Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr09 ID=Chr09-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: 70713020
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1142373 characters in sequence are not A, C, G, or T
File 30 of 226
Found at i:13373020 original size:13 final size:13
Alignment explanation
Indices: 13373002--13373026 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
13372992 TACCTATCTA
13373002 AAGAAAGTCTGCG
1 AAGAAAGTCTGCG
13373015 AAGAAAGTCTGC
1 AAGAAAGTCTGC
13373027 CCAAGACAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.16, G:0.28, T:0.16
Consensus pattern (13 bp):
AAGAAAGTCTGCG
Found at i:13373232 original size:12 final size:12
Alignment explanation
Indices: 13373215--13373240 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
13373205 AAACCAGATC
13373215 AAGGGAGAACGA
1 AAGGGAGAACGA
13373227 AAGGGAGAACGA
1 AAGGGAGAACGA
13373239 AA
1 AA
13373241 CCAAATCAGT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.54, C:0.08, G:0.38, T:0.00
Consensus pattern (12 bp):
AAGGGAGAACGA
Found at i:13374653 original size:23 final size:23
Alignment explanation
Indices: 13374627--13374697 Score: 124
Period size: 23 Copynumber: 3.1 Consensus size: 23
13374617 AGTGTTATTG
13374627 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
13374650 ATCAGTGGTAGCTTCGACTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
*
13374673 TTCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
13374696 AT
1 AT
13374698 TTGTGTGGCA
Statistics
Matches: 44, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 44 1.00
ACGTcount: A:0.23, C:0.21, G:0.24, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:13374874 original size:38 final size:37
Alignment explanation
Indices: 13374832--13374904 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 37
13374822 ATGTATGGAA
* *
13374832 TTGAATTGAATATTGACTTGAAAA-TGGAAAAGTGAATT
1 TTGAATTGAATAGTGA-TT-AAAAGTGAAAAAGTGAATT
13374870 TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAA
1 TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAA
13374905 ATTATGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 4 0.12
37 13 0.41
38 15 0.47
ACGTcount: A:0.45, C:0.01, G:0.22, T:0.32
Consensus pattern (37 bp):
TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAATT
Found at i:13375914 original size:2 final size:2
Alignment explanation
Indices: 13375907--13375968 Score: 124
Period size: 2 Copynumber: 31.0 Consensus size: 2
13375897 TGGTATTGAA
13375907 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13375949 AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT
13375969 TGGATTGAGA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 60 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13376427 original size:14 final size:14
Alignment explanation
Indices: 13376408--13376434 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
13376398 CGGAAAATTC
13376408 GAAAAATATTTTCT
1 GAAAAATATTTTCT
13376422 GAAAAATATTTTC
1 GAAAAATATTTTC
13376435 CACCAAACAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.41
Consensus pattern (14 bp):
GAAAAATATTTTCT
Found at i:13396479 original size:21 final size:21
Alignment explanation
Indices: 13396440--13396481 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
13396430 TTTTCCTAAG
*
13396440 ATGTGAATTAGATTGAATTGA
1 ATGTGAATTAGATTAAATTGA
**
13396461 ATGTGAATTTTATTAAATTGA
1 ATGTGAATTAGATTAAATTGA
13396482 GTTAAATTTA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.19, T:0.43
Consensus pattern (21 bp):
ATGTGAATTAGATTAAATTGA
Found at i:13397194 original size:25 final size:25
Alignment explanation
Indices: 13397124--13397195 Score: 63
Period size: 25 Copynumber: 2.9 Consensus size: 25
13397114 TATGCCTCTT
* ** **
13397124 ATGAGCTTCCCGTTATAAGGCCCGG
1 ATGAGCTTCCCGTTATATGGTTCAC
* * * *
13397149 ATAAGCCTCCTGTTACATGGTTCAC
1 ATGAGCTTCCCGTTATATGGTTCAC
13397174 ATGAGCTTCCCGTTATATGGTT
1 ATGAGCTTCCCGTTATATGGTT
13397196 TGAAAGAGTG
Statistics
Matches: 34, Mismatches: 13, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
25 34 1.00
ACGTcount: A:0.21, C:0.25, G:0.22, T:0.32
Consensus pattern (25 bp):
ATGAGCTTCCCGTTATATGGTTCAC
Found at i:13398363 original size:23 final size:25
Alignment explanation
Indices: 13398325--13398371 Score: 71
Period size: 23 Copynumber: 2.0 Consensus size: 25
13398315 TTCGTGTAAC
13398325 TTAATTGTGCAATTATATGTTTGAA
1 TTAATTGTGCAATTATATGTTTGAA
*
13398350 TTAATT-TG-AATTATTTGTTTGA
1 TTAATTGTGCAATTATATGTTTGA
13398372 GAATTGTCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 13 0.62
24 2 0.10
25 6 0.29
ACGTcount: A:0.30, C:0.02, G:0.15, T:0.53
Consensus pattern (25 bp):
TTAATTGTGCAATTATATGTTTGAA
Found at i:13403333 original size:24 final size:24
Alignment explanation
Indices: 13403297--13403344 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
13403287 CAAATGAATG
*
13403297 GTAAGATAATTTTCGTTATACGAA
1 GTAAGATAATTTTCATTATACGAA
*
13403321 GTAAGATAGTTTTCATTATACGAA
1 GTAAGATAATTTTCATTATACGAA
13403345 CTTACTAAGC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.38, C:0.08, G:0.17, T:0.38
Consensus pattern (24 bp):
GTAAGATAATTTTCATTATACGAA
Found at i:13406667 original size:22 final size:21
Alignment explanation
Indices: 13406629--13406669 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
13406619 CATTTGAAAT
**
13406629 AAATTTTAAAATTTATTTTTA
1 AAATTTTAAAAAATATTTTTA
13406650 AAATTTTCAAAAAATATTTT
1 AAATTTT-AAAAAATATTTT
13406670 CGGTAAATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 7 0.41
22 10 0.59
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.51
Consensus pattern (21 bp):
AAATTTTAAAAAATATTTTTA
Found at i:13421819 original size:2 final size:2
Alignment explanation
Indices: 13421812--13421837 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13421802 ATATAAAGTA
13421812 AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT
13421838 TTTGCTTAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:13435837 original size:19 final size:21
Alignment explanation
Indices: 13435805--13435843 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
13435795 AGACTAGTTT
*
13435805 TTTTTTTTTGAGAA-ATAAAG
1 TTTTTGTTTGAGAATATAAAG
13435825 TTTTTGTTT-AGAATATAAA
1 TTTTTGTTTGAGAATATAAA
13435844 TCAAATTGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (21 bp):
TTTTTGTTTGAGAATATAAAG
Found at i:13437615 original size:25 final size:24
Alignment explanation
Indices: 13437569--13437616 Score: 69
Period size: 25 Copynumber: 2.0 Consensus size: 24
13437559 TATTTCATTG
* *
13437569 TTTATTAAAAAATTCATTCATTTA
1 TTTATTAAAAAATCCATCCATTTA
13437593 TTTAGTTAAAAAATCCATCCATTT
1 TTTA-TTAAAAAATCCATCCATTT
13437617 TTTTTTTGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 4 0.19
25 17 0.81
ACGTcount: A:0.40, C:0.12, G:0.02, T:0.46
Consensus pattern (24 bp):
TTTATTAAAAAATCCATCCATTTA
Found at i:13454133 original size:33 final size:33
Alignment explanation
Indices: 13454096--13454217 Score: 113
Period size: 33 Copynumber: 3.7 Consensus size: 33
13454086 GTTTAAATGT
* *
13454096 AAGACCATAGCTTGGTTATGACATTTTAATGAA
1 AAGACCATAGCTGGGTTATGACATTCTAATGAA
* * * * * *
13454129 AAGACCTTAACTGGGTTATGGCACTACAAATG-T
1 AAGACCATAGCTGGGTTATGACA-TTCTAATGAA
* * *
13454162 AAGACCATAGCTGGGCTATGGCATTCTGATGAA
1 AAGACCATAGCTGGGTTATGACATTCTAATGAA
13454195 AAGACCAT-GACTGGGTTATGACA
1 AAGACCATAG-CTGGGTTATGACA
13454218 CTACAAATGT
Statistics
Matches: 69, Mismatches: 17, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
32 6 0.09
33 58 0.84
34 5 0.07
ACGTcount: A:0.34, C:0.16, G:0.23, T:0.27
Consensus pattern (33 bp):
AAGACCATAGCTGGGTTATGACATTCTAATGAA
Found at i:13454171 original size:66 final size:66
Alignment explanation
Indices: 13454090--13454235 Score: 220
Period size: 66 Copynumber: 2.2 Consensus size: 66
13454080 GGAAATGTTT
* * * * *
13454090 AAATGTAAGACCATAGCTTGGTTATGACATTTTAATGAAAAGACCTTAACTGGGTTATGGCACTA
1 AAATGTAAGACCATAGCTGGGCTATGACATTCTAATGAAAAGACCATAACTGGGTTATGACACTA
13454155 C
66 C
* * *
13454156 AAATGTAAGACCATAGCTGGGCTATGGCATTCTGATGAAAAGACCATGACTGGGTTATGACACTA
1 AAATGTAAGACCATAGCTGGGCTATGACATTCTAATGAAAAGACCATAACTGGGTTATGACACTA
13454221 C
66 C
13454222 AAATGTAAGACCAT
1 AAATGTAAGACCAT
13454236 GACAAGGCCA
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
66 72 1.00
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (66 bp):
AAATGTAAGACCATAGCTGGGCTATGACATTCTAATGAAAAGACCATAACTGGGTTATGACACTA
C
Found at i:13454238 original size:33 final size:31
Alignment explanation
Indices: 13454090--13454235 Score: 103
Period size: 33 Copynumber: 4.5 Consensus size: 31
13454080 GGAAATGTTT
* **
13454090 AAATGTAAGACCATAGCTTGGTTATGACATTT
1 AAATGTAAGACCATA-CTGGGTTATGACATAC
* * * *
13454122 TAATGAAAAGACCTTAACTGGGTTATGGCACTAC
1 AAATG-TAAGACCAT-ACTGGGTTATGACA-TAC
* * *
13454156 AAATGTAAGACCATAGCTGGGCTATGGCATTC
1 AAATGTAAGACCATA-CTGGGTTATGACATAC
** *
13454188 TGATGAAAAGACCATGACTGGGTTATGACACTAC
1 AAATG-TAAGACCAT-ACTGGGTTATGACA-TAC
13454222 AAATGTAAGACCAT
1 AAATGTAAGACCAT
13454236 GACAAGGCCA
Statistics
Matches: 86, Mismatches: 21, Indels: 13
0.72 0.17 0.11
Matches are distributed among these distances:
32 10 0.12
33 64 0.74
34 12 0.14
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.27
Consensus pattern (31 bp):
AAATGTAAGACCATACTGGGTTATGACATAC
Found at i:13458472 original size:13 final size:13
Alignment explanation
Indices: 13458454--13458483 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
13458444 TCCAGCAACT
13458454 ATGAATTTATTTC
1 ATGAATTTATTTC
*
13458467 ATGAATTTATTTG
1 ATGAATTTATTTC
13458480 ATGA
1 ATGA
13458484 TGGTCCAAGC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.33, C:0.03, G:0.13, T:0.50
Consensus pattern (13 bp):
ATGAATTTATTTC
Found at i:13458651 original size:50 final size:50
Alignment explanation
Indices: 13458576--13458818 Score: 342
Period size: 50 Copynumber: 4.8 Consensus size: 50
13458566 ATTTGGGTAA
* ** *
13458576 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGATATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
*
13458626 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGACG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
* * *
13458676 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
* * * * *
13458726 AGAGGTCCCCTATAAGACCATGTCTGGGACATGGCATGGGCACCAACATG
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
* *
13458776 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCA
13458819 TGTCATTATC
Statistics
Matches: 171, Mismatches: 21, Indels: 1
0.89 0.11 0.01
Matches are distributed among these distances:
50 137 0.80
51 34 0.20
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (50 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCATTGGCACCAAGATG
Found at i:13458754 original size:100 final size:100
Alignment explanation
Indices: 13458576--13458818 Score: 378
Period size: 100 Copynumber: 2.4 Consensus size: 100
13458566 ATTTGGGTAA
* * *
13458576 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACTGATATGAGAGATCCCATGTAA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGATCCCATATAA
* *
13458641 GACCATGTCTGGGACATGGCATTGGCACCAAGACG
66 GACCATGTCTGGGACATGGCATGGGCACCAACACG
* * *
13458676 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGGTCCCCTATAA
1 AGAGATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGATCCCATATAA
*
13458741 GACCATGTCTGGGACATGGCATGGGCACCAACATG
66 GACCATGTCTGGGACATGGCATGGGCACCAACACG
* *
13458776 AGAACATCCCATGTAAGACCATGTCTGGGACATGGCTTTGGCA
1 AG-AGATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA
13458819 TGTCATTATC
Statistics
Matches: 130, Mismatches: 12, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
100 93 0.72
101 37 0.28
ACGTcount: A:0.27, C:0.23, G:0.29, T:0.21
Consensus pattern (100 bp):
AGAGATCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGAGAGATCCCATATAA
GACCATGTCTGGGACATGGCATGGGCACCAACACG
Found at i:13461475 original size:17 final size:18
Alignment explanation
Indices: 13461453--13461486 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
13461443 TAACAATCAT
13461453 TAAAAGAAT-AAAGAAAC
1 TAAAAGAATAAAAGAAAC
13461470 TAAAAGAATAAAAGAAA
1 TAAAAGAATAAAAGAAA
13461487 GAAAAGAAGG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.74, C:0.03, G:0.12, T:0.12
Consensus pattern (18 bp):
TAAAAGAATAAAAGAAAC
Found at i:13461491 original size:17 final size:17
Alignment explanation
Indices: 13461454--13461494 Score: 57
Period size: 17 Copynumber: 2.4 Consensus size: 17
13461444 AACAATCATT
*
13461454 AAAAGAATAAAGAAACT
1 AAAAGAATAAAGAAACG
13461471 AAAAGAATAAAAGAAA-G
1 AAAAGAAT-AAAGAAACG
13461488 AAAAGAA
1 AAAAGAA
13461495 GGAGAAAAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 15 0.68
18 7 0.32
ACGTcount: A:0.76, C:0.02, G:0.15, T:0.07
Consensus pattern (17 bp):
AAAAGAATAAAGAAACG
Found at i:13468430 original size:44 final size:44
Alignment explanation
Indices: 13468380--13468543 Score: 238
Period size: 44 Copynumber: 3.6 Consensus size: 44
13468370 TACGTATGAT
13468380 CACTTATCACTTGTCACTGATCAGATAAGTGTAGCCAAAGCTAC
1 CACTTATCACTTGTCACTGATCAGATAAGTGTAGCCAAAGCTAC
*
13468424 CACTTATCACTTGTCACTGATCAGATAACTGTAGCCAAAGCTAC
1 CACTTATCACTTGTCACTGATCAGATAAGTGTAGCCAAAGCTAC
* *
13468468 CACCTATCACTTGTCACTTGTCACTGATCAGATAAGTGCAGCTAAAGCTAC
1 CA-CT-T-A----TCACTTGTCACTGATCAGATAAGTGTAGCCAAAGCTAC
13468519 CACTTATCACTTGTCACTGATCAGA
1 CACTTATCACTTGTCACTGATCAGA
13468544 AGTACTCAAA
Statistics
Matches: 109, Mismatches: 4, Indels: 14
0.86 0.03 0.11
Matches are distributed among these distances:
44 64 0.59
45 2 0.02
46 1 0.01
47 1 0.01
48 1 0.01
49 1 0.01
50 2 0.02
51 37 0.34
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (44 bp):
CACTTATCACTTGTCACTGATCAGATAAGTGTAGCCAAAGCTAC
Found at i:13468479 original size:51 final size:51
Alignment explanation
Indices: 13468424--13468536 Score: 181
Period size: 51 Copynumber: 2.2 Consensus size: 51
13468414 CCAAAGCTAC
* *
13468424 CACTTATCACTTGTCACTGATCAGATAACTGTAGCCAAAGCTACCACCTAT
1 CACTTGTCACTTGTCACTGATCAGATAACTGCAGCCAAAGCTACCACCTAT
* * *
13468475 CACTTGTCACTTGTCACTGATCAGATAAGTGCAGCTAAAGCTACCACTTAT
1 CACTTGTCACTTGTCACTGATCAGATAACTGCAGCCAAAGCTACCACCTAT
13468526 CACTTGTCACT
1 CACTTGTCACT
13468537 GATCAGAAGT
Statistics
Matches: 57, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
51 57 1.00
ACGTcount: A:0.29, C:0.28, G:0.13, T:0.29
Consensus pattern (51 bp):
CACTTGTCACTTGTCACTGATCAGATAACTGCAGCCAAAGCTACCACCTAT
Found at i:13480267 original size:14 final size:14
Alignment explanation
Indices: 13480250--13480280 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
13480240 TAAAAATAAA
13480250 TTTTTAATTTTATT
1 TTTTTAATTTTATT
13480264 TTTTTAATTTTATT
1 TTTTTAATTTTATT
13480278 TTT
1 TTT
13480281 AAAATTTTGG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (14 bp):
TTTTTAATTTTATT
Found at i:13480286 original size:14 final size:14
Alignment explanation
Indices: 13480255--13480288 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
13480245 ATAAATTTTT
**
13480255 AATTTTATTTTTTT
1 AATTTTATTTTTAA
13480269 AATTTTATTTTTAA
1 AATTTTATTTTTAA
13480283 AATTTT
1 AATTTT
13480289 GGAAACATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (14 bp):
AATTTTATTTTTAA
Found at i:13483691 original size:49 final size:46
Alignment explanation
Indices: 13483559--13483693 Score: 191
Period size: 45 Copynumber: 2.9 Consensus size: 46
13483549 CCATGGAAAA
* *
13483559 TTGTGAAAAGTAGGTATGGTGTTTTAGTGAA-AAAAGCATATTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATATTGAG
*
13483604 TTGTGAAAAGTAGGCATGGTGTTTCAGTGAAGAAAACCATATTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATATTGAG
* *
13483650 TTGTGAAAAGTAGGAGGTATGGTATTTCAGTGAAGGAAACCATA
1 TTGTGAAAAGT---AGGTATGGTGTTTCAGTGAAGAAAACCATA
13483694 CTGAATTATA
Statistics
Matches: 80, Mismatches: 6, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
45 29 0.36
46 24 0.30
49 27 0.34
ACGTcount: A:0.36, C:0.06, G:0.29, T:0.30
Consensus pattern (46 bp):
TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATATTGAG
Found at i:13488518 original size:8 final size:9
Alignment explanation
Indices: 13488491--13488555 Score: 53
Period size: 10 Copynumber: 7.1 Consensus size: 9
13488481 CTCTCTTTTA
13488491 TATATATAT
1 TATATATAT
13488500 ATATATATAT
1 -TATATATAT
13488510 TATA-ATAT
1 TATATATAT
* *
13488518 TTTATAAAT
1 TATATATAT
* *
13488527 TACTCTTTAT
1 TA-TATATAT
13488537 GTATATATAT
1 -TATATATAT
13488547 TATA-ATAT
1 TATATATAT
13488555 T
1 T
13488556 TAATAAATTA
Statistics
Matches: 44, Mismatches: 8, Indels: 8
0.73 0.13 0.13
Matches are distributed among these distances:
8 12 0.27
9 12 0.27
10 18 0.41
11 2 0.05
ACGTcount: A:0.42, C:0.03, G:0.02, T:0.54
Consensus pattern (9 bp):
TATATATAT
Found at i:13488792 original size:13 final size:13
Alignment explanation
Indices: 13488774--13488809 Score: 51
Period size: 11 Copynumber: 3.0 Consensus size: 13
13488764 CCGGCCCGCC
13488774 TATATTAATTTTT
1 TATATTAATTTTT
13488787 TATATT-A-TTTT
1 TATATTAATTTTT
13488798 TATA-TAATTTTT
1 TATATTAATTTTT
13488810 AAATATTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
10 1 0.05
11 9 0.43
12 5 0.24
13 6 0.29
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (13 bp):
TATATTAATTTTT
Found at i:13488925 original size:30 final size:31
Alignment explanation
Indices: 13488891--13488953 Score: 101
Period size: 30 Copynumber: 2.1 Consensus size: 31
13488881 ACTTCACAAG
13488891 CAAATGCCTCTAAAATAATAAC-AAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAAATTAA
* *
13488921 CAAATGTCTTTAAAATAATAACAAAAATTAA
1 CAAATGCCTCTAAAATAATAACAAAAATTAA
13488952 CA
1 CA
13488954 GTAAAATAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
30 20 0.67
31 10 0.33
ACGTcount: A:0.57, C:0.14, G:0.03, T:0.25
Consensus pattern (31 bp):
CAAATGCCTCTAAAATAATAACAAAAATTAA
Found at i:13490582 original size:46 final size:46
Alignment explanation
Indices: 13490510--13490609 Score: 173
Period size: 46 Copynumber: 2.2 Consensus size: 46
13490500 ACGATGCTAT
13490510 AACTCAGTATGGTTTCCTTCACTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTCCTTCACTGAAACACCATACCTACTTTTCAC
* * *
13490556 AACTTAGTATGGTTTTCTTCATTGAAACACCATACCTACTTTTCAC
1 AACTCAGTATGGTTTCCTTCACTGAAACACCATACCTACTTTTCAC
13490602 AACTCAGT
1 AACTCAGT
13490610 TTTATTGTTA
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 50 1.00
ACGTcount: A:0.29, C:0.27, G:0.09, T:0.35
Consensus pattern (46 bp):
AACTCAGTATGGTTTCCTTCACTGAAACACCATACCTACTTTTCAC
Found at i:13495776 original size:23 final size:23
Alignment explanation
Indices: 13495708--13495775 Score: 118
Period size: 23 Copynumber: 2.9 Consensus size: 23
13495698 TACCTACTTT
*
13495708 CACTACACCAAAACAAGCTTTTA
1 CACTACACCAAAACAGGCTTTTA
13495731 CACTACACCAAAACAGGCTTTTA
1 CACTACACCAAAACAGGCTTTTA
13495754 CACTACACCAAAACAGGTCTTT
1 CACTACACCAAAACAGG-CTTT
13495776 AGCGGCGTAT
Statistics
Matches: 43, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
23 39 0.91
24 4 0.09
ACGTcount: A:0.40, C:0.31, G:0.07, T:0.22
Consensus pattern (23 bp):
CACTACACCAAAACAGGCTTTTA
Found at i:13496492 original size:18 final size:21
Alignment explanation
Indices: 13496446--13496494 Score: 59
Period size: 18 Copynumber: 2.5 Consensus size: 21
13496436 TAGTTCGACT
13496446 AAATTAATATATAAATCAAAC
1 AAATTAATATATAAATCAAAC
* *
13496467 AAAGTAATATA-AAA-C-ACC
1 AAATTAATATATAAATCAAAC
13496485 AAATTAATAT
1 AAATTAATAT
13496495 CGTGATTAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
18 11 0.44
19 1 0.04
20 3 0.12
21 10 0.40
ACGTcount: A:0.61, C:0.10, G:0.02, T:0.27
Consensus pattern (21 bp):
AAATTAATATATAAATCAAAC
Found at i:13496770 original size:15 final size:16
Alignment explanation
Indices: 13496752--13496782 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
13496742 GCTTTAAGAC
13496752 TTAGGGTT-TAGGGGT
1 TTAGGGTTATAGGGGT
13496767 TTAGGGTTATAGGGGT
1 TTAGGGTTATAGGGGT
13496783 CGGGTTAGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.53
16 7 0.47
ACGTcount: A:0.16, C:0.00, G:0.45, T:0.39
Consensus pattern (16 bp):
TTAGGGTTATAGGGGT
Found at i:13497072 original size:20 final size:20
Alignment explanation
Indices: 13497039--13497077 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
13497029 GGGATTCTTG
* *
13497039 GTTTTTGTGTTTGGGGTTTA
1 GTTTTCGTGGTTGGGGTTTA
13497059 GTTTTCGTGGTTGGGGTTT
1 GTTTTCGTGGTTGGGGTTT
13497078 GGGGTTGGAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.03, C:0.03, G:0.38, T:0.56
Consensus pattern (20 bp):
GTTTTCGTGGTTGGGGTTTA
Found at i:13497960 original size:230 final size:231
Alignment explanation
Indices: 13497544--13498046 Score: 776
Period size: 230 Copynumber: 2.2 Consensus size: 231
13497534 AGTTGTGAAG
* *
13497544 AAAACGGCGCCGTTTTCTTATTACATTTAGTGGCGTTTTATACAAAACGCCGCAAGTATGTTTTC
1 AAAACGGCGCCGTTTTCTTATTATATTTAGTGGCGTTTTAGACAAAACGCCGCAAGTATGTTTTC
* * ** *
13497609 TTTGTTACGGGAACGGCGTCGTTTTCCATTGTTATTAGTGGCGTTACACCCAAAACGCCACAAAT
66 TTTGTTACAGAAACGGCGTCGTTTTCCAAGGATATTAGTGGCGTTACACCCAAAACGCCACAAAT
*
13497674 ATATTTTAAAGATTACACGAGTTTGCGTTAAACGACTGCGTTTGACATTATATTTAGTGGCACTT
131 ATATTTTAAAGATTACACGAGTTTGCGTTAAACGACTGCGTTTGACATTATATTTAGTGGCACCT
*
13497739 ATATATAAACGCCGCAAACTCGAAATGGTGTTACGA
196 ATATATAAACGCCGCAAAATCGAAATGGTGTTACGA
*
13497775 AAAACGGCGCCGTTTTCTTATTATATTTAGTGGCGTTTTAGATAAAACGCCGCAAGTATGTTTTC
1 AAAACGGCGCCGTTTTCTTATTATATTTAGTGGCGTTTTAGACAAAACGCCGCAAGTATGTTTTC
* * *
13497840 TTTGTTACAGAAATGGCGTCGTTTT-CAAGGATATTTGTGGCGTTACACCCAAAACGCCGCAAAT
66 TTTGTTACAGAAACGGCGTCGTTTTCCAAGGATATTAGTGGCGTTACACCCAAAACGCCACAAAT
* * * *
13497904 ATATTTTAAAGATTACATGAGTTTGCTTTAAACGACTGCGTTTGACCTTATATTTAGTGGCGCCT
131 ATATTTTAAAGATTACACGAGTTTGCGTTAAACGACTGCGTTTGACATTATATTTAGTGGCACCT
*
13497969 ATATATAAACGCCGCAAAATCGAAATGGTGTTACGG
196 ATATATAAACGCCGCAAAATCGAAATGGTGTTACGA
* * *
13498005 AAAACGGCGTCGTTTACTTAGTTGGT-TTTAGTGGCGCTTTTA
1 AAAACGGCGCCGTTTTCTTA-TT-ATATTTAGTGGCG-TTTTA
13498047 TTAAATGCCG
Statistics
Matches: 248, Mismatches: 21, Indels: 5
0.91 0.08 0.02
Matches are distributed among these distances:
230 146 0.59
231 96 0.39
232 6 0.02
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (231 bp):
AAAACGGCGCCGTTTTCTTATTATATTTAGTGGCGTTTTAGACAAAACGCCGCAAGTATGTTTTC
TTTGTTACAGAAACGGCGTCGTTTTCCAAGGATATTAGTGGCGTTACACCCAAAACGCCACAAAT
ATATTTTAAAGATTACACGAGTTTGCGTTAAACGACTGCGTTTGACATTATATTTAGTGGCACCT
ATATATAAACGCCGCAAAATCGAAATGGTGTTACGA
Found at i:13498409 original size:19 final size:19
Alignment explanation
Indices: 13498387--13498430 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
13498377 CAGACATCTC
*
13498387 CCCCAAATCCCTAAAATTT
1 CCCCAAATCCCTAAAAGTT
* *
13498406 CCCCTAATCCCTAACAGTT
1 CCCCAAATCCCTAAAAGTT
13498425 CCCCAA
1 CCCCAA
13498431 CGTAGTCCAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.32, C:0.43, G:0.02, T:0.23
Consensus pattern (19 bp):
CCCCAAATCCCTAAAAGTT
Found at i:13500492 original size:19 final size:20
Alignment explanation
Indices: 13500449--13500992 Score: 121
Period size: 20 Copynumber: 28.9 Consensus size: 20
13500439 TACAATTTCT
*
13500449 TAACTTATATAATATTAAGA
1 TAACTTATATAATATTAACA
13500469 TAACTTATATAATATT-ACA
1 TAACTTATATAATATTAACA
* *
13500488 TAACTTATATAATGTTAAGA
1 TAACTTATATAATATTAACA
* * *
13500508 TAA--AAAATCGA-ATT-ACA
1 TAACTTATAT-AATATTAACA
* * **
13500525 TAACTTACACAATATTAAGG
1 TAACTTATATAATATTAACA
* *
13500545 TAAAATT-TCT-A-ATT-ACA
1 T-AACTTATATAATATTAACA
* *
13500562 TAACTTATACAATATTAAGA
1 TAACTTATATAATATTAACA
* *
13500582 TAAAATT-T-TGA-ATT-ACA
1 T-AACTTATATAATATTAACA
*
13500599 TAACTTATATAATATTAATA
1 TAACTTATATAATATTAACA
* * *
13500619 TTACTTTTATAATATTAAGA
1 TAACTTATATAATATTAACA
* **
13500639 TCAAATT-T-CGA-ATT-ACA
1 T-AACTTATATAATATTAACA
* * **
13500656 TAACTTATACAATAATAAGG
1 TAACTTATATAATATTAACA
* *
13500676 TAAAATT-TCT-A-ATT-ACA
1 T-AACTTATATAATATTAACA
* *
13500693 TAACTTATACAATATTAAGA
1 TAACTTATATAATATTAACA
** ***
13500713 TAAAAT-TCCGA-ATT-ACA
1 TAACTTATATAATATTAACA
*
13500730 TAACTTATATAATATTAAGA
1 TAACTTATATAATATTAACA
* * *
13500750 TTACTTTTATAATATTAAGA
1 TAACTTATATAATATTAACA
* **
13500770 TCAAATT-T-CGA-ATT-ACA
1 T-AACTTATATAATATTAACA
13500787 TAACTTATATAATATT-ACA
1 TAACTTATATAATATTAACA
* * *
13500806 TAACTTACACAATATTAAGA
1 TAACTTATATAATATTAACA
* **
13500826 TAAAATT-T-CGA-ATT-ACA
1 T-AACTTATATAATATTAACA
* *
13500843 TAAGTTATATAATATTAAGA
1 TAACTTATATAATATTAACA
* * *
13500863 TTACTTTTATAATATTAAGA
1 TAACTTATATAATATTAACA
* **
13500883 TCAAATT-T-CGA-ATT-ACA
1 T-AACTTATATAATATTAACA
** *
13500900 TAACTTATATAAT-TTTCCG
1 TAACTTATATAATATTAACA
*
13500919 TAACTTATATAATATTAAGA
1 TAACTTATATAATATTAACA
* **
13500939 TAAAATT-T-CGA-ATT-ACA
1 T-AACTTATATAATATTAACA
13500956 TAACTTATATAATATT-ACA
1 TAACTTATATAATATTAACA
*
13500975 TAACTTTTATAATATTAA
1 TAACTTATATAATATTAA
13500993 GANNNNNNNN
Statistics
Matches: 363, Mismatches: 111, Indels: 100
0.63 0.19 0.17
Matches are distributed among these distances:
16 32 0.09
17 41 0.11
18 46 0.13
19 107 0.29
20 108 0.30
21 29 0.08
ACGTcount: A:0.46, C:0.10, G:0.05, T:0.39
Consensus pattern (20 bp):
TAACTTATATAATATTAACA
Found at i:13500543 original size:37 final size:37
Alignment explanation
Indices: 13500482--13500616 Score: 189
Period size: 37 Copynumber: 3.6 Consensus size: 37
13500472 CTTATATAAT
* * **
13500482 ATTACATAACTTATATAATGTTAAGATAAAAAATCGA
1 ATTACATAACTTATACAATATTAAGATAAAATTTCGA
* * *
13500519 ATTACATAACTTACACAATATTAAGGTAAAATTTCTA
1 ATTACATAACTTATACAATATTAAGATAAAATTTCGA
*
13500556 ATTACATAACTTATACAATATTAAGATAAAATTTTGA
1 ATTACATAACTTATACAATATTAAGATAAAATTTCGA
*
13500593 ATTACATAACTTATATAATATTAA
1 ATTACATAACTTATACAATATTAA
13500617 TATTACTTTT
Statistics
Matches: 86, Mismatches: 12, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 86 1.00
ACGTcount: A:0.49, C:0.10, G:0.05, T:0.36
Consensus pattern (37 bp):
ATTACATAACTTATACAATATTAAGATAAAATTTCGA
Found at i:13500653 original size:94 final size:93
Alignment explanation
Indices: 13500533--13500863 Score: 321
Period size: 94 Copynumber: 3.5 Consensus size: 93
13500523 CATAACTTAC
* *
13500533 ACAATATTAAGGTAAAATTTCTAATTACATAACTTATACAATATTAAGATAAAATTTTGAATTAC
1 ACAATATTAAGATAAAATTTCGAATTACATAACTTATACAATATTAAGATAAAATTTTGAATTAC
13500598 ATAACTTATATAATATTAATATTACTTTT
66 ATAACTTATATAATATTAATA-TACTTTT
* * * *
13500627 ATAATATTAAGATCAAATTTCGAATTACATAACTTATACAATAATAAGGTAAAATTTCT-AATTA
1 ACAATATTAAGATAAAATTTCGAATTACATAACTTATACAATATTAAGATAAAATTT-TGAATTA
* * ***
13500691 CATAACTTATACAATATTAAGATAAAATT
65 CATAACTTATATAATATTAATATACTTTT
* * * * ** * * * * * *
13500720 CCGA-ATT-ACAT-AACTTATATAATATTAAGATTACTTTTATAATATTAAGATCAAATTTCGAA
1 ACAATATTAAGATAAAATT-T-CGA-ATT-ACATAACTTATACAATATTAAGATAAAATTTTGAA
**
13500782 TTACATAACTTATATAATATTACATA-ACTTAC
62 TTACATAACTTATATAATATTA-ATATACTTTT
* *
13500814 ACAATATTAAGATAAAATTTCGAATTACATAAGTTATATAATATTAAGAT
1 ACAATATTAAGATAAAATTTCGAATTACATAACTTATACAATATTAAGAT
13500864 TACTTTTATA
Statistics
Matches: 184, Mismatches: 43, Indels: 21
0.74 0.17 0.08
Matches are distributed among these distances:
90 4 0.02
91 4 0.02
92 4 0.02
93 28 0.15
94 129 0.70
95 7 0.04
96 4 0.02
97 4 0.02
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (93 bp):
ACAATATTAAGATAAAATTTCGAATTACATAACTTATACAATATTAAGATAAAATTTTGAATTAC
ATAACTTATATAATATTAATATACTTTT
Found at i:13500675 original size:131 final size:131
Alignment explanation
Indices: 13500468--13500800 Score: 544
Period size: 131 Copynumber: 2.5 Consensus size: 131
13500458 TAATATTAAG
* * * **
13500468 ATAACTTATATAATATTACATA--ACTTATATAATGTTAAGATAAAAAATCGAATTACATAACTT
1 ATAACTTATATAATATTA-ATATTACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTT
* * **
13500531 ACACAATATTAAGGTAAAATTTCTAATTACATAACTTATACAATATTAAGATAAAATTTTGAATT
65 ATACAATAATAAGGTAAAATTTCTAATTACATAACTTATACAATATTAAGATAAAATTCCGAATT
13500596 AC
130 AC
13500598 ATAACTTATATAATATTAATATTACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTA
1 ATAACTTATATAATATTAATATTACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTA
13500663 TACAATAATAAGGTAAAATTTCTAATTACATAACTTATACAATATTAAGATAAAATTCCGAATTA
66 TACAATAATAAGGTAAAATTTCTAATTACATAACTTATACAATATTAAGATAAAATTCCGAATTA
13500728 C
131 C
*
13500729 ATAACTTATATAATATTAAGATTACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTA
1 ATAACTTATATAATATTAATATTACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTA
*
13500794 TATAATA
66 TACAATA
13500801 TTACATAACT
Statistics
Matches: 190, Mismatches: 11, Indels: 3
0.93 0.05 0.01
Matches are distributed among these distances:
129 3 0.02
130 18 0.09
131 169 0.89
ACGTcount: A:0.47, C:0.10, G:0.05, T:0.38
Consensus pattern (131 bp):
ATAACTTATATAATATTAATATTACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTA
TACAATAATAAGGTAAAATTTCTAATTACATAACTTATACAATATTAAGATAAAATTCCGAATTA
C
Found at i:13500683 original size:37 final size:37
Alignment explanation
Indices: 13500629--13500750 Score: 190
Period size: 37 Copynumber: 3.3 Consensus size: 37
13500619 TTACTTTTAT
*
13500629 AATATTAAGATCAAATTTCGAATTACATAACTTATAC
1 AATATTAAGATAAAATTTCGAATTACATAACTTATAC
* * *
13500666 AATAATAAGGTAAAATTTCTAATTACATAACTTATAC
1 AATATTAAGATAAAATTTCGAATTACATAACTTATAC
* *
13500703 AATATTAAGATAAAATTCCGAATTACATAACTTATAT
1 AATATTAAGATAAAATTTCGAATTACATAACTTATAC
13500740 AATATTAAGAT
1 AATATTAAGAT
13500751 TACTTTTATA
Statistics
Matches: 76, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
37 76 1.00
ACGTcount: A:0.48, C:0.11, G:0.06, T:0.35
Consensus pattern (37 bp):
AATATTAAGATAAAATTTCGAATTACATAACTTATAC
Found at i:13500822 original size:113 final size:113
Alignment explanation
Indices: 13500687--13500994 Score: 528
Period size: 113 Copynumber: 2.7 Consensus size: 113
13500677 AAAATTTCTA
*
13500687 ATTACATAACTTATACAATATTAAGATAAAATTCCGAATTACATAACTTATATAATATTAAGATT
1 ATTACATAACTTATACAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAGATT
13500752 ACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATATAAT
66 ACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATATAAT
* *
13500800 ATTACATAACTTACACAATATTAAGATAAAATTTCGAATTACATAAGTTATATAATATTAAGATT
1 ATTACATAACTTATACAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAGATT
13500865 ACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATATAAT
66 ACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATATAAT
* * * * * *
13500913 TTTCCGTAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATT-ACATA
1 ATTACATAACTTATACAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAGATT
13500977 ACTTTTATAATATTAAGA
66 ACTTTTATAATATTAAGA
13500995 NNNNNNNNNN
Statistics
Matches: 184, Mismatches: 11, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
112 21 0.11
113 163 0.89
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (113 bp):
ATTACATAACTTATACAATATTAAGATAAAATTTCGAATTACATAACTTATATAATATTAAGATT
ACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATATAAT
Found at i:13500842 original size:56 final size:56
Alignment explanation
Indices: 13500687--13500994 Score: 445
Period size: 56 Copynumber: 5.5 Consensus size: 56
13500677 AAAATTTCTA
* *
13500687 ATTACATAACTTATACAATATTAAGATAAAATTCCGAATTACATAACTTATATAAT
1 ATTACATAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAAT
* * * *
13500743 ATTAAGATTACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATATAAT
1 ATT-ACATAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAAT
* * *
13500800 ATTACATAACTTACACAATATTAAGATAAAATTTCGAATTACATAAGTTATATAAT
1 ATTACATAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAAT
* * * *
13500856 ATTAAGATTACTTTTATAATATTAAGATCAAATTTCGAATTACATAACTTATATAAT
1 ATT-ACATAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAAT
* * *
13500913 TTTCCGTAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAAT
1 ATTACATAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAAT
*
13500969 ATTACATAACTTTTATAATATTAAGA
1 ATTACATAACTTATATAATATTAAGA
13500995 NNNNNNNNNN
Statistics
Matches: 219, Mismatches: 31, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
56 121 0.55
57 98 0.45
ACGTcount: A:0.45, C:0.10, G:0.05, T:0.40
Consensus pattern (56 bp):
ATTACATAACTTATATAATATTAAGATAAAATTTCGAATTACATAACTTATATAAT
Found at i:13501554 original size:57 final size:57
Alignment explanation
Indices: 13501465--13501673 Score: 289
Period size: 57 Copynumber: 3.7 Consensus size: 57
13501455 NNNNNNCATA
* *
13501465 ACTTATACAATATTAAGGTAAGATTTCGAATTACATAACTCATACAATATTAAGATT
1 ACTTATACAATATTAAGATAAAATTTCGAATTACATAACTCATACAATATTAAGATT
* * * * *
13501522 ACTTATATAATATTAAGATAAAATTTCTAATTACATAACT--TACATAAATT-ACATA
1 ACTTATACAATATTAAGATAAAATTTCGAATTACATAACTCATACA-ATATTAAGATT
* *
13501577 ACTTATACAATATTAAGGTAAGATTTCGAATTACATAACTCATACAATATTAAGATT
1 ACTTATACAATATTAAGATAAAATTTCGAATTACATAACTCATACAATATTAAGATT
* *
13501634 ACTTATATAATATTAAGATAAAATTTCTAATTACATAACT
1 ACTTATACAATATTAAGATAAAATTTCGAATTACATAACT
13501674 TACATAAATT
Statistics
Matches: 130, Mismatches: 18, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
55 43 0.33
56 8 0.06
57 79 0.61
ACGTcount: A:0.46, C:0.11, G:0.06, T:0.37
Consensus pattern (57 bp):
ACTTATACAATATTAAGATAAAATTTCGAATTACATAACTCATACAATATTAAGATT
Found at i:13501566 original size:9 final size:9
Alignment explanation
Indices: 13501552--13501581 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
13501542 AAATTTCTAA
13501552 TTACATAAC
1 TTACATAAC
*
13501561 TTACATAAA
1 TTACATAAC
13501570 TTACATAAC
1 TTACATAAC
13501579 TTA
1 TTA
13501582 TACAATATTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.47, C:0.17, G:0.00, T:0.37
Consensus pattern (9 bp):
TTACATAAC
Found at i:13501658 original size:112 final size:112
Alignment explanation
Indices: 13501461--13501693 Score: 466
Period size: 112 Copynumber: 2.1 Consensus size: 112
13501451 NNNNNNNNNN
13501461 CATAACTTATACAATATTAAGGTAAGATTTCGAATTACATAACTCATACAATATTAAGATTACTT
1 CATAACTTATACAATATTAAGGTAAGATTTCGAATTACATAACTCATACAATATTAAGATTACTT
13501526 ATATAATATTAAGATAAAATTTCTAATTACATAACTTACATAAATTA
66 ATATAATATTAAGATAAAATTTCTAATTACATAACTTACATAAATTA
13501573 CATAACTTATACAATATTAAGGTAAGATTTCGAATTACATAACTCATACAATATTAAGATTACTT
1 CATAACTTATACAATATTAAGGTAAGATTTCGAATTACATAACTCATACAATATTAAGATTACTT
13501638 ATATAATATTAAGATAAAATTTCTAATTACATAACTTACATAAATTA
66 ATATAATATTAAGATAAAATTTCTAATTACATAACTTACATAAATTA
13501685 CATAACTTA
1 CATAACTTA
13501694 CATAACTTAC
Statistics
Matches: 121, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
112 121 1.00
ACGTcount: A:0.46, C:0.12, G:0.05, T:0.36
Consensus pattern (112 bp):
CATAACTTATACAATATTAAGGTAAGATTTCGAATTACATAACTCATACAATATTAAGATTACTT
ATATAATATTAAGATAAAATTTCTAATTACATAACTTACATAAATTA
Found at i:13501678 original size:9 final size:9
Alignment explanation
Indices: 13501664--13501844 Score: 128
Period size: 9 Copynumber: 20.9 Consensus size: 9
13501654 AAATTTCTAA
13501664 TTACATAAC
1 TTACATAAC
*
13501673 TTACATAAA
1 TTACATAAC
13501682 TTACATAAC
1 TTACATAAC
13501691 TTACATAAC
1 TTACATAAC
*
13501700 TTACATAAA
1 TTACATAAC
*
13501709 TTAAATAAC
1 TTACATAAC
*
13501718 TTGCATAAC
1 TTACATAAC
*
13501727 TTAAATAAC
1 TTACATAAC
13501736 TTACATAAC
1 TTACATAAC
13501745 --ACATAACC
1 TTACATAA-C
* *
13501753 TT-CCTAGC
1 TTACATAAC
* *
13501761 TTACATTAT
1 TTACATAAC
*
13501770 TTAGATAA-
1 TTACATAAC
13501778 -TACA-AACC
1 TTACATAA-C
* *
13501786 TT-CCTAGC
1 TTACATAAC
* *
13501794 TTACATTAT
1 TTACATAAC
*
13501803 TTAGATAA-
1 TTACATAAC
*
13501811 -TACATAGC
1 TTACATAAC
*
13501819 CTACATAAC
1 TTACATAAC
13501828 TTACATAAC
1 TTACATAAC
13501837 TTACATAA
1 TTACATAA
13501845 ATTGGACGCC
Statistics
Matches: 130, Mismatches: 31, Indels: 22
0.71 0.17 0.12
Matches are distributed among these distances:
6 2 0.02
7 14 0.11
8 8 0.06
9 106 0.82
ACGTcount: A:0.43, C:0.20, G:0.03, T:0.34
Consensus pattern (9 bp):
TTACATAAC
Found at i:13501791 original size:33 final size:34
Alignment explanation
Indices: 13501740--13501816 Score: 138
Period size: 33 Copynumber: 2.3 Consensus size: 34
13501730 AATAACTTAC
*
13501740 ATAACACATAACCTTCCTAGCTTACATTATTTAG
1 ATAATACATAACCTTCCTAGCTTACATTATTTAG
13501774 ATAATACA-AACCTTCCTAGCTTACATTATTTAG
1 ATAATACATAACCTTCCTAGCTTACATTATTTAG
13501807 ATAATACATA
1 ATAATACATA
13501817 GCCTACATAA
Statistics
Matches: 41, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
33 33 0.80
34 8 0.20
ACGTcount: A:0.39, C:0.21, G:0.05, T:0.35
Consensus pattern (34 bp):
ATAATACATAACCTTCCTAGCTTACATTATTTAG
Found at i:13502872 original size:40 final size:40
Alignment explanation
Indices: 13502809--13502884 Score: 107
Period size: 40 Copynumber: 1.9 Consensus size: 40
13502799 GTTTGGACAA
* *
13502809 AAAACGCCGCTAAAAATCAAGCATTAGCGGCGCTTTAAAT
1 AAAACGCCGCTAAAAACCAAGCATTAGCGGCACTTTAAAT
* * *
13502849 AAAACGCCGTTAAAGACCGAGCATTAGCGGCACTTT
1 AAAACGCCGCTAAAAACCAAGCATTAGCGGCACTTT
13502885 CAGGAAAATG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 31 1.00
ACGTcount: A:0.37, C:0.24, G:0.20, T:0.20
Consensus pattern (40 bp):
AAAACGCCGCTAAAAACCAAGCATTAGCGGCACTTTAAAT
Found at i:13503038 original size:41 final size:40
Alignment explanation
Indices: 13502978--13503214 Score: 305
Period size: 41 Copynumber: 5.8 Consensus size: 40
13502968 CGACCTTTCG
13502978 GGGCTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
1 GGGC-TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* *
13503019 GGAGCTTTAGCGGCGTTTTTGAGAAAGCGCAGCTAATGCTC
1 GG-GCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* *
13503060 AGGCTTTTAGCGGCGTTTTTGAAAAAGCGTCGCTAATGCTC
1 GGGC-TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
* * *
13503101 AGGCTTTTAGCAGCGTTTTTG-AAAAGCGCCGCTAATGCCC
1 GGGC-TTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
** * *
13503141 GGGGCTTTAGCGGCGTTTTCCAAGAAGCGCCGCTAATGCTTA
1 -GGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGC-TC
*
13503183 GGGCTTTAGCGGCGTTTTTGAAAAAGCACCGC
1 GGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGC
13503215 AAAAACATTT
Statistics
Matches: 171, Mismatches: 20, Indels: 10
0.85 0.10 0.05
Matches are distributed among these distances:
40 32 0.19
41 137 0.80
42 2 0.01
ACGTcount: A:0.21, C:0.22, G:0.29, T:0.28
Consensus pattern (40 bp):
GGGCTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTC
Found at i:13503157 original size:81 final size:81
Alignment explanation
Indices: 13502976--13503206 Score: 322
Period size: 81 Copynumber: 2.8 Consensus size: 81
13502966 TTCGACCTTT
*
13502976 CGGGGCTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGAGCTTTAGCGGCGTTTTTGA
1 CGGGGCTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAG-GCTTTAGCGGCGTTTTTGA
*
13503041 GAAAGCGCAGCTAATGCT
65 -AAAGCGCAGCTAATGCC
* * *
13503059 C-AGGCTTTTAGCGGCGTTTTTGAAAAAGCGTCGCTAATGCTCAGGCTTTTAGCAGCGTTTTTGA
1 CGGGGCTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGGC-TTTAGCGGCGTTTTTGA
*
13503123 AAAGCGCCGCTAATGCC
65 AAAGCGCAGCTAATGCC
** * *
13503140 CGGGGC-TTTAGCGGCGTTTTCCAAGAAGCGCCGCTAATGCTTAGGGCTTTAGCGGCGTTTTTGA
1 CGGGGCTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCA-GGCTTTAGCGGCGTTTTTGA
13503204 AAA
65 AAA
13503207 AGCACCGCAA
Statistics
Matches: 132, Mismatches: 13, Indels: 8
0.86 0.08 0.05
Matches are distributed among these distances:
81 69 0.52
82 62 0.47
83 1 0.01
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (81 bp):
CGGGGCTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCAGGCTTTAGCGGCGTTTTTGAA
AAGCGCAGCTAATGCC
Found at i:13503197 original size:122 final size:123
Alignment explanation
Indices: 13502979--13503209 Score: 360
Period size: 122 Copynumber: 1.9 Consensus size: 123
13502969 GACCTTTCGG
* * **
13502979 GGCTTTTAGCGGCGTTTTTGAAAAAGCGCCGCTAATGCTCGGAGCTTTAGCGGCGTTTTTGAGAA
1 GGCTTTTAGCAGCGTTTTTGAAAAAGCGCCGCTAATGCCCGGAGCTTTAGCGGCGTTTTCAAGAA
13503044 AGCGCAGCTAATGCTCAGGCTTTTAGCGGCGTTTTTGAAAAAGCGTCGCTAATGCTCA
66 AGCGCAGCTAATGCTCAGGCTTTTAGCGGCGTTTTTGAAAAAGCGTCGCTAATGCTCA
*
13503102 GGCTTTTAGCAGCGTTTTTG-AAAAGCGCCGCTAATGCCCGGGGCTTTAGCGGCGTTTTCCAAG-
1 GGCTTTTAGCAGCGTTTTTGAAAAAGCGCCGCTAATGCCCGGAGCTTTAGCGGCGTTTT-CAAGA
* *
13503165 AAGCGCCGCTAATGCTTAGGGC-TTTAGCGGCGTTTTTGAAAAAGC
65 AAGCGCAGCTAATGCTCA-GGCTTTTAGCGGCGTTTTTGAAAAAGC
13503210 ACCGCAAAAA
Statistics
Matches: 99, Mismatches: 7, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
122 75 0.76
123 24 0.24
ACGTcount: A:0.21, C:0.21, G:0.29, T:0.29
Consensus pattern (123 bp):
GGCTTTTAGCAGCGTTTTTGAAAAAGCGCCGCTAATGCCCGGAGCTTTAGCGGCGTTTTCAAGAA
AGCGCAGCTAATGCTCAGGCTTTTAGCGGCGTTTTTGAAAAAGCGTCGCTAATGCTCA
Found at i:13503766 original size:14 final size:14
Alignment explanation
Indices: 13503743--13503787 Score: 65
Period size: 14 Copynumber: 3.2 Consensus size: 14
13503733 TAAATAAGGT
13503743 TTAGGGGTTAGTA-G
1 TTAGGGGTTAG-AGG
*
13503757 TTATGGGTTAGAGG
1 TTAGGGGTTAGAGG
13503771 TTAGGGGTTAGAGG
1 TTAGGGGTTAGAGG
13503785 TTA
1 TTA
13503788 AGAGTTAGTG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
13 1 0.04
14 27 0.96
ACGTcount: A:0.22, C:0.00, G:0.42, T:0.36
Consensus pattern (14 bp):
TTAGGGGTTAGAGG
Found at i:13505604 original size:17 final size:17
Alignment explanation
Indices: 13505584--13505620 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
13505574 AATTTTTGAA
*
13505584 TTAGTGAATTCTGTGAT
1 TTAGTAAATTCTGTGAT
*
13505601 TTAGTAAATTTTGTGAT
1 TTAGTAAATTCTGTGAT
13505618 TTA
1 TTA
13505621 AAAAGAATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.27, C:0.03, G:0.19, T:0.51
Consensus pattern (17 bp):
TTAGTAAATTCTGTGAT
Found at i:13506428 original size:46 final size:45
Alignment explanation
Indices: 13506370--13506509 Score: 226
Period size: 46 Copynumber: 3.0 Consensus size: 45
13506360 CCATGGAAAA
*
13506370 TTGTGAACAGTAGGTATGGTGTTTCAGTGAAGAAAGCCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAA-CCATACTGAG
*
13506416 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAAACCATATTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAG-AAACCATACTGAG
*
13506462 TTGTGAAAAGTAGGTATGGTATTTCAGTGAAGGAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAA-GAAACCATACTGAG
13506508 TT
1 TT
13506510 ATAGCATTGT
Statistics
Matches: 88, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
46 84 0.95
47 4 0.05
ACGTcount: A:0.33, C:0.09, G:0.29, T:0.30
Consensus pattern (45 bp):
TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAACCATACTGAG
Found at i:13535455 original size:7 final size:7
Alignment explanation
Indices: 13535438--13535480 Score: 50
Period size: 7 Copynumber: 5.9 Consensus size: 7
13535428 AAGTATTTTA
13535438 AAAATTTT
1 AAAA-TTT
13535446 AAAATTT
1 AAAATTT
13535453 AAAATTT
1 AAAATTT
*
13535460 AAAATTA
1 AAAATTT
*
13535467 ATAAAGTT
1 A-AAATTT
13535475 AAAATT
1 AAAATT
13535481 ATACTTTGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
7 21 0.70
8 9 0.30
ACGTcount: A:0.58, C:0.00, G:0.02, T:0.40
Consensus pattern (7 bp):
AAAATTT
Found at i:13535988 original size:17 final size:17
Alignment explanation
Indices: 13535968--13536013 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
13535958 AAACATTCTC
*
13535968 ATTAAATTTATATTAGT
1 ATTAAATTTAAATTAGT
*
13535985 ATTAAATGTAAATTAGT
1 ATTAAATTTAAATTAGT
13536002 -TTAAAATTTAAA
1 ATT-AAATTTAAA
13536014 AATATTTTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 2 0.08
17 23 0.92
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.46
Consensus pattern (17 bp):
ATTAAATTTAAATTAGT
Found at i:13536845 original size:37 final size:35
Alignment explanation
Indices: 13536779--13536889 Score: 98
Period size: 36 Copynumber: 3.0 Consensus size: 35
13536769 ATAAATTTAA
*
13536779 AAAACTTTTTAATGATTTTCACAATTTTAAAAAAAATT
1 AAAAC-TTTTAAT-ATTTT-ATAATTTTAAAAAAAATT
* * **
13536817 ACAATCTTTATAA-ATATTTATAATTTTAAGAAATTTT
1 A-AAACTTT-TAATAT-TTTATAATTTTAAAAAAAATT
*
13536854 AAAACTTTTAATATTTTATATATTTTAAAATAAATT
1 AAAACTTTTAATATTTTATA-ATTTTAAAAAAAATT
13536890 TTAAATTTTT
Statistics
Matches: 58, Mismatches: 10, Indels: 12
0.73 0.12 0.15
Matches are distributed among these distances:
35 9 0.16
36 19 0.33
37 17 0.29
38 7 0.12
39 6 0.10
ACGTcount: A:0.46, C:0.05, G:0.02, T:0.47
Consensus pattern (35 bp):
AAAACTTTTAATATTTTATAATTTTAAAAAAAATT
Found at i:13536912 original size:21 final size:21
Alignment explanation
Indices: 13536866--13536911 Score: 76
Period size: 20 Copynumber: 2.2 Consensus size: 21
13536856 AACTTTTAAT
*
13536866 ATTTTATATATTTTAAAATAA
1 ATTTTAAATATTTTAAAATAA
13536887 ATTTTAAAT-TTTTAAAATAA
1 ATTTTAAATATTTTAAAATAA
13536907 ATTTT
1 ATTTT
13536912 TACTAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 16 0.67
21 8 0.33
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (21 bp):
ATTTTAAATATTTTAAAATAA
Found at i:13541140 original size:33 final size:33
Alignment explanation
Indices: 13541098--13541166 Score: 129
Period size: 33 Copynumber: 2.1 Consensus size: 33
13541088 GATCAAGTTG
*
13541098 AAGCAGATACAAAGCGTGTCGTTGGAACATAGT
1 AAGCAGATACAAAGCGTGCCGTTGGAACATAGT
13541131 AAGCAGATACAAAGCGTGCCGTTGGAACATAGT
1 AAGCAGATACAAAGCGTGCCGTTGGAACATAGT
13541164 AAG
1 AAG
13541167 TGCATAAAAC
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.38, C:0.16, G:0.28, T:0.19
Consensus pattern (33 bp):
AAGCAGATACAAAGCGTGCCGTTGGAACATAGT
Found at i:13542685 original size:20 final size:20
Alignment explanation
Indices: 13542662--13542707 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
13542652 ATTCATTTAT
**
13542662 TAAAATAATAATTTTATAAA
1 TAAAATAATAATACTATAAA
13542682 TAAAATAATAATACTATAAA
1 TAAAATAATAATACTATAAA
13542702 TAAAAT
1 TAAAAT
13542708 TGTTTAAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (20 bp):
TAAAATAATAATACTATAAA
Found at i:13557024 original size:157 final size:157
Alignment explanation
Indices: 13556823--13557139 Score: 589
Period size: 157 Copynumber: 2.0 Consensus size: 157
13556813 TAGAATACCC
*
13556823 TTAGCATAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTAGTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTAGTA
* *
13556888 TTATCAATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
13556953 TATATAATTGAATAAAATTCTTAATAA
131 TATATAATTGAATAAAATTCTTAATAA
* *
13556980 TTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATTTAAATTTTAATAAGATTATTA
1 TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTAGTA
13557045 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
66 ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
13557110 TATATAATTGAATAAAATTCTTAATAA
131 TATATAATTGAATAAAATTCTTAATAA
13557137 TTA
1 TTA
13557140 ATATTCTTAT
Statistics
Matches: 155, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
157 155 1.00
ACGTcount: A:0.44, C:0.03, G:0.06, T:0.47
Consensus pattern (157 bp):
TTAGCAGAAATTTGTTTTGGTAAATGATTATTGTTATTGTTATTTAAATTTTAATAAGATTAGTA
ATATCAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAA
TATATAATTGAATAAAATTCTTAATAA
Found at i:13557136 original size:82 final size:82
Alignment explanation
Indices: 13556893--13557142 Score: 222
Period size: 76 Copynumber: 3.1 Consensus size: 82
13556883 TAGTATTATC
*
13556893 AATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATAT
1 AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATAT
13556958 AATTGAATAAAATTCTT
66 AATTGAATAAAATTCTT
* * * * * * **
13556975 AATAATTAGCAGA-AATTT-GT--T-TTGGT-AA-ATTATTATTGTT-ATTGTTATTTAAATTTT
1 AATAA-TA--A-ATAATTTAATCATATT--TAAACATAATTATTATTAAAT-ATATTTTAATTAA
* * *
13557032 AATA-A-GATT-ATTAATA-TC--
59 AATATATAATTGAATAAAATTCTT
13557050 AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATAT
1 AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATAT
13557115 AATTGAATAAAATTCTT
66 AATTGAATAAAATTCTT
*
13557132 AATAATTAATA
1 AATAATAAATA
13557143 TTCTTATATG
Statistics
Matches: 123, Mismatches: 24, Indels: 42
0.65 0.13 0.22
Matches are distributed among these distances:
71 1 0.01
72 6 0.05
73 1 0.01
74 3 0.02
75 8 0.07
76 25 0.20
77 5 0.04
78 8 0.07
79 8 0.07
80 5 0.04
81 25 0.20
82 18 0.15
83 3 0.02
84 1 0.01
85 5 0.04
86 1 0.01
ACGTcount: A:0.47, C:0.03, G:0.04, T:0.46
Consensus pattern (82 bp):
AATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATAT
AATTGAATAAAATTCTT
Found at i:13557223 original size:157 final size:154
Alignment explanation
Indices: 13556894--13557224 Score: 355
Period size: 157 Copynumber: 2.1 Consensus size: 154
13556884 AGTATTATCA
13556894 ATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATA
1 ATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATA
* * * * ** * * * * * *
13556959 ATTGAATAAAATTCTTAATAATTAGCAGAAATTTGTTTTGGTAAATTATTATTGTTATTGTTATT
66 ATTGAATAAAATTCTTAATAATTAACACAAATATGATTTACTAAATTAATATTGATACTATAAAT
* * * *
13557024 TAAATTTTAATAAGATTATTAATAT
131 GAAAATTT-AGAAGATAATTAATAT
*
13557049 CAATAATAAATAATTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATA
1 --ATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATA
* **
13557114 TAATTGAATAAAATTCTTAATAATTAATATTCTTATATGAATTTACTCAAATCATAATATATGAT
64 TAATTGAATAAAATTCTTAATAATTAACA--CAAATATG-ATTTACT-AAAT--TAATAT-TGAT
13557179 ACTATAAATGAAAATTT-GAA-ATAATTAATAT
122 ACTATAAATGAAAATTTAGAAGATAATTAATAT
*
13557210 -TAA-ATATATTTTAAT
1 ATAATAAATATTTTAAT
13557225 TAAAATATAT
Statistics
Matches: 145, Mismatches: 22, Indels: 14
0.80 0.12 0.08
Matches are distributed among these distances:
157 99 0.68
158 3 0.02
159 4 0.03
160 4 0.03
161 14 0.10
162 2 0.01
163 5 0.03
164 14 0.10
ACGTcount: A:0.47, C:0.04, G:0.04, T:0.45
Consensus pattern (154 bp):
ATAATAAATATTTTAATCATATTTAAACATAATTATTATTAAATATATTTTAATTAAAATATATA
ATTGAATAAAATTCTTAATAATTAACACAAATATGATTTACTAAATTAATATTGATACTATAAAT
GAAAATTTAGAAGATAATTAATAT
Found at i:13557335 original size:24 final size:25
Alignment explanation
Indices: 13557289--13557336 Score: 64
Period size: 26 Copynumber: 1.9 Consensus size: 25
13557279 TATGAATTTG
13557289 TATAATTTAAAATAATAATTATTACA
1 TATAATTTAAAAT-ATAATTATTACA
13557315 TATAATTTAATAAT-TAA-TATTA
1 TATAATTTAA-AATATAATTATTA
13557337 AATTTCATAA
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
24 5 0.24
25 3 0.14
26 10 0.48
27 3 0.14
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (25 bp):
TATAATTTAAAATATAATTATTACA
Found at i:13557340 original size:92 final size:92
Alignment explanation
Indices: 13557244--13557472 Score: 236
Period size: 92 Copynumber: 2.5 Consensus size: 92
13557234 TGATTTAATA
* * *
13557244 AAATTT-AAAATAATT-ATAACTAATAAATTATATTTTATGAATTTGTATAATTTAAAATAA-TA
1 AAATTTCAAAA-AATTCATAA-TAATAAATTATATTATATGAATTTATACAATTTAAAATAATTA
*
13557306 ATTATTACATATAATTTAATAATTAATATT
64 A-TATTAAATATAATTTAATAATTAATATT
* * * * *
13557336 AAATTTCATAAAATTCTTGATAATAAATTTTCTTATATGAATTTATACAATTTAAAATAATTAAT
1 AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
* *
13557401 ATTAAATATAATTTAAT-AGTGATA-T
66 ATTAAATATAATTTAATAATTAATATT
* * *
13557426 ATAATTTCATAAAATTCTTAATAATAAAATGT-TCTTATATGAATTTA
1 A-AATTTCAAAAAATTCATAATAAT-AAAT-TATATTATATGAATTTA
13557473 CTAAAATCAA
Statistics
Matches: 119, Mismatches: 12, Indels: 12
0.83 0.08 0.08
Matches are distributed among these distances:
90 2 0.02
91 27 0.23
92 81 0.68
93 9 0.08
ACGTcount: A:0.48, C:0.04, G:0.03, T:0.45
Consensus pattern (92 bp):
AAATTTCAAAAAATTCATAATAATAAATTATATTATATGAATTTATACAATTTAAAATAATTAAT
ATTAAATATAATTTAATAATTAATATT
Found at i:13560013 original size:33 final size:33
Alignment explanation
Indices: 13559974--13560049 Score: 143
Period size: 33 Copynumber: 2.3 Consensus size: 33
13559964 ATTATAAAAC
*
13559974 ATGTATAATTGACCTAAAATTAATTGTTGGTGT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
13560007 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
1 ATGTATAATTGACCTAAAATTAATTGTTGGTAT
13560040 ATGTATAATT
1 ATGTATAATT
13560050 CAAGTTTTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.36, C:0.05, G:0.16, T:0.43
Consensus pattern (33 bp):
ATGTATAATTGACCTAAAATTAATTGTTGGTAT
Found at i:13560147 original size:37 final size:37
Alignment explanation
Indices: 13560092--13560178 Score: 147
Period size: 37 Copynumber: 2.4 Consensus size: 37
13560082 GTATAAATAT
* * *
13560092 ATTGATTAGTTCATTAAAGCATGTTCAAAGTTTTAAC
1 ATTGATTAGTTTAATAAAGCATGTTCAAAGTTTGAAC
13560129 ATTGATTAGTTTAATAAAGCATGTTCAAAGTTTGAAC
1 ATTGATTAGTTTAATAAAGCATGTTCAAAGTTTGAAC
13560166 ATTGATTAGTTTA
1 ATTGATTAGTTTA
13560179 TTTATTTATG
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
37 47 1.00
ACGTcount: A:0.36, C:0.08, G:0.15, T:0.41
Consensus pattern (37 bp):
ATTGATTAGTTTAATAAAGCATGTTCAAAGTTTGAAC
Found at i:13563250 original size:7 final size:7
Alignment explanation
Indices: 13563238--13563264 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
13563228 GAAAAAGAAA
13563238 AGAAGGT
1 AGAAGGT
13563245 AGAAGGT
1 AGAAGGT
13563252 AGAAGGT
1 AGAAGGT
13563259 AGAAGG
1 AGAAGG
13563265 AAATCGGTCG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.44, T:0.11
Consensus pattern (7 bp):
AGAAGGT
Found at i:13574384 original size:53 final size:53
Alignment explanation
Indices: 13574324--13574447 Score: 203
Period size: 53 Copynumber: 2.3 Consensus size: 53
13574314 ATTTTGTTAG
* * *
13574324 TCAAATTATTAATTGTTAATTACATTGATTGTTAGTAAATTTATCAAATTATA
1 TCAAATTATTAATTGTTAATTACATTAATTGCTAGTAAAATTATCAAATTATA
**
13574377 TCAAATTATTAATTGTTAATTGTATTAATTGCTAGTAAAATTATCAAATTATA
1 TCAAATTATTAATTGTTAATTACATTAATTGCTAGTAAAATTATCAAATTATA
13574430 TCAAATTATTAATTGTTA
1 TCAAATTATTAATTGTTA
13574448 GTACCAGTCA
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 66 1.00
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.47
Consensus pattern (53 bp):
TCAAATTATTAATTGTTAATTACATTAATTGCTAGTAAAATTATCAAATTATA
Found at i:13574644 original size:22 final size:22
Alignment explanation
Indices: 13574619--13574737 Score: 197
Period size: 22 Copynumber: 5.5 Consensus size: 22
13574609 AGGGTTATGA
13574619 TTAGGGTTTTTAAGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGT
13574641 TTAGGGTTTTTAAGTTAAGGG-
1 TTAGGGTTTTTAAGTTAAGGGT
*
13574662 TTAGGGTTTTTAAGTTAAAGGT
1 TTAGGGTTTTTAAGTTAAGGGT
*
13574684 TTAAGGTTTTTAAGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAGGGT
*
13574706 TTAGGGTTTTTAAGTTAATGG-
1 TTAGGGTTTTTAAGTTAAGGGT
13574727 TTAGGGTTTTT
1 TTAGGGTTTTT
13574738 GTTAGGGTAA
Statistics
Matches: 91, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
21 31 0.34
22 60 0.66
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (22 bp):
TTAGGGTTTTTAAGTTAAGGGT
Found at i:13574668 original size:43 final size:44
Alignment explanation
Indices: 13574619--13574737 Score: 197
Period size: 43 Copynumber: 2.8 Consensus size: 44
13574609 AGGGTTATGA
*
13574619 TTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAAGTTAAGGG-
1 TTAGGGTTTTTAAGTTAAAGGTTTAGGGTTTTTAAGTTAAGGGT
*
13574662 TTAGGGTTTTTAAGTTAAAGGTTTAAGGTTTTTAAGTTAAGGGT
1 TTAGGGTTTTTAAGTTAAAGGTTTAGGGTTTTTAAGTTAAGGGT
*
13574706 TTAGGGTTTTTAAGTTAATGG-TTAGGGTTTTT
1 TTAGGGTTTTTAAGTTAAAGGTTTAGGGTTTTT
13574738 GTTAGGGTAA
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
43 51 0.72
44 20 0.28
ACGTcount: A:0.24, C:0.00, G:0.29, T:0.47
Consensus pattern (44 bp):
TTAGGGTTTTTAAGTTAAAGGTTTAGGGTTTTTAAGTTAAGGGT
Found at i:13574774 original size:8 final size:8
Alignment explanation
Indices: 13574754--13574786 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
13574744 GTAAATTTAA
13574754 TTATAAA-
1 TTATAAAT
13574761 TTATAAAT
1 TTATAAAT
*
13574769 TTATAAAG
1 TTATAAAT
13574777 TTATAAAT
1 TTATAAAT
13574785 TT
1 TT
13574787 TTAATAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
7 7 0.30
8 16 0.70
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (8 bp):
TTATAAAT
Found at i:13574782 original size:16 final size:15
Alignment explanation
Indices: 13574754--13574786 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
13574744 GTAAATTTAA
13574754 TTATAAATTATAAAT
1 TTATAAATTATAAAT
13574769 TTATAAAGTTATAAAT
1 TTATAAA-TTATAAAT
13574785 TT
1 TT
13574787 TTAATAAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (15 bp):
TTATAAATTATAAAT
Found at i:13575002 original size:21 final size:21
Alignment explanation
Indices: 13574978--13575017 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
13574968 TTATCCAGTT
*
13574978 TCTGGCCGGGG-TTGTGGTTGC
1 TCTGG-CGGGGATTCTGGTTGC
13574999 TCTGGCGGGGATTCTGGTT
1 TCTGGCGGGGATTCTGGTT
13575018 CTTCCGGTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.03, C:0.17, G:0.45, T:0.35
Consensus pattern (21 bp):
TCTGGCGGGGATTCTGGTTGC
Found at i:13575979 original size:7 final size:7
Alignment explanation
Indices: 13575969--13575994 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
13575959 TTATATACAT
13575969 AATACTA
1 AATACTA
13575976 AATACTA
1 AATACTA
13575983 AATACTA
1 AATACTA
13575990 AATAC
1 AATAC
13575995 CAATCGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:13576200 original size:20 final size:20
Alignment explanation
Indices: 13576163--13576200 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
13576153 ATTATTTTTA
*
13576163 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
13576183 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
13576201 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:13577190 original size:51 final size:50
Alignment explanation
Indices: 13577128--13577225 Score: 144
Period size: 51 Copynumber: 1.9 Consensus size: 50
13577118 TAATTTTTAA
13577128 AAATAGGGATTTAAGAGAAATTT-AAGAGAAAATTGAGAGCAAATTGAAATT
1 AAATAGGGATTTAAGAGAAATTTGAAG-G-AAATTGAGAGCAAATTGAAATT
* *
13577179 AAATATGGATTTGAGAGAAATTTGGAAGGAAATTGAGAGCAAATTGA
1 AAATAGGGATTTAAGAGAAATTT-GAAGGAAATTGAGAGCAAATTGA
13577226 GAGCAAATTG
Statistics
Matches: 43, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
51 39 0.91
52 1 0.02
53 3 0.07
ACGTcount: A:0.48, C:0.02, G:0.24, T:0.26
Consensus pattern (50 bp):
AAATAGGGATTTAAGAGAAATTTGAAGGAAATTGAGAGCAAATTGAAATT
Found at i:13585393 original size:40 final size:40
Alignment explanation
Indices: 13585338--13585558 Score: 388
Period size: 40 Copynumber: 5.5 Consensus size: 40
13585328 AGGCTTGTGC
13585338 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
* *
13585378 CTAGCAGGCTTAATGCAGGTGAAATATTCAGATTATACGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
* *
13585418 CTAGCAGGCTTAATGCCGATGAAATATTCAGATTATACGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
13585458 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
*
13585498 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACAT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
*
13585538 CTAGCAGGCTTCATGCCGGTG
1 CTAGCAGGCTTAATGCCGGTG
13585559 TACAGAATCA
Statistics
Matches: 173, Mismatches: 8, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 173 1.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (40 bp):
CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
Found at i:13590538 original size:46 final size:45
Alignment explanation
Indices: 13590471--13590656 Score: 246
Period size: 46 Copynumber: 4.0 Consensus size: 45
13590461 CCATGGAAAA
* *
13590471 TTGTGAAAAGTAGGTATGGTGTTTCAGTAAAGAAAGCTATATTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAA-CTATACTGAG
* *
13590517 TTGTGAAAAATAGGTATGGTGTTTCAGTGAAGAAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAG-AAACTATACTGAG
* * *
13590563 TTGTGAAAAGTAAGTATGGTGTTTCAGTGAAGAAAATCATACTGCG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAACT-ATACTGAG
* * *
13590609 TTGTGAAAAGTAGGTATGGTATTTCAATGAAGGAAACCATACTGAG
1 TTGTGAAAAGTAGGTATGGTGTTTCAGTGAA-GAAACTATACTGAG
13590655 TT
1 TT
13590657 ATAGCATTGT
Statistics
Matches: 122, Mismatches: 15, Indels: 6
0.85 0.10 0.04
Matches are distributed among these distances:
45 3 0.02
46 112 0.92
47 7 0.06
ACGTcount: A:0.35, C:0.08, G:0.26, T:0.31
Consensus pattern (45 bp):
TTGTGAAAAGTAGGTATGGTGTTTCAGTGAAGAAACTATACTGAG
Found at i:13590628 original size:92 final size:92
Alignment explanation
Indices: 13590471--13590656 Score: 275
Period size: 92 Copynumber: 2.0 Consensus size: 92
13590461 CCATGGAAAA
* *
13590471 TTGTGAAAAGTAGGTATGGTGTTTCAGTAAAGAAAGCTATATTGAGTTGTGAAAAATAGGTATGG
1 TTGTGAAAAGTAAGTATGGTGTTTCAGTAAAGAAAGCTATACTGAGTTGTGAAAAATAGGTATGG
* *
13590536 TGTTTCAGTGAAGAAAACCATACTGAG
66 TATTTCAATGAAGAAAACCATACTGAG
* * * *
13590563 TTGTGAAAAGTAAGTATGGTGTTTCAGTGAAGAAA-ATCATACTGCGTTGTGAAAAGTAGGTATG
1 TTGTGAAAAGTAAGTATGGTGTTTCAGTAAAGAAAGCT-ATACTGAGTTGTGAAAAATAGGTATG
*
13590627 GTATTTCAATGAAGGAAACCATACTGAG
65 GTATTTCAATGAAGAAAACCATACTGAG
13590655 TT
1 TT
13590657 ATAGCATTGT
Statistics
Matches: 84, Mismatches: 9, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
91 1 0.01
92 83 0.99
ACGTcount: A:0.35, C:0.08, G:0.26, T:0.31
Consensus pattern (92 bp):
TTGTGAAAAGTAAGTATGGTGTTTCAGTAAAGAAAGCTATACTGAGTTGTGAAAAATAGGTATGG
TATTTCAATGAAGAAAACCATACTGAG
Found at i:13592497 original size:31 final size:31
Alignment explanation
Indices: 13592462--13592524 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
13592452 ATTAATGTAC
13592462 TAATTAATTTGGAATGGATAAGTTTCTTTCA
1 TAATTAATTTGGAATGGATAAGTTTCTTTCA
13592493 TAATTAATTTGGAATGGATAAGTTTCTTTCA
1 TAATTAATTTGGAATGGATAAGTTTCTTTCA
13592524 T
1 T
13592525 TGAAATTCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.32, C:0.06, G:0.16, T:0.46
Consensus pattern (31 bp):
TAATTAATTTGGAATGGATAAGTTTCTTTCA
Found at i:13594332 original size:3 final size:3
Alignment explanation
Indices: 13594324--13594364 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
13594314 TATTCCTAGT
13594324 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
13594365 TATTTTAATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:13594506 original size:14 final size:14
Alignment explanation
Indices: 13594487--13594532 Score: 83
Period size: 14 Copynumber: 3.3 Consensus size: 14
13594477 TATTTAAAAT
13594487 ATAATAATAATTTA
1 ATAATAATAATTTA
*
13594501 ATAATACTAATTTA
1 ATAATAATAATTTA
13594515 ATAATAATAATTTA
1 ATAATAATAATTTA
13594529 ATAA
1 ATAA
13594533 CATTTTTTAA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (14 bp):
ATAATAATAATTTA
Found at i:13596130 original size:44 final size:46
Alignment explanation
Indices: 13596037--13596196 Score: 231
Period size: 46 Copynumber: 3.6 Consensus size: 46
13596027 TTTGAGTACT
* * *
13596037 TCTGATCAAGTGACAAAGTAATAAGTGATAGC-TTAGTTACACTTA
1 TCTGATCAAGTAACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
*
13596082 TCTGATCAAG-AAC-AAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGTAACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
*
13596126 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAGTAACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
*
13596172 TCTGATC-AGGAAC-AAGTGATAAGTG
1 TCTGATCAAGTAACAAAGTGATAAGTG
13596197 GTGATAAAAT
Statistics
Matches: 104, Mismatches: 8, Indels: 7
0.87 0.07 0.06
Matches are distributed among these distances:
43 15 0.14
44 36 0.35
45 16 0.15
46 37 0.36
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (46 bp):
TCTGATCAAGTAACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
Found at i:13596159 original size:46 final size:45
Alignment explanation
Indices: 13596037--13596196 Score: 229
Period size: 44 Copynumber: 3.6 Consensus size: 45
13596027 TTTGAGTACT
* *
13596037 TCTGATCAAGTGACAAAGTAATAAGTGATAGC-TTAGTTACACTTA
1 TCTGATCAAG-GACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
* *
13596082 TCTGATCAAGAAC-AAGTGATAAGTGGTAGCTTTAGCTACACTTA
1 TCTGATCAAGGACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
13596126 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
1 TCTGATCAAG-GACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
13596172 TCTGATC-AGGA-ACAAGTGATAAGTG
1 TCTGATCAAGGACA-AAGTGATAAGTG
13596197 GTGATAAAAT
Statistics
Matches: 105, Mismatches: 6, Indels: 9
0.88 0.05 0.08
Matches are distributed among these distances:
43 16 0.15
44 38 0.36
45 14 0.13
46 37 0.35
ACGTcount: A:0.36, C:0.14, G:0.21, T:0.29
Consensus pattern (45 bp):
TCTGATCAAGGACAAAGTGATAAGTGATAGCTTTAGCTACACTTA
Found at i:13596241 original size:62 final size:64
Alignment explanation
Indices: 13596135--13596260 Score: 195
Period size: 62 Copynumber: 2.0 Consensus size: 64
13596125 ATCTGATCAA
*
13596135 GTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATC-AG-GA-ACAAGTGATAAGTG
1 GTGACAAAATGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACA-AAGTGATAAGTG
* *
13596197 GTGATAAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
1 GTGACAAAATGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
13596261 ATAGTCTAGC
Statistics
Matches: 58, Mismatches: 3, Indels: 4
0.89 0.05 0.06
Matches are distributed among these distances:
62 41 0.71
63 2 0.03
64 14 0.24
65 1 0.02
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.29
Consensus pattern (64 bp):
GTGACAAAATGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAAGTGATAAGTG
Found at i:13596275 original size:45 final size:46
Alignment explanation
Indices: 13596197--13596305 Score: 161
Period size: 45 Copynumber: 2.4 Consensus size: 46
13596187 GTGATAAGTG
* * * *
13596197 GTGATAAAATGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAA
1 GTGACAAAGTGATAAGTGATAGCTCTAGCTACACTTATCTGATCAA
13596243 GTGACAAAGTGATAAGTGATAG-TCTAGCTACACTTATCTGATCAA
1 GTGACAAAGTGATAAGTGATAGCTCTAGCTACACTTATCTGATCAA
13596288 G-GAC-AAGTGATAAGTGAT
1 GTGACAAAGTGATAAGTGAT
13596306 CATACGTAAG
Statistics
Matches: 59, Mismatches: 4, Indels: 3
0.89 0.06 0.05
Matches are distributed among these distances:
43 14 0.24
44 3 0.05
45 23 0.39
46 19 0.32
ACGTcount: A:0.36, C:0.13, G:0.22, T:0.29
Consensus pattern (46 bp):
GTGACAAAGTGATAAGTGATAGCTCTAGCTACACTTATCTGATCAA
Found at i:13600784 original size:46 final size:46
Alignment explanation
Indices: 13600675--13600928 Score: 406
Period size: 46 Copynumber: 5.6 Consensus size: 46
13600665 TACATATGAT
* *
13600675 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-AGGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
*
13600718 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
13600764 CACTTATCACTTTGTTACTTGATCAGATAAGTGTAGTTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
13600810 CACTTATCACTTTGTCACTTGATCAGCTAAGTGTAGCTAAAGCTAT
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
* *
13600856 CACTTATCACTTTGTTACTTGATCATATAAGTGTAGCTAAAGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
13600902 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
13600929 AGTACTCAAA
Statistics
Matches: 192, Mismatches: 16, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
43 10 0.05
44 5 0.03
45 20 0.10
46 157 0.82
ACGTcount: A:0.29, C:0.21, G:0.15, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAAAGCTAC
Found at i:13602383 original size:16 final size:17
Alignment explanation
Indices: 13602359--13602392 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
13602349 TAACTATATG
13602359 TTTAGTTATTT-GTTTT
1 TTTAGTTATTTAGTTTT
*
13602375 TTTATTTATTTAGTTTT
1 TTTAGTTATTTAGTTTT
13602392 T
1 T
13602393 CACATAATAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.15, C:0.00, G:0.09, T:0.76
Consensus pattern (17 bp):
TTTAGTTATTTAGTTTT
Found at i:13610185 original size:39 final size:39
Alignment explanation
Indices: 13610131--13610210 Score: 160
Period size: 39 Copynumber: 2.1 Consensus size: 39
13610121 TAGTTTATAC
13610131 TTGTGTTTTTGTGAGTGGTGGGAAGGATTGTTTTTTCTT
1 TTGTGTTTTTGTGAGTGGTGGGAAGGATTGTTTTTTCTT
13610170 TTGTGTTTTTGTGAGTGGTGGGAAGGATTGTTTTTTCTT
1 TTGTGTTTTTGTGAGTGGTGGGAAGGATTGTTTTTTCTT
13610209 TT
1 TT
13610211 TCTTTCTTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 41 1.00
ACGTcount: A:0.10, C:0.03, G:0.33, T:0.55
Consensus pattern (39 bp):
TTGTGTTTTTGTGAGTGGTGGGAAGGATTGTTTTTTCTT
Found at i:13613120 original size:22 final size:23
Alignment explanation
Indices: 13613067--13613120 Score: 76
Period size: 22 Copynumber: 2.4 Consensus size: 23
13613057 TACAGAAACG
*
13613067 GAAGAAATAAGAAGGAAGGAAGCA
1 GAAGAAA-AAGAAGGAAGGAAGAA
13613091 GAAG-AAAAGAAGGAAGGAA-AA
1 GAAGAAAAAGAAGGAAGGAAGAA
13613112 GAAGAAAAA
1 GAAGAAAAA
13613121 ACTAGGTATT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
21 5 0.18
22 17 0.61
23 2 0.07
24 4 0.14
ACGTcount: A:0.65, C:0.02, G:0.31, T:0.02
Consensus pattern (23 bp):
GAAGAAAAAGAAGGAAGGAAGAA
Found at i:13618098 original size:16 final size:15
Alignment explanation
Indices: 13618067--13618108 Score: 57
Period size: 16 Copynumber: 2.7 Consensus size: 15
13618057 ACAAAATCAA
*
13618067 ATAAAATTTAATTAT
1 ATAAAAGTTAATTAT
13618082 ATAAAAGTTACATTAT
1 ATAAAAGTTA-ATTAT
*
13618098 ATAAAAATTAA
1 ATAAAAGTTAA
13618109 ATGAGTTAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
15 10 0.42
16 14 0.58
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.38
Consensus pattern (15 bp):
ATAAAAGTTAATTAT
Found at i:13618195 original size:37 final size:38
Alignment explanation
Indices: 13618145--13618225 Score: 112
Period size: 37 Copynumber: 2.2 Consensus size: 38
13618135 AAAATGTCAG
13618145 TTATAATTAAACTTTTAAAAAAATG-TATTTTAA-TTTT
1 TTATAATTAAACTTTTAAAAAAATGAT-TTTTAATTTTT
***
13618182 TTATAATTAAACTTTTAGTGAAATGATTTTTAATTTTT
1 TTATAATTAAACTTTTAAAAAAATGATTTTTAATTTTT
13618220 TTATAA
1 TTATAA
13618226 ACTTTATATG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
37 28 0.72
38 11 0.28
ACGTcount: A:0.40, C:0.02, G:0.05, T:0.53
Consensus pattern (38 bp):
TTATAATTAAACTTTTAAAAAAATGATTTTTAATTTTT
Found at i:13618376 original size:59 final size:60
Alignment explanation
Indices: 13618259--13618379 Score: 156
Period size: 60 Copynumber: 2.0 Consensus size: 60
13618249 ATACTAAACT
* * * * *
13618259 AAACACAACAACTTATAACTTAATCCTAAATTACTAATAAATTAAATTTTAAATAATTAC
1 AAACACAAAAACTTATAACATAATCCCAAATTACTAACAAATTAAATTTAAAATAATTAC
* *
13618319 AAACACAAAAATTTATAACATAATCCCAAA-TACTAGCAAATT-AATTATAAAATAATTAC
1 AAACACAAAAACTTATAACATAATCCCAAATTACTAACAAATTAAATT-TAAAATAATTAC
13618378 AA
1 AA
13618380 TATTCATACA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
58 4 0.08
59 23 0.43
60 26 0.49
ACGTcount: A:0.55, C:0.15, G:0.01, T:0.30
Consensus pattern (60 bp):
AAACACAAAAACTTATAACATAATCCCAAATTACTAACAAATTAAATTTAAAATAATTAC
Found at i:13618456 original size:27 final size:25
Alignment explanation
Indices: 13618420--13618639 Score: 207
Period size: 27 Copynumber: 9.0 Consensus size: 25
13618410 ATATCTCCAC
13618420 ATTACAATATTCATACAAAATTACAA
1 ATTACAATATTCATACAAAA-TACAA
13618446 TATTACAATATTCATAC--AA-A-AA
1 -ATTACAATATTCATACAAAATACAA
* *
13618468 ATTGCAATATTCATACAAAATTATAA
1 ATTACAATATTCATACAAAA-TACAA
13618494 TATTACAATATTCATAC-AAA-ACAA
1 -ATTACAATATTCATACAAAATACAA
*
13618518 A-TATAATATTCATACAAAATTACAAA
1 ATTACAATATTCATACAAAA-TAC-AA
13618544 ATTACAATATTCATAC--AA-A-AA
1 ATTACAATATTCATACAAAATACAA
*
13618565 ATTACAATATTCATACAAAACTATAA
1 ATTACAATATTCATACAAAA-TACAA
13618591 TATTACAATATTCATAC-AAA-A-AA
1 -ATTACAATATTCATACAAAATACAA
* *
13618614 ATTATAATATTCAAACAAAATTACAA
1 ATTACAATATTCATACAAAA-TACAA
13618640 TATTCATACA
Statistics
Matches: 165, Mismatches: 7, Indels: 43
0.77 0.03 0.20
Matches are distributed among these distances:
21 33 0.20
22 29 0.18
23 15 0.09
24 4 0.02
25 9 0.05
26 15 0.09
27 60 0.36
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (25 bp):
ATTACAATATTCATACAAAATACAA
Found at i:13618496 original size:48 final size:48
Alignment explanation
Indices: 13618367--13618643 Score: 373
Period size: 48 Copynumber: 5.7 Consensus size: 48
13618357 AATTAATTAT
13618367 AAAATAATTACAATATTCATACAAAAAATTACAATATTACAATATATC-T-C
1 AAAA-AATTACAATATTCATAC--AAAATTACAATATTACAATAT-TCATAC
* *
13618417 --CACATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
1 AAAAAATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
* *
13618463 AAAAAATTGCAATATTCATACAAAATTATAATATTACAATATTCATAC
1 AAAAAATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
* * *
13618511 AAAACAAATATAATATTCATACAAAATTACAAAATTACAATATTCATAC
1 AAAA-AATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
* *
13618560 AAAAAATTACAATATTCATACAAAACTATAATATTACAATATTCATAC
1 AAAAAATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
* *
13618608 AAAAAAATTATAATATTCAAACAAAATTACAATATT
1 -AAAAAATTACAATATTCATACAAAATTACAATATT
13618644 CATACAAAAA
Statistics
Matches: 201, Mismatches: 20, Indels: 13
0.86 0.09 0.06
Matches are distributed among these distances:
44 2 0.01
45 22 0.11
46 1 0.00
47 16 0.08
48 86 0.43
49 74 0.37
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.31
Consensus pattern (48 bp):
AAAAAATTACAATATTCATACAAAATTACAATATTACAATATTCATAC
Found at i:13618541 original size:97 final size:97
Alignment explanation
Indices: 13618367--13618643 Score: 395
Period size: 97 Copynumber: 2.9 Consensus size: 97
13618357 AATTAATTAT
* * * *
13618367 AAAATAATTACAATATTCATACAAAAAATTACAATATTACAATATATC-T-C--CAC-ATTACAA
1 AAAA-AATTACAATATTCATAC--AAAATTATAATATTACAATAT-TCATACAAAACAAATATAA
13618427 TATTCATACAAAATTACAATATTACAATATTCATAC
62 TATTCATACAAAATTACAATATTACAATATTCATAC
*
13618463 AAAAAATTGCAATATTCATACAAAATTATAATATTACAATATTCATACAAAACAAATATAATATT
1 AAAAAATTACAATATTCATACAAAATTATAATATTACAATATTCATACAAAACAAATATAATATT
*
13618528 CATACAAAATTACAAAATTACAATATTCATAC
66 CATACAAAATTACAATATTACAATATTCATAC
*
13618560 AAAAAATTACAATATTCATACAAAACTATAATATTACAATATTCATACAAAA-AAATTATAATAT
1 AAAAAATTACAATATTCATACAAAATTATAATATTACAATATTCATACAAAACAAA-TATAATAT
*
13618624 TCAAACAAAATTACAATATT
65 TCATACAAAATTACAATATT
13618644 CATACAAAAA
Statistics
Matches: 165, Mismatches: 10, Indels: 11
0.89 0.05 0.06
Matches are distributed among these distances:
92 2 0.01
93 21 0.13
94 1 0.01
95 16 0.10
96 9 0.05
97 116 0.70
ACGTcount: A:0.54, C:0.14, G:0.00, T:0.31
Consensus pattern (97 bp):
AAAAAATTACAATATTCATACAAAATTATAATATTACAATATTCATACAAAACAAATATAATATT
CATACAAAATTACAATATTACAATATTCATAC
Found at i:13618571 original size:70 final size:67
Alignment explanation
Indices: 13618420--13618652 Score: 233
Period size: 70 Copynumber: 3.3 Consensus size: 67
13618410 ATATCTCCAC
* * *
13618420 ATTACAATATTCATACAAAATTACAATATTACAATATTCATAC-AAAAAATTGCAATATTCATAC
1 ATTACAATATTCATACAAAACTATAATATTA-AATATTCATACAAAAAAATTACAATA-T--T-C
13618484 AAAATTATAA
61 AAAA--A-AA
13618494 TATTACAATATTCATACAAAAC-A-AATA-T-AATATTCATACAAAATTACAAAATTACAATATT
1 -ATTACAATATTCATACAAAACTATAATATTAAATATTCATAC--AA--A-AAAATTACAATATT
13618555 CATACAAAAA
60 CA-A-AAAAA
* *
13618565 ATTACAATATTCATACAAAACTATAATATTACAATATTCATACAAAAAAATTATAATATTCAAAC
1 ATTACAATATTCATACAAAACTATAATATTA-AATATTCATACAAAAAAATTACAATATTCAAAA
13618630 AAA
65 AAA
13618633 ATTACAATATTCATACAAAA
1 ATTACAATATTCATACAAAA
13618653 AATTACTAAT
Statistics
Matches: 141, Mismatches: 4, Indels: 33
0.79 0.02 0.19
Matches are distributed among these distances:
68 24 0.17
69 1 0.01
70 47 0.33
71 4 0.03
72 8 0.06
73 10 0.07
74 3 0.02
75 33 0.23
76 11 0.08
ACGTcount: A:0.55, C:0.14, G:0.00, T:0.31
Consensus pattern (67 bp):
ATTACAATATTCATACAAAACTATAATATTAAATATTCATACAAAAAAATTACAATATTCAAAAA
AA
Found at i:13618640 original size:89 final size:89
Alignment explanation
Indices: 13618442--13618777 Score: 351
Period size: 97 Copynumber: 3.8 Consensus size: 89
13618432 ATACAAAATT
* * *
13618442 ACAATATTACAATATTCATACAAAAAATTGCAATATTCATACAAAATTATAATATTACAATATTC
1 ACAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAAACTATAATATTACAATATTC
*
13618507 ATACAAAACAAATATA-ATATTCATACAAAA
66 ATACAAAA-AAAT-TACA-A-T-ATTC--AA
13618537 TTACAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAAACTATAATATTACAATAT
1 --ACAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAAACTATAATATTACAATAT
*
13618602 TCATACAAAAAAATTATAATATTCAA
64 TCATACAAAAAAATTACAATATTCAA
*
13618628 ACAAAATTACAATATTCATACAAAAAATTAC--TA---ATCCAAAACTATAA-A-TACAA-ATTT
1 ACAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAAACTATAATATTACAATA-TT
* * * *
13618685 AATTATAAAATAATTACAATATTCAT
65 CA-TACAAAAAAATTACAATATTCAA
* * *
13618711 ACAACATTACAATATTCATA-AAAAAATTATAATATTCATAC-AAA--A-AAT-TTAAAATATTC
1 ACAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAAACTATAATATTACAATATTC
13618770 ATACAAAA
66 ATACAAAA
13618778 TTCTAATCTA
Statistics
Matches: 212, Mismatches: 16, Indels: 36
0.80 0.06 0.14
Matches are distributed among these distances:
81 1 0.00
82 17 0.08
83 47 0.22
84 23 0.11
85 1 0.00
86 3 0.01
87 5 0.02
89 31 0.15
91 2 0.01
93 3 0.01
94 1 0.00
95 3 0.01
96 5 0.02
97 70 0.33
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (89 bp):
ACAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAAACTATAATATTACAATATTC
ATACAAAAAAATTACAATATTCAA
Found at i:13618736 original size:83 final size:84
Alignment explanation
Indices: 13618538--13618744 Score: 253
Period size: 83 Copynumber: 2.4 Consensus size: 84
13618528 CATACAAAAT
13618538 TACAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAAACTATAATATTACAATATT
1 TACAAAATTACAATATTCATACAAAAAATTAC--TA---ATACAAAACTATAATATTACAATATT
* *
13618603 CATACAAAAAAATTATAATATTCA
61 AATACAAAAAAATTACAATATTCA
* *
13618627 AACAAAATTACAATATTCATACAAAAAATTACTAATCCAAAACTATAA-A-TACAA-ATTTAATT
1 TACAAAATTACAATATTCATACAAAAAATTACTAATACAAAACTATAATATTACAATA-TTAA-T
* *
13618689 ATAAAATAATTACAATATTCA
64 ACAAAAAAATTACAATATTCA
*
13618710 TACAACATTACAATATTCATA-AAAAAATTA-TAATA
1 TACAAAATTACAATATTCATACAAAAAATTACTAATA
13618745 TTCATACAAA
Statistics
Matches: 107, Mismatches: 9, Indels: 12
0.84 0.07 0.09
Matches are distributed among these distances:
81 5 0.05
82 17 0.16
83 39 0.36
84 13 0.12
87 2 0.02
89 31 0.29
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (84 bp):
TACAAAATTACAATATTCATACAAAAAATTACTAATACAAAACTATAATATTACAATATTAATAC
AAAAAAATTACAATATTCA
Found at i:13618778 original size:83 final size:84
Alignment explanation
Indices: 13618538--13618778 Score: 251
Period size: 83 Copynumber: 2.8 Consensus size: 84
13618528 CATACAAAAT
* *
13618538 TACAAAATTACAATATTCATACAAAAAATTACAATATTCATACAAAACTATAATATTACAATATT
1 TACAAAATTACAATATTCATACAAAAAATTATAATATTCATAC-AAA--A-AAT-TTAAAATATT
* *
13618603 CATACAAAAAAATTATAATATTCA
61 CATACAAAATAATTACAATATTCA
* * * * * *
13618627 AACAAAATTACAATATTCATACAAAAAATTACT-A-ATCCAAAACTATAAA--TACAAAT-TTAA
1 TACAAAATTACAATATTCATACAAAAAATTA-TAATATTC-ATACAAAAAATTTA-AAATATTCA
*
13618687 TTATAAAATAATTACAATATTCA
63 -TACAAAATAATTACAATATTCA
*
13618710 TACAACATTACAATATTCATA-AAAAAATTATAATATTCATACAAAAAATTTAAAATATTCATAC
1 TACAAAATTACAATATTCATACAAAAAATTATAATATTCATACAAAAAATTTAAAATATTCATAC
13618774 AAAAT
66 AAAAT
13618779 TCTAATCTAA
Statistics
Matches: 124, Mismatches: 19, Indels: 24
0.74 0.11 0.14
Matches are distributed among these distances:
81 1 0.01
82 22 0.18
83 55 0.44
84 5 0.04
85 2 0.02
86 1 0.01
88 4 0.03
89 34 0.27
ACGTcount: A:0.56, C:0.13, G:0.00, T:0.31
Consensus pattern (84 bp):
TACAAAATTACAATATTCATACAAAAAATTATAATATTCATACAAAAAATTTAAAATATTCATAC
AAAATAATTACAATATTCA
Found at i:13618779 original size:20 final size:20
Alignment explanation
Indices: 13618702--13618779 Score: 86
Period size: 20 Copynumber: 3.9 Consensus size: 20
13618692 AAATAATTAC
* *
13618702 AATATTCATACAACA-TTAC
1 AATATTCATACAAAATTTAA
* * *
13618721 AATATTCATAAAAAAATTAT
1 AATATTCATACAAAATTTAA
13618741 AATATTCATACAAAAAATTTAA
1 AATATTCATAC--AAAATTTAA
13618763 AATATTCATACAAAATT
1 AATATTCATACAAAATT
13618780 CTAATCTAAA
Statistics
Matches: 50, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
19 13 0.26
20 19 0.38
22 18 0.36
ACGTcount: A:0.55, C:0.12, G:0.00, T:0.33
Consensus pattern (20 bp):
AATATTCATACAAAATTTAA
Found at i:13621565 original size:19 final size:18
Alignment explanation
Indices: 13621543--13621590 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
13621533 GTTCTTTTAA
13621543 CTTTTTTTTCTTTA-TTTTC
1 CTTTTTTTTC--TACTTTTC
*
13621562 CTTTCTTTTCTACTTTTC
1 CTTTTTTTTCTACTTTTC
13621580 CTTTTGTTTTC
1 CTTTT-TTTTC
13621591 CTCCCTTCTC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
17 2 0.08
18 9 0.36
19 14 0.56
ACGTcount: A:0.04, C:0.21, G:0.02, T:0.73
Consensus pattern (18 bp):
CTTTTTTTTCTACTTTTC
Found at i:13622791 original size:29 final size:31
Alignment explanation
Indices: 13622720--13622796 Score: 104
Period size: 29 Copynumber: 2.5 Consensus size: 31
13622710 TTAACGGCTC
* *
13622720 AGTGACTAAAATGTTACAATACGATAACGTA
1 AGTGACTAAAATGTAACAATACGATAACATA
* *
13622751 AGTGACTAAAATGTAACATTTC-A-AACATA
1 AGTGACTAAAATGTAACAATACGATAACATA
13622780 AGTGACTAAAATGTAAC
1 AGTGACTAAAATGTAAC
13622797 CTGAGGTAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
29 22 0.52
30 1 0.02
31 19 0.45
ACGTcount: A:0.47, C:0.13, G:0.14, T:0.26
Consensus pattern (31 bp):
AGTGACTAAAATGTAACAATACGATAACATA
Found at i:13622841 original size:3 final size:3
Alignment explanation
Indices: 13622835--13622867 Score: 57
Period size: 3 Copynumber: 11.0 Consensus size: 3
13622825 TAGTTTACCC
*
13622835 TTA TTA TTG TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
13622868 AAACTGTTAA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.30, C:0.00, G:0.03, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:13635228 original size:25 final size:23
Alignment explanation
Indices: 13635200--13635246 Score: 67
Period size: 25 Copynumber: 2.0 Consensus size: 23
13635190 AAATTCATTA
13635200 AAATTATATATAAATATATCAAATT
1 AAATTATA-ATAAAT-TATCAAATT
*
13635225 AAATTATAATAAATTATTAAAT
1 AAATTATAATAAATTATCAAAT
13635247 GTTTGCTTTA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 7 0.33
24 6 0.29
25 8 0.38
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (23 bp):
AAATTATAATAAATTATCAAATT
Found at i:13639901 original size:20 final size:20
Alignment explanation
Indices: 13639864--13639902 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
13639854 AGTCTTGTTT
* *
13639864 TATTATTTTAATTTGATTTG
1 TATTATTTTAAGTAGATTTG
*
13639884 TATTTTTTTAAGTAGATTT
1 TATTATTTTAAGTAGATTT
13639903 AAATTATATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.00, G:0.10, T:0.64
Consensus pattern (20 bp):
TATTATTTTAAGTAGATTTG
Found at i:13643457 original size:49 final size:49
Alignment explanation
Indices: 13643385--13643491 Score: 214
Period size: 49 Copynumber: 2.2 Consensus size: 49
13643375 ATGGATTATA
13643385 AATTCATTGGCAGTATGTCTATGCTGGTTTAAATCTAGCTCAACCCAAT
1 AATTCATTGGCAGTATGTCTATGCTGGTTTAAATCTAGCTCAACCCAAT
13643434 AATTCATTGGCAGTATGTCTATGCTGGTTTAAATCTAGCTCAACCCAAT
1 AATTCATTGGCAGTATGTCTATGCTGGTTTAAATCTAGCTCAACCCAAT
13643483 AATTCATTG
1 AATTCATTG
13643492 ATCCATTATA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 58 1.00
ACGTcount: A:0.29, C:0.20, G:0.16, T:0.36
Consensus pattern (49 bp):
AATTCATTGGCAGTATGTCTATGCTGGTTTAAATCTAGCTCAACCCAAT
Found at i:13643700 original size:13 final size:15
Alignment explanation
Indices: 13643662--13643691 Score: 51
Period size: 15 Copynumber: 1.9 Consensus size: 15
13643652 AAAAAATTAA
13643662 AATATAATATATATAT
1 AATATAA-ATATATAT
13643678 AATATAAATATATA
1 AATATAAATATATA
13643692 AATTGAATAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (15 bp):
AATATAAATATATAT
Found at i:13643755 original size:21 final size:21
Alignment explanation
Indices: 13643731--13643772 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
13643721 AGTAAATTAC
13643731 TAAA-AAAATTAATACATAAAA
1 TAAATAAAA-TAATACATAAAA
* *
13643752 TAAATACAATAATAGATAAAA
1 TAAATAAAATAATACATAAAA
13643773 ACGAGATGCG
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.69, C:0.05, G:0.02, T:0.24
Consensus pattern (21 bp):
TAAATAAAATAATACATAAAA
Found at i:13644424 original size:3 final size:3
Alignment explanation
Indices: 13644418--13644446 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
13644408 CTATTTTTTT
13644418 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
13644447 GGGTTAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:13650219 original size:5 final size:5
Alignment explanation
Indices: 13650209--13650234 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
13650199 TGAGCATTCG
13650209 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
13650235 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:13651271 original size:9 final size:9
Alignment explanation
Indices: 13651257--13651293 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
13651247 TATAGTTTGA
13651257 TATTCGAAT
1 TATTCGAAT
13651266 TATTCGAAT
1 TATTCGAAT
*
13651275 TATTCGAGT
1 TATTCGAAT
13651284 TATTCGAAT
1 TATTCGAAT
13651293 T
1 T
13651294 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:13652306 original size:24 final size:21
Alignment explanation
Indices: 13652247--13652306 Score: 54
Period size: 20 Copynumber: 2.8 Consensus size: 21
13652237 GATTAATGGT
13652247 GATT-AAGTTTAATTAATTAA
1 GATTAAAGTTTAATTAATTAA
*
13652267 GGTTAAA--TTAAGTTAATTAA
1 GATTAAAGTTTAA-TTAATTAA
13652287 GTAATTAAAAGTTTAATTAA
1 G--ATT-AAAGTTTAATTAA
13652307 AGTATATAAG
Statistics
Matches: 31, Mismatches: 2, Indels: 10
0.72 0.05 0.23
Matches are distributed among these distances:
19 4 0.13
20 12 0.39
21 2 0.06
22 2 0.06
23 3 0.10
24 4 0.13
25 4 0.13
ACGTcount: A:0.47, C:0.00, G:0.12, T:0.42
Consensus pattern (21 bp):
GATTAAAGTTTAATTAATTAA
Found at i:13654951 original size:67 final size:67
Alignment explanation
Indices: 13654872--13655003 Score: 246
Period size: 67 Copynumber: 2.0 Consensus size: 67
13654862 TTCTCAATTC
13654872 AGAGAGCACACTCCCACGAACCTCATTTCTTACAACGGGATTACCAGTCCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCACGAACCTCATTTCTTACAACGGGATTACCAGTCCAGGCTAAATCCCCTG
13654937 CG
66 CG
* *
13654939 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCAGTCCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCACGAACCTCATTTCTTACAACGGGATTACCAGTCCAGGCTAAATCCCCTG
13655004 TAATATAAAC
Statistics
Matches: 63, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
67 63 1.00
ACGTcount: A:0.27, C:0.34, G:0.19, T:0.20
Consensus pattern (67 bp):
AGAGAGCACACTCCCACGAACCTCATTTCTTACAACGGGATTACCAGTCCAGGCTAAATCCCCTG
CG
Found at i:13655218 original size:57 final size:57
Alignment explanation
Indices: 13655130--13655238 Score: 168
Period size: 57 Copynumber: 1.9 Consensus size: 57
13655120 AATTCGGATT
13655130 ACCCGTCCGGGCTAAATCCATTTTCCACATATTCTTCGGG-AGGACTATATCAAGATC
1 ACCCGTCCGGGCTAAATCCATTTTCCACATATTCTTCGGGAAGG-CTATATCAAGATC
* *
13655187 ACCCGTCCGGGCTAGAT-CTTTTTCACACATATTCTTCGGGAAGGCTATATCA
1 ACCCGTCCGGGCTAAATCCATTTTC-CACATATTCTTCGGGAAGGCTATATCA
13655239 GTATGAGATC
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
56 6 0.12
57 39 0.81
58 3 0.06
ACGTcount: A:0.25, C:0.28, G:0.18, T:0.29
Consensus pattern (57 bp):
ACCCGTCCGGGCTAAATCCATTTTCCACATATTCTTCGGGAAGGCTATATCAAGATC
Found at i:13658606 original size:31 final size:31
Alignment explanation
Indices: 13658571--13658663 Score: 95
Period size: 32 Copynumber: 3.0 Consensus size: 31
13658561 ATATTATCAT
13658571 CGAATGTATATACACTTTAAACATGAATAGC
1 CGAATGTATATACACTTTAAACATGAATAGC
* *
13658602 CGAATGCT-TATACAC-ATAACAAAT-ATTATCA-C
1 CGAATG-TATATACACTTTAA-ACATGA--AT-AGC
13658634 CGAATGTATATACACTTTAAACATGAATAG
1 CGAATGTATATACACTTTAAACATGAATAG
13658664 TTGAATGCAT
Statistics
Matches: 49, Mismatches: 4, Indels: 18
0.69 0.06 0.25
Matches are distributed among these distances:
30 5 0.10
31 19 0.39
32 20 0.41
33 5 0.10
ACGTcount: A:0.43, C:0.17, G:0.11, T:0.29
Consensus pattern (31 bp):
CGAATGTATATACACTTTAAACATGAATAGC
Found at i:13658654 original size:63 final size:67
Alignment explanation
Indices: 13658497--13658716 Score: 241
Period size: 63 Copynumber: 3.2 Consensus size: 67
13658487 AACACTTAAA
* * * * ** *
13658497 ACCGAATGCATATACAATTTAAAACATGAATCGCCAAATGTGTATATACATATATGCTTAACAAA
1 ACCGAATGTATATACACTTT-AAACATGAATAGCCGAATGCATATATAC--A-A-GCATAACAAA
13658562 TATTATC
61 TATTATC
*
13658569 ATCGAATGTATATACACTTTAAACATGAATAGCCGAATGC-T-TATAC-A-CATAACAAATATTA
1 ACCGAATGTATATACACTTTAAACATGAATAGCCGAATGCATATATACAAGCATAACAAATATTA
13658630 TC
66 TC
** * *
13658632 ACCGAATGTATATACACTTTAAACATGAATAGTTGAATGCATATATACATATGCCTAACAAGTAT
1 ACCGAATGTATATACACTTTAAACATGAATAGCCGAATGCATATATACA-A-GCATAACAAATAT
13658697 TATC
64 TATC
13658701 ACCGAATGTATATACA
1 ACCGAATGTATATACA
13658717 TGTTCTTCAA
Statistics
Matches: 130, Mismatches: 12, Indels: 15
0.83 0.08 0.10
Matches are distributed among these distances:
63 52 0.40
64 1 0.01
65 6 0.05
67 1 0.01
69 35 0.27
70 1 0.01
71 17 0.13
72 17 0.13
ACGTcount: A:0.42, C:0.17, G:0.10, T:0.30
Consensus pattern (67 bp):
ACCGAATGTATATACACTTTAAACATGAATAGCCGAATGCATATATACAAGCATAACAAATATTA
TC
Done.