Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold407
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: 4418299
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 127125 characters in sequence are not A, C, G, or T
File 11 of 28
Found at i:1566891 original size:22 final size:21
Alignment explanation
Indices: 1566851--1566891 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
1566841 TAATAAAATA
* *
1566851 TAAATAAAATTATATTTATGT
1 TAAATAAAATTAAAATTATGT
1566872 TAAATAATAATTAAAATTAT
1 TAAATAA-AATTAAAATTAT
1566892 TTTTTATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
TAAATAAAATTAAAATTATGT
Found at i:1566901 original size:27 final size:27
Alignment explanation
Indices: 1566846--1566902 Score: 71
Period size: 27 Copynumber: 2.1 Consensus size: 27
1566836 TTAAATAATA
*
1566846 AAATATAAATAAAATTATATTTATGTT
1 AAATATAAATAAAATTATATTTATATT
* *
1566873 AAATAATAATTAAAATTAT-TTTTTATT
1 AAAT-ATAAATAAAATTATATTTATATT
1566900 AAA
1 AAA
1566903 AATTATATAC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
27 13 0.50
28 13 0.50
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.46
Consensus pattern (27 bp):
AAATATAAATAAAATTATATTTATATT
Found at i:1574370 original size:20 final size:20
Alignment explanation
Indices: 1574345--1574421 Score: 93
Period size: 20 Copynumber: 3.9 Consensus size: 20
1574335 GTAAAAAGAC
1574345 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
*
1574365 AGAATGTATCGATACATTCA
1 AGAATGTATCGATACATTGA
* * *
1574385 TA-CATATATCGATATATTGA
1 -AGAATGTATCGATACATTGA
*
1574405 AAAATGTATCGATACAT
1 AGAATGTATCGATACAT
1574422 CTGGGTAAAA
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
19 1 0.02
20 45 0.96
21 1 0.02
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:1574405 original size:91 final size:90
Alignment explanation
Indices: 1574297--1574468 Score: 281
Period size: 91 Copynumber: 1.9 Consensus size: 90
1574287 TTTTACCTAG
* *
1574297 ATATATCGATACATTGAAAAATGTATCTATACATCTGGGTAAAAAGACAGAATGTATCGATACAT
1 ATATATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAA-ACAGAATATATCGATACAT
*
1574362 TGAAGAATGTATCGATACATTCATAC
65 TGAAAAATGTATCGATACATTCATAC
* *
1574388 ATATATCGATATATTGAAAAATGTATCGATACATCTGGGTAAAAAATAGAATATATCGATACATT
1 ATATATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAACAGAATATATCGATACATT
*
1574453 GAAAAATGTATTGATA
66 GAAAAATGTATCGATA
1574469 TATCTAGGTA
Statistics
Matches: 75, Mismatches: 6, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
90 32 0.43
91 43 0.57
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.31
Consensus pattern (90 bp):
ATATATCGATACATTGAAAAATGTATCGATACATCTGGGTAAAAAACAGAATATATCGATACATT
GAAAAATGTATCGATACATTCATAC
Found at i:1574463 original size:50 final size:50
Alignment explanation
Indices: 1574388--1574482 Score: 154
Period size: 50 Copynumber: 1.9 Consensus size: 50
1574378 ACATTCATAC
* *
1574388 ATATATCGATATATTGAAAAATGTATCGATACATCTGGGTAAAAAATAGA
1 ATATATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAAAATAGA
* *
1574438 ATATATCGATACATTGAAAAATGTATTGATATATCTAGGTAAAAA
1 ATATATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAAA
1574483 TGTAACTTTT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
50 41 1.00
ACGTcount: A:0.46, C:0.07, G:0.15, T:0.32
Consensus pattern (50 bp):
ATATATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAAAATAGA
Found at i:1575576 original size:45 final size:46
Alignment explanation
Indices: 1575456--1575577 Score: 129
Period size: 49 Copynumber: 2.6 Consensus size: 46
1575446 AGATGAGAGG
* *
1575456 AGTGCCAATGTGCTAATTCAAGGCCAACAACATTGGGCTAAGGGAAA
1 AGTGCCAATGTGCTAATTCAAAGCCAGCAACATTGGGCTAA-GGAAA
* ** *
1575503 AGTGGACCAATGTGCTGATTCAAAGCCAGTGACATTGGGCTAA-TAAA
1 AGT-G-CCAATGTGCTAATTCAAAGCCAGCAACATTGGGCTAAGGAAA
* * *
1575550 GGTGCCAATGTGCTTATTCAATGCCAGC
1 AGTGCCAATGTGCTAATTCAAAGCCAGC
1575578 GATATTGAAC
Statistics
Matches: 63, Mismatches: 10, Indels: 6
0.80 0.13 0.08
Matches are distributed among these distances:
45 21 0.33
46 1 0.02
47 8 0.13
48 1 0.02
49 32 0.51
ACGTcount: A:0.32, C:0.20, G:0.25, T:0.23
Consensus pattern (46 bp):
AGTGCCAATGTGCTAATTCAAAGCCAGCAACATTGGGCTAAGGAAA
Found at i:1575693 original size:32 final size:32
Alignment explanation
Indices: 1575630--1575722 Score: 109
Period size: 32 Copynumber: 2.9 Consensus size: 32
1575620 GTTACCACCG
*
1575630 ACTTGTGTGGGCTTTAAAAAAAAGATGCCACTA
1 ACTTGTGTGGGCTTT-AAAAAGAGATGCCACTA
* * *
1575663 ACTTGTGTGGGCTTTAAAAAGAGTTTCCACTG
1 ACTTGTGTGGGCTTTAAAAAGAGATGCCACTA
* *
1575695 ACTTGTGTAGGCTTTGAAAAG-G-TGCCAC
1 ACTTGTGTGGGCTTTAAAAAGAGATGCCAC
1575723 CGACTTATGA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
30 5 0.09
31 1 0.02
32 32 0.60
33 15 0.28
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.30
Consensus pattern (32 bp):
ACTTGTGTGGGCTTTAAAAAGAGATGCCACTA
Found at i:1575738 original size:28 final size:28
Alignment explanation
Indices: 1575668--1575968 Score: 284
Period size: 28 Copynumber: 10.5 Consensus size: 28
1575658 CACTAACTTG
* * *
1575668 TGTGGGCTTTAAAAAGAGTTTCCACTGACT
1 TGTGGGCTTTGAAAAG-G-TGCCACCGACT
1575698 TGTGTAGGCTTTGAAAAGGTGCCACCGACT
1 TGTG--GGCTTTGAAAAGGTGCCACCGACT
* **
1575728 TATGAACTTTGAAAAGGTGCCACCGACT
1 TGTGGGCTTTGAAAAGGTGCCACCGACT
*
1575756 TGTGGGCTTTGAAAAGGTATGTCACTC-ACT
1 TGTGGGCTTTGAAAAGG--TGCCAC-CGACT
* *
1575786 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAAGGTGCCACCGACT
* *
1575814 TGTGGGCTTTGGAAGGGTGCCACCGACT
1 TGTGGGCTTTGAAAAGGTGCCACCGACT
* *
1575842 TGTGAGCTTT-AAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAAGG-TGCCACCGACT
*
1575870 TGTGGGCTTTG-AAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAAGG-TGCCACCGACT
* * * *
1575898 TATGGGCTTTGAAAAGAGTTACCACTGATT
1 TGTGGGCTTTGAAAAG-G-TGCCACCGACT
* * * *
1575928 TGTGGGCTTTGAAACGATGCCACTGACC
1 TGTGGGCTTTGAAAAGGTGCCACCGACT
1575956 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
1575969 CGTTATAGAT
Statistics
Matches: 231, Mismatches: 30, Indels: 22
0.82 0.11 0.08
Matches are distributed among these distances:
27 4 0.02
28 146 0.63
29 4 0.02
30 64 0.28
31 2 0.01
32 11 0.05
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTGAAAAGGTGCCACCGACT
Found at i:1575797 original size:58 final size:57
Alignment explanation
Indices: 1575653--1575968 Score: 311
Period size: 58 Copynumber: 5.5 Consensus size: 57
1575643 TTAAAAAAAA
* * *
1575653 GATGCCACTAACTTGTGTGGGCTTTAAAAAGAGTTTCCACTGACTTGTGTAGGCTTTGAAAAG
1 GATGCCACTCAC-T-TGTGGGCTTTGAAAAG-GTTGCCACTGACTTGTG--GGCTTTG-AAAG
* ** *
1575716 G-TGCCAC-CGACTTATGAACTTTGAAAAGG-TGCCACCGACTTGTGGGCTTTGAAAAG
1 GATGCCACTC-ACTTGTGGGCTTTGAAAAGGTTGCCACTGACTTGTGGGCTTTG-AAAG
* * *
1575772 GTATGTCACTCACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCTTTGGAAG
1 G-ATGCCACTCACTTGTGGGCTTTGAAAAGGTTGCCACTGACTTGTGGGCTTTGAAAG
* * *
1575829 GGTGCCAC-CGACTTGTGAGCTTT-AAAAGGATGCCACTGACTTGTGGGCTTTGAAAG
1 GATGCCACTC-ACTTGTGGGCTTTGAAAAGGTTGCCACTGACTTGTGGGCTTTGAAAG
* * * * *
1575885 GATGCCACTGACTTATGGGCTTTGAAAAGAGTTACCACTGATTTGTGGGCTTTGAAAC
1 GATGCCACTCACTTGTGGGCTTTGAAAAG-GTTGCCACTGACTTGTGGGCTTTGAAAG
* *
1575943 GATGCCACTGACCTGTGGGCTTTGAA
1 GATGCCACTCACTTGTGGGCTTTGAA
1575969 CGTTATAGAT
Statistics
Matches: 215, Mismatches: 28, Indels: 25
0.80 0.10 0.09
Matches are distributed among these distances:
55 1 0.00
56 78 0.36
57 14 0.07
58 98 0.46
59 2 0.01
60 12 0.06
61 1 0.00
62 8 0.04
63 1 0.00
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (57 bp):
GATGCCACTCACTTGTGGGCTTTGAAAAGGTTGCCACTGACTTGTGGGCTTTGAAAG
Found at i:1575814 original size:86 final size:85
Alignment explanation
Indices: 1575668--1575968 Score: 363
Period size: 86 Copynumber: 3.5 Consensus size: 85
1575658 CACTAACTTG
* * * * * *
1575668 TGTGGGCTTTAAAAAGAGTTTCCACTGACTTGTGTAGGCTTTGAAAAGGTGCCACCGACTTATGA
1 TGTGGGCTTTGAAAAG-GATGCCACTGACTTGTG--GGCTTTGAAAGGGTGCCACTGACTTATGG
*
1575733 ACTTTGAAAAGGTGCCACCGACT
63 GCTTTGAAAAGGTGCCACCGACT
* * *
1575756 TGTGGGCTTTGAAAAGGTATGTCACTCACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGC
1 TGTGGGCTTTGAAAAGG-ATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTATGGGC
* *
1575821 TTTGGAAGGGTGCCACCGACT
65 TTTGAAAAGGTGCCACCGACT
* *
1575842 TGTGAGCTTT-AAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTATGGGCT
1 TGTGGGCTTTGAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTATGGGCT
* * *
1575906 TTGAAAAGAGTTACCACTGATT
66 TTGAAAAG-G-TGCCACCGACT
* *
1575928 TGTGGGCTTTG-AAACGATGCCACTGACCTGTGGGCTTTGAA
1 TGTGGGCTTTGAAAAGGATGCCACTGACTTGTGGGCTTTGAA
1575969 CGTTATAGAT
Statistics
Matches: 184, Mismatches: 25, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
84 50 0.27
85 7 0.04
86 99 0.54
87 1 0.01
88 27 0.15
ACGTcount: A:0.24, C:0.18, G:0.29, T:0.29
Consensus pattern (85 bp):
TGTGGGCTTTGAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTATGGGCT
TTGAAAAGGTGCCACCGACT
Found at i:1575842 original size:114 final size:114
Alignment explanation
Indices: 1575670--1575950 Score: 352
Period size: 114 Copynumber: 2.4 Consensus size: 114
1575660 CTAACTTGTG
* * *
1575670 TGGGCTTTAAAAAGAGTTTCCACTGACTTGTGTAGGCTTTGAAAAGGTGCCACCGACTTATGAAC
1 TGGGCTTTGAAAAGAGGTACCACTGACTTGTG--GGCTTTGAAAAGGTGCCACCGACTTATGAAC
* *
1575735 TTTGAAAAGG-TGCCACCGACTTGTGGGCTTTGAAAAGGTATGTCACTCACTTG
64 TTT-AAAAGGATGCCACCGACTTGTGGGCTTTG-AAAGG-ATGCCACTCACTTA
* * * * *
1575788 TGGGCTTTG-AAAG-GGTGCCACTGACTTGTGGGCTTTGGAAGGGTGCCACCGACTTGTGAGCTT
1 TGGGCTTTGAAAAGAGGTACCACTGACTTGTGGGCTTTGAAAAGGTGCCACCGACTTATGAACTT
* *
1575851 TAAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTA
66 TAAAAGGATGCCACCGACTTGTGGGCTTTGAAAGGATGCCACTCACTTA
