Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr1
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: 96304692
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2448173 characters in sequence are not A, C, G, or T
File 16 of 313
Found at i:5255071 original size:19 final size:19
Alignment explanation
Indices: 5255029--5255072 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
5255019 TTGTTGAAAA
5255029 TTTATTTAGGTAGATAAAT
1 TTTATTTAGGTAGATAAAT
*
5255048 CTTATTTAGGTAGATAAAT
1 TTTATTTAGGTAGATAAAT
5255067 TTTATT
1 TTTATT
5255073 CATATTCTAG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.34, C:0.02, G:0.14, T:0.50
Consensus pattern (19 bp):
TTTATTTAGGTAGATAAAT
Found at i:5261847 original size:5 final size:5
Alignment explanation
Indices: 5261837--5261868 Score: 55
Period size: 5 Copynumber: 6.4 Consensus size: 5
5261827 CTGTGTGTTC
*
5261837 TTTAT TTTAT TTTAT TTTAT TTCAT TTTAT TT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTTAT TT
5261869 ACAGTTTTCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
5 25 1.00
ACGTcount: A:0.19, C:0.03, G:0.00, T:0.78
Consensus pattern (5 bp):
TTTAT
Found at i:5263249 original size:29 final size:29
Alignment explanation
Indices: 5263207--5263265 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
5263197 TCAAGGTGAA
5263207 TGTTCTTTATTAGAATGTTGGACTCCACC
1 TGTTCTTTATTAGAATGTTGGACTCCACC
5263236 TGTTCTTTATTAGAATGTTGGACTCCACC
1 TGTTCTTTATTAGAATGTTGGACTCCACC
5263265 T
1 T
5263266 AGTCCTTCAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.20, C:0.20, G:0.17, T:0.42
Consensus pattern (29 bp):
TGTTCTTTATTAGAATGTTGGACTCCACC
Found at i:5265628 original size:50 final size:51
Alignment explanation
Indices: 5265551--5265659 Score: 184
Period size: 50 Copynumber: 2.2 Consensus size: 51
5265541 CACCATGGCA
* * *
5265551 ACAAGTGATAAGTGATAGCTTTGGCTACACTTATCTGATCAAGGATAAGTG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
5265602 A-AAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
1 ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
5265652 ACAAGTGA
1 ACAAGTGA
5265660 AAAATGGTAG
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
50 47 0.87
51 7 0.13
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.27
Consensus pattern (51 bp):
ACAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGGACAAATG
Found at i:5265693 original size:31 final size:31
Alignment explanation
Indices: 5265655--5265802 Score: 206
Period size: 31 Copynumber: 4.8 Consensus size: 31
5265645 ACAAATGACA
* * * *
5265655 AGTGAAAAATGGTAGTTTCGGTTACCTAATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
5265686 AGTGAAAAGTGGTAGTTTCGGGTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
5265717 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
5265748 AGTGAAAAATGGTAGCTCCGGCTACCTGATC
1 AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
* *
5265779 AGTGAATAGTGGTAGCTTTGGCTA
1 AGTGAAAAGTGGTAGCTTCGGCTA
5265803 AAAGTGACAA
Statistics
Matches: 106, Mismatches: 11, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 106 1.00
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (31 bp):
AGTGAAAAGTGGTAGCTTCGGCTACCTGATC
Found at i:5269714 original size:37 final size:38
Alignment explanation
Indices: 5269657--5269736 Score: 117
Period size: 37 Copynumber: 2.1 Consensus size: 38
5269647 CAAAAAGCTA
** *
5269657 GATTATAGGGAAAGGCTACACACAGAATTAAGGCATTC
1 GATTATAGGGAAAGGCTACACACAGAAAGAAAGCATTC
*
5269695 GATTA-AGGGAAAGGGTACACACAGAAAGAAAGCATTC
1 GATTATAGGGAAAGGCTACACACAGAAAGAAAGCATTC
5269732 GATTA
1 GATTA
5269737 CAATGAGACC
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
37 33 0.87
38 5 0.13
ACGTcount: A:0.42, C:0.14, G:0.25, T:0.19
Consensus pattern (38 bp):
GATTATAGGGAAAGGCTACACACAGAAAGAAAGCATTC
Found at i:5269886 original size:26 final size:26
Alignment explanation
Indices: 5269850--5269907 Score: 89
Period size: 26 Copynumber: 2.2 Consensus size: 26
5269840 ACATTCTCGA
5269850 ATGGCTATCTTCATGAGAAAATTTAC
1 ATGGCTATCTTCATGAGAAAATTTAC
* **
5269876 ATGGCTATCTTGATGAGACCATTTAC
1 ATGGCTATCTTCATGAGAAAATTTAC
5269902 ATGGCT
1 ATGGCT
5269908 CAACCTATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 29 1.00
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.34
Consensus pattern (26 bp):
ATGGCTATCTTCATGAGAAAATTTAC
Found at i:5270471 original size:28 final size:28
Alignment explanation
Indices: 5270406--5270464 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
5270396 CAAAATTCAA
*
5270406 ACTTTAATTA-TAAAATAATTAATTTTC
1 ACTTAAATTATTAAAATAATTAATTTTC
*
5270433 ACTTAAATTATTAAAATATTTAATTTT-
1 ACTTAAATTATTAAAATAATTAATTTTC
5270460 ACTTA
1 ACTTA
5270465 TTTTTATAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 14 0.48
28 15 0.52
ACGTcount: A:0.44, C:0.07, G:0.00, T:0.49
Consensus pattern (28 bp):
ACTTAAATTATTAAAATAATTAATTTTC
Found at i:5271936 original size:47 final size:47
Alignment explanation
Indices: 5271847--5271936 Score: 119
Period size: 47 Copynumber: 1.9 Consensus size: 47
5271837 GGTAAGGTGC
* * *
5271847 CGATGCCATGTCCTAGACACAGTCTTATACTGGCTCATATCTCAAGT
1 CGATGCCATGTCCCAGACACAGTCTTACACTGACTCATATCTCAAGT
**
5271894 CGATGCCATGTCCCAGACATGGTCTTACACTGACT-ATCATCTC
1 CGATGCCATGTCCCAGACACAGTCTTACACTGACTCAT-ATCTC
5271937 GTACTACACC
Statistics
Matches: 37, Mismatches: 5, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
46 2 0.05
47 35 0.95
ACGTcount: A:0.24, C:0.30, G:0.17, T:0.29
Consensus pattern (47 bp):
CGATGCCATGTCCCAGACACAGTCTTACACTGACTCATATCTCAAGT
Found at i:5272093 original size:211 final size:211
Alignment explanation
Indices: 5271729--5272144 Score: 823
Period size: 211 Copynumber: 2.0 Consensus size: 211
5271719 AATTAGGTAC
5271729 CTACACCACTCACAACATGGTTATACTTTCCTTGTTAGTTTAAGAACATAACTTTTACCGTTGAA
1 CTACACCACTCACAACATGGTTATACTTTCCTTGTTAGTTTAAGAACATAACTTTTACCGTTGAA
5271794 CCATTCGGAATACTACCTGATATTACATAAGCCTCAAGCATAGGGTAAGGTGCCGATGCCATGTC
66 CCATTCGGAATACTACCTGATATTACATAAGCCTCAAGCATAGGGTAAGGTGCCGATGCCATGTC
5271859 CTAGACACAGTCTTATACTGGCTCATATCTCAAGTCGATGCCATGTCCCAGACATGGTCTTACAC
131 CTAGACACAGTCTTATACTGGCTCATATCTCAAGTCGATGCCATGTCCCAGACATGGTCTTACAC
5271924 TGACTATCATCTCGTA
196 TGACTATCATCTCGTA
5271940 CTACACCACTCACAACATGGTTATACTTTCCTTGTTAGTTTAAGAACATAACTTTTACCGTTGAA
1 CTACACCACTCACAACATGGTTATACTTTCCTTGTTAGTTTAAGAACATAACTTTTACCGTTGAA
5272005 CCATTCGGAATACTACCTGATATTACATAAGCCTCAAGCATAGGGTAAGGTGCCGATGCCATGTC
66 CCATTCGGAATACTACCTGATATTACATAAGCCTCAAGCATAGGGTAAGGTGCCGATGCCATGTC
5272070 CTAGACACAGTCTTATACTGGCTCATATCTCAAGTCGATGCCATGTCCCAGACATGGTCTTACAC
131 CTAGACACAGTCTTATACTGGCTCATATCTCAAGTCGATGCCATGTCCCAGACATGGTCTTACAC
*
5272135 TGACTCTCAT
196 TGACTATCAT
5272145 AATGTGGCTG
Statistics
Matches: 204, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
211 204 1.00
ACGTcount: A:0.28, C:0.26, G:0.16, T:0.30
Consensus pattern (211 bp):
CTACACCACTCACAACATGGTTATACTTTCCTTGTTAGTTTAAGAACATAACTTTTACCGTTGAA
CCATTCGGAATACTACCTGATATTACATAAGCCTCAAGCATAGGGTAAGGTGCCGATGCCATGTC
CTAGACACAGTCTTATACTGGCTCATATCTCAAGTCGATGCCATGTCCCAGACATGGTCTTACAC
TGACTATCATCTCGTA
Found at i:5283205 original size:3 final size:3
Alignment explanation
Indices: 5283177--5283239 Score: 63
Period size: 3 Copynumber: 20.3 Consensus size: 3
5283167 TATTTTTATG
* * *
5283177 TTA TTA GTA TTA TTA GTA TTA CTA TTA TTA TTA TTA TTA TGTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
* *
5283223 GTA TATA TTT TTA TTA T
1 TTA T-TA TTA TTA TTA T
5283240 GTAAATATAT
Statistics
Matches: 48, Mismatches: 10, Indels: 4
0.77 0.16 0.06
Matches are distributed among these distances:
3 42 0.88
4 6 0.12
ACGTcount: A:0.32, C:0.02, G:0.06, T:0.60
Consensus pattern (3 bp):
TTA
Found at i:5283250 original size:23 final size:23
Alignment explanation
Indices: 5283184--5283250 Score: 61
Period size: 21 Copynumber: 3.1 Consensus size: 23
5283174 ATGTTATTAG
* * *
5283184 TATTATTAGTAT-TACTATTAT-
1 TATTATTATTATGTAATAGTATA
*
5283205 TATTATTATTATGTATTAGTATA
1 TATTATTATTATGTAATAGTATA
*
5283228 TATTTTTATTATGTAA-A-TATA
1 TATTATTATTATGTAATAGTATA
5283249 TA
1 TA
5283251 CATATATATA
Statistics
Matches: 39, Mismatches: 5, Indels: 4
