Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr01 113035596
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: 113035596
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Warning! 271 characters in sequence are not A, C, G, or T
File 76 of 378
Found at i:20315063 original size:46 final size:46
Alignment explanation
Indices: 20315012--20315106 Score: 147
Period size: 46 Copynumber: 2.1 Consensus size: 46
20315002 TTAAAAAAAA
* *
20315012 TTACTAGTGTATTGCCGGCCATTAGAAGGTCAGAA-CTAATTTTTTT
1 TTACTAGTGTAGTGCCGGCCATTAGAAGGCCAGAATC-AATTTTTTT
*
20315058 TTACTAGTGTGGTGCCGGCCATTAGAAGGCCAGAATCAATTTTTTT
1 TTACTAGTGTAGTGCCGGCCATTAGAAGGCCAGAATCAATTTTTTT
20315104 TTA
1 TTA
20315107 TTTTTTTCCT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
46 44 0.98
47 1 0.02
ACGTcount: A:0.25, C:0.16, G:0.21, T:0.38
Consensus pattern (46 bp):
TTACTAGTGTAGTGCCGGCCATTAGAAGGCCAGAATCAATTTTTTT
Found at i:20315157 original size:54 final size:54
Alignment explanation
Indices: 20315053--20315206 Score: 168
Period size: 54 Copynumber: 2.9 Consensus size: 54
20315043 AGAACTAATT
**
20315053 TTTTTTTACTAGTGTGGTGC-CGGCCATTAGAAGGCCAGAATCAATTTTTTTTTA
1 TTTTTTTACTAGTGTGGTGCTC-GCCATTAGAAGGCCAGAATCAAAATTTTTTTA
* * * *
20315107 TTTTTTTCCTAGTGTGGTGCTCACCATTAGAAGGTCAGAA-CTAAAATTTTTTTC
1 TTTTTTTACTAGTGTGGTGCTCGCCATTAGAAGGCCAGAATC-AAAATTTTTTTA
* * * * * *
20315161 CTTTTTTACTAGTGTAGTGGTCGCTATTAGAAGACCAGAATAAAAA
1 TTTTTTTACTAGTGTGGTGCTCGCCATTAGAAGGCCAGAATCAAAA
20315207 AAAAAATTAT
Statistics
Matches: 82, Mismatches: 15, Indels: 6
0.80 0.15 0.06
Matches are distributed among these distances:
53 1 0.01
54 80 0.98
55 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.19, T:0.40
Consensus pattern (54 bp):
TTTTTTTACTAGTGTGGTGCTCGCCATTAGAAGGCCAGAATCAAAATTTTTTTA
Found at i:20315239 original size:47 final size:49
Alignment explanation
Indices: 20315166--20315289 Score: 155
Period size: 49 Copynumber: 2.6 Consensus size: 49
20315156 TTTTCCTTTT
* * *
20315166 TTACTAGTGTAGTGGTC-GCTATTAGAAGACCAGAA-T-AAAAAAAAAAA
1 TTACTAGTGTAGT-GCCAGCCATTAGAAGACCAAAACTAAAAAAAAAAAA
* * * *
20315213 TTATTAGTGTGGTGCCGGTCATTAGAAGACCAAAACTAAAAAAAAAAAA
1 TTACTAGTGTAGTGCCAGCCATTAGAAGACCAAAACTAAAAAAAAAAAA
20315262 TTACTAGTGTAGTGCCAGCCATTAGAAG
1 TTACTAGTGTAGTGCCAGCCATTAGAAG
20315290 GCTAGAACCA
Statistics
Matches: 64, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
46 2 0.03
47 26 0.41
48 1 0.02
49 35 0.55
ACGTcount: A:0.43, C:0.13, G:0.20, T:0.24
Consensus pattern (49 bp):
TTACTAGTGTAGTGCCAGCCATTAGAAGACCAAAACTAAAAAAAAAAAA
Found at i:20317510 original size:3 final size:3
Alignment explanation
Indices: 20317502--20317542 Score: 82
Period size: 3 Copynumber: 13.7 Consensus size: 3
20317492 TCTTAATCTA
20317502 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
20317543 AAGAAACCAC
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:20321535 original size:30 final size:30
Alignment explanation
Indices: 20321492--20321548 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
20321482 GACGAACGGG
*
20321492 TAACCTCGATATAATGTCATCTTGTGTGAT
1 TAACCTCGATATAATGTCAGCTTGTGTGAT
* *
20321522 TAACCTGGTTATAATGTCAGCTTGTGT
1 TAACCTCGATATAATGTCAGCTTGTGT
20321549 AAGCAACCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.25, C:0.16, G:0.19, T:0.40
Consensus pattern (30 bp):
TAACCTCGATATAATGTCAGCTTGTGTGAT
Found at i:20321557 original size:30 final size:30
Alignment explanation
Indices: 20321501--20321557 Score: 78
Period size: 30 Copynumber: 1.9 Consensus size: 30
20321491 GTAACCTCGA
* * **
20321501 TATAATGTCATCTTGTGTGATTAACCTGGT
1 TATAATGTCAGCTTGTGTAAGCAACCTGGT
20321531 TATAATGTCAGCTTGTGTAAGCAACCT
1 TATAATGTCAGCTTGTGTAAGCAACCT
20321558 TGAAATATTG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
30 23 1.00
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (30 bp):
TATAATGTCAGCTTGTGTAAGCAACCTGGT
Found at i:20323210 original size:14 final size:15
Alignment explanation
Indices: 20323191--20323227 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
20323181 ATAATTTAAA
20323191 ATATAATAATAAT-G
1 ATATAATAATAATAG
20323205 ATATAAT-ATAATAG
1 ATATAATAATAATAG
*
20323219 TTATAATAA
1 ATATAATAA
20323228 ATAAAAGAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 5 0.25
14 14 0.70
15 1 0.05
ACGTcount: A:0.57, C:0.00, G:0.05, T:0.38
Consensus pattern (15 bp):
ATATAATAATAATAG
Found at i:20324377 original size:2 final size:2
Alignment explanation
Indices: 20324364--20324421 Score: 71
Period size: 2 Copynumber: 29.0 Consensus size: 2
20324354 GTGATAAGAA
* * * * *
20324364 AT AT AT AA AT AT AT AC AT AT AC AT AT AC AT AT AC 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
20324406 AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT
20324422 GAATTGCTTA
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (2 bp):
AT
Found at i:20331499 original size:50 final size:50
Alignment explanation
Indices: 20331419--20331523 Score: 192
Period size: 50 Copynumber: 2.1 Consensus size: 50
20331409 TTGGCTTAAA
* *
20331419 TAAGACTTGAAACATGATATTTGTCAATATGTATGGGTATGTGTTATGGT
1 TAAGGCTTGAAACATGATATTTGTCAATATGTATAGGTATGTGTTATGGT
20331469 TAAGGCTTGAAACATGATATTTGTCAATATGTATAGGTATGTGTTATGGT
1 TAAGGCTTGAAACATGATATTTGTCAATATGTATAGGTATGTGTTATGGT
20331519 TAAGG
1 TAAGG
20331524 TAGGTGAAAA
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
50 53 1.00
ACGTcount: A:0.30, C:0.06, G:0.25, T:0.39
Consensus pattern (50 bp):
TAAGGCTTGAAACATGATATTTGTCAATATGTATAGGTATGTGTTATGGT
Found at i:20331985 original size:33 final size:33
Alignment explanation
Indices: 20331947--20332009 Score: 90
Period size: 33 Copynumber: 1.9 Consensus size: 33
20331937 TTCTGATATG
* *
20331947 ATATGACATTTTGATATGATATATGCTTCTGAA
1 ATATGACATTCTAATATGATATATGCTTCTGAA
* *
20331980 ATATGACATTCTAATATTATATATGTTTCT
1 ATATGACATTCTAATATGATATATGCTTCT
20332010 AGTGATGCGA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 26 1.00
ACGTcount: A:0.33, C:0.10, G:0.11, T:0.46
Consensus pattern (33 bp):
ATATGACATTCTAATATGATATATGCTTCTGAA
Found at i:20343683 original size:51 final size:50
Alignment explanation
Indices: 20343524--20343680 Score: 251
Period size: 51 Copynumber: 3.1 Consensus size: 50
20343514 ACTTCTGATC
* *
20343524 AGTGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGATA
1 AGTGACAAGTGATAAGTGGTAG-CTTAGCTACACTTATCTGATCAGTGACA
* *
20343575 AGTGACAAATGATAAGTGGTAGCTTAGCTACTCTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA
*
20343625 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAGTGACA
20343676 AGTGA
1 AGTGA
20343681 TAAATGTGAT
Statistics
Matches: 98, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
50 46 0.47
51 52 0.53
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (50 bp):
AGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA
Found at i:20351478 original size:51 final size:50
Alignment explanation
Indices: 20351319--20351475 Score: 251
Period size: 51 Copynumber: 3.1 Consensus size: 50
20351309 ACTTCTGATC
* *
20351319 AGTGACAAGTGATAAGTGGTAGCCTCAGCTACACTTATCTGATCAGTGATA
1 AGTGACAAGTGATAAGTGGTAG-CTTAGCTACACTTATCTGATCAGTGACA
* *
20351370 AGTGACAAATGATAAGTGGTAGCTTAGCTACTCTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA
*
20351420 AGTGATAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA
1 AGTGACAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTGATCAGTGACA
20351471 AGTGA
1 AGTGA
20351476 TAAATGTGAT
Statistics
Matches: 98, Mismatches: 7, Indels: 2
0.92 0.07 0.02
Matches are distributed among these distances:
50 46 0.47
51 52 0.53
ACGTcount: A:0.32, C:0.15, G:0.24, T:0.29
Consensus pattern (50 bp):
AGTGACAAGTGATAAGTGGTAGCTTAGCTACACTTATCTGATCAGTGACA
Found at i:20358193 original size:32 final size:31
Alignment explanation
Indices: 20358098--20358238 Score: 106
Period size: 32 Copynumber: 4.5 Consensus size: 31
20358088 TGGGAGACCT
* * *
20358098 ATTAAAATTTTCAAAAATTTTAGGA-GTTTT
1 ATTAAAATTTTCAAAAATTTTAGAAGGTATA
* **
20358128 ATGAAAATTTTCAAAAATTTTA-AGAGAACATA
1 ATTAAAATTTTCAAAAATTTTAGA-AG-GTATA
*
20358160 ATTAAAATTTTCAAAAAGTATTAGAAGGTATA
1 ATTAAAATTTTCAAAAA-TTTTAGAAGGTATA
* * * * * *
20358192 ATTAGACTTTTAAAAAATTTGAGAGGGTCTA
1 ATTAAAATTTTCAAAAATTTTAGAAGGTATA
* *
20358223 ATTAAACTTTTTAAAA
1 ATTAAAATTTTCAAAA
20358239 GCCTTAAGGG
Statistics
Matches: 87, Mismatches: 19, Indels: 9
0.76 0.17 0.08
Matches are distributed among these distances:
30 22 0.25
31 24 0.28
32 34 0.39
33 6 0.07
34 1 0.01
ACGTcount: A:0.46, C:0.05, G:0.11, T:0.38
Consensus pattern (31 bp):
ATTAAAATTTTCAAAAATTTTAGAAGGTATA
Found at i:20372540 original size:6 final size:6
Alignment explanation
Indices: 20372514--20372553 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
20372504 TTAAAGATAT
* *
20372514 AAATAA AGATAA AAGTAA AAATAA AAATAA TAAATAA AAA
1 AAATAA AAATAA AAATAA AAATAA AAATAA -AAATAA AAA
20372554 GTTTTTAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
6 23 0.79
7 6 0.21
ACGTcount: A:0.78, C:0.00, G:0.05, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:20374253 original size:40 final size:40
Alignment explanation
Indices: 20374157--20374454 Score: 399
Period size: 40 Copynumber: 7.5 Consensus size: 40
20374147 AAGCCAAGTA
* * *
20374157 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTC-AATG
1 CCTTCGGGACTTAGCCCGGATATAG-TAACTCGCACAAATG
* *
20374195 CCTTCGGGACATAGCCCGGATATAGTAACTCGCACCAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
20374235 CCTTCGGGACTTAACCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
20374275 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * * *
20374315 CCTTCGGGACTTAGCCCAGATGTAATAACTTGCACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
* * *
20374355 CCTTCGGGACTTAGCCCGGATGTAATAACTCACACAAATG
1 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
*
20374395 CCTTCGGGACTTAGCCCGGA-ACTAGTCACTAGCGCA-AAATG
1 CCTTCGGGACTTAGCCCGGATA-TAGTAACT--CGCACAAATG
20374436 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
20374455 TTATCATCCA
Statistics
Matches: 235, Mismatches: 19, Indels: 9
0.89 0.07 0.03
Matches are distributed among these distances:
38 12 0.05
39 17 0.07
40 179 0.76
41 24 0.10
42 3 0.01
ACGTcount: A:0.27, C:0.28, G:0.22, T:0.23
Consensus pattern (40 bp):
CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
Found at i:20379997 original size:21 final size:21
Alignment explanation
Indices: 20379972--20380035 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 21
20379962 TAGCCTTCGG
20379972 GCTTCCGTTTAGCACTTATGT
1 GCTTCCGTTTAGCACTTATGT
* * *
20379993 GCTTCAG-TTAGC-CTT-CGG
1 GCTTCCGTTTAGCACTTATGT
20380011 GCTTCCGTTTAGCACTTATGT
1 GCTTCCGTTTAGCACTTATGT
20380032 GCTT
1 GCTT
20380036 GAGCTAGACT
Statistics
Matches: 34, Mismatches: 6, Indels: 6
0.74 0.13 0.13
Matches are distributed among these distances:
18 7 0.21
19 8 0.24
20 8 0.24
21 11 0.32
ACGTcount: A:0.12, C:0.25, G:0.22, T:0.41
Consensus pattern (21 bp):
GCTTCCGTTTAGCACTTATGT
Found at i:20380000 original size:39 final size:39
Alignment explanation
Indices: 20379954--20380054 Score: 175
Period size: 39 Copynumber: 2.6 Consensus size: 39
20379944 GCTCTGGTGA
20379954 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
20379993 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
* * *
20380032 GCTTGAGCTAGACTTCGGGCTTC
1 GCTTCAGTTAGCCTTCGGGCTTC
20380055 AGATCACGAT
Statistics
Matches: 59, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 59 1.00
ACGTcount: A:0.13, C:0.26, G:0.25, T:0.37
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
Found at i:20388234 original size:33 final size:33
Alignment explanation
Indices: 20388167--20388234 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
20388157 TCAAGGCTGC
* *
20388167 CATCATAGTCTCAATGGCATCAGCCTTACCAGT
1 CATCATAGCCTCAATGGCATCAGCCCTACCAGT
* *
20388200 CATCATAGCCTCAATGGCATCATCCCTACTAGT
1 CATCATAGCCTCAATGGCATCAGCCCTACCAGT
20388233 CA
1 CA
20388235 GTTTTTCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.28, C:0.32, G:0.13, T:0.26
Consensus pattern (33 bp):
CATCATAGCCTCAATGGCATCAGCCCTACCAGT
Found at i:20388888 original size:22 final size:24
Alignment explanation
Indices: 20388858--20388901 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
20388848 CTATCTAGAT
20388858 ATCAAATC-TCT-AAGATTACAAA
1 ATCAAATCTTCTAAAGATTACAAA
*
20388880 ATCATATCTTCTAAAGATTACA
1 ATCAAATCTTCTAAAGATTACA
20388902 TTTAATGTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
22 7 0.37
23 3 0.16
24 9 0.47
ACGTcount: A:0.45, C:0.18, G:0.05, T:0.32
Consensus pattern (24 bp):
ATCAAATCTTCTAAAGATTACAAA
Found at i:20388958 original size:35 final size:35
Alignment explanation
Indices: 20388930--20389048 Score: 140
Period size: 35 Copynumber: 3.5 Consensus size: 35
20388920 ATATTTTTAG
*
20388930 AGATCCCCTTCCATATTTAACGAGCATATCTTTGA
1 AGATCACCTTCCATATTTAACGAGCATATCTTTGA
* *
20388965 AGATCACTTTCCATATTT-AC---CA-ATCTTTGG
1 AGATCACCTTCCATATTTAACGAGCATATCTTTGA
* **
20388995 AGATCCCCTTCCATATTTGCCGAGCATATCTTTGA
1 AGATCACCTTCCATATTTAACGAGCATATCTTTGA
*
20389030 AGATCACTTTCCATATTTA
1 AGATCACCTTCCATATTTA
20389049 CCAAGCTCCG
Statistics
Matches: 69, Mismatches: 10, Indels: 10
0.78 0.11 0.11
Matches are distributed among these distances:
30 23 0.33
31 3 0.04
34 4 0.06
35 39 0.57
ACGTcount: A:0.27, C:0.25, G:0.11, T:0.37
Consensus pattern (35 bp):
AGATCACCTTCCATATTTAACGAGCATATCTTTGA
Found at i:20388993 original size:30 final size:30
Alignment explanation
Indices: 20388957--20389052 Score: 111
Period size: 30 Copynumber: 3.0 Consensus size: 30
20388947 TAACGAGCAT
20388957 ATCTTTGAAGATCACTTTCCATATTTACCA
1 ATCTTTGAAGATCACTTTCCATATTTACCA
* * * *
20388987 ATCTTTGGAGATCCCCTTCCATATTTGCCGAGCA
1 ATCTTTGAAGATCACTTTCCATATTT----ACCA
20389021 TATCTTTGAAGATCACTTTCCATATTTACCA
1 -ATCTTTGAAGATCACTTTCCATATTTACCA
20389052 A
1 A
20389053 GCTCCGGAGA
Statistics
Matches: 53, Mismatches: 8, Indels: 10
0.75 0.11 0.14
Matches are distributed among these distances:
30 24 0.45
31 3 0.06
34 3 0.06
35 23 0.43
ACGTcount: A:0.27, C:0.25, G:0.10, T:0.38
Consensus pattern (30 bp):
ATCTTTGAAGATCACTTTCCATATTTACCA
Found at i:20389033 original size:65 final size:65
Alignment explanation
Indices: 20388929--20389052 Score: 230
Period size: 65 Copynumber: 1.9 Consensus size: 65
20388919 CATATTTTTA
20388929 GAGATCCCCTTCCATATTTAACGAGCATATCTTTGAAGATCACTTTCCATATTTACCAATCTTTG
1 GAGATCCCCTTCCATATTTAACGAGCATATCTTTGAAGATCACTTTCCATATTTACCAATCTTTG
**
20388994 GAGATCCCCTTCCATATTTGCCGAGCATATCTTTGAAGATCACTTTCCATATTTACCAA
1 GAGATCCCCTTCCATATTTAACGAGCATATCTTTGAAGATCACTTTCCATATTTACCAA
20389053 GCTCCGGAGA
Statistics
Matches: 57, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
65 57 1.00
ACGTcount: A:0.27, C:0.26, G:0.11, T:0.35
Consensus pattern (65 bp):
GAGATCCCCTTCCATATTTAACGAGCATATCTTTGAAGATCACTTTCCATATTTACCAATCTTTG
Found at i:20396329 original size:31 final size:31
Alignment explanation
Indices: 20396286--20396347 Score: 90
Period size: 31 Copynumber: 2.0 Consensus size: 31
20396276 TGTATTGATG
*
20396286 TATTAAATTATTTAAATATATTTTATCATTA
1 TATTAAATTATTTAAATATAATTTATCATTA
*
20396317 TATT-AATGTATTTAAATATAATTTATTATTA
1 TATTAAAT-TATTTAAATATAATTTATCATTA
20396348 GATTTAAGTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
30 3 0.11
31 25 0.89
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.55
Consensus pattern (31 bp):
TATTAAATTATTTAAATATAATTTATCATTA
Found at i:20397010 original size:31 final size:30
Alignment explanation
Indices: 20396968--20397073 Score: 81
Period size: 31 Copynumber: 3.4 Consensus size: 30
20396958 AGTGGAAAAG
*
20396968 TTTGAGCAAAAATATAAATTTAAAAATTAGA
1 TTTGAGAAAAAATA-AAATTTAAAAATTAGA
* **
20396999 TTTGAGAAAAAA-AAACTTGTTTAGAAAACGAG-
1 TTTGAGAAAAAATAAA---ATTTA-AAAATTAGA
* *
20397031 TTTGAGCAAAAATAAAAACTTAAAAATTAGA
1 TTTGAGAAAAAAT-AAAATTTAAAAATTAGA
*
20397062 TTTAAGAAAAAA
1 TTTGAGAAAAAA
20397074 AAACTCGTTT
Statistics
Matches: 57, Mismatches: 11, Indels: 14
0.70 0.13 0.17
Matches are distributed among these distances:
29 2 0.04
30 7 0.12
31 24 0.42
32 15 0.26
33 6 0.11
34 3 0.05
ACGTcount: A:0.56, C:0.05, G:0.12, T:0.27
Consensus pattern (30 bp):
TTTGAGAAAAAATAAAATTTAAAAATTAGA
Found at i:20397033 original size:63 final size:63
Alignment explanation
Indices: 20396966--20397097 Score: 228
Period size: 63 Copynumber: 2.1 Consensus size: 63
20396956 AAAGTGGAAA
* * * *
20396966 AGTTTGAGCAAAAATATAAATTTAAAAATTAGATTTGAGAAAAAAAAACTTGTTTAGAAAACG
1 AGTTTGAGCAAAAATAAAAACTTAAAAATTAGATTTAAGAAAAAAAAACTCGTTTAGAAAACG
20397029 AGTTTGAGCAAAAATAAAAACTTAAAAATTAGATTTAAGAAAAAAAAACTCGTTTAGAAAACG
1 AGTTTGAGCAAAAATAAAAACTTAAAAATTAGATTTAAGAAAAAAAAACTCGTTTAGAAAACG
20397092 AGTTTG
1 AGTTTG
20397098 GCCTCAAGTA
Statistics
Matches: 65, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 65 1.00
ACGTcount: A:0.52, C:0.06, G:0.14, T:0.27
Consensus pattern (63 bp):
AGTTTGAGCAAAAATAAAAACTTAAAAATTAGATTTAAGAAAAAAAAACTCGTTTAGAAAACG
Found at i:20397035 original size:32 final size:31
Alignment explanation
Indices: 20396999--20397097 Score: 89
Period size: 32 Copynumber: 3.1 Consensus size: 31
20396989 AAAAATTAGA
20396999 TTTGAGAAAAAAAAACTTGTTTAGAAAACGAG
1 TTTGAGAAAAAAAAAC-TGTTTAGAAAACGAG
**
20397031 TTTGAGCAAAAATAAAAAC---TTA-AAAATTAG
1 TTTGAG--AAAA-AAAAACTGTTTAGAAAACGAG
*
20397061 ATTTAAGAAAAAAAAACTCGTTTAGAAAACGAG
1 -TTTGAGAAAAAAAAACT-GTTTAGAAAACGAG
20397094 TTTG
1 TTTG
20397098 GCCTCAAGTA
Statistics
Matches: 52, Mismatches: 6, Indels: 18
0.68 0.08 0.24
Matches are distributed among these distances:
28 6 0.12
29 4 0.08
30 6 0.12
31 8 0.15
32 12 0.23
33 6 0.12
34 4 0.08
35 6 0.12
ACGTcount: A:0.52, C:0.07, G:0.15, T:0.26
Consensus pattern (31 bp):
TTTGAGAAAAAAAAACTGTTTAGAAAACGAG
Found at i:20406759 original size:2 final size:2
Alignment explanation
Indices: 20406752--20406794 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
20406742 AGTCATGTGA
20406752 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
20406794 A
1 A
20406795 AGTGGTTTTG
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:20408284 original size:49 final size:49
Alignment explanation
Indices: 20408184--20408288 Score: 117
Period size: 49 Copynumber: 2.1 Consensus size: 49
20408174 AATGTTTTAT
** * * *
20408184 TTTTTTATGTAATTTATTTGTTATGTGTGTTTTAGGTTGATTAAATTTA
1 TTTTTTATGTAATTTATTTGGCATGTGTATTTTAGATTGATTAAATATA
20408233 TTTTTTATGTAATTTATTTGGCATGT-TATTTT-GATT-ATTTTAATATATA
1 TTTTTTATGTAATTTATTTGGCATGTGTATTTTAGATTGA--TTAA-ATATA
20408282 TTTTTTA
1 TTTTTTA
20408289 ATTTTTTATG
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
46 1 0.02
47 3 0.06
48 9 0.19
49 35 0.73
ACGTcount: A:0.24, C:0.01, G:0.12, T:0.63
Consensus pattern (49 bp):
TTTTTTATGTAATTTATTTGGCATGTGTATTTTAGATTGATTAAATATA
Found at i:20409890 original size:14 final size:14
Alignment explanation
Indices: 20409871--20409905 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
20409861 GACATTTTTT
* *
20409871 TTCTAATGATATTA
1 TTCTAACGATACTA
20409885 TTCTAACGATACTA
1 TTCTAACGATACTA
20409899 TTCTAAC
1 TTCTAAC
20409906 ATGTAATTTG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.34, C:0.17, G:0.06, T:0.43
Consensus pattern (14 bp):
TTCTAACGATACTA
Found at i:20411126 original size:14 final size:14
Alignment explanation
Indices: 20411107--20411135 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
20411097 TGGAACAAAC
20411107 TTTGTAATATAAAT
1 TTTGTAATATAAAT
20411121 TTTGTAATATAAAT
1 TTTGTAATATAAAT
20411135 T
1 T
20411136 AAATACATTG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.07, T:0.52
Consensus pattern (14 bp):
TTTGTAATATAAAT
Found at i:20411164 original size:62 final size:62
Alignment explanation
Indices: 20411016--20411184 Score: 218
Period size: 62 Copynumber: 2.7 Consensus size: 62
20411006 AATTAGATTA
* ** *
20411016 ATTACAATATTAAAACTTGGAACAAACTTTGTTGTCATAAATTAATTAATTGCAACATTATAAC
1 ATTACAACATTAAAACTTGGAACAAACTTTGTAAT-ATAAATTAATTAATT-CAACATTAAAAC
*
20411080 ATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATT-TTGTAATAT-AA-ATTAAATAC
1 ATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTAAT-TAAT-TCAACATTAAA-AC
*
20411142 ATTGCAACATTAAAACTTGGAACAAACTTTGTAATATAAATTA
1 ATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTA
20411185 GGTACGTTGG
Statistics
Matches: 95, Mismatches: 6, Indels: 9
0.86 0.05 0.08
Matches are distributed among these distances:
61 5 0.05
62 46 0.48
63 11 0.12
64 33 0.35
ACGTcount: A:0.46, C:0.11, G:0.08, T:0.35
Consensus pattern (62 bp):
ATTACAACATTAAAACTTGGAACAAACTTTGTAATATAAATTAATTAATTCAACATTAAAAC
Found at i:20415715 original size:21 final size:21
Alignment explanation
Indices: 20415667--20415715 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
20415657 AACAGTTTTA
*
20415667 ATAACGAAAGGACTTGATGAT
1 ATAACGTAAGGACTTGATGAT
20415688 ATAACGTAAGGACTTGATGAT
1 ATAACGTAAGGACTTGATGAT
20415709 ATAACGT
1 ATAACGT
20415716 CAATAGTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.41, C:0.10, G:0.22, T:0.27
Consensus pattern (21 bp):
ATAACGTAAGGACTTGATGAT
Found at i:20417538 original size:49 final size:49
Alignment explanation
Indices: 20417466--20417563 Score: 196
Period size: 49 Copynumber: 2.0 Consensus size: 49
20417456 GTCATATAGG
20417466 CCTTATAAATAACAGTGTTGGTTTTATGACACAAAGAGAGCGTGTGGTC
1 CCTTATAAATAACAGTGTTGGTTTTATGACACAAAGAGAGCGTGTGGTC
20417515 CCTTATAAATAACAGTGTTGGTTTTATGACACAAAGAGAGCGTGTGGTC
1 CCTTATAAATAACAGTGTTGGTTTTATGACACAAAGAGAGCGTGTGGTC
20417564 TTGTGGCAAG
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.31, C:0.14, G:0.24, T:0.31
Consensus pattern (49 bp):
CCTTATAAATAACAGTGTTGGTTTTATGACACAAAGAGAGCGTGTGGTC
Found at i:20420484 original size:20 final size:19
Alignment explanation
Indices: 20420456--20420541 Score: 84
Period size: 20 Copynumber: 4.3 Consensus size: 19
20420446 TTTTAAAATA
*
20420456 AAGTGAAAATGATTTTAACC
1 AAGTCAAAATGATTTTAA-C
*
20420476 AAGTCAAAATGATTTTCATC
1 AAGTCAAAATGATTTT-AAC
* *
20420496 AAGTTAAAATCATTTTAAC
1 AAGTCAAAATGATTTTAAC
20420515 ATA-TCAAAATGATTTTCAAAC
1 A-AGTCAAAATGATTTT--AAC
20420536 AAGTCA
1 AAGTCA
20420542 GAATTGCTCT
Statistics
Matches: 54, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
19 14 0.26
20 32 0.59
21 8 0.15
ACGTcount: A:0.45, C:0.13, G:0.09, T:0.33
Consensus pattern (19 bp):
AAGTCAAAATGATTTTAAC
Found at i:20420530 original size:39 final size:40
Alignment explanation
Indices: 20420456--20420532 Score: 113
Period size: 39 Copynumber: 1.9 Consensus size: 40
20420446 TTTTAAAATA
*
20420456 AAGTGAAAATGATTTTAACCAAGTCAAAATGATTTTCATC
1 AAGTGAAAATCATTTTAACCAAGTCAAAATGATTTTCATC
*
20420496 AAGTTAAAATCATTTTAA-CATA-TCAAAATGATTTTCA
1 AAGTGAAAATCATTTTAACCA-AGTCAAAATGATTTTCA
20420533 AACAAGTCAG
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
39 17 0.50
40 17 0.50
ACGTcount: A:0.44, C:0.12, G:0.09, T:0.35
Consensus pattern (40 bp):
AAGTGAAAATCATTTTAACCAAGTCAAAATGATTTTCATC
Found at i:20420539 original size:40 final size:40
Alignment explanation
Indices: 20420456--20420539 Score: 109
Period size: 40 Copynumber: 2.1 Consensus size: 40
20420446 TTTTAAAATA
* *
20420456 AAGTGAAAATGATTTTAACCAAGTCAAAATGATTTTCATC
1 AAGTGAAAATCATTTTAACCAAGTCAAAATGATTTTCAAC
*
20420496 AAGTTAAAATCATTTTAA-CATA-TCAAAATGATTTTCAAAC
1 AAGTGAAAATCATTTTAACCA-AGTCAAAATGATTTTC-AAC
20420536 AAGT
1 AAGT
20420540 CAGAATTGCT
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
39 16 0.41
40 23 0.59
ACGTcount: A:0.45, C:0.12, G:0.10, T:0.33
Consensus pattern (40 bp):
AAGTGAAAATCATTTTAACCAAGTCAAAATGATTTTCAAC
Found at i:20423230 original size:2 final size:2
Alignment explanation
Indices: 20423223--20423256 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
20423213 TAGGGTAAAA
20423223 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
20423257 TATTTTGAGG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20424459 original size:44 final size:45
Alignment explanation
Indices: 20424369--20424497 Score: 152
Period size: 44 Copynumber: 2.8 Consensus size: 45
20424359 GACAGAACGA
*
20424369 AATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGG
* *
20424415 ATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGG
1 AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
* ** * * *
20424459 AATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 AATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
20424498 CAGGATATTG
Statistics
Matches: 70, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
44 36 0.51
45 1 0.01
46 33 0.47
ACGTcount: A:0.34, C:0.14, G:0.24, T:0.28
Consensus pattern (45 bp):
AATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGG
Found at i:20443370 original size:40 final size:40
Alignment explanation
Indices: 20443242--20443393 Score: 164
Period size: 40 Copynumber: 3.8 Consensus size: 40
20443232 ATCACGATTT
* * * * *
20443242 GCACAAATGCCTTCGGGTCTTAGCCCAGATTTAACAACTT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAACTACTA
*
20443282 GCACGAA-TGCCTTCGGGTCTTAGCCCGGATATAGCTACTA
1 GCAC-AATTGCCTTCGGGTCTTAGCCCGGATATAACTACTA
* * *
20443322 GCACAATTGCCTTCGGGTCTTAACCCGGATATAAAT-TTCA
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATATAACTACT-A
* * *
20443362 GCATAATTGTCTTCGGGGCTTAGCCCGGATAT
1 GCACAATTGCCTTCGGGTCTTAGCCCGGATAT
20443394 CATTCAATTT
Statistics
Matches: 96, Mismatches: 13, Indels: 6
0.83 0.11 0.05
Matches are distributed among these distances:
39 3 0.03
40 91 0.95
41 2 0.02
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (40 bp):
GCACAATTGCCTTCGGGTCTTAGCCCGGATATAACTACTA
Found at i:20454595 original size:18 final size:19
Alignment explanation
Indices: 20454568--20454603 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
20454558 ATCAATACCG
20454568 TTTTAAAAA-TATTGATAA
1 TTTTAAAAATTATTGATAA
*
20454586 TTTTATAAATTATTGATA
1 TTTTAAAAATTATTGATA
20454604 CTCATGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (19 bp):
TTTTAAAAATTATTGATAA
Found at i:20454601 original size:19 final size:18
Alignment explanation
Indices: 20454568--20454603 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
20454558 ATCAATACCG
20454568 TTTTAAAAATATTGATAA
1 TTTTAAAAATATTGATAA
*
20454586 TTTTATAAATTATTGATA
1 TTTTA-AAAATATTGATA
20454604 CTCATGAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.44, C:0.00, G:0.06, T:0.50
Consensus pattern (18 bp):
TTTTAAAAATATTGATAA
Found at i:20455624 original size:22 final size:22
Alignment explanation
Indices: 20455599--20455649 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 22
20455589 TAGCAATAAG
* * *
20455599 GTGCTATATAGAGAGCACGGAT
1 GTGCTAAACAGAGAGCACGAAT
*
20455621 GTGCTAAACAGAGAGCACTAAT
1 GTGCTAAACAGAGAGCACGAAT
20455643 GTGCTAA
1 GTGCTAA
20455650 TAATCAGATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.35, C:0.16, G:0.27, T:0.22
Consensus pattern (22 bp):
GTGCTAAACAGAGAGCACGAAT
Found at i:20460258 original size:35 final size:35
Alignment explanation
Indices: 20460219--20460313 Score: 172
Period size: 35 Copynumber: 2.7 Consensus size: 35
20460209 GTATGGATTT
*
20460219 GATAATACCATACCTACATTTCACAGCTCAGTATG
1 GATAATACCATACCTACATTTCACAACTCAGTATG
20460254 GATAATACCATACCTACATTTCACAACTCAGTATG
1 GATAATACCATACCTACATTTCACAACTCAGTATG
*
20460289 GATGATACCATACCTACATTTCACA
1 GATAATACCATACCTACATTTCACA
20460314 CTTTGCCATG
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 58 1.00
ACGTcount: A:0.36, C:0.26, G:0.09, T:0.28
Consensus pattern (35 bp):
GATAATACCATACCTACATTTCACAACTCAGTATG
Found at i:20461708 original size:20 final size:20
Alignment explanation
Indices: 20461683--20461753 Score: 81
Period size: 20 Copynumber: 3.5 Consensus size: 20
20461673 GGCCGTTACA
20461683 TTCAATCAAGTCAAAATGAT
1 TTCAATCAAGTCAAAATGAT
* *
20461703 TTCAATCAAGTTAAAATCAT
1 TTCAATCAAGTCAAAATGAT
* *
20461723 TTTAA-CACGTCAAAATGATT
1 TTCAATCAAGTCAAAATGA-T
*
20461743 TTCAAACAAGT
1 TTCAATCAAGT
20461754 TAGAATTGCT
Statistics
Matches: 41, Mismatches: 8, Indels: 3
0.79 0.15 0.06
Matches are distributed among these distances:
19 10 0.24
20 27 0.66
21 4 0.10
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.32
Consensus pattern (20 bp):
TTCAATCAAGTCAAAATGAT
Found at i:20465184 original size:16 final size:16
Alignment explanation
Indices: 20465163--20465198 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 16
20465153 TAGTAGACAT
20465163 TATAATAT-AGTTAACA
1 TATAATATCA-TTAACA
20465179 TATAATATCATTAACA
1 TATAATATCATTAACA
20465195 TATA
1 TATA
20465199 TGAAATTACA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 18 0.95
17 1 0.05
ACGTcount: A:0.50, C:0.08, G:0.03, T:0.39
Consensus pattern (16 bp):
TATAATATCATTAACA
Found at i:20466274 original size:20 final size:20
Alignment explanation
Indices: 20466249--20466286 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20466239 GTTTATTCAC
*
20466249 GATTTTCAATATTTTGTAAA
1 GATTTTCAAAATTTTGTAAA
*
20466269 GATTTTTAAAATTTTGTA
1 GATTTTCAAAATTTTGTA
20466287 TTTGGATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.53
Consensus pattern (20 bp):
GATTTTCAAAATTTTGTAAA
Found at i:20467944 original size:28 final size:28
Alignment explanation
Indices: 20467912--20467980 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
20467902 GCGTAGATCA
20467912 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
20467940 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
20467968 CGATA-TACCCCTA
1 CGAAATTACCCCTA
20467981 GGGTTTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 8 0.20
28 32 0.80
ACGTcount: A:0.43, C:0.28, G:0.10, T:0.19
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:20474277 original size:20 final size:20
Alignment explanation
Indices: 20474252--20474289 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
20474242 GTTTATTCGC
*
20474252 GATTTTCAATATTTTGTAAA
1 GATTTTCAAAATTTTGTAAA
*
20474272 GATTTTTAAAATTTTGTA
1 GATTTTCAAAATTTTGTA
20474290 TTTGGATGTG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.53
Consensus pattern (20 bp):
GATTTTCAAAATTTTGTAAA
Found at i:20475949 original size:28 final size:28
Alignment explanation
Indices: 20475917--20475985 Score: 122
Period size: 28 Copynumber: 2.5 Consensus size: 28
20475907 GCGTAGATCA
20475917 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
20475945 CGAAATTACCCCTAAAGAGCAAAATTAC
1 CGAAATTACCCCTAAAGAGCAAAATTAC
*
20475973 CGATA-TACCCCTA
1 CGAAATTACCCCTA
20475986 GGGTTTTAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 1
0.95 0.02 0.02
Matches are distributed among these distances:
27 8 0.20
28 32 0.80
ACGTcount: A:0.43, C:0.28, G:0.10, T:0.19
Consensus pattern (28 bp):
CGAAATTACCCCTAAAGAGCAAAATTAC
Found at i:20479222 original size:58 final size:57
Alignment explanation
Indices: 20479103--20479222 Score: 154
Period size: 57 Copynumber: 2.1 Consensus size: 57
20479093 TTCTCATTTT
* *
20479103 CATTTTCATTTCCATTTTGGAGAAAACCACATTCATTTCCAAATGATTTTATTTCTC
1 CATTTTCATTTCCATTTTAGAGAAAACCACAATCATTTCCAAATGATTTTATTTCTC
* **
20479160 CATTTTCATTTTCC-TTTTAGAGATAACCTTAATCATTTCCAAATG-TTTCATATTTCTC
1 CATTTTCA-TTTCCATTTTAGAGAAAACCACAATCATTTCCAAATGATTT--TATTTCTC
20479218 CATTT
1 CATTT
20479223 CACCATTTCT
Statistics
Matches: 55, Mismatches: 5, Indels: 5
0.85 0.08 0.08
Matches are distributed among these distances:
56 3 0.05
57 34 0.62
58 18 0.33
ACGTcount: A:0.27, C:0.21, G:0.06, T:0.47
Consensus pattern (57 bp):
CATTTTCATTTCCATTTTAGAGAAAACCACAATCATTTCCAAATGATTTTATTTCTC
Found at i:20485028 original size:28 final size:28
Alignment explanation
Indices: 20484996--20485110 Score: 131
Period size: 29 Copynumber: 4.0 Consensus size: 28
20484986 TACCTGTATC
*
20484996 TGGCCCATTAAGCCCAATCATATTCATA
1 TGGCCCATTAAGCCCAATCACATTCATA
* * * *
20485024 TGGCCCATTAGGTCCAAATCACCTGCATA
1 TGGCCCATTAAG-CCCAATCACATTCATA
* *
20485053 TGGCCCATTAGGCCCAAATCACATTTATA
1 TGGCCCATTAAGCCC-AATCACATTCATA
* *
20485082 TGGCCCATTAAGCCTAGTCACATTCATA
1 TGGCCCATTAAGCCCAATCACATTCATA
20485110 T
1 T
20485111 TCATGCTCAC
Statistics
Matches: 72, Mismatches: 13, Indels: 4
0.81 0.15 0.04
Matches are distributed among these distances:
28 25 0.35
29 47 0.65
ACGTcount: A:0.30, C:0.29, G:0.14, T:0.28
Consensus pattern (28 bp):
TGGCCCATTAAGCCCAATCACATTCATA
Found at i:20485362 original size:16 final size:16
Alignment explanation
Indices: 20485321--20485363 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
20485311 GTAGCCAAAC
20485321 TTTCGGCTTTTCAGCA
1 TTTCGGCTTTTCAGCA
** *
20485337 TTTCAACTTTTCGGCA
1 TTTCGGCTTTTCAGCA
20485353 TTTCGGCTTTT
1 TTTCGGCTTTT
20485364 ACCGATACAT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.12, C:0.23, G:0.16, T:0.49
Consensus pattern (16 bp):
TTTCGGCTTTTCAGCA
Found at i:20486481 original size:16 final size:16
Alignment explanation
Indices: 20486440--20486487 Score: 53
Period size: 16 Copynumber: 3.0 Consensus size: 16
20486430 AAATTCAAGA
* *
20486440 TTTCGGGGTTTTTGGAA
1 TTTCGGGATTTTTGG-G
*
20486457 TTT-GAGATTTTTGGG
1 TTTCGGGATTTTTGGG
20486472 TTTCGGGATTTTTGGG
1 TTTCGGGATTTTTGGG
20486488 GCATTACATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 3 0.12
16 20 0.77
17 3 0.12
ACGTcount: A:0.10, C:0.04, G:0.35, T:0.50
Consensus pattern (16 bp):
TTTCGGGATTTTTGGG
Found at i:20487871 original size:30 final size:30
Alignment explanation
Indices: 20487831--20487887 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
20487821 AGACTAATTA
* *
20487831 CACACGGGCTGAG-CACACGCCCGTGTGAGG
1 CACACAGGCTG-GCCACACGCCCATGTGAGG
20487861 CACACAGGCTGGCCACACGCCCATGTG
1 CACACAGGCTGGCCACACGCCCATGTG
20487888 GCAGCCCGTG
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 1 0.04
30 23 0.96
ACGTcount: A:0.21, C:0.37, G:0.32, T:0.11
Consensus pattern (30 bp):
CACACAGGCTGGCCACACGCCCATGTGAGG
Found at i:20490467 original size:166 final size:167
Alignment explanation
Indices: 20490184--20490517 Score: 467
Period size: 166 Copynumber: 2.0 Consensus size: 167
20490174 CTTCACATAG
** * * * *
20490184 ACACTACGAGTTTCTAGCAATGTTGTTTGGGCTAACCAATGCCCAATCCACTTTTATGGATTTGA
1 ACACTACGAGTTTCTAGCAATGTCATTTGGACCAACCAACGCCCAATCCACTTTTATGGATCTGA
* * * * *
20490249 TGAACATAATTTTTCATTTGTATCTTTATAGATTTTTTGTTGTGTTCATAGATTATATATTTATC
66 TGAACATAATTTTTCATTTGTATCTTGATAAATTTGTTGTTGTGTTCATAGATGATATATTAATC
20490314 TACTC-AAAAAATAAAAATGATCATGATCAGCATCTA
131 TACTCAAAAAAATAAAAATGATCATGATCAGCATCTA
* * *
20490350 ACACTAGGGGTTTCTAGTAATGTCATTTGGACCAACCAACGCCCAATCCACTTTTATGGATCTGA
1 ACACTACGAGTTTCTAGCAATGTCATTTGGACCAACCAACGCCCAATCCACTTTTATGGATCTGA
*
20490415 TGAACATAATTTTTCATGTT-TAT-TTGGATAAATTTGTTGTTGTTTTCATAGATGATATATTAA
66 TGAACATAATTTTTCAT-TTGTATCTT-GATAAATTTGTTGTTGTGTTCATAGATGATATATTAA
* * *
20490478 TCTACTCAAAAAAATGAAAATGATCATGATTAGTATCTA
129 TCTACTCAAAAAAATAAAAATGATCATGATCAGCATCTA
20490517 A
1 A
20490518 GAGTTTTACT
Statistics
Matches: 147, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
165 2 0.01
166 114 0.78
167 31 0.21
ACGTcount: A:0.32, C:0.15, G:0.14, T:0.39
Consensus pattern (167 bp):
ACACTACGAGTTTCTAGCAATGTCATTTGGACCAACCAACGCCCAATCCACTTTTATGGATCTGA
TGAACATAATTTTTCATTTGTATCTTGATAAATTTGTTGTTGTGTTCATAGATGATATATTAATC
TACTCAAAAAAATAAAAATGATCATGATCAGCATCTA
Found at i:20490705 original size:162 final size:163
Alignment explanation
Indices: 20490437--20490766 Score: 608
Period size: 162 Copynumber: 2.0 Consensus size: 163
20490427 TTCATGTTTA
20490437 TTTGGATAAATTTGTTGTTGTTTTCATAGATGATATATTAATCTACTCAAAAAAATGAAAATGAT
1 TTTGGATAAATTTGTTGTTGTTTTCATAGATGATATATTAATCTACTCAAAAAAATGAAAATGAT
*
20490502 CATGATTAGTATCTAAGAGTTTTACTACAAACCTTGCAAGAAAAATAATTGTTTTCAAAAGTCTA
66 CATGATTAGTATCTAAGAGTTTTACAACAAACCTTGCAAGAAAAATAATTGTTTTCAAAAGTCTA
20490567 CAAATGTGAGTTCTGGCTACGAGAAGTGAGATT
131 CAAATGTGAGTTCTGGCTACGAGAAGTGAGATT
*
20490600 TTTGGATAAATTTGTTTTTGTTTTCATAGATGATATATTAATCTACTC-AAAAAATGAAAATGAT
1 TTTGGATAAATTTGTTGTTGTTTTCATAGATGATATATTAATCTACTCAAAAAAATGAAAATGAT
*
20490664 CATGATTAGTATCTAATAGTTTTACAACAAACCTTGCAAGAAAAATAATTGTTTTCAAAAGTCTA
66 CATGATTAGTATCTAAGAGTTTTACAACAAACCTTGCAAGAAAAATAATTGTTTTCAAAAGTCTA
* *
20490729 CAAATGTGAGTTTTGGCTACGAGAAGTGGGATT
131 CAAATGTGAGTTCTGGCTACGAGAAGTGAGATT
20490762 TTTGG
1 TTTGG
20490767 GTTACCTAAT
Statistics
Matches: 162, Mismatches: 5, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
162 115 0.71
163 47 0.29
ACGTcount: A:0.37, C:0.10, G:0.17, T:0.37
Consensus pattern (163 bp):
TTTGGATAAATTTGTTGTTGTTTTCATAGATGATATATTAATCTACTCAAAAAAATGAAAATGAT
CATGATTAGTATCTAAGAGTTTTACAACAAACCTTGCAAGAAAAATAATTGTTTTCAAAAGTCTA
CAAATGTGAGTTCTGGCTACGAGAAGTGAGATT
Found at i:20494391 original size:19 final size:19
Alignment explanation
Indices: 20494367--20494403 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
20494357 TCTATAAATA
20494367 TCAGCTTGTGTGAGCAATG
1 TCAGCTTGTGTGAGCAATG
20494386 TCAGCTTGTGTGAGCAAT
1 TCAGCTTGTGTGAGCAAT
20494404 ATAGTCTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.22, C:0.16, G:0.30, T:0.32
Consensus pattern (19 bp):
TCAGCTTGTGTGAGCAATG
Found at i:20504294 original size:12 final size:12
Alignment explanation
Indices: 20504277--20504303 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
20504267 GTCATACACA
20504277 GCCTACCACATG
1 GCCTACCACATG
20504289 GCCTACCACATG
1 GCCTACCACATG
20504301 GCC
1 GCC
20504304 GTGTGGTGTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.44, G:0.19, T:0.15
Consensus pattern (12 bp):
GCCTACCACATG
Found at i:20508932 original size:30 final size:31
Alignment explanation
Indices: 20508898--20508958 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 31
20508888 GGTAATAGTT
*
20508898 AGAGGTTT-TGGGGTTCTAAGGGCGTCCTAA
1 AGAGGTTTACGGGGTTCTAAGGGCGTCCTAA
20508928 AGAGGTTTACGGGGTTCTAAGGGCGTCCTAA
1 AGAGGTTTACGGGGTTCTAAGGGCGTCCTAA
20508959 GGGAAATCTT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 8 0.28
31 21 0.72
ACGTcount: A:0.21, C:0.15, G:0.36, T:0.28
Consensus pattern (31 bp):
AGAGGTTTACGGGGTTCTAAGGGCGTCCTAA
Found at i:20514046 original size:20 final size:20
Alignment explanation
Indices: 20514008--20514048 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
20513998 CATGAACAAT
**
20514008 TTTGTGCCTACTAACACTAA
1 TTTGTGCCTAAAAACACTAA
*
20514028 TTTGTGCCTAAAAAGACTAA
1 TTTGTGCCTAAAAACACTAA
20514048 T
1 T
20514049 GGCTGATGCA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.34, C:0.20, G:0.12, T:0.34
Consensus pattern (20 bp):
TTTGTGCCTAAAAACACTAA
Found at i:20518933 original size:28 final size:29
Alignment explanation
Indices: 20518897--20518961 Score: 123
Period size: 29 Copynumber: 2.3 Consensus size: 29
20518887 GCATGTGGCT
20518897 AGGCCGTGTGAGCCACA-GGGCATGTGAG
1 AGGCCGTGTGAGCCACACGGGCATGTGAG
20518925 AGGCCGTGTGAGCCACACGGGCATGTGAG
1 AGGCCGTGTGAGCCACACGGGCATGTGAG
20518954 AGGCCGTG
1 AGGCCGTG
20518962 CGACTGGCCG
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
28 17 0.47
29 19 0.53
ACGTcount: A:0.20, C:0.23, G:0.43, T:0.14
Consensus pattern (29 bp):
AGGCCGTGTGAGCCACACGGGCATGTGAG
Found at i:20531203 original size:25 final size:26
Alignment explanation
Indices: 20531163--20531214 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 26
20531153 TTTATTTTAT
*
20531163 TTTGGGTTTTATTTTTGTTTTATTGG
1 TTTGGGTTTTATTTTTGGTTTATTGG
*
20531189 TTTGGG-TTTATTTTTGGTTTGTTGG
1 TTTGGGTTTTATTTTTGGTTTATTGG
20531214 T
1 T
20531215 CTGAGCCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
25 18 0.75
26 6 0.25
ACGTcount: A:0.06, C:0.00, G:0.27, T:0.67
Consensus pattern (26 bp):
TTTGGGTTTTATTTTTGGTTTATTGG
Found at i:20531694 original size:44 final size:43
Alignment explanation
Indices: 20531629--20532105 Score: 235
Period size: 44 Copynumber: 10.7 Consensus size: 43
20531619 CTATTTTTAG
*
20531629 TCTGTTCCACTGCAACTTCAGGGAGATAAGACCTGTAACTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCTGT-ACTTCAA
* * * * *
20531673 -CTTGCTCCACTGCATCTTCAGGAAGATAGGACTTGTACTTTAA
1 TC-TGCTCCACTGCAACTTCAGGGAGATAAGACCTGTACTTCAA
* * * **
20531716 TCTGCTCCACTGTAACTTTAGGGAGATAAGATTCACCATGGTAGATTTGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAG----ACC-T-GTA-CTTCAA
* ** * * *** * *
20531766 TCTGAC-CTACTGCGGCTTCAGAGG-TATAGGGTTTATAGCTTTAA
1 TCTG-CTCCACTGCAACTTCAG-GGAGATAAGACCTGTA-CTTCAA
* * * * * ** * *
20531810 TCTACTCTACTGCAACCTGAGAGAGATAAGATTTGCTATTTTCAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCTG-TA-CTTCAA
* * *
20531855 TCTGTTCCACTGCAACTTCAGGGAGATAAAACTTGTAACTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCTGT-ACTTCAA
* * * * *
20531899 CCCGCTCCACTGCATCTTCAGGGAGATAGGACTTGTACTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCTGTACTTCAA
* * *** *
20531942 CCTGCCCCACTGCAACTTCAGGG-GATAAGGTTTGCTATCTTCGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCTG-TA-CTTCAA
* * * *
20531986 TCTGTTCCACTGCAACTTCAGGAATATAAGATCTGTGACTTCAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCTGT-ACTTCAA
* * ** *
20532030 TCTGCTCCGCTGCAACTTCAGAGAGATAAGATTTACG-ACTTAAAA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACCT--GTACTT-CAA
* *
20532075 TATGCTCTACTGCAACTTCAGGGAGATAAGA
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGA
20532106 TTCACTATGG
Statistics
Matches: 328, Mismatches: 83, Indels: 43
0.72 0.18 0.09
Matches are distributed among these distances:
42 8 0.02
43 61 0.19
44 155 0.47
45 72 0.22
46 1 0.00
47 2 0.01
48 1 0.00
49 3 0.01
50 22 0.07
51 3 0.01
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.30
Consensus pattern (43 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACCTGTACTTCAA
Found at i:20531802 original size:226 final size:226
Alignment explanation
Indices: 20531407--20531970 Score: 828
Period size: 226 Copynumber: 2.5 Consensus size: 226
20531397 TTTGATTTAC
* * * * *
20531407 TCCACTGCAACTTCAGAGAGATAAGA-ATCGTAACTTCAACCTGCTCTACTACAACTTTAGGGAG
1 TCCACTGCAACTTCAGGGAGATAAGACAT-GTAACTTCAACCTGCTCCACTGCATCTTCAGGGAG
* * * * **
20531471 ATGAGG-TTTGTGACTTTAATCTGCTCCATTGCAACTTCAGGAAGATAAAATTTGCCATGGTAGA
65 AT-AGGACTTGT-ACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCACCATGGTAGA
*
20531535 TTTGATCTGACCTACTACGACTTCAGAGGTATAGGGTTTATAGCTTTAATCTACTCTATTGCAAC
128 TTTGATCTGACCTACTACGACTTCAGAGGTATAGGGTTTATAGCTTTAATCTACTCTACTGCAAC
* *
20531600 TTCAGAGAGATAAGATTTGCTATTTTTAGTCTGT
193 CTCAGAGAGATAAGATTTGCTATTTTCAGTCTGT
* * *
20531634 TCCACTGCAACTTCAGGGAGATAAGACCTGTAACTTCAACTTGCTCCACTGCATCTTCAGGAAGA
1 TCCACTGCAACTTCAGGGAGATAAGACATGTAACTTCAACCTGCTCCACTGCATCTTCAGGGAGA
* *
20531699 TAGGACTTGTACTTTAATCTGCTCCACTGTAACTTTAGGGAGATAAGATTCACCATGGTAGATTT
66 TAGGACTTGTACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCACCATGGTAGATTT
* * *
20531764 GATCTGACCTACTGCGGCTTCAGAGGTATAGGGTTTATAGCTTTAATCTACTCTACTGCAACCTG
131 GATCTGACCTACTACGACTTCAGAGGTATAGGGTTTATAGCTTTAATCTACTCTACTGCAACCTC
20531829 AGAGAGATAAGATTTGCTATTTTCAGTCTGT
196 AGAGAGATAAGATTTGCTATTTTCAGTCTGT
* * *
20531860 TCCACTGCAACTTCAGGGAGATAAAACTTGTAACTTCAACCCGCTCCACTGCATCTTCAGGGAGA
1 TCCACTGCAACTTCAGGGAGATAAGACATGTAACTTCAACCTGCTCCACTGCATCTTCAGGGAGA
* * *
20531925 TAGGACTTGTACTTCAACCTGCCCCACTGCAACTTCAGGG-GATAAG
66 TAGGACTTGTACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAG
20531971 GTTTGCTATC
Statistics
Matches: 303, Mismatches: 32, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
225 6 0.02
226 236 0.78
227 60 0.20
228 1 0.00
ACGTcount: A:0.28, C:0.21, G:0.20, T:0.31
Consensus pattern (226 bp):
TCCACTGCAACTTCAGGGAGATAAGACATGTAACTTCAACCTGCTCCACTGCATCTTCAGGGAGA
TAGGACTTGTACTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCACCATGGTAGATTT
GATCTGACCTACTACGACTTCAGAGGTATAGGGTTTATAGCTTTAATCTACTCTACTGCAACCTC
AGAGAGATAAGATTTGCTATTTTCAGTCTGT
Found at i:20540279 original size:12 final size:12
Alignment explanation
Indices: 20540264--20540290 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
20540254 CTCCTGCATC
20540264 TGCGTTTGTAAT
1 TGCGTTTGTAAT
20540276 TGCGTTTGTAAT
1 TGCGTTTGTAAT
20540288 TGC
1 TGC
20540291 TCTTGCATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.15, C:0.11, G:0.26, T:0.48
Consensus pattern (12 bp):
TGCGTTTGTAAT
Found at i:20545640 original size:25 final size:26
Alignment explanation
Indices: 20545605--20545661 Score: 80
Period size: 25 Copynumber: 2.2 Consensus size: 26
20545595 TTTATTTTAT
*
20545605 TTTGGGTTTTATTTTTGTTTTATTGG
1 TTTGGGTTTTATTTTTGGTTTATTGG
*
20545631 TTTGGG-TTTATTTTTGGTTTGTTGG
1 TTTGGGTTTTATTTTTGGTTTATTGG
*
20545656 TCTGGG
1 TTTGGG
20545662 CCAAAATTGG
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
25 22 0.79
26 6 0.21
ACGTcount: A:0.05, C:0.02, G:0.30, T:0.63
Consensus pattern (26 bp):
TTTGGGTTTTATTTTTGGTTTATTGG
Found at i:20547350 original size:12 final size:11
Alignment explanation
Indices: 20547313--20547348 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
20547303 AAATAAATAC
*
20547313 AATAATAAAGG
1 AATAATAAAGA
20547324 AATAATAAATGA
1 AATAATAAA-GA
20547336 AATAATAAAGA
1 AATAATAAAGA
20547347 AA
1 AA
20547349 ATTCTAGTGA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.69, C:0.00, G:0.11, T:0.19
Consensus pattern (11 bp):
AATAATAAAGA
Found at i:20547438 original size:3 final size:3
Alignment explanation
Indices: 20547430--20547620 Score: 146
Period size: 3 Copynumber: 65.7 Consensus size: 3
20547420 ATGGTTTAAA
* * * *
20547430 AAT AAT AAT GAT AAT AAT AAT AAT AGT AAT AAT AAT AAT CAT ACT -AT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * ** * *
20547477 AAT GAT AGT AAT AAT GGT AA- AAT AAT AAT AAT GAT AAT AAT AA- AAA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * * * *
20547523 AAT -AT AA- AAA AAT TAG CA- AAT GAT AAT AAT AAT ATT GAT AAT AAAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AAT
*
20547569 AAT AAT AGT AA- AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AACT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA-T
20547614 AA- AAT AA
1 AAT AAT AA
20547621 CTAAAAAGGA
Statistics
Matches: 146, Mismatches: 32, Indels: 20
0.74 0.16 0.10
Matches are distributed among these distances:
2 14 0.10
3 126 0.86
4 6 0.04
ACGTcount: A:0.62, C:0.02, G:0.06, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:20553354 original size:21 final size:21
Alignment explanation
Indices: 20553328--20553368 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
20553318 CTTAACAGGA
20553328 TAGCTGACATGGCCAGTTAAT
1 TAGCTGACATGGCCAGTTAAT
**
20553349 TAGCTGATGTGGCCAGTTAA
1 TAGCTGACATGGCCAGTTAA
20553369 CTTGCCACGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.29
Consensus pattern (21 bp):
TAGCTGACATGGCCAGTTAAT
Found at i:20559333 original size:21 final size:21
Alignment explanation
Indices: 20559309--20559349 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
20559299 ACGTGACAAG
*
20559309 TTAACTGGCCACGTCAGCTAA
1 TTAACTAGCCACGTCAGCTAA
*
20559330 TTAACTAGCCATGTCAGCTA
1 TTAACTAGCCACGTCAGCTA
20559350 TTCCGTTAAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (21 bp):
TTAACTAGCCACGTCAGCTAA
Found at i:20559447 original size:30 final size:32
Alignment explanation
Indices: 20559380--20559447 Score: 79
Period size: 31 Copynumber: 2.2 Consensus size: 32
20559370 AAAACGTTAA
20559380 TGAGTGACTGATTTGTCAGTTTTTAATAACGT
1 TGAGTGACTGATTTGTCAGTTTTTAATAACGT
* * * *
20559412 T-AGTGACTGTTTTGTTATTTTTTCA-AA-GT
1 TGAGTGACTGATTTGTCAGTTTTTAATAACGT
20559441 TGAGTGA
1 TGAGTGA
20559448 TTGAAATGAA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
29 3 0.10
30 7 0.23
31 20 0.65
32 1 0.03
ACGTcount: A:0.24, C:0.07, G:0.22, T:0.47
Consensus pattern (32 bp):
TGAGTGACTGATTTGTCAGTTTTTAATAACGT
Found at i:20560015 original size:12 final size:12
Alignment explanation
Indices: 20559998--20560030 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
20559988 CGACCCTTCC
20559998 ATATTAATTTTT
1 ATATTAATTTTT
20560010 ATATT-ATTTTT
1 ATATTAATTTTT
20560021 ATA-TAATTTT
1 ATATTAATTTT
20560031 AAAATATATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
10 1 0.05
11 14 0.70
12 5 0.25
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (12 bp):
ATATTAATTTTT
Found at i:20560291 original size:22 final size:22
Alignment explanation
Indices: 20560243--20560291 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
20560233 ATATCCAAAC
*
20560243 AATAACAACAAAATAGTAGCAA
1 AATAACAACAAAATAGTAACAA
* * * *
20560265 CATAATAATAAAATGGTAACAA
1 AATAACAACAAAATAGTAACAA
20560287 AATAA
1 AATAA
20560292 GGAGAAAACA
Statistics
Matches: 21, Mismatches: 6, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.63, C:0.10, G:0.08, T:0.18
Consensus pattern (22 bp):
AATAACAACAAAATAGTAACAA
Found at i:20566747 original size:5 final size:5
Alignment explanation
Indices: 20566731--20566760 Score: 51
Period size: 5 Copynumber: 5.8 Consensus size: 5
20566721 AAATTACTAA
20566731 GCCCG AGCCCG GCCCG GCCCG GCCCG GCCC
1 GCCCG -GCCCG GCCCG GCCCG GCCCG GCCC
20566761 ATATTAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 19 0.79
6 5 0.21
ACGTcount: A:0.03, C:0.60, G:0.37, T:0.00
Consensus pattern (5 bp):
GCCCG
Found at i:20566844 original size:12 final size:12
Alignment explanation
Indices: 20566829--20566857 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
20566819 ATATATTTAA
20566829 AAATATTAAAAT
1 AAATATTAAAAT
20566841 AAATATTAAAAT
1 AAATATTAAAAT
20566853 AAATA
1 AAATA
20566858 AAAATAATAC
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:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AAATATTAAAAT
Found at i:20566844 original size:24 final size:24
Alignment explanation
Indices: 20566783--20566846 Score: 76
Period size: 26 Copynumber: 2.6 Consensus size: 24
20566773 TTTCTTATTT
* *
20566783 TATT-AAATAAAAAAATTTAAAAA
1 TATTAAAATAAATATATTTAAAAA
*
20566806 TATAATAAATCAAATATATTTAAAAA
1 TATTA-AAAT-AAATATATTTAAAAA
20566832 TATTAAAATAAATAT
1 TATTAAAATAAATAT
20566847 TAAAATAAAT
Statistics
Matches: 34, Mismatches: 4, Indels: 5
0.79 0.09 0.12
Matches are distributed among these distances:
23 3 0.09
24 6 0.18
25 8 0.24
26 17 0.50
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (24 bp):
TATTAAAATAAATATATTTAAAAA
Found at i:20566866 original size:21 final size:20
Alignment explanation
Indices: 20566786--20566872 Score: 61
Period size: 21 Copynumber: 4.0 Consensus size: 20
20566776 CTTATTTTAT
20566786 TAAATAAAAAAAT-TTAAAAA
1 TAAATAAAAAAATATT-AAAA
20566806 TATAATAAATCAAATATATTTAAAA
1 TA-AATAAA--AAA-ATA-TTAAAA
*
20566831 -ATATTAAAATAAATATTAAAA
1 TA-AATAAAA-AAATATTAAAA
*
20566852 TAAATAAAAATAATACTAAAA
1 TAAATAAAAA-AATATTAAAA
20566873 CAATTCTTAA
Statistics
Matches: 55, Mismatches: 3, Indels: 17
0.73 0.04 0.23
Matches are distributed among these distances:
20 3 0.05
21 27 0.49
22 5 0.09
23 5 0.09
24 9 0.16
25 4 0.07
26 2 0.04
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (20 bp):
TAAATAAAAAAATATTAAAA
Found at i:20567510 original size:28 final size:28
Alignment explanation
Indices: 20567477--20567530 Score: 74
Period size: 28 Copynumber: 1.9 Consensus size: 28
20567467 AGTGGTATAC
20567477 TTTTT-AAATAATTTGAATAATTTTTAAT
1 TTTTTAAAAT-ATTTGAATAATTTTTAAT
**
20567505 TTTTTAAAATATTTTTATAATTTTTA
1 TTTTTAAAATATTTGAATAATTTTTA
20567531 TTGAAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
28 19 0.83
29 4 0.17
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (28 bp):
TTTTTAAAATATTTGAATAATTTTTAAT
Found at i:20577597 original size:24 final size:24
Alignment explanation
Indices: 20577559--20577614 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
20577549 TCTTCCAGTT
* *
20577559 AAACTATGTTTATTTGTTTCAATC
1 AAACTCTGTTGATTTGTTTCAATC
*
20577583 ATACTCTGTTGATTTGTTTCAATC
1 AAACTCTGTTGATTTGTTTCAATC
20577607 AAACTCTG
1 AAACTCTG
20577615 ATTAGTCTAG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.27, C:0.16, G:0.11, T:0.46
Consensus pattern (24 bp):
AAACTCTGTTGATTTGTTTCAATC
Found at i:20579135 original size:2 final size:2
Alignment explanation
Indices: 20579128--20579164 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
20579118 TTATTTGTTT
20579128 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
20579165 TATTCATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:20579262 original size:3 final size:3
Alignment explanation
Indices: 20579254--20579301 Score: 87
Period size: 3 Copynumber: 15.7 Consensus size: 3
20579244 ATTTAGGCCT
20579254 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TCTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA TTA TTA
20579300 TT
1 TT
20579302 TATTTATTCA
Statistics
Matches: 44, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 41 0.93
4 3 0.07
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:20582416 original size:26 final size:26
Alignment explanation
Indices: 20582358--20582410 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
20582348 TAAATAATGC
**
20582358 TTAATTAAAATTTAAGTTTTTATACA
1 TTAATTAAAATTTAAGTTTAAATACA
20582384 TTAATTAAAATTTAA-TTTAAATTACA
1 TTAATTAAAATTTAAGTTTAAA-TACA
20582410 T
1 T
20582411 ATATTACAGA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 4 0.17
26 20 0.83
ACGTcount: A:0.45, C:0.04, G:0.02, T:0.49
Consensus pattern (26 bp):
TTAATTAAAATTTAAGTTTAAATACA
Found at i:20582897 original size:15 final size:15
Alignment explanation
Indices: 20582877--20582942 Score: 55
Period size: 14 Copynumber: 4.3 Consensus size: 15
20582867 ACTACAAAAC
20582877 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
20582892 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
20582911 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
*
20582926 A-TTAATATTAA-AT
1 ATTTATTATTAATAT
20582939 ATTT
1 ATTT
20582943 TCAACAATAT
Statistics
Matches: 42, Mismatches: 4, Indels: 11
0.74 0.07 0.19
Matches are distributed among these distances:
13 3 0.07
14 11 0.26
15 10 0.24
16 1 0.02
17 7 0.17
18 1 0.02
19 9 0.21
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:20590986 original size:13 final size:13
Alignment explanation
Indices: 20590965--20590999 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
20590955 AAATTTTTTC
*
20590965 AAAGCACTTCTCA
1 AAAGTACTTCTCA
20590978 AAAGTACTTCTCA
1 AAAGTACTTCTCA
*
20590991 AAAATACTT
1 AAAGTACTT
20591000 TTTCACAGCA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.43, C:0.23, G:0.06, T:0.29
Consensus pattern (13 bp):
AAAGTACTTCTCA
Found at i:20593467 original size:5 final size:5
Alignment explanation
Indices: 20593457--20593484 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
20593447 GGAAGATATG
20593457 ATTTT ATTTT ATTTT ATTTT ATTTT ATT
1 ATTTT ATTTT ATTTT ATTTT ATTTT ATT
20593485 ATTAAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.21, C:0.00, G:0.00, T:0.79
Consensus pattern (5 bp):
ATTTT
Found at i:20594062 original size:15 final size:15
Alignment explanation
Indices: 20594042--20594093 Score: 54
Period size: 15 Copynumber: 3.5 Consensus size: 15
20594032 TTCTAATACT
*
20594042 ATTATTTTTTATCTA
1 ATTATTATTTATCTA
20594057 ATTATTATTTATCTA
1 ATTATTATTTATCTA
* *
20594072 TTTA-TATTTCTACT-
1 ATTATTATTTAT-CTA
20594086 ATTATTAT
1 ATTATTAT
20594094 ATTTCTATTT
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
14 9 0.29
15 22 0.71
ACGTcount: A:0.29, C:0.08, G:0.00, T:0.63
Consensus pattern (15 bp):
ATTATTATTTATCTA
Found at i:20594064 original size:18 final size:21
Alignment explanation
Indices: 20594016--20594066 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
20594006 TGTTTCTATT
20594016 TATATTTATTTTGTTATTCTAA
1 TATA-TTATTTTGTTATTCTAA
20594038 TACTATTATTTT-TTA-TCTAA
1 TA-TATTATTTTGTTATTCTAA
20594058 T-TATTATTT
1 TATATTATTT
20594067 ATCTATTTAT
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
18 8 0.29
20 6 0.21
21 3 0.11
22 9 0.32
23 2 0.07
ACGTcount: A:0.27, C:0.06, G:0.02, T:0.65
Consensus pattern (21 bp):
TATATTATTTTGTTATTCTAA
Found at i:20594103 original size:29 final size:29
Alignment explanation
Indices: 20593989--20594103 Score: 83
Period size: 29 Copynumber: 4.0 Consensus size: 29
20593979 TTTAATATAT
* * *
20593989 TATTGCTATTATTATTATGTTTCTATTTA
1 TATTTCTACTATTATTATATTTCTATTTA
* ** * * * *
20594018 TATTTATTTTGTTATTCTAATACTA-TTA
1 TATTTCTACTATTATTATATTTCTATTTA
*
20594046 T-TTTTTATCTAATTATTAT-TTATCTATTTA
1 TATTTCTA-CT-ATTATTATATT-TCTATTTA
20594076 TATTTCTACTATTATTATATTTCTATTT
1 TATTTCTACTATTATTATATTTCTATTT
20594104 GTTATATATT
Statistics
Matches: 64, Mismatches: 16, Indels: 12
0.70 0.17 0.13
Matches are distributed among these distances:
27 4 0.06
28 6 0.09
29 41 0.64
30 8 0.12
31 5 0.08
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (29 bp):
TATTTCTACTATTATTATATTTCTATTTA
Found at i:20594118 original size:44 final size:44
Alignment explanation
Indices: 20594038--20594124 Score: 104
Period size: 44 Copynumber: 2.0 Consensus size: 44
20594028 GTTATTCTAA
* *
20594038 TACTATTATTTTTTATCTAATTATTATTTATCTATTTATATTTC
1 TACTATTATTTATTATCTAATTATTATATATCTATTTATATTTC
* * * *
20594082 TACTATTATTATATT-TCTATTTGTTATATATTTATTTCTATTT
1 TACTATTATT-TATTATCTAATTATTATATATCTATTTATATTT
20594125 ATATACTAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
44 33 0.92
45 3 0.08
ACGTcount: A:0.26, C:0.08, G:0.01, T:0.64
Consensus pattern (44 bp):
TACTATTATTTATTATCTAATTATTATATATCTATTTATATTTC
Found at i:20594291 original size:25 final size:25
Alignment explanation
Indices: 20594263--20594357 Score: 66
Period size: 25 Copynumber: 3.7 Consensus size: 25
20594253 CTCATTTCAA
20594263 ATTTTTATACATTATTTATTTTAAT
1 ATTTTTATACATTATTTATTTTAAT
* * * *
20594288 ATTTTCATATATTATGTATTTCAAACT
1 ATTTTTATACATTATTTATTT-TAA-T
* * *
20594315 TTTTTTCACACATTATATATTTTGAAT
1 ATTTTT-ATACATTATTTATTTT-AAT
* *
20594342 -TATTTATATATTATTT
1 ATTTTTATACATTATTT
20594358 TTAAAGAGTT
Statistics
Matches: 52, Mismatches: 14, Indels: 8
0.70 0.19 0.11
Matches are distributed among these distances:
25 26 0.50
26 6 0.12
27 6 0.12
28 14 0.27
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (25 bp):
ATTTTTATACATTATTTATTTTAAT
Found at i:20594358 original size:21 final size:22
Alignment explanation
Indices: 20594328--20594381 Score: 58
Period size: 23 Copynumber: 2.5 Consensus size: 22
20594318 TTTCACACAT
**
20594328 TATA-TATTTTGAATTA-TTTA
1 TATATTATTTTGAAAGAGTTTA
*
20594348 TATATTATTTTTAAAGAGTTTTA
1 TATATTATTTTGAAAGAG-TTTA
20594371 TATATTATTTT
1 TATATTATTTT
20594382 ATCTTGAATG
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
20 4 0.14
21 9 0.32
23 15 0.54
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (22 bp):
TATATTATTTTGAAAGAGTTTA
Found at i:20606362 original size:15 final size:15
Alignment explanation
Indices: 20606342--20606370 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
20606332 TTACCAGACA
20606342 TGGATAATGAAAAAT
1 TGGATAATGAAAAAT
20606357 TGGATAATGAAAAA
1 TGGATAATGAAAAA
20606371 CAAGTCACTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.55, C:0.00, G:0.21, T:0.24
Consensus pattern (15 bp):
TGGATAATGAAAAAT
Found at i:20609142 original size:39 final size:39
Alignment explanation
Indices: 20609088--20609165 Score: 147
Period size: 39 Copynumber: 2.0 Consensus size: 39
20609078 AGGTCATGAT
20609088 TGTCACGGTGTCATCTCAAGTCTTAAAGGCTCAGTATAC
1 TGTCACGGTGTCATCTCAAGTCTTAAAGGCTCAGTATAC
*
20609127 TGTCATGGTGTCATCTCAAGTCTTAAAGGCTCAGTATAC
1 TGTCACGGTGTCATCTCAAGTCTTAAAGGCTCAGTATAC
20609166 CCTCTGTGCA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.26, C:0.22, G:0.21, T:0.32
Consensus pattern (39 bp):
TGTCACGGTGTCATCTCAAGTCTTAAAGGCTCAGTATAC
Found at i:20609470 original size:50 final size:50
Alignment explanation
Indices: 20609407--20609502 Score: 138
Period size: 50 Copynumber: 1.9 Consensus size: 50
20609397 CAGCAAAAAC
* * *
20609407 ATGGTCCAAAGAGCGAAACTTGGTTTCAAGTTACGGAAATAAGTCTCATT
1 ATGGTCCAAAGAGCAAAACTTGGTTTCAAGTTACAGAAAGAAGTCTCATT
* * *
20609457 ATGGTCCATAGAGCAAAATTTTGTTTCAAGTTACAGAAAGAAGTCT
1 ATGGTCCAAAGAGCAAAACTTGGTTTCAAGTTACAGAAAGAAGTCT
20609503 AAATTAAACA
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
50 40 1.00
ACGTcount: A:0.35, C:0.15, G:0.21, T:0.29
Consensus pattern (50 bp):
ATGGTCCAAAGAGCAAAACTTGGTTTCAAGTTACAGAAAGAAGTCTCATT
Found at i:20610788 original size:17 final size:17
Alignment explanation
Indices: 20610766--20610800 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
20610756 CAAAGTAAAA
20610766 AACAGATATGAAGATAT
1 AACAGATATGAAGATAT
*
20610783 AACAGATATGAAGGTAT
1 AACAGATATGAAGATAT
20610800 A
1 A
20610801 TGCACTTGCA
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:0.51, C:0.06, G:0.20, T:0.23
Consensus pattern (17 bp):
AACAGATATGAAGATAT
Found at i:20614801 original size:2 final size:2
Alignment explanation
Indices: 20614794--20614828 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
20614784 AATAATCGAC
20614794 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20614829 ACCTACCCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:20615947 original size:50 final size:50
Alignment explanation
Indices: 20615888--20616002 Score: 151
Period size: 50 Copynumber: 2.3 Consensus size: 50
20615878 CTACTTATTT
* * *
20615888 GGCCGAATATGCAAGAT-CAAGAATAATATCACATATGTACATATCTATAA
1 GGCCGAATATGCAAGATCCAA-AATAACATCACATAAGTACATACCTATAA
* * **
20615938 GGCCGAATATGCAAGTTCCAATATAACATCACATAAGTACATACCTATGT
1 GGCCGAATATGCAAGATCCAAAATAACATCACATAAGTACATACCTATAA
20615988 GGCCGAATATGCAAG
1 GGCCGAATATGCAAG
20616003 GTCATTTAAC
Statistics
Matches: 57, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
50 54 0.95
51 3 0.05
ACGTcount: A:0.40, C:0.19, G:0.17, T:0.24
Consensus pattern (50 bp):
GGCCGAATATGCAAGATCCAAAATAACATCACATAAGTACATACCTATAA
Found at i:20617680 original size:18 final size:19
Alignment explanation
Indices: 20617638--20617682 Score: 56
Period size: 18 Copynumber: 2.4 Consensus size: 19
20617628 CAAGCTTAAT
20617638 ATTAAATTAATTAAGATTTA
1 ATTAAA-TAATTAAGATTTA
* *
20617658 GTTAAATATTTAAG-TTTA
1 ATTAAATAATTAAGATTTA
20617676 ATTAAAT
1 ATTAAAT
20617683 GTTAAACTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 10 0.45
19 7 0.32
20 5 0.23
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (19 bp):
ATTAAATAATTAAGATTTA
Found at i:20620276 original size:14 final size:14
Alignment explanation
Indices: 20620243--20620292 Score: 52
Period size: 13 Copynumber: 3.6 Consensus size: 14
20620233 ATAAAGTTTA
20620243 TAAATTTAA-CAAAT
1 TAAA-TTAATCAAAT
*
20620257 TCAATTAATC-AAT
1 TAAATTAATCAAAT
20620270 ATAAATT-ATCAAAT
1 -TAAATTAATCAAAT
20620284 TAAATTAAT
1 TAAATTAAT
20620293 TGATTTATAG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
13 16 0.53
14 14 0.47
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAATTAATCAAAT
Found at i:20628612 original size:11 final size:11
Alignment explanation
Indices: 20628596--20628631 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
20628586 ACCAGTGGAG
20628596 AAAATTAAATT
1 AAAATTAAATT
20628607 AAAATTAAATT
1 AAAATTAAATT
*
20628618 AAAAATAAGATT
1 AAAATTAA-ATT
20628630 AA
1 AA
20628632 GAGTTGGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 18 0.78
12 5 0.22
ACGTcount: A:0.67, C:0.00, G:0.03, T:0.31
Consensus pattern (11 bp):
AAAATTAAATT
Found at i:20629396 original size:2 final size:2
Alignment explanation
Indices: 20629389--20629430 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
20629379 TACTTAAATG
20629389 AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T 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
20629430 A
1 A
20629431 AAAGCTATAT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20629439 original size:19 final size:19
Alignment explanation
Indices: 20629389--20629440 Score: 54
Period size: 19 Copynumber: 2.8 Consensus size: 19
20629379 TACTTAAATG
*
20629389 ATATATATA-TATATATAT
1 ATATATAAACTATATATAT
* *
20629407 ATATATATATTATATATAT
1 ATATATAAACTATATATAT
20629426 ATATA-AAAGCTATAT
1 ATATATAAA-CTATAT
20629441 TAGAAATGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
18 11 0.37
19 19 0.63
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.46
Consensus pattern (19 bp):
ATATATAAACTATATATAT
Found at i:20631360 original size:26 final size:26
Alignment explanation
Indices: 20631323--20631406 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
20631313 TGATACAAAT
* *
20631323 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
20631349 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
20631375 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
20631401 TGATAA
1 TGATAA
20631407 GAATTTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:20632924 original size:26 final size:26
Alignment explanation
Indices: 20632894--20632946 Score: 72
Period size: 26 Copynumber: 2.0 Consensus size: 26
20632884 TTTATAGTTT
20632894 TACCCCTAGGAGATAAATT-ACCGAAA
1 TACCCCTAGG-GATAAATTGACCGAAA
* *
20632920 TACCCCTAGGGTTAAATTGACCTAAA
1 TACCCCTAGGGATAAATTGACCGAAA
20632946 T
1 T
20632947 GCATGTTTAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.38, C:0.23, G:0.15, T:0.25
Consensus pattern (26 bp):
TACCCCTAGGGATAAATTGACCGAAA
Found at i:20636294 original size:17 final size:17
Alignment explanation
Indices: 20636196--20636299 Score: 88
Period size: 17 Copynumber: 6.1 Consensus size: 17
20636186 TAATCAAACC
*
20636196 TTGAACTTAAG-AATGTT
1 TTGAACTTAAGTAA-ATT
20636213 TTGAACTTAAAG-AAATT
1 TTGAACTT-AAGTAAATT
*
20636230 TT-AGGCTTAAGTGAAATT
1 TTGA-ACTTAAGT-AAATT
* **
20636248 TTGAACTTAAGCATGTT
1 TTGAACTTAAGTAAATT
20636265 TTGAACTTAAGTAAATT
1 TTGAACTTAAGTAAATT
* *
20636282 TTGAATTTGAGTAAATT
1 TTGAACTTAAGTAAATT
20636299 T
1 T
20636300 CAAACTGCTT
Statistics
Matches: 71, Mismatches: 11, Indels: 10
0.77 0.12 0.11
Matches are distributed among these distances:
16 4 0.06
17 48 0.68
18 18 0.25
19 1 0.01
ACGTcount: A:0.37, C:0.06, G:0.16, T:0.41
Consensus pattern (17 bp):
TTGAACTTAAGTAAATT
Found at i:20638017 original size:30 final size:30
Alignment explanation
Indices: 20637981--20638049 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
20637971 TGCAGGACAC
20637981 AATAAATTGTTTTAATCTATCATGTAATTG
1 AATAAATTGTTTTAATCTATCATGTAATTG
* **
20638011 AATAAATTATTTTAATCTATTGTGTAATTG
1 AATAAATTGTTTTAATCTATCATGTAATTG
20638041 AATAAATTG
1 AATAAATTG
20638050 ACAAATATCT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 35 1.00
ACGTcount: A:0.39, C:0.04, G:0.10, T:0.46
Consensus pattern (30 bp):
AATAAATTGTTTTAATCTATCATGTAATTG
Found at i:20641807 original size:50 final size:50
Alignment explanation
Indices: 20641732--20641908 Score: 264
Period size: 50 Copynumber: 3.5 Consensus size: 50
20641722 CCATGGCAAC
*
20641732 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATAAAGGACAAATGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * *
20641782 AAGTGATCAGTAATAGCTTCGGCTACACTTATCTGATCAAGGACAAGTGA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* *
20641832 AAGTGATAAGTGATAACTTCGGCTACACTTATCTGATCAAGGACAAATAA
1 AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
* * *
20641882 CAAGTGAAAAGTGGTAGCTTCTGCTAC
1 -AAGTGATAAGTGATAGCTTCGGCTAC
20641909 CTAATCAGTG
Statistics
Matches: 113, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
50 91 0.81
51 22 0.19
ACGTcount: A:0.36, C:0.16, G:0.21, T:0.26
Consensus pattern (50 bp):
AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATGA
Found at i:20641922 original size:31 final size:31
Alignment explanation
Indices: 20641884--20642001 Score: 173
Period size: 31 Copynumber: 3.8 Consensus size: 31
20641874 ACAAATAACA
* * *
20641884 AGTGAAAAGTGGTAGCTTCTGCTACCTAATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
20641915 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
* *
20641946 AGTGAAAAATGGTAGCTCCAGCTACCTGATC
1 AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
* *
20641977 AGTGAATAGTGGTAGCTTCGGCTAC
1 AGTGAAAAGTGGTAGCTCCGGCTAC
20642002 AAGTGACAAG
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 78 1.00
ACGTcount: A:0.28, C:0.20, G:0.26, T:0.25
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTCCGGCTACCTGATC
Found at i:20642127 original size:49 final size:46
Alignment explanation
Indices: 20642023--20642226 Score: 214
Period size: 42 Copynumber: 4.5 Consensus size: 46
20642013 GATTTCCGTA
* * * *
20642023 TAAGACCATATCTGGGATATGGCATCA-GTGAGATATGTGATTCGTG
1 TAAGACCATAGCTGGGCTATGGCATCATATGTGATATGT-ATTCGTG
20642069 TAAGACCATAGCTGGGCTATGGCATCGATATGTGATATGTCATTACGTG
1 TAAGACCATAGCTGGGCTATGGCATC-ATATGTGATATGT-ATT-CGTG
20642118 TAAGACCATAGCTGGGCTATGGCATCGATATGTGA-A--TA-T-GTG
1 TAAGACCATAGCTGGGCTATGGCATC-ATATGTGATATGTATTCGTG
20642160 TAAGACCATAGCTGGGCTATGGCATCATTATGTGA-A-G-A-T-GTG
1 TAAGACCATAGCTGGGCTATGGCATCA-TATGTGATATGTATTCGTG
* **
20642202 TAAGACCATAGTTGAACTATGGCAT
1 TAAGACCATAGCTGGGCTATGGCAT
20642227 TGAGAAAACG
Statistics
Matches: 145, Mismatches: 8, Indels: 14
0.87 0.05 0.08
Matches are distributed among these distances:
41 1 0.01
42 64 0.44
44 1 0.01
45 1 0.01
46 25 0.17
47 1 0.01
48 13 0.09
49 39 0.27
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.29
Consensus pattern (46 bp):
TAAGACCATAGCTGGGCTATGGCATCATATGTGATATGTATTCGTG
Found at i:20664266 original size:196 final size:196
Alignment explanation
Indices: 20663919--20664300 Score: 514
Period size: 196 Copynumber: 1.9 Consensus size: 196
20663909 TTGGCTTTTT
* * *
20663919 CCACAGGCTCATCAAACAACTCTGTATTTTAGGCCGCTAAATAAACTCAAATCTCACGATTGAGC
1 CCACAAGCTCATCAAACAACTCTGTATTTTAGGCCACTAAATAAACCCAAATCTCACGATTGAGC
* * * * * ** *
20663984 CTAAAGCGAAACCTCTTATAGCGATACTTATCAGTCAAAACCATCTTAGGAGTATACTGACAAAG
66 CCAAAGCGAAACCTCTTACAACGATACTTATAAGTCAAAACCATCTCAAAAGCATACTGACAAAG
*
20664049 GCACACAAACTCTGCCTCATAGTCAGCCACAGACAAGCTACCTTGCACAAGATCCAAAAATTCCC
131 GCACACAAACTCTGCCTCATAGTCAGCCACAAACAAGCTACCTTGCACAAGATCCAAAAATTCCC
20664114 A
196 A
* * *
20664115 CCACAAGCTCATCAAACAACTTTGTATTTTGGGCCACTAAATAAACCCTAATCTCACGATTGAGC
1 CCACAAGCTCATCAAACAACTCTGTATTTTAGGCCACTAAATAAACCCAAATCTCACGATTGAGC
* * * * * *
20664180 CCAGAGC-AGAACCTCTTACAATGATCCTTCTAAGTCAAAACTATCTCAAAAGCATACTGACTAA
66 CCAAAGCGA-AACCTCTTACAACGATACTTATAAGTCAAAACCATCTCAAAAGCATACTGACAAA
* * * * *
20664244 GGCGCACAAACTTTGTCTCATAGTCAGCCACAAACGAGCTACCTTGCGCAAGATCCA
130 GGCACACAAACTCTGCCTCATAGTCAGCCACAAACAAGCTACCTTGCACAAGATCCA
20664301 TAAACTGCTT
Statistics
Matches: 159, Mismatches: 26, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
195 1 0.01
196 158 0.99
ACGTcount: A:0.35, C:0.28, G:0.14, T:0.23
Consensus pattern (196 bp):
CCACAAGCTCATCAAACAACTCTGTATTTTAGGCCACTAAATAAACCCAAATCTCACGATTGAGC
CCAAAGCGAAACCTCTTACAACGATACTTATAAGTCAAAACCATCTCAAAAGCATACTGACAAAG
GCACACAAACTCTGCCTCATAGTCAGCCACAAACAAGCTACCTTGCACAAGATCCAAAAATTCCC
A
Found at i:20666134 original size:10 final size:10
Alignment explanation
Indices: 20666102--20666144 Score: 52
Period size: 10 Copynumber: 4.4 Consensus size: 10
20666092 ATTCTGACAC
20666102 ACAT-CAATT
1 ACATACAATT
**
20666111 ACATACAAGC
1 ACATACAATT
*
20666121 ACATATAATT
1 ACATACAATT
20666131 ACATACAATT
1 ACATACAATT
20666141 ACAT
1 ACAT
20666145 TTAATCAAAA
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
9 4 0.15
10 23 0.85
ACGTcount: A:0.49, C:0.21, G:0.02, T:0.28
Consensus pattern (10 bp):
ACATACAATT
Found at i:20673457 original size:26 final size:28
Alignment explanation
Indices: 20673426--20673480 Score: 96
Period size: 26 Copynumber: 2.0 Consensus size: 28
20673416 AATATGAAAA
20673426 TACAAATAAATTC-A-TTTTTTTATTTT
1 TACAAATAAATTCAATTTTTTTTATTTT
20673452 TACAAATAAATTCAATTTTTTTTATTTT
1 TACAAATAAATTCAATTTTTTTTATTTT
20673480 T
1 T
20673481 CTTTCAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 13 0.48
27 1 0.04
28 13 0.48
ACGTcount: A:0.35, C:0.07, G:0.00, T:0.58
Consensus pattern (28 bp):
TACAAATAAATTCAATTTTTTTTATTTT
Found at i:20675391 original size:20 final size:20
Alignment explanation
Indices: 20675368--20675405 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
20675358 ATGAAAATAA
20675368 TTAG-AATTAAATATTAAGGT
1 TTAGAAATTAAA-ATTAAGGT
20675388 TTAGAAATTAAAATTAAG
1 TTAGAAATTAAAATTAAG
20675406 TACCTGAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 10 0.59
21 7 0.41
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (20 bp):
TTAGAAATTAAAATTAAGGT
Found at i:20678542 original size:27 final size:27
Alignment explanation
Indices: 20678494--20678652 Score: 184
Period size: 27 Copynumber: 5.9 Consensus size: 27
20678484 GCGAGGCTGC
* *
20678494 CAGATATTGTGAC-GAAGTCACCAGATA
1 CAGATATTGTGGCAG-AGCCACCAGATA
20678521 CAGATATTGTGGCAGAGCCACCAGA-A
1 CAGATATTGTGGCAGAGCCACCAGATA
20678547 CAGATATATGTGGCAGAGCCACCAGAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
* *
20678574 CAGATAATTGTGGCATAGCCACCAG-GA
1 CAGAT-ATTGTGGCAGAGCCACCAGATA
*
20678601 CAGATATATGTGGCAGAGCCACCAAAT-
1 CAGATAT-TGTGGCAGAGCCACCAGATA
*
20678628 CAGATAATTGTGGCATAGCCACCAG
1 CAGAT-ATTGTGGCAGAGCCACCAG
20678653 GACGCTTCCT
Statistics
Matches: 115, Mismatches: 9, Indels: 16
0.82 0.06 0.11
Matches are distributed among these distances:
26 10 0.09
27 100 0.87
28 5 0.04
ACGTcount: A:0.35, C:0.22, G:0.25, T:0.19
Consensus pattern (27 bp):
CAGATATTGTGGCAGAGCCACCAGATA
Found at i:20678653 original size:54 final size:54
Alignment explanation
Indices: 20678512--20678655 Score: 245
Period size: 54 Copynumber: 2.7 Consensus size: 54
20678502 GTGACGAAGT
* *
20678512 CACCAGATACAGAT-ATTGTGGCAGAGCCACCAGAACAGATATATGTGGCAGAGC
1 CACCAGAT-CAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
20678566 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
*
20678620 CACCAAATCAGATAATTGTGGCATAGCCACCAGGAC
1 CACCAGATCAGATAATTGTGGCATAGCCACCAGGAC
20678656 GCTTCCTCCA
Statistics
Matches: 86, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
53 5 0.06
54 81 0.94
ACGTcount: A:0.35, C:0.24, G:0.24, T:0.17
Consensus pattern (54 bp):
CACCAGATCAGATAATTGTGGCATAGCCACCAGGACAGATATATGTGGCAGAGC
Found at i:20679058 original size:8 final size:8
Alignment explanation
Indices: 20679042--20679071 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
20679032 CTCAAAATAC
20679042 CGGCTTTT
1 CGGCTTTT
*
20679050 CGGCATTT
1 CGGCTTTT
20679058 CGGCTTTT
1 CGGCTTTT
20679066 CGGCTT
1 CGGCTT
20679072 GTGCCGATCT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.03, C:0.27, G:0.27, T:0.43
Consensus pattern (8 bp):
CGGCTTTT
Found at i:20680279 original size:26 final size:26
Alignment explanation
Indices: 20680248--20680381 Score: 241
Period size: 26 Copynumber: 5.2 Consensus size: 26
20680238 TGAAATTTCC
20680248 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
20680274 ATCATGGAATATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
20680300 ATCATGGAATATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
*
20680326 ATCATGAAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
20680352 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
20680378 ATCA
1 ATCA
20680382 ATTTGTATCA
Statistics
Matches: 104, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 104 1.00
ACGTcount: A:0.36, C:0.25, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:20684246 original size:47 final size:46
Alignment explanation
Indices: 20684126--20684303 Score: 200
Period size: 47 Copynumber: 3.8 Consensus size: 46
20684116 ATAATTTCAC
* *
20684126 CCATAATGAACTCGGAACGCAACTCAACGAGCTCGGGTGTTCACAT
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGTTCACAT
* * *
20684172 CCATAATGAACTCGGAACACAACTCAACGAGTTCTGATGCTT-GCAT
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATG-TTCACAT
*
20684218 CCATAAGTGAACTCGGAACGCAACTCAACGAGTTCGGAT-TCCTCATAAT
1 CCATAA-TGAACTCGGAACGCAACTCAACGAGTTCGGATGT--TCA-CAT
* * * *
20684267 TC-TCACGAACTCGGAACGCAACTCAATGAGTTCGGAT
1 CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGAT
20684304 CTCAATTTCC
Statistics
Matches: 113, Mismatches: 13, Indels: 11
0.82 0.09 0.08
Matches are distributed among these distances:
45 1 0.01
46 44 0.39
47 63 0.56
48 2 0.02
49 3 0.03
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (46 bp):
CCATAATGAACTCGGAACGCAACTCAACGAGTTCGGATGTTCACAT
Found at i:20688675 original size:39 final size:39
Alignment explanation
Indices: 20688632--20688722 Score: 119
Period size: 39 Copynumber: 2.3 Consensus size: 39
20688622 TGTTTTTGAG
*
20688632 TATTGTGATATATGATTGAATGCTATGTGATTATATGAC
1 TATTGTGATATATGATTAAATGCTATGTGATTATATGAC
* ** *
20688671 TATTGTGATATATGCTTAAATTTTATGTGATTATATGCC
1 TATTGTGATATATGATTAAATGCTATGTGATTATATGAC
* *
20688710 AAATGTGATATAT
1 TATTGTGATATAT
20688723 CCTTAAAAGT
Statistics
Matches: 45, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
39 45 1.00
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (39 bp):
TATTGTGATATATGATTAAATGCTATGTGATTATATGAC
Found at i:20693044 original size:28 final size:28
Alignment explanation
Indices: 20693012--20693138 Score: 155
Period size: 28 Copynumber: 4.5 Consensus size: 28
20693002 CCATGGCATA
* ** *
20693012 TTCAAGTAAGAGTTTGCATGGACTACCT
1 TTCAAGCAAGAGTCCGCATGGACTATCT
* *
20693040 TTCAAGTAAGAGTCTGCATGGACTATCT
1 TTCAAGCAAGAGTCCGCATGGACTATCT
* *
20693068 ATCAAGCAAGAGTCCGCATGGGCTATCT
1 TTCAAGCAAGAGTCCGCATGGACTATCT
* * *
20693096 TTCAAGAAAGAGTTCGCAAGGACTATCT
1 TTCAAGCAAGAGTCCGCATGGACTATCT
20693124 TTCAAGCAAGAGTCC
1 TTCAAGCAAGAGTCC
20693139 ACAAGGATTG
Statistics
Matches: 86, Mismatches: 13, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
28 86 1.00
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (28 bp):
TTCAAGCAAGAGTCCGCATGGACTATCT
Done.