* * * *
1575900 TGGGCTTTGAAAAGAGTTACCACTGATTTGTGGGCTTTGAAACGATGCCAC
1 TGGGCTTTGAAAAGAGGTACCACTGACTTGTGGGCTTTGAAAAGGTGCCAC
1575951 TGACCTGTGG
Statistics
Matches: 143, Mismatches: 17, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
112 20 0.14
113 15 0.10
114 81 0.57
116 15 0.10
117 4 0.03
118 8 0.06
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (114 bp):
TGGGCTTTGAAAAGAGGTACCACTGACTTGTGGGCTTTGAAAAGGTGCCACCGACTTATGAACTT
TAAAAGGATGCCACCGACTTGTGGGCTTTGAAAGGATGCCACTCACTTA
Found at i:1575870 original size:142 final size:144
Alignment explanation
Indices: 1575689--1575966 Score: 368
Period size: 142 Copynumber: 1.9 Consensus size: 144
1575679 AAAAGAGTTT
*
1575689 CCACTGACTTGTGTAGGCTTTGAAAAGGTGCCACCGACTTATGAACTTTGAAAAGG-TGCCACCG
1 CCACCGACTTGTGTAGGCTTTGAAAAGGTGCCACCGACTTATGAACTTTG-AAAGGATGCCACCG
* ** * * *
1575753 ACTTGTGGGCTTTGAAAAG-GTATGTCACTCACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGT
65 ACTTATGGGCTTTGAAAAGAGT-TACCACTCACTTGTGGGCTTTGAAACGATGCCACTGACCTGT
1575817 GGGCTTTGGAAGGGTG
129 GGGCTTTGGAAGGGTG
* * ** *
1575833 CCACCGACTTGTG-A-GCTTT-AAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTG
1 CCACCGACTTGTGTAGGCTTTGAAAAGG-TGCCACCGACTTATGAACTTTGAAAGGATGCCACCG
* *
1575895 ACTTATGGGCTTTGAAAAGAGTTACCACTGATTTGTGGGCTTTGAAACGATGCCACTGACCTGTG
65 ACTTATGGGCTTTGAAAAGAGTTACCACTCACTTGTGGGCTTTGAAACGATGCCACTGACCTGTG
1575960 GGCTTTG
130 GGCTTTG
1575967 AACGTTATAG
Statistics
Matches: 117, Mismatches: 14, Indels: 8
0.84 0.10 0.06
Matches are distributed among these distances:
141 11 0.09
142 91 0.78
143 3 0.03
144 12 0.10
ACGTcount: A:0.23, C:0.19, G:0.29, T:0.29
Consensus pattern (144 bp):
CCACCGACTTGTGTAGGCTTTGAAAAGGTGCCACCGACTTATGAACTTTGAAAGGATGCCACCGA
CTTATGGGCTTTGAAAAGAGTTACCACTCACTTGTGGGCTTTGAAACGATGCCACTGACCTGTGG
GCTTTGGAAGGGTG
Found at i:1577190 original size:10 final size:9
Alignment explanation
Indices: 1577177--1577220 Score: 52
Period size: 9 Copynumber: 4.7 Consensus size: 9
1577167 GACCCTTCTA
1577177 TTTTTGTTTG
1 TTTTT-TTTG
1577187 TTTTTTTTTG
1 -TTTTTTTTG
*
1577197 GTTTTTTTG
1 TTTTTTTTG
*
1577206 TTTTTTTGG
1 TTTTTTTTG
1577215 TTTTTT
1 TTTTTT
1577221 ATTTTTTGGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
9 21 0.70
10 4 0.13
11 5 0.17
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:1577200 original size:15 final size:14
Alignment explanation
Indices: 1577177--1577229 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 14
1577167 GACCCTTCTA
1577177 TTTTT-GTTTGTTTT
1 TTTTTGGTTT-TTTT
1577191 TTTTTGGTTTTTTTGTT
1 TTTTTGG--TTTTT-TT
1577208 TTTTTGGTTTTTTAT
1 TTTTTGGTTTTTT-T
1577223 TTTTTGG
1 TTTTTGG
1577230 GGGTTTCTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
14 6 0.18
15 14 0.41
16 2 0.06
17 12 0.35
ACGTcount: A:0.02, C:0.00, G:0.17, T:0.81
Consensus pattern (14 bp):
TTTTTGGTTTTTTT
Found at i:1577201 original size:9 final size:9
Alignment explanation
Indices: 1577189--1577220 Score: 57
Period size: 9 Copynumber: 3.7 Consensus size: 9
1577179 TTTGTTTGTT
1577189 TTTTTTTGG
1 TTTTTTTGG
1577198 TTTTTTT-G
1 TTTTTTTGG
1577206 TTTTTTTGG
1 TTTTTTTGG
1577215 TTTTTT
1 TTTTTT
1577221 ATTTTTTGGG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 8 0.36
9 14 0.64
ACGTcount: A:0.00, C:0.00, G:0.16, T:0.84
Consensus pattern (9 bp):
TTTTTTTGG
Found at i:1577211 original size:17 final size:17
Alignment explanation
Indices: 1577189--1577247 Score: 66
Period size: 17 Copynumber: 3.4 Consensus size: 17
1577179 TTTGTTTGTT
1577189 TTTTTTTGGTTTTTTTG
1 TTTTTTTGGTTTTTTTG
1577206 TTTTTTTGGTTTTTTAT-
1 TTTTTTTGGTTTTTT-TG
**
1577223 TTTTTGGGGGTTTCTTTTG
1 TTTTT-TTGGTTT-TTTTG
1577242 TTTTTT
1 TTTTTT
1577248 CGTTTTTTAT
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
17 20 0.57
18 7 0.20
19 8 0.23
ACGTcount: A:0.02, C:0.02, G:0.19, T:0.78
Consensus pattern (17 bp):
TTTTTTTGGTTTTTTTG
Found at i:1577235 original size:35 final size:35
Alignment explanation
Indices: 1577196--1577264 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
1577186 GTTTTTTTTT
*
1577196 GGTTT-TTTTGTTTTTTTGGTTTTTTATTTTTTGGG
1 GGTTTCTTTTG-TTTTTTCGTTTTTTATTTTTTGGG
1577231 GGTTTCTTTTGTTTTTTCGTTTTTTATTTTTTGG
1 GGTTTCTTTTGTTTTTTCGTTTTTTATTTTTTGG
1577265 TACGAAGGAT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 27 0.84
36 5 0.16
ACGTcount: A:0.03, C:0.03, G:0.20, T:0.74
Consensus pattern (35 bp):
GGTTTCTTTTGTTTTTTCGTTTTTTATTTTTTGGG
Found at i:1591092 original size:13 final size:13
Alignment explanation
Indices: 1591074--1591099 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1591064 CATTATTCAA
1591074 TGTATCGATACAT
1 TGTATCGATACAT
1591087 TGTATCGATACAT
1 TGTATCGATACAT
1591100 CGATCTTTGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1591163 original size:20 final size:20
Alignment explanation
Indices: 1591138--1591191 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
1591128 TTTACCCAGA
*
1591138 TGTATCGATACATTT-TGTAT
1 TGTATCGATACATTTCT-CAT
1591158 TGTATCGATACATTTCTCAT
1 TGTATCGATACATTTCTCAT
1591178 TGTATCGATACATT
1 TGTATCGATACATT
1591192 CAGGCATTTT
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.26, C:0.15, G:0.13, T:0.46
Consensus pattern (20 bp):
TGTATCGATACATTTCTCAT
Found at i:1593511 original size:51 final size:51
Alignment explanation
Indices: 1593449--1593682 Score: 204
Period size: 51 Copynumber: 4.5 Consensus size: 51
1593439 ATTTTTCATC
* * * *
1593449 TCGGAGATACTCCAATCCCGATTTCATTTTCAAAACATTAATTTTTCTTAA
1 TCGGGGATACTCCAATCCCGATTTCATTTCCAAAACATCAATTTTTCTCAA
* * * * ** ** *
1593500 TCGGGGATACTCCAA-CTCCGATTTTATTTCTAAAGCCTTGATTTACCGCAA
1 TCGGGGATACTCCAATC-CCGATTTCATTTCCAAAACATCAATTTTTCTCAA
* * * *
1593551 -CTGGGGATACTCCAATCCTGGTTTCATCTCCAAAACATCAATTTTTCTTAA
1 TC-GGGGATACTCCAATCCCGATTTCATTTCCAAAACATCAATTTTTCTCAA
* * * *
1593602 TCGGGGATACTCCAA-CTCCGATTTTATTTCCAAAATACCAATTTTTCACAA
1 TCGGGGATACTCCAATC-CCGATTTCATTTCCAAAACATCAATTTTTCTCAA
*
1593653 TTGGGGATACTCCAATCCCGTCATTTCATT
1 TCGGGGATACTCCAATCCCG--ATTTCATT
1593683 GGGGATACTC
Statistics
Matches: 141, Mismatches: 34, Indels: 14
0.75 0.18 0.07
Matches are distributed among these distances:
50 3 0.02
51 128 0.91
52 3 0.02
53 7 0.05
ACGTcount: A:0.28, C:0.25, G:0.12, T:0.35
Consensus pattern (51 bp):
TCGGGGATACTCCAATCCCGATTTCATTTCCAAAACATCAATTTTTCTCAA
Found at i:1593658 original size:102 final size:101
Alignment explanation
Indices: 1593454--1593681 Score: 296
Period size: 102 Copynumber: 2.2 Consensus size: 101
1593444 TCATCTCGGA
* * *
1593454 GATACTCCAATCCCGATTTCATTTTCAAAACATTAATTTTTCTTAATCGGGGATACTCCAACTCC
1 GATACTCCAATCCCGATTTCATCTCCAAAACATCAATTTTTCTTAATCGGGGATACTCCAACTCC
* * * *
1593519 GATTTTATTTCTAAAGCCTTGATTTACCGCAACTGGG
66 GATTTTATTTCAAAAACC-TAATTTACCACAACTGGG
* *
1593556 GATACTCCAATCCTGGTTTCATCTCCAAAACATCAATTTTTCTTAATCGGGGATACTCCAACTCC
1 GATACTCCAATCCCGATTTCATCTCCAAAACATCAATTTTTCTTAATCGGGGATACTCCAACTCC
** *
1593621 GATTTTATTTCCAAAATACC-AATTTTTCACAATTGGG
66 GATTTTATTT-CAAAA-ACCTAATTTACCACAACTGGG
1593658 GATACTCCAATCCCGTCATTTCAT
1 GATACTCCAATCCCG--ATTTCAT
1593682 TGGGGATACT
Statistics
Matches: 108, Mismatches: 14, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
102 96 0.89
103 4 0.04
104 8 0.07
ACGTcount: A:0.28, C:0.25, G:0.11, T:0.36
Consensus pattern (101 bp):
GATACTCCAATCCCGATTTCATCTCCAAAACATCAATTTTTCTTAATCGGGGATACTCCAACTCC
GATTTTATTTCAAAAACCTAATTTACCACAACTGGG
Found at i:1593700 original size:28 final size:28
Alignment explanation
Indices: 1593652--1593707 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
1593642 ATTTTTCACA
*
1593652 ATTGGGGATACTCCAATCCCGTCATTTC
1 ATTGGGGATACTCCAACCCCGTCATTTC
* *
1593680 ATTGGGGATACTCCAGCCCCGTTATTTC
1 ATTGGGGATACTCCAACCCCGTCATTTC
1593708 CGAGAGGATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.20, C:0.29, G:0.20, T:0.32
Consensus pattern (28 bp):
ATTGGGGATACTCCAACCCCGTCATTTC
Found at i:1593849 original size:108 final size:106
Alignment explanation
Indices: 1593606--1593891 Score: 313
Period size: 108 Copynumber: 2.7 Consensus size: 106
1593596 TCTTAATCGG
* * *
1593606 GGATACTCCAACTCCGATTTTATTTCCAAAATACCAATTTTTCACAATTGGGGATACTCCAATCC
1 GGATACTCCAACTCCGA-TTTATTTCCAAAATATCAATTTTTCACAATCGGGGATACTCCAACCC
* * ** *
1593671 CGTCATTTCATTGGGGATACTCCAGCCCCGTTATTTCCGAGA
65 CGTTATATCATCAGGGATACTCCAACCCCGTTATTTCCGAGA
* * * * * * * * *
1593713 GGATACTTCAACCTCGGCTTTATATCCAAAATATTGATTTTTTCATAATCGGGGGTACTCTAACC
1 GGATACTCCAA-CTCCGATTTATTTCCAAAATA-TCAATTTTTCACAATCGGGGATACTCCAACC
* **
1593778 CCGTTATATCATCAGGGATACTCCAATCCCGTTATTTTTGAG-
64 CCGTTATATCATCAGGGATACTCCAACCCCGTTATTTCCGAGA
* *
1593820 GTGATACTCCAACTCCGATTGTATTTCCAAAACATCAATTTCTCACAATCGGGGATACTCCAACC
1 G-GATACTCCAACTCCGATT-TATTTCCAAAATATCAATTTTTCACAATCGGGGATACTCCAACC
*
1593885 CCATTAT
64 CCGTTAT
1593892 TTTCGCGAGG
Statistics
Matches: 143, Mismatches: 32, Indels: 8
0.78 0.17 0.04
Matches are distributed among these distances:
107 62 0.43
108 81 0.57
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.33
Consensus pattern (106 bp):
GGATACTCCAACTCCGATTTATTTCCAAAATATCAATTTTTCACAATCGGGGATACTCCAACCCC
GTTATATCATCAGGGATACTCCAACCCCGTTATTTCCGAGA
Found at i:1593925 original size:79 final size:79
Alignment explanation
Indices: 1593788--1593993 Score: 211
Period size: 79 Copynumber: 2.6 Consensus size: 79
1593778 CCGTTATATC
* * * * ** *
1593788 ATCAGGGATACTCCAATCCCGTTATTTTTGAG-GTGATACTCCAACTCC-GATTGTATTTCCAAA
1 ATCAGGGATACTCCAACCCCATTATTTTCGAGAG-GATACTCCAACCCCGGCCT-CATTTCCAAA
1593851 ACATCAA-TTTCTCACA
64 ACATCAATTTTCT-ACA
* * * *
1593867 ATCGGGGATACTCCAACCCCATTATTTTCGCGAGGATACTCCAACCCCGGCCTCATTTCTAAAGC
