTTTTTTTATTGTT
Found at i:62509572 original size:13 final size:13
Alignment explanation
Indices: 62509554--62509578 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
62509544 TAACTCGTTT
62509554 TATATTTTTATAA
1 TATATTTTTATAA
62509567 TATATTTTTATA
1 TATATTTTTATA
62509579 TTTTGTGTAA
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (13 bp):
TATATTTTTATAA
Found at i:62516227 original size:21 final size:21
Alignment explanation
Indices: 62516201--62516253 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
62516191 CGCTGTTTTT
*
62516201 AATCTCACCGCTACAATATCC
1 AATCTCACCGCTACAATAACC
** * *
62516222 AATCTCACTACTTCAATAACT
1 AATCTCACCGCTACAATAACC
62516243 AATCTCACCGC
1 AATCTCACCGC
62516254 CACCGTTGTT
Statistics
Matches: 25, Mismatches: 7, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.34, C:0.36, G:0.04, T:0.26
Consensus pattern (21 bp):
AATCTCACCGCTACAATAACC
Found at i:62521605 original size:84 final size:84
Alignment explanation
Indices: 62521464--62521619 Score: 201
Period size: 84 Copynumber: 1.9 Consensus size: 84
62521454 ATGTGTTTTC
* * *
62521464 GTGTAAGACCACGTCTGGGACGTTGGCATCGACTTGTGTTTACGCGTAAGACCATGTCTGGGACA
1 GTGTAAGACCACGTCTAGGACGTTGGCATCGACTTGTGATTACACGTAAGACCATGTCTGGGACA
62521529 TTGGCATCGTATTTGATTT
66 TTGGCATCGTATTTGATTT
* *
62521548 GTGTAAGACC-CTGTCTAGGACAG-TGGCATCGA-TATGTGATTACATGTAAGATCATGTCTGGG
1 GTGTAAGACCAC-GTCTAGGAC-GTTGGCATCGACT-TGTGATTACACGTAAGACCATGTCTGGG
**
62521610 ATGTTGGCAT
63 ACATTGGCAT
62521620 TGTACGAGTC
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
83 2 0.03
84 59 0.95
85 1 0.02
ACGTcount: A:0.22, C:0.17, G:0.29, T:0.31
Consensus pattern (84 bp):
GTGTAAGACCACGTCTAGGACGTTGGCATCGACTTGTGATTACACGTAAGACCATGTCTGGGACA
TTGGCATCGTATTTGATTT
Found at i:62521618 original size:43 final size:43
Alignment explanation
Indices: 62521449--62521619 Score: 179
Period size: 43 Copynumber: 4.0 Consensus size: 43
62521439 ACATAGGATT
* * *
62521449 TCGATATGTGTTTTCGTGTAAGACCACGTCTGGGACGTTGGCA
1 TCGATATGTGATTACGTGTAAGACCATGTCTGGGACGTTGGCA
* * *
62521492 TCGACT-TGTGTTTACGCGTAAGACCATGTCTGGGACATTGGCA
1 TCGA-TATGTGATTACGTGTAAGACCATGTCTGGGACGTTGGCA
* * * *
62521535 TCG-TATTTGATT-TGTGTAAGACCCTGTCTAGGACAG-TGGCA
1 TCGATATGTGATTACGTGTAAGACCATGTCTGGGAC-GTTGGCA
* * *
62521576 TCGATATGTGATTACATGTAAGATCATGTCTGGGATGTTGGCA
1 TCGATATGTGATTACGTGTAAGACCATGTCTGGGACGTTGGCA
62521619 T
1 T
62521620 TGTACGAGTC
Statistics
Matches: 104, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
41 27 0.26
42 14 0.13
43 62 0.60
44 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.28, T:0.33
Consensus pattern (43 bp):
TCGATATGTGATTACGTGTAAGACCATGTCTGGGACGTTGGCA
Found at i:62529621 original size:15 final size:15
Alignment explanation
Indices: 62529601--62529631 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
62529591 TGAAACCTAC
*
62529601 CTTAACCAATGAGAT
1 CTTAACCAATAAGAT
62529616 CTTAACCAATAAGAT
1 CTTAACCAATAAGAT
62529631 C
1 C
62529632 AAGGCTAAAC
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:0.42, C:0.23, G:0.10, T:0.26
Consensus pattern (15 bp):
CTTAACCAATAAGAT
Found at i:62566453 original size:23 final size:21
Alignment explanation
Indices: 62566427--62566470 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
