Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008138.1 Hibiscus syriacus cultivar Beakdansim tig00110694_pilon, whole genome shotgun sequence
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: 3838456
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 16 of 18
Found at i:3258628 original size:18 final size:18
Alignment explanation
Indices: 3258605--3258641 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
3258595 CTAACAGTTT
3258605 CTATATGGTCCTTACTAA
1 CTATATGGTCCTTACTAA
3258623 CTATATGGTCCTTACTAA
1 CTATATGGTCCTTACTAA
3258641 C
1 C
3258642 ATTATCCATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.27, C:0.24, G:0.11, T:0.38
Consensus pattern (18 bp):
CTATATGGTCCTTACTAA
Found at i:3260052 original size:29 final size:28
Alignment explanation
Indices: 3259981--3260052 Score: 83
Period size: 29 Copynumber: 2.5 Consensus size: 28
3259971 ATTCAATTTA
*
3259981 AAAAGTTCAGTGAGCAAATTAGAAAAAT
1 AAAAGTTCAGTGAGCAAAATAGAAAAAT
* *
3260009 AGAAAGTACAATGAGCAAAATAGGAAAAAAT
1 A-AAAGTTCAGTGAGCAAAATA-G-AAAAAT
3260040 AAAA-TTCAGTGAG
1 AAAAGTTCAGTGAG
3260053 GAATGGTGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
28 1 0.03
29 24 0.67
30 4 0.11
31 7 0.19
ACGTcount: A:0.56, C:0.07, G:0.19, T:0.18
Consensus pattern (28 bp):
AAAAGTTCAGTGAGCAAAATAGAAAAAT
Found at i:3264460 original size:22 final size:21
Alignment explanation
Indices: 3264428--3264486 Score: 77
Period size: 20 Copynumber: 2.9 Consensus size: 21
3264418 TTTAAAAATT
*
3264428 AATATTTTATTATTTTTTTTT
1 AATATTTTATTATTTTTTTTA
*
3264449 TATA-TTT-TTATTTCTTTTTA
1 AATATTTTATTATTT-TTTTTA
3264469 AATATTTTATTATTTTTT
1 AATATTTTATTATTTTTT
3264487 ATATTAACAT
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
19 6 0.19
20 11 0.34
21 9 0.28
22 6 0.19
ACGTcount: A:0.24, C:0.02, G:0.00, T:0.75
Consensus pattern (21 bp):
AATATTTTATTATTTTTTTTA
Found at i:3264461 original size:19 final size:18
Alignment explanation
Indices: 3264441--3264491 Score: 66
Period size: 19 Copynumber: 2.8 Consensus size: 18
3264431 ATTTTATTAT
3264441 TTTTTTTTTATATTTTTA
1 TTTTTTTTTATATTTTTA
* *
3264459 TTTCTTTTTAAATATTTTA
1 TTTTTTTTTATAT-TTTTA
*
3264478 TTATTTTTTATATT
1 TTTTTTTTTATATT
3264492 AACATTCCCT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
18 12 0.44
19 15 0.56
ACGTcount: A:0.22, C:0.02, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTTTTTTATATTTTTA
Found at i:3264476 original size:27 final size:27
Alignment explanation
Indices: 3264398--3264485 Score: 82
Period size: 27 Copynumber: 3.4 Consensus size: 27
3264388 ATTTCCTAAT
3264398 TTTTATATTTTCTATTTCTTTTTAAA-A
1 TTTTATATTTT-TATTTCTTTTTAAATA
* * *
3264425 ATTAATA-TTTTA-TTATTTTT---T-
1 TTTTATATTTTTATTTCTTTTTAAATA
3264446 TTTTATATTTTTATTTCTTTTTAAATA
1 TTTTATATTTTTATTTCTTTTTAAATA
3264473 TTTTATTATTTTT
1 TTTTA-TATTTTT
3264486 TATATTAACA
Statistics
Matches: 47, Mismatches: 6, Indels: 15
0.69 0.09 0.22
Matches are distributed among these distances:
21 5 0.11
22 5 0.11
23 7 0.15
24 7 0.15
25 2 0.04
26 4 0.09
27 10 0.21
28 7 0.15
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (27 bp):
TTTTATATTTTTATTTCTTTTTAAATA
Found at i:3270174 original size:65 final size:65
Alignment explanation
Indices: 3270070--3270243 Score: 250
Period size: 65 Copynumber: 2.8 Consensus size: 65
3270060 GAGACACAAT
* * *
3270070 TTACTCGAGATTGGATTTCAACTTCACAACGAAGGATATCTAACTTAAAGCCAATTTGGTGAAAC
1 TTACTCGAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAATTTGGTGAAAC
*
3270135 TTACTCGAGATTGGATTTCAACTTCACGACGAAGGATATCCAACTCAAAACCAATTTGGTGAAAC
1 TTACTCGAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAATTTGGTGAAAC
* * *
3270200 --AATC--G-TTGGATTTCAACTTGACAACGAAGGATATCCAATTCAAA
1 TTACTCGAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAA
3270244 GCTCAACTTC
Statistics
Matches: 101, Mismatches: 8, Indels: 5
0.89 0.07 0.04
Matches are distributed among these distances:
60 36 0.36
61 1 0.01
63 3 0.03
65 61 0.60
ACGTcount: A:0.36, C:0.20, G:0.17, T:0.28
Consensus pattern (65 bp):
TTACTCGAGATTGGATTTCAACTTCACAACGAAGGATATCCAACTCAAAACCAATTTGGTGAAAC
Found at i:3270298 original size:66 final size:65
Alignment explanation
Indices: 3270208--3270424 Score: 194
Period size: 66 Copynumber: 3.4 Consensus size: 65
3270198 ACAATCGTTG
*
3270208 GATTTCAACTTGACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGTCATCCA
1 GATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAG-CATCCA
3270273 T
65 T
* * *
3270274 GATTTCAACTTCACGAC-AATGGATAT-C-GTTCCCACAAG-T-AGTA-TTCATC-TC---T-AG
1 GATTTCAACTTCACAACGAA-GGATATCCAATT--CA-AAGCTCA--ACTTCA-CAACGAATGAG
3270328 -AT---T
59 CATCCAT
3270331 GGATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCCATCC
1 -GATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAG-CATCC
3270396 AT
64 AT
*
3270398 GATTTCAACTTCACAACGAATGATATC
1 GATTTCAACTTCACAACGAAGGATATC
3270425 GTGCTCGAGT
Statistics
Matches: 119, Mismatches: 8, Indels: 48
0.68 0.05 0.27
Matches are distributed among these distances:
57 6 0.05
58 30 0.25
59 4 0.03
60 4 0.03
61 1 0.01
62 4 0.03
63 1 0.01
64 4 0.03
65 4 0.03
66 55 0.46
67 6 0.05
ACGTcount: A:0.35, C:0.24, G:0.13, T:0.27
Consensus pattern (65 bp):
GATTTCAACTTCACAACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGAGCATCCAT
Found at i:3270652 original size:85 final size:85
Alignment explanation
Indices: 3270500--3270716 Score: 247
Period size: 85 Copynumber: 2.5 Consensus size: 85
3270490 CTCCAGCCTA
* *
3270500 TTACAACATAGCTCAAGGCGAGAAAGGATATCTGTCAACAATGAAACCTTCGAGTTCGATTACAT
1 TTACAACATAGCTCAAGGCGAGAAGGGATATTTGTCAACAA--AAACCTTCGAGTTCGATTACAT
* *
3270565 TCAACTCA-AGGACATGTCAAAT
64 TCAACGCAGAGG-CATATCAAAT
* * * * * * * *
3270587 TTACACCATAACTCAAGGCGAGAAGGGTTATTTTTCATCAAAGACCTTGGAGTTCGATTAGATTC
1 TTACAACATAGCTCAAGGCGAGAAGGGATATTTGTCAACAAAAACCTTCGAGTTCGATTACATTC
* *
3270652 AGCGCAGAGGCATATTAAAT
66 AACGCAGAGGCATATCAAAT
* * *
3270672 TTACAGCATAGCTCAAGGCGAGAAGGGCTATTTGTCAGCAAAAAC
1 TTACAACATAGCTCAAGGCGAGAAGGGATATTTGTCAACAAAAAC
3270717 TAACGATTTC
Statistics
Matches: 109, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
85 72 0.66
86 3 0.03
87 34 0.31
ACGTcount: A:0.35, C:0.19, G:0.20, T:0.25
Consensus pattern (85 bp):
TTACAACATAGCTCAAGGCGAGAAGGGATATTTGTCAACAAAAACCTTCGAGTTCGATTACATTC
AACGCAGAGGCATATCAAAT
Found at i:3271763 original size:21 final size:21
Alignment explanation
Indices: 3271733--3271816 Score: 136
Period size: 21 Copynumber: 4.1 Consensus size: 21
3271723 AATCAGATTG
3271733 CCCA-GGGGTACAGATTCCCC
1 CCCAGGGGGTACAGATTCCCC
3271753 CCCAGGGGGTACAGATT-CCC
1 CCCAGGGGGTACAGATTCCCC
*
3271773 CCCAGGGGGAACAGATTCCCC
1 CCCAGGGGGTACAGATTCCCC
*
3271794 CCCAGGGGGTACCGATTCCCC
1 CCCAGGGGGTACAGATTCCCC
3271815 CC
1 CC
3271817 TGTCTAACGG
Statistics
Matches: 59, Mismatches: 3, Indels: 3
0.91 0.05 0.05
Matches are distributed among these distances:
20 23 0.39
21 36 0.61
ACGTcount: A:0.19, C:0.40, G:0.27, T:0.13
Consensus pattern (21 bp):
CCCAGGGGGTACAGATTCCCC
Found at i:3271790 original size:41 final size:40
Alignment explanation
Indices: 3271733--3271816 Score: 141
Period size: 41 Copynumber: 2.1 Consensus size: 40
3271723 AATCAGATTG
*
3271733 CCCAGGGGTACAGATTCCCCCCCAGGGGGTACAGATTCCC
1 CCCAGGGGAACAGATTCCCCCCCAGGGGGTACAGATTCCC
*
3271773 CCCAGGGGGAACAGATTCCCCCCCAGGGGGTACCGATTCCC
1 CCCA-GGGGAACAGATTCCCCCCCAGGGGGTACAGATTCCC
3271814 CCC
1 CCC
3271817 TGTCTAACGG
Statistics
Matches: 41, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
40 4 0.10
41 37 0.90
ACGTcount: A:0.19, C:0.40, G:0.27, T:0.13
Consensus pattern (40 bp):
CCCAGGGGAACAGATTCCCCCCCAGGGGGTACAGATTCCC
Found at i:3272892 original size:15 final size:16
Alignment explanation
Indices: 3272866--3272896 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
3272856 TATATTTTAG
3272866 TCATTGAATTTAATTT
1 TCATTGAATTTAATTT
3272882 TCATT-AATTTAATTT
1 TCATTGAATTTAATTT
3272897 GGATTTCGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 10 0.67
16 5 0.33
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.58
Consensus pattern (16 bp):
TCATTGAATTTAATTT
Found at i:3273180 original size:23 final size:24
Alignment explanation
Indices: 3273128--3273182 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 24
3273118 TTTTTATAAA
* *
3273128 TTATTATTTTATTATTTCTTATAT
1 TTATTATTTAATTATTTCTAATAT
3273152 TT-TTATTTAATT-TTT-TAATATT
1 TTATTATTTAATTATTTCTAATA-T
3273174 TTATTATTT
1 TTATTATTT
3273183 TTTATATTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 4 0.15
22 6 0.22
23 15 0.56
24 2 0.07
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.73
Consensus pattern (24 bp):
TTATTATTTAATTATTTCTAATAT
Found at i:3273247 original size:3 final size:3
Alignment explanation
Indices: 3273239--3273264 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3273229 TTATTTTACC
3273239 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
3273265 TTTAATTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:3273393 original size:6 final size:6
Alignment explanation
Indices: 3273384--3273413 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
3273374 AAGCAATTCG
3273384 AATTTT AATTTT AATTTT AATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT
3273414 CGCAATTAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
AATTTT
Found at i:3273399 original size:18 final size:18
Alignment explanation
Indices: 3273378--3273413 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
3273368 AAAGGTAAGC
3273378 AATTCGAATTTTAATTTT
1 AATTCGAATTTTAATTTT
**
3273396 AATTTTAATTTTAATTTT
1 AATTCGAATTTTAATTTT
3273414 CGCAATTAAG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.03, T:0.61
Consensus pattern (18 bp):
AATTCGAATTTTAATTTT
Found at i:3275921 original size:3 final size:3
Alignment explanation
Indices: 3275913--3275955 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
3275903 TTTGTTTCAT
*
3275913 TTA TTA TTA TTA TTA TT- TTA TT- TTA ATA TTA TTA TTA -TA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3275956 ATTTATTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 6 0.17
3 29 0.83
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3275942 original size:22 final size:23
Alignment explanation
Indices: 3275911--3275960 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
3275901 CATTTGTTTC
* *
3275911 ATTTATTATTATTATTATTTTAT
1 ATTTAATATTATTATTATATTAT
3275934 -TTTAATATTATTATTATATTAT
1 ATTTAATATTATTATTATATTAT
3275956 ATTTA
1 ATTTA
3275961 TTAAATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
ATTTAATATTATTATTATATTAT
Found at i:3276440 original size:18 final size:16
Alignment explanation
Indices: 3276402--3276431 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3276392 CCTGCAAAAC
3276402 AAAGA-AAAAAAAAGG
1 AAAGACAAAAAAAAGG
3276417 AAAGACAAAAAAAAG
1 AAAGACAAAAAAAAG
3276432 AGACGAGACC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (16 bp):
AAAGACAAAAAAAAGG
Found at i:3277633 original size:119 final size:116
Alignment explanation
Indices: 3277497--3277732 Score: 287
Period size: 119 Copynumber: 2.0 Consensus size: 116
3277487 ATTTTAATCA
* * * * *
3277497 TGTTTTAATATTTATTTATTTTTCAATAT-TAAG-AAAGGGCAGTCTTAAAACAATTGGATGTCC
1 TGTTTTAATATTTATTTATTTTT-AATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGT-C
* * *
3277560 ATTTTCTGATTTTTTTAAATAAATAAATATCCTATTTTATAAATTATATATTAAT
64 ATTTTCTGATATTTCTAAATAAATAAATATCCTATTTT-TAAA-TATATATAAAT
* ** *
3277615 TGTTTTAATTATTTATTTATTTTTAATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCA
1 TGTTTTAA-TATTTATTTATTTTTAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCA
**
3277680 TTTTCTGATATTTCTAAATAAATAAATATTTTATTTTTAAATATATATAAAT
65 TTTTCTGATATTTCTAAATAAATAAATATCCTATTTTTAAATATATATAAAT
3277732 T
1 T
3277733 AATATTTTTT
Statistics
Matches: 101, Mismatches: 14, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
117 11 0.11
118 17 0.17
119 53 0.52
120 20 0.20
ACGTcount: A:0.37, C:0.08, G:0.09, T:0.47
Consensus pattern (116 bp):
TGTTTTAATATTTATTTATTTTTAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCAT
TTTCTGATATTTCTAAATAAATAAATATCCTATTTTTAAATATATATAAAT
Found at i:3277753 original size:29 final size:29
Alignment explanation
Indices: 3277697--3277753 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
3277687 ATATTTCTAA
*
3277697 ATAAATAAATATTTTATTTTTAAATATAT
1 ATAAATAAATATTTTATTTATAAATATAT
* *
3277726 ATAAATTAATATTTT-TTTCATAATTATA
1 ATAAATAAATATTTTATTT-ATAAATATA
3277754 ATTTTGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (29 bp):
ATAAATAAATATTTTATTTATAAATATAT
Found at i:3277812 original size:47 final size:47
Alignment explanation
Indices: 3277725--3277814 Score: 110
Period size: 47 Copynumber: 1.9 Consensus size: 47
3277715 TTTAAATATA
* * * * *
3277725 TATAAATTAATATTTTTTTCATAATTATAATTTTGAAATAATATGAT
1 TATAAATTAATATATTTTTAAAAATTATAAATTTCAAATAATATGAT
*
3277772 TATAAATTAAATATATTTTTAAAAATT-TAAATTTCTAATAATA
1 TATAAATT-AATATATTTTTAAAAATTATAAATTTCAAATAATA
3277815 GAGACAATTT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
47 21 0.58
48 15 0.42
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.49
Consensus pattern (47 bp):
TATAAATTAATATATTTTTAAAAATTATAAATTTCAAATAATATGAT
Found at i:3279773 original size:8 final size:7
Alignment explanation
Indices: 3279749--3279790 Score: 50
Period size: 7 Copynumber: 6.0 Consensus size: 7
3279739 TTTTCATATA
3279749 TGCA-TT
1 TGCATTT
3279755 TGCATTT
1 TGCATTT
3279762 TGCATCTT
1 TGCAT-TT
3279770 TGCATTT
1 TGCATTT
* *
3279777 TTCATTG
1 TGCATTT
3279784 TGCATTT
1 TGCATTT
3279791 ATACTTTTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
6 4 0.13
7 19 0.63
8 7 0.23
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (7 bp):
TGCATTT
Found at i:3279773 original size:15 final size:14
Alignment explanation
Indices: 3279749--3279790 Score: 50
Period size: 15 Copynumber: 3.0 Consensus size: 14
3279739 TTTTCATATA
3279749 TGCA-TTTGCATTT
1 TGCATTTTGCATTT
3279762 TGCATCTTTGCATTT
1 TGCAT-TTTGCATTT
* *
3279777 TTCATTGTGCATTT
1 TGCATTTTGCATTT
3279791 ATACTTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 4 0.16
14 8 0.32
15 13 0.52
ACGTcount: A:0.14, C:0.17, G:0.14, T:0.55
Consensus pattern (14 bp):
TGCATTTTGCATTT
Found at i:3279866 original size:12 final size:12
Alignment explanation
Indices: 3279849--3279896 Score: 60
Period size: 12 Copynumber: 3.8 Consensus size: 12
3279839 ACATTCACAT
3279849 ATTTACATTTGC
1 ATTTACATTTGC
3279861 ATTTACATTTGC
1 ATTTACATTTGC
* *
3279873 ATTTTTACGTTTGT
1 A--TTTACATTTGC
3279887 ATTTACATTT
1 ATTTACATTT
3279897 TTATTTTTAC
Statistics
Matches: 31, Mismatches: 3, Indels: 4
0.82 0.08 0.11
Matches are distributed among these distances:
12 21 0.68
14 10 0.32
ACGTcount: A:0.23, C:0.12, G:0.08, T:0.56
Consensus pattern (12 bp):
ATTTACATTTGC
Found at i:3279879 original size:26 final size:26
Alignment explanation
Indices: 3279850--3279908 Score: 82
Period size: 26 Copynumber: 2.3 Consensus size: 26
3279840 CATTCACATA
3279850 TTTACATTTGCATTTACATTTGCATT
1 TTTACATTTGCATTTACATTTGCATT
* * **
3279876 TTTACGTTTGTATTTACATTTTTATT
1 TTTACATTTGCATTTACATTTGCATT
3279902 TTTACAT
1 TTTACAT
3279909 AATTACATTT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
26 28 1.00
ACGTcount: A:0.22, C:0.12, G:0.07, T:0.59
Consensus pattern (26 bp):
TTTACATTTGCATTTACATTTGCATT
Found at i:3279901 original size:12 final size:12
Alignment explanation
Indices: 3279848--3279902 Score: 56
Period size: 12 Copynumber: 4.4 Consensus size: 12
3279838 TACATTCACA
3279848 TATTTACATTTG
1 TATTTACATTTG
*
3279860 CATTTACATTTG
1 TATTTACATTTG
* *
3279872 CATTTTTACGTTTG
1 --TATTTACATTTG
*
3279886 TATTTACATTTT
1 TATTTACATTTG
3279898 TATTT
1 TATTT
3279903 TTACATAATT
Statistics
Matches: 34, Mismatches: 7, Indels: 4
0.76 0.16 0.09
Matches are distributed among these distances:
12 25 0.74
14 9 0.26
ACGTcount: A:0.22, C:0.11, G:0.07, T:0.60
Consensus pattern (12 bp):
TATTTACATTTG
Found at i:3279905 original size:14 final size:14
Alignment explanation
Indices: 3279850--3279908 Score: 54
Period size: 12 Copynumber: 4.5 Consensus size: 14
3279840 CATTCACATA
*
3279850 TTTACATTTGCA--
1 TTTACATTTGTATT
*
3279862 TTTACATTTGCATT
1 TTTACATTTGTATT
*
3279876 TTTACGTTTGTA--
1 TTTACATTTGTATT
*
3279888 TTTACATTTTTATT
1 TTTACATTTGTATT
3279902 TTTACAT
1 TTTACAT
3279909 AATTACATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
12 22 0.56
14 17 0.44
ACGTcount: A:0.22, C:0.12, G:0.07, T:0.59
Consensus pattern (14 bp):
TTTACATTTGTATT
Found at i:3284191 original size:114 final size:114
Alignment explanation
Indices: 3283972--3284180 Score: 355
Period size: 114 Copynumber: 1.8 Consensus size: 114
3283962 CACGTTCTCG
* *
3283972 TAGTAGAAATAAGGAGACCCAATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTT
1 TAGTAGAAATAAGGAGACCCAATAGAATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
*
3284037 GGTATGAACCCCAAAACCAATCATTAGATTTAAAAGATGAATTTGCTCA
66 GGTAGGAACCCCAAAACCAATCATTAGATTTAAAAGATGAATTTGCTCA
* *
3284086 TAGTAGAAATAAGGAGACCCAATAGAATCTTTTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTC
1 TAGTAGAAATAAGGAGACCCAATAGAATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
* *
3284151 GGTAGGAACCCCAGAACCAATCATTGGATT
66 GGTAGGAACCCCAAAACCAATCATTAGATT
3284181 AGGAAGATGA
Statistics
Matches: 88, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
114 88 1.00
ACGTcount: A:0.33, C:0.16, G:0.21, T:0.31
Consensus pattern (114 bp):
TAGTAGAAATAAGGAGACCCAATAGAATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGATTC
GGTAGGAACCCCAAAACCAATCATTAGATTTAAAAGATGAATTTGCTCA
Found at i:3285434 original size:73 final size:74
Alignment explanation
Indices: 3285342--3285512 Score: 202
Period size: 76 Copynumber: 2.3 Consensus size: 74
3285332 ATTAACAAGA
* * *
3285342 AGCAAATGTTGGGGCATGCTGAAA-ACTTTTT-TTCAGAATCAGGAATGTTGATGTATCCTGAAT
1 AGCAAATGTTGGGGCATGCTGAAAGACTTTTTAATCAGAATCAAGAATGTTGATGTATCCTGAAC
*
3285405 GTTTATATC
66 GTTCATATC
* * * * **
3285414 AGCAAAATGCTGGGGCATGCTGAAAGCCTTTTTCAATCCGAATGAAGAATGTTGATGTATTTTGA
1 AGC-AAATGTTGGGGCATGCTGAAAGACTTTTT-AATCAGAATCAAGAATGTTGATGTATCCTGA
*
3285479 ACGTTCGTATC
64 ACGTTCATATC
*
3285490 AGCAATTGTTGGGGCATGCTGAA
1 AGCAAATGTTGGGGCATGCTGAA
3285513 GGCCCACATC
Statistics
Matches: 82, Mismatches: 13, Indels: 5
0.82 0.13 0.05
Matches are distributed among these distances:
72 3 0.04
73 20 0.24
74 6 0.07
75 18 0.22
76 35 0.43
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.33
Consensus pattern (74 bp):
AGCAAATGTTGGGGCATGCTGAAAGACTTTTTAATCAGAATCAAGAATGTTGATGTATCCTGAAC
GTTCATATC
Found at i:3286094 original size:54 final size:54
Alignment explanation
Indices: 3286035--3286141 Score: 128
Period size: 54 Copynumber: 2.0 Consensus size: 54
3286025 TGTTGTCAAA
* *
3286035 TAGCATCTGTGCA-AAAGCCACAGGAAAGGATGAATGTGTTG-TCAAATGTTTTAC
1 TAGCATCTGAGCATAAA-CCACAGGAAAGGATGAATGTATTGAT-AAATGTTTTAC
* * * *
3286089 TAGCATTTGAGCATAAACCACATGAGATGATGAATGTATTGATAAATGTTTTA
1 TAGCATCTGAGCATAAACCACAGGAAAGGATGAATGTATTGATAAATGTTTTA
3286142 TGAACCAGTC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
54 41 0.91
55 4 0.09
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (54 bp):
TAGCATCTGAGCATAAACCACAGGAAAGGATGAATGTATTGATAAATGTTTTAC
Found at i:3286541 original size:22 final size:22
Alignment explanation
Indices: 3286513--3286634 Score: 201
Period size: 22 Copynumber: 5.6 Consensus size: 22
3286503 ACATCTACAT
3286513 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
3286535 TCTTC-AAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
3286556 TTTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
3286578 TCTTCAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
* *
3286600 TTTTTAAAGATGATAGATTCTC
1 TCTTCAAAGATGATAGATTCTC
*
3286622 TTTTCAAAGATGA
1 TCTTCAAAGATGA
3286635 AAGCTTTATT
Statistics
Matches: 94, Mismatches: 5, Indels: 2
0.93 0.05 0.02
Matches are distributed among these distances:
21 20 0.21
22 74 0.79
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (22 bp):
TCTTCAAAGATGATAGATTCTC
Found at i:3287439 original size:78 final size:76
Alignment explanation
Indices: 3287308--3287491 Score: 273
Period size: 76 Copynumber: 2.4 Consensus size: 76
3287298 CTATTTCTCA
* *
3287308 CATCTGTAAGTCCTACAATGCATGATGTTTCCAAAAAGCCTTCGGGAGTTTTTTTTGATGTTTTC
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAG--CTTTTTGATGTTTTC
*
3287373 AAAGCCTT-AGGGT
64 AAAACCTTCA-GGT
3287386 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
3287451 AACCTTCAGGT
66 AACCTTCAGGT
* *
3287462 CAGCTGTAAGCCCTACAGTGCA-GAATGTTT
1 CATCTGTAAGTCCTACAGTGCATG-ATGTTT
3287492 TTTCTTAAAA
Statistics
Matches: 99, Mismatches: 5, Indels: 6
0.90 0.05 0.05
Matches are distributed among these distances:
75 1 0.01
76 50 0.51
77 1 0.01
78 47 0.47
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AACCTTCAGGT
Found at i:3287710 original size:112 final size:112
Alignment explanation
Indices: 3287500--3288368 Score: 1415
Period size: 112 Copynumber: 7.7 Consensus size: 112
3287490 TTTTTCTTAA
* *
3287500 AACATTTCCAGGTAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAATAAGAAGTTCATAAT
1 AACATTTCCA-GAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAAT
3287565 GAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGGATC
65 GAGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGGATC
3287613 AACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
1 AACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
*
3287678 AGGAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGGATC
66 AGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGGATC
3287725 AACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
1 AACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
3287790 AGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGGATC
66 AGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGGATC
* * *
3287837 AGCATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTAAAGAATGAAGAAGAAGTTCATAATG
1 AACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
*
3287902 AGAAGAACTTGTTCAA-TCTTTTGCTTGAATTCATCATTCGATGGATT
66 AGAAGAACTTGTTCAACT-TTTTGCTTGAATTCATCATTCGATGGATC
*
3287949 AGCATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
1 AACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
3288014 AGAAGAACTTGTTCAA-TATTTTGCTTGAATTCATCATTCGATGGATC
66 AGAAGAACTTGTTCAACT-TTTTGCTTGAATTCATCATTCGATGGATC
*
3288061 AGCATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
1 AACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
3288126 AGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGGATC
66 AGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGGATC
*
3288173 AGCATTTCCAGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA-AAGTTCATAATG
1 AACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
* * * * * *** *
3288236 AGAAGAGCTTGTTCAACCTTTTGTTTGACTTTATCACAGAAGGAGATAGATC
66 AGAAGAACTTGTTCAACTTTTTGCTTGAATTCAT--C---ATTCGATGGATC
* * * *
3288288 AACATTTCCAGAAGTGTTTATAATGAGAAGAACTCATCTGAAGAATG-AGAAGAAATTCATAATG
1 AACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
*
3288352 AGAAGAATTTGTTCAAC
66 AGAAGAACTTGTTCAAC
3288369 CTTGCCTTAA
Statistics
Matches: 719, Mismatches: 28, Indels: 15
0.94 0.04 0.02
Matches are distributed among these distances:
110 41 0.06
111 39 0.05
112 548 0.76
113 11 0.02
115 24 0.03
116 56 0.08
ACGTcount: A:0.38, C:0.14, G:0.20, T:0.29
Consensus pattern (112 bp):
AACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATG
AGAAGAACTTGTTCAACTTTTTGCTTGAATTCATCATTCGATGGATC
Found at i:3288711 original size:3 final size:3
Alignment explanation
Indices: 3288703--3288745 Score: 56
Period size: 3 Copynumber: 15.3 Consensus size: 3
3288693 TTTGTTTCAT
*
3288703 TTA TTA TTA TTA TTA TT- TTA TT- TTA ATA TTA TTA TTA -TA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3288746 ATTTATTAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
2 6 0.17
3 29 0.83
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:3288732 original size:22 final size:23
Alignment explanation
Indices: 3288701--3288750 Score: 75
Period size: 22 Copynumber: 2.2 Consensus size: 23
3288691 CATTTGTTTC
* *
3288701 ATTTATTATTATTATTATTTTAT
1 ATTTAATATTATTATTATATTAT
3288724 -TTTAATATTATTATTATATTAT
1 ATTTAATATTATTATTATATTAT
3288746 ATTTA
1 ATTTA
3288751 TTAAATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 20 0.83
23 4 0.17
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (23 bp):
ATTTAATATTATTATTATATTAT
Found at i:3288834 original size:14 final size:14
Alignment explanation
Indices: 3288806--3288839 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
3288796 GGCCCGATTA
*
3288806 CAAACCAGACTGGCC
1 CAAA-CAGACCGGCC
3288821 CAAACAGACCGGCC
1 CAAACAGACCGGCC
3288835 CAAAC
1 CAAAC
3288840 CTAATAACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 14 0.78
15 4 0.22
ACGTcount: A:0.38, C:0.41, G:0.18, T:0.03
Consensus pattern (14 bp):
CAAACAGACCGGCC
Found at i:3290195 original size:21 final size:21
Alignment explanation
Indices: 3290169--3290231 Score: 60
Period size: 22 Copynumber: 3.0 Consensus size: 21
3290159 TTATTTAGCC
3290169 ATAAATATATATATTTATA-TA
1 ATAAATATAT-TATTTATATTA
*
3290190 ATAAATAATATTTATTT-TATTT
1 ATAAAT-ATA-TTATTTATATTA
*
3290212 ATAAAAATATTATTTA-ATTA
1 ATAAATATATTATTTATATTA
3290232 CTTTTAATTT
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
20 9 0.26
21 11 0.31
22 14 0.40
23 1 0.03
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
ATAAATATATTATTTATATTA
Found at i:3290199 original size:24 final size:21
Alignment explanation
Indices: 3290171--3290231 Score: 61
Period size: 20 Copynumber: 2.8 Consensus size: 21
3290161 ATTTAGCCAT
3290171 AAATATATATATTTATATAATAA
1 AAATATATAT-TTTAT-TAATAA
* *
3290194 ATAATATTTATTTTATTTATAA
1 A-AATATATATTTTATTAATAA
*
3290216 AAATAT-TATTTAATTA
1 AAATATATATTTTATTA
3290232 CTTTTAATTT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
20 8 0.24
21 5 0.15
22 6 0.18
23 6 0.18
24 8 0.24
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (21 bp):
AAATATATATTTTATTAATAA
Found at i:3290393 original size:119 final size:116
Alignment explanation
Indices: 3290254--3290487 Score: 292
Period size: 119 Copynumber: 2.0 Consensus size: 116
3290244 TTTAATCCTA
* * *
3290254 TTTTAATATTTATTTATTTTTCAATAT-TAAG-AAAGGGCAGTCTTAAAACAACTAGATGTTCAT
1 TTTTAATATTTATTTATTTTT-AATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAG-TCAT
** *
3290317 TTTCTGATATTTTTAAATAAATAAATATCCTATTTTATAAATTATATATTAATTG
64 TTTCTGATATTCCTAAATAAATAAATATCCTATTTT-TAAA-TATATATAAATTG
* ** *
3290372 TTTTAATTATTTATTTATTTTTAATATCGAAGAAAAGAGCTGTCTTAAGGCACCTAGAAGTCATT
1 TTTTAA-TATTTATTTATTTTTAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCATT
* **
3290437 TTTTGATATTCCTAAATAAATAAATATTTTATTTTTAAATATATATAAATT
65 TTCTGATATTCCTAAATAAATAAATATCCTATTTTTAAATATATATAAATT
3290488 AATATTTTTT
Statistics
Matches: 100, Mismatches: 13, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
117 11 0.11
118 15 0.15
119 53 0.53
120 21 0.21
ACGTcount: A:0.38, C:0.08, G:0.08, T:0.46
Consensus pattern (116 bp):
TTTTAATATTTATTTATTTTTAATATCGAAGAAAAGAGCAGTCTTAAAACAACTAGAAGTCATTT
TCTGATATTCCTAAATAAATAAATATCCTATTTTTAAATATATATAAATTG
Found at i:3290508 original size:29 final size:29
Alignment explanation
Indices: 3290452--3290508 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
3290442 ATATTCCTAA
*
3290452 ATAAATAAATATTTTATTTTTAAATATAT
1 ATAAATAAATATTTTATTTATAAATATAT
* *
3290481 ATAAATTAATATTTT-TTTCATAATTATA
1 ATAAATAAATATTTTATTT-ATAAATATA
3290509 ATTTTGAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 3 0.12
29 21 0.88
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.53
Consensus pattern (29 bp):
ATAAATAAATATTTTATTTATAAATATAT
Found at i:3290567 original size:47 final size:47
Alignment explanation
Indices: 3290480--3290570 Score: 112
Period size: 47 Copynumber: 1.9 Consensus size: 47
3290470 TTTAAATATA
* * *
3290480 TATAAATTAATATTTTTTTCATAATTATAATTTTGAAATAATAGGAT
1 TATAAATTAATATATTTTTCATAATTATAAATTTCAAATAATAGGAT
* * *
3290527 TATAAATTAAATATATTTTTGA-AATTTTAAATTTCTAATAATAG
1 TATAAATT-AATATATTTTTCATAATTATAAATTTCAAATAATAG
3290571 AGACAATTTA
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
47 26 0.70
48 11 0.30
ACGTcount: A:0.44, C:0.02, G:0.05, T:0.48
Consensus pattern (47 bp):
TATAAATTAATATATTTTTCATAATTATAAATTTCAAATAATAGGAT
Found at i:3295927 original size:30 final size:30
Alignment explanation
Indices: 3295856--3295915 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
3295846 ACAATTTAAG
3295856 GCAAAATGTTTTTGGACTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
*
3295886 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
3295916 ATTCAAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTTGAATTGAATTT
Found at i:3296122 original size:21 final size:21
Alignment explanation
Indices: 3296096--3296171 Score: 118
Period size: 21 Copynumber: 3.7 Consensus size: 21
3296086 ATGCAATTAG
*
3296096 TGCATCGATGCATCCTTGCCA
1 TGCATCCATGCATCCTTGCCA
*
3296117 TGCATCCATGTATCCTTGCCA
1 TGCATCCATGCATCCTTGCCA
*
3296138 TGCATCGATGCATCC-TGCCA
1 TGCATCCATGCATCCTTGCCA
3296158 TGCATCCATGCATC
1 TGCATCCATGCATC
3296172 AAGGCTGCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
20 18 0.36
21 32 0.64
ACGTcount: A:0.20, C:0.34, G:0.17, T:0.29
Consensus pattern (21 bp):
TGCATCCATGCATCCTTGCCA
Found at i:3297507 original size:20 final size:19
Alignment explanation
Indices: 3297466--3297514 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 19
3297456 AACGATTTTC
*
3297466 TTTTGAAAACAAAAATAGA
1 TTTTGAAAACAAAAATAAA
* *
3297485 TTTTGAAAGCCAAAATGAAA
1 TTTTGAAAACAAAAAT-AAA
3297505 TTTTGGAAAA
1 TTTT-GAAAA
3297515 GGATTTAGAG
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
19 14 0.58
20 6 0.25
21 4 0.17
ACGTcount: A:0.51, C:0.06, G:0.14, T:0.29
Consensus pattern (19 bp):
TTTTGAAAACAAAAATAAA
Found at i:3298856 original size:30 final size:30
Alignment explanation
Indices: 3298785--3298844 Score: 111
Period size: 30 Copynumber: 2.0 Consensus size: 30
3298775 AATATTTAAG
3298785 GCAAAATGTTTTTGGACTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
*
3298815 GCAAAATGTTTTTGGATTTGAATTGAATTT
1 GCAAAATGTTTTTGGACTTGAATTGAATTT
3298845 ATTCAAAGTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 29 1.00
ACGTcount: A:0.30, C:0.05, G:0.20, T:0.45
Consensus pattern (30 bp):
GCAAAATGTTTTTGGACTTGAATTGAATTT
Found at i:3299054 original size:8 final size:8
Alignment explanation
Indices: 3299043--3299160 Score: 67
Period size: 8 Copynumber: 17.1 Consensus size: 8
3299033 TGCATCCTTG
3299043 CCATGCAT
1 CCATGCAT
3299051 CCATGCAT
1 CCATGCAT
*
3299059 CCTTG---
1 CCATGCAT
3299064 CCATGCAT
1 CCATGCAT
*
3299072 CGATGCAT
1 CCATGCAT
3299080 CC-TG---
1 CCATGCAT
3299084 CCATGCAT
1 CCATGCAT
3299092 CCATGCAT
1 CCATGCAT
3299100 CC-TG---
1 CCATGCAT
3299104 CCATGCAT
1 CCATGCAT
3299112 CCATGCAT
1 CCATGCAT
3299120 CC-TG---
1 CCATGCAT
3299124 CCATGCAT
1 CCATGCAT
* *
3299132 CTATACAT
1 CCATGCAT
3299140 CC-TG---
1 CCATGCAT
3299144 CCATGCAT
1 CCATGCAT
3299152 CCATGCAT
1 CCATGCAT
3299160 C
1 C
3299161 AAGGCTGCAA
Statistics
Matches: 83, Mismatches: 8, Indels: 38
0.64 0.06 0.29
Matches are distributed among these distances:
4 8 0.10
5 12 0.14
7 7 0.08
8 56 0.67
ACGTcount: A:0.21, C:0.38, G:0.14, T:0.26
Consensus pattern (8 bp):
CCATGCAT
Found at i:3299087 original size:20 final size:20
Alignment explanation
Indices: 3299025--3299160 Score: 218
Period size: 20 Copynumber: 6.7 Consensus size: 20
3299015 ATGCAATTAG
*
3299025 TGCATCGATGCATCCTTGCCA
1 TGCATCCATGCATCC-TGCCA
3299046 TGCATCCATGCATCCTTGCCA
1 TGCATCCATGCATCC-TGCCA
*
3299067 TGCATCGATGCATCCTGCCA
1 TGCATCCATGCATCCTGCCA
3299087 TGCATCCATGCATCCTGCCA
1 TGCATCCATGCATCCTGCCA
3299107 TGCATCCATGCATCCTGCCA
1 TGCATCCATGCATCCTGCCA
* *
3299127 TGCATCTATACATCCTGCCA
1 TGCATCCATGCATCCTGCCA
3299147 TGCATCCATGCATC
1 TGCATCCATGCATC
3299161 AAGGCTGCAA
Statistics
Matches: 108, Mismatches: 7, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
20 74 0.69
21 34 0.31
ACGTcount: A:0.21, C:0.37, G:0.15, T:0.27
Consensus pattern (20 bp):
TGCATCCATGCATCCTGCCA
Found at i:3299565 original size:34 final size:32
Alignment explanation
Indices: 3299526--3299595 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
3299516 TTTTGTAAAG
* * *
3299526 GGGAAATGTTCTAGCTTATCCCGTGTAAAAGCTA
1 GGGAAAGGTTCTAGCTTAGCCCG-G-AAAAACTA
*
3299560 GGGAAAGGTTCTAGTTTAGCCCGGAAAAACTA
1 GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
3299592 GGGA
1 GGGA
3299596 GTTGTAAGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 11 0.34
33 1 0.03
34 20 0.62
ACGTcount: A:0.31, C:0.16, G:0.29, T:0.24
Consensus pattern (32 bp):
GGGAAAGGTTCTAGCTTAGCCCGGAAAAACTA
Found at i:3302021 original size:47 final size:47
Alignment explanation
Indices: 3301967--3302134 Score: 221
Period size: 47 Copynumber: 3.6 Consensus size: 47
3301957 GAATAAATGT
* * *
3301967 ATGCGAACTAGAAATCATGCAGTTATGTTTATTTTTCTCGAACAAGC
1 ATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTTCTTGAACAAGC
* * * *
3302014 ATGCGAACTAGAAATCATGTGGTTAGGTTTATTTTT-TTAAACATGT
1 ATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTTCTTGAACAAGC
*
3302060 ATGTGAACTAGAAATCATGCGGTTAGGTTTATTTTTTCTTGAACAAGC
1 ATGCGAACTAGAAATCATGCGGTTAGGTTTA-TTTTTCTTGAACAAGC
* * *
3302108 ATGCAAATTAGATATCATGCGGTTAGG
1 ATGCGAACTAGAAATCATGCGGTTAGG
3302135 ATTTTTTGTG
Statistics
Matches: 103, Mismatches: 16, Indels: 3
0.84 0.13 0.02
Matches are distributed among these distances:
46 35 0.34
47 38 0.37
48 30 0.29
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.36
Consensus pattern (47 bp):
ATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTTCTTGAACAAGC
Found at i:3302084 original size:46 final size:46
Alignment explanation
Indices: 3301963--3302134 Score: 191
Period size: 46 Copynumber: 3.7 Consensus size: 46
3301953 TTTTGAATAA
* * *
3301963 ATGTATGCGAACTAGAAATCATGCAGTTATGTTTATTTTTCTCGAAC
1 ATGTATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTT-TCAAAC
* * * *
3302010 AAGCATGCGAACTAGAAATCATGTGGTTAGGTTTATTTTTTTAAAC
1 ATGTATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTTTCAAAC
* *
3302056 ATGTATGTGAACTAGAAATCATGCGGTTAGGTTTATTTTTTCTTGAAC
1 ATGTATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTTTC--AAAC
* * * * *
3302104 AAGCATGCAAATTAGATATCATGCGGTTAGG
1 ATGTATGCGAACTAGAAATCATGCGGTTAGG
3302135 ATTTTTTGTG
Statistics
Matches: 104, Mismatches: 19, Indels: 3
0.83 0.15 0.02
Matches are distributed among these distances:
46 41 0.39
47 35 0.34
48 28 0.27
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (46 bp):
ATGTATGCGAACTAGAAATCATGCGGTTAGGTTTATTTTTTCAAAC
Found at i:3302133 original size:94 final size:93
Alignment explanation
Indices: 3301963--3302134 Score: 263
Period size: 94 Copynumber: 1.8 Consensus size: 93
3301953 TTTTGAATAA
* *
3301963 ATGTATGCGAACTAGAAATCATGCAGTTATGTTTATTTTTCTCGAACAAGCATGCGAACTAGAAA
1 ATGTATGCGAACTAGAAATCATGCAGTTAGGTTTATTTTTCTCGAACAAGCATGCAAACTAGAAA
*
3302028 TCATGTGGTTAGGTTTATTTTTTTAAAC
66 TCATGCGGTTAGGTTTATTTTTTTAAAC
* * * * *
3302056 ATGTATGTGAACTAGAAATCATGCGGTTAGGTTTATTTTTTCTTGAACAAGCATGCAAATTAGAT
1 ATGTATGCGAACTAGAAATCATGCAGTTAGGTTTA-TTTTTCTCGAACAAGCATGCAAACTAGAA
3302121 ATCATGCGGTTAGG
65 ATCATGCGGTTAGG
3302135 ATTTTTTGTG
Statistics
Matches: 70, Mismatches: 8, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
93 32 0.46
94 38 0.54
ACGTcount: A:0.31, C:0.12, G:0.20, T:0.37
Consensus pattern (93 bp):
ATGTATGCGAACTAGAAATCATGCAGTTAGGTTTATTTTTCTCGAACAAGCATGCAAACTAGAAA
TCATGCGGTTAGGTTTATTTTTTTAAAC
Found at i:3304679 original size:7 final size:6
Alignment explanation
Indices: 3304652--3304694 Score: 52
Period size: 6 Copynumber: 7.2 Consensus size: 6
3304642 ATTGACACCT
* *
3304652 TTTGTA TTTGCA TTTGCA TTTGGCA TTTTCA TTTGCA -TTGCA T
1 TTTGCA TTTGCA TTTGCA TTT-GCA TTTGCA TTTGCA TTTGCA T
3304695 GCATTTATTT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
5 5 0.16
6 21 0.66
7 6 0.19
ACGTcount: A:0.16, C:0.14, G:0.16, T:0.53
Consensus pattern (6 bp):
TTTGCA
Found at i:3308748 original size:22 final size:21
Alignment explanation
Indices: 3308719--3308782 Score: 78
Period size: 20 Copynumber: 3.0 Consensus size: 21
3308709 AACCCATCAG
3308719 TAAGTCTTTCGAGCATGATGA
1 TAAGTCTTTCGAGCATGATGA
* *
3308740 TGAAGTCTTTCGGGCCATCA-G-
1 T-AAGTCTTTCGAG-CATGATGA
3308761 TAAGTCTTTCGAGCATGATGA
1 TAAGTCTTTCGAGCATGATGA
3308782 T
1 T
3308783 TAAATCCTTC
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
19 4 0.11
20 12 0.34
21 3 0.09
22 12 0.34
23 4 0.11
ACGTcount: A:0.25, C:0.17, G:0.25, T:0.33
Consensus pattern (21 bp):
TAAGTCTTTCGAGCATGATGA
Found at i:3308767 original size:20 final size:20
Alignment explanation
Indices: 3308712--3308774 Score: 74
Period size: 20 Copynumber: 3.0 Consensus size: 20
3308702 TGAAGCGAAC
3308712 CCATCAGTAAGTCTTTCGAG
1 CCATCAGTAAGTCTTTCGAG
* *
3308732 -CATGATGATGAAGTCTTTCGGG
1 CCATCA-G-T-AAGTCTTTCGAG
3308754 CCATCAGTAAGTCTTTCGAG
1 CCATCAGTAAGTCTTTCGAG
3308774 C
1 C
3308775 ATGATGATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
19 4 0.11
20 13 0.37
21 2 0.06
22 12 0.34
23 4 0.11
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (20 bp):
CCATCAGTAAGTCTTTCGAG
Found at i:3308806 original size:42 final size:42
Alignment explanation
Indices: 3308717--3309103 Score: 155
Period size: 42 Copynumber: 8.8 Consensus size: 42
3308707 CGAACCCATC
* * * ** *
3308717 AGTAAGTCTTTCGAGCATGATGATGAAGTCTTTCGGGCCATC
1 AGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATT
3308759 AGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATT
1 AGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATT
* * * ** * * *
3308801 TGTAAGCCTTCACGGAAG-A-GTAGTGAAGCAAACCCATC-AGTAAGTGCCAT
1 AGTAAGTCTT-TC-G-AGCATG-A-TG-ATTAAATCCTTCGGGTAA-T----T
* * *
3308851 CAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGG-ACATC
1 -AGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTA-ATT
* * * * ** *
3308894 AGTAAGTTTTTCGAGCATGATGATGAAGTCCTTTGGGCCATC
1 AGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATT
* *
3308936 AGTAAGTCTTTCGAGCATGATGATTAAATCTTTCAGGTAATT
1 AGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATT
* * ** *
3308978 TGTAAGCCTTCATCGAAG-A-GTAGTGAAGCAAAT-CTATC-AGTAAGTGCCAT
1 AGTAAGTCTT--TCG-AGCATG-A-TG-ATTAAATCCT-TCGGGTAA-T----T
*
3309028 CAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTCATT
1 -AGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATT
* *
3309071 TGTGAGTCTTTCGAGCAAT-ATGA-TAAATCCTTC
1 AGTAAGTCTTTCGAGC-ATGATGATTAAATCCTTC
3309104 AGGTTATCCA
Statistics
Matches: 260, Mismatches: 50, Indels: 71
0.68 0.13 0.19
Matches are distributed among these distances:
41 10 0.04
42 141 0.54
43 6 0.02
44 8 0.03
45 17 0.07
46 17 0.07
47 17 0.07
48 15 0.06
49 8 0.03
50 5 0.02
51 16 0.06
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (42 bp):
AGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATT
Found at i:3308843 original size:122 final size:126
Alignment explanation
Indices: 3308620--3308926 Score: 406
Period size: 122 Copynumber: 2.4 Consensus size: 126
3308610 TAAACAATTT
* * *
3308620 AAGTTCTTCGGGTCATCAGTAAGTCTTTCGAGCATGATGATTAAATCTTTCGAGTAATTTGTAAG
1 AAGTCCTTCGGGACATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGAGTAATTTGTAAG
*
3308685 CCTTCACAGAAGAGTAGTGAAGC-GA-A-C-CCATCAGTAAGTCTTTCGAGCATGATGATG
66 CCTTCACAGAAGAGTAGTGAAGCAAACATCACCATCAGTAAGTCTTTCGAGCATGATGATG
* * *
3308742 AAGTCTTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGTAATTTGTAAG
1 AAGTCCTTCGGGACATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGAGTAATTTGTAAG
*
3308807 CCTTCACGGAAGAGTAGTGAAGCAAACCCATCAGTAAGTGCCATCAGTAAGTCTTTCGAGCATGA
66 CCTTCACAGAAGAGTAGTGAAGCAAA--CATC----A---CCATCAGTAAGTCTTTCGAGCATGA
3308872 TGATG
122 TGATG
* * *
3308877 AAGTCCTTCGGGACATCAGTAAGTTTTTCGAGCATGATGATGAAGTCCTT
1 AAGTCCTTCGGGACATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTT
3308927 TGGGCCATCA
Statistics
Matches: 160, Mismatches: 12, Indels: 13
0.86 0.06 0.07
Matches are distributed among these distances:
122 82 0.51
123 1 0.01
126 1 0.01
127 1 0.01
135 75 0.47
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (126 bp):
AAGTCCTTCGGGACATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGAGTAATTTGTAAG
CCTTCACAGAAGAGTAGTGAAGCAAACATCACCATCAGTAAGTCTTTCGAGCATGATGATG
Found at i:3308852 original size:13 final size:13
Alignment explanation
Indices: 3308834--3308858 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3308824 TGAAGCAAAC
3308834 CCATCAGTAAGTG
1 CCATCAGTAAGTG
3308847 CCATCAGTAAGT
1 CCATCAGTAAGT
3308859 CTTTCGAGCA
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:0.24, G:0.20, T:0.24
Consensus pattern (13 bp):
CCATCAGTAAGTG
Found at i:3309009 original size:177 final size:177
Alignment explanation
Indices: 3308713--3309087 Score: 619
Period size: 177 Copynumber: 2.1 Consensus size: 177
3308703 GAAGCGAACC
3308713 CATCAGTAAGTCTTTCGAGCATGATGATGAAGTCTTTCGGGCCATCAGTAAGTCTTTCGAGCATG
1 CATCAGTAAGTCTTTCGAGCATGATGATGAAGTCTTTCGGGCCATCAGTAAGTCTTTCGAGCATG
*
3308778 ATGATTAAATCCTTCGGGTAATTTGTAAGCCTTCACGGAAGAGTAGTGAAGCAAACCCATCAGTA
66 ATGATTAAATCCTTCAGGTAATTTGTAAGCCTTCACGGAAGAGTAGTGAAGCAAACCCATCAGTA
*
3308843 AGTGCCATCAGTAAGTCTTTCGAGCATGATGATGAAGTCCTTCGGGA
131 AGTGCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGA
*
3308890 CATCAGTAAGTTTTTCGAGCATGATGATGAAGTCCTTT-GGGCCATCAGTAAGTCTTTCGAGCAT
1 CATCAGTAAGTCTTTCGAGCATGATGATGAAGT-CTTTCGGGCCATCAGTAAGTCTTTCGAGCAT
* * *
3308954 GATGATTAAATCTTTCAGGTAATTTGTAAGCCTTCATC-GAAGAGTAGTGAAGCAAATCTATCAG
65 GATGATTAAATCCTTCAGGTAATTTGTAAGCCTTCA-CGGAAGAGTAGTGAAGCAAACCCATCAG
* *
3309018 TAAGTGCCATCAGTAAGTCTTTCGAGCATGATGATTAAATCCTTCGGGT
129 TAAGTGCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGA
** *
3309067 CATTTGTGAGTCTTTCGAGCA
1 CATCAGTAAGTCTTTCGAGCA
3309088 ATATGATAAA
Statistics
Matches: 184, Mismatches: 12, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
177 179 0.97
178 5 0.03
ACGTcount: A:0.28, C:0.18, G:0.23, T:0.31
Consensus pattern (177 bp):
CATCAGTAAGTCTTTCGAGCATGATGATGAAGTCTTTCGGGCCATCAGTAAGTCTTTCGAGCATG
ATGATTAAATCCTTCAGGTAATTTGTAAGCCTTCACGGAAGAGTAGTGAAGCAAACCCATCAGTA
AGTGCCATCAGTAAGTCTTTCGAGCATGATGATGAAATCCTTCGGGA
Found at i:3309207 original size:37 final size:37
Alignment explanation
Indices: 3309166--3309236 Score: 124
Period size: 37 Copynumber: 1.9 Consensus size: 37
3309156 CATCCGGGCT
* *
3309166 ATCCTAAGCCTTCACCGAAGAGTAGTGAAGCAAATCC
1 ATCCTAAGCCTTCACCAAAGAGTAGTAAAGCAAATCC
3309203 ATCCTAAGCCTTCACCAAAGAGTAGTAAAGCAAA
1 ATCCTAAGCCTTCACCAAAGAGTAGTAAAGCAAA
3309237 ACGATCTCGA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 32 1.00
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.18
Consensus pattern (37 bp):
ATCCTAAGCCTTCACCAAAGAGTAGTAAAGCAAATCC
Found at i:3317088 original size:15 final size:14
Alignment explanation
Indices: 3317052--3317098 Score: 58
Period size: 15 Copynumber: 3.2 Consensus size: 14
3317042 GGATAAATAA
*
3317052 TTTTTAAAATATAT
1 TTTTTAATATATAT
3317066 TATTTTAATATATAT
1 T-TTTTAATATATAT
*
3317081 TTTATTAATATATGT
1 TTT-TTAATATATAT
3317096 TTT
1 TTT
3317099 GTGGGGGGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
14 3 0.10
15 26 0.90
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (14 bp):
TTTTTAATATATAT
Found at i:3317883 original size:12 final size:13
Alignment explanation
Indices: 3317839--3317882 Score: 65
Period size: 13 Copynumber: 3.5 Consensus size: 13
3317829 CGACCCGATT
3317839 ACCCGATTACCCG
1 ACCCGATTACCCG
*
3317852 CCCCGATTACCCG
1 ACCCGATTACCCG
3317865 -CCCGA-TACCCG
1 ACCCGATTACCCG
3317876 ACCCGAT
1 ACCCGAT
3317883 AAATATTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
11 6 0.21
12 10 0.36
13 12 0.43
ACGTcount: A:0.20, C:0.50, G:0.16, T:0.14
Consensus pattern (13 bp):
ACCCGATTACCCG
Found at i:3317964 original size:35 final size:35
Alignment explanation
Indices: 3317906--3317987 Score: 119
Period size: 35 Copynumber: 2.3 Consensus size: 35
3317896 AATTATTTAT
3317906 ATATATATAATATTAATAAATTTAATTTAAATAAAA
1 ATATATAT-ATATTAATAAATTTAATTTAAATAAAA
* * * *
3317942 ATATATATATATTTATATATTTAATTTAAATATAT
1 ATATATATATATTAATAAATTTAATTTAAATAAAA
3317977 ATATATATATA
1 ATATATATATA
3317988 CTCGGCCCGA
Statistics
Matches: 42, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
35 34 0.81
36 8 0.19
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (35 bp):
ATATATATATATTAATAAATTTAATTTAAATAAAA
Found at i:3318017 original size:12 final size:12
Alignment explanation
Indices: 3318002--3318027 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
3317992 GCCCGATTCT
3318002 CGGCCCAATACC
1 CGGCCCAATACC
3318014 CGGCCCAATACC
1 CGGCCCAATACC
3318026 CG
1 CG
3318028 TTTAAATAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.23, C:0.50, G:0.19, T:0.08
Consensus pattern (12 bp):
CGGCCCAATACC
Found at i:3319295 original size:21 final size:21
Alignment explanation
Indices: 3319262--3319301 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
3319252 AAATTTTTAA
*
3319262 ATAAAATTTATTTTATAATTT
1 ATAAAATTAATTTTATAATTT
* *
3319283 ATAAGATTAATTTTTTAAT
1 ATAAAATTAATTTTATAAT
3319302 ATTTTATAGT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (21 bp):
ATAAAATTAATTTTATAATTT
Found at i:3319315 original size:24 final size:25
Alignment explanation
Indices: 3319266--3319326 Score: 63
Period size: 24 Copynumber: 2.5 Consensus size: 25
3319256 TTTTAAATAA
*
3319266 AATTTATTTTATAATTTATAAGATT
1 AATTTATTTAATAATTTATAAGATT
*
3319291 AATTT-TTTAATATTTTAT-AGTATT
1 AATTTATTTAATAATTTATAAG-ATT
**
3319315 AAAATATTTAAT
1 AATTTATTTAAT
3319327 TTTTATCCAC
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 2 0.07
24 17 0.57
25 11 0.37
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (25 bp):
AATTTATTTAATAATTTATAAGATT
Found at i:3320314 original size:17 final size:17
Alignment explanation
Indices: 3320294--3320351 Score: 82
Period size: 17 Copynumber: 3.5 Consensus size: 17
3320284 AAAAATATAT
*
3320294 AATATATGGTTTTTGAA
1 AATATATAGTTTTTGAA
*
3320311 AATATATAATTTTTGAA
1 AATATATAGTTTTTGAA
3320328 AATATATAG-TTTTGAA
1 AATATATAGTTTTTGAA
*
3320344 AACATATA
1 AATATATA
3320352 ATATATATGG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
16 14 0.38
17 23 0.62
ACGTcount: A:0.45, C:0.02, G:0.10, T:0.43
Consensus pattern (17 bp):
AATATATAGTTTTTGAA
Found at i:3320411 original size:39 final size:39
Alignment explanation
Indices: 3320368--3320480 Score: 102
Period size: 39 Copynumber: 3.2 Consensus size: 39
3320358 ATGGCTTTTG
3320368 AAAATAGTTTTTAAAAACATATATAATATATATAATTTA
1 AAAATAGTTTTTAAAAACATATATAATATATATAATTTA
** *** *
3320407 AAAATA-----T----A-ATATATGTTATATAGCTTTTG
1 AAAATAGTTTTTAAAAACATATATAATATATATAATTTA
3320436 AAAATAGTTTTTAAAAACATATATAATATATATAATTTA
1 AAAATAGTTTTTAAAAACATATATAATATATATAATTTA
3320475 AAAATA
1 AAAATA
3320481 TAATATATGT
Statistics
Matches: 52, Mismatches: 12, Indels: 20
0.62 0.14 0.24
Matches are distributed among these distances:
29 21 0.40
30 1 0.02
34 2 0.04
38 1 0.02
39 27 0.52
ACGTcount: A:0.52, C:0.03, G:0.04, T:0.41
Consensus pattern (39 bp):
AAAATAGTTTTTAAAAACATATATAATATATATAATTTA
Found at i:3320427 original size:68 final size:68
Alignment explanation
Indices: 3320355--3320508 Score: 292
Period size: 68 Copynumber: 2.3 Consensus size: 68
3320345 ACATATAATA
*
3320355 TATATGGCTTTTGAAAATAGTTTTTAAAAACATATATAATATATATAATTTAAAAATATAATATA
1 TATATAGCTTTTGAAAATAGTTTTTAAAAACATATATAATATATATAATTTAAAAATATAATATA
3320420 TGT
66 TGT
3320423 TATATAGCTTTTGAAAATAGTTTTTAAAAACATATATAATATATATAATTTAAAAATATAATATA
1 TATATAGCTTTTGAAAATAGTTTTTAAAAACATATATAATATATATAATTTAAAAATATAATATA
3320488 TGT
66 TGT
3320491 TATATAGCTTTT-AAAATA
1 TATATAGCTTTTGAAAATA
3320509 AATATAGCAT
Statistics
Matches: 85, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
67 6 0.07
68 79 0.93
ACGTcount: A:0.47, C:0.03, G:0.06, T:0.43
Consensus pattern (68 bp):
TATATAGCTTTTGAAAATAGTTTTTAAAAACATATATAATATATATAATTTAAAAATATAATATA
TGT
Found at i:3320532 original size:7 final size:7
Alignment explanation
Indices: 3320522--3320582 Score: 54
Period size: 7 Copynumber: 8.4 Consensus size: 7
3320512 ATAGCATATG
3320522 TATTATT
1 TATTATT
3320529 TATTATT
1 TATTATT
3320536 TATTTATAT
1 TA-TTAT-T
*
3320545 GTATTATA
1 -TATTATT
3320553 TATTATT
1 TATTATT
*
3320560 TA-TA-G
1 TATTATT
3320565 TATTATT
1 TATTATT
3320572 TATTATGT
1 TATTAT-T
3320580 TAT
1 TAT
3320583 GTTATGTTAT
Statistics
Matches: 44, Mismatches: 4, Indels: 11
0.75 0.07 0.19
Matches are distributed among these distances:
5 2 0.05
6 4 0.09
7 23 0.52
8 8 0.18
9 5 0.11
10 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.05, T:0.64
Consensus pattern (7 bp):
TATTATT
Found at i:3320544 original size:24 final size:24
Alignment explanation
Indices: 3320517--3320587 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 24
3320507 TAAATATAGC
3320517 ATATGTATTATTTATTATTTATTT
1 ATATGTATTATTTATTATTTATTT
3320541 ATATGTATTA--TA-TA-TTATTT
1 ATATGTATTATTTATTATTTATTT
3320561 ATA-GTATTATTTATTATGTTATGTT
1 ATATGTATTATTTATTAT-TTAT-TT
3320586 AT
1 AT
3320588 GTTATGTTAT
Statistics
Matches: 41, Mismatches: 0, Indels: 11
0.79 0.00 0.21
Matches are distributed among these distances:
19 6 0.15
20 9 0.22
21 4 0.10
22 4 0.10
24 14 0.34
25 4 0.10
ACGTcount: A:0.31, C:0.00, G:0.07, T:0.62
Consensus pattern (24 bp):
ATATGTATTATTTATTATTTATTT
Found at i:3320569 original size:19 final size:20
Alignment explanation
Indices: 3320535--3320582 Score: 71
Period size: 19 Copynumber: 2.4 Consensus size: 20
3320525 TATTTATTAT
3320535 TTATTTATATGTATTATATA
1 TTATTTATATGTATTATATA
*
3320555 TTATTTATA-GTATTATTTA
1 TTATTTATATGTATTATATA
3320574 TTATGTTAT
1 TTAT-TTAT
3320583 GTTATGTTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.62
Consensus pattern (20 bp):
TTATTTATATGTATTATATA
Found at i:3320584 original size:5 final size:5
Alignment explanation
Indices: 3320574--3322272 Score: 3331
Period size: 5 Copynumber: 340.8 Consensus size: 5
3320564 GTATTATTTA
3320574 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
3320624 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
3320674 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
3320724 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
3320774 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TT-TG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
3320823 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
3320873 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
3320923 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG -TATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
3320972 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
3321022 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
3321072 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
3321122 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
3321172 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
3321222 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
3321272 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
3321322 TTATG TTATG TTATG TTATG -T-TG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
3321370 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
3321420 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
3321470 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
3321520 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
3321570 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
3321620 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
3321670 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
3321720 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
3321770 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
3321820 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
3321870 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
3321920 TTATG TTATG TTATG -T-TG TTATG TTATG TTATG TTATG TTATG TTATTTG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTA--TG
3321970 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
3322020 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
3322070 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
3322120 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
3322170 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
3322220 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTAT-
1 TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG TTATG
3322269 TTAT
1 TTAT
3322273 TTCATTTTAA
Statistics
Matches: 1686, Mismatches: 0, Indels: 17
0.99 0.00 0.01
Matches are distributed among these distances:
3 4 0.00
4 16 0.01
5 1661 0.99
7 5 0.00
ACGTcount: A:0.20, C:0.00, G:0.20, T:0.60
Consensus pattern (5 bp):
TTATG
Found at i:3323434 original size:18 final size:17
Alignment explanation
Indices: 3323393--3323436 Score: 52
Period size: 19 Copynumber: 2.4 Consensus size: 17
3323383 TTTGAAGTTT
*
3323393 TTATTTATTTATTTAATG
1 TTATTT-TTTATTTAATA
3323411 TGTATTTTTTAATTTAATA
1 T-TATTTTTT-ATTTAATA
3323430 TTATTTT
1 TTATTTT
3323437 ATTTTATTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 10 0.43
19 13 0.57
ACGTcount: A:0.27, C:0.00, G:0.05, T:0.68
Consensus pattern (17 bp):
TTATTTTTTATTTAATA
Found at i:3327374 original size:15 final size:15
Alignment explanation
Indices: 3327354--3327386 Score: 66
Period size: 15 Copynumber: 2.2 Consensus size: 15
3327344 ACATTCTCCT
3327354 ATTATCCTTTGAATC
1 ATTATCCTTTGAATC
3327369 ATTATCCTTTGAATC
1 ATTATCCTTTGAATC
3327384 ATT
1 ATT
3327387 CTTTTTACAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.27, C:0.18, G:0.06, T:0.48
Consensus pattern (15 bp):
ATTATCCTTTGAATC
Found at i:3328176 original size:23 final size:23
Alignment explanation
Indices: 3328143--3328213 Score: 90
Period size: 23 Copynumber: 3.1 Consensus size: 23
3328133 GGTTGTGCAC
3328143 AATGCACCGAAGTGCCACATAGA
1 AATGCACCGAAGTGCCACATAGA
* * * *
3328166 AGTGCATCGAAGTGCCGCGTAGA
1 AATGCACCGAAGTGCCACATAGA
*
3328189 AATGCACCGAAGTGCCATATA-A
1 AATGCACCGAAGTGCCACATAGA
3328211 AAT
1 AAT
3328214 ATCTATAAAG
Statistics
Matches: 39, Mismatches: 9, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
22 4 0.10
23 35 0.90
ACGTcount: A:0.37, C:0.23, G:0.24, T:0.17
Consensus pattern (23 bp):
AATGCACCGAAGTGCCACATAGA
Found at i:3335563 original size:15 final size:14
Alignment explanation
Indices: 3335543--3335643 Score: 69
Period size: 15 Copynumber: 6.8 Consensus size: 14
3335533 ATCCTTGATT
3335543 TTTAATTTTTTTCAA
1 TTTAATTTTTTT-AA
3335558 TTTAATAATTTTTTAA
1 TTTAAT--TTTTTTAA
*
3335574 TTTGAAGTTTTTTATTA
1 TTT-AA-TTTTTT-TAA
* *
3335591 TTTTATTTATTTAA
1 TTTAATTTTTTTAA
* * *
3335605 TAT-GTATTTTTAA
1 TTTAATTTTTTTAA
*
3335618 TTTAATTTAATTTAA
1 TTTAATTT-TTTTAA
3335633 TTTAATTTTTT
1 TTTAATTTTTT
3335644 AGGAAATTTT
Statistics
Matches: 66, Mismatches: 13, Indels: 15
0.70 0.14 0.16
Matches are distributed among these distances:
13 9 0.14
14 8 0.12
15 24 0.36
16 11 0.17
17 13 0.20
18 1 0.02
ACGTcount: A:0.30, C:0.01, G:0.03, T:0.66
Consensus pattern (14 bp):
TTTAATTTTTTTAA
Found at i:3335623 original size:5 final size:5
Alignment explanation
Indices: 3335613--3335640 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
3335603 AATATGTATT
3335613 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
1 TTTAA TTTAA TTTAA TTTAA TTTAA TTT
3335641 TTTAGGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (5 bp):
TTTAA
Found at i:3337880 original size:51 final size:51
Alignment explanation
Indices: 3337797--3337896 Score: 164
Period size: 51 Copynumber: 2.0 Consensus size: 51
3337787 GTCTTAATAG
**
3337797 ACAAGTCCCCAAAACTCTTTGATTTCACACTTGTCTAAGTGGGAGTGAGAA
1 ACAAGTCCCCAAAACTCTTTGATCGCACACTTGTCTAAGTGGGAGTGAGAA
* *
3337848 ACAAGTCTCCAAAACTCTTTGATCGCATACTTGTCTAAGTGGGAGTGAG
1 ACAAGTCCCCAAAACTCTTTGATCGCACACTTGTCTAAGTGGGAGTGAG
3337897 TGCGGATTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 45 1.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.28
Consensus pattern (51 bp):
ACAAGTCCCCAAAACTCTTTGATCGCACACTTGTCTAAGTGGGAGTGAGAA
Found at i:3339301 original size:16 final size:17
Alignment explanation
Indices: 3339276--3339313 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
3339266 TCAAAAGTTT
3339276 TTTA-TTTT-AATAAAA
1 TTTATTTTTAAATAAAA
3339291 TTTATTTTTAAATAAAA
1 TTTATTTTTAAATAAAA
3339308 TTTATT
1 TTTATT
3339314 AAAATCATAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
15 4 0.19
16 4 0.19
17 13 0.62
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTTATTTTTAAATAAAA
Found at i:3340890 original size:60 final size:59
Alignment explanation
Indices: 3340826--3340995 Score: 225
Period size: 60 Copynumber: 2.8 Consensus size: 59
3340816 ATTTTTCTTT
* * * *
3340826 TAAATTGGTCCCTAAACTTTTAAATATTCCAATTTCATCCCTAAACTATGA-CTATCATTC
1 TAAATTAGTCCCTAAACTTTTGAATATTTCAATTTCATCCC-AAACTATAACCT-TCATTC
* * *
3340886 TAAATTAATCCTTAAACTTTTGAACATTTCAATTTCATCCCCAAACTATAACCTTCATTC
1 TAAATTAGTCCCTAAACTTTTGAATATTTCAATTTCAT-CCCAAACTATAACCTTCATTC
*
3340946 TAAATCAGTCCCTAAACTTTTTGAATATTTCAATTTCATCCCAAACTATA
1 TAAATTAGTCCCTAAAC-TTTTGAATATTTCAATTTCATCCCAAACTATA
3340996 CGCATATACT
Statistics
Matches: 96, Mismatches: 11, Indels: 6
0.85 0.10 0.05
Matches are distributed among these distances:
60 71 0.74
61 25 0.26
ACGTcount: A:0.35, C:0.24, G:0.04, T:0.38
Consensus pattern (59 bp):
TAAATTAGTCCCTAAACTTTTGAATATTTCAATTTCATCCCAAACTATAACCTTCATTC
Found at i:3341301 original size:60 final size:60
Alignment explanation
Indices: 3341189--3341303 Score: 160
Period size: 60 Copynumber: 1.9 Consensus size: 60
3341179 ACTTTAGGGT
* * *
3341189 TGAAATTAAAATGTTCAAAAGTTTAAGGACTAATTTAGAATGAAAGTCATAATTTGAAGA
1 TGAAATTAAAATATTCAAAAGTTTAAGGACTAATTTAAAATGAAACTCATAATTTGAAGA
* * *
3341249 TGAAATTAAAATATTTAAAAGTTTAAGGA-TCAATTTAAAATGAGACTTATAATTT
1 TGAAATTAAAATATTCAAAAGTTTAAGGACT-AATTTAAAATGAAACTCATAATTT
3341304 AGAGAAATAC
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
59 1 0.02
60 47 0.98
ACGTcount: A:0.47, C:0.04, G:0.14, T:0.35
Consensus pattern (60 bp):
TGAAATTAAAATATTCAAAAGTTTAAGGACTAATTTAAAATGAAACTCATAATTTGAAGA
Found at i:3346480 original size:9 final size:9
Alignment explanation
Indices: 3346443--3346506 Score: 58
Period size: 10 Copynumber: 6.7 Consensus size: 9
3346433 GAAAAGCATT
3346443 AAATATTAA
1 AAATATTAA
*
3346452 AAGTAATTAA
1 AAAT-ATTAA
3346462 AAACTATTAA
1 AAA-TATTAA
*
3346472 AAATCTT-A
1 AAATATTAA
3346480 AAATATCCTGAA
1 AAATAT--T-AA
3346492 AAATATTAA
1 AAATATTAA
3346501 AAATAT
1 AAATAT
3346507 ATGAAAAGCA
Statistics
Matches: 45, Mismatches: 4, Indels: 12
0.74 0.07 0.20
Matches are distributed among these distances:
8 6 0.13
9 14 0.31
10 17 0.38
11 1 0.02
12 7 0.16
ACGTcount: A:0.59, C:0.06, G:0.03, T:0.31
Consensus pattern (9 bp):
AAATATTAA
Found at i:3347518 original size:2 final size:2
Alignment explanation
Indices: 3347511--3347541 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
3347501 TTTCTTTCAT
3347511 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
3347542 GTTTTTCGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:3350969 original size:2 final size:2
Alignment explanation
Indices: 3350962--3351036 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
3350952 TATTGGTTGC
3350962 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3351004 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3351037 GATAGATAAA
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3353180 original size:224 final size:225
Alignment explanation
Indices: 3352627--3354424 Score: 2996
Period size: 224 Copynumber: 8.0 Consensus size: 225
3352617 GATTGAAACC
*
3352627 AAACTCTCACACCTCAGAACAGTTATACCTTACGAAGCGAAGCAACACTAAACAGCCCAAGGAAG
1 AAACTCTCACACCTCAGAACAGTTATACCTTACGAAGCGGAGCAACACTAAACAGCCCAAGGAAG
*
3352692 CTGACAACAAAGAGGAAACCAATCATCCATCCAATCCCCAGGTTCTTAACATCTTCCGCTCGGTT
66 CTGACAACAAAGAGGAAACCAATCATCCATCCAATCCCCGGGTTCTTAACATCTTCCGCTCGGTT
*
3352757 TCCAGGGTAATCAACATCGATAAGATTATATGTTCTTTCATCCATAT-CAATCAGATACGATCCA
131 TCCAGGGTAATCAACACCGATAAGATTATATGTTCTTTCATCCAT-TGCAATCAGATACGATCCA
*
3352821 AAACCCCCTACAAGAAACACAATCAGATATT
195 AAACCCCCTATAAGAAACACAATCAGATATT
* * *
3352852 AAACTCTCACACCTCAGAACAGTTATACCTTACAAAGTGGAGCAACACTAAACAGTCCAAGGAAG
1 AAACTCTCACACCTCAGAACAGTTATACCTTACGAAGCGGAGCAACACTAAACAGCCCAAGGAAG
3352917 CTGACAACAAAGAGGAAACCAATCATCCATCCAATCCCCGGGTTCTTAACATCTTCCGCTCGGTT
66 CTGACAACAAAGAGGAAACCAATCATCCATCCAATCCCCGGGTTCTTAACATCTTCCGCTCGGTT
* * *
3352982 TCCATGGTAATCAACACCGATAAAATTATATGTTCTTTCATCCATTGCAATCAGACACGATCC-A
131 TCCAGGGTAATCAACACCGATAAGATTATATGTTCTTTCATCCATTGCAATCAGATACGATCCAA
*
3353046 AACCCCCTATAAGAAACACAATCAGATAAT
196 AACCCCCTATAAGAAACACAATCAGATATT
* *
3353076 AAACTCTCACACCTCAGAACATTTATACTTTACGAAGCGGAGCAACACTAAACAGCCCAAGGAAG
1 AAACTCTCACACCTCAGAACAGTTATACCTTACGAAGCGGAGCAACACTAAACAGCCCAAGGAAG
* * *
3353141 CTGACAACAAAGAGGAAACCGAGCATCCATCCAATCCCCGGTTTCTTAACATCTT-CGCTCGGTT
66 CTGACAACAAAGAGGAAACCAATCATCCATCCAATCCCCGGGTTCTTAACATCTTCCGCTCGGTT
* * *
3353205 TCCAGGGTAATCAACACTGATAAGTTTATATGTTCTTTCATCCATTGCAATCAGATACAATCCAA
131 TCCAGGGTAATCAACACCGATAAGATTATATGTTCTTTCATCCATTGCAATCAGATACGATCCAA
*
3353270 AACCTCCTATAAGAAACACAATCAGATATT
196 AACCCCCTATAAGAAACACAATCAGATATT
* *
3353300 AAACTGTCACACCTCAGAACAGTTATACCTTACGAAGCGGAGCAACACTAAACAGTCCAAGGAAG
1 AAACTCTCACACCTCAGAACAGTTATACCTTACGAAGCGGAGCAACACTAAACAGCCCAAGGAAG
*
3353365 CTGACAACAAAGAGGAAACCAATCATCCATCCAATCCTCGGGTTCTTAACATCTTCCGCTCGGTT
66 CTGACAACAAAGAGGAAACCAATCATCCATCCAATCCCCGGGTTCTTAACATCTTCCGCTCGGTT
* *
3353430 TCCATGGTAATCAACACCGATAAGATTATATGTTCTTTCATCCATTGCAATCAGACACGATCCAA
131 TCCAGGGTAATCAACACCGATAAGATTATATGTTCTTTCATCCATTGCAATCAGATACGATCCAA
*
3353495 AA-CCCCTATAAGAAACACAATCAGATAAT
196 AACCCCCTATAAGAAACACAATCAGATATT
* * *
3353524 AAACTCTCACACCTCAGAACATTTATACTTTACGAAGCGCAGCAACACTAAACAGCCCAAGGAAG
1 AAACTCTCACACCTCAGAACAGTTATACCTTACGAAGCGGAGCAACACTAAACAGCCCAAGGAAG
* * * *
3353589 CTGACAACAAAGAGGAAACCGAGCATCCATCCAATCCCCGGTTTCTTAACATCTT-CGCTCAGTT
66 CTGACAACAAAGAGGAAACCAATCATCCATCCAATCCCCGGGTTCTTAACATCTTCCGCTCGGTT
*
3353653 TCCAGGGTAATCAACACTGATAAGATTATATGTTCTTTCATCCCATTGCAATCAGATACGATCCA
131 TCCAGGGTAATCAACACCGATAAGATTATATGTTCTTTCAT-CCATTGCAATCAGATACGATCCA
* * *
3353718 AAACCTCCTATAAGACACACAATCAGTTATT
195 AAACCCCCTATAAGAAACACAATCAGATATT
* * *
3353749 AAACTGTCACAACTCAGAACAGTTATACCTTACGAAGCGGAGCAACACTAAACAGTCCAAGGAAG
1 AAACTCTCACACCTCAGAACAGTTATACCTTACGAAGCGGAGCAACACTAAACAGCCCAAGGAAG
3353814 CTGACAACAAAGAGGAAACCAATCATCCATCCAATCCCCGGGTTCTTAACATCTTCCGCTCGGTT
66 CTGACAACAAAGAGGAAACCAATCATCCATCCAATCCCCGGGTTCTTAACATCTTCCGCTCGGTT
* *
3353879 TCCATGGTAATCAACACCGATAAGATTATATGTTCTTTCATCCATTGCAATCAGACACGATCCAA
131 TCCAGGGTAATCAACACCGATAAGATTATATGTTCTTTCATCCATTGCAATCAGATACGATCCAA
* *
3353944 AA-CCCCTACAAGAAACACAATCAGATAAT
196 AACCCCCTATAAGAAACACAATCAGATATT
* *
3353973 AAAGTCTCACACCTCAGAACAGTTATACTTTACGAAGCGGAGCAACACTAAACAGCCCAAGGAAG
1 AAACTCTCACACCTCAGAACAGTTATACCTTACGAAGCGGAGCAACACTAAACAGCCCAAGGAAG
* * * *
3354038 CTGACAACAAAGAGGAAACCGATCATCCATCCAATCCCTGGTTTCTTAACATCTTCCGCTCTGTT
66 CTGACAACAAAGAGGAAACCAATCATCCATCCAATCCCCGGGTTCTTAACATCTTCCGCTCGGTT
* *
3354103 TCCAGGGTAATCAACACTGATAAGATTATATGTTCTTTGATCCATTGCAATCAGATACGATCCAA
131 TCCAGGGTAATCAACACCGATAAGATTATATGTTCTTTCATCCATTGCAATCAGATACGATCCAA
**
3354168 AACGTCCTATAAGAAACACAATCAGATATT
196 AACCCCCTATAAGAAACACAATCAGATATT
*
3354198 AAACTGTCACACCTCAGAACAGTTATACCTTACGAAGCGGAGCAACACTAAACAGCCCAAGGAAG
1 AAACTCTCACACCTCAGAACAGTTATACCTTACGAAGCGGAGCAACACTAAACAGCCCAAGGAAG
* * *
3354263 CTGACAGCGAAGAGGAAACCCATCATCCATCCAATCCCCGGGTTCTTAACATCTTCCGCTCGGTT
66 CTGACAACAAAGAGGAAACCAATCATCCATCCAATCCCCGGGTTCTTAACATCTTCCGCTCGGTT
*
3354328 TCCAGGGTAATCAACACCGATACGATTATATGTTCTTTCATCCATTGCAATCAGATACGATCCAA
131 TCCAGGGTAATCAACACCGATAAGATTATATGTTCTTTCATCCATTGCAATCAGATACGATCCAA
*
3354393 ATCCCCCTATAAGAAACACAATCAGATATT
196 AACCCCCTATAAGAAACACAATCAGATATT
3354423 AA
1 AA
3354425 GATAGAGACA
Statistics
Matches: 1457, Mismatches: 109, Indels: 14
0.92 0.07 0.01
Matches are distributed among these distances:
223 113 0.08
224 650 0.45
225 647 0.44
226 47 0.03
ACGTcount: A:0.36, C:0.27, G:0.14, T:0.23
Consensus pattern (225 bp):
AAACTCTCACACCTCAGAACAGTTATACCTTACGAAGCGGAGCAACACTAAACAGCCCAAGGAAG
CTGACAACAAAGAGGAAACCAATCATCCATCCAATCCCCGGGTTCTTAACATCTTCCGCTCGGTT
TCCAGGGTAATCAACACCGATAAGATTATATGTTCTTTCATCCATTGCAATCAGATACGATCCAA
AACCCCCTATAAGAAACACAATCAGATATT
Found at i:3353883 original size:449 final size:449
Alignment explanation
Indices: 3352627--3354420 Score: 3184
Period size: 449 Copynumber: 4.0 Consensus size: 449
3352617 GATTGAAACC
* *
3352627 AAACTCTCACACCTCAGAACAGTTATACCTTACGAAGCGAAGCAACACTAAACAGCCCAAGGAAG
1 AAACTCTCACACCTCAGAACAGTTATACTTTACGAAGCGGAGCAACACTAAACAGCCCAAGGAAG
* *
3352692 CTGACAACAAAGAGGAAACCAATCATCCATCCAATCCCCAGG-TTCTTAACATCTTCCGCTCGGT
66 CTGACAACAAAGAGGAAACCGAGCATCCATCCAATCCCC-GGTTTCTTAACATCTTCCGCTCGGT
3352756 TTCCAGGGTAATCAACA-TCGATAAGATTATATGTTCTTTCATCCATAT-CAATCAGATACGATC
130 TTCCAGGGTAATCAACACT-GATAAGATTATATGTTCTTTCATCCAT-TGCAATCAGATACGATC
* * *
3352819 CAAAACCCCCTACAAGAAACACAATCAGATATTAAACTCTCACACCTCAGAACAGTTATACCTTA
193 CAAAACCTCCTATAAGAAACACAATCAGATATTAAACTGTCACACCTCAGAACAGTTATACCTTA
* *
3352884 CAAAGTGGAGCAACACTAAACAGTCCAAGGAAGCTGACAACAAAGAGGAAACCAATCATCCATCC
258 CGAAGCGGAGCAACACTAAACAGTCCAAGGAAGCTGACAACAAAGAGGAAACCAATCATCCATCC
*
3352949 AATCCCCGGGTTCTTAACATCTTCCGCTCGGTTTCCATGGTAATCAACACCGATAAAATTATATG
323 AATCCCCGGGTTCTTAACATCTTCCGCTCGGTTTCCATGGTAATCAACACCGATAAGATTATATG
*
3353014 TTCTTTCATCCATTGCAATCAGACACGATCCAAACCCCCTATAAGAAACACAATCAGATAAT
388 TTCTTTCATCCATTGCAATCAGACACGATCCAAAACCCCTATAAGAAACACAATCAGATAAT
*
3353076 AAACTCTCACACCTCAGAACATTTATACTTTACGAAGCGGAGCAACACTAAACAGCCCAAGGAAG
1 AAACTCTCACACCTCAGAACAGTTATACTTTACGAAGCGGAGCAACACTAAACAGCCCAAGGAAG
3353141 CTGACAACAAAGAGGAAACCGAGCATCCATCCAATCCCCGGTTTCTTAACATCTT-CGCTCGGTT
66 CTGACAACAAAGAGGAAACCGAGCATCCATCCAATCCCCGGTTTCTTAACATCTTCCGCTCGGTT
* *
3353205 TCCAGGGTAATCAACACTGATAAGTTTATATGTTCTTTCATCCATTGCAATCAGATACAATCCAA
131 TCCAGGGTAATCAACACTGATAAGATTATATGTTCTTTCATCCATTGCAATCAGATACGATCCAA
3353270 AACCTCCTATAAGAAACACAATCAGATATTAAACTGTCACACCTCAGAACAGTTATACCTTACGA
196 AACCTCCTATAAGAAACACAATCAGATATTAAACTGTCACACCTCAGAACAGTTATACCTTACGA
3353335 AGCGGAGCAACACTAAACAGTCCAAGGAAGCTGACAACAAAGAGGAAACCAATCATCCATCCAAT
261 AGCGGAGCAACACTAAACAGTCCAAGGAAGCTGACAACAAAGAGGAAACCAATCATCCATCCAAT
*
3353400 CCTCGGGTTCTTAACATCTTCCGCTCGGTTTCCATGGTAATCAACACCGATAAGATTATATGTTC
326 CCCCGGGTTCTTAACATCTTCCGCTCGGTTTCCATGGTAATCAACACCGATAAGATTATATGTTC
3353465 TTTCATCCATTGCAATCAGACACGATCCAAAACCCCTATAAGAAACACAATCAGATAAT
391 TTTCATCCATTGCAATCAGACACGATCCAAAACCCCTATAAGAAACACAATCAGATAAT
* *
3353524 AAACTCTCACACCTCAGAACATTTATACTTTACGAAGCGCAGCAACACTAAACAGCCCAAGGAAG
1 AAACTCTCACACCTCAGAACAGTTATACTTTACGAAGCGGAGCAACACTAAACAGCCCAAGGAAG
*
3353589 CTGACAACAAAGAGGAAACCGAGCATCCATCCAATCCCCGGTTTCTTAACATCTT-CGCTCAGTT
66 CTGACAACAAAGAGGAAACCGAGCATCCATCCAATCCCCGGTTTCTTAACATCTTCCGCTCGGTT
3353653 TCCAGGGTAATCAACACTGATAAGATTATATGTTCTTTCATCCCATTGCAATCAGATACGATCCA
131 TCCAGGGTAATCAACACTGATAAGATTATATGTTCTTTCAT-CCATTGCAATCAGATACGATCCA
* * *
3353718 AAACCTCCTATAAGACACACAATCAGTTATTAAACTGTCACAACTCAGAACAGTTATACCTTACG
195 AAACCTCCTATAAGAAACACAATCAGATATTAAACTGTCACACCTCAGAACAGTTATACCTTACG
3353783 AAGCGGAGCAACACTAAACAGTCCAAGGAAGCTGACAACAAAGAGGAAACCAATCATCCATCCAA
260 AAGCGGAGCAACACTAAACAGTCCAAGGAAGCTGACAACAAAGAGGAAACCAATCATCCATCCAA
3353848 TCCCCGGGTTCTTAACATCTTCCGCTCGGTTTCCATGGTAATCAACACCGATAAGATTATATGTT
325 TCCCCGGGTTCTTAACATCTTCCGCTCGGTTTCCATGGTAATCAACACCGATAAGATTATATGTT
*
3353913 CTTTCATCCATTGCAATCAGACACGATCCAAAACCCCTACAAGAAACACAATCAGATAAT
390 CTTTCATCCATTGCAATCAGACACGATCCAAAACCCCTATAAGAAACACAATCAGATAAT
*
3353973 AAAGTCTCACACCTCAGAACAGTTATACTTTACGAAGCGGAGCAACACTAAACAGCCCAAGGAAG
1 AAACTCTCACACCTCAGAACAGTTATACTTTACGAAGCGGAGCAACACTAAACAGCCCAAGGAAG
* * *
3354038 CTGACAACAAAGAGGAAACCGATCATCCATCCAATCCCTGGTTTCTTAACATCTTCCGCTCTGTT
66 CTGACAACAAAGAGGAAACCGAGCATCCATCCAATCCCCGGTTTCTTAACATCTTCCGCTCGGTT
*
3354103 TCCAGGGTAATCAACACTGATAAGATTATATGTTCTTTGATCCATTGCAATCAGATACGATCCAA
131 TCCAGGGTAATCAACACTGATAAGATTATATGTTCTTTCATCCATTGCAATCAGATACGATCCAA
*
3354168 AACGTCCTATAAGAAACACAATCAGATATTAAACTGTCACACCTCAGAACAGTTATACCTTACGA
196 AACCTCCTATAAGAAACACAATCAGATATTAAACTGTCACACCTCAGAACAGTTATACCTTACGA
* * * *
3354233 AGCGGAGCAACACTAAACAGCCCAAGGAAGCTGACAGCGAAGAGGAAACCCATCATCCATCCAAT
261 AGCGGAGCAACACTAAACAGTCCAAGGAAGCTGACAACAAAGAGGAAACCAATCATCCATCCAAT
* *
3354298 CCCCGGGTTCTTAACATCTTCCGCTCGGTTTCCAGGGTAATCAACACCGATACGATTATATGTTC
326 CCCCGGGTTCTTAACATCTTCCGCTCGGTTTCCATGGTAATCAACACCGATAAGATTATATGTTC
* *
3354363 TTTCATCCATTGCAATCAGATACGATCCAAATCCCCCTATAAGAAACACAATCAGATA
391 TTTCATCCATTGCAATCAGACACGATCCAAA-ACCCCTATAAGAAACACAATCAGATA
3354421 TTAAGATAGA
Statistics
Matches: 1295, Mismatches: 44, Indels: 11
0.96 0.03 0.01
Matches are distributed among these distances:
447 1 0.00
448 483 0.37
449 739 0.57
450 72 0.06
ACGTcount: A:0.36, C:0.27, G:0.14, T:0.23
Consensus pattern (449 bp):
AAACTCTCACACCTCAGAACAGTTATACTTTACGAAGCGGAGCAACACTAAACAGCCCAAGGAAG
CTGACAACAAAGAGGAAACCGAGCATCCATCCAATCCCCGGTTTCTTAACATCTTCCGCTCGGTT
TCCAGGGTAATCAACACTGATAAGATTATATGTTCTTTCATCCATTGCAATCAGATACGATCCAA
AACCTCCTATAAGAAACACAATCAGATATTAAACTGTCACACCTCAGAACAGTTATACCTTACGA
AGCGGAGCAACACTAAACAGTCCAAGGAAGCTGACAACAAAGAGGAAACCAATCATCCATCCAAT
CCCCGGGTTCTTAACATCTTCCGCTCGGTTTCCATGGTAATCAACACCGATAAGATTATATGTTC
TTTCATCCATTGCAATCAGACACGATCCAAAACCCCTATAAGAAACACAATCAGATAAT
Found at i:3355346 original size:22 final size:22
Alignment explanation
Indices: 3355315--3355374 Score: 59
Period size: 22 Copynumber: 2.7 Consensus size: 22
3355305 ACTCTTATAT
* * * *
3355315 ATATTATTATTTAATTAAAATT
1 ATATTTTTATTAAATAAAAATA
*
3355337 TTATTTTTATTAAATAAAAATA
1 ATATTTTTATTAAATAAAAATA
3355359 ATATTTTT-TATAAATA
1 ATATTTTTAT-TAAATA
3355375 TATTATCTCG
Statistics
Matches: 31, Mismatches: 6, Indels: 2
0.79 0.15 0.05
Matches are distributed among these distances:
21 1 0.03
22 30 0.97
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (22 bp):
ATATTTTTATTAAATAAAAATA
Found at i:3359763 original size:37 final size:37
Alignment explanation
Indices: 3359665--3359784 Score: 174
Period size: 35 Copynumber: 3.3 Consensus size: 37
3359655 TGGTAACCAA
* *
3359665 CTTTGAAAAAAATGGTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATA-GTTTTTCAAAGTTTGGTAAATGTTT
3359703 CTTTG-AAAAT-GTTTTTCAAAGTTTGGTAAATGTTT
1 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAAATGTTT
*
3359738 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAGATGTTT
1 CTTTGAAAAATAGTTTTTCAAAGTTTGGTAAATGTTT
*
3359775 -GTTGAAAAAT
1 CTTTGAAAAAT
3359785 GATAATGAGA
Statistics
Matches: 76, Mismatches: 4, Indels: 6
0.88 0.05 0.07
Matches are distributed among these distances:
35 29 0.38
36 14 0.18
37 28 0.37
38 5 0.07
ACGTcount: A:0.33, C:0.05, G:0.18, T:0.44
Consensus pattern (37 bp):
CTTTGAAAAATAGTTTTTCAAAGTTTGGTAAATGTTT
Found at i:3364277 original size:36 final size:37
Alignment explanation
Indices: 3364237--3364314 Score: 113
Period size: 37 Copynumber: 2.1 Consensus size: 37
3364227 CCAACTTTGA
*
3364237 AAAAAAT-GGTTTTCAAAGTTTGGTAAATGTTTCTTT
1 AAAAAATAGGTTTTCAAAGTTTGGTAAATGTTTCTTG
* * *
3364273 AAAAAATAGTTTTTCAAAGTTTGGTAGATGTTTGTTG
1 AAAAAATAGGTTTTCAAAGTTTGGTAAATGTTTCTTG
3364310 AAAAA
1 AAAAA
3364315 TGATAATGGG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
36 7 0.19
37 30 0.81
ACGTcount: A:0.37, C:0.04, G:0.18, T:0.41
Consensus pattern (37 bp):
AAAAAATAGGTTTTCAAAGTTTGGTAAATGTTTCTTG
Found at i:3364315 original size:36 final size:36
Alignment explanation
Indices: 3364204--3364316 Score: 108
Period size: 36 Copynumber: 3.2 Consensus size: 36
3364194 TGAAAGTATT
** *
3364204 AAAATGGTTTTC-AAGTTTGGTAACCAACTTT-G-AAA
1 AAAATGGTTTTCAAAGTTTGGTAA--ATGTTTCGTTAA
*
3364239 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTAA
1 AAAATGGTTTTCAAAGTTTGGTAAATGTTTCGTTAA
* * *
3364275 AAAATAGTTTTTCAAAGTTTGGTAGATGTTT-GTTGA
1 AAAAT-GGTTTTCAAAGTTTGGTAAATGTTTCGTTAA
3364311 AAAATG
1 AAAATG
3364317 ATAATGGGAT
Statistics
Matches: 66, Mismatches: 8, Indels: 8
0.80 0.10 0.10
Matches are distributed among these distances:
34 4 0.06
35 13 0.20
36 26 0.39
37 23 0.35
ACGTcount: A:0.35, C:0.06, G:0.19, T:0.40
Consensus pattern (36 bp):
AAAATGGTTTTCAAAGTTTGGTAAATGTTTCGTTAA
Found at i:3366288 original size:37 final size:36
Alignment explanation
Indices: 3366172--3366272 Score: 159
Period size: 35 Copynumber: 2.8 Consensus size: 36
3366162 AATCAACCAA
3366172 TTTGAAAAAATGATTTTCAAAGTTTGGTAAATGTTTC
1 TTTG-AAAAATGATTTTCAAAGTTTGGTAAATGTTTC
*
3366209 TTTG-AAAATGATTTTCAAAGTTTGGTAAACGTTTC
1 TTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTTC
*
3366244 TTTGAAAAATGGTTTTTCAAAGTTTGGTA
1 TTTGAAAAAT-GATTTTCAAAGTTTGGTA
3366273 GATATTTGTT
Statistics
Matches: 60, Mismatches: 2, Indels: 4
0.91 0.03 0.06
Matches are distributed among these distances:
35 34 0.57
36 5 0.08
37 21 0.35
ACGTcount: A:0.33, C:0.06, G:0.18, T:0.44
Consensus pattern (36 bp):
TTTGAAAAATGATTTTCAAAGTTTGGTAAATGTTTC
Found at i:3370792 original size:21 final size:20
Alignment explanation
Indices: 3370768--3370831 Score: 59
Period size: 21 Copynumber: 3.4 Consensus size: 20
3370758 ACTTTGAAAA
3370768 AAATGATTTTCAAAGTTTGGT
1 AAATG-TTTTCAAAGTTTGGT
*
3370789 AAATG-TTTC----TTT-GA
1 AAATGTTTTCAAAGTTTGGT
3370803 AAATGGTTTTCAAAGTTTGGT
1 AAAT-GTTTTCAAAGTTTGGT
3370824 AAATGTTT
1 AAATGTTT
3370832 CTTTGAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 4 0.12
16 4 0.12
19 4 0.12
20 7 0.21
21 10 0.29
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (20 bp):
AAATGTTTTCAAAGTTTGGT
Found at i:3370859 original size:37 final size:36
Alignment explanation
Indices: 3370766--3370877 Score: 172
Period size: 35 Copynumber: 3.1 Consensus size: 36
3370756 CAACTTTGAA
*
3370766 AAAAATGATTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
3370802 -AAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
1 AAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
* * *
3370837 AAAAATGGTTTTTCAAAGTTTGGTAGATGTTTGTTGG
1 AAAAATGG-TTTTCAAAGTTTGGTAAATGTTTCTTTG
3370874 AAAA
1 AAAA
3370878 TTGTAATGAG
Statistics
Matches: 70, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
35 34 0.49
36 7 0.10
37 29 0.41
ACGTcount: A:0.32, C:0.04, G:0.21, T:0.43
Consensus pattern (36 bp):
AAAAATGGTTTTCAAAGTTTGGTAAATGTTTCTTTG
Found at i:3371029 original size:101 final size:101
Alignment explanation
Indices: 3370854--3371055 Score: 395
Period size: 101 Copynumber: 2.0 Consensus size: 101
3370844 GTTTTTCAAA
*
3370854 GTTTGGTAGATGTTTGTTGGAAAATTGTAATGAGATAATTATTATTGTTCACTGGACTTTAGGGT
1 GTTTGGTAAATGTTTGTTGGAAAATTGTAATGAGATAATTATTATTGTTCACTGGACTTTAGGGT
3370919 ATTTATAAGATTAGTCCTTAACCTTCAACTATAAAT
66 ATTTATAAGATTAGTCCTTAACCTTCAACTATAAAT
3370955 GTTTGGTAAATGTTTGTTGGAAAATTGTAATGAGATAATTATTATTGTTCACTGGACTTTAGGGT
1 GTTTGGTAAATGTTTGTTGGAAAATTGTAATGAGATAATTATTATTGTTCACTGGACTTTAGGGT
3371020 ATTTATAAGATTAGTCCTTAACCTTCAACTATAAAT
66 ATTTATAAGATTAGTCCTTAACCTTCAACTATAAAT
3371056 ACCCTAGCTC
Statistics
Matches: 100, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
101 100 1.00
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (101 bp):
GTTTGGTAAATGTTTGTTGGAAAATTGTAATGAGATAATTATTATTGTTCACTGGACTTTAGGGT
ATTTATAAGATTAGTCCTTAACCTTCAACTATAAAT
Found at i:3373751 original size:20 final size:20
Alignment explanation
Indices: 3373715--3373752 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
3373705 ATACTATTCC
**
3373715 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
3373735 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
3373753 GTGAACCAAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:3377528 original size:23 final size:23
Alignment explanation
Indices: 3377489--3377534 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
3377479 CCAAATAAAA
* *
3377489 CAAAAAATATTCTTTTGGATTCT
1 CAAAAAATATACTTTTGAATTCT
3377512 CAAAGAAATATAC-TTTGAATTCT
1 CAAA-AAATATACTTTTGAATTCT
3377535 TTGGAGCATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 13 0.65
24 7 0.35
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (23 bp):
CAAAAAATATACTTTTGAATTCT
Found at i:3383244 original size:20 final size:21
Alignment explanation
Indices: 3383214--3383254 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
3383204 AATAGAATGC
3383214 CCTATGGGTACCGATACCCCT
1 CCTATGGGTACCGATACCCCT
3383235 CCTA-GGGTACCGATACCCCT
1 CCTATGGGTACCGATACCCCT
3383255 ATGTAAGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.20, C:0.39, G:0.20, T:0.22
Consensus pattern (21 bp):
CCTATGGGTACCGATACCCCT
Found at i:3387088 original size:15 final size:15
Alignment explanation
Indices: 3387065--3387099 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
3387055 ATCAAAGGAA
*
3387065 GAAATGAAAGATGAG
1 GAAACGAAAGATGAG
3387080 GAAACGAAAGATGAG
1 GAAACGAAAGATGAG
3387095 GAAAC
1 GAAAC
3387100 TCATAATGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.54, C:0.06, G:0.31, T:0.09
Consensus pattern (15 bp):
GAAACGAAAGATGAG
Found at i:3389557 original size:13 final size:13
Alignment explanation
Indices: 3389534--3389572 Score: 69
Period size: 13 Copynumber: 2.9 Consensus size: 13
3389524 AAAACTACAT
3389534 ATTGATTTTCAAAC
1 ATTG-TTTTCAAAC
3389548 ATTGTTTTCAAAC
1 ATTGTTTTCAAAC
3389561 ATTGTTTTCAAA
1 ATTGTTTTCAAA
3389573 GTTTTCTCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
13 21 0.84
14 4 0.16
ACGTcount: A:0.33, C:0.13, G:0.08, T:0.46
Consensus pattern (13 bp):
ATTGTTTTCAAAC
Found at i:3391631 original size:20 final size:21
Alignment explanation
Indices: 3391601--3391641 Score: 75
Period size: 20 Copynumber: 2.0 Consensus size: 21
3391591 AACAGAATGC
3391601 CCTATGGGTACCGATACCCCT
1 CCTATGGGTACCGATACCCCT
3391622 CCTA-GGGTACCGATACCCCT
1 CCTATGGGTACCGATACCCCT
3391642 ATGTAAGTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.20, C:0.39, G:0.20, T:0.22
Consensus pattern (21 bp):
CCTATGGGTACCGATACCCCT
Found at i:3391699 original size:20 final size:20
Alignment explanation
Indices: 3391674--3391714 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
3391664 AAACAGAATG
3391674 CCTTATGGGTACCGATACCC
1 CCTTATGGGTACCGATACCC
3391694 CCTTATGGGTACCGATACCC
1 CCTTATGGGTACCGATACCC
3391714 C
1 C
3391715 TAGTCATATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.20, C:0.37, G:0.20, T:0.24
Consensus pattern (20 bp):
CCTTATGGGTACCGATACCC
Found at i:3396961 original size:21 final size:22
Alignment explanation
Indices: 3396935--3396981 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
3396925 AAAATGTTAG
3396935 GAAAAATGTAACATTTTCGGTT
1 GAAAAATGTAACATTTTCGGTT
3396957 GAAAAATGTAACATTTTCGGTT
1 GAAAAATGTAACATTTTCGGTT
3396979 GAA
1 GAA
3396982 CAAAAAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.38, C:0.09, G:0.19, T:0.34
Consensus pattern (22 bp):
GAAAAATGTAACATTTTCGGTT
Found at i:3397368 original size:12 final size:12
Alignment explanation
Indices: 3397351--3397395 Score: 72
Period size: 12 Copynumber: 3.8 Consensus size: 12
3397341 TCTTTATTTC
3397351 AAAATTTTAATT
1 AAAATTTTAATT
*
3397363 AAAATTTTATTT
1 AAAATTTTAATT
*
3397375 CAAATTTTAATT
1 AAAATTTTAATT
3397387 AAAATTTTA
1 AAAATTTTA
3397396 TTTCGTTCGA
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
12 29 1.00
ACGTcount: A:0.47, C:0.02, G:0.00, T:0.51
Consensus pattern (12 bp):
AAAATTTTAATT
Found at i:3397384 original size:24 final size:25
Alignment explanation
Indices: 3397343--3397399 Score: 107
Period size: 24 Copynumber: 2.3 Consensus size: 25
3397333 ATCTTTCTTC
3397343 TTTATTTCAAAATTTTAATTAAAAT
1 TTTATTTCAAAATTTTAATTAAAAT
3397368 TTTATTTC-AAATTTTAATTAAAAT
1 TTTATTTCAAAATTTTAATTAAAAT
3397392 TTTATTTC
1 TTTATTTC
3397400 GTTCGACAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
24 24 0.75
25 8 0.25
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (25 bp):
TTTATTTCAAAATTTTAATTAAAAT
Found at i:3406030 original size:2 final size:2
Alignment explanation
Indices: 3406023--3406086 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
3406013 CGATCTAACC
3406023 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
3406065 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
3406087 TTACAATTTT
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:3412489 original size:103 final size:103
Alignment explanation
Indices: 3412224--3412782 Score: 715
Period size: 103 Copynumber: 5.5 Consensus size: 103
3412214 AAGAGAAGCT
* * * *
3412224 ATCTCAAATGAGATAAAATTTTGTTTCGAGTGAAACAATTTTAACATTTGTGTTTCAAGGGAAAC
1 ATCTCAAGTGAGATAAAATTTTGTTTCGAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAAT
* *
3412289 TGTCTCAAGCGAGACAG-AGTTTGTTTTTAAGAAAAAAAA
66 TGTCTCAAGCGAGA-AGAAATTTGTTTTTAAG-AAAAATA
** * **
3412328 ATCTCAAGTGAGAT--AATTTT-TTTTAAGTGAACCAATTTCAAAATTTACGTTTCAAGGGAAAT
1 ATCTCAAGTGAGATAAAATTTTGTTTCGAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAAT
3412390 TGTCTCAAGCGAGAAGAAATTTGTTTTTAAGAAAAATA
66 TGTCTCAAGCGAGAAGAAATTTGTTTTTAAGAAAAATA
*
3412428 ATCTCAAGTGAGATAAAATTTTGTTTCTAGTGAAACAATTTCAAAATTTGTGTTTCAAGGG-AAT
1 ATCTCAAGTGAGATAAAATTTTGTTTCGAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAAT
*
3412492 TGTCTCAAGCGAGACGAAATTTGTTTTTAAGAAAAATA
66 TGTCTCAAGCGAGAAGAAATTTGTTTTTAAGAAAAATA
* * * *
3412530 ATCTCAAGTGAGAT--AATATT-TTTCGAGTGAAATAATTTCAAAATTTTTGTTTCAAGAGAAAT
1 ATCTCAAGTGAGATAAAATTTTGTTTCGAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAAT
* * * *
3412592 TGTCTCAAGTGA-AATGGAATTTATTTTTAACAAAAATA
66 TGTCTCAAGCGAGAA-GAAATTTGTTTTTAAGAAAAATA
* * * * *
3412630 ATCTTAAGTGAGATAAATTTTTGTTTCGAGTGAAAAAATTTCAAAATTTATGTTTCATGGGAAAT
1 ATCTCAAGTGAGATAAAATTTTGTTTCGAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAAT
* * * *
3412695 TGTCTCAAGCGA-AACAAAATTTATTTTTAAGTAAAACA
66 TGTCTCAAGCGAGAA-GAAATTTGTTTTTAAGAAAAATA
* * *
3412733 ATCTCAAGTGAGATAAATTTTTGTTTCGAGTAAAATAATTTCAAAATTTG
1 ATCTCAAGTGAGATAAAATTTTGTTTCGAGTGAAACAATTTCAAAATTTG
3412783 CGATACAAAA
Statistics
Matches: 401, Mismatches: 45, Indels: 19
0.86 0.10 0.04
Matches are distributed among these distances:
99 35 0.09
100 74 0.18
101 61 0.15
102 70 0.17
103 148 0.37
104 13 0.03
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (103 bp):
ATCTCAAGTGAGATAAAATTTTGTTTCGAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAAT
TGTCTCAAGCGAGAAGAAATTTGTTTTTAAGAAAAATA
Found at i:3412621 original size:202 final size:202
Alignment explanation
Indices: 3412224--3412781 Score: 769
Period size: 202 Copynumber: 2.7 Consensus size: 202
3412214 AAGAGAAGCT
* * * *
3412224 ATCTCAAATGAGATAAAATTTTGTTTCGAGTGAAACAATTTTAACATTTGTGTTTCAAGGGAAAC
1 ATCTCAAGTGAGATAAAATTTTGTTTCGAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAAT
* **
3412289 TGTCTCAAGCGAGACAGAGTTTGTTTTTAAGAAAAAAAAATCTCAAGTGAGATAATTTTTTTTAA
66 TGTCTCAAGCGAGACA-AATTTGTTTTTAAG-AAAAAAAATCTCAAGTGAGATAATTTTTTTCGA
** * *
3412354 GTGAACCAATTTCAAAATTTACGTTTCAAGGGAAATTGTCTCAAGCGAGAAGAAATTTGTTTTTA
129 GTGAAATAATTTCAAAATTTACGTTTCAAGAGAAATTGTCTCAAGCGAGAAGAAATTTATTTTTA
*
3412419 AGAAAAATA
194 ACAAAAATA
*
3412428 ATCTCAAGTGAGATAAAATTTTGTTTCTAGTGAAACAATTTCAAAATTTGTGTTTCAAGGG-AAT
1 ATCTCAAGTGAGATAAAATTTTGTTTCGAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAAT
* *
3412492 TGTCTCAAGCGAGACGAAATTTGTTTTTAAGAAAAATAATCTCAAGTGAGATAATATTTTTCGAG
66 TGTCTCAAGCGAGAC-AAATTTGTTTTTAAGAAAAAAAATCTCAAGTGAGATAATTTTTTTCGAG
** * *
3412557 TGAAATAATTTCAAAATTTTTGTTTCAAGAGAAATTGTCTCAAGTGA-AATGGAATTTATTTTTA
130 TGAAATAATTTCAAAATTTACGTTTCAAGAGAAATTGTCTCAAGCGAGAA-GAAATTTATTTTTA
3412621 ACAAAAATA
194 ACAAAAATA
* * * * *
3412630 ATCTTAAGTGAGATAAATTTTTGTTTCGAGTGAAAAAATTTCAAAATTTATGTTTCATGGGAAAT
1 ATCTCAAGTGAGATAAAATTTTGTTTCGAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAAT
* * * *
3412695 TGTCTCAAGCGAAACAAAATTTATTTTTAAGTAAAACAATCTCAAGTGAGATAAATTTTTGTTTC
66 TGTCTCAAGCGAGAC-AAATTTGTTTTTAAGAAAAAAAATCTCAAGTGAGAT-AA-TTTT-TTTC
*
3412760 GAGTAAAATAATTTCAAAATTT
127 GAGTGAAATAATTTCAAAATTT
3412782 GCGATACAAA
Statistics
Matches: 316, Mismatches: 32, Indels: 10
0.88 0.09 0.03
Matches are distributed among these distances:
201 2 0.01
202 146 0.46
203 80 0.25
204 60 0.19
205 3 0.01
206 25 0.08
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.36
Consensus pattern (202 bp):
ATCTCAAGTGAGATAAAATTTTGTTTCGAGTGAAACAATTTCAAAATTTGTGTTTCAAGGGAAAT
TGTCTCAAGCGAGACAAATTTGTTTTTAAGAAAAAAAATCTCAAGTGAGATAATTTTTTTCGAGT
GAAATAATTTCAAAATTTACGTTTCAAGAGAAATTGTCTCAAGCGAGAAGAAATTTATTTTTAAC
AAAAATA
Found at i:3412757 original size:305 final size:305
Alignment explanation
Indices: 3412224--3412929 Score: 784
Period size: 305 Copynumber: 2.4 Consensus size: 305
3412214 AAGAGAAGCT
* * * *
3412224 ATCTCAAATGAGATAAAATTTTGTTTCGAGTGAAACAATTTTAACATTTGTGTTTCAAGGGAAAC
1 ATCTCAAATGAGAT-AAATATTGTTTCGAGTGAAACAATTTCAAAATTTGTGTTTCAAGAGAAAC
* * *
3412289 TGTCTCAAGCGAGACAGAGTTTGTTTTTAAGAAAAAAAAATCTCAAGTGAGATAATTTTTTTTAA
65 TGTCTCAAGCGAAACAGAATTTATTTTTAAGAAAAAAAAATCTCAAGTGAGATAATTTTTTTTAA
** * *
3412354 GTGAACCAATTTCAAAATTTACGTTTCAAGGGAAATTGTCTCAAGCGAGAAGAAATTTGTTTTTA
130 GTGAAAAAATTTCAAAATTTACGTTTCAAGGGAAATTGTCTCAAGCGAGAAAAAATTTATTTTTA
* * *
3412419 AGAAAAATAATCTCAAGTGAGATAAAATTTTGTTTCTAGTGAAACAATTTCAAAATTTGTGTTTC
195 AGAAAAACAATCTCAAGTGAGATAAAATTTTGTTTCGAGTAAAACAATTTCAAAATTTGTGTTTC
3412484 AAGGGAATTGTCTCAAGCGAGACGAAATTTGTTTTTAAGAAAAATA
260 AAGGGAATTGTCTCAAGCGAGACGAAATTTGTTTTTAAGAAAAATA
* * * *
3412530 ATCTCAAGTGAGAT-AATATT-TTTCGAGTGAAATAATTTCAAAATTTTTGTTTCAAGAGAAATT
1 ATCTCAAATGAGATAAATATTGTTTCGAGTGAAACAATTTCAAAATTTGTGTTTCAAGAGAAACT
* ** * * *
3412593 GTCTCAAGTGAAATGGAATTTATTTTTAA-CAAAAATAATCTTAAGTGAGATAAATTTTTGTTTC
66 GTCTCAAGCGAAACAGAATTTATTTTTAAGAAAAAAAAATCTCAAGTGAGAT-AATTTTT-TTT-
* * *
3412657 GAGTGAAAAAATTTCAAAATTTATGTTTCATGGGAAATTGTCTCAAGCGA-AACAAAATTTATTT
128 AAGTGAAAAAATTTCAAAATTTACGTTTCAAGGGAAATTGTCTCAAGCGAGAA-AAAATTTATTT
* * *
3412721 TTAAGTAAAACAATCTCAAGTGAGATAAATTTTTGTTTCGAGTAAAATAATTTCAAAA-TT-TG-
192 TTAAGAAAAACAATCTCAAGTGAGATAAAATTTTGTTTCGAGTAAAACAATTTCAAAATTTGTGT
*
3412783 --C----G-A-----T--A-C---A--AAATTTGTTTTTAAGAAAAACA
257 TTCAAGGGAATTGTCTCAAGCGAGACGAAATTTGTTTTTAAGAAAAATA
* * * * * * *
3412812 ATATTAAGTGAGATAAATTTTTGTTTCAAGTGAAATAATTTCAAAATTTGTGTTTCAAGAGAAAT
1 ATCTCAAATGAGATAAA-TATTGTTTCGAGTGAAACAATTTCAAAATTTGTGTTTCAAGAGAAAC
* * * *
3412877 TGTCTCAAGTGAGACAAAATTTATTTTTAAG-AAAAACAATCTCAAGTGAGATA
65 TGTCTCAAGCGAAACAGAATTTATTTTTAAGAAAAAAAAATCTCAAGTGAGATA
3412930 TAAAAAAATC
Statistics
Matches: 350, Mismatches: 42, Indels: 38
0.81 0.10 0.09
Matches are distributed among these distances:
282 33 0.09
283 2 0.01
284 5 0.01
285 85 0.24
287 1 0.00
288 1 0.00
290 1 0.00
295 1 0.00
296 1 0.00
300 1 0.00
302 19 0.05
303 69 0.20
304 12 0.03
305 106 0.30
306 13 0.04
ACGTcount: A:0.40, C:0.09, G:0.16, T:0.36
Consensus pattern (305 bp):
ATCTCAAATGAGATAAATATTGTTTCGAGTGAAACAATTTCAAAATTTGTGTTTCAAGAGAAACT
GTCTCAAGCGAAACAGAATTTATTTTTAAGAAAAAAAAATCTCAAGTGAGATAATTTTTTTTAAG
TGAAAAAATTTCAAAATTTACGTTTCAAGGGAAATTGTCTCAAGCGAGAAAAAATTTATTTTTAA
GAAAAACAATCTCAAGTGAGATAAAATTTTGTTTCGAGTAAAACAATTTCAAAATTTGTGTTTCA
AGGGAATTGTCTCAAGCGAGACGAAATTTGTTTTTAAGAAAAATA
Found at i:3412801 original size:79 final size:79
Alignment explanation
Indices: 3412703--3412861 Score: 255
Period size: 79 Copynumber: 2.0 Consensus size: 79
3412693 ATTGTCTCAA
* * *
3412703 GCGAAACAAAATTTATTTTTAAGTAAAACAATCTCAAGTGAGATAAATTTTTGTTTCGAGTAAAA
1 GCGAAACAAAATTTATTTTTAAGAAAAACAATATCAAGTGAGATAAATTTTTGTTTCAAGTAAAA
3412768 TAATTTCAAAATTT
66 TAATTTCAAAATTT
* * * *
3412782 GCGATACAAAATTTGTTTTTAAGAAAAACAATATTAAGTGAGATAAATTTTTGTTTCAAGTGAAA
1 GCGAAACAAAATTTATTTTTAAGAAAAACAATATCAAGTGAGATAAATTTTTGTTTCAAGTAAAA
3412847 TAATTTCAAAATTT
66 TAATTTCAAAATTT
3412861 G
1 G
3412862 TGTTTCAAGA
Statistics
Matches: 73, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
79 73 1.00
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.37
Consensus pattern (79 bp):
GCGAAACAAAATTTATTTTTAAGAAAAACAATATCAAGTGAGATAAATTTTTGTTTCAAGTAAAA
TAATTTCAAAATTT
Found at i:3417852 original size:56 final size:59
Alignment explanation
Indices: 3417744--3417883 Score: 160
Period size: 56 Copynumber: 2.4 Consensus size: 59
3417734 TTTGAAATAC
*
3417744 CGTGAATTGAGCAATAGGAAATGTTAATCCCTCAAGTGGGGCGTCACTGATTCAAAATGT
1 CGTGAATTGAGCAATAGGAAATGTT-ATCCCTCAAGTGAGGCGTCACTGATTCAAAATGT
* * * * *
3417804 CGTGAATTGAGTAA-AGGAAATG-T-TCCCTCAAGTGAGGTGTTATTGATTCGAAATGT
1 CGTGAATTGAGCAATAGGAAATGTTATCCCTCAAGTGAGGCGTCACTGATTCAAAATGT
* ** *
3417860 CATGAATCAAGCAATATGAAATGT
1 CGTGAATTGAGCAATAGGAAATGT
3417884 GAAAATATCC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
56 38 0.57
57 7 0.10
58 1 0.01
59 8 0.12
60 13 0.19
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.29
Consensus pattern (59 bp):
CGTGAATTGAGCAATAGGAAATGTTATCCCTCAAGTGAGGCGTCACTGATTCAAAATGT
Found at i:3418022 original size:42 final size:42
Alignment explanation
Indices: 3417911--3418026 Score: 112
Period size: 42 Copynumber: 2.8 Consensus size: 42
3417901 AGGAATTATG
* *
3417911 GATGGCACGAAGGACTT--TCATCTTGCTCAAAAGACTAATA
1 GATGGCCCGAAGGACTTAATCATCTTGCTTAAAAGACTAATA
* * * * * * *
3417951 GATGACCCGAAGGATTTAAGCACCATGCTTGAAAGACTTACT-
1 GATGGCCCGAAGGACTTAATCATCTTGCTTAAAAGAC-TAATA
*
3417993 GATGGCCCAAAGGACTTAATCATCTTGCTTAAAA
1 GATGGCCCGAAGGACTTAATCATCTTGCTTAAAA
3418027 TTGATGGGTT
Statistics
Matches: 57, Mismatches: 16, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
40 14 0.25
42 40 0.70
43 3 0.05
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (42 bp):
GATGGCCCGAAGGACTTAATCATCTTGCTTAAAAGACTAATA
Found at i:3426084 original size:34 final size:32
Alignment explanation
Indices: 3426018--3426086 Score: 84
Period size: 32 Copynumber: 2.1 Consensus size: 32
3426008 GTTCAAAATT
**
3426018 CACAGGTATCGATACATGCCTGTGTATAGATA
1 CACAGGTATCGATACACCCCTGTGTATAGATA
* *
3426050 CACAGGTATCGGTACACCCCTGAATGTATTGATA
1 CACAGGTATCGATACACCCCTG--TGTATAGATA
3426084 CAC
1 CAC
3426087 CATGAAGTTG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 19 0.61
34 12 0.39
ACGTcount: A:0.30, C:0.23, G:0.20, T:0.26
Consensus pattern (32 bp):
CACAGGTATCGATACACCCCTGTGTATAGATA
Found at i:3427309 original size:18 final size:18
Alignment explanation
Indices: 3427286--3427329 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
3427276 CCAAACCGTA
*
3427286 ATACTTTCTTCCAGGGAG
1 ATACTTTCTTCCAAGGAG
3427304 ATACTTTCTTCCAAGGAG
1 ATACTTTCTTCCAAGGAG
3427322 ATACTTTC
1 ATACTTTC
3427330 AGGAAAACTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.25, C:0.23, G:0.16, T:0.36
Consensus pattern (18 bp):
ATACTTTCTTCCAAGGAG
Found at i:3432256 original size:22 final size:23
Alignment explanation
Indices: 3432207--3432264 Score: 82
Period size: 23 Copynumber: 2.6 Consensus size: 23
3432197 TCGTATAAAG
*
3432207 CACCAAAGTGCCACGTAGAATTA
1 CACCGAAGTGCCACGTAGAATTA
*
3432230 CACCGAAGTGCCGCGTAGAA-TA
1 CACCGAAGTGCCACGTAGAATTA
*
3432252 CACCGTAGTGCCA
1 CACCGAAGTGCCA
3432265 TGATTACATG
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
22 13 0.42
23 18 0.58
ACGTcount: A:0.33, C:0.29, G:0.22, T:0.16
Consensus pattern (23 bp):
CACCGAAGTGCCACGTAGAATTA
Found at i:3432699 original size:23 final size:23
Alignment explanation
Indices: 3432663--3432726 Score: 74
Period size: 23 Copynumber: 2.8 Consensus size: 23
3432653 CAGCTCGTAT
*
3432663 AAATGCACCAAAGTGCCACATAG
1 AAATGCACCGAAGTGCCACATAG
* * *
3432686 AATTGCACCGAAGTGCCGCGTAG
1 AAATGCACCGAAGTGCCACATAG
* *
3432709 AAATACACCGTAGTGCCA
1 AAATGCACCGAAGTGCCA
3432727 TATATATAAT
Statistics
Matches: 33, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.36, C:0.27, G:0.22, T:0.16
Consensus pattern (23 bp):
AAATGCACCGAAGTGCCACATAG
Found at i:3443128 original size:39 final size:39
Alignment explanation
Indices: 3443085--3443250 Score: 154
Period size: 39 Copynumber: 4.3 Consensus size: 39
3443075 AATTTGCGAC
* * *
3443085 AAGGACTTACCCTGAGCAAAAAGTCGAGGAGCCTGTGGT
1 AAGGACTTACCCTAAGCAAAAAGTCAAGGAGCCTGCGGT
* * * * *
3443124 AAGGACTTACTCTAAGCACAAAGTTAAGGAGCATGTGGT
1 AAGGACTTACCCTAAGCAAAAAGTCAAGGAGCCTGCGGT
* * * *
3443163 AAGGACTTACCCTAATCACAAA-TCCGAGGAGCTTGCGGT
1 AAGGACTTACCCTAAGCAAAAAGT-CAAGGAGCCTGCGGT
* * ** * *
3443202 AAAGACTTACCCTGAGCAAAAAACCAAGGAGCCTACGAT
1 AAGGACTTACCCTAAGCAAAAAGTCAAGGAGCCTGCGGT
3443241 AAGGACTTAC
1 AAGGACTTAC
3443251 AAGTCATAGA
Statistics
Matches: 103, Mismatches: 22, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
38 1 0.01
39 102 0.99
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.19
Consensus pattern (39 bp):
AAGGACTTACCCTAAGCAAAAAGTCAAGGAGCCTGCGGT
Found at i:3443231 original size:78 final size:78
Alignment explanation
Indices: 3443085--3443233 Score: 174
Period size: 78 Copynumber: 1.9 Consensus size: 78
3443075 AATTTGCGAC
* * * * * ***
3443085 AAGGACTTACCCTGAGCAAAAAGTCGAGGAGCCTGTGGTAAGGACTTACTCTAAGCACAAAGTTA
1 AAGGACTTACCCTAAGCAAAAAGTCGAGGAGCCTGCGGTAAAGACTTACCCTAAGCAAAAAACCA
3443150 AGGAGCATGTGGT
66 AGGAGCATGTGGT
* * * *
3443163 AAGGACTTACCCTAATCACAAA-TCCGAGGAGCTTGCGGTAAAGACTTACCCTGAGCAAAAAACC
1 AAGGACTTACCCTAAGCAAAAAGT-CGAGGAGCCTGCGGTAAAGACTTACCCTAAGCAAAAAACC
3443227 AAGGAGC
65 AAGGAGC
3443234 CTACGATAAG
Statistics
Matches: 58, Mismatches: 12, Indels: 2
0.81 0.17 0.03
Matches are distributed among these distances:
77 1 0.02
78 57 0.98
ACGTcount: A:0.36, C:0.21, G:0.25, T:0.18
Consensus pattern (78 bp):
AAGGACTTACCCTAAGCAAAAAGTCGAGGAGCCTGCGGTAAAGACTTACCCTAAGCAAAAAACCA
AGGAGCATGTGGT
Found at i:3453057 original size:27 final size:27
Alignment explanation
Indices: 3453026--3453087 Score: 115
Period size: 27 Copynumber: 2.3 Consensus size: 27
3453016 GTATGAAAGA
3453026 TTGTCAAATTTTTTAATTGAAAAAGGT
1 TTGTCAAATTTTTTAATTGAAAAAGGT
3453053 TTGTCAAATTTTTTAATTGAAAAAGGT
1 TTGTCAAATTTTTTAATTGAAAAAGGT
*
3453080 TTTTCAAA
1 TTGTCAAA
3453088 AGGGAAGGTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 34 1.00
ACGTcount: A:0.37, C:0.05, G:0.13, T:0.45
Consensus pattern (27 bp):
TTGTCAAATTTTTTAATTGAAAAAGGT
Found at i:3454429 original size:20 final size:21
Alignment explanation
Indices: 3454390--3454429 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
3454380 CCCCCTTTGA
*
3454390 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATTACCCCCAC
*
3454411 AGGGGAATCGA-TACCCCCA
1 AGGGGAACCGATTACCCCCA
3454430 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.38, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATTACCCCCAC
Found at i:3460861 original size:21 final size:21
Alignment explanation
Indices: 3460835--3460876 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
3460825 CAATTATGAA
*
3460835 TCAAGGAGCTTTACTTCAAAG
1 TCAAGGAGCCTTACTTCAAAG
* *
3460856 TCAAGGTGCCTTACTTTAAAG
1 TCAAGGAGCCTTACTTCAAAG
3460877 CCATAGCTCG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Consensus pattern (21 bp):
TCAAGGAGCCTTACTTCAAAG
Done.