Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008121.1 Hibiscus syriacus cultivar Beakdansim tig00110674_pilon, whole genome shotgun sequence
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: 1116347
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 4
Found at i:1007 original size:20 final size:23
Alignment explanation
Indices: 965--1006 Score: 61
Period size: 21 Copynumber: 1.9 Consensus size: 23
955 ATTGATAATC
965 TAATTATGTGTTTTAAAATTTTA
1 TAATTATGTGTTTTAAAATTTTA
*
988 TAATTAT-T-TTTTATAATTT
1 TAATTATGTGTTTTAAAATTT
1007 AAAATTGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 10 0.56
22 1 0.06
23 7 0.39
ACGTcount: A:0.33, C:0.00, G:0.05, T:0.62
Consensus pattern (23 bp):
TAATTATGTGTTTTAAAATTTTA
Found at i:2044 original size:37 final size:35
Alignment explanation
Indices: 1973--2045 Score: 85
Period size: 37 Copynumber: 2.0 Consensus size: 35
1963 GTTGAAAAAT
*
1973 ATTTATATATTTCTTTAAAAAATTAAATTCATAAA
1 ATTTATATATTTCTTTAAAAAATTAAAATCATAAA
* *
2008 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-A-TTTCTTTAAAAAATT-AAAATCATAAA
2045 A
1 A
2046 GGTTTAATGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
35 8 0.25
36 1 0.03
37 19 0.59
38 4 0.12
ACGTcount: A:0.49, C:0.04, G:0.01, T:0.45
Consensus pattern (35 bp):
ATTTATATATTTCTTTAAAAAATTAAAATCATAAA
Found at i:8304 original size:43 final size:43
Alignment explanation
Indices: 8247--8334 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 43
8237 CAAAAACCAG
* *
8247 ACTTTTCCAACAATCCAAATACTTAACAGCCTTTTCATCAACC
1 ACTTTTCCAACAATCCAAATACCTAACAGCCTTTTCATAAACC
8290 ACTTTTCCAACAATCCAAATACCTAACAGCCTTTTCATAAACC
1 ACTTTTCCAACAATCCAAATACCTAACAGCCTTTTCATAAACC
8333 AC
1 AC
8335 CTTATGCTGA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.36, C:0.33, G:0.02, T:0.28
Consensus pattern (43 bp):
ACTTTTCCAACAATCCAAATACCTAACAGCCTTTTCATAAACC
Found at i:14125 original size:105 final size:105
Alignment explanation
Indices: 13998--14951 Score: 1523
Period size: 105 Copynumber: 9.1 Consensus size: 105
13988 CTCGAGAGTA
* * * * * *
13998 AATTTCAACTTCTCAACGAAGGATCTT-GAATCCAAGACAACACAAGCTCAACTTCATGACGAAG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCC-AGACAACGCAAGTTCAACTTCACGACGAAG
* * *
14062 GGGCGGCTGATTGTCAACAAACATTTCTCAATTTCAGAGCC
65 GGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCC
* *
14103 AATTTCAACTTCACCACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
14168 GACCGCTGGTTGTCAACAAACATTTCTCGATTTCAGAGTC
66 GACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCC
*
14208 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGATGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
14273 GACCGCTGGTTGTCAACAAACATTTCTCGATTTCAGAGTC
66 GACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCC
14313 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
14378 GACCGCTGGTTGTCAACAAACATTTCTCGATTTCAGAGTC
66 GACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCC
* *
14418 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACAACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
14483 GACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCC
* *
14523 AATTTCAACTTCACCACGAAGGATATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
14588 GACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAAC-ATTTCTCAATTTCAGAGCC
* * *
14629 AATTTCAACTTCGCCACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
*
14694 GACCGTTGGTTGTCAACAAACATTTCTCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCC
*
14734 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCCCGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* * *
14799 GACTGCTGGTTGTCAATAAACATTTCCCAATTTCAGAGCC
66 GACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCC
* *
14839 AATTTCGACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTTAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
** * * *
14904 GACCGCTGGTTGTCATTAAACAACTTCCCAATTTCAGAACC
66 GACCGCTGGTTGTCAACAAAC-ATTTCTCAATTTCAGAGCC
14945 AATTTCA
1 AATTTCA
14952 GATAGGTTCG
Statistics
Matches: 799, Mismatches: 47, Indels: 5
0.94 0.06 0.01
Matches are distributed among these distances:
105 672 0.84
106 127 0.16
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (105 bp):
AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
GACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCC
Found at i:14773 original size:316 final size:316
Alignment explanation
Indices: 13998--14951 Score: 1552
Period size: 316 Copynumber: 3.0 Consensus size: 316
13988 CTCGAGAGTA
* * * * * *
13998 AATTTCAACTTCTCAACGAAGGATCTT-GAATCCAAGACAACACAAGCTCAACTTCATGACGAAG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCC-AGACAACGCAAGTTCAACTTCACGACGAAG
* * * *
14062 GGGCGGCTGATTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACCACGAAGGAT
65 GGACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGAT
*
14127 ATTGGACTCCAGACAACACAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATT
130 ATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATT
* *
14192 TCTCGATTTCAGAGTCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTC
195 TCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTC
* * * * *
14257 AACTTCACGATGAAGGGACCGCTGGTTGTCAACAAAC-ATTTCTCGATTTCAGAGTC
260 AACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCC
14313 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
* *
14378 GACCGCTGGTTGTCAACAAACATTTCTCGATTTCAGAGTCAATTTCAACTTCACAACGAAGGATA
66 GACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATA
* *
14443 TTGGACTCCAGACAACGTAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACATTT
131 TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTT
* *
14508 CTCAATTTCAGAGCCAATTTCAACTTCACCACGAAGGATATTGGACTCCAGACAACACAAGTTCA
196 CTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCA
14573 ACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCC
261 ACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCC
* * *
14629 AATTTCAACTTCGCCACGAAGGATATTGGACTTCAGACAACGCAAGTTCAACTTCACGACGAAGG
1 AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
*
14694 GACCGTTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATA
66 GACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATA
* * *
14759 TTGGACTCCAGACAACGCAAGTTCAACTTCCCGACGAAGGGACTGCTGGTTGTCAATAAACATTT
131 TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTT
* * *
14824 CCCAATTTCAGAGCCAATTTCGACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTTA
196 CTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCA
* * *
14889 ACTTCACGACGAAGGGACCGCTGGTTGTCATTAAACAACTTCCCAATTTCAGAACC
261 ACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCC
14945 AATTTCA
1 AATTTCA
14952 GATAGGTTCG
Statistics
Matches: 594, Mismatches: 43, Indels: 3
0.93 0.07 0.00
Matches are distributed among these distances:
315 269 0.45
316 325 0.55
ACGTcount: A:0.33, C:0.25, G:0.18, T:0.24
Consensus pattern (316 bp):
AATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGG
GACCGCTGGTTGTCAACAAACATTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATA
TTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACATTT
CTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCA
ACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATTTCAGAGCC
Found at i:15492 original size:81 final size:82
Alignment explanation
Indices: 15263--15493 Score: 286
Period size: 84 Copynumber: 2.8 Consensus size: 82
15253 CACAAAGACC
*
15263 TTCGATTACACTCAGCTTCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT
1 TTCGATTACACTCAGCTCCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT
*
15328 GCCAACCAAAGACCTTTGAG
66 G---ACCAAAGACCTTCGAG
* * * * * *
15348 TTCGACTACGCTTAGCTCC-AAGGCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCT
1 TTCGATTACACTCAGCTCCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT
*
15412 G-CCAAAGACCTTCGGG
66 GACCAAAGACCTTCGAG
* * * * * *
15428 TTCGATTATACTCAGCTCCGAGGGCACATCATTTACAGCATAACTCAAGACTAGAAGAGTTATCT
1 TTCGATTACACTCAGCTCCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT
15493 G
66 G
15494 TCAACAAAAA
Statistics
Matches: 124, Mismatches: 21, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
80 28 0.23
81 38 0.31
84 43 0.35
85 15 0.12
ACGTcount: A:0.29, C:0.24, G:0.21, T:0.26
Consensus pattern (82 bp):
TTCGATTACACTCAGCTCCGAGGGCACATCATTTGCAGCATAACTTAAGTCGAGAAGGGTTATCT
GACCAAAGACCTTCGAG
Found at i:15555 original size:36 final size:36
Alignment explanation
Indices: 15515--15710 Score: 295
Period size: 36 Copynumber: 5.4 Consensus size: 36
15505 CTTTGAGATT
* *
15515 GTTTCCCTTGAGACAAATTTCGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACA
*
15551 GTTTCCCTTGAAAGAAATTTCGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACA
* *
15587 GTTTCCCTTGAAACATATTTTGTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACA
* *
15623 GTTTCCCTTGAAACAAAATTCGTCTCCCTTGAGACA
1 GTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACA
15659 GTTTCCCTTGAAACAAATTGGT-GTCTCTCTTGAGACA
1 GTTTCCCTTGAAACAAATT--TCGTCTCTCTTGAGACA
*
15696 GTTTCTCTTGAAACA
1 GTTTCCCTTGAAACA
15711 CCAAACCCTT
Statistics
Matches: 145, Mismatches: 13, Indels: 3
0.90 0.08 0.02
Matches are distributed among these distances:
36 116 0.80
37 28 0.19
38 1 0.01
ACGTcount: A:0.24, C:0.24, G:0.16, T:0.36
Consensus pattern (36 bp):
GTTTCCCTTGAAACAAATTTCGTCTCTCTTGAGACA
Found at i:22219 original size:34 final size:34
Alignment explanation
Indices: 22176--22244 Score: 120
Period size: 34 Copynumber: 2.0 Consensus size: 34
22166 GTATCTGGAT