62566417 TTTCTACCTT
*
62566427 AAAATCATACATTATATTTTTCA
1 AAAATCATA-ATT-TACTTTTCA
*
62566450 AAAATTATAATTTACTTTTCA
1 AAAATCATAATTTACTTTTCA
62566471 GATTTTAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 8 0.42
22 3 0.16
23 8 0.42
ACGTcount: A:0.43, C:0.11, G:0.00, T:0.45
Consensus pattern (21 bp):
AAAATCATAATTTACTTTTCA
Found at i:62573307 original size:15 final size:16
Alignment explanation
Indices: 62573267--62573311 Score: 51
Period size: 15 Copynumber: 2.9 Consensus size: 16
62573257 AATAAATAAA
*
62573267 AAATATTTTAAATTATT
1 AAATAATTTAAA-TATT
62573284 AAAT-A-TTAAAT-TT
1 AAATAATTTAAATATT
62573297 AAATAATTTAAATAT
1 AAATAATTTAAATAT
62573312 ATTTTTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
13 6 0.25
14 2 0.08
15 11 0.46
16 1 0.04
17 4 0.17
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (16 bp):
AAATAATTTAAATATT
Found at i:62573318 original size:21 final size:21
Alignment explanation
Indices: 62573271--62573319 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
62573261 AATAAAAAAT
*
62573271 ATTTTAAATTATTAAATATTA
1 ATTTTAAATAATTAAATATTA
*
62573292 AATTTAAATAATTTAAATA-TA
1 ATTTTAAATAA-TTAAATATTA
*
62573313 TTTTTAA
1 ATTTTAA
62573320 TTTTTTTTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 16 0.70
22 7 0.30
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATTTTAAATAATTAAATATTA
Found at i:62573918 original size:2 final size:2
Alignment explanation
Indices: 62573911--62573935 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
62573901 ATTAACACAA
62573911 AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG A
62573936 TGCATACCAT
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:62580473 original size:24 final size:24
Alignment explanation
Indices: 62580446--62580492 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
62580436 ATTGAAATGA
62580446 ATTGA-TTTAGTATGTGA-TGAATTT
1 ATTGAGTTTA-TAT-TGATTGAATTT
62580470 ATTGAGTTTATATTGATTGAATT
1 ATTGAGTTTATATTGATTGAATT
62580493 GGTATATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
23 3 0.14
24 14 0.67
25 4 0.19
ACGTcount: A:0.30, C:0.00, G:0.19, T:0.51
Consensus pattern (24 bp):
ATTGAGTTTATATTGATTGAATTT
Found at i:62580771 original size:40 final size:39
Alignment explanation
Indices: 62580648--62580788 Score: 117
Period size: 40 Copynumber: 3.6 Consensus size: 39
62580638 CGACTTCGAG
* * * *
62580648 TCGATGAGACACTAGGTGTCAATTTACTACTTCAAATATA
1 TCGATGAGACACTGGGTGTCAAATTATTACTTCGAAT-TA
* * * **
62580688 TTTGATGAGGCACTGGGTG-CCAA-T-TTACTTCGGTTTA
1 -TCGATGAGACACTGGGTGTCAAATTATTACTTCGAATTA
62580725 GTCGATGAGACACTGGGTGTCAAATTATTACTTCGAATTA
1 -TCGATGAGACACTGGGTGTCAAATTATTACTTCGAATTA
* * *
62580765 TCCGATGAGGCATTGGGTGCCAAA
1 T-CGATGAGACACTGGGTGTCAAA
62580789 CTGTGTGTTT
Statistics
Matches: 78, Mismatches: 18, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
37 18 0.23
38 10 0.13
39 3 0.04
40 32 0.41
41 15 0.19
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (39 bp):
TCGATGAGACACTGGGTGTCAAATTATTACTTCGAATTA
Found at i:62583032 original size:18 final size:18
Alignment explanation
Indices: 62583006--62583040 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
62582996 ATATTTTGTT
