Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_019167849.1 Durio zibethinus cultivar Musang King isolate D1 unplaced genomic scaffold, Duzib1.0 scaffold_12, whole genome shotgun sequence
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 22966848
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 129000 characters in sequence are not A, C, G, or T
File 110 of 129
Found at i:18419564 original size:29 final size:29
Alignment explanation
Indices: 18419522--18419606 Score: 154
Period size: 29 Copynumber: 3.0 Consensus size: 29
18419512 GATGCTGTGG
18419522 TAGTTGATTGTATGGATTAGGGAGGTTGA
1 TAGTTGATTGTATGGATTAGGGAGGTTGA
18419551 TAGTTGATTGTATGGATTAGGGAGGTTGA
1 TAGTTGATTGTATGGATTAGGGAGGTTGA
*
18419580 TAGTTGATTGTATGG-TTAGGGAAGTTG
1 TAGTTGATTGTATGGATTAGGGAGGTTG
18419607 TAAATAGGGG
Statistics
Matches: 55, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
28 11 0.20
29 44 0.80
ACGTcount: A:0.24, C:0.00, G:0.38, T:0.39
Consensus pattern (29 bp):
TAGTTGATTGTATGGATTAGGGAGGTTGA
Found at i:18421797 original size:21 final size:23
Alignment explanation
Indices: 18421772--18421822 Score: 63
Period size: 23 Copynumber: 2.3 Consensus size: 23
18421762 TCTTCATTTG
18421772 AATTCATA-T-TCT-TTTTCTAAA
1 AATTCATACTCTCTCTTTT-TAAA
18421793 AATTCATACTCTCTCTTTTTAAA
1 AATTCATACTCTCTCTTTTTAAA
*
18421816 AAATCAT
1 AATTCAT
18421823 TCTTTCCTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
21 8 0.31
22 1 0.04
23 13 0.50
24 4 0.15
ACGTcount: A:0.35, C:0.18, G:0.00, T:0.47
Consensus pattern (23 bp):
AATTCATACTCTCTCTTTTTAAA
Found at i:18422761 original size:19 final size:21
Alignment explanation
Indices: 18422721--18422761 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
18422711 TTGGTTTTCA
*
18422721 AGAAAGAGTATGGATTTTTAG
1 AGAAAGAGTATGGATATTTAG
18422742 AGAAAGAGTAT-GA-ATTTAG
1 AGAAAGAGTATGGATATTTAG
18422761 A
1 A
18422762 TAAAAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 6 0.32
20 2 0.11
21 11 0.58
ACGTcount: A:0.44, C:0.00, G:0.27, T:0.29
Consensus pattern (21 bp):
AGAAAGAGTATGGATATTTAG
Found at i:18423506 original size:19 final size:19
Alignment explanation
Indices: 18423482--18423559 Score: 86
Period size: 20 Copynumber: 4.1 Consensus size: 19
18423472 CTTTAAATTA
18423482 TAAAAAATTCAAAAATTTT
1 TAAAAAATTCAAAAATTTT
* * *
18423501 TAAAAAGTTC-AAAATATC
1 TAAAAAATTCAAAAATTTT
*
18423519 TAAAAAATTCAAAAAAATTT
1 TAAAAAATTC-AAAAATTTT
*
18423539 TAAAAAATATAAAAAATTTT
1 TAAAAAAT-TCAAAAATTTT
18423559 T
1 T
18423560 TAAATTGTAA
Statistics
Matches: 47, Mismatches: 9, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
18 15 0.32
19 9 0.19
20 22 0.47
21 1 0.02
ACGTcount: A:0.60, C:0.05, G:0.01, T:0.33
Consensus pattern (19 bp):
TAAAAAATTCAAAAATTTT
Found at i:18423525 original size:11 final size:10
Alignment explanation
Indices: 18423476--18423598 Score: 71
Period size: 9 Copynumber: 12.9 Consensus size: 10
18423466 TAATTTCTTT
*
18423476 AAATTATAAA
1 AAATTCTAAA
18423486 AAATTC-AAA
1 AAATTCTAAA
* *
18423495 AATTTTTAAA
1 AAATTCTAAA
*
18423505 AAGTTC-AAA
1 AAATTCTAAA
*
18423514 ATA-TCTAAA
1 AAATTCTAAA
*
18423523 AAATTCAAAA
1 AAATTCTAAA
*
18423533 AAATTTTAAA
1 AAATTCTAAA
*
18423543 AAA-TATAAA
1 AAATTCTAAA
***
18423552 AAATT-TTTT
1 AAATTCTAAA
*
18423561 AAATTGTAAA
1 AAATTCTAAA
18423571 ATAATTCT-AA
1 A-AATTCTAAA
*
18423581 AAATT-AAAA
1 AAATTCTAAA
18423590 AAATTCTAA
1 AAATTCTAA
18423599 TTGTCTTTTA
Statistics
Matches: 84, Mismatches: 21, Indels: 16
0.69 0.17 0.13
Matches are distributed among these distances:
8 2 0.02
9 41 0.49
10 36 0.43
11 5 0.06
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (10 bp):
AAATTCTAAA
Found at i:18423693 original size:7 final size:7
Alignment explanation
Indices: 18423672--18423707 Score: 51
Period size: 7 Copynumber: 5.6 Consensus size: 7
18423662 AAAATTTTCA
18423672 AAAATTC
1 AAAATTC
18423679 AAAA---
1 AAAATTC
18423683 AAAATTC
1 AAAATTC
18423690 AAAATTC
1 AAAATTC
18423697 AAAATTC
1 AAAATTC
18423704 AAAA
1 AAAA
18423708 ATTTTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
4 4 0.15
7 22 0.85
ACGTcount: A:0.67, C:0.11, G:0.00, T:0.22
Consensus pattern (7 bp):
AAAATTC
Found at i:18423693 original size:18 final size:20
Alignment explanation
Indices: 18423656--18423700 Score: 67
Period size: 18 Copynumber: 2.4 Consensus size: 20
18423646 AGAAAATAAT
*
18423656 TTCAAAAAAATTTTCAAAAA
1 TTCAAAAAAATATTCAAAAA
18423676 TTCAAAAAAA-ATTC-AAAA
1 TTCAAAAAAATATTCAAAAA
18423694 TTCAAAA
1 TTCAAAA
18423701 TTCAAAAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 11 0.46
19 3 0.12
20 10 0.42
ACGTcount: A:0.62, C:0.11, G:0.00, T:0.27
Consensus pattern (20 bp):
TTCAAAAAAATATTCAAAAA
Found at i:18423884 original size:19 final size:18
Alignment explanation
Indices: 18423862--18423902 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 18
18423852 TTAATTTCTT
18423862 AATTTTT-TAAAATTTTCA
1 AATTTTTGT-AAATTTTCA
18423880 GAATTTTTGTAAATTTTCA
1 -AATTTTTGTAAATTTTCA
18423899 AATT
1 AATT
18423903 ATGATAGTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.19
19 16 0.76
20 1 0.05
ACGTcount: A:0.37, C:0.05, G:0.05, T:0.54
Consensus pattern (18 bp):
AATTTTTGTAAATTTTCA
Found at i:18424111 original size:10 final size:10
Alignment explanation
Indices: 18424079--18424145 Score: 62
Period size: 10 Copynumber: 6.6 Consensus size: 10
18424069 ATATTTAAAT
18424079 TTTTTAAAAA
1 TTTTTAAAAA
** *
18424089 TTTTTTCATA
1 TTTTTAAAAA
18424099 TTTTTAAAAA
1 TTTTTAAAAA
* *
18424109 TTTTTAGAAT
1 TTTTTAAAAA
*
18424119 TTTTCTCAAAA
1 TTTT-TAAAAA
18424130 TTTTTAAAAA
1 TTTTTAAAAA
*
18424140 GTTTTA
1 TTTTTA
18424146 TAATTGTTTT
Statistics
Matches: 43, Mismatches: 13, Indels: 2
0.74 0.22 0.03
Matches are distributed among these distances:
10 36 0.84
11 7 0.16
ACGTcount: A:0.37, C:0.04, G:0.03, T:0.55
Consensus pattern (10 bp):
TTTTTAAAAA
Found at i:18424122 original size:20 final size:19
Alignment explanation
Indices: 18424072--18424137 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 19
18424062 AAATTCAATA
18424072 TTTAAATTTTTTAAAAATT
1 TTTAAATTTTTTAAAAATT
**
18424091 TTTTCATATTTTTAAAAATT
1 TTTAAAT-TTTTTAAAAATT
*
18424111 TTTAGAATTTTTCTCAAAATT
1 TTTA-AATTTTT-TAAAAATT
18424132 TTTAAA
1 TTTAAA
18424138 AAGTTTTATA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
19 5 0.13
20 21 0.54
21 13 0.33
ACGTcount: A:0.38, C:0.05, G:0.02, T:0.56
Consensus pattern (19 bp):
TTTAAATTTTTTAAAAATT
Found at i:18424171 original size:16 final size:15
Alignment explanation
Indices: 18424149--18424187 Score: 55
Period size: 15 Copynumber: 2.7 Consensus size: 15
18424139 AGTTTTATAA
18424149 TTGTTTTGAATTTTT
1 TTGTTTTGAATTTTT
18424164 TATGTTTTG-ATTTTT
1 T-TGTTTTGAATTTTT
18424179 TT-TTTTGAA
1 TTGTTTTGAA
18424188 AATTTTGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
13 5 0.23
14 2 0.09
15 8 0.36
16 7 0.32
ACGTcount: A:0.15, C:0.00, G:0.13, T:0.72
Consensus pattern (15 bp):
TTGTTTTGAATTTTT
Found at i:18424223 original size:19 final size:19
Alignment explanation
Indices: 18424187--18424233 Score: 55
Period size: 18 Copynumber: 2.6 Consensus size: 19
18424177 TTTTTTTTGA
18424187 AAATTTTG--AATTTATAG
1 AAATTTTGAAAATTTATAG
*
18424204 AAATTTTGAAAATTTTTAG
1 AAATTTTGAAAATTTATAG
*
18424223 -AATTTTCAAAA
1 AAATTTTGAAAA
18424234 AATTTTAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 8 0.31
18 10 0.38
19 8 0.31
ACGTcount: A:0.45, C:0.02, G:0.09, T:0.45
Consensus pattern (19 bp):
AAATTTTGAAAATTTATAG
Found at i:18424261 original size:22 final size:19
Alignment explanation
Indices: 18424236--18424279 Score: 61
Period size: 22 Copynumber: 2.2 Consensus size: 19
18424226 TTTCAAAAAA
18424236 TTTTAAAAAACTTTTAGAATTT
1 TTTTAAAAAA-TTTT--AATTT
18424258 TTTTAAAAAATTTTAATTT
1 TTTTAAAAAATTTTAATTT
18424277 TTT
1 TTT
18424280 AAATTTTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
19 8 0.36
21 4 0.18
22 10 0.45
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (19 bp):
TTTTAAAAAATTTTAATTT
Found at i:18424265 original size:21 final size:19
Alignment explanation
Indices: 18424236--18424282 Score: 58
Period size: 21 Copynumber: 2.4 Consensus size: 19
18424226 TTTCAAAAAA
*
18424236 TTTTAAAAAACTTTTAGAATT
1 TTTTAAAAAAATTTT--AATT
*
18424257 TTTTTAAAAAATTTTAATT
1 TTTTAAAAAAATTTTAATT
18424276 TTTTAAA
1 TTTTAAA
18424283 TTTTTTTAAT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
19 10 0.43
21 13 0.57
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (19 bp):
TTTTAAAAAAATTTTAATT
Found at i:18424279 original size:18 final size:18
Alignment explanation
Indices: 18424236--18424301 Score: 60
Period size: 18 Copynumber: 3.4 Consensus size: 18
18424226 TTTCAAAAAA
18424236 TTTTAAAAAACTTTTAGAATTT
1 TTTTAAAAAA-TTTT--AA-TT
18424258 TTTTAAAAAATTTTAATT
1 TTTTAAAAAATTTTAATT
*** *
18424276 TTTTAAATTTTTTTAATA
1 TTTTAAAAAATTTTAATT
18424294 TTTTAAAA
1 TTTTAAAA
18424302 GTTTTAGAAT
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
18 23 0.59
19 2 0.05
21 4 0.10
22 10 0.26
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.56
Consensus pattern (18 bp):
TTTTAAAAAATTTTAATT
Found at i:18424306 original size:18 final size:18
Alignment explanation
Indices: 18424258--18424306 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 18
18424248 TTTAGAATTT
* *
18424258 TTTTAAAAAATTTTAATT
1 TTTTAAAAATTTTTAATA
**
18424276 TTTTAAATTTTTTTAATA
1 TTTTAAAAATTTTTAATA
*
18424294 TTTTAAAAGTTTT
1 TTTTAAAAATTTT
18424307 AGAATTCCTA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (18 bp):
TTTTAAAAATTTTTAATA
Found at i:18424385 original size:31 final size:30
Alignment explanation
Indices: 18424334--18424452 Score: 107
Period size: 30 Copynumber: 3.9 Consensus size: 30
18424324 TTAAAATTAA
* * *
18424334 AATTTTTTTGTAAATGTTAAAAAAATTTTA-
1 AATTATTTTG-AAATTTTTAAAAAATTTTAG
*
18424364 AATTATTTTAGAATTTTTTAAAAAATTTTAG
1 AATTATTTT-GAAATTTTTAAAAAATTTTAG
* * ** *
18424395 AATTGTTTTGAAATTTTTGAAATTTTTTAA
1 AATTATTTTGAAATTTTTAAAAAATTTTAG
*
18424425 AATT-TTTTGAAAATTTTTGAAAAATTTT
1 AATTATTTTG-AAATTTTTAAAAAATTTT
18424453 TAAATTGTAG
Statistics
Matches: 74, Mismatches: 12, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
29 5 0.07
30 60 0.81
31 9 0.12
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (30 bp):
AATTATTTTGAAATTTTTAAAAAATTTTAG
Found at i:18424387 original size:30 final size:30
Alignment explanation
Indices: 18424353--18424476 Score: 117
Period size: 30 Copynumber: 4.1 Consensus size: 30
18424343 GTAAATGTTA
* *
18424353 AAAAAATTTTAAATTATTTTAGAATTTTTT
1 AAAAAATTTTAAATTGTTTTAAAATTTTTT
*
18424383 AAAAAATTTTAGAATTGTTTTGAAA-TTTTT
1 AAAAAATTTTA-AATTGTTTTAAAATTTTTT
* ** *
18424413 GAAATTTTTTAAAATT-TTTTGAAAATTTTTG
1 AAAAAATTTT-AAATTGTTTT-AAAATTTTTT
* **
18424444 AAAAATTTTTAAATTGTAGTAAAATTTTTT
1 AAAAAATTTTAAATTGTTTTAAAATTTTTT
18424474 AAA
1 AAA
18424477 GTTTTTTAAT
Statistics
Matches: 76, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
29 4 0.05
30 47 0.62
31 25 0.33
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (30 bp):
AAAAAATTTTAAATTGTTTTAAAATTTTTT
Found at i:18424431 original size:20 final size:19
Alignment explanation
Indices: 18424369--18424485 Score: 92
Period size: 20 Copynumber: 5.8 Consensus size: 19
18424359 TTTTAAATTA
*
18424369 TTTTAGAATTTTTTAAAAAA
1 TTTTA-AATTTTTTAAAAAT
*
18424389 TTTTAGAATTGTTTT-GAAAT
1 TTTTA-AATT-TTTTAAAAAT
*
18424409 TTTTGAAATTTTTTAAAATT
1 TTTT-AAATTTTTTAAAAAT
*
18424429 TTTTGAAAATTTTTGAAAAAT
1 TTTT--AAATTTTTTAAAAAT
** *
18424450 TTTTAAATTGTAGTAAAATT
1 TTTTAAATT-TTTTAAAAAT
18424470 TTTTAAAGTTTTTTAA
1 TTTTAAA-TTTTTTAA
18424486 TTTTTTAGAA
Statistics
Matches: 78, Mismatches: 13, Indels: 12
0.76 0.13 0.12
Matches are distributed among these distances:
19 9 0.12
20 45 0.58
21 24 0.31
ACGTcount: A:0.38, C:0.00, G:0.09, T:0.54
Consensus pattern (19 bp):
TTTTAAATTTTTTAAAAAT
Found at i:18424490 original size:9 final size:9
Alignment explanation
Indices: 18424359--18424492 Score: 81
Period size: 10 Copynumber: 13.6 Consensus size: 9
18424349 GTTAAAAAAA
18424359 TTTTAAATT
1 TTTTAAATT
18424368 ATTTTAGAATT
1 -TTTTA-AATT
**
18424379 TTTTAAAAAA
1 TTTT-AAATT
18424389 TTTTAGAATT
1 TTTTA-AATT
18424399 GTTTTGAAATT
1 -TTTT-AAATT
*
18424410 TTTGAAATT
1 TTTTAAATT
18424419 TTTTAAAATT
1 TTTT-AAATT
18424429 TTTTGAAAATT
1 TTTT--AAATT
* *
18424440 TTTGAAAAAT
1 TTT-TAAATT
18424450 TTTTAAATT
1 TTTTAAATT
* *
18424459 GTAGTAAAATT
1 -T-TTTAAATT
18424470 TTTTAAAGTT
1 TTTTAAA-TT
18424480 TTTT-AATT
1 TTTTAAATT
18424488 TTTTA
1 TTTTA
18424493 GAACTTGTTG
Statistics
Matches: 98, Mismatches: 14, Indels: 25
0.72 0.10 0.18
Matches are distributed among these distances:
8 6 0.06
9 19 0.19
10 44 0.45
11 28 0.29
12 1 0.01
ACGTcount: A:0.37, C:0.00, G:0.07, T:0.56
Consensus pattern (9 bp):
TTTTAAATT
Found at i:18425457 original size:4 final size:4
Alignment explanation
Indices: 18425443--18425474 Score: 55
Period size: 4 Copynumber: 7.8 Consensus size: 4
18425433 ACTTCAATAA
18425443 AAAT AAAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT -AAAT AAAT AAAT AAAT AAAT AAAT AAA
18425475 AACTCTTCTG
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 23 0.85
5 4 0.15
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:18432568 original size:161 final size:161
Alignment explanation
Indices: 18432349--18433433 Score: 860
Period size: 161 Copynumber: 6.8 Consensus size: 161
18432339 CATTTTAACC
* * * *
18432349 TTTCACACATATCAATCATG-G-AAATCAAATTCAATCATTTGGACAAA-TTTAATATCATGTAT
1 TTTCACACATATCAA-C-TGTGAAAACCAAGTTCAATCATTT-AAAAAAGTTTAATATCATGTAT
* * * *
18432411 TGAAGCTATCTAAAATGTTAAAACAAAACAATAAC-G-ACAATTTTGTATTTTTACCTTTTAACC
63 TGAAGCTATCCAAACTGTTAAAATAAAACAATAACAGTA-AA-TTTGTATTTTTACCTTTTAACG
*
18432474 GCAAAAAAAGTCCTAAACAGAAGTAAACAATAA-TT
126 GCAAAAAAAGTCCTAAACAGAAGTAAATAATAACTT
* *
18432509 ATTTCACATATATCAACTGTGAAAATCAAGTTCAATCATTTAAAAAAGTTTAATATCATGTATTG
1 -TTTCACACATATCAACTGTGAAAACCAAGTTCAATCATTTAAAAAAGTTTAATATCATGTATTG
* * * * **
18432574 AAACTATCCAAACTGTTAAAATAGAACAATAACAGTAAATTTGTATTTTTATCTTTCAATAGCAT
65 AAGCTATCCAAACTGTTAAAATAAAACAATAACAGTAAATTTGTATTTTTACCTTTTAACGGCA-
* * *
18432639 GAAAAA-TCCTAAACA-AAGGTAAACAGTAACTT
129 AAAAAAGTCCTAAACAGAA-GTAAATAATAACTT
* * * ** * ** *
18432671 TTTCATATATATTAACTACGAAAACCAAGTTCAATGATTCCAAAAAGTTTAATATCATGTATTAA
1 TTTCACACATATCAACTGTGAAAACCAAGTTCAATCATTTAAAAAAGTTTAATATCATGTATTGA
* * * * * * *
18432736 AGCCATCCAAACTGTTAAAATAAAATAACAACAGTAAATTTGTATATTTGCCTTTTAATGGTAAA
66 AGCTATCCAAACTGTTAAAATAAAACAATAACAGTAAATTTGTATTTTTACCTTTTAACGGCAAA
* * *
18432801 AATAGTCCTAAATAGACA-TAAATGATAACTT
131 AAAAGTCCTAAACAGA-AGTAAATAATAACTT
* * * *
18432832 TTTCACACATATCAACCGT-AGAAACCAAGCTCAATCATTCAAACAAGTTTAATATCATGTATTG
1 TTTCACACATATCAACTGTGA-AAACCAAGTTCAATCATTTAAAAAAGTTTAATATCATGTATTG
* * * * ** * * *
18432896 AAACTATCCAAACTATTAAAACAGAACAATATTA-TAAATTTGCA-TTTTGCCTTTTAACGGTAT
65 AAGCTATCCAAACTGTTAAAATAAAACAATAACAGTAAATTTGTATTTTTACCTTTTAACGGCA-
* * **
18432959 AAAAAAATCCTAAACAGACGTAAATGTTAGA-TT
129 AAAAAAGTCCTAAACAGAAGTAAATAATA-ACTT
* * * *** * * *
18432992 TTTCATACATATCAACTATGAAAACCAAGTTCAATTATTCCGACAAGTTTAATACCATATATTGA
1 TTTCACACATATCAACTGTGAAAACCAAGTTCAATCATTTAAAAAAGTTTAATATCATGTATTGA
* * ** *
18433057 AGCTATGCAAACTGTTAAAATAAAACAATAAC----AA-TTG--------CCTCTTAATAGCACA
66 AGCTATCCAAACTGTTAAAATAAAACAATAACAGTAAATTTGTATTTTTACCTTTTAACGGCAAA
* * * *
18433109 AAAAGTCTTAAACATATGTAAATGATAAC-T
131 AAAAGTCCTAAACAGAAGTAAATAATAACTT
* * ** * *
18433139 TTTCACACATATCAACTGTTAAAACTAAGTTCAATCATTTGGACAAGTTTAATATCATATATTGA
1 TTTCACACATATCAACTGTGAAAACCAAGTTCAATCATTTAAAAAAGTTTAATATCATGTATTGA
* * * * * * * *
18433204 AGCTATCTAAACTGTTAAAATAGAACATTAACAGTAAATTTATATTTTTACCTATTAATGACATA
66 AGCTATCCAAACTGTTAAAATAAAACAATAACAGTAAATTTGTATTTTTACCTTTTAACGGCAAA
* *
18433269 AAAAGTCCTAAATAGACGTAAATAATAACTT
131 AAAAGTCCTAAACAGAAGTAAATAATAACTT
* * ** * * * * * * *
18433300 TTTCATATATATCAACCATAAAAACTAAGTTCAAT-AATTAGGATAAGTTTAATTTCATGCATTG
1 TTTCACACATATCAACTGTGAAAACCAAGTTCAATCATTTA-AAAAAGTTTAATATCATGTATTG
* * * * * **
18433364 AAACTATCAAAACTATTAAAACT-AAATAATAACTGTAAATTTACATTTTTACCTTTTAACGGCA
65 AAGCTATCCAAACTGTTAAAA-TAAAACAATAACAGTAAATTTGTATTTTTACCTTTTAACGGCA
*
18433428 CAAAAA
129 AAAAAA
18433434 TTTGTAAACA
Statistics
Matches: 751, Mismatches: 140, Indels: 66
0.78 0.15 0.07
Matches are distributed among these distances:
147 87 0.12
148 23 0.03
149 9 0.01
151 2 0.00
152 2 0.00
156 3 0.00
157 2 0.00
159 18 0.02
160 164 0.22
161 427 0.57
162 12 0.02
163 2 0.00
ACGTcount: A:0.44, C:0.15, G:0.09, T:0.32
Consensus pattern (161 bp):
TTTCACACATATCAACTGTGAAAACCAAGTTCAATCATTTAAAAAAGTTTAATATCATGTATTGA
AGCTATCCAAACTGTTAAAATAAAACAATAACAGTAAATTTGTATTTTTACCTTTTAACGGCAAA
AAAAGTCCTAAACAGAAGTAAATAATAACTT
Found at i:18434624 original size:13 final size:13
Alignment explanation
Indices: 18434589--18434625 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
18434579 ATAAAAGCAA
*
18434589 ATATATAAAAAAC
1 ATATATAAAGAAC
*
18434602 ATATGTAAAGAAC
1 ATATATAAAGAAC
18434615 ATATATAAAGA
1 ATATATAAAGA
18434626 CATTGAGAAG
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
13 21 1.00
ACGTcount: A:0.62, C:0.05, G:0.08, T:0.24
Consensus pattern (13 bp):
ATATATAAAGAAC
Found at i:18438334 original size:26 final size:27
Alignment explanation
Indices: 18438280--18438332 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
18438270 TTCTTTATTG
*
18438280 ATTTGTATAATTTTATTATTTTAGAAA
1 ATTTGTATAATTTTATTATTTTAAAAA
*
18438307 ATTT-TATTATTTTATT-TTTTAAAAA
1 ATTTGTATAATTTTATTATTTTAAAAA
18438332 A
1 A
18438333 ATATTCAGAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 9 0.38
26 11 0.46
27 4 0.17
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (27 bp):
ATTTGTATAATTTTATTATTTTAAAAA
Found at i:18438445 original size:10 final size:10
Alignment explanation
Indices: 18438432--18438522 Score: 60
Period size: 10 Copynumber: 9.0 Consensus size: 10
18438422 AAATTTAAAC
18438432 TTTTTTATAA
1 TTTTTTATAA
** *
18438442 TTTTCCAAAA
1 TTTTTTATAA
* *
18438452 TTTGTTAGAA
1 TTTTTTATAA
* *
18438462 TTTGTTAGAA
1 TTTTTTATAA
18438472 TTTTTT-TAA
1 TTTTTTATAA
* *
18438481 TGTTTTAGAA
1 TTTTTTATAA
18438491 TTTTTT-TAA
1 TTTTTTATAA
18438500 TTTTTTGAGTAA
1 TTTTTT-A-TAA
18438512 TTTTTTGATAA
1 TTTTTT-ATAA
18438523 GTTTAAAAAA
Statistics
Matches: 64, Mismatches: 13, Indels: 7
0.76 0.15 0.08
Matches are distributed among these distances:
9 15 0.23
10 35 0.55
11 3 0.05
12 11 0.17
ACGTcount: A:0.29, C:0.02, G:0.10, T:0.59
Consensus pattern (10 bp):
TTTTTTATAA
Found at i:18438490 original size:19 final size:19
Alignment explanation
Indices: 18438466--18438517 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 19
18438456 TTAGAATTTG
18438466 TTAGAATTTTTTTAATGTT
1 TTAGAATTTTTTTAATGTT
*
18438485 TTAGAATTTTTTTAATTTT
1 TTAGAATTTTTTTAATGTT
18438504 TTGAGTAATTTTTT
1 TT-AG-AATTTTTT
18438518 GATAAGTTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 20 0.67
20 2 0.07
21 8 0.27
ACGTcount: A:0.25, C:0.00, G:0.10, T:0.65
Consensus pattern (19 bp):
TTAGAATTTTTTTAATGTT
Found at i:18438591 original size:21 final size:21
Alignment explanation
Indices: 18438543--18438588 Score: 69
Period size: 21 Copynumber: 2.3 Consensus size: 21
18438533 ATTTTAAAAT
*
18438543 ATTTTTAGAATTTTTATTAGA
1 ATTTTTAAAATTTTTATTAGA
18438564 ATTTTTAAAATTTTT-TT-GA
1 ATTTTTAAAATTTTTATTAGA
18438583 ATTTTT
1 ATTTTT
18438589 TTATATGTTA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 8 0.33
20 2 0.08
21 14 0.58
ACGTcount: A:0.30, C:0.00, G:0.07, T:0.63
Consensus pattern (21 bp):
ATTTTTAAAATTTTTATTAGA
Found at i:18438634 original size:28 final size:28
Alignment explanation
Indices: 18438565--18438634 Score: 95
Period size: 28 Copynumber: 2.5 Consensus size: 28
18438555 TTTATTAGAA
* *
18438565 TTTTTAAAATTTTTTTGAATTTTTTTAT
1 TTTTTAAAATTTTTTTGAAATTTTTGAT
* *
18438593 ATGTTAAAATTTTTTTGAAATTTTTGAT
1 TTTTTAAAATTTTTTTGAAATTTTTGAT
18438621 TTTTTAGAAATTTT
1 TTTTTA-AAATTTT
18438635 AAAAGTTTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 1
0.83 0.14 0.02
Matches are distributed among these distances:
28 28 0.80
29 7 0.20
ACGTcount: A:0.29, C:0.00, G:0.07, T:0.64
Consensus pattern (28 bp):
TTTTTAAAATTTTTTTGAAATTTTTGAT
Found at i:18438690 original size:20 final size:19
Alignment explanation
Indices: 18438631--18438895 Score: 74
Period size: 20 Copynumber: 14.1 Consensus size: 19
18438621 TTTTTAGAAA
*
18438631 TTTTAAAAGTTTTTAAA-T
1 TTTTAAAAATTTTTAAATT
* *
18438649 TTTCACAAAACTTTTAGAATT
1 TTTTA-AAAATTTTTA-AATT
*
18438670 TTTTAAAAATTTTT-AATA
1 TTTTAAAAATTTTTAAATT
*
18438688 TTTT-AAAATATTTATAA-T
1 TTTTAAAAATTTTTA-AATT
* * *
18438706 TCTTATAATTTTTTAAA--
1 TTTTAAAAATTTTTAAATT
* * *
18438723 --AT-AAAATTTTTTAATA
1 TTTTAAAAATTTTTAAATT
** *
18438739 AATGATAAAATATTTTAGAA-T
1 TTTTA-AAAAT-TTTTA-AATT
18438760 TTTTAAAAATTTTTAGAATT
1 TTTTAAAAATTTTTA-AATT
* * *
18438780 GTTTT-GAAACTTTGAAA--
1 -TTTTAAAAATTTTTAAATT
* *
18438797 TTTT-GAAATTTTAAAATT
1 TTTTAAAAATTTTTAAATT
*** * **
18438815 TTTTTTCAAGTTTTAAAAA
1 TTTTAAAAATTTTTAAATT
18438834 TTTTAGTAAAATTTTTAAAGTT
1 TTTTA--AAAATTTTTAAA-TT
*
18438856 TTTTAAAACTTTTT-AATT
1 TTTTAAAAATTTTTAAATT
*
18438874 TTTTAAAACTTTTTGAAATT
1 TTTTAAAAATTTTT-AAATT
18438894 TT
1 TT
18438896 GAATTTTTTA
Statistics
Matches: 182, Mismatches: 41, Indels: 46
0.68 0.15 0.17
Matches are distributed among these distances:
14 9 0.05
15 1 0.01
16 14 0.08
17 8 0.04
18 36 0.20
19 41 0.23
20 42 0.23
21 24 0.13
22 7 0.04
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (19 bp):
TTTTAAAAATTTTTAAATT
Found at i:18438700 original size:19 final size:19
Alignment explanation
Indices: 18438670--18438774 Score: 57
Period size: 18 Copynumber: 5.8 Consensus size: 19
18438660 TTTTAGAATT
18438670 TTTTAAAA-ATTTTTAATA
1 TTTTAAAATATTTTTAATA
*
18438688 TTTTAAAATATTTATAAT-
1 TTTTAAAATATTTTTAATA
* *
18438706 TCTTATAAT-TTTTTAA-A
1 TTTTAAAATATTTTTAATA
*
18438723 --ATAAAAT-TTTTTAATAAA
1 TTTTAAAATATTTTTAAT--A
** *
18438741 TGATAAAATATTTTAGAAT-
1 TTTTAAAATATTTT-TAATA
18438760 TTTTAAAA-ATTTTTA
1 TTTTAAAATATTTTTA
18438775 GAATTGTTTT
Statistics
Matches: 68, Mismatches: 10, Indels: 19
0.70 0.10 0.20
Matches are distributed among these distances:
15 12 0.18
17 7 0.10
18 21 0.31
19 14 0.21
20 7 0.10
21 4 0.06
22 3 0.04
ACGTcount: A:0.45, C:0.01, G:0.02, T:0.52
Consensus pattern (19 bp):
TTTTAAAATATTTTTAATA
Found at i:18438775 original size:19 final size:19
Alignment explanation
Indices: 18438621--18438779 Score: 75
Period size: 19 Copynumber: 8.6 Consensus size: 19
18438611 AATTTTTGAT
* *
18438621 TTTTTAGAAATTTTAAAAG
1 TTTTTAGAATTTTTAAAAA
*
18438640 TTTTTA-AATTTTCACAAAA
1 TTTTTAGAATTTTTA-AAAA
*
18438659 CTTTTAGAATTTTTTAAAAA
1 TTTTTAGAA-TTTTTAAAAA
18438679 TTTTT--AATATTTT-AAAA
1 TTTTTAGAAT-TTTTAAAAA
* * * * *
18438696 TATTTATAATTCTTATAAT
1 TTTTTAGAATTTTTAAAAA
* *
18438715 TTTTTA-AA---ATAAAAT
1 TTTTTAGAATTTTTAAAAA
* * **
18438730 TTTTTAATAAATGAT-AAAA
1 TTTTT-AGAATTTTTAAAAA
18438749 TATTTTAGAATTTTTAAAAA
1 T-TTTTAGAATTTTTAAAAA
18438769 TTTTTAGAATT
1 TTTTTAGAATT
18438780 GTTTTGAAAC
Statistics
Matches: 108, Mismatches: 18, Indels: 28
0.70 0.12 0.18
Matches are distributed among these distances:
15 10 0.09
16 1 0.01
17 11 0.10
18 17 0.16
19 43 0.40
20 21 0.19
21 5 0.05
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.51
Consensus pattern (19 bp):
TTTTTAGAATTTTTAAAAA
Found at i:18438805 original size:8 final size:8
Alignment explanation
Indices: 18438781--18438816 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
18438771 TTTAGAATTG
18438781 TTTTGAAA
1 TTTTGAAA
*
18438789 CTTTGAAA
1 TTTTGAAA
18438797 TTTTGAAA
1 TTTTGAAA
*
18438805 TTTTAAAA
1 TTTTGAAA
18438813 TTTT
1 TTTT
18438817 TTTTCAAGTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
8 25 1.00
ACGTcount: A:0.36, C:0.03, G:0.08, T:0.53
Consensus pattern (8 bp):
TTTTGAAA
Found at i:18438877 original size:18 final size:20
Alignment explanation
Indices: 18438840--18438887 Score: 75
Period size: 18 Copynumber: 2.5 Consensus size: 20
18438830 AAAATTTTAG
18438840 TAAAA-TTTTTAAAGTTTTT
1 TAAAACTTTTTAAAGTTTTT
18438859 TAAAACTTTTT-AA-TTTTT
1 TAAAACTTTTTAAAGTTTTT
18438877 TAAAACTTTTT
1 TAAAACTTTTT
18438888 GAAATTTTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
18 16 0.57
19 7 0.25
20 5 0.18
ACGTcount: A:0.35, C:0.04, G:0.02, T:0.58
Consensus pattern (20 bp):
TAAAACTTTTTAAAGTTTTT
Found at i:18439849 original size:14 final size:14
Alignment explanation
Indices: 18439830--18439857 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
18439820 TAGCAACTTC
18439830 AATAAAAATAAAAA
1 AATAAAAATAAAAA
18439844 AATAAAAATAAAAA
1 AATAAAAATAAAAA
18439858 CTCTTCTGAT
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:0.86, C:0.00, G:0.00, T:0.14
Consensus pattern (14 bp):
AATAAAAATAAAAA
Found at i:18442873 original size:15 final size:15
Alignment explanation
Indices: 18442853--18442883 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
18442843 GAAATCGGCA
18442853 AACTTAAAGTTCCTC
1 AACTTAAAGTTCCTC
18442868 AACTTAAAGTTCCTC
1 AACTTAAAGTTCCTC
18442883 A
1 A
18442884 TGTGAAAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.26, G:0.06, T:0.32
Consensus pattern (15 bp):
AACTTAAAGTTCCTC
Found at i:18444583 original size:170 final size:160
Alignment explanation
Indices: 18444396--18444790 Score: 391
Period size: 161 Copynumber: 2.4 Consensus size: 160
18444386 AACTGTAAAA
* *
18444396 TTATATTTTTGCCTTTTAACA-ATACAAAAGTCTTAAACAAACGTAAACAATTAAAACATTTTAG
1 TTATATTTTTGCCTTTTAACACA-AAAAAAATCTTAAACAAACGTAAAC-A--AAAAC---TT--
* * * *
18444460 CCTTTCACACATATTAATCATG-G-AAACCAAATTCAATCATTTGAACAAGTTAAATATCATGTA
57 --TTTCACACATATCAA-C-TGTGAAAACCAAATTCAATCATTCGAAAAAGTTAAATATCACGTA
*
18444523 TTGAAACTATCCAAACTGTTAAAACAGAACAATAATAGCAACT
118 TTGAAACTATCCAAACTGTTAAAACAGAACAATAATAACAACT
* * * * * *
18444566 TTGTATTTTTGCCTTTTAACAGCAAAAAAAATTTTAAACAGAGGTAAACAAAAACTTTTTCATAT
1 TTATATTTTTGCCTTTTAACA-CAAAAAAAATCTTAAACAAACGTAAACAAAAACTTTTTCACAC
* * * * *
18444631 ATATCAACTGTGAAAATCAAGTTCAATCATTCGAAAAAGTTTAATATCACGTATTGAAGCTATGC
65 ATATCAACTGTGAAAACCAAATTCAATCATTCGAAAAAGTTAAATATCACGTATTGAAACTATCC
*
18444696 AAACTGTTAAAACAGAACAATAATAACAATT
130 AAACTGTTAAAACAGAACAATAATAACAACT
* ** ** * **
18444727 TTATATTTTTACCTTTTAATGGCACGAAAAATCTTAAACAAAGGTAAACAGTAACTTTTTCACA
1 TTATATTTTTGCCTTTTAA-CACAAAAAAAATCTTAAACAAACGTAAACAAAAACTTTTTCACA
18444791 TAAACTATTT
Statistics
Matches: 190, Mismatches: 30, Indels: 19
0.79 0.13 0.08
Matches are distributed among these distances:
159 2 0.01
160 2 0.01
161 137 0.72
165 2 0.01
168 5 0.03
170 21 0.11
171 20 0.11
172 1 0.01
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.32
Consensus pattern (160 bp):
TTATATTTTTGCCTTTTAACACAAAAAAAATCTTAAACAAACGTAAACAAAAACTTTTTCACACA
TATCAACTGTGAAAACCAAATTCAATCATTCGAAAAAGTTAAATATCACGTATTGAAACTATCCA
AACTGTTAAAACAGAACAATAATAACAACT
Found at i:18444701 original size:161 final size:161
Alignment explanation
Indices: 18444491--18444788 Score: 434
Period size: 161 Copynumber: 1.9 Consensus size: 161
18444481 GGAAACCAAA
* * *
18444491 TTCAATCATTTGAACAAGTTAAATATCATGTATTGAAACTATCCAAACTGTTAAAACAGAACAAT
1 TTCAATCATTCGAAAAAGTTAAATATCACGTATTGAAACTATCCAAACTGTTAAAACAGAACAAT
* * * * *
18444556 AATAGCAACTTTGTATTTTTGCCTTTTAACAGCAAAAAAAATTTTAAACAGAGGTAAACAAAAAC
66 AATAACAACTTTATATTTTTACCTTTTAACAGCAAAAAAAATCTTAAACAAAGGTAAACAAAAAC
18444621 TTTTTCATATATATCAACTGTGAAAATCAAG
131 TTTTTCATATATATCAACTGTGAAAATCAAG
* * *
18444652 TTCAATCATTCGAAAAAGTTTAATATCACGTATTGAAGCTATGCAAACTGTTAAAACAGAACAAT
1 TTCAATCATTCGAAAAAGTTAAATATCACGTATTGAAACTATCCAAACTGTTAAAACAGAACAAT
* ** ** **
18444717 AATAACAATTTTATATTTTTACCTTTTAATGGCACGAAAAATCTTAAACAAAGGTAAACAGTAAC
66 AATAACAACTTTATATTTTTACCTTTTAACAGCAAAAAAAATCTTAAACAAAGGTAAACAAAAAC
18444782 TTTTTCA
131 TTTTTCA
18444789 CATAAACTAT
Statistics
Matches: 119, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
161 119 1.00
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.32
Consensus pattern (161 bp):
TTCAATCATTCGAAAAAGTTAAATATCACGTATTGAAACTATCCAAACTGTTAAAACAGAACAAT
AATAACAACTTTATATTTTTACCTTTTAACAGCAAAAAAAATCTTAAACAAAGGTAAACAAAAAC
TTTTTCATATATATCAACTGTGAAAATCAAG
Found at i:18445039 original size:299 final size:299
Alignment explanation
Indices: 18444498--18445044 Score: 686
Period size: 300 Copynumber: 1.8 Consensus size: 299
18444488 AAATTCAATC
* * * * *
18444498 ATTTGAACAAGTTAAATATCATGTATTGAAACTATCCAAACTGTTAAAACAGAACAATAATAGCA
1 ATTTGAAAAAATTAAATATCATGTATTGAAACCATCCAAACTGTTAAAACAAAACAATAACAGCA
* * * ** *
18444563 ACTTTGTATTTTTGCCTTTTAACAGCAAAAAAAATTTTAAACAGAGGTAAACAAAAACTTTTTCA
66 AATGTGTATTTTTGCCTTTTAACAACAAAAAAAATCCTAAACAGACGTAAACAAAAACTTTTTCA
* * * * *
18444628 TATATATCAACTGTGAAAATCAAGTTCAATCATTCGAAAAAGTTTAATATCACGTATTGAAGCTA
131 TACATATCAACCGTGAAAATCAAGTTCAATAATTCGAAAAAGTTTAATATCACGTATTAAAACTA
* * * *
18444693 TGCAAACTGTTAAAACAGAACAATAATAACAATTTTATATTTTTACCTTTTAATGGCACGAAAAA
196 TCCAAACTATTAAAACAGAACAATAATAACAATTTTACATATTTACCTTTTAATGGCACGAAAAA
18444758 TCTTAAACAAAGGTAAACAGTAACTTTTTCACATAAACT
261 TCTTAAACAAAGGTAAACAGTAACTTTTTCACATAAACT
* * * *
18444797 ATTTGAAAAAATTTAATATCATGTATT-AAAGCCATCTAAACTGTTAAAATAAAATAATAACAGC
1 ATTTGAAAAAATTAAATATCATGTATTGAAA-CCATCCAAACTGTTAAAACAAAACAATAACAGC
* * * * * *
18444861 AAATGTGTATTTTTGCCTTTTTAACAACAAAAATAGTCCTAAATAGACGTAAACGATAATTTTTT
65 AAATGTGTATTTTTGCC-TTTTAACAACAAAAAAAATCCTAAACAGACGTAAACAAAAACTTTTT
* * * *
18444926 TATACATATCAACCGT-AGAAATCAAGTTCAATAATTCGGACAAGTTTAATATCATGTATTAAAA
129 CATACATATCAACCGTGA-AAATCAAGTTCAATAATTCGAAAAAGTTTAATATCACGTATTAAAA
* * * ** *
18444990 CTATCCAAACTATTAAAATAGAATAATATTATTAATTTTGCA-ATTTACCTTTTAA
193 CTATCCAAACTATTAAAACAGAACAATAATAACAATTTTACATATTTACCTTTTAA
18445045 CGACATAAAA
Statistics
Matches: 205, Mismatches: 40, Indels: 6
0.82 0.16 0.02
Matches are distributed among these distances:
298 3 0.01
299 79 0.39
300 123 0.60
ACGTcount: A:0.44, C:0.14, G:0.09, T:0.33
Consensus pattern (299 bp):
ATTTGAAAAAATTAAATATCATGTATTGAAACCATCCAAACTGTTAAAACAAAACAATAACAGCA
AATGTGTATTTTTGCCTTTTAACAACAAAAAAAATCCTAAACAGACGTAAACAAAAACTTTTTCA
TACATATCAACCGTGAAAATCAAGTTCAATAATTCGAAAAAGTTTAATATCACGTATTAAAACTA
TCCAAACTATTAAAACAGAACAATAATAACAATTTTACATATTTACCTTTTAATGGCACGAAAAA
TCTTAAACAAAGGTAAACAGTAACTTTTTCACATAAACT
Found at i:18445098 original size:160 final size:156
Alignment explanation
Indices: 18444879--18445251 Score: 345
Period size: 156 Copynumber: 2.4 Consensus size: 156
18444869 ATTTTTGCCT
* * * *
18444879 TTTTAACAACAAAAATAGTCCTAAATAGACGTAAACGATAATTTTTTTATACATATCAACCGTAG
1 TTTTAACAACAAAAATAGTCCTAAATAAACGTAAACGATAACTTTTTCACACATATCAA-C-T-G
*
18444944 AAATCAAGTTCAATAATTCGGACAAGTTTAATATCATGTATTAAAACTATCCAAACTATTAAAAT
63 AAAT-AAGTTCAATAATTCGGACAAGTTTAATACCATGTATTAAAACTATCCAAACTATTAAAAT
18445009 AGAATAATATTATTAATTTTGCAATTTACC
127 AGAATAATATTATTAATTTTGCAATTTACC
* * * * * *
18445039 TTTTAACGACATAAAA-AGTCCTAAATAAACGTAAATGTTAGCTTTTTCACCCATATCAACTGTA
1 TTTTAACAACA-AAAATAGTCCTAAATAAACGTAAACGATAACTTTTTCACACATATCAACTGAA
* * * * * * * * * *
18445103 CTAAGTTTAATTATTCTGATAAGTTTAATACCATGTATTGAAGCTATGCAAATTGTTAAAATAGA
65 ATAAGTTCAATAATTCGGACAAGTTTAATACCATGTATTAAAACTATCCAAACTATTAAAATAGA
* * * ** * *
18445168 ACAAAAATAACAATTTTACATTTTTACC
130 ATAATATTATTAATTTTGCA-ATTTACC
* * * ** * * *
18445196 TCTTAACAGCATCAAA-AGTTTTAAACAGATGTAAACGATAACTTTTTCACACATAT
1 TTTTAACAACA-AAAATAGTCCTAAATAAACGTAAACGATAACTTTTTCACACATAT
18445252 TTTAAAAATT
Statistics
Matches: 170, Mismatches: 41, Indels: 7
0.78 0.19 0.03
Matches are distributed among these distances:
156 67 0.39
157 52 0.31
158 1 0.01
159 1 0.01
160 45 0.26
161 4 0.02
ACGTcount: A:0.42, C:0.15, G:0.09, T:0.35
Consensus pattern (156 bp):
TTTTAACAACAAAAATAGTCCTAAATAAACGTAAACGATAACTTTTTCACACATATCAACTGAAA
TAAGTTCAATAATTCGGACAAGTTTAATACCATGTATTAAAACTATCCAAACTATTAAAATAGAA
TAATATTATTAATTTTGCAATTTACC
Found at i:18445291 original size:19 final size:19
Alignment explanation
Indices: 18445251--18445403 Score: 96
Period size: 20 Copynumber: 7.8 Consensus size: 19
18445241 TTCACACATA
*
18445251 TTTTAAAAATTTTATCAAAAT
1 TTTTAAAAATTTT-T-AGAAT
* *
18445272 TTTTAAATATTTTTATAAT
1 TTTTAAAAATTTTTAGAAT
** ***
18445291 TGTTT-TGAATTTTTTTTAT
1 T-TTTAAAAATTTTTAGAAT
18445310 CTTTTAAAAAAATTTTT-GAAT
1 -TTTT-A-AAAATTTTTAGAAT
* * *
18445331 TTTT-CAAATTTTTTGAAA
1 TTTTAAAAATTTTTAGAAT
18445349 TTTTAAAAATTTTTAGAAT
1 TTTTAAAAATTTTTAGAAT
* *
18445368 TTTCAAAAAACTTTTAGAATT
1 TTT-TAAAAATTTTTAGAA-T
18445389 TTTTAAAAATTTTTA
1 TTTTAAAAATTTTTA
18445404 ATATTCTTAA
Statistics
Matches: 103, Mismatches: 20, Indels: 19
0.73 0.14 0.13
Matches are distributed among these distances:
17 8 0.08
18 7 0.07
19 31 0.30
20 32 0.31
21 18 0.17
22 7 0.07
ACGTcount: A:0.38, C:0.03, G:0.04, T:0.55
Consensus pattern (19 bp):
TTTTAAAAATTTTTAGAAT
Found at i:18445334 original size:20 final size:18
Alignment explanation
Indices: 18445317--18445402 Score: 91
Period size: 18 Copynumber: 4.6 Consensus size: 18
18445307 TATCTTTTAA
18445317 AAAAATTTTTGAATTTTT
1 AAAAATTTTTGAATTTTT
* * *
18445335 CAAATTTTTTGAAATTTT
1 AAAAATTTTTGAATTTTT
*
18445353 AAAAATTTTTAGAATTTTCA
1 AAAAATTTTT-GAATTTT-T
*
18445373 AAAAACTTTTAGAATTTTTT
1 AAAAA-TTTTTGAA-TTTTT
18445393 AAAAATTTTT
1 AAAAATTTTT
18445403 AATATTCTTA
Statistics
Matches: 54, Mismatches: 10, Indels: 7
0.76 0.14 0.10
Matches are distributed among these distances:
18 23 0.43
19 10 0.19
20 13 0.24
21 8 0.15
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (18 bp):
AAAAATTTTTGAATTTTT
Found at i:18445343 original size:18 final size:18
Alignment explanation
Indices: 18445322--18445374 Score: 63
Period size: 19 Copynumber: 2.9 Consensus size: 18
18445312 TTTAAAAAAA
18445322 TTTTTGAATTTTTCAAAT
1 TTTTTGAATTTTTCAAAT
**
18445340 TTTTTGAAATTTTAAAAAT
1 TTTTTG-AATTTTTCAAAT
*
18445359 TTTTAGAA-TTTTCAAA
1 TTTTTGAATTTTTCAAA
18445375 AAACTTTTAG
Statistics
Matches: 29, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
17 6 0.21
18 8 0.28
19 15 0.52
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.55
Consensus pattern (18 bp):
TTTTTGAATTTTTCAAAT
Found at i:18445403 original size:20 final size:19
Alignment explanation
Indices: 18445317--18445403 Score: 97
Period size: 20 Copynumber: 4.6 Consensus size: 19
18445307 TATCTTTTAA
18445317 AAAAATTTTT-GAATTTTT
1 AAAAATTTTTAGAATTTTT
* * *
18445335 -CAAATTTTTTGAAATTTT
1 AAAAATTTTTAGAATTTTT
*
18445353 AAAAATTTTTAGAATTTTCA
1 AAAAATTTTTAGAATTTT-T
*
18445373 AAAAACTTTTAGAATTTTTT
1 AAAAATTTTTAGAA-TTTTT
18445393 AAAAATTTTTA
1 AAAAATTTTTA
18445404 ATATTCTTAA
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
17 8 0.14
18 7 0.12
19 14 0.25
20 23 0.41
21 4 0.07
ACGTcount: A:0.41, C:0.03, G:0.05, T:0.51
Consensus pattern (19 bp):
AAAAATTTTTAGAATTTTT
Found at i:18445524 original size:19 final size:18
Alignment explanation
Indices: 18445502--18445621 Score: 64
Period size: 20 Copynumber: 6.3 Consensus size: 18
18445492 TGTTTTGATA
*
18445502 TTTTGAAATTTTTAAATT
1 TTTTTAAATTTTTAAATT
* *
18445520 TTTTTCAAGTTTTAAAAATT
1 TTTTT-AAATTTT-TAAATT
** *
18445540 TTAATAAACTTTTTAAAAATC
1 TTTTTAAA-TTTTT--AAATT
* *
18445561 TTTTTAAGTTCTTTAAAACT
1 TTTTTAAATT-TTT-AAATT
18445581 TTTTTAAATTTTT-AA-T
1 TTTTTAAATTTTTAAATT
*
18445597 TTTTTAGAGCTTTTTAAATT
1 TTTTTA-A-ATTTTTAAATT
18445617 TTTTT
1 TTTTT
18445622 TTGAATTTTT
Statistics
Matches: 77, Mismatches: 15, Indels: 18
0.70 0.14 0.16
Matches are distributed among these distances:
16 7 0.09
17 3 0.04
18 9 0.12
19 13 0.17
20 33 0.43
21 12 0.16
ACGTcount: A:0.33, C:0.05, G:0.04, T:0.58
Consensus pattern (18 bp):
TTTTTAAATTTTTAAATT
Found at i:18445540 original size:20 final size:20
Alignment explanation
Indices: 18445515--18445595 Score: 65
Period size: 20 Copynumber: 4.0 Consensus size: 20
18445505 TGAAATTTTT
*
18445515 AAATTTTTTTCAAGTTTTAA
1 AAATTTTTTTAAAGTTTTAA
** *
18445535 AAATTTTAATAAACTTTTTAA
1 AAATTTTTTTAAA-GTTTTAA
* *
18445556 AAATCTTTTT-AAGTTCTTTA
1 AAATTTTTTTAAAGTT-TTAA
* *
18445576 AAACTTTTTTAAATTTTTAA
1 AAATTTTTTTAAAGTTTTAA
18445596 TTTTTTAGAG
Statistics
Matches: 45, Mismatches: 13, Indels: 6
0.70 0.20 0.09
Matches are distributed among these distances:
19 2 0.04
20 26 0.58
21 17 0.38
ACGTcount: A:0.38, C:0.06, G:0.02, T:0.53
Consensus pattern (20 bp):
AAATTTTTTTAAAGTTTTAA
Found at i:18445805 original size:27 final size:27
Alignment explanation
Indices: 18445771--18445824 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
18445761 AATAGATTTC
* *
18445771 AAAATTAAAATACTAATGTGATAAAAA
1 AAAATTAAAATACTAATATGACAAAAA
18445798 AAAATTAAAATACTAATATGACAAAAA
1 AAAATTAAAATACTAATATGACAAAAA
18445825 TTTTAAAATT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.65, C:0.06, G:0.06, T:0.24
Consensus pattern (27 bp):
AAAATTAAAATACTAATATGACAAAAA
Found at i:18449132 original size:19 final size:20
Alignment explanation
Indices: 18449108--18449147 Score: 73
Period size: 19 Copynumber: 2.0 Consensus size: 20
18449098 TCTTAAATTT
18449108 ATTAAATATTATTT-TTAAA
1 ATTAAATATTATTTCTTAAA
18449127 ATTAAATATTATTTCTTAAA
1 ATTAAATATTATTTCTTAAA
18449147 A
1 A
18449148 ATAATTACGT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.70
20 6 0.30
ACGTcount: A:0.47, C:0.03, G:0.00, T:0.50
Consensus pattern (20 bp):
ATTAAATATTATTTCTTAAA
Found at i:18449304 original size:2 final size:2
Alignment explanation
Indices: 18449297--18449333 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
18449287 TCCCCACTCA
18449297 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
18449334 GAAAAAGTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:18451576 original size:12 final size:12
Alignment explanation
Indices: 18451559--18451587 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
18451549 TATTAGATTC
18451559 AACTTTGCTTTT
1 AACTTTGCTTTT
18451571 AACTTTGCTTTT
1 AACTTTGCTTTT
18451583 AACTT
1 AACTT
18451588 GCATTTGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.21, C:0.17, G:0.07, T:0.55
Consensus pattern (12 bp):
AACTTTGCTTTT
Found at i:18460584 original size:13 final size:12
Alignment explanation
Indices: 18460567--18460605 Score: 60
Period size: 12 Copynumber: 3.2 Consensus size: 12
18460557 AATTCTTTAA
18460567 TTTTTAATATAT
1 TTTTTAATATAT
*
18460579 TATTTTAATATAA
1 T-TTTTAATATAT
18460592 TTTTTAATATAT
1 TTTTTAATATAT
18460604 TT
1 TT
18460606 AAATAAATTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
12 13 0.54
13 11 0.46
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
TTTTTAATATAT
Found at i:18460862 original size:15 final size:14
Alignment explanation
Indices: 18460825--18460864 Score: 53
Period size: 15 Copynumber: 2.7 Consensus size: 14
18460815 TTTTAAATCA
*
18460825 ATTTTTTTAATATT
1 ATTTTTTAAATATT
18460839 ATTTATTTAAATAATT
1 ATTT-TTTAAAT-ATT
18460855 ATTTTTTAAA
1 ATTTTTTAAA
18460865 AGTGAATATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
14 4 0.17
15 12 0.52
16 7 0.30
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
ATTTTTTAAATATT
Found at i:18461476 original size:18 final size:18
Alignment explanation
Indices: 18461439--18461479 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
18461429 TAAAATATCC
*
18461439 ATAAATATAAGTATAGAA
1 ATAAATATAAGTATAAAA
18461457 ATAAATATAA-TATAAAAA
1 ATAAATATAAGTAT-AAAA
18461475 ATAAA
1 ATAAA
18461480 AAATGAGAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (18 bp):
ATAAATATAAGTATAAAA
Found at i:18464319 original size:19 final size:18
Alignment explanation
Indices: 18464282--18464352 Score: 60
Period size: 18 Copynumber: 4.1 Consensus size: 18
18464272 ATCTCATGAT
**
18464282 TAAAATATTTGTATTATA
1 TAAAATATTTAAATTATA
18464300 TAAAATATTTAAATT-TA
1 TAAAATATTTAAATTATA
* * *
18464317 T---ATATTTATATCAAA
1 TAAAATATTTAAATTATA
18464332 TAAAATATTTAAATTTATA
1 TAAAATATTTAAA-TTATA
18464351 TA
1 TA
18464353 TTTATTTTAT
Statistics
Matches: 40, Mismatches: 8, Indels: 9
0.70 0.14 0.16
Matches are distributed among these distances:
14 9 0.22
15 2 0.05
17 3 0.08
18 21 0.52
19 5 0.12
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (18 bp):
TAAAATATTTAAATTATA
Found at i:18464322 original size:32 final size:32
Alignment explanation
Indices: 18464286--18464364 Score: 122
Period size: 32 Copynumber: 2.5 Consensus size: 32
18464276 CATGATTAAA
*
18464286 ATATTTGTATTATATAAAATATTTAAATTTAT
1 ATATTTATATTATATAAAATATTTAAATTTAT
* *
18464318 ATATTTATATCAAATAAAATATTTAAATTTAT
1 ATATTTATATTATATAAAATATTTAAATTTAT
*
18464350 ATATTTATTTTATAT
1 ATATTTATATTATAT
18464365 TTTAAATACA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.44, C:0.01, G:0.01, T:0.53
Consensus pattern (32 bp):
ATATTTATATTATATAAAATATTTAAATTTAT
Found at i:18464474 original size:22 final size:22
Alignment explanation
Indices: 18464424--18464464 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
18464414 TATATTTTTT
*
18464424 TAATT-TTATTAAACTTTTATA
1 TAATTATTATTAAAATTTTATA
18464445 TAATTATTATTAAAATTTTA
1 TAATTATTATTAAAATTTTA
18464465 ACTCATTATT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.56
Consensus pattern (22 bp):
TAATTATTATTAAAATTTTATA
Found at i:18464487 original size:13 final size:13
Alignment explanation
Indices: 18464471--18464500 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
18464461 TTTAACTCAT
*
18464471 TATTTTTATATTA
1 TATTTTTATACTA
18464484 TATTTTTATACTA
1 TATTTTTATACTA
18464497 TATT
1 TATT
18464501 CATAAAATAT
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:0.30, C:0.03, G:0.00, T:0.67
Consensus pattern (13 bp):
TATTTTTATACTA
Found at i:18465907 original size:2 final size:2
Alignment explanation
Indices: 18465900--18465946 Score: 67
Period size: 2 Copynumber: 23.0 Consensus size: 2
18465890 CCATTATCCA
* *
18465900 AT AT AT AT AA AT AT AT AT AT AT AT AT CAA 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
18465943 AT AT
1 AT AT
18465947 CACTATCCAG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
2 39 0.98
3 1 0.03
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:18472150 original size:12 final size:12
Alignment explanation
Indices: 18472133--18472157 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
18472123 AATTCTTAGC
18472133 TAAAAGGTCAAA
1 TAAAAGGTCAAA
18472145 TAAAAGGTCAAA
1 TAAAAGGTCAAA
18472157 T
1 T
18472158 CTTAAAATTA
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:0.56, C:0.08, G:0.16, T:0.20
Consensus pattern (12 bp):
TAAAAGGTCAAA
Found at i:18475805 original size:32 final size:32
Alignment explanation
Indices: 18475735--18475798 Score: 128
Period size: 32 Copynumber: 2.0 Consensus size: 32
18475725 TCAAGCTTAA
18475735 ACAACTTGATTTAAGTCAATTACATAACCAAT
1 ACAACTTGATTTAAGTCAATTACATAACCAAT
18475767 ACAACTTGATTTAAGTCAATTACATAACCAAT
1 ACAACTTGATTTAAGTCAATTACATAACCAAT
18475799 GTAACTTTGC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.44, C:0.19, G:0.06, T:0.31
Consensus pattern (32 bp):
ACAACTTGATTTAAGTCAATTACATAACCAAT
Found at i:18488259 original size:16 final size:15
Alignment explanation
Indices: 18488231--18488264 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
18488221 TAATTAAAAT
*
18488231 TAATTATAGAATTAA
1 TAATTATAAAATTAA
18488246 TAATATATAAAATTAA
1 TAAT-TATAAAATTAA
18488262 TAA
1 TAA
18488265 AAAAATAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 4 0.24
16 13 0.76
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (15 bp):
TAATTATAAAATTAA
Found at i:18488274 original size:17 final size:18
Alignment explanation
Indices: 18488252--18488286 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
18488242 TTAATAATAT
18488252 ATAAAA-TTAATAAAAAA
1 ATAAAAGTTAATAAAAAA
18488269 ATAAAATGTTAATAAAAA
1 ATAAAA-GTTAATAAAAA
18488287 TGATTAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
19 10 0.62
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (18 bp):
ATAAAAGTTAATAAAAAA
Found at i:18488440 original size:30 final size:30
Alignment explanation
Indices: 18488399--18488467 Score: 95
Period size: 30 Copynumber: 2.3 Consensus size: 30
18488389 ATTTAATTTT
*
18488399 TTTTTACTAATTTTCATATA-AAATATTTCC
1 TTTTTATTAATTTT-ATATATAAATATTTCC
* *
18488429 TTTTTATTAATTTTATGTATAAATATTTCT
1 TTTTTATTAATTTTATATATAAATATTTCC
18488459 TTTTTATTA
1 TTTTTATTA
18488468 CATAAAGATT
Statistics
Matches: 35, Mismatches: 3, Indels: 2
0.88 0.08 0.05
Matches are distributed among these distances:
29 4 0.11
30 31 0.89
ACGTcount: A:0.30, C:0.07, G:0.01, T:0.61
Consensus pattern (30 bp):
TTTTTATTAATTTTATATATAAATATTTCC
Found at i:18492094 original size:21 final size:21
Alignment explanation
Indices: 18492070--18492114 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
18492060 GGTTGCTTCC
* * *
18492070 AAATCAAGAAAAACAAGACAA
1 AAATCAAAAAAAAAAAGAAAA
*
18492091 AAATTAAAAAAAAAAAGAAAA
1 AAATCAAAAAAAAAAAGAAAA
18492112 AAA
1 AAA
18492115 CACACACACA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.80, C:0.07, G:0.07, T:0.07
Consensus pattern (21 bp):
AAATCAAAAAAAAAAAGAAAA
Found at i:18492977 original size:15 final size:16
Alignment explanation
Indices: 18492957--18492986 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
18492947 TACTATTAAT
18492957 TAATTATT-ATACTAC
1 TAATTATTAATACTAC
18492972 TAATTATTAATACTA
1 TAATTATTAATACTA
18492987 ATAAAATATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 8 0.57
16 6 0.43
ACGTcount: A:0.43, C:0.10, G:0.00, T:0.47
Consensus pattern (16 bp):
TAATTATTAATACTAC
Found at i:18493483 original size:23 final size:23
Alignment explanation
Indices: 18493445--18493501 Score: 66
Period size: 23 Copynumber: 2.5 Consensus size: 23
18493435 AATTAATAAA
18493445 TATAAATTTTTAATTT-TAATATT
1 TATAAATTTTTAATTTCTAA-ATT
18493468 TATAACATTTTT-ATTTCTAAATT
1 TATAA-ATTTTTAATTTCTAAATT
*
18493491 TA-AATTTTTTA
1 TATAAATTTTTA
18493502 TAAAAAAAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 5 0.17
22 2 0.07
23 14 0.47
24 9 0.30
ACGTcount: A:0.37, C:0.04, G:0.00, T:0.60
Consensus pattern (23 bp):
TATAAATTTTTAATTTCTAAATT
Found at i:18494794 original size:22 final size:21
Alignment explanation
Indices: 18494760--18494819 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
18494750 ATTTAAAAAA
18494760 ATGTAATTATTAAATTTATTAG
1 ATGTAATTATTAAA-TTATTAG
* * *
18494782 ATGTTATTTTTAAATTATTAT
1 ATGTAATTATTAAATTATTAG
18494803 ATG-AATTAATTAAATTA
1 ATGTAATT-ATTAAATTA
18494820 AATTTTAAGA
Statistics
Matches: 32, Mismatches: 5, Indels: 3
0.80 0.12 0.08
Matches are distributed among these distances:
20 3 0.09
21 17 0.53
22 12 0.38
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.52
Consensus pattern (21 bp):
ATGTAATTATTAAATTATTAG
Found at i:18495812 original size:24 final size:23
Alignment explanation
Indices: 18495785--18495862 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 23
18495775 AATTTTCATC
*
18495785 ATTTTTTTTAATTCAATTACAATA
1 ATTTTTTTTAATT-AATTATAATA
18495809 A-TTTTTTTAATTATAATTATAATA
1 ATTTTTTTTAA-T-TAATTATAATA
*
18495833 ATTTTTATT-A-TAATTATAATA
1 ATTTTTTTTAATTAATTATAATA
18495854 ATTTTTTTT
1 ATTTTTTTT
18495863 TTTTAATTTT
Statistics
Matches: 48, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
21 19 0.40
23 9 0.19
24 13 0.27
25 7 0.15
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (23 bp):
ATTTTTTTTAATTAATTATAATA
Found at i:18499228 original size:2 final size:2
Alignment explanation
Indices: 18499221--18499248 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
18499211 ACCCCTCTGA
18499221 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
18499249 CAAGAGCATA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:18504466 original size:15 final size:17
Alignment explanation
Indices: 18504446--18504484 Score: 55
Period size: 17 Copynumber: 2.4 Consensus size: 17
18504436 TGAAATATTG
*
18504446 TTAAAAA-TTAT-AAGA
1 TTAAAAATTTATGAAAA
18504461 TTAAAAATTTATGAAAA
1 TTAAAAATTTATGAAAA
18504478 TTAAAAA
1 TTAAAAA
18504485 ATTCGAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 7 0.33
16 4 0.19
17 10 0.48
ACGTcount: A:0.62, C:0.00, G:0.05, T:0.33
Consensus pattern (17 bp):
TTAAAAATTTATGAAAA
Found at i:18504821 original size:12 final size:10
Alignment explanation
Indices: 18504793--18504818 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
18504783 TAAAATTTTC
18504793 TAAAAATGAG
1 TAAAAATGAG
18504803 TAAAAATGAG
1 TAAAAATGAG
18504813 TAAAAA
1 TAAAAA
18504819 AATTAAATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.19
Consensus pattern (10 bp):
TAAAAATGAG
Found at i:18509863 original size:23 final size:23
Alignment explanation
Indices: 18509826--18509873 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
18509816 CTCAAAAAAT
*
18509826 TTTTGATAATCTTAAAATTATTC
1 TTTTGATAATATTAAAATTATTC
* **
18509849 TTTTGATATTATTAATTTTATTC
1 TTTTGATAATATTAAAATTATTC
18509872 TT
1 TT
18509874 AGCCCCTTTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.29, C:0.06, G:0.04, T:0.60
Consensus pattern (23 bp):
TTTTGATAATATTAAAATTATTC
Found at i:18513368 original size:34 final size:33
Alignment explanation
Indices: 18513330--18513394 Score: 76
Period size: 33 Copynumber: 1.9 Consensus size: 33
18513320 TTTGAGTTTA
* *
18513330 TTGTTAAATTTTTTTGTTATAGATTTGTTGAGAT
1 TTGTT-AAGTTTTTTGCTATAGATTTGTTGAGAT
** *
18513364 TTGTTGGGTTTTTTGCTATATATTTGTTGAG
1 TTGTTAAGTTTTTTGCTATAGATTTGTTGAG
18513395 TTTTTTTTGG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
33 21 0.81
34 5 0.19
ACGTcount: A:0.18, C:0.02, G:0.22, T:0.58
Consensus pattern (33 bp):
TTGTTAAGTTTTTTGCTATAGATTTGTTGAGAT
Found at i:18513752 original size:123 final size:123
Alignment explanation
Indices: 18513570--18513793 Score: 299
Period size: 123 Copynumber: 1.8 Consensus size: 123
18513560 ATGTGTAAGA
* * * *
18513570 TTTATGTTGATTTGTTGGTAAATTTGGATTTAATGTGTATTAAGATATATATTTGTTTTTATAGA
1 TTTATGTTGATTTGATGGTAAATTTGGATTTAATGTGGAATAAGATATATATTTATTTTTATA-A
** *
18513635 TGTTTTATATTT-ATTTTTTTTAAAATTTAATAATAATAATAATAATAGAAATTAAAATT
65 -AATTTATATTTGATATTTTTTAAAATTTAATAATAATAATAATAATAGAAATTAAAATT
* * * * *
18513694 TTTATTTTGATTTGATGTTAAATTTGG-TTTGATGTGGAATAAGATTTATATTTATTTTTTTAAA
1 TTTATGTTGATTTGATGGTAAATTTGGATTTAATGTGGAATAAGATATATATTTATTTTTATAAA
*
18513758 ATTTATATTTGATATTTTTTAAAATTTATTAATAAT
66 ATTTATATTTGATATTTTTTAAAATTTAATAATAAT
18513794 TATTGAAATA
Statistics
Matches: 86, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
121 9 0.10
122 24 0.28
123 29 0.34
124 24 0.28
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.54
Consensus pattern (123 bp):
TTTATGTTGATTTGATGGTAAATTTGGATTTAATGTGGAATAAGATATATATTTATTTTTATAAA
ATTTATATTTGATATTTTTTAAAATTTAATAATAATAATAATAATAGAAATTAAAATT
Found at i:18513761 original size:21 final size:23
Alignment explanation
Indices: 18513737--18513786 Score: 86
Period size: 23 Copynumber: 2.3 Consensus size: 23
18513727 GTGGAATAAG
18513737 ATTTATATTT-AT-TTTTTTAAA
1 ATTTATATTTGATATTTTTTAAA
18513758 ATTTATATTTGATATTTTTTAAA
1 ATTTATATTTGATATTTTTTAAA
18513781 ATTTAT
1 ATTTAT
18513787 TAATAATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
21 10 0.37
22 2 0.07
23 15 0.56
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (23 bp):
ATTTATATTTGATATTTTTTAAA
Found at i:18515000 original size:28 final size:27
Alignment explanation
Indices: 18514927--18515000 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 27
18514917 AGTGTTTGAT
*
18514927 TTTTTTTCTTCTTTTTTTTATGTTTTAG
1 TTTTTTT-TTCTTTTTTTTATGTTTAAG
*
18514955 TTTTGTTTTTAGC-TTTTTTAATG-TTAAG
1 TTTT-TTTTT--CTTTTTTTTATGTTTAAG
*
18514983 TTTTTTTTTCTTTGTTTT
1 TTTTTTTTTCTTTTTTTT
18515001 GTAGGTAATA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
25 1 0.03
26 5 0.13
27 5 0.13
28 14 0.37
29 12 0.32
30 1 0.03
ACGTcount: A:0.09, C:0.05, G:0.09, T:0.76
Consensus pattern (27 bp):
TTTTTTTTTCTTTTTTTTATGTTTAAG
Found at i:18515000 original size:29 final size:29
Alignment explanation
Indices: 18514926--18515000 Score: 66
Period size: 29 Copynumber: 2.6 Consensus size: 29
18514916 AAGTGTTTGA
* *
18514926 TTTTTTTTCTTCT-TTTTTTTATGTTTTAG
1 TTTTTTTTCTT-TGTTTTTTAATGTTTAAG
* *
18514955 TTTTGTTT-TTAGCTTTTTTAATG-TTAAG
1 TTTTTTTTCTTTG-TTTTTTAATGTTTAAG
18514983 TTTTTTTTTCTTTGTTTT
1 -TTTTTTTTCTTTGTTTT
18515001 GTAGGTAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 8
0.72 0.12 0.16
Matches are distributed among these distances:
28 6 0.17
29 27 0.75
30 3 0.08
ACGTcount: A:0.09, C:0.05, G:0.09, T:0.76
Consensus pattern (29 bp):
TTTTTTTTCTTTGTTTTTTAATGTTTAAG
Found at i:18516374 original size:39 final size:40
Alignment explanation
Indices: 18516301--18516378 Score: 122
Period size: 40 Copynumber: 2.0 Consensus size: 40
18516291 AAAGTGTTGT
* *
18516301 TTTTTTTATTATATTTGATAATCTAAAGTAAAAATTATTG
1 TTTTTTTATTACATTTCATAATCTAAAGTAAAAATTATTG
*
18516341 TTTTTTTATTGCATTTCATAATCTAAAGT-AAAATTATT
1 TTTTTTTATTACATTTCATAATCTAAAGTAAAAATTATT
18516379 CCAAAATCTA
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
39 9 0.26
40 26 0.74
ACGTcount: A:0.36, C:0.05, G:0.06, T:0.53
Consensus pattern (40 bp):
TTTTTTTATTACATTTCATAATCTAAAGTAAAAATTATTG
Found at i:18519459 original size:22 final size:22
Alignment explanation
Indices: 18519434--18519477 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
18519424 TATATATTTA
18519434 TATTTGTAT-CTCTAGAATTAAG
1 TATTTGTATCCT-TAGAATTAAG
18519456 TATTTGTATCCTTAGAATTAAG
1 TATTTGTATCCTTAGAATTAAG
18519478 GATAAAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 19 0.90
23 2 0.10
ACGTcount: A:0.32, C:0.09, G:0.14, T:0.45
Consensus pattern (22 bp):
TATTTGTATCCTTAGAATTAAG
Found at i:18519661 original size:25 final size:25
Alignment explanation
Indices: 18519618--18519667 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
18519608 AATATACATT
*
18519618 CAGTTTTACTCTT-AGTTTTTCACA
1 CAGTTTTACTCTTAATTTTTTCACA
*
18519642 CAGTTTTATTTCTTAATTTTTTCACA
1 CAGTTTTA-CTCTTAATTTTTTCACA
18519668 AACATTGGCA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
24 8 0.36
25 4 0.18
26 10 0.45
ACGTcount: A:0.22, C:0.18, G:0.06, T:0.54
Consensus pattern (25 bp):
CAGTTTTACTCTTAATTTTTTCACA
Found at i:18525735 original size:153 final size:153
Alignment explanation
Indices: 18525457--18525742 Score: 509
Period size: 153 Copynumber: 1.9 Consensus size: 153
18525447 GCTAAAAAAT
*
18525457 GTCTTTTTGGTAGATTATGATAGAAATACATGTTGGAATATTATCAGACAACTTCTTGTTGTTAG
1 GTCTTTTCGGTAGATTATGATAGAAATACATGTTGGAATATTATCAGACAACTTCTTGTTGTTAG
* *
18525522 AATCACCATTGAATGGTTAACCTGGATTGCTTAGTGGTGGAAAATAGGGCTCTAGTCTTGTCTGC
66 AATCACCATTGAATGGTTAACCTGGATTGCTTAGCGGTGGAAAATAGGGCTCTAGTCTTGTCTAC
18525587 CCTTGGATACCAACTTAAAGAAG
131 CCTTGGATACCAACTTAAAGAAG
*
18525610 GTCTTTTCGGTAGATTATGATAGAAATACATGTTGGAATATTATCAGACAGCTTCTTGTTGTTAG
1 GTCTTTTCGGTAGATTATGATAGAAATACATGTTGGAATATTATCAGACAACTTCTTGTTGTTAG
* * *
18525675 AATCACCATTGATTGGTTAACCTGGATTGCTTAGCGGTGGAAAGTAGGGCTCTTGTCTTGTCTAC
66 AATCACCATTGAATGGTTAACCTGGATTGCTTAGCGGTGGAAAATAGGGCTCTAGTCTTGTCTAC
18525740 CCT
131 CCT
18525743 CTGACACCAA
Statistics
Matches: 126, Mismatches: 7, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
153 126 1.00
ACGTcount: A:0.27, C:0.15, G:0.23, T:0.36
Consensus pattern (153 bp):
GTCTTTTCGGTAGATTATGATAGAAATACATGTTGGAATATTATCAGACAACTTCTTGTTGTTAG
AATCACCATTGAATGGTTAACCTGGATTGCTTAGCGGTGGAAAATAGGGCTCTAGTCTTGTCTAC
CCTTGGATACCAACTTAAAGAAG
Found at i:18533420 original size:20 final size:19
Alignment explanation
Indices: 18533366--18533413 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
18533356 AATGATTATC
* *
18533366 ATTTTAT-TAT-ATATATT
1 ATTTTATGTATCAAATATG
18533383 ATTTTATGTATCAAATATG
1 ATTTTATGTATCAAATATG
18533402 ATTTTAATGTAT
1 ATTTT-ATGTAT
18533414 TTAATATTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
17 7 0.27
18 3 0.12
19 10 0.38
20 6 0.23
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.56
Consensus pattern (19 bp):
ATTTTATGTATCAAATATG
Found at i:18537850 original size:36 final size:37
Alignment explanation
Indices: 18537810--18537884 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 37
18537800 TATAAATTCC
18537810 AAATGATAATAAAGAAACAAAAA-AAAAAGAAGAACA
1 AAATGATAATAAAGAAACAAAAAGAAAAAGAAGAACA
18537846 AAATGATAATAAAGAAACAAAAAGAAAAAGAAGAACA
1 AAATGATAATAAAGAAACAAAAAGAAAAAGAAGAACA
18537883 AA
1 AA
18537885 TGTTCATACA
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
36 23 0.61
37 15 0.39
ACGTcount: A:0.75, C:0.05, G:0.12, T:0.08
Consensus pattern (37 bp):
AAATGATAATAAAGAAACAAAAAGAAAAAGAAGAACA
Found at i:18543460 original size:35 final size:36
Alignment explanation
Indices: 18543421--18543495 Score: 100
Period size: 36 Copynumber: 2.1 Consensus size: 36
18543411 CTAATTAAAG
* * *
18543421 TATTATAGGT-ATTTTTAT-AATTATGATAGGAGTGA
1 TATTATA-GTCATTTTGATCAATTATGATAGAAATGA
18543456 TATTATAGTCATTTTGATCAATTATGATAGAAATGA
1 TATTATAGTCATTTTGATCAATTATGATAGAAATGA
18543492 TATT
1 TATT
18543496 TCTTTAATTA
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
34 2 0.06
35 14 0.40
36 19 0.54
ACGTcount: A:0.36, C:0.03, G:0.16, T:0.45
Consensus pattern (36 bp):
TATTATAGTCATTTTGATCAATTATGATAGAAATGA
Found at i:18543943 original size:17 final size:17
Alignment explanation
Indices: 18543899--18543933 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
18543889 AAATTTATCC
*
18543899 AATAAAAAATATTAAAA
1 AATAAAAAAAATTAAAA
18543916 AATAAAAAAAATTAAAA
1 AATAAAAAAAATTAAAA
18543933 A
1 A
18543934 TGAGAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (17 bp):
AATAAAAAAAATTAAAA
Found at i:18544069 original size:25 final size:27
Alignment explanation
Indices: 18544022--18544072 Score: 79
Period size: 27 Copynumber: 1.9 Consensus size: 27
18544012 AAATAATTTT
18544022 ATTAATATAATATATATACATGTATAAA
1 ATTAATATAATATATATA-ATGTATAAA
18544050 ATTAA-ATAATATATAT-ATGTATA
1 ATTAATATAATATATATAATGTATA
18544073 TATCTTAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
25 7 0.30
27 11 0.48
28 5 0.22
ACGTcount: A:0.53, C:0.02, G:0.04, T:0.41
Consensus pattern (27 bp):
ATTAATATAATATATATAATGTATAAA
Found at i:18544350 original size:18 final size:17
Alignment explanation
Indices: 18544327--18544383 Score: 55
Period size: 18 Copynumber: 3.3 Consensus size: 17
18544317 TGGAAGAGAT
*
18544327 AAAAAAAATTGAAATTAA
1 AAAAAAAATT-AAATAAA
*
18544345 AAAAAATATTAAATAAA
1 AAAAAAAATTAAATAAA
18544362 AATAAAAAA-T-AATAGAA
1 AA-AAAAAATTAAATA-AA
18544379 AAAAA
1 AAAAA
18544384 CACGTAATAT
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 7 0.21
17 13 0.38
18 14 0.41
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (17 bp):
AAAAAAAATTAAATAAA
Found at i:18544361 original size:16 final size:15
Alignment explanation
Indices: 18544325--18544363 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
18544315 TATGGAAGAG
18544325 ATAAAAAAAATTGAA
1 ATAAAAAAAATTGAA
*
18544340 ATTAAAAAAAATATTAA
1 A-TAAAAAAAAT-TGAA
18544357 ATAAAAA
1 ATAAAAA
18544364 TAAAAAATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
15 1 0.05
16 16 0.76
17 4 0.19
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (15 bp):
ATAAAAAAAATTGAA
Found at i:18544735 original size:21 final size:21
Alignment explanation
Indices: 18544711--18544750 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
18544701 AAAATAAAAA
18544711 TAGAAAAATCTTTT-ATTTATT
1 TAGAAAAAT-TTTTAATTTATT
*
18544732 TAGATAAATTTTTAATTTA
1 TAGAAAAATTTTTAATTTA
18544751 AAAGAAAGTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.53
Consensus pattern (21 bp):
TAGAAAAATTTTTAATTTATT
Found at i:18545448 original size:28 final size:29
Alignment explanation
Indices: 18545416--18545476 Score: 108
Period size: 27 Copynumber: 2.2 Consensus size: 29
18545406 AAAAAGGTAA
18545416 AAATAATTTTATAATTTAATA-TTTTAAT
1 AAATAATTTTATAATTTAATATTTTTAAT
18545444 AAAT-ATTTTATAATTTAATATTTTTAAT
1 AAATAATTTTATAATTTAATATTTTTAAT
18545472 AAATA
1 AAATA
18545477 GTAAGGGAGC
Statistics
Matches: 31, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
27 16 0.52
28 15 0.48
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (29 bp):
AAATAATTTTATAATTTAATATTTTTAAT
Found at i:18545450 original size:12 final size:13
Alignment explanation
Indices: 18545433--18545476 Score: 54
Period size: 15 Copynumber: 3.3 Consensus size: 13
18545423 TTTATAATTT
18545433 AATA-TTTTAATA
1 AATATTTTTAATA
*
18545445 AATATTTTATAATTT
1 AATATTTT-TAA-TA
18545460 AATATTTTTAATA
1 AATATTTTTAATA
18545473 AATA
1 AATA
18545477 GTAAGGGAGC
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
12 4 0.15
13 8 0.30
14 6 0.22
15 9 0.33
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
AATATTTTTAATA
Found at i:18545521 original size:15 final size:16
Alignment explanation
Indices: 18545501--18545533 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
18545491 TTTACACTAA
18545501 TTTTAAA-AAAATTAT
1 TTTTAAATAAAATTAT
18545516 TTTTAAATAAAATTAT
1 TTTTAAATAAAATTAT
18545532 TT
1 TT
18545534 AATTATTCTT
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:0.00, T:0.52
Consensus pattern (16 bp):
TTTTAAATAAAATTAT
Found at i:18546059 original size:17 final size:17
Alignment explanation
Indices: 18546039--18546083 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 17
18546029 CATATTAGAT
*
18546039 AAATTATATAATTTAAC
1 AAATTTTATAATTTAAC
*
18546056 AAATTTTCAT-ATTTAAT
1 AAATTTT-ATAATTTAAC
18546073 AAATTTTATAA
1 AAATTTTATAA
18546084 CTTACATGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
16 2 0.08
17 20 0.83
18 2 0.08
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (17 bp):
AAATTTTATAATTTAAC
Found at i:18574868 original size:19 final size:22
Alignment explanation
Indices: 18574822--18574871 Score: 61
Period size: 19 Copynumber: 2.4 Consensus size: 22
18574812 AATAATTCAT
18574822 ATTTAATATGTAATCAATTTGA
1 ATTTAATATGTAATCAATTTGA
* *
18574844 AATTAAT-T-TAAT-AATTTTA
1 ATTTAATATGTAATCAATTTGA
18574863 ATTTAATAT
1 ATTTAATAT
18574872 AAATTTATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
19 12 0.50
20 5 0.21
21 1 0.04
22 6 0.25
ACGTcount: A:0.44, C:0.02, G:0.04, T:0.50
Consensus pattern (22 bp):
ATTTAATATGTAATCAATTTGA
Found at i:18579577 original size:15 final size:15
Alignment explanation
Indices: 18579548--18579576 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
18579538 CGTCAAATAC
18579548 CAAAAAAAGCAAAAA
1 CAAAAAAAGCAAAAA
18579563 CAAAAAAA-CAAAAA
1 CAAAAAAAGCAAAAA
18579577 AAACAAGAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.83, C:0.14, G:0.03, T:0.00
Consensus pattern (15 bp):
CAAAAAAAGCAAAAA
Found at i:18580691 original size:12 final size:14
Alignment explanation
Indices: 18580676--18580707 Score: 50
Period size: 12 Copynumber: 2.4 Consensus size: 14
18580666 AAATTTAAAA
18580676 TTTTTATT-AA-TG
1 TTTTTATTGAATTG
18580688 TTTTTATTGAATTG
1 TTTTTATTGAATTG
18580702 TTTTTA
1 TTTTTA
18580708 ATAAATAACT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 8 0.44
13 2 0.11
14 8 0.44
ACGTcount: A:0.22, C:0.00, G:0.09, T:0.69
Consensus pattern (14 bp):
TTTTTATTGAATTG
Found at i:18581479 original size:13 final size:13
Alignment explanation
Indices: 18581461--18581485 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
18581451 TTCTACAATT
18581461 TTTTTTCCTTTCC
1 TTTTTTCCTTTCC
18581474 TTTTTTCCTTTC
1 TTTTTTCCTTTC
18581486 AAGTAAAAAA
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:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (13 bp):
TTTTTTCCTTTCC
Found at i:18588024 original size:2 final size:2
Alignment explanation
Indices: 18588017--18588041 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
18588007 AAAATAATAA
18588017 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
18588042 AAGATAACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:18589344 original size:15 final size:15
Alignment explanation
Indices: 18589324--18589354 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
18589314 ACAAAGCTAA
18589324 TGGTTGTAGGCAATT
1 TGGTTGTAGGCAATT
18589339 TGGTTGTAGGCAATT
1 TGGTTGTAGGCAATT
18589354 T
1 T
18589355 TGTAAGAACA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.32, T:0.42
Consensus pattern (15 bp):
TGGTTGTAGGCAATT
Found at i:18589740 original size:29 final size:29
Alignment explanation
Indices: 18589698--18589755 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
18589688 GGCACCCGTC
18589698 CTGGTACTGTTTCCAGTGAAAGCCTAAAG
1 CTGGTACTGTTTCCAGTGAAAGCCTAAAG
18589727 CTGGTACTGTTTCCAGTGAAAGCCTAAAG
1 CTGGTACTGTTTCCAGTGAAAGCCTAAAG
18589756 AAAACAATTC
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.21, G:0.24, T:0.28
Consensus pattern (29 bp):
CTGGTACTGTTTCCAGTGAAAGCCTAAAG
Found at i:18592397 original size:14 final size:14
Alignment explanation
Indices: 18592380--18592407 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
18592370 TTTTACTTAG
18592380 AAAATTTCATCTAA
1 AAAATTTCATCTAA
18592394 AAAATTTCATCTAA
1 AAAATTTCATCTAA
18592408 GTCTTACTTA
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:0.50, C:0.14, G:0.00, T:0.36
Consensus pattern (14 bp):
AAAATTTCATCTAA
Found at i:18604288 original size:20 final size:19
Alignment explanation
Indices: 18604263--18604339 Score: 75
Period size: 19 Copynumber: 3.9 Consensus size: 19
18604253 AGCCCATTTT
*
18604263 TTTTATTTTGTATTTTATAA
1 TTTTATTTTAT-TTTTATAA
*
18604283 TTTTATTTTATTTTTATTA
1 TTTTATTTTATTTTTATAA
*
18604302 TTTT-TATTATTTTATATATA
1 TTTTATTTTATTTT-TATA-A
*
18604322 TATTTCTTTTATTTTTAT
1 T-TTTATTTTATTTTTAT
18604340 CTTATGTATT
Statistics
Matches: 48, Mismatches: 5, Indels: 7
0.80 0.08 0.12
Matches are distributed among these distances:
18 8 0.17
19 14 0.29
20 12 0.25
21 6 0.12
22 8 0.17
ACGTcount: A:0.23, C:0.01, G:0.01, T:0.74
Consensus pattern (19 bp):
TTTTATTTTATTTTTATAA
Found at i:18604523 original size:41 final size:43
Alignment explanation
Indices: 18604442--18604525 Score: 109
Period size: 42 Copynumber: 2.0 Consensus size: 43
18604432 TTATATATAT
18604442 TTATCTGATTATATAATATAATTTATCTAGTATTTATTTTTAG
1 TTATCTGATTATATAATATAATTTATCTAGTATTTATTTTTAG
* * * *
18604485 TTATCTG-TTA-ATATTATTATTTATCTGATTATTTTTTTTTA
1 TTATCTGATTATATAATATAATTTATCT-AGTATTTATTTTTA
18604526 AAATTATCTA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
41 14 0.39
42 15 0.42
43 7 0.19
ACGTcount: A:0.29, C:0.05, G:0.06, T:0.61
Consensus pattern (43 bp):
TTATCTGATTATATAATATAATTTATCTAGTATTTATTTTTAG
Found at i:18604542 original size:44 final size:41
Alignment explanation
Indices: 18604442--18604543 Score: 105
Period size: 44 Copynumber: 2.4 Consensus size: 41
18604432 TTATATATAT
* *
18604442 TTATCTGATTATATAATATAATTTATCTAGTATTTATTTTTAG
1 TTATCT-ATTA-ATATTATAATTTATCTAGTATTTATTTTTAA
* * * *
18604485 TTATCTGTTAATATTATTATTTATCTGATTATTTTTTTTTAAAA
1 TTATCTATTAATATTATAATTTATCT-AGTATTTATTTTT--AA
18604529 TTATCTATTAATATT
1 TTATCTATTAATATT
18604544 TTTTATTTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
41 14 0.29
42 14 0.29
43 6 0.12
44 15 0.31
ACGTcount: A:0.31, C:0.05, G:0.05, T:0.59
Consensus pattern (41 bp):
TTATCTATTAATATTATAATTTATCTAGTATTTATTTTTAA
Found at i:18605394 original size:4 final size:4
Alignment explanation
Indices: 18605383--18605477 Score: 74
Period size: 4 Copynumber: 23.8 Consensus size: 4
18605373 TTTGTTTCCT
* * * *
18605383 TTTA -TTA TTTA TTTA TTTA TTTA -TTA TTATA TTAA GATTG TTTA -ATA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TT-TA TTTA -TTTA TTTA TTTA
18605430 TTT- TTTA TTT- TTTA TTTA TTTTCA TTTA TTTA TTTA TTTA TTTTA TTT
1 TTTA TTTA TTTA TTTA TTTA -TTT-A TTTA TTTA TTTA TTTA -TTTA TTT
18605478 TCTTTAAATA
Statistics
Matches: 73, Mismatches: 8, Indels: 20
0.72 0.08 0.20
Matches are distributed among these distances:
3 14 0.19
4 43 0.59
5 15 0.21
6 1 0.01
ACGTcount: A:0.25, C:0.01, G:0.02, T:0.72
Consensus pattern (4 bp):
TTTA
Found at i:18605400 original size:8 final size:8
Alignment explanation
Indices: 18605383--18605477 Score: 74
Period size: 7 Copynumber: 11.9 Consensus size: 8
18605373 TTTGTTTCCT
18605383 TTTA-TTA
1 TTTATTTA
18605390 TTTATTTA
1 TTTATTTA
18605398 TTTATTTA
1 TTTATTTA
18605406 -TTATTATA
1 TTTATT-TA
* * *
18605414 TTAAGATTG
1 TTTA-TTTA
*
18605423 TTTA-ATA
1 TTTATTTA
18605430 TTT-TTTA
1 TTTATTTA
18605437 TTT-TTTA
1 TTTATTTA
18605444 TTTATTTTCA
1 TTTA-TTT-A
18605454 TTTATTTA
1 TTTATTTA
18605462 TTTATTTA
1 TTTATTTA
18605470 TTTTATTT
1 -TTTATTT
18605478 TCTTTAAATA
Statistics
Matches: 72, Mismatches: 7, Indels: 16
0.76 0.07 0.17
Matches are distributed among these distances:
7 25 0.35
8 22 0.31
9 19 0.26
10 6 0.08
ACGTcount: A:0.25, C:0.01, G:0.02, T:0.72
Consensus pattern (8 bp):
TTTATTTA
Found at i:18605451 original size:18 final size:18
Alignment explanation
Indices: 18605428--18605478 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 18
18605418 GATTGTTTAA
18605428 TATTTTTTATTTTTTATT
1 TATTTTTTATTTTTTATT
*
18605446 TA-TTTTCATTTATTTATT
1 TATTTTTTATTT-TTTATT
18605464 TATTTATTTTATTTT
1 TA-TT-TTTTATTTT
18605479 CTTTAAATAA
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
17 8 0.30
18 10 0.37
20 2 0.07
21 7 0.26
ACGTcount: A:0.20, C:0.02, G:0.00, T:0.78
Consensus pattern (18 bp):
TATTTTTTATTTTTTATT
Found at i:18605483 original size:22 final size:23
Alignment explanation
Indices: 18605432--18605483 Score: 74
Period size: 22 Copynumber: 2.4 Consensus size: 23
18605422 GTTTAATATT
18605432 TTTTATTT-TTTATTTATTTTCA
1 TTTTATTTATTTATTTATTTTCA
18605454 -TTTATTTATTTATTTATTTT-A
1 TTTTATTTATTTATTTATTTTCA
*
18605475 TTTTCTTTA
1 TTTTATTTA
18605484 AATAAAATTA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
21 8 0.30
22 19 0.70
ACGTcount: A:0.19, C:0.04, G:0.00, T:0.77
Consensus pattern (23 bp):
TTTTATTTATTTATTTATTTTCA
Found at i:18605575 original size:59 final size:59
Alignment explanation
Indices: 18605510--18605780 Score: 325
Period size: 58 Copynumber: 4.5 Consensus size: 59
18605500 AAAAAACAAA
*
18605510 TTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAGAATGAATTTTCAAAAAAAGGTTT
1 TTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAGAATAAATTTTCAAAAAAAGGTTT
* * **
18605569 TTTGAGGAAAAGTTGAAAGTATCAA-TTTTCTTCAA-AATTAAAAATTCCAAAAAAATATTT
1 TTTGAGGAAAAGTTGAAAGTATCAATTTTTCTT-AAGAA-T-AAATTTTCAAAAAAAGGTTT
* * *
18605629 TTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTT-TAAAAAAGGTTT
1 TTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAGAATAAATTTTCAAAAAAAGGTTT
* * *
18605686 TTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAAAAGAGTTTTT
1 TTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAGAATAAATTTTC---AAAAAAAG-G--TTT
*
18605751 TTTTAGGAAAAGTTGAAAGTATCAATTTTT
1 TTTGAGGAAAAGTTGAAAGTATCAATTTTT
18605781 TCTTGTACAA
Statistics
Matches: 180, Mismatches: 19, Indels: 20
0.82 0.09 0.09
Matches are distributed among these distances:
57 12 0.07
58 53 0.29
59 51 0.28
60 26 0.14
62 7 0.04
63 1 0.01
65 30 0.17
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.37
Consensus pattern (59 bp):
TTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAGAATAAATTTTCAAAAAAAGGTTT
Found at i:18605707 original size:58 final size:59
Alignment explanation
Indices: 18605510--18605779 Score: 314
Period size: 59 Copynumber: 4.5 Consensus size: 59
18605500 AAAAAACAAA
* * *
18605510 TTTGAGGAAAAGTTGAAAGTATCAATTTTTCTTAAGAATGAATTTTCAAAAAAAGGTTT
1 TTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTTAAAAAAAAGGTTT
* ** **
18605569 TTTGAGGAAAAGTTGAAAGTATCAATTTT-CTTCAA-AATTAAAAATTCCAAAAAAATATTT
1 TTTGAGGAAAAGTTGAAAGTATCAATTTTCCTT-AAGAA-T-AAATTTTAAAAAAAAGGTTT
* *
18605629 TTAG-GGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTT-TAAAAAAGGTTT
1 TTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTTAAAAAAAAGGTTT
* *
18605686 TTTGAGAAAAAGTTGAAAGTATCAATTTTCCTTAAAAATAAATTTTCAAAAAAAAAAGAGTTTTT
1 TTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTT---AAAAAAAAG-G--TTT
*
18605751 TTTTAGGAAAAGTTGAAAGTATCAATTTT
1 TTTGAGGAAAAGTTGAAAGTATCAATTTT
18605780 TTCTTGTACA
Statistics
Matches: 181, Mismatches: 17, Indels: 20
0.83 0.08 0.09
Matches are distributed among these distances:
57 12 0.07
58 49 0.27
59 59 0.33
60 23 0.13
62 7 0.04
63 1 0.01
65 30 0.17
ACGTcount: A:0.44, C:0.06, G:0.14, T:0.37
Consensus pattern (59 bp):
TTTGAGGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTTAAAAAAAAGGTTT
Found at i:18605738 original size:117 final size:118
Alignment explanation
Indices: 18605515--18605740 Score: 357
Period size: 117 Copynumber: 1.9 Consensus size: 118
18605505 ACAAATTTGA
* * *
18605515 GGAAAAGTTGAAAGTATCAATTTTTCTTAAGAATGAATTTTCAAAAAAAGGTTTTTTGAGGAAAA
1 GGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTTCAAAAAAAGGTTTTTTGAGAAAAA
* *
18605580 GTTGAAAGTATCAATTTTCTTCAAAATTAAAAATTCCAAAAAAATATTTTTAG
66 GTTGAAAGTATCAATTTTCTTCAAAAATAAAAATTCAAAAAAAATATTTTTAG
*
18605633 GGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTT-TAAAAAAGGTTTTTTGAGAAAAA
1 GGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTTCAAAAAAAGGTTTTTTGAGAAAAA
**
18605697 GTTGAAAGTATCAATTTTCCTT-AAAAATAAATTTTCAAAAAAAA
66 GTTGAAAGTATCAATTTT-CTTCAAAAATAAAAATTCAAAAAAAA
18605741 AAGAGTTTTT
Statistics
Matches: 99, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
117 57 0.58
118 42 0.42
ACGTcount: A:0.46, C:0.07, G:0.13, T:0.35
Consensus pattern (118 bp):
GGAAAAGTTGAAAGTATCAATTTTCCTTAAGAATAAATTTTCAAAAAAAGGTTTTTTGAGAAAAA
GTTGAAAGTATCAATTTTCTTCAAAAATAAAAATTCAAAAAAAATATTTTTAG
Found at i:18608961 original size:15 final size:15
Alignment explanation
Indices: 18608941--18608972 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
18608931 TACATGCATT
*
18608941 TTTCATTCATTGCAC
1 TTTCATTCATTACAC
18608956 TTTCATTCATTACAC
1 TTTCATTCATTACAC
18608971 TT
1 TT
18608973 AACAAAGTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.22, C:0.25, G:0.03, T:0.50
Consensus pattern (15 bp):
TTTCATTCATTACAC
Found at i:18615900 original size:9 final size:9
Alignment explanation
Indices: 18615869--18615926 Score: 64
Period size: 9 Copynumber: 6.2 Consensus size: 9
18615859 TACTATGCTT
18615869 AAAAAAATG
1 AAAAAAATG
*
18615878 AAAATGAAAAG
1 AAAA--AAATG
18615889 AAAAAAATG
1 AAAAAAATG
18615898 -AAAAAATG
1 AAAAAAATG
*
18615906 AAAAAAAGG
1 AAAAAAATG
18615915 AAAAAAAGTG
1 AAAAAAA-TG
18615925 AA
1 AA
18615927 TGAAAAAAGA
Statistics
Matches: 41, Mismatches: 4, Indels: 7
0.79 0.08 0.13
Matches are distributed among these distances:
8 8 0.20
9 22 0.54
10 3 0.07
11 8 0.20
ACGTcount: A:0.76, C:0.00, G:0.16, T:0.09
Consensus pattern (9 bp):
AAAAAAATG
Found at i:18617030 original size:28 final size:29
Alignment explanation
Indices: 18616988--18617090 Score: 102
Period size: 29 Copynumber: 3.4 Consensus size: 29
18616978 GATCAGCCAT
* *
18616988 TTTTTCAAGCGTTTTCTTTAGAAGCA-TTA
1 TTTTTCAA-AGTTTTATTTAGAAGCATTTA
*
18617017 TTTTTCAAAGTTTTATTAATG-AGCATTTA
1 TTTTTCAAAGTTTTATTTA-GAAGCATTTA
18617046 TTTTTCAAAGTTTAATTGATTTAGAAGTCATTTA
1 TTTTTCAAAG-TT--TT-ATTTAGAAG-CATTTA
18617080 TTTTTCAAAGT
1 TTTTTCAAAGT
18617091 CGTTGAGCCT
Statistics
Matches: 62, Mismatches: 4, Indels: 12
0.79 0.05 0.15
Matches are distributed among these distances:
28 12 0.19
29 22 0.35
30 2 0.03
32 3 0.05
33 7 0.11
34 16 0.26
ACGTcount: A:0.29, C:0.09, G:0.12, T:0.50
Consensus pattern (29 bp):
TTTTTCAAAGTTTTATTTAGAAGCATTTA
Found at i:18617083 original size:34 final size:32
Alignment explanation
Indices: 18617004--18617090 Score: 110
Period size: 29 Copynumber: 2.8 Consensus size: 32
18616994 AAGCGTTTTC
*
18617004 TTTAGAAGCA-TTATTTTTCAAAGTTTTATTA
1 TTTAGAAGCATTTATTTTTCAAAGTTTAATTA
*
18617035 -AT-G-AGCATTTATTTTTCAAAGTTTAATTGA
1 TTTAGAAGCATTTATTTTTCAAAGTTTAATT-A
18617065 TTTAGAAGTCATTTATTTTTCAAAGT
1 TTTAGAAG-CATTTATTTTTCAAAGT
18617091 CGTTGAGCCT
Statistics
Matches: 47, Mismatches: 3, Indels: 9
0.80 0.05 0.15
Matches are distributed among these distances:
28 4 0.09
29 20 0.43
30 2 0.04
31 1 0.02
32 1 0.02
33 2 0.04
34 17 0.36
ACGTcount: A:0.32, C:0.07, G:0.11, T:0.49
Consensus pattern (32 bp):
TTTAGAAGCATTTATTTTTCAAAGTTTAATTA
Found at i:18617481 original size:25 final size:23
Alignment explanation
Indices: 18617432--18617479 Score: 80
Period size: 23 Copynumber: 2.1 Consensus size: 23
18617422 GGGTAAGCCC
18617432 ATTTTTTTTATTTTGTATTTTAT
1 ATTTTTTTTATTTTGTATTTTAT
18617455 ATTTTTTTTATTTT-TATTATTAT
1 ATTTTTTTTATTTTGTATT-TTAT
18617478 AT
1 AT
18617480 ATATATTTTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 4 0.17
23 20 0.83
ACGTcount: A:0.21, C:0.00, G:0.02, T:0.77
Consensus pattern (23 bp):
ATTTTTTTTATTTTGTATTTTAT
Found at i:18617488 original size:25 final size:22
Alignment explanation
Indices: 18617432--18617499 Score: 66
Period size: 23 Copynumber: 2.9 Consensus size: 22
18617422 GGGTAAGCCC
*
18617432 ATTTTTTTTATTTTGTATTTTAT
1 ATTTATTTTATTTT-TATTTTAT
*
18617455 ATTTTTTTTATTTTTATTATTAT
1 ATTTATTTTATTTTTATT-TTAT
18617478 ATATATATTTT-TCTTTTATTTT
1 AT-T-TATTTTAT-TTTTATTTT
18617500 TGTCTTATGT
Statistics
Matches: 40, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
22 4 0.10
23 20 0.50
24 4 0.10
25 12 0.30
ACGTcount: A:0.21, C:0.01, G:0.01, T:0.76
Consensus pattern (22 bp):
ATTTATTTTATTTTTATTTTAT
Found at i:18617522 original size:15 final size:15
Alignment explanation
Indices: 18617504--18617534 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
18617494 TATTTTTGTC
18617504 TTATGTATTTATTAT
1 TTATGTATTTATTAT
*
18617519 TTATTTATTTATTAT
1 TTATGTATTTATTAT
18617534 T
1 T
18617535 ACTATTTAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.71
Consensus pattern (15 bp):
TTATGTATTTATTAT
Found at i:18617689 original size:28 final size:25
Alignment explanation
Indices: 18617658--18617709 Score: 68
Period size: 28 Copynumber: 2.0 Consensus size: 25
18617648 TGTTAATATT
*
18617658 ATTATTTATCTAATTATTTTCTTTTTAA
1 ATTATCTAT-TAA-TATTTT-TTTTTAA
18617686 ATTATCTATTAATATTTTTTTTTA
1 ATTATCTATTAATATTTTTTTTTA
18617710 TTTTTCTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 6 0.26
26 6 0.26
27 3 0.13
28 8 0.35
ACGTcount: A:0.29, C:0.06, G:0.00, T:0.65
Consensus pattern (25 bp):
ATTATCTATTAATATTTTTTTTTAA
Found at i:18617692 original size:44 final size:41
Alignment explanation
Indices: 18617584--18617710 Score: 128
Period size: 43 Copynumber: 3.0 Consensus size: 41
18617574 TTTTTTCTGT
* * * *
18617584 TAATATTTATATATATTTATCTGATTATATATTATAATTTATC
1 TAATATTTATTTTTAATTATCTG-TTA-ATATTATTATTTATC
*
18617627 TAATATTTATTTTTAGTTATCTGTTAATATTATTATTTATC
1 TAATATTTATTTTTAATTATCTGTTAATATTATTATTTATC
* * * *
18617668 TAATTATTTTCTTTTTAAATTATCTATTAATATTTTTTTTTAT
1 TAA-TA-TTTATTTTT-AATTATCTGTTAATATTATTATTTAT
18617711 TTTTCTTTTT
Statistics
Matches: 72, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
41 17 0.24
42 5 0.07
43 28 0.39
44 22 0.31
ACGTcount: A:0.31, C:0.05, G:0.02, T:0.61
Consensus pattern (41 bp):
TAATATTTATTTTTAATTATCTGTTAATATTATTATTTATC
Found at i:18618602 original size:9 final size:9
Alignment explanation
Indices: 18618588--18618641 Score: 51
Period size: 9 Copynumber: 6.2 Consensus size: 9
18618578 GATTGTTTAA
18618588 TATTTTTTT
1 TATTTTTTT
18618597 TA--TTTTT
1 TATTTTTTT
18618604 TATTTATTTT
1 TATTT-TTTT
* *
18618614 CA-TTTATT
1 TATTTTTTT
*
18618622 TATTTATTT
1 TATTTTTTT
18618631 TATTTTTTT
1 TATTTTTTT
18618640 TA
1 TA
18618642 AATAAAATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
7 7 0.20
8 4 0.11
9 19 0.54
10 5 0.14
ACGTcount: A:0.19, C:0.02, G:0.00, T:0.80
Consensus pattern (9 bp):
TATTTTTTT
Done.