0.81 0.10 0.08
Matches are distributed among these distances:
21 17 0.44
22 8 0.21
23 14 0.36
ACGTcount: A:0.36, C:0.01, G:0.06, T:0.57
Consensus pattern (23 bp):
TATTATTATTATGTAATAGTATA
Found at i:5283354 original size:3 final size:3
Alignment explanation
Indices: 5283341--5283376 Score: 63
Period size: 3 Copynumber: 12.0 Consensus size: 3
5283331 TATTTCAATG
*
5283341 TTA TCA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5283377 GTTTATGCTT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:5283548 original size:22 final size:24
Alignment explanation
Indices: 5283502--5283548 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
5283492 TATTTTAGTA
*
5283502 ATATGTATATTCTTCATATATTAT
1 ATATGTATATTCTTCATATACTAT
*
5283526 ATATGTGTATTCTT-A-ATACTAT
1 ATATGTATATTCTTCATATACTAT
5283548 A
1 A
5283549 CTTTATATGT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 7 0.33
23 1 0.05
24 13 0.62
ACGTcount: A:0.34, C:0.09, G:0.06, T:0.51
Consensus pattern (24 bp):
ATATGTATATTCTTCATATACTAT
Found at i:5283595 original size:21 final size:22
Alignment explanation
Indices: 5283569--5283612 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
5283559 ATCATGTATT
*
5283569 TTTTAATGTTACATTAT-TATA
1 TTTTAATATTACATTATATATA
*
5283590 TTTTAATATTATATTATATATA
1 TTTTAATATTACATTATATATA
5283612 T
1 T
5283613 ATTTTCCTAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.59
Consensus pattern (22 bp):
TTTTAATATTACATTATATATA
Found at i:5283617 original size:24 final size:25
Alignment explanation
Indices: 5283586--5283687 Score: 84
Period size: 24 Copynumber: 4.0 Consensus size: 25
5283576 GTTACATTAT
5283586 TATATTTTAATATTA-TATTATATA
1 TATATTTTAATATTATTATTATATA
**
5283610 TATATTTTCCTATTA-TATTATATTCA
1 TATATTTTAATATTATTATTATA-T-A
* * *
5283636 TATATCTTTTATA-TATTACTATGTA
1 TATAT-TTTAATATTATTATTATATA
* *
5283661 AATATTTTGATATTATTAGTTATATA
1 TATATTTTAATATTATTA-TTATATA
5283687 T
1 T
5283688 TACTTATATA
Statistics
Matches: 61, Mismatches: 11, Indels: 10
0.74 0.13 0.12
Matches are distributed among these distances:
24 26 0.43
25 11 0.18
26 14 0.23
27 10 0.16
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (25 bp):
TATATTTTAATATTATTATTATATA
Found at i:5290821 original size:40 final size:40
Alignment explanation
Indices: 5290777--5291041 Score: 367
Period size: 40 Copynumber: 6.7 Consensus size: 40
5290767 GCTACTCGTT
* *
5290777 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
5290817 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
5290857 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
5290897 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* *
5290937 CAAATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * * * *
5290976 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGATTTAGTAAC-TCGCA
5291017 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
5291042 CATCATTCAA
Statistics
Matches: 206, Mismatches: 14, Indels: 10
0.90 0.06 0.04
Matches are distributed among these distances:
38 2 0.01
39 33 0.16
40 158 0.77
41 13 0.06
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:5291032 original size:119 final size:121
Alignment explanation
Indices: 5290777--5291041 Score: 369
Period size: 119 Copynumber: 2.2 Consensus size: 121
5290767 GCTACTCGTT
* *
5290777 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCACAAATGCCTTCGGGACTTAACCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
* * *
5290841 GATTTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
66 GAATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCA
* *
5290897 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCACAAATGCCTTCGGG-CTTAGCCCG
1 CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
* ** * *
5290960 GAATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
66 GAATTAGTAACTCGCACAAATGCCTTCGGGA-CTTAACCCGGATATAGTAAC-TAGCA
5291017 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
5291042 CATCATTCAA
Statistics
Matches: 129, Mismatches: 13, Indels: 7
0.87 0.09 0.05
Matches are distributed among these distances:
118 3 0.02
119 68 0.53
120 56 0.43
121 2 0.02
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (121 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTATAGTAACTCGCACAAATGCCTTCGGGACTTAACCCG
GAATTAGTAACTCGCACAAATGCCTTCGGGACTTAACCCGGATATAGTAACTAGCA
Found at i:5300972 original size:40 final size:40
Alignment explanation
Indices: 5300874--5301176 Score: 380
Period size: 40 Copynumber: 7.6 Consensus size: 40
5300864 TCCTCGTTCA
* * * ** *
5300874 AATGCCTTCGGGACATAGCCCGGTTTTAGTAACTCACAC-
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
5300913 AATGCCTTCGGGACATAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
5300953 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
5300993 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
*
5301033 AATGCCTTCGGGACTTAACCCGGATTTAATAACTCGCACG
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
** * *
5301073 AATGCCTTCGGGACTTAACCCGGATTTAGTATCTCGCACA
1 AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
* * * * *
5301113 AAGGCCTTC-GGATCTTAATCCGGATATATTC-ACTTAGCAC-
1 AATGCCTTCGGGA-CTTAACCCGGATTTA-ACAAC-TCGCACG
* *
5301153 AAAGCCTTCGGGACTTAGCCCGGA
1 AATGCCTTCGGGACTTAACCCGGA
5301177 CAGCATTCAA
Statistics
Matches: 239, Mismatches: 20, Indels: 9
0.89 0.07 0.03
Matches are distributed among these distances:
39 37 0.15
40 194 0.81
41 8 0.03
ACGTcount: A:0.27, C:0.28, G:0.20, T:0.24
Consensus pattern (40 bp):
AATGCCTTCGGGACTTAACCCGGATTTAACAACTCGCACG
Found at i:5303589 original size:79 final size:81
Alignment explanation
Indices: 5303472--5303625 Score: 260
Period size: 79 Copynumber: 1.9 Consensus size: 81
5303462 TCAATTTATG
* *
5303472 TTTCAAAAGAATCAACTCATATTGCGAGATGTGAGTTGAGCCTCAGGACACGCTGAGGTAATTTT
1 TTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGT-ATTTT
5303537 -AATTTCTGTTTCTGCT
65 CAATTTCTGTTTCTGCT
5303553 TTTC-AAA-AATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTC
1 TTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTC
5303616 AATTTCTGTT
66 AATTTCTGTT
5303626 CTTCCAATTT
Statistics
Matches: 70, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
78 5 0.07
79 58 0.83
80 3 0.04
81 4 0.06
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.34
Consensus pattern (81 bp):
TTTCAAAAGAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTC
AATTTCTGTTTCTGCT
Found at i:5303705 original size:178 final size:185
Alignment explanation
Indices: 5303445--5303776 Score: 430
Period size: 185 Copynumber: 1.8 Consensus size: 185
5303435 ACTGAGGTAT
* *
5303445 TTCCAATTTCTGTTCTTTCAATTTATGTTTCAAAAGAATCAACTCATATTGCGAGATGTGAGTTG
1 TTCCAATTTCTGTTCTTTCAATTCATGTTTCAAAAGAATCAACTCATATTGCGAGAAGTGAGTTG
* * * *
5303510 AGCCTCAGGACACGCTGAG-GT-AATTT-TAATTTCT-GTTTCTGCTTTTCAAAAATCAACTCAT
66 AGCCTCAAGAAACGCTGAGAGTCAATTTCT-ATTTCTAATTTATGCTTTTCAAAAATCAACTCAT
*
5303571 ATTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTCAATTTCTGTTC
130 ACTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTCAATTTCTGTTC
* *
5303627 TTCCAATTTCTG-T-TTT-AATTCATGATTTC-AAA-ATTTAACTCATATTGCGAGAAGTGAGTT
1 TTCCAATTTCTGTTCTTTCAATTCATG-TTTCAAAAGAATCAACTCATATTGCGAGAAGTGAGTT
* * * *
5303687 GAGCTTCAAGAAACGCTGAGAAATCTTCAATTTCTATTTTTAATTTATGTTTTTCAAAAATCAAC
65 GAGCCTCAAGAAACGCTGAG--A--GTCAATTTCTATTTCTAATTTATGCTTTTCAAAAATCAAC
5303752 TCATACTGCGAGAGGTGAGTTGAGC
126 TCATACTGCGAGAGGTGAGTTGAGC
5303777 TTTTTAATTT
Statistics
Matches: 128, Mismatches: 13, Indels: 15
0.82 0.08 0.10
Matches are distributed among these distances:
178 42 0.33
179 10 0.08
180 7 0.05
181 1 0.01
182 12 0.09
183 1 0.01
184 10 0.08
185 45 0.35
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (185 bp):
TTCCAATTTCTGTTCTTTCAATTCATGTTTCAAAAGAATCAACTCATATTGCGAGAAGTGAGTTG
AGCCTCAAGAAACGCTGAGAGTCAATTTCTATTTCTAATTTATGCTTTTCAAAAATCAACTCATA
CTGCGAGAGGTGAGTTGAGCCTCAGGACACACTGAGGTATTTTCAATTTCTGTTC
Found at i:5303807 original size:54 final size:54
Alignment explanation
Indices: 5303723--5303830 Score: 153
Period size: 54 Copynumber: 2.0 Consensus size: 54
5303713 TCAATTTCTA
** *
5303723 TTTTTAATTTATGTTTTTCAAAAATCAACTCATACTGCGAGAGGTGAGTTGAGC
