Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr10
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: 95480121
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.31
Warning! 2980117 characters in sequence are not A, C, G, or T
File 216 of 284
Found at i:71686734 original size:24 final size:24
Alignment explanation
Indices: 71686702--71686748 Score: 76
Period size: 24 Copynumber: 2.0 Consensus size: 24
71686692 ACCTGTTGTT
*
71686702 GCTGCAAATAATTTTGAACTGAAC
1 GCTGCAAATAAGTTTGAACTGAAC
*
71686726 GCTGCAAATAAGTTTGAATTGAA
1 GCTGCAAATAAGTTTGAACTGAA
71686749 ACGTAACACG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.38, C:0.13, G:0.19, T:0.30
Consensus pattern (24 bp):
GCTGCAAATAAGTTTGAACTGAAC
Found at i:71687290 original size:25 final size:25
Alignment explanation
Indices: 71687261--71687314 Score: 99
Period size: 25 Copynumber: 2.2 Consensus size: 25
71687251 TTGAAGAGAT
*
71687261 GTCACTGAATAACTATCAGTGGCAA
1 GTCACTGAATAACTATCAGTAGCAA
71687286 GTCACTGAATAACTATCAGTAGCAA
1 GTCACTGAATAACTATCAGTAGCAA
71687311 GTCA
1 GTCA
71687315 TGAGAACAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.37, C:0.20, G:0.19, T:0.24
Consensus pattern (25 bp):
GTCACTGAATAACTATCAGTAGCAA
Found at i:71689809 original size:15 final size:16
Alignment explanation
Indices: 71689773--71689812 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
71689763 CCTCACTTTC
*
71689773 TCTTTTTTCTTTTTCT
1 TCTTTTTTCTTTTCCT
*
71689789 TATTTTTTC-TTTCCT
1 TCTTTTTTCTTTTCCT
71689804 TCTTTTTTC
1 TCTTTTTTC
71689813 CCTTTTTTCT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.03, C:0.20, G:0.00, T:0.78
Consensus pattern (16 bp):
TCTTTTTTCTTTTCCT
Found at i:71689835 original size:24 final size:24
Alignment explanation
Indices: 71689791--71689836 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
71689781 CTTTTTCTTA
*
71689791 TTTTTTCTTTCCTTCTTTTTTCCC
1 TTTTTTCTTTCCTTCTCTTTTCCC
71689815 TTTTTTC-TTCCTTCATCTTTTC
1 TTTTTTCTTTCCTTC-TCTTTTC
71689837 TCCCTATTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 7 0.35
24 13 0.65
ACGTcount: A:0.02, C:0.28, G:0.00, T:0.70
Consensus pattern (24 bp):
TTTTTTCTTTCCTTCTCTTTTCCC
Found at i:71696678 original size:138 final size:138
Alignment explanation
Indices: 71696428--71696703 Score: 383
Period size: 138 Copynumber: 2.0 Consensus size: 138
71696418 AGGAAATTTC
* *
71696428 CTTTTGCACCCTTGGCTTGATTCATTTCCTACGTTTCCACTGGTAAATGCATCAGATGTGGAGGT
1 CTTTTGCACACTTGGCTTGATTCATTCCCTACGTTTCCACTGGTAAATGCATCAGATGTGGAGGT
*
71696493 TTTAATTGCAACTCAGTCTATAATTATGTTTATTATCAGAACCTCCTCCTCATACTCTC-TTCTA
66 TTTAATTGCAACTCAGTCTATAATTATGTTTATTATAAGAACCTCCTCCTCATACTCTCTTTC-A
71696557 TGAGACCTT
130 TGAGACCTT
* * * * * * *
71696566 CTTTTGTACACTTGGCTTGATTCATTCCCTGCGTTTCCACTTGTGAGTGCGTCAGATGTTGAGGT
1 CTTTTGCACACTTGGCTTGATTCATTCCCTACGTTTCCACTGGTAAATGCATCAGATGTGGAGGT
* * * * * * *
71696631 TTTAATTGCAACTCAGTCTGTTATTATGTTTATTATAAGGACTTCCTCCTTATAGTTTCTTTCAT
66 TTTAATTGCAACTCAGTCTATAATTATGTTTATTATAAGAACCTCCTCCTCATACTCTCTTTCAT
71696696 GAGACCTT
131 GAGACCTT
71696704 TTCCAAACCC
Statistics
Matches: 120, Mismatches: 17, Indels: 2
0.86 0.12 0.01
Matches are distributed among these distances:
138 117 0.98
139 3 0.03
ACGTcount: A:0.21, C:0.22, G:0.16, T:0.41
Consensus pattern (138 bp):
CTTTTGCACACTTGGCTTGATTCATTCCCTACGTTTCCACTGGTAAATGCATCAGATGTGGAGGT
TTTAATTGCAACTCAGTCTATAATTATGTTTATTATAAGAACCTCCTCCTCATACTCTCTTTCAT
GAGACCTT
Found at i:71697167 original size:22 final size:22
Alignment explanation
Indices: 71697142--71697186 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
71697132 AATTCGTTAA
71697142 AGACTAAATTTCTTGTCCAATG
1 AGACTAAATTTCTTGTCCAATG
71697164 AGACTAAATTTCTTGTCCAATG
1 AGACTAAATTTCTTGTCCAATG
71697186 A
1 A
71697187 ATTCTAGGAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.33, C:0.18, G:0.13, T:0.36
Consensus pattern (22 bp):
AGACTAAATTTCTTGTCCAATG
Found at i:71704535 original size:22 final size:23
Alignment explanation
Indices: 71704492--71704540 Score: 57
Period size: 22 Copynumber: 2.2 Consensus size: 23
71704482 AATTTAACCC
* *
71704492 TTAATTTTTTATGAATAGTAAA-
1 TTAATTTTTTATAAATAATAAAG
71704514 TTAATTTTTTA-AAACTAATAAAG
1 TTAATTTTTTATAAA-TAATAAAG
71704537 TTAA
1 TTAA
71704541 ATGGTAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
21 2 0.09
22 17 0.74
23 4 0.17
ACGTcount: A:0.45, C:0.02, G:0.06, T:0.47
Consensus pattern (23 bp):
TTAATTTTTTATAAATAATAAAG
Found at i:71706115 original size:19 final size:19
Alignment explanation
Indices: 71706091--71706145 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
71706081 TTAATAAGGA
71706091 TAATAATAATAATAAATAG
1 TAATAATAATAATAAATAG
* *
71706110 TAATAATAATATATTATTAG
1 TAATAATAATA-ATAAATAG
*
71706130 TAATAGAAAATAATAA
1 TAATA-ATAATAATAA
71706146 TGATAAAGGG
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
19 11 0.37
20 14 0.47
21 5 0.17
ACGTcount: A:0.60, C:0.00, G:0.05, T:0.35
Consensus pattern (19 bp):
TAATAATAATAATAAATAG
Found at i:71706276 original size:3 final size:3
Alignment explanation
Indices: 71706256--71706356 Score: 57
Period size: 3 Copynumber: 33.7 Consensus size: 3
71706246 TTGATACTGG
* * *
71706256 TAA TAA T-A TAA AACA TAA TAA -AA GAA TAA TAA TATG TAA TAA TAA
1 TAA TAA TAA TAA TA-A TAA TAA TAA TAA TAA TAA TA-A TAA TAA TAA
* * * * * *
71706301 TAG TAA TAA -AA AAA TAA CAG TAA CAA CAA TAA TAA TAAA TAA -AA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA
71706345 TAA TAAA TAA TA
1 TAA T-AA TAA TA
71706357 TTAAAAAAAA
Statistics
Matches: 76, Mismatches: 14, Indels: 16
0.72 0.13 0.15
Matches are distributed among these distances:
2 8 0.11
3 58 0.76
4 10 0.13
ACGTcount: A:0.66, C:0.04, G:0.04, T:0.26
Consensus pattern (3 bp):
TAA
Found at i:71706298 original size:13 final size:12
Alignment explanation
Indices: 71706270--71706309 Score: 55
Period size: 13 Copynumber: 3.3 Consensus size: 12
71706260 AATATAAAAC
*
71706270 ATAATAAAAG-A
1 ATAATAATAGTA
71706281 ATAATAATATGTA
1 ATAATAATA-GTA
71706294 ATAATAATAGTA
1 ATAATAATAGTA
71706306 ATAA
1 ATAA
71706310 AAAAATAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
11 8 0.31
12 8 0.31
13 10 0.38
ACGTcount: A:0.62, C:0.00, G:0.07, T:0.30
Consensus pattern (12 bp):
ATAATAATAGTA
Found at i:71706355 original size:22 final size:22
Alignment explanation
Indices: 71706328--71706369 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
71706318 CAGTAACAAC
*
71706328 AATAATAATAAATAAAATAATA
1 AATAATAATAAAAAAAATAATA
*
71706350 AATAATATTAAAAAAAATAA
1 AATAATAATAAAAAAAATAA
71706370 GAATGTCCAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (22 bp):
AATAATAATAAAAAAAATAATA
Found at i:71707705 original size:45 final size:45
Alignment explanation
Indices: 71707631--71707933 Score: 147
Period size: 45 Copynumber: 6.7 Consensus size: 45
71707621 GTAGCTTTAA
* * *
71707631 TCTGTTCCACTGCCACTTCAGGGAAATAAGATTTGCTATCTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAG
* *
71707676 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTCGTTG-TAACTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-T--TTGCTATCTTCAG
* * * *
71707723 CCTGCTCCACTACAACTTTAGGGAGATAACG-TTTG-T-T-TTGA-
1 TCTGCTCCACTGCAACTTCAGGGAGATAA-GATTTGCTATCTTCAG
* * * ** *
71707764 TCTGC-CCTACTACAACTTTAGAGAGATAAGATCTATAATTTATCTTCAA
1 TCTGCTCC-ACTGCAACTTCAGGGAGATAAGAT-T-T--GCTATCTTCAG
* * * * * *
71707813 TCTGTTCCATTACTACTTCATGGAAATAAGATTCT-CTATCTTC-G
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGATT-TGCTATCTTCAG
* * * * * * * * *
71707857 ATCTACTCCATTGCTACCTCATGGAGATAAGATCTACAATCTTTAG
1 -TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAG
** *
71707903 TCTGCTCCACTGTTACTTTAGGGAGATAAGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA
71707934 GTTGTGTCTT
Statistics
Matches: 202, Mismatches: 38, Indels: 36
0.73 0.14 0.13
Matches are distributed among these distances:
40 3 0.01
41 25 0.12
42 4 0.02
43 1 0.00
44 5 0.02
45 93 0.46
46 4 0.02
47 34 0.17
48 9 0.04
49 22 0.11
50 2 0.01
ACGTcount: A:0.28, C:0.23, G:0.16, T:0.34
Consensus pattern (45 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGATTTGCTATCTTCAG
Found at i:71708099 original size:132 final size:132
Alignment explanation
Indices: 71707922--71708160 Score: 318
Period size: 132 Copynumber: 1.8 Consensus size: 132
71707912 CTGTTACTTT
* * * * * *
71707922 AGGGAGATAAGAGTTGTGTCTTAAATCTACTTCTCTACTATCTCGGGAAGATAAGATTCACCGTT
1 AGGGAGATAAGAGTAGTGGCTTAAATCTACTTCCCTACTACCTCGGGAAGATAAGATTCACCATC
**
71707987 TTCGATCTACTTTACTACTGCTTAGGAAAATAAGATCTGTGATCTTCAGCCTTCTCCACTACTGC
66 TTCGATCTACTCCACTACTGCTTAGGAAAATAAGATCTGTGATCTTCAGCCTTCTCCACTACTGC
71708052 TC
131 TC
* * *
71708054 AGGGAGATAAG-GCTAGTGGCTTAAATTTGCTTCCCTACTACCTCGGGAAGATAAGATTCGCCAT
1 AGGGAGATAAGAG-TAGTGGCTTAAATCTACTTCCCTACTACCTCGGGAAGATAAGATTCACCAT
** * * *
71708118 CTTCGATCTGGTCCACTGCTGCTTAGGGAGATAAGATCTGTGA
65 CTTCGATCTACTCCACTACTGCTTAGGAAAATAAGATCTGTGA
71708161 ATTCATCAAT
Statistics
Matches: 90, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
131 1 0.01
132 89 0.99
ACGTcount: A:0.26, C:0.21, G:0.21, T:0.31
Consensus pattern (132 bp):
AGGGAGATAAGAGTAGTGGCTTAAATCTACTTCCCTACTACCTCGGGAAGATAAGATTCACCATC
TTCGATCTACTCCACTACTGCTTAGGAAAATAAGATCTGTGATCTTCAGCCTTCTCCACTACTGC
TC
Found at i:71712814 original size:20 final size:20
Alignment explanation
Indices: 71712789--71712831 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
71712779 ATTTGTATGG
*
71712789 TAAAGAATATTTGCTCAGGA
1 TAAAGAATATTTGCTCAGAA
71712809 TAAAGAATATTTGCTCAGAA
1 TAAAGAATATTTGCTCAGAA
71712829 TAA
1 TAA
71712832 GACATAAAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.16, T:0.30
Consensus pattern (20 bp):
TAAAGAATATTTGCTCAGAA
Found at i:71716391 original size:19 final size:20
Alignment explanation
Indices: 71716367--71716413 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
71716357 TTGTGAAATT
* *
71716367 TAATGCACATG-ATGCGATG
1 TAATGCAAATGCATGAGATG
71716386 TAATGCAAATGCATGAGATG
1 TAATGCAAATGCATGAGATG
71716406 -AATGCAAA
1 TAATGCAAA
71716414 ACTAAAAAAG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.40, C:0.13, G:0.23, T:0.23
Consensus pattern (20 bp):
TAATGCAAATGCATGAGATG
Found at i:71724040 original size:10 final size:10
Alignment explanation
Indices: 71724025--71724052 Score: 56
Period size: 10 Copynumber: 2.8 Consensus size: 10
71724015 GGCTTAGGTT
71724025 AAGGGTATGG
1 AAGGGTATGG
71724035 AAGGGTATGG
1 AAGGGTATGG
71724045 AAGGGTAT
1 AAGGGTAT
71724053 ACATAGTGAC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.32, C:0.00, G:0.46, T:0.21
Consensus pattern (10 bp):
AAGGGTATGG
Found at i:71724483 original size:30 final size:30
Alignment explanation
Indices: 71724447--71724507 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
71724437 ACGTGGAAGT
*
71724447 AAGGGTCGAGTGATGCATAAGCTTCTTGGG
1 AAGGGTCGAGTGATGCATAAGCTTATTGGG
71724477 AAGGGTCGAGTGATGCATAAGCTTATTGGG
1 AAGGGTCGAGTGATGCATAAGCTTATTGGG
71724507 A
1 A
71724508 CATCATAGCA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.26, C:0.11, G:0.36, T:0.26
Consensus pattern (30 bp):
AAGGGTCGAGTGATGCATAAGCTTATTGGG
Found at i:71730984 original size:28 final size:28
Alignment explanation
Indices: 71730944--71731001 Score: 116
Period size: 28 Copynumber: 2.1 Consensus size: 28
71730934 GGATTTGGGG
71730944 TTTCTTGAGAGGAATTAGTTGGTATAAA
1 TTTCTTGAGAGGAATTAGTTGGTATAAA
71730972 TTTCTTGAGAGGAATTAGTTGGTATAAA
1 TTTCTTGAGAGGAATTAGTTGGTATAAA
71731000 TT
1 TT
71731002 ATGTGTTCTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 30 1.00
ACGTcount: A:0.31, C:0.03, G:0.24, T:0.41
Consensus pattern (28 bp):
TTTCTTGAGAGGAATTAGTTGGTATAAA
Found at i:71731313 original size:17 final size:18
Alignment explanation
Indices: 71731293--71731326 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
71731283 TGTTTTTTCT
*
71731293 TTATTT-TTTTCTTTTAG
1 TTATTTATTTACTTTTAG
71731310 TTATTTATTTACTTTTA
1 TTATTTATTTACTTTTA
71731327 TCTCTCAACC
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.18, C:0.06, G:0.03, T:0.74
Consensus pattern (18 bp):
TTATTTATTTACTTTTAG
Found at i:71737267 original size:27 final size:26
Alignment explanation
Indices: 71737209--71737275 Score: 82
Period size: 27 Copynumber: 2.5 Consensus size: 26
71737199 TGAAAATTTG
*
71737209 AAAAAATATAAAAATTATTAAATCTT
1 AAAAAATATAAAAATTATTAAATATT
*
71737235 AAAAAATATGAAAATTGATATAAA-ATT
1 AAAAAATATAAAAATT-AT-TAAATATT
*
71737262 ATAAAATATAAAAA
1 AAAAAATATAAAAA
71737276 ATCTAATAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
26 15 0.43
27 16 0.46
28 4 0.11
ACGTcount: A:0.66, C:0.01, G:0.03, T:0.30
Consensus pattern (26 bp):
AAAAAATATAAAAATTATTAAATATT
Found at i:71737287 original size:37 final size:38
Alignment explanation
Indices: 71737214--71737287 Score: 89
Period size: 37 Copynumber: 2.0 Consensus size: 38
71737204 ATTTGAAAAA
* * *
71737214 ATATAAAAATTATTAAATCTTAAAAAATATGAAAATTG
1 ATATAAAAATTATAAAATCATAAAAAATATAAAAATTG
*
71737252 ATAT-AAAATTATAAAAT-ATAAAAAATCTAATAAATT
1 ATATAAAAATTATAAAATCATAAAAAATATAA-AAATT
71737288 ATTAATAAAA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
36 10 0.32
37 17 0.55
38 4 0.13
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.34
Consensus pattern (38 bp):
ATATAAAAATTATAAAATCATAAAAAATATAAAAATTG
Found at i:71737316 original size:21 final size:24
Alignment explanation
Indices: 71737283--71737330 Score: 66
Period size: 21 Copynumber: 2.1 Consensus size: 24
71737273 AAAATCTAAT
71737283 AAATTATTAATAAAACATA-TTTA
1 AAATTATTAATAAAACATATTTTA
*
71737306 AAATT-TT-ATAAAACCTATTTTA
1 AAATTATTAATAAAACATATTTTA
71737328 AAA
1 AAA
71737331 CTATACAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 9 0.39
22 9 0.39
23 5 0.22
ACGTcount: A:0.54, C:0.06, G:0.00, T:0.40
Consensus pattern (24 bp):
AAATTATTAATAAAACATATTTTA
Found at i:71743434 original size:19 final size:20
Alignment explanation
Indices: 71743410--71743451 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
71743400 CATTCCAATC
*
71743410 CATTTCACATA-TTACATTT
1 CATTTCACATATTTAAATTT
71743429 CATTTCACATATTTAAATTT
1 CATTTCACATATTTAAATTT
71743449 CAT
1 CAT
71743452 AATTCATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 11 0.52
20 10 0.48
ACGTcount: A:0.33, C:0.19, G:0.00, T:0.48
Consensus pattern (20 bp):
CATTTCACATATTTAAATTT
Found at i:71746349 original size:21 final size:21
Alignment explanation
Indices: 71746320--71746360 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
71746310 CATATAAAGA
*
71746320 AAAACTTATAATTAATTTTTG
1 AAAACTTATAATGAATTTTTG
* *
71746341 AAAATTTATTATGAATTTTT
1 AAAACTTATAATGAATTTTT
71746361 AAAGTCAGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.41, C:0.02, G:0.05, T:0.51
Consensus pattern (21 bp):
AAAACTTATAATGAATTTTTG
Found at i:71747295 original size:46 final size:46
Alignment explanation
Indices: 71747228--71747352 Score: 223
Period size: 46 Copynumber: 2.7 Consensus size: 46
71747218 AACCCGCCCC
* *
71747228 TAAGTGAACTCAGTCTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
71747274 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
*
71747320 TAAGTGAACTCGGACTCAACTCAACGAGTTCGG
1 TAAGTGAACTCGGACTCAACTCAACGAGCTCGG
71747353 ATGCTCAACC
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
46 76 1.00
ACGTcount: A:0.27, C:0.29, G:0.23, T:0.21
Consensus pattern (46 bp):
TAAGTGAACTCGGACTCAACTCAACGAGCTCGGGCGTTCGCATCCA
Found at i:71748940 original size:28 final size:28
Alignment explanation
Indices: 71748887--71748941 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 28
71748877 ATCATTAAAT
* * **
71748887 TAATTAATTTTAATATTATTTTTATTAG
1 TAATTAATTTTAATAATAATAATATTAG
71748915 TAATTAATTTTAATAATAATAATATTA
1 TAATTAATTTTAATAATAATAATATTA
71748942 TTATTATTAC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
28 23 1.00
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.55
Consensus pattern (28 bp):
TAATTAATTTTAATAATAATAATATTAG
Found at i:71748943 original size:3 final size:3
Alignment explanation
Indices: 71748937--71749071 Score: 125
Period size: 3 Copynumber: 45.3 Consensus size: 3
71748927 ATAATAATAA
* * *
71748937 TAT TAT TAT TAT TAC TAT TAT TAT TAT TAC TAT TAT CTTT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT
** * * *
71748983 TAT TCC TAT TAT TAT TAA CA- TAT TAT TAT TCT TAT TAT TAT T-T T-T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
71749028 TA- TAT TAT TAT CAT TAT TAGCT TAT TAT TAT TAT TAT TAC TAT T
1 TAT TAT TAT TAT TAT TAT TA--T TAT TAT TAT TAT TAT TAT TAT T
71749072 TTTGTTATCT
Statistics
Matches: 107, Mismatches: 19, Indels: 12
0.78 0.14 0.09
Matches are distributed among these distances:
2 7 0.07
3 95 0.89
4 2 0.02
5 3 0.03
ACGTcount: A:0.30, C:0.07, G:0.01, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:71749324 original size:26 final size:27
Alignment explanation
Indices: 71749295--71749359 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
71749285 ATATTATTTA
71749295 TTTTAAATTATT-TTT-AT-TATCACTTG
1 TTTTAAATT-TTCTTTCATATATCA-TTG
*
71749321 TTTTAAATTTTCTTTCATATATTATTG
1 TTTTAAATTTTCTTTCATATATCATTG
*
71749348 TTTTAAAATTTC
1 TTTTAAATTTTC
71749360 ATATTGTTTT
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
25 2 0.06
26 12 0.35
27 16 0.47
28 4 0.12
ACGTcount: A:0.28, C:0.08, G:0.03, T:0.62
Consensus pattern (27 bp):
TTTTAAATTTTCTTTCATATATCATTG
Found at i:71749353 original size:27 final size:27
Alignment explanation
Indices: 71749263--71749359 Score: 94
Period size: 26 Copynumber: 3.7 Consensus size: 27
71749253 TATAAATTTG
* *
71749263 TACTTGTTTTAAA-TCTCTTAATATAT
1 TACTTGTTTTAAATTTTCTTTATATAT
* *
71749289 TATTTATTTTAAATTATT-TTTAT-TAT
1 TACTTGTTTTAAATT-TTCTTTATATAT
*
71749315 CACTTGTTTTAAATTTTCTTTCATATAT
1 TACTTGTTTTAAATTTTCTTT-ATATAT
*
71749343 TA-TTGTTTTAAAATTTC
1 TACTTGTTTTAAATTTTC
71749360 ATATTGTTTT
Statistics
Matches: 57, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
25 2 0.04
26 29 0.51
27 21 0.37
28 5 0.09
ACGTcount: A:0.29, C:0.08, G:0.03, T:0.60
Consensus pattern (27 bp):
TACTTGTTTTAAATTTTCTTTATATAT
Found at i:71754482 original size:25 final size:27
Alignment explanation
Indices: 71754435--71754485 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
71754425 AAACTAAATT
*
71754435 ATAATTATTTTTAAATGTGTAATTATC
1 ATAATTATTTTTAAATGTATAATTATC
71754462 ATAATT-TTTTTAAAT-TATAATTAT
1 ATAATTATTTTTAAATGTATAATTAT
71754486 TTTTAAATGT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 8 0.35
26 9 0.39
27 6 0.26
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.55
Consensus pattern (27 bp):
ATAATTATTTTTAAATGTATAATTATC
Found at i:71754483 original size:16 final size:18
Alignment explanation
Indices: 71754462--71754503 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
71754452 TGTAATTATC
71754462 ATAATT-TTTTTAAAT-T
1 ATAATTATTTTTAAATGT
71754478 ATAATTATTTTTAAATGT
1 ATAATTATTTTTAAATGT
71754496 ATAATTAT
1 ATAATTAT
71754504 GACAACTTCT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 6 0.25
17 9 0.38
18 9 0.38
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (18 bp):
ATAATTATTTTTAAATGT
Found at i:71755716 original size:26 final size:26
Alignment explanation
Indices: 71755662--71755719 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
71755652 CAACATTCAC
*
71755662 AATAAT-GTAAATATTATTAAAATCA
1 AATAATAGTAAATATTATCAAAATCA
*
71755687 AATAATAGTAAA-ATTATCAAATATCT
1 AATAATAGTAAATATTATCAAA-ATCA
71755713 AATAATA
1 AATAATA
71755720 ATAACTAAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
25 14 0.48
26 15 0.52
ACGTcount: A:0.57, C:0.05, G:0.03, T:0.34
Consensus pattern (26 bp):
AATAATAGTAAATATTATCAAAATCA
Found at i:71759496 original size:39 final size:39
Alignment explanation
Indices: 71759453--71759573 Score: 118
Period size: 39 Copynumber: 3.1 Consensus size: 39
71759443 AGTCTAGCTG
* * * * * *
71759453 AAGCACATAAGTGCCAAACGAAAGATCGAAGGTTAACTA
1 AAGCACACAAGTGCTAAACAAAAGACCAAAGGCTAACTA
* * *
71759492 AAGCACACAAGTGTTAAACAAAAGCCCAAAGGCTAACTG
1 AAGCACACAAGTGCTAAACAAAAGACCAAAGGCTAACTA
* * *
71759531 AAGCACACAAGTGCTAAACAGAAG-CCTGAAGGCTAACTG
1 AAGCACACAAGTGCTAAACAAAAGACC-AAAGGCTAACTA
71759570 AAGC
1 AAGC
71759574 TCATCAGAGC
Statistics
Matches: 69, Mismatches: 12, Indels: 2
0.83 0.14 0.02
Matches are distributed among these distances:
38 2 0.03
39 67 0.97
ACGTcount: A:0.45, C:0.21, G:0.21, T:0.13
Consensus pattern (39 bp):
AAGCACACAAGTGCTAAACAAAAGACCAAAGGCTAACTA
Found at i:71759516 original size:21 final size:21
Alignment explanation
Indices: 71759491--71759555 Score: 64
Period size: 21 Copynumber: 3.2 Consensus size: 21
71759481 AAGGTTAACT
*
71759491 AAAGCACACAAGTGTTAAACA
1 AAAGCACACAAGTGCTAAACA
* *
71759512 AAAGCCCA-AAG-GCT-AACT
1 AAAGCACACAAGTGCTAAACA
*
71759530 GAAGCACACAAGTGCTAAACA
1 AAAGCACACAAGTGCTAAACA
*
71759551 GAAGC
1 AAAGC
71759556 CTGAAGGCTA
Statistics
Matches: 35, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 9 0.26
19 5 0.14
20 6 0.17
21 15 0.43
ACGTcount: A:0.48, C:0.23, G:0.18, T:0.11
Consensus pattern (21 bp):
AAAGCACACAAGTGCTAAACA
Found at i:71762149 original size:40 final size:40
Alignment explanation
Indices: 71762086--71762169 Score: 107
Period size: 40 Copynumber: 2.1 Consensus size: 40
71762076 AAAATCGAAT
* * * *
71762086 AGATCGAGTATTAGCGGCATTTTTATGAAAGTGCCGCTAA
1 AGATCGAGCATTAGCGGCATTTTTAAGAAAGCGCCACTAA
*
71762126 AGATCGAGCATTAGCGG-ATTTTTTAAGGAAGCGCCACTAA
1 AGATCGAGCATTAGCGGCA-TTTTTAAGAAAGCGCCACTAA
71762166 AGAT
1 AGAT
71762170 TGACCTATAG
Statistics
Matches: 38, Mismatches: 5, Indels: 2
0.84 0.11 0.04
Matches are distributed among these distances:
39 1 0.03
40 37 0.97
ACGTcount: A:0.32, C:0.15, G:0.25, T:0.27
Consensus pattern (40 bp):
AGATCGAGCATTAGCGGCATTTTTAAGAAAGCGCCACTAA
Found at i:71762373 original size:153 final size:155
Alignment explanation
Indices: 71762145--71762435 Score: 401
Period size: 153 Copynumber: 1.9 Consensus size: 155
71762135 ATTAGCGGAT
** * *
71762145 TTTTTAAGGAAGCGCCACTAAAGATTGACCTATAGCGACGTTTTTTTAAAAACGACGCTAAAAGA
1 TTTTTAACAAAGCGCCACTAAAGATTGACCTATAGCGACGCTTTCTTAAAAACGACGCTAAAAGA
*
71762210 TTAAAGAGAACGACATCGT-T-TTTCTGAGCTTCAGTGGCATTAGCGGCGCTACC-C-GAAAAAC
66 TTAAACAGAACGACATCGTCTGTTT-TGAGCTTCAGTGGCATTAGCGGCGCTACCTCAG-AAAAC
71762271 GCAGCAATAGATCCAACATTAGAGGCG
129 GCAGCAATAGATCCAACATTAGAGGCG
* * * * * *
71762298 TTTTTAACAAAGCGCCGCTATAGGTTGATCTATAGCGGCGCTTTCTTAAAAACGCCGCTAAAAGA
1 TTTTTAACAAAGCGCCACTAAAGATTGACCTATAGCGACGCTTTCTTAAAAACGACGCTAAAAGA
* * *
71762363 TTAAACAGAACGACGTCGTCTGTTTTGAGCTTCAGTGGCATTAGTGGCGCTTCCTCAGAAAACGC
66 TTAAACAGAACGACATCGTCTGTTTTGAGCTTCAGTGGCATTAGCGGCGCTACCTCAGAAAACGC
*
71762428 CGCAATAG
131 AGCAATAG
71762436 TTTGGGTTCT
Statistics
Matches: 119, Mismatches: 15, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
153 72 0.61
154 28 0.24
155 18 0.15
156 1 0.01
ACGTcount: A:0.31, C:0.21, G:0.22, T:0.25
Consensus pattern (155 bp):
TTTTTAACAAAGCGCCACTAAAGATTGACCTATAGCGACGCTTTCTTAAAAACGACGCTAAAAGA
TTAAACAGAACGACATCGTCTGTTTTGAGCTTCAGTGGCATTAGCGGCGCTACCTCAGAAAACGC
AGCAATAGATCCAACATTAGAGGCG
Found at i:71763076 original size:21 final size:21
Alignment explanation
Indices: 71763052--71763104 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
71763042 TTTATAGTCG
*
71763052 TAAATCATAAAT-TATAAACCT
1 TAAATCCTAAATAT-TAAACCT
*
71763073 TAAACCCTAAATATTAAACCT
1 TAAATCCTAAATATTAAACCT
*
71763094 TGAATCCTAAA
1 TAAATCCTAAA
71763105 CCATAAAACC
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 26 0.96
22 1 0.04
ACGTcount: A:0.49, C:0.19, G:0.02, T:0.30
Consensus pattern (21 bp):
TAAATCCTAAATATTAAACCT
Found at i:71763247 original size:21 final size:21
Alignment explanation
Indices: 71763213--71763277 Score: 76
Period size: 21 Copynumber: 3.0 Consensus size: 21
71763203 TTATAAAACG
*
71763213 TCTTAAAACTATAAACCTTAAA
1 TCTT-AAACCATAAACCTTAAA
*
71763235 TCTTAAACCATAAACCCTAAA
1 TCTTAAACCATAAACCTTAAA
**
71763256 TCCAAAACCATAAAACCTTAAA
1 TCTTAAACCAT-AAACCTTAAA
71763278 CTATAGACAG
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 24 0.65
22 13 0.35
ACGTcount: A:0.51, C:0.25, G:0.00, T:0.25
Consensus pattern (21 bp):
TCTTAAACCATAAACCTTAAA
Found at i:71763636 original size:3 final size:3
Alignment explanation
Indices: 71763628--71763668 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
71763618 ATTAATAGTA
71763628 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
71763669 GGATTTATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:71763891 original size:72 final size:74
Alignment explanation
Indices: 71763757--71763932 Score: 202
Period size: 72 Copynumber: 2.4 Consensus size: 74
71763747 TGAAGCTTTG
*
71763757 TTATTAGTGGCGCTTTTA-AAAAATGCCACAAAACATCTATTAAGAGAATGTAAAACGGCATCG-
1 TTATTAGTGGCGCTTTTATAAACA-GCCACAAAACATCTA-TAAGAGAATGTAAAACGGCATCGT
*
71763820 TTTACATCATT
64 TTTACAGCATT
* * * *
71763831 CTTATTAGTGGCGCTTCTATAAACA-CCGCAAAACATCTA-AAGAG-ATTTCAAAACGTCATCGT
1 -TTATTAGTGGCGCTTTTATAAACAGCCACAAAACATCTATAAGAGAATGT-AAAACGGCATCGT
* *
71763893 TTTATAGCCTT
64 TTTACAGCATT
71763904 TTATTAGTGGCGCTTTTATAAAC-GCCACA
1 TTATTAGTGGCGCTTTTATAAACAGCCACA
71763933 GAAGATGTGA
Statistics
Matches: 87, Mismatches: 10, Indels: 11
0.81 0.09 0.10
Matches are distributed among these distances:
71 3 0.03
72 42 0.48
73 8 0.09
74 13 0.15
75 17 0.20
76 4 0.05
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (74 bp):
TTATTAGTGGCGCTTTTATAAACAGCCACAAAACATCTATAAGAGAATGTAAAACGGCATCGTTT
TACAGCATT
Found at i:71769794 original size:40 final size:39
Alignment explanation
Indices: 71769739--71769815 Score: 145
Period size: 40 Copynumber: 1.9 Consensus size: 39
71769729 GACATCCAAT
71769739 GCTGGAGAAATTATGGTATATTTACTTAATAAAATTTNAA
1 GCTGGAGAAATTATGGTATATTTACTTAATAAAATTT-AA
71769779 GCTGGAGAAATTATGGTATATTTACTTAATAAAATTT
1 GCTGGAGAAATTATGGTATATTTACTTAATAAAATTT
71769816 GATTTATTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 37 1.00
ACGTcount: A:0.39, C:0.05, G:0.16, T:0.39
Consensus pattern (39 bp):
GCTGGAGAAATTATGGTATATTTACTTAATAAAATTTAA
Found at i:71770294 original size:21 final size:21
Alignment explanation
Indices: 71770270--71770324 Score: 85
Period size: 21 Copynumber: 2.7 Consensus size: 21
71770260 AACTTAGAGC
*
71770270 GGAGGCAGCGGCAGCAGCGAG
1 GGAGGCAGCAGCAGCAGCGAG
*
71770291 GGAGGCAGCAGTAGCAGCGAG
1 GGAGGCAGCAGCAGCAGCGAG
71770312 GGAGGCAG-AGCAG
1 GGAGGCAGCAGCAG
71770325 AGCAGAAAGT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
20 4 0.13
21 27 0.87
ACGTcount: A:0.27, C:0.20, G:0.51, T:0.02
Consensus pattern (21 bp):
GGAGGCAGCAGCAGCAGCGAG
Found at i:71770588 original size:31 final size:31
Alignment explanation
Indices: 71770552--71770612 Score: 104
Period size: 31 Copynumber: 2.0 Consensus size: 31
71770542 TATATTTTTT
*
71770552 ATGCTATATTTGCTATTTTTGGTTGGATTTC
1 ATGCTATATTTGCTATTTTTGGTTGAATTTC
*
71770583 ATGCTATATTTGCTGTTTTTGGTTGAATTT
1 ATGCTATATTTGCTATTTTTGGTTGAATTT
71770613 AATGAAGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.16, C:0.08, G:0.20, T:0.56
Consensus pattern (31 bp):
ATGCTATATTTGCTATTTTTGGTTGAATTTC
Found at i:71773105 original size:39 final size:39
Alignment explanation
Indices: 71773059--71773182 Score: 176
Period size: 39 Copynumber: 3.2 Consensus size: 39
71773049 CAAAGTCTAG
* *
71773059 CTGAAGCACATAAGTGCTAAACGGAAGCCTGAAGGTTAA
1 CTGAAGCACACAAGTGCTAAACGGAAGCCTGAAGGCTAA
* * * ** *
71773098 CTAAAGCACAGAAGTGTTAAACAAAAGCCCGAAGGCTAA
1 CTGAAGCACACAAGTGCTAAACGGAAGCCTGAAGGCTAA
71773137 CTGAAGCACACAAGTGCTAAACGGAAGCCTGAAGGCTAA
1 CTGAAGCACACAAGTGCTAAACGGAAGCCTGAAGGCTAA
71773176 CTGAAGC
1 CTGAAGC
71773183 TCATCAGAGC
Statistics
Matches: 72, Mismatches: 13, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
39 72 1.00
ACGTcount: A:0.40, C:0.21, G:0.24, T:0.15
Consensus pattern (39 bp):
CTGAAGCACACAAGTGCTAAACGGAAGCCTGAAGGCTAA
Found at i:71773125 original size:21 final size:21
Alignment explanation
Indices: 71773062--71773125 Score: 53
Period size: 21 Copynumber: 3.2 Consensus size: 21
71773052 AGTCTAGCTG
* * **
71773062 AAGCACATAAGTGCTAAACGG
1 AAGCACAGAAGTGTTAAACAA
* *
71773083 AAGC-CTGAAG-GTT-AACTA
1 AAGCACAGAAGTGTTAAACAA
71773101 AAGCACAGAAGTGTTAAACAA
1 AAGCACAGAAGTGTTAAACAA
71773122 AAGC
1 AAGC
71773126 CCGAAGGCTA
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
18 7 0.21
19 7 0.21
20 7 0.21
21 12 0.36
ACGTcount: A:0.45, C:0.17, G:0.22, T:0.16
Consensus pattern (21 bp):
AAGCACAGAAGTGTTAAACAA
Found at i:71775606 original size:20 final size:21
Alignment explanation
Indices: 71775573--71775613 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
71775563 AGCACATGTA
*
71775573 TTCATGAAAATTCA-AAATTT
1 TTCATCAAAATTCACAAATTT
*
71775593 TTCATCAAATTTCACAAATTT
1 TTCATCAAAATTCACAAATTT
71775614 ACATTTTAGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 12 0.67
21 6 0.33
ACGTcount: A:0.41, C:0.15, G:0.02, T:0.41
Consensus pattern (21 bp):
TTCATCAAAATTCACAAATTT
Found at i:71783657 original size:24 final size:25
Alignment explanation
Indices: 71783630--71783686 Score: 89
Period size: 24 Copynumber: 2.3 Consensus size: 25
71783620 AAGCTCTTCT
*
71783630 GAGCTGAATAACAGGAAGCT-ATGA
1 GAGCTGAATAACAGGAAGCTCATAA
*
71783654 GAGCTGAATAACTGGAAGCTCATAA
1 GAGCTGAATAACAGGAAGCTCATAA
71783679 GAGCTGAA
1 GAGCTGAA
71783687 ATTTGTGACC
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
24 19 0.63
25 11 0.37
ACGTcount: A:0.40, C:0.14, G:0.28, T:0.18
Consensus pattern (25 bp):
GAGCTGAATAACAGGAAGCTCATAA
Found at i:71788616 original size:13 final size:13
Alignment explanation
Indices: 71788598--71788633 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
71788588 GCCATGTGTC
* *
71788598 ACACACGGCTGAG
1 ACACACGCCCGAG
71788611 ACACACGCCCGAG
1 ACACACGCCCGAG
71788624 ACACACGCCC
1 ACACACGCCC
71788634 TTGTCTCTGC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.31, C:0.44, G:0.22, T:0.03
Consensus pattern (13 bp):
ACACACGCCCGAG
Found at i:71792162 original size:46 final size:46
Alignment explanation
Indices: 71792018--71792228 Score: 158
Period size: 46 Copynumber: 4.5 Consensus size: 46
71792008 TGTGTAAGCT
* * * * * * *
71792018 AGTGTAAGACATGTCTGGCACATGCATCGACCAT-ATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCAACGGCTATGA-GACGATAGCC
* * * * ** *
71792064 GGTGTAAGACCATGTCTGGGAAATGGAATTGGC-ATTGAGACGAGGGCT
1 AGTGTAAGA-CATGTCTGGGACATGCAA-CGGCTA-TGAGACGATAGCC
* *
71792112 AGTGTAAGACATGTTTGGGACATGCAACGGCCT-TGAGACGTTAGCC
1 AGTGTAAGACATGTCTGGGACATGCAACGG-CTATGAGACGATAGCC
* * **
71792158 AGTGTAAGACATGTCTGGGACATGCATCGGCTATGAGATGATAGTT
1 AGTGTAAGACATGTCTGGGACATGCAACGGCTATGAGACGATAGCC
*
71792204 AGTATAAGACCATGTCTGGGACATG
1 AGTGTAAGA-CATGTCTGGGACATG
71792229 ACATCAACTT
Statistics
Matches: 130, Mismatches: 27, Indels: 15
0.76 0.16 0.09
Matches are distributed among these distances:
45 2 0.02
46 64 0.49
47 46 0.35
48 17 0.13
49 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.30, T:0.25
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCAACGGCTATGAGACGATAGCC
Found at i:71792242 original size:47 final size:47
Alignment explanation
Indices: 71792162--71792280 Score: 127
Period size: 47 Copynumber: 2.5 Consensus size: 47
71792152 TTAGCCAGTG
** * *
71792162 TAAGA-CATGTCTGGGACATGCATCGGCTATGAGATGA-TAGTTAGTA
1 TAAGACCATGTCTGGGACATGCATCAACTATGAGAT-ACGAGCTAGTA
71792208 TAAGACCATGTCTGGGACATGACATCAACT-TGAGATACGAGCTAGTA
1 TAAGACCATGTCTGGGACATG-CATCAACTATGAGATACGAGCTAGTA
* * *
71792255 TAATACCGTGTCTAGGACATGGCATC
1 TAAGACCATGTCTGGGACAT-GCATC
71792281 GACACCTTAC
Statistics
Matches: 62, Mismatches: 7, Indels: 7
0.82 0.09 0.09
Matches are distributed among these distances:
46 6 0.10
47 49 0.79
48 7 0.11
ACGTcount: A:0.31, C:0.18, G:0.25, T:0.26
Consensus pattern (47 bp):
TAAGACCATGTCTGGGACATGCATCAACTATGAGATACGAGCTAGTA
Found at i:71800578 original size:49 final size:49
Alignment explanation
Indices: 71800506--71800693 Score: 232
Period size: 49 Copynumber: 3.8 Consensus size: 49
71800496 TGAGGTCACG
*
71800506 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
* * * * * * *
71800555 TGTGTAGTGCTAAGTGCAGGCTACTATGCGTACCCGAAAATTGTGATCACG
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTG-G-TCGCA
* * *
71800606 TGTGTAGTACTAAGTGTAGGCTACTACGTGTACCAGATTATTGGCCGCA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
* * *
71800655 TGTGTAGTACTAAGTTCAGGCTACTATGCGTACCAGATA
1 TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATA
71800694 GCTTCGGCTA
Statistics
Matches: 115, Mismatches: 22, Indels: 4
0.82 0.16 0.03
Matches are distributed among these distances:
49 74 0.64
50 2 0.02
51 39 0.34
ACGTcount: A:0.26, C:0.19, G:0.27, T:0.29
Consensus pattern (49 bp):
TGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGTCGCA
Found at i:71800675 original size:100 final size:101
Alignment explanation
Indices: 71800492--71800688 Score: 324
Period size: 100 Copynumber: 2.0 Consensus size: 101
71800482 CAAATGAACT
* *
71800492 ATTGTGAGGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCGGATAATTGGTCGCATG
1 ATTGTGA-GTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGCCGCATG
*
71800557 TGTAGTGCTAAGTGCAGGCTACTATGCGTACCCGAAA
65 TGTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAA
* *
71800594 ATTGTGA-TCACGTGTGTAGTACTAAGTGTAGGCTACTACGTGTACCAGATTATTGGCCGCATGT
1 ATTGTGAGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGCCGCATGT
*
71800658 GTAGTACTAAGTTCAGGCTACTATGCGTACC
66 GTAGTACTAAGTGCAGGCTACTATGCGTACC
71800689 AGATAGCTTC
Statistics
Matches: 89, Mismatches: 6, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
100 82 0.92
102 7 0.08
ACGTcount: A:0.24, C:0.19, G:0.27, T:0.29
Consensus pattern (101 bp):
ATTGTGAGTCACGTGTGTAGTACTAAGTGCAGGCTACTACGTGTACCAGATAATTGGCCGCATGT
GTAGTACTAAGTGCAGGCTACTATGCGTACCCGAAA
Found at i:71803715 original size:15 final size:15
Alignment explanation
Indices: 71803695--71803750 Score: 62
Period size: 15 Copynumber: 3.7 Consensus size: 15
71803685 GTATCTTGGG
71803695 TTTCTTTATTCTGGA
1 TTTCTTTATTCTGGA
71803710 TTTCTTTATTCT-GA
1 TTTCTTTATTCTGGA
* *
71803724 GTTTTTTTA-TCTTGAA
1 -TTTCTTTATTC-TGGA
71803740 TTTCTTTATTC
1 TTTCTTTATTC
71803751 AGTTTTCTTG
Statistics
Matches: 34, Mismatches: 3, Indels: 7
0.77 0.07 0.16
Matches are distributed among these distances:
14 4 0.12
15 27 0.79
16 3 0.09
ACGTcount: A:0.14, C:0.12, G:0.09, T:0.64
Consensus pattern (15 bp):
TTTCTTTATTCTGGA
Found at i:71815199 original size:25 final size:25
Alignment explanation
Indices: 71815171--71815239 Score: 102
Period size: 25 Copynumber: 2.8 Consensus size: 25
71815161 TCTTCTGAGT
*
71815171 TGAATAACGGGAAGCTCATGCAAGC
1 TGAAGAACGGGAAGCTCATGCAAGC
* *
71815196 TGAAGAATGGGAAGCTCATGCGAGC
1 TGAAGAACGGGAAGCTCATGCAAGC
*
71815221 CGAAGAACGGGAAGCTCAT
1 TGAAGAACGGGAAGCTCAT
71815240 AAGAGCTGAA
Statistics
Matches: 39, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
25 39 1.00
ACGTcount: A:0.35, C:0.19, G:0.32, T:0.14
Consensus pattern (25 bp):
TGAAGAACGGGAAGCTCATGCAAGC
Found at i:71821201 original size:43 final size:42
Alignment explanation
Indices: 71821103--71821212 Score: 123
Period size: 43 Copynumber: 2.6 Consensus size: 42
71821093 TGATTACATG
* *
71821103 TAAGACCATGTCTGGGACATTGGCATTGTATTGAGATTATGTG
1 TAAGACCATGTCTGGGACATTGGCATCGTATT-AGATTATGTA
* *
71821146 TAAGACCATGTCTAGGACATTGGCATCGTTAATT-GATTTTGTA
1 TAAGACCATGTCTGGGACATTGGCATCG-T-ATTAGATTATGTA
* * *
71821189 TAAGTCCCTGTCTGGGACAATGGC
1 TAAGACCATGTCTGGGACATTGGC
71821213 GTCGATATGT
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
43 53 0.93
44 1 0.02
45 3 0.05
ACGTcount: A:0.25, C:0.15, G:0.25, T:0.34
Consensus pattern (42 bp):
TAAGACCATGTCTGGGACATTGGCATCGTATTAGATTATGTA
Found at i:71822346 original size:21 final size:22
Alignment explanation
Indices: 71822322--71822362 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
71822312 ATATTTATTC
71822322 TTAGT-TCTTAATTTTCTTTTT
1 TTAGTGTCTTAATTTTCTTTTT
* *
71822343 TTAGTGTTTTCATTTTCTTT
1 TTAGTGTCTTAATTTTCTTT
71822363 AATTTCTAAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 5 0.29
22 12 0.71
ACGTcount: A:0.12, C:0.10, G:0.07, T:0.71
Consensus pattern (22 bp):
TTAGTGTCTTAATTTTCTTTTT
Found at i:71822840 original size:4 final size:4
Alignment explanation
Indices: 71822833--71822887 Score: 92
Period size: 4 Copynumber: 13.8 Consensus size: 4
71822823 TTCATGTATG
* *
71822833 TGTA TGTA AGTA TGTA TGTA AGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
71822881 TGTA TGT
1 TGTA TGT
71822888 GAATAAAAAA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
4 47 1.00
ACGTcount: A:0.27, C:0.00, G:0.25, T:0.47
Consensus pattern (4 bp):
TGTA
Found at i:71827446 original size:23 final size:23
Alignment explanation
Indices: 71827420--71827467 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
71827410 ATTAAATGAT
71827420 TTCTCCAGCACAAAACCTCCTAA
1 TTCTCCAGCACAAAACCTCCTAA
** * *
71827443 TTCTCCTTCTCAAAACCTCTTAA
1 TTCTCCAGCACAAAACCTCCTAA
71827466 TT
1 TT
71827468 TTCTTTCGAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.29, C:0.35, G:0.02, T:0.33
Consensus pattern (23 bp):
TTCTCCAGCACAAAACCTCCTAA
Found at i:71831549 original size:40 final size:40
Alignment explanation
Indices: 71831490--71832477 Score: 1940
Period size: 40 Copynumber: 24.7 Consensus size: 40
71831480 GAGCATTGGT
*
71831490 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
*
71831530 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
71831570 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
71831610 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
71831650 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
71831690 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
71831730 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
71831770 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
71831810 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
71831850 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
71831890 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
71831930 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
71831970 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
71832010 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
71832050 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
71832090 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
71832130 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
71832170 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
71832210 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
71832250 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
71832290 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
71832330 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
71832370 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
*
71832410 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
*
71832450 ATATGTCCGGGCTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
71832478 ATGTGTTTGC
Statistics
Matches: 943, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
40 943 1.00
ACGTcount: A:0.32, C:0.20, G:0.28, T:0.20
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGATG
Found at i:71834674 original size:79 final size:79
Alignment explanation
Indices: 71834580--71834790 Score: 305
Period size: 79 Copynumber: 2.7 Consensus size: 79
71834570 CAATTATACT
* * *
71834580 TAAGGATACAAAAGATCATAAAATCAACTTATATATTCATGGATTGTATATATCAATATACAATC
1 TAAGGATACAAAAGATCATAAAGTCAGCTAATATATTCATGGATTGTATATATCAATATACAATC
71834645 AATTATCCTTAATA
66 AATTATCCTTAATA
* * * * *
71834659 TAAGGATACAAAAGATCATAAAGTCAGCTCATATATTTATGGATTGCATATCTCAATATATAATC
1 TAAGGATACAAAAGATCATAAAGTCAGCTAATATATTCATGGATTGTATATATCAATATACAATC
*
71834724 AATTGTCCTTAATA
66 AATTATCCTTAATA
* * * *
71834738 TAAGGATACAATAGATTATAAAGTTAGCTAATATATTCATGGATTGTACATAT
1 TAAGGATACAAAAGATCATAAAGTCAGCTAATATATTCATGGATTGTATATAT
71834791 ATTCATGGAT
Statistics
Matches: 116, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
79 116 1.00
ACGTcount: A:0.43, C:0.12, G:0.11, T:0.35
Consensus pattern (79 bp):
TAAGGATACAAAAGATCATAAAGTCAGCTAATATATTCATGGATTGTATATATCAATATACAATC
AATTATCCTTAATA
Found at i:71834792 original size:19 final size:19
Alignment explanation
Indices: 71834768--71834804 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
71834758 AAGTTAGCTA
71834768 ATATATTCATGGATTGTAC
1 ATATATTCATGGATTGTAC
71834787 ATATATTCATGGATTGTA
1 ATATATTCATGGATTGTA
71834805 TATCTCAACA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.08, G:0.16, T:0.43
Consensus pattern (19 bp):
ATATATTCATGGATTGTAC
Found at i:71836352 original size:16 final size:15
Alignment explanation
Indices: 71836326--71836357 Score: 55
Period size: 16 Copynumber: 2.1 Consensus size: 15
71836316 ACTAGATCAG
71836326 CAAAAGCCGAAAAGC
1 CAAAAGCCGAAAAGC
71836341 CAAAATGCCGAAAAGC
1 CAAAA-GCCGAAAAGC
71836357 C
1 C
71836358 GGTATTTTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 5 0.31
16 11 0.69
ACGTcount: A:0.50, C:0.28, G:0.19, T:0.03
Consensus pattern (15 bp):
CAAAAGCCGAAAAGC
Found at i:71836802 original size:27 final size:26
Alignment explanation
Indices: 71836759--71836869 Score: 150
Period size: 27 Copynumber: 4.2 Consensus size: 26
71836749 AGGAAGCGTC
* * *
71836759 CTGGTGGCTATGGCACAATTATCTGAT
1 CTGGTGGCTCTGCCAC-ATTATCTGTT
71836786 CTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTCTGCCACAT-TATCTGTT
71836813 CTGGTGGCTCTGCCACAATTATCTGTT
1 CTGGTGGCTCTGCCAC-ATTATCTGTT
* *
71836840 CTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTCTGCCACATTATCTGTT
71836866 CTGG
1 CTGG
71836870 CAGCCATGCT
Statistics
Matches: 77, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
26 16 0.21
27 59 0.77
28 2 0.03
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.37
Consensus pattern (26 bp):
CTGGTGGCTCTGCCACATTATCTGTT
Found at i:71836817 original size:54 final size:53
Alignment explanation
Indices: 71836759--71836869 Score: 168
Period size: 54 Copynumber: 2.1 Consensus size: 53
71836749 AGGAAGCGTC
* *
71836759 CTGGTGGCTATGGCACAATTATCTGATCTGGTGGCTCTGCCACATATATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACAT-TATCTGTT
* * *
71836813 CTGGTGGCTCTGCCACAATTATCTGTTCTGGTGACTCTGTCACATTATCTGTT
1 CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATTATCTGTT
71836866 CTGG
1 CTGG
71836870 CAGCCATGCT
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
53 12 0.23
54 40 0.77
ACGTcount: A:0.16, C:0.23, G:0.23, T:0.37
Consensus pattern (53 bp):
CTGGTGGCTATGCCACAATTATCTGATCTGGTGACTCTGCCACATTATCTGTT
Found at i:71840140 original size:23 final size:18
Alignment explanation
Indices: 71840086--71840159 Score: 105
Period size: 18 Copynumber: 4.1 Consensus size: 18
71840076 CCCATTTCAA
*
71840086 TAACATTAATCAGTGCAG
1 TAACAGTAATCAGTGCAG
71840104 TAACAGTAATCAGTGCAG
1 TAACAGTAATCAGTGCAG
* *
71840122 TAACCA-TGATCAATGCAG
1 TAA-CAGTAATCAGTGCAG
71840140 TAACAGTAATCAGTGCAG
1 TAACAGTAATCAGTGCAG
71840158 TA
1 TA
71840160 TGCAAGCAGA
Statistics
Matches: 49, Mismatches: 5, Indels: 4
0.84 0.09 0.07
Matches are distributed among these distances:
17 2 0.04
18 45 0.92
19 2 0.04
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (18 bp):
TAACAGTAATCAGTGCAG
Found at i:71840512 original size:27 final size:27
Alignment explanation
Indices: 71840470--71840600 Score: 113
Period size: 27 Copynumber: 4.8 Consensus size: 27
71840460 GAACAAATCT
** *
71840470 GTCATTTTACTTTACAAGGGTATTACA
1 GTCATTTTACCCTACAAGGGTATTTCA
*
71840497 GTCATTTTACCCTACAAGGGTATTTTCC
1 GTCATTTTACCCTACAAGGGTA-TTTCA
* **
71840525 GTCATTTTACCTTA-TGGAGGTATTTC-
1 GTCATTTTACCCTACAAG-GGTATTTCA
** *
71840551 GATCATTTTACCCTATGAGGGTATTTCG
1 G-TCATTTTACCCTACAAGGGTATTTCA
* *
71840579 GTCATTTTATCCTATAAGGGTA
1 GTCATTTTACCCTACAAGGGTA
71840601 AAACAGTCAT
Statistics
Matches: 87, Mismatches: 12, Indels: 10
0.80 0.11 0.09
Matches are distributed among these distances:
26 1 0.01
27 64 0.74
28 22 0.25
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.41
Consensus pattern (27 bp):
GTCATTTTACCCTACAAGGGTATTTCA
Found at i:71840533 original size:55 final size:54
Alignment explanation
Indices: 71840470--71840587 Score: 132
Period size: 55 Copynumber: 2.2 Consensus size: 54
71840460 GAACAAATCT
*
71840470 GTCATTTTACTTTACAAG-GGTATTAC-AGTCATTTTACCCTACAAGGGTATTTTCC
1 GTCATTTTACCTTA-AAGAGGTATTACGA-TCATTTTACCCTACAAGGGTA-TTTCC
** * ** *
71840525 GTCATTTTACCTTATGGAGGTATTTCGATCATTTTACCCTATGAGGGTATTTCG
1 GTCATTTTACCTTAAAGAGGTATTACGATCATTTTACCCTACAAGGGTATTTCC
71840579 GTCATTTTA
1 GTCATTTTA
71840588 TCCTATAAGG
Statistics
Matches: 54, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
54 14 0.26
55 39 0.72
56 1 0.02
ACGTcount: A:0.23, C:0.18, G:0.17, T:0.42
Consensus pattern (54 bp):
GTCATTTTACCTTAAAGAGGTATTACGATCATTTTACCCTACAAGGGTATTTCC
Found at i:71840546 original size:28 final size:27
Alignment explanation
Indices: 71840486--71840600 Score: 117
Period size: 27 Copynumber: 4.2 Consensus size: 27
71840476 TTACTTTACA
* * **
71840486 AGGGTATTACAGTCATTTTACCCTACA
1 AGGGTATTTCCGTCATTTTACCCTATG
*
71840513 AGGGTATTTTCCGTCATTTTACCTTATG
1 AGGGTA-TTTCCGTCATTTTACCCTATG
71840541 -GAGGTATTT-CGATCATTTTACCCTATG
1 AG-GGTATTTCCG-TCATTTTACCCTATG
* * *
71840568 AGGGTATTTCGGTCATTTTATCCTATA
1 AGGGTATTTCCGTCATTTTACCCTATG
71840595 AGGGTA
1 AGGGTA
71840601 AAACAGTCAT
Statistics
Matches: 74, Mismatches: 9, Indels: 10
0.80 0.10 0.11
Matches are distributed among these distances:
26 2 0.03
27 50 0.68
28 22 0.30
ACGTcount: A:0.23, C:0.17, G:0.19, T:0.40
Consensus pattern (27 bp):
AGGGTATTTCCGTCATTTTACCCTATG
Found at i:71843505 original size:37 final size:37
Alignment explanation
Indices: 71843454--71843527 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
71843444 AATTTGATCC
*
71843454 CTAATGTAGTAAAGTTAACAAATAAGCCAAACTAACT
1 CTAATGTAGCAAAGTTAACAAATAAGCCAAACTAACT
*
71843491 CTAATGTAGCAAAGTTAACAAATAAGTCAAACTAACT
1 CTAATGTAGCAAAGTTAACAAATAAGCCAAACTAACT
71843528 TGATAATCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.49, C:0.16, G:0.11, T:0.24
Consensus pattern (37 bp):
CTAATGTAGCAAAGTTAACAAATAAGCCAAACTAACT
Found at i:71845142 original size:14 final size:14
Alignment explanation
Indices: 71845125--71845155 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
71845115 AGTAAAATGT
71845125 TTTCTAAAAAATAA
1 TTTCTAAAAAATAA
*
71845139 TTTCTGAAAAATAA
1 TTTCTAAAAAATAA
71845153 TTT
1 TTT
71845156 ATTTTTCTGA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.42
Consensus pattern (14 bp):
TTTCTAAAAAATAA
Found at i:71845181 original size:18 final size:20
Alignment explanation
Indices: 71845139--71845181 Score: 54
Period size: 18 Copynumber: 2.2 Consensus size: 20
71845129 TAAAAAATAA
*
71845139 TTTCTGAAAAATAATTTATT
1 TTTCTGAAAAATAATTTACT
*
71845159 TTTCTG-AAAATGA-TTACT
1 TTTCTGAAAAATAATTTACT
71845177 TTTCT
1 TTTCT
71845182 ATTGTTTGGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
18 9 0.43
19 6 0.29
20 6 0.29
ACGTcount: A:0.33, C:0.09, G:0.07, T:0.51
Consensus pattern (20 bp):
TTTCTGAAAAATAATTTACT
Found at i:71846835 original size:28 final size:28
Alignment explanation
Indices: 71846802--71846862 Score: 113
Period size: 28 Copynumber: 2.2 Consensus size: 28
71846792 CAAGGAAGAA
*
71846802 CAAACCCGAAAGTGGAACTCAAAGAGGG
1 CAAACCCGAAAGTGGAACTCAAAGAGAG
71846830 CAAACCCGAAAGTGGAACTCAAAGAGAG
1 CAAACCCGAAAGTGGAACTCAAAGAGAG
71846858 CAAAC
1 CAAAC
71846863 TGAAAACCCA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.46, C:0.23, G:0.25, T:0.07
Consensus pattern (28 bp):
CAAACCCGAAAGTGGAACTCAAAGAGAG
Found at i:71853425 original size:24 final size:24
Alignment explanation
Indices: 71853397--71853447 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
71853387 TTCTAGAAGG
*
71853397 TTTAGTATTTACTAGTATAATATA
1 TTTAGCATTTACTAGTATAATATA
* *
71853421 TTTAGCATTTATTAGTATAATTTA
1 TTTAGCATTTACTAGTATAATATA
71853445 TTT
1 TTT
71853448 GACTTACTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.33, C:0.04, G:0.08, T:0.55
Consensus pattern (24 bp):
TTTAGCATTTACTAGTATAATATA
Found at i:71856020 original size:30 final size:30
Alignment explanation
Indices: 71855984--71856041 Score: 107
Period size: 30 Copynumber: 1.9 Consensus size: 30
71855974 CTTGTAAAAC
71855984 TTGATTGGAATTTAAGTTAATGGATTGGAA
1 TTGATTGGAATTTAAGTTAATGGATTGGAA
*
71856014 TTGATTGGAATTTAGGTTAATGGATTGG
1 TTGATTGGAATTTAAGTTAATGGATTGG
71856042 GGCCACTTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.29, C:0.00, G:0.29, T:0.41
Consensus pattern (30 bp):
TTGATTGGAATTTAAGTTAATGGATTGGAA
Found at i:71859217 original size:23 final size:24
Alignment explanation
Indices: 71859187--71859232 Score: 67
Period size: 24 Copynumber: 2.0 Consensus size: 24
71859177 AGAACTTTTA
* *
71859187 ATCAGGAA-GCTCACGAAGAGCCT
1 ATCAGGAATACTCACAAAGAGCCT
71859210 ATCAGGAATACTCACAAAGAGCC
1 ATCAGGAATACTCACAAAGAGCC
71859233 ATGTAACAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
23 8 0.40
24 12 0.60
ACGTcount: A:0.39, C:0.26, G:0.22, T:0.13
Consensus pattern (24 bp):
ATCAGGAATACTCACAAAGAGCCT
Found at i:71862498 original size:21 final size:22
Alignment explanation
Indices: 71862481--71862536 Score: 66
Period size: 21 Copynumber: 2.7 Consensus size: 22
71862471 AGAAAATTCA
71862481 ATCAAAT-TAGAATTAAATAAG
1 ATCAAATATAGAATTAAATAAG
*
71862502 ATCAAATATAGAATTGAA-AAG
1 ATCAAATATAGAATTAAATAAG
71862523 ATTC-AATATA-AATT
1 A-TCAAATATAGAATT
71862537 TGATGTTGTT
Statistics
Matches: 32, Mismatches: 1, Indels: 5
0.84 0.03 0.13
Matches are distributed among these distances:
20 4 0.12
21 17 0.53
22 11 0.34
ACGTcount: A:0.55, C:0.05, G:0.09, T:0.30
Consensus pattern (22 bp):
ATCAAATATAGAATTAAATAAG
Found at i:71865228 original size:16 final size:16
Alignment explanation
Indices: 71865205--71865238 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
71865195 AATTTTAGAT
71865205 AAATAATTA-TTTAAC
1 AAATAATTAGTTTAAC
71865220 AAATAAATTAGTTTAAC
1 AAAT-AATTAGTTTAAC
71865237 AA
1 AA
71865239 TCGAATCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 4 0.24
16 5 0.29
17 8 0.47
ACGTcount: A:0.56, C:0.06, G:0.03, T:0.35
Consensus pattern (16 bp):
AAATAATTAGTTTAAC
Found at i:71865679 original size:18 final size:19
Alignment explanation
Indices: 71865656--71865693 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
71865646 ACGTTCAGGC
71865656 TTTA-TGGCTCAAAATAGG
1 TTTAGTGGCTCAAAATAGG
*
71865674 TTTATGTGGCTCAACATAGG
1 TTTA-GTGGCTCAAAATAGG
71865694 GTTGTTGTGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 4 0.24
20 13 0.76
ACGTcount: A:0.29, C:0.13, G:0.24, T:0.34
Consensus pattern (19 bp):
TTTAGTGGCTCAAAATAGG
Found at i:71877646 original size:14 final size:14
Alignment explanation
Indices: 71877610--71877653 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
71877600 GTACAATATA
71877610 TATATGATATAATAAT
1 TATATG-TAT-ATAAT
* *
71877626 AAAATGTATATAAT
1 TATATGTATATAAT
71877640 TATATGTATATAAT
1 TATATGTATATAAT
71877654 AAAAGTTATG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
14 17 0.71
15 3 0.12
16 4 0.17
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (14 bp):
TATATGTATATAAT
Found at i:71882185 original size:45 final size:44
Alignment explanation
Indices: 71882121--71882248 Score: 195
Period size: 45 Copynumber: 2.9 Consensus size: 44
71882111 TGTGCAGTAC
*
71882121 TATTCGGGCCTTTGAGCCTAGCAGGCTATAATGCCGGTGAGATAT
1 TATTCGGG-CTTTGAGCCTAGCAGGCTATAATACCGGTGAGATAT
71882166 TATTCGGGTCTTTGAGCCTAGCAGGCTATAATACCGGTGAGATAT
1 TATTCGGG-CTTTGAGCCTAGCAGGCTATAATACCGGTGAGATAT
* * *
71882211 TATTCGGGCCTCGAGCCTAGCAGGCGA-AATACCGGTGA
1 TATTCGGGCTTTGAGCCTAGCAGGCTATAATACCGGTGA
71882249 AGGAATTCGG
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
43 11 0.14
44 16 0.21
45 51 0.65
ACGTcount: A:0.23, C:0.21, G:0.29, T:0.27
Consensus pattern (44 bp):
TATTCGGGCTTTGAGCCTAGCAGGCTATAATACCGGTGAGATAT
Found at i:71886076 original size:13 final size:13
Alignment explanation
Indices: 71886058--71886082 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
71886048 TATATGATAT
71886058 GTGTGAAAATTTC
1 GTGTGAAAATTTC
71886071 GTGTGAAAATTT
1 GTGTGAAAATTT
71886083 TATCGTTTGT
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:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:71887334 original size:23 final size:23
Alignment explanation
Indices: 71887308--71887351 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
71887298 TATATCCATA
* *
71887308 CCAAAATCATGCCAAATCATAAG
1 CCAAAATCATACCAAAACATAAG
*
71887331 CCAAAGTCATACCAAAACATA
1 CCAAAATCATACCAAAACATA
71887352 TGTTTCATAA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.50, C:0.27, G:0.07, T:0.16
Consensus pattern (23 bp):
CCAAAATCATACCAAAACATAAG
Found at i:71888213 original size:86 final size:85
Alignment explanation
Indices: 71888058--71888219 Score: 220
Period size: 86 Copynumber: 1.9 Consensus size: 85
71888048 CAATGCCAAC
* *
71888058 GTCCCAGACGTAGTCTTACATGTAATTAAATATCAATGCCACTGTCCCAGACAGGGTCTTACACG
1 GTCCCAGACATAGTCTTACATGTAATTAAATATCAATGCCAATGTCCCAGACAGGGTCTTACACG
71888123 AAATCAAATATGATGCCGAT
66 AAATCAAATATGATGCCGAT
* * * *
71888143 GTCCCAGACATGGTCTTACATGTAAATCTCAA-ATCGATGCCAATGTCTCAGAC-GTGGTCTTAC
1 GTCCCAGACATAGTCTTACATGT-AAT-TAAATATCAATGCCAATGTCCCAGACAG-GGTCTTAC
*
71888206 ACGAAATCACATAT
63 ACGAAATCAAATAT
71888220 TGGAATCCTA
Statistics
Matches: 67, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
85 22 0.33
86 42 0.63
87 3 0.04
ACGTcount: A:0.32, C:0.24, G:0.17, T:0.27
Consensus pattern (85 bp):
GTCCCAGACATAGTCTTACATGTAATTAAATATCAATGCCAATGTCCCAGACAGGGTCTTACACG
AAATCAAATATGATGCCGAT
Found at i:71888233 original size:44 final size:42
Alignment explanation
Indices: 71888050--71888219 Score: 160
Period size: 43 Copynumber: 4.0 Consensus size: 42
71888040 AGCTCGTACA
* * * * * * * *
71888050 ATGCCAACGTCCCAGACGTAGTCTTACATGTAATTAAATATCA
1 ATGCCAATGTCCCAGACATGGTCTTACACGAAATCACATAT-G
* * *
71888093 ATGCCACTGTCCCAGACAGGGTCTTACACGAAATCAAATATG
1 ATGCCAATGTCCCAGACATGGTCTTACACGAAATCACATATG
* * * *
71888135 ATGCCGATGTCCCAGACATGGTCTTACATGTAAATCTCAAATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACG-AAATCACATAT-G
* *
71888179 ATGCCAATGTCTCAGACGTGGTCTTACACGAAATCACATAT
1 ATGCCAATGTCCCAGACATGGTCTTACACGAAATCACATAT
71888220 TGGAATCCTA
Statistics
Matches: 103, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
42 26 0.25
43 50 0.49
44 27 0.26
ACGTcount: A:0.32, C:0.25, G:0.17, T:0.26
Consensus pattern (42 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGAAATCACATATG
Found at i:71890629 original size:16 final size:17
Alignment explanation
Indices: 71890608--71890640 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
71890598 CACATTGAAG
71890608 TGTTTT-TTGAAAACCA
1 TGTTTTATTGAAAACCA
71890624 TGTTTTCATTGAAAACC
1 TGTTTT-ATTGAAAACC
71890641 CTTTTTACTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
18 9 0.60
ACGTcount: A:0.30, C:0.15, G:0.12, T:0.42
Consensus pattern (17 bp):
TGTTTTATTGAAAACCA
Found at i:71891743 original size:27 final size:27
Alignment explanation
Indices: 71891713--71891785 Score: 74
Period size: 27 Copynumber: 2.7 Consensus size: 27
71891703 CCCTACAGGG
*
71891713 GTATGTCGACCATTTTACACTACAATA
1 GTATGTCGACAATTTTACACTACAATA
* ** **
71891740 GTATTTCGGTAATTTTACACTACAAGG
1 GTATGTCGACAATTTTACACTACAATA
* *
71891767 GTATTTCGATAATTTTACA
1 GTATGTCGACAATTTTACA
71891786 AATCGGGGGT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.38
Consensus pattern (27 bp):
GTATGTCGACAATTTTACACTACAATA
Found at i:71892096 original size:27 final size:27
Alignment explanation
Indices: 71891740--71892104 Score: 403
Period size: 27 Copynumber: 13.6 Consensus size: 27
71891730 CACTACAATA
* *
71891740 GTATTTCGGTAATTTTAC-ACTACAAGG
1 GTATTTCGGTAATTTTACAAAT-CGAGG
* *
71891767 GTATTTCGATAATTTTACAAATCGGGG
1 GTATTTCGGTAATTTTACAAATCGAGG
*
71891794 GTGTTTCGGTAATTTTACAAATCGAGG
1 GTATTTCGGTAATTTTACAAATCGAGG
** * *
71891821 GTATTTTAGTAATTTTACAAACCAAGG
1 GTATTTCGGTAATTTTACAAATCGAGG
* *
71891848 GTATTTCGATAATTTTACAAATCAAGG
1 GTATTTCGGTAATTTTACAAATCGAGG
* *
71891875 GTATTTCAGTAATTTTACAAATCAAGG
1 GTATTTCGGTAATTTTACAAATCGAGG
*
71891902 GTGTTTCGGTAATTTTACAAATCGAGG
1 GTATTTCGGTAATTTTACAAATCGAGG
* * *
71891929 GT-GTTCTGATAATTTTACAAATTGAGG
1 GTATTTC-GGTAATTTTACAAATCGAGG
* * * *
71891956 GTGTTTCGGTAATTTCACAAATTGGGG
1 GTATTTCGGTAATTTTACAAATCGAGG
*
71891983 GTATTTTGGTAATTTTACAAATCGAGG
1 GTATTTCGGTAATTTTACAAATCGAGG
** * *
71892010 GTATTTTAGTAATTTCAC-AATTGAGG
1 GTATTTCGGTAATTTTACAAATCGAGG
*
71892036 GTATTTCAGTAATTTTACAAATCGAGG
1 GTATTTCGGTAATTTTACAAATCGAGG
* * *
71892063 GTGTTTTGGTAATTTCACAAATCGAGG
1 GTATTTCGGTAATTTTACAAATCGAGG
**
71892090 GTATTTTAGTAATTT
1 GTATTTCGGTAATTT
71892105 CTCTTTATTA
Statistics
Matches: 289, Mismatches: 45, Indels: 8
0.85 0.13 0.02
Matches are distributed among these distances:
26 26 0.09
27 258 0.89
28 5 0.02
ACGTcount: A:0.30, C:0.10, G:0.21, T:0.39
Consensus pattern (27 bp):
GTATTTCGGTAATTTTACAAATCGAGG
Found at i:71892465 original size:28 final size:28
Alignment explanation
Indices: 71892404--71892484 Score: 108
Period size: 28 Copynumber: 2.9 Consensus size: 28
71892394 ATCCACACTT
* *
71892404 ATTCATTTGGCCCCTTTAGGCCCAATCTC
1 ATTCATTTGG-CCCATTAGGCCCAATCAC
* *
71892433 GTTCATTTGGCCCATCAGGCCCAATCAC
1 ATTCATTTGGCCCATTAGGCCCAATCAC
*
71892461 ATTCATATGGCCCATTAGGCCCAA
1 ATTCATTTGGCCCATTAGGCCCAA
71892485 CTACTTCCCA
Statistics
Matches: 45, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
28 36 0.80
29 9 0.20
ACGTcount: A:0.22, C:0.33, G:0.16, T:0.28
Consensus pattern (28 bp):
ATTCATTTGGCCCATTAGGCCCAATCAC
Found at i:71897489 original size:43 final size:43
Alignment explanation
Indices: 71897441--71897625 Score: 214
Period size: 43 Copynumber: 4.3 Consensus size: 43
71897431 CACATATCGG
** *
71897441 AATCACATATCGACT-CCAACATATTAAACGTGGTCTTAC-TCGT
1 AATCACATATCGA-TGCCAACATCCTAGACGTGGTCTTACAT-GT
* * * *
71897484 AATCACATATCGATGCCAACAT-TTCAGATGTAGTTTTACATGT
1 AATCACATATCGATGCCAACATCCT-AGACGTGGTCTTACATGT
* * **
71897527 AATCACATATCGATGCTAACATCCGAGACGTGGTCTTACACAT
1 AATCACATATCGATGCCAACATCCTAGACGTGGTCTTACATGT
*
71897570 AATCACATATCGATGCCAACGTCCTAGACGTGGTCTTACATGT
1 AATCACATATCGATGCCAACATCCTAGACGTGGTCTTACATGT
71897613 AATCACATATCGA
1 AATCACATATCGA
71897626 AAATCCTATG
Statistics
Matches: 121, Mismatches: 17, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
42 3 0.02
43 117 0.97
44 1 0.01
ACGTcount: A:0.32, C:0.24, G:0.15, T:0.29
Consensus pattern (43 bp):
AATCACATATCGATGCCAACATCCTAGACGTGGTCTTACATGT
Found at i:71897493 original size:168 final size:168
Alignment explanation
Indices: 71897192--71897496 Score: 443
Period size: 168 Copynumber: 1.8 Consensus size: 168
71897182 TCCTAGACAG
* * * *
71897192 GGTCTTACTCATAAACCCATATCAAAATCACCTATCGATGCCAACGTATTAAACGTGGTCTTACT
1 GGTCTTACTCATAAACACATATCAAAATCACATATCGATGCCAACGTATTAAACATAGTCTTACT
* * * * *
71897257 CGTACACACATATCAGAATCACATATTGATGCCAACGTGTTAAATGTGGTCTTACTTGCACACAC
66 CGTACACACATATCAGAATCACATATCGATGCCAACATATTAAACGTGGTCTTACTCGCACACAC
71897322 ATATCGAAATCACATATCGATGCCAACGTATTAAACAT
131 ATATCGAAATCACATATCGATGCCAACGTATTAAACAT
** * *
71897360 GGTCTTACTCATACGCAGATATCAGAATCACATATCGATGCCAACGTATTAAACATAGTCTTACT
1 GGTCTTACTCATAAACACATATCAAAATCACATATCGATGCCAACGTATTAAACATAGTCTTACT
* *
71897425 CGTACACACATATCGGAATCACATATCGACT-CCAACATATTAAACGTGGTCTTACTCGTA-ATC
66 CGTACACACATATCAGAATCACATATCGA-TGCCAACATATTAAACGTGGTCTTACTCGCACA-C
71897488 ACATATCGA
129 ACATATCGA
71897497 TGCCAACATT
Statistics
Matches: 120, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
167 1 0.01
168 118 0.98
169 1 0.01
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (168 bp):
GGTCTTACTCATAAACACATATCAAAATCACATATCGATGCCAACGTATTAAACATAGTCTTACT
CGTACACACATATCAGAATCACATATCGATGCCAACATATTAAACGTGGTCTTACTCGCACACAC
ATATCGAAATCACATATCGATGCCAACGTATTAAACAT
Found at i:71897495 original size:56 final size:56
Alignment explanation
Indices: 71897192--71897494 Score: 396
Period size: 56 Copynumber: 5.4 Consensus size: 56
71897182 TCCTAGACAG
* * * * *
71897192 GGTCTTACTCATAAACCCATATCAAAATCACCTATCGATGCCAACGTATTAAACGT
1 GGTCTTACTCGTACACACATATCAGAATCACATATCGATGCCAACGTATTAAACGT
* * *
71897248 GGTCTTACTCGTACACACATATCAGAATCACATATTGATGCCAACGTGTTAAATGT
1 GGTCTTACTCGTACACACATATCAGAATCACATATCGATGCCAACGTATTAAACGT
* * *
71897304 GGTCTTACTTGCACACACATATC-GAAATCACATATCGATGCCAACGTATTAAACAT
1 GGTCTTACTCGTACACACATATCAG-AATCACATATCGATGCCAACGTATTAAACGT
* * * *
71897360 GGTCTTACTCATACGCAGATATCAGAATCACATATCGATGCCAACGTATTAAACAT
1 GGTCTTACTCGTACACACATATCAGAATCACATATCGATGCCAACGTATTAAACGT
* * *
71897416 AGTCTTACTCGTACACACATATCGGAATCACATATCGACT-CCAACATATTAAACGT
1 GGTCTTACTCGTACACACATATCAGAATCACATATCGA-TGCCAACGTATTAAACGT
71897472 GGTCTTACTCGTA-ATCACATATC
1 GGTCTTACTCGTACA-CACATATC
71897495 GATGCCAACA
Statistics
Matches: 216, Mismatches: 27, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
55 2 0.01
56 212 0.98
57 2 0.01
ACGTcount: A:0.34, C:0.25, G:0.13, T:0.28
Consensus pattern (56 bp):
GGTCTTACTCGTACACACATATCAGAATCACATATCGATGCCAACGTATTAAACGT
Found at i:71897586 original size:86 final size:86
Alignment explanation
Indices: 71897468--71897625 Score: 237
Period size: 86 Copynumber: 1.8 Consensus size: 86
71897458 AACATATTAA
* * * * * *
71897468 ACGTGGTCTTACTCGTAATCACATATCGATGCCAACAT-TTCAGATGTAGTTTTACATGTAATCA
1 ACGTGGTCTTACACATAATCACATATCGATGCCAACGTCCT-AGACGTAGTCTTACATGTAATCA
71897532 CATATCGATGCTAACATCCGAG
65 CATATCGATGCTAACATCCGAG
*
71897554 ACGTGGTCTTACACATAATCACATATCGATGCCAACGTCCTAGACGTGGTCTTACATGTAATCAC
1 ACGTGGTCTTACACATAATCACATATCGATGCCAACGTCCTAGACGTAGTCTTACATGTAATCAC
71897619 ATATCGA
66 ATATCGA
71897626 AAATCCTATG
Statistics
Matches: 64, Mismatches: 7, Indels: 2
0.88 0.10 0.03
Matches are distributed among these distances:
86 63 0.98
87 1 0.02
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (86 bp):
ACGTGGTCTTACACATAATCACATATCGATGCCAACGTCCTAGACGTAGTCTTACATGTAATCAC
ATATCGATGCTAACATCCGAG
Found at i:71899519 original size:27 final size:27
Alignment explanation
Indices: 71899462--71899519 Score: 80
Period size: 27 Copynumber: 2.1 Consensus size: 27
71899452 ACCCATAATC
* * *
71899462 GATAAAATGACTATTATGCCTCTGTGT
1 GATAAAATGACTATTATGCCCCTATGA
*
71899489 GATAAAATGACTGTTATGCCCCTATGA
1 GATAAAATGACTATTATGCCCCTATGA
71899516 GATA
1 GATA
71899520 TAAGATTATA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.33
Consensus pattern (27 bp):
GATAAAATGACTATTATGCCCCTATGA
Found at i:71900155 original size:18 final size:19
Alignment explanation
Indices: 71900121--71900162 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 19
71900111 ATAAAGCCTC
*
71900121 TTTGG-ATTTTATTTTTAA
1 TTTGGTATTTTATATTTAA
71900139 TTTGGTATTTTA-ATTTAA
1 TTTGGTATTTTATATTTAA
71900157 TTTGGT
1 TTTGGT
71900163 TATAACTGCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
18 16 0.73
19 6 0.27
ACGTcount: A:0.21, C:0.00, G:0.14, T:0.64
Consensus pattern (19 bp):
TTTGGTATTTTATATTTAA
Found at i:71903081 original size:22 final size:22
Alignment explanation
Indices: 71903053--71903117 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
71903043 GCAAATACGT
*
71903053 TTGGCACACAGCCATAATCAGG
1 TTGGCACAAAGCCATAATCAGG
* *
71903075 TTGGCACAGAGCCAT-ATGTAGG
1 TTGGCACAAAGCCATAAT-CAGG
*
71903097 TTGGCGCAAAGCCATAATCAG
1 TTGGCACAAAGCCATAATCAG
71903118 AATAATTGGC
Statistics
Matches: 36, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
21 2 0.06
22 32 0.89
23 2 0.06
ACGTcount: A:0.31, C:0.23, G:0.26, T:0.20
Consensus pattern (22 bp):
TTGGCACAAAGCCATAATCAGG
Found at i:71903321 original size:41 final size:41
Alignment explanation
Indices: 71903260--71903381 Score: 181
Period size: 41 Copynumber: 3.0 Consensus size: 41
71903250 AAAAGCCACT
* * *
71903260 GGTGGATCCACAGTCATCAAGCAACCATGCGATCCTTAATC
1 GGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAATC
71903301 GGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAATC
1 GGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAATC
* * * *
71903342 AGTGGATCCACGATCGTTAAGCAACCATGCAATCCTCAAT
1 GGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAAT
71903382 TTCTTCCTCC
Statistics
Matches: 74, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
41 74 1.00
ACGTcount: A:0.29, C:0.30, G:0.20, T:0.21
Consensus pattern (41 bp):
GGTGGATCCACGGTCGTCAAGCAACCATGCGATCCTCAATC
Found at i:71903662 original size:27 final size:27
Alignment explanation
Indices: 71903632--71903683 Score: 68
Period size: 27 Copynumber: 1.9 Consensus size: 27
71903622 AGGTGTTTTG
71903632 GTAAATCTACAAACCAAGGGTATTTCA
1 GTAAATCTACAAACCAAGGGTATTTCA
* * * *
71903659 GTAATTTTGCAAACCAATGGTATTT
1 GTAAATCTACAAACCAAGGGTATTT
71903684 TTGTAATTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 21 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (27 bp):
GTAAATCTACAAACCAAGGGTATTTCA
Found at i:71903689 original size:27 final size:27
Alignment explanation
Indices: 71903641--71904015 Score: 208
Period size: 27 Copynumber: 13.9 Consensus size: 27
71903631 GGTAAATCTA
* *
71903641 CAAACCAAGGGTATTTCAGTAATTTTG
1 CAAATCAAGGGTATTTCTGTAATTTTG
* * *
71903668 CAAACCAATGGTATTTTTGTAATTTTTG
1 CAAATCAAGGGTATTTCTGTAA-TTTTG
* *
71903696 -AAAGTCAAAGGTATTTCTATAATTTTG
1 CAAA-TCAAGGGTATTTCTGTAATTTTG
* * * *
71903723 TAAATTAGGGGTATTTCTGTAATTTTT
1 CAAATCAAGGGTATTTCTGTAATTTTG
** *
71903750 CAAATCAAGGGTATTTCAATAATTTTC
1 CAAATCAAGGGTATTTCTGTAATTTTG
* * *
71903777 CAAATTAGGGGTATTT-TGGTAATTTTA
1 CAAATCAAGGGTATTTCT-GTAATTTTG
* * *
71903804 CAAATCTAGGGTATTTCGGTAATTTTA
1 CAAATCAAGGGTATTTCTGTAATTTTG
* ** * *
71903831 CAAGTTGAGGGTATTTCGGTAATTTTA
1 CAAATCAAGGGTATTTCTGTAATTTTG
** * **
71903858 CAGGTCAAGAGTATTT-TGGTAATTTCA
1 CAAATCAAGGGTATTTCT-GTAATTTTG
* * *
71903885 CAAATCTAGGGTATTTCGGGAATTTT-
1 CAAATCAAGGGTATTTCTGTAATTTTG
* * * *
71903911 CAAGTCGAGGGTATTTCAGTAATTTTA
1 CAAATCAAGGGTATTTCTGTAATTTTG
* * * *
71903938 TAAA-CCAGGGTTATTT-TGGTAGTTTTA
1 CAAATCAAGGG-TATTTCT-GTAATTTTG
* *
71903965 CTAATCGAGGGTATTT-TGGTAATTTTG
1 CAAATCAAGGGTATTTCT-GTAATTTTG
* * *
71903992 TAAA-CCAGGGTTATTTCAGTAATT
1 CAAATCAAGGG-TATTTCTGTAATT
71904016 CTACCCTACA
Statistics
Matches: 274, Mismatches: 61, Indels: 26
0.76 0.17 0.07
Matches are distributed among these distances:
26 32 0.12
27 215 0.78
28 27 0.10
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.41
Consensus pattern (27 bp):
CAAATCAAGGGTATTTCTGTAATTTTG
Found at i:71903782 original size:54 final size:54
Alignment explanation
Indices: 71903641--71903936 Score: 244
Period size: 54 Copynumber: 5.5 Consensus size: 54
71903631 GGTAAATCTA
* * ** ** *
71903641 CAAACCAAGGGTATTTCAGTAATTTTGCAAACCAATGGTATTTTTGTAATTTTT
1 CAAATCAAGGGTATTTCAGTAATTTTCCAAATTAGGGGTATTTCTGTAATTTTT
* * **
71903695 GAAAGTCAAAGGTATTTCTA-TAATTTTGTAAATTAGGGGTATTTCTGTAATTTTT
1 CAAA-TCAAGGGTATTTC-AGTAATTTTCCAAATTAGGGGTATTTCTGTAATTTTT
* *
71903750 CAAATCAAGGGTATTTCAATAATTTTCCAAATTAGGGGTATTT-TGGTAATTTTA
1 CAAATCAAGGGTATTTCAGTAATTTTCCAAATTAGGGGTATTTCT-GTAATTTTT
* * * * * *
71903804 CAAATCTAGGGTATTTCGGTAATTTTACAAGTT-GAGGGTATTTCGGTAATTTTA
1 CAAATCAAGGGTATTTCAGTAATTTTCCAAATTAG-GGGTATTTCTGTAATTTTT
** * ** * *
71903858 CAGGTCAAGAGTATTTTGGTAA-TTTCACAAATCTA-GGGTATTTCGGGAA-TTTT
1 CAAATCAAGGGTATTTCAGTAATTTTC-CAAAT-TAGGGGTATTTCTGTAATTTTT
* *
71903911 CAAGTCGAGGGTATTTCAGTAATTTT
1 CAAATCAAGGGTATTTCAGTAATTTT
71903937 ATAAACCAGG
Statistics
Matches: 198, Mismatches: 34, Indels: 20
0.79 0.13 0.08
Matches are distributed among these distances:
53 26 0.13
54 127 0.64
55 44 0.22
56 1 0.01
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.41
Consensus pattern (54 bp):
CAAATCAAGGGTATTTCAGTAATTTTCCAAATTAGGGGTATTTCTGTAATTTTT
Found at i:71903826 original size:81 final size:81
Alignment explanation
Indices: 71903627--71904015 Score: 320
Period size: 81 Copynumber: 4.8 Consensus size: 81
71903617 TACAAAGGTG
* * * * * * * * * **
71903627 TTTTGGTAAATCTACAAACCAAGGGTATTTCAGTAATTTTGCAAACCAATGGTATTTTTGTAATT
1 TTTTGGTAATTTTACAAATCTAGGGTATTTCGGTAATTTTTCAAATCGAGGGTATTTCAGTAATT
** **
71903692 TTTGAAAGTCAAAGGTA
66 TTACAAA-TCAGGGGTA
* ** * * *
71903709 TTTCT-ATAATTTTGTAAAT-TAGGGGTATTTCTGTAATTTTTCAAATCAAGGGTATTTCAATAA
1 TTT-TGGTAATTTTACAAATCTA-GGGTATTTCGGTAATTTTTCAAATCGAGGGTATTTCAGTAA
* *
71903772 TTTTCCAAATTAGGGGTA
64 TTTTACAAATCAGGGGTA
* * * *
71903790 TTTTGGTAATTTTACAAATCTAGGGTATTTCGGTAATTTTACAAGTTGAGGGTATTTCGGTAATT
1 TTTTGGTAATTTTACAAATCTAGGGTATTTCGGTAATTTTTCAAATCGAGGGTATTTCAGTAATT
** * *
71903855 TTACAGGTCAAGAGTA
66 TTACAAATCAGGGGTA
* * *
71903871 TTTTGGTAATTTCACAAATCTAGGGTATTTCGGGAA-TTTTCAAGTCGAGGGTATTTCAGTAATT
1 TTTTGGTAATTTTACAAATCTAGGGTATTTCGGTAATTTTTCAAATCGAGGGTATTTCAGTAATT
* * *
71903935 TTATAAACCAGGGTTA
66 TTACAAATCAGGGGTA
* * * * *
71903951 TTTTGGTAGTTTTACTAATCGAGGGTATTTTGGTAATTTTGT-AAA-CCAGGGTTATTTCAGTAA
1 TTTTGGTAATTTTACAAATCTAGGGTATTTCGGTAATTTT-TCAAATCGAGGG-TATTTCAGTAA
71904014 TT
64 TT
71904016 CTACCCTACA
Statistics
Matches: 245, Mismatches: 55, Indels: 15
0.78 0.17 0.05
Matches are distributed among these distances:
80 70 0.29
81 119 0.49
82 55 0.22
83 1 0.00
ACGTcount: A:0.30, C:0.10, G:0.20, T:0.41
Consensus pattern (81 bp):
TTTTGGTAATTTTACAAATCTAGGGTATTTCGGTAATTTTTCAAATCGAGGGTATTTCAGTAATT
TTACAAATCAGGGGTA
Found at i:71903980 original size:54 final size:52
Alignment explanation
Indices: 71903646--71904015 Score: 231
Period size: 54 Copynumber: 6.9 Consensus size: 52
71903636 ATCTACAAAC
* * * **
71903646 CAAGGGTATTTCAGTAATTTTGCAAACCAATGGTATTTTTGTAATTTTTGA-AAGT
1 CAAGGGTATTTCGGTAATTTTACAAACC-AGGGTATTTCGGTAA-TTTT-ACAA-T
* ** ** ** * *
71903701 CAAAGGTATTTCTATAATTTTGTAAATTAGGGGTATTTCTGTAATTTTTCAAAT
1 CAAGGGTATTTCGGTAATTTTACAAACCA-GGGTATTTCGGTAATTTTAC-AAT
** * ** *
71903755 CAAGGGTATTTCAATAATTTTCCAAATTAGGGGTATTTTGGTAATTTTACAAAT
1 CAAGGGTATTTCGGTAATTTTACAAACCA-GGGTATTTCGGTAATTTTAC-AAT
* *** *
71903809 CTAGGGTATTTCGGTAATTTTACAAGTTGAGGGTATTTCGGTAATTTTACAGGT
1 CAAGGGTATTTCGGTAATTTTACAA-ACCAGGGTATTTCGGTAATTTTACA-AT
* * * * *
71903863 CAAGAGTATTTTGGTAATTTCACAAATCTAGGGTATTTCGGGAATTTT-CAAGT
1 CAAGGGTATTTCGGTAATTTTACAAA-CCAGGGTATTTCGGTAATTTTACAA-T
* * * * *
71903916 CGAGGGTATTTCAGTAATTTTATAAACCAGGGTTATTTTGGTAGTTTTACTAAT
1 CAAGGGTATTTCGGTAATTTTACAAACCAGGG-TATTTCGGTAATTTTAC-AAT
* * ** *
71903970 CGAGGGTATTTTGGTAATTTTGTAAACCAGGGTTATTTCAGTAATT
1 CAAGGGTATTTCGGTAATTTTACAAACCAGGG-TATTTCGGTAATT
71904016 CTACCCTACA
Statistics
Matches: 256, Mismatches: 49, Indels: 21
0.79 0.15 0.06
Matches are distributed among these distances:
52 5 0.02
53 36 0.14
54 175 0.68
55 40 0.16
ACGTcount: A:0.29, C:0.09, G:0.20, T:0.42
Consensus pattern (52 bp):
CAAGGGTATTTCGGTAATTTTACAAACCAGGGTATTTCGGTAATTTTACAAT
Found at i:71904041 original size:54 final size:53
Alignment explanation
Indices: 71903916--71904041 Score: 139
Period size: 54 Copynumber: 2.3 Consensus size: 53
71903906 ATTTTCAAGT
** * *
71903916 CGAGGGTATTTCAGTAATTTTATAAACCAGGGTTATTTTGGTAGTTTTACTAA
1 CGAGGGTATTTCAGTAATTTTATAAACCAGGGTTATTTCAGTAATTCTACTAA
** *
71903969 TCGAGGGTATTTTGGTAATTTTGTAAACCAGGGTTATTTCAGTAATTCTACCCT-A
1 -CGAGGGTATTTCAGTAATTTTATAAACCAGGGTTATTTCAGTAATTCTA--CTAA
71904024 C-AGGGGTATTTCAGTAAT
1 CGA-GGGTATTTCAGTAAT
71904042 ACTAGCTTAC
Statistics
Matches: 60, Mismatches: 9, Indels: 6
0.80 0.12 0.08
Matches are distributed among these distances:
53 1 0.02
54 56 0.93
55 1 0.02
56 2 0.03
ACGTcount: A:0.27, C:0.12, G:0.21, T:0.40
Consensus pattern (53 bp):
CGAGGGTATTTCAGTAATTTTATAAACCAGGGTTATTTCAGTAATTCTACTAA
Found at i:71909276 original size:40 final size:40
Alignment explanation
Indices: 71909199--71909462 Score: 372
Period size: 40 Copynumber: 6.5 Consensus size: 40
71909189 ACCCAAGTAT
* *
71909199 CTTCGGGATTTAG-CCGGATATAG-CAACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTAGCACAAATGC
* * *
71909238 CTTCGGGTCTTAGCCCAGATATAGTCACTAGCATAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
71909278 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
71909318 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
* *
71909358 CTTCGAGACTTAGCCCGGGTATAG-CAACTACTCGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTC-ACTA---GCACAAATGC
* *
71909401 CTTCGGGACTTAGCCCGGATATAGTAACTTGCACAAATGC
1 CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
*
71909441 CTTCAGGACTTAGCCCGGATAT
1 CTTCGGGACTTAGCCCGGATAT
71909463 CATCCGAATA
Statistics
Matches: 203, Mismatches: 15, Indels: 13
0.88 0.06 0.06
Matches are distributed among these distances:
39 12 0.06
40 155 0.76
41 1 0.00
43 35 0.17
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.24
Consensus pattern (40 bp):
CTTCGGGACTTAGCCCGGATATAGTCACTAGCACAAATGC
Found at i:71911469 original size:13 final size:13
Alignment explanation
Indices: 71911451--71911483 Score: 66
Period size: 13 Copynumber: 2.5 Consensus size: 13
71911441 ACACGGGCGT
71911451 GTGTGTCTTGGCC
1 GTGTGTCTTGGCC
71911464 GTGTGTCTTGGCC
1 GTGTGTCTTGGCC
71911477 GTGTGTC
1 GTGTGTC
71911484 CCCTAGGTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.00, C:0.21, G:0.39, T:0.39
Consensus pattern (13 bp):
GTGTGTCTTGGCC
Found at i:71913906 original size:12 final size:13
Alignment explanation
Indices: 71913870--71913907 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
71913860 AAATATTTGA
71913870 CTTGTTCTTAATT
1 CTTGTTCTTAATT
*
71913883 ATGTGTTCTTAATT
1 CT-TGTTCTTAATT
71913897 CTTG-TCTTAAT
1 CTTGTTCTTAAT
71913908 ATTCCAGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 7 0.32
13 3 0.14
14 12 0.55
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.58
Consensus pattern (13 bp):
CTTGTTCTTAATT
Found at i:71921939 original size:12 final size:13
Alignment explanation
Indices: 71921903--71921940 Score: 51
Period size: 14 Copynumber: 2.9 Consensus size: 13
71921893 AAATATTTGA
71921903 CTTGTTCTTAATT
1 CTTGTTCTTAATT
*
71921916 ATGTGTTCTTAATT
1 CT-TGTTCTTAATT
71921930 CTTG-TCTTAAT
1 CTTGTTCTTAAT
71921941 ATTCCAGGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
12 7 0.32
13 3 0.14
14 12 0.55
ACGTcount: A:0.18, C:0.13, G:0.11, T:0.58
Consensus pattern (13 bp):
CTTGTTCTTAATT
Found at i:71924288 original size:32 final size:32
Alignment explanation
Indices: 71924252--71924330 Score: 124
Period size: 32 Copynumber: 2.5 Consensus size: 32
71924242 ACAGTATTAA
*
71924252 TTGGGCCTAGCCCA-ACTCAGAATCAATATCAG
1 TTGGGCCTAGCCCATA-TCAGAACCAATATCAG
*
71924284 TTGGGCCTAGCCCATATCAGAACCAGTATCAG
1 TTGGGCCTAGCCCATATCAGAACCAATATCAG
71924316 TTGGGCCTAGCCCAT
1 TTGGGCCTAGCCCAT
71924331 TTCAATATCA
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
32 43 0.98
33 1 0.02
ACGTcount: A:0.27, C:0.29, G:0.22, T:0.23
Consensus pattern (32 bp):
TTGGGCCTAGCCCATATCAGAACCAATATCAG
Found at i:71924840 original size:19 final size:19
Alignment explanation
Indices: 71924783--71924846 Score: 94
Period size: 19 Copynumber: 3.4 Consensus size: 19
71924773 AGTGTAAATG
71924783 GGCCCAAGG-CCATTACTC
1 GGCCCAAGGCCCATTACTC
* *
71924801 GACACAAGGCCCATTACTC
1 GGCCCAAGGCCCATTACTC
71924820 GGCCCAAGGCCCATTACTC
1 GGCCCAAGGCCCATTACTC
*
71924839 GGTCCAAG
1 GGCCCAAG
71924847 TAGACCCACA
Statistics
Matches: 40, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
18 7 0.17
19 33 0.82
ACGTcount: A:0.25, C:0.38, G:0.22, T:0.16
Consensus pattern (19 bp):
GGCCCAAGGCCCATTACTC
Found at i:71927277 original size:15 final size:15
Alignment explanation
Indices: 71927245--71927273 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
71927235 ATTTTTAGTG
71927245 TTTATTATGTGTGAA
1 TTTATTATGTGTGAA
71927260 TTTA-TATGTGTGAA
1 TTTATTATGTGTGAA
71927274 ATTTTCGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.28, C:0.00, G:0.21, T:0.52
Consensus pattern (15 bp):
TTTATTATGTGTGAA
Found at i:71928612 original size:43 final size:43
Alignment explanation
Indices: 71928547--71928893 Score: 430
Period size: 43 Copynumber: 8.1 Consensus size: 43
71928537 ATATATGTGA
*
71928547 CATCGATATGTGATTACGAGTAAGACCACGTCTGGGATGTTGG
1 CATCGATATGTGATTACGAGTAAGACCACGTCTGGGACGTTGG
* * *
71928590 CATCGATATGTGATTACAAGTAAGACTACGTCTGGGATGTTGG
1 CATCGATATGTGATTACGAGTAAGACCACGTCTGGGACGTTGG
* * *
71928633 CATCAATATGTGATTATGAGTAAGACCACATCTGGGACGTTGG
1 CATCGATATGTGATTACGAGTAAGACCACGTCTGGGACGTTGG
* * *
71928676 CATCGATATGTAATTATGAATAAGACCACGTCTGGGACGTTGG
1 CATCGATATGTGATTACGAGTAAGACCACGTCTGGGACGTTGG
* * *
71928719 AATCCATATGTGATTACGTGTAAGACCACGTCTGGGACGTTGG
1 CATCGATATGTGATTACGAGTAAGACCACGTCTGGGACGTTGG
* *
71928762 CATCGATATGTGATTACGTGTAAGACCACGTCTGGGATGTTGG
1 CATCGATATGTGATTACGAGTAAGACCACGTCTGGGACGTTGG
* * * **
71928805 GATCGATATGTGGTTACGTGTAAGA-CACTGTCTGGGACAATGG
1 CATCGATATGTGATTACGAGTAAGACCAC-GTCTGGGACGTTGG
** * *
71928848 CATCGATATAAGA-TA-GCATGTAAGACCACGTTTGGGATGTTGG
1 CATCGATATGTGATTACG-A-GTAAGACCACGTCTGGGACGTTGG
71928891 CAT
1 CAT
71928894 TGTACGATAT
Statistics
Matches: 265, Mismatches: 35, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
41 1 0.00
42 5 0.02
43 256 0.97
44 3 0.01
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (43 bp):
CATCGATATGTGATTACGAGTAAGACCACGTCTGGGACGTTGG
Found at i:71937972 original size:13 final size:13
Alignment explanation
Indices: 71937950--71937982 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
71937940 AAGGGCTTGC
71937950 TTAT-TAAACTAA
1 TTATCTAAACTAA
71937962 TTATCTAAACTAA
1 TTATCTAAACTAA
*
71937975 TTAACTAA
1 TTATCTAA
71937983 TTTAATTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 4 0.21
13 15 0.79
ACGTcount: A:0.48, C:0.12, G:0.00, T:0.39
Consensus pattern (13 bp):
TTATCTAAACTAA
Found at i:71944613 original size:9 final size:9
Alignment explanation
Indices: 71944595--71944641 Score: 80
Period size: 9 Copynumber: 5.4 Consensus size: 9
71944585 AAATGAAAAT
71944595 AAAAAT-AA
1 AAAAATAAA
71944603 AAAAATAAA
1 AAAAATAAA
71944612 AAAAAT-AA
1 AAAAATAAA
71944620 AAAAATAAA
1 AAAAATAAA
71944629 AAAAATAAA
1 AAAAATAAA
71944638 AAAA
1 AAAA
71944642 GAATAAAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 3
0.93 0.00 0.08
Matches are distributed among these distances:
8 14 0.38
9 23 0.62
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (9 bp):
AAAAATAAA
Found at i:71944650 original size:1 final size:1
Alignment explanation
Indices: 71944590--71944641 Score: 50
Period size: 1 Copynumber: 52.0 Consensus size: 1
71944580 AATTGAAATG
* * * * * *
71944590 AAAATAAAAATAAAAAAATAAAAAAAATAAAAAAATAAAAAAAATAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
71944642 GAATAAAAAG
Statistics
Matches: 39, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
1 39 1.00
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (1 bp):
A
Found at i:71944650 original size:17 final size:17
Alignment explanation
Indices: 71944595--71944641 Score: 94
Period size: 17 Copynumber: 2.8 Consensus size: 17
71944585 AAATGAAAAT
71944595 AAAAATAAAAAAATAAA
1 AAAAATAAAAAAATAAA
71944612 AAAAATAAAAAAATAAA
1 AAAAATAAAAAAATAAA
71944629 AAAAATAAAAAAA
1 AAAAATAAAAAAA
71944642 GAATAAAAAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 30 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (17 bp):
AAAAATAAAAAAATAAA
Found at i:71944652 original size:9 final size:8
Alignment explanation
Indices: 71944595--71944641 Score: 76
Period size: 8 Copynumber: 5.6 Consensus size: 8
71944585 AAATGAAAAT
71944595 AAAAATAA
1 AAAAATAA
71944603 AAAAATAAA
1 AAAAAT-AA
71944612 AAAAATAA
1 AAAAATAA
71944620 AAAAATAAA
1 AAAAAT-AA
71944629 AAAAATAA
1 AAAAATAA
71944637 AAAAA
1 AAAAA
71944642 GAATAAAAAG
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
8 21 0.57
9 16 0.43
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAAATAA
Found at i:71953203 original size:45 final size:45
Alignment explanation
Indices: 71953136--71953224 Score: 169
Period size: 45 Copynumber: 2.0 Consensus size: 45
71953126 GACCTCTATA
*
71953136 TTAATCGAAAACTATTTTCAATTCTCACATTTGCTTTCACTTTTC
1 TTAATCGAAAACTATTTCCAATTCTCACATTTGCTTTCACTTTTC
71953181 TTAATCGAAAACTATTTCCAATTCTCACATTTGCTTTCACTTTT
1 TTAATCGAAAACTATTTCCAATTCTCACATTTGCTTTCACTTTT
71953225 TTTTAAACCA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 43 1.00
ACGTcount: A:0.27, C:0.22, G:0.04, T:0.46
Consensus pattern (45 bp):
TTAATCGAAAACTATTTCCAATTCTCACATTTGCTTTCACTTTTC
Found at i:71957695 original size:34 final size:34
Alignment explanation
Indices: 71957647--71957716 Score: 131
Period size: 34 Copynumber: 2.1 Consensus size: 34
71957637 TGCAACTGAG
71957647 TTCATTTATGAAACCATTCTCAAATGCTATCACA
1 TTCATTTATGAAACCATTCTCAAATGCTATCACA
*
71957681 TTCATTTATTAAACCATTCTCAAATGCTATCACA
1 TTCATTTATGAAACCATTCTCAAATGCTATCACA
71957715 TT
1 TT
71957717 ATCAATTAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 35 1.00
ACGTcount: A:0.34, C:0.23, G:0.04, T:0.39
Consensus pattern (34 bp):
TTCATTTATGAAACCATTCTCAAATGCTATCACA
Found at i:71965617 original size:27 final size:27
Alignment explanation
Indices: 71965587--71965671 Score: 84
Period size: 27 Copynumber: 3.2 Consensus size: 27
71965577 AATTTAGTTC
71965587 TAAAAGTCCAATTAAGCACTTTATCAG
1 TAAAAGTCCAATTAAGCACTTTATCAG
* * * * * *
71965614 TAAAATTACTATT-TGCAATTTAGTC-C
1 TAAAAGTCCAATTAAGCACTTTA-TCAG
*
71965640 TCAAAGTCCAATTAAGCACTTTATCAG
1 TAAAAGTCCAATTAAGCACTTTATCAG
71965667 TAAAA
1 TAAAA
71965672 TTACTTAGCG
Statistics
Matches: 41, Mismatches: 14, Indels: 6
0.67 0.23 0.10
Matches are distributed among these distances:
26 18 0.44
27 23 0.56
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.33
Consensus pattern (27 bp):
TAAAAGTCCAATTAAGCACTTTATCAG
Found at i:71965652 original size:53 final size:53
Alignment explanation
Indices: 71965572--71965676 Score: 192
Period size: 53 Copynumber: 2.0 Consensus size: 53
71965562 TTTTGCAACT
*
71965572 TTTGCAATTTAGTTCTAAAAGTCCAATTAAGCACTTTATCAGTAAAATTACTA
1 TTTGCAATTTAGTCCTAAAAGTCCAATTAAGCACTTTATCAGTAAAATTACTA
*
71965625 TTTGCAATTTAGTCCTCAAAGTCCAATTAAGCACTTTATCAGTAAAATTACT
1 TTTGCAATTTAGTCCTAAAAGTCCAATTAAGCACTTTATCAGTAAAATTACT
71965677 TAGCGATATT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
53 50 1.00
ACGTcount: A:0.36, C:0.17, G:0.10, T:0.37
Consensus pattern (53 bp):
TTTGCAATTTAGTCCTAAAAGTCCAATTAAGCACTTTATCAGTAAAATTACTA
Found at i:71967888 original size:46 final size:46
Alignment explanation
Indices: 71967838--71968061 Score: 232
Period size: 46 Copynumber: 4.8 Consensus size: 46
71967828 TGGTTGAGCA
* * *
71967838 TCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCAAATG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAAACG
* *** * ** ** *
71967884 TCCGAACTCGTTGAGTTGAGTCCGAGTTCGAGAGATGTAACTAGGCA
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTC-ACTTATGGATGTAAACG
*
71967931 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTGAACG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAAACG
* * ** *
71967977 CCCGAGCTCGTTGAATTGAGTCCGAGTTCACTTATGGGCGGGTGAACG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTAT-GG-ATGTAAACG
* *
71968025 CCCGAGCTCGTTGAGTTGTGTCCGAGTTCACTTATGG
1 TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGG
71968062 GCGGGTTACA
Statistics
Matches: 147, Mismatches: 28, Indels: 5
0.82 0.16 0.03
Matches are distributed among these distances:
46 69 0.47
47 38 0.26
48 40 0.27
ACGTcount: A:0.21, C:0.21, G:0.30, T:0.29
Consensus pattern (46 bp):
TCCGAGCTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGTAAACG
Done.