*
62583006 ATTAGATATCGATACCAA
1 ATTAAATATCGATACCAA
62583024 ATTAAATATCGATACCA
1 ATTAAATATCGATACCA
62583041 TTTTGACATA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.29
Consensus pattern (18 bp):
ATTAAATATCGATACCAA
Found at i:62585165 original size:266 final size:267
Alignment explanation
Indices: 62584691--62585227 Score: 988
Period size: 266 Copynumber: 2.0 Consensus size: 267
62584681 ACTAGTGAGT
62584691 AATTTTCTCTTTTCCATAATTTTCTATCGGTTCTTGATCTATACGATAATTTATTTCAATTATCA
1 AATTTTCTCTTTTCCATAATTTTCTATCGGTTCTTGATCTATACGATAATTTATTTCAATTATCA
* * *
62584756 ATCCCAAGTACATTATAAACGTCCATTTGATGCATATGACTTTTTTATTGACATTTTTCATAATT
66 ATCCCAAGTACATTATAAAAGTCCACTTGATGCATATGAATTTTTTATTGACATTTTTCATAATT
*
62584821 TCCCTAAAATTTTACATTTTATTCAATTTAGTCCCTAAAACCGAAACAAGCTCATTTTTTTCTTA
131 GCCCTAAAATTTTACATTTTATTCAATTTAGTCCCTAAAACCGAAACAAGCTCATTTTTTTCTTA
*
62584886 ATTAAGCCC-AAAAATATTATGCCTAATTCATTATTATCCTAAAAAACCCTCAAGTCACAAAATT
196 ATTAAGCCCAAAAAATATTATGCCTAATTCATTATCATCCTAAAAAACCCTCAAGTCACAAAATT
62584950 TACAAGA
261 TACAAGA
*
62584957 AATTTTCTTTTTTCCATAATTTTCTATCGGTTCTTGATCTATACGATAATTTATTTCAATTATCA
1 AATTTTCTCTTTTCCATAATTTTCTATCGGTTCTTGATCTATACGATAATTTATTTCAATTATCA
*
62585022 GTCCCAAGTACATTATAAAAGTCCACTTGATGCATATGAATTTTTTATTGACATTTTTCATAATT
66 ATCCCAAGTACATTATAAAAGTCCACTTGATGCATATGAATTTTTTATTGACATTTTTCATAATT
62585087 GCCCTAAAATTTTACATTTTATTCAATTTAGTCCCTAAAACCGAAACAAGCTCATTTTTTTTCTT
131 GCCCTAAAATTTTACATTTTATTCAATTTAGTCCCTAAAACCGAAACAAGCTCA-TTTTTTTCTT
62585152 AATTAAG-CCAAAAAATATTATGCCTAATTCATTATCATCCTAAAAAACCCTCAAGTCACAAAAT
195 AATTAAGCCCAAAAAATATTATGCCTAATTCATTATCATCCTAAAAAACCCTCAAGTCACAAAAT
62585216 TTACAAGA
260 TTACAAGA
62585224 AATT
1 AATT
62585228 AATTCCATTC
Statistics
Matches: 262, Mismatches: 7, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
266 180 0.69
267 82 0.31
ACGTcount: A:0.34, C:0.19, G:0.07, T:0.40
Consensus pattern (267 bp):
AATTTTCTCTTTTCCATAATTTTCTATCGGTTCTTGATCTATACGATAATTTATTTCAATTATCA
ATCCCAAGTACATTATAAAAGTCCACTTGATGCATATGAATTTTTTATTGACATTTTTCATAATT
GCCCTAAAATTTTACATTTTATTCAATTTAGTCCCTAAAACCGAAACAAGCTCATTTTTTTCTTA
ATTAAGCCCAAAAAATATTATGCCTAATTCATTATCATCCTAAAAAACCCTCAAGTCACAAAATT
TACAAGA
Found at i:62588707 original size:21 final size:22
Alignment explanation
Indices: 62588659--62588732 Score: 62
Period size: 23 Copynumber: 3.3 Consensus size: 22
62588649 ATTGATAAGA
* *
62588659 TGCACTGAAGTGCCACTATTC-TT
1 TGCACCGAAGTGCCAC--TTCACT
*
62588682 TGCACCGAAGTGTCAC-TCACT
1 TGCACCGAAGTGCCACTTCACT
* *
62588703 TGCACAGTAGTGCCACTTTCACT
1 TGCACCGAAGTGCCAC-TTCACT
62588726 TGCACCG
1 TGCACCG
62588733 TAGTACCATT
Statistics
Matches: 41, Mismatches: 7, Indels: 6
0.76 0.13 0.11
Matches are distributed among these distances:
20 2 0.05
21 14 0.34
23 25 0.61
ACGTcount: A:0.22, C:0.31, G:0.19, T:0.28
Consensus pattern (22 bp):
TGCACCGAAGTGCCACTTCACT
Found at i:62592810 original size:35 final size:35
Alignment explanation
Indices: 62592771--62592840 Score: 140
Period size: 35 Copynumber: 2.0 Consensus size: 35
62592761 TATTTTATTA
62592771 CATACATCTGAATAAGATGTTTTGTAATGTTATGG
1 CATACATCTGAATAAGATGTTTTGTAATGTTATGG
62592806 CATACATCTGAATAAGATGTTTTGTAATGTTATGG
1 CATACATCTGAATAAGATGTTTTGTAATGTTATGG