1 TTTTTAATTTATGTTTCCCAAAAATCAACTCATACTGCGAGAAGTGAGTTGAGC
* * * *
5303777 TTTTTAATTTCTGTTTCCCAAAAATGAACTCATATTGTGAGAAGTGAGTTGAGC
1 TTTTTAATTTATGTTTCCCAAAAATCAACTCATACTGCGAGAAGTGAGTTGAGC
5303831 CTTAGGACAC
Statistics
Matches: 47, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
54 47 1.00
ACGTcount: A:0.30, C:0.13, G:0.19, T:0.39
Consensus pattern (54 bp):
TTTTTAATTTATGTTTCCCAAAAATCAACTCATACTGCGAGAAGTGAGTTGAGC
Found at i:5305913 original size:3 final size:3
Alignment explanation
Indices: 5305891--5305953 Score: 72
Period size: 3 Copynumber: 20.3 Consensus size: 3
5305881 GATTTTTATG
* *
5305891 TTA TTA GTA TTA TTA GTA TTA TTA TTA TTA TTA TTA TTA TGTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA TTA
* *
5305937 GTA TATA TTT TTA TTA T
1 TTA T-TA TTA TTA TTA T
5305954 GTAAATATAT
Statistics
Matches: 50, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
3 44 0.88
4 6 0.12
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:5305964 original size:23 final size:23
Alignment explanation
Indices: 5305898--5305964 Score: 61
Period size: 21 Copynumber: 3.1 Consensus size: 23
5305888 ATGTTATTAG
* * *
5305898 TATTATTAGTAT-TATTATTAT-
1 TATTATTATTATGTAATAGTATA
*
5305919 TATTATTATTATGTATTAGTATA
1 TATTATTATTATGTAATAGTATA
*
5305942 TATTTTTATTATGTAA-A-TATA
1 TATTATTATTATGTAATAGTATA
5305963 TA
1 TA
5305965 CATATATATA
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
21 17 0.43
22 9 0.22
23 14 0.35
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (23 bp):
TATTATTATTATGTAATAGTATA
Found at i:5306066 original size:3 final size:3
Alignment explanation
Indices: 5306053--5306130 Score: 129
Period size: 3 Copynumber: 26.0 Consensus size: 3
5306043 TATTTCAATG
* * *
5306053 TTA TCA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA TTA TCA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5306101 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
5306131 GTTTATGCTT
Statistics
Matches: 69, Mismatches: 6, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:5306130 original size:18 final size:18
Alignment explanation
Indices: 5306053--5306128 Score: 143
Period size: 18 Copynumber: 4.2 Consensus size: 18
5306043 TATTTCAATG
5306053 TTATCATTATTATTATTA
1 TTATCATTATTATTATTA
5306071 TTATCATTATTATTATTA
1 TTATCATTATTATTATTA
5306089 TTATCATTATTATTATTA
1 TTATCATTATTATTATTA
*
5306107 TTATTATTATTATTATTA
1 TTATCATTATTATTATTA
5306125 TTAT
1 TTAT
5306129 TAGTTTATGC
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
18 57 1.00
ACGTcount: A:0.33, C:0.04, G:0.00, T:0.63
Consensus pattern (18 bp):
TTATCATTATTATTATTA
Found at i:5306362 original size:22 final size:22
Alignment explanation
Indices: 5306320--5306436 Score: 85
Period size: 21 Copynumber: 5.0 Consensus size: 22
5306310 ATCATGTATT
* *
5306320 TTTTAATGTTACATTAT-TATA
1 TTTTAATATTATATTATATATA
5306341 TTTTAATATTATATTATATATA
1 TTTTAATATTATATTATATATA
*
5306363 TATTCCTATTATATTATATTCATATATC
1 T-TT--TA--ATATTATATT-ATATATA
*
5306391 TTTTATATATTACTA-TGTATATA
1 TTTTA-ATATTA-TATTATATATA
*
5306414 TTTTGATATTATTAGTTATATAT
1 TTTTAATATTA-TA-TTATATAT
5306437 TACTTATATA
Statistics
Matches: 78, Mismatches: 8, Indels: 17
0.76 0.08 0.17
Matches are distributed among these distances:
21 15 0.19
22 13 0.17
23 11 0.14
24 14 0.18
25 6 0.08
27 12 0.15
28 7 0.09
ACGTcount: A:0.34, C:0.05, G:0.03, T:0.57
Consensus pattern (22 bp):
TTTTAATATTATATTATATATA
Found at i:5306366 original size:11 final size:11
Alignment explanation
Indices: 5306332--5306448 Score: 50
Period size: 11 Copynumber: 10.3 Consensus size: 11
5306322 TTAATGTTAC
5306332 ATTAT-TATAT
1 ATTATATATAT
*
5306342 TTTA-ATATTAT
1 ATTATATA-TAT
5306353 ATTATATATAT
1 ATTATATATAT
*
5306364 ATTCCTAT-TAT
1 ATT-ATATATAT
5306375 ATTATATTCATAT
1 ATTATA-T-ATAT
*
5306388 ATCT-TTTATAT
1 AT-TATATATAT
5306399 ATTACTATGTATAT
1 ATTA-TA--TATAT
*
5306413 ATTTTGATAT-T
1 ATTAT-ATATAT
5306424 ATTAGT-TATAT
1 ATTA-TATATAT
5306435 ATTACT-TATAT
1 ATTA-TATATAT
5306446 ATT
1 ATT
5306449 TCCATGTATA
Statistics
Matches: 83, Mismatches: 9, Indels: 29
0.69 0.07 0.24
Matches are distributed among these distances:
10 11 0.13
11 43 0.52
12 12 0.14
13 7 0.08
14 10 0.12
ACGTcount: A:0.35, C:0.05, G:0.03, T:0.57
Consensus pattern (11 bp):
ATTATATATAT
Found at i:5306474 original size:23 final size:22
Alignment explanation
Indices: 5306385--5306486 Score: 75
Period size: 23 Copynumber: 4.4 Consensus size: 22
5306375 ATTATATTCA
* * *
5306385 TATATCTTTTATATATTACTATG
1 TATATATTTTATAT-TTTCCATG
5306408 TATATATTTTGATATTATT--A-G
1 TATATATTTT-ATATT-TTCCATG
5306429 TTATATATTACTTATATATTTCCATG
1 -TATATATT--TTATAT-TTTCCATG
5306455 TATATATTTTATATTGTTCCATG
1 TATATATTTTATATT-TTCCATG
*
5306478 TACATATTT
1 TATATATTT
5306487 GAGTAGTGTT
Statistics
Matches: 66, Mismatches: 3, Indels: 20
0.74 0.03 0.22
Matches are distributed among these distances:
21 1 0.02
22 10 0.15
23 37 0.56
24 8 0.12
25 9 0.14
26 1 0.02
ACGTcount: A:0.30, C:0.08, G:0.06, T:0.56
Consensus pattern (22 bp):
TATATATTTTATATTTTCCATG
Found at i:5323168 original size:104 final size:104
Alignment explanation
Indices: 5322983--5323190 Score: 389
Period size: 104 Copynumber: 2.0 Consensus size: 104
5322973 AATAGGTTAC
*
5322983 AAAATTTGCATTCTAGAAGTTTCTAGTATGAAATTGCTTGGAAATATTAATTAGGAGGTATTAAA
1 AAAACTTGCATTCTAGAAGTTTCTAGTATGAAATTGCTTGGAAATATTAATTAGGAGGTATTAAA
5323048 TAGAAATTTGACCAATTTCTAAGTTTATGGACAAAAATT
66 TAGAAATTTGACCAATTTCTAAGTTTATGGACAAAAATT
* *
5323087 AAAACTTGCATTCTAGAAGTTTCTAGTATGAAATTGCTTTGAAATATTAATTAGGAGGTCTTAAA
1 AAAACTTGCATTCTAGAAGTTTCTAGTATGAAATTGCTTGGAAATATTAATTAGGAGGTATTAAA
5323152 TAGAAATTTGACCAATTTCTAAGTTTATGGACAAAAATT
66 TAGAAATTTGACCAATTTCTAAGTTTATGGACAAAAATT
5323191 GGACATGGAT
Statistics
Matches: 101, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
104 101 1.00
ACGTcount: A:0.39, C:0.09, G:0.16, T:0.37
Consensus pattern (104 bp):
AAAACTTGCATTCTAGAAGTTTCTAGTATGAAATTGCTTGGAAATATTAATTAGGAGGTATTAAA
TAGAAATTTGACCAATTTCTAAGTTTATGGACAAAAATT
Found at i:5324227 original size:46 final size:46
Alignment explanation
Indices: 5324168--5324283 Score: 178
Period size: 46 Copynumber: 2.5 Consensus size: 46
5324158 AATATTTGAG
*
5324168 CATCCGAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
1 CATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
* * *
5324214 CGTCCAAACTCGTTGAGTTGAGTCTGAGTTCACTTATGGATGTGAA
1 CATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
* *
5324260 TATCCGAACTCGTTGAGTTGAGTC
1 CATCCAAACTCGTTGAGTTGAGTC
5324284 ATGCGAATGT
Statistics
Matches: 63, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
46 63 1.00
ACGTcount: A:0.23, C:0.20, G:0.26, T:0.31
Consensus pattern (46 bp):
CATCCAAACTCGTTGAGTTGAGTCCGAGTTCACTTATGGATGCGAA
Found at i:5331851 original size:26 final size:26
Alignment explanation
Indices: 5331822--5331929 Score: 198
Period size: 26 Copynumber: 4.2 Consensus size: 26
5331812 TGATACAAAT
5331822 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
5331848 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
5331874 TGATAATGGGTTAGGTAAATGTTCAA
1 TGATAATGGGTTAGGTAAATGTTCCA
5331900 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
5331926 TGAT
1 TGAT
5331930 GATAATTTCA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 78 1.00
ACGTcount: A:0.31, C:0.06, G:0.27, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:5333624 original size:27 final size:27
Alignment explanation
Indices: 5333527--5333631 Score: 135
Period size: 27 Copynumber: 3.9 Consensus size: 27
5333517 AGGAAGCGTC
*
5333527 CTGGTGGCTATGCCACAATTATCTG-AT
1 CTGGTGGCTCTGCCACAA-TATCTGTAT
5333554 CTGGTGGCTCTGCCACATATATCTGT-T
1 CTGGTGGCTCTGCCACA-ATATCTGTAT
5333581 CTGGTGGCTCTGCCACAATATCTGTAT
1 CTGGTGGCTCTGCCACAATATCTGTAT
* *
5333608 CTGGTGACT-TCGTCACAATATCTG
1 CTGGTGGCTCT-GCCACAATATCTG
5333632 GCAGCCTCCC
Statistics
Matches: 71, Mismatches: 3, Indels: 8
0.87 0.04 0.10
Matches are distributed among these distances:
26 9 0.13
27 61 0.86
28 1 0.01
ACGTcount: A:0.19, C:0.25, G:0.22, T:0.34
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATATCTGTAT
Found at i:5341196 original size:27 final size:27
Alignment explanation
Indices: 5341156--5341242 Score: 88
Period size: 27 Copynumber: 3.2 Consensus size: 27
5341146 AGGAAGCGTC
*
5341156 CTGGTGGCTATGCCACAATTATCTGAT
1 CTGGTGGCTCTGCCACAATTATCTGAT
* *
5341183 CTGGTGGCTCTGCCGC-ATATATCTGTT
1 CTGGTGGCTCTGCCACAAT-TATCTGAT
* * *
5341210 TTGGTAGCTCTACCACAA-TATCTGTAT
1 CTGGTGGCTCTGCCACAATTATCTG-AT
5341237 CTGGTG
1 CTGGTG
5341243 ACTTCGTCAC
Statistics
Matches: 47, Mismatches: 10, Indels: 6
0.75 0.16 0.10
Matches are distributed among these distances:
26 8 0.17
27 38 0.81
28 1 0.02
ACGTcount: A:0.18, C:0.23, G:0.23, T:0.36
Consensus pattern (27 bp):
CTGGTGGCTCTGCCACAATTATCTGAT
Found at i:5342483 original size:13 final size:15
Alignment explanation
Indices: 5342449--5342550 Score: 54
Period size: 16 Copynumber: 6.7 Consensus size: 15
5342439 TACTGGATTT
5342449 TAAAATATATATATA
1 TAAAATATATATATA
*
5342464 TACAATATATAT-TA
1 TAAAATATATATATA
5342478 -AAAATAGTA-ATAATA
1 TAAAATA-TATAT-ATA
5342493 TAAAACTA-ACTA-ATAA
1 TAAAA-TATA-TATAT-A
* *
5342509 TAACTATATATAAATA
1 TAA-AATATATATATA
* *
5342525 TATACATATATGTAT-
1 TA-AAATATATATATA
5342540 TAAAATATATA
1 TAAAATATATA
5342551 CGTAATAATA
Statistics
Matches: 67, Mismatches: 8, Indels: 25
0.67 0.08 0.25
Matches are distributed among these distances:
13 7 0.10
14 11 0.16
15 18 0.27
16 23 0.34
17 8 0.12
ACGTcount: A:0.57, C:0.05, G:0.02, T:0.36
Consensus pattern (15 bp):
TAAAATATATATATA
Found at i:5342604 original size:11 final size:11
Alignment explanation
Indices: 5342572--5342612 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
5342562 GAATAAAATG
*
5342572 TATATACATAG
1 TATATACATAA
*
5342583 TAT-TA-AAAA
1 TATATACATAA
5342592 TATATACATAA
1 TATATACATAA
5342603 TATATACATA
1 TATATACATA
5342613 TTAGAAATAA
Statistics
Matches: 25, Mismatches: 3, Indels: 4
0.78 0.09 0.12
Matches are distributed among these distances:
9 5 0.20
10 4 0.16
11 16 0.64
ACGTcount: A:0.54, C:0.07, G:0.02, T:0.37
Consensus pattern (11 bp):
TATATACATAA
Found at i:5342721 original size:26 final size:26
Alignment explanation
Indices: 5342674--5342758 Score: 93
Period size: 26 Copynumber: 3.3 Consensus size: 26
5342664 TTGAAAATTT
* * *
5342674 ATACATAATA-ATGATATTAAAAGTAT
1 ATACATAATATA-GTTATTAAAAATAC
* *
5342700 GTACGTAATATAG-TATTAAAAATAC
1 ATACATAATATAGTTATTAAAAATAC
*
5342725 ATACATAATATAGTTATTAAAAATAT
1 ATACATAATATAGTTATTAAAAATAC
5342751 ATACATAA
1 ATACATAA
5342759 GATAATATGT
Statistics
Matches: 50, Mismatches: 7, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
25 21 0.42
26 28 0.56
27 1 0.02
ACGTcount: A:0.53, C:0.06, G:0.07, T:0.34
Consensus pattern (26 bp):
ATACATAATATAGTTATTAAAAATAC
Found at i:5342904 original size:23 final size:23
Alignment explanation
Indices: 5342866--5342922 Score: 66
Period size: 23 Copynumber: 2.6 Consensus size: 23
5342856 ACCTAAATGT
5342866 ATACAT-AT-ATATTAAAAATAA
1 ATACATAATAATATTAAAAATAA
* *
5342887 ATACATAATAATATTAAAAGTAT
1 ATACATAATAATATTAAAAATAA
*
5342910 GTACATAA-AATAT
1 ATACATAATAATAT
5342923 ATACATATGA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
21 6 0.19
22 7 0.23
23 18 0.58
ACGTcount: A:0.58, C:0.05, G:0.04, T:0.33
Consensus pattern (23 bp):
ATACATAATAATATTAAAAATAA
Found at i:5343115 original size:48 final size:45
Alignment explanation
Indices: 5343041--5343134 Score: 118
Period size: 48 Copynumber: 2.0 Consensus size: 45
5343031 AATAATAATA
* * *
5343041 ATGTTAAAAACAATTATTAATAATATTACATAAATATATAC-ATATAT
1 ATGTTAAAAAAAATAAATAATAATATTA-A-AAATA-ATACTATATAT
5343088 ATGTTAAAAATAAATAAATAATAATATTAAAAATAATACTATATAT
1 ATGTTAAAAA-AAATAAATAATAATATTAAAAATAATACTATATAT
5343134 A
1 A
5343135 AAGAGTGTAT
Statistics
Matches: 42, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
45 4 0.10
46 12 0.29
47 11 0.26
48 15 0.36
ACGTcount: A:0.57, C:0.04, G:0.02, T:0.36
Consensus pattern (45 bp):
ATGTTAAAAAAAATAAATAATAATATTAAAAATAATACTATATAT
Found at i:5343135 original size:27 final size:25
Alignment explanation
Indices: 5343035--5343135 Score: 74
Period size: 23 Copynumber: 4.2 Consensus size: 25
5343025 CTAAGAAATA
* *
5343035 ATAATAATGTTAAAAACAAT-T-AT
1 ATAATAATATTAAAAATAATATAAT
5343058 -TAATAATATTACATAAAT-ATATACAT
1 ATAATAATATTA-A-AAATAATATA-AT
*
5343084 AT-AT-ATGTTAAAAATAA-ATAA-
1 ATAATAATATTAAAAATAATATAAT
5343105 ATAATAATATTAAAAATAATACTATAT
1 ATAATAATATTAAAAATAATA-TA-AT
5343132 ATAA
1 ATAA
5343136 AGAGTGTATA
Statistics
Matches: 61, Mismatches: 4, Indels: 22
0.70 0.05 0.25
Matches are distributed among these distances:
21 2 0.03
22 13 0.21
23 22 0.36
24 7 0.11
25 7 0.11
26 5 0.08
27 5 0.08
ACGTcount: A:0.58, C:0.04, G:0.02, T:0.36
Consensus pattern (25 bp):
ATAATAATATTAAAAATAATATAAT
Found at i:5343170 original size:12 final size:13
Alignment explanation
Indices: 5343096--5343257 Score: 101
Period size: 12 Copynumber: 12.1 Consensus size: 13
5343086 ATATGTTAAA
5343096 AATAA-ATA-AAT
1 AATAATATATAAT
*
5343107 AATAATAT-TAAA
1 AATAATATATAAT
5343119 AATAATACTATATAT
1 AATAATA-TATA-AT
*
5343134 AA-AGAGTGTATATAT
1 AATA-A-TATATA-AT
5343149 ATATACATATATAAT
1 A-ATA-ATATATAAT
5343164 AA-AATATACGGTAAT
1 AATAATATA---TAAT
5343179 AATAATAATGATAAT
1 AATAAT-AT-ATAAT
5343194 AATAATAT-TAAT
1 AATAATATATAAT
5343206 AGTAGTAA-ATATAAT
1 A--A-TAATATATAAT
5343221 AATAATA-ATAAT
1 AATAATATATAAT
5343233 AATAATA-ATAAT
1 AATAATATATAAT
5343245 AATAATA-ATAAT
1 AATAATATATAAT
5343257 A
1 A
5343258 TCATCGATAA
Statistics
Matches: 126, Mismatches: 5, Indels: 39
0.74 0.03 0.23
Matches are distributed among these distances:
11 5 0.04
12 54 0.43
13 4 0.03
14 9 0.07
15 39 0.31
16 10 0.08
17 4 0.03
18 1 0.01
ACGTcount: A:0.59, C:0.02, G:0.05, T:0.34
Consensus pattern (13 bp):
AATAATATATAAT
Found at i:5343181 original size:3 final size:3
Alignment explanation
Indices: 5343175--5343257 Score: 114
Period size: 3 Copynumber: 27.7 Consensus size: 3
5343165 AAATATACGG
* * * *
5343175 TAA TAA TAA TAA TGA TAA TAA TAA TAT TAA TAG TAG TAA -ATA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA-A TAA
5343220 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
5343258 TCATCGATAA
Statistics
Matches: 72, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
2 1 0.01
3 70 0.97
4 1 0.01
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:5353029 original size:27 final size:26
Alignment explanation
Indices: 5352981--5353039 Score: 84
Period size: 27 Copynumber: 2.2 Consensus size: 26
5352971 AGCAGCAACT
*
5352981 ATTAAATTTGTCCCTAAGCTAGACAC
1 ATTAAATTTGTCCCTAAACTAGACAC
5353007 ATTAAATTGATGT-CCTAAACTAGACAC
1 ATTAAATT--TGTCCCTAAACTAGACAC
5353034 ATTAAA
1 ATTAAA
5353040 ACTATGTATT
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 8 0.27
27 19 0.63
28 3 0.10
ACGTcount: A:0.41, C:0.19, G:0.10, T:0.31
Consensus pattern (26 bp):
ATTAAATTTGTCCCTAAACTAGACAC
Found at i:5363454 original size:5 final size:6
Alignment explanation
Indices: 5363415--5363461 Score: 67
Period size: 6 Copynumber: 7.5 Consensus size: 6
5363405 TAATTTTAAT
*
5363415 AAATAA AAATAA AAATCTAA AAGTAA AAATAA AAATAA AAATAA AAA
1 AAATAA AAATAA AAA--TAA AAATAA AAATAA AAATAA AAATAA AAA
5363462 ACATATAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
6 32 0.86
8 5 0.14
ACGTcount: A:0.79, C:0.02, G:0.02, T:0.17
Consensus pattern (6 bp):
AAATAA
Found at i:5363462 original size:20 final size:20
Alignment explanation
Indices: 5363415--5363455 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
5363405 TAATTTTAAT
**
5363415 AAATAAAAATAAAAATCTAA
1 AAATAAAAATAAAAATAAAA
*
5363435 AAGTAAAAATAAAAATAAAA
1 AAATAAAAATAAAAATAAAA
5363455 A
1 A
5363456 TAAAAAACAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.78, C:0.02, G:0.02, T:0.17
Consensus pattern (20 bp):
AAATAAAAATAAAAATAAAA
Found at i:5363495 original size:9 final size:9
Alignment explanation
Indices: 5363481--5363548 Score: 91
Period size: 9 Copynumber: 7.6 Consensus size: 9
5363471 TTTATACAAA
5363481 TAATTCGAT
1 TAATTCGAT
*
5363490 TAATTCGGT
1 TAATTCGAT
* *
5363499 TAATTTGAG
1 TAATTCGAT
*
5363508 TAATTCGGT
1 TAATTCGAT
*
5363517 TAATTCGGT
1 TAATTCGAT
5363526 TAATTCGAT
1 TAATTCGAT