1 ATCAGGGATACTCCAACCCCATTATTTTCGAGAGGATACTCCAACCCCGGCCTCATTTCCAAAAC
** *
1593932 ATTGATTTTCTATA
66 ATCAATTTTCTACA
* * *
1593946 ATCAGGGATACTCCTACCCTATTATTTTCGAGGGGATACTCCAACCCC
1 ATCAGGGATACTCCAACCCCATTATTTTCGAGAGGATACTCCAACCCC
1593994 AATTTTTCAT
Statistics
Matches: 105, Mismatches: 19, Indels: 6
0.81 0.15 0.05
Matches are distributed among these distances:
79 97 0.92
80 8 0.08
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.31
Consensus pattern (79 bp):
ATCAGGGATACTCCAACCCCATTATTTTCGAGAGGATACTCCAACCCCGGCCTCATTTCCAAAAC
ATCAATTTTCTACA
Found at i:1594038 original size:81 final size:79
Alignment explanation
Indices: 1593866--1594039 Score: 206
Period size: 79 Copynumber: 2.2 Consensus size: 79
1593856 AATTTCTCAC
*
1593866 AATCGGGGATACTCCAACCCCATTATTTTCGCGAGGATACTCCAACCCCGGCCTCATTTCTAAAG
1 AATCGGGGATACTCCAACCCCATTATTTTCGAGAGGATACTCCAACCCCGGCCTCATTTCTAAAG
** *
1593931 CATTGATTTTCTAT
66 CACCGATTTTCCAT
* * * * ****
1593945 AATCAGGGATACTCCTACCCTATTATTTTCGAGGGGATACTCCAACCCCAATTTTTCATTTCTAG
1 AATCGGGGATACTCCAACCCCATTATTTTCGAGAGGATACTCCAACCCC--GGCCTCATTTCTA-
1594010 AA-CACCGATTTTCCAT
63 AAGCACCGATTTTCCAT
1594026 AATCGGGGATACTC
1 AATCGGGGATACTC
1594040 TAGCCCCGTT
Statistics
Matches: 79, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
79 44 0.56
81 33 0.42
82 2 0.03
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.31
Consensus pattern (79 bp):
AATCGGGGATACTCCAACCCCATTATTTTCGAGAGGATACTCCAACCCCGGCCTCATTTCTAAAG
CACCGATTTTCCAT
Found at i:1595543 original size:20 final size:19
Alignment explanation
Indices: 1595516--1595592 Score: 100
Period size: 20 Copynumber: 3.9 Consensus size: 19
1595506 GTAAAAAGAC
1595516 AAAATGTATCGATACATTG
1 AAAATGTATCGATACATTG
*
1595535 AAGAATGTATCGATACATTC
1 AA-AATGTATCGATACATTG
* *
1595555 ATACATGTATTGATACATTG
1 A-AAATGTATCGATACATTG
1595575 AAAAATGTATCGATACAT
1 -AAAATGTATCGATACAT
1595593 CTGGGTAAAA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
19 2 0.04
20 45 0.92
21 2 0.04
ACGTcount: A:0.42, C:0.12, G:0.14, T:0.32
Consensus pattern (19 bp):
AAAATGTATCGATACATTG
Found at i:1595652 original size:24 final size:24
Alignment explanation
Indices: 1595575--1595656 Score: 64
Period size: 20 Copynumber: 3.3 Consensus size: 24
1595565 TGATACATTG
1595575 AAAAATGTATCGATACATCTGGGT
1 AAAAATGTATCGATACATCTGGGT
* *
1595599 AAAAGACAGAACGTATCGATACAT-T---A
1 ---A-A-A-AATGTATCGATACATCTGGGT
1595625 AAAAATGTATCGATACATCTGGGT
1 AAAAATGTATCGATACATCTGGGT
1595649 AAAAATGT
1 AAAAATGT
1595657 GATTTTTTCA
Statistics
Matches: 44, Mismatches: 4, Indels: 17
0.68 0.06 0.26
Matches are distributed among these distances:
20 14 0.32
21 2 0.05
22 1 0.02
23 1 0.02
24 8 0.18
27 1 0.02
28 1 0.02
29 2 0.05
30 14 0.32
ACGTcount: A:0.44, C:0.12, G:0.18, T:0.26
Consensus pattern (24 bp):
AAAAATGTATCGATACATCTGGGT
Found at i:1596596 original size:35 final size:35
Alignment explanation
Indices: 1596550--1596617 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
1596540 CAGACTATGC
* *
1596550 TCACCCCTATCTCTATCTGCATTATAAAAAAAATT
1 TCACCCCTATCTCTATCTACATTACAAAAAAAATT
1596585 TCACCCCTATCTCTATCTACATTACAAAAAAAA
1 TCACCCCTATCTCTATCTACATTACAAAAAAAA
1596618 ATCAAAAACA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.40, C:0.28, G:0.01, T:0.31
Consensus pattern (35 bp):
TCACCCCTATCTCTATCTACATTACAAAAAAAATT
Found at i:1597012 original size:35 final size:35
Alignment explanation
Indices: 1596966--1597034 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
1596956 CCAGACTATG
*
1596966 CTCACCCCTATCTCTATCTGCATTATAAAAAAAAT
1 CTCACCCCTATCTCTATCTGCATTACAAAAAAAAT
1597001 CTCACCCCTATCTCTATCTGCATTACAAAAAAAA
1 CTCACCCCTATCTCTATCTGCATTACAAAAAAAA
1597035 ATCAAAAACA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.38, C:0.30, G:0.03, T:0.29
Consensus pattern (35 bp):
CTCACCCCTATCTCTATCTGCATTACAAAAAAAAT
Found at i:1597129 original size:417 final size:416
Alignment explanation
Indices: 1596356--1597188 Score: 1639
Period size: 417 Copynumber: 2.0 Consensus size: 416
1596346 GCCTGGGCTC
1596356 AAAACCTAGGTCACTCATTCTTTTTTTTTTTGAAAAAAAACGAGTGTCTTAAAAATAGCTAGACA
1 AAAACCTAGGTCACTCATTCTTTTTTTTTTTGAAAAAAAACGAGTGTCTTAAAAATAGCTAGACA
1596421 AAATCTGGTATCTACAGTGTTGAATGAAATTCAAGAAAAGAAGTTCACGCCATATAAACCAAATT
66 AAATCTGGTATCTACAGTGTTGAATGAAATTCAAGAAAAGAAGTTCACGCCATATAAACCAAATT
1596486 TTAGTGCCAACCTTACATAGTTAATTAATGATTTTAATTACAAAATTGTTTATCCAGACTATGCT
131 TTAGTGCCAACCTTACATAGTTAATTAATGATTTTAATTACAAAATTGTTTATCCAGACTATGCT
*
1596551 CACCCCTATCTCTATCTGCATTATAAAAAAAATTTCACCCCTATCTCTATCTACATTACAAAAAA
196 CACCCCTATCTCTATCTGCATTATAAAAAAAATCTCACCCCTATCTCTATCTACATTACAAAAAA
1596616 AAATCAAAAACACTTCAATTTCCAAATGATACTCACTTAAACCAAAATTAGTAAATTTATGAAAT
261 AAATCAAAAACACTTCAATTTCCAAATGATACTCACTTAAACCAAAATTAGTAAATTTATGAAAT
1596681 GTAAATGCTAGTTGTAAAAATAAGTTGTCAAGTACAAGTGCATTCCCATTCATCTCATCTCATGT
326 GTAAATGCTAGTTGTAAAAATAAGTTGTCAAGTACAAGTGCATTCCCATTCATCTCATCTCATGT
1596746 AGTTGGTGTTAGGATCTTAGTTTTGA
391 AGTTGGTGTTAGGATCTTAGTTTTGA
1596772 AAAACCTAGGTCACTCATTCTTTTTTTTTTTTGAAAAAAAACGAGTGTCTTAAAAATAGCTAGAC
1 AAAACCTAGGTCACTCATTC-TTTTTTTTTTTGAAAAAAAACGAGTGTCTTAAAAATAGCTAGAC
1596837 AAAATCTGGTATCTACAGTGTTGAATGAAATTCAAGAAAAGAAGTTCACGCCATATAAACCAAAT
65 AAAATCTGGTATCTACAGTGTTGAATGAAATTCAAGAAAAGAAGTTCACGCCATATAAACCAAAT
1596902 TTTAGTGCCAACCTTACATAGTTAATTAATGATTTTAATTACAAAATTGTTTATCCAGACTATGC
130 TTTAGTGCCAACCTTACATAGTTAATTAATGATTTTAATTACAAAATTGTTTATCCAGACTATGC
*
1596967 TCACCCCTATCTCTATCTGCATTATAAAAAAAATCTCACCCCTATCTCTATCTGCATTACAAAAA
195 TCACCCCTATCTCTATCTGCATTATAAAAAAAATCTCACCCCTATCTCTATCTACATTACAAAAA
1597032 AAAATCAAAAACACTTCAATTTCCAAATGATACTCACTTAAACCAAAATTAGTAAATTTATGAAA
260 AAAATCAAAAACACTTCAATTTCCAAATGATACTCACTTAAACCAAAATTAGTAAATTTATGAAA
1597097 TGTAAATGCTAGTTGTAAAAATAAGTTGTCAAGTACAAGTGCATTCCCATTCATCTCATCTCATG
325 TGTAAATGCTAGTTGTAAAAATAAGTTGTCAAGTACAAGTGCATTCCCATTCATCTCATCTCATG
1597162 TAGTTGGTGTTAGGATCTTAGTTTTGA
390 TAGTTGGTGTTAGGATCTTAGTTTTGA
1597189 TATAACAAAG
Statistics
Matches: 414, Mismatches: 2, Indels: 1
0.99 0.00 0.00
Matches are distributed among these distances:
416 20 0.05
417 394 0.95
ACGTcount: A:0.38, C:0.18, G:0.11, T:0.33
Consensus pattern (416 bp):
AAAACCTAGGTCACTCATTCTTTTTTTTTTTGAAAAAAAACGAGTGTCTTAAAAATAGCTAGACA
AAATCTGGTATCTACAGTGTTGAATGAAATTCAAGAAAAGAAGTTCACGCCATATAAACCAAATT
TTAGTGCCAACCTTACATAGTTAATTAATGATTTTAATTACAAAATTGTTTATCCAGACTATGCT
CACCCCTATCTCTATCTGCATTATAAAAAAAATCTCACCCCTATCTCTATCTACATTACAAAAAA
AAATCAAAAACACTTCAATTTCCAAATGATACTCACTTAAACCAAAATTAGTAAATTTATGAAAT
GTAAATGCTAGTTGTAAAAATAAGTTGTCAAGTACAAGTGCATTCCCATTCATCTCATCTCATGT
AGTTGGTGTTAGGATCTTAGTTTTGA
Found at i:1597352 original size:17 final size:18
Alignment explanation
Indices: 1597322--1597356 Score: 54
Period size: 17 Copynumber: 1.9 Consensus size: 18
1597312 GTATAAATAT
1597322 TTTTCAAGCATAAAAAATG
1 TTTTCAAG-ATAAAAAATG
1597341 TTTTCAAG-TAAAAAAT
1 TTTTCAAGATAAAAAAT
1597357 AATCCAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
19 8 0.50
ACGTcount: A:0.49, C:0.09, G:0.09, T:0.34
Consensus pattern (18 bp):
TTTTCAAGATAAAAAATG
Found at i:1598536 original size:13 final size:13
Alignment explanation
Indices: 1598518--1598543 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1598508 CAATTTTTTG
1598518 TGTATCGATACAT
1 TGTATCGATACAT
1598531 TGTATCGATACAT
1 TGTATCGATACAT
1598544 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1599293 original size:21 final size:21
Alignment explanation
Indices: 1599252--1599295 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
1599242 CTCCCCTTTA
* *
1599252 TCTCCCCCGTTTATTAATAAT
1 TCTCCCCCGTTAATCAATAAT
1599273 TCTCCCCC-TTAATCAAGTAAT
1 TCTCCCCCGTTAATCAA-TAAT
1599294 TC
1 TC
1599296 ATATCAAAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 6 0.30
21 14 0.70
ACGTcount: A:0.25, C:0.32, G:0.05, T:0.39
Consensus pattern (21 bp):
TCTCCCCCGTTAATCAATAAT
Found at i:1599312 original size:25 final size:25
Alignment explanation
Indices: 1599284--1599335 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
1599274 CTCCCCCTTA
1599284 ATCAAGTAATTCATATCAAAAATTT
1 ATCAAGTAATTCATATCAAAAATTT
1599309 ATCAAGTAATTCATATCAAAAATTT
1 ATCAAGTAATTCATATCAAAAATTT
1599334 AT
1 AT
1599336 TTGCACATAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.48, C:0.12, G:0.04, T:0.37
Consensus pattern (25 bp):
ATCAAGTAATTCATATCAAAAATTT
Found at i:1599327 original size:14 final size:14
Alignment explanation
Indices: 1599284--1599327 Score: 58
Period size: 14 Copynumber: 3.4 Consensus size: 14
1599274 CTCCCCCTTA
1599284 ATCAAGTAATTCAT
1 ATCAAGTAATTCAT
*
1599298 ATCAA-AAATT--T
1 ATCAAGTAATTCAT
1599309 ATCAAGTAATTCAT
1 ATCAAGTAATTCAT
1599323 ATCAA
1 ATCAA
1599328 AAATTTATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
11 6 0.24
12 4 0.16
13 4 0.16
14 11 0.44
ACGTcount: A:0.48, C:0.14, G:0.05, T:0.34
Consensus pattern (14 bp):
ATCAAGTAATTCAT
Found at i:1601145 original size:13 final size:13
Alignment explanation
Indices: 1601127--1601165 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
1601117 ATAATCACCC
1601127 TGTATCGATACAA
1 TGTATCGATACAA
1601140 TGTATCGATACAA
1 TGTATCGATACAA
1601153 TGTATCGATACAA
1 TGTATCGATACAA
1601166 AGAAAAATGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1601176 original size:20 final size:20
Alignment explanation
Indices: 1601151--1601229 Score: 68
Period size: 20 Copynumber: 3.7 Consensus size: 20
1601141 GTATCGATAC
1601151 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
* **
1601171 AATGTACCGATACATTGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
*
