Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr6
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: 56482370
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 1659275 characters in sequence are not A, C, G, or T
File 10 of 172
Found at i:3055075 original size:41 final size:41
Alignment explanation
Indices: 3055018--3055099 Score: 155
Period size: 41 Copynumber: 2.0 Consensus size: 41
3055008 TAATTCATGA
3055018 AATTAACATTTAACCATTAAATTTCAGCCACATGAACTTAC
1 AATTAACATTTAACCATTAAATTTCAGCCACATGAACTTAC
*
3055059 AATTAACATTTAACCATTAAATTTCAGCCATATGAACTTAC
1 AATTAACATTTAACCATTAAATTTCAGCCACATGAACTTAC
3055100 TATTTCATTA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 40 1.00
ACGTcount: A:0.41, C:0.21, G:0.05, T:0.33
Consensus pattern (41 bp):
AATTAACATTTAACCATTAAATTTCAGCCACATGAACTTAC
Found at i:3059364 original size:67 final size:66
Alignment explanation
Indices: 3059256--3059386 Score: 226
Period size: 67 Copynumber: 2.0 Consensus size: 66
3059246 TTCCCAATTC
*
3059256 AGAGAGCACACTCCCGCAAACCTCATTTCTTACAGTGGGATTACTAGTCCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCGCAAACCTCATTTCTTACAGCGGGATTAC-AGTCCAGGCTAAATCCCCTG
3059321 CA
65 CA
* *
3059323 AGAGAGCACACTCCCGCGAACCTCATTTCTTACAGCGGGATTACCGTCCAGGCTAAATCCCCTG
1 AGAGAGCACACTCCCGCAAACCTCATTTCTTACAGCGGGATTACAGTCCAGGCTAAATCCCCTG
3059387 TAATATAAAC
Statistics
Matches: 61, Mismatches: 3, Indels: 1
0.94 0.05 0.02
Matches are distributed among these distances:
66 19 0.31
67 42 0.69
ACGTcount: A:0.27, C:0.33, G:0.19, T:0.21
Consensus pattern (66 bp):
AGAGAGCACACTCCCGCAAACCTCATTTCTTACAGCGGGATTACAGTCCAGGCTAAATCCCCTGC
A
Found at i:3065011 original size:40 final size:41
Alignment explanation
Indices: 3064943--3065019 Score: 111
Period size: 40 Copynumber: 1.9 Consensus size: 41
3064933 GTTGATGGAA
* *
3064943 AATAGAAATTGTGATTATTATGCATTTAAAAATAATAATTT
1 AATAAAAATTGTGATTATTATACATTTAAAAATAATAATTT
**
3064984 AATAAAAATTGTGA-TATTATATTTTTAAAAATAATA
1 AATAAAAATTGTGATTATTATACATTTAAAAATAATA
3065020 TAATTTAACT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
40 19 0.59
41 13 0.41
ACGTcount: A:0.49, C:0.01, G:0.08, T:0.42
Consensus pattern (41 bp):
AATAAAAATTGTGATTATTATACATTTAAAAATAATAATTT
Found at i:3068985 original size:32 final size:32
Alignment explanation
Indices: 3068942--3069023 Score: 155
Period size: 32 Copynumber: 2.6 Consensus size: 32
3068932 ACGAGACTTG
3068942 TACAACGCATTAATTAAATGTGTATATTCATA
1 TACAACGCATTAATTAAATGTGTATATTCATA
*
3068974 TACAACTCATTAATTAAATGTGTATATTCATA
1 TACAACGCATTAATTAAATGTGTATATTCATA
3069006 TACAACGCATTAATTAAA
1 TACAACGCATTAATTAAA
3069024 AATATTTCTA
Statistics
Matches: 48, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (32 bp):
TACAACGCATTAATTAAATGTGTATATTCATA
Found at i:3069300 original size:62 final size:62
Alignment explanation
Indices: 3069141--3069352 Score: 379
Period size: 62 Copynumber: 3.4 Consensus size: 62
3069131 ATAAAATAAA
* *
3069141 AATTGGATCATTACATATAATCAAGTAAACAAATTGATTAAAAAACATATGGATAATATATT
1 AATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACATATGGATAATATATT
*
3069203 AAAATTGAATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACATATGGATAATATATT
1 --AATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACATATGGATAATATATT
3069267 AATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACATATGGATAATATATT
1 AATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACATATGGATAATATATT
3069329 AATTGGATCATTAGATATAATCAA
1 AATTGGATCATTAGATATAATCAA
3069353 CTTGATTCTA
Statistics
Matches: 144, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
62 85 0.59
64 59 0.41
ACGTcount: A:0.50, C:0.08, G:0.10, T:0.32
Consensus pattern (62 bp):
AATTGGATCATTAGATATAATCAAGTAAACAACTTGATTAAAAAACATATGGATAATATATT
Found at i:3072782 original size:111 final size:112
Alignment explanation
Indices: 3072664--3072895 Score: 294
Period size: 117 Copynumber: 2.0 Consensus size: 112
3072654 AAGTAGATTA
*
3072664 TAAATTATATTTAATAATAATTATATATTATGA-TT-TTAGTAAATTCATATAAG-A-A-TAAGA
1 TAAATTATATTT--TAAT-ATTATATATTATGATTTATTAGTAAATTCATATAAGAATATTAACA
* *
3072724 ATTTTATTAAATTATATAATATTATTAAATTATATTTAATAATAATTATTT
63 ATTTTATTAAATTATAT-ATATTATTAAATTATATTTAATAACAATTATAT
*
3072775 TAAATTATATTTTAGTATTATATATTATGATTTTATTAGTAAATTCATATAAGAATATTTATTAA
1 TAAATTATATTTTAATATTATATATTATGA-TTTATTAGTAAATTCATATAAG-A-A--TATTAA
* *
3072840 CAATTTTATTAAATTATATATTTTATTAAATTATATTTTATAACAATTATAT
61 CAATTTTATTAAATTATATATATTATTAAATTATATTTAATAACAATTATAT
3072892 TAAA
1 TAAA
3072896 ATATGATTAA
Statistics
Matches: 105, Mismatches: 6, Indels: 14
0.84 0.05 0.11
Matches are distributed among these distances:
108 14 0.13
109 3 0.03
110 2 0.02
111 30 0.29
114 1 0.01
117 34 0.32
118 21 0.20
ACGTcount: A:0.45, C:0.02, G:0.03, T:0.50
Consensus pattern (112 bp):
TAAATTATATTTTAATATTATATATTATGATTTATTAGTAAATTCATATAAGAATATTAACAATT
TTATTAAATTATATATATTATTAAATTATATTTAATAACAATTATAT
Found at i:3072794 original size:44 final size:44
Alignment explanation
Indices: 3072664--3072794 Score: 114
Period size: 44 Copynumber: 3.0 Consensus size: 44
3072654 AAGTAGATTA
*
3072664 TAAATTATATTTAATAATAATTA---TATATTATGATTTTAG---
1 TAAATTATATTTAATAATAATTATTTTAAATTAT-ATTTTAGTAT
** * ** *
3072703 TAAATTCATATAAGAATAAGAATT-TTATTAAATTATATAATATTAT
1 TAAATT-ATAT-TTAATAATAATTATT-TTAAATTATATTTTAGTAT
3072749 TAAATTATATTTAATAATAATTATTTTAAATTATATTTTAGTAT
1 TAAATTATATTTAATAATAATTATTTTAAATTATATTTTAGTAT
3072793 TA
1 TA
3072795 TATATTATGA
Statistics
Matches: 69, Mismatches: 13, Indels: 15
0.71 0.13 0.15
Matches are distributed among these distances:
39 6 0.09
40 4 0.06
41 9 0.13
43 4 0.06
44 34 0.49
45 6 0.09
46 6 0.09
ACGTcount: A:0.46, C:0.01, G:0.04, T:0.50
Consensus pattern (44 bp):
TAAATTATATTTAATAATAATTATTTTAAATTATATTTTAGTAT
Found at i:3072862 original size:17 final size:17
Alignment explanation
Indices: 3072842--3072875 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
3072832 TTTATTAACA
3072842 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
3072859 ATTTTATTAAATTATAT
1 ATTTTATTAAATTATAT
3072876 TTTATAACAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
ATTTTATTAAATTATAT
Found at i:3072889 original size:16 final size:15
Alignment explanation
Indices: 3072842--3072892 Score: 57
Period size: 16 Copynumber: 3.2 Consensus size: 15
3072832 TTTATTAACA
*
3072842 ATTTTATTAAATTATAT
1 ATTTTA-TAAAAT-TAT
*
3072859 ATTTTATTAAATTAT
1 ATTTTATAAAATTAT
3072874 ATTTTATAACAATTAT
1 ATTTTATAA-AATTAT
3072890 ATT
1 ATT
3072893 AAAATATGAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
15 11 0.37
16 13 0.43
17 6 0.20
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (15 bp):
ATTTTATAAAATTAT
Found at i:3074329 original size:18 final size:18
Alignment explanation
Indices: 3074306--3074353 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
3074296 GATTTTTTTA
3074306 TTTTATAATTT-AATAGAT
1 TTTTATAATTTGAATA-AT
3074324 TTTTATAAATTTGAATAAT
1 TTTTAT-AATTTGAATAAT
* *
3074343 CTTTATGATTT
1 TTTTATAATTT
3074354 CATTATTCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 10 0.38
19 12 0.46
20 4 0.15
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.56
Consensus pattern (18 bp):
TTTTATAATTTGAATAAT
Found at i:3081842 original size:20 final size:19
Alignment explanation
Indices: 3081810--3081847 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
3081800 TTTTTTATTT
3081810 TTTAAATAAATATTTTTAA
1 TTTAAATAAATATTTTTAA
*
3081829 TTTAATATATATATTTTTA
1 TTTAA-ATAAATATTTTTA
3081848 TAAAAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTTAAATAAATATTTTTAA
Found at i:3083371 original size:13 final size:13
Alignment explanation
Indices: 3083353--3083377 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3083343 AGAAACTTGT
3083353 TTAAACAAACAAG
1 TTAAACAAACAAG
3083366 TTAAACAAACAA
1 TTAAACAAACAA
3083378 TAAAATAAGA
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:0.64, C:0.16, G:0.04, T:0.16
Consensus pattern (13 bp):
TTAAACAAACAAG
Found at i:3085356 original size:9 final size:9
Alignment explanation
Indices: 3085342--3085419 Score: 58
Period size: 9 Copynumber: 9.2 Consensus size: 9
3085332 AGAAAGAAAT
3085342 TATTTTTAA
1 TATTTTTAA
3085351 TA-TTTTAA
1 TATTTTTAA
*
3085359 TATTTGT-A
1 TATTTTTAA
* *
3085367 CA-TTTTAT
1 TATTTTTAA
*
3085375 TATTTTAAA
1 TATTTTTAA
*
3085384 TATTTTTAT
1 TATTTTTAA
*
3085393 TGTTTTTAA
1 TATTTTTAA
*
3085402 AATTTTT-A
1 TATTTTTAA
3085410 -ATTTTTAA
1 TATTTTTAA
3085418 TA
1 TA
3085420 AATTCAATTC
Statistics
Matches: 51, Mismatches: 13, Indels: 10
0.69 0.18 0.14
Matches are distributed among these distances:
7 9 0.18
8 13 0.25
9 29 0.57
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (9 bp):
TATTTTTAA
Found at i:3096810 original size:21 final size:21
Alignment explanation
Indices: 3096786--3096832 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
3096776 AAACAGTGGT
* *
3096786 AAAAAATGATAAAACAGCAAC
1 AAAAAATGAAAAAACAACAAC
*
3096807 AAAACATGAAAAAACAACAAC
1 AAAAAATGAAAAAACAACAAC
3096828 AAAAA
1 AAAAA
3096833 TAGCAGGGGG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.72, C:0.15, G:0.06, T:0.06
Consensus pattern (21 bp):
AAAAAATGAAAAAACAACAAC
Found at i:3097826 original size:21 final size:22
Alignment explanation
Indices: 3097793--3097833 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
3097783 TCGAAGAAAT
3097793 TTAATTAAAAATTTTAAAAAAA
1 TTAATTAAAAATTTTAAAAAAA
3097815 TTAATT-AAAATTTTAAAAA
1 TTAATTAAAAATTTTAAAAA
3097834 TTATCATAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
TTAATTAAAAATTTTAAAAAAA
Found at i:3099005 original size:17 final size:17
Alignment explanation
Indices: 3098978--3099023 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
3098968 CCGATATAAT
* * *
3098978 AAATATATTTATTTTTT
1 AAATATTTTTAATTTTA
*
3098995 AAATTTTTTTAATTTTA
1 AAATATTTTTAATTTTA
3099012 AAATATTTTTAA
1 AAATATTTTTAA
3099024 AATACTTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (17 bp):
AAATATTTTTAATTTTA
Found at i:3099021 original size:11 final size:11
Alignment explanation
Indices: 3099007--3099054 Score: 53
Period size: 11 Copynumber: 4.4 Consensus size: 11
3098997 ATTTTTTTAA
3099007 TTTTAAAATAT
1 TTTTAAAATAT
3099018 TTTTAAAATACT
1 TTTTAAAATA-T
***
3099030 TTTTTTTA-AT
1 TTTTAAAATAT
3099040 TTTTAAAATAT
1 TTTTAAAATAT
3099051 TTTT
1 TTTT
3099055 TGGTATTTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
10 6 0.21
11 17 0.59
12 6 0.21
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.62
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:3099067 original size:22 final size:21
Alignment explanation
Indices: 3099015--3099069 Score: 67
Period size: 22 Copynumber: 2.5 Consensus size: 21
3099005 AATTTTAAAA
*
3099015 TATTTTTAAAATACTTTTTTT
1 TATTTTTAAAATACTTTTTTG
3099036 TAATTTTTAAAATA-TTTTTTGG
1 T-ATTTTTAAAATACTTTTTT-G
3099058 TATTTATTAAAA
1 TATTT-TTAAAA
3099070 AATGGGCCGG
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
21 11 0.37
22 19 0.63
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.60
Consensus pattern (21 bp):
TATTTTTAAAATACTTTTTTG
Found at i:3109758 original size:15 final size:15
Alignment explanation
Indices: 3109729--3109763 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
3109719 AACTCTATTT
3109729 TAATT-ATATTAAGA
1 TAATTAATATTAAGA
*
3109743 TAATTAATATTGAGA
1 TAATTAATATTAAGA
3109758 TAATTA
1 TAATTA
3109764 TTAAGGATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 5 0.26
15 14 0.74
ACGTcount: A:0.49, C:0.00, G:0.09, T:0.43
Consensus pattern (15 bp):
TAATTAATATTAAGA
Found at i:3129458 original size:22 final size:22
Alignment explanation
Indices: 3129432--3129477 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
3129422 ATATTTTTAT
* *
3129432 AATTTTTAAAGAATTAAATTAA
1 AATTTTAAAAGAATTAAATAAA
* *
3129454 AATTTTAAAATATTTAAATAAA
1 AATTTTAAAAGAATTAAATAAA
3129476 AA
1 AA
3129478 AAGTTATTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.02, T:0.39
Consensus pattern (22 bp):
AATTTTAAAAGAATTAAATAAA
Found at i:3134333 original size:18 final size:18
Alignment explanation
Indices: 3134306--3134347 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
3134296 CTTATTTAAT
*
3134306 AATA-TTTTTATTTCAAA
1 AATATTTTTTATTCCAAA
*
3134323 CATATTTTTTATTCCAAA
1 AATATTTTTTATTCCAAA
3134341 AATATTT
1 AATATTT
3134348 GTAAGAAACA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
17 3 0.14
18 18 0.86
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.52
Consensus pattern (18 bp):
AATATTTTTTATTCCAAA
Found at i:3138381 original size:310 final size:312
Alignment explanation
Indices: 3137847--3138425 Score: 781
Period size: 310 Copynumber: 1.9 Consensus size: 312
3137837 ATTTAGAATT
* ***
3137847 TATATGTGTTTAAAAATAATATATAATAAACAATATGTGTATGATTTGAAACTAATTAATCACAA
1 TATATGTGTTTAAAAATAACATATAATAAACAATAAACGTATGATTTGAAACTAATTAATCACAA
* * * * *
3137912 TAACACATGAAATATATATAATATTAAAATAAAAAAAATAGAATAATTTGTGAGAAAAAATAAAA
66 TAACAAATGAAATATATACAATATTAAAAT-AAAAAAATAGAATAAATTATAAGAAAAAATAAAA
* ** * *
3137977 TGTAAACACACGAATATGTCATATTAACAACACTAAATGCATTACAATTATTTATCATGATGTTG
130 TGTAAACACACAAATACATCATATAAACAACACTAAATGCACTACAATTATTTATCATGATGTTG
* * * * *
3138042 TCATCAATTGTGAGTTAGTGTTGAGTTGACATATGGCA-CTAACTCAATTAACAATATTATTAAT
195 TCATCAATTGTAAATTAGTGTTAAGTTGACATATGACATC-AACTCAATTAACAACATTATTAAT
3138106 ATATA-AATTCTATCACACATGTATGCGTGCGAAAACTACGAATTTATAACACA
259 ATATACAATTCTATCACACATGTATGCGTGCGAAAACTACGAATTTATAACACA
* * *
3138159 TATATGTGTTTAAAAATAACGTATAATAAACAATAAAACGTATGTTTTGAAACTAATTAATCATA
1 TATATGTGTTTAAAAATAACATATAATAAACAAT-AAACGTATGATTTGAAACTAATTAATCACA
* * * *
3138224 ATAACAAATTAAATATGTACAGTATTAAAAT-AAAAAATAGAATAAATTATAAGTAAAACA-AAA
65 ATAACAAATGAAATATATACAATATTAAAATAAAAAAATAGAATAAATTATAAG-AAAAAATAAA
* * * *
3138287 AT-TAAACACATAAATACATCATATAAACGATACTAAATGCACTACAATTATTTATCATGATTTT
129 ATGTAAACACACAAATACATCATATAAACAACACTAAATGCACTACAATTATTTATCATGATGTT
* * * *
3138351 GTCATTAGTTGTAAATTAGTGTTAAGTTGACTTATGACATCAACTCAATTAACAACATTGTTAAT
194 GTCATCAATTGTAAATTAGTGTTAAGTTGACATATGACATCAACTCAATTAACAACATTATTAAT
3138416 ATATACAATT
259 ATATACAATT
3138426 GATGAAGATA
Statistics
Matches: 229, Mismatches: 34, Indels: 9
0.84 0.12 0.03
Matches are distributed among these distances:
310 112 0.49
311 29 0.13
312 37 0.16
313 51 0.22
ACGTcount: A:0.47, C:0.11, G:0.10, T:0.33
Consensus pattern (312 bp):
TATATGTGTTTAAAAATAACATATAATAAACAATAAACGTATGATTTGAAACTAATTAATCACAA
TAACAAATGAAATATATACAATATTAAAATAAAAAAATAGAATAAATTATAAGAAAAAATAAAAT
GTAAACACACAAATACATCATATAAACAACACTAAATGCACTACAATTATTTATCATGATGTTGT
CATCAATTGTAAATTAGTGTTAAGTTGACATATGACATCAACTCAATTAACAACATTATTAATAT
ATACAATTCTATCACACATGTATGCGTGCGAAAACTACGAATTTATAACACA
Found at i:3140332 original size:14 final size:14
Alignment explanation
Indices: 3140315--3140350 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
3140305 TTTAGTAATA
3140315 TTAATGTAATGTTT
1 TTAATGTAATGTTT
*
3140329 TTAATTTAATGTTT
1 TTAATGTAATGTTT
*
3140343 TTATTGTA
1 TTAATGTA
3140351 TTATTTGTTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.28, C:0.00, G:0.11, T:0.61
Consensus pattern (14 bp):
TTAATGTAATGTTT
Found at i:3140338 original size:25 final size:25
Alignment explanation
Indices: 3140285--3140332 Score: 80
Period size: 25 Copynumber: 2.0 Consensus size: 25
3140275 ATTATGAAAA
*
3140285 TAATATTAATGTAATGTGTTTTTAG
1 TAATATTAATGTAATGTGTTTTAAG
3140310 TAATATTAATGTAATGT-TTTTAA
1 TAATATTAATGTAATGTGTTTTAA
3140333 TTTAATGTTT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 5 0.23
25 17 0.77
ACGTcount: A:0.35, C:0.00, G:0.12, T:0.52
Consensus pattern (25 bp):
TAATATTAATGTAATGTGTTTTAAG
Found at i:3141204 original size:14 final size:16
Alignment explanation
Indices: 3141185--3141219 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
3141175 TTCCACCCTG
3141185 AAAAAG-AAGAAAA-A
1 AAAAAGAAAGAAAAGA
3141199 AAAAAGAAAGAAAAGA
1 AAAAAGAAAGAAAAGA
3141215 AAAAA
1 AAAAA
3141220 AAGCTGCTTC
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.32
15 7 0.37
16 6 0.32
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAGAAAAGA
Found at i:3141210 original size:18 final size:18
Alignment explanation
Indices: 3141187--3141222 Score: 56
Period size: 18 Copynumber: 2.0 Consensus size: 18
3141177 CCACCCTGAA
3141187 AAAGAAGAA-AAAAAAAAG
1 AAAGAA-AAGAAAAAAAAG
3141205 AAAGAAAAGAAAAAAAAG
1 AAAGAAAAGAAAAAAAAG
3141223 CTGCTTCACC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 2 0.12
18 15 0.88
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (18 bp):
AAAGAAAAGAAAAAAAAG
Found at i:3141222 original size:14 final size:14
Alignment explanation
Indices: 3141184--3141222 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 14
3141174 TTTCCACCCT
*
3141184 GAAAAAGAAGAAAA
1 GAAAAAAAAGAAAA
*
3141198 AAAAAAGAAAGAAAA
1 GAAAAA-AAAGAAAA
3141213 GAAAAAAAAG
1 GAAAAAAAAG
3141223 CTGCTTCACC
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
14 9 0.43
15 12 0.57
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (14 bp):
GAAAAAAAAGAAAA
Found at i:3145172 original size:24 final size:24
Alignment explanation
Indices: 3145145--3145198 Score: 99
Period size: 24 Copynumber: 2.2 Consensus size: 24
3145135 AGTATGCGTT
3145145 AAATTTGACGTGTTCAATTTGCTA
1 AAATTTGACGTGTTCAATTTGCTA
*
3145169 AAATTTGACGTGTTCAGTTTGCTA
1 AAATTTGACGTGTTCAATTTGCTA
3145193 AAATTT
1 AAATTT
3145199 ATTAGCTCAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.30, C:0.11, G:0.17, T:0.43
Consensus pattern (24 bp):
AAATTTGACGTGTTCAATTTGCTA
Found at i:3151254 original size:29 final size:28
Alignment explanation
Indices: 3151183--3151260 Score: 72
Period size: 29 Copynumber: 2.7 Consensus size: 28
3151173 ACGATAGAAA
3151183 AAAATATAATTTTATAGTTTTTAAAAGATT
1 AAAAT-TAATTTTATA-TTTTTAAAAGATT
*
3151213 -AAATTAAATTTTTATATTTTT-AAGGAGTT
1 AAAATT-AA-TTTTATATTTTTAAAAGA-TT
3151242 AAAATGTAATTTTAT-TTTT
1 AAAAT-TAATTTTATATTTT
3151261 ATCGATTTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
28 9 0.21
29 19 0.45
30 13 0.31
31 1 0.02
ACGTcount: A:0.41, C:0.00, G:0.08, T:0.51
Consensus pattern (28 bp):
AAAATTAATTTTATATTTTTAAAAGATT
Found at i:3156289 original size:16 final size:16
Alignment explanation
Indices: 3156264--3156294 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
3156254 TTACTGATTA
*
3156264 CAACTTTATTTCATTC
1 CAACTCTATTTCATTC
3156280 CAACTCTATTTCATT
1 CAACTCTATTTCATT
3156295 ACAGTAAACC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.26, C:0.26, G:0.00, T:0.48
Consensus pattern (16 bp):
CAACTCTATTTCATTC
Found at i:3165903 original size:31 final size:32
Alignment explanation
Indices: 3165850--3165915 Score: 89
Period size: 31 Copynumber: 2.1 Consensus size: 32
3165840 GGTACCTAAT
* *
3165850 TTTTTTTATCCAATTAGCTACTTGAAAATGAC
1 TTTTTTGATCAAATTAGCTACTTGAAAATGAC
**
3165882 TTTTTTGATCAAATTAG-TACTTGAACTTGAC
1 TTTTTTGATCAAATTAGCTACTTGAAAATGAC
3165913 TTT
1 TTT
3165916 ATAGTTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 15 0.50
32 15 0.50
ACGTcount: A:0.29, C:0.14, G:0.11, T:0.47
Consensus pattern (32 bp):
TTTTTTGATCAAATTAGCTACTTGAAAATGAC
Found at i:3169275 original size:12 final size:12
Alignment explanation
Indices: 3169258--3169282 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
3169248 CGTCGAATCG
3169258 GATTCAAGTCGA
1 GATTCAAGTCGA
3169270 GATTCAAGTCGA
1 GATTCAAGTCGA
3169282 G
1 G
3169283 TTTAAGTATG
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:0.32, C:0.16, G:0.28, T:0.24
Consensus pattern (12 bp):
GATTCAAGTCGA
Found at i:3176196 original size:9 final size:9
Alignment explanation
Indices: 3176182--3176212 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
3176172 TTGTTAACTG
3176182 TTTTATTTT
1 TTTTATTTT
3176191 TTTTATTTT
1 TTTTATTTT
3176200 TTTTATATTT
1 TTTTAT-TTT
3176210 TTT
1 TTT
3176213 GGTCATATCT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 15 0.71
10 6 0.29
ACGTcount: A:0.13, C:0.00, G:0.00, T:0.87
Consensus pattern (9 bp):
TTTTATTTT
Found at i:3184855 original size:20 final size:20
Alignment explanation
Indices: 3184827--3184873 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
3184817 CCCATTTTAA
* **
3184827 TAAATATTAAAAATTTATTT
1 TAAAAATTAAAAAAATATTT
3184847 TAAAAATTAAAAAAATATTT
1 TAAAAATTAAAAAAATATTT
3184867 TAAAAAT
1 TAAAAAT
3184874 ATTTTAAAAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (20 bp):
TAAAAATTAAAAAAATATTT
Found at i:3184863 original size:31 final size:29
Alignment explanation
Indices: 3184828--3184912 Score: 84
Period size: 30 Copynumber: 2.8 Consensus size: 29
3184818 CCATTTTAAT
3184828 AAATA-TTAAAAATTTATTTTAAAAATTAAAA
1 AAATATTTAAAAA--TATTTT-AAAATTAAAA
3184859 AAATATTTTAAAAATATTTTAAAATTAAAA
1 AAATA-TTTAAAAATATTTTAAAATTAAAA
* **
3184889 AATTA-AAAAAAAGTATTTTAAAAT
1 AAATATTTAAAAA-TATTTTAAAAT
3184913 ATTTTAAAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 8
0.81 0.05 0.14
Matches are distributed among these distances:
28 5 0.10
29 11 0.23
30 14 0.29
31 11 0.23
33 7 0.15
ACGTcount: A:0.61, C:0.00, G:0.01, T:0.38
Consensus pattern (29 bp):
AAATATTTAAAAATATTTTAAAATTAAAA
Found at i:3184873 original size:11 final size:11
Alignment explanation
Indices: 3184820--3184882 Score: 53
Period size: 11 Copynumber: 5.8 Consensus size: 11
3184810 GGCCCGACCC
3184820 ATTTTAATAAAT
1 ATTTTAA-AAAT
3184832 A--TTAAAAATTT
1 ATTTTAAAAA--T
3184843 ATTTT-AAAA-
1 ATTTTAAAAAT
**
3184852 ATTAAAAAAAT
1 ATTTTAAAAAT
3184863 ATTTTAAAAAT
1 ATTTTAAAAAT
3184874 ATTTTAAAA
1 ATTTTAAAA
3184883 TTAAAAAATT
Statistics
Matches: 41, Mismatches: 4, Indels: 13
0.71 0.07 0.22
Matches are distributed among these distances:
9 6 0.15
10 8 0.20
11 20 0.49
12 5 0.12
13 2 0.05
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (11 bp):
ATTTTAAAAAT
Found at i:3184912 original size:39 final size:40
Alignment explanation
Indices: 3184848--3184939 Score: 154
Period size: 39 Copynumber: 2.4 Consensus size: 40
3184838 AATTTATTTT
3184848 AAAAATT-AAAAAAATATTTTAAAAATATTTTAAAATT-A
1 AAAAATTAAAAAAAATATTTTAAAAATATTTTAAAATTAA
3184886 AAAAATTAAAAAAAAGTATTTT-AAAATATTTTAAAATTAA
1 AAAAATTAAAAAAAA-TATTTTAAAAATATTTTAAAATTAA
3184926 AAAAATTAAAAAAA
1 AAAAATTAAAAAAA
3184940 TAAATATATT
Statistics
Matches: 51, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
38 7 0.14
39 23 0.45
40 21 0.41
ACGTcount: A:0.66, C:0.00, G:0.01, T:0.33
Consensus pattern (40 bp):
AAAAATTAAAAAAAATATTTTAAAAATATTTTAAAATTAA
Found at i:3185516 original size:11 final size:11
Alignment explanation
Indices: 3185500--3185533 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
3185490 ATCCAAACAT
3185500 TAATAATAAAA
1 TAATAATAAAA
* *
3185511 TAATAACAACA
1 TAATAATAAAA
3185522 TAATAATAAAA
1 TAATAATAAAA
3185533 T
1 T
3185534 TATAGCAAAA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (11 bp):
TAATAATAAAA
Found at i:3186347 original size:16 final size:16
Alignment explanation
Indices: 3186326--3186359 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
3186316 TGCATATTTA
*
3186326 ATCATTTATATAATAT
1 ATCATTTACATAATAT
*
3186342 ATCATTTACATATTAT
1 ATCATTTACATAATAT
3186358 AT
1 AT
3186360 TTATTTTCAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.41, C:0.09, G:0.00, T:0.50
Consensus pattern (16 bp):
ATCATTTACATAATAT
Found at i:3188250 original size:276 final size:264
Alignment explanation
Indices: 3187734--3188273 Score: 855
Period size: 276 Copynumber: 2.0 Consensus size: 264
3187724 AAGTTGAAAG
*
3187734 AACATAAAAGAAAAAATTAAATTGCTCAAAACGAAAAAAATTGGTATCAATTGTATAATTTAACC
1 AACATAAAAGAAAAAATTAAATTGCTCAAAACGAAAAAAATTAGTATCAATTGTATAATTTAACC
*
3187799 TAAAATTTTTGTTTGAAATGATAGTTTAACATGCCACGTCAGCTTATTATTACACCGTATGACTA
66 TAAAATTTTTGTTTGAAATGATAGTTTAACATGCCACGTCAGCTTACTATTACACCGTATGACTA
* * *
3187864 AAATGTTACAACACGTTAACGTAAGTAACTAAAACATAGCATTTCAAACATAAGTGATTAAAATG
131 AAATGTTACAACACGTTAACGCAAGTAACTAAAACATAACATTTCAAACATAAGTGACTAAAATG
* * *
3187929 TAAATTGAGGGAAACAAAAGTGACTATTTTCATAGTTTACCCTAAATAATTTTTTTCACGTGGGA
196 TAAACTGAGGGAAACAAAAATAACTATTTTCATAGTTTACCCTAAATAATTTTTTTCACGTGGGA
3187994 TTAA
261 TTAA
*
3187998 AACATAAAAGAAAAAAATTAAATTGCTCAAACCGAAAAAAAATTAGTATCAATTGTATAATTTAA
1 AACATAAAAG-AAAAAATTAAATTGCTCAAAACG-AAAAAAATTAGTATCAATTGTATAATTTAA
3188063 CCTAAAATTTTTGTTTGAAATGATAGTTTAACATGCCACGTCAGCTTACTATTACACCGTTAATG
64 CCTAAAATTTTTGTTTGAAATGATAGTTTAACATGCCACGTCAGCTTACTATTACACC-------
* * *
3188128 GCTCAGTGACTAAAATGTTACAACACGTTAACGCATGTGACTAAAACATAACATTTTAAACATAA
122 G-T-A-TGACTAAAATGTTACAACACGTTAACGCAAGTAACTAAAACATAACATTTCAAACATAA
*
3188193 GTGACTAAAATGTAAACTGAGGGAAACAAAAATAACTATTTTTATAGTTTACCCTAAATAATTTT
184 GTGACTAAAATGTAAACTGAGGGAAACAAAAATAACTATTTTCATAGTTTACCCTAAATAATTTT
3188258 TTTCACGTGGGATTAA
249 TTTCACGTGGGATTAA
3188274 CTTAGTTGTT
Statistics
Matches: 251, Mismatches: 13, Indels: 12
0.91 0.05 0.04
Matches are distributed among these distances:
264 10 0.04
265 22 0.09
266 86 0.34
273 1 0.00
274 1 0.00
275 1 0.00
276 130 0.52
ACGTcount: A:0.42, C:0.14, G:0.13, T:0.31
Consensus pattern (264 bp):
AACATAAAAGAAAAAATTAAATTGCTCAAAACGAAAAAAATTAGTATCAATTGTATAATTTAACC
TAAAATTTTTGTTTGAAATGATAGTTTAACATGCCACGTCAGCTTACTATTACACCGTATGACTA
AAATGTTACAACACGTTAACGCAAGTAACTAAAACATAACATTTCAAACATAAGTGACTAAAATG
TAAACTGAGGGAAACAAAAATAACTATTTTCATAGTTTACCCTAAATAATTTTTTTCACGTGGGA
TTAA
Found at i:3190325 original size:60 final size:58
Alignment explanation
Indices: 3190192--3190339 Score: 172
Period size: 60 Copynumber: 2.5 Consensus size: 58
3190182 TATACATTTT
*
3190192 GGTACCTAAACTTGGCTTCAAAGTTCAAATTGGTACTAAGGTTTTTTTGGTCCAATTA
1 GGTACCTAAACTTGGCTTCAAAGTTCAAATTGGTACTAAAGTTTTTTTGGTCCAATTA
* * * * * *
3190250 AGTACTTGAACTTGGCTTTAAGGTTCAATTTGGTACCTAAAGTTTAGTTTT-GTCCAATTA
1 GGTACCTAAACTTGGCTTCAAAGTTCAAATTGGTA-CTAAAGTTT--TTTTGGTCCAATTA
* **
3190310 GGTACCTAAATTTGGCTTCTTAGTTCAAAT
1 GGTACCTAAACTTGGCTTCAAAGTTCAAAT
3190340 AAGTAAATTA
Statistics
Matches: 71, Mismatches: 16, Indels: 4
0.78 0.18 0.04
Matches are distributed among these distances:
58 29 0.41
59 8 0.11
60 30 0.42
61 4 0.06
ACGTcount: A:0.27, C:0.15, G:0.18, T:0.40
Consensus pattern (58 bp):
GGTACCTAAACTTGGCTTCAAAGTTCAAATTGGTACTAAAGTTTTTTTGGTCCAATTA
Found at i:3191026 original size:6 final size:6
Alignment explanation
Indices: 3191015--3191042 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
3191005 AAGTTATGGT
3191015 ATCGTC ATCGTC ATCGTC ATCGTC ATCG
1 ATCGTC ATCGTC ATCGTC ATCGTC ATCG
3191043 GTGAAAGGCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.18, C:0.32, G:0.18, T:0.32
Consensus pattern (6 bp):
ATCGTC
Found at i:3193638 original size:38 final size:37
Alignment explanation
Indices: 3193596--3193670 Score: 141
Period size: 38 Copynumber: 2.0 Consensus size: 37
3193586 CAATTTGCCC
3193596 AAAACAGGGGAGGTTGGTTTTGCGGCCCTAGGCAAAGG
1 AAAACAGGGGAGGTTGGTTTTGCGGCCCTAGG-AAAGG
3193634 AAAACAGGGGAGGTTGGTTTTGCGGCCCTAGGAAAGG
1 AAAACAGGGGAGGTTGGTTTTGCGGCCCTAGGAAAGG
3193671 GAGCCATGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
37 5 0.14
38 32 0.86
ACGTcount: A:0.27, C:0.15, G:0.40, T:0.19
Consensus pattern (37 bp):
AAAACAGGGGAGGTTGGTTTTGCGGCCCTAGGAAAGG
Found at i:3216264 original size:31 final size:29
Alignment explanation
Indices: 3216221--3216282 Score: 88
Period size: 31 Copynumber: 2.1 Consensus size: 29
3216211 ATTTCAAAAT
* *
3216221 TATATATGAACTTTGATTTAATGTGCAATTA
1 TATATATAAACTTTAATTT--TGTGCAATTA
3216252 TATATATAAACTTTAATTTTGTGCAATTA
1 TATATATAAACTTTAATTTTGTGCAATTA
3216281 TA
1 TA
3216283 CACTTAAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 12 0.41
31 17 0.59
ACGTcount: A:0.37, C:0.06, G:0.10, T:0.47
Consensus pattern (29 bp):
TATATATAAACTTTAATTTTGTGCAATTA
Found at i:3216290 original size:29 final size:29
Alignment explanation
Indices: 3216242--3216347 Score: 79
Period size: 31 Copynumber: 3.5 Consensus size: 29
3216232 TTTGATTTAA
*
3216242 TGTGCAATTATATA-TATAAACTTTAATTT
1 TGTGCAATTATACACT-TAAACTTTAATTT
*
3216271 TGTGCAATTATACACTTAAAATTCTAATTGT
1 TGTGCAATTATACACTTAAACTT-TAATT-T
* * * * *
3216302 AGTTCAAATGTATACTTGAAACTTTAATTT
1 TGTGCAATTATACACTT-AAACTTTAATTT
**
3216332 TGATTTAATTATACAC
1 TG-TGCAATTATACAC
3216348 ATTTAAATAA
Statistics
Matches: 59, Mismatches: 13, Indels: 8
0.74 0.16 0.10
Matches are distributed among these distances:
29 19 0.32
30 8 0.14
31 27 0.46
32 5 0.08
ACGTcount: A:0.37, C:0.10, G:0.08, T:0.44
Consensus pattern (29 bp):
TGTGCAATTATACACTTAAACTTTAATTT
Found at i:3238967 original size:37 final size:37
Alignment explanation
Indices: 3238916--3238999 Score: 134
Period size: 37 Copynumber: 2.3 Consensus size: 37
3238906 ACACCTTAAG
* *
3238916 AATTTGCTTGATAGAATGTAAATAAAATAATATATAT
1 AATTTGCTTCATAGAATGTAAAGAAAATAATATATAT
3238953 AATTTGCTTCATAGAATGTAAAGAAAATAATATATAT
1 AATTTGCTTCATAGAATGTAAAGAAAATAATATATAT
3238990 ATATTT-CTTC
1 A-ATTTGCTTC
3239000 TTTTCATTAG
Statistics
Matches: 44, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
37 40 0.91
38 4 0.09
ACGTcount: A:0.45, C:0.06, G:0.10, T:0.39
Consensus pattern (37 bp):
AATTTGCTTCATAGAATGTAAAGAAAATAATATATAT
Found at i:3241113 original size:18 final size:19
Alignment explanation
Indices: 3241074--3241114 Score: 64
Period size: 19 Copynumber: 2.2 Consensus size: 19
3241064 AATATTTCTC
* *
3241074 AAAAGTGCTTTTGGGACAA
1 AAAAATGCTTTTGAGACAA
3241093 AAAAATGCTTTTGAGACAA
1 AAAAATGCTTTTGAGACAA
3241112 AAA
1 AAA
3241115 CATTCCCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.46, C:0.10, G:0.20, T:0.24
Consensus pattern (19 bp):
AAAAATGCTTTTGAGACAA
Found at i:3244704 original size:20 final size:20
Alignment explanation
Indices: 3244667--3244705 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
3244657 AATAAACACA
**
3244667 TAACTATTCATTTAATATTG
1 TAACTATTCAAATAATATTG
*
3244687 TAACTATTCAAATCATATT
1 TAACTATTCAAATAATATT
3244706 ATTTAAATAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.38, C:0.13, G:0.03, T:0.46
Consensus pattern (20 bp):
TAACTATTCAAATAATATTG
Found at i:3249808 original size:20 final size:20
Alignment explanation
Indices: 3249773--3249811 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3249763 AATAAACACA
**
3249773 TAACTATTCATTTAATATTG
1 TAACTATTCAAATAATATTG
3249793 TAACTATTCAAATAATATT
1 TAACTATTCAAATAATATT
3249812 ATTTAAATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (20 bp):
TAACTATTCAAATAATATTG
Found at i:3251816 original size:20 final size:20
Alignment explanation
Indices: 3251781--3251819 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
3251771 AATAAACACA
**
3251781 TAACTATTCATTTAATATTG
1 TAACTATTCAAATAATATTG
3251801 TAACTATTCAAATAATATT
1 TAACTATTCAAATAATATT
3251820 ATTTAAATGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.41, C:0.10, G:0.03, T:0.46
Consensus pattern (20 bp):
TAACTATTCAAATAATATTG
Found at i:3255972 original size:33 final size:33
Alignment explanation
Indices: 3255907--3255972 Score: 78
Period size: 33 Copynumber: 2.0 Consensus size: 33
3255897 TCAAATACTA
* * *
3255907 TTTAAAAAATCATTAAAAATATTTTTTATTTAT
1 TTTAAAAAATAAATAAAAATATATTTTATTTAT
* * *
3255940 TTTAAAAAATAAATATACATATATTTTCTTTAT
1 TTTAAAAAATAAATAAAAATATATTTTATTTAT
3255973 ATGTTATTTC
Statistics
Matches: 27, Mismatches: 6, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (33 bp):
TTTAAAAAATAAATAAAAATATATTTTATTTAT
Found at i:3256759 original size:30 final size:31
Alignment explanation
Indices: 3256700--3256760 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
3256690 AATTTTTTGC
3256700 CATTGAACTATTCAAAAATTTTCATTTAAGT
1 CATTGAACTATTCAAAAATTTTCATTTAAGT
* * * *
3256731 CATTGAATTATT-TAAATTTTTTATTTAAGT
1 CATTGAACTATTCAAAAATTTTCATTTAAGT
3256761 TACTAAACTG
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.36, C:0.08, G:0.07, T:0.49
Consensus pattern (31 bp):
CATTGAACTATTCAAAAATTTTCATTTAAGT
Found at i:3262585 original size:102 final size:100
Alignment explanation
Indices: 3262430--3262627 Score: 265
Period size: 102 Copynumber: 2.0 Consensus size: 100
3262420 AATAATCATA
* * *
3262430 ATTTTTAAAAGAGTAACTAAGTGTATTTCTAAGCATTTTTAAAAAAATTTAAAATATTAATTT-T
1 ATTTTCAAAAGAGTAACTAAGTGTATTTATAAGCACTTTTAAAAAAATTTAAAATATTAATTTAT
**
3262494 TT-ACTTTTAAAAAAACATTCTTTTATTTTTTTTAT
66 TTGACTTTT-AAAAAACATTAATTTATTTTTTTTAT
* * * *
3262529 ATTTTCAAAAGAGTAATTAAGTGTTATATATATAAGCGCTTTTAAGAAAATTTAAAATATTATTT
1 ATTTTCAAAAGAGTAACTAAGTG-TAT-T-TATAAGCACTTTTAAAAAAATTTAAAATATTAATT
3262594 TATTTGACTTTTAAAAAACATTAATTTATTTTTT
63 TATTTGACTTTTAAAAAACATTAATTTATTTTTT
3262628 ATTAATAAAC
Statistics
Matches: 85, Mismatches: 9, Indels: 6
0.85 0.09 0.06
Matches are distributed among these distances:
99 21 0.25
100 3 0.04
101 1 0.01
102 31 0.36
103 23 0.27
104 6 0.07
ACGTcount: A:0.40, C:0.06, G:0.07, T:0.48
Consensus pattern (100 bp):
ATTTTCAAAAGAGTAACTAAGTGTATTTATAAGCACTTTTAAAAAAATTTAAAATATTAATTTAT
TTGACTTTTAAAAAACATTAATTTATTTTTTTTAT
Found at i:3278064 original size:35 final size:35
Alignment explanation
Indices: 3278013--3278087 Score: 141
Period size: 35 Copynumber: 2.1 Consensus size: 35
3278003 CGTTACGTTC
*
3278013 AAAGAAATTCCCACTACCTCAAATGATAGGGCACA
1 AAAGCAATTCCCACTACCTCAAATGATAGGGCACA
3278048 AAAGCAATTCCCACTACCTCAAATGATAGGGCACA
1 AAAGCAATTCCCACTACCTCAAATGATAGGGCACA
3278083 AAAGC
1 AAAGC
3278088 CTAAAGTATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
35 39 1.00
ACGTcount: A:0.43, C:0.27, G:0.15, T:0.16
Consensus pattern (35 bp):
AAAGCAATTCCCACTACCTCAAATGATAGGGCACA
Found at i:3282987 original size:31 final size:31
Alignment explanation
Indices: 3282935--3283010 Score: 98
Period size: 31 Copynumber: 2.5 Consensus size: 31
3282925 ATAAAAATTG
* * * *
3282935 ATAGTTGCGCGACCAAAAAAGAAAAGAGTCA
1 ATAGTTGGGTGACTAAAAAAGAAAAGAGACA
* *
3282966 ATGGTTGGGTGACTAAAAAAGAAAGGAGACA
1 ATAGTTGGGTGACTAAAAAAGAAAAGAGACA
3282997 ATAGTTGGGTGACT
1 ATAGTTGGGTGACT
3283011 TGTGGTGTAA
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 38 1.00
ACGTcount: A:0.42, C:0.11, G:0.29, T:0.18
Consensus pattern (31 bp):
ATAGTTGGGTGACTAAAAAAGAAAAGAGACA
Found at i:3288738 original size:16 final size:17
Alignment explanation
Indices: 3288717--3288749 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
3288707 TTCCATTTTG
3288717 ATACAAA-ATAAAAATA
1 ATACAAATATAAAAATA
*
3288733 ATACAAATATAAGAATA
1 ATACAAATATAAAAATA
3288750 TCCAAACACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 7 0.47
17 8 0.53
ACGTcount: A:0.70, C:0.06, G:0.03, T:0.21
Consensus pattern (17 bp):
ATACAAATATAAAAATA
Found at i:3292937 original size:236 final size:236
Alignment explanation
Indices: 3292524--3292995 Score: 863
Period size: 236 Copynumber: 2.0 Consensus size: 236
3292514 ATCTTGACTC
* * *
3292524 CGGCCTCTACGTAATCTACCCAGTTGACAATGAATGGAAGAAATCCCCAAAACTGTTTTTAAAAA
1 CGGCCTCTACGTAATCCACCCAGTTGACAATGAACGGAAGAAATCCCCAAAACTGTTTTGAAAAA
3292589 AAATTGCTTTGACGGCTGCTAGACCCCAAGCAAAGAAAAAATGAGATTTTTATATCTATTTTTAG
66 AAATTGCTTTGACGGCTGCTAGACCCCAAGCAAAGAAAAAATGAGATTTTTATATCTATTTTTAG
3292654 GGTTTTTAGAAATTAAATAAATATAACTACGTTTTAAACCGAAAATTATAATTACATTAATTATA
131 GGTTTTTAGAAATTAAATAAATATAACTACGTTTTAAACCGAAAATTATAATTACATTAATTATA
3292719 ATAATGATTTCGGTAAACTATATATTTATTTGAATTTATAT
196 ATAATGATTTCGGTAAACTATATATTTATTTGAATTTATAT
* *
3292760 CGGCCTCTACGTAATCCACCCAGTTGACAATGAACGGAAGGAATCCCCAAAACTGTTTTGGAAAA
1 CGGCCTCTACGTAATCCACCCAGTTGACAATGAACGGAAGAAATCCCCAAAACTGTTTTGAAAAA
** * *
3292825 ACTTTTCTTTGACTGCTGCTAGACCCCAAGCAAAGAAAAAATGAGATTTTTATATCTATTTTTAG
66 AAATTGCTTTGACGGCTGCTAGACCCCAAGCAAAGAAAAAATGAGATTTTTATATCTATTTTTAG
3292890 GGTTTTTAGAAATTAAATAAATATAACTACGTTTTAAACCGAAAATTATAATTACATTAATTATA
131 GGTTTTTAGAAATTAAATAAATATAACTACGTTTTAAACCGAAAATTATAATTACATTAATTATA
3292955 ATAATGATTTCGGTAAACTATATATTTATTTGAATTTATAT
196 ATAATGATTTCGGTAAACTATATATTTATTTGAATTTATAT
3292996 ACTAACCAAA
Statistics
Matches: 227, Mismatches: 9, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
236 227 1.00
ACGTcount: A:0.38, C:0.14, G:0.13, T:0.35
Consensus pattern (236 bp):
CGGCCTCTACGTAATCCACCCAGTTGACAATGAACGGAAGAAATCCCCAAAACTGTTTTGAAAAA
AAATTGCTTTGACGGCTGCTAGACCCCAAGCAAAGAAAAAATGAGATTTTTATATCTATTTTTAG
GGTTTTTAGAAATTAAATAAATATAACTACGTTTTAAACCGAAAATTATAATTACATTAATTATA
ATAATGATTTCGGTAAACTATATATTTATTTGAATTTATAT
Found at i:3300614 original size:21 final size:21
Alignment explanation
Indices: 3300581--3300626 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
3300571 AAAATCTAAT
3300581 TCAAT-TTTT-TTTGGTTAAA
1 TCAATCTTTTATTTGGTTAAA
* *
3300600 TTAATCTTTTATTTGGTTCAA
1 TCAATCTTTTATTTGGTTAAA
3300621 TCAATC
1 TCAATC
3300627 CGTACAATTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 4 0.18
20 4 0.18
21 14 0.64
ACGTcount: A:0.26, C:0.11, G:0.09, T:0.54
Consensus pattern (21 bp):
TCAATCTTTTATTTGGTTAAA
Found at i:3303409 original size:3 final size:3
Alignment explanation
Indices: 3303401--3303439 Score: 78
Period size: 3 Copynumber: 13.0 Consensus size: 3
3303391 TTGCTTTGTG
3303401 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
3303440 GTCTAAGTTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 36 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:3312162 original size:18 final size:18
Alignment explanation
Indices: 3312139--3312175 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3312129 AAATATGTAG
3312139 ATAAATATATAA-ACTAAT
1 ATAAATA-ATAATACTAAT
3312157 ATAAATAATAATACTAAT
1 ATAAATAATAATACTAAT
3312175 A
1 A
3312176 ATAATGATGA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 4 0.22
18 14 0.78
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.32
Consensus pattern (18 bp):
ATAAATAATAATACTAAT
Found at i:3315086 original size:14 final size:14
Alignment explanation
Indices: 3315063--3315092 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
3315053 AGTTTGAATC
3315063 AAAATAATTATTAT
1 AAAATAATTATTAT
*
3315077 AAAATGATTATTAT
1 AAAATAATTATTAT
3315091 AA
1 AA
3315093 CATTTTGACA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.57, C:0.00, G:0.03, T:0.40
Consensus pattern (14 bp):
AAAATAATTATTAT
Found at i:3315155 original size:21 final size:21
Alignment explanation
Indices: 3315131--3315182 Score: 52
Period size: 21 Copynumber: 2.5 Consensus size: 21
3315121 TTTTTTTTGA
*
3315131 AATATTTAAAATATAAAGAAT
1 AATATTTAAAAGATAAAGAAT
* *
3315152 AATA-ATATAACGATAAAGAAT
1 AATATTTA-AAAGATAAAGAAT
*
3315173 AACATTTAAA
1 AATATTTAAA
3315183 TTGATTTCGA
Statistics
Matches: 24, Mismatches: 5, Indels: 4
0.73 0.15 0.12
Matches are distributed among these distances:
20 2 0.08
21 20 0.83
22 2 0.08
ACGTcount: A:0.62, C:0.04, G:0.06, T:0.29
Consensus pattern (21 bp):
AATATTTAAAAGATAAAGAAT
Found at i:3326077 original size:45 final size:44
Alignment explanation
Indices: 3326005--3326110 Score: 119
Period size: 45 Copynumber: 2.4 Consensus size: 44
3325995 TGGCTTTAAC
* *
3326005 CTGCTCCACTACAACTTCAGGGAGATAAGA-TTCGCCAT-CTTCAGT
1 CTGCCCCACTGCAACTTCAGGGAGATAAGACTT-G-CATCCTT-AGT
**
3326050 CTGCCCCACTGCAACTTCA-GGAGGATAAGACTTGTTTCCTTAGT
1 CTGCCCCACTGCAACTTCAGGGA-GATAAGACTTGCATCCTTAGT
3326094 CTGCCCCACTGCAACTT
1 CTGCCCCACTGCAACTT
3326111 TGATCTACTT
Statistics
Matches: 54, Mismatches: 4, Indels: 7
0.83 0.06 0.11
Matches are distributed among these distances:
44 24 0.44
45 28 0.52
46 2 0.04
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (44 bp):
CTGCCCCACTGCAACTTCAGGGAGATAAGACTTGCATCCTTAGT
Found at i:3326296 original size:44 final size:43
Alignment explanation
Indices: 3326126--3326577 Score: 125
Period size: 44 Copynumber: 10.3 Consensus size: 43
3326116 TACTTCGCTG
*
3326126 CCTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTA
1 CCTAGGGAGATAAGATCTGTAATCTTCAATCTACTCCACT-CTA
* * * * * *
3326170 CCCAGGAAGAT-AGA-AT-TACTGGCTTCAATGTACTCCACTGTAA
1 CCTAGGGAGATAAGATCTGTAAT--CTTCAATCTACTCCACTCT-A
* * * * ** * * *
3326213 CTTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTG
1 CCT-AGGGAGATAAGATCTGTAATCTTCAATCTACTCCACT-CTA
* * * *
3326258 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTG
1 CCTAGGGAGATAAGATCTGTAATCTTCAATCTACTCCACT-CTA
* * * * * *
3326302 CCCATGGAGATAGAGTTACTG---GCTTCAATGC-ACTCCATTGTAA
1 CCTAGGGAGATA-AGAT-CTGTAATCTTCAAT-CTACTCCACTCT-A
* * **** ** *
3326345 CCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCACTACTA
1 CCT-AGGGAGATAAGATCTGTAATCTTCAATCTACTCCACT-CTA
* * * *
3326390 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTG
1 CCTAGGGAGATAAGATCTGTAATCTTCAATCTACTCCACT-CTA
* * * * * *
3326434 CCCAGAGAGAT-AGA-AT-TACTGGCTTCAATGTACTCCACTGTAA
1 CCTAGGGAGATAAGATCTGTAAT--CTTCAATCTACTCCACTCT-A
* * * ** * * *
3326477 CCTCAGGGAGGTAAAATCCGCCATCATT-GATCTGCTCCACTACTG
1 CCT-AGGGAGATAAGATCTGTAATC-TTCAATCTACTCCACT-CTA
* *
3326522 CTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTA
1 CCTAGGGAGATAAGATCTGTAATCTTCAATCTACTCCACT-CTA
* *
3326566 CCGAGAGAGATA
1 CCTAGGGAGATA
3326578 GAATTACTGG
Statistics
Matches: 275, Mismatches: 105, Indels: 56
0.63 0.24 0.13
Matches are distributed among these distances:
41 6 0.02
42 6 0.02
43 59 0.21
44 143 0.52
45 51 0.19
46 8 0.03
47 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (43 bp):
CCTAGGGAGATAAGATCTGTAATCTTCAATCTACTCCACTCTA
Found at i:3326369 original size:132 final size:131
Alignment explanation
Indices: 3326123--3326628 Score: 836
Period size: 132 Copynumber: 3.8 Consensus size: 131
3326113 ATCTACTTCG
*
3326123 CTGCCTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTACCCAG-GAAGATAGAATT
1 CTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTACCCAGAG-AGATAGAATT
* *
3326187 ACTGGCTTCAATGTACTCCACTGTAACTTCAGGGAGGTAAAATCCGCCATCTTCGATCTGCTCCA
65 ACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCTT-GATCTGCTCCA
3326252 CTA
129 CTA
* * *
3326255 CTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCATG-GAGATAGAGTT
1 CTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTACCCA-GAGAGATAGAATT
* *
3326319 ACTGGCTTCAATGCACTCCATTGTAACCTCAGGGAGGTAAAATCCACCATCTTTGATCTGCTCCA
65 ACTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATC-TTGATCTGCTCCA
3326384 CTA
129 CTA
* * *
3326387 CTACTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGTTGCCCAGAGAGATAGAATTA
1 CTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTACCCAGAGAGATAGAATTA
*
3326452 CTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCGCCATCATTGATCTGCTCCAC
66 CTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATC-TTGATCTGCTCCAC
3326517 TA
130 TA
*
3326519 CTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTACCGAGAGAGATAGAATTA
1 CTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTACCCAGAGAGATAGAATTA
3326584 CTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCA
66 CTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCA
3326629 ACTAGACTCA
Statistics
Matches: 352, Mismatches: 19, Indels: 6
0.93 0.05 0.02
Matches are distributed among these distances:
131 1 0.00
132 347 0.99
133 4 0.01
ACGTcount: A:0.28, C:0.24, G:0.19, T:0.29
Consensus pattern (131 bp):
CTGCTTAGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTACCCAGAGAGATAGAATTA
CTGGCTTCAATGTACTCCACTGTAACCTCAGGGAGGTAAAATCCACCATCTTGATCTGCTCCACT
A
Found at i:3334704 original size:23 final size:23
Alignment explanation
Indices: 3334678--3334752 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
3334668 ATAAGTGCCA
3334678 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* *
3334701 CACTG-GATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
3334723 CACTGAAATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
3334746 CACTGAT
1 CACTGAT
3334753 CAATAACACT
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
22 20 0.43
23 26 0.57
ACGTcount: A:0.32, C:0.27, G:0.21, T:0.20
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:3336336 original size:132 final size:132
Alignment explanation
Indices: 3336075--3336527 Score: 652
Period size: 132 Copynumber: 3.5 Consensus size: 132
3336065 GGGCTATCAC
* ** * * *
3336075 AGAATTACTGGCTTCAATGTACTCTACTGTAACCTTAGAGAGGTAAAATCTGCCA---TCAACCT
1 AGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCT
* ** ** * *
3336137 GCTCCACTGCAACCGAGGGAGATAAGACCTGAAATCTTCAATCTATTCTACTGTTGTCCAGGGAA
66 GCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCAACTGTTGTCCAGGGAA
3336202 GT
131 GT
** * *
3336204 AGAATTACTGGCTTCAATGTACTTTACTGTAACTACAGGGAGGTAAAATCCGCCATCTTCGATCT
1 AGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCT
* * * *
3336269 GCTCCACTACTGCTTAGGAAGATAAGATCTGAAATCTTCAATCTATTCCACTGTTGTCTAGGAAA
66 GCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCAACTGTTGTCCAGGGAA
3336334 GT
131 GT
3336336 AGAATTACT-G--T--ATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCT
1 AGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCT
3336396 GCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCAACTGTTGTCCAGGGAA
66 GCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCAACTGTTGTCCAGGGAA
3336461 GT
131 GT
*
3336463 AGAATTACTGACTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCT
1 AGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCT
3336528 ACTTCACTTT
Statistics
Matches: 289, Mismatches: 27, Indels: 13
0.88 0.08 0.04
Matches are distributed among these distances:
127 117 0.40
129 50 0.17
130 1 0.00
131 1 0.00
132 120 0.42
ACGTcount: A:0.30, C:0.23, G:0.19, T:0.29
Consensus pattern (132 bp):
AGAATTACTGGCTTCAATGTACTCCACTGTAACCACAGGGAGGTAAAATCTGCCATCTTCGATCT
GCTCCACTACTGCTTAGGGAGATAAGATCTGAAATCTTCAATCTATTCAACTGTTGTCCAGGGAA
GT
Found at i:3337683 original size:7 final size:7
Alignment explanation
Indices: 3337673--3337711 Score: 53
Period size: 7 Copynumber: 5.6 Consensus size: 7
3337663 CCGGTTTTAC
3337673 TTTTTCA
1 TTTTTCA
3337680 TTTTTCA
1 TTTTTCA
3337687 TTTTTCA
1 TTTTTCA
3337694 -TTTTCA
1 TTTTTCA
*
3337700 TCTCTTCA
1 T-TTTTCA
3337708 TTTT
1 TTTT
3337712 CCACATCACT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
6 6 0.21
7 16 0.57
8 6 0.21
ACGTcount: A:0.13, C:0.18, G:0.00, T:0.69
Consensus pattern (7 bp):
TTTTTCA
Found at i:3338681 original size:19 final size:19
Alignment explanation
Indices: 3338657--3338694 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
3338647 TAATTTGGAA
3338657 GAAAAAATC-TGAAAGAATG
1 GAAAAAATCGT-AAAGAATG
3338676 GAAAAAATCGTAAAGAATG
1 GAAAAAATCGTAAAGAATG
3338695 AAAGAACATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.58, C:0.05, G:0.21, T:0.16
Consensus pattern (19 bp):
GAAAAAATCGTAAAGAATG
Found at i:3340597 original size:19 final size:20
Alignment explanation
Indices: 3340573--3340612 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
3340563 AACTGTGTTT
* *
3340573 AATGCATATG-ATGTAATGA
1 AATGCAAATGCATGAAATGA
3340592 AATGCAAATGCATGAAATGA
1 AATGCAAATGCATGAAATGA
3340612 A
1 A
3340613 TGCGAAAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.47, C:0.07, G:0.20, T:0.25
Consensus pattern (20 bp):
AATGCAAATGCATGAAATGA
Found at i:3340664 original size:13 final size:13
Alignment explanation
Indices: 3340646--3340671 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
3340636 ATTCAATTTT
3340646 TTTACTAGAAAAC
1 TTTACTAGAAAAC
3340659 TTTACTAGAAAAC
1 TTTACTAGAAAAC
3340672 AAATCTCTTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.15, G:0.08, T:0.31
Consensus pattern (13 bp):
TTTACTAGAAAAC
Found at i:3342587 original size:3 final size:3
Alignment explanation
Indices: 3342579--3342611 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
3342569 ATATGTGTAG
3342579 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
3342612 ATATAACATG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:3352344 original size:25 final size:25
Alignment explanation
Indices: 3352311--3352360 Score: 100
Period size: 25 Copynumber: 2.0 Consensus size: 25
3352301 AGTGAAAGAA
3352311 AAAGTCATTTTGTCACCGGTTACTG
1 AAAGTCATTTTGTCACCGGTTACTG
3352336 AAAGTCATTTTGTCACCGGTTACTG
1 AAAGTCATTTTGTCACCGGTTACTG
3352361 GGGGAAGTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 25 1.00
ACGTcount: A:0.24, C:0.20, G:0.20, T:0.36
Consensus pattern (25 bp):
AAAGTCATTTTGTCACCGGTTACTG
Found at i:3355517 original size:107 final size:106
Alignment explanation
Indices: 3355319--3355577 Score: 317
Period size: 107 Copynumber: 2.4 Consensus size: 106
3355309 GAGAAAAAGG
3355319 AAAAAAAAATTTGGGTGCTGGCCTATCAATGGCCGGCACCCAACAGTAAAAAAAAAAATTTACTT
1 AAAAAAAAATTTGGGTGCTGGCCTATCAATGGCCGGCA-CC-ACAGTAAAAAAAAAAATTTACTT
* * **
3355384 TTTTTTTCATGTTAAAATCAGGTATCAGTATACGAAAAAAGTA
64 TTTTTTTCATGTCAAAATCAGATATCAAAATACGAAAAAAGTA
*
3355427 AAAAAAAAATTTGGGTGCTGGCCTGTCAATGGCCGGCACCA-AGTACAATTTAAAAAAAA-TT-C
1 AAAAAAAAATTTGGGTGCTGGCCTATCAATGGCCGGCACCACAGTA-AA---AAAAAAAATTTAC
* *
3355489 TTTTTTTTTCGTGTCAGAATCAGATATCAAAATACGAAAAAAGTA
62 TTTTTTTTTCATGTCAAAATCAGATATCAAAATACGAAAAAAGTA
*** * *
3355534 AAAAATATTTTTTTTGGTGCTGGCCTATCAATGGTCGGCACCAC
1 AAAAA-A-AAATTTGGGTGCTGGCCTATCAATGGCCGGCACCAC
3355578 CTTGTAATGG
Statistics
Matches: 131, Mismatches: 13, Indels: 12
0.84 0.08 0.08
Matches are distributed among these distances:
105 4 0.03
106 3 0.02
107 47 0.36
108 40 0.31
109 37 0.28
ACGTcount: A:0.38, C:0.16, G:0.17, T:0.29
Consensus pattern (106 bp):
AAAAAAAAATTTGGGTGCTGGCCTATCAATGGCCGGCACCACAGTAAAAAAAAAAATTTACTTTT
TTTTTCATGTCAAAATCAGATATCAAAATACGAAAAAAGTA
Found at i:3356108 original size:108 final size:107
Alignment explanation
Indices: 3355882--3356166 Score: 292
Period size: 110 Copynumber: 2.7 Consensus size: 107
3355872 AATGTGGTGT
* * * *
3355882 AGGCTAGCACCCAAAAATTTTTTTTACTTTTTTCGTATACTGATATCTGATTCTGACACGAAAAA
1 AGGCCAGCACCCAAAAATTTTTTTTACTTTTTTCATATACTGATACCTGATTCTAACACGAAAAA
* * * * *
3355947 AAAGAAAAAAATTTTTTAAATTGTACTTGGTGCCGGCTATTGAC
66 AAAGAAAAAAAATTATT-AACTGTA-TAGGTGCCGGCCATTGAC
* * ***
3355991 AGGCCAGCACCCAAAATTTTTTTTTTACTTTTTTCATATACTGATACCTGATTTTAAGGTGAAAA
1 AGGCCAGCACCCAAAA-ATTTTTTTTACTTTTTTCATATACTGATACCTGATTCTAACACGAAAA
3356056 AAAAGTAAAAAAAAATTATT-ACTGT-TAGGTGCCGGCCATTGAC
65 AAAAG--AAAAAAAATTATTAACTGTATAGGTGCCGGCCATTGAC
**** * ** *
3356099 AGGCCAGCA-CCAAAAA-AAAATTTAATTTTTTCATATACTGATATTTGATTCTGACAC-AAAAA
1 AGGCCAGCACCCAAAAATTTTTTTTACTTTTTTCATATACTGATACCTGATTCTAACACGAAAAA
3356161 AAAGAA
66 AAAGAA
3356167 TTTTCTTTTA
Statistics
Matches: 146, Mismatches: 27, Indels: 13
0.78 0.15 0.07
Matches are distributed among these distances:
102 2 0.01
104 9 0.06
105 29 0.20
107 6 0.04
108 25 0.17
109 15 0.10
110 49 0.34
112 11 0.08
ACGTcount: A:0.38, C:0.15, G:0.14, T:0.33
Consensus pattern (107 bp):
AGGCCAGCACCCAAAAATTTTTTTTACTTTTTTCATATACTGATACCTGATTCTAACACGAAAAA
AAAGAAAAAAAATTATTAACTGTATAGGTGCCGGCCATTGAC
Found at i:3358831 original size:13 final size:13
Alignment explanation
Indices: 3358815--3358845 Score: 62
Period size: 13 Copynumber: 2.4 Consensus size: 13
3358805 CTCCTCACAC
3358815 GAATACATTATTT
1 GAATACATTATTT
3358828 GAATACATTATTT
1 GAATACATTATTT
3358841 GAATA
1 GAATA
3358846 ACGAATCTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.42, C:0.06, G:0.10, T:0.42
Consensus pattern (13 bp):
GAATACATTATTT
Found at i:3368279 original size:12 final size:12
Alignment explanation
Indices: 3368262--3368288 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
3368252 AGCGTGTGAG
3368262 ACATGAACTCAA
1 ACATGAACTCAA
3368274 ACATGAACTCAA
1 ACATGAACTCAA
3368286 ACA
1 ACA
3368289 GGTAATTTAA
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:0.52, C:0.26, G:0.07, T:0.15
Consensus pattern (12 bp):
ACATGAACTCAA
Found at i:3373280 original size:26 final size:25
Alignment explanation
Indices: 3373221--3373281 Score: 70
Period size: 26 Copynumber: 2.4 Consensus size: 25
3373211 AGCCATTTCG
*
3373221 GGAAGCTCACAAAGAGCCTTTAATC
1 GGAAGCTCACAAAGAGCCTATAATC
*
3373246 GAGAAGCTCACGAAGAGCCATATAAT-
1 G-GAAGCTCACAAAGAGCC-TATAATC
3373272 GGAATGCTCA
1 GGAA-GCTCA
3373282 TAAGAGTTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 4 0.13
26 22 0.71
27 5 0.16
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (25 bp):
GGAAGCTCACAAAGAGCCTATAATC
Found at i:3374460 original size:11 final size:11
Alignment explanation
Indices: 3374444--3374468 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3374434 CCGTTTAGAA
3374444 TTTTTTTTATT
1 TTTTTTTTATT
3374455 TTTTTTTTATT
1 TTTTTTTTATT
3374466 TTT
1 TTT
3374469 AAAATACTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.08, C:0.00, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTATT
Found at i:3374507 original size:28 final size:27
Alignment explanation
Indices: 3374456--3374508 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
3374446 TTTTTTATTT
*
3374456 TTTTTTTATTTTTAAAATACTTTTTTA
1 TTTTTTTATTTTTAAAATAATTTTTTA
*
3374483 TTTTTTTATTTTTAAAATAAATTTTT
1 TTTTTTTATTTTTAAAATAATTTTTT
3374509 GGTGTTTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (27 bp):
TTTTTTTATTTTTAAAATAATTTTTTA
Found at i:3374516 original size:26 final size:27
Alignment explanation
Indices: 3374460--3374518 Score: 66
Period size: 27 Copynumber: 2.2 Consensus size: 27
3374450 TTATTTTTTT
** ** *
3374460 TTTATTTTTAAAATACTTTTTTATTTT
1 TTTATTTTTAAAATAAATTTTTAGGTG
3374487 TTTATTTTTAAAATAAATTTTT-GGTG
1 TTTATTTTTAAAATAAATTTTTAGGTG
3374513 TTTATT
1 TTTATT
3374519 AAAAAATGGG
Statistics
Matches: 27, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
26 7 0.26
27 20 0.74
ACGTcount: A:0.27, C:0.02, G:0.05, T:0.66
Consensus pattern (27 bp):
TTTATTTTTAAAATAAATTTTTAGGTG
Found at i:3375804 original size:18 final size:19
Alignment explanation
Indices: 3375781--3375835 Score: 53
Period size: 18 Copynumber: 2.9 Consensus size: 19
3375771 GAACAAGAAC
3375781 TTGAGAAAATTGAGAGAG-
1 TTGAGAAAATTGAGAGAGA
*
3375799 TTGAGAGAATT-AGGAGAGA
1 TTGAGAAAATTGA-GAGAGA
3375818 TT-AGAAATAATTGAGAGA
1 TTGAG-AA-AATTGAGAGA
3375836 ATAGGATGCG
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
17 1 0.03
18 17 0.57
19 3 0.10
20 8 0.27
21 1 0.03
ACGTcount: A:0.45, C:0.00, G:0.31, T:0.24
Consensus pattern (19 bp):
TTGAGAAAATTGAGAGAGA
Found at i:3376219 original size:26 final size:27
Alignment explanation
Indices: 3376169--3376237 Score: 115
Period size: 26 Copynumber: 2.6 Consensus size: 27
3376159 AAAAATAAAA
*
3376169 ATTTACCAAAATATTATAACTTTTTTT
1 ATTTACCAAAATATTATAAATTTTTTT
3376196 ATTTACCAAAATA-TATAAATTTTTTT
1 ATTTACCAAAATATTATAAATTTTTTT
3376222 ATTTACCAAAAT-TTAT
1 ATTTACCAAAATATTAT
3376238 CAAAAATAAA
Statistics
Matches: 40, Mismatches: 1, Indels: 3
0.91 0.02 0.07
Matches are distributed among these distances:
26 27 0.68
27 13 0.32
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (27 bp):
ATTTACCAAAATATTATAAATTTTTTT
Found at i:3376337 original size:27 final size:27
Alignment explanation
Indices: 3376297--3376373 Score: 93
Period size: 27 Copynumber: 2.9 Consensus size: 27
3376287 TAACTGTTCA
**
3376297 TGCCAATGGTATTGGCGGCACCAAAGG
1 TGCCAATGCAATTGGCGGCACCAAAGG
* *
3376324 TGCCAATGCCATTGGCGGCACCAATGG
1 TGCCAATGCAATTGGCGGCACCAAAGG
*
3376351 TGCC-ATACTAATTGGCGGCACCA
1 TGCCAATGC-AATTGGCGGCACCA
3376374 CTCGTATTAT
Statistics
Matches: 44, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
26 3 0.07
27 41 0.93
ACGTcount: A:0.25, C:0.27, G:0.29, T:0.19
Consensus pattern (27 bp):
TGCCAATGCAATTGGCGGCACCAAAGG
Found at i:3376470 original size:11 final size:11
Alignment explanation
Indices: 3376454--3376490 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
3376444 GTTGGCGCGG
3376454 AAAAGAAGAGA
1 AAAAGAAGAGA
3376465 AAAAG-AGAGA
1 AAAAGAAGAGA
*
3376475 AAAAGAGGAGA
1 AAAAGAAGAGA
3376486 AAAAG
1 AAAAG
3376491 GAGGTATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 10 0.42
11 14 0.58
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (11 bp):
AAAAGAAGAGA
Found at i:3376555 original size:19 final size:21
Alignment explanation
Indices: 3376517--3376555 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
3376507 AATAATTGAT
*
3376517 TATATTGTTGTTATTATTTTG
1 TATATTGTTGTTAATATTTTG
3376538 TATATT-TTG-TAATATTTT
1 TATATTGTTGTTAATATTTT
3376556 TTTGTTTTAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 8 0.47
20 3 0.18
21 6 0.35
ACGTcount: A:0.23, C:0.00, G:0.10, T:0.67
Consensus pattern (21 bp):
TATATTGTTGTTAATATTTTG
Found at i:3376906 original size:12 final size:12
Alignment explanation
Indices: 3376889--3376919 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
3376879 ATAATTTTAG
3376889 TGTGTATTATTT
1 TGTGTATTATTT
3376901 TGTGTATTATTT
1 TGTGTATTATTT
*
3376913 TGAGTAT
1 TGTGTAT
3376920 AAATTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.19, C:0.00, G:0.19, T:0.61
Consensus pattern (12 bp):
TGTGTATTATTT
Found at i:3377516 original size:18 final size:18
Alignment explanation
Indices: 3377473--3377517 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
3377463 TTGACATGGT
*
3377473 TGGTGGTGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
***
3377491 TACCGGCGAAGAAGAAGG
1 TGGTGGCGAAGAAGAAGG
3377509 TGGTGGCGA
1 TGGTGGCGA
3377518 TTGTCGAATC
Statistics
Matches: 20, Mismatches: 7, Indels: 0
0.74 0.26 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.31, C:0.09, G:0.47, T:0.13
Consensus pattern (18 bp):
TGGTGGCGAAGAAGAAGG
Found at i:3379494 original size:12 final size:11
Alignment explanation
Indices: 3379457--3379494 Score: 51
Period size: 10 Copynumber: 3.5 Consensus size: 11
3379447 AGGAGAGGAA
3379457 AAAAATAAAAT
1 AAAAATAAAAT
3379468 -AAAATAAAAT
1 AAAAATAAAAT
*
3379478 AAAAATGAAACT
1 AAAAAT-AAAAT
3379490 AAAAA
1 AAAAA
3379495 CACTCGACTC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 10 0.42
11 5 0.21
12 9 0.38
ACGTcount: A:0.79, C:0.03, G:0.03, T:0.16
Consensus pattern (11 bp):
AAAAATAAAAT
Found at i:3381280 original size:552 final size:552
Alignment explanation
Indices: 3380536--3381639 Score: 2208
Period size: 552 Copynumber: 2.0 Consensus size: 552
3380526 TGAGTCTCAT
3380536 ATCGGAAGGCATGGGTAGTTAAACAGATGGCGATGGAGCAACTGTATGGGGATTACGATTCATCG
1 ATCGGAAGGCATGGGTAGTTAAACAGATGGCGATGGAGCAACTGTATGGGGATTACGATTCATCG
3380601 TATAACGAGCTTCAAGGTTGGATAGCTGTTATGCAGGAGTACGTACCGGGGACTGTGATTGAGTT
66 TATAACGAGCTTCAAGGTTGGATAGCTGTTATGCAGGAGTACGTACCGGGGACTGTGATTGAGTT
3380666 GCAGACAAGTCTATATTACAGCCCGGATGAGCAGTTATAGCCGGCAAAAAGGATTTTCCATCAGA
131 GCAGACAAGTCTATATTACAGCCCGGATGAGCAGTTATAGCCGGCAAAAAGGATTTTCCATCAGA
3380731 TGTTCTGGACGTTCGATCCATGTGTGCGGGCATTTCCCCACTGCAAGCCACTTGTGCAGGTGGAT
196 TGTTCTGGACGTTCGATCCATGTGTGCGGGCATTTCCCCACTGCAAGCCACTTGTGCAGGTGGAT
3380796 GAGACCTGGTTGTATGGAAAATATACACAGATACTGCTTCTTGCAATTACTCAAGACGGTAACAG
261 GAGACCTGGTTGTATGGAAAATATACACAGATACTGCTTCTTGCAATTACTCAAGACGGTAACAG
3380861 AAACGTGCTCCCGATAGCATTTGCTATCTTAGATAAAGGGAACATGGAGTCTTGGGAATTCTTCT
326 AAACGTGCTCCCGATAGCATTTGCTATCTTAGATAAAGGGAACATGGAGTCTTGGGAATTCTTCT
3380926 TCACAAATCTGCGGAGGTATGTTATTAGGAACGATAACATTTGCATCATCTCCGATAGAGGGAAG
391 TCACAAATCTGCGGAGGTATGTTATTAGGAACGATAACATTTGCATCATCTCCGATAGAGGGAAG
3380991 GGTTTAATTGCAGCTATTAGGCGTTCCGATGTGCCATGGAGATCTGCTTACTGCATTCGTCACAT
456 GGTTTAATTGCAGCTATTAGGCGTTCCGATGTGCCATGGAGATCTGCTTACTGCATTCGTCACAT
3381056 TGCGTCAAACTTCCATAAAGATTACAAGAATA
521 TGCGTCAAACTTCCATAAAGATTACAAGAATA
3381088 ATCGGAAGGCATGGGTAGTTAAACAGATGGCGATGGAGCAACTGTATGGGGATTACGATTCATCG
1 ATCGGAAGGCATGGGTAGTTAAACAGATGGCGATGGAGCAACTGTATGGGGATTACGATTCATCG
3381153 TATAACGAGCTTCAAGGTTGGATAGCTGTTATGCAGGAGTACGTACCGGGGACTGTGATTGAGTT
66 TATAACGAGCTTCAAGGTTGGATAGCTGTTATGCAGGAGTACGTACCGGGGACTGTGATTGAGTT
3381218 GCAGACAAGTCTATATTACAGCCCGGATGAGCAGTTATAGCCGGCAAAAAGGATTTTCCATCAGA
131 GCAGACAAGTCTATATTACAGCCCGGATGAGCAGTTATAGCCGGCAAAAAGGATTTTCCATCAGA
3381283 TGTTCTGGACGTTCGATCCATGTGTGCGGGCATTTCCCCACTGCAAGCCACTTGTGCAGGTGGAT
196 TGTTCTGGACGTTCGATCCATGTGTGCGGGCATTTCCCCACTGCAAGCCACTTGTGCAGGTGGAT
3381348 GAGACCTGGTTGTATGGAAAATATACACAGATACTGCTTCTTGCAATTACTCAAGACGGTAACAG
261 GAGACCTGGTTGTATGGAAAATATACACAGATACTGCTTCTTGCAATTACTCAAGACGGTAACAG
3381413 AAACGTGCTCCCGATAGCATTTGCTATCTTAGATAAAGGGAACATGGAGTCTTGGGAATTCTTCT
326 AAACGTGCTCCCGATAGCATTTGCTATCTTAGATAAAGGGAACATGGAGTCTTGGGAATTCTTCT
3381478 TCACAAATCTGCGGAGGTATGTTATTAGGAACGATAACATTTGCATCATCTCCGATAGAGGGAAG
391 TCACAAATCTGCGGAGGTATGTTATTAGGAACGATAACATTTGCATCATCTCCGATAGAGGGAAG
3381543 GGTTTAATTGCAGCTATTAGGCGTTCCGATGTGCCATGGAGATCTGCTTACTGCATTCGTCACAT
456 GGTTTAATTGCAGCTATTAGGCGTTCCGATGTGCCATGGAGATCTGCTTACTGCATTCGTCACAT
3381608 TGCGTCAAACTTCCATAAAGATTACAAGAATA
521 TGCGTCAAACTTCCATAAAGATTACAAGAATA
3381640 CAGACTAGAA
Statistics
Matches: 552, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
552 552 1.00
ACGTcount: A:0.28, C:0.19, G:0.26, T:0.27
Consensus pattern (552 bp):
ATCGGAAGGCATGGGTAGTTAAACAGATGGCGATGGAGCAACTGTATGGGGATTACGATTCATCG
TATAACGAGCTTCAAGGTTGGATAGCTGTTATGCAGGAGTACGTACCGGGGACTGTGATTGAGTT
GCAGACAAGTCTATATTACAGCCCGGATGAGCAGTTATAGCCGGCAAAAAGGATTTTCCATCAGA
TGTTCTGGACGTTCGATCCATGTGTGCGGGCATTTCCCCACTGCAAGCCACTTGTGCAGGTGGAT
GAGACCTGGTTGTATGGAAAATATACACAGATACTGCTTCTTGCAATTACTCAAGACGGTAACAG
AAACGTGCTCCCGATAGCATTTGCTATCTTAGATAAAGGGAACATGGAGTCTTGGGAATTCTTCT
TCACAAATCTGCGGAGGTATGTTATTAGGAACGATAACATTTGCATCATCTCCGATAGAGGGAAG
GGTTTAATTGCAGCTATTAGGCGTTCCGATGTGCCATGGAGATCTGCTTACTGCATTCGTCACAT
TGCGTCAAACTTCCATAAAGATTACAAGAATA
Found at i:3385678 original size:41 final size:41
Alignment explanation
Indices: 3385621--3385824 Score: 336
Period size: 41 Copynumber: 5.0 Consensus size: 41
3385611 GCATATTCGG
* *
3385621 ATCACCGGTACTTAGCCTGCTAGGTTTATAACCTGATTAAT
1 ATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAT
* * *
3385662 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAG
1 ATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAT
3385703 ATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAT
1 ATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAT
* * *
3385744 ATCACCGGCACTTAGCCTGCTAGGCTTATAGCCTGATTCAG
1 ATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAT
3385785 ATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCA
1 ATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCA
3385825 ATTCACCAAT
Statistics
Matches: 150, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
41 150 1.00
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (41 bp):
ATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAT
Found at i:3385720 original size:82 final size:82
Alignment explanation
Indices: 3385615--3385831 Score: 391
Period size: 82 Copynumber: 2.6 Consensus size: 82
3385605 AATTTAGCAT
* *
3385615 ATTCGGATCACCGGTACTTAGCCTGCTAGGTTTATAACCTGATTAATATCACCGGCACTTAGCCT
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTAATATCACCGGCACTTAGCCT
3385680 GCTAGGCTTATAGCCTG
66 GCTAGGCTTATAGCCTG
*
3385697 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCATATCACCGGCACTTAGCCT
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTAATATCACCGGCACTTAGCCT
3385762 GCTAGGCTTATAGCCTG
66 GCTAGGCTTATAGCCTG
3385779 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTCAAT-TCACC
1 ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATT-AATATCACC
3385832 AATTCCAAAC
Statistics
Matches: 130, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
82 128 0.98
83 2 0.02
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (82 bp):
ATTCAGATCACCGGCACTTAGCCTGCTAGGTTTATAACCTGATTAATATCACCGGCACTTAGCCT
GCTAGGCTTATAGCCTG
Found at i:3388815 original size:39 final size:40
Alignment explanation
Indices: 3388757--3388922 Score: 135
Period size: 40 Copynumber: 4.0 Consensus size: 40
3388747 TAAAATTACC
* * *
3388757 TTTTTTTTCTTTTTTTCCTTCCTTCCTTCCCTC-TTCTTCT
1 TTTTTTTTC-TCTTCTCCTTCCTTCCTTCCTTCTTTCTTCT
* *
3388797 TTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCATTCTTTCATTCT
1 TTTTTTTTCTCTTCTCC-TTCC--TTCCTTCCTTCTTTC-TTCT
* *
3388841 TTTTTCTTCTCTTTTCCTTCTCTT-CTT-CTTCTTTCTT-T
1 TTTTTTTTCTCTTCTCCTTC-CTTCCTTCCTTCTTTCTTCT
* *
3388879 CTTTTTTTCTCTTCTCCTTTCCATTTCTTTCCTTCTTT-TTCT
1 TTTTTTTTCTCTTCTCC-TTCC--TTCCTTCCTTCTTTCTTCT
3388921 TT
1 TT
3388923 CTTCCCTCTC
Statistics
Matches: 100, Mismatches: 14, Indels: 22
0.74 0.10 0.16
Matches are distributed among these distances:
38 16 0.16
39 11 0.11
40 22 0.22
41 6 0.06
42 19 0.19
43 6 0.06
44 20 0.20
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.69
Consensus pattern (40 bp):
TTTTTTTTCTCTTCTCCTTCCTTCCTTCCTTCTTTCTTCT
Found at i:3388841 original size:44 final size:42
Alignment explanation
Indices: 3388790--3388922 Score: 159
Period size: 44 Copynumber: 3.2 Consensus size: 42
3388780 TCCTTCCCTC
3388790 TTCTTCTTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCATTCT
1 TTCTTCTTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTC-TTCT
* * *
3388833 TTCATTCTTTTTTCTTCTCTTTTCC-TT-CTCTTC-TTCTTCT
1 TTC-TTCTTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCTTCT
* *
3388873 TTCTT-TCTTTTTTTCTCTTCTCCTTTCCATTTCTTTCCTTCT
1 TTCTTCTTTTTTTTTCTCTTCTCCTTTCCTTTTCTTT-CTTCT
3388915 TT-TTCTTT
1 TTCTTCTTT
3388923 CTTCCCTCTC
Statistics
Matches: 75, Mismatches: 9, Indels: 13
0.77 0.09 0.13
Matches are distributed among these distances:
38 15 0.20
39 4 0.05
40 11 0.15
41 7 0.09
42 14 0.19
43 5 0.07
44 19 0.25
ACGTcount: A:0.02, C:0.29, G:0.00, T:0.69
Consensus pattern (42 bp):
TTCTTCTTTTTTTTTCTCTTCTCCTTTCCTTTTCTTTCTTCT
Found at i:3388856 original size:29 final size:28
Alignment explanation
Indices: 3388806--3388893 Score: 83
Period size: 29 Copynumber: 3.1 Consensus size: 28
3388796 TTTTTTTTTC
*
3388806 TCTTCTCCTTTCCTTT-TCTTTCATTCT-T
1 TCTTCTTCTTT-CTTTCT-TTTCATTCTCT
* *
3388834 TCATTCTTTTTTCTTCTCTTTTCCTTCTCT
1 TC-TTCTTCTTTCTT-TCTTTTCATTCTCT
*
3388864 TCTTCTTCTTTCTTTCTTTT-TTTCTCT
1 TCTTCTTCTTTCTTTCTTTTCATTCTCT
3388891 TCT
1 TCT
3388894 CCTTTCCATT
Statistics
Matches: 51, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
27 9 0.18
28 11 0.22
29 27 0.53
30 4 0.08
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.68
Consensus pattern (28 bp):
TCTTCTTCTTTCTTTCTTTTCATTCTCT
Found at i:3388868 original size:19 final size:19
Alignment explanation
Indices: 3388844--3388897 Score: 56
Period size: 19 Copynumber: 2.8 Consensus size: 19
3388834 TCATTCTTTT
3388844 TTCTTCTCTTTTCCTTCTC
1 TTCTTCTCTTTTCCTTCTC
* *
3388863 TTCTTCT-TCTTTCTTTCTT
1 TTCTTCTCT-TTTCCTTCTC
* *
3388882 TTTTTCTCTTCTCCTT
1 TTCTTCTCTTTTCCTT
3388898 TCCATTTCTT
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
18 1 0.04
19 26 0.93
20 1 0.04
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (19 bp):
TTCTTCTCTTTTCCTTCTC
Found at i:3388878 original size:4 final size:4
Alignment explanation
Indices: 3388820--3388961 Score: 80
Period size: 4 Copynumber: 35.0 Consensus size: 4
3388810 CTCCTTTCCT
* * *
3388820 TTTC TTTC ATTC TTTC ATTC TTT- TTTC TTCTC TTTTC CTTC TCTTC -TTC
1 TTTC TTTC TTTC TTTC TTTC TTTC TTTC TT-TC -TTTC TTTC T-TTC TTTC
* * *
3388869 -TTC TTTC TTTC TTTT TTTC TCTTC -TCC TTTCC ATTTC TTTC CTTC -TT-
1 TTTC TTTC TTTC TTTC TTTC T-TTC TTTC TTT-C -TTTC TTTC TTTC TTTC
* * * *
3388916 TTTC TTTC TTCCC TCTC ATTTC TTCC TCTC TTTC TTTC TTTC TTTC
1 TTTC TTTC TT-TC TTTC -TTTC TTTC TTTC TTTC TTTC TTTC TTTC
3388962 CCTCTCCTTT
Statistics
Matches: 106, Mismatches: 19, Indels: 26
0.70 0.13 0.17
Matches are distributed among these distances:
3 15 0.14
4 69 0.65
5 17 0.16
6 5 0.05
ACGTcount: A:0.03, C:0.31, G:0.00, T:0.66
Consensus pattern (4 bp):
TTTC
Found at i:3388906 original size:82 final size:79
Alignment explanation
Indices: 3388759--3388960 Score: 227
Period size: 82 Copynumber: 2.5 Consensus size: 79
3388749 AAATTACCTT
* * *
3388759 TTTTTTCTT-T-TTTTCCTTCCTTCCTTC-CCTCTTCTTCTTTTTTTTTCTCTTCTCCTTTCCTT
1 TTTTTTCTTCTCTTTTCCTTCCTT-CTTCTTCT-TTCTT-TCTTTTTTTCTCTTCTCCTTTCCAT
3388821 TTCTTTCATTCTTTCATTC
63 TTCTTTCATTCTTT--TTC
3388840 TTTTTTCTTCTCTTTTCCTTCTCTTCTTCTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCATTT
1 TTTTTTCTTCTCTTTTCCTTC-CTTCTTCTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCATTT
*
3388905 CTTTCCTTCTTTTTC
65 CTTTCATTCTTTTTC
* * *
3388920 TTTCTTCCCTCTCATTT-CTTCC-TC-TCTTTCTTTCTTTCTTT
1 TTT-TTTCTTCTCTTTTCCTTCCTTCTTC-TTCTTTCTTTCTTT
3388961 CCCTCTCCTT
Statistics
Matches: 108, Mismatches: 7, Indels: 15
0.83 0.05 0.12
Matches are distributed among these distances:
77 2 0.02
78 16 0.15
79 1 0.01
80 10 0.09
81 19 0.18
82 37 0.34
83 18 0.17
84 5 0.05
ACGTcount: A:0.02, C:0.31, G:0.00, T:0.67
Consensus pattern (79 bp):
TTTTTTCTTCTCTTTTCCTTCCTTCTTCTTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCATTTC
TTTCATTCTTTTTC
Found at i:3388907 original size:74 final size:72
Alignment explanation
Indices: 3388829--3388971 Score: 175
Period size: 74 Copynumber: 1.9 Consensus size: 72
3388819 TTTTCTTTCA
* * *
3388829 TTCTTTCATTCTTTTTTCTTCTCTTTTCCTTCTC-TTCTT-CT-TCTTTCTTTCTTTTTTTCTCT
1 TTCTTTCATTC-TTTTTCTT-TC--TTCCCTCTCATTCTTCCTCTCTTTCTTTCTTTCTTTC-CC
3388891 TCTCCTTTCCAT
61 TCTCCTTTCCAT
*
3388903 TTCTTTCCTTCTTTTTCTTTCTTCCCTCTCATTTCTTCCTCTCTTTCTTTCTTTCTTTCCCTCTC
1 TTCTTTCATTCTTTTTCTTTCTTCCCTCTCA-TTCTTCCTCTCTTTCTTTCTTTCTTTCCCTCTC
3388968 CTTT
65 CTTT
3388972 TGCCCCCCCC
Statistics
Matches: 61, Mismatches: 4, Indels: 9
0.82 0.05 0.12
Matches are distributed among these distances:
70 8 0.13
72 7 0.11
73 19 0.31
74 27 0.44
ACGTcount: A:0.02, C:0.33, G:0.00, T:0.65
Consensus pattern (72 bp):
TTCTTTCATTCTTTTTCTTTCTTCCCTCTCATTCTTCCTCTCTTTCTTTCTTTCTTTCCCTCTCC
TTTCCAT
Found at i:3388914 original size:48 final size:44
Alignment explanation
Indices: 3388801--3388925 Score: 97
Period size: 39 Copynumber: 2.9 Consensus size: 44
3388791 TCTTCTTTTT
* * *
3388801 TTTTCTCTTCTCCTTTCCTTTTCTTTCATTC-TTTCATTC--T--
1 TTTT-TCTTCTCCTTTCCTTCTCTTTCCTTCTTTTCTTTCTTTAC
* *
3388841 TTTTTCTTCTCTTTTCCTTCTCTTCTTCTTC-TTTCTTTCTTT--
1 TTTTTCTTCTCCTTTCCTTCTCTT-TCCTTCTTTTCTTTCTTTAC
3388883 TTTTCTCTTCTCCTTTCCATT-TCTTTCCTTCTTTTTCTTTCTT
1 TTTT-TCTTCTCCTTTCC-TTCTCTTTCCTTC-TTTTCTTTCTT
3388926 CCCTCTCATT
Statistics
Matches: 71, Mismatches: 7, Indels: 10
0.81 0.08 0.11
Matches are distributed among these distances:
39 18 0.25
40 15 0.21
42 10 0.14
43 16 0.23
44 12 0.17
ACGTcount: A:0.02, C:0.30, G:0.00, T:0.68
Consensus pattern (44 bp):
TTTTTCTTCTCCTTTCCTTCTCTTTCCTTCTTTTCTTTCTTTAC
Found at i:3388915 original size:34 final size:33
Alignment explanation
Indices: 3388869--3388958 Score: 98
Period size: 34 Copynumber: 2.8 Consensus size: 33
3388859 TCTCTTCTTC
* *
3388869 TTCTTTCTTTCTTTTTTTCTCTTCTCCTTTCCAT
1 TTCTTTCCTTCTTTTTTTCTCTTCTCCTCT-CAT
3388903 TTCTTTCCTTCTTTTTCTT-TCTTC-CCTCTCAT
1 TTCTTTCCTTCTTTTT-TTCTCTTCTCCTCTCAT
*
3388935 TTC-TTCCTCTCTTTCTTTCT-TTCT
1 TTCTTTCCT-TCTTTTTTTCTCTTCT
3388959 TTCCCTCTCC
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
31 10 0.20
32 13 0.27
33 4 0.08
34 20 0.41
35 2 0.04
ACGTcount: A:0.02, C:0.32, G:0.00, T:0.66
Consensus pattern (33 bp):
TTCTTTCCTTCTTTTTTTCTCTTCTCCTCTCAT
Found at i:3388943 original size:13 final size:13
Alignment explanation
Indices: 3388918--3388951 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
3388908 TCCTTCTTTT
3388918 TCTTTCTTCCCTC
1 TCTTTCTTCCCTC
3388931 TCATTTCTT-CCTC
1 TC-TTTCTTCCCTC
3388944 TCTTTCTT
1 TCTTTCTT
3388952 TCTTTCTTTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
12 6 0.30
13 8 0.40
14 6 0.30
ACGTcount: A:0.03, C:0.38, G:0.00, T:0.59
Consensus pattern (13 bp):
TCTTTCTTCCCTC
Found at i:3389078 original size:27 final size:27
Alignment explanation
Indices: 3389003--3389069 Score: 116
Period size: 27 Copynumber: 2.5 Consensus size: 27
3388993 TATTATTAAC
3389003 TGGTGCCGCCAATGGTATTGGCACCAT
1 TGGTGCCGCCAATGGTATTGGCACCAT
* *
3389030 TGGTGCCGCCAATGGTTTTGGCACCTT
1 TGGTGCCGCCAATGGTATTGGCACCAT
3389057 TGGTGCCGCCAAT
1 TGGTGCCGCCAAT
3389070 CCCATTGGCG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.15, C:0.27, G:0.30, T:0.28
Consensus pattern (27 bp):
TGGTGCCGCCAATGGTATTGGCACCAT
Found at i:3389173 original size:26 final size:25
Alignment explanation
Indices: 3389138--3389205 Score: 100
Period size: 26 Copynumber: 2.6 Consensus size: 25
3389128 GGTTTTTTTG
*
3389138 ATATATTTTGGTAAATAAAAAAATTT
1 ATATATTTTGGTAAAT-AAAAAAGTT
*
3389164 ATATTTTTTGGTAAATAAAAAAGTT
1 ATATATTTTGGTAAATAAAAAAGTT
3389189 ATAATATTTTGGTAAAT
1 AT-ATATTTTGGTAAAT
3389206 TTTTATTTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
25 10 0.26
26 28 0.74
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (25 bp):
ATATATTTTGGTAAATAAAAAAGTT
Found at i:3393117 original size:20 final size:21
Alignment explanation
Indices: 3393092--3393135 Score: 72
Period size: 21 Copynumber: 2.1 Consensus size: 21
3393082 GGAGAAATAG
3393092 AAAAGAAT-GAAAAAAAAATT
1 AAAAGAATAGAAAAAAAAATT
*
3393112 AAAAGAATATAAAAAAAAATT
1 AAAAGAATAGAAAAAAAAATT
3393133 AAA
1 AAA
3393136 TTGCTCAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 8 0.36
21 14 0.64
ACGTcount: A:0.77, C:0.00, G:0.07, T:0.16
Consensus pattern (21 bp):
AAAAGAATAGAAAAAAAAATT
Found at i:3399529 original size:12 final size:12
Alignment explanation
Indices: 3399514--3399563 Score: 64
Period size: 12 Copynumber: 4.2 Consensus size: 12
3399504 TGATGAGGGT
*
3399514 GAGGAAGAGGAA
1 GAGGAAGAAGAA
*
3399526 GAGGAGGAAGAA
1 GAGGAAGAAGAA
*
3399538 GAGGAAGAAGAT
1 GAGGAAGAAGAA
*
3399550 GAGGAGGAAGAA
1 GAGGAAGAAGAA
3399562 GA
1 GA
3399564 ACTTCAGCCA
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
12 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.48, T:0.02
Consensus pattern (12 bp):
GAGGAAGAAGAA
Found at i:3399534 original size:9 final size:9
Alignment explanation
Indices: 3399517--3399548 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
3399507 TGAGGGTGAG
3399517 GAAGAGGAA
1 GAAGAGGAA
*
3399526 GAGGAGGAA
1 GAAGAGGAA
3399535 GAAGAGGAA
1 GAAGAGGAA
3399544 GAAGA
1 GAAGA
3399549 TGAGGAGGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.47, T:0.00
Consensus pattern (9 bp):
GAAGAGGAA
Found at i:3399541 original size:24 final size:24
Alignment explanation
Indices: 3399514--3399563 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
3399504 TGATGAGGGT
*
3399514 GAGGAAGAGGAAGAGGAGGAAGAA
1 GAGGAAGAAGAAGAGGAGGAAGAA
*
3399538 GAGGAAGAAGATGAGGAGGAAGAA
1 GAGGAAGAAGAAGAGGAGGAAGAA
3399562 GA
1 GA
3399564 ACTTCAGCCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.48, T:0.02
Consensus pattern (24 bp):
GAGGAAGAAGAAGAGGAGGAAGAA
Found at i:3406502 original size:9 final size:9
Alignment explanation
Indices: 3406488--3406512 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
3406478 TATTATAAAA
3406488 TAATTATAT
1 TAATTATAT
3406497 TAATTATAT
1 TAATTATAT
3406506 TAATTAT
1 TAATTAT
3406513 CTATACTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (9 bp):
TAATTATAT
Found at i:3420530 original size:27 final size:26
Alignment explanation
Indices: 3420500--3420582 Score: 94
Period size: 27 Copynumber: 3.1 Consensus size: 26
3420490 GGCAAAATGG
* * *
3420500 TAATTTTACCCCACAAGGGTATCTCGA
1 TAATTCTACCCTAC-AGGGTATTTCGA
* *
3420527 TAATTCTACCCTACAGGGATATTTTGG
1 TAATTCTACCCTACAGGG-TATTTCGA
3420554 TAATTCTACCCTACAGTGGTATTTCGA
1 TAATTCTACCCTACAG-GGTATTTCGA
3420581 TA
1 TA
3420583 TTTTACAAAT
Statistics
Matches: 47, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
26 4 0.09
27 41 0.87
28 2 0.04
ACGTcount: A:0.28, C:0.22, G:0.16, T:0.35
Consensus pattern (26 bp):
TAATTCTACCCTACAGGGTATTTCGA
Found at i:3420655 original size:53 final size:53
Alignment explanation
Indices: 3420598--3420747 Score: 178
Period size: 53 Copynumber: 2.8 Consensus size: 53
3420588 CAAATCGAGA
* * * *
3420598 GTATTTCGATAATTTCATAGATCAGGGGTATTTTGGTAATTTTACAAGCTA-GG
1 GTATTTTGGTAATTTTATA-ATCAGGGGTATTTTGGTAATTTTACAAACTAGGG
* * *
3420651 GTATTTTGGTAATTTTACAAACCAGGGGTATTTTAGTAATTTTACAAACTAGGG
1 GTATTTTGGTAATTTTA-TAATCAGGGGTATTTTGGTAATTTTACAAACTAGGG
*
3420705 GTATTTTGGTAATTTTACTAATC-GAGGGTATTTTGTTAATTTT
1 GTATTTTGGTAATTTTA-TAATCAG-GGGTATTTTGGTAATTTT
3420748 GTAGACCAAG
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
53 43 0.52
54 40 0.48
ACGTcount: A:0.28, C:0.08, G:0.21, T:0.43
Consensus pattern (53 bp):
GTATTTTGGTAATTTTATAATCAGGGGTATTTTGGTAATTTTACAAACTAGGG
Found at i:3420658 original size:26 final size:27
Alignment explanation
Indices: 3420621--3420747 Score: 177
Period size: 27 Copynumber: 4.7 Consensus size: 27
3420611 TTCATAGATC
*
3420621 AGGGGTATTTTGGTAATTTTACAAGCT
1 AGGGGTATTTTGGTAATTTTACAAACT
*
3420648 A-GGGTATTTTGGTAATTTTACAAACC
1 AGGGGTATTTTGGTAATTTTACAAACT
*
3420674 AGGGGTATTTTAGTAATTTTACAAACT
1 AGGGGTATTTTGGTAATTTTACAAACT
*
3420701 AGGGGTATTTTGGTAATTTTACTAA-T
1 AGGGGTATTTTGGTAATTTTACAAACT
* *
3420727 CGAGGGTATTTTGTTAATTTT
1 AG-GGGTATTTTGGTAATTTT
3420748 GTAGACCAAG
Statistics
Matches: 90, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
26 26 0.29
27 64 0.71
ACGTcount: A:0.28, C:0.07, G:0.22, T:0.43
Consensus pattern (27 bp):
AGGGGTATTTTGGTAATTTTACAAACT
Found at i:3420759 original size:27 final size:27
Alignment explanation
Indices: 3420623--3420764 Score: 160
Period size: 27 Copynumber: 5.3 Consensus size: 27
3420613 CATAGATCAG
* *
3420623 GGGTATTTTGGTAATTTTAC-AAGCTA
1 GGGTATTTTGGTAATTTTACAAACCAA
*
3420649 GGGTATTTTGGTAATTTTACAAACCAG
1 GGGTATTTTGGTAATTTTACAAACCAA
* * *
3420676 GGGTATTTTAGTAATTTTACAAACTAG
1 GGGTATTTTGGTAATTTTACAAACCAA
* * *
3420703 GGGTATTTTGGTAATTTTACTAATCGA
1 GGGTATTTTGGTAATTTTACAAACCAA
* ** *
3420730 GGGTATTTTGTTAATTTTGTAGACCAA
1 GGGTATTTTGGTAATTTTACAAACCAA
3420757 GGGTATTT
1 GGGTATTT
3420765 AAATCCACAA
Statistics
Matches: 97, Mismatches: 18, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
26 20 0.21
27 77 0.79
ACGTcount: A:0.27, C:0.08, G:0.23, T:0.42
Consensus pattern (27 bp):
GGGTATTTTGGTAATTTTACAAACCAA
Found at i:3429256 original size:17 final size:17
Alignment explanation
Indices: 3429234--3429267 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3429224 ATCCACTAAT
*
3429234 CCACTACCACCAACAAC
1 CCACTACCAACAACAAC
3429251 CCACTACCAACAACAAC
1 CCACTACCAACAACAAC
3429268 AATCCACTAC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.50, G:0.00, T:0.06
Consensus pattern (17 bp):
CCACTACCAACAACAAC
Found at i:3439305 original size:29 final size:28
Alignment explanation
Indices: 3439272--3439330 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
3439262 AATTTTATTG
* *
3439272 ATTTTTTTTA--AAAAAATTTGTATTTT
1 ATTTTTTTTAGTAAAAAAATAGTATTTT
*
3439298 CTTTTTTTTAGTAAAAAAATAGTATTTT
1 ATTTTTTTTAGTAAAAAAATAGTATTTT
3439326 ATTTT
1 ATTTT
3439331 AAAAACCGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 9 0.33
28 18 0.67
ACGTcount: A:0.34, C:0.02, G:0.05, T:0.59
Consensus pattern (28 bp):
ATTTTTTTTAGTAAAAAAATAGTATTTT
Found at i:3450126 original size:15 final size:16
Alignment explanation
Indices: 3450106--3450139 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
3450096 ATGAGTGAAG
*
3450106 ATTAAGAGTT-ATTAA
1 ATTAAGAATTAATTAA
3450121 ATTAAGAATTAATTAA
1 ATTAAGAATTAATTAA
3450137 ATT
1 ATT
3450140 TTTAATAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.50, C:0.00, G:0.09, T:0.41
Consensus pattern (16 bp):
ATTAAGAATTAATTAA
Found at i:3455028 original size:15 final size:15
Alignment explanation
Indices: 3455008--3455037 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
3454998 GGCAATCACT
3455008 CATTCTTAAAACCAA
1 CATTCTTAAAACCAA
*
3455023 CATTCTTAATACCAA
1 CATTCTTAAAACCAA
3455038 AGAGTCAGAC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.27, G:0.00, T:0.30
Consensus pattern (15 bp):
CATTCTTAAAACCAA
Found at i:3457199 original size:40 final size:40
Alignment explanation
Indices: 3457144--3457284 Score: 255
Period size: 40 Copynumber: 3.5 Consensus size: 40
3457134 AGGCTTGTGC
3457144 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
*
3457184 CTAGCAGGCTTAATGCCGGTGAAATATTCAGATTATACGT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
*
3457224 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACAT
1 CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
*
3457264 CTAGCAGGCTTCATGCCGGTG
1 CTAGCAGGCTTAATGCCGGTG
3457285 TACGGAATCA
Statistics
Matches: 97, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 97 1.00
ACGTcount: A:0.28, C:0.21, G:0.23, T:0.28
Consensus pattern (40 bp):
CTAGCAGGCTTAATGCCGGTGAAATATTCAGACTATACGT
Found at i:3458521 original size:17 final size:17
Alignment explanation
Indices: 3458499--3458534 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
3458489 AATGATGGGG
3458499 TGGTTGTTGTTAAAAAA
1 TGGTTGTTGTTAAAAAA
*
3458516 TGGTTGTTGTTAAATAA
1 TGGTTGTTGTTAAAAAA
3458533 TG
1 TG
3458535 AACTTTGCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.44
Consensus pattern (17 bp):
TGGTTGTTGTTAAAAAA
Found at i:3460816 original size:26 final size:25
Alignment explanation
Indices: 3460766--3460818 Score: 63
Period size: 26 Copynumber: 2.1 Consensus size: 25
3460756 AATCGAAACA
* *
3460766 ATTTATTTTATATTATTTTAAAAAT
1 ATTTATTTTATAATATTATAAAAAT
3460791 ATTTATTTTTATAATA-TATAATAAAT
1 ATTTA-TTTTATAATATTATAA-AAAT
3460817 AT
1 AT
3460819 ATAACTATAT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
25 9 0.38
26 15 0.62
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (25 bp):
ATTTATTTTATAATATTATAAAAAT
Done.