62592841 AACTACTACA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.31, C:0.09, G:0.20, T:0.40
Consensus pattern (35 bp):
CATACATCTGAATAAGATGTTTTGTAATGTTATGG
Found at i:62604598 original size:22 final size:22
Alignment explanation
Indices: 62604563--62604616 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
62604553 ATTTAGTCAT
* *
62604563 ATAATAAATCATTAATATAATAA
1 ATAATAATTTATTAATATAA-AA
* *
62604586 AT-ATAATTTATTATTTTAAAA
1 ATAATAATTTATTAATATAAAA
62604607 ATAATAATTT
1 ATAATAATTT
62604617 TAAATAATAT
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
21 4 0.15
22 20 0.77
23 2 0.08
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (22 bp):
ATAATAATTTATTAATATAAAA
Found at i:62617718 original size:12 final size:11
Alignment explanation
Indices: 62617683--62617714 Score: 55
Period size: 12 Copynumber: 2.8 Consensus size: 11
62617673 CAAAATTAAG
62617683 TAAATAAATAT
1 TAAATAAATAT
62617694 TAAATGAAATAT
1 TAAAT-AAATAT
62617706 TAAATAAAT
1 TAAATAAAT
62617715 TATTTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (11 bp):
TAAATAAATAT
Found at i:62619502 original size:50 final size:50
Alignment explanation
Indices: 62619448--62619986 Score: 293
Period size: 50 Copynumber: 10.8 Consensus size: 50
62619438 TACACCGCCA
** *
62619448 GGGAAGTAAGATTCATCGTTGTGGCTTCAATCTTTTCAATTGCAATACCG
1 GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTCAATTGCAATGCCG
** * * * * * **
62619498 GGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCACTGCACCGCCAG
1 GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTCAATTGCAATGCC-G
* * * *
62619549 TGG-AGTAAGATTCGCCGTTGCGGCTTTAATCTTTT-AATTGCAATGTCG
1 GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTCAATTGCAATGCCG
** ** * * * * * **
62619597 GGGAAACAAGATTCTTCGTCGTAGCTTCAATCTATTCCACTGCACCGCCAG
1 GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTCAATTGCAATGCC-G
* **
62619648 GGG-AGTAAGATTCACCGTTGTGGCTTCAATCTTTT-AATTGCAATGTGG
1 GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTCAATTGCAATGCCG
** * * * * ** * * * * *
62619696 GGGAAACAAGATTCACCGTCGTAGCTTTAATCTGCTCCACTACACTGCCA
1 GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTCAATTGCAATGCCG
** * ** * *
62619746 GAAAAGTAAGATTCGTCGTTACGGCTTCAATCTTTTTAATTGCAATGTCG
1 GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTCAATTGCAATGCCG
* * ** * *
62619796 GGGAACG--AGATTCGCTGTTGTAGCTTCAATCTGATCCACTGC-AT-CACG
1 GGGAA-GTAAGATTCGCCGTTGTGGCTTCAATCTTTTCAATTGCAATGC-CG
* * * * *
62619844 AAGGAAGTAAGATTCACCGTTGCGGCTTCAATCTTTTTAATTGCAATGTCG
1 -GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTCAATTGCAATGCCG
* * * * * ** * * * * *
62619895 GGGAAGCAAGATTCGTCGTCGTAGCTTTAATCTGCTCCACTGCACTGTCA
1 GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTCAATTGCAATGCCG
* * *
62619945 GGAAAGTAAGATTCGCCGTTGCGGCTTCAATCTTTTTAATTG
1 GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTCAATTG
62619987 TAAACTATGG
Statistics
Matches: 338, Mismatches: 138, Indels: 26
0.67 0.27 0.05
Matches are distributed among these distances:
48 12 0.04
49 90 0.27
50 224 0.66
51 12 0.04
ACGTcount: A:0.25, C:0.22, G:0.23, T:0.31
Consensus pattern (50 bp):
GGGAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTCAATTGCAATGCCG
Done.