Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A01
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: 104050246
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4660000 characters in sequence are not A, C, G, or T
File 10 of 316
Found at i:2986959 original size:27 final size:27
Alignment explanation
Indices: 2986921--2986994 Score: 89
Period size: 27 Copynumber: 2.7 Consensus size: 27
2986911 GCCTGATCAG
*
2986921 GCCAATTAAATTGGCGGCACCAA-AGGT
1 GCCAAATAAATTGGCGGCACCAATA-GT
*
2986948 GCCAAATAAATTGGTGGCACCAATAGT
1 GCCAAATAAATTGGCGGCACCAATAGT
*
2986975 GCCAAAGT-CATTGGCGGCAC
1 GCCAAA-TAAATTGGCGGCAC
2986995 TGCCAAAGGA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
27 39 0.95
28 2 0.05
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (27 bp):
GCCAAATAAATTGGCGGCACCAATAGT
Found at i:2987102 original size:19 final size:19
Alignment explanation
Indices: 2987072--2987144 Score: 82
Period size: 19 Copynumber: 4.0 Consensus size: 19
2987062 CCTTTTAATT
2987072 CTTT-TTTT-ATTTAATAA
1 CTTTATTTTAATTTAATAA
2987089 CTTTATTTTAATTTAATAAA
1 CTTTATTTTAATTTAAT-AA
* *
2987109 C--TATTCTCATTTAATAA
1 CTTTATTTTAATTTAATAA
*
2987126 CTCTATTTTAATTTAATAA
1 CTTTATTTTAATTTAATAA
2987145 ACTATTAAGT
Statistics
Matches: 47, Mismatches: 4, Indels: 8
0.80 0.07 0.14
Matches are distributed among these distances:
17 7 0.15
18 16 0.34
19 21 0.45
20 3 0.06
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.55
Consensus pattern (19 bp):
CTTTATTTTAATTTAATAA
Found at i:2987113 original size:18 final size:18
Alignment explanation
Indices: 2987092--2987150 Score: 82
Period size: 18 Copynumber: 3.2 Consensus size: 18
2987082 TTAATAACTT
2987092 TATTTTAATTTAATAAAC
1 TATTTTAATTTAATAAAC
* * *
2987110 TATTCTCATTTAATAACTC
1 TATTTTAATTTAATAA-AC
2987129 TATTTTAATTTAATAAAC
1 TATTTTAATTTAATAAAC
2987147 TATT
1 TATT
2987151 AAGTAATACT
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
18 19 0.56
19 15 0.44
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (18 bp):
TATTTTAATTTAATAAAC
Found at i:2987133 original size:37 final size:37
Alignment explanation
Indices: 2987080--2987150 Score: 133
Period size: 37 Copynumber: 1.9 Consensus size: 37
2987070 TTCTTTTTTT
*
2987080 ATTTAATAACTTTATTTTAATTTAATAAACTATTCTC
1 ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
2987117 ATTTAATAACTCTATTTTAATTTAATAAACTATT
1 ATTTAATAACTCTATTTTAATTTAATAAACTATT
2987151 AAGTAATACT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 33 1.00
ACGTcount: A:0.39, C:0.10, G:0.00, T:0.51
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAACTATTCTC
Found at i:2987392 original size:19 final size:19
Alignment explanation
Indices: 2987365--2987434 Score: 97
Period size: 19 Copynumber: 3.7 Consensus size: 19
2987355 TCAACTCAAT
*
2987365 TTTTTATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
*
2987384 TTTTAATTTAATAA-ACTA
1 TTTTAATTTAATAACTCTA
* *
2987402 TTATCATTTAATAACTCTA
1 TTTTAATTTAATAACTCTA
2987421 TTTTAATTTAATAA
1 TTTTAATTTAATAA
2987435 AATATTAAGT
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
18 15 0.35
19 28 0.65
ACGTcount: A:0.39, C:0.09, G:0.00, T:0.53
Consensus pattern (19 bp):
TTTTAATTTAATAACTCTA
Found at i:2987415 original size:37 final size:37
Alignment explanation
Indices: 2987370--2987441 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
2987360 TCAATTTTTT
*
2987370 ATTTAATAACTCTATTTTAATTTAATAAACTATTATC
1 ATTTAATAACTCTATTTTAATTTAATAAAATATTATC
2987407 ATTTAATAACTCTATTTTAATTTAATAAAATATTA
1 ATTTAATAACTCTATTTTAATTTAATAAAATATTA
2987442 AGTAATACTT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (37 bp):
ATTTAATAACTCTATTTTAATTTAATAAAATATTATC
Found at i:2987737 original size:19 final size:19
Alignment explanation
Indices: 2987713--2987770 Score: 64
Period size: 19 Copynumber: 3.1 Consensus size: 19
2987703 ACTTAATATT
*
2987713 TTATTAAATTAAAATAGAG
1 TTATTAAATAAAAATAGAG
* * *
2987732 TTATTAAATGAGAATAG-T
1 TTATTAAATAAAAATAGAG
*
2987750 TTATTAAATAAAAAAAGAG
1 TTATTAAATAAAAATAGAG
2987769 TT
1 TT
2987771 GAAGGGGAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 2
0.77 0.17 0.05
Matches are distributed among these distances:
18 14 0.45
19 17 0.55
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (19 bp):
TTATTAAATAAAAATAGAG
Found at i:2987755 original size:18 final size:18
Alignment explanation
Indices: 2987707--2987762 Score: 60
Period size: 19 Copynumber: 3.1 Consensus size: 18
2987697 AGTATTACTT
* *
2987707 AATATTTTATTAAATTAA
1 AATAGTTTATTAAATGAA
* *
2987725 AATAGAGTTATTAAATGAG
1 AATAG-TTTATTAAATGAA
2987744 AATAGTTTATTAAAT-AA
1 AATAGTTTATTAAATGAA
2987761 AA
1 AA
2987763 AAAGAGTTGA
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
17 3 0.10
18 13 0.42
19 15 0.48
ACGTcount: A:0.52, C:0.00, G:0.09, T:0.39
Consensus pattern (18 bp):
AATAGTTTATTAAATGAA
Found at i:2988270 original size:18 final size:18
Alignment explanation
Indices: 2988247--2988283 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
2988237 GATTTGTATC
2988247 GATATTGTTATCAATGTA
1 GATATTGTTATCAATGTA
2988265 GATATTGTTATCAATGTA
1 GATATTGTTATCAATGTA
2988283 G
1 G
2988284 GAAGTCGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.32, C:0.05, G:0.19, T:0.43
Consensus pattern (18 bp):
GATATTGTTATCAATGTA
Found at i:2989586 original size:49 final size:49
Alignment explanation
Indices: 2989529--2989623 Score: 172
Period size: 49 Copynumber: 1.9 Consensus size: 49
2989519 TAGTAAATTG
* *
2989529 GCATGACATTACACATGTGATAATATGTTTGATGCATCAGATTTTAGAA
1 GCATGACATTACACATCTGATAATATGTTTGACGCATCAGATTTTAGAA
2989578 GCATGACATTACACATCTGATAATATGTTTGACGCATCAGATTTTA
1 GCATGACATTACACATCTGATAATATGTTTGACGCATCAGATTTTA
2989624 TAAGTAATAG
Statistics
Matches: 44, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
49 44 1.00
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.35
Consensus pattern (49 bp):
GCATGACATTACACATCTGATAATATGTTTGACGCATCAGATTTTAGAA
Found at i:2990750 original size:17 final size:17
Alignment explanation
Indices: 2990708--2990754 Score: 62
Period size: 17 Copynumber: 2.8 Consensus size: 17
2990698 AATTCAATTT
2990708 TAATATAAAT-ATTCAA
1 TAATATAAATAATTCAA
2990724 T-ATGACTAAATAATTCAA
1 TAAT-A-TAAATAATTCAA
2990742 TAATATAAATAAT
1 TAATATAAATAAT
2990755 ATAAAATGTG
Statistics
Matches: 27, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
15 2 0.07
16 2 0.07
17 13 0.48
18 8 0.30
19 2 0.07
ACGTcount: A:0.55, C:0.06, G:0.02, T:0.36
Consensus pattern (17 bp):
TAATATAAATAATTCAA
Found at i:2991058 original size:30 final size:31
Alignment explanation
Indices: 2991019--2991078 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
2991009 AGAGGTGAGA
*
2991019 TGGGAAGGGAATAAAAGTTTTAGG-GGAAAAG
1 TGGGAAGGGAATAAAAATTTT-GGTGGAAAAG
*
2991050 TGGG-AGGGAGTAAAAATTTTGGTGGAAAA
1 TGGGAAGGGAATAAAAATTTTGGTGGAAAA
2991079 TAAAAGGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 2 0.08
30 20 0.77
31 4 0.15
ACGTcount: A:0.40, C:0.00, G:0.38, T:0.22
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTGGTGGAAAAG
Found at i:2991247 original size:21 final size:21
Alignment explanation
Indices: 2991213--2991253 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
2991203 GGGAGAAAGT
*
2991213 GGGAAAGAGTAAAAGTTTTGA
1 GGGAAAGAGTAAAAGGTTTGA
2991234 GGGAAA-AGTAAAAAGGTTTG
1 GGGAAAGAGT-AAAAGGTTTG
2991254 GGAGTTTAGG
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.44, C:0.00, G:0.34, T:0.22
Consensus pattern (21 bp):
GGGAAAGAGTAAAAGGTTTGA
Found at i:2991248 original size:29 final size:30
Alignment explanation
Indices: 2991189--2991248 Score: 70
Period size: 30 Copynumber: 2.0 Consensus size: 30
2991179 GAGGGGAGGG
**
2991189 GAGTAAAAATTTTAGGGAGAAAGTGGGAAA
1 GAGTAAAAATTTTAGGGAGAAAGTGAAAAA
*
2991219 GAGTAAAAGTTTTGAGGGA-AAAGT-AAAAA
1 GAGTAAAAATTTT-AGGGAGAAAGTGAAAAA
2991248 G
1 G
2991249 GTTTGGGAGT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
29 4 0.15
30 17 0.65
31 5 0.19
ACGTcount: A:0.48, C:0.00, G:0.32, T:0.20
Consensus pattern (30 bp):
GAGTAAAAATTTTAGGGAGAAAGTGAAAAA
Found at i:2991716 original size:28 final size:29
Alignment explanation
Indices: 2991675--2991746 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
2991665 GTACAATTAA
*
2991675 TTTTATATGATTAATTACA-ATTTTTATTT
1 TTTTATAT-TTTAATTACATATTTTTATTT
*
2991704 TTTTATATTTTAATTAGATATTTTTATTT
1 TTTTATATTTTAATTACATATTTTTATTT
*
2991733 TTTTA-AGTTTAATT
1 TTTTATATTTTAATT
2991747 TATAAAGATG
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
28 16 0.41
29 23 0.59
ACGTcount: A:0.29, C:0.01, G:0.04, T:0.65
Consensus pattern (29 bp):
TTTTATATTTTAATTACATATTTTTATTT
Found at i:2993841 original size:14 final size:15
Alignment explanation
Indices: 2993822--2993853 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2993812 AGGGTCTAAC
2993822 ATATTTTATA-ATAT
1 ATATTTTATATATAT
2993836 ATA-TTTATATATAT
1 ATATTTTATATATAT
2993850 ATAT
1 ATAT
2993854 AGTGAACAGT
Statistics
Matches: 16, Mismatches: 0, Indels: 3
0.84 0.00 0.16
Matches are distributed among these distances:
13 6 0.38
14 10 0.62
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (15 bp):
ATATTTTATATATAT
Found at i:2997015 original size:30 final size:31
Alignment explanation
Indices: 2996979--2997059 Score: 89
Period size: 30 Copynumber: 2.7 Consensus size: 31
2996969 TAATTGGACT
*
2996979 TAAATTTTAAAATATAAAAAAT-AAAGAGAA
1 TAAATTTTAAAATATAAAAAATAAAAAAGAA
* *
2997009 TAAATTTCATAAAT-T-AAAAATAAAAAAGAC
1 TAAATTTTA-AAATATAAAAAATAAAAAAGAA
2997039 TAAATTTT-AAATATACAAAAA
1 TAAATTTTAAAATATA-AAAAA
2997060 GTTCTAACCT
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
28 4 0.10
29 7 0.17
30 22 0.52
31 9 0.21
ACGTcount: A:0.64, C:0.04, G:0.04, T:0.28
Consensus pattern (31 bp):
TAAATTTTAAAATATAAAAAATAAAAAAGAA
Found at i:2997792 original size:31 final size:33
Alignment explanation
Indices: 2997727--2997794 Score: 95
Period size: 31 Copynumber: 2.1 Consensus size: 33
2997717 TAAAAAATTC
*
2997727 ATTTGGACTCTTTTTCAAAAAATTGATGACCAA
1 ATTTGGACTCTTTTTCAAAAAATTGAGGACCAA
* *
2997760 ATTT-GACTCTTTTT-AAAATATTGAGGATCAA
1 ATTTGGACTCTTTTTCAAAAAATTGAGGACCAA
2997791 ATTT
1 ATTT
2997795 AACTAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 2
0.86 0.08 0.05
Matches are distributed among these distances:
31 18 0.56
32 10 0.31
33 4 0.12
ACGTcount: A:0.35, C:0.12, G:0.12, T:0.41
Consensus pattern (33 bp):
ATTTGGACTCTTTTTCAAAAAATTGAGGACCAA
Found at i:3000277 original size:9 final size:9
Alignment explanation
Indices: 3000265--3000295 Score: 53
Period size: 9 Copynumber: 3.3 Consensus size: 9
3000255 AATATATTTA
3000265 TTTTTTAATT
1 TTTTTTAA-T
3000275 TTTTTTAAT
1 TTTTTTAAT
3000284 TTTTTTAAT
1 TTTTTTAAT
3000293 TTT
1 TTT
3000296 AAAATATTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 13 0.62
10 8 0.38
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTAAT
Found at i:3000280 original size:10 final size:10
Alignment explanation
Indices: 3000265--3000295 Score: 55
Period size: 10 Copynumber: 3.2 Consensus size: 10
3000255 AATATATTTA
3000265 TTTTTTAATT
1 TTTTTTAATT
3000275 TTTTTTAA-T
1 TTTTTTAATT
3000284 TTTTTTAATT
1 TTTTTTAATT
3000294 TT
1 TT
3000296 AAAATATTTT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
9 9 0.45
10 11 0.55
ACGTcount: A:0.19, C:0.00, G:0.00, T:0.81
Consensus pattern (10 bp):
TTTTTTAATT
Found at i:3000334 original size:39 final size:41
Alignment explanation
Indices: 3000273--3000366 Score: 158
Period size: 39 Copynumber: 2.4 Consensus size: 41
3000263 TATTTTTTAA
3000273 TTTTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATAC
*
3000314 TTTTTTTTTA-TTTTTT-ATTTTAAAATATTTTTAAAATAC
1 TTTTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATAC
3000353 -TTTTTTTAATTTTT
1 TTTTTTTTAATTTTT
3000367 AAAATAAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
38 8 0.16
39 27 0.54
40 6 0.12
41 9 0.18
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (41 bp):
TTTTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATAC
Found at i:3000377 original size:38 final size:39
Alignment explanation
Indices: 3000273--3000377 Score: 113
Period size: 39 Copynumber: 2.7 Consensus size: 39
3000263 TATTTTTTAA
** *
3000273 TTTTTTTTAATTTTTTTAATTTTAAAATATTTTTAAAATAC
1 TTTTTTTTAA--TTTTTAAAATAAAAATATTTTTAAAATAC
* * ** *
3000314 TTTTTTTTTATTTTTTATTTTAAAATATTTTTAAAATAC
1 TTTTTTTTAATTTTTAAAATAAAAATATTTTTAAAATAC
3000353 -TTTTTTTAATTTTTAAAATAAAAAT
1 TTTTTTTTAATTTTTAAAATAAAAAT
3000378 TTGGTATTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
38 20 0.35
39 28 0.49
41 9 0.16
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (39 bp):
TTTTTTTTAATTTTTAAAATAAAAATATTTTTAAAATAC
Found at i:3012149 original size:21 final size:24
Alignment explanation
Indices: 3012104--3012151 Score: 66
Period size: 21 Copynumber: 2.1 Consensus size: 24
3012094 ATAGATAATC
*
3012104 TTTAAAAAGAACTTTTATGATTTT
1 TTTAAAAAGAACTTTTATAATTTT
3012128 TTTAAAAA-AA-TTTTA-AATTTT
1 TTTAAAAAGAACTTTTATAATTTT
3012149 TTT
1 TTT
3012152 TTTAATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 8 0.35
22 5 0.22
23 2 0.09
24 8 0.35
ACGTcount: A:0.40, C:0.02, G:0.04, T:0.54
Consensus pattern (24 bp):
TTTAAAAAGAACTTTTATAATTTT
Found at i:3018142 original size:20 final size:19
Alignment explanation
Indices: 3018117--3018154 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
3018107 AGTATATATT
3018117 AAAAAA-TTCAATAAGATTTC
1 AAAAAAGTT-AATAA-ATTTC
3018137 AAAAAAGTTAATAAATTT
1 AAAAAAGTTAATAAATTT
3018155 ATTTTAAAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.24
20 11 0.65
21 2 0.12
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.32
Consensus pattern (19 bp):
AAAAAAGTTAATAAATTTC
Found at i:3018684 original size:12 final size:12
Alignment explanation
Indices: 3018652--3018685 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
3018642 AAAAGTATAG
3018652 ATAATAATAACA
1 ATAATAATAACA
* *
3018664 ACAACAATAACA
1 ATAATAATAACA
3018676 ATAATAATAA
1 ATAATAATAA
3018686 TTTTGAGGGC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.68, C:0.12, G:0.00, T:0.21
Consensus pattern (12 bp):
ATAATAATAACA
Found at i:3022693 original size:7 final size:8
Alignment explanation
Indices: 3022673--3022701 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
3022663 ATAAATATAT
3022673 ATTTTTTA
1 ATTTTTTA
3022681 ATTTTTTA
1 ATTTTTTA
3022689 ATTTTTTA
1 ATTTTTTA
3022697 ATTTT
1 ATTTT
3022702 AAAATACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (8 bp):
ATTTTTTA
Found at i:3023197 original size:32 final size:31
Alignment explanation
Indices: 3023149--3023278 Score: 103
Period size: 32 Copynumber: 4.3 Consensus size: 31
3023139 TTAATATCAT
* *
3023149 ATTTGGTATCTGAACTTACCACTTTTTTTCTA
1 ATTTGGTACCTAAACTTA-CACTTTTTTTCTA
* * *
3023181 ATTTGGTACATAAAC-T----TTTTTGTCCA
1 ATTTGGTACCTAAACTTACACTTTTTTTCTA
* *
3023207 ATTTGGTACCTAAGCTTAACACTTTTTTCCTA
1 ATTTGGTACCTAAACTT-ACACTTTTTTTCTA
3023239 ATTTGGTACCTAAACTTGACA--TTTTTTCTTA
1 ATTTGGTACCTAAACTT-ACACTTTTTTTC-TA
*
3023270 AGTTGGTAC
1 ATTTGGTAC
3023279 TTAATCTTTT
Statistics
Matches: 77, Mismatches: 14, Indels: 15
0.73 0.13 0.14
Matches are distributed among these distances:
26 21 0.27
27 1 0.01
30 6 0.08
31 11 0.14
32 38 0.49
ACGTcount: A:0.25, C:0.18, G:0.12, T:0.46
Consensus pattern (31 bp):
ATTTGGTACCTAAACTTACACTTTTTTTCTA
Found at i:3023315 original size:60 final size:59
Alignment explanation
Indices: 3023237--3023375 Score: 142
Period size: 60 Copynumber: 2.3 Consensus size: 59
3023227 ACTTTTTTCC
* * *
3023237 TAATTTGGTACCTAAACTTGACA-TTTTTT-CTTAAGTTGGTA-CTTAATCTTTTTTGGGGT
1 TAATTTGGTACTTGAACTTGA-ATTTTTTTCCCTAAGTTGGTATC-TAATCTTTTTT-GGGT
* **
3023296 ATAATTTGGTACTTGAACTT-AATTTTTTTCCCTAATTTGGTATCTAATCTTTTTTTTGT
1 -TAATTTGGTACTTGAACTTGAATTTTTTTCCCTAAGTTGGTATCTAATCTTTTTTGGGT
*
3023355 TCAATTTGATACTTGAACTTG
1 T-AATTTGGTACTTGAACTTG
3023376 TCAAACATTT
Statistics
Matches: 67, Mismatches: 7, Indels: 10
0.80 0.08 0.12
Matches are distributed among these distances:
58 2 0.03
59 26 0.39
60 38 0.57
61 1 0.01
ACGTcount: A:0.23, C:0.12, G:0.14, T:0.51
Consensus pattern (59 bp):
TAATTTGGTACTTGAACTTGAATTTTTTTCCCTAAGTTGGTATCTAATCTTTTTTGGGT
Found at i:3023801 original size:58 final size:56
Alignment explanation
Indices: 3023716--3023881 Score: 181
Period size: 58 Copynumber: 2.9 Consensus size: 56
3023706 TTAAACCTAA
* * * * * *
3023716 AAAAAGCTTAGGTATCATATTAGGAAAAAATATCAAGTTCAAGTACCAAATAGGGCCC
1 AAAAAGATTAAGTACCATATTAAGAAAAAATATCAAGTTCATGTACCAAATA-AG-CC
* * * * *
3023774 AAAAAGTTTATGTACCAAATTAAGAAAAAATGTCAAGTTCATGTATCAAATTAAGCC
1 AAAAAGATTAAGTACCATATTAAGAAAAAATATCAAGTTCATGTACCAAA-TAAGCC
* *
3023831 AAAAAAATTAAGTACCATATTAA-AAAAAATATCAAATTCATGTACCAAATA
1 AAAAAGATTAAGTACCATATTAAGAAAAAATATCAAGTTCATGTACCAAATA
3023882 TTATATTAAA
Statistics
Matches: 91, Mismatches: 16, Indels: 5
0.81 0.14 0.04
Matches are distributed among these distances:
55 2 0.02
56 23 0.25
57 21 0.23
58 43 0.47
59 2 0.02
ACGTcount: A:0.50, C:0.13, G:0.11, T:0.25
Consensus pattern (56 bp):
AAAAAGATTAAGTACCATATTAAGAAAAAATATCAAGTTCATGTACCAAATAAGCC
Found at i:3023818 original size:31 final size:30
Alignment explanation
Indices: 3023777--3023880 Score: 85
Period size: 31 Copynumber: 3.6 Consensus size: 30
3023767 AGGGCCCAAA
*
3023777 AAGTTTATGTACCAAATTAAGAAAAAATGTC
1 AAGTTCATGTACCAAATTAAGAAAAAAT-TC
* *
3023808 AAGTTCATGTATCAAATTAAGCCAAAAA---
1 AAGTTCATGTACCAAATTAAG-AAAAAATTC
* *
3023836 AA-TT-AAGTACCATATTAA-AAAAAATATC
1 AAGTTCATGTACCAAATTAAGAAAAAAT-TC
*
3023864 AAATTCATGTACCAAAT
1 AAGTTCATGTACCAAAT
3023881 ATTATATTAA
Statistics
Matches: 57, Mismatches: 9, Indels: 15
0.70 0.11 0.19
Matches are distributed among these distances:
24 5 0.09
26 11 0.19
27 2 0.04
28 4 0.07
29 2 0.04
30 9 0.16
31 19 0.33
32 5 0.09
ACGTcount: A:0.51, C:0.12, G:0.09, T:0.28
Consensus pattern (30 bp):
AAGTTCATGTACCAAATTAAGAAAAAATTC
Found at i:3024064 original size:22 final size:21
Alignment explanation
Indices: 3024028--3024087 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
3024018 GACCCAGGCC
*
3024028 ATTT-TTTTAATAAATACTAAAA
1 ATTTATTTTAA-AAATA-AAAAA
3024050 ATTTATTTTAAAAATTAAAAAA
1 ATTTATTTTAAAAA-TAAAAAA
**
3024072 AAGTATTTTAAAAATA
1 ATTTATTTTAAAAATA
3024088 TTTTAAAGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
21 2 0.06
22 23 0.70
23 8 0.24
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.42
Consensus pattern (21 bp):
ATTTATTTTAAAAATAAAAAA
Found at i:3024145 original size:42 final size:43
Alignment explanation
Indices: 3024059--3024157 Score: 159
Period size: 43 Copynumber: 2.4 Consensus size: 43
3024049 AATTTATTTT
*
3024059 AAAAA-TT-AAAAAAAAGTATTTTAAAAATATTTTAAAGTTAA
1 AAAAATTTAAAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
3024100 AAAAATTTAAAAAAAAAGTATTTTAAAAATATTTTAAAATT-A
1 AAAAATTTAAAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
*
3024142 AAAAATGTAAAAAAAA
1 AAAAATTTAAAAAAAA
3024158 TAAATATATT
Statistics
Matches: 54, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
41 5 0.09
42 18 0.33
43 31 0.57
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (43 bp):
AAAAATTTAAAAAAAAAGTATTTTAAAAATATTTTAAAATTAA
Found at i:3028227 original size:29 final size:29
Alignment explanation
Indices: 3028193--3028250 Score: 98
Period size: 29 Copynumber: 2.0 Consensus size: 29
3028183 TTAAAAATAA
*
3028193 AAAAAATATTTTAAAAATATTTATTATATT
1 AAAAAAT-TTTAAAAAATATTTATTATATT
3028223 AAAAAATTTTAAAAAATATTTATTATAT
1 AAAAAATTTTAAAAAATATTTATTATAT
3028251 ATTTGGCCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
29 20 0.74
30 7 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (29 bp):
AAAAAATTTTAAAAAATATTTATTATATT
Found at i:3033402 original size:30 final size:30
Alignment explanation
Indices: 3033342--3033404 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
3033332 AATTTGGAAG
* *
3033342 TTAATTTATATATTTTTTATTTTTAGAAAT
1 TTAATTTATATATTTTTTAATTTCAGAAAT
*
3033372 TTAATTTATTTATTTTTTAGATTTCA-AAAT
1 TTAATTTATATATTTTTTA-ATTTCAGAAAT
3033402 TTA
1 TTA
3033405 TGTTCAATTA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
30 25 0.86
31 4 0.14
ACGTcount: A:0.33, C:0.02, G:0.03, T:0.62
Consensus pattern (30 bp):
TTAATTTATATATTTTTTAATTTCAGAAAT
Found at i:3035689 original size:40 final size:40
Alignment explanation
Indices: 3035634--3035718 Score: 170
Period size: 40 Copynumber: 2.1 Consensus size: 40
3035624 CATGTTCACA
3035634 AAATATACAAACTTCTTACTTGCCTAGATTTGCATCTAAT
1 AAATATACAAACTTCTTACTTGCCTAGATTTGCATCTAAT
3035674 AAATATACAAACTTCTTACTTGCCTAGATTTGCATCTAAT
1 AAATATACAAACTTCTTACTTGCCTAGATTTGCATCTAAT
3035714 AAATA
1 AAATA
3035719 GTTCTCGGAA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 45 1.00
ACGTcount: A:0.38, C:0.19, G:0.07, T:0.36
Consensus pattern (40 bp):
AAATATACAAACTTCTTACTTGCCTAGATTTGCATCTAAT
Found at i:3037225 original size:36 final size:36
Alignment explanation
Indices: 3037185--3037259 Score: 141
Period size: 36 Copynumber: 2.1 Consensus size: 36
3037175 TCATGTTTCT
3037185 TCAAGAAACTGGATTTGCTTCGCTCCAAGAACTGCA
1 TCAAGAAACTGGATTTGCTTCGCTCCAAGAACTGCA
*
3037221 TCAAGAAAGTGGATTTGCTTCGCTCCAAGAACTGCA
1 TCAAGAAACTGGATTTGCTTCGCTCCAAGAACTGCA
3037257 TCA
1 TCA
3037260 TCGTTTGCAA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (36 bp):
TCAAGAAACTGGATTTGCTTCGCTCCAAGAACTGCA
Found at i:3044712 original size:65 final size:65
Alignment explanation
Indices: 3044642--3044772 Score: 235
Period size: 65 Copynumber: 2.0 Consensus size: 65
3044632 GATTTTGATT
*
3044642 TGATATAATTATATAAATAAAATTTCGATTTAATTTAAAATTTCACATATCTCTAATTAGATTTG
1 TGATATAATTATATAAATAAAATTTCGACTTAATTTAAAATTTCACATATCTCTAATTAGATTTG
* *
3044707 TGATATAATTATATAAATAAAATTTTGACTTAATTTAAAATTTCACATATTTCTAATTAGATTTG
1 TGATATAATTATATAAATAAAATTTCGACTTAATTTAAAATTTCACATATCTCTAATTAGATTTG
3044772 T
1 T
3044773 CTATGGGTCG
Statistics
Matches: 63, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
65 63 1.00
ACGTcount: A:0.41, C:0.07, G:0.06, T:0.46
Consensus pattern (65 bp):
TGATATAATTATATAAATAAAATTTCGACTTAATTTAAAATTTCACATATCTCTAATTAGATTTG
Found at i:3052864 original size:21 final size:21
Alignment explanation
Indices: 3052838--3052878 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
3052828 ATCTGCTCAA
* *
3052838 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
3052859 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
3052879 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:3058908 original size:3 final size:3
Alignment explanation
Indices: 3058897--3058987 Score: 78
Period size: 3 Copynumber: 30.3 Consensus size: 3
3058887 ATTATTTTGT
*
3058897 TTA TT- TTA TTA TTA TTA TTA TTA TTA TTTA CTA TTA TTA TCT- TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA T-TA TTA
* * * * * * *
3058942 CTA TTA TTG TTA GTA TTA TTA CTA CTA TTA TTA TTA CTA TCA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3058988 ATTTATACCT
Statistics
Matches: 70, Mismatches: 14, Indels: 8
0.76 0.15 0.09
Matches are distributed among these distances:
2 3 0.04
3 63 0.90
4 4 0.06
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:3058917 original size:12 final size:12
Alignment explanation
Indices: 3058903--3058987 Score: 89
Period size: 12 Copynumber: 6.8 Consensus size: 12
3058893 TTGTTTATTT
*
3058903 TATTATTATTAT
1 TATTATTATTAC
3058915 TATTATTATTTAC
1 TATTATTA-TTAC
3058928 TATTATTATCTTTAC
1 TATTATTA---TTAC
* *
3058943 TATTATTGTTAG
1 TATTATTATTAC
*
3058955 TATTATTACTAC
1 TATTATTATTAC
3058967 TATTATTATTAC
1 TATTATTATTAC
*
3058979 TATCATTAT
1 TATTATTAT
3058988 ATTTATACCT
Statistics
Matches: 62, Mismatches: 8, Indels: 6
0.82 0.11 0.08
Matches are distributed among these distances:
12 39 0.63
13 11 0.18
15 12 0.19
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.59
Consensus pattern (12 bp):
TATTATTATTAC
Found at i:3071635 original size:44 final size:44
Alignment explanation
Indices: 3071494--3071835 Score: 177
Period size: 44 Copynumber: 7.9 Consensus size: 44
3071484 ATTATATAGG
* * * *
3071494 TCTTATCTCCCTGAGATTACAGTGGAACAGACCAAAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAA-GT-AGA
* ** *
3071540 TCTTATCTCCCTGAGGTTACAGCGGAGCAGATTGAAGCCAG-AGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAG-AAGTAGA
* *
3071584 TTTTATCTCCTTGAGATTACAGCGGAGCAGATCAAAGATAGTA-A
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGA-AGTAGA
* * ** * *
3071628 TCCTATCTCCTTGAGATTACAATGGAGCGGAT--TA-AAG--GA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAAGTAGA
* *** * * **
3071667 TCTTATCTCTCTGA-AGTTACAATAGAGAAGATCACATCAG--G-
1 TCTTATCTCCCTGAGA-TTACAGCGGAGCAGATCAAAGAAGTAGA
* * * * * ** *
3071708 TCTTATTTCCCTGAGGTTACAGTGGAGTAGACCGGAGAATTTCAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAA-GT-AGA
* * ** *
3071754 TCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG-AGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAG-AAGTAGA
* *
3071798 TCTTATCTCCCTGAGATTACAGCGGAGCAAATCGAAGA
1 TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGA
3071836 CACTATCCTA
Statistics
Matches: 229, Mismatches: 52, Indels: 33
0.73 0.17 0.11
Matches are distributed among these distances:
38 1 0.00
39 25 0.11
40 2 0.01
41 29 0.13
42 4 0.02
44 101 0.44
45 2 0.01
46 63 0.28
47 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.23, T:0.27
Consensus pattern (44 bp):
TCTTATCTCCCTGAGATTACAGCGGAGCAGATCAAAGAAGTAGA
Found at i:3071862 original size:43 final size:44
Alignment explanation
Indices: 3071751--3071867 Score: 130
Period size: 44 Copynumber: 2.7 Consensus size: 44
3071741 GGAGAATTTC
* * * * *
3071751 AGATCTTATCTCCCTGAGGTTACAGTGGAGCAGATTGAAGCCAG
1 AGATCCTATCTCCCTGAAGTTACAGTGGAGCAAATCGAAGACAG
* *
3071795 AGATCTTATCTCCCTG-AGATTACAGCGGAGCAAATCGAAGACA-
1 AGATCCTATCTCCCTGAAG-TTACAGTGGAGCAAATCGAAGACAG
**
3071838 CTATCCTATCTCCCTGAAGTTACAGTGGAG
1 AGATCCTATCTCCCTGAAGTTACAGTGGAG
3071868 TGGATTAAAA
Statistics
Matches: 62, Mismatches: 9, Indels: 5
0.82 0.12 0.07
Matches are distributed among these distances:
43 24 0.39
44 38 0.61
ACGTcount: A:0.29, C:0.23, G:0.23, T:0.25
Consensus pattern (44 bp):
AGATCCTATCTCCCTGAAGTTACAGTGGAGCAAATCGAAGACAG
Found at i:3072752 original size:14 final size:15
Alignment explanation
Indices: 3072728--3072756 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3072718 TTTTTGCATA
3072728 CTTTGATTTTTTTTT
1 CTTTGATTTTTTTTT
3072743 CTTT-ATTTTTTTTT
1 CTTTGATTTTTTTTT
3072757 TGCCTTTTAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 10 0.71
15 4 0.29
ACGTcount: A:0.07, C:0.07, G:0.03, T:0.83
Consensus pattern (15 bp):
CTTTGATTTTTTTTT
Found at i:3073410 original size:3 final size:3
Alignment explanation
Indices: 3073399--3073486 Score: 72
Period size: 3 Copynumber: 29.3 Consensus size: 3
3073389 ATTATTTTGT
* *
3073399 TTA TT- TTA TTA TTA TTA TTA TTA TTTA CTA TTA TTA TCT- TTA CTA
1 TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA T-TA TTA TTA
* * * * * *
3073444 TTA TTG TTA GTA TTA TTA CTA CTA TTA TTA TTA CTA TCA TTA T
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T
3073487 ATTTATACCT
Statistics
Matches: 67, Mismatches: 14, Indels: 8
0.75 0.16 0.09
Matches are distributed among these distances:
2 3 0.04
3 60 0.90
4 4 0.06
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:3073419 original size:12 final size:12
Alignment explanation
Indices: 3073404--3073486 Score: 85
Period size: 12 Copynumber: 6.6 Consensus size: 12
3073394 TTTGTTTATT
*
3073404 TTATTATTATTA
1 TTATTATTACTA
3073416 TTATTATTTACTA
1 TTATTA-TTACTA
3073429 TTATTATCTTTACTA
1 TTATTA---TTACTA
* *
3073444 TTATTGTTAGTA
1 TTATTATTACTA
*
3073456 TTATTACTACTA
1 TTATTATTACTA
3073468 TTATTATTACTA
1 TTATTATTACTA
*
3073480 TCATTAT
1 TTATTAT
3073487 ATTTATACCT
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
12 37 0.62
13 11 0.18
15 12 0.20
ACGTcount: A:0.30, C:0.08, G:0.02, T:0.59
Consensus pattern (12 bp):
TTATTATTACTA
Found at i:3073807 original size:13 final size:12
Alignment explanation
Indices: 3073786--3073819 Score: 50
Period size: 13 Copynumber: 2.7 Consensus size: 12
3073776 AATATCACTA
3073786 TTTACTTTTTTAT
1 TTTA-TTTTTTAT
3073799 TTTATTTTTTAT
1 TTTATTTTTTAT
3073811 TATTATTTT
1 T-TTATTTT
3073820 CAAATTTTGA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
12 9 0.45
13 11 0.55
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (12 bp):
TTTATTTTTTAT
Found at i:3077564 original size:24 final size:24
Alignment explanation
Indices: 3077531--3077582 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
3077521 TTTCTAAAAG
3077531 ATTTAATATTTA-TGAGTATAATAT
1 ATTTAATATTTATTG-GTATAATAT
*
3077555 ATTTAGTATTTATTGGTATAATAT
1 ATTTAATATTTATTGGTATAATAT
3077579 ATTT
1 ATTT
3077583 GACTTTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
24 24 0.92
25 2 0.08
ACGTcount: A:0.37, C:0.00, G:0.10, T:0.54
Consensus pattern (24 bp):
ATTTAATATTTATTGGTATAATAT
Found at i:3077590 original size:24 final size:24
Alignment explanation
Indices: 3077531--3077592 Score: 74
Period size: 24 Copynumber: 2.6 Consensus size: 24
3077521 TTTCTAAAAG
*
3077531 ATTTAATATTTA-TGAGTATAATAT
1 ATTTACTATTTATTG-GTATAATAT
*
3077555 ATTTAGTATTTATTGGTATAATAT
1 ATTTACTATTTATTGGTATAATAT
3077579 ATTTGACT-TTTATT
1 ATTT-ACTATTTATT
3077593 AGAATTAGGT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
24 30 0.88
25 4 0.12
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.55
Consensus pattern (24 bp):
ATTTACTATTTATTGGTATAATAT
Found at i:3081475 original size:14 final size:15
Alignment explanation
Indices: 3081448--3081476 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
3081438 ACTTGATTTC
3081448 TATTGATGTAATAAT
1 TATTGATGTAATAAT
3081463 TATTGAT-TAATAAT
1 TATTGATGTAATAAT
3081477 ATGCAAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 7 0.50
15 7 0.50
ACGTcount: A:0.41, C:0.00, G:0.10, T:0.48
Consensus pattern (15 bp):
TATTGATGTAATAAT
Found at i:3091569 original size:17 final size:17
Alignment explanation
Indices: 3091492--3091569 Score: 59
Period size: 17 Copynumber: 4.5 Consensus size: 17
3091482 TATCTTCATA
*
3091492 AATATTAGATTTAATTT
1 AATATTAAATTTAATTT
** *
3091509 AATATTAACGTTAAATT
1 AATATTAAATTTAATTT
* * **
3091526 AA-ATTTAATGCTAAGAT
1 AATATTAAAT-TTAATTT
3091543 AATTATTAAATTTAATTT
1 AA-TATTAAATTTAATTT
3091561 AATATTAAA
1 AATATTAAA
3091570 CTATTAAAAA
Statistics
Matches: 44, Mismatches: 14, Indels: 6
0.69 0.22 0.09
Matches are distributed among these distances:
16 4 0.09
17 28 0.64
18 6 0.14
19 6 0.14
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (17 bp):
AATATTAAATTTAATTT
Found at i:3092942 original size:29 final size:29
Alignment explanation
Indices: 3092878--3092944 Score: 71
Period size: 29 Copynumber: 2.3 Consensus size: 29
3092868 ATTTAGTCAT
** *
3092878 ATTTAATCTTTTTAATAATAACAAAACTA
1 ATTTAATCCATTTAATAAAAACAAAACTA
** * *
3092907 AAGTAATCCATTTAATAAAAATAAGACTA
1 ATTTAATCCATTTAATAAAAACAAAACTA
3092936 ATTTAATCC
1 ATTTAATCC
3092945 GGTTTTTATA
Statistics
Matches: 29, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.49, C:0.12, G:0.03, T:0.36
Consensus pattern (29 bp):
ATTTAATCCATTTAATAAAAACAAAACTA
Found at i:3093509 original size:11 final size:11
Alignment explanation
Indices: 3093493--3093534 Score: 52
Period size: 11 Copynumber: 3.9 Consensus size: 11
3093483 ATATTTTTAA
3093493 TTTTAAAATAT
1 TTTTAAAATAT
3093504 TTTTAAAATACT
1 TTTTAAAATA-T
*
3093516 TTTT--TATAT
1 TTTTAAAATAT
3093525 TTTTAAAATA
1 TTTTAAAATA
3093535 AATTTTTGGT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
9 5 0.19
10 3 0.12
11 13 0.50
12 5 0.19
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:3093540 original size:21 final size:21
Alignment explanation
Indices: 3093500--3093541 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
3093490 TAATTTTAAA
**
3093500 ATATTTTTAAAATACTTTTTT
1 ATATTTTTAAAATAAATTTTT
3093521 ATATTTTTAAAATAAATTTTT
1 ATATTTTTAAAATAAATTTTT
3093542 GGTGTTTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (21 bp):
ATATTTTTAAAATAAATTTTT
Found at i:3100455 original size:13 final size:13
Alignment explanation
Indices: 3100437--3100461 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
3100427 GGTCCTTTTG
3100437 TTATTTTAAATTT
1 TTATTTTAAATTT
3100450 TTATTTTAAATT
1 TTATTTTAAATT
3100462 ATGTTACTTA
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:0.00, G:0.00, T:0.68
Consensus pattern (13 bp):
TTATTTTAAATTT
Found at i:3105518 original size:15 final size:15
Alignment explanation
Indices: 3105498--3105545 Score: 51
Period size: 15 Copynumber: 3.2 Consensus size: 15
3105488 TGTTTATAAA
*
3105498 TATTTAATTATTATT
1 TATTTAAATATTATT
*
3105513 TATTTAAATATTATG
1 TATTTAAATATTATT
* * *
3105528 AATTTCAATAATATT
1 TATTTAAATATTATT
3105543 TAT
1 TAT
3105546 ATCAGCATAT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.56
Consensus pattern (15 bp):
TATTTAAATATTATT
Found at i:3106240 original size:83 final size:83
Alignment explanation
Indices: 3106086--3106240 Score: 188
Period size: 83 Copynumber: 1.9 Consensus size: 83
3106076 CCACCTCGCG
* * * * *
3106086 AGGTGGAGCATAAGGGAGATGCGTGAGCCGCGAGATGGACTGCCTCATCGCGTCTCACATCCCAT
1 AGGTGGAGCACAAGAGAGATGCGTGAGCCGCGAGATGGACTACCTCATCGCGTCTCACACCCCAC
3106151 CAACATGATGACCTGGCT
66 CAACATGATGACCTGGCT
* * * *
3106169 AGGTGGAGCACAAGAGAGATGTGTGAGTCGTGAGATGGA-TCACCTCATTGTC-TCTCACACCCC
1 AGGTGGAGCACAAGAGAGATGCGTGAGCCGCGAGATGGACT-ACCTCATCG-CGTCTCACACCCC
*
3106232 ACCGACATG
64 ACCAACATG
3106241 GCGACCTCAT
Statistics
Matches: 60, Mismatches: 10, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
82 1 0.02
83 58 0.97
84 1 0.02
ACGTcount: A:0.25, C:0.26, G:0.29, T:0.20
Consensus pattern (83 bp):
AGGTGGAGCACAAGAGAGATGCGTGAGCCGCGAGATGGACTACCTCATCGCGTCTCACACCCCAC
CAACATGATGACCTGGCT
Found at i:3108200 original size:22 final size:22
Alignment explanation
Indices: 3108148--3108200 Score: 52
Period size: 22 Copynumber: 2.4 Consensus size: 22
3108138 GTTACTGTTA
* *
3108148 TGTTGTTGTTTTGCTACTATTT
1 TGTTGTTATATTGCTACTATTT
*** *
3108170 CACTATTATATTGCTACTATTT
1 TGTTGTTATATTGCTACTATTT
3108192 TGTTGTTAT
1 TGTTGTTAT
3108201 TGTTTGAATC
Statistics
Matches: 21, Mismatches: 10, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.17, C:0.11, G:0.13, T:0.58
Consensus pattern (22 bp):
TGTTGTTATATTGCTACTATTT
Found at i:3109268 original size:15 final size:16
Alignment explanation
Indices: 3109248--3109283 Score: 56
Period size: 15 Copynumber: 2.3 Consensus size: 16
3109238 TAAAAAAAAA
3109248 ATTGAGTTATAGCT-G
1 ATTGAGTTATAGCTCG
*
3109263 ATTGAGTTTTAGCTCG
1 ATTGAGTTATAGCTCG
3109279 ATTGA
1 ATTGA
3109284 CATGGGTACT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 13 0.68
16 6 0.32
ACGTcount: A:0.25, C:0.08, G:0.25, T:0.42
Consensus pattern (16 bp):
ATTGAGTTATAGCTCG
Found at i:3110534 original size:18 final size:18
Alignment explanation
Indices: 3110507--3110546 Score: 55
Period size: 17 Copynumber: 2.2 Consensus size: 18
3110497 TTGGGGTTTT
3110507 TTTTTAAAAAAATACAAAA
1 TTTTTAAAAAAATA-AAAA
*
3110526 TTTTT-AAAAATTAAAAA
1 TTTTTAAAAAAATAAAAA
3110543 TTTT
1 TTTT
3110547 CATTTTGTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 7 0.35
19 5 0.25
ACGTcount: A:0.55, C:0.03, G:0.00, T:0.42
Consensus pattern (18 bp):
TTTTTAAAAAAATAAAAA
Found at i:3111487 original size:10 final size:10
Alignment explanation
Indices: 3111455--3111498 Score: 56
Period size: 10 Copynumber: 4.6 Consensus size: 10
3111445 TGAAGTGATC
3111455 TTTTATA-AT
1 TTTTATATAT
*
3111464 TTTTA-ATAA
1 TTTTATATAT
*
3111473 GTTTATATAT
1 TTTTATATAT
3111483 TTTTATATAT
1 TTTTATATAT
3111493 TTTTAT
1 TTTTAT
3111499 TGTTTATTAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
8 1 0.03
9 10 0.34
10 18 0.62
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (10 bp):
TTTTATATAT
Found at i:3111936 original size:18 final size:18
Alignment explanation
Indices: 3111913--3111977 Score: 51
Period size: 18 Copynumber: 3.4 Consensus size: 18
3111903 ATTCAAATAT
3111913 TAAATTACATATTAAAAC
1 TAAATTACATATTAAAAC
** *
3111931 TAAATTA-ATGTACCAAATAATA
1 TAAATTACA--TA-TTAA-AA-C
3111953 TAAATTACATATTAAAAC
1 TAAATTACATATTAAAAC
3111971 TAAATTA
1 TAAATTA
3111978 ATGTACCAAA
Statistics
Matches: 35, Mismatches: 6, Indels: 12
0.66 0.11 0.23
Matches are distributed among these distances:
17 1 0.03
18 14 0.40
19 4 0.11
20 4 0.11
21 4 0.11
22 7 0.20
23 1 0.03
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.34
Consensus pattern (18 bp):
TAAATTACATATTAAAAC
Found at i:3111959 original size:40 final size:40
Alignment explanation
Indices: 3111908--3111994 Score: 165
Period size: 40 Copynumber: 2.1 Consensus size: 40
3111898 AAAAAATTCA
3111908 AATATTAAATTACATATTAAAACTAAATTAATGTACCAAAT
1 AATA-TAAATTACATATTAAAACTAAATTAATGTACCAAAT
3111949 AATATAAATTACATATTAAAACTAAATTAATGTACCAAAT
1 AATATAAATTACATATTAAAACTAAATTAATGTACCAAAT
3111989 AATATA
1 AATATA
3111995 TTAACCCAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
40 42 0.91
41 4 0.09
ACGTcount: A:0.55, C:0.09, G:0.02, T:0.33
Consensus pattern (40 bp):
AATATAAATTACATATTAAAACTAAATTAATGTACCAAAT
Found at i:3112591 original size:4 final size:4
Alignment explanation
Indices: 3112582--3112609 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
3112572 TACAAACTAA
3112582 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT
3112610 CTTAAGGAGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
ATTT
Found at i:3121949 original size:18 final size:17
Alignment explanation
Indices: 3121929--3121962 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
3121919 TATATTTATT
3121929 TTTTAAAAAATTTTTAA
1 TTTTAAAAAATTTTTAA
*
3121946 TTTTAAAATATTTTTAA
1 TTTTAAAAAATTTTTAA
3121963 AATACTTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TTTTAAAAAATTTTTAA
Found at i:3121960 original size:11 final size:11
Alignment explanation
Indices: 3121946--3122051 Score: 63
Period size: 11 Copynumber: 10.4 Consensus size: 11
3121936 AAATTTTTAA
3121946 TTTTAAAATAT
1 TTTTAAAATAT
3121957 TTTTAAAATACT
1 TTTTAAAATA-T
* *
3121969 TTTT-TATTAT
1 TTTTAAAATAT
3121979 TTTT---A-A-
1 TTTTAAAATAT
3121985 TTTTAAAATAT
1 TTTTAAAATAT
3121996 TTTTAAAATACT
1 TTTTAAAATA-T
* *
3122008 TTTT-TATTAT
1 TTTTAAAATAT
*
3122018 TTTT----TAA
1 TTTTAAAATAT
3122025 TTTTAAAATAT
1 TTTTAAAATAT
3122036 TTTTAAAATACT
1 TTTTAAAATA-T
3122048 TTTT
1 TTTT
3122052 TTAATTTTTA
Statistics
Matches: 76, Mismatches: 7, Indels: 23
0.72 0.07 0.22
Matches are distributed among these distances:
6 4 0.05
7 7 0.09
9 1 0.01
10 11 0.14
11 38 0.50
12 15 0.20
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:3121983 original size:39 final size:39
Alignment explanation
Indices: 3121938--3122062 Score: 225
Period size: 39 Copynumber: 3.2 Consensus size: 39
3121928 TTTTTAAAAA
3121938 ATTTTTAATTTTAAAATATTTTTAAAATACTTTTTTATT
1 ATTTTTAATTTTAAAATATTTTTAAAATACTTTTTTATT
3121977 ATTTTTAATTTTAAAATATTTTTAAAATACTTTTTTATT
1 ATTTTTAATTTTAAAATATTTTTAAAATACTTTTTTATT
*
3122016 ATTTTTTAATTTTAAAATATTTTTAAAATACTTTTTT-TA
1 A-TTTTTAATTTTAAAATATTTTTAAAATACTTTTTTATT
3122055 ATTTTTAA
1 ATTTTTAA
3122063 AATAAATTTT
Statistics
Matches: 84, Mismatches: 1, Indels: 3
0.95 0.01 0.03
Matches are distributed among these distances:
38 7 0.08
39 42 0.50
40 35 0.42
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (39 bp):
ATTTTTAATTTTAAAATATTTTTAAAATACTTTTTTATT
Found at i:3122010 original size:28 final size:28
Alignment explanation
Indices: 3121957--3122010 Score: 65
Period size: 28 Copynumber: 1.9 Consensus size: 28
3121947 TTTAAAATAT
* * *
3121957 TTTTAAAATACTTTTTTATTATTTTTAA
1 TTTTAAAATACTTTTTAAATACTTTTAA
3121985 TTTTAAAATA-TTTTTAAAATACTTTT
1 TTTTAAAATACTTTTT-AAATACTTTT
3122011 TTATTATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
27 5 0.23
28 17 0.77
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTTAAAATACTTTTTAAATACTTTTAA
Found at i:3122072 original size:21 final size:21
Alignment explanation
Indices: 3122034--3122073 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
3122024 ATTTTAAAAT
**
3122034 ATTTTTAAAATACTTTTTTTA
1 ATTTTTAAAATAAATTTTTTA
3122055 ATTTTTAAAATAAATTTTT
1 ATTTTTAAAATAAATTTTT
3122074 GGTATTTATT
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:0.38, C:0.03, G:0.00, T:0.60
Consensus pattern (21 bp):
ATTTTTAAAATAAATTTTTTA
Found at i:3122080 original size:22 final size:21
Alignment explanation
Indices: 3122033--3122091 Score: 59
Period size: 22 Copynumber: 2.8 Consensus size: 21
3122023 AATTTTAAAA
* *
3122033 TATTTTTAAAAT-ACTTTTTT
1 TATTTTTAAAATAAATTTTTG
3122053 TAATTTTTAAAATAAATTTTTGG
1 T-ATTTTTAAAATAAATTTTT-G
3122076 TATTTATTAAAA-AAAT
1 TATTT-TTAAAATAAAT
3122092 GGACCGGGCC
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
20 1 0.03
21 11 0.33
22 14 0.42
23 7 0.21
ACGTcount: A:0.41, C:0.02, G:0.03, T:0.54
Consensus pattern (21 bp):
TATTTTTAAAATAAATTTTTG
Found at i:3122411 original size:9 final size:11
Alignment explanation
Indices: 3122389--3122420 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
3122379 ATTATTTATT
3122389 TATTTTAAATA
1 TATTTTAAATA
3122400 TATTTTAAATA
1 TATTTTAAATA
*
3122411 TAATTTAAAT
1 TATTTTAAAT
3122421 TAATCCGATT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TATTTTAAATA
Found at i:3123191 original size:28 final size:28
Alignment explanation
Indices: 3123149--3123208 Score: 75
Period size: 28 Copynumber: 2.1 Consensus size: 28
3123139 CTGATTATTC
* *
3123149 AACTAGTAAGTGAAGTACGAGACCATTT
1 AACTAGTAAGCGAAGTACAAGACCATTT
* **
3123177 AACTAGTAGGCGAAGTACAAGATTATTT
1 AACTAGTAAGCGAAGTACAAGACCATTT
3123205 AACT
1 AACT
3123209 TAATGATTTC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (28 bp):
AACTAGTAAGCGAAGTACAAGACCATTT
Found at i:3134793 original size:45 final size:45
Alignment explanation
Indices: 3134724--3134826 Score: 138
Period size: 45 Copynumber: 2.3 Consensus size: 45
3134714 AATCAGTAAC
*
3134724 GGTAGCAGTAACAGTAACAGTATTCAACACACAAAGTG-CTGAATCT
1 GGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGTC-GAAT-T
* * *
3134770 -GTAACAGTAACGGTAACAGTATTCGACACACAAGGTGTCGAATT
1 GGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGTCGAATT
3134814 GGTAACAGTAACA
1 GGTAACAGTAACA
3134827 ATAGTCAGCA
Statistics
Matches: 50, Mismatches: 5, Indels: 5
0.83 0.08 0.08
Matches are distributed among these distances:
44 1 0.02
45 48 0.96
46 1 0.02
ACGTcount: A:0.39, C:0.18, G:0.21, T:0.21
Consensus pattern (45 bp):
GGTAACAGTAACAGTAACAGTATTCAACACACAAAGTGTCGAATT
Found at i:3141655 original size:51 final size:51
Alignment explanation
Indices: 3141579--3141873 Score: 383
Period size: 51 Copynumber: 5.9 Consensus size: 51
3141569 TAATCAATGA
* **
3141579 CAAGTGATAAATGGTAGCTTTAGCTACACTTATCTGATTGGTGACAAGTGG
1 CAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGG
* * * *
3141630 CAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAGTGACATGTGA
1 CAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGG
*
3141681 CAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTTATCAGTGACAAGTGG
1 CAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGG
* * * *
3141732 CAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGAGCAGTGACATA-TGA
1 CAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACA-AGTGG
*
3141783 CAAGTGATAAGTGGTAGCTTTAGCTATACTTATCTG---A-T--C-AGTGG
1 CAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGG
* *
3141827 CAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTAATCAGGGACAAG
1 CAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAG
3141874 CCATAAGTGA
Statistics
Matches: 211, Mismatches: 24, Indels: 19
0.83 0.09 0.07
Matches are distributed among these distances:
43 16 0.08
44 20 0.09
45 1 0.00
46 1 0.00
47 1 0.00
48 1 0.00
49 1 0.00
50 2 0.01
51 167 0.79
52 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (51 bp):
CAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAGTGACAAGTGG
Found at i:3141745 original size:102 final size:101
Alignment explanation
Indices: 3141575--3141871 Score: 439
Period size: 102 Copynumber: 3.0 Consensus size: 101
3141565 CTTCTAATCA
* * *
3141575 ATGACAAGTGATAAATGGTAGCTTTAGCTACACTTATCTGATTGGTGACAAGTGGCAAGTGATAA
1 ATGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTTA-TCGTGACAAGTGGCAAGTGATAA
3141640 GTGATAGCTTCAGCTACACTTATCTGATCAGTGACAT
65 GTGATAGCTTCAGCTACACTTATCTGATCAGTGACAT
*
3141677 GTGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTTATCAGTGACAAGTGGCAAGTGATAA
1 ATGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTTATC-GTGACAAGTGGCAAGTGATAA
*
3141742 GTGATAGCTTCAGCTACACTTATCTGAGCAGTGACAT
65 GTGATAGCTTCAGCTACACTTATCTGATCAGTGACAT
3141779 ATGACAAGTGATAAGTGGTAGCTTTAGCT--A--TA-CTTATC-TGATC-AGTGGCAAGTGATAA
1 ATGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTTATCGTGA-CAAGTGGCAAGTGATAA
* * *
3141837 GTGGTAGCTT-AGCTACACTTATCTAATCAGGGACA
65 GTGATAGCTTCAGCTACACTTATCTGATCAGTGACA
3141872 AGCCATAAGT
Statistics
Matches: 183, Mismatches: 10, Indels: 12
0.89 0.05 0.06
Matches are distributed among these distances:
94 22 0.12
95 27 0.15
96 1 0.01
97 6 0.03
98 2 0.01
100 1 0.01
101 1 0.01
102 123 0.67
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (101 bp):
ATGACAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTTATCGTGACAAGTGGCAAGTGATAAG
TGATAGCTTCAGCTACACTTATCTGATCAGTGACAT
Found at i:3141866 original size:43 final size:44
Alignment explanation
Indices: 3141783--3141866 Score: 143
Period size: 43 Copynumber: 1.9 Consensus size: 44
3141773 TGACATATGA
* *
3141783 CAAGTGATAAGTGGTAGCTTTAGCTATACTTATCTGATCAGTGG
1 CAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAGTGG
3141827 CAAGTGATAAGTGGTAGC-TTAGCTACACTTATCTAATCAG
1 CAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAG
3141867 GGACAAGCCA
Statistics
Matches: 38, Mismatches: 2, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
43 20 0.53
44 18 0.47
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (44 bp):
CAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTAATCAGTGG
Found at i:3141880 original size:43 final size:44
Alignment explanation
Indices: 3141789--3141882 Score: 129
Period size: 43 Copynumber: 2.2 Consensus size: 44
3141779 ATGACAAGTG
* * **
3141789 ATAAGTGGTAGCTTTAGCTATACTTATCTGATCAGTGGCAAGTG
1 ATAAGTGGTAGCTTTAGCTACACTTATCTAATCAGTGGCAAGCC
3141833 ATAAGTGGTAGC-TTAGCTACACTTATCTAATCAG-GGACAAGCC
1 ATAAGTGGTAGCTTTAGCTACACTTATCTAATCAGTGG-CAAGCC
3141876 ATAAGTG
1 ATAAGTG
3141883 ATCATACGTA
Statistics
Matches: 45, Mismatches: 4, Indels: 3
0.87 0.08 0.06
Matches are distributed among these distances:
42 2 0.04
43 31 0.69
44 12 0.27
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (44 bp):
ATAAGTGGTAGCTTTAGCTACACTTATCTAATCAGTGGCAAGCC
Found at i:3142013 original size:24 final size:24
Alignment explanation
Indices: 3141981--3142031 Score: 102
Period size: 24 Copynumber: 2.1 Consensus size: 24
3141971 GGTAAGTGAC
3141981 AAATGGGCCCAAAAGAATTATAGT
1 AAATGGGCCCAAAAGAATTATAGT
3142005 AAATGGGCCCAAAAGAATTATAGT
1 AAATGGGCCCAAAAGAATTATAGT
3142029 AAA
1 AAA
3142032 AGAATAAGTA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.49, C:0.12, G:0.20, T:0.20
Consensus pattern (24 bp):
AAATGGGCCCAAAAGAATTATAGT
Found at i:3145447 original size:30 final size:31
Alignment explanation
Indices: 3145423--3145481 Score: 84
Period size: 30 Copynumber: 1.9 Consensus size: 31
3145413 GTAAATACTT
* **
3145423 AAAATTTGAGGGGTTAA-AGTGTAAATATGA
1 AAAATTTGAAGGACTAATAGTGTAAATATGA
3145453 AAAATTTGAAGGACTAATAGTGTAAATAT
1 AAAATTTGAAGGACTAATAGTGTAAATAT
3145482 TTTAAGGGTG
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
30 14 0.56
31 11 0.44
ACGTcount: A:0.46, C:0.02, G:0.22, T:0.31
Consensus pattern (31 bp):
AAAATTTGAAGGACTAATAGTGTAAATATGA
Found at i:3149335 original size:16 final size:18
Alignment explanation
Indices: 3149303--3149338 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
3149293 ATATGCTTAC
3149303 ATATATGTACATATTTAT
1 ATATATGTACATATTTAT
3149321 ATATATGTAC-T-TTTAT
1 ATATATGTACATATTTAT
3149337 AT
1 AT
3149339 TTTTTATAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 7 0.39
17 1 0.06
18 10 0.56
ACGTcount: A:0.36, C:0.06, G:0.06, T:0.53
Consensus pattern (18 bp):
ATATATGTACATATTTAT
Found at i:3152678 original size:20 final size:20
Alignment explanation
Indices: 3152650--3152701 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
3152640 TTTTTTAAAT
3152650 ATTTG-TATAAAATTTTACA
1 ATTTGTTATAAAATTTTACA
**
3152669 ATTTGTTATAATTCTTTTACA
1 ATTTGTTATAA-AATTTTACA
3152690 ATTT-TTATAAAA
1 ATTTGTTATAAAA
3152702 AAAATTAATT
Statistics
Matches: 27, Mismatches: 4, Indels: 4
0.77 0.11 0.11
Matches are distributed among these distances:
19 5 0.19
20 11 0.41
21 11 0.41
ACGTcount: A:0.38, C:0.06, G:0.04, T:0.52
Consensus pattern (20 bp):
ATTTGTTATAAAATTTTACA
Found at i:3152770 original size:18 final size:18
Alignment explanation
Indices: 3152706--3152769 Score: 78
Period size: 19 Copynumber: 3.5 Consensus size: 18
3152696 ATAAAAAAAA
3152706 TTAAT-TTTTAT-TAAAAT
1 TTAATATTTTATCT-AAAT
*
3152723 TTAAATTTTTTATCTAAAT
1 TT-AATATTTTATCTAAAT
3152742 TTAATATTTTATCTAAATT
1 TTAATATTTTATCTAAA-T
3152761 TTAATATTT
1 TTAATATTT
3152770 AATATTTTTA
Statistics
Matches: 42, Mismatches: 1, Indels: 6
0.86 0.02 0.12
Matches are distributed among these distances:
17 2 0.05
18 17 0.40
19 22 0.52
20 1 0.02
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.59
Consensus pattern (18 bp):
TTAATATTTTATCTAAAT
Found at i:3158976 original size:31 final size:31
Alignment explanation
Indices: 3158911--3158976 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
3158901 AATATCAGTA
* *
3158911 TTTTAATTTGATTAATTTTAATCTTTTAATT
1 TTTTAATTTGATTAATTTTAATCCTGTAATT
* *
3158942 TTTTGATTTGGTTAATTTTAATTCCTGTAATT
1 TTTTAATTTGATTAATTTTAA-TCCTGTAATT
3158974 TTT
1 TTT
3158977 AAAATTTAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
31 19 0.63
32 11 0.37
ACGTcount: A:0.24, C:0.05, G:0.08, T:0.64
Consensus pattern (31 bp):
TTTTAATTTGATTAATTTTAATCCTGTAATT
Found at i:3159952 original size:20 final size:21
Alignment explanation
Indices: 3159913--3159954 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
3159903 ATTAATATTC
3159913 AATAAATTATTCAATATTTTAA
1 AATAAATTA-TCAATATTTTAA
*
3159935 AATAAATTA-CAATTTTTTAA
1 AATAAATTATCAATATTTTAA
3159955 GTGAAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
22 9 0.47
ACGTcount: A:0.50, C:0.05, G:0.00, T:0.45
Consensus pattern (21 bp):
AATAAATTATCAATATTTTAA
Found at i:3160847 original size:91 final size:91
Alignment explanation
Indices: 3160729--3160894 Score: 244
Period size: 91 Copynumber: 1.8 Consensus size: 91
3160719 CGAGATTCTT
* ***
3160729 TTTTTGTTCCGTGGTTAAGAAAATGTTTGGCTTGAATTCGCACTAGAATTTTCTGTTT-CTTTGC
1 TTTTCGTTCCGTGGTTAAGAAAATGTTTAAATTGAATTCGCACTAGAATTTTCTGTTTGC-TTGC
*
3160793 TGCGAAACACTGTTTGAATTCTTTTTA
65 TGAGAAACACTGTTTGAATTCTTTTTA
* * *
3160820 TTTTCGTTGCGTGGTTAAGAAACTGTTTAAATTGAATTCGCACTAGAATTTTTTGTTTGCTTGCT
1 TTTTCGTTCCGTGGTTAAGAAAATGTTTAAATTGAATTCGCACTAGAATTTTCTGTTTGCTTGCT
3160885 GAGAAACACT
66 GAGAAACACT
3160895 CTGAGAAAAA
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
91 65 0.98
92 1 0.02
ACGTcount: A:0.23, C:0.14, G:0.19, T:0.44
Consensus pattern (91 bp):
TTTTCGTTCCGTGGTTAAGAAAATGTTTAAATTGAATTCGCACTAGAATTTTCTGTTTGCTTGCT
GAGAAACACTGTTTGAATTCTTTTTA
Found at i:3161095 original size:100 final size:100
Alignment explanation
Indices: 3160796--3161180 Score: 418
Period size: 106 Copynumber: 3.8 Consensus size: 100
3160786 TCTTTGCTGC
* * * *
3160796 GAAACACTGTTTGAATTCTTTTTATTTTCGTTGCGTGGTTAAGAAACTGTTTAAATTGAATTCGC
1 GAAAAACTGTTTGAATTC-TTTT-TTTTCGTTGCGCGGTTAAGAAAATGTTTAATTTGAATTCGC
* *
3160861 ACTAGAATTTTTTGTTTGCTTGCTGAGAAACACTCTGA
64 ACTAGAATTTTCTGATTGCTTGCTGAGAAACACT-TGA
* * * * *
3160899 GAAAAACTGGTTGAATTCCTTGTTTTTT-TTTGGTCGCGTGGATAAGAAAATGTTTGATTCGAAT
1 GAAAAACTGTTTGAATT-CTT-TTTTTTCGTT-G-CGC--GGTTAAGAAAATGTTTAATTTGAAT
** * *
3160963 TCGCGTTAGAGTTTTCTGATTGTTTGCTGAGAAACACTGTGA
60 TCGCACTAGAATTTTCTGATTGCTTGCTGAGAAACACT-TGA
* * *
3161005 GAAAAACTGTTTGAGTTCTTTTTTTTCGTTGCGCGGTTAAGAAAATG-TTAGTTTTAATTCGCAC
1 GAAAAACTGTTTGAATTCTTTTTTTTCGTTGCGCGGTTAAGAAAATGTTTAATTTGAATTCGCAC
* *
3161069 TAGAATTATCTGATTGGTTGCTGAGAAACAC-TGA
66 TAGAATTTTCTGATTGCTTGCTGAGAAACACTTGA
* * * *
3161103 GAAAAAATCGTTTGAATT-TTTTTATTTCGTTGCGTGGTTAAGAAATTGTTTAATTTGAACTCGC
1 GAAAAACT-GTTTGAATTCTTTTT-TTTCGTTGCGCGGTTAAGAAAATGTTTAATTTGAATTCGC
3161167 ACTAGAATTTTCTG
64 ACTAGAATTTTCTG
3161181 TTTCTGGTTG
Statistics
Matches: 235, Mismatches: 37, Indels: 23
0.80 0.13 0.08
Matches are distributed among these distances:
98 15 0.06
99 30 0.13
100 64 0.27
101 12 0.05
102 2 0.01
103 25 0.11
104 12 0.05
105 5 0.02
106 70 0.30
ACGTcount: A:0.26, C:0.12, G:0.21, T:0.41
Consensus pattern (100 bp):
GAAAAACTGTTTGAATTCTTTTTTTTCGTTGCGCGGTTAAGAAAATGTTTAATTTGAATTCGCAC
TAGAATTTTCTGATTGCTTGCTGAGAAACACTTGA
Found at i:3161193 original size:56 final size:56
Alignment explanation
Indices: 3161131--3161236 Score: 160
Period size: 56 Copynumber: 1.9 Consensus size: 56
3161121 TTTTTATTTC
3161131 GTTGCGTGGTTAAGAA-ATTGTTTAATTTGAACTCGCACTAGAATTTTCTGTTTCTG
1 GTTGCGTGGTTAAGAAGA-TGTTTAATTTGAACTCGCACTAGAATTTTCTGTTTCTG
* * * *
3161187 GTTGCGTGGTTAATAAGATGTTTAATTTGAATTCGGATTAGAATTTTCTG
1 GTTGCGTGGTTAAGAAGATGTTTAATTTGAACTCGCACTAGAATTTTCTG
3161237 ATTGTTTCCC
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
56 44 0.98
57 1 0.02
ACGTcount: A:0.25, C:0.09, G:0.23, T:0.43
Consensus pattern (56 bp):
GTTGCGTGGTTAAGAAGATGTTTAATTTGAACTCGCACTAGAATTTTCTGTTTCTG
Found at i:3161335 original size:158 final size:155
Alignment explanation
Indices: 3161032--3161319 Score: 362
Period size: 156 Copynumber: 1.8 Consensus size: 155
3161022 CTTTTTTTTC
* * * *
3161032 GTTGCGCGGTTAAGAAAATGTTAGTTTTAATTCGCACTAGAATTATCTGATTGGTTGCTGAGAAA
1 GTTGCGCGGTTAAGAAAATGTTAATTTGAATTCGCACTAGAATTATCTGATTGGTTCCCGAGAAA
* * * **
3161097 CACTGAGAAAAAATCGTTTGAATTTTTTTATTTCGTTGCGTGGTTAAGAAATTGTTTAATTTGAA
66 CACTGAGAAAAAATCGTTTGAATTTTTTTATTTCGTTGCATGGTTAAGAAAATATTTAATTCAAA
3161162 CTCGCACTAGAATTTTCTGTTTCTG
131 CTCGCACTAGAATTTTCTGTTTCTG
* * * * * * *
3161187 GTTGCGTGGTTAATAAGATGTTTAATTTGAATTCGGATTAGAATTTTCTGATTGTTTCCCGAGAA
1 GTTGCGCGGTTAAGAAAATG-TTAATTTGAATTCGCACTAGAATTATCTGATTGGTTCCCGAGAA
* * *
3161252 ACACTGAG-AAAAATTGTTTGAATTTCTTTTTTTTTTCGTTGCATGGTTAAGAAAATATTTGATT
65 ACACTGAGAAAAAATCGTTTGAA--T-TTTTTTATTTCGTTGCATGGTTAAGAAAATATTTAATT
3161316 CAAA
127 CAAA
3161320 TTCGGATCAG
Statistics
Matches: 110, Mismatches: 19, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
155 30 0.27
156 44 0.40
157 1 0.01
158 35 0.32
ACGTcount: A:0.28, C:0.10, G:0.20, T:0.41
Consensus pattern (155 bp):
GTTGCGCGGTTAAGAAAATGTTAATTTGAATTCGCACTAGAATTATCTGATTGGTTCCCGAGAAA
CACTGAGAAAAAATCGTTTGAATTTTTTTATTTCGTTGCATGGTTAAGAAAATATTTAATTCAAA
CTCGCACTAGAATTTTCTGTTTCTG
Found at i:3166994 original size:13 final size:13
Alignment explanation
Indices: 3166976--3167002 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
3166966 AATTTAAAAG
3166976 TTAGATATGATTA
1 TTAGATATGATTA
3166989 TTAGATATGATTA
1 TTAGATATGATTA
3167002 T
1 T
3167003 ATAATAAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.00, G:0.15, T:0.48
Consensus pattern (13 bp):
TTAGATATGATTA
Found at i:3179731 original size:20 final size:20
Alignment explanation
Indices: 3179703--3179742 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
3179693 ACGTTATCGC
* *
3179703 ATAATTTTTTTAATTTTTTT
1 ATAAATTTTATAATTTTTTT
3179723 ATAAATTTTATAATTTTTTT
1 ATAAATTTTATAATTTTTTT
3179743 TATTCTTAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (20 bp):
ATAAATTTTATAATTTTTTT
Found at i:3180115 original size:39 final size:37
Alignment explanation
Indices: 3180039--3180130 Score: 114
Period size: 39 Copynumber: 2.4 Consensus size: 37
3180029 GCATTTAATT
* * *
3180039 AAAT-TTTTTAAATTTTAAAAATTATAAAAATTCAAAA
1 AAATATTTTTAAA-ATTAAAAATCATAAAAATTAAAAA
*
3180076 AAATATTTTTAAAATTAAAAATCATTAAAATTATAAAAA
1 AAATATTTTTAAAATTAAAAATCA-TAAAAAT-TAAAAA
3180115 AAATATTTTTAAAATT
1 AAATATTTTTAAAATT
3180131 TTAAAAATTA
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
37 13 0.27
38 14 0.29
39 21 0.44
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (37 bp):
AAATATTTTTAAAATTAAAAATCATAAAAATTAAAAA
Found at i:3183476 original size:18 final size:18
Alignment explanation
Indices: 3183450--3183502 Score: 79
Period size: 18 Copynumber: 2.9 Consensus size: 18
3183440 TTGGTTAAAA
* *
3183450 ATTAACCGAGTTAACCGG
1 ATTACCCGAATTAACCGG
3183468 ATTACCCGAATTAACCGG
1 ATTACCCGAATTAACCGG
*
3183486 ATTACCCAAATTAACCG
1 ATTACCCGAATTAACCG
3183503 AATTGAATCA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 32 1.00
ACGTcount: A:0.36, C:0.26, G:0.15, T:0.23
Consensus pattern (18 bp):
ATTACCCGAATTAACCGG
Found at i:3183506 original size:9 final size:9
Alignment explanation
Indices: 3183449--3183506 Score: 62
Period size: 9 Copynumber: 6.4 Consensus size: 9
3183439 TTTGGTTAAA
3183449 AATTAACCG
1 AATTAACCG
*
3183458 AGTTAACCG
1 AATTAACCG
* *
3183467 GATTACCCG
1 AATTAACCG
3183476 AATTAACCG
1 AATTAACCG
* * *
3183485 GATTACCCA
1 AATTAACCG
3183494 AATTAACCG
1 AATTAACCG
3183503 AATT
1 AATT
3183507 GAATCACTAC
Statistics
Matches: 37, Mismatches: 12, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
9 37 1.00
ACGTcount: A:0.38, C:0.24, G:0.14, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:3183735 original size:107 final size:107
Alignment explanation
Indices: 3183621--3183824 Score: 399
Period size: 107 Copynumber: 1.9 Consensus size: 107
3183611 GAGTTGGGTA
*
3183621 ATTGGGTTGGGTTGAATACTTGAGTTTGGATTGGGTTTAGGTGAATAATGGGCCTATTTATATAT
1 ATTGGGTTGGGTTGAATACTTGAGTTTGGATTGAGTTTAGGTGAATAATGGGCCTATTTATATAT
3183686 TATAATTTTATTTATTAATTTTTTCGGTTAACTGAATTTATG
66 TATAATTTTATTTATTAATTTTTTCGGTTAACTGAATTTATG
3183728 ATTGGGTTGGGTTGAATACTTGAGTTTGGATTGAGTTTAGGTGAATAATGGGCCTATTTATATAT
1 ATTGGGTTGGGTTGAATACTTGAGTTTGGATTGAGTTTAGGTGAATAATGGGCCTATTTATATAT
3183793 TATAATTTTATTTATTAATTTTTTCGGTTAAC
66 TATAATTTTATTTATTAATTTTTTCGGTTAAC
3183825 CGACCGGTTT
Statistics
Matches: 96, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
107 96 1.00
ACGTcount: A:0.25, C:0.05, G:0.22, T:0.48
Consensus pattern (107 bp):
ATTGGGTTGGGTTGAATACTTGAGTTTGGATTGAGTTTAGGTGAATAATGGGCCTATTTATATAT
TATAATTTTATTTATTAATTTTTTCGGTTAACTGAATTTATG
Found at i:3184619 original size:3 final size:3
Alignment explanation
Indices: 3184611--3184675 Score: 58
Period size: 3 Copynumber: 21.7 Consensus size: 3
3184601 CGAAGAGGAA
* * * * * * * *
3184611 GAC GAC GAC GAC GAC GAC GAG GAT GAT GAA GGC GAA GAT GGC GAC GAC
1 GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC GAC
3184659 GAC GAC GAC GAC GAC GA
1 GAC GAC GAC GAC GAC GA
3184676 AGGAGAGGAG
Statistics
Matches: 51, Mismatches: 11, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.34, C:0.23, G:0.38, T:0.05
Consensus pattern (3 bp):
GAC
Found at i:3184779 original size:12 final size:12
Alignment explanation
Indices: 3184764--3184838 Score: 69
Period size: 12 Copynumber: 6.2 Consensus size: 12
3184754 GGATGTTAAA
*
3184764 GACGATGATGAC
1 GACGACGATGAC
* * *
3184776 GACGATGAAGGC
1 GACGACGATGAC
* *
3184788 GACGGCGATGGC
1 GACGACGATGAC
*
3184800 GATGACGATGAC
1 GACGACGATGAC
* *
3184812 GATGACGACGAC
1 GACGACGATGAC
3184824 GACGACGATGAC
1 GACGACGATGAC
3184836 GAC
1 GAC
3184839 AGTGATGAAG
Statistics
Matches: 52, Mismatches: 11, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 52 1.00
ACGTcount: A:0.31, C:0.21, G:0.37, T:0.11
Consensus pattern (12 bp):
GACGACGATGAC
Found at i:3184816 original size:6 final size:6
Alignment explanation
Indices: 3184793--3184837 Score: 63
Period size: 6 Copynumber: 7.5 Consensus size: 6
3184783 AAGGCGACGG
* * *
3184793 CGATGG CGATGA CGATGA CGATGA CGACGA CGACGA CGATGA CGA
1 CGATGA CGATGA CGATGA CGATGA CGATGA CGATGA CGATGA CGA
3184838 CAGTGATGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
6 36 1.00
ACGTcount: A:0.31, C:0.22, G:0.36, T:0.11
Consensus pattern (6 bp):
CGATGA
Found at i:3184838 original size:18 final size:18
Alignment explanation
Indices: 3184787--3184838 Score: 68
Period size: 18 Copynumber: 2.9 Consensus size: 18
3184777 ACGATGAAGG
* * *
3184787 CGACGGCGATGGCGATGA
1 CGACGACGATGACGACGA
*
3184805 CGATGACGATGACGACGA
1 CGACGACGATGACGACGA
3184823 CGACGACGATGACGAC
1 CGACGACGATGACGAC
3184839 AGTGATGAAG
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
18 29 1.00
ACGTcount: A:0.29, C:0.25, G:0.37, T:0.10
Consensus pattern (18 bp):
CGACGACGATGACGACGA
Found at i:3185851 original size:11 final size:11
Alignment explanation
Indices: 3185835--3185859 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
3185825 GGTGTGTTAG
3185835 AAAAAACAAAA
1 AAAAAACAAAA
3185846 AAAAAACAAAA
1 AAAAAACAAAA
3185857 AAA
1 AAA
3185860 GTAGAAAGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.92, C:0.08, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAACAAAA
Found at i:3186143 original size:3 final size:3
Alignment explanation
Indices: 3186135--3186169 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
3186125 TTTTTGCATC
3186135 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
1 ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG ATG AT
3186170 AGCCATTTAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.31, T:0.34
Consensus pattern (3 bp):
ATG
Found at i:3193161 original size:60 final size:59
Alignment explanation
Indices: 3193080--3193256 Score: 187
Period size: 61 Copynumber: 2.9 Consensus size: 59
3193070 CGAAATTGAA
** *
3193080 TCCAAAAAAAAGCTTGGGTACCAAATTAGAAAAAAATGGCATGTTCAAGTACCAAATTTGG
1 TCCAAAAAAAAG-TTCAGTACCAAATTAGAAAAAAATGGCAAGTTCAAGTACCAAA-TTGG
* *
3193141 TCCAAAAAAAAGTTCAGTACCAAATTTTA-AAAAAAATGGCAAGTTCAGGTACCTAATTGG
1 TCCAAAAAAAAGTTCAGTACCAAA--TTAGAAAAAAATGGCAAGTTCAAGTACCAAATTGG
* * * * *
3193201 -GCAAAAAAAATTTTAGATACCAAATTAGAAAAAAAAGTGTCAAGTTCAAGAACCAA
1 TCCAAAAAAAAGTTCAG-TACCAAATTAG-AAAAAAA-TGGCAAGTTCAAGTACCAA
3193257 TGTTATATTA
Statistics
Matches: 98, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
58 3 0.03
59 13 0.13
60 28 0.29
61 51 0.52
62 3 0.03
ACGTcount: A:0.48, C:0.14, G:0.15, T:0.23
Consensus pattern (59 bp):
TCCAAAAAAAAGTTCAGTACCAAATTAGAAAAAAATGGCAAGTTCAAGTACCAAATTGG
Found at i:3193188 original size:31 final size:31
Alignment explanation
Indices: 3193097--3193198 Score: 81
Period size: 31 Copynumber: 3.3 Consensus size: 31
3193087 AAAAGCTTGG
*
3193097 GTACCAAA--TTAGAAAAAAATGGCATGTTCAA
1 GTACCAAATTTTA-AAAAAAATGGCAAGTTC-A
**
3193128 GTACCAAATTTGGTCCAAAAAA----AAGTTCA
1 GTACCAAATTT--TAAAAAAAATGGCAAGTTCA
3193157 GTACCAAATTTTAAAAAAAATGGCAAGTTCA
1 GTACCAAATTTTAAAAAAAATGGCAAGTTCA
*
3193188 GGTACCTAATT
1 -GTACCAAATT
3193199 GGGCAAAAAA
Statistics
Matches: 56, Mismatches: 6, Indels: 17
0.71 0.08 0.22
Matches are distributed among these distances:
27 7 0.12
29 12 0.21
30 5 0.09
31 15 0.27
32 9 0.16
33 1 0.02
34 6 0.11
35 1 0.02
ACGTcount: A:0.45, C:0.15, G:0.15, T:0.25
Consensus pattern (31 bp):
GTACCAAATTTTAAAAAAAATGGCAAGTTCA
Found at i:3199010 original size:14 final size:14
Alignment explanation
Indices: 3198991--3199018 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
3198981 GGCCTGTGAT
3198991 TCAAGATTTTAAAC
1 TCAAGATTTTAAAC
3199005 TCAAGATTTTAAAC
1 TCAAGATTTTAAAC
3199019 AACTAAGAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.43, C:0.14, G:0.07, T:0.36
Consensus pattern (14 bp):
TCAAGATTTTAAAC
Found at i:3202645 original size:2 final size:2
Alignment explanation
Indices: 3202638--3202669 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
3202628 CATTTGACTC
3202638 CT 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 CT
3202670 TAATACTTTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
CT
Found at i:3215692 original size:11 final size:11
Alignment explanation
Indices: 3215672--3215708 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
3215662 AGCCCTGCCC
*
3215672 ATATTAAATAT
1 ATATTTAATAT
3215683 ATATTTAATAT
1 ATATTTAATAT
3215694 ATA--TAATAT
1 ATATTTAATAT
3215703 ATATTT
1 ATATTT
3215709 GATTAAAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
9 9 0.39
11 14 0.61
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (11 bp):
ATATTTAATAT
Found at i:3221174 original size:9 final size:9
Alignment explanation
Indices: 3221157--3221187 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
3221147 TCGAGTTGAT
3221157 TCGAATAAC
1 TCGAATAAC
*
3221166 TCGATTAAC
1 TCGAATAAC
3221175 TCGAATAAC
1 TCGAATAAC
3221184 TCGA
1 TCGA
3221188 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:3222986 original size:29 final size:29
Alignment explanation
Indices: 3222945--3223028 Score: 80
Period size: 31 Copynumber: 2.8 Consensus size: 29
3222935 ATAAATTTCA
3222945 AAAT-TACACATGAACTTTGATTTGGTGC
1 AAATATACACATGAACTTTGATTTGGTGC
* * *
3222973 AATTATACACATGAAACCTTGATTGTGGTTC
1 AAATATACACATG-AACTTTGATT-TGGTGC
* * *
3223004 AAATATATATATGAAGCTTTAATTT
1 AAATATACACATGAA-CTTTGATTT
3223029 CAATTAAATC
Statistics
Matches: 44, Mismatches: 8, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
28 3 0.07
29 8 0.18
30 12 0.27
31 21 0.48
ACGTcount: A:0.36, C:0.12, G:0.14, T:0.38
Consensus pattern (29 bp):
AAATATACACATGAACTTTGATTTGGTGC
Found at i:3226661 original size:48 final size:48
Alignment explanation
Indices: 3226579--3226671 Score: 136
Period size: 48 Copynumber: 1.9 Consensus size: 48
3226569 TTTCTTGGCT
* *
3226579 TAAAAACGCCTAAGTCAGCCTAACTTCCACCAATAATGGATTCAATCG
1 TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAATCG
3226627 TAAAAACGCCTAAGTCAG-CTCAAC-TCGCAACAATAAAGGATTCAA
1 TAAAAACGCCTAAGTCAGCCT-AACTTC-CAACAATAAAGGATTCAA
3226672 CAGAATTCCC
Statistics
Matches: 41, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
47 4 0.10
48 37 0.90
ACGTcount: A:0.41, C:0.26, G:0.13, T:0.20
Consensus pattern (48 bp):
TAAAAACGCCTAAGTCAGCCTAACTTCCAACAATAAAGGATTCAATCG
Found at i:3227995 original size:19 final size:19
Alignment explanation
Indices: 3227959--3227994 Score: 58
Period size: 18 Copynumber: 2.0 Consensus size: 19
3227949 ATGAACTTTA
3227959 TTTTATTTTATTTATATAT
1 TTTTATTTTATTTATATAT
3227978 TTTTA-TTTATTTA-ATAT
1 TTTTATTTTATTTATATAT
3227995 AAAAAAAGTC
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 4 0.24
18 8 0.47
19 5 0.29
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTTATTTTATTTATATAT
Found at i:3235198 original size:4 final size:4
Alignment explanation
Indices: 3235189--3235215 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
3235179 AAGTAAAGTA
3235189 AAAT AAAT AAAT AAAT AAAT AAAT AAA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAA
3235216 AAGAAAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.78, C:0.00, G:0.00, T:0.22
Consensus pattern (4 bp):
AAAT
Found at i:3236032 original size:20 final size:21
Alignment explanation
Indices: 3236007--3236045 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 21
3235997 AATGGAAAAT
3236007 AAAGAA-A-AAAAATAAAGTTA
1 AAAGAACATAAAAA-AAAGTTA
3236027 AAAGAACATAAAAAAAAGT
1 AAAGAACATAAAAAAAAGT
3236046 GCTCAAAATA
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:0.74, C:0.03, G:0.10, T:0.13
Consensus pattern (21 bp):
AAAGAACATAAAAAAAAGTTA
Found at i:3236173 original size:16 final size:16
Alignment explanation
Indices: 3236149--3236182 Score: 59
Period size: 16 Copynumber: 2.1 Consensus size: 16
3236139 CTTATCATTA
*
3236149 TACCGTTAAGGGCAAT
1 TACCATTAAGGGCAAT
3236165 TACCATTAAGGGCAAT
1 TACCATTAAGGGCAAT
3236181 TA
1 TA
3236183 ATAGCTCAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.35, C:0.18, G:0.21, T:0.26
Consensus pattern (16 bp):
TACCATTAAGGGCAAT
Found at i:3238247 original size:10 final size:10
Alignment explanation
Indices: 3238228--3238257 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
3238218 ATTTTACTAT
3238228 TATATATATG
1 TATATATATG
*
3238238 TATATGTATG
1 TATATATATG
3238248 TATATATATG
1 TATATATATG
3238258 CTTCAGTTTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (10 bp):
TATATATATG
Found at i:3246847 original size:19 final size:20
Alignment explanation
Indices: 3246837--3246873 Score: 67
Period size: 19 Copynumber: 1.9 Consensus size: 20
3246827 TAATTAATAA
3246837 TTATAAAAAT-ATAAAAAAT
1 TTATAAAAATAATAAAAAAT
3246856 TTATAAAAATAATAAAAA
1 TTATAAAAATAATAAAAA
3246874 CATATTTAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (20 bp):
TTATAAAAATAATAAAAAAT
Found at i:3247513 original size:28 final size:28
Alignment explanation
Indices: 3247471--3247553 Score: 91
Period size: 28 Copynumber: 2.9 Consensus size: 28
3247461 AAATTCAAGT
3247471 TTTTATGATTTTTTTTATAAGTTTATATAA
1 TTTTATGA--TTTTTTATAAGTTTATATAA
*
3247501 TTTTA--ATGTTTTTATTAA-TTTTTAATAA
1 TTTTATGAT-TTTTTA-TAAGTTTAT-ATAA
3247529 TTTTATGATTTTTTATAAGTTTATA
1 TTTTATGATTTTTTATAAGTTTATA
3247554 AGAATGTTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 14
0.74 0.03 0.23
Matches are distributed among these distances:
26 1 0.02
27 10 0.22
28 17 0.38
29 10 0.22
30 7 0.16
ACGTcount: A:0.30, C:0.00, G:0.06, T:0.64
Consensus pattern (28 bp):
TTTTATGATTTTTTATAAGTTTATATAA
Found at i:3247532 original size:19 final size:19
Alignment explanation
Indices: 3247481--3247552 Score: 58
Period size: 19 Copynumber: 3.8 Consensus size: 19
3247471 TTTTATGATT
*
3247481 TTTTTTATAAGTTTATATAA
1 TTTTTAATAAGTTTAT-TAA
***
3247501 -TTTTAATGTTTTTATTAA
1 TTTTTAATAAGTTTATTAA
* *
3247519 TTTTTAATAATTTTA-TGA
1 TTTTTAATAAGTTTATTAA
*
3247537 TTTTTTATAAGTTTAT
1 TTTTTAATAAGTTTAT
3247553 AAGAATGTTA
Statistics
Matches: 41, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
18 18 0.44
19 23 0.56
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.64
Consensus pattern (19 bp):
TTTTTAATAAGTTTATTAA
Found at i:3247539 original size:18 final size:18
Alignment explanation
Indices: 3247518--3247552 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
3247508 GTTTTTATTA
*
3247518 ATTTTTAATAATTTTATG
1 ATTTTTAATAAGTTTATG
*
3247536 ATTTTTTATAAGTTTAT
1 ATTTTTAATAAGTTTAT
3247553 AAGAATGTTA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (18 bp):
ATTTTTAATAAGTTTATG
Found at i:3247570 original size:29 final size:28
Alignment explanation
Indices: 3247482--3247575 Score: 95
Period size: 29 Copynumber: 3.3 Consensus size: 28
3247472 TTTATGATTT
3247482 TTTTTATAAGTTTAT-ATAATTTTA-ATG
1 TTTTTATAAGTTTATAATAATTTTATA-G
* *
3247509 TTTTTATTAA-TTTTTAATAATTTTATGAT
1 TTTTTA-TAAGTTTATAATAATTTTAT-AG
* *
3247538 TTTTTATAAGTTTATAAGAATGTTATACG
1 TTTTTATAAGTTTATAATAATTTTATA-G
3247567 TTTTTATAA
1 TTTTTATAA
3247576 AATTTTAGAT
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
27 10 0.18
28 16 0.29
29 28 0.51
30 1 0.02
ACGTcount: A:0.33, C:0.01, G:0.07, T:0.59
Consensus pattern (28 bp):
TTTTTATAAGTTTATAATAATTTTATAG
Found at i:3247608 original size:19 final size:19
Alignment explanation
Indices: 3247492--3247636 Score: 75
Period size: 19 Copynumber: 7.5 Consensus size: 19
3247482 TTTTTATAAG
3247492 TTTATATAATTT-TAATGTT
1 TTTATATAATTTATAAT-TT
* *
3247511 TTTAT-TAATTTTTAATAAT
1 TTTATATAATTTATAAT-TT
** *
3247530 TTTATGATTTTTTATAAGTT
1 TTTAT-ATAATTTATAATTT
* * **
3247550 TATA-AGAATGTTATACGTT
1 TTTATATAAT-TTATAATTT
* *
3247569 TTTATAAAATTTTAGATATTT
1 TTTATATAA-TTTATA-ATTT
3247590 TTTAT-TAATTCTATAATTT
1 TTTATATAATT-TATAATTT
* *
3247609 TTTTTATAATTTATTATTT
1 TTTATATAATTTATAATTT
3247628 TTT-TATAAT
1 TTTATATAAT
3247637 ATTTATAAGT
Statistics
Matches: 96, Mismatches: 21, Indels: 19
0.71 0.15 0.14
Matches are distributed among these distances:
18 14 0.15
19 46 0.48
20 21 0.22
21 15 0.16
ACGTcount: A:0.32, C:0.01, G:0.05, T:0.61
Consensus pattern (19 bp):
TTTATATAATTTATAATTT
Found at i:3247628 original size:18 final size:20
Alignment explanation
Indices: 3247587--3247636 Score: 68
Period size: 18 Copynumber: 2.5 Consensus size: 20
3247577 ATTTTAGATA
3247587 TTTTTTATTAATTCTATAATT
1 TTTTTTA-TAATTCTATAATT
*
3247608 TTTTTTATAATT-TATTA-T
1 TTTTTTATAATTCTATAATT
3247626 TTTTTTATAAT
1 TTTTTTATAAT
3247637 ATTTATAAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 12 0.43
19 4 0.14
20 5 0.18
21 7 0.25
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (20 bp):
TTTTTTATAATTCTATAATT
Found at i:3247792 original size:7 final size:7
Alignment explanation
Indices: 3247768--3247817 Score: 73
Period size: 7 Copynumber: 6.9 Consensus size: 7
3247758 ATTAAAATAA
3247768 ATTTTAT
1 ATTTTAT
3247775 ATTTTTAAT
1 A-TTTT-AT
3247784 ATTTTAT
1 ATTTTAT
3247791 ATTTTAT
1 ATTTTAT
3247798 ATTTTAT
1 ATTTTAT
3247805 ATTTTAT
1 ATTTTAT
*
3247812 AATTTA
1 ATTTTA
3247818 AAACAAGTTA
Statistics
Matches: 40, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
7 29 0.73
8 8 0.20
9 3 0.08
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (7 bp):
ATTTTAT
Done.