5363535 TAATTCGAT
1 TAATTCGAT
5363544 TAATT
1 TAATT
5363549 TTATACTTTT
Statistics
Matches: 51, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 51 1.00
ACGTcount: A:0.29, C:0.09, G:0.16, T:0.46
Consensus pattern (9 bp):
TAATTCGAT
Found at i:5363519 original size:27 final size:27
Alignment explanation
Indices: 5363481--5363548 Score: 109
Period size: 27 Copynumber: 2.5 Consensus size: 27
5363471 TTTATACAAA
*
5363481 TAATTCGATTAATTCGGTTAATTTGAG
1 TAATTCGATTAATTCGGTTAATTCGAG
* *
5363508 TAATTCGGTTAATTCGGTTAATTCGAT
1 TAATTCGATTAATTCGGTTAATTCGAG
5363535 TAATTCGATTAATT
1 TAATTCGATTAATT
5363549 TTATACTTTT
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 37 1.00
ACGTcount: A:0.29, C:0.09, G:0.16, T:0.46
Consensus pattern (27 bp):
TAATTCGATTAATTCGGTTAATTCGAG
Found at i:5369539 original size:54 final size:55
Alignment explanation
Indices: 5369475--5369581 Score: 180
Period size: 54 Copynumber: 2.0 Consensus size: 55
5369465 ACTAGCGGTA
* *
5369475 GGGAAAGACGCGAGTTTTTAAAAAGATAAATGCTTTT-TAAATACCACGAATACG
1 GGGAAAGACGCGAGTTTTCAAAAAGATAAATGCTTTTCAAAATACCACGAATACG
*
5369529 GGGAAAGACGCGAGTTTTCAAAAAGATAAATTCTTTTCAAAATACCACGAATA
1 GGGAAAGACGCGAGTTTTCAAAAAGATAAATGCTTTTCAAAATACCACGAATA
5369582 TGTAGCTTGT
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
54 35 0.71
55 14 0.29
ACGTcount: A:0.42, C:0.14, G:0.19, T:0.25
Consensus pattern (55 bp):
GGGAAAGACGCGAGTTTTCAAAAAGATAAATGCTTTTCAAAATACCACGAATACG
Found at i:5384946 original size:47 final size:47
Alignment explanation
Indices: 5384892--5385038 Score: 172
Period size: 47 Copynumber: 3.1 Consensus size: 47
5384882 TTAAGATTTT
*
5384892 ATGTGATGAATGTG-G-ATGAGTATATATGAGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAGCAT--GCATATATGAGATAAGGCCGAATGGCCA
* *
5384939 ATGTGATGAATGTGAGCATGCATATGTGTGATAAGGCCGAATGGCCA
1 ATGTGATGAATGTGAGCATGCATATATGAGATAAGGCCGAATGGCCA
* * * * * * *
5384986 ATGTGGTGAATATGAACATGCATATATGTGGTAAAGCCGAATGGCTA
1 ATGTGATGAATGTGAGCATGCATATATGAGATAAGGCCGAATGGCCA
5385033 ATGTGA
1 ATGTGA
5385039 AATATATATG
Statistics
Matches: 87, Mismatches: 11, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
47 84 0.97
48 1 0.01
49 2 0.02
ACGTcount: A:0.33, C:0.10, G:0.31, T:0.27
Consensus pattern (47 bp):
ATGTGATGAATGTGAGCATGCATATATGAGATAAGGCCGAATGGCCA
Found at i:5384994 original size:25 final size:25
Alignment explanation
Indices: 5384921--5384994 Score: 59
Period size: 23 Copynumber: 3.1 Consensus size: 25
5384911 GTATATATGA
*
5384921 GATAAGGCCGAATGGCCAATGTGAT
1 GATAAGGCCGAATGGCCAATGTGGT
* * *
5384946 GA-ATGTG-AGCAT-G-CATATGT-GT
1 GATAAG-GCCGAATGGCCA-ATGTGGT
5384968 GATAAGGCCGAATGGCCAATGTGGT
1 GATAAGGCCGAATGGCCAATGTGGT
5384993 GA
1 GA
5384995 ATATGAACAT
Statistics
Matches: 35, Mismatches: 7, Indels: 14
0.62 0.12 0.25
Matches are distributed among these distances:
22 6 0.17
23 10 0.29
24 10 0.29
25 9 0.26
ACGTcount: A:0.30, C:0.14, G:0.34, T:0.23
Consensus pattern (25 bp):
GATAAGGCCGAATGGCCAATGTGGT
Found at i:5385163 original size:98 final size:98
Alignment explanation
Indices: 5385013--5385878 Score: 1636
Period size: 98 Copynumber: 8.9 Consensus size: 98
5385003 ATGCATATAT
5385013 GTGGTAAAGCCGAATGG-CTAATGTG-AA-ATATATATGAGATATGTATATGTGGTAAAGTCGAA
1 GTGGTAAAGCCGAATGGTC-AATGTGAAATATATATATGAGATATGTATATGTGGTAAAGTCGAA
5385075 TGGCTAATGTGAAATATGTATGAGATATGCATAC
65 TGGCTAATGTGAAATATGTATGAGATATGCATAC
5385109 GTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGTCGAAT
1 GTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGTCGAAT
5385174 GGCTAATGTGAAATATGTATGAGATATGCATAC
66 GGCTAATGTGAAATATGTATGAGATATGCATAC
5385207 GTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGTCGAAT
1 GTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGTCGAAT
5385272 GGCTAATGTGAAATATGTATGAGATATGCATAC
66 GGCTAATGTGAAATATGTATGAGATATGCATAC
5385305 GTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGTCGAAT
1 GTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGTCGAAT
5385370 GGCTAATGTGAAATATGTATGAGATATGCATAC
66 GGCTAATGTGAAATATGTATGAGATATGCATAC
5385403 GTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGTCGAAT
1 GTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGTCGAAT
5385468 GGCTAATGTGAAATATGTATGAGATATGCATAC
66 GGCTAATGTGAAATATGTATGAGATATGCATAC
5385501 GTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGTCGAAT
1 GTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGTCGAAT
5385566 GGCTAATGTGAAATATGTATGAGATATGCATAC
66 GGCTAATGTGAAATATGTATGAGATATGCATAC
5385599 GTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGTCGAAT
1 GTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGTCGAAT
5385664 GGCTAATGTGAAATATGTATGAGATATGCATAC
66 GGCTAATGTGAAATATGTATGAGATATGCATAC
5385697 GTGGGGTAAAGCCGAATGG-CTAATGTG-AA-ATATATATGAGATATGTATATGTGGTAAAGTCG
1 GT--GGTAAAGCCGAATGGTC-AATGTGAAATATATATATGAGATATGTATATGTGGTAAAGTCG
5385759 AATGGCTAATGTGAAATATGTATGAGATATGCATAC
63 AATGGCTAATGTGAAATATGTATGAGATATGCATAC
*
5385795 GTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGCCGAAT
1 GTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGTCGAAT
*
5385860 GGCTAGTGTGAAATATGTA
66 GGCTAATGTGAAATATGTA
5385879 GGCGATGTGC
Statistics
Matches: 759, Mismatches: 2, Indels: 16
0.98 0.00 0.02
Matches are distributed among these distances:
96 44 0.06
97 6 0.01
98 685 0.90
99 3 0.00
100 21 0.03
ACGTcount: A:0.36, C:0.07, G:0.26, T:0.30
Consensus pattern (98 bp):
GTGGTAAAGCCGAATGGTCAATGTGAAATATATATATGAGATATGTATATGTGGTAAAGTCGAAT
GGCTAATGTGAAATATGTATGAGATATGCATAC
Found at i:5386207 original size:37 final size:37
Alignment explanation
Indices: 5386033--5386206 Score: 258
Period size: 37 Copynumber: 4.7 Consensus size: 37
5386023 ATTCCGGATG
5386033 AGACCCGATGACTACGTGTGGAGATTATGTCCGGGTA
1 AGACCCGATGACTACGTGTGGAGATTATGTCCGGGTA
* *
5386070 AGACCCGATGACAACGTGTGGGGATTATGTCCGGGTA
1 AGACCCGATGACTACGTGTGGAGATTATGTCCGGGTA
* *
5386107 AGACCCGATGACTACGTGTGGGGAGTATGTCCGGGTA
1 AGACCCGATGACTACGTGTGGAGATTATGTCCGGGTA
* *
5386144 AGACCCGATGACTACATGTGGAGATTTTGTCCGGGTA
1 AGACCCGATGACTACGTGTGGAGATTATGTCCGGGTA
* * * *
5386181 AGAACCGATAACTTCTTGTGGAGATT
1 AGACCCGATGACTACGTGTGGAGATT
5386207 TCGTCTGAGC
Statistics
Matches: 125, Mismatches: 12, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
37 125 1.00
ACGTcount: A:0.25, C:0.18, G:0.32, T:0.25
Consensus pattern (37 bp):
AGACCCGATGACTACGTGTGGAGATTATGTCCGGGTA
Found at i:5391119 original size:46 final size:46
Alignment explanation
Indices: 5391012--5391182 Score: 134
Period size: 46 Copynumber: 3.7 Consensus size: 46
5391002 GCCACATTAT
* * *
5391012 GATAG-CAAGTGTAAGACCATGTCTGGGACATGGCATTGGC-ATTGAGAA
1 GATAGCCAA-TGTAAGACC-TGTCTGGGACAT-GCATCGGCTA-CGAGAC
* ** * * *
5391060 GAGAGTTAGTGTAAGACCTGTTTGGGACATGCATTGGCCT-CGAGAC
1 GATAGCCAATGTAAGACCTGTCTGGGACATGCATCGG-CTACGAGAC
* * *
5391106 G-TAAGCCAATGTAAGACATGTCTAGGACATGCATCGGCTACGAGAT
1 GAT-AGCCAATGTAAGACCTGTCTGGGACATGCATCGGCTACGAGAC
*
5391152 GATAGTCAATGTAAGACCGTGTCTGGGACAT
1 GATAGCCAATGTAAGACC-TGTCTGGGACAT
5391183 CGTATTGACT
Statistics
Matches: 98, Mismatches: 18, Indels: 15
0.75 0.14 0.11
Matches are distributed among these distances:
45 2 0.02
46 58 0.59
47 24 0.24
48 13 0.13
49 1 0.01
ACGTcount: A:0.29, C:0.17, G:0.30, T:0.24
Consensus pattern (46 bp):
GATAGCCAATGTAAGACCTGTCTGGGACATGCATCGGCTACGAGAC
Found at i:5394307 original size:47 final size:47
Alignment explanation
Indices: 5394237--5394367 Score: 165
Period size: 47 Copynumber: 2.8 Consensus size: 47
5394227 CACAATCGAT
* *
5394237 AAGTACCTATACCATGGCTCGTAGCCAAATCAAGGTAACTTATCTCA
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCTCA
* * *
5394284 GAGTACCTATACCATAGCCCGTAGCCAAATCAAGAG-AACTCCTCTCA
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAG-GTAACTCATCTCA
* * * *
5394331 AAATACCTATATCATGGCCCGTAGCCAAGTTAAGGTA
1 AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTA
5394368 TTATTCGCAC
Statistics
Matches: 71, Mismatches: 11, Indels: 4
0.83 0.13 0.05
Matches are distributed among these distances:
46 1 0.01
47 69 0.97
48 1 0.01
ACGTcount: A:0.34, C:0.27, G:0.16, T:0.23
Consensus pattern (47 bp):
AAGTACCTATACCATGGCCCGTAGCCAAATCAAGGTAACTCATCTCA
