Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr5
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: 43060996
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 2186021 characters in sequence are not A, C, G, or T
File 5 of 128
Found at i:1542229 original size:18 final size:18
Alignment explanation
Indices: 1542181--1542593 Score: 105
Period size: 18 Copynumber: 22.1 Consensus size: 18
1542171 TTTTTTCGTG
1542181 TTTTCGTGTTTTCAAAAAA
1 TTTTCGTGTTTTC-AAAAA
* *
1542200 TTCTCATG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
1542217 TTTTTGTGTTTTCAAAATTTTCA
1 TTTTCGTGTTTTCAAAA-----A
1542240 TGTTTTCGTGTTTTCAAAAAAA
1 --TTTTCGTGTTTTC--AAAAA
* *
1542262 TTCTCGTGTTTTTAAAAA
1 TTTTCGTGTTTTCAAAAA
** * *
1542280 AATTCGTATTTTAAAAAA
1 TTTTCGTGTTTTCAAAAA
** * *
1542298 AATTCATGTTTTC-GAAA
1 TTTTCGTGTTTTCAAAAA
1542315 TTTTCGTG---TCAAAAAA
1 TTTTCGTGTTTTC-AAAAA
* *
1542331 TTCTCATG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
1542348 TTTTCGTGTTTTAAAAAAA
1 TTTTCGTGTTTT-CAAAAA
**
1542367 TTCCCGTGTTTTCAAAATTTTCA
1 TTTTCGTGTTTTCAAAA-----A
1542390 TGCTTTCGTGTTTTCAAAAAA
1 T--TTTCGTGTTTTC-AAAAA
*
1542411 TTCTT-GTGTTTTTTAAAAAAA
1 TT-TTCGTG--TTTT-CAAAAA
** * **
1542432 AATTCATGTTTAAAAAAA
1 TTTTCGTGTTTTCAAAAA
** ** *
1542450 AATTCAAGTTTTC-GAAA
1 TTTTCGTGTTTTCAAAAA
*
1542467 TTTTCGTGTTTTCAAAAT
1 TTTTCGTGTTTTCAAAAA
1542485 TTTTCGTG---TCAAAAAA
1 TTTTCGTGTTTTC-AAAAA
* * * *
1542501 TTCTCATG-TATCGAAAA
1 TTTTCGTGTTTTCAAAAA
* * *
1542518 TTTCCTTATTTTCAAAAAAA
1 TTTTCGTGTTTTC--AAAAA
** *
1542538 AATCCGTGTTTTCAAAAAA
1 TTTTCGTGTTTTC-AAAAA
*
1542557 ATTTCGTG-TTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
*
1542574 TCTTCGTGTTTTCAAAAA
1 TTTTCGTGTTTTCAAAAA
1542592 TT
1 TT
1542594 ATTATTGTGT
Statistics
Matches: 292, Mismatches: 65, Indels: 75
0.68 0.15 0.17
Matches are distributed among these distances:
14 2 0.01
15 2 0.01
16 19 0.07
17 60 0.21
18 94 0.32
19 40 0.14
20 28 0.10
21 13 0.04
22 1 0.00
23 3 0.01
25 22 0.08
26 4 0.01
27 4 0.01
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (18 bp):
TTTTCGTGTTTTCAAAAA
Found at i:1542243 original size:17 final size:18
Alignment explanation
Indices: 1542181--1542246 Score: 73
Period size: 17 Copynumber: 3.7 Consensus size: 18
1542171 TTTTTTCGTG
*
1542181 TTTTCGTGTTTTCAAAAAA
1 TTTTCATGTTTTC-AAAAA
*
1542200 TTCTCATG-TTTCAAAAA
1 TTTTCATGTTTTCAAAAA
**
1542217 TTTTTGTGTTTTC-AAAA
1 TTTTCATGTTTTCAAAAA
1542234 TTTTCATGTTTTC
1 TTTTCATGTTTTC
1542247 GTGTTTTCAA
Statistics
Matches: 39, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
17 25 0.64
18 8 0.21
19 6 0.15
ACGTcount: A:0.26, C:0.12, G:0.09, T:0.53
Consensus pattern (18 bp):
TTTTCATGTTTTCAAAAA
Found at i:1542329 original size:33 final size:33
Alignment explanation
Indices: 1542293--1542388 Score: 97
Period size: 33 Copynumber: 2.8 Consensus size: 33
1542283 TCGTATTTTA
*
1542293 AAAAAAATTCATGTTTTCGAAATTTTCGTG-TC
1 AAAAAAATTCATGTTTTCAAAATTTTCGTGTTC
* *
1542325 AAAAAATTCTCATG-TTTCAAAAATTTTCGTGTTTT
1 AAAAAAAT-TCATGTTTTC-AAAATTTTCGTG-TTC
*
1542360 AAAAAAATTCCCGTGTTTTCAAAATTTTC
1 AAAAAAATT--CATGTTTTCAAAATTTTC
1542389 ATGCTTTCGT
Statistics
Matches: 52, Mismatches: 5, Indels: 10
0.78 0.07 0.15
Matches are distributed among these distances:
32 11 0.21
33 16 0.31
34 1 0.02
35 8 0.15
36 12 0.23
37 4 0.08
ACGTcount: A:0.35, C:0.14, G:0.09, T:0.42
Consensus pattern (33 bp):
AAAAAAATTCATGTTTTCAAAATTTTCGTGTTC
Found at i:1542348 original size:17 final size:17
Alignment explanation
Indices: 1542326--1542364 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
1542316 TTTCGTGTCA
1542326 AAAAATTCTCATGTTTC
1 AAAAATTCTCATGTTTC
* * *
1542343 AAAAATTTTCGTGTTTT
1 AAAAATTCTCATGTTTC
1542360 AAAAA
1 AAAAA
1542365 AATTCCCGTG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (17 bp):
AAAAATTCTCATGTTTC
Found at i:1542421 original size:19 final size:19
Alignment explanation
Indices: 1542323--1542422 Score: 53
Period size: 19 Copynumber: 5.1 Consensus size: 19
1542313 AATTTTCGTG
**
1542323 TCAAAAAATTCTCATG-TT
1 TCAAAAAATTCTTGTGTTT
1542341 TC-AAAAATT-TTCGTGTTT
1 TCAAAAAATTCTT-GTGTTT
* **
1542359 TAAAAAAATTCCCGTGTTT
1 TCAAAAAATTCTTGTGTTT
* *
1542378 TCAAAATTTTCATGCTTTCGTGTTT
1 TCAAAA----AATTC-TT-GTGTTT
1542403 TCAAAAAATTCTTGTGTTT
1 TCAAAAAATTCTTGTGTTT
1542422 T
1 T
1542423 TTAAAAAAAA
Statistics
Matches: 60, Mismatches: 12, Indels: 19
0.66 0.13 0.21
Matches are distributed among these distances:
16 1 0.02
17 9 0.15
18 5 0.08
19 25 0.42
20 2 0.03
21 3 0.05
23 3 0.05
25 12 0.20
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (19 bp):
TCAAAAAATTCTTGTGTTT
Found at i:1542479 original size:17 final size:18
Alignment explanation
Indices: 1542457--1542493 Score: 58
Period size: 17 Copynumber: 2.1 Consensus size: 18
1542447 AAAAATTCAA
*
1542457 GTTTTCGAAA-TTTTCGT
1 GTTTTCAAAATTTTTCGT
1542474 GTTTTCAAAATTTTTCGT
1 GTTTTCAAAATTTTTCGT
1542492 GT
1 GT
1542494 CAAAAAATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.19, C:0.11, G:0.16, T:0.54
Consensus pattern (18 bp):
GTTTTCAAAATTTTTCGT
Found at i:1542554 original size:19 final size:19
Alignment explanation
Indices: 1542526--1542591 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
1542516 AATTTCCTTA
*
1542526 TTTTCAAAAAAAAATCCGTG
1 TTTTC-AAAAAAAATTCGTG
*
1542546 TTTTCAAAAAAATTTCGTG
1 TTTTCAAAAAAAATTCGTG
**
1542565 -TTTC-AAAAATCTTCGTG
1 TTTTCAAAAAAAATTCGTG
1542582 TTTTCAAAAA
1 TTTTCAAAAA
1542592 TTATTATTGT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
17 11 0.28
18 8 0.20
19 16 0.40
20 5 0.12
ACGTcount: A:0.39, C:0.14, G:0.09, T:0.38
Consensus pattern (19 bp):
TTTTCAAAAAAAATTCGTG
Found at i:1542582 original size:36 final size:36
Alignment explanation
Indices: 1542535--1542609 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
1542525 ATTTTCAAAA
1542535 AAAAATCCGTGTTTTCAAAAA-AATT-TCGTGTTTC
1 AAAAATCCGTGTTTTCAAAAATAATTATCGTGTTTC
* *
1542569 AAAAATCTTCGTGTTTTCAAAAATTATTATTGTGTTTC
1 AAAAATC--CGTGTTTTCAAAAATAATTATCGTGTTTC
1542607 AAA
1 AAA
1542610 GTTCTCGTGT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
34 7 0.20
36 14 0.40
37 3 0.09
38 11 0.31
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.41
Consensus pattern (36 bp):
AAAAATCCGTGTTTTCAAAAATAATTATCGTGTTTC
Found at i:1548435 original size:18 final size:16
Alignment explanation
Indices: 1548382--1548447 Score: 69
Period size: 18 Copynumber: 3.8 Consensus size: 16
1548372 AAAAAAAGGG
1548382 ACAAAAAAAATAAAAAA
1 ACAAAAAAAA-AAAAAA
1548399 ACAAAAACAAAAATAAAA
1 ACAAAAA-AAAAA-AAAA
1548417 ACAAAAAAAACAAAGAAA
1 ACAAAAAAAA-AAA-AAA
*
1548435 AGAAAAAGAAAAA
1 ACAAAAA-AAAAA
1548448 TCAAGATGAA
Statistics
Matches: 43, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
17 13 0.30
18 27 0.63
19 3 0.07
ACGTcount: A:0.85, C:0.08, G:0.05, T:0.03
Consensus pattern (16 bp):
ACAAAAAAAAAAAAAA
Found at i:1548447 original size:6 final size:6
Alignment explanation
Indices: 1548382--1548423 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
1548372 AAAAAAAGGG
*
1548382 ACAAAA A-AAATA A-AAAA ACAAAA ACAAAA ATAAAA ACAAAA A
1 ACAAAA ACAAA-A ACAAAA ACAAAA ACAAAA ACAAAA ACAAAA A
1548424 AAACAAAGAA
Statistics
Matches: 32, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
5 5 0.16
6 27 0.84
ACGTcount: A:0.86, C:0.10, G:0.00, T:0.05
Consensus pattern (6 bp):
ACAAAA
Found at i:1548447 original size:12 final size:12
Alignment explanation
Indices: 1548382--1548441 Score: 59
Period size: 12 Copynumber: 4.9 Consensus size: 12
1548372 AAAAAAAGGG
*
1548382 ACAAAAAAAATA
1 ACAAAAAAAAAA
*
1548394 A-AAAAACAAAA
1 ACAAAAAAAAAA
*
1548405 ACAAAAATAAAA
1 ACAAAAAAAAAA
1548417 ACAAAAAAAACAA
1 ACAAAAAAAA-AA
*
1548430 AGAAAAGAAAAA
1 ACAAAA-AAAAA
1548442 GAAAAATCAA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
11 9 0.22
12 19 0.47
13 8 0.20
14 4 0.10
ACGTcount: A:0.85, C:0.08, G:0.03, T:0.03
Consensus pattern (12 bp):
ACAAAAAAAAAA
Found at i:1549511 original size:73 final size:74
Alignment explanation
Indices: 1549289--1549658 Score: 444
Period size: 73 Copynumber: 4.8 Consensus size: 74
1549279 TTTCAAGAAA
* *
1549289 TATTTTTAAAATTCTGT-TTTTTGCAAGAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGG
1 TATTTTTAAATTTCTGTCTTTTT--TA-AAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGG
1549353 GTCACGCTGAGG
63 GTCACGCTGAGG
1549365 TATTTTTAAATTTCTG-CTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCG
1 TATTTTTAAATTTCTGTC-TTTTTT---AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCG
1549429 GGTCACGCTGAGG
62 GGTCACGCTGAGG
1549442 TATTTTT-AATTTCTGTCTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
1 TATTTTTAAATTTCTGTCTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
1549506 ACGCTGAGG
66 ACGCTGAGG
* * * **
1549515 TATTTTT-AATTCCTGTCTTTTTTTAAATCAACTCATAATATGAGAGGTGAGTTGAGGCCTCACG
1 TATTTTTAAATTTCTGTCTTTTTTAAAATCAACTCATAATA-CAGAGGTGAGTTGA-GCCTCGGG
*
1549579 TC-CCCTGAGG
64 TCACGCTGAGG
* * * *
1549589 TATTTCTTTTAAATTTTTGTTTTTTTTTTTTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 TA--T-TTTTAAATTTCTG----TCTTTTTTAAAATCAACTCATAATAC-AGAGGTGAGTTGAGC
1549654 CTCGG
58 CTCGG
1549659 ACCAANNNNN
Statistics
Matches: 260, Mismatches: 17, Indels: 29
0.85 0.06 0.09
Matches are distributed among these distances:
73 88 0.34
74 22 0.08
75 8 0.03
76 30 0.12
77 66 0.25
78 7 0.03
81 5 0.02
82 34 0.13
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (74 bp):
TATTTTTAAATTTCTGTCTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTC
ACGCTGAGG
Found at i:1549599 original size:150 final size:149
Alignment explanation
Indices: 1549289--1549658 Score: 455
Period size: 150 Copynumber: 2.4 Consensus size: 149
1549279 TTTCAAGAAA
* **
1549289 TATTTTTAAAATTCTGTT-TTTTGCAAGAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGG
1 TATTTTTAAATTTCTGTTCTTTT-TTA-AAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGG
*
1549353 GTCACGCTGAGGTATTTTTAAATTTCTGCTTTTTTTCAAAAAATCAACTCATAATACAGAGGTGA
64 GTCACGCTGAGGTATTTTTAAATTCCTGCTTTTTTT---AAAATCAACTCATAATACAGAGGTGA
** *
1549418 GTTGAGCCTCGGGTCACGCTGAGG
126 GTTGAGCCTCACGTCACCCTGAGG
1549442 TATTTTT-AATTTCTG-TCTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
1 TATTTTTAAATTTCTGTTCTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
*
1549505 CACGCTGAGGTATTTTT-AATTCCTGTCTTTTTTT-AAATCAACTCATAATATGAGAGGTGAGTT
66 CACGCTGAGGTATTTTTAAATTCCTG-CTTTTTTTAAAATCAACTCATAATA-CAGAGGTGAGTT
1549568 GAGGCCTCACGTC-CCCTGAGG
129 GA-GCCTCACGTCACCCTGAGG
* * * *
1549589 TATTTCTTTTAAATTTTTGTTTTTTTTTTTTAAAATCAACTCATATTGCGAGAGGTGAGTTGAGC
1 TA--T-TTTTAAATTTCTG---TTCTTTTTTAAAATCAACTCATAATAC-AGAGGTGAGTTGAGC
1549654 CTCGG
59 CTCGG
1549659 ACCAANNNNN
Statistics
Matches: 192, Mismatches: 12, Indels: 23
0.85 0.05 0.10
Matches are distributed among these distances:
146 16 0.08
147 22 0.11
148 8 0.04
149 8 0.04
150 68 0.35
151 9 0.05
152 11 0.06
153 7 0.04
155 23 0.12
156 20 0.10
ACGTcount: A:0.26, C:0.16, G:0.20, T:0.38
Consensus pattern (149 bp):
TATTTTTAAATTTCTGTTCTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGT
CACGCTGAGGTATTTTTAAATTCCTGCTTTTTTTAAAATCAACTCATAATACAGAGGTGAGTTGA
GCCTCACGTCACCCTGAGG
Found at i:1549918 original size:75 final size:77
Alignment explanation
Indices: 1549816--1550006 Score: 282
Period size: 75 Copynumber: 2.5 Consensus size: 77
1549806 AAATAAAAAT
* *
1549816 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGCACACGCCGAGGTA-T-TTTTCAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGAC-CACGCCGAGGTATTCTTTTAAA
1549879 -TTATGGTTTTT-A
65 TTTAT-GTTTTTAA
* *
1549891 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCATGCCGATGTATTTCTTTTAAA
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCACGCCGAGGTA-TTCTTTTAAA
1549956 TTTATGTTTTTCAA
65 TTTATGTTTTT-AA
1549970 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1 AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCT
1550007 NNNNNNNNNN
Statistics
Matches: 106, Mismatches: 4, Indels: 8
0.90 0.03 0.07
Matches are distributed among these distances:
74 10 0.09
75 41 0.39
76 1 0.01
77 12 0.11
78 4 0.04
79 38 0.36
ACGTcount: A:0.30, C:0.17, G:0.22, T:0.31
Consensus pattern (77 bp):
AAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGACCACGCCGAGGTATTCTTTTAAAT
TTATGTTTTTAA
Found at i:1551850 original size:20 final size:20
Alignment explanation
Indices: 1551825--1551862 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
1551815 AAAAATATTC
1551825 AAAAATCCTCGTATTTTAAT
1 AAAAATCCTCGTATTTTAAT
* *
1551845 AAAAATTCTCGTGTTTTA
1 AAAAATCCTCGTATTTTA
1551863 TTAGAATCCC
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:0.37, C:0.13, G:0.08, T:0.42
Consensus pattern (20 bp):
AAAAATCCTCGTATTTTAAT
Found at i:1552015 original size:19 final size:21
Alignment explanation
Indices: 1551979--1552018 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
1551969 AAAAAATAAA
*
1551979 AAAATAAAAATCTTGTGTTTT
1 AAAATAAAAATCTCGTGTTTT
1552000 AAAA-AAAAAT-TCGTGTTTT
1 AAAATAAAAATCTCGTGTTTT
1552019 TAAAGTTTCC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 6 0.33
21 4 0.22
ACGTcount: A:0.45, C:0.05, G:0.10, T:0.40
Consensus pattern (21 bp):
AAAATAAAAATCTCGTGTTTT
Found at i:1552059 original size:18 final size:18
Alignment explanation
Indices: 1552024--1552142 Score: 97
Period size: 18 Copynumber: 6.8 Consensus size: 18
1552014 GTTTTTAAAG
1552024 TTTCCATGTTTT--AAAA
1 TTTCCATGTTTTCAAAAA
*
1552040 TTTCCGTGTTTTCAAAAA
1 TTTCCATGTTTTCAAAAA
*
1552058 TTCCCATG-TTT-AAAAA
1 TTTCCATGTTTTCAAAAA
* *
1552074 TTTTTTCGTGTTTTCAAAAA
1 --TTTCCATGTTTTCAAAAA
*
1552094 ATTCTCATG-TTTCAAAAA
1 TTTC-CATGTTTTCAAAAA
* *
1552112 TTTTCGTGTTTTC-AAAA
1 TTTCCATGTTTTCAAAAA
*
1552129 TTTTCATGTTTTCA
1 TTTCCATGTTTTCA
1552143 TGTTTTTTAA
Statistics
Matches: 81, Mismatches: 13, Indels: 16
0.74 0.12 0.15
Matches are distributed among these distances:
16 16 0.20
17 22 0.27
18 32 0.40
19 6 0.07
20 5 0.06
ACGTcount: A:0.29, C:0.14, G:0.08, T:0.49
Consensus pattern (18 bp):
TTTCCATGTTTTCAAAAA
Found at i:1552091 original size:36 final size:34
Alignment explanation
Indices: 1552009--1552128 Score: 143
Period size: 36 Copynumber: 3.4 Consensus size: 34
1551999 TAAAAAAAAA
* * * *
1552009 TTCGTGTTTT-TAAAGTTTCCATGTTTTAAAATT
1 TTCGTGTTTTCAAAAATTCCCATGTTTAAAAATT
*
1552042 TCCGTGTTTTCAAAAATTCCCATGTTTAAAAATTTT
1 TTCGTGTTTTCAAAAATTCCCATGTTTAAAAA--TT
*
1552078 TTCGTGTTTTCAAAAAATTCTCATGTTTCAAAAATT
1 TTCGTGTTTTC-AAAAATTCCCATGTTT-AAAAATT
1552114 TTCGTGTTTTCAAAA
1 TTCGTGTTTTCAAAA
1552129 TTTTCATGTT
Statistics
Matches: 75, Mismatches: 7, Indels: 8
0.83 0.08 0.09
Matches are distributed among these distances:
33 9 0.12
34 17 0.23
35 4 0.05
36 25 0.33
37 15 0.20
38 5 0.07
ACGTcount: A:0.29, C:0.13, G:0.10, T:0.47
Consensus pattern (34 bp):
TTCGTGTTTTCAAAAATTCCCATGTTTAAAAATT
Found at i:1552185 original size:18 final size:18
Alignment explanation
Indices: 1552139--1552185 Score: 58
Period size: 18 Copynumber: 2.6 Consensus size: 18
1552129 TTTTCATGTT
*
1552139 TTCATGTTTTTTAAAAAAA
1 TTCATG-TTTTAAAAAAAA
* *
1552158 TTCGTATTTTAAAAAAAA
1 TTCATGTTTTAAAAAAAA
1552176 TTCATGTTTT
1 TTCATGTTTT
1552186 CGAAATTTTC
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
18 19 0.83
19 4 0.17
ACGTcount: A:0.38, C:0.06, G:0.06, T:0.49
Consensus pattern (18 bp):
TTCATGTTTTAAAAAAAA
Found at i:1552241 original size:19 final size:17
Alignment explanation
Indices: 1552009--1552267 Score: 97
Period size: 17 Copynumber: 15.4 Consensus size: 17
1551999 TAAAAAAAAA
* *
1552009 TTCGTGTTTTTAAAGTT
1 TTCGTGTTTTAAAAATT
* *
1552026 TCCATGTTTT-AAAATT
1 TTCGTGTTTTAAAAATT
*
1552042 TCCGTGTTTTCAAAAATT
1 TTCGTGTTTT-AAAAATT
** *
1552060 CCCATG-TTTAAAAATTTT
1 TTCGTGTTTTAAAAA--TT
1552078 TTCGTGTTTTCAAAAAATT
1 TTCGTGTTTT--AAAAATT
* * *
1552097 CTCATGTTTCAAAAATT
1 TTCGTGTTTTAAAAATT
*
1552114 TTCGTGTTTTCAAAATT
1 TTCGTGTTTTAAAAATT
* *
1552131 TTCATGTTTT---CA--
1 TTCGTGTTTTAAAAATT
* **
1552143 -T-GTTTTTTAAAAAAA
1 TTCGTGTTTTAAAAATT
* **
1552158 TTCGTATTTTAAAAAAAA
1 TTCGTGTTTT-AAAAATT
* **
1552176 TTCATGTTTTCGAAATT
1 TTCGTGTTTTAAAAATT
**
1552193 TTCGTG-TCAAAAAATT
1 TTCGTGTTTTAAAAATT
* * *
1552209 CTCATGTTTCAAAAATT
1 TTCGTGTTTTAAAAATT
1552226 TTCGTGTTTTAAAAAAATT
1 TTCGTGTTTT--AAAAATT
** *
1552245 CCCGTGTTTTCAAAATT
1 TTCGTGTTTTAAAAATT
1552262 TTCGTG
1 TTCGTG
1552268 CTTTCGTGTT
Statistics
Matches: 179, Mismatches: 45, Indels: 36
0.69 0.17 0.14
Matches are distributed among these distances:
10 5 0.03
11 1 0.01
13 1 0.01
14 1 0.01
16 30 0.17
17 79 0.44
18 30 0.17
19 27 0.15
21 5 0.03
ACGTcount: A:0.31, C:0.12, G:0.10, T:0.47
Consensus pattern (17 bp):
TTCGTGTTTTAAAAATT
Found at i:1552335 original size:18 final size:17
Alignment explanation
Indices: 1552298--1552335 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
1552288 TCTCGTGTTT
*
1552298 TTTAAAAAAAAATCATG
1 TTTAAAAAAAAATCAAG
1552315 TTTAAAAAAAAATTCAAG
1 TTTAAAAAAAAA-TCAAG
1552333 TTT
1 TTT
1552336 TCGAAATTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.55, C:0.05, G:0.05, T:0.34
Consensus pattern (17 bp):
TTTAAAAAAAAATCAAG
Found at i:1552354 original size:17 final size:18
Alignment explanation
Indices: 1552332--1552409 Score: 67
Period size: 17 Copynumber: 4.6 Consensus size: 18
1552322 AAAAATTCAA
*
1552332 GTTTTCGAAA-TTTTCGT
1 GTTTTCAAAATTTTTCGT
1552349 GTTTTCAAAATTTTTCGT
1 GTTTTCAAAATTTTTCGT
**
1552367 G---TCAAAAAAATTTCGT
1 GTTTTC-AAAATTTTTCGT
* *
1552383 G-TTTCAAAAATCTTCGT
1 GTTTTCAAAATTTTTCGT
1552400 GTTTTCAAAA
1 GTTTTCAAAA
1552410 ATTATTATTG
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
15 2 0.04
16 11 0.22
17 20 0.39
18 18 0.35
ACGTcount: A:0.29, C:0.13, G:0.13, T:0.45
Consensus pattern (18 bp):
GTTTTCAAAATTTTTCGT
Found at i:1552365 original size:18 final size:18
Alignment explanation
Indices: 1552339--1552412 Score: 84
Period size: 18 Copynumber: 4.3 Consensus size: 18
1552329 CAAGTTTTCG
1552339 AAATTTTCGTGTTTTCAA
1 AAATTTTCGTGTTTTCAA
*
1552357 AATTTTTCGTG---TCAAA
1 AAATTTTCGTGTTTTC-AA
*
1552373 AAAATTTCGTG-TTTCAA
1 AAATTTTCGTGTTTTCAA
*
1552390 AAATCTTCGTGTTTTCAA
1 AAATTTTCGTGTTTTCAA
1552408 AAATT
1 AAATT
1552413 ATTATTGTGT
Statistics
Matches: 46, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
15 2 0.04
16 11 0.24
17 11 0.24
18 22 0.48
ACGTcount: A:0.32, C:0.12, G:0.11, T:0.45
Consensus pattern (18 bp):
AAATTTTCGTGTTTTCAA
Found at i:1560460 original size:12 final size:12
Alignment explanation
Indices: 1560443--1560474 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
1560433 AAATTGTGTA
1560443 ATATTCGAGTTC
1 ATATTCGAGTTC
1560455 ATATTCGAGTTC
1 ATATTCGAGTTC
1560467 ATATTCGA
1 ATATTCGA
1560475 ATTAAACCAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.41
Consensus pattern (12 bp):
ATATTCGAGTTC
Found at i:1560800 original size:57 final size:57
Alignment explanation
Indices: 1560694--1560847 Score: 168
Period size: 57 Copynumber: 2.7 Consensus size: 57
1560684 TATGTCGGAA
* * * * * *
1560694 ATTATGAAAACAACGGCCGTTTTGGACAACCATTTCTT-AAATGTCAGACATAATA-
1 ATTATGAAAACAACAGCCATTTTAGACAACCATATCTTCATATGTCAGACAAAATAT
* * * *
1560749 AGTTCTGGAAACAGCAGCCATTTTAGACAATCATATCTTCATATGTCAGACAAAATAT
1 A-TTATGAAAACAACAGCCATTTTAGACAACCATATCTTCATATGTCAGACAAAATAT
* * *
1560807 ATTATGAAAACAACAGTCATTTTGGACAACCATTTCTTCAT
1 ATTATGAAAACAACAGCCATTTTAGACAACCATATCTTCAT
1560848 TTATCCAACA
Statistics
Matches: 79, Mismatches: 17, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
55 1 0.01
56 29 0.37
57 48 0.61
58 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.13, T:0.31
Consensus pattern (57 bp):
ATTATGAAAACAACAGCCATTTTAGACAACCATATCTTCATATGTCAGACAAAATAT
Found at i:1563162 original size:56 final size:57
Alignment explanation
Indices: 1563030--1563171 Score: 144
Period size: 56 Copynumber: 2.5 Consensus size: 57
1563020 CACACATAAT
* ** *
1563030 ACAACAGCTATTTTAGACAACCATTTCTTCGTATGTCAGACATAATAAATTATGAAA
1 ACAACAGCCATTTTAGACAACCATTTCTTCAAATATCAGACATAATAAATTATGAAA
* * * * * * *
1563087 ACAACGGTCA-TTAAGGACAACCATTTCTT-AAATATCAGATATAATAAGTTCTGGAA
1 ACAACAGCCATTTTA-GACAACCATTTCTTCAAATATCAGACATAATAAATTATGAAA
* *
1563143 ACAGCAGCCATTTTAGACAATCATTTCTT
1 ACAACAGCCATTTTAGACAACCATTTCTT
1563172 GATATGTCAG
Statistics
Matches: 67, Mismatches: 16, Indels: 5
0.76 0.18 0.06
Matches are distributed among these distances:
56 43 0.64
57 24 0.36
ACGTcount: A:0.39, C:0.18, G:0.12, T:0.31
Consensus pattern (57 bp):
ACAACAGCCATTTTAGACAACCATTTCTTCAAATATCAGACATAATAAATTATGAAA
Found at i:1565104 original size:23 final size:21
Alignment explanation
Indices: 1565059--1565104 Score: 56
Period size: 23 Copynumber: 2.1 Consensus size: 21
1565049 ATTTCTTAAA
* *
1565059 TATTATTTTTTATGAATTTAT
1 TATTATTCTTTATGAACTTAT
1565080 TATTATATCTTTATCGAACTTAT
1 TATTAT-TCTTTAT-GAACTTAT
1565103 TA
1 TA
1565105 AATCGACGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.29
22 6 0.29
23 9 0.43
ACGTcount: A:0.30, C:0.07, G:0.04, T:0.59
Consensus pattern (21 bp):
TATTATTCTTTATGAACTTAT
Found at i:1571421 original size:24 final size:24
Alignment explanation
Indices: 1571394--1571493 Score: 68
Period size: 24 Copynumber: 4.3 Consensus size: 24
1571384 AATATGAATT
1571394 TTAAAATAATTATACATAATACAA
1 TTAAAATAATTATACATAATACAA
* * *
1571418 TTAAAAT-ATGCATACATAATAGAT
1 TTAAAATAAT-TATACATAATACAA
* ** * *
1571442 TTAAAAATAATGATGTATGATACAT
1 TT-AAAATAATTATACATAATACAA
1571467 TTAAAAT-A-T-T-CATAATA-AA
1 TTAAAATAATTATACATAATACAA
1571486 TTAAAATA
1 TTAAAATA
1571494 TACATGACTA
Statistics
Matches: 60, Mismatches: 12, Indels: 12
0.71 0.14 0.14
Matches are distributed among these distances:
19 8 0.13
20 5 0.08
21 1 0.02
23 3 0.05
24 25 0.42
25 16 0.27
26 2 0.03
ACGTcount: A:0.54, C:0.06, G:0.05, T:0.35
Consensus pattern (24 bp):
TTAAAATAATTATACATAATACAA
Found at i:1571491 original size:19 final size:20
Alignment explanation
Indices: 1571467--1571513 Score: 60
Period size: 19 Copynumber: 2.4 Consensus size: 20
1571457 TATGATACAT
*
1571467 TTAAAATATTCAT-AATAAA
1 TTAAAATATACATGAATAAA
* *
1571486 TTAAAATATACATGACTAAC
1 TTAAAATATACATGAATAAA
1571506 TTAAAATA
1 TTAAAATA
1571514 ATAATCCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
19 12 0.50
20 12 0.50
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (20 bp):
TTAAAATATACATGAATAAA
Found at i:1573490 original size:530 final size:532
Alignment explanation
Indices: 1572473--1573534 Score: 1882
Period size: 530 Copynumber: 2.0 Consensus size: 532
1572463 TTTCAAAATT
1572473 TTTAACCGTTAACCGAACCGAAAATTTTTCAAAAAAATTAACCGAACCGAAATTTTTCAGTTAAT
1 TTTAACCGTTAACCGAACCGAAAATTTTTCAAAAAAATTAACCGAACCGAAATTTTTCAGTTAAT
1572538 TCGGTCGGTTATCTGAATTAACCGAAAATTATATGTTTTTTATTTTTGGTTAAAAATTAACCGAA
66 TCGGTCGGTTATCTGAATTAACCGAAAATTATATGTTTTTTATTTTTGGTTAAAAATTAACCGAA
1572603 TTACCAGAATTAACCGAATTGAATCACTACATAATTAAATTATATTTAGACTTTTAGACTTTAGT
131 TTACCAGAATTAACCGAATTGAATCACTACATAATTAAATTATATTTAGACTTTTAGACTTTAGT
1572668 TTTAGTTTTAGTTTTAGAATTTTATTTTTATTTATTAAATTATTTGTAATTTTTATGATTGGGTT
196 TTTAGTTTTAGTTTTAGAATTTTATTTTTATTTATTAAATTATTTGTAATTTTTATGATTGGGTT
1572733 GAGTTGGGTAATTGGGTTGGATTGAATACTTGGGTTTGGATTGGGTTTAGGTGAATAGTGGGCCT
261 GAGTTGGGTAATTGGGTTGGATTGAATACTTGGGTTTGGATTGGGTTTAGGTGAATAGTGGGCCT
** *
1572798 ATTTATATATTATAATTTTATTTATTAATTTTTTCGGTTAAACCAAAAAAATTCGGTTCACCGAC
326 ATTTATATATTATAATTTTATTTATTAATTTTTTCACTTAAACCAAAAAAATTCGGTTAACCGAC
* * *
1572863 CGATTTCGAACCGAATTAACAGGTAACCGAAAAATCAAAAAATAATTAACCGACCTCCGACCGAA
391 AGATTTCGAACCGAATTAACAGGTAACCAAAAAATCAAAAAATAATTAACCGACCTCCGACCAAA
* * * *
1572928 AAAATTTGGTTAACTGACCGATTAACCGAATTC-GATCGTTTAAC-CAAATTTTTTCGATTTTAC
456 AAAATTCGGTTAACCGACCAATTAACCGAATTCAG-TCGGTTAACTCAAATTTTTTCGATTTTAC
*
1572991 CCGAATTTTGCAC
520 ACGAATTTTGCAC
1573004 TTTAACCGTT-ACCGAACCGAAAATTTTTCAAAAAAATTAACCGAACCGAAATTTTTCAGTTAAT
1 TTTAACCGTTAACCGAACCGAAAATTTTTCAAAAAAATTAACCGAACCGAAATTTTTCAGTTAAT
1573068 TCGGTCGGTTATCTGAATTAACCGAAAATTATATGTTTTTTATTTTTGGTTAAAAATTAACCGAA
66 TCGGTCGGTTATCTGAATTAACCGAAAATTATATGTTTTTTATTTTTGGTTAAAAATTAACCGAA
1573133 TTACCAGAATTAACCGAATTGAATCACTACATAATTAAATTATATTTAGACTTTTAGACTTTAGT
131 TTACCAGAATTAACCGAATTGAATCACTACATAATTAAATTATATTTAGACTTTTAGACTTTAGT
1573198 TTTAGTTTTAGTTTTAGAATTTTATTTTTATTTATTAAATTATTTGTAATTTTTATGATTGGGTT
196 TTTAGTTTTAGTTTTAGAATTTTATTTTTATTTATTAAATTATTTGTAATTTTTATGATTGGGTT
1573263 GAGTTGGGTAATTGGGTTGGATTGAATACTTGGGTTTGGATTGGGTTTAGGTGAATAGTGGGCCT
261 GAGTTGGGTAATTGGGTTGGATTGAATACTTGGGTTTGGATTGGGTTTAGGTGAATAGTGGGCCT
* * *
1573328 ATTTATATATTATAATTTTATTTATTAATTTTTTTACTTAAACCGAAAAAATTCGGTTAATCGAC
326 ATTTATATATTATAATTTTATTTATTAATTTTTTCACTTAAACCAAAAAAATTCGGTTAACCGAC
* * *
1573393 TAG-TTTCGAACCGAATTAACCGTTAACCAAAAAATTAAAAAATAATTAACCGACC-CTCGACCA
391 -AGATTTCGAACCGAATTAACAGGTAACCAAAAAATCAAAAAATAATTAACCGACCTC-CGACCA
* * *
1573456 AAAAAATTCGGTTAACCGACCAATTAATCGAATTCAGTCGGTTAACTGAATTTTTTTCGATTTTA
454 AAAAAATTCGGTTAACCGACCAATTAACCGAATTCAGTCGGTTAACTCAAATTTTTTCGATTTTA
1573521 CACGAATTTTGCAC
519 CACGAATTTTGCAC
1573535 ACCCCCTAGT
Statistics
Matches: 507, Mismatches: 20, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
529 1 0.00
530 465 0.92
531 41 0.08
ACGTcount: A:0.33, C:0.13, G:0.15, T:0.39
Consensus pattern (532 bp):
TTTAACCGTTAACCGAACCGAAAATTTTTCAAAAAAATTAACCGAACCGAAATTTTTCAGTTAAT
TCGGTCGGTTATCTGAATTAACCGAAAATTATATGTTTTTTATTTTTGGTTAAAAATTAACCGAA
TTACCAGAATTAACCGAATTGAATCACTACATAATTAAATTATATTTAGACTTTTAGACTTTAGT
TTTAGTTTTAGTTTTAGAATTTTATTTTTATTTATTAAATTATTTGTAATTTTTATGATTGGGTT
GAGTTGGGTAATTGGGTTGGATTGAATACTTGGGTTTGGATTGGGTTTAGGTGAATAGTGGGCCT
ATTTATATATTATAATTTTATTTATTAATTTTTTCACTTAAACCAAAAAAATTCGGTTAACCGAC
AGATTTCGAACCGAATTAACAGGTAACCAAAAAATCAAAAAATAATTAACCGACCTCCGACCAAA
AAAATTCGGTTAACCGACCAATTAACCGAATTCAGTCGGTTAACTCAAATTTTTTCGATTTTACA
CGAATTTTGCAC
Found at i:1574589 original size:57 final size:57
Alignment explanation
Indices: 1574479--1574620 Score: 173
Period size: 57 Copynumber: 2.5 Consensus size: 57
1574469 TAAATTACGA
* * * * *
1574479 AGTCGTTTTGGACAACCATTTCTT-AAATGTCAGACATAATAAGTTCTGGAAACAGC
1 AGTCCTTTTGGACAACCATTTCTTCAAATGTCAGACAAAATAAGTTATGAAAACAAC
* * *
1574535 AG-CCATTTTAGACAATCATTTCTTCATATGTCAGACAAAATATA-TTATGAAAACAAC
1 AGTCC-TTTTGGACAACCATTTCTTCAAATGTCAGACAAAATA-AGTTATGAAAACAAC
1574592 AGTCCTTTTGGACAACCATTTCTTCAAAT
1 AGTCCTTTTGGACAACCATTTCTTCAAAT
1574621 TTCCAACACG
Statistics
Matches: 71, Mismatches: 11, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
55 1 0.01
56 19 0.27
57 48 0.68
58 3 0.04
ACGTcount: A:0.36, C:0.19, G:0.13, T:0.32
Consensus pattern (57 bp):
AGTCCTTTTGGACAACCATTTCTTCAAATGTCAGACAAAATAAGTTATGAAAACAAC
Found at i:1579157 original size:56 final size:57
Alignment explanation
Indices: 1579015--1579165 Score: 153
Period size: 56 Copynumber: 2.7 Consensus size: 57
1579005 GAAAGAAATG
* * * * *
1579015 AATTATGAAAACCACATACATTTTAGACAACCATTTCTTCATATGTTAGACATAATA
1 AATTATGAAAACAACGTCCATTTTAGACAACCATTTCTTCAAATGTCAGACATAATA
* * * *
1579072 AATTATGAAAACAACGTTCGTTTTGGACAACCATTTCTT-AAATGTCAGACGTAATA
1 AATTATGAAAACAACGTCCATTTTAGACAACCATTTCTTCAAATGTCAGACATAATA
* * * * *
1579128 AGTTCTGGAAACAGCAG-CCATTTTAGACAATCATTTCT
1 AATTATGAAAACAAC-GTCCATTTTAGACAACCATTTCT
1579166 GAAAACAACA
Statistics
Matches: 77, Mismatches: 16, Indels: 3
0.80 0.17 0.03
Matches are distributed among these distances:
56 42 0.55
57 35 0.45
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.32
Consensus pattern (57 bp):
AATTATGAAAACAACGTCCATTTTAGACAACCATTTCTTCAAATGTCAGACATAATA
Found at i:1579597 original size:56 final size:57
Alignment explanation
Indices: 1579464--1579641 Score: 207
Period size: 57 Copynumber: 3.1 Consensus size: 57
1579454 ACCATAACCC
* * *
1579464 AACAACAGCCATTTTAGGCAACAATTTCTTCATATGTCGGACATAATAAATTATGAA
1 AACAACAGCCATTTTAGACAACCATTTCTTCATATGTCAGACATAATAAATTATGAA
* * * * * * *
1579521 AACAACGGCCGTTTTGGACAACCATTTCTT-AAATGTCAGATATAA-AAAGTTCTGGA
1 AACAACAGCCATTTTAGACAACCATTTCTTCATATGTCAGACATAATAAA-TTATGAA
* * * *
1579577 AACAGCAGCCATTTTAGACAATCATTTCTTCATATGTCAGACAAAATATATTATGAA
1 AACAACAGCCATTTTAGACAACCATTTCTTCATATGTCAGACATAATAAATTATGAA
1579634 AACAACAG
1 AACAACAG
1579642 AACTCATTTT
Statistics
Matches: 96, Mismatches: 22, Indels: 6
0.77 0.18 0.05
Matches are distributed among these distances:
55 3 0.03
56 42 0.44
57 49 0.51
58 2 0.02
ACGTcount: A:0.40, C:0.18, G:0.13, T:0.29
Consensus pattern (57 bp):
AACAACAGCCATTTTAGACAACCATTTCTTCATATGTCAGACATAATAAATTATGAA
Found at i:1589127 original size:15 final size:15
Alignment explanation
Indices: 1589109--1589138 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
1589099 AAAATAAGGG
1589109 TTGAAAAATTAAGTA
1 TTGAAAAATTAAGTA
*
1589124 TTGAAAATTTAAGTA
1 TTGAAAAATTAAGTA
1589139 CCGAATTTTA
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:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (15 bp):
TTGAAAAATTAAGTA
Found at i:1595490 original size:29 final size:28
Alignment explanation
Indices: 1595438--1595521 Score: 84
Period size: 30 Copynumber: 2.9 Consensus size: 28
1595428 AAATTATAAA
1595438 ATTTTGAAAGG-TTAAAAT-GTAATTTATC
1 ATTTT-AAAGGATTAAAATAG-AATTTATC
*
1595466 ATATTTAAAGGGATT-AAATAGAATTGTTTTC
1 AT-TTTAAA-GGATTAAAATAGAA-T-TTATC
1595497 ATTTTAAAGGATTAAAATAGAATTT
1 ATTTTAAAGGATTAAAATAGAATTT
1595522 TTACTATATA
Statistics
Matches: 48, Mismatches: 1, Indels: 14
0.76 0.02 0.22
Matches are distributed among these distances:
28 7 0.15
29 17 0.35
30 18 0.38
31 6 0.12
ACGTcount: A:0.42, C:0.02, G:0.14, T:0.42
Consensus pattern (28 bp):
ATTTTAAAGGATTAAAATAGAATTTATC
Found at i:1596319 original size:18 final size:18
Alignment explanation
Indices: 1596286--1596333 Score: 55
Period size: 17 Copynumber: 2.7 Consensus size: 18
1596276 TAAAATCAAA
*
1596286 AAATAATTTTAATTTTTCT-
1 AAATTATTTT-ATTTTT-TG
1596305 AAATT-TTTTATTTTTTG
1 AAATTATTTTATTTTTTG
1596322 AAATTATTTTAT
1 AAATTATTTTAT
1596334 ACAAAGAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
16 1 0.04
17 11 0.42
18 10 0.38
19 4 0.15
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.62
Consensus pattern (18 bp):
AAATTATTTTATTTTTTG
Found at i:1602092 original size:15 final size:15
Alignment explanation
Indices: 1602072--1602101 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1602062 CTGAACTTGA
1602072 CAACAATTCTCACAT
1 CAACAATTCTCACAT
1602087 CAACAATTCTCACAT
1 CAACAATTCTCACAT
1602102 TAGAGTTTGA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.33, G:0.00, T:0.27
Consensus pattern (15 bp):
CAACAATTCTCACAT
Found at i:1604659 original size:23 final size:23
Alignment explanation
Indices: 1604631--1604677 Score: 94
Period size: 23 Copynumber: 2.0 Consensus size: 23
1604621 GATATATGGC
1604631 AATAATAAATAGAATTAAAGTTT
1 AATAATAAATAGAATTAAAGTTT
1604654 AATAATAAATAGAATTAAAGTTT
1 AATAATAAATAGAATTAAAGTTT
1604677 A
1 A
1604678 GGTATCAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (23 bp):
AATAATAAATAGAATTAAAGTTT
Found at i:1611690 original size:14 final size:14
Alignment explanation
Indices: 1611671--1611701 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
1611661 CAATGAGACT
1611671 TGACTTCGTTGTTA
1 TGACTTCGTTGTTA
1611685 TGACTTCGTTGTTA
1 TGACTTCGTTGTTA
1611699 TGA
1 TGA
1611702 TTTTGAATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.16, C:0.13, G:0.23, T:0.48
Consensus pattern (14 bp):
TGACTTCGTTGTTA
Found at i:1615048 original size:3 final size:3
Alignment explanation
Indices: 1615020--1615119 Score: 107
Period size: 3 Copynumber: 33.7 Consensus size: 3
1615010 TCTACATAAA
* * * * **
1615020 TAT TA- TAT ATAT AAT TAT TAT AAT TAT TAAC CAT TAT TAT GGT T-T
1 TAT TAT TAT -TAT TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT TAT
1615065 TA- TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1615112 TAT TAT TA
1 TAT TAT TA
1615120 GATTTTTCTG
Statistics
Matches: 81, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
2 6 0.07
3 71 0.88
4 4 0.05
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:1615412 original size:18 final size:18
Alignment explanation
Indices: 1615386--1615445 Score: 79
Period size: 18 Copynumber: 3.3 Consensus size: 18
1615376 TAAATAAAAT
*
1615386 AAAGTAAATAAAAGAAACT
1 AAAG-AAATAAAAGAAACA
1615405 AAAGAAATAAAAGAAA-A
1 AAAGAAATAAAAGAAACA
1615422 AAAGAAGA-AAAAGAAACA
1 AAAGAA-ATAAAAGAAACA
1615440 AAAGAA
1 AAAGAA
1615446 CAGCAAAAGC
Statistics
Matches: 38, Mismatches: 1, Indels: 5
0.86 0.02 0.11
Matches are distributed among these distances:
17 14 0.37
18 20 0.53
19 4 0.11
ACGTcount: A:0.77, C:0.03, G:0.13, T:0.07
Consensus pattern (18 bp):
AAAGAAATAAAAGAAACA
Found at i:1615417 original size:9 final size:9
Alignment explanation
Indices: 1615382--1615445 Score: 64
Period size: 9 Copynumber: 7.2 Consensus size: 9
1615372 TAAGTAAATA
1615382 AAAT-AAAG
1 AAATAAAAG
1615390 TAAATAAAAG
1 -AAATAAAAG
1615400 AAACT-AAAG
1 AAA-TAAAAG
1615409 AAATAAAAG
1 AAATAAAAG
1615418 AAA-AAAAG
1 AAATAAAAG
1615426 AAGA-AAAAG
1 AA-ATAAAAG
*
1615435 AAACAAAAG
1 AAATAAAAG
1615444 AA
1 AA
1615446 CAGCAAAAGC
Statistics
Matches: 50, Mismatches: 0, Indels: 10
0.83 0.00 0.17
Matches are distributed among these distances:
8 9 0.18
9 36 0.72
10 5 0.10
ACGTcount: A:0.77, C:0.03, G:0.12, T:0.08
Consensus pattern (9 bp):
AAATAAAAG
Found at i:1615728 original size:24 final size:24
Alignment explanation
Indices: 1615697--1615744 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
1615687 AGAAATTTTG
1615697 ATTGGAATTGAATAAAGGATTGAA
1 ATTGGAATTGAATAAAGGATTGAA
*
1615721 ATTGGAATTTAATAAAGGATTGAA
1 ATTGGAATTGAATAAAGGATTGAA
1615745 TTGTAAACTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.46, C:0.00, G:0.23, T:0.31
Consensus pattern (24 bp):
ATTGGAATTGAATAAAGGATTGAA
Found at i:1616269 original size:21 final size:21
Alignment explanation
Indices: 1616243--1616306 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
1616233 TTGTTTTGAA
1616243 TACTGAATTGAATTGTGAAGT
1 TACTGAATTGAATTGTGAAGT
*
1616264 TACTGAA-T--ATTGTTAAGT
1 TACTGAATTGAATTGTGAAGT
* * *
1616282 GTACTGCATTGAACTGTGAAAT
1 -TACTGAATTGAATTGTGAAGT
1616304 TAC
1 TAC
1616307 CGAAGTAATG
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
18 9 0.26
19 6 0.18
20 2 0.06
21 10 0.29
22 7 0.21
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38
Consensus pattern (21 bp):
TACTGAATTGAATTGTGAAGT
Found at i:1616828 original size:45 final size:45
Alignment explanation
Indices: 1616759--1616859 Score: 141
Period size: 45 Copynumber: 2.2 Consensus size: 45
1616749 GCCGACTACT
* * *
1616759 GTTACTGTTACTGATTCGATACTTTGTGTGTCGAATACTGTTACC
1 GTTACTGTTACAGATTCGACACTTTGTGTGTCGAACACTGTTACC
* *
1616804 GTTACTGTTACAGATTC-AGCACTTTGTGTGTTGAACACTGTTACT
1 GTTACTGTTACAGATTCGA-CACTTTGTGTGTCGAACACTGTTACC
1616849 GTTACTGTTAC
1 GTTACTGTTAC
1616860 TGCTATCGTT
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
44 1 0.02
45 49 0.98
ACGTcount: A:0.21, C:0.18, G:0.20, T:0.42
Consensus pattern (45 bp):
GTTACTGTTACAGATTCGACACTTTGTGTGTCGAACACTGTTACC
Found at i:1616851 original size:6 final size:6
Alignment explanation
Indices: 1616840--1616887 Score: 53
Period size: 6 Copynumber: 7.7 Consensus size: 6
1616830 TGTGTTGAAC
*
1616840 ACTGTT ACTGTT ACTGTT ACTGCT A-TCGTT ACTGATT ACTGATT ACTG
1 ACTGTT ACTGTT ACTGTT ACTGTT ACT-GTT ACTG-TT ACTG-TT ACTG
1616888 ATCAGGTACT
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
5 1 0.03
6 22 0.59
7 14 0.38
ACGTcount: A:0.21, C:0.19, G:0.17, T:0.44
Consensus pattern (6 bp):
ACTGTT
Found at i:1624483 original size:57 final size:58
Alignment explanation
Indices: 1624408--1624555 Score: 162
Period size: 56 Copynumber: 2.6 Consensus size: 58
1624398 ACCGAACAAG
*
1624408 AGCCATTGTAGACAACCATTTCTTCATATGTCAGAA-ATAATAAATTATGAAAAC-GAC
1 AGCCATTTTAGACAACCATTTCTTCATATGTCAGAACATAATAAATTATGAAAACAG-C
* * * * * * *
1624465 GGTCGTTTT-GAACAACCATTTCTT-AAATGTCA-AACATAATAAGTTCTGGAAACAGC
1 AGCCATTTTAG-ACAACCATTTCTTCATATGTCAGAACATAATAAATTATGAAAACAGC
*
1624521 AGCCATTTTAGACAATCATTTCTTCATATGTCAGA
1 AGCCATTTTAGACAACCATTTCTTCATATGTCAGA
1624556 TGAAAACAAC
Statistics
Matches: 72, Mismatches: 13, Indels: 11
0.75 0.14 0.11
Matches are distributed among these distances:
55 2 0.03
56 42 0.58
57 27 0.38
58 1 0.01
ACGTcount: A:0.37, C:0.18, G:0.14, T:0.31
Consensus pattern (58 bp):
AGCCATTTTAGACAACCATTTCTTCATATGTCAGAACATAATAAATTATGAAAACAGC
Found at i:1626174 original size:11 final size:11
Alignment explanation
Indices: 1626136--1626175 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
1626126 AAAATGTAAT
1626136 TTTTTTAATAA
1 TTTTTTAATAA
*
1626147 TTATTTAATAA
1 TTTTTTAATAA
*
1626158 TATTTTTAGTAA
1 T-TTTTTAATAA
1626170 TTTTTT
1 TTTTTT
1626176 TCATGTCATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 16 0.64
12 9 0.36
ACGTcount: A:0.33, C:0.00, G:0.03, T:0.65
Consensus pattern (11 bp):
TTTTTTAATAA
Found at i:1626176 original size:12 final size:12
Alignment explanation
Indices: 1626132--1626176 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
1626122 GAATAAAATG
1626132 TAATTTTTTTAA
1 TAATTTTTTTAA
*
1626144 TAA-TTATTTAA
1 TAATTTTTTTAA
* *
1626155 TAATATTTTTAG
1 TAATTTTTTTAA
1626167 TAATTTTTTT
1 TAATTTTTTT
1626177 CATGTCATTG
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
11 10 0.37
12 17 0.63
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.64
Consensus pattern (12 bp):
TAATTTTTTTAA
Found at i:1626812 original size:15 final size:15
Alignment explanation
Indices: 1626794--1626827 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1626784 GCATAAAAAA
*
1626794 TAAGGGTTGAAAATT
1 TAAGGATTGAAAATT
*
1626809 TAAGTATTGAAAATT
1 TAAGGATTGAAAATT
1626824 TAAG
1 TAAG
1626828 TACCGAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.35
Consensus pattern (15 bp):
TAAGGATTGAAAATT
Found at i:1626828 original size:15 final size:15
Alignment explanation
Indices: 1626800--1626829 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1626790 AAAATAAGGG
1626800 TTGAAAATTTAAGTA
1 TTGAAAATTTAAGTA
1626815 TTGAAAATTTAAGTA
1 TTGAAAATTTAAGTA
1626830 CCGAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (15 bp):
TTGAAAATTTAAGTA
Found at i:1627076 original size:20 final size:20
Alignment explanation
Indices: 1627048--1627089 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1627038 TTTTCCCGTT
* *
1627048 TATTCATTTTTTTATATTTA
1 TATTCATTTATCTATATTTA
*
1627068 TATTTATTTATCTATATTTA
1 TATTCATTTATCTATATTTA
1627088 TA
1 TA
1627090 GCCAAAATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (20 bp):
TATTCATTTATCTATATTTA
Found at i:1629577 original size:25 final size:25
Alignment explanation
Indices: 1629543--1629593 Score: 102
Period size: 25 Copynumber: 2.0 Consensus size: 25
1629533 ACTTCGGATG
1629543 TTCCGATGATGTAACACCTCTTACC
1 TTCCGATGATGTAACACCTCTTACC
1629568 TTCCGATGATGTAACACCTCTTACC
1 TTCCGATGATGTAACACCTCTTACC
1629593 T
1 T
1629594 AACTCATTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.24, C:0.31, G:0.12, T:0.33
Consensus pattern (25 bp):
TTCCGATGATGTAACACCTCTTACC
Found at i:1636235 original size:34 final size:36
Alignment explanation
Indices: 1636161--1636235 Score: 84
Period size: 38 Copynumber: 2.1 Consensus size: 36
1636151 TTGATTTTTA
* *
1636161 TATTTATTAATCTATACCTATATGGTAAGAGAGCGGTT
1 TATTTATTAATCTATACCTATA-GATAAGAAAGC-GTT
1636199 TATTTATTAATCTATACCTATA-AT-AGCAAAGC-TT
1 TATTTATTAATCTATACCTATAGATAAG-AAAGCGTT
1636233 TAT
1 TAT
1636236 CGAGCCGAAG
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
34 5 0.15
35 2 0.06
36 5 0.15
38 22 0.65
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (36 bp):
TATTTATTAATCTATACCTATAGATAAGAAAGCGTT
Found at i:1637850 original size:57 final size:57
Alignment explanation
Indices: 1637780--1637933 Score: 175
Period size: 56 Copynumber: 2.7 Consensus size: 57
1637770 ACCATAACCG
1637780 AACAACAGCCATTTTAGACAACCATTTCCTCATATGTCAGACATAATAAATTATGAA
1 AACAACAGCCATTTTAGACAACCATTTCCTCATATGTCAGACATAATAAATTATGAA
* * * * * * * * * **
1637837 AACAACGGTCATTTTGGACAACCATTT-CTTAAATATCAGATATAATAAGTTCTGGT
1 AACAACAGCCATTTTAGACAACCATTTCCTCATATGTCAGACATAATAAATTATGAA
* * *
1637893 AACAGCAGCCATTTTAGACAATCATTTCTTCATATGTCAGA
1 AACAACAGCCATTTTAGACAACCATTTCCTCATATGTCAGA
1637934 TGAAAATACC
Statistics
Matches: 76, Mismatches: 20, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
56 43 0.57
57 33 0.43
ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31
Consensus pattern (57 bp):
AACAACAGCCATTTTAGACAACCATTTCCTCATATGTCAGACATAATAAATTATGAA
Found at i:1640817 original size:6 final size:6
Alignment explanation
Indices: 1640806--1640849 Score: 61
Period size: 6 Copynumber: 7.0 Consensus size: 6
1640796 TTATTGATTT
*
1640806 TTTATA TTTATA TTTATA TTTATA TTTATTTA TTAATA TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTA--TA TTTATA TTTATA
1640850 GCCAAAATTA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 29 0.85
8 5 0.15
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (6 bp):
TTTATA
Found at i:1645101 original size:26 final size:25
Alignment explanation
Indices: 1645050--1645108 Score: 64
Period size: 26 Copynumber: 2.3 Consensus size: 25
1645040 AATATTTGTA
* *
1645050 TTATATTATTTTAATATTTAATATTT
1 TTATA-TATTTTAATATTAAAAATTT
*
1645076 TTATATATTTTATTCATTAAAAATTT
1 TTATATATTTTAAT-ATTAAAAATTT
*
1645102 TCATATA
1 TTATATA
1645109 GTCATCTTAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
25 8 0.29
26 20 0.71
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.59
Consensus pattern (25 bp):
TTATATATTTTAATATTAAAAATTT
Found at i:1648232 original size:23 final size:23
Alignment explanation
Indices: 1648205--1648248 Score: 88
Period size: 23 Copynumber: 1.9 Consensus size: 23
1648195 AACTGGACGC
1648205 ACTTTCATACAATCTCATCAAGT
1 ACTTTCATACAATCTCATCAAGT
1648228 ACTTTCATACAATCTCATCAA
1 ACTTTCATACAATCTCATCAA
1648249 AATTAACCTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.36, C:0.27, G:0.02, T:0.34
Consensus pattern (23 bp):
ACTTTCATACAATCTCATCAAGT
Found at i:1650313 original size:49 final size:49
Alignment explanation
Indices: 1650241--1650346 Score: 151
Period size: 49 Copynumber: 2.1 Consensus size: 49
1650231 AATTTTGAAG
* * *
1650241 ACAACATTGTTAGAAGGGACAGCCATGAATTCCAAACATAAATCATAAA
1 ACAACATTGTTAGAAGGGACAGCCACGAACTCCAAACATAAACCATAAA
*
1650290 ACAACATTGTTAGAAGAGG-CAGCCACGAACTCTAAACATAAACCATAAA
1 ACAACATTGTTAGAAG-GGACAGCCACGAACTCCAAACATAAACCATAAA
1650339 ACAGACAT
1 ACA-ACAT
1650347 ACATAATAAT
Statistics
Matches: 51, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
49 45 0.88
50 6 0.12
ACGTcount: A:0.47, C:0.21, G:0.14, T:0.18
Consensus pattern (49 bp):
ACAACATTGTTAGAAGGGACAGCCACGAACTCCAAACATAAACCATAAA
Found at i:1653527 original size:86 final size:86
Alignment explanation
Indices: 1653382--1653549 Score: 309
Period size: 86 Copynumber: 2.0 Consensus size: 86
1653372 GATTGTATTT
1653382 AGGCTGACCAAGAACAGTCCAAATCCCCCCACCTAAAACAATTATATAATGGCCACTAGTTTACT
1 AGGCTGACCAAGAACAGTCCAAATCCCCCCACCTAAAACAATTATATAATGGCCACTAGTTTACT
1653447 TCACAAAACAAAGACCAAGAC
66 TCACAAAACAAAGACCAAGAC
* *
1653468 AGGCTGACCAAGAACAGTCCAAATCCCCCCACCTAAAACAATTATATAATGTCCCCTAGTTTACT
1 AGGCTGACCAAGAACAGTCCAAATCCCCCCACCTAAAACAATTATATAATGGCCACTAGTTTACT
*
1653533 TCACAAAACAGAGACCA
66 TCACAAAACAAAGACCA
1653550 CCATGGATGA
Statistics
Matches: 79, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
86 79 1.00
ACGTcount: A:0.40, C:0.30, G:0.11, T:0.18
Consensus pattern (86 bp):
AGGCTGACCAAGAACAGTCCAAATCCCCCCACCTAAAACAATTATATAATGGCCACTAGTTTACT
TCACAAAACAAAGACCAAGAC
Found at i:1656668 original size:6 final size:6
Alignment explanation
Indices: 1656657--1656690 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
1656647 TTACCTCAAC
1656657 CCCACT CCCACT CCCACT CCCACT CCCACT CCCA
1 CCCACT CCCACT CCCACT CCCACT CCCACT CCCA
1656691 TTCCACTTTA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.18, C:0.68, G:0.00, T:0.15
Consensus pattern (6 bp):
CCCACT
Found at i:1657110 original size:34 final size:35
Alignment explanation
Indices: 1657066--1657132 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
1657056 CAGTAAAATA
*
1657066 TTTTCCGTAAAATGATTT-CGGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
* *
1657100 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACGGGAAAATATTTT
1657133 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 17 0.59
35 12 0.41
ACGTcount: A:0.31, C:0.09, G:0.15, T:0.45
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACGGGAAAATATTTTAC
Found at i:1663682 original size:17 final size:17
Alignment explanation
Indices: 1663660--1663692 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
1663650 TAAAGAAAGA
1663660 AAGAAGAAAGTAGGAGG
1 AAGAAGAAAGTAGGAGG
*
1663677 AAGAAGGAAGTAGGAG
1 AAGAAGAAAGTAGGAG
1663693 AGGACACTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.52, C:0.00, G:0.42, T:0.06
Consensus pattern (17 bp):
AAGAAGAAAGTAGGAGG
Found at i:1665572 original size:26 final size:27
Alignment explanation
Indices: 1665524--1665578 Score: 103
Period size: 26 Copynumber: 2.1 Consensus size: 27
1665514 TCTAAAATAG
1665524 TAGCAAAATTGACAATAAAATAAGAGT
1 TAGCAAAATTGACAATAAAATAAGAGT
1665551 TAGCAAAATTG-CAATAAAATAAGAGT
1 TAGCAAAATTGACAATAAAATAAGAGT
1665577 TA
1 TA
1665579 TACAATATCC
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 17 0.61
27 11 0.39
ACGTcount: A:0.55, C:0.07, G:0.15, T:0.24
Consensus pattern (27 bp):
TAGCAAAATTGACAATAAAATAAGAGT
Found at i:1667560 original size:24 final size:25
Alignment explanation
Indices: 1667519--1667566 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
1667509 TTATGGCTGG
1667519 TTGATTTAAGGTCACAAAATCTTGA
1 TTGATTTAAGGTCACAAAATCTTGA
*
1667544 TTGATTT-ATGTCACAAAATCTTG
1 TTGATTTAAGGTCACAAAATCTTG
1667567 TTGGTGGTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (25 bp):
TTGATTTAAGGTCACAAAATCTTGA
Found at i:1670446 original size:49 final size:49
Alignment explanation
Indices: 1670354--1670447 Score: 136
Period size: 49 Copynumber: 1.9 Consensus size: 49
1670344 AGGCTGATGG
* *
1670354 GTAAATATTTATTAAAACAACGTAATTTTTCCTTTTAACTTTAGAGGAA
1 GTAAATATTTATCAAAACAACGTAATTTTGCCTTTTAACTTTAGAGGAA
* *
1670403 GTAAATATTTATCAAAACAATGTAATTTTGCACTTTTTA-TTTAGA
1 GTAAATATTTATCAAAACAACGTAATTTTGC-CTTTTAACTTTAGA
1670448 TTTTCATATA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
49 34 0.85
50 6 0.15
ACGTcount: A:0.38, C:0.10, G:0.10, T:0.43
Consensus pattern (49 bp):
GTAAATATTTATCAAAACAACGTAATTTTGCCTTTTAACTTTAGAGGAA
Found at i:1671809 original size:22 final size:23
Alignment explanation
Indices: 1671775--1671819 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
1671765 ATTTCTTAAA
* * *
1671775 TATTATTTTTTTAT-GAATTTAT
1 TATTATATCTTTATCGAACTTAT
1671797 TATTATATCTTTATCGAACTTAT
1 TATTATATCTTTATCGAACTTAT
1671820 CAAATCGAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.60
Consensus pattern (23 bp):
TATTATATCTTTATCGAACTTAT
Found at i:1673467 original size:15 final size:15
Alignment explanation
Indices: 1673449--1673482 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1673439 GCAGAAAAAA
*
1673449 TAAGGGTTGAAAATT
1 TAAGGATTGAAAATT
*
1673464 TAAGTATTGAAAATT
1 TAAGGATTGAAAATT
1673479 TAAG
1 TAAG
1673483 TACCGAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.35
Consensus pattern (15 bp):
TAAGGATTGAAAATT
Found at i:1673483 original size:15 final size:15
Alignment explanation
Indices: 1673455--1673484 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1673445 AAAATAAGGG
1673455 TTGAAAATTTAAGTA
1 TTGAAAATTTAAGTA
1673470 TTGAAAATTTAAGTA
1 TTGAAAATTTAAGTA
1673485 CCGAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (15 bp):
TTGAAAATTTAAGTA
Found at i:1676870 original size:22 final size:22
Alignment explanation
Indices: 1676845--1676895 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
1676835 TTTTCCACAA
*
1676845 ATTAATCCATGATTTTTGAACC
1 ATTAAACCATGATTTTTGAACC
*
1676867 ATTAAACTATGATTTTTGAACC
1 ATTAAACCATGATTTTTGAACC
1676889 ATTAAAC
1 ATTAAAC
1676896 TTTCATATTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.37, C:0.16, G:0.08, T:0.39
Consensus pattern (22 bp):
ATTAAACCATGATTTTTGAACC
Found at i:1676896 original size:22 final size:22
Alignment explanation
Indices: 1676853--1676896 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
1676843 AAATTAATCC
1676853 ATGATTTTTGAACCATTAAACT
1 ATGATTTTTGAACCATTAAACT
1676875 ATGATTTTTGAACCATTAAACT
1 ATGATTTTTGAACCATTAAACT
1676897 TTCATATTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.14, G:0.09, T:0.41
Consensus pattern (22 bp):
ATGATTTTTGAACCATTAAACT
Found at i:1678496 original size:29 final size:31
Alignment explanation
Indices: 1678444--1678510 Score: 72
Period size: 29 Copynumber: 2.3 Consensus size: 31
1678434 TTACTTTTCA
*
1678444 TATATTT--GGAATTTAGTTGATTTA-ATTT
1 TATATTTCAGGAATTTAATTGATTTACATTT
*
1678472 TAT-TTTCAGGAATTTAATT-ATTTTACTTTT
1 TATATTTCAGGAATTTAATTGA-TTTACATTT
1678502 TATATTTCA
1 TATATTTCA
1678511 AAATTTATGT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
27 3 0.09
28 4 0.12
29 14 0.44
30 6 0.19
31 5 0.16
ACGTcount: A:0.28, C:0.04, G:0.09, T:0.58
Consensus pattern (31 bp):
TATATTTCAGGAATTTAATTGATTTACATTT
Found at i:1680015 original size:15 final size:16
Alignment explanation
Indices: 1679987--1680019 Score: 50
Period size: 15 Copynumber: 2.1 Consensus size: 16
1679977 TTTTTATAGG
*
1679987 ATAACATAATATTAAA
1 ATAACATAAAATTAAA
1680003 ATAA-ATAAAATTAAA
1 ATAACATAAAATTAAA
1680018 AT
1 AT
1680020 TGGTTTATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
15 12 0.75
16 4 0.25
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.30
Consensus pattern (16 bp):
ATAACATAAAATTAAA
Found at i:1683258 original size:56 final size:57
Alignment explanation
Indices: 1683192--1683339 Score: 185
Period size: 57 Copynumber: 2.6 Consensus size: 57
1683182 ACCATAACCG
** * *
1683192 AACAACAGCCATTTTGGACAACCATTTCTT-AAATGTCAGACATGATA-AGTTCTGGA
1 AACAACAGCCATTTTGGACAACCATTTCTTCAAATGTCAGACAAAATATA-TTATGAA
* * * *
1683248 AACAGCAGCCATTTTAGG-CAATCATATCTTCATATGTCAGACAAAATATATTATGAA
1 AACAACAGCCATTTT-GGACAACCATTTCTTCAAATGTCAGACAAAATATATTATGAA
1683305 AACAACAGCCATTTTGGACAACCATTTCTTCAAAT
1 AACAACAGCCATTTTGGACAACCATTTCTTCAAAT
1683340 TTCCAACACG
Statistics
Matches: 76, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
56 26 0.34
57 49 0.64
58 1 0.01
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.29
Consensus pattern (57 bp):
AACAACAGCCATTTTGGACAACCATTTCTTCAAATGTCAGACAAAATATATTATGAA
Found at i:1684327 original size:22 final size:23
Alignment explanation
Indices: 1684293--1684337 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 23
1684283 ATTTCTTAAA
* * *
1684293 TATTATTTTTTTAT-GAATTTAT
1 TATTATATCTTTATCGAACTTAT
1684315 TATTATATCTTTATCGAACTTAT
1 TATTATATCTTTATCGAACTTAT
1684338 CAAATCGAAG
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
22 12 0.63
23 7 0.37
ACGTcount: A:0.29, C:0.07, G:0.04, T:0.60
Consensus pattern (23 bp):
TATTATATCTTTATCGAACTTAT
Found at i:1685410 original size:20 final size:20
Alignment explanation
Indices: 1685382--1685423 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
1685372 TTTTCCCGTT
* *
1685382 TATTCATTTTTTTATATTTA
1 TATTCATTTATCTATATTTA
*
1685402 TATTTATTTATCTATATTTA
1 TATTCATTTATCTATATTTA
1685422 TA
1 TA
1685424 GCCAAAATTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.67
Consensus pattern (20 bp):
TATTCATTTATCTATATTTA
Found at i:1686026 original size:15 final size:15
Alignment explanation
Indices: 1686008--1686041 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
1685998 GCATAAAAAA
*
1686008 TAAGGGTTGAAAATT
1 TAAGGATTGAAAATT
*
1686023 TAAGTATTGAAAATT
1 TAAGGATTGAAAATT
1686038 TAAG
1 TAAG
1686042 TACCGAATTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.44, C:0.00, G:0.21, T:0.35
Consensus pattern (15 bp):
TAAGGATTGAAAATT
Found at i:1686042 original size:15 final size:15
Alignment explanation
Indices: 1686014--1686043 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
1686004 AAAATAAGGG
1686014 TTGAAAATTTAAGTA
1 TTGAAAATTTAAGTA
1686029 TTGAAAATTTAAGTA
1 TTGAAAATTTAAGTA
1686044 CCGAATTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.13, T:0.40
Consensus pattern (15 bp):
TTGAAAATTTAAGTA
Found at i:1691758 original size:29 final size:28
Alignment explanation
Indices: 1691706--1691789 Score: 84
Period size: 30 Copynumber: 2.9 Consensus size: 28
1691696 AAATTATAAA
1691706 ATTTTGAAAGG-TTAAAAT-GTAATTTATC
1 ATTTT-AAAGGATTAAAATAG-AATTTATC
*
1691734 ATATTTAAAGGGATT-AAATAGAATTGTTTTC
1 AT-TTTAAA-GGATTAAAATAGAA-T-TTATC
1691765 ATTTTAAAGGATTAAAATAGAATTT
1 ATTTTAAAGGATTAAAATAGAATTT
1691790 TTACTATATA
Statistics
Matches: 48, Mismatches: 1, Indels: 14
0.76 0.02 0.22
Matches are distributed among these distances:
28 7 0.15
29 17 0.35
30 18 0.38
31 6 0.12
ACGTcount: A:0.42, C:0.02, G:0.14, T:0.42
Consensus pattern (28 bp):
ATTTTAAAGGATTAAAATAGAATTTATC
Found at i:1697624 original size:59 final size:57
Alignment explanation
Indices: 1697516--1697627 Score: 143
Period size: 57 Copynumber: 1.9 Consensus size: 57
1697506 TTTTTTTTTT
*
1697516 TAATTTGGTACTTAAATTTAATATTTTTTTAAGATGATATTTAAACTTTTTTAGGTC
1 TAATTTGGTACTTAAATTTAATATTTTTTTAAGATGATACTTAAACTTTTTTAGGTC
* * ** * *
1697573 TAATTTGGTACTTAAATTTGACTCTTTTTTCTAATTTGATACTTGATCTTTTTTA
1 TAATTTGGTACTTAAATTT-AATATTTTTT-TAAGATGATACTTAAACTTTTTTA
1697628 TTTTTGTTTG
Statistics
Matches: 46, Mismatches: 7, Indels: 2
0.84 0.13 0.04
Matches are distributed among these distances:
57 19 0.41
58 8 0.17
59 19 0.41
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.54
Consensus pattern (57 bp):
TAATTTGGTACTTAAATTTAATATTTTTTTAAGATGATACTTAAACTTTTTTAGGTC
Found at i:1703839 original size:30 final size:30
Alignment explanation
Indices: 1703805--1703869 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 30
1703795 TAATCCTCCA
*
1703805 CCCAAAGTTTTGAAAAATTACAATTTTGCC
1 CCCAAACTTTTGAAAAATTACAATTTTGCC
* * *
1703835 CCCAAACTTTTGAATAATTACATTTTTGTC
1 CCCAAACTTTTGAAAAATTACAATTTTGCC
1703865 CCCAA
1 CCCAA
1703870 GCTCGGAAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.34, C:0.23, G:0.08, T:0.35
Consensus pattern (30 bp):
CCCAAACTTTTGAAAAATTACAATTTTGCC
Found at i:1709161 original size:10 final size:11
Alignment explanation
Indices: 1709149--1709200 Score: 56
Period size: 10 Copynumber: 4.9 Consensus size: 11
1709139 GTTTTTTTAA
1709149 TTTTAAAATAT
1 TTTTAAAATAT
1709160 TTTTAAAATACT
1 TTTTAAAATA-T
**
1709172 TTTT-TTA-AT
1 TTTTAAAATAT
1709181 TTTTAAAA-AT
1 TTTTAAAATAT
1709191 TTTTAAAATA
1 TTTTAAAATA
1709201 AAAATGGGCC
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
9 5 0.15
10 12 0.35
11 12 0.35
12 5 0.15
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:1709175 original size:31 final size:32
Alignment explanation
Indices: 1709117--1709200 Score: 113
Period size: 31 Copynumber: 2.7 Consensus size: 32
1709107 NNNNNNAAAT
* *
1709117 ATTTTTAAAATACTTTTT-TAAT-GTTTTTTTA
1 ATTTTTAAAATA-TTTTTAAAATACTTTTTTTA
1709148 A-TTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATATTTTTAAAATACTTTTTTTA
1709179 ATTTTTAAAA-ATTTTTAAAATA
1 ATTTTTAAAATATTTTTAAAATA
1709201 AAAATGGGCC
Statistics
Matches: 48, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
29 5 0.10
30 13 0.27
31 22 0.46
32 8 0.17
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.58
Consensus pattern (32 bp):
ATTTTTAAAATATTTTTAAAATACTTTTTTTA
Found at i:1709192 original size:41 final size:42
Alignment explanation
Indices: 1709113--1709200 Score: 126
Period size: 41 Copynumber: 2.1 Consensus size: 42
1709103 NNNNNNNNNN
***
1709113 AAATATTTTTAAAATACTTTTTTAATGTTTTTTTAA-TTTTA
1 AAATATTTTTAAAATACTTTTTTAATGTTTTAAAAATTTTTA
1709154 AAATATTTTTAAAATACTTTTTTTAAT-TTTTAAAAATTTTTA
1 AAATATTTTTAAAATAC-TTTTTTAATGTTTTAAAAATTTTTA
1709196 AAATA
1 AAATA
1709201 AAAATGGGCC
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
41 23 0.55
42 19 0.45
ACGTcount: A:0.40, C:0.02, G:0.01, T:0.57
Consensus pattern (42 bp):
AAATATTTTTAAAATACTTTTTTAATGTTTTAAAAATTTTTA
Found at i:1711818 original size:30 final size:29
Alignment explanation
Indices: 1711784--1711848 Score: 76
Period size: 30 Copynumber: 2.2 Consensus size: 29
1711774 TAATCCTCCA
1711784 CCCAACTTTTTGAAAAATTACAATTTTGCC
1 CCCAAC-TTTTGAAAAATTACAATTTTGCC
* * * *
1711814 CCCAAACTTTTGCATAATTACATTTTTGTC
1 CCC-AACTTTTGAAAAATTACAATTTTGCC
1711844 CCCAA
1 CCCAA
1711849 GCTCGGAAGT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
29 2 0.07
30 25 0.83
31 3 0.10
ACGTcount: A:0.31, C:0.26, G:0.06, T:0.37
Consensus pattern (29 bp):
CCCAACTTTTGAAAAATTACAATTTTGCC
Found at i:1711822 original size:31 final size:30
Alignment explanation
Indices: 1711791--1711848 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
1711781 CCACCCAACT
1711791 TTTTGAAAAATTACAATTTTGCCCCCAAAC
1 TTTTGAAAAATTACAATTTTGCCCCCAAAC
* * * *
1711821 TTTTGCATAATTACATTTTTGTCCCCAA
1 TTTTGAAAAATTACAATTTTGCCCCCAA
1711849 GCTCGGAAGT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (30 bp):
TTTTGAAAAATTACAATTTTGCCCCCAAAC
Found at i:1719640 original size:65 final size:66
Alignment explanation
Indices: 1719548--1719680 Score: 214
Period size: 66 Copynumber: 2.0 Consensus size: 66
1719538 GCTATGCCCG
* ** * *
1719548 AACAGTCATGGACTGACTTAATTGCTGAG-CATTCATCTGGATAAATTCGGTTCTTGAGCTGGAG
1 AACAGCCATGGACTGACGAAATAGCTGAGTAATTCATCTGGATAAATTCGGTTCTTGAGCTGGAG
1719612 T
66 T
1719613 AACAGCCATGGACTGACGAAATAGCTGAGTAATTCATCTGGATAAATTCGGTTCTTGAGCTGGAG
1 AACAGCCATGGACTGACGAAATAGCTGAGTAATTCATCTGGATAAATTCGGTTCTTGAGCTGGAG
1719678 T
66 T
1719679 AA
1 AA
1719681 TTGAGTCAGC
Statistics
Matches: 62, Mismatches: 5, Indels: 1
0.91 0.07 0.01
Matches are distributed among these distances:
65 25 0.40
66 37 0.60
ACGTcount: A:0.29, C:0.17, G:0.25, T:0.29
Consensus pattern (66 bp):
AACAGCCATGGACTGACGAAATAGCTGAGTAATTCATCTGGATAAATTCGGTTCTTGAGCTGGAG
T
Found at i:1720275 original size:26 final size:25
Alignment explanation
Indices: 1720221--1720275 Score: 65
Period size: 26 Copynumber: 2.2 Consensus size: 25
1720211 TGAGTCACAA
* * *
1720221 TTAAGTTGTCTAAATTAAGACCTAT
1 TTAAGTTGTCTAAACTAAGACCAAG
*
1720246 TTAATTTGTTCTAAACTAAGACCAAG
1 TTAAGTTG-TCTAAACTAAGACCAAG
1720272 TTAA
1 TTAA
1720276 ATCTCATATT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
25 7 0.28
26 18 0.72
ACGTcount: A:0.38, C:0.13, G:0.11, T:0.38
Consensus pattern (25 bp):
TTAAGTTGTCTAAACTAAGACCAAG
Found at i:1728479 original size:20 final size:20
Alignment explanation
Indices: 1728440--1728479 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
1728430 GTCTTTAATA
**
1728440 ATATACTTTAAGTTTTAAAT
1 ATATACTTTAAGTTGAAAAT
*
1728460 ATATATTTTAAGTTGAAAAT
1 ATATACTTTAAGTTGAAAAT
1728480 TTTACTATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.03, G:0.07, T:0.47
Consensus pattern (20 bp):
ATATACTTTAAGTTGAAAAT
Found at i:1740334 original size:606 final size:591
Alignment explanation
Indices: 1739138--1740336 Score: 2148
Period size: 606 Copynumber: 2.0 Consensus size: 591
1739128 TATGTTTGGA
*
1739138 ATCTTCAGATGATCCGAATGTGGGTTCAAGAGATTGAAGTACCTTTTAGAGTTCATTTAGGTTTT
1 ATCTTCAGATGATACGAATGTGGGTTCAAGAGATTGAAGTACCTTTTAGAGTTCATTTAGGTTTT
1739203 TTTTTTTTTAAAGAATAAGGAAGAAAATGTTCTTTATTAATGGAAAAAGTGTTTAGTTTAATTTA
66 TTTTTTTTTAAAGAATAAGGAAGAAAATGTTCTTTATTAATGGAAAAAGTGTTTAGTTTAATTTA
* *
1739268 TTAATATTTTAAAATTAGCAGCTTAATATTAAATTATTTAAGAATTTGAAATTTTAAAAATAATG
131 TTAATATTTTAAAATGAGCAGCTTAATATTAAATTATTTAAGAATTTGAAATTTTAAAAATAATA
1739333 ATTAAAAAAAAGTCAGACATTAAGTTTTAATATTTAATTTTTTTAATTTTATAAAATAATTAATT
196 ATTAAAAAAAAGTCAGACATTAAGTTTTAATATTTAATTTTTTTAATTTTATAAAATAATTAATT
1739398 TCTAATGACATGATACACGTGTATTTTCATGAATGTCACATAAACGTCAATCATTCCCATCATCA
261 TCTAATGACATGATACACGTGTATTTTCATGAATGTCACATAAACGTCAATCATTCCCATCATCA
1739463 AAATTAACGACTCGTTAATTTTTTCACCTAATTCTGAATAATTTGATAAAAAGAAAAATAAAAGA
326 AAATTAACGACTCGTTAATTTTTTCACCTAATTCTGAATAATTTGATAAAAAGAAAAATAAAAGA
1739528 AATGGGGTTGTTCTTAATATTTTGAGGGCAAAGAAAAAAAAAAGGACTTTTTGCCTAAATTGACT
391 AATGGGGTTGTTCTTAATATTTTGAGGGCAAAGAAAAAAAAAAGGACTTTTTGCCTAAATTGACT
*
1739593 TTATTCTTTTCTAAGTTGTGAAAAGTGCTGATTTATCTTTGAAATGAAATTACAATAAAATCTGA
456 TTATTCTTTTCTAAGTTGTGAAAAGTGCTGATTTATCTTTAAAATGAAATTACAATAAAATCTGA
1739658 TGGAAAATTCAAAAAATTTAGAATAAGATCTAAAACAAAGAAAAAATTATTTTCTAGAATTTAGG
521 TGGAAAATTCAAAAAATTTAGAATAAGATCTAAAACAAAGAAAAAATTATTTTCTAGAATTTAGG
1739723 CATAAT
586 CATAAT
*
1739729 ATCTTCAGATGATACGAATGTGGGTTCGAGAGATTGAAGTACCTTTTAGAGTTCATTTAGGTTTT
1 ATCTTCAGATGATACGAATGTGGGTTCAAGAGATTGAAGTACCTTTTAGAGTTCATTTAGGTTTT
1739794 GTTTTTTTTTAAAGAATAAGGAAGAAAATGTTCTTTATTAATGGAAAAAGTGTTTAGTTTAATTT
66 -TTTTTTTTTAAAGAATAAGGAAGAAAATGTTCTTTATTAATGGAAAAAGTGTTTAGTTTAATTT
1739859 ATTAATATTTTAAAATGAGCAGCTTAATATTAAATTATTTAAGAATTTGAAATTTTAAAAATAAT
130 ATTAATATTTTAAAATGAGCAGCTTAATATTAAATTATTTAAGAATTTGAAATTTTAAAAATAAT
1739924 AATTAAAAAAAAGTCAGACATTAAGTTTTAATATTTAATATTTTTTTAATTTTATAAAATAATTA
195 AATTAAAAAAAAGTCAGACATTAAGTTTTAATATTT-A-ATTTTTTTAATTTTATAAAATAATTA
* *
1739989 ATTTCTAATGACGTGATACACGTGTATTTTCATGAATGTCACGTAAACGTCAATCATTCCCATCA
258 ATTTCTAATGACATGATACACGTGTATTTTCATGAATGTCACATAAACGTCAATCATTCCCATCA
* *
1740054 TCAAAATTAATGACTCGTTAATTTTTTCACCTAATTCTGGATAATTTGATAAAAATAAAAATTAA
323 TCAAAATTAACGACTCGTTAATTTTTTCACCTAATTCTGAATAATTTG------------A-TAA
* *
1740119 AAAGCAAAATAAAAGAAATGGGGTTTTTCTTAATATTTTGAGGGCAAAG-AAAAAAAAAGGACTT
375 AAAGAAAAATAAAAGAAATGGGGTTGTTCTTAATATTTTGAGGGCAAAGAAAAAAAAAAGGACTT
1740183 TTTGCCTAAATTGACTTTATTCTTTTCTAAGTTGTGAAAAGTGCTGATTTATCTTTAAAATGAAA
440 TTTGCCTAAATTGACTTTATTCTTTTCTAAGTTGTGAAAAGTGCTGATTTATCTTTAAAATGAAA
1740248 TTACAATAAAATCTGATGGAAAATTCAAAAAATTTAGAATAAGATCTAAAACAAAGAAAAAATTA
505 TTACAATAAAATCTGATGGAAAATTCAAAAAATTTAGAATAAGATCTAAAACAAAGAAAAAATTA
1740313 TTTTCTAGAATTTAGGCATAAT
570 TTTTCTAGAATTTAGGCATAAT
1740335 AT
1 AT
1740337 TATTATTTTG
Statistics
Matches: 581, Mismatches: 11, Indels: 17
0.95 0.02 0.03
Matches are distributed among these distances:
591 63 0.11
592 163 0.28
593 1 0.00
594 135 0.23
606 169 0.29
607 50 0.09
ACGTcount: A:0.41, C:0.09, G:0.13, T:0.38
Consensus pattern (591 bp):
ATCTTCAGATGATACGAATGTGGGTTCAAGAGATTGAAGTACCTTTTAGAGTTCATTTAGGTTTT
TTTTTTTTTAAAGAATAAGGAAGAAAATGTTCTTTATTAATGGAAAAAGTGTTTAGTTTAATTTA
TTAATATTTTAAAATGAGCAGCTTAATATTAAATTATTTAAGAATTTGAAATTTTAAAAATAATA
ATTAAAAAAAAGTCAGACATTAAGTTTTAATATTTAATTTTTTTAATTTTATAAAATAATTAATT
TCTAATGACATGATACACGTGTATTTTCATGAATGTCACATAAACGTCAATCATTCCCATCATCA
AAATTAACGACTCGTTAATTTTTTCACCTAATTCTGAATAATTTGATAAAAAGAAAAATAAAAGA
AATGGGGTTGTTCTTAATATTTTGAGGGCAAAGAAAAAAAAAAGGACTTTTTGCCTAAATTGACT
TTATTCTTTTCTAAGTTGTGAAAAGTGCTGATTTATCTTTAAAATGAAATTACAATAAAATCTGA
TGGAAAATTCAAAAAATTTAGAATAAGATCTAAAACAAAGAAAAAATTATTTTCTAGAATTTAGG
CATAAT
Found at i:1740481 original size:24 final size:25
Alignment explanation
Indices: 1740440--1740487 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 25
1740430 TTATGGCTGG
1740440 TTGATTTAAGGTCACAAAATCTTGA
1 TTGATTTAAGGTCACAAAATCTTGA
*
1740465 TTGATTT-ATGTCACAAAATCTTG
1 TTGATTTAAGGTCACAAAATCTTG
1740488 TTGGTGGTGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 15 0.68
25 7 0.32
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.40
Consensus pattern (25 bp):
TTGATTTAAGGTCACAAAATCTTGA
Found at i:1746277 original size:19 final size:19
Alignment explanation
Indices: 1746253--1746290 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
1746243 TTCAATTAAG
*
1746253 TCTTTCATT-AAGTGTTTTT
1 TCTTTC-TTCAAGTATTTTT
1746272 TCTTTCTTCAAGTATTTTT
1 TCTTTCTTCAAGTATTTTT
1746291 CATCTAGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.12
19 15 0.88
ACGTcount: A:0.16, C:0.13, G:0.08, T:0.63
Consensus pattern (19 bp):
TCTTTCTTCAAGTATTTTT
Found at i:1746339 original size:12 final size:12
Alignment explanation
Indices: 1746279--1746379 Score: 60
Period size: 12 Copynumber: 7.8 Consensus size: 12
1746269 TTTTCTTTCT
1746279 TCAAGTATTTTTCA
1 TCAAGT-TTTTT-A
*
1746293 TCTAGTTCTTTTA
1 TCAAGTT-TTTTA
1746306 TCAAGTTTTAAATTA
1 TCAAGTTTT---TTA
*
1746321 CCAAGTTTTTTA
1 TCAAGTTTTTTA
**
1746333 TCAAGTTTTGCA
1 TCAAGTTTTTTA
*
1746345 GCAAGTTCTTTT-
1 TCAAGTT-TTTTA
* *
1746357 TAAAGTTTTTCA
1 TCAAGTTTTTTA
1746369 TCAAGTCTTTT
1 TCAAGT-TTTT
1746380 CCTAAAATTT
Statistics
Matches: 67, Mismatches: 13, Indels: 15
0.71 0.14 0.16
Matches are distributed among these distances:
11 3 0.04
12 30 0.45
13 14 0.21
14 9 0.13
15 11 0.16
ACGTcount: A:0.26, C:0.14, G:0.10, T:0.50
Consensus pattern (12 bp):
TCAAGTTTTTTA
Found at i:1746385 original size:25 final size:23
Alignment explanation
Indices: 1746322--1746403 Score: 69
Period size: 24 Copynumber: 3.4 Consensus size: 23
1746312 TTTAAATTAC
* *
1746322 CAAGT-TTTTTATCAAGTTTTGCAG
1 CAAGTCTTTTTA--AAGTTTTCCAT
*
1746346 CAAGTTCTTTTTAAAGTTTTTCAT
1 CAAG-TCTTTTTAAAGTTTTCCAT
*
1746370 CAAGTCTTTTCCTAAAATTTTCCAT
1 CAAGTCTTTT--TAAAGTTTTCCAT
1746395 CAAGT-TTTT
1 CAAGTCTTTT
1746404 AATCATTTCG
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
23 6 0.12
24 21 0.42
25 17 0.34
26 6 0.12
ACGTcount: A:0.26, C:0.16, G:0.10, T:0.49
Consensus pattern (23 bp):
CAAGTCTTTTTAAAGTTTTCCAT
Found at i:1749258 original size:5 final size:5
Alignment explanation
Indices: 1749250--1749274 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1749240 ATCATATCAT
1749250 ATTAA ATTAA ATTAA ATTAA ATTAA
1 ATTAA ATTAA ATTAA ATTAA ATTAA
1749275 TTATAAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (5 bp):
ATTAA
Found at i:1749295 original size:16 final size:16
Alignment explanation
Indices: 1749250--1749286 Score: 51
Period size: 15 Copynumber: 2.4 Consensus size: 16
1749240 ATCATATCAT
*
1749250 ATTAAATTAAAT-TAA
1 ATTAAATTAATTATAA
1749265 ATTAAATTAATTATAA
1 ATTAAATTAATTATAA
1749281 A-TAAAT
1 ATTAAAT
1749287 CTATTTATAG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 16 0.80
16 4 0.20
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATTAAATTAATTATAA
Found at i:1755074 original size:48 final size:48
Alignment explanation
Indices: 1754980--1755079 Score: 155
Period size: 48 Copynumber: 2.1 Consensus size: 48
1754970 CTAAATTAAA
*
1754980 TTGAATTGTTAATTTTTAAGAGTCTAAAATCGCCTGAGTTTGAGTGTG
1 TTGAATTGTTAATTTTTAAGAGTCTAAAATCGCCTGAGTTTAAGTGTG
* ** *
1755028 TTGAATTGTTAATTTTTAAGAGTCTAAAATTGTGTGGGTTTAAGTGTG
1 TTGAATTGTTAATTTTTAAGAGTCTAAAATCGCCTGAGTTTAAGTGTG
1755076 TTGA
1 TTGA
1755080 TGTGCATTAT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.27, C:0.05, G:0.24, T:0.44
Consensus pattern (48 bp):
TTGAATTGTTAATTTTTAAGAGTCTAAAATCGCCTGAGTTTAAGTGTG
Found at i:1758648 original size:24 final size:25
Alignment explanation
Indices: 1758620--1758671 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
1758610 TAGGTGTTAA
1758620 GCAGCCGTTA-TTCTGTTAATAACT
1 GCAGCCGTTATTTCTGTTAATAACT
*
1758644 GCAGCTGTTATTTCTGTTAATAACT
1 GCAGCCGTTATTTCTGTTAATAACT
1758669 GCA
1 GCA
1758672 ATGTATTTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 9 0.35
25 17 0.65
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.38
Consensus pattern (25 bp):
GCAGCCGTTATTTCTGTTAATAACT
Found at i:1759815 original size:18 final size:18
Alignment explanation
Indices: 1759792--1759826 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
1759782 CTGTTAACTA
*
1759792 TCATCAATTCCATGATGG
1 TCATCAACTCCATGATGG
1759810 TCATCAACTCCATGATG
1 TCATCAACTCCATGATG
1759827 CTCCTACAAA
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:0.29, C:0.26, G:0.14, T:0.31
Consensus pattern (18 bp):
TCATCAACTCCATGATGG
Found at i:1763195 original size:24 final size:25
Alignment explanation
Indices: 1763167--1763218 Score: 88
Period size: 25 Copynumber: 2.1 Consensus size: 25
1763157 TAGGTGTTAA
1763167 GCAGCCGTTA-TTCTGTTAATAACT
1 GCAGCCGTTATTTCTGTTAATAACT
*
1763191 GCAGCTGTTATTTCTGTTAATAACT
1 GCAGCCGTTATTTCTGTTAATAACT
1763216 GCA
1 GCA
1763219 TTGTATTTAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
24 9 0.35
25 17 0.65
ACGTcount: A:0.25, C:0.19, G:0.17, T:0.38
Consensus pattern (25 bp):
GCAGCCGTTATTTCTGTTAATAACT
Found at i:1767710 original size:24 final size:23
Alignment explanation
Indices: 1767663--1767707 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1767653 TTCGAATATG
1767663 TATTTTATTTTTAGATATTCAAT
1 TATTTTATTTTTAGATATTCAAT
*
1767686 TATTTTATTATTTATAT-TTCAA
1 TATTTTATT-TTTAGATATTCAA
1767708 ATTTTAAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.62
Consensus pattern (23 bp):
TATTTTATTTTTAGATATTCAAT
Found at i:1772762 original size:30 final size:28
Alignment explanation
Indices: 1772724--1772803 Score: 90
Period size: 29 Copynumber: 2.8 Consensus size: 28
1772714 TTTGGACTTG
*
1772724 AATTTTAAAATCTAAAAAATATAG-GATTA
1 AATTTTAAAAT-TAAAAAA-ATAGTGACTA
1772753 AATTCTTAAAATTAAAAAAATAGTGACTA
1 AATT-TTAAAATTAAAAAAATAGTGACTA
* *
1772782 AATTTTGAATTTATAAAAAATA
1 AATTTTAAAATTA-AAAAAATA
1772804 CAAGGACTTA
Statistics
Matches: 45, Mismatches: 3, Indels: 6
0.83 0.06 0.11
Matches are distributed among these distances:
28 11 0.24
29 27 0.60
30 7 0.16
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.35
Consensus pattern (28 bp):
AATTTTAAAATTAAAAAAATAGTGACTA
Found at i:1774721 original size:34 final size:34
Alignment explanation
Indices: 1774677--1774742 Score: 105
Period size: 34 Copynumber: 1.9 Consensus size: 34
1774667 CCCATTATTG
*
1774677 TTTATCTATTCTTAATTGTGGCATTTTAAAGCTA
1 TTTATCTATTCTTAATTATGGCATTTTAAAGCTA
* *
1774711 TTTATTTATTCTTAATTATGGCATTTTTAAGC
1 TTTATCTATTCTTAATTATGGCATTTTAAAGC
1774743 GACTGTGTAG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.26, C:0.11, G:0.11, T:0.53
Consensus pattern (34 bp):
TTTATCTATTCTTAATTATGGCATTTTAAAGCTA
Found at i:1796791 original size:20 final size:20
Alignment explanation
Indices: 1796755--1796792 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
1796745 CATGTAATTC
*
1796755 ATAAAAATTTTAGAAAATAA
1 ATAAAAATTGTAGAAAATAA
1796775 ATAAAAATTAGTA-AAAAT
1 ATAAAAATT-GTAGAAAAT
1796793 GTTCATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 14 0.88
21 2 0.12
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (20 bp):
ATAAAAATTGTAGAAAATAA
Found at i:1801259 original size:23 final size:23
Alignment explanation
Indices: 1801195--1801260 Score: 71
Period size: 23 Copynumber: 2.9 Consensus size: 23
1801185 TTTTATGTTC
*
1801195 ACGAACATATTCATTTAAC-TTAA
1 ACGAACATATTCA-TAAACATTAA
* * **
1801218 TCGAACATGTTCACGAACATTAA
1 ACGAACATATTCATAAACATTAA
1801241 ACGAACATATTCATAAACAT
1 ACGAACATATTCATAAACAT
1801261 ATGATTGAAC
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
22 3 0.09
23 31 0.91
ACGTcount: A:0.44, C:0.20, G:0.08, T:0.29
Consensus pattern (23 bp):
ACGAACATATTCATAAACATTAA
Found at i:1801411 original size:12 final size:12
Alignment explanation
Indices: 1801371--1801413 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 12
1801361 ATTATTAATA
*
1801371 AATAAACGAGTC
1 AATAAACGAGCC
* *
1801383 AATAAGCGAGCT
1 AATAAACGAGCC
*
1801395 TATAAACGAGCC
1 AATAAACGAGCC
1801407 AATAAAC
1 AATAAAC
1801414 AAGCTTGTTC
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.49, C:0.19, G:0.16, T:0.16
Consensus pattern (12 bp):
AATAAACGAGCC
Found at i:1801418 original size:24 final size:24
Alignment explanation
Indices: 1801372--1801419 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1801362 TTATTAATAA
* * *
1801372 ATAAACGAGTCAATAAGCGAGCTT
1 ATAAACGAGCCAATAAACAAGCTT
1801396 ATAAACGAGCCAATAAACAAGCTT
1 ATAAACGAGCCAATAAACAAGCTT
1801420 GTTCGTAAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.46, C:0.19, G:0.17, T:0.19
Consensus pattern (24 bp):
ATAAACGAGCCAATAAACAAGCTT
Found at i:1805928 original size:18 final size:20
Alignment explanation
Indices: 1805905--1805947 Score: 54
Period size: 20 Copynumber: 2.2 Consensus size: 20
1805895 ATTAAAGGAT
1805905 TTTTAG-ATGG-GTATTTAC
1 TTTTAGTATGGTGTATTTAC
* *
1805923 TTTTAGTATGGTGTGTTTAG
1 TTTTAGTATGGTGTATTTAC
1805943 TTTTA
1 TTTTA
1805948 TATTTGTCTC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 6 0.29
19 4 0.19
20 11 0.52
ACGTcount: A:0.19, C:0.02, G:0.23, T:0.56
Consensus pattern (20 bp):
TTTTAGTATGGTGTATTTAC
Found at i:1807768 original size:18 final size:18
Alignment explanation
Indices: 1807742--1807782 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
1807732 CATAAGTATC
1807742 TAAAAAAATGGAAATAAA
1 TAAAAAAATGGAAATAAA
* *
1807760 TAAATAAATGTAAATAAA
1 TAAAAAAATGGAAATAAA
1807778 -AAAAA
1 TAAAAA
1807783 GTAAATACAT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 4 0.20
18 16 0.80
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (18 bp):
TAAAAAAATGGAAATAAA
Found at i:1807773 original size:14 final size:14
Alignment explanation
Indices: 1807756--1807789 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
1807746 AAAATGGAAA
* *
1807756 TAAATAAATAAATG
1 TAAATAAAAAAAAG
1807770 TAAATAAAAAAAAG
1 TAAATAAAAAAAAG
1807784 TAAATA
1 TAAATA
1807790 CATATTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.24
Consensus pattern (14 bp):
TAAATAAAAAAAAG
Found at i:1807938 original size:23 final size:23
Alignment explanation
Indices: 1807910--1807954 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
1807900 ATATATTTGG
1807910 ACTATA-AAATATACATAAAACAA
1 ACTATACAAATAT-CATAAAACAA
*
1807933 ACTATACAAATATTATAAAACA
1 ACTATACAAATATCATAAAACA
1807955 GAAATATATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 14 0.70
24 6 0.30
ACGTcount: A:0.62, C:0.13, G:0.00, T:0.24
Consensus pattern (23 bp):
ACTATACAAATATCATAAAACAA
Found at i:1808538 original size:14 final size:13
Alignment explanation
Indices: 1808517--1808581 Score: 53
Period size: 14 Copynumber: 4.8 Consensus size: 13
1808507 ATACAGATAC
1808517 AATAATAATAACAT
1 AATAATAATAA-AT
*
1808531 AGTAATAATTAAA-
1 AATAATAA-TAAAT
1808544 AATAGATAA-AAAT
1 AATA-ATAATAAAT
1808557 AATAATAATAACAT
1 AATAATAATAA-AT
* *
1808571 ATTAAAAATAA
1 AATAATAATAA
1808582 TCTAAAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 10
0.75 0.07 0.18
Matches are distributed among these distances:
12 7 0.17
13 9 0.21
14 23 0.55
15 3 0.07
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (13 bp):
AATAATAATAAAT
Found at i:1808582 original size:20 final size:19
Alignment explanation
Indices: 1808517--1808582 Score: 53
Period size: 20 Copynumber: 3.3 Consensus size: 19
1808507 ATACAGATAC
1808517 AATAATAATAACATAGTAATA
1 AATAATAATAACATA-TAA-A
* * * *
1808538 ATTAAAAAT-AGATAAAAA
1 AATAATAATAACATATAAA
1808556 TAATAATAATAACATATTAAA
1 -AATAATAATAACATA-TAAA
1808577 AATAAT
1 AATAAT
1808583 CTAAAAAAAC
Statistics
Matches: 34, Mismatches: 8, Indels: 7
0.69 0.16 0.14
Matches are distributed among these distances:
18 1 0.03
19 9 0.26
20 14 0.41
21 10 0.29
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (19 bp):
AATAATAATAACATATAAA
Found at i:1809463 original size:14 final size:14
Alignment explanation
Indices: 1809444--1809480 Score: 74
Period size: 14 Copynumber: 2.6 Consensus size: 14
1809434 AGTTGCTGAT
1809444 CGTGGGTGAAGCGA
1 CGTGGGTGAAGCGA
1809458 CGTGGGTGAAGCGA
1 CGTGGGTGAAGCGA
1809472 CGTGGGTGA
1 CGTGGGTGA
1809481 TGGGTAGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.19, C:0.14, G:0.51, T:0.16
Consensus pattern (14 bp):
CGTGGGTGAAGCGA
Found at i:1812488 original size:66 final size:66
Alignment explanation
Indices: 1812379--1812512 Score: 241
Period size: 66 Copynumber: 2.0 Consensus size: 66
1812369 GAAGCAAAAA
*
1812379 CTATGATGCCAGTACACACTACAATCTCTTCCAATTTCTGTCTTTTCTTCCTGATCAAACTGGCC
1 CTATGATGCCAGTACACACTACAATCTCTTCCAATTTCAGTCTTTTCTTCCTGATCAAACTGGCC
1812444 T
66 T
**
1812445 CTATGATGCCAGTACACACTACAATCTCTTCCAATTTCAGTCTTTTCTTTTTGATCAAACTGGCC
1 CTATGATGCCAGTACACACTACAATCTCTTCCAATTTCAGTCTTTTCTTCCTGATCAAACTGGCC
1812510 T
66 T
1812511 CT
1 CT
1812513 TCAACAGTTG
Statistics
Matches: 65, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 65 1.00
ACGTcount: A:0.23, C:0.29, G:0.10, T:0.37
Consensus pattern (66 bp):
CTATGATGCCAGTACACACTACAATCTCTTCCAATTTCAGTCTTTTCTTCCTGATCAAACTGGCC
T
Found at i:1812960 original size:21 final size:21
Alignment explanation
Indices: 1812934--1812977 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
1812924 ACTTGCTATT
1812934 GTCATTTTTGTTAGTGTCGGA
1 GTCATTTTTGTTAGTGTCGGA
**
1812955 GTCATTTTTGTTCTTGTCGGA
1 GTCATTTTTGTTAGTGTCGGA
1812976 GT
1 GT
1812978 TGAAAGAGGG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.11, C:0.11, G:0.27, T:0.50
Consensus pattern (21 bp):
GTCATTTTTGTTAGTGTCGGA
Found at i:1821131 original size:87 final size:88
Alignment explanation
Indices: 1821021--1821197 Score: 347
Period size: 87 Copynumber: 2.0 Consensus size: 88
1821011 ATAATTTTTT
1821021 ATTGATTTATAAACACGTAATGATGAATAATATTAACTTAATTAAGAATAGATAAATATATATAT
1 ATTGATTTATAAACACGTAATGATGAATAATATTAACTTAATTAAGAATAGATAAATATATATAT
1821086 ATTGATATAATATAAATATACGA
66 ATTGATATAATATAAATATACGA
1821109 ATTGATTTAT-AACACGTAATGATGAATAATATTAACTTAATTAAGAATAGATAAATATATATAT
1 ATTGATTTATAAACACGTAATGATGAATAATATTAACTTAATTAAGAATAGATAAATATATATAT
1821173 ATTGATATAATATAAATATACGA
66 ATTGATATAATATAAATATACGA
1821196 AT
1 AT
1821198 GTTTTTAAAT
Statistics
Matches: 89, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
87 79 0.89
88 10 0.11
ACGTcount: A:0.50, C:0.05, G:0.09, T:0.37
Consensus pattern (88 bp):
ATTGATTTATAAACACGTAATGATGAATAATATTAACTTAATTAAGAATAGATAAATATATATAT
ATTGATATAATATAAATATACGA
Found at i:1823105 original size:18 final size:17
Alignment explanation
Indices: 1823078--1823113 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
1823068 TCCCATATTT
*
1823078 CGGGCGGGCCGTCGGGC
1 CGGGCGGGCCGTCCGGC
1823095 CGGGCCGGGCCGTCCGGC
1 CGGG-CGGGCCGTCCGGC
1823113 C
1 C
1823114 CATGGACAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 4 0.24
18 13 0.76
ACGTcount: A:0.00, C:0.42, G:0.53, T:0.06
Consensus pattern (17 bp):
CGGGCGGGCCGTCCGGC
Found at i:1834950 original size:23 final size:23
Alignment explanation
Indices: 1834917--1834986 Score: 122
Period size: 23 Copynumber: 3.0 Consensus size: 23
1834907 AAAGATCCCT
*
1834917 TGTAATAAAGTACATAAGCTTTA
1 TGTAATAAAGTACATAAACTTTA
*
1834940 TGTAATGAAGTACATAAACTTTA
1 TGTAATAAAGTACATAAACTTTA
1834963 TGTAATAAAGTACATAAACTTTA
1 TGTAATAAAGTACATAAACTTTA
1834986 T
1 T
1834987 CACAAGTGAG
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.44, C:0.09, G:0.11, T:0.36
Consensus pattern (23 bp):
TGTAATAAAGTACATAAACTTTA
Found at i:1836173 original size:11 final size:11
Alignment explanation
Indices: 1836157--1836182 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1836147 CCAGGCGATT
1836157 AACACTATAAA
1 AACACTATAAA
1836168 AACACTATAAA
1 AACACTATAAA
1836179 AACA
1 AACA
1836183 AGAAAAAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.65, C:0.19, G:0.00, T:0.15
Consensus pattern (11 bp):
AACACTATAAA
Done.