Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold326
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: 1352760
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
File 8 of 8
Found at i:1235770 original size:156 final size:153
Alignment explanation
Indices: 1235395--1235978 Score: 518
Period size: 156 Copynumber: 3.8 Consensus size: 153
1235385 CGAGATTGTT
* * *
1235395 TTTTATGCCAAATGTGTGCATTTAGGATAGGTTAGTTATTTTCCTTATCTTTTTTATATCTTTAA
1 TTTTATGCCAAAGGTGTGCATTTAGGATAGGTTAGTCATTTTCCTTATC-TTTTTATATCTTTTA
* * * * * *
1235460 GGGTTATTAAGATACTTTTATGTTGAAGGTATACATACCTCAAG-GGTATTTTGGTAATTTTTCT
65 GGGTTATCAAGATACTTTCATGTTAAAAGTATAC-T--CT-AAGAGGCATTTTGGTAATTTCTCT
*
1235524 AGAATCGAGT-CTTAG--GTCATAGTTGC
126 AGAAT-GAGTCCTAAGTCGTCATAGTTGC
* * *
1235550 TTTTATGCCAAAGGTGTGCATCCTA--ATAAGTTAGTCCTTTTCCTTATCTTTTTCATATCTTTT
1 TTTTATGCCAAAGGTGTGCAT-TTAGGATAGGTTAGTCATTTTCCTTATCTTTTT-ATATCTTTT
*
1235613 AGGGTTATCAAGATATTTTCATGTTAAAAGTATACTCTAAGA-GCATTTTGGTAATTTCTCTAGA
64 AGGGTTATCAAGATACTTTCATGTTAAAAGTATACTCTAAGAGGCATTTTGGTAATTTCTCTAGA
* *
1235677 ACTGAGTCCTAAGTCGTCATTGGGTTAC
129 A-TGAGTCCTAAGTCGTCA-T-AGTTGC
* * *
1235705 TTTTATGCCAAAGGTGGGCATTTAGGATAGGTTAGTCATTTTCTTTATCTTTTTAATGTCTTTTA
1 TTTTATGCCAAAGGTGTGCATTTAGGATAGGTTAGTCATTTTCCTTATCTTTTT-ATATCTTTTA
** * * * *
1235770 GAATTAGT-AAGATACTTTCAT-TTCAAAAATATACCCT-AGAGGCATTTTGATAATTTCTTTAG
65 GGGTTA-TCAAGATACTTTCATGTT-AAAAGTATACTCTAAGAGGCATTTTGGTAATTTCTCTAG
* * *
1235832 AATTGAGTCCTAGGTCGTCACCAAGTCGC
128 AA-TGAGTCCTAAGTCGTCA--TAGTTGC
* * * * *
1235861 TTTTATGCCAAAGGTGTG-TTTTCAAGATAGGTTCA-TCATTTT-ATTATCTTTTTGTGTGC-TT
1 TTTTATGCCAAAGGTGTGCATTT-AGGATAGGTT-AGTCATTTTCCTTATCTTTTTATAT-CTTT
** * * *
1235922 TAGGGTTA-CCGGAATACTTTCACGTCAAAACTATAC-CTAA-AGGCATTTTGGTAATTT
63 TAGGGTTATCAAG-ATACTTTCATGTTAAAAGTATACTCTAAGAGGCATTTTGGTAATTT
1235979 TTCAGATCGA
Statistics
Matches: 357, Mismatches: 50, Indels: 46
0.79 0.11 0.10
Matches are distributed among these distances:
150 28 0.08
151 7 0.02
153 29 0.08
154 91 0.25
155 64 0.18
156 136 0.38
157 2 0.01
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.42
Consensus pattern (153 bp):
TTTTATGCCAAAGGTGTGCATTTAGGATAGGTTAGTCATTTTCCTTATCTTTTTATATCTTTTAG
GGTTATCAAGATACTTTCATGTTAAAAGTATACTCTAAGAGGCATTTTGGTAATTTCTCTAGAAT
GAGTCCTAAGTCGTCATAGTTGC
Found at i:1235926 original size:310 final size:307
Alignment explanation
Indices: 1235395--1235978 Score: 639
Period size: 310 Copynumber: 1.9 Consensus size: 307
1235385 CGAGATTGTT
* * * *
1235395 TTTTATGCCAAATGTGTGCATTTAGGATAGGTTAGTTATTTTCCTTATCTTTTTTATATCTTTAA
1 TTTTATGCCAAAGGTGGGCATTTAGGATAGGTTAGTCATTTTCCTTATCTTTTTAATATCTTTAA
** * * * * * *
1235460 GGGTTATTAAGATACTTTTATGTTGAAGGTATACATACCTCAAGGGTATTTTGGTAATTTTTCTA
66 GAATTAGTAAGATACTTTCATGTTCAA-G-AAACATACCTCAAGGGCATTTTGATAATTTTTCTA
* * * * *
1235525 GAATCGAGTCTTAGGTCATAGTTGCTTTTATGCCAAAGGTGTGCATCCTAATAAGTTAGTCCTTT
129 GAATCGAGTCCTAGGTCAAAGTCGCTTTTATGCCAAAGGTGTGCATCCAAATAAGTTAGTCATTT
* * * * *
1235590 TCCTTATCTTTTTCATATCTTTTAGGGTTATCAAG-ATATTTTCATGTTAAAAGTATACTCT-AA
194 TCATTATCTTTTTCATATCTTTTAGGGTTA-CAAGAATACTTTCACGTCAAAACTATAC-CTAAA
1235653 GAGCATTTTGGTAATTTCTCTAGAACTGAGTCCTAAGTCGTCATTGGGTTAC
257 G-GCATTTTGGTAATTTCTCTAGAACTGAGTCCTAAGTCGTCATTGGGTTAC
* * *
1235705 TTTTATGCCAAAGGTGGGCATTTAGGATAGGTTAGTCATTTTCTTTATCTTTTTAATGTCTTTTA
1 TTTTATGCCAAAGGTGGGCATTTAGGATAGGTTAGTCATTTTCCTTATCTTTTTAATATCTTTAA
* *
1235770 GAATTAGTAAGATACTTTCAT-TTCAA-AAATATACC-CTAGAGGCATTTTGATAATTTCTT-TA
66 GAATTAGTAAGATACTTTCATGTTCAAGAAACATACCTCAAG-GGCATTTTGATAATTT-TTCTA
* ** * *
1235831 GAATTGAGTCCTAGGTCGTCACCAAGTCGCTTTTATGCCAAAGGTGTGTTTTCAAGATAGGTTCA
129 GAATCGAGTCCTA-G--GTCA--AAGTCGCTTTTATGCCAAAGGTGTGCATCCAA-ATAAGTT-A
* * **
1235896 -TCATTTT-ATTATCTTTTT-GTGTGC-TTTAGGGTTACCGGAATACTTTCACGTCAAAACTATA
187 GTCATTTTCATTATCTTTTTCATAT-CTTTTAGGGTTACAAGAATACTTTCACGTCAAAACTATA
1235957 CCTAAAGGCATTTTGGTAATTT
251 CCTAAAGGCATTTTGGTAATTT
1235979 TTCAGATCGA
Statistics
Matches: 226, Mismatches: 36, Indels: 25
0.79 0.13 0.09
Matches are distributed among these distances:
305 3 0.01
306 34 0.15
307 3 0.01
309 27 0.12
310 109 0.48
311 37 0.16
312 12 0.05
313 1 0.00
ACGTcount: A:0.26, C:0.14, G:0.17, T:0.42
Consensus pattern (307 bp):
TTTTATGCCAAAGGTGGGCATTTAGGATAGGTTAGTCATTTTCCTTATCTTTTTAATATCTTTAA
GAATTAGTAAGATACTTTCATGTTCAAGAAACATACCTCAAGGGCATTTTGATAATTTTTCTAGA
ATCGAGTCCTAGGTCAAAGTCGCTTTTATGCCAAAGGTGTGCATCCAAATAAGTTAGTCATTTTC
ATTATCTTTTTCATATCTTTTAGGGTTACAAGAATACTTTCACGTCAAAACTATACCTAAAGGCA
TTTTGGTAATTTCTCTAGAACTGAGTCCTAAGTCGTCATTGGGTTAC
Found at i:1246704 original size:21 final size:21
Alignment explanation
Indices: 1246671--1246720 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
1246661 TTGCAAGTTG
*
1246671 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
1246693 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
1246714 AAATAAA
1 AAATAAA
1246721 AACTTGCATA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:1250587 original size:13 final size:13
Alignment explanation
Indices: 1250569--1250607 Score: 78
Period size: 13 Copynumber: 3.0 Consensus size: 13
1250559 ACATTTTTCT
1250569 TTGTATCGATACA
1 TTGTATCGATACA
1250582 TTGTATCGATACA
1 TTGTATCGATACA
1250595 TTGTATCGATACA
1 TTGTATCGATACA
1250608 GGGTGATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1259352 original size:32 final size:32
Alignment explanation
Indices: 1259308--1259370 Score: 99
Period size: 32 Copynumber: 2.0 Consensus size: 32
1259298 TAATTTAATT
* *
1259308 TATTTTTTATTAATATTTAATAATAAAAATAA
1 TATTTTTAATTAAAATTTAATAATAAAAATAA
*
1259340 TATTTTTAATTAAAATTTAATTATAAAAATA
1 TATTTTTAATTAAAATTTAATAATAAAAATA
1259371 TATAAATATT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (32 bp):
TATTTTTAATTAAAATTTAATAATAAAAATAA
Found at i:1259354 original size:18 final size:19
Alignment explanation
Indices: 1259318--1259425 Score: 70
Period size: 18 Copynumber: 5.9 Consensus size: 19
1259308 TATTTTTTAT
1259318 TAATATTTAATAATAAAAA
1 TAATATTTAATAATAAAAA
* *
1259337 TAATATTT-TTAATTAAAA
1 TAATATTTAATAATAAAAA
* *
1259355 T-TTAATT-ATAA-AAATATA
1 TAATATTTAATAATAAA-A-A
1259373 TAA-ATATTAA-AATAAAAA
1 TAATAT-TTAATAATAAAAA
* *
1259391 TAATATATTAATAATATAAT
1 TAATAT-TTAATAATAAAAA
1259411 TAATA-TTAA-AATAAA
1 TAATATTTAATAATAAA
1259426 TTTTTAAATT
Statistics
Matches: 70, Mismatches: 11, Indels: 18
0.71 0.11 0.18
Matches are distributed among these distances:
16 2 0.03
17 13 0.19
18 20 0.29
19 20 0.29
20 15 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (19 bp):
TAATATTTAATAATAAAAA
Found at i:1259376 original size:23 final size:24
Alignment explanation
Indices: 1259346--1259397 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 24
1259336 ATAATATTTT
*
1259346 TAAT-TAAAAT-TTAATTATAAAAA
1 TAATATAAAATATTAA-AATAAAAA
1259369 T-ATAT-AAATATTAAAATAAAAA
1 TAATATAAAATATTAAAATAAAAA
1259391 TAATATA
1 TAATATA
1259398 TTAATAATAT
Statistics
Matches: 24, Mismatches: 1, Indels: 7
0.75 0.03 0.22
Matches are distributed among these distances:
22 14 0.58
23 10 0.42
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (24 bp):
TAATATAAAATATTAAAATAAAAA
Found at i:1259409 original size:22 final size:22
Alignment explanation
Indices: 1259361--1259409 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
1259351 AAAATTTAAT
*
1259361 TATAAAAATATATAAATATTAA
1 TATAAAAATATATAAATAATAA
* *
1259383 AATAAAAATA-ATATATTAATAA
1 TATAAAAATATATA-AATAATAA
1259405 TATAA
1 TATAA
1259410 TTAATATTAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (22 bp):
TATAAAAATATATAAATAATAA
Found at i:1259414 original size:54 final size:55
Alignment explanation
Indices: 1259319--1259423 Score: 128
Period size: 54 Copynumber: 1.9 Consensus size: 55
1259309 ATTTTTTATT
* *
1259319 AATATTTAATAATAAAAATAATATTTTTAATTAAAATTTAATTATAAAAATATATA
1 AATATTTAATAATAAAAATAATATTATTAATTAAAAATTAA-TATAAAAATATATA
*
1259375 AATA-TTAA-AATAAAAATAATA-TATTAA-TAATATAATTAATATTAAAATA
1 AATATTTAATAATAAAAATAATATTATTAATTAA-A-AATTAATATAAAAATA
1259424 AATTTTTAAA
Statistics
Matches: 44, Mismatches: 3, Indels: 7
0.81 0.06 0.13
Matches are distributed among these distances:
52 3 0.07
53 15 0.34
54 18 0.41
55 4 0.09
56 4 0.09
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (55 bp):
AATATTTAATAATAAAAATAATATTATTAATTAAAAATTAATATAAAAATATATA
Found at i:1262332 original size:79 final size:79
Alignment explanation
Indices: 1262165--1262368 Score: 214
Period size: 79 Copynumber: 2.6 Consensus size: 79
1262155 GAGATAATAA
* * ** * *
1262165 CGGGGTTGGAGTGTTCCCTT-GAAAATAACGGGGCTGGAGTATCCCCGGTTGTGAGAAATCGATG
1 CGGGGTTGGAGT-ATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATG
*
1262229 ATTAGAAAAAAAAAT
65 ATTAGAAAAAAAAAC
* *
1262244 CGGGATTGGAGTATCCCTTCGAAAATAGCGGGGTTGGAGTATCCCCAATTATGAGAAATCAAT-A
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATGA
* ** * *
1262308 TTTTGGGAATAAAGC
66 -TTAGAAAAAAAAAC
* * * *
1262323 CGGGGTTGGAGTATCCCCTCGGAAGTAATGGGGTTGGAGTATCCCC
1 CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCC
1262369 GATGAAATAA
Statistics
Matches: 103, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
78 7 0.07
79 96 0.93
ACGTcount: A:0.28, C:0.16, G:0.30, T:0.25
Consensus pattern (79 bp):
CGGGGTTGGAGTATCCCTTCGAAAATAACGGGGTTGGAGTATCCCCAATTATGAGAAATCAATGA
TTAGAAAAAAAAAC
Found at i:1262385 original size:28 final size:28
Alignment explanation
Indices: 1262326--1262399 Score: 85
Period size: 28 Copynumber: 2.6 Consensus size: 28
1262316 ATAAAGCCGG
*** * * *
1262326 GGTTGGAGTATCCCCTCGGAAGTAATGG
1 GGTTGGAGTATCCCCGATGAAATAACGA
1262354 GGTTGGAGTATCCCCGATGAAATAACGA
1 GGTTGGAGTATCCCCGATGAAATAACGA
*
1262382 GGTTGGAGTATCCTCGAT
1 GGTTGGAGTATCCCCGAT
1262400 TGTGAAAAAT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.18, G:0.32, T:0.26
Consensus pattern (28 bp):
GGTTGGAGTATCCCCGATGAAATAACGA
Found at i:1264888 original size:13 final size:13
Alignment explanation
Indices: 1264870--1264895 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1264860 ACAAAGATCC
1264870 ATGTATCGATACA
1 ATGTATCGATACA
1264883 ATGTATCGATACA
1 ATGTATCGATACA
1264896 CAGAAAAATG
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:1264891 original size:33 final size:33
Alignment explanation
Indices: 1264849--1264915 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1264839 AAAATTTCCA
***
1264849 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1264882 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1264915 A
1 A
1264916 TTTCCTTGGC
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:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1265666 original size:55 final size:55
Alignment explanation
Indices: 1265533--1266506 Score: 1453
Period size: 55 Copynumber: 17.5 Consensus size: 55
1265523 TGGGAAGGTT
* *
1265533 TGCCACTAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGACTGG-AAA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAA
* *
1265587 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCTTGCTCTTTGAGGACT-GAAAGG
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAA-A
** *
1265642 TGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTGAAAAA
1 TGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTGTCCTGCTCTTTGAGGACTGGAAAA
* * *
1265703 TGCCACCAACCTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGATTGGAAAA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAA
**
1265758 TGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGACTGGAAGG
1 TGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGACTGGAAAA
*
1265813 CGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGACTGGAAAA
1 TGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGACTGGAAAA
**
1265868 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAGGA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAA
* *
1265923 TGCCACCAACTTGTGTGGGCTTTAAAAGGTGTCCTGCTCTTTGAGGATTGGAAAA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAA
**
1265978 TGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGACTGGAAGG
1 TGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGACTGGAAAA
**
1266033 CACCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGACTGGAAAA
1 TGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGACTGGAAAA
1266088 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAA
* *
1266143 TGCCACCAACTTGTGCGGGCTTTGAAAGGTGTCCTGCTCTTTGGGGACT--AAAA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAA
1266196 GGTGCCACCAACTTGTGTGGGCTTT-AAGAGGTGTCCTGCTCTTTGAGGACTGGAAAA
1 --TGCCACCAACTTGTGTGGGCTTTGAA-AGGTGTCCTGCTCTTTGAGGACTGGAAAA
1266253 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAA
*
1266308 TGCCACCAACTTGTGTGGGCTTTGAGAGGTGTCCTGCTCTTTGAGGACTGGAAAA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAA
*
1266363 TGCCACCAACTTGTGTGGGCTTTGAGAGGTGTCCTGCTCTTTGAGGACTGGAAAA
1 TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAA
** *
1266418 TGCCACCAACTTGTGTGGGCTTTGAAAAGAAAAAGCATCCTGCTCTTTGAGGACTAGAAAA
1 TGCCACCAACTTGTGTGGGCTTTG-AAAG-----GTGTCCTGCTCTTTGAGGACTGGAAAA
1266479 TGCCACCAACTTGTGTGGGCTTTGAAAG
1 TGCCACCAACTTGTGTGGGCTTTGAAAG
1266507 AAAAAGGCGT
Statistics
Matches: 848, Mismatches: 47, Indels: 44
0.90 0.05 0.05
Matches are distributed among these distances:
53 5 0.01
54 54 0.06
55 673 0.79
56 13 0.02
57 4 0.00
60 8 0.01
61 88 0.10
62 3 0.00
ACGTcount: A:0.22, C:0.20, G:0.29, T:0.29
Consensus pattern (55 bp):
TGCCACCAACTTGTGTGGGCTTTGAAAGGTGTCCTGCTCTTTGAGGACTGGAAAA
Found at i:1266141 original size:27 final size:27
Alignment explanation
Indices: 1266059--1266141 Score: 62
Period size: 27 Copynumber: 3.0 Consensus size: 27
1266049 GGGCTTTAAG
1266059 AGGTGTCCTGCTCTTTGAGGACTGGAA
1 AGGTGTCCTGCTCTTTGAGGACTGGAA
* ** * * * *
1266086 A-ATG-CCACCAACTTGTGTGGGCTTTGAA
1 AGGTGTCCTGC-TCTT-TGAGGAC-TGGAA
1266114 AGGTGTCCTGCTCTTTGAGGACTGGAA
1 AGGTGTCCTGCTCTTTGAGGACTGGAA
1266141 A
1 A
1266142 ATGCCACCAA
Statistics
Matches: 37, Mismatches: 14, Indels: 10
0.61 0.23 0.16
Matches are distributed among these distances:
25 3 0.08
26 5 0.14
27 11 0.30
28 10 0.27
29 5 0.14
30 3 0.08
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (27 bp):
AGGTGTCCTGCTCTTTGAGGACTGGAA
Found at i:1266306 original size:27 final size:27
Alignment explanation
Indices: 1266224--1266306 Score: 62
Period size: 27 Copynumber: 3.0 Consensus size: 27
1266214 GGGCTTTAAG
1266224 AGGTGTCCTGCTCTTTGAGGACTGGAA
1 AGGTGTCCTGCTCTTTGAGGACTGGAA
* ** * * * *
1266251 A-ATG-CCACCAACTTGTGTGGGCTTTGAA
1 AGGTGTCCTGC-TCTT-TGAGGAC-TGGAA
1266279 AGGTGTCCTGCTCTTTGAGGACTGGAA
1 AGGTGTCCTGCTCTTTGAGGACTGGAA
1266306 A
1 A
1266307 ATGCCACCAA
Statistics
Matches: 37, Mismatches: 14, Indels: 10
0.61 0.23 0.16
Matches are distributed among these distances:
25 3 0.08
26 5 0.14
27 11 0.30
28 10 0.27
29 5 0.14
30 3 0.08
ACGTcount: A:0.22, C:0.19, G:0.30, T:0.29
Consensus pattern (27 bp):
AGGTGTCCTGCTCTTTGAGGACTGGAA
Found at i:1272836 original size:28 final size:28
Alignment explanation
Indices: 1272796--1272867 Score: 99
Period size: 28 Copynumber: 2.6 Consensus size: 28
1272786 GGAATAAAGC
** *
1272796 CGGGGTTGGAGTATCCCCTCGGAAGTAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
1272824 CGGGGTTGGAGTATCCCCGATGAAATAA
1 CGGGGTTGGAGTATCCCCGAGGAAATAA
*
1272852 CGAGGTTGGAGTATCC
1 CGGGGTTGGAGTATCC
1272868 TCGATTGTGA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 39 1.00
ACGTcount: A:0.24, C:0.19, G:0.35, T:0.22
Consensus pattern (28 bp):
CGGGGTTGGAGTATCCCCGAGGAAATAA
Found at i:1275360 original size:13 final size:13
Alignment explanation
Indices: 1275342--1275367 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1275332 ACAAAGATCC
1275342 ATGTATCGATACA
1 ATGTATCGATACA
1275355 ATGTATCGATACA
1 ATGTATCGATACA
1275368 CAGAAAAATG
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:1275363 original size:33 final size:33
Alignment explanation
Indices: 1275321--1275387 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1275311 AAAATTTCCA
***
1275321 AATGTATCGATACAAAGATCCATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
*
1275354 AATGTATCGATACACAGAAAAATGTATCGATAC
1 AATGTATCGATACAAAGAAAAATGTATCGATAC
1275387 A
1 A
1275388 TTTCCTTGGC
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:0.43, C:0.16, G:0.15, T:0.25
Consensus pattern (33 bp):
AATGTATCGATACAAAGAAAAATGTATCGATAC
Found at i:1275431 original size:19 final size:18
Alignment explanation
Indices: 1275407--1275474 Score: 83
Period size: 19 Copynumber: 3.9 Consensus size: 18
1275397 CAGTAGCTAA
1275407 TTATGTATCGATACAATAC
1 TTATGTATCGATACAA-AC
1275426 TTATGTATCGATAC--A-
1 TTATGTATCGATACAAAC
1275441 -T-TGTATCGATACAAAAC
1 TTATGTATCGATAC-AAAC
1275458 TTATGTATCGATACAAA
1 TTATGTATCGATACAAA
1275475 TCGTTGAATT
Statistics
Matches: 43, Mismatches: 0, Indels: 13
0.77 0.00 0.23
Matches are distributed among these distances:
13 11 0.26
14 1 0.02
16 2 0.05
18 4 0.09
19 25 0.58
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (18 bp):
TTATGTATCGATACAAAC
Found at i:1275447 original size:13 final size:13
Alignment explanation
Indices: 1275429--1275453 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1275419 ACAATACTTA
1275429 TGTATCGATACAT
1 TGTATCGATACAT
1275442 TGTATCGATACA
1 TGTATCGATACA
1275454 AAACTTATGT
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:1275451 original size:32 final size:32
Alignment explanation
Indices: 1275410--1275472 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
1275400 TAGCTAATTA
*
1275410 TGTATCGATACAATACTTATGTATCGATACAT
1 TGTATCGATACAAAACTTATGTATCGATACAT
1275442 TGTATCGATACAAAACTTATGTATCGATACA
1 TGTATCGATACAAAACTTATGTATCGATACA
1275473 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.35
Consensus pattern (32 bp):
TGTATCGATACAAAACTTATGTATCGATACAT
Found at i:1276576 original size:19 final size:19
Alignment explanation
Indices: 1276532--1276587 Score: 76
Period size: 19 Copynumber: 2.9 Consensus size: 19
1276522 TTGCCAGTTT
**
1276532 CATGTATCGATACAATTGTG
1 CATGTATCGATACAA-TGAA
1276552 CATGTATCGATACAATGAA
1 CATGTATCGATACAATGAA
*
1276571 CATGTATTGATACAATG
1 CATGTATCGATACAATG
1276588 TATCAATACA
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
19 18 0.55
20 15 0.45
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.32
Consensus pattern (19 bp):
CATGTATCGATACAATGAA
Found at i:1280557 original size:13 final size:13
Alignment explanation
Indices: 1280539--1280563 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1280529 ACAAGTTCAA
1280539 CATATTGTAAAAC
1 CATATTGTAAAAC
1280552 CATATTGTAAAA
1 CATATTGTAAAA
1280564 ATGTTTTTTA
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:0.48, C:0.12, G:0.08, T:0.32
Consensus pattern (13 bp):
CATATTGTAAAAC
Found at i:1284360 original size:25 final size:25
Alignment explanation
Indices: 1284309--1284360 Score: 61
Period size: 25 Copynumber: 2.1 Consensus size: 25
1284299 AAACTTTCTA
** *
1284309 TTCAAAACAATGTTCAAAGGTTTAT
1 TTCAAAACAAAATTCAAAGGTTGAT
1284334 TTCAAAACAAAATTCAATA-GTTGAT
1 TTCAAAACAAAATTCAA-AGGTTGAT
1284359 TT
1 TT
1284361 TCACATATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 22 0.96
26 1 0.04
ACGTcount: A:0.42, C:0.12, G:0.10, T:0.37
Consensus pattern (25 bp):
TTCAAAACAAAATTCAAAGGTTGAT
Found at i:1289188 original size:76 final size:77
Alignment explanation
Indices: 1289079--1289515 Score: 334
Period size: 76 Copynumber: 5.6 Consensus size: 77
1289069 TCTATCGGAA
* * *
1289079 ATACTCCAACCCCATAATTTTCGAGAGGATACTCCAACCCCGTTTTTA-TTCAAAATATCAATTT
1 ATACTCCAA-CCCATCATTTTCGAGGGGATACTCCAACCCCATTTTTATTTCAAAATATCAATTT
**
1289143 TTCATTA-TCGAG
65 TTCACCATTCGAG
* * * **
1289155 ATACTCCAACCTCATCA-TTTCTAAGGGGATACTCCAACCCCATTTTT-TTCCAAAGTATTGATT
1 ATACTCCAACC-CATCATTTTC-GAGGGGATACTCCAACCCCATTTTTATTTCAAAATATCAATT
* *
1289218 TTTCACCATTAGGG
64 TTTCACCATTCGAG
* * *
1289232 ATACTCCAACCCATCATTTTCGAGGGGATACTCCAACCCCTATTTTTATTTTCAAAATTTCGATA
1 ATACTCCAACCCATCATTTTCGAGGGGATACTCCAACCCC-ATTTTTA-TTTCAAAATATCAATT
* *
1289297 TTTCACCATTGGGG
64 TTTCACCATTCGAG
* * * **
1289311 ATACTCCAGCCCTATCATTTAT-GAAGGGATACTTCAA--CTTTTTTTATTTCTAAAATATCAAT
1 ATACTCCAACCC-ATCATTT-TCGAGGGGATACTCCAACCCCATTTTTATTTC-AAAATATCAAT
*
1289373 TTTTCACCA-TCAGAA
63 TTTTCACCATTC-GAG
* *** * *
1289388 ATACTCCAACCCCATTATTTTCGAGGGGATACTCCAATCTCTTTTTTTTACTTCTAAAAGCATCA
1 ATACTCCAA-CCCATCATTTTCGAGGGGATACTCCAA-C-CCCATTTTTATTTC-AAAA-TATC-
*
1289453 AAATTTTCACCATT-GAGG
60 AATTTTTCACCATTCGA-G
** * * * *
1289471 ATACTCCAAACCTGTTATTTCCAAAGGGATACTCCAACCCCATTT
1 ATACTCC-AACCCATCATTTTCGAGGGGATACTCCAACCCCATTT
1289516 CTACTTCCAA
Statistics
Matches: 291, Mismatches: 47, Indels: 41
0.77 0.12 0.11
Matches are distributed among these distances:
75 6 0.02
76 81 0.28
77 75 0.26
78 4 0.01
79 35 0.12
80 20 0.07
81 21 0.07
82 6 0.02
83 40 0.14
84 3 0.01
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.35
Consensus pattern (77 bp):
ATACTCCAACCCATCATTTTCGAGGGGATACTCCAACCCCATTTTTATTTCAAAATATCAATTTT
TCACCATTCGAG
Found at i:1289380 original size:77 final size:77
Alignment explanation
Indices: 1289079--1289479 Score: 316
Period size: 77 Copynumber: 5.1 Consensus size: 77
1289069 TCTATCGGAA
* * **
1289079 ATACTCCAACCCCATAATTTTCGAGAGGATACTCCAACCCCGTTTTTA-TTC-AAAATATCAATT
1 ATACTCCAA-CCCATCATTTTCGAGGGGATACTCCAA-CCTTTTTTTATTTCTAAAATATCAATT
** * *
1289142 TTTCATTA-TCGAG
64 TTTCACCATTAGGG
* *** * * **
1289155 ATACTCCAACCTCATCA-TTTCTAAGGGGATACTCCAACCCCATTTT-TTTCCAAAGTATTGATT
1 ATACTCCAACC-CATCATTTTC-GAGGGGATACTCCAACCTTTTTTTATTTCTAAAATATCAATT
1289218 TTTCACCATTAGGG
64 TTTCACCATTAGGG
* * *
1289232 ATACTCCAACCCATCATTTTCGAGGGGATACTCCAACCCCTATTTTTATTT-TCAAAATTTCGAT
1 ATACTCCAACCCATCATTTTCGAGGGGATACTCCAA--CCTTTTTTTATTTCT-AAAATATCAAT
* *
1289296 ATTTCACCATTGGGG
63 TTTTCACCATTAGGG
* * *
1289311 ATACTCCAGCCCTATCATTTAT-GAAGGGATACTTCAA-CTTTTTTTATTTCTAAAATATCAATT
1 ATACTCCAACCC-ATCATTT-TCGAGGGGATACTCCAACCTTTTTTTATTTCTAAAATATCAATT
* **
1289374 TTTCACCATCAGAA
64 TTTCACCATTAGGG
* * *
1289388 ATACTCCAACCCCATTATTTTCGAGGGGATACTCCAATCTCTTTTTTTTACTTCTAAAAGCATCA
1 ATACTCCAA-CCCATCATTTTCGAGGGGATACTCCAA-C-C-TTTTTTTATTTCTAAAA-TATC-
*
1289453 AAATTTTCACCATT-GAGG
60 AATTTTTCACCATTAG-GG
1289471 ATACTCCAA
1 ATACTCCAA
1289480 ACCTGTTATT
Statistics
Matches: 260, Mismatches: 43, Indels: 37
0.76 0.13 0.11
Matches are distributed among these distances:
75 16 0.06
76 61 0.23
77 75 0.29
78 10 0.04
79 35 0.13
80 21 0.08
81 17 0.07
82 4 0.02
83 21 0.08
ACGTcount: A:0.30, C:0.24, G:0.10, T:0.36
Consensus pattern (77 bp):
ATACTCCAACCCATCATTTTCGAGGGGATACTCCAACCTTTTTTTATTTCTAAAATATCAATTTT
TCACCATTAGGG
Found at i:1289382 original size:156 final size:153
Alignment explanation
Indices: 1289076--1289515 Score: 395
Period size: 156 Copynumber: 2.8 Consensus size: 153
1289066 TTATCTATCG
* *
1289076 GAAATACTCCAACCCCATAATTTTCGAGAGGATACTCCAACCCCGTTTTTATTCAAAATATCAAT
1 GAAATACTCCAACCCCATAATTTTCGAGGGGATACTCCAACCCCATTTTTATTCAAAATATCAAT
* ** *
1289141 TTTTCATTATCGAGATACTCCAACCTCATCATTTCTAAGGGGATACTCCAACCCCATTTTTTTCC
66 ATTTCACCATCGAGATACTCCAACCTCATCATTTATAAGGGGATACTCCAACCCCATTTTTTTCC
* ** *
1289206 AAAGTATTGATTTTTCACCATTA
131 AAAATATCAATTTTTCACCATCA
** * *
1289229 GGGATACTCCAA-CCCATCATTTTCGAGGGGATACTCCAACCCCTATTTTTATTTTCAAAATTTC
1 GAAATACTCCAACCCCATAATTTTCGAGGGGATACTCCAACCCC-ATTTTTA--TTCAAAATATC
* * * * * ***
1289293 GATATTTCACCATTGGGGATACTCCAGCC-CTATCATTTATGAA-GGGATACTTCAA-CTTTTTT
63 AATATTTCACCA-TCGAGATACTCCAACCTC-ATCATTTAT-AAGGGGATACTCCAACCCCATTT
*
1289355 TATTTCTAAAATATCAATTTTTCACCATCA
125 T-TTTCCAAAATATCAATTTTTCACCATCA
* *** *
1289385 GAAATACTCCAACCCCATTATTTTCGAGGGGATACTCCAATCTCTTTTTTTTACTTCTAAAAGCA
1 GAAATACTCCAACCCCATAATTTTCGAGGGGATACTCCAA-C-CCCATTTTTA-TTC-AAAA-TA
* * * * ** *
1289450 TCAAAATTTTCACCATTGAGGATACTCCAAACCT-GTTATTTCCAAAGGGATACTCCAACCCCAT
61 TCAATA-TTTCACCATCGA-GATACTCC-AACCTCATCATTTATAAGGGGATACTCCAACCCCAT
1289514 TT
123 TT
1289516 CTACTTCCAA
Statistics
Matches: 224, Mismatches: 45, Indels: 28
0.75 0.15 0.09
Matches are distributed among these distances:
152 29 0.13
153 16 0.07
155 24 0.11
156 65 0.29
157 31 0.14
158 11 0.05
159 9 0.04
160 32 0.14
161 7 0.03
ACGTcount: A:0.30, C:0.25, G:0.10, T:0.35
Consensus pattern (153 bp):
GAAATACTCCAACCCCATAATTTTCGAGGGGATACTCCAACCCCATTTTTATTCAAAATATCAAT
ATTTCACCATCGAGATACTCCAACCTCATCATTTATAAGGGGATACTCCAACCCCATTTTTTTCC
AAAATATCAATTTTTCACCATCA
Found at i:1292584 original size:13 final size:13
Alignment explanation
Indices: 1292566--1292590 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1292556 ATTACTCAAA
1292566 TGTATCGATACAT
1 TGTATCGATACAT
1292579 TGTATCGATACA
1 TGTATCGATACA
1292591 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:1292724 original size:52 final size:52
Alignment explanation
Indices: 1292601--1292724 Score: 194
Period size: 52 Copynumber: 2.4 Consensus size: 52
1292591 CTGATCTTTG
*
1292601 TATCGATACCTGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATA
1 TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATA
* * *
1292653 TATCGATACATACACGCAAATTTGCCCAGATGTATCGATACACTATGAAATG
1 TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATA
* *
1292705 TATTGATATATGCAGGCAAA
1 TATCGATACATGCAGGCAAA
1292725 ATTTCATATT
Statistics
Matches: 64, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
52 64 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.27
Consensus pattern (52 bp):
TATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATGAAATA
Found at i:1296769 original size:22 final size:22
Alignment explanation
Indices: 1296744--1296835 Score: 75
Period size: 22 Copynumber: 4.3 Consensus size: 22
1296734 ACTACGTTGT
1296744 ATAC-TGCTAAGAAAATGTATCG
1 ATACATGCTAA-AAAATGTATCG
*
1296766 ATACA---TAGGAAAATGTATCG
1 ATACATGCTA-AAAAATGTATCG
* * *
1296786 ATACATGCTTACAATTGTATCG
1 ATACATGCTAAAAAATGTATCG
* * *
1296808 ATACATGCTTACAATTGTATCG
1 ATACATGCTAAAAAATGTATCG
1296830 ATACAT
1 ATACAT
1296836 TTCTTACTGT
Statistics
Matches: 60, Mismatches: 5, Indels: 10
0.80 0.07 0.13
Matches are distributed among these distances:
20 18 0.30
22 41 0.68
23 1 0.02
ACGTcount: A:0.38, C:0.15, G:0.15, T:0.32
Consensus pattern (22 bp):
ATACATGCTAAAAAATGTATCG
Found at i:1296779 original size:20 final size:20
Alignment explanation
Indices: 1296754--1296791 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
1296744 ATACTGCTAA
1296754 GAAAATGTATCGATACATAG
1 GAAAATGTATCGATACATAG
1296774 GAAAATGTATCGATACAT
1 GAAAATGTATCGATACAT
1296792 GCTTACAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.11, G:0.18, T:0.26
Consensus pattern (20 bp):
GAAAATGTATCGATACATAG
Found at i:1297252 original size:21 final size:21
Alignment explanation
Indices: 1297223--1297262 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
1297213 AAAGAGAAAA
1297223 TCCCATAATGCCT-TTGGTTTG
1 TCCCATAAT-CCTATTGGTTTG
*
1297244 TCCCCTAATCCTATTGGTT
1 TCCCATAATCCTATTGGTT
1297263 GAGCATGTAG
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:0.15, C:0.28, G:0.15, T:0.42
Consensus pattern (21 bp):
TCCCATAATCCTATTGGTTTG
Found at i:1299501 original size:28 final size:29
Alignment explanation
Indices: 1299464--1299534 Score: 87
Period size: 28 Copynumber: 2.6 Consensus size: 29
1299454 ATCTCAGGGT
* *
1299464 TACTCCAACCCT-GTTATTT-TCGAGGGGA
1 TACTCTAACCCTCGTTATTTCT-GAGAGGA
1299492 TACTCTAA-CCTCGTTATTTCTGAGAGGA
1 TACTCTAACCCTCGTTATTTCTGAGAGGA
1299520 TACTCTAA-CCTCGTT
1 TACTCTAACCCTCGTT
1299535 TTTATTTCCA
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
27 3 0.08
28 35 0.90
29 1 0.03
ACGTcount: A:0.23, C:0.25, G:0.17, T:0.35
Consensus pattern (29 bp):
TACTCTAACCCTCGTTATTTCTGAGAGGA
Found at i:1299538 original size:182 final size:187
Alignment explanation
Indices: 1299305--1299691 Score: 493
Period size: 182 Copynumber: 2.1 Consensus size: 187
1299295 ATTTATTATT
* * * *
1299305 GGGGATATTCCAATCTCGTTAGTTCTGAAGGGATACTCCAACCCTGTTTTTATTTCCAAAAATAT
1 GGGGATACTCTAACCTCGTTAGTTCTGAAGGGATACTCCAACCCTGTTTTTATTTCCAAAAAAAT
* * *
1299370 CAAATTTTTCATCGCGAGGATACTACAACCCTATTATTTTTTGAGGGGATACTCCTAGCC-CGTT
66 CAAAATTTTCATCGCAAGGATACTACAACCCTATTATTTTTTGAGGGGATACT-CTAACCTCGTT
* * *
1299434 TTTATTTTC-AAAA-T-A-TTTTCATCTCAGGGTTACTCCAACCCTGTTA-TTTTCGA
130 TTTATTTCCAAAAATTAATTTTTCATCGCAGGGATACTCCAACCCTGTTATTTTTCGA
* *
1299487 GGGGATACTCTAACCTCGTTATTTCTG-AGAGGATACTCTAA-CCTCGTTTTTATTTCCAAAAAA
1 GGGGATACTCTAACCTCGTTAGTTCTGAAG-GGATACTCCAACCCT-GTTTTTATTTCCAAAAAA
* * * *
1299550 ATTAAAATTTTCATTGCAAGGATACTCCAACCCTGTTATTTTTTGAGGGGATACTCTAACCTCGT
64 ATCAAAATTTTCATCGCAAGGATACTACAACCCTATTATTTTTTGAGGGGATACTCTAACCTCGT
* *
1299615 TTTTATTTCCAAAAAAATTAAATTTTTTATCGCAGGGATACTCCAACCCTGTTATTTTTTGA
129 TTTTATTTCC--AAAAATT-AATTTTTCATCGCAGGGATACTCCAACCCTGTTATTTTTCGA
*
1299677 GGAGATACTCTAACC
1 GGGGATACTCTAACC
1299692 CCATTTTTAT
Statistics
Matches: 175, Mismatches: 19, Indels: 14
0.84 0.09 0.07
Matches are distributed among these distances:
181 10 0.06
182 111 0.63
185 4 0.02
186 1 0.01
188 1 0.01
189 28 0.16
190 20 0.11
ACGTcount: A:0.28, C:0.20, G:0.14, T:0.37
Consensus pattern (187 bp):
GGGGATACTCTAACCTCGTTAGTTCTGAAGGGATACTCCAACCCTGTTTTTATTTCCAAAAAAAT
CAAAATTTTCATCGCAAGGATACTACAACCCTATTATTTTTTGAGGGGATACTCTAACCTCGTTT
TTATTTCCAAAAATTAATTTTTCATCGCAGGGATACTCCAACCCTGTTATTTTTCGA
Found at i:1299612 original size:81 final size:81
Alignment explanation
Indices: 1299489--1299709 Score: 329
Period size: 81 Copynumber: 2.7 Consensus size: 81
1299479 ATTTTCGAGG
* * *
1299489 GGATACTCTAA-CCTCGTTA-TTTCTGAGAGGATACTCTAACCTCGTTTTTATTTCCAAAAAAAT
1 GGATACTCCAACCCT-GTTATTTTTTGAGGGGATACTCTAACCTCGTTTTTATTTCCAAAAAAAT
*
1299552 TAAAATTTTCATTGCAA
65 TAAAATTTTCATCGCAA
1299569 GGATACTCCAACCCTGTTATTTTTTGAGGGGATACTCTAACCTCGTTTTTATTTCCAAAAAAATT
1 GGATACTCCAACCCTGTTATTTTTTGAGGGGATACTCTAACCTCGTTTTTATTTCCAAAAAAATT
* * *
1299634 AAATTTTTTATCGCAG
66 AAAATTTTCATCGCAA
* * *
1299650 GGATACTCCAACCCTGTTATTTTTTGAGGAGATACTCTAACCCCATTTTTATTTCCAAAA
1 GGATACTCCAACCCTGTTATTTTTTGAGGGGATACTCTAACCTCGTTTTTATTTCCAAAA
1299710 TATTTTCATC
Statistics
Matches: 129, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
80 14 0.11
81 115 0.89
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (81 bp):
GGATACTCCAACCCTGTTATTTTTTGAGGGGATACTCTAACCTCGTTTTTATTTCCAAAAAAATT
AAAATTTTCATCGCAA
Found at i:1299701 original size:263 final size:259
Alignment explanation
Indices: 1299230--1299739 Score: 649
Period size: 263 Copynumber: 2.0 Consensus size: 259
1299220 TTTTTCTCGA
*
1299230 GGATACTCTAACCCTGTTATTTTCAAGAGGATACTCCAACCCCATTTTTATTTCCAAAATATTAA
1 GGATACTCTAACCCTGTTATTTTCAAGAGGATACTCCAACCCCATTTTTATTTCCAAAAAATTAA
* * * *
1299295 ATTTATTATTGGGGATATTCCAATCTCGTTAGTTCTGAAGGGATACTCCAACCCTGTTTTTATTT
66 ATTTATCATTGAGGATACTCCAACCTCGTTAGTTCTGAAGGGATACTCCAACCCTGTTTTTATTT
* *
1299360 CCAAAAATATCAAATTTTTCATCGCGAGGATACTACAACCCTATTATTTTTTGAGGGGATACTCC
131 CCAAAAAAATCAAATTTTTCATCGCGAGGATACTACAACCCTATTATTTTTTGAGGAGATACTCC
* * * *
1299425 TAGCCCGTTTTTATTTTCAAAATATTTTCATCTC-AGGGTTACTCCAACCCTGTTATTTTCGAGG
196 TACCCCATTTTTATTTCCAAAATATTTTCATCTCGA-GGATACTCCAACCCTGTTATTTTCGAGG
* * * *
1299489 GGATACTCTAA-CCTCGTTA-TTTCTGAGAGGATACTCTAACCTCGTTTTTATTTCCAAAAAAAT
1 GGATACTCTAACCCT-GTTATTTTC-AAGAGGATACTCCAACCCCATTTTTATTTCC-AAAAAAT
* * * *
1299552 TAAAATTT-TCATTGCAAGGATACTCCAACC-CTGTTATTTTTTGAGGGGATACTCTAA-CCTCG
63 T-AAATTTATCATTG--AGGATACTCCAACCTC-GTTA-GTTCTGAAGGGATACTCCAACCCT-G
* * * *
1299614 TTTTTATTTCCAAAAAAATTAAATTTTTTATCGC-AGGGATACTCCAACCCTGTTATTTTTTGAG
122 TTTTTATTTCCAAAAAAATCAAATTTTTCATCGCGA-GGATACTACAACCCTATTATTTTTTGAG
1299678 GAGATACT-CTAACCCCATTTTTATTTCCAAAATATTTTCATCTCGAGGATACTCCAACCCTG
186 GAGATACTCCT-ACCCCATTTTTATTTCCAAAATATTTTCATCTCGAGGATACTCCAACCCTG
1299740 GTTTTATTTC
Statistics
Matches: 216, Mismatches: 23, Indels: 20
0.83 0.09 0.08
Matches are distributed among these distances:
258 7 0.03
259 42 0.19
260 12 0.06
261 7 0.03
262 21 0.10
263 126 0.58
264 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.13, T:0.38
Consensus pattern (259 bp):
GGATACTCTAACCCTGTTATTTTCAAGAGGATACTCCAACCCCATTTTTATTTCCAAAAAATTAA
ATTTATCATTGAGGATACTCCAACCTCGTTAGTTCTGAAGGGATACTCCAACCCTGTTTTTATTT
CCAAAAAAATCAAATTTTTCATCGCGAGGATACTACAACCCTATTATTTTTTGAGGAGATACTCC
TACCCCATTTTTATTTCCAAAATATTTTCATCTCGAGGATACTCCAACCCTGTTATTTTCGAGG
Found at i:1299815 original size:79 final size:79
Alignment explanation
Indices: 1299724--1299926 Score: 250
Period size: 79 Copynumber: 2.6 Consensus size: 79
1299714 TTCATCTCGA
*
1299724 GGATACTCCAACCCTGGTTTTATTTCTAAAATATCGA-TTTTCTATCATCAGGGATACTCCAACC
1 GGATACTCCAACCCTGGTTTTATTTCTAAAATATCGATTTTTC-ACCATCAGGGATACTCCAACC
**
1299788 CCGTTATTTT-TGAG
65 CCGTTATTTTCAAAG
*** ** *
1299802 GGAATACTCCAACCCCATTTTTATTTCTAAAATATCGATTTTTCACCATTGGGGATACTTCAACC
1 GG-ATACTCCAACCCTGGTTTTATTTCTAAAATATCGATTTTTCACCATCAGGGATACTCCAACC
*
1299867 CTGTTATTTTCAAAG
65 CCGTTATTTTCAAAG
* *
1299882 GGATACTCCAACCTTGGTTTTATTT-TGAAAATATCAATTTTTCAC
1 GGATACTCCAACCCTGGTTTTATTTCT-AAAATATCGATTTTTCAC
1299927 ATTGGGGATC
Statistics
Matches: 106, Mismatches: 15, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
78 3 0.03
79 94 0.89
80 9 0.08
ACGTcount: A:0.28, C:0.22, G:0.12, T:0.38
Consensus pattern (79 bp):
GGATACTCCAACCCTGGTTTTATTTCTAAAATATCGATTTTTCACCATCAGGGATACTCCAACCC
CGTTATTTTCAAAG
Found at i:1304703 original size:62 final size:61
Alignment explanation
Indices: 1304606--1304798 Score: 287
Period size: 62 Copynumber: 3.1 Consensus size: 61
1304596 ACCTATTTTA
* * * *
1304606 ACCTTTTAGTCCTCAAAGAGAAAGATGTTTTTTTCTTTTTAAAACTCACATGAGTTGGTGGC
1 ACCTTTTAGTCCTCAAAGAGTAGGATGTTTTTTTCTTTTTAAAGC-CACACGAGTTGGTGGC
*
1304668 ACCTTTTAGTCCTCAAAGAGTAGGATGTTTTTTTCTTTTTAAAGCCTATACGAGTTGGTGGC
1 ACCTTTTAGTCCTCAAAGAGTAGGATGTTTTTTTCTTTTTAAAGCC-ACACGAGTTGGTGGC
**
1304730 ACCTTTTAGTCCTCAAAGAGTAGGATGCCTTTTTCTTTTTAAAGCCCACACGAGTTGGTGGC
1 ACCTTTTAGTCCTCAAAGAGTAGGATGTTTTTTTCTTTTTAAAG-CCACACGAGTTGGTGGC
*
1304792 ATCTTTT
1 ACCTTTT
1304799 TCCTTTTCTT
Statistics
Matches: 120, Mismatches: 9, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
61 1 0.01
62 117 0.98
63 2 0.02
ACGTcount: A:0.24, C:0.18, G:0.19, T:0.39
Consensus pattern (61 bp):
ACCTTTTAGTCCTCAAAGAGTAGGATGTTTTTTTCTTTTTAAAGCCACACGAGTTGGTGGC
Found at i:1306268 original size:17 final size:17
Alignment explanation
Indices: 1306246--1306292 Score: 55
Period size: 16 Copynumber: 2.8 Consensus size: 17
1306236 CTTTTGACTT
1306246 ACAAAAACAAAAACAA-A
1 ACAAAAACAAAAA-AATA
1306263 AC-AAAACAAAAAAATA
1 ACAAAAACAAAAAAATA
1306279 ACCAAAAA-AAAAAA
1 A-CAAAAACAAAAAA
1306293 GAAACCAACT
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
15 2 0.07
16 12 0.44
17 9 0.33
18 4 0.15
ACGTcount: A:0.83, C:0.15, G:0.00, T:0.02
Consensus pattern (17 bp):
ACAAAAACAAAAAAATA
Found at i:1306298 original size:17 final size:16
Alignment explanation
Indices: 1306247--1306300 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
1306237 TTTTGACTTA
1306247 CAAAAACAAAAACAAAA-
1 CAAAAA-AAAAA-AAAAC
*
1306264 CAAAACAAAAAAATAAC
1 CAAAA-AAAAAAAAAAC
1306281 CAAAAAAAAAAAGAAAC
1 CAAAAAAAAAAA-AAAC
1306298 CAA
1 CAA
1306301 CTTAAGTTGA
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
16 10 0.31
17 21 0.66
18 1 0.03
ACGTcount: A:0.80, C:0.17, G:0.02, T:0.02
Consensus pattern (16 bp):
CAAAAAAAAAAAAAAC
Found at i:1307444 original size:64 final size:63
Alignment explanation
Indices: 1307254--1308080 Score: 447
Period size: 63 Copynumber: 12.9 Consensus size: 63
1307244 TTATCTCTTA
* * * * * *
1307254 AGTCCTCAAATAGCAGGATGCATTTT-TCTTTTAAAAAACCCACACAAGTTGGTGGCAAC-TTTT
1 AGTCCTCAAAGAGCATGACGCCTTTTCT-TTTTTAAAAGCCCACACAAGTTGGTGGC-ACTTTTT
* * * * * * *
1307317 AGTCTTCAAAGAGTAAGACGCGTTTTCCTTTTT-AAAGCCCACATAAGTTGATGGCACTTTTT
1 AGTCCTCAAAGAGCATGACGCCTTTTCTTTTTTAAAAGCCCACACAAGTTGGTGGCACTTTTT
* * *
1307379 AGTCCTCAAAGAGCGTGACTGCCTTTTCTTTTTTAAAAGCCCACACAAGTTAGTGACA-TCTTTT
1 AGTCCTCAAAGAGCATGAC-GCCTTTTCTTTTTTAAAAGCCCACACAAGTTGGTGGCACT-TTTT
* * * *
1307443 AGTCTTCAAAGAACATGACG-CTTTTTTTTCCTTTAAAAGCCCATACAAGTTGGTGGCACCTTTT
1 AGTCCTCAAAGAGCATGACGCCTTTTCTTT--TTTAAAAGCCCACACAAGTTGGTGGCA-CTTTT
1307507 T
63 T
* * * * * * *
1307508 AGTCCTCAAAAAACAGGACACCTTTCCTTTTCCTTTTAAAGCTCACACAAGTTGGTGGCACATTT
1 AGTCCTCAAAGAGCATGACGCCTTTTC-TTT--TTTAAAAGCCCACACAAGTTGGTGGCAC-TTT
1307573 TT
62 TT
* * * * * * * *
1307575 AGTCCTAAAAAAGCAGGACGCCTTTCCTTTTCCTTTTAAAGCCCACACATGTTGATGGTACTTTT
1 AGTCCTCAAAGAGCATGACGCCTTTTC-TTT--TTTAAAAGCCCACACAAGTTGGTGGCACTTTT
1307640 T
63 T
* * * * ** *
1307641 AGTTCTCAAAGAACAGGACACCTTTTCTTTTCCTTTTGAAGCCCACAC---------G-AGTTTT
1 AGTCCTCAAAGAGCATGACGCCTTTTC-TTT--TTTAAAAGCCCACACAAGTTGGTGGCACTTTT
1307696 T
63 T
* * * * * *
1307697 -GTCCTTAAAGAGCAGGACGCCTTTTC-CTTTT-AAAGCTCACACAAGTTGGTGGCACATTTG
1 AGTCCTCAAAGAGCATGACGCCTTTTCTTTTTTAAAAGCCCACACAAGTTGGTGGCACTTTTT
* * * * * * * * *
1307757 AGTCTCTTAAAGAGTAGGATGCTTTTTCTTTTTTAGAAGCCCACACAAGCTAGTGGCACCTTTT
1 AGTC-CTCAAAGAGCATGACGCCTTTTCTTTTTTAAAAGCCCACACAAGTTGGTGGCACTTTTT
** * * * *
1307821 AGTTTTTAAGGAGCAAGACACCTTTTCTTTTTTAAAAGCCCACACAAGTTGGTAGGC-CTTTTT
1 AGTCCTCAAAGAGCATGACGCCTTTTCTTTTTTAAAAGCCCACACAAGTTGGT-GGCACTTTTT
* ** * * * * * *
1307884 AGCCCTCAAAGAGCAAAAGGCCTTTTCCTTTTTTTAAAAAAAAGCCTACACAAGCTAGCGGCACC
1 AGTCCTCAAAGAGCATGACGCCTTTT-C-TTTTTT----AAAAGCCCACACAAGTTGGTGGCACT
1307949 TTTT
60 TTTT
* *
1307953 AGTCCTCAAAGAGCAGGACGCTTTTTTTTTTCTTTTTTAAAAAAGCCCACACAAGTTGGTGGCAC
1 AGTCCTCAAAGAGCATGACGC-----CTTTTCTTTTTT--AAAAGCCCACACAAGTTGGTGGCA-
1308018 TCATTTTT
58 -C-TTTTT
** * * * * * *
1308026 AGTCCT-AAA-AAAATGACTCATTTTCTTTCTCAAAA-CCCATACAAGTTGGTAGCAC
1 AGTCCTCAAAGAGCATGACGCCTTTTCTTTTTTAAAAGCCCACACAAGTTGGTGGCAC
1308081 CTATCTACTT
Statistics
Matches: 606, Mismatches: 116, Indels: 86
0.75 0.14 0.11
Matches are distributed among these distances:
50 9 0.01
51 3 0.00
53 1 0.00
55 22 0.04
56 6 0.01
57 1 0.00
59 1 0.00
60 4 0.01
61 6 0.01
62 66 0.11
63 121 0.20
64 97 0.16
65 26 0.04
66 61 0.10
67 88 0.15
68 3 0.00
69 38 0.06
70 22 0.04
71 6 0.01
72 10 0.02
73 11 0.02
74 4 0.01
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.34
Consensus pattern (63 bp):
AGTCCTCAAAGAGCATGACGCCTTTTCTTTTTTAAAAGCCCACACAAGTTGGTGGCACTTTTT
Found at i:1307675 original size:66 final size:66
Alignment explanation
Indices: 1307339--1307693 Score: 368
Period size: 67 Copynumber: 5.4 Consensus size: 66
1307329 GTAAGACGCG
* * *
1307339 TTTTCCTTTTTAAAGCCCACATAAGTTGATGGCACTTTTTAGTCCTCAAAGAGC-GTGACTGCCT
1 TTTTCC-TTTTAAAGCCCACACAAGTTGATGGCACTTTTTAGTCCTCAAAGAACAG-GAC-ACCT
1307403 TTTC
63 TTTC
* * * * *
1307407 -TTT--TTTAAAAGCCCACACAAGTT-AGTGACA-TCTTTTAGTCTTCAAAGAACATGAC-GCTT
1 TTTTCCTTTTAAAGCCCACACAAGTTGA-TGGCACT-TTTTAGTCCTCAAAGAACAGGACACCTT
1307466 TT-
64 TTC
* * * *
1307468 TTTTCCTTTAAAAGCCCATACAAGTTGGTGGCACCTTTTTAGTCCTCAAAAAACAGGACACCTTT
1 TTTTCCTTTTAAAGCCCACACAAGTTGATGGCA-CTTTTTAGTCCTCAAAGAACAGGACACCTTT
*
1307533 CC
65 TC
* * * *
1307535 TTTTCCTTTTAAAGCTCACACAAGTTGGTGGCACATTTTTAGTCCT-AAAAAAGCAGGACGCCTT
1 TTTTCCTTTTAAAGCCCACACAAGTTGATGGCAC-TTTTTAGTCCTCAAAGAA-CAGGACACCTT
*
1307599 TCC
64 TTC
* * *
1307602 TTTTCCTTTTAAAGCCCACACATGTTGATGGTACTTTTTAGTTCTCAAAGAACAGGACACCTTTT
1 TTTTCCTTTTAAAGCCCACACAAGTTGATGGCACTTTTTAGTCCTCAAAGAACAGGACACCTTTT
1307667 C
66 C
* *
1307668 TTTTCCTTTTGAAGCCCACACGAGTT
1 TTTTCCTTTTAAAGCCCACACAAGTT
1307694 TTTGTCCTTA
Statistics
Matches: 243, Mismatches: 30, Indels: 30
0.80 0.10 0.10
Matches are distributed among these distances:
62 8 0.03
63 2 0.01
64 64 0.26
65 20 0.08
66 57 0.23
67 92 0.38
ACGTcount: A:0.26, C:0.24, G:0.15, T:0.35
Consensus pattern (66 bp):
TTTTCCTTTTAAAGCCCACACAAGTTGATGGCACTTTTTAGTCCTCAAAGAACAGGACACCTTTT
C
Found at i:1308017 original size:70 final size:70
Alignment explanation
Indices: 1307842--1308031 Score: 190
Period size: 69 Copynumber: 2.7 Consensus size: 70
1307832 AGCAAGACAC
* * *
1307842 CTTTTCTTTTTT--AAAAGCCCACACAAGTTGGTAGGC-CTTTTTAGCCCTCAAAGAGCAAAAGG
1 CTTTTCTTTTTTAAAAAAGCCCACACAAGTTGGT-GGCACCTTTTAGTCCTCAAAGAGCAAAACG
1307904 CCTTTT
65 CCTTTT
* ** * * * * **
1307910 CCTTT-TTTTAAAAAAAAGCCTACACAAGCTAGCGGCACCTTTTAGTCCTCAAAGAGCAGGACGC
1 CTTTTCTTTTTTAAAAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAAACGC
*
1307974 TTTTT
66 CTTTT
*
1307979 TTTTTCTTTTTTAAAAAAGCCCACACAAGTTGGTGGCACTCATTTTTAGTCCT
1 CTTTTCTTTTTTAAAAAAGCCCACACAAGTTGGTGGCAC-C--TTTTAGTCCT
1308032 AAAAAAATGA
Statistics
Matches: 94, Mismatches: 21, Indels: 9
0.76 0.17 0.07
Matches are distributed among these distances:
67 4 0.04
68 7 0.07
69 45 0.48
70 27 0.29
71 1 0.01
73 10 0.11
ACGTcount: A:0.27, C:0.23, G:0.15, T:0.34
Consensus pattern (70 bp):
CTTTTCTTTTTTAAAAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAAACGC
CTTTT
Found at i:1308598 original size:21 final size:20
Alignment explanation
Indices: 1308572--1308622 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
1308562 CTACAATTTA
1308572 TATCGATACAAATAGTGAATG
1 TATCGATACAAA-AGTGAATG
* *
1308593 TATCGATACATAAGTGATTG
1 TATCGATACAAAAGTGAATG
*
1308613 TATCAATACA
1 TATCGATACA
1308623 TGTTTGAAAT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 16 0.59
21 11 0.41
ACGTcount: A:0.41, C:0.12, G:0.16, T:0.31
Consensus pattern (20 bp):
TATCGATACAAAAGTGAATG
Found at i:1308614 original size:20 final size:21
Alignment explanation
Indices: 1308572--1308643 Score: 76
Period size: 21 Copynumber: 3.5 Consensus size: 21
1308562 CTACAATTTA
*
1308572 TATCGATACAAATAGTGAATG
1 TATCGATACATATAGTGAATG
*
1308593 TATCGATACATA-AGTGATTG
1 TATCGATACATATAGTGAATG
* * *
1308613 TATCAATACATGT-TTGAAATG
1 TATCGATACATATAGTG-AATG
1308634 TATCGATACA
1 TATCGATACA
1308644 GGACCATGTT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
20 19 0.45
21 23 0.55
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (21 bp):
TATCGATACATATAGTGAATG
Found at i:1308735 original size:51 final size:51
Alignment explanation
Indices: 1308680--1308776 Score: 149
Period size: 51 Copynumber: 1.9 Consensus size: 51
1308670 TCTGGAGAGA
* * * *
1308680 AAATGTATCGATACATTTTTCATTGTATCGATACATTTTGGGTTTTAGCCT
1 AAATGTATCGATACATTTTACATTGTATCAATACATTCTAGGTTTTAGCCT
*
1308731 AAATGTATTGATACATTTTACATTGTATCAATACATTCTAGGTTTT
1 AAATGTATCGATACATTTTACATTGTATCAATACATTCTAGGTTTT
1308777 TGACCCAAAT
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
51 41 1.00
ACGTcount: A:0.29, C:0.12, G:0.13, T:0.45
Consensus pattern (51 bp):
AAATGTATCGATACATTTTACATTGTATCAATACATTCTAGGTTTTAGCCT
Found at i:1309207 original size:12 final size:12
Alignment explanation
Indices: 1309190--1309216 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
1309180 TTGGCTCAGC
1309190 AGAGAAAAAAAA
1 AGAGAAAAAAAA
1309202 AGAGAAAAAAAA
1 AGAGAAAAAAAA
1309214 AGA
1 AGA
1309217 AGATTTTCAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (12 bp):
AGAGAAAAAAAA
Found at i:1322920 original size:11 final size:10
Alignment explanation
Indices: 1322895--1322936 Score: 50
Period size: 10 Copynumber: 4.2 Consensus size: 10
1322885 TTTTTGACTT
1322895 ACAAAAACAAA
1 ACAAAAA-AAA
1322906 A-AAAAAAAA
1 ACAAAAAAAA
**
1322915 TTAAAAAAAA
1 ACAAAAAAAA
1322925 ACAAAAAAAA
1 ACAAAAAAAA
1322935 AC
1 AC
1322937 CAACTTAAGT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
9 3 0.11
10 23 0.85
11 1 0.04
ACGTcount: A:0.86, C:0.10, G:0.00, T:0.05
Consensus pattern (10 bp):
ACAAAAAAAA
Found at i:1322930 original size:20 final size:20
Alignment explanation
Indices: 1322897--1322934 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1322887 TTTGACTTAC
1322897 AAAAACAAAAAAAAAAAATT
1 AAAAACAAAAAAAAAAAATT
1322917 AAAAA-AAAACAAAAAAAA
1 AAAAACAAAA-AAAAAAAA
1322935 ACCAACTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.89, C:0.05, G:0.00, T:0.05
Consensus pattern (20 bp):
AAAAACAAAAAAAAAAAATT
Found at i:1324004 original size:62 final size:62
Alignment explanation
Indices: 1323913--1324474 Score: 355
Period size: 62 Copynumber: 8.8 Consensus size: 62
1323903 AGTAGGATGC
* * * * *
1323913 CTTTTTTCTTTTAAAAAGCTCACACAAGTTGGTGACACCTTTTAGTCTTCAAAGAGCAGGACG
1 CTTTTTCCTTTTTAAAA-CCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACG
*** * * * *
1323976 CTTTTTCCTTTTTAAAACCTGTACAAGTTAGTGGCACCTTTTAGTCCTTAAAGAGCAAGATG
1 CTTTTTCCTTTTTAAAACCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACG
* * * * * *
1324038 CTTTTTCCTTTTTGAAAGCCCATATAAGCTGGTGGCACATTTTAGTCCTCAAAGAGCAGGATG
1 CTTTTTCCTTTTT-AAAACCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACG
* * * * **
1324101 -TTTTTCTTTTCCTTTAAAAGCCCACAAAACTTGGTGGCACCTTTTTAGTCCTTAAAGAGCAAAA
1 CTTTTTC-CTT--TTTAAAA-CCCACACAAGTTGGTGGCACC-TTTTAGTCCTCAAAGAGCAGGA
*
1324165 CAC
61 C-G
** * * * * *
1324168 CTTTACTTTTTCTTTTAAAGCCTATACAAGTTGGTGGCACCTTCTTAGTCCT-AAA-A-AAGTGC
1 CTTT--TTCCT-TTTTAAAACCCACACAAGTTGGTGGCACCTT-TTAGTCCTCAAAGAGCAG-GA
*
1324230 CTTT
61 C--G
* * * ** * * *
1324234 CCTTTTCC-TTTTAAAGCCTACACAAGTTGGTAACATCTTTTAGTCCTCAAAAAGCAGGACA
1 CTTTTTCCTTTTTAAAACCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACG
* * * *
1324295 CTTTTTCC-TTTTAAAAGCCCACACAAGTTGGTGGTATCTTTTAGTCCTCAAAAAGCAAGACG
1 CTTTTTCCTTTTTAAAA-CCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACG
* * * * * ** *
1324357 CTTTTTTCTTTTTCTTTTAAAGCCTACACAAGCTAGTGATACCTTTTAGTCCTCAAAGAGTA-GA
1 C-TTTTTC---CT-TTTTAAAACCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGA
*
1324421 CA
61 CG
* * * *
1324423 CTTTTTCCTTCTTAAAAGTCCACACAAGTTGGTGGTACCTTTTAGTCATCAA
1 CTTTTTCCTTTTTAAAA-CCCACACAAGTTGGTGGCACCTTTTAGTCCTCAA
1324475 GGAATAAGAG
Statistics
Matches: 392, Mismatches: 82, Indels: 51
0.75 0.16 0.10
Matches are distributed among these distances:
61 28 0.07
62 153 0.39
63 66 0.17
64 8 0.02
65 27 0.07
66 31 0.08
67 58 0.15
68 16 0.04
69 2 0.01
70 3 0.01
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.36
Consensus pattern (62 bp):
CTTTTTCCTTTTTAAAACCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAGGACG
Found at i:1324160 original size:66 final size:63
Alignment explanation
Indices: 1323892--1324162 Score: 217
Period size: 63 Copynumber: 4.3 Consensus size: 63
1323882 TTATCCCTTA
* * * * * * * ** *
1323892 AGTCCTTTAAGAGTAGGATGCCTTTTTTCTTTTAAAAAGCTCACACAAGTTGGTGACACCTTTT
1 AGTCCTTAAAGAGCAAGATG-CTTTTTCCTTTTTAAAAGCCCACATAAACTGGTGGCACCTTTT
* * *** * ** *
1323956 AGT-CTTCAAAGAGCAGGACGCTTTTTCCTTTTTAAAA-CCTGTACAAGTTAGTGGCACCTTTT
1 AGTCCTT-AAAGAGCAAGATGCTTTTTCCTTTTTAAAAGCCCACATAAACTGGTGGCACCTTTT
* * * *
1324018 AGTCCTTAAAGAGCAAGATGCTTTTTCCTTTTTGAAAGCCCATATAAGCTGGTGGCACATTTT
1 AGTCCTTAAAGAGCAAGATGCTTTTTCCTTTTTAAAAGCCCACATAAACTGGTGGCACCTTTT
* * *
1324081 AGTCCTCAAAGAGCAGGATG-TTTTTCTTTTCCTTTAAAAGCCCACA-AAACTTGGTGGCACCTT
1 AGTCCTTAAAGAGCAAGATGCTTTTTC-CTT--TTTAAAAGCCCACATAAAC-TGGTGGCACC-T
1324144 TTT
61 TTT
1324147 AGTCCTTAAAGAGCAA
1 AGTCCTTAAAGAGCAA
1324163 AACACCTTTA
Statistics
Matches: 170, Mismatches: 29, Indels: 14
0.80 0.14 0.07
Matches are distributed among these distances:
62 55 0.32
63 60 0.35
64 16 0.09
65 21 0.12
66 18 0.11
ACGTcount: A:0.27, C:0.20, G:0.18, T:0.35
Consensus pattern (63 bp):
AGTCCTTAAAGAGCAAGATGCTTTTTCCTTTTTAAAAGCCCACATAAACTGGTGGCACCTTTT
Found at i:1324467 original size:191 final size:186
Alignment explanation
Indices: 1323913--1324474 Score: 513
Period size: 191 Copynumber: 2.9 Consensus size: 186
1323903 AGTAGGATGC
* * * * *
1323913 CTTTTTTCTTTTAAAAAGCTCACACAAGTTGGTGACACCTTTTAGTCTTCAAAGAGCAGGACGCT
1 CTTTTTCCTTTT-AAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAGACGCT
* * * * * **
1323978 TTTTC---CT-TTTTAAAACCTGTACAAGTTAGTGGCACCTTTTAGTCCTTAAAGAGCAAGATGC
65 TTTTCTTTTTCTTTTAAAGCCTATACAAGTTAGTGGCACCTTTTAGTCCTAAAAGAG-TAGACAC
* * * * * *
1324039 TTTTTCCTTTTTGAAAGCCCATATAAGCTGGTGGCACATTTTAGTCCTCAAAGAGCAGGAT
129 TTTTTCC-TTTT-AAAG-CCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAAAGCAGGAA
* * * * * *
1324100 GTTTTTCTTTTCCTTTAAAAGCCCACAAAACTTGGTGGCACCTTTTTAGTCCTTAAAGAGCAAAA
1 CTTTTTC----CTTTTAAAAGCCCACACAAGTTGGTGGCACC-TTTTAGTCCTCAAAGAGCAAGA
* * * * *
1324165 CACCTTTACTTTTTCTTTTAAAGCCTATACAAGTTGGTGGCACCTTCTTAGTCCTAAAAAAGT-G
61 CGCTTTTTCTTTTTCTTTTAAAGCCTATACAAGTTAGTGGCACCTT-TTAGTCCTAAAAGAGTAG
* * * ** *
1324229 CCTTTCCTTTTCCTTTTAAAGCCTACACAAGTTGGTAACATCTTTTAGTCCTCAAAAAGCAGGAC
125 AC--ACTTTTTCCTTTTAAAGCC-ACACAAGTTGGTGGCACCTTTTAGTCCTCAAAAAGCAGGA-
1324294 A
186 A
* * *
1324295 CTTTTTCCTTTTAAAAGCCCACACAAGTTGGTGGTATCTTTTAGTCCTCAAAAAGCAAGACGCTT
1 CTTTTTCCTTTTAAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAGACGC-T
* * ** *
1324360 TTTTCTTTTTCTTTTAAAGCCTACACAAGCTAGTGATACCTTTTAGTCCTCAAAGAGTAGACACT
65 TTTTCTTTTTCTTTTAAAGCCTATACAAGTTAGTGGCACCTTTTAGTCCTAAAAGAGTAGACACT
* *
1324425 TTTTCCTTCTTAAAAGTCCACACAAGTTGGTGGTACCTTTTAGTCATCAA
130 TTTTCCTT-TT-AAAG-CCACACAAGTTGGTGGCACCTTTTAGTCCTCAA
1324475 GGAATAAGAG
Statistics
Matches: 295, Mismatches: 61, Indels: 34
0.76 0.16 0.09
Matches are distributed among these distances:
187 5 0.02
189 9 0.03
190 59 0.20
191 122 0.41
192 2 0.01
193 2 0.01
194 38 0.13
195 38 0.13
196 20 0.07
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.36
Consensus pattern (186 bp):
CTTTTTCCTTTTAAAAGCCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAGAGCAAGACGCTT
TTTCTTTTTCTTTTAAAGCCTATACAAGTTAGTGGCACCTTTTAGTCCTAAAAGAGTAGACACTT
TTTCCTTTTAAAGCCACACAAGTTGGTGGCACCTTTTAGTCCTCAAAAAGCAGGAA
Found at i:1324492 original size:129 final size:130
Alignment explanation
Indices: 1323913--1324505 Score: 373
Period size: 129 Copynumber: 4.6 Consensus size: 130
1323903 AGTAGGATGC
* * ** * * *
1323913 CTTTTTTCTTTTAAAAAGCTCACACAAGTTGGTGACACCTTTTAGTCTTCAAAGAGCAGGACG-C
1 CTTTTTCCTTTT-AAAAGCCCACACAAGTTGGTGGTACCTTTTAGTCATCAAAAAGCAAGACGCC
* * ** * ** * * * *
1323977 -TTTTTC---CT-TTTTAAAACCTGTACAAGTTAGTGGCACCTTTTAGTCCTTAAAGAGCAAGAT
65 TTTTTTCTTTTTCTTTTAAAGCCTACACAAGCTAGTAACACCTTTTAGTCCTCAAAAAGCAGGAC
*
1324037 G
130 A
* * * * * * * * * *
1324038 CTTTTTCCTTTTTGAAAGCCCATATAAGCTGGTGGCACATTTTAGTCCTCAAAGAGCAGGATG--
1 CTTTTTCC-TTTTAAAAGCCCACACAAGTTGGTGGTACCTTTTAGTCATCAAAAAGCAAGACGCC
* * * * * ** * * **
1324101 -TTTTTCTTTTCCTTTAAAAGCCCACA-AAACTTGGTGGCACCTTTTTAGTCCTTAAAGAGCAAA
65 TTTTTTCTTTTTCTTTTAAAGCCTACACAAGC-TAGTAACACC-TTTTAGTCCTCAAAAAGCAGG
1324164 ACA
128 ACA
* * * * *
1324167 CCTTTACTTTTTCTTTT-AAAGCCTATACAAGTTGGTGGCACCTTCTTAGTC--CTAAAA--AAG
1 -C--T--TTTTCCTTTTAAAAGCCCACACAAGTTGGTGGTACCTT-TTAGTCATCAAAAAGCAAG
* * * * * *
1324227 -TGCC--TTTCCTTTTCCTTTTAAAGCCTACACAAGTTGGTAACATCTTTTAGTCCTCAAAAAGC
60 ACGCCTTTTTTCTTTTTCTTTTAAAGCCTACACAAGCTAGTAACACCTTTTAGTCCTCAAAAAGC
1324289 AGGACA
125 AGGACA
* *
1324295 CTTTTTCCTTTTAAAAGCCCACACAAGTTGGTGGTATCTTTTAGTCCTCAAAAAGCAAGACG-CT
1 CTTTTTCCTTTTAAAAGCCCACACAAGTTGGTGGTACCTTTTAGTCATCAAAAAGCAAGACGCCT
* * * *
1324359 TTTTTCTTTTTCTTTTAAAGCCTACACAAGCTAGTGATACCTTTTAGTCCTCAAAGAGTA-GACA
66 TTTTTCTTTTTCTTTTAAAGCCTACACAAGCTAGTAACACCTTTTAGTCCTCAAAAAGCAGGACA
* * * *
1324423 CTTTTTCCTTCTTAAAAGTCCACACAAGTTGGTGGTACCTTTTAGTCATCAAGGAA-TAAGAGGC
1 CTTTTTCCTT-TTAAAAGCCCACACAAGTTGGTGGTACCTTTTAGTCATCAA-AAAGCAAGACGC
1324487 CTTTTTTTCTTTTTCTTTT
64 C-TTTTTTCTTTTTCTTTT
1324506 TTAAAAAAAG
Statistics
Matches: 375, Mismatches: 65, Indels: 50
0.77 0.13 0.10
Matches are distributed among these distances:
123 15 0.04
124 29 0.08
125 54 0.14
126 4 0.01
127 7 0.02
128 55 0.15
129 145 0.39
130 6 0.02
131 21 0.06
132 24 0.06
133 10 0.03
134 5 0.01
ACGTcount: A:0.27, C:0.21, G:0.15, T:0.37
Consensus pattern (130 bp):
CTTTTTCCTTTTAAAAGCCCACACAAGTTGGTGGTACCTTTTAGTCATCAAAAAGCAAGACGCCT
TTTTTCTTTTTCTTTTAAAGCCTACACAAGCTAGTAACACCTTTTAGTCCTCAAAAAGCAGGACA
Found at i:1325138 original size:20 final size:21
Alignment explanation
Indices: 1325094--1325147 Score: 74
Period size: 20 Copynumber: 2.6 Consensus size: 21
1325084 TTCTACAATT
* *
1325094 TGTATAGATACAAACAGTAAA
1 TGTATCGATACATACAGTAAA
*
1325115 TGTATCGATACATA-AGTGAA
1 TGTATCGATACATACAGTAAA
1325135 TGTATCGATACAT
1 TGTATCGATACAT
1325148 GTCTGAAATG
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 18 0.60
21 12 0.40
ACGTcount: A:0.43, C:0.11, G:0.17, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATACAGTAAA
Found at i:1325159 original size:21 final size:21
Alignment explanation
Indices: 1325094--1325167 Score: 71
Period size: 21 Copynumber: 3.6 Consensus size: 21
1325084 TTCTACAATT
* *
1325094 TGTATAGATACA-AACAGTAAA
1 TGTATCGATACATAACTG-AAA
*
1325115 TGTATCGATACATAAGTG-AA
1 TGTATCGATACATAACTGAAA
**
1325135 TGTATCGATACATGTCTGAAA
1 TGTATCGATACATAACTGAAA
*
1325156 TGTATCAATACA
1 TGTATCGATACA
1325168 GGATCATGTC
Statistics
Matches: 44, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
20 17 0.39
21 24 0.55
22 3 0.07
ACGTcount: A:0.42, C:0.12, G:0.16, T:0.30
Consensus pattern (21 bp):
TGTATCGATACATAACTGAAA
Found at i:1327777 original size:51 final size:51
Alignment explanation
Indices: 1327714--1327824 Score: 152
Period size: 51 Copynumber: 2.2 Consensus size: 51
1327704 AGGGATAATT
* *
1327714 CAACCCCGTTTTTATTTTCAAAATATCAAATTTTCACCATCGA-AGATACTC
1 CAACCCCATTTTTATTTCCAAAATATCAAATTTTCACCAT-GAGAGATACTC
* * *
1327765 CAACCCCATTTTTATTTCCAAAATATCGATTTTTCACCATTAGAGATACTC
1 CAACCCCATTTTTATTTCCAAAATATCAAATTTTCACCATGAGAGATACTC
*
1327816 CAATCCCAT
1 CAACCCCAT
1327825 CATTTTTTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 1 0.02
51 52 0.98
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.35
Consensus pattern (51 bp):
CAACCCCATTTTTATTTCCAAAATATCAAATTTTCACCATGAGAGATACTC
Found at i:1327896 original size:79 final size:79
Alignment explanation
Indices: 1327758--1328088 Score: 308
Period size: 79 Copynumber: 4.2 Consensus size: 79
1327748 CACCATCGAA
* * * * *
1327758 GATACTCCAACCCCATTTTTATTTCCAAAATATCGATTTTTCACCAT-TAGAGATACTCCAATCC
1 GATACTCCAACCCCGTTTTTATTTCCAAAATATCAAATTTTCACCATCGAGA-ATACTCCAACCC
*
1327822 CATCATTTTTTAAGG
65 CATCATTTTTGAAGG
* * * *
1327837 GATGCTTCAACCCCGTTTTTATTTCGAAAATATCAAATTTTCACTATCGAGAATACTCCAACCCC
1 GATACTCCAACCCCGTTTTTATTTCCAAAATATCAAATTTTCACCATCGAGAATACTCCAACCCC
*
1327902 ATTATTTTTGAAGG
66 ATCATTTTTGAAGG
* * * * *
1327916 GATACTCCAATCTCGTTTTGTATTTCCAAAAGCATTAAATTTCTCACCATCGGGAATACTCCAAC
1 GATACTCCAACCCCGTTTT-TATTTCCAAAA-TATCAAATTT-TCACCATCGAGAATACTCCAAC
* * ***
1327981 CTCATTATTTCCAAAGG
63 CCCATCATTTTTGAAGG
* *** * * *
1327998 GATACTCTAACCTTATTTTTACTTT-CAAAATATTAAATTTTTCATC-TCGAGGATACTCCAACC
1 GATACTCCAACCCCGTTTTTA-TTTCCAAAATATCAAA-TTTTCACCATCGAGAATACTCCAACC
* * *
1328061 TCACCATCTTTGAAGG
64 CCATCATTTTTGAAGG
1328077 GATACTCCAACC
1 GATACTCCAACC
1328089 TCGATTTTCA
Statistics
Matches: 207, Mismatches: 39, Indels: 12
0.80 0.15 0.05
Matches are distributed among these distances:
79 115 0.56
80 23 0.11
81 18 0.09
82 51 0.25
ACGTcount: A:0.31, C:0.25, G:0.10, T:0.35
Consensus pattern (79 bp):
GATACTCCAACCCCGTTTTTATTTCCAAAATATCAAATTTTCACCATCGAGAATACTCCAACCCC
ATCATTTTTGAAGG
Found at i:1332365 original size:21 final size:21
Alignment explanation
Indices: 1332339--1332428 Score: 55
Period size: 21 Copynumber: 4.2 Consensus size: 21
1332329 AAAACAACTA
1332339 AAAATTAATAAAATTTAAATG
1 AAAATTAATAAAATTTAAATG
1332360 AAAATT--TAAAA--TAAA-G
1 AAAATTAATAAAATTTAAATG
* * * *
1332376 AAAATAAAAAAAAATTAAAAACAACTA
1 AAAAT-TAATAAAATT---TA-AA-TG
1332403 AAAATTAATAAAATTTAAATG
1 AAAATTAATAAAATTTAAATG
1332424 AAAAT
1 AAAAT
1332429 CTCTAAGGCT
Statistics
Matches: 50, Mismatches: 8, Indels: 22
0.62 0.10 0.28
Matches are distributed among these distances:
16 6 0.12
17 4 0.08
19 9 0.18
21 12 0.24
22 2 0.04
23 1 0.02
24 1 0.02
25 2 0.04
26 8 0.16
27 5 0.10
ACGTcount: A:0.69, C:0.02, G:0.03, T:0.26
Consensus pattern (21 bp):
AAAATTAATAAAATTTAAATG
Found at i:1336803 original size:20 final size:21
Alignment explanation
Indices: 1336759--1336803 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 21
1336749 TTTAATATTA
* *
1336759 ATTAAAAATTAAAAAATTTAT
1 ATTAAAAATTAAAAAAGTTAG
*
1336780 ATTAAAAATT-AAAAAGTTCG
1 ATTAAAAATTAAAAAAGTTAG
1336800 ATTA
1 ATTA
1336804 GATTTGTAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 11 0.52
21 10 0.48
ACGTcount: A:0.58, C:0.02, G:0.04, T:0.36
Consensus pattern (21 bp):
ATTAAAAATTAAAAAAGTTAG
Found at i:1340634 original size:52 final size:52
Alignment explanation
Indices: 1340556--1340683 Score: 224
Period size: 52 Copynumber: 2.5 Consensus size: 52
1340546 CGAAATATGA
*
1340556 AAATTTGCCTGCATGTATCGATACA-TTTAATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAA-AATGTATCGATACATCTGGGC
1340608 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
1340660 AAA-TTGCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
1340684 AAGATCAGTG
Statistics
Matches: 74, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 21 0.28
52 48 0.65
53 5 0.07
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.34
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTTAAAATGTATCGATACATCTGGGC
Found at i:1340710 original size:13 final size:13
Alignment explanation
Indices: 1340692--1340716 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1340682 CAAAGATCAG
1340692 TGTATCGATACAA
1 TGTATCGATACAA
1340705 TGTATCGATACA
1 TGTATCGATACA
1340717 TTTGAGTAAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1340794 original size:33 final size:33
Alignment explanation
Indices: 1340757--1340823 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1340747 AGTAGCTTAA
1340757 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1340790 ATTGTATCGATACAACATTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1340823 A
1 A
1340824 AATCGTTGAA
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:0.40, C:0.13, G:0.12, T:0.34
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1340797 original size:13 final size:13
Alignment explanation
Indices: 1340779--1340803 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1340769 CAAAAAAATA
1340779 TGTATCGATACAT
1 TGTATCGATACAT
1340792 TGTATCGATACA
1 TGTATCGATACA
1340804 ACATTTTATG
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:1341103 original size:49 final size:49
Alignment explanation
Indices: 1341031--1341714 Score: 901
Period size: 49 Copynumber: 14.6 Consensus size: 49
1341021 CTTATTCAAG
1341031 GCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGT
1 GCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGT
*
1341080 GCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG-AGGTGCCAATGT
1 GCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGT
1341128 GCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGT
1 GCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGT
* * * *
1341177 GCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGATGATGCCAATAT
1 GCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGT
* *
1341226 GCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATGT
1 GCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGT
* * *
1341269 GCTGATTCAAGGCCAGCTACATTGGACTTAAAGATAAAGATGCCAATAT
1 GCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGT
* * *
1341318 GCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAGTGT
1 GCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGT
* * *
1341361 GCTGATTCAAGGCCAGGTACATTGGACTTAAAGATGAAGATGCCAATAT
1 GCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGT
* *
1341410 GCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATGT
1 GCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGT
* *
1341453 GCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATAT
1 GCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGT
* *
1341502 GCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATGT
1 GCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGT
* *
1341545 GCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATAT
1 GCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGT
* *
1341594 GCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATGT
1 GCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGT
*
1341637 GCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGGTGCCAATGT
1 GCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGT
1341685 GCTGATTCAAGGCCAGCTACATTGGACTTA
1 GCTGATTCAAGGCCAGCTACATTGGACTTA
1341715 GAAGGGTTGC
Statistics
Matches: 553, Mismatches: 51, Indels: 63
0.83 0.08 0.09
Matches are distributed among these distances:
43 187 0.34
45 5 0.01
47 4 0.01
48 89 0.16
49 268 0.48
ACGTcount: A:0.31, C:0.19, G:0.26, T:0.25
Consensus pattern (49 bp):
GCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGT
Found at i:1341311 original size:92 final size:92
Alignment explanation
Indices: 1341031--1341719 Score: 1094
Period size: 92 Copynumber: 7.4 Consensus size: 92
1341021 CTTATTCAAG
* * *
1341031 GCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAG
1 GCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATGTGCTGATTCAAGGCCAG
* *
1341096 CTACATTGGACTTAAAGATG-AGGTGCCAATGT
60 CTACATTGGACTTAAAGATGAAGATGCCAATAT
* * *
1341128 GCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATGTGCTGAGTCAAGGCCAG
1 GCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGGTGCCAATGTGCTGATTCAAGGCCAG
*
1341193 CTACATTGGACTTAAAGATGATGATGCCAATAT
60 CTACATTGGACTTAAAGATGAAGATGCCAATAT
1341226 GCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACAT
1 GCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACAT
*
1341291 TGGACTTAAAGATAAAGATGCCAATAT
66 TGGACTTAAAGATGAAGATGCCAATAT
* *
1341318 GCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAGTGTGCTGATTCAAGGCCAGGTACAT
1 GCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACAT
1341383 TGGACTTAAAGATGAAGATGCCAATAT
66 TGGACTTAAAGATGAAGATGCCAATAT
1341410 GCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACAT
1 GCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACAT
1341475 TGGACTTAAAGATGAAGATGCCAATAT
66 TGGACTTAAAGATGAAGATGCCAATAT
1341502 GCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACAT
1 GCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACAT
1341567 TGGACTTAAAGATGAAGATGCCAATAT
66 TGGACTTAAAGATGAAGATGCCAATAT
1341594 GCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACAT
1 GCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACAT
* * *
1341659 TGGACTTAAAGGTG-AGGTGCCAATGT
66 TGGACTTAAAGATGAAGATGCCAATAT
* *
1341685 GCTGATTCAAGGCCAGCTACATTGGACTTAGAAGG
1 GCTGATTCAAGGCCAGCGATATTGGACTTA-AAGG
1341720 GTTGCCACCG
Statistics
Matches: 572, Mismatches: 18, Indels: 9
0.95 0.03 0.02
Matches are distributed among these distances:
91 38 0.07
92 412 0.72
94 1 0.00
97 85 0.15
98 36 0.06
ACGTcount: A:0.31, C:0.18, G:0.26, T:0.25
Consensus pattern (92 bp):
GCTGATTCAAGGCCAGCGATATTGGACTTAAAGGTGCCAATGTGCTGATTCAAGGCCAGCTACAT
TGGACTTAAAGATGAAGATGCCAATAT
Found at i:1341796 original size:67 final size:68
Alignment explanation
Indices: 1341714--1341887 Score: 284
Period size: 67 Copynumber: 2.6 Consensus size: 68
1341704 CATTGGACTT
*
1341714 AGAAGGG-TTGCCACCGACTTGTGTGGGCTTTAGAGAATGG-TTGCCACCAACTTGTGTGGGCTT
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTTGCCACCAACTTGTGTGGGCTT
*
1341777 TGG
66 TAG
* *
1341780 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAAAGAAGGGTTTGCCACCGACTTGTGTGGGCTT
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTTGCCACCAACTTGTGTGGGCTT
1341845 TAG
66 TAG
1341848 AGAA-GGTTTGCCACCGACTTGTGTGGGCTTTAGA-AAGGGT
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGT
1341888 GAAAGATGCC
Statistics
Matches: 101, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
66 13 0.13
67 60 0.59
68 28 0.28
ACGTcount: A:0.20, C:0.17, G:0.34, T:0.29
Consensus pattern (68 bp):
AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTTGCCACCAACTTGTGTGGGCTT
TAG
Found at i:1341801 original size:34 final size:34
Alignment explanation
Indices: 1341714--1341887 Score: 284
Period size: 33 Copynumber: 5.2 Consensus size: 34
1341704 CATTGGACTT
1341714 AGAAGGG-TTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
* * *
1341747 AGAATGG-TTGCCACCAACTTGTGTGGGCTTTGG
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
*
1341780 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAA
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
1341814 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
1341848 AGAA-GGTTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
1341881 A-AAGGGT
1 AGAAGGGT
1341888 GAAAGATGCC
Statistics
Matches: 131, Mismatches: 8, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
32 2 0.02
33 69 0.53
34 60 0.46
ACGTcount: A:0.20, C:0.17, G:0.34, T:0.29
Consensus pattern (34 bp):
AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:1341999 original size:34 final size:35
Alignment explanation
Indices: 1341869--1342965 Score: 1215
Period size: 34 Copynumber: 32.3 Consensus size: 35
1341859 CACCGACTTG
** *
1341869 TGTGGGCTTTAGAAAGGGTGAAAGA-TGCCACGAAGT
1 TGTGGGCTTTA-AAA-GGAAAAAGAGTGCCACGGAGT
* * *
1341905 TGTGGAC-TTAAAAAGAACAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
1341938 TGTGGGCTTTAAAAGGGAAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAAA-GG-AAAAAGAGTGCCACGGAGT
*
1341975 TGTGGGC-TTAGAAGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
* *
1342009 TGTGGGC-TTAGAAGG-AAAAGAGTGCCACGTAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
* *
1342042 TGTGGGCTTT-AAAGG-AAAAGAGTGCTACGTAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
* *
1342075 CGTGGAC-TTAAAA-G-----G-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
1342102 TGTGGGCTTTGAAAA-G---AAG-GTGCCACGGAGT
1 TGTGGGCTTT-AAAAGGAAAAAGAGTGCCACGGAGT
1342133 TGTGGGCTTTAACAAGGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAA-AA-GGAAAAAGAGTGCCACGGAGT
* * *
1342170 TGTGGACTGTAAAAAGAAAAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
1342204 TGTGGGCTTTGAAAAGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTT-AAAAGGAAAAAGAGTGCCACGGAGT
* *
1342240 TGTGGGC-TTAGAAGG-AAAAGAGTGCCACGTAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
*
1342273 TGTGGGCTTTGAAAAGGAAAAAGAGTGCCGCGGAGT
1 TGTGGGCTTT-AAAAGGAAAAAGAGTGCCACGGAGT
1342309 TGTGGGCTTTAACAAGGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAA-AA-GGAAAAAGAGTGCCACGGAGT
* *
1342346 TGTGGGCTGTAAAAAGAAAAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
**
1342380 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACAAAGT
1 TGTGGGCTTT-AAAA-GGAAAAAGAGTGCCACGGAGT
* * *
1342417 TGTGGGCTTTAAAAAGAAAAAGTGTGCCACAGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
**
1342452 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACAAAGT
1 TGTGGGCTTT-AAAA-GGAAAAAGAGTGCCACGGAGT
* * *
1342489 TGTGGGCTTTAAAAAGAAAAAGTGTGCCACAGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
*
1342524 TGTGGGCTTTAAAAAGAAAAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
* *
1342558 TGTGGAC-TTAAAGATGAAAAA-AGTGCCACGGAGT
1 TGTGGGCTTTAAA-AGGAAAAAGAGTGCCACGGAGT
*
1342592 TGTGGGCTTTGAAA-G---AAG-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
*
1342622 TGTGGGCTTTGAAAA-GAAGAAG-GTGCCACGGAGT
1 TGTGGGCTTT-AAAAGGAAAAAGAGTGCCACGGAGT
*
1342656 TGTGGGCTTT-AAAGG-AAAAG-GTGCCACAGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
1342688 TGTGGGCTTTAAAA-GAAAAA-AGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
1342721 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTT-AAAA-GGAAAAAGAGTGCCACGGAGT
1342758 TGTGGGCTTTAAACA-GAAAAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAA-AGGAAAAAGAGTGCCACGGAGT
* *
1342792 TGTGGGCTTTAAAAAGAAAAAG-GTGCCACGGTGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
* *
1342826 TGTGGAC-TTAAAGATGAAAAA-AGTGCCACGGAGT
1 TGTGGGCTTTAAA-AGGAAAAAGAGTGCCACGGAGT
*
1342860 TGTGGGCTTTGAAA-G---AAG-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
* *
1342890 TGTGGGCTTTGAAAA-GAAGAAG-GTGCCACAGAGT
1 TGTGGGCTTT-AAAAGGAAAAAGAGTGCCACGGAGT
1342924 TGTGGGCTTT-AAAGG-AAAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
1342956 TGTGGGCTTT
1 TGTGGGCTTT
1342966 GAAGAAAAAA
Statistics
Matches: 939, Mismatches: 65, Indels: 118
0.84 0.06 0.11
Matches are distributed among these distances:
27 15 0.02
28 3 0.00
29 5 0.01
30 50 0.05
31 33 0.04
32 60 0.06
33 141 0.15
34 263 0.28
35 127 0.14
36 98 0.10
37 144 0.15
ACGTcount: A:0.32, C:0.12, G:0.35, T:0.21
Consensus pattern (35 bp):
TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
Found at i:1342001 original size:71 final size:69
Alignment explanation
Indices: 1341869--1342965 Score: 1215
Period size: 71 Copynumber: 16.1 Consensus size: 69
1341859 CACCGACTTG
** * * * *
1341869 TGTGGGCTTTAGAAAGGGTGAAAGA-TGCCACGAAGTTGTGGAC-TTAAAAAGAACAAGGTGCCA
1 TGTGGGCTTTA-AAA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGGTGCCA
1341932 CGGAGT
64 CGGAGT
*
1341938 TGTGGGCTTTAAAAGGGAAAAAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGGAAAAAGAGTGCC
1 TGTGGGCTTTAAAA-GG-AAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAG-GTGCC
1342002 ACGGAGT
63 ACGGAGT
* * *
1342009 TGTGGGC-TTAGAAGG-AAAAGAGTGCCACGTAGTTGTGGGCTTT-AAAGG-AAAAGAGTGCTAC
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAG-GTGCCAC
*
1342070 GTAGT
65 GGAGT
* *
1342075 CGTGGAC-TTAAAA-G-----G-GTGCCACGGAGTTGTGGGCTTTGAAAA-G---AAGGTGCCAC
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAAGGAAAAAGGTGCCAC
1342128 GGAGT
65 GGAGT
* * *
1342133 TGTGGGCTTTAACAAGGGAAAAAGAGTGCCACGGAGTTGTGGACTGTAAAAAGAAAAAGGTGCCA
1 TGTGGGCTTTAA-AA-GGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGGTGCCA
1342198 CGGAGT
64 CGGAGT
*
1342204 TGTGGGCTTTGAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGG-AAAAGAGTGCCA
1 TGTGGGCTTT-AAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAG-GTGCCA
*
1342267 CGTAGT
64 CGGAGT
*
1342273 TGTGGGCTTTGAAAAGGAAAAAGAGTGCCGCGGAGTTGTGGGCTTTAACAAGGGAAAAAGAGTGC
1 TGTGGGCTTT-AAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAA-AA-GGAAAAAG-GTGC
1342338 CACGGAGT
62 CACGGAGT
* *
1342346 TGTGGGCTGTAAAAAGAAAAAG-GTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCC
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA-GGAAAAAG-GTGCC
**
1342410 ACAAAGT
63 ACGGAGT
* * *
1342417 TGTGGGCTTTAAAAAGAAAAAGTGTGCCACAGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCC
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA-GGAAAAAG-GTGCC
**
1342482 ACAAAGT
63 ACGGAGT
* * * *
1342489 TGTGGGCTTTAAAAAGAAAAAGTGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACG
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGGTGCCACG
1342554 GAGT
66 GAGT
* * *
1342558 TGTGGAC-TTAAAGATGAAAAA-AGTGCCACGGAGTTGTGGGCTTTGAAA-G---AAGGTGCCAC
1 TGTGGGCTTTAAA-AGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGGTGCCAC
1342617 GGAGT
65 GGAGT
*
1342622 TGTGGGCTTTGAAAA-GAAGAAG-GTGCCACGGAGTTGTGGGCTTT-AAAGG-AAAAGGTGCCAC
1 TGTGGGCTTT-AAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGGTGCCAC
*
1342683 AGAGT
65 GGAGT
1342688 TGTGGGCTTTAAAA-GAAAAA-AGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCC
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT-AAAA-GGAAAAAG-GTGCC
1342751 ACGGAGT
63 ACGGAGT
*
1342758 TGTGGGCTTTAAACA-GAAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCAC
1 TGTGGGCTTTAAA-AGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGGTGCCAC
*
1342821 GGTGT
65 GGAGT
* * *
1342826 TGTGGAC-TTAAAGATGAAAAA-AGTGCCACGGAGTTGTGGGCTTTGAAA-G---AAGGTGCCAC
1 TGTGGGCTTTAAA-AGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGGTGCCAC
1342885 GGAGT
65 GGAGT
* *
1342890 TGTGGGCTTTGAAAA-GAAGAAG-GTGCCACAGAGTTGTGGGCTTT-AAAGG-AAAAGGTGCCAC
1 TGTGGGCTTT-AAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGGTGCCAC
1342951 GGAGT
65 GGAGT
1342956 TGTGGGCTTT
1 TGTGGGCTTT
1342966 GAAGAAAAAA
Statistics
Matches: 918, Mismatches: 59, Indels: 105
0.85 0.05 0.10
Matches are distributed among these distances:
58 15 0.02
59 7 0.01
60 23 0.03
61 2 0.00
62 4 0.00
63 6 0.01
64 96 0.10
65 38 0.04
66 81 0.09
67 44 0.05
68 113 0.12
69 111 0.12
70 97 0.11
71 145 0.16
72 110 0.12
73 26 0.03
ACGTcount: A:0.32, C:0.12, G:0.35, T:0.21
Consensus pattern (69 bp):
TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAAAGGAAAAAGGTGCCACG
GAGT
Found at i:1342106 original size:27 final size:29
Alignment explanation
Indices: 1341991--1342220 Score: 95
Period size: 33 Copynumber: 7.2 Consensus size: 29
1341981 CTTAGAAGGA
* * *
1341991 AAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGG
1 AAAAGGGTGCCACGGAGTTGTGGACTT----TG
* * *
1342024 AAAAGAGTGCCACGTAGTTGTGGGCTTTAAAGG
1 AAAAGGGTGCCACGGAGTTGTGGACTTT----G
* * * *
1342057 AAAAGAGTGCTACGTAGTCGTGGAC-TT-
1 AAAAGGGTGCCACGGAGTTGTGGACTTTG
*
1342084 AAAAGGGTGCCACGGAGTTGTGGGCTTTG
1 AAAAGGGTGCCACGGAGTTGTGGACTTTG
*
1342113 AAAAGAAGGTGCCACGGAGTTGTGGGCTTTAACAAGGG
1 AAAAG--GGTGCCACGGAGTTGTGGACTTT-------G
* *
1342151 AAAAAGAGTGCCACGGAGTTGTGGACTGTAAAAAG
1 -AAAAGGGTGCCACGGAGTTGTGGACT-T----TG
* *
1342186 AAAAAGGTGCCACGGAGTTGTGGGCTTTG
1 AAAAGGGTGCCACGGAGTTGTGGACTTTG
1342215 AAAAGG
1 AAAAGG
1342221 AAAAAGAGTG
Statistics
Matches: 158, Mismatches: 18, Indels: 46
0.71 0.08 0.21
Matches are distributed among these distances:
27 20 0.13
28 2 0.01
29 11 0.07
31 23 0.15
32 2 0.01
33 50 0.32
34 23 0.15
35 1 0.01
37 19 0.12
38 2 0.01
39 5 0.03
ACGTcount: A:0.31, C:0.13, G:0.36, T:0.21
Consensus pattern (29 bp):
AAAAGGGTGCCACGGAGTTGTGGACTTTG
Found at i:1342848 original size:268 final size:270
Alignment explanation
Indices: 1341889--1342996 Score: 1338
Period size: 268 Copynumber: 4.1 Consensus size: 270
1341879 AGAAAGGGTG
* *
1341889 AAAGATGCCACGAAGTTGTGGAC-TTAAAAAGAACAAGGTGCCACGGAGTTGTGGGCTTTAAAAG
1 AAAG-TGCCACGGAGTTGTGGACTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAA-
* * *
1341953 GGAAAAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTT
64 GG-AAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAAGAAAAAGAGTGCCACGGAGTTGTGGACTT
* * * * *
1342018 AGAAG--GAAAAGAGTGCCACGTAGTTGTGGGCTTT-AAAGGAAAAGAGTGCTACGTAGTCGTGG
128 A-AAGATGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAGG-AAAGAGTGCCACGGAGTTGTGG
* * *
1342080 AC-TT---AA-AAG--GGTGCCACGGAGTTGTGGGCTTTGAAA--AGAAGGTGCCACGGAGTTGT
191 GCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAGGAAAAGGTGCCACAGAGTTGT
1342136 GGGCTTTAACAAGGGAAA
256 GGGCTTTAA-AA--GAAA
*
1342154 AAGAGTGCCACGGAGTTGTGGACTGTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAA
1 AA-AGTGCCACGGAGTTGTGGACTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTT-AAAA
* * * *
1342219 GGAAAAAGAGTGCCACGGAGTTGTGGGCTT-AGAAGGAAAAGAGTGCCACGTAGTTGTGGGCTTT
64 GGAAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAAGAAAAAGAGTGCCACGGAGTTGTGGAC-TT
* * *
1342283 GAAA-AGGAAAAAGAGTGCCGCGGAGTTGTGGGCTTTAACAAGGGAAAAAGAGTGCCACGGAGTT
128 -AAAGATGAAAAA-AGTGCCACGGAGTTGTGGGCTTTGA-AA-GG--AAAGAGTGCCACGGAGTT
* * *
1342347 GTGGGCTGTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCAC
187 GTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTG-AAA-GG-AAAAG-GTGCCAC
*
1342412 AAAGTTGTGGGCTTTAAAAAGAAA
248 AGAGTTGTGGGCTTT-AAAAGAAA
* * * * **
1342436 AAGTGTGCCACAGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACAAAGTTGTGGGCTTTAA
1 AA-AGTGCCACGGAGTTGTGGACTTT-AAAA-AGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAA
* * *
1342501 AAAGAAAAAGTGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAG-GTGCCACGGAGTTGTGGAC
62 AAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TTAAAAAGAAAAAGAGTGCCACGGAGTTGTGGAC
1342565 TTAAAGATGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAA-G-AAG-GTGCCACGGAGTTGTGG
126 TTAAAGATGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAGGAAAGAGTGCCACGGAGTTGTGG
1342627 GCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTT-AAAGGAAAAGGTGCCACAGAGTTGT
191 GCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAGGAAAAGGTGCCACAGAGTTGT
1342691 GGGCTTTAAAAGAAA
256 GGGCTTTAAAAGAAA
* *
1342706 AAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
1 AAAGTGCCACGGAGTTGTGGACTTT-AAAA-AGAAAAAG-GTGCCACGGAGTTGTGGGCTTTAAA
*
1342771 CA-GAAAAAG-GTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAG-GTGCCACGGTGTTGTGGAC
63 -AGGAAAAAGAGTGCCACGGAGTTGTGGGC-TTAAAAAGAAAAAGAGTGCCACGGAGTTGTGGAC
1342833 TTAAAGATGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAA-G-AAG-GTGCCACGGAGTTGTGG
126 TTAAAGATGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAGGAAAGAGTGCCACGGAGTTGTGG
* *
1342895 GCTTTGAAAAGAAGAAGGTGCCACAGAGTTGTGGGCTTT-AAAGGAAAAGGTGCCACGGAGTTGT
191 GCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAGGAAAAGGTGCCACAGAGTTGT
*
1342959 GGGCTTT-GAAGAAA
256 GGGCTTTAAAAGAAA
** *
1342973 AAA-TGCCACTAAGTCGTGGACTTT
1 AAAGTGCCACGGAGTTGTGGACTTT
1342997 GAGATAAAAT
Statistics
Matches: 756, Mismatches: 54, Indels: 65
0.86 0.06 0.07
Matches are distributed among these distances:
264 26 0.03
265 51 0.07
266 61 0.08
267 34 0.04
268 183 0.24
269 68 0.09
270 13 0.02
271 42 0.06
272 6 0.01
273 2 0.00
274 3 0.00
275 2 0.00
276 55 0.07
277 3 0.00
278 24 0.03
279 3 0.00
280 1 0.00
282 28 0.04
283 34 0.04
284 67 0.09
285 41 0.05
286 9 0.01
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.21
Consensus pattern (270 bp):
AAAGTGCCACGGAGTTGTGGACTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAGG
AAAAAGAGTGCCACGGAGTTGTGGGCTTAAAAAGAAAAAGAGTGCCACGGAGTTGTGGACTTAAA
GATGAAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAGGAAAGAGTGCCACGGAGTTGTGGGCTTT
GAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAGGAAAAGGTGCCACAGAGTTGTGGGCT
TTAAAAGAAA
Found at i:1343053 original size:63 final size:60
Alignment explanation
Indices: 1342945--1343156 Score: 219
Period size: 63 Copynumber: 3.4 Consensus size: 60
1342935 AAGGAAAAGG
* * * * * *
1342945 TGCCACGGAGTTGTGGGCTTTGAAGAAAAAATGCCACTAAGTCGTGGACTTTGAGATAAAA
1 TGCCACTGAGTCGTGGACTTTAAAGAAAAGATGCCACTGAGTCGTGGACTTTGAGA-AAAA
*
1343006 TGCCACTGAGTCGTGGACTTTAAAGATAAAGGATGCCACTGAGTCGTGGACTTTAAAGAAAAGGA
1 TGCCACTGAGTCGTGGACTTTAAAGA-AAA-GATGCCACTGAGTCGTGGACTTT-GAGAAAA--A
* * * * *
1343071 TGCCACTGGGTCGTGGACTTT-GAGCAGAGATTGCCACTGAGTCGTGGACTTTGAGAAGAGAT
1 TGCCACTGAGTCGTGGACTTTAAAGAAAAGA-TGCCACTGAGTCGTGGACTTTGAGAA-A-AA
*
1343133 TGCCACTTAGTCGTGGACTTTAAA
1 TGCCACTGAGTCGTGGACTTTAAA
1343157 AAGGTATTTG
Statistics
Matches: 126, Mismatches: 16, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
61 22 0.17
62 28 0.22
63 49 0.39
64 6 0.05
65 21 0.17
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (60 bp):
TGCCACTGAGTCGTGGACTTTAAAGAAAAGATGCCACTGAGTCGTGGACTTTGAGAAAAA
Found at i:1343092 original size:126 final size:126
Alignment explanation
Indices: 1342501--1343156 Score: 368
Period size: 132 Copynumber: 5.0 Consensus size: 126
1342491 TGGGCTTTAA
* * * * *
1342501 AAAGAAAAAGTGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACT
1 AAAGATAAAG-GTGCCACAGAGTCGTGGACTTT--AAAGGAAAAGGTGCCACGGAGTCGTGGACT
* ** * * * * * *
1342566 TAAAGATG-AAAAAAGTGCCACGGAGTTGTGGGCTTTGA-AAGA-AGGTGCCACGGAGTTGTGGG
63 T--TGA-GCAAAAAA-TGCCACTAAGTCGTGGACTTTGAGAAGAGA-ATGCCACTGAGTCGTGGA
1342628 CTTT
123 CTTT
* * * * * *
1342632 GAAAAGA-AGAAGGTGCCACGGAGTTGTGGGCTTTAAAGGAAAAGGTGCCACAGAGTTGTGGGCT
1 --AAAGATA-AAGGTGCCACAGAGTCGTGGACTTTAAAGGAAAAGGTGCCACGGAGTCGTGGACT
* ** * * * * * *
1342696 TTAAAAG-AAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTG
63 TT--GAGCAAAAAA-TGCCACTAAGTCGTGGACTTTG---A--G-AAGAGAATGCCACTGAGTCG
*
1342760 TGGGCTTT
119 TGGACTTT
* * * * * * *
1342768 AAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGTGTTGTGGAC
1 -AA-AGATAAAGGTGCCACAGAGTCGTGGACTTT--AAAGGAAAAGGTGCCACGGAGTCGTGGAC
* ** * * * * *
1342833 TTAAAGATG-AAAAAAGTGCCACGGAGTTGTGGGCTTTGA-AAGA-AGGTGCCACGGAGTTGTGG
62 TT--TGA-GCAAAAAA-TGCCACTAAGTCGTGGACTTTGAGAAGAGA-ATGCCACTGAGTCGTGG
*
1342895 GCTTT
122 ACTTT
* * * *
1342900 GAAAAGA-AGAAGGTGCCACAGAGTTGTGGGCTTTAAAGGAAAAGGTGCCACGGAGTTGTGGGCT
1 --AAAGATA-AAGGTGCCACAGAGTCGTGGACTTTAAAGGAAAAGGTGCCACGGAGTCGTGGACT
1342964 TTGAAG-AAAAAATGCCACTAAGTCGTGGACTTTGAGATA-A-AATGCCACTGAGTCGTGGACTT
63 TTG-AGCAAAAAATGCCACTAAGTCGTGGACTTTGAGA-AGAGAATGCCACTGAGTCGTGGACTT
1343026 T
126 T
*
1343027 AAAGATAAAGGATGCCACTGAGTCGTGGACTTTAAA-GAAAAGGATGCCACTGG-GTCGTGGACT
1 AAAGATAAAGG-TGCCACAGAGTCGTGGACTTTAAAGGAAAAGG-TGCCAC-GGAGTCGTGGACT
* * * * * *
1343090 TTGAGCAGAGATTGCCACTGAGTCGTGGACTTTGAGAAGAGATTGCCACTTAGTCGTGGACTTT
63 TTGAGCAAAAAATGCCACTAAGTCGTGGACTTTGAGAAGAGAATGCCACTGAGTCGTGGACTTT
1343154 AAA
1 AAA
1343157 AAGGTATTTG
Statistics
Matches: 454, Mismatches: 38, Indels: 68
0.81 0.07 0.12
Matches are distributed among these distances:
125 19 0.04
126 67 0.15
127 63 0.14
128 11 0.02
129 32 0.07
130 57 0.13
131 2 0.00
132 75 0.17
133 11 0.02
135 3 0.01
136 54 0.12
137 2 0.00
138 28 0.06
139 30 0.07
ACGTcount: A:0.32, C:0.13, G:0.32, T:0.22
Consensus pattern (126 bp):
AAAGATAAAGGTGCCACAGAGTCGTGGACTTTAAAGGAAAAGGTGCCACGGAGTCGTGGACTTTG
AGCAAAAAATGCCACTAAGTCGTGGACTTTGAGAAGAGAATGCCACTGAGTCGTGGACTTT
Found at i:1343109 original size:31 final size:30
Alignment explanation
Indices: 1342844--1343153 Score: 230
Period size: 31 Copynumber: 9.9 Consensus size: 30
1342834 TAAAGATGAA
* * *
1342844 AAAAG-TGCCACGGAGTTGTGGGCTTTGA-
1 AAAAGATGCCACTGAGTCGTGGACTTTGAG
* * * *
1342872 AAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAG
1 AA-AAGATGCCACTGAGTCGTGGACTTTG---AG
* * * * *
1342906 AAGAAGGTGCCACAGAGTTGTGGGCTTTAAAGG
1 AA-AAGATGCCACTGAGTCGTGGACTTT-GA-G
* * * *
1342939 AAAAGGTGCCACGGAGTTGTGGGCTTTGAAG
1 AAAAGATGCCACTGAGTCGTGGACTTTG-AG
* *
1342970 AAAAAATGCCACTAAGTCGTGGACTTTGAG
1 AAAAGATGCCACTGAGTCGTGGACTTTGAG
*
1343000 ATAAA-ATGCCACTGAGTCGTGGACTTTAAAG
1 A-AAAGATGCCACTGAGTCGTGGACTTT-GAG
*
1343031 ATAAAGGATGCCACTGAGTCGTGGACTTTAAAG
1 A-AAA-GATGCCACTGAGTCGTGGACTTT-GAG
*
1343064 AAAAGGATGCCACTGGGTCGTGGACTTTGAG
1 AAAA-GATGCCACTGAGTCGTGGACTTTGAG
* *
1343095 CAGAGATTGCCACTGAGTCGTGGACTTTGAG
1 AAAAGA-TGCCACTGAGTCGTGGACTTTGAG
* *
1343126 AAGAGATTGCCACTTAGTCGTGGACTTT
1 AAAAGA-TGCCACTGAGTCGTGGACTTT
1343154 AAAAAGGTAT
Statistics
Matches: 249, Mismatches: 19, Indels: 25
0.85 0.06 0.09
Matches are distributed among these distances:
28 2 0.01
29 3 0.01
30 48 0.19
31 86 0.35
32 52 0.21
33 31 0.12
34 27 0.11
ACGTcount: A:0.29, C:0.15, G:0.32, T:0.24
Consensus pattern (30 bp):
AAAAGATGCCACTGAGTCGTGGACTTTGAG
Found at i:1344911 original size:49 final size:49
Alignment explanation
Indices: 1344699--1345534 Score: 1050
Period size: 49 Copynumber: 17.8 Consensus size: 49
1344689 TCTTGCATTA
* * * *
1344699 TGCCACTGTGCAGATTCAAGGCCTGCCACACTT-GACTTAAAGATGGAAAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCTACA-TTGGACTTAAAGAT-G--AAGG
* * *
1344751 TGCCGATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGG
*
1344794 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGG
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGG
1344842 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGG
*
1344891 TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG-AGG
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGG
1344939 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGG
* * *
1344988 TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGATGA
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGG
* * *
1345037 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGG
*
1345080 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGG
* * * *
1345129 TGCCAATATGCTGATTCAAGTCCAGCGATATTGGACTT----A--AAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGG
* *
1345172 TGCCAGTGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGG
* * *
1345221 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGG
*
1345264 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGG
* * *
1345313 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGG
*
1345356 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGA
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGG
* * *
1345405 TGCCAATATGCTGATTCAAGGCCAGCGATATTGGACTT----A--AAGG
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGG
*
1345448 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGG
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGG
1345496 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
1345535 GAAGGGTTGC
Statistics
Matches: 682, Mismatches: 63, Indels: 82
0.82 0.08 0.10
Matches are distributed among these distances:
43 226 0.33
45 5 0.01
47 4 0.01
48 137 0.20
49 280 0.41
51 2 0.00
52 28 0.04
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (49 bp):
TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGG
Found at i:1345131 original size:92 final size:92
Alignment explanation
Indices: 1344699--1345539 Score: 1267
Period size: 92 Copynumber: 9.0 Consensus size: 92
1344689 TCTTGCATTA
* * * * * *
1344699 TGCCACTGTGCAGATTCAAGGCCTGCCACACTT-GACTTAAAGATGGAAAAGGTGCCGATATGCT
1 TGCCAATGTGCTGATTCAAGGCCAGCTACA-TTGGACTTAAAGAT-G--AAGATGCCAATATGCT
*
1344763 GATTCAAGGCCAGCTATATTGGACTTAAAGG
62 GATTCAAGGCCAGCGATATTGGACTTAAAGG
* * *
1344794 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGGTGCCAATGTGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATT
* *
1344858 CAAGGCCAGCTACATTGGACTTAAAGATGAAGG
66 CAAGGCCAGCGATATTGGACTT----A--AAGG
* * *
1344891 TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATG-AGGTGCCAATGTGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATT
* *
1344955 CAAGGCCAGCTACATTGGACTTAAAGATGAAGG
66 CAAGGCCAGCGATATTGGACTT----A--AAGG
* *
1344988 TGCCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGATGATGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATT
1345053 CAAGGCCAGCGATATTGGACTTAAAGG
66 CAAGGCCAGCGATATTGGACTTAAAGG
1345080 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATT
*
1345145 CAAGTCCAGCGATATTGGACTTAAAGG
66 CAAGGCCAGCGATATTGGACTTAAAGG
*
1345172 TGCCAGTGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATT
1345237 CAAGGCCAGCGATATTGGACTTAAAGG
66 CAAGGCCAGCGATATTGGACTTAAAGG
1345264 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATT
1345329 CAAGGCCAGCGATATTGGACTTAAAGG
66 CAAGGCCAGCGATATTGGACTTAAAGG
1345356 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATT
1345421 CAAGGCCAGCGATATTGGACTTAAAGG
66 CAAGGCCAGCGATATTGGACTTAAAGG
* * *
1345448 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGGTG-AGGTGCCAATGTGCTGATT
1 TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATT
* *
1345512 CAAGGCCAGCTACATTGGACTTAGAAGG
66 CAAGGCCAGCGATATTGGACTTA-AAGG
1345540 GTTGCCACCG
Statistics
Matches: 711, Mismatches: 26, Indels: 21
0.94 0.03 0.03
Matches are distributed among these distances:
91 76 0.11
92 414 0.58
94 4 0.01
95 37 0.05
97 144 0.20
98 36 0.05
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (92 bp):
TGCCAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGATGCCAATATGCTGATT
CAAGGCCAGCGATATTGGACTTAAAGG
Found at i:1345616 original size:67 final size:68
Alignment explanation
Indices: 1345534--1345707 Score: 284
Period size: 67 Copynumber: 2.6 Consensus size: 68
1345524 CATTGGACTT
*
1345534 AGAAGGG-TTGCCACCGACTTGTGTGGGCTTTAGAGAATGG-TTGCCACCAACTTGTGTGGGCTT
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTTGCCACCAACTTGTGTGGGCTT
*
1345597 TGG
66 TAG
* *
1345600 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAAAGAAGGGTTTGCCACCGACTTGTGTGGGCTT
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTTGCCACCAACTTGTGTGGGCTT
1345665 TAG
66 TAG
1345668 AGAA-GGTTTGCCACCGACTTGTGTGGGCTTTAGA-AAGGGT
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGT
1345708 GAAAGATGCC
Statistics
Matches: 101, Mismatches: 5, Indels: 4
0.92 0.05 0.04
Matches are distributed among these distances:
66 13 0.13
67 60 0.59
68 28 0.28
ACGTcount: A:0.20, C:0.17, G:0.34, T:0.29
Consensus pattern (68 bp):
AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAGAGAAGGGTTTGCCACCAACTTGTGTGGGCTT
TAG
Found at i:1345621 original size:34 final size:34
Alignment explanation
Indices: 1345534--1345707 Score: 284
Period size: 33 Copynumber: 5.2 Consensus size: 34
1345524 CATTGGACTT
1345534 AGAAGGG-TTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
* * *
1345567 AGAATGG-TTGCCACCAACTTGTGTGGGCTTTGG
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
*
1345600 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAA
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
1345634 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
1345668 AGAA-GGTTTGCCACCGACTTGTGTGGGCTTTAG
1 AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
1345701 A-AAGGGT
1 AGAAGGGT
1345708 GAAAGATGCC
Statistics
Matches: 131, Mismatches: 8, Indels: 4
0.92 0.06 0.03
Matches are distributed among these distances:
32 2 0.02
33 69 0.53
34 60 0.46
ACGTcount: A:0.20, C:0.17, G:0.34, T:0.29
Consensus pattern (34 bp):
AGAAGGGTTTGCCACCGACTTGTGTGGGCTTTAG
Found at i:1345819 original size:34 final size:35
Alignment explanation
Indices: 1345689--1346608 Score: 954
Period size: 34 Copynumber: 27.3 Consensus size: 35
1345679 CACCGACTTG
** *
1345689 TGTGGGCTTTAGAAAGGGTGAAAGA-TGCCACGAAGT
1 TGTGGGCTTTA-AAA-GGAAAAAGAGTGCCACGGAGT
* * *
1345725 TGTGGAC-TTAAAAAGAACAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
1345758 TGTGGGCTTTAAAAGGGAAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAAA-GG-AAAAAGAGTGCCACGGAGT
*
1345795 TGTGGGC-TTAGAAGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
* *
1345829 TGTGGGC-TTAGAAGG-AAAAGAGTGCCACGTAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
* *
1345862 TGTGGGCTTT-AAAGG-AAAAGAGTGCTACGTAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
* *
1345895 CGTGGAC-TTAAAA-G-----G-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
1345922 TGTGGGCTTTGAAAA-G---AAG-GTGCCACGGAGT
1 TGTGGGCTTT-AAAAGGAAAAAGAGTGCCACGGAGT
*
1345953 TGTGGGCTTTAACAAGGGAAAAGAGTGCCACGGAGT
1 TGTGGGCTTTAA-AAGGAAAAAGAGTGCCACGGAGT
* * *
1345989 TGTGGACTGTAAAAAGAAAAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
**
1346023 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACAAAGT
1 TGTGGGCTTT-AAAA-GGAAAAAGAGTGCCACGGAGT
* * *
1346060 TGTGGGCTTTAAAAAGAAAAAGTGTGCCACAGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
**
1346095 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACAAAGT
1 TGTGGGCTTT-AAAA-GGAAAAAGAGTGCCACGGAGT
* * * *
1346132 TATGGGCTTTAAAAAGAAAAAGTGTGCCACAGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
*
1346167 TGTGGGCTTTAAAAAGAAAAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
* *
1346201 TGTGGAC-TTAAAGATGAAAAA-AGTGCCACGGAGT
1 TGTGGGCTTTAAA-AGGAAAAAGAGTGCCACGGAGT
*
1346235 TGTGGGCTTTGAAA-G---AAG-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
*
1346265 TGTGGGCTTTGAAAA-GAAGAAG-GTGCCACGGAGT
1 TGTGGGCTTT-AAAAGGAAAAAGAGTGCCACGGAGT
**
1346299 TGTGGGCTTT-AAAGG-AAAAG-GTGCCATAGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
1346331 TGTGGGCTTTAAAA-GAAAAA-AGTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
1346364 TGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGT
1 TGTGGGCTTT-AAAA-GGAAAAAGAGTGCCACGGAGT
1346401 TGTGGGCTTTAAACA-GAAAAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAA-AGGAAAAAGAGTGCCACGGAGT
* *
1346435 TGTGGGCTTTAAAAAGAAAAAG-GTGCCACGGTGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
* *
1346469 TGTGGAC-TTAAAGATGAAAAA-AGTGCCACGGAGT
1 TGTGGGCTTTAAA-AGGAAAAAGAGTGCCACGGAGT
*
1346503 TGTGGGCTTTGAAA-G---AAG-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
*
1346533 TGTGGGCTTTGAAAA-GAAGAAG-GTGCCACGGAGT
1 TGTGGGCTTT-AAAAGGAAAAAGAGTGCCACGGAGT
1346567 TGTGGGCTTT-AAAGG-AAAAG-GTGCCACGGAGT
1 TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
1346599 TGTGGGCTTT
1 TGTGGGCTTT
1346609 GAAGAAAAAA
Statistics
Matches: 777, Mismatches: 58, Indels: 102
0.83 0.06 0.11
Matches are distributed among these distances:
27 15 0.02
28 3 0.00
29 5 0.01
30 50 0.06
31 33 0.04
32 61 0.08
33 115 0.15
34 236 0.30
35 103 0.13
36 66 0.08
37 90 0.12
ACGTcount: A:0.32, C:0.12, G:0.34, T:0.21
Consensus pattern (35 bp):
TGTGGGCTTTAAAAGGAAAAAGAGTGCCACGGAGT
Found at i:1345926 original size:27 final size:29
Alignment explanation
Indices: 1345811--1346040 Score: 104
Period size: 33 Copynumber: 7.2 Consensus size: 29
1345801 CTTAGAAGGA
* * *
1345811 AAAAGAGTGCCACGGAGTTGTGGGCTTAGAAGG
1 AAAAGGGTGCCACGGAGTTGTGGACTT----TG
* * *
1345844 AAAAGAGTGCCACGTAGTTGTGGGCTTTAAAGG
1 AAAAGGGTGCCACGGAGTTGTGGACTTT----G
* * * *
1345877 AAAAGAGTGCTACGTAGTCGTGGAC-TT-
1 AAAAGGGTGCCACGGAGTTGTGGACTTTG
*
1345904 AAAAGGGTGCCACGGAGTTGTGGGCTTTG
1 AAAAGGGTGCCACGGAGTTGTGGACTTTG
*
1345933 AAAAGAAGGTGCCACGGAGTTGTGGGCTTTAACAAGGG
1 AAAAG--GGTGCCACGGAGTTGTGGACTTT-------G
* *
1345971 AAAAGAGTGCCACGGAGTTGTGGACTGTAAAAAG
1 AAAAGGGTGCCACGGAGTTGTGGACT-T----TG
* *
1346005 AAAAAGGTGCCACGGAGTTGTGGGCTTTG
1 AAAAGGGTGCCACGGAGTTGTGGACTTTG
1346034 AAAAGGG
1 AAAAGGG
1346041 AAAAAGAGTG
Statistics
Matches: 159, Mismatches: 18, Indels: 44
0.72 0.08 0.20
Matches are distributed among these distances:
27 20 0.13
28 2 0.01
29 12 0.08
31 23 0.14
32 2 0.01
33 50 0.31
34 24 0.15
36 19 0.12
37 1 0.01
38 6 0.04
ACGTcount: A:0.30, C:0.13, G:0.36, T:0.21
Consensus pattern (29 bp):
AAAAGGGTGCCACGGAGTTGTGGACTTTG
Found at i:1346486 original size:268 final size:273
Alignment explanation
Indices: 1345714--1346624 Score: 1193
Period size: 268 Copynumber: 3.4 Consensus size: 273
1345704 GGGTGAAAGA
* *
1345714 TGCCACGAAGTTGTGGAC-TTAAAAAGAACAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAA
1 TGCCACGGAGTTGTGGACTTTAAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGG-AA
* * *
1345778 AAAGAGTGCCACGGAGTTGTGGGC-TTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGC-TT-AG
65 AAAGAGTGCCACAGAGTTGTGGGCTTTA-AAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAA
* * * * * *
1345840 AA-GG-AAAAGAGTGCCACGTAGTTGTGGGCTTT-AAAGGAAAAGAGTGCTACGTAGTCGTGGAC
129 AAGGGAAAAAGAGTGCCACGAAGTTGTGGGCTTTAAAAGAAAAAGAGTGCCACGGAGTTGTGGGC
*
1345902 -TT-AAAAG-----GGTGCCACGGAGTTGTGGGCTT-----TGAAAAGAAGGTGCCACGGAGTTG
194 TTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAGATGAAAA-AA-GTGCCACGGAGTTG
*
1345955 TGGGCTTTAACAAGGGAAAAGAG
257 TGGGCTTTGA-AA--G--AAG-G
* *
1345978 TGCCACGGAGTTGTGGACTGTAAAAAGAAAAAGGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAA
1 TGCCACGGAGTTGTGGACTTTAAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTT-AAAAGGGAA
* * *
1346043 AAAGAGTGCCACAAAGTTGTGGGCTTTAAAAAGAAAAAGTGTGCCACAGAGTTGTGGGCTTTGAA
65 AAAGAGTGCCACAGAGTTGTGGGCTTT-AAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAA
* * * *
1346108 AAGGGAAAAAGAGTGCCACAAAGTTATGGGCTTTAAAAAGAAAAAGTGTGCCACAGAGTTGTGGG
129 AAGGGAAAAAGAGTGCCACGAAGTTGTGGGCTTT-AAAAGAAAAAGAGTGCCACGGAGTTGTGGG
1346173 CTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAGTTGT
193 CTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAGTTGT
1346238 GGGCTTTGAAAGAAGG
258 GGGCTTTGAAAGAAGG
* *
1346254 TGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTT-AAA-GG-AA
1 TGCCACGGAGTTGTGGACTTTAAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAA
*
1346316 AAG-GTGCCATAGAGTTGTGGGCTTTAAAAGAAAAA-AGTGCCACGGAGTTGTGGGCTTTGAAAA
66 AAGAGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAA
*
1346379 GGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAACAGAAAAAG-GTGCCACGGAGTTGTGGGCT
131 GGGAAAAAGAGTGCCACGAAGTTGTGGGCTTTAAA-AGAAAAAGAGTGCCACGGAGTTGTGGGCT
*
1346443 TTAAAAAGAAAAAGGTGCCACGGTGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAGTTGTGG
195 TTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAGTTGTGG
1346508 GCTTTGAAAGAAGG
260 GCTTTGAAAGAAGG
* *
1346522 TGCCACGGAGTTGTGGGCTTTGAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTT-AAA-GG-AA
1 TGCCACGGAGTTGTGGACTTTAAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAA
* *
1346584 AAG-GTGCCACGGAGTTGTGGGCTTT-GAAGAAAAA-A-TGCCAC
66 AAGAGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGAGTGCCAC
1346625 TAAGTCGTGG
Statistics
Matches: 587, Mismatches: 37, Indels: 44
0.88 0.06 0.07
Matches are distributed among these distances:
264 17 0.03
265 58 0.10
266 42 0.07
267 12 0.02
268 188 0.32
269 65 0.11
270 35 0.06
271 20 0.03
272 28 0.05
273 4 0.01
274 8 0.01
276 52 0.09
277 3 0.01
279 22 0.04
281 2 0.00
282 23 0.04
283 2 0.00
284 6 0.01
ACGTcount: A:0.33, C:0.12, G:0.34, T:0.21
Consensus pattern (273 bp):
TGCCACGGAGTTGTGGACTTTAAAAAGAAGAAGGTGCCACGGAGTTGTGGGCTTTAAAAGGGAAA
AAGAGTGCCACAGAGTTGTGGGCTTTAAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTTTGAAAA
GGGAAAAAGAGTGCCACGAAGTTGTGGGCTTTAAAAGAAAAAGAGTGCCACGGAGTTGTGGGCTT
TAAAAAGAAAAAGGTGCCACGGAGTTGTGGACTTAAAGATGAAAAAAGTGCCACGGAGTTGTGGG
CTTTGAAAGAAGG
Found at i:1346696 original size:63 final size:60
Alignment explanation
Indices: 1346588--1346799 Score: 219
Period size: 63 Copynumber: 3.4 Consensus size: 60
1346578 AAGGAAAAGG
* * * * * *
1346588 TGCCACGGAGTTGTGGGCTTTGAAGAAAAAATGCCACTAAGTCGTGGACTTTGAGATAAAA
1 TGCCACTGAGTCGTGGACTTTAAAGAAAAGATGCCACTGAGTCGTGGACTTTGAGA-AAAA
*
1346649 TGCCACTGAGTCGTGGACTTTAAAGATAAAGGATGCCACTGAGTCGTGGACTTTAAAGAAAAGGA
1 TGCCACTGAGTCGTGGACTTTAAAGA-AAA-GATGCCACTGAGTCGTGGACTTT-GAGAAAA--A
* * * * *
1346714 TGCCACTGGGTCGTGGACTTT-GAGCAGAGATTGCCACTGAGTCGTGGACTTTGAGAAGAGAT
1 TGCCACTGAGTCGTGGACTTTAAAGAAAAGA-TGCCACTGAGTCGTGGACTTTGAGAA-A-AA
*
1346776 TGCCACTTAGTCGTGGACTTTAAA
1 TGCCACTGAGTCGTGGACTTTAAA
1346800 AAGGTATTTG
Statistics
Matches: 126, Mismatches: 16, Indels: 16
0.80 0.10 0.10
Matches are distributed among these distances:
61 22 0.17
62 28 0.22
63 49 0.39
64 6 0.05
65 21 0.17
ACGTcount: A:0.29, C:0.17, G:0.29, T:0.25
Consensus pattern (60 bp):
TGCCACTGAGTCGTGGACTTTAAAGAAAAGATGCCACTGAGTCGTGGACTTTGAGAAAAA
Found at i:1346735 original size:126 final size:126
Alignment explanation
Indices: 1346144--1346799 Score: 368
Period size: 132 Copynumber: 5.0 Consensus size: 126
1346134 TGGGCTTTAA
* * * * * *
1346144 AAAGAAAAAGTGTGCCACAGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGAGTTGTGGACT
1 AAAGATAAAG-GTGCCACGGAGTCGTGGACTTT--AAAGGAAAAGGTGCCACGGAGTCGTGGACT
* ** * * * * * *
1346209 TAAAGATG-AAAAAAGTGCCACGGAGTTGTGGGCTTTGA-AAGA-AGGTGCCACGGAGTTGTGGG
63 T--TGA-GCAAAAAA-TGCCACTAAGTCGTGGACTTTGAGAAGAGA-ATGCCACTGAGTCGTGGA
1346271 CTTT
123 CTTT
* * ** * *
1346275 GAAAAGA-AGAAGGTGCCACGGAGTTGTGGGCTTTAAAGGAAAAGGTGCCATAGAGTTGTGGGCT
1 --AAAGATA-AAGGTGCCACGGAGTCGTGGACTTTAAAGGAAAAGGTGCCACGGAGTCGTGGACT
* ** * * * * * *
1346339 TTAAAAG-AAAAAAGTGCCACGGAGTTGTGGGCTTTGAAAAGGGAAAAAGAGTGCCACGGAGTTG
63 TT--GAGCAAAAAA-TGCCACTAAGTCGTGGACTTTG---A--G-AAGAGAATGCCACTGAGTCG
*
1346403 TGGGCTTT
119 TGGACTTT
* * * * * *
1346411 AAACAGAAAAAGGTGCCACGGAGTTGTGGGCTTTAAAAAGAAAAAGGTGCCACGGTGTTGTGGAC
1 -AA-AGATAAAGGTGCCACGGAGTCGTGGACTTT--AAAGGAAAAGGTGCCACGGAGTCGTGGAC
* ** * * * * *
1346476 TTAAAGATG-AAAAAAGTGCCACGGAGTTGTGGGCTTTGA-AAGA-AGGTGCCACGGAGTTGTGG
62 TT--TGA-GCAAAAAA-TGCCACTAAGTCGTGGACTTTGAGAAGAGA-ATGCCACTGAGTCGTGG
*
1346538 GCTTT
122 ACTTT
* * * *
1346543 GAAAAGA-AGAAGGTGCCACGGAGTTGTGGGCTTTAAAGGAAAAGGTGCCACGGAGTTGTGGGCT
1 --AAAGATA-AAGGTGCCACGGAGTCGTGGACTTTAAAGGAAAAGGTGCCACGGAGTCGTGGACT
1346607 TTGAAG-AAAAAATGCCACTAAGTCGTGGACTTTGAGATA-A-AATGCCACTGAGTCGTGGACTT
63 TTG-AGCAAAAAATGCCACTAAGTCGTGGACTTTGAGA-AGAGAATGCCACTGAGTCGTGGACTT
1346669 T
126 T
*
1346670 AAAGATAAAGGATGCCACTGAGTCGTGGACTTTAAA-GAAAAGGATGCCACTGG-GTCGTGGACT
1 AAAGATAAAGG-TGCCACGGAGTCGTGGACTTTAAAGGAAAAGG-TGCCAC-GGAGTCGTGGACT
* * * * * *
1346733 TTGAGCAGAGATTGCCACTGAGTCGTGGACTTTGAGAAGAGATTGCCACTTAGTCGTGGACTTT
63 TTGAGCAAAAAATGCCACTAAGTCGTGGACTTTGAGAAGAGAATGCCACTGAGTCGTGGACTTT
1346797 AAA
1 AAA
1346800 AAGGTATTTG
Statistics
Matches: 453, Mismatches: 39, Indels: 68
0.81 0.07 0.12
Matches are distributed among these distances:
125 19 0.04
126 67 0.15
127 63 0.14
128 11 0.02
129 32 0.07
130 56 0.12
131 2 0.00
132 76 0.17
133 11 0.02
135 3 0.01
136 54 0.12
137 2 0.00
138 27 0.06
139 30 0.07
ACGTcount: A:0.32, C:0.13, G:0.32, T:0.23
Consensus pattern (126 bp):
AAAGATAAAGGTGCCACGGAGTCGTGGACTTTAAAGGAAAAGGTGCCACGGAGTCGTGGACTTTG
AGCAAAAAATGCCACTAAGTCGTGGACTTTGAGAAGAGAATGCCACTGAGTCGTGGACTTT
Found at i:1346752 original size:31 final size:30
Alignment explanation
Indices: 1346487--1346796 Score: 230
Period size: 31 Copynumber: 9.9 Consensus size: 30
1346477 TAAAGATGAA
* * *
1346487 AAAAG-TGCCACGGAGTTGTGGGCTTTGA-
1 AAAAGATGCCACTGAGTCGTGGACTTTGAG
* * * *
1346515 AAGAAGGTGCCACGGAGTTGTGGGCTTTGAAAAG
1 AA-AAGATGCCACTGAGTCGTGGACTTTG---AG
* * * * *
1346549 AAGAAGGTGCCACGGAGTTGTGGGCTTTAAAGG
1 AA-AAGATGCCACTGAGTCGTGGACTTT-GA-G
* * * *
1346582 AAAAGGTGCCACGGAGTTGTGGGCTTTGAAG
1 AAAAGATGCCACTGAGTCGTGGACTTTG-AG
* *
1346613 AAAAAATGCCACTAAGTCGTGGACTTTGAG
1 AAAAGATGCCACTGAGTCGTGGACTTTGAG
*
1346643 ATAAA-ATGCCACTGAGTCGTGGACTTTAAAG
1 A-AAAGATGCCACTGAGTCGTGGACTTT-GAG
*
1346674 ATAAAGGATGCCACTGAGTCGTGGACTTTAAAG
1 A-AAA-GATGCCACTGAGTCGTGGACTTT-GAG
*
1346707 AAAAGGATGCCACTGGGTCGTGGACTTTGAG
1 AAAA-GATGCCACTGAGTCGTGGACTTTGAG
* *
1346738 CAGAGATTGCCACTGAGTCGTGGACTTTGAG
1 AAAAGA-TGCCACTGAGTCGTGGACTTTGAG
* *
1346769 AAGAGATTGCCACTTAGTCGTGGACTTT
1 AAAAGA-TGCCACTGAGTCGTGGACTTT
1346797 AAAAAGGTAT
Statistics
Matches: 251, Mismatches: 17, Indels: 25
0.86 0.06 0.09
Matches are distributed among these distances:
28 2 0.01
29 3 0.01
30 48 0.19
31 86 0.34
32 53 0.21
33 31 0.12
34 28 0.11
ACGTcount: A:0.29, C:0.15, G:0.32, T:0.24
Consensus pattern (30 bp):
AAAAGATGCCACTGAGTCGTGGACTTTGAG
Found at i:1348114 original size:15 final size:17
Alignment explanation
Indices: 1348094--1348133 Score: 57
Period size: 15 Copynumber: 2.5 Consensus size: 17
1348084 CTTTGCACCC
1348094 TTTTTTTTACAC-CT-T
1 TTTTTTTTACACTCTCT
*
1348109 TTTTTTTTACTCTCTCT
1 TTTTTTTTACACTCTCT
1348126 TTTTTTTT
1 TTTTTTTT
1348134 TTTTTGACTT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 11 0.50
16 2 0.09
17 9 0.41
ACGTcount: A:0.07, C:0.17, G:0.00, T:0.75
Consensus pattern (17 bp):
TTTTTTTTACACTCTCT
Done.