Found at i:5404962 original size:22 final size:22
Alignment explanation
Indices: 5404931--5404979 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 22
5404921 CCATGTCTTG
* *
5404931 AGACATATAGGCTTTTT-TTTCA
1 AGACAAATAGG-TTTTTGTCTCA
5404953 AGACAAATAGGTTTTTGTCTCA
1 AGACAAATAGGTTTTTGTCTCA
5404975 AGACA
1 AGACA
5404980 TGCAAGCTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 5 0.21
22 19 0.79
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (22 bp):
AGACAAATAGGTTTTTGTCTCA
Found at i:5405727 original size:16 final size:15
Alignment explanation
Indices: 5405708--5405755 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
5405698 AGTTTTATTG
*
5405708 TTTATATGTTTATAAT
1 TTTATATATTT-TAAT
5405724 TTTATA-ATTTTAAT
1 TTTATATATTTTAAT
5405738 TTTATATCATTTTAAT
1 TTTATAT-ATTTTAAT
5405754 TT
1 TT
5405756 AGAATGTTGT
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
14 10 0.34
15 3 0.10
16 16 0.55
ACGTcount: A:0.31, C:0.02, G:0.02, T:0.65
Consensus pattern (15 bp):
TTTATATATTTTAAT
Found at i:5405739 original size:14 final size:15
Alignment explanation
Indices: 5405720--5405755 Score: 56
Period size: 14 Copynumber: 2.4 Consensus size: 15
5405710 TATATGTTTA
5405720 TAATTTTATA-ATTT
1 TAATTTTATACATTT
5405734 TAATTTTATATCATTT
1 TAATTTTATA-CATTT
5405750 TAATTT
1 TAATTT
5405756 AGAATGTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 10 0.50
16 10 0.50
ACGTcount: A:0.33, C:0.03, G:0.00, T:0.64
Consensus pattern (15 bp):
TAATTTTATACATTT
Found at i:5405833 original size:20 final size:21
Alignment explanation
Indices: 5405796--5405835 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
5405786 ACTTTATATG
*
5405796 TTTAAGTTTTCTAATTTTAAT
1 TTTAAGTTTTATAATTTTAAT
*
5405817 TTTAA-TTTTATACTTTTAA
1 TTTAAGTTTTATAATTTTAA
5405836 AATTTAAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (21 bp):
TTTAAGTTTTATAATTTTAAT
Found at i:5406053 original size:15 final size:17
Alignment explanation
Indices: 5406022--5406053 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
5406012 AATTTTTTTA
5406022 ATTTATAAATGATTATT
1 ATTTATAAATGATTATT
5406039 ATTT-TAAAT-ATTATT
1 ATTTATAAATGATTATT
5406054 TACATTGAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 5 0.33
17 4 0.27
ACGTcount: A:0.41, C:0.00, G:0.03, T:0.56
Consensus pattern (17 bp):
ATTTATAAATGATTATT
Found at i:5406741 original size:15 final size:15
Alignment explanation
Indices: 5406721--5406749 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
5406711 GTTAGTTAAT
5406721 TTTTTATTTTTATTA
1 TTTTTATTTTTATTA
5406736 TTTTTATTTTTATT
1 TTTTTATTTTTATT
5406750 TTGTTTTTCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (15 bp):
TTTTTATTTTTATTA
Found at i:5415689 original size:52 final size:52
Alignment explanation
Indices: 5415611--5415722 Score: 170
Period size: 52 Copynumber: 2.2 Consensus size: 52
5415601 GTCACATGGT
* * * *
5415611 CGTGTCTGGTGTTGTTCGTTTCTCCCACGCCCGTGTATGCAATCCCCACACC
1 CGTGTCTAGCGTTGTTCGTTTCTCCCACGCCCGTGTATGCAAGCCCCACACA
* *
5415663 CGTGTCTAGCGTTGTTCGTTTCTCCCACGCCTGTGTATGCAAGCCCCACGCA
1 CGTGTCTAGCGTTGTTCGTTTCTCCCACGCCCGTGTATGCAAGCCCCACACA
5415715 CGTGTCTA
1 CGTGTCTA
5415723 TCTAACAGGT
Statistics
Matches: 54, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
52 54 1.00
ACGTcount: A:0.12, C:0.35, G:0.22, T:0.30
Consensus pattern (52 bp):
CGTGTCTAGCGTTGTTCGTTTCTCCCACGCCCGTGTATGCAAGCCCCACACA
Found at i:5425910 original size:16 final size:15
Alignment explanation
Indices: 5425864--5425912 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 15
5425854 ATTTGGGTGA
5425864 TTTATTTATTTTTAT
1 TTTATTTATTTTTAT
* **
5425879 TTAAAAATATTTTTAT
1 TT-TATTTATTTTTAT
5425895 TTTATTTATTTATTAT
1 TTTATTTATTT-TTAT
5425911 TT
1 TT
5425913 CGTTTAATTC
Statistics
Matches: 26, Mismatches: 6, Indels: 3
0.74 0.17 0.09
Matches are distributed among these distances:
15 8 0.31
16 18 0.69
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (15 bp):
TTTATTTATTTTTAT
Found at i:5434308 original size:6 final size:6
Alignment explanation
Indices: 5434272--5434314 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
5434262 AAGTACTTTT
* * *
5434272 AATAAA AATTAA CATAAA ACATAAA ATTAAA AATAAA AATAAA
1 AATAAA AATAAA AATAAA A-ATAAA AATAAA AATAAA AATAAA
5434315 TGTTTCTAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
6 24 0.80
7 6 0.20
ACGTcount: A:0.74, C:0.05, G:0.00, T:0.21
Consensus pattern (6 bp):
AATAAA
Found at i:5436808 original size:27 final size:27
Alignment explanation
Indices: 5436778--5436869 Score: 114
Period size: 27 Copynumber: 3.4 Consensus size: 27
5436768 ATTACCAAAG
*
5436778 TACCCTCGATTTATAGAATTACTGTTT
1 TACCCTCGATTTACAGAATTACTGTTT
* *
5436805 TACCCTTGATTTACAGAATTACTATTT
1 TACCCTCGATTTACAGAATTACTGTTT
* * *
5436832 CACCCTCAATTTACAAAATTA-TCGTTT
1 TACCCTCGATTTACAGAATTACT-GTTT
5436859 TACCCTCGATT
1 TACCCTCGATT
5436870 GTGAAATTAC
Statistics
Matches: 54, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
26 1 0.02
27 53 0.98
ACGTcount: A:0.28, C:0.23, G:0.08, T:0.41
Consensus pattern (27 bp):
TACCCTCGATTTACAGAATTACTGTTT
Found at i:5436931 original size:27 final size:27
Alignment explanation
Indices: 5436901--5437113 Score: 101
Period size: 27 Copynumber: 7.7 Consensus size: 27
5436891 TATAGGGTAG
*
5436901 AATTACCAAAATACCCTTAGTTTTTAA
1 AATTACCAAAATACCCTTAGTTTATAA
* * *
5436928 AATTACCAAAATACCACTGGTTGGTTTGTGA
1 AATTACCAAAATACC-C---TTAGTTTATAA
** *
5436959 AATTACTGAAATA-CCTTCAATTTATAA
1 AATTACCAAAATACCCTT-AGTTTATAA
* *
5436986 AATTACCAAAATACCCCT-GATTTACAA
1 AATTACCAAAATACCCTTAG-TTTATAA
* *
5437013 AATTA-CAGAAATACCCTTGACTTTCTAAA
1 AATTACCA-AAATACCCTT-AGTTTAT-AA
* * * *
5437042 AATTA-TAGAAATACCATTGGTTTACAA
1 AATTACCA-AAATACCCTTAGTTTATAA
* ** * * *
5437069 AATTGCTGAAATACCCTTGGTTTGTAG
1 AATTACCAAAATACCCTTAGTTTATAA
* *
5437096 ATTTACCAAAACACCCTT
1 AATTACCAAAATACCCTT
5437114 GTAGGATGAA
Statistics
Matches: 139, Mismatches: 35, Indels: 24
0.70 0.18 0.12
Matches are distributed among these distances:
26 4 0.03
27 85 0.61
28 11 0.08
29 19 0.14
30 1 0.01
31 19 0.14
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (27 bp):
AATTACCAAAATACCCTTAGTTTATAA
Found at i:5438025 original size:25 final size:25
Alignment explanation
Indices: 5437992--5438061 Score: 122
Period size: 25 Copynumber: 2.8 Consensus size: 25
5437982 AGGAAGTGCT
*
5437992 AAAAGGGCTATGCCCCAGTTTACCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
*
5438017 AAAAGGGCTTTGCCCCAGTTTATCA
1 AAAAGGGCTTTGCCCCAGTTTACCA
5438042 AAAAGGGCTTTGCCCCAGTT
1 AAAAGGGCTTTGCCCCAGTT
5438062 ATTAAAAGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 43 1.00
ACGTcount: A:0.29, C:0.26, G:0.21, T:0.24
Consensus pattern (25 bp):
AAAAGGGCTTTGCCCCAGTTTACCA
Found at i:5439892 original size:19 final size:19
Alignment explanation
Indices: 5439868--5439911 Score: 88
Period size: 19 Copynumber: 2.3 Consensus size: 19
5439858 TCAATTAGCC
5439868 TCTCAATTGAGCTGATTTT
1 TCTCAATTGAGCTGATTTT
5439887 TCTCAATTGAGCTGATTTT
1 TCTCAATTGAGCTGATTTT
5439906 TCTCAA
1 TCTCAA
5439912 CTAGTTTACA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.23, C:0.18, G:0.14, T:0.45
Consensus pattern (19 bp):
TCTCAATTGAGCTGATTTT
Found at i:5447596 original size:19 final size:19
Alignment explanation
Indices: 5447568--5447611 Score: 79
Period size: 19 Copynumber: 2.3 Consensus size: 19
5447558 TCAATTAGCC
*
5447568 TCTCATTTGAGCTGATTTT
1 TCTCAATTGAGCTGATTTT
5447587 TCTCAATTGAGCTGATTTT
1 TCTCAATTGAGCTGATTTT
5447606 TCTCAA
1 TCTCAA
5447612 CTAGTTTACA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.20, C:0.18, G:0.14, T:0.48
Consensus pattern (19 bp):
TCTCAATTGAGCTGATTTT
Found at i:5448140 original size:64 final size:64
Alignment explanation
Indices: 5448065--5448192 Score: 229
Period size: 64 Copynumber: 2.0 Consensus size: 64
5448055 TTATCAATTT
*
5448065 TCCTGCTGATTTCATGCCCTTGCCGTCCAGCCCAAATAAATTTTGGGTCTAATTGCCTTTTAAA
1 TCCTGCTGATTTCATGCCCTTGCCATCCAGCCCAAATAAATTTTGGGTCTAATTGCCTTTTAAA
**
5448129 TCCTGCTGATTTCATGCCCTTGCCATCCAGCCGTAATAAATTTTGGGTCTAATTGCCTTTTAAA
1 TCCTGCTGATTTCATGCCCTTGCCATCCAGCCCAAATAAATTTTGGGTCTAATTGCCTTTTAAA
