Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold629
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: 578285
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
File 3 of 5
Found at i:280781 original size:10 final size:10
Alignment explanation
Indices: 280737--280773 Score: 65
Period size: 10 Copynumber: 3.6 Consensus size: 10
280727 AGGAAAAGAT
280737 AAAAAAAAAG
1 AAAAAAAAAG
280747 TAAAAAAAAAG
1 -AAAAAAAAAG
280758 AAAAAAAAAG
1 AAAAAAAAAG
280768 AAAAAA
1 AAAAAA
280774 TGAGAAAATA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 16 0.62
11 10 0.38
ACGTcount: A:0.89, C:0.00, G:0.08, T:0.03
Consensus pattern (10 bp):
AAAAAAAAAG
Found at i:285525 original size:20 final size:20
Alignment explanation
Indices: 285500--285617 Score: 110
Period size: 20 Copynumber: 5.8 Consensus size: 20
285490 TTTTAACTAG
*
285500 ATGTATCGATACATTGTACA
1 ATGTATCGATACATTGAACA
** *
285520 ATGTATTAATACATCTGAGTAGA
1 ATGTATCGATACAT-TGA--ACA
*
285543 ATGTATCGATACATTGAAGA
1 ATGTATCGATACATTGAACA
* * * *
285563 ATGTATCAATACATTCATCC
1 ATGTATCGATACATTGAACA
*
285583 ATGTATCGATACATTGAAAA
1 ATGTATCGATACATTGAACA
*
285603 ATATATCGATACATT
1 ATGTATCGATACATT
285618 CATCCATGAA
Statistics
Matches: 78, Mismatches: 17, Indels: 6
0.77 0.17 0.06
Matches are distributed among these distances:
20 59 0.76
21 2 0.03
22 3 0.04
23 14 0.18
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.34
Consensus pattern (20 bp):
ATGTATCGATACATTGAACA
Found at i:285598 original size:40 final size:40
Alignment explanation
Indices: 285500--285625 Score: 144
Period size: 40 Copynumber: 3.1 Consensus size: 40
285490 TTTTAACTAG
* * * * **
285500 ATGTATCGATACATTGTACAATGTATTAATACATCTGAGTAGA
1 ATGTATCGATACATTGAAAAATGTATCAATACAT-TCA-T-CC
*
285543 ATGTATCGATACATTGAAGAATGTATCAATACATTCATCC
1 ATGTATCGATACATTGAAAAATGTATCAATACATTCATCC
* *
285583 ATGTATCGATACATTGAAAAATATATCGATACATTCATCC
1 ATGTATCGATACATTGAAAAATGTATCAATACATTCATCC
285623 ATG
1 ATG
285626 AAAAGACAGA
Statistics
Matches: 74, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
40 40 0.54
41 1 0.01
42 2 0.03
43 31 0.42
ACGTcount: A:0.38, C:0.15, G:0.13, T:0.33
Consensus pattern (40 bp):
ATGTATCGATACATTGAAAAATGTATCAATACATTCATCC
Found at i:288173 original size:10 final size:10
Alignment explanation
Indices: 288143--288176 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
288133 TTAGGATCAA
*
288143 TTTAAAAATA
1 TTTAAAAATC
288153 TTTCAAAAATC
1 TTT-AAAAATC
288164 TTTAAAAATC
1 TTTAAAAATC
288174 TTT
1 TTT
288177 TTCCCAGTGG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 13 0.59
11 9 0.41
ACGTcount: A:0.47, C:0.09, G:0.00, T:0.44
Consensus pattern (10 bp):
TTTAAAAATC
Found at i:289624 original size:28 final size:28
Alignment explanation
Indices: 289551--290022 Score: 593
Period size: 28 Copynumber: 16.5 Consensus size: 28
289541 CACTAACTTG
*
289551 TGTGGGCTTTGAAAAGAGTTGCCTACTGACT
1 TGTGGGCTTTG-AAAG-GGTGCC-ACTGACT
*
289582 CGTGTGGGCTTTGAAAGGGTGCCACTAACT
1 --TGTGGGCTTTGAAAGGGTGCCACTGACT
289612 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
289640 TGTGGGCTTTGAATGGGTGCCATTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
289668 TGTGGGCTTTGAATAGAGTGCCATTGACT
1 TGTGGGCTTTGAA-AGGGTGCCACTGACT
*
289697 TGTGGGCTTTGAAAGGGTGTCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
*
289725 TGTGGGCTTTGAAAAGAGTGCCACTGACT
1 TGTGGGCTTTG-AAAGGGTGCCACTGACT
*
289754 TGTGGGGTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
** *
289782 TGCATGGGCTTTGAAAGAATGCCACTAACT
1 TG--TGGGCTTTGAAAGGGTGCCACTGACT
* * * *
289812 TATGGGCTTTGAAAGGATGCCATTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
289840 TGTGAGCTTTGAAAGGGTGCCATTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
289868 TGTGGGCTTTGAAAGGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
289896 TGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
289924 TATGGGCTTTGAAAAGAGTTGCCACTAACT
1 TGTGGGCTTTG-AAAG-GGTGCCACTGACT
* * *
289954 CGTGGGCTTTGAAAGGATGCCACTAACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
* *
289982 TGTGGGCTTTAAAATGGTGCCACTGACT
1 TGTGGGCTTTGAAAGGGTGCCACTGACT
290010 TGTGGGCTTTGAA
1 TGTGGGCTTTGAA
290023 GAGATGAACA
Statistics
Matches: 393, Mismatches: 40, Indels: 17
0.87 0.09 0.04
Matches are distributed among these distances:
28 264 0.67
29 59 0.15
30 50 0.13
31 5 0.01
32 4 0.01
33 11 0.03
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (28 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:289781 original size:114 final size:113
Alignment explanation
Indices: 289551--290028 Score: 624
Period size: 114 Copynumber: 4.2 Consensus size: 113
289541 CACTAACTTG
* * *
289551 TGTGGGCTTTGAAAAGAGTTGCCTACTGACTCGTGTGGGCTTTGAAAGGGTGCCACTAACTTGTG
1 TGTGGGCTTTG-AAAGAGATGCC-ACTAACT--TATGGGCTTTGAAAGGGTGCCACTAACTTGTG
* * *
289616 GGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAATGGGTGCCATTGACT
62 GGCTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
* * * * *
289668 TGTGGGCTTTGAATAGAG-TGCCATTGACTTGTGGGCTTTGAAAGGGTGTCACTGACTTGTGGGC
1 TGTGGGCTTTGAA-AGAGATGCCACTAACTTATGGGCTTTGAAAGGGTGCCACTAACTTGTGGGC
*
289732 TTTGAAAAGAGTGCCACTGACTTGTGGGGTTTGAAAGGGTGCCACTGACT
65 TTTG-AAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
* * *
289782 TGCATGGGCTTTGAAAGA-ATGCCACTAACTTATGGGCTTTGAAAGGATGCCATTAACTTGTGAG
1 TG--TGGGCTTTGAAAGAGATGCCACTAACTTATGGGCTTTGAAAGGGTGCCACTAACTTGTGGG
* *
289846 CTTTGAAAGGGTGCCATTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
64 CTTTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
* *
289896 TGTGGGCTTTGAAAG-GATGCCACTAACTTATGGGCTTTGAAAAGAGTTGCCACTAACTCGTGGG
1 TGTGGGCTTTGAAAGAGATGCCACTAACTTATGGGCTTTG-AAAG-GGTGCCACTAACTTGTGGG
* * *
289960 CTTTGAAAG-GATGCCACTAACTTGTGGGCTTTAAAATGGTGCCACTGACT
64 CTTTGAAAGAG-TGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
290010 TGTGGGCTTTG-AAGAGATG
1 TGTGGGCTTTGAAAGAGATG
290029 AACATTCTAG
Statistics
Matches: 325, Mismatches: 26, Indels: 23
0.87 0.07 0.06
Matches are distributed among these distances:
112 36 0.11
113 45 0.14
114 161 0.50
115 51 0.16
116 17 0.05
117 15 0.05
ACGTcount: A:0.22, C:0.16, G:0.31, T:0.30
Consensus pattern (113 bp):
TGTGGGCTTTGAAAGAGATGCCACTAACTTATGGGCTTTGAAAGGGTGCCACTAACTTGTGGGCT
TTGAAAGAGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACT
Found at i:289890 original size:142 final size:141
Alignment explanation
Indices: 289551--290022 Score: 635
Period size: 142 Copynumber: 3.3 Consensus size: 141
289541 CACTAACTTG
* *
289551 TGTGGGCTTTGAAAAGAGTTGCCTACTGACTCGTGTGGGCTTTGAAAGGGTGCCACTAACTTGTG
1 TGTGGGCTTTG-AAAG-GGTGCC-ACTGACT--TGTGGGCTTTGAAAGGGTGCCACTGACTTGTG
* ** * *
289616 GGCTTTGAAAGGGTGCCACTGACTTG-TGGGCTTTGAATGGGTGCCATTGACTTGTGGGCTTTGA
61 GGCTTTGAAAGGGTGCCACTGACTTGATGGGCTTTGAAAGAATGCCACTAACTTGTGGGCTTTGA
*
289680 ATA-GAGTGCCATTGACT
126 A-AGGA-TGCCATTAACT
* * *
289697 TGTGGGCTTTGAAAGGGTGTCACTGACTTGTGGGCTTTGAAAAGAGTGCCACTGACTTGTGGGGT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTG-AAAGGGTGCCACTGACTTGTGGGCT
*
289762 TTGAAAGGGTGCCACTGACTTGCATGGGCTTTGAAAGAATGCCACTAACTTATGGGCTTTGAAAG
65 TTGAAAGGGTGCCACTGACTTG-ATGGGCTTTGAAAGAATGCCACTAACTTGTGGGCTTTGAAAG
289827 GATGCCATTAACT
129 GATGCCATTAACT
* *
289840 TGTGAGCTTTGAAAGGGTGCCATTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTT
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTT
* * * *
289905 TGAAAGGATGCCACTAACTT-ATGGGCTTTGAAAAGAGTTGCCACTAACTCGTGGGCTTTGAAAG
66 TGAAAGGGTGCCACTGACTTGATGGGCTTTG-AAAGA-ATGCCACTAACTTGTGGGCTTTGAAAG
*
289969 GATGCCACTAACT
129 GATGCCATTAACT
* *
289982 TGTGGGCTTTAAAATGGTGCCACTGACTTGTGGGCTTTGAA
1 TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAA
290023 GAGATGAACA
Statistics
Matches: 293, Mismatches: 27, Indels: 16
0.87 0.08 0.05
Matches are distributed among these distances:
140 10 0.03
141 16 0.05
142 159 0.54
143 54 0.18
144 39 0.13
145 4 0.01
146 11 0.04
ACGTcount: A:0.22, C:0.17, G:0.31, T:0.30
Consensus pattern (141 bp):
TGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTTTGAAAGGGTGCCACTGACTTGTGGGCTT
TGAAAGGGTGCCACTGACTTGATGGGCTTTGAAAGAATGCCACTAACTTGTGGGCTTTGAAAGGA
TGCCATTAACT
Found at i:291258 original size:11 final size:10
Alignment explanation
Indices: 291242--291312 Score: 54
Period size: 11 Copynumber: 6.6 Consensus size: 10
291232 CCCCTTTCTG
291242 TTTTTTGTTAT
1 TTTTTTGTT-T
* *
291253 TTTTTTCTTGG
1 TTTTTTGTT-T
*
291264 TTTTTT-ATT
1 TTTTTTGTTT
291273 TTTTTTGTTTT
1 TTTTTTG-TTT
291284 TTTTTTGGGTTTT
1 TTTTTT--G-TTT
291297 TTTTTTGTTT
1 TTTTTTGTTT
291307 TTTTTT
1 TTTTTT
291313 TTGGTATGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 9
0.77 0.09 0.14
Matches are distributed among these distances:
9 6 0.12
10 10 0.20
11 23 0.46
13 11 0.22
ACGTcount: A:0.03, C:0.01, G:0.11, T:0.85
Consensus pattern (10 bp):
TTTTTTGTTT
Found at i:291268 original size:13 final size:12
Alignment explanation
Indices: 291242--291317 Score: 62
Period size: 12 Copynumber: 5.8 Consensus size: 12
291232 CCCCTTTCTG
*
291242 TTTTTTGTTATTT
1 TTTTTTGGT-TTT
291255 TTTTCTTGGTTTTTT
1 TTTT-TTGG--TTTT
*
291270 ATTTTTTTTGTTTT
1 -TT-TTTTGGTTTT
291284 TTTTTTGGGTTTT
1 TTTTTT-GGTTTT
*
291297 TTTTTTGTTTTT
1 TTTTTTGGTTTT
291309 TTTTTTGGT
1 TTTTTTGGT
291318 ATGAAGGACG
Statistics
Matches: 52, Mismatches: 5, Indels: 13
0.74 0.07 0.19
Matches are distributed among these distances:
12 17 0.33
13 17 0.33
14 7 0.13
15 3 0.06
16 6 0.12
17 2 0.04
ACGTcount: A:0.03, C:0.01, G:0.13, T:0.83
Consensus pattern (12 bp):
TTTTTTGGTTTT
Found at i:291283 original size:28 final size:27
Alignment explanation
Indices: 291242--291314 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 27
291232 CCCCTTTCTG
* *
291242 TTTTTTGTTATTTTTTTCTT-GGTTTT
1 TTTTTTTTTTTTTTTTTCTTGGGTTTT
*
291268 TTATTTTTTTTGTTTTTTTTTTGGGTTTT
1 TT-TTTTTTTT-TTTTTTTCTTGGGTTTT
291297 TTTTTTGTTTTTTTTTTT
1 TTTTTT-TTTTTTTTTTT
291315 GGTATGAAGG
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
26 2 0.05
27 6 0.15
28 20 0.50
29 12 0.30
ACGTcount: A:0.03, C:0.01, G:0.11, T:0.85
Consensus pattern (27 bp):
TTTTTTTTTTTTTTTTTCTTGGGTTTT
Found at i:291313 original size:11 final size:11
Alignment explanation
Indices: 291271--291313 Score: 68
Period size: 11 Copynumber: 3.7 Consensus size: 11
291261 TGGTTTTTTA
291271 TTTTTTTTGTT
1 TTTTTTTTGTT
291282 TTTTTTTTGGGTT
1 TTTTTTTT--GTT
291295 TTTTTTTTGTT
1 TTTTTTTTGTT
291306 TTTTTTTT
1 TTTTTTTT
291314 TGGTATGAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 19 0.63
13 11 0.37
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (11 bp):
TTTTTTTTGTT
Found at i:295215 original size:13 final size:13
Alignment explanation
Indices: 295197--295222 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
295187 CAATTTTTTG
295197 TGTATCGATACAT
1 TGTATCGATACAT
295210 TGTATCGATACAT
1 TGTATCGATACAT
295223 ACTTGCTGTA
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:295334 original size:20 final size:20
Alignment explanation
Indices: 295285--295336 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
295275 CTTTTTCATC
*
295285 TATCGATACATTGCAACTTG
1 TATCGATACTTTGCAACTTG
*
295305 TATCGATACTTTG-AATTGTG
1 TATCGATACTTTGCAACT-TG
295325 TATCGATACTTT
1 TATCGATACTTT
295337 TAAAGGTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 3 0.10
20 26 0.90
ACGTcount: A:0.27, C:0.15, G:0.15, T:0.42
Consensus pattern (20 bp):
TATCGATACTTTGCAACTTG
Found at i:297616 original size:21 final size:21
Alignment explanation
Indices: 297592--297638 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
297582 TTTGATGCTG
297592 ATTTTG-A-TGAAAAACGAAGT
1 ATTTTGAAGTGAAAAAC-AAGT
297612 -TATTTGAAGTGAAAAACAAGT
1 AT-TTTGAAGTGAAAAACAAGT
297633 ATTTTG
1 ATTTTG
297639 CAAAAGATTT
Statistics
Matches: 23, Mismatches: 0, Indels: 7
0.77 0.00 0.23
Matches are distributed among these distances:
19 1 0.04
20 4 0.17
21 9 0.39
22 9 0.39
ACGTcount: A:0.43, C:0.04, G:0.19, T:0.34
Consensus pattern (21 bp):
ATTTTGAAGTGAAAAACAAGT
Found at i:297777 original size:13 final size:13
Alignment explanation
Indices: 297759--297797 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
297749 ATAATCACCC
*
297759 TGTATCGATACAG
1 TGTATCGATACAA
297772 TGTATCGATACAA
1 TGTATCGATACAA
297785 TGTATCGATACAA
1 TGTATCGATACAA
297798 AGAAAAATGT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.36, C:0.15, G:0.18, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:297808 original size:20 final size:20
Alignment explanation
Indices: 297783--297861 Score: 77
Period size: 20 Copynumber: 3.7 Consensus size: 20
297773 GTATCGATAC
297783 AATGTATCGATACAAAGAAA
1 AATGTATCGATACAAAGAAA
*
297803 AATGTATCGATACATAGAATTTCCA
1 AATGTATCGATACAAAGAA-----A
* *
297828 GATGTATCGATACACAGAAA
1 AATGTATCGATACAAAGAAA
*
297848 CATGTATCGATACA
1 AATGTATCGATACA
297862 TTTTGGACAT
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
20 32 0.64
25 18 0.36
ACGTcount: A:0.44, C:0.15, G:0.15, T:0.25
Consensus pattern (20 bp):
AATGTATCGATACAAAGAAA
Found at i:299889 original size:15 final size:15
Alignment explanation
Indices: 299869--299899 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
299859 ATTTCGTTTG
*
299869 GAGCTTCTTCATTTT
1 GAGCTTCCTCATTTT
299884 GAGCTTCCTCATTTT
1 GAGCTTCCTCATTTT
299899 G
1 G
299900 GACATTTTTA
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:0.13, C:0.23, G:0.16, T:0.48
Consensus pattern (15 bp):
GAGCTTCCTCATTTT
Found at i:301732 original size:21 final size:21
Alignment explanation
Indices: 301703--301747 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
301693 AAGTTTTCAT
*
301703 TTTTCTTAGCTAAC-TCATTA
1 TTTTCTTAGCCAACTTCATTA
*
301723 TTTTCATTAGCCAACTTCTTTA
1 TTTTC-TTAGCCAACTTCATTA
301745 TTT
1 TTT
301748 CAACTTGCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 8 0.38
22 8 0.38
ACGTcount: A:0.22, C:0.20, G:0.04, T:0.53
Consensus pattern (21 bp):
TTTTCTTAGCCAACTTCATTA
Found at i:305265 original size:13 final size:13
Alignment explanation
Indices: 305240--305265 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
305230 GGTTGGAGTA
305240 TCCCCTTGGAGGC
1 TCCCCTTGGAGGC
305253 TCCCCTTGGAGGC
1 TCCCCTTGGAGGC
305266 ATGGGGTTGG
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:0.08, C:0.38, G:0.31, T:0.23
Consensus pattern (13 bp):
TCCCCTTGGAGGC
Found at i:307502 original size:20 final size:20
Alignment explanation
Indices: 307477--307553 Score: 102
Period size: 20 Copynumber: 3.9 Consensus size: 20
307467 GTAAAAAAAC
307477 AGAATGTATCGATACATTGA
1 AGAATGTATCGATACATTGA
* *
307497 AGAATGTATTGATACATTCA
1 AGAATGTATCGATACATTGA
*
307517 TA-CATGTATCGATACATTGA
1 -AGAATGTATCGATACATTGA
*
307537 AAAATGTATCGATACAT
1 AGAATGTATCGATACAT
307554 CTGGGTACTT
Statistics
Matches: 49, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
19 1 0.02
20 47 0.96
21 1 0.02
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.32
Consensus pattern (20 bp):
AGAATGTATCGATACATTGA
Found at i:309859 original size:20 final size:21
Alignment explanation
Indices: 309825--309863 Score: 71
Period size: 20 Copynumber: 1.9 Consensus size: 21
309815 AGGTCAAAAC
309825 CCTAGAAAGTATCGATACAAA
1 CCTAGAAAGTATCGATACAAA
309846 CCTAGAAA-TATCGATACA
1 CCTAGAAAGTATCGATACA
309864 TATTGCTTTG
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.46, C:0.21, G:0.13, T:0.21
Consensus pattern (21 bp):
CCTAGAAAGTATCGATACAAA
Found at i:312078 original size:21 final size:21
Alignment explanation
Indices: 312054--312100 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
312044 AAAAAAGAAA
312054 AATTAGAAAAGAAGATAAGTG
1 AATTAGAAAAGAAGATAAGTG
*
312075 AATTAGAAAAGAAGATAATTG
1 AATTAGAAAAGAAGATAAGTG
312096 AATTA
1 AATTA
312101 CAAGATGGTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.57, C:0.00, G:0.19, T:0.23
Consensus pattern (21 bp):
AATTAGAAAAGAAGATAAGTG
Found at i:312141 original size:21 final size:21
Alignment explanation
Indices: 312117--312156 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
312107 GGTAATAAAG
312117 AATTAGCTAATGAA-AACAACA
1 AATTAGCTAA-GAAGAACAACA
*
312138 AATTGGCTAAGAAGAACAA
1 AATTAGCTAAGAAGAACAA
312157 GAACTTGCAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.55, C:0.12, G:0.15, T:0.17
Consensus pattern (21 bp):
AATTAGCTAAGAAGAACAACA
Found at i:312667 original size:13 final size:13
Alignment explanation
Indices: 312649--312674 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
312639 TACACCAAGT
312649 ATGTATCGATACA
1 ATGTATCGATACA
312662 ATGTATCGATACA
1 ATGTATCGATACA
312675 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:312672 original size:32 final size:33
Alignment explanation
Indices: 312631--312694 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
312621 TAGCCAAACT
* **
312631 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
312663 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
312695 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:313195 original size:34 final size:35
Alignment explanation
Indices: 313132--313198 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
313122 CTAAGTGATT
313132 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
313168 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
313199 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:317983 original size:13 final size:13
Alignment explanation
Indices: 317965--317990 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
317955 TACACCAAGT
317965 ATGTATCGATACA
1 ATGTATCGATACA
317978 ATGTATCGATACA
1 ATGTATCGATACA
317991 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:317988 original size:32 final size:33
Alignment explanation
Indices: 317947--318010 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 33
317937 TAGCCAAACT
* **
317947 TGTATCGATACACCAAGTA-TGTATCGATACAA
1 TGTATCGATACACAAAAAATTGTATCGATACAA
317979 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
318011 TTGGCTTGTA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 16 0.57
33 12 0.43
ACGTcount: A:0.41, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:318511 original size:34 final size:35
Alignment explanation
Indices: 318448--318514 Score: 102
Period size: 37 Copynumber: 1.9 Consensus size: 35
318438 CTAAGTGATT
318448 GAGAGGTTCTATCTTAGCCTTTGAAAAAGATAGAGA
1 GAGAGGTTCTATCTTAGCCTTTG-AAAAGATAGAGA
318484 GAGAGGTTTCTATCTTAGCC-TTG-AAAGATAG
1 GAGAGG-TTCTATCTTAGCCTTTGAAAAGATAG
318515 TGTTGTAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
34 8 0.27
36 9 0.30
37 13 0.43
ACGTcount: A:0.33, C:0.12, G:0.25, T:0.30
Consensus pattern (35 bp):
GAGAGGTTCTATCTTAGCCTTTGAAAAGATAGAGA
Found at i:322222 original size:11 final size:11
Alignment explanation
Indices: 322206--322239 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
322196 CTTGGATTTT
322206 TCTTTTTTCTC
1 TCTTTTTTCTC
322217 TCTTTTTTCT-
1 TCTTTTTTCTC
*
322227 TCTTTTTTTTC
1 TCTTTTTTCTC
322238 TC
1 TC
322240 ACTTGCTGCC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 9 0.43
11 12 0.57
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (11 bp):
TCTTTTTTCTC
Found at i:322234 original size:12 final size:12
Alignment explanation
Indices: 322206--322238 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
322196 CTTGGATTTT
322206 TCTTTTTTC-TC
1 TCTTTTTTCTTC
322217 TCTTTTTTCTTC
1 TCTTTTTTCTTC
*
322229 TTTTTTTTCT
1 TCTTTTTTCT
322239 CACTTGCTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
11 9 0.45
12 11 0.55
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (12 bp):
TCTTTTTTCTTC
Found at i:322563 original size:5 final size:5
Alignment explanation
Indices: 322553--322578 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
322543 ATGAGTAAAT
322553 AATAA AATAA AATAA AATAA AATAA A
1 AATAA AATAA AATAA AATAA AATAA A
322579 TCCGAAAATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (5 bp):
AATAA
Found at i:323335 original size:334 final size:333
Alignment explanation
Indices: 322793--323551 Score: 894
Period size: 334 Copynumber: 2.3 Consensus size: 333
322783 GTTCAATGAA
* * ** * * * *
322793 AATATTAGATGCATTTTAAAAATTTTAAACCAA-AGAAAATCTCTTCGAAAATATCTATGGAA-T
1 AATATTTGATGAATTTTAAAAATTGAAAACCAAGA-AAAATCTCCTCGAAAAAATTTA-AGAAGT
* * * * * * * *
322856 AGAAAAC-TCGATTTTTTGAGAAAAAGGGAAATTTCAAAGAAAAAATCCAAATCTTATGAAAATA
64 AGAAAACACCG-TATTTCGAAAAAAAGAGAAATTTCAAAGAAAAAATCAAAAACTCATGAAAATA
* * *
322920 AATTAATTTTTTAAAAATAAATTAATATGAATCAAATAATGATGTTTGATGAATTTTAAAAATTG
128 AATTAATTTTTTAAAAAGAAATTAATATGAATCAAATAATAATATTTGATGAATTTTAAAAATTG
* * * *
322985 AAAACTGAGAAAAATCCCCTCGAAAAAATTTATGGAGTAGAAAACA-TCATATTTTGAAAAAAAA
193 AAAACTAAGAAAAATCCCCTCAAAAAAATTTACGGAGTAGAAAACACT-ATATTTAGAAAAAAAA
*
323049 G-AATTTCAAGGAAAAAAAT-AAAAATCTCATGAAAATGAATTTATTTTTTAAAAATGAATTAAT
257 GAAATTTCAAGG-AAAAAATCAAAAA-CTCATGAAAATGAATTTATTTTTTAAAAAGGAATTAAT
323112 ATGAAATAAATAAT
320 ATGAAATAAATAAT
* * * *
323126 GATGTTTTATGAATTTTAAAAATTGAAAACCAAGAAAAATCTCCT-TAAGAAAACTTTACAG-AG
1 AATATTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATCTCCTCGAA-AAAA-TTTA-AGAAG
* *
323189 TAGAAAATATCGTATTTCGAAAAAAAGAG-AATTTC-AAGAAAACAAATCAAAAACTCATGAAAA
63 TAGAAAACACCGTATTTCGAAAAAAAGAGAAATTTCAAAG-AAA-AAATCAAAAACTCATGAAAA
* * * * **
323252 TGAATTTATTTTTTAAAACGGAATTAATATGAAAT-AAATGTTAATATTTGATGAATTTTAAAAA
126 TAAATTAATTTTTTAAAAAGAAATTAATATG-AATCAAATAATAATATTTGATGAATTTTAAAAA
* *
323316 TTGAAAAGC-AAGAAAAATCCCCTCAAAAAAATTTACGGAGTAGAAAATACTGTATTTAGAAAAA
190 TTGAAAA-CTAAGAAAAATCCCCTCAAAAAAATTTACGGAGTAGAAAACACTATATTTAGAAAAA
** * *
323380 AGGGAAATTTTAAGGAAAAAATCAAAAACTCATGAAAATGAATTTATTTTTTAAAACGGAATTAA
254 AAAGAAATTTCAAGGAAAAAATCAAAAACTCATGAAAATGAATTTATTTTTTAAAAAGGAATTAA
*
323445 TATGAAATAAATGAT
319 TATGAAATAAATAAT
* *
323460 AATATTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATTTCCTCGAAAAAATTTATGAAGTAG
1 AATATTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATCTCCTCGAAAAAATTTAAGAAGTAG
*
323525 AAAACCCCGTATTTCGAAAAAAGAGAG
66 AAAACACCGTATTTCGAAAAAA-AGAG
323552 TTTTAATGAA
Statistics
Matches: 360, Mismatches: 51, Indels: 29
0.82 0.12 0.07
Matches are distributed among these distances:
332 6 0.02
333 76 0.21
334 254 0.71
335 24 0.07
ACGTcount: A:0.50, C:0.08, G:0.12, T:0.30
Consensus pattern (333 bp):
AATATTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATCTCCTCGAAAAAATTTAAGAAGTAG
AAAACACCGTATTTCGAAAAAAAGAGAAATTTCAAAGAAAAAATCAAAAACTCATGAAAATAAAT
TAATTTTTTAAAAAGAAATTAATATGAATCAAATAATAATATTTGATGAATTTTAAAAATTGAAA
ACTAAGAAAAATCCCCTCAAAAAAATTTACGGAGTAGAAAACACTATATTTAGAAAAAAAAGAAA
TTTCAAGGAAAAAATCAAAAACTCATGAAAATGAATTTATTTTTTAAAAAGGAATTAATATGAAA
TAAATAAT
Found at i:323547 original size:166 final size:166
Alignment explanation
Indices: 322787--323550 Score: 864
Period size: 166 Copynumber: 4.6 Consensus size: 166
322777 ATAGGAGTTC
* * * ** * * *
322787 AATGAAAATATTAGATGCATTTTAAAAATTTTAAACCAA-AGAAAATCTCTTCGAAAATATCTAT
1 AATGATAATATTTGATGAATTTTAAAAATTGAAAACCAAGA-AAAATCTCCTCGAAAAAATTTAT
* * * * * * *
322851 GGAA-TAGAAAAC-TCGATTTTTTGAGAAAAAGGGAAATTTCAAAGAAAAAATCCAAATCTTATG
65 -GAAGTAGAAAACATCG-TATTTCGA-AAAAAGAGAAATTTCAAGGAAAAAATCAAAAACTCATG
* * **
322914 AAAATAAATTAATTTTTTAAAAATAAATTAATATG-AATCA
127 AAAATGAATTTATTTTTTAAAAAGGAATTAATATGAAAT-A
* * * ** *
322954 AATAATGATGTTTGATGAATTTTAAAAATTGAAAACTGAGAAAAATCCCCTCGAAAAAATTTATG
1 AATGATAATATTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATCTCCTCGAAAAAATTTATG
* * * *
323019 GAGTAGAAAACATCATATTTTGAAAAAAAAG-AATTTCAAGGAAAAAAAT-AAAAATCTCATGAA
66 AAGTAGAAAACATCGTATTTCGAAAAAAGAGAAATTTCAAGG-AAAAAATCAAAAA-CTCATGAA
*
323082 AATGAATTTATTTTTTAAAAATGAATTAATATGAAATA
129 AATGAATTTATTTTTTAAAAAGGAATTAATATGAAATA
* * * * *
323120 AATAATGATGTTTTATGAATTTTAAAAATTGAAAACCAAGAAAAATCTCCT-TAAGAAAACTTTA
1 AATGATAATATTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATCTCCTCGAA-AAAA-TTTA
* * *
323184 -CAGAGTAGAAAATATCGTATTTCGAAAAAA-AGAGAATTTCAAGAAAACAAATCAAAAACTCAT
64 TGA-AGTAGAAAACATCGTATTTCGAAAAAAGAGA-AATTTCAAGGAAA-AAATCAAAAACTCAT
*
323247 GAAAATGAATTTATTTTTTAAAACGGAATTAATATGAAATA
126 GAAAATGAATTTATTTTTTAAAAAGGAATTAATATGAAATA
* * * * *
323288 AATGTTAATATTTGATGAATTTTAAAAATTGAAAAGCAAGAAAAATCCCCTCAAAAAAATTTACG
1 AATGATAATATTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATCTCCTCGAAAAAATTTATG
* * * * *
323353 GAGTAGAAAATA-CTGTATTTAGAAAAAAGGGAAATTTTAAGGAAAAAATCAAAAACTCATGAAA
66 AAGTAGAAAACATC-GTATTTCGAAAAAAGAGAAATTTCAAGGAAAAAATCAAAAACTCATGAAA
*
323417 ATGAATTTATTTTTTAAAACGGAATTAATATGAAATA
130 ATGAATTTATTTTTTAAAAAGGAATTAATATGAAATA
*
323454 AATGATAATATTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATTTCCTCGAAAAAATTTATG
1 AATGATAATATTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATCTCCTCGAAAAAATTTATG
**
323519 AAGTAGAAAACCCCGTATTTCGAAAAAAGAGA
66 AAGTAGAAAACATCGTATTTCGAAAAAAGAGA
323551 GTTTTAATGA
Statistics
Matches: 515, Mismatches: 64, Indels: 37
0.84 0.10 0.06
Matches are distributed among these distances:
165 14 0.03
166 247 0.48
167 137 0.27
168 110 0.21
169 7 0.01
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.29
Consensus pattern (166 bp):
AATGATAATATTTGATGAATTTTAAAAATTGAAAACCAAGAAAAATCTCCTCGAAAAAATTTATG
AAGTAGAAAACATCGTATTTCGAAAAAAGAGAAATTTCAAGGAAAAAATCAAAAACTCATGAAAA
TGAATTTATTTTTTAAAAAGGAATTAATATGAAATA
Found at i:324860 original size:20 final size:19
Alignment explanation
Indices: 324832--324872 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 19
324822 TTTTTTTGAA
324832 TTTTGATTTTT-TCATTTTT
1 TTTTGATTTTTGT-ATTTTT
324851 TTTTGTATTTTTGTATTTTT
1 TTTTG-ATTTTTGTATTTTT
324871 TT
1 TT
324873 CATTTTTGGA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 5 0.25
20 14 0.70
21 1 0.05
ACGTcount: A:0.10, C:0.02, G:0.07, T:0.80
Consensus pattern (19 bp):
TTTTGATTTTTGTATTTTT
Found at i:324860 original size:26 final size:29
Alignment explanation
Indices: 324820--324879 Score: 90
Period size: 29 Copynumber: 2.2 Consensus size: 29
324810 TTTATCCAAC
324820 TTTTTTTTTGAA-TTTTG-A-TTTTTTCA
1 TTTTTTTTTGAATTTTTGTATTTTTTTCA
*
324846 TTTTTTTTTGTATTTTTGTATTTTTTTCA
1 TTTTTTTTTGAATTTTTGTATTTTTTTCA
324875 TTTTT
1 TTTTT
324880 GGATTTCCTT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 11 0.37
27 5 0.17
28 1 0.03
29 13 0.43
ACGTcount: A:0.12, C:0.03, G:0.07, T:0.78
Consensus pattern (29 bp):
TTTTTTTTTGAATTTTTGTATTTTTTTCA
Found at i:324916 original size:6 final size:6
Alignment explanation
Indices: 324895--324928 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
324885 TCCTTTAAAG
* *
324895 TAAAAT TGAAAT TAAAAC TAAAAT TAAAAT TAAA
1 TAAAAT TAAAAT TAAAAT TAAAAT TAAAAT TAAA
324929 GACATACTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.65, C:0.03, G:0.03, T:0.29
Consensus pattern (6 bp):
TAAAAT
Found at i:325293 original size:33 final size:33
Alignment explanation
Indices: 325256--325337 Score: 103
Period size: 33 Copynumber: 2.5 Consensus size: 33
325246 CCATTAATCG
*
325256 AGGCATCAACTTTTAATGAAAACTACTTCACTA
1 AGGCATCAACTTTAAATGAAAACTACTTCACTA
* *
325289 AGGCATCAACTTTAAATGAACACTTCTTCA-TCA
1 AGGCATCAACTTTAAATGAAAACTACTTCACT-A
* *
325322 AGGCTTTAACTTTAAA
1 AGGCATCAACTTTAAA
325338 AATGTAAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
32 1 0.02
33 42 0.98
ACGTcount: A:0.38, C:0.21, G:0.10, T:0.32
Consensus pattern (33 bp):
AGGCATCAACTTTAAATGAAAACTACTTCACTA
Found at i:325574 original size:24 final size:24
Alignment explanation
Indices: 325492--325595 Score: 68
Period size: 24 Copynumber: 4.2 Consensus size: 24
325482 TTAAAAGTGA
*
325492 AAAACAT-CTCATAAAAGGCTTT-
1 AAAACATCCTCATGAAAGGCTTTG
* * * *
325514 AAAACATACTCTTGAGAGCCTTTG
1 AAAACATCCTCATGAAAGGCTTTG
*
325538 AAAATGAATATCCTCATGAAAGGCTTTG
1 --AA--AACATCCTCATGAAAGGCTTTG
** * *
325566 AAAACATCCTTGTGAAAAGCTTAG
1 AAAACATCCTCATGAAAGGCTTTG
325590 AAAACA
1 AAAACA
325596 AACATTCTCA
Statistics
Matches: 62, Mismatches: 14, Indels: 10
0.72 0.16 0.12
Matches are distributed among these distances:
22 7 0.11
23 11 0.18
24 23 0.37
26 4 0.06
28 17 0.27
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.26
Consensus pattern (24 bp):
AAAACATCCTCATGAAAGGCTTTG
Found at i:325638 original size:24 final size:24
Alignment explanation
Indices: 325608--325712 Score: 111
Period size: 24 Copynumber: 4.4 Consensus size: 24
325598 CATTCTCATT
* *
325608 AGAGGCTTAGAAAATGTCCTTGTT
1 AGAGGCTTTGAAAATGTCCTTGTG
* *
325632 AGAGGCTTTGAAAATGTTCTCGTG
1 AGAGGCTTTGAAAATGTCCTTGTG
* **
325656 AGAGACTTTGAAAACATCCTTGTG
1 AGAGGCTTTGAAAATGTCCTTGTG
* * *
325680 AAAGGCTTTGATAATGTCCTTGCG
1 AGAGGCTTTGAAAATGTCCTTGTG
*
325704 AAAGGCTTT
1 AGAGGCTTT
325713 AATAACATCC
Statistics
Matches: 66, Mismatches: 15, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 66 1.00
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (24 bp):
AGAGGCTTTGAAAATGTCCTTGTG
Found at i:325720 original size:48 final size:48
Alignment explanation
Indices: 325624--325723 Score: 112
Period size: 48 Copynumber: 2.1 Consensus size: 48
325614 TTAGAAAATG
* * * * *
325624 TCCTTGTTAGAGGCTTTGAAAATGTTCTCGTGAGAGACTTTGAAAACA
1 TCCTTGTGAAAGGCTTTGAAAATGTCCTCGCGAAAGACTTTGAAAACA
* * *
325672 TCCTTGTGAAAGGCTTTGATAATGTCCTTGCGAAAGGCTTT-AATAACA
1 TCCTTGTGAAAGGCTTTGAAAATGTCCTCGCGAAAGACTTTGAA-AACA
325720 TCCT
1 TCCT
325724 CAGTAGAGGC
Statistics
Matches: 43, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
47 2 0.05
48 41 0.95
ACGTcount: A:0.28, C:0.17, G:0.21, T:0.34
Consensus pattern (48 bp):
TCCTTGTGAAAGGCTTTGAAAATGTCCTCGCGAAAGACTTTGAAAACA
Found at i:325723 original size:24 final size:24
Alignment explanation
Indices: 325668--325723 Score: 76
Period size: 24 Copynumber: 2.3 Consensus size: 24
325658 AGACTTTGAA
* *
325668 AACATCCTTGTGAAAGGCTTTGAT
1 AACATCCTTGCGAAAGGCTTTAAT
**
325692 AATGTCCTTGCGAAAGGCTTTAAT
1 AACATCCTTGCGAAAGGCTTTAAT
325716 AACATCCT
1 AACATCCT
325724 CAGTAGAGGC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.30, C:0.20, G:0.18, T:0.32
Consensus pattern (24 bp):
AACATCCTTGCGAAAGGCTTTAAT
Found at i:327140 original size:166 final size:166
Alignment explanation
Indices: 326912--327253 Score: 410
Period size: 166 Copynumber: 2.1 Consensus size: 166
326902 TTCAATTATA
* * * * * *
326912 AAAATTCTTTAAATATCATCATTTAATTACTATCAAGTTAGTTTTGAAAAATTCCTTTTA-TTTC
1 AAAATTCATCAAATATCATCATTTAATTACTATCAAATCAGTTTTAAAAAATTCCATTTATTTTC
* * *
326976 ATTAATTTTCCATTATTTTCCTTCAAATTCT-TTTGTTTTCAAAAAATCGAGTTTTCTTTTTCAT
66 ATGAATTTTCCATT-TTTTCCTTCAAATTCTCTAT-TTTT-AAAAAATCGAGTTTTCTTTTCCAT
* *
327040 AAAGGTTTTCGTGGGGT-TTTTT-TTAGTTCAAAATTTTT
128 AAAGGTTTTCG-AGAGTATTTTTCTTAGTTCAAAATTTTT
327078 AAAATTCATCAAATATCATCATTTAATT-CATAGT-AAATCAGTTTTTAAAAAATT-CATTTATT
1 AAAATTCATCAAATATCATCATTTAATTAC-TA-TCAAATCAG-TTTTAAAAAATTCCATTTATT
* * * * *
327140 TTCATGAGTTTTTCATTTTTTCCTTGAAATTCTCTATTTTTGAAAAATTGAGTTTTCTTTTCCAT
63 TTCATGAATTTTCCATTTTTTCCTTCAAATTCTCTATTTTTAAAAAATCGAGTTTTCTTTTCCAT
* *
327205 AAAGGTTTTCGAGAGTATTTTTCTTCGTTTAAAATTTTT
128 AAAGGTTTTCGAGAGTATTTTTCTTAGTTCAAAATTTTT
327244 AAAATTCATC
1 AAAATTCATC
327254 TAACATTTTC
Statistics
Matches: 151, Mismatches: 18, Indels: 14
0.83 0.10 0.08
Matches are distributed among these distances:
164 3 0.02
165 38 0.25
166 81 0.54
167 29 0.19
ACGTcount: A:0.30, C:0.12, G:0.08, T:0.50
Consensus pattern (166 bp):
AAAATTCATCAAATATCATCATTTAATTACTATCAAATCAGTTTTAAAAAATTCCATTTATTTTC
ATGAATTTTCCATTTTTTCCTTCAAATTCTCTATTTTTAAAAAATCGAGTTTTCTTTTCCATAAA
GGTTTTCGAGAGTATTTTTCTTAGTTCAAAATTTTT
Found at i:327749 original size:20 final size:19
Alignment explanation
Indices: 327706--327757 Score: 77
Period size: 20 Copynumber: 2.7 Consensus size: 19
327696 CAATTCAGTG
*
327706 TGTATCGATACTAAGAACA
1 TGTATCGATACTTAGAACA
*
327725 TGTATCGATACTTAGCAATA
1 TGTATCGATACTTAG-AACA
327745 TGTATCGATACTT
1 TGTATCGATACTT
327758 TTTAGGGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
19 14 0.47
20 16 0.53
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Consensus pattern (19 bp):
TGTATCGATACTTAGAACA
Found at i:328816 original size:13 final size:13
Alignment explanation
Indices: 328798--328822 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
328788 CATAAAGTGT
328798 TGTATCGATACAA
1 TGTATCGATACAA
328811 TGTATCGATACA
1 TGTATCGATACA
328823 TAAGTGTTGT
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:328833 original size:32 final size:33
Alignment explanation
Indices: 328778--328841 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 33
328768 TTCAACGATT
328778 TGTACCGATACATAAAGTGTTGTATCGATACAA
1 TGTACCGATACATAAAGTGTTGTATCGATACAA
*
328811 TGTATCGATACAT-AAGTGTTGTATCGATACA
1 TGTACCGATACATAAAGTGTTGTATCGATACA
328842 TAAGTTTTGT
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
32 18 0.60
33 12 0.40
ACGTcount: A:0.34, C:0.14, G:0.19, T:0.33
Consensus pattern (33 bp):
TGTACCGATACATAAAGTGTTGTATCGATACAA
Found at i:328835 original size:19 final size:19
Alignment explanation
Indices: 328777--328860 Score: 99
Period size: 19 Copynumber: 4.7 Consensus size: 19
328767 TTTCAACGAT
*
328777 TTGTACCGATACATAAAGTG
1 TTGTATCGATACAT-AAGTG
328797 TTGTATCGATAC--AA---
1 TTGTATCGATACATAAGTG
328811 -TGTATCGATACATAAGTG
1 TTGTATCGATACATAAGTG
*
328829 TTGTATCGATACATAAGTT
1 TTGTATCGATACATAAGTG
328848 TTGTATCGATACA
1 TTGTATCGATACA
328861 ATATAGGCTA
Statistics
Matches: 56, Mismatches: 2, Indels: 13
0.79 0.03 0.18
Matches are distributed among these distances:
13 11 0.20
15 2 0.04
17 2 0.04
19 30 0.54
20 11 0.20
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (19 bp):
TTGTATCGATACATAAGTG
Found at i:328919 original size:13 final size:13
Alignment explanation
Indices: 328901--328925 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
328891 ACATTTTAAA
328901 TGTATCGATACAT
1 TGTATCGATACAT
328914 TGTATCGATACA
1 TGTATCGATACA
328926 CTGATCTTTG
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:329851 original size:20 final size:20
Alignment explanation
Indices: 329806--329852 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 20
329796 TATAACAACC
*
329806 CATGATTCATGCATTTTGAG
1 CATGTTTCATGCATTTTGAG
329826 CTATGTTTCATGCA-TTTGCAG
1 C-ATGTTTCATGCATTTTG-AG
329847 CATGTT
1 CATGTT
329853 CAGCACCTCC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.43
Consensus pattern (20 bp):
CATGTTTCATGCATTTTGAG
Found at i:331966 original size:13 final size:13
Alignment explanation
Indices: 331948--331975 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
331938 ATACAAAGAT
331948 CAATGTATCGATA
1 CAATGTATCGATA
331961 CAATGTATCGATA
1 CAATGTATCGATA
331974 CA
1 CA
331976 TTGAATAATG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:331972 original size:33 final size:33
Alignment explanation
Indices: 331930--331995 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
331920 AAATTCCTAG
331930 ATGTATCGATACAAAG-ATCAATGTATCGATACA
1 ATGTATCGATACAAAGAAT-AATGTATCGATACA
**
331963 ATGTATCGATACATTGAATAATGTATCGATACA
1 ATGTATCGATACAAAGAATAATGTATCGATACA
331996 TTGAATAATG
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 28 0.93
34 2 0.07
ACGTcount: A:0.41, C:0.14, G:0.15, T:0.30
Consensus pattern (33 bp):
ATGTATCGATACAAAGAATAATGTATCGATACA
Found at i:331987 original size:20 final size:20
Alignment explanation
Indices: 331962--332017 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
331952 GTATCGATAC
331962 AATGTATCGATACATTGAAT
1 AATGTATCGATACATTGAAT
331982 AATGTATCGATACATTGAAT
1 AATGTATCGATACATTGAAT
332002 AATGTATCGATACATT
1 AATGTATCGATACATT
332018 TCCTTAGCAG
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.39, C:0.11, G:0.14, T:0.36
Consensus pattern (20 bp):
AATGTATCGATACATTGAAT
Found at i:334690 original size:20 final size:20
Alignment explanation
Indices: 334665--334719 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
334655 GTTAGACTCA
* *
334665 ATGTATCGATACATTTCACC
1 ATGTATCGATACAATCCACC
**
334685 ATGTATCGATACAATCCTTC
1 ATGTATCGATACAATCCACC
334705 ATGTATCGATACAAT
1 ATGTATCGATACAAT
334720 GTATCGATAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.35
Consensus pattern (20 bp):
ATGTATCGATACAATCCACC
Found at i:334723 original size:13 final size:13
Alignment explanation
Indices: 334705--334732 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
334695 ACAATCCTTC
334705 ATGTATCGATACA
1 ATGTATCGATACA
334718 ATGTATCGATACA
1 ATGTATCGATACA
334731 AT
1 AT
334733 ATGAGTTTTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.14, G:0.14, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:337855 original size:51 final size:51
Alignment explanation
Indices: 337800--337919 Score: 159
Period size: 51 Copynumber: 2.4 Consensus size: 51
337790 TGGAAAATAA
* *
337800 TGGGGTTGGAGTATCCCCGATTATGAGAAATCAAAATTTTAGAAATAAAGT
1 TGGGGTTGGAGTATCCCCAATTATGAGAAATCAAAATTTTAGAAATAAAGG
** * * * *
337851 TGGGGTTAAAGTATCCCTAATTGTGAGAAATCAATATTTTGGAAATAAAGG
1 TGGGGTTGGAGTATCCCCAATTATGAGAAATCAAAATTTTAGAAATAAAGG
*
337902 CGGGGTTGGAGTATCCCC
1 TGGGGTTGGAGTATCCCC
337920 TAGAAAATAA
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
TGGGGTTGGAGTATCCCCAATTATGAGAAATCAAAATTTTAGAAATAAAGG
Found at i:337986 original size:130 final size:133
Alignment explanation
Indices: 337748--337997 Score: 364
Period size: 130 Copynumber: 1.9 Consensus size: 133
337738 TGAAAAACTT
* * *
337748 AATATTTTGGAGATAACAACGGGGTTGGAGTATCCTCGATTATGGAAAATAATGGGGTTGGAGTA
1 AATATTTTGGAAATAACAACGGGGTTGGAGTATCCTC-ACTA-GGAAAATAATGGGGTTAGAGTA
**
337813 TCCCCGATTATGAGAAATCAAAATTTTAGAAATAAAGTTGGGGTTAAAGTATCCCTAATTGTGAG
64 TCCCCGATTATGAGAAATCAAAATTTTAGAAATAAAGCCGGGGTTAAAGTATCCCTAATTGTGAG
337878 AAATC
129 AAATC
*
337883 AATATTTTGGAAATAA-AGGCGGGGTTGGAGTATCC-C-CTA-GAAAATAATGGGGTTAGAGTAT
1 AATATTTTGGAAATAACA-ACGGGGTTGGAGTATCCTCACTAGGAAAATAATGGGGTTAGAGTAT
* * *
337944 CCCCGATTATGAGAAATCAATATTTTAGGAATAAAGCCGGGGTTAGAGTATCCC
65 CCCCGATTATGAGAAATCAAAATTTTAGAAATAAAGCCGGGGTTAAAGTATCCC
337998 CTCGGAAATA
Statistics
Matches: 105, Mismatches: 9, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
130 70 0.67
132 2 0.02
134 2 0.02
135 31 0.30
ACGTcount: A:0.35, C:0.12, G:0.25, T:0.28
Consensus pattern (133 bp):
AATATTTTGGAAATAACAACGGGGTTGGAGTATCCTCACTAGGAAAATAATGGGGTTAGAGTATC
CCCGATTATGAGAAATCAAAATTTTAGAAATAAAGCCGGGGTTAAAGTATCCCTAATTGTGAGAA
ATC
Found at i:338020 original size:28 final size:27
Alignment explanation
Indices: 337981--338053 Score: 83
Period size: 27 Copynumber: 2.7 Consensus size: 27
337971 GGAATAAAGC
* **
337981 CGGGGTTAGAGTATCCCCTCGGAAATAA
1 CGGGGTTGGAGTATCCCCGAGG-AATAA
* *
338009 CGGGGTTGGAGTATCCCCGATGATTAA
1 CGGGGTTGGAGTATCCCCGAGGAATAA
*
338036 CGGGGTTGGGGTATCCCC
1 CGGGGTTGGAGTATCCCC
338054 AATTGTGAAA
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
27 21 0.54
28 18 0.46
ACGTcount: A:0.21, C:0.22, G:0.34, T:0.23
Consensus pattern (27 bp):
CGGGGTTGGAGTATCCCCGAGGAATAA
Found at i:338027 original size:79 final size:79
Alignment explanation
Indices: 337852--338029 Score: 250
Period size: 79 Copynumber: 2.3 Consensus size: 79
337842 AAATAAAGTT
* ** * * *
337852 GGGGTTAAAGTATCCCTAATTGTGAGAAATCAATATTTTGGAAATAAAGGCGGGGTTGGAGTATC
1 GGGGTTAGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTAGAGTATC
*
337917 CCCTAGAAAATAAT
66 CCCTAGAAAATAAC
337931 GGGGTTAGAGTATCCCCGATTATGAGAAATCAATATTTTAGG-AATAAAGCCGGGGTTAGAGTAT
1 GGGGTTAGAGTATCCCCGATTATGAGAAATCAATATTTT-GGAAATAAAGCCGGGGTTAGAGTAT
* *
337995 CCCCTCGGAAATAAC
65 CCCCTAGAAAATAAC
*
338010 GGGGTTGGAGTATCCCCGAT
1 GGGGTTAGAGTATCCCCGAT
338030 GATTAACGGG
Statistics
Matches: 88, Mismatches: 10, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
79 86 0.98
80 2 0.02
ACGTcount: A:0.32, C:0.15, G:0.27, T:0.26
Consensus pattern (79 bp):
GGGGTTAGAGTATCCCCGATTATGAGAAATCAATATTTTGGAAATAAAGCCGGGGTTAGAGTATC
CCCTAGAAAATAAC
Found at i:338220 original size:102 final size:103
Alignment explanation
Indices: 338038--338273 Score: 334
Period size: 102 Copynumber: 2.3 Consensus size: 103
338028 ATGATTAACG
* * * *
338038 GGGTTGGGGTATCCCCAATTGTGAAAAATTGGTGTTTTTGGAAATAAAATCGAAGTTGGAGTATC
1 GGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTCGAAAATAAAATCGAAGTTGGAGTATC
*
338103 CCCGATTATAGAAAATTGGTGTTTT-GAAAATAAAACCA
66 CCCGATTATAGAAAATTAGTGTTTTAG-AAATAAAACCA
* *
338141 GGGTTGGAGTATCCCCGATTGTGGAAAATTGGTG-TTTCGAAAATAAAATCGGAGTTGGAGTATC
1 GGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTCGAAAATAAAATCGAAGTTGGAGTATC
* *
338205 CCCGATTGT-GAAAAATTAGTGTTTTAGAAATAAAACCG
66 CCCGATTATAG-AAAATTAGTGTTTTAGAAATAAAACCA
* *
338243 GGGTTGGAGTACCCCCGATTATGAAAAATTG
1 GGGTTGGAGTATCCCCGATTGTGAAAAATTG
338274 AGAAACTTAA
Statistics
Matches: 119, Mismatches: 12, Indels: 5
0.88 0.09 0.04
Matches are distributed among these distances:
101 1 0.01
102 86 0.72
103 32 0.27
ACGTcount: A:0.33, C:0.12, G:0.26, T:0.30
Consensus pattern (103 bp):
GGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTCGAAAATAAAATCGAAGTTGGAGTATC
CCCGATTATAGAAAATTAGTGTTTTAGAAATAAAACCA
Found at i:338270 original size:51 final size:51
Alignment explanation
Indices: 338036--338273 Score: 300
Period size: 51 Copynumber: 4.6 Consensus size: 51
338026 CGATGATTAA
* * * *
338036 CGGGGTTGGGGTATCCCCAATTGTGAAAAATTGGTGTTTTTGGAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTG-TTTTGAAAATAAAAC
** *
338088 CGAAGTTGGAGTATCCCCGATTAT-AGAAAATTGGTGTTTTGAAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTGTGA-AAAATTGGTGTTTTGAAAATAAAAC
* * * *
338139 CAGGGTTGGAGTATCCCCGATTGTGGAAAATTGGTGTTTCGAAAATAAAAT
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAAC
* *
338190 CGGAGTTGGAGTATCCCCGATTGTGAAAAATTAGTGTTTT-AGAAATAAAAC
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGA-AAATAAAAC
* *
338241 CGGGGTTGGAGTACCCCCGATTATGAAAAATTG
1 CGGGGTTGGAGTATCCCCGATTGTGAAAAATTG
338274 AGAAACTTAA
Statistics
Matches: 159, Mismatches: 24, Indels: 7
0.84 0.13 0.04
Matches are distributed among these distances:
50 1 0.01
51 129 0.81
52 29 0.18
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.29
Consensus pattern (51 bp):
CGGGGTTGGAGTATCCCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAAC
Found at i:340653 original size:13 final size:13
Alignment explanation
Indices: 340635--340660 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
340625 ACAAAGATCG
340635 ATGTATCGATACA
1 ATGTATCGATACA
340648 ATGTATCGATACA
1 ATGTATCGATACA
340661 TTCTACAAAT
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:340737 original size:19 final size:21
Alignment explanation
Indices: 340713--340764 Score: 72
Period size: 19 Copynumber: 2.6 Consensus size: 21
340703 AGCGATACAC
*
340713 TGTATCGATACA-TTACT-TA
1 TGTATCGATACATTTACTGAA
340732 TGTATCGATACATTTACTGAA
1 TGTATCGATACATTTACTGAA
*
340753 TGTATCAATACA
1 TGTATCGATACA
340765 AATTATTGAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 12 0.41
20 5 0.17
21 12 0.41
ACGTcount: A:0.35, C:0.15, G:0.12, T:0.38
Consensus pattern (21 bp):
TGTATCGATACATTTACTGAA
Found at i:341897 original size:79 final size:79
Alignment explanation
Indices: 341699--342409 Score: 521
Period size: 79 Copynumber: 9.1 Consensus size: 79
341689 TATTTTGGAG
* * * * * * ** *
341699 ATAAAAACGGGGTTGGAGTATCCCCTCGAAAATAA-TAGGGTTAGAGTTTCCCTAATGGTG-AAA
1 ATAAAACCAGGGTTGGAGTATCCCTTCGAAAATAACGA-GGTTGGAGTATCCCCGATTGTGAAAA
* * *
341762 ATCAATATTTTGGAA
65 ATCAGTGTTTTGAAA
* * * * * *
341777 AT-AAATC-GTGATTGGAGTATCCCCTCGAAAATAA-TAGGGTTGGAGTATCTCTGATTGTGAAA
1 ATAAAACCAG-GGTTGGAGTATCCCTTCGAAAATAACGA-GGTTGGAGTATCCCCGATTGTGAAA
* *
341839 AATTAGTGTTTTAAAA
64 AATCAGTGTTTTGAAA
** * * *
341855 ATAAAATTAGGGTTGTAGTATCCCTTCGAAAATAACGAGGTTGGAGTATCCCCGATTATGGAAAA
1 ATAAAACCAGGGTTGGAGTATCCCTTCGAAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAA
* *
341920 TCAATGTTTTGGAA
66 TCAGTGTTTTGAAA
* * * * *
341934 ATAAAACCAAGGATGGAGTATCCCCTT-GGAAATAAC--GG--GGAGTATCCTCGATTGTGAAAT
1 ATAAAACCAGGGTTGGAGTAT-CCCTTCGAAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAA
*
341994 ATCAGTATTTTGAAA
65 ATCAGTGTTTTGAAA
* *
342009 ATAAAACCAGGGTTGGAGTAT-CCTCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTAAAAA
1 ATAAAACCAGGGTTGGAGTATCCCT-TCGAAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAA
* *
342073 ATCGGTGTTTTGGAA
65 ATCAGTGTTTTGAAA
* * * * * *
342088 ATAAAATC-GAGGTTGTAGTAT--CTTCTCAGAAATAACGGGGTTGAAGTATCCCTGATTGTGAA
1 ATAAAACCAG-GGTTGGAGTATCCCTTC-GA-AAATAACGAGGTTGGAGTATCCCCGATTGTGAA
*
342150 AAATC-GATATTTT-AGAA
63 AAATCAG-TGTTTTGA-AA
* * * * *
342167 ATAAAACTAGGTTTGAAGTATCCCCTT-GAAAATAACGGGGTTGGAGTATCTCCGATTGTGAAAA
1 ATAAAACCAGGGTTGGAGTAT-CCCTTCGAAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAA
**
342231 ATTGGTGTTTTGAAA
65 ATCAGTGTTTTGAAA
* * *
342246 ATAAAA-CAGGGGTTGGAGTATCCAC-TCGAAAATAAC-AGGGTTGGAGTATCCCCAATTATGGA
1 ATAAAACCA-GGGTTGGAGTATCC-CTTCGAAAATAACGA-GGTTGGAGTATCCCCGATTGTGAA
*
342308 AAATCAATGTTTTGAAA
63 AAATCAGTGTTTTGAAA
* * ** * * * * * *
342325 ATAAAATCGGGGTTAAAGTACCTCCTTTG-AAATAACAAAGTTGGAGTATCCCCGATGGTGGAAA
1 ATAAAACCAGGGTTGGAGTATC-CCTTCGAAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAA
* *
342389 ATCGGTATTTT-AGAA
65 ATCAGTGTTTTGA-AA
342404 ATAAAA
1 ATAAAA
342410 ACATGAATGA
Statistics
Matches: 513, Mismatches: 88, Indels: 63
0.77 0.13 0.09
Matches are distributed among these distances:
73 3 0.01
74 1 0.00
75 57 0.11
76 1 0.00
77 54 0.11
78 27 0.05
79 351 0.68
80 16 0.03
82 3 0.01
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (79 bp):
ATAAAACCAGGGTTGGAGTATCCCTTCGAAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAA
TCAGTGTTTTGAAA
Found at i:342213 original size:158 final size:158
Alignment explanation
Indices: 341708--342409 Score: 644
Period size: 158 Copynumber: 4.5 Consensus size: 158
341698 GATAAAAACG
* * * * * ** * ** *
341708 GGGTTGGAGTATCCCCTCGAAAATAA-TAGGGTTAGAGTTTCCCTAATGGTG-AAAATCAATATT
1 GGGTTGAAGTATCCCCTTGAAAATAACGA-GGTTGGAGTATCCCCGATTGTGAAAAATCGGTGTT
* * * *
341771 TTGGAAAT-AAATCGTGATTGGAGTATCCCCTCGAAAATAATAGGGTTGGAGTATCTCTGATTGT
65 TTGGAAATAAAATCGAGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCTGATTGT
* * * *
341835 GAAAAATTAGTGTTTTAAAAATAAAATTA
130 GAAAAATCAGTATTTTGAAAATAAAACTA
* * * **
341864 GGGTTGTAGTAT-CCCTTCGAAAATAACGAGGTTGGAGTATCCCCGATTATGGAAAATCAATGTT
1 GGGTTGAAGTATCCCCTT-GAAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATCGGTGTT
* * * * *
341928 TTGGAAATAAAACCAAGGATGGAGTATCCCCTTGGAAATAAC--GG--GGAGTAT-CCTCGATTG
65 TTGGAAATAAAATCGAGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCT-GATTG
* *
341988 TGAAATATCAGTATTTTGAAAATAAAACCA
129 TGAAAAATCAGTATTTTGAAAATAAAACTA
* * * * *
342018 GGGTTGGAGTATCCTCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTAAAAAATCGGTGTTT
1 GGGTTGAAGTATCCCCTTGAAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATCGGTGTTT
* ** * *
342083 TGGAAATAAAATCGAGGTTGTAGTATCTTCTC-AGAAATAACGGGGTTGAAGTATCCCTGATTGT
66 TGGAAATAAAATCGAGGTTGGAGTATCCCCTCGA-AAATAACAGGGTTGGAGTATCCCTGATTGT
342147 GAAAAATC-GATATTTT-AGAAATAAAACTA
130 GAAAAATCAG-TATTTTGA-AAATAAAACTA
* * * *
342176 GGTTTGAAGTATCCCCTTGAAAATAACGGGGTTGGAGTATCTCCGATTGTGAAAAATTGGTGTTT
1 GGGTTGAAGTATCCCCTTGAAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATCGGTGTTT
* * * ** *
342241 TGAAAATAAAA-CAGGGGTTGGAGTATCCACTCGAAAATAACAGGGTTGGAGTATCCCCAATTAT
66 TGGAAATAAAATC-GAGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCTGATTGT
* * * *
342305 GGAAAATCAATGTTTTGAAAATAAAA-TCG
130 GAAAAATCAGTATTTTGAAAATAAAACT-A
* * * * * *
342334 GGGTTAAAGTA-CCTCCTTTG-AAATAACAAAGTTGGAGTATCCCCGATGGTGGAAAATCGGTAT
1 GGGTTGAAGTATCC-CC-TTGAAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATCGGTGT
*
342397 TTTAGAAATAAAA
64 TTTGGAAATAAAA
342410 ACATGAATGA
Statistics
Matches: 447, Mismatches: 78, Indels: 40
0.79 0.14 0.07
Matches are distributed among these distances:
153 2 0.00
154 120 0.27
155 7 0.02
156 39 0.09
157 26 0.06
158 245 0.55
159 8 0.02
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (158 bp):
GGGTTGAAGTATCCCCTTGAAAATAACGAGGTTGGAGTATCCCCGATTGTGAAAAATCGGTGTTT
TGGAAATAAAATCGAGGTTGGAGTATCCCCTCGAAAATAACAGGGTTGGAGTATCCCTGATTGTG
AAAAATCAGTATTTTGAAAATAAAACTA
Found at i:342321 original size:237 final size:232
Alignment explanation
Indices: 341788--342409 Score: 723
Period size: 237 Copynumber: 2.7 Consensus size: 232
341778 TAAATCGTGA
* * * * * *
341788 TTGGAGTATCCCCTCGAAAATAATAGGGTTGGAGTATCTCTGATTGTGAAAAATTAGTGTTTTAA
1 TTGGAGTATCCACTCGAAAATAACAGGGTTGGAGTATCCCCGATTGTGAAAAATCAGTGTTTTGA
* *
341853 AAATAAAAT-TAGGGTTGTAGTATC-CCTTCGAAAATAACGAGGTTGGAGTATCCCCGATTATGG
66 AAATAAAATCGA-GGTTGTAGTATCTCC-TCG-AAATAACGAGGTTGGAGTATCCCCGATTGTGG
* * * * *
341916 AAAATCAATGTTTTGGAAATAAAACCAAGGATGGAGTATCCCCTTGGAAATAACGGGGAGTATCC
128 AAAATCGATATTTTAGAAATAAAACCAAGGATGAAGTATCCCCTTGAAAATAACGGGGAGTATCC
*
341981 TCGATTGTGAAATATCAGTATTTTGAAAATAAAACCAGGG
193 TCGATTGTGAAAAATCAGTATTTTGAAAATAAAACCAGGG
* * * * *
342021 TTGGAGTATCCTCTCGAAAATAACGGGGTTGGAGTATCCCCGATTGTAAAAAATCGGTGTTTTGG
1 TTGGAGTATCCACTCGAAAATAACAGGGTTGGAGTATCCCCGATTGTGAAAAATCAGTGTTTTGA
* * * * *
342086 AAATAAAATCGAGGTTGTAGTATCTTCTCAGAAATAACGGGGTTGAAGTATCCCTGATTGTGAAA
66 AAATAAAATCGAGGTTGTAGTATCTCCTC-GAAATAACGAGGTTGGAGTATCCCCGATTGTGGAA
* *
342151 AATCGATATTTTAGAAATAAAA-CTAGGTTTGAAGTATCCCCTTGAAAATAACGGGGTTGGAGTA
130 AATCGATATTTTAGAAATAAAACCAAGG-ATGAAGTATCCCCTTGAAAATAAC--GG--GGAGTA
** *
342215 T-CTCCGATTGTGAAAAATTGGTGTTTTGAAAATAAAA-CAGGGG
190 TCCT-CGATTGTGAAAAATCAGTATTTTGAAAATAAAACCA-GGG
* * * *
342258 TTGGAGTATCCACTCGAAAATAACAGGGTTGGAGTATCCCCAATTATGGAAAATCAATGTTTTGA
1 TTGGAGTATCCACTCGAAAATAACAGGGTTGGAGTATCCCCGATTGTGAAAAATCAGTGTTTTGA
* ** * * * * *
342323 AAATAAAATCGGGGTTAAAGTACCTCCTTTGAAATAACAAAGTTGGAGTATCCCCGATGGTGGAA
66 AAATAAAATCGAGGTTGTAGTATCTCC-TCGAAATAACGAGGTTGGAGTATCCCCGATTGTGGAA
*
342388 AATCGGTATTTTAGAAATAAAA
130 AATCGATATTTTAGAAATAAAA
342410 ACATGAATGA
Statistics
Matches: 327, Mismatches: 51, Indels: 18
0.83 0.13 0.05
Matches are distributed among these distances:
232 4 0.01
233 147 0.45
234 3 0.01
235 2 0.01
236 4 0.01
237 166 0.51
238 1 0.00
ACGTcount: A:0.35, C:0.13, G:0.23, T:0.29
Consensus pattern (232 bp):
TTGGAGTATCCACTCGAAAATAACAGGGTTGGAGTATCCCCGATTGTGAAAAATCAGTGTTTTGA
AAATAAAATCGAGGTTGTAGTATCTCCTCGAAATAACGAGGTTGGAGTATCCCCGATTGTGGAAA
ATCGATATTTTAGAAATAAAACCAAGGATGAAGTATCCCCTTGAAAATAACGGGGAGTATCCTCG
ATTGTGAAAAATCAGTATTTTGAAAATAAAACCAGGG
Found at i:352558 original size:34 final size:35
Alignment explanation
Indices: 352490--352560 Score: 92
Period size: 34 Copynumber: 2.1 Consensus size: 35
352480 GTGTTTGTGA
*
352490 AAAGAATAAGCACAAAGGAATACAAATGAGCTTTG
1 AAAGAATAAGCACAAAGGAATACAAAAGAGCTTTG
**
352525 AAAGAATAA-CAACAAA-GAATACAAAAGCTCTTTG
1 AAAGAATAAGC-ACAAAGGAATACAAAAGAGCTTTG
352559 AA
1 AA
352561 GTGTAGAAAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
34 18 0.56
35 14 0.44
ACGTcount: A:0.55, C:0.13, G:0.15, T:0.17
Consensus pattern (35 bp):
AAAGAATAAGCACAAAGGAATACAAAAGAGCTTTG
Found at i:354893 original size:20 final size:20
Alignment explanation
Indices: 354870--354944 Score: 60
Period size: 26 Copynumber: 3.3 Consensus size: 20
354860 ATTTTTATAT
354870 ATTTTAATTATTATAATTAA
1 ATTTTAATTATTATAATTAA
*
354890 ATTTAAATTATTTTATATTTATATAA
1 ATTTTAATTA--TTATA---AT-TAA
354916 ATTTTAATATATTAATAATTAA
1 ATTTTAAT-TATT-ATAATTAA
354938 TATTTTA
1 -ATTTTA
354945 TTTAAAACAT
Statistics
Matches: 44, Mismatches: 2, Indels: 15
0.72 0.03 0.25
Matches are distributed among these distances:
20 9 0.20
22 8 0.18
23 8 0.18
25 4 0.09
26 13 0.30
27 2 0.05
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (20 bp):
ATTTTAATTATTATAATTAA
Found at i:355285 original size:11 final size:11
Alignment explanation
Indices: 355266--355301 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
355256 AAATCATATT
355266 TTATATTTATA
1 TTATATTTATA
*
355277 TTATTTTTATA
1 TTATATTTATA
*
355288 TTATAATTATA
1 TTATATTTATA
355299 TTA
1 TTA
355302 AAGGTATTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (11 bp):
TTATATTTATA
Found at i:357047 original size:174 final size:174
Alignment explanation
Indices: 356750--357337 Score: 655
Period size: 174 Copynumber: 3.4 Consensus size: 174
356740 GAGTCTACCA
* ** * *
356750 ATATATACAAATTCATCAATTTG-AATATTAATTACCAATTTAAAGTAAAATTAGTGTAACTATA
1 ATATACACAAATTCATCAA-TTGAAATACCAATCACCAATTTAAAGTAGAATTAGTGTAACTATA
* ** * * *
356814 TATGCAATTAGAGTAGTAGTAACCAATTTCAAGTAGGACTAGTGTAAGTGTATATTAAATTAGAC
65 TATGCAATTGGAGTAGTAACAACCAATTTCAATTAGAACTAGTGTAAGTGTATATTAAATTGGAC
* * * *
356879 TATTTGGGCAAGTAAAGACCAATTTTAATTACAATTAGTATTACT
130 TATTTGAGCAAGTAATGACCAATTTTAATTAGAATTAGTATAACT
* ** * * * * *
356924 GTATATGCAAATTCATTAATTGAAATACTAATCATCAATTTAAAGTAGAATTAGTATAACTATAC
1 ATATACACAAATTCATCAATTGAAATACCAATCACCAATTTAAAGTAGAATTAGTGTAACTATAT
*** * * *
356989 ACATAATTGGAGTAGAAACAACCAATTTCAATTAGAACTAGTATAAGTGTCTATTAAATTGGACT
66 ATGCAATTGGAGTAGTAACAACCAATTTCAATTAGAACTAGTGTAAGTGTATATTAAATTGGACT
* *
357054 ATTTAGAG-AAGTAATGGCCAATTTTAATTAGAATTGGTATAACT
131 ATTT-GAGCAAGTAATGACCAATTTTAATTAGAATTAGTATAACT
* * * *
357098 CTATACACAAATTCATCAATT-AGAATACCAATCACTAATTTAAAGTAGAATTAGTGTCAGTATA
1 ATATACACAAATTCATCAATTGA-AATACCAATCACCAATTTAAAGTAGAATTAGTGTAACTATA
* * ** *
357162 TATGCAATTAGG-GCAGTAACAACCAATTTTAATTAGATTTAGTGTAAGTGTATATTTAATTGGA
65 TATGCAATT-GGAGTAGTAACAACCAATTTCAATTAGAACTAGTGTAAGTGTATATTAAATTGGA
* * * *
357226 CTATTTGAACAAGTAATGACC-ATTTCAATTAGAATTACTGTAACT
129 CTATTTGAGCAAGTAATGACCAATTTTAATTAGAATTAGTATAACT
* * * * * *
357271 ATATACACAAATTTATCAATTGGACTACCAATCACCAATTTCAACTACAATTAGTGTAACTATAT
1 ATATACACAAATTCATCAATTGAAATACCAATCACCAATTTAAAGTAGAATTAGTGTAACTATAT
357336 AT
66 AT
357338 ACAAATTCAT
Statistics
Matches: 343, Mismatches: 65, Indels: 13
0.81 0.15 0.03
Matches are distributed among these distances:
173 82 0.24
174 257 0.75
175 4 0.01
ACGTcount: A:0.41, C:0.12, G:0.13, T:0.35
Consensus pattern (174 bp):
ATATACACAAATTCATCAATTGAAATACCAATCACCAATTTAAAGTAGAATTAGTGTAACTATAT
ATGCAATTGGAGTAGTAACAACCAATTTCAATTAGAACTAGTGTAAGTGTATATTAAATTGGACT
ATTTGAGCAAGTAATGACCAATTTTAATTAGAATTAGTATAACT
Found at i:357371 original size:61 final size:61
Alignment explanation
Indices: 357247--357398 Score: 169
Period size: 61 Copynumber: 2.5 Consensus size: 61
357237 AGTAATGACC
* * * * *
357247 ATTTCAATTAGAATTACTGTAACTATATACACAAATTTATCAATTGGACTACCAATCACCA
1 ATTTCAAATAGAATTAGTGTAACTATATATACAAATTCATCAATTGGACTACAAATCACCA
* * * * ***
357308 ATTTCAACTACAATTAGTGTAACTATATATACAAATTCATTAATTGGATTACAAATTTTCA
1 ATTTCAAATAGAATTAGTGTAACTATATATACAAATTCATCAATTGGACTACAAATCACCA
* * *
357369 ATTTAAAATAGAATAAGTGTAACAATATAT
1 ATTTCAAATAGAATTAGTGTAACTATATAT
357399 GCAATTAGAG
Statistics
Matches: 75, Mismatches: 16, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
61 75 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (61 bp):
ATTTCAAATAGAATTAGTGTAACTATATATACAAATTCATCAATTGGACTACAAATCACCA
Found at i:358055 original size:14 final size:15
Alignment explanation
Indices: 358028--358056 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
358018 AAAAAACTAA
358028 AAAGAAAGATAAATT
1 AAAGAAAGATAAATT
358043 AAAGAAA-ATAAATT
1 AAAGAAAGATAAATT
358057 CTTGTATTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.69, C:0.00, G:0.10, T:0.21
Consensus pattern (15 bp):
AAAGAAAGATAAATT
Found at i:358978 original size:19 final size:19
Alignment explanation
Indices: 358949--359006 Score: 80
Period size: 20 Copynumber: 3.0 Consensus size: 19
358939 ATTATTATTA
358949 AATAATATTTTATATAATT
1 AATAATATTTTATATAATT
* *
358968 CATATTATTTTTATATAATT
1 AATAATA-TTTTATATAATT
*
358988 AATAATATTTTATTTAATT
1 AATAATATTTTATATAATT
359007 TTAACGAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
19 16 0.48
20 17 0.52
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (19 bp):
AATAATATTTTATATAATT
Found at i:360557 original size:2 final size:2
Alignment explanation
Indices: 360550--360588 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
360540 AAAATGGTAC
360550 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
360589 ATGTAATTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:361351 original size:13 final size:13
Alignment explanation
Indices: 361333--361360 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
361323 ATATAATCAA
361333 TTTTTTTATAAAT
1 TTTTTTTATAAAT
361346 TTTTTTTATAAAT
1 TTTTTTTATAAAT
361359 TT
1 TT
361361 AAAAAATCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
TTTTTTTATAAAT
Found at i:361417 original size:13 final size:13
Alignment explanation
Indices: 361399--361423 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
361389 AATATGTATT
361399 AAATATAAATATC
1 AAATATAAATATC
361412 AAATATAAATAT
1 AAATATAAATAT
361424 TTTTTAAAAG
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:0.64, C:0.04, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATATAAATATC
Found at i:361957 original size:41 final size:40
Alignment explanation
Indices: 361908--361991 Score: 141
Period size: 41 Copynumber: 2.1 Consensus size: 40
361898 ATTGAGTTGG
*
361908 TATTACTTGACTTATGACATCAATTTAGTTACTCTTGTTA
1 TATTACTTGACTTATGACATCAATTTAGTTACTCTCGTTA
*
361948 TATTCACTTGACTTGTGACATCAATTTAGTTACTCTCGTTA
1 TATT-ACTTGACTTATGACATCAATTTAGTTACTCTCGTTA
361989 TAT
1 TAT
361992 ATAGTATAAG
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
40 4 0.10
41 37 0.90
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (40 bp):
TATTACTTGACTTATGACATCAATTTAGTTACTCTCGTTA
Found at i:364921 original size:24 final size:24
Alignment explanation
Indices: 364873--364924 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
364863 TTCAATCAAG
*
364873 ATTTTTTTAATTATTTCATTCTAA
1 ATTTTTTTAATTATTTAATTCTAA
364897 ATTTTTTTATGATTA-TTAATT-TAA
1 ATTTTTTTA--ATTATTTAATTCTAA
364921 ATTT
1 ATTT
364925 AAATTTTATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
24 16 0.64
25 5 0.20
26 4 0.16
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (24 bp):
ATTTTTTTAATTATTTAATTCTAA
Found at i:367044 original size:153 final size:156
Alignment explanation
Indices: 366776--367078 Score: 339
Period size: 153 Copynumber: 2.0 Consensus size: 156
366766 TCACTGGTCA
** * * *
366776 CTTTTATGCCAAAGGTGTGTGTTTAGTATAGGTTCACCCTATTTTTATGTTTATTTTCGTGTCCT
1 CTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCACCCTA-TTTTATGATGATTTTCGTGTCCT
* * * * * *
366841 TTAGGATTACTGGATACTTTCATATTGAAGGTATAACCAAAAGACTTTTTGGTGATTTCTCTAAA
65 TTAAGATTACTAGATACTTTCACATCGAAAGTATAACCAAAAGACTTTTTGGTAATTTCTCTAAA
366906 ACCAAGTCCAATATAGTCATTAGGTTG
130 ACCAAGTCCAATATAGTCATTAGGTTG
* *
366933 CTTTTATGCCAAA-GTGTGCATTTAGGATAGGTTCA-TC-A-TTTATGATGATTTTTGTGTCCTT
1 CTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCACCCTATTTTATGATGATTTTCGTGTCCTT
* ** *
366994 TAA-AGTTACCTAGATACTTTCACATCGAAAGTAT-ACCCAAAGGGTATTTTGGTAATTTCTTTA
66 TAAGA-TTA-CTAGATACTTTCACATCGAAAGTATAACCAAAAGACT-TTTTGGTAATTTCTCTA
** **
367057 AAACTGAGTCTGATATAGTCAT
128 AAACCAAGTCCAATATAGTCAT
367079 CGTCTCATTT
Statistics
Matches: 122, Mismatches: 21, Indels: 10
0.80 0.14 0.07
Matches are distributed among these distances:
151 1 0.01
152 33 0.27
153 54 0.44
154 1 0.01
155 1 0.01
156 19 0.16
157 13 0.11
ACGTcount: A:0.27, C:0.15, G:0.17, T:0.41
Consensus pattern (156 bp):
CTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCACCCTATTTTATGATGATTTTCGTGTCCTT
TAAGATTACTAGATACTTTCACATCGAAAGTATAACCAAAAGACTTTTTGGTAATTTCTCTAAAA
CCAAGTCCAATATAGTCATTAGGTTG
Found at i:371954 original size:33 final size:33
Alignment explanation
Indices: 371917--371983 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
371907 TTCAACGATT
371917 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
371950 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
371983 T
1 T
371984 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:371955 original size:13 final size:13
Alignment explanation
Indices: 371937--371961 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
371927 CATAAAATGT
371937 TGTATCGATACAA
1 TGTATCGATACAA
371950 TGTATCGATACA
1 TGTATCGATACA
371962 TATTTTTTTG
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:372042 original size:13 final size:13
Alignment explanation
Indices: 372024--372048 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
372014 ATTACTCAAA
372024 TGTATCGATACAT
1 TGTATCGATACAT
372037 TGTATCGATACA
1 TGTATCGATACA
372049 CTGATCTTTG
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:372150 original size:52 final size:52
Alignment explanation
Indices: 372057--372186 Score: 201
Period size: 52 Copynumber: 2.5 Consensus size: 52
372047 CACTGATCTT
* *
372057 TGTATCGATACATGCAGGC-AATTTGCCCAGATGTATCGATACA-TTTTAAAA
1 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATT-AAA
372108 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATTAAA
* *
372160 TGTATCGATACATGCAAGCAACTTTTC
1 TGTATCGATACATGCAGGCAAATTTTC
372187 ATATTTCGGG
Statistics
Matches: 73, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
51 19 0.26
52 51 0.70
53 3 0.04
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTTCCCAGATGTATCGATACACTATTAAA
Found at i:385790 original size:1 final size:1
Alignment explanation
Indices: 385786--385872 Score: 66
Period size: 1 Copynumber: 87.0 Consensus size: 1
385776 AAAAATTAAT
* * * * * * * * *
385786 AAAAACAAAAACAAGAAAAAAAAAACAAACACAAAAAAAAAACAAAAAAAACAAAAAAACAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* * *
385851 AAAGAAGAAAAAAAGAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAA
385873 TGGGGAAGAA
Statistics
Matches: 62, Mismatches: 24, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
1 62 1.00
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:385806 original size:17 final size:17
Alignment explanation
Indices: 385786--385871 Score: 84
Period size: 17 Copynumber: 4.8 Consensus size: 17
385776 AAAAATTAAT
*
385786 AAAAACAAAAACAAGAA
1 AAAAACAAAAAAAAGAA
* *
385803 AAAAAAAACAAACACAAAAA
1 AAAAACAA-AAA-A-AAGAA
*
385823 AAAAACAAAAAAAACAA
1 AAAAACAAAAAAAAGAA
385840 AAAAACAAAAAAAAGAA
1 AAAAACAAAAAAAAGAA
385857 GAAAAA-AAGAAAAAA
1 -AAAAACAA-AAAAAA
385872 ATGGGGAAGA
Statistics
Matches: 58, Mismatches: 6, Indels: 9
0.79 0.08 0.12
Matches are distributed among these distances:
17 29 0.50
18 15 0.26
19 3 0.05
20 11 0.19
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (17 bp):
AAAAACAAAAAAAAGAA
Found at i:385811 original size:20 final size:19
Alignment explanation
Indices: 385786--385870 Score: 91
Period size: 20 Copynumber: 4.3 Consensus size: 19
385776 AAAAATTAAT
385786 AAAAACAAAAACAAGAAAAA
1 AAAAACAAAAACAA-AAAAA
*
385806 AAAAACAAACACAAAAAAA
1 AAAAACAAAAACAAAAAAA
*
385825 AAACAAAAAAAACAAAAAAA
1 AAA-AACAAAAACAAAAAAA
*
385845 CAAAAA-AAAGAAGAAAAAAA
1 -AAAAACAAA-AACAAAAAAA
385865 GAAAAA
1 -AAAAA
385871 AATGGGGAAG
Statistics
Matches: 57, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
19 11 0.19
20 43 0.75
21 3 0.05
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (19 bp):
AAAAACAAAAACAAAAAAA
Found at i:385823 original size:28 final size:29
Alignment explanation
Indices: 385787--385872 Score: 88
Period size: 29 Copynumber: 3.0 Consensus size: 29
385777 AAAATTAATA
*
385787 AAAACAAAAACAAG-AAAAAAA-AAACAAAC
1 AAAA-AAAAA-AAGAAAAAAAACAAAAAAAC
*
385816 ACAAAAAAAAAACAAAAAAAACAAAAAAAC
1 A-AAAAAAAAAAGAAAAAAAACAAAAAAAC
* *
385846 AAAAAAAAGAAG-AAAAAAAGAAAAAAA
1 AAAAAAAAAAAGAAAAAAAACAAAAAAA
385873 TGGGGAAGAA
Statistics
Matches: 49, Mismatches: 5, Indels: 7
0.80 0.08 0.11
Matches are distributed among these distances:
28 16 0.33
29 22 0.45
30 11 0.22
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (29 bp):
AAAAAAAAAAAGAAAAAAAACAAAAAAAC
Found at i:385832 original size:37 final size:37
Alignment explanation
Indices: 385786--385872 Score: 104
Period size: 37 Copynumber: 2.4 Consensus size: 37
385776 AAAAATTAAT
* * *
385786 AAAAACAAAAACAAGAAAAAAA-AAACAAACACAAAAA
1 AAAAACAAAAAAAACAAAAAAACAAA-AAAAACAAAAA
* *
385823 AAAAACAAAAAAAACAAAAAAACAAAAAAAAGAAGAA
1 AAAAACAAAAAAAACAAAAAAACAAAAAAAACAAAAA
*
385860 AAAAAGAAAAAAA
1 AAAAACAAAAAAA
385873 TGGGGAAGAA
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
37 40 0.93
38 3 0.07
ACGTcount: A:0.86, C:0.09, G:0.05, T:0.00
Consensus pattern (37 bp):
AAAAACAAAAAAAACAAAAAAACAAAAAAAACAAAAA
Found at i:389352 original size:52 final size:52
Alignment explanation
Indices: 389274--389402 Score: 213
Period size: 52 Copynumber: 2.5 Consensus size: 52
389264 CGAAATATGA
*
389274 AAATTTGCTTGCATGTATCGATACATTTCATAGCATATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGCATATCGATACATCTGGGC
* **
389326 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGCATATCGATACATCTGGGC
*
389378 AAATTTGCCTGCATGTATCAATACA
1 AAATTTGCCTGCATGTATCGATACA
389403 AAGATCAGTG
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
52 72 1.00
ACGTcount: A:0.29, C:0.19, G:0.17, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGCATATCGATACATCTGGGC
Found at i:389413 original size:52 final size:52
Alignment explanation
Indices: 389274--389422 Score: 183
Period size: 52 Copynumber: 2.9 Consensus size: 52
389264 CGAAATATGA
* * *** **
389274 AAATTTGCTTGCATGTATCGATACATTTCATAGCATATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCAATACATAAGATAGTGTATCGATACATCTGGGC
* ***
389326 AAATTTGCCTGCATGTATCGATACATTTTATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCAATACATAAGATAGTGTATCGATACATCTGGGC
389378 AAATTTGCCTGCATGTATCAATACA-AAGATCAGTGTATCGATACA
1 AAATTTGCCTGCATGTATCAATACATAAGAT-AGTGTATCGATACA
389423 ATGTATCGAT
Statistics
Matches: 88, Mismatches: 8, Indels: 2
0.90 0.08 0.02
Matches are distributed among these distances:
51 2 0.02
52 86 0.98
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCAATACATAAGATAGTGTATCGATACATCTGGGC
Found at i:389429 original size:13 final size:13
Alignment explanation
Indices: 389411--389435 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
389401 CAAAGATCAG
389411 TGTATCGATACAA
1 TGTATCGATACAA
389424 TGTATCGATACA
1 TGTATCGATACA
389436 TTTGAAATGT
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:389500 original size:19 final size:18
Alignment explanation
Indices: 389476--389573 Score: 90
Period size: 19 Copynumber: 5.8 Consensus size: 18
389466 TAGCTTATAT
389476 TGTATCGATACAAAACTTA
1 TGTATCGATAC-AAACTTA
389495 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
389508 TGTATCGATACAACACTTA
1 TGTATCGATACAA-ACTTA
389527 TGTATCGATAC--A--T-
1 TGTATCGATACAAACTTA
389540 TGTATCGATACAACACTTTA
1 TGTATCGATACAA-AC-TTA
389560 TGTATCGATACAAA
1 TGTATCGATACAAA
389574 TCGTTGAAAT
Statistics
Matches: 66, Mismatches: 0, Indels: 26
0.72 0.00 0.28
Matches are distributed among these distances:
13 22 0.33
14 2 0.03
16 4 0.06
18 1 0.02
19 24 0.36
20 13 0.20
ACGTcount: A:0.37, C:0.17, G:0.12, T:0.34
Consensus pattern (18 bp):
TGTATCGATACAAACTTA
Found at i:389513 original size:13 final size:13
Alignment explanation
Indices: 389495--389551 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
389485 ACAAAACTTA
389495 TGTATCGATACAT
1 TGTATCGATACAT
389508 TGTATCGATACAACACTT
1 TGTATCGAT---ACA--T
389526 ATGTATCGATACAT
1 -TGTATCGATACAT
389540 TGTATCGATACA
1 TGTATCGATACA
389552 ACACTTTATG
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 21 0.55
14 1 0.03
16 6 0.16
18 1 0.03
19 9 0.24
ACGTcount: A:0.33, C:0.18, G:0.14, T:0.35
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:389515 original size:32 final size:32
Alignment explanation
Indices: 389474--389571 Score: 178
Period size: 32 Copynumber: 3.0 Consensus size: 32
389464 AGTAGCTTAT
*
389474 ATTGTATCGATACAAAACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
389506 ATTGTATCGATACAACACTTATGTATCGATAC
1 ATTGTATCGATACAACACTTATGTATCGATAC
389538 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAACAC-TTATGTATCGATAC
389571 A
1 A
389572 AATCGTTGAA
Statistics
Matches: 64, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
32 49 0.77
33 15 0.23
ACGTcount: A:0.36, C:0.17, G:0.12, T:0.35
Consensus pattern (32 bp):
ATTGTATCGATACAACACTTATGTATCGATAC
Found at i:391140 original size:32 final size:32
Alignment explanation
Indices: 391099--391576 Score: 514
Period size: 32 Copynumber: 14.9 Consensus size: 32
391089 CCAGTGGAGA
391099 AACCTTCTTCAAAGCCCACACAAGCTGGTGGC
1 AACCTTCTTCAAAGCCCACACAAGCTGGTGGC
* * * *
391131 AACCTTCTTCAAAGTCTACACAAGTTGGTAGC
1 AACCTTCTTCAAAGCCCACACAAGCTGGTGGC
391163 AACCTTTCTTCAAAGCCCACACAAGCTGGTGGC
1 AACC-TTCTTCAAAGCCCACACAAGCTGGTGGC
391196 AACCTTCTTCAAAGCCCACACAAGCTGGTGGC
1 AACCTTCTTCAAAGCCCACACAAGCTGGTGGC
* *
391228 AACCTTCTTCAAAG-CCACACAAGTTGGTGGT
1 AACCTTCTTCAAAGCCCACACAAGCTGGTGGC
*
391259 GACCTT-TTCTAAAGCCCACACAAG-TCGGTGGC
1 AACCTTCTTC-AAAGCCCACACAAGCT-GGTGGC
391291 AACCATTAC--CAAAGCCCACACAAG-TAGGTGGC
1 AACC-TT-CTTCAAAGCCCACACAAGCT-GGTGGC
* * *
391323 AACCTTCTTCATAGGCCACACAAGTTGGTGGC
1 AACCTTCTTCAAAGCCCACACAAGCTGGTGGC
* * *
391355 GACCCT-TTCTAAAGCCCACACAAGTTGGTGGC
1 AACCTTCTTC-AAAGCCCACACAAGCTGGTGGC
* * * *
391387 GACCCT-TTCTAAAGCCCACATAAGTTGGTGGC
1 AACCTTCTTC-AAAGCCCACACAAGCTGGTGGC
* * *
391419 GACCATT-TCCAAAGTCCACACAAGCTGGTGGC
1 AACC-TTCTTCAAAGCCCACACAAGCTGGTGGC
*
391451 AACATT-TGTCAAAGCCCACACAAG-TCGGTGGC
1 AACCTTCT-TCAAAGCCCACACAAGCT-GGTGGC
391483 AACCCTT-TTCAAAGCCCACACAAGCTGGTGGC
1 AA-CCTTCTTCAAAGCCCACACAAGCTGGTGGC
* *
391515 AACTTTCTTTAAAGCCCACACAAGCTGGTGGC
1 AACCTTCTTCAAAGCCCACACAAGCTGGTGGC
* * *
391547 AA-CTTTTTCTAAAACCCACACAAGTTGGTG
1 AACCTTCTTC-AAAGCCCACACAAGCTGGTG
391577 CTATCTCTTT
Statistics
Matches: 390, Mismatches: 38, Indels: 36
0.84 0.08 0.08
Matches are distributed among these distances:
30 4 0.01
31 41 0.11
32 305 0.78
33 40 0.10
ACGTcount: A:0.29, C:0.30, G:0.19, T:0.22
Consensus pattern (32 bp):
AACCTTCTTCAAAGCCCACACAAGCTGGTGGC
Found at i:396714 original size:21 final size:21
Alignment explanation
Indices: 396670--396724 Score: 67
Period size: 21 Copynumber: 2.7 Consensus size: 21
396660 ATTTGCCTGC
396670 ATGTATCGATACA-AAGAATA
1 ATGTATCGATACATAAGAATA
** *
396690 ATGTATCGATACATCTGAGTA
1 ATGTATCGATACATAAGAATA
*
396711 ATGTATAGATACAT
1 ATGTATCGATACAT
396725 TTCCTTGGCA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
20 13 0.43
21 17 0.57
ACGTcount: A:0.42, C:0.11, G:0.16, T:0.31
Consensus pattern (21 bp):
ATGTATCGATACATAAGAATA
Found at i:397867 original size:16 final size:17
Alignment explanation
Indices: 397848--397885 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 17
397838 TAGGCTTTTA
397848 TTATTTATTA-CTTGAT
1 TTATTTATTATCTTGAT
*
397864 TTA-TTATTATCTTTAT
1 TTATTTATTATCTTGAT
397880 TTATTT
1 TTATTT
397886 TTCTTTACAA
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
15 6 0.32
16 11 0.58
17 2 0.11
ACGTcount: A:0.24, C:0.05, G:0.03, T:0.68
Consensus pattern (17 bp):
TTATTTATTATCTTGAT
Found at i:399357 original size:165 final size:157
Alignment explanation
Indices: 399127--399517 Score: 408
Period size: 154 Copynumber: 2.5 Consensus size: 157
399117 GTTTTGAATC
*
399127 TTAAAATTCTTTAAATATTCA-CATTTAATT-ATTATTAAATTAGTTTTAAAATATTC-ATCTTA
1 TTAAAATTCTTTAAATATT-ATTATTTAATTCA-TATTAAATTAG-TTTAAAA-ATTCAAT-TTA
*
399189 TTTTATAAATTTTGCATTTTCTTTCAG-ATTTTTCCTATT-TTCAAAATACAGAGTTTTTTACTC
61 TTTTAT-AATTTTG-A--GT-TTT-AGAATTTTTCCTATTGTT-AAAATACAGAGTTTTTTACTC
* *
399252 CGTAAATTTCTCCTGTAAGATTTTTCTAAGTTTATAGCTT
119 CGTAAATTTCTCCGGTAAGATTTTTCTAAGTTTATA-ATT
* *
399292 TTAAAATTTTTTAAATATTATTATTTAATTCATATTAAATTAGTTTAGACAAAATCAATTTA-TT
1 TTAAAATTCTTTAAATATTATTATTTAATTCATATTAAATTAGTTTA-A-AAATTCAATTTATTT
* * * * * * *
399356 T-T-A---TGAGTTTTAGAATTTTTCTTGTTGTTGAGATACGGAGTTTTTTACTTCGTAAATTTT
64 TATAATTTTGAGTTTTAGAATTTTTCCTATTGTTAAAATACAGAGTTTTTTACTCCGTAAATTTC
*
399416 TTCGGTAAGATTTTTCTAAGTTTATAATT
129 TCCGGTAAGATTTTTCTAAGTTTATAATT
* * *
399445 TCAAAATTCTTCAAATATTATTATTTAATTCATATTAAATCAGTTTAAAAATTCAATTTATTTTA
1 TTAAAATTCTTTAAATATTATTATTTAATTCATATTAAATTAGTTTAAAAATTCAATTTATTTTA
399510 TGAATTTT
66 T-AATTTT
399518 AGAATTTTTC
Statistics
Matches: 193, Mismatches: 19, Indels: 35
0.78 0.08 0.14
Matches are distributed among these distances:
151 11 0.06
152 4 0.02
153 48 0.25
154 63 0.33
155 4 0.02
157 1 0.01
158 3 0.02
161 1 0.01
163 1 0.01
164 8 0.04
165 44 0.23
166 5 0.03
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (157 bp):
TTAAAATTCTTTAAATATTATTATTTAATTCATATTAAATTAGTTTAAAAATTCAATTTATTTTA
TAATTTTGAGTTTTAGAATTTTTCCTATTGTTAAAATACAGAGTTTTTTACTCCGTAAATTTCTC
CGGTAAGATTTTTCTAAGTTTATAATT
Found at i:399374 original size:154 final size:150
Alignment explanation
Indices: 399216--399836 Score: 520
Period size: 153 Copynumber: 4.1 Consensus size: 150
399206 TTTCTTTCAG
* *
399216 ATTTTTCCTATTTTCAAAATACAGAGTTTTTTACTCCGTAAATTTCTCCTGTAAGATTTTTCTAA
1 ATTTTTCCT-TTTTCGAGATACAGAGTTTTTTACTCCGTAAATTTCTCC-GTAAGATTTTTCTAA
* * * *
399281 GTTTATAGCTTTTAAAATTTTTTAAATATTATTATTTAATTCATATTAAATTAGTTTAGACAAAA
64 GTTTATA-ATTTTAAAATTCTTCAAATATTATTATTTAATTCATATTAAATTAGTTTAGA-AAAT
399346 TCAATTTATTTTATGAGTTTTAGA
127 TCAATTTATTTTATGAGTTTTAGA
* * * * *
399370 ATTTTT-CTTGTTGTTGAGATACGGAGTTTTTTACTTCGTAAATTTTTTCGGTAAGATTTTTCTA
1 ATTTTTCCTT-TT-TCGAGATACAGAGTTTTTTACTCCGTAAA-TTTCTCCGTAAGATTTTTCTA
* *
399434 AGTTTATAATTTCAAAATTCTTCAAATATTATTATTTAATTCATATTAAATCAGTTTA-AAAATT
63 AGTTTATAATTTTAAAATTCTTCAAATATTATTATTTAATTCATATTAAATTAGTTTAGAAAATT
*
399498 CAATTTATTTTATGAATTTTAGA
128 CAATTTATTTTATGAGTTTTAGA
* * * ** *
399521 ATTTTT-CTTTTAACCGAGATACAGAGTTTTCTACTCAGTAAAAATCTCCG-ATAGAATTTTCCT
1 ATTTTTCCTTTT--TCGAGATACAGAGTTTTTTACTCCGTAAATTTCTCCGTA-AG-ATTTTTCT
* * * ** * *
399584 AAGTTTTTAATTTTCAAAGTTCTTCAAATATTATTGTTTAACCCATA-TAAATTCAATTTTGAAA
62 AAGTTTATAATTTT-AAAATTCTTCAAATATTATTATTTAATTCATATTAAATT-AGTTTAGAAA
* *
399648 ATTTCAGTTTATTTTATGAGTTTTAAA
125 A-TTCAATTTATTTTATGAGTTTTAGA
*** * ** * * * ***
399675 ATTTTT--TTGACACCAAGATATGGAGTTTTCTATTCCATAAATTTCTCCAGTTTTATTTTTCTC
1 ATTTTTCCTT--TTTCGAGATACAGAGTTTTTTACTCCGTAAATTTCTCC-GTAAGATTTTTCT-
* * * * * * * *
399738 AA-TTTAAAATTTTTAAAATGCATCAAATATTTTTATTAAATTCATATTAAATCAATTTGTGAAA
62 AAGTTTATAA-TTTTAAAATTCTTCAAATATTATTATTTAATTCATATTAAATTAGTTT-AGAAA
* * *
399802 ATTTAATTTATTTTTATGAATTTTACA
125 ATTCAATTTA-TTTTATGAGTTTTAGA
*
399829 TTTTTTCC
1 ATTTTTCC
399837 ATATAATAAA
Statistics
Matches: 378, Mismatches: 68, Indels: 40
0.78 0.14 0.08
Matches are distributed among these distances:
149 1 0.00
150 8 0.02
151 82 0.22
152 34 0.09
153 131 0.35
154 117 0.31
155 5 0.01
ACGTcount: A:0.33, C:0.10, G:0.08, T:0.49
Consensus pattern (150 bp):
ATTTTTCCTTTTTCGAGATACAGAGTTTTTTACTCCGTAAATTTCTCCGTAAGATTTTTCTAAGT
TTATAATTTTAAAATTCTTCAAATATTATTATTTAATTCATATTAAATTAGTTTAGAAAATTCAA
TTTATTTTATGAGTTTTAGA
Found at i:402023 original size:151 final size:150
Alignment explanation
Indices: 401833--402230 Score: 397
Period size: 156 Copynumber: 2.6 Consensus size: 150
401823 GAATCAAGTC
** * * * *
401833 TTAGGTTGTCACCAAGATACTTTTATGCCAAATGAGTGCATTTAGGATAGGTTCATCGCATTTAT
1 TTAGGTTGTCACCGGGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCCATTTAT
* * *
401898 GATAATTTTAAACTCCTCATTTGGGGTTATCGGGATACTTTAATGTCGAAGGTATACCTTAAAGA
66 GATAATTTTAAACT-C-C-TTTAGGGTTA-CGAGATACTTTAATGTCGAAAGTATACCTTAAAGA
*
401963 CATTTTCATAA-TTTTC-CTAGAA
127 CATTTTCATAATTTTTCACGAGAA
* * *
401985 TT-GGTTGTCATCGGGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAAGTTCATCCCATTGAT
1 TTAGGTTGTCACCGGGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCCATTTAT
* * * * * * **
402049 GATCATTTTTAAGTCCTTTAGGGTTACGAGATACTTTCATGTTGAAAGTATACCTTAAGGGTATT
66 GATAATTTTAAACTCCTTTAGGGTTACGAGATACTTTAATGTCGAAAGTATACCTTAAAGACATT
** **
402114 TTTGTAATTTTTTTCAAAATCGAGTC
131 TTCATAA--TTTTTC---A-CGAGAA
* * *
402140 TTAGGTTGTCACCGGGATGCTTTTATGCTAAAGGTGGGTATTTAGGATAGGTTCATCCCATTTAT
1 TTAGGTTGTCACCGGGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCCATTTAT
** * *
402205 GACCATTTTCAAGTCCTTTAGGGTTA
66 GATAATTTTAAACTCCTTTAGGGTTA
402231 TCGGAATACT
Statistics
Matches: 204, Mismatches: 33, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
147 37 0.18
148 9 0.04
149 1 0.00
150 6 0.03
151 64 0.31
152 2 0.01
155 5 0.02
156 80 0.39
ACGTcount: A:0.26, C:0.15, G:0.20, T:0.39
Consensus pattern (150 bp):
TTAGGTTGTCACCGGGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAGGTTCATCCCATTTAT
GATAATTTTAAACTCCTTTAGGGTTACGAGATACTTTAATGTCGAAAGTATACCTTAAAGACATT
TTCATAATTTTTCACGAGAA
Found at i:402173 original size:156 final size:157
Alignment explanation
Indices: 401987--402281 Score: 425
Period size: 156 Copynumber: 1.9 Consensus size: 157
401977 TCCTAGAATT
* * *
401987 GGTTGTCATCGGGATGCTTTTATGCCAAAGGTGTGCATTTAGGATAAGTTCATCCCATTGATGAT
1 GGTTGTCACCGGGATGCTTTTATGCCAAAGGTGGGCATTTAGGATAAGTTCATCCCATTGATGAC
* ** *
402052 CATTTTTAAGTCCTTTAGGGTTA-C-GAGATACTTTCATGTTGAAAGTATAC-CTTAAGGGTATT
66 CATTTTCAAGTCCTTTAGGGTTATCGGA-ATACTTTCACATTGAAAGTAGACTC-TAAGGGTATT
*
402114 TTTGTAATTTTTTTCAAAATCGAGTCTTA
129 TTGGTAATTTTTTTCAAAATCGAGTCTTA
* * * *
402143 GGTTGTCACCGGGATGCTTTTATGCTAAAGGTGGGTATTTAGGATAGGTTCATCCCATTTATGAC
1 GGTTGTCACCGGGATGCTTTTATGCCAAAGGTGGGCATTTAGGATAAGTTCATCCCATTGATGAC
* *
402208 CATTTTCAAGTCCTTTAGGGTTATCGGAATACTTTCACATTGAAGGTAGATTCTAAGGGTATTTT
66 CATTTTCAAGTCCTTTAGGGTTATCGGAATACTTTCACATTGAAAGTAGACTCTAAGGGTATTTT
402273 GGTAATTTT
131 GGTAATTTT
402282 ATATTTAACC
Statistics
Matches: 122, Mismatches: 14, Indels: 5
0.87 0.10 0.04
Matches are distributed among these distances:
156 80 0.66
157 39 0.32
158 3 0.02
ACGTcount: A:0.25, C:0.14, G:0.22, T:0.40
Consensus pattern (157 bp):
GGTTGTCACCGGGATGCTTTTATGCCAAAGGTGGGCATTTAGGATAAGTTCATCCCATTGATGAC
CATTTTCAAGTCCTTTAGGGTTATCGGAATACTTTCACATTGAAAGTAGACTCTAAGGGTATTTT
GGTAATTTTTTTCAAAATCGAGTCTTA
Found at i:406165 original size:14 final size:13
Alignment explanation
Indices: 406145--406199 Score: 69
Period size: 14 Copynumber: 4.2 Consensus size: 13
406135 TCATATAAAA
406145 TTTTAATTTAATT
1 TTTTAATTTAATT
406158 TTTATAATTTAATT
1 TTT-TAATTTAATT
406172 TTTT-A-TTAATT
1 TTTTAATTTAATT
406183 TTTTATATTGTAATT
1 TTTTA-ATT-TAATT
406198 TT
1 TT
406200 ACAGATATTA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
11 10 0.27
12 1 0.03
13 5 0.14
14 14 0.38
15 7 0.19
ACGTcount: A:0.29, C:0.00, G:0.02, T:0.69
Consensus pattern (13 bp):
TTTTAATTTAATT
Found at i:406171 original size:25 final size:27
Alignment explanation
Indices: 406143--406200 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 27
406133 GATCATATAA
406143 AATTTTAAT-TTAA-TTTTTATAATT-T
1 AATTTTAATATTAATTTTTTAT-ATTGT
*
406168 AATTTT-TTATTAATTTTTTATATTGT
1 AATTTTAATATTAATTTTTTATATTGT
406194 AATTTTA
1 AATTTTA
406201 CAGATATTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
24 1 0.04
25 13 0.46
26 14 0.50
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.66
Consensus pattern (27 bp):
AATTTTAATATTAATTTTTTATATTGT
Found at i:410554 original size:19 final size:19
Alignment explanation
Indices: 410530--410566 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
410520 TTTTCAAAAA
*
410530 AAAAAAAAGCAAAAAGAAG
1 AAAAAAAAGAAAAAAGAAG
410549 AAAAAAAAGAAAAAAGAA
1 AAAAAAAAGAAAAAAGAA
410567 AATTCAGTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.84, C:0.03, G:0.14, T:0.00
Consensus pattern (19 bp):
AAAAAAAAGAAAAAAGAAG
Found at i:411735 original size:112 final size:113
Alignment explanation
Indices: 411537--411747 Score: 302
Period size: 112 Copynumber: 1.9 Consensus size: 113
411527 AACTTGGAAG
* **
411537 AACATTAAATTTGTCTGGTTTTCAAAGAAATTCATACTTTATACATTCCAATGCATTCGTGCCTA
1 AACATCAAATTTGTCTAATTTTCAAAGAAATTCATACTTTATACATTCCAATGCATTCGTGCCTA
411602 GGAAAATAGGGCATATATCCTATAAGTTCTGAAAGTCTTGAGCCCAAC
66 GGAAAATAGGGCATATATCCTATAAGTTCTGAAAGTCTTGAGCCCAAC
* * *
411650 AACATCAAATTTGTCTAATTTTC-AAGAAATTCATATTTTATACATTTCAAT-CAATTCGTTCCT
1 AACATCAAATTTGTCTAATTTTCAAAGAAATTCATACTTTATACATTCCAATGC-ATTCGTGCCT
* * *
411713 AGGAAAAGTA-GGCATGTATCCTATCAGTTTTGAAA
65 AGGAAAA-TAGGGCATATATCCTATAAGTTCTGAAA
411748 TTTTTAGGCT
Statistics
Matches: 87, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
111 1 0.01
112 64 0.74
113 22 0.25
ACGTcount: A:0.35, C:0.17, G:0.13, T:0.35
Consensus pattern (113 bp):
AACATCAAATTTGTCTAATTTTCAAAGAAATTCATACTTTATACATTCCAATGCATTCGTGCCTA
GGAAAATAGGGCATATATCCTATAAGTTCTGAAAGTCTTGAGCCCAAC
Found at i:413158 original size:44 final size:44
Alignment explanation
Indices: 413109--413361 Score: 144
Period size: 44 Copynumber: 5.8 Consensus size: 44
413099 TATGTTTGAT
* *
413109 ATATGGTTACCACTCTAGTCAAACTCTTCTCATT-TCGGTCTAAC
1 ATATGGTTACCACCCTAGTCAAACTCTTCTCATTCT-GATCTAAC
* * * *
413153 ATATGGTTACCACCCTAGTCAGATTCTTTTCATTCTGATTTAAC
1 ATATGGTTACCACCCTAGTCAAACTCTTCTCATTCTGATCTAAC
* * * * * *
413197 ACATGGTTACCACCTTGGTCAAA-T-TGCCTCATTTCT-ATTTAAT
1 ATATGGTTACCACCCTAGTCAAACTCT-TCTCA-TTCTGATCTAAC
* * * * * *
413240 GTATGGTTACTACCCTGGTCAAACTCTTTTTATGT-TGGAT-TGAC
1 ATATGGTTACCACCCTAGTCAAACTCTTCTCAT-TCT-GATCTAAC
* * * * *
413284 ATATGGATACCACCTTGGTCAGACTCTTCTCATTCCT-A-CTTGAC
1 ATATGGTTACCACCCTAGTCAAACTCTTCTCATT-CTGATC-TAAC
* * * *
413328 GTATGGTTACCACCCTGGTCAAGCTCTTTTCATT
1 ATATGGTTACCACCCTAGTCAAACTCTTCTCATT
413362 TTCGTTTGAT
Statistics
Matches: 162, Mismatches: 35, Indels: 24
0.73 0.16 0.11
Matches are distributed among these distances:
42 1 0.01
43 33 0.20
44 123 0.76
45 5 0.03
ACGTcount: A:0.23, C:0.25, G:0.14, T:0.38
Consensus pattern (44 bp):
ATATGGTTACCACCCTAGTCAAACTCTTCTCATTCTGATCTAAC
Found at i:413269 original size:87 final size:87
Alignment explanation
Indices: 413149--413362 Score: 227
Period size: 87 Copynumber: 2.4 Consensus size: 87
413139 CATTTCGGTC
* * * * *
413149 TAACATATGGTTACCACCCTAGTCAGATTCTTTTCATTCT-GATTTAACACATGGTTACCACCTT
1 TAACGTATGGTTACCACCCTGGTCAAACTCTTTTCATT-TGGA-TTAACACATGGATACCACCTT
* *
413213 GGTCA-AAT-TGCCTCATTTCTATT
64 GGTCAGAATCT-CCTCATTCCTACT
* * * * *
413236 TAATGTATGGTTACTACCCTGGTCAAACTCTTTTTATGTTGGATTGACATATGGATACCACCTTG
1 TAACGTATGGTTACCACCCTGGTCAAACTCTTTTCAT-TTGGATTAACACATGGATACCACCTTG
* *
413301 GTCAGACTCTTCTCATTCCTACT
65 GTCAGAATCTCCTCATTCCTACT
* *
413324 TGACGTATGGTTACCACCCTGGTCAAGCTCTTTTCATTT
1 TAACGTATGGTTACCACCCTGGTCAAACTCTTTTCATTT
413363 TCGTTTGATG
Statistics
Matches: 104, Mismatches: 19, Indels: 8
0.79 0.15 0.06
Matches are distributed among these distances:
87 56 0.54
88 47 0.45
89 1 0.01
ACGTcount: A:0.23, C:0.24, G:0.14, T:0.39
Consensus pattern (87 bp):
TAACGTATGGTTACCACCCTGGTCAAACTCTTTTCATTTGGATTAACACATGGATACCACCTTGG
TCAGAATCTCCTCATTCCTACT
Found at i:413383 original size:88 final size:87
Alignment explanation
Indices: 413240--413405 Score: 194
Period size: 88 Copynumber: 1.9 Consensus size: 87
413230 TCTATTTAAT
* * *
413240 GTATGGTTACTACCCTGGTCAAACTCTTTTTATGTTGGATTGACATATGGATACCAC-CTTGGTC
1 GTATGGTTACCACCCTGGTCAAACTCTTTTCATGTTCGATTGA-ATATGGATACCACTCTT-GTC
*
413304 AGAC-TCTTCTCATTCCTACTTGAC
64 AAACAT-TTCTCATTCCTACTTGAC
* * * *
413328 GTATGGTTACCACCCTGGTCAAGCTCTTTTCATTTTCGTTTG-ATGTGTGATTACCACTCTTGTC
1 GTATGGTTACCACCCTGGTCAAACTCTTTTCATGTTCGATTGAATATG-GA-TACCACTCTTGTC
413392 AAACATTTCTCATT
64 AAACATTTCTCATT
413406 TCAGTCTGGT
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
86 4 0.06
87 2 0.03
88 56 0.85
89 4 0.06
ACGTcount: A:0.20, C:0.23, G:0.16, T:0.40
Consensus pattern (87 bp):
GTATGGTTACCACCCTGGTCAAACTCTTTTCATGTTCGATTGAATATGGATACCACTCTTGTCAA
ACATTTCTCATTCCTACTTGAC
Found at i:413692 original size:42 final size:43
Alignment explanation
Indices: 413628--413765 Score: 117
Period size: 42 Copynumber: 3.3 Consensus size: 43
413618 TCAACTCAAT
* * *
413628 CCCTGGTAAACTCCTTTA-CCCTTTGTTGACTTATTAATTCAG
1 CCCTGGTCAACTCTTTTATCCCTTTGTTGACTTATTGATTCAG
* **
413670 CCCTGGTCAAC-CTTTTATCCCTTAT-TT-ACCTT-GTGGCTCAG
1 CCCTGGTCAACTCTTTTATCCCTT-TGTTGA-CTTATTGATTCAG
* * *
413711 TCCCTAGTGAACTCTTTTAT-CCTTTGTTGACTTATTGATTTAG
1 -CCCTGGTCAACTCTTTTATCCCTTTGTTGACTTATTGATTCAG
*
413754 CCTTGGTCAACT
1 CCCTGGTCAACT
413766 TTTCATCTCT
Statistics
Matches: 73, Mismatches: 15, Indels: 16
0.70 0.14 0.15
Matches are distributed among these distances:
41 12 0.16
42 47 0.64
43 14 0.19
ACGTcount: A:0.18, C:0.26, G:0.14, T:0.42
Consensus pattern (43 bp):
CCCTGGTCAACTCTTTTATCCCTTTGTTGACTTATTGATTCAG
Found at i:413715 original size:84 final size:85
Alignment explanation
Indices: 413622--413865 Score: 302
Period size: 84 Copynumber: 2.9 Consensus size: 85
413612 TGCTTGTCAA
*
413622 CTCAATCCCTGGTAAACTCCTTTACCCTTTGTTGACTTATTAATTCAGCCCTGGTCAACCTTTTA
1 CTCAATCCCTGGTAAACTCCTTTACCCTTTGTTGACTTATTAATTCAGCCTTGGTCAACCTTTTA
413687 TCCCTTATTTACCTTGT-GG
66 TCCCTTATTTACCTTGTCGG
* * * * * * *
413706 CTCAGTCCCTAGTGAACTCTTTTATCCTTTGTTGACTTATTGATTTAGCCTTGGTCAA-CTTTTC
1 CTCAATCCCTGGTAAACTCCTTTACCCTTTGTTGACTTATTAATTCAGCCTTGGTCAACCTTTT-
*
413770 ATCTC-TATTTA-CTTGTCGG
65 ATCCCTTATTTACCTTGTCGG
* *
413789 CTTAATCCCTGGTAAACTTCC-TTACCTTTTGTTGACTTA-TAAGTTCAGCCTTGGTCAACCTTT
1 CTCAATCCCTGGTAAAC-TCCTTTACCCTTTGTTGACTTATTAA-TTCAGCCTTGGTCAACCTTT
* *
413852 CATCCCTTGTTTAC
64 TATCCCTTATTTAC
413866 GTTACCCCTC
Statistics
Matches: 132, Mismatches: 21, Indels: 13
0.80 0.13 0.08
Matches are distributed among these distances:
82 7 0.05
83 60 0.45
84 65 0.49
ACGTcount: A:0.18, C:0.26, G:0.13, T:0.43
Consensus pattern (85 bp):
CTCAATCCCTGGTAAACTCCTTTACCCTTTGTTGACTTATTAATTCAGCCTTGGTCAACCTTTTA
TCCCTTATTTACCTTGTCGG
Found at i:413822 original size:83 final size:82
Alignment explanation
Indices: 413622--413865 Score: 280
Period size: 83 Copynumber: 2.9 Consensus size: 82
413612 TGCTTGTCAA
*
413622 CTCAATCCCTGGTAAACTCCTTTACCCTTTGTTGACTTATTAATTCAGCCCTGGTCAACCTTTT-
1 CTCAATCCCTGGTAAACTCC-TTA-CCTTTGTTGACTTATTAATTCAGCCTTGGTCAA-CTTTTC
413686 ATCCCTTATTTACCTTGTGG
63 ATCCCTTATTTACCTTGTGG
* * * * * *
413706 CTCAGTCCCTAGTGAACTCTTTTATCCTTTGTTGACTTATTGATTTAGCCTTGGTCAACTTTTCA
1 CTCAATCCCTGGTAAACTC-CTTA-CCTTTGTTGACTTATTAATTCAGCCTTGGTCAACTTTTCA
*
413771 TCTC-TATTTA-CTTGTCGG
64 TCCCTTATTTACCTTGT-GG
* *
413789 CTTAATCCCTGGTAAACTTCCTTACCTTTTGTTGACTTA-TAAGTTCAGCCTTGGTCAACCTTTC
1 CTCAATCCCTGGTAAAC-TCCTTACC-TTTGTTGACTTATTAA-TTCAGCCTTGGTCAACTTTTC
*
413853 ATCCCTTGTTTAC
63 ATCCCTTATTTAC
413866 GTTACCCCTC
Statistics
Matches: 133, Mismatches: 19, Indels: 15
0.80 0.11 0.09
Matches are distributed among these distances:
82 9 0.07
83 64 0.48
84 60 0.45
ACGTcount: A:0.18, C:0.26, G:0.13, T:0.43
Consensus pattern (82 bp):
CTCAATCCCTGGTAAACTCCTTACCTTTGTTGACTTATTAATTCAGCCTTGGTCAACTTTTCATC
CCTTATTTACCTTGTGG
Found at i:414384 original size:83 final size:83
Alignment explanation
Indices: 414176--414412 Score: 196
Period size: 83 Copynumber: 2.8 Consensus size: 83
414166 ACCTAGGCTA
* * * * *
414176 AACCGACAAGCCAAAAAAGGATAAAAGGATTTACCCGAGACTAATCCGATAGGTAAACAA-AGGA
1 AACCGACAAGTC-AATAAGGATAAAA-GATTTACCCGAGACTAAACCGACAAGTAAACAAGA-GA
* * * *
414240 T-GAAAGATTGATTAGGATTG
63 TAAAAAGACTAATTAGGATCG
** * * ** * *
414260 GGCCAATGAA-TCAATAATGGATAAAAGATTTACTTGGGACTAAGCCGACAAGTAAACAAGAGAT
1 AACCGA-CAAGTCAATAA-GGATAAAAGATTTACCCGAGACTAAACCGACAAGTAAACAAGAGAT
414324 AAAAAG-CTAATTAGGATCG
64 AAAAAGACTAATTAGGATCG
* * *
414343 AACCGACAAGTCAATAGAGGATAAAAGATTTACCCGAGACTAAACTGACATGTAAATAATG-GAT
1 AACCGACAAGTCAATA-AGGATAAAAGATTTACCCGAGACTAAACCGACAAGTAAACAA-GAGAT
414407 AAAAAG
64 AAAAAG
414413 TTAACCAGGA
Statistics
Matches: 119, Mismatches: 27, Indels: 15
0.74 0.17 0.09
Matches are distributed among these distances:
82 2 0.02
83 96 0.81
84 19 0.16
85 2 0.02
ACGTcount: A:0.46, C:0.14, G:0.21, T:0.19
Consensus pattern (83 bp):
AACCGACAAGTCAATAAGGATAAAAGATTTACCCGAGACTAAACCGACAAGTAAACAAGAGATAA
AAAGACTAATTAGGATCG
Found at i:414981 original size:88 final size:88
Alignment explanation
Indices: 414850--415265 Score: 428
Period size: 88 Copynumber: 4.7 Consensus size: 88
414840 GCAAATCATA
* * ** * * *
414850 TGACCAAGGTGGTAACCATACATCAAATTAGAATTAAAAGAATCTAACCAAGGTGGTAACCCTAC
1 TGACTAAGGTGGTAACCATACGTCAAATCGGAATGAAAAGAATCTGACCAAGGTGGTAACCATA-
414915 T-TTAGACAAGAA-ATAGGCAGATT
65 TGTTAGACAAGAAGA-AGGCAGATT
* * * * * * *
414938 TGACTAGGGTGGTAACCATACGTCAAATCGGAATGAAACGAATCTGACTAGGGTGGAAACCACAC
1 TGACTAAGGTGGTAACCATACGTCAAATCGGAATGAAAAGAATCTGACCAAGGTGGTAACCATAT
* * * * * *
415003 GTCAGA-TAGAAAGGATGCAAACT
66 GTTAGACAAG-AAGAAGGCAGATT
* * * *
415026 TGA-TCAGGGTGGTAACCATACGTCAAATCGAAATGAAAAGAATCTGACTAGGGTGGTAACCATA
1 TGACT-AAGGTGGTAACCATACGTCAAATCGGAATGAAAAGAATCTGACCAAGGTGGTAACCATA
* *
415090 TGCTAGACAAGAAGAAGGCATATT
65 TGTTAGACAAGAAGAAGGCAGATT
* ** *
415114 TCAAAAAGGTGGTAACCATAC-TACAAATCAGAATGAAAAGAATCTGACCAAGGTGGTAACCATA
1 TGACTAAGGTGGTAACCATACGT-CAAATCGGAATGAAAAGAATCTGACCAAGGTGGTAACCATA
*
415178 TGTTAGAGAAGAAGAAGGCAGATT
65 TGTTAGACAAGAAGAAGGCAGATT
* * * * *
415202 TAACCAAGGTGGTAACCATATGTCAAATCGAAATGAAAAAAATCTGACCAAGGTGGTAACCATA
1 TGACTAAGGTGGTAACCATACGTCAAATCGGAATGAAAAGAATCTGACCAAGGTGGTAACCATA
415266 CATCAAATTG
Statistics
Matches: 271, Mismatches: 49, Indels: 16
0.81 0.15 0.05
Matches are distributed among these distances:
87 4 0.01
88 264 0.97
89 3 0.01
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.20
Consensus pattern (88 bp):
TGACTAAGGTGGTAACCATACGTCAAATCGGAATGAAAAGAATCTGACCAAGGTGGTAACCATAT
GTTAGACAAGAAGAAGGCAGATT
Found at i:414986 original size:44 final size:44
Alignment explanation
Indices: 414938--415397 Score: 239
Period size: 44 Copynumber: 10.5 Consensus size: 44
414928 TAGGCAGATT
*
414938 TGACTAGGGTGGTAACCATACGTCAAATCGGAATGAAACGAATC
1 TGACTAGGGTGGTAACCATACGTCAAATCGGAATGAAAAGAATC
* * * * * * * *
414982 TGACTAGGGTGGAAACCACACGTCAGAT-AGAAAG-GATGCAAAC
1 TGACTAGGGTGGTAACCATACGTCAAATCGGAATGAAAAG-AATC
*
415025 TTGA-TCAGGGTGGTAACCATACGTCAAATCGAAATGAAAAGAATC
1 -TGACT-AGGGTGGTAACCATACGTCAAATCGGAATGAAAAGAATC
* * *
415070 TGACTAGGGTGGTAACCATATG-CTAGA-C--AA-GAAGAAGGCATATT
1 TGACTAGGGTGGTAACCATACGTC-AAATCGGAATGAA-AA-G-A-ATC
* ** * *
415114 TCAAAAAGGTGGTAACCATAC-TACAAATCAGAATGAAAAGAATC
1 TGACTAGGGTGGTAACCATACGT-CAAATCGGAATGAAAAGAATC
* * * * * *
415158 TGACCAAGGTGGTAACCATATGTTAGA---GAA-GAAGAAGGCAGATT
1 TGACTAGGGTGGTAACCATACGTCAAATCGGAATGAA-AA-G-A-ATC
* * * * * *
415202 TAACCAAGGTGGTAACCATATGTCAAATCGAAATGAAAAAAATC
1 TGACTAGGGTGGTAACCATACGTCAAATCGGAATGAAAAGAATC
* * * * *
415246 TGACCAAGGTGGTAACCATACATCAAATTGAAATGAAAAGAATC
1 TGACTAGGGTGGTAACCATACGTCAAATCGGAATGAAAAGAATC
* * * ** * ** *
415290 TAACCAGAGTGGTAACCATACGTCAAATAAGAAGGATGTAGACT-
1 TGACTAGGGTGGTAACCATACGTCAAATCGGAATGA-AAAGAATC
* * *
415334 TGACTACGGTGGTAACCATATGTCAAATTGGAATGAAAAGAATC
1 TGACTAGGGTGGTAACCATACGTCAAATCGGAATGAAAAGAATC
* *
415378 T-AGCCAAGGTGGTAACCATA
1 TGA-CTAGGGTGGTAACCATA
415398 TGCCATACAA
Statistics
Matches: 318, Mismatches: 69, Indels: 58
0.71 0.16 0.13
Matches are distributed among these distances:
40 6 0.02
41 9 0.03
42 4 0.01
43 17 0.05
44 249 0.78
45 16 0.05
46 3 0.01
47 8 0.03
48 6 0.02
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.20
Consensus pattern (44 bp):
TGACTAGGGTGGTAACCATACGTCAAATCGGAATGAAAAGAATC
Found at i:415151 original size:176 final size:176
Alignment explanation
Indices: 414852--415266 Score: 471
Period size: 176 Copynumber: 2.4 Consensus size: 176
414842 AAATCATATG
* * * * *
414852 ACCAAGGTGGTAACCATACATCAAAT-TAGAATTAAAAGAATCTAACCAAGGTGGTAACCCTACT
1 ACCAAGGTGGTAACCATACGTCAAATCGA-AATGAAAAGAATCTGACCAAGGTGGTAACCATACT
* * ** * * *
414916 TTAGACAAGAAATAGGCAGATTTGACTAGGGTGGTAACCATACGTCAAATCGGAATGAAACGAAT
65 CTAGACAAGAAATAGGCAGATTTCAAAAAGGTGGTAACCATACGTCAAATCAGAATGAAAAGAAT
* * * * * *
414981 CTGACTAGGGTGGAAACCACACGTCAGA-TAGAAAGGATGCAAACTTG
130 CTGACCAAGGTGGAAACCACACGTCAGAGAAG-AAGAAGGCAAACTTA
* * * *
415028 ATCAGGGTGGTAACCATACGTCAAATCGAAATGAAAAGAATCTGACTAGGGTGGTAACCATA-TG
1 ACCAAGGTGGTAACCATACGTCAAATCGAAATGAAAAGAATCTGACCAAGGTGGTAACCATACT-
*
415092 CTAGACAAGAAGA-AGGCATATTTCAAAAAGGTGGTAACCATAC-TACAAATCAGAATGAAAAGA
65 CTAGACAAGAA-ATAGGCAGATTTCAAAAAGGTGGTAACCATACGT-CAAATCAGAATGAAAAGA
* * * * * *
415155 ATCTGACCAAGGTGGTAACCATATGTTAGAGAAGAAGAAGGCAGATTTA
128 ATCTGACCAAGGTGGAAACCACACGTCAGAGAAGAAGAAGGCAAACTTA
* *
415204 ACCAAGGTGGTAACCATATGTCAAATCGAAATGAAAAAAATCTGACCAAGGTGGTAACCATAC
1 ACCAAGGTGGTAACCATACGTCAAATCGAAATGAAAAGAATCTGACCAAGGTGGTAACCATAC
415267 ATCAAATTGA
Statistics
Matches: 198, Mismatches: 35, Indels: 11
0.81 0.14 0.05
Matches are distributed among these distances:
175 2 0.01
176 192 0.97
177 4 0.02
ACGTcount: A:0.41, C:0.16, G:0.22, T:0.20
Consensus pattern (176 bp):
ACCAAGGTGGTAACCATACGTCAAATCGAAATGAAAAGAATCTGACCAAGGTGGTAACCATACTC
TAGACAAGAAATAGGCAGATTTCAAAAAGGTGGTAACCATACGTCAAATCAGAATGAAAAGAATC
TGACCAAGGTGGAAACCACACGTCAGAGAAGAAGAAGGCAAACTTA
Found at i:415281 original size:132 final size:132
Alignment explanation
Indices: 415119--415397 Score: 350
Period size: 132 Copynumber: 2.1 Consensus size: 132
415109 ATATTTCAAA
* * *
415119 AAGGTGGTAACCATACTACAAATCAGAATGAAAAGAATCTGACCA-AGGTGGTAACCATATGTTA
1 AAGGTGGTAACCATACTACAAATCAGAATGAAAAGAATCTAACCAGA-GTGGTAACCATACGTCA
* *
415183 GAGAAGAAGAAGGCAGATTTAACCAAGGTGGTAACCATATGTCAAATCGAAATGAAAAAAATCT-
65 AAGAAGAAGAAGGCAGACTTAACCAAGGTGGTAACCATATGTCAAATCGAAATGAAAAAAATCTA
415247 GACC
130 G-CC
*
415251 AAGGTGGTAACCATAC-ATCAAAT-TGAAATGAAAAGAATCTAACCAGAGTGGTAACCATACGTC
1 AAGGTGGTAACCATACTA-CAAATCAG-AATGAAAAGAATCTAACCAGAGTGGTAACCATACGTC
* * * * * * * * * *
415314 AAATAAGAAGGATGTAGACTTGACTACGGTGGTAACCATATGTCAAATTGGAATGAAAAGAATCT
64 AAAGAAGAAGAAGGCAGACTTAACCAAGGTGGTAACCATATGTCAAATCGAAATGAAAAAAATCT
415379 AGCC
129 AGCC
415383 AAGGTGGTAACCATA
1 AAGGTGGTAACCATA
415398 TGCCATACAA
Statistics
Matches: 127, Mismatches: 16, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
131 2 0.02
132 123 0.97
133 2 0.02
ACGTcount: A:0.43, C:0.15, G:0.22, T:0.21
Consensus pattern (132 bp):
AAGGTGGTAACCATACTACAAATCAGAATGAAAAGAATCTAACCAGAGTGGTAACCATACGTCAA
AGAAGAAGAAGGCAGACTTAACCAAGGTGGTAACCATATGTCAAATCGAAATGAAAAAAATCTAG
CC
Found at i:415294 original size:88 final size:87
Alignment explanation
Indices: 415033--415399 Score: 285
Period size: 88 Copynumber: 4.2 Consensus size: 87
415023 ACTTGATCAG
* * *
415033 GGTGGTAACCATACGTCAAATCGAAATGAAAAGAATCTGACTAGGGTGGTAACCATATG-CTAGA
1 GGTGGTAACCATATGTCAAATCGAAATGAAAAGAATCTGACCAAGGTGGTAACCATATGTC-A-A
* * * *
415097 CA-AGAA-G-AAGGCATATTTCAA-AAA
64 -ATTGAATGAAAAG-A-ATCT-AACCAA
* * *
415121 GGTGGTAACCATACT-ACAAATC-AGAATGAAAAGAATCTGACCAAGGTGGTAACCATATGTTAG
1 GGTGGTAACCATA-TGTCAAATCGA-AATGAAAAGAATCTGACCAAGGTGGTAACCATATGTCAA
*
415184 A--GAA-GAAGAAGGCAGATTTAACCAA
64 ATTGAATGAA-AA-G-A-ATCTAACCAA
* **
415209 GGTGGTAACCATATGTCAAATCGAAATGAAAAAAATCTGACCAAGGTGGTAACCATACATCAAAT
1 GGTGGTAACCATATGTCAAATCGAAATGAAAAGAATCTGACCAAGGTGGTAACCATATGTCAAAT
415274 TGAAATGAAAAGAATCTAACC-A
66 TG-AATGAAAAGAATCTAACCAA
* * * * * *
415296 GAGTGGTAACCATACGTCAAATAAGAAGGATG--TAGACT-TGACTACGGTGGTAACCATATGTC
1 G-GTGGTAACCATATGTCAAAT-CGAA--ATGAAAAGAATCTGACCAAGGTGGTAACCATATGTC
*
415358 AAATTGGAATGAAAAGAATCTAGCCAA
62 AAATT-GAATGAAAAGAATCTAACCAA
415385 GGTGGTAACCATATG
1 GGTGGTAACCATATG
415400 CCATACAAGA
Statistics
Matches: 233, Mismatches: 27, Indels: 38
0.78 0.09 0.13
Matches are distributed among these distances:
85 4 0.02
86 2 0.01
87 7 0.03
88 197 0.85
89 11 0.05
90 2 0.01
91 7 0.03
92 3 0.01
ACGTcount: A:0.42, C:0.15, G:0.22, T:0.21
Consensus pattern (87 bp):
GGTGGTAACCATATGTCAAATCGAAATGAAAAGAATCTGACCAAGGTGGTAACCATATGTCAAAT
TGAATGAAAAGAATCTAACCAA
Found at i:415410 original size:88 final size:88
Alignment explanation
Indices: 415253--415460 Score: 240
Period size: 88 Copynumber: 2.4 Consensus size: 88
415243 ATCTGACCAA
** * *
415253 GGTGGTAACCATACATCAAATTGAAATGAAAAGAATCTAACCAGAGTGGTAACCATACGTCAAAT
1 GGTGGTAACCATATGTCAAATTGAAATGAAAAGAATCTAACCAGAGTGGTAACCATACGCCAAAC
* * *
415318 AAGAAGGATG-TAGACTTGACTAC
66 AAGAA-GAAGACAAACTTGACTAC
* * * *
415341 GGTGGTAACCATATGTCAAATTGGAATGAAAAGAATCTAGCCA-AGGTGGTAACCATATGCCATA
1 GGTGGTAACCATATGTCAAATTGAAATGAAAAGAATCTAACCAGA-GTGGTAACCATACGCCAAA
* * *
415405 CAAGAAGAAGACAAATTTGATTAG
65 CAAGAAGAAGACAAACTTGACTAC
* *
415429 GGTGGTAACCATGTGTCAAATCGAAATGAAAA
1 GGTGGTAACCATATGTCAAATTGAAATGAAAA
415461 AGGTGGTAAC
Statistics
Matches: 101, Mismatches: 17, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
87 4 0.04
88 97 0.96
ACGTcount: A:0.41, C:0.14, G:0.22, T:0.22
Consensus pattern (88 bp):
GGTGGTAACCATATGTCAAATTGAAATGAAAAGAATCTAACCAGAGTGGTAACCATACGCCAAAC
AAGAAGAAGACAAACTTGACTAC
Found at i:415641 original size:44 final size:44
Alignment explanation
Indices: 415583--415733 Score: 153
Period size: 44 Copynumber: 3.4 Consensus size: 44
415573 AATGAGGCAG
*
415583 ATTTGACCAGGGTGGGT-ACCATACATCAAATCAAAAAGAAAAGA
1 ATTTGACCAAGGT-GGTAACCATACATCAAATCAAAAAGAAAAGA
* * * ** **
415627 ATTTGACCAAGGTGGTAACCATACGTCAGAT-AGGAGGGAGGCAGA
1 ATTTGACCAAGGTGGTAACCATACATCAAATCA-AAAAGA-AAAGA
* * *
415672 TTTTGACCAAAGTGGTAACCATACATCAAATCAAAATGAAAAGA
1 ATTTGACCAAGGTGGTAACCATACATCAAATCAAAAAGAAAAGA
*
415716 ATCTGACCAAGGTGGTAA
1 ATTTGACCAAGGTGGTAA
415734 TTATAGACAC
Statistics
Matches: 83, Mismatches: 20, Indels: 8
0.75 0.18 0.07
Matches are distributed among these distances:
43 4 0.05
44 45 0.54
45 33 0.40
46 1 0.01
ACGTcount: A:0.41, C:0.16, G:0.23, T:0.20
Consensus pattern (44 bp):
ATTTGACCAAGGTGGTAACCATACATCAAATCAAAAAGAAAAGA
Found at i:415704 original size:89 final size:88
Alignment explanation
Indices: 415460--415733 Score: 331
Period size: 87 Copynumber: 3.1 Consensus size: 88
415450 CGAAATGAAA
* * * ** *
415460 AAGGTGGTAACCATACGTTAGATAAGAGAGAGGTAGATTTGA-CTAGGATGGTAACCATATGTTA
1 AAGGTGGTAACCATACGTCAGATAAGAGAGAGGCAGATTTGACCAAGG-TGGTAACCATACATCA
* **
415524 AATCGAAATGAAAAGAATCTGAAT
65 AATCAAAATGAAAAGAATCTGACC
* * *
415548 AAGGTGGTAACCATAAG-CAGACAAGA-ATGAGGCAGATTTGACCAGGGTGGGT-ACCATACATC
1 AAGGTGGTAACCATACGTCAGATAAGAGA-GAGGCAGATTTGACCAAGGT-GGTAACCATACATC
* *
415610 AAATCAAAAAGAAAAGAATTTGACC
64 AAATCAAAATGAAAAGAATCTGACC
* * *
415635 AAGGTGGTAACCATACGTCAGATAGGAGGGAGGCAGATTTTGACCAAAGTGGTAACCATACATCA
1 AAGGTGGTAACCATACGTCAGATAAGAGAGAGGCAGA-TTTGACCAAGGTGGTAACCATACATCA
415700 AATCAAAATGAAAAGAATCTGACC
65 AATCAAAATGAAAAGAATCTGACC
415724 AAGGTGGTAA
1 AAGGTGGTAA
415734 TTATAGACAC
Statistics
Matches: 157, Mismatches: 22, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
86 1 0.01
87 63 0.40
88 40 0.25
89 53 0.34
ACGTcount: A:0.41, C:0.14, G:0.25, T:0.20
Consensus pattern (88 bp):
AAGGTGGTAACCATACGTCAGATAAGAGAGAGGCAGATTTGACCAAGGTGGTAACCATACATCAA
ATCAAAATGAAAAGAATCTGACC
Found at i:416077 original size:20 final size:20
Alignment explanation
Indices: 416033--416106 Score: 85
Period size: 21 Copynumber: 3.6 Consensus size: 20
416023 TTTCATAATT
* *
416033 TGTATCGATACAAATAGTAAA
1 TGTATCGATACATA-AGTGAA
416054 TGTATCGATACATAAGTGAA
1 TGTATCGATACATAAGTGAA
***
416074 TGTATCGATACATGCCTGAAA
1 TGTATCGATACATAAGTG-AA
416095 TGTATCGATACA
1 TGTATCGATACA
416107 AAACCACTCT
Statistics
Matches: 47, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
20 20 0.43
21 27 0.57
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.30
Consensus pattern (20 bp):
TGTATCGATACATAAGTGAA
Done.