1601196 AATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
1601216 CATGTATCGATACA
1 AATGTATCGATACA
1601230 TTTTGGACAT
Statistics
Matches: 47, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
20 30 0.64
25 17 0.36
ACGTcount: A:0.44, C:0.16, G:0.14, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:1605107 original size:21 final size:21
Alignment explanation
Indices: 1605078--1605122 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1605068 AAGTTTTCAT
*
1605078 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
1605098 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
1605120 TTT
1 TTT
1605123 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:1606208 original size:13 final size:13
Alignment explanation
Indices: 1606190--1606215 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1606180 TACAGCAAGT
1606190 ATGTATCGATACA
1 ATGTATCGATACA
1606203 ATGTATCGATACA
1 ATGTATCGATACA
1606216 CAAAAAATTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1608471 original size:21 final size:21
Alignment explanation
Indices: 1608433--1608477 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
1608423 TTGCAAGTTC
*
1608433 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1608455 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
1608475 AAA
1 AAA
1608478 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1610301 original size:15 final size:15
Alignment explanation
Indices: 1610281--1610311 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1610271 TAAAAATGTC
*
1610281 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1610296 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1610311 C
1 C
1610312 CAAACGAAAT
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:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1612404 original size:20 final size:20
Alignment explanation
Indices: 1612325--1612404 Score: 79
Period size: 20 Copynumber: 3.8 Consensus size: 20
1612315 AATGTCCAAA
*
1612325 ATGTATCGATACATGTTTCT
1 ATGTATCGATACATTTTTCT
* *
1612345 GTGTATCGATACATCTGGAAATTCT
1 ATGTATCGATACAT-T----TTTCT
1612370 ATGTATCGATACATTTTTCT
1 ATGTATCGATACATTTTTCT
*
1612390 TTGTATCGATACATT
1 ATGTATCGATACATT
1612405 GTATCGATAC
Statistics
Matches: 49, Mismatches: 6, Indels: 10
0.75 0.09 0.15
Matches are distributed among these distances:
20 31 0.63
24 1 0.02
25 17 0.35
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (20 bp):
ATGTATCGATACATTTTTCT
Found at i:1612408 original size:13 final size:13
Alignment explanation
Indices: 1612390--1612426 Score: 65
Period size: 13 Copynumber: 2.8 Consensus size: 13
1612380 ACATTTTTCT
1612390 TTGTATCGATACA
1 TTGTATCGATACA
1612403 TTGTATCGATACA
1 TTGTATCGATACA
*
1612416 CTGTATCGATA
1 TTGTATCGATA
1612427 TAGGGTGATT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.30, C:0.16, G:0.16, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1617301 original size:13 final size:13
Alignment explanation
Indices: 1617283--1617308 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1617273 CAATTTTTTG
1617283 TGTATCGATACAT
1 TGTATCGATACAT
1617296 TGTATCGATACAT
1 TGTATCGATACAT
1617309 ACTTGCTGTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1621596 original size:52 final size:51
Alignment explanation
Indices: 1621518--1621666 Score: 235
Period size: 52 Copynumber: 2.9 Consensus size: 51
1621508 CGAAATATGA
1621518 AAATTTGCCTGCATGTATCGATACATTGAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTG-ATAGTGTATCGATACATCTGGGC
* *
1621570 AAATTTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACA-TTGATAGTGTATCGATACATCTGGGC
**
1621622 AAATTTGCCTGCATGTATCGATACAAAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACATTGAT-AGTGTATCGATACA
1621667 ATGTATCGAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 85 0.96
53 2 0.02
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (51 bp):
AAATTTGCCTGCATGTATCGATACATTGATAGTGTATCGATACATCTGGGC
Found at i:1621673 original size:13 final size:13
Alignment explanation
Indices: 1621655--1621679 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1621645 CAAAGATCAG
1621655 TGTATCGATACAA
1 TGTATCGATACAA
1621668 TGTATCGATACA
1 TGTATCGATACA
1621680 CTTAAGTGAT
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:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1621757 original size:33 final size:33
Alignment explanation
Indices: 1621720--1621786 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1621710 AGTAGCTTAA
1621720 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1621753 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1621786 A
1 A
1621787 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1621760 original size:13 final size:13
Alignment explanation
Indices: 1621742--1621766 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1621732 CAAAAAAATA
1621742 TGTATCGATACAT
1 TGTATCGATACAT
1621755 TGTATCGATACA
1 TGTATCGATACA
1621767 ACACTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1622768 original size:12 final size:12
Alignment explanation
Indices: 1622751--1622781 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
1622741 CAAGTCAACG
1622751 ATGATGATGAAA
1 ATGATGATGAAA
*
1622763 ATGATGATGATA
1 ATGATGATGAAA
1622775 ATGATGA
1 ATGATGA
1622782 AGAAGTTGAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.45, C:0.00, G:0.26, T:0.29
Consensus pattern (12 bp):
ATGATGATGAAA
Found at i:1629696 original size:19 final size:18
Alignment explanation
Indices: 1629652--1629703 Score: 52
Period size: 20 Copynumber: 2.7 Consensus size: 18
1629642 TTTTAGAGTT
*
1629652 AAGTATAAAT-ATTTTTC
1 AAGTAAAAATAATTTTTC
1629669 AAGCATAAAAATAATGTTTTC
1 AAG--TAAAAATAAT-TTTTC
1629690 AAGTAAAAAATAAT
1 AAGT-AAAAATAAT
1629704 CCAAAGTATC
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
17 3 0.10
19 7 0.24
20 11 0.38
21 8 0.28
ACGTcount: A:0.52, C:0.06, G:0.08, T:0.35
Consensus pattern (18 bp):
AAGTAAAAATAATTTTTC
Found at i:1629700 original size:20 final size:21
Alignment explanation
Indices: 1629664--1629703 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
1629654 GTATAAATAT
1629664 TTTTCAAGCATAAAAATAATG
1 TTTTCAAGCATAAAAATAATG
*
1629685 TTTTCAAGTA-AAAAATAAT
1 TTTTCAAGCATAAAAATAAT
1629704 CCAAAGTATC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.50, C:0.07, G:0.07, T:0.35
Consensus pattern (21 bp):
TTTTCAAGCATAAAAATAATG
Found at i:1629911 original size:13 final size:13
Alignment explanation
Indices: 1629874--1629911 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
1629864 GCTAAACTCA
*
1629874 GTATCGATACAGT
1 GTATCGATACATT
*
1629887 GTAGCGATACATT
1 GTATCGATACATT
1629900 GTATCGATACAT
1 GTATCGATACAT
1629912 GGTGAAATGT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.32
Consensus pattern (13 bp):
GTATCGATACATT
Found at i:1631185 original size:16 final size:16
Alignment explanation
Indices: 1631147--1631186 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
1631137 AGTCTAAAAA
*
1631147 AACTTGAAATTGAAAC
1 AACTTGAAATCGAAAC
*
1631163 GACTTGAAATCGAAAC
1 AACTTGAAATCGAAAC
*
1631179 AATTTGAA
1 AACTTGAA
1631187 CTTAAAATTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.47, C:0.12, G:0.15, T:0.25
Consensus pattern (16 bp):
AACTTGAAATCGAAAC
Found at i:1633358 original size:24 final size:24
Alignment explanation
Indices: 1633331--1633381 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
1633321 AGTAAAATTA
*
1633331 AATTAAAAGAAAAATAATTAAAGC
1 AATTAAAAGAAAAATAATTAAAAC
*
1633355 AATTAAAAGGAAAATAATTAAAAC
1 AATTAAAAGAAAAATAATTAAAAC
1633379 AAT
1 AAT
1633382 CATAATGGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.67, C:0.04, G:0.08, T:0.22
Consensus pattern (24 bp):
AATTAAAAGAAAAATAATTAAAAC
Found at i:1633626 original size:19 final size:21
Alignment explanation
Indices: 1633602--1633654 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
1633592 TTTATTAAAA
1633602 ATATTAAAATTT-TAT-TTTT
1 ATATTAAAATTTATATATTTT
*
1633621 ATATTAATATTTATATATTTT
1 ATATTAAAATTTATATATTTT
1633642 ATAATT-AAATTTA
1 AT-ATTAAAATTTA
1633655 AATAAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 11 0.38
20 3 0.10
21 12 0.41
22 3 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (21 bp):
ATATTAAAATTTATATATTTT
Found at i:1634814 original size:10 final size:10
Alignment explanation
Indices: 1634755--1634815 Score: 50
Period size: 10 Copynumber: 5.8 Consensus size: 10
1634745 GAAGAGATAA
1634755 AAATAAAAAT
1 AAATAAAAAT
*
1634765 AAACAAAAAT
1 AAATAAAAAT
* *
1634775 AAATAAATGAG
1 AAATAAA-AAT
* *
1634786 AAATGTATAAT
1 AAAT-AAAAAT
1634797 ATAATAAAAAT
1 A-AATAAAAAT
1634808 AAATAAAA
1 AAATAAAA
1634816 CACTTCAAAG
Statistics
Matches: 38, Mismatches: 10, Indels: 6
0.70 0.19 0.11
Matches are distributed among these distances:
10 22 0.58
11 12 0.32
12 4 0.11
ACGTcount: A:0.72, C:0.02, G:0.05, T:0.21
Consensus pattern (10 bp):
AAATAAAAAT
Found at i:1635611 original size:44 final size:44
Alignment explanation
Indices: 1635528--1635650 Score: 103
Period size: 44 Copynumber: 2.8 Consensus size: 44
1635518 GACTCAAAAT
* *
1635528 TTTAAATTATTATTTATAAATTAATAAATATTAAAAATTTTAAC
1 TTTAAATTAATATTTATAAATTAATAAATATAAAAAATTTTAAC
* * ** *
1635572 TTTATATTAATATTTATATATTTTTAAATA-AAAATAATTTT-AT
1 TTTAAATTAATATTTATAAATTAATAAATATAAAA-AATTTTAAC
*
1635615 TATTAAA-TAATAATTA-AAATTAAAATAAAT-TAAAAA
1 T-TTAAATTAATATTTATAAATT--AATAAATATAAAAA
1635651 TTAAATAAAA
Statistics
Matches: 62, Mismatches: 12, Indels: 11
0.73 0.14 0.13
Matches are distributed among these distances:
42 4 0.06
43 14 0.23
44 44 0.71
