Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 132 of 198
Found at i:42112074 original size:21 final size:21
Alignment explanation
Indices: 42112050--42112204 Score: 79
Period size: 21 Copynumber: 7.4 Consensus size: 21
42112040 TTTTTTGCTG
42112050 AATCGATTGTTTATTGTTTTA
1 AATCGATTGTTTATTGTTTTA
* *
42112071 AATC-AGTTCTTT-TCT-TCTTTG
1 AATCGA-TTGTTTAT-TGT-TTTA
42112092 AATCGATTGTTTATTGTTTTA
1 AATCGATTGTTTATTGTTTTA
* * * * *
42112113 AATCTATTCTTTGCTT-CTTTG
1 AATCGATTGTTT-ATTGTTTTA
* *
42112134 AATCAATTGCTTATTGTTTTA
1 AATCGATTGTTTATTGTTTTA
* * * *
42112155 ATTTGATTCTTT-TCT-TCTTTG
1 AATCGATTGTTTAT-TGT-TTTA
* *
42112176 AATCAATTGTTTGTTGTTTTA
1 AATCGATTGTTTATTGTTTTA
42112197 AATCGATT
1 AATCGATT
42112205 CTTGGCTTCT
Statistics
Matches: 95, Mismatches: 27, Indels: 24
0.65 0.18 0.16
Matches are distributed among these distances:
20 7 0.07
21 81 0.85
22 7 0.07
ACGTcount: A:0.21, C:0.11, G:0.12, T:0.57
Consensus pattern (21 bp):
AATCGATTGTTTATTGTTTTA
Found at i:42112107 original size:42 final size:43
Alignment explanation
Indices: 42112048--42112280 Score: 262
Period size: 42 Copynumber: 5.5 Consensus size: 43
42112038 TTTTTTTTGC
* *
42112048 TGAATCGATTGTTTATTGTTTTAAATCAG-TTCTTTTCTTCTT
1 TGAATCAATTGTTTATTGTTTTAAATCAGATTCTTTGCTTCTT
* *
42112090 TGAATCGATTGTTTATTGTTTTAAATC-TATTCTTTGCTTCTT
1 TGAATCAATTGTTTATTGTTTTAAATCAGATTCTTTGCTTCTT
* ** *
42112132 TGAATCAATTGCTTATTGTTTT-AATTTGATTCTTTTCTTCTT
1 TGAATCAATTGTTTATTGTTTTAAATCAGATTCTTTGCTTCTT
* *
42112174 TGAATCAATTGTTTGTTGTTTTAAATC-GATTCTTGGCTTCTT
1 TGAATCAATTGTTTATTGTTTTAAATCAGATTCTTTGCTTCTT
* * *
42112216 TAAACCAATTCGTTATTGTTGTTTTAAAT-AGATTCTTTGCTTCTT
1 TGAATCAATT-G-T-TTATTGTTTTAAATCAGATTCTTTGCTTCTT
*
42112261 TGAATCGATT-TATTATTGTT
1 TGAATCAATTGT-TTATTGTT
42112281 GTTTTAAATC
Statistics
Matches: 165, Mismatches: 19, Indels: 14
0.83 0.10 0.07
Matches are distributed among these distances:
41 3 0.02
42 122 0.74
43 4 0.02
44 1 0.01
45 35 0.21
ACGTcount: A:0.21, C:0.12, G:0.12, T:0.55
Consensus pattern (43 bp):
TGAATCAATTGTTTATTGTTTTAAATCAGATTCTTTGCTTCTT
Found at i:42112237 original size:45 final size:44
Alignment explanation
Indices: 42112063--42112324 Score: 254
Period size: 42 Copynumber: 6.0 Consensus size: 44
42112053 CGATTGTTTA
* * *
42112063 TTGTTTTAAATC-AGTTCTTTTCTTCTTTGAATCGATTG-T-TTA
1 TTGTTTTAAATCGA-TTCTTTGCTTCTTTGAATCAATTGTTATTG
*
42112105 TTGTTTTAAATCTATTCTTTGCTTCTTTGAATCAATTGCTTA---
1 TTGTTTTAAATCGATTCTTTGCTTCTTTGAATCAATTG-TTATTG
* * *
42112147 TTGTTTTAATTTGATTCTTTTCTTCTTTGAATCAATTG-T-TTG
1 TTGTTTTAAATCGATTCTTTGCTTCTTTGAATCAATTGTTATTG
* * *
42112189 TTGTTTTAAATCGATTCTTGGCTTCTTTAAACCAATTCGTTATTG
1 TTGTTTTAAATCGATTCTTTGCTTCTTTGAATCAATT-GTTATTG
* * *
42112234 TTGTTTTAAATAGATTCTTTGCTTCTTTGAATCGATTTATTATTG
1 TTGTTTTAAATCGATTCTTTGCTTCTTTGAATC-AATTGTTATTG
* * * **
42112279 TTGTTTTAAATCTATTATTTACTTCTTT-AATTGATTCGTTATTG
1 TTGTTTTAAATCGATTCTTTGCTTCTTTGAATCAATT-GTTATTG
42112323 TT
1 TT
42112325 AGCAATGTAG
Statistics
Matches: 182, Mismatches: 26, Indels: 22
0.79 0.11 0.10
Matches are distributed among these distances:
40 1 0.01
42 99 0.54
43 4 0.02
44 13 0.07
45 62 0.34
46 3 0.02
ACGTcount: A:0.21, C:0.11, G:0.11, T:0.56
Consensus pattern (44 bp):
TTGTTTTAAATCGATTCTTTGCTTCTTTGAATCAATTGTTATTG
Found at i:42112270 original size:21 final size:21
Alignment explanation
Indices: 42112067--42112270 Score: 80
Period size: 21 Copynumber: 9.6 Consensus size: 21
42112057 TGTTTATTGT
*
42112067 TTTAAATC-AGTTCTTTTCTTC
1 TTTAAATCGA-TTCTTTGCTTC
* * * *
42112088 TTTGAATCGATTGTTT-ATTGT
1 TTTAAATCGATTCTTTGCTT-C
*
42112109 TTTAAATCTATTCTTTGCTTC
1 TTTAAATCGATTCTTTGCTTC
* *
42112130 TTTGAATCAATTGCTTAT--TGT-
1 TTTAAATCGATT-CTT-TGCT-TC
* * *
42112151 TTTAATTTGATTCTTTTCTTC
1 TTTAAATCGATTCTTTGCTTC
* * * *
42112172 TTTGAATCAATTGTTTG-TTGT
1 TTTAAATCGATTCTTTGCTT-C
*
42112193 TTTAAATCGATTCTTGGCTTC
1 TTTAAATCGATTCTTTGCTTC
* * *
42112214 TTTAAACCAATTCGTTATTG-TTGT
1 TTTAAATCGATTC--T-TTGCTT-C
*
42112238 TTTAAATAGATTCTTTGCTTC
1 TTTAAATCGATTCTTTGCTTC
*
42112259 TTTGAATCGATT
1 TTTAAATCGATT
42112271 TATTATTGTT
Statistics
Matches: 130, Mismatches: 37, Indels: 32
0.65 0.19 0.16
Matches are distributed among these distances:
19 1 0.01
20 8 0.06
21 93 0.72
22 12 0.09
23 4 0.03
24 12 0.09
ACGTcount: A:0.21, C:0.13, G:0.12, T:0.55
Consensus pattern (21 bp):
TTTAAATCGATTCTTTGCTTC
Found at i:42113065 original size:42 final size:42
Alignment explanation
Indices: 42113009--42113219 Score: 208
Period size: 42 Copynumber: 4.9 Consensus size: 42
42112999 ATTTTTCCTA
* * *
42113009 AATCGATTGTTTGTTATTTTAAATTGATTCTTTTCTTCTTTG
1 AATCGATTGTTTGTTGTTTTAAATCGATTCTTTGCTTCTTTG
* * *
42113051 AATCAATTGTTTGTTGTTTTAAATCAATTATTTGCTTCTTTG
1 AATCGATTGTTTGTTGTTTTAAATCGATTCTTTGCTTCTTTG
* * * *
42113093 AATTGATTCATTATTGTTGTTTT-AATCGTTTCTTTGGTTCTTTG
1 AATCGATT--GT-TTGTTGTTTTAAATCGATTCTTTGCTTCTTTG
* * *
42113137 AATCGATTGTTTGTTGTTTTAAATTGATTTTTTTCTTCTTTG
1 AATCGATTGTTTGTTGTTTTAAATCGATTCTTTGCTTCTTTG
* * * *
42113179 AATTGATTCTTTATTTTTGTTTTAAATTGATTCTTTGCTTC
1 AATCGA-T-TGT-TTGTTGTTTTAAATCGATTCTTTGCTTC
42113220 AAAAGCCCGT
Statistics
Matches: 137, Mismatches: 25, Indels: 11
0.79 0.14 0.06
Matches are distributed among these distances:
41 10 0.07
42 64 0.47
43 1 0.01
44 27 0.20
45 35 0.26
ACGTcount: A:0.19, C:0.09, G:0.13, T:0.59
Consensus pattern (42 bp):
AATCGATTGTTTGTTGTTTTAAATCGATTCTTTGCTTCTTTG
Found at i:42113139 original size:86 final size:86
Alignment explanation
Indices: 42113044--42113203 Score: 257
Period size: 86 Copynumber: 1.9 Consensus size: 86
42113034 GATTCTTTTC
42113044 TTCTTTGAATCAATTGTTTGTTGTTTTAAATCAATTATTTGCTTCTTTGAATTGATTCATTATTG
1 TTCTTTGAATCAATTGTTTGTTGTTTTAAATCAATTATTTGCTTCTTTGAATTGATTCATTATTG
42113109 TTGTTTTAATCGTTTCTTTGG
66 TTGTTTTAATCGTTTCTTTGG
* ** * * * *
42113130 TTCTTTGAATCGATTGTTTGTTGTTTTAAATTGATTTTTTTCTTCTTTGAATTGATTCTTTATTT
1 TTCTTTGAATCAATTGTTTGTTGTTTTAAATCAATTATTTGCTTCTTTGAATTGATTCATTATTG
42113195 TTGTTTTAA
66 TTGTTTTAA
42113204 ATTGATTCTT
Statistics
Matches: 67, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
86 67 1.00
ACGTcount: A:0.19, C:0.08, G:0.13, T:0.60
Consensus pattern (86 bp):
TTCTTTGAATCAATTGTTTGTTGTTTTAAATCAATTATTTGCTTCTTTGAATTGATTCATTATTG
TTGTTTTAATCGTTTCTTTGG
Found at i:42113165 original size:21 final size:20
Alignment explanation
Indices: 42113007--42113165 Score: 70
Period size: 21 Copynumber: 7.5 Consensus size: 20
42112997 ATATTTTTCC
42113007 TAAATCGATTGTTTGTTATTT
1 TAAATCGATTGTTTGTT-TTT
* *
42113028 TAAATTGATTCTTT-TCTTCTT
1 TAAATCGATTGTTTGT-TT-TT
* *
42113049 TGAATCAATTGTTTGTTGTTT
1 TAAATCGATTGTTTGTT-TTT
* * *
42113070 TAAATCAATTATTTGCTTCTT
1 TAAATCGATTGTTTG-TTTTT
* * *
42113091 TGAATTGATTCATTATTGTTGTTT
1 TAAATCGATT--GT-TTGTT-TTT
* * *
42113115 T-AATCGTTTCTTTGGTTCTT
1 TAAATCGATTGTTT-GTTTTT
*
42113135 TGAATCGATTGTTTGTTGTTT
1 TAAATCGATTGTTTGTT-TTT
*
42113156 TAAATTGATT
1 TAAATCGATT
42113166 TTTTTCTTCT
Statistics
Matches: 103, Mismatches: 23, Indels: 24
0.69 0.15 0.16
Matches are distributed among these distances:
20 10 0.10
21 74 0.72
22 4 0.04
23 9 0.09
24 6 0.06
ACGTcount: A:0.21, C:0.08, G:0.14, T:0.57
Consensus pattern (20 bp):
TAAATCGATTGTTTGTTTTT
Found at i:42113207 original size:24 final size:23
Alignment explanation
Indices: 42113150--42113214 Score: 80
Period size: 24 Copynumber: 2.9 Consensus size: 23
42113140 CGATTGTTTG
42113150 TTGTTTTAAATTGATT-TTTTTC
1 TTGTTTTAAATTGATTCTTTTTC
* * *
42113172 TT-CTTTGAATTGATTCTTTATTT
1 TTGTTTTAAATTGATTCTTT-TTC
42113195 TTGTTTTAAATTGATTCTTT
1 TTGTTTTAAATTGATTCTTT
42113215 GCTTCAAAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 11 0.31
22 5 0.14
23 4 0.11
24 15 0.43
ACGTcount: A:0.18, C:0.06, G:0.09, T:0.66
Consensus pattern (23 bp):
TTGTTTTAAATTGATTCTTTTTC
Found at i:42113596 original size:16 final size:15
Alignment explanation
Indices: 42113575--42113604 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
42113565 CCCAATTTAA
42113575 TTTAATTTTCTATTTC
1 TTTAATTTT-TATTTC
42113591 TTTAATTTTTATTT
1 TTTAATTTTTATTT
42113605 TTTTCTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.20, C:0.07, G:0.00, T:0.73
Consensus pattern (15 bp):
TTTAATTTTTATTTC
Found at i:42120210 original size:14 final size:14
Alignment explanation
Indices: 42120191--42120217 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
42120181 TATGGCCTGG
42120191 AGTCTTTTATCATC
1 AGTCTTTTATCATC
42120205 AGTCTTTTATCAT
1 AGTCTTTTATCAT
42120218 GTAATGGTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.19, G:0.07, T:0.52
Consensus pattern (14 bp):
AGTCTTTTATCATC
Found at i:42120625 original size:21 final size:21
Alignment explanation
Indices: 42120599--42120639 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
42120589 TAAACAAAAA
* *
42120599 ATGCTCATAACCGCAGCACAG
1 ATGCTCATAACAGCAACACAG
*
42120620 ATGCTCGTAACAGCAACACA
1 ATGCTCATAACAGCAACACA
42120640 TAACAATCCT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.37, C:0.32, G:0.17, T:0.15
Consensus pattern (21 bp):
ATGCTCATAACAGCAACACAG
Found at i:42127463 original size:11 final size:11
Alignment explanation
Indices: 42127447--42127472 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
42127437 TATTTTTTAA
42127447 TTTTAAAATAC
1 TTTTAAAATAC
42127458 TTTTAAAATAC
1 TTTTAAAATAC
42127469 TTTT
1 TTTT
42127473 TTTAATTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (11 bp):
TTTTAAAATAC
Found at i:42127481 original size:39 final size:39
Alignment explanation
Indices: 42127432--42127561 Score: 176
Period size: 39 Copynumber: 3.3 Consensus size: 39
42127422 AATATTTTTA
*
42127432 TTTTTT-ATTTTTTAATTTTAAAATACTTTTAAAATACT
1 TTTTTTAATTTTTTAATTTTAAAATATTTTTAAAATACT
* *
42127470 TTTTTTAATTTTTAAATTTTAAAAT-TTTTTAAAAAAAC-
1 TTTTTTAATTTTTTAATTTTAAAATATTTTT-AAAATACT
*
42127508 TTCTTTAATTTTTTTTAATTTTAAAATATTTTTAAAATACT
1 TTTTTTAA--TTTTTTAATTTTAAAATATTTTTAAAATACT
42127549 TTTTTTAATTTTT
1 TTTTTTAATTTTT
42127562 GTTTTAATTT
Statistics
Matches: 79, Mismatches: 7, Indels: 11
0.81 0.07 0.11
Matches are distributed among these distances:
38 17 0.22
39 28 0.35
40 22 0.28
41 12 0.15
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.62
Consensus pattern (39 bp):
TTTTTTAATTTTTTAATTTTAAAATATTTTTAAAATACT
Found at i:42130547 original size:19 final size:18
Alignment explanation
Indices: 42130513--42130548 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
42130503 TGTGTTTACA
*
42130513 AAATATGTATATAAATAT
1 AAATATGTACATAAATAT
42130531 AAATATGATACATAAATA
1 AAATATG-TACATAAATA
42130549 AATTTTGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.58, C:0.03, G:0.06, T:0.33
Consensus pattern (18 bp):
AAATATGTACATAAATAT
Found at i:42132584 original size:129 final size:129
Alignment explanation
Indices: 42132436--42132720 Score: 437
Period size: 129 Copynumber: 2.2 Consensus size: 129
42132426 TTCTGATCCA
* *
42132436 CTCCACTGCAACTTTAGGGAGATAAGACTAGTTGCGATCTGCTCTACTGCAACTTCAAAGAGATA
1 CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTACTGCAACTTCAAAGAGATA
* * *
42132501 AGATCTGTAGTTTTAATTCGCTCCACTAG-AACTTCAGGGAGATAGAATTGGTTTCCTCTGCCTG
66 AGATCTATAGTTTTAATCCGCTCCACT-GCAACTTCAGGGAGATAGAATTGATTTCCTCTGCCTG
* *
42132565 CTCCACTGCAACTTCAGGGAAATAAGACTAGATGCGATCTGCTCTACTGCAACTTCAGAGAGATA
1 CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTACTGCAACTTCAAAGAGATA
* * * * *
42132630 AGATCTATGGTTTTAATCCGTTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCTGTCTG
66 AGATCTATAGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGAATTGATTTCCTCTGCCTG
*
42132694 CTCCACTGCTACTTCAGGGAGATAAGA
1 CTCCACTGCAACTTCAGGGAGATAAGA
42132721 AAAAATCTTC
Statistics
Matches: 141, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
128 1 0.01
129 140 0.99
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.29