*
22176 CGGACGTATTAGGCAATTGGCATTCGGTTTCTGC
1 CGGACGTATTAGACAATTGGCATTCGGTTTCTGC
*
22210 CGGACGTATTAGACAATTGGCTTTCGGTTTCTGC
1 CGGACGTATTAGACAATTGGCATTCGGTTTCTGC
22244 C
1 C
22245 CTCATGGATA
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.17, C:0.22, G:0.28, T:0.33
Consensus pattern (34 bp):
CGGACGTATTAGACAATTGGCATTCGGTTTCTGC
Found at i:24730 original size:17 final size:18
Alignment explanation
Indices: 24710--24744 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
24700 GACGAGGCAA
*
24710 ACCAAAT-AGCAGATGGC
1 ACCAAATAAGAAGATGGC
24727 ACCAAATAAGAAGATGGC
1 ACCAAATAAGAAGATGGC
24745 CGGTTGAGCT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.46, C:0.20, G:0.23, T:0.11
Consensus pattern (18 bp):
ACCAAATAAGAAGATGGC
Found at i:29524 original size:30 final size:30
Alignment explanation
Indices: 29490--29561 Score: 99
Period size: 30 Copynumber: 2.4 Consensus size: 30
29480 AACCCGTCCT
*
29490 CATCCCCGTTTAGCATAAACAGTTTTTCCC
1 CATCCCCGTTTAGCATAAACAATTTTTCCC
* * *
29520 CATCCCCATTTAGCATAAACAATTTTTTCT
1 CATCCCCGTTTAGCATAAACAATTTTTCCC
*
29550 CGTCCCCGTTTA
1 CATCCCCGTTTA
29562 ATTCAGTTTT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.24, C:0.32, G:0.08, T:0.36
Consensus pattern (30 bp):
CATCCCCGTTTAGCATAAACAATTTTTCCC
Found at i:30529 original size:23 final size:23
Alignment explanation
Indices: 30492--30535 Score: 70
Period size: 23 Copynumber: 1.9 Consensus size: 23
30482 TAGTAGAGGG
30492 TCTACGCGGTCATTCGGGACAAT
1 TCTACGCGGTCATTCGGGACAAT
* *
30515 TCTACGTGGTTATTCGGGACA
1 TCTACGCGGTCATTCGGGACA
30536 TATATGTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.20, C:0.23, G:0.27, T:0.30
Consensus pattern (23 bp):
TCTACGCGGTCATTCGGGACAAT
Found at i:31333 original size:21 final size:21
Alignment explanation
Indices: 31307--31346 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
31297 CGATATTTTT
* *
31307 GTGCATCGGTACATTGTAGTA
1 GTGCATCGATACACTGTAGTA
31328 GTGCATCGATACACTGTAG
1 GTGCATCGATACACTGTAG
31347 CACTGTTCAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.17, G:0.28, T:0.30
Consensus pattern (21 bp):
GTGCATCGATACACTGTAGTA
Found at i:40145 original size:27 final size:25
Alignment explanation
Indices: 40091--40147 Score: 64
Period size: 25 Copynumber: 2.2 Consensus size: 25
40081 AAAAAGTATT
*
40091 TTTA-TATTAACTTATTAAATATAT
1 TTTATTATTAACTTATTAAATATAA
40115 TTTATTATTAACTTAATTTTAAA-ATAA
1 TTTATTATTAACTT-A--TTAAATATAA
40142 TTTATT
1 TTTATT
40148 TTATTTTCAT
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
24 4 0.14
25 9 0.32
26 1 0.04
27 9 0.32
28 5 0.18
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (25 bp):
TTTATTATTAACTTATTAAATATAA
Found at i:40371 original size:31 final size:31
Alignment explanation
Indices: 40308--40376 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 31
40298 TGATCACCAC
*
40308 ATCTTGATTAAATAAAAAATAAAACTGACTAT
1 ATCTTAATTAAAT-AAAAATAAAACTGACTAT
*
40340 ATCTTAATTAAAT-AAAATCAAAAGTGACTAT
1 ATCTTAATTAAATAAAAAT-AAAACTGACTAT
40371 ATCTTA
1 ATCTTA
40377 TGTTTTTTTG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 5 0.15
31 17 0.50
32 12 0.35
ACGTcount: A:0.51, C:0.10, G:0.06, T:0.33
Consensus pattern (31 bp):
ATCTTAATTAAATAAAAATAAAACTGACTAT
Found at i:47295 original size:33 final size:32
Alignment explanation
Indices: 47246--47312 Score: 107
Period size: 33 Copynumber: 2.1 Consensus size: 32
47236 TTTATTTTGT
*
47246 TCGGGTTGGGTTTTTTAAGTGAGATATTCGGG
1 TCGGGTCGGGTTTTTTAAGTGAGATATTCGGG
*
47278 TCGGGTCGGGTGTTTTTAAGTGTGATATTCGGG
1 TCGGGTCGGGT-TTTTTAAGTGAGATATTCGGG
47311 TC
1 TC
47313 AGGTTTGGGT
Statistics
Matches: 32, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 10 0.31
33 22 0.69
ACGTcount: A:0.13, C:0.09, G:0.37, T:0.40
Consensus pattern (32 bp):
TCGGGTCGGGTTTTTTAAGTGAGATATTCGGG
Found at i:50329 original size:19 final size:20
Alignment explanation
Indices: 50291--50329 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
50281 AGTACTTCAA
50291 GGAGGAGATGAATGGGAATTT
1 GGAGGAGATGAA-GGGAATTT
*
50312 GGAGGAGTTGAA-GGAATT
1 GGAGGAGATGAAGGGAATT
50330 CCCCCAGTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 6 0.35
21 11 0.65
ACGTcount: A:0.33, C:0.00, G:0.44, T:0.23
Consensus pattern (20 bp):
GGAGGAGATGAAGGGAATTT
Found at i:62143 original size:18 final size:18
Alignment explanation
Indices: 62120--62159 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
62110 TTCTATTAGT
* *
62120 ATTTATTTATGATGTGTC
1 ATTTATGTATGATGTATC
62138 ATTTATGTATGATGTATC
1 ATTTATGTATGATGTATC
62156 ATTT
1 ATTT
62160 TTTTCTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.25, C:0.05, G:0.15, T:0.55
Consensus pattern (18 bp):
ATTTATGTATGATGTATC
Found at i:64121 original size:18 final size:19
Alignment explanation
Indices: 64098--64140 Score: 70
Period size: 20 Copynumber: 2.3 Consensus size: 19
64088 CAGTAATCCT
64098 ATTCC-CTGGTAATCTTAC
1 ATTCCACTGGTAATCTTAC
64116 ATTCCCACTGGTAATCTTAC
1 ATT-CCACTGGTAATCTTAC
64136 ATTCC
1 ATTCC
64141 GTGAACCAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 3 0.13
19 4 0.17
20 16 0.70
ACGTcount: A:0.23, C:0.30, G:0.09, T:0.37
Consensus pattern (19 bp):
ATTCCACTGGTAATCTTAC
Found at i:64128 original size:20 final size:20
Alignment explanation
Indices: 64103--64140 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
64093 ATCCTATTCC
64103 CTGGTAATCTTACATTCCCA
1 CTGGTAATCTTACATTCCCA
64123 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
64141 GTGAACCAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.29, G:0.11, T:0.37
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:74937 original size:17 final size:18
Alignment explanation
Indices: 74917--74950 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
74907 TTTATAAGAT
74917 ATATTTTATTA-TATTTA
1 ATATTTTATTAGTATTTA
*
74934 ATATTTTGTTAGTATTT
1 ATATTTTATTAGTATTT
74951 TATTTAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (18 bp):
ATATTTTATTAGTATTTA
Found at i:74967 original size:13 final size:13
Alignment explanation
Indices: 74946--75006 Score: 63
Period size: 13 Copynumber: 4.8 Consensus size: 13
74936 ATTTTGTTAG
74946 TATTTTATTTAAT
1 TATTTTATTTAAT
* *
74959 TATTGTA-TTATT
1 TATTTTATTTAAT
*
74971 TAATTTT-TTTTAT
1 T-ATTTTATTTAAT
*
74984 TATTTTATTTAAA
1 TATTTTATTTAAT
74997 TATTTTATTT
1 TATTTTATTT
75007 TTTTGCTGTT
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
12 10 0.26
13 28 0.74
ACGTcount: A:0.28, C:0.00, G:0.02, T:0.70
Consensus pattern (13 bp):
TATTTTATTTAAT
Found at i:74986 original size:17 final size:17
Alignment explanation
Indices: 74950--74994 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
74940 TGTTAGTATT
74950 TTATTTAA-TTATTGTA
1 TTATTTAATTTATTGTA
* *
74966 TTATTTAATTTTTTTTA
1 TTATTTAATTTATTGTA
*
74983 TTATTTTATTTA
1 TTATTTAATTTA
74995 AATATTTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
16 8 0.33
17 16 0.67
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (17 bp):
TTATTTAATTTATTGTA
Found at i:74989 original size:8 final size:8
Alignment explanation
Indices: 74918--74992 Score: 53
Period size: 8 Copynumber: 9.1 Consensus size: 8
74908 TTATAAGATA
74918 TATTTTAT
1 TATTTTAT
*
74926 TATATTTAA
1 TAT-TTTAT
*
74935 TATTTTGT
1 TATTTTAT
*
74943 TAGTATT-T
1 TA-TTTTAT
*
74951 TATTTAAT
1 TATTTTAT
*
74959 TATTGTAT
1 TATTTTAT
*
74967 TATTTAATT
1 TATTTTA-T
*
74976 TTTTTTAT
1 TATTTTAT
74984 TATTTTAT
1 TATTTTAT
74992 T
1 T
74993 TAAATATTTT
Statistics
Matches: 50, Mismatches: 13, Indels: 8
0.70 0.18 0.11
Matches are distributed among these distances:
7 2 0.04
8 32 0.64
9 16 0.32
ACGTcount: A:0.27, C:0.00, G:0.04, T:0.69
Consensus pattern (8 bp):
TATTTTAT
Found at i:74991 original size:38 final size:39
Alignment explanation
Indices: 74928--75005 Score: 113
Period size: 38 Copynumber: 2.0 Consensus size: 39
74918 TATTTTATTA
*
74928 TATTTAATATTTTGTTAGTATTTTATTTAATTATTGTAT
1 TATTTAATATTTTGTTAGTATTTTATTTAAATATTGTAT
* * *
74967 TATTTAAT-TTTTTTTATTATTTTATTTAAATATTTTAT
1 TATTTAATATTTTGTTAGTATTTTATTTAAATATTGTAT
75005 T
1 T
75006 TTTTTGCTGT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
38 27 0.77
39 8 0.23
ACGTcount: A:0.28, C:0.00, G:0.04, T:0.68
Consensus pattern (39 bp):
TATTTAATATTTTGTTAGTATTTTATTTAAATATTGTAT
Found at i:75002 original size:22 final size:21
Alignment explanation
Indices: 74922--75010 Score: 69
Period size: 21 Copynumber: 4.3 Consensus size: 21
74912 AAGATATATT
* *
74922 TTATTATATTTAATATTTTGTTA
1 TTATTTTATTTAA-ATATT-TTA
* * *
74945 GTATTTTATTTAATTATTGTA
1 TTATTTTATTTAAATATTTTA
*
74966 TTATTTAATTT---T-TTTTA
1 TTATTTTATTTAAATATTTTA
74983 TTATTTTATTTAAATATTTTA
1 TTATTTTATTTAAATATTTTA
*
75004 TTTTTTT
1 TTATTTT
75011 GCTGTTATAA
Statistics
Matches: 52, Mismatches: 10, Indels: 10
0.72 0.14 0.14
Matches are distributed among these distances:
17 14 0.27
18 1 0.02
20 1 0.02
21 22 0.42
22 3 0.06
23 11 0.21
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (21 bp):
TTATTTTATTTAAATATTTTA
Found at i:75083 original size:18 final size:17
Alignment explanation
Indices: 75062--75124 Score: 58
Period size: 18 Copynumber: 3.6 Consensus size: 17
75052 TATTTTGTTA
75062 GTATTTTATTTAATTATT
1 GTATTTT-TTTAATTATT
*
75080 GTATTATTTTTTATTA-T
1 GTATT-TTTTTAATTATT
*
75097 -TATTTTATTTAAATATT
1 GTATTTT-TTTAATTATT
*
75114 TTATTTTTTTA
1 GTATTTTTTTA
75125 CAGTTATAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
15 2 0.05
16 10 0.26
17 6 0.16
18 18 0.47
19 2 0.05
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (17 bp):
GTATTTTTTTAATTATT
Found at i:75096 original size:10 final size:11
Alignment explanation
Indices: 75052--75105 Score: 56
Period size: 11 Copynumber: 4.8 Consensus size: 11
75042 TTATATTTAA
* *
75052 TATTTTGTTAG
1 TATTTTATTAT
75063 TATTTTATTTAAT
1 TATTTTA-TT-AT
*
75076 TATTGTATTAT
1 TATTTTATTAT
75087 T-TTTTATTAT
1 TATTTTATTAT
75097 TATTTTATT
1 TATTTTATT
75106 TAAATATTTT
Statistics
Matches: 36, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
10 9 0.25
11 16 0.44
12 4 0.11
13 7 0.19
ACGTcount: A:0.24, C:0.00, G:0.06, T:0.70
Consensus pattern (11 bp):
TATTTTATTAT
Found at i:75102 original size:34 final size:33
Alignment explanation
Indices: 75054--75123 Score: 95
Period size: 34 Copynumber: 2.1 Consensus size: 33
75044 ATATTTAATA
* *
75054 TTTTGTTAGTATTTTATTTAATTATTGTATTATT
1 TTTTATTAGTATTTTATTTAAATATTGTATT-TT
* *
75088 TTTTATTATTATTTTATTTAAATATTTTATTTT
1 TTTTATTAGTATTTTATTTAAATATTGTATTTT
75121 TTT
1 TTT
75124 ACAGTTATAA
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
33 5 0.16
34 27 0.84
ACGTcount: A:0.24, C:0.00, G:0.04, T:0.71
Consensus pattern (33 bp):
TTTTATTAGTATTTTATTTAAATATTGTATTTT
Found at i:75143 original size:113 final size:114
Alignment explanation
Indices: 74925--75269 Score: 557
Period size: 113 Copynumber: 3.0 Consensus size: 114
74915 ATATATTTTA
74925 TTATATTTAATATTTTGTTAGTATTTTATTTAATTATTGTATTATTTAATTTTTTTTATTATTTT
1 TTATATTTAATATTTTGTTAGTATTTTATTTAATTATTGTATTA-TT--TTTTTTTTATTATTTT
* * *
74990 ATTTAAATATTTTATTTTTTTGCTGTTATAAAATGGAAAGCAGTCTGCTTCG
63 ATTTAAATATTTTATTTTTTTACAGTTATAAAATGAAAAGCAGTCTGCTTCG
*
75042 TTATATTTAATATTTTGTTAGTATTTTATTTAATTATTGTATTA-TTTTTTATTATTATTTTATT
1 TTATATTTAATATTTTGTTAGTATTTTATTTAATTATTGTATTATTTTTTTTTTATTATTTTATT
*
75106 TAAATATTTTATTTTTTTACAGTTATAAAATAAAAAGCAGTCTGCTTCG
66 TAAATATTTTATTTTTTTACAGTTATAAAATGAAAAGCAGTCTGCTTCG
*
75155 TTATATTTAATATTTTGTTAATATTTTATTTAATTATTGTATTATTTAATTTTTTTATTATTTTA
1 TTATATTTAATATTTTGTTAGTATTTTATTTAATTATTGTATTATTT--TTTTTTTATTATTTTA
* * *
75220 TTTAAATATTCTATTTTTTTACAGTTATAAAATGAAAATCGGTCTGCTTC
64 TTTAAATATTTTATTTTTTTACAGTTATAAAATGAAAAGCAGTCTGCTTC
75270 ATTTGGATGA
Statistics
Matches: 214, Mismatches: 11, Indels: 7
0.92 0.05 0.03
Matches are distributed among these distances:
113 106 0.50
114 2 0.01
115 1 0.00
116 61 0.29
117 44 0.21
ACGTcount: A:0.30, C:0.05, G:0.08, T:0.58
Consensus pattern (114 bp):
TTATATTTAATATTTTGTTAGTATTTTATTTAATTATTGTATTATTTTTTTTTTATTATTTTATT
TAAATATTTTATTTTTTTACAGTTATAAAATGAAAAGCAGTCTGCTTCG
Found at i:75217 original size:37 final size:39
Alignment explanation
Indices: 75158--75234 Score: 113
Period size: 37 Copynumber: 2.0 Consensus size: 39
75148 TGCTTCGTTA
* *
75158 TATTTAATATTTTGTTAATATTTTATTTAATTATTGTAT
1 TATTTAATATTTTGTTAATATTTTATTTAAATATTCTAT
*
75197 TATTTAAT-TTTT-TTATTATTTTATTTAAATATTCTAT
1 TATTTAATATTTTGTTAATATTTTATTTAAATATTCTAT
75234 T
1 T
75235 TTTTTACAGT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
37 23 0.66
38 4 0.11
39 8 0.23
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (39 bp):
TATTTAATATTTTGTTAATATTTTATTTAAATATTCTAT
Found at i:75222 original size:16 final size:16
Alignment explanation
Indices: 75180--75222 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
75170 TGTTAATATT
*
75180 TTATTTAATTATTGTA
1 TTATTTAATTTTTGTA
*
75196 TTATTTAATTTTTTTA
1 TTATTTAATTTTTGTA
*
75212 TTATTTTATTT
1 TTATTTAATTT
75223 AAATATTCTA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (16 bp):
TTATTTAATTTTTGTA
Found at i:75234 original size:21 final size:19
Alignment explanation
Indices: 75176--75240 Score: 55
Period size: 21 Copynumber: 3.4 Consensus size: 19
75166 ATTTTGTTAA
75176 TATTTTATTTAATTATTGTAT
1 TATTTTATTTAA-TATT-TAT
*
75197 TATTTAATTT--T-TTTAT
1 TATTTTATTTAATATTTAT
75213 TATTTTATTTAAATATTCTAT
1 TATTTTATTT-AATATT-TAT
*
75234 TTTTTTA
1 TATTTTA
75241 CAGTTATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 10
0.73 0.06 0.20
Matches are distributed among these distances:
16 12 0.33
17 2 0.06
18 1 0.03
19 1 0.03
20 2 0.06
21 18 0.50
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.69
Consensus pattern (19 bp):
TATTTTATTTAATATTTAT
Found at i:77255 original size:33 final size:34
Alignment explanation
Indices: 77192--77272 Score: 137
Period size: 33 Copynumber: 2.4 Consensus size: 34
77182 CGATTATATA
77192 TATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
77226 TATATATATAATATTTTATA-TTTTTATATTAAT
1 TATATATATAATATTTTATATTTTTTATATTAAT
* *
77259 TGTATATAAAATAT
1 TATATATATAATAT
77273 GTTTGGGTTC
Statistics
Matches: 45, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
33 25 0.56
34 20 0.44
ACGTcount: A:0.41, C:0.00, G:0.01, T:0.58
Consensus pattern (34 bp):
TATATATATAATATTTTATATTTTTTATATTAAT
Found at i:99252 original size:2 final size:2
Alignment explanation
Indices: 99245--99273 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
99235 AAATAAAAAT
99245 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
99274 TCTATAGATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:101267 original size:34 final size:34
Alignment explanation
Indices: 101224--101302 Score: 149
Period size: 34 Copynumber: 2.3 Consensus size: 34
101214 TTCCGCAAAA
101224 ATTAATATTTCGTATTCTCAATTTGTTCTCATCG
1 ATTAATATTTCGTATTCTCAATTTGTTCTCATCG
*
101258 ATTAATATTTCGTATTGTCAATTTGTTCTCATCG
1 ATTAATATTTCGTATTCTCAATTTGTTCTCATCG
101292 ATTAATATTTC
1 ATTAATATTTC
101303 TGTTATTGAC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.25, C:0.15, G:0.09, T:0.51
Consensus pattern (34 bp):
ATTAATATTTCGTATTCTCAATTTGTTCTCATCG
Found at i:102156 original size:36 final size:37
Alignment explanation
Indices: 102103--102201 Score: 159
Period size: 36 Copynumber: 2.8 Consensus size: 37
102093 AATTACATCC
102103 ACTTTAGC-TTAGGTAAAAGCTTAA-ACGTAATATGA
1 ACTTTAGCTTTAGGTAAAAGCTTAATACGTAATATGA
* *
102138 ACTTTAGCTTTAGGTAAAAAC-TAATATGTAATATGA
1 ACTTTAGCTTTAGGTAAAAGCTTAATACGTAATATGA
102174 ACTTTAGCTTTAGGTAAAAGCTTAATAC
1 ACTTTAGCTTTAGGTAAAAGCTTAATAC
102202 TTATGAAATA
Statistics
Matches: 57, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
35 11 0.19
36 41 0.72
37 5 0.09
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.34
Consensus pattern (37 bp):
ACTTTAGCTTTAGGTAAAAGCTTAATACGTAATATGA
Found at i:102225 original size:13 final size:13
Alignment explanation
Indices: 102207--102243 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
102197 AATACTTATG
102207 AAATAAAATTGAA
1 AAATAAAATTGAA
102220 AAATAAAATTGAA
1 AAATAAAATTGAA
102233 AAATAAAATTG
1 AAATAAAATTG
102244 TTTAGAATTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (13 bp):
AAATAAAATTGAA
Found at i:106436 original size:14 final size:14
Alignment explanation
Indices: 106417--106454 Score: 76
Period size: 14 Copynumber: 2.7 Consensus size: 14
106407 CAAACAACGT
106417 AATTGGTTTTCTGG
1 AATTGGTTTTCTGG
106431 AATTGGTTTTCTGG
1 AATTGGTTTTCTGG
106445 AATTGGTTTT
1 AATTGGTTTT
106455 TCAGAAAACC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.16, C:0.05, G:0.26, T:0.53
Consensus pattern (14 bp):
AATTGGTTTTCTGG
Found at i:106990 original size:13 final size:14
Alignment explanation
Indices: 106969--106998 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
106959 ATTTATTTTA
106969 ATAATTTTTAAAAT
1 ATAATTTTTAAAAT
106983 ATAA-TTTTAAAAT
1 ATAATTTTTAAAAT
106996 ATA
1 ATA
106999 TATTAATTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
ATAATTTTTAAAAT
Found at i:107124 original size:15 final size:15
Alignment explanation
Indices: 107088--107122 Score: 63
Period size: 14 Copynumber: 2.4 Consensus size: 15
107078 ATTTAGAAAT
107088 TAATTTAAATTTTTA
1 TAATTTAAATTTTTA
107103 TAATTTAAA-TTTTA
1 TAATTTAAATTTTTA
107117 TAATTT
1 TAATTT
107123 TATTTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 11 0.55
15 9 0.45
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (15 bp):
TAATTTAAATTTTTA
Found at i:112169 original size:52 final size:52
Alignment explanation
Indices: 112092--112199 Score: 173
Period size: 52 Copynumber: 2.1 Consensus size: 52
112082 AAACAGTCGT
* *
112092 ATAGTTTAATGATCTCTAGTGTATCTTACTTTGAACTTACG-TTTAAAGTATA
1 ATAGTTTAATGATCCCTAGTATATCTTACTTTGAACTTA-GATTTAAAGTATA
*
112144 ATAGTTTAATGATCCCTAGTATATCTTACTTTGAACTTAGATTTAGAGTATA
1 ATAGTTTAATGATCCCTAGTATATCTTACTTTGAACTTAGATTTAAAGTATA
112196 ATAG
1 ATAG
112200 GTTTCGAGTA
Statistics
Matches: 52, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
51 1 0.02
52 51 0.98
ACGTcount: A:0.32, C:0.11, G:0.14, T:0.43
Consensus pattern (52 bp):
ATAGTTTAATGATCCCTAGTATATCTTACTTTGAACTTAGATTTAAAGTATA
Found at i:117368 original size:22 final size:21
Alignment explanation
Indices: 117340--117427 Score: 72
Period size: 21 Copynumber: 4.0 Consensus size: 21
117330 GATTTCTATT
117340 ATATATATAATTTTTGAAAAC
1 ATATATATAATTTTTGAAAAC
* * *
117361 ATAT-TATATAGTTTTGGAAAT
1 ATATATATA-ATTTTTGAAAAC
117382 ATATA-ATAATTGTTTTGAAAAC
1 ATATATATAA-T-TTTTGAAAAC
*
117404 ATAAAATGTATAATTTTTGAAAAC
1 AT---ATATATAATTTTTGAAAAC
117428 TTAGTTTTTG
Statistics
Matches: 52, Mismatches: 7, Indels: 13
0.72 0.10 0.18
Matches are distributed among these distances:
20 5 0.10
21 20 0.38
22 10 0.19
24 10 0.19
25 3 0.06
26 4 0.08
ACGTcount: A:0.45, C:0.03, G:0.09, T:0.42
Consensus pattern (21 bp):
ATATATATAATTTTTGAAAAC
Found at i:120009 original size:20 final size:21
Alignment explanation
Indices: 119986--120025 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
119976 TAATATAAGA
119986 TAAATT-TTACTTTTAGTATC
1 TAAATTATTACTTTTAGTATC
*
120006 TAAATTATTAGTTTTAGTAT
1 TAAATTATTACTTTTAGTAT
120026 ATTTTAGTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.33, C:0.05, G:0.07, T:0.55
Consensus pattern (21 bp):
TAAATTATTACTTTTAGTATC
Found at i:122617 original size:51 final size:51
Alignment explanation
Indices: 122562--122659 Score: 187
Period size: 51 Copynumber: 1.9 Consensus size: 51
122552 CATGTTCTAG
*
122562 AAACAGATTCATTTATCAATGATGTAACTAGGCCATCTTCAATGTTCCTTC
1 AAACAGATTCATTTATCAATGATGTAACTAGGCCACCTTCAATGTTCCTTC
122613 AAACAGATTCATTTATCAATGATGTAACTAGGCCACCTTCAATGTTC
1 AAACAGATTCATTTATCAATGATGTAACTAGGCCACCTTCAATGTTC
122660 TTTCCCTCGA
Statistics
Matches: 46, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 46 1.00
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (51 bp):
AAACAGATTCATTTATCAATGATGTAACTAGGCCACCTTCAATGTTCCTTC
Found at i:123267 original size:54 final size:54
Alignment explanation
Indices: 123181--123345 Score: 224
Period size: 54 Copynumber: 3.1 Consensus size: 54
123171 TTACCTTTTC
* * * * * *
123181 TGACAGTTATCCTGCGATATTGCAAGATAGACATGATTTTCAAGTGCAAGAGTG
1 TGACAGGTATCCTACGTTATTACAAGACAGACATGATTTTCAAGTGCAAGAGAG
* *
123235 TGACAGGTATCCTACGTTATTACAAGGCAGACATGATTTTCAAGAT-CAAGAGCG
1 TGACAGGTATCCTACGTTATTACAAGACAGACATGATTTTCAAG-TGCAAGAGAG
* *
123289 TGACAGGTATCCTATGTTATTACAAGACAGACATTATTTTCAAGTGCAAGAGAG
1 TGACAGGTATCCTACGTTATTACAAGACAGACATGATTTTCAAGTGCAAGAGAG
123343 TGA
1 TGA
123346 AAATGATGCA
Statistics
Matches: 98, Mismatches: 11, Indels: 4
0.87 0.10 0.04
Matches are distributed among these distances:
53 1 0.01
54 96 0.98
55 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.22, T:0.28
Consensus pattern (54 bp):
TGACAGGTATCCTACGTTATTACAAGACAGACATGATTTTCAAGTGCAAGAGAG
Found at i:131497 original size:20 final size:21
Alignment explanation
Indices: 131472--131515 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
131462 ACGATAATAG
*
131472 TAGAATGCTT-AATTGAGGTT
1 TAGAATGCTTAAATTGAGATT
*
131492 TAGAATGTTTAAATTGAGATT
1 TAGAATGCTTAAATTGAGATT
131513 TAG
1 TAG
131516 CCACACACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 9 0.43
21 12 0.57
ACGTcount: A:0.34, C:0.02, G:0.23, T:0.41
Consensus pattern (21 bp):
TAGAATGCTTAAATTGAGATT
Found at i:136841 original size:2 final size:2
Alignment explanation
Indices: 136836--136862 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
136826 AACATACTCG
136836 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
136863 TTTGTTTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:140024 original size:186 final size:186
Alignment explanation
Indices: 139697--140088 Score: 646
Period size: 186 Copynumber: 2.1 Consensus size: 186
139687 TTTTCTAATT
* * *
139697 TATATAA-AAATTAAATATTTTATAATTCAAAAAAACAGTTTCTAATTAATTTAAATAATATATA
1 TATATAATATATTTAATATTTTATAATTCAAAAAAACAATTTCTAATTAATTTAAATAATATATA
139761 ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTA
66 ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTA
*
139826 TTGGATCTTAAATTATTAATTGGGTTTTAAATGGATTGGGCTGAG-TCCATATATTA
131 TTGGATCTTAAATTATTAATTGAGTTTTAAATGGATTGGGCTGAGCT-CATATATTA
* * *
139882 TATATAATATATTTAATATTTTTTAATTCAGAAAAATAATTTAC-AATTAATTTAAATAATATAT
1 TATATAATATATTTAATATTTTATAATTCAAAAAAACAATTT-CTAATTAATTTAAATAATATAT
*
139946 AATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGGTTTAAAAGTT
65 AATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTT
* *
140011 ATTGGATCTTAAATTATTAATTGAGTTTTAAATGGTTTGGGTTGAGCTCATATATTA
130 ATTGGATCTTAAATTATTAATTGAGTTTTAAATGGATTGGGCTGAGCTCATATATTA
*
140068 TATATAATATATTTAAAATTT
1 TATATAATATATTTAATATTT
140089 AAAATTTTAT
Statistics
Matches: 193, Mismatches: 11, Indels: 5
0.92 0.05 0.02
Matches are distributed among these distances:
185 7 0.04
186 184 0.95
187 2 0.01
ACGTcount: A:0.43, C:0.03, G:0.08, T:0.46
Consensus pattern (186 bp):
TATATAATATATTTAATATTTTATAATTCAAAAAAACAATTTCTAATTAATTTAAATAATATATA
ATTATAAAATAAAAATTTTATATAAATTTTTTAATTAATTAATATTGATTTAGATTTAAAAGTTA
TTGGATCTTAAATTATTAATTGAGTTTTAAATGGATTGGGCTGAGCTCATATATTA
Found at i:141080 original size:31 final size:32
Alignment explanation
Indices: 141027--141094 Score: 95
Period size: 31 Copynumber: 2.2 Consensus size: 32
141017 CACCCCAATT
141027 AAAAAAATATAATATAGACCTTTAAAATTTTC
1 AAAAAAATATAATATAGACCTTTAAAATTTTC
* *
141059 AAAAAAAT-TAAT-TCGACCCTTTAAAATTTTT
1 AAAAAAATATAATATAGA-CCTTTAAAATTTTC
141090 AAAAA
1 AAAAA
141095 TTTAGATCAT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
30 3 0.09
31 22 0.67
32 8 0.24
ACGTcount: A:0.53, C:0.10, G:0.03, T:0.34
Consensus pattern (32 bp):
AAAAAAATATAATATAGACCTTTAAAATTTTC
Found at i:153567 original size:197 final size:199
Alignment explanation
Indices: 153232--153627 Score: 769
Period size: 197 Copynumber: 2.0 Consensus size: 199
153222 GTTCGATTTT
153232 GAGTTTGAATTTCAACTTCAAGTCAAGCTTGAAAGTTTTAGTCTCTTAAGCTTTTGAGCCGAGTC
1 GAGTTTGAATTTCAACTTCAAGTCAAGCTTGAAAGTTTTAGTCTCTTAAGCTTTTGAGCCGAGTC
*
153297 GAGCTCCATTTTAAAGTTTCGAGTTTAGTTGAACTCAATAATACTCGCGCTCATTTACAACCCTA
66 GAGCTCCATTTTAAAGTTTCGAGTTTAGTTGAACTCAATAATACTCGAGCTCATTTACAACCCTA
153362 AACTCAATCCTCCTCTATC-CCCATGACAAAG-AATTAGACACCAACCAACAATTGTACTCAATT
131 AACTCAATCCTCCTCTATCTCCCATGACAAAGAAATTAGACACCAACCAACAATTGTACTCAATT
153425 ATAA
196 ATAA
153429 GAGTTTGAATTTCAACTTCAAGTCAAGCTTGAAAGTTTTAGTCTCTTAAGCTTTTGAGCCGAGTC
1 GAGTTTGAATTTCAACTTCAAGTCAAGCTTGAAAGTTTTAGTCTCTTAAGCTTTTGAGCCGAGTC
153494 GAGCTCCATTTTAAAGTTTCGAGTTTAGTTGAACTCAATAATACTCGAGCTCATTTACAACCCTA
66 GAGCTCCATTTTAAAGTTTCGAGTTTAGTTGAACTCAATAATACTCGAGCTCATTTACAACCCTA
153559 AACTCAATCCTCCTCTATCTCCCATGACAAAGAAATTAGACACCAACCAACAATTGTACTCAATT
131 AACTCAATCCTCCTCTATCTCCCATGACAAAGAAATTAGACACCAACCAACAATTGTACTCAATT
153624 ATAA
196 ATAA
153628 TTCTCCATCT
Statistics
Matches: 196, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
197 148 0.76
198 12 0.06
199 36 0.18
ACGTcount: A:0.32, C:0.23, G:0.13, T:0.32
Consensus pattern (199 bp):
GAGTTTGAATTTCAACTTCAAGTCAAGCTTGAAAGTTTTAGTCTCTTAAGCTTTTGAGCCGAGTC
GAGCTCCATTTTAAAGTTTCGAGTTTAGTTGAACTCAATAATACTCGAGCTCATTTACAACCCTA
AACTCAATCCTCCTCTATCTCCCATGACAAAGAAATTAGACACCAACCAACAATTGTACTCAATT
ATAA
Found at i:167345 original size:24 final size:23
Alignment explanation
Indices: 167318--167395 Score: 61
Period size: 24 Copynumber: 3.3 Consensus size: 23
167308 AGGCAGCGGG
167318 AGAGACGGAGCAGGAGGAAGAGGC
1 AGAGA-GGAGCAGGAGGAAGAGGC
*
167342 AGAGGAGGA-CGAGGAGGCAGAGTG-
1 AGA-GAGGAGC-AGGAGGAAGAG-GC
* * *
167366 AGAGGTGGAGAAGGTGGAAGAGGC
1 AGA-GAGGAGCAGGAGGAAGAGGC
167390 AGAGAG
1 AGAGAG
167396 AGAGGGAGAG
Statistics
Matches: 43, Mismatches: 6, Indels: 11
0.72 0.10 0.18
Matches are distributed among these distances:
23 4 0.09
24 36 0.84
25 3 0.07
ACGTcount: A:0.36, C:0.08, G:0.53, T:0.04
Consensus pattern (23 bp):
AGAGAGGAGCAGGAGGAAGAGGC
Found at i:167350 original size:18 final size:18
Alignment explanation
Indices: 167329--167363 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
167319 GAGACGGAGC
*
167329 AGGAGGAAGAGGCAGAGG
1 AGGACGAAGAGGCAGAGG
*
167347 AGGACGAGGAGGCAGAG
1 AGGACGAAGAGGCAGAG
167364 TGAGAGGTGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.37, C:0.09, G:0.54, T:0.00
Consensus pattern (18 bp):
AGGACGAAGAGGCAGAGG
Found at i:177266 original size:13 final size:13
Alignment explanation
Indices: 177250--177274 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
177240 ACAAATATAT
177250 TAAAAAATAATGG
1 TAAAAAATAATGG
177263 TAAAAAATAATG
1 TAAAAAATAATG
177275 CAAAAATATA
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:0.64, C:0.00, G:0.12, T:0.24
Consensus pattern (13 bp):
TAAAAAATAATGG
Found at i:178077 original size:17 final size:18
Alignment explanation
Indices: 178031--178092 Score: 101
Period size: 18 Copynumber: 3.6 Consensus size: 18
178021 TCATTATTAT
178031 TTTTATTAAAAATTATAA
1 TTTTATTAAAAATTATAA
178049 TTTTATTAAAAATTATAA
1 TTTTATTAAAAATTATAA
178067 TTTTATT-AAAATTA-AA
1 TTTTATTAAAAATTATAA
*
178083 TTTTAATAAA
1 TTTTATTAAA
178093 TGTTTAAATT
Statistics
Matches: 42, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
16 8 0.19
17 9 0.21
18 25 0.60
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (18 bp):
TTTTATTAAAAATTATAA
Found at i:178101 original size:18 final size:18
Alignment explanation
Indices: 178078--178128 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
178068 TTTATTAAAA
*
178078 TTAAATTTTAATAAATGT
1 TTAAATTTAAATAAATGT
*
178096 TTAAATTTAAATAAATTT
1 TTAAATTTAAATAAATGT
*
178114 TTAATATTTATATAA
1 TTAA-ATTTAAATAA
178129 TAAGGATAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
18 20 0.69
19 9 0.31
ACGTcount: A:0.47, C:0.00, G:0.02, T:0.51
Consensus pattern (18 bp):
TTAAATTTAAATAAATGT
Found at i:183401 original size:27 final size:28
Alignment explanation
Indices: 183370--183432 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 28
183360 GCCCAATTTT
* *
183370 TTTATAATT-AGGGCCTCAATTTTTAT-A
1 TTTATAATTAAAGCCCT-AATTTTTATAA
183397 TTTATAATTAAAGCCCTAATTTTTATAA
1 TTTATAATTAAAGCCCTAATTTTTATAA
183425 TTTCATAA
1 TTT-ATAA
183433 ATTTTTTAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
27 18 0.58
28 9 0.29
29 4 0.13
ACGTcount: A:0.35, C:0.11, G:0.06, T:0.48
Consensus pattern (28 bp):
TTTATAATTAAAGCCCTAATTTTTATAA
Found at i:184121 original size:22 final size:21
Alignment explanation
Indices: 184096--184162 Score: 57
Period size: 21 Copynumber: 3.1 Consensus size: 21
184086 TATTCTAATT
184096 ATAAATTATTATTATTATAGAA
1 ATAAATTATT-TTATTATAGAA
* *
184118 AT-AATTAATTTATAACTA-AA
1 ATAAATTATTTTATTA-TAGAA
* *
184138 ATATATTATTTGCATTATAGAA
1 ATAAATTATTT-TATTATAGAA
184160 ATA
1 ATA
184163 GGTAATTTAA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
20 9 0.26
21 16 0.46
22 10 0.29
ACGTcount: A:0.49, C:0.03, G:0.04, T:0.43
Consensus pattern (21 bp):
ATAAATTATTTTATTATAGAA
Found at i:188085 original size:2 final size:2
Alignment explanation
Indices: 188080--188116 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
188070 AAACGCGCGC
188080 AT AT AT 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 AT AT AT A
188117 CAGTGTCTTG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:190178 original size:30 final size:30
Alignment explanation
Indices: 190142--190214 Score: 101
Period size: 30 Copynumber: 2.4 Consensus size: 30
190132 AATCTCATAT
*
190142 AGATGTCAGAACGGGGAATTTATCCCATGC
1 AGATGTCAGAACGGAGAATTTATCCCATGC
* * *
190172 AGATGTCAAAACGGAGAGTTTATCCCATGT
1 AGATGTCAGAACGGAGAATTTATCCCATGC
*
190202 AGATGTTAGAACG
1 AGATGTCAGAACG
190215 AGGACTAAGC
Statistics
Matches: 37, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.33, C:0.16, G:0.26, T:0.25
Consensus pattern (30 bp):
AGATGTCAGAACGGAGAATTTATCCCATGC
Found at i:190230 original size:29 final size:28
Alignment explanation
Indices: 190195--190266 Score: 90
Period size: 28 Copynumber: 2.5 Consensus size: 28
190185 GAGAGTTTAT
* *
190195 CCCATGTAGATGTTAGAACGAGGACTAAG
1 CCCATGTAGA-ATCAGAACGAGGACTAAG
* *
190224 CCCATGTAGAATCAGGACGGGGACTAAG
1 CCCATGTAGAATCAGAACGAGGACTAAG
*
190252 CCCATGCAGAATCAG
1 CCCATGTAGAATCAG
190267 GATGGAGATT
Statistics
Matches: 38, Mismatches: 5, Indels: 1
0.86 0.11 0.02
Matches are distributed among these distances:
28 28 0.74
29 10 0.26
ACGTcount: A:0.33, C:0.22, G:0.28, T:0.17
Consensus pattern (28 bp):
CCCATGTAGAATCAGAACGAGGACTAAG
Found at i:202031 original size:24 final size:23
Alignment explanation
Indices: 201982--202031 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 23
201972 TATGGCATGG
*
201982 TTTTTCAAAAATCATTTTTCATA
1 TTTTTCAAAAATCATTTTTCAAA
202005 TTTTTCTAAAAATC-TTTTTGCAAA
1 TTTTTC-AAAAATCATTTTT-CAAA
202029 TTT
1 TTT
202032 GTTTTAAATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
23 11 0.46
24 13 0.54
ACGTcount: A:0.32, C:0.12, G:0.02, T:0.54
Consensus pattern (23 bp):
TTTTTCAAAAATCATTTTTCAAA
Found at i:202800 original size:30 final size:30
Alignment explanation
Indices: 202659--202800 Score: 131
Period size: 30 Copynumber: 4.7 Consensus size: 30
202649 GATATAATCT
* * **
202659 CATGCATATGTTAGAACGACGAATTTATCC
1 CATGCAGATGTCAGAACGGGGAATTTATCC
* *
202689 CATGCAGATGTCAGAACGAGGAGTTTATCC
1 CATGCAGATGTCAGAACGGGGAATTTATCC
* * ** *
202719 TATGCAGATTTCAGAACGGATAGTTTATCC
1 CATGCAGATGTCAGAACGGGGAATTTATCC
* * * * *
202749 CATGTAGATGTTATAATGGGGAATTTATCA
1 CATGCAGATGTCAGAACGGGGAATTTATCC
*
202779 CATGTAGATGTCAGAACGGGGA
1 CATGCAGATGTCAGAACGGGGA
202801 CTAAGCCCAT
Statistics
Matches: 90, Mismatches: 22, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
30 90 1.00
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (30 bp):
CATGCAGATGTCAGAACGGGGAATTTATCC
Found at i:203335 original size:12 final size:12
Alignment explanation
Indices: 203315--203344 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
203305 TGTTATTACG
*
203315 AAATTATTAAAA
1 AAATAATTAAAA
203327 AAATAATTAAAA
1 AAATAATTAAAA
203339 AAATAA
1 AAATAA
203345 GGAGCCTCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (12 bp):
AAATAATTAAAA
Found at i:203654 original size:14 final size:14
Alignment explanation
Indices: 203635--203662 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
203625 CGTTGGGCAT
203635 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
203649 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
203663 GAGCATCCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.43, G:0.29, T:0.07
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:203669 original size:34 final size:33
Alignment explanation
Indices: 203631--203707 Score: 109
Period size: 34 Copynumber: 2.3 Consensus size: 33
203621 AACACGTTGG
*
203631 GCATCCGAGGCCATCCGACCGAGGCCATCCGAGA
1 GCATCCGAGGCCATCCGAACGA-GCCATCCGAGA
* * *
203665 GCATCCGAGGCCATCCGAACGAGCTATGCGAGG
1 GCATCCGAGGCCATCCGAACGAGCCATCCGAGA
203698 GCATCCGAGG
1 GCATCCGAGG
203708 GTAACCGAGC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
33 18 0.46
34 21 0.54
ACGTcount: A:0.23, C:0.34, G:0.32, T:0.10
Consensus pattern (33 bp):
GCATCCGAGGCCATCCGAACGAGCCATCCGAGA
Found at i:203674 original size:20 final size:21
Alignment explanation
Indices: 203649--203706 Score: 73
Period size: 20 Copynumber: 2.7 Consensus size: 21
203639 GGCCATCCGA
203649 CCGAGGCCATCCGAGAGC-AT
1 CCGAGGCCATCCGAGAGCTAT
203669 CCGAGGCCATCCGAACGAGCTAT
1 CCGAGGCCATCCG-A-GAGCTAT
* *
203692 GCGAGGGCATCCGAG
1 CCGAGGCCATCCGAG
203707 GGTAACCGAG
Statistics
Matches: 33, Mismatches: 2, Indels: 5
0.82 0.05 0.12
Matches are distributed among these distances:
20 13 0.39
21 2 0.06
22 5 0.15
23 13 0.39
ACGTcount: A:0.24, C:0.33, G:0.33, T:0.10
Consensus pattern (21 bp):
CCGAGGCCATCCGAGAGCTAT
Found at i:203707 original size:33 final size:33
Alignment explanation
Indices: 203629--203740 Score: 125
Period size: 33 Copynumber: 3.4 Consensus size: 33
203619 CCAACACGTT
* * *
203629 GGGCATCCGAGGCCATCCGACCGAGGCCATCCGA
1 GGGCATCCGAGGCCATCCGAACGA-GCTATGCGA
*
203663 GAGCATCCGAGGCCATCCGAACGAGCTATGCGA
1 GGGCATCCGAGGCCATCCGAACGAGCTATGCGA
** * * *
203696 GGGCATCCGAGGGTAACCGAGCGAGCTATGCAA
1 GGGCATCCGAGGCCATCCGAACGAGCTATGCGA
*
203729 GGGAATCCGAGG
1 GGGCATCCGAGG
203741 GCAGCCGAGC
Statistics
Matches: 67, Mismatches: 11, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
33 45 0.67
34 22 0.33
ACGTcount: A:0.25, C:0.29, G:0.35, T:0.11
Consensus pattern (33 bp):
GGGCATCCGAGGCCATCCGAACGAGCTATGCGA
Found at i:203708 original size:10 final size:10
Alignment explanation
Indices: 203629--203749 Score: 53
Period size: 10 Copynumber: 11.1 Consensus size: 10
203619 CCAACACGTT
203629 GGGCATCCGA
1 GGGCATCCGA
*
203639 GGCCATCCGA
1 GGGCATCCGA
203649 CCGAGGCCATCCGA
1 --G-GG-CATCCGA
*
203663 GAGCATCCGA
1 GGGCATCCGA
*
203673 GGCCATCCGAA
1 GGGCATCCG-A
* *
203684 CGAGCTATGCGA
1 -GGGC-ATCCGA
203696 GGGCATCCGA
1 GGGCATCCGA
* *
203706 GGGTAACCGA
1 GGGCATCCGA
* *
203716 GCGAGCTATGCAA
1 G-G-GC-ATCCGA
*
203729 GGGAATCCGA
1 GGGCATCCGA
*
203739 GGGCAGCCGA
1 GGGCATCCGA
203749 G
1 G
203750 CGACCTACAA
Statistics
Matches: 80, Mismatches: 21, Indels: 20
0.66 0.17 0.17
Matches are distributed among these distances:
10 50 0.62
11 7 0.09
12 7 0.09
13 9 0.11
14 7 0.09
ACGTcount: A:0.25, C:0.30, G:0.36, T:0.10
Consensus pattern (10 bp):
GGGCATCCGA
Found at i:203741 original size:33 final size:33
Alignment explanation
Indices: 203667--203752 Score: 109
Period size: 33 Copynumber: 2.6 Consensus size: 33
203657 ATCCGAGAGC
* * * * *
203667 ATCCGAGGCCATCCGAACGAGCTATGCGAGGGC
1 ATCCGAGGGCAACCGAGCGAGCTATGCAAGGGA
*
203700 ATCCGAGGGTAACCGAGCGAGCTATGCAAGGGA
1 ATCCGAGGGCAACCGAGCGAGCTATGCAAGGGA
*
203733 ATCCGAGGGCAGCCGAGCGA
1 ATCCGAGGGCAACCGAGCGA
203753 CCTACAAGGT
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.27, C:0.27, G:0.36, T:0.10
Consensus pattern (33 bp):
ATCCGAGGGCAACCGAGCGAGCTATGCAAGGGA
Found at i:203782 original size:29 final size:29
Alignment explanation
Indices: 203749--203814 Score: 114
Period size: 29 Copynumber: 2.3 Consensus size: 29
203739 GGGCAGCCGA
*
203749 GCGACCTACAAGGTCGCCCGGAGTGCATG
1 GCGACCTACAAGGTCGCCCGGAGGGCATG
203778 GCGACCTACAAGGTCGCCCGGAGGGCATG
1 GCGACCTACAAGGTCGCCCGGAGGGCATG
*
203807 ACGACCTA
1 GCGACCTA
203815 TGTGTTGGGC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
29 35 1.00
ACGTcount: A:0.23, C:0.32, G:0.33, T:0.12
Consensus pattern (29 bp):
GCGACCTACAAGGTCGCCCGGAGGGCATG
Found at i:203919 original size:29 final size:29
Alignment explanation
Indices: 203873--203957 Score: 145
Period size: 29 Copynumber: 2.9 Consensus size: 29
203863 GAGCAAGGGT
*
203873 AGGTCGCCCG-GAGTGCATGGCGACCTATA
1 AGGTCGCCCGAAAG-GCATGGCGACCTATA
203902 AGGTCGCCCGAAAGGCATGGCGACCTATA
1 AGGTCGCCCGAAAGGCATGGCGACCTATA
203931 AGGTCGCCCGAAAGGCATGGCGACCTA
1 AGGTCGCCCGAAAGGCATGGCGACCTA
203958 CGGCCAATAC
Statistics
Matches: 54, Mismatches: 1, Indels: 2
0.95 0.02 0.04
Matches are distributed among these distances:
29 52 0.96
30 2 0.04
ACGTcount: A:0.25, C:0.28, G:0.33, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGAAAGGCATGGCGACCTATA
Found at i:205102 original size:21 final size:21
Alignment explanation
Indices: 205076--205125 Score: 68
Period size: 21 Copynumber: 2.5 Consensus size: 21
205066 CGCCGCGACG
205076 ATTTTCTTACTGTTATTTCTT
1 ATTTTCTTACTGTTATTTCTT
* *
205097 ATTTTCTTAATTTTATTTCTT
1 ATTTTCTTACTGTTATTTCTT
205118 -TTTT-TTAC
1 ATTTTCTTAC
205126 CTCCTCTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
19 3 0.12
20 4 0.15
21 19 0.73
ACGTcount: A:0.16, C:0.12, G:0.02, T:0.70
Consensus pattern (21 bp):
ATTTTCTTACTGTTATTTCTT
Found at i:210143 original size:5 final size:5
Alignment explanation
Indices: 210133--210157 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
210123 GGAAGAATTT
210133 TTAGC TTAGC TTAGC TTAGC TTAGC
1 TTAGC TTAGC TTAGC TTAGC TTAGC
210158 GATGAAGTTG
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:0.20, C:0.20, G:0.20, T:0.40
Consensus pattern (5 bp):
TTAGC
Found at i:210245 original size:23 final size:23
Alignment explanation
Indices: 210202--210246 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
210192 ATTATTTATT
* * *
210202 ATTTAAAAATATTTATGATTTTA
1 ATTTAAAAAAATTGATAATTTTA
210225 ATTTAAAAAAATTGATAATTTT
1 ATTTAAAAAAATTGATAATTTT
210247 GGATTAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (23 bp):
ATTTAAAAAAATTGATAATTTTA
Found at i:210341 original size:16 final size:16
Alignment explanation
Indices: 210320--210357 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
210310 CTAAAGCGTC
* *
210320 TTTTAAAAATAATTTT
1 TTTTAAAAAAAATATT
210336 TTTTAAAAAAAATATT
1 TTTTAAAAAAAATATT
210352 TTTTAA
1 TTTTAA
210358 GACAAAAGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (16 bp):
TTTTAAAAAAAATATT
Found at i:210658 original size:30 final size:30
Alignment explanation
Indices: 210588--210722 Score: 127
Period size: 30 Copynumber: 4.6 Consensus size: 30
210578 ATAATAGATC
* *
210588 TAGCAAAAACATGAACTTAAATGA-TTAAA
1 TAGCAAAAACATAAACTTAAATGACTAAAA
* * *
210617 T-GATAAAAACATAAACTCAAAAGACTAAAA
1 TAG-CAAAAACATAAACTTAAATGACTAAAA
* *
210647 TAGCTAAAACATAAATTTAAATGAC-ATAAA
1 TAGCAAAAACATAAACTTAAATGACTA-AAA
* *
210677 TAGCAAAAACAGAAACTTAAGTGACTAAAA
1 TAGCAAAAACATAAACTTAAATGACTAAAA
210707 TA--AAATAACATAAACT
1 TAGCAAA-AACATAAACT
210723 AAAGTGTCAA
Statistics
Matches: 85, Mismatches: 15, Indels: 12
0.76 0.13 0.11
Matches are distributed among these distances:
28 4 0.05
29 28 0.33
30 51 0.60
31 2 0.02
ACGTcount: A:0.59, C:0.12, G:0.08, T:0.21
Consensus pattern (30 bp):
TAGCAAAAACATAAACTTAAATGACTAAAA
Found at i:211595 original size:3 final size:3
Alignment explanation
Indices: 211587--211621 Score: 54
Period size: 3 Copynumber: 12.0 Consensus size: 3
211577 TAATTAGATG
*
211587 ATA ATA ATA ATT ATA ATA ATA ATA ATA AT- ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
211622 TACTTTTTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
2 2 0.07
3 27 0.93
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (3 bp):
ATA
Found at i:212813 original size:2 final size:2
Alignment explanation
Indices: 212774--212799 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
212764 TTGCTTCGAC
212774 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
212800 GGGTAAAGTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:213058 original size:35 final size:34
Alignment explanation
Indices: 213012--213108 Score: 124
Period size: 35 Copynumber: 2.8 Consensus size: 34
213002 AACACAATCA
*
213012 TCAATTACATTCTAAACCCCAAAATTCAAAATGCT
1 TCAATTACATTCTAAACCCC-AAATTCAAAATACT
**
213047 TCAATTACATTCTAAACCTTAAATTCCAAAATACT
1 TCAATTACATTCTAAACCCCAAATT-CAAAATACT
*
213082 TCAATTACATGGCT-AACCCCAAATTCA
1 TCAATTACAT-TCTAAACCCCAAATTCA
213109 CAATCCATTC
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
34 7 0.13
35 45 0.83
36 2 0.04
ACGTcount: A:0.41, C:0.26, G:0.03, T:0.30
Consensus pattern (34 bp):
TCAATTACATTCTAAACCCCAAATTCAAAATACT
Found at i:213467 original size:148 final size:147
Alignment explanation
Indices: 213262--213553 Score: 485
Period size: 148 Copynumber: 2.0 Consensus size: 147
213252 AAATACTCAA
* * * * *
213262 TTCAGTTTATAAAATAGTTGACTCAATTTTTTTTGATTTGAGTTTATAAAATTTAAATCAAGTCG
1 TTCAGTTTATAAAATAGTTGACTCAAATATTTTCGATTTGAGTTTATAAAATTTAAATAAAGTCA
* * *
213327 AATTGAATTGAACTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATCATATTATAATATT
66 AATTAAATTGAACTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATATT
213392 ATTTGATTCTAATTCAG
131 ATTTGATTCTAATTCAG
*
213409 TTCAGTTTATAAAATAGTTGACTCGAAATATTTTCGATTTGAGTTTATAAAATTTAAATAAATTC
1 TTCAGTTTATAAAATAGTTGACTC-AAATATTTTCGATTTGAGTTTATAAAATTTAAATAAAGTC
*
213474 AAATTAAATTGAATTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATAT
65 AAATTAAATTGAACTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATAT
213539 TATTTGATTCTAATT
130 TATTTGATTCTAATT
213554 TAAATAGTTT
Statistics
Matches: 134, Mismatches: 10, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
147 24 0.18
148 110 0.82
ACGTcount: A:0.37, C:0.07, G:0.09, T:0.47
Consensus pattern (147 bp):
TTCAGTTTATAAAATAGTTGACTCAAATATTTTCGATTTGAGTTTATAAAATTTAAATAAAGTCA
AATTAAATTGAACTTTCGAGTTTCTGTTTAAATTTAATTATAAATATTTATAATACTATAATATT
ATTTGATTCTAATTCAG
Found at i:214125 original size:35 final size:36
Alignment explanation
Indices: 214058--214134 Score: 129
Period size: 35 Copynumber: 2.2 Consensus size: 36
214048 GGGGTTGTCT
*
214058 ATGTAATTGAAGTATTTTTAGAATTTGAGGTTTAGA
1 ATGTAATTGAAGTATTTTTAGAAATTGAGGTTTAGA
*
214094 ATGTAATTGAAGTA-TTTTAGAAATTGGGGTTTAGA
1 ATGTAATTGAAGTATTTTTAGAAATTGAGGTTTAGA
214129 ATGTAA
1 ATGTAA
214135 ATGATGATTG
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
35 25 0.64
36 14 0.36
ACGTcount: A:0.35, C:0.00, G:0.23, T:0.42
Consensus pattern (36 bp):
ATGTAATTGAAGTATTTTTAGAAATTGAGGTTTAGA
Found at i:218211 original size:37 final size:38
Alignment explanation
Indices: 218165--218323 Score: 137
Period size: 37 Copynumber: 4.3 Consensus size: 38
218155 TTATCTAAGG
* *
218165 ATTTGTATTCAATTAAAATACGATTATA-TAATTACAA
1 ATTTATATTCAATTAAAATACGAATATATTAATTACAA
* * * * *
218202 ATTTATATTCGATTGAAATATGAATATATTATTTATAA
1 ATTTATATTCAATTAAAATACGAATATATTAATTACAA
* * * **
218240 ATTTATA-TCTGATT-AAATACAAATATATTATTTATGA
1 ATTTATATTC-AATTAAAATACGAATATATTAATTACAA
* * * *
218277 ATTTATGTTCAATTAAAATATGGATATATT-ATTACGA
1 ATTTATATTCAATTAAAATACGAATATATTAATTACAA
218314 ATTTATATTC
1 ATTTATATTC
218324 GTTTGGAATA
Statistics
Matches: 100, Mismatches: 18, Indels: 8
0.79 0.14 0.06
Matches are distributed among these distances:
37 68 0.68
38 32 0.32
ACGTcount: A:0.42, C:0.06, G:0.07, T:0.45
Consensus pattern (38 bp):
ATTTATATTCAATTAAAATACGAATATATTAATTACAA
Found at i:221173 original size:37 final size:37
Alignment explanation
Indices: 221017--221179 Score: 112
Period size: 37 Copynumber: 4.4 Consensus size: 37
221007 TTATTTAAGG
* * * *
221017 ATTTATATTTAATTAAAATTTGAATATGTTATTACAA
1 ATTTATATTCAATTAAAATATGAATATATAATTACAA
* * * * * * *
221054 ACTTATATTCGATTGAAATAGGAATAGATTATCTGCAA
1 ATTTATATTCAATTAAAATATGAATATATAAT-TACAA
* ** ** * * *
221092 ATGTATATTTGATT-AAATACAAAAATATTATTTATAA
1 ATTTATATTCAATTAAAATATGAATATA-TAATTACAA
* *
221129 ATCTATATTCAATTAAAATATGAATATATAATTACTA
1 ATTTATATTCAATTAAAATATGAATATATAATTACAA
221166 ATTTATATTCAATT
1 ATTTATATTCAATT
221180 GGAATACAAT
Statistics
Matches: 93, Mismatches: 30, Indels: 6
0.72 0.23 0.05
Matches are distributed among these distances:
37 66 0.71
38 27 0.29
ACGTcount: A:0.44, C:0.06, G:0.07, T:0.43
Consensus pattern (37 bp):
ATTTATATTCAATTAAAATATGAATATATAATTACAA
Found at i:222069 original size:20 final size:20
Alignment explanation
Indices: 221994--222166 Score: 233
Period size: 20 Copynumber: 8.7 Consensus size: 20
221984 GCGAATATGA
* *
221994 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
222014 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
222034 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
222054 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
222074 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
222094 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* *
222114 AAATCGCAACG-ATAATCAGT
1 AAATCGCAACGCGT-ATCCGT
*
222134 AAATTGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
222154 AAATTGCAACGCG
1 AAATCGCAACGCG
222167 ATTTTTAAAG
Statistics
Matches: 137, Mismatches: 13, Indels: 6
0.88 0.08 0.04
Matches are distributed among these distances:
19 1 0.01
20 133 0.97
21 3 0.02
ACGTcount: A:0.34, C:0.27, G:0.19, T:0.21
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:222585 original size:33 final size:33
Alignment explanation
Indices: 222546--222616 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
222536 TTCACTTAGA
222546 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
222579 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
222612 TTTCA
1 TTTCA
222617 AGTTAGTATT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:222722 original size:21 final size:20
Alignment explanation
Indices: 222696--222802 Score: 102
Period size: 21 Copynumber: 5.5 Consensus size: 20
222686 TGCAGAAGAG
222696 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGA-AAATGAAAA
* **
222717 TCGCAACGTGAAAATGACTA
1 TCGCAACGAGAAAATGAAAA
222737 TCTGCAACGAGAAAAATGAAAA
1 TC-GCAACGAG-AAAATGAAAA
222759 TCGCAACGAG---A-G--AA
1 TCGCAACGAGAAAATGAAAA
*
222773 TCGCAACGCG-AAATGAAAA
1 TCGCAACGAGAAAATGAAAA
222792 TCGCAACGAGA
1 TCGCAACGAGA
222803 GAATCGCAAC
Statistics
Matches: 70, Mismatches: 8, Indels: 17
0.74 0.08 0.18
Matches are distributed among these distances:
14 11 0.16
16 2 0.03
17 2 0.03
19 11 0.16
20 9 0.13
21 25 0.36
22 10 0.14
ACGTcount: A:0.47, C:0.19, G:0.21, T:0.13
Consensus pattern (20 bp):
TCGCAACGAGAAAATGAAAA
Found at i:222776 original size:14 final size:14
Alignment explanation
Indices: 222757--222813 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
222747 GAAAAATGAA
222757 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
222771 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
222790 AATCGCAACGAGAG
1 AATCGCAACGAGAG
222804 AATCGCAACG
1 AATCGCAACG
222814 CGAAACCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.28
ACGTcount: A:0.44, C:0.23, G:0.25, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:222788 original size:33 final size:33
Alignment explanation
Indices: 222750--222829 Score: 142
Period size: 33 Copynumber: 2.4 Consensus size: 33
222740 GCAACGAGAA
222750 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
222783 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
1 AAATGAAAATCGCAACGAGAGAATCGCAACGCG
**
222816 AAACCAAAATCGCA
1 AAATGAAAATCGCA
222830 TTGCGATTTT
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 45 1.00
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (33 bp):
AAATGAAAATCGCAACGAGAGAATCGCAACGCG
Found at i:222847 original size:19 final size:19
Alignment explanation
Indices: 222825--222952 Score: 87
Period size: 19 Copynumber: 7.1 Consensus size: 19
222815 GAAACCAAAA
*
222825 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
222844 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
222858 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
222877 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
222891 TCTCGTTGCGATTTTCATTT
1 TCGCGTTGCGATTTTCA-TT
* ***
222911 CTCTCGTTGCGACAGTCATT
1 -TCGCGTTGCGATTTTCATT
*
222931 CTCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
222951 TC
1 TC
222953 AACCAAAAGA
Statistics
Matches: 87, Mismatches: 10, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
14 20 0.23
16 6 0.07
17 6 0.07
19 22 0.25
20 19 0.22
21 14 0.16
ACGTcount: A:0.11, C:0.25, G:0.19, T:0.45
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:222866 original size:14 final size:14
Alignment explanation
Indices: 222847--222903 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
222837 TTTCATTTCG
222847 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
222861 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
222880 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
222894 CGTTGCGATT
1 CGTTGCGATT
222904 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:222872 original size:33 final size:33
Alignment explanation
Indices: 222830--222952 Score: 165
Period size: 33 Copynumber: 3.5 Consensus size: 33
222820 CAAAATCGCA
222830 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
222863 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
*
222896 TTGCGATTTTCATTTCTCTCGTTGCGACAGTCATTCTCTCG
1 TTGCGATTTTCA-TT-TCGCGTT--G-C-G--ATTCTCTCG
222937 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
222953 AACCAAAAGA
Statistics
Matches: 81, Mismatches: 1, Indels: 10
0.88 0.01 0.11
Matches are distributed among these distances:
33 45 0.56
34 2 0.02
35 6 0.07
37 1 0.01
38 1 0.01
39 3 0.04
40 2 0.02
41 21 0.26
ACGTcount: A:0.11, C:0.24, G:0.19, T:0.46
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:222914 original size:21 final size:21
Alignment explanation
Indices: 222888--222952 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
222878 CGCGTTGCGA
222888 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
222909 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
222929 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
222950 TTC
1 TTC
222953 AACCAAAAGA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
20 17 0.46
21 20 0.54
ACGTcount: A:0.11, C:0.26, G:0.15, T:0.48
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:223157 original size:24 final size:24
Alignment explanation
Indices: 223123--223169 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
223113 CTGAAACATC
223123 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
223147 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
223170 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:223891 original size:20 final size:20
Alignment explanation
Indices: 223862--224032 Score: 136
Period size: 20 Copynumber: 8.6 Consensus size: 20
223852 AAATTTCAGT
* *
223862 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACAGATTATC
* *
223882 GTTGCAATTTACGGATTATC
1 GTTGCGATTTACAGATTATC
*
223902 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACAGATTATC
*
223922 GTTGCGATTTACTGATTATC
1 GTTGCGATTTACAGATTATC
* *
223942 GTTGCGATTTACGGA-TACGC
1 GTTGCGATTTACAGATTA-TC
* *
223962 GTTGCGATATACGGA-TA-C
1 GTTGCGATTTACAGATTATC
* *
223980 GCATTGCGATTTACGGA-TACGC
1 G--TTGCGATTTACAGATTA-TC
* *
224002 GTTGCGATTTACGGA-TACAC
1 GTTGCGATTTACAGATTA-TC
224022 GTTGCGATTTA
1 GTTGCGATTTA
224033 TGTGTTCGCG
Statistics
Matches: 132, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
18 2 0.02
19 2 0.02
20 126 0.95
22 2 0.02
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTACAGATTATC
Found at i:223965 original size:60 final size:60
Alignment explanation
Indices: 223862--224032 Score: 193
Period size: 60 Copynumber: 2.9 Consensus size: 60
223852 AAATTTCAGT
* * * * * *
223862 GTTGTGATTTACAGATTCTCGTTGCAATTTACGGATTA-TCGTTGCGATTTACAGATTCTC
1 GTTGCGATTTACAGATTATCGTTGCGATTTACGGA-TACACGTTGCGATTTACAGATACGC
* * * *
223922 GTTGCGATTTACTGATTATCGTTGCGATTTACGGATACGCGTTGCGATATACGGATACGC
1 GTTGCGATTTACAGATTATCGTTGCGATTTACGGATACACGTTGCGATTTACAGATACGC
* * *
223982 ATTGCGATTTACGGA-TACGCGTTGCGATTTACGGATACACGTTGCGATTTA
1 GTTGCGATTTACAGATTA-TCGTTGCGATTTACGGATACACGTTGCGATTTA
224033 TGTGTTCGCG
Statistics
Matches: 95, Mismatches: 14, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
59 4 0.04
60 91 0.96
ACGTcount: A:0.22, C:0.18, G:0.24, T:0.36
Consensus pattern (60 bp):
GTTGCGATTTACAGATTATCGTTGCGATTTACGGATACACGTTGCGATTTACAGATACGC
Found at i:224043 original size:40 final size:40
Alignment explanation
Indices: 223862--224051 Score: 199
Period size: 40 Copynumber: 4.8 Consensus size: 40
223852 AAATTTCAGT
* * * * *
223862 GTTGTGATTTACAGATTCTCGTTGCAATTTACGGATTATC
1 GTTGCGATTTACGGATACGCGTTGCGATTTACGGATTATC
* * * *
223902 GTTGCGATTTACAGATTCTCGTTGCGATTTACTGATTATC
1 GTTGCGATTTACGGATACGCGTTGCGATTTACGGATTATC
*
223942 GTTGCGATTTACGGATACGCGTTGCGATATACGGA-TA-C
1 GTTGCGATTTACGGATACGCGTTGCGATTTACGGATTATC
*
223980 GCATTGCGATTTACGGATACGCGTTGCGATTTACGGA-TACAC
1 G--TTGCGATTTACGGATACGCGTTGCGATTTACGGATTA-TC
* *
224022 GTTGCGATTTATGTG-TTCGCGTTGCGATTT
1 GTTGCGATTTACG-GATACGCGTTGCGATTT
224052 TCATATTCGC
Statistics
Matches: 134, Mismatches: 11, Indels: 10
0.86 0.07 0.06
Matches are distributed among these distances:
38 2 0.01
39 2 0.01
40 127 0.95
41 1 0.01
42 2 0.01
ACGTcount: A:0.21, C:0.17, G:0.25, T:0.37
Consensus pattern (40 bp):
GTTGCGATTTACGGATACGCGTTGCGATTTACGGATTATC
Found at i:224044 original size:20 final size:20
Alignment explanation
Indices: 223999--224070 Score: 67
Period size: 20 Copynumber: 3.6 Consensus size: 20
223989 TTTACGGATA
* *
223999 CGCGTTGCGATTTACG-GATA
1 CGCGTTGCGATTTATGTG-TT
*
224019 CACGTTGCGATTTATGTGTT
1 CGCGTTGCGATTTATGTGTT
* *
224039 CGCGTTGCGATTT-TCATATT
1 CGCGTTGCGATTTAT-GTGTT
224059 CGCGTTGCGATT
1 CGCGTTGCGATT
224071 CTGTAAAATC
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
19 1 0.02
20 42 0.95
21 1 0.02
ACGTcount: A:0.15, C:0.19, G:0.26, T:0.39
Consensus pattern (20 bp):
CGCGTTGCGATTTATGTGTT
Found at i:224047 original size:60 final size:59
Alignment explanation
Indices: 223862--224070 Score: 188
Period size: 60 Copynumber: 3.5 Consensus size: 59
223852 AAATTTCAGT
* * * * * * *
223862 GTTGTGATTTACAGATTCTCGTTGCAATTTACGGATTA-TCGTTGCGATTTACAGATTCTC
1 GTTGCGATTTACAGATACGCGTTGCGATTTACGGA-TACACGTTGCGATTTA-AGGTTCGC
* * * * * *
223922 GTTGCGATTTACTGATTA-TCGTTGCGATTTACGGATACGCGTTGCGATATACGGATACGC
1 GTTGCGATTTACAGA-TACGCGTTGCGATTTACGGATACACGTTGCGATTTAAGG-TTCGC
* * *
223982 ATTGCGATTTACGGATACGCGTTGCGATTTACGGATACACGTTGCGATTTATGTGTTCGC
1 GTTGCGATTTACAGATACGCGTTGCGATTTACGGATACACGTTGCGATTTAAG-GTTCGC
* * *
224042 GTTGCGATTTTCATATTCGCGTTGCGATT
1 GTTGCGATTTACAGATACGCGTTGCGATT
224071 CTGTAAAATC
Statistics
Matches: 122, Mismatches: 22, Indels: 10
0.79 0.14 0.06
Matches are distributed among these distances:
59 5 0.04
60 115 0.94
61 2 0.02
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (59 bp):
GTTGCGATTTACAGATACGCGTTGCGATTTACGGATACACGTTGCGATTTAAGGTTCGC
Found at i:224088 original size:21 final size:20
Alignment explanation
Indices: 224064--224134 Score: 54
Period size: 21 Copynumber: 3.4 Consensus size: 20
224054 ATATTCGCGT
224064 TGCGATTCTGTAAAATCGCAA
1 TGCGATT-TGTAAAATCGCAA
** *
224085 TGCGAATTTGTACTATCGCAT
1 TGCG-ATTTGTAAAATCGCAA
**
224106 TGCGA-TTGTCAAGAATCGCGT
1 TGCGATTTGT-AA-AATCGCAA
224127 TGCGATTT
1 TGCGATTT
224135 TGGAAACTGG
Statistics
Matches: 40, Mismatches: 6, Indels: 7
0.75 0.11 0.13
Matches are distributed among these distances:
19 4 0.10
20 2 0.05
21 29 0.73
22 5 0.12
ACGTcount: A:0.25, C:0.18, G:0.23, T:0.34
Consensus pattern (20 bp):
TGCGATTTGTAAAATCGCAA
Found at i:224722 original size:15 final size:15
Alignment explanation
Indices: 224702--224754 Score: 56
Period size: 16 Copynumber: 3.4 Consensus size: 15
224692 ATGTAAGATT
224702 AAGAAAATGTGTTAC
1 AAGAAAATGTGTTAC
224717 AAGAAAAATGTAAGATT--
1 AAG-AAAATGT--G-TTAC
224734 AAGAAAATGTGTTAC
1 AAGAAAATGTGTTAC
224749 AAGAAA
1 AAGAAA
224755 TATTAATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
13 2 0.06
14 1 0.03
15 9 0.28
16 14 0.44
17 3 0.09
18 1 0.03
19 2 0.06
ACGTcount: A:0.55, C:0.04, G:0.19, T:0.23
Consensus pattern (15 bp):
AAGAAAATGTGTTAC
Found at i:224727 original size:32 final size:32
Alignment explanation
Indices: 224691--224754 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
224681 AATACAACTT
224691 AATGTAAGATTAAGAAAATGTGTTACAAGAAA
1 AATGTAAGATTAAGAAAATGTGTTACAAGAAA
224723 AATGTAAGATTAAGAAAATGTGTTACAAGAAA
1 AATGTAAGATTAAGAAAATGTGTTACAAGAAA
224755 TATTAATTTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.53, C:0.03, G:0.19, T:0.25
Consensus pattern (32 bp):
AATGTAAGATTAAGAAAATGTGTTACAAGAAA
Found at i:224908 original size:21 final size:21
Alignment explanation
Indices: 224884--224940 Score: 69
Period size: 22 Copynumber: 2.7 Consensus size: 21
224874 CGAAAATATT
*
224884 CATTTTAAGTAGCAAAATTAA
1 CATTTTAAGTAGCAAAAATAA
* *
224905 CATTTTTAGTAGAAAAAAATAA
1 CATTTTAAGTAG-CAAAAATAA
*
224927 CATATTAAGTAGCA
1 CATTTTAAGTAGCA
224941 CTCAATTGAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
21 12 0.41
22 17 0.59
ACGTcount: A:0.49, C:0.09, G:0.11, T:0.32
Consensus pattern (21 bp):
CATTTTAAGTAGCAAAAATAA
Found at i:226849 original size:10 final size:10
Alignment explanation
Indices: 226834--226894 Score: 68
Period size: 10 Copynumber: 5.7 Consensus size: 10
226824 AAACGTATTT
226834 ATGAACAGTA
1 ATGAACAGTA
*
226844 ATGAACATTA
1 ATGAACAGTA
226854 CCATGAACAGTA
1 --ATGAACAGTA
*
226866 ATGAACAATA
1 ATGAACAGTA
226876 CCATGAACAGTA
1 --ATGAACAGTA
226888 ATGAACA
1 ATGAACA
226895 ATACCGAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
10 25 0.58
12 18 0.42
ACGTcount: A:0.49, C:0.16, G:0.15, T:0.20
Consensus pattern (10 bp):
ATGAACAGTA
Found at i:226862 original size:22 final size:22
Alignment explanation
Indices: 226834--226899 Score: 123
Period size: 22 Copynumber: 3.0 Consensus size: 22
226824 AAACGTATTT
*
226834 ATGAACAGTAATGAACATTACC
1 ATGAACAGTAATGAACAATACC
226856 ATGAACAGTAATGAACAATACC
1 ATGAACAGTAATGAACAATACC
226878 ATGAACAGTAATGAACAATACC
1 ATGAACAGTAATGAACAATACC
226900 GAATACTAAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.20
Consensus pattern (22 bp):
ATGAACAGTAATGAACAATACC
Found at i:227718 original size:23 final size:23
Alignment explanation
Indices: 227628--227711 Score: 114
Period size: 23 Copynumber: 3.7 Consensus size: 23
227618 CACCACAGCT
*
227628 CGTATAAATGCACCGAAGTACAA
1 CGTAGAAATGCACCGAAGTACAA
*
227651 CGTAGAATTGCACCGAAGTACAA
1 CGTAGAAATGCACCGAAGTACAA
* * **
227674 CGTAGAATTGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTACAA
227697 CGTAGAAATGCACCG
1 CGTAGAAATGCACCG
227712 TAGTGCCATA
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 55 1.00
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTACAA
Found at i:227868 original size:23 final size:23
Alignment explanation
Indices: 227832--227875 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
227822 AATACATATA
* *
227832 TGTCCCGAAGGACCACGTAGAAT
1 TGTCCCAAAAGACCACGTAGAAT
*
227855 TGTCCCAAAAGACCTCGTAGA
1 TGTCCCAAAAGACCACGTAGA
227876 CCCTCGACTC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.32, C:0.27, G:0.23, T:0.18
Consensus pattern (23 bp):
TGTCCCAAAAGACCACGTAGAAT
Found at i:228544 original size:22 final size:22
Alignment explanation
Indices: 228518--228559 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
228508 TAATTTCTGA
*
228518 TCATAT-ACTTTATTATACAAAT
1 TCATATGA-TTTATTACACAAAT
228540 TCATATGATTTATTACACAA
1 TCATATGATTTATTACACAA
228560 TCATTTATTC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 17 0.94
23 1 0.06
ACGTcount: A:0.40, C:0.14, G:0.02, T:0.43
Consensus pattern (22 bp):
TCATATGATTTATTACACAAAT
Found at i:228563 original size:20 final size:21
Alignment explanation
Indices: 228517--228563 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 21
228507 CTAATTTCTG
*
228517 ATCATATACTTTATTATACAA
1 ATCATATACTTTATTACACAA
228538 ATTCATATGA-TTTATTACAC-A
1 A-TCATAT-ACTTTATTACACAA
228559 ATCAT
1 ATCAT
228564 TTATTCCTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
20 4 0.17
21 3 0.13
22 15 0.65
23 1 0.04
ACGTcount: A:0.40, C:0.15, G:0.02, T:0.43
Consensus pattern (21 bp):
ATCATATACTTTATTACACAA
Found at i:230788 original size:12 final size:12
Alignment explanation
Indices: 230771--230820 Score: 55
Period size: 12 Copynumber: 4.2 Consensus size: 12
230761 ATAACCGTTT
*
230771 TACATGCATATA
1 TACATGCATACA
*
230783 TACATGCATGCA
1 TACATGCATACA
*
230795 TGCATGCATACA
1 TACATGCATACA
* *
230807 TGCATGCATGCA
1 TACATGCATACA
230819 TA
1 TA
230821 ACTGGTGAAA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.34, C:0.22, G:0.16, T:0.28
Consensus pattern (12 bp):
TACATGCATACA
Found at i:230794 original size:4 final size:4
Alignment explanation
Indices: 230785--230819 Score: 61
Period size: 4 Copynumber: 8.8 Consensus size: 4
230775 TGCATATATA
*
230785 CATG CATG CATG CATG CATA CATG CATG CATG CAT
1 CATG CATG CATG CATG CATG CATG CATG CATG CAT
230820 AACTGGTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.29, C:0.26, G:0.20, T:0.26
Consensus pattern (4 bp):
CATG
Found at i:231506 original size:2 final size:2
Alignment explanation
Indices: 231495--231528 Score: 54
Period size: 2 Copynumber: 18.0 Consensus size: 2
231485 ATAAACAAAA
231495 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
231529 TATGATGTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
1 2 0.07
2 28 0.93
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:231967 original size:10 final size:10
Alignment explanation
Indices: 231952--231989 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
231942 TATCACACCT
231952 AATTCTCTCA
1 AATTCTCTCA
231962 AATTCTCT-A
1 AATTCTCTCA
231971 AATTTCTCTCA
1 AA-TTCTCTCA
*
231982 AATACTCT
1 AATTCTCT
231990 ATCTCTTTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
9 3 0.12
10 19 0.76
11 3 0.12
ACGTcount: A:0.32, C:0.26, G:0.00, T:0.42
Consensus pattern (10 bp):
AATTCTCTCA
Found at i:232311 original size:111 final size:111
Alignment explanation
Indices: 232117--232449 Score: 630
Period size: 111 Copynumber: 3.0 Consensus size: 111
232107 TGAAAATCAT
*
232117 ATATCTCTACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
232182 TATTTAGTTGATTTATTTAATGCATGATTATTAAATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAAATTAAGAATTAA
*
232228 ATATCTCGACACTTTGCTGATACGGTAATATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
*
232293 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAAATTAAGAATTAA
232339 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
232404 TAATTAGTTGATTTATTTAATGCATGATTATTAAATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAAATTAAGAATTAA
232450 TTATTGTAAT
Statistics
Matches: 216, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 216 1.00
ACGTcount: A:0.36, C:0.08, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTGCTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAAATTAAGAATTAA
Found at i:234327 original size:27 final size:27
Alignment explanation
Indices: 234281--234332 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
234271 ACCTGCTCAA
*
234281 GACGACGACAATGACAATGACGATGGT
1 GACGACGACAACGACAATGACGATGGT
* * *
234308 GACGACGACGACGACGATGATGATG
1 GACGACGACAACGACAATGACGATG
234333 ACAATGAGGA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.35, C:0.19, G:0.33, T:0.13
Consensus pattern (27 bp):
GACGACGACAACGACAATGACGATGGT
Found at i:234518 original size:26 final size:25
Alignment explanation
Indices: 234444--234514 Score: 67
Period size: 25 Copynumber: 2.8 Consensus size: 25
234434 TTTATATTTG
234444 TATTTACTTTATTTTGTTTAATTGTAA
1 TATTTACTTTATTTTG-TTAATT-TAA
* *
234471 T-TTT-TTTTATTATT-TCTCATTTAA
1 TATTTACTTTATT-TTGT-TAATTTAA
234495 TATTTACTTTATTTTGTTAA
1 TATTTACTTTATTTTGTTAA
234515 ATTTGTTGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 12
0.69 0.08 0.24
Matches are distributed among these distances:
24 5 0.14
25 17 0.49
26 12 0.34
27 1 0.03
ACGTcount: A:0.24, C:0.06, G:0.04, T:0.66
Consensus pattern (25 bp):
TATTTACTTTATTTTGTTAATTTAA
Found at i:234586 original size:35 final size:32
Alignment explanation
Indices: 234551--234631 Score: 83
Period size: 35 Copynumber: 2.3 Consensus size: 32
234541 TTTAGTTAAT
234551 TTTGTT-TATTACCATTTAATATCAGTTATTGTAA
1 TTTGTTATATTACCATTTAAT-TC--TTATTGTAA
234585 TTTGATTATCATTTACCATTTAATTCTTATTGTAA
1 TTTG-TTAT-A-TTACCATTTAATTCTTATTGTAA
*
234620 GTTTGTTGTATT
1 -TTTGTTATATT
234632 TAAATACCAA
Statistics
Matches: 41, Mismatches: 1, Indels: 11
0.77 0.02 0.21
Matches are distributed among these distances:
33 2 0.05
34 5 0.12
35 14 0.34
36 5 0.12
37 3 0.07
38 12 0.29
ACGTcount: A:0.26, C:0.09, G:0.10, T:0.56
Consensus pattern (32 bp):
TTTGTTATATTACCATTTAATTCTTATTGTAA
Found at i:249083 original size:15 final size:15
Alignment explanation
Indices: 249063--249113 Score: 57
Period size: 16 Copynumber: 3.3 Consensus size: 15
249053 GTTTACTTTA
*
249063 GAATGATTAAGCGTT
1 GAATGATTAAACGTT
*
249078 GAATGATTTAAATGTT
1 GAATGA-TTAAACGTT
*
249094 GAATGATTCAAATGTT
1 GAATGATT-AAACGTT
249110 GAAT
1 GAAT
249114 AATTCAGAGA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
15 8 0.25
16 24 0.75
ACGTcount: A:0.37, C:0.04, G:0.22, T:0.37
Consensus pattern (15 bp):
GAATGATTAAACGTT
Found at i:249094 original size:16 final size:16
Alignment explanation
Indices: 249075--249119 Score: 72
Period size: 16 Copynumber: 2.8 Consensus size: 16
249065 ATGATTAAGC
*
249075 GTTGAATGATTTAAAT
1 GTTGAATGATTCAAAT
249091 GTTGAATGATTCAAAT
1 GTTGAATGATTCAAAT
*
249107 GTTGAATAATTCA
1 GTTGAATGATTCA
249120 GAGACTCTGT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 27 1.00
ACGTcount: A:0.38, C:0.04, G:0.18, T:0.40
Consensus pattern (16 bp):
GTTGAATGATTCAAAT
Found at i:251129 original size:12 final size:12
Alignment explanation
Indices: 251112--251141 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
251102 CATTAAAATT
251112 CAAAATACGAAA
1 CAAAATACGAAA
*
251124 CAAAATACGAGA
1 CAAAATACGAAA
251136 CAAAAT
1 CAAAAT
251142 GATCATGTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.63, C:0.17, G:0.10, T:0.10
Consensus pattern (12 bp):
CAAAATACGAAA
Found at i:252248 original size:2 final size:2
Alignment explanation
Indices: 252241--252273 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
252231 CTGAAATTAT
252241 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
252274 TATTTAGCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Done.