Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr11 124536837
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: 124536837
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 312 characters in sequence are not A, C, G, or T
File 19 of 427
Found at i:5225097 original size:30 final size:31
Alignment explanation
Indices: 5225036--5225098 Score: 94
Period size: 30 Copynumber: 2.1 Consensus size: 31
5225026 ATATGAGATA
5225036 AGTCTTTGTATTTTTTTCAAATTTGAAATTT
1 AGTCTTTGTATTTTTTTCAAATTTGAAATTT
*
5225067 AGTCTTTGTA-TTTTTT-AAATTTCGAGATTT
1 AGTCTTTGTATTTTTTTCAAATTT-GAAATTT
5225097 AG
1 AG
5225099 GTTCAATGGT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
29 6 0.20
30 14 0.47
31 10 0.33
ACGTcount: A:0.25, C:0.06, G:0.13, T:0.56
Consensus pattern (31 bp):
AGTCTTTGTATTTTTTTCAAATTTGAAATTT
Found at i:5225195 original size:2 final size:2
Alignment explanation
Indices: 5225188--5225214 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5225178 CAAGTGAGTT
5225188 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
5225215 TTAAATTACC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5230379 original size:2 final size:2
Alignment explanation
Indices: 5230368--5230402 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
5230358 AACAAAAAGA
5230368 AT AT -T 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
5230403 GCAGTAGCGA
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:5235135 original size:299 final size:292
Alignment explanation
Indices: 5234508--5235482 Score: 1086
Period size: 299 Copynumber: 3.3 Consensus size: 292
5234498 TAAAAGTAAC
* * * * *
5234508 GGAGATAATAACTTATGCATATTAAAAATGAAAATGTATAAATTAGAATAAAATGAAGTTTTGGT
1 GGAGATAATAACTTGTGCATATT-AAAAT-AAAATGTATAAAATATATTAAAATAAAGTTTTGGT
* * *
5234573 TGATTGGTAAAATTAA-AGTTTTGCTAACTCAATTAGTGTGGGTTCAAATCCTACTATATGCATA
64 TGAGTGGTAAATTTAATA-TTTT-CTAATTCAATTAGTGT-GGTTCAAATCC-ACTATATGCATA
* * * **
5234637 TTTTAATTTGTTTTTGTTAAAAAGAAAATACTAAAATACTCTTTAATAGTATAACTTATTTTAAT
125 TTTTAATTTGTTTTTGTTAAAATGAAAAGACTAAAATACCCTCAAATAGTATAACTTATTTTAAT
* * * ** * *
5234702 TATGAAAAGGTATTTTTGTAATTTTTTAACCGAGTTGGTGACCCAATTGAATGTGACAGCAATTT
190 TA-CAAAAGGCATTTTTGTAATTTCTTAACCGAGTTGGTGA-CCAATTGAGGGTGACACCAACTT
* *
5234767 AGTAAAACGCTTAAT-AATATTAACTATAGATATACAACTAT
253 AGTAAAACACTTAATAAATAGTAA-TATA-ATATACAACTAT
*
5234808 GGGAGATAATAACTTGTGCAAATTAAAATAAAATTGTATAAAATATATTAAAATAAAGTTTTGGT
1 -GGAGATAATAACTTGTGCATATTAAAATAAAA-TGTATAAAATATATTAAAATAAAGTTTTGGT
* * * * * *
5234873 TAAGTGGTAAATTTAATATTTTACAAATTTAATTGGGGTAGGTTCAAATTCCACTATGTGCATAT
64 TGAGTGGTAAATTTAATATTTT-CTAATTCAATTAGTGT-GGTTCAAA-TCCACTATATGCATAT
* *
5234938 TTTAATTTATTTTTGTTAAAATGAAAAGA-TAAAATACCCTCAAATAGTATAAGTTATTTTAATT
126 TTTAATTTGTTTTTGTTAAAATGAAAAGACTAAAATACCCTCAAATAGTATAACTTATTTTAATT
* ** * * * * *
5235002 ACAAAATGCATTTTTGTAATTTCTTAATTGATTTGGTGACTCGATCGAGGGTGACACCAACATAA
191 ACAAAAGGCATTTTTGTAATTTCTTAACCGAGTTGGTGAC-CAATTGAGGGTGACACCAACTTAG
5235067 TAAAACACTTAATAAATAGTAAGTATAAATATACAACTAGT
255 TAAAACACTTAATAAATAGTAA-TAT-AATATACAACTA-T
* * *
5235108 GGAGATAGTAATTTGTGCATTTTAAAATAAAAATGTATAAAATATATTAAAATGAAA-TTTTGGT
1 GGAGATAATAACTTGTGCATATTAAAAT-AAAATGTATAAAATATATTAAAAT-AAAGTTTTGGT
* * * * *
5235172 TGAGTGATAAATTTAAGATTTTTTAATCCAATTTGTGTGAGTTCAAATCTCAC-ATATGCATATT
64 TGAGTGGTAAATTTAATATTTTCTAATTCAATTAGTGTG-GTTCAAATC-CACTATATGCATATT
*
5235236 TTAATTTGTTTTTGTTAAAATGAAAAGACTAAAATACCCTCAAACAGTATAACTTATTTTAATTA
127 TTAATTTGTTTTTGTTAAAATGAAAAGACTAAAATACCCTCAAATAGTATAACTTATTTTAATTA
* * * *
5235301 CGAAAGGACATTTTTATAATTTCCTAACCGAGTTGGTGACCTAGTTGAGGGTGACACCAACTTAG
192 CAAAAGG-CATTTTTGTAATTTCTTAACCGAGTTGGTGACC-AATTGAGGGTGACACCAACTTAG
*
5235366 TAAAATACTTAATAAATAGT-ATAGT--TATACAACTAAT
255 TAAAACACTTAATAAATAGTAATA-TAATATACAACT-AT
* * * * * ** *
5235403 GAAGAGAACAACTTGTGCCTATTAAAATACAAAAGTATAAAATATATTAAAAT-AAGGCTTAGTT
1 GGAGATAATAACTTGTGCATATTAAAATA-AAATGTATAAAATATATTAAAATAAAGTTTTGGTT
5235467 GAGTGGTAAATTTAAT
65 GAGTGGTAAATTTAAT
5235483 GTAACACCCC
Statistics
Matches: 571, Mismatches: 85, Indels: 43
0.82 0.12 0.06
Matches are distributed among these distances:
293 2 0.00
294 20 0.04
295 53 0.09
296 1 0.00
297 43 0.08
298 121 0.21
299 191 0.33
300 115 0.20
301 25 0.04
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (292 bp):
GGAGATAATAACTTGTGCATATTAAAATAAAATGTATAAAATATATTAAAATAAAGTTTTGGTTG
AGTGGTAAATTTAATATTTTCTAATTCAATTAGTGTGGTTCAAATCCACTATATGCATATTTTAA
TTTGTTTTTGTTAAAATGAAAAGACTAAAATACCCTCAAATAGTATAACTTATTTTAATTACAAA
AGGCATTTTTGTAATTTCTTAACCGAGTTGGTGACCAATTGAGGGTGACACCAACTTAGTAAAAC
ACTTAATAAATAGTAATATAATATACAACTAT
Found at i:5235812 original size:18 final size:19
Alignment explanation
Indices: 5235791--5235832 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
5235781 GGAAGTTCCC
5235791 TTTTCTTCT-TTTC-TTTCT
1 TTTTC-TCTGTTTCTTTTCT
5235809 TTTTCTCTGTTTCTTTTCT
1 TTTTCTCTGTTTCTTTTCT
5235828 TTTTC
1 TTTTC
5235833 CTTTGAAAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 3 0.14
18 9 0.41
19 10 0.45
ACGTcount: A:0.00, C:0.21, G:0.02, T:0.76
Consensus pattern (19 bp):
TTTTCTCTGTTTCTTTTCT
Found at i:5236429 original size:21 final size:20
Alignment explanation
Indices: 5236392--5236430 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
5236382 GGGATTTATG
* *
5236392 GATCCCACACGAGCGTGTAA
1 GATCCCACACAACCGTGTAA
5236412 GATCCTCACACAACCGTGT
1 GATCC-CACACAACCGTGT
5236431 CAGTCCTGTA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.28, C:0.33, G:0.21, T:0.18
Consensus pattern (20 bp):
GATCCCACACAACCGTGTAA
Found at i:5236898 original size:181 final size:181
Alignment explanation
Indices: 5236594--5236955 Score: 688
Period size: 181 Copynumber: 2.0 Consensus size: 181
5236584 TTCTATTCAG
*
5236594 CTGTTTGGTCCTAAGTCACCAATTTTAGTTTATGTATGTTTTTTATTTGAAAATGCGTCTGTGTA
1 CTGTTTGGTCCTAAGTCACCAATTTTAGTTTATGTATGTTTTTTATCTGAAAATGCGTCTGTGTA
*
5236659 TTCCGACCCTTGGCTAGACTTTAGTGAGGGTAACTAAGTCTCTATATCTATGGCTATGTGTTCTG
66 TTCCGACCCTTGGCTAGACTTTAGTGAGGGTAACTAAGTCTCTATATATATGGCTATGTGTTCTG
5236724 TTAATGTGTAATTCGTGACTGTTGTGGGTGAGATGTCTGTTTTCTGAACCC
131 TTAATGTGTAATTCGTGACTGTTGTGGGTGAGATGTCTGTTTTCTGAACCC
* *
5236775 CTGTTTGGTCCTAAGTCACCACTTTTAGTTTGTGTATGTTTTTTATCTGAAAATGCGTCTGTGTA
1 CTGTTTGGTCCTAAGTCACCAATTTTAGTTTATGTATGTTTTTTATCTGAAAATGCGTCTGTGTA
5236840 TTCCGACCCTTGGCTAGACTTTAGTGAGGGTAACTAAGTCTCTATATATATGGCTATGTGTTCTG
66 TTCCGACCCTTGGCTAGACTTTAGTGAGGGTAACTAAGTCTCTATATATATGGCTATGTGTTCTG
5236905 TTAATGTGTAATTCGTGACTGTTGTGGGTGAGATGTCTGTTTTCTGAACCC
131 TTAATGTGTAATTCGTGACTGTTGTGGGTGAGATGTCTGTTTTCTGAACCC
5236956 GATTAGCTGG
Statistics
Matches: 177, Mismatches: 4, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
181 177 1.00
ACGTcount: A:0.20, C:0.16, G:0.23, T:0.42
Consensus pattern (181 bp):
CTGTTTGGTCCTAAGTCACCAATTTTAGTTTATGTATGTTTTTTATCTGAAAATGCGTCTGTGTA
TTCCGACCCTTGGCTAGACTTTAGTGAGGGTAACTAAGTCTCTATATATATGGCTATGTGTTCTG
TTAATGTGTAATTCGTGACTGTTGTGGGTGAGATGTCTGTTTTCTGAACCC
Found at i:5244490 original size:36 final size:37
Alignment explanation
Indices: 5244439--5244517 Score: 99
Period size: 38 Copynumber: 2.2 Consensus size: 37
5244429 AATACAACTC
* * *
5244439 TTTTTAACTAATAATTGT-AATTTAA-ATTCTAATTA
1 TTTTTAAATAATAATTGTAAATTAAATATTATAATTA
*
5244474 TTTTTAAATAAATAATTTTAAATTAAATATTATAATTA
1 TTTTTAAAT-AATAATTGTAAATTAAATATTATAATTA
5244512 TTTTTA
1 TTTTTA
5244518 TATGTAAAAT
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
35 8 0.22
36 8 0.22
37 6 0.16
38 15 0.41
ACGTcount: A:0.43, C:0.03, G:0.01, T:0.53
Consensus pattern (37 bp):
TTTTTAAATAATAATTGTAAATTAAATATTATAATTA
Found at i:5244602 original size:2 final size:2
Alignment explanation
Indices: 5244595--5244627 Score: 59
Period size: 2 Copynumber: 17.0 Consensus size: 2
5244585 CGTGCTTATT
5244595 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5244628 GATGAAGAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 29 0.97
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5250047 original size:23 final size:24
Alignment explanation
Indices: 5250006--5250053 Score: 64
Period size: 23 Copynumber: 2.0 Consensus size: 24
5249996 TTTTTTTAAA
*
5250006 AATATTTATATTATTTTTT-ATTT
1 AATATTTATAATATTTTTTCATTT
5250029 AATATTTAATAAT-TTTTTTCATTT
1 AATATTT-ATAATATTTTTTCATTT
5250053 A
1 A
5250054 TTAAAATGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
23 13 0.59
24 9 0.41
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (24 bp):
AATATTTATAATATTTTTTCATTT
Found at i:5252754 original size:46 final size:44
Alignment explanation
Indices: 5252650--5252757 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
5252640 TATCTTTGAC
** * * *
5252650 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
5252694 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
5252740 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
5252758 TTTCGTTCTG
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:5253902 original size:2 final size:2
Alignment explanation
Indices: 5253895--5253920 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5253885 ATAATAATAA
5253895 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
5253921 TTTACCCTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5254791 original size:30 final size:30
Alignment explanation
Indices: 5254750--5254808 Score: 84
Period size: 31 Copynumber: 2.0 Consensus size: 30
5254740 TAAATCCATG
5254750 TTATTTTATACAT-ATAATTTCTTTTAAAT
1 TTATTTTATACATCATAATTTCTTTTAAAT
* *
5254779 TTATTTGTATACATCATTATTTTTTTTAAA
1 TTATTT-TATACATCATAATTTCTTTTAAA
5254809 ATCTATTACA
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 6 0.23
30 7 0.27
31 13 0.50
ACGTcount: A:0.32, C:0.07, G:0.02, T:0.59
Consensus pattern (30 bp):
TTATTTTATACATCATAATTTCTTTTAAAT
Found at i:5257684 original size:34 final size:34
Alignment explanation
Indices: 5257587--5257686 Score: 128
Period size: 34 Copynumber: 2.9 Consensus size: 34
5257577 GTTTCAGTTA
* * * *
5257587 GGGCCTTAGCCCATTTCAATAACAGTAGCAGTTT
1 GGGCCTAAGCCCATTTCAGTAACAGTATCAGTCT
* *
5257621 GGGCCTAAGCCTATTTTAGTAACAGTATCAGTCT
1 GGGCCTAAGCCCATTTCAGTAACAGTATCAGTCT
* *
5257655 GGGCCTGAGCCCATTTCAGTAACAATATCAGT
1 GGGCCTAAGCCCATTTCAGTAACAGTATCAGT
5257687 GAGGCCTATG
Statistics
Matches: 56, Mismatches: 10, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 56 1.00
ACGTcount: A:0.27, C:0.23, G:0.21, T:0.29
Consensus pattern (34 bp):
GGGCCTAAGCCCATTTCAGTAACAGTATCAGTCT
Found at i:5258465 original size:2 final size:2
Alignment explanation
Indices: 5258458--5258513 Score: 85
Period size: 2 Copynumber: 28.0 Consensus size: 2
5258448 TGATAGTGTT
* * *
5258458 AC AC AC AC AC AC GC AC AC GC AC AC AC AC AC AC GC AC AC AC AC
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC
5258500 AC AC AC AC AC AC AC
1 AC AC AC AC AC AC AC
5258514 CCCCTATTAT
Statistics
Matches: 48, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.45, C:0.50, G:0.05, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5260015 original size:164 final size:164
Alignment explanation
Indices: 5259744--5260067 Score: 621
Period size: 164 Copynumber: 2.0 Consensus size: 164
5259734 ATTTCCAGAG
*
5259744 CACATAACCACTAAGCCAGACATACTTTCACGTCACAAACATACACAAATAATTTTATCAGAGAT
1 CACATAACCACTAAGCCAGACATACTTTCACGTCACAAACATACACAAATAATTTTAGCAGAGAT
5259809 TTTGAGATTTAGGGCGTTACAGATTCAATGACTATTTTGTAATTTTTTGATAGGTGGGAGATTCA
66 TTTGAGATTTAGGGCGTTACAGATTCAATGACTATTTTGTAATTTTTTGATAGGTGGGAGATTCA
5259874 ACGCTATGTGCATATTTTATTGTAATAGTTAGAA
131 ACGCTATGTGCATATTTTATTGTAATAGTTAGAA
*
5259908 CACATAACCACTAAGCCAGACATACTTTCACGTCACAAACATACACAAGTAATTTTAGCAGAGAT
1 CACATAACCACTAAGCCAGACATACTTTCACGTCACAAACATACACAAATAATTTTAGCAGAGAT
*
5259973 TTTGAGATTTGGGGCGTTACAGATTCAATGACTATTTTGTAATTTTTTGATAGGTGGGAGATTCA
66 TTTGAGATTTAGGGCGTTACAGATTCAATGACTATTTTGTAATTTTTTGATAGGTGGGAGATTCA
5260038 ACGCTATGTGCATATTTTATTGTAATAGTT
131 ACGCTATGTGCATATTTTATTGTAATAGTT
5260068 CTCTAGTACA
Statistics
Matches: 157, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
164 157 1.00
ACGTcount: A:0.33, C:0.15, G:0.17, T:0.34
Consensus pattern (164 bp):
CACATAACCACTAAGCCAGACATACTTTCACGTCACAAACATACACAAATAATTTTAGCAGAGAT
TTTGAGATTTAGGGCGTTACAGATTCAATGACTATTTTGTAATTTTTTGATAGGTGGGAGATTCA
ACGCTATGTGCATATTTTATTGTAATAGTTAGAA
Found at i:5264596 original size:22 final size:22
Alignment explanation
Indices: 5264569--5264634 Score: 78
Period size: 22 Copynumber: 3.0 Consensus size: 22
5264559 CGATTATTAG
5264569 CACATTAGTGCTCTCTGTTTAA
1 CACATTAGTGCTCTCTGTTTAA
* * * *
5264591 CACATTCGTGTTCTCTGTATAG
1 CACATTAGTGCTCTCTGTTTAA
* *
5264613 CACTTTAGTGCTCTTTGTTTAA
1 CACATTAGTGCTCTCTGTTTAA
5264635 TAGTGCATAA
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
22 34 1.00
ACGTcount: A:0.20, C:0.21, G:0.15, T:0.44
Consensus pattern (22 bp):
CACATTAGTGCTCTCTGTTTAA
Found at i:5269292 original size:42 final size:42
Alignment explanation
Indices: 5269245--5269331 Score: 156
Period size: 42 Copynumber: 2.1 Consensus size: 42
5269235 GATTTTTCTA
5269245 TTAATAACAAGTAAATATGACAATGCACATGTAATAATTTAT
1 TTAATAACAAGTAAATATGACAATGCACATGTAATAATTTAT
* *
5269287 TTAATAACAAGTTAATATGACAATGCACATGTGATAATTTAT
1 TTAATAACAAGTAAATATGACAATGCACATGTAATAATTTAT
5269329 TTA
1 TTA
5269332 TCGTGCAAGT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.45, C:0.09, G:0.10, T:0.36
Consensus pattern (42 bp):
TTAATAACAAGTAAATATGACAATGCACATGTAATAATTTAT
Found at i:5275315 original size:13 final size:14
Alignment explanation
Indices: 5275289--5275321 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
5275279 TATTAAATTC
5275289 AAAAAATGAATTTTA
1 AAAAAATG-ATTTTA
5275304 AAAAAATG-TTTTA
1 AAAAAATGATTTTA
5275317 AAAAA
1 AAAAA
5275322 TATACCCATA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.56
15 8 0.44
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (14 bp):
AAAAAATGATTTTA
Found at i:5277552 original size:29 final size:29
Alignment explanation
Indices: 5277502--5277573 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
5277492 CAATTCAATT
** * * *
5277502 TAAATGTTTAAATCATACAAATAAAGAGAC
1 TAAAT-TTTAAAAAATAAAAATAAAAAGAA
*
5277532 TAAATTTTAAAAAATAAAAATAAAAATAA
1 TAAATTTTAAAAAATAAAAATAAAAAGAA
5277561 TAAATTTTAAAAA
1 TAAATTTTAAAAA
5277574 TCTGAAAATT
Statistics
Matches: 36, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 31 0.86
30 5 0.14
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.29
Consensus pattern (29 bp):
TAAATTTTAAAAAATAAAAATAAAAAGAA
Found at i:5278972 original size:126 final size:126
Alignment explanation
Indices: 5278745--5278993 Score: 417
Period size: 126 Copynumber: 2.0 Consensus size: 126
5278735 GAGGTACACG
* *
5278745 TGTAGTTGTCTAGTTATTTCGTCACTCACACTAGTTTTTAACTGTAAAAATGGATGAAATTTTTA
1 TGTAGTTGTCTAGTTATTTCGTCACCCACACTAGTTTTTAACTGTAAAAATAGATGAAATTTTTA
* * *
5278810 ATAGAAATAATCAATTTGTTTTTTAATCTAACGTACATTAACTGATTTGTCTATTTTTACA
66 ATAGAAATAATCAATTTGCTTTTTAATCTAACGTACATTAACTAATTTATCTATTTTTACA
*
5278871 TGTAGTTGTCTAGTTATTTCGTCACCCACGCTAGTTTTTAACTGTAAAAATAGATGAAATTTTTA
1 TGTAGTTGTCTAGTTATTTCGTCACCCACACTAGTTTTTAACTGTAAAAATAGATGAAATTTTTA
* * *
5278936 ATAGAAATGATTAATTTGCTTTTTAATCTAATGTACATTAACTAATTTATCTATTTTT
66 ATAGAAATAATCAATTTGCTTTTTAATCTAACGTACATTAACTAATTTATCTATTTTT
5278994 TAGTAAAAGT
Statistics
Matches: 114, Mismatches: 9, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
126 114 1.00
ACGTcount: A:0.32, C:0.12, G:0.12, T:0.45
Consensus pattern (126 bp):
TGTAGTTGTCTAGTTATTTCGTCACCCACACTAGTTTTTAACTGTAAAAATAGATGAAATTTTTA
ATAGAAATAATCAATTTGCTTTTTAATCTAACGTACATTAACTAATTTATCTATTTTTACA
Found at i:5280387 original size:14 final size:14
Alignment explanation
Indices: 5280370--5280411 Score: 50
Period size: 14 Copynumber: 3.1 Consensus size: 14
5280360 TATAATATTC
5280370 AAATAATAACAACA
1 AAATAATAACAACA
*
5280384 AAATAGTAACAACA
1 AAATAATAACAACA
* *
5280398 TAGTAATAA-AACA
1 AAATAATAACAACA
5280411 A
1 A
5280412 TAAGAAAATA
Statistics
Matches: 23, Mismatches: 5, Indels: 1
0.79 0.17 0.03
Matches are distributed among these distances:
13 4 0.17
14 19 0.83
ACGTcount: A:0.67, C:0.12, G:0.05, T:0.17
Consensus pattern (14 bp):
AAATAATAACAACA
Found at i:5281469 original size:16 final size:16
Alignment explanation
Indices: 5281448--5281480 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
5281438 TTTAAAGAAA
5281448 GATGAAGAAATTTTGG
1 GATGAAGAAATTTTGG
5281464 GATGAAGAAATTTTGG
1 GATGAAGAAATTTTGG
5281480 G
1 G
5281481 GTTTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.00, G:0.33, T:0.30
Consensus pattern (16 bp):
GATGAAGAAATTTTGG
Found at i:5288583 original size:21 final size:22
Alignment explanation
Indices: 5288550--5288600 Score: 79
Period size: 22 Copynumber: 2.4 Consensus size: 22
5288540 CATGATACAT
*
5288550 AAGT-GCACTTAT-ATATGGTC
1 AAGTGGCAATTATAATATGGTC
5288570 AAGTGGCAATTATAATATGGTC
1 AAGTGGCAATTATAATATGGTC
5288592 AAGTGGCAA
1 AAGTGGCAA
5288601 CATATAATTG
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
20 4 0.14
21 7 0.25
22 17 0.61
ACGTcount: A:0.35, C:0.12, G:0.24, T:0.29
Consensus pattern (22 bp):
AAGTGGCAATTATAATATGGTC
Found at i:5292885 original size:26 final size:27
Alignment explanation
Indices: 5292826--5292890 Score: 71
Period size: 26 Copynumber: 2.4 Consensus size: 27
5292816 CATAAAAAAT
* *
5292826 TATATTATATATTTTTTTAATATTTAA
1 TATATTTTATATTTTTTTAATATTGAA
*
5292853 TA-ATTTTATATTTTTTTATTTATTGAA
1 TATATTTTATATTTTTTTA-ATATTGAA
*
5292880 -ATTTTTTATAT
1 TATATTTTATAT
5292891 AGTGATCTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
26 16 0.50
27 16 0.50
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (27 bp):
TATATTTTATATTTTTTTAATATTGAA
Found at i:5293270 original size:1 final size:1
Alignment explanation
Indices: 5293264--5293290 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
5293254 AAACTCTGAA
5293264 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
5293291 GCTTATTGGC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:5294893 original size:29 final size:28
Alignment explanation
Indices: 5294810--5294893 Score: 77
Period size: 28 Copynumber: 3.0 Consensus size: 28
5294800 ATATAGTTTT
5294810 ATTTTT-AATTTCTTGAT-AATTATATATA
1 ATTTTTAAATTT-TT-ATAAATTATATATA
* *
5294838 A-ATTTAAATATTTTATATA-TATAATATA
1 ATTTTTAAAT-TTTTATAAATTAT-ATATA
5294866 ATTTTTAAATTTTTAATAAATTATATAT
1 ATTTTTAAATTTTT-ATAAATTATATAT
5294894 TGTTTTAATA
Statistics
Matches: 45, Mismatches: 4, Indels: 13
0.73 0.06 0.21
Matches are distributed among these distances:
27 8 0.18
28 17 0.38
29 17 0.38
30 3 0.07
ACGTcount: A:0.43, C:0.01, G:0.01, T:0.55
Consensus pattern (28 bp):
ATTTTTAAATTTTTATAAATTATATATA
Found at i:5300080 original size:39 final size:39
Alignment explanation
Indices: 5300037--5300112 Score: 125
Period size: 39 Copynumber: 1.9 Consensus size: 39
5300027 ACCTGCTAAA
5300037 CAGTTCCTCGATCCAAACTCGAAACTCAGTTAAACTCAG
1 CAGTTCCTCGATCCAAACTCGAAACTCAGTTAAACTCAG
* * *
5300076 CAGTTCCTCGATCCGAACTTGAAACTCTGTTAAACTC
1 CAGTTCCTCGATCCAAACTCGAAACTCAGTTAAACTC
5300113 GTTACCTATA
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 34 1.00
ACGTcount: A:0.30, C:0.30, G:0.13, T:0.26
Consensus pattern (39 bp):
CAGTTCCTCGATCCAAACTCGAAACTCAGTTAAACTCAG
Found at i:5303411 original size:9 final size:9
Alignment explanation
Indices: 5303397--5303427 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
5303387 AAAATTAGAT
5303397 AATTAATCA
1 AATTAATCA
*
5303406 AATTAATCG
1 AATTAATCA
5303415 AATTAATCA
1 AATTAATCA
5303424 AATT
1 AATT
5303428 TAATAATTAA
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:0.52, C:0.10, G:0.03, T:0.35
Consensus pattern (9 bp):
AATTAATCA
Found at i:5303497 original size:44 final size:44
Alignment explanation
Indices: 5303448--5303536 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
5303438 TATTATGTAT
5303448 TAATTTCAATACTTATGTAGTATTTTTAATTATGTAGTGTTTCA
1 TAATTTCAATACTTATGTAGTATTTTTAATTATGTAGTGTTTCA
5303492 TAATTTCAATACTTATGTAGTATTTTTAATTATGTAGTGTTTCA
1 TAATTTCAATACTTATGTAGTATTTTTAATTATGTAGTGTTTCA
5303536 T
1 T
5303537 GACATAAAAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.29, C:0.07, G:0.11, T:0.53
Consensus pattern (44 bp):
TAATTTCAATACTTATGTAGTATTTTTAATTATGTAGTGTTTCA
Found at i:5306864 original size:4 final size:4
Alignment explanation
Indices: 5306855--5306879 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5306845 AGTTAGAATC
5306855 ATAA ATAA ATAA ATAA ATAA ATAA A
1 ATAA ATAA ATAA ATAA ATAA ATAA A
5306880 AACCTCTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (4 bp):
ATAA
Found at i:5307186 original size:68 final size:68
Alignment explanation
Indices: 5307077--5307215 Score: 219
Period size: 68 Copynumber: 2.0 Consensus size: 68
5307067 GTATCCAGCC
*
5307077 TGGGGAGTACATTCGCAAGAATGAAACTAAAAGGAATTGAC-AGGGGACTGCACAAGTAGTGGAG
1 TGGGGAGTACATTCGCAAGAATGAAACTAAAAGGAATTGACAAGGGG-CCGCACAAGTAGTGGAG
5307141 CATG
65 CATG
* *
5307145 TGGGGAGTACA-TCTGCAAGAATGAAACTTAAAGGAATTGACAAGGGGCCGCACAAGTGGTGGAG
1 TGGGGAGTACATTC-GCAAGAATGAAACTAAAAGGAATTGACAAGGGGCCGCACAAGTAGTGGAG
5307209 CATG
65 CATG
5307213 TGG
1 TGG
5307216 TTTAATTTGA
Statistics
Matches: 66, Mismatches: 3, Indels: 4
0.90 0.04 0.05
Matches are distributed among these distances:
67 2 0.03
68 59 0.89
69 5 0.08
ACGTcount: A:0.35, C:0.14, G:0.34, T:0.18
Consensus pattern (68 bp):
TGGGGAGTACATTCGCAAGAATGAAACTAAAAGGAATTGACAAGGGGCCGCACAAGTAGTGGAGC
ATG
Found at i:5310380 original size:6 final size:6
Alignment explanation
Indices: 5310371--5310406 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
5310361 CTATGGAGTT
5310371 GGATTA GGATTA GGATTA GGATTA GGATTA GGATTA
1 GGATTA GGATTA GGATTA GGATTA GGATTA GGATTA
5310407 ATCAAAATCC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (6 bp):
GGATTA
Found at i:5310441 original size:25 final size:24
Alignment explanation
Indices: 5310408--5310457 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 24
5310398 TTAGGATTAA
5310408 TCAAAATCCTATTTCTATTTATAT
1 TCAAAATCCTATTTCTATTTATAT
*
5310432 TCAATAATCCTATTTCTATTTGTAT
1 TCAA-AATCCTATTTCTATTTATAT
5310457 T
1 T
5310458 TGGATTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
24 4 0.17
25 20 0.83
ACGTcount: A:0.30, C:0.16, G:0.02, T:0.52
Consensus pattern (24 bp):
TCAAAATCCTATTTCTATTTATAT
Found at i:5311849 original size:19 final size:20
Alignment explanation
Indices: 5311825--5311868 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
5311815 ATTACAAAAA
5311825 AAAAATT-AAAATAATTTTC
1 AAAAATTCAAAATAATTTTC
5311844 AAAAATTCAAAATAATTTTC
1 AAAAATTCAAAATAATTTTC
5311864 AAAAA
1 AAAAA
5311869 AATTTCAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 7 0.29
20 17 0.71
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAAATTCAAAATAATTTTC
Found at i:5313335 original size:31 final size:31
Alignment explanation
Indices: 5313300--5313364 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
5313290 CAAAATGGTC
*
5313300 ATTAAATTATTCGAAAGTTTTTATTTAAGTT
1 ATTAAATTATTCGAAAATTTTTATTTAAGTT
* * *
5313331 ATTAACTTGTTTGAAAATTTTTATTTAAGTT
1 ATTAAATTATTCGAAAATTTTTATTTAAGTT
5313362 ATT
1 ATT
5313365 GAGCTGTTAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.34, C:0.03, G:0.09, T:0.54
Consensus pattern (31 bp):
ATTAAATTATTCGAAAATTTTTATTTAAGTT
Found at i:5314651 original size:17 final size:17
Alignment explanation
Indices: 5314629--5314675 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
5314619 AAATTTGAAA
**
5314629 TTTAAAATTTAT-ATTT
1 TTTAAAATTTATAAGAT
* *
5314645 TTTTAAATTTTTAAGAT
1 TTTAAAATTTATAAGAT
5314662 TTTAAAATTTATAA
1 TTTAAAATTTATAA
5314676 CTATTAACAT
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
16 10 0.42
17 14 0.58
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.57
Consensus pattern (17 bp):
TTTAAAATTTATAAGAT
Found at i:5315406 original size:100 final size:100
Alignment explanation
Indices: 5315167--5315365 Score: 380
Period size: 100 Copynumber: 2.0 Consensus size: 100
5315157 AATATTCACT
*
5315167 TTATAATCACGTATCAATAAAAAATGATACTAAAAATATTGATAATTTTTAAAAAGAAAATGTTC
1 TTATAATCACGTATCAATAAAAAATGACACTAAAAATATTGATAATTTTTAAAAAGAAAATGTTC
*
5315232 ATTCAAATTTTTCATGATAAAATAATCTTTTTCTG
66 ATTCAAACTTTTCATGATAAAATAATCTTTTTCTG
5315267 TTATAATCACGTATCAATAAAAAATGACACTAAAAATATTGATAATTTTTAAAAAGAAAATGTTC
1 TTATAATCACGTATCAATAAAAAATGACACTAAAAATATTGATAATTTTTAAAAAGAAAATGTTC
5315332 ATTCAAACTTTTCATGATAAAATAATCTTTTTCT
66 ATTCAAACTTTTCATGATAAAATAATCTTTTTCT
5315366 ATTTGAATAA
Statistics
Matches: 97, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
100 97 1.00
ACGTcount: A:0.45, C:0.10, G:0.07, T:0.38
Consensus pattern (100 bp):
TTATAATCACGTATCAATAAAAAATGACACTAAAAATATTGATAATTTTTAAAAAGAAAATGTTC
ATTCAAACTTTTCATGATAAAATAATCTTTTTCTG
Found at i:5315624 original size:27 final size:27
Alignment explanation
Indices: 5315586--5315641 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
5315576 TAATACATTC
5315586 AAATTATATATAACCATATTGTATATT
1 AAATTATATATAACCATATTGTATATT
5315613 AAATTATATATAACCATATTGTATATT
1 AAATTATATATAACCATATTGTATATT
5315640 AA
1 AA
5315642 CGAAAAGTTG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.46, C:0.07, G:0.04, T:0.43
Consensus pattern (27 bp):
AAATTATATATAACCATATTGTATATT
Found at i:5315637 original size:17 final size:16
Alignment explanation
Indices: 5315590--5315642 Score: 53
Period size: 12 Copynumber: 3.6 Consensus size: 16
5315580 ACATTCAAAT
5315590 TATATATAACCATATTG
1 TATAT-TAACCATATTG
*
5315607 TATATT-A--A-ATTA
1 TATATTAACCATATTG
5315619 TATA-TAACCATATTG
1 TATATTAACCATATTG
5315634 TATATTAAC
1 TATATTAAC
5315643 GAAAAGTTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 11
0.69 0.05 0.26
Matches are distributed among these distances:
11 1 0.03
12 8 0.28
13 1 0.03
14 1 0.03
15 8 0.28
16 5 0.17
17 5 0.17
ACGTcount: A:0.43, C:0.09, G:0.04, T:0.43
Consensus pattern (16 bp):
TATATTAACCATATTG
Found at i:5318039 original size:26 final size:27
Alignment explanation
Indices: 5317982--5318040 Score: 111
Period size: 27 Copynumber: 2.2 Consensus size: 27
5317972 CAAAAAGTCA
5317982 AACTATGCCCTTTTTTTAAGGAAATCG
1 AACTATGCCCTTTTTTTAAGGAAATCG
5318009 AACTATGCCCTTTTTTTAAGGAAATCG
1 AACTATGCCCTTTTTTTAAGGAAATCG
5318036 -ACTAT
1 AACTAT
5318041 ATGGAAAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
26 5 0.16
27 27 0.84
ACGTcount: A:0.31, C:0.19, G:0.14, T:0.37
Consensus pattern (27 bp):
AACTATGCCCTTTTTTTAAGGAAATCG
Found at i:5322586 original size:17 final size:17
Alignment explanation
Indices: 5322557--5322599 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 17
5322547 TCTCTTATTT
5322557 TTAAATAAAAAAAAGAC
1 TTAAATAAAAAAAAGAC
5322574 TTAAA-AAAGAAAAAGAC
1 TTAAATAAA-AAAAAGAC
5322591 TTAGAATAA
1 TTA-AATAA
5322600 GGAGTTTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
16 3 0.13
17 16 0.70
18 2 0.09
19 2 0.09
ACGTcount: A:0.67, C:0.05, G:0.09, T:0.19
Consensus pattern (17 bp):
TTAAATAAAAAAAAGAC
Found at i:5324067 original size:2 final size:2
Alignment explanation
Indices: 5324060--5324098 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
5324050 AACCATACAT
5324060 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC AC A
5324099 TATATATATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.51, C:0.49, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:5324665 original size:22 final size:22
Alignment explanation
Indices: 5324617--5324665 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
5324607 TTGAAATTTG
* *
5324617 ATTTTATTATTTAATGTTAATT
1 ATTTTATTATTTAATATCAATT
*
5324639 TTTTTATTATTTATATATCAA-T
1 ATTTTATTATTTA-ATATCAATT
5324661 ATTTT
1 ATTTT
5324666 TATATTTTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (22 bp):
ATTTTATTATTTAATATCAATT
Found at i:5324758 original size:18 final size:21
Alignment explanation
Indices: 5324737--5324779 Score: 56
Period size: 20 Copynumber: 2.1 Consensus size: 21
5324727 TACAATAATT
5324737 TAATTT-TTTTTAT-TCTA-A
1 TAATTTATTTTTATGTCTATA
5324755 TAATTTAATTTTTATGTCTATA
1 TAATTT-ATTTTTATGTCTATA
5324777 TAA
1 TAA
5324780 CTAGGGACTT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
18 6 0.29
20 7 0.33
21 4 0.19
22 4 0.19
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (21 bp):
TAATTTATTTTTATGTCTATA
Found at i:5324989 original size:3 final size:3
Alignment explanation
Indices: 5324981--5325023 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
5324971 ATATAACATC
5324981 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
5325024 GTAAATAAAG
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
ATT
Found at i:5328371 original size:24 final size:24
Alignment explanation
Indices: 5328327--5328372 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
5328317 CGCGACACCC
*
5328327 CCACCTACTGCTGCTATTGCCGCT
1 CCACCTACTGCTGCTACTGCCGCT
*
5328351 CCACCTACTGCTGCTGCTGCCG
1 CCACCTACTGCTGCTACTGCCG
5328373 TTGCTTTTGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.11, C:0.43, G:0.20, T:0.26
Consensus pattern (24 bp):
CCACCTACTGCTGCTACTGCCGCT
Found at i:5329069 original size:113 final size:114
Alignment explanation
Indices: 5328815--5329248 Score: 649
Period size: 113 Copynumber: 3.9 Consensus size: 114
5328805 TTTTATAGTT
* * * *
5328815 GATTAGGTTATATAAATTGTTAGTGTTTAGTAGTTTAGTGCATTACTGTATTGTGATTTTTTTAG
1 GATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAGTGTATTGTAATTTTTTTAG
5328880 TAATATATTTTAAAAAAATAATTTTATAGCTATTTTATTAGTAATTTAA
66 TAATATATTTTAAAAAAATAATTTTATAGCTATTTTATTAGTAATTTAA
5328929 GATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAGTGTATTGTAATTTTTTTAG
1 GATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAGTGTATTGTAATTTTTTTAG
*
5328994 TAATATA-TTTAAAAAAATATTTTTATAGCTATTTTATTAGTAATTTAA
66 TAATATATTTTAAAAAAATAATTTTATAGCTATTTTATTAGTAATTTAA
* *
5329042 GATTAAGTTATATAAATTGTTAGTGTTTAGTGGTTCAGTGTATT-GTG-A---T--TTTTTTTAG
1 GATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAGTGTATTGTAATTTTTTTAG
*
5329100 TAATATATTTTAAAAAAATATTTTTATAGCTATTTTATTAGTAATTTAA
66 TAATATATTTTAAAAAAATAATTTTATAGCTATTTTATTAGTAATTTAA
* *
5329149 GATTAGGTTATAT--ATTGTTAGTGTTTAATGGTTTAGTGTGTATTAGTGTATTGTGATTTTTTT
1 GATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTA--GTGTATTAGTGTATTGT-AATTTTTT
* *
5329212 TAGTAATGTA-TTT-AAAAAATAATTTTATAGTTATTTT
63 TAGTAATATATTTTAAAAAAATAATTTTATAGCTATTTT
5329249 GTGTTAGTAT
Statistics
Matches: 296, Mismatches: 13, Indels: 23
0.89 0.04 0.07
Matches are distributed among these distances:
105 20 0.07
106 16 0.05
107 60 0.20
108 4 0.01
109 1 0.00
111 1 0.00
112 4 0.01
113 104 0.35
114 71 0.24
115 15 0.05
ACGTcount: A:0.32, C:0.01, G:0.15, T:0.52
Consensus pattern (114 bp):
GATTAGGTTATATAAATTGTTAGTGTTTAGTGGTTTAGTGTATTAGTGTATTGTAATTTTTTTAG
TAATATATTTTAAAAAAATAATTTTATAGCTATTTTATTAGTAATTTAA
Found at i:5329334 original size:15 final size:16
Alignment explanation
Indices: 5329305--5329336 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
5329295 TGTGATTTTT
5329305 TAATGTAATTTTTATA
1 TAATGTAATTTTTATA
5329321 TAATGTAA-TTTTATA
1 TAATGTAATTTTTATA
5329336 T
1 T
5329337 TATTATATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.38, C:0.00, G:0.06, T:0.56
Consensus pattern (16 bp):
TAATGTAATTTTTATA
Found at i:5333378 original size:27 final size:27
Alignment explanation
Indices: 5333316--5333378 Score: 81
Period size: 27 Copynumber: 2.3 Consensus size: 27
5333306 CCTACCAAGA
*
5333316 AGGCACAACTAGTCGTGCCTGTCAGAT
1 AGGCACAACTAGTCGAGCCTGTCAGAT
* * *
5333343 ATGCTCAACTAGTTGAGCCTGTCAGAT
1 AGGCACAACTAGTCGAGCCTGTCAGAT
*
5333370 AGGCGCAAC
1 AGGCACAAC
5333379 ATGTATGTAT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.27, C:0.25, G:0.25, T:0.22
Consensus pattern (27 bp):
AGGCACAACTAGTCGAGCCTGTCAGAT
Found at i:5333612 original size:2 final size:2
Alignment explanation
Indices: 5333607--5333638 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5333597 ACCCAAAATC
5333607 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
5333639 TAAGATGTAT
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5333757 original size:17 final size:18
Alignment explanation
Indices: 5333715--5333759 Score: 58
Period size: 17 Copynumber: 2.6 Consensus size: 18
5333705 ATAACTTTCG
5333715 AAAAA-TAATTTTTAGAA
1 AAAAATTAATTTTTAGAA
*
5333732 AATAAATTAATTTTTTG-A
1 AA-AAATTAATTTTTAGAA
5333750 AAAAATTAAT
1 AAAAATTAAT
5333760 ATATTTCTGG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
17 10 0.40
18 6 0.24
19 9 0.36
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (18 bp):
AAAAATTAATTTTTAGAA
Found at i:5334018 original size:2 final size:2
Alignment explanation
Indices: 5334011--5334043 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
5334001 ATTTAACTTT
5334011 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5334044 GAGAGTATGT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5334590 original size:17 final size:18
Alignment explanation
Indices: 5334558--5334591 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
5334548 ATATTATTTT
*
5334558 TAAAATTTATTATTAAAA
1 TAAAATTTAATATTAAAA
5334576 TAAAA-TTAATATTAAA
1 TAAAATTTAATATTAAA
5334592 TACTTTTATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (18 bp):
TAAAATTTAATATTAAAA
Found at i:5334591 original size:30 final size:31
Alignment explanation
Indices: 5334557--5334632 Score: 77
Period size: 30 Copynumber: 2.5 Consensus size: 31
5334547 AATATTATTT
*
5334557 TTAAAATTTATTATTAAAAT-A-AAATTAATA
1 TTAAAAATTATTATTAAAATAATAAATT-ATA
* *
5334587 TTAAATACTT-TTATTAAATTAATAAATTATA
1 TTAAA-AATTATTATTAAAATAATAAATTATA
5334618 TTAATAAATTATTAT
1 TTAA-AAATTATTAT
5334633 ATTATTAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
30 14 0.37
31 14 0.37
32 10 0.26
ACGTcount: A:0.51, C:0.01, G:0.00, T:0.47
Consensus pattern (31 bp):
TTAAAAATTATTATTAAAATAATAAATTATA
Found at i:5334629 original size:13 final size:13
Alignment explanation
Indices: 5334599--5334629 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
5334589 AAATACTTTT
*
5334599 ATTAAATTAATAA
1 ATTATATTAATAA
5334612 ATTATATTAATAA
1 ATTATATTAATAA
5334625 ATTAT
1 ATTAT
5334630 TATATTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (13 bp):
ATTATATTAATAA
Found at i:5334631 original size:16 final size:16
Alignment explanation
Indices: 5334612--5334660 Score: 57
Period size: 16 Copynumber: 3.1 Consensus size: 16
5334602 AAATTAATAA
5334612 ATTATATTAATAAATT
1 ATTATATTAATAAATT
*
5334628 ATTATATTATTAAA-T
1 ATTATATTAATAAATT
5334643 A-TATATTTAATAATATT
1 ATTATA-TTAATAA-ATT
5334660 A
1 A
5334661 AAAATTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
14 4 0.14
15 8 0.29
16 14 0.50
17 2 0.07
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (16 bp):
ATTATATTAATAAATT
Found at i:5334638 original size:37 final size:37
Alignment explanation
Indices: 5334597--5334697 Score: 109
Period size: 37 Copynumber: 2.7 Consensus size: 37
5334587 TTAAATACTT
*
5334597 TTATTAAATTAA-TAAATTATATTAATAAATTATTATA
1 TTATTAAATTAATTAAATTATATTAA-AAATTATAATA
* *
5334634 TTATTAAATATATATTTAATAATATTAAAAATTATAATA
1 TTATTAAAT-TA-ATTAAATTATATTAAAAATTATAATA
5334673 -T-TTAATATTAATTAAATATATATTA
1 TTATTAA-ATTAATTAAAT-TATATTA
5334698 TTTAAGATAA
Statistics
Matches: 54, Mismatches: 5, Indels: 10
0.78 0.07 0.14
Matches are distributed among these distances:
36 6 0.11
37 21 0.39
38 5 0.09
39 11 0.20
40 11 0.20
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (37 bp):
TTATTAAATTAATTAAATTATATTAAAAATTATAATA
Found at i:5334678 original size:22 final size:24
Alignment explanation
Indices: 5334600--5334702 Score: 72
Period size: 24 Copynumber: 4.2 Consensus size: 24
5334590 AATACTTTTA
5334600 TTAA-ATTAATAAATTATATTAATAAAT
1 TTAATATTAATAAA-TATA-TAAT--AT
* *
5334627 TATTATATTATTAAATATAT-AT-T
1 T-TAATATTAATAAATATATAATAT
5334650 TAATAATATTAA-AAAT-TATAATAT
1 T--TAATATTAATAAATATATAATAT
*
5334674 TTAATATTAATTAAATATATATTAT
1 TTAATATTAA-TAAATATATAATAT
5334699 TTAA
1 TTAA
5334703 GATAATTTTG
Statistics
Matches: 63, Mismatches: 5, Indels: 18
0.73 0.06 0.21
Matches are distributed among these distances:
22 12 0.19
23 8 0.13
24 14 0.22
25 11 0.17
26 2 0.03
27 2 0.03
28 6 0.10
29 8 0.13
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (24 bp):
TTAATATTAATAAATATATAATAT
Found at i:5334679 original size:25 final size:25
Alignment explanation
Indices: 5334639--5334702 Score: 78
Period size: 25 Copynumber: 2.6 Consensus size: 25
5334629 TTATATTATT
5334639 AAATAT-ATATTTAATAAT-ATTAA
1 AAATATAATATTTAATAATAATTAA
*
5334662 AAATTATAATATTTAATATTAATTAA
1 AAA-TATAATATTTAATAATAATTAA
* *
5334688 ATATATATTATTTAA
1 AAATATAATATTTAA
5334703 GATAATTTTG
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
23 3 0.09
24 3 0.09
25 22 0.63
26 7 0.20
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
AAATATAATATTTAATAATAATTAA
Found at i:5334680 original size:36 final size:37
Alignment explanation
Indices: 5334604--5334697 Score: 97
Period size: 36 Copynumber: 2.5 Consensus size: 37
5334594 CTTTTATTAA
5334604 ATTAA-TAAAT-TATATTAATAAATTATTATATTATTAAAT
1 ATTAATTAAATATATATTAA-AAATTA-TA-A-TATTAAAT
* *
5334643 A-TATATTTAATA-ATATTAAAAATTATAATATTTAAT
1 ATTA-ATTAAATATATATTAAAAATTATAATATTAAAT
5334679 ATTAATTAAATATATATTA
1 ATTAATTAAATATATATTA
5334698 TTTAAGATAA
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
36 15 0.32
37 9 0.19
38 4 0.09
39 8 0.17
40 11 0.23
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (37 bp):
ATTAATTAAATATATATTAAAAATTATAATATTAAAT
Found at i:5338595 original size:26 final size:26
Alignment explanation
Indices: 5338560--5338620 Score: 67
Period size: 26 Copynumber: 2.4 Consensus size: 26
5338550 TGTTAATACA
5338560 TAAATA-TATAAAT-TTAAAT-ATAT
1 TAAATATTATAAATCTTAAATAATAT
*
5338583 TGAAATAATTAT-ACTCTTAAATAATAT
1 T-AAAT-ATTATAAATCTTAAATAATAT
5338610 TAAATATTATA
1 TAAATATTATA
5338621 TTAAAAATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
23 1 0.03
24 4 0.13
25 8 0.26
26 13 0.42
27 5 0.16
ACGTcount: A:0.52, C:0.03, G:0.02, T:0.43
Consensus pattern (26 bp):
TAAATATTATAAATCTTAAATAATAT
Found at i:5339825 original size:6 final size:6
Alignment explanation
Indices: 5339816--5339841 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
5339806 AAAAAAAAAA
5339816 AAAGTG AAAGTG AAAGTG AAAGTG AA
1 AAAGTG AAAGTG AAAGTG AAAGTG AA
5339842 TTCTTTGCTA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.54, C:0.00, G:0.31, T:0.15
Consensus pattern (6 bp):
AAAGTG
Found at i:5341929 original size:2 final size:2
Alignment explanation
Indices: 5341922--5341958 Score: 56
Period size: 2 Copynumber: 18.5 Consensus size: 2
5341912 TTTTGTAGGT
* *
5341922 TA TA TA TA TA TA TA TT TA TA TA TA AA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5341959 GAGTTATATT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5351506 original size:21 final size:21
Alignment explanation
Indices: 5351476--5351516 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
5351466 TGAATAAAAA
*
5351476 AATTTAAATATCT-TAAATTT
1 AATTTAAATATATATAAATTT
5351496 AATTTCAAATATATATAAATT
1 AATTT-AAATATATATAAATT
5351517 ATTTTTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 5 0.28
21 7 0.39
22 6 0.33
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.46
Consensus pattern (21 bp):
AATTTAAATATATATAAATTT
Found at i:5352079 original size:13 final size:13
Alignment explanation
Indices: 5352061--5352086 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5352051 TAAGATCTTT
5352061 TTTAAAATTAAAA
1 TTTAAAATTAAAA
5352074 TTTAAAATTAAAA
1 TTTAAAATTAAAA
5352087 GGTTTTTAAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (13 bp):
TTTAAAATTAAAA
Found at i:5356160 original size:11 final size:11
Alignment explanation
Indices: 5356144--5356173 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
5356134 TAACATTAAG
5356144 AATATATATAT
1 AATATATATAT
*
5356155 AATATAAATAT
1 AATATATATAT
5356166 AATATATA
1 AATATATA
5356174 CAATATACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AATATATATAT
Found at i:5356578 original size:27 final size:27
Alignment explanation
Indices: 5356545--5356613 Score: 138
Period size: 27 Copynumber: 2.6 Consensus size: 27
5356535 ACCGGTCGAT
5356545 CGTCGGCCACCGCCCGTCACCGACCAC
1 CGTCGGCCACCGCCCGTCACCGACCAC
5356572 CGTCGGCCACCGCCCGTCACCGACCAC
1 CGTCGGCCACCGCCCGTCACCGACCAC
5356599 CGTCGGCCACCGCCC
1 CGTCGGCCACCGCCC
5356614 ACGGTGGCCG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.13, C:0.57, G:0.23, T:0.07
Consensus pattern (27 bp):
CGTCGGCCACCGCCCGTCACCGACCAC
Found at i:5356582 original size:17 final size:17
Alignment explanation
Indices: 5356562--5356615 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 17
5356552 CACCGCCCGT
5356562 CACCGACCACCGTCGGC
1 CACCGACCACCGTCGGC
5356579 CACCG--C-CCGT----
1 CACCGACCACCGTCGGC
5356589 CACCGACCACCGTCGGC
1 CACCGACCACCGTCGGC
*
5356606 CACCGCCCAC
1 CACCGACCAC
5356616 GGTGGCCGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
10 5 0.17
12 1 0.03
13 4 0.14
14 4 0.14
15 1 0.03
17 14 0.48
ACGTcount: A:0.17, C:0.57, G:0.20, T:0.06
Consensus pattern (17 bp):
CACCGACCACCGTCGGC
Found at i:5357026 original size:15 final size:15
Alignment explanation
Indices: 5357008--5357042 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
5356998 TCTTCTTTTT
*
5357008 TTTTTTTGGGTTAGG
1 TTTTTTTGGGGTAGG
5357023 TTTTTTTGGGGTAGG
1 TTTTTTTGGGGTAGG
5357038 TTTTT
1 TTTTT
5357043 CTTTTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.06, C:0.00, G:0.31, T:0.63
Consensus pattern (15 bp):
TTTTTTTGGGGTAGG
Found at i:5357057 original size:16 final size:15
Alignment explanation
Indices: 5357038--5357073 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
5357028 TTGGGGTAGG
*
5357038 TTTTTCTTTTTCTTTT
1 TTTTTCTTTGT-TTTT
5357054 TTTTTCTTTGTTTTT
1 TTTTTCTTTGTTTTT
5357069 TTTTT
1 TTTTT
5357074 GGGTTAGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.00, C:0.08, G:0.03, T:0.89
Consensus pattern (15 bp):
TTTTTCTTTGTTTTT
Found at i:5357826 original size:88 final size:81
Alignment explanation
Indices: 5357719--5358795 Score: 310
Period size: 88 Copynumber: 13.0 Consensus size: 81
5357709 AACAGACATT
** * *
5357719 AAAAACAGAAATTGAAAATAGCTCAGCGCGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGATTTTGAAAATACCTC-GCACGTGA-CCAAGGCTCAACTCACCTCTCGCAATATGAG
5357784 TTGATTTTTTGAAACTTAACTTG
64 TTGATTTTTTGAAA---AA--TG
* * * ** *
5357807 AAAAGCAGATTTTGAAAATACCTCGATATGTGACTGGAGGTTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGATTTTGAAAATACCTCG-CACGTGAC-CAAGGCTCAACTCACCTCTCGCAATATGAG
*
5357872 TTGA-TTTTTGAAAAACAG
64 TTGATTTTTTGAAAAA-TG
* * * * * * *
5357890 AAATTAAAAGA--CT-CAACTCAACTCTCGCA-GAAATTA-AAAAGCTCAACTCACCTCTCGCAA
1 AAA--AACAGATTTTGAAAAT--AC-CTCGCACG---TGACCAAGGCTCAACTCACCTCTCGCAA
5357950 TATGAGTTGAATTTTTTTGAAAAA--
58 TATGAGTTG-A-TTTTTTGAAAAATG
** * *
5357974 AAAAACAGAAATTGAAAATAGCTCAGCACGTGAGCCAAGGCTCAACTCACTTCTCGCAATATGAG
1 AAAAACAGATTTTGAAAATACCTC-GCACGTGA-CCAAGGCTCAACTCACCTCTCGCAATATGAG
5358039 TTGA-TTTTTGAAAACAGAATCTG
64 TTGATTTTTTG--AA-A-AA--TG
* * * * * *
5358062 AAAAATAGATTTTGAAAATACCTCGACATGTGACTCGAGGCTCAACTCACATCTCACAATGTGAG
1 AAAAACAGATTTTGAAAATACCTCG-CACGTGAC-CAAGGCTCAACTCACCTCTCGCAATATGAG
5358127 TTGATTTTTTTGAAAAAT-
64 TTGA-TTTTTTGAAAAATG
* *** *** * *
5358145 --ATA-A-ATTGAAAAAATACCTCAGTGTGTGATCTGAA-GCTCAACTCACCTTTCGCAATATGA
1 AAAAACAGATTTTGAAAATACCTC-GCACGTGA-C-CAAGGCTCAACTCACCTCTCGCAATATGA
5358205 GTTGATTTTTTTG--AAA-G
63 GTTGA-TTTTTTGAAAAATG
* * **
5358222 ACAAA-A-A--TTGAAAATAGCTCAGCGTGTGAGCCAAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGATTTTGAAAATACCTC-GCACGTGA-CCAAGGCTCAACTCACCTCTCGCAATATGAG
5358283 TTGATTTTTTTGAAAGGCAGAAATTG
64 TTGA-TTTTTTG--A---A-AAA-TG
* ** * * * * * *
5358309 AAAAACGGAAATTGAAAATACCTTG-GCGTTTGACCTGAGGCTCAACTCGCCTCTCACAATACGA
1 AAAAACAGATTTTGAAAATACCTCGCACG--TGACC-AAGGCTCAACTCACCTCTCGCAATATGA
5358373 GTTGATTTTTT------TG
63 GTTGATTTTTTGAAAAATG
* ** * * *
5358386 -ACAACAGAAATTGAAATTACCT--CAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGATTTTGAAAATACCTCGCA-CGTGACC-AAGGCTCAACTCACCTCTCGCAATATGAG
*
5358448 TTAATTTTTTTTTGAAAGGCAGAAATTG
64 TTGA---TTTTTTG--A---A-AAA-TG
* ** * * * * * *
5358476 AAAAACGGAAATTGAAAATACCTCGGCATGTGACCTGAGGCTCAACTCGCCGCTCGTAATACGAG
1 AAAAACAGATTTTGAAAATACCTC-GCACGTGACC-AAGGCTCAACTCACCTCTCGCAATATGAG
5358541 TTGATTTTTT------TG
64 TTGATTTTTTGAAAAATG
* ** * * *
5358553 -ACAACAGAAATTGAAATTACCT--CAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGATTTTGAAAATACCTCGCA-CGTGACC-AAGGCTCAACTCACCTCTCGCAATATGAG
5358615 TTGATTTTTTTTGAAAGGCAGAAATTG
64 TTGA--TTTTTTG--A---A-AAA-TG
** ** ** ** *
5358642 AAAAATGGAAATTGAAAATACCTCGGCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAG
1 AAAAACAGATTTTGAAAATACCTC-GCACGTGA-CCAAGGCTCAACTCACCTCTCGCAATATGAG
*
5358707 TTGACTTTTT------TG
64 TTGATTTTTTGAAAAATG
* ** * * *
5358719 -ACAACAGAAATTGAAATTACCT--CAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAG
1 AAAAACAGATTTTGAAAATACCTCGCA-CGTGACC-AAGGCTCAACTCACCTCTCGCAATATGAG
5358781 TTGATTTTTTTGAAA
64 TTGA-TTTTTTGAAA
5358796 GGCAGAAATT
Statistics
Matches: 765, Mismatches: 119, Indels: 219
0.69 0.11 0.20
Matches are distributed among these distances:
73 4 0.01
74 104 0.14
75 5 0.01
76 66 0.09
77 70 0.09
79 56 0.07
80 11 0.01
81 4 0.01
82 14 0.02
83 41 0.05
84 42 0.05
85 15 0.02
86 4 0.01
87 30 0.04
88 113 0.15
89 5 0.01
90 46 0.06
91 62 0.08
92 35 0.05
93 36 0.05
94 2 0.00
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (81 bp):
AAAAACAGATTTTGAAAATACCTCGCACGTGACCAAGGCTCAACTCACCTCTCGCAATATGAGTT
GATTTTTTGAAAAATG
Found at i:5357923 original size:30 final size:30
Alignment explanation
Indices: 5357887--5357948 Score: 99
Period size: 30 Copynumber: 2.1 Consensus size: 30
5357877 TTTTGAAAAA
5357887 CAGAAATT-AAAAGACTCAACTCAACTCTCG
1 CAGAAATTAAAAAG-CTCAACTCAACTCTCG
*
5357917 CAGAAATTAAAAAGCTCAACTCACCTCTCG
1 CAGAAATTAAAAAGCTCAACTCAACTCTCG
5357947 CA
1 CA
5357949 ATATGAGTTG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
30 25 0.83
31 5 0.17
ACGTcount: A:0.42, C:0.29, G:0.10, T:0.19
Consensus pattern (30 bp):
CAGAAATTAAAAAGCTCAACTCAACTCTCG
Found at i:5358261 original size:77 final size:78
Alignment explanation
Indices: 5358073--5358312 Score: 290
Period size: 77 Copynumber: 3.1 Consensus size: 78
5358063 AAAATAGATT
* * * * *
5358073 TTGAAAATACCTC-GACATGTGA-CTCGAGGCTCAACTCACATCTCACAATGTGAGTTGATTTTT
1 TTGAAAATACCTCAG-CGTGTGAGCTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
* * *
5358136 TTGAAAAATATAAA
65 TTGAAAGACAAAAA
* * * *
5358150 TTGAAAAAATACCTCAGTGTGTGATCTGAA-GCTCAACTCACCTTTCGCAATATGAGTTGATTTT
1 TTG--AAAATACCTCAGCGTGTGAGCTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
5358214 TTTGAAAGACAAAAA
64 TTTGAAAGACAAAAA
*
5358229 TTGAAAATAGCTCAGCGTGTGAGC-CAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
1 TTGAAAATACCTCAGCGTGTGAGCTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
* *
5358293 TGAAAGGCAGAAA
66 TGAAAGACAAAAA
5358306 TTGAAAA
1 TTGAAAA
5358313 ACGGAAATTG
Statistics
Matches: 140, Mismatches: 18, Indels: 10
0.83 0.11 0.06
Matches are distributed among these distances:
76 2 0.01
77 74 0.53
79 60 0.43
80 4 0.03
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (78 bp):
TTGAAAATACCTCAGCGTGTGAGCTCAAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTT
TGAAAGACAAAAA
Found at i:5358637 original size:76 final size:75
Alignment explanation
Indices: 5358483--5358810 Score: 227
Period size: 74 Copynumber: 4.1 Consensus size: 75
5358473 TTGAAAAACG
* * *
5358483 GAAATTGAAAATACCTCGGCATGTGACCTGAGGCTCAACTCGCCGCTCGTAATACGAGTTGATTT
1 GAAATTGAAAATACCTCAGCA-GTGACCTGAGGCTCAACTCACCGCTCGCAATACGAGTTGATTT
5358548 TTTTGACAACA
65 TTTTGACAACA
* * * *
5358559 GAAATTGAAATTACCTCAGC-GTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 GAAATTGAAAATACCTCAGCAGTGACCTGAGGCTCAACTCACCGCTCGCAATACGAGTTGA-TTT
5358623 TTTTGA-AAGGCA
65 TTTTGACAA--CA
** * * * * * *
5358635 GAAATTGAAAAATGGAAAT-TGAAAAT-ACCTCGGCGTGTGATCTGAGGCTCAACTCACCTCTCG
1 GAAATTG-AAAAT--ACCTCAG-CAGTGACCT----GAG-G--CT----C-A-ACTCACCGCTCG
*
5358698 CAATACGAGTTGACTTTTTTGACAACA
49 CAATACGAGTTGATTTTTTTGACAACA
* * * *
5358725 GAAATTGAAATTACCTCAGC-GTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 GAAATTGAAAATACCTCAGCAGTGACCTGAGGCTCAACTCACCGCTCGCAATACGAGTTGATTTT
5358789 TTTGA-AAGGCA
66 TTTGACAA--CA
5358800 GAAATTGAAAA
1 GAAATTGAAAA
5358811 ACGGAAATTG
Statistics
Matches: 196, Mismatches: 30, Indels: 53
0.70 0.11 0.19
Matches are distributed among these distances:
73 2 0.01
74 69 0.35
75 21 0.11
76 28 0.14
77 4 0.02
78 1 0.01
79 5 0.03
80 3 0.02
82 1 0.01
83 4 0.02
84 1 0.01
86 3 0.02
87 5 0.03
88 1 0.01
89 4 0.02
90 10 0.05
91 8 0.04
92 26 0.13
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (75 bp):
GAAATTGAAAATACCTCAGCAGTGACCTGAGGCTCAACTCACCGCTCGCAATACGAGTTGATTTT
TTTGACAACA
Found at i:5358689 original size:333 final size:329
Alignment explanation
Indices: 5358155--5359083 Score: 1214
Period size: 333 Copynumber: 2.9 Consensus size: 329
5358145 ATAAATTGAA
* * * * ** * *
5358155 AAAATACCTCAGTGTGTGATCTGAAGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTTTGAA
1 AAAATACCTCGGCGTGTGACCTGAGGCTCAACTC-CCACTCG-AATACGAGTTGATTTTTTTGAC
* * * *
5358220 AGACAAAAATTGAAAATAGCTCAGCGTGTGAGCC-AAGGCTCAACTCACCTCTCGCAATATGAGT
64 A-ACAGAAATTGAAATTACCTCAGCGTGT---CCTGAGGCTCAACTCACCTCTCGCAATATGAGT
* * *
5358284 TGATTTTTTTGAAAGGCAGAAATTGAAAAACGGAAATTGAAAATACCTTGGCGTTTGACCTGAGG
125 TGATTTTTTTGAAAGGCAGAAATTGAAAAATGGAAATTGAAAATACCTCGGCGTGTGACCTGAGG
* *
5358349 CTCAACTCGCCTCTCACAATACGAGTTGATTTTTTTGACAACAGAAATTGAAATTACCTCAGCGT
190 CTCAACTCACCTCTCGCAATACGAGTTGA-TTTTTTGACAACAGAAATTGAAATTACCTCAGCGT
*
5358414 GTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTAATTTTTTTTTGAAAGGCAGAAATTGAAA
254 GTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAGGCAGAAATTGAAA
5358479 AACGGAAATTG
319 AACGGAAATTG
* *
5358490 AAAATACCTCGGCATGTGACCTGAGGCTCAACTCGCCGCTCGTAATACGAGTTGATTTTTTTGAC
1 AAAATACCTCGGCGTGTGACCTGAGGCTCAACTC-CCACTCG-AATACGAGTTGATTTTTTTGAC
5358555 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
64 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
*
5358620 TTTTTTTGAAAGGCAGAAATTGAAAAATGGAAATTGAAAATACCTCGGCGTGTGATCTGAGGCTC
128 TTTTTTTGAAAGGCAGAAATTGAAAAATGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTC
5358685 AACTCACCTCTCGCAATACGAGTTGACTTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTC
193 AACTCACCTCTCGCAATACGAGTTGA-TTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTC
5358750 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA--TTTTTTTGAAAGGCAGAAATTGAAAAAC
257 CTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAGGCAGAAATTGAAAAAC
5358813 GGAAATTG
322 GGAAATTG
*
5358821 AAAATACCTCGGCGTGTGACCTGAGGCTCAACT--CAC-C----AC------------TCG-CAA
1 AAAATACCTCGGCGTGTGACCTGAGGCTCAACTCCCACTCGAATACGAGTTGATTTTTTTGACAA
5358866 CAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
66 CAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
* * * * *
5358931 TTTTG--A---A-AAA-T-----AT--AAGTTGAAAACACCTCAGTGTGTGACCCGAGGCTCAAC
131 TTTTGAAAGGCAGAAATTGAAAAATGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAAC
* * *
5358982 TCACCTCTCGCAATATGAGTTGA-TTTTTGAAAACAGAAATTGAAATTACCTCAGCGTGTCCCGA
196 TCACCTCTCGCAATACGAGTTGATTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGA
*
5359046 GGCTCAACTCACCTCTCACAATATGAGTTGATTTTTTT
261 GGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTT
5359084 GAAAAACAGA
Statistics
Matches: 554, Mismatches: 36, Indels: 49
0.87 0.06 0.08
Matches are distributed among these distances:
292 69 0.12
294 59 0.11
296 2 0.00
301 1 0.00
302 3 0.01
303 1 0.00
306 1 0.00
308 8 0.01
309 65 0.12
310 2 0.00
322 2 0.00
327 1 0.00
328 2 0.00
331 70 0.13
332 32 0.06
333 157 0.28
334 24 0.04
335 55 0.10
ACGTcount: A:0.31, C:0.21, G:0.19, T:0.29
Consensus pattern (329 bp):
AAAATACCTCGGCGTGTGACCTGAGGCTCAACTCCCACTCGAATACGAGTTGATTTTTTTGACAA
CAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
TTTTGAAAGGCAGAAATTGAAAAATGGAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAAC
TCACCTCTCGCAATACGAGTTGATTTTTTGACAACAGAAATTGAAATTACCTCAGCGTGTCCTGA
GGCTCAACTCACCTCTCGCAATATGAGTTGATTTTTTTTTGAAAGGCAGAAATTGAAAAACGGAA
ATTG
Found at i:5358727 original size:166 final size:165
Alignment explanation
Indices: 5358155--5358865 Score: 1136
Period size: 167 Copynumber: 4.3 Consensus size: 165
5358145 ATAAATTGAA
* * * * * * *
5358155 AAAATACCTCAGTGTGTGATCTGAAGCTCAACTCACCTTTCGCAATATGAGTTGATTTTTTTGAA
1 AAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTTTTTGAC
* * * *
5358220 AGACAAAAATTGAAAATAGCTCAGCGTGTGAGCC-AAGGCTCAACTCACCTCTCGCAATATGAGT
66 A-ACAGAAATTGAAATTACCTCAGCGTGT---CCTGAGGCTCAACTCACCTCTCGCAATATGAGT
5358284 TGATTTTTTTGAAAGGCAGAAATTGAAAAACGGAAATTG
127 TGATTTTTTTGAAAGGCAGAAATTGAAAAACGGAAATTG
* * * *
5358323 AAAATACCTTGGCGTTTGACCTGAGGCTCAACTCGCCTCTCACAATACGAGTTGATTTTTTTGAC
1 AAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTTTTTGAC
*
5358388 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTAAT
66 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
5358453 TTTTTTTTGAAAGGCAGAAATTGAAAAACGGAAATTG
130 -TTTTTTTGAAAGGCAGAAATTGAAAAACGGAAATTG
* * * *
5358490 AAAATACCTCGGCATGTGACCTGAGGCTCAACTCGCCGCTCGTAATACGAGTTGATTTTTTTGAC
1 AAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTTTTTGAC
5358555 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
66 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
*
5358620 TTTTTTTGAAAGGCAGAAATTGAAAAATGGAAATTG
130 TTTTTTTGAAAGGCAGAAATTGAAAAACGGAAATTG
* *
5358656 AAAATACCTCGGCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGACTTTTTTGAC
1 AAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTTTTTGAC
5358721 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
66 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
5358786 TTTTTTGAAAGGCAGAAATTGAAAAACGGAAATTG
131 TTTTTTGAAAGGCAGAAATTGAAAAACGGAAATTG
*
5358821 AAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCACTCGCAA
1 AAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAA
5358866 CAGAAATTGA
Statistics
Matches: 507, Mismatches: 33, Indels: 9
0.92 0.06 0.02
Matches are distributed among these distances:
164 2 0.00
165 109 0.21
166 159 0.31
167 182 0.36
168 55 0.11
ACGTcount: A:0.32, C:0.21, G:0.20, T:0.28
Consensus pattern (165 bp):
AAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGATTTTTTTGAC
AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
TTTTTTGAAAGGCAGAAATTGAAAAACGGAAATTG
Found at i:5358729 original size:90 final size:89
Alignment explanation
Indices: 5358559--5358734 Score: 257
Period size: 92 Copynumber: 2.0 Consensus size: 89
5358549 TTTGACAACA
* * *
5358559 GAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTTT
1 GAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGATCTTT
5358624 TTTGAAAGGCAGAAATTGAAAAATG
66 TTTGAAA-GCAGAAATTGAAAAATG
* *
5358649 GAAATTGAAAATACCTCGGCGTGTGATCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGA-CT
1 GAAATTGAAAATACCTCAGCGTGT--CCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGATCT
5358713 TTTTTGACAA-CAGAAATTGAAA
64 TTTTTGA-AAGCAGAAATTGAAA
5358735 TTACCTCAGC
Statistics
Matches: 78, Mismatches: 5, Indels: 6
0.88 0.06 0.07
Matches are distributed among these distances:
90 34 0.44
91 8 0.10
92 36 0.46
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.28
Consensus pattern (89 bp):
GAAATTGAAAATACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATACGAGTTGATCTTT
TTTGAAAGCAGAAATTGAAAAATG
Found at i:5358915 original size:52 final size:53
Alignment explanation
Indices: 5358814--5358917 Score: 165
Period size: 52 Copynumber: 2.0 Consensus size: 53
5358804 TTGAAAAACG
*
5358814 GAAATTGAAAATACCTCGGCGTGTGACCTGAGGCTCAACTCACCACTCGCAACA
1 GAAATTGAAAATACCTCAGCGTGT-ACCTGAGGCTCAACTCACCACTCGCAACA
* *
5358868 GAAATTGAAATTACCTCAGCGTGT-CCTGAGGCTCAACTCACCTCTCGCAA
1 GAAATTGAAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCACTCGCAA
5358918 TATGAGTTGA
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
52 25 0.53
54 22 0.47
ACGTcount: A:0.30, C:0.30, G:0.19, T:0.21
Consensus pattern (53 bp):
GAAATTGAAAATACCTCAGCGTGTACCTGAGGCTCAACTCACCACTCGCAACA
Found at i:5358984 original size:77 final size:73
Alignment explanation
Indices: 5358867--5359089 Score: 315
Period size: 72 Copynumber: 3.0 Consensus size: 73
5358857 CACTCGCAAC
** *
5358867 AGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
1 AGAAATTGAAAACACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
5358932 TTTGAAAA
66 TTTGAAAA
* *
5358940 ATATAAGTTGAAAACACCTCAGTGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
1 AGA-AA-TTGAAAACACCTCAGCGTGT--CCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA
5359005 --TTTTTGAAAA
62 TTTTTTTGAAAA
** *
5359015 CAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCACAATATGAGTTGATTT
1 -AGAAATTGAAAACACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTT
5359080 TTTTGAAAA
65 TTTTGAAAA
5359089 A
1 A
5359090 CAGAAATTAA
Statistics
Matches: 133, Mismatches: 10, Indels: 14
0.85 0.06 0.09
Matches are distributed among these distances:
72 35 0.26
73 3 0.02
74 29 0.22
75 29 0.22
76 2 0.02
77 35 0.26
ACGTcount: A:0.31, C:0.22, G:0.17, T:0.30
Consensus pattern (73 bp):
AGAAATTGAAAACACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGATTTT
TTTGAAAA
Found at i:5359079 original size:72 final size:73
Alignment explanation
Indices: 5358864--5359097 Score: 337
Period size: 75 Copynumber: 3.1 Consensus size: 73
5358854 CACCACTCGC
*
5358864 AACAGAAATTGAAATTACCTCAGCGTGTCCTGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
1 AACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
5358929 TTTTTTGAA
65 TTTTTTGAA
* ** *
5358938 AA-ATATAAGTTGAAAACACCTCAGTGTGTGACCCGAGGCTCAACTCACCTCTCGCAATATGAGT
1 AACAGA-AA-TTGAAATTACCTCAGCGTGT--CCCGAGGCTCAACTCACCTCTCGCAATATGAGT
5359002 TGA-TTTTTGAA
62 TGATTTTTTGAA
*
5359013 AACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCACAATATGAGTTGAT
1 AACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGA-
5359078 TTTTTTGAAA
65 TTTTTTG-AA
5359088 AACAGAAATT
1 AACAGAAATT
5359098 AAAAGGCTTA
Statistics
Matches: 142, Mismatches: 10, Indels: 15
0.85 0.06 0.09
Matches are distributed among these distances:
72 35 0.25
73 2 0.01
74 27 0.19
75 41 0.29
76 2 0.01
77 35 0.25
ACGTcount: A:0.32, C:0.21, G:0.17, T:0.29
Consensus pattern (73 bp):
AACAGAAATTGAAATTACCTCAGCGTGTCCCGAGGCTCAACTCACCTCTCGCAATATGAGTTGAT
TTTTTGAA
Found at i:5366041 original size:2 final size:2
Alignment explanation
Indices: 5366028--5366062 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
5366018 TAAAACATAC
*
5366028 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
5366063 CATGACATAC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:5366577 original size:11 final size:11
Alignment explanation
Indices: 5366561--5366590 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
5366551 TAACATTAAG
5366561 AATATATATAT
1 AATATATATAT
*
5366572 AATATAAATAT
1 AATATATATAT
5366583 AATATATA
1 AATATATA
5366591 CAATATACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AATATATATAT
Found at i:5366996 original size:27 final size:27
Alignment explanation
Indices: 5366963--5367031 Score: 138
Period size: 27 Copynumber: 2.6 Consensus size: 27
5366953 ACCGGTCGAT
5366963 CGTCGGCCACCGCCCGTCACCGACCAC
1 CGTCGGCCACCGCCCGTCACCGACCAC
5366990 CGTCGGCCACCGCCCGTCACCGACCAC
1 CGTCGGCCACCGCCCGTCACCGACCAC
5367017 CGTCGGCCACCGCCC
1 CGTCGGCCACCGCCC
5367032 ACGGTGGCCG
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 42 1.00
ACGTcount: A:0.13, C:0.57, G:0.23, T:0.07
Consensus pattern (27 bp):
CGTCGGCCACCGCCCGTCACCGACCAC
Found at i:5367000 original size:17 final size:17
Alignment explanation
Indices: 5366980--5367033 Score: 50
Period size: 17 Copynumber: 3.6 Consensus size: 17
5366970 CACCGCCCGT
5366980 CACCGACCACCGTCGGC
1 CACCGACCACCGTCGGC
5366997 CACCG--C-CCGT----
1 CACCGACCACCGTCGGC
5367007 CACCGACCACCGTCGGC
1 CACCGACCACCGTCGGC
*
5367024 CACCGCCCAC
1 CACCGACCAC
5367034 GGTGGCCGAA
Statistics
Matches: 29, Mismatches: 1, Indels: 14
0.66 0.02 0.32
Matches are distributed among these distances:
10 5 0.17
12 1 0.03
13 4 0.14
14 4 0.14
15 1 0.03
17 14 0.48
ACGTcount: A:0.17, C:0.57, G:0.20, T:0.06
Consensus pattern (17 bp):
CACCGACCACCGTCGGC
Found at i:5367448 original size:15 final size:15
Alignment explanation
Indices: 5367430--5367464 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
5367420 GCTTCTTTTT
*
5367430 TTTTTTTGGGTTAGG
1 TTTTTTTGGGGTAGG
5367445 TTTTTTTGGGGTAGG
1 TTTTTTTGGGGTAGG
5367460 TTTTT
1 TTTTT
5367465 CTTTTTCTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.06, C:0.00, G:0.31, T:0.63
Consensus pattern (15 bp):
TTTTTTTGGGGTAGG
Found at i:5367479 original size:16 final size:15
Alignment explanation
Indices: 5367460--5367495 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
5367450 TTGGGGTAGG
*
5367460 TTTTTCTTTTTCTTTT
1 TTTTTCTTTGT-TTTT
5367476 TTTTTCTTTGTTTTT
1 TTTTTCTTTGTTTTT
5367491 TTTTT
1 TTTTT
5367496 GGGTTAGGTT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.47
16 10 0.53
ACGTcount: A:0.00, C:0.08, G:0.03, T:0.89
Consensus pattern (15 bp):
TTTTTCTTTGTTTTT
Found at i:5371001 original size:18 final size:18
Alignment explanation
Indices: 5370980--5371017 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
5370970 ATTCGAGTAA
5370980 AACCGAAAAAATTCGGTT
1 AACCGAAAAAATTCGGTT
**
5370998 AACCGACCAAATTCGGTT
1 AACCGAAAAAATTCGGTT
5371016 AA
1 AA
5371018 TCGGTCGGTT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.21, G:0.16, T:0.21
Consensus pattern (18 bp):
AACCGAAAAAATTCGGTT
Found at i:5371259 original size:13 final size:13
Alignment explanation
Indices: 5371243--5371267 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5371233 CAAGTACCTC
5371243 ACCCAACCCAATT
1 ACCCAACCCAATT
5371256 ACCCAACCCAAT
1 ACCCAACCCAAT
5371268 CATAAAAATT
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:0.48, G:0.00, T:0.12
Consensus pattern (13 bp):
ACCCAACCCAATT
Found at i:5371305 original size:5 final size:6
Alignment explanation
Indices: 5371292--5371332 Score: 55
Period size: 6 Copynumber: 6.5 Consensus size: 6
5371282 ATAATTTAAT
*
5371292 AAATAA AAATAA AATTCTAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AA--ATAA AAATAA AAATAA AAATAA AAA
5371333 ACATATAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
6 26 0.84
8 5 0.16
ACGTcount: A:0.78, C:0.02, G:0.00, T:0.20
Consensus pattern (6 bp):
AAATAA
Found at i:5371333 original size:20 final size:20
Alignment explanation
Indices: 5371292--5371333 Score: 57
Period size: 20 Copynumber: 2.1 Consensus size: 20
5371282 ATAATTTAAT
* **
5371292 AAATAAAAATAAAATTCTAA
1 AAATAAAAATAAAAATAAAA
5371312 AAATAAAAATAAAAATAAAA
1 AAATAAAAATAAAAATAAAA
5371332 AA
1 AA
5371334 CATATAATTT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.79, C:0.02, G:0.00, T:0.19
Consensus pattern (20 bp):
AAATAAAAATAAAAATAAAA
Found at i:5372528 original size:2 final size:2
Alignment explanation
Indices: 5372523--5372549 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
5372513 ATTCTCTCCA
5372523 TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC T
5372550 TTTTTTTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:5389650 original size:12 final size:11
Alignment explanation
Indices: 5389633--5389674 Score: 52
Period size: 12 Copynumber: 3.9 Consensus size: 11
5389623 AAAAGGCAAG
5389633 ATTATTAAATAA
1 ATTATTAAA-AA
5389645 ATTATTAAAAA
1 ATTATTAAAAA
*
5389656 A-T-TTATAAA
1 ATTATTAAAAA
5389665 ATTATTAAAA
1 ATTATTAAAA
5389675 TAGAAGAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
9 7 0.27
10 2 0.08
11 8 0.31
12 9 0.35
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
ATTATTAAAAA
Found at i:5389936 original size:20 final size:20
Alignment explanation
Indices: 5389906--5389985 Score: 74
Period size: 21 Copynumber: 4.0 Consensus size: 20
5389896 CAAAACAATG
*
5389906 AAATCTTAAACTTAGAATTTT
1 AAATCTCAAACTTA-AATTTT
* *
5389927 AAAT-TTAAACTTTAAACTTT
1 AAATCTCAAAC-TTAAATTTT
*
5389947 AAATCTCAAACCTTAAATTAT
1 AAATCTCAAA-CTTAAATTTT
*
5389968 AAAT-TCGAACTTAAATTT
1 AAATCTCAAACTTAAATTT
5389986 GAATCCTGAA
Statistics
Matches: 50, Mismatches: 6, Indels: 8
0.78 0.09 0.12
Matches are distributed among these distances:
19 8 0.16
20 19 0.38
21 22 0.44
22 1 0.02
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.40
Consensus pattern (20 bp):
AAATCTCAAACTTAAATTTT
Found at i:5406572 original size:40 final size:39
Alignment explanation
Indices: 5406510--5406807 Score: 429
Period size: 40 Copynumber: 7.5 Consensus size: 39
5406500 AAACCAAGTA
* * *
5406510 CCTTCGGGATTTA-ACCGGATATAGCT-ACTCGCTCAAATG
1 CCTTCGGGACTTAGCCCGGA-ATAG-TAACTCGCACAAATG
**
5406549 CCTTCGGGACTTAGCCCGGATATAGTAGTTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGA-ATAGTAACTCGCACAAATG
5406589 CCTTCGGGACTTAGCCCGGATATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGA-ATAGTAACTCGCACAAATG
5406629 CCTTCGGGACTTAGCCCGGAAATAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGG-AATAGTAACTCGCACAAATG
5406669 CCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGAA-TAGTAACTCGCACAAATG
5406709 CCTTCGGGACTTAGCCCGGAATTAGTAACTCGCACAAATG
1 CCTTCGGGACTTAGCCCGGAA-TAGTAACTCGCACAAATG
* * * *
5406749 ACTTCGGGACTTAGCCCGGAATTAGTCACTAGCACAGATG
1 CCTTCGGGACTTAGCCCGGAA-TAGTAACTCGCACAAATG
5406789 CCTTCGGGACTTAGCCCGG
1 CCTTCGGGACTTAGCCCGG
5406808 TTATCATCCG
Statistics
Matches: 243, Mismatches: 12, Indels: 7
0.93 0.05 0.03
Matches are distributed among these distances:
39 15 0.06
40 227 0.93
41 1 0.00
ACGTcount: A:0.26, C:0.27, G:0.23, T:0.23
Consensus pattern (39 bp):
CCTTCGGGACTTAGCCCGGAATAGTAACTCGCACAAATG
Found at i:5423385 original size:18 final size:18
Alignment explanation
Indices: 5423357--5423449 Score: 96
Period size: 18 Copynumber: 5.2 Consensus size: 18
5423347 CCCAACTACT
* *
5423357 GTATACGTGAACAGTACC
1 GTATACATGAATAGTACC
* *
5423375 GTATTCATGAATAGTGCC
1 GTATACATGAATAGTACC
* *
5423393 GTATACGTGAATAGTACT
1 GTATACATGAATAGTACC
* *
5423411 GTATACATGAATAGTGCT
1 GTATACATGAATAGTACC
* *
5423429 ATATACGTGAATAGTACC
1 GTATACATGAATAGTACC
5423447 GTA
1 GTA
5423450 AACGGTCGTA
Statistics
Matches: 60, Mismatches: 15, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 60 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (18 bp):
GTATACATGAATAGTACC
Found at i:5423409 original size:36 final size:36
Alignment explanation
Indices: 5423357--5423449 Score: 141
Period size: 36 Copynumber: 2.6 Consensus size: 36
5423347 CCCAACTACT
* *
5423357 GTATACGTGAACAGTACCGTATTCATGAATAGTGCC
1 GTATACGTGAATAGTACCGTATACATGAATAGTGCC
* *
5423393 GTATACGTGAATAGTACTGTATACATGAATAGTGCT
1 GTATACGTGAATAGTACCGTATACATGAATAGTGCC
*
5423429 ATATACGTGAATAGTACCGTA
1 GTATACGTGAATAGTACCGTA
5423450 AACGGTCGTA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
36 51 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (36 bp):
GTATACGTGAATAGTACCGTATACATGAATAGTGCC
Found at i:5426115 original size:15 final size:16
Alignment explanation
Indices: 5426086--5426117 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
5426076 TATATGATAA
5426086 AATTTTATGTTTTATT
1 AATTTTATGTTTTATT
5426102 AATTTTAT-TTTTATT
1 AATTTTATGTTTTATT
5426117 A
1 A
5426118 TATATTTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 8 0.50
16 8 0.50
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (16 bp):
AATTTTATGTTTTATT
Found at i:5428093 original size:137 final size:137
Alignment explanation
Indices: 5427847--5428133 Score: 538
Period size: 137 Copynumber: 2.1 Consensus size: 137
5427837 CATTGGGCCT
** * *
5427847 AAGCCCATTCAGGTAATAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCAAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
5427912 AGCCCCTTATTCAGATAATAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAATAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
5427977 CATATGC
131 CATATGC
5427984 AAGCCCATTTGGGTAACAGTGGTACTGGGCAAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAACAGTGGTACTGGGCAAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
5428049 AGCCCCTTATTCAGATAATAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
66 AGCCCCTTATTCAGATAATAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
5428114 CATATGC
131 CATATGC
5428121 AAGCCCATTTGGG
1 AAGCCCATTTGGG
5428134 GAGACTACTC
Statistics
Matches: 146, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
137 146 1.00
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (137 bp):
AAGCCCATTTGGGTAACAGTGGTACTGGGCAAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
AGCCCCTTATTCAGATAATAGTATGGCCCATAGGCCCATTTCAAAATACATGCAACATCAGTAAA
CATATGC
Found at i:5429956 original size:26 final size:26
Alignment explanation
Indices: 5429920--5430055 Score: 227
Period size: 26 Copynumber: 5.2 Consensus size: 26
5429910 CATGATATTC
5429920 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
5429946 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
5429972 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
5429998 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* **
5430024 TTATCATGGAACATTTACCTAACTTA
1 TTATCATGAAACATTTACCTAACCCA
5430050 TTATCA
1 TTATCA
5430056 ATTTGTATCA
Statistics
Matches: 103, Mismatches: 7, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 103 1.00
ACGTcount: A:0.37, C:0.24, G:0.05, T:0.34
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:5440685 original size:7 final size:7
Alignment explanation
Indices: 5440668--5440702 Score: 52
Period size: 7 Copynumber: 4.7 Consensus size: 7
5440658 CAAAAATAAC
5440668 CTTTCTTT
1 CTTT-TTT
5440676 CTTTTTT
1 CTTTTTT
5440683 CTTTTTT
1 CTTTTTT
5440690 CTTTTTCT
1 CTTTTT-T
5440698 CTTTT
1 CTTTT
5440703 CTCTCTAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 16 0.62
8 10 0.38
ACGTcount: A:0.00, C:0.20, G:0.00, T:0.80
Consensus pattern (7 bp):
CTTTTTT
Found at i:5445551 original size:9 final size:10
Alignment explanation
Indices: 5445528--5445571 Score: 51
Period size: 9 Copynumber: 4.8 Consensus size: 10
5445518 TTCTTTATTA
5445528 AATATTAT-T
1 AATATTATCT
*
5445537 ATTATT-TCT
1 AATATTATCT
5445546 AATATTAT-T
1 AATATTATCT
5445555 AATATTATC-
1 AATATTATCT
5445564 AATATTAT
1 AATATTAT
5445572 TTTTTTATAT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
8 1 0.03
9 28 0.93
10 1 0.03
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (10 bp):
AATATTATCT
Found at i:5445551 original size:18 final size:18
Alignment explanation
Indices: 5445528--5445572 Score: 65
Period size: 18 Copynumber: 2.5 Consensus size: 18
5445518 TTCTTTATTA
*
5445528 AATATTATTATTATT-TC
1 AATATTATTAATATTATC
5445545 TAATATTATTAATATTATC
1 -AATATTATTAATATTATC
5445564 AATATTATT
1 AATATTATT
5445573 TTTTTATATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
18 23 0.92
19 2 0.08
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (18 bp):
AATATTATTAATATTATC
Found at i:5445691 original size:28 final size:29
Alignment explanation
Indices: 5445637--5445692 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 29
5445627 ATATATGGTA
* *
5445637 TTATTTTTAGTTATTTTAATTTCATATTG
1 TTATTATTAGTTATTATAATTTCATATTG
5445666 TTATTATTAG-TATTATAATATT-ATATT
1 TTATTATTAGTTATTATAAT-TTCATATT
5445693 TATTTTAATA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
28 13 0.54
29 11 0.46
ACGTcount: A:0.30, C:0.02, G:0.05, T:0.62
Consensus pattern (29 bp):
TTATTATTAGTTATTATAATTTCATATTG
Found at i:5445725 original size:22 final size:21
Alignment explanation
Indices: 5445676--5445733 Score: 54
Period size: 17 Copynumber: 2.9 Consensus size: 21
5445666 TTATTATTAG
5445676 TATTATAATA--T-TATA-TT
1 TATTATAATATGTATATATTT
*
5445693 TATTTTAATATTGGTATATATTT
1 TATTATAATA-T-GTATATATTT
5445716 TATTAT-ATATGTATATAT
1 TATTATAATATGTATATAT
5445734 ATACTTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 9
0.75 0.05 0.20
Matches are distributed among these distances:
17 9 0.27
20 8 0.24
21 2 0.06
22 7 0.21
23 7 0.21
ACGTcount: A:0.36, C:0.00, G:0.05, T:0.59
Consensus pattern (21 bp):
TATTATAATATGTATATATTT
Found at i:5445791 original size:12 final size:12
Alignment explanation
Indices: 5445666--5445791 Score: 65
Period size: 12 Copynumber: 10.7 Consensus size: 12
5445656 TTTCATATTG
5445666 TTATTATTAGTAT
1 TTATTATTA-TAT
*
5445679 TATAATATTATAT
1 T-TATTATTATAT
5445692 TTATT-TTAATAT
1 TTATTATT-ATAT
5445704 TGGTA-TA-TAT-T
1 T--TATTATTATAT
5445715 TTATTA-TATAT
1 TTATTATTATAT
*
5445726 GTA-TATATATACT
1 TTATTAT-TATA-T
5445739 TT-TTA-TATA-
1 TTATTATTATAT
* *
5445748 GTATTATCAT-T
1 TTATTATTATAT
5445759 TCTATTATTATAT
1 T-TATTATTATAT
*
5445772 TTATTATTATGT
1 TTATTATTATAT
5445784 TTATTATT
1 TTATTATT
5445792 TTCACTATTA
Statistics
Matches: 88, Mismatches: 9, Indels: 33
0.68 0.07 0.25
Matches are distributed among these distances:
9 3 0.03
10 10 0.11
11 13 0.15
12 40 0.45
13 13 0.15
14 9 0.10
ACGTcount: A:0.33, C:0.02, G:0.05, T:0.60
Consensus pattern (12 bp):
TTATTATTATAT
Found at i:5445800 original size:21 final size:21
Alignment explanation
Indices: 5445763--5445802 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
5445753 ATCATTTCTA
*
5445763 TTATTATATTTATTATTATGT
1 TTATTATATTTACTATTATGT
5445784 TTATTAT-TTTCACTATTAT
1 TTATTATATTT-ACTATTAT
5445803 TATTTTTTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 3 0.18
21 14 0.82
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.65
Consensus pattern (21 bp):
TTATTATATTTACTATTATGT
Found at i:5445935 original size:38 final size:40
Alignment explanation
Indices: 5445858--5445940 Score: 100
Period size: 38 Copynumber: 2.1 Consensus size: 40
5445848 ACTTATTATG
* * *
5445858 AATATTATTTTCTTATTATATTATTACGTATATTCTTTTT
1 AATATTATCTTCTTATTATATTATTACATATATTATTTTT
*
5445898 AATATTATCTT-TTA-TATATTA-TGCATATATATATTTTT
1 AATATTATCTTCTTATTATATTATTACATATAT-TATTTTT
5445936 AATAT
1 AATAT
5445941 CCTATTATTC
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
37 7 0.18
38 18 0.47
39 3 0.08
40 10 0.26
ACGTcount: A:0.33, C:0.06, G:0.02, T:0.59
Consensus pattern (40 bp):
AATATTATCTTCTTATTATATTATTACATATATTATTTTT
Found at i:5445989 original size:26 final size:26
Alignment explanation
Indices: 5445960--5446031 Score: 83
Period size: 25 Copynumber: 2.8 Consensus size: 26
5445950 CATATATTTT
5445960 ATTATGTATATATTTTTAATAACTAC
1 ATTATGTATATATTTTTAATAACTAC
* * * *
5445986 ATTATGTATGTATTTGTAA-CACTAT
1 ATTATGTATATATTTTTAATAACTAC
* *
5446011 ATTATGTACATACTTTTAATA
1 ATTATGTATATATTTTTAATA
5446032 TTATTATGTA
Statistics
Matches: 36, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
25 19 0.53
26 17 0.47
ACGTcount: A:0.36, C:0.08, G:0.07, T:0.49
Consensus pattern (26 bp):
ATTATGTATATATTTTTAATAACTAC
Found at i:5446015 original size:25 final size:26
Alignment explanation
Indices: 5445959--5446053 Score: 85
Period size: 26 Copynumber: 3.8 Consensus size: 26
5445949 TCATATATTT
*
5445959 TATTATGTATATATTTTTAATAACTA
1 TATTATGTATATATTTGTAATAACTA
* * *
5445985 CATTATGTATGTATTTGTAA-CACTA
1 TATTATGTATATATTTGTAATAACTA
*
5446010 TATTATGTACATACTTT-TAAT-A-T-
1 TATTATGTATATA-TTTGTAATAACTA
*
5446033 TATTATGTATTTATTT-TAATA
1 TATTATGTATATATTTGTAATA
5446054 TATATGTACA
Statistics
Matches: 57, Mismatches: 9, Indels: 9
0.76 0.12 0.12
Matches are distributed among these distances:
22 7 0.12
23 11 0.19
24 1 0.02
25 18 0.32
26 20 0.35
ACGTcount: A:0.35, C:0.06, G:0.06, T:0.53
Consensus pattern (26 bp):
TATTATGTATATATTTGTAATAACTA
Found at i:5446067 original size:20 final size:21
Alignment explanation
Indices: 5446008--5446068 Score: 79
Period size: 20 Copynumber: 2.9 Consensus size: 21
5445998 TTTGTAACAC
5446008 TATATTATGTACATACTTTTAA
1 TATATTATGTACATA-TTTTAA
**
5446030 TATTATTATGTATTTATTTTAA
1 TA-TATTATGTACATATTTTAA
5446052 TATA-TATGTACATATTT
1 TATATTATGTACATATTT
5446069 ATGTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
20 11 0.32
21 2 0.06
22 10 0.29
23 11 0.32
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.56
Consensus pattern (21 bp):
TATATTATGTACATATTTTAA
Found at i:5446067 original size:24 final size:22
Alignment explanation
Indices: 5446024--5446101 Score: 61
Period size: 22 Copynumber: 3.5 Consensus size: 22
5446014 ATGTACATAC
**
5446024 TTTTAATATTATTATGTATTTA
1 TTTTAATATTATTACATATTTA
5446046 TTTTAATATATATGTACATATTTA
1 TTTTAATAT-TAT-TACATATTTA
* * *
5446070 -TGTAGTATTATTA-ATACATATA
1 TTTTAATATTATTACAT--ATTTA
5446092 TTTTAATATT
1 TTTTAATATT
5446102 TCTAATATAT
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
20 2 0.05
21 2 0.05
22 16 0.36
23 16 0.36
24 8 0.18
ACGTcount: A:0.36, C:0.03, G:0.05, T:0.56
Consensus pattern (22 bp):
TTTTAATATTATTACATATTTA
Found at i:5446135 original size:26 final size:26
Alignment explanation
Indices: 5446098--5446151 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
5446088 TATATTTTAA
*
5446098 TATTTCTAATATA-TATTGTATATGTT
1 TATTTCTAATATATTA-TGTATATATT
5446124 TATTT-TATATATATTATGTATATATT
1 TATTTCTA-ATATATTATGTATATATT
5446150 TA
1 TA
5446152 AAATTATTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
25 2 0.08
26 21 0.84
27 2 0.08
ACGTcount: A:0.33, C:0.02, G:0.06, T:0.59
Consensus pattern (26 bp):
TATTTCTAATATATTATGTATATATT
Found at i:5446208 original size:2 final size:2
Alignment explanation
Indices: 5446201--5446232 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5446191 ATTTACTTTA
5446201 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
5446233 GGCACTATTA
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:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5449853 original size:2 final size:2
Alignment explanation
Indices: 5449846--5449899 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
5449836 TGCCTTTGAG
5449846 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
5449888 TA TA TA TT TA TA
1 TA TA TA TA TA TA
5449900 AATTATAATT
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 50 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:5452588 original size:82 final size:82
Alignment explanation
Indices: 5452449--5452613 Score: 312
Period size: 82 Copynumber: 2.0 Consensus size: 82
5452439 GTTCATTACA
*
5452449 GTATAAAAGAAAATTAGTTCTTTGGTCACTAGTGTTGGCCTTTCCAGTGATTCCTAGTGATGATT
1 GTATAAAAGAAAATTAGTTCTCTGGTCACTAGTGTTGGCCTTTCCAGTGATTCCTAGTGATGATT
5452514 TAAATCTTGTAAATCAT
66 TAAATCTTGTAAATCAT
*
5452531 GTATAAAAGAAAATTAGTTCTCTGGTCACTAGTGTTGGCCTTTCCAGTGATTTCTAGTGATGATT
1 GTATAAAAGAAAATTAGTTCTCTGGTCACTAGTGTTGGCCTTTCCAGTGATTCCTAGTGATGATT
5452596 TAAATCTTGTAAATCAT
66 TAAATCTTGTAAATCAT
5452613 G
1 G
5452614 GTAAGTGTCT
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.29, C:0.13, G:0.19, T:0.39
Consensus pattern (82 bp):
GTATAAAAGAAAATTAGTTCTCTGGTCACTAGTGTTGGCCTTTCCAGTGATTCCTAGTGATGATT
TAAATCTTGTAAATCAT
Found at i:5454868 original size:18 final size:19
Alignment explanation
Indices: 5454845--5454880 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
5454835 ATTGTTTTCA
5454845 TACCTT-TAGGTATATCAC
1 TACCTTGTAGGTATATCAC
5454863 TACCTTGTAGGTATATCA
1 TACCTTGTAGGTATATCA
5454881 TTAATATCAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.28, C:0.19, G:0.14, T:0.39
Consensus pattern (19 bp):
TACCTTGTAGGTATATCAC
Found at i:5455937 original size:21 final size:21
Alignment explanation
Indices: 5455911--5455963 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
5455901 CGCTGTTTCT
*
5455911 AATCTCACCGCTACAGTATCC
1 AATCTCACCGCTACAGTAACC
*
5455932 AATCTCACCGCTACAGTAACT
1 AATCTCACCGCTACAGTAACC
5455953 AATCTCACCGC
1 AATCTCACCGC
5455964 CACCGCTGTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.30, C:0.38, G:0.09, T:0.23
Consensus pattern (21 bp):
AATCTCACCGCTACAGTAACC
Found at i:5456063 original size:2 final size:2
Alignment explanation
Indices: 5456050--5456098 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
5456040 AGGTATATGC
*
5456050 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5456092 AT AT AT A
1 AT AT AT A
5456099 CACACATACA
Statistics
Matches: 45, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:5456449 original size:22 final size:22
Alignment explanation
Indices: 5456424--5456468 Score: 56
Period size: 22 Copynumber: 2.0 Consensus size: 22
5456414 TACATATAAA
5456424 TATTACATA-TAATATTTGATTT
1 TATTA-ATATTAATATTTGATTT
* *
5456446 TATTAATATTTATGTTTGATTT
1 TATTAATATTAATATTTGATTT
5456468 T
1 T
5456469 TTTGAAATGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 3 0.15
22 17 0.85
ACGTcount: A:0.31, C:0.02, G:0.07, T:0.60
Consensus pattern (22 bp):
TATTAATATTAATATTTGATTT
Done.