Consensus pattern (129 bp):
CTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTACTGCAACTTCAAAGAGATA
AGATCTATAGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGAATTGATTTCCTCTGCCTG
Found at i:42132699 original size:44 final size:43
Alignment explanation
Indices: 42132436--42132720 Score: 155
Period size: 44 Copynumber: 6.6 Consensus size: 43
42132426 TTCTGATCCA
* * * *
42132436 CTCCACTGCAACTTTAGGGAGATAAGACT-A-GTTGC-GATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTGATTTTTCTG-TCTG
* ** **
42132477 CTCTACTGCAACTTCAAAGAGATAAGATCTGTAGTTTTAAT-TC-G
1 CTCCACTGCAACTTCAGGGAGATAAGAT-TG-A-TTTTTCTGTCTG
* * *
42132521 CTCCACTAG-AACTTCAGGGAGAT-AGAATTGGTTTCCTCTGCCTG
1 CTCCACT-GCAACTTCAGGGAGATAAG-ATTGATTT-TTCTGTCTG
* * *
42132565 CTCCACTGCAACTTCAGGGAAATAAGACTAGA---TGC-GATCTG
1 CTCCACTGCAACTTCAGGGAGATAAGA-TTGATTTTTCTG-TCTG
* * ** *
42132606 CTCTACTGCAACTTCAGAGAGATAAGATCT-ATGGTTTT-AATCCG
1 CTCCACTGCAACTTCAGGGAGATAAGAT-TGAT--TTTTCTGTCTG
* *
42132650 TTCCACTGCAACTTCAGGGAGATAGGATTGATTTCTTCTGTCTG
1 CTCCACTGCAACTTCAGGGAGATAAGATTGATTT-TTCTGTCTG
*
42132694 CTCCACTGCTACTTCAGGGAGATAAGA
1 CTCCACTGCAACTTCAGGGAGATAAGA
42132721 AAAAATCTTC
Statistics
Matches: 180, Mismatches: 39, Indels: 47
0.68 0.15 0.18
Matches are distributed among these distances:
40 3 0.02
41 54 0.30
42 4 0.02
43 9 0.05
44 100 0.56
45 8 0.04
46 2 0.01
ACGTcount: A:0.27, C:0.22, G:0.21, T:0.29
Consensus pattern (43 bp):
CTCCACTGCAACTTCAGGGAGATAAGATTGATTTTTCTGTCTG
Found at i:42132836 original size:46 final size:45
Alignment explanation
Indices: 42132752--42132911 Score: 178
Period size: 46 Copynumber: 3.5 Consensus size: 45
42132742 CTGTCAATAC
* ** *
42132752 AGGAAGACAAGATTTGCTACCTTCGATCTACTTCGCCACCAGTAT
1 AGGAAGACAAGATCTGCTATTTTTGATCTACTTCGCCACCAGTAT
* *
42132797 AGGAAAATAAGATCTGCTATTTTCTGATCTACTTCGCCACCAGTAT
1 AGGAAGACAAGATCTGCTATTTT-TGATCTACTTCGCCACCAGTAT
* * * *** *
42132843 GGGAAGACAAGATCCGCTATTTTT-ATCTACTTTGTTGCCAGTAC
1 AGGAAGACAAGATCTGCTATTTTTGATCTACTTCGCCACCAGTAT
42132887 AGGAAGACAAGATCTGCTACTTTTT
1 AGGAAGACAAGATCTGCTA-TTTTT
42132912 AACTTACTCC
Statistics
Matches: 96, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
44 32 0.33
45 24 0.25
46 40 0.42
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (45 bp):
AGGAAGACAAGATCTGCTATTTTTGATCTACTTCGCCACCAGTAT
Found at i:42145846 original size:299 final size:298
Alignment explanation
Indices: 42145073--42146149 Score: 1807
Period size: 298 Copynumber: 3.6 Consensus size: 298
42145063 CCGATAATGC
* * **
42145073 CATTGATGCTTACTCTATTGTTGTTATCAAAGTTGGTCCATGTAGCTTACCGATGTCTCGCAATG
1 CATTGATGCTTACTCTATTGTTGTTATCAAAGCTAGTCCATGTAGCTTACCGATGTCTCGTGATG
*
42145138 GAAGTTTTGGGAGTCAGGTCATTCTTCCCTTACCTCATACGATGAACATGAAGAGGTAAGAAACC
66 GAAGTTTTGGGAGTCAAGTCATTCTTCCCTTACCTCATACGATGAACATGAAGAGGTAAGAAACC
*
42145203 AAAATTTGAACCTCCTGTCATCAGTGTTGTCAAATCATCGATATCAAATCTGACATCTCTGACTC
131 AAAATTCGAACCTCCTGTCATCAGTGTTGTCAAATCATCGATATCAAATCTGACATCTCTGACTC
42145268 CATTTCAGTAGCAAAGTGTAGGACTTTGAAGGACTCAAATGCTTAAGGCTAAGCAGTGCTTCAAT
196 CATTTCAGTAGCAAAGTGTAGGACTTTGAAGGACTCAAATGCTTAAGGCTAAGCAGTGCTTCAAT
42145333 GGTTATTTTTTTCTCGTTAATAGAAAACGCAATAGTGG
261 GGTTATTTTTTTCTCGTTAATAGAAAACGCAATAGTGG
42145371 CATTGATGCTTACTCTATTGTTGTTATCAAAGCTAGTCCATGTAGCTTACCGATGTCTCGTGATG
1 CATTGATGCTTACTCTATTGTTGTTATCAAAGCTAGTCCATGTAGCTTACCGATGTCTCGTGATG
* *
42145436 GAAGTTTTGGGAGTTAGGTCATTCTTCCCTTACCTCATACGATGAACATGAAGAGGTAAGAAACC
66 GAAGTTTTGGGAGTCAAGTCATTCTTCCCTTACCTCATACGATGAACATGAAGAGGTAAGAAACC
*
42145501 AAAATTTGAACCTCCTGTCATCAGTGTTGTCAAATCATCGATATCAAATCTGACATCTCTGACTC
131 AAAATTCGAACCTCCTGTCATCAGTGTTGTCAAATCATCGATATCAAATCTGACATCTCTGACTC
*
42145566 CATTTCAGTAGCAAAGTGTAGGACTTTGAAGGGCTCAAATGCTTAAGGCTAAGCAGTGCTTCAAT
196 CATTTCAGTAGCAAAGTGTAGGACTTTGAAGGACTCAAATGCTTAAGGCTAAGCAGTGCTTCAAT
42145631 GGTTATTTTTTTTCTCGTTAATAGAAAACGCAATAGTGG
261 GGTTA-TTTTTTTCTCGTTAATAGAAAACGCAATAGTGG
42145670 CATTGATGCTTACTCTATTGTTGTTATCAAAGCTAGTCCATGTAGCTTACCGATGTCTCGTGATG
1 CATTGATGCTTACTCTATTGTTGTTATCAAAGCTAGTCCATGTAGCTTACCGATGTCTCGTGATG
* *
42145735 GAAGTTTTGGGAGTCAAGTCATTCTTCCTTTACCTCATACGATGAGCATGAAGAGGTAAGAAACC
66 GAAGTTTTGGGAGTCAAGTCATTCTTCCCTTACCTCATACGATGAACATGAAGAGGTAAGAAACC
* * * * *
42145800 AAGATTCGAGCCTCTTGTCATCAATGTTGTCAAATCATCGATATCAAATCTGACATCTCTAACTC
131 AAAATTCGAACCTCCTGTCATCAGTGTTGTCAAATCATCGATATCAAATCTGACATCTCTGACTC
* * *
42145865 CATTTCAGTAGCAAAG-GTTAGGACTTTGAAAGACTCAAATTCTTAAGGCTAAGTAGTGCTTCAA
196 CATTTCAGTAGCAAAGTG-TAGGACTTTGAAGGACTCAAATGCTTAAGGCTAAGCAGTGCTTCAA
* * * *
42145929 TGGTCGA-TTTTTTCCCTTTAATAGAAAATGCAATAGTGG
260 TGGT-TATTTTTTTCTCGTTAATAGAAAACGCAATAGTGG
* * ** * *
42145968 CATTGATGCTTACTCTATTATTGTTATCAAATCCGGTCTATGTAGCTTACCGATGTCTCGTGGTG
1 CATTGATGCTTACTCTATTGTTGTTATCAAAGCTAGTCCATGTAGCTTACCGATGTCTCGTGATG
* *
42146033 GAAGTTTTGGGAGTCAAGTCATTCTTCTCTTACCTCATACGATGAGCATGAAGAGGTAAGAAACC
66 GAAGTTTTGGGAGTCAAGTCATTCTTCCCTTACCTCATACGATGAACATGAAGAGGTAAGAAACC
* *
42146098 AAAATTCAAACCTTCTGTCATCAGTGTTGTCAAATCATCGATATCAAATCTG
131 AAAATTCGAACCTCCTGTCATCAGTGTTGTCAAATCATCGATATCAAATCTG
42146150 TAACACTCTA
Statistics
Matches: 738, Mismatches: 38, Indels: 6
0.94 0.05 0.01
Matches are distributed among these distances:
298 457 0.62
299 280 0.38
300 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.19, T:0.33
Consensus pattern (298 bp):
CATTGATGCTTACTCTATTGTTGTTATCAAAGCTAGTCCATGTAGCTTACCGATGTCTCGTGATG
GAAGTTTTGGGAGTCAAGTCATTCTTCCCTTACCTCATACGATGAACATGAAGAGGTAAGAAACC
AAAATTCGAACCTCCTGTCATCAGTGTTGTCAAATCATCGATATCAAATCTGACATCTCTGACTC
CATTTCAGTAGCAAAGTGTAGGACTTTGAAGGACTCAAATGCTTAAGGCTAAGCAGTGCTTCAAT
GGTTATTTTTTTCTCGTTAATAGAAAACGCAATAGTGG
Found at i:42147648 original size:9 final size:10
Alignment explanation
Indices: 42147624--42147648 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
42147614 ACCCATAATT
42147624 ATTTTTTACA
1 ATTTTTTACA
42147634 ATTTTTTACA
1 ATTTTTTACA
42147644 ATTTT
1 ATTTT
42147649 CCAAAGTCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.28, C:0.08, G:0.00, T:0.64
Consensus pattern (10 bp):
ATTTTTTACA
Found at i:42148256 original size:45 final size:45
Alignment explanation
Indices: 42148192--42148279 Score: 158
Period size: 45 Copynumber: 2.0 Consensus size: 45
42148182 ACAGATACTC
* *
42148192 GGTGGATTCAGCACATAGCAACCACCTTATTAATCAATGATGTCA
1 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCA
42148237 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
1 GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGT
42148280 TCGGTTCACA
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (45 bp):
GGTGGAATCAGCACATAGCAACCACCTTACTAATCAATGATGTCA
Found at i:42148351 original size:51 final size:51
Alignment explanation
Indices: 42148286--42148426 Score: 183
Period size: 51 Copynumber: 2.8 Consensus size: 51
42148276 ATGTTCGGTT
* * * *
42148286 CACATAGTAGCCTGCACATAGTACTACATATGTGACCATTACCATCCGATA
1 CACATAATAGCCTGCACATAGTACTACACACGTGACCATAACCATCCGATA
* * * * *
42148337 CACGTAATAGCCTGCACATAGTACTACACACGTGATCAAAACTATCCGGTA
1 CACATAATAGCCTGCACATAGTACTACACACGTGACCATAACCATCCGATA
* *
42148388 CGCATAGTAGCCTGCACATAGTACTACACACGTGACCAT
1 CACATAATAGCCTGCACATAGTACTACACACGTGACCAT
42148427 CACTTTCACT
Statistics
Matches: 76, Mismatches: 14, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
51 76 1.00
ACGTcount: A:0.33, C:0.28, G:0.16, T:0.23
Consensus pattern (51 bp):
CACATAATAGCCTGCACATAGTACTACACACGTGACCATAACCATCCGATA
Found at i:42152027 original size:21 final size:19
Alignment explanation
Indices: 42151986--42152028 Score: 50
Period size: 21 Copynumber: 2.2 Consensus size: 19
42151976 ACAATATATC
* *
42151986 TTTTTATAATTTTATACTT
1 TTTTTATAATTTAATAATT
42152005 TTTTTAATAAATTTAATAATT
1 TTTTT-AT-AATTTAATAATT
42152026 TTT
1 TTT
42152029 AAATTTTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 5 0.25
20 2 0.10
21 13 0.65
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (19 bp):
TTTTTATAATTTAATAATT
Found at i:42152504 original size:26 final size:31
Alignment explanation
Indices: 42152451--42152509 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 31
42152441 TAAAGTACTC
42152451 AATTATTCAATTTATTTTATTGTAGTTATTT
1 AATTATTCAATTTATTTTATTGTAGTTATTT
42152482 AATTATT-AA-TT-TTTTATT-T-GTTATTT
1 AATTATTCAATTTATTTTATTGTAGTTATTT
42152508 AA
1 AA
42152510 CTTTTAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
26 9 0.32
27 1 0.04
28 7 0.25
29 2 0.07
30 2 0.07
31 7 0.25
ACGTcount: A:0.31, C:0.02, G:0.05, T:0.63
Consensus pattern (31 bp):
AATTATTCAATTTATTTTATTGTAGTTATTT
Found at i:42157605 original size:21 final size:21
Alignment explanation
Indices: 42157575--42157651 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
42157565 AGCTCGAAAA
*
42157575 TTGAATAGAAGCTCATAAGAG
1 TTGAACAGAAGCTCATAAGAG
*
42157596 TTGAACAGAAACTCATAAGAG
1 TTGAACAGAAGCTCATAAGAG
42157617 TTGAACAGAAGCTCATAAGAG
1 TTGAACAGAAGCTCATAAGAG
* * *
42157638 CTGACCAAAAGCTC
1 TTGAACAGAAGCTC
42157652 GAAAGAGCTA
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 50 1.00
ACGTcount: A:0.43, C:0.17, G:0.21, T:0.19
Consensus pattern (21 bp):
TTGAACAGAAGCTCATAAGAG
Found at i:42157657 original size:21 final size:21
Alignment explanation
Indices: 42157620--42157691 Score: 74
Period size: 21 Copynumber: 3.4 Consensus size: 21
42157610 ATAAGAGTTG
* *
42157620 AACAGAAGCTC-ATAAGAGCTG
1 AACAAAAGCTCGA-AAGAGCTA
*
42157641 ACCAAAAGCTCGAAAGAGCTA
1 AACAAAAGCTCGAAAGAGCTA
* *
42157662 AATAGAAGCTCGAAAGAGCTA
1 AACAAAAGCTCGAAAGAGCTA
42157683 AACAGAAAG
1 AACA-AAAG
42157692 TAAAACACGA
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
21 37 0.90
22 4 0.10
ACGTcount: A:0.49, C:0.18, G:0.22, T:0.11
Consensus pattern (21 bp):
AACAAAAGCTCGAAAGAGCTA
Found at i:42157658 original size:42 final size:43
Alignment explanation
Indices: 42157562--42157691 Score: 146
Period size: 42 Copynumber: 3.1 Consensus size: 43
42157552 ATAAGCCAAC
*
42157562 GAAAGCTCGAAA-A-TTGAATAGAAGCTCATAAGAGTTGAACA
1 GAAAGCTCGAAAGAGTTGAATAGAAGCTCATAAGAGCTGAACA
* *
42157603 GAAA-CTC-ATAAGAGTTGAACAGAAGCTCATAAGAGCTGACCA
1 GAAAGCTCGA-AAGAGTTGAATAGAAGCTCATAAGAGCTGAACA
* * *
42157645 -AAAGCTCGAAAGAGCTAAATAGAAGCTCGA-AAGAGCTAAACA
1 GAAAGCTCGAAAGAGTTGAATAGAAGCTC-ATAAGAGCTGAACA
42157687 GAAAG
1 GAAAG
42157692 TAAAACACGA
Statistics
Matches: 74, Mismatches: 8, Indels: 12
0.79 0.09 0.13
Matches are distributed among these distances:
39 1 0.01
40 5 0.07
41 8 0.11
42 54 0.73
43 6 0.08
ACGTcount: A:0.47, C:0.15, G:0.22, T:0.15
Consensus pattern (43 bp):
GAAAGCTCGAAAGAGTTGAATAGAAGCTCATAAGAGCTGAACA
Found at i:42164577 original size:16 final size:16
Alignment explanation
Indices: 42164556--42164586 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
42164546 GAGAATTAAG
42164556 TAAAAATCAAATAAAC
1 TAAAAATCAAATAAAC
42164572 TAAAAATCAAATAAA
1 TAAAAATCAAATAAA
42164587 AAAAAAATTT
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:0.71, C:0.10, G:0.00, T:0.19
Consensus pattern (16 bp):
TAAAAATCAAATAAAC
Found at i:42164592 original size:16 final size:16
Alignment explanation
Indices: 42164557--42164594 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
42164547 AGAATTAAGT
**
42164557 AAAAATCAAATAAACT
1 AAAAATCAAATAAAAA
42164573 AAAAATCAAATAAAAA
1 AAAAATCAAATAAAAA
42164589 AAAAAT
1 AAAAAT
42164595 TTTGTATCTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.76, C:0.08, G:0.00, T:0.16
Consensus pattern (16 bp):
AAAAATCAAATAAAAA
Found at i:42166277 original size:30 final size:30
Alignment explanation
Indices: 42166224--42166282 Score: 84
Period size: 30 Copynumber: 2.0 Consensus size: 30
42166214 AAACATTTTA
*
42166224 TTTTCCCCAAAATTTTTACTCCC-TCCCAC
1 TTTTCCCCAAAACTTTTACTCCCTTCCCAC
*
42166253 TTTTCCCCTAAAACTTTTATTCCCTTCCCA
1 TTTTCCCC-AAAACTTTTACTCCCTTCCCA