5448193 GCTTTTCTCA
Statistics
Matches: 61, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
64 61 1.00
ACGTcount: A:0.22, C:0.26, G:0.16, T:0.37
Consensus pattern (64 bp):
TCCTGCTGATTTCATGCCCTTGCCATCCAGCCCAAATAAATTTTGGGTCTAATTGCCTTTTAAA
Found at i:5454139 original size:68 final size:68
Alignment explanation
Indices: 5454030--5454184 Score: 310
Period size: 68 Copynumber: 2.3 Consensus size: 68
5454020 TACAAATAGT
5454030 ATGTAGCTAGGTCACATGTATGGTGCTGAGTGCACATCATGTGTACAAGAGAGCTACAAGACATT
1 ATGTAGCTAGGTCACATGTATGGTGCTGAGTGCACATCATGTGTACAAGAGAGCTACAAGACATT
5454095 ATG
66 ATG
5454098 ATGTAGCTAGGTCACATGTATGGTGCTGAGTGCACATCATGTGTACAAGAGAGCTACAAGACATT
1 ATGTAGCTAGGTCACATGTATGGTGCTGAGTGCACATCATGTGTACAAGAGAGCTACAAGACATT
5454163 ATG
66 ATG
5454166 ATGTAGCTAGGTCACATGT
1 ATGTAGCTAGGTCACATGT
5454185 GTGATACTAT
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 87 1.00
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.27
Consensus pattern (68 bp):
ATGTAGCTAGGTCACATGTATGGTGCTGAGTGCACATCATGTGTACAAGAGAGCTACAAGACATT
ATG
Found at i:5454207 original size:68 final size:68
Alignment explanation
Indices: 5454030--5454282 Score: 304
Period size: 68 Copynumber: 3.8 Consensus size: 68
5454020 TACAAATAGT
* *
5454030 ATGTAGCTAGGTCACATGTATGGTGCTGAGTGCACATCATGTGTACAAGAGAGCTACAAGACATT
1 ATGTAGCTAGGTCACATGTATGGTACTGAGTGCACACCATGTGTACAAGAGAGCTACAAGACATT
5454095 ATG
66 ATG
* *
5454098 ATGTAGCTAGGTCACATGTATGGTGCTGAGTGCACATCATGTGTACAAGAGAGCTACAAGACATT
1 ATGTAGCTAGGTCACATGTATGGTACTGAGTGCACACCATGTGTACAAGAGAGCTACAAGACATT
5454163 ATG
66 ATG
* * * **
5454166 ATGTAGCTAGGTCACATGTGTGATACT-ATGTGTACACCATGTAG-ACAAGAGAGCTAC--GGGA
1 ATGTAGCTAGGTCACATGTATGGTACTGA-GTGCACACCATGT-GTACAAGAGAGCTACAAGACA
*
5454227 -TA-A
64 TTATG
* ** **
5454230 AT-TGGCTAGGTCACATGGGTGGTACTGAGTGTTCACCATGTGTACAAGAGAGC
1 ATGTAGCTAGGTCACATGTATGGTACTGAGTGCACACCATGTGTACAAGAGAGC
5454283 CGAACTATAT
Statistics
Matches: 169, Mismatches: 12, Indels: 13
0.87 0.06 0.07
Matches are distributed among these distances:
62 1 0.01
63 43 0.25
64 3 0.02
65 2 0.01
66 2 0.01
67 1 0.01
68 116 0.69
69 1 0.01
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (68 bp):
ATGTAGCTAGGTCACATGTATGGTACTGAGTGCACACCATGTGTACAAGAGAGCTACAAGACATT
ATG
Found at i:5458197 original size:18 final size:18
Alignment explanation
Indices: 5458174--5458210 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
5458164 TCTCACGAAA
5458174 ACTTTAGCATCTCATAAT
1 ACTTTAGCATCTCATAAT
5458192 ACTTTAGCATCTCATAAT
1 ACTTTAGCATCTCATAAT
5458210 A
1 A
5458211 TACTGTTCAT
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:0.35, C:0.22, G:0.05, T:0.38
Consensus pattern (18 bp):
ACTTTAGCATCTCATAAT
Found at i:5460000 original size:56 final size:56
Alignment explanation
Indices: 5459933--5460108 Score: 334
Period size: 56 Copynumber: 3.1 Consensus size: 56
5459923 TATTAGTTTA
*
5459933 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
5459989 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
*
5460045 TTGCCCATGCTTCTTATTTTGTTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
5460101 TTGCCCAT
1 TTGCCCAT
5460109 CATCCCTTGT
Statistics
Matches: 118, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
56 118 1.00
ACGTcount: A:0.22, C:0.23, G:0.10, T:0.45
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:5463126 original size:29 final size:29
Alignment explanation
Indices: 5463063--5463130 Score: 84
Period size: 29 Copynumber: 2.3 Consensus size: 29
5463053 TAATCAACCG
*
5463063 CGCACACTTAGTGCCATGTACTTTAAACT
1 CGCACACTTAGTGCCATGCACTTTAAACT
* **
5463092 CACACACTTAGTGCCATGCA-TTTCAAGTT
1 CGCACACTTAGTGCCATGCACTTT-AAACT
5463121 CGCACACTTA
1 CGCACACTTA
5463131 CCTTTTCCGC
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 3 0.09
29 30 0.91
ACGTcount: A:0.28, C:0.29, G:0.13, T:0.29
Consensus pattern (29 bp):
CGCACACTTAGTGCCATGCACTTTAAACT
Found at i:5463242 original size:174 final size:174
Alignment explanation
Indices: 5462952--5463279 Score: 602
Period size: 174 Copynumber: 1.9 Consensus size: 174
5462942 AACTCAAGGT
* * *
5462952 ACTTACCTTTTCCGCTGTCCAAAATTGACTCGGTAAAGTCGCACCCTTCATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTATCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
5463017 GAAAATATATATTGAGTTCGCACACATAGTGCTTAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGAGTTCGCACACATAGTGCTCAATAATCAACCGCGCACACTTAGTGCCATGT
5463082 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
131 ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
5463126 ACTTACCTTTTCCGCTATCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
1 ACTTACCTTTTCCGCTATCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
*
5463191 GAAAATATATATTGGGTTCGCACACATAGTGCTCAATAATCAACCGCGCACACTTAGTGCCATGT
66 GAAAATATATATTGAGTTCGCACACATAGTGCTCAATAATCAACCGCGCACACTTAGTGCCATGT
*
5463256 ACTTTAAACTCGCACACTTAGTGC
131 ACTTTAAACTCACACACTTAGTGC
5463280 TGTACAATTT
Statistics
Matches: 148, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
174 148 1.00
ACGTcount: A:0.31, C:0.25, G:0.14, T:0.30
Consensus pattern (174 bp):
ACTTACCTTTTCCGCTATCCAAAATCGACTCGGTAAAGTCGCACCCTTAATGTAAATAATTTATA
GAAAATATATATTGAGTTCGCACACATAGTGCTCAATAATCAACCGCGCACACTTAGTGCCATGT
ACTTTAAACTCACACACTTAGTGCCATGCATTTCAAGTTCGCAC
Found at i:5463271 original size:29 final size:30
Alignment explanation
Indices: 5463232--5463310 Score: 110
Period size: 29 Copynumber: 2.7 Consensus size: 30
5463222 CTCAATAATC
5463232 AACCGCGCACACTTAGTGCCATGTAC-TTTA
1 AACC-CGCACACTTAGTGCCATGTACATTTA
*
5463262 AACTCGCACACTTAGTG-C-TGTACAATTTA
1 AACCCGCACACTTAGTGCCATGTAC-ATTTA
5463291 AACCCGCACACTTAGTGCCA
1 AACCCGCACACTTAGTGCCA
5463311 ATCTCATGAC
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 5 0.12
28 1 0.02
29 33 0.77
30 4 0.09
ACGTcount: A:0.29, C:0.30, G:0.15, T:0.25
Consensus pattern (30 bp):
AACCCGCACACTTAGTGCCATGTACATTTA
Found at i:5469207 original size:40 final size:40
Alignment explanation
Indices: 5469170--5469394 Score: 262
Period size: 40 Copynumber: 5.7 Consensus size: 40
5469160 GCTACTCGTT
* *
5469170 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATT-TAGTAACTCGCA
*
5469210 CAAATGCCTTCGGGATTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
5469250 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
* * *
5469290 TC-AATGCCTTCGGG-CTTAGCCCGGAATTAGTATCTCGCA
1 -CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
** * * * *
5469329 CAAATGCCTTC-GGATCTTAGTCCGGATATGGTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAACCCGGATTTAGTAAC-TCGCA
*
5469370 CAAA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAACCCGGA
5469395 CATCATTCGA
Statistics
Matches: 163, Mismatches: 15, Indels: 14
0.85 0.08 0.07
Matches are distributed among these distances:
38 3 0.02
39 31 0.19
40 115 0.71
41 14 0.09
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
Found at i:5469354 original size:119 final size:120
Alignment explanation
Indices: 5469172--5469394 Score: 301
Period size: 119 Copynumber: 1.9 Consensus size: 120
5469162 TACTCGTTCA
*
5469172 AATGCCTTCGGGACATAGCCCGGTTATAGTAACTCGCACAAATGCCTTCGGGATTTAACCCGGAT
1 AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGATTTAACCCGGAT
* *
5469237 TTAGTAAC-TCGCACAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCATC
66 ATAGTAACTTAGCACAAA-GCCTTCGGGACTTAACCCGGATTTAGTAACTCGCATC
* * **
5469292 AATGCCTTCGGG-CTTAGCCCGGA-ATTAGTATCTCGCACAAATGCCTTC-GGATCTTAGTCCGG
1 AATGCCTTCGGGACATAGCCCGGATA-TAGTAACTCGCACAAATGCCTTCGGGAT-TTAACCCGG
* * *
5469354 ATATGGTCACTTAGCACAAAGCCTTCGGGACTTAGCCCGGA
64 ATATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGA
5469395 CATCATTCGA
Statistics
Matches: 90, Mismatches: 10, Indels: 7
0.84 0.09 0.07
Matches are distributed among these distances:
118 5 0.06
119 65 0.72
120 20 0.22
ACGTcount: A:0.25, C:0.27, G:0.22, T:0.26
Consensus pattern (120 bp):
AATGCCTTCGGGACATAGCCCGGATATAGTAACTCGCACAAATGCCTTCGGGATTTAACCCGGAT
ATAGTAACTTAGCACAAAGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCATC
Found at i:5470091 original size:150 final size:150
Alignment explanation
Indices: 5469820--5470119 Score: 591
