Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032250.1 Gossypioides kirkii chromosome KI_08
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: 39602670
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 500 characters in sequence are not A, C, G, or T
File 16 of 125
Found at i:5156113 original size:14 final size:16
Alignment explanation
Indices: 5156083--5156128 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
5156073 AAATAAAATT
5156083 ATAAAAAC-TAT-AAA
1 ATAAAAACATATAAAA
*
5156097 AT-AGAA-ATATAAAA
1 ATAAAAACATATAAAA
5156111 ATAAAAACATATAAAA
1 ATAAAAACATATAAAA
5156127 AT
1 AT
5156129 TGTTTAAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 6 0.23
14 7 0.27
15 3 0.12
16 10 0.38
ACGTcount: A:0.72, C:0.04, G:0.02, T:0.22
Consensus pattern (16 bp):
ATAAAAACATATAAAA
Found at i:5156212 original size:18 final size:18
Alignment explanation
Indices: 5156189--5156223 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
5156179 CATTCTGGAA
5156189 ATTAAAATATTATTTTTT
1 ATTAAAATATTATTTTTT
*
5156207 ATTAAAATATTGTTTTT
1 ATTAAAATATTATTTTT
5156224 ATAGGTGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.03, T:0.60
Consensus pattern (18 bp):
ATTAAAATATTATTTTTT
Found at i:5157038 original size:2 final size:2
Alignment explanation
Indices: 5157031--5157060 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5157021 TGGTACTTTC
5157031 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
5157061 TTCAATAATG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:5158817 original size:19 final size:18
Alignment explanation
Indices: 5158795--5158838 Score: 61
Period size: 18 Copynumber: 2.4 Consensus size: 18
5158785 AAATTACGAA
*
5158795 AAAAATTAAAATAATTTTT
1 AAAAATTAAAAT-ATTTAT
*
5158814 AAAATTTAAAATATTTAT
1 AAAAATTAAAATATTTAT
5158832 AAAAATT
1 AAAAATT
5158839 TCAAAATTTA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 11 0.50
19 11 0.50
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
AAAAATTAAAATATTTAT
Found at i:5158839 original size:19 final size:19
Alignment explanation
Indices: 5158794--5158850 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
5158784 AAAATTACGA
*
5158794 AAAAAATTAAAATAATTT-T
1 AAAAATTTAAAAT-ATTTAT
*
5158813 TAAAATTTAAAATATTTAT
1 AAAAATTTAAAATATTTAT
*
5158832 AAAAATTTCAAA-ATTTAT
1 AAAAATTTAAAATATTTAT
5158850 A
1 A
5158851 TTTTTAAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
18 11 0.33
19 22 0.67
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (19 bp):
AAAAATTTAAAATATTTAT
Found at i:5160051 original size:17 final size:17
Alignment explanation
Indices: 5160020--5160053 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
5160010 AATTAATAAT
*
5160020 TATTTATAATTTATATA
1 TATTTATAATGTATATA
5160037 TATTTATAATGTATATA
1 TATTTATAATGTATATA
5160054 AAAATACGAG
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:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
TATTTATAATGTATATA
Found at i:5160138 original size:15 final size:15
Alignment explanation
Indices: 5160111--5160146 Score: 56
Period size: 14 Copynumber: 2.5 Consensus size: 15
5160101 TTGTTTATTA
5160111 TATTATTAATTTTTT
1 TATTATTAATTTTTT
5160126 TATT-TTAATTTTTT
1 TATTATTAATTTTTT
*
5160140 CATTATT
1 TATTATT
5160147 GATAAGATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.25, C:0.03, G:0.00, T:0.72
Consensus pattern (15 bp):
TATTATTAATTTTTT
Found at i:5160388 original size:20 final size:20
Alignment explanation
Indices: 5160348--5160384 Score: 58
Period size: 19 Copynumber: 1.9 Consensus size: 20
5160338 AATAAAGAAA
*
5160348 AATATATTTTATTTTAATAT
1 AATATATTTTATATTAATAT
5160368 AATATA-TTTATATTAAT
1 AATATATTTTATATTAAT
5160385 TATATACTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
19 10 0.62
20 6 0.38
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
AATATATTTTATATTAATAT
Found at i:5174706 original size:17 final size:17
Alignment explanation
Indices: 5174684--5174768 Score: 89
Period size: 17 Copynumber: 4.9 Consensus size: 17
5174674 GGTCCAATAG
5174684 ATTTAAATTTATTTTAA
1 ATTTAAATTTATTTTAA
* *
5174701 ATTTAAGTTTATATTAA
1 ATTTAAATTTATTTTAA
** *
5174718 ATTTAAATCCATTTAAA
1 ATTTAAATTTATTTTAA
*
5174735 ATTTAAATTTATTATAA
1 ATTTAAATTTATTTTAA
* *
5174752 ATATTAAGTTTAATTTA
1 AT-TTAAATTTATTTTA
5174769 TTTAAATCAA
Statistics
Matches: 53, Mismatches: 14, Indels: 1
0.78 0.21 0.01
Matches are distributed among these distances:
17 42 0.79
18 11 0.21
ACGTcount: A:0.44, C:0.02, G:0.02, T:0.52
Consensus pattern (17 bp):
ATTTAAATTTATTTTAA
Found at i:5174788 original size:51 final size:51
Alignment explanation
Indices: 5174684--5174788 Score: 124
Period size: 51 Copynumber: 2.1 Consensus size: 51
5174674 GGTCCAATAG
* * **
5174684 ATTTAAATTTATTTTAAATTTAAGTTTATATTAAATTTAAATCCATTTAAA
1 ATTTAAATTTATTATAAATTTAAGTTTATATTAAATTTAAATCAATCCAAA
* *
5174735 ATTTAAATTTATTATAAATATTAAGTTTA-ATT-TATTTAAATCAATGCCCAA
1 ATTTAAATTTATTATAAAT-TTAAGTTTATATTAAATTTAAATCAAT-CCAAA
5174786 ATT
1 ATT
5174789 ACAAGCCTAA
Statistics
Matches: 46, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
50 11 0.24
51 26 0.57
52 9 0.20
ACGTcount: A:0.43, C:0.06, G:0.03, T:0.49
Consensus pattern (51 bp):
ATTTAAATTTATTATAAATTTAAGTTTATATTAAATTTAAATCAATCCAAA
Found at i:5175500 original size:16 final size:16
Alignment explanation
Indices: 5175481--5175536 Score: 58
Period size: 16 Copynumber: 3.4 Consensus size: 16
5175471 GATAATGTTT
*
5175481 ATAACAAATAACATTA
1 ATAATAAATAACATTA
* *
5175497 ATAATAACAAAATATTA
1 ATAATAA-ATAACATTA
**
5175514 ATAATAAATGGCATTA
1 ATAATAAATAACATTA
5175530 ATAATAA
1 ATAATAA
5175537 TAATGATAAT
Statistics
Matches: 32, Mismatches: 7, Indels: 2
0.78 0.17 0.05
Matches are distributed among these distances:
16 18 0.56
17 14 0.44
ACGTcount: A:0.61, C:0.07, G:0.04, T:0.29
Consensus pattern (16 bp):
ATAATAAATAACATTA
Found at i:5175555 original size:30 final size:31
Alignment explanation
Indices: 5175512--5175569 Score: 100
Period size: 30 Copynumber: 1.9 Consensus size: 31
5175502 AACAAAATAT
5175512 TAATAATAAATGGCATTAATAATAATAATGA
1 TAATAATAAATGGCATTAATAATAATAATGA
*
5175543 TAATAAT-GATGGCATTAATAATAATAA
1 TAATAATAAATGGCATTAATAATAATAA
5175570 AAAGTTGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
30 19 0.73
31 7 0.27
ACGTcount: A:0.53, C:0.03, G:0.10, T:0.33
Consensus pattern (31 bp):
TAATAATAAATGGCATTAATAATAATAATGA
Found at i:5176720 original size:30 final size:29
Alignment explanation
Indices: 5176676--5176778 Score: 86
Period size: 30 Copynumber: 3.5 Consensus size: 29
5176666 TTAAACTGTC
5176676 CAAAAA-TCATATTTTGACCCCTGAACTTTT
1 CAAAAATTCAT-TTTT-ACCCCTGAACTTTT
* * * **
5176706 CCAAAATTCCATTTTTAACTCTGATTTTTT
1 CAAAAATT-CATTTTTACCCCTGAACTTTT
*
5176736 CAAAAATTCATTTTTACCCCTAAAC--TT
1 CAAAAATTCATTTTTACCCCTGAACTTTT
*
5176763 AAAAAATTCAATTTTT
1 CAAAAATTC-ATTTTT
5176779 TACCTCAATT
Statistics
Matches: 58, Mismatches: 12, Indels: 8
0.74 0.15 0.10
Matches are distributed among these distances:
27 10 0.17
28 6 0.10
29 12 0.21
30 22 0.38
31 5 0.09
32 3 0.05
ACGTcount: A:0.35, C:0.20, G:0.03, T:0.42
Consensus pattern (29 bp):
CAAAAATTCATTTTTACCCCTGAACTTTT
Found at i:5176807 original size:59 final size:58
Alignment explanation
Indices: 5176708--5177106 Score: 233
Period size: 59 Copynumber: 6.8 Consensus size: 58
5176698 GAACTTTTCC
* * ** *
5176708 AAAATTCCATTTTTAACTCTGATTTTTTCAAAAATT--CATTTTTACCCCTAAACTTAA
1 AAAATTCCATTTTTGACCCCAATTTTTCCAAAAATTACCA-TTTTACCCCTAAACTTAA
* * * * **
5176765 AAAATTCAATTTTTTACCTCAATTTTTCCAAAAATTACCATTTTACCCCCGAATGTCTAA
1 AAAATTCCATTTTTGACCCCAATTTTTCCAAAAATTACCATTTTA-CCCCTAAACT-TAA
* ** * * *
5176825 AAAA-TCCATTGTTGACCTTAA--TTTCCAAAAATGACCATTTTA-CCCTAGGA-TGTCTA
1 AAAATTCCATTTTTGACCCCAATTTTTCCAAAAATTACCATTTTACCCCTA-AACT-T-AA
** * * * * *
5176881 AAAATTCTGTTTTTGACCCCAA-CTTTCCCAAAATTACCATTTTACTCCGAAACTTCCA
1 AAAATTCCATTTTTGACCCCAATTTTTCCAAAAATTACCATTTTACCCCTAAACTT-AA
* * * *
5176939 AAACTTCCATTTTTGACCCCTATTTTTCCAAAAATGACCATTTTA-CCCTCAAACTTTCA
1 AAAATTCCATTTTTGACCCCAATTTTTCCAAAAATTACCATTTTACCCCT-AAAC-TTAA
* * * * ** * ** * **
5176998 AAAATTCCATTCTTGATCTCGATTCCTCCAAAAAGTAAAATTTTACCCTCGAATGTCT-A
1 AAAATTCCATTTTTGACCCCAATTTTTCCAAAAATTACCATTTTACCC-CTAAACT-TAA
* * *
5177057 AAAATTCCATTTTTGACCCCTAACTTTTCCCAAAATTACCATTTTGCCCC
1 AAAATTCCATTTTTGACCCC-AATTTTTCCAAAAATTACCATTTTACCCC
5177107 GAGTGATCGA
Statistics
Matches: 259, Mismatches: 66, Indels: 32
0.73 0.18 0.09
Matches are distributed among these distances:
55 6 0.02
56 5 0.02
57 61 0.24
58 48 0.19
59 105 0.41
60 33 0.13
61 1 0.00
ACGTcount: A:0.33, C:0.25, G:0.05, T:0.37
Consensus pattern (58 bp):
AAAATTCCATTTTTGACCCCAATTTTTCCAAAAATTACCATTTTACCCCTAAACTTAA
Found at i:5176923 original size:29 final size:29
Alignment explanation
Indices: 5176891--5177013 Score: 69
Period size: 29 Copynumber: 4.2 Consensus size: 29
5176881 AAAATTCTGT
*
5176891 TTTTGACCC-C-AACTTTCCCAAAATTACCA
1 TTTTGACCCGCAAACTTT-CAAAAATT-CCA
* *
5176920 TTTT-ACTCCG-AAACTTCCAAAACTTCCA
1 TTTTGAC-CCGCAAACTTTCAAAAATTCCA
* ** *
5176948 TTTTTGACCC-CTATTTTTCCAAAAATGACCA
1 -TTTTGACCCGCAAACTTT-CAAAAAT-TCCA
*
5176979 TTTT-ACCCTCAAACTTTCAAAAATTCCA
1 TTTTGACCCGCAAACTTTCAAAAATTCCA
5177007 TTCTTGA
1 TT-TTGA
5177014 TCTCGATTCC
Statistics
Matches: 70, Mismatches: 13, Indels: 21
0.67 0.12 0.20
Matches are distributed among these distances:
28 10 0.14
29 34 0.49
30 23 0.33
31 3 0.04
ACGTcount: A:0.31, C:0.29, G:0.04, T:0.36
Consensus pattern (29 bp):
TTTTGACCCGCAAACTTTCAAAAATTCCA
Found at i:5188526 original size:23 final size:22
Alignment explanation
Indices: 5188486--5188531 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 22
5188476 TGAATATTCA
*
5188486 AAAAATAATAATTAAATTATTTT
1 AAAAATAAAAATTAAATT-TTTT
5188509 AAAAATAAAAAATT-AATTTTTT
1 AAAAAT-AAAAATTAAATTTTTT
5188531 A
1 A
5188532 TATCGTACTT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 5 0.24
23 10 0.48
24 6 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (22 bp):
AAAAATAAAAATTAAATTTTTT
Found at i:5191787 original size:29 final size:28
Alignment explanation
Indices: 5191723--5191831 Score: 71
Period size: 29 Copynumber: 3.8 Consensus size: 28
5191713 CTTAAATAAA
*
5191723 AACTTTTTAATAATTAAATGATTAAAAT
1 AACTTTTTAATAATTAAGTGATTAAAAT
* * **
5191751 AATTTTTTTAATAATTCAGTGATTATGTAT
1 AA-CTTTTTAATAATTAAGTGATTA-AAAT
* **
5191781 AAC-TTTTAA-AATTGAGTGAGCAAAATTT
1 AACTTTTTAATAATTAAGTGATTAAAA--T
*
5191809 AAATTTATTAATAATT-AGTGATT
1 AACTTT-TTAATAATTAAGTGATT
5191832 TTGTGTATAG
Statistics
Matches: 60, Mismatches: 14, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
26 1 0.02
27 10 0.17
28 11 0.18
29 21 0.35
30 13 0.22
31 4 0.07
ACGTcount: A:0.42, C:0.04, G:0.09, T:0.45
Consensus pattern (28 bp):
AACTTTTTAATAATTAAGTGATTAAAAT
Found at i:5192116 original size:14 final size:14
Alignment explanation
Indices: 5192097--5192143 Score: 51
Period size: 14 Copynumber: 3.2 Consensus size: 14
5192087 AAAGTCGTGA
5192097 TTTAATTTATATAT
1 TTTAATTTATATAT
*
5192111 TTTAATTTAGCAT-T
1 TTTAATTTA-TATAT
5192125 TTTATAGTTTATATAT
1 TTTA-A-TTTATATAT
5192141 TTT
1 TTT
5192144 TTTAAAAATT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
14 14 0.52
15 5 0.19
16 8 0.30
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (14 bp):
TTTAATTTATATAT
Found at i:5199428 original size:23 final size:23
Alignment explanation
Indices: 5199373--5199430 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
5199363 CTGACGTGGC
* *
5199373 ATCCAGTCAGCAGCTTCTAGAAG
1 ATCCAGTCAGCAGCTTCCAAAAG
*
5199396 ATCCAATCAGCAGCTTCCAAAAG
1 ATCCAGTCAGCAGCTTCCAAAAG
* *
5199419 GTCTAGTCAGCA
1 ATCCAGTCAGCA
5199431 AGGATGGACG
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.33, C:0.28, G:0.19, T:0.21
Consensus pattern (23 bp):
ATCCAGTCAGCAGCTTCCAAAAG
Found at i:5202972 original size:3 final size:3
Alignment explanation
Indices: 5202964--5203007 Score: 81
Period size: 3 Copynumber: 15.0 Consensus size: 3
5202954 GGGCAAAGGA
5202964 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
5203008 TGTATTATTT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
2 2 0.05
3 38 0.95
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:5203287 original size:17 final size:17
Alignment explanation
Indices: 5203235--5203297 Score: 60
Period size: 18 Copynumber: 3.7 Consensus size: 17
5203225 TTTAAATATG
5203235 TATATATTTTATTTTATT
1 TATATATTTTATTTT-TT
*
5203253 T-TAATATTTAATTATTTT
1 TAT-ATATTTTATT-TTTT
*
5203271 TATATTTTTTATTTTTT
1 TATATATTTTATTTTTT
5203288 TA-A-ATTTTAT
1 TATATATTTTAT
5203298 ATTTAATTAT
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
15 6 0.16
16 1 0.03
17 7 0.18
18 21 0.55
19 3 0.08
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (17 bp):
TATATATTTTATTTTTT
Found at i:5203300 original size:17 final size:17
Alignment explanation
Indices: 5203240--5203301 Score: 58
Period size: 17 Copynumber: 3.6 Consensus size: 17
5203230 ATATGTATAT
5203240 ATTTTAT-TTTATTTT-A
1 ATTTTATATTT-TTTTAA
*
5203256 ATATTTA-ATTATTTTTAT
1 AT-TTTATATT-TTTTTAA
*
5203274 ATTTTTTATTTTTTTAA
1 ATTTTATATTTTTTTAA
5203291 ATTTTATATTT
1 ATTTTATATTT
5203302 AATTATCTTA
Statistics
Matches: 37, Mismatches: 4, Indels: 9
0.74 0.08 0.18
Matches are distributed among these distances:
16 2 0.05
17 29 0.78
18 6 0.16
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (17 bp):
ATTTTATATTTTTTTAA
Found at i:5208036 original size:2 final size:2
Alignment explanation
Indices: 5208029--5208089 Score: 68
Period size: 2 Copynumber: 30.5 Consensus size: 2
5208019 CGAAATAGAA
* * * * *
5208029 AT AT AT AT AT AT AT GT AT AT AT AC GT AT AC AT AT AT AT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
5208071 AT AT AT GT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
5208090 CACAATGAAA
Statistics
Matches: 47, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (2 bp):
AT
Found at i:5210178 original size:11 final size:11
Alignment explanation
Indices: 5210147--5210176 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
5210137 ATAATTTATT
5210147 ATTATATTTAA
1 ATTATATTTAA
5210158 ATTATATTTAA
1 ATTATATTTAA
5210169 ATT-TATTT
1 ATTATATTT
5210177 TATACTACCT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 5 0.26
11 14 0.74
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (11 bp):
ATTATATTTAA
Found at i:5211467 original size:4 final size:4
Alignment explanation
Indices: 5211458--5211551 Score: 84
Period size: 4 Copynumber: 23.2 Consensus size: 4
5211448 AAATAAACGG
* * *
5211458 GAAA GAAA GAAA GAAAA GAAA GAAA GAAA GGAA GAAG GAGAG GAAA GAAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA GAAA
* * * *
5211508 G-AA GAAG GAAA GAAG GAGAG GAAA GAAA G-AA GAAA AAAA GAAA G
1 GAAA GAAA GAAA GAAA GA-AA GAAA GAAA GAAA GAAA GAAA GAAA G
5211552 GTAATGTGTT
Statistics
Matches: 75, Mismatches: 10, Indels: 10
0.79 0.11 0.11
Matches are distributed among these distances:
3 6 0.08
4 57 0.76
5 12 0.16
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (4 bp):
GAAA
Found at i:5211547 original size:28 final size:28
Alignment explanation
Indices: 5211458--5211549 Score: 121
Period size: 28 Copynumber: 3.2 Consensus size: 28
5211448 AAATAAACGG
* * *
5211458 GAAAGAAAGAAAGAAAAGAAAGAAAGAAA
1 GAAAGAAGGAGAGGAAAGAAAG-AAGAAA
* *
5211487 GGAAGAAGGAGAGGAAAGAAAGAAGAAG
1 GAAAGAAGGAGAGGAAAGAAAGAAGAAA
5211515 GAAAGAAGGAGAGGAAAGAAAGAAGAAA
1 GAAAGAAGGAGAGGAAAGAAAGAAGAAA
*
5211543 AAAAGAA
1 GAAAGAA
5211550 AGGTAATGTG
Statistics
Matches: 55, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 37 0.67
29 18 0.33
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (28 bp):
GAAAGAAGGAGAGGAAAGAAAGAAGAAA
Found at i:5214577 original size:21 final size:22
Alignment explanation
Indices: 5214553--5214599 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
5214543 GTTTCATGTA
5214553 TAGGATCTAGGGTTTGAAGT-T
1 TAGGATCTAGGGTTTGAAGTAT
* * *
5214574 TAGGGTTTAGGGTTTTAAGTAT
1 TAGGATCTAGGGTTTGAAGTAT
5214596 TAGG
1 TAGG
5214600 TTTAGGTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.23, C:0.02, G:0.34, T:0.40
Consensus pattern (22 bp):
TAGGATCTAGGGTTTGAAGTAT
Found at i:5214601 original size:21 final size:21
Alignment explanation
Indices: 5214560--5214610 Score: 70
Period size: 21 Copynumber: 2.5 Consensus size: 21
5214550 GTATAGGATC
*
5214560 TAGGGTTTGAAGTTTAGGGTT
1 TAGGGTTTTAAGTTTAGGGTT
5214581 TAGGGTTTTAAGTATTA-GGTT
1 TAGGGTTTTAAGT-TTAGGGTT
5214602 TA-GGTTTTA
1 TAGGGTTTTA
5214611 GGGTTTAATA
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 7 0.25
21 18 0.64
22 3 0.11
ACGTcount: A:0.22, C:0.00, G:0.31, T:0.47
Consensus pattern (21 bp):
TAGGGTTTTAAGTTTAGGGTT
Found at i:5214603 original size:28 final size:26
Alignment explanation
Indices: 5214571--5214623 Score: 79
Period size: 28 Copynumber: 2.0 Consensus size: 26
5214561 AGGGTTTGAA
5214571 GTTTAGGGTTTAGGGTTTTAAGTATTAG
1 GTTTAGGGTTTAGGG-TTTAA-TATTAG
*
5214599 GTTTAGGTTTTAGGGTTTAATATTA
1 GTTTAGGGTTTAGGGTTTAATATTA
5214624 TGAAATTTAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 5 0.21
27 5 0.21
28 14 0.58
ACGTcount: A:0.23, C:0.00, G:0.28, T:0.49
Consensus pattern (26 bp):
GTTTAGGGTTTAGGGTTTAATATTAG
Found at i:5214863 original size:21 final size:21
Alignment explanation
Indices: 5214837--5214883 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
5214827 TTAGGGTCCA
*
5214837 ATTGCCCCGGAGGAGTAGAGT
1 ATTGCCCCGGAGGAGTAAAGT
*
5214858 ATTGCCCGGGAGGAGTAAAGT
1 ATTGCCCCGGAGGAGTAAAGT
5214879 ATTGC
1 ATTGC
5214884 GATGGTTCGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.26, C:0.17, G:0.36, T:0.21
Consensus pattern (21 bp):
ATTGCCCCGGAGGAGTAAAGT
Found at i:5216846 original size:16 final size:16
Alignment explanation
Indices: 5216825--5216874 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
5216815 TGATGGGGAT
5216825 ATTATTTTGATAATTA
1 ATTATTTTGATAATTA
*
5216841 ATTATTTT-TTATATT-
1 ATTATTTTGATA-ATTA
*
5216856 A-TATTTTGGTAATTA
1 ATTATTTTGATAATTA
5216871 ATTA
1 ATTA
5216875 GCTAGATTTA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
14 9 0.32
15 6 0.21
16 13 0.46
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.60
Consensus pattern (16 bp):
ATTATTTTGATAATTA
Found at i:5217418 original size:20 final size:21
Alignment explanation
Indices: 5217393--5217435 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
5217383 TACTCACTAC
5217393 TACTAAC-AACAAAATAAAAT
1 TACTAACTAACAAAATAAAAT
*
5217413 TACTAACTAACAAAATTAAAT
1 TACTAACTAACAAAATAAAAT
5217434 TA
1 TA
5217436 AAGTAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 7 0.33
21 14 0.67
ACGTcount: A:0.60, C:0.14, G:0.00, T:0.26
Consensus pattern (21 bp):
TACTAACTAACAAAATAAAAT
Found at i:5217609 original size:12 final size:12
Alignment explanation
Indices: 5217592--5217622 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
5217582 ATTAAAATAT
5217592 TTTAAAATTAAA
1 TTTAAAATTAAA
5217604 TTTAAAATTAAA
1 TTTAAAATTAAA
*
5217616 CTTAAAA
1 TTTAAAA
5217623 AATTAATTAA
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:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (12 bp):
TTTAAAATTAAA
Found at i:5217818 original size:10 final size:10
Alignment explanation
Indices: 5217803--5217827 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
5217793 GTCGTCCCCT
5217803 TTCTTCTTCC
1 TTCTTCTTCC
5217813 TTCTTCTTCC
1 TTCTTCTTCC
5217823 TTCTT
1 TTCTT
5217828 TCTTTCTTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.00, C:0.36, G:0.00, T:0.64
Consensus pattern (10 bp):
TTCTTCTTCC
Found at i:5217830 original size:4 final size:4
Alignment explanation
Indices: 5217823--5217871 Score: 66
Period size: 4 Copynumber: 12.8 Consensus size: 4
5217813 TTCTTCTTCC
* *
5217823 TTCT TTCT TTCT TTCT TTCT TTTT TTCT CTC- TTCT TTCT TTCT TT-T
1 TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT TTCT
5217869 TTC
1 TTC
5217872 CTTCAATTTT
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
3 5 0.13
4 34 0.87
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (4 bp):
TTCT
Found at i:5217862 original size:7 final size:7
Alignment explanation
Indices: 5217801--5217867 Score: 59
Period size: 8 Copynumber: 9.6 Consensus size: 7
5217791 CCGTCGTCCC
5217801 CTTTCTT
1 CTTTCTT
*
5217808 CTTCCTT
1 CTTTCTT
5217815 C-TTCTT
1 CTTTCTT
*
5217821 CCTTCTTT
1 CTTTC-TT
5217829 CTTTCTTT
1 CTTTC-TT
5217837 CTTTCTT
1 CTTTCTT
5217844 -TTT-TT
1 CTTTCTT
*
5217849 CTCTCTT
1 CTTTCTT
5217856 CTTTCTTT
1 CTTTC-TT
5217864 CTTT
1 CTTT
5217868 TTTCCTTCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 9
0.78 0.08 0.14
Matches are distributed among these distances:
5 2 0.04
6 10 0.20
7 18 0.36
8 20 0.40
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (7 bp):
CTTTCTT
Found at i:5226487 original size:21 final size:23
Alignment explanation
Indices: 5226463--5226541 Score: 83
Period size: 24 Copynumber: 3.5 Consensus size: 23
5226453 AAAAACGCAT
*
5226463 AAAAATAACATTC-AAACAAC-C
1 AAAAATAACAATCAAAACAACAC
*
5226484 -AAAATAATAATCAAAACAACAAC
1 AAAAATAACAATCAAAACAAC-AC
* *
5226507 AAAAATAATAATCAAAACAGCAAC
1 AAAAATAACAATCAAAACAAC-AC
5226531 AAAAATAACAA
1 AAAAATAACAA
5226542 CATCAAAATA
Statistics
Matches: 50, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
20 10 0.20
21 7 0.14
23 1 0.02
24 32 0.64
ACGTcount: A:0.68, C:0.18, G:0.01, T:0.13
Consensus pattern (23 bp):
AAAAATAACAATCAAAACAACAC
Found at i:5226511 original size:24 final size:24
Alignment explanation
Indices: 5226477--5226538 Score: 106
Period size: 24 Copynumber: 2.6 Consensus size: 24
5226467 ATAACATTCA
*
5226477 AACAACCAAAATAATAATCAAAAC
1 AACAACAAAAATAATAATCAAAAC
5226501 AACAACAAAAATAATAATCAAAAC
1 AACAACAAAAATAATAATCAAAAC
*
5226525 AGCAACAAAAATAA
1 AACAACAAAAATAA
5226539 CAACATCAAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
24 36 1.00
ACGTcount: A:0.69, C:0.18, G:0.02, T:0.11
Consensus pattern (24 bp):
AACAACAAAAATAATAATCAAAAC
Found at i:5226965 original size:2 final size:2
Alignment explanation
Indices: 5226958--5226993 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
5226948 ATAACATGCA
5226958 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
5226994 TTATCGTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5228069 original size:14 final size:14
Alignment explanation
Indices: 5228050--5228090 Score: 57
Period size: 14 Copynumber: 2.9 Consensus size: 14
5228040 AGCCTTAAAT
5228050 CCTAAAT-CTTAAC
1 CCTAAATCCTTAAC
*
5228063 CCTTAAATCCATAAC
1 CC-TAAATCCTTAAC
5228078 CCTAAATCCTTAA
1 CCTAAATCCTTAA
5228091 ATCCAAAACC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 2 0.08
14 15 0.62
15 7 0.29
ACGTcount: A:0.39, C:0.32, G:0.00, T:0.29
Consensus pattern (14 bp):
CCTAAATCCTTAAC
Found at i:5228104 original size:21 final size:20
Alignment explanation
Indices: 5228042--5228111 Score: 77
Period size: 21 Copynumber: 3.4 Consensus size: 20
5228032 AACTCTTGAG
* * *
5228042 CCTTAAATCCTAAATCTTAAC
1 CCTTAAATCC-AAAACCTAAA
*
5228063 CCTTAAATCCATAACCCTAAA
1 CCTTAAATCCA-AAACCTAAA
5228084 TCCTTAAATCCAAAACCTAAA
1 -CCTTAAATCCAAAACCTAAA
5228105 CCTTAAA
1 CCTTAAA
5228112 CCTTGAATCT
Statistics
Matches: 43, Mismatches: 4, Indels: 5
0.83 0.08 0.10
Matches are distributed among these distances:
20 8 0.19
21 24 0.56
22 11 0.26
ACGTcount: A:0.43, C:0.30, G:0.00, T:0.27
Consensus pattern (20 bp):
CCTTAAATCCAAAACCTAAA
Found at i:5228106 original size:28 final size:29
Alignment explanation
Indices: 5228075--5228140 Score: 75
Period size: 28 Copynumber: 2.4 Consensus size: 29
5228065 TTAAATCCAT
*
5228075 AACCCTAAATCCTTAAATC-CAAAACCTA
1 AACCCTAAATCCTTAAATCTCAAAACCAA
* * *
5228103 AACCTTAAA-CCTTGAATCTCAAATCCAA
1 AACCCTAAATCCTTAAATCTCAAAACCAA
5228131 AACCC-AAATC
1 AACCCTAAATC
5228141 TAAACTCTAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
27 11 0.35
28 20 0.65
ACGTcount: A:0.45, C:0.32, G:0.02, T:0.21
Consensus pattern (29 bp):
AACCCTAAATCCTTAAATCTCAAAACCAA
Found at i:5228764 original size:20 final size:21
Alignment explanation
Indices: 5228726--5228764 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
5228716 TGTGTATATA
5228726 TAAATTAATATATTAAAATTT
1 TAAATTAATATATTAAAATTT
5228747 TAAATATAATA-A-TAAAAT
1 TAAAT-TAATATATTAAAAT
5228765 ACATTATATA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 6 0.35
21 6 0.35
22 5 0.29
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (21 bp):
TAAATTAATATATTAAAATTT
Found at i:5229049 original size:17 final size:18
Alignment explanation
Indices: 5229021--5229055 Score: 63
Period size: 17 Copynumber: 2.0 Consensus size: 18
5229011 CGTTAGTATT
5229021 AACAGAAAAAAAAATTAA
1 AACAGAAAAAAAAATTAA
5229039 AACAG-AAAAAAAATTAA
1 AACAGAAAAAAAAATTAA
5229056 GTGTAAATAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.77, C:0.06, G:0.06, T:0.11
Consensus pattern (18 bp):
AACAGAAAAAAAAATTAA
Found at i:5234102 original size:18 final size:18
Alignment explanation
Indices: 5234076--5234115 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
5234066 TACAAATATA
5234076 AAAAATAAATAAAAGATG
1 AAAAATAAATAAAAGATG
* *
5234094 AAAAGTAAATAAAAGATT
1 AAAAATAAATAAAAGATG
5234112 AAAA
1 AAAA
5234116 TAATTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.72, C:0.00, G:0.10, T:0.17
Consensus pattern (18 bp):
AAAAATAAATAAAAGATG
Found at i:5240005 original size:19 final size:20
Alignment explanation
Indices: 5239973--5240010 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
5239963 TAAAATTTAA
5239973 TTTAAATATATAAACTATAT
1 TTTAAATATATAAACTATAT
*
5239993 TTTAAATAT-TAAATTATA
1 TTTAAATATATAAACTATA
5240011 ATAATTACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (20 bp):
TTTAAATATATAAACTATAT
Found at i:5243149 original size:13 final size:13
Alignment explanation
Indices: 5243133--5243157 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5243123 TGTTGTGAAA
5243133 AAATACTTTTGAG
1 AAATACTTTTGAG
5243146 AAATACTTTTGA
1 AAATACTTTTGA
5243158 AAAGTTTGGT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.40, C:0.08, G:0.12, T:0.40
Consensus pattern (13 bp):
AAATACTTTTGAG
Found at i:5244095 original size:22 final size:22
Alignment explanation
Indices: 5244069--5244111 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 22
5244059 AACACTAAGG
5244069 TATG-TTTACTAACACAAAATTA
1 TATGATTTA-TAACACAAAATTA
5244091 TATGTATTTATAACACAAAAT
1 TATG-ATTTATAACACAAAAT
5244112 ATTGATGTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 4 0.21
23 11 0.58
24 4 0.21
ACGTcount: A:0.47, C:0.12, G:0.05, T:0.37
Consensus pattern (22 bp):
TATGATTTATAACACAAAATTA
Found at i:5245359 original size:6 final size:6
Alignment explanation
Indices: 5245348--5245375 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
5245338 ATATAATTAA
5245348 AAAATT AAAATT AAAATT AAAATT AAAA
1 AAAATT AAAATT AAAATT AAAATT AAAA
5245376 AAGCAAGCCA
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:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (6 bp):
AAAATT
Found at i:5258986 original size:19 final size:19
Alignment explanation
Indices: 5258951--5258987 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
5258941 CTATTGAATC
**
5258951 ATTTTTTTAATTTTTTATG
1 ATTTTTTTAATAATTTATG
5258970 ATTTTTTTAATAATTTAT
1 ATTTTTTTAATAATTTAT
5258988 TTAATTGAAC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (19 bp):
ATTTTTTTAATAATTTATG
Found at i:5266356 original size:5 final size:5
Alignment explanation
Indices: 5266316--5266355 Score: 62
Period size: 5 Copynumber: 8.0 Consensus size: 5
5266306 ATTCTGAAAA
* *
5266316 TCATC TCATC TCATT TCATC TCATC TCATC TCATC ACATC
1 TCATC TCATC TCATC TCATC TCATC TCATC TCATC TCATC
5266356 ATTACAATCT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
5 32 1.00
ACGTcount: A:0.23, C:0.38, G:0.00, T:0.40
Consensus pattern (5 bp):
TCATC
Found at i:5270465 original size:12 final size:12
Alignment explanation
Indices: 5270448--5270483 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
5270438 ACTCTTAGTG
*
5270448 CAGGCACAGGCA
1 CAGGCACTGGCA
5270460 CAGGCACTGGCA
1 CAGGCACTGGCA
*
5270472 CTGGCACTGGCA
1 CAGGCACTGGCA
5270484 AAGCCAAACC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.25, C:0.33, G:0.33, T:0.08
Consensus pattern (12 bp):
CAGGCACTGGCA
Found at i:5272594 original size:28 final size:27
Alignment explanation
Indices: 5272560--5272680 Score: 82
Period size: 29 Copynumber: 4.2 Consensus size: 27
5272550 ATCGGGGTTA
5272560 AAAATGGGATTTAGGGAAGTTTGAGGGT
1 AAAATGGGATTTAGGGAAGTTTG-GGGT
* * * * *
5272588 GAAATGGTAATTTTAGTGAA-ATCGGGGTTT
1 AAAATGG-GA-TTTAGGGAAGTTTGGGG--T
5272618 AAAATGGGATTTAGGGAAGTTTGGGGGT
1 AAAATGGGATTTAGGGAAGTTT-GGGGT
* ** *
5272646 AAAATGGTAATTTTTGAAAGTTTCGGGGT
1 AAAATGG-GATTTAGGGAAGTTT-GGGGT
5272675 AAAATG
1 AAAATG
5272681 TAATTTTTTG
Statistics
Matches: 71, Mismatches: 15, Indels: 13
0.72 0.15 0.13
Matches are distributed among these distances:
28 25 0.35
29 27 0.38
30 19 0.27
ACGTcount: A:0.32, C:0.02, G:0.34, T:0.32
Consensus pattern (27 bp):
AAAATGGGATTTAGGGAAGTTTGGGGT
Found at i:5272601 original size:58 final size:58
Alignment explanation
Indices: 5272530--5272659 Score: 215
Period size: 58 Copynumber: 2.2 Consensus size: 58
5272520 ACCCGGGGGC
* *
5272530 AAATGGTAGATTTTGGTGAAATCGGGGTTAAAAATGGGATTTAGGGAAGTTTGAGGGTG
1 AAATGGTA-ATTTTAGTGAAATCGGGGTTAAAAATGGGATTTAGGGAAGTTTGAGGGTA
* *
5272589 AAATGGTAATTTTAGTGAAATCGGGGTTTAAAATGGGATTTAGGGAAGTTTGGGGGTA
1 AAATGGTAATTTTAGTGAAATCGGGGTTAAAAATGGGATTTAGGGAAGTTTGAGGGTA
5272647 AAATGGTAATTTT
1 AAATGGTAATTTT
5272660 TGAAAGTTTC
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
58 59 0.88
59 8 0.12
ACGTcount: A:0.32, C:0.02, G:0.34, T:0.33
Consensus pattern (58 bp):
AAATGGTAATTTTAGTGAAATCGGGGTTAAAAATGGGATTTAGGGAAGTTTGAGGGTA
Found at i:5272623 original size:30 final size:30
Alignment explanation
Indices: 5272530--5272624 Score: 72
Period size: 30 Copynumber: 3.2 Consensus size: 30
5272520 ACCCGGGGGC
* *
5272530 AAATGGTAGATTTTGGTGAAATCGGGGTTAA
1 AAATGGTA-ATTTTAGTGAAATCGGGGTTTA
* * * * *
5272561 AAATGG-GA-TTTAGGGAAGTTTGAGGG--TG
1 AAATGGTAATTTTAGTGAA-ATCG-GGGTTTA
5272589 AAATGGTAATTTTAGTGAAATCGGGGTTTA
1 AAATGGTAATTTTAGTGAAATCGGGGTTTA
5272619 AAATGG
1 AAATGG
5272625 GATTTAGGGA
Statistics
Matches: 46, Mismatches: 12, Indels: 13
0.65 0.17 0.18
Matches are distributed among these distances:
28 16 0.35
29 6 0.13
30 18 0.39
31 6 0.13
ACGTcount: A:0.33, C:0.02, G:0.34, T:0.32
Consensus pattern (30 bp):
AAATGGTAATTTTAGTGAAATCGGGGTTTA
Found at i:5272835 original size:60 final size:60
Alignment explanation
Indices: 5272662--5272929 Score: 335
Period size: 60 Copynumber: 4.5 Consensus size: 60
5272652 GTAATTTTTG
* * **
5272662 AAAGTTTCGGGGT-AAAATGTAATTTTTTGG-AAA-TTTTGGGGTCAAAATATGATTTTGGA
1 AAAGTTTTGGGGTCAAAATGTAA--TTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTCAA
* * *
5272721 AAAGTTTTGGGGTCAAAATATATAATTTTGGAAGAGTTTTGGGGCCAAAATATAATTTTCAA
1 AAAGTTTTGGGGTC-AAA-ATGTAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTCAA
* *
5272783 AAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTTAAAATATAATTTTCAG
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTCAA
* * * * * *
5272843 AAAGTTTTGGGGTCAAAATATAATTTTGGAAAAGTTTAGGGGTTAAAATGTAATTTTTAG
1 AAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTCAA
*
5272903 AAAGCTTTGGGGTCAAAATGTAATTTT
1 AAAGTTTTGGGGTCAAAATGTAATTTT
5272930 TAGATAATTT
Statistics
Matches: 186, Mismatches: 18, Indels: 9
0.87 0.08 0.04
Matches are distributed among these distances:
59 12 0.06
60 125 0.67
61 8 0.04
62 41 0.22
ACGTcount: A:0.35, C:0.04, G:0.23, T:0.38
Consensus pattern (60 bp):
AAAGTTTTGGGGTCAAAATGTAATTTTGGAAAAGTTTTGGGGTCAAAATATAATTTTCAA
Found at i:5272933 original size:30 final size:30
Alignment explanation
Indices: 5272634--5272930 Score: 302
Period size: 30 Copynumber: 9.9 Consensus size: 30
5272624 GGATTTAGGG
* *
5272634 AAGTTTGGGGGT-AAAATGGTAATTTTT-GA
1 AAGTTTTGGGGTCAAAAT-ATAATTTTTGGA
* *
5272663 AAGTTTCGGGGT-AAAATGTAATTTTTTGGA
1 AAGTTTTGGGGTCAAAATATAA-TTTTTGGA
*
5272693 AA-TTTTGGGGTCAAAATATGA-TTTTGGAA
1 AAGTTTTGGGGTCAAAATATAATTTTTGG-A
*
5272722 AAGTTTTGGGGTCAAAATATATAATTTTGGA
1 AAGTTTTGGGGTCAAAATATA-ATTTTTGGA
* ***
5272753 AGAGTTTTGGGGCCAAAATATAATTTTCAAA
1 A-AGTTTTGGGGTCAAAATATAATTTTTGGA
*
5272784 AAGTTTTGGGGTCAAAATGTAA-TTTTGGAA
1 AAGTTTTGGGGTCAAAATATAATTTTTGG-A
* **
5272814 AAGTTTTGGGGTTAAAATATAATTTTCAGA
1 AAGTTTTGGGGTCAAAATATAATTTTTGGA
5272844 AAGTTTTGGGGTCAAAATATAA-TTTTGGAA
1 AAGTTTTGGGGTCAAAATATAATTTTTGG-A
* * * *
5272874 AAGTTTAGGGGTTAAAATGTAATTTTTAGA
1 AAGTTTTGGGGTCAAAATATAATTTTTGGA
* *
5272904 AAGCTTTGGGGTCAAAATGTAATTTTT
1 AAGTTTTGGGGTCAAAATATAATTTTT
5272931 AGATAATTTA
Statistics
Matches: 227, Mismatches: 29, Indels: 23
0.81 0.10 0.08
Matches are distributed among these distances:
28 10 0.04
29 39 0.17
30 135 0.59
31 18 0.08
32 25 0.11
ACGTcount: A:0.34, C:0.04, G:0.24, T:0.38
Consensus pattern (30 bp):
AAGTTTTGGGGTCAAAATATAATTTTTGGA
Found at i:5273238 original size:162 final size:162
Alignment explanation
Indices: 5273026--5273340 Score: 533
Period size: 162 Copynumber: 1.9 Consensus size: 162
5273016 ATTTGAAAAT
*
5273026 CTTGAAAAAATTTTGGACCAATTTTATAATTAAATAAAAGTTGATTTAAAGATTAAATTAAAACA
1 CTTGAAAAAATTTTGGACCAATTTGATAATTAAATAAAAGTTGATTTAAAGATTAAATTAAAACA
* *
5273091 AATTAAAAATGTCGGGGACTAAATGCATAAATAATCCAAAAAGTGACACGTGGCAACCTCTAGTA
66 AATTAAAAAAGTCAGGGACTAAATGCATAAATAATCCAAAAAGTGACACGTGGCAACCTCTAGTA
5273156 CAGTCAAACAGTCAAAGGACTAACTTATAAAC
131 CAGTCAAACAGTCAAAGGACTAACTTATAAAC
* * *
5273188 CTTG-AAAAATTCTTGGGCCAATTTGATAATTAAATAAAAGTTTATTTAAAGATTAAATTAAAAT
1 CTTGAAAAAATT-TTGGACCAATTTGATAATTAAATAAAAGTTGATTTAAAGATTAAATTAAAAC
* *
5273252 AAATTAAAAAAGTCAGGGACTAAATTCATAAATAATCCAAAAAGTGACACGTGGCAGCCTCTAGT
65 AAATTAAAAAAGTCAGGGACTAAATGCATAAATAATCCAAAAAGTGACACGTGGCAACCTCTAGT
*
5273317 ACAGTCAAACTGTCAAAGGACTAA
130 ACAGTCAAACAGTCAAAGGACTAA
5273341 ATTGAAAGCT
Statistics
Matches: 143, Mismatches: 9, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
161 7 0.05
162 136 0.95
ACGTcount: A:0.46, C:0.13, G:0.14, T:0.27
Consensus pattern (162 bp):
CTTGAAAAAATTTTGGACCAATTTGATAATTAAATAAAAGTTGATTTAAAGATTAAATTAAAACA
AATTAAAAAAGTCAGGGACTAAATGCATAAATAATCCAAAAAGTGACACGTGGCAACCTCTAGTA
CAGTCAAACAGTCAAAGGACTAACTTATAAAC
Found at i:5274919 original size:6 final size:6
Alignment explanation
Indices: 5274887--5274935 Score: 53
Period size: 6 Copynumber: 7.5 Consensus size: 6
5274877 GACATTGGAC
*
5274887 TTTTAA TTTTTAA TGTTTAGTA TTTTAA TTTTAA TTTTAA TTTAAA TTT
1 TTTTAA -TTTTAA T-TTTA--A TTTTAA TTTTAA TTTTAA TTTTAA TTT
5274936 AAAGTAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
6 22 0.58
7 10 0.26
8 4 0.11
9 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (6 bp):
TTTTAA
Found at i:5274936 original size:6 final size:6
Alignment explanation
Indices: 5274908--5274976 Score: 58
Period size: 6 Copynumber: 12.2 Consensus size: 6
5274898 AATGTTTAGT
* * * *
5274908 ATTTTA ATTTTA ATTTTA ATTTAA ATTTAA A-GTAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA
5274955 GA--TAA ATTTAA A--TAA ATTTAA A
1 -ATTTAA ATTTAA ATTTAA ATTTAA A
5274977 ATCAATTTAT
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
4 5 0.09
5 7 0.13
6 41 0.76
7 1 0.02
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.48
Consensus pattern (6 bp):
ATTTAA
Found at i:5274936 original size:11 final size:11
Alignment explanation
Indices: 5274910--5274975 Score: 53
Period size: 11 Copynumber: 6.0 Consensus size: 11
5274900 TGTTTAGTAT
*
5274910 TTTAATTTTAA
1 TTTAAATTTAA
*
5274921 TTTTAATTTAAA
1 TTTAAATTT-AA
* *
5274933 TTTAAAGTAAA
1 TTTAAATTTAA
5274944 TTTAAATTTAA
1 TTTAAATTTAA
**
5274955 GATAAATTTAA
1 TTTAAATTTAA
*
5274966 -ATAAATTTAA
1 TTTAAATTTAA
5274976 AATCAATTTA
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
10 10 0.22
11 27 0.60
12 8 0.18
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (11 bp):
TTTAAATTTAA
Found at i:5274971 original size:10 final size:10
Alignment explanation
Indices: 5274946--5274976 Score: 53
Period size: 10 Copynumber: 3.0 Consensus size: 10
5274936 AAAGTAAATT
5274946 TAAATTTAAGA
1 TAAATTTAA-A
5274957 TAAATTTAAA
1 TAAATTTAAA
5274967 TAAATTTAAA
1 TAAATTTAAA
5274977 ATCAATTTAT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
10 11 0.55
11 9 0.45
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (10 bp):
TAAATTTAAA
Found at i:5274972 original size:21 final size:21
Alignment explanation
Indices: 5274946--5274985 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
5274936 AAAGTAAATT
*
5274946 TAAATTTAAGATAAATTTAAA
1 TAAATTTAAAATAAATTTAAA
*
5274967 TAAATTTAAAATCAATTTA
1 TAAATTTAAAATAAATTTA
5274986 TCTCCAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (21 bp):
TAAATTTAAAATAAATTTAAA
Found at i:5274978 original size:11 final size:11
Alignment explanation
Indices: 5274946--5274985 Score: 55
Period size: 11 Copynumber: 3.7 Consensus size: 11
5274936 AAAGTAAATT
*
5274946 TAAATTTAAGA
1 TAAATTTAAAA
5274957 TAAATTT-AAA
1 TAAATTTAAAA
5274967 TAAATTTAAAA
1 TAAATTTAAAA
*
5274978 TCAATTTA
1 TAAATTTA
5274986 TCTCCAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.55, C:0.03, G:0.03, T:0.40
Consensus pattern (11 bp):
TAAATTTAAAA
Found at i:5274978 original size:17 final size:18
Alignment explanation
Indices: 5274925--5274967 Score: 72
Period size: 17 Copynumber: 2.5 Consensus size: 18
5274915 TTTTAATTTT
5274925 AATTTAAATTTAA-AGTA
1 AATTTAAATTTAAGAGTA
5274942 AATTTAAATTTAAGA-TA
1 AATTTAAATTTAAGAGTA
5274959 AATTTAAAT
1 AATTTAAAT
5274968 AAATTTAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
17 24 0.96
18 1 0.04
ACGTcount: A:0.53, C:0.00, G:0.05, T:0.42
Consensus pattern (18 bp):
AATTTAAATTTAAGAGTA
Found at i:5275349 original size:38 final size:38
Alignment explanation
Indices: 5275298--5275933 Score: 282
Period size: 38 Copynumber: 17.4 Consensus size: 38
5275288 CTATCCAACT
*
5275298 TTACTTCAATTTCAAGAGGATGGGAAAAGATCTTGCTC
1 TTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTC
* * * *
5275336 TTACTTCAATTTC-AGA-GATAAAGACGTAATATCTAGCT-
1 TTACTTCAATTTCAAGAGGAT-AGGA--AAAGATCTTGCTC
*
5275374 TTACTTCAATTTCAAAAGGATAGGAAAAGATCTTGCTC
1 TTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTC
* * * **
5275412 TTACTTC-A----AAGA--CT-TG---ATATCCAGCT-
1 TTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTC
*
5275438 TTACTTCAATTTCAAGAGGATAGGAAAAGATCTGGCTC
1 TTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTC
* * * **
5275476 TTACTTC-A----AAGA--CT-TG---ATATCCAGCT-
1 TTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTC
5275502 TTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTC
1 TTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTC
* *** ***
5275540 TTACTTCAATTTC-AGAGG-TAAAGACGTGTTATCCAACTC
1 TTACTTCAATTTCAAGAGGAT-AGGAAAAG--ATCTTGCTC
*
5275579 -TACTTCAATTTCAAGCGGATAGGAAAAGATCTTGCTC
1 TTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTC
* ** * *
5275616 TTACTTCAATTTC-AGA-GATA--AAGACTTGTTGTCCAAC
1 TTACTTCAATTTCAAGAGGATAGGAAAAGATCTTG--C-TC
5275653 TCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTC
1 T-TACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTC
* ** * *
5275692 TTACTTCAATTTCAA-A-GATA--AAGACTTGTTGTCCAAC
1 TTACTTCAATTTCAAGAGGATAGGAAAAGATCTTG--C-TC
5275729 TCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTC
1 T-TACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTC
* *** **
5275768 TTACTTCAATTTCAA-A-GATAAAGATTTGTTATCTCACTC
1 TTACTTCAATTTCAAGAGGAT-AGGAAAAG--ATCTTGCTC
* *
5275807 -TACTTCAATTTCAAGAGGATAGGAAACA-ATGTTACTC
1 TTACTTCAATTTCAAGAGGATAGGAAA-AGATCTTGCTC
* *** ***
5275844 TTACTTCAATTTC-AGA-GATAATGACTTGTTATCCCACTC
1 TTACTTCAATTTCAAGAGGAT-AGGAAAAG--ATCTTGCTC
* ** *
5275883 -TACTTCAATTTCAAGAGAATAGGAATCGATGTTGCTC
1 TTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTC
5275920 TTACTTCAATTTCA
1 TTACTTCAATTTCA
5275934 GAGATAAAGA
Statistics
Matches: 438, Mismatches: 94, Indels: 132
0.66 0.14 0.20
Matches are distributed among these distances:
26 14 0.03
27 16 0.04
30 2 0.00
31 10 0.02
33 9 0.02
34 16 0.04
36 20 0.05
37 75 0.17
38 182 0.42
39 61 0.14
40 19 0.04
42 14 0.03
ACGTcount: A:0.33, C:0.18, G:0.15, T:0.33
Consensus pattern (38 bp):
TTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTC
Found at i:5275400 original size:76 final size:76
Alignment explanation
Indices: 5275273--5275994 Score: 884
Period size: 76 Copynumber: 9.8 Consensus size: 76
5275263 TGCTCTTTAG
* * *
5275273 AGAGATAAAGACTTGCTATCCAACTTTACTTCAATTTCAAGAGGATGGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
5275338 ACTTCAATTTC
66 ACTTCAATTTC
* ** * * * *
5275349 AGAGATAAAGACGTAATATCTAGCTTTACTTCAATTTCAAAAGGATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
5275414 A---C---TTC
66 ACTTCAATTTC
* * * *
5275419 ------AAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTGGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
5275478 A---C---TTC
66 ACTTCAATTTC
* * *
5275483 ------AAAGACTTGATATCCAGCTTTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
5275542 ACTTCAATTTC
66 ACTTCAATTTC
* * *
5275553 AGAGGTAAAGACGTGTTATCCAACTCTACTTCAATTTCAAGCGGATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
5275618 ACTTCAATTTC
66 ACTTCAATTTC
*
5275629 AGAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
5275694 ACTTCAATTTC
66 ACTTCAATTTC
* *
5275705 AAAGATAAAGACTTGTTGTCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
5275770 ACTTCAATTTC
66 ACTTCAATTTC
* * * *
5275781 AAAGATAAAGATTTGTTATCTC-ACTCTACTTCAATTTCAAGAGGATAGGAAACA-ATGTTACTC
1 AGAGATAAAGACTTGTTATC-CAACTCTACTTCAATTTCAAGAGGATAGGAAA-AGATCTTGCTC
5275844 TTACTTCAATTTC
64 TTACTTCAATTTC
* * * ** *
5275857 AGAGATAATGACTTGTTATCCCACTCTACTTCAATTTCAAGAGAATAGGAATCGATGTTGCTCTT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
5275922 ACTTCAATTTC
66 ACTTCAATTTC
* * * * * * *
5275933 AGAGATAAAGACGTGTTATCCAACTTTACTGCAATTTCAAGCGAATAGGAAAAAATTTTGCT
1 AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCT
5275995 GTGGTCTGAT
Statistics
Matches: 586, Mismatches: 44, Indels: 32
0.89 0.07 0.05
Matches are distributed among these distances:
64 118 0.20
67 1 0.00
70 6 0.01
73 1 0.00
75 1 0.00
76 457 0.78
77 2 0.00
ACGTcount: A:0.34, C:0.18, G:0.15, T:0.33
Consensus pattern (76 bp):
AGAGATAAAGACTTGTTATCCAACTCTACTTCAATTTCAAGAGGATAGGAAAAGATCTTGCTCTT
ACTTCAATTTC
Found at i:5287732 original size:58 final size:58
Alignment explanation
Indices: 5287632--5287762 Score: 181
Period size: 58 Copynumber: 2.2 Consensus size: 58
5287622 ACCCGGGGGC
* * *
5287632 AAAATGGTAGATTTTGGTAAAATTGGGGTTAAAAATGAGATTTAGGGAAGTTTGAGGGT
1 AAAATGGTA-ATTTTAGTAAAATCGAGGTTAAAAATGAGATTTAGGGAAGTTTGAGGGT
* * * * *
5287691 GAAATGGTAATTTTAGTGAAATCGAGGTTTAAAATGGGATTTAGGGAAGTTTGGGGGT
1 AAAATGGTAATTTTAGTAAAATCGAGGTTAAAAATGAGATTTAGGGAAGTTTGAGGGT
5287749 AAAATGGTAATTTT
1 AAAATGGTAATTTT
5287763 TGAAAGTTTC
Statistics
Matches: 63, Mismatches: 9, Indels: 1
0.86 0.12 0.01
Matches are distributed among these distances:
58 55 0.87
59 8 0.13
ACGTcount: A:0.34, C:0.01, G:0.31, T:0.34
Consensus pattern (58 bp):
AAAATGGTAATTTTAGTAAAATCGAGGTTAAAAATGAGATTTAGGGAAGTTTGAGGGT
Found at i:5287769 original size:29 final size:28
Alignment explanation
Indices: 5287737--5288035 Score: 233
Period size: 30 Copynumber: 10.0 Consensus size: 28
5287727 GGATTTAGGG
* *
5287737 AAGTTTGGGGGTAAAATGGTAATTTTTGA
1 AAGTTTTGGGGTAAAAT-ATAATTTTTGA
* * *
5287766 AAGTTTCGAGGTAAAATGTAATTTTTTAGA
1 AAGTTTTGGGGTAAAATATAA-TTTTT-GA
*
5287796 AA-TTTTGGGGTCAAAATATGA-TTTTGAAA
1 AAGTTTTGGGGT-AAAATATAATTTTTG--A
*
5287825 AAGTTTTGGGGTCAAAATATATAATTTTGGA
1 AAGTTTTGGGGT--AAA-ATATAATTTTTGA
* *
5287856 AGATTTTTGAGGCTAAAATATAATTTTTAGA
1 A-AGTTTTG-GGGTAAAATATAATTTTT-GA
* *
5287887 AAGTTTTGGGGTTAAATGTAATTTTTGAA
1 AAGTTTTGGGGTAAAATATAATTTTTG-A
* *
5287916 AAGTTTTAGGGTTAAAATATAATTTTGGAA
1 AAGTTTT-GGGGTAAAATATAATTTTTG-A
* *
5287946 AAGTTTAGGGGTTAAAATGTAATTTTTAGA
1 AAGTTTTGGGG-TAAAATATAATTTTT-GA
*
5287976 AAGTTTTAGGGTCAAAATATAATTTTTAGA
1 AAGTTTTGGGGT-AAAATATAATTTTT-GA
* * *
5288006 AAGTTTTAAGGTTAAAATGTAATTTTTGA
1 AAGTTTT-GGGGTAAAATATAATTTTTGA
5288035 A
1 A
5288036 TAATTTAGGG
Statistics
Matches: 223, Mismatches: 29, Indels: 36
0.77 0.10 0.12
Matches are distributed among these distances:
27 1 0.00
28 9 0.04
29 60 0.27
30 119 0.53
31 16 0.07
32 11 0.05
33 7 0.03
ACGTcount: A:0.37, C:0.02, G:0.21, T:0.40
Consensus pattern (28 bp):
AAGTTTTGGGGTAAAATATAATTTTTGA
Found at i:5287889 original size:121 final size:119
Alignment explanation
Indices: 5287756--5288035 Score: 350
Period size: 121 Copynumber: 2.3 Consensus size: 119
5287746 GGTAAAATGG
* * * *
5287756 TAATTTTT-GAAAGTTTCGAGGTAAAATGTAATTTTTTAGAAA-TTTTGGGGTCAAAATATGATT
1 TAATTTTTAGAAAGTTTTGAGGTAAAATGTAATTTTTGA-AAAGTTTTAGGGTCAAAATATAATT
* * *
5287819 TTGAAAAAGTTTTGGGGTCAAAATATATAATTTTGGAAGATTTTTGAGGCT-AAAATA
65 TTGAAAAAGTTTAGGGGTCAAAATATA-AATTTTAGAA-AGTTTT-AGGCTCAAAATA
* * *
5287876 TAATTTTTAGAAAGTTTTGGGGTTAAATGTAATTTTTGAAAAGTTTTAGGGTTAAAATATAATTT
1 TAATTTTTAGAAAGTTTTGAGGTAAAATGTAATTTTTGAAAAGTTTTAGGGTCAAAATATAATTT
* * * * *
5287941 TGGAAAAGTTTAGGGGTTAAAATGTAATTTTTAGAAAGTTTTAGGGTCAAAATA
66 TGAAAAAGTTTAGGGGTCAAAATATAAATTTTAGAAAGTTTTAGGCTCAAAATA
*
5287995 TAATTTTTAGAAAGTTTTAAGGTTAAAATGTAATTTTTGAA
1 TAATTTTTAGAAAGTTTTGAGG-TAAAATGTAATTTTTGAA
5288036 TAATTTAGGG
Statistics
Matches: 138, Mismatches: 18, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
118 4 0.03
119 31 0.22
120 36 0.26
121 67 0.49
ACGTcount: A:0.37, C:0.02, G:0.20, T:0.41
Consensus pattern (119 bp):
TAATTTTTAGAAAGTTTTGAGGTAAAATGTAATTTTTGAAAAGTTTTAGGGTCAAAATATAATTT
TGAAAAAGTTTAGGGGTCAAAATATAAATTTTAGAAAGTTTTAGGCTCAAAATA
Found at i:5287993 original size:60 final size:59
Alignment explanation
Indices: 5287760--5288032 Score: 263
Period size: 60 Copynumber: 4.6 Consensus size: 59
5287750 AAATGGTAAT
* * * *
5287760 TTTTG-AAAGTTTCGAGG-TAAAATGTAATTTTTTAGAAA-TTTTGGGGTCAAAATATGA
1 TTTTGAAAAGTTTAGGGGTTAAAATGTAA-TTTTTAGAAAGTTTTAGGGTCAAAATATAA
* * * * * * *
5287817 TTTTGAAAAAGTTTTGGGGTCAAAATATATAATTTTGGAAGATTTTTGAGGCT-AAAATATAA
1 TTTTG-AAAAGTTTAGGGGTTAAAATGTA-ATTTTTAGAA-AGTTTT-AGGGTCAAAATATAA
* * *
5287879 TTTTTAGAAAGTTTTGGGGTT-AAATGTAATTTTT-GAAAAGTTTTAGGGTTAAAATATAA
1 TTTTGA-AAAGTTTAGGGGTTAAAATGTAATTTTTAG-AAAGTTTTAGGGTCAAAATATAA
5287938 TTTTGGAAAAGTTTAGGGGTTAAAATGTAATTTTTAGAAAGTTTTAGGGTCAAAATATAA
1 TTTT-GAAAAGTTTAGGGGTTAAAATGTAATTTTTAGAAAGTTTTAGGGTCAAAATATAA
* *
5287998 TTTTTAGAAAGTTTTA-AGGTTAAAATGTAATTTTT
1 TTTTGA-AAAG-TTTAGGGGTTAAAATGTAATTTTT
5288033 GAATAATTTA
Statistics
Matches: 181, Mismatches: 20, Indels: 27
0.79 0.09 0.12
Matches are distributed among these distances:
57 5 0.03
58 4 0.02
59 43 0.24
60 83 0.46
61 14 0.08
62 29 0.16
63 3 0.02
ACGTcount: A:0.37, C:0.02, G:0.20, T:0.42
Consensus pattern (59 bp):
TTTTGAAAAGTTTAGGGGTTAAAATGTAATTTTTAGAAAGTTTTAGGGTCAAAATATAA
Found at i:5289857 original size:6 final size:6
Alignment explanation
Indices: 5289825--5289873 Score: 53
Period size: 6 Copynumber: 7.5 Consensus size: 6
5289815 GACATTGGAC
*
5289825 TTTTAA TTTTTAA TGTTTAGTA TTTTAA TTTTAA TTTTAA TTTAAA TTT
1 TTTTAA -TTTTAA T-TTTA--A TTTTAA TTTTAA TTTTAA TTTTAA TTT
5289874 AAAGTAAATT
Statistics
Matches: 38, Mismatches: 1, Indels: 7
0.83 0.02 0.15
Matches are distributed among these distances:
6 22 0.58
7 10 0.26
8 4 0.11
9 2 0.05
ACGTcount: A:0.31, C:0.00, G:0.04, T:0.65
Consensus pattern (6 bp):
TTTTAA
Found at i:5289874 original size:6 final size:6
Alignment explanation
Indices: 5289846--5289934 Score: 80
Period size: 6 Copynumber: 15.2 Consensus size: 6
5289836 AATGTTTAGT
* * * *
5289846 ATTTTA ATTTTA ATTTTA ATTTAA ATTTAA A-GTAA ATTTAA ATAATTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA AT--TTAA
5289895 ATTTAA ATTTAA GA--TAA ATTTAA ATTTAA A--TAA ATTTAA A
1 ATTTAA ATTTAA -ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
5289935 ATCAATTTAT
Statistics
Matches: 72, Mismatches: 3, Indels: 16
0.79 0.03 0.18
Matches are distributed among these distances:
4 5 0.07
5 7 0.10
6 53 0.74
7 1 0.01
8 6 0.08
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (6 bp):
ATTTAA
Found at i:5289874 original size:11 final size:11
Alignment explanation
Indices: 5289848--5289934 Score: 63
Period size: 11 Copynumber: 8.0 Consensus size: 11
5289838 TGTTTAGTAT
*
5289848 TTTAATTTTAAT
1 TTTAA-TTTAAA
5289860 TTTAATTTAAA
1 TTTAATTTAAA
**
5289871 TTTAAAGTAAA
1 TTTAATTTAAA
*
5289882 TTTAA-AT-AA
1 TTTAATTTAAA
*
5289891 TTAAATTTAAA
1 TTTAATTTAAA
**
5289902 TTTAAGATAAA
1 TTTAATTTAAA
5289913 TTTAAATTTAAA
1 TTT-AATTTAAA
*
5289925 -TAAATTTAAA
1 TTTAATTTAAA
5289935 ATCAATTTAT
Statistics
Matches: 60, Mismatches: 12, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
9 6 0.10
10 10 0.17
11 33 0.55
12 11 0.18
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (11 bp):
TTTAATTTAAA
Found at i:5289874 original size:17 final size:16
Alignment explanation
Indices: 5289848--5289934 Score: 88
Period size: 17 Copynumber: 5.4 Consensus size: 16
5289838 TGTTTAGTAT
* *
5289848 TTTAATTTTAATTTTAA
1 TTTAAATTTAA-TTAAA
*
5289865 TTTAAATTTAAAGTAAA
1 TTTAAATTT-AATTAAA
5289882 TTTAAA--TAATTAAA
1 TTTAAATTTAATTAAA
*
5289896 TTTAAATTTAAGATAAA
1 TTTAAATTTAA-TTAAA
*
5289913 TTTAAATTTAAATAAA
1 TTTAAATTTAATTAAA
5289929 TTTAAA
1 TTTAAA
5289935 ATCAATTTAT
Statistics
Matches: 61, Mismatches: 5, Indels: 9
0.81 0.07 0.12
Matches are distributed among these distances:
14 12 0.20
15 1 0.02
16 14 0.23
17 32 0.52
18 2 0.03
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (16 bp):
TTTAAATTTAATTAAA
Found at i:5289901 original size:31 final size:32
Alignment explanation
Indices: 5289863--5289934 Score: 103
Period size: 31 Copynumber: 2.2 Consensus size: 32
5289853 TTTTAATTTT
*
5289863 AATTTAAATTTAA-AGTAAATTTAAA-TAATTA
1 AATTTAAATTTAAGA-TAAATTTAAATTAAATA
5289894 AATTTAAATTTAAGATAAATTTAAATTTAAATA
1 AATTTAAATTTAAGATAAATTTAAA-TTAAATA
5289927 AATTTAAA
1 AATTTAAA
5289935 ATCAATTTAT
Statistics
Matches: 37, Mismatches: 1, Indels: 4
0.88 0.02 0.10
Matches are distributed among these distances:
31 23 0.62
32 1 0.03
33 13 0.35
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (32 bp):
AATTTAAATTTAAGATAAATTTAAATTAAATA
Found at i:5289936 original size:17 final size:16
Alignment explanation
Indices: 5289863--5289934 Score: 103
Period size: 17 Copynumber: 4.5 Consensus size: 16
5289853 TTTTAATTTT
5289863 AATTTAAATTTAAAGTA
1 AATTTAAATTTAAA-TA
*
5289880 AATTTAAA--TAATTA
1 AATTTAAATTTAAATA
5289894 AATTTAAATTTAAGATA
1 AATTTAAATTTAA-ATA
5289911 AATTTAAATTTAAATA
1 AATTTAAATTTAAATA
5289927 AATTTAAA
1 AATTTAAA
5289935 ATCAATTTAT
Statistics
Matches: 50, Mismatches: 2, Indels: 7
0.85 0.03 0.12
Matches are distributed among these distances:
14 10 0.20
15 3 0.06
16 14 0.28
17 23 0.46
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.42
Consensus pattern (16 bp):
AATTTAAATTTAAATA
Found at i:5289951 original size:27 final size:27
Alignment explanation
Indices: 5289867--5289952 Score: 73
Period size: 27 Copynumber: 3.0 Consensus size: 27
5289857 AATTTTAATT
* *
5289867 TAAATTTAAAGTAAATTTAAATAATTAAA
1 TAAATTTAAAATAAATTTAAAT--CTAAA
* *
5289896 TTTAAATTTAAGATAAATTTAAATTTAAA
1 --TAAATTTAAAATAAATTTAAATCTAAA
* **
5289925 TAAATTTAAAATCAATTTATCTCTAAA
1 TAAATTTAAAATAAATTTAAATCTAAA
5289952 T
1 T
5289953 TAAAACCAAA
Statistics
Matches: 48, Mismatches: 7, Indels: 4
0.81 0.12 0.07
Matches are distributed among these distances:
27 23 0.48
29 5 0.10
31 20 0.42
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.42
Consensus pattern (27 bp):
TAAATTTAAAATAAATTTAAATCTAAA
Found at i:5290644 original size:31 final size:31
Alignment explanation
Indices: 5290609--5290668 Score: 93
Period size: 31 Copynumber: 1.9 Consensus size: 31
5290599 AAAAAACTTA
* *
5290609 ACAATTCAGTGACTTGAATAAAAACTTTCGC
1 ACAATTCAGTGACTTAAACAAAAACTTTCGC
*
5290640 ACAATTCAGTGACTTAAACGAAAACTTTC
1 ACAATTCAGTGACTTAAACAAAAACTTTC
5290669 AAATAGTTCA
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.40, C:0.20, G:0.12, T:0.28
Consensus pattern (31 bp):
ACAATTCAGTGACTTAAACAAAAACTTTCGC
Found at i:5294298 original size:29 final size:29
Alignment explanation
Indices: 5294240--5294304 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
5294230 AGTCATCCAT
** *
5294240 AAAGGCTCGCATATAACAAAGTTAATCAC
1 AAAGGCTTACATATAACAAAGTTAACCAC
* * *
5294269 AGAGGCTTACATATAACAGAGTTAGCCAC
1 AAAGGCTTACATATAACAAAGTTAACCAC
5294298 AAAGGCT
1 AAAGGCT
5294305 CTTTTTCAAG
Statistics
Matches: 29, Mismatches: 7, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.42, C:0.20, G:0.18, T:0.20
Consensus pattern (29 bp):
AAAGGCTTACATATAACAAAGTTAACCAC
Found at i:5300282 original size:24 final size:24
Alignment explanation
Indices: 5300255--5300317 Score: 65
Period size: 24 Copynumber: 2.6 Consensus size: 24
5300245 TTTTTTACTA
* *
5300255 TTTTGGTGTTGTTTTTAT-TGTTAT
1 TTTTGCTGTTGTTTTT-TCTATTAT
* * *
5300279 TTTTGTTGCTATTTTTTCTATTAT
1 TTTTGCTGTTGTTTTTTCTATTAT
5300303 TTTTGCTGTTGTTTT
1 TTTTGCTGTTGTTTT
5300318 GGTTGTTTGG
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
23 1 0.03
24 30 0.97
ACGTcount: A:0.08, C:0.05, G:0.16, T:0.71
Consensus pattern (24 bp):
TTTTGCTGTTGTTTTTTCTATTAT
Found at i:5300842 original size:32 final size:32
Alignment explanation
Indices: 5300780--5300842 Score: 76
Period size: 32 Copynumber: 2.0 Consensus size: 32
5300770 TCATAGACTT
* *
5300780 ATAAATTGATTATTTGAATTTAGTATTTCATG
1 ATAAATTAATTATTTGAATTTAGTAATTCATG
5300812 ATAAATTAATTAATTT-AATTT-GATAATTCAT
1 ATAAATTAATT-ATTTGAATTTAG-TAATTCAT
5300843 ATTGATTAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
31 1 0.04
32 22 0.81
33 4 0.15
ACGTcount: A:0.40, C:0.03, G:0.08, T:0.49
Consensus pattern (32 bp):
ATAAATTAATTATTTGAATTTAGTAATTCATG
Found at i:5313121 original size:31 final size:31
Alignment explanation
Indices: 5313065--5313153 Score: 83
Period size: 31 Copynumber: 2.9 Consensus size: 31
5313055 TTAATAATAC
* *
5313065 ATAAAATAT-TTTAAA-ATTTTAAATATAATG
1 ATAAATTATATTTAAATAATTT-AATATAATG
**
5313095 ATAAATTATATTTAAATAATTTAATATCGTG
1 ATAAATTATATTTAAATAATTTAATATAATG
* * * *
5313126 GTAAATAATATTTATATGATTTAATATA
1 ATAAATTATATTTAAATAATTTAATATA
5313154 GTGCTGCATA
Statistics
Matches: 48, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
30 8 0.17
31 36 0.75
32 4 0.08
ACGTcount: A:0.48, C:0.01, G:0.06, T:0.45
Consensus pattern (31 bp):
ATAAATTATATTTAAATAATTTAATATAATG
Found at i:5324276 original size:19 final size:21
Alignment explanation
Indices: 5324254--5324310 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 21
5324244 GAAAATTACA
5324254 AAAAAAT-GTAAAAAA-ATAT
1 AAAAAATCGTAAAAAACATAT
5324273 --AAAATCGTAAAAAACATAT
1 AAAAAATCGTAAAAAACATAT
5324292 AAAAATTATCGTACAAAAA
1 AAAAA--ATCGTA-AAAAA
5324311 GAATCATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
17 5 0.16
18 8 0.26
19 4 0.13
21 3 0.10
23 6 0.19
24 5 0.16
ACGTcount: A:0.67, C:0.07, G:0.05, T:0.21
Consensus pattern (21 bp):
AAAAAATCGTAAAAAACATAT
Found at i:5324482 original size:19 final size:18
Alignment explanation
Indices: 5324458--5324538 Score: 90
Period size: 19 Copynumber: 4.3 Consensus size: 18
5324448 GTTAAAGGAC
5324458 ATTTTTTATGCATTTTATA
1 ATTTTTTATG-ATTTTATA
5324477 ATTTTTTATGATTTTTATA
1 ATTTTTTATGA-TTTTATA
** ** *
5324496 AAATTTTACAATTTTTTA
1 ATTTTTTATGATTTTATA
5324514 TATTTTTTATGATTTTATA
1 -ATTTTTTATGATTTTATA
5324533 ATTTTT
1 ATTTTT
5324539 AATAAAATTT
Statistics
Matches: 50, Mismatches: 10, Indels: 5
0.77 0.15 0.08
Matches are distributed among these distances:
18 13 0.26
19 37 0.74
ACGTcount: A:0.28, C:0.02, G:0.04, T:0.65
Consensus pattern (18 bp):
ATTTTTTATGATTTTATA
Found at i:5324483 original size:10 final size:10
Alignment explanation
Indices: 5324470--5324543 Score: 66
Period size: 10 Copynumber: 7.8 Consensus size: 10
5324460 TTTTTATGCA
5324470 TTTTATAATT
1 TTTTATAATT
*
5324480 TTTTATGA-T
1 TTTTATAATT
**
5324489 TTTTATAAAA
1 TTTTATAATT
*
5324499 TTTTACAATT
1 TTTTATAATT
5324509 TTTTAT-ATT
1 TTTTATAATT
*
5324518 TTTTATGA--
1 TTTTATAATT
5324526 TTTTATAATT
1 TTTTATAATT
*
5324536 TTTAATAA
1 TTTTATAA
5324544 AATTTAAATA
Statistics
Matches: 51, Mismatches: 9, Indels: 8
0.75 0.13 0.12
Matches are distributed among these distances:
8 7 0.14
9 17 0.33
10 27 0.53
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.64
Consensus pattern (10 bp):
TTTTATAATT
Found at i:5324579 original size:28 final size:29
Alignment explanation
Indices: 5324525--5324581 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
5324515 ATTTTTTATG
* *
5324525 ATTTTATAATTTTTAATAAAATTTAAATA
1 ATTTTATAATTTTCAATAAAATATAAATA
*
5324554 ATTTTTTAATTTTCAA-AAAATATAAATA
1 ATTTTATAATTTTCAATAAAATATAAATA
5324582 CTTAAGAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
28 11 0.44
29 14 0.56
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (29 bp):
ATTTTATAATTTTCAATAAAATATAAATA
Found at i:5325273 original size:24 final size:24
Alignment explanation
Indices: 5325242--5325291 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
5325232 ATGTTCACGA
* *
5325242 ATAAGCTCGTTTATTGACTTGTTT
1 ATAAGCTCGTTTATTGAATCGTTT
5325266 ATAAGCTCGTTTATTGAATCGTTT
1 ATAAGCTCGTTTATTGAATCGTTT
5325290 AT
1 AT
5325292 TTATTAATAA
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:0.24, C:0.12, G:0.16, T:0.48
Consensus pattern (24 bp):
ATAAGCTCGTTTATTGAATCGTTT
Found at i:5325414 original size:24 final size:24
Alignment explanation
Indices: 5325382--5325489 Score: 157
Period size: 24 Copynumber: 4.5 Consensus size: 24
5325372 TCATTAACAT
*
5325382 TGTTCGTGAACATGTGT-AATTCTA
1 TGTTCGTGAACATGT-TCAATTATA
5325406 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCAATTATA
5325430 TGTTCGTGAACATGTTCAATTATA
1 TGTTCGTGAACATGTTCAATTATA
* *
5325454 TGTTCATGAACATGTTCATTTA-A
1 TGTTCGTGAACATGTTCAATTATA
*
5325477 TGTTCGTAAACAT
1 TGTTCGTGAACAT
5325490 ATTTGATTAA
Statistics
Matches: 78, Mismatches: 5, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
23 13 0.17
24 65 0.83
ACGTcount: A:0.29, C:0.13, G:0.17, T:0.42
Consensus pattern (24 bp):
TGTTCGTGAACATGTTCAATTATA
Found at i:5325468 original size:12 final size:12
Alignment explanation
Indices: 5325405--5325472 Score: 50
Period size: 12 Copynumber: 5.7 Consensus size: 12
5325395 GTGTAATTCT
*
5325405 ATGTTCGTGAAC
1 ATGTTCATGAAC
* *
5325417 ATGTTCAAT-TAT
1 ATGTTC-ATGAAC
*
5325429 ATGTTCGTGAAC
1 ATGTTCATGAAC
* *
5325441 ATGTTCAAT-TAT
1 ATGTTC-ATGAAC
5325453 ATGTTCATGAAC
1 ATGTTCATGAAC
5325465 ATGTTCAT
1 ATGTTCAT
5325473 TTAATGTTCG
Statistics
Matches: 41, Mismatches: 11, Indels: 8
0.68 0.18 0.13
Matches are distributed among these distances:
11 3 0.07
12 36 0.88
13 2 0.05
ACGTcount: A:0.29, C:0.13, G:0.16, T:0.41
Consensus pattern (12 bp):
ATGTTCATGAAC
Found at i:5325548 original size:21 final size:21
Alignment explanation
Indices: 5325524--5325563 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
5325514 TTCGTGAACA
5325524 TTAAACAAACGAACATGAATT
1 TTAAACAAACGAACATGAATT
*
5325545 TTAAATAAACGAACATGAA
1 TTAAACAAACGAACATGAA
5325564 CAAAAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.12, G:0.10, T:0.23
Consensus pattern (21 bp):
TTAAACAAACGAACATGAATT
Found at i:5327067 original size:17 final size:17
Alignment explanation
Indices: 5327045--5327080 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
5327035 TAAATCAATG
*
5327045 ATAAATAAAATATAAAT
1 ATAAATAAAATAAAAAT
*
5327062 ATAAATAAGATAAAAAT
1 ATAAATAAAATAAAAAT
5327079 AT
1 AT
5327081 CATAAATAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.28
Consensus pattern (17 bp):
ATAAATAAAATAAAAAT
Found at i:5327089 original size:15 final size:16
Alignment explanation
Indices: 5327045--5327097 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 16
5327035 TAAATCAATG
*
5327045 ATAAATAAAATATAAAT
1 ATAAAT-AAATAAAAAT
5327062 ATAAATAAGATAAAAATAT
1 ATAAATAA-AT-AAAA-AT
5327081 CATAAATAAATAAAAAT
1 -ATAAATAAATAAAAAT
5327098 TACGAATTTA
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
16 2 0.06
17 10 0.32
18 7 0.23
19 4 0.13
20 8 0.26
ACGTcount: A:0.70, C:0.02, G:0.02, T:0.26
Consensus pattern (16 bp):
ATAAATAAATAAAAAT
Found at i:5327637 original size:59 final size:60
Alignment explanation
Indices: 5327477--5327645 Score: 191
Period size: 60 Copynumber: 2.8 Consensus size: 60
5327467 TAATAAATTT
* * * *
5327477 AAGTACCAAATTGAA-TCTAAAAAAAAGCTTAGGTGCCAAATTAGGAAAAAATGCCAAGTTC
1 AAGTACCAAATT-AAGTC-CAAAAAAAGTTTAGGTGCCAAATTAAGAAAAAACGCCAAGTTC
* ** *
5327538 AGGTACCAAATTGTGTCCAAAAAAAGTTTAGGTGCCAAATTAAGAAAAAGCGCCAAGTTC
1 AAGTACCAAATTAAGTCCAAAAAAAGTTTAGGTGCCAAATTAAGAAAAAACGCCAAGTTC
* * * *
5327598 AAGTATCAAATTAAGT-CAAAAAAAGTTTAAGTACTAAATTAA-AAAAAA
1 AAGTACCAAATTAAGTCCAAAAAAAGTTTAGGTGCCAAATTAAGAAAAAA
5327646 TATCAAATTT
Statistics
Matches: 91, Mismatches: 16, Indels: 5
0.81 0.14 0.04
Matches are distributed among these distances:
58 5 0.05
59 23 0.25
60 50 0.55
61 13 0.14
ACGTcount: A:0.49, C:0.13, G:0.15, T:0.22
Consensus pattern (60 bp):
AAGTACCAAATTAAGTCCAAAAAAAGTTTAGGTGCCAAATTAAGAAAAAACGCCAAGTTC
Found at i:5332389 original size:2 final size:2
Alignment explanation
Indices: 5332382--5332411 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
5332372 CAAGATATGT
5332382 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
5332412 CTGATTTTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:5339787 original size:21 final size:21
Alignment explanation
Indices: 5339758--5339799 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
5339748 TTTTGATTTG
5339758 ATATATAATCAAATACACTAT
1 ATATATAATCAAATACACTAT
*
5339779 ATATGTAATCAAATACACTAT
1 ATATATAATCAAATACACTAT
5339800 CATTAGTGGT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.50, C:0.14, G:0.02, T:0.33
Consensus pattern (21 bp):
ATATATAATCAAATACACTAT
Found at i:5358004 original size:19 final size:19
Alignment explanation
Indices: 5357976--5358014 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
5357966 TTGTGCTATG
*
5357976 TGTGTTTGTTTATTTTATT
1 TGTGTATGTTTATTTTATT
5357995 TGTGTATGTTTATTTTATT
1 TGTGTATGTTTATTTTATT
5358014 T
1 T
5358015 TGATTGTAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.13, C:0.00, G:0.15, T:0.72
Consensus pattern (19 bp):
TGTGTATGTTTATTTTATT
Found at i:5358111 original size:4 final size:4
Alignment explanation
Indices: 5358102--5358158 Score: 78
Period size: 4 Copynumber: 13.8 Consensus size: 4
5358092 AAATAAACGG
*
5358102 GAAA GAAA GAAA GAAAA GAAA GAAA GAAA GAAA GAAA GAAA GAGAG GAAA
1 GAAA GAAA GAAA G-AAA GAAA GAAA GAAA GAAA GAAA GAAA GA-AA GAAA
*
5358152 TAAA GAA
1 GAAA GAA
5358159 GAAGGAGAGA
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
4 40 0.85
5 7 0.15
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (4 bp):
GAAA
Found at i:5358160 original size:20 final size:20
Alignment explanation
Indices: 5358105--5358171 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
5358095 TAAACGGGAA
* *
5358105 AGAAAGAAAGAAAAGAAAGAA
1 AGAAATAAAG-AAAGAAAGAG
*
5358126 AGAAAGAAAGAAAGAAAGAG
1 AGAAATAAAGAAAGAAAGAG
*
5358146 AGGAAATAAAG-AAGAAGGAG
1 A-GAAATAAAGAAAGAAAGAG
5358166 AGAAAT
1 AGAAAT
5358172 GTAATGTGTT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
19 5 0.12
20 19 0.45
21 18 0.43
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (20 bp):
AGAAATAAAGAAAGAAAGAG
Found at i:5361191 original size:7 final size:7
Alignment explanation
Indices: 5361181--5361266 Score: 68
Period size: 7 Copynumber: 12.3 Consensus size: 7
5361171 ATGTATAGGA
*
5361181 TTTATGG
1 TTTAAGG
*
5361188 TTTAGGG
1 TTTAAGG
5361195 CTTTAA-G
1 -TTTAAGG
*
5361202 TTTAAGA
1 TTTAAGG
5361209 TTTAAGG
1 TTTAAGG
* *
5361216 TTTATGA
1 TTTAAGG
5361223 TTCTAA-G
1 TT-TAAGG
*
5361230 TTTAGGG
1 TTTAAGG
*
5361237 TTTAGGG
1 TTTAAGG
5361244 TTTAAGG
1 TTTAAGG
*
5361251 TTTAGGG
1 TTTAAGG
5361258 TTTAAGG
1 TTTAAGG
5361265 TT
1 TT
5361267 ATGAAATTTA
Statistics
Matches: 63, Mismatches: 12, Indels: 8
0.76 0.14 0.10
Matches are distributed among these distances:
6 7 0.11
7 50 0.79
8 6 0.10
ACGTcount: A:0.23, C:0.02, G:0.28, T:0.47
Consensus pattern (7 bp):
TTTAAGG
Found at i:5361266 original size:21 final size:21
Alignment explanation
Indices: 5361181--5361266 Score: 86
Period size: 21 Copynumber: 4.1 Consensus size: 21
5361171 ATGTATAGGA
*
5361181 TTTATGGTTTAGGGCTTTAA-G
1 TTTAAGGTTTAGGG-TTTAAGG
* * * *
5361202 TTTAAGATTTAAGGTTTATGA
1 TTTAAGGTTTAGGGTTTAAGG
*
5361223 TTCTAA-GTTTAGGGTTTAGGG
1 TT-TAAGGTTTAGGGTTTAAGG
5361244 TTTAAGGTTTAGGGTTTAAGG
1 TTTAAGGTTTAGGGTTTAAGG
5361265 TT
1 TT
5361267 ATGAAATTTA
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
20 7 0.13
21 42 0.81
22 3 0.06
ACGTcount: A:0.23, C:0.02, G:0.28, T:0.47
Consensus pattern (21 bp):
TTTAAGGTTTAGGGTTTAAGG
Found at i:5363869 original size:17 final size:18
Alignment explanation
Indices: 5363837--5363870 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
5363827 TTAATTCGAT
5363837 TCGAAATTAGATAATTAG
1 TCGAAATTAGATAATTAG
*
5363855 TCGAACTTA-ATAATTA
1 TCGAAATTAGATAATTA
5363871 ATATTATGTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 7 0.47
18 8 0.53
ACGTcount: A:0.44, C:0.09, G:0.12, T:0.35
Consensus pattern (18 bp):
TCGAAATTAGATAATTAG
Found at i:5366179 original size:120 final size:114
Alignment explanation
Indices: 5366038--5366273 Score: 280
Period size: 115 Copynumber: 2.0 Consensus size: 114
5366028 ATTATCAAAA
* * *
5366038 TAAATTTTAGAATGATCAAAATAAAATCGACAATATTTTAAT-ATGACCTG-CAATATAATTTAC
1 TAAATTTTAAAATGATCAAAATAAAA---AC-A-ACTTT-ATCATGAACTGAC-ATATAATTTAC
5366101 CTTATAATAAAATACGAAAAATCTCTATAATTTATATTATAAATATTCATCCATTTT
59 CTTATAATAAAATACGAAAAATCTCTATAATTTATATTATAAATA-TCATCCATTTT
* * * * *
5366158 TAAATTTTAAAATGAAT-AAAATAAAAACACCTTTATCCTGAAGTGACTTATAATTTATCTTATA
1 TAAATTTTAAAATG-ATCAAAATAAAAACAACTTTATCATGAACTGACATATAATTTACCTTATA
* *
5366222 ATAAAATACGAAAAATCTCTATACTTTATATTATGAATATCATCCATTTT
65 ATAAAATACGAAAAATCTCTATAATTTATATTATAAATATCATCCATTTT
5366272 TA
1 TA
5366274 GAAACCGAAT
Statistics
Matches: 103, Mismatches: 10, Indels: 12
0.82 0.08 0.10
Matches are distributed among these distances:
114 15 0.15
115 60 0.58
116 2 0.02
117 2 0.02
120 22 0.21
121 2 0.02
ACGTcount: A:0.44, C:0.12, G:0.05, T:0.39
Consensus pattern (114 bp):
TAAATTTTAAAATGATCAAAATAAAAACAACTTTATCATGAACTGACATATAATTTACCTTATAA
TAAAATACGAAAAATCTCTATAATTTATATTATAAATATCATCCATTTT
Found at i:5367563 original size:21 final size:21
Alignment explanation
Indices: 5367537--5367583 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
5367527 GTATGCTTCT
* *
5367537 TTCTTTCACCTTCTTTAATAC
1 TTCTTTCACCTTCTTGAATAA
**
5367558 TTCTTTCATTTTCTTGAATAA
1 TTCTTTCACCTTCTTGAATAA
5367579 TTCTT
1 TTCTT
5367584 CAATTACTAA
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:0.19, C:0.21, G:0.02, T:0.57
Consensus pattern (21 bp):
TTCTTTCACCTTCTTGAATAA
Found at i:5372649 original size:14 final size:15
Alignment explanation
Indices: 5372616--5372657 Score: 50
Period size: 14 Copynumber: 2.7 Consensus size: 15
5372606 TTCCAAATGA
5372616 AATTAGAATAAATCTTT
1 AATTA-AATAAA-CTTT
5372633 AATTAAATAAA-TTT
1 AATTAAATAAACTTT
*
5372647 AATTAATTAAA
1 AATTAAATAAA
5372658 ATTTTTAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
14 13 0.54
16 6 0.25
17 5 0.21
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (15 bp):
AATTAAATAAACTTT
Found at i:5373552 original size:2 final size:2
Alignment explanation
Indices: 5373545--5373573 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
5373535 TACTTTAATC
5373545 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5373574 ACTTTCAATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5391695 original size:23 final size:23
Alignment explanation
Indices: 5391669--5391834 Score: 141
Period size: 23 Copynumber: 7.4 Consensus size: 23
5391659 AGTGCTGGGC
5391669 AACAGAGAGCACACAAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
5391692 AACAGAGAGTACACAAA--G-T-
1 AACAGAGAGCACACAAAGTGCTA
* *
5391711 -AC--TGAGCACACAAAGTGCCA
1 AACAGAGAGCACACAAAGTGCTA
* *
5391731 ATCAGAGAGCACACGAAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
* * *
5391754 ATCGGAGAGCACGCAAAGTGCTAA
1 AACAGAGAGCACACAAAGTGCT-A
* *
5391778 TAACAGAGAGCACGA-GACGTGCTA
1 -AACAGAGAGCAC-ACAAAGTGCTA
*
5391802 AACAGAGAGCACACACAGTGCTA
1 AACAGAGAGCACACAAAGTGCTA
*
5391825 ATCAGAGAGC
1 AACAGAGAGC
5391835 GCGCTAGTGT
Statistics
Matches: 112, Mismatches: 20, Indels: 22
0.73 0.13 0.14
Matches are distributed among these distances:
16 10 0.09
18 3 0.03
20 1 0.01
21 2 0.02
22 1 0.01
23 77 0.69
24 2 0.02
25 16 0.14
ACGTcount: A:0.42, C:0.22, G:0.25, T:0.11
Consensus pattern (23 bp):
AACAGAGAGCACACAAAGTGCTA
Found at i:5391719 original size:39 final size:39
Alignment explanation
Indices: 5391675--5391749 Score: 114
Period size: 39 Copynumber: 1.9 Consensus size: 39
5391665 GGGCAACAGA
* *
5391675 GAGCACACAAAGTGCTAAACAGAGAGTACACAAAGTACT
1 GAGCACACAAAGTGCCAAACAGAGAGCACACAAAGTACT
* *
5391714 GAGCACACAAAGTGCCAATCAGAGAGCACACGAAGT
1 GAGCACACAAAGTGCCAAACAGAGAGCACACAAAGT
5391750 GCTAATCGGA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
39 32 1.00
ACGTcount: A:0.44, C:0.23, G:0.23, T:0.11
Consensus pattern (39 bp):
GAGCACACAAAGTGCCAAACAGAGAGCACACAAAGTACT
Found at i:5391810 original size:48 final size:46
Alignment explanation
Indices: 5391714--5391834 Score: 154
Period size: 48 Copynumber: 2.6 Consensus size: 46
5391704 ACAAAGTACT
* * *
5391714 GAGCACACAAAGTGCCAATCAGAGAGCACACGAAGTGCTAATCGGA
1 GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGTGCTAAACAGA
* *
5391760 GAGCACGCAAAGTGCTAATAACAGAGAGCACGA-GACGTGCTAAACAGA
1 GAGCACACAAAGTGCTAAT--CAGAGAGCAC-ACGAAGTGCTAAACAGA
*
5391808 GAGCACACACAGTGCTAATCAGAGAGC
1 GAGCACACAAAGTGCTAATCAGAGAGC
5391835 GCGCTAGTGT
Statistics
Matches: 65, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
46 25 0.38
48 39 0.60
49 1 0.02
ACGTcount: A:0.40, C:0.23, G:0.26, T:0.11
Consensus pattern (46 bp):
GAGCACACAAAGTGCTAATCAGAGAGCACACGAAGTGCTAAACAGA
Found at i:5394990 original size:35 final size:35
Alignment explanation
Indices: 5394919--5394991 Score: 89
Period size: 35 Copynumber: 2.1 Consensus size: 35
5394909 AAAAATAATC
*
5394919 GAGGATTGAGAATGGTAAATTGGAAAATGAAAATT
1 GAGGATTGAGAATGGTAAAATGGAAAATGAAAATT
5394954 GAGGATTGAGGAAT-G-AAAATGGAGAAAT-AAATATT
1 GAGGATTGA-GAATGGTAAAATGGA-AAATGAAA-ATT
5394989 GAG
1 GAG
5394992 TATTTGGTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 6
0.83 0.02 0.15
Matches are distributed among these distances:
34 10 0.29
35 20 0.59
36 4 0.12
ACGTcount: A:0.47, C:0.00, G:0.30, T:0.23
Consensus pattern (35 bp):
GAGGATTGAGAATGGTAAAATGGAAAATGAAAATT
Found at i:5403026 original size:21 final size:20
Alignment explanation
Indices: 5403002--5403043 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
5402992 TAATATAACA
*
5403002 TCAATAATTTTATTTTAAATT
1 TCAAGAATTTTA-TTTAAATT
*
5403023 TCAAGATTTTTATTTAAATT
1 TCAAGAATTTTATTTAAATT
5403043 T
1 T
5403044 AATTTTTTTT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.36, C:0.05, G:0.02, T:0.57
Consensus pattern (20 bp):
TCAAGAATTTTATTTAAATT
Found at i:5405288 original size:6 final size:6
Alignment explanation
Indices: 5405277--5405318 Score: 84
Period size: 6 Copynumber: 7.0 Consensus size: 6
5405267 TAACTTATGC
5405277 CCTTCT CCTTCT CCTTCT CCTTCT CCTTCT CCTTCT CCTTCT
1 CCTTCT CCTTCT CCTTCT CCTTCT CCTTCT CCTTCT CCTTCT
5405319 ATTCTAGGAT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (6 bp):
CCTTCT
Found at i:5410884 original size:3 final size:3
Alignment explanation
Indices: 5410876--5410903 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
5410866 AAAGAAAAGC
5410876 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
5410904 CAACAATTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:5417069 original size:17 final size:17
Alignment explanation
Indices: 5417047--5417085 Score: 53
Period size: 17 Copynumber: 2.3 Consensus size: 17
5417037 CACATATTTC
*
5417047 ATTATAATTGTATAAT-A
1 ATTATAA-TGGATAATAA
5417064 ATTATAATGGATAATAA
1 ATTATAATGGATAATAA
5417081 ATTAT
1 ATTAT
5417086 TAGGCTTCTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.49, C:0.00, G:0.08, T:0.44
Consensus pattern (17 bp):
ATTATAATGGATAATAA
Found at i:5417506 original size:15 final size:15
Alignment explanation
Indices: 5417486--5417516 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
5417476 AAGTATATTT
*
5417486 AATAATTCTAAATGA
1 AATAATTATAAATGA
5417501 AATAATTATAAATGA
1 AATAATTATAAATGA
5417516 A
1 A
5417517 GAGAGATTTT
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:0.58, C:0.03, G:0.06, T:0.32
Consensus pattern (15 bp):
AATAATTATAAATGA
Found at i:5418283 original size:19 final size:19
Alignment explanation
Indices: 5418261--5418303 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
5418251 TAAAATATTT
5418261 TAAAAACTATCA-AACATTA
1 TAAAAACTATCAGAA-ATTA
* *
5418280 TAAAAATTATTAGAAATTA
1 TAAAAACTATCAGAAATTA
5418299 TAAAA
1 TAAAA
5418304 TGTTGTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.60, C:0.07, G:0.02, T:0.30
Consensus pattern (19 bp):
TAAAAACTATCAGAAATTA
Found at i:5418341 original size:19 final size:19
Alignment explanation
Indices: 5418276--5418342 Score: 66
Period size: 19 Copynumber: 3.6 Consensus size: 19
5418266 ACTATCAAAC
*
5418276 ATTATAAAAATTATTAGAA
1 ATTATAAAAAATATTAGAA
** *
5418295 ATTATAAAATGT-TGTAAAA
1 ATTATAAAAAATAT-TAGAA
5418314 ATTAT-AAAAATATTAGAA
1 ATTATAAAAAATATTAGAA
*
5418332 ATCATAAAAAA
1 ATTATAAAAAA
5418343 AAAGTGTAAC
Statistics
Matches: 38, Mismatches: 7, Indels: 6
0.75 0.14 0.12
Matches are distributed among these distances:
18 13 0.34
19 25 0.66
ACGTcount: A:0.60, C:0.01, G:0.06, T:0.33
Consensus pattern (19 bp):
ATTATAAAAAATATTAGAA
Found at i:5426318 original size:21 final size:22
Alignment explanation
Indices: 5426294--5426338 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
5426284 AATATCTAAT
*
5426294 AATAAA-TGTTTT-ATAATATAA
1 AATAAAGTATTTTAATAATA-AA
5426315 AATAAAGTATTTTAATAATAAA
1 AATAAAGTATTTTAATAATAAA
5426337 AA
1 AA
5426339 CGTGAATATT
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
21 6 0.29
22 9 0.43
23 6 0.29
ACGTcount: A:0.58, C:0.00, G:0.04, T:0.38
Consensus pattern (22 bp):
AATAAAGTATTTTAATAATAAA
Found at i:5428404 original size:90 final size:89
Alignment explanation
Indices: 5428233--5428426 Score: 250
Period size: 90 Copynumber: 2.2 Consensus size: 89
5428223 TTAAGGGTGT
* * * *
5428233 AAAAAGCCCTCAAA-TTTTCTCAAAAAAAGCAATTAAGCCTCTCTTTTTTTTGCACTTATTTGAG
1 AAAAAACCCTCAAACCTTTCTCAAAAAAAGCAATTAAGCCTATCTTTTTTTTGCACTTAATTGAG
*
5428297 TACTTGAACTTTCAAAATGCATCA
66 TACTTGAACTTTCAAAATGCATAA
*
5428321 AAAAAACCCTCAAACCTTT-TCAAAAAAAGCAATTAAGCCCCTATTTTTTTTTTGCA-TTCAATT
1 AAAAAACCCTCAAACCTTTCTCAAAAAAAGCAATTAAG--CCTATCTTTTTTTTGCACTT-AATT
* * *
5428384 GGGTACTTGAAGTTTTAAAATGCATAA
63 GAGTACTTGAACTTTCAAAATGCATAA
5428411 AAAAAGACCCTCAAAC
1 AAAAA-ACCCTCAAAC
5428427 TTAAAAAAAA
Statistics
Matches: 92, Mismatches: 9, Indels: 7
0.85 0.08 0.06
Matches are distributed among these distances:
88 31 0.34
89 5 0.05
90 46 0.50
91 10 0.11
ACGTcount: A:0.38, C:0.20, G:0.09, T:0.32
Consensus pattern (89 bp):
AAAAAACCCTCAAACCTTTCTCAAAAAAAGCAATTAAGCCTATCTTTTTTTTGCACTTAATTGAG
TACTTGAACTTTCAAAATGCATAA
Found at i:5428436 original size:90 final size:91
Alignment explanation
Indices: 5428254--5428462 Score: 239
Period size: 90 Copynumber: 2.3 Consensus size: 91
5428244 AAATTTTCTC
* * *
5428254 AAAAAAAGCAATTAAG--CCTCTCTTTTTTTTGCACTTATTTGAGTACTTGAACTTTCAAAATGC
1 AAAAAAAGCAATTAAGCCCCTATTTTTTTTTTGCACTTAATTGAGTACTTGAACTTTCAAAATGC
* ***
5428317 ATCAAAAAAACCCTCAAACCTT-TTC
66 ATAAAAAAAACCCTCAAACCTTAAAA
* * *
5428342 AAAAAAAGCAATTAAGCCCCTATTTTTTTTTTGCA-TTCAATTGGGTACTTGAAGTTTTAAAATG
1 AAAAAAAGCAATTAAGCCCCTATTTTTTTTTTGCACTT-AATTGAGTACTTGAACTTTCAAAATG
5428406 CATAAAAAAAGACCCTCAAA-CTTAAAAAA
65 CATAAAAAAA-ACCCTCAAACCTT--AAAA
*
5428435 AAAAAGAAGCAATTAAGCCCCTACTTTT
1 AAAAA-AAGCAATTAAGCCCCTATTTTT
5428463 ATTAAAAATA
Statistics
Matches: 102, Mismatches: 11, Indels: 10
0.83 0.09 0.08
Matches are distributed among these distances:
88 16 0.16
89 2 0.02
90 49 0.48
91 9 0.09
93 5 0.05
94 21 0.21
ACGTcount: A:0.40, C:0.19, G:0.10, T:0.32
Consensus pattern (91 bp):
AAAAAAAGCAATTAAGCCCCTATTTTTTTTTTGCACTTAATTGAGTACTTGAACTTTCAAAATGC
ATAAAAAAAACCCTCAAACCTTAAAA
Done.