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (44 bp):
TTTAAATTAATATTTATAAATTAATAAATATAAAAAATTTTAAC
Found at i:1635638 original size:17 final size:19
Alignment explanation
Indices: 1635616--1635658 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
1635606 TAATTTTATT
1635616 ATTAAATAAT-AATT-AAA
1 ATTAAATAATAAATTAAAA
1635633 ATT-AA-AATAAATTAAAA
1 ATTAAATAATAAATTAAAA
1635650 ATTAAATAA
1 ATTAAATAA
1635659 AACATCAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 6
0.79 0.00 0.21
Matches are distributed among these distances:
15 3 0.14
16 6 0.27
17 9 0.41
18 2 0.09
19 2 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (19 bp):
ATTAAATAATAAATTAAAA
Found at i:1635647 original size:16 final size:16
Alignment explanation
Indices: 1635616--1635659 Score: 54
Period size: 16 Copynumber: 2.6 Consensus size: 16
1635606 TAATTTTATT
1635616 ATTAAATAATAATT-AAA
1 ATTAAAT-A-AATTAAAA
1635633 ATTAAAATAAATTAAAA
1 ATT-AAATAAATTAAAA
1635650 ATTAAATAAA
1 ATTAAATAAA
1635660 ACATCAAATC
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
16 11 0.44
17 10 0.40
18 4 0.16
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTAAATAAATTAAAA
Found at i:1636422 original size:8 final size:8
Alignment explanation
Indices: 1636409--1636502 Score: 73
Period size: 8 Copynumber: 10.9 Consensus size: 8
1636399 CCAAAAGTTA
1636409 TAAAAATT
1 TAAAAATT
1636417 TAAAAATT
1 TAAAAATT
*
1636425 TAGAAATTT
1 TA-AAAATT
*
1636434 TAAAAACTC
1 TAAAAA-TT
1636443 TATAAAATT
1 TA-AAAATT
1636452 ATAAAAATTAT
1 -TAAAAA-T-T
*
1636463 TAAAATTT
1 TAAAAATT
*
1636471 TAAAAAAT
1 TAAAAATT
1636479 TAAAAA-T
1 TAAAAATT
1636486 TATAAAATT
1 TA-AAAATT
1636495 ATAAAAAT
1 -TAAAAAT
1636503 ATATATTCAA
Statistics
Matches: 70, Mismatches: 7, Indels: 17
0.74 0.07 0.18
Matches are distributed among these distances:
7 3 0.04
8 30 0.43
9 22 0.31
10 14 0.20
11 1 0.01
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.36
Consensus pattern (8 bp):
TAAAAATT
Found at i:1636422 original size:9 final size:9
Alignment explanation
Indices: 1636410--1636501 Score: 50
Period size: 9 Copynumber: 10.4 Consensus size: 9
1636400 CAAAAGTTAT
1636410 AAAAATTT-
1 AAAAATTTA
1636418 AAAAATTTA
1 AAAAATTTA
* *
1636427 GAAATTTTA
1 AAAAATTTA
* *
1636436 AAAACTCTA
1 AAAAATTTA
*
1636445 TAAAA-TTA
1 AAAAATTTA
*
1636453 TAAAAATTATT
1 -AAAAATT-TA
*
1636464 AAAATTTTA
1 AAAAATTTA
1636473 AAAAA-TT-
1 AAAAATTTA
1636480 AAAAA-TTA
1 AAAAATTTA
*
1636488 TAAAATTATA
1 AAAAATT-TA
1636498 AAAA
1 AAAA
1636502 TATATATTCA
Statistics
Matches: 62, Mismatches: 15, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
7 7 0.11
8 16 0.26
9 26 0.42
10 12 0.19
11 1 0.02
ACGTcount: A:0.62, C:0.02, G:0.01, T:0.35
Consensus pattern (9 bp):
AAAAATTTA
Found at i:1636439 original size:26 final size:26
Alignment explanation
Indices: 1636410--1636492 Score: 78
Period size: 26 Copynumber: 3.1 Consensus size: 26
1636400 CAAAAGTTAT
*
1636410 AAAAATTTAAAAATTTAGAAATTTTA
1 AAAAATTTAAAAATTTAAAAATTTTA
* *
1636436 AAAACTCTATAAAATTATAAAAATTATT-
1 AAAAATTTA-AAAATT-TAAAAATT-TTA
* * *
1636464 AAAATTTTAAAAAATTAAAAATTATA
1 AAAAATTTAAAAATTTAAAAATTTTA
1636490 AAA
1 AAA
1636493 TTATAAAAAT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
25 1 0.02
26 18 0.39
27 11 0.24
28 14 0.30
29 2 0.04
ACGTcount: A:0.61, C:0.02, G:0.01, T:0.35
Consensus pattern (26 bp):
AAAAATTTAAAAATTTAAAAATTTTA
Found at i:1636485 original size:7 final size:8
Alignment explanation
Indices: 1636347--1636505 Score: 71
Period size: 8 Copynumber: 19.1 Consensus size: 8
1636337 AACAATTAGA
1636347 AAAATATAT
1 AAAAT-TAT
*
1636356 AAAATTAA
1 AAAATTAT
1636364 AAATATTAT
1 AAA-ATTAT
1636373 AAAATT-T
1 AAAATTAT
*
1636380 -AAA-CAT
1 AAAATTAT
*
1636386 AAAACTA-
1 AAAATTAT
* **
1636393 AAATTTCC
1 AAAATTAT
1636401 AAAAGTTAT
1 AAAA-TTAT
1636410 AAAAATT-T
1 -AAAATTAT
1636418 AAAAATT-T
1 -AAAATTAT
*
1636426 AGAAATTTT
1 A-AAATTAT
1636435 AAAAACTCTAT
1 -AAAA-T-TAT
1636446 AAAATTAT
1 AAAATTAT
1636454 AAAAATTATT
1 -AAAATTA-T
*
1636464 AAAATTTTAA
1 AAAA--TTAT
1636474 AAAATTA-
1 AAAATTAT
1636481 AAAATTAT
1 AAAATTAT
1636489 AAAATTAT
1 AAAATTAT
*
1636497 AAAAATAT
1 AAAATTAT
1636505 A
1 A
1636506 TATTCAAAAA
Statistics
Matches: 120, Mismatches: 13, Indels: 35
0.71 0.08 0.21
Matches are distributed among these distances:
6 4 0.03
7 16 0.13
8 48 0.40
9 32 0.27
10 15 0.12
11 5 0.04
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.34
Consensus pattern (8 bp):
AAAATTAT
Found at i:1636507 original size:18 final size:17
Alignment explanation
Indices: 1636346--1636500 Score: 97
Period size: 18 Copynumber: 8.8 Consensus size: 17
1636336 AAACAATTAG
1636346 AAAAATATATAAAA-TT
1 AAAAATATATAAAATTT
1636362 AAAAATATTATAAAATTT
1 AAAAATA-TATAAAATTT
* *
1636380 AAACATAAAACTAAAATTT
1 AAAAAT-ATA-TAAAATTT
*
1636399 CCAAAAGT-TATAAAAATTT
1 --AAAAATATAT-AAAATTT
* * *
1636418 AAAAATTTAGAAATTTT
1 AAAAATATATAAAATTT
*
1636435 AAAAACTCTATAAAATTAT
1 AAAAA-TATATAAAATT-T
1636454 AAAAAT-TATTAAAATTTT
1 AAAAATATA-TAAAA-TTT
*
1636472 AAAAA-AT-TAAAAATT
1 AAAAATATATAAAATTT
1636487 ATAAAAT-TATAAAA
1 A-AAAATATATAAAA
1636501 ATATATATTC
Statistics
Matches: 111, Mismatches: 12, Indels: 31
0.72 0.08 0.20
Matches are distributed among these distances:
15 3 0.03
16 17 0.15
17 30 0.27
18 32 0.29
19 25 0.23
21 4 0.04
ACGTcount: A:0.61, C:0.04, G:0.01, T:0.34
Consensus pattern (17 bp):
AAAAATATATAAAATTT
Found at i:1636573 original size:29 final size:27
Alignment explanation
Indices: 1636538--1636673 Score: 98
Period size: 28 Copynumber: 4.8 Consensus size: 27
1636528 GTGAGTTCTA
1636538 ATATATTTTTAAAAATTTTTTGAATTTT
1 ATATATTTTTAAAAATTTTTT-AATTTT
* * *
1636566 ATTTTATTTTT-ATAATTTTTTTATTTT
1 A-TATATTTTTAAAAATTTTTTAATTTT
1636593 ATATATTTTTAAAATATTTAAAATTTAAAATTTT
1 ATATATTTTTAAAA-ATTT----TTT--AATTTT
*
1636627 -T-TATTTTTATAAAATTTTTAAATTTT
1 ATATATTTTTA-AAAATTTTTTAATTTT
* * *
1636653 ATAGATTTTTTATAATTTTTT
1 ATATATTTTTAAAAATTTTTT
1636674 TGATAATTTG
Statistics
Matches: 85, Mismatches: 11, Indels: 25
0.70 0.09 0.21
Matches are distributed among these distances:
26 14 0.16
27 17 0.20
28 22 0.26
29 8 0.09
32 15 0.18
33 4 0.05
34 5 0.06
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (27 bp):
ATATATTTTTAAAAATTTTTTAATTTT
Found at i:1636592 original size:16 final size:18
Alignment explanation
Indices: 1636567--1636602 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1636557 TTGAATTTTA
1636567 TTTTATTTTTATA-ATTT
1 TTTTATTTTTATATATTT
1636584 TTTTA-TTTTATATATTT
1 TTTTATTTTTATATATTT
1636601 TT
1 TT
1636603 AAAATATTTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 11 0.61
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (18 bp):
TTTTATTTTTATATATTT
Found at i:1636640 original size:34 final size:35
Alignment explanation
Indices: 1636588--1636672 Score: 102
Period size: 34 Copynumber: 2.4 Consensus size: 35
1636578 TAATTTTTTT
*
1636588 ATTTTATATATTTTTAAAATATTTAAAATTTA-AA
1 ATTTTTTATATTTTTAAAATATTTAAAATTTATAA
* * *
1636622 ATTTTTTAT-TTTTATAAAATTTTTAAATTTTATAG
1 ATTTTTTATATTTT-TAAAATATTTAAAATTTATAA
1636657 ATTTTTTATAATTTTT
1 ATTTTTTAT-ATTTTT
1636673 TTGATAATTT
Statistics
Matches: 43, Mismatches: 4, Indels: 6
0.81 0.08 0.11
Matches are distributed among these distances:
33 4 0.09
34 24 0.56
35 10 0.23
36 1 0.02
37 4 0.09
ACGTcount: A:0.38, C:0.00, G:0.01, T:0.61
Consensus pattern (35 bp):
ATTTTTTATATTTTTAAAATATTTAAAATTTATAA
Found at i:1636641 original size:18 final size:18
Alignment explanation
Indices: 1636618--1636665 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
1636608 ATTTAAAATT
1636618 TAAAATTTTTTATTTTTA
1 TAAAATTTTTTATTTTTA
* *
1636636 TAAAATTTTTAAATTTTA
1 TAAAATTTTTTATTTTTA
*
1636654 T-AGATTTTTTAT
1 TAAAATTTTTTAT
1636666 AATTTTTTTG
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
17 8 0.32
18 17 0.68
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.62
Consensus pattern (18 bp):
TAAAATTTTTTATTTTTA
Found at i:1636663 original size:11 final size:10
Alignment explanation
Indices: 1636649--1636761 Score: 65
Period size: 10 Copynumber: 11.1 Consensus size: 10
1636639 AATTTTTAAA
1636649 TTTTATAGATT
1 TTTTATA-ATT
1636660 TTTTATAATTT
1 TTTTATAA-TT
1636671 TTTTGATAATT
1 TTTT-ATAATT
*
1636682 TGTTTTTAATT
1 T-TTTATAATT
*
1636693 CTATTGAT--TT
1 -T-TTTATAATT
*
1636703 TTTTATTATT
1 TTTTATAATT
*
1636713 TTTTA-ATTT
1 TTTTATAATT
*
1636722 TTATTTTAA-T
1 TT-TTATAATT
1636732 TTTTA-AATT
1 TTTTATAATT
*
1636741 TGTTATAATT
1 TTTTATAATT
*
1636751 TTTTCTAATT
1 TTTTATAATT
1636761 T
1 T
1636762 AAAAATATTC
Statistics
Matches: 79, Mismatches: 13, Indels: 21
0.70 0.12 0.19
Matches are distributed among these distances:
8 6 0.08
9 12 0.15
10 28 0.35
11 22 0.28
12 11 0.14
ACGTcount: A:0.25, C:0.02, G:0.04, T:0.69
Consensus pattern (10 bp):
TTTTATAATT
Found at i:1636721 original size:19 final size:19
Alignment explanation
Indices: 1636699--1636754 Score: 60
Period size: 19 Copynumber: 2.9 Consensus size: 19
1636689 AATTCTATTG
1636699 ATTTTTTTATTATTTTTTA
1 ATTTTTTTATTATTTTTTA
*
1636718 ATTTTTATT-TTAATTTTTA
1 ATTTTT-TTATTATTTTTTA
* * *
1636737 AATTTGTTATAATTTTTT
1 ATTTTTTTATTATTTTTT
1636755 CTAATTTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
18 2 0.07
19 26 0.87
20 2 0.07
ACGTcount: A:0.25, C:0.00, G:0.02, T:0.73
Consensus pattern (19 bp):
ATTTTTTTATTATTTTTTA
Found at i:1637018 original size:20 final size:18
Alignment explanation
Indices: 1636981--1637015 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1636971 GATTAACATG
1636981 ATAAATATAATATATTTA
1 ATAAATATAATATATTTA
*
1636999 ATAAATATATTATATTT
1 ATAAATATAATATATTT
