Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold6
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: 4312818
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 226954 characters in sequence are not A, C, G, or T
File 13 of 14
Found at i:4034288 original size:14 final size:14
Alignment explanation
Indices: 4034266--4034326 Score: 56
Period size: 14 Copynumber: 4.4 Consensus size: 14
4034256 TTTAAAATAA
*
4034266 TTTAATGTTTAGAG
1 TTTAGTGTTTAGAG
*
4034280 TTTAGTGTTTACAG
1 TTTAGTGTTTAGAG
4034294 TTTAG-GTTGTAG-G
1 TTTAGTGTT-TAGAG
*
4034307 TTTA-TGGTTTAGTG
1 TTTAGT-GTTTAGAG
4034321 TTTAGT
1 TTTAGT
4034327 TTGGGTTTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
13 11 0.28
14 27 0.69
15 1 0.03
ACGTcount: A:0.20, C:0.02, G:0.26, T:0.52
Consensus pattern (14 bp):
TTTAGTGTTTAGAG
Found at i:4034354 original size:21 final size:20
Alignment explanation
Indices: 4034312--4034369 Score: 59
Period size: 21 Copynumber: 3.0 Consensus size: 20
4034302 GTAGGTTTAT
*
4034312 GGTTTAGTGTTTA--GTTTG
1 GGTTTAATGTTTAGGGTTTG
*
4034330 GGTTTTAA-GTTTTGGGTTTAG
1 GG-TTTAATGTTTAGGGTTT-G
4034351 GGTTTAATGTTTAGGGTTT
1 GGTTTAATGTTTAGGGTTT
4034370 TTGGGTTAGG
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 6 0.19
19 4 0.12
20 9 0.28
21 13 0.41
ACGTcount: A:0.14, C:0.00, G:0.33, T:0.53
Consensus pattern (20 bp):
GGTTTAATGTTTAGGGTTTG
Found at i:4040216 original size:71 final size:71
Alignment explanation
Indices: 4040128--4040259 Score: 264
Period size: 71 Copynumber: 1.9 Consensus size: 71
4040118 TAATATCAAA
4040128 AGTTTGCAGTCTGTTCACGATTAATGCCATATCGCCTAAAAAAAAGATGGCGCAAAAAAAAAACT
1 AGTTTGCAGTCTGTTCACGATTAATGCCATATCGCCTAAAAAAAAGATGGCGCAAAAAAAAAACT
4040193 CTATCG
66 CTATCG
4040199 AGTTTGCAGTCTGTTCACGATTAATGCCATATCGCCTAAAAAAAAGATGGCGCAAAAAAAA
1 AGTTTGCAGTCTGTTCACGATTAATGCCATATCGCCTAAAAAAAAGATGGCGCAAAAAAAA
4040260 CCGGGGCAAT
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
71 61 1.00
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.23
Consensus pattern (71 bp):
AGTTTGCAGTCTGTTCACGATTAATGCCATATCGCCTAAAAAAAAGATGGCGCAAAAAAAAAACT
CTATCG
Found at i:4040529 original size:14 final size:15
Alignment explanation
Indices: 4040503--4040535 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
4040493 TCCCAAGCTG
4040503 GGAAGGACCTTATGT
1 GGAAGGACCTTATGT
*
4040518 GGAAGG-CCTTATTT
1 GGAAGGACCTTATGT
4040532 GGAA
1 GGAA
4040536 AAACGTCAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.12, G:0.33, T:0.27
Consensus pattern (15 bp):
GGAAGGACCTTATGT
Found at i:4042034 original size:88 final size:88
Alignment explanation
Indices: 4041877--4042624 Score: 1208
Period size: 88 Copynumber: 8.5 Consensus size: 88
4041867 ATAACAAATA
* *
4041877 TTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTCCCTGGGTTGTAGCA
1 TTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGTAGCG
4041942 GAGCAGGTTAAAAATAGCAGATC
66 GAGCAGGTTAAAAATAGCAGATC
*
4041965 TTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGCAGCG
1 TTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGTAGCG
*
4042030 GAGCAGGTTAAAAATAACAGATC
66 GAGCAGGTTAAAAATAGCAGATC
*
4042053 TTCCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGTAGCG
1 TTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGTAGCG
*
4042118 GAGCAGGTAAAAAATAGCAGATC
66 GAGCAGGTTAAAAATAGCAGATC
* * * *
4042141 TTGCTTTCCTGCAGCGACAGCGAAGCAGATCGAAGACACCAACCTTGCCTACCTGGGTTGTAGCG
1 TTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGTAGCG
*
4042206 GAGCAAGTTAAAAATAGCAGATC
66 GAGCAGGTTAAAAATAGCAGATC
*
4042229 TTGCCTTCCTGCACCGACAGCGAAGTAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGTAGCG
1 TTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGTAGCG
4042294 GAGCAGGTTAAAAATAGCAGATC
66 GAGCAGGTTAAAAATAGCAGATC
* * *
4042317 TTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAACCTTACCTACCTGGGTTGTAGCG
1 TTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGTAGCG
4042382 GAGCAGGTTAAAAATAGCAGATC
66 GAGCAGGTTAAAAATAGCAGATC
* * *
4042405 TTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGGCACCAGCCTTGCCTCCCTGGGTTGCAGCA
1 TTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGTAGCG
4042470 GAGCAGGTTAAAAATAGCAGATC
66 GAGCAGGTTAAAAATAGCAGATC
* * * * * *
4042493 TTGCCTTCTTGTACCGATAGCGAAGCAGATCGAAGACACTAGCCTTGCCTCACTGGGTTGCAGCG
1 TTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGTAGCG
* *
4042558 AAGCAGGTTAAAAATAACAGATC
66 GAGCAGGTTAAAAATAGCAGATC
* * ** * *
4042581 TTGCCTTCCTACACCGACAGTGAAATAGATCGATGACCCCAGCC
1 TTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCC
4042625 CTATCTCCCT
Statistics
Matches: 610, Mismatches: 50, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
88 610 1.00
ACGTcount: A:0.28, C:0.28, G:0.24, T:0.20
Consensus pattern (88 bp):
TTGCCTTCCTGCACCGACAGCGAAGCAGATCGAAGACACCAGCCTTGCCTCCCTGGGTTGTAGCG
GAGCAGGTTAAAAATAGCAGATC
Found at i:4042718 original size:44 final size:44
Alignment explanation
Indices: 4042625--4042723 Score: 121
Period size: 44 Copynumber: 2.2 Consensus size: 44
4042615 GACCCCAGCC
* * * *
4042625 CTATCTCCCTAGACAGCAGTGGAATATGTTGAAGATTGTAAGTT
1 CTATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATGGGAAGTT
*
4042669 CTATCTCCCTGGTCAGCAGTGGAATAGGTTGAAGATGGCGAA--T
1 CTATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATGG-GAAGTT
4042712 CTTATCTCCCTG
1 C-TATCTCCCTG
4042724 AAGTTACAGT
Statistics
Matches: 48, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
43 2 0.04
44 44 0.92
45 2 0.04
ACGTcount: A:0.25, C:0.20, G:0.24, T:0.30
Consensus pattern (44 bp):
CTATCTCCCTGGACAGCAGTGGAATAGGTTGAAGATGGGAAGTT
Found at i:4042757 original size:44 final size:43
Alignment explanation
Indices: 4042709--4043525 Score: 310
Period size: 44 Copynumber: 18.9 Consensus size: 43
4042699 GAAGATGGCG
*
4042709 AATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CAAT
* ** *
4042753 AATCTTATCTCCCTAAAGTTGCAGTGGAGTGGATTAAAATCACA-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGCA-AT
* * * *
4042797 GATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T--CGC-AT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAAT
** * * * *** * *
4042835 CGGGTCTTATCTCCTTGAAGTTGCAATGGAGTA-ACCCAAGAAAGCG
1 --AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAA--T
*
4042881 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CAAT
* ** *
4042925 AATCTTATCTCCCTAAAGTTGCAGTGGAGTGGATTAAAATCACA-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGCA-AT
* * * *
4042969 GATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-T--CGC-AT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAAT
** * * * *** * *
4043007 CGGGTCTTATCTCCTTGAAGTTGCAATGGAGTA-ACCCAAGAAAGCG
1 --AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAA--T
*
4043053 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CAAT
* *
4043097 AATCTTATCTCCCTGAAGTCGCAGTGGAGCAGATTAAAATCACA-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGCA-AT
* * * * * *
4043141 GATCTTATTTCTCTGAAGTTGCAG-AGAGCAGA-T--CGCATCT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCA-AT
* * * * * * *
4043181 AGTCTTATCTCCCTAAAGTTGCAGTGGAACAAACT-AAGTAAGC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAA-T
* * *
4043224 AAGCCTTATC-CTCCTGAAGTTGTAGT-GAGGCAGACTGAAGATGGC-A-
1 AA-TCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAA-A--GCAAT
* *
4043270 AATCTTATCTCCCTGAAGTTACAGTGGAGCATATTAAAGCCAAT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CAAT
* ** *
4043314 AAT-TGTATCTCCCTGAAGTTGCAATGGAGTGGATTAAAATCACA-
1 AATCT-TATCTCCCTGAAGTTGCAGTGGAGCAGATT-AAAGCA-AT
* * * * * *
4043358 GATCTTATCTCTCTGAAGTTGTAG-AGAGTAGA-T--CGC-AT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAAT
** * *** * *
4043396 CGGGTCTTATCTCCCTGAAGTTGCAGTGGAGTAGACCCAAGAAAGC
1 --AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAA-T
* * * * *
4043442 AAGTCTTATCTCCCTGAAGTTGTAGTGGACCAGACTCAAGAAAT
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAAT
* * * * *
4043486 CAAGTCTTATCCCCCTGAAATTGTAGTGGGGCAGACTAAA
1 -AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAA
4043526 TAAACAAATC
Statistics
Matches: 574, Mismatches: 136, Indels: 125
0.69 0.16 0.15
Matches are distributed among these distances:
37 3 0.01
39 5 0.01
40 82 0.14
41 21 0.04
42 6 0.01
43 34 0.06
44 292 0.51
45 118 0.21
46 10 0.02
47 1 0.00
48 1 0.00
49 1 0.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAAT
Found at i:4042956 original size:172 final size:172
Alignment explanation
Indices: 4042706--4043208 Score: 898
Period size: 172 Copynumber: 2.9 Consensus size: 172
4042696 GTTGAAGATG
* *
4042706 GCGAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCCAATAATCTTATCTCCCTAAAG
1 GCGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCTTATCTCCCTAAAG
4042771 TTGCAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATC
66 TTGCAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATC
4042836 GGGTCTTATCTCCTTGAAGTTGCAATGGAGTAACCCAAGAAA
131 GGGTCTTATCTCCTTGAAGTTGCAATGGAGTAACCCAAGAAA
4042878 GCGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCTTATCTCCCTAAAG
1 GCGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCTTATCTCCCTAAAG
4042943 TTGCAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATC
66 TTGCAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATC
4043008 GGGTCTTATCTCCTTGAAGTTGCAATGGAGTAACCCAAGAAA
131 GGGTCTTATCTCCTTGAAGTTGCAATGGAGTAACCCAAGAAA
*
4043050 GCGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCTTATCTCCCTGAAG
1 GCGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCTTATCTCCCTAAAG
* ** *
4043115 TCGCAGTGGAGCAGATTAAAATCACAGATCTTATTTCTCTGAAGTTGCAGAGAGCAGATCGCATC
66 TTGCAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATC
** * * *
4043180 TAGTCTTATCTCCCTAAAGTTGCAGTGGA
131 GGGTCTTATCTCCTTGAAGTTGCAATGGA
4043209 ACAAACTAAG
Statistics
Matches: 319, Mismatches: 12, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
172 319 1.00
ACGTcount: A:0.30, C:0.21, G:0.22, T:0.28
Consensus pattern (172 bp):
GCGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCTTATCTCCCTAAAG
TTGCAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATC
GGGTCTTATCTCCTTGAAGTTGCAATGGAGTAACCCAAGAAA
Found at i:4043014 original size:128 final size:126
Alignment explanation
Indices: 4042882--4043426 Score: 399
Period size: 128 Copynumber: 4.2 Consensus size: 126
4042872 AAGAAAGCGA
4042882 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCTTATCTCCCTAAAGTTGC
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CAATAATCTTATCTCCCTAAAGTTGC
**
4042947 AGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCGG
65 AGTGGAGCAGATTAAAATCA-AGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCGG
* * * *** * * * *
4043010 GTCTTATCTCCTTGAAGTTGCAATGGAGTA-ACCCAAGAAAGCGAGTCTTATCTCCCTGAAGTTG
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAA--TAATCTTATCTCCCTAAAGTTG
** * * * * ***
4043074 CAGTGGAGCAGATTAAAGCCAATAATCTTATCTCCCTGAAGTCGCAGTGGAGCAGATTAAAATCA
64 CAGTGGAGCAGATTAAAATCAA-GATCTTATCTCTCTGAAGTTGCAG-AGAGCAGA-TCGCAT--
*
4043139 CAG
124 CGG
* * * * * * *
4043142 ATCTTATTTCTCTGAAGTTGCAG-AGAGCAGA-T--CGCATCTAGTCTTATCTCCCTAAAGTTGC
1 GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCA-ATAATCTTATCTCCCTAAAGTTGC
* * * * * * * *
4043203 AGTGGAACAAACTAAGTAAGCAAG-CCTTATC-CTCCTGAAGTTGTAGTGAGGCAGA-CTGAAGA
65 AGTGGAGCAGATTAA--AATCAAGATCTTATCTCT-CTGAAGTTGCAGAGA-GCAGATC-G--CA
4043265 T-GG
123 TCGG
* * * *
4043268 CAAATCTTATCTCCCTGAAGTTACAGTGGAGCATATTAAAGCCAATAAT-TGTATCTCCCTGAAG
1 ---GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG-CAATAATCT-TATCTCCCTAAAG
* ** * *
4043332 TTGCAATGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGTAGAGAGTAGATCGCATC
61 TTGCAGTGGAGCAGATTAAAATCA-AGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATC
4043397 GG
125 GG
4043399 GTCTTATCTCCCTGAAGTTGCAGTGGAG
1 GTCTTATCTCCCTGAAGTTGCAGTGGAG
4043427 TAGACCCAAG
Statistics
Matches: 315, Mismatches: 72, Indels: 60
0.70 0.16 0.13
Matches are distributed among these distances:
126 3 0.01
127 8 0.03
128 164 0.52
129 31 0.10
130 15 0.05
131 11 0.03
132 29 0.09
133 50 0.16
134 4 0.01
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (126 bp):
GTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCAATAATCTTATCTCCCTAAAGTTGCA
GTGGAGCAGATTAAAATCAAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCGG
Found at i:4043242 original size:172 final size:172
Alignment explanation
Indices: 4042706--4043307 Score: 888
Period size: 172 Copynumber: 3.5 Consensus size: 172
4042696 GTTGAAGATG
* *
4042706 GCGAATCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCCAATAATCTTATCTCCCTAAAG
1 GCGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCTTATCTCCCTAAAG
**
4042771 TTGCAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATC
66 TTGCAGTGGAGCAGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATC
4042836 GGGTCTTATCTCCTTGAAGTTGCAATGGAGTAACCCAAGAAA
131 GGGTCTTATCTCCTTGAAGTTGCAATGGAGTAACCCAAGAAA
4042878 GCGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCTTATCTCCCTAAAG
1 GCGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCTTATCTCCCTAAAG
**
4042943 TTGCAGTGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATC
66 TTGCAGTGGAGCAGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATC
4043008 GGGTCTTATCTCCTTGAAGTTGCAATGGAGTAACCCAAGAAA
131 GGGTCTTATCTCCTTGAAGTTGCAATGGAGTAACCCAAGAAA
*
4043050 GCGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCTTATCTCCCTGAAG
1 GCGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCTTATCTCCCTAAAG
* *
4043115 TCGCAGTGGAGCAGATTAAAATCACAGATCTTATTTCTCTGAAGTTGCAGAGAGCAGATCGCATC
66 TTGCAGTGGAGCAGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATC
** * * * ** * * *
4043180 TAGTCTTATCTCCCTAAAGTTGCAGTGGAACAAACTAAGTAA
131 GGGTCTTATCTCCTTGAAGTTGCAATGGAGTAACCCAAGAAA
* * * * *
4043222 GCAAGCCTTATC-CTCCTGAAGTTGTAGT-GAGGCAGACTGAAGATGGC-A-AATCTTATCTCCC
1 GCGAGTCTTATCTC-CCTGAAGTTGCAGTGGA-GCAGA-TTAA-A-GCCAATAATCTTATCTCCC
* * *
4043283 TGAAGTTACAGTGGAGCATATTAAA
61 TAAAGTTGCAGTGGAGCAGATTAAA
4043308 GCCAATAATT
Statistics
Matches: 400, Mismatches: 25, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
171 3 0.01
172 355 0.89
173 38 0.09
174 2 0.00
175 2 0.00
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.27
Consensus pattern (172 bp):
GCGAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCTTATCTCCCTAAAG
TTGCAGTGGAGCAGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATC
GGGTCTTATCTCCTTGAAGTTGCAATGGAGTAACCCAAGAAA
Found at i:4043331 original size:217 final size:218
Alignment explanation
Indices: 4043055--4043468 Score: 627
Period size: 217 Copynumber: 1.9 Consensus size: 218
4043045 AGAAAGCGAG
*
4043055 TCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCCAATAATCTTATCTCCCTGAAGTCGCA
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCCAATAATCTTATCTCCCTGAAGTCGCA
* * *
4043120 GTGGAGCAGATTAAAATCACAGATCTTATTTCTCTGAAGTTGCAGAGAGCAGATCGCATCTAGTC
66 ATGGAGCAGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCGAGTC
* *
4043185 TTATCTCCCTAAAGTTGCAGTGGAACA-AACTAAGTAAGCAAGCCTTATC-CTCCTGAAGTTGTA
131 TTATCTCCCTAAAGTTGCAGTGGAACAGAACCAAGAAAGCAAGCCTTATCTC-CCTGAAGTTGTA
4043248 GTGAGGCAGACTGAAGATGGCAAA
195 GTGAGGCAGACTGAAGATGGCAAA
* *
4043272 TCTTATCTCCCTGAAGTTACAGTGGAGCATATTAAAGCCAATAAT-TGTATCTCCCTGAAGTTGC
1 TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCCAATAATCT-TATCTCCCTGAAGTCGC
** * * *
4043336 AATGGAGTGGATTAAAATCACAGATCTTATCTCTCTGAAGTTGTAGAGAGTAGATCGCATCGGGT
65 AATGGAGCAGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCGAGT
* ** * *
4043401 CTTATCTCCCTGAAGTTGCAGTGGAGTAGACCCAAGAAAGCAAGTCTTATCTCCCTGAAGTTGTA
130 CTTATCTCCCTAAAGTTGCAGTGGAACAGAACCAAGAAAGCAAGCCTTATCTCCCTGAAGTTGTA
4043466 GTG
195 GTG
4043469 GACCAGACTC
Statistics
Matches: 176, Mismatches: 18, Indels: 5
0.88 0.09 0.03
Matches are distributed among these distances:
216 1 0.01
217 141 0.80
218 33 0.19
219 1 0.01
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (218 bp):
TCTTATCTCCCTGAAGTTACAGTGGAGCAGATTAAAGCCAATAATCTTATCTCCCTGAAGTCGCA
ATGGAGCAGATTAAAATCACAGATCTTATCTCTCTGAAGTTGCAGAGAGCAGATCGCATCGAGTC
TTATCTCCCTAAAGTTGCAGTGGAACAGAACCAAGAAAGCAAGCCTTATCTCCCTGAAGTTGTAG
TGAGGCAGACTGAAGATGGCAAA
Found at i:4044024 original size:19 final size:19
Alignment explanation
Indices: 4043993--4044185 Score: 233
Period size: 19 Copynumber: 9.9 Consensus size: 19
4043983 TCATTTGGCC
*
4043993 ATGATATGCAATCTTAGAT
1 ATGATATGTAATCTTAGAT
* *
4044012 ATAATATATAATCTTAGAT
1 ATGATATGTAATCTTAGAT
*
4044031 ATGATATGCAATCTTAGAT
1 ATGATATGTAATCTTAGAT
* *
4044050 ATAATATATAATCTTAGAT
1 ATGATATGTAATCTTAGAT
*
4044069 ATGATATGCAATCTTAGAT
1 ATGATATGTAATCTTAGAT
* *
4044088 ATAATATATAATCTTAGAT
1 ATGATATGTAATCTTAGAT
*
4044107 ATGATATGCAATCTTAGAT
1 ATGATATGTAATCTTAGAT
4044126 ATGATATGTAATCTTAGAT
1 ATGATATGTAATCTTAGAT
* *
4044145 ATGATATGCAGTCTTAGAAGAT
1 ATGATATGTAATCTT---AGAT
*
4044167 ATGATTTTGTAATCTTAGA
1 ATGA-TATGTAATCTTAGA
4044186 GATTTAATTT
Statistics
Matches: 146, Mismatches: 24, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
19 127 0.87
20 3 0.02
22 8 0.05
23 8 0.05
ACGTcount: A:0.39, C:0.08, G:0.13, T:0.39
Consensus pattern (19 bp):
ATGATATGTAATCTTAGAT
Found at i:4044035 original size:38 final size:38
Alignment explanation
Indices: 4043993--4044162 Score: 313
Period size: 38 Copynumber: 4.5 Consensus size: 38
4043983 TCATTTGGCC
4043993 ATGATATGCAATCTTAGATATAATATATAATCTTAGAT
1 ATGATATGCAATCTTAGATATAATATATAATCTTAGAT
4044031 ATGATATGCAATCTTAGATATAATATATAATCTTAGAT
1 ATGATATGCAATCTTAGATATAATATATAATCTTAGAT
4044069 ATGATATGCAATCTTAGATATAATATATAATCTTAGAT
1 ATGATATGCAATCTTAGATATAATATATAATCTTAGAT
* *
4044107 ATGATATGCAATCTTAGATATGATATGTAATCTTAGAT
1 ATGATATGCAATCTTAGATATAATATATAATCTTAGAT
*
4044145 ATGATATGCAGTCTTAGA
1 ATGATATGCAATCTTAGA
4044163 AGATATGATT
Statistics
Matches: 129, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
38 129 1.00
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (38 bp):
ATGATATGCAATCTTAGATATAATATATAATCTTAGAT
Found at i:4044286 original size:27 final size:27
Alignment explanation
Indices: 4044256--4044397 Score: 169
Period size: 27 Copynumber: 5.3 Consensus size: 27
4044246 TTTGATAGAT
* *
4044256 GGTATTTCAGTTATTTTACCCATTGAG
1 GGTATTTCGGTCATTTTACCCATTGAG
* * *
4044283 GGTATTTCGGTTACTTTACCCACTGAG
1 GGTATTTCGGTCATTTTACCCATTGAG
* *
4044310 GGTATTTCGGTCATTTTACCAATCGAG
1 GGTATTTCGGTCATTTTACCCATTGAG
* * *
4044337 GGTATTTCGATCATTTTACCTATCGAG
1 GGTATTTCGGTCATTTTACCCATTGAG
*
4044364 GGTATTTTGGTCATTTTACCC-TTCGAG
1 GGTATTTCGGTCATTTTACCCATT-GAG
4044391 GGTATTT
1 GGTATTT
4044398 AAATAATTTA
Statistics
Matches: 100, Mismatches: 14, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
26 1 0.01
27 99 0.99
ACGTcount: A:0.20, C:0.18, G:0.21, T:0.42
Consensus pattern (27 bp):
GGTATTTCGGTCATTTTACCCATTGAG
Found at i:4047077 original size:43 final size:43
Alignment explanation
Indices: 4047015--4047097 Score: 107
Period size: 43 Copynumber: 1.9 Consensus size: 43
4047005 AAGTGTGTAT
* *
4047015 AATTCAAAAATAAGGTCACACGGTCATGTCACCAGACCGTGCGC
1 AATTCAAAAATAAGGTCACACAGCCATGTCA-CAGACCGTGCGC
*
4047059 AATTC-AAAAT-AGGTTCACACAGCCGTGTCACAGACCGTG
1 AATTCAAAAATAAGG-TCACACAGCCATGTCACAGACCGTG
4047098 TGTGATTCGA
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
42 12 0.34
43 18 0.51
44 5 0.14
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.19
Consensus pattern (43 bp):
AATTCAAAAATAAGGTCACACAGCCATGTCACAGACCGTGCGC
Found at i:4048319 original size:24 final size:24
Alignment explanation
Indices: 4048287--4048347 Score: 88
Period size: 23 Copynumber: 2.6 Consensus size: 24
4048277 GTACATAATA
4048287 CCTGCTAAATACACCAGCACAAAG
1 CCTGCTAAATACACCAGCACAAAG
* * *
4048311 CCTGCTAAA-AAACCTGCTCAAAG
1 CCTGCTAAATACACCAGCACAAAG
4048334 CCTGCTAAATACAC
1 CCTGCTAAATACAC
4048348 TGACACGTAG
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
23 20 0.62
24 12 0.38
ACGTcount: A:0.39, C:0.33, G:0.11, T:0.16
Consensus pattern (24 bp):
CCTGCTAAATACACCAGCACAAAG
Found at i:4052021 original size:13 final size:13
Alignment explanation
Indices: 4052003--4052030 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
4051993 TTTATTATAG
4052003 TTTTTCATAATTT
1 TTTTTCATAATTT
4052016 TTTTTCATAATTT
1 TTTTTCATAATTT
4052029 TT
1 TT
4052031 AAAACCTTTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.21, C:0.07, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTTCATAATTT
Found at i:4052204 original size:13 final size:13
Alignment explanation
Indices: 4052186--4052211 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
4052176 CTAGGCTTTC
4052186 TTATAATTTTTTT
1 TTATAATTTTTTT
4052199 TTATAATTTTTTT
1 TTATAATTTTTTT
4052212 CAACTTAGCG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (13 bp):
TTATAATTTTTTT
Found at i:4053257 original size:9 final size:9
Alignment explanation
Indices: 4053240--4053270 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
4053230 TCGAGTTGAT
4053240 TCGAATAAC
1 TCGAATAAC
*
4053249 TCGATTAAC
1 TCGAATAAC
4053258 TCGAATAAC
1 TCGAATAAC
4053267 TCGA
1 TCGA
4053271 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:4059597 original size:45 final size:45
Alignment explanation
Indices: 4059528--4059727 Score: 179
Period size: 45 Copynumber: 4.5 Consensus size: 45
4059518 TACACGGTGG
** * *
4059528 ATCAGCACGCAGC-ACCACCCTTATAGTCAATAGTACTC-GGTGAA
1 ATCAGCACATAGCAACCACCTTTATAATCAATAGTA-TCGGGTGAA
* * *
4059572 ATCAGCACATAGCAACCACCTTTATACTCAATGGTACCGGGTGAA
1 ATCAGCACATAGCAACCACCTTTATAATCAATAGTATCGGGTGAA
* * * * * * * *
4059617 ATCAGCACATAGTAACAACCTATGTAACCATTGGTATCCGGTGAA
1 ATCAGCACATAGCAACCACCTTTATAATCAATAGTATCGGGTGAA
* ** * * *
4059662 ATCAGCACATAGCAACCACTTTTATTTTCATTAATATCGGGTGGA
1 ATCAGCACATAGCAACCACCTTTATAATCAATAGTATCGGGTGAA
*
4059707 ATCAGCACATAGCATCCACCT
1 ATCAGCACATAGCAACCACCT
4059728 ATATTTCCAA
Statistics
Matches: 125, Mismatches: 29, Indels: 3
0.80 0.18 0.02
Matches are distributed among these distances:
44 12 0.10
45 113 0.90
ACGTcount: A:0.33, C:0.26, G:0.17, T:0.24
Consensus pattern (45 bp):
ATCAGCACATAGCAACCACCTTTATAATCAATAGTATCGGGTGAA
Found at i:4059728 original size:90 final size:90
Alignment explanation
Indices: 4059565--4059729 Score: 231
Period size: 90 Copynumber: 1.8 Consensus size: 90
4059555 CAATAGTACT
** *
4059565 CGGTGAAATCAGCACATAGCAACCACCTTTATACTCAATGGTACCGGGTGAAATCAGCACATAGT
1 CGGTGAAATCAGCACATAGCAACCACCTTTATACTCAATAATACCGGGTGAAATCAGCACATAGC
4059630 AACAACCTATGTAACCATTGGTATC
66 AACAACCTATGTAACCATTGGTATC
* ** * * *
4059655 CGGTGAAATCAGCACATAGCAACCACTTTTATTTTCATTAATATCGGGTGGAATCAGCACATAGC
1 CGGTGAAATCAGCACATAGCAACCACCTTTATACTCAATAATACCGGGTGAAATCAGCACATAGC
* *
4059720 ATCCACCTAT
66 AACAACCTAT
4059730 ATTTCCAATG
Statistics
Matches: 64, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
90 64 1.00
ACGTcount: A:0.33, C:0.24, G:0.17, T:0.25
Consensus pattern (90 bp):
CGGTGAAATCAGCACATAGCAACCACCTTTATACTCAATAATACCGGGTGAAATCAGCACATAGC
AACAACCTATGTAACCATTGGTATC
Found at i:4066670 original size:45 final size:45
Alignment explanation
Indices: 4066603--4066692 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 45
4066593 AGCACCACAG
* *
4066603 TTATAGTCAATAGTACTCGGTGAAATCAACACTTAGCAACCACCT
1 TTATACTCAATAGTACTCGGTGAAATCAACACATAGCAACCACCT
* *
4066648 TTATACTCAATGGTAC-CGGGTGAAATCAACACATAGCATCCACCT
1 TTATACTCAATAGTACTC-GGTGAAATCAACACATAGCAACCACCT
4066693 ATATTTCCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
44 1 0.03
45 39 0.98
ACGTcount: A:0.34, C:0.26, G:0.14, T:0.26
Consensus pattern (45 bp):
TTATACTCAATAGTACTCGGTGAAATCAACACATAGCAACCACCT
Found at i:4069394 original size:25 final size:25
Alignment explanation
Indices: 4069366--4069418 Score: 70
Period size: 25 Copynumber: 2.1 Consensus size: 25
4069356 TGAATAACTT
4069366 TAAGCTCATACGAAATGAGTAATGG
1 TAAGCTCATACGAAATGAGTAATGG
* ** *
4069391 TAAGCTTATACGAGCTGAGTATTGG
1 TAAGCTCATACGAAATGAGTAATGG
4069416 TAA
1 TAA
4069419 CCCTAATGAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.36, C:0.11, G:0.25, T:0.28
Consensus pattern (25 bp):
TAAGCTCATACGAAATGAGTAATGG
Found at i:4070541 original size:23 final size:23
Alignment explanation
Indices: 4070510--4070554 Score: 81
Period size: 23 Copynumber: 2.0 Consensus size: 23
4070500 AACAAAATTT
4070510 TATACGGTATTTCTATCATTCTA
1 TATACGGTATTTCTATCATTCTA
*
4070533 TATATGGTATTTCTATCATTCT
1 TATACGGTATTTCTATCATTCT
4070555 GTAGGAAATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.24, C:0.16, G:0.09, T:0.51
Consensus pattern (23 bp):
TATACGGTATTTCTATCATTCTA
Found at i:4071785 original size:30 final size:30
Alignment explanation
Indices: 4071742--4071801 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 30
4071732 AATTTTTTGC
*
4071742 GAGCTGAACTAAGCTC-CATTTCAGCTCAAT
1 GAGCTGAACTAAGCTCAAATTT-AGCTCAAT
4071772 GAGCTCGAA-TAAGCTCAAATTTAGCTCAAT
1 GAGCT-GAACTAAGCTCAAATTTAGCTCAAT
4071802 TCCATTTAGA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
30 20 0.74
31 7 0.26
ACGTcount: A:0.33, C:0.23, G:0.17, T:0.27
Consensus pattern (30 bp):
GAGCTGAACTAAGCTCAAATTTAGCTCAAT
Found at i:4073020 original size:6 final size:6
Alignment explanation
Indices: 4073011--4073121 Score: 69
Period size: 6 Copynumber: 18.0 Consensus size: 6
4073001 AATGAAAAAG
** * * * *
4073011 AAGAAA AAGAAA AAGAAA GTGAAG GAGAAA AAGAAA AAGAAA ATGCAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA
** ** * * *
4073059 AAGAAA AAGAAA TCGAAA AAGTGA GAGAAA AGGAAA ACGAAGAA AAGAAA
1 AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAGAAA AAG-A-AA AAGAAA
*
4073109 ATTGAAA AAGAAA
1 A-AGAAA AAGAAA
4073122 TTGAGATTGA
Statistics
Matches: 77, Mismatches: 25, Indels: 6
0.71 0.23 0.06
Matches are distributed among these distances:
6 66 0.86
7 7 0.09
8 4 0.05
ACGTcount: A:0.69, C:0.03, G:0.23, T:0.05
Consensus pattern (6 bp):
AAGAAA
Found at i:4073022 original size:15 final size:16
Alignment explanation
Indices: 4072998--4073027 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
4072988 ACATTGTAAT
4072998 AAAAATGAAAAAGAAG
1 AAAAATGAAAAAGAAG
4073014 AAAAA-GAAAAAGAA
1 AAAAATGAAAAAGAA
4073028 AGTGAAGGAG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (16 bp):
AAAAATGAAAAAGAAG
Found at i:4073044 original size:24 final size:24
Alignment explanation
Indices: 4073011--4073070 Score: 86
Period size: 24 Copynumber: 2.5 Consensus size: 24
4073001 AATGAAAAAG
*
4073011 AAGAAAAAGAAAAAGAAAGTG-AA
1 AAGAAAAAGAAAAAGAAAATGCAA
*
4073034 GGAGAAAAAGAAAAAGAAAATGCAA
1 -AAGAAAAAGAAAAAGAAAATGCAA
4073059 AAGAAAAAGAAA
1 AAGAAAAAGAAA
4073071 TCGAAAAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
24 30 0.94
25 2 0.06
ACGTcount: A:0.73, C:0.02, G:0.22, T:0.03
Consensus pattern (24 bp):
AAGAAAAAGAAAAAGAAAATGCAA
Found at i:4073078 original size:18 final size:18
Alignment explanation
Indices: 4072999--4073121 Score: 76
Period size: 18 Copynumber: 6.8 Consensus size: 18
4072989 CATTGTAATA
4072999 AAAATGAAAAAG---AAG
1 AAAATGAAAAAGAAAAAG
* **
4073014 AAAAAGAAAAAGAAAGTG
1 AAAATGAAAAAGAAAAAG
*
4073032 AAGGA-GAAAAAGAAAAAG
1 AA-AATGAAAAAGAAAAAG
*
4073050 AAAATGCAAAAGAAAAAG
1 AAAATGAAAAAGAAAAAG
** *
4073068 -AAATCGAAAAAGTGAGAG
1 AAAAT-GAAAAAGAAAAAG
* *
4073086 AAAAGGAAAACGAAGAAAAG
1 AAAATGAAAAAG-A-AAAAG
4073106 AAAATTGAAAAAGAAA
1 AAAA-TGAAAAAGAAA
4073122 TTGAGATTGA
Statistics
Matches: 79, Mismatches: 19, Indels: 16
0.69 0.17 0.14
Matches are distributed among these distances:
15 11 0.14
17 5 0.06
18 43 0.54
19 6 0.08
20 8 0.10
21 6 0.08
ACGTcount: A:0.70, C:0.02, G:0.22, T:0.06
Consensus pattern (18 bp):
AAAATGAAAAAGAAAAAG
Found at i:4073130 original size:18 final size:18
Alignment explanation
Indices: 4073109--4073143 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
4073099 AGAAAAGAAA
4073109 ATTGA-AAAAGAAATTGAG
1 ATTGAGAAAA-AAATTGAG
4073127 ATTGAGAAAAAAATTGA
1 ATTGAGAAAAAAATTGA
4073144 AAAAGAAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.57, C:0.00, G:0.20, T:0.23
Consensus pattern (18 bp):
ATTGAGAAAAAAATTGAG
Found at i:4079273 original size:25 final size:25
Alignment explanation
Indices: 4079208--4079389 Score: 159
Period size: 25 Copynumber: 7.3 Consensus size: 25
4079198 GGCACTTCGA
* *
4079208 ATAATTCGCCACAAAGTCTCTTCAG
1 ATAATTCGCCACAAAGGCTTTTCAG
** * * *
4079233 ATAATTTACTAGAAAGGCTTTTTAG
1 ATAATTCGCCACAAAGGCTTTTCAG
*
4079258 ATAATTCGCCACAAAGGCTTTTTAG
1 ATAATTCGCCACAAAGGCTTTTCAG
* * * *
4079283 ATAATTCACCGCAAAGGATTTTTAG
1 ATAATTCGCCACAAAGGCTTTTCAG
* *
4079308 TTAATTTGCCACAAAGGCTTTTCAG
1 ATAATTCGCCACAAAGGCTTTTCAG
** * * *
4079333 ATAATTC-AAAAATAAGGCTCTTAAG
1 ATAATTCGCCACA-AAGGCTTTTCAG
*
4079358 ATAATTCGCCATAAAGGCTTTTCAG
1 ATAATTCGCCACAAAGGCTTTTCAG
*
4079383 AAAATTC
1 ATAATTC
4079390 ACTGAAAAGG
Statistics
Matches: 122, Mismatches: 33, Indels: 4
0.77 0.21 0.03
Matches are distributed among these distances:
24 2 0.02
25 118 0.97
26 2 0.02
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (25 bp):
ATAATTCGCCACAAAGGCTTTTCAG
Found at i:4079285 original size:50 final size:51
Alignment explanation
Indices: 4079208--4079402 Score: 220
Period size: 50 Copynumber: 3.9 Consensus size: 51
4079198 GGCACTTCGA
* * *
4079208 ATAATTCGCCACAAAGTCTCTTCAGATAATTTACTAG-AAAGGCTTTTTAG
1 ATAATTCGCCACAAAGGCTTTTCAGATAATTCACTAGAAAAGGCTTTTTAG
* * * *
4079258 ATAATTCGCCACAAAGGCTTTTTAGATAATTCAC-CGCAAAGGATTTTTAG
1 ATAATTCGCCACAAAGGCTTTTCAGATAATTCACTAGAAAAGGCTTTTTAG
* * * * *
4079308 TTAATTTGCCACAAAGGCTTTTCAGATAATTCA--AAAATAAGGCTCTTAAG
1 ATAATTCGCCACAAAGGCTTTTCAGATAATTCACTAGAA-AAGGCTTTTTAG
* *
4079358 ATAATTCGCCATAAAGGCTTTTCAGAAAATTCACT-GAAAAGGCTT
1 ATAATTCGCCACAAAGGCTTTTCAGATAATTCACTAGAAAAGGCTT
4079403 GGTTTTGTTT
Statistics
Matches: 120, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
49 2 0.02
50 116 0.97
51 2 0.02
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (51 bp):
ATAATTCGCCACAAAGGCTTTTCAGATAATTCACTAGAAAAGGCTTTTTAG
Found at i:4079360 original size:100 final size:100
Alignment explanation
Indices: 4079209--4079391 Score: 251
Period size: 100 Copynumber: 1.8 Consensus size: 100
4079199 GCACTTCGAA
* * * * * *
4079209 TAATTCGCCACAAAGTCTCTTCAGATAATTTACTAGAAAGGCTTTTTAGATAATTCGCCACAAAG
1 TAATTCGCCACAAAGGCTCTTCAGATAATTCACAAAAAAGGCTCTTAAGATAATTCGCCACAAAG
* *
4079274 GCTTTTTAGATAATTCACCGCAAAGGATTTTTAGT
66 GCTTTTCAGAAAATTCACCGCAAAGGATTTTTAGT
* * *
4079309 TAATTTGCCACAAAGGCTTTTCAGATAATTCA-AAAATAAGGCTCTTAAGATAATTCGCCATAAA
1 TAATTCGCCACAAAGGCTCTTCAGATAATTCACAAAA-AAGGCTCTTAAGATAATTCGCCACAAA
4079373 GGCTTTTCAGAAAATTCAC
65 GGCTTTTCAGAAAATTCAC
4079392 TGAAAAGGCT
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
99 2 0.03
100 69 0.97
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.32
Consensus pattern (100 bp):
TAATTCGCCACAAAGGCTCTTCAGATAATTCACAAAAAAGGCTCTTAAGATAATTCGCCACAAAG
GCTTTTCAGAAAATTCACCGCAAAGGATTTTTAGT
Found at i:4081354 original size:32 final size:32
Alignment explanation
Indices: 4081313--4081377 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
4081303 TTTCCTTTAC
4081313 ATCGTTGCTCACACGAGTTGTGAAATGGGTCT
1 ATCGTTGCTCACACGAGTTGTGAAATGGGTCT
4081345 ATCGTTGCTCACACGAGTTGTGAAATGGGTCT
1 ATCGTTGCTCACACGAGTTGTGAAATGGGTCT
4081377 A
1 A
4081378 CTCACACGAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.31
Consensus pattern (32 bp):
ATCGTTGCTCACACGAGTTGTGAAATGGGTCT
Found at i:4081392 original size:26 final size:27
Alignment explanation
Indices: 4081320--4081392 Score: 85
Period size: 32 Copynumber: 2.6 Consensus size: 27
4081310 TACATCGTTG
4081320 CTCACACGAGTTGTGAAATGGGTCTATCGTT
1 CTCACACGAGTTGTGAAATGGGTCTA----T
4081351 GCTCACACGAGTTGTGAAATGGGTCTA-
1 -CTCACACGAGTTGTGAAATGGGTCTAT
*
4081378 CTCACACGAGCTGTG
1 CTCACACGAGTTGTG
4081393 GGTCGAAATG
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
26 14 0.35
32 26 0.65
ACGTcount: A:0.23, C:0.22, G:0.27, T:0.27
Consensus pattern (27 bp):
CTCACACGAGTTGTGAAATGGGTCTAT
Found at i:4087333 original size:35 final size:35
Alignment explanation
Indices: 4087269--4087335 Score: 89
Period size: 35 Copynumber: 1.9 Consensus size: 35
4087259 CTGTATGCCT
*
4087269 CACATGGCTGAAACACACACCTGTATCTCAGGGGA
1 CACATGGCTGAAACACACACCCGTATCTCAGGGGA
** * *
4087304 CACATGGCTGAGTCACATACCCGTGTCTCAGG
1 CACATGGCTGAAACACACACCCGTATCTCAGG
4087336 CCATGTGGAC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 27 1.00
ACGTcount: A:0.27, C:0.30, G:0.24, T:0.19
Consensus pattern (35 bp):
CACATGGCTGAAACACACACCCGTATCTCAGGGGA
Found at i:4090661 original size:33 final size:33
Alignment explanation
Indices: 4090619--4090684 Score: 132
Period size: 33 Copynumber: 2.0 Consensus size: 33
4090609 AAAGCTTCTT
4090619 GAATTGCACCTCCTATTTCTGCTTGTGTTGCTG
1 GAATTGCACCTCCTATTTCTGCTTGTGTTGCTG
4090652 GAATTGCACCTCCTATTTCTGCTTGTGTTGCTG
1 GAATTGCACCTCCTATTTCTGCTTGTGTTGCTG
4090685 CAATCTTTAC
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.12, C:0.24, G:0.21, T:0.42
Consensus pattern (33 bp):
GAATTGCACCTCCTATTTCTGCTTGTGTTGCTG
Found at i:4093583 original size:11 final size:11
Alignment explanation
Indices: 4093567--4093603 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
4093557 AAGAGAGAAT
*
4093567 GATGCTTGATG
1 GATGCTTGAGG
4093578 GATGCTTGAGG
1 GATGCTTGAGG
*
4093589 GATGATTGAGG
1 GATGCTTGAGG
4093600 GATG
1 GATG
4093604 ATGAATGAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.22, C:0.05, G:0.43, T:0.30
Consensus pattern (11 bp):
GATGCTTGAGG
Found at i:4099329 original size:39 final size:39
Alignment explanation
Indices: 4099270--4099344 Score: 107
Period size: 39 Copynumber: 1.9 Consensus size: 39
4099260 ACCACCTGTG
*
4099270 TTTATTATCCTGGCAGACTACCCTGTGTTTAGTGTCCCA
1 TTTATTATCCCGGCAGACTACCCTGTGTTTAGTGTCCCA
* *
4099309 TTTATTATCCCGGC-GAACTACCTTGTGTTTCGTGTC
1 TTTATTATCCCGGCAG-ACTACCCTGTGTTTAGTGTC
4099345 TCGATGGACT
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
38 1 0.03
39 31 0.97
ACGTcount: A:0.16, C:0.25, G:0.19, T:0.40
Consensus pattern (39 bp):
TTTATTATCCCGGCAGACTACCCTGTGTTTAGTGTCCCA
Found at i:4101096 original size:16 final size:17
Alignment explanation
Indices: 4101075--4101109 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
4101065 TTCACTTAAC
*
4101075 TTAACA-TTACAACAAA
1 TTAACATTTAAAACAAA
4101091 TTAACATTTAAAACAAA
1 TTAACATTTAAAACAAA
4101108 TT
1 TT
4101110 TGTATTTAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 6 0.35
17 11 0.65
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.31
Consensus pattern (17 bp):
TTAACATTTAAAACAAA
Found at i:4104446 original size:41 final size:41
Alignment explanation
Indices: 4104392--4104469 Score: 102
Period size: 41 Copynumber: 1.9 Consensus size: 41
4104382 CTTTCACAAC
* *
4104392 ATTAACCAAAAAGGCTTCCCATAAAATAGACCACAAATAAG
1 ATTAACCAAAAAGGCTTCCCAGAAAATACACCACAAATAAG
* * * *
4104433 ATTAGCCACAAAGGCTTTCCAGATAATACACCACAAA
1 ATTAACCAAAAAGGCTTCCCAGAAAATACACCACAAA
4104470 GGCTTTCTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
41 31 1.00
ACGTcount: A:0.47, C:0.24, G:0.10, T:0.18
Consensus pattern (41 bp):
ATTAACCAAAAAGGCTTCCCAGAAAATACACCACAAATAAG
Found at i:4110481 original size:8 final size:8
Alignment explanation
Indices: 4110468--4110493 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
4110458 TAATGTTGAA
4110468 GCCCCCAC
1 GCCCCCAC
4110476 GCCCCCAC
1 GCCCCCAC
4110484 GCCCCCAC
1 GCCCCCAC
4110492 GC
1 GC
4110494 TCTCACTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.12, C:0.73, G:0.15, T:0.00
Consensus pattern (8 bp):
GCCCCCAC
Found at i:4112078 original size:35 final size:35
Alignment explanation
Indices: 4112039--4112109 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
4112029 GATTTATAGG
* *
4112039 TATTCTGATTATGACTCCCATGTTAAGCATGCCAT
1 TATTCTAATTATGACTCCCATGTTAAACATGCCAT
* * *
4112074 TATTCTAATTCTGATTCGCATGTTAAACATGCCAT
1 TATTCTAATTATGACTCCCATGTTAAACATGCCAT
4112109 T
1 T
4112110 GTGTTAAACT
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.27, C:0.21, G:0.13, T:0.39
Consensus pattern (35 bp):
TATTCTAATTATGACTCCCATGTTAAACATGCCAT
Found at i:4117152 original size:25 final size:25
Alignment explanation
Indices: 4117124--4117212 Score: 85
Period size: 25 Copynumber: 3.6 Consensus size: 25
4117114 TAGTACTTCA
4117124 CCACAAAGGCGTTTCACAACATTAG
1 CCACAAAGGCGTTTCACAACATTAG
* * * *
4117149 CCAC-AACG-GTTTCCCATATAATACG
1 CCACAAAGGCGTTTCACA-ACATTA-G
* *
4117174 CCACAAAGGCTTTTCACAAGATTAG
1 CCACAAAGGCGTTTCACAACATTAG
4117199 CCACAAAGGC-TTTC
1 CCACAAAGGCGTTTC
4117213 CAGATAATAC
Statistics
Matches: 51, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
23 7 0.14
24 11 0.22
25 20 0.39
26 7 0.14
27 6 0.12
ACGTcount: A:0.34, C:0.29, G:0.15, T:0.22
Consensus pattern (25 bp):
CCACAAAGGCGTTTCACAACATTAG
Found at i:4117183 original size:50 final size:50
Alignment explanation
Indices: 4117124--4117242 Score: 168
Period size: 50 Copynumber: 2.4 Consensus size: 50
4117114 TAGTACTTCA
* * *
4117124 CCACAAAGGCGTTTCACAACATTAGCCACAACGG-TTTCCCATATAATACG
1 CCACAAAGGCTTTTCACAACATTAGCCACAAAGGCTTT-CCAGATAATACG
*
4117174 CCACAAAGGCTTTTCACAAGATTAGCCACAAAGGCTTTCCAGATAATACG
1 CCACAAAGGCTTTTCACAACATTAGCCACAAAGGCTTTCCAGATAATACG
* *
4117224 CTATAAAGGCTTTTCACAA
1 CCACAAAGGCTTTTCACAA
4117243 TGTTAGTTGT
Statistics
Matches: 62, Mismatches: 6, Indels: 2
0.89 0.09 0.03
Matches are distributed among these distances:
50 59 0.95
51 3 0.05
ACGTcount: A:0.35, C:0.27, G:0.14, T:0.24
Consensus pattern (50 bp):
CCACAAAGGCTTTTCACAACATTAGCCACAAAGGCTTTCCAGATAATACG
Found at i:4119107 original size:25 final size:25
Alignment explanation
Indices: 4119076--4119143 Score: 93
Period size: 26 Copynumber: 2.7 Consensus size: 25
4119066 GTTTACATTA
*
4119076 GCCACAAAGGCTTTCTAGATAATAC
1 GCCACAAAGGCTTTCCAGATAATAC
* *
4119101 GCTACAAAAGGTTTTCCAGATAATAC
1 GCCAC-AAAGGCTTTCCAGATAATAC
4119127 GCCACAAA-GCTTTCCAG
1 GCCACAAAGGCTTTCCAG
4119144 GTAACCTATC
Statistics
Matches: 37, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
24 8 0.22
25 7 0.19
26 22 0.59
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (25 bp):
GCCACAAAGGCTTTCCAGATAATAC
Found at i:4121462 original size:21 final size:20
Alignment explanation
Indices: 4121419--4121461 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
4121409 CAGAAAATTA
*
4121419 TTTCTGGAAATTGATTTACT
1 TTTCTGGAAAATGATTTACT
4121439 TTTCTGGAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
4121459 TTT
1 TTT
4121462 TTGGTGTTTG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.26, C:0.09, G:0.14, T:0.51
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:4124424 original size:50 final size:50
Alignment explanation
Indices: 4124361--4124462 Score: 186
Period size: 50 Copynumber: 2.0 Consensus size: 50
4124351 ACCTTTGGTG
* *
4124361 TCGCCCTGCTTTATCCAACTTCCAATGGACTCGGCTGGCCTTTTGATCTT
1 TCGCCCTGCTTTATCCAACTTCCAATGGACTCAGCTGACCTTTTGATCTT
4124411 TCGCCCTGCTTTATCCAACTTCCAATGGACTCAGCTGACCTTTTGATCTT
1 TCGCCCTGCTTTATCCAACTTCCAATGGACTCAGCTGACCTTTTGATCTT
4124461 TC
1 TC
4124463 TATTATTTTA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 50 1.00
ACGTcount: A:0.16, C:0.32, G:0.16, T:0.36
Consensus pattern (50 bp):
TCGCCCTGCTTTATCCAACTTCCAATGGACTCAGCTGACCTTTTGATCTT
Found at i:4129550 original size:21 final size:21
Alignment explanation
Indices: 4129524--4129591 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
4129514 GGAGCATAAA
*
4129524 CAGGGGCACGTATGTACAATT
1 CAGGGGCACATATGTACAATT
* * *
4129545 CAGGGGTACCA-AAGTACAAAT
1 CAGGGGCA-CATATGTACAATT
**
4129566 -AGGGGCACATATGTGTAATT
1 CAGGGGCACATATGTACAATT
4129586 CAGGGG
1 CAGGGG
4129592 TATCAAAGTA
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
19 2 0.06
20 12 0.34
21 20 0.57
22 1 0.03
ACGTcount: A:0.32, C:0.16, G:0.31, T:0.21
Consensus pattern (21 bp):
CAGGGGCACATATGTACAATT
Found at i:4129586 original size:41 final size:41
Alignment explanation
Indices: 4129525--4129667 Score: 196
Period size: 41 Copynumber: 3.5 Consensus size: 41
4129515 GAGCATAAAC
* *
4129525 AGGGGCACGTATGTACAATTCAGGGGTACCAAAGTACAAAT
1 AGGGGCACATATGTGCAATTCAGGGGTACCAAAGTACAAAT
* * *
4129566 AGGGGCACATATGTGTAATTCAGGGGTATCAAAGTATAAAT
1 AGGGGCACATATGTGCAATTCAGGGGTACCAAAGTACAAAT
* * * *
4129607 AAGGGCACGTATGTGCAATTCAGGAGTACCAAAGTACAAAC
1 AGGGGCACATATGTGCAATTCAGGGGTACCAAAGTACAAAT
*
4129648 AGGGGAACATATGTGCAATT
1 AGGGGCACATATGTGCAATT
4129668 TAGGTAATAA
Statistics
Matches: 87, Mismatches: 15, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
41 87 1.00
ACGTcount: A:0.37, C:0.15, G:0.27, T:0.22
Consensus pattern (41 bp):
AGGGGCACATATGTGCAATTCAGGGGTACCAAAGTACAAAT
Found at i:4132039 original size:46 final size:46
Alignment explanation
Indices: 4131948--4132039 Score: 105
Period size: 46 Copynumber: 2.0 Consensus size: 46
4131938 GCAATCAGCC
** *
4131948 TTGAATACCAAAAAATCCCAATCTCTAAACAATTCAAGTAACAAAT
1 TTGAATACCAAAAAATCCCAATCTCTAAACAAAACAAGAAACAAAT
* * * *
4131994 TTGAATTCCAAAAAATCCTAGTCTCTTAACAAAACAA-AAACCAAAT
1 TTGAATACCAAAAAATCCCAATCTCTAAACAAAACAAGAAA-CAAAT
4132040 ATACCAAATA
Statistics
Matches: 38, Mismatches: 7, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
45 2 0.05
46 36 0.95
ACGTcount: A:0.50, C:0.22, G:0.04, T:0.24
Consensus pattern (46 bp):
TTGAATACCAAAAAATCCCAATCTCTAAACAAAACAAGAAACAAAT
Found at i:4132560 original size:28 final size:28
Alignment explanation
Indices: 4132518--4132590 Score: 101
Period size: 28 Copynumber: 2.6 Consensus size: 28
4132508 GCTGATAAAC
4132518 AGAGTGAAAGGAGAATGACTGTTCTGATG
1 AGAGTG-AAGGAGAATGACTGTTCTGATG
* * *
4132547 AGAGTGAAGGAGAACGATTGTTGTGATG
1 AGAGTGAAGGAGAATGACTGTTCTGATG
*
4132575 AGATTGAAGGAGAATG
1 AGAGTGAAGGAGAATG
4132591 GAAAATATCT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
28 33 0.85
29 6 0.15
ACGTcount: A:0.36, C:0.04, G:0.37, T:0.23
Consensus pattern (28 bp):
AGAGTGAAGGAGAATGACTGTTCTGATG
Found at i:4133581 original size:28 final size:28
Alignment explanation
Indices: 4133548--4133610 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
4133538 GACAGAGAGA
* *
4133548 AAGGAGAATGATTGTTGTGATGAGAATG
1 AAGGAGAATGACTGTTGTGATAAGAATG
*
4133576 AAGGAGAATGACTGTTGTGATAAGAGTG
1 AAGGAGAATGACTGTTGTGATAAGAATG
4133604 AAGGAGA
1 AAGGAGA
4133611 GTGGAAAATA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.38, C:0.02, G:0.37, T:0.24
Consensus pattern (28 bp):
AAGGAGAATGACTGTTGTGATAAGAATG
Found at i:4135124 original size:26 final size:26
Alignment explanation
Indices: 4135088--4135151 Score: 94
Period size: 26 Copynumber: 2.5 Consensus size: 26
4135078 ACGAACTTTC
4135088 TCAAAATTTTACCGAGGGTTAA-ATCG
1 TCAAAATTTTACCGAGGG-TAAGATCG
* *
4135114 TCAAAATTTTACCGAGGGTAAGTTTG
1 TCAAAATTTTACCGAGGGTAAGATCG
4135140 TCAAAATTTTAC
1 TCAAAATTTTAC
4135152 TATTGTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
25 3 0.09
26 32 0.91
ACGTcount: A:0.34, C:0.14, G:0.17, T:0.34
Consensus pattern (26 bp):
TCAAAATTTTACCGAGGGTAAGATCG
Found at i:4153451 original size:9 final size:9
Alignment explanation
Indices: 4153437--4153554 Score: 70
Period size: 9 Copynumber: 13.6 Consensus size: 9
4153427 TGAGATATAT
4153437 TTATGTAAG
1 TTATGTAAG
*
4153446 TTATGTAAC
1 TTATGTAAG
*
4153455 TTATGATATG
1 TTATG-TAAG
* * *
4153465 ATATAT-AT
1 TTATGTAAG
4153473 TTATGT-AG
1 TTATGTAAG
4153481 -TATGTAAG
1 TTATGTAAG
4153489 TTATGTAAG
1 TTATGTAAG
*
4153498 TTATG-ACAT
1 TTATGTA-AG
*
4153507 TTATGATATG
1 TTATG-TAAG
* * *
4153517 ATATAT-AT
1 TTATGTAAG
4153525 TTATGT-A-
1 TTATGTAAG
4153532 TTATGTAAG
1 TTATGTAAG
4153541 TTATGTAAG
1 TTATGTAAG
4153550 TTATG
1 TTATG
4153555 AAATTTGAAA
Statistics
Matches: 82, Mismatches: 19, Indels: 16
0.70 0.16 0.14
Matches are distributed among these distances:
7 11 0.13
8 14 0.17
9 48 0.59
10 8 0.10
11 1 0.01
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.47
Consensus pattern (9 bp):
TTATGTAAG
Found at i:4153472 original size:36 final size:34
Alignment explanation
Indices: 4153425--4153493 Score: 102
Period size: 36 Copynumber: 2.0 Consensus size: 34
4153415 TAAGTATAAT
4153425 TATGAGATATATTTATGTAAGTTATGTAACTTATGA
1 TATGAGATATATTTATGT-AG-TATGTAACTTATGA
* *
4153461 TATGATATATATTTATGTAGTATGTAAGTTATG
1 TATGAGATATATTTATGTAGTATGTAACTTATG
4153494 TAAGTTATGA
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
34 12 0.39
35 2 0.06
36 17 0.55
ACGTcount: A:0.35, C:0.01, G:0.17, T:0.46
Consensus pattern (34 bp):
TATGAGATATATTTATGTAGTATGTAACTTATGA
Found at i:4153476 original size:18 final size:17
Alignment explanation
Indices: 4153425--4153532 Score: 67
Period size: 18 Copynumber: 6.2 Consensus size: 17
4153415 TAAGTATAAT
*
4153425 TATGAGATATATTTATG
1 TATGATATATATTTATG
* * * *
4153442 TAAGTTATGTAACTTATG
1 TATGATATAT-ATTTATG
4153460 ATATGATATATATTTATG
1 -TATGATATATATTTATG
* *
4153478 TA-G-TATGTAAGTTATG
1 TATGATATAT-ATTTATG
* * *
4153494 TAAGTTATGACATTTATG
1 TATGATAT-ATATTTATG
4153512 ATATGATATATATTTATG
1 -TATGATATATATTTATG
4153530 TAT
1 TAT
4153533 TATGTAAGTT
Statistics
Matches: 67, Mismatches: 17, Indels: 14
0.68 0.17 0.14
Matches are distributed among these distances:
15 4 0.06
16 9 0.13
17 12 0.18
18 29 0.43
19 13 0.19
ACGTcount: A:0.35, C:0.02, G:0.16, T:0.47
Consensus pattern (17 bp):
TATGATATATATTTATG
Found at i:4153499 original size:52 final size:52
Alignment explanation
Indices: 4153437--4153555 Score: 204
Period size: 52 Copynumber: 2.3 Consensus size: 52
4153427 TGAGATATAT
4153437 TTATGTAAGTTATGTA-ACTTATGATATGATATATATTTATGTAGTATGTAAG
1 TTATGTAAGTTATG-ACACTTATGATATGATATATATTTATGTAGTATGTAAG
* *
4153489 TTATGTAAGTTATGACATTTATGATATGATATATATTTATGTATTATGTAAG
1 TTATGTAAGTTATGACACTTATGATATGATATATATTTATGTAGTATGTAAG
4153541 TTATGTAAGTTATGA
1 TTATGTAAGTTATGA
4153556 AATTTGAAAT
Statistics
Matches: 64, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
51 1 0.02
52 63 0.98
ACGTcount: A:0.34, C:0.02, G:0.17, T:0.47
Consensus pattern (52 bp):
TTATGTAAGTTATGACACTTATGATATGATATATATTTATGTAGTATGTAAG
Found at i:4155277 original size:29 final size:29
Alignment explanation
Indices: 4155230--4155285 Score: 71
Period size: 29 Copynumber: 1.9 Consensus size: 29
4155220 GGCAAAATAT
4155230 TTATAAAATTACAAATATT-TTATAAAACC
1 TTATAAAATTACAAATATTGTT-TAAAACC
*
4155259 TTATCAAATTA-AAACTATTGTTTAAAA
1 TTATAAAATTACAAA-TATTGTTTAAAA
4155286 ATATGATTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 3 0.12
29 19 0.79
30 2 0.08
ACGTcount: A:0.50, C:0.09, G:0.02, T:0.39
Consensus pattern (29 bp):
TTATAAAATTACAAATATTGTTTAAAACC
Found at i:4155919 original size:24 final size:25
Alignment explanation
Indices: 4155882--4155935 Score: 74
Period size: 24 Copynumber: 2.2 Consensus size: 25
4155872 CTTACACGGT
* *
4155882 GATGCGGCAAAGGAGTGT-GATGGC
1 GATGCGACAAAGGAGGGTCGATGGC
*
4155906 GATGCGACAGAGGAGGGTCGATGGC
1 GATGCGACAAAGGAGGGTCGATGGC
4155931 GATGC
1 GATGC
4155936 AGCAAACGGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 15 0.58
25 11 0.42
ACGTcount: A:0.24, C:0.15, G:0.46, T:0.15
Consensus pattern (25 bp):
GATGCGACAAAGGAGGGTCGATGGC
Found at i:4158528 original size:14 final size:14
Alignment explanation
Indices: 4158509--4158536 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
4158499 AGAAAAAGAA
4158509 ACTCCCCATGTATG
1 ACTCCCCATGTATG
4158523 ACTCCCCATGTATG
1 ACTCCCCATGTATG
4158537 TCAACGTCGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.36, G:0.14, T:0.29
Consensus pattern (14 bp):
ACTCCCCATGTATG
Found at i:4158689 original size:6 final size:6
Alignment explanation
Indices: 4158673--4158718 Score: 58
Period size: 6 Copynumber: 7.5 Consensus size: 6
4158663 ATGTTCCCTG
*
4158673 TAAAAA T-AAAA TAAAAA TAAAAA TAAAATA GTAAAAA TAATAA TAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAA-A -TAAAAA TAAAAA TAA
4158719 TAGGAAACAT
Statistics
Matches: 36, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
5 5 0.14
6 24 0.67
7 2 0.06
8 5 0.14
ACGTcount: A:0.76, C:0.00, G:0.02, T:0.22
Consensus pattern (6 bp):
TAAAAA
Found at i:4164559 original size:15 final size:15
Alignment explanation
Indices: 4164541--4164586 Score: 60
Period size: 15 Copynumber: 3.1 Consensus size: 15
4164531 CTAAAACACT
*
4164541 AAACCATAAGCCCTA
1 AAACCATAAACCCTA
4164556 AAACCATAAACCCTA
1 AAACCATAAACCCTA
4164571 AATA-C-TAAACCCTA
1 AA-ACCATAAACCCTA
4164585 AA
1 AA
4164587 CCTTAAATCA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
14 11 0.38
15 17 0.59
16 1 0.03
ACGTcount: A:0.52, C:0.30, G:0.02, T:0.15
Consensus pattern (15 bp):
AAACCATAAACCCTA
Found at i:4164572 original size:7 final size:7
Alignment explanation
Indices: 4164522--4164614 Score: 60
Period size: 7 Copynumber: 13.0 Consensus size: 7
4164512 TTATCAAAAC
4164522 CCCTAAA
1 CCCTAAA
*
4164529 CTCTAAAA
1 CCCT-AAA
*
4164537 CACTAAA
1 CCCTAAA
* *
4164544 CCATAAG
1 CCCTAAA
4164551 CCCTAAAA
1 CCCT-AAA
*
4164559 CCATAAA
1 CCCTAAA
4164566 CCCTAAA
1 CCCTAAA
**
4164573 TACTAAA
1 CCCTAAA
4164580 CCCTAAA
1 CCCTAAA
*
4164587 CCTTAAA
1 CCCTAAA
* *
4164594 TCATAAA
1 CCCTAAA
*
4164601 CCTTAAA
1 CCCTAAA
*
4164608 CCTTAAA
1 CCCTAAA
4164615 ATAAAATGAT
Statistics
Matches: 66, Mismatches: 18, Indels: 4
0.75 0.20 0.05
Matches are distributed among these distances:
7 55 0.83
8 11 0.17
ACGTcount: A:0.48, C:0.30, G:0.01, T:0.20
Consensus pattern (7 bp):
CCCTAAA
Found at i:4164586 original size:21 final size:21
Alignment explanation
Indices: 4164556--4164614 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
4164546 ATAAGCCCTA
*
4164556 AAACCATAAACCCTAAAT-ACT
1 AAACCATAAACCTTAAATCA-T
*
4164577 AAACCCTAAACCTTAAATCAT
1 AAACCATAAACCTTAAATCAT
*
4164598 AAACCTTAAACCTTAAA
1 AAACCATAAACCTTAAA
4164615 ATAAAATGAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
21 33 0.97
22 1 0.03
ACGTcount: A:0.51, C:0.27, G:0.00, T:0.22
Consensus pattern (21 bp):
AAACCATAAACCTTAAATCAT
Found at i:4164593 original size:14 final size:14
Alignment explanation
Indices: 4164522--4164614 Score: 71
Period size: 14 Copynumber: 6.5 Consensus size: 14
4164512 TTATCAAAAC
*
4164522 CCCTAAACTCTAAAA
1 CCCTAAAC-CTTAAA
* * *
4164537 CACTAAACCATAAG
1 CCCTAAACCTTAAA
*
4164551 CCCTAAAACCATAAA
1 CCCT-AAACCTTAAA
*
4164566 CCCTAAATAC-TAAA
1 CCCTAAA-CCTTAAA
4164580 CCCTAAACCTTAAA
1 CCCTAAACCTTAAA
* *
4164594 TCATAAACCTTAAA
1 CCCTAAACCTTAAA
*
4164608 CCTTAAA
1 CCCTAAA
4164615 ATAAAATGAT
Statistics
Matches: 63, Mismatches: 12, Indels: 7
0.77 0.15 0.09
Matches are distributed among these distances:
13 1 0.02
14 41 0.65
15 21 0.33
ACGTcount: A:0.48, C:0.30, G:0.01, T:0.20
Consensus pattern (14 bp):
CCCTAAACCTTAAA
Found at i:4165036 original size:124 final size:124
Alignment explanation
Indices: 4164816--4165044 Score: 368
Period size: 124 Copynumber: 1.8 Consensus size: 124
4164806 GTTTTTCATG
* * * *
4164816 TATAACCTTTGTGGCATTTCCAGTCAAAACGCCACTAAAAACTTAATTCCCTATAGTGAAACGAC
1 TATAACCTTTGCGGCATTTCCAGTCAAAACACCACCAAAAACTTAACTCCCTATAGTGAAACGAC
*
4164881 GCTGTTTAAGTCAAATTGGTATTGCAATTTTGCGGCATTTATGAAAAACGCCACTAATA
66 GCCGTTTAAGTCAAATTGGTATTGCAATTTTGCGGCATTTATGAAAAACGCCACTAATA
* * * *
4164940 TATAACCTTTGCGGCATTTTCTGTCGAAACACCACCAAAAACTTAACTCCCTGTAGTGAAACGAC
1 TATAACCTTTGCGGCATTTCCAGTCAAAACACCACCAAAAACTTAACTCCCTATAGTGAAACGAC
*
4165005 GCCGTTTAAGTCAAATTGGTATTGCATTTTTGCGGCATTT
66 GCCGTTTAAGTCAAATTGGTATTGCAATTTTGCGGCATTT
4165045 TCGGTCAAAA
Statistics
Matches: 95, Mismatches: 10, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
124 95 1.00
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.31
Consensus pattern (124 bp):
TATAACCTTTGCGGCATTTCCAGTCAAAACACCACCAAAAACTTAACTCCCTATAGTGAAACGAC
GCCGTTTAAGTCAAATTGGTATTGCAATTTTGCGGCATTTATGAAAAACGCCACTAATA
Found at i:4165096 original size:86 final size:86
Alignment explanation
Indices: 4164947--4165126 Score: 279
Period size: 86 Copynumber: 2.1 Consensus size: 86
4164937 ATATATAACC
* * * **
4164947 TTTGCGGCATTTTCTGTCGAAACACCACCAAAAACTTAACTCCCTGTAGTGAAACGACGCCGTTT
1 TTTGCGGCATTTTCGGTCAAAACACCACCAAAAACTTAACTCCCTATAGTGAAACGAAACCGTTT
*
4165012 AAGTCAAATTGGTATTGCATT
66 AAGTCAAATTGGTATTGCAAT
* * *
4165033 TTTGCGGCATTTTCGGTCAAAACACCACTAAAAATTTAATTCCCTATAGTGAAACGAAACCGTTT
1 TTTGCGGCATTTTCGGTCAAAACACCACCAAAAACTTAACTCCCTATAGTGAAACGAAACCGTTT
4165098 AAGTCAAATTGGTATTGCAAT
66 AAGTCAAATTGGTATTGCAAT
4165119 TTTGCGGC
1 TTTGCGGC
4165127 GTTTATGAAA
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
86 85 1.00
ACGTcount: A:0.31, C:0.21, G:0.17, T:0.31
Consensus pattern (86 bp):
TTTGCGGCATTTTCGGTCAAAACACCACCAAAAACTTAACTCCCTATAGTGAAACGAAACCGTTT
AAGTCAAATTGGTATTGCAAT
Found at i:4165206 original size:210 final size:210
Alignment explanation
Indices: 4164823--4165250 Score: 608
Period size: 210 Copynumber: 2.0 Consensus size: 210
4164813 ATGTATAACC
* * ** *
4164823 TTTGTGGCATTTCCAGTCAAAACGCCACTAAAAACTTAATTCCCTATAGTGAAACGACGCTGTTT
1 TTTGCGGCATTTCCAGTCAAAACACCACTAAAAACTTAATTCCCTATAGTGAAACGAAACCGTTT
* *
4164888 AAGTCAAATTGGTATTGCAATTTTGCGGCATTTATGAAAAACGCCACTAATATATAACCTTTGCG
66 AAGTCAAATTGGTATTGCAATTTTGCGGCATTTATGAAAAACACCACTAATATATAACCTTTGCC
* *
4164953 GCATTTTCTGTCGAAACACCACCAAAAACTTAACTCCCTGTAGTGAAACGACGCCGTTTAAGTCA
131 GCATTTTCTGTCAAAACACCACAAAAAACTTAACTCCCTGTAGTGAAACGACGCCGTTTAAGTCA
*
4165018 AATTGGTATTGCATT
196 AATTGGTATTGCAAT
* * *
4165033 TTTGCGGCATTTTCGGTCAAAACACCACTAAAAATTTAATTCCCTATAGTGAAACGAAACCGTTT
1 TTTGCGGCATTTCCAGTCAAAACACCACTAAAAACTTAATTCCCTATAGTGAAACGAAACCGTTT
* * * *
4165098 AAGTCAAATTGGTATTGCAATTTTGCGGCGTTTATGAAAAACACCACTAATGTATGATCTTTGCC
66 AAGTCAAATTGGTATTGCAATTTTGCGGCATTTATGAAAAACACCACTAATATATAACCTTTGCC
* * * * *
4165163 GCGTTTT-TAGTCAAAACGCCACAAAAAATTTAA-TGCTCTGTAGTGAAACGACGTCGTTTAAGT
131 GCATTTTCT-GTCAAAACACCACAAAAAACTTAACT-CCCTGTAGTGAAACGACGCCGTTTAAGT
**
4165226 TGAATTGGTATTGCAAT
194 CAAATTGGTATTGCAAT
4165243 TTTGCGGC
1 TTTGCGGC
4165251 GTTTATGAAA
Statistics
Matches: 192, Mismatches: 24, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
209 2 0.01
210 190 0.99
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.32
Consensus pattern (210 bp):
TTTGCGGCATTTCCAGTCAAAACACCACTAAAAACTTAATTCCCTATAGTGAAACGAAACCGTTT
AAGTCAAATTGGTATTGCAATTTTGCGGCATTTATGAAAAACACCACTAATATATAACCTTTGCC
GCATTTTCTGTCAAAACACCACAAAAAACTTAACTCCCTGTAGTGAAACGACGCCGTTTAAGTCA
AATTGGTATTGCAAT
Found at i:4165211 original size:124 final size:123
Alignment explanation
Indices: 4165033--4165344 Score: 408
Period size: 124 Copynumber: 2.5 Consensus size: 123
4165023 GTATTGCATT
* * * * * *
4165033 TTTGCGGCATTTTCGGTCAAAACACCACTAAAAATTTAATTCCCTATAGTGAAACGAAACCGTTT
1 TTTGCCGCATTTTCAGTCAAAACGCCACAAAAAATTTAATT-CCTGTAGTGAAACGACACCGTTT
*
4165098 AAGTCAAATTGGTATTGCAATTTTGCGGCGTTTATGAAAAACACCACTAATGTATGATC
65 AAGTCAAATTGGTATTGCAATTTTGCGGCGTTTATGAAAAACACCACTAATGTATGACC
* * * **
4165157 TTTGCCGCGTTTTTAGTCAAAACGCCACAAAAAATTTAATGCTCTGTAGTGAAACGACGTCGTTT
1 TTTGCCGCATTTTCAGTCAAAACGCCACAAAAAATTTAATTC-CTGTAGTGAAACGACACCGTTT
** * *
4165222 AAGTTGAATTGGTATTGCAATTTTGCGGCGTTTATGAAAAGCGCCACTAATGTATGACC
65 AAGTCAAATTGGTATTGCAATTTTGCGGCGTTTATGAAAAACACCACTAATGTATGACC
** * * * *
4165281 TTTGTGGCATTTTCAGTCAAAACGCCATAAAAAAATTATTTCCTGTAGTGAAACGGCACCGTTT
1 TTTGCCGCATTTTCAGTCAAAACGCCACAAAAAATTTAATTCCTGTAGTGAAACGACACCGTTT
4165345 TGCAAAATTT
Statistics
Matches: 160, Mismatches: 27, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
123 20 0.12
124 140 0.88
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.32
Consensus pattern (123 bp):
TTTGCCGCATTTTCAGTCAAAACGCCACAAAAAATTTAATTCCTGTAGTGAAACGACACCGTTTA
AGTCAAATTGGTATTGCAATTTTGCGGCGTTTATGAAAAACACCACTAATGTATGACC
Found at i:4178124 original size:43 final size:43
Alignment explanation
Indices: 4178065--4178256 Score: 138
Period size: 44 Copynumber: 4.4 Consensus size: 43
4178055 CCCTGAGGTT
*
4178065 GCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCA
1 GCAGTGGAGTAGATTGAAGCCAGTAATTCTACTTCCCTGGGCA
* ** * **
4178108 GCAGTGGAATAGATTGAAGATTTTAG-ATATTGT-C-TCCCTAAGCA
1 GCAGTGGAGTAGATTGAAG---CCAGTA-ATTCTACTTCCCTGGGCA
* * ** ** * * **
4178152 GTAGTGGAGCAGATCAAAGATAGTGAATTTTACCTCCCTGAGGTT
1 GCAGTGGAGTAGATTGAAGCCAGT-AATTCTACTTCCCTG-GGCA
*
4178197 GCAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCA
1 GCAGTGGAGTAGATTGAAGCCAGTAATTCTACTTCCCTGGGCA
*
4178240 GCAGTGGAATAGATTGA
1 GCAGTGGAGTAGATTGA
4178257 GGATTTTAGA
Statistics
Matches: 109, Mismatches: 31, Indels: 18
0.69 0.20 0.11
Matches are distributed among these distances:
41 3 0.03
42 4 0.04
43 36 0.33
44 40 0.37
45 20 0.18
46 6 0.06
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.28
Consensus pattern (43 bp):
GCAGTGGAGTAGATTGAAGCCAGTAATTCTACTTCCCTGGGCA
Found at i:4178203 original size:132 final size:131
Alignment explanation
Indices: 4178025--4178629 Score: 934
Period size: 132 Copynumber: 4.6 Consensus size: 131
4178015 CATAGACAGC
4178025 GGAGCAGATCAAAGATAGTGAATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTA
1 GGAGCAGATCAAAGAT-GTGAATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTA
*
4178090 ATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTTAGATATTGTCTCCCTAAGCAGTA
65 ATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATATTGTCTCCCTAAGCAGTA
4178155 GT
130 GT
4178157 GGAGCAGATCAAAGATAGTGAATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTA
1 GGAGCAGATCAAAGAT-GTGAATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTA
* * *
4178222 ATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAGGATTTTAGATCTTGTCTCCCTAAGCAGTA
65 ATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATATTGTCTCCCTAAGCAGTA
4178287 GT
130 GT
* *
4178289 GGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA-TA
1 GGAGCAGATCAAAGAT-GTGAATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGT-
* * * * *
4178353 AATTCTACTACCCTGGGCAGCAGCGGAATAGATTGAAGATTTCAG--ATTGCCTCCCTACGTAGT
64 AATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATATTGTCTCCCTAAGCAGT
4178416 AGT
129 AGT
* * * *
4178419 GGAGCAGATCAAAGATG-GCAGATTGTACCTCCCTGTGGTTACAGTGAAGTACATTGAAGCCAGT
1 GGAGCAGATCAAAGATGTG-A-ATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGT
* *
4178483 AATTCTACTTCCTTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGT
64 AATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATATTGTCTCCCTAAGCAGT
4178548 AGT
129 AGT
4178551 GGAGCAGATCAAAGATG-GCAGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGT
1 GGAGCAGATCAAAGATGTG-A-ATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGT
4178615 AATTCTA-TCTCCCTG
64 AATTCTACT-TCCCTG
4178630 NNNNNNNNNN
Statistics
Matches: 439, Mismatches: 27, Indels: 14
0.91 0.06 0.03
Matches are distributed among these distances:
128 1 0.00
129 2 0.00
130 114 0.26
131 3 0.01
132 319 0.73
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (131 bp):
GGAGCAGATCAAAGATGTGAATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTAA
TTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATATTGTCTCCCTAAGCAGTAG
T
Found at i:4178532 original size:262 final size:262
Alignment explanation
Indices: 4178025--4178629 Score: 959
Period size: 262 Copynumber: 2.3 Consensus size: 262
4178015 CATAGACAGC
*
4178025 GGAGCAGATCAAAGATAGTGAATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTA
1 GGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTA
* * *
4178090 ATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTTAGATATTGTCTCCCTAAGCAGTA
66 ATTCTAC-TCCCTGGGCAGCAGCGGAATAGATTGAAGATTTCAGA-ATTGCCTCCCTAAGCAGTA
* * *
4178155 GTGGAGCAGATCAAAGATAGTGAATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAG
129 GTGGAGCAGATCAAAGATAGTGAATTGTACCTCCCTGAGGTTACAGTGAAGTACATTGAAGCCAG
* *
4178220 TAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAGGATTTTAGATCTTGTCTCCCTAAGCAG
194 TAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAG
4178285 TAGT
259 TAGT
* *
4178289 GGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGTACATTGAAGCCA-TA
1 GGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGT-
* *
4178353 AATTCTACTACCCTGGGCAGCAGCGGAATAGATTGAAGATTTCAG-ATTGCCTCCCTACGTAGTA
65 AATTCTACT-CCCTGGGCAGCAGCGGAATAGATTGAAGATTTCAGAATTGCCTCCCTAAGCAGTA
*
4178417 GTGGAGCAGATCAAAGAT-G-GCAGATTGTACCTCCCTGTGGTTACAGTGAAGTACATTGAAGCC
129 GTGGAGCAGATCAAAGATAGTG-A-ATTGTACCTCCCTGAGGTTACAGTGAAGTACATTGAAGCC
*
4178480 AGTAATTCTACTTCCTTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGC
192 AGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGC
4178545 AGTAGT
257 AGTAGT
*
4178551 GGAGCAGATCAAAGATGG-CAGATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGT
1 GGAGCAGATCAAAGATGGTGA-ATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGT
4178615 AATTCTATCTCCCTG
65 AATTCTA-CTCCCTG
4178630 NNNNNNNNNN
Statistics
Matches: 316, Mismatches: 18, Indels: 16
0.90 0.05 0.05
Matches are distributed among these distances:
260 1 0.00
261 3 0.01
262 207 0.66
263 5 0.02
264 100 0.32
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.28
Consensus pattern (262 bp):
GGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGAGGTTGCAGTGGAGTACATTGAAGCCAGTA
ATTCTACTCCCTGGGCAGCAGCGGAATAGATTGAAGATTTCAGAATTGCCTCCCTAAGCAGTAGT
GGAGCAGATCAAAGATAGTGAATTGTACCTCCCTGAGGTTACAGTGAAGTACATTGAAGCCAGTA
ATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCTCCCTAAGCAGTA
GT
Found at i:4179210 original size:132 final size:131
Alignment explanation
Indices: 4178973--4180466 Score: 1966
Period size: 132 Copynumber: 11.3 Consensus size: 131
4178963 NNNNNNNNNN
*
4178973 ATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTTAGATCTTGTC
1 ATTGAAGCCAGTAATTCTAC-TCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTC
* * * * * *
4179038 TCCTTAAGCAGTAGTGGATCAGATCAAAGATGGCGGATTTTACCTCCCTGAGGTTGCAGTGTAGT
65 TCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGAGGTTACAGTGGAGT
4179103 AC
130 AC
* * *
4179105 ATTGAAGCCAGTAATTCTATCTCCTTGGGCGGCAGTGGAATAGATTGAAGATTTCAGATTTTGTC
1 ATTGAAGCCAGTAATTCTA-CTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTC
* *
4179170 TCCCTAAGCAATAGTGG-GCCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAG
65 TCCCTAAGCAGTAGTGGAG-CAGATCAAAGATGGTGAATTTTACCTCCCTGAGGTTACAGTGGAG
4179234 TAC
129 TAC
4179237 ATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTC
1 ATTGAAGCCAGTAATTCTAC-TCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTC
* * * *
4179302 TCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGCGGATTTTACCTCCCTGAGGTTGCAGTGTAGT
65 TCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGAGGTTACAGTGGAGT
4179367 AC
130 AC
* * *
4179369 ATTGAAGCCAGTAATTCTATCTCCTTGGGCGGCAGTGGAATAGATTGAAGATTTCAGATTTTGTC
1 ATTGAAGCCAGTAATTCTA-CTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTC
* *
4179434 TCCCTAAGCAATAGTGG-GCCAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAG
65 TCCCTAAGCAGTAGTGGAG-CAGATCAAAGATGGTGAATTTTACCTCCCTGAGGTTACAGTGGAG
4179498 TAC
129 TAC
* * *
4179501 ATTGAAGCCAGTAATTCCACTTCCCTTGGCAGCAGTGGAATAGATTAAAGATTTCAGATCTTGTC
1 ATTGAAGCCAGTAATTCTAC-TCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTC
* *
4179566 TTCCC-AAGCAGTAGTGGAGCAGATCAAAGATGATGAATTTTACCTCCCTGTGGTTACAGTGGAG
65 -TCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGAGGTTACAGTGGAG
*
4179630 TAA
129 TAC
* * * *
4179633 ATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAATGGAATAGATTAAAGATTACAGATCTTATC
1 ATTGAAGCCAGTAATTCTAC-TCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTC
* * * * * *
4179698 TCCCTAGGCAGTAGTGGAGTAGATCGAAGATGG-CAGATTTTACCTCCCTGAAGTTATAGTGGAG
65 TCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGA-ATTTTACCTCCCTGAGGTTACAGTGGAG
*
4179762 TAT
129 TAC
* * * ** * *
4179765 ATTGATGCCAGTAATTTTATCTCCCTGGGCAGCAGTGGAATAGATTAAAGATAACATATCTTATC
1 ATTGAAGCCAGTAATTCTA-CTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTC
* *
4179830 TCCCTAAGCAGTAGTGGAGCAGATCAAAGATGG-CAGATTTTACCTCCCTGAGGTTGC-GTGGAG
65 TCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGA-ATTTTACCTCCCTGAGGTTACAGTGGAG
*
4179893 TAT
129 TAC
* * * * *
4179896 ATTGAAGCCAGTAACTCTATCTCCCTGGGCAGCAGTGGAATAGATTGAGGATTACAGATATTATC
1 ATTGAAGCCAGTAATTCTA-CTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTC
* * *
4179961 TCCCTAAGCAGTAGAGGAGCAGATCAAAGATGGTGGACTTTACCTCCCTGAGGTTACAGTGGAGT
65 TCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGAGGTTACAGTGGAGT
4180026 AC
130 AC
* * ** *
4180028 ATTGAAGCCAATAATTCTATCTCCCTGGGCAGCAGTGGAATAGATTAAAGATAACAGATCTTATC
1 ATTGAAGCCAGTAATTCTA-CTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTC
* * *
4180093 TCCCTAAGAAGTAGTGGAGCAGATCAAAGATGG-CAGATTTTACCTCCCTGAGGTTGCAGTGGAG
65 TCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGA-ATTTTACCTCCCTGAGGTTACAGTGGAG
**
4180157 TGT
129 TAC
* *
4180160 ATTGAAGCCAGTAATTCTACTTCCCTGGGCAGAAGTGGAATAGATTAAAGATTTCAGATCTTGTC
1 ATTGAAGCCAGTAATTCTAC-TCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTC
* *
4180225 TCCCTAAGCAGTAGTGGAGTAGATCAAAGATGGTGAATTTTACCTCCCTGTGGTTACAGTGGAGT
65 TCCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGAGGTTACAGTGGAGT
4180290 AC
130 AC
* * * *
4180292 ATTGAAGCCAGTAATTCTACTTCTCTGGGTAGCAGCGGAATAGATTGAAGATTTCAGATCTTGCC
1 ATTGAAGCCAGTAATTCTAC-TCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTC
* * * *
4180357 TTCCT--GCA-TAGATAGCGAAACAGATCGAAGATGGT-AGATTTTACCTCCCTGAGGTTACCGT
65 TCCCTAAGCAGTAG-T-G-G-AGCAGATCAAAGATGGTGA-ATTTTACCTCCCTGAGGTTACAGT
4180418 GGAGTAC
125 GGAGTAC
* * * *
4180425 ATTGAAGCCAGCAATTCAATCTCCCAGGGCAACAGTGGAATA
1 ATTGAAGCCAGTAATTCTA-CTCCCTGGGCAGCAGTGGAATA
4180467 AACAGAAGAA
Statistics
Matches: 1216, Mismatches: 123, Indels: 45
0.88 0.09 0.03
Matches are distributed among these distances:
129 3 0.00
130 4 0.00
131 127 0.10
132 995 0.82
133 86 0.07
134 1 0.00
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.28
Consensus pattern (131 bp):
ATTGAAGCCAGTAATTCTACTCCCTGGGCAGCAGTGGAATAGATTGAAGATTTCAGATCTTGTCT
CCCTAAGCAGTAGTGGAGCAGATCAAAGATGGTGAATTTTACCTCCCTGAGGTTACAGTGGAGTA
C
Found at i:4181948 original size:3 final size:3
Alignment explanation
Indices: 4181928--4181993 Score: 55
Period size: 3 Copynumber: 21.3 Consensus size: 3
4181918 GGGTTCCTTG
** *
4181928 TTA TTAA TTA TT- TTA TTA TTA AAA TTAA TTA TTT TTA TTA -TA TTA
1 TTA TT-A TTA TTA TTA TTA TTA TTA TT-A TTA TTA TTA TTA TTA TTA
4181973 GTTA TTA TTA TTGA TTA TTA T
1 -TTA TTA TTA TT-A TTA TTA T
4181994 CATATTTTCT
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
2 4 0.08
3 35 0.69
4 12 0.24
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:4181989 original size:7 final size:6
Alignment explanation
Indices: 4181928--4181993 Score: 55
Period size: 7 Copynumber: 10.7 Consensus size: 6
4181918 GGGTTCCTTG
** *
4181928 TTATTAA TTATT- TTATTA TTAAAA TTAATTA TTTTTA TTA-TA TTAGTTA
1 TTATT-A TTATTA TTATTA TTATTA TT-ATTA TTATTA TTATTA TTA-TTA
4181977 TTATTA TTGATTA TTAT
1 TTATTA TT-ATTA TTAT
4181994 CATATTTTCT
Statistics
Matches: 48, Mismatches: 6, Indels: 11
0.74 0.09 0.17
Matches are distributed among these distances:
5 10 0.21
6 18 0.38
7 20 0.42
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (6 bp):
TTATTA
Found at i:4183225 original size:20 final size:21
Alignment explanation
Indices: 4183188--4183231 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
4183178 ATTATTGATA
* *
4183188 ATTTTTTATAATAATTAATATT
1 ATTTTTTAGAAT-ATTAAAATT
4183210 ATTTTTTAGAAT-TTAAAATT
1 ATTTTTTAGAATATTAAAATT
4183230 AT
1 AT
4183232 GTAATTATGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 9 0.45
22 11 0.55
ACGTcount: A:0.41, C:0.00, G:0.02, T:0.57
Consensus pattern (21 bp):
ATTTTTTAGAATATTAAAATT
Found at i:4186872 original size:22 final size:22
Alignment explanation
Indices: 4186844--4186893 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
4186834 AAGAAACTAA
* *
4186844 TGTTTTCTTGTTGTTTTTTCAT
1 TGTTTTCTTGTTGCTTTCTCAT
4186866 TGTTTTCTTGTTGCTTTCTCAT
1 TGTTTTCTTGTTGCTTTCTCAT
4186888 TGTTTT
1 TGTTTT
4186894 GCTGTAATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.04, C:0.12, G:0.14, T:0.70
Consensus pattern (22 bp):
TGTTTTCTTGTTGCTTTCTCAT
Found at i:4187453 original size:22 final size:20
Alignment explanation
Indices: 4187405--4187454 Score: 55
Period size: 22 Copynumber: 2.4 Consensus size: 20
4187395 TTTTTTTATG
*
4187405 ATTTTTTTAATTTTTTGAGA
1 ATTTTTTTAATTTTTTGACA
*
4187425 TTGTTTTTTGAATTTGTTTGACA
1 AT-TTTTTT-AATTT-TTTGACA
4187448 ATTTTTT
1 ATTTTTT
4187455 ATATTTTATC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
20 1 0.04
21 6 0.25
22 10 0.42
23 7 0.29
ACGTcount: A:0.20, C:0.02, G:0.12, T:0.66
Consensus pattern (20 bp):
ATTTTTTTAATTTTTTGACA
Found at i:4187751 original size:27 final size:25
Alignment explanation
Indices: 4187706--4187756 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
4187696 TAACATATTG
*
4187706 AAAATTTTAAGTACCAAATAGATAAA
1 AAAAATTTAAGTACCAAATA-ATAAA
4187732 AAAAATTTAAGTACCAAAATAATAA
1 AAAAATTTAAGTACC-AAATAATAA
4187757 TTTGGTGGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 18 0.78
27 5 0.22
ACGTcount: A:0.61, C:0.08, G:0.06, T:0.25
Consensus pattern (25 bp):
AAAAATTTAAGTACCAAATAATAAA
Found at i:4191151 original size:20 final size:19
Alignment explanation
Indices: 4191128--4191194 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 19
4191118 AGGCAAAAAT
*
4191128 GTGCAATCAGAGGCACCGTA
1 GTGCAAT-AGAGGCACCGAA
*
4191148 GTGCAAATAGAGACACCGAA
1 GTGC-AATAGAGGCACCGAA
*
4191168 GTGTATATAGAGGCACCGAA
1 GTGCA-ATAGAGGCACCGAA
4191188 GTGCAAT
1 GTGCAAT
4191195 CCCGTACAAG
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
19 3 0.08
20 34 0.85
21 3 0.08
ACGTcount: A:0.36, C:0.19, G:0.28, T:0.16
Consensus pattern (19 bp):
GTGCAATAGAGGCACCGAA
Found at i:4193581 original size:5 final size:5
Alignment explanation
Indices: 4193571--4193596 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
4193561 GAAGAGAGAA
4193571 AAAAT AAAAT AAAAT AAAAT AAAAT A
1 AAAAT AAAAT AAAAT AAAAT AAAAT A
4193597 GGATTTAAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AAAAT
Found at i:4194591 original size:75 final size:79
Alignment explanation
Indices: 4194503--4194688 Score: 247
Period size: 83 Copynumber: 2.4 Consensus size: 79
4194493 TAATTAATGG
*
4194503 TGGTGGAGCCATTCTAAATGGCGCCACCACTTTATGTTAG-GTTT-TTTT-TTT-AATTTAAAAA
1 TGGTGGAGCCATTCTAAATGGCGCCACCACTTTATGTTAGTGTTTGTTTTCTTTAAATTAAAAAA
*
4194564 AATGTTATTCTATT
66 AATATTATTCTATT
* *
4194578 TGGTGGAGTCATTCTAAATGGCGCCACCACTTTATGTTAGTTTTTTTAGGTTTTCTTTAAATTAA
1 TGGTGGAGCCATTCTAAATGGCGCCACCACTTTATGTTAG--TGTTT--GTTTTCTTTAAATTAA
*
4194643 AAAAAATATTATTTTATT
62 AAAAAATATTATTCTATT
*
4194661 TGGTGGAGCCATTCTAAATAGCG-CACCA
1 TGGTGGAGCCATTCTAAATGGCGCCACCA
4194689 GTGTAATCTA
Statistics
Matches: 96, Mismatches: 7, Indels: 9
0.86 0.06 0.08
Matches are distributed among these distances:
75 39 0.41
78 3 0.03
81 4 0.04
82 8 0.08
83 42 0.44
ACGTcount: A:0.28, C:0.14, G:0.17, T:0.41
Consensus pattern (79 bp):
TGGTGGAGCCATTCTAAATGGCGCCACCACTTTATGTTAGTGTTTGTTTTCTTTAAATTAAAAAA
AATATTATTCTATT
Found at i:4194715 original size:83 final size:82
Alignment explanation
Indices: 4194545--4194718 Score: 181
Period size: 83 Copynumber: 2.1 Consensus size: 82
4194535 TATGTTAGGT
* * * * * *
4194545 TTTTTTTTTAATTTAAAAAAATGTTATTCTATTTGGTGGAGTCATTCTAAATGGCGCCACCACTT
1 TTTTCTTTAAATTAAAAAAAATATTATTCTATTTGGTGGAGCCATTCTAAATAGCGCCACCACTT
* * * * *
4194610 TATGTTAGTTTTTTTAGG
66 AATCTTACTATTTTTA-C
* *
4194628 TTTTCTTTAAATTAAAAAAAATATTATTTTATTTGGTGGAGCCATTCTAAATAGCG-CACCAGTG
1 TTTTCTTTAAATTAAAAAAAATATTATTCTATTTGGTGGAGCCATTCTAAATAGCGCCACCACT-
4194692 TAATCTATCACTATTTTT-C
65 TAATCT-T-ACTATTTTTAC
4194711 TTTTCTTT
1 TTTTCTTT
4194719 TTTAATATAT
Statistics
Matches: 75, Mismatches: 13, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
82 6 0.08
83 61 0.81
84 1 0.01
85 7 0.09
ACGTcount: A:0.28, C:0.13, G:0.13, T:0.47
Consensus pattern (82 bp):
TTTTCTTTAAATTAAAAAAAATATTATTCTATTTGGTGGAGCCATTCTAAATAGCGCCACCACTT
AATCTTACTATTTTTAC
Found at i:4195279 original size:21 final size:20
Alignment explanation
Indices: 4195253--4195301 Score: 55
Period size: 20 Copynumber: 2.4 Consensus size: 20
4195243 TTTTGGAATG
**
4195253 TTGTAAATGTAAAATTATATT
1 TTGTAAATAAAAAATT-TATT
4195274 TTGTAAA-AAAAAATTTATT
1 TTGTAAATAAAAAATTTATT
4195293 TATGTAAAT
1 T-TGTAAAT
4195302 TGATAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
19 5 0.21
20 12 0.50
21 7 0.29
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (20 bp):
TTGTAAATAAAAAATTTATT
Found at i:4195288 original size:20 final size:20
Alignment explanation
Indices: 4195263--4195300 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
4195253 TTGTAAATGT
4195263 AAAATTATATTT-TGTAAAAA
1 AAAATT-TATTTATGTAAAAA
4195283 AAAATTTATTTATGTAAA
1 AAAATTTATTTATGTAAA
4195301 TTGATAATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (20 bp):
AAAATTTATTTATGTAAAAA
Found at i:4195549 original size:12 final size:12
Alignment explanation
Indices: 4195534--4195558 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
4195524 TTTTAAATTT
4195534 AAAAAAAGAAAA
1 AAAAAAAGAAAA
4195546 AAAAAAAGAAAA
1 AAAAAAAGAAAA
4195558 A
1 A
4195559 TGGTGATAGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAAAAGAAAA
Found at i:4195658 original size:9 final size:9
Alignment explanation
Indices: 4195627--4195661 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
4195617 TTTTTAAATT
4195627 TAAAAAAAC
1 TAAAAAAAC
*
4195636 TAAAAGAAAT
1 TAAAA-AAAC
4195646 TAAAAAAAC
1 TAAAAAAAC
4195655 TAAAAAA
1 TAAAAAA
4195662 TAATAATAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
9 15 0.65
10 8 0.35
ACGTcount: A:0.77, C:0.06, G:0.03, T:0.14
Consensus pattern (9 bp):
TAAAAAAAC
Found at i:4199189 original size:22 final size:24
Alignment explanation
Indices: 4199167--4199226 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 24
4199157 CAAATCGTTC
4199167 TCTTTT-TT-ATTC-CT-CTTTTT
1 TCTTTTATTGATTCTCTCCTTTTT
4199187 TCTTTTATTGATTCTCTCC---TT
1 TCTTTTATTGATTCTCTCCTTTTT
4199208 T-TTTTATTGATTCTCTCCT
1 TCTTTTATTGATTCTCTCCT
4199227 CTCCTACAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 9
0.80 0.00 0.20
Matches are distributed among these distances:
20 23 0.66
21 5 0.14
22 4 0.11
23 2 0.06
24 1 0.03
ACGTcount: A:0.08, C:0.22, G:0.03, T:0.67
Consensus pattern (24 bp):
TCTTTTATTGATTCTCTCCTTTTT
Found at i:4199214 original size:20 final size:20
Alignment explanation
Indices: 4199189--4199226 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
4199179 CTCTTTTTTC
4199189 TTTTATTGATTCTCTCCTTT
1 TTTTATTGATTCTCTCCTTT
4199209 TTTTATTGATTCTCTCCT
1 TTTTATTGATTCTCTCCT
4199227 CTCCTACAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.11, C:0.21, G:0.05, T:0.63
Consensus pattern (20 bp):
TTTTATTGATTCTCTCCTTT
Found at i:4199386 original size:21 final size:21
Alignment explanation
Indices: 4199360--4199477 Score: 186
Period size: 21 Copynumber: 5.7 Consensus size: 21
4199350 AATCATATCT
*
4199360 TCTAAGATTGTATATATCATA
1 TCTAAGATTGCATATATCATA
*
4199381 TCTAAGATTACATATATCATA
1 TCTAAGATTGCATATATCATA
4199402 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
*
4199423 TCTAAGATTACATATATCATA
1 TCTAAGATTGCATATATCATA
4199444 TCTAAGATTGCATATA--ATA
1 TCTAAGATTGCATATATCATA
*
4199463 TCTAAGATTGTATAT
1 TCTAAGATTGCATAT
4199478 CCTCGAAAAT
Statistics
Matches: 91, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
19 17 0.19
21 74 0.81
ACGTcount: A:0.40, C:0.12, G:0.08, T:0.40
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:4199417 original size:42 final size:42
Alignment explanation
Indices: 4199337--4199471 Score: 204
Period size: 42 Copynumber: 3.2 Consensus size: 42
4199327 AAATTAAATC
* *
4199337 TCTAAGATTACA-AAATCATATCTTCTAAGATTGTATATATCATA
1 TCTAAGATTACATATATCATA---TCTAAGATTGCATATATCATA
4199381 TCTAAGATTACATATATCATATCTAAGATTGCATATATCATA
1 TCTAAGATTACATATATCATATCTAAGATTGCATATATCATA
4199423 TCTAAGATTACATATATCATATCTAAGATTGCATATA--ATA
1 TCTAAGATTACATATATCATATCTAAGATTGCATATATCATA
4199463 TCTAAGATT
1 TCTAAGATT
4199472 GTATATCCTC
Statistics
Matches: 88, Mismatches: 2, Indels: 6
0.92 0.02 0.06
Matches are distributed among these distances:
40 12 0.14
42 57 0.65
44 12 0.14
45 7 0.08
ACGTcount: A:0.41, C:0.13, G:0.07, T:0.39
Consensus pattern (42 bp):
TCTAAGATTACATATATCATATCTAAGATTGCATATATCATA
Found at i:4199740 original size:44 final size:44
Alignment explanation
Indices: 4199681--4199765 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 44
4199671 AGGAATTCGT
*
4199681 GCTTCAATCTACTCCACTGTAACTTCAGG-GAGATAAGACTTATA
1 GCTTCAATCTACTCCACTGCAACTTCAGGAG-GATAAGACTTATA
* * *
4199725 GCTTTAATCTGCTCCACTGCCACTTCAGGAGGATAAGACTT
1 GCTTCAATCTACTCCACTGCAACTTCAGGAGGATAAGACTT
4199766 GCTGGCTTAA
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
44 35 0.97
45 1 0.03
ACGTcount: A:0.28, C:0.25, G:0.18, T:0.29
Consensus pattern (44 bp):
GCTTCAATCTACTCCACTGCAACTTCAGGAGGATAAGACTTATA
Found at i:4199847 original size:44 final size:44
Alignment explanation
Indices: 4199799--4200115 Score: 157
Period size: 44 Copynumber: 7.2 Consensus size: 44
4199789 TATCTTGGAA
*
4199799 AGATAAGATTTGCCTTCTTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCCTTCTTTAATCTGCTCCACTACTGCTTAGGG
* * ** * * * * * *
4199843 AGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGG
1 AGATAAGATTTGCCTTCTTTAATCTGCTCCACTACTGCTTAGGG
* ** * * * *
4199887 AGACAAGGCTTG-GTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTTGCCT-TCTTTAATCTGC-T-CCACTACTGCTTAGG-G
*
4199931 AGATAAGATTTGCCGTT-TTTGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATTTGCC-TTCTTTAATCTGCTCCACTACTGCTTAGGG
* * ** * * * * *
4199975 AGATAAGATCTACAATCTTTAACCTACTCCGCTGCTGCTCAGGG
1 AGATAAGATTTGCCTTCTTTAATCTGCTCCACTACTGCTTAGGG
* ** * * * *
4200019 AGACAAGGCTTG-GTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAAGATTTGCCT-TCTTTAATCTGC-T-CCACTACTGCTTAGG-G
* *
4200063 AGATAAGATTTGCCTTCTTTGATCTGCTTCACTACTGCTTAGGG
1 AGATAAGATTTGCCTTCTTTAATCTGCTCCACTACTGCTTAGGG
4200107 AGATAAGAT
1 AGATAAGAT
4200116 CTGTAATTTT
Statistics
Matches: 187, Mismatches: 68, Indels: 36
0.64 0.23 0.12
Matches are distributed among these distances:
42 11 0.06
43 9 0.05
44 149 0.80
45 9 0.05
46 9 0.05
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.32
Consensus pattern (44 bp):
AGATAAGATTTGCCTTCTTTAATCTGCTCCACTACTGCTTAGGG
Found at i:4199944 original size:132 final size:132
Alignment explanation
Indices: 4199763--4200160 Score: 690
Period size: 132 Copynumber: 3.0 Consensus size: 132
4199753 GAGGATAAGA
*
4199763 CTTGCTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCTTCTTTGATCTGCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCTTCTTTGATCTGCTC
*
4199828 CACTACTGCTTAGGGAGATAAGATCTACAATCTTCAACCTACTCCGCTGCTGCTCAGGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTAAACCTACTCCGCTGCTGCTCAGGGAGACAA
4199893 GG
131 GG
4199895 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCGTT-TTTGATCTGCT
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCC-TTCTTTGATCTGCT
*
4199959 CCACTACTGCTTAGGGAGATAAGATCTACAATCTTTAACCTACTCCGCTGCTGCTCAGGGAGACA
65 CCACTACTGCTTAGGGAGATAAGATCTACAATCTTAAACCTACTCCGCTGCTGCTCAGGGAGACA
4200024 AGG
130 AGG
*
4200027 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCTTCTTTGATCTGCTT
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCTTCTTTGATCTGCTC
** * * * *
4200092 CACTACTGCTTAGGGAGATAAGATCTGTAATTTTAAACCTACTCCACTGCTGCTCAGGAAGATAA
66 CACTACTGCTTAGGGAGATAAGATCTACAATCTTAAACCTACTCCGCTGCTGCTCAGGGAGACAA
4200157 GG
131 GG
4200159 CT
1 CT
4200161 GGAGTCTTTG
Statistics
Matches: 254, Mismatches: 10, Indels: 4
0.95 0.04 0.01
Matches are distributed among these distances:
131 2 0.01
132 250 0.98
133 2 0.01
ACGTcount: A:0.25, C:0.24, G:0.20, T:0.32
Consensus pattern (132 bp):
CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTTGCCTTCTTTGATCTGCTC
CACTACTGCTTAGGGAGATAAGATCTACAATCTTAAACCTACTCCGCTGCTGCTCAGGGAGACAA
GG
Found at i:4200154 original size:88 final size:88
Alignment explanation
Indices: 4200078--4200389 Score: 220
Period size: 88 Copynumber: 3.6 Consensus size: 88
4200068 AGATTTGCCT
* *
4200078 TCTTTGATCTGCTTCACTA-CTGCT-TAGGGAGATAAGATCTG-TAATTTTAAACCTACTCCACT
1 TCTTTGATCTGCTTCACTATC-GCTGTAGGAAGACAAGATCTGCT-ATTTTAAACCTACTCCACT
*
4200140 GCTGCTCAGGAAGATAAGGCTGGAG
64 GCTGCTCAGGAAGATAAGGCTGCAG
* * *
4200165 TCTTTGATCTGCTTCACTATCGGTGTAGGAAGGCAAGATCTGCTATTTTTAACCTACTCCACTGC
1 TCTTTGATCTGCTTCACTATCGCTGTAGGAAGACAAGATCTGCTATTTTAAACCTACTCCACTGC
** * **
4200230 AACACAGGAAGGCAAGGCTG-ATG
66 TGCTCAGGAAGATAAGGCTGCA-G
* * * ** * * * * * ** *
4200253 TCTTCGATCTACTTCGCCGTCGGTGCAGGAAGGCAAGATCTGTTATTTTTAACCTGTTCCGCTGC
1 TCTTTGATCTGCTTCACTATCGCTGTAGGAAGACAAGATCTGCTATTTTAAACCTACTCCACTGC
** * * **
4200318 AACACAGGGAGGCAAGGCTG-ATG
66 TGCTCAGGAAGATAAGGCTGCA-G
* * * * * * *
4200341 TCTTCGGTCTGCTTCGCTGTCGGTGCAGGAAGGCAAGATCTGCTATTTT
1 TCTTTGATCTGCTTCACTATCGCTGTAGGAAGACAAGATCTGCTATTTT
4200390 CACTAATCTG
Statistics
Matches: 196, Mismatches: 25, Indels: 7
0.86 0.11 0.03
Matches are distributed among these distances:
87 22 0.11
88 173 0.88
89 1 0.01
ACGTcount: A:0.23, C:0.22, G:0.25, T:0.30
Consensus pattern (88 bp):
TCTTTGATCTGCTTCACTATCGCTGTAGGAAGACAAGATCTGCTATTTTAAACCTACTCCACTGC
TGCTCAGGAAGATAAGGCTGCAG
Found at i:4200375 original size:44 final size:44
Alignment explanation
Indices: 4200234--4200377 Score: 121
Period size: 44 Copynumber: 3.3 Consensus size: 44
4200224 CACTGCAACA
* *
4200234 CAGGAAGGCAAGGCTGATGTCTTCGATCTACTTCGCCGTCGGTG
1 CAGGAAGGCAAGGCTGATGTCTTCGATCTGCTTCGCTGTCGGTG
* * * * ** * ****
4200278 CAGGAAGGCAAGATCTGTTATTTTTAACCTG-TTCCGCTG-CAACA
1 CAGGAAGGCAAG-GCTGATGTCTTCGATCTGCTT-CGCTGTCGGTG
* *
4200322 CAGGGAGGCAAGGCTGATGTCTTCGGTCTGCTTCGCTGTCGGTG
1 CAGGAAGGCAAGGCTGATGTCTTCGATCTGCTTCGCTGTCGGTG
4200366 CAGGAAGGCAAG
1 CAGGAAGGCAAG
4200378 ATCTGCTATT
Statistics
Matches: 69, Mismatches: 27, Indels: 8
0.66 0.26 0.08
Matches are distributed among these distances:
43 15 0.22
44 40 0.58
45 14 0.20
ACGTcount: A:0.21, C:0.23, G:0.31, T:0.25
Consensus pattern (44 bp):
CAGGAAGGCAAGGCTGATGTCTTCGATCTGCTTCGCTGTCGGTG
Found at i:4207797 original size:22 final size:22
Alignment explanation
Indices: 4207772--4207825 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
4207762 TCTATTTTTT
*
4207772 ATTC-CTCCTTTTTCTTTTGTTG
1 ATTCTCTCCTTTTT-TTTTATTG
4207794 ATTCTCTCCTTTTTTTTTATTG
1 ATTCTCTCCTTTTTTTTTATTG
4207816 ATTCTCTCCT
1 ATTCTCTCCT
4207826 CTCCTACAAT
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
22 21 0.70
23 9 0.30
ACGTcount: A:0.07, C:0.24, G:0.06, T:0.63
Consensus pattern (22 bp):
ATTCTCTCCTTTTTTTTTATTG
Found at i:4207985 original size:21 final size:21
Alignment explanation
Indices: 4207959--4208055 Score: 153
Period size: 21 Copynumber: 4.7 Consensus size: 21
4207949 AATCATATCT
*
4207959 TCTAAGATTGTATATATCATA
1 TCTAAGATTGCATATATCATA
*
4207980 TCTAAGATTACATATATCATA
1 TCTAAGATTGCATATATCATA
4208001 TCTAAGATTGCATATATCATA
1 TCTAAGATTGCATATATCATA
4208022 TCTAAGATTGCATATA--ATA
1 TCTAAGATTGCATATATCATA
*
4208041 TCTAAGATTGTATAT
1 TCTAAGATTGCATAT
4208056 CCTCGAAAAT
Statistics
Matches: 72, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
19 17 0.24
21 55 0.76
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.40
Consensus pattern (21 bp):
TCTAAGATTGCATATATCATA
Found at i:4208380 original size:13 final size:13
Alignment explanation
Indices: 4208362--4208413 Score: 52
Period size: 13 Copynumber: 3.9 Consensus size: 13
4208352 GAGTTAGATA
*
4208362 AAATAATTAAAAT
1 AAATAAATAAAAT
* *
4208375 AAATAACTAAGAT
1 AAATAAATAAAAT
4208388 AAATAAAATAAAAT
1 AAAT-AAATAAAAT
4208402 -AATAAAATAAAA
1 AAAT-AAATAAAA
4208414 GATTGGACAA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
13 27 0.79
14 7 0.21
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.23
Consensus pattern (13 bp):
AAATAAATAAAAT
Found at i:4208394 original size:22 final size:22
Alignment explanation
Indices: 4208359--4208412 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
4208349 TCCGAGTTAG
*
4208359 ATAAAATAATTAAAAT-AAATA
1 ATAAAATAAATAAAATAAAATA
*
4208380 ACTAAGATAAATAAAATAAAATA
1 A-TAAAATAAATAAAATAAAATA
4208403 ATAAAATAAA
1 ATAAAATAAA
4208413 AGATTGGACA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
21 1 0.04
22 21 0.75
23 6 0.21
ACGTcount: A:0.72, C:0.02, G:0.02, T:0.24
Consensus pattern (22 bp):
ATAAAATAAATAAAATAAAATA
Found at i:4210223 original size:33 final size:33
Alignment explanation
Indices: 4210186--4210258 Score: 92
Period size: 33 Copynumber: 2.2 Consensus size: 33
4210176 ACTTTCTGTT
* *
4210186 TGGTGTGTTGGTTGGACTAGCTCTTATGAGCAC
1 TGGTGTGATGGTTGGACTAGCTCTTATAAGCAC
* * * *
4210219 TGGTGTGATGGTTGGATTAGTTCTTCTAAGCAT
1 TGGTGTGATGGTTGGACTAGCTCTTATAAGCAC
4210252 TGGTGTG
1 TGGTGTG
4210259 GATGAAGGAT
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.15, C:0.11, G:0.34, T:0.40
Consensus pattern (33 bp):
TGGTGTGATGGTTGGACTAGCTCTTATAAGCAC
Found at i:4219281 original size:50 final size:50
Alignment explanation
Indices: 4219178--4219419 Score: 238
Period size: 50 Copynumber: 4.7 Consensus size: 50
4219168 GGGAATGAGA
**
4219178 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCATTATTGAGATTATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGC---ACCGAG---ATGAGAGG
* *
4219234 TCCCATATAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGG
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * **
4219284 TCCTCA-GTAAGACCATGTCTGGGACATGGCATGGGCACCGATATGAGAAC
1 TCC-CATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
* * * * * **
4219334 TCCCATGTAAGACCATATCTGGGATATGGCATTGGCA--GTACAGGAAACA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCG-AGATGAGAGG
* *
4219383 TCCCATGTAAGACCATGTCTAGGACATGGCTTTGGCA
1 TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
4219420 TGTTATTATC
Statistics
Matches: 161, Mismatches: 22, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
48 1 0.01
49 40 0.25
50 80 0.50
51 2 0.01
53 4 0.02
56 34 0.21
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.24
Consensus pattern (50 bp):
TCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCGAGATGAGAGG
Found at i:4219647 original size:20 final size:20
Alignment explanation
Indices: 4219622--4219660 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
4219612 TGAGTTATTT
4219622 AAGTAAGCA-AGTAAGTAAAC
1 AAGTAAG-AGAGTAAGTAAAC
4219642 AAGTAAGAGAGTAAGTAAA
1 AAGTAAGAGAGTAAGTAAA
4219661 GAAGAAAGTA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.56, C:0.05, G:0.23, T:0.15
Consensus pattern (20 bp):
AAGTAAGAGAGTAAGTAAAC
Found at i:4234972 original size:27 final size:28
Alignment explanation
Indices: 4234940--4235063 Score: 97
Period size: 30 Copynumber: 4.2 Consensus size: 28
4234930 ATATCGCCGT
* *
4234940 AAAGGCTCACGTAT-AACAAAGAGCCAC
1 AAAGGCTCACGTATCAAAAAACAGCCAC
*
4234967 AAAGGCTTTCACTTATCAAAAAACAGCCAC
1 AAAGGC--TCACGTATCAAAAAACAGCCAC
* * * *
4234997 AAAGGCTTTCTCATATCTAATAACAGCCAC
1 AAAGGC--TCACGTATCAAAAAACAGCCAC
* * *
4235027 AAAGGCTTTCACATATCTAATAACAGCCAC
1 AAAGGC--TCACGTATCAAAAAACAGCCAC
4235057 AAAGGCT
1 AAAGGCT
4235064 TTCACATTTC
Statistics
Matches: 86, Mismatches: 8, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
27 6 0.07
28 1 0.01
29 7 0.08
30 72 0.84
ACGTcount: A:0.41, C:0.26, G:0.13, T:0.20
Consensus pattern (28 bp):
AAAGGCTCACGTATCAAAAAACAGCCAC
Found at i:4234997 original size:30 final size:30
Alignment explanation
Indices: 4234961--4235070 Score: 184
Period size: 30 Copynumber: 3.7 Consensus size: 30
4234951 TATAACAAAG
* * *
4234961 AGCCACAAAGGCTTTCACTTATCAAAAAAC
1 AGCCACAAAGGCTTTCACATATCTAATAAC
*
4234991 AGCCACAAAGGCTTTCTCATATCTAATAAC
1 AGCCACAAAGGCTTTCACATATCTAATAAC
4235021 AGCCACAAAGGCTTTCACATATCTAATAAC
1 AGCCACAAAGGCTTTCACATATCTAATAAC
4235051 AGCCACAAAGGCTTTCACAT
1 AGCCACAAAGGCTTTCACAT
4235071 TTCGATAATG
Statistics
Matches: 75, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 75 1.00
ACGTcount: A:0.39, C:0.27, G:0.11, T:0.23
Consensus pattern (30 bp):
AGCCACAAAGGCTTTCACATATCTAATAAC
Found at i:4235322 original size:55 final size:54
Alignment explanation
Indices: 4235179--4235329 Score: 171
Period size: 55 Copynumber: 2.7 Consensus size: 54
4235169 ATTTCCCTAC
* * * *
4235179 ATGACGCCATAGTCCCAAACTAGGTCTTATACTATGTGGTTCTCTTATCCCCAT
1 ATGATGCCATAGTCCCAGACTAGGTCTTACACTATATGGTTCTCTTATCCCCAT
* **
4235233 ATGATGCCACAACCACCATGACTAGGTCTTACACTATATGGTT-T-TTCACTTCCCCAT
1 ATGATGCCATAGTC-CCA-GACTAGGTCTTACACTATATGGTTCTCTT-A--TCCCCAT
*
4235290 ATGATGCCATAGTCTCAGACTAGGTCTTACACTATATGGT
1 ATGATGCCATAGTCCCAGACTAGGTCTTACACTATATGGT
4235330 CTTCTTGCCA
Statistics
Matches: 81, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
54 12 0.15
55 28 0.35
56 23 0.28
57 18 0.22
ACGTcount: A:0.26, C:0.26, G:0.15, T:0.32
Consensus pattern (54 bp):
ATGATGCCATAGTCCCAGACTAGGTCTTACACTATATGGTTCTCTTATCCCCAT
Found at i:4236042 original size:34 final size:34
Alignment explanation
Indices: 4235999--4236068 Score: 113
Period size: 34 Copynumber: 2.1 Consensus size: 34
4235989 ATATAGGCAG
4235999 AGAATACTTCCTAAGGAAGTAATGCGCAGTTCCC
1 AGAATACTTCCTAAGGAAGTAATGCGCAGTTCCC
* * *
4236033 AGAATACTTCCTGAGGAAGTAATGTGCAGTTGCC
1 AGAATACTTCCTAAGGAAGTAATGCGCAGTTCCC
4236067 AG
1 AG
4236069 CACTTATCCG
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.31, C:0.20, G:0.24, T:0.24
Consensus pattern (34 bp):
AGAATACTTCCTAAGGAAGTAATGCGCAGTTCCC
Found at i:4238631 original size:27 final size:27
Alignment explanation
Indices: 4238601--4238654 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
4238591 ATTCACTGAA
*
4238601 TGACTT-ATGCTTGGACTGTCCACCATG
1 TGACTTCA-GCTTGAACTGTCCACCATG
4238628 TGACTTCGAGCTTGAACTGTCCACCAT
1 TGACTTC-AGCTTGAACTGTCCACCAT
4238655 ATGTACTCGC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
27 6 0.25
28 17 0.71
29 1 0.04
ACGTcount: A:0.20, C:0.28, G:0.20, T:0.31
Consensus pattern (27 bp):
TGACTTCAGCTTGAACTGTCCACCATG
Found at i:4239956 original size:18 final size:18
Alignment explanation
Indices: 4239922--4239970 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 18
4239912 GGGTGTGCAT
4239922 AATTCGGTTAAAACCGAAAA
1 AATTCGGTT--AACCGAAAA
***
4239942 AATTCGGTTAACCGACCG
1 AATTCGGTTAACCGAAAA
4239960 AATTCGGTTAA
1 AATTCGGTTAA
4239971 GCGGTCGGTT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 17 0.65
20 9 0.35
ACGTcount: A:0.39, C:0.18, G:0.18, T:0.24
Consensus pattern (18 bp):
AATTCGGTTAACCGAAAA
Found at i:4240742 original size:27 final size:27
Alignment explanation
Indices: 4240704--4240756 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
4240694 AACTATGTCG
4240704 TTGTATACTATTGTCTTAATTTTTTCA
1 TTGTATACTATTGTCTTAATTTTTTCA
4240731 TTGTATACTATTGTCTTAATTTTTTC
1 TTGTATACTATTGTCTTAATTTTTTC
4240757 TTTCATCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.21, C:0.11, G:0.08, T:0.60
Consensus pattern (27 bp):
TTGTATACTATTGTCTTAATTTTTTCA
Found at i:4240874 original size:8 final size:8
Alignment explanation
Indices: 4240861--4240885 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
4240851 CCTATATTGT
4240861 TAATTAAA
1 TAATTAAA
4240869 TAATTAAA
1 TAATTAAA
4240877 TAATTAAA
1 TAATTAAA
4240885 T
1 T
4240886 GCGAACATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (8 bp):
TAATTAAA
Found at i:4241114 original size:17 final size:17
Alignment explanation
Indices: 4241092--4241127 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
4241082 AATTCAGTCG
4241092 TATAAGATTATTTTTCA
1 TATAAGATTATTTTTCA
4241109 TATAAGATTATTTTTCA
1 TATAAGATTATTTTTCA
4241126 TA
1 TA
4241128 CCTTAATTCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.53
Consensus pattern (17 bp):
TATAAGATTATTTTTCA
Found at i:4244600 original size:37 final size:37
Alignment explanation
Indices: 4244550--4245139 Score: 1153
Period size: 37 Copynumber: 15.9 Consensus size: 37
4244540 NNNNNNNNNN
4244550 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
4244587 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
4244624 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
4244661 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
4244698 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
4244735 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
4244772 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
4244809 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
4244846 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
4244883 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
4244920 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
4244957 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
4244994 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
4245031 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
4245068 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
1 AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
* * *
4245105 AATATTTATGTAATGTTTTTAATTATGTAGTGATT
1 AAGACTTATGTAATATTTTTAATTATGTAGTGATT
4245140 TAATTCGGGT
Statistics
Matches: 550, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
37 550 1.00
ACGTcount: A:0.35, C:0.05, G:0.14, T:0.46
Consensus pattern (37 bp):
AAGACTTATGTAATATTTTTAATTATGTAGTGATTCA
Found at i:4245154 original size:9 final size:9
Alignment explanation
Indices: 4245140--4245268 Score: 132
Period size: 9 Copynumber: 13.6 Consensus size: 9
4245130 TGTAGTGATT
4245140 TAATTCGGG
1 TAATTCGGG
4245149 TAATTCGGG
1 TAATTCGGG
*
4245158 TAATTTGGG
1 TAATTCGGG
*
4245167 TATTTTCGGG
1 TA-ATTCGGG
*
4245177 TAATTTGGG
1 TAATTCGGG
4245186 TAATTTTCGGG
1 TAA--TTCGGG
*
4245197 TAATTTGGG
1 TAATTCGGG
*
4245206 TAATTTTTGGG
1 TAA--TTCGGG
4245217 TAATTCGGG
1 TAATTCGGG
4245226 TAATATTCGGG
1 T-A-ATTCGGG
4245237 TAATTCGGG
1 TAATTCGGG
*
4245246 TAAGTCGGG
1 TAATTCGGG
*
4245255 TAAGTCGGG
1 TAATTCGGG
4245264 TAATT
1 TAATT
4245269 TTTAACCAAA
Statistics
Matches: 103, Mismatches: 10, Indels: 14
0.81 0.08 0.11
Matches are distributed among these distances:
9 69 0.67
10 9 0.09
11 25 0.24
ACGTcount: A:0.22, C:0.07, G:0.32, T:0.40
Consensus pattern (9 bp):
TAATTCGGG
Found at i:4245193 original size:20 final size:20
Alignment explanation
Indices: 4245140--4245270 Score: 164
Period size: 20 Copynumber: 6.8 Consensus size: 20
4245130 TGTAGTGATT
4245140 TAATTCGGGTAA--TTCGGG
1 TAATTCGGGTAATTTTCGGG
*
4245158 TAATTTGGGT-ATTTTCGGG
1 TAATTCGGGTAATTTTCGGG
*
4245177 TAATTTGGGTAATTTTCGGG
1 TAATTCGGGTAATTTTCGGG
* *
4245197 TAATTTGGGTAATTTTTGGG
1 TAATTCGGGTAATTTTCGGG
*
4245217 TAATTCGGGTAATATTCGGG
1 TAATTCGGGTAATTTTCGGG
*
4245237 TAATTCGGGTAA--GTCGGG
1 TAATTCGGGTAATTTTCGGG
*
4245255 TAAGTCGGGTAATTTT
1 TAATTCGGGTAATTTT
4245271 TAACCAAAAA
Statistics
Matches: 100, Mismatches: 8, Indels: 8
0.86 0.07 0.07
Matches are distributed among these distances:
17 1 0.01
18 25 0.25
19 16 0.16
20 58 0.58
ACGTcount: A:0.21, C:0.07, G:0.31, T:0.40
Consensus pattern (20 bp):
TAATTCGGGTAATTTTCGGG
Found at i:4245211 original size:29 final size:28
Alignment explanation
Indices: 4245140--4245268 Score: 120
Period size: 29 Copynumber: 4.5 Consensus size: 28
4245130 TGTAGTGATT
*
4245140 TAATTCGGGTAATTCGGGTAATTT-GGG
1 TAATTTGGGTAATTCGGGTAATTTCGGG
* *
4245167 TATTTTCGGGTAATTTGGGTAATTTTCGGG
1 TAATTT-GGGTAATTCGGGTAA-TTTCGGG
*
4245197 TAATTTGGGTAATTTTTGGGTAA-TTCGGG
1 TAATTTGGGTAA--TTCGGGTAATTTCGGG
*
4245226 TAATATTCGGGTAATTCGGGTAA-GTCGGG
1 TAAT-TT-GGGTAATTCGGGTAATTTCGGG
* *
4245255 TAAGTCGGGTAATT
1 TAATTTGGGTAATT
4245269 TTTAACCAAA
Statistics
Matches: 87, Mismatches: 8, Indels: 14
0.80 0.07 0.13
Matches are distributed among these distances:
27 12 0.14
28 15 0.17
29 35 0.40
30 10 0.11
31 15 0.17
ACGTcount: A:0.22, C:0.07, G:0.32, T:0.40
Consensus pattern (28 bp):
TAATTTGGGTAATTCGGGTAATTTCGGG
Found at i:4248457 original size:9 final size:9
Alignment explanation
Indices: 4248443--4248467 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
4248433 ATTATCTAAT
4248443 ATTAAATTA
1 ATTAAATTA
4248452 ATTAAATTA
1 ATTAAATTA
4248461 ATTAAAT
1 ATTAAAT
4248468 ACAAAAATTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (9 bp):
ATTAAATTA
Found at i:4256486 original size:10 final size:10
Alignment explanation
Indices: 4256467--4256533 Score: 52
Period size: 10 Copynumber: 6.7 Consensus size: 10
4256457 TTAAATTCTA
4256467 ATAAAAATAT
1 ATAAAAATAT
4256477 A-AAAATATAT
1 ATAAAA-ATAT
*
4256487 TTAAAAAT-T
1 ATAAAAATAT
4256496 ATAAAAA-ACT
1 ATAAAAATA-T
4256506 ATAAAAATCAT
1 ATAAAAAT-AT
*
4256517 A-AAAAAAACT
1 ATAAAAATA-T
4256527 ATAAAAA
1 ATAAAAA
4256534 GTTGTNNNNN
Statistics
Matches: 46, Mismatches: 3, Indels: 15
0.72 0.05 0.23
Matches are distributed among these distances:
9 12 0.26
10 22 0.48
11 11 0.24
12 1 0.02
ACGTcount: A:0.70, C:0.04, G:0.00, T:0.25
Consensus pattern (10 bp):
ATAAAAATAT
Found at i:4256627 original size:21 final size:20
Alignment explanation
Indices: 4256601--4256657 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 20
4256591 NNNNNNNGAT
* *
4256601 AATTTTATAATTTTTTTTATG
1 AATTTTATAATTTTCTTTA-C
4256622 AATTTTAT-A-TTTCTTTAC
1 AATTTTATAATTTTCTTTAC
4256640 AATTTTTATAATTTTCTT
1 AA-TTTTATAATTTTCTT
4256658 ACGACTTTAT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
18 2 0.06
19 13 0.42
20 2 0.06
21 14 0.45
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (20 bp):
AATTTTATAATTTTCTTTAC
Done.