Period size: 150 Copynumber: 2.0 Consensus size: 150
5469810 CATCAAGCAA
*
5469820 TTTAATACAATTCATTCGAACATCAAAAGAGAAGCTCAAGGTACTTAGCCCATATATACATTAGA
1 TTTAATACAATTCATTCGAACATCAAAACAGAAGCTCAAGGTACTTAGCCCATATATACATTAGA
5469885 CACTAGAGTCACATATGTACGAAATCACGAATCGAATTCAACATACTAGCTAATATTTCCCCTTA
66 CACTAGAGTCACATATGTACGAAATCACGAATCGAATTCAACATACTAGCTAATATTTCCCCTTA
5469950 GCCGAATTTTCTAAGTCAAG
131 GCCGAATTTTCTAAGTCAAG
5469970 TTTAATACAATTCATTCGAACATCAAAACAGAAGCTCAAGGTACTTAGCCCATATATACATTAGA
1 TTTAATACAATTCATTCGAACATCAAAACAGAAGCTCAAGGTACTTAGCCCATATATACATTAGA
5470035 CACTAGAGTCACATATGTACGAAATCACGAATCGAATTCAACATACTAGCTAATATTTCCCCTTA
66 CACTAGAGTCACATATGTACGAAATCACGAATCGAATTCAACATACTAGCTAATATTTCCCCTTA
5470100 GCCGAATTTTCTAAGTCAAG
131 GCCGAATTTTCTAAGTCAAG
5470120 CTAAAGCCAT
Statistics
Matches: 149, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
150 149 1.00
ACGTcount: A:0.38, C:0.22, G:0.12, T:0.28
Consensus pattern (150 bp):
TTTAATACAATTCATTCGAACATCAAAACAGAAGCTCAAGGTACTTAGCCCATATATACATTAGA
CACTAGAGTCACATATGTACGAAATCACGAATCGAATTCAACATACTAGCTAATATTTCCCCTTA
GCCGAATTTTCTAAGTCAAG
Found at i:5470741 original size:56 final size:56
Alignment explanation
Indices: 5470674--5471073 Score: 773
Period size: 56 Copynumber: 7.1 Consensus size: 56
5470664 TATTAGTTTA
*
5470674 TTGCCCATGCTTCTTATTTTATTCTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
5470730 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
5470786 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
5470842 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
5470898 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
5470954 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
* *
5471010 TTGCCCATGCTTTTTATTTTATATTTCCATTAACACAACATGTTTCATGACATGTT
1 TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
5471066 TTGCCCAT
1 TTGCCCAT
5471074 CATCCCTTGT
Statistics
Matches: 341, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
56 341 1.00
ACGTcount: A:0.23, C:0.22, G:0.09, T:0.46
Consensus pattern (56 bp):
TTGCCCATGCTTCTTATTTTATTTTTCCATTAACACAACATGTTTCATGACATGTT
Found at i:5471765 original size:84 final size:84
Alignment explanation
Indices: 5471624--5471786 Score: 299
Period size: 84 Copynumber: 1.9 Consensus size: 84
5471614 AAGACTTACC
*
5471624 TCGGATGTTGTCGAACGACTTCAATGGCTATTGAATTACTTTTTCCTTCCCTTTATCGGATTTAG
1 TCGGATGTTGTCGAACGACTTCAATGGCTATTCAATTACTTTTTCCTTCCCTTTATCGGATTTAG
5471689 TTCCCCTTTGCTCTCGAGT
66 TTCCCCTTTGCTCTCGAGT
*
5471708 TCGGATGTTGTCGAACGACTTCAATGGCTATTCAATTACTTTTTCCTTCCCTTTATCGGATTTTG
1 TCGGATGTTGTCGAACGACTTCAATGGCTATTCAATTACTTTTTCCTTCCCTTTATCGGATTTAG
*
5471773 TTTCCCTTTGCTCT
66 TTCCCCTTTGCTCT
5471787 TGAGCTTAAA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
84 76 1.00
ACGTcount: A:0.16, C:0.24, G:0.17, T:0.44
Consensus pattern (84 bp):
TCGGATGTTGTCGAACGACTTCAATGGCTATTCAATTACTTTTTCCTTCCCTTTATCGGATTTAG
TTCCCCTTTGCTCTCGAGT
Found at i:5475144 original size:54 final size:54
Alignment explanation
Indices: 5475062--5475169 Score: 207
Period size: 54 Copynumber: 2.0 Consensus size: 54
5475052 TAGTAAAAGT
5475062 AACATAAATCCTACCTTAATCAACCCCTTTTGAGTTGGCCAAATGTCTAGAGCA
1 AACATAAATCCTACCTTAATCAACCCCTTTTGAGTTGGCCAAATGTCTAGAGCA
*
5475116 AACATAAATCCTACCTTAATCAACCCCTTTTGAGTTGGCCGAATGTCTAGAGCA
1 AACATAAATCCTACCTTAATCAACCCCTTTTGAGTTGGCCAAATGTCTAGAGCA
5475170 TTTCTTCCTT
Statistics
Matches: 53, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
54 53 1.00
ACGTcount: A:0.32, C:0.26, G:0.14, T:0.28
Consensus pattern (54 bp):
AACATAAATCCTACCTTAATCAACCCCTTTTGAGTTGGCCAAATGTCTAGAGCA
Found at i:5479280 original size:39 final size:39
Alignment explanation
Indices: 5479116--5479298 Score: 170
Period size: 40 Copynumber: 4.6 Consensus size: 39
5479106 TTGAATGCTG
* * * * * * *
5479116 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTATGTCCCGAAGGCATTGTGC-GAGTTACTAAA
* * * *
5479156 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTATG-TCCCGAAGG-CATTGTGCGAGTTACTAAA
* **
5479196 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTATGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
5479236 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTATGTCCCGAAGGCATTGTGCGAGTTACTAAA
* *
5479275 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTATGTCCCGAAGGCATT
5479299 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
39 38 0.31
40 74 0.61
41 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (39 bp):
TCCGGGTTATGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:5479318 original size:79 final size:80
Alignment explanation
Indices: 5479152--5479333 Score: 190
Period size: 79 Copynumber: 2.3 Consensus size: 80
5479142 GCTAAGTGAA
* * * *
5479152 TATATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGG
1 TATATCCGGGTTAAG-TCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGG
** ** *
5479216 CATTCGTGCGAGTTGT
65 CATTCGAACGAGGAGC
* * * * *
5479232 TAAATCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGC
1 TATATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGC
*
5479296 ATTTGAACGAGGAGC
66 ATTCGAACGAGGAGC
*
5479311 TATATCC-GGTTAAATCCCGAAGG
1 TATATCCGGGTTAAGTCCCGAAGG
5479334 TACGTGATTT
Statistics
Matches: 83, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
78 14 0.17
79 50 0.60
80 19 0.23
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (80 bp):
TATATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGC
ATTCGAACGAGGAGC
Found at i:5495808 original size:422 final size:422
Alignment explanation
Indices: 5495024--5496293 Score: 2477
Period size: 422 Copynumber: 3.0 Consensus size: 422
5495014 TGGGAGTATT
*
5495024 TATAAAGGTAATCTGCGTCATACCACTGTGGCTATAAAGATGTTGCATTCTAATAGCTTGCAAGG
1 TATAAAGGTAATCTGTGTCATACCACTGTGGCTATAAAGATGTTGCATTCTAATAGCTTGCAAGG
5495089 TCCATCGGAATTTCAACAAGAGGTATAGTCCCCTAAGTATTGTTTTATTTATTGTTTGGATGGAC
66 TCCATCGGAATTTCAACAAGAGGTATAGTCCCCTAAGTATTGTTTTATTTATTGTTTGGATGGAC
5495154 TTCATGTTACATTGAGTTGAACATATTATTAGTGGTATCCGTGTCATAAATTCAGAGCCTATGAT
131 TTCATGTTACATTGAGTTGAACATATTATTAGTGGTATCCGTGTCATAAATTCAGAGCCTATGAT
5495219 ATATCCAGAAAAAGCCCAAGGAGTTAATTATAGATTCTGTTATTTGGTTATTGTGTTTGCTGCAT
196 ATATCCAGAAAAAGCCCAAGGAGTTAATTATAGATTCTGTTATTTGGTTATTGTGTTTGCTGCAT
5495284 TCCTTGTACATATCTCAAAGTTAATTGTCCCCCATCCTGGAACTGTATTTTGTGCCTTAGACTGT
261 TCCTTGTACATATCTCAAAGTTAATTGTCCCCCATCCTGGAACTGTATTTTGTGCCTTAGACTGT
5495349 CTATGTTCTTCCCTCTCTAGCAATTCTGCATCCTCAAAAATAAGCTTAAAATTATCTATTTGTTA
326 CTATGTTCTTCCCTCTCTAGCAATTCTGCATCCTCAAAAATAAGCTTAAAATTATCTATTTGTTA
5495414 ACAGTAGTATCATGTTGCACGTGTAAAATATA
391 ACAGTAGTATCATGTTGCACGTGTAAAATATA
5495446 TATAAAGGTAATCTGTGTCATACCACTGTGGCTATAAAGATGTTGCATTCTAATAGCTTGCAAGG
1 TATAAAGGTAATCTGTGTCATACCACTGTGGCTATAAAGATGTTGCATTCTAATAGCTTGCAAGG
5495511 TCCATCGGAATTTCAACAAGAGGTATAGTCCCCTAAGTATTGTTTTATTTATTGTTTGGATGGAC
66 TCCATCGGAATTTCAACAAGAGGTATAGTCCCCTAAGTATTGTTTTATTTATTGTTTGGATGGAC
5495576 TTCATGTTACATTGAGTTGAACATATTATTAGTGGTATCCGTGTCATAAATTCAGAGCCTATGAT
131 TTCATGTTACATTGAGTTGAACATATTATTAGTGGTATCCGTGTCATAAATTCAGAGCCTATGAT
5495641 ATATCCAGAAAAAGCCCAAGGAGTTAATTATAGATTCTGTTATTTGGTTATTGTGTTTGCTGCAT
196 ATATCCAGAAAAAGCCCAAGGAGTTAATTATAGATTCTGTTATTTGGTTATTGTGTTTGCTGCAT
*
5495706 TCCTTGTACATATCTCAAAGTTAATTGTCCCCCATCCTGGAACTGTATTTTGTGCCTCAGACTGT
261 TCCTTGTACATATCTCAAAGTTAATTGTCCCCCATCCTGGAACTGTATTTTGTGCCTTAGACTGT
5495771 CTATGTTCTTCCCTCTCTAGCAATTCTGCATCCTCAAAAATAAGCTTAAAATTATCTATTTGTTA
326 CTATGTTCTTCCCTCTCTAGCAATTCTGCATCCTCAAAAATAAGCTTAAAATTATCTATTTGTTA
5495836 ACAGTAGTATCATGTTGCACGTGTAAAATATA
391 ACAGTAGTATCATGTTGCACGTGTAAAATATA
5495868 TATAAAGGTAATCTGTGTCATACCACTGTGGCTATAAAGATGTTGCATTCTAATAGCTTGCAAGG
1 TATAAAGGTAATCTGTGTCATACCACTGTGGCTATAAAGATGTTGCATTCTAATAGCTTGCAAGG
5495933 TCCATCGGAATTTCAACAAGAGGTATAGTCCCCTAAGTATTGTTTTATTTATTGTTTGGATGGAC
66 TCCATCGGAATTTCAACAAGAGGTATAGTCCCCTAAGTATTGTTTTATTTATTGTTTGGATGGAC
5495998 TTCATGTTACATTGAGTTGAACATATTATTAGTGGTATCCGTGTCATAAATTCAGAGCCTATGAT
131 TTCATGTTACATTGAGTTGAACATATTATTAGTGGTATCCGTGTCATAAATTCAGAGCCTATGAT
* *
5496063 ATATCCAGAAAAAGCCCAAGGAGTTAATTATAGATTCTGTTATTTGGTTATTATGTTTGCAGCAT
196 ATATCCAGAAAAAGCCCAAGGAGTTAATