Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold2
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: 5794061
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 68655 characters in sequence are not A, C, G, or T
File 9 of 38
Found at i:1404884 original size:27 final size:27
Alignment explanation
Indices: 1404832--1404885 Score: 83
Period size: 26 Copynumber: 2.0 Consensus size: 27
1404822 TAGGTTCAGA
*
1404832 TTAAATTATTTTTAAATTTAAATTTTT
1 TTAAATTATTTTCAAATTTAAATTTTT
*
1404859 TTAAATTA-TTTCGAATTTAAATTTTT
1 TTAAATTATTTTCAAATTTAAATTTTT
1404885 T
1 T
1404886 GAATTCGGAT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 17 0.68
27 8 0.32
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (27 bp):
TTAAATTATTTTCAAATTTAAATTTTT
Found at i:1405834 original size:23 final size:23
Alignment explanation
Indices: 1405802--1405845 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
1405792 TTAATAATGT
*
1405802 ATTATTAATATAATTATATAATA
1 ATTATAAATATAATTATATAATA
* *
1405825 ATTATAAATATATTTTTATAA
1 ATTATAAATATAATTATATAA
1405846 ATTAAATATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
ATTATAAATATAATTATATAATA
Found at i:1405853 original size:19 final size:20
Alignment explanation
Indices: 1405829--1405876 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 20
1405819 ATAATAATTA
1405829 TAAATATATTT-TTATAAAT
1 TAAATATATTTATTATAAAT
*
1405848 TAAATAT-TTTATTTTAAAT
1 TAAATATATTTATTATAAAT
*
1405867 AAAATTATAT
1 TAAA-TATAT
1405877 AATTATAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
18 3 0.12
19 17 0.71
20 3 0.12
21 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (20 bp):
TAAATATATTTATTATAAAT
Found at i:1406355 original size:28 final size:28
Alignment explanation
Indices: 1406292--1406398 Score: 94
Period size: 29 Copynumber: 3.8 Consensus size: 28
1406282 GTGTTTATTT
* *
1406292 AAATATTAAT-TAAAAAATTATTTTG-TA
1 AAATATAAATATAAAAATTTA-TTTGATA
1406319 TAAAT-TAAATATAAAAATTTATTTGATA
1 -AAATATAAATATAAAAATTTATTTGATA
* *
1406347 AAATATAAAATTTAAAAATTTATTTAGATG
1 AAATAT-AAATATAAAAATTTATTT-GATA
* * *
1406377 CAATAAAAATATATAAATTTAT
1 AAATATAAATATAAAAATTTAT
1406399 CAAAATAAAG
Statistics
Matches: 66, Mismatches: 8, Indels: 9
0.80 0.10 0.11
Matches are distributed among these distances:
27 12 0.18
28 16 0.24
29 31 0.47
30 7 0.11
ACGTcount: A:0.54, C:0.01, G:0.04, T:0.41
Consensus pattern (28 bp):
AAATATAAATATAAAAATTTATTTGATA
Found at i:1406362 original size:29 final size:29
Alignment explanation
Indices: 1406325--1406398 Score: 96
Period size: 29 Copynumber: 2.6 Consensus size: 29
1406315 TGTATAAATT
1406325 AAATATAAAAATTTATTTGATAAAATATA
1 AAATATAAAAATTTATTTGATAAAATATA
* **
1406354 AAATTTAAAAATTTATTTAGATGCAATA-A
1 AAATATAAAAATTTATTT-GATAAAATATA
*
1406383 AAATATATAAATTTAT
1 AAATATAAAAATTTAT
1406399 CAAAATAAAG
Statistics
Matches: 39, Mismatches: 5, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
29 32 0.82
30 7 0.18
ACGTcount: A:0.55, C:0.01, G:0.04, T:0.39
Consensus pattern (29 bp):
AAATATAAAAATTTATTTGATAAAATATA
Found at i:1408356 original size:19 final size:19
Alignment explanation
Indices: 1408313--1408356 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
1408303 TGAGTTTTAG
*
1408313 ATTTTTTTCTTGAAATTCT
1 ATTTTTTTCTTGAAATACT
*
1408332 CTTTTTTT-TTGAAATACT
1 ATTTTTTTCTTGAAATACT
*
1408350 ATGTTTT
1 ATTTTTT
1408357 CTACTCCGTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 14 0.67
19 7 0.33
ACGTcount: A:0.20, C:0.09, G:0.07, T:0.64
Consensus pattern (19 bp):
ATTTTTTTCTTGAAATACT
Found at i:1408463 original size:167 final size:162
Alignment explanation
Indices: 1408128--1408577 Score: 479
Period size: 167 Copynumber: 2.6 Consensus size: 162
1408118 ATATCAAATA
* * * * *
1408128 TCATAAGTTTTGGATTTTTTCCTTCAAATTCCCTTTTTTTGAAATACGATATATTCTACTCCGTA
1 TCATAAGTTTTAGATTTTTTTCTT-AAATTCCTTTTTTTTGAAATACAAT-TTTTCTACTCCGTA
* * * *
1408193 AATTTTTTAAAGAGAATTTTTCTTAATTTTTAATTTTTGATTTTTAAAATTCATCAAATATCATC
64 AATTTTTT-CAGAAAATTTTTCTTAATTTTT-A------ATTTTTAAAATTCATCAAACACCATC
* *
1408258 ATTTATTTTATATTAGTTCAGTTTTAAAAAATAAATTCATTT
121 ATTTATTTCATATTAATTCAGTTTTAAAAAATAAATTCATTT
* *
1408300 TCATGAGTTTTAGATTTTTTTCTTGAAATTCTCTTTTTTTTTGAAATACTATGTTTTCTACTCCG
1 TCATAAGTTTTAGATTTTTTTCTT-AAATTC-C-TTTTTTTTGAAATACAAT-TTTTCTACTCCG
* *
1408365 TAAATTTTTTCAGGAAAATTTTTCTTAATTTTTAATTTTTAAAATTCATCAAACGCCATTATTTA
62 TAAATTTTTTCA-GAAAATTTTTCTTAATTTTTAATTTTTAAAATTCATCAAACACCATCATTTA
*
1408430 TTTCATATTAATTCAGTTTTCAAAAATAAATTCATTT
126 TTTCATATTAATTCAGTTTTAAAAAATAAATTCATTT
* * *
1408467 TCATAAGTTTTAGATTTTTTTTCCTTAAAATCCCTTTTTTTCGAAAAAAACGAATTTTT-TACTC
1 TCATAAGTTTTAGA-TTTTTTT-CTT-AAATTCCTTTTTTTTG--AAATAC-AATTTTTCTACTC
* ** **
1408531 TGTAAATTTTTTCAGAAGAATTTTTCTCGATTTAAAATTTTTAAAAT
60 CGTAAATTTTTTCAGAA-AATTTTTCTTAATTTTTAATTTTTAAAAT
1408578 GTATCTAATA
Statistics
Matches: 241, Mismatches: 28, Indels: 22
0.83 0.10 0.08
Matches are distributed among these distances:
167 85 0.35
168 51 0.21
169 17 0.07
170 2 0.01
172 27 0.11
173 3 0.01
174 56 0.23
ACGTcount: A:0.31, C:0.12, G:0.07, T:0.50
Consensus pattern (162 bp):
TCATAAGTTTTAGATTTTTTTCTTAAATTCCTTTTTTTTGAAATACAATTTTTCTACTCCGTAAA
TTTTTTCAGAAAATTTTTCTTAATTTTTAATTTTTAAAATTCATCAAACACCATCATTTATTTCA
TATTAATTCAGTTTTAAAAAATAAATTCATTT
Found at i:1408614 original size:168 final size:168
Alignment explanation
Indices: 1408128--1408655 Score: 405
Period size: 168 Copynumber: 3.1 Consensus size: 168
1408118 ATATCAAATA
* * * * * * * *
1408128 TCATAAGTTTTGGA-TTTTTTCCTTCAAATTC-CCTTTTTTT-GAAATACGATATATTCTACTCC
1 TCATAAGTTTTAGATTTTTTTTCTTGAAAATCTCCTTTTTTTCGAAAAACAATGTTTTCTACTCC
* * * * * * *
1408190 GTAAATTTTTTAAAGAGAATTTTTCTTAATTTTTAATTTTTGATTTTTAAAATTCATCAAATATC
66 GTAAATTTTTTCAGGAAAATTTTTCTCAA--TTTAA-----AATTTTTAAAATTCATCAAACACC
* ** * * *
1408255 ATCATTTATTTTATATTAGTTCAGTTTTAAAAAATAAATTCATTT
124 ATCATTGAACTCACATTAATTCAGTTTTAAAAAATAAATTCATTT
* * * * * *
1408300 TCATGAGTTTTAGA-TTTTTTTCTTGAAATTCTCTTTTTTTTTGAAATACTATGTTTTCTACTCC
1 TCATAAGTTTTAGATTTTTTTTCTTGAAAATCTCCTTTTTTTCGAAAAACAATGTTTTCTACTCC
* ** * * *
1408364 GTAAATTTTTTCAGGAAAATTTTTCTTAATTTTTAATTTTTAAAATTCATCAAACGCCATTATTT
66 GTAAATTTTTTCAGGAAAATTTTTCTCAATTTAAAATTTTTAAAATTCATCAAACACCATCATTG
** * *
1408429 ATTTCATATTAATTCAGTTTTCAAAAATAAATTCATTT
131 AACTCACATTAATTCAGTTTTAAAAAATAAATTCATTT
1408467 TCATAAGTTTTAGATTTTTTTTCCTT-AAAATC-CCTTTTTTTCGAAAAAAACGAAT-TTTT-TA
1 TCATAAGTTTTAGATTTTTTTT-CTTGAAAATCTCCTTTTTTTCG--AAAAAC-AATGTTTTCTA
* * * * **
1408528 CTCTGTAAATTTTTTCA-GAAGAATTTTTCTCGATTTAAAATTTTTAAAATGT-ATCTAATATTA
62 CTCCGTAAATTTTTTCAGGAA-AATTTTTCTCAATTTAAAATTTTTAAAAT-TCATCAAACACCA
* * * *
1408591 TCATTGAACTCCCATTGATTCAGTTTTAAAAAATTTAATTTATTT
125 TCATTGAACTCACATTAATTCAGTTTTAAAAAA-TAAATTCATTT
*
1408636 T-ATTAA-TTTTAAATTTTTTT
1 TCA-TAAGTTTTAGATTTTTTT
1408656 ATATATATTA
Statistics
Matches: 297, Mismatches: 48, Indels: 26
0.80 0.13 0.07
Matches are distributed among these distances:
167 86 0.29
168 100 0.34
169 26 0.09
170 2 0.01
172 30 0.10
173 8 0.03
174 45 0.15
ACGTcount: A:0.32, C:0.11, G:0.06, T:0.51
Consensus pattern (168 bp):
TCATAAGTTTTAGATTTTTTTTCTTGAAAATCTCCTTTTTTTCGAAAAACAATGTTTTCTACTCC
GTAAATTTTTTCAGGAAAATTTTTCTCAATTTAAAATTTTTAAAATTCATCAAACACCATCATTG
AACTCACATTAATTCAGTTTTAAAAAATAAATTCATTT
Found at i:1408804 original size:12 final size:12
Alignment explanation
Indices: 1408789--1408828 Score: 57
Period size: 12 Copynumber: 3.4 Consensus size: 12
1408779 TTAATTTTAA
1408789 ATTTATTTTATT
1 ATTTATTTTATT
1408801 ATTTA-TTTATTT
1 ATTTATTTTA-TT
1408813 ATTTATTTTA-T
1 ATTTATTTTATT
1408824 ATTTA
1 ATTTA
1408829 AATTGTTAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
11 10 0.38
12 12 0.46
13 4 0.15
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (12 bp):
ATTTATTTTATT
Found at i:1409211 original size:25 final size:23
Alignment explanation
Indices: 1409150--1409214 Score: 76
Period size: 25 Copynumber: 2.7 Consensus size: 23
1409140 GAACTCGGCT
1409150 GAAAATAGAGAAAAAAAAATAAA
1 GAAAATAGAGAAAAAAAAATAAA
* *
1409173 GAAAGAAAAGAGAAAGAAAAATAAA
1 G-AA-AATAGAGAAAAAAAAATAAA
1409198 GAAAATAGGTAGAAAAA
1 GAAAATA-G-AGAAAAA
1409215 CAAGAAAACT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
23 4 0.12
24 5 0.15
25 25 0.74
ACGTcount: A:0.74, C:0.00, G:0.18, T:0.08
Consensus pattern (23 bp):
GAAAATAGAGAAAAAAAAATAAA
Found at i:1412166 original size:18 final size:18
Alignment explanation
Indices: 1412123--1412166 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
1412113 TTTAACTTAT
1412123 TAATTTTTTTAAACAAAA
1 TAATTTTTTTAAACAAAA
*
1412141 TAAATTTTTTAAA-AAAA
1 TAATTTTTTTAAACAAAA
1412158 T-ATTTTTTT
1 TAATTTTTTT
1412167 CACCCACAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
16 7 0.29
17 5 0.21
18 12 0.50
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.52
Consensus pattern (18 bp):
TAATTTTTTTAAACAAAA
Found at i:1412492 original size:15 final size:16
Alignment explanation
Indices: 1412472--1412502 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1412462 AACTTTTGCT
1412472 TTTATTTTTTA-TTTA
1 TTTATTTTTTACTTTA
1412487 TTTATTTTTTACTTTA
1 TTTATTTTTTACTTTA
1412503 AAAAAATCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTATTTTTTACTTTA
Found at i:1413290 original size:17 final size:17
Alignment explanation
Indices: 1413241--1413290 Score: 52
Period size: 18 Copynumber: 3.0 Consensus size: 17
1413231 ATGTCATAAA
1413241 ATAC-ATTAA-TATTTT
1 ATACTATTAATTATTTT
*
1413256 ATATTATTTAAATT-TTTT
1 ATACTA-TT-AATTATTTT
1413274 ATACTATTAATTATTTT
1 ATACTATTAATTATTTT
1413291 TCTTAATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
15 3 0.11
16 5 0.18
17 8 0.29
18 11 0.39
19 1 0.04
ACGTcount: A:0.36, C:0.04, G:0.00, T:0.60
Consensus pattern (17 bp):
ATACTATTAATTATTTT
Found at i:1413354 original size:29 final size:31
Alignment explanation
Indices: 1413299--1413360 Score: 92
Period size: 29 Copynumber: 2.1 Consensus size: 31
1413289 TTTCTTAATT
1413299 TATTATAATTTAAGAATATCAAAAATTAAAA
1 TATTATAATTTAAGAATATCAAAAATTAAAA
* *
1413330 TATTA-AATTTAATATTAT-AAAAATTAAAA
1 TATTATAATTTAAGAATATCAAAAATTAAAA
1413359 TA
1 TA
1413361 AATCTTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 13 0.45
30 11 0.38
31 5 0.17
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.39
Consensus pattern (31 bp):
TATTATAATTTAAGAATATCAAAAATTAAAA
Found at i:1413383 original size:31 final size:29
Alignment explanation
Indices: 1413337--1413405 Score: 77
Period size: 31 Copynumber: 2.3 Consensus size: 29
1413327 AAATATTAAA
*
1413337 TTTAATATTATAAAAATTA-AAATAAATCT
1 TTTAATATTATAAAAACTACAAATAAA-CT
*
1413366 TTTAATATACTATAAAAACTACTAATAAACT
1 TTTAATAT--TATAAAAACTACAAATAAACT
*
1413397 TTTACTATT
1 TTTAATATT
1413406 TAATCGTGGG
Statistics
Matches: 34, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
29 9 0.26
31 19 0.56
32 6 0.18
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.42
Consensus pattern (29 bp):
TTTAATATTATAAAAACTACAAATAAACT
Found at i:1414618 original size:17 final size:18
Alignment explanation
Indices: 1414580--1414642 Score: 51
Period size: 17 Copynumber: 3.6 Consensus size: 18
1414570 AGATCAGGTT
**
1414580 TATTTTTTAAACTATCTA
1 TATTTTTTAAACTAAATA
1414598 -ATTTTTT-AACTAAATA
1 TATTTTTTAAACTAAATA
* *
1414614 TA-TTTTTAAATTTAATA
1 TATTTTTTAAACTAAATA
*
1414631 TTTTTATTTAAA
1 TATTT-TTTAAA
1414643 TTTTTTTCAA
Statistics
Matches: 36, Mismatches: 5, Indels: 7
0.75 0.10 0.15
Matches are distributed among these distances:
16 12 0.33
17 16 0.44
18 2 0.06
19 6 0.17
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTTTTTAAACTAAATA
Found at i:1415791 original size:2 final size:2
Alignment explanation
Indices: 1415784--1415808 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
1415774 CTGTCTTACC
1415784 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
1415809 CACACATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:1417713 original size:6 final size:7
Alignment explanation
Indices: 1417687--1417724 Score: 60
Period size: 7 Copynumber: 5.6 Consensus size: 7
1417677 AAGCTATATC
1417687 AAAATTT
1 AAAATTT
1417694 AAAATTT
1 AAAATTT
1417701 AAAATTT
1 AAAATTT
1417708 -AAATTT
1 AAAATTT
*
1417714 AAATTTT
1 AAAATTT
1417721 AAAA
1 AAAA
1417725 ATCTAGATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
6 6 0.21
7 22 0.79
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (7 bp):
AAAATTT
Found at i:1417713 original size:13 final size:13
Alignment explanation
Indices: 1417687--1417723 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
1417677 AAGCTATATC
1417687 AAAATTTAAAATTT
1 AAAATTT-AAATTT
1417701 AAAATTTAAATTT
1 AAAATTTAAATTT
*
1417714 AAATTTTAAA
1 AAAATTTAAA
1417724 AATCTAGATA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
13 15 0.68
14 7 0.32
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (13 bp):
AAAATTTAAATTT
Found at i:1418999 original size:8 final size:7
Alignment explanation
Indices: 1418979--1419020 Score: 52
Period size: 7 Copynumber: 6.1 Consensus size: 7
1418969 GCTTCAATAA
1418979 TATATTT
1 TATATTT
1418986 TATATTT
1 TATATTT
1418993 GTATATTT
1 -TATATTT
1419001 T-T-TTT
1 TATATTT
*
1419006 TATATTA
1 TATATTT
1419013 TATATTT
1 TATATTT
1419020 T
1 T
1419021 TATAAATTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
5 4 0.13
6 2 0.07
7 17 0.57
8 7 0.23
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (7 bp):
TATATTT
Found at i:1418999 original size:15 final size:14
Alignment explanation
Indices: 1418979--1419020 Score: 52
Period size: 15 Copynumber: 3.1 Consensus size: 14
1418969 GCTTCAATAA
1418979 TATATTTTATATTT
1 TATATTTTATATTT
1418993 GTATATTTT-T-TTT
1 -TATATTTTATATTT
*
1419006 TATATTATATATTT
1 TATATTTTATATTT
1419020 T
1 T
1419021 TATAAATTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 5
0.80 0.03 0.17
Matches are distributed among these distances:
12 7 0.29
13 4 0.17
14 5 0.21
15 8 0.33
ACGTcount: A:0.26, C:0.00, G:0.02, T:0.71
Consensus pattern (14 bp):
TATATTTTATATTT
Found at i:1419009 original size:27 final size:27
Alignment explanation
Indices: 1418978--1419039 Score: 79
Period size: 27 Copynumber: 2.3 Consensus size: 27
1418968 AGCTTCAATA
* **
1418978 ATATATTTTATATTTGTATATTTTTTT
1 ATATATTATATATTTGTATAAATTTTT
* *
1419005 TTATATTATATATTTTTATAAATTTTT
1 ATATATTATATATTTGTATAAATTTTT
1419032 ATATATTA
1 ATATATTA
1419040 AATAATTCGT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (27 bp):
ATATATTATATATTTGTATAAATTTTT
Found at i:1419016 original size:19 final size:20
Alignment explanation
Indices: 1418983--1419021 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
1418973 CAATAATATA
*
1418983 TTTTATATTTGTATATTTTT
1 TTTTATATTTATATATTTTT
1419003 TTTTATA-TTATATATTTTT
1 TTTTATATTTATATATTTTT
1419022 ATAAATTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (20 bp):
TTTTATATTTATATATTTTT
Found at i:1419095 original size:14 final size:14
Alignment explanation
Indices: 1419076--1419126 Score: 50
Period size: 14 Copynumber: 3.4 Consensus size: 14
1419066 AAAATTTATA
1419076 TATTTTTTATTAAT
1 TATTTTTTATTAAT
*
1419090 TATTTTTTA-TATTT
1 TATTTTTTATTA-AT
1419104 TATTTTTATCATATAAT
1 TATTTTT-T-AT-TAAT
1419121 TATTTT
1 TATTTT
1419127 ATATATAAAG
Statistics
Matches: 30, Mismatches: 2, Indels: 7
0.77 0.05 0.18
Matches are distributed among these distances:
13 2 0.07
14 17 0.57
15 1 0.03
16 1 0.03
17 7 0.23
18 2 0.07
ACGTcount: A:0.27, C:0.02, G:0.00, T:0.71
Consensus pattern (14 bp):
TATTTTTTATTAAT
Found at i:1419140 original size:17 final size:16
Alignment explanation
Indices: 1419086--1419134 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
1419076 TATTTTTTAT
*
1419086 TAATTATTTT-TTATA
1 TAATTATTTTATCATA
*
1419101 T-TTTATTTTTATCATA
1 TAATTA-TTTTATCATA
1419117 TAATTATTTTAT-ATA
1 TAATTATTTTATCATA
1419132 TAA
1 TAA
1419135 AGTTATCGGA
Statistics
Matches: 28, Mismatches: 3, Indels: 6
0.76 0.08 0.16
Matches are distributed among these distances:
14 3 0.11
15 11 0.39
16 11 0.39
17 3 0.11
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (16 bp):
TAATTATTTTATCATA
Found at i:1419757 original size:21 final size:22
Alignment explanation
Indices: 1419728--1419768 Score: 66
Period size: 21 Copynumber: 1.9 Consensus size: 22
1419718 TTCTTTATTT
1419728 ATATAATATT-AAAGAAAAACC
1 ATATAATATTAAAAGAAAAACC
*
1419749 ATATTATATTAAAAGAAAAA
1 ATATAATATTAAAAGAAAAA
1419769 TTTATTATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.63, C:0.05, G:0.05, T:0.27
Consensus pattern (22 bp):
ATATAATATTAAAAGAAAAACC
Found at i:1419774 original size:21 final size:20
Alignment explanation
Indices: 1419733--1419776 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
1419723 TATTTATATA
**
1419733 ATATTAAAGAAAAACCATATT
1 ATATTAAAGAAAAA-TTTATT
1419754 ATATTAAAAGAAAAATTTATT
1 ATATT-AAAGAAAAATTTATT
1419775 AT
1 AT
1419777 TAAATATTTA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 11 0.55
22 9 0.45
ACGTcount: A:0.57, C:0.05, G:0.05, T:0.34
Consensus pattern (20 bp):
ATATTAAAGAAAAATTTATT
Found at i:1421535 original size:23 final size:24
Alignment explanation
Indices: 1421487--1421533 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
1421477 TTGACACATT
* *
1421487 ATTTTATTCTTATTATATCATTAA
1 ATTTTATTATTATAATATCATTAA
1421511 ATTTTA-TATTATAATAT-ATTAA
1 ATTTTATTATTATAATATCATTAA
1421533 A
1 A
1421534 ATATAATAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 6 0.29
23 9 0.43
24 6 0.29
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.55
Consensus pattern (24 bp):
ATTTTATTATTATAATATCATTAA
Found at i:1424526 original size:3 final size:3
Alignment explanation
Indices: 1424518--1424542 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
1424508 TGTTATGCTT
1424518 TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA T
1424543 TTTTCTTTGT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:1427213 original size:17 final size:19
Alignment explanation
Indices: 1427191--1427229 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 19
1427181 ATCATTATGC
*
1427191 AATTAAAGTAAG-G-TTTA
1 AATTAAAATAAGAGTTTTA
1427208 AATTAAAATAAGAGTTTTA
1 AATTAAAATAAGAGTTTTA
1427227 AAT
1 AAT
1427230 AAGATCTTCT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 11 0.58
18 1 0.05
19 7 0.37
ACGTcount: A:0.51, C:0.00, G:0.13, T:0.36
Consensus pattern (19 bp):
AATTAAAATAAGAGTTTTA
Found at i:1428023 original size:2 final size:2
Alignment explanation
Indices: 1428016--1428063 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
1428006 CACTACATAA
1428016 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1428058 AT AT AT
1 AT AT AT
1428064 TTCTCAACAT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1428198 original size:14 final size:14
Alignment explanation
Indices: 1428176--1428208 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
1428166 ATTTTCTTTT
1428176 GGGGGG-GGGGG-G
1 GGGGGGAGGGGGAG
1428188 GGGGGGAGGGGGAG
1 GGGGGGAGGGGGAG
1428202 GGGGGGA
1 GGGGGGA
1428209 TAAAACAAGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 6 0.32
13 5 0.26
14 8 0.42
ACGTcount: A:0.09, C:0.00, G:0.91, T:0.00
Consensus pattern (14 bp):
GGGGGGAGGGGGAG
Found at i:1428886 original size:15 final size:16
Alignment explanation
Indices: 1428866--1428896 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
1428856 AATTTTTAAG
1428866 TATAAATATAA-AAAA
1 TATAAATATAATAAAA
1428881 TATAAATATAATAAAA
1 TATAAATATAATAAAA
1428897 ATACATGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (16 bp):
TATAAATATAATAAAA
Found at i:1432833 original size:13 final size:13
Alignment explanation
Indices: 1432815--1432839 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1432805 CTATTCATAA
1432815 TGTATCGATACAC
1 TGTATCGATACAC
1432828 TGTATCGATACA
1 TGTATCGATACA
1432840 TGAATAGTGA
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:0.32, C:0.20, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:1433030 original size:13 final size:13
Alignment explanation
Indices: 1433012--1433036 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1433002 CTGCCAGTTT
1433012 ATGTATCGATACA
1 ATGTATCGATACA
1433025 ATGTATCGATAC
1 ATGTATCGATAC
1433037 TAAGCAAAAT
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1437253 original size:15 final size:15
Alignment explanation
Indices: 1437233--1437261 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
1437223 TATGCATATT
1437233 TAGCAACTTGATAGA
1 TAGCAACTTGATAGA
1437248 TAGCAACTTGATAG
1 TAGCAACTTGATAG
1437262 GTTCCATGAG
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:0.38, C:0.14, G:0.21, T:0.28
Consensus pattern (15 bp):
TAGCAACTTGATAGA
Found at i:1438748 original size:78 final size:79
Alignment explanation
Indices: 1438619--1438880 Score: 239
Period size: 79 Copynumber: 3.3 Consensus size: 79
1438609 CTCGTTTTCA
* * * ** * *
1438619 TTTCTAAAACACCAAAATTTTCATCTCGATGATACTCAAACCTGATTATTTTTGAGGAGATATTC
1 TTTCTAAAACACCAAAATTTTCATCTTGAGGATACTCCAACCCCATCATTTTTGAGGAGATACTC
* *
1438684 TAACTAAGTTTTAT
66 CAACTCAGTTTTAT
**
1438698 TTTCT-AAACACCAAAATTTTCATCTTGAGGATACTCCAACCCCATCATTTTCAAAGG-GATACT
1 TTTCTAAAACACCAAAATTTTCATCTTGAGGATACTCCAACCCCATCATTTT-TGAGGAGATACT
* *
1438761 CCAACCCCGCTTTTAT
65 CCAACTCAG-TTTTAT
* *** * *
1438777 TTCCT-AAACATTGAATTTTTCATCTT-AGGGATACTCCAACCCTATCATTTTTGA-GAGGATAC
1 TTTCTAAAACACCAAAATTTTCATCTTGA-GGATACTCCAACCCCATCATTTTTGAGGA-GATAC
*
1438839 TCCAACCTCATTTTTA-
64 TCCAA-CTCAGTTTTAT
* *
1438855 CTTCTAAAACACCTAAATTTTCATCT
1 TTTCTAAAACACCAAAATTTTCATCT
1438881 CAGGGGATAT
Statistics
Matches: 146, Mismatches: 30, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
77 1 0.01
78 55 0.38
79 88 0.60
80 2 0.01
ACGTcount: A:0.31, C:0.23, G:0.09, T:0.37
Consensus pattern (79 bp):
TTTCTAAAACACCAAAATTTTCATCTTGAGGATACTCCAACCCCATCATTTTTGAGGAGATACTC
CAACTCAGTTTTAT
Found at i:1439210 original size:19 final size:18
Alignment explanation
Indices: 1439185--1439281 Score: 97
Period size: 19 Copynumber: 5.8 Consensus size: 18
1439175 ATTTCAACGA
1439185 TTTGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1439203 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1439219 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1439235 TGTTGTATCGATAC--AA-
1 T-TTGTATCGATACATAAG
1439251 --TGTATCGATACATAAG
1 TTTGTATCGATACATAAG
1439267 TTTTGTATCGATACA
1 -TTTGTATCGATACA
1439282 ATGTATCACT
Statistics
Matches: 66, Mismatches: 0, Indels: 25
0.73 0.00 0.27
Matches are distributed among these distances:
13 22 0.33
15 4 0.06
17 4 0.06
18 1 0.02
19 35 0.53
ACGTcount: A:0.33, C:0.12, G:0.18, T:0.37
Consensus pattern (18 bp):
TTTGTATCGATACATAAG
Found at i:1439223 original size:32 final size:32
Alignment explanation
Indices: 1439187--1439288 Score: 195
Period size: 32 Copynumber: 3.2 Consensus size: 32
1439177 TTCAACGATT
1439187 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1439219 TGTATCGATACATAAGTGTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
*
1439251 TGTATCGATACATAAGTTTTGTATCGATACAA
1 TGTATCGATACATAAGTGTTGTATCGATACAA
1439283 TGTATC
1 TGTATC
1439289 ACTACGAAGC
Statistics
Matches: 69, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
32 69 1.00
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (32 bp):
TGTATCGATACATAAGTGTTGTATCGATACAA
Found at i:1439224 original size:13 final size:13
Alignment explanation
Indices: 1439206--1439262 Score: 60
Period size: 13 Copynumber: 3.9 Consensus size: 13
1439196 ACATAAGTGT
1439206 TGTATCGATACAA
1 TGTATCGATACAA
1439219 TGTATCGATACATAA
1 TGTATCGATAC--AA
1439234 GTGTTGTATCGATACAA
1 ----TGTATCGATACAA
1439251 TGTATCGATACA
1 TGTATCGATACA
1439263 TAAGTTTTGT
Statistics
Matches: 38, Mismatches: 0, Indels: 12
0.76 0.00 0.24
Matches are distributed among these distances:
13 23 0.61
15 2 0.05
17 2 0.05
19 11 0.29
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1439350 original size:13 final size:13
Alignment explanation
Indices: 1439334--1439358 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1439324 ATTACTCAAA
1439334 TGTATCGATACAT
1 TGTATCGATACAT
1439347 TGTATCGATACA
1 TGTATCGATACA
1439359 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1441184 original size:24 final size:26
Alignment explanation
Indices: 1441157--1441205 Score: 66
Period size: 27 Copynumber: 1.9 Consensus size: 26
1441147 AAAAAAATTT
1441157 ATTCAT-C-GGGGACACTCCAACCTC
1 ATTCATCCAGGGGACACTCCAACCTC
*
1441181 ATTCCTCCGAGGGGACACTCCAACC
1 ATTCATCC-AGGGGACACTCCAACC
1441206 CCGTTTTCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 5 0.24
25 1 0.05
27 15 0.71
ACGTcount: A:0.24, C:0.39, G:0.18, T:0.18
Consensus pattern (26 bp):
ATTCATCCAGGGGACACTCCAACCTC
Found at i:1447235 original size:31 final size:32
Alignment explanation
Indices: 1447198--1447259 Score: 83
Period size: 32 Copynumber: 2.0 Consensus size: 32
1447188 ATTATATAAT
*
1447198 AAAAAAT-ATTTTATTTTGAA-AATAAAAATTA
1 AAAAAATAACTTTATTTT-AAGAATAAAAATTA
*
1447229 AAAAAATAACTTTATTTTAAGATTAAAAATT
1 AAAAAATAACTTTATTTTAAGAATAAAAATT
1447260 TTAAATATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 9 0.33
32 18 0.67
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.39
Consensus pattern (32 bp):
AAAAAATAACTTTATTTTAAGAATAAAAATTA
Found at i:1447665 original size:22 final size:21
Alignment explanation
Indices: 1447627--1447676 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
1447617 TATATTTATA
*
1447627 TATATTTGTGACATTTTATTT
1 TATATTTGTGACATTTTATGT
** *
1447648 TATATCTTGTGATGTTTTGTGT
1 TATAT-TTGTGACATTTTATGT
1447670 TATATTT
1 TATATTT
1447677 TAAATTTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.20, C:0.04, G:0.14, T:0.62
Consensus pattern (21 bp):
TATATTTGTGACATTTTATGT
Found at i:1448106 original size:13 final size:12
Alignment explanation
Indices: 1448088--1448126 Score: 53
Period size: 11 Copynumber: 3.2 Consensus size: 12
1448078 AATTCCCAAC
1448088 ATAAATATTAAAT
1 ATAAATA-TAAAT
*
1448101 ATAAATATATAT
1 ATAAATATAAAT
1448113 -TAAATATAAAT
1 ATAAATATAAAT
1448124 ATA
1 ATA
1448127 TTTTAAAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
11 10 0.43
12 6 0.26
13 7 0.30
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (12 bp):
ATAAATATAAAT
Found at i:1448107 original size:6 final size:6
Alignment explanation
Indices: 1448088--1448126 Score: 53
Period size: 6 Copynumber: 6.5 Consensus size: 6
1448078 AATTCCCAAC
*
1448088 ATAAAT ATTAAAT ATAAAT ATATAT -TAAAT ATAAAT ATA
1 ATAAAT A-TAAAT ATAAAT ATAAAT ATAAAT ATAAAT ATA
1448127 TTTTAAAATT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 4 0.14
6 19 0.66
7 6 0.21
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (6 bp):
ATAAAT
Found at i:1448125 original size:15 final size:17
Alignment explanation
Indices: 1448092--1448133 Score: 75
Period size: 17 Copynumber: 2.5 Consensus size: 17
1448082 CCCAACATAA
1448092 ATATTAAATATAAATAT
1 ATATTAAATATAAATAT
1448109 ATATTAAATATAAATAT
1 ATATTAAATATAAATAT
*
1448126 ATTTTAAA
1 ATATTAAA
1448134 ATTTTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (17 bp):
ATATTAAATATAAATAT
Found at i:1448206 original size:13 final size:13
Alignment explanation
Indices: 1448188--1448218 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
1448178 ATTAAAATAT
1448188 ATATTAAATACAA
1 ATATTAAATACAA
*
1448201 ATATTAAATATAA
1 ATATTAAATACAA
1448214 ATATT
1 ATATT
1448219 TAAAAATTTC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (13 bp):
ATATTAAATACAA
Found at i:1449690 original size:2 final size:2
Alignment explanation
Indices: 1449683--1449721 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
1449673 TGCTTGTTTA
*
1449683 TC TC TC TC TC TC TC TT TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1449722 ATTTTCTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.00, C:0.46, G:0.00, T:0.54
Consensus pattern (2 bp):
TC
Found at i:1451950 original size:16 final size:17
Alignment explanation
Indices: 1451930--1451963 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
1451920 CTTTTTTTAA
*
1451930 TTTTTAAAATATTTATC
1 TTTTGAAAATATTTATC
*
1451947 TTTTGAAATTATTTATC
1 TTTTGAAAATATTTATC
1451964 AAAATGCATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.32, C:0.06, G:0.03, T:0.59
Consensus pattern (17 bp):
TTTTGAAAATATTTATC
Found at i:1456768 original size:13 final size:13
Alignment explanation
Indices: 1456750--1456775 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1456740 CTATTTATGA
1456750 TGTATCGATACAC
1 TGTATCGATACAC
1456763 TGTATCGATACAC
1 TGTATCGATACAC
1456776 ACAAATATGT
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:0.31, C:0.23, G:0.15, T:0.31
Consensus pattern (13 bp):
TGTATCGATACAC
Found at i:1456870 original size:10 final size:10
Alignment explanation
Indices: 1456843--1456881 Score: 53
Period size: 10 Copynumber: 4.0 Consensus size: 10
1456833 TAGTGATACG
1456843 TGAACAGTG-
1 TGAACAGTGA
1456852 TGAACAGTGA
1 TGAACAGTGA
*
1456862 TGAATAGTGA
1 TGAACAGTGA
*
1456872 TCAACAGTGA
1 TGAACAGTGA
1456882 AAATGAGATT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
9 9 0.35
10 17 0.65
ACGTcount: A:0.38, C:0.10, G:0.28, T:0.23
Consensus pattern (10 bp):
TGAACAGTGA
Found at i:1456969 original size:53 final size:53
Alignment explanation
Indices: 1456905--1457041 Score: 247
Period size: 53 Copynumber: 2.6 Consensus size: 53
1456895 CTACTTCCAA
1456905 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
* *
1456958 TGTATCGATACATATTGTGTGTATCGATACAAATTTGGCTACTGCCAATGTCC
1 TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
1457011 TGTATCGATACATATTTGTGTGTATCGATAC
1 TGTATCGATACATATTT-TGTGTATCGATAC
1457042 TATGCAATTT
Statistics
Matches: 80, Mismatches: 3, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
53 67 0.84
54 13 0.16
ACGTcount: A:0.27, C:0.18, G:0.18, T:0.37
Consensus pattern (53 bp):
TGTATCGATACATATTTTGTGTATCGATACAAATTTGGCTACTGCCAATGACC
Found at i:1457074 original size:20 final size:20
Alignment explanation
Indices: 1457011--1457081 Score: 74
Period size: 20 Copynumber: 3.5 Consensus size: 20
1457001 GCCAATGTCC
**
1457011 TGTATCGATACATATTTGTG
1 TGTATCGATACATATTAATG
* *
1457031 TGTATCGATAC-TATGCAATT
1 TGTATCGATACATAT-TAATG
1457051 TGTATCGATACAT-TTAAATG
1 TGTATCGATACATATT-AATG
1457071 TGTATCGATAC
1 TGTATCGATAC
1457082 TTTTCAGGGT
Statistics
Matches: 42, Mismatches: 6, Indels: 6
0.78 0.11 0.11
Matches are distributed among these distances:
19 3 0.07
20 38 0.90
21 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.17, T:0.41
Consensus pattern (20 bp):
TGTATCGATACATATTAATG
Found at i:1457147 original size:21 final size:21
Alignment explanation
Indices: 1457121--1457161 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
1457111 GTCAACCTTG
1457121 TGTATTAATACCAATA-GTATA
1 TGTATTAATA-CAATACGTATA
*
1457142 TGTATTGATACAATACGTAT
1 TGTATTAATACAATACGTAT
1457162 TTTTACTTAG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 13 0.72
ACGTcount: A:0.39, C:0.10, G:0.12, T:0.39
Consensus pattern (21 bp):
TGTATTAATACAATACGTATA
Found at i:1457508 original size:20 final size:20
Alignment explanation
Indices: 1457480--1457530 Score: 75
Period size: 20 Copynumber: 2.5 Consensus size: 20
1457470 CGATACATTT
* *
1457480 TATCGATACATAATGAATTG
1 TATCAATACATAATAAATTG
*
1457500 TATCAATACATAGTAAATTG
1 TATCAATACATAATAAATTG
1457520 TATCAATACAT
1 TATCAATACAT
1457531 TGAGCCTAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.43, C:0.12, G:0.10, T:0.35
Consensus pattern (20 bp):
TATCAATACATAATAAATTG
Found at i:1461592 original size:40 final size:40
Alignment explanation
Indices: 1461518--1461598 Score: 135
Period size: 40 Copynumber: 2.0 Consensus size: 40
1461508 ATCCTTATAG
*
1461518 TTTGATATTTACAATCCATGCATTAGTCTTATCAACTTCT
1 TTTGATATTTACAATCCATGCATTAGACTTATCAACTTCT
* *
1461558 TTTGATATTTATAATTCATGCATTAGACTTATCAACTTCT
1 TTTGATATTTACAATCCATGCATTAGACTTATCAACTTCT
1461598 T
1 T
1461599 CCATATTAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
40 38 1.00
ACGTcount: A:0.28, C:0.17, G:0.07, T:0.47
Consensus pattern (40 bp):
TTTGATATTTACAATCCATGCATTAGACTTATCAACTTCT
Found at i:1461786 original size:126 final size:127
Alignment explanation
Indices: 1461629--1461877 Score: 455
Period size: 127 Copynumber: 2.0 Consensus size: 127
1461619 TTCCCATAAA
*
1461629 AAATTCATGCGTCAATCACATCTATTCTAAAAAA-AATCTATGTATTAGTCTTATTTTTCAAATT
1 AAATTCATGCGTCAATCACATCTATTCTAAAAAAGAATCTATGTATTAGTCTTATCTTTCAAATT
*
1461693 CAAATAAGAATTTAAATATTAGTCACATCTTTTAGATTCCAATAAATAATTCATACATTACT
66 CAAATAAAAATTTAAATATTAGTCACATCTTTTAGATTCCAATAAATAATTCATACATTACT
*
1461755 AAATTCATGCGTCAATCATATCTATTCTAAAAAAGAATCTATGTATTAGTCTTATCTTTCAAATT
1 AAATTCATGCGTCAATCACATCTATTCTAAAAAAGAATCTATGTATTAGTCTTATCTTTCAAATT
*
1461820 CAAATAAAAATTTACATATTAGTCACATCTTTTAGATTCCAATAAATAATTCATACAT
66 CAAATAAAAATTTAAATATTAGTCACATCTTTTAGATTCCAATAAATAATTCATACAT
1461878 GTAAGCTCAA
Statistics
Matches: 118, Mismatches: 4, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
126 33 0.28
127 85 0.72
ACGTcount: A:0.41, C:0.15, G:0.06, T:0.39
Consensus pattern (127 bp):
AAATTCATGCGTCAATCACATCTATTCTAAAAAAGAATCTATGTATTAGTCTTATCTTTCAAATT
CAAATAAAAATTTAAATATTAGTCACATCTTTTAGATTCCAATAAATAATTCATACATTACT
Found at i:1462621 original size:13 final size:13
Alignment explanation
Indices: 1462603--1462627 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1462593 CAATTCTTCA
1462603 TGTATTGATACAT
1 TGTATTGATACAT
1462616 TGTATTGATACA
1 TGTATTGATACA
1462628 ATATGCCATG
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:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (13 bp):
TGTATTGATACAT
Found at i:1462702 original size:20 final size:19
Alignment explanation
Indices: 1462676--1462749 Score: 85
Period size: 20 Copynumber: 3.8 Consensus size: 19
1462666 ATTGCCAGTT
* *
1462676 TCATGTATTGATACAATTA
1 TCATGTATCGATACAATGA
1462695 TGCATGTATCGATACAATGA
1 T-CATGTATCGATACAATGA
* *
1462715 TTATGTATCGATACAAAGCA
1 TCATGTATCGATACAATG-A
*
1462735 TAATGTATCGATACA
1 TCATGTATCGATACA
1462750 GCTGGATGTG
Statistics
Matches: 48, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
19 16 0.33
20 32 0.67
ACGTcount: A:0.38, C:0.14, G:0.15, T:0.34
Consensus pattern (19 bp):
TCATGTATCGATACAATGA
Found at i:1463380 original size:36 final size:37
Alignment explanation
Indices: 1463339--1463413 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 37
1463329 TAAAAGGATT
* *
1463339 TTCAAGATTTTCTTCCCCTTATTGTTA-AAAAAAATC
1 TTCAAGATTTTCTCCCCCTTAATGTTATAAAAAAATC
1463375 TTCAAGATTTTCTCCCCCTTAATGTTATAAAAAAATC
1 TTCAAGATTTTCTCCCCCTTAATGTTATAAAAAAATC
1463412 TT
1 TT
1463414 TTTATTTCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
36 25 0.69
37 11 0.31
ACGTcount: A:0.33, C:0.20, G:0.05, T:0.41
Consensus pattern (37 bp):
TTCAAGATTTTCTCCCCCTTAATGTTATAAAAAAATC
Found at i:1465240 original size:32 final size:33
Alignment explanation
Indices: 1465177--1465245 Score: 106
Period size: 32 Copynumber: 2.1 Consensus size: 33
1465167 TTCAACGATT
1465177 TGTATCGATACATAAAGTGTTGTATCAATACAA
1 TGTATCGATACATAAAGTGTTGTATCAATACAA
*
1465210 TGTATCGATACAT-AAGT-TCTGTATCGATACAA
1 TGTATCGATACATAAAGTGT-TGTATCAATACAA
1465242 TGTA
1 TGTA
1465246 AGTTACTGCC
Statistics
Matches: 34, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
31 1 0.03
32 20 0.59
33 13 0.38
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (33 bp):
TGTATCGATACATAAAGTGTTGTATCAATACAA
Found at i:1465301 original size:13 final size:13
Alignment explanation
Indices: 1465283--1465307 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1465273 ATTACTCAAA
1465283 TGTATCGATACAT
1 TGTATCGATACAT
1465296 TGTATCGATACA
1 TGTATCGATACA
1465308 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1465356 original size:52 final size:52
Alignment explanation
Indices: 1465316--1465441 Score: 234
Period size: 52 Copynumber: 2.4 Consensus size: 52
1465306 CACTGATCTT
1465316 TGTATCGATACATGCAGGCAAATCTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATCTGCCCAGATGTATCGATACACTATGAAA
* *
1465368 TGTATCGATACATACAGGCAAATTTGCCCAGATGTATCGATACACTATGAAA
1 TGTATCGATACATGCAGGCAAATCTGCCCAGATGTATCGATACACTATGAAA
1465420 TGTATCGATACATGCAGGCAAA
1 TGTATCGATACATGCAGGCAAA
1465442 ATTTCATATT
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 71 1.00
ACGTcount: A:0.36, C:0.20, G:0.19, T:0.25
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATCTGCCCAGATGTATCGATACACTATGAAA
Found at i:1468922 original size:13 final size:13
Alignment explanation
Indices: 1468884--1468922 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1468874 TAGTAACCCT
*
1468884 TGTATTGATACAT
1 TGTATTGATACAA
1468897 TGTATTGATACAA
1 TGTATTGATACAA
*
1468910 TGTATCGATACAA
1 TGTATTGATACAA
1468923 AGAACATTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.38
Consensus pattern (13 bp):
TGTATTGATACAA
Found at i:1475210 original size:20 final size:20
Alignment explanation
Indices: 1475185--1475238 Score: 76
Period size: 19 Copynumber: 2.8 Consensus size: 20
1475175 GTCAGTTTCG
1475185 TGTATCGATACAATTG-TGCA
1 TGTATCGATACAATTGAT-CA
1475205 TGTATCGATACAA-TGATCA
1 TGTATCGATACAATTGATCA
*
1475224 TGCATCGATACAATT
1 TGTATCGATACAATT
1475239 TATCGATACA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Consensus pattern (20 bp):
TGTATCGATACAATTGATCA
Found at i:1477374 original size:22 final size:22
Alignment explanation
Indices: 1477344--1477385 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
1477334 AAAAGAAAAT
*
1477344 AACGAACAAATTTACATAAACA
1 AACGAACAAATATACATAAACA
*
1477366 AACGCACAAATATACATAAA
1 AACGAACAAATATACATAAA
1477386 GAGGGGCAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.60, C:0.19, G:0.05, T:0.17
Consensus pattern (22 bp):
AACGAACAAATATACATAAACA
Found at i:1477846 original size:28 final size:25
Alignment explanation
Indices: 1477806--1477859 Score: 81
Period size: 28 Copynumber: 2.0 Consensus size: 25
1477796 AGAAGTAAAA
1477806 ATGGGGTTGGAGTATTCCCTCAGAGATG
1 ATGGGGTTGGAGTA-T-CC-CAGAGATG
1477834 ATGGGGTTGGAGTATCCCAGAGATG
1 ATGGGGTTGGAGTATCCCAGAGATG
1477859 A
1 A
1477860 AAAATTCGGT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
25 9 0.35
26 2 0.08
27 1 0.04
28 14 0.54
ACGTcount: A:0.24, C:0.13, G:0.37, T:0.26
Consensus pattern (25 bp):
ATGGGGTTGGAGTATCCCAGAGATG
Found at i:1477872 original size:79 final size:79
Alignment explanation
Indices: 1477775--1478058 Score: 320
Period size: 79 Copynumber: 3.6 Consensus size: 79
1477765 CATCCCTTTA
* * * *
1477775 AGATGAAAATTTCAGTGTTTTAGAAGTAAAAATGGGGTTGGAGTAT-TCCCTCAGAGATGATGGG
1 AGATGAAAAATTCAATGTTTTAGAAGTAAAAACGGGGTTGGAGTATCT-CCTCAGAAATGATGGG
1477839 GTTGGAGTATCCCAG
65 GTTGGAGTATCCCAG
** ** * * * * * *
1477854 AGATGAAAAATTCGGTGTTTGGGAAATAAAAAAGGGGTTAGAGTATCTCCTCAAAAATGGTGTGG
1 AGATGAAAAATTCAATGTTTTAGAAGTAAAAACGGGGTTGGAGTATCTCCTCAGAAATGATGGGG
***
1477919 TT-GAGTATCTTGG
66 TTGGAGTATCCCAG
* * *
1477932 AGATGAAGAAGTTCAATGTTTTAGAAGTAAATACAGGGTTGGAGTATCTCCTCAGAAATGATGGG
1 AGATGAA-AAATTCAATGTTTTAGAAGTAAAAACGGGGTTGGAGTATCTCCTCAGAAATGATGGG
*
1477997 GTTGGAGTATCCCCG
65 GTTGGAGTATCCCAG
* * *
1478012 AGATGAAAAATTCAATGTTTTGGAAGCAAAAACGGAGTTGGAGTATC
1 AGATGAAAAATTCAATGTTTTAGAAGTAAAAACGGGGTTGGAGTATC
1478059 CCCTTTTGAT
Statistics
Matches: 166, Mismatches: 36, Indels: 6
0.80 0.17 0.03
Matches are distributed among these distances:
78 15 0.09
79 135 0.81
80 16 0.10
ACGTcount: A:0.33, C:0.10, G:0.29, T:0.28
Consensus pattern (79 bp):
AGATGAAAAATTCAATGTTTTAGAAGTAAAAACGGGGTTGGAGTATCTCCTCAGAAATGATGGGG
TTGGAGTATCCCAG
Found at i:1479654 original size:22 final size:21
Alignment explanation
Indices: 1479605--1479659 Score: 67
Period size: 20 Copynumber: 2.6 Consensus size: 21
1479595 GTAGCCAAAC
* **
1479605 TTGTATCGATACACCAAAGTA
1 TTGTATCGATACACAAAAAAA
1479626 -TGTATCGATACACAAAAAAAA
1 TTGTATCGATACAC-AAAAAAA
1479647 TTGTATCGATACA
1 TTGTATCGATACA
1479660 TTGGCTTATA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
20 13 0.45
21 4 0.14
22 12 0.41
ACGTcount: A:0.44, C:0.16, G:0.13, T:0.27
Consensus pattern (21 bp):
TTGTATCGATACACAAAAAAA
Found at i:1485826 original size:13 final size:13
Alignment explanation
Indices: 1485808--1485846 Score: 69
Period size: 13 Copynumber: 3.0 Consensus size: 13
1485798 ACATTTTTCT
1485808 TTGTATCGATACA
1 TTGTATCGATACA
1485821 TTGTATCGATACA
1 TTGTATCGATACA
*
1485834 CTGTATCGATACA
1 TTGTATCGATACA
1485847 GGGGGATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 25 1.00
ACGTcount: A:0.31, C:0.18, G:0.15, T:0.36
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1486010 original size:20 final size:20
Alignment explanation
Indices: 1485967--1486012 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1485957 AAATCTTTTG
1485967 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1485988 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1486008 CAAAA
1 CAAAA
1486013 CCAGCATAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1490239 original size:52 final size:52
Alignment explanation
Indices: 1490165--1490289 Score: 223
Period size: 52 Copynumber: 2.4 Consensus size: 52
1490155 ATATGAAAAA
* *
1490165 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
1490217 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
1490269 TTGCCTGCATGTATCGATACA
1 TTGCCTGCATGTATCGATACA
1490290 AAGATCAATG
Statistics
Matches: 70, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 70 1.00
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:1490300 original size:52 final size:52
Alignment explanation
Indices: 1490165--1490309 Score: 204
Period size: 52 Copynumber: 2.8 Consensus size: 52
1490155 ATATGAAAAA
* * *
1490165 TTGCTTGCATGTATCGATACATTTA-ATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TAAGATAATGTATCGATACATCTGGGCAAAT
***
1490217 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATAAGATAATGTATCGATACATCTGGGCAAAT
1490269 TTGCCTGCATGTATCGATACA-AAGATCAATGTATCGATACA
1 TTGCCTGCATGTATCGATACATAAGAT-AATGTATCGATACA
1490310 ATGTATCGAT
Statistics
Matches: 85, Mismatches: 6, Indels: 4
0.89 0.06 0.04
Matches are distributed among these distances:
51 4 0.05
52 81 0.95
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.34
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATAAGATAATGTATCGATACATCTGGGCAAAT
Found at i:1490313 original size:13 final size:13
Alignment explanation
Indices: 1490295--1490322 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1490285 ATACAAAGAT
1490295 CAATGTATCGATA
1 CAATGTATCGATA
1490308 CAATGTATCGATA
1 CAATGTATCGATA
1490321 CA
1 CA
1490323 TTTGAGTAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.18, G:0.14, T:0.29
Consensus pattern (13 bp):
CAATGTATCGATA
Found at i:1490400 original size:33 final size:33
Alignment explanation
Indices: 1490363--1490429 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1490353 AGTAGCTTAA
1490363 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
* ***
1490396 ATTGTATCGATACAACACTTTATGTATCGATAC
1 ATTGTATCGATACAAAAAAATATGTATCGATAC
1490429 A
1 A
1490430 AATCGTTGAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.40, C:0.15, G:0.12, T:0.33
Consensus pattern (33 bp):
ATTGTATCGATACAAAAAAATATGTATCGATAC
Found at i:1490403 original size:13 final size:13
Alignment explanation
Indices: 1490385--1490409 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1490375 CAAAAAAATA
1490385 TGTATCGATACAT
1 TGTATCGATACAT
1490398 TGTATCGATACA
1 TGTATCGATACA
1490410 ACACTTTATG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1491311 original size:67 final size:68
Alignment explanation
Indices: 1491189--1491315 Score: 184
Period size: 67 Copynumber: 1.9 Consensus size: 68
1491179 ATTGGGTTTT
* * *
1491189 AAAGATGATGAAGGTGCCAATATGCTGATTCAAGGCCAGCAATATTGGACTTAAAGATGAAGATG
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
1491254 AGA
66 AGA
* * * *
1491257 AAAG-TGATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGA
1 AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGA
1491316 GAAAAAGGAT
Statistics
Matches: 52, Mismatches: 7, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
67 48 0.92
68 4 0.08
ACGTcount: A:0.39, C:0.12, G:0.25, T:0.24
Consensus pattern (68 bp):
AAAGATGATAAAGATGCCAATATGCTGATTCAAGGCCAACAATATTGGACTTAAAGATGAAGATG
AGA
Found at i:1491537 original size:49 final size:49
Alignment explanation
Indices: 1491328--1491940 Score: 768
Period size: 49 Copynumber: 12.7 Consensus size: 49
1491318 AAAAGGATGT
* *
1491328 CAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAAGATGGAAAATGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGAT-G--AAGGTGC
* *
1491380 CAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
1491423 CAATGTGCTGATTCAAGGCCAGCTACACTGGACTTAAAGGTG-AGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
*
1491471 CAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
1491520 CAATGTGCTGAGTCAAGGCCAGCTACATTGGTCTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
1491569 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * *
1491618 CAATGTGCTGAGTCAAGGCCAGCTACATTGGTCTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
1491667 CAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
1491716 CAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATAAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
1491765 CAATATGCTGATTGAAGGCCAGCTATATTAGACTT--A-AT---GGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
1491808 CAATGTGCTGAGTCAAGGCTAGCTACATTGGACTTAAAGGTG-AGGTAC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* *
1491856 CAATATGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
* * * *
1491905 CAATATGCTGATTCAGGGCCAGCTATATTGGGCTTA
1 CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTA
1491941 GAAGGGTTGC
Statistics
Matches: 485, Mismatches: 63, Indels: 29
0.84 0.11 0.05
Matches are distributed among these distances:
43 72 0.15
45 1 0.00
46 3 0.01
47 1 0.00
48 89 0.18
49 287 0.59
52 32 0.07
ACGTcount: A:0.30, C:0.18, G:0.26, T:0.26
Consensus pattern (49 bp):
CAATGTGCTGATTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGC
Found at i:1491603 original size:98 final size:98
Alignment explanation
Indices: 1491262--1491940 Score: 873
Period size: 98 Copynumber: 7.0 Consensus size: 98
1491252 TGAGAAAAGT
* * * * * *
1491262 GATAAAGATGCCAATATGTTGATTCATGGCCAACGATATTGGGCTTAAAGATGAGAAAAAGGATG
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGAT--G---AAGG-TG
* * *
1491327 TCAATGTGCTGATTCAAGGCCAGCTACATTGAACTTAAA
60 CCAATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
*
1491366 GATGGAAAATGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTT----A--AAGGTGCCA
1 GAT---AAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCA
* *
1491425 ATGTGCTGATTCAAGGCCAGCTACACTGGACTTAAA
63 ATGTGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
* * *
1491461 GGT-GAGGTGCCAATGTGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
*
1491525 TGCTGAGTCAAGGCCAGCTACATTGGTCTTAAA
66 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
* *
1491558 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGCCAATG
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
*
1491623 TGCTGAGTCAAGGCCAGCTACATTGGTCTTAAA
66 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
* *
1491656 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAATGGTGAAGGTGCCAATG
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
1491721 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
66 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
* *
1491754 GATAAAGGTGCCAATATGCTGATTGAAGGCCAGCTATATTAGACTT--A-AT---GGTGCCAATG
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
*
1491813 TGCTGAGTCAAGGCTAGCTACATTGGACTTAAA
66 TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
* * * * * *
1491846 GGT-GAGGTACCAATATGCTGAGTCAAGGCCAGCTACATTGGACTTAAAGATGAAGGTGCCAATA
1 GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
* * * *
1491910 TGCTGATTCAGGGCCAGCTATATTGGGCTTA
66 TGCTGAGTCAAGGCCAGCTACATTGGACTTA
1491941 GAAGGGTTGC
Statistics
Matches: 518, Mismatches: 41, Indels: 39
0.87 0.07 0.07
Matches are distributed among these distances:
91 75 0.14
92 44 0.08
93 1 0.00
94 2 0.00
95 42 0.08
96 4 0.01
97 79 0.15
98 231 0.45
103 1 0.00
104 3 0.01
107 36 0.07
ACGTcount: A:0.31, C:0.17, G:0.26, T:0.26
Consensus pattern (98 bp):
GATAAAGGTGCCAATATGCTGATTCAAGGCCAGCTATATTGGACTTAAAGATGAAGGTGCCAATG
TGCTGAGTCAAGGCCAGCTACATTGGACTTAAA
Found at i:1492042 original size:33 final size:33
Alignment explanation
Indices: 1491933--1492051 Score: 176
Period size: 33 Copynumber: 3.7 Consensus size: 33
1491923 CCAGCTATAT
1491933 TGGGC-TTAGAAG--GGTTGCCACCGACTTGTG
1 TGGGCTTTAGAAGAAGGTTGCCACCGACTTGTG
*
1491963 TGGGCTTTAG-AGAGTGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAAGA-AGGTTGCCACCGACTTGTG
*
1491996 TGGGCTTTGGAAGAAGGTTGCCACCGACTTGTG
1 TGGGCTTTAGAAGAAGGTTGCCACCGACTTGTG
1492029 TGGGCTTTAGAAGAAGG-TGCCAC
1 TGGGCTTTAGAAGAAGGTTGCCAC
1492052 GGAGTCGTGG
Statistics
Matches: 81, Mismatches: 3, Indels: 8
0.88 0.03 0.09
Matches are distributed among these distances:
30 7 0.09
31 4 0.05
32 6 0.07
33 61 0.75
34 3 0.04
ACGTcount: A:0.18, C:0.18, G:0.36, T:0.27
Consensus pattern (33 bp):
TGGGCTTTAGAAGAAGGTTGCCACCGACTTGTG
Found at i:1492143 original size:27 final size:28
Alignment explanation
Indices: 1492112--1492630 Score: 249
Period size: 27 Copynumber: 16.9 Consensus size: 28
1492102 AGGAAAAAGA
*
1492112 TGCCACGGAGTTGTGGGCTT-AAAATGG
1 TGCCACGGAGTTGTGGGCTTAAAAAGGG
** * *
1492139 TGCCACAAAGTTGTGGACTTAAAAGGAAAAGAG
1 TGCCACGGAGTTGTGGGCTT---A--AAAAGGG
*
1492172 TGCCACGTAGTTGTGGGCTTTAAAGGAAAAAAGGG
1 TGCCACGGAGTTGTGGGC-TT------AAAAAGGG
* * *
1492207 TGCCACGGAGTCGT-GGATTTAAAAGGG
1 TGCCACGGAGTTGTGGGCTTAAAAAGGG
*
1492234 TGCCACGGAGTTGTGGGCTT-AAACGGG
1 TGCCACGGAGTTGTGGGCTTAAAAAGGG
* *
1492261 TGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAG
1 TGCCACGGAGTTGTGGGCTT------AAAAAGGG
1492295 TGCCACGGAGTTGTGGGCTTTAAAAAGGAAAAAG
1 TGCCACGGAGTTGTGGGC-TTAAAAAGG-----G
* *
1492329 ATGCCACGGAGTTGTGGGCTT-TAAATGG
1 -TGCCACGGAGTTGTGGGCTTAAAAAGGG
* * *
1492357 TGCCACAGAGTTGTGGACTTAAAAGGAAAAGAG
1 TGCCACGGAGTTGTGGGCTT---A--AAAAGGG
*
1492390 TGCCACGTAGTTGTGGGCTTTAAAGGAAAAAAGGG
1 TGCCACGGAGTTGTGGGC-TT------AAAAAGGG
* * *
1492425 TGCCACAGAGTCGTGGACTT-AAAAGGG
1 TGCCACGGAGTTGTGGGCTTAAAAAGGG
*
1492452 TGCCACGGAGTTGTGGGCTTTAAAAAGAG
1 TGCCACGGAGTTGTGGGC-TTAAAAAGGG
* *
1492481 TGCCACGGAGTCGTGGACTTAAAAGGAAAAAGGG
1 TGCCACGGAGTTGTGGGCTT------AAAAAGGG
* *
1492515 TGCCACGGAGTTGTGGTCTTTGAAAAGAAGG
1 TGCCACGGAGTTGTGGGC-TT-AAAA-AGGG
*
1492546 TGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAG
1 TGCCACGGAGTTGTGGGCTT------AAAAAGGG
* * *
1492580 TGCCACGGAGTCGTGGGC-TCAAACGGG
1 TGCCACGGAGTTGTGGGCTTAAAAAGGG
1492607 TGCCACGGAGTTGTGGGCTTAAAA
1 TGCCACGGAGTTGTGGGCTTAAAA
1492631 GGAAAAGAGT
Statistics
Matches: 382, Mismatches: 59, Indels: 101
0.70 0.11 0.19
Matches are distributed among these distances:
27 124 0.32
28 13 0.03
29 28 0.07
30 7 0.02
31 20 0.05
33 46 0.12
34 75 0.20
35 65 0.17
37 4 0.01
ACGTcount: A:0.30, C:0.14, G:0.35, T:0.21
Consensus pattern (28 bp):
TGCCACGGAGTTGTGGGCTTAAAAAGGG
Found at i:1492151 original size:60 final size:61
Alignment explanation
Indices: 1492072--1492565 Score: 282
Period size: 60 Copynumber: 8.0 Consensus size: 61
1492062 ACTTAAAAGG
* * *
1492072 AAAAGAGTGCCACGTAGTTGTGGGCTTTAAAGGAAAA-AGATGCCACGGAGTTGTGGGC-TT
1 AAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGAAAAGAG-TGCCACGGAGTTGTGGGCTTT
* ** * *
1492132 AAAATGGTGCCACAAAGTTGTGGACTTAAAAGGAAAAGAGTGCCACGTAGTTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTT
* *
1492193 AAAGGAAAAAAGGGTGCCACGGAGTCGTGGA-TTT-----AAAAGGGTGCCACGGAGTTGTGGGC
1 -------AAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGAAAAGAGTGCCACGGAGTTGTGGGC
1492252 -TT
59 TTT
*
1492254 AAACGGGTGCCACGGAGTTGTGGAC-TTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTTA-AAGG-AAAAGAGTGCCACGGAGTTGTGGGCTTT
* * * *
1492316 AAAAAGGAAAAAGATGCCACGGAGTTGTGGGCTTT-----AAATG-GTGCCACAGAGTTGTGGAC
1 -AAAAGG-----G-TGCCACGGAGTTGTGGACTTTAAAGGAAAAGAGTGCCACGGAGTTGTGGGC
1492375 -TT
59 TTT
* * * * * *
1492377 AAAAGGAAAAGAGTGCCACGTAGTTGTGGGCTTTAAAGGAAAAAAGGGTGCCACAGAGTCGTGGA
1 AAAA-G----G-GTGCCACGGAGTTGTGGACTTTAAAGG--AAAAGAGTGCCACGGAGTTGTGGG
1492442 C-TT
58 CTTT
* * *
1492445 AAAAGGGTGCCACGGAGTTGTGGGCTTT--A--AAAAGAGTGCCACGGAGTCGTGGACTTAAAAG
1 AAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGAAAAGAGTGCCACGGAGTTGTGGGCTT-----
*
1492506 GA
61 -T
* *
1492508 AAAAGGGTGCCACGGAGTTGTGGTCTTTGAAA--AGAAG-GTGCCACGGAGTTGTGGGCTT
1 AAAAGGGTGCCACGGAGTTGTGGACTTT-AAAGGAAAAGAGTGCCACGGAGTTGTGGGCTT
1492566 AGAAGGAAAA
Statistics
Matches: 352, Mismatches: 33, Indels: 93
0.74 0.07 0.19
Matches are distributed among these distances:
54 24 0.07
56 23 0.07
57 1 0.00
60 73 0.21
61 35 0.10
62 63 0.18
63 37 0.11
65 20 0.06
66 5 0.01
67 7 0.02
68 45 0.13
69 17 0.05
70 2 0.01
ACGTcount: A:0.31, C:0.14, G:0.34, T:0.22
Consensus pattern (61 bp):
AAAAGGGTGCCACGGAGTTGTGGACTTTAAAGGAAAAGAGTGCCACGGAGTTGTGGGCTTT
Found at i:1492405 original size:218 final size:219
Alignment explanation
Indices: 1492027--1492566 Score: 873
Period size: 218 Copynumber: 2.5 Consensus size: 219
1492017 CACCGACTTG
*
1492027 TGTGGGCTTTAGAAGAA-GGTGCCACGGAGTCGTGGACTTAAAAGG-AAAAGAGTGCCACGTAGT
1 TGTGGGCTTTA-AA-AAGGGTGCCACGGAGTCGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGT
1492090 TGTGGGCTTT-AAAGGAAAAAGATGCCACGGAGTTGTGGGCTTAAAATGGTGCCACAAAGTTGTG
64 TGTGGGCTTTAAAAGGAAAAAGATGCCACGGAGTTGTGGGCTTAAAATGGTGCCACAAAGTTGTG
*
1492154 GACTTAAAAGGAAAAGAGTGCCACGTAGTTGTGGGCTTTAAAGGAAAAAAGGGTGCCACGGAGTC
129 GACTTAAAAGGAAAAGAGTGCCACGTAGTTGTGGGCTTTAAAGGAAAAAAGGGTGCCACAGAGTC
*
1492219 GTGGATTTAAAAGGGTGCCACGGAGT
194 GTGGACTTAAAAGGGTGCCACGGAGT
* * *
1492245 TGTGGGC-TT-AAACGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTG
1 TGTGGGCTTTAAAAAGGGTGCCACGGAGTCGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTG
* *
1492308 TGGGCTTTAAAAAGGAAAAAGATGCCACGGAGTTGTGGGCTTTAAATGGTGCCACAGAGTTGTGG
66 TGGGCTTT-AAAAGGAAAAAGATGCCACGGAGTTGTGGGCTTAAAATGGTGCCACAAAGTTGTGG
1492373 ACTTAAAAGGAAAAGAGTGCCACGTAGTTGTGGGCTTTAAAGGAAAAAAGGGTGCCACAGAGTCG
130 ACTTAAAAGGAAAAGAGTGCCACGTAGTTGTGGGCTTTAAAGGAAAAAAGGGTGCCACAGAGTCG
1492438 TGGACTTAAAAGGGTGCCACGGAGT
195 TGGACTTAAAAGGGTGCCACGGAGT
* *
1492463 TGTGGGCTTTAAAAAGAGTGCCACGGAGTCGTGGACTTAAAAGGAAAAAGGGTGCCACGGAGTTG
1 TGTGGGCTTTAAAAAGGGTGCCACGGAGTCGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTG
* *
1492528 TGGTCTTTGAAAA-G---AAGGTGCCACGGAGTTGTGGGCTTA
66 TGGGCTTT-AAAAGGAAAAAGATGCCACGGAGTTGTGGGCTTA
1492567 GAAGGAAAAA
Statistics
Matches: 299, Mismatches: 17, Indels: 14
0.91 0.05 0.04
Matches are distributed among these distances:
214 1 0.00
215 28 0.09
216 50 0.17
217 2 0.01
218 155 0.52
219 3 0.01
220 60 0.20
ACGTcount: A:0.30, C:0.14, G:0.34, T:0.22
Consensus pattern (219 bp):
TGTGGGCTTTAAAAAGGGTGCCACGGAGTCGTGGACTTAAAAGGAAAAAGAGTGCCACGGAGTTG
TGGGCTTTAAAAGGAAAAAGATGCCACGGAGTTGTGGGCTTAAAATGGTGCCACAAAGTTGTGGA
CTTAAAAGGAAAAGAGTGCCACGTAGTTGTGGGCTTTAAAGGAAAAAAGGGTGCCACAGAGTCGT
GGACTTAAAAGGGTGCCACGGAGT
Found at i:1492454 original size:95 final size:95
Alignment explanation
Indices: 1492165--1492632 Score: 476
Period size: 95 Copynumber: 5.1 Consensus size: 95
1492155 ACTTAAAAGG
* * * * *
1492165 AAAAGAGTGCCACGTAGTTGTGGGCTTTA-AAGGAAAAAAGGGTGCCACGGAGTCGT-GGATTT-
1 AAAAGGGTGCCACGGAGTTGTGGAC-TTAGAAGG-AAAAAGAGTGCCACGGAGTCGTGGGCTTTA
1492227 -----AAAAGGGTGCCACGGAGTTGTGGGCTT
64 AAGGAAAAAGGGTGCCACGGAGTTGTGGGCTT
* *
1492254 AAACGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTTGTGGGCTTTAAA
1 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTCGTGGGCTTT--A
*
1492319 AAGGAAAAA-GATGCCACGGAGTTGTGGGCTT
64 AAGGAAAAAGGGTGCCACGGAGTTGTGGGCTT
* * * * * *
1492350 TAAATGGTGCCACAGAGTTGTGGACTTAAAAGG-AAAAGAGTGCCACGTAGTTGTGGGCTTTAAA
1 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTCGTGGGCTTTAAA
* * *
1492414 GGAAAAAAGGGTGCCACAGAGTCGTGGACTT
66 GG-AAAAAGGGTGCCACGGAGTTGTGGGCTT
* * * *
1492445 AAAAGGGTGCCACGGAGTTGTGGGCTT-----TAAAAAGAGTGCCACGGAGTCGTGGACTTAAAA
1 AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTCGTGGGCTTTAAA
*
1492505 GGAAAAAGGGTGCCACGGAGTTGTGGTCTTT
66 GGAAAAAGGGTGCCACGGAGTTGTGGGC-TT
*
1492536 GAAAAGAAGGTGCCACGGAGTTGTGGGCTTAGAAGGAAAAAGAGTGCCACGGAGTCGTGGGC--T
1 -AAAAG--GGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTCGTGGGCTTT
* *
1492599 -----CAAACGGGTGCCACGGAGTTGTGGGCTT
63 AAAGGAAAAAGGGTGCCACGGAGTTGTGGGCTT
1492627 AAAAGG
1 AAAAGG
1492633 AAAAGAGTGC
Statistics
Matches: 321, Mismatches: 36, Indels: 45
0.80 0.09 0.11
Matches are distributed among these distances:
88 24 0.07
89 30 0.09
90 28 0.09
91 33 0.10
92 28 0.09
93 5 0.02
94 27 0.08
95 68 0.21
96 49 0.15
97 4 0.01
99 25 0.08
ACGTcount: A:0.30, C:0.14, G:0.35, T:0.21
Consensus pattern (95 bp):
AAAAGGGTGCCACGGAGTTGTGGACTTAGAAGGAAAAAGAGTGCCACGGAGTCGTGGGCTTTAAA
GGAAAAAGGGTGCCACGGAGTTGTGGGCTT
Found at i:1492788 original size:63 final size:63
Alignment explanation
Indices: 1492715--1492948 Score: 321
Period size: 63 Copynumber: 3.7 Consensus size: 63
1492705 CACTAAATTA
* * *
1492715 TGGACTTTAGGACAAAATGCCATTGAATCGCGGGCTTTGAGAAGAAAAGGTGCCACAGAGTCG
1 TGGACTTTAGGACAAAATGCCACTGATTCGTGGGCTTTGAGAAGAAAAGGTGCCACAGAGTCG
* *
1492778 TGGACTTTAGGACAAAATGCCACTGATTCGTGGGTTTTGAGAAGAAAAGGTGCCACGGAGTCG
1 TGGACTTTAGGACAAAATGCCACTGATTCGTGGGCTTTGAGAAGAAAAGGTGCCACAGAGTCG
*
1492841 TGGACTTTAGGACAAAATGCCACTGATTCATGGGCTTT--GAAGAAAAGGATGCCACTA-AGTCG
1 TGGACTTTAGGACAAAATGCCACTGATTCGTGGGCTTTGAGAAGAAAAGG-TGCCAC-AGAGTCG
* * * * *
1492903 TGGACTTTGAGAAGAGATTGCCACTGAGTCGTGGGCTTTGAGAAGA
1 TGGACTTT-AGGACAAAATGCCACTGATTCGTGGGCTTTGAGAAGA
1492949 GATTTGAAGA
Statistics
Matches: 152, Mismatches: 14, Indels: 8
0.87 0.08 0.05
Matches are distributed among these distances:
61 10 0.07
62 19 0.12
63 118 0.78
65 5 0.03
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.24
Consensus pattern (63 bp):
TGGACTTTAGGACAAAATGCCACTGATTCGTGGGCTTTGAGAAGAAAAGGTGCCACAGAGTCG
Found at i:1492799 original size:30 final size:30
Alignment explanation
Indices: 1492715--1492941 Score: 150
Period size: 30 Copynumber: 7.3 Consensus size: 30
1492705 CACTAAATTA
* *
1492715 TGGACTTTAGGACAAAATGCCATTGAATCG
1 TGGACTTTAGGACAAAATGCCACTGAGTCG
* * * * *
1492745 CGGGCTTTGAGAAGAAAAGGTGCCACAGAGTCG
1 TGGACTTT-AGGACAAAA--TGCCACTGAGTCG
*
1492778 TGGACTTTAGGACAAAATGCCACTGATTCG
1 TGGACTTTAGGACAAAATGCCACTGAGTCG
** * * *
1492808 TGGGTTTTGAGAAGAAAAGGTGCCACGGAGTCG
1 TGGACTTT-AGGACAAAA--TGCCACTGAGTCG
* *
1492841 TGGACTTTAGGACAAAATGCCACTGATTCA
1 TGGACTTTAGGACAAAATGCCACTGAGTCG
* * *
1492871 TGGGCTTTGAAGA-AAAGGATGCCACTAAGTCG
1 TGGACTTT-AGGACAAA--ATGCCACTGAGTCG
* * * *
1492903 TGGACTTTGAGAAGAGATTGCCACTGAGTCG
1 TGGACTTT-AGGACAAAATGCCACTGAGTCG
*
1492934 TGGGCTTT
1 TGGACTTT
1492942 GAGAAGAGAT
Statistics
Matches: 149, Mismatches: 38, Indels: 19
0.72 0.18 0.09
Matches are distributed among these distances:
30 43 0.29
31 36 0.24
32 35 0.23
33 35 0.23
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (30 bp):
TGGACTTTAGGACAAAATGCCACTGAGTCG
Found at i:1492952 original size:31 final size:31
Alignment explanation
Indices: 1492652--1492948 Score: 206
Period size: 31 Copynumber: 9.5 Consensus size: 31
1492642 CCACGTAGTT
* * * *
1492652 GTGGGCTTTGAGAAGAGATTGCCACTGACTT
1 GTGGGCTTTGAGAAGAAAATGCCACTGAGTC
* * * * * *
1492683 GTGGGCTTTAAGAAGGAGATGCCACTAAATT
1 GTGGGCTTTGAGAAGAAAATGCCACTGAGTC
* * * * * *
1492714 ATGGACTTT-AGGACAAAATGCCATTGAATC
1 GTGGGCTTTGAGAAGAAAATGCCACTGAGTC
* *
1492744 GCGGGCTTTGAGAAGAAAAGGTGCCACAGAGTC
1 GTGGGCTTTGAGAAGAAAA--TGCCACTGAGTC
* * * *
1492777 GTGGACTTT-AGGACAAAATGCCACTGATTC
1 GTGGGCTTTGAGAAGAAAATGCCACTGAGTC
* *
1492807 GTGGGTTTTGAGAAGAAAAGGTGCCACGGAGTC
1 GTGGGCTTTGAGAAGAAAA--TGCCACTGAGTC
* * * *
1492840 GTGGACTTT-AGGACAAAATGCCACTGATTC
1 GTGGGCTTTGAGAAGAAAATGCCACTGAGTC
* * *
1492870 ATGGGCTTTGAAGAA-AAGGATGCCACTAAGTC
1 GTGGGCTTTG-AGAAGAA-AATGCCACTGAGTC
* * *
1492902 GTGGACTTTGAGAAGAGATTGCCACTGAGTC
1 GTGGGCTTTGAGAAGAAAATGCCACTGAGTC
1492933 GTGGGCTTTGAGAAGA
1 GTGGGCTTTGAGAAGA
1492949 GATTTGAAGA
Statistics
Matches: 201, Mismatches: 55, Indels: 20
0.73 0.20 0.07
Matches are distributed among these distances:
30 54 0.27
31 77 0.38
32 37 0.18
33 33 0.16
ACGTcount: A:0.30, C:0.16, G:0.30, T:0.24
Consensus pattern (31 bp):
GTGGGCTTTGAGAAGAAAATGCCACTGAGTC
Found at i:1501247 original size:52 final size:52
Alignment explanation
Indices: 1501162--1501285 Score: 221
Period size: 52 Copynumber: 2.4 Consensus size: 52
1501152 ATATGAAAAG
* *
1501162 TTGCTTGCATGTATCGATACATTTAATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
*
1501214 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
1501266 TTGCCTGCATGTATCGATAC
1 TTGCCTGCATGTATCGATAC
1501286 CAAGATCAAT
Statistics
Matches: 69, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 69 1.00
ACGTcount: A:0.27, C:0.18, G:0.19, T:0.36
Consensus pattern (52 bp):
TTGCCTGCATGTATCGATACATTTAATAATGTATCGATACATCTGGGCAAAT
Found at i:1501297 original size:52 final size:51
Alignment explanation
Indices: 1501162--1501307 Score: 197
Period size: 52 Copynumber: 2.8 Consensus size: 51
1501152 ATATGAAAAG
* *
1501162 TTGCTTGCATGTATCGATACATTTA-ATAGTGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA--TAGATAATGTATCGATACATCTGGGCAAAT
**
1501214 TTGCCTGCATGTATCGATACATTTTATAATGTATCGATACATCTGGGCAAAT
1 TTGCCTGCATGTATCGATACA-TAGATAATGTATCGATACATCTGGGCAAAT
1501266 TTGCCTGCATGTATCGATACCA-AGATCAATGTATCGATACAT
1 TTGCCTGCATGTATCGATA-CATAGAT-AATGTATCGATACAT
1501308 TTTTTGGCAG
Statistics
Matches: 86, Mismatches: 5, Indels: 6
0.89 0.05 0.06
Matches are distributed among these distances:
51 4 0.05
52 80 0.93
53 2 0.02
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (51 bp):
TTGCCTGCATGTATCGATACATAGATAATGTATCGATACATCTGGGCAAAT
Found at i:1501368 original size:33 final size:33
Alignment explanation
Indices: 1501326--1501392 Score: 89
Period size: 33 Copynumber: 2.0 Consensus size: 33
1501316 AGTAGCTTAA
*
1501326 ATTGTATCGATACAAAAAAATATGTATCGATAC
1 ATTGAATCGATACAAAAAAATATGTATCGATAC
* ***
1501359 ATTGAATCGATACAACACTTTATGTATCGATAC
1 ATTGAATCGATACAAAAAAATATGTATCGATAC
1501392 A
1 A
1501393 AATCATTGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
33 29 1.00
ACGTcount: A:0.42, C:0.15, G:0.12, T:0.31
Consensus pattern (33 bp):
ATTGAATCGATACAAAAAAATATGTATCGATAC
Found at i:1502354 original size:41 final size:41
Alignment explanation
Indices: 1502281--1502388 Score: 168
Period size: 41 Copynumber: 2.7 Consensus size: 41
1502271 AGAATGCGTA
* *
1502281 AATTTGCTAAAATTGC--CTTATTAAGGGGGAGAATGTACG
1 AATTTGTTAAAATTACTTCTTATTAAGGGGGAGAATGTACG
1502320 AATTTGTTAAAATTACTTCTTATTAAGGGGGAGAATGTACG
1 AATTTGTTAAAATTACTTCTTATTAAGGGGGAGAATGTACG
*
1502361 AATTTGTTAAAATTACTT-TAATTAAGGG
1 AATTTGTTAAAATTACTTCTTATTAAGGG
1502389 AGAAAGAAAA
Statistics
Matches: 64, Mismatches: 3, Indels: 3
0.91 0.04 0.04
Matches are distributed among these distances:
39 14 0.22
40 9 0.14
41 41 0.64
ACGTcount: A:0.35, C:0.07, G:0.21, T:0.36
Consensus pattern (41 bp):
AATTTGTTAAAATTACTTCTTATTAAGGGGGAGAATGTACG
Found at i:1503053 original size:13 final size:13
Alignment explanation
Indices: 1503035--1503060 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1503025 ACACCAAAGT
1503035 ATGTATCGATACA
1 ATGTATCGATACA
1503048 ATGTATCGATACA
1 ATGTATCGATACA
1503061 CAAAAAAAAT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1505064 original size:50 final size:51
Alignment explanation
Indices: 1505005--1505139 Score: 182
Period size: 52 Copynumber: 2.6 Consensus size: 51
1504995 TGCCTGTATA
* ** * *
1505005 TATCGATACATTCTTTAATGTGTCGATACATTTGGGT-CAAACCCAGAATG
1 TATCGATACAATCAATAATGTATCAATACATTTGGGTACAAACCCAGAATG
*
1505055 TATCGATACAATGAATAATGTATCAATACATTTGGGTCACAAACCCAGAATG
1 TATCGATACAATCAATAATGTATCAATACATTTGGGT-ACAAACCCAGAATG
* *
1505107 TATCGATACAATAAAAAATGTATCAATACATTT
1 TATCGATACAATCAATAATGTATCAATACATTT
1505140 TCTTTACAAA
Statistics
Matches: 75, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
50 31 0.41
52 44 0.59
ACGTcount: A:0.39, C:0.16, G:0.14, T:0.31
Consensus pattern (51 bp):
TATCGATACAATCAATAATGTATCAATACATTTGGGTACAAACCCAGAATG
Found at i:1505114 original size:52 final size:50
Alignment explanation
Indices: 1505020--1505139 Score: 186
Period size: 52 Copynumber: 2.4 Consensus size: 50
1505010 ATACATTCTT
* * *
1505020 TAATGTGTCGATACATTTGGGTCAAACCCAGAATGTATCGATACAATGAA
1 TAATGTATCAATACATTTGGGTCAAACCCAGAATGTATCGATACAATAAA
1505070 TAATGTATCAATACATTTGGGTCACAAACCCAGAATGTATCGATACAATAAA
1 TAATGTATCAATACATTTGGGT--CAAACCCAGAATGTATCGATACAATAAA
*
1505122 AAATGTATCAATACATTT
1 TAATGTATCAATACATTT
1505140 TCTTTACAAA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
50 20 0.31
52 44 0.69
ACGTcount: A:0.40, C:0.16, G:0.15, T:0.29
Consensus pattern (50 bp):
TAATGTATCAATACATTTGGGTCAAACCCAGAATGTATCGATACAATAAA
Found at i:1505219 original size:20 final size:20
Alignment explanation
Indices: 1505196--1505242 Score: 85
Period size: 20 Copynumber: 2.3 Consensus size: 20
1505186 TATTTCAGAC
1505196 ATGTATCGATACATTCACTT
1 ATGTATCGATACATTCACTT
1505216 ATGTATCGATACATTCACTT
1 ATGTATCGATACATTCACTT
1505236 ATTGTAT
1 A-TGTAT
1505243 AAATACCAAC
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 21 0.81
21 5 0.19
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.43
Consensus pattern (20 bp):
ATGTATCGATACATTCACTT
Found at i:1505248 original size:21 final size:20
Alignment explanation
Indices: 1505204--1505248 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
1505194 ACATGTATCG
**
1505204 ATACATTCACTTATGTATCG
1 ATACATTCACTTATGTATAA
1505224 ATACATTCACTTATTGTATAA
1 ATACATTCACTTA-TGTATAA
1505245 ATAC
1 ATAC
1505249 CAACTATAGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
20 13 0.59
21 9 0.41
ACGTcount: A:0.36, C:0.18, G:0.07, T:0.40
Consensus pattern (20 bp):
ATACATTCACTTATGTATAA
Found at i:1514338 original size:81 final size:81
Alignment explanation
Indices: 1514192--1514359 Score: 255
Period size: 81 Copynumber: 2.1 Consensus size: 81
1514182 AAGTATGATT
* * * * *
1514192 TTGACAAACAAATCATGAATAAAATACCACATGCATAAAGATGAACAAGTATCATACATGCAAAC
1 TTGACAAACAAATCATAAATAAAATAACACATGCACAAAAATGAACAAGTATCACACATGCAAAC
1514257 ACACAAAGATGACATA
66 ACACAAAGATGACATA
* *
1514273 TTGACAAACAAATCATAAATAAAATAACACATGCACAAAAATGAACAAGTATCACGCATGTAAAC
1 TTGACAAACAAATCATAAATAAAATAACACATGCACAAAAATGAACAAGTATCACACATGCAAAC
* *
1514338 ATACAAAGATGACATC
66 ACACAAAGATGACATA
1514354 TTGACA
1 TTGACA
1514360 CGAGAAAGGT
Statistics
Matches: 78, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
81 78 1.00
ACGTcount: A:0.52, C:0.18, G:0.11, T:0.19
Consensus pattern (81 bp):
TTGACAAACAAATCATAAATAAAATAACACATGCACAAAAATGAACAAGTATCACACATGCAAAC
ACACAAAGATGACATA
Found at i:1517069 original size:20 final size:20
Alignment explanation
Indices: 1517046--1517091 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
1517036 AAATGTATTG
1517046 ATACATACCCAAAAGTATCA
1 ATACATACCCAAAAGTATCA
** * *
1517066 ATACATAGGCTAAGGTATCA
1 ATACATACCCAAAAGTATCA
1517086 ATACAT
1 ATACAT
1517092 TTTGGTCATG
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.46, C:0.20, G:0.11, T:0.24
Consensus pattern (20 bp):
ATACATACCCAAAAGTATCA
Found at i:1518663 original size:18 final size:19
Alignment explanation
Indices: 1518642--1518682 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 19
1518632 AATTGTCAAA
1518642 ACAC-TTAAAAGTATCGAT
1 ACACATTAAAAGTATCGAT
*
1518660 ACACAATTCAAAGTATCGAT
1 ACAC-ATTAAAAGTATCGAT
1518680 ACA
1 ACA
1518683 AGTTGCAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
20 16 0.80
ACGTcount: A:0.46, C:0.20, G:0.10, T:0.24
Consensus pattern (19 bp):
ACACATTAAAAGTATCGAT
Found at i:1518793 original size:13 final size:13
Alignment explanation
Indices: 1518775--1518800 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
1518765 ACACCAAAGT
1518775 ATGTATCGATACA
1 ATGTATCGATACA
1518788 ATGTATCGATACA
1 ATGTATCGATACA
1518801 CAAAAAATTG
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:1518798 original size:33 final size:33
Alignment explanation
Indices: 1518756--1518820 Score: 96
Period size: 33 Copynumber: 2.0 Consensus size: 33
1518746 TAGCCAAACT
* *
1518756 TGTATCGATACAC-CAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAAT-TGTATCGATACAA
1518789 TGTATCGATACACAAAAAATTGTATCGATACA
1 TGTATCGATACACAAAAAATTGTATCGATACA
1518821 TTCGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
33 25 0.86
34 4 0.14
ACGTcount: A:0.42, C:0.17, G:0.14, T:0.28
Consensus pattern (33 bp):
TGTATCGATACACAAAAAATTGTATCGATACAA
Found at i:1523015 original size:15 final size:15
Alignment explanation
Indices: 1522995--1523025 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
1522985 TAAAAATGTC
*
1522995 CAAAATGAGGAAGCT
1 CAAAATGAAGAAGCT
1523010 CAAAATGAAGAAGCT
1 CAAAATGAAGAAGCT
1523025 C
1 C
1523026 CAAACGAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.48, C:0.16, G:0.23, T:0.13
Consensus pattern (15 bp):
CAAAATGAAGAAGCT
Found at i:1525124 original size:13 final size:13
Alignment explanation
Indices: 1525106--1525144 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
1525096 ACATTTTTCT
*
1525106 TTGTATTGATACA
1 TTGTATCGATACA
1525119 TTGTATCGATACA
1 TTGTATCGATACA
*
1525132 CTGTATCGATACA
1 TTGTATCGATACA
1525145 GGGGGATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.31, C:0.15, G:0.15, T:0.38
Consensus pattern (13 bp):
TTGTATCGATACA
Found at i:1525308 original size:20 final size:20
Alignment explanation
Indices: 1525265--1525310 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
1525255 AAATCTTTTG
1525265 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
1525286 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
1525306 CAAAA
1 CAAAA
1525311 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:1529639 original size:29 final size:30
Alignment explanation
Indices: 1529607--1529664 Score: 82
Period size: 29 Copynumber: 2.0 Consensus size: 30
1529597 TAGTAAAGAG
*
1529607 AGTATTTTAGTCCTTATA-TTATTAAATTT
1 AGTATTTTAATCCTTATACTTATTAAATTT
* *
1529636 AGTATTTTAATCTTTATACTTTTTAAATT
1 AGTATTTTAATCCTTATACTTATTAAATT
1529665 ATAGCAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 16 0.64
30 9 0.36
ACGTcount: A:0.31, C:0.07, G:0.05, T:0.57
Consensus pattern (30 bp):
AGTATTTTAATCCTTATACTTATTAAATTT
Found at i:1530055 original size:122 final size:122
Alignment explanation
Indices: 1529919--1530160 Score: 367
Period size: 122 Copynumber: 2.0 Consensus size: 122
1529909 ATTTACAAAG
* ** * *
1529919 ACTAAAATACTAAATTTAATAGTACATGAATTAAAATGTTTCCTTCACTGTAGTATAGGGACTCT
1 ACTAAAATACTAAATTTAATAATACATGAATTAAAATACTTCCTTCACTATAGTATAGGAACTCT
*
1529984 AAATGAACTATTACCATTTTCAAAATCTCCTCAAAAATTAAAATTCTCTCTTTCCTA
66 AAATAAACTATTACCATTTTCAAAATCTCCTCAAAAATTAAAATTCTCTCTTTCCTA
* * * *
1530041 ACTAAGATACTAAATTTAATAATACATGGATTAAAATACTTCCTTCACTATAGTATATGAACTTT
1 ACTAAAATACTAAATTTAATAATACATGAATTAAAATACTTCCTTCACTATAGTATAGGAACTCT
* * *
1530106 AAATAAACTATTACCGTTTTCAAAATCTCCTCGAAAATTAAAATTTTCTCTTTCC
66 AAATAAACTATTACCATTTTCAAAATCTCCTCAAAAATTAAAATTCTCTCTTTCC
1530161 CAAGTATTTT
Statistics
Matches: 107, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
122 107 1.00
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.37
Consensus pattern (122 bp):
ACTAAAATACTAAATTTAATAATACATGAATTAAAATACTTCCTTCACTATAGTATAGGAACTCT
AAATAAACTATTACCATTTTCAAAATCTCCTCAAAAATTAAAATTCTCTCTTTCCTA
Found at i:1533326 original size:16 final size:16
Alignment explanation
Indices: 1533264--1533331 Score: 52
Period size: 16 Copynumber: 4.2 Consensus size: 16
1533254 ATTTGGGTTA
* *
1533264 TTTTAATTTTAGATTT
1 TTTTAAGTTTAGATAT
*
1533280 ATTTTGAGTTT-GA-AT
1 -TTTTAAGTTTAGATAT
*
1533295 TATTTCAAGCTTAGATAT
1 T-TTT-AAGTTTAGATAT
1533313 TTTTAAGTTTAGAT-T
1 TTTTAAGTTTAGATAT
1533328 TTTT
1 TTTT
1533332 CGGGTTCGGA
Statistics
Matches: 41, Mismatches: 6, Indels: 10
0.72 0.11 0.18
Matches are distributed among these distances:
14 1 0.02
15 9 0.22
16 15 0.37
17 13 0.32
18 3 0.07
ACGTcount: A:0.26, C:0.03, G:0.12, T:0.59
Consensus pattern (16 bp):
TTTTAAGTTTAGATAT
Found at i:1533875 original size:3 final size:3
Alignment explanation
Indices: 1533869--1533902 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
1533859 ATAATAATAG
1533869 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
1533903 GTTGAGTACT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:1534749 original size:135 final size:135
Alignment explanation
Indices: 1534598--1534860 Score: 359
Period size: 135 Copynumber: 1.9 Consensus size: 135
1534588 ATTATTTGTG
* * ** * *
1534598 TATATTATTAATATTTAATTTTATATGGTTA-CTATATACTTCATGTTATTGTATTGCTACTA-A
1 TATATTATTAACATTTAAATTTATAAAGTTATC-ATATACTTCATGTTATTATATTACTA-TATA
* * * * * *
1534661 AATGTTATTTGATATTATTAAATTATACTATTAATACATTTACTTCATATTTAATACATGTAATA
64 AATATTAATTGATATTACTAAATTATACTATTAATAAATTTACTCCATATTTAATACACGTAATA
1534726 TGTACTA
129 TGTACTA
*
1534733 TATATTATTAACATTTAAATTTATAAAGTTATCATATACTTCGTGTTATTATATTACTATATAAA
1 TATATTATTAACATTTAAATTTATAAAGTTATCATATACTTCATGTTATTATATTACTATATAAA
* *
1534798 TATTAATTGTTATTACTAAATTATACTATTAATAAATTTACTCCATATTTAATATACGTAATA
66 TATTAATTGATATTACTAAATTATACTATTAATAAATTTACTCCATATTTAATACACGTAATA
1534861 CATATTATAT
Statistics
Matches: 111, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
134 2 0.02
135 108 0.97
136 1 0.01
ACGTcount: A:0.38, C:0.08, G:0.05, T:0.48
Consensus pattern (135 bp):
TATATTATTAACATTTAAATTTATAAAGTTATCATATACTTCATGTTATTATATTACTATATAAA
TATTAATTGATATTACTAAATTATACTATTAATAAATTTACTCCATATTTAATACACGTAATATG
TACTA
Found at i:1537439 original size:13 final size:13
Alignment explanation
Indices: 1537421--1537445 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1537411 CATAAAATGT
1537421 TGTATCGATACAA
1 TGTATCGATACAA
1537434 TGTATCGATACA
1 TGTATCGATACA
1537446 TATTTTTTTG
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:0.36, C:0.16, G:0.16, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:1537443 original size:33 final size:33
Alignment explanation
Indices: 1537401--1537467 Score: 98
Period size: 33 Copynumber: 2.0 Consensus size: 33
1537391 TTCAACGATT
1537401 TGTATCGATACATAAAATGTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
*** *
1537434 TGTATCGATACATATTTTTTTGTATCGATACAA
1 TGTATCGATACATAAAATGTTGTATCGATACAA
1537467 T
1 T
1537468 TTAAGCTACT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.40
Consensus pattern (33 bp):
TGTATCGATACATAAAATGTTGTATCGATACAA
Found at i:1537528 original size:13 final size:13
Alignment explanation
Indices: 1537510--1537534 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
1537500 ATTACTCACA
1537510 TGTATCGATACAT
1 TGTATCGATACAT
1537523 TGTATCGATACA
1 TGTATCGATACA
1537535 CTGATCTTTG
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:0.32, C:0.16, G:0.16, T:0.36
Consensus pattern (13 bp):
TGTATCGATACAT
Found at i:1537599 original size:52 final size:52
Alignment explanation
Indices: 1537543--1537664 Score: 226
Period size: 52 Copynumber: 2.3 Consensus size: 52
1537533 CACTGATCTT
*
1537543 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACATTATAAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
*
1537595 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATTAAA
1 TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
1537647 TGTATCGATACATGCAGG
1 TGTATCGATACATGCAGG
1537665 AAGTGAGCTA
Statistics
Matches: 68, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
52 68 1.00
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.29
Consensus pattern (52 bp):
TGTATCGATACATGCAGGCAAATTTGCCCAGATGTATCGATACACTATAAAA
Found at i:1541545 original size:12 final size:11
Alignment explanation
Indices: 1541519--1541544 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
1541509 AAAAATATGC
1541519 AAAAGAAAAAA
1 AAAAGAAAAAA
1541530 AAAAGAAAAAA
1 AAAAGAAAAAA
1541541 AAAA
1 AAAA
1541545 ACCCCTTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.08, T:0.00
Consensus pattern (11 bp):
AAAAGAAAAAA
Found at i:1542546 original size:31 final size:31
Alignment explanation
Indices: 1542508--1542652 Score: 199
Period size: 31 Copynumber: 4.7 Consensus size: 31
1542498 AAAAAAAAAA
1542508 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
*
1542539 AAAGTCCACGACTCAGTGGCAATCTCTGCTC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
*
1542570 AAAGTCCACGACGCAGTGGC-ATC-CTTCTC
1 AAAGTCCACGACTCAGTGGCAATCTCTTCTC
*
1542599 TTTAAAGTCCACGACTCAGTGGC-AT-TTTGTCTC
1 ---AAAGTCCACGACTCAGTGGCAATCTCT-TCTC
1542632 AAAGTCCACGACTCAGTGGCA
1 AAAGTCCACGACTCAGTGGCA
1542653 TTTTTTCTTC
Statistics
Matches: 103, Mismatches: 5, Indels: 12
0.86 0.04 0.10
Matches are distributed among these distances:
29 5 0.05
30 23 0.22
31 49 0.48
32 22 0.21
33 4 0.04
ACGTcount: A:0.26, C:0.30, G:0.19, T:0.25
Consensus pattern (31 bp):
AAAGTCCACGACTCAGTGGCAATCTCTTCTC
Found at i:1542653 original size:62 final size:61
Alignment explanation
Indices: 1542508--1542671 Score: 208
Period size: 62 Copynumber: 2.6 Consensus size: 61
1542498 AAAAAAAAAA
1542508 AAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCAATCTCTGCTC
1 AAAGTCCACGACTCAGTGGC-ATCTCTTCTCAAAGTCCACGACTCAGTGGCAATCTCTGCTC
* *
1542570 AAAGTCCACGACGCAGTGGCATC-CTTCTCTTTAAAGTCCACGACTCAGTGGC-AT-TTTGTCTC
1 AAAGTCCACGACTCAGTGGCATCTCTTCTC---AAAGTCCACGACTCAGTGGCAATCTCTG-CTC
* * *
1542632 AAAGTCCACGACTCAGTGGCATTTTTTCTTCAAAGCCCAC
1 AAAGTCCACGACTCAGTGGCATCTCTTC-TCAAAGTCCAC
1542672 AACTTCGTGG
Statistics
Matches: 90, Mismatches: 6, Indels: 13
0.83 0.06 0.12
Matches are distributed among these distances:
60 6 0.07
61 14 0.16
62 45 0.50
63 23 0.26
64 2 0.02
ACGTcount: A:0.25, C:0.30, G:0.18, T:0.27
Consensus pattern (61 bp):
AAAGTCCACGACTCAGTGGCATCTCTTCTCAAAGTCCACGACTCAGTGGCAATCTCTGCTC
Found at i:1542665 original size:93 final size:93
Alignment explanation
Indices: 1542508--1542724 Score: 244
Period size: 93 Copynumber: 2.3 Consensus size: 93
1542498 AAAAAAAAAA
1542508 AAAGTCCACGACTCAGTGGCAATCTCTTCTCAAAGTCCACGACTCAGTGGCAATCTCTGCTCAAA
1 AAAGTCCACGACTCAGTGGC-ATCTCTTCTCAAAGTCCACGACTCAGTGGCAATCTCTGCTCAAA
* *
1542573 GTCCACGAC-GCAGTGGCATCCTTCT-CTTT
65 GCCCACAACTGC-GTGGCA-CCTTCTCCTTT
* * * *
1542602 AAAGTCCACGACTCAGTGGCAT-TTTGTCTCAAAGTCCACGACTCAGTGGC-ATTTTTTCTTCAA
1 AAAGTCCACGACTCAGTGGCATCTCT-TCTCAAAGTCCACGACTCAGTGGCAATCTCTGC-TCAA
* *
1542665 AGCCCACAACTTCGTGGCACCTTTTCCTTT
64 AGCCCACAACTGCGTGGCACCTTCTCCTTT
* * * *
1542695 AAAGCCCACAACTCCGTGGCACCTTCTTCT
1 AAAGTCCACGACTCAGTGGCATC-TCTTCT
1542725 TTTCAAAGCC
Statistics
Matches: 104, Mismatches: 13, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
92 12 0.12
93 66 0.63
94 24 0.23
95 2 0.02
ACGTcount: A:0.24, C:0.32, G:0.17, T:0.28
Consensus pattern (93 bp):
AAAGTCCACGACTCAGTGGCATCTCTTCTCAAAGTCCACGACTCAGTGGCAATCTCTGCTCAAAG
CCCACAACTGCGTGGCACCTTCTCCTTT
Found at i:1542741 original size:34 final size:34
Alignment explanation
Indices: 1542663--1543379 Score: 874
Period size: 34 Copynumber: 20.6 Consensus size: 34
1542653 TTTTTTCTTC
* *
1542663 AAAGCCCACAACTTCGTGGCACC-TTTTC-CTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
* *
1542695 AAAGCCCACAACTCCGTGGCACCTTCTTCTTTTC
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
* * *
1542729 AAAGCCCGCAACTCCGTGGCACTTTTTTCATCTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTC-TTTTT
*
1542764 -AAGTCCACAACTCCGTGGCACCTTTTTCTTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
*
1542797 AAAGCCCACAACTCCATGGCACCTTTTTC-TTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
*
1542830 AAAGCCCACAACTCTGTGGCACACTTTTTCTTTTT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTTCTTTTT
*
1542865 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTC
1 AAAGCCCACAACTCCGTGGCAC-CTTTTT--CTTTTT
1542902 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
*
1542936 AAAGCCCACAACTCTGTGGCACACTTTTTCTTTTT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTTCTTTTT
*
1542971 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTC
1 AAAGCCCACAACTCCGTGGCAC-CTTTTT--CTTTTT
1543008 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
* *
1543042 AAAGCCTACAACTCTGTGGCACACTTTTTCTTTTT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTTCTTTTT
* *
1543077 AAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTTC
1 AAAGCCCACAACTCCGTGGCAC-CTTTTT--CTTTTT
1543114 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
*
1543148 AAAGCCCACAACTCCGTGGCACTTTTTTTCCCTTTTT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTT--CTTTTT
* * *
1543185 AAAGCCCACAACTCCGTGGCACTTTCTTTTCCTTCT
1 AAAGCCCACAACTCCGTGGCAC-CT-TTTTCTTTTT
* * * *
1543221 -AAGCCCATAACTCCGTGGCACTCCTTTTCCTTCT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTTCTTTTT
* * *
1543255 -AAGCCTACAACTCCGTGGCACTCTTTTTCCTTCT
1 AAAGCCCACAACTCCGTGGCAC-CTTTTTCTTTTT
1543289 -AAGCCCACAACTCCGTGGCACTCTTTTTTTCCTTTTT
1 AAAGCCCACAACTCCGTGGCAC-C--TTTTT-CTTTTT
* *
1543326 AAAGCCCACAACTCTGTGGCACCTTGTTCTTTTT
1 AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
* *
1543360 -AAGTCCACAACTTCGTGGCA
1 AAAGCCCACAACTCCGTGGCA
1543380 TCTTCCACCC
Statistics
Matches: 613, Mismatches: 50, Indels: 43
0.87 0.07 0.06
Matches are distributed among these distances:
32 22 0.04
33 49 0.08
34 233 0.38
35 142 0.23
36 27 0.04
37 116 0.19
38 24 0.04
ACGTcount: A:0.20, C:0.33, G:0.12, T:0.35
Consensus pattern (34 bp):
AAAGCCCACAACTCCGTGGCACCTTTTTCTTTTT
Found at i:1542968 original size:106 final size:106
Alignment explanation
Indices: 1542663--1543379 Score: 966
Period size: 106 Copynumber: 6.9 Consensus size: 106
1542653 TTTTTTCTTC
* *
1542663 AAAGCCCACAACTTCGTGGCAC-C-TTTT-CC-TTT-AAAGCCCACAACTCCGTGGCACCTTCTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTT
* * * * *
1542723 CTTTTCAAAGCCCGCAACTCCGTGGCAC-TTTTTTCATCTTT
66 CTTTTTAAAGCCCACAACTCTGTGGCACACTTTTTC-TTTTT
* * *
1542764 -AAGTCCACAACTCCGTGGCAC-CTTTTT--CTTTTTAAAGCCCACAACTCCATGGCACCTTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTT
1542825 C-TTTTAAAGCCCACAACTCTGTGGCACACTTTTTCTTTTT
66 CTTTTTAAAGCCCACAACTCTGTGGCACACTTTTTCTTTTT
1542865 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTT
1542930 CTTTTTAAAGCCCACAACTCTGTGGCACACTTTTTCTTTTT
66 CTTTTTAAAGCCCACAACTCTGTGGCACACTTTTTCTTTTT
1542971 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTT
*
1543036 CTTTTTAAAGCCTACAACTCTGTGGCACACTTTTTCTTTTT
66 CTTTTTAAAGCCCACAACTCTGTGGCACACTTTTTCTTTTT
*
1543077 AAAGCCCACAACTCTGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTT
1 AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTT
* **
1543142 CTTTTTAAAGCCCACAACTCCGTGGCACTTTTTTTCCCTTTTT
66 CTTTTTAAAGCCCACAACTCTGTGGCACACTTTTT--CTTTTT
* * * *
1543185 AAAGCCCACAACTCCGTGGCACT-TTCTTTTCC--TTCTAAGCCCATAACTCCGTGGCACTCCTT
1 AAAGCCCACAACTCCGTGGCACTCTT-TTTCCCTTTTCAAAGCCCACAACTCCGTGGCAC-CTTT
* * * * * * *
1543247 TTCCTTCT-AAGCCTACAACTCCGTGGCACTCTTTTTCCTTCT
64 TTCTTTTTAAAGCCCACAACTCTGTGGCACACTTTTTCTTTTT
* * * *
1543289 -AAGCCCACAACTCCGTGGCACTCTTTTTTTCCTTTTTAAAGCCCACAACTCTGTGGCACCTTGT
1 AAAGCCCACAACTCCGTGGCACTC-TTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTT
*
1543353 TCTTTTT-AAGTCCACAACT-TCGTGGCA
65 TCTTTTTAAAGCCCACAACTCT-GTGGCA
1543380 TCTTCCACCC
Statistics
Matches: 558, Mismatches: 40, Indels: 32
0.89 0.06 0.05
Matches are distributed among these distances:
100 21 0.04
101 34 0.06
102 53 0.09
103 28 0.05
104 10 0.02
105 59 0.11
106 309 0.55
107 11 0.02
108 33 0.06
ACGTcount: A:0.20, C:0.33, G:0.12, T:0.35
Consensus pattern (106 bp):
AAAGCCCACAACTCCGTGGCACTCTTTTTCCCTTTTCAAAGCCCACAACTCCGTGGCACCTTTTT
CTTTTTAAAGCCCACAACTCTGTGGCACACTTTTTCTTTTT
Done.