Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr2
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: 41236440
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 2030548 characters in sequence are not A, C, G, or T
File 83 of 106
Found at i:31548258 original size:111 final size:108
Alignment explanation
Indices: 31548108--31548322 Score: 340
Period size: 111 Copynumber: 2.0 Consensus size: 108
31548098 ATATTCATAC
* ** *
31548108 ATAAGCTAAAAGAAATTGAAACAAACTATCAAGGTCATCATCAAAATATAAGAATTAAGACTAAT
1 ATAAGCTAAAAAAAATTGAAACAAACTATCAAAATCATCATCAAAATATAAGAATCAAGACTAAT
**
31548173 TCCCATTCATGTTTACAATAAAAAAATGTTAACAAAAACATGCCAT
66 TCCCACACATGTTTAC---AAAAAAATGTTAACAAAAACATGCCAT
*
31548219 ATAAGCTAAAAAAAATTGAAACAAACTATCAAAATCATCATCAAAATGTAAGAATCAAGACTAAT
1 ATAAGCTAAAAAAAATTGAAACAAACTATCAAAATCATCATCAAAATATAAGAATCAAGACTAAT
31548284 TCCCACACATGTTTACAAAAAAATGTTAACAAAAACATG
66 TCCCACACATGTTTACAAAAAAATGTTAACAAAAACATG
31548323 ACATTCTAAC
Statistics
Matches: 97, Mismatches: 7, Indels: 3
0.91 0.07 0.03
Matches are distributed among these distances:
108 23 0.24
111 74 0.76
ACGTcount: A:0.52, C:0.16, G:0.08, T:0.24
Consensus pattern (108 bp):
ATAAGCTAAAAAAAATTGAAACAAACTATCAAAATCATCATCAAAATATAAGAATCAAGACTAAT
TCCCACACATGTTTACAAAAAAATGTTAACAAAAACATGCCAT
Found at i:31555376 original size:23 final size:23
Alignment explanation
Indices: 31555299--31555416 Score: 145
Period size: 23 Copynumber: 5.2 Consensus size: 23
31555289 TGACTTTGGA
*
31555299 CATTGCATGACTAGTT-G-ATAGG
1 CATTGCATGACTTGTTAGTA-AGG
*
31555321 CATTGCGTGACTTGTT-G-ATAGG
1 CATTGCATGACTTGTTAGTA-AGG
*
31555343 CATTGCGTGACTTGTTAGTAAGG
1 CATTGCATGACTTGTTAGTAAGG
*
31555366 TATTGCATGACTTGTTAGTAAGG
1 CATTGCATGACTTGTTAGTAAGG
*
31555389 CATTGCATGACTAGTTAGTAAGG
1 CATTGCATGACTTGTTAGTAAGG
31555412 CATTG
1 CATTG
31555417 TGTGACTTAG
Statistics
Matches: 88, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
22 36 0.41
23 51 0.58
24 1 0.01
ACGTcount: A:0.25, C:0.13, G:0.28, T:0.35
Consensus pattern (23 bp):
CATTGCATGACTTGTTAGTAAGG
Found at i:31555422 original size:23 final size:23
Alignment explanation
Indices: 31555318--31555424 Score: 146
Period size: 23 Copynumber: 4.7 Consensus size: 23
31555308 ACTAGTTGAT
31555318 AGGCATTGCGTGACTTGTT-G-A
1 AGGCATTGCGTGACTTGTTAGTA
31555339 TAGGCATTGCGTGACTTGTTAGTA
1 -AGGCATTGCGTGACTTGTTAGTA
* *
31555363 AGGTATTGCATGACTTGTTAGTA
1 AGGCATTGCGTGACTTGTTAGTA
* *
31555386 AGGCATTGCATGACTAGTTAGTA
1 AGGCATTGCGTGACTTGTTAGTA
*
31555409 AGGCATTGTGTGACTT
1 AGGCATTGCGTGACTT
31555425 AGGCATTGCT
Statistics
Matches: 76, Mismatches: 7, Indels: 3
0.88 0.08 0.03
Matches are distributed among these distances:
22 19 0.25
23 56 0.74
24 1 0.01
ACGTcount: A:0.23, C:0.12, G:0.29, T:0.36
Consensus pattern (23 bp):
AGGCATTGCGTGACTTGTTAGTA
Found at i:31555468 original size:22 final size:22
Alignment explanation
Indices: 31555435--31555510 Score: 75
Period size: 22 Copynumber: 3.5 Consensus size: 22
31555425 AGGCATTGCT
* *
31555435 TAAAAATCAGTCACGCAATGCC
1 TAAAAATCAGTCACACAATGCA
31555457 TAAAAA-CTAGTCACACAATGCA
1 TAAAAATC-AGTCACACAATGCA
* * * *
31555479 T-AAAACCAATCACATAATGCT
1 TAAAAATCAGTCACACAATGCA
31555500 TAAAAATCAGT
1 TAAAAATCAGT
31555511 TATGCAGTGA
Statistics
Matches: 44, Mismatches: 7, Indels: 6
0.77 0.12 0.11
Matches are distributed among these distances:
21 17 0.39
22 27 0.61
ACGTcount: A:0.47, C:0.22, G:0.09, T:0.21
Consensus pattern (22 bp):
TAAAAATCAGTCACACAATGCA
Found at i:31556753 original size:63 final size:63
Alignment explanation
Indices: 31556627--31556755 Score: 177
Period size: 63 Copynumber: 2.0 Consensus size: 63
31556617 GTAAATCCTC
* * *
31556627 TTGGTTTGGTGGACTAAAATAGGAAACAGTGAACATGCAGCACAGATAGAGCCATATATAGGG
1 TTGGTTTGATGGACTAAAATAGGAAACAATGAACATGCAGCACAGATAGAGCCATATAAAGGG
* * * * * *
31556690 TTGGTTTGATGGACTAAAATAGGGAACAATGAACATGCAGTAGAGATTGAGCGATGTAAAGGG
1 TTGGTTTGATGGACTAAAATAGGAAACAATGAACATGCAGCACAGATAGAGCCATATAAAGGG
31556753 TTG
1 TTG
31556756 CCGCTTGATT
Statistics
Matches: 57, Mismatches: 9, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
63 57 1.00
ACGTcount: A:0.36, C:0.10, G:0.30, T:0.24
Consensus pattern (63 bp):
TTGGTTTGATGGACTAAAATAGGAAACAATGAACATGCAGCACAGATAGAGCCATATAAAGGG
Found at i:31568522 original size:2 final size:2
Alignment explanation
Indices: 31568515--31568540 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31568505 GTAGAATTTG
31568515 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
31568541 GGGAACGGCA
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):
AT
Found at i:31574485 original size:2 final size:2
Alignment explanation
Indices: 31574478--31574506 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31574468 TCACATTAAC
31574478 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 A
31574507 CNATACATAA
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31574578 original size:97 final size:96
Alignment explanation
Indices: 31574411--31574603 Score: 359
Period size: 97 Copynumber: 2.0 Consensus size: 96
31574401 AACAAAATGT
31574411 CATACATAAATATTTTAAATTATAATTTCCTTACAACCATGGATTGGCTTACAAGGCTCACATTA
1 CATACATAAATATTTTAAATTATAATTTCCTTACAACCATGGATTGGCTTACAAGGCTCACATTA
31574476 ACATATATATATATATATATATATATATATA
66 ACATATATATATATATATATATATATATATA
31574507 CNATACATAAATATTTTAAATTATAATTTCCTTACAACCATGGATTGGCTTACAAGGCTCACATT
1 C-ATACATAAATATTTTAAATTATAATTTCCTTACAACCATGGATTGGCTTACAAGGCTCACATT
* *
31574572 AACATATATATATTTGTATATATATATATATA
65 AACATATATATATATATATATATATATATATA
31574604 TACTTCGGTT
Statistics
Matches: 94, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
96 1 0.01
97 93 0.99
ACGTcount: A:0.40, C:0.13, G:0.07, T:0.39
Consensus pattern (96 bp):
CATACATAAATATTTTAAATTATAATTTCCTTACAACCATGGATTGGCTTACAAGGCTCACATTA
ACATATATATATATATATATATATATATATA
Found at i:31592889 original size:17 final size:16
Alignment explanation
Indices: 31592861--31592893 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
31592851 TGTACAATGA
31592861 TTAAATATATAAATAG
1 TTAAATATATAAATAG
31592877 TTAAATAATATAAATAG
1 TTAAAT-ATATAAATAG
31592894 AAAGAAGAAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.58, C:0.00, G:0.06, T:0.36
Consensus pattern (16 bp):
TTAAATATATAAATAG
Found at i:31598319 original size:22 final size:24
Alignment explanation
Indices: 31598280--31598325 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
31598270 ACCATTATAG
*
31598280 CAAAATACATAACGAAATA-AAAA
1 CAAAATACATAAAGAAATATAAAA
*
31598303 CAAAATA-ATAAATAAATATAAAA
1 CAAAATACATAAAGAAATATAAAA
31598326 TATTTATTCA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.72, C:0.09, G:0.02, T:0.17
Consensus pattern (24 bp):
CAAAATACATAAAGAAATATAAAA
Found at i:31600226 original size:234 final size:233
Alignment explanation
Indices: 31599817--31600287 Score: 746
Period size: 234 Copynumber: 2.0 Consensus size: 233
31599807 GGCTAATCAT
* * *
31599817 TTCTATGTTTACATTCTTCAATAAATATAAGTTCAAGATCTTTGTTTTTCTTTCATAATATTGAG
1 TTCTATGTTTACATTCTTCAATAAATATAAATTCAAGATCCTTGTTTTTCTTTCATAATATTAAG
* *
31599882 CACTATATTATATGCAAAAATATCGTCGACATTTATTTCATTCCAATTCCATCTTTTCTCGTCAT
66 CACTATATTATATGAAAAAATATCGTCCACATTTATTTCATTCCAATTCCATCTTTTCTCGTCAT
* * * * * *
31599947 GACATAATTGATTGTGATCTTTTTATTTTCAATGATTTCAGGTACTTGAATTTTTTTTGAAATTT
131 AACATAAGTGAATGAGATCTTTTCATTTTCAATGATTTCAGGTACTTGAATTTTTTCTGAAATTT
*
31600012 TTATCAATTATGTC-GAGGGTCTCTTCTAGAGTTTCGAC
196 TTATCAATTATGTCAG-GGGTCTCTTCTAGAGTTTCAAC
31600050 TTCTATGTTTACATTCTTCAATAAATATAAATTCAAGATCCTTGTTTTTCTTTCATAATATTAAG
1 TTCTATGTTTACATTCTTCAATAAATATAAATTCAAGATCCTTGTTTTTCTTTCATAATATTAAG
* * ** *
31600115 CGCTATATTATATATAAAAAATATCGTCCATGTTTATTTCATTCCAATTTCATCTTTTCTCGTCA
66 CACTATATTATAT-GAAAAAATATCGTCCACATTTATTTCATTCCAATTCCATCTTTTCTCGTCA
*
31600180 TAACATAAGTGAATGAGATCTTTTCATTTTCAATGATTTTAGGTACTTGAATTTTTTCTGAAATT
130 TAACATAAGTGAATGAGATCTTTTCATTTTCAATGATTTCAGGTACTTGAATTTTTTCTGAAATT
*
31600245 TTTATCAGTTATGTCAGGGGTCTCTTCTAGAGTTTCAAC
195 TTTATCAATTATGTCAGGGGTCTCTTCTAGAGTTTCAAC
31600284 TTCT
1 TTCT
31600288 TCTTTCTGAC
Statistics
Matches: 217, Mismatches: 19, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
233 74 0.34
234 142 0.65
235 1 0.00
ACGTcount: A:0.28, C:0.15, G:0.11, T:0.46
Consensus pattern (233 bp):
TTCTATGTTTACATTCTTCAATAAATATAAATTCAAGATCCTTGTTTTTCTTTCATAATATTAAG
CACTATATTATATGAAAAAATATCGTCCACATTTATTTCATTCCAATTCCATCTTTTCTCGTCAT
AACATAAGTGAATGAGATCTTTTCATTTTCAATGATTTCAGGTACTTGAATTTTTTCTGAAATTT
TTATCAATTATGTCAGGGGTCTCTTCTAGAGTTTCAAC
Found at i:31603228 original size:2 final size:2
Alignment explanation
Indices: 31603221--31603317 Score: 176
Period size: 2 Copynumber: 48.0 Consensus size: 2
31603211 CATCTAGATC
31603221 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
31603263 NA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
31603305 TA TA TA TA GTA TA
1 TA TA TA TA -TA TA
31603318 AATGGATATT
Statistics
Matches: 92, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
2 90 0.98
3 2 0.02
ACGTcount: A:0.49, C:0.00, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:31609182 original size:2 final size:2
Alignment explanation
Indices: 31609175--31609206 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
31609165 AATAGAAATA
31609175 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31609207 GAAGGGACTA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:31611917 original size:16 final size:16
Alignment explanation
Indices: 31611896--31611926 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
31611886 ATCATGGAAA
31611896 TCAATGATTCTGCAAG
1 TCAATGATTCTGCAAG
31611912 TCAATGATTCTGCAA
1 TCAATGATTCTGCAA
31611927 TTATGGAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.32, C:0.19, G:0.16, T:0.32
Consensus pattern (16 bp):
TCAATGATTCTGCAAG
Found at i:31611973 original size:35 final size:35
Alignment explanation
Indices: 31611932--31612001 Score: 113
Period size: 35 Copynumber: 2.0 Consensus size: 35
31611922 TGCAATTATG
* *
31611932 GAAAGGATTCTGTAAATATTATGGAGAGGAGTGAT
1 GAAAGGATTCTGCAAATATTATGGAAAGGAGTGAT
*
31611967 GAAAGGATTCTGCAAATATTATGGAAAGGATTGAT
1 GAAAGGATTCTGCAAATATTATGGAAAGGAGTGAT
31612002 TCTGTACATC
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
35 32 1.00
ACGTcount: A:0.39, C:0.04, G:0.29, T:0.29
Consensus pattern (35 bp):
GAAAGGATTCTGCAAATATTATGGAAAGGAGTGAT
Found at i:31616800 original size:35 final size:35
Alignment explanation
Indices: 31616748--31616817 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
31616738 TGCAATCATG
*
31616748 GAAAAGATTCTGCAAATATTATGGAGAGGAGTGAT
1 GAAAAGATTCTGCAAATATTATGGAAAGGAGTGAT
* * *
31616783 GAAAGGATTCTGTAAATATTATGGAAAGGATTGAT
1 GAAAAGATTCTGCAAATATTATGGAAAGGAGTGAT
31616818 TTTGTACATC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.40, C:0.04, G:0.27, T:0.29
Consensus pattern (35 bp):
GAAAAGATTCTGCAAATATTATGGAAAGGAGTGAT
Found at i:31618839 original size:17 final size:18
Alignment explanation
Indices: 31618819--31618853 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
31618809 ATTAGGCTAG
*
31618819 ATTTGTGAGT-TTGTGAA
1 ATTTGTGAATGTTGTGAA
31618836 ATTTGTGAATGTTGTGAA
1 ATTTGTGAATGTTGTGAA
31618854 CCGAGTTTGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.26, C:0.00, G:0.29, T:0.46
Consensus pattern (18 bp):
ATTTGTGAATGTTGTGAA
Found at i:31618956 original size:16 final size:16
Alignment explanation
Indices: 31618931--31618967 Score: 56
Period size: 16 Copynumber: 2.3 Consensus size: 16
31618921 TCAATTAACT
*
31618931 TAATGCAAAGTATTAA
1 TAATGCAAAGCATTAA
*
31618947 TAATGGAAAGCATTAA
1 TAATGCAAAGCATTAA
31618963 TAATG
1 TAATG
31618968 TCCGAAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.16, T:0.30
Consensus pattern (16 bp):
TAATGCAAAGCATTAA
Found at i:31624187 original size:13 final size:16
Alignment explanation
Indices: 31624155--31624190 Score: 51
Period size: 13 Copynumber: 2.4 Consensus size: 16
31624145 TTATTCTTCT
31624155 AACTTTTTGACATGTA
1 AACTTTTTGACATGTA
31624171 AACTTTTT-A-AT-TA
1 AACTTTTTGACATGTA
31624184 AACTTTT
1 AACTTTT
31624191 AGAATTAAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 9 0.45
14 2 0.10
15 1 0.05
16 8 0.40
ACGTcount: A:0.33, C:0.11, G:0.06, T:0.50
Consensus pattern (16 bp):
AACTTTTTGACATGTA
Found at i:31630259 original size:12 final size:12
Alignment explanation
Indices: 31630242--31630268 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
31630232 TCCGTTTGCG
31630242 CTCCCTCTCTTT
1 CTCCCTCTCTTT
31630254 CTCCCTCTCTTT
1 CTCCCTCTCTTT
31630266 CTC
1 CTC
31630269 ATACTGTCTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (12 bp):
CTCCCTCTCTTT
Found at i:31630404 original size:24 final size:24
Alignment explanation
Indices: 31630358--31630404 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 24
31630348 TCAATCTTCC
31630358 TTCTTTGCTCCCTCTCTTTTCTTA
1 TTCTTTGCTCCCTCTCTTTTCTTA
* *
31630382 TTCTTT-CTCGCTCTGTTTCTCTT
1 TTCTTTGCTCCCTCTCTTT-TCTT
31630405 TCTAATCTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 10 0.50
24 10 0.50
ACGTcount: A:0.02, C:0.32, G:0.06, T:0.60
Consensus pattern (24 bp):
TTCTTTGCTCCCTCTCTTTTCTTA
Found at i:31634630 original size:6 final size:6
Alignment explanation
Indices: 31634619--31634649 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
31634609 AGTGGCGCAC
31634619 TAGGGT TAGGGT TAGGGT TAGGGT TAGGGT T
1 TAGGGT TAGGGT TAGGGT TAGGGT TAGGGT T
31634650 TGGTTGGAGC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.16, C:0.00, G:0.48, T:0.35
Consensus pattern (6 bp):
TAGGGT
Found at i:31635273 original size:22 final size:23
Alignment explanation
Indices: 31635230--31635278 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 23
31635220 TGTGTTTGTT
**
31635230 TTTTATTAAATCAATTTTTTAA-
1 TTTTATTAAATCAATTAATTAAG
* *
31635252 TTTTATTTAATTAATTAATTAAG
1 TTTTATTAAATCAATTAATTAAG
31635275 TTTT
1 TTTT
31635279 TATCTTTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 18 0.82
23 4 0.18
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (23 bp):
TTTTATTAAATCAATTAATTAAG
Found at i:31635776 original size:33 final size:33
Alignment explanation
Indices: 31635739--31635802 Score: 101
Period size: 33 Copynumber: 1.9 Consensus size: 33
31635729 AATAAATTTT
* *
31635739 TAATTTAATATATTTTATTTTTATTTTTTATTA
1 TAATTTAATATATTTTATTTTCATTTATTATTA
*
31635772 TAATTTTATATATTTTATTTTCATTTATTAT
1 TAATTTAATATATTTTATTTTCATTTATTAT
31635803 AGCACAAATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 28 1.00
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.69
Consensus pattern (33 bp):
TAATTTAATATATTTTATTTTCATTTATTATTA
Found at i:31635803 original size:20 final size:18
Alignment explanation
Indices: 31635749--31635803 Score: 56
Period size: 20 Copynumber: 2.8 Consensus size: 18
31635739 TAATTTAATA
*
31635749 TATTTTATTTTTATTTTT
1 TATTTTATTTTTATATTT
*
31635767 TATTATAATTTTATATATTT
1 TATT-TTATTTT-TATATTT
31635787 TATTTTCATTTATTATA
1 TATTTT-ATTT-TTATA
31635804 GCACAAATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
18 4 0.13
19 7 0.23
20 18 0.60
21 1 0.03
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (18 bp):
TATTTTATTTTTATATTT
Found at i:31636859 original size:30 final size:30
Alignment explanation
Indices: 31636823--31636881 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
31636813 ATGGTTGACA
* *
31636823 TACCAAACCAGTAAGTGATTCTTAAAAATG
1 TACCAAACCAGTAAGAGATTCTAAAAAATG
*
31636853 TACCAAACTAGTAAGAGATTCTAAAAAAT
1 TACCAAACCAGTAAGAGATTCTAAAAAAT
31636882 ATAATAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.47, C:0.15, G:0.12, T:0.25
Consensus pattern (30 bp):
TACCAAACCAGTAAGAGATTCTAAAAAATG
Found at i:31637531 original size:36 final size:36
Alignment explanation
Indices: 31637484--31637553 Score: 106
Period size: 36 Copynumber: 1.9 Consensus size: 36
31637474 TAGAAAAAGA
* *
31637484 TTCAATACAATGTCTTTTATGGA-TCAAGCACAACTT
1 TTCAATACAATGCCTTTTAT-GATTAAAGCACAACTT
31637520 TTCAATACAATGCCTTTTATGATTAAAGCACAAC
1 TTCAATACAATGCCTTTTATGATTAAAGCACAAC
31637554 CGCTCAACCT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
35 2 0.06
36 29 0.94
ACGTcount: A:0.36, C:0.20, G:0.10, T:0.34
Consensus pattern (36 bp):
TTCAATACAATGCCTTTTATGATTAAAGCACAACTT
Found at i:31656448 original size:23 final size:23
Alignment explanation
Indices: 31656422--31656498 Score: 75
Period size: 23 Copynumber: 3.3 Consensus size: 23
31656412 GAGATTAATT
31656422 TCCCATTCTTGTTGGTTTGAGAC
1 TCCCATTCTTGTTGGTTTGAGAC
* * * * *
31656445 TCCCACCTTTTCTCTTGCTTTAAG-T
1 TCCCA--TTCT-TGTTGGTTTGAGAC
31656470 TCCCATTCTTGTTGGTTTGAGAC
1 TCCCATTCTTGTTGGTTTGAGAC
31656493 TCCCAT
1 TCCCAT
31656499 CTTTTCTCTA
Statistics
Matches: 40, Mismatches: 10, Indels: 8
0.69 0.17 0.14
Matches are distributed among these distances:
22 9 0.22
23 14 0.35
25 8 0.20
26 9 0.22
ACGTcount: A:0.13, C:0.27, G:0.16, T:0.44
Consensus pattern (23 bp):
TCCCATTCTTGTTGGTTTGAGAC
Found at i:31656477 original size:48 final size:48
Alignment explanation
Indices: 31656416--31656521 Score: 167
Period size: 48 Copynumber: 2.2 Consensus size: 48
31656406 CTCGTTGAGA
* **
31656416 TTAATTTCCCATTCTTGTTGGTTTGAGACTCCCACCTTTTCTCTTGCT
1 TTAAGTTCCCATTCTTGTTGGTTTGAGACTCCCACCTTTTCTCTACCT
*
31656464 TTAAGTTCCCATTCTTGTTGGTTTGAGACTCCCATCTTTTCTCTACCT
1 TTAAGTTCCCATTCTTGTTGGTTTGAGACTCCCACCTTTTCTCTACCT
*
31656512 TTAAGATCCC
1 TTAAGTTCCC
31656522 GCATTGCCCA
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 53 1.00
ACGTcount: A:0.15, C:0.27, G:0.12, T:0.45
Consensus pattern (48 bp):
TTAAGTTCCCATTCTTGTTGGTTTGAGACTCCCACCTTTTCTCTACCT
Found at i:31657225 original size:23 final size:23
Alignment explanation
Indices: 31657199--31657244 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
31657189 ATATTAATAA
**
31657199 ATATCTATTTATAATTTATATTT
1 ATATCTATAAATAATTTATATTT
*
31657222 ATATTTATAAATAATTTATATTT
1 ATATCTATAAATAATTTATATTT
31657245 GCTATATTGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (23 bp):
ATATCTATAAATAATTTATATTT
Found at i:31657238 original size:17 final size:19
Alignment explanation
Indices: 31657204--31657244 Score: 59
Period size: 17 Copynumber: 2.3 Consensus size: 19
31657194 AATAAATATC
*
31657204 TATTTATAATTTATATTTA
1 TATTTATAATATATATTTA
31657223 TATTTATAA-ATA-ATTTA
1 TATTTATAATATATATTTA
31657240 TATTT
1 TATTT
31657245 GCTATATTGT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 10 0.48
18 2 0.10
19 9 0.43
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (19 bp):
TATTTATAATATATATTTA
Found at i:31657473 original size:24 final size:24
Alignment explanation
Indices: 31657441--31657486 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
31657431 GCCACTATAT
*
31657441 AAATATTTAAAGATAAACATTTAA
1 AAATATTTAAAAATAAACATTTAA
* *
31657465 AAATCTTTAAAAATAAATATTT
1 AAATATTTAAAAATAAACATTT
31657487 TTAAAATTAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.37
Consensus pattern (24 bp):
AAATATTTAAAAATAAACATTTAA
Found at i:31661535 original size:33 final size:31
Alignment explanation
Indices: 31661492--31661552 Score: 86
Period size: 33 Copynumber: 1.9 Consensus size: 31
31661482 CATGAGACCT
* *
31661492 AAAAATTCAAACAAATTATTGAGCAAAAAAAAA
1 AAAAAATCAAACAAATAATTG-G-AAAAAAAAA
31661525 AAAAAATCAAACAAATAATTGGAAAAAA
1 AAAAAATCAAACAAATAATTGGAAAAAA
31661553 TGGATTAACG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
31 6 0.23
32 1 0.04
33 19 0.73
ACGTcount: A:0.69, C:0.08, G:0.07, T:0.16
Consensus pattern (31 bp):
AAAAAATCAAACAAATAATTGGAAAAAAAAA
Found at i:31674495 original size:36 final size:36
Alignment explanation
Indices: 31674455--31674637 Score: 226
Period size: 36 Copynumber: 5.1 Consensus size: 36
31674445 AAGTACTTGG
* * *
31674455 TTAAAATTATTTAATTAAGTTGTTGGGTTTAATTAA
1 TTAAAATTATTTAATTAAGTTATTGGGCTTAATTGA
* *
31674491 TT-AAATTATTTAATTAAGTCATTGGACTTAATTGA
1 TTAAAATTATTTAATTAAGTTATTGGGCTTAATTGA
* * *
31674526 TTAAAATTGTTTAATTAAGTAATTGGGCCTAATTGA
1 TTAAAATTATTTAATTAAGTTATTGGGCTTAATTGA
* * *
31674562 TTAAAATTATTTAATTAAATTGTTGGGCTTAATTAA
1 TTAAAATTATTTAATTAAGTTATTGGGCTTAATTGA
* * *
31674598 TT-ATATTGTTTAATTAAGTTATTGGGCCTAATTGA
1 TTAAAATTATTTAATTAAGTTATTGGGCTTAATTGA
31674633 TTAAA
1 TTAAA
31674638 TTAAACAATT
Statistics
Matches: 123, Mismatches: 22, Indels: 4
0.83 0.15 0.03
Matches are distributed among these distances:
35 59 0.48
36 64 0.52
ACGTcount: A:0.36, C:0.04, G:0.14, T:0.46
Consensus pattern (36 bp):
TTAAAATTATTTAATTAAGTTATTGGGCTTAATTGA
Found at i:31674530 original size:71 final size:71
Alignment explanation
Indices: 31674455--31674640 Score: 248
Period size: 71 Copynumber: 2.6 Consensus size: 71
31674445 AAGTACTTGG
* * ** * *
31674455 TTAAAATTATTTAATTAAGTTGTTGGGTTTAATTAATTAAATTATTTAATTAAGTCATTGGACTT
1 TTAAAATTGTTTAATTAAGTTATTGGGCCTAATTGATTAAATTATTTAATTAAATCATTGGACTT
*
31674520 AATTGA
66 AATTAA
* ** *
31674526 TTAAAATTGTTTAATTAAGTAATTGGGCCTAATTGATTAAAATTATTTAATTAAATTGTTGGGCT
1 TTAAAATTGTTTAATTAAGTTATTGGGCCTAATTGATT-AAATTATTTAATTAAATCATTGGACT
31674591 TAATTAA
65 TAATTAA
*
31674598 TT-ATATTGTTTAATTAAGTTATTGGGCCTAATTGATTAAATTA
1 TTAAAATTGTTTAATTAAGTTATTGGGCCTAATTGATTAAATTA
31674641 AACAATTAAG
Statistics
Matches: 101, Mismatches: 13, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
70 6 0.06
71 65 0.64
72 30 0.30
ACGTcount: A:0.36, C:0.04, G:0.13, T:0.47
Consensus pattern (71 bp):
TTAAAATTGTTTAATTAAGTTATTGGGCCTAATTGATTAAATTATTTAATTAAATCATTGGACTT
AATTAA
Found at i:31674653 original size:35 final size:35
Alignment explanation
Indices: 31674458--31674640 Score: 222
Period size: 35 Copynumber: 5.2 Consensus size: 35
31674448 TACTTGGTTA
* * *
31674458 AAATTATTTAATTAAGTTGTTGGGTTTAATTAATT
1 AAATTATTTAATTAAGTTATTGGGCTTAATTGATT
* *
31674493 AAATTATTTAATTAAGTCATTGGACTTAATTGATT
1 AAATTATTTAATTAAGTTATTGGGCTTAATTGATT
* * *
31674528 AAAATTGTTTAATTAAGTAATTGGGCCTAATTGATT
1 -AAATTATTTAATTAAGTTATTGGGCTTAATTGATT
* * *
31674564 AAAATTATTTAATTAAATTGTTGGGCTTAATTAATT
1 -AAATTATTTAATTAAGTTATTGGGCTTAATTGATT
* * *
31674600 ATATTGTTTAATTAAGTTATTGGGCCTAATTGATT
1 AAATTATTTAATTAAGTTATTGGGCTTAATTGATT
31674635 AAATTA
1 AAATTA
31674641 AACAATTAAG
Statistics
Matches: 124, Mismatches: 23, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
35 63 0.51
36 61 0.49
ACGTcount: A:0.36, C:0.04, G:0.14, T:0.46
Consensus pattern (35 bp):
AAATTATTTAATTAAGTTATTGGGCTTAATTGATT
Found at i:31684200 original size:17 final size:17
Alignment explanation
Indices: 31684157--31684206 Score: 57
Period size: 17 Copynumber: 2.9 Consensus size: 17
31684147 GAATAAAGAA
*
31684157 AAATAAAATCCTAAA-C
1 AAATAAAATTCTAAATC
31684173 AAACTAAAATTCTAAATC
1 AAA-TAAAATTCTAAATC
* *
31684191 AAATAGAATTATAAAT
1 AAATAAAATTCTAAAT
31684207 ACACTTGTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
16 3 0.10
17 22 0.76
18 4 0.14
ACGTcount: A:0.60, C:0.12, G:0.02, T:0.26
Consensus pattern (17 bp):
AAATAAAATTCTAAATC
Found at i:31685154 original size:36 final size:36
Alignment explanation
Indices: 31685107--31685203 Score: 149
Period size: 36 Copynumber: 2.7 Consensus size: 36
31685097 CTCAACACAA
** *
31685107 GTCATGTGCACTTTCACACCGCATATAGCTATTATC
1 GTCATGTGCACTCCCACACCGCACATAGCTATTATC
* *
31685143 GTCATGTGCACTCCCACATCGCACATAGCTATTATT
1 GTCATGTGCACTCCCACACCGCACATAGCTATTATC
31685179 GTCATGTGCACTCCCACACCGCACA
1 GTCATGTGCACTCCCACACCGCACA
31685204 CAGTCATCGT
Statistics
Matches: 55, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 55 1.00
ACGTcount: A:0.25, C:0.33, G:0.14, T:0.28
Consensus pattern (36 bp):
GTCATGTGCACTCCCACACCGCACATAGCTATTATC
Found at i:31689017 original size:19 final size:20
Alignment explanation
Indices: 31688988--31689027 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
31688978 TCACTTTTAA
31688988 ACTTCAAATCATACTCCAAT
1 ACTTCAAATCATACTCCAAT
31689008 ACTT-AAATCATACTCCAAT
1 ACTTCAAATCATACTCCAAT
31689027 A
1 A
31689028 AGTCAAATGG
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.42, C:0.28, G:0.00, T:0.30
Consensus pattern (20 bp):
ACTTCAAATCATACTCCAAT
Found at i:31689680 original size:16 final size:18
Alignment explanation
Indices: 31689656--31689692 Score: 51
Period size: 16 Copynumber: 2.2 Consensus size: 18
31689646 ATTAAAATTT
31689656 TAATATTT-AATCATA-A
1 TAATATTTAAATCATATA
*
31689672 TAATGTTTAAATCATATA
1 TAATATTTAAATCATATA
31689690 TAA
1 TAA
31689693 AATATATAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 7 0.39
18 4 0.22
ACGTcount: A:0.49, C:0.05, G:0.03, T:0.43
Consensus pattern (18 bp):
TAATATTTAAATCATATA
Found at i:31689755 original size:18 final size:20
Alignment explanation
Indices: 31689729--31689771 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
31689719 TGTTTAATTA
*
31689729 TAAATAAAA-TATTAATATT
1 TAAATAAAATTATTAAGATT
*
31689748 TAAA-AAAATTGTTAAGATT
1 TAAATAAAATTATTAAGATT
31689767 TAAAT
1 TAAAT
31689772 TATAAATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 3
0.80 0.08 0.12
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (20 bp):
TAAATAAAATTATTAAGATT
Found at i:31689761 original size:44 final size:43
Alignment explanation
Indices: 31689674--31689779 Score: 119
Period size: 43 Copynumber: 2.4 Consensus size: 43
31689664 AATCATAATA
* *
31689674 ATGTTTAAATCATATATAAAATATATAATATATTAAAAATGTT
1 ATGTTTAAATTATAAATAAAATATATAATATATTAAAAATGTT
31689717 ATTGTTT-AATTATAAATAAAATAT-TAATAT-TTAAAAAAATTGTT
1 A-TGTTTAAATTATAAATAAAATATATAATATATT--AAAAA-TGTT
*
31689761 AAGATTTAAATTATAAATA
1 ATG-TTTAAATTATAAATA
31689780 TTCCAATCAT
Statistics
Matches: 54, Mismatches: 3, Indels: 10
0.81 0.04 0.15
Matches are distributed among these distances:
41 2 0.04
42 6 0.11
43 22 0.41
44 13 0.24
45 11 0.20
ACGTcount: A:0.52, C:0.01, G:0.05, T:0.42
Consensus pattern (43 bp):
ATGTTTAAATTATAAATAAAATATATAATATATTAAAAATGTT
Found at i:31689816 original size:23 final size:24
Alignment explanation
Indices: 31689790--31689840 Score: 59
Period size: 24 Copynumber: 2.2 Consensus size: 24
31689780 TTCCAATCAT
**
31689790 AATACTA-TTTGAATTATAGATAA
1 AATACTATTTTGAAAAATAGATAA
* *
31689813 AATATTATTTTTAAAAATAGATAA
1 AATACTATTTTGAAAAATAGATAA
31689837 AATA
1 AATA
31689841 ATCATATTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.53, C:0.02, G:0.06, T:0.39
Consensus pattern (24 bp):
AATACTATTTTGAAAAATAGATAA
Found at i:31689850 original size:24 final size:24
Alignment explanation
Indices: 31689805--31689850 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
31689795 TATTTGAATT
* *
31689805 ATAGATAAAATATTATTTTTAAAA
1 ATAGATAAAATATCATTATTAAAA
31689829 ATAGATAAAATAATCA-TATTAA
1 ATAGATAAAAT-ATCATTATTAA
31689851 TGTTAAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 16 0.84
25 3 0.16
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (24 bp):
ATAGATAAAATATCATTATTAAAA
Found at i:31690329 original size:13 final size:12
Alignment explanation
Indices: 31690305--31690344 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
31690295 AATAGAGAAT
31690305 GAAAGGAAAAGA
1 GAAAGGAAAAGA
31690317 GAAAGGAAAA-A
1 GAAAGGAAAAGA
* *
31690328 GAGAGGAAGAGA
1 GAAAGGAAAAGA
31690340 GAAAG
1 GAAAG
31690345 TTAGATGGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.62, C:0.00, G:0.38, T:0.00
Consensus pattern (12 bp):
GAAAGGAAAAGA
Found at i:31694682 original size:2 final size:2
Alignment explanation
Indices: 31694675--31694703 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
31694665 AGAAACCGTG
31694675 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
31694704 GTATTTTTTT
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:31696066 original size:15 final size:15
Alignment explanation
Indices: 31696046--31696085 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
31696036 AAGTGAGCTT
31696046 ATTTTGACTAGTGAC
1 ATTTTGACTAGTGAC
31696061 ATTTTGACTAGTGAC
1 ATTTTGACTAGTGAC
31696076 ATTTTGACTA
1 ATTTTGACTA
31696086 TTAACGATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.28, C:0.12, G:0.17, T:0.42
Consensus pattern (15 bp):
ATTTTGACTAGTGAC
Found at i:31699221 original size:15 final size:15
Alignment explanation
Indices: 31699201--31699232 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
31699191 TTGTTTTAGG
31699201 ATTATTATCCTATAT
1 ATTATTATCCTATAT
31699216 ATTATTATCCTATAT
1 ATTATTATCCTATAT
31699231 AT
1 AT
31699233 ATATATATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.34, C:0.12, G:0.00, T:0.53
Consensus pattern (15 bp):
ATTATTATCCTATAT
Found at i:31700119 original size:32 final size:32
Alignment explanation
Indices: 31700078--31700141 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
31700068 ATATTAAAAG
31700078 ACAAAATAACAGATAGTAACAGCTAGAAACTA
1 ACAAAATAACAGATAGTAACAGCTAGAAACTA
31700110 ACAAAATAACAGATAGTAACAGCTAGAAACTA
1 ACAAAATAACAGATAGTAACAGCTAGAAACTA
31700142 TCTCTAATGG
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:0.56, C:0.16, G:0.12, T:0.16
Consensus pattern (32 bp):
ACAAAATAACAGATAGTAACAGCTAGAAACTA
Found at i:31718889 original size:16 final size:15
Alignment explanation
Indices: 31718870--31718912 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
31718860 TTACTTATTT
31718870 TTAGTTATTTTTATAA
1 TTAGTTATTTTTA-AA
* *
31718886 TTAGGTTACTTTTAAG
1 TTA-GTTATTTTTAAA
31718902 TTAGTTATTTT
1 TTAGTTATTTT
31718913 AATTTTATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
15 7 0.30
16 7 0.30
17 9 0.39
ACGTcount: A:0.26, C:0.02, G:0.12, T:0.60
Consensus pattern (15 bp):
TTAGTTATTTTTAAA
Found at i:31718924 original size:20 final size:20
Alignment explanation
Indices: 31718895--31718937 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
31718885 ATTAGGTTAC
31718895 TTTTAAGTTAGTT-ATTTTAA
1 TTTTAAGTTA-TTGATTTTAA
* *
31718915 TTTTATGTTATTGCTTTTAA
1 TTTTAAGTTATTGATTTTAA
31718935 TTT
1 TTT
31718938 GTTTATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.23, C:0.02, G:0.09, T:0.65
Consensus pattern (20 bp):
TTTTAAGTTATTGATTTTAA
Found at i:31726488 original size:19 final size:22
Alignment explanation
Indices: 31726461--31726501 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
31726451 TACATGTTGA
31726461 TTAGTTTAA-TTTATG-TATTT
1 TTAGTTTAATTTTATGTTATTT
31726481 TTAG-TTAATTTTATGTTATTT
1 TTAGTTTAATTTTATGTTATTT
31726502 GATTTTAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 4 0.21
20 10 0.53
21 5 0.26
ACGTcount: A:0.24, C:0.00, G:0.10, T:0.66
Consensus pattern (22 bp):
TTAGTTTAATTTTATGTTATTT
Found at i:31735703 original size:60 final size:60
Alignment explanation
Indices: 31735580--31735748 Score: 203
Period size: 60 Copynumber: 2.8 Consensus size: 60
31735570 TAATTGATGT
***
31735580 AACCGTGCATGTGCAGAGTGGGTAGTGCACATGCCGGTTGAATGACAATGTCATGATAATTAC
1 AACCGTGCATGTGCA-AGTGGGTAGTGCACATGCCGG-T-AATGATGCTGTCATGATAATTAC
* * *
31735643 AACCGTGCATGTGCAAGTGGGCACTGCACATGCCGGTAATGATGCTGTCATGATATTTAC
1 AACCGTGCATGTGCAAGTGGGTAGTGCACATGCCGGTAATGATGCTGTCATGATAATTAC
** * * *
31735703 AGTCGTGCATGTGCGGAGTGGGTAGTGCACATGCCAGTGATGATGC
1 AACCGTGCATGTGC-AAGTGGGTAGTGCACATGCCGGTAATGATGC
31735749 ACATGAGCTG
Statistics
Matches: 92, Mismatches: 13, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
60 31 0.34
61 27 0.29
62 19 0.21
63 15 0.16
ACGTcount: A:0.25, C:0.19, G:0.31, T:0.25
Consensus pattern (60 bp):
AACCGTGCATGTGCAAGTGGGTAGTGCACATGCCGGTAATGATGCTGTCATGATAATTAC
Found at i:31739968 original size:73 final size:73
Alignment explanation
Indices: 31739881--31740077 Score: 225
Period size: 73 Copynumber: 2.7 Consensus size: 73
31739871 AAGTGGGATG
* * * * * * *
31739881 AGAAGAATCAATATCTCAAGAATGCAAAGATCGATTCTTAAAAAATAGAAAGCTCCAAATTTGAA
1 AGAAGAATCGATATCTCAAGAATGGAAAGGTCGATTCTAAAAAAACAGAAAGCTCCAAACTTCAA
31739946 CTGAAACA
66 CTGAAACA
* * * * * *
31739954 AGAAGAATCGATATCTCAAGAATGGAATGGTCGATTCTCAAAAGACAAAAAGCTTCATACTTCAA
1 AGAAGAATCGATATCTCAAGAATGGAAAGGTCGATTCTAAAAAAACAGAAAGCTCCAAACTTCAA
* *
31740019 GTGAGACA
66 CTGAAACA
* *
31740027 AGAAAAAGT-GATATCTCAAGAATGGAAAGGTTGATTCTAAAAAAACAGAAA
1 AGAAGAA-TCGATATCTCAAGAATGGAAAGGTCGATTCTAAAAAAACAGAAA
31740078 ATTTTGGGAT
Statistics
Matches: 103, Mismatches: 20, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
73 102 0.99
74 1 0.01
ACGTcount: A:0.48, C:0.14, G:0.17, T:0.21
Consensus pattern (73 bp):
AGAAGAATCGATATCTCAAGAATGGAAAGGTCGATTCTAAAAAAACAGAAAGCTCCAAACTTCAA
CTGAAACA
Found at i:31740507 original size:31 final size:31
Alignment explanation
Indices: 31740469--31740639 Score: 123
Period size: 31 Copynumber: 5.5 Consensus size: 31
31740459 AATCCATTAT
* * *
31740469 TGTAAGGTTATACATCCATTGCAAAAGGTAG
1 TGTAAGGTTATACCTCCACTGTAAAAGGTAG
* * *
31740500 TGTAAGGTTATACCTCCACTATAAAAGATAA
1 TGTAAGGTTATACCTCCACTGTAAAAGGTAG
* * * * * *
31740531 AGAAAGGTTATACTTCTAGTGTAAAAGGTTG
1 TGTAAGGTTATACCTCCACTGTAAAAGGTAG
*
31740562 TGT--GTGTCTATACCTCCACTGTAAAAGGTAA
1 TGTAAG-GT-TATACCTCCACTGTAAAAGGTAG
* * * ** *
31740593 TG-AACAGTTATACCTCTATTACAAAAAGTAG
1 TGTAA-GGTTATACCTCCACTGTAAAAGGTAG
31740624 TGTAAGGTTATACCTC
1 TGTAAGGTTATACCTC
31740640 TTCAAGAAAG
Statistics
Matches: 104, Mismatches: 30, Indels: 12
0.71 0.21 0.08
Matches are distributed among these distances:
29 1 0.01
30 2 0.02
31 97 0.93
32 4 0.04
ACGTcount: A:0.36, C:0.15, G:0.19, T:0.31
Consensus pattern (31 bp):
TGTAAGGTTATACCTCCACTGTAAAAGGTAG
Found at i:31740636 original size:62 final size:62
Alignment explanation
Indices: 31740472--31740639 Score: 189
Period size: 62 Copynumber: 2.7 Consensus size: 62
31740462 CCATTATTGT
*
31740472 AAGGTTATACATCCATTGCAAAAGGTAGTGTAAGGTTATACCTCCACTATAAAAGATAAAGA
1 AAGGTTATACATCTATTGCAAAAGGTAGTGTAAGGTTATACCTCCACTATAAAAGATAAAGA
* * * * * * *
31740534 AAGGTTATACTTCTAGTGTAAAAGGTTGTGT--GTGTCTATACCTCCACTGTAAAAGGTAATGA
1 AAGGTTATACATCTATTGCAAAAGGTAGTGTAAG-GT-TATACCTCCACTATAAAAGATAAAGA
* * *
31740596 ACA-GTTATACCTCTATTACAAAAAGTAGTGTAAGGTTATACCTC
1 A-AGGTTATACATCTATTGCAAAAGGTAGTGTAAGGTTATACCTC
31740640 TTCAAGAAAG
Statistics
Matches: 87, Mismatches: 14, Indels: 10
0.78 0.13 0.09
Matches are distributed among these distances:
60 1 0.01
61 2 0.02
62 80 0.92
63 3 0.03
64 1 0.01
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.30
Consensus pattern (62 bp):
AAGGTTATACATCTATTGCAAAAGGTAGTGTAAGGTTATACCTCCACTATAAAAGATAAAGA
Found at i:31748794 original size:22 final size:22
Alignment explanation
Indices: 31748769--31748810 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
31748759 GAAATTGATT
*
31748769 AGACTAGTTTTTAAGTATTGTG
1 AGACTAATTTTTAAGTATTGTG
*
31748791 AGACTAATTTTTAGGTATTG
1 AGACTAATTTTTAAGTATTG
31748811 CGTGACTTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.29, C:0.05, G:0.21, T:0.45
Consensus pattern (22 bp):
AGACTAATTTTTAAGTATTGTG
Found at i:31748821 original size:23 final size:22
Alignment explanation
Indices: 31748769--31748817 Score: 62
Period size: 22 Copynumber: 2.2 Consensus size: 22
31748759 GAAATTGATT
* *
31748769 AGACTAGTTTTTAAGTATTGTG
1 AGACTAATTTTTAAGTATTGCG
*
31748791 AGACTAATTTTTAGGTATTGCG
1 AGACTAATTTTTAAGTATTGCG
*
31748813 TGACT
1 AGACT
31748818 TAATCACTGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.27, C:0.08, G:0.22, T:0.43
Consensus pattern (22 bp):
AGACTAATTTTTAAGTATTGCG
Found at i:31748860 original size:22 final size:22
Alignment explanation
Indices: 31748828--31748894 Score: 82
Period size: 22 Copynumber: 3.1 Consensus size: 22
31748818 TAATCACTGT
*
31748828 GTGACTAGTTTTTAGGCATTAT
1 GTGACTAGTTTTTAGGCATTAC
* *
31748850 GTGA-TTGGTTTTAGGCATTAC
1 GTGACTAGTTTTTAGGCATTAC
**
31748871 GTGACTAGTTTTTAGATATTAC
1 GTGACTAGTTTTTAGGCATTAC
31748893 GT
1 GT
31748895 TACTGATTTT
Statistics
Matches: 37, Mismatches: 7, Indels: 2
0.80 0.15 0.04
Matches are distributed among these distances:
21 18 0.49
22 19 0.51
ACGTcount: A:0.22, C:0.09, G:0.24, T:0.45
Consensus pattern (22 bp):
GTGACTAGTTTTTAGGCATTAC
Found at i:31748881 original size:21 final size:21
Alignment explanation
Indices: 31748828--31748882 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
31748818 TAATCACTGT
*
31748828 GTGACTAGTTTTTAGGCATTAT
1 GTGACTAG-TTTTAGGCATTAC
* *
31748850 GTGATTGGTTTTAGGCATTAC
1 GTGACTAGTTTTAGGCATTAC
31748871 GTGACTAGTTTT
1 GTGACTAGTTTT
31748883 TAGATATTAC
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 22 0.79
22 6 0.21
ACGTcount: A:0.20, C:0.09, G:0.25, T:0.45
Consensus pattern (21 bp):
GTGACTAGTTTTAGGCATTAC
Found at i:31748936 original size:23 final size:23
Alignment explanation
Indices: 31748909--31749098 Score: 249
Period size: 23 Copynumber: 8.3 Consensus size: 23
31748899 GATTTTTAAA
*
31748909 CAATGCCTTACTAGCAAGTCACG
1 CAATGCCTTACTAACAAGTCACG
*
31748932 CAATGTCTTACTAACAAGTCACG
1 CAATGCCTTACTAACAAGTCACG
* * *
31748955 TAATACCTTACTAATAAGTCACG
1 CAATGCCTTACTAACAAGTCACG
*
31748978 CAATGCCTTACTAATAAGTCACG
1 CAATGCCTTACTAACAAGTCACG
*
31749001 CAATGTCTTACTAACAAGTCACG
1 CAATGCCTTACTAACAAGTCACG
* * *
31749024 TAATACCTTACTAATAAGTCACG
1 CAATGCCTTACTAACAAGTCACG
*
31749047 CAATGCCTTACTAATAAGTCACG
1 CAATGCCTTACTAACAAGTCACG
*
31749070 CAATGCC-TA-TCAACTAGTCACG
1 CAATGCCTTACT-AACAAGTCACG
31749092 CAATGCC
1 CAATGCC
31749099 ATATCAACCA
Statistics
Matches: 148, Mismatches: 18, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
21 1 0.01
22 18 0.12
23 129 0.87
ACGTcount: A:0.35, C:0.27, G:0.13, T:0.26
Consensus pattern (23 bp):
CAATGCCTTACTAACAAGTCACG
Found at i:31749020 original size:69 final size:69
Alignment explanation
Indices: 31748909--31749074 Score: 314
Period size: 69 Copynumber: 2.4 Consensus size: 69
31748899 GATTTTTAAA
**
31748909 CAATGCCTTACTAGCAAGTCACGCAATGTCTTACTAACAAGTCACGTAATACCTTACTAATAAGT
1 CAATGCCTTACTAATAAGTCACGCAATGTCTTACTAACAAGTCACGTAATACCTTACTAATAAGT
31748974 CACG
66 CACG
31748978 CAATGCCTTACTAATAAGTCACGCAATGTCTTACTAACAAGTCACGTAATACCTTACTAATAAGT
1 CAATGCCTTACTAATAAGTCACGCAATGTCTTACTAACAAGTCACGTAATACCTTACTAATAAGT
31749043 CACG
66 CACG
31749047 CAATGCCTTACTAATAAGTCACGCAATG
1 CAATGCCTTACTAATAAGTCACGCAATG
31749075 CCTATCAACT
Statistics
Matches: 95, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
69 95 1.00
ACGTcount: A:0.36, C:0.25, G:0.13, T:0.27
Consensus pattern (69 bp):
CAATGCCTTACTAATAAGTCACGCAATGTCTTACTAACAAGTCACGTAATACCTTACTAATAAGT
CACG
Found at i:31749091 original size:22 final size:22
Alignment explanation
Indices: 31749040--31749186 Score: 122
Period size: 22 Copynumber: 6.6 Consensus size: 22
31749030 CTTACTAATA
31749040 AGTCACGCAATGCCT-TACTAA-T
1 AGTCACGCAATGCCTAT-C-AACT
31749062 AAGTCACGCAATGCCTATCAACT
1 -AGTCACGCAATGCCTATCAACT
*
31749085 AGTCACGCAATGCCATATCAACC
1 AGTCACGCAATGCC-TATCAACT
* *** **
31749108 AGTCACACAATATTTAAAAACT
1 AGTCACGCAATGCCTATCAACT
* *
31749130 AGTCACGCAATGCCCA--AAGT
1 AGTCACGCAATGCCTATCAACT
**
31749150 CAGTCACGCAATGCCTAAAAACT
1 -AGTCACGCAATGCCTATCAACT
31749173 AGTCACGCAATGCC
1 AGTCACGCAATGCC
31749187 CAAAAACCAC
Statistics
Matches: 102, Mismatches: 16, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
20 3 0.03
21 15 0.15
22 46 0.45
23 37 0.36
24 1 0.01
ACGTcount: A:0.37, C:0.29, G:0.14, T:0.20
Consensus pattern (22 bp):
AGTCACGCAATGCCTATCAACT
Found at i:31749111 original size:23 final size:22
Alignment explanation
Indices: 31748923--31749186 Score: 123
Period size: 23 Copynumber: 11.7 Consensus size: 22
31748913 GCCTTACTAG
*
31748923 CAAGTCACGCAATGTCT-TACTAA
1 CAAGTCACGCAATGCCTAT-C-AA
* *
31748946 CAAGTCACGTAATACCT-TACTAA
1 CAAGTCACGCAATGCCTAT-C-AA
*
31748969 TAAGTCACGCAATGCCT-TACTAA
1 CAAGTCACGCAATGCCTAT-C-AA
* *
31748992 TAAGTCACGCAATGTCT-TACTAA
1 CAAGTCACGCAATGCCTAT-C-AA
* *
31749015 CAAGTCACGTAATACCT-TACTAA
1 CAAGTCACGCAATGCCTAT-C-AA
*
31749038 TAAGTCACGCAATGCCT-TACTAA
1 CAAGTCACGCAATGCCTAT-C-AA
*
31749061 TAAGTCACGCAATGCCTATCAA
1 CAAGTCACGCAATGCCTATCAA
*
31749083 CTAGTCACGCAATGCCATATCAA
1 CAAGTCACGCAATGCC-TATCAA
* * *** **
31749106 CCAGTCACACAATATTTAAAAA
1 CAAGTCACGCAATGCCTATCAA
* *
31749128 CTAGTCACGCAATGCCCA--AA
1 CAAGTCACGCAATGCCTATCAA
**
31749148 GTC-AGTCACGCAATGCCTAAAAA
1 --CAAGTCACGCAATGCCTATCAA
*
31749171 CTAGTCACGCAATGCC
1 CAAGTCACGCAATGCC
31749187 CAAAAACCAC
Statistics
Matches: 204, Mismatches: 30, Indels: 15
0.82 0.12 0.06
Matches are distributed among these distances:
20 2 0.01
21 16 0.08
22 47 0.23
23 138 0.68
24 1 0.00
ACGTcount: A:0.37, C:0.27, G:0.12, T:0.23
Consensus pattern (22 bp):
CAAGTCACGCAATGCCTATCAA
Found at i:31749112 original size:45 final size:44
Alignment explanation
Indices: 31749040--31749186 Score: 163
Period size: 45 Copynumber: 3.3 Consensus size: 44
31749030 CTTACTAATA
* * **
31749040 AGTCACGCAATGCCTTACTAATAAGTCACGCAATGCCTATCAACT
1 AGTCACGCAATGCCATAC-AATCAGTCACGCAATGCCTAAAAACT
* * ***
31749085 AGTCACGCAATGCCATATCAACCAGTCACACAATATTTAAAAACT
1 AGTCACGCAATGCCATA-CAATCAGTCACGCAATGCCTAAAAACT
*
31749130 AGTCACGCAATGCCCA-A-AGTCAGTCACGCAATGCCTAAAAACT
1 AGTCACGCAATG-CCATACAATCAGTCACGCAATGCCTAAAAACT
31749173 AGTCACGCAATGCC
1 AGTCACGCAATGCC
31749187 CAAAAACCAC
Statistics
Matches: 85, Mismatches: 15, Indels: 7
0.79 0.14 0.07
Matches are distributed among these distances:
42 2 0.02
43 32 0.38
45 47 0.55
46 4 0.05
ACGTcount: A:0.37, C:0.29, G:0.14, T:0.20
Consensus pattern (44 bp):
AGTCACGCAATGCCATACAATCAGTCACGCAATGCCTAAAAACT
Found at i:31749169 original size:43 final size:43
Alignment explanation
Indices: 31749063--31749191 Score: 152
Period size: 43 Copynumber: 3.0 Consensus size: 43
31749053 CTTACTAATA
**
31749063 AGTCACGCAATGCCTATCAACTAGTCACGCAATG-CCATATCAACC
1 AGTCACGCAATGCCTAAAAACTAGTCACGCAATGCCCA-A--AACC
* *** **
31749108 AGTCACACAATATTTAAAAACTAGTCACGCAATGCCCAAAGTC
1 AGTCACGCAATGCCTAAAAACTAGTCACGCAATGCCCAAAACC
31749151 AGTCACGCAATGCCTAAAAACTAGTCACGCAATGCCCAAAA
1 AGTCACGCAATGCCTAAAAACTAGTCACGCAATGCCCAAAA
31749192 ACCACAAAAA
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
43 38 0.54
45 29 0.41
46 3 0.04
ACGTcount: A:0.39, C:0.29, G:0.13, T:0.19
Consensus pattern (43 bp):
AGTCACGCAATGCCTAAAAACTAGTCACGCAATGCCCAAAACC
Found at i:31749356 original size:10 final size:10
Alignment explanation
Indices: 31749330--31749366 Score: 56
Period size: 10 Copynumber: 3.6 Consensus size: 10
31749320 TCTTCATATA
31749330 TCAAAAATCAC
1 TCAAAAAT-AC
31749341 TCAAAAATAC
1 TCAAAAATAC
*
31749351 TTAAAAATAC
1 TCAAAAATAC
31749361 TCAAAA
1 TCAAAA
31749367 CGCTCAAAGG
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.59, C:0.19, G:0.00, T:0.22
Consensus pattern (10 bp):
TCAAAAATAC
Found at i:31755264 original size:15 final size:15
Alignment explanation
Indices: 31755244--31755273 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
31755234 ACTGAATTTG
*
31755244 GGCATTACGTGACTA
1 GGCATTACGTAACTA
31755259 GGCATTACGTAACTA
1 GGCATTACGTAACTA
31755274 AATTTGGGCA
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:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (15 bp):
GGCATTACGTAACTA
Found at i:31755270 original size:36 final size:36
Alignment explanation
Indices: 31755221--31755294 Score: 112
Period size: 36 Copynumber: 2.1 Consensus size: 36
31755211 GACTAGTTTT
* * *
31755221 TAGGTATTGCGTAACTGAATTTGGGCATTACGTGAC
1 TAGGCATTACGTAACTAAATTTGGGCATTACGTGAC
*
31755257 TAGGCATTACGTAACTAAATTTGGGCATTGCGTGAC
1 TAGGCATTACGTAACTAAATTTGGGCATTACGTGAC
31755293 TA
1 TA
31755295 ATTTCTGATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 34 1.00
ACGTcount: A:0.27, C:0.15, G:0.26, T:0.32
Consensus pattern (36 bp):
TAGGCATTACGTAACTAAATTTGGGCATTACGTGAC
Found at i:31755316 original size:26 final size:26
Alignment explanation
Indices: 31755280--31755375 Score: 147
Period size: 26 Copynumber: 3.7 Consensus size: 26
31755270 ACTAAATTTG
* * *
31755280 GGCATTGCGTGACTAATTTCTGATAA
1 GGCATTGCATGACTAGTTTTTGATAA
* *
31755306 GGCATTGCGTGACTAGTTTTTTATAA
1 GGCATTGCATGACTAGTTTTTGATAA
31755332 GGCATTGCATGACTAGTTTTTGATAA
1 GGCATTGCATGACTAGTTTTTGATAA
31755358 GGCATTGCATGACTAGTT
1 GGCATTGCATGACTAGTT
31755376 GATAGGCATG
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 65 1.00
ACGTcount: A:0.25, C:0.14, G:0.24, T:0.38
Consensus pattern (26 bp):
GGCATTGCATGACTAGTTTTTGATAA
Found at i:31755439 original size:23 final size:23
Alignment explanation
Indices: 31755303--31755432 Score: 115
Period size: 26 Copynumber: 5.4 Consensus size: 23
31755293 TAATTTCTGA
*
31755303 TAAGGCATTGCGTGACTAGTTTTTTA-
1 TAAGGCATTGCATGACTAG----TTAG
*
31755329 TAAGGCATTGCATGACTAGTTTTTG
1 TAAGGCATTGCATGACTAG--TTAG
31755354 ATAAGGCATTGCATGACTAGTT-G
1 -TAAGGCATTGCATGACTAGTTAG
*
31755377 -ATAGGCA-TGACATGACTTGTTAG
1 TA-AGGCATTG-CATGACTAGTTAG
*
31755400 TAAGGTATTGCATGACTAGTTAG
1 TAAGGCATTGCATGACTAGTTAG
31755423 TAAGGCATTG
1 TAAGGCATTG
31755433 TGTGACTTAA
Statistics
Matches: 91, Mismatches: 6, Indels: 17
0.80 0.05 0.15
Matches are distributed among these distances:
21 3 0.03
22 15 0.16
23 27 0.30
24 9 0.10
26 37 0.41
ACGTcount: A:0.28, C:0.12, G:0.25, T:0.35
Consensus pattern (23 bp):
TAAGGCATTGCATGACTAGTTAG
Found at i:31755498 original size:22 final size:22
Alignment explanation
Indices: 31755473--31755521 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 22
31755463 AGTCAATGTG
* * *
31755473 TAAAAACTAGTCACGTAATGCC
1 TAAAAACCAATCACGTAATGAC
*
31755495 T-AAAACCAATTACGTAATGAC
1 TAAAAACCAATCACGTAATGAC
31755516 TAAAAA
1 TAAAAA
31755522 TTGTCACACG
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.49, C:0.18, G:0.10, T:0.22
Consensus pattern (22 bp):
TAAAAACCAATCACGTAATGAC
Found at i:31756023 original size:65 final size:65
Alignment explanation
Indices: 31755917--31756048 Score: 228
Period size: 65 Copynumber: 2.0 Consensus size: 65
31755907 GTTCTTTCTC
*
31755917 CCTGAGCAAAATCACTGCTTGCAAAGAGCAAAATTGCTGTTCATCGCCCTTAAGAACCCTAAGAT
1 CCTGAGCAAAATCACTGCCTGCAAAGAGCAAAATTGCTGTTCATCGCCCTTAAGAACCCTAAGAT
* * *
31755982 CCTGAGCAAAATCGCTGCCTGCAAAGAGCAAAATTGTTGTTCATCTCCCTTAAGAACCCTAAGAT
1 CCTGAGCAAAATCACTGCCTGCAAAGAGCAAAATTGCTGTTCATCGCCCTTAAGAACCCTAAGAT
31756047 CC
1 CC
31756049 ACCATTCAAA
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (65 bp):
CCTGAGCAAAATCACTGCCTGCAAAGAGCAAAATTGCTGTTCATCGCCCTTAAGAACCCTAAGAT
Found at i:31764004 original size:8 final size:8
Alignment explanation
Indices: 31763982--31764025 Score: 54
Period size: 8 Copynumber: 5.5 Consensus size: 8
31763972 AAAATTAGTT
31763982 AAAAA-TA
1 AAAAATTA
*
31763989 ATAAATTA
1 AAAAATTA
31763997 AAAAATTA
1 AAAAATTA
31764005 AAAAATTA
1 AAAAATTA
*
31764013 AAATATATA
1 AAAAAT-TA
31764022 AAAA
1 AAAA
31764026 TAAATGCTAT
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
7 4 0.13
8 22 0.71
9 5 0.16
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (8 bp):
AAAAATTA
Found at i:31764074 original size:10 final size:10
Alignment explanation
Indices: 31764054--31764092 Score: 51
Period size: 10 Copynumber: 3.7 Consensus size: 10
31764044 TGTTCAAAAA
31764054 AATATAATAAT
1 AATA-AATAAT
31764065 AATAAATAAT
1 AATAAATAAT
*
31764075 AATAAAATAAG
1 AAT-AAATAAT
31764086 AATAAAT
1 AATAAAT
31764093 TTAAAAAAAG
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
10 13 0.50
11 13 0.50
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (10 bp):
AATAAATAAT
Found at i:31764082 original size:11 final size:11
Alignment explanation
Indices: 31764054--31764091 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
31764044 TGTTCAAAAA
*
31764054 AATATAATAAT
1 AATAAAATAAT
31764065 AAT-AAATAAT
1 AATAAAATAAT
*
31764075 AATAAAATAAG
1 AATAAAATAAT
31764086 AATAAA
1 AATAAA
31764092 TTTAAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
10 9 0.38
11 15 0.62
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:31766043 original size:17 final size:18
Alignment explanation
Indices: 31766023--31766056 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
31766013 TGTCAAGGAA
31766023 TAGCTAATTTT-AAATTT
1 TAGCTAATTTTCAAATTT
*
31766040 TAGCTATTTTTCAAATT
1 TAGCTAATTTTCAAATT
31766057 CAGTAATAAC
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:0.32, C:0.09, G:0.06, T:0.53
Consensus pattern (18 bp):
TAGCTAATTTTCAAATTT
Found at i:31767078 original size:47 final size:46
Alignment explanation
Indices: 31766983--31767117 Score: 148
Period size: 47 Copynumber: 2.9 Consensus size: 46
31766973 CCATTTTTAA
* * ** *
31766983 AAATATGTGAGTAAATTATAATTAAGTATATTTTTAG-CATTTGGGAT
1 AAATATGTGA-TAAATTATAATTAAGGATAATTTT-GTTTTTTGAGAT
*
31767030 AAATATGTGATAAAATTATAATTATGGATAATTTTGTTTTTTGAGAT
1 AAATATGTGAT-AAATTATAATTAAGGATAATTTTGTTTTTTGAGAT
**
31767077 AAATATGTTTTTAAATTATAA-TAAGGATAATTTTGTTTTTT
1 AAATATG-TGATAAATTATAATTAAGGATAATTTTGTTTTTT
31767118 ATAAAAATAA
Statistics
Matches: 76, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
46 21 0.28
47 53 0.70
48 2 0.03
ACGTcount: A:0.38, C:0.01, G:0.14, T:0.47
Consensus pattern (46 bp):
AAATATGTGATAAATTATAATTAAGGATAATTTTGTTTTTTGAGAT
Found at i:31769400 original size:33 final size:33
Alignment explanation
Indices: 31769362--31769427 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
31769352 TTAATCATGA
* * *
31769362 TTCCTTGCACCCGAGCATTTGGCTCATTGGTTG
1 TTCCTTACACCCGAGCATTTAGCTCATTAGTTG
*
31769395 TTCCTTACACCTGAGCATTTAGCTCATTAGTTG
1 TTCCTTACACCCGAGCATTTAGCTCATTAGTTG
31769428 GTCTATGATC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.17, C:0.26, G:0.20, T:0.38
Consensus pattern (33 bp):
TTCCTTACACCCGAGCATTTAGCTCATTAGTTG
Found at i:31792155 original size:21 final size:21
Alignment explanation
Indices: 31792126--31792167 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
31792116 TTTAAATTAC
31792126 TCTAATGAAACAAGAATATTT
1 TCTAATGAAACAAGAATATTT
* **
31792147 TCTAGTGAAATTAGAATATTT
1 TCTAATGAAACAAGAATATTT
31792168 ATTAACCTTT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.43, C:0.07, G:0.12, T:0.38
Consensus pattern (21 bp):
TCTAATGAAACAAGAATATTT
Found at i:31792948 original size:31 final size:30
Alignment explanation
Indices: 31792911--31793018 Score: 80
Period size: 31 Copynumber: 3.5 Consensus size: 30
31792901 AAAAATACCT
31792911 AATTTAATCCTTATATAATAAATTTTTATTC
1 AATTTAATCCTTATAT-ATAAATTTTTATTC
* * *
31792942 AATTTAATCTCTAAATTTTATAAA--TTTATTT
1 AATTTAATC-CT-TA-TATATAAATTTTTATTC
* *
31792973 AATTTAAT--TTCGATACTTTATATTTTTATTC
1 AATTTAATCCTT--ATA-TATAAATTTTTATTC
31793004 AATTTAATCCTTATA
1 AATTTAATCCTTATA
31793019 ACATGACATT
Statistics
Matches: 59, Mismatches: 8, Indels: 20
0.68 0.09 0.23
Matches are distributed among these distances:
28 2 0.03
29 5 0.08
31 40 0.68
32 2 0.03
33 8 0.14
34 2 0.03
ACGTcount: A:0.36, C:0.09, G:0.01, T:0.54
Consensus pattern (30 bp):
AATTTAATCCTTATATATAAATTTTTATTC
Found at i:31793189 original size:58 final size:58
Alignment explanation
Indices: 31793088--31793206 Score: 193
Period size: 58 Copynumber: 2.1 Consensus size: 58
31793078 TTCAAACATG
* * * *
31793088 ACACCTCTTTATTGCCACATTAGCATATCAACACCTCAGCATCACCTTGTGAACAGTC
1 ACACATCTTCATTGCCACATTAGCATATCAACACCTCAACATCACCTTGTGAACAATC
*
31793146 ACACATCTTCATTGCCACATTAGCATATCAACGCCTCAACATCACCTTGTGAACAATC
1 ACACATCTTCATTGCCACATTAGCATATCAACACCTCAACATCACCTTGTGAACAATC
31793204 ACA
1 ACA
31793207 TTAATGTCAC
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
58 56 1.00
ACGTcount: A:0.32, C:0.33, G:0.09, T:0.26
Consensus pattern (58 bp):
ACACATCTTCATTGCCACATTAGCATATCAACACCTCAACATCACCTTGTGAACAATC
Found at i:31798948 original size:21 final size:21
Alignment explanation
Indices: 31798922--31798962 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
31798912 GGCAGCAAGT
31798922 TTCTCGCTGCAGCAAAATTCA
1 TTCTCGCTGCAGCAAAATTCA
* *
31798943 TTCTCGCTGTAGCGAAATTC
1 TTCTCGCTGCAGCAAAATTC
31798963 GGGCGGCCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.24, C:0.27, G:0.17, T:0.32
Consensus pattern (21 bp):
TTCTCGCTGCAGCAAAATTCA
Found at i:31799389 original size:251 final size:252
Alignment explanation
Indices: 31799004--31799456 Score: 631
Period size: 251 Copynumber: 1.8 Consensus size: 252
31798994 GAGAAAATAT
* * *
31799004 TGTTAGTTTGCATATGTTTCAGTTTTTCTAGTAGATCTCTCGCTACAGAAGTACAATTGACCTGA
1 TGTTAGTTTGCATATGTTTCAGTTTTTCTAGCAGATCGCTCACTACAGAAGTACAATTGACCTGA
*
31799069 TTTTTAGACCATTAGAAAGATAAGAGACAAGGCTACAACTTTGATGTTTACCACTTTTCCCATTT
66 TTTTTAGACCATTAGAAAGATAAGAGACAAGGCTACAACTTTGATGTTTACCACTTTTCCCAATT
* ** * * *
31799134 CGGACGGGAAAGTGGTCAAAATCTTTAT-TAAGTGAAGATACTGCATTAGAA-CCTAAGAGTTTC
131 CGGACGAGAAAGTAATCAAAATCTTCATCAAAGTGAAGACACTGCATTAGAATCC-AAGAGTTTC
*
31799197 TCGCTGCAGTGAGTTGTTGGCTACCAAAACAGAATGTTTCTCGCTCAGCGAGAAACAC
195 TCACTGCAGTGAGTTGTTGGCTACCAAAACAGAATGTTTCTCGCTCAGCGAGAAACAC
* * * ** * * *
31799255 TGTTAGTTTGTATGTGTTTTAGTTTTTCTAGCATTTCGCTCACTATATAAGTTCAATTGACCTGA
1 TGTTAGTTTGCATATGTTTCAGTTTTTCTAGCAGATCGCTCACTACAGAAGTACAATTGACCTGA
* * * * **
31799320 TTTTTAGATCATTAGAAAGCTAAGAGACAGGGCTACAACTTTGATGTTTACCATTTTTCTTAATT
66 TTTTTAGACCATTAGAAAGATAAGAGACAAGGCTACAACTTTGATGTTTACCACTTTTCCCAATT
* * *
31799385 CGGACGAGAAGGTAATCAAAATCTTCATCAAAGTGAAGGCACTGCATTAGAATCCGAGAGTTTCT
131 CGGACGAGAAAGTAATCAAAATCTTCATCAAAGTGAAGACACTGCATTAGAATCCAAGAGTTTCT
31799450 CACTGCA
196 CACTGCA
31799457 ACAAGATTTA
Statistics
Matches: 172, Mismatches: 28, Indels: 3
0.85 0.14 0.01
Matches are distributed among these distances:
251 135 0.78
252 35 0.20
253 2 0.01
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (252 bp):
TGTTAGTTTGCATATGTTTCAGTTTTTCTAGCAGATCGCTCACTACAGAAGTACAATTGACCTGA
TTTTTAGACCATTAGAAAGATAAGAGACAAGGCTACAACTTTGATGTTTACCACTTTTCCCAATT
CGGACGAGAAAGTAATCAAAATCTTCATCAAAGTGAAGACACTGCATTAGAATCCAAGAGTTTCT
CACTGCAGTGAGTTGTTGGCTACCAAAACAGAATGTTTCTCGCTCAGCGAGAAACAC
Found at i:31799546 original size:22 final size:21
Alignment explanation
Indices: 31799499--31799546 Score: 51
Period size: 22 Copynumber: 2.2 Consensus size: 21
31799489 GCTGCCAAAA
* *
31799499 CAGAATGTTTCTCGCTGCAGC
1 CAGAATGTTTCTCACTACAGC
* *
31799520 TAGAATGCTTTCTCACTATAGC
1 CAGAATG-TTTCTCACTACAGC
31799542 CAGAA
1 CAGAA
31799547 GTAGGGCACC
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
21 6 0.29
22 15 0.71
ACGTcount: A:0.27, C:0.25, G:0.19, T:0.29
Consensus pattern (21 bp):
CAGAATGTTTCTCACTACAGC
Found at i:31799906 original size:38 final size:40
Alignment explanation
Indices: 31799812--31799918 Score: 146
Period size: 38 Copynumber: 2.7 Consensus size: 40
31799802 CTCACCCAGC
* *
31799812 TCATGTGCATCCCCCCACATCGTGCACATAGCCGGAGTCA
1 TCATGTGCATCCCCCCACATCGTGCACATAGCCAGAGCCA
* ** *
31799852 TCGTGTGCATCCCCCCACATCGTGCACA-A-TTAGTGCCA
1 TCATGTGCATCCCCCCACATCGTGCACATAGCCAGAGCCA
31799890 TCATGTGCATCCCCCCACATCGTGCACAT
1 TCATGTGCATCCCCCCACATCGTGCACAT
31799919 GGGCACTTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
38 31 0.53
39 1 0.02
40 27 0.46
ACGTcount: A:0.21, C:0.38, G:0.18, T:0.22
Consensus pattern (40 bp):
TCATGTGCATCCCCCCACATCGTGCACATAGCCAGAGCCA
Found at i:31807142 original size:2 final size:2
Alignment explanation
Indices: 31807135--31807161 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
31807125 CATGCACAAC
31807135 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 A
31807162 CCAACACAAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31813243 original size:54 final size:53
Alignment explanation
Indices: 31813171--31813275 Score: 122
Period size: 54 Copynumber: 2.0 Consensus size: 53
31813161 TTACCGATTG
* * *
31813171 AAATTTTTGTTCGAAATATGATT-CCAATGAAAATCCATTGGAAATTACCAACA
1 AAATTTTTGTTAGAAATATG-TTACCAACGAAAATCCATTCGAAATTACCAACA
* * * *
31813224 AAATTTTCTGTTAGTAATATGTTACCAACGAAATTTCTTTCGAAATTACCAA
1 AAATTTT-TGTTAGAAATATGTTACCAACGAAAATCCATTCGAAATTACCAA
31813276 TGGAGTTTTT
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
53 9 0.21
54 34 0.79
ACGTcount: A:0.39, C:0.15, G:0.10, T:0.35
Consensus pattern (53 bp):
AAATTTTTGTTAGAAATATGTTACCAACGAAAATCCATTCGAAATTACCAACA
Found at i:31813327 original size:57 final size:57
Alignment explanation
Indices: 31813248--31813426 Score: 202
Period size: 57 Copynumber: 3.1 Consensus size: 57
31813238 TAATATGTTA
* * *
31813248 CCAACGAAATTTCTTTCG-AAATTACCAATGGAGTTTTTGTTGATAATTTAGTCATTT
1 CCAATGAAATTTCATT-GAAAATTACCAATGGAATTTTTGTTGATAATTTAGTCATTT
** *
31813305 CCAATGAAA-TTCTATTGAAAATTACCAGCGAAATTTTTGTTGATAATTTAGTCATTT
1 CCAATGAAATTTC-ATTGAAAATTACCAATGGAATTTTTGTTGATAATTTAGTCATTT
* * * * *
31813362 -TAGATGAAATTTCATTGGAAATTACCAATGGAATTTTTGTTGGTAATTTAATCATTG
1 CCA-ATGAAATTTCATTGAAAATTACCAATGGAATTTTTGTTGATAATTTAGTCATTT
*
31813419 CCTATGAA
1 CCAATGAA
31813427 TTTGAGTTTG
Statistics
Matches: 101, Mismatches: 16, Indels: 10
0.80 0.13 0.08
Matches are distributed among these distances:
56 5 0.05
57 93 0.92
58 3 0.03
ACGTcount: A:0.33, C:0.12, G:0.15, T:0.41
Consensus pattern (57 bp):
CCAATGAAATTTCATTGAAAATTACCAATGGAATTTTTGTTGATAATTTAGTCATTT
Found at i:31816239 original size:36 final size:35
Alignment explanation
Indices: 31816199--31816322 Score: 146
Period size: 36 Copynumber: 3.5 Consensus size: 35
31816189 CTCAACTTAG
* *
31816199 CTCATGTGCACTGCCACACCGCACATAGCTAATATC
1 CTCATGTGCACTCCCACACCGCACATGGC-AATATC
* *
31816235 CTCATGTGCACTTCCACATCGCACATGGCAAGTA--
1 CTCATGTGCACTCCCACACCGCACATGGCAA-TATC
*
31816269 -TCATGTGCACTCCCACACTGCACATGGCATATATC
1 CTCATGTGCACTCCCACACCGCACATGGCA-ATATC
*
31816304 ATCATGTGCACTCCCACAC
1 CTCATGTGCACTCCCACAC
31816323 TGCTCACCAC
Statistics
Matches: 77, Mismatches: 6, Indels: 10
0.83 0.06 0.11
Matches are distributed among these distances:
33 28 0.36
34 1 0.01
35 2 0.03
36 46 0.60
ACGTcount: A:0.27, C:0.35, G:0.15, T:0.23
Consensus pattern (35 bp):
CTCATGTGCACTCCCACACCGCACATGGCAATATC
Found at i:31822496 original size:38 final size:40
Alignment explanation
Indices: 31822453--31822558 Score: 130
Period size: 40 Copynumber: 2.7 Consensus size: 40
31822443 ATAGTGCCCG
*
31822453 TGTGCACGATGTGGGGGGATGTACATGAT-G-GCACTGAT-
1 TGTGCACGATGTGGGGGGATGTACATGATAGTGC-CGGATA
* * *
31822491 TGTGCACGATGTAGGGGGATGCACACT-ATAGTGCCGGCTA
1 TGTGCACGATGTGGGGGGATGTACA-TGATAGTGCCGGATA
31822531 TGTGCACGATGTGGGGGGATGTACATGA
1 TGTGCACGATGTGGGGGGATGTACATGA
31822559 GCCGGGTGTG
Statistics
Matches: 57, Mismatches: 6, Indels: 8
0.80 0.08 0.11
Matches are distributed among these distances:
38 25 0.44
39 6 0.11
40 26 0.46
ACGTcount: A:0.22, C:0.15, G:0.39, T:0.25
Consensus pattern (40 bp):
TGTGCACGATGTGGGGGGATGTACATGATAGTGCCGGATA
Found at i:31827199 original size:43 final size:43
Alignment explanation
Indices: 31827129--31827247 Score: 177
Period size: 43 Copynumber: 2.8 Consensus size: 43
31827119 GTAATTATGT
* *
31827129 TGACTCGGCTATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCG-GTGA
*
31827172 TGACCCGGTTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
* *
31827215 TGACCCAGCCATGTGCGAGTAGGGAGTGCGCAT
1 TGACCCGGCTATGTGCGAGTAGGGAGTGCGCAT
31827248 GAGCTGGTGA
Statistics
Matches: 69, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
42 1 0.01
43 68 0.99
ACGTcount: A:0.22, C:0.21, G:0.38, T:0.19
Consensus pattern (43 bp):
TGACCCGGCTATGTGCGAGTAGGGAGTGCGCATAACCCGGTGA
Found at i:31827257 original size:43 final size:43
Alignment explanation
Indices: 31827139--31827260 Score: 174
Period size: 43 Copynumber: 2.8 Consensus size: 43
31827129 TGACTCGGCT
* **
31827139 ATGTGCGAGTAGGGAGTGCGCATAAGCCGAG-GATGACCCGGTT
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCG-GTGATGACCCAGCC
*
31827182 ATGTGCGAGTAGGGAGTGCGCATAACCCGGTGATGACCCAGCC
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
* *
31827225 ATGTGCGAGTAGGGAGTGCGCATGAGCTGGTGATGA
1 ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGA
31827261 TGATGATGAG
Statistics
Matches: 71, Mismatches: 7, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
42 1 0.01
43 70 0.99
ACGTcount: A:0.23, C:0.19, G:0.39, T:0.19
Consensus pattern (43 bp):
ATGTGCGAGTAGGGAGTGCGCATAAGCCGGTGATGACCCAGCC
Found at i:31827271 original size:20 final size:20
Alignment explanation
Indices: 31827246--31827308 Score: 101
Period size: 20 Copynumber: 3.2 Consensus size: 20
31827236 GGGAGTGCGC
31827246 ATGAGCTGGTGATGATGATG
1 ATGAGCTGGTGATGATGATG
31827266 ATGAGCTGGTGATGATGATG
1 ATGAGCTGGTGATGATGATG
* *
31827286 ATGGGTTGGTGA-GATGATG
1 ATGAGCTGGTGATGATGATG
31827305 ATGA
1 ATGA
31827309 TGGGTATATA
Statistics
Matches: 40, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
19 10 0.25
20 30 0.75
ACGTcount: A:0.25, C:0.03, G:0.41, T:0.30
Consensus pattern (20 bp):
ATGAGCTGGTGATGATGATG
Found at i:31833589 original size:18 final size:18
Alignment explanation
Indices: 31833553--31833592 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
31833543 TTAATATTTT
31833553 AATATTATTTTTTAATTAA
1 AATATTATTTTTT-ATTAA
31833572 AATATTATTTTATT-TTAA
1 AATATTATTTT-TTATTAA
31833590 AAT
1 AAT
31833593 TTTTCACTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 7 0.35
19 11 0.55
20 2 0.10
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
AATATTATTTTTTATTAA
Found at i:31836071 original size:17 final size:19
Alignment explanation
Indices: 31836049--31836093 Score: 67
Period size: 17 Copynumber: 2.5 Consensus size: 19
31836039 CATAATATAT
*
31836049 TATATATTAATGT-T-TTA
1 TATATATTAATATATATTA
31836066 TATATATTAATATATATTA
1 TATATATTAATATATATTA
31836085 TATATATTA
1 TATATATTA
31836094 TTTTGTTGAT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
17 12 0.48
18 1 0.04
19 12 0.48
ACGTcount: A:0.42, C:0.00, G:0.02, T:0.56
Consensus pattern (19 bp):
TATATATTAATATATATTA
Found at i:31836269 original size:2 final size:2
Alignment explanation
Indices: 31836211--31836251 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
31836201 ATAAGTAAGT
* * *
31836211 TA TA TG TA TG TA TC 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 TA TA TA TA T
31836252 TTCATAACCA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31836384 original size:2 final size:2
Alignment explanation
Indices: 31836377--31836402 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
31836367 CGATTTAATG
31836377 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
31836403 GTATGTAGGT
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):
AT
Found at i:31838060 original size:23 final size:23
Alignment explanation
Indices: 31838034--31838078 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
31838024 ACAAAATCTA
31838034 AATGAGAAAAAAATAAAAAAATC
1 AATGAGAAAAAAATAAAAAAATC
* **
31838057 AATGTGAAAAATCTAAAAAAAT
1 AATGAGAAAAAAATAAAAAAAT
31838079 AAAAAAGTAA
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:0.69, C:0.04, G:0.09, T:0.18
Consensus pattern (23 bp):
AATGAGAAAAAAATAAAAAAATC
Found at i:31844363 original size:62 final size:62
Alignment explanation
Indices: 31844291--31844412 Score: 212
Period size: 62 Copynumber: 2.0 Consensus size: 62
31844281 CATATATATA
31844291 AAAAGAAGAAGAAGAAGAAGATATATATATATATATATATATAATAAA-TAAAAA-GTAAANTT
1 AAAAGAAGAAGAAGAAGAAGATATATATATATATATATATAT-ATAAATTAAAAAGGTAAA-TT
31844353 AAAAGAAGAAGAAGAAGAAGATATATATATATATATATATATATAAATTAAAAAGGTAAA
1 AAAAGAAGAAGAAGAAGAAGATATATATATATATATATATATATAAATTAAAAAGGTAAA
31844413 ATATCACCAC
Statistics
Matches: 58, Mismatches: 0, Indels: 3
0.95 0.00 0.05
Matches are distributed among these distances:
61 5 0.09
62 48 0.83
63 5 0.09
ACGTcount: A:0.61, C:0.00, G:0.12, T:0.25
Consensus pattern (62 bp):
AAAAGAAGAAGAAGAAGAAGATATATATATATATATATATATATAAATTAAAAAGGTAAATT
Found at i:31844380 original size:2 final size:2
Alignment explanation
Indices: 31844373--31844397 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
31844363 GAAGAAGAAG
31844373 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 A
31844398 AATTAAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:31846348 original size:23 final size:24
Alignment explanation
Indices: 31846291--31846355 Score: 78
Period size: 25 Copynumber: 2.7 Consensus size: 24
31846281 TTTTTTTAAA
* *
31846291 AAAAAATTTATAATTTTGTCTCTAT
1 AAAAATTTTATAATTTTATCTC-AT
31846316 AAAAATTTTATAATTTTATCTC-T
1 AAAAATTTTATAATTTTATCTCAT
* *
31846339 ACAAATTTTAAAATTTT
1 AAAAATTTTATAATTTT
31846356 TCTAACATAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
23 16 0.44
25 20 0.56
ACGTcount: A:0.42, C:0.08, G:0.02, T:0.49
Consensus pattern (24 bp):
AAAAATTTTATAATTTTATCTCAT
Found at i:31846406 original size:83 final size:86
Alignment explanation
Indices: 31846229--31846412 Score: 221
Period size: 83 Copynumber: 2.1 Consensus size: 86
31846219 TTTATTTTTT
* *
31846229 TAATTTTATAACTTTACCTCTACAAAAATTTTAAGATTTTTTTAACATACTCTTTTTTTAAAAAA
1 TAATTTTATAACTTTACCTCTAC-AAAATTTTAAAATTTTTCTAACATA--CTTTTTTTAAAAAA
* * *
31846294 AAATTTATAATTTTGTCTCTATAA
63 AAATTTATAATTTTATCCCTACAA
* * * ***
31846318 AAATTTTATAATTTTATCTCTAC-AAATTTTAAAATTTTTCTAACATA-TTTTTTT-AAAAATTT
1 TAATTTTATAACTTTACCTCTACAAAATTTTAAAATTTTTCTAACATACTTTTTTTAAAAAAAAA
31846380 TTTATAATTTTATCCCTACAA
66 TTTATAATTTTATCCCTACAA
31846401 TAATTTTATAAC
1 TAATTTTATAAC
31846413 ATATCATAAT
Statistics
Matches: 82, Mismatches: 13, Indels: 6
0.81 0.13 0.06
Matches are distributed among these distances:
83 33 0.40
84 7 0.09
87 22 0.27
89 20 0.24
ACGTcount: A:0.38, C:0.11, G:0.01, T:0.50
Consensus pattern (86 bp):
TAATTTTATAACTTTACCTCTACAAAATTTTAAAATTTTTCTAACATACTTTTTTTAAAAAAAAA
TTTATAATTTTATCCCTACAA
Found at i:31847877 original size:16 final size:16
Alignment explanation
Indices: 31847858--31847907 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 16
31847848 TCTGCGATTG
31847858 GGAGAAAGAGGAAGAA
1 GGAGAAAGAGGAAGAA
* *
31847874 GGAGAAGGAGAAAGAA
1 GGAGAAAGAGGAAGAA
31847890 --AGAAAGAGTGAAGAA
1 GGAGAAAGAG-GAAGAA
31847905 GGA
1 GGA
31847908 AGGGGAGCGG
Statistics
Matches: 27, Mismatches: 4, Indels: 5
0.75 0.11 0.14
Matches are distributed among these distances:
14 7 0.26
15 5 0.19
16 14 0.52
17 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.42, T:0.02
Consensus pattern (16 bp):
GGAGAAAGAGGAAGAA
Found at i:31847984 original size:13 final size:12
Alignment explanation
Indices: 31847939--31848001 Score: 60
Period size: 13 Copynumber: 5.2 Consensus size: 12
31847929 AAAAAGAATG
31847939 AAAAAG-AAA-A
1 AAAAAGAAAAGA
*
31847949 AATAAGAAGAAGA
1 AAAAAGAA-AAGA
31847962 AATAAAGAAAAGA
1 AA-AAAGAAAAGA
*
31847975 AAAAAGGAAA-A
1 AAAAAGAAAAGA
31847986 AAAAAGAAAAGGA
1 AAAAAGAAAA-GA
31847999 AAA
1 AAA
31848002 GGATTTGGGT
Statistics
Matches: 43, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
10 5 0.12
11 11 0.26
12 9 0.21
13 13 0.30
14 5 0.12
ACGTcount: A:0.79, C:0.00, G:0.17, T:0.03
Consensus pattern (12 bp):
AAAAAGAAAAGA
Found at i:31848300 original size:33 final size:31
Alignment explanation
Indices: 31848261--31848356 Score: 77
Period size: 33 Copynumber: 2.8 Consensus size: 31
31848251 TAGTGTTAGA
31848261 AAATAAAAAAATGGAAAGTAAAAATAATAATA-
1 AAATAAAAAAAT--AAAGTAAAAATAATAATAC
* *
31848293 ATAATAAATAAATAAATGATAAAAATCATAATAC
1 A-AATAAAAAAATAAA-G-TAAAAATAATAATAC
31848327 AAATATAAAAATTATAAAAAGTAAAAATAA
1 AAATA-AAAAA--AT--AAAGTAAAAATAA
31848357 ATTATGAAGA
Statistics
Matches: 51, Mismatches: 4, Indels: 14
0.74 0.06 0.20
Matches are distributed among these distances:
31 3 0.06
32 2 0.04
33 27 0.53
34 5 0.10
36 10 0.20
37 1 0.02
38 3 0.06
ACGTcount: A:0.70, C:0.02, G:0.05, T:0.23
Consensus pattern (31 bp):
AAATAAAAAAATAAAGTAAAAATAATAATAC
Found at i:31848323 original size:20 final size:19
Alignment explanation
Indices: 31848300--31848344 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
31848290 ATAATAATAA
*
31848300 ATAAATAAATGATAAAAATC
1 ATAAACAAAT-ATAAAAATC
*
31848320 ATAATACAAATATAAAAATT
1 ATAA-ACAAATATAAAAATC
31848340 ATAAA
1 ATAAA
31848345 AAGTAAAAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 1 0.05
20 16 0.73
21 5 0.23
ACGTcount: A:0.67, C:0.04, G:0.02, T:0.27
Consensus pattern (19 bp):
ATAAACAAATATAAAAATC
Found at i:31850761 original size:60 final size:60
Alignment explanation
Indices: 31850635--31850768 Score: 162
Period size: 60 Copynumber: 2.2 Consensus size: 60
31850625 ATAGAAAGTT
* * * * *
31850635 TTTCGCTGCAGCGAAATTGTAACCCAGAAACAGAAAGTTTCTAGTTGCAACGAGATTCAA
1 TTTCGCTACAGCGAAATTGCAACCCAGAAACAGAAAGTTTCTAGCTGCAACAAGAATCAA
* * * *
31850695 TCTCGCTACAGTGAAATTGCAACCCAGAAACAGAAAGTTTCTCA-CTGCAGCAAGAATGAA
1 TTTCGCTACAGCGAAATTGCAACCCAGAAACAGAAAGTTTCT-AGCTGCAACAAGAATCAA
*
31850755 TTTCGCTGCAGCGA
1 TTTCGCTACAGCGA
31850769 GAAGCTACAG
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
60 60 0.98
61 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.23
Consensus pattern (60 bp):
TTTCGCTACAGCGAAATTGCAACCCAGAAACAGAAAGTTTCTAGCTGCAACAAGAATCAA
Found at i:31851187 original size:43 final size:43
Alignment explanation
Indices: 31851122--31851244 Score: 147
Period size: 43 Copynumber: 2.9 Consensus size: 43
31851112 CCCATCATCA
* * * ** *
31851122 TCATCACCAGCTCATGCACACTCCCTACTCGCACATGGCTGGG
1 TCATCACCGGCTTATGCGCACTCCCTACTCGCACATAACCGGG
* *
31851165 TCATCACCGGGTTATGCGCACTCCTTACTCGCACATAACCGGG
1 TCATCACCGGCTTATGCGCACTCCCTACTCGCACATAACCGGG
***
31851208 TCATTGTCGGCTTATGCGCACTCCCTACTCGCACATA
1 TCATCACCGGCTTATGCGCACTCCCTACTCGCACATA
31851245 GCCAAGTCAA
Statistics
Matches: 67, Mismatches: 13, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 67 1.00
ACGTcount: A:0.20, C:0.37, G:0.19, T:0.24
Consensus pattern (43 bp):
TCATCACCGGCTTATGCGCACTCCCTACTCGCACATAACCGGG
Found at i:31852962 original size:2 final size:2
Alignment explanation
Indices: 31852955--31853101 Score: 124
Period size: 2 Copynumber: 74.5 Consensus size: 2
31852945 AACTTGATTC
31852955 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * ** ** * *
31852997 AT AT AT AT AT AT AT AT A- ACG AA AG CT CG AT -T GC A- AT TT NT
1 AT AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT
* *
31853037 GAT TT A- AG AT AT AT ACT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 -AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT
31853080 AT AT AT AT A- AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
31853102 ACGAAAGCTC
Statistics
Matches: 122, Mismatches: 15, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
1 5 0.04
2 113 0.93
3 4 0.03
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.45
Consensus pattern (2 bp):
AT
Found at i:31864611 original size:43 final size:43
Alignment explanation
Indices: 31864564--31864672 Score: 139
Period size: 43 Copynumber: 2.5 Consensus size: 43
31864554 TCAGCTCATA
* * **
31864564 CGCACTCCCTACTTGCACATGGCTGGGTCATCAC-CGGGTTATG
1 CGCACTCCCTACTCGCACATAGCTGGGTCATC-CTCGACTTATG
* *
31864607 CGCACTCCCTACTCACACATAGCTGGGTCATCCTTGACTTATG
1 CGCACTCCCTACTCGCACATAGCTGGGTCATCCTCGACTTATG
*
31864650 CACACTCCCTACTCGCACATAGC
1 CGCACTCCCTACTCGCACATAGC
31864673 CGAGTCAATG
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 1 0.02
43 56 0.98
ACGTcount: A:0.20, C:0.37, G:0.18, T:0.25
Consensus pattern (43 bp):
CGCACTCCCTACTCGCACATAGCTGGGTCATCCTCGACTTATG
Found at i:31864709 original size:2 final size:2
Alignment explanation
Indices: 31864704--31864750 Score: 94
Period size: 2 Copynumber: 23.5 Consensus size: 2
31864694 CAATATATTC
31864704 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
31864746 AT AT A
1 AT AT A
31864751 NNNNNNNNNN
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31868244 original size:14 final size:14
Alignment explanation
Indices: 31868225--31868257 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
31868215 TCATCCCTAC
*
31868225 GGATGCCTAACCAA
1 GGATGCCTAAACAA
31868239 GGATGCCTAAACAA
1 GGATGCCTAAACAA
31868253 -GATGC
1 GGATGC
31868258 TTTTAGGTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.15
Consensus pattern (14 bp):
GGATGCCTAAACAA
Found at i:31869661 original size:18 final size:18
Alignment explanation
Indices: 31869638--31869676 Score: 78
Period size: 18 Copynumber: 2.2 Consensus size: 18
31869628 TTTTGTTGGA
31869638 AAACAAGAAGTAAGTTTT
1 AAACAAGAAGTAAGTTTT
31869656 AAACAAGAAGTAAGTTTT
1 AAACAAGAAGTAAGTTTT
31869674 AAA
1 AAA
31869677 ACGGTTGGGA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.54, C:0.05, G:0.15, T:0.26
Consensus pattern (18 bp):
AAACAAGAAGTAAGTTTT
Found at i:31881593 original size:19 final size:19
Alignment explanation
Indices: 31881569--31881606 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
31881559 ACTTCTAAAC
31881569 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
31881588 CTCAAATCATACTCCAATA
1 CTCAAATCATACTCCAATA
31881607 AGTCAAATGA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (19 bp):
CTCAAATCATACTCCAATA
Found at i:31883211 original size:84 final size:85
Alignment explanation
Indices: 31883045--31883251 Score: 197
Period size: 84 Copynumber: 2.4 Consensus size: 85
31883035 ATCATCATCG
* * * * *
31883045 GCTTATGCGCACTCCCTACTCGCACATAGTCGGGTCAACATCGGCTTCTGTGCACTTCCACTCAC
1 GCTTATGCACACTCCCTACTCACACATAGTCGGGTCAACATCGACTTATGCGCACTTCCACTCAC
*
31883110 ATATATCCAGGTCAGCATTA
66 ACATATCCAGGTCAGCATTA
* *
31883130 GCTTATGCACACT-CTTACTCACACATAG-CTGGGTCAGCATCGACTTATGCGCAC-TCCTACTC
1 GCTTATGCACACTCCCTACTCACACATAGTC-GGGTCAACATCGACTTATGCGCACTTCC-ACTC
* * * *
31883192 GCACATAGT-CGGGTTAGCATTG
64 ACACATA-TCCAGGTCAGCATTA
** * ** *
31883214 GCTTATGTGCATTCCCTACTTGCACATAGTCGAGTCAA
1 GCTTATGCACACTCCCTACTCACACATAGTCGGGTCAA
31883252 TATCATCACA
Statistics
Matches: 97, Mismatches: 20, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
83 4 0.04
84 62 0.64
85 30 0.31
86 1 0.01
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (85 bp):
GCTTATGCACACTCCCTACTCACACATAGTCGGGTCAACATCGACTTATGCGCACTTCCACTCAC
ACATATCCAGGTCAGCATTA
Found at i:31883241 original size:43 final size:42
Alignment explanation
Indices: 31883040--31883250 Score: 169
Period size: 42 Copynumber: 5.0 Consensus size: 42
31883030 TCATCATCAT
* *
31883040 CATCGGCTTATGCGCACTCCCTACTCGCACATAGTCGGGTCAA
1 CATCGACTTATGCGCACT-CCTACTCGCACATAGTCGGGTCAG
* * * * * *
31883083 CATCGGCTTCTGTGCACTTCC-ACTCACATATA-TCCAGGTCAG
1 CATCGACTTATGCGCAC-TCCTACTCGCACATAGT-CGGGTCAG
* * * *
31883125 CAT-TAGCTTATGCACACTCTTACTCACACATAG-CTGGGTCAG
1 CATCGA-CTTATGCGCACTCCTACTCGCACATAGTC-GGGTCAG
*
31883167 CATCGACTTATGCGCACTCCTACTCGCACATAGTCGGGTTAG
1 CATCGACTTATGCGCACTCCTACTCGCACATAGTCGGGTCAG
* * * * * *
31883209 CATTGGCTTATGTGCATTCCCTACTTGCACATAGTCGAGTCA
1 CATCGACTTATGCGCACT-CCTACTCGCACATAGTCGGGTCA
31883251 ATATCATCAC
Statistics
Matches: 133, Mismatches: 26, Indels: 18
0.75 0.15 0.10
Matches are distributed among these distances:
41 4 0.03
42 89 0.67
43 39 0.29
44 1 0.01
ACGTcount: A:0.22, C:0.31, G:0.19, T:0.28
Consensus pattern (42 bp):
CATCGACTTATGCGCACTCCTACTCGCACATAGTCGGGTCAG
Found at i:31884420 original size:10 final size:10
Alignment explanation
Indices: 31884405--31884437 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
31884395 TTATTATTTA
31884405 TTTATTTATT
1 TTTATTTATT
31884415 TTTATTTATT
1 TTTATTTATT
31884425 TATTA-TTATT
1 T-TTATTTATT
31884435 TTT
1 TTT
31884438 TCACTCACAA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
9 2 0.09
10 17 0.77
11 3 0.14
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTATTTATT
Found at i:31884420 original size:14 final size:14
Alignment explanation
Indices: 31884394--31884435 Score: 66
Period size: 14 Copynumber: 2.9 Consensus size: 14
31884384 CTTTCCATTG
31884394 TTTATTATTTATTTA
1 TTTATT-TTTATTTA
31884409 TTTATTTTTATTTA
1 TTTATTTTTATTTA
*
31884423 TTTATTATTATTT
1 TTTATTTTTATTT
31884436 TTTCACTCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
14 20 0.77
15 6 0.23
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTATTTTTATTTA
Found at i:31884669 original size:92 final size:91
Alignment explanation
Indices: 31884502--31884773 Score: 314
Period size: 92 Copynumber: 3.0 Consensus size: 91
31884492 AATTTTTGCC
* * * *
31884502 CCTTTCAACC-TCAAAAATCAGCAGCCT-AAGCTGCTCATTTCACCCTTAAAATCGATAGCCAAA
1 CCTTTCAGCCTTCAAAAATCAGCAG-CTAAAGCTACTCATCTCA-CCTCAAAATCGATAGCCAAA
* *
31884565 ACCTCAAAAATCAGCAACTAAAGCTTCT
64 ACCTCAAAAATCAGCAGCTAAAGCTGCT
* *
31884593 CCTTTCAGCCTTCAAAAATCAGCAGCTAAAGCTACTCATCTGATCCTCAAAATCGATAACCAAAA
1 CCTTTCAGCCTTCAAAAATCAGCAGCTAAAGCTACTCATCTCA-CCTCAAAATCGATAGCCAAAA
* * * *
31884658 CCTCAACAATCAGTAGCAAAAGGTGCT
65 CCTCAAAAATCAGCAGCTAAAGCTGCT
* * * * * **
31884685 TCTTTTAGCCTTCAAAAATCAGTAGCTAAAGCTACTAATCTCACCTTCAAAATCAACGGCCAAAA
1 CCTTTCAGCCTTCAAAAATCAGCAGCTAAAGCTACTCATCTCACC-TCAAAATCGATAGCCAAAA
*
31884750 CCTCAAAAATCAACAGCTAAAGCT
65 CCTCAAAAATCAGCAGCTAAAGCT
31884774 ACTTATCTCA
Statistics
Matches: 151, Mismatches: 27, Indels: 5
0.83 0.15 0.03
Matches are distributed among these distances:
91 13 0.09
92 138 0.91
ACGTcount: A:0.39, C:0.29, G:0.10, T:0.23
Consensus pattern (91 bp):
CCTTTCAGCCTTCAAAAATCAGCAGCTAAAGCTACTCATCTCACCTCAAAATCGATAGCCAAAAC
CTCAAAAATCAGCAGCTAAAGCTGCT
Done.