1637016 TTATTTAAAA
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:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (18 bp):
ATAAATATAATATATTTA
Found at i:1638104 original size:20 final size:20
Alignment explanation
Indices: 1638079--1638116 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1638069 ATTATATTTA
*
1638079 ATATATAAATATATATTAGC
1 ATATATAAAGATATATTAGC
*
1638099 ATATATATAGATATATTA
1 ATATATAAAGATATATTA
1638117 AAGTGATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (20 bp):
ATATATAAAGATATATTAGC
Found at i:1638249 original size:7 final size:7
Alignment explanation
Indices: 1638186--1638280 Score: 63
Period size: 7 Copynumber: 13.0 Consensus size: 7
1638176 CCTTGACCAC
1638186 AATTAATA
1 AATT-ATA
1638194 ATATTAATA
1 A-ATT-ATA
*
1638203 AAATATA
1 AATTATA
1638210 AA-TATA
1 AATTATA
1638216 AA-TATA
1 AATTATA
*
1638222 TATTA-A
1 AATTATA
1638228 AATTTATA
1 AA-TTATA
1638236 TAA-TATA
1 -AATTATA
1638243 AATTATA
1 AATTATA
1638250 AATTATTAA
1 AATTA-T-A
1638259 AATTTATA
1 AA-TTATA
*
1638267 TATTATA
1 AATTATA
1638274 AATTATA
1 AATTATA
1638281 TGTTATTAAA
Statistics
Matches: 73, Mismatches: 5, Indels: 19
0.75 0.05 0.20
Matches are distributed among these distances:
6 15 0.21
7 34 0.47
8 7 0.10
9 14 0.19
10 3 0.04
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (7 bp):
AATTATA
Found at i:1638260 original size:31 final size:31
Alignment explanation
Indices: 1638186--1638294 Score: 121
Period size: 31 Copynumber: 3.5 Consensus size: 31
1638176 CCTTGACCAC
* * * *
1638186 AATTAATAATATTAATAAAATATAAA-TATAA
1 AATTATTAAAATTTATATAATATAAATTAT-A
1638217 ATATATATTAAAATTTATATAATATAAATTATA
1 A-AT-TATTAAAATTTATATAATATAAATTATA
*
1638250 AATTATTAAAATTTATATATTATAAATTATA
1 AATTATTAAAATTTATATAATATAAATTATA
**
1638281 TGTTATTAAAATTT
1 AATTATTAAAATTT
1638295 TTATGTATAA
Statistics
Matches: 68, Mismatches: 7, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
31 40 0.59
32 4 0.06
33 21 0.31
34 3 0.04
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (31 bp):
AATTATTAAAATTTATATAATATAAATTATA
Found at i:1638279 original size:14 final size:14
Alignment explanation
Indices: 1638194--1638286 Score: 75
Period size: 14 Copynumber: 6.5 Consensus size: 14
1638184 ACAATTAATA
*
1638194 ATATTAATAAAATAT
1 ATATT-ATAAATTAT
*
1638209 A-AATATAAA-TAT
1 ATATTATAAATTAT
1638221 ATATTA-AAATTTAT
1 ATATTATAAA-TTAT
*
1638235 ATAATATAAATTAT
1 ATATTATAAATTAT
*
1638249 AAATTATTAAAATTTAT
1 ATATTA-T-AAA-TTAT
1638266 ATATTATAAATTAT
1 ATATTATAAATTAT
*
1638280 ATGTTAT
1 ATATTAT
1638287 TAAAATTTTT
Statistics
Matches: 64, Mismatches: 7, Indels: 15
0.74 0.08 0.17
Matches are distributed among these distances:
12 7 0.11
13 8 0.12
14 28 0.44
15 8 0.12
16 4 0.06
17 9 0.14
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.45
Consensus pattern (14 bp):
ATATTATAAATTAT
Found at i:1638299 original size:17 final size:17
Alignment explanation
Indices: 1638222--1638300 Score: 62
Period size: 17 Copynumber: 5.0 Consensus size: 17
1638212 TATAAATATA
**
1638222 TATTAAAATTTATATAA
1 TATTAAAATTTATATGT
**
1638239 TA-T-AAA-TTATAAAT
1 TATTAAAATTTATATGT
*
1638253 TATTAAAATTTATATAT
1 TATTAAAATTTATATGT
1638270 TA-T-AAA-TTATATGT
1 TATTAAAATTTATATGT
*
1638284 TATTAAAATTTTTATGT
1 TATTAAAATTTATATGT
1638301 ATAATATTTA
Statistics
Matches: 51, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
14 17 0.33
15 8 0.16
16 8 0.16
17 18 0.35
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.51
Consensus pattern (17 bp):
TATTAAAATTTATATGT
Found at i:1638538 original size:54 final size:54
Alignment explanation
Indices: 1638456--1638563 Score: 198
Period size: 54 Copynumber: 2.0 Consensus size: 54
1638446 GGGATATTTA
*
1638456 GAGTAATTTCCTTTTCAGGGTTTCGCCATTTATGTTTGTAAAGCAAAAATGGAT
1 GAGTAATTTCCTTTTCACGGTTTCGCCATTTATGTTTGTAAAGCAAAAATGGAT
*
1638510 GAGTAATTTCCTTTTCACTGTTTCGCCATTTATGTTTGTAAAGCAAAAATGGAT
1 GAGTAATTTCCTTTTCACGGTTTCGCCATTTATGTTTGTAAAGCAAAAATGGAT
1638564 AATTTTTTTT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 52 1.00
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.40
Consensus pattern (54 bp):
GAGTAATTTCCTTTTCACGGTTTCGCCATTTATGTTTGTAAAGCAAAAATGGAT
Found at i:1638897 original size:30 final size:33
Alignment explanation
Indices: 1638863--1638923 Score: 83
Period size: 33 Copynumber: 1.9 Consensus size: 33
1638853 GGGTATTTTT
1638863 TAATA-TTAATT-AATAT-ATTAATTATAATAA
1 TAATATTTAATTAAATATAATTAATTATAATAA
* *
1638893 TAATATTTTATTAAATATAATTATTTATAAT
1 TAATATTTAATTAAATATAATTAATTATAAT
1638924 TTTATATAGA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
30 5 0.19
31 5 0.19
32 5 0.19
33 11 0.42
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (33 bp):
TAATATTTAATTAAATATAATTAATTATAATAA
Found at i:1639647 original size:16 final size:15
Alignment explanation
Indices: 1639628--1639657 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
1639618 ATGCCCTAAC
1639628 TAAAAAAAAACAAAAT
1 TAAAAAAAAA-AAAAT
1639644 TAAAAAAAAAAAAA
1 TAAAAAAAAAAAAA
1639658 CATGACAGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.87, C:0.03, G:0.00, T:0.10
Consensus pattern (15 bp):
TAAAAAAAAAAAAAT
Found at i:1640017 original size:5 final size:5
Alignment explanation
Indices: 1640009--1640081 Score: 55
Period size: 5 Copynumber: 15.2 Consensus size: 5
1639999 CTTTATTTTA
* * * *
1640009 AATAT AATAT AAT-T -ATAT GATAT AAAAT AATAT AAAAT AATTAA AATAT
1 AATAT AATAT AATAT AATAT AATAT AATAT AATAT AATAT AA-TAT AATAT
* *
1640058 AATAT TATAT AA-AA AATA- AATAT A
1 AATAT AATAT AATAT AATAT AATAT A
1640082 TTAAAAATTT
Statistics
Matches: 53, Mismatches: 10, Indels: 10
0.73 0.14 0.14
Matches are distributed among these distances:
3 2 0.04
4 9 0.17
5 39 0.74
6 3 0.06
ACGTcount: A:0.63, C:0.00, G:0.01, T:0.36
Consensus pattern (5 bp):
AATAT
Found at i:1640058 original size:16 final size:16
Alignment explanation
Indices: 1640037--1640087 Score: 50
Period size: 16 Copynumber: 3.1 Consensus size: 16
1640027 GATATAAAAT
1640037 AATATAAAATAATTAA
1 AATATAAAATAATTAA
* *
1640053 AATATAATATTATATAA
1 AATATAAAATAAT-TAA
*
1640070 AAAAT-AAATATATTAA
1 AATATAAAATA-ATTAA
1640086 AA
1 AA
1640088 ATTTATATAA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
16 19 0.68
17 9 0.32
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AATATAAAATAATTAA
Found at i:1640069 original size:21 final size:19
Alignment explanation
Indices: 1640035--1640081 Score: 51
Period size: 21 Copynumber: 2.4 Consensus size: 19
1640025 ATGATATAAA
1640035 ATAATATAAAATAATTAAAAT
1 ATAATATAAAATAA--AAAAT
* *
1640056 ATAATATTATATAAAAAAT
1 ATAATATAAAATAAAAAAT
1640075 A-AATATA
1 ATAATATA
1640082 TTAAAAATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 5 0.22
19 6 0.26
21 12 0.52
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (19 bp):
ATAATATAAAATAAAAAAT
Found at i:1640079 original size:18 final size:17
Alignment explanation
Indices: 1640051--1640088 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 17
1640041 TAAAATAATT
1640051 AAAATATAATATTATATAA
1 AAAATATAATA-TAT-TAA
1640070 AAAATA-AATATATTAA
1 AAAATATAATATATTAA
1640086 AAA
1 AAA
1640089 TTTATATAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
16 6 0.32
17 3 0.16
18 4 0.21
19 6 0.32
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (17 bp):
AAAATATAATATATTAA
Found at i:1640096 original size:15 final size:15
Alignment explanation
Indices: 1640043--1640089 Score: 51
Period size: 15 Copynumber: 3.0 Consensus size: 15
1640033 AAATAATATA
1640043 AAATA-ATTAAAATAT
1 AAATATATTAAAA-AT
*
1640058 AATATTATATAAAAAAT
1 AA-A-TATATTAAAAAT
1640075 AAATATATTAAAAAT
1 AAATATATTAAAAAT
1640090 TTATATAATA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
15 13 0.48
16 2 0.07
17 6 0.22
18 6 0.22
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (15 bp):
AAATATATTAAAAAT
Found at i:1642590 original size:72 final size:73
Alignment explanation
Indices: 1642502--1642640 Score: 208
Period size: 73 Copynumber: 1.9 Consensus size: 73
1642492 TCAGAACACC
* * * **
1642502 TTTTAAAATTAATATTCGAATGTCCTT-GAAGGGTATATAAATATTATTATGCAAAATATTAGAA
1 TTTTAAAATTAATATTCGAATCTCCTTAGAAAGATATATAAATACCATTATGCAAAATATTAGAA
1642566 AAACTTAT
66 AAACTTAT
* *
1642574 TTTTAAAATTAGTATTCGAATCTCCTTAGAAAGATATATAAATACCATTATGTAAAATATTAGAA
1 TTTTAAAATTAATATTCGAATCTCCTTAGAAAGATATATAAATACCATTATGCAAAATATTAGAA
1642639 AA
66 AA
1642641 GTTTATTTCT
Statistics
Matches: 59, Mismatches: 7, Indels: 1
0.88 0.10 0.01
Matches are distributed among these distances:
72 25 0.42
73 34 0.58
ACGTcount: A:0.45, C:0.08, G:0.10, T:0.37
Consensus pattern (73 bp):
TTTTAAAATTAATATTCGAATCTCCTTAGAAAGATATATAAATACCATTATGCAAAATATTAGAA
AAACTTAT
Found at i:1643770 original size:18 final size:19
Alignment explanation
Indices: 1643734--1643777 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 19
1643724 GTCAATAAAA
1643734 ATTTTATTTTTATATTAAT
1 ATTTTATTTTTATATTAAT
1643753 ATTTATATTTTTTATAATTAA-
1 ATTT-TA-TTTTTAT-ATTAAT
1643774 ATTT
1 ATTT
1643778 AAATAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.18
20 2 0.09
21 11 0.50
22 5 0.23
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (19 bp):
ATTTTATTTTTATATTAAT
Found at i:1645904 original size:13 final size:13
Alignment explanation
Indices: 1645888--1645963 Score: 67
Period size: 13 Copynumber: 6.3 Consensus size: 13
1645878 ATATTAAAAA
*
1645888 ATAATATAATTAT
1 ATAATATAAATAT
1645901 ATAATATAAATAT
1 ATAATATAAATAT
1645914 AT-ATA-AAA-A-
1 ATAATATAAATAT
* *
1645923 ATAAAATATA-AT
1 ATAATATAAATAT
1645935 ATAATATTAAA-A-
1 ATAATA-TAAATAT
1645947 ATAATATAAATAT
1 ATAATATAAATAT
1645960 ATAA
1 ATAA
1645964 ATTTATATTA
Statistics
Matches: 52, Mismatches: 5, Indels: 12
0.75 0.07 0.17
Matches are distributed among these distances:
9 2 0.04
10 3 0.06
11 10 0.19
12 15 0.29
13 22 0.42
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (13 bp):
ATAATATAAATAT
Found at i:1645937 original size:34 final size:36
Alignment explanation
Indices: 1645876--1645956 Score: 105
Period size: 35 Copynumber: 2.3 Consensus size: 36
1645866 TGATGTAAAC
* *
1645876 AAATAT-TAAAAAATAATATAATTATATAATA-TAA
1 AAATATATAAAAAATAAAATAATAATATAATATTAA
*
1645910 ATATATATAAAAAATAAAAT-ATAATATAATATTAA
1 AAATATATAAAAAATAAAATAATAATATAATATTAA
1645945 AAATAATATAAA
1 AAAT-ATATAAA
1645957 TATATAAATT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
34 15 0.38
35 18 0.45
36 7 0.17
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (36 bp):
AAATATATAAAAAATAAAATAATAATATAATATTAA
Found at i:1645941 original size:24 final size:25
Alignment explanation
Indices: 1645903--1645962 Score: 81
Period size: 24 Copynumber: 2.5 Consensus size: 25
1645893 ATAATTATAT
1645903 AATATAA-ATATATATAAAAAATAA
1 AATATAATATATATATAAAAAATAA
*
1645927 AATATAATATA-ATATTAAAAATAA
1 AATATAATATATATATAAAAAATAA
*
1645951 TATA-AATATATA
1 AATATAATATATA
1645963 AATTTATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 6 0.19
24 23 0.72
25 3 0.09
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (25 bp):
AATATAATATATATATAAAAAATAA
Found at i:1646053 original size:62 final size:60
Alignment explanation
Indices: 1645924--1646063 Score: 142
Period size: 62 Copynumber: 2.3 Consensus size: 60
1645914 ATATAAAAAA
* * * *
1645924 TAAAATATAATATAATATTAAAAATAATATAAATATATAAATTTATATTAAATTTTATAT
1 TAAAAAATAATAAAATATTAAAAATAATATAAAAATATAAATTTATAATAAATTTTATAT
* *
1645984 AATAAAAATAATAAATATATTAAAAA-ATATGTAAAAATATAATATTT-TAAATAAATTATTAT-
1 TA-AAAAATAATAAA-ATATTAAAAATA-ATATAAAAATATAA-ATTTAT-AATAAATT-TTATA
1646046 T
60 T
1646047 TAAAAAATAATATAAAT
1 TAAAAAATAATA-AAAT
1646064 GTAATGAAAA
Statistics
Matches: 66, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
60 1 0.02
61 11 0.17
62 35 0.53
63 15 0.23
64 4 0.06
ACGTcount: A:0.60, C:0.00, G:0.01, T:0.39
Consensus pattern (60 bp):
TAAAAAATAATAAAATATTAAAAATAATATAAAAATATAAATTTATAATAAATTTTATAT
Found at i:1646739 original size:112 final size:112
Alignment explanation
Indices: 1646549--1646750 Score: 260
Period size: 112 Copynumber: 1.8 Consensus size: 112
1646539 ATATCGGTTA
* * * **
1646549 ATAAATTTAATAATATTATTTTATTAAAAAATTTTAAAATAAATATATAATTTTATATTTAATAA
1 ATAAATTAAATAATATCATCTTATTAAAAAATTTTAAAATAAATATATAATCCTATATTTAATAA
* *
1646614 AATAAAAGGTATTATCTAATTTATTAATATTATATAAATTTATCTTC
66 AATAAAAGATATTAGCTAATTTATTAATATTATATAAATTTATCTTC
* * * * *
1646661 ATAAATTAAATAATATCATCTTATTAAAAATTTTTAAAGTAAATATATAATCCTATTTTTATTGA
1 ATAAATTAAATAATATCATCTTATTAAAAAATTTTAAAATAAATATATAATCCTATATTTAATAA
* * * *
1646726 AGTGAATGATATTAGGTAATTTATT
66 AATAAAAGATATTAGCTAATTTATT
1646751 GATAAGAGTA
Statistics
Matches: 74, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
112 74 1.00
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (112 bp):
ATAAATTAAATAATATCATCTTATTAAAAAATTTTAAAATAAATATATAATCCTATATTTAATAA
AATAAAAGATATTAGCTAATTTATTAATATTATATAAATTTATCTTC
Found at i:1646967 original size:15 final size:15
Alignment explanation
Indices: 1646947--1646984 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
1646937 GTGACGTAAT
1646947 AAATTTGAATTAAAA
1 AAATTTGAATTAAAA
* *
1646962 AAATTT-ATTTTAAA
1 AAATTTGAATTAAAA
1646976 AAATTTGAA
1 AAATTTGAA
1646985 ATCAAACTCT
Statistics
Matches: 19, Mismatches: 3, Indels: 2
0.79 0.12 0.08
Matches are distributed among these distances:
14 12 0.63
15 7 0.37
ACGTcount: A:0.55, C:0.00, G:0.05, T:0.39
Consensus pattern (15 bp):
AAATTTGAATTAAAA
Found at i:1647556 original size:27 final size:26
Alignment explanation
Indices: 1647521--1647600 Score: 81
Period size: 28 Copynumber: 2.9 Consensus size: 26
1647511 TTTCTAATAT
*
1647521 TAAATAATTAAAAGAATAAAAATAATTCA
1 TAAA-AATTAAAAAAATAAAAA-AA-TCA
1647550 -AAAAATTCAAAGAAAATAAAAAAATCA
1 TAAAAATT-AAA-AAAATAAAAAAATCA
* *
1647577 TAAAAATTAAAAATATAAATAAAT
1 TAAAAATTAAAAAAATAAAAAAAT
1647601 AAATTCTCAA
Statistics
Matches: 45, Mismatches: 3, Indels: 9
0.79 0.05 0.16
Matches are distributed among these distances:
26 11 0.24
27 10 0.22
28 15 0.33
29 9 0.20
ACGTcount: A:0.70, C:0.04, G:0.03, T:0.24
Consensus pattern (26 bp):
TAAAAATTAAAAAAATAAAAAAATCA
Found at i:1647637 original size:22 final size:23
Alignment explanation
Indices: 1647609--1647657 Score: 73
Period size: 22 Copynumber: 2.2 Consensus size: 23
1647599 ATAAATTCTC
* *
1647609 AAAATTCTAAAGA-AAAAAATAA
1 AAAATTCTAAAAACAAAAAAGAA
1647631 AAAATTCTAAAAACAAAAAAGAA
1 AAAATTCTAAAAACAAAAAAGAA
1647654 AAAA
1 AAAA
1647658 GAAAACCTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 12 0.50
23 12 0.50
ACGTcount: A:0.76, C:0.06, G:0.04, T:0.14
Consensus pattern (23 bp):
AAAATTCTAAAAACAAAAAAGAA
Found at i:1648211 original size:2 final size:2
Alignment explanation
Indices: 1648204--1648234 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1648194 TGTTAGATTG
1648204 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1648235 ATTCAAAATT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1649086 original size:17 final size:17
Alignment explanation
Indices: 1649047--1649113 Score: 57
Period size: 17 Copynumber: 3.8 Consensus size: 17
1649037 TAATAATTTA
1649047 TAATTTAAATTAATTTGATT
1 TAATTTAAATT-A-TT-ATT
1649067 TAATTTAAATTATTATT
1 TAATTTAAATTATTATT
* *
1649084 TAA-ATAATATTTTTATT
1 TAATTTAA-ATTATTATT
1649101 TAAATTT-AATTAT
1 T-AATTTAAATTAT
1649114 CAAAATATAT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
16 3 0.08
17 19 0.47
18 5 0.12
19 2 0.05
20 11 0.28
ACGTcount: A:0.42, C:0.00, G:0.01, T:0.57
Consensus pattern (17 bp):
TAATTTAAATTATTATT
Found at i:1649745 original size:5 final size:5
Alignment explanation
Indices: 1649729--1649763 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
1649719 TATATTGATG
*
1649729 ATATT A-ATT ATATT ATATT ATATT ACATT ATATT A
1 ATATT ATATT ATATT ATATT ATATT ATATT ATATT A
1649764 GAACAACAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (5 bp):
ATATT
Found at i:1649750 original size:10 final size:9
Alignment explanation
Indices: 1649719--1649763 Score: 54
Period size: 10 Copynumber: 4.8 Consensus size: 9
1649709 AATTGTAAAA
*
1649719 TATATTGAT
1 TATATTAAT
*
1649728 GATATTAAT
1 TATATTAAT
1649737 TATATTATAT
1 TATATTA-AT
1649747 TATATTACAT
1 TATATTA-AT
1649757 TATATTA
1 TATATTA
1649764 GAACAACAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
9 13 0.42
10 18 0.58
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.53
Consensus pattern (9 bp):
TATATTAAT
Found at i:1650200 original size:5 final size:5
Alignment explanation
Indices: 1650185--1650216 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
1650175 AGACTTTGTC
*
1650185 GTTTT GCTTT GTTTT GTTTT GTTTT GTTTT GT
1 GTTTT GTTTT GTTTT GTTTT GTTTT GTTTT GT
1650217 GTGTTTGAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.00, C:0.03, G:0.22, T:0.75
Consensus pattern (5 bp):
GTTTT
Found at i:1650692 original size:12 final size:12
Alignment explanation
Indices: 1650675--1650710 Score: 58
Period size: 11 Copynumber: 3.2 Consensus size: 12
1650665 ATTTGATGTA
1650675 TATTATATATTT
1 TATTATATATTT
1650687 TATTATAT-TTT
1 TATTATATATTT
1650698 TATTA-ATATTT
1 TATTATATATTT
1650709 TA
1 TA
1650711 AATATTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 2 0.09
11 13 0.57
12 8 0.35
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
TATTATATATTT
Found at i:1650700 original size:11 final size:11
Alignment explanation
Indices: 1650675--1650709 Score: 52
Period size: 12 Copynumber: 3.0 Consensus size: 11
1650665 ATTTGATGTA
1650675 TATTATATATTT
1 TATTATAT-TTT
1650687 TATTATATTTT
1 TATTATATTTT
1650698 TATTAATATTTT
1 TATT-ATATTTT
1650710 AAATATTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
11 7 0.32
12 15 0.68
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (11 bp):
TATTATATTTT
Found at i:1650707 original size:22 final size:22
Alignment explanation
Indices: 1650673--1650728 Score: 69
Period size: 22 Copynumber: 2.5 Consensus size: 22
1650663 TGATTTGATG
*
1650673 TATATTATATATTTTATTATATTT
1 TATATTA-ATATTTTA-AATATTT
1650697 T-TATTAATATTTTAAATATTT
1 TATATTAATATTTTAAATATTT
*
1650718 TATATTTATAT
1 TATATTAATAT
1650729 AAATTTTAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
21 7 0.24
22 16 0.55
23 5 0.17
24 1 0.03
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
TATATTAATATTTTAAATATTT
Found at i:1650763 original size:31 final size:31
Alignment explanation
Indices: 1650720--1650870 Score: 83
Period size: 30 Copynumber: 4.6 Consensus size: 31
1650710 AAATATTTTA
*
1650720 TATTTATATAAATTTTAATAAAATTATAATT
1 TATTTATTTAAATTTTAATAAAATTATAATT
*
1650751 TATTTATTTAAATATTATAATCATATAATATTAATACTT
1 TATTTATTTAAAT-TT-T-A--ATA-AA-ATT-ATAATT
** * * * * *
1650790 TATAAATATTATATTTATATTTAAAATAT-TTT
1 TATTTAT-TTAAATTT-TAATAAAATTATAATT
*
1650822 ATATTTATATAAATTTTAA-AAAA-TATAATT
1 -TATTTATTTAAATTTTAATAAAATTATAATT
1650852 TATATTATTTAAATTTTAA
1 TAT-TTATTTAAATTTTAA
1650871 AATATATATA
Statistics
Matches: 91, Mismatches: 17, Indels: 25
0.68 0.13 0.19
Matches are distributed among these distances:
29 6 0.07
30 19 0.21
31 14 0.15
32 10 0.11
33 8 0.09
34 3 0.03
35 2 0.02
36 4 0.04
37 2 0.02
38 4 0.04
39 14 0.15
40 5 0.05
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.52
Consensus pattern (31 bp):
TATTTATTTAAATTTTAATAAAATTATAATT
Found at i:1650798 original size:22 final size:20
Alignment explanation
Indices: 1650773--1650818 Score: 56
Period size: 22 Copynumber: 2.2 Consensus size: 20
1650763 TATTATAATC
1650773 ATATAATATTAATACTTTATAA
1 ATATAATATTAATA-TTTA-AA
* *
1650795 ATATTATATTTATATTTAAA
1 ATATAATATTAATATTTAAA
1650815 ATAT
1 ATAT
1650819 TTTATATTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 6 0.27
21 4 0.18
22 12 0.55
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (20 bp):
ATATAATATTAATATTTAAA
Found at i:1650829 original size:28 final size:28
Alignment explanation
Indices: 1650798--1650905 Score: 73
Period size: 28 Copynumber: 3.9 Consensus size: 28
1650788 TTTATAAATA
1650798 TTATATTTATATTTAAAATATTTTATAT
1 TTATATTTATATTTAAAATATTTTATAT
** * * *
1650826 TTATATAAAT-TTTAAAAAATATAAT-T
1 TTATATTTATATTTAAAATATTTTATAT
* *
1650852 TATATTATTTAAATTTTAAAATA-TATATAT
1 T-TA-TATTTATA-TTTAAAATATTTTATAT
*
1650882 TGATATTATATATTT--AATATTTTA
1 TTATATT-TATATTTAAAATATTTTA
1650906 AAAATATCAC
Statistics
Matches: 58, Mismatches: 15, Indels: 15
0.66 0.17 0.17
Matches are distributed among these distances:
26 6 0.10
27 17 0.29
28 19 0.33
29 6 0.10
30 10 0.17
ACGTcount: A:0.44, C:0.00, G:0.01, T:0.55
Consensus pattern (28 bp):
TTATATTTATATTTAAAATATTTTATAT
Found at i:1650901 original size:103 final size:106
Alignment explanation
Indices: 1650674--1650902 Score: 294
Period size: 103 Copynumber: 2.2 Consensus size: 106
1650664 GATTTGATGT
* *
1650674 ATATTATATATTTTATTATATTTTTATTAATATTTTAAATATTTTATATTTATATAAATTTTAAT
1 ATATTATATA-TTTA--ATA-TTATATTAATATTTAAAATATTTTATATTTATATAAATTTTAAT
*
1650739 AAAATTATAATTTATTTATTTAAATATTATAATCATATAATATTA
62 AAAATTATAATTTATTTATTTAAATATTAAAATCATATAATATTA
*
1650784 ATACTT-TATA---AATATTATATTTATATTTAAAATATTTTATATTTATATAAATTTTAA-AAA
1 ATA-TTATATATTTAATATTATATTAATATTTAAAATATTTTATATTTATATAAATTTTAATAAA
* *
1650844 A-TATAATTTATATTATTTAAATTTTAAAAT-ATAT-ATATTG
65 ATTATAATTTAT-TTATTTAAATATTAAAATCATATAATATTA
1650884 ATATTATATATTTAATATT
1 ATATTATATATTTAATATT
1650903 TTAAAAATAT
Statistics
Matches: 107, Mismatches: 6, Indels: 19
0.81 0.05 0.14
Matches are distributed among these distances:
99 2 0.02
100 12 0.11
101 14 0.13
102 20 0.19
103 46 0.43
104 3 0.03
106 1 0.01
110 7 0.07
111 2 0.02
ACGTcount: A:0.44, C:0.01, G:0.00, T:0.55
Consensus pattern (106 bp):
ATATTATATATTTAATATTATATTAATATTTAAAATATTTTATATTTATATAAATTTTAATAAAA
TTATAATTTATTTATTTAAATATTAAAATCATATAATATTA
Found at i:1651196 original size:13 final size:13
Alignment explanation
Indices: 1651180--1651205 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1651170 ATGAGAGACA
1651180 AATATATATATAT
1 AATATATATATAT
1651193 AATATATATATAT
1 AATATATATATAT
1651206 CTATTAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
AATATATATATAT
Found at i:1654257 original size:2 final size:2
Alignment explanation
Indices: 1654252--1654276 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1654242 ATATATATAT
1654252 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
1654277 AGAAAAAGAG
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:1657289 original size:3 final size:3
Alignment explanation
Indices: 1657281--1657323 Score: 68
Period size: 3 Copynumber: 14.3 Consensus size: 3
1657271 GCCACCGTCT
* *
1657281 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCT TCG TCA TCA T
1 TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA TCA T
1657324 TTACGCTTTC
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.28, C:0.33, G:0.02, T:0.37
Consensus pattern (3 bp):
TCA
Found at i:1657443 original size:6 final size:6
Alignment explanation
Indices: 1657434--1657528 Score: 59
Period size: 6 Copynumber: 15.8 Consensus size: 6
1657424 CCTTTCTCTC
* * * *
1657434 TCTCGT TCTCGT TGTC-T GTCCCGC TCTC-T ATCTCTT TCTCGT TCTCGT
1 TCTCGT TCTCGT TCTCGT -TCTCGT TCTCGT -TCTCGT TCTCGT TCTCGT
* * * * * * *
1657482 TCCCTT TCTCGA TCTCTT TCTCGT TCTCGT TCCCTT TCTCGA TCTCG
1 TCTCGT TCTCGT TCTCGT TCTCGT TCTCGT TCTCGT TCTCGT TCTCG
1657529 ATCCTTCTTT
Statistics
Matches: 65, Mismatches: 20, Indels: 8
0.70 0.22 0.09
Matches are distributed among these distances:
5 1 0.02
6 63 0.97
7 1 0.02
ACGTcount: A:0.03, C:0.37, G:0.13, T:0.47
Consensus pattern (6 bp):
TCTCGT
Found at i:1657516 original size:30 final size:30
Alignment explanation
Indices: 1657416--1657527 Score: 136
Period size: 30 Copynumber: 3.7 Consensus size: 30
1657406 ACTTAACCGA
* ** *
1657416 TCTCTTTCCCTTTCTCTCTCTCGTTCTCGT
1 TCTCGTTCCCTTTCTCGATCTCTTTCTCGT
* ** *
1657446 TGTC-TGTCCCGCTCTCTATCTCTTTCTCGT
1 TCTCGT-TCCCTTTCTCGATCTCTTTCTCGT
1657476 TCTCGTTCCCTTTCTCGATCTCTTTCTCGT
1 TCTCGTTCCCTTTCTCGATCTCTTTCTCGT
1657506 TCTCGTTCCCTTTCTCGATCTC
1 TCTCGTTCCCTTTCTCGATCTC
1657528 GATCCTTCTT
Statistics
Matches: 71, Mismatches: 9, Indels: 4
0.85 0.11 0.05
Matches are distributed among these distances:
29 1 0.01
30 69 0.97
31 1 0.01
ACGTcount: A:0.03, C:0.38, G:0.10, T:0.49
Consensus pattern (30 bp):
TCTCGTTCCCTTTCTCGATCTCTTTCTCGT
Found at i:1660067 original size:23 final size:23
Alignment explanation
Indices: 1660022--1660067 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
1660012 AAAAAGATTG
* *
1660022 TTAAAAAATTTTTTAATTATTAT
1 TTAAAAAATTTATAAATTATTAT
1660045 TTAAAACAATTTATAAATT-TTAT
1 TTAAAA-AATTTATAAATTATTAT
1660068 ATATTATTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (23 bp):
TTAAAAAATTTATAAATTATTAT
Found at i:1660103 original size:30 final size:26
Alignment explanation
Indices: 1660069--1660134 Score: 64
Period size: 30 Copynumber: 2.5 Consensus size: 26
1660059 AAATTTTATA
1660069 TATTATTTTTATTTATTCAAAAATATAATT
1 TATTATTTTTATTT-TT-AAAAA-ATAA-T
* *
1660099 TATTAATTATA-TTTTAAAAAATAAT
1 TATTATTTTTATTTTTAAAAAATAAT
1660124 TA-TATTTTTAT
1 TATTATTTTTAT
1660135 ATCATATTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 7
0.74 0.10 0.17
Matches are distributed among these distances:
24 6 0.19
25 3 0.10
26 4 0.13
27 5 0.16
28 2 0.06
29 2 0.06
30 9 0.29
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (26 bp):
TATTATTTTTATTTTTAAAAAATAAT
Found at i:1660134 original size:26 final size:28
Alignment explanation
Indices: 1660071--1660136 Score: 77
Period size: 27 Copynumber: 2.4 Consensus size: 28
1660061 ATTTTATATA
1660071 TTATTTTTAT-TTATTCAAAAATATAAT
1 TTATTTTTATATTATTCAAAAATATAAT
*
1660098 TTATTAATTATATT-TT-AAAAA-ATAAT
1 TTATT-TTTATATTATTCAAAAATATAAT
1660124 TATATTTTTATAT
1 T-TATTTTTATAT
1660137 CATATTTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
26 12 0.35
27 14 0.41
28 6 0.18
29 2 0.06
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (28 bp):
TTATTTTTATATTATTCAAAAATATAAT
Found at i:1660959 original size:13 final size:13
Alignment explanation
Indices: 1660920--1660963 Score: 54
Period size: 13 Copynumber: 3.5 Consensus size: 13
1660910 TATTTAAAAA
*
1660920 TTTTAAATATATT
1 TTTTAATTATATT
**
1660933 TTTTTTTTAT-TT
1 TTTTAATTATATT
1660945 TTTTAATTATATT
1 TTTTAATTATATT
1660958 TTTTAA
1 TTTTAA
1660964 ATAAATAAAA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
12 10 0.40
13 15 0.60
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (13 bp):
TTTTAATTATATT
Found at i:1660996 original size:13 final size:14
Alignment explanation
Indices: 1660980--1661008 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
1660970 AAAAAATATC
1660980 AAATAA-AATAAAA
1 AAATAATAATAAAA
1660993 AAATAATAATAAAA
1 AAATAATAATAAAA
1661007 AA
1 AA
1661009 TATATTCAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.40
14 9 0.60
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (14 bp):
AAATAATAATAAAA
Found at i:1661007 original size:20 final size:19
Alignment explanation
Indices: 1660962--1661006 Score: 58
Period size: 19 Copynumber: 2.4 Consensus size: 19
1660952 TATATTTTTT
*
1660962 AAAT-AAATAAAAAATATC
1 AAATAAAATAAAAAATATA
1660980 AAATAAAATAAAAAA-ATA
1 AAATAAAATAAAAAATATA
1660998 ATAATAAAA
1 A-AATAAAA
1661007 AATATATTCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
18 7 0.29
19 17 0.71
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (19 bp):
AAATAAAATAAAAAATATA
Found at i:1661212 original size:16 final size:17
Alignment explanation
Indices: 1661187--1661220 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
1661177 AATTTTTATG
1661187 AATTTGAATTAAATTTA
1 AATTTGAATTAAATTTA
1661204 AATTT-AATTAAATTTA
1 AATTTGAATTAAATTTA
1661220 A
1 A
1661221 TTATAATTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (17 bp):
AATTTGAATTAAATTTA
Found at i:1661248 original size:30 final size:31
Alignment explanation
Indices: 1661214--1661280 Score: 77
Period size: 31 Copynumber: 2.2 Consensus size: 31
1661204 AATTTAATTA
1661214 AATTTAATTAT-AATTTT-TTAATAAAA-ATAT
1 AATTTAATTATAAATTTTATT-ATAAAATAT-T
* *
1661244 AATTTTATTTTAAATTTTATTATAAAATATT
1 AATTTAATTATAAATTTTATTATAAAATATT
1661275 AATTTA
1 AATTTA
1661281 TTAACATAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
30 9 0.29
31 18 0.58
32 4 0.13
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (31 bp):
AATTTAATTATAAATTTTATTATAAAATATT
Found at i:1661474 original size:15 final size:15
Alignment explanation
Indices: 1661454--1661500 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
1661444 ATAAAATATG
1661454 AAATAAAAATAATTA
1 AAATAAAAATAATTA
**
1661469 AAATAAATTTTAA-TA
1 AAATAAA-AATAATTA
1661484 AAATAAAAATAATTA
1 AAATAAAAATAATTA
1661499 AA
1 AA
1661501 TATGATATAA
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
14 3 0.12
15 20 0.77
16 3 0.12
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (15 bp):
AAATAAAAATAATTA
Done.