Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold506
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: 486993
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 2 of 3
Found at i:194307 original size:13 final size:13
Alignment explanation
Indices: 194289--194314 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
194279 CAATTTTTGG
194289 TGTATCGATACAT
1 TGTATCGATACAT
194302 TGTATCGATACAT
1 TGTATCGATACAT
194315 ACTTGGTGTA
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:194326 original size:32 final size:33
Alignment explanation
Indices: 194269--194332 Score: 103
Period size: 32 Copynumber: 2.0 Consensus size: 33
194259 TACAAGCCAA
**
194269 TGTATCGATACAATTTTTGGTGTATCGATACAT
1 TGTATCGATACAATACTTGGTGTATCGATACAT
194302 TGTATCGATAC-ATACTTGGTGTATCGATACA
1 TGTATCGATACAATACTTGGTGTATCGATACA
194333 AGTTTGGCTA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
32 18 0.62
33 11 0.38
ACGTcount: A:0.28, C:0.14, G:0.19, T:0.39
Consensus pattern (33 bp):
TGTATCGATACAATACTTGGTGTATCGATACAT
Found at i:194339 original size:19 final size:18
Alignment explanation
Indices: 194269--194339 Score: 62
Period size: 19 Copynumber: 4.0 Consensus size: 18
194259 TACAAGCCAA
194269 TGTATCGATACAATTTTTGG
1 TGTATCGATACAA--TTTGG
194289 TGTATCGATAC-A--T--
1 TGTATCGATACAATTTGG
*
194302 TGTATCGATACATACTTGG
1 TGTATCGATACA-ATTTGG
194321 TGTATCGATACAAGTTTGG
1 TGTATCGATACAA-TTTGG
194340 CTACTGCCAA
Statistics
Matches: 43, Mismatches: 1, Indels: 15
0.73 0.02 0.25
Matches are distributed among these distances:
13 11 0.26
15 2 0.05
17 1 0.02
18 1 0.02
19 17 0.40
20 11 0.26
ACGTcount: A:0.27, C:0.13, G:0.21, T:0.39
Consensus pattern (18 bp):
TGTATCGATACAATTTGG
Found at i:196009 original size:60 final size:60
Alignment explanation
Indices: 195904--196047 Score: 164
Period size: 60 Copynumber: 2.4 Consensus size: 60
195894 TGCTCATACA
* * ** * *
195904 AAGTTATTGTTTGGGTTTCTAATTTCATCCAAGCCATTTAGTTGAGTCTTGGTTGTGCCC
1 AAGTCATTGTTTAGGTTTCTGGTTTCATCCAAGCCATTTAATTGAGTCTTAGTTGTGCCC
* * * * * *
195964 CAGTCATTGTTTAGGTTTCTGGTTTCGTCCATGCCGTTTAATTGAGTCTTAGTTTTGCCT
1 AAGTCATTGTTTAGGTTTCTGGTTTCATCCAAGCCATTTAATTGAGTCTTAGTTGTGCCC
*
196024 AAGTCATT-TTTAGGTTTTTGGTTT
1 AAGTCATTGTTTAGGTTTCTGGTTT
196048 TGTCTAGACA
Statistics
Matches: 70, Mismatches: 14, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
59 15 0.21
60 55 0.79
ACGTcount: A:0.16, C:0.15, G:0.22, T:0.47
Consensus pattern (60 bp):
AAGTCATTGTTTAGGTTTCTGGTTTCATCCAAGCCATTTAATTGAGTCTTAGTTGTGCCC
Found at i:199244 original size:13 final size:13
Alignment explanation
Indices: 199226--199250 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
199216 CAAAGATCAG
199226 TGTATCGATACAA
1 TGTATCGATACAA
199239 TGTATCGATACA
1 TGTATCGATACA
199251 TTTCGGTAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:206291 original size:52 final size:52
Alignment explanation
Indices: 206213--206341 Score: 231
Period size: 52 Copynumber: 2.5 Consensus size: 52
206203 CGAAATATGA
206213 AAATTTGCCTACATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTACATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
* *
206265 AAATTTGACTACATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTACATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
*
206317 AAATTTGCCTGCATGTATCGATACA
1 AAATTTGCCTACATGTATCGATACA
206342 AAGATCAGTG
Statistics
Matches: 73, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 73 1.00
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTACATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
Found at i:206352 original size:52 final size:51
Alignment explanation
Indices: 206213--206361 Score: 219
Period size: 52 Copynumber: 2.9 Consensus size: 51
206203 CGAAATATGA
206213 AAATTTGCCTACATGTATCGATACATTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTACATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
* *
206265 AAATTTGACTACATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTACATGTATCGATACA-TTAATAGTGTATCGATACATCTGGGC
* *
206317 AAATTTGCCTGCATGTATCGATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTACATGTATCGATACATTA-AT-AGTGTATCGATACA
206362 ATGTATCGAT
Statistics
Matches: 89, Mismatches: 6, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
51 2 0.02
52 87 0.98
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (51 bp):
AAATTTGCCTACATGTATCGATACATTAATAGTGTATCGATACATCTGGGC
Found at i:206368 original size:13 final size:13
Alignment explanation
Indices: 206350--206374 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
206340 CAAAGATCAG
206350 TGTATCGATACAA
1 TGTATCGATACAA
206363 TGTATCGATACA
1 TGTATCGATACA
206375 TTTAGGTAGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:206448 original size:32 final size:33
Alignment explanation
Indices: 206412--206480 Score: 104
Period size: 32 Copynumber: 2.1 Consensus size: 33
206402 GGCAATAGCT
*
206412 TACATTATATCGGTACAAAAC-TTATGTATCGA
1 TACATTATATCGATACAAAACTTTATGTATCGA
* *
206444 TACATTGTATCGATACAACACTTTATGTATCGA
1 TACATTATATCGATACAAAACTTTATGTATCGA
206477 TACA
1 TACA
206481 AATCGTTGAA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 18 0.55
33 15 0.45
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (33 bp):
TACATTATATCGATACAAAACTTTATGTATCGA
Found at i:206454 original size:13 final size:13
Alignment explanation
Indices: 206436--206460 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
206426 ACAAAACTTA
206436 TGTATCGATACAT
1 TGTATCGATACAT
206449 TGTATCGATACA
1 TGTATCGATACA
206461 ACACTTTATG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:207278 original size:66 final size:65
Alignment explanation
Indices: 207152--207281 Score: 163
Period size: 66 Copynumber: 2.0 Consensus size: 65
207142 TCAAATAACC
* * * *
207152 TCTTTTTGACTTAGGTTCCACCTTGGTCATCTTTAGTTGACTTTATCGATTTTGCTTTAGTCAAA
1 TCTTTTTGACTTAGGTTCCACCTTGGTCACCTTTAGTTGACTTTATAGATTTTACCTTAGTCAAA
*** *
207217 TCTTTTTCGACTTAGGTTTGGCCTTGGTTACCTTTAGTTGACTTTACTAG-TTTTACCTTAGTCA
1 TCTTTTT-GACTTAGGTTCCACCTTGGTCACCTTTAGTTGACTTTA-TAGATTTTACCTTAGTCA
207281 A
64 A
207282 CCCCTCTAAC
Statistics
Matches: 55, Mismatches: 8, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
65 7 0.13
66 46 0.84
67 2 0.04
ACGTcount: A:0.18, C:0.18, G:0.16, T:0.48
Consensus pattern (65 bp):
TCTTTTTGACTTAGGTTCCACCTTGGTCACCTTTAGTTGACTTTATAGATTTTACCTTAGTCAAA
Found at i:207418 original size:41 final size:40
Alignment explanation
Indices: 207365--207508 Score: 155
Period size: 41 Copynumber: 3.5 Consensus size: 40
207355 CCCCTCTAGA
* * **
207365 TAGTTGACTTTTATTAGTTTTGCCCTAGTTAACACTTCAAAC
1 TAGTTGA-TTTTATTAGTTTTG-CCTAGTCAACCCTTTTAAC
*
207407 TAGTTGATTTTAGTAGTTTCAT-CCTAGTCAACCCTTTTAAC
1 TAGTTGATTTTATTAGTTT--TGCCTAGTCAACCCTTTTAAC
* * *
207448 TAGTTGACTTTATTACTTTTGCCTCGGTCAACCCTTTTAAC
1 TAGTTGATTTTATTAGTTTTGCCT-AGTCAACCCTTTTAAC
207489 TTAGTTGATTTTATTAGTTT
1 -TAGTTGATTTTATTAGTTT
207509 CACTGTGGTT
Statistics
Matches: 86, Mismatches: 11, Indels: 10
0.80 0.10 0.09
Matches are distributed among these distances:
39 1 0.01
40 3 0.03
41 57 0.66
42 24 0.28
43 1 0.01
ACGTcount: A:0.23, C:0.18, G:0.12, T:0.47
Consensus pattern (40 bp):
TAGTTGATTTTATTAGTTTTGCCTAGTCAACCCTTTTAAC
Found at i:207494 original size:83 final size:83
Alignment explanation
Indices: 207407--207564 Score: 212
Period size: 83 Copynumber: 1.9 Consensus size: 83
207397 CACTTCAAAC
* *
207407 TAGTTGATTTTAGTAGTTTCA-TCCTAGTCAACCCTTTTAACTAGTTGACTTTATT-ACTTTTGC
1 TAGTTGATTTTAGTAGTTTCACT-CTAGTCAACCCCTTTAACTAGTTAACTTTATTGA-TTTTGC
207470 CTCGGTCAACCCTTTTAACT
64 CTCGGTCAACCCTTTTAACT
* * * * *
207490 TAGTTGATTTTATTAGTTTCACTGTGGTTAACCCCTTTAACTAGTTAACTTTATTGATTTTTCCT
1 TAGTTGATTTTAGTAGTTTCACTCTAGTCAACCCCTTTAACTAGTTAACTTTATTGATTTTGCCT
*
207555 TGGTCAACCC
66 CGGTCAACCC
207565 CCTTTTTGAT
Statistics
Matches: 65, Mismatches: 8, Indels: 4
0.84 0.10 0.05
Matches are distributed among these distances:
83 63 0.97
84 2 0.03
ACGTcount: A:0.22, C:0.20, G:0.13, T:0.46
Consensus pattern (83 bp):
TAGTTGATTTTAGTAGTTTCACTCTAGTCAACCCCTTTAACTAGTTAACTTTATTGATTTTGCCT
CGGTCAACCCTTTTAACT
Found at i:207523 original size:42 final size:40
Alignment explanation
Indices: 207404--207564 Score: 146
Period size: 41 Copynumber: 3.9 Consensus size: 40
207394 TAACACTTCA
* * * *
207404 AACTAGTTGATTTTAGTAGTTTCATCCTAGTCAACCCTTTT
1 AACTAGTTGACTTTATTAGTTTCA-CTTGGTCAACCCTTTT
* *
207445 AACTAGTTGACTTTATTACTTTTGC-CTCGGTCAACCCTTTT
1 AACTAGTTGACTTTATTA-GTTT-CACTTGGTCAACCCTTTT
* * *
207486 AACTTAGTTGATTTTATTAGTTTCACTGTGGTTAACCCCTTT
1 AAC-TAGTTGACTTTATTAGTTTCACT-TGGTCAACCCTTTT
* *
207528 AACTAGTTAACTTTATTGATTTTTC-CTTGGTCAACCC
1 AACTAGTTGACTTTATT-A-GTTTCACTTGGTCAACCC
207565 CCTTTTTGAT
Statistics
Matches: 98, Mismatches: 15, Indels: 14
0.77 0.12 0.11
Matches are distributed among these distances:
40 1 0.01
41 58 0.59
42 34 0.35
43 5 0.05
ACGTcount: A:0.22, C:0.20, G:0.12, T:0.45
Consensus pattern (40 bp):
AACTAGTTGACTTTATTAGTTTCACTTGGTCAACCCTTTT
Found at i:207998 original size:41 final size:42
Alignment explanation
Indices: 207937--208031 Score: 147
Period size: 41 Copynumber: 2.3 Consensus size: 42
207927 AACTCTTTCT
*
207937 TTTACTTAGGTTTAGCCTTGGTCAACCTCTTTAACTAGTGGAC
1 TTTA-TTAGTTTTAGCCTTGGTCAACCTCTTTAACTAGTGGAC
* *
207980 TTTATTAGTTTTA-CCTTGGTCAACCTTTTTAACTAGTTGAC
1 TTTATTAGTTTTAGCCTTGGTCAACCTCTTTAACTAGTGGAC
208021 TTTATTAGTTT
1 TTTATTAGTTT
208032 CATCCTAGTT
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
41 37 0.76
42 8 0.16
43 4 0.08
ACGTcount: A:0.21, C:0.17, G:0.15, T:0.47
Consensus pattern (42 bp):
TTTATTAGTTTTAGCCTTGGTCAACCTCTTTAACTAGTGGAC
Found at i:208928 original size:66 final size:64
Alignment explanation
Indices: 208752--208969 Score: 188
Period size: 66 Copynumber: 3.3 Consensus size: 64
208742 ATGTAACTAG
* * *
208752 TTGACTTTATCAATTTTGCCTTAATCAAACCTTTTTTTTAATTTAGGTTCTGCCTTAGTCA-CTC
1 TTGACTTTATCAATTTTGCCTTAGTC-AA-C-TTTTTTTAACTTAGGTTATGCC-TAGTCACCT-
208816 TTAA
61 TTAA
* * *** * * * *
208820 TTGATTTTATCAATTTCGCCTTAGTCAACACCATTTTGACTTAGGTTTTTTCCTAGTTACCTTTA
1 TTGACTTTATCAATTTTGCCTTAGTCAAC-TTTTTTTAACTTAGG-TTATGCCTAGTCACCTTTA
208885 A
64 A
* * *
208886 TTGACTTTATCGATTTTGTCTTAGTCAACTTTTTTTCAACTTAGGTTATGCCTTGTCACCTTTAG
1 TTGACTTTATCAATTTTGCCTTAGTCAACTTTTTTT-AACTTAGGTTATGCCTAGTCACCTTTA-
*
208951 C
64 A
*
208952 TT-ACTTTATCGATTTTGC
1 TTGACTTTATCAATTTTGC
208970 TCTAGTTAGC
Statistics
Matches: 120, Mismatches: 26, Indels: 11
0.76 0.17 0.07
Matches are distributed among these distances:
65 34 0.28
66 54 0.45
67 9 0.08
68 23 0.19
ACGTcount: A:0.21, C:0.19, G:0.11, T:0.49
Consensus pattern (64 bp):
TTGACTTTATCAATTTTGCCTTAGTCAACTTTTTTTAACTTAGGTTATGCCTAGTCACCTTTAA
Found at i:209068 original size:73 final size:73
Alignment explanation
Indices: 208979--209409 Score: 322
Period size: 73 Copynumber: 5.7 Consensus size: 73
208969 CTCTAGTTAG
* * * * *
208979 CCTCTCTAACTAGTTGATTTTATTAATTTTACCCTAGTCAACTCCTTTTTTGACTTAGCTTTTGC
1 CCTCTCAAACTAGTTGACTTTATTAATTTTACCCTAGTCAACCCCTTTTTTGACTTAGATTTAGC
209044 CTGGTCAA
66 CTGGTCAA
**
209052 CCTCTCAAACTAGTTGACTTTATCGATTTTACCCTAGTCAACCCCTTTAACTAGTTGACTTGATC
1 CCTCTCAAACTAGTTGACTTTATTAATTTTACCCTAGTCAACCCCTTT---T--TTGACTT-A--
** *
209117 GATTTCAGCCTAATTAA
58 GATTT-AGCCTGGTCAA
* ** * * * ** * * * *
209134 CCCCTTTAACTAGTTGACTTTGTTAGTTTGACTATGGTTAACCCCTTTTTTGACTTAGGTTTCGC
1 CCTCTCAAACTAGTTGACTTTATTAATTTTACCCTAGTCAACCCCTTTTTTGACTTAGATTTAGC
209199 CTGGTCAA
66 CTGGTCAA
* * *
209207 CCTCTCAAACTAATTGACTTTATTGATTTTACCCTAGTCAACACCTTTAACTAGTTGACTTGATC
1 CCTCTCAAACTAGTTGACTTTATTAATTTTACCCTAGTCAACCCCTTT---T--TTGACTT-A--
** *
209272 GATTTCAGCCTAATTAA
58 GATTT-AGCCTGGTCAA
** * * * ** * * * *
209289 CCTCTTTAACTAGTTGATTTTATTAGTTTGACTATGGTTAACCCCTTTTTTGACTTAGGTTTCGC
1 CCTCTCAAACTAGTTGACTTTATTAATTTTACCCTAGTCAACCCCTTTTTTGACTTAGATTTAGC
209354 CTGGTCAA
66 CTGGTCAA
* * *
209362 CCTCTCAAACTAATTGACTTTATTGATTTTACCCTAGTCAACACCTTT
1 CCTCTCAAACTAGTTGACTTTATTAATTTTACCCTAGTCAACCCCTTT
209410 AACTAGTTGA
Statistics
Matches: 266, Mismatches: 74, Indels: 36
0.71 0.20 0.10
Matches are distributed among these distances:
73 128 0.48
74 8 0.03
76 4 0.02
77 14 0.05
78 14 0.05
79 4 0.02
81 8 0.03
82 86 0.32
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.41
Consensus pattern (73 bp):
CCTCTCAAACTAGTTGACTTTATTAATTTTACCCTAGTCAACCCCTTTTTTGACTTAGATTTAGC
CTGGTCAA
Found at i:209094 original size:41 final size:41
Alignment explanation
Indices: 209059--209466 Score: 219
Period size: 41 Copynumber: 10.4 Consensus size: 41
209049 CAACCTCTCA
*
209059 AACTAGTTGACTTTATCGATTTTACCCTAGTCAACCCCTTT
1 AACTAGTTGACTTTATCGATTTCACCCTAGTCAACCCCTTT
* * * *
209100 AACTAGTTGACTTGATCGATTTCAGCCTAATTAACCCCTTT
1 AACTAGTTGACTTTATCGATTTCACCCTAGTCAACCCCTTT
* * * ** * *
209141 AACTAGTTGACTTTGT-TAGTTTGACTATGGTTAACCCCTTT
1 AACTAGTTGACTTTATCGA-TTTCACCCTAGTCAACCCCTTT
* * * * **
209182 ---T--TTGAC-TTA--GGTTTC-GCCTGGTCAACCTCTCA
1 AACTAGTTGACTTTATCGATTTCACCCTAGTCAACCCCTTT
* * * *
209214 AACTAATTGACTTTATTGATTTTACCCTAGTCAACACCTTT
1 AACTAGTTGACTTTATCGATTTCACCCTAGTCAACCCCTTT
* * * * *
209255 AACTAGTTGACTTGATCGATTTCAGCCTAATTAACCTCTTT
1 AACTAGTTGACTTTATCGATTTCACCCTAGTCAACCCCTTT
* * * ** * *
209296 AACTAGTTGATTTTAT-TAGTTTGACTATGGTTAACCCCTTT
1 AACTAGTTGACTTTATCGA-TTTCACCCTAGTCAACCCCTTT
* * * * **
209337 ---T--TTGAC-TTA--GGTTTC-GCCTGGTCAACCTCTCA
1 AACTAGTTGACTTTATCGATTTCACCCTAGTCAACCCCTTT
* * * *
209369 AACTAATTGACTTTATTGATTTTACCCTAGTCAACACCTTT
1 AACTAGTTGACTTTATCGATTTCACCCTAGTCAACCCCTTT
* * *
209410 AACTAGTTGACTTGATCGATTTCAGCCTA-ACTAACCCCTTT
1 AACTAGTTGACTTTATCGATTTCACCCTAGTC-AACCCCTTT
209451 AACTAGTTGACTTTAT
1 AACTAGTTGACTTTAT
209467 TAGTTTGACT
Statistics
Matches: 267, Mismatches: 79, Indels: 42
0.69 0.20 0.11
Matches are distributed among these distances:
32 20 0.07
33 6 0.02
35 7 0.03
36 9 0.03
37 10 0.04
38 8 0.03
40 11 0.04
41 196 0.73
ACGTcount: A:0.25, C:0.23, G:0.13, T:0.40
Consensus pattern (41 bp):
AACTAGTTGACTTTATCGATTTCACCCTAGTCAACCCCTTT
Found at i:209208 original size:155 final size:155
Alignment explanation
Indices: 208985--209504 Score: 878
Period size: 155 Copynumber: 3.4 Consensus size: 155
208975 TTAGCCTCTC
* * * ** * * * * *
208985 TAACTAGTTGATTTTATTAATTTTACCCTAGTCAACTCCTTTTTTGACTTAGCTTTTGCCTGGTC
1 TAACTAGTTGACTTTATTAGTTTGACTATGGTTAACCCCTTTTTTGACTTAGGTTTCGCCTGGTC
* * *
209050 AACCTCTCAAACTAGTTGACTTTATCGATTTTACCCTAGTCAACCCCTTTAACTAGTTGACTTGA
66 AACCTCTCAAACTAATTGACTTTATTGATTTTACCCTAGTCAACACCTTTAACTAGTTGACTTGA
209115 TCGATTTCAGCCTAATTAACCCCTT
131 TCGATTTCAGCCTAATTAACCCCTT
*
209140 TAACTAGTTGACTTTGTTAGTTTGACTATGGTTAACCCCTTTTTTGACTTAGGTTTCGCCTGGTC
1 TAACTAGTTGACTTTATTAGTTTGACTATGGTTAACCCCTTTTTTGACTTAGGTTTCGCCTGGTC
209205 AACCTCTCAAACTAATTGACTTTATTGATTTTACCCTAGTCAACACCTTTAACTAGTTGACTTGA
66 AACCTCTCAAACTAATTGACTTTATTGATTTTACCCTAGTCAACACCTTTAACTAGTTGACTTGA
*
209270 TCGATTTCAGCCTAATTAACCTCTT
131 TCGATTTCAGCCTAATTAACCCCTT
*
209295 TAACTAGTTGATTTTATTAGTTTGACTATGGTTAACCCCTTTTTTGACTTAGGTTTCGCCTGGTC
1 TAACTAGTTGACTTTATTAGTTTGACTATGGTTAACCCCTTTTTTGACTTAGGTTTCGCCTGGTC
209360 AACCTCTCAAACTAATTGACTTTATTGATTTTACCCTAGTCAACACCTTTAACTAGTTGACTTGA
66 AACCTCTCAAACTAATTGACTTTATTGATTTTACCCTAGTCAACACCTTTAACTAGTTGACTTGA
*
209425 TCGATTTCAGCCTAACTAACCCCTT
131 TCGATTTCAGCCTAATTAACCCCTT
*
209450 TAACTAGTTGACTTTATTAGTTTGACTATGGTTAACCCTTTTTTTGACTTAGGTT
1 TAACTAGTTGACTTTATTAGTTTGACTATGGTTAACCCCTTTTTTGACTTAGGTT
209505 CTATCCTAGT
Statistics
Matches: 344, Mismatches: 21, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
155 344 1.00
ACGTcount: A:0.24, C:0.22, G:0.13, T:0.41
Consensus pattern (155 bp):
TAACTAGTTGACTTTATTAGTTTGACTATGGTTAACCCCTTTTTTGACTTAGGTTTCGCCTGGTC
AACCTCTCAAACTAATTGACTTTATTGATTTTACCCTAGTCAACACCTTTAACTAGTTGACTTGA
TCGATTTCAGCCTAATTAACCCCTT
Found at i:209689 original size:66 final size:66
Alignment explanation
Indices: 209604--209849 Score: 262
Period size: 66 Copynumber: 3.7 Consensus size: 66
209594 CCCTTTCAAG
* * *
209604 TTAGGTTTTACCCTAGTCACCCTTAGTTGACTTTATCAGTTTCACCTTAGTTAACTTCTTTTTAA
1 TTAGGTTCTGCCCTAGTCACCCTTAGTTGACTTTATTAGTTTCACCTTAGTTAACTTCTTTTTAA
209669 C
66 C
* * ** *
209670 TTAGATTCTGCCCTAGTCACCTTTAGTTGACTTTATTAGTTTTGCCTTGGTTAACCTT-TTTTTA
1 TTAGGTTCTGCCCTAGTCACCCTTAGTTGACTTTATTAGTTTCACCTTAGTTAA-CTTCTTTTTA
209734 AC
65 AC
* ** ** * *** * *
209736 TTTGGTTCCACTTTGGTCAGTTTTAGTTGACTTTATTAATTTCACCTTAGTCAA-TTCTTTTTCA
1 TTAGGTTCTGCCCTAGTCACCCTTAGTTGACTTTATTAGTTTCACCTTAGTTAACTTCTTTTT-A
209800 AC
65 AC
* * *
209802 TTAGGTTCTGCCCTGGTCATCCTTAGTTGGCTTTATTAGTTTCACCTT
1 TTAGGTTCTGCCCTAGTCACCCTTAGTTGACTTTATTAGTTTCACCTT
209850 GGTCAACCCT
Statistics
Matches: 145, Mismatches: 32, Indels: 6
0.79 0.17 0.03
Matches are distributed among these distances:
64 2 0.01
65 5 0.03
66 135 0.93
67 3 0.02
ACGTcount: A:0.18, C:0.21, G:0.13, T:0.48
Consensus pattern (66 bp):
TTAGGTTCTGCCCTAGTCACCCTTAGTTGACTTTATTAGTTTCACCTTAGTTAACTTCTTTTTAA
C
Found at i:209968 original size:41 final size:40
Alignment explanation
Indices: 209922--210035 Score: 131
Period size: 41 Copynumber: 2.8 Consensus size: 40
209912 TGGTTTTGCT
* * *
209922 TTAGTCAACTTCTCTAATTAGTTGACTTTATTAGTTTTTC
1 TTAGTCAACTCCTCTAACTAGTTGACTTTATCAGTTTTTC
* * * *
209962 TCTAGTCAACTCCTTTAACCAGTTGACTTTATCAATTTCGTC
1 T-TAGTCAACTCCTCTAACTAGTTGACTTTATCAGTTT-TTC
*
210004 TTAGTCAACCCCTCTAACTAGTT-ACTTTATCA
1 TTAGTCAACTCCTCTAACTAGTTGACTTTATCA
210036 ATTCACCCTA
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
40 10 0.16
41 49 0.79
42 3 0.05
ACGTcount: A:0.25, C:0.23, G:0.09, T:0.44
Consensus pattern (40 bp):
TTAGTCAACTCCTCTAACTAGTTGACTTTATCAGTTTTTC
Found at i:210383 original size:42 final size:41
Alignment explanation
Indices: 210249--210394 Score: 145
Period size: 42 Copynumber: 3.6 Consensus size: 41
210239 TAGGCTCTTT
* * *
210249 TAGTTGACTTTATCGATTTTGCTTTGGTCAACCACTCTAAC
1 TAGTTGACTTTATCGATTTTGCTTTTGTTAACCCCTCTAAC
* * * *
210290 TAGTTG-CTTTAT-TAATTTGAC-ATTGCTTAACCCCTCAAAC
1 TAGTTGACTTTATCGATTTTG-CTTTTG-TTAACCCCTCTAAC
*
210330 TAGTTGACTTTATCGATTTTGCTTTTGTTAACCCCTTTTAAC
1 TAGTTGACTTTATCGATTTTGCTTTTGTTAACCCC-TCTAAC
* **
210372 TAGTTAACTTTATTAATTTTGCT
1 TAGTTGACTTTATCGATTTTGCT
210395 CTAGTCAACC
Statistics
Matches: 84, Mismatches: 15, Indels: 11
0.76 0.14 0.10
Matches are distributed among these distances:
39 7 0.08
40 24 0.29
41 21 0.25
42 32 0.38
ACGTcount: A:0.23, C:0.19, G:0.12, T:0.46
Consensus pattern (41 bp):
TAGTTGACTTTATCGATTTTGCTTTTGTTAACCCCTCTAAC
Found at i:212591 original size:51 final size:52
Alignment explanation
Indices: 212483--212603 Score: 122
Period size: 51 Copynumber: 2.3 Consensus size: 52
212473 TCTGAAATGA
* *
212483 AAATGTATCGATACATTTTCCATTGTATCGATATACATTATGGGTTTTCATCC
1 AAATGGATCGATACATTTTCCATTGTATCGA-ATACATTATGAGTTTTCATCC
* * * *
212536 AAATGGATCGATGCATTATT-CATTGTATTG-ATACATTCTGAGTTTTGA-CTC
1 AAATGGATCGATACATT-TTCCATTGTATCGAATACATTATGAGTTTTCATC-C
* *
212587 AAATGTATTGATACATT
1 AAATGGATCGATACATT
212604 CTTTAATGTA
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
50 1 0.02
51 30 0.53
53 24 0.42
54 2 0.04
ACGTcount: A:0.30, C:0.14, G:0.15, T:0.41
Consensus pattern (52 bp):
AAATGGATCGATACATTTTCCATTGTATCGAATACATTATGAGTTTTCATCC
Found at i:225610 original size:20 final size:21
Alignment explanation
Indices: 225582--225621 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
225572 TGAATTGAAT
225582 TTTAAATAAAATATT-TTTAA
1 TTTAAATAAAATATTATTTAA
* *
225602 TTTAGATAAATTATTATTTA
1 TTTAAATAAAATATTATTTA
225622 TAATAAAAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.53
Consensus pattern (21 bp):
TTTAAATAAAATATTATTTAA
Found at i:225625 original size:23 final size:23
Alignment explanation
Indices: 225593--225657 Score: 62
Period size: 23 Copynumber: 2.8 Consensus size: 23
225583 TTAAATAAAA
*
225593 TATTTTTAATTTAGATAA-ATTAT
1 TATTTATAATTTA-ATAATATTAT
** *
225616 TATTTATAATAAAAATAATATTTT
1 TATTTATAAT-TTAATAATATTAT
225640 TATTTA-AATTTAATAATA
1 TATTTATAATTTAATAATA
225658 AAAATATATA
Statistics
Matches: 34, Mismatches: 6, Indels: 5
0.76 0.13 0.11
Matches are distributed among these distances:
22 7 0.21
23 16 0.47
24 11 0.32
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (23 bp):
TATTTATAATTTAATAATATTAT
Found at i:226079 original size:15 final size:15
Alignment explanation
Indices: 226059--226094 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
226049 TCATATACTA
226059 TTATTTTATAATTAT
1 TTATTTTATAATTAT
*
226074 TTATTTTTTAATTAT
1 TTATTTTATAATTAT
*
226089 TAATTT
1 TTATTT
226095 ACTATTATAT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (15 bp):
TTATTTTATAATTAT
Found at i:226119 original size:22 final size:22
Alignment explanation
Indices: 226042--226120 Score: 60
Period size: 22 Copynumber: 3.8 Consensus size: 22
226032 ATTATATATG
* *
226042 TTATTTATCATATACTATTATT
1 TTATTAATCATATACTATTATA
* * * *
226064 TTA-TAATTATTTA-TTTTTTAA
1 TTATTAATCATATACTATTAT-A
226085 TTATTAAT--T-TACTATTATA
1 TTATTAATCATATACTATTATA
226104 TTATTAATCATATACTA
1 TTATTAATCATATACTA
226121 ATGGTTTCTG
Statistics
Matches: 43, Mismatches: 8, Indels: 12
0.68 0.13 0.19
Matches are distributed among these distances:
19 11 0.26
20 9 0.21
21 11 0.26
22 12 0.28
ACGTcount: A:0.35, C:0.06, G:0.00, T:0.58
Consensus pattern (22 bp):
TTATTAATCATATACTATTATA
Found at i:227933 original size:51 final size:51
Alignment explanation
Indices: 227812--227954 Score: 186
Period size: 51 Copynumber: 2.9 Consensus size: 51
227802 AAAAATCACA
* * * *
227812 TTTTTACCCAGATGTATCGATACA---TTGAATGTATCGATACATTTTGTC
1 TTTTTACCTAGATGTATCGATACATTTTTCAATGTATCGATACATTCTATC
* * *
227860 -TTTTACCTAGATTTATCAATACATTTTTCAATGTATCGATGCATTCTATC
1 TTTTTACCTAGATGTATCGATACATTTTTCAATGTATCGATACATTCTATC
*
227910 TTTTTACCTAGATGTATCGATACATTTTTTAATGTATCGATACAT
1 TTTTTACCTAGATGTATCGATACATTTTTCAATGTATCGATACAT
227955 CAAGTTAAAA
Statistics
Matches: 80, Mismatches: 11, Indels: 5
0.83 0.11 0.05
Matches are distributed among these distances:
47 20 0.25
50 20 0.25
51 40 0.50
ACGTcount: A:0.28, C:0.16, G:0.11, T:0.45
Consensus pattern (51 bp):
TTTTTACCTAGATGTATCGATACATTTTTCAATGTATCGATACATTCTATC
Found at i:233029 original size:21 final size:21
Alignment explanation
Indices: 233003--233045 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
232993 GACGAATTTC
233003 AGATTATAATGACTTTCTTTT
1 AGATTATAATGACTTTCTTTT
*
233024 AGATTATAATGACTTTTTTTT
1 AGATTATAATGACTTTCTTTT
233045 A
1 A
233046 AGCTTGAATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.30, C:0.07, G:0.09, T:0.53
Consensus pattern (21 bp):
AGATTATAATGACTTTCTTTT
Found at i:234771 original size:21 final size:20
Alignment explanation
Indices: 234743--234781 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
234733 ATTGCATGTT
234743 TAAAAATTATTT-TAAAATAC
1 TAAAAATT-TTTATAAAATAC
234763 TAAACAATTTTTATAAAAT
1 TAAA-AATTTTTATAAAAT
234782 GTTTTAGTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.54, C:0.05, G:0.00, T:0.41
Consensus pattern (20 bp):
TAAAAATTTTTATAAAATAC
Found at i:239023 original size:20 final size:19
Alignment explanation
Indices: 238998--239072 Score: 78
Period size: 20 Copynumber: 3.8 Consensus size: 19
238988 AAAAAGACAT
*
238998 AATGTATCGATATATTGAA
1 AATGTATCGATACATTGAA
*
239017 GAATGTATCGATACATTCATA
1 -AATGTATCGATACATTGA-A
*
239038 CATGTATCGATACATTGAAA
1 AATGTATCGATACATTG-AA
* *
239058 AAGGTATTGATACAT
1 AATGTATCGATACAT
239073 CTAGGTAAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
20 44 0.96
21 2 0.04
ACGTcount: A:0.40, C:0.11, G:0.16, T:0.33
Consensus pattern (19 bp):
AATGTATCGATACATTGAA
Found at i:239024 original size:51 final size:51
Alignment explanation
Indices: 238948--239134 Score: 209
Period size: 51 Copynumber: 3.9 Consensus size: 51
238938 TTTTAACTAG
* *
238948 ATGTATCGAAACATTAAAAAATGTATCGATACATCTAGGTAAAAAGACATA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAAAGACATA
* *
238999 ATGTATCGATATATTGAAGAATGTATCGATACA--T---T-------CATA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAAAGACATA
* *
239038 CATGTATCGATACATTGAAAAAGGTATTGATACATCTAGGTAAAAAGACATA
1 -ATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAAAGACATA
* *
239090 ATGTATAGATACATTGAAAAATGTATCGATACATCTGGGTAAAAA
1 ATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAAA
239135 TGTGACTTTT
Statistics
Matches: 111, Mismatches: 12, Indels: 26
0.74 0.08 0.17
Matches are distributed among these distances:
39 4 0.04
40 29 0.26
42 1 0.01
45 1 0.01
46 1 0.01
49 1 0.01
51 70 0.63
52 4 0.04
ACGTcount: A:0.44, C:0.11, G:0.16, T:0.29
Consensus pattern (51 bp):
ATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAAAGACATA
Found at i:239043 original size:91 final size:91
Alignment explanation
Indices: 238948--239123 Score: 289
Period size: 91 Copynumber: 1.9 Consensus size: 91
238938 TTTTAACTAG
* * *
238948 ATGTATCGAAACATTAAAAAATGTATCGATACATCTAGGTAAAAAGACATAATGTATCGATATAT
1 ATGTATCGAAACATTAAAAAAGGTATCGATACATCTAGGTAAAAAGACATAATGTATAGATACAT
*
239013 TGAAGAATGTATCGATACATTCATAC
66 TGAAAAATGTATCGATACATTCATAC
* * *
239039 ATGTATCGATACATTGAAAAAGGTATTGATACATCTAGGTAAAAAGACATAATGTATAGATACAT
1 ATGTATCGAAACATTAAAAAAGGTATCGATACATCTAGGTAAAAAGACATAATGTATAGATACAT
239104 TGAAAAATGTATCGATACAT
66 TGAAAAATGTATCGATACAT
239124 CTGGGTAAAA
Statistics
Matches: 78, Mismatches: 7, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
91 78 1.00
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.30
Consensus pattern (91 bp):
ATGTATCGAAACATTAAAAAAGGTATCGATACATCTAGGTAAAAAGACATAATGTATAGATACAT
TGAAAAATGTATCGATACATTCATAC
Found at i:239055 original size:40 final size:39
Alignment explanation
Indices: 238995--239072 Score: 111
Period size: 40 Copynumber: 2.0 Consensus size: 39
238985 GGTAAAAAGA
* * *
238995 CATAATGTATCGATATATTGAAGAATGTATCGATACATT
1 CATAATGTATCGATACATTGAAAAAGGTATCGATACATT
*
239034 CATACATGTATCGATACATTGAAAAAGGTATTGATACAT
1 CATA-ATGTATCGATACATTGAAAAAGGTATCGATACAT
239073 CTAGGTAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
39 4 0.12
40 30 0.88
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (39 bp):
CATAATGTATCGATACATTGAAAAAGGTATCGATACATT
Found at i:239976 original size:50 final size:50
Alignment explanation
Indices: 239860--240004 Score: 184
Period size: 50 Copynumber: 2.9 Consensus size: 50
239850 TTTTAACTAG
* * * * * * *
239860 ATGTATCGATACATTAAAAAAGGTATTGATACAT-TTGGCTAAAAAGACAGA
1 ATGTATCGATACATTGAAAAATGTATCGATAAATCTAGG-T-AAAATATAGA
*
239911 ATGTATCGATACATTGAGAAATGTATCGATAAATCTAGGTAAAATATAGA
1 ATGTATCGATACATTGAAAAATGTATCGATAAATCTAGGTAAAATATAGA
*
239961 ATGTATCGATACATTGAAAAATGTATCGATACATCTAGGTAAAA
1 ATGTATCGATACATTGAAAAATGTATCGATAAATCTAGGTAAAA
240005 ATGCGATTTT
Statistics
Matches: 83, Mismatches: 10, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
50 50 0.60
51 30 0.36
52 3 0.04
ACGTcount: A:0.44, C:0.10, G:0.17, T:0.29
Consensus pattern (50 bp):
ATGTATCGATACATTGAAAAATGTATCGATAAATCTAGGTAAAATATAGA
Found at i:241002 original size:28 final size:28
Alignment explanation
Indices: 240873--241814 Score: 746
Period size: 28 Copynumber: 32.4 Consensus size: 28
240863 AAAGTGGTGA
*
240873 TTTGAAAAGGGTTACCACTGACTTGCGTGGGC
1 TTTGAAAA-GG-TGCCACTGACTT--GTGGGC
*
240905 TTTGAAAAAAGGTGCCACTAACTTGTATGGGC
1 TTTG--AAAAGGTGCCACTGACTTG--TGGGC
*
240937 TTTGAAAAGAGTTGCCACCGACTTGTGTGGGC
1 TTTGAAAAG-G-TGCCACTGAC-T-TGTGGGC
*
240969 TTTGAAAAGGTGCCACCGACTTGTGGGC
1 TTTGAAAAGGTGCCACTGACTTGTGGGC
* *
240997 TTTGAAAGGGTGCCACCGACTTGTGGGC
1 TTTGAAAAGGTGCCACTGACTTGTGGGC
* *
241025 TTTGAAAGGGTGCCACCGACTTGTGGGC
1 TTTGAAAAGGTGCCACTGACTTGTGGGC
* *
241053 TTCGAAATA-GTGCCACTAACTTGTGGGC
1 TTTGAAA-AGGTGCCACTGACTTGTGGGC
* * *
241081 TTCGAAATGATGCCACTGACTTGTGGGC
1 TTTGAAAAGGTGCCACTGACTTGTGGGC
* *
241109 TTTG-AAAGGATACTACT-ATCTTGTGGGC
1 TTTGAAAAGG-TGCCACTGA-CTTGTGGGC
* * *
241137 TTTGAAAGGGTGCTACTGACTTATGGGC
1 TTTGAAAAGGTGCCACTGACTTGTGGGC
* *
241165 TTTGAAAGGGTATGCCACTGACTTATGGGC
1 TTTGAAAAGG--TGCCACTGACTTGTGGGC
* *
241195 TTTG-AAAGGATGCCACTAACTTGTGAGC
1 TTTGAAAAGG-TGCCACTGACTTGTGGGC
* * * *
241223 TTTGGAAGGGTGCCACCGATTTTGTATGGGC
1 TTTGAAAAGGTGCCACTGA-CTTG--TGGGC
* * ** *
241254 CTTGAACAGAGTTGCCACCAACTTATGCGGAC
1 TTTGAA-A-AGGTGCCACTGACTTGTG-GG-C
* *
241286 TTTGAAAGAGTTACCACTGACTTGTGGGC
1 TTTGAAA-AGGTGCCACTGACTTGTGGGC
241315 TTTGAAAAGGATGCCACTGACTTGTGGGC
1 TTTGAAAAGG-TGCCACTGACTTGTGGGC
* * *
241344 TTTGAAAGGGTGGCACTGACTTATGGGC
1 TTTGAAAAGGTGCCACTGACTTGTGGGC
* * * * *
241372 TTTGAAAAGATGCCATTGTCTTATGGGG
1 TTTGAAAAGGTGCCACTGACTTGTGGGC
* *
241400 TTTAAAAAGGTGCCACCGAC-TGTGGGC
1 TTTGAAAAGGTGCCACTGACTTGTGGGC
* *
241427 TTTGAAAGGGTATGCCACTGACTTGTGGTC
1 TTTGAAAAGG--TGCCACTGACTTGTGGGC
* ** * * *
241457 GTTGAAGGGGTGTGCCACTAACTTGTTGAC
1 TTTGAA-AAG-GTGCCACTGACTTGTGGGC
* *
241487 TTTGAAAGGGTGCCACTAACTTGTGGGC
1 TTTGAAAAGGTGCCACTGACTTGTGGGC
* * * *
241515 TTTGGAAGGGTGCCACCGATTTGTGTGGGC
1 TTTGAAAAGGTGCCACTGA-CT-TGTGGGC
* *
241545 TTTGAATAGAGTTGCCACCGACTTGTGTGGAC
1 TTTGAA-A-AGGTGCCACTGACTTGTG-GG-C
* * * * *
241577 ATTAAAAAGTGTTACCACTAACTTATGGGC
1 TTTGAAAAG-G-TGCCACTGACTTGTGGGC
*
241607 TTTAAAAAGGGTGCCACTGACTTGTGGGC
1 TTTGAAAA-GGTGCCACTGACTTGTGGGC
* * *
241636 TTTGAAAGGGTGCCACTAACTTATGGGC
1 TTTGAAAAGGTGCCACTGACTTGTGGGC
241664 TTTG-AAAGGATGCCACTGACTTGTGGGC
1 TTTGAAAAGG-TGCCACTGACTTGTGGGC
* * *
241692 TTTGAAAGGGTGCCACTAACTTATGGGC
1 TTTGAAAAGGTGCCACTGACTTGTGGGC
*
241720 TTTG-AAAGGATGCCACTGGCTTGTGGGC
1 TTTGAAAAGG-TGCCACTGACTTGTGGGC
* *
241748 TTTGAAAAGATGCCACTGACTTATGGGC
1 TTTGAAAAGGTGCCACTGACTTGTGGGC
* * * *
241776 TTTGAGAAGGATGGCACTAACTTGTGGCC
1 TTTGAAAAGG-TGCCACTGACTTGTGGGC
241805 TTTGAAAAGG
1 TTTGAAAAGG
241815 GTCATATTGA
Statistics
Matches: 750, Mismatches: 116, Indels: 91
0.78 0.12 0.10
Matches are distributed among these distances:
27 25 0.03
28 374 0.50
29 115 0.15
30 99 0.13
31 38 0.05
32 81 0.11
33 12 0.02
34 6 0.01
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (28 bp):
TTTGAAAAGGTGCCACTGACTTGTGGGC
Found at i:241536 original size:292 final size:287
Alignment explanation
Indices: 240915--241808 Score: 1039
Period size: 292 Copynumber: 3.1 Consensus size: 287
240905 TTTGAAAAAA
* * * *
240915 GGTGCCACTAACTTGTATGGGCTTTGAAAAGAGTTGCCACCGACTTGTGTGGGCTTTGAAA-AGG
1 GGTGCCACTAACTTG--TGGGCTTTG-GAAG-GGTGCCACCGATTTGTGTGGGCTTTGAAAGAGT
* * * *
240979 TGCCACCGACTTGTGGG-CTTTGAAAGGGTGCCACCGACTTGTGGGCTTTG-AAAGGGTGCCACC
62 TGCCACCGACTTGTGGGACTTTGAAAGGTTACCACTGACTTGTGGGCTTTGAAAAGGGTGCCACT
* ** * * *
241042 GACTTGTGGGCTTCGAAATAGTGCCACTAACTTGTGGGCTTCGAAATGATGCCACTGACTTGTGG
127 GACTTGTGGGCTTTGAAAGGGTGCCACTAACTTATGGGCTTTGAAAAGATGCCACTGACTTGTGG
* * * * * * * *
241107 GCTTTGAAAGGATACTACTATCTTGTGGGCTTTGAAAGGG-TGCTACTGACTTATGGGCTTTGAA
192 GCTTTAAAAGG-TGCCACCAACTTGTGGGCTTTGAAAGGGATGCCACTGACTTGTGGGCGTTGAA
* *
241171 AGGGTATGCCACTGACTTATGGGCTTTGAAAG
256 AGGGTATGCCACTAACTTATGGACTTTGAAAG
* * * *
241203 GATGCCACTAACTTGTGAGCTTTGGAAGGGTGCCACCGATTTTGTATGGGCCTTGAACAGAGTTG
1 GGTGCCACTAACTTGTGGGCTTTGGAAGGGTGCCACCGA-TTTGTGTGGGCTTTGAA-AGAGTTG
* * *
241268 CCACCAACTTATGCGGACTTTGAAAGAGTTACCACTGACTTGTGGGCTTTGAAAAGGATGCCACT
64 CCACCGACTTGTG-GGACTTTGAAAG-GTTACCACTGACTTGTGGGCTTTGAAAAGGGTGCCACT
* * * * *
241333 GACTTGTGGGCTTTGAAAGGGTGGCACTGACTTATGGGCTTTGAAAAGATGCCATTGTCTTATGG
127 GACTTGTGGGCTTTGAAAGGGTGCCACTAACTTATGGGCTTTGAAAAGATGCCACTGACTTGTGG
* * *
241398 GGTTTAAAAAGGTGCCACCGAC-TGTGGGCTTTGAAAGGGTATGCCACTGACTTGTGGTCGTTGA
192 GCTTT-AAAAGGTGCCACCAACTTGTGGGCTTTGAAAGGG-ATGCCACTGACTTGTGGGCGTTGA
* * * *
241462 AGGGGTGTGCCACTAACTTGTTGACTTTGAAAG
255 AAGGGTATGCCACTAACTTATGGACTTTGAAAG
241495 GGTGCCACTAACTTGTGGGCTTTGGAAGGGTGCCACCGATTTGTGTGGGCTTTGAATAGAGTTGC
1 GGTGCCACTAACTTGTGGGCTTTGGAAGGGTGCCACCGATTTGTGTGGGCTTTGAA-AGAGTTGC
** * * *
241560 CACCGACTTGTGTGGACATTAAAAAGTGTTACCACTAACTTATGGGCTTTAAAAAGGGTGCCACT
65 CACCGACTTGTG-GGAC-TTTGAAAG-GTTACCACTGACTTGTGGGCTTTGAAAAGGGTGCCACT
*
241625 GACTTGTGGGCTTTGAAAGGGTGCCACTAACTTATGGGCTTTGAAAGGATGCCACTGACTTGTGG
127 GACTTGTGGGCTTTGAAAGGGTGCCACTAACTTATGGGCTTTGAAAAGATGCCACTGACTTGTGG
* * * * *
241690 GCTTTGAAAGGGTGCCACTAACTTATGGGCTTTGAAA-GGATGCCACTGGCTTGTGGGCTTTGAA
192 GCTTT-AAAAGGTGCCACCAACTTGTGGGCTTTGAAAGGGATGCCACTGACTTGTGGGCGTTGAA
* * *
241754 A-AG-ATGCCACTGACTTATGGGCTTTGAGAAG
256 AGGGTATGCCACTAACTTATGGACTTTGA-AAG
* * *
241785 GATGGCACTAACTTGTGGCCTTTG
1 GGTGCCACTAACTTGTGGGCTTTG
241809 AAAAGGGTCA
Statistics
Matches: 510, Mismatches: 83, Indels: 24
0.83 0.13 0.04
Matches are distributed among these distances:
284 10 0.02
285 17 0.03
286 9 0.02
287 15 0.03
288 16 0.03
289 28 0.05
290 63 0.12
291 133 0.26
292 206 0.40
293 13 0.03
ACGTcount: A:0.23, C:0.18, G:0.30, T:0.29
Consensus pattern (287 bp):
GGTGCCACTAACTTGTGGGCTTTGGAAGGGTGCCACCGATTTGTGTGGGCTTTGAAAGAGTTGCC
ACCGACTTGTGGGACTTTGAAAGGTTACCACTGACTTGTGGGCTTTGAAAAGGGTGCCACTGACT
TGTGGGCTTTGAAAGGGTGCCACTAACTTATGGGCTTTGAAAAGATGCCACTGACTTGTGGGCTT
TAAAAGGTGCCACCAACTTGTGGGCTTTGAAAGGGATGCCACTGACTTGTGGGCGTTGAAAGGGT
ATGCCACTAACTTATGGACTTTGAAAG
Found at i:241851 original size:26 final size:26
Alignment explanation
Indices: 241821--241893 Score: 71
Period size: 26 Copynumber: 2.8 Consensus size: 26
241811 AAGGGTCATA
241821 TTGACGAAAATTTCTTGACAAAGTT-
1 TTGACGAAAATTTCTTGACAAAGTTC
* *
241846 TCTGAC-AAACA-TTCTCGATAGAAGTTC
1 T-TGACGAAA-ATTTCTTGACA-AAGTTC
*
241873 TTGACGATAATTTCTTGACAA
1 TTGACGAAAATTTCTTGACAA
241894 CCATTTCTTG
Statistics
Matches: 37, Mismatches: 5, Indels: 11
0.70 0.09 0.21
Matches are distributed among these distances:
25 11 0.30
26 16 0.43
27 10 0.27
ACGTcount: A:0.34, C:0.16, G:0.15, T:0.34
Consensus pattern (26 bp):
TTGACGAAAATTTCTTGACAAAGTTC
Found at i:244279 original size:33 final size:33
Alignment explanation
Indices: 244239--244307 Score: 104
Period size: 33 Copynumber: 2.1 Consensus size: 33
244229 CCGTTACAAG
* *
244239 CAATGTATCGATACAAT-TCATCATGTATTGATA
1 CAATGTATCAATACAATGT-ACCATGTATTGATA
244272 CAATGTATCAATACAATGTACCATGTATTGATA
1 CAATGTATCAATACAATGTACCATGTATTGATA
244305 CAA
1 CAA
244308 ACAGTGGTAG
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
33 32 0.97
34 1 0.03
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.33
Consensus pattern (33 bp):
CAATGTATCAATACAATGTACCATGTATTGATA
Found at i:245026 original size:21 final size:22
Alignment explanation
Indices: 244997--245037 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
244987 AGATAAACAT
*
244997 ATTTCTCCCCCTTTATCAAAGC
1 ATTTCTCCCCCATTATCAAAGC
*
245019 ATTT-TCCCCCATTGTCAAA
1 ATTTCTCCCCCATTATCAAA
245038 TCTTAAAAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.24, C:0.34, G:0.05, T:0.37
Consensus pattern (22 bp):
ATTTCTCCCCCATTATCAAAGC
Found at i:252975 original size:14 final size:14
Alignment explanation
Indices: 252956--252984 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
252946 ATATCCGTTG
252956 GAGGTTGAATGATT
1 GAGGTTGAATGATT
252970 GAGGTTGAATGATT
1 GAGGTTGAATGATT
252984 G
1 G
252985 TGTTTCTAGC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.28, C:0.00, G:0.38, T:0.34
Consensus pattern (14 bp):
GAGGTTGAATGATT
Found at i:253267 original size:32 final size:33
Alignment explanation
Indices: 253223--253285 Score: 83
Period size: 32 Copynumber: 1.9 Consensus size: 33
253213 ACAATTGTCC
* **
253223 ATGTATCGATACAGTGAAT-ATGTATCGATATA
1 ATGTATCAATACAAAGAATAATGTATCGATATA
*
253255 ATGTATCAATACAAAGCATAATGTATCGATA
1 ATGTATCAATACAAAGAATAATGTATCGATA
253286 CATCTAGGTA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
32 15 0.58
33 11 0.42
ACGTcount: A:0.41, C:0.11, G:0.16, T:0.32
Consensus pattern (33 bp):
ATGTATCAATACAAAGAATAATGTATCGATATA
Found at i:277394 original size:28 final size:28
Alignment explanation
Indices: 277362--277691 Score: 414
Period size: 28 Copynumber: 11.8 Consensus size: 28
277352 AACTTTTGTC
*
277362 TGGCATCCTTTCAAAGCCCATAAGTCAG
1 TGGCATCCTTTCAAAGCCCACAAGTCAG
277390 TGGCAT-CTCTTCAAAGCCCACAAGTCAG
1 TGGCATCCT-TTCAAAGCCCACAAGTCAG
* * *
277418 TGGCATGCTTTCAAAGCTCGCAAGTCAG
1 TGGCATCCTTTCAAAGCCCACAAGTCAG
* *
277446 TGGCATCTTTTCCAAGCCCACAAGTCAG
1 TGGCATCCTTTCAAAGCCCACAAGTCAG
* *
277474 TGGCATCCGTTT-AAAGCCCATAAGTCAA
1 TGGCATCC-TTTCAAAGCCCACAAGTCAG
*
277502 TGGCATCCTTTCAATGCCCACAAGTCAG
1 TGGCATCCTTTCAAAGCCCACAAGTCAG
* * *
277530 TGGCATATCTTT-ACAGCCCATAAGTCAG
1 TGGCAT-CCTTTCAAAGCCCACAAGTCAG
*
277558 TGGCATCCTTTCAAAGCCCACAAGTCAA
1 TGGCATCCTTTCAAAGCCCACAAGTCAG
*
277586 TGGCACCCTTTCAAAGCCCACAAGTCAG
1 TGGCATCCTTTCAAAGCCCACAAGTCAG
** * * *
277614 TGTTACCCTTTTAAAGCCCACAAGTTAG
1 TGGCATCCTTTCAAAGCCCACAAGTCAG
* * *
277642 TGGCATTCTTTCAAAGCCCATAAGTTAG
1 TGGCATCCTTTCAAAGCCCACAAGTCAG
277670 TGGCATCCTTTCAAAGCCCACA
1 TGGCATCCTTTCAAAGCCCACA
277692 CAAGTCGGTG
Statistics
Matches: 259, Mismatches: 37, Indels: 12
0.84 0.12 0.04
Matches are distributed among these distances:
27 9 0.03
28 241 0.93
29 9 0.03
ACGTcount: A:0.28, C:0.29, G:0.18, T:0.25
Consensus pattern (28 bp):
TGGCATCCTTTCAAAGCCCACAAGTCAG
Found at i:283271 original size:18 final size:18
Alignment explanation
Indices: 283245--283280 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
283235 TTGTACACAT
283245 CAAACGAATCCATTATCA
1 CAAACGAATCCATTATCA
* *
283263 CAAATGAATTCATTATCA
1 CAAACGAATCCATTATCA
283281 GAACTTTGTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.44, C:0.22, G:0.06, T:0.28
Consensus pattern (18 bp):
CAAACGAATCCATTATCA
Found at i:284485 original size:21 final size:22
Alignment explanation
Indices: 284461--284501 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
284451 AAATCAGTTA
* *
284461 ATAACAATT-ATATATTTAAGT
1 ATAAAAATTCATAAATTTAAGT
284482 ATAAAAATTCATAAATTTAA
1 ATAAAAATTCATAAATTTAA
284502 CTAATTATTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.54, C:0.05, G:0.02, T:0.39
Consensus pattern (22 bp):
ATAAAAATTCATAAATTTAAGT
Found at i:286260 original size:19 final size:19
Alignment explanation
Indices: 286211--286266 Score: 76
Period size: 20 Copynumber: 2.9 Consensus size: 19
286201 ACTGCCAATT
* *
286211 TCATGTATCAATACAATTA
1 TCATGTATCGATACAATGA
286230 TGCATGTATCGATACAATGA
1 T-CATGTATCGATACAATGA
*
286250 TCATTTATCGATACAAT
1 TCATGTATCGATACAAT
286267 ATATCAATAC
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.38, C:0.16, G:0.11, T:0.36
Consensus pattern (19 bp):
TCATGTATCGATACAATGA
Found at i:288739 original size:13 final size:13
Alignment explanation
Indices: 288721--288745 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
288711 TAGTAACCCA
288721 TGTATCGATACAT
1 TGTATCGATACAT
288734 TGTATCGATACA
1 TGTATCGATACA
288746 AAGAACATTG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:288805 original size:20 final size:20
Alignment explanation
Indices: 288780--288817 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
288770 GGTTTTTCCA
* *
288780 AATGTATCGATACATTTTTC
1 AATGTATCAACACATTTTTC
288800 AATGTATCAACACATTTT
1 AATGTATCAACACATTTT
288818 GAAAATTTTC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.16, G:0.08, T:0.42
Consensus pattern (20 bp):
AATGTATCAACACATTTTTC
Found at i:297042 original size:21 final size:21
Alignment explanation
Indices: 297016--297071 Score: 112
Period size: 21 Copynumber: 2.7 Consensus size: 21
297006 ACATGTTGCA
297016 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
297037 ATGTATCGATACATGAAAAAG
1 ATGTATCGATACATGAAAAAG
297058 ATGTATCGATACAT
1 ATGTATCGATACAT
297072 TTCTTGGGAG
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 35 1.00
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.27
Consensus pattern (21 bp):
ATGTATCGATACATGAAAAAG
Found at i:297128 original size:13 final size:13
Alignment explanation
Indices: 297110--297135 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
297100 TACAGCAAGT
297110 ATGTATCGATACA
1 ATGTATCGATACA
297123 ATGTATCGATACA
1 ATGTATCGATACA
297136 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:299387 original size:21 final size:21
Alignment explanation
Indices: 299354--299398 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
299344 TTGCAAGTTG
*
299354 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
299376 AAATAATG-AGTTAGCTAAGA
1 AAATAAAGAAGTTAGCTAAGA
299396 AAA
1 AAA
299399 ATGAAAACTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 9 0.43
22 7 0.33
ACGTcount: A:0.53, C:0.04, G:0.20, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:301221 original size:15 final size:15
Alignment explanation
Indices: 301201--301231 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
301191 TAAAAATGTC
*
301201 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
301216 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
301231 C
1 C
301232 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:303319 original size:13 final size:13
Alignment explanation
Indices: 303301--303326 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
303291 ACATTTTTCC
303301 TTGTATCGATACA
1 TTGTATCGATACA
303314 TTGTATCGATACA
1 TTGTATCGATACA
303327 GGGTGATTAT
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:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:305901 original size:13 final size:13
Alignment explanation
Indices: 305883--305908 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
305873 TATAGCAAGT
305883 ATGTATCGATACA
1 ATGTATCGATACA
305896 ATGTATCGATACA
1 ATGTATCGATACA
305909 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:307556 original size:7 final size:7
Alignment explanation
Indices: 307544--307607 Score: 62
Period size: 7 Copynumber: 9.4 Consensus size: 7
307534 AAGAAATCCC
307544 TTTTTCT
1 TTTTTCT
307551 TTTTTCT
1 TTTTTCT
307558 TTTTTCT
1 TTTTTCT
*
307565 CTTATT-T
1 -TTTTTCT
*
307572 TTTTTCC
1 TTTTTCT
307579 TTTTTC-
1 TTTTTCT
*
307585 TTTTGCT
1 TTTTTCT
*
307592 CTTTT-T
1 TTTTTCT
307598 TTTTTCT
1 TTTTTCT
307605 TTT
1 TTT
307608 CTTTTTGGCT
Statistics
Matches: 46, Mismatches: 7, Indels: 8
0.75 0.11 0.13
Matches are distributed among these distances:
6 14 0.30
7 28 0.61
8 4 0.09
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.81
Consensus pattern (7 bp):
TTTTTCT
Found at i:307567 original size:9 final size:8
Alignment explanation
Indices: 307544--307628 Score: 57
Period size: 8 Copynumber: 10.1 Consensus size: 8
307534 AAGAAATCCC
307544 TTTTTC-T
1 TTTTTCTT
307551 TTTTTCTT
1 TTTTTCTT
307559 TTTTCTCTT
1 TTTT-TCTT
*
307568 ATTTTTTTT
1 -TTTTTCTT
307577 CCTTTTTCTT
1 --TTTTTCTT
**
307587 TTGCTCTT
1 TTTTTCTT
307595 TTTTT-TT
1 TTTTTCTT
307602 TCTTTTCTT
1 T-TTTTCTT
**
307611 TTTGGCTT
1 TTTTTCTT
307619 TCTTTTCTT
1 T-TTTTCTT
307628 T
1 T
307629 GTAGTTGAAA
Statistics
Matches: 60, Mismatches: 11, Indels: 12
0.72 0.13 0.14
Matches are distributed among these distances:
7 9 0.15
8 24 0.40
9 16 0.27
10 11 0.18
ACGTcount: A:0.01, C:0.16, G:0.04, T:0.79
Consensus pattern (8 bp):
TTTTTCTT
Found at i:307612 original size:13 final size:12
Alignment explanation
Indices: 307544--307613 Score: 59
Period size: 13 Copynumber: 5.2 Consensus size: 12
307534 AAGAAATCCC
307544 TTTTTCTTTTTTCT
1 TTTTTC-TTTTT-T
307558 TTTTTCTCTTATTT
1 TTTTTCT-TT-TTT
*
307572 TTTTTCCTTTTTC
1 TTTTT-CTTTTTT
*
307585 TTTTGCTCTTTTT
1 TTTTTCT-TTTTT
307598 TTTTTCTTTTCTT
1 TTTTTCTTTT-TT
307611 TTT
1 TTT
307614 GGCTTTCTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 11
0.76 0.06 0.18
Matches are distributed among these distances:
12 5 0.11
13 22 0.47
14 16 0.34
15 4 0.09
ACGTcount: A:0.01, C:0.16, G:0.01, T:0.81
Consensus pattern (12 bp):
TTTTTCTTTTTT
Found at i:307614 original size:25 final size:26
Alignment explanation
Indices: 307544--307614 Score: 85
Period size: 25 Copynumber: 2.8 Consensus size: 26
307534 AAGAAATCCC
* *
307544 TTTTTCTT-TTTTCTTTTTTCTCTTA
1 TTTTTTTTCTTTTCTTTTTGCTCTTA
307569 TTTTTTTTCCTTTT-TCTTTTGCTCTT-
1 TTTTTTTT-CTTTTCT-TTTTGCTCTTA
307595 TTTTTTTTCTTTTCTTTTTG
1 TTTTTTTTCTTTTCTTTTTG
307615 GCTTTCTTTT
Statistics
Matches: 40, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
25 17 0.43
26 10 0.25
27 13 0.32
ACGTcount: A:0.01, C:0.15, G:0.03, T:0.80
Consensus pattern (26 bp):
TTTTTTTTCTTTTCTTTTTGCTCTTA
Found at i:311422 original size:20 final size:21
Alignment explanation
Indices: 311397--311454 Score: 64
Period size: 20 Copynumber: 2.8 Consensus size: 21
311387 CTACCAAGGG
*
311397 AATGTATCGATACATTATTA-
1 AATGTATCGATACATTATGAC
* **
311417 AATGTATCAATACATGCTGAC
1 AATGTATCGATACATTATGAC
311438 AATTGTATCGATACATT
1 AA-TGTATCGATACATT
311455 TTGGATTTTT
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
20 16 0.53
21 2 0.07
22 12 0.40
ACGTcount: A:0.38, C:0.14, G:0.12, T:0.36
Consensus pattern (21 bp):
AATGTATCGATACATTATGAC
Found at i:312797 original size:37 final size:33
Alignment explanation
Indices: 312747--312834 Score: 97
Period size: 32 Copynumber: 2.5 Consensus size: 33
312737 ACCTTTTAGC
* *
312747 CTAAGGTATAACCTTACAACACTATCATTTACAAAGG
1 CTAAGATAGAACCTT-CAACACTATC-TTT-C-AAGG
*
312784 CTAAGATAGAACC-TCTACACTATCTTTCAAGG
1 CTAAGATAGAACCTTCAACACTATCTTTCAAGG
312816 CTAAGATAGAACCTCTCAA
1 CTAAGATAGAACCT-TCAA
312835 TCACCTGGAG
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
32 17 0.38
33 1 0.02
34 6 0.13
35 9 0.20
36 1 0.02
37 11 0.24
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.26
Consensus pattern (33 bp):
CTAAGATAGAACCTTCAACACTATCTTTCAAGG
Found at i:312819 original size:32 final size:35
Alignment explanation
Indices: 312765--312831 Score: 113
Period size: 32 Copynumber: 2.0 Consensus size: 35
312755 TAACCTTACA
312765 ACACTATCATTTACAAAGGCTAAGATAGAACCTCT
1 ACACTATCATTTACAAAGGCTAAGATAGAACCTCT
312800 ACACTATC-TTT-C-AAGGCTAAGATAGAACCTCT
1 ACACTATCATTTACAAAGGCTAAGATAGAACCTCT
312832 CAATCACCTG
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
32 20 0.62
33 1 0.03
34 3 0.09
35 8 0.25
ACGTcount: A:0.37, C:0.24, G:0.12, T:0.27
Consensus pattern (35 bp):
ACACTATCATTTACAAAGGCTAAGATAGAACCTCT
Found at i:313312 original size:13 final size:13
Alignment explanation
Indices: 313291--313329 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
313281 TACTATTCAC
313291 ATGTATCGATACA
1 ATGTATCGATACA
* *
313304 ATGTGTCGATATA
1 ATGTATCGATACA
313317 ATGTATCGATACA
1 ATGTATCGATACA
313330 TGAACAGTGA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.36, C:0.13, G:0.18, T:0.33
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:313348 original size:10 final size:10
Alignment explanation
Indices: 313329--313360 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
313319 GTATCGATAC
*
313329 ATGAACAGTG
1 ATGAATAGTG
313339 ATGAATAGTG
1 ATGAATAGTG
313349 ATGAATAGTG
1 ATGAATAGTG
313359 AT
1 AT
313361 ACATGAACAG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.41, C:0.03, G:0.28, T:0.28
Consensus pattern (10 bp):
ATGAATAGTG
Found at i:314525 original size:7 final size:7
Alignment explanation
Indices: 314513--314539 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
314503 TTTCATTTAT
314513 AAAAATA
1 AAAAATA
314520 AAAAATA
1 AAAAATA
314527 AAAAATA
1 AAAAATA
314534 AAAAAT
1 AAAAAT
314540 GTGATTAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (7 bp):
AAAAATA
Found at i:315249 original size:18 final size:18
Alignment explanation
Indices: 315226--315261 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
315216 TAAAGGAGAT
315226 TGATACCAATTGATGAAA
1 TGATACCAATTGATGAAA
*
315244 TGATACCAATTGTTGAAA
1 TGATACCAATTGATGAAA
315262 GATTAATGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.42, C:0.11, G:0.17, T:0.31
Consensus pattern (18 bp):
TGATACCAATTGATGAAA
Found at i:316716 original size:21 final size:21
Alignment explanation
Indices: 316674--316738 Score: 62
Period size: 21 Copynumber: 3.1 Consensus size: 21
316664 ATGCAAATTT
**
316674 TTATTTTTATTAGTTAACTCA
1 TTATTTTTATTAGCCAACTCA
*
316695 TTATTTTTATTAGCCAATTCA
1 TTATTTTTATTAGCCAACTCA
*
316716 TCATTTTCTAGTT-G-CAACTCA
1 TTATTTT-TA-TTAGCCAACTCA
316737 TT
1 TT
316739 TCTTTTCTCC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
21 31 0.86
22 3 0.08
23 2 0.06
ACGTcount: A:0.26, C:0.15, G:0.06, T:0.52
Consensus pattern (21 bp):
TTATTTTTATTAGCCAACTCA
Found at i:316801 original size:21 final size:21
Alignment explanation
Indices: 316756--316801 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
316746 TCCTTTGATT
**
316756 CATTTAATTTCTTTTCTAATT
1 CATTTAATTTCTTTTCTAAAA
316777 CATTTAATTTCTTTT-TAAGAA
1 CATTTAATTTCTTTTCTAA-AA
316798 CATT
1 CATT
316802 ATTCTCTAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 3 0.14
21 19 0.86
ACGTcount: A:0.28, C:0.13, G:0.02, T:0.57
Consensus pattern (21 bp):
CATTTAATTTCTTTTCTAAAA
Found at i:322791 original size:29 final size:29
Alignment explanation
Indices: 322758--322815 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
322748 GTCTAAATGC
322758 CATCACTTGTTTGAATATGTTATTTATAT
1 CATCACTTGTTTGAATATGTTATTTATAT
322787 CATCACTTGTTTGAATATGTTATTTATAT
1 CATCACTTGTTTGAATATGTTATTTATAT
322816 TCACTATTAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.52
Consensus pattern (29 bp):
CATCACTTGTTTGAATATGTTATTTATAT
Found at i:324284 original size:82 final size:80
Alignment explanation
Indices: 324181--324629 Score: 336
Period size: 82 Copynumber: 5.5 Consensus size: 80
324171 TTTTTGAGGG
* *
324181 GATACTCTAACCTCGT-TTTTCTTCCAAAAAATCTTGAATTTACATTCTCAAATATACTCCAACC
1 GATACTCTAACCT--TATTTTCTTACAAAAAATCTTGAATTTACATTCTCAAAGATACTCCAACC
*
324245 CCATCTCTGTAAACAAGA
64 CCATCTCTCTAAA-AAGA
* * * * *
324263 GATGCTCTAACCTTATATTTCTAACAAAAAATTCTTCAATTTACATTCTCAAGGATACTTCAACC
1 GATACTCTAACCTTAT-TTTCTTACAAAAAA-TCTTGAATTTACATTCTCAAAGATACTCCAACC
* * *
324328 GCATCTCTC--CAAAGG
64 CCATCTCTCTAAAAAGA
* * ** *
324343 GATACT-TCAATCTCACTTTTCTTACAAAAGAATCTTGAATTTACATTCTTGAGGATACTCCAAC
1 GATACTCT-AACCTTA-TTTTCTTACAAAA-AATCTTGAATTTACATTCTCAAAGATACTCCAAC
* * *
324407 CCCATCTCTCCAAAATGGT
63 CCCATCTCTCTAAAA-AGA
* ** * * *
324426 GATACTCTAACCCTATTTTTCTTGGAAAAAATCTTGATTTTACATTCTCAATGATACTCCAACCT
1 GATACTCTAACCTTA-TTTTCTTACAAAAAATCTTGAATTTACATTCTCAAAGATACTCCAACCC
* *
324491 TATCTCTCTAAAAAAAA
65 CATCTCTCT-AAAAAGA
* * * * * * * *
324508 GATACTTTAACCTTATCTTT-TTACTAAAAAATGTTGAATTTTCATTCTCTAGGATGCCCCAAAC
1 GATACTCTAACCTTAT-TTTCTTAC-AAAAAATCTTGAATTTACATTCTCAAAGATACTCCAACC
* *
324572 CCATATCTCCAAAGAAG-
64 CCATCTCTCTAAA-AAGA
* * * *
324589 GATACTCTTACCTCATTTTTCATATAAAAAGA-CTTGAATTT
1 GATACTCTAACCTTA-TTTTCTTACAAAAA-ATCTTGAATTT
324630 TCTTTTAGAT
Statistics
Matches: 288, Mismatches: 62, Indels: 35
0.75 0.16 0.09
Matches are distributed among these distances:
79 1 0.00
80 62 0.22
81 39 0.14
82 123 0.43
83 62 0.22
84 1 0.00
ACGTcount: A:0.34, C:0.24, G:0.08, T:0.35
Consensus pattern (80 bp):
GATACTCTAACCTTATTTTCTTACAAAAAATCTTGAATTTACATTCTCAAAGATACTCCAACCCC
ATCTCTCTAAAAAGA
Found at i:324457 original size:163 final size:161
Alignment explanation
Indices: 324197--324498 Score: 381
Period size: 163 Copynumber: 1.9 Consensus size: 161
324187 CTAACCTCGT
* * **
324197 TTTTCTTCCAAAAAATCTTGAATTTACATTCTCAAATATACTCCAACCCCATCTCTGTAAACAAG
1 TTTTCTTACAAAAAATCTTGAATTTACATTCTCAAAGATACTCCAACCCCATCTCTCCAAACAAG
* * *
324262 AGATGCTCTAACCTTATATTTCTAACAAAAAATTCTTCAATTTACATTCTCAAGGATACTTCAAC
66 AGATACTCTAACCCTATATTTCTAACAAAAAA-TCTTCAATTTACATTCTCAAGGATACTCCAAC
324327 CGCATCTCTCCAAAGGGATACTTCAATCTCAC
130 CGCATCTCTCCAAAGGGATACTTCAATCTCAC
** *
324359 TTTTCTTACAAAAGAATCTTGAATTTACATTCTTGAGGATACTCCAACCCCATCTCTCCAAA-AT
1 TTTTCTTACAAAA-AATCTTGAATTTACATTCTCAAAGATACTCCAACCCCATCTCTCCAAACA-
* * * *** * * *
324423 GGTGATACTCTAACCCTATTTTTCTTGGAAAAAATCTTGATTTTACATTCTCAATGATACTCCAA
64 AGAGATACTCTAACCCTATATTTCTAACAAAAAATCTTCAATTTACATTCTCAAGGATACTCCAA
**
324488 CCTTATCTCTC
129 CCGCATCTCTC
324499 TAAAAAAAAG
Statistics
Matches: 117, Mismatches: 21, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
162 49 0.42
163 68 0.58
ACGTcount: A:0.32, C:0.25, G:0.08, T:0.35
Consensus pattern (161 bp):
TTTTCTTACAAAAAATCTTGAATTTACATTCTCAAAGATACTCCAACCCCATCTCTCCAAACAAG
AGATACTCTAACCCTATATTTCTAACAAAAAATCTTCAATTTACATTCTCAAGGATACTCCAACC
GCATCTCTCCAAAGGGATACTTCAATCTCAC
Found at i:331254 original size:15 final size:16
Alignment explanation
Indices: 331230--331259 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
331220 TTTTCACAAA
331230 AAAAATGAAAAAGAAG
1 AAAAATGAAAAAGAAG
331246 AAAAA-GAAAAAGAA
1 AAAAATGAAAAAGAA
331260 AATTCACTTG
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:332946 original size:88 final size:87
Alignment explanation
Indices: 332834--333080 Score: 282
Period size: 88 Copynumber: 2.8 Consensus size: 87
332824 TTTGTATCTA
* * * * * * *
332834 CATTATTT-TCATGCATTTTCCTCTTCACTGATACTTGTATTTGGATTATTTCATATACTTTTGC
1 CATTATTTCACATGCATTTT-CTCTTCACTGACACTTG-ATTTGCATCATTTCACATACATCTGC
*
332898 ACCATTAGAT-GTATTGGCATTTG
64 ACCATTAGATGGAATTGGCATTTG
* * * *
332921 CATTATTTCACATGCATTTGTCTCTTCACTAACACTTGATTTGCATCGTTTCACATGCATCTACA
1 CATTATTTCACATGCATTT-TCTCTTCACTGACACTTGATTTGCATCATTTCACATACATCTGCA
332986 CCATTAGATGGAATTGGCATTTG
65 CCATTAGATGGAATTGGCATTTG
* * * * *
333009 CGTTGTTTCACAAGCATTTTCTTCTTTACTGACATTTGCATTTGCATCATTTCACATACATCTGC
1 CATTATTTCACATGCATTTTC-TCTTCACTGACACTTG-ATTTGCATCATTTCACATACATCTGC
333074 ACCATTA
64 ACCATTA
333081 CCAATACTTG
Statistics
Matches: 134, Mismatches: 21, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
87 38 0.28
88 65 0.49
89 31 0.23
ACGTcount: A:0.23, C:0.21, G:0.12, T:0.43
Consensus pattern (87 bp):
CATTATTTCACATGCATTTTCTCTTCACTGACACTTGATTTGCATCATTTCACATACATCTGCAC
CATTAGATGGAATTGGCATTTG
Found at i:333920 original size:55 final size:56
Alignment explanation
Indices: 333861--333970 Score: 132
Period size: 56 Copynumber: 2.0 Consensus size: 56
333851 AAAATTTTCG
* * * *
333861 ATGGTGCAACC-AAAGCTTTTGGTAGTGGTAATCAGAATAAATGTTAAAGTCTTTA
1 ATGGTGCAACCAAAAACTTCTGGTAGTCGTAATCAGAATAAATGTTAAACTCTTTA
* * * **
333916 ATGGTGTATCCAAAAACTTCTGGTGGTCGTAATCAGAATGGATGTTAAACTCTTT
1 ATGGTGCAACCAAAAACTTCTGGTAGTCGTAATCAGAATAAATGTTAAACTCTTT
333971 GTTGGTGTAT
Statistics
Matches: 45, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
55 9 0.20
56 36 0.80
ACGTcount: A:0.32, C:0.13, G:0.22, T:0.34
Consensus pattern (56 bp):
ATGGTGCAACCAAAAACTTCTGGTAGTCGTAATCAGAATAAATGTTAAACTCTTTA
Found at i:334024 original size:54 final size:56
Alignment explanation
Indices: 333888--334039 Score: 166
Period size: 56 Copynumber: 2.8 Consensus size: 56
333878 TTTGGTAGTG
*
333888 GTAATCAGAATAAATGTTAAAGTCTTTAATGGTGTATCCAAAAACTTCTGGTGGTC
1 GTAATCAGAATAAATGTTAAAGTCTTTGATGGTGTATCCAAAAACTTCTGGTGGTC
** * * * *
333944 GTAATCAGAATGGATGTTAAACTCTTTGTTGGTGTATTC-AAAACTTCT-GTGGTT
1 GTAATCAGAATAAATGTTAAAGTCTTTGATGGTGTATCCAAAAACTTCTGGTGGTC
* * * * *
333998 GTAACCAGAAT-AATTTTCAAAGTCTTTGGTTGTATATCCAAA
1 GTAATCAGAATAAATGTT-AAAGTCTTTGATGGTGTATCCAAA
334040 CCTTCTAATG
Statistics
Matches: 79, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
53 4 0.05
54 31 0.39
55 11 0.14
56 33 0.42
ACGTcount: A:0.32, C:0.12, G:0.19, T:0.37
Consensus pattern (56 bp):
GTAATCAGAATAAATGTTAAAGTCTTTGATGGTGTATCCAAAAACTTCTGGTGGTC
Found at i:341031 original size:141 final size:143
Alignment explanation
Indices: 340868--341241 Score: 488
Period size: 141 Copynumber: 2.6 Consensus size: 143
340858 GAACCAAAGG
* * *
340868 GATACAGAAAAGTTTTGAAGATTTTTATAACCTTACGGAAAACCATAGGAATATTAGAAATTTTG
1 GATAC-GAAAAGTTTTGAAGATTTCTATACCCCTACGGAAAACCATAGGAATATTAGAAATTTTG
* * * *
340933 AAAAATTAAGAGAATAATTTTTATTTAATTTTTAATTTTC-AAAAAAATTTATTCCGTACCTTAA
65 AAAAATTAAGAGAATAATTTTTATCTAATTTTTAATTTCCAAAAAAAAATCATTCCGTACCTTAA
* *
340997 TAGG-GAACTGAAAA
130 T-GGACAACCGAAAA
* *
341011 GATACG-AAAGTTTTGAAGATTTCTATACCCCTACGAAAAATCATAGGAATATTAGAAATTTTGA
1 GATACGAAAAGTTTTGAAGATTTCTATACCCCTACGGAAAACCATAGGAATATTAGAAATTTTGA
**
341075 AAAATTAAGAGAATAATTTTTATCTAATTTTTAATTTCCAAAAAAAAATCATTTTGTACCTTAAT
66 AAAATTAAGAGAATAATTTTTATCTAATTTTTAATTTCCAAAAAAAAATCATTCCGTACCTTAAT
*
341140 GGACAACCGAAAT
131 GGACAACCGAAAA
* * * * * *
341153 GATACGAAAAGTTTTGAAAATTTCCATACCCCCACGGATACCCAT-GGAAATATTAGAAATTTTA
1 GATACGAAAAGTTTTGAAGATTTCTATACCCCTACGGAAAACCATAGG-AATATTAGAAATTTTG
*
341217 AAAAATTAAG-GTGATAATTTTTATC
65 AAAAATTAAGAG-AATAATTTTTATC
341242 AGATAAAATA
Statistics
Matches: 203, Mismatches: 23, Indels: 10
0.86 0.10 0.04
Matches are distributed among these distances:
141 92 0.45
142 38 0.19
143 73 0.36
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.34
Consensus pattern (143 bp):
GATACGAAAAGTTTTGAAGATTTCTATACCCCTACGGAAAACCATAGGAATATTAGAAATTTTGA
AAAATTAAGAGAATAATTTTTATCTAATTTTTAATTTCCAAAAAAAAATCATTCCGTACCTTAAT
GGACAACCGAAAA
Found at i:343113 original size:166 final size:160
Alignment explanation
Indices: 342741--343197 Score: 383
Period size: 166 Copynumber: 2.8 Consensus size: 160
342731 AAATTCCCAT
* * * * *
342741 GAAAACATTTATGGATAGAAA-TTCGGT-TATTGGAAATAGGGGCATTTCAAGGAAAAAAATGAA
1 GAAAACATTTATGGATAGAAACTT-TGTATTTTGAAAATAGGGGAATTTCAA-GAAAAAAATCAA
* * * *
342804 AAACTCATAAAAATGAATGAATTTTTTAAAACT-AGTCTAATATGAATTAAATGATAATATTTGG
64 AAACT-AAAAAAATGAATGAATTTTTCAAAACTGA-TTTAATATG-ATTAAATGATAATATTTGA
* *
342868 TGAATTTAAAAAAATTTGACCCGAGAAAACCCCCGG
126 TGAATTTAAAAAAATTTGAACCAAGAAAACCCCC-G
* * * *
342904 AGAAAACCTTTATGGAATAAAAAAC-TTG-ATCTTTCAAAAATAGGGAAATTTCAAGAAAAAAAT
1 -GAAAACATTTATGG-AT-AGAAACTTTGTAT-TTT-GAAAATAGGGGAATTTCAAGAAAAAAAT
* * * * *
342967 TAAAAACTAACGAAAATGAATGAATTTTTGAAAAATGATTTAATATGAGTTAAATAATAATATTT
61 CAAAAACTAA-AAAAATGAATGAATTTTTCAAAACTGATTTAATATGA-TTAAATGATAATATTT
*
343032 GATGAATTT-TAAAAA-TTGAAAACCAAGATAAATCTCCCC-
124 GATGAATTTAAAAAAATTTG--AACCAAGA-AAA-C-CCCCG
* *
343071 GAAAACATTTATGGAGTAGAACACTTTGTATTTTGTAAATAGGAGGAATTTCAA-AAGAAAATCA
1 GAAAACATTTATGGA-TAGAA-ACTTTGTATTTTGAAAATAGG-GGAATTTCAAGAAAAAAATCA
* * * * * *
343135 ATAACTTATAAAATAAAAGGAATTTTTCAAAACTGATTTAATGGTGATTAAATGATAATATTT
63 AAAACTAAAAAAAT-GAATGAATTTTTCAAAACTGATTTAAT-ATGATTAAATGATAATATTT
343198 AGAAAATTTT
Statistics
Matches: 237, Mismatches: 35, Indels: 40
0.76 0.11 0.13
Matches are distributed among these distances:
164 16 0.07
165 20 0.08
166 157 0.66
167 37 0.16
168 3 0.01
169 4 0.02
ACGTcount: A:0.47, C:0.09, G:0.14, T:0.30
Consensus pattern (160 bp):
GAAAACATTTATGGATAGAAACTTTGTATTTTGAAAATAGGGGAATTTCAAGAAAAAAATCAAAA
ACTAAAAAAATGAATGAATTTTTCAAAACTGATTTAATATGATTAAATGATAATATTTGATGAAT
TTAAAAAAATTTGAACCAAGAAAACCCCCG
Found at i:343613 original size:22 final size:22
Alignment explanation
Indices: 343588--343634 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
343578 ATACGAATGT
* * *
343588 CAATTCTCGAATATTTTCAGAA
1 CAATTCTCAAAAATTTTAAGAA
343610 CAA-TCTCAAAAATTTTAAGAA
1 CAATTCTCAAAAATTTTAAGAA
343631 -AATT
1 CAATT
343635 GACCGTGACA
Statistics
Matches: 21, Mismatches: 3, Indels: 3
0.78 0.11 0.11
Matches are distributed among these distances:
20 2 0.10
21 16 0.76
22 3 0.14
ACGTcount: A:0.45, C:0.15, G:0.06, T:0.34
Consensus pattern (22 bp):
CAATTCTCAAAAATTTTAAGAA
Found at i:344315 original size:42 final size:43
Alignment explanation
Indices: 344189--344324 Score: 136
Period size: 42 Copynumber: 3.2 Consensus size: 43
344179 GGTAAATAAA
* * *
344189 GATG-AAAAGGTTGATCGAGATTGAACCGACAAGTCAATAAAG
1 GATGAAAAAGGTTGATCGGGATTGAACTGACAAGTCAACAAAG
* * * * * *
344231 GAT-AAAAAGATTTACTCGGGAAT-AAGTCGATAAGTAAACAAAG
1 GATGAAAAAGGTTGA-TCGGGATTGAACT-GACAAGTCAACAAAG
344274 GATGAAAAAGGTTGAT-GGGATTGAACTGACAAGTCAACAAAG
1 GATGAAAAAGGTTGATCGGGATTGAACTGACAAGTCAACAAAG
*
344316 GATAAAAAA
1 GATGAAAAA
344325 CTTAACTGAT
Statistics
Matches: 73, Mismatches: 16, Indels: 10
0.74 0.16 0.10
Matches are distributed among these distances:
42 39 0.53
43 25 0.34
44 9 0.12
ACGTcount: A:0.47, C:0.10, G:0.24, T:0.19
Consensus pattern (43 bp):
GATGAAAAAGGTTGATCGGGATTGAACTGACAAGTCAACAAAG
Found at i:344578 original size:47 final size:47
Alignment explanation
Indices: 344421--344913 Score: 468
Period size: 47 Copynumber: 10.5 Consensus size: 47
344411 TAATTGATAT
* * * ** * *
344421 AGTCAAATGAGGATGAAAAGAGTTTGACTA-GAACTAACGCTAATAC
1 AGTCAAACGAGGGTGAAAAGAGTTTGACCAGGTCCTAATGCCAATAC
* * ** *
344467 AGTCAAACAATGAAGAAAAGAGTTTGACCAGGTCCTAATGCCAATAT
1 AGTCAAACGAGGGTGAAAAGAGTTTGACCAGGTCCTAATGCCAATAC
* ** * * * * * * *
344514 AGTTAAATAATGATGAAATGAGTTTGACCAAGTCTTAATGCTAGTAC
1 AGTCAAACGAGGGTGAAAAGAGTTTGACCAGGTCCTAATGCCAATAC
* * *
344561 AGTCAAACGAGGGTGAAAAGAGTTTGACGAGGTCCTAACGCGAATAC
1 AGTCAAACGAGGGTGAAAAGAGTTTGACCAGGTCCTAATGCCAATAC
* * * * * **
344608 AATCAAATGAAGGTGAAATGAGTTTGACCATGTCCTAACACCAATAC
1 AGTCAAACGAGGGTGAAAAGAGTTTGACCAGGTCCTAATGCCAATAC
* ** * *
344655 AGTCAAACTAGGGCAAAAAAAGTTTAACCAGGTCCTAATGCCAATAC
1 AGTCAAACGAGGGTGAAAAGAGTTTGACCAGGTCCTAATGCCAATAC
* * *
344702 AGTTAAACGAGGGTGAAAAGAGTTTGACCAGGTCCTAATACCAATAT
1 AGTCAAACGAGGGTGAAAAGAGTTTGACCAGGTCCTAATGCCAATAC
* **
344749 AGTCAAACGAGGGTGAAAAGAGTTTAACCAGGTCCTAACACCAATAC
1 AGTCAAACGAGGGTGAAAAGAGTTTGACCAGGTCCTAATGCCAATAC
* * * * *
344796 AATCAAACAAGGGTGAAAAGAGTTTGACCAGATCCTAATGCAAATAT
1 AGTCAAACGAGGGTGAAAAGAGTTTGACCAGGTCCTAATGCCAATAC
* * * *
344843 AGTCAAATGAGGATGAAAAGAGTTTGACGAGGTCCTATTGCCAATAC
1 AGTCAAACGAGGGTGAAAAGAGTTTGACCAGGTCCTAATGCCAATAC
* * *
344890 ATTCAAA-AAGAGGTGAGAAGAGTT
1 AGTCAAACGAG-GGTGAAAAGAGTT
344914 CAGCAAAGAG
Statistics
Matches: 361, Mismatches: 84, Indels: 3
0.81 0.19 0.01
Matches are distributed among these distances:
46 27 0.07
47 334 0.93
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.22
Consensus pattern (47 bp):
AGTCAAACGAGGGTGAAAAGAGTTTGACCAGGTCCTAATGCCAATAC
Found at i:355325 original size:20 final size:20
Alignment explanation
Indices: 355300--355404 Score: 84
Period size: 20 Copynumber: 4.7 Consensus size: 20
355290 TTTTAACTAG
355300 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
355320 ATGTATCGATACATCTGGGTAAAAAGATAGA
1 ATGTATCGATACAT-T--G-----A-A-A-A
* *
355351 ATGTATTGATACATTGAAGA
1 ATGTATCGATACATTGAAAA
355371 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAAAA
*
355391 ATGTATCAATACAT
1 ATGTATCGATACAT
355405 CTGGGTACTT
Statistics
Matches: 69, Mismatches: 5, Indels: 22
0.72 0.05 0.23
Matches are distributed among these distances:
20 46 0.67
21 1 0.01
22 1 0.01
23 2 0.03
28 2 0.03
29 1 0.01
30 2 0.03
31 14 0.20
ACGTcount: A:0.43, C:0.10, G:0.17, T:0.30
Consensus pattern (20 bp):
ATGTATCGATACATTGAAAA
Found at i:356407 original size:28 final size:28
Alignment explanation
Indices: 356326--357235 Score: 581
Period size: 28 Copynumber: 31.6 Consensus size: 28
356316 CACCGACTCG
*
356326 TGTGGGCTTTGAAAAGAGTGCCACT-AGCT
1 TGTGGGCTTTGAAAGGA-TGCCACTGA-CT
* * *
356355 TGTGGGCTTTCAAAAGAGTGCCACTAACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
*
356384 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
356412 TGTGGGTTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
*
356440 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTGAAAGGA-TGCCACTGACT
*
356469 TGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
356497 TGTGTGCTTTGAAATGGGTTGCCA-TCGACT
1 TGTGGGCTTTGAAA--GGATGCCACT-GACT
* **
356527 TGTGTGGCTTTGAAATAGGTTGCCACCAACTT
1 TGTG-GGCTTTG-AA-AGGATGCCACTGAC-T
* * * *
356559 GTGTGGGCTTTCAAATGAGTTGCCACAGATTT
1 -TGTGGGCTTTGAAA-G-GATGCCACTGA-CT
*
356591 GTGTGGGCTTTGAAATGATGCCACTGACT
1 -TGTGGGCTTTGAAAGGATGCCACTGACT
* *
356620 TGTGGGCTTTGAAATAGGTTGCCACCGACTT
1 TGTGGGCTTTG-AA-AGGATGCCACTGAC-T
* **
356651 GTGTGGGCTTTGAAATGGGTTGCCACCAACTT
1 -TGTGGGCTTTGAAA--GGATGCCACTGAC-T
356683 GTGTGGGCTTTGAAAAGGATGCCACTGACT
1 -TGTGGGCTTTG-AAAGGATGCCACTGACT
356713 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
356741 TGTGGGCTTTGAAATGGGTTGCCACCGACTT
1 TGTGGGCTTTGAAA--GGATGCCACTGAC-T
* * *
356772 GTGTGGGCTTTGAATTGAGTTGCCACCGACTT
1 -TGTGGGCTTTGAA-AG-GATGCCACTGAC-T
* *
356804 GTGTGGGCTTTGAAATGATGCTACTGACT
1 -TGTGGGCTTTGAAAGGATGCCACTGACT
* *
356833 TGTGGGCTTTGAAATGATACCACTGACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
356861 TATGGGCTTTGAAATGATGCCACTGATT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
356889 TGTGGGCTTTAAAATGATGCCACTAACT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * * *
356917 TGTGGCCTTTAAAAGGGTGCTGCCACGGAGT
1 TGTGGGCTTTGAAA--G-GATGCCACTGACT
* * * **
356948 TGTGGAC-TTAAAAGGATGCCACGGGGT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * * *
356975 TGTGGACTTTAAAAGGGTGCCACGGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
357003 TGTGGACTTTAAAAGGATGCCACGGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
357031 TGTGGAC-TTAAAAGGATGCCACAGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * * * *
357058 GGTGGACTTTAAAAGGGTGCCACAGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
357086 GGTGGACTTT-AAAGGGTGCCA-TGGAGT
1 TGTGGGCTTTGAAAGGATGCCACT-GACT
* * * *
357113 TATGGACTTTAAAAAGG-TGCCA-TAGAGT
1 TGTGGGCTTT-GAAAGGATGCCACT-GACT
* *
357141 TGTGGACTTTAAAAGGATG-C-C--AC-
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * *
357164 TGTGGACTTT-AAAGGATGCCACGGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* * * *
357191 TGTGGAC-TTAAAAGGATGCCACAGAGT
1 TGTGGGCTTTGAAAGGATGCCACTGACT
* *
357218 TGTGGTCTTTGAAGGGAT
1 TGTGGGCTTTGAAAGGAT
357236 CAGGTGCTTG
Statistics
Matches: 759, Mismatches: 78, Indels: 89
0.82 0.08 0.10
Matches are distributed among these distances:
22 8 0.01
23 11 0.01
24 2 0.00
26 3 0.00
27 102 0.13
28 314 0.41
29 87 0.11
30 64 0.08
31 49 0.06
32 111 0.15
33 8 0.01
ACGTcount: A:0.24, C:0.16, G:0.31, T:0.29
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGATGCCACTGACT
Found at i:356754 original size:121 final size:119
Alignment explanation
Indices: 356289--356920 Score: 734
Period size: 121 Copynumber: 5.3 Consensus size: 119
356279 GGTGCCATTA
** * * *
356289 ACTTGTGTGGGCTTTGAGAATAATTACCACCGACTCGTGTGGGCTTTGAAAAGAGTGCCACT-AG
1 ACTTGTGTGGGCTTTGA-AATGGTTGCCACCAACTTGTGTGGGCTTTGAAAAGA-TGCCACTGA-
* * * * *
356353 CTTGTGGGCTTTCAAAAGAGTGCCACTAACTTGTGGGCTTTG-AA-AGGGTGCCACTG
63 CTTGTGGGCTTTGAAAGGA-TGCCACTGACTTGTGGGCTTTGAAATAGGTTGCCACCG
* * *
356409 AC-T-TGTGGGTTTTGAAA-GGATGCCACTAAC-T-TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 ACTTGTGTGGGCTTTGAAATGGTTGCCACCAACTTGTGTGGGCTTTGAAAAGA-TGCCACTGACT
* * * *
356469 TGTGGGCTTTGAAAGGATGCCACTAACTTGTGTGCTTTGAAATGGGTTGCCATCG
65 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAATAGGTTGCCACCG
* * *
356524 ACTTGTGT-GGCTTTGAAATAGGTTGCCACCAACTTGTGTGGGCTTTCAAATGAGTTGCCACAGA
1 ACTTGTGTGGGCTTTGAAAT-GGTTGCCACCAACTTGTGTGGGCTTTGAAA--AGATGCCACTGA
* *
356588 TTTGTGTGGGCTTTGAAATGATGCCACTGACTTGTGGGCTTTGAAATAGGTTGCCACCG
63 -CT-TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAATAGGTTGCCACCG
356647 ACTTGTGTGGGCTTTGAAATGGGTTGCCACCAACTTGTGTGGGCTTTGAAAAGGATGCCACTGAC
1 ACTTGTGTGGGCTTTGAAAT-GGTTGCCACCAACTTGTGTGGGCTTTGAAAA-GATGCCACTGAC
*
356712 TTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAATGGGTTGCCACCG
64 TTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAATAGGTTGCCACCG
* * * *
356768 ACTTGTGTGGGCTTTGAATTGAGTTGCCACCGACTTGTGTGGGCTTTGAAATGATGCTACTGACT
1 ACTTGTGTGGGCTTTGAAATG-GTTGCCACCAACTTGTGTGGGCTTTGAAAAGATGCCACTGACT
* * * * *
356833 TGTGGGCTTTGAAATGATACCACTGACTTATGGGCTTTGAAAT--GATGCCACTG
65 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAATAGGTTGCCACCG
* * *
356886 A-TT-TGTGGGCTTTAAAAT-GATGCCACTAACTTGTG
1 ACTTGTGTGGGCTTTGAAATGGTTGCCACCAACTTGTG
356921 GCCTTTAAAA
Statistics
Matches: 448, Mismatches: 48, Indels: 38
0.84 0.09 0.07
Matches are distributed among these distances:
113 21 0.05
114 58 0.13
115 11 0.02
116 30 0.07
117 7 0.02
118 31 0.07
119 2 0.00
120 68 0.15
121 108 0.24
122 5 0.01
123 67 0.15
124 40 0.09
ACGTcount: A:0.22, C:0.18, G:0.29, T:0.31
Consensus pattern (119 bp):
ACTTGTGTGGGCTTTGAAATGGTTGCCACCAACTTGTGTGGGCTTTGAAAAGATGCCACTGACTT
GTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAATAGGTTGCCACCG
Found at i:357002 original size:55 final size:56
Alignment explanation
Indices: 356867--357227 Score: 384
Period size: 55 Copynumber: 6.6 Consensus size: 56
356857 GACTTATGGG
* * * * * * ** * *
356867 CTTTGAAATGATGCCACTGATTTGTGGGCTTTAAAATGATGCCACTAACTTGTGGC
1 CTTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGA
* *
356923 CTTTAAAAGGGTGCTGCCACGGAGTTGTGGAC-TTAAAAGGATGCCACGGGGTTGTGGA
1 CTTTAAAA--G-GATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGA
*
356981 CTTTAAAAGGGTGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGA
1 CTTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGA
* * * * *
357037 C-TTAAAAGGATGCCACAGAGTGGTGGACTTTAAAAGGGTGCCACAGAGTGGTGGA
1 CTTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGA
* * * **
357092 CTTT-AAAGGGTGCCATGGAGTTATGGACTTTAAAAAGG-TGCCATAGAGTTGTGGA
1 CTTTAAAAGGATGCCACGGAGTTGTGGACTTT-AAAAGGATGCCACGGAGTTGTGGA
357147 CTTTAAAAGGATGCCAC-----TGTGGACTTT-AAAGGATGCCACGGAGTTGTGGA
1 CTTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGA
* *
357197 C-TTAAAAGGATGCCACAGAGTTGTGGTCTTT
1 CTTTAAAAGGATGCCACGGAGTTGTGGACTTT
357228 GAAGGGATCA
Statistics
Matches: 259, Mismatches: 33, Indels: 28
0.81 0.10 0.09
Matches are distributed among these distances:
49 20 0.08
50 16 0.06
51 9 0.03
54 9 0.03
55 109 0.42
56 52 0.20
58 28 0.11
59 16 0.06
ACGTcount: A:0.27, C:0.15, G:0.31, T:0.27
Consensus pattern (56 bp):
CTTTAAAAGGATGCCACGGAGTTGTGGACTTTAAAAGGATGCCACGGAGTTGTGGA
Found at i:357232 original size:27 final size:27
Alignment explanation
Indices: 356937--357232 Score: 334
Period size: 27 Copynumber: 11.0 Consensus size: 27
356927 AAAAGGGTGC
*
356937 TGCCACGGAGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTTAAAGGA
* *
356964 TGCCACGGGGTTGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTT-AAAGGA
356992 TGCCACGGAGTTGTGGACTTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTT-AAAGGA
*
357020 TGCCACGGAGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTTAAAGGA
* * *
357047 TGCCACAGAGTGGTGGACTTTAAAAGGG
1 TGCCACGGAGTTGTGGACTTT-AAAGGA
* * *
357075 TGCCACAGAGTGGTGGACTTTAAAGGG
1 TGCCACGGAGTTGTGGACTTTAAAGGA
* *
357102 TGCCATGGAGTTATGGACTTTAAAAAGG-
1 TGCCACGGAGTTGTGGACTTT--AAAGGA
**
357130 TGCCATAGAGTTGTGGACTTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTT-AAAGGA
357158 TGCCAC-----TGTGGACTTTAAAGGA
1 TGCCACGGAGTTGTGGACTTTAAAGGA
*
357180 TGCCACGGAGTTGTGGACTTAAAAGGA
1 TGCCACGGAGTTGTGGACTTTAAAGGA
* * *
357207 TGCCACAGAGTTGTGGTCTTTGAAGG
1 TGCCACGGAGTTGTGGACTTTAAAGG
357233 GATCAGGTGC
Statistics
Matches: 237, Mismatches: 22, Indels: 20
0.85 0.08 0.07
Matches are distributed among these distances:
22 12 0.05
23 10 0.04
27 109 0.46
28 101 0.43
29 5 0.02
ACGTcount: A:0.28, C:0.14, G:0.33, T:0.25
Consensus pattern (27 bp):
TGCCACGGAGTTGTGGACTTTAAAGGA
Found at i:365713 original size:52 final size:52
Alignment explanation
Indices: 365633--365747 Score: 203
Period size: 52 Copynumber: 2.2 Consensus size: 52
365623 AAAAGTTGTT
* *
365633 TGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAATTTGCC
*
365685 TGCATGTATCGATACATTTTATAATGTATCGATACATCTAGGCAAATTTGCC
1 TGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAATTTGCC
365737 TGCATGTATCG
1 TGCATGTATCG
365748 TCCCCACATA
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
52 60 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (52 bp):
TGCATGTATCGATACATTTAATAATGTATCGATACATCTAGGCAAATTTGCC
Found at i:367243 original size:20 final size:20
Alignment explanation
Indices: 367220--367287 Score: 59
Period size: 20 Copynumber: 3.3 Consensus size: 20
367210 AGAATGCATT
367220 GATACAATGAGAAATGTATC
1 GATACAATGAGAAATGTATC
367240 GATACAATTGTA-AATATGTATCC
1 GATACAA-TG-AGAA-ATGTAT-C
* * *
367263 G-TACATTTAGTAATGTATC
1 GATACAATGAGAAATGTATC
367282 GATACA
1 GATACA
367288 TTTCTTTGGC
Statistics
Matches: 39, Mismatches: 3, Indels: 12
0.72 0.06 0.22
Matches are distributed among these distances:
19 2 0.05
20 18 0.46
21 6 0.15
22 11 0.28
23 2 0.05
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (20 bp):
GATACAATGAGAAATGTATC
Found at i:368186 original size:20 final size:20
Alignment explanation
Indices: 368161--368214 Score: 83
Period size: 20 Copynumber: 2.7 Consensus size: 20
368151 GTTAGAAGCA
*
368161 ATGTATCGATACAAT-TCATC
1 ATGTATCGATACAATGT-ACC
368181 ATGTATCGATACAATGTACC
1 ATGTATCGATACAATGTACC
368201 ATGTATCGATACAA
1 ATGTATCGATACAA
368215 ACAGTGGTAG
Statistics
Matches: 32, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
20 31 0.97
21 1 0.03
ACGTcount: A:0.37, C:0.19, G:0.13, T:0.31
Consensus pattern (20 bp):
ATGTATCGATACAATGTACC
Found at i:369667 original size:22 final size:20
Alignment explanation
Indices: 369621--369668 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
369611 TTTTGTTGAT
369621 AATTTTGATGAAAAAGGAAG
1 AATTTTGATGAAAAAGGAAG
*
369641 TATTTTGAAGTGAAAAA-GAAG
1 AATTTTG-A-TGAAAAAGGAAG
*
369662 AAATTTG
1 AATTTTG
369669 TAAAAGATTT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
20 6 0.26
21 10 0.43
22 7 0.30
ACGTcount: A:0.48, C:0.00, G:0.23, T:0.29
Consensus pattern (20 bp):
AATTTTGATGAAAAAGGAAG
Found at i:369806 original size:13 final size:13
Alignment explanation
Indices: 369788--369814 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
369778 ATAGTAACCC
369788 ATGTATCGATACA
1 ATGTATCGATACA
369801 ATGTATCGATACA
1 ATGTATCGATACA
369814 A
1 A
369815 AGAATATTGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:376095 original size:13 final size:13
Alignment explanation
Indices: 376077--376103 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
376067 ACAATTGCCC
376077 ATGTATCGATACA
1 ATGTATCGATACA
376090 ATGTATCGATACA
1 ATGTATCGATACA
376103 A
1 A
376104 AGCATAATCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:379669 original size:13 final size:13
Alignment explanation
Indices: 379651--379677 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
379641 GCATTATGCT
379651 TTGTATTGATACA
1 TTGTATTGATACA
379664 TTGTATTGATACA
1 TTGTATTGATACA
379677 T
1 T
379678 ATTCATTGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.07, G:0.15, T:0.48
Consensus pattern (13 bp):
TTGTATTGATACA
Found at i:379686 original size:19 final size:19
Alignment explanation
Indices: 379662--379716 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
379652 TGTATTGATA
*
379662 CATTGTATTGATACATATT
1 CATTGTATTGATACATACT
* *
379681 CATTGTATTAATACACACT
1 CATTGTATTGATACATACT
*
379700 CAATTGTATCGATACAT
1 C-ATTGTATTGATACAT
379717 GAAACTGGCA
Statistics
Matches: 29, Mismatches: 6, Indels: 1
0.81 0.17 0.03
Matches are distributed among these distances:
19 17 0.59
20 12 0.41
ACGTcount: A:0.35, C:0.16, G:0.09, T:0.40
Consensus pattern (19 bp):
CATTGTATTGATACATACT
Found at i:388330 original size:51 final size:51
Alignment explanation
Indices: 388214--388343 Score: 147
Period size: 52 Copynumber: 2.5 Consensus size: 51
388204 ATTTGTCTAC
* * *
388214 ATGTATTGATACATTAAAGAATATATCTCTATATTTGGGTAAAAAACTCAAA
1 ATGTATCGATACAAT-AAGAATATATCTCTAAATTTGGGTAAAAAACTCAAA
* * * *
388266 ATGTATCGATACAATGAAGAATGTAT-TGCTAAATTTGGGTTAAAACCT-AGA
1 ATGTATCGATACAAT-AAGAATATATCT-CTAAATTTGGGTAAAAAACTCAAA
388317 ATGTATCGATACAATAAGAAATATATC
1 ATGTATCGATACAATAAG-AATATATC
388344 GATACATTTT
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
50 3 0.05
51 24 0.36
52 39 0.59
ACGTcount: A:0.43, C:0.10, G:0.15, T:0.32
Consensus pattern (51 bp):
ATGTATCGATACAATAAGAATATATCTCTAAATTTGGGTAAAAAACTCAAA
Found at i:391727 original size:20 final size:20
Alignment explanation
Indices: 391701--391755 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 20
391691 AAAAAGATAG
*
391701 AATGTATCAATACATTCATA
1 AATGTATCAATACATTCAAA
* * * *
391721 CATGTATCGATACGTTGAAA
1 AATGTATCAATACATTCAAA
391741 AATGTATCAATACAT
1 AATGTATCAATACAT
391756 CTGGGTAAAA
Statistics
Matches: 27, Mismatches: 8, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.42, C:0.15, G:0.11, T:0.33
Consensus pattern (20 bp):
AATGTATCAATACATTCAAA
Found at i:392759 original size:32 final size:32
Alignment explanation
Indices: 392712--392796 Score: 116
Period size: 32 Copynumber: 2.7 Consensus size: 32
392702 AAAAGGGTTG
*
392712 CCACCGACTTGTGTGGGCTTTAAAAACAGGTA
1 CCACCAACTTGTGTGGGCTTTAAAAACAGGTA
* * * *
392744 CCACTAACTTGTGTGGGCTTTAAAAAGAGTTG
1 CCACCAACTTGTGTGGGCTTTAAAAACAGGTA
*
392776 CCACCGACTTGTGTGGGCTTT
1 CCACCAACTTGTGTGGGCTTT
392797 GAAAGGTGAT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.24, C:0.21, G:0.26, T:0.29
Consensus pattern (32 bp):
CCACCAACTTGTGTGGGCTTTAAAAACAGGTA
Found at i:392847 original size:28 final size:28
Alignment explanation
Indices: 392755--393312 Score: 598
Period size: 28 Copynumber: 19.6 Consensus size: 28
392745 CACTAACTTG
* * *
392755 TGTGGGCTTTAAAAAGAGTTGCCACCGACTT
1 TGTGGGCTTTGAAATGA--TGCCACTGAC-T
*
392786 GTGTGGGCTTTGAAAGGTGATGCCACTAACT
1 -TGTGGGCTTTGAAA--TGATGCCACTGACT
* * * *
392817 TGTGGGTTTTGAAATGTTGCCACTCATT
1 TGTGGGCTTTGAAATGATGCCACTGACT
392845 TGTGGGCTTTGAAATGATGCCACTGACT
1 TGTGGGCTTTGAAATGATGCCACTGACT
* * *
392873 TGTGGGCTTTAAAAAGGTG-CACTGACT
1 TGTGGGCTTTGAAATGATGCCACTGACT
* *
392900 TGTGGGCTTTGAAAGGATGTCACTGACT
1 TGTGGGCTTTGAAATGATGCCACTGACT
* *
392928 TATGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAATGATGCCACTGACT
* * *
392956 TGTGGACTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAATGATGCCACTGACT
*
392984 TGTGGGCTTTGAAATGGTGCCACTGACT
1 TGTGGGCTTTGAAATGATGCCACTGACT
* * *
393012 TGTGGGCTTTGAAACGGTGCCATTGACT
1 TGTGGGCTTTGAAATGATGCCACTGACT
* *
393040 TGTGGGCTTTGAAAATAGTTACCACTGACT
1 TGTGGGCTTTG-AAAT-GATGCCACTGACT
* * * * *
393070 TATAGGCTTTGAAAAAGGTGCCATTGACT
1 TGTGGGCTTTG-AAATGATGCCACTGACT
* * *
393099 TGTGGGCTTTAAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAATGATGCCACTGACT
*
393127 TGTGGGCTTTGAAAGGATGCCACTGACT
1 TGTGGGCTTTGAAATGATGCCACTGACT
* *
393155 TATGGGCTTTGAACA-GATGCCACTAACT
1 TGTGGGCTTTGAA-ATGATGCCACTGACT
* *
393183 TGGGGGCTTTGATAAGGATGCCACTGACT
1 TGTGGGCTTTGA-AATGATGCCACTGACT
* * *
393212 TGCGAGCTTTGAAAAGATGCCACTGACT
1 TGTGGGCTTTGAAATGATGCCACTGACT
* *
393240 TGTGGGCTTTGAAAAGATGCGACTGACT
1 TGTGGGCTTTGAAATGATGCCACTGACT
*
393268 TGTGGGCTTTGAGAAGGATGCCACTGACT
1 TGTGGGCTTTGA-AATGATGCCACTGACT
*
393297 TGTGGGCTTCGAAATG
1 TGTGGGCTTTGAAATG
393313 GGTTGTATTG
Statistics
Matches: 458, Mismatches: 59, Indels: 22
0.85 0.11 0.04
Matches are distributed among these distances:
27 24 0.05
28 304 0.66
29 70 0.15
30 36 0.08
31 1 0.00
32 21 0.05
34 2 0.00
ACGTcount: A:0.23, C:0.17, G:0.30, T:0.30
Consensus pattern (28 bp):
TGTGGGCTTTGAAATGATGCCACTGACT
Found at i:393205 original size:85 final size:84
Alignment explanation
Indices: 392755--393310 Score: 634
Period size: 85 Copynumber: 6.5 Consensus size: 84
392745 CACTAACTTG
* * * *
392755 TGTGGGCTTTAAAAAGAGTTGCCACCGACTTGTGTGGGCTTTGAAAGGTGATGCCACTAACTTGT
1 TGTGGGCTTT-GAAAG-GATGCCACTGAC-T-TGTGGGCTTTGAAA-G-GATGCCACTGACTTGT
* * * *
392820 GGGTTTTGAAATGTTGCCACTCATT
60 GGGCTTTGAAATGATGCCACTGACT
* *
392845 TGTGGGCTTTGAAATGATGCCACTGACTTGTGGGCTTTAAAAAGG-TG-CACTGACTTGTGGGCT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTT-GAAAGGATGCCACTGACTTGTGGGCT
* *
392908 TTGAAAGGATGTCACTGACT
65 TTGAAATGATGCCACTGACT
* * *
392928 TATGGGCTTTGAAAGGATGCCACTGACTTGTGGACTTTGAAAGGGTGCCACTGACTTGTGGGCTT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTT
*
392993 TGAAATGGTGCCACTGACT
66 TGAAATGATGCCACTGACT
* * * * * *
393012 TGTGGGCTTTGAAACGG-TGCCATTGACTTGTGGGCTTTGAAAATAGTTACCACTGACTTATAGG
1 TGTGGGCTTTGAAA-GGATGCCACTGACTTGTGGGCTTTG-AAA-GGATGCCACTGACTTGTGGG
* * *
393076 CTTTGAAAAAGGTGCCATTGACT
63 CTTTG-AAATGATGCCACTGACT
* * *
393099 TGTGGGCTTTAAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTATGGGCTT
1 TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTT
*
393164 TGAACA-GATGCCACTAACT
66 TGAA-ATGATGCCACTGACT
* * * *
393183 TGGGGGCTTTGATAAGGATGCCACTGACTTGCGAGCTTTGAAAAGATGCCACTGACTTGTGGGCT
1 TGTGGGCTTTGA-AAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCT
* *
393248 TTGAAAAGATGCGACTGACT
65 TTGAAATGATGCCACTGACT
*
393268 TGTGGGCTTTGAGAAGGATGCCACTGACTTGTGGGCTTCGAAA
1 TGTGGGCTTTGA-AAGGATGCCACTGACTTGTGGGCTTTGAAA
393311 TGGGTTGTAT
Statistics
Matches: 403, Mismatches: 52, Indels: 27
0.84 0.11 0.06
Matches are distributed among these distances:
82 5 0.01
83 66 0.16
84 91 0.23
85 129 0.32
86 36 0.09
87 53 0.13
88 10 0.02
89 3 0.01
90 10 0.02
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.30
Consensus pattern (84 bp):
TGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTTTGAAAGGATGCCACTGACTTGTGGGCTT
TGAAATGATGCCACTGACT
Found at i:406038 original size:27 final size:26
Alignment explanation
Indices: 405999--406049 Score: 75
Period size: 27 Copynumber: 1.9 Consensus size: 26
405989 ATTTTTTATT
405999 GAAAAATGAGGTTGGAGTATCCCCTC
1 GAAAAATGAGGTTGGAGTATCCCCTC
* *
406025 GAAAGAATGGGGTTGGAGTGTCCCC
1 GAAA-AATGAGGTTGGAGTATCCCC
406050 GATGATGAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
26 4 0.18
27 18 0.82
ACGTcount: A:0.27, C:0.18, G:0.33, T:0.22
Consensus pattern (26 bp):
GAAAAATGAGGTTGGAGTATCCCCTC
Found at i:411898 original size:31 final size:31
Alignment explanation
Indices: 411862--411922 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
411852 CTTTAAATCA
* *
411862 ATTTCAAATTTCTTCAATTTCA-CATCAAAAC
1 ATTTC-AATTTCATCAATATCATCATCAAAAC
*
411893 ATTTCATTTTCATCAATATCATCATCAAAA
1 ATTTCAATTTCATCAATATCATCATCAAAA
411923 ACAGTTTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
30 13 0.50
31 13 0.50
ACGTcount: A:0.39, C:0.21, G:0.00, T:0.39
Consensus pattern (31 bp):
ATTTCAATTTCATCAATATCATCATCAAAAC
Found at i:413712 original size:8 final size:8
Alignment explanation
Indices: 413699--413727 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
413689 AAATTTTCAA
413699 AATAAAAT
1 AATAAAAT
413707 AAT-AAAT
1 AATAAAAT
413714 AATAAAAT
1 AATAAAAT
413722 AATAAA
1 AATAAA
413728 TAAATATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
7 7 0.35
8 13 0.65
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AATAAAAT
Found at i:413717 original size:15 final size:15
Alignment explanation
Indices: 413699--413730 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
413689 AAATTTTCAA
413699 AATAAAATAATAAAT
1 AATAAAATAATAAAT
413714 AATAAAATAATAAAT
1 AATAAAATAATAAAT
413729 AA
1 AA
413731 ATATTTTTAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.75, C:0.00, G:0.00, T:0.25
Consensus pattern (15 bp):
AATAAAATAATAAAT
Found at i:415511 original size:31 final size:32
Alignment explanation
Indices: 415467--415542 Score: 120
Period size: 32 Copynumber: 2.4 Consensus size: 32
415457 TACATTGAAG
*
415467 AATGTAT-GATACATTTGGG-TCAAAACCCAA
1 AATGTATCGATACATTTGGGTTAAAAACCCAA
*
415497 AATGTATCGATACATTTGGGTTAAAAACCCAT
1 AATGTATCGATACATTTGGGTTAAAAACCCAA
415529 AATGTATCGATACA
1 AATGTATCGATACA
415543 ATGATAAATG
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
30 7 0.17
31 12 0.29
32 23 0.55
ACGTcount: A:0.39, C:0.16, G:0.16, T:0.29
Consensus pattern (32 bp):
AATGTATCGATACATTTGGGTTAAAAACCCAA
Found at i:423184 original size:24 final size:23
Alignment explanation
Indices: 423152--423199 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 23
423142 AAGCTAGCCT
*
423152 TATTTTTTTCTACCTATTTGTTTC
1 TATTTTTTTCTACCT-TTTCTTTC
*
423176 TATTTTTTTCTCCCTTTTCTTTC
1 TATTTTTTTCTACCTTTTCTTTC
423199 T
1 T
423200 CCCTTTTTTC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.36
24 14 0.64
ACGTcount: A:0.08, C:0.21, G:0.02, T:0.69
Consensus pattern (23 bp):
TATTTTTTTCTACCTTTTCTTTC
Found at i:423200 original size:13 final size:12
Alignment explanation
Indices: 423178--423208 Score: 53
Period size: 13 Copynumber: 2.5 Consensus size: 12
423168 TTTGTTTCTA
423178 TTTTTTTCTCCC
1 TTTTTTTCTCCC
423190 TTTTCTTTCTCCC
1 TTTT-TTTCTCCC
423203 TTTTTT
1 TTTTTT
423209 CTCTTTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.33
13 12 0.67
ACGTcount: A:0.00, C:0.29, G:0.00, T:0.71
Consensus pattern (12 bp):
TTTTTTTCTCCC
Found at i:424027 original size:17 final size:18
Alignment explanation
Indices: 424007--424041 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
423997 AAAATACTAT
424007 ATTTCAA-AAAAAAAGAA
1 ATTTCAAGAAAAAAAGAA
424024 ATTTCAAGGAAAAAAAGA
1 ATTTCAA-GAAAAAAAGA
424042 TCAAAAACTC
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.44
19 9 0.56
ACGTcount: A:0.66, C:0.06, G:0.11, T:0.17
Consensus pattern (18 bp):
ATTTCAAGAAAAAAAGAA
Found at i:424086 original size:170 final size:170
Alignment explanation
Indices: 423873--424433 Score: 839
Period size: 169 Copynumber: 3.3 Consensus size: 170
423863 AAAGAAAAAT
* * ** *
423873 TCAAAAGC-CATGAAAATGAATTAATTTTTTAAAATTGAATTAATATAAAATAAATAATGATGTT
1 TCAAAAACTCATGAAAATGAATGAATTTTCAAAAAATGAATTAATATAAAATAAATAATGATGTT
* *
423937 TGATGAATTTAAAAAATTGAAAACCCAGAAAAATCCTCTTGAAAAAAATTTACGGAGTTGAAAAT
66 TGATGAATTTAAAAAATTGAAAACCAAGAAAAATCCTCTTGAAAAAAATTTACGGAGTTGAAAAC
424002 ACTATATTTCAAAAAAAAAGAAATTTCAAGGAAAAAAAGA
131 ACTATATTTCAAAAAAAAAGAAATTTCAAGGAAAAAAAGA
424042 TCAAAAACTCATGAAAATGAATGAATTTTCAAAAAATGAATTAATATAAAATAAATAATGATGTT
1 TCAAAAACTCATGAAAATGAATGAATTTTCAAAAAATGAATTAATATAAAATAAATAATGATGTT
* *
424107 TGATGAATTTAAAAAATTGAAAAGCAAGAAAAATCCTTTTGAAAAAAATTTACGGAGTTGAAAAC
66 TGATGAATTTAAAAAATTGAAAACCAAGAAAAATCCTCTTGAAAAAAATTTACGGAGTTGAAAAC
*
424172 ACTATATTTC-AAGAAAAAGAAATTTCAAGGAAAAAAAGA
131 ACTATATTTCAAAAAAAAAGAAATTTCAAGGAAAAAAAGA
* * *
424211 TCAAAAACTCATGATAATGAATGAATTTTCAAAAACTGAATTAATATAAAATAAATAATGTTGTT
1 TCAAAAACTCATGAAAATGAATGAATTTTCAAAAAATGAATTAATATAAAATAAATAATGATGTT
* ** *
424276 TGATGAATTTTAAAAATTGAAAACCAAGAAAAAT-CTCATTGAAAAAAATTTACAAAGTTAAAAA
66 TGATGAATTTAAAAAATTGAAAACCAAGAAAAATCCTC-TTGAAAAAAATTTACGGAGTTGAAAA
** *
424340 CACCGTATTTCAAAAAAAAAG-AATTTCAA-GAAAGAAA-A
130 CACTATATTTCAAAAAAAAAGAAATTTCAAGGAAAAAAAGA
* * **
424378 TTATAAACTCATGAAAATGAATGAATTTTTGAAAAATGAATTAATA-AGAAATAAAT
1 TCAAAAACTCATGAAAATGAATGAATTTTCAAAAAATGAATTAATATA-AAATAAAT
424434 GATAATATGT
Statistics
Matches: 359, Mismatches: 29, Indels: 10
0.90 0.07 0.03
Matches are distributed among these distances:
166 1 0.00
167 49 0.14
168 9 0.03
169 169 0.47
170 131 0.36
ACGTcount: A:0.53, C:0.07, G:0.11, T:0.28
Consensus pattern (170 bp):
TCAAAAACTCATGAAAATGAATGAATTTTCAAAAAATGAATTAATATAAAATAAATAATGATGTT
TGATGAATTTAAAAAATTGAAAACCAAGAAAAATCCTCTTGAAAAAAATTTACGGAGTTGAAAAC
ACTATATTTCAAAAAAAAAGAAATTTCAAGGAAAAAAAGA
Found at i:425159 original size:27 final size:27
Alignment explanation
Indices: 425039--425485 Score: 392
Period size: 28 Copynumber: 15.9 Consensus size: 27
425029 AGTCGGATAT
* *
425039 AGGTGCCACTAAATTGTGTAGGCTTTGAAA
1 AGGTGCCACTGACTTGTG--GGCTTTG-AA
* * *
425069 AGGGTTACCACTGACTTGTAGACTTTGAAA
1 A-GG-TGCCACTGACTTGTGGGCTTTG-AA
* *
425099 AGGTGCCATTGACTTGTTGGCTTTTGAA
1 AGGTGCCACTGACTTGTGGGC-TTTGAA
*
425127 AGGTGCCACTAACTTGTGGGCTTTGAA
1 AGGTGCCACTGACTTGTGGGCTTTGAA
* * *
425154 ATGTGCCACTAACTTGTGGGCATTGAA
1 AGGTGCCACTGACTTGTGGGCTTTGAA
425181 AGGTGCCACTGACTTGTGGGCTTTGAA
1 AGGTGCCACTGACTTGTGGGCTTTGAA
* * *
425208 TGGATG-CATTGAGTTGTGGGCTTTGAA
1 AGG-TGCCACTGACTTGTGGGCTTTGAA
* *
425235 AGGATGCCACCGACTTGTGGGCTTTTAAAA
1 AGG-TGCCACTGACTTGTGGGC-TTT-GAA
** * * *
425265 ATATCCCACTAACTTGTGGCCTTTGAAA
1 AGGTGCCACTGACTTGTGGGCTTTG-AA
** *
425293 AGGTAACACTTACTTGTGGGCTTTTGAA
1 AGGTGCCACTGACTTGTGGGC-TTTGAA
* * * *
425321 AGAATGTCACTAACTTATGGGCTTTGAA
1 AG-GTGCCACTGACTTGTGGGCTTTGAA
* *
425349 AGGATGCCACTGACTTATGGGTTTTGAA
1 AGG-TGCCACTGACTTGTGGGCTTTGAA
*
425377 AGGATGCCACTGACTTGTGGGTTTTGAAA
1 AGG-TGCCACTGACTTGTGGGCTTTG-AA
*
425406 AGGTACCACTGACTTGTGGGCTTTGAAA
1 AGGTGCCACTGACTTGTGGGCTTTG-AA
* ** *
425434 ATGTGGTACTGCCTTGTGGGCTTTGAA
1 AGGTGCCACTGACTTGTGGGCTTTGAA
425461 AGGATGCCACTGACTTGTGGGCTTT
1 AGG-TGCCACTGACTTGTGGGCTTT
425486 TAAAATGGTC
Statistics
Matches: 345, Mismatches: 59, Indels: 28
0.80 0.14 0.06
Matches are distributed among these distances:
27 85 0.25
28 187 0.54
29 46 0.13
30 14 0.04
31 2 0.01
32 11 0.03
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.32
Consensus pattern (27 bp):
AGGTGCCACTGACTTGTGGGCTTTGAA
Found at i:426816 original size:12 final size:12
Alignment explanation
Indices: 426801--426850 Score: 66
Period size: 12 Copynumber: 4.2 Consensus size: 12
426791 CTTTTTCTTG
*
426801 TTTTT-TTTGTT
1 TTTTTGTTTTTT
426812 TTTTTGTTTTTT
1 TTTTTGTTTTTT
*
426824 ATTTTTGTTTTTG
1 -TTTTTGTTTTTT
426837 TTTTTGTTTTTT
1 TTTTTGTTTTTT
426849 TT
1 TT
426851 GAAAAAGAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
11 5 0.15
12 18 0.53
13 11 0.32
ACGTcount: A:0.02, C:0.00, G:0.10, T:0.88
Consensus pattern (12 bp):
TTTTTGTTTTTT
Found at i:426821 original size:6 final size:6
Alignment explanation
Indices: 426798--426847 Score: 59
Period size: 6 Copynumber: 8.3 Consensus size: 6
426788 TTCCTTTTTC
*
426798 TTGTTT TT-TTT GTT-TTT TTGTTTT TTATTT TTGTTT TTGTTT TTGTTT
1 TTGTTT TTGTTT -TTGTTT TTG-TTT TTGTTT TTGTTT TTGTTT TTGTTT
426846 TT
1 TT
426848 TTTGAAAAAG
Statistics
Matches: 39, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
5 5 0.13
6 29 0.74
7 5 0.13
ACGTcount: A:0.02, C:0.00, G:0.12, T:0.86
Consensus pattern (6 bp):
TTGTTT
Found at i:426828 original size:21 final size:21
Alignment explanation
Indices: 426798--426851 Score: 76
Period size: 21 Copynumber: 2.6 Consensus size: 21
426788 TTCCTTTTTC
426798 TTGTTTTTTTTGTTTTT-TTGT
1 TTGTTTTTTTTGTTTTTGTT-T
426819 TT-TTTATTTTTGTTTTTGTTT
1 TTGTTT-TTTTTGTTTTTGTTT
426840 TTGTTTTTTTTG
1 TTGTTTTTTTTG
426852 AAAAAGAATG
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
20 3 0.10
21 22 0.73
22 5 0.17
ACGTcount: A:0.02, C:0.00, G:0.13, T:0.85
Consensus pattern (21 bp):
TTGTTTTTTTTGTTTTTGTTT
Found at i:431684 original size:52 final size:52
Alignment explanation
Indices: 431614--431734 Score: 215
Period size: 52 Copynumber: 2.3 Consensus size: 52
431604 GAAAATTTAT
*
431614 CTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
* *
431666 TTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
431718 CTGCATGTATCGATACA
1 CTGCATGTATCGATACA
431735 AAGATCGGTG
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 65 1.00
ACGTcount: A:0.29, C:0.17, G:0.18, T:0.36
Consensus pattern (52 bp):
CTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAATTTGC
Found at i:431747 original size:52 final size:52
Alignment explanation
Indices: 431614--431754 Score: 187
Period size: 52 Copynumber: 2.7 Consensus size: 52
431604 GAAAATTTAT
*
431614 CTGCATGTATCGATACATTTA-ATAGTGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACA-TAAGATAGTGTATCGATACATCTGGGCAAATTTGC
* *** *
431666 TTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAATTTGC
1 CTGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGC
*
431718 CTGCATGTATCGATACA-AAGATCGGTGTATCGATACA
1 CTGCATGTATCGATACATAAGAT-AGTGTATCGATACA
431755 ATGTATCGAT
Statistics
Matches: 78, Mismatches: 9, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
51 4 0.05
52 74 0.95
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.34
Consensus pattern (52 bp):
CTGCATGTATCGATACATAAGATAGTGTATCGATACATCTGGGCAAATTTGC
Found at i:431761 original size:13 final size:13
Alignment explanation
Indices: 431743--431767 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
431733 CAAAGATCGG
431743 TGTATCGATACAA
1 TGTATCGATACAA
431756 TGTATCGATACA
1 TGTATCGATACA
431768 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:431866 original size:33 final size:33
Alignment explanation
Indices: 431809--431875 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
431799 AGTAGCTTAA
*
431809 ATTGTATCGATACAAAAAAATATGTATCTATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
431842 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
431875 A
1 A
431876 AATCGTTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.40, C:0.13, G:0.10, T:0.36
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:434485 original size:79 final size:79
Alignment explanation
Indices: 434180--434485 Score: 382
Period size: 79 Copynumber: 3.9 Consensus size: 79
434170 AGATAACCAT
* * * * * *
434180 GGGGCTGGAGTATCCCTGATTATGGAAAATCGGTGTTTTGGAAGTAAAATCGGGGTTGGAATATC
1 GGGGTTGGAGTATCCTTGATTATAGAAAATTGGTGTTTTGGAAATAAAATCGGGGTTGGAGTATC
*
434245 CCC-TCAGAAATAAC
66 CCCGTGA-AAATAAC
* *
434259 AGGGTTGGAGTATCCTTGATTATAGAAAATTGGTGTTTTGAAAATAAAATCGGGGTTGGAGTATC
1 GGGGTTGGAGTATCCTTGATTATAGAAAATTGGTGTTTTGGAAATAAAATCGGGGTTGGAGTATC
* *
434324 CTCTTGAAAATAAC
66 CCCGTGAAAATAAC
* * * ** *
434338 GGGGTTGGAGTATCCTTGATTATAGAAAATTGATGCTTTAGAAATAAGGTCGGGGTTGAAGTATC
1 GGGGTTGGAGTATCCTTGATTATAGAAAATTGGTGTTTTGGAAATAAAATCGGGGTTGGAGTATC
434403 CCCGTGAAAATAAC
66 CCCGTGAAAATAAC
* * * * *
434417 GGGGTTAGAGTATCGTCGATTGT-GAGAAATTGGTGTTTTGGAAATAAAATCGGAGTTGGAGTAT
1 GGGGTTGGAGTATCCTTGATTATAGA-AAATTGGTGTTTTGGAAATAAAATCGGGGTTGGAGTAT
434481 CCCCG
65 CCCCG
434486 ATTGTGAAAA
Statistics
Matches: 194, Mismatches: 31, Indels: 4
0.85 0.14 0.02
Matches are distributed among these distances:
78 2 0.01
79 190 0.98
80 2 0.01
ACGTcount: A:0.30, C:0.11, G:0.29, T:0.30
Consensus pattern (79 bp):
GGGGTTGGAGTATCCTTGATTATAGAAAATTGGTGTTTTGGAAATAAAATCGGGGTTGGAGTATC
CCCGTGAAAATAAC
Found at i:434488 original size:51 final size:51
Alignment explanation
Indices: 434419--434535 Score: 173
Period size: 51 Copynumber: 2.3 Consensus size: 51
434409 AAAATAACGG
** *
434419 GGTTAGAGTATCGTCGATTGTGAGAAATTGGTGTTTTGGAAATAAAATCG-
1 GGTTAGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGA
* *
434469 GAGTTGGAGTATCCCCGATTGTGAAAAATTGGTTTTTTGGAAATAAAATCGA
1 G-GTTAGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGA
434521 GGTTAGAGTATCCCC
1 GGTTAGAGTATCCCC
434536 TCGAAAATAA
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
50 1 0.02
51 57 0.97
52 1 0.02
ACGTcount: A:0.30, C:0.10, G:0.27, T:0.32
Consensus pattern (51 bp):
GGTTAGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGA
Found at i:434668 original size:28 final size:28
Alignment explanation
Indices: 434627--434698 Score: 117
Period size: 28 Copynumber: 2.6 Consensus size: 28
434617 TATAAAGCCA
* *
434627 GGGTTAGAGCATCCCCTCGGAAATAACG
1 GGGTTGGAGTATCCCCTCGGAAATAACG
434655 GGGTTGGAGTATCCCCTCGGAAATAACG
1 GGGTTGGAGTATCCCCTCGGAAATAACG
*
434683 AGGTTGGAGTATCCCC
1 GGGTTGGAGTATCCCC
434699 AATTGTGAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 41 1.00
ACGTcount: A:0.25, C:0.24, G:0.31, T:0.21
Consensus pattern (28 bp):
GGGTTGGAGTATCCCCTCGGAAATAACG
Found at i:434744 original size:51 final size:51
Alignment explanation
Indices: 434685--434828 Score: 180
Period size: 51 Copynumber: 2.8 Consensus size: 51
434675 AAATAACGAG
** *
434685 GTTGGAGTATCCCCAATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGA
1 GTTGGAGTATCCCCAATTAAGAAAAATTGATGTTTTGGAAATAAAATCGGA
** * ** * * * *
434736 GTTGGAGTATCCCCGGTTACGGTAAATCGATGCTTTAGAAATAAAATCGGT
1 GTTGGAGTATCCCCAATTAAGAAAAATTGATGTTTTGGAAATAAAATCGGA
434787 GTTGGAGTATCCCCAATTAAGAAAAATTGATGTTTTGGAAAT
1 GTTGGAGTATCCCCAATTAAGAAAAATTGATGTTTTGGAAAT
434829 GGAACCGGGA
Statistics
Matches: 74, Mismatches: 19, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
51 74 1.00
ACGTcount: A:0.33, C:0.12, G:0.24, T:0.31
Consensus pattern (51 bp):
GTTGGAGTATCCCCAATTAAGAAAAATTGATGTTTTGGAAATAAAATCGGA
Found at i:434748 original size:107 final size:106
Alignment explanation
Indices: 434471--434749 Score: 307
Period size: 107 Copynumber: 2.6 Consensus size: 106
434461 TAAAATCGGA
* *
434471 GTTGGAGTATCCCCGATTGTGAAAAATTGGTTTTTTGGAAATAAAATC-GAGGTTAGAGTATCCC
1 GTTGGAGTATCCCCAATTGTGAAAAATTGGTATTTTGGAAATAAAATCGGA-GTTAGAGTATCCC
434535 CTCGAAAATAACGGGATTGGAGTATCCTCGATGACAAAACAAG
65 CTCGAAAATAACGGGATTGGAGTATCCTCGA-GACAAAACAAG
* *** * * * ** *
434578 GTTGGAGTA-CCCACAATTATGAAAAATCAATAATTTAGATATAAAGCCAGG-GTTAGAGCATCC
1 GTTGGAGTATCCC-CAATTGTGAAAAATTGGTATTTTGGAAATAAAATC-GGAGTTAGAGTATCC
* * *
434641 CCTCGGAAATAACGGGGTTGGAGTATCCCCTCG-GA-AATAACGAG
64 CCTCGAAAATAACGGGATTGGAGTAT--CCTCGAGACAA-AACAAG
* *
434685 GTTGGAGTATCCCCAATTGTGAAAAATTGGTGTTTTGGAAATAAAATCGGAGTTGGAGTATCCCC
1 GTTGGAGTATCCCCAATTGTGAAAAATTGGTATTTTGGAAATAAAATCGGAGTTAGAGTATCCCC
434750 GGTTACGGTA
Statistics
Matches: 137, Mismatches: 27, Indels: 16
0.76 0.15 0.09
Matches are distributed among these distances:
106 7 0.05
107 121 0.88
108 3 0.02
109 6 0.04
ACGTcount: A:0.33, C:0.16, G:0.24, T:0.26
Consensus pattern (106 bp):
GTTGGAGTATCCCCAATTGTGAAAAATTGGTATTTTGGAAATAAAATCGGAGTTAGAGTATCCCC
TCGAAAATAACGGGATTGGAGTATCCTCGAGACAAAACAAG
Found at i:434843 original size:51 final size:51
Alignment explanation
Indices: 434686--434851 Score: 165
Period size: 51 Copynumber: 3.3 Consensus size: 51
434676 AATAACGAGG
** *
434686 TTGGAGTATCCCCAATTGTGAAAAATTGGTGTTTTGGAAATAAAATC-GGA
1 TTGGAGTATCCCCAATTAAGAAAAATTGATGTTTTGGAAATAAAATCGGGA
** * ** * * *
434736 GTTGGAGTATCCCCGGTTACGGTAAATCGATGCTTTAGAAATAAAATCGGTG-
1 -TTGGAGTATCCCCAATTAAGAAAAATTGATGTTTTGGAAATAAAATCGG-GA
** *
434788 TTGGAGTATCCCCAATTAAGAAAAATTGATGTTTTGGAAATGGAACCGGGA
1 TTGGAGTATCCCCAATTAAGAAAAATTGATGTTTTGGAAATAAAATCGGGA
*
434839 TTGGAATATCCCC
1 TTGGAGTATCCCC
434852 GAGATGAAAA
Statistics
Matches: 90, Mismatches: 22, Indels: 6
0.76 0.19 0.05
Matches are distributed among these distances:
50 1 0.01
51 87 0.97
52 1 0.01
53 1 0.01
ACGTcount: A:0.32, C:0.14, G:0.25, T:0.30
Consensus pattern (51 bp):
TTGGAGTATCCCCAATTAAGAAAAATTGATGTTTTGGAAATAAAATCGGGA
Done.