Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 ID=Chr01-JGI_221_v2.0
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: 55868233
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 983842 characters in sequence are not A, C, G, or T
File 107 of 187
Found at i:31737825 original size:32 final size:32
Alignment explanation
Indices: 31737734--31737835 Score: 107
Period size: 32 Copynumber: 3.2 Consensus size: 32
31737724 TTTGCTGCGA
* *
31737734 TGCTATTGACGGCTTTGTGCCGATCATATTAC
1 TGCTACTGATGGCTTTGTGCCGATCATATTAC
* * * * * *
31737766 CGTTACTGATGGCTGTGTGCTGGTCATATCAC
1 TGCTACTGATGGCTTTGTGCCGATCATATTAC
* *
31737798 TGCTACTGATGGCTTTATGCCAATCATATTAC
1 TGCTACTGATGGCTTTGTGCCGATCATATTAC
31737830 TG-TACT
1 TGCTACT
31737836 TAGGGATTGT
Statistics
Matches: 54, Mismatches: 16, Indels: 1
0.76 0.23 0.01
Matches are distributed among these distances:
31 4 0.07
32 50 0.93
ACGTcount: A:0.20, C:0.22, G:0.22, T:0.37
Consensus pattern (32 bp):
TGCTACTGATGGCTTTGTGCCGATCATATTAC
Found at i:31746012 original size:42 final size:42
Alignment explanation
Indices: 31745926--31746012 Score: 140
Period size: 42 Copynumber: 2.1 Consensus size: 42
31745916 TGCCAGGCTG
*
31745926 TGTAACTTTCGAAATGGCCTCACACGCCCGTGTGTCAGGTCA
1 TGTAACTTTCGAAATGGCCTCACACGCCCGTGTGTCAGGCCA
*
31745968 TGTAACTTTTGAAATGGCCTCACACGCCCGTGT-TCCAGGCCA
1 TGTAACTTTCGAAATGGCCTCACACGCCCGTGTGT-CAGGCCA
31746010 TGT
1 TGT
31746013 GCTAGGTAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
41 1 0.02
42 41 0.98
ACGTcount: A:0.21, C:0.29, G:0.23, T:0.28
Consensus pattern (42 bp):
TGTAACTTTCGAAATGGCCTCACACGCCCGTGTGTCAGGCCA
Found at i:31757182 original size:59 final size:60
Alignment explanation
Indices: 31757114--31757238 Score: 218
Period size: 60 Copynumber: 2.1 Consensus size: 60
31757104 ACATTGAACA
*
31757114 TTAAA-AAATATTTCTTTTTTTAATT-TTTTTCCATATCATATATTTTAACTTTTTAACT
1 TTAAATAAATACTTCTTTTTTTAATTCTTTTTCCATATCATATATTTTAACTTTTTAACT
*
31757172 TTAAATAAATACTTCTTTTTTTATTTCTTTTTCCATATCATATATTTTAACTTTTTAACT
1 TTAAATAAATACTTCTTTTTTTAATTCTTTTTCCATATCATATATTTTAACTTTTTAACT
31757232 TTAAATA
1 TTAAATA
31757239 TTTATGTAAT
Statistics
Matches: 63, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
58 5 0.08
59 18 0.29
60 40 0.63
ACGTcount: A:0.31, C:0.11, G:0.00, T:0.58
Consensus pattern (60 bp):
TTAAATAAATACTTCTTTTTTTAATTCTTTTTCCATATCATATATTTTAACTTTTTAACT
Found at i:31760009 original size:27 final size:27
Alignment explanation
Indices: 31759969--31760111 Score: 189
Period size: 27 Copynumber: 5.3 Consensus size: 27
31759959 AAGGACTGAA
**
31759969 TAAAATGATTGAATTACCCCCATAGGG
1 TAAAATGACCGAATTACCCCCATAGGG
* * *
31759996 TAAAATGATCGAATTACTCCTATAGGG
1 TAAAATGACCGAATTACCCCCATAGGG
* * *
31760023 TAGAATGACCGAATTACCCTCACAGGG
1 TAAAATGACCGAATTACCCCCATAGGG
*
31760050 TAAAATGACCAAATTA-CCCCATAGGG
1 TAAAATGACCGAATTACCCCCATAGGG
*
31760076 TAAAATGACCGAATTAGCCCCATAGGG
1 TAAAATGACCGAATTACCCCCATAGGG
31760103 TAAAATGAC
1 TAAAATGAC
31760112 TATTATACCC
Statistics
Matches: 101, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
26 23 0.23
27 78 0.77
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.22
Consensus pattern (27 bp):
TAAAATGACCGAATTACCCCCATAGGG
Found at i:31760103 original size:53 final size:53
Alignment explanation
Indices: 31759969--31760111 Score: 189
Period size: 53 Copynumber: 2.7 Consensus size: 53
31759959 AAGGACTGAA
** * * *
31759969 TAAAATGATTGAATTACCCCCATAGGGTAAAATGATCGAATTACTCCTATAGGG
1 TAAAATGACCGAATTA-CCCCATAGGGTAAAATGACCAAATTACTCCCATAGGG
* *
31760023 TAGAATGACCGAATTACCCTCACAGGGTAAAATGACCAAATTAC-CCCATAGGG
1 TAAAATGACCGAATTACCC-CATAGGGTAAAATGACCAAATTACTCCCATAGGG
31760076 TAAAATGACCGAATTAGCCCCATAGGGTAAAATGAC
1 TAAAATGACCGAATTA-CCCCATAGGGTAAAATGAC
31760112 TATTATACCC
Statistics
Matches: 78, Mismatches: 9, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
53 41 0.53
54 37 0.47
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.22
Consensus pattern (53 bp):
TAAAATGACCGAATTACCCCATAGGGTAAAATGACCAAATTACTCCCATAGGG
Found at i:31763338 original size:43 final size:43
Alignment explanation
Indices: 31763255--31763380 Score: 121
Period size: 43 Copynumber: 2.9 Consensus size: 43
31763245 CATAAAAACG
* * * * *
31763255 CCGCTAAAGAACATGATCTTTAACGGCGTTT-TCAGTAAAAGCA
1 CCGCTAAAGATCATGTTCTTTAGCGGCGTTTGT-GGGAAAAGCA
* **
31763298 CCGCTAAAGATCATGTTCTTTAGCGGCATTTGTGGGAAAAGTG
1 CCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGGAAAAGCA
* * *
31763341 CCGATAAATG-TCATGTTCTTTAGTGGTGTTTGTGGGAAAA
1 CCGCTAAA-GATCATGTTCTTTAGCGGCGTTTGTGGGAAAA
31763381 CGCCACTAAC
Statistics
Matches: 69, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
43 67 0.97
44 2 0.03
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.31
Consensus pattern (43 bp):
CCGCTAAAGATCATGTTCTTTAGCGGCGTTTGTGGGAAAAGCA
Found at i:31775586 original size:18 final size:19
Alignment explanation
Indices: 31775563--31775601 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
31775553 CTTGGCCCAT
* *
31775563 TACAGTATCA-ATATTCAG
1 TACAGTAACAGATATGCAG
31775581 TACAGTAACAGATATGCAG
1 TACAGTAACAGATATGCAG
31775600 TA
1 TA
31775602 TCAAATCCTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 9 0.50
19 9 0.50
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.28
Consensus pattern (19 bp):
TACAGTAACAGATATGCAG
Found at i:31775963 original size:247 final size:247
Alignment explanation
Indices: 31775524--31776012 Score: 807
Period size: 247 Copynumber: 2.0 Consensus size: 247
31775514 TTAGCCCATT
*
31775524 ACAATACAGAAGCAGTCATGCATTTGGGCCTTGGCCCATTACAGTATCAATATTCAGTACAGTAA
1 ACAATACAGAAGCAGTCATGCATTTGGGCCTTGGCCCATTACAGTATCAATACTCAGTACAGTAA
* * *
31775589 CAGATATGCAGTATCAAATCCTACCCAACTAGCCTCTACACTCCAACTCTATCTAACCCTACACT
66 CAGATATGCAGTATCAAATCCTACCCAACCAGCCTCTACACTCCAACTCCATCCAACCCTACACT
* *
31775654 CCATGTGGGGATATAATCAACCCACCCATCCCTACACTCCAAAAAGTACCAAATCCGGCACTAGA
131 CCATGTGAGGATATAATCAACCCACCCATCCCTACACTCCAAAAAGAACCAAATCCGGCACTAGA
*
31775719 TAGTGGTTTGCAGTTGAACTGCCAGTAAATTAGGCTCGAGGCCTTTCTCCGA
196 TAGTGGTTTGCAGCTGAACTGCCAGTAAATTAGGCTCGAGGCCTTTCTCCGA
* *
31775771 ACAATACATAAGCAGTCATGCATTTGGGCCTTGGCCCATTACAGTATCAATACTCAGTACCGTAA
1 ACAATACAGAAGCAGTCATGCATTTGGGCCTTGGCCCATTACAGTATCAATACTCAGTACAGTAA
* *
31775836 CAGATATGCAGTATCAAATCCTACCCAGCCAGCCTCTACACTCCAACTCCGTCCAACCCTACACT
66 CAGATATGCAGTATCAAATCCTACCCAACCAGCCTCTACACTCCAACTCCATCCAACCCTACACT
* * ** **
31775901 CCATGTGAGGATATAATCAACCCACCCATCCTTACCCTCCAAAAAGAACTGAATGTGGCACTAGA
131 CCATGTGAGGATATAATCAACCCACCCATCCCTACACTCCAAAAAGAACCAAATCCGGCACTAGA
* *
31775966 TAGTGGTTTGCAGCTGAGCTGCCTGTAAATTAGGCTCGAGGCCTTTC
196 TAGTGGTTTGCAGCTGAACTGCCAGTAAATTAGGCTCGAGGCCTTTC
31776013 AGTGCACTTC
Statistics
Matches: 223, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
247 223 1.00
ACGTcount: A:0.30, C:0.29, G:0.16, T:0.24
Consensus pattern (247 bp):
ACAATACAGAAGCAGTCATGCATTTGGGCCTTGGCCCATTACAGTATCAATACTCAGTACAGTAA
CAGATATGCAGTATCAAATCCTACCCAACCAGCCTCTACACTCCAACTCCATCCAACCCTACACT
CCATGTGAGGATATAATCAACCCACCCATCCCTACACTCCAAAAAGAACCAAATCCGGCACTAGA
TAGTGGTTTGCAGCTGAACTGCCAGTAAATTAGGCTCGAGGCCTTTCTCCGA
Found at i:31784016 original size:34 final size:35
Alignment explanation
Indices: 31783978--31784053 Score: 127
Period size: 34 Copynumber: 2.2 Consensus size: 35
31783968 ACTTTAAATG
31783978 TTTAAATGTTTATGTAAGTTATGATAATC-TTAAC
1 TTTAAATGTTTATGTAAGTTATGATAATCATTAAC
* *
31784012 TTTAAATGTTTATTTAAGTTATGATTATCATTAAC
1 TTTAAATGTTTATGTAAGTTATGATAATCATTAAC
31784047 TTTAAAT
1 TTTAAAT
31784054 ATGATTATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
34 27 0.69
35 12 0.31
ACGTcount: A:0.36, C:0.05, G:0.09, T:0.50
Consensus pattern (35 bp):
TTTAAATGTTTATGTAAGTTATGATAATCATTAAC
Found at i:31784034 original size:43 final size:43
Alignment explanation
Indices: 31783937--31784023 Score: 158
Period size: 43 Copynumber: 2.0 Consensus size: 43
31783927 TTATATTCTC
*
31783937 TAAATGTTTATATAAGTTATGATAATCATTAACTTTAAATGTT
1 TAAATGTTTATGTAAGTTATGATAATCATTAACTTTAAATGTT
31783980 TAAATGTTTATGTAAGTTATGATAATC-TTAACTTTAAATGTT
1 TAAATGTTTATGTAAGTTATGATAATCATTAACTTTAAATGTT
31784022 TA
1 TA
31784024 TTTAAGTTAT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
42 17 0.40
43 26 0.60
ACGTcount: A:0.38, C:0.05, G:0.10, T:0.47
Consensus pattern (43 bp):
TAAATGTTTATGTAAGTTATGATAATCATTAACTTTAAATGTT
Found at i:31784091 original size:19 final size:19
Alignment explanation
Indices: 31784067--31784162 Score: 68
Period size: 19 Copynumber: 4.9 Consensus size: 19
31784057 ATTATTTATT
31784067 TAATTAATCAAAAATTAAA
1 TAATTAATCAAAAATTAAA
* *
31784086 TAATTATTCATAAAATTATTA
1 TAATTAATCA-AAAATTA-AA
* * ** **
31784107 TGAAAT-ATGATTAATTATT
1 T-AATTAATCAAAAATTAAA
31784126 TAATTAATCAAAAATTAAA
1 TAATTAATCAAAAATTAAA
*
31784145 TAATTATTCATAAAATTA
1 TAATTAATCA-AAAATTA
31784163 TTATGAAATA
Statistics
Matches: 57, Mismatches: 15, Indels: 9
0.70 0.19 0.11
Matches are distributed among these distances:
18 3 0.05
19 28 0.49
20 19 0.33
21 4 0.07
22 3 0.05
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (19 bp):
TAATTAATCAAAAATTAAA
Found at i:31784142 original size:59 final size:59
Alignment explanation
Indices: 31784050--31784355 Score: 504
Period size: 59 Copynumber: 5.2 Consensus size: 59
31784040 CATTAACTTT
*
31784050 AAATATGATTATTTATTTAATTAATCAAAAATTAAATAATTATTCATAAAATTATTATG
1 AAATATGATTATTTATTTAATTAATCAAAAATTAATTAATTATTCATAAAATTATTATG
* *
31784109 AAATATGATTAATTATTTAATTAATCAAAAATTAAATAATTATTCATAAAATTATTATG
1 AAATATGATTATTTATTTAATTAATCAAAAATTAATTAATTATTCATAAAATTATTATG
** * * * * *
31784168 AAATATGATTATTTATTTAATTAATTGAAAACTAATTAATTAATAATAGAATTATTATA
1 AAATATGATTATTTATTTAATTAATCAAAAATTAATTAATTATTCATAAAATTATTATG
31784227 AAATATGATTATTTATTTAATTAATCAAAAATTAATTAATTATTCATAAAATTATTATG
1 AAATATGATTATTTATTTAATTAATCAAAAATTAATTAATTATTCATAAAATTATTATG
* *
31784286 AAATATGATTATTTATTTAATTAATCAAAACTTAATTAATTATTCATAGAATTATTATG
1 AAATATGATTATTTATTTAATTAATCAAAAATTAATTAATTATTCATAAAATTATTATG
31784345 AAATATGATTA
1 AAATATGATTA
31784356 ATAGTTAAAT
Statistics
Matches: 228, Mismatches: 19, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
59 228 1.00
ACGTcount: A:0.48, C:0.03, G:0.04, T:0.44
Consensus pattern (59 bp):
AAATATGATTATTTATTTAATTAATCAAAAATTAATTAATTATTCATAAAATTATTATG
Found at i:31784267 original size:19 final size:20
Alignment explanation
Indices: 31784243--31784280 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
31784233 GATTATTTAT
31784243 TTAATTAATCA-AAAATTAA
1 TTAATTAATCATAAAATTAA
*
31784262 TTAATTATTCATAAAATTA
1 TTAATTAATCATAAAATTA
31784281 TTATGAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.53, C:0.05, G:0.00, T:0.42
Consensus pattern (20 bp):
TTAATTAATCATAAAATTAA
Found at i:31787115 original size:17 final size:18
Alignment explanation
Indices: 31787093--31787135 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
31787083 AATGAGATAA
*
31787093 AAATAAATAA-AATAAAT
1 AAATAAATAAGAAAAAAT
31787110 AAATAAATAAGAAAAAAT
1 AAATAAATAAGAAAAAAT
*
31787128 AAACAAAT
1 AAATAAAT
31787136 GACAAAAATC
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 10 0.43
18 13 0.57
ACGTcount: A:0.77, C:0.02, G:0.02, T:0.19
Consensus pattern (18 bp):
AAATAAATAAGAAAAAAT
Found at i:31787142 original size:18 final size:18
Alignment explanation
Indices: 31787097--31787143 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
31787087 AGATAAAAAT
* *
31787097 AAATAA-AATAAATAAAT
1 AAATAACAAAAAATAAAC
*
31787114 AAATAAGAAAAAATAAAC
1 AAATAACAAAAAATAAAC
*
31787132 AAATGACAAAAA
1 AAATAACAAAAA
31787144 TCAATAAACT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
17 6 0.24
18 19 0.76
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.15
Consensus pattern (18 bp):
AAATAACAAAAAATAAAC
Found at i:31788594 original size:20 final size:20
Alignment explanation
Indices: 31788565--31788604 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
31788555 CAAATAGGGC
*
31788565 TAAATTGAAATTAAAAAAAT
1 TAAATGGAAATTAAAAAAAT
31788585 TAAATGGAAATTAAAAAAAT
1 TAAATGGAAATTAAAAAAAT
31788605 AAAAAAAACT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.65, C:0.00, G:0.07, T:0.28
Consensus pattern (20 bp):
TAAATGGAAATTAAAAAAAT
Found at i:31790314 original size:50 final size:50
Alignment explanation
Indices: 31790170--31790316 Score: 132
Period size: 50 Copynumber: 2.9 Consensus size: 50
31790160 ACTGGAATAT
* * * ** *
31790170 CGGGGAAACAAGATTCGCCATCGTAGCTTTAATCTATTCCACTATACTGC
1 CGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTATTCCATTGCAATGC
** * * * * * ** *
31790220 CAAGGAAATAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGT
1 CGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTATTCCATTGCAATGC
* *
31790270 TGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTGTTCCATTGCAA
1 CGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTATTCCATTGCAA
31790317 CATCAAGGCG
Statistics
Matches: 71, Mismatches: 26, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
50 71 1.00
ACGTcount: A:0.28, C:0.22, G:0.20, T:0.31
Consensus pattern (50 bp):
CGGGGAAACAAGATTCGCCGTCGTAGCTTCAATCTATTCCATTGCAATGC
Found at i:31790435 original size:44 final size:44
Alignment explanation
Indices: 31790389--31791315 Score: 971
Period size: 44 Copynumber: 21.7 Consensus size: 44
31790379 TGCTATTTTC
* * ** *
31790389 AACCTACTCCACTGCTG-CTCAGGGAGATAGGGTTCATGATCTTC
1 AACCTATTCCACTGCTGAC-CAGGGAGATAGGATTCACAATCTTT
* *
31790433 AACCTATTCCACTGCTGACCAGGGAGATAGGA-CCTACAATCTTC
1 AACCTATTCCACTGCTGACCAGGGAGATAGGATTC-ACAATCTTT
* * * * * *
31790477 AATCTATTCCACTGCTGCCCAGAGAGATAGAATTCTCAATCTTC
1 AACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTT
*
31790521 AACCTATTCCAAC-GCTGACCAGAGAGATAGGATTCACAATCTTT
1 AACCTATTCC-ACTGCTGACCAGGGAGATAGGATTCACAATCTTT
* *
31790565 AACCTATTCCACTGCTGTCCAGAGAGATAGGATTCACAATCTTT
1 AACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTT
* * *
31790609 AACCTATTCCA-TGCTGACTAGCGAGATAGG----GC--TCTTT
1 AACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTT
* * * * *
31790646 AATCTATTCCACTGCT-CCCTAGGGAGATAGAATTCTCAATCTTC
1 AACCTATTCCACTGCTGACC-AGGGAGATAGGATTCACAATCTTT
* * *
31790690 AACTTATCCCACTGCTGACCAGGGAGATAGAATTCACAATCTTT
1 AACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTT
* * *
31790734 AACCTATTCCACTACTGTCCAAGGAGATAGGATTCACAATCTTT
1 AACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTT
* *
31790778 AACCTATTCCACTACTGACCAGGGAGATAGG----GC--TCTTT
1 AACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTT
* * ** * *
31790816 AATCTATTCCACTGCT-TCCTAGGGAGATAAAATTCTCAATCTTC
1 AACCTATTCCACTGCTGACC-AGGGAGATAGGATTCACAATCTTT
*
31790860 AACCTATTCCACTGCTGACCAGGGAAATAGGATTCACAATCTTT
1 AACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTT
*
31790904 AACCTATTCCACTGCTGTCCAGGGAGATAGGATTCACAATCTTT
1 AACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTT
* * * *
31790948 AACGTATTCCACTACTGACCAGGGAGATAGG----GC--TTTTT
1 AACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTT
* * * *
31790986 AATCTATTCCACTGCTGACCAAGGAGATAGGATTCTCAATCTTC
1 AACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTT
*
31791030 AACCTATTCCACTACTGACCAGGGAGATAGGATTCACAATCTTT
1 AACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTT
* * *
31791074 AACTTATTCCACTACTGACCAGGGAGATAGG----GC--TCTTT
1 AACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTT
* * * * ** *
31791112 AATCTATTCCACTACTGCCCAGGGAGATAGAATTCTTAATCTTC
1 AACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTT
* *
31791156 AACCTATTCCACTACTGACCATGGAGATAGGATTCACAATCTTT
1 AACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTT
* * * * *
31791200 AACCTATTCCTCTACTGTCCAAGGAGATAAGATTCACAATCTTT
1 AACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTT
* * *
31791244 AACCTATTCCACT-TTGTCCAGGGAGATAGGATTCACAATCTCT
1 AACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTT
31791287 AACCTATTCCACTGCTGACCAGGGAGATA
1 AACCTATTCCACTGCTGACCAGGGAGATA
31791316 TGGCTGGGGT
Statistics
Matches: 745, Mismatches: 103, Indels: 70
0.81 0.11 0.08
Matches are distributed among these distances:
37 18 0.02
38 104 0.14
39 1 0.00
40 3 0.00
42 3 0.00
43 58 0.08
44 550 0.74
45 8 0.01
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (44 bp):
AACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTT
Found at i:31790654 original size:37 final size:38
Alignment explanation
Indices: 31790604--31790675 Score: 101
Period size: 37 Copynumber: 1.9 Consensus size: 38
31790594 GGATTCACAA
*
31790604 TCTTTAACCTATTCCA-TGCTGACTAGCGAGATAGGGC
1 TCTTTAACCTATTCCACTGCTCACTAGCGAGATAGGGC
* * *
31790641 TCTTTAATCTATTCCACTGCTCCCTAGGGAGATAG
1 TCTTTAACCTATTCCACTGCTCACTAGCGAGATAG
31790676 AATTCTCAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
37 15 0.50
38 15 0.50
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (38 bp):
TCTTTAACCTATTCCACTGCTCACTAGCGAGATAGGGC
Found at i:31790850 original size:126 final size:126
Alignment explanation
Indices: 31790427--31791315 Score: 672
Period size: 126 Copynumber: 7.0 Consensus size: 126
31790417 AGGGTTCATG
* * * * * * *
31790427 ATCTTCAACCTATTCCACTGCTGACCAGGGAGATAGGA-CCTACAATCTTCAATCTATTCCACTG
1 ATCTTTAACGTATTCCACTACTGACCAGGGAGATA--ATTC-ACAATCTTTAACCTATTCCACTA
* * * * * * *
31790491 CTGCCCAGAGAGATAGAATTCTCAATCTTCAACCTATTCCAAC-GCTGACCAGAGAGATAGGATT
63 CTGACCAGGGAGATAGGATTCACAATCTTTAACCTATTCC-ACTACTGACCAGGGAGATAGG--T
31790555 CAC
125 -AC
* * * * *
31790558 AATCTTTAACCTATTCCACTGCTGTCCAGAGAGATAGGATTCACAATCTTTAACCTATTCCA-TG
1 -ATCTTTAACGTATTCCACTACTGACCAGGGAGATA--ATTCACAATCTTTAACCTATTCCACTA
* * * * * * *
31790622 CTGACTAGCGAGATAGG----GC--TCTTTAATCTATTCCACTGCT-CCCTAGGGAGATAGAATT
63 CTGACCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTACTGACC-AGGGAGATAG--GT
*
31790680 CTC
125 -AC
* * * *
31790683 AATCTTCAACTTATCCCACTGCTGACCAGGGAGATAGAATTCACAATCTTTAACCTATTCCACTA
1 -ATCTTTAACGTATTCCACTACTGACCAGGGAGAT--AATTCACAATCTTTAACCTATTCCACTA
* * *
31790748 CTGTCCAAGGAGATAGGATTCACAATCTTTAACCTATTCCACTACTGACCAGGGAGATAGG-GC
63 CTGACCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTACTGACCAGGGAGATAGGTAC
* * * *
31790811 -TCTTTAATC-TATTCCACTGCT-TCCTAGGGAGATAAAATTCTCAATCTTCAACCTATTCCACT
1 ATCTTTAA-CGTATTCCACTACTGACC-AGGGAGAT--AATTCACAATCTTTAACCTATTCCACT
* * * *
31790873 GCTGACCAGGGAAATAGGATTCACAATCTTTAACCTATTCCACTGCTGTCCAGGGAGATAGGATT
62 ACTGACCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTACTGACCAGGGAGATAGG--T
31790938 CAC
125 -AC
*** * * *
31790941 AATCTTTAACGTATTCCACTACTGACCAGGGAGAT-A-GGGC--TTTTTAATCTATTCCACTGCT
1 -ATCTTTAACGTATTCCACTACTGACCAGGGAGATAATTCACAATCTTTAACCTATTCCACTACT
* * *
31791002 GACCAAGGAGATAGGATTCTCAATCTTCAACCTATTCCACTACTGACCAGGGAGATAGGATTCAC
65 GACCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTACTGACCAGGGAGATAGG--T-AC
* *** *
31791067 AATCTTTAACTTATTCCACTACTGACCAGGGAGAT-A-GGGC--TCTTTAATCTATTCCACTACT
1 -ATCTTTAACGTATTCCACTACTGACCAGGGAGATAATTCACAATCTTTAACCTATTCCACTACT
* * ** * *
31791128 GCCCAGGGAGATAGAATTCTTAATCTTCAACCTATTCCACTACTGACCATGGAGATAGGATTCAC
65 GACCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTACTGACCAGGGAGATAGG--T-AC
* * * *
31791193 AATCTTTAACCTATTCCTCTACTGTCCAAGGAGATAAGATTCACAATCTTTAACCTATTCCACT-
1 -ATCTTTAACGTATTCCACTACTGACCAGGGAGAT-A-ATTCACAATCTTTAACCTATTCCACTA
* * * *
31791257 TTGTCCAGGGAGATAGGATTCACAATCTCTAACCTATTCCACTGCTGACCAGGGAGATA
63 CTGACCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTACTGACCAGGGAGATA
31791316 TGGCTGGGGT
Statistics
Matches: 641, Mismatches: 85, Indels: 63
0.81 0.11 0.08
Matches are distributed among these distances:
124 4 0.01
125 84 0.13
126 347 0.54
127 3 0.00
128 2 0.00
129 2 0.00
130 3 0.00
131 66 0.10
132 125 0.20
133 5 0.01
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.29
Consensus pattern (126 bp):
ATCTTTAACGTATTCCACTACTGACCAGGGAGATAATTCACAATCTTTAACCTATTCCACTACTG
ACCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTACTGACCAGGGAGATAGGTAC
Found at i:31790880 original size:170 final size:169
Alignment explanation
Indices: 31790389--31791320 Score: 1155
Period size: 170 Copynumber: 5.5 Consensus size: 169
31790379 TGCTATTTTC
* * ** * *
31790389 AACCTACTCCACTGCTG-CTCAGGGAGATAGGGTTCATGATCTTCAACCTATTCCACTGCTGACC
1 AACCTATTCCACTGCTGTC-CAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTACTGACC
* * *
31790453 AGGGAGATAGGACCTACAATCTTCAATCTATTCCACTGCTGCCCAGAGAGATAGAATTCTCAATC
65 AGGGAGATAGG-GCT-C--T-TT-AATCTATTCCACTGCT-ACCAGGGAGATAGAATTCTCAATC
*
31790518 TTCAACCTATTCCAAC-GCTGACCAGAGAGATAGGATTCACAATCTTT
123 TTCAACCTATTCC-ACTGCTGACCAGGGAGATAGGATTCACAATCTTT
* * *
31790565 AACCTATTCCACTGCTGTCCAGAGAGATAGGATTCACAATCTTTAACCTATTCCA-TGCTGACTA
1 AACCTATTCCACTGCTGTCCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTACTGACCA
* * *
31790629 GCGAGATAGGGCTCTTTAATCTATTCCACTGCTCCCTAGGGAGATAGAATTCTCAATCTTCAACT
66 GGGAGATAGGGCTCTTTAATCTATTCCACTGCTACC-AGGGAGATAGAATTCTCAATCTTCAACC
* *
31790694 TATCCCACTGCTGACCAGGGAGATAGAATTCACAATCTTT
130 TATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTT
* *
31790734 AACCTATTCCACTACTGTCCAAGGAGATAGGATTCACAATCTTTAACCTATTCCACTACTGACCA
1 AACCTATTCCACTGCTGTCCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTACTGACCA
* *
31790799 GGGAGATAGGGCTCTTTAATCTATTCCACTGCTTCCTAGGGAGATAAAATTCTCAATCTTCAACC
66 GGGAGATAGGGCTCTTTAATCTATTCCACTGCTACC-AGGGAGATAGAATTCTCAATCTTCAACC
*
31790864 TATTCCACTGCTGACCAGGGAAATAGGATTCACAATCTTT
130 TATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTT
*
31790904 AACCTATTCCACTGCTGTCCAGGGAGATAGGATTCACAATCTTTAACGTATTCCACTACTGACCA
1 AACCTATTCCACTGCTGTCCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTACTGACCA
* * *
31790969 GGGAGATAGGGCTTTTTAATCTATTCCACTGCTGACCAAGGAGATAGGATTCTCAATCTTCAACC
66 GGGAGATAGGGCTCTTTAATCTATTCCACTGCT-ACCAGGGAGATAGAATTCTCAATCTTCAACC
*
31791034 TATTCCACTACTGACCAGGGAGATAGGATTCACAATCTTT
130 TATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTT
* * * * * *
31791074 AACTTATTCCACTACTGACCAGGGAGATAGG----GC--TCTTTAATCTATTCCACTACTGCCCA
1 AACCTATTCCACTGCTGTCCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTACTGACCA
** * * * * * *
31791133 GGGAGATAGAATTCTTAATCTTCAACCTATTCCACTACTGACCATGGAGATAGGATTCACAATCT
66 GGGAGATAG--GGC----TCTTTAATCTATTCCACTGCT-ACCAGGGAGATAGAATTCTCAATCT
* * * * * *
31791198 TTAACCTATTCCTCTACTGTCCAAGGAGATAAGATTCACAATCTTT
124 TCAACCTATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTT
* * *
31791244 AACCTATTCCACT-TTGTCCAGGGAGATAGGATTCACAATCTCTAACCTATTCCACTGCTGACCA
1 AACCTATTCCACTGCTGTCCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTACTGACCA
*
31791308 GGGAGATATGGCT
66 GGGAGATAGGGCT
31791321 GGGGTCATTA
Statistics
Matches: 672, Mismatches: 67, Indels: 41
0.86 0.09 0.05
Matches are distributed among these distances:
164 32 0.05
166 2 0.00
168 5 0.01
169 144 0.21
170 386 0.57
171 3 0.00
173 3 0.00
174 2 0.00
175 47 0.07
176 47 0.07
177 1 0.00
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.29
Consensus pattern (169 bp):
AACCTATTCCACTGCTGTCCAGGGAGATAGGATTCACAATCTTTAACCTATTCCACTACTGACCA
GGGAGATAGGGCTCTTTAATCTATTCCACTGCTACCAGGGAGATAGAATTCTCAATCTTCAACCT
ATTCCACTGCTGACCAGGGAGATAGGATTCACAATCTTT
Found at i:31791491 original size:79 final size:78
Alignment explanation
Indices: 31791360--31791607 Score: 280
Period size: 79 Copynumber: 3.0 Consensus size: 78
31791350 TAGGAAGGCA
* * *
31791360 AGATCTTCTATTTTTAGCCTGCTCCGCTGCAACCCAGGGAGGCAAGGCTGGTGTATTCGATCTGC
1 AGATCTGCTATTTTTAGCCTGCTCCGCTGCAA-CCATGGAGGCAAGGCTGGTGTCTTCGATCTGC
31791425 TTCGCTGTCGGTGC
65 TTCGCTGTCGGTGC
* * * *
31791439 AGATCTGCTATTTTTAGCCTGCTTCGCTGCAACCAATGGAGACAAGGTTGGTGTCTTCGATTTGC
1 AGATCTGCTATTTTTAGCCTGCTCCGCTGCAACC-ATGGAGGCAAGGCTGGTGTCTTCGATCTGC
* *
31791504 TTCGTTGTCGATGCAGGAAGGC
65 TTCG--CT-G-T-C-GG--TGC
* *
31791526 AAGATCTGATATTTTTAGCCTGCTCCGCTACAATCCATGGAGGCAAGGCTGGTGTCTTCGATCTG
1 -AGATCTGCTATTTTTAGCCTGCTCCGCTGCAA-CCATGGAGGCAAGGCTGGTGTCTTCGATCTG
*
31791591 CTTCACTGTCGGTGC
64 CTTCGCTGTCGGTGC
31791606 AG
1 AG
31791608 GAAGGCAAGA
Statistics
Matches: 140, Mismatches: 18, Indels: 22
0.78 0.10 0.12
Matches are distributed among these distances:
78 2 0.01
79 61 0.44
80 2 0.01
81 1 0.01
82 3 0.02
83 2 0.01
84 2 0.01
85 3 0.02
86 1 0.01
87 2 0.01
88 59 0.42
89 2 0.01
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (78 bp):
AGATCTGCTATTTTTAGCCTGCTCCGCTGCAACCATGGAGGCAAGGCTGGTGTCTTCGATCTGCT
TCGCTGTCGGTGC
Found at i:31791593 original size:88 final size:88
Alignment explanation
Indices: 31791439--31791621 Score: 269
Period size: 88 Copynumber: 2.1 Consensus size: 88
31791429 CTGTCGGTGC
* * * * *
31791439 AGATCTGCTATTTTTAGCCTGCTTCGCTGCAACCAATGGAGACAAGGTTGGTGTCTTCGATTTGC
1 AGATCTGATATTTTTAGCCTGCTCCGCTACAACCAATGGAGACAAGGCTGGTGTCTTCGATCTGC
**
31791504 TTCGTTGTCGATGCAGGAAGGCA
66 TTCACTGTCGATGCAGGAAGGCA
*
31791527 AGATCTGATATTTTTAGCCTGCTCCGCTACAATCC-ATGGAGGCAAGGCTGGTGTCTTCGATCTG
1 AGATCTGATATTTTTAGCCTGCTCCGCTACAA-CCAATGGAGACAAGGCTGGTGTCTTCGATCTG
*
31791591 CTTCACTGTCGGTGCAGGAAGGCA
65 CTTCACTGTCGATGCAGGAAGGCA
31791615 AGATCTG
1 AGATCTG
31791622 CTCTCTGGGG
Statistics
Matches: 85, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
88 83 0.98
89 2 0.02
ACGTcount: A:0.21, C:0.22, G:0.27, T:0.30
Consensus pattern (88 bp):
AGATCTGATATTTTTAGCCTGCTCCGCTACAACCAATGGAGACAAGGCTGGTGTCTTCGATCTGC
TTCACTGTCGATGCAGGAAGGCA
Found at i:31798579 original size:17 final size:19
Alignment explanation
Indices: 31798559--31798622 Score: 69
Period size: 21 Copynumber: 3.4 Consensus size: 19
31798549 GATTACAAAA
31798559 TCATATC-T-TCCAAGATT
1 TCATATCATATCCAAGATT
31798576 TCATATCATATCCAAGATT
1 TCATATCATATCCAAGATT
* *
31798595 GCATATATCATATCTAAGATT
1 TC--ATATCATATCCAAGATT
*
31798616 GCATATC
1 TCATATC
31798623 CTTGAAGATT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
17 7 0.17
18 1 0.02
19 15 0.37
21 18 0.44
ACGTcount: A:0.34, C:0.20, G:0.08, T:0.38
Consensus pattern (19 bp):
TCATATCATATCCAAGATT
Found at i:31798591 original size:19 final size:19
Alignment explanation
Indices: 31798567--31798622 Score: 76
Period size: 21 Copynumber: 2.8 Consensus size: 19
31798557 AATCATATCT
*
31798567 TCCAAGATTTCATATCATA
1 TCCAAGATTGCATATCATA
31798586 TCCAAGATTGCATATATCATA
1 TCCAAGATTGC--ATATCATA
*
31798607 TCTAAGATTGCATATC
1 TCCAAGATTGCATATC
31798623 CTTGAAGATT
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
19 15 0.45
21 18 0.55
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.36
Consensus pattern (19 bp):
TCCAAGATTGCATATCATA
Found at i:31798604 original size:21 final size:21
Alignment explanation
Indices: 31798578--31798621 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
31798568 CCAAGATTTC
31798578 ATATCATATCCAAGATTGCAT
1 ATATCATATCCAAGATTGCAT
*
31798599 ATATCATATCTAAGATTGCAT
1 ATATCATATCCAAGATTGCAT
31798620 AT
1 AT
31798622 CCTTGAAGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.39, C:0.16, G:0.09, T:0.36
Consensus pattern (21 bp):
ATATCATATCCAAGATTGCAT
Found at i:31804012 original size:48 final size:48
Alignment explanation
Indices: 31803941--31804038 Score: 196
Period size: 48 Copynumber: 2.0 Consensus size: 48
31803931 TTTTAAGTCA
31803941 TCCAATTAGTTAATTATCATTATTACATGTAAATCATTCGTTAATCGG
1 TCCAATTAGTTAATTATCATTATTACATGTAAATCATTCGTTAATCGG
31803989 TCCAATTAGTTAATTATCATTATTACATGTAAATCATTCGTTAATCGG
1 TCCAATTAGTTAATTATCATTATTACATGTAAATCATTCGTTAATCGG
31804037 TC
1 TC
31804039 TTACATACAA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
48 50 1.00
ACGTcount: A:0.33, C:0.15, G:0.10, T:0.42
Consensus pattern (48 bp):
TCCAATTAGTTAATTATCATTATTACATGTAAATCATTCGTTAATCGG
Found at i:31807580 original size:41 final size:41
Alignment explanation
Indices: 31807512--31807614 Score: 154
Period size: 41 Copynumber: 2.5 Consensus size: 41
31807502 CTTAGTGGAT
* *
31807512 TCAGCACTTAGCAACAACC-TTAAATTCAGTGATACAGGGAA
1 TCAGCACATAGCAAC-CCCTTTAAATTCAGTGATACAGGGAA
* *
31807553 TCAGCACATAGCAACCCCTTTATATTCAGTGATACGGGGAA
1 TCAGCACATAGCAACCCCTTTAAATTCAGTGATACAGGGAA
31807594 TCAGCACATAGCAACCCCTTT
1 TCAGCACATAGCAACCCCTTT
31807615 CATAATCAAA
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
40 2 0.04
41 55 0.96
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (41 bp):
TCAGCACATAGCAACCCCTTTAAATTCAGTGATACAGGGAA
Found at i:31808816 original size:11 final size:11
Alignment explanation
Indices: 31808788--31808828 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
31808778 GCCCAAATGT
31808788 CGAAATTTTTGAA
1 CGAAATTTTT--A
31808801 CGAAATTTTTA
1 CGAAATTTTTA
*
31808812 CGAAATCTTTA
1 CGAAATTTTTA
31808823 CGAAAT
1 CGAAAT
31808829 AATTTTGTGA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
11 17 0.63
13 10 0.37
ACGTcount: A:0.39, C:0.12, G:0.12, T:0.37
Consensus pattern (11 bp):
CGAAATTTTTA
Found at i:31811567 original size:20 final size:19
Alignment explanation
Indices: 31811542--31811581 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
31811532 CATCTTTAAA
*
31811542 ATCAAATTAAAATGATTTTT
1 ATCAAA-TAAAATAATTTTT
*
31811562 ATCAAATCAAATAATTTTT
1 ATCAAATAAAATAATTTTT
31811581 A
1 A
31811582 AACTAGTCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.47, C:0.07, G:0.03, T:0.42
Consensus pattern (19 bp):
ATCAAATAAAATAATTTTT
Found at i:31811799 original size:103 final size:103
Alignment explanation
Indices: 31811609--31811826 Score: 233
Period size: 103 Copynumber: 2.1 Consensus size: 103
31811599 CCAGGCCAAA
* * * *
31811609 AAGTATCGATACCTTTTTGGCCAATTATTGATATTTTATGAATTATCGATACCCTTATGAAAAGC
1 AAGTATCGATACCTTTTCGGCCAAGTATTGATATTTTATGAAATATCGATACCCTTATGAAAAAC
* *
31811674 AATACCAAAACGACATTATATTTTTCACAAACCCTATT
66 AATACCAAAAAGACATTATATTTCTCACAAACCCTATT
* * * * *
31811712 AAGTATTGATACC-TTTCGGTCAAGTATTGATATTTTTTGAAATATCGATACCCCTTCTTAAAAA
1 AAGTATCGATACCTTTTCGGCCAAGTATTGATATTTTATGAAATATCGATA-CCCTTATGAAAAA
** * * * * **
31811776 TGATACTAAAATAG-CATTCTATTTCTCACAAAACTTACA
65 CAATACCAAAA-AGACATTATATTTCTCACAAACCCTATT
31811815 AAGTATCGATAC
1 AAGTATCGATAC
31811827 AGTATCAATA
Statistics
Matches: 93, Mismatches: 20, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
102 32 0.34
103 60 0.65
104 1 0.01
ACGTcount: A:0.36, C:0.18, G:0.10, T:0.36
Consensus pattern (103 bp):
AAGTATCGATACCTTTTCGGCCAAGTATTGATATTTTATGAAATATCGATACCCTTATGAAAAAC
AATACCAAAAAGACATTATATTTCTCACAAACCCTATT
Found at i:31812843 original size:17 final size:17
Alignment explanation
Indices: 31812794--31812847 Score: 58
Period size: 17 Copynumber: 3.2 Consensus size: 17
31812784 TGTCCTTAAG
31812794 CAAACT-AAAC-GAAAA
1 CAAACTAAAACTGAAAA
*
31812809 CAAAATAAAAACCTGAAAA
1 CAAACT-AAAA-CTGAAAA
*
31812828 TAAACTAAAACTGAAAA
1 CAAACTAAAACTGAAAA
31812845 CAA
1 CAA
31812848 GAAATAAACA
Statistics
Matches: 31, Mismatches: 4, Indels: 6
0.76 0.10 0.15
Matches are distributed among these distances:
15 5 0.16
17 12 0.39
18 5 0.16
19 9 0.29
ACGTcount: A:0.67, C:0.17, G:0.06, T:0.11
Consensus pattern (17 bp):
CAAACTAAAACTGAAAA
Found at i:31813599 original size:12 final size:11
Alignment explanation
Indices: 31813582--31813615 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
31813572 ATCATGAATG
31813582 CTTTTCATTTC
1 CTTTTCATTTC
*
31813593 TCTTTTCCTTTC
1 -CTTTTCATTTC
31813605 CTTTTCATTTC
1 CTTTTCATTTC
31813616 ATTAATTTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.06, C:0.29, G:0.00, T:0.65
Consensus pattern (11 bp):
CTTTTCATTTC
Found at i:31823255 original size:32 final size:31
Alignment explanation
Indices: 31823210--31823269 Score: 75
Period size: 32 Copynumber: 1.9 Consensus size: 31
31823200 TTTCTAAAGG
* * *
31823210 TATGTTATATATATGTATGTGTATGTGTTTT
1 TATGGTATATATATCTATGTCTATGTGTTTT
*
31823241 TATGGTATAATATATCTATTTCTATGTGT
1 TATGGTAT-ATATATCTATGTCTATGTGT
31823270 GTGGGACAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
31 7 0.29
32 17 0.71
ACGTcount: A:0.25, C:0.03, G:0.17, T:0.55
Consensus pattern (31 bp):
TATGGTATATATATCTATGTCTATGTGTTTT
Found at i:31828044 original size:27 final size:26
Alignment explanation
Indices: 31827810--31828042 Score: 322
Period size: 27 Copynumber: 8.7 Consensus size: 26
31827800 GTAATGGGCC
31827810 TAAAATGACCGAAATACCCTCGAAGGG
1 TAAAATGACCGAAATACCC-CGAAGGG
*
31827837 TAAAATGACCGAAATACCCCCGAATGG
1 TAAAATGACCGAAATA-CCCCGAAGGG
*
31827864 TAAAATGACCGAAATACCCCGAGGGG
1 TAAAATGACCGAAATACCCCGAAGGG
*
31827890 TAAAATGGCCGAAATACCCCTGAAGGG
1 TAAAATGACCGAAATACCCC-GAAGGG
* *
31827917 TAAAATGACCAAAATACCCCAGAAGAG
1 TAAAATGACCGAAATACCCC-GAAGGG
*
31827944 TAAAATGACCGAAACACCCCTGAAGGG
1 TAAAATGACCGAAATACCCC-GAAGGG
*
31827971 TAAAATGACCAAAATACCCCCGAAGGG
1 TAAAATGACCGAAATA-CCCCGAAGGG
*
31827998 TAAAATGACTGAAATACCTCCGAAGGG
1 TAAAATGACCGAAATACC-CCGAAGGG
*
31828025 TAAAATGACTGAAATACC
1 TAAAATGACCGAAATACC
31828043 TCTAGGAGTT
Statistics
Matches: 185, Mismatches: 17, Indels: 8
0.88 0.08 0.04
Matches are distributed among these distances:
26 29 0.16
27 149 0.81
28 7 0.04
ACGTcount: A:0.42, C:0.23, G:0.21, T:0.14
Consensus pattern (26 bp):
TAAAATGACCGAAATACCCCGAAGGG
Found at i:31830012 original size:16 final size:16
Alignment explanation
Indices: 31829988--31830022 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
31829978 TTTTTTATCA
31829988 AAAACAAAATATTTTC
1 AAAACAAAATATTTTC
*
31830004 AAAATAAAATATTTTC
1 AAAACAAAATATTTTC
31830020 AAA
1 AAA
31830023 CTAATAACAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.60, C:0.09, G:0.00, T:0.31
Consensus pattern (16 bp):
AAAACAAAATATTTTC
Found at i:31845089 original size:15 final size:15
Alignment explanation
Indices: 31845069--31845112 Score: 88
Period size: 15 Copynumber: 2.9 Consensus size: 15
31845059 TCAATCAAAT
31845069 CATACTTATAGTGAC
1 CATACTTATAGTGAC
31845084 CATACTTATAGTGAC
1 CATACTTATAGTGAC
31845099 CATACTTATAGTGA
1 CATACTTATAGTGA
31845113 ACATCTAACT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.34, C:0.18, G:0.14, T:0.34
Consensus pattern (15 bp):
CATACTTATAGTGAC
Found at i:31848877 original size:50 final size:50
Alignment explanation
Indices: 31848825--31849109 Score: 363
Period size: 50 Copynumber: 5.7 Consensus size: 50
31848815 TACTGCCTAT
* * * * ** * * * *
31848825 GCCATATCCTAGATATGGTCTTACATGAGAGTTCTCATATAGGTGCCTAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
* ** * * *
31848875 GCCATGTCCCAGACACGGTCTTACGGGGGACCTCTCATCTTGGCGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
* * *
31848925 GCCATGTCCCAAACATGGTCTTACATGGGACATGTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
*
31848975 ACCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
*
31849025 GTCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
* *
31849075 GCCATGTCCCAGATATGGTCTTACATGGGATCTCT
1 GCCATGTCCCAGACATGGTCTTACATGGGACCTCT
31849110 TTACCCAAAT
Statistics
Matches: 204, Mismatches: 31, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 204 1.00
ACGTcount: A:0.22, C:0.29, G:0.22, T:0.27
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCAAC
Found at i:31854988 original size:20 final size:20
Alignment explanation
Indices: 31854965--31855017 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
31854955 ACCCTTTCAA
*
31854965 ATTTTCTTA-TTTTCATTTGC
1 ATTTTCTTACTTTCCA-TTGC
31854985 A-TTTCATTACTTTCCATTGC
1 ATTTTC-TTACTTTCCATTGC
*
31855005 ATTTTCTTTCTTT
1 ATTTTCTTACTTT
31855018 AGCTTAAATA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
19 4 0.14
20 15 0.54
21 9 0.32
ACGTcount: A:0.15, C:0.19, G:0.04, T:0.62
Consensus pattern (20 bp):
ATTTTCTTACTTTCCATTGC
Found at i:31855685 original size:25 final size:26
Alignment explanation
Indices: 31855657--31855777 Score: 93
Period size: 25 Copynumber: 4.7 Consensus size: 26
31855647 TGTACATATA
*
31855657 TGCTCACACGAGCTATGAATATGCG-
1 TGCTCACACGAGCTATGAAAATGCGC
* * * *
31855682 TGCTTACATGAGCTGTGAAAATGGGTC
1 TGCTCACACGAGCTATGAAAATGCG-C
* * *
31855709 TACTCACACGAGATATGAATATGCG-
1 TGCTCACACGAGCTATGAAAATGCGC
** * *
31855734 TGCTCACATAAGCTGTGAAAATGGGTC
1 TGCTCACACGAGCTATGAAAATGCG-C
*
31855761 TGCTCAGACGAGCTATG
1 TGCTCACACGAGCTATG
31855778 GGTCAGAATG
Statistics
Matches: 69, Mismatches: 23, Indels: 6
0.70 0.23 0.06
Matches are distributed among these distances:
25 38 0.55
27 31 0.45
ACGTcount: A:0.29, C:0.20, G:0.26, T:0.26
Consensus pattern (26 bp):
TGCTCACACGAGCTATGAAAATGCGC
Found at i:31855737 original size:52 final size:52
Alignment explanation
Indices: 31855659--31855777 Score: 193
Period size: 52 Copynumber: 2.3 Consensus size: 52
31855649 TACATATATG
* *
31855659 CTCACACGAGCTATGAATATGCGTGCTTACATGAGCTGTGAAAATGGGTCTA
1 CTCACACGAGCTATGAATATGCGTGCTCACATAAGCTGTGAAAATGGGTCTA
* *
31855711 CTCACACGAGATATGAATATGCGTGCTCACATAAGCTGTGAAAATGGGTCTG
1 CTCACACGAGCTATGAATATGCGTGCTCACATAAGCTGTGAAAATGGGTCTA
*
31855763 CTCAGACGAGCTATG
1 CTCACACGAGCTATG
31855778 GGTCAGAATG
Statistics
Matches: 61, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
52 61 1.00
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.25
Consensus pattern (52 bp):
CTCACACGAGCTATGAATATGCGTGCTCACATAAGCTGTGAAAATGGGTCTA
Found at i:31860068 original size:31 final size:31
Alignment explanation
Indices: 31860033--31860108 Score: 143
Period size: 31 Copynumber: 2.5 Consensus size: 31
31860023 AAATTTTGTT
*
31860033 ATTTTAATCACTCTTATTAGATAAGTTGTCA
1 ATTTTAGTCACTCTTATTAGATAAGTTGTCA
31860064 ATTTTAGTCACTCTTATTAGATAAGTTGTCA
1 ATTTTAGTCACTCTTATTAGATAAGTTGTCA
31860095 ATTTTAGTCACTCT
1 ATTTTAGTCACTCT
31860109 AAGTCACTTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
31 44 1.00
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.46
Consensus pattern (31 bp):
ATTTTAGTCACTCTTATTAGATAAGTTGTCA
Found at i:31868934 original size:16 final size:17
Alignment explanation
Indices: 31868907--31868938 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
31868897 ATAATGATAT
31868907 AAATTAATATATTAGTG
1 AAATTAATATATTAGTG
31868924 AAATT-ATATATTAGT
1 AAATTAATATATTAGT
31868939 TTTTATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 10 0.67
17 5 0.33
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (17 bp):
AAATTAATATATTAGTG
Found at i:31869622 original size:15 final size:15
Alignment explanation
Indices: 31869602--31869632 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31869592 TATATTTATG
*
31869602 TATGAAATTATAATA
1 TATGAAATTAAAATA
31869617 TATGAAATTAAAATA
1 TATGAAATTAAAATA
31869632 T
1 T
31869633 CAAAAAATTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (15 bp):
TATGAAATTAAAATA
Found at i:31882065 original size:26 final size:26
Alignment explanation
Indices: 31882036--31882085 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
31882026 GATACAAACG
31882036 TATACCTATAAAATAAATCTATATTC
1 TATACCTATAAAATAAATCTATATTC
** *
31882062 TATATGTTTAAAATAAATCTATAT
1 TATACCTATAAAATAAATCTATAT
31882086 GTTATCCCCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.42
Consensus pattern (26 bp):
TATACCTATAAAATAAATCTATATTC
Found at i:31883380 original size:78 final size:78
Alignment explanation
Indices: 31883230--31883413 Score: 230
Period size: 78 Copynumber: 2.4 Consensus size: 78
31883220 AATTCAACTA
*
31883230 AACAATTCTGTTTCAGGATTTTATTCCTGCAATTTAACAGGATTTGTTCGATTTTTGTTTCAAAC
1 AACAATTCTGTTTCAGGATTTTATTCCTGCAATTTAACAGGATTTGTTCAATTTTTGTTTCAAAC
*
31883295 AAAAAATCTATTG
66 AAAAAATCGATTG
* ** *
31883308 AACAATTCTGTTTTAGGATTTTATTTTTGTC-ATTTAATAGGATTTGTTCAATTTCTTGTTTCAA
1 AACAATTCTGTTTCAGGATTTTATTCCTG-CAATTTAACAGGATTTGTTCAATTT-TTGTTTCAA
* *
31883372 A-TAGAAATCGATTG
64 ACAAAAAATCGATTG
* *
31883386 AACAATTATGTTTCAAGATTCTT-TTCCT
1 AACAATTCTGTTTCAGGATT-TTATTCCT
31883414 ATCATTCAGC
Statistics
Matches: 90, Mismatches: 13, Indels: 6
0.83 0.12 0.06
Matches are distributed among these distances:
78 77 0.86
79 13 0.14
ACGTcount: A:0.29, C:0.12, G:0.12, T:0.46
Consensus pattern (78 bp):
AACAATTCTGTTTCAGGATTTTATTCCTGCAATTTAACAGGATTTGTTCAATTTTTGTTTCAAAC
AAAAAATCGATTG
Found at i:31886152 original size:20 final size:21
Alignment explanation
Indices: 31886113--31886153 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
31886103 ATTCGAAATT
31886113 AAATCAAAACAAAATAGAAAA
1 AAATCAAAACAAAATAGAAAA
* *
31886134 AAATTAAAA-AAAATTGAAAA
1 AAATCAAAACAAAATAGAAAA
31886154 TTTGAAAAGC
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.76, C:0.05, G:0.05, T:0.15
Consensus pattern (21 bp):
AAATCAAAACAAAATAGAAAA
Found at i:31887525 original size:40 final size:40
Alignment explanation
Indices: 31887475--31887665 Score: 213
Period size: 40 Copynumber: 4.8 Consensus size: 40
31887465 AATGGAATCG
* * * *
31887475 AAGTGCAAACAGGGGAAAAAATGTGCATTCAGGGACACCA
1 AAGTACAAACAGGGGCACATATGTGCATTCAGGGACACCA
* * * * *
31887515 AAGTAAAAACAGGGGTAGATATGTGCATTCAGGGGCACCG
1 AAGTACAAACAGGGGCACATATGTGCATTCAGGGACACCA
* **
31887555 AAGTGCAAACAGGGGCACATATGTGCATTCAGGGACACTG
1 AAGTACAAACAGGGGCACATATGTGCATTCAGGGACACCA
* ** * *
31887595 AAGTGCAAACAGGGGCATGTATGTGCGTTCAAGGG-TACCA
1 AAGTACAAACAGGGGCACATATGTGCATTC-AGGGACACCA
31887635 AAGTACAAACAGGGGCACATATGTGCATTCA
1 AAGTACAAACAGGGGCACATATGTGCATTCA
31887666 ATAGTAGTTT
Statistics
Matches: 127, Mismatches: 23, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
39 1 0.01
40 122 0.96
41 4 0.03
ACGTcount: A:0.36, C:0.18, G:0.29, T:0.17
Consensus pattern (40 bp):
AAGTACAAACAGGGGCACATATGTGCATTCAGGGACACCA
Found at i:31887547 original size:20 final size:20
Alignment explanation
Indices: 31887524--31887588 Score: 62
Period size: 20 Copynumber: 3.2 Consensus size: 20
31887514 AAAGTAAAAA
*
31887524 CAGGGGTAGATATGTGCATT
1 CAGGGGCAGATATGTGCATT
**
31887544 CAGGGGCACCGA-A-GTGCAAA
1 CAGGGGCA--GATATGTGCATT
*
31887564 CAGGGGCACATATGTGCATT
1 CAGGGGCAGATATGTGCATT
31887584 CAGGG
1 CAGGG
31887589 ACACTGAAGT
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
18 1 0.03
19 1 0.03
20 30 0.86
21 1 0.03
22 2 0.06
ACGTcount: A:0.28, C:0.18, G:0.35, T:0.18
Consensus pattern (20 bp):
CAGGGGCAGATATGTGCATT
Found at i:31887563 original size:80 final size:80
Alignment explanation
Indices: 31887473--31887665 Score: 253
Period size: 80 Copynumber: 2.4 Consensus size: 80
31887463 TCAATGGAAT
* * * *
31887473 CGAAGTGCAAACAGGGGAAAAAATGTGCATTCAGGGACACCAAAGTAAAAACAGGGGTA-GATAT
1 CGAAGTGCAAACAGGGGCACATATGTGCATTCAGGGACACCAAAGTAAAAACAGGGGCATG-TAT
*
31887537 GTGCATTCAGGGGCAC
65 GTGCATTCAAGGGCAC
** **
31887553 CGAAGTGCAAACAGGGGCACATATGTGCATTCAGGGACACTGAAGTGCAAACAGGGGCATGTATG
1 CGAAGTGCAAACAGGGGCACATATGTGCATTCAGGGACACCAAAGTAAAAACAGGGGCATGTATG
* *
31887618 TGCGTTCAAGGGTAC
66 TGCATTCAAGGGCAC
* *
31887633 CAAAGTACAAACAGGGGCACATATGTGCATTCA
1 CGAAGTGCAAACAGGGGCACATATGTGCATTCA
31887666 ATAGTAGTTT
Statistics
Matches: 99, Mismatches: 13, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
80 98 0.99
81 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.30, T:0.17
Consensus pattern (80 bp):
CGAAGTGCAAACAGGGGCACATATGTGCATTCAGGGACACCAAAGTAAAAACAGGGGCATGTATG
TGCATTCAAGGGCAC
Found at i:31887600 original size:20 final size:20
Alignment explanation
Indices: 31887537--31887611 Score: 71
Period size: 20 Copynumber: 3.8 Consensus size: 20
31887527 GGGTAGATAT
*
31887537 GTGCATTCAGGGGCACCGAA
1 GTGCATTCAGGGGCACTGAA
** *
31887557 GTGCAAACAGGGGCACAT-AT
1 GTGCATTCAGGGGCAC-TGAA
*
31887577 GTGCATTCAGGGACACTGAA
1 GTGCATTCAGGGGCACTGAA
**
31887597 GTGCAAACAGGGGCA
1 GTGCATTCAGGGGCA
31887612 TGTATGTGCG
Statistics
Matches: 42, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
19 1 0.02
20 41 0.98
ACGTcount: A:0.31, C:0.21, G:0.33, T:0.15
Consensus pattern (20 bp):
GTGCATTCAGGGGCACTGAA
Found at i:31887620 original size:20 final size:20
Alignment explanation
Indices: 31887557--31887620 Score: 58
Period size: 20 Copynumber: 3.2 Consensus size: 20
31887547 GGGCACCGAA
**
31887557 GTGCAAACAGGGGCACATAT
1 GTGCAAACAGGGGCATGTAT
** * *
31887577 GTGCATTCAGGGACACTG-AA
1 GTGCAAACAGGGGCA-TGTAT
31887597 GTGCAAACAGGGGCATGTAT
1 GTGCAAACAGGGGCATGTAT
31887617 GTGC
1 GTGC
31887621 GTTCAAGGGT
Statistics
Matches: 32, Mismatches: 10, Indels: 4
0.70 0.22 0.09
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.30, C:0.19, G:0.33, T:0.19
Consensus pattern (20 bp):
GTGCAAACAGGGGCATGTAT
Found at i:31887666 original size:40 final size:40
Alignment explanation
Indices: 31887427--31887666 Score: 209
Period size: 40 Copynumber: 6.0 Consensus size: 40
31887417 TGCATAAAAG
* * *
31887427 GGGCACCAAAGTGCAATCAGGAGCACGA-ATGTGTGA-TCAA
1 GGGCACCAAAGTGCAAACAGGGGCAC-ATATGTG-CATTCAA
* * * * * * *
31887467 TGGAATCGAAGTGCAAACAGGGGAAAAAATGTGCATTC-A
1 GGGCACCAAAGTGCAAACAGGGGCACATATGTGCATTCAA
** * * *
31887506 GGGACACCAAAGTAAAAACAGGGGTAGATATGTGCATTCAG
1 GGG-CACCAAAGTGCAAACAGGGGCACATATGTGCATTCAA
*
31887547 GGGCACCGAAGTGCAAACAGGGGCACATATGTGCATTC-A
1 GGGCACCAAAGTGCAAACAGGGGCACATATGTGCATTCAA
** ** *
31887586 GGGACACTGAAGTGCAAACAGGGGCATGTATGTGCGTTCAA
1 GGG-CACCAAAGTGCAAACAGGGGCACATATGTGCATTCAA
* *
31887627 GGGTACCAAAGTACAAACAGGGGCACATATGTGCATTCAA
1 GGGCACCAAAGTGCAAACAGGGGCACATATGTGCATTCAA
31887667 TAGTAGTTTC
Statistics
Matches: 158, Mismatches: 36, Indels: 12
0.77 0.17 0.06
Matches are distributed among these distances:
39 8 0.05
40 143 0.91
41 7 0.04
ACGTcount: A:0.35, C:0.18, G:0.30, T:0.17
Consensus pattern (40 bp):
GGGCACCAAAGTGCAAACAGGGGCACATATGTGCATTCAA
Found at i:31888052 original size:17 final size:18
Alignment explanation
Indices: 31888014--31888052 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
31888004 AATATAATTT
*
31888014 ATTTCATTTATTAGCTTAA
1 ATTTCATATATTAGC-TAA
31888033 ATTTCATATATTAG-TAA
1 ATTTCATATATTAGCTAA
31888050 ATT
1 ATT
31888053 CTAAAATTTG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 6 0.32
19 13 0.68
ACGTcount: A:0.36, C:0.08, G:0.05, T:0.51
Consensus pattern (18 bp):
ATTTCATATATTAGCTAA
Found at i:31888586 original size:13 final size:13
Alignment explanation
Indices: 31888565--31888598 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
31888555 GAGATAATAG
*
31888565 TTTTGATTTATAT
1 TTTTTATTTATAT
*
31888578 TTTTTATTTATGT
1 TTTTTATTTATAT
31888591 TTTTTATT
1 TTTTTATT
31888599 AATTAAATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.18, C:0.00, G:0.06, T:0.76
Consensus pattern (13 bp):
TTTTTATTTATAT
Found at i:31894103 original size:30 final size:30
Alignment explanation
Indices: 31894069--31894126 Score: 98
Period size: 30 Copynumber: 1.9 Consensus size: 30
31894059 CATACTTATG
*
31894069 TTATGGAGGTGAGTGATTCTTTCAAGTTGT
1 TTATGGAGGTGAGTAATTCTTTCAAGTTGT
*
31894099 TTATGGTGGTGAGTAATTCTTTCAAGTT
1 TTATGGAGGTGAGTAATTCTTTCAAGTT
31894127 AGCCAAAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.21, C:0.07, G:0.28, T:0.45
Consensus pattern (30 bp):
TTATGGAGGTGAGTAATTCTTTCAAGTTGT
Found at i:31906477 original size:20 final size:20
Alignment explanation
Indices: 31906440--31906479 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
31906430 CGAGACTAAA
* *
31906440 TCAGAAATTTAGAGAATTTT
1 TCAGAAACTTAGAAAATTTT
*
31906460 TCAGAAACTTATAAAATTTT
1 TCAGAAACTTAGAAAATTTT
31906480 CAAAACTGCA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.07, G:0.10, T:0.40
Consensus pattern (20 bp):
TCAGAAACTTAGAAAATTTT
Found at i:31907857 original size:25 final size:25
Alignment explanation
Indices: 31907811--31907879 Score: 68
Period size: 25 Copynumber: 2.8 Consensus size: 25
31907801 GCTCTAAACG
* *
31907811 GTAAGCTCC-TCTGCGCTAAATAACA
1 GTAAGCTCCTTC-GAGCTGAATAACA
**
31907836 GTAAGCTCCTTCGAGCTGAATAATG
1 GTAAGCTCCTTCGAGCTGAATAACA
* *
31907861 GTAAGCTCATACGAGCTGA
1 GTAAGCTCCTTCGAGCTGA
31907880 GTATCGGTAA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
25 35 0.95
26 2 0.05
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.25
Consensus pattern (25 bp):
GTAAGCTCCTTCGAGCTGAATAACA
Found at i:31907888 original size:25 final size:25
Alignment explanation
Indices: 31907836--31907896 Score: 70
Period size: 25 Copynumber: 2.4 Consensus size: 25
31907826 CTAAATAACA
* *
31907836 GTAAGCTCCTTCGAGCTGAATAATG
1 GTAAGCTCATACGAGCTGAATAATG
*
31907861 GTAAGCTCATACGAGCTGAGT-ATCG
1 GTAAGCTCATACGAGCTGAATAAT-G
*
31907886 GTAACCTCATA
1 GTAAGCTCATA
31907897 TAAGCTTAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
24 2 0.06
25 29 0.94
ACGTcount: A:0.30, C:0.21, G:0.23, T:0.26
Consensus pattern (25 bp):
GTAAGCTCATACGAGCTGAATAATG
Found at i:31907902 original size:25 final size:24
Alignment explanation
Indices: 31907860--31907915 Score: 58
Period size: 25 Copynumber: 2.3 Consensus size: 24
31907850 GCTGAATAAT
* * *
31907860 GGTAAGCTCATACGAGCTGAGTATC
1 GGTAACCTCATACAAGCTGA-AATC
* *
31907885 GGTAACCTCATATAAGCTTAAATC
1 GGTAACCTCATACAAGCTGAAATC
31907909 GGTAACC
1 GGTAACC
31907916 CTAATGACAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
24 10 0.38
25 16 0.62
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.25
Consensus pattern (24 bp):
GGTAACCTCATACAAGCTGAAATC
Found at i:31915435 original size:25 final size:24
Alignment explanation
Indices: 31915394--31915450 Score: 69
Period size: 25 Copynumber: 2.3 Consensus size: 24
31915384 TCCTATACAT
*
31915394 GTATGCTCATACGAGCTCTAAATCG
1 GTATGCTCATACGAGCTATAAA-CG
* *
31915419 GTATGCTCTTACTAGCTATAAACG
1 GTATGCTCATACGAGCTATAAACG
*
31915443 GTAAGCTC
1 GTATGCTC
31915451 CTTTGAGTTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
24 9 0.32
25 19 0.68
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (24 bp):
GTATGCTCATACGAGCTATAAACG
Found at i:31915509 original size:25 final size:25
Alignment explanation
Indices: 31915459--31915537 Score: 79
Period size: 25 Copynumber: 3.2 Consensus size: 25
31915449 TCCTTTGAGT
* * *
31915459 TGAATAACAGTAAGCTCCTCCTAGC
1 TGAATAACAGTAAGCTCATACAAGC
* *
31915484 TGAATAACAGTAAGCTCATGCGAGC
1 TGAATAACAGTAAGCTCATACAAGC
* *
31915509 TGAGTATC-GATAAGCTCATACAAGC
1 TGAATAACAG-TAAGCTCATACAAGC
31915534 TGAA
1 TGAA
31915538 ATCGGTAACC
Statistics
Matches: 45, Mismatches: 8, Indels: 2
0.82 0.15 0.04
Matches are distributed among these distances:
24 1 0.02
25 44 0.98
ACGTcount: A:0.35, C:0.22, G:0.20, T:0.23
Consensus pattern (25 bp):
TGAATAACAGTAAGCTCATACAAGC
Found at i:31919469 original size:12 final size:12
Alignment explanation
Indices: 31919439--31919487 Score: 73
Period size: 13 Copynumber: 4.0 Consensus size: 12
31919429 AAAAATAAAT
31919439 AAATAAACAAAA
1 AAATAAACAAAA
31919451 GAAATAAACAAAA
1 -AAATAAACAAAA
31919464 AAATAAACAAAAA
1 AAATAAAC-AAAA
31919477 AAATAAA-AAAA
1 AAATAAACAAAA
31919488 CCAATCAGGA
Statistics
Matches: 35, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
11 4 0.11
12 8 0.23
13 23 0.66
ACGTcount: A:0.84, C:0.06, G:0.02, T:0.08
Consensus pattern (12 bp):
AAATAAACAAAA
Found at i:31919470 original size:25 final size:25
Alignment explanation
Indices: 31919421--31919487 Score: 82
Period size: 25 Copynumber: 2.6 Consensus size: 25
31919411 AAAATAGATC
31919421 AAGAGAATAAAAATAAATAAATAAACAA
1 AAGA-AAT-AAAA-AAATAAATAAACAA
31919449 AAGAAATAAACAAAA-AAATAAACAA
1 AAGAAATAAA-AAAATAAATAAACAA
*
31919474 AAAAAATAAAAAAA
1 AAGAAATAAAAAAA
31919488 CCAATCAGGA
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
24 4 0.11
25 19 0.51
26 6 0.16
27 4 0.11
28 4 0.11
ACGTcount: A:0.81, C:0.04, G:0.04, T:0.10
Consensus pattern (25 bp):
AAGAAATAAAAAAATAAATAAACAA
Found at i:31920511 original size:19 final size:19
Alignment explanation
Indices: 31920487--31920524 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
31920477 CAACACTTAC
31920487 AAAATGTGTTAAAAATACT
1 AAAATGTGTTAAAAATACT
31920506 AAAATGTGTTAAAAATACT
1 AAAATGTGTTAAAAATACT
31920525 TATTTTTTAA
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:0.53, C:0.05, G:0.11, T:0.32
Consensus pattern (19 bp):
AAAATGTGTTAAAAATACT
Found at i:31922332 original size:29 final size:28
Alignment explanation
Indices: 31922241--31922335 Score: 73
Period size: 29 Copynumber: 3.2 Consensus size: 28
31922231 TCCTTAGGTT
* * *
31922241 TTATCAGGCACTAGGTATCGGTGATTATA
1 TTATCAGGTACTACGTACCGGTGA-TATA
* * ** *
31922270 TTTATCAGATACTACATACCAATGAGTATT
1 -TTATCAGGTACTACGTACCGGTGA-TATA
*
31922300 TTATCAGGTACTATGTACCGGTGATCATA
1 TTATCAGGTACTACGTACCGGTGAT-ATA
31922329 TTATCAG
1 TTATCAG
31922336 ATAGTTTGTA
Statistics
Matches: 49, Mismatches: 15, Indels: 3
0.73 0.22 0.04
Matches are distributed among these distances:
28 1 0.02
29 28 0.57
30 20 0.41
ACGTcount: A:0.31, C:0.16, G:0.18, T:0.36
Consensus pattern (28 bp):
TTATCAGGTACTACGTACCGGTGATATA
Found at i:31924572 original size:26 final size:26
Alignment explanation
Indices: 31924543--31924623 Score: 62
Period size: 26 Copynumber: 3.2 Consensus size: 26
31924533 CGATATGAGA
31924543 ACATCCCATGTAAGACCATGTCTGGG
1 ACATCCCATGTAAGACCATGTCTGGG
** * * *
31924569 ACATGGCATG--GGCACC--GATATGAGA
1 ACATCCCATGTAAG-ACCATG-TCTG-GG
31924594 ACATCCCATGTAAGACCATGTCTGGG
1 ACATCCCATGTAAGACCATGTCTGGG
31924620 ACAT
1 ACAT
31924624 GGCTTTGGCA
Statistics
Matches: 38, Mismatches: 10, Indels: 14
0.61 0.16 0.23
Matches are distributed among these distances:
23 1 0.03
24 4 0.11
25 12 0.32
26 16 0.42
27 4 0.11
28 1 0.03
ACGTcount: A:0.30, C:0.25, G:0.25, T:0.21
Consensus pattern (26 bp):
ACATCCCATGTAAGACCATGTCTGGG
Found at i:31924574 original size:51 final size:50
Alignment explanation
Indices: 31924342--31924633 Score: 377
Period size: 50 Copynumber: 5.8 Consensus size: 50
31924332 TTGGGTAAAA
* * *
31924342 AGGTCCCATGTAAGACCATGTTTGGGACATGGCGTTGACACCAAGATGAG
1 AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAG
* * *
31924392 AGGTCCCATTTAAGACCATGTCTGAGACATGGCGTTGGCACTGAGATGAG
1 AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAG
* *
31924442 AGGTCTCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGACATGAG
1 AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAG
** * * *
31924492 AGGTCCCCCGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAG
1 AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAG
** * * *
31924542 AACATCCCATGTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAG
1 -AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAG
** *
31924593 AACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 -AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
31924634 TGTTATTATC
Statistics
Matches: 218, Mismatches: 23, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
50 133 0.61
51 85 0.39
ACGTcount: A:0.26, C:0.23, G:0.29, T:0.22
Consensus pattern (50 bp):
AGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAG
Found at i:31929736 original size:50 final size:50
Alignment explanation
Indices: 31929656--31929822 Score: 219
Period size: 50 Copynumber: 3.3 Consensus size: 50
31929646 CAAAGTCATA
* * ** *
31929656 TCCCAGATATAGTCTTACATGGGAGTTCTCATATCGGTGCCCATGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATG
* * * *
31929706 TCCCAGGCATGGTCTTATATGGGACCTCTCATCTCGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATG
*
31929756 TCCCAGACATGGCCTTACATGGGACCTCTCATCTCGGTG-CCAGTGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCA-TGCCATG
*
31929806 TCCCAAACATGGTCTTA
1 TCCCAGACATGGTCTTA
31929823 TACTGGCTCA
Statistics
Matches: 100, Mismatches: 16, Indels: 2
0.85 0.14 0.02
Matches are distributed among these distances:
49 2 0.02
50 98 0.98
ACGTcount: A:0.20, C:0.31, G:0.22, T:0.27
Consensus pattern (50 bp):
TCCCAGACATGGTCTTACATGGGACCTCTCATCTCGGTGCCCATGCCATG
Found at i:31930980 original size:21 final size:22
Alignment explanation
Indices: 31930947--31930987 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
31930937 CAATTTTTCA
* *
31930947 ATCTAATATATATATTTCAATC
1 ATCTAAGATATATAATTCAATC
31930969 ATCTAAGA-ATATAATTCAA
1 ATCTAAGATATATAATTCAA
31930988 GTTACATGAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.46, C:0.12, G:0.02, T:0.39
Consensus pattern (22 bp):
ATCTAAGATATATAATTCAATC
Found at i:31934784 original size:29 final size:29
Alignment explanation
Indices: 31934712--31934797 Score: 84
Period size: 29 Copynumber: 2.9 Consensus size: 29
31934702 ACTATGTGTT
*
31934712 GGTGATTATATTTATTAGATACTATGTACC
1 GGTGATCATA-TTATTAGATACTATGTACC
* * * *
31934742 GAT-AACTATTTTATTAGGTACTATGTACC
1 GGTGATC-ATATTATTAGATACTATGTACC
* *
31934771 GGTGATCATATTATCAGATATTATGTA
1 GGTGATCATATTATTAGATACTATGTA
31934798 TTGGTGTTCA
Statistics
Matches: 43, Mismatches: 11, Indels: 5
0.73 0.19 0.08
Matches are distributed among these distances:
29 37 0.86
30 6 0.14
ACGTcount: A:0.31, C:0.10, G:0.16, T:0.42
Consensus pattern (29 bp):
GGTGATCATATTATTAGATACTATGTACC
Found at i:31936977 original size:20 final size:20
Alignment explanation
Indices: 31936952--31936994 Score: 86
Period size: 20 Copynumber: 2.1 Consensus size: 20
31936942 CTGTGTGCCA
31936952 GACCGTGTGCAGCATAAAGT
1 GACCGTGTGCAGCATAAAGT
31936972 GACCGTGTGCAGCATAAAGT
1 GACCGTGTGCAGCATAAAGT
31936992 GAC
1 GAC
31936995 TTTACATGCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.30, C:0.21, G:0.30, T:0.19
Consensus pattern (20 bp):
GACCGTGTGCAGCATAAAGT
Found at i:31961463 original size:15 final size:16
Alignment explanation
Indices: 31961434--31961463 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31961424 CAAACATGCT
31961434 TTAACACATTATCAAA
1 TTAACACATTATCAAA
31961450 TTAACACA-TATCAA
1 TTAACACATTATCAA
31961464 CAACGCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:31967688 original size:15 final size:16
Alignment explanation
Indices: 31967659--31967688 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
31967649 CAAACATGCT
31967659 TTAACACATTATCAAA
1 TTAACACATTATCAAA
31967675 TTAACACA-TATCAA
1 TTAACACATTATCAA
31967689 CAAGGCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:31975104 original size:27 final size:27
Alignment explanation
Indices: 31975067--31975130 Score: 119
Period size: 27 Copynumber: 2.4 Consensus size: 27
31975057 ATGTGTTCTT
31975067 TTTTTAATTTAAAATTTAAAAAAAATA
1 TTTTTAATTTAAAATTTAAAAAAAATA
31975094 TTTTTAATTTAAAATTTAAAAAAAATA
1 TTTTTAATTTAAAATTTAAAAAAAATA
*
31975121 TTTTTTATTT
1 TTTTTAATTT
31975131 GGTGGATCCA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 36 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (27 bp):
TTTTTAATTTAAAATTTAAAAAAAATA
Found at i:31977067 original size:14 final size:15
Alignment explanation
Indices: 31977050--31977079 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
31977040 CATAATTCAA
31977050 AAAATAT-ATTTTAC
1 AAAATATAATTTTAC
31977064 AAAATATAATTTTAC
1 AAAATATAATTTTAC
31977079 A
1 A
31977080 TTTCAAACAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 7 0.47
15 8 0.53
ACGTcount: A:0.53, C:0.07, G:0.00, T:0.40
Consensus pattern (15 bp):
AAAATATAATTTTAC
Found at i:31977666 original size:39 final size:41
Alignment explanation
Indices: 31977623--31977722 Score: 150
Period size: 39 Copynumber: 2.5 Consensus size: 41
31977613 AAATATATTT
* *
31977623 ATTTTTTTTAATTTTAAAATATTTTT-ACATAC-TTTTTTA
1 ATTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTA
31977662 ATTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTA
1 ATTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTA
* *
31977703 ATTTTTTAAAATTTTTAAAT
1 ATTTTTTTAAATTTTAAAAT
31977723 TAAAAATGGG
Statistics
Matches: 55, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
39 25 0.45
40 5 0.09
41 25 0.45
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (41 bp):
ATTTTTTTAAATTTTAAAATATTTTTAAAATACTTTTTTTA
Found at i:31977687 original size:11 final size:10
Alignment explanation
Indices: 31977634--31977718 Score: 52
Period size: 8 Copynumber: 8.3 Consensus size: 10
31977624 TTTTTTTTAA
31977634 TTTTAAAATAT
1 TTTTAAAAT-T
*
31977645 TTTTACATACTT
1 TTTTA-A-AATT
31977657 TTTT--AATT
1 TTTTAAAATT
*
31977665 TTTTTAAA--
1 TTTTAAAATT
31977673 TTTTAAAATAT
1 TTTTAAAAT-T
31977684 TTTTAAAATACT
1 TTTTAAAAT--T
**
31977696 TTTTTTAATT
1 TTTTAAAATT
31977706 TTTTAAAATT
1 TTTTAAAATT
31977716 TTT
1 TTT
31977719 AAATTAAAAA
Statistics
Matches: 58, Mismatches: 8, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
8 14 0.24
10 14 0.24
11 14 0.24
12 14 0.24
13 2 0.03
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.62
Consensus pattern (10 bp):
TTTTAAAATT
Found at i:31980930 original size:3 final size:3
Alignment explanation
Indices: 31980922--31981006 Score: 70
Period size: 3 Copynumber: 28.7 Consensus size: 3
31980912 TTAGTCCTCG
* * *
31980922 TTA TTA TTA TTA TTA TTA -TA TTA TTA TTA TTA TCA -AA CTAA TTAA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TT-A
* *
31980967 TT- TTA TCA TTA TTA -AA TTTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA TTA TT
31981007 TACTCATTTA
Statistics
Matches: 68, Mismatches: 7, Indels: 14
0.76 0.08 0.16
Matches are distributed among these distances:
2 6 0.09
3 56 0.82
4 6 0.09
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:31981049 original size:2 final size:2
Alignment explanation
Indices: 31981042--31981099 Score: 62
Period size: 2 Copynumber: 28.5 Consensus size: 2
31981032 TAGATTTAAT
* * * * *
31981042 TA TA TA TA TA TA TA TA TA TA CA TA CA TA TC TT TGA TT TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T-A TA TA TA TA
31981085 TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA T
31981100 GCATACTTCT
Statistics
Matches: 46, Mismatches: 9, Indels: 2
0.81 0.16 0.04
Matches are distributed among these distances:
2 45 0.98
3 1 0.02
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:31981262 original size:18 final size:17
Alignment explanation
Indices: 31981238--31981306 Score: 70
Period size: 18 Copynumber: 3.9 Consensus size: 17
31981228 ACATACATAC
31981238 TTATATATTCTATATAT
1 TTATATATTCTATATAT
*
31981255 TCTATATATTTTATA-AT
1 T-TATATATTCTATATAT
31981272 TTATATACATATCTATATAT
1 TTATAT--AT-TCTATATAT
*
31981292 ATATATATT-TATATA
1 TTATATATTCTATATA
31981307 CATTTTTTAC
Statistics
Matches: 44, Mismatches: 3, Indels: 11
0.76 0.05 0.19
Matches are distributed among these distances:
16 11 0.25
17 5 0.11
18 16 0.36
19 5 0.11
20 7 0.16
ACGTcount: A:0.39, C:0.06, G:0.00, T:0.55
Consensus pattern (17 bp):
TTATATATTCTATATAT
Found at i:31981326 original size:2 final size:2
Alignment explanation
Indices: 31981215--31981306 Score: 50
Period size: 2 Copynumber: 48.0 Consensus size: 2
31981205 ATAACTTATT
* * * *
31981215 TA TA TA TA TG TA TA CA TA CA TA CT- TA TA TA T- TC 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 TA
* * * * *
31981255 TC TA TA TA T- TT TA TA -A TT TA TA TA CA TA TC 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
*
31981295 TA TA TT TA TA TA
1 TA TA TA TA TA TA
31981307 CATTTTTTAC
Statistics
Matches: 67, Mismatches: 17, Indels: 12
0.70 0.18 0.12
Matches are distributed among these distances:
1 5 0.07
2 61 0.91
3 1 0.01
ACGTcount: A:0.40, C:0.08, G:0.01, T:0.51
Consensus pattern (2 bp):
TA
Found at i:31981326 original size:37 final size:36
Alignment explanation
Indices: 31981248--31981327 Score: 85
Period size: 37 Copynumber: 2.2 Consensus size: 36
31981238 TTATATATTC
*
31981248 TATATAT-TCTATATATTTTATAATTTATATACATA
1 TATATATATATATATATTTTATAATTTATATACATA
* *
31981283 TCTATATATATATATATTTATATACATTT-TTTACGA-A
1 TATATATATATATATATTT-TATA-ATTTATATAC-ATA
31981320 TATATATA
1 TATATATA
31981328 CATACTTATA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
35 6 0.16
36 10 0.27
37 16 0.43
38 5 0.14
ACGTcount: A:0.40, C:0.06, G:0.01, T:0.53
Consensus pattern (36 bp):
TATATATATATATATATTTTATAATTTATATACATA
Found at i:31981694 original size:20 final size:20
Alignment explanation
Indices: 31981671--31981708 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
31981661 TTGCTCATAT
31981671 TATTT-TTATTCACATTATCA
1 TATTTATTATTC-CATTATCA
31981691 TATTTATTATTCCATTAT
1 TATTTATTATTCCATTAT
31981709 GCATGTTAAC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.29, C:0.13, G:0.00, T:0.58
Consensus pattern (20 bp):
TATTTATTATTCCATTATCA
Found at i:31981982 original size:108 final size:107
Alignment explanation
Indices: 31981750--31982060 Score: 448
Period size: 106 Copynumber: 2.9 Consensus size: 107
31981740 TTATTCTAAA
31981750 TAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTT-
1 TAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTC
*
31981814 TCGTTCGACCAAATAGCTAAATATCCTTTTAAAATTTCAAAG
66 TCGTTCGACCAAATAGCCAAATATCCTTTTAAAATTTCAAAG
* *
31981856 TAAGGCGATATTTTGCGTTTGAAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTT
1 TAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGA-TTTT
* * * **
31981921 CTCGTTCGACCAAATAACCAAATATCTTTTTTAAATTTTGAAG
65 CTCGTTCGACCAAATAGCCAAATATCCTTTTAAAATTTCAAAG
* * *
31981964 TAAGGTAATATTTTGCGTTTGGAAATTC-AAATAAACGTGCCCTAATGTGCTGGGTTTTGA-TTT
1 TAAGGCAATATTTTGCGTTTGGAAATTCGAGA-AAACGTGCCCTAATGTGCTGGGTTTCGATTTT
* * * *
31982027 CCCATTTGACCAAATAGCCAAATATCCTCTTAAA
65 CTCGTTCGACCAAATAGCCAAATATCCTTTTAAA
31982061 TCTCAATCCA
Statistics
Matches: 182, Mismatches: 20, Indels: 6
0.88 0.10 0.03
Matches are distributed among these distances:
106 88 0.48
107 6 0.03
108 88 0.48
ACGTcount: A:0.30, C:0.16, G:0.18, T:0.36
Consensus pattern (107 bp):
TAAGGCAATATTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATTTTC
TCGTTCGACCAAATAGCCAAATATCCTTTTAAAATTTCAAAG
Found at i:31982287 original size:22 final size:22
Alignment explanation
Indices: 31982244--31982288 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
31982234 TCGTGGATTA
* *
31982244 AAATCGTTGTTTTAATAAAATC
1 AAATCGTTGTATTAAAAAAATC
31982266 AAATCGTT-TATTAAAAACAATC
1 AAATCGTTGTATTAAAAA-AATC
31982288 A
1 A
31982289 CTTGTTAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 7 0.35
22 13 0.65
ACGTcount: A:0.47, C:0.11, G:0.07, T:0.36
Consensus pattern (22 bp):
AAATCGTTGTATTAAAAAAATC
Found at i:31987093 original size:3 final size:3
Alignment explanation
Indices: 31987087--31987131 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
31987077 AGTACCGTTG
31987087 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
31987132 AAGATAGATT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:32003438 original size:56 final size:55
Alignment explanation
Indices: 32003352--32003459 Score: 180
Period size: 56 Copynumber: 1.9 Consensus size: 55
32003342 GTATCCATTG
*
32003352 GATGATAAATCATCACTTTTAATTTGAATAGTGCTTACAAATAATTAAATTTGTAA
1 GATGATAAATCATCACTTTTAATTTGAATAGTGCTCACAAATAATT-AATTTGTAA
**
32003408 GATGATAAATCATCACTTTTAATTTGAATAGTGCTCATGAATAATTAATTTG
1 GATGATAAATCATCACTTTTAATTTGAATAGTGCTCACAAATAATTAATTTG
32003460 CAATCTACAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
55 6 0.12
56 43 0.88
ACGTcount: A:0.39, C:0.09, G:0.12, T:0.40
Consensus pattern (55 bp):
GATGATAAATCATCACTTTTAATTTGAATAGTGCTCACAAATAATTAATTTGTAA
Found at i:32008486 original size:25 final size:26
Alignment explanation
Indices: 32008440--32008708 Score: 169
Period size: 25 Copynumber: 10.8 Consensus size: 26
32008430 TACGAGCATG
* * **
32008440 TAATCAGGAAGCTCTTTCGAGCCATA
1 TAATCGGGAAGCTCATGAGAGCCATA
* *
32008466 TAAT-GGGAAGCTCATGTGAGCCATG
1 TAATCGGGAAGCTCATGAGAGCCATA
* * *
32008491 TAAT-GGTAAGCTCATAAGAGTC--A
1 TAATCGGGAAGCTCATGAGAGCCATA
* *
32008514 TAATCGAGAAGCTCATGCGAGCCA-A
1 TAATCGGGAAGCTCATGAGAGCCATA
*
32008539 T-ATCGGAAAGCTC-TGGAGAGCCAT-
1 TAATCGGGAAGCTCAT-GAGAGCCATA
* *
32008563 TAATCGAGAAGCTCGTGAGAGCCAGT-
1 TAATCGGGAAGCTCATGAGAGCCA-TA
**
32008589 T-ATCATGAAGCTCAT-ACGAGCCATA
1 TAATCGGGAAGCTCATGA-GAGCCATA
* *
32008614 -AA-CGGGAAGCT-TTGAAGAGCTAT-
1 TAATCGGGAAGCTCATG-AGAGCCATA
32008637 TAATCGGGAAGCTCATGAGAGCCA-A
1 TAATCGGGAAGCTCATGAGAGCCATA
* * *
32008662 TTATCGAGAAGCTC-TGGAGAGCCAAA
1 TAATCGGGAAGCTCAT-GAGAGCCATA
*
32008688 TAA-CGGGAAGCTCATAAGAGC
1 TAATCGGGAAGCTCATGAGAGC
32008709 TATGGTGTGT
Statistics
Matches: 190, Mismatches: 34, Indels: 39
0.72 0.13 0.15
Matches are distributed among these distances:
23 6 0.03
24 49 0.26
25 122 0.64
26 13 0.07
ACGTcount: A:0.34, C:0.19, G:0.26, T:0.21
Consensus pattern (26 bp):
TAATCGGGAAGCTCATGAGAGCCATA
Found at i:32008684 original size:74 final size:74
Alignment explanation
Indices: 32008458--32008708 Score: 223
Period size: 74 Copynumber: 3.4 Consensus size: 74
32008448 AAGCTCTTTC
* * * * *
32008458 GAGCCATATAATGGGAAGCTCATG-TGAGCCATGTAAT-G-GTAAGCTCATAAGAGTC-ATAATC
1 GAGCCA-ATAACGGGAAGCTC-TGAAGAGCCAT-TAATCGAG-AAGCTCATGAGAGCCAATTATC
*
32008519 GAGAAGCTCATGC
62 GAGAAGCTCATGA
* * * * *
32008532 GAGCCAATATCGGAAAGCTCTGGAGAGCCATTAATCGAGAAGCTCGTGAGAGCCAGTTATC-ATG
1 GAGCCAATAACGGGAAGCTCTGAAGAGCCATTAATCGAGAAGCTCATGAGAGCCAATTATCGA-G
32008596 AAGCTCAT-A
65 AAGCTCATGA
* * *
32008605 CGAGCC-ATAAACGGGAAGCTTTGAAGAGCTATTAATCGGGAAGCTCATGAGAGCCAATTATCGA
1 -GAGCCAAT-AACGGGAAGCTCTGAAGAGCCATTAATCGAGAAGCTCATGAGAGCCAATTATCGA
32008669 GAAGCTC-TGGA
64 GAAGCTCAT-GA
32008680 GAGCCAAATAACGGGAAGCTCAT-AAGAGC
1 GAGCC-AATAACGGGAAGCTC-TGAAGAGC
32008709 TATGGTGTGT
Statistics
Matches: 145, Mismatches: 19, Indels: 25
0.77 0.10 0.13
Matches are distributed among these distances:
72 6 0.04
73 35 0.24
74 82 0.57
75 19 0.13
76 3 0.02
ACGTcount: A:0.34, C:0.19, G:0.27, T:0.20
Consensus pattern (74 bp):
GAGCCAATAACGGGAAGCTCTGAAGAGCCATTAATCGAGAAGCTCATGAGAGCCAATTATCGAGA
AGCTCATGA
Found at i:32008845 original size:8 final size:8
Alignment explanation
Indices: 32008832--32008872 Score: 82
Period size: 8 Copynumber: 5.1 Consensus size: 8
32008822 ATACTTTCGG
32008832 ATATGTTT
1 ATATGTTT
32008840 ATATGTTT
1 ATATGTTT
32008848 ATATGTTT
1 ATATGTTT
32008856 ATATGTTT
1 ATATGTTT
32008864 ATATGTTT
1 ATATGTTT
32008872 A
1 A
32008873 AGTAATCATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 33 1.00
ACGTcount: A:0.27, C:0.00, G:0.12, T:0.61
Consensus pattern (8 bp):
ATATGTTT
Found at i:32011363 original size:55 final size:55
Alignment explanation
Indices: 32011279--32011385 Score: 180
Period size: 55 Copynumber: 1.9 Consensus size: 55
32011269 GTATCCATTG
*
32011279 GATGATAAATCATCACTTTTACTTTGAATAGTGC-AATGAATAATTAAATTTGTAA
1 GATGATAAATCATCACTTTTAATTTGAATAGTGCTAATGAATAATT-AATTTGTAA
*
32011334 GATGATAAATCATCACTTTTAATTTGAATAGTGCTCATGAATAATTAATTTG
1 GATGATAAATCATCACTTTTAATTTGAATAGTGCTAATGAATAATTAATTTG
32011386 CAATCTATAA
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
55 39 0.80
56 10 0.20
ACGTcount: A:0.38, C:0.09, G:0.13, T:0.39
Consensus pattern (55 bp):
GATGATAAATCATCACTTTTAATTTGAATAGTGCTAATGAATAATTAATTTGTAA
Found at i:32011821 original size:18 final size:18
Alignment explanation
Indices: 32011776--32011821 Score: 74
Period size: 18 Copynumber: 2.6 Consensus size: 18
32011766 TGGCTAGGGT
*
32011776 ACGAAGAATCTGAAAGGC
1 ACGAAGAATTTGAAAGGC
32011794 ACGAAGAATTTGAAAGGC
1 ACGAAGAATTTGAAAGGC
*
32011812 ATGAAGAATT
1 ACGAAGAATT
32011822 GAGGCAGCCT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.46, C:0.11, G:0.26, T:0.17
Consensus pattern (18 bp):
ACGAAGAATTTGAAAGGC
Found at i:32014324 original size:16 final size:16
Alignment explanation
Indices: 32014303--32014338 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
32014293 TTTGGTTTGC
32014303 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
32014319 TGTATTGGATTAGAGG
1 TGTATTGGATTAGAGG
32014335 TGTA
1 TGTA
32014339 ATAGCAAATC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.25, C:0.00, G:0.36, T:0.39
Consensus pattern (16 bp):
TGTATTGGATTAGAGG
Found at i:32014595 original size:18 final size:17
Alignment explanation
Indices: 32014574--32014608 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
32014564 TTATTATTAA
*
32014574 ATATATTTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
32014592 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
32014609 TCTTATAATT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 6 0.38
18 10 0.62
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:32014745 original size:156 final size:157
Alignment explanation
Indices: 32014461--32014776 Score: 553
Period size: 156 Copynumber: 2.0 Consensus size: 157
32014451 TAGAATACCC
*
32014461 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAAATTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAAATTTAATAAGATTATTA
* * ** *
32014526 TTATCAGTAATAAATTTTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
32014591 TATATAATTTAATAAAATTCTT-ATAA
131 TATATAATTTAATAAAATTCTTAATAA
* *
32014617 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAAATTTAATAAGATTATTA
32014682 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
32014747 TATATAATTTAATAAAATTCTTAATAA
131 TATATAATTTAATAAAATTCTTAATAA
32014774 TTA
1 TTA
32014777 ATATTCTTAT
Statistics
Matches: 151, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
156 144 0.95
157 7 0.05
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.48
Consensus pattern (157 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAAATTTAATAAGATTATTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTATAATTAAAA
TATATAATTTAATAAAATTCTTAATAA
Found at i:32014747 original size:16 final size:16
Alignment explanation
Indices: 32014710--32014751 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
32014700 TTAATCATAT
*
32014710 TTAAACATA-ATTATTA
1 TTAAA-ATATATTATAA
32014726 TT-AAATATATTATAA
1 TTAAAATATATTATAA
32014741 TTAAAATATAT
1 TTAAAATATAT
32014752 AATTTAATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 3 0.13
15 10 0.43
16 10 0.43
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.45
Consensus pattern (16 bp):
TTAAAATATATTATAA
Found at i:32014758 original size:14 final size:15
Alignment explanation
Indices: 32014719--32014760 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
32014709 TTTAAACATA
*
32014719 ATTATTATTAAATAT
1 ATTATAATTAAATAT
32014734 ATTATAATTAAA-AT
1 ATTATAATTAAATAT
*
32014748 A-TATAATTTAATA
1 ATTATAATTAAATA
32014761 AAATTCTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 9 0.38
14 4 0.17
15 11 0.46
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTATAATTAAATAT
Found at i:32014810 original size:61 final size:60
Alignment explanation
Indices: 32014745--32014932 Score: 172
Period size: 61 Copynumber: 3.1 Consensus size: 60
32014735 TTATAATTAA
32014745 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAGATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCA-ATCAT
** * * * * * * * * *
32014806 AATATATGGTACT-GTAAAA-TATAAATTAACATAATTATTATTAAAT--ATATTA-T-AATTAA
1 AATATATAAT-TTAATAAAATTCTTAA-TAA-TTAA-TATTCTTATATGAAT-TTACTCAATCAT
32014865 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCAT
1 AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTC-AATCAT
32014926 AATATAT
1 AATATAT
32014933 GATACTGTAA
Statistics
Matches: 93, Mismatches: 22, Indels: 24
0.67 0.16 0.17
Matches are distributed among these distances:
57 9 0.10
58 7 0.08
59 22 0.24
60 9 0.10
61 30 0.32
62 7 0.08
63 9 0.10
ACGTcount: A:0.47, C:0.06, G:0.03, T:0.43
Consensus pattern (60 bp):
AATATATAATTTAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAATCAT
Found at i:32014847 original size:120 final size:120
Alignment explanation
Indices: 32014713--32014952 Score: 446
Period size: 120 Copynumber: 2.0 Consensus size: 120
32014703 ATCATATTTA
32014713 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
* *
32014778 TATTCTTATATGAATTTACTCAGATCATAATATATGGTACTGTAAAAT-ATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGT-AAATGATAAATT
32014833 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
1 AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
32014898 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAATGATAAATT
66 TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAATGATAAATT
32014953 TTAATAAAAG
Statistics
Matches: 117, Mismatches: 2, Indels: 2
0.97 0.02 0.02
Matches are distributed among these distances:
119 4 0.03
120 113 0.97
ACGTcount: A:0.48, C:0.06, G:0.04, T:0.42
Consensus pattern (120 bp):
AACATAATTATTATTAAATATATTATAATTAAAATATATAATTTAATAAAATTCTTAATAATTAA
TATTCTTATATGAATTTACTCAAATCATAATATATGATACTGTAAATGATAAATT
Found at i:32014878 original size:14 final size:15
Alignment explanation
Indices: 32014829--32014880 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
32014819 GTAAAATATA
32014829 AATTAACATA-ATTAT
1 AATTAA-ATATATTAT
*
32014844 TATTAAATATATTAT
1 AATTAAATATATTAT
32014859 AATTAAA-ATA-TAT
1 AATTAAATATATTAT
*
32014872 AATTTAATA
1 AATTAAATA
32014881 AAATTCTTAA
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
13 9 0.28
14 7 0.22
15 16 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (15 bp):
AATTAAATATATTAT
Found at i:32018714 original size:9 final size:9
Alignment explanation
Indices: 32018695--32018732 Score: 53
Period size: 9 Copynumber: 4.3 Consensus size: 9
32018685 GTGTTGATTC
32018695 TTAAAAA-T
1 TTAAAAATT
32018703 TTAAAAATT
1 TTAAAAATT
32018712 TTAAAAATAT
1 TTAAAAAT-T
32018722 TT-AAAATT
1 TTAAAAATT
32018730 TTA
1 TTA
32018733 TTTTATAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
8 10 0.37
9 14 0.52
10 3 0.11
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (9 bp):
TTAAAAATT
Found at i:32018753 original size:23 final size:23
Alignment explanation
Indices: 32018709--32018756 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
32018699 AAATTTAAAA
**
32018709 ATTTTAAAAATATTTAAAATTTT
1 ATTTTAAAAATACATAAAATTTT
* *
32018732 ATTTTATAAATACATAAGATTTT
1 ATTTTAAAAATACATAAAATTTT
32018755 AT
1 AT
32018757 AAAATACATA
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (23 bp):
ATTTTAAAAATACATAAAATTTT
Found at i:32022198 original size:2 final size:2
Alignment explanation
Indices: 32022191--32022229 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
32022181 GAAGGACAAA
32022191 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
32022230 AGTACCTCAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:32024829 original size:20 final size:22
Alignment explanation
Indices: 32024791--32024838 Score: 66
Period size: 20 Copynumber: 2.3 Consensus size: 22
32024781 TAGAAATTAG
32024791 TAGAATTGTAATTCCTAGAAAA
1 TAGAATTGTAATTCCTAGAAAA
*
32024813 TAGAATT-T-ATTCTTAGAAAA
1 TAGAATTGTAATTCCTAGAAAA
32024833 TA-AATT
1 TAGAATT
32024839 CTCACTATTT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
19 4 0.16
20 13 0.52
21 1 0.04
22 7 0.28
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (22 bp):
TAGAATTGTAATTCCTAGAAAA
Found at i:32026437 original size:48 final size:49
Alignment explanation
Indices: 32026378--32026610 Score: 209
Period size: 50 Copynumber: 4.7 Consensus size: 49
32026368 GGGATGAGAC
* * **
32026378 CCCATGTAAGACCATGTTTGGGACATGGCATTGGCATTA-ATGAGAGGT
1 CCCACGTAAGACCATGTCTGGGACATGGCATTGGCACGACATGAGAGGT
* * *
32026426 CCCACATAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGT
1 CCCACGTAAGACCATGTCTGGGACATGGCATTGGCA-CGACATGAGAGGT
* * * * **
32026476 CCCCCGTAAGATCATGTCTGGGACATGGCATGGGCACCGATATGAGAACT
1 CCCACGTAAGACCATGTCTGGGACATGGCATTGGCA-CGACATGAGAGGT
* * * * * * **
32026526 CCCATGTAAGACCATATCTGGGATATGGCATTGG-AAGTACAGGAAACAT
1 CCCACGTAAGACCATGTCTGGGACATGGCATTGGCACG-ACATGAGAGGT
* * *
32026575 CCCATGTAAGACCATGTATGGGACATGGCTTTGGCA
1 CCCACGTAAGACCATGTCTGGGACATGGCATTGGCA
32026611 TGTTATTTTC
Statistics
Matches: 151, Mismatches: 30, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
48 33 0.22
49 38 0.25
50 80 0.53
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.22
Consensus pattern (49 bp):
CCCACGTAAGACCATGTCTGGGACATGGCATTGGCACGACATGAGAGGT
Found at i:32026492 original size:50 final size:49
Alignment explanation
Indices: 32026378--32026559 Score: 213
Period size: 50 Copynumber: 3.7 Consensus size: 49
32026368 GGGATGAGAC
* * **
32026378 CCCATGTAAGACCATGTTTGGGACATGGCATTGGCA-TTAATGAGAGGT
1 CCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAATGAGAGGT
* *
32026426 CCCACATAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGT
1 CCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGA-ATGAGAGGT
* * * **
32026476 CCCCCGTAAGATCATGTCTGGGACATGGCATGGGCACCGATATGAGAACT
1 CCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGA-ATGAGAGGT
* * *
32026526 CCCATGTAAGACCATATCTGGGATATGGCATTGG
1 CCCACGTAAGACCATGTCTGGGACATGGCATTGG
32026560 AAGTACAGGA
Statistics
Matches: 112, Mismatches: 20, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
48 32 0.29
49 1 0.01
50 79 0.71
ACGTcount: A:0.26, C:0.22, G:0.29, T:0.23
Consensus pattern (49 bp):
CCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAATGAGAGGT
Found at i:32026837 original size:20 final size:20
Alignment explanation
Indices: 32026812--32026860 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
32026802 TGAGTTATTT
32026812 AAGTAAGCAAGTAAGTAAAC
1 AAGTAAGCAAGTAAGTAAAC
*
32026832 AAGTAAG-AGAGTAAGTAAAG
1 AAGTAAGCA-AGTAAGTAAAC
32026852 AAG-AAGCAA
1 AAGTAAGCAA
32026861 AGACCATGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
19 5 0.19
20 21 0.81
ACGTcount: A:0.57, C:0.06, G:0.24, T:0.12
Consensus pattern (20 bp):
AAGTAAGCAAGTAAGTAAAC
Found at i:32030712 original size:20 final size:20
Alignment explanation
Indices: 32030673--32030736 Score: 60
Period size: 20 Copynumber: 3.2 Consensus size: 20
32030663 ACACCAGGGA
*
32030673 GCACCGTAGTGCTATCAGAG
1 GCACCGTAGTGCAATCAGAG
32030693 GCACCGTAGTGCAAAT-AGAG
1 GCACCGTAGTGC-AATCAGAG
* * *
32030713 GTA-CGATTGTGCAGTCAGAG
1 GCACCG-TAGTGCAATCAGAG
32030733 GCAC
1 GCAC
32030737 TGGAGTGAAA
Statistics
Matches: 35, Mismatches: 5, Indels: 7
0.74 0.11 0.15
Matches are distributed among these distances:
19 4 0.11
20 29 0.83
21 2 0.06
ACGTcount: A:0.28, C:0.22, G:0.31, T:0.19
Consensus pattern (20 bp):
GCACCGTAGTGCAATCAGAG
Found at i:32030763 original size:20 final size:20
Alignment explanation
Indices: 32030740--32030782 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
32030730 GAGGCACTGG
*
32030740 AGTGAAAATAGAGACACCAA
1 AGTGAAAACAGAGACACCAA
* *
32030760 AGTGTAAACAGAGGCACCAA
1 AGTGAAAACAGAGACACCAA
32030780 AGT
1 AGT
32030783 CCAAGTAGAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.16, G:0.23, T:0.12
Consensus pattern (20 bp):
AGTGAAAACAGAGACACCAA
Found at i:32035312 original size:36 final size:36
Alignment explanation
Indices: 32035263--32035335 Score: 94
Period size: 36 Copynumber: 2.0 Consensus size: 36
32035253 TCAGTTTATC
*
32035263 TCAGCCTACTTCTTTTC-ATTGCAGATATCTTCAATT
1 TCAGCCTACTTC-TTTCAAATGCAGATATCTTCAATT
** *
32035299 TCAGCCTGTTTCTTTCAAATGCAGATATCTTCCATT
1 TCAGCCTACTTCTTTCAAATGCAGATATCTTCAATT
32035335 T
1 T
32035336 TATATGCTCG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
35 4 0.12
36 28 0.88
ACGTcount: A:0.22, C:0.25, G:0.10, T:0.44
Consensus pattern (36 bp):
TCAGCCTACTTCTTTCAAATGCAGATATCTTCAATT
Found at i:32037606 original size:24 final size:24
Alignment explanation
Indices: 32037570--32037616 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
32037560 CACACGACCG
*
32037570 TGTCACAGCCCATGTCCTAGGCCA
1 TGTCACAGCCCATGTCCCAGGCCA
*
32037594 TGTCACAGTCCATGTCCCAGGCC
1 TGTCACAGCCCATGTCCCAGGCC
32037617 CTGTGCTTTG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.19, C:0.38, G:0.21, T:0.21
Consensus pattern (24 bp):
TGTCACAGCCCATGTCCCAGGCCA
Found at i:32038361 original size:20 final size:20
Alignment explanation
Indices: 32038335--32038382 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
32038325 TTCCATATTT
32038335 CAGAGGCACCATAGTGCTTA
1 CAGAGGCACCATAGTGCTTA
*
32038355 TAGAGGCACCATAGTGCTTA
1 CAGAGGCACCATAGTGCTTA
32038375 CAGAGGCA
1 CAGAGGCA
32038383 TGAATGTGCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.31, C:0.23, G:0.27, T:0.19
Consensus pattern (20 bp):
CAGAGGCACCATAGTGCTTA
Found at i:32038490 original size:60 final size:60
Alignment explanation
Indices: 32038391--32038504 Score: 147
Period size: 60 Copynumber: 1.9 Consensus size: 60
32038381 CATGAATGTG
* * * *
32038391 CAAACAAGGGTACCGAAGTACAAATAGGGGAACTAAAGTAAAAACAGGAGTACCAAAGTA
1 CAAACAAGGGTACCGAAGTACAAACAGGAGAACCAAAGTAAAAACAGAAGTACCAAAGTA
* * * * *
32038451 CAAACAGGGGTACCGAAGTACAAGCAGGAGTACCGAAGTACAAACAGAAGTACC
1 CAAACAAGGGTACCGAAGTACAAACAGGAGAACCAAAGTAAAAACAGAAGTACC
32038505 TGTAACAACC
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
60 45 1.00
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (60 bp):
CAAACAAGGGTACCGAAGTACAAACAGGAGAACCAAAGTAAAAACAGAAGTACCAAAGTA
Found at i:32038502 original size:20 final size:20
Alignment explanation
Indices: 32038391--32038504 Score: 122
Period size: 20 Copynumber: 5.7 Consensus size: 20
32038381 CATGAATGTG
32038391 CAAACAAGG-GTACCGAAGTA
1 CAAAC-AGGAGTACCGAAGTA
* * * **
32038411 CAAATAGGGGAACTAAAGTA
1 CAAACAGGAGTACCGAAGTA
* *
32038431 AAAACAGGAGTACCAAAGTA
1 CAAACAGGAGTACCGAAGTA
*
32038451 CAAACAGGGGTACCGAAGTA
1 CAAACAGGAGTACCGAAGTA
*
32038471 CAAGCAGGAGTACCGAAGTA
1 CAAACAGGAGTACCGAAGTA
*
32038491 CAAACAGAAGTACC
1 CAAACAGGAGTACC
32038505 TGTAACAACC
Statistics
Matches: 77, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
19 3 0.04
20 74 0.96
ACGTcount: A:0.46, C:0.18, G:0.25, T:0.11
Consensus pattern (20 bp):
CAAACAGGAGTACCGAAGTA
Found at i:32046952 original size:20 final size:20
Alignment explanation
Indices: 32046926--32046977 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
32046916 GGCGTGTTAC
*
32046926 AGTACCGAAGTCCAAACAGG
1 AGTACCGAAGTACAAACAGG
*
32046946 GGTACCGAAGTACAAACAGG
1 AGTACCGAAGTACAAACAGG
32046966 AGTACCGAAGTA
1 AGTACCGAAGTA
32046978 AATTCCTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.40, C:0.21, G:0.27, T:0.12
Consensus pattern (20 bp):
AGTACCGAAGTACAAACAGG
Found at i:32051166 original size:16 final size:17
Alignment explanation
Indices: 32051136--32051168 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
32051126 TGCCAAAATG
*
32051136 AGATCAAAATCATCAAA
1 AGATAAAAATCATCAAA
32051153 AGATAAAAAT-ATCAAA
1 AGATAAAAATCATCAAA
32051169 CTAGCAGGGA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 6 0.40
17 9 0.60
ACGTcount: A:0.64, C:0.12, G:0.06, T:0.18
Consensus pattern (17 bp):
AGATAAAAATCATCAAA
Found at i:32054189 original size:20 final size:19
Alignment explanation
Indices: 32054166--32054332 Score: 122
Period size: 20 Copynumber: 8.4 Consensus size: 19
32054156 TTACAGAGGC
32054166 ACAAATGTACAAACAGGGGT
1 ACAAA-GTACAAACAGGGGT
*
32054186 ACAAAAGTACAAATAGGGGT
1 AC-AAAGTACAAACAGGGGT
* **
32054206 ACCGAAGTACAAGTA-GGGT
1 A-CAAAGTACAAACAGGGGT
* *
32054225 ACCAAAGTATAAACGGGGGT
1 A-CAAAGTACAAACAGGGGT
* *
32054245 ACTGAAGTACAAACAGTGGT
1 AC-AAAGTACAAACAGGGGT
* *
32054265 ACTGAAGTACAAATA-GGGT
1 AC-AAAGTACAAACAGGGGT
32054284 ACGAAAGTACAAACAGGGGT
1 AC-AAAGTACAAACAGGGGT
* * *
32054304 ACCAGAGTACAAATAGGAGT
1 A-CAAAGTACAAACAGGGGT
32054324 ACCAAAGTA
1 A-CAAAGTA
32054333 AATTCCCATA
Statistics
Matches: 120, Mismatches: 21, Indels: 12
0.78 0.14 0.08
Matches are distributed among these distances:
19 30 0.25
20 85 0.71
21 5 0.04
ACGTcount: A:0.44, C:0.14, G:0.26, T:0.16
Consensus pattern (19 bp):
ACAAAGTACAAACAGGGGT
Found at i:32054232 original size:39 final size:39
Alignment explanation
Indices: 32054172--32054332 Score: 164
Period size: 39 Copynumber: 4.1 Consensus size: 39
32054162 AGGCACAAAT
*
32054172 GTACAAACAGGGGTACAAAAGTACAAATAGGGGTACCGAA
1 GTACAAACA-GGGTACCAAAGTACAAATAGGGGTACCGAA
** * ** *
32054212 GTACAAGTAGGGTACCAAAGTATAAACGGGGGTACTGAA
1 GTACAAACAGGGTACCAAAGTACAAATAGGGGTACCGAA
**
32054251 GTACAAACAGTGGTACTGAAGTACAAATA-GGGTA-CGAAA
1 GTACAAACAG-GGTACCAAAGTACAAATAGGGGTACCG-AA
* * *
32054290 GTACAAACAGGGGTACCAGAGTACAAATAGGAGTACCAAA
1 GTACAAACA-GGGTACCAAAGTACAAATAGGGGTACCGAA
32054330 GTA
1 GTA
32054333 AATTCCCATA
Statistics
Matches: 96, Mismatches: 20, Indels: 10
0.76 0.16 0.08
Matches are distributed among these distances:
38 1 0.01
39 64 0.67
40 30 0.31
41 1 0.01
ACGTcount: A:0.43, C:0.14, G:0.27, T:0.16
Consensus pattern (39 bp):
GTACAAACAGGGTACCAAAGTACAAATAGGGGTACCGAA
Found at i:32054254 original size:59 final size:58
Alignment explanation
Indices: 32054167--32054332 Score: 197
Period size: 59 Copynumber: 2.8 Consensus size: 58
32054157 TACAGAGGCA
*
32054167 CAAATGTACAAACAGGGGTACAAAAGTACAAATAGGGGTACCGAAGTACAAGTAGGGTAC
1 CAAA-GTACAAACAGGGGTAC-AAAGTACAAATAGGGGTACCGAAGTACAAATAGGGTAC
* * * * * *
32054227 CAAAGTATAAACGGGGGTACTGAAGTACAAACAGTGGTACTGAAGTACAAATAGGGTAC
1 CAAAGTACAAACAGGGGTAC-AAAGTACAAATAGGGGTACCGAAGTACAAATAGGGTAC
* * * *
32054286 GAAAGTACAAACAGGGGTACCAGAGTACAAATAGGAGTACCAAAGTA
1 CAAAGTACAAACAGGGGTA-CAAAGTACAAATAGGGGTACCGAAGTA
32054333 AATTCCCATA
Statistics
Matches: 87, Mismatches: 18, Indels: 3
0.81 0.17 0.03
Matches are distributed among these distances:
59 82 0.94
60 5 0.06
ACGTcount: A:0.43, C:0.14, G:0.27, T:0.16
Consensus pattern (58 bp):
CAAAGTACAAACAGGGGTACAAAGTACAAATAGGGGTACCGAAGTACAAATAGGGTAC
Done.