42166283 TCCCACCTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 8 0.31
30 13 0.50
31 5 0.19
ACGTcount: A:0.20, C:0.39, G:0.00, T:0.41
Consensus pattern (30 bp):
TTTTCCCCAAAACTTTTACTCCCTTCCCAC
Found at i:42166430 original size:20 final size:18
Alignment explanation
Indices: 42166370--42166430 Score: 61
Period size: 19 Copynumber: 3.2 Consensus size: 18
42166360 TATTTACTTT
42166370 CCCTCAAACTTTTATTC-C
1 CCCT-AAACTTTTATTCTC
* *
42166388 CCCAAAATTTTTATTTCTC
1 CCCTAAACTTTTA-TTCTC
42166407 CCCTAAACTTTTACTTCTC
1 CCCTAAACTTTTA-TTCTC
42166426 ACCCT
1 -CCCT
42166431 TTACTCTCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 8 0.23
18 6 0.17
19 17 0.49
20 4 0.11
ACGTcount: A:0.23, C:0.36, G:0.00, T:0.41
Consensus pattern (18 bp):
CCCTAAACTTTTATTCTC
Found at i:42171382 original size:12 final size:13
Alignment explanation
Indices: 42171365--42171393 Score: 51
Period size: 12 Copynumber: 2.3 Consensus size: 13
42171355 TTCTACTTGC
42171365 TTTGATTTTCT-T
1 TTTGATTTTCTGT
42171377 TTTGATTTTCTGT
1 TTTGATTTTCTGT
42171390 TTTG
1 TTTG
42171394 TTCTGCACTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 11 0.69
13 5 0.31
ACGTcount: A:0.07, C:0.07, G:0.14, T:0.72
Consensus pattern (13 bp):
TTTGATTTTCTGT
Found at i:42184566 original size:25 final size:25
Alignment explanation
Indices: 42184537--42184708 Score: 107
Period size: 25 Copynumber: 7.4 Consensus size: 25
42184527 GGAGTTTAGC
*
42184537 GTGCTCTTTGATTATTAGCACATCA
1 GTGCTCTCTGATTATTAGCACATCA
* * **
42184562 ATGCTCTCTGGTTATTAGCATGTCA
1 GTGCTCTCTGATTATTAGCACATCA
* *
42184587 GTGCTCTTTGATTACTAG--CA-CA
1 GTGCTCTCTGATTATTAGCACATCA
* * *
42184609 ---CTCTCTGATTACTAGCACGTTA
1 GTGCTCTCTGATTATTAGCACATCA
**
42184631 GTGCTCTCTGATTATTAGCACATTG
1 GTGCTCTCTGATTATTAGCACATCA
* **
42184656 GTGCTCTCCG--T-TTAGCACATTT
1 GTGCTCTCTGATTATTAGCACATCA
* *
42184678 GTGCTCTCTG--TA-TAGCACTTTA
1 GTGCTCTCTGATTATTAGCACATCA
42184700 GTGCTCTCT
1 GTGCTCTCT
42184709 ATTTAATAGT
Statistics
Matches: 118, Mismatches: 22, Indels: 17
0.75 0.14 0.11
Matches are distributed among these distances:
19 14 0.12
21 1 0.01
22 40 0.34
23 1 0.01
25 62 0.53
ACGTcount: A:0.19, C:0.23, G:0.18, T:0.40
Consensus pattern (25 bp):
GTGCTCTCTGATTATTAGCACATCA
Found at i:42184615 original size:44 final size:44
Alignment explanation
Indices: 42184565--42184652 Score: 122
Period size: 44 Copynumber: 2.0 Consensus size: 44
42184555 CACATCAATG
* * * *
42184565 CTCTCTGGTTATTAGCATGTCAGTGCTCTTTGATTACTAGCACA
1 CTCTCTGATTACTAGCACGTCAGTGCTCTCTGATTACTAGCACA
* *
42184609 CTCTCTGATTACTAGCACGTTAGTGCTCTCTGATTATTAGCACA
1 CTCTCTGATTACTAGCACGTCAGTGCTCTCTGATTACTAGCACA
42184653 TTGGTGCTCT
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 38 1.00
ACGTcount: A:0.22, C:0.24, G:0.17, T:0.38
Consensus pattern (44 bp):
CTCTCTGATTACTAGCACGTCAGTGCTCTCTGATTACTAGCACA
Found at i:42184617 original size:19 final size:19
Alignment explanation
Indices: 42184590--42184626 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
42184580 CATGTCAGTG
*
42184590 CTCTTTGATTACTAGCACA
1 CTCTCTGATTACTAGCACA
42184609 CTCTCTGATTACTAGCAC
1 CTCTCTGATTACTAGCAC
42184627 GTTAGTGCTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.24, C:0.30, G:0.11, T:0.35
Consensus pattern (19 bp):
CTCTCTGATTACTAGCACA
Found at i:42184684 original size:47 final size:44
Alignment explanation
Indices: 42184621--42184707 Score: 111
Period size: 47 Copynumber: 1.9 Consensus size: 44
42184611 CTCTGATTAC
* *
42184621 TAGCACGTTAGTGCTCTCTGATTATTAGCACATTGGTGCTCTCCGTT
1 TAGCACATTAGTGCTCTCTG--TA-TAGCACATTAGTGCTCTCCGTT
* *
42184668 TAGCACATTTGTGCTCTCTGTATAGCACTTTAGTGCTCTC
1 TAGCACATTAGTGCTCTCTGTATAGCACATTAGTGCTCTC
42184708 TATTTAATAG
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
44 16 0.44
45 2 0.06
47 18 0.50
ACGTcount: A:0.17, C:0.24, G:0.20, T:0.39
Consensus pattern (44 bp):
TAGCACATTAGTGCTCTCTGTATAGCACATTAGTGCTCTCCGTT
Found at i:42184708 original size:22 final size:22
Alignment explanation
Indices: 42184621--42184708 Score: 88
Period size: 22 Copynumber: 3.9 Consensus size: 22
42184611 CTCTGATTAC
*
42184621 TAGCACGTTAGTGCTCTCTGATTA
1 TAGCACTTTAGTGCTCTCTG--TA
* * * *
42184645 TTAGCACATTGGTGCTCTCCGTT
1 -TAGCACTTTAGTGCTCTCTGTA
42184668 TAGCACATTT-GTGCTCTCTGTA
1 TAGCAC-TTTAGTGCTCTCTGTA
42184690 TAGCACTTTAGTGCTCTCT
1 TAGCACTTTAGTGCTCTCT
42184709 ATTTAATAGT
Statistics
Matches: 54, Mismatches: 7, Indels: 7
0.79 0.10 0.10
Matches are distributed among these distances:
21 3 0.06
22 31 0.57
23 3 0.06
25 17 0.31
ACGTcount: A:0.17, C:0.24, G:0.19, T:0.40
Consensus pattern (22 bp):
TAGCACTTTAGTGCTCTCTGTA
Found at i:42194684 original size:50 final size:50
Alignment explanation
Indices: 42194588--42194823 Score: 201
Period size: 50 Copynumber: 4.6 Consensus size: 50
42194578 AGATCCCACA
* *
42194588 TAAGACCATGTCTGGGACATGACATTGACATCATTGAGGTTATGAGAAGTCCCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCATC---GA-G--ATGAGAAGTCCCATG
* * **
42194644 TAAGACCATGTCTGGGACATGGCGTTGGCATCGAGATGAGAGGTCCCCCG
1 TAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAAGTCCCATG
* * * * * *
42194694 TAAGACCATGTTTGGGACATGGCATGGGCACCAATATGAGAACTCCCATG
1 TAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAAGTCCCATG
* * * *
42194744 TAAGACCATATCTGGGATATGGCATTGGCGGTAC-A-A-GA-AACATCCCATG
1 TAAGACCATGTCTGGGACATGGCATTGGC-AT-CGAGATGAGAA-GTCCCATG
* *
42194793 TAAGACCATGTCTGGGACATGACTTTGGCAT
1 TAAGACCATGTCTGGGACATGGCATTGGCAT
42194824 GTTATTATCA
Statistics
Matches: 149, Mismatches: 28, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
48 3 0.02
49 34 0.23
50 78 0.52
51 1 0.01
52 2 0.01
53 2 0.01
56 29 0.19
ACGTcount: A:0.28, C:0.21, G:0.27, T:0.24
Consensus pattern (50 bp):
TAAGACCATGTCTGGGACATGGCATTGGCATCGAGATGAGAAGTCCCATG
Found at i:42203823 original size:9 final size:9
Alignment explanation
Indices: 42203809--42203839 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
42203799 TAACAATAAT
42203809 AAGAAAAGA
1 AAGAAAAGA
42203818 AAGAAAAGAA
1 AAGAAAAG-A
42203828 AAGAAAAGA
1 AAGAAAAGA
42203837 AAG
1 AAG
42203840 TAAATCACGA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 12 0.57
10 9 0.43
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (9 bp):
AAGAAAAGA
Found at i:42203839 original size:4 final size:5
Alignment explanation
Indices: 42203809--42203838 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
42203799 TAACAATAAT
42203809 AAGAA AAG-A AAGAA AAGAA AAGAA AAGAA A
1 AAGAA AAGAA AAGAA AAGAA AAGAA AAGAA A
42203839 GTAAATCACG
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAGAA
Found at i:42203839 original size:14 final size:15
Alignment explanation
Indices: 42203809--42203838 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
42203799 TAACAATAAT
42203809 AAGAAAAG-AAAGAA
1 AAGAAAAGAAAAGAA
42203823 AAGAAAAGAAAAGAA
1 AAGAAAAGAAAAGAA
42203838 A
1 A
42203839 GTAAATCACG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (15 bp):
AAGAAAAGAAAAGAA
Found at i:42207968 original size:252 final size:252
Alignment explanation
Indices: 42207523--42208025 Score: 918
Period size: 252 Copynumber: 2.0 Consensus size: 252
42207513 AGAGGGAATA
42207523 AAATTAACATTTCAGGCTTTGGGTTTTTGTAATATGGTACATCAAGAAGTGTTTACAAGCTCAAA
1 AAATTAACATTTCAGGCTTTGGGTTTTTGTAATATGGTACATCAAGAAGTGTTTACAAGCTCAAA
42207588 TTAGGTACTATGGGTGAATAACTAGAGGTAAGCTTTTTGGTTATGGATATGTTCCAAACAATGCC
66 TTAGGTACTATGGGTGAATAACTAGAGGTAAGCTTTTTGGTTATGGATATGTTCCAAACAATGCC
*
42207653 TTAGGTTATCCCTTAAGCATATCAATATGGACAAATTTAATCAACCAAACAAACTTAAATTAAAC
131 TTAGGTTATCCCTTAAGCATATCAATATGCACAAATTTAATCAACCAAACAAACTTAAATTAAAC
42207718 CATTTTTCATTCATACTAGCATG-TTTGTTTTCTTGTATTCCCTATATCATTTGGTAC
196 CATTTTTCATTCATACTAGCATGCTTTG-TTTCTTGTATTCCCTATATCATTTGGTAC
* *
42207775 AAATTAACATTTTAGGCTTTGGGTTTTTGTAATATGGTACATCAAGAAGTTTTTACAAGCTCAAA
1 AAATTAACATTTCAGGCTTTGGGTTTTTGTAATATGGTACATCAAGAAGTGTTTACAAGCTCAAA
* *
42207840 TTAGGTACTATGGGTGAATAAGTAGAGGTAAGCTTTTTGTTTATGGATATGTTCCAAACAATGCC
66 TTAGGTACTATGGGTGAATAACTAGAGGTAAGCTTTTTGGTTATGGATATGTTCCAAACAATGCC
* * *
42207905 TTAGGTTATCCCTTAAGCATCTCAATATGCACAAATTTAATCAACCGAACAAACTTAAATTAAAG
131 TTAGGTTATCCCTTAAGCATATCAATATGCACAAATTTAATCAACCAAACAAACTTAAATTAAAC
42207970 CATTTTTCATTCATACTAGCATGCTTTGTTTCTTGTATTCCCTATATCATTTGGTA
196 CATTTTTCATTCATACTAGCATGCTTTGTTTCTTGTATTCCCTATATCATTTGGTA
42208026 TAGTTGATTG
Statistics
Matches: 242, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
252 238 0.98
253 4 0.02
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (252 bp):
AAATTAACATTTCAGGCTTTGGGTTTTTGTAATATGGTACATCAAGAAGTGTTTACAAGCTCAAA
TTAGGTACTATGGGTGAATAACTAGAGGTAAGCTTTTTGGTTATGGATATGTTCCAAACAATGCC
TTAGGTTATCCCTTAAGCATATCAATATGCACAAATTTAATCAACCAAACAAACTTAAATTAAAC
CATTTTTCATTCATACTAGCATGCTTTGTTTCTTGTATTCCCTATATCATTTGGTAC
Found at i:42208471 original size:18 final size:18
Alignment explanation
Indices: 42208437--42208477 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 18
42208427 TCCTACATAG
42208437 AAAATCAAAAGAAAACTA
1 AAAATCAAAAGAAAACTA
42208455 CAAAA-CAAAA-AACAACTA
1 -AAAATCAAAAGAA-AACTA
42208473 AAAAT
1 AAAAT
42208478 TTATTTCTAC
Statistics
Matches: 20, Mismatches: 0, Indels: 5
0.80 0.00 0.20
Matches are distributed among these distances:
17 6 0.30
18 10 0.50
19 4 0.20
ACGTcount: A:0.73, C:0.15, G:0.02, T:0.10
Consensus pattern (18 bp):
AAAATCAAAAGAAAACTA
Found at i:42209600 original size:227 final size:228
Alignment explanation
Indices: 42209324--42209763 Score: 706
Period size: 227 Copynumber: 1.9 Consensus size: 228
42209314 CACACTATAG
*
42209324 GAATTATTGTAGGCTCTTCAGATGACAAAAAAAAATTGGTCCATTCTCTTTCTATTTTTGTTCTC
1 GAATTATTGTAGGCTCTTCAGATCACAAAAAAAAATTGGTCCATTCTCTTTCTATTTTTGTTCTC
* *
42209389 CCAAATTCCTTTACAATTCCTCATTAAAGGATCAAATTCC-TACTCTTGGATAAAAGTATACGGC
66 CAAAATTCCTTTACAATTCCTCATTAAAGGATCAAA-TCCTTACTCTTGGATAAAAGTATACGAC
42209453 TATAGTTGTGGCAAATATTTATCCA-TGTCACTTTCCTGGAATTCAATTGATAGACTTGAAGTGA
130 TATAGTTGTGGCAAATATTT-TCCACTGTCACTTTCCTGGAATTCAATTGATAGACTTGAAGTGA
*
42209517 TTACATTGAAACTTGCCATTGGAATTCAATTGATT
194 TTACATTGAAACTCGCCATTGGAATTCAATTGATT
* *
42209552 GAATTGTTGTAGGCTCTTCAGA-CAGAAAAAAAAATTGGTCCATTCTCTTTCTATTTTTGTTCTC
1 GAATTATTGTAGGCTCTTCAGATCACAAAAAAAAATTGGTCCATTCTCTTTCTATTTTTGTTCTC
* *
42209616 CAAAATTCTTTTACAATTCCTCATTAAAGGATCAAATCCTTTCTCTTGGATAAAAGTATACGACT
66 CAAAATTCCTTTACAATTCCTCATTAAAGGATCAAATCCTTACTCTTGGATAAAAGTATACGACT
* * * * * * *
42209681 ATAGTTGTTGTAAGTATTTTTCACTGTCATTTTCCTGGAATTCAATTGATGGACTTGAAGTGCTT
131 ATAGTTGTGGCAAATATTTTCCACTGTCACTTTCCTGGAATTCAATTGATAGACTTGAAGTGATT
42209746 ACATTGAAACTCGCCATT
196 ACATTGAAACTCGCCATT
42209764 CAATAATCTA
Statistics
Matches: 195, Mismatches: 15, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
226 6 0.03
227 168 0.86
228 21 0.11
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (228 bp):
GAATTATTGTAGGCTCTTCAGATCACAAAAAAAAATTGGTCCATTCTCTTTCTATTTTTGTTCTC
CAAAATTCCTTTACAATTCCTCATTAAAGGATCAAATCCTTACTCTTGGATAAAAGTATACGACT
ATAGTTGTGGCAAATATTTTCCACTGTCACTTTCCTGGAATTCAATTGATAGACTTGAAGTGATT
ACATTGAAACTCGCCATTGGAATTCAATTGATT
Found at i:42228219 original size:27 final size:27
Alignment explanation
Indices: 42228175--42228370 Score: 218
Period size: 27 Copynumber: 7.3 Consensus size: 27
42228165 AGAGACATGT
* *
42228175 GTAAAATAACCGATATACCCCCGAAGG
1 GTAAAATGACCGAAATACCCCCGAAGG
* * * * *
42228202 GTAATATAACCAAAATACTCTCGAAGG
1 GTAAAATGACCGAAATACCCCCGAAGG
42228229 GTAAAATGACCGAAATA-CCCCGAAGG
1 GTAAAATGACCGAAATACCCCCGAAGG
* **
42228255 GTAAAATGACCAAAATACCCCTAAAGG
1 GTAAAATGACCGAAATACCCCCGAAGG
* * *
42228282 GTAAAATGACCGGAACACCCTCGAAGG
1 GTAAAATGACCGAAATACCCCCGAAGG
* *
42228309 GT-AAATAACTGAAATACCCCCGAAGG
1 GTAAAATGACCGAAATACCCCCGAAGG
*
42228335 GTAAAATGATCGAAATACCCCC-ATAGG
1 GTAAAATGACCGAAATACCCCCGA-AGG
42228362 GTAAAATGA
1 GTAAAATGA
42228371 ATTTTATACC
Statistics
Matches: 139, Mismatches: 27, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
26 45 0.32
27 94 0.68
ACGTcount: A:0.43, C:0.22, G:0.19, T:0.16
Consensus pattern (27 bp):
GTAAAATGACCGAAATACCCCCGAAGG
Found at i:42228268 original size:53 final size:52
Alignment explanation
Indices: 42228175--42228368 Score: 219
Period size: 53 Copynumber: 3.6 Consensus size: 52
42228165 AGAGACATGT
* * * *
42228175 GTAAAATAACCGATATACCCCCGAAGGGTAATATAACCAAAATACTCTCGAAGG
1 GTAAAATGACCGAAATA-CCCCGAAGGGTAAAATAACCAAAATAC-CCCGAAGG
* *
42228229 GTAAAATGACCGAAATACCCCGAAGGGTAAAATGACCAAAATACCCCTAAAGG
1 GTAAAATGACCGAAATACCCCGAAGGGTAAAATAACCAAAATACCCC-GAAGG
* * **
42228282 GTAAAATGACCGGAACACCCTCGAAGGGT-AAATAACTGAAATACCCCCGAAGG
1 GTAAAATGACCGAAATACCC-CGAAGGGTAAAATAACCAAAATA-CCCCGAAGG
* *
42228335 GTAAAATGATCGAAATACCCCCATAGGGTAAAAT
1 GTAAAATGACCGAAATACCCCGA-AGGGTAAAAT
42228369 GAATTTTATA
Statistics
Matches: 119, Mismatches: 16, Indels: 10
0.82 0.11 0.07
Matches are distributed among these distances:
52 4 0.03
53 84 0.71
54 31 0.26
ACGTcount: A:0.43, C:0.22, G:0.19, T:0.16
Consensus pattern (52 bp):
GTAAAATGACCGAAATACCCCGAAGGGTAAAATAACCAAAATACCCCGAAGG
Found at i:42228282 original size:80 final size:80
Alignment explanation
Indices: 42228175--42228368 Score: 237
Period size: 80 Copynumber: 2.4 Consensus size: 80
42228165 AGAGACATGT
* * * * * * *
42228175 GTAAAATAACCGATATACCCCCGAAGGGTAATATAACCAAAATACTCTCGAAGGGTAAAATGACC
1 GTAAAATGACCGAAATACCCCCAAAGGGTAAAATAACCAAAACACCCTCGAAGGGT-AAATAACC
42228240 GAAATA-CCCCGAAGG
65 GAAATACCCCCGAAGG
* * * ** *
42228255 GTAAAATGACCAAAATACCCCTAAAGGGTAAAATGACCGGAACACCCTCGAAGGGTAAATAACTG
1 GTAAAATGACCGAAATACCCCCAAAGGGTAAAATAACCAAAACACCCTCGAAGGGTAAATAACCG
42228320 AAATACCCCCGAAGG
66 AAATACCCCCGAAGG
* *
42228335 GTAAAATGATCGAAATACCCCCATAGGGTAAAAT
1 GTAAAATGACCGAAATACCCCCAAAGGGTAAAAT
42228369 GAATTTTATA
Statistics
Matches: 96, Mismatches: 17, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
79 12 0.12
80 84 0.88
ACGTcount: A:0.43, C:0.22, G:0.19, T:0.16
Consensus pattern (80 bp):
GTAAAATGACCGAAATACCCCCAAAGGGTAAAATAACCAAAACACCCTCGAAGGGTAAATAACCG
AAATACCCCCGAAGG
Found at i:42234692 original size:20 final size:20
Alignment explanation
Indices: 42234667--42234745 Score: 70
Period size: 20 Copynumber: 4.0 Consensus size: 20
42234657 ATGTGACGTC
*
42234667 AGGGGCACCGAAGTGCAAAT
1 AGGGGCACAGAAGTGCAAAT
* * * *
42234687 AGGGGCATAGATGTGTAAAC
1 AGGGGCACAGAAGTGCAAAT
* *
42234707 AGGGGCAC-GAATGTGTAATT
1 AGGGGCACAGAA-GTGCAAAT
*
42234727 AGGGGCACAGATGTGCAAA
1 AGGGGCACAGAAGTGCAAA
42234746 CAGTGATACC
Statistics
Matches: 45, Mismatches: 12, Indels: 4
0.74 0.20 0.07
Matches are distributed among these distances:
19 2 0.04
20 41 0.91
21 2 0.04
ACGTcount: A:0.34, C:0.14, G:0.35, T:0.16
Consensus pattern (20 bp):
AGGGGCACAGAAGTGCAAAT
Found at i:42234696 original size:40 final size:40
Alignment explanation
Indices: 42234643--42234748 Score: 117
Period size: 40 Copynumber: 2.6 Consensus size: 40
42234633 CATAGATGCA
* **
42234643 AAATAGGGACATAGATGTG-ACGTCAGGGGCACCGAA-GTGC
1 AAATAGGGGCATAGATGTGTA-AACAGGGGCA-CGAATGTGC
*
42234683 AAATAGGGGCATAGATGTGTAAACAGGGGCACGAATGTGT
1 AAATAGGGGCATAGATGTGTAAACAGGGGCACGAATGTGC
* * *
42234723 AATTAGGGGCACAGATGTGCAAACAG
1 AAATAGGGGCATAGATGTGTAAACAG
42234749 TGATACCAAA
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
39 4 0.07
40 52 0.91
41 1 0.02
ACGTcount: A:0.35, C:0.14, G:0.34, T:0.17
Consensus pattern (40 bp):
AAATAGGGGCATAGATGTGTAAACAGGGGCACGAATGTGC
Found at i:42241695 original size:51 final size:51
Alignment explanation
Indices: 42241563--42241750 Score: 211
Period size: 51 Copynumber: 3.7 Consensus size: 51
42241553 GAAAGTGATG
* * * *
42241563 GTCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCAGA-A-TGATA
1 GTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTATCGGATAGTAATA
* *
42241612 GGTCACATGTGTAGTACTATGTGCAGGCTACTATGCGTATCGGATAGT-TTCA
1 -GTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTATCGGATAGTAAT-A
* * * * * *
42241664 ATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATGGGATGGTAATG
1 GTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTATCGGATAGTAATA
* *
42241715 GTCACATGTGTGGTACTATGTGCAGGCTACTGTGTG
1 GTCACATGTGTAGTACTATGTGCAGGCTACTATGTG
42241751 AACCAAACAT
Statistics
Matches: 116, Mismatches: 18, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
50 39 0.34
51 74 0.64
52 3 0.03
ACGTcount: A:0.23, C:0.16, G:0.29, T:0.32
Consensus pattern (51 bp):
GTCACATGTGTAGTACTATGTGCAGGCTACTATGTGTATCGGATAGTAATA
Found at i:42241918 original size:38 final size:37
Alignment explanation
Indices: 42241876--42241948 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 37
42241866 AGGTGTGGAA
*
42241876 TTGAATTGAATAT-TGACTTAGAAA-TGGAAAAGTGAATT
1 TTGAATTGAAT-TGTGA-TT-GAAAGTGAAAAAGTGAATT
42241914 TTGAATTGAATTGTGATTGAAAGTGAAAAAGTGAA
1 TTGAATTGAATTGTGATTGAAAGTGAAAAAGTGAA
42241949 ATTATGAAAG
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
36 4 0.12
37 14 0.44
38 14 0.44
ACGTcount: A:0.42, C:0.01, G:0.23, T:0.33
Consensus pattern (37 bp):
TTGAATTGAATTGTGATTGAAAGTGAAAAAGTGAATT
Found at i:42245277 original size:55 final size:55
Alignment explanation
Indices: 42245193--42245299 Score: 169
Period size: 55 Copynumber: 1.9 Consensus size: 55
42245183 AGACCATACC
* *
42245193 AATTTTTGTTTAATTCCCACCTTGATAACTTCCTAGGGTCGTCAAGCCTAAGGTT
1 AATTTTGGTTTAATTCCCACCTTAATAACTTCCTAGGGTCGTCAAGCCTAAGGTT
* **
42245248 AATTTTGGTTTAATTCCCACCTTAATAACTTCCTAGGTTTTTCAAGCCTAAG
1 AATTTTGGTTTAATTCCCACCTTAATAACTTCCTAGGGTCGTCAAGCCTAAG
42245300 TTTATTCTTT
Statistics
Matches: 47, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 47 1.00
ACGTcount: A:0.25, C:0.21, G:0.14, T:0.39
Consensus pattern (55 bp):
AATTTTGGTTTAATTCCCACCTTAATAACTTCCTAGGGTCGTCAAGCCTAAGGTT
Found at i:42254979 original size:2 final size:2
Alignment explanation
Indices: 42254974--42255000 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
42254964 TATATTTAAA
42254974 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 A
42255001 AAAGTGAGAA
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:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:42259368 original size:503 final size:503
Alignment explanation
Indices: 42258421--42259429 Score: 1653
Period size: 503 Copynumber: 2.0 Consensus size: 503
42258411 AGGAAAATAG
* * *
42258421 TAGTTCATTTTGGTATTCGATACCATTTCTCAAGTATCTATACTCGGGGTAAAAATACCGATACG
1 TAGTTCATTTTGGTATTCGATACCATTTCTCAAGTATCGATACTCGAGGTAAAAATACCGATACA
* *
42258486 TTTTGGATTTCTATCTATAATTGATGGGTTTTAGCTTTTGCAGAAAAATTGAATACTGATTTGAT
66 TTTTGGATTTCTATCTATAATTGATGGGTTTTAACTTTTGCAGAAAAATTGAATACTAATTTGAT
* *
42258551 ACTGATTTTTTGATCGGTATCGATACCATATATGAGAAATATCGATATCATTGAATTAGTATCGG
131 ACTGATTTTTTGATCGGTATCGATACCATATATGAGAAATATCGATACCATTGAATTAGTATCAG
**
42258616 TACCTACGTGATTTTTGATAATTTTTGTTAAGTGGTCTTAAAGCATGCTTTAAATTTGTTATAGA
196 TACCTACGTGATTTTTGATAATTTTTGTTAAGTGGAATTAAAGCATGCTTTAAATTTGTTATAGA
42258681 CTCATTTTTATGTATGTTTGGCATAACTTAATGTAACCTAGGGTATTCTTGGCTTGATATCTCTA
261 CTCATTTTTATGTATGTTTGGCATAACTTAATGTAACCTAGGGTATTCTTGGCTTGATATCTCTA
* *
42258746 TAATTGGTTCAAATTTGGTGACGTTTGCATTCTAGTGAGACTTTATGTGATGTGTGATGTTGTGA
326 TAATTGGTTCAAATTTGGTGACGTTTACATTCTAATGAGACTTTATGTGATGTGTGATGTTGTGA
* * ** *
42258811 CGGTGGTGTAGCGTCATGTTACTTGGGCTCAGTGACCGGGCTAAGTATAAGGTGTTACATTTCAT
391 CGGTGGTGTAGAGTCATGTTACTGGGGCTCAACGACCGGGCGAAGTATAAGGTGTTACATTTCAT
* *
42258876 GCATTATAAGATTATGGGAATGGTCAGCATTTTGAAACATGACTTGGT
456 GCATTATAAGATTATGAGAATGGTCAGCATTTTGAAAAATGACTTGGT
** *
42258924 TAGTTCATTTTGGTA-TCGATACCATTTCTTGAGTATCGATACTCGAGGTAGAAATACCGATACA
1 TAGTTCATTTTGGTATTCGATACCATTTCTCAAGTATCGATACTCGAGGTAAAAATACCGATACA
** *
42258988 TTTTTTATTTCTATCTATAATTGATGGGTTTTAACTTTTGCAGAAAAATTGAATACTAATTTGGT
66 TTTTGGATTTCTATCTATAATTGATGGGTTTTAACTTTTGCAGAAAAATTGAATACTAATTTGAT
*
42259053 ACTGATTTTTTTTATCGGTATCGATACCATATATGAGAAATATCGATACCATTGAATTAGTATCA
131 ACTGA-TTTTTTGATCGGTATCGATACCATATATGAGAAATATCGATACCATTGAATTAGTATCA
* * *
42259118 GTACCTATGTGATTTTTGATAATTTTTGTTAAGTGGAATTAAAGCATGCTTTTAATTTGTTATGG
195 GTACCTACGTGATTTTTGATAATTTTTGTTAAGTGGAATTAAAGCATGCTTTAAATTTGTTATAG
* **
42259183 GCTCATTTTTATGTATGTTTGGCATAACTTAATGTCGCCTAGGGTATTCTTGGCTTGGA-ATCTC
260 ACTCATTTTTATGTATGTTTGGCATAACTTAATGTAACCTAGGGTATTCTTGGCTT-GATATCTC
*
42259247 TATGATTGGTTCAAATTTGGTGACGTTTACATTCTAATGAGACTTTATGTGATGTGTGATGTTGT
324 TATAATTGGTTCAAATTTGGTGACGTTTACATTCTAATGAGACTTTATGTGATGTGTGATGTTGT
* **
42259312 GACGGTGGTGTAGAGTCATGTTACTGGGGCTCAACGACCGTGCGGGGTATAAGGTGTTACATTTC
389 GACGGTGGTGTAGAGTCATGTTACTGGGGCTCAACGACCGGGCGAAGTATAAGGTGTTACATTTC
**
42259377 ATGCATTATAAGATTATGAGAATGGTTGGCATTTTGAAAAATGACTTGGT
454 ATGCATTATAAGATTATGAGAATGGTCAGCATTTTGAAAAATGACTTGGT
42259427 TAG
1 TAG
42259430 GTAATGGATG
Statistics
Matches: 467, Mismatches: 37, Indels: 4
0.92 0.07 0.01
Matches are distributed among these distances:
502 108 0.23
503 357 0.76
504 2 0.00
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (503 bp):
TAGTTCATTTTGGTATTCGATACCATTTCTCAAGTATCGATACTCGAGGTAAAAATACCGATACA
TTTTGGATTTCTATCTATAATTGATGGGTTTTAACTTTTGCAGAAAAATTGAATACTAATTTGAT
ACTGATTTTTTGATCGGTATCGATACCATATATGAGAAATATCGATACCATTGAATTAGTATCAG
TACCTACGTGATTTTTGATAATTTTTGTTAAGTGGAATTAAAGCATGCTTTAAATTTGTTATAGA
CTCATTTTTATGTATGTTTGGCATAACTTAATGTAACCTAGGGTATTCTTGGCTTGATATCTCTA
TAATTGGTTCAAATTTGGTGACGTTTACATTCTAATGAGACTTTATGTGATGTGTGATGTTGTGA
CGGTGGTGTAGAGTCATGTTACTGGGGCTCAACGACCGGGCGAAGTATAAGGTGTTACATTTCAT
GCATTATAAGATTATGAGAATGGTCAGCATTTTGAAAAATGACTTGGT
Found at i:42260190 original size:72 final size:72
Alignment explanation
Indices: 42260099--42260238 Score: 280
Period size: 72 Copynumber: 1.9 Consensus size: 72
42260089 TTATAACTGG
42260099 TTATATTAATAATTTCGGTAAAATATGTATAATTAATTTTTTTGTATGAATCACATTCATATTTT
1 TTATATTAATAATTTCGGTAAAATATGTATAATTAATTTTTTTGTATGAATCACATTCATATTTT
42260164 AATAATT
66 AATAATT
42260171 TTATATTAATAATTTCGGTAAAATATGTATAATTAATTTTTTTGTATGAATCACATTCATATTTT
1 TTATATTAATAATTTCGGTAAAATATGTATAATTAATTTTTTTGTATGAATCACATTCATATTTT
42260236 AAT
66 AAT
42260239 TTTATCAATG
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 68 1.00
ACGTcount: A:0.37, C:0.06, G:0.07, T:0.50
Consensus pattern (72 bp):
TTATATTAATAATTTCGGTAAAATATGTATAATTAATTTTTTTGTATGAATCACATTCATATTTT
AATAATT
Found at i:42263685 original size:24 final size:24
Alignment explanation
Indices: 42263658--42263704 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
42263648 AAAAAAACAC
42263658 TTAGTTTATTATCTTATTACCATA
1 TTAGTTTATTATCTTATTACCATA
42263682 TTAGTTTATTATCTTATTACCAT
1 TTAGTTTATTATCTTATTACCAT
42263705 TCATATTTCT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.28, C:0.13, G:0.04, T:0.55
Consensus pattern (24 bp):
TTAGTTTATTATCTTATTACCATA
Found at i:42275129 original size:32 final size:32
Alignment explanation
Indices: 42275083--42275150 Score: 95
Period size: 32 Copynumber: 2.1 Consensus size: 32
42275073 CATCTTTTGT
42275083 TTAATTAACATTTAACATAATTATCA-AATTAC-
1 TTAATTAACATTTAA-A-AATTATCATAATTACA
*
42275115 TTAATTAACCTTTAAAAATTATCATAATTACA
1 TTAATTAACATTTAAAAATTATCATAATTACA
42275147 TTAA
1 TTAA
42275151 AACCTATCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 4
0.87 0.03 0.11
Matches are distributed among these distances:
30 8 0.24
31 7 0.21
32 18 0.55
ACGTcount: A:0.47, C:0.12, G:0.00, T:0.41
Consensus pattern (32 bp):
TTAATTAACATTTAAAAATTATCATAATTACA
Found at i:42275329 original size:13 final size:13
Alignment explanation
Indices: 42275311--42275346 Score: 63
Period size: 13 Copynumber: 2.8 Consensus size: 13
42275301 ACTTAAACAT
*
42275311 CAAAATTTCTTAA
1 CAAAATTTCATAA
42275324 CAAAATTTCATAA
1 CAAAATTTCATAA
42275337 CAAAATTTCA
1 CAAAATTTCA
42275347 ATATGAACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (13 bp):
CAAAATTTCATAA
Found at i:42279283 original size:56 final size:51
Alignment explanation
Indices: 42279217--42279409 Score: 210
Period size: 50 Copynumber: 3.7 Consensus size: 51
42279207 GGGGATGAGA
* **
42279217 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGGTTATGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGC---ACCGA-G-TATGAGAGG
* **
42279273 TCCCACGTAAGACCATGTCTTGGACATGGGGTTGGCACCGAG-ATGAGAGG
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGTATGAGAGG
* * * **
42279323 TCCCCCGTAAGACTATGTCTGGGACATGGCATGGGCACCGA-TATGAGAAC
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGTATGAGAGG
* *
42279373 TCCCACGTAAGACCATATCTGGGATATGGCATTGGCA
1 TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCA
42279410 GTACAAGAAA
Statistics
Matches: 117, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
50 81 0.69
52 1 0.01
53 3 0.03
56 32 0.27
ACGTcount: A:0.25, C:0.22, G:0.30, T:0.23
Consensus pattern (51 bp):
TCCCACGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGTATGAGAGG
Found at i:42285647 original size:25 final size:25
Alignment explanation
Indices: 42285619--42285666 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
42285609 GAGATTGTCG
42285619 TTATTCAGCTCGGAGGAGCTTACCT
1 TTATTCAGCTCGGAGGAGCTTACCT
* *
42285644 TTATTCAGCTTGGAGGAGTTTAC
1 TTATTCAGCTCGGAGGAGCTTAC
42285667 TGTTTATAGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.21, C:0.19, G:0.25, T:0.35
Consensus pattern (25 bp):
TTATTCAGCTCGGAGGAGCTTACCT
Found at i:42299401 original size:9 final size:9
Alignment explanation
Indices: 42299387--42299471 Score: 107
Period size: 9 Copynumber: 9.4 Consensus size: 9
42299377 TTTGGTTAAA
*
42299387 AATTAACTG
1 AATTAACCG
*
42299396 AATTAATCG
1 AATTAACCG
42299405 AATTAACCG
1 AATTAACCG
*
42299414 AATTACCCG
1 AATTAACCG
42299423 AATTAACCG
1 AATTAACCG
*
42299432 AATTAACCA
1 AATTAACCG
* *
42299441 AATTACCCA
1 AATTAACCG
*
42299450 AATTACCCG
1 AATTAACCG
42299459 AATTAACCG
1 AATTAACCG
42299468 AATT
1 AATT
42299472 GAATCACTAC
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
9 67 1.00
ACGTcount: A:0.44, C:0.22, G:0.08, T:0.26
Consensus pattern (9 bp):
AATTAACCG
Found at i:42299418 original size:27 final size:27
Alignment explanation
Indices: 42299395--42299471 Score: 118
Period size: 27 Copynumber: 2.9 Consensus size: 27
42299385 AAAATTAACT
*
42299395 GAATTAATCGAATTAACCGAATTACCC
1 GAATTAACCGAATTAACCGAATTACCC
*
42299422 GAATTAACCGAATTAACCAAATTACCC
1 GAATTAACCGAATTAACCGAATTACCC
* *
42299449 AAATTACCCGAATTAACCGAATT
1 GAATTAACCGAATTAACCGAATT
42299472 GAATCACTAC
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 45 1.00
ACGTcount: A:0.43, C:0.23, G:0.09, T:0.25
Consensus pattern (27 bp):
GAATTAACCGAATTAACCGAATTACCC
Found at i:42299639 original size:18 final size:18
Alignment explanation
Indices: 42299616--42299659 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
42299606 ATTTTTTATG
*
42299616 ATTGGGTTGGGTTGGGTA
1 ATTGGGTTGGGTTGGATA
42299634 ATTGGGTTGGGTTGGATA
1 ATTGGGTTGGGTTGGATA
*
42299652 CTTGGGTT
1 ATTGGGTT
42299660 TGGATTGAGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.11, C:0.02, G:0.45, T:0.41
Consensus pattern (18 bp):
ATTGGGTTGGGTTGGATA
Found at i:42306338 original size:29 final size:29
Alignment explanation
Indices: 42306290--42306360 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
42306280 TAAAAATTTT
* *
42306290 AAAAAATAAATCAGGGTTTAGAGTTTTAA
1 AAAAAATAAATTAGGGTTTAGAGGTTTAA
* *
42306319 AAAAAATAAATTAGGTTTTAGGGGTTTAA
1 AAAAAATAAATTAGGGTTTAGAGGTTTAA
* *
42306348 AATAAATTAATTA
1 AAAAAATAAATTA
42306361 AATTAGGATT
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
29 36 1.00
ACGTcount: A:0.49, C:0.01, G:0.15, T:0.34
Consensus pattern (29 bp):
AAAAAATAAATTAGGGTTTAGAGGTTTAA
Found at i:42306365 original size:34 final size:33
Alignment explanation
Indices: 42306325--42306407 Score: 94
Period size: 34 Copynumber: 2.5 Consensus size: 33
42306315 TTAAAAAAAA
42306325 TAAATTAGGTTTTAGGGGTTTAAAATAAATTAAT
1 TAAATTAGGTTTTAGGGGTTTAAAA-AAATTAAT
* * ** *
42306359 TAAATTAGGATTTAAAGTTTTTAAGAAAATTAAT
1 TAAATTAGG-TTTTAGGGGTTTAAAAAAATTAAT
*
42306393 TAAATTAGGGTTTAG
1 TAAATTAGGTTTTAG
42306408 TTTTTTTTAA
Statistics
Matches: 40, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
33 3 0.08
34 26 0.65
35 11 0.28
ACGTcount: A:0.42, C:0.00, G:0.17, T:0.41
Consensus pattern (33 bp):
TAAATTAGGTTTTAGGGGTTTAAAAAAATTAAT
Found at i:42306738 original size:126 final size:126
Alignment explanation
Indices: 42306513--42306902 Score: 565
Period size: 124 Copynumber: 3.1 Consensus size: 126
42306503 GTTTTATTTG
* * * * *
42306513 CTACAGTAGTTTCAGAAAAATTAATTTTGAGAAGACGTTTCTGAAAAAATAATGTCAAAAACGCT
1 CTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAAACGCT
* *
42306578 TCAAGCAGGATGTACTGTCAGCAAAATTACTGAAAAAAGCTCTCATATGGACGCTCCTTTT
66 TCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCTCATATGGACGCTCTTTTT
*
42306639 CTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGATGGTTCTGAAAAAATAGTGTCAAAAACGCT
1 CTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAAACGCT
*
42306704 TCAATCAGGATGCACTGTCAGCAAAATTACTGAAAAAA-CTCCTACATA--GACGCTCTTTTT
66 TCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCT-CT-CATATGGACGCTCTTTTT
* *
42306764 CTACAGTAGTTCCT-AAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTAAAAAATGCT
1 CTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAAACGCT
* * * ** **
42306828 TTAAGCAGGATGCACTGTCAACAAAATTACTGAAAAAAGCTCCCACGTGGACAAT-TTTTT
66 TCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCTCATATGGACGCTCTTTTT
42306888 CTACAGTAGTTCCTG
1 CTACAGTAGTTCCTG
42306903 CTTGGCCTTA
Statistics
Matches: 238, Mismatches: 20, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
123 2 0.01
124 102 0.43
125 33 0.14
126 97 0.41
127 4 0.02
ACGTcount: A:0.38, C:0.17, G:0.17, T:0.28
Consensus pattern (126 bp):
CTACAGTAGTTCCTGAAAAAATAATTTTGAGAAGACGGTTCTGAAAAAATAGTGTCAAAAACGCT
TCAAGCAGGATGCACTGTCAGCAAAATTACTGAAAAAAGCTCTCATATGGACGCTCTTTTT
Found at i:42313285 original size:19 final size:19
Alignment explanation
Indices: 42313254--42313291 Score: 51
Period size: 19 Copynumber: 2.0 Consensus size: 19
42313244 GACATACAAT
*
42313254 TGTACAAAATTAAATTTTA
1 TGTACAAAATTAAAATTTA
42313273 TGTA-AAAATTTAAAATTTA
1 TGTACAAAA-TTAAAATTTA
42313292 CCAGATTAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
19 13 0.76
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (19 bp):
TGTACAAAATTAAAATTTA
Found at i:42316678 original size:51 final size:52
Alignment explanation
Indices: 42316570--42316681 Score: 131
Period size: 54 Copynumber: 2.1 Consensus size: 52
42316560 AAACGTGTTG
*
42316570 TTAATAATAAAAATTATTGAAAAATATTATTAAATATTTAATTCAAATATTTTT
1 TTAATAATAAAAATGATTGAAAAATATTA-TAAATATTTAATT-AAATATTTTT
* * *
42316624 TTAATAATAAAAATGATTG-AAAATGTTA-AAATATATTAATT-TATCTTTTAT
1 TTAATAATAAAAATGATTGAAAAATATTATAAATAT-TTAATTAAATATTTT-T
42316675 TTAATAA
1 TTAATAA
42316682 GGATAAATTT
Statistics
Matches: 52, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
50 6 0.12
51 14 0.27
52 6 0.12
53 8 0.15
54 18 0.35
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.46
Consensus pattern (52 bp):
TTAATAATAAAAATGATTGAAAAATATTATAAATATTTAATTAAATATTTTT
Found at i:42322104 original size:17 final size:16
Alignment explanation
Indices: 42322084--42322117 Score: 50
Period size: 17 Copynumber: 2.1 Consensus size: 16
42322074 TTTAAGATTG
42322084 AAAAGGAAAGAAGAAGA
1 AAAAGGAAAGAA-AAGA
*
42322101 AAAAGGAGAGAAAAGA
1 AAAAGGAAAGAAAAGA
42322117 A
1 A
42322118 TAAACATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (16 bp):
AAAAGGAAAGAAAAGA
Found at i:42328208 original size:54 final size:54
Alignment explanation
Indices: 42328106--42328209 Score: 136
Period size: 54 Copynumber: 1.9 Consensus size: 54
42328096 CTATGGCAAA
* * * * * *
42328106 AAGACTATATAGTGTAAGACCTAGTCTGGGATTATGGCATCATATGGGGATAAG
1 AAGACCATATAGTGTAAGACCTAATCTAGAACTATGCCATCATATGGGGATAAG
* *
42328160 AAGACCATATAGTGTAAGACCTAATCTAGAACTATGCCGTCATGTGGGGA
1 AAGACCATATAGTGTAAGACCTAATCTAGAACTATGCCATCATATGGGGA
42328210 AAAAGATAAA
Statistics
Matches: 42, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
54 42 1.00
ACGTcount: A:0.34, C:0.14, G:0.26, T:0.26
Consensus pattern (54 bp):
AAGACCATATAGTGTAAGACCTAATCTAGAACTATGCCATCATATGGGGATAAG
Found at i:42331525 original size:39 final size:37
Alignment explanation
Indices: 42331458--42331550 Score: 98
Period size: 39 Copynumber: 2.5 Consensus size: 37
42331448 ACCAGAATGG
* *
42331458 CACCCAGTGCCTCATCGGATAGTTCGAAGCAATAGTTGA
1 CACCCAGTGCCTCATCGGAAAGTCCGAAG-AA-AGTTGA
* *
42331497 CACCCAGTGTCTCATCGGCAAAG-CCGAAGAAAGTTGG
1 CACCCAGTGCCTCATCGG-AAAGTCCGAAGAAAGTTGA
* *
42331534 TACCCAGTACCTCATCG
1 CACCCAGTGCCTCATCG
42331551 AATCTATCCG
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
37 19 0.41
38 2 0.04
39 22 0.48
40 3 0.07
ACGTcount: A:0.28, C:0.29, G:0.23, T:0.20
Consensus pattern (37 bp):
CACCCAGTGCCTCATCGGAAAGTCCGAAGAAAGTTGA
Found at i:42331745 original size:24 final size:26
Alignment explanation
Indices: 42331708--42331762 Score: 71
Period size: 24 Copynumber: 2.2 Consensus size: 26
42331698 TTCAATCACA
*
42331708 ATTTCTCACACTTTCAATTCAATCATT
1 ATTTCTCACACTTTCAA-TCAATAATT
42331735 -TTTC-CAC-CTTTCAATCAATAATT
1 ATTTCTCACACTTTCAATCAATAATT
42331758 ATTTC
1 ATTTC
42331763 ACAAATTCAC
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
23 8 0.31
24 11 0.42
25 3 0.12
26 4 0.15
ACGTcount: A:0.29, C:0.25, G:0.00, T:0.45
Consensus pattern (26 bp):
ATTTCTCACACTTTCAATCAATAATT
Found at i:42332884 original size:14 final size:14
Alignment explanation
Indices: 42332865--42332910 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
42332855 TTTTTTTATT
42332865 ATAATAATAATTTA
1 ATAATAATAATTTA
*
42332879 ATAATACTAATTTA
1 ATAATAATAATTTA
42332893 ATAATAATAATTTA
1 ATAATAATAATTTA
42332907 ATAA
1 ATAA
42332911 CATTTTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAATAATAATTTA
Found at i:42337780 original size:21 final size:21
Alignment explanation
Indices: 42337738--42337780 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
42337728 TTCAGTATAC
*
42337738 ATTCTTTCATCAGTATCATTT
1 ATTCTTTCATCAGCATCATTT
*
42337759 ATTCTTTCTTCAGACATC-TTT
1 ATTCTTTCATCAG-CATCATTT
42337780 A
1 A
42337781 ATTTATAAAC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 16 0.84
22 3 0.16
ACGTcount: A:0.23, C:0.21, G:0.05, T:0.51
Consensus pattern (21 bp):
ATTCTTTCATCAGCATCATTT
Found at i:42339350 original size:6 final size:6
Alignment explanation
Indices: 42339339--42339378 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
42339329 CACTTCACCT
* * *
42339339 TACTAA TACTAA TAATAA TATTAA TACTAA TATTAA TACT
1 TACTAA TACTAA TACTAA TACTAA TACTAA TACTAA TACT
42339379 TACCTCACAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (6 bp):
TACTAA
Found at i:42339365 original size:18 final size:18
Alignment explanation
Indices: 42339342--42339376 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
42339332 TTCACCTTAC
42339342 TAATACTAATAATAATAT
1 TAATACTAATAATAATAT
*
42339360 TAATACTAATATTAATA
1 TAATACTAATAATAATA
42339377 CTTACCTCAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (18 bp):
TAATACTAATAATAATAT
Found at i:42339377 original size:12 final size:12
Alignment explanation
Indices: 42339339--42339378 Score: 62
Period size: 12 Copynumber: 3.3 Consensus size: 12
42339329 CACTTCACCT
*
42339339 TACTAATACTAA
1 TACTAATATTAA
*
42339351 TAATAATATTAA
1 TACTAATATTAA
42339363 TACTAATATTAA
1 TACTAATATTAA
42339375 TACT
1 TACT
42339379 TACCTCACAT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.50, C:0.10, G:0.00, T:0.40
Consensus pattern (12 bp):
TACTAATATTAA
Found at i:42340423 original size:5 final size:5
Alignment explanation
Indices: 42340415--42340481 Score: 79
Period size: 5 Copynumber: 14.2 Consensus size: 5
42340405 TATTTAATTT
* * *
42340415 ATATA ATATA AAACA ATATA ATATA ATATA ATATA ATAT- ATATT ATATA
1 ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA ATATA
42340464 ATA-A A-ATA ATAT- ATATA A
1 ATATA ATATA ATATA ATATA A
42340482 AACATAAAAA
Statistics
Matches: 53, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
3 1 0.02
4 12 0.23
5 40 0.75
ACGTcount: A:0.61, C:0.01, G:0.00, T:0.37
Consensus pattern (5 bp):
ATATA
Found at i:42340461 original size:7 final size:7
Alignment explanation
Indices: 42340414--42340478 Score: 51
Period size: 7 Copynumber: 8.9 Consensus size: 7
42340404 CTATTTAATT
42340414 TATATAA
1 TATATAA
*
42340421 TATAAAA
1 TATATAA
*
42340428 CAATATAA
1 -TATATAA
42340436 TATA-ATA
1 TATATA-A
42340443 TAATATAA
1 T-ATATAA
*
42340451 TATATAT
1 TATATAA
42340458 TATATAA
1 TATATAA
*
42340465 TAAAATAA
1 T-ATATAA
42340473 TATATA
1 TATATA
42340479 TAAAACATAA
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
6 1 0.02
7 27 0.60
8 16 0.36
9 1 0.02
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (7 bp):
TATATAA
Found at i:42340479 original size:22 final size:22
Alignment explanation
Indices: 42340413--42340479 Score: 75
Period size: 22 Copynumber: 3.0 Consensus size: 22
42340403 TCTATTTAAT
* *
42340413 TTATATAATATAA-AACA-ATA
1 TTATATAATAAAATAATATATA
*
42340433 TAATATAATATAATATAATATATA
1 TTATATAATA-AA-ATAATATATA
42340457 TTATATAATAAAATAATATATA
1 TTATATAATAAAATAATATATA
42340479 T
1 T
42340480 AAAACATAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
20 9 0.23
21 1 0.03
22 12 0.31
23 5 0.13
24 12 0.31
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.40
Consensus pattern (22 bp):
TTATATAATAAAATAATATATA
Found at i:42342848 original size:54 final size:53
Alignment explanation
Indices: 42342782--42342898 Score: 137
Period size: 54 Copynumber: 2.2 Consensus size: 53
42342772 GGTTACATGT
* * *
42342782 TCTAAGACCGTGTGAAA-ATTTGAAGCCATGTAAGGTGGAGTCACATAGTCGTGTA
1 TCTAA-ACCGTGT-AAATA-TTGAAGCCATATAAGCTGGAGTCACACAGTCGTGTA
* *
42342837 TCTAAACCGTGTAACTCATTGAAGCCATATAAGCTGGAGTCATACAGTCGTGTA
1 TCTAAACCGTGTAAAT-ATTGAAGCCATATAAGCTGGAGTCACACAGTCGTGTA
*
42342891 TCCAAACC
1 TCTAAACC
42342899 ATATAACTCA
Statistics
Matches: 54, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
53 2 0.04
54 46 0.85
55 6 0.11
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.26
Consensus pattern (53 bp):
TCTAAACCGTGTAAATATTGAAGCCATATAAGCTGGAGTCACACAGTCGTGTA
Found at i:42342906 original size:54 final size:54
Alignment explanation
Indices: 42342801--42342908 Score: 153
Period size: 54 Copynumber: 2.0 Consensus size: 54
42342791 GTGTGAAAAT
* * * * * *
42342801 TTGAAGCCATGTAAGGTGGAGTCACATAGTCGTGTATCTAAACCGTGTAACTCA
1 TTGAAGCCATATAAGCTGGAGTCACACAGTCGTGTATCCAAACCATATAACTCA
*
42342855 TTGAAGCCATATAAGCTGGAGTCATACAGTCGTGTATCCAAACCATATAACTCA
1 TTGAAGCCATATAAGCTGGAGTCACACAGTCGTGTATCCAAACCATATAACTCA
42342909 CTAAGATTGT
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.32, C:0.20, G:0.20, T:0.27
Consensus pattern (54 bp):
TTGAAGCCATATAAGCTGGAGTCACACAGTCGTGTATCCAAACCATATAACTCA
Found at i:42345676 original size:17 final size:19
Alignment explanation
Indices: 42345648--42345688 Score: 61
Period size: 17 Copynumber: 2.3 Consensus size: 19
42345638 ATTTTACAAC
42345648 AATTATACATTTAA-AAAT
1 AATTATACATTTAATAAAT
42345666 AATTATA-ATTTAATAAAT
1 AATTATACATTTAATAAAT
42345684 -ATTAT
1 AATTAT
42345689 GATAATTACA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.50
18 11 0.50
ACGTcount: A:0.54, C:0.02, G:0.00, T:0.44
Consensus pattern (19 bp):
AATTATACATTTAATAAAT
Found at i:42345714 original size:27 final size:26
Alignment explanation
Indices: 42345664--42345715 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
42345654 ACATTTAAAA
*
42345664 ATAATTATAATTTAATAAATATTATG
1 ATAATTACAATTTAATAAATATTATG
42345690 ATAATTACATATTTAA-AAATAATTAT
1 ATAATTACA-ATTTAATAAAT-ATTAT
42345716 AATTATAATT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (26 bp):
ATAATTACAATTTAATAAATATTATG
Found at i:42346689 original size:12 final size:11
Alignment explanation
Indices: 42346665--42346703 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
42346655 TAATAATTAC
42346665 TAATTTTTTTA
1 TAATTTTTTTA
42346676 TAATTTTTTCTA
1 TAATTTTTT-TA
42346688 T-ATATTTTTTA
1 TAAT-TTTTTTA
42346699 TAATT
1 TAATT
42346704 ATCTAAAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.28, C:0.03, G:0.00, T:0.69
Consensus pattern (11 bp):
TAATTTTTTTA
Found at i:42346708 original size:21 final size:19
Alignment explanation
Indices: 42346657--42346709 Score: 54
Period size: 23 Copynumber: 2.6 Consensus size: 19
42346647 ATAATGACTA
42346657 ATAATTA-CTAATTTTTTT
1 ATAATTATCTAATTTTTTT
*
42346675 ATAATTTTTTCTATATATTTTTT
1 ATAA--TTATCTA-AT-TTTTTT
42346698 ATAATTATCTAA
1 ATAATTATCTAA
42346710 AAAGTTACAG
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
18 4 0.14
20 3 0.11
21 9 0.32
22 2 0.07
23 10 0.36
ACGTcount: A:0.34, C:0.06, G:0.00, T:0.60
Consensus pattern (19 bp):
ATAATTATCTAATTTTTTT
Found at i:42351035 original size:19 final size:19
Alignment explanation
Indices: 42351008--42351044 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
42350998 TAGCTTTCAA
*
42351008 TGAACATATAAATAAATAG
1 TGAAAATATAAATAAATAG
*
42351027 TGAAAATATATATAAATA
1 TGAAAATATAAATAAATA
42351045 ATTAACTAGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.59, C:0.03, G:0.08, T:0.30
Consensus pattern (19 bp):
TGAAAATATAAATAAATAG
Found at i:42353010 original size:21 final size:21
Alignment explanation
Indices: 42352977--42353022 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
42352967 CGGTCTGGCA
* *
42352977 ACACGAGCCTGTGGAGTAGCC
1 ACACGAGCATGTGGAGAAGCC
* *
42352998 ACACGGGCATGTGGGGAAGCC
1 ACACGAGCATGTGGAGAAGCC
42353019 ACAC
1 ACAC
42353023 AAACATGTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.26, C:0.28, G:0.35, T:0.11
Consensus pattern (21 bp):
ACACGAGCATGTGGAGAAGCC
Found at i:42353760 original size:25 final size:25
Alignment explanation
Indices: 42353721--42353819 Score: 117
Period size: 25 Copynumber: 3.9 Consensus size: 25
42353711 AAAGTCTTTT
** * *
42353721 CAGAGAATTTGCCACAAAGTCTTTA
1 CAGAGAATTCACCACAAAGGCTTCA
*
42353746 CAGAGAGTTCACCACAAAGGCTTCA
1 CAGAGAATTCACCACAAAGGCTTCA
* **
42353771 CAGAGCATTCATTACAAAGGCTTCA
1 CAGAGAATTCACCACAAAGGCTTCA
42353796 CTAGAGAATTCACCACAAAGGCTT
1 C-AGAGAATTCACCACAAAGGCTT
42353820 GGTTTCGTTT
Statistics
Matches: 61, Mismatches: 12, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
25 42 0.69
26 19 0.31
ACGTcount: A:0.36, C:0.24, G:0.17, T:0.22
Consensus pattern (25 bp):
CAGAGAATTCACCACAAAGGCTTCA
Found at i:42359345 original size:3 final size:3
Alignment explanation
Indices: 42359339--42359430 Score: 105
Period size: 3 Copynumber: 29.7 Consensus size: 3
42359329 GCTAATTAGT
*
42359339 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* * *
42359387 TTA TT- GTA TTTA TTA TTA TTA CATA CCTTA TTA TTA TTT TTA TT
1 TTA TTA TTA -TTA TTA TTA TTA -TTA --TTA TTA TTA TTA TTA TT
42359431 TACCCATTTA
Statistics
Matches: 77, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
2 1 0.01
3 69 0.90
4 4 0.05
5 3 0.04
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:42362131 original size:30 final size:28
Alignment explanation
Indices: 42362074--42362180 Score: 85
Period size: 30 Copynumber: 3.8 Consensus size: 28
42362064 ATCATATATT
*
42362074 TTAT-TATAATTTATATTATAATAATAG
1 TTATATATTATTTATATTATAATAATAG
* *
42362101 TTATATATGTATTTATATTTTTAGTAATAG
1 TTATATAT-TATTTATA-TTATAATAATAG
*
42362131 TTATATATTATATTAT-TAATAATATATTAG
1 TTATATATTAT-TTATATTATAATA-A-TAG
* * *
42362161 TAATATACTAATT-TATTATA
1 TTATATATTATTTATATTATA
42362181 TCAATTTAAG
Statistics
Matches: 63, Mismatches: 10, Indels: 12
0.74 0.12 0.14
Matches are distributed among these distances:
27 4 0.06
28 9 0.14
29 17 0.27
30 33 0.52
ACGTcount: A:0.41, C:0.01, G:0.05, T:0.53
Consensus pattern (28 bp):
TTATATATTATTTATATTATAATAATAG
Found at i:42362157 original size:19 final size:18
Alignment explanation
Indices: 42362133--42362181 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
42362123 AGTAATAGTT
42362133 ATATATTATATTATTAATA
1 ATATATTATATTA-TAATA
* *
42362152 ATATATTAGTAATATACTA
1 ATATATTA-TATTATAATA
*
42362171 ATTTATTATAT
1 ATATATTATAT
42362182 CAATTTAAGG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 2 0.08
19 19 0.76
20 4 0.16
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (18 bp):
ATATATTATATTATAATA
Found at i:42366473 original size:127 final size:126
Alignment explanation
Indices: 42366145--42366715 Score: 855
Period size: 127 Copynumber: 4.5 Consensus size: 126
42366135 GATAAAATTA
* * * * * *
42366145 AAGCAGGATGCT-TTATCAGAAGGATTTCT-AAAGTCGCGCCCACGTGTACGCGCTTTTGCTATA
1 AAGCAGGATGCTATT-TGAGAAGAATTTGTGAAA-TCGCGCCCTCGTGGACGCGCTTTTGCTACA
* * * *
42366208 GTAGGTCCTGGAAAAATAATTTCGAGTTGACGTTTTTGAGCTAATAGTAT-AAAAAATGCTTC
64 GTAGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAACGCTTC
*
42366270 AAGCAGGATGCT-TTATGAGAAGAAATTGTGAAATCGCG-CCTCGTGGACGCGCTTTTGCTACAG
1 AAGCAGGATGCTATT-TGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAG
*
42366333 TAGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGTAAATAGTTTAAAAAAACGCTTC
65 TAGGTCCTGGAA-AAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAACGCTTC
* * *
42366396 AAGCAGGATGCTATTTGAGAAGAATCTGTGAAATCGCACCCTCGTGGACGCGCTTTTGCTATAGT
1 AAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
42366461 AGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAACGCTTC
66 AGGTCCTGGAA-AAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAACGCTTC
* * * *
42366523 AAACAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGAGCTTTTACTACAAT
1 AAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
*
42366588 AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATGGTTTAAAAAAACGCTTC
66 AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAACGCTTC
* * *
42366649 TAGTAGGATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
42366714 AG
66 AG
42366716 CATGTTTGGG
Statistics
Matches: 409, Mismatches: 32, Indels: 9
0.91 0.07 0.02
Matches are distributed among these distances:
124 34 0.08
125 63 0.15
126 155 0.38
127 157 0.38
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (126 bp):
AAGCAGGATGCTATTTGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAACGCTTC
Found at i:42366605 original size:253 final size:251
Alignment explanation
Indices: 42366145--42366715 Score: 860
Period size: 253 Copynumber: 2.3 Consensus size: 251
42366135 GATAAAATTA
* * * * * * *
42366145 AAGCAGGATGCT-TTATCAGAAGGATTTCTAAAGTCGCGCCCACGTGTACGCGCTTTTGCTATAG
1 AAGCAGGATGCTATT-TGAGAAGAATCTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTATAG
* * * *
42366209 TAGGTCCTGGAAAAATAATTTCGAGTTGACGTTTTTGAGCTAATAGTATAAAAAATGCTTCAAGC
65 TAGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAAC
* * *
42366274 AGGATGCTTTATGAGAAGAAATTGTGAAATCGCGCCTCGTGGACGCGCTTTTGCTACAGTAGGTC
130 AGGATGCTTTATGAGAAGAAATTGTGAAATCGCGCCTCGTGGACGAGCTTTTACTACAATAGGTC
*
42366339 CTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGTAAATAGTTTAAAAAAACGCTTC
195 CTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAACGCTTC
* *
42366396 AAGCAGGATGCTATTTGAGAAGAATCTGTGAAATCGCACCCTCGTGGACGCGCTTTTGCTATAGT
1 AAGCAGGATGCTATTTGAGAAGAATCTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTATAGT
*
42366461 AGGTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAACGCTTCAAA
66 AGGTCCTGGAA-AAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTAT-AAAAAACGCTTCAAA
*
42366526 CAGGATGCTATT-TGAGAAGAATTTGTGAAATCGCGCCCTCGTGGACGAGCTTTTACTACAATAG
129 CAGGATGCT-TTATGAGAAGAAATTGTGAAATCGCG-CCTCGTGGACGAGCTTTTACTACAATAG
*
42366590 GTCCTGGAA-AAATAATTTCGAGTTGACGTTTCTGAGCAAATGGTTTAAAAAAACGCTTC
192 GTCCTGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAACGCTTC
* * * *
42366649 TAGTAGGATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
1 AAGCAGGATGCTATTTGAGAAGAATCTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTATAGT
42366714 AG
66 AG
42366716 CATGTTTGGG
Statistics
Matches: 289, Mismatches: 26, Indels: 8
0.89 0.08 0.02
Matches are distributed among these distances:
251 64 0.22
252 36 0.12
253 153 0.53
254 36 0.12
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (251 bp):
AAGCAGGATGCTATTTGAGAAGAATCTGTAAAATCGCGCCCTCGTGGACGCGCTTTTGCTATAGT
AGGTCCTGGAAAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTATAAAAAACGCTTCAAACA
GGATGCTTTATGAGAAGAAATTGTGAAATCGCGCCTCGTGGACGAGCTTTTACTACAATAGGTCC
TGGAAGAAATAATTTCGAGTTGACGTTTCTGAGCAAATAGTTTAAAAAAACGCTTC
Found at i:42369917 original size:114 final size:114
Alignment explanation
Indices: 42369786--42369995 Score: 411
Period size: 114 Copynumber: 1.8 Consensus size: 114
42369776 TATATCAAAT
*
42369786 TACCAGTCAAAACATTTTTTCAAATCTAACATTATGTGAATGTAAAATTATTAATTGATAATTGT
1 TACCAGTAAAAACATTTTTTCAAATCTAACATTATGTGAATGTAAAATTATTAATTGATAATTGT
42369851 ATTAATGGTTAGTAAAATTATCAAATTATATCAAATTATTAATTGTTAG
66 ATTAATGGTTAGTAAAATTATCAAATTATATCAAATTATTAATTGTTAG
42369900 TACCAGTAAAAACATTTTTTCAAATCTAACATTATGTGAATGTAAAATTATTAATTGATAATTGT
1 TACCAGTAAAAACATTTTTTCAAATCTAACATTATGTGAATGTAAAATTATTAATTGATAATTGT
42369965 ATTAATGGTTAGTAAAATTATCAAATTATAT
66 ATTAATGGTTAGTAAAATTATCAAATTATAT
42369996 TTAAGTTAAG
Statistics
Matches: 95, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
114 95 1.00
ACGTcount: A:0.42, C:0.08, G:0.10, T:0.41
Consensus pattern (114 bp):
TACCAGTAAAAACATTTTTTCAAATCTAACATTATGTGAATGTAAAATTATTAATTGATAATTGT
ATTAATGGTTAGTAAAATTATCAAATTATATCAAATTATTAATTGTTAG
Found at i:42370097 original size:43 final size:43
Alignment explanation
Indices: 42369995--42370691 Score: 864
Period size: 43 Copynumber: 16.1 Consensus size: 43
42369985 TCAAATTATA
42369995 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGG-TTAGGG-T
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
42370036 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* *
42370080 TTTAAGTTAAGGGTTAGGGTTTTAAAGTTAAAGGTTTAGGG-T
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
*
42370122 TTTAAGTTAAGGGTTAGGGTTTTAAAGTTAAGGG-TTAGGGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTA-GGGTT
* * *
42370165 TTAAAGTTAAGGGTTAGGGGTTTTAAAGTTAAGGGTTTAAGG--
1 TTTAAGTTAAGGGTTA-GGGTTTTTAAGTTAAGGGTTTAGGGTT
*
42370207 TTTAAGGGTTTAAGGTTTAAGGG-TTTTAAGTTAAGGG-TTAGGGTT
1 TTTAA--G-TTAAGGGTT-AGGGTTTTTAAGTTAAGGGTTTAGGGTT
* *
42370252 TTTAAGTTAAGGGTTTAGTGTTTTAAAGTTAA-GGTTTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* *
42370295 TTAAAGTTAAGGGTTAGGAGTTTTTAAGTTAAGGGTTTAAGGTT
1 TTTAAGTTAAGGGTTAGG-GTTTTTAAGTTAAGGGTTTAGGGTT
* * *
42370339 TTTAAGTTAAAGGTTTAGGGTTTTAAAGTTAAGAG-TTAGGGTT
1 TTTAAGTT-AAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* *
42370382 TTTAAGTTAAAGGTTAGTGTTTTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * *
42370425 TTAAAGTCAAGGGTTAGGATTTTTAAG-TAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* *
42370467 TTTAAGTTAAGAGTTTATGGTTTTTAAGTTAAGGGTTTAGGG-T
1 TTTAAGTTAAG-GGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* * * *
42370510 TTTACAGTCAAAGGTTAGGGTTTTTAAGTTAAGGGTTCATGGTT
1 TTTA-AGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
* *
42370554 TTTAACTTAAGGGTTTAGGGTTTTAAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
*
42370597 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAAGG-TTAGGGTT
1 TTTAAGTTAAGGG-TTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
42370640 TTTAAGTTAAGGGTTAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTT-A-----AGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
42370689 TTT
1 TTT
42370692 CAATTAAATT
Statistics
Matches: 572, Mismatches: 52, Indels: 56
0.84 0.08 0.08
Matches are distributed among these distances:
41 16 0.03
42 122 0.21
43 247 0.43
44 123 0.22
45 28 0.05
46 1 0.00
48 20 0.03
49 15 0.03
ACGTcount: A:0.26, C:0.01, G:0.31, T:0.42
Consensus pattern (43 bp):
TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTT
Found at i:42370195 original size:15 final size:15
Alignment explanation
Indices: 42370177--42370245 Score: 72
Period size: 15 Copynumber: 4.7 Consensus size: 15
42370167 AAAGTTAAGG
*
42370177 GTTAGGGGTTTTAAA
1 GTTAAGGGTTTTAAA
*
42370192 GTTAAGGG-TTTAAG
1 GTTAAGGGTTTTAAA
*
42370206 GTTTAAGGG-TTTAAG
1 G-TTAAGGGTTTTAAA
42370221 GTTTAAGGGTTTT-AA
1 G-TTAAGGGTTTTAAA
42370236 GTTAAGGGTT
1 GTTAAGGGTT
42370246 AGGGTTTTTA
Statistics
Matches: 49, Mismatches: 3, Indels: 5
0.86 0.05 0.09
Matches are distributed among these distances:
14 15 0.31
15 31 0.63
16 3 0.06
ACGTcount: A:0.26, C:0.00, G:0.33, T:0.41
Consensus pattern (15 bp):
GTTAAGGGTTTTAAA
Found at i:42370206 original size:8 final size:8
Alignment explanation
Indices: 42370193--42370232 Score: 66
Period size: 8 Copynumber: 5.2 Consensus size: 8
42370183 GGTTTTAAAG
42370193 TTAAGGGT
1 TTAAGGGT
42370201 TTAA-GGT
1 TTAAGGGT
42370208 TTAAGGGT
1 TTAAGGGT
42370216 TTAA-GGT
1 TTAAGGGT
42370223 TTAAGGGT
1 TTAAGGGT
42370231 TT
1 TT
42370233 TAAGTTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
7 14 0.47
8 16 0.53
ACGTcount: A:0.25, C:0.00, G:0.33, T:0.42
Consensus pattern (8 bp):
TTAAGGGT
Found at i:42370652 original size:15 final size:15
Alignment explanation
Indices: 42370634--42370682 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
42370624 GTTAAAGGTT
42370634 AGGGTTTTTAAGTTA
1 AGGGTTTTTAAGTTA
*
42370649 AGGG---TTAGGGTT-
1 AGGGTTTTTA-AGTTA
42370661 AGGGTTTTTAAGTTA
1 AGGGTTTTTAAGTTA
42370676 AGGGTTT
1 AGGGTTT
42370683 AGGGTTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 10
0.69 0.05 0.26
Matches are distributed among these distances:
12 7 0.26
13 3 0.11
14 3 0.11
15 14 0.52
ACGTcount: A:0.22, C:0.00, G:0.35, T:0.43
Consensus pattern (15 bp):
AGGGTTTTTAAGTTA
Found at i:42370672 original size:65 final size:63
Alignment explanation
Indices: 42369995--42370660 Score: 626
Period size: 64 Copynumber: 10.3 Consensus size: 63
42369985 TCAAATTATA
*
42369995 TTTAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGG-TTA-GGGTTTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTT-A-TTAAGGGTTTATGGTTTTTAAGTTAAGGGTTTAGGGTT
* * *
42370058 TTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGG-TTAGGGTTTTAAAGTTAAAGGTTTAGGG-
1 TTTAAGTTAAGGG-TTAGGGTTTTT-A-TTAAGGGTTTATGGTTTTTAAGTTAAGGGTTTAGGGT
42370121 T
63 T
* * *
42370122 TTTAAGTTAAGGGTTAGGGTTTTAAAGTTAAGGG-TTAGGGGTTTTAAAGTTAAGGG-TTAGGGG
1 TTTAAGTTAAGGGTTAGGGTTTT-TA-TTAAGGGTTTA-TGGTTTTTAAGTTAAGGGTTTA-GGG
42370185 TT
62 TT
* * * * *
42370187 TTAAAGTTAAGGGTTTAAGG-TTTAAGGGTTTAA-GGTTTAAGGGTTTTAAGTTAAGGG-TTAGG
1 TTTAAGTTAAGGG-TTAGGGTTTTTA----TTAAGGGTTTATGGTTTTTAAGTTAAGGGTTTAGG
42370249 GTT
61 GTT
* * * *
42370252 TTTAAGTTAAGGGTTTAGTGTTTTAAAGTTAA-GGTTTAGGGTTTTAAAGTTAAGGG-TTAGGAG
1 TTTAAGTTAAGGG-TTAGGGTTTT-TA-TTAAGGGTTTATGGTTTTTAAGTTAAGGGTTTAGG-G
42370315 TT
62 TT
* * * * *
42370317 TTTAAGTTAAGGGTTTAAGGTTTTTAAGTTAAAGGTTTAGGGTTTTAAAGTTAAGAG-TTAGGGT
1 TTTAAGTTAAGGG-TTAGGGTTTTT-A-TTAAGGGTTTATGGTTTTTAAGTTAAGGGTTTAGGGT
42370381 T
63 T
* * * * * *
42370382 TTTAAGTTAAAGGTTAGTGTTTTTAAGTTAAGGGTTTAGGGTTTTAAAGTCAAGGG-TTAGGATT
1 TTTAAGTTAAGGGTTAGGGTTTTT-A-TTAAGGGTTTATGGTTTTTAAGTTAAGGGTTTAGGGTT
*
42370446 TTTAAG-TAAGGGTTTAGGGTTTTTAAGTTAAGAGTTTATGGTTTTTAAGTTAAGGGTTTAGGG-
1 TTTAAGTTAAGGG-TTAGGGTTTTT-A-TTAAGGGTTTATGGTTTTTAAGTTAAGGGTTTAGGGT
42370509 T
63 T
* * * *
42370510 TTTACAGTCAAAGGTTAGGGTTTTTAAGTTAAGGGTTCATGGTTTTTAACTTAAGGGTTTAGGGT
1 TTTA-AGTTAAGGGTTAGGGTTTTT-A-TTAAGGGTTTATGGTTTTTAAGTTAAGGGTTTAGGGT
42370575 T
63 T
* * *
42370576 TTAAAGTTAAGGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAAGG-TTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTTTTT-A-TTAAGGGTTTATGGTTTTTAAGTTAAGGGTTTAGGGTT
42370640 TTTAAGTTAAGGGTTAGGGTT
1 TTTAAGTTAAGGGTTAGGGTT
42370661 AGGGTTTTTA
Statistics
Matches: 533, Mismatches: 49, Indels: 41
0.86 0.08 0.07
Matches are distributed among these distances:
63 43 0.08
64 212 0.40
65 205 0.38
66 64 0.12
67 9 0.02
ACGTcount: A:0.26, C:0.01, G:0.31, T:0.42
Consensus pattern (63 bp):
TTTAAGTTAAGGGTTAGGGTTTTTATTAAGGGTTTATGGTTTTTAAGTTAAGGGTTTAGGGTT
Found at i:42370677 original size:27 final size:28
Alignment explanation
Indices: 42370630--42370688 Score: 111
Period size: 27 Copynumber: 2.1 Consensus size: 28
42370620 TTAAGTTAAA
42370630 GGTTAGGGTTTTTAAGTTAAGGG-TTAG
1 GGTTAGGGTTTTTAAGTTAAGGGTTTAG
42370657 GGTTAGGGTTTTTAAGTTAAGGGTTTAG
1 GGTTAGGGTTTTTAAGTTAAGGGTTTAG
42370685 GGTT
1 GGTT
42370689 TTTCAATTAA
Statistics
Matches: 31, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 23 0.74
28 8 0.26
ACGTcount: A:0.20, C:0.00, G:0.37, T:0.42
Consensus pattern (28 bp):
GGTTAGGGTTTTTAAGTTAAGGGTTTAG
Found at i:42370698 original size:22 final size:22
Alignment explanation
Indices: 42369995--42370691 Score: 873
Period size: 22 Copynumber: 32.1 Consensus size: 22
42369985 TCAAATTATA
42369995 TTTAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
42370016 TTTAAGTTAAGGG-TTAGGG-T
1 TTTAAGTTAAGGGTTTAGGGTT
42370036 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
42370058 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
42370080 TTTAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
42370101 TTAAAGTTAAAGGTTTAGGG-T
1 TTTAAGTTAAGGGTTTAGGGTT
42370122 TTTAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
42370143 TTAAAGTTAAGGG-TTAGGGGTT
1 TTTAAGTTAAGGGTTTA-GGGTT
*
42370165 TTAAAGTTAAGGG-TTAGGGGTT
1 TTTAAGTTAAGGGTTTA-GGGTT
* *
42370187 TTAAAGTTAAGGGTTTAAGG--
1 TTTAAGTTAAGGGTTTAGGGTT
42370207 TTTAAGGGTTTAA-GGTTTAAGGG-T
1 TTTAA--G-TTAAGGGTTT-AGGGTT
42370231 TTTAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
42370252 TTTAAGTTAAGGGTTTAGTGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
42370274 TTAAAGTTAA-GGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
42370295 TTAAAGTTAAGGG-TTAGGAGTT
1 TTTAAGTTAAGGGTTTAGG-GTT
*
42370317 TTTAAGTTAAGGGTTTAAGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
42370339 TTTAAGTTAAAGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
42370361 TTAAAGTTAAGAG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
42370382 TTTAAGTTAAAGG-TTAGTGTT
1 TTTAAGTTAAGGGTTTAGGGTT
42370403 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* * *
42370425 TTAAAGTCAAGGG-TTAGGATT
1 TTTAAGTTAAGGGTTTAGGGTT
42370446 TTTAAG-TAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
* *
42370467 TTTAAGTTAAGAGTTTATGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
42370489 TTTAAGTTAAGGGTTTAGGG-T
1 TTTAAGTTAAGGGTTTAGGGTT
* *
42370510 TTTACAGTCAAAGG-TTAGGGTT
1 TTTA-AGTTAAGGGTTTAGGGTT
* *
42370532 TTTAAGTTAAGGGTTCATGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
42370554 TTTAACTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
42370576 TTAAAGTTAAGGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
42370597 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
*
42370619 TTTAAGTTAAAGG-TTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
42370640 TTTAAGTTAAGGGTTAGGGTTAGGGTT
1 TTTAAGTTAAGGG-T----TTAGGGTT
42370667 TTTAAGTTAAGGGTTTAGGGTT
1 TTTAAGTTAAGGGTTTAGGGTT
42370689 TTT
1 TTT
42370692 CAATTAAATT
Statistics
Matches: 598, Mismatches: 48, Indels: 59
0.85 0.07 0.08
Matches are distributed among these distances:
20 33 0.06
21 237 0.40
22 287 0.48
23 14 0.02
24 5 0.01
26 1 0.00
27 21 0.04
ACGTcount: A:0.26, C:0.01, G:0.31, T:0.42
Consensus pattern (22 bp):
TTTAAGTTAAGGGTTTAGGGTT
Found at i:42371256 original size:18 final size:18
Alignment explanation
Indices: 42371230--42371273 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
42371220 GACTCGAAAA
* *
42371230 AGGAAACATATAAGGGTT
1 AGGAAACATAAAAGGGAT
*
42371248 AGGATACATAAAAGGGAT
1 AGGAAACATAAAAGGGAT
42371266 AGGAAACA
1 AGGAAACA
42371274 CACCTGGCAT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.50, C:0.07, G:0.27, T:0.16
Consensus pattern (18 bp):
AGGAAACATAAAAGGGAT
Found at i:42371929 original size:7 final size:7
Alignment explanation
Indices: 42371919--42371943 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
42371909 TTATATACAT
42371919 AATACTA
1 AATACTA
42371926 AATACTA
1 AATACTA
42371933 AATACTA
1 AATACTA
42371940 AATA
1 AATA
42371944 TCAATCAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:42372138 original size:20 final size:20
Alignment explanation
Indices: 42372113--42372150 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
42372103 TTTATTTTTA
42372113 AAAATCT-ATATAATAATTGT
1 AAAATCTAATATAA-AATTGT
42372133 AAAATCTAATATAAAATT
1 AAAATCTAATATAAAATT
42372151 TACCTCGTTA
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:0.55, C:0.05, G:0.03, T:0.37
Consensus pattern (20 bp):
AAAATCTAATATAAAATTGT
Found at i:42373182 original size:11 final size:12
Alignment explanation
Indices: 42373165--42373197 Score: 50
Period size: 11 Copynumber: 2.8 Consensus size: 12
42373155 ATTTGGAAGG
42373165 AATTTGAGAGCA
1 AATTTGAGAGCA
*
42373177 AA-TTGAGAGGA
1 AATTTGAGAGCA
42373188 AATTTGAGAG
1 AATTTGAGAG
42373198 AGGATTAGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
11 10 0.53
12 9 0.47
ACGTcount: A:0.42, C:0.03, G:0.30, T:0.24
Consensus pattern (12 bp):
AATTTGAGAGCA
Found at i:42377924 original size:19 final size:19
Alignment explanation
Indices: 42377883--42377925 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 19
42377873 ATGATATTTT
* *
42377883 TTATTATTGATGTAATTAT
1 TTATTATTGATGTAAATAA
* *
42377902 TTATTATTTATTTAAATAA
1 TTATTATTGATGTAAATAA
42377921 TTATT
1 TTATT
42377926 TGCTTTAATT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.35, C:0.00, G:0.05, T:0.60
Consensus pattern (19 bp):
TTATTATTGATGTAAATAA
Found at i:42386327 original size:62 final size:62
Alignment explanation
Indices: 42386252--42386377 Score: 198
Period size: 62 Copynumber: 2.0 Consensus size: 62
42386242 GGCCATGTAG
* * * * *
42386252 GATTTTATTGATGATTTATTAAGGATTTTTCAAATATATCCAAACCCTTGTGTGTATTGTTA
1 GATTTTATCGATGATTTATTAAGAATTTTTCAAATATATCCAAACCCCTATGTATATTGTTA
*
42386314 GATTTTATCGATGATTTATTAATAATTTTTCAAATATATCCAAACCCCTATGTATATTGTTA
1 GATTTTATCGATGATTTATTAAGAATTTTTCAAATATATCCAAACCCCTATGTATATTGTTA
42386376 GA
1 GA
42386378 ACATAATAGA
Statistics
Matches: 58, Mismatches: 6, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
62 58 1.00
ACGTcount: A:0.32, C:0.11, G:0.12, T:0.45
Consensus pattern (62 bp):
GATTTTATCGATGATTTATTAAGAATTTTTCAAATATATCCAAACCCCTATGTATATTGTTA
Found at i:42391878 original size:12 final size:12
Alignment explanation
Indices: 42391858--42391893 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
42391848 AAATCTATGT
*
42391858 CAATGCTTAAAA
1 CAATACTTAAAA
*
42391870 CAATTCTTAAAA
1 CAATACTTAAAA
42391882 CAATACTTAAAA
1 CAATACTTAAAA
42391894 AACTTTGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.53, C:0.17, G:0.03, T:0.28
Consensus pattern (12 bp):
CAATACTTAAAA
Found at i:42395211 original size:39 final size:39
Alignment explanation
Indices: 42395148--42395268 Score: 206
Period size: 39 Copynumber: 3.1 Consensus size: 39
42395138 TTAAGTGTAG
42395148 TATCCGCTGAGTTTCGTTCTGGAAATCATATCCAAATAC
1 TATCCGCTGAGTTTCGTTCTGGAAATCATATCCAAATAC
* * * *
42395187 TATCTGCTAAGTTTCATTTTGGAAATCATATCCAAATAC
1 TATCCGCTGAGTTTCGTTCTGGAAATCATATCCAAATAC
42395226 TATCCGCTGAGTTTCGTTCTGGAAATCATATCCAAATAC
1 TATCCGCTGAGTTTCGTTCTGGAAATCATATCCAAATAC
42395265 TATC
1 TATC
42395269 TCCAAAGAAA
Statistics
Matches: 74, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
39 74 1.00
ACGTcount: A:0.30, C:0.21, G:0.13, T:0.36
Consensus pattern (39 bp):
TATCCGCTGAGTTTCGTTCTGGAAATCATATCCAAATAC
Found at i:42399523 original size:21 final size:21
Alignment explanation
Indices: 42399494--42399534 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
42399484 CAGATCTCTC
* * *
42399494 AAAATAGAAATCTAACCTAAG
1 AAAAGAGAAAACTAAACTAAG
42399515 AAAAGAGAAAACTAAACTAA
1 AAAAGAGAAAACTAAACTAA
42399535 AATTAAAAGA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.63, C:0.12, G:0.10, T:0.15
Consensus pattern (21 bp):
AAAAGAGAAAACTAAACTAAG
Found at i:42403551 original size:15 final size:16
Alignment explanation
Indices: 42403527--42403560 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
42403517 TAATTGTGAG
*
42403527 TAAAGTTTAATTAA-T
1 TAAAGATTAATTAAGT
42403542 TAAAGATTAATTAAGT
1 TAAAGATTAATTAAGT
42403558 TAA
1 TAA
42403561 TTAAATGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (16 bp):
TAAAGATTAATTAAGT
Found at i:42405620 original size:16 final size:16
Alignment explanation
Indices: 42405587--42405622 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
42405577 GACACAGTGT
**
42405587 ATGTATTAACACGTGA
1 ATGTATTAACACAAGA
42405603 ATGTATTAACACAAGA
1 ATGTATTAACACAAGA
42405619 ATGT
1 ATGT
42405623 GCTTACTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.31
Consensus pattern (16 bp):
ATGTATTAACACAAGA
Found at i:42407595 original size:31 final size:32
Alignment explanation
Indices: 42407555--42407614 Score: 79
Period size: 31 Copynumber: 1.9 Consensus size: 32
42407545 ACAAAGGTTA
*
42407555 ATTTAAGGGGATA-AGGGTTGTTGTCAGGCAGC
1 ATTTAAGGGG-TAGAGGGTTGGTGTCAGGCAGC
*
42407587 ATTT-AGGGGTAGAGGGTTGGTGTTAGGC
1 ATTTAAGGGGTAGAGGGTTGGTGTCAGGC
42407615 GGCACCAGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 2 0.08
31 19 0.76
32 4 0.16
ACGTcount: A:0.22, C:0.07, G:0.42, T:0.30
Consensus pattern (32 bp):
ATTTAAGGGGTAGAGGGTTGGTGTCAGGCAGC
Found at i:42408714 original size:42 final size:42
Alignment explanation
Indices: 42408657--42408743 Score: 140
Period size: 42 Copynumber: 2.1 Consensus size: 42
42408647 GTTTACAAAC
42408657 AAAAACGCCGCTAAAG-ACCATGTTCTTTAGCGGCGCTTAGAA
1 AAAAACGCCGCTAAAGCA-CATGTTCTTTAGCGGCGCTTAGAA
* *
42408699 AAAAACGCTGCTAAAGCACATGTTCTTTAGCGGCGCTTTGAA
1 AAAAACGCCGCTAAAGCACATGTTCTTTAGCGGCGCTTAGAA
42408741 AAA
1 AAA
42408744 GTTCTTTAGC
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
42 41 0.98
43 1 0.02
ACGTcount: A:0.34, C:0.22, G:0.21, T:0.23
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGCACATGTTCTTTAGCGGCGCTTAGAA
Found at i:42408752 original size:24 final size:24
Alignment explanation
Indices: 42408720--42408767 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
42408710 TAAAGCACAT
*
42408720 GTTCTTTAGCGGCGCTTTGAAAAA
1 GTTCTTTAGCGGCGCTTAGAAAAA
42408744 GTTCTTTAGCGGCGCTTAGAAAAA
1 GTTCTTTAGCGGCGCTTAGAAAAA
42408768 AACGTCTCTA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.27, C:0.17, G:0.25, T:0.31
Consensus pattern (24 bp):
GTTCTTTAGCGGCGCTTAGAAAAA
Found at i:42408760 original size:66 final size:66
Alignment explanation
Indices: 42408678--42408809 Score: 214
Period size: 66 Copynumber: 2.0 Consensus size: 66
42408668 TAAAGACCAT
* *
42408678 GTTCTTTAGCGGCGCTTAGAAAAAAACG-CTGCTAAAG-CACATGTTCTTTAGCGGCGCTTTGAA
1 GTTCTTTAGCGGCGCTTAGAAAAAAACGTCT-CTAAAGAC-CATGTTCTTTAGCGACGCTTAGAA
42408741 AAA
64 AAA
42408744 GTTCTTTAGCGGCGCTTAGAAAAAAACGTCTCTAAAGACCATGTTCTTTAGCGACGCTTAGAAAA
1 GTTCTTTAGCGGCGCTTAGAAAAAAACGTCTCTAAAGACCATGTTCTTTAGCGACGCTTAGAAAA
42408809 A
66 A
42408810 AACGCCGCTA
Statistics
Matches: 62, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
66 59 0.95
67 3 0.05
ACGTcount: A:0.32, C:0.20, G:0.21, T:0.27
Consensus pattern (66 bp):
GTTCTTTAGCGGCGCTTAGAAAAAAACGTCTCTAAAGACCATGTTCTTTAGCGACGCTTAGAAAA
A
Found at i:42408791 original size:108 final size:108
Alignment explanation
Indices: 42408657--42408851 Score: 329
Period size: 108 Copynumber: 1.8 Consensus size: 108
42408647 GTTTACAAAC
* *
42408657 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAAAAACGCTGCTAAAG-CACATG
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGACGCTTAGAAAAAAACGCCGCTAAAGACA-ATG
*
42408721 TTCTTTAGCGGCGCTTTGAAAAAGTTCTTTAGCGGCGCTTAGAA
65 TTCTTTAGCGGCGCTTAGAAAAAGTTCTTTAGCGGCGCTTAGAA
* *
42408765 AAAAACGTCTCTAAAGACCATGTTCTTTAGCGACGCTTAGAAAAAAACGCCGCTAAAGACAATGT
1 AAAAACGCCGCTAAAGACCATGTTCTTTAGCGACGCTTAGAAAAAAACGCCGCTAAAGACAATGT
42408830 TCTTTAGCGGCGCTTAGAAAAA
66 TCTTTAGCGGCGCTTAGAAAAA
42408852 AAACGCCTCT
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
108 79 0.98
109 2 0.02
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (108 bp):
AAAAACGCCGCTAAAGACCATGTTCTTTAGCGACGCTTAGAAAAAAACGCCGCTAAAGACAATGT
TCTTTAGCGGCGCTTAGAAAAAGTTCTTTAGCGGCGCTTAGAA
Found at i:42408803 original size:42 final size:42
Alignment explanation
Indices: 42408744--42409010 Score: 383
Period size: 42 Copynumber: 6.3 Consensus size: 42
42408734 CTTTGAAAAA
* *
42408744 GTTCTTTAGCGGCGCTTAGAAAAAAACGTCTCTAAAGACCAT
1 GTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACCAT
* *
42408786 GTTCTTTAGCGACGCTTAGAAAAAAACGCCGCTAAAGACAAT
1 GTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACCAT
* *
42408828 GTTCTTTAGCGGCGCTTAGAAAAAAAACGCCTCTAAAGATCAT
1 GTTCTTTAGCGGCGCTTAG-AAAAAAACGCCGCTAAAGACCAT
* * * *
42408871 GTTCTGTA-CTGGTGCTTAGGAAAAAACGCCGCTAAAGACAAT
1 GTTCTTTAGC-GGCGCTTAGAAAAAAACGCCGCTAAAGACCAT
* *
42408913 GTTCTTTAGCGACGCTTAGAAAAAAATGCCGCTAAAGACCAT
1 GTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACCAT
* *
42408955 GTACTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCAT
1 GTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACCAT
42408997 GTTCTTTAGCGGCG
1 GTTCTTTAGCGGCG
42409011 TTTATTCTTA
Statistics
Matches: 197, Mismatches: 25, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
42 161 0.82
43 36 0.18
ACGTcount: A:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (42 bp):
GTTCTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGACCAT
Found at i:42408970 original size:127 final size:126
Alignment explanation
Indices: 42408757--42409001 Score: 409
Period size: 127 Copynumber: 1.9 Consensus size: 126
42408747 CTTTAGCGGC
* * *
42408757 GCTTAGAAAAAAACGTCTCTAAAGACCATGTTCTTTAGCGACGCTTAGAAAAAAACGCCGCTAAA
1 GCTTAGAAAAAAACGCCGCTAAAGACAATGTTCTTTAGCGACGCTTAGAAAAAAACGCCGCTAAA
* *
42408822 GACAATGTTCTTTAGCGGCGCTTAGAAAAAAAACGCCTCTAAAGATCATGTTCTGTACTGGT
66 GACAATGTACTTTAGCGGCGCTTAG-AAAAAAACGCCGCTAAAGATCATGTTCTGTACTGGT
* *
42408884 GCTTAGGAAAAAACGCCGCTAAAGACAATGTTCTTTAGCGACGCTTAGAAAAAAATGCCGCTAAA
1 GCTTAGAAAAAAACGCCGCTAAAGACAATGTTCTTTAGCGACGCTTAGAAAAAAACGCCGCTAAA
*
42408949 GACCATGTACTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCT
66 GACAATGTACTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCT
42409002 TTAGCGGCGT
Statistics
Matches: 110, Mismatches: 8, Indels: 1
0.92 0.07 0.01
Matches are distributed among these distances:
126 27 0.25
127 83 0.75
ACGTcount: A:0.36, C:0.21, G:0.20, T:0.24
Consensus pattern (126 bp):
GCTTAGAAAAAAACGCCGCTAAAGACAATGTTCTTTAGCGACGCTTAGAAAAAAACGCCGCTAAA
GACAATGTACTTTAGCGGCGCTTAGAAAAAAACGCCGCTAAAGATCATGTTCTGTACTGGT
Found at i:42409422 original size:21 final size:21
Alignment explanation
Indices: 42409395--42409444 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
42409385 TTTTGGCCTG
* *
42409395 CTCTGCTTCTCTCGCTGCAGC
1 CTCTGCTTCCCTCACTGCAGC
* *
42409416 TTCTGCTTCCCTCACTGCCGC
1 CTCTGCTTCCCTCACTGCAGC
42409437 CTCTGCTT
1 CTCTGCTT
42409445 TAAGTTGTAG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.04, C:0.44, G:0.16, T:0.36
Consensus pattern (21 bp):
CTCTGCTTCCCTCACTGCAGC
Done.