Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 ID=Chr03-JGI_221_v2.0
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: 45765648
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 655849 characters in sequence are not A, C, G, or T
File 58 of 150
Found at i:17407027 original size:69 final size:70
Alignment explanation
Indices: 17406799--17407056 Score: 423
Period size: 70 Copynumber: 3.7 Consensus size: 70
17406789 CTATATTTAA
* * *
17406799 ATATTGTT-AATAATAAATTTTATATTTTTA-AAACTAATTGTACATGTTATTTTTCTAAATATT
1 ATATT-TTCAATAATAAATTTTATAATTTTAGAAA-GAATTGTAAATGTTATTTTTCTAAATATT
17406862 AACATCT
64 AACATCT
* *
17406869 ATATTTTCAATAATAAATTTTATAATTTTAGAAATAATTGTACATGTTATTTTTCTAAATATTAA
1 ATATTTTCAATAATAAATTTTATAATTTTAGAAAGAATTGTAAATGTTATTTTTCTAAATATTAA
17406934 CATCT
66 CATCT
*
17406939 ATATTTTCAATAATTAATTTTATAATTTTAGAAAGAATTGTAAATGTTA-TTTTCTAAATATTAA
1 ATATTTTCAATAATAAATTTTATAATTTTAGAAAGAATTGTAAATGTTATTTTTCTAAATATTAA
17407003 CATCT
66 CATCT
17407008 ATATTTTCAATAATAAATTTTATAATTTTAGAAAGAATTGTAAATGTTA
1 ATATTTTCAATAATAAATTTTATAATTTTAGAAAGAATTGTAAATGTTA
17407057 CATAATTCAA
Statistics
Matches: 181, Mismatches: 5, Indels: 5
0.95 0.03 0.03
Matches are distributed among these distances:
69 70 0.39
70 108 0.60
71 3 0.02
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.48
Consensus pattern (70 bp):
ATATTTTCAATAATAAATTTTATAATTTTAGAAAGAATTGTAAATGTTATTTTTCTAAATATTAA
CATCT
Found at i:17407055 original size:139 final size:140
Alignment explanation
Indices: 17406799--17407056 Score: 423
Period size: 139 Copynumber: 1.9 Consensus size: 140
17406789 CTATATTTAA
* * *
17406799 ATATTGTTAATAATAAATTTTATATTTTTAAAACTAATTGTACATGTTATTTTTCTAAATATTAA
1 ATATTGTTAATAATAAATTTTATAATTTTAAAACGAATTGTAAATGTTATTTTTCTAAATATTAA
* *
17406864 CATCTATATTTTCAATAATAAATTTTATAATTTTAGAAATAATTGTACATGTTATTTTTCTAAAT
66 CATCTATATTTTCAATAATAAATTTTATAATTTTAGAAAGAATTGTAAATGTTATTTTTCTAAAT
17406929 ATTAACATCT
131 ATTAACATCT
*
17406939 ATATT-TTCAATAATTAATTTTATAATTTTAGAAA-GAATTGTAAATGTTA-TTTTCTAAATATT
1 ATATTGTT-AATAATAAATTTTATAATTTTA-AAACGAATTGTAAATGTTATTTTTCTAAATATT
17407001 AACATCTATATTTTCAATAATAAATTTTATAATTTTAGAAAGAATTGTAAATGTTA
64 AACATCTATATTTTCAATAATAAATTTTATAATTTTAGAAAGAATTGTAAATGTTA
17407057 CATAATTCAA
Statistics
Matches: 110, Mismatches: 6, Indels: 5
0.91 0.05 0.04
Matches are distributed among these distances:
139 69 0.63
140 38 0.35
141 3 0.03
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.48
Consensus pattern (140 bp):
ATATTGTTAATAATAAATTTTATAATTTTAAAACGAATTGTAAATGTTATTTTTCTAAATATTAA
CATCTATATTTTCAATAATAAATTTTATAATTTTAGAAAGAATTGTAAATGTTATTTTTCTAAAT
ATTAACATCT
Found at i:17407184 original size:19 final size:19
Alignment explanation
Indices: 17407160--17407282 Score: 106
Period size: 19 Copynumber: 7.5 Consensus size: 19
17407150 ATATATAAAC
17407160 TTACATAATACATAACTTA
1 TTACATAATACATAACTTA
17407179 TTACATAATACATAACTTA
1 TTACATAATACATAACTTA
17407198 -T--AT-AT--A-AAC---
1 TTACATAATACATAACTTA
17407207 TTACATAATACATAACTTA
1 TTACATAATACATAACTTA
17407226 TTACATAATACATAACTTA
1 TTACATAATACATAACTTA
17407245 -T--AT-AT--A-AAC---
1 TTACATAATACATAACTTA
17407254 TTACATAATACATAACTTA
1 TTACATAATACATAACTTA
17407273 TTACATAATA
1 TTACATAATA
17407283 AGTTACGTAA
Statistics
Matches: 84, Mismatches: 0, Indels: 40
0.68 0.00 0.32
Matches are distributed among these distances:
10 2 0.02
12 10 0.12
13 6 0.07
15 6 0.07
16 10 0.12
18 2 0.02
19 48 0.57
ACGTcount: A:0.49, C:0.15, G:0.00, T:0.37
Consensus pattern (19 bp):
TTACATAATACATAACTTA
Found at i:17407201 original size:47 final size:47
Alignment explanation
Indices: 17407145--17407282 Score: 276
Period size: 47 Copynumber: 2.9 Consensus size: 47
17407135 ATTATATAAC
17407145 AACTTATATATAAACTTACATAATACATAACTTATTACATAATACAT
1 AACTTATATATAAACTTACATAATACATAACTTATTACATAATACAT
17407192 AACTTATATATAAACTTACATAATACATAACTTATTACATAATACAT
1 AACTTATATATAAACTTACATAATACATAACTTATTACATAATACAT
17407239 AACTTATATATAAACTTACATAATACATAACTTATTACATAATA
1 AACTTATATATAAACTTACATAATACATAACTTATTACATAATA
17407283 AGTTACGTAA
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
47 91 1.00
ACGTcount: A:0.49, C:0.14, G:0.00, T:0.36
Consensus pattern (47 bp):
AACTTATATATAAACTTACATAATACATAACTTATTACATAATACAT
Found at i:17407213 original size:28 final size:28
Alignment explanation
Indices: 17407179--17407273 Score: 127
Period size: 28 Copynumber: 3.7 Consensus size: 28
17407169 ACATAACTTA
17407179 TTACATAATACATAACTTATATATAAAC
1 TTACATAATACATAACTTATATATAAAC
17407207 TTACATAATACATAAC-----T-T--A-
1 TTACATAATACATAACTTATATATAAAC
17407226 TTACATAATACATAACTTATATATAAAC
1 TTACATAATACATAACTTATATATAAAC
17407254 TTACATAATACATAACTTAT
1 TTACATAATACATAACTTAT
17407274 TACATAATAA
Statistics
Matches: 58, Mismatches: 0, Indels: 18
0.76 0.00 0.24
Matches are distributed among these distances:
19 16 0.28
20 1 0.02
22 1 0.02
23 1 0.02
24 1 0.02
25 1 0.02
27 1 0.02
28 36 0.62
ACGTcount: A:0.48, C:0.15, G:0.00, T:0.37
Consensus pattern (28 bp):
TTACATAATACATAACTTATATATAAAC
Found at i:17407389 original size:126 final size:126
Alignment explanation
Indices: 17407321--17407680 Score: 677
Period size: 126 Copynumber: 2.8 Consensus size: 126
17407311 TAACAACTTG
17407321 CATAACTCACATAACTAAATTAATTTATATTATACATTAACTTGTCGGACTTGCATAACTTATAT
1 CATAACTCACATAACTAAATTAATTTATATTATACATTAACTTGTCGGACTTGCATAACTTATAT
17407386 AATACTTAACTTACATAATACATAACTTACATAATAACATAATAAGTTACATAATATTATA
66 AATACTTAACTTACATAATACATAACTTACATAATAACATAATAAGTTACATAATATTATA
*
17407447 CATAACTCACATAACTAAATTAATTTATATTATACATTAACTTGTAGGACTTGCATAACTTATAT
1 CATAACTCACATAACTAAATTAATTTATATTATACATTAACTTGTCGGACTTGCATAACTTATAT
17407512 AATACTTAACTTACATAATACATAACTTACATAATAACATAATAAGTTACATAATATTATA
66 AATACTTAACTTACATAATACATAACTTACATAATAACATAATAAGTTACATAATATTATA
*
17407573 CATAACTGACATAACTAAATTAATTTATATTATACATTAACTTGTCGGACTTGCATAACTTATAT
1 CATAACTCACATAACTAAATTAATTTATATTATACATTAACTTGTCGGACTTGCATAACTTATAT
17407638 AATACTTAACTTACATAACGTACATAACTTACATAAT-ACATAA
66 AATACTTAACTTACATAA--TACATAACTTACATAATAACATAA
17407681 CTTACATAAT
Statistics
Matches: 229, Mismatches: 3, Indels: 3
0.97 0.01 0.01
Matches are distributed among these distances:
126 206 0.90
127 6 0.03
128 17 0.07
ACGTcount: A:0.44, C:0.15, G:0.04, T:0.36
Consensus pattern (126 bp):
CATAACTCACATAACTAAATTAATTTATATTATACATTAACTTGTCGGACTTGCATAACTTATAT
AATACTTAACTTACATAATACATAACTTACATAATAACATAATAAGTTACATAATATTATA
Found at i:17407448 original size:41 final size:43
Alignment explanation
Indices: 17407403--17407590 Score: 137
Period size: 41 Copynumber: 4.5 Consensus size: 43
17407393 AACTTACATA
17407403 ATACATAACTTACATAA-TAACATAATAAGTTACATA-ATATT
1 ATACATAACTTACATAACTAACATAATAAGTTACATACATATT
* * * * *
17407444 ATACATAACTCACATAACTAA-AT--TAATTTATATTATACATT
1 ATACATAACTTACATAACTAACATAATAAGTTACA-TACATATT
* * * * * *
17407485 A-ACTTGTAGGACTTGCATAACTTATATAAT-ACTTAACTTACATA--
1 ATAC--ATA--ACTTACATAACTAACATAATAAGTT-ACATACATATT
17407529 ATACATAACTTACATAA-TAACATAATAAGTTACATA-ATATT
1 ATACATAACTTACATAACTAACATAATAAGTTACATACATATT
*
17407570 ATACATAACTGACATAACTAA
1 ATACATAACTTACATAACTAA
17407591 ATTAATTTAT
Statistics
Matches: 111, Mismatches: 20, Indels: 31
0.69 0.12 0.19
Matches are distributed among these distances:
39 10 0.09
40 15 0.14
41 51 0.46
42 8 0.07
43 2 0.02
44 12 0.11
45 4 0.04
46 7 0.06
47 2 0.02
ACGTcount: A:0.47, C:0.14, G:0.04, T:0.35
Consensus pattern (43 bp):
ATACATAACTTACATAACTAACATAATAAGTTACATACATATT
Found at i:17407639 original size:9 final size:9
Alignment explanation
Indices: 17407621--17407723 Score: 105
Period size: 9 Copynumber: 12.3 Consensus size: 9
17407611 AACTTGTCGG
*
17407621 ACTTGCATA
1 ACTTACATA
*
17407630 ACTTATATA
1 ACTTACATA
*
17407639 A--TACTTA
1 ACTTACATA
17407646 ACTTACATA
1 ACTTACATA
*
17407655 ACGTACATA
1 ACTTACATA
17407664 ACTTACATA
1 ACTTACATA
17407673 A--TACATA
1 ACTTACATA
17407680 ACTTACATA
1 ACTTACATA
17407689 A--TACATA
1 ACTTACATA
*
17407696 ACTTACGTA
1 ACTTACATA
17407705 A--TACATA
1 ACTTACATA
17407712 ACTTACATA
1 ACTTACATA
17407721 ACT
1 ACT
17407724 CATATATACT
Statistics
Matches: 77, Mismatches: 9, Indels: 16
0.75 0.09 0.16
Matches are distributed among these distances:
7 25 0.32
9 52 0.68
ACGTcount: A:0.45, C:0.19, G:0.03, T:0.33
Consensus pattern (9 bp):
ACTTACATA
Found at i:17407727 original size:16 final size:16
Alignment explanation
Indices: 17407157--17407721 Score: 169
Period size: 16 Copynumber: 34.7 Consensus size: 16
17407147 CTTATATATA
17407157 AACTTACATAATACAT
1 AACTTACATAATACAT
17407173 AACTTATTACATAATACAT
1 AAC---TTACATAATACAT
*
17407192 AACTT--AT-ATATA-
1 AACTTACATAATACAT
17407204 AACTTACATAATACAT
1 AACTTACATAATACAT
17407220 AACTTATTACATAATACAT
1 AAC---TTACATAATACAT
*
17407239 AACTT--AT-ATATA-
1 AACTTACATAATACAT
17407251 AACTTACATAATACAT
1 AACTTACATAATACAT
*
17407267 AACTTA-TTACATA-AT
1 AACTTACATA-ATACAT
* * *
17407282 AAGTTACGTAACTTATAT
1 AACTTACATAA--TACAT
* *
17407300 AGAAACTTATATAACAACTTGCAT
1 ---AACTTACAT---AA--TACAT
* *
17407324 AACTCACATAACTAAATT
1 AACTTACATAA-TACA-T
* * *
17407342 AATTTATATTATACATT
1 AACTTACATAATACA-T
* ** * *
17407359 AACTTGTCGGACTTGCAT
1 AACTT-ACATA-ATACAT
* *
17407377 AACTTATATAATACTT
1 AACTTACATAATACAT
17407393 AACTTACATAATACAT
1 AACTTACATAATACAT
17407409 AACTTACATAATAACAT
1 AACTTACATAAT-ACAT
17407426 AA--TA-AGT--TACAT
1 AACTTACA-TAATACAT
*
17407438 AA--T--ATTATACAT
1 AACTTACATAATACAT
* *
17407450 AACTCACATAACTAAATT
1 AACTTACATAA-TACA-T
* * *
17407468 AATTTATATTATACATT
1 AACTTACATAATACA-T
** * * *
17407485 AACTTGTAGGACTTGCAT
1 AACTTACA-TA-ATACAT
* *
17407503 AACTTATATAATACTT
1 AACTTACATAATACAT
17407519 AACTTACATAATACAT
1 AACTTACATAATACAT
17407535 AACTTACATAATAACAT
1 AACTTACATAAT-ACAT
17407552 AA--TA-AGT--TACAT
1 AACTTACA-TAATACAT
*
17407564 AA--T--ATTATACAT
1 AACTTACATAATACAT
* *
17407576 AACTGACATAACTAAATT
1 AACTTACATAA-TACA-T
* * *
17407594 AATTTATATTATACATT
1 AACTTACATAATACA-T
* ** * *
17407611 AACTTGTCGGACTTGCAT
1 AACTT-ACATA-ATACAT
* *
17407629 AACTTATATAATACTT
1 AACTTACATAATACAT
17407645 AACTTACATAACGTACAT
1 AACTTACATAA--TACAT
17407663 AACTTACATAATACAT
1 AACTTACATAATACAT
17407679 AACTTACATAATACAT
1 AACTTACATAATACAT
*
17407695 AACTTACGTAATACAT
1 AACTTACATAATACAT
17407711 AACTTACATAA
1 AACTTACATAA
17407722 CTCATATATA
Statistics
Matches: 408, Mismatches: 87, Indels: 108
0.68 0.14 0.18
Matches are distributed among these distances:
10 2 0.00
11 2 0.00
12 38 0.09
13 10 0.02
14 10 0.02
15 24 0.06
16 144 0.35
17 54 0.13
18 63 0.15
19 41 0.10
21 13 0.03
24 7 0.02
ACGTcount: A:0.45, C:0.15, G:0.04, T:0.36
Consensus pattern (16 bp):
AACTTACATAATACAT
Found at i:17413919 original size:42 final size:42
Alignment explanation
Indices: 17413860--17414080 Score: 148
Period size: 42 Copynumber: 5.2 Consensus size: 42
17413850 CATATATAGT
* *
17413860 GGCGTTTGTAAATAAAGCGCCGCTATAGGCT-AATGTATTTGC
1 GGCGTTTGT-AGTAAAGCGCCGCTAAAGGCTCAATGTATTTGC
* *** *
17413902 GGCGTTTGTAGTGAAAGCGTCGCTAAAAAATCAGA-GTTTTTAGC
1 GGCGTTTGTAGT-AAAGCGCCGCTAAAGGCTCA-ATGTATTT-GC
* * * * *
17413946 GGCGTTTGTTGTCAAAGCGCTGCTAAAGG-TCAAGGTATCTAGT
1 GGCGTTTGTAGT-AAAGCGCCGCTAAAGGCTCAATGTAT-TTGC
* * * *
17413989 GGCGTTTGTAAATAAAGTGCCGCTATAGGCT-AATGTTTTTGC
1 GGCGTTTGT-AGTAAAGCGCCGCTAAAGGCTCAATGTATTTGC
* *
17414031 GGCGTTTTTAGTGAAAGCGCCGCTAAAGG-TCAA-GCTCTTTAGC
1 GGCGTTTGTAGT-AAAGCGCCGCTAAAGGCTCAATG-TATTT-GC
17414074 GGCGTTT
1 GGCGTTT
17414081 TAGGTTTAAG
Statistics
Matches: 137, Mismatches: 30, Indels: 23
0.72 0.16 0.12
Matches are distributed among these distances:
41 6 0.04
42 53 0.39
43 49 0.36
44 29 0.21
ACGTcount: A:0.24, C:0.16, G:0.28, T:0.31
Consensus pattern (42 bp):
GGCGTTTGTAGTAAAGCGCCGCTAAAGGCTCAATGTATTTGC
Found at i:17413943 original size:129 final size:130
Alignment explanation
Indices: 17413748--17414057 Score: 396
Period size: 129 Copynumber: 2.4 Consensus size: 130
17413738 TGGGAAAATT
* * * * *
17413748 GCCGCTAAAGGTTAATGCATTTAGTGGCGTTTTTA-TGAAAAGCGTCGCT-AAAAGCCAAGGTCT
1 GCCGCTATAGGCTAATGTATTT-GCGGCGTTTTTAGTG-AAAGCGTCGCTAAAAAACCAAGGTCT
17413811 TTTAGCGGCGTTCG-TGCCCAAAGCACCGCTAAAGGTCAACATATATAGTGGCGTTTGTAAATAA
64 TTTAGCGGCGTTCGTTG-CCAAAGCACCGCTAAAGGTCAACATATATAGTGGCGTTTGTAAATAA
17413875 AGC
128 AGC
* *
17413878 GCCGCTATAGGCTAATGTATTTGCGGCGTTTGTAGTGAAAGCGTCGCTAAAAAATC-AGAGT-TT
1 GCCGCTATAGGCTAATGTATTTGCGGCGTTTTTAGTGAAAGCGTCGCTAAAAAACCAAG-GTCTT
* * * * ** *
17413941 TTAGCGGCGTTTGTTGTCAAAGCGCTGCTAAAGGTCAAGGTATCTAGTGGCGTTTGTAAATAAAG
65 TTAGCGGCGTTCGTTGCCAAAGCACCGCTAAAGGTCAACATATATAGTGGCGTTTGTAAATAAAG
*
17414006 T
130 C
* *
17414007 GCCGCTATAGGCTAATGTTTTTGCGGCGTTTTTAGTGAAAGCGCCGCTAAA
1 GCCGCTATAGGCTAATGTATTTGCGGCGTTTTTAGTGAAAGCGTCGCTAAA
17414058 GGTCAAGCTC
Statistics
Matches: 158, Mismatches: 18, Indels: 9
0.85 0.10 0.05
Matches are distributed among these distances:
129 128 0.81
130 30 0.19
ACGTcount: A:0.27, C:0.17, G:0.26, T:0.29
Consensus pattern (130 bp):
GCCGCTATAGGCTAATGTATTTGCGGCGTTTTTAGTGAAAGCGTCGCTAAAAAACCAAGGTCTTT
TAGCGGCGTTCGTTGCCAAAGCACCGCTAAAGGTCAACATATATAGTGGCGTTTGTAAATAAAGC
Found at i:17414643 original size:31 final size:32
Alignment explanation
Indices: 17414582--17414655 Score: 107
Period size: 31 Copynumber: 2.4 Consensus size: 32
17414572 TACAATAAAT
**
17414582 GTCACCCAACTATTATTTTTTTCTCTTTTTTG
1 GTCACCCAACTATTATAATTTTCTCTTTTTTG
*
17414614 GTCACCCAACTATT-TAATTTTGTCTTTTTTG
1 GTCACCCAACTATTATAATTTTCTCTTTTTTG
17414645 GTCA-CCAACTA
1 GTCACCCAACTA
17414656 ACAACGTAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 2
0.89 0.07 0.05
Matches are distributed among these distances:
30 7 0.18
31 18 0.46
32 14 0.36
ACGTcount: A:0.20, C:0.23, G:0.08, T:0.49
Consensus pattern (32 bp):
GTCACCCAACTATTATAATTTTCTCTTTTTTG
Found at i:17414798 original size:54 final size:56
Alignment explanation
Indices: 17414720--17414826 Score: 150
Period size: 54 Copynumber: 1.9 Consensus size: 56
17414710 GACAAAATGG
* *
17414720 AATAGTTGAATGATCATTTTTGTAACTTATT-ATAATTTGGTGA-TAAAAAAATACT
1 AATAATTGAATGATCATTTTTGTAACTT-TTCATAATTAGGTGACTAAAAAAATACT
17414775 AATAATTGAATGA-C-TATTTTGTAACTTTTCATAATTAGGTGACTAAAAAAAT
1 AATAATTGAATGATCAT-TTTTGTAACTTTTCATAATTAGGTGACTAAAAAAAT
17414827 TAAAAAACCA
Statistics
Matches: 47, Mismatches: 2, Indels: 6
0.85 0.04 0.11
Matches are distributed among these distances:
53 3 0.06
54 23 0.49
55 21 0.45
ACGTcount: A:0.41, C:0.07, G:0.12, T:0.40
Consensus pattern (56 bp):
AATAATTGAATGATCATTTTTGTAACTTTTCATAATTAGGTGACTAAAAAAATACT
Found at i:17425111 original size:43 final size:44
Alignment explanation
Indices: 17425064--17425211 Score: 140
Period size: 43 Copynumber: 3.4 Consensus size: 44
17425054 AAGTTGTTCA
* * * * *
17425064 ATTTAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGGTTAATG-C
1 ATTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAAGTCAAGGTC
* * * *
17425107 ATTTAGTGACGTTT-TTATGAAAAGCGTCGCTAAAAGTCAAGGTC
1 ATTTAGCGGCGTTTGTGA-GAAAAGCGCCGCTAAAAGTCAAGGTC
* * *
17425151 TTTTCGCGGCGTTTGTGAGAAAAGCGCCGCTAAAAGTCAGGGT-
1 ATTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAAGTCAAGGTC
*
17425194 TTTTAGCGGCGCTTTGTG
1 ATTTAGCGGCG-TTTGTG
17425212 CAAAGCACCG
Statistics
Matches: 84, Mismatches: 17, Indels: 7
0.78 0.16 0.06
Matches are distributed among these distances:
42 1 0.01
43 41 0.49
44 40 0.48
45 2 0.02
ACGTcount: A:0.24, C:0.16, G:0.30, T:0.30
Consensus pattern (44 bp):
ATTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAAGTCAAGGTC
Found at i:17425295 original size:43 final size:43
Alignment explanation
Indices: 17425230--17425455 Score: 255
Period size: 43 Copynumber: 5.2 Consensus size: 43
17425220 CGCTATTATC
17425230 TTTAGCGGCGCTTAAGTCACAAACGCCGCTAAAGAGCTTGACT
1 TTTAGCGGCGCTTAAGTCACAAACGCCGCTAAAGAGCTTGACT
* * * * * *
17425273 TTTAGCGGCGCTTCCACT-ACAAACGCCGCAAAATACCTTGACC
1 TTTAGCGGCGCTT-AAGTCACAAACGCCGCTAAAGAGCTTGACT
* * *
17425316 TTTAGCGGCGCTT-TGATCACAAACGCCGCTAAA-AGGCACT-AGGT
1 TTTAGCGGCGCTTAAG-TCACAAACGCCGCTAAAGA-GC-TTGA-CT
17425360 TTTAGCGGCGCTTAAGTCACAAACGCCGCTAAAGAGCTTGACT
1 TTTAGCGGCGCTTAAGTCACAAACGCCGCTAAAGAGCTTGACT
* * *
17425403 TTTAGCGGCGCTTAAGTCACAAACACCGCTAAAG-GCCGTGACC
1 TTTAGCGGCGCTTAAGTCACAAACGCCGCTAAAGAG-CTTGACT
17425446 TTTAGCGGCG
1 TTTAGCGGCG
17425456 TTTGTTTCTA
Statistics
Matches: 154, Mismatches: 19, Indels: 20
0.80 0.10 0.10
Matches are distributed among these distances:
42 3 0.02
43 113 0.73
44 36 0.23
45 2 0.01
ACGTcount: A:0.27, C:0.28, G:0.23, T:0.22
Consensus pattern (43 bp):
TTTAGCGGCGCTTAAGTCACAAACGCCGCTAAAGAGCTTGACT
Found at i:17425471 original size:87 final size:85
Alignment explanation
Indices: 17425229--17425480 Score: 267
Period size: 87 Copynumber: 2.9 Consensus size: 85
17425219 CCGCTATTAT
* * *
17425229 CTTTAGCGGCGCTTAAGTCACAAACGCCGCTAAAGAGCTTGACTTTTAGCGGCGCTTCCACTACA
1 CTTTAGCGGCGCTTAAGTCACAAACGCCGCTAAAG-GCCTGACTTTTAGCGGCGCTTACTCTACA
* *
17425294 AACGCCGCAAAATACCTTGAC
65 AACGCCGCTAAAGACCTTGAC
* * *
17425315 CTTTAGCGGCGCTT-TGATCACAAACGCCGCTAAAAGGCACT-AGGTTTTAGCGGCGCTTAAGTC
1 CTTTAGCGGCGCTTAAG-TCACAAACGCCGCT-AAAGGC-CTGA-CTTTTAGCGGCGCTT-ACTC
*
17425378 -ACAAACGCCGCTAAAGAGCTTGAC
61 TACAAACGCCGCTAAAGACCTTGAC
* * * * ** *
17425402 TTTTAGCGGCGCTTAAGTCACAAACACCGCTAAAGGCCGTGACCTTTAGCGGCGTTTGTTTCTAT
1 CTTTAGCGGCGCTTAAGTCACAAACGCCGCTAAAGGCC-TGACTTTTAGCGGCGCTT-ACTCTAC
17425467 AAACGCCGCTAAAG
64 AAACGCCGCTAAAG
17425481 TTAACGACGC
Statistics
Matches: 138, Mismatches: 19, Indels: 17
0.79 0.11 0.10
Matches are distributed among these distances:
85 2 0.01
86 52 0.38
87 82 0.59
88 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.23
Consensus pattern (85 bp):
CTTTAGCGGCGCTTAAGTCACAAACGCCGCTAAAGGCCTGACTTTTAGCGGCGCTTACTCTACAA
ACGCCGCTAAAGACCTTGAC
Found at i:17425542 original size:14 final size:14
Alignment explanation
Indices: 17425523--17425561 Score: 78
Period size: 14 Copynumber: 2.8 Consensus size: 14
17425513 TTATTTTACT
17425523 GATTCGTAAAAATC
1 GATTCGTAAAAATC
17425537 GATTCGTAAAAATC
1 GATTCGTAAAAATC
17425551 GATTCGTAAAA
1 GATTCGTAAAA
17425562 GAAATTTTTG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.44, C:0.13, G:0.15, T:0.28
Consensus pattern (14 bp):
GATTCGTAAAAATC
Found at i:17430379 original size:4 final size:4
Alignment explanation
Indices: 17430370--17430396 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
17430360 CTTTATCAAT
17430370 TTTA TTTA TTTA TTTA TTTA TTTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTT
17430397 TATCATTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.22, C:0.00, G:0.00, T:0.78
Consensus pattern (4 bp):
TTTA
Found at i:17432025 original size:109 final size:109
Alignment explanation
Indices: 17431703--17432237 Score: 851
Period size: 109 Copynumber: 4.9 Consensus size: 109
17431693 AATTTTTTTT
*
17431703 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGTTGGGTTTCGATT
1 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATT
*
17431768 TTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAAATTTTA
66 TTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAAATTTCA
* * * * *
17431812 ACATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAATCGTG-CATTATGTGCTGGGTTTCGTTT
1 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATT
*
17431876 TTTCTCGTTCGACCATATAGCCAAATATCCTTTTAAAAATTTCA
66 TTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAAATTTCA
*
17431920 ACATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATT
1 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATT
* *
17431985 TTTCTCGTTCGAACAAATAACCAAATATCCTTTTAAAAATTTCA
66 TTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAAATTTCA
*
17432029 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTTGATT
1 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATT
* * *
17432094 TTTCTCGCTCGACCAAATAGCTAAATATCCTTTCAAAAATTTCA
66 TTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAAATTTCA
* * * * *
17432138 AAATAAGGTAATGTTTTGCGTTTGGAAACTCGAGAAAACTTGCTCTAATGCGCTGGGTTTCGA--
1 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATT
* *
17432201 TTTCTCGTTGGACCAAATAGCCAAATATCCTCTTAAA
66 TTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAA
17432238 TCTTAATCCA
Statistics
Matches: 392, Mismatches: 33, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
107 32 0.08
108 101 0.26
109 259 0.66
ACGTcount: A:0.30, C:0.17, G:0.19, T:0.35
Consensus pattern (109 bp):
AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATT
TTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAAATTTCA
Found at i:17435453 original size:12 final size:12
Alignment explanation
Indices: 17435436--17435460 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17435426 GGTGTTCAGT
17435436 CGGTTAACCGAC
1 CGGTTAACCGAC
17435448 CGGTTAACCGAC
1 CGGTTAACCGAC
17435460 C
1 C
17435461 CGAAATTCTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.24, C:0.36, G:0.24, T:0.16
Consensus pattern (12 bp):
CGGTTAACCGAC
Found at i:17435637 original size:9 final size:9
Alignment explanation
Indices: 17435621--17435775 Score: 193
Period size: 9 Copynumber: 16.6 Consensus size: 9
17435611 TTTGGTTAAA
17435621 AATTACCCG
1 AATTACCCG
*
17435630 ACTTACCCG
1 AATTACCCG
*
17435639 ACTTACCCG
1 AATTACCCG
17435648 AATTACCCG
1 AATTACCCG
17435657 AATTACCCG
1 AATTACCCG
*
17435666 ACTTACCCG
1 AATTACCCG
17435675 AATTACCCG
1 AATTACCCG
17435684 AATTACCCG
1 AATTACCCG
17435693 AAAATTACCCG
1 --AATTACCCG
17435704 AATTACCCG
1 AATTACCCG
* *
17435713 AAAATGACCCA
1 --AATTACCCG
*
17435724 AATTACCCA
1 AATTACCCG
17435733 AATTACCCG
1 AATTACCCG
*
17435742 AAAATTACCCA
1 --AATTACCCG
17435753 AATTACCCG
1 AATTACCCG
17435762 AATTACCCG
1 AATTACCCG
17435771 AATTA
1 AATTA
17435776 AATCACTACA
Statistics
Matches: 130, Mismatches: 10, Indels: 12
0.86 0.07 0.08
Matches are distributed among these distances:
9 106 0.82
11 24 0.18
ACGTcount: A:0.37, C:0.33, G:0.09, T:0.21
Consensus pattern (9 bp):
AATTACCCG
Found at i:17435710 original size:29 final size:27
Alignment explanation
Indices: 17435621--17435775 Score: 193
Period size: 29 Copynumber: 5.5 Consensus size: 27
17435611 TTTGGTTAAA
* *
17435621 AATTACCCGACTTACCCGACTTACCCG
1 AATTACCCGAATTACCCGAATTACCCG
*
17435648 AATTACCCGAATTACCCGACTTACCCG
1 AATTACCCGAATTACCCGAATTACCCG
17435675 AATTACCCGAATTACCCGAAAATTACCCG
1 AATTACCCGAATTACCCG--AATTACCCG
* * *
17435704 AATTACCCGAAAATGACCCAAATTACCCA
1 AATTACCCG--AATTACCCGAATTACCCG
*
17435733 AATTACCCGAAAATTACCCAAATTACCCG
1 AATTACCCG--AATTACCCGAATTACCCG
17435762 AATTACCCGAATTA
1 AATTACCCGAATTA
17435776 AATCACTACA
Statistics
Matches: 117, Mismatches: 7, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
27 49 0.42
29 61 0.52
31 7 0.06
ACGTcount: A:0.37, C:0.33, G:0.09, T:0.21
Consensus pattern (27 bp):
AATTACCCGAATTACCCGAATTACCCG
Found at i:17435804 original size:17 final size:17
Alignment explanation
Indices: 17435782--17435879 Score: 52
Period size: 17 Copynumber: 5.4 Consensus size: 17
17435772 ATTAAATCAC
17435782 TACATAATTAAAAACAT
1 TACATAATTAAAAACAT
** * *
17435799 TACATAAATATTTGAATCAC
1 TACAT--A-ATTAAAAACAT
*
17435819 TACATAATTAAAAATAT
1 TACATAATTAAAAACAT
** * *
17435836 TACATAAGTCTTTGAATCAC
1 TACATAA---TTAAAAACAT
*
17435856 TACATAATTAAAAATAT
1 TACATAATTAAAAACAT
17435873 TACATAA
1 TACATAA
17435880 GTCTTGAATT
Statistics
Matches: 56, Mismatches: 19, Indels: 12
0.64 0.22 0.14
Matches are distributed among these distances:
17 30 0.54
18 1 0.02
19 1 0.02
20 24 0.43
ACGTcount: A:0.51, C:0.12, G:0.03, T:0.34
Consensus pattern (17 bp):
TACATAATTAAAAACAT
Found at i:17435880 original size:37 final size:37
Alignment explanation
Indices: 17435776--17435888 Score: 192
Period size: 37 Copynumber: 3.1 Consensus size: 37
17435766 ACCCGAATTA
* * *
17435776 AATCACTACATAATTAAAAACATTACATAAATATTTG
1 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
17435813 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
1 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
17435850 AATCACTACATAATTAAAAATATTACATAAGTC-TTG
1 AATCACTACATAATTAAAAATATTACATAAGTCTTTG
17435886 AAT
1 AAT
17435889 TAACACATAA
Statistics
Matches: 73, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
36 6 0.08
37 67 0.92
ACGTcount: A:0.49, C:0.13, G:0.04, T:0.34
Consensus pattern (37 bp):
AATCACTACATAATTAAAAATATTACATAAGTCTTTG
Found at i:17435956 original size:24 final size:24
Alignment explanation
Indices: 17435929--17435987 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
17435919 ATTCTCCATT
*
17435929 TATATCCATTTCATCTTTCCAAAA
1 TATATCCATTTCATCTCTCCAAAA
17435953 TATATCCATTTCATCTCTCCAAAA
1 TATATCCATTTCATCTCTCCAAAA
*
17435977 TATCTCCATTT
1 TATATCCATTT
17435988 GCATTAAACC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 33 1.00
ACGTcount: A:0.31, C:0.27, G:0.00, T:0.42
Consensus pattern (24 bp):
TATATCCATTTCATCTCTCCAAAA
Found at i:17445962 original size:8 final size:8
Alignment explanation
Indices: 17445949--17445973 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
17445939 AAATGTTCGC
17445949 ATTTAATT
1 ATTTAATT
17445957 ATTTAATT
1 ATTTAATT
17445965 ATTTAATT
1 ATTTAATT
17445973 A
1 A
17445974 ACAATATAGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
ATTTAATT
Found at i:17446108 original size:27 final size:27
Alignment explanation
Indices: 17446078--17446130 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
17446068 AAAGATGAAA
17446078 GAAAAAATTAAGACAATAGTATACAAT
1 GAAAAAATTAAGACAATAGTATACAAT
17446105 GAAAAAATTAAGACAATAGTATACAA
1 GAAAAAATTAAGACAATAGTATACAA
17446131 CGACATAGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.60, C:0.08, G:0.11, T:0.21
Consensus pattern (27 bp):
GAAAAAATTAAGACAATAGTATACAAT
Found at i:17446389 original size:19 final size:19
Alignment explanation
Indices: 17446365--17446416 Score: 68
Period size: 20 Copynumber: 2.7 Consensus size: 19
17446355 TTATTACTAA
17446365 CATAAAAGTAAGCAAAACC
1 CATAAAAGTAAGCAAAACC
** *
17446384 CATAAATAAAAAGAAAAACC
1 CATAAA-AGTAAGCAAAACC
17446404 CATAAAAGTAAGC
1 CATAAAAGTAAGC
17446417 TGAAAGCACA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.62, C:0.17, G:0.10, T:0.12
Consensus pattern (19 bp):
CATAAAAGTAAGCAAAACC
Found at i:17446920 original size:18 final size:19
Alignment explanation
Indices: 17446885--17446933 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
17446875 AACCGACCGC
17446885 TTAACCGAATTCGGTCGG-
1 TTAACCGAATTCGGTCGGT
***
17446903 TTAACCGAATTTTTTCGGTT
1 TTAACCGAATTCGGTCGG-T
17446923 TTAACCGAATT
1 TTAACCGAATT
17446934 ATGCACACCC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
18 15 0.58
20 11 0.42
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (19 bp):
TTAACCGAATTCGGTCGGT
Found at i:17447481 original size:21 final size:20
Alignment explanation
Indices: 17447451--17447515 Score: 60
Period size: 21 Copynumber: 3.1 Consensus size: 20
17447441 TAAAAAAGAG
*
17447451 AGAGAGAAAAAAGAAGGAAAA
1 AGAGAAAAAAAAGAA-GAAAA
* *
17447472 AGAGAAAAAATAGAAAGAAGA
1 AGAGAAAAAAAAG-AAGAAAA
*
17447493 AGAAGAAAAGAAA-AAGAAAA
1 AG-AGAAAAAAAAGAAGAAAA
17447513 AGA
1 AGA
17447516 AAAGGAGAGG
Statistics
Matches: 36, Mismatches: 6, Indels: 6
0.75 0.12 0.12
Matches are distributed among these distances:
19 1 0.03
20 8 0.22
21 17 0.47
22 10 0.28
ACGTcount: A:0.74, C:0.00, G:0.25, T:0.02
Consensus pattern (20 bp):
AGAGAAAAAAAAGAAGAAAA
Found at i:17447497 original size:6 final size:6
Alignment explanation
Indices: 17447467--17447518 Score: 54
Period size: 6 Copynumber: 8.8 Consensus size: 6
17447457 AAAAAAGAAG
* * *
17447467 GAAAAA GAGAAA -AAATA GAAAGAA GAAGAA G-AAAA GAAAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAA-AA GAAAAA GAAAAA GAAAAA GAAAAA
17447514 GAAAA
1 GAAAA
17447519 GGAGAGGCCA
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
5 7 0.19
6 26 0.70
7 4 0.11
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (6 bp):
GAAAAA
Found at i:17447879 original size:22 final size:22
Alignment explanation
Indices: 17447851--17447897 Score: 94
Period size: 22 Copynumber: 2.1 Consensus size: 22
17447841 GAATTTGTTG
17447851 TTCTTGGAATACTTCTTTCTTT
1 TTCTTGGAATACTTCTTTCTTT
17447873 TTCTTGGAATACTTCTTTCTTT
1 TTCTTGGAATACTTCTTTCTTT
17447895 TTC
1 TTC
17447898 AAGATACGTG
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:0.13, C:0.19, G:0.09, T:0.60
Consensus pattern (22 bp):
TTCTTGGAATACTTCTTTCTTT
Found at i:17449023 original size:132 final size:131
Alignment explanation
Indices: 17448793--17449289 Score: 649
Period size: 132 Copynumber: 3.8 Consensus size: 131
17448783 TGGAGCCATT
* * * * *
17448793 AGTCCTATCTCCCTGATCAGCAGTGGAGTAGATTGAAGATTGTAGATTCTGTCTCCCTAAGCAGT
1 AGTCCTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCCTGTCTCCCTAAGCAGT
* * * *
17448858 AGTGAAGCAGATTGAAGATGGTGAATCTTATCTTCCCGAGATAGTGGAGAAACAGATTTAAGCCA
66 AGTGAAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAG-TAGTGGAGAAGCAGATTTAAACCA
**
17448923 TA
130 CC
* * * *
17448925 AATCTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATTCTGTCTCCCTAAGAAGT
1 AGTCCTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCCTGTCTCCCTAAGCAGT
* *
17448990 AGTGAAACAGATCGAAGATGGTGAATCTTATCTTCCCAAGTTAGTGGAGAAGTAGATTTAAACCA
66 AGTGAAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAG-TAGTGGAGAAGCAGATTTAAACCA
17449055 CC
130 CC
* *
17449057 AGTCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGATCCTGTCTCCCTAAGTAGT
1 AGTCCTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCCTGTCTCCCTAAGCAGT
* * *
17449122 AGTGGAGCAGATCAAAGACGGCT-AATCTTATCTTCCCAATGTAGTAGG-GAAGCAGATTTAAAC
66 AGTGAAGCAGATCGAAGATGG-TGAATCTTATCTTCCCAA-GTAGT-GGAGAAGCAGATTTAAAC
17449185 CACC
128 CACC
* * * * *
17449189 AGTCCTATCTCCCTAAGTAGTAGTGGAGTAGGTCGAAGATTGTAAATCCTGTCTCCCTAAGCAGT
1 AGTCCTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCCTGTCTCCCTAAGCAGT
* * * *
17449254 AGTGGAGCAGATCGAAGATAGCGAATTTTA-CTTCCC
66 AGTGAAGCAGATCGAAGATGGTGAATCTTATCTTCCC
17449290 TAGCGGTGCA
Statistics
Matches: 325, Mismatches: 36, Indels: 9
0.88 0.10 0.02
Matches are distributed among these distances:
131 6 0.02
132 315 0.97
133 4 0.01
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (131 bp):
AGTCCTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGCAGATCCTGTCTCCCTAAGCAGT
AGTGAAGCAGATCGAAGATGGTGAATCTTATCTTCCCAAGTAGTGGAGAAGCAGATTTAAACCAC
C
Found at i:17449115 original size:44 final size:44
Alignment explanation
Indices: 17448795--17449272 Score: 166
Period size: 44 Copynumber: 10.9 Consensus size: 44
17448785 GAGCCATTAG
* * *
17448795 TCCTATCTCCCTGA-TCAGCAGTGGAGTAGATTGAAGATTGTAGA
1 TCCTATCTCCCTAAGT-AGTAGTGGAGTAGATTGAAGATTGCAGA
* * * * *
17448839 TTCTGTCTCCCTAAGCAGTAGTGAAGCAGATTGAAGATGGTG-A-A
1 TCCTATCTCCCTAAGTAGTAGTGGAGTAGATTGAAGAT--TGCAGA
* * * * *
17448883 TCTTATCTTCCC-GAG-A-TAGTGGAGAAACAGATTTAAGCCA-T--AAA
1 TCCTATC-TCCCTAAGTAGTAGTGGAG---TAGATTGAAG--ATTGCAGA
* * * *
17448927 TCTTATCTCCCTAAGCAGCAGTGGAGTAGGTTGAAGATTGCAGA
1 TCCTATCTCCCTAAGTAGTAGTGGAGTAGATTGAAGATTGCAGA
* * * * ** *
17448971 TTCTGTCTCCCTAAGAAGTAGTGAAACAGATCGAAGATGGTG-A-A
1 TCCTATCTCCCTAAGTAGTAGTGGAGTAGATTGAAGAT--TGCAGA
* * * * * ***
17449015 TCTTATCTTCCC-AAGTTAGTGGAGAAGTAGATTTAA-ACCACCAG-
1 TCCTATC-TCCCTAAG-TAGTAGTGGAGTAGATTGAAGA-TTGCAGA
* *
17449059 TCCTATCTCCCTAAGCAGTAGTGGAGTAGGTTGAAGATTGCAGA
1 TCCTATCTCCCTAAGTAGTAGTGGAGTAGATTGAAGATTGCAGA
* * ** **
17449103 TCCTGTCTCCCTAAGTAGTAGTGGAGCAGATCAAAGACGGCTA-A
1 TCCTATCTCCCTAAGTAGTAGTGGAGTAGATTGAAGATTGC-AGA
* * * ***
17449147 TCTTATCTTCCC-AATGTAGTAG-GGAAGCAGATTTAA-ACCACCAG-
1 TCCTATC-TCCCTAA-GTAGTAGTGG-AGTAGATTGAAGA-TTGCAGA
* * * *
17449191 TCCTATCTCCCTAAGTAGTAGTGGAGTAGGTCGAAGATTGTAAA
1 TCCTATCTCCCTAAGTAGTAGTGGAGTAGATTGAAGATTGCAGA
* * * *
17449235 TCCTGTCTCCCTAAGCAGTAGTGGAGCAGATCGAAGAT
1 TCCTATCTCCCTAAGTAGTAGTGGAGTAGATTGAAGAT
17449273 AGCGAATTTT
Statistics
Matches: 318, Mismatches: 80, Indels: 72
0.68 0.17 0.15
Matches are distributed among these distances:
41 1 0.00
42 8 0.03
43 53 0.17
44 188 0.59
45 56 0.18
46 11 0.03
47 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (44 bp):
TCCTATCTCCCTAAGTAGTAGTGGAGTAGATTGAAGATTGCAGA
Found at i:17449604 original size:99 final size:99
Alignment explanation
Indices: 17449274--17449965 Score: 947
Period size: 99 Copynumber: 7.0 Consensus size: 99
17449264 ATCGAAGATA
* * * * * *
17449274 GCGAATTTTACTTCCCTA-GCGGTGCAGTGGAATAGATTGAAGCTACAATGACGAATCTGGCTTC
1 GCGAATCTTACTTCCC-AGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGCAAATCTCGCTTC
* * *
17449338 CTCGATATTGCAATTAAAAGATTGAGGCCTCAACG
65 CCCGACATTGCAATTAAAAGATTGAGGCCACAACG
* * * * * * * * *
17449373 ACAAATCTTATTTCCCTGGTGGTGCAGTAGAGCAGATTGAAGCTACAACTGCAAATCTTGCTTCC
1 GCGAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGCAAATCTCGCTTCC
* *
17449438 CTGACATTGCAATTAAAAAATTTGAGGCCACAACG
66 CCGACATTGCAATTAAAAGA-TTGAGGCCACAACG
* *
17449473 GCGAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTGAAGCTACAACGACAAATCTTGCTTCC
1 GCGAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGCAAATCTCGCTTCC
*
17449538 CCGACATTGCAATTAAGAGATTGAGGCCACAACG
66 CCGACATTGCAATTAAAAGATTGAGGCCACAACG
*
17449572 GCGAATCTTACTTCCCAGGCGGTGTAGTGGAACAGATTGAAGCTACAACGGCAAATCTCGCTTCC
1 GCGAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGCAAATCTCGCTTCC
* * *
17449637 TCGACATTGCAATTAAAAAAATTGAAGCCACAACG
66 CCGACATTGCAATT-AAAAGATTGAGGCCACAACG
** * * * * * ** *
17449672 ATGAATCTTACTTCTCTGGCGGTGTAGTGGAATAGATTGAAGCTACAATGGTGAATCTTGC-TCC
1 GCGAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGCAAATCTCGCTTCC
*
17449736 CCTAACATTGCAATTAAAAAGATTGAGGCCACAACG
66 CC-GACATTGCAATT-AAAAGATTGAGGCCACAACG
* *
17449772 GCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAATGGCAAATCTCGCTTCC
1 GCGAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGCAAATCTCGCTTCC
17449837 CCGACATTGCAATTAAAAGATTGAGGCCACAACG
66 CCGACATTGCAATTAAAAGATTGAGGCCACAACG
* *
17449871 GCGAATCTTACTTCTCAGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTCGCTTCC
1 GCGAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGCAAATCTCGCTTCC
17449936 CCGACATTGCAATTAAAAGATTGAGGCCAC
66 CCGACATTGCAATTAAAAGATTGAGGCCAC
17449966 GAATAGATTG
Statistics
Matches: 524, Mismatches: 64, Indels: 10
0.88 0.11 0.02
Matches are distributed among these distances:
99 270 0.52
100 249 0.48
101 5 0.01
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.24
Consensus pattern (99 bp):
GCGAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGCAAATCTCGCTTCC
CCGACATTGCAATTAAAAGATTGAGGCCACAACG
Found at i:17449628 original size:199 final size:198
Alignment explanation
Indices: 17449274--17449965 Score: 985
Period size: 199 Copynumber: 3.5 Consensus size: 198
17449264 ATCGAAGATA
* * * *
17449274 GCGAATTTTACTTCCCTA-GCGGTGCAGTGGAATAGATTGAAGCTACAATGACGAATCTGGCTTC
1 GCGAATCTTACTTCCC-AGGCGGTGCAGTGGAACAGATTGAAGCTACAACGACGAATCTTGCTTC
* * * * * * * *
17449338 CTCGATATTGCAATTAAAAGATTGAGGCCTCAACGACAAATCTTATTTCCCTGGTGGTGCAGTAG
65 CCCGACATTGCAATTAAAAGATTGAGGCCACAACGGCGAATCTTACTTCCCTGGCGGTGCAGTGG
* * *
17449403 AGCAGATTGAAGCTACAACTGCAAATCTTGCTTCCCTGACATTGCAATTAAAAAATTTGAGGCCA
130 AACAGATTGAAGCTACAACGGCAAATCTCGCTTCCCTGACATTGCAATTAAAAAA-TTGAGGCCA
17449468 CAACG
194 CAACG
*
17449473 GCGAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTGAAGCTACAACGACAAATCTTGCTTCC
1 GCGAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTGAAGCTACAACGACGAATCTTGCTTCC
* * *
17449538 CCGACATTGCAATTAAGAGATTGAGGCCACAACGGCGAATCTTACTTCCCAGGCGGTGTAGTGGA
66 CCGACATTGCAATTAAAAGATTGAGGCCACAACGGCGAATCTTACTTCCCTGGCGGTGCAGTGGA
*
17449603 ACAGATTGAAGCTACAACGGCAAATCTCGCTT-CCTCGACATTGCAATTAAAAAAATTGAAGCCA
131 ACAGATTGAAGCTACAACGGCAAATCTCGCTTCCCT-GACATTGCAATT-AAAAAATTGAGGCCA
17449667 CAACG
194 CAACG
** * * * * * **
17449672 ATGAATCTTACTTCTCTGGCGGTGTAGTGGAATAGATTGAAGCTACAATGGTGAATCTTGC-TCC
1 GCGAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTGAAGCTACAACGACGAATCTTGCTTCC
*
17449736 CCTAACATTGCAATTAAAAAGATTGAGGCCACAACGGCGAATCTTACTTCCCTGGCGGTGCAGTG
66 CC-GACATTGCAATT-AAAAGATTGAGGCCACAACGGCGAATCTTACTTCCCTGGCGGTGCAGTG
* * *
17449801 GAACAGATTGAAGCTACAATGGCAAATCTCGCTTCCCCGACATTGCAATTAAAAGATTGAGGCCA
129 GAACAGATTGAAGCTACAACGGCAAATCTCGCTTCCCTGACATTGCAATTAAAAAATTGAGGCCA
17449866 CAACG
194 CAACG
* * *
17449871 GCGAATCTTACTTCTCAGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTCGCTTCC
1 GCGAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTGAAGCTACAACGACGAATCTTGCTTCC
17449936 CCGACATTGCAATTAAAAGATTGAGGCCAC
66 CCGACATTGCAATTAAAAGATTGAGGCCAC
17449966 GAATAGATTG
Statistics
Matches: 439, Mismatches: 47, Indels: 15
0.88 0.09 0.03
Matches are distributed among these distances:
198 25 0.06
199 310 0.71
200 102 0.23
201 2 0.00
ACGTcount: A:0.30, C:0.23, G:0.22, T:0.24
Consensus pattern (198 bp):
GCGAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTGAAGCTACAACGACGAATCTTGCTTCC
CCGACATTGCAATTAAAAGATTGAGGCCACAACGGCGAATCTTACTTCCCTGGCGGTGCAGTGGA
ACAGATTGAAGCTACAACGGCAAATCTCGCTTCCCTGACATTGCAATTAAAAAATTGAGGCCACA
ACG
Found at i:17449818 original size:299 final size:299
Alignment explanation
Indices: 17449274--17449953 Score: 1026
Period size: 299 Copynumber: 2.3 Consensus size: 299
17449264 ATCGAAGATA
* * * * *
17449274 GCGAATTTTACTTCCCTA-GCGGTGCAGTGGAATAGATTGAAGCTACAATGACGAATCTGGCTTC
1 GCGAATCTTACTTCCC-AGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTCGCTTC
* * * * * *
17449338 CTCGATATTGCAATT-AAAAGATTGAGGCCTCAACGACAAATCTTATTTCCCTGGTGGTGCAGTA
65 CTCGACATTGCAATTAAAAAAATTGAAGCCACAACGACAAATCTTACTTCCCTGGCGGTGCAGTA
* * *
17449402 GAGCAGATTGAAGCTACAACTGCAAATCTTGCTTCCCTGACATTGCAATTAAAAAATTTGAGGCC
130 GAACAGATTGAAGCTACAACTGCAAATCTTGCTCCCCTAACATTGCAATTAAAAAATTTGAGGCC
*
17449467 ACAACGGCGAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTGAAGCTACAACGACAAATCTT
195 ACAACGGCGAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTGAAGCTACAACGACAAATCTC
*
17449532 GCTTCCCCGACATTGCAATTAAGAGATTGAGGCCACAACG
260 GCTTCCCCGACATTGCAATTAAAAGATTGAGGCCACAACG
* *
17449572 GCGAATCTTACTTCCCAGGCGGTGTAGTGGAACAGATTGAAGCTACAACGGCAAATCTCGCTTCC
1 GCGAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTCGCTTCC
** * * *
17449637 TCGACATTGCAATTAAAAAAATTGAAGCCACAACGATGAATCTTACTTCTCTGGCGGTGTAGTGG
66 TCGACATTGCAATTAAAAAAATTGAAGCCACAACGACAAATCTTACTTCCCTGGCGGTGCAGTAG
* **
17449702 AATAGATTGAAGCTACAA-TGGTGAATCTTGCTCCCCTAACATTGCAATTAAAAAGA-TTGAGGC
131 AACAGATTGAAGCTACAACT-GCAAATCTTGCTCCCCTAACATTGCAATTAAAAA-ATTTGAGGC
* * *
17449765 CACAACGGCGAATCTTACTTCCCTGGCGGTGCAGTGGAACAGATTGAAGCTACAATGGCAAATCT
194 CACAACGGCGAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTGAAGCTACAACGACAAATCT
17449830 CGCTTCCCCGACATTGCAATTAAAAGATTGAGGCCACAACG
259 CGCTTCCCCGACATTGCAATTAAAAGATTGAGGCCACAACG
*
17449871 GCGAATCTTACTTCTCAGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTCGCTTCC
1 GCGAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTCGCTTCC
*
17449936 CCGACATTGCAATTAAAA
66 TCGACATTGCAATTAAAA
17449954 GATTGAGGCC
Statistics
Matches: 345, Mismatches: 33, Indels: 7
0.90 0.09 0.02
Matches are distributed among these distances:
297 1 0.00
298 70 0.20
299 273 0.79
300 1 0.00
ACGTcount: A:0.31, C:0.23, G:0.22, T:0.24
Consensus pattern (299 bp):
GCGAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTGAAGCTACAACGGCGAATCTCGCTTCC
TCGACATTGCAATTAAAAAAATTGAAGCCACAACGACAAATCTTACTTCCCTGGCGGTGCAGTAG
AACAGATTGAAGCTACAACTGCAAATCTTGCTCCCCTAACATTGCAATTAAAAAATTTGAGGCCA
CAACGGCGAATCTTACTTCCCAGGCGGTGCAGTGGAACAGATTGAAGCTACAACGACAAATCTCG
CTTCCCCGACATTGCAATTAAAAGATTGAGGCCACAACG
Found at i:17450037 original size:66 final size:66
Alignment explanation
Indices: 17449904--17450028 Score: 169
Period size: 66 Copynumber: 1.9 Consensus size: 66
17449894 GCAGTGGAAC
* *
17449904 AGATTGAAGCTACAACGGCGAATCTCGCTTCCCCGACATTGCAATTAAAAGATTGAGGCCACGAA
1 AGATTGAAGCTACAACGGCGAATCTCGCTTACCCGACATTGCAATTAAAAGATTGAAGCCACGAA
17449969 T
66 T
* * ** * *
17449970 AGATTGAAGCTACAATGGCGAATTTTTCTTACTCGACATTGCAGTTAAATAGATTGAAG
1 AGATTGAAGCTACAACGGCGAATCTCGCTTACCCGACATTGCAATTAAA-AGATTGAAG
17450029 TTACAATAGC
Statistics
Matches: 50, Mismatches: 8, Indels: 1
0.85 0.14 0.02
Matches are distributed among these distances:
66 42 0.84
67 8 0.16
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (66 bp):
AGATTGAAGCTACAACGGCGAATCTCGCTTACCCGACATTGCAATTAAAAGATTGAAGCCACGAA
T
Found at i:17451655 original size:3 final size:3
Alignment explanation
Indices: 17451647--17451674 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
17451637 ACATCATTTA
17451647 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
17451675 TACTTATACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:17452397 original size:109 final size:109
Alignment explanation
Indices: 17452206--17452632 Score: 653
Period size: 109 Copynumber: 3.9 Consensus size: 109
17452196 AAATTTTTTT
* * * *
17452206 AAATAAGGCAATGTTTTGGGTTTGGAAATTCGAGAAAACGTGCCATAATGTGGTGGGTTTCAATT
1 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCTTAATGTGCTGGGTTTCGATT
17452271 TTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAAATTTCA
66 TTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAAATTTCA
* * * *
17452315 AAATAAGACAATATTTTGCGTTTGGAAATTTGAGAAAACGTGCCTTAATGTGCTGGGTTTCGATC
1 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCTTAATGTGCTGGGTTTCGATT
* *
17452380 TTTCTCGTTCGACCAAATAACCAAATATCCTTTTAAAAATTTTA
66 TTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAAATTTCA
*
17452424 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCCTAATGTGCTGGGTTTCGATT
1 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCTTAATGTGCTGGGTTTCGATT
* * *
17452489 TTTCTCGCTCGACCAAATAGCTAAATATCCTTTCAAAAATTTCA
66 TTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAAATTTCA
* *
17452533 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACTTG-CTCTAATGCGCTGGGTTTCGA-
1 AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCT-TAATGTGCTGGGTTTCGAT
* * *
17452596 -TTTCTCGTTGGACCAAATAGCCGAATATCCTCTTAAA
65 TTTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAA
17452633 TCTTAATCCA
Statistics
Matches: 288, Mismatches: 29, Indels: 4
0.90 0.09 0.01
Matches are distributed among these distances:
107 31 0.11
108 1 0.00
109 256 0.89
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.34
Consensus pattern (109 bp):
AAATAAGGCAATGTTTTGCGTTTGGAAATTCGAGAAAACGTGCCTTAATGTGCTGGGTTTCGATT
TTTCTCGTTCGACCAAATAGCCAAATATCCTTTTAAAAATTTCA
Found at i:17453609 original size:30 final size:30
Alignment explanation
Indices: 17453575--17453645 Score: 133
Period size: 30 Copynumber: 2.4 Consensus size: 30
17453565 GCGTGATTAA
*
17453575 ACAAAAGATTCTTATTGTCTGGAAAAAAAC
1 ACAAAAGATTCTTATTGTCCGGAAAAAAAC
17453605 ACAAAAGATTCTTATTGTCCGGAAAAAAAC
1 ACAAAAGATTCTTATTGTCCGGAAAAAAAC
17453635 ACAAAAGATTC
1 ACAAAAGATTC
17453646 GTCTGTTGTT
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
30 40 1.00
ACGTcount: A:0.48, C:0.15, G:0.13, T:0.24
Consensus pattern (30 bp):
ACAAAAGATTCTTATTGTCCGGAAAAAAAC
Found at i:17457531 original size:21 final size:20
Alignment explanation
Indices: 17457507--17457582 Score: 75
Period size: 21 Copynumber: 3.8 Consensus size: 20
17457497 TTTTTTATGA
17457507 TTTTATATAAATTTTAATACT
1 TTTTATA-AAATTTTAATACT
*** *
17457528 TTTTAT-TGTTTTTATTA-T
1 TTTTATAAAATTTTAATACT
*
17457546 TTTTATAGAATTTTAATACAT
1 TTTTATAAAATTTTAATAC-T
17457567 TTTTATAAAATTTTAA
1 TTTTATAAAATTTTAA
17457583 ATATGTTTTA
Statistics
Matches: 43, Mismatches: 9, Indels: 6
0.74 0.16 0.10
Matches are distributed among these distances:
18 7 0.16
19 14 0.33
21 22 0.51
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (20 bp):
TTTTATAAAATTTTAATACT
Found at i:17457540 original size:19 final size:20
Alignment explanation
Indices: 17457507--17457582 Score: 77
Period size: 19 Copynumber: 3.9 Consensus size: 20
17457497 TTTTTTATGA
17457507 TTTTATATA-AATTTTAATAC
1 TTTT-TATAGAATTTTAATAC
* * *
17457527 TTTTTATTG-TTTTTATTA-
1 TTTTTATAGAATTTTAATAC
17457545 TTTTTATAGAATTTTAATAC
1 TTTTTATAGAATTTTAATAC
*
17457565 ATTTTTATAAAATTTTAA
1 -TTTTTATAGAATTTTAA
17457583 ATATGTTTTA
Statistics
Matches: 45, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
18 8 0.18
19 17 0.38
20 4 0.09
21 16 0.36
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.61
Consensus pattern (20 bp):
TTTTTATAGAATTTTAATAC
Found at i:17457548 original size:38 final size:39
Alignment explanation
Indices: 17457498--17457572 Score: 118
Period size: 38 Copynumber: 1.9 Consensus size: 39
17457488 CAATTCAGTT
17457498 TTTTTATGATTTTATATA-AATTTTAATAC-TTTTTATTG
1 TTTTTATGATTTT-TATAGAATTTTAATACATTTTTATTG
*
17457536 TTTTTATTATTTTTATAGAATTTTAATACATTTTTAT
1 TTTTTATGATTTTTATAGAATTTTAATACATTTTTAT
17457573 AAAATTTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
37 4 0.12
38 23 0.68
39 7 0.21
ACGTcount: A:0.29, C:0.03, G:0.04, T:0.64
Consensus pattern (39 bp):
TTTTTATGATTTTTATAGAATTTTAATACATTTTTATTG
Found at i:17457658 original size:9 final size:9
Alignment explanation
Indices: 17457498--17457762 Score: 87
Period size: 9 Copynumber: 27.7 Consensus size: 9
17457488 CAATTCAGTT
*
17457498 TTTTTATGA
1 TTTTTATAA
17457507 TTTTATATAAA
1 TTTT-TAT-AA
* *
17457518 TTTTAATAC
1 TTTTTATAA
**
17457527 TTTTTATTG
1 TTTTTATAA
*
17457536 TTTTTATTA
1 TTTTTATAA
17457545 TTTTTATAGAA
1 TTTTTAT--AA
*
17457556 TTTTAATACA
1 TTTTTATA-A
17457566 TTTTTATAAA
1 TTTTTAT-AA
* *
17457576 ATTTTAAATA
1 TTTTTATA-A
17457586 TGTTTTATTAA
1 T-TTTTA-TAA
17457597 -TTTTATAA
1 TTTTTATAA
*
17457605 TTTATTA-GA
1 TTT-TTATAA
17457614 TTTATTAT-A
1 TTT-TTATAA
17457623 TTTTTGATAGTA
1 TTTTT-ATA--A
*
17457635 TTTATTAT-T
1 TTT-TTATAA
17457644 TTTTTATAA
1 TTTTTATAA
*
17457653 TTTTTAAAA
1 TTTTTATAA
**
17457662 GTTTAAATCAA
1 -TTTTTAT-AA
*
17457673 TTTTCATATA
1 TTTTTATA-A
17457683 TTTTT-TAA
1 TTTTTATAA
*
17457691 TATTTA-AA
1 TTTTTATAA
17457699 TTTTT-TAA
1 TTTTTATAA
*
17457707 TATTTTTTATA
1 T-TTTTATA-A
17457718 TTTTTATAA
1 TTTTTATAA
* *
17457727 TTTTTTTTCTGA
1 ---TTTTTATAA
17457739 TTTTTATAA
1 TTTTTATAA
17457748 TTTTT-TAA
1 TTTTTATAA
17457756 TATTTTA
1 T-TTTTA
17457763 ATAGAAAAAT
Statistics
Matches: 194, Mismatches: 31, Indels: 61
0.68 0.11 0.21
Matches are distributed among these distances:
8 27 0.14
9 84 0.43
10 44 0.23
11 23 0.12
12 14 0.07
13 2 0.01
ACGTcount: A:0.32, C:0.02, G:0.03, T:0.63
Consensus pattern (9 bp):
TTTTTATAA
Found at i:17457693 original size:10 final size:10
Alignment explanation
Indices: 17457680--17457761 Score: 63
Period size: 10 Copynumber: 8.7 Consensus size: 10
17457670 CAATTTTCAT
17457680 ATATTTTTTA
1 ATATTTTTTA
17457690 ATA---TTTA
1 ATATTTTTTA
17457697 A-ATTTTTTA
1 ATATTTTTTA
17457706 ATATTTTTT-
1 ATATTTTTTA
17457715 ATATTTTTATA
1 ATATTTTT-TA
*
17457726 AT-TTTTTTT
1 ATATTTTTTA
*
17457735 CTGA-TTTTT-
1 AT-ATTTTTTA
17457744 ATAATTTTTTA
1 AT-ATTTTTTA
17457755 ATATTTT
1 ATATTTT
17457762 AATAGAAAAA
Statistics
Matches: 58, Mismatches: 4, Indels: 20
0.71 0.05 0.24
Matches are distributed among these distances:
6 1 0.02
7 5 0.09
9 17 0.29
10 31 0.53
11 4 0.07
ACGTcount: A:0.28, C:0.01, G:0.01, T:0.70
Consensus pattern (10 bp):
ATATTTTTTA
Found at i:17457714 original size:28 final size:28
Alignment explanation
Indices: 17457673--17457732 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
17457663 TTTAAATCAA
* *
17457673 TTTTCATATATTTTTTAATATTTA-AATT
1 TTTTAATATATTTTAT-ATATTTATAATT
* *
17457701 TTTTAATATTTTTTATATTTTTATAATT
1 TTTTAATATATTTTATATATTTATAATT
17457729 TTTT
1 TTTT
17457733 TTCTGATTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
27 6 0.22
28 21 0.78
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (28 bp):
TTTTAATATATTTTATATATTTATAATT
Found at i:17457741 original size:21 final size:20
Alignment explanation
Indices: 17457693--17457753 Score: 79
Period size: 21 Copynumber: 3.0 Consensus size: 20
17457683 TTTTTTAATA
* *
17457693 TTTAAATTTTT-TAATATTT
1 TTTATATTTTTATAATTTTT
17457712 TTTATATTTTTATAATTTTT
1 TTTATATTTTTATAATTTTT
*
17457732 TTTCTGATTTTTATAATTTTT
1 TTTAT-ATTTTTATAATTTTT
17457753 T
1 T
17457754 AATATTTTAA
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
19 10 0.27
20 11 0.30
21 16 0.43
ACGTcount: A:0.25, C:0.02, G:0.02, T:0.72
Consensus pattern (20 bp):
TTTATATTTTTATAATTTTT
Found at i:17458220 original size:19 final size:21
Alignment explanation
Indices: 17458198--17458237 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
17458188 CTTCAACATT
17458198 AATAATATT-TTAA-ATTTTA
1 AATAATATTCTTAATATTTTA
*
17458217 AATAGTATTCTTAATATTTTA
1 AATAATATTCTTAATATTTTA
17458238 TTGAGAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 8 0.44
20 4 0.22
21 6 0.33
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.53
Consensus pattern (21 bp):
AATAATATTCTTAATATTTTA
Found at i:17469132 original size:3 final size:3
Alignment explanation
Indices: 17469100--17469168 Score: 53
Period size: 3 Copynumber: 24.3 Consensus size: 3
17469090 TTATACTCAT
17469100 TTA TTCA TTA TTA -TA TT- TCTA -TA TTA -TA TTA TTA TT- TT- TGTA
1 TTA TT-A TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA T-TA
*
17469142 TTA TTA TTA -TA TTA TTA TCA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA T
17469169 AGTTGCTCTT
Statistics
Matches: 55, Mismatches: 2, Indels: 18
0.73 0.03 0.24
Matches are distributed among these distances:
2 12 0.22
3 39 0.71
4 4 0.07
ACGTcount: A:0.30, C:0.04, G:0.01, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:17469143 original size:11 final size:11
Alignment explanation
Indices: 17469101--17469168 Score: 50
Period size: 11 Copynumber: 5.8 Consensus size: 11
17469091 TATACTCATT
17469101 TATTCATTATTA
1 TATT-ATTATTA
*
17469113 TATTTCTATATTA
1 TA-TTAT-TATTA
17469126 TATTATTATT-
1 TATTATTATTA
*
17469136 TTTGTATTATTA
1 TAT-TATTATTA
17469148 T-TATATTATTA
1 TAT-TATTATTA
17469159 TCATTATTAT
1 T-ATTATTAT
17469169 AGTTGCTCTT
Statistics
Matches: 46, Mismatches: 4, Indels: 12
0.74 0.06 0.19
Matches are distributed among these distances:
10 2 0.04
11 21 0.46
12 13 0.28
13 10 0.22
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.63
Consensus pattern (11 bp):
TATTATTATTA
Found at i:17469164 original size:17 final size:16
Alignment explanation
Indices: 17469121--17469169 Score: 55
Period size: 17 Copynumber: 2.9 Consensus size: 16
17469111 TATATTTCTA
17469121 TATTATATTATTAT-T
1 TATTATATTATTATAT
*
17469136 TTTGTATTATTATTATAT
1 TAT-TA-TATTATTATAT
17469154 TATTATCATTATTATA
1 TATTAT-ATTATTATA
17469170 GTTGCTCTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
15 2 0.07
16 3 0.11
17 20 0.71
18 3 0.11
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (16 bp):
TATTATATTATTATAT
Found at i:17469199 original size:21 final size:21
Alignment explanation
Indices: 17469175--17469217 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
17469165 TTATAGTTGC
*
17469175 TCTTACATATATACGTATATT
1 TCTTACATATATACATATATT
**
17469196 TCTTTTATATATACATATATT
1 TCTTACATATATACATATATT
17469217 T
1 T
17469218 TTCTAGATAT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.33, C:0.12, G:0.02, T:0.53
Consensus pattern (21 bp):
TCTTACATATATACATATATT
Found at i:17470860 original size:17 final size:16
Alignment explanation
Indices: 17470834--17470865 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
17470824 TCAAGCAAAT
17470834 CAAAACAAGATTCAAC
1 CAAAACAAGATTCAAC
17470850 CAAATACAAGATTCAA
1 CAAA-ACAAGATTCAA
17470866 GGACGAATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.56, C:0.22, G:0.06, T:0.16
Consensus pattern (16 bp):
CAAAACAAGATTCAAC
Found at i:17471731 original size:12 final size:12
Alignment explanation
Indices: 17471716--17471740 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
17471706 TCTTTCCATC
17471716 TTTCTTCTTTAT
1 TTTCTTCTTTAT
17471728 TTTCTTCTTTAT
1 TTTCTTCTTTAT
17471740 T
1 T
17471741 AATTCTAATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.08, C:0.16, G:0.00, T:0.76
Consensus pattern (12 bp):
TTTCTTCTTTAT
Found at i:17473911 original size:41 final size:41
Alignment explanation
Indices: 17473860--17473971 Score: 161
Period size: 41 Copynumber: 2.7 Consensus size: 41
17473850 CTTAATTATA
*
17473860 CCCTGAATTGCACTTATGTGCCCCTGTTTATACTTCAGTAC
1 CCCTGAATTGCACTTATGTGCCACTGTTTATACTTCAGTAC
* * *
17473901 CCCTAAATTGCACTTATGTGCCACTGTTTGTACTTCGGTAC
1 CCCTGAATTGCACTTATGTGCCACTGTTTATACTTCAGTAC
* * *
17473942 CCCTGAATTGCACATACGTGCCATTGTTTA
1 CCCTGAATTGCACTTATGTGCCACTGTTTA
17473972 CACTCCGATA
Statistics
Matches: 62, Mismatches: 9, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
41 62 1.00
ACGTcount: A:0.21, C:0.28, G:0.16, T:0.36
Consensus pattern (41 bp):
CCCTGAATTGCACTTATGTGCCACTGTTTATACTTCAGTAC
Found at i:17477423 original size:33 final size:32
Alignment explanation
Indices: 17477319--17477431 Score: 156
Period size: 32 Copynumber: 3.5 Consensus size: 32
17477309 TAGAGGAATA
*
17477319 TTGTTATCATTTAACAAAATTAAAGTTGATAT
1 TTGTTATCATTTCACAAAATTAAAGTTGATAT
* *
17477351 TTTTTATCATTTTACAAAATTAAAGTTG-TAAT
1 TTGTTATCATTTCACAAAATTAAAGTTGAT-AT
* *
17477383 TTGTTATCATTTCACAAAATGAAAAGCTGATAT
1 TTGTTATCATTTCACAAAAT-TAAAGTTGATAT
17477416 TTGTTATCATTTCACA
1 TTGTTATCATTTCACA
17477432 GAACCACACG
Statistics
Matches: 72, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
31 1 0.01
32 46 0.64
33 24 0.33
34 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.09, T:0.44
Consensus pattern (32 bp):
TTGTTATCATTTCACAAAATTAAAGTTGATAT
Found at i:17482308 original size:51 final size:51
Alignment explanation
Indices: 17482253--17482696 Score: 382
Period size: 51 Copynumber: 8.7 Consensus size: 51
17482243 GTGAAAGTGT
* *
17482253 TGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATAA
* * * ** * * * *
17482304 TGGTCACATGTGTAGTACTAAGTGAAGGCTACAATATGTACCGAGAAGCT-T
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAA-ATAA
* * * *
17482355 TGGTCACGTGTGTAGTACTGTGTGAAGGCTATTAAGTGAATCGATAAATAA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATAA
* * * * ** * * * * *
17482406 TGGTCACATGTGTAGTACTAAGTGAAAGCTACAATATGTACCAAGAAGCT-T
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAA-ATAA
* * ** *
17482457 TGGTCACGTGCGTAGTACTGTGTGAAGGCTACTACGTGAATTGATAAATGA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATAA
* * * * *
17482508 TGGTCACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGA-AAAGCT-T
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAA--TAA
* * *
17482559 TAGTCACGTATGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAA-ACT
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATA-A
* * * *
17482609 TGATCATGTATGTAGTACTATGTGAAGGCTATTACGTGAACCG-TAAA-AA
1 TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATAA
*
17482658 TTGATCACGTGTGTAGTACTATGTGAAGGCTACTACGTG
1 -TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTG
17482697 TATCGAATGA
Statistics
Matches: 308, Mismatches: 75, Indels: 21
0.76 0.19 0.05
Matches are distributed among these distances:
50 85 0.28
51 220 0.71
52 3 0.01
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (51 bp):
TGGTCACGTGTGTAGTACTATGTGAAGGCTACTACGTGAACCGATAAATAA
Found at i:17482411 original size:102 final size:102
Alignment explanation
Indices: 17482252--17482702 Score: 586
Period size: 102 Copynumber: 4.4 Consensus size: 102
17482242 AGTGAAAGTG
17482252 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
1 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
17482317 AGTACTAAGTGAAGGCTACAATATGTACCGAGAAGCT
66 AGTACTAAGTGAAGGCTACAATATGTACCGAGAAGCT
* *
17482354 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTATTAAGTGAATCGATAAATAATGGTCACATGTGT
1 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
* *
17482419 AGTACTAAGTGAAAGCTACAATATGTACCAAGAAGCT
66 AGTACTAAGTGAAGGCTACAATATGTACCGAGAAGCT
* * *
17482456 TTGGTCACGTGCGTAGTACTGTGTGAAGGCTACTACGTGAATTGATAAATGATGGTCACATGTGT
1 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
* * *
17482521 AGTACTAAGTGAAGGCTACTATGTGTACCGAAAAGCT
66 AGTACTAAGTGAAGGCTACAATATGTACCGAGAAGCT
* * * * * * ** *
17482558 TTAGTCACGTATGTAGTACTATGTGAAGGCTACTACGTGAACCG-TAAA-ACTTGATCATGTATG
1 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATA-ATGGTCACATGTG
* ** ** * **
17482621 TAGTACTATGTGAAGGCTATTACGTGAACCGTA-AA-AA
65 TAGTACTAAGTGAAGGCTACAATATGTACCG-AGAAGCT
* * *
17482658 TTGATCACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGA
17482703 ATGATAATAG
Statistics
Matches: 309, Mismatches: 37, Indels: 7
0.88 0.10 0.02
Matches are distributed among these distances:
100 39 0.13
101 41 0.13
102 229 0.74
ACGTcount: A:0.31, C:0.14, G:0.25, T:0.30
Consensus pattern (102 bp):
TTGGTCACGTGTGTAGTACTGTGTGAAGGCTACTACGTGAATCGATAAATAATGGTCACATGTGT
AGTACTAAGTGAAGGCTACAATATGTACCGAGAAGCT
Found at i:17483609 original size:5 final size:5
Alignment explanation
Indices: 17483599--17483661 Score: 72
Period size: 5 Copynumber: 12.6 Consensus size: 5
17483589 TGCTTGATGA
* * * * *
17483599 AATGG AATGG AATGG AATGG TATGA AATGG AATAG TATAG AATGG AATGG
1 AATGG AATGG AATGG AATGG AATGG AATGG AATGG AATGG AATGG AATGG
*
17483649 TATGG AATGG AAT
1 AATGG AATGG AAT
17483662 ATACATATAT
Statistics
Matches: 48, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
5 48 1.00
ACGTcount: A:0.41, C:0.00, G:0.33, T:0.25
Consensus pattern (5 bp):
AATGG
Found at i:17483900 original size:40 final size:40
Alignment explanation
Indices: 17483856--17483983 Score: 114
Period size: 40 Copynumber: 3.2 Consensus size: 40
17483846 AGCGGCGTTT
*
17483856 TTAGCGGCGCTTGGACAAAAACGCCACTAAAAATCGAGCA
1 TTAGCGGCGCTTGGACAAAAACGCCACTAAAAATAGAGCA
** * * * **
17483896 TTAGCGGCGCTTTTATAAAAATGCCTCTAAAGGTAGAGCA
1 TTAGCGGCGCTTGGACAAAAACGCCACTAAAAATAGAGCA
*** * **
17483936 TTAGCGGCGCTTCTCCGAAAACGCTGCTAAAAATA-AGCA
1 TTAGCGGCGCTTGGACAAAAACGCCACTAAAAATAGAGCA
*
17483975 TTAGGGGCG
1 TTAGCGGCG
17483984 TTTTCTGAAA
Statistics
Matches: 70, Mismatches: 18, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
39 12 0.17
40 58 0.83
ACGTcount: A:0.33, C:0.22, G:0.24, T:0.21
Consensus pattern (40 bp):
TTAGCGGCGCTTGGACAAAAACGCCACTAAAAATAGAGCA
Found at i:17484006 original size:38 final size:39
Alignment explanation
Indices: 17483873--17484006 Score: 101
Period size: 40 Copynumber: 3.4 Consensus size: 39
17483863 CGCTTGGACA
* * * ***
17483873 AAAACGCCACTAAAAATCGAGCATTAGCGGCGCTTTTATA
1 AAAACGCCGCTAAAAAT-AAGCATTAGCGGCGCTTCTCCG
* * **
17483913 AAAATGCCTCTAAAGGTAGAGCATTAGCGGCGCTTCTCCG
1 AAAACGCCGCTAAAAATA-AGCATTAGCGGCGCTTCTCCG
* * * *
17483953 AAAACGCTGCTAAAAATAAGCATTAGGGGCG-TTTTCTG
1 AAAACGCCGCTAAAAATAAGCATTAGCGGCGCTTCTCCG
17483991 AAAAGCGCCGC-AAAAA
1 AAAA-CGCCGCTAAAAA
17484007 GCCTAAGCCA
Statistics
Matches: 74, Mismatches: 18, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
38 14 0.19
39 17 0.23
40 43 0.58
ACGTcount: A:0.36, C:0.22, G:0.22, T:0.21
Consensus pattern (39 bp):
AAAACGCCGCTAAAAATAAGCATTAGCGGCGCTTCTCCG
Found at i:17484100 original size:41 final size:41
Alignment explanation
Indices: 17484043--17484160 Score: 209
Period size: 41 Copynumber: 2.9 Consensus size: 41
17484033 GAGTTTTTGG
17484043 GGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCT
1 GGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCT
* *
17484084 GGCCTTTAGCGGCGTTTTTGAAGAAGCACCGTTAATGCTCT
1 GGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCT
*
17484125 GGCCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAAT
1 GGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAAT
17484161 AATAATCAAA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
41 72 1.00
ACGTcount: A:0.19, C:0.23, G:0.28, T:0.30
Consensus pattern (41 bp):
GGCCTTTAGCGGCGTTTTTGAAGAAGCGCCGCTAATGCTCT
Found at i:17485233 original size:7 final size:7
Alignment explanation
Indices: 17485193--17485335 Score: 59
Period size: 7 Copynumber: 20.6 Consensus size: 7
17485183 ATTAAATAAT
17485193 GTTTAAGG
1 GTTT-AGG
17485201 G-TTAGG
1 GTTTAGG
*
17485207 GATTTTGG
1 G-TTTAGG
17485215 G-TT-GG
1 GTTTAGG
17485220 G-TTAGG
1 GTTTAGG
17485226 GTTTAGG
1 GTTTAGG
*
17485233 GATTAGG
1 GTTTAGG
17485240 GATTTAGG
1 G-TTTAGG
*
17485248 G--TCGG
1 GTTTAGG
17485253 G-TTAGG
1 GTTTAGG
* *
17485259 ATTTAAG
1 GTTTAGG
17485266 GTTTATGG
1 GTTTA-GG
*
17485274 G-TTAAG
1 GTTTAGG
*
17485280 ATTTAGAG
1 GTTTAG-G
17485288 GTTTAAGG
1 GTTT-AGG
17485296 GTTTAGGG
1 GTTTA-GG
* *
17485304 GTTAAGA
1 GTTTAGG
*
17485311 GTTAAGG
1 GTTTAGG
* *
17485318 ATTTAGA
1 GTTTAGG
17485325 GTTTAGG
1 GTTTAGG
17485332 GTTT
1 GTTT
17485336 CATGGGTCGA
Statistics
Matches: 102, Mismatches: 21, Indels: 25
0.69 0.14 0.17
Matches are distributed among these distances:
5 9 0.09
6 13 0.13
7 49 0.48
8 29 0.28
9 2 0.02
ACGTcount: A:0.22, C:0.01, G:0.38, T:0.38
Consensus pattern (7 bp):
GTTTAGG
Found at i:17485239 original size:33 final size:32
Alignment explanation
Indices: 17485193--17485268 Score: 98
Period size: 33 Copynumber: 2.3 Consensus size: 32
17485183 ATTAAATAAT
* *
17485193 GTTTAAGGGTTAGGGATTTTGGGTTGGGTTAGG
1 GTTT-AGGGTTAGGGATTTAGGGTCGGGTTAGG
17485226 GTTTAGGGATTAGGGATTTAGGGTCGGGTTAGG
1 GTTTAGGG-TTAGGGATTTAGGGTCGGGTTAGG
* *
17485259 ATTTAAGGTT
1 GTTTAGGGTT
17485269 TATGGGTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
32 6 0.16
33 32 0.84
ACGTcount: A:0.18, C:0.01, G:0.42, T:0.38
Consensus pattern (32 bp):
GTTTAGGGTTAGGGATTTAGGGTCGGGTTAGG
Found at i:17485617 original size:21 final size:20
Alignment explanation
Indices: 17485583--17485633 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 20
17485573 TATGGATTTA
*
17485583 GGGATTATGGTTTAAGGGTT
1 GGGATTAAGGTTTAAGGGTT
*
17485603 GGGATTTAAGGTTTAGGGGTT
1 GGGA-TTAAGGTTTAAGGGTT
*
17485624 AGGGGTTAAG
1 -GGGATTAAG
17485634 AACTAGGGAT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
20 4 0.15
21 19 0.73
22 3 0.12
ACGTcount: A:0.22, C:0.00, G:0.43, T:0.35
Consensus pattern (20 bp):
GGGATTAAGGTTTAAGGGTT
Found at i:17489340 original size:9 final size:9
Alignment explanation
Indices: 17489308--17489350 Score: 52
Period size: 9 Copynumber: 4.8 Consensus size: 9
17489298 TGTCTGTCTT
17489308 TTTTATTGC
1 TTTTATTGC
* *
17489317 TTTCA-CGC
1 TTTTATTGC
17489325 TTTTTATTGC
1 -TTTTATTGC
17489335 TTTTATTGC
1 TTTTATTGC
17489344 TTTTATT
1 TTTTATT
17489351 TTATTTTTTA
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
8 2 0.07
9 24 0.86
10 2 0.07
ACGTcount: A:0.12, C:0.14, G:0.09, T:0.65
Consensus pattern (9 bp):
TTTTATTGC
Found at i:17491340 original size:43 final size:43
Alignment explanation
Indices: 17491203--17491389 Score: 232
Period size: 43 Copynumber: 4.4 Consensus size: 43
17491193 TAAAGCTTTA
* *
17491203 TTCTTTAGCGGCGTTTGTGACAAAA-CGCCGCTAAAGATCATA
1 TTCTTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATG
* * * ** *
17491245 TTCTTTAGTGGCGTTTGTGGCTAAAGCGCCGCTAAAACTCACG
1 TTCTTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATG
* * *
17491288 ATCTGTAGCGGTGTTTGTGACAAAAGCGCCGCTAAAGGTCATG
1 TTCTTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATG
* * *
17491331 TTCTTTAGCGGCGTTTGTTATAAAAGCGCCACTAAAGGTCATG
1 TTCTTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATG
*
17491374 ATCTTTAGCGGCGTTT
1 TTCTTTAGCGGCGTTT
17491390 TTTCACATAA
Statistics
Matches: 121, Mismatches: 23, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
42 22 0.18
43 99 0.82
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.30
Consensus pattern (43 bp):
TTCTTTAGCGGCGTTTGTGACAAAAGCGCCGCTAAAGGTCATG
Found at i:17492950 original size:18 final size:19
Alignment explanation
Indices: 17492929--17492964 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
17492919 GTATACAGAG
*
17492929 GTAATAATAG-TTTGGAAA
1 GTAAAAATAGTTTTGGAAA
17492947 GTAAAAATAGTTTTGGAA
1 GTAAAAATAGTTTTGGAA
17492965 TAAATATTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 9 0.56
19 7 0.44
ACGTcount: A:0.44, C:0.00, G:0.22, T:0.33
Consensus pattern (19 bp):
GTAAAAATAGTTTTGGAAA
Found at i:17493105 original size:16 final size:15
Alignment explanation
Indices: 17493080--17493110 Score: 53
Period size: 16 Copynumber: 2.0 Consensus size: 15
17493070 GTTTGCTGAA
17493080 ATTAACCTAGAAAAT
1 ATTAACCTAGAAAAT
17493095 ATTAGACCTAGAAAAT
1 ATTA-ACCTAGAAAAT
17493111 GAGCTTAGGT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 4 0.27
16 11 0.73
ACGTcount: A:0.52, C:0.13, G:0.10, T:0.26
Consensus pattern (15 bp):
ATTAACCTAGAAAAT
Found at i:17493378 original size:16 final size:16
Alignment explanation
Indices: 17493359--17493395 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
17493349 TAAAACTATT
17493359 AAATATTAAATTAAAA
1 AAATATTAAATTAAAA
*
17493375 AAATA-TAATTTAAAA
1 AAATATTAAATTAAAA
17493390 AAATAT
1 AAATAT
17493396 GGGTGGACCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (16 bp):
AAATATTAAATTAAAA
Found at i:17495530 original size:18 final size:16
Alignment explanation
Indices: 17495507--17495552 Score: 56
Period size: 18 Copynumber: 2.7 Consensus size: 16
17495497 TAGAAAAAAA
17495507 ATATTTTTATTAATTTAT
1 ATATTTTTATT-ATTT-T
17495525 ATATTTTTATGTATTTT
1 ATATTTTTAT-TATTTT
*
17495542 TTATTTTTATT
1 ATATTTTTATT
17495553 TATGTTTTCC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
16 1 0.04
17 10 0.38
18 14 0.54
19 1 0.04
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.72
Consensus pattern (16 bp):
ATATTTTTATTATTTT
Found at i:17495560 original size:18 final size:17
Alignment explanation
Indices: 17495508--17495560 Score: 61
Period size: 17 Copynumber: 3.1 Consensus size: 17
17495498 AGAAAAAAAA
* *
17495508 TATTTTTATTAATTTATA
1 TATTTTTATTTATTT-TT
*
17495526 TATTTTTATGTATTTTT
1 TATTTTTATTTATTTTT
*
17495543 TATTTTTATTTATGTTT
1 TATTTTTATTTATTTTT
17495560 T
1 T
17495561 CCACATGGCA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 17 0.57
18 13 0.43
ACGTcount: A:0.23, C:0.00, G:0.04, T:0.74
Consensus pattern (17 bp):
TATTTTTATTTATTTTT
Found at i:17496475 original size:24 final size:24
Alignment explanation
Indices: 17496447--17496498 Score: 86
Period size: 24 Copynumber: 2.2 Consensus size: 24
17496437 TTACAACTTC
17496447 ATCTTCGAGATGTCGAAAGATTCA
1 ATCTTCGAGATGTCGAAAGATTCA
* *
17496471 ATCTTCGGGATGTTGAAAGATTCA
1 ATCTTCGAGATGTCGAAAGATTCA
17496495 ATCT
1 ATCT
17496499 CAGAATAGAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.31, C:0.15, G:0.21, T:0.33
Consensus pattern (24 bp):
ATCTTCGAGATGTCGAAAGATTCA
Found at i:17507528 original size:3 final size:3
Alignment explanation
Indices: 17507522--17507586 Score: 71
Period size: 3 Copynumber: 21.7 Consensus size: 3
17507512 GTTATCTTTG
* *
17507522 TTA TTA -TA TTA TATA TTA CTA TTA TTA TTA TTA -TA TTAA TTA TTG
1 TTA TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TT-A TTA TTA
*
17507567 TTA TTT TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TT
17507587 TTAATACATA
Statistics
Matches: 52, Mismatches: 6, Indels: 8
0.79 0.09 0.12
Matches are distributed among these distances:
2 4 0.08
3 42 0.81
4 6 0.12
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:17507555 original size:27 final size:27
Alignment explanation
Indices: 17507522--17507582 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
17507512 GTTATCTTTG
17507522 TTATTATATT-ATATATTACTATTATTA
1 TTATTATATTAAT-TATTACTATTATTA
** *
17507549 TTATTATATTAATTATTGTTATTTTTA
1 TTATTATATTAATTATTACTATTATTA
17507576 TTATTAT
1 TTATTAT
17507583 TATTTTAATA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
27 28 0.93
28 2 0.07
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.64
Consensus pattern (27 bp):
TTATTATATTAATTATTACTATTATTA
Found at i:17514418 original size:42 final size:44
Alignment explanation
Indices: 17514353--17514474 Score: 124
Period size: 42 Copynumber: 2.8 Consensus size: 44
17514343 TCAAATAACA
* * * * *
17514353 ATGCCACTATCCCAAACAGGGTCTTACACGAAATCAT-ATAT-G
1 ATGCCAATGTCCCAGACATGGTCTTACACGAAATCATCAAATCG
17514395 ATGCCAATGTCCCAGACATGGTCTTACACGTAAATC-TCAAATCG
1 ATGCCAATGTCCCAGACATGGTCTTACACG-AAATCATCAAATCG
* ** * *
17514439 ATGCCAACGTCCCAGATGTGGTCTTATACGATATCA
1 ATGCCAATGTCCCAGACATGGTCTTACACGAAATCA
17514475 CGTATCAGAA
Statistics
Matches: 66, Mismatches: 10, Indels: 6
0.80 0.12 0.07
Matches are distributed among these distances:
42 27 0.41
43 12 0.18
44 27 0.41
ACGTcount: A:0.32, C:0.26, G:0.16, T:0.25
Consensus pattern (44 bp):
ATGCCAATGTCCCAGACATGGTCTTACACGAAATCATCAAATCG
Found at i:17514600 original size:33 final size:32
Alignment explanation
Indices: 17514558--17514635 Score: 90
Period size: 33 Copynumber: 2.5 Consensus size: 32
17514548 TCTTATGCTA
* *
17514558 AATTCAATTCAACAT-TGTAGTATACATACATAC
1 AATTCAATTCAACATATGTA-TA-AAATAAATAC
17514591 AATTCAATTCAAC-TATGTATAAAATAAATAC
1 AATTCAATTCAACATATGTATAAAATAAATAC
*
17514622 -ATTCAATTTAACAT
1 AATTCAATTCAACAT
17514636 CATTTATTCA
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
30 11 0.28
31 9 0.22
32 3 0.08
33 17 0.43
ACGTcount: A:0.46, C:0.15, G:0.04, T:0.35
Consensus pattern (32 bp):
AATTCAATTCAACATATGTATAAAATAAATAC
Found at i:17517397 original size:18 final size:18
Alignment explanation
Indices: 17517341--17517397 Score: 62
Period size: 18 Copynumber: 3.1 Consensus size: 18
17517331 ATATAAATAT
*
17517341 AAATTTTAAAAAGTCAAAA
1 AAATTATAAAAA-TCAAAA
*
17517360 TAATATATAAAAAT-AGAAA
1 AAAT-TATAAAAATCA-AAA
17517379 AAATTATAAAAATCAAAA
1 AAATTATAAAAATCAAAA
17517397 A
1 A
17517398 GAGGTATTTA
Statistics
Matches: 32, Mismatches: 3, Indels: 7
0.76 0.07 0.17
Matches are distributed among these distances:
18 14 0.44
19 11 0.34
20 7 0.22
ACGTcount: A:0.68, C:0.04, G:0.04, T:0.25
Consensus pattern (18 bp):
AAATTATAAAAATCAAAA
Found at i:17517578 original size:30 final size:29
Alignment explanation
Indices: 17517537--17517612 Score: 89
Period size: 29 Copynumber: 2.6 Consensus size: 29
17517527 TAGAATATAT
***
17517537 AATTTTGAAAATTTAAGTTTTATTTTTTCAA
1 AATTTT-AAAATTTAAACATTA-TTTTTCAA
*
17517568 AATTTTAAAATCTAAACATTATTTTTCAA
1 AATTTTAAAATTTAAACATTATTTTTCAA
*
17517597 AAATTTAAAATTTAAA
1 AATTTTAAAATTTAAA
17517613 TGCTTTTCTC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
29 22 0.56
30 11 0.28
31 6 0.15
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (29 bp):
AATTTTAAAATTTAAACATTATTTTTCAA
Found at i:17518879 original size:17 final size:17
Alignment explanation
Indices: 17518838--17518880 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
17518828 TTTGTTAGGG
*
17518838 TTAAGATTTTTTAAGAA
1 TTAAGGTTTTTTAAGAA
17518855 TTAAGGTTTTTTAAGAA
1 TTAAGGTTTTTTAAGAA
*
17518872 TTAGGGTTT
1 TTAAGGTTT
17518881 AAGGTTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.49
Consensus pattern (17 bp):
TTAAGGTTTTTTAAGAA
Found at i:17523923 original size:25 final size:25
Alignment explanation
Indices: 17523889--17523971 Score: 71
Period size: 25 Copynumber: 3.4 Consensus size: 25
17523879 TGCTAGACAG
*
17523889 AATATGCCACAAAGGCAATATACAT
1 AATACGCCACAAAGGCAATATACAT
* * *
17523914 AATACGCCACAAGGGTAATATATAT
1 AATACGCCACAAAGGCAATATACAT
* * * *
17523939 AGTATGCAACAAAGGCTAA-AT-CAG
1 AATACGCCACAAAGGC-AATATACAT
17523963 AATACGCCA
1 AATACGCCA
17523972 TAGAGGCTAT
Statistics
Matches: 43, Mismatches: 14, Indels: 3
0.72 0.23 0.05
Matches are distributed among these distances:
24 7 0.16
25 34 0.79
26 2 0.05
ACGTcount: A:0.46, C:0.19, G:0.16, T:0.19
Consensus pattern (25 bp):
AATACGCCACAAAGGCAATATACAT
Found at i:17528483 original size:105 final size:101
Alignment explanation
Indices: 17528337--17528530 Score: 255
Period size: 105 Copynumber: 1.9 Consensus size: 101
17528327 CTCATAATGT
* ** * *
17528337 CATAACCCAGTTATGGTATTATCATTAGGATGCCATAGCCCAGCTATGGTCTTACACATATACAT
1 CATAACACAGTTATGGTATTATCATTACAATGCCATAGCCCAACTATGGTCTTACACATAAACAT
*
17528402 TTACTGCCATGGTCCAACTATGGTCTTACGTTTAAGATGC
66 TT--T--CATGGTCCAACCATGGTCTTACGTTTAAGATGC
* **
17528442 CATAACACAGTTATGGT-CTATTCATTACAATGCCATAGCCCAACTATGGTCTTACATTTAAACA
1 CATAACACAGTTATGGTATTA-TCATTACAATGCCATAGCCCAACTATGGTCTTACACATAAACA
17528506 TTTTCATGGTCCAACCATGGTCTTA
65 TTTTCATGGTCCAACCATGGTCTTA
17528531 TCCGTCAATT
Statistics
Matches: 79, Mismatches: 9, Indels: 6
0.84 0.10 0.06
Matches are distributed among these distances:
101 20 0.25
103 1 0.01
104 2 0.03
105 56 0.71
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (101 bp):
CATAACACAGTTATGGTATTATCATTACAATGCCATAGCCCAACTATGGTCTTACACATAAACAT
TTTCATGGTCCAACCATGGTCTTACGTTTAAGATGC
Found at i:17530669 original size:26 final size:23
Alignment explanation
Indices: 17530636--17530687 Score: 68
Period size: 26 Copynumber: 2.1 Consensus size: 23
17530626 GAAATAAGTC
*
17530636 AAAGAAAATAAAAATTAAACAACTA
1 AAAGAAAATAAAAAAT-AA-AACTA
17530661 AAAGCAAAATAAAAAATAAAACTA
1 AAAG-AAAATAAAAAATAAAACTA
17530685 AAA
1 AAA
17530688 ATAAAATCAG
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 8 0.32
25 6 0.24
26 11 0.44
ACGTcount: A:0.75, C:0.08, G:0.04, T:0.13
Consensus pattern (23 bp):
AAAGAAAATAAAAAATAAAACTA
Found at i:17532802 original size:6 final size:6
Alignment explanation
Indices: 17532789--17532821 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
17532779 TAGGAATTAT
*
17532789 GGAAA- GGAAAA GGAAAG GGAAAG GGAAAG GGAA
1 GGAAAG GGAAAG GGAAAG GGAAAG GGAAAG GGAA
17532822 TGTGGCTAGT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
5 5 0.19
6 21 0.81
ACGTcount: A:0.55, C:0.00, G:0.45, T:0.00
Consensus pattern (6 bp):
GGAAAG
Found at i:17538628 original size:19 final size:20
Alignment explanation
Indices: 17538591--17538635 Score: 56
Period size: 19 Copynumber: 2.2 Consensus size: 20
17538581 TTATTTTGTC
*
17538591 ACTAGAAAAAGAGAGATTACT
1 ACTA-AAAAAGAGAGATTACA
*
17538612 ACTAAAAAA-AGATATTACA
1 ACTAAAAAAGAGAGATTACA
17538631 ACTAA
1 ACTAA
17538636 TATTACGTGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
19 13 0.59
20 5 0.23
21 4 0.18
ACGTcount: A:0.58, C:0.11, G:0.11, T:0.20
Consensus pattern (20 bp):
ACTAAAAAAGAGAGATTACA
Found at i:17539665 original size:114 final size:114
Alignment explanation
Indices: 17539466--17540036 Score: 765
Period size: 113 Copynumber: 5.0 Consensus size: 114
17539456 AAAATAAGCA
*** *
17539466 TTAGCGGCGTTTTCCAGAAAGCGCCAC-AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* *
17539530 TCGAGGG-TTTCGCGGCGTTTTTAAGAAAGCGCCACTAATGCTCAGGTAT
66 TCG-GGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGTAT
* * * **
17539579 TTAGCAGCATTTTTGGGAAAGCGCCGCAAAAAAACCTATGCCCAACGACGCTATTTTCTGAGCTT
1 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* ***
17539644 TCGGGGATTTCGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGCCC
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGTAT
* * * *
17539693 TTAGCGGCGTTTTTAGGAAAGCTCCGC-AAAATACCTAAGCCCAACGACGCCGTTTACTGAGCTT
1 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* * * *
17539757 ACGGTGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAAGTCT
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGTAT
* * *
17539806 TTAGTGGCGTTTTTGGG-AAGCTCCGCAAAAAAACCTAAGCCCAACGACACCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* * *
17539870 TCGGGGATTTAGCAGCGTTTTGTAAGAAAGCGCCGCTAATTCTCAGGGAT
66 TCGGGGATTTAGCGGCGTTTT-TAAGAAAGCGCCGCTAATGCTCAGGTAT
* * * *
17539920 TTAGCGGCGTTGTTGGTAAAGCGCCGCAAAAAAACCTAATCCCAACGACTCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* *
17539985 TTGGGGATTTAGCGACGTTTTTAAGAAAGCGCCGCTAATGCTCAAGG-AT
66 TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTC-AGGTAT
17540034 TTA
1 TTA
17540037 AAATAATTTA
Statistics
Matches: 402, Mismatches: 50, Indels: 11
0.87 0.11 0.02
Matches are distributed among these distances:
112 9 0.02
113 166 0.41
114 162 0.40
115 65 0.16
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (114 bp):
TTAGCGGCGTTTTTGGGAAAGCGCCGCAAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
TCGGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAGGTAT
Found at i:17539898 original size:227 final size:226
Alignment explanation
Indices: 17539466--17540036 Score: 779
Period size: 227 Copynumber: 2.5 Consensus size: 226
17539456 AAAATAAGCA
* *
17539466 TTAGCGGCGTTTTCCA-GAAAGCGCCACAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
1 TTAGCGGCGTTTT-TAGGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTT
* * * *
17539530 TCGAGGGTTTCGCGGCGTTTTTAAGAAAGCGCCACTAATGCTCAGGTATTTAGCAGCATTTTTGG
65 TCG-GGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAAGTATTTAGCAGCATTTTTGG
* * * * *
17539595 GAAAGCGCCGCAAAAAAACCTATGCCCAACGACGCTATTTTCTGAGCTTTCGGGGATTTCGCGGC
129 GAAAGCGCCGCAAAAAAACCTAAGCCCAACGACACCATTTTCTGAGCTTTCGGGGATTTAGCAGC
*
17539660 GTTTTTAAGAAAGCGCCGCTAATGCTCAGGCCC
194 GTTTTTAAGAAAGCGCCGCTAATGCTCAGGCAC
* * * *
17539693 TTAGCGGCGTTTTTAGGAAAGCTCCGCAAAATACCTAAGCCCAACGACGCCGTTTACTGAGCTTA
1 TTAGCGGCGTTTTTAGGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTT
* ** *
17539758 CGGTGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAAGTCTTTAGTGGCGTTTTTGGG
66 CGG-GATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAAGTATTTAGCAGCATTTTTGGG
* *
17539823 -AAGCTCCGCAAAAAAACCTAAGCCCAACGACACCGTTTTCTGAGCTTTCGGGGATTTAGCAGCG
130 AAAGCGCCGCAAAAAAACCTAAGCCCAACGACACCATTTTCTGAGCTTTCGGGGATTTAGCAGCG
* * *
17539887 TTTTGTAAGAAAGCGCCGCTAATTCTCAGGGAT
195 TTTT-TAAGAAAGCGCCGCTAATGCTCAGGCAC
* * *
17539920 TTAGCGGCGTTGTT-GGTAAAGCGCCGCAAAAAAACCTAATCCCAACGACTCCGTTTTCTGAGCT
1 TTAGCGGCGTTTTTAGG-AAAGCGCCGC-AAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGC-
* * *
17539984 TTTGGGGATTTAGCGACGTTTTTAAGAAAGCGCCGCTAATGCTCAAGGATTTA
63 TTTCGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAAGTATTTA
17540037 AAATAATTTA
Statistics
Matches: 302, Mismatches: 36, Indels: 11
0.87 0.10 0.03
Matches are distributed among these distances:
226 65 0.22
227 158 0.52
228 75 0.25
229 4 0.01
ACGTcount: A:0.26, C:0.24, G:0.24, T:0.26
Consensus pattern (226 bp):
TTAGCGGCGTTTTTAGGAAAGCGCCGCAAAAAACCTAAGCCCAACGACGCCGTTTTCTGAGCTTT
CGGGATTTAGCGGCGTTTTTAAGAAAGCGCCGCTAATGCTCAAGTATTTAGCAGCATTTTTGGGA
AAGCGCCGCAAAAAAACCTAAGCCCAACGACACCATTTTCTGAGCTTTCGGGGATTTAGCAGCGT
TTTTAAGAAAGCGCCGCTAATGCTCAGGCAC
Found at i:17540277 original size:15 final size:15
Alignment explanation
Indices: 17540259--17540297 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 15
17540249 TACCATTTTA
17540259 AGGTTTATGGATTAT
1 AGGTTTATGGATTAT
* *
17540274 AGGTTTAGGGGTTAT
1 AGGTTTATGGATTAT
17540289 -GGTTTATGG
1 AGGTTTATGG
17540298 TTTAAAGGCC
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.21, C:0.00, G:0.36, T:0.44
Consensus pattern (15 bp):
AGGTTTATGGATTAT
Found at i:17540280 original size:22 final size:21
Alignment explanation
Indices: 17540205--17540302 Score: 72
Period size: 22 Copynumber: 4.6 Consensus size: 21
17540195 ATTAATTATC
* *
17540205 ATTATAGTTTAGGGTATATGG
1 ATTATAGTTTAAGGTTTATGG
*
17540226 TTTATAGTTTAAGGTTTA-GG
1 ATTATAGTTTAAGGTTTATGG
* * *
17540246 TGTTACCATTTTAAGGTTTATGG
1 -ATTA-TAGTTTAAGGTTTATGG
* *
17540269 ATTATAGGTTTAGGGGTTATGG
1 ATTATA-GTTTAAGGTTTATGG
* *
17540291 TTTATGGTTTAA
1 ATTATAGTTTAA
17540303 AGGCCGGGGT
Statistics
Matches: 59, Mismatches: 14, Indels: 8
0.73 0.17 0.10
Matches are distributed among these distances:
20 2 0.03
21 24 0.41
22 31 0.53
23 2 0.03
ACGTcount: A:0.24, C:0.02, G:0.27, T:0.47
Consensus pattern (21 bp):
ATTATAGTTTAAGGTTTATGG
Found at i:17540345 original size:15 final size:15
Alignment explanation
Indices: 17540309--17540387 Score: 51
Period size: 14 Copynumber: 5.5 Consensus size: 15
17540299 TTAAAGGCCG
* *
17540309 GGGTTTAAGGTTTAA
1 GGGTTTATGGGTTAA
* *
17540324 AGG-TTATGTGTTAA
1 GGGTTTATGGGTTAA
*
17540338 GGGTTTATGGGTTTA
1 GGGTTTATGGGTTAA
17540353 GGGTTT-TAGGGTTTAA
1 GGGTTTAT-GGG-TTAA
*
17540369 --GTTTATGGTTTAA
1 GGGTTTATGGGTTAA
17540382 -GGTTTA
1 GGGTTTA
17540388 GATTAACTAG
Statistics
Matches: 50, Mismatches: 9, Indels: 11
0.71 0.13 0.16
Matches are distributed among these distances:
13 4 0.08
14 22 0.44
15 21 0.42
16 3 0.06
ACGTcount: A:0.22, C:0.00, G:0.33, T:0.46
Consensus pattern (15 bp):
GGGTTTATGGGTTAA
Found at i:17540378 original size:13 final size:14
Alignment explanation
Indices: 17540334--17540388 Score: 58
Period size: 13 Copynumber: 3.8 Consensus size: 14
17540324 AGGTTATGTG
17540334 TTAAGGGTTTATGGGT
1 TTAA-GGTTTA-GGGT
*
17540350 TTAGGGTTTTAGGGT
1 TTAAGG-TTTAGGGT
*
17540365 TTAA-GTTTATGGT
1 TTAAGGTTTAGGGT
17540378 TTAAGGTTTAG
1 TTAAGGTTTAG
17540389 ATTAACTAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
13 11 0.33
14 6 0.18
15 9 0.27
16 7 0.21
ACGTcount: A:0.20, C:0.00, G:0.33, T:0.47
Consensus pattern (14 bp):
TTAAGGTTTAGGGT
Found at i:17540378 original size:21 final size:20
Alignment explanation
Indices: 17540348--17540387 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
17540338 GGGTTTATGG
*
17540348 GTTTAGGGTTTTAGGGTTTAA
1 GTTTAGGG-TTTAAGGTTTAA
*
17540369 GTTTATGGTTTAAGGTTTA
1 GTTTAGGGTTTAAGGTTTA
17540388 GATTAACTAG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.20, C:0.00, G:0.30, T:0.50
Consensus pattern (20 bp):
GTTTAGGGTTTAAGGTTTAA
Found at i:17540709 original size:22 final size:21
Alignment explanation
Indices: 17540679--17540753 Score: 53
Period size: 22 Copynumber: 3.4 Consensus size: 21
17540669 TGGGATTTAA
*
17540679 GGTTTAGGGGTTAGTAGTTAGG
1 GGTTAAGGGGTTAG-AGTTAGG
*
17540701 GGTTAA-GGGTTAAGAGTTAGT
1 GGTTAAGGGGTT-AGAGTTAGG
* * *
17540722 GATTTAGGGGTTAGGATTTAGG
1 GGTTAAGGGGTTA-GAGTTAGG
*
17540744 GATTTAAGGG
1 G-GTTAAGGG
17540754 TCGGGTTAGG
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
21 16 0.39
22 19 0.46
23 6 0.15
ACGTcount: A:0.24, C:0.00, G:0.41, T:0.35
Consensus pattern (21 bp):
GGTTAAGGGGTTAGAGTTAGG
Found at i:17540741 original size:14 final size:14
Alignment explanation
Indices: 17540681--17540744 Score: 58
Period size: 14 Copynumber: 4.5 Consensus size: 14
17540671 GGATTTAAGG
*
17540681 TTTAGGGGTTAGTA
1 TTTAGGGGTTAGGA
*
17540695 GTTAGGGGTTAAGG-
1 TTTAGGGGTT-AGGA
* * *
17540709 GTTAAGAGTTAGTGA
1 TTTAGGGGTTAG-GA
17540724 TTTAGGGGTTAGGA
1 TTTAGGGGTTAGGA
17540738 TTTAGGG
1 TTTAGGG
17540745 ATTTAAGGGT
Statistics
Matches: 40, Mismatches: 7, Indels: 6
0.75 0.13 0.11
Matches are distributed among these distances:
13 2 0.05
14 27 0.68
15 11 0.28
ACGTcount: A:0.23, C:0.00, G:0.41, T:0.36
Consensus pattern (14 bp):
TTTAGGGGTTAGGA
Found at i:17540754 original size:22 final size:21
Alignment explanation
Indices: 17540664--17540768 Score: 79
Period size: 21 Copynumber: 5.0 Consensus size: 21
17540654 GTTAATTTTG
* * *
17540664 AGGGTTGGGATTTAAGGTTTA
1 AGGGTTAGGAGTTAGGGTTTA
* * *
17540685 GGGGTTAGTAGTTAGGGGTTA
1 AGGGTTAGGAGTTAGGGTTTA
* *
17540706 AGGGTTAAGAGTTAGTGATTTA
1 AGGGTTAGGAGTTAG-GGTTTA
* *
17540728 GGGGTTAGGATTTAGGGATTTA
1 AGGGTTAGGAGTTAGGG-TTTA
*
17540750 AGGG-TCGG-GTTAGGGTTTA
1 AGGGTTAGGAGTTAGGGTTTA
17540769 GATTAATTAG
Statistics
Matches: 64, Mismatches: 18, Indels: 6
0.73 0.20 0.07
Matches are distributed among these distances:
19 4 0.06
20 6 0.09
21 31 0.48
22 23 0.36
ACGTcount: A:0.23, C:0.01, G:0.41, T:0.35
Consensus pattern (21 bp):
AGGGTTAGGAGTTAGGGTTTA
Found at i:17543541 original size:49 final size:46
Alignment explanation
Indices: 17543405--17543542 Score: 117
Period size: 49 Copynumber: 3.0 Consensus size: 46
17543395 AAAGATTGCT
* *
17543405 TATGTAAGCTATATTTAAATTTTATTAATAATAAATTGATAACTTA
1 TATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAATTTA
* * * *
17543451 -A-ATAAG-TAT-TATTATA-TTT-TTAATATTATACATATATTAATTTA
1 TATGTAAGCTATAT-TTAAATTTTATTAATA--ATAAATTTA-TAATTTA
17543495 CGTATGTAAGCTATATTTAAATTTTATTAATAATAAATTTTATAATTT
1 --TATGTAAGCTATATTTAAATTTTATTAATAATAAA-TTTATAATTT
17543543 TAAAAAAAAA
Statistics
Matches: 69, Mismatches: 10, Indels: 23
0.68 0.10 0.23
Matches are distributed among these distances:
41 6 0.09
42 4 0.06
43 13 0.19
44 10 0.14
45 1 0.01
47 1 0.01
48 4 0.06
49 17 0.25
50 7 0.10
51 6 0.09
ACGTcount: A:0.42, C:0.04, G:0.05, T:0.49
Consensus pattern (46 bp):
TATGTAAGCTATATTTAAATTTTATTAATAATAAATTTATAATTTA
Found at i:17543574 original size:21 final size:23
Alignment explanation
Indices: 17543559--17543659 Score: 61
Period size: 21 Copynumber: 4.4 Consensus size: 23
17543549 AAAATTCTAA
17543559 ATCT-TATTTTCTAAATATTAAC
1 ATCTATATTTTCTAAATATTAAC
*
17543581 ATCTATATTTTC--AATAATAA-
1 ATCTATATTTTCTAAATATTAAC
* **
17543601 ATTTTATAATTTTAGAAATGACTGTAA-
1 A-TCTAT-ATTTTCTAAAT-A-T-TAAC
*
17543628 ATGT-TATTTTCTAAATATTAAC
1 ATCTATATTTTCTAAATATTAAC
*
17543650 ATATATATTT
1 ATCTATATTT
17543660 GGAATAATAA
Statistics
Matches: 61, Mismatches: 8, Indels: 19
0.69 0.09 0.22
Matches are distributed among these distances:
20 1 0.02
21 14 0.23
22 13 0.21
23 13 0.21
24 12 0.20
25 2 0.03
26 2 0.03
27 4 0.07
ACGTcount: A:0.40, C:0.08, G:0.04, T:0.49
Consensus pattern (23 bp):
ATCTATATTTTCTAAATATTAAC
Found at i:17543647 original size:69 final size:69
Alignment explanation
Indices: 17543523--17543734 Score: 298
Period size: 69 Copynumber: 3.1 Consensus size: 69
17543513 AAATTTTATT
* * *
17543523 AATAATAAATTTTATAATTTTAAAAAAAAATTCTAAATCTTATTTTCTAAATATTAACATCTATA
1 AATAATAAATTTTATAATTTT-AAAAATAATTGTAAATGTTATTTTCTAAATATTAACATCTATA
17543588 TTTTC
65 TTTTC
* * * *
17543593 AATAATAAATTTTATAATTTTAGAAATGACTGTAAATGTTATTTTCTAAATATTAACATATATAT
1 AATAATAAATTTTATAATTTTAAAAATAATTGTAAATGTTATTTTCTAAATATTAACATCTATAT
**
17543658 TTGG
66 TTTC
* * *
17543662 AATAATAAATTTTACAATTTGAAAAATAATTGTAAATGTTATTTTCTAAATATTAACACCTATAT
1 AATAATAAATTTTATAATTTTAAAAATAATTGTAAATGTTATTTTCTAAATATTAACATCTATAT
*
17543727 TTTT
66 TTTC
17543731 AATA
1 AATA
17543735 TATCACCCAT
Statistics
Matches: 124, Mismatches: 18, Indels: 1
0.87 0.13 0.01
Matches are distributed among these distances:
69 103 0.83
70 21 0.17
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (69 bp):
AATAATAAATTTTATAATTTTAAAAATAATTGTAAATGTTATTTTCTAAATATTAACATCTATAT
TTTC
Found at i:17543953 original size:19 final size:19
Alignment explanation
Indices: 17543901--17543953 Score: 70
Period size: 19 Copynumber: 2.8 Consensus size: 19
17543891 ACATAACTTA
* *
17543901 TTAATATTTATATACATTT
1 TTAATATTTATATATATAT
*
17543920 TTAATATATATATATATAT
1 TTAATATTTATATATATAT
*
17543939 TTAAAATTTATATAT
1 TTAATATTTATATAT
17543954 TTTTTCAAAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
TTAATATTTATATATATAT
Found at i:17543963 original size:19 final size:18
Alignment explanation
Indices: 17543901--17543963 Score: 54
Period size: 19 Copynumber: 3.3 Consensus size: 18
17543891 ACATAACTTA
* *
17543901 TTAATATTTATATACATTT
1 TTAAAATTTATATA-TTTT
* * *
17543920 TTAATATATATATATATAT
1 TTAAAATTTATATAT-TTT
17543939 TTAAAATTTATATATTTT
1 TTAAAATTTATATATTTT
17543957 TTCAAAA
1 TT-AAAA
17543964 CTTTCAAAAC
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
18 4 0.11
19 32 0.89
ACGTcount: A:0.43, C:0.03, G:0.00, T:0.54
Consensus pattern (18 bp):
TTAAAATTTATATATTTT
Found at i:17545897 original size:21 final size:21
Alignment explanation
Indices: 17545873--17545946 Score: 80
Period size: 21 Copynumber: 3.6 Consensus size: 21
17545863 CTACAACTTA
17545873 AAGCAGAAGCAGCAGCGAGGG
1 AAGCAGAAGCAGCAGCGAGGG
* * *
17545894 AAGCAGCAGCTGCAGCAAGGG
1 AAGCAGAAGCAGCAGCGAGGG
* *
17545915 AAGCA-AAGGCTGCAGCGAGAG
1 AAGCAGAA-GCAGCAGCGAGGG
17545936 AAGCAG-AGCAG
1 AAGCAGAAGCAG
17545947 AGCAAAAAGT
Statistics
Matches: 44, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
20 4 0.09
21 40 0.91
ACGTcount: A:0.38, C:0.20, G:0.39, T:0.03
Consensus pattern (21 bp):
AAGCAGAAGCAGCAGCGAGGG
Found at i:17546359 original size:42 final size:42
Alignment explanation
Indices: 17546263--17546393 Score: 136
Period size: 42 Copynumber: 3.1 Consensus size: 42
17546253 TTTTGTATAA
* ** ***
17546263 AAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGCTTAGAAAA
1 AAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTTTATCT
* * *
17546305 AAACGCCGCTAAAGACCATGTTCTTTAGCGACGTTTTTCTCT
1 AAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTTTATCT
* * * *
17546347 AAGCGCCTCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTTCT
1 AAGCGCCGCTAAAGACCATGTTCTTTAGCGGCG-TTTTTATCT
17546390 AAGC
1 AAGC
17546394 AGTCTTTAGC
Statistics
Matches: 73, Mismatches: 15, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
42 61 0.84
43 12 0.16
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.30
Consensus pattern (42 bp):
AAGCGCCGCTAAAGACCATGTTCTTTAGCGGCGTTTTTATCT
Found at i:17550268 original size:31 final size:31
Alignment explanation
Indices: 17550233--17550300 Score: 84
Period size: 31 Copynumber: 2.2 Consensus size: 31
17550223 TACAATTAAT
* * *
17550233 AAAAATTAAAGTTTTATGTATATATTT-CAAC
1 AAAAATCAAACTTTAATGTATATATTTGC-AC
*
17550264 AAAAATCAAACTTTAATGTGTATATTTGCAC
1 AAAAATCAAACTTTAATGTATATATTTGCAC
17550295 AAAAAT
1 AAAAAT
17550301 AAAAAATTTT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
31 31 0.97
32 1 0.03
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.37
Consensus pattern (31 bp):
AAAAATCAAACTTTAATGTATATATTTGCAC
Found at i:17550688 original size:21 final size:22
Alignment explanation
Indices: 17550642--17550688 Score: 53
Period size: 21 Copynumber: 2.2 Consensus size: 22
17550632 GATTTAAAAT
* *
17550642 ATTTTAAAAATTTTAATCTTAT
1 ATTTTAAAAATTGTAATCTTAA
17550664 ATTTT-AAAATTGT-ATCTTGAA
1 ATTTTAAAAATTGTAATCTT-AA
17550685 ATTT
1 ATTT
17550689 CTAGTTTCAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 12 0.55
22 5 0.23
ACGTcount: A:0.38, C:0.04, G:0.04, T:0.53
Consensus pattern (22 bp):
ATTTTAAAAATTGTAATCTTAA
Found at i:17551177 original size:21 final size:21
Alignment explanation
Indices: 17551153--17551192 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
17551143 TTTTCTAAAT
* *
17551153 TTAAAAGTCAAAACTATTAAG
1 TTAAAAGACAAAACCATTAAG
17551174 TTAAAAGACAAAACCATTA
1 TTAAAAGACAAAACCATTA
17551193 TATTGTTTAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.12, G:0.07, T:0.25
Consensus pattern (21 bp):
TTAAAAGACAAAACCATTAAG
Found at i:17551859 original size:2 final size:2
Alignment explanation
Indices: 17551847--17551886 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
17551837 CAAATCTTCC
* *
17551847 TA TA CA TA TA TA TA TA TA TA TA TA AA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
17551887 ATCAATTCAA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (2 bp):
TA
Found at i:17554347 original size:24 final size:26
Alignment explanation
Indices: 17554302--17554349 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 26
17554292 CACATATTTT
*
17554302 GTATAACTACTTTATTACTATTTTCA
1 GTATAACTACTGTATTACTATTTTCA
*
17554328 GTATAACTA-TGTA-TAGTATTTT
1 GTATAACTACTGTATTACTATTTT
17554350 TCTCTGATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 8 0.40
25 3 0.15
26 9 0.45
ACGTcount: A:0.31, C:0.10, G:0.08, T:0.50
Consensus pattern (26 bp):
GTATAACTACTGTATTACTATTTTCA
Found at i:17558548 original size:34 final size:34
Alignment explanation
Indices: 17558441--17558540 Score: 139
Period size: 34 Copynumber: 2.9 Consensus size: 34
17558431 CTAAGCTGAT
*
17558441 CTATTATAAGCATA-TTACTTGTTACTGTATTGAA
1 CTATTATAAGCATATTTA-TTGATACTGTATTGAA
* * *
17558475 CTGTTATAAGCATATTAATTGATATTGTATTGAA
1 CTATTATAAGCATATTTATTGATACTGTATTGAA
*
17558509 CTATTATAAGCATATTTATTGCTACTGTATTG
1 CTATTATAAGCATATTTATTGATACTGTATTG
17558541 TTCTATTAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
34 55 0.96
35 2 0.04
ACGTcount: A:0.32, C:0.10, G:0.13, T:0.45
Consensus pattern (34 bp):
CTATTATAAGCATATTTATTGATACTGTATTGAA
Found at i:17563754 original size:17 final size:18
Alignment explanation
Indices: 17563722--17563756 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
17563712 TCATGATGTT
17563722 CGCCCGTGTGGGCCCACA
1 CGCCCGTGTGGGCCCACA
*
17563740 CGCCTGTGT-GGCCCACA
1 CGCCCGTGTGGGCCCACA
17563757 TGACCCAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.11, C:0.43, G:0.31, T:0.14
Consensus pattern (18 bp):
CGCCCGTGTGGGCCCACA
Found at i:17568135 original size:14 final size:14
Alignment explanation
Indices: 17568116--17568143 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
17568106 AGAATTGAAA
17568116 ATATTTAAAAAAAT
1 ATATTTAAAAAAAT
17568130 ATATTTAAAAAAAT
1 ATATTTAAAAAAAT
17568144 TTGTAAGTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (14 bp):
ATATTTAAAAAAAT
Found at i:17568343 original size:29 final size:28
Alignment explanation
Indices: 17568293--17568348 Score: 67
Period size: 29 Copynumber: 2.0 Consensus size: 28
17568283 TTTATCAGCA
** *
17568293 TTAACTAAGGATTAATTTTATTGAAACT
1 TTAACTAAGGATTAATAGTATTAAAACT
*
17568321 TTAATTAAGGAATTAATAGTATTAAAAC
1 TTAACTAAGG-ATTAATAGTATTAAAAC
17568349 ATAAAAAGTT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 9 0.39
29 14 0.61
ACGTcount: A:0.45, C:0.05, G:0.11, T:0.39
Consensus pattern (28 bp):
TTAACTAAGGATTAATAGTATTAAAACT
Found at i:17571430 original size:83 final size:81
Alignment explanation
Indices: 17571286--17571472 Score: 230
Period size: 83 Copynumber: 2.2 Consensus size: 81
17571276 GTGTTACACC
* * *
17571286 TTGGCCCCTCAAAAATGAAAATTTCAATTCAATCCTCTTATAAATAGAGAATTTATAAATTAATA
1 TTGGCCCCT-AAAAATGAAAATTTCAATACAATCCTCTTATAAATAAAGAAATTATAAATTAATA
* *
17571351 TATAGTGAAATTGTACT
65 TATAGTAAAATTATACT
* * * * *
17571368 TTGGCCCCTTAAAATTAAAATTTTTCAATACAGTCCTCTTATAAATAAAGAAATTGTTAATTAAT
1 TTGGCCCCTAAAAATGAAAA--TTTCAATACAATCCTCTTATAAATAAAGAAATTATAAATTAAT
17571433 ATATAGTAAAATTATACT
64 ATATAGTAAAATTATACT
*
17571451 TTAGCCCTCTAAAAATGGAAAA
1 TTGGCCC-CTAAAAAT-GAAAA
17571473 ATATATGGTT
Statistics
Matches: 88, Mismatches: 13, Indels: 5
0.83 0.12 0.05
Matches are distributed among these distances:
81 9 0.10
82 9 0.10
83 59 0.67
84 7 0.08
85 4 0.05
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.35
Consensus pattern (81 bp):
TTGGCCCCTAAAAATGAAAATTTCAATACAATCCTCTTATAAATAAAGAAATTATAAATTAATAT
ATAGTAAAATTATACT
Found at i:17572431 original size:30 final size:30
Alignment explanation
Indices: 17572405--17572477 Score: 91
Period size: 28 Copynumber: 2.5 Consensus size: 30
17572395 AATTAAAATT
17572405 TTAAAAATTCAA-AAAATTATTTTTAAAAAA
1 TTAAAAA-TCAATAAAATTATTTTTAAAAAA
*
17572435 TTAAAAATCAATAAAATTA--TTTAAAAAG
1 TTAAAAATCAATAAAATTATTTTTAAAAAA
17572463 TATAAAAATC-ATAAA
1 T-TAAAAATCAATAAA
17572478 TAAATTAATT
Statistics
Matches: 40, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
28 14 0.35
29 12 0.30
30 14 0.35
ACGTcount: A:0.62, C:0.04, G:0.01, T:0.33
Consensus pattern (30 bp):
TTAAAAATCAATAAAATTATTTTTAAAAAA
Found at i:17572485 original size:27 final size:28
Alignment explanation
Indices: 17572427--17572485 Score: 68
Period size: 28 Copynumber: 2.1 Consensus size: 28
17572417 AAAATTATTT
* *
17572427 TTAAAAAATTAAAAATCAATAAAATTAT
1 TTAAAAAATTAAAAATCAATAAAATAAA
*
17572455 TTAAAAAGTATAAAAATC-AT-AAATAAA
1 TTAAAAAAT-TAAAAATCAATAAAATAAA
17572482 TTAA
1 TTAA
17572486 TTAAATACTG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 9 0.33
28 10 0.37
29 8 0.30
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (28 bp):
TTAAAAAATTAAAAATCAATAAAATAAA
Found at i:17580802 original size:18 final size:18
Alignment explanation
Indices: 17580779--17580814 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
17580769 GTTTTATGCT
17580779 GAGAAGAAGAAGATGAAG
1 GAGAAGAAGAAGATGAAG
*
17580797 GAGAAGAAGATGATGAAG
1 GAGAAGAAGAAGATGAAG
17580815 AGTATGAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.53, C:0.00, G:0.39, T:0.08
Consensus pattern (18 bp):
GAGAAGAAGAAGATGAAG
Found at i:17582830 original size:162 final size:163
Alignment explanation
Indices: 17582656--17582969 Score: 569
Period size: 162 Copynumber: 1.9 Consensus size: 163
17582646 AGGTACCAAC
* *
17582656 TTGACAACTGAGTCCATTTTAGTCCCAAACTTGAAACCTATAAAAGTTTGATGATGTGGCATTAT
1 TTGACAACTGAGTCCATTTTAGTCCCAAACTTGAAAACTATAAAAGTTTGATGATGTGGCACTAT
17582721 GAGATTGTGCAACATCATCACTTGAAAA-TT-AAAAAATATATATGAATTTTCAGGTGATGATGT
66 GAGATTGTGCAACATCATCACTTGAAAATTTAAAAAAAT-TATATGAATTTTCAGGTGATGATGT
17582784 GATACAATTTCAAAGTTTCACATGGCACTTAAAT
130 GATACAATTTCAAAGTTTCACATGGCACTTAAAT
17582818 TTGACAACTGAGTCCATTTTAGTCCCAAACTTGAAAACTATAAAAGTTTGATGATGTGGCACTAT
1 TTGACAACTGAGTCCATTTTAGTCCCAAACTTGAAAACTATAAAAGTTTGATGATGTGGCACTAT
*
17582883 GAGATTGTGCTACATCATCACTTGAAAATTTAAAAAAATTATATGAATTTTCAGGTGATGATGTG
66 GAGATTGTGCAACATCATCACTTGAAAATTTAAAAAAATTATATGAATTTTCAGGTGATGATGTG
*
17582948 GTACAATTTCAAAGTTTCACAT
131 ATACAATTTCAAAGTTTCACAT
17582970 ACAATATTTT
Statistics
Matches: 146, Mismatches: 4, Indels: 3
0.95 0.03 0.02
Matches are distributed among these distances:
162 90 0.62
163 49 0.34
164 7 0.05
ACGTcount: A:0.36, C:0.14, G:0.16, T:0.34
Consensus pattern (163 bp):
TTGACAACTGAGTCCATTTTAGTCCCAAACTTGAAAACTATAAAAGTTTGATGATGTGGCACTAT
GAGATTGTGCAACATCATCACTTGAAAATTTAAAAAAATTATATGAATTTTCAGGTGATGATGTG
ATACAATTTCAAAGTTTCACATGGCACTTAAAT
Found at i:17586489 original size:45 final size:46
Alignment explanation
Indices: 17586427--17586522 Score: 133
Period size: 45 Copynumber: 2.1 Consensus size: 46
17586417 CAATTTGACC
*
17586427 TACTAAATAATTAACTAAATTACATAGTATATATT-TTAAATTATTTA
1 TACTAAAT-ATTAACTAAATTACATAGTATATATTATT-AATTATCTA
* *
17586474 TACTAAAT-TTAACTAAATTAGATAGTATTTATTATTAATTATCTA
1 TACTAAATATTAACTAAATTACATAGTATATATTATTAATTATCTA
17586519 TACT
1 TACT
17586523 TGATCAAGGG
Statistics
Matches: 45, Mismatches: 3, Indels: 4
0.87 0.06 0.08
Matches are distributed among these distances:
45 35 0.78
46 2 0.04
47 8 0.18
ACGTcount: A:0.44, C:0.07, G:0.03, T:0.46
Consensus pattern (46 bp):
TACTAAATATTAACTAAATTACATAGTATATATTATTAATTATCTA
Found at i:17593551 original size:3 final size:3
Alignment explanation
Indices: 17593543--17593584 Score: 59
Period size: 3 Copynumber: 14.3 Consensus size: 3
17593533 TGATATAAAA
* *
17593543 AAT AAT AAT AA- ACT AAT AAT AAT AAT AGT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
17593585 TTAAACCAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
2 1 0.03
3 33 0.97
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:17595118 original size:45 final size:45
Alignment explanation
Indices: 17594883--17595805 Score: 558
Period size: 44 Copynumber: 20.7 Consensus size: 45
17594873 ACTAGGCTTC
* * *
17594883 AATCTGCCCCGCTGCAACTTCAGGGGGATAAGA-TTCGCTA----T
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GCTATCTTT
* * * * * * *
17594924 GATCTACTCTACTGCAACTTCAGAGAGATAAAATCTGTAACCAGTCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-T-GCTA-TCTTT
* * * * * * *
17594973 AATCTGCTCCACCGTAATTTCAGGGA-AGTGAGATTTGCTATATTC
1 AATCTGCTCCACTGCAACTTCAGGGAGA-TAAGACTTGCTATCTTT
* * * * *
17595018 AGTCTGC-CCTACTGCAACTTTAGGGGGATAGGACTTG---T-TAT
1 AATCTGCTCC-ACTGCAACTTCAGGGAGATAAGACTTGCTATCTTT
** * * ** *
17595059 GGTCTGCTCTACTGCAACTTCAGAGAGATAAGACCCGCTATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTT
* * * * * *
17595104 AGTCTGCTCCACTGCAACTTCAGAGAGATAAGA-GTGGTGTCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTT
* * * * * * *
17595148 AATCCGCTCCACTACAACTTCAAGGAGAT-AGAATT-ATTTGCTGT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTAT-CTTT
* * *
17595192 AATCTGCTCCACTGTAACTTCAGGGAGATAAGATTTGC---C-AT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTT
* * * *
17595233 GATCTGCTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTATAGCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-TG--CTAT--CTTT
* * * *
17595284 AATCTGTTCCACTACAACTTCAGAGAAATAAGA-TTCGCTATCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GCTATCTTT
*
17595329 AATCTGCTCCACTACAACTTCAGGGAGATAAGACTTG-TCA-CTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCT-ATCTTT
* * ** **
17595373 AATCCGCTCCACTGCAACTTCAGGGAGATAGGA-TTATTGGCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTT
* * * * * *
17595417 AATTTACTCCACTGCAACTTCAAGGAGATAAGA-TTCACCATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GCTATCTTT
* * * * * *
17595462 ATTCTGCCCCACTGCAACTTTAGGGGGATAAGACTTGTTTTCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTT
* * * *
17595507 AGTCTGCTCCACTGTAACTTCAAGGAGATAAGACTTG-TAACTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTT
* * * * * **
17595551 AACCCGCTCCACTGTAACTTCAGGGAGATATGA-TTACTGGCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTT
* *
17595595 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTCGCCATCTTC
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GCTATCTTT
* * * *
17595640 AGTCTG-TCCCACTGCAACTTCAGGGGGATAAGACTTGCTTTCTTC
1 AATCTGCT-CCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTT
* * *
17595685 AGTCTGCTCCACTGTAACTTCAGGGAGATAAGACTTG-TAACTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTT
* ** **
17595729 AAT-TCGCTCCACTACAACTTCAGGGAGAT-AGTA-TTATTGGCTTT
1 AATCT-GCTCCACTGCAACTTCAGGGAGATAAG-ACTTGCTATCTTT
*
17595773 AATCTGCTCCACTACAACTTCAGGGAGATAAGA
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA
17595806 TTCGCCATCT
Statistics
Matches: 683, Mismatches: 152, Indels: 91
0.74 0.16 0.10
Matches are distributed among these distances:
41 83 0.12
42 4 0.01
43 17 0.02
44 267 0.39
45 240 0.35
46 10 0.01
47 4 0.01
48 3 0.00
49 25 0.04
50 1 0.00
51 29 0.04
ACGTcount: A:0.27, C:0.23, G:0.19, T:0.30
Consensus pattern (45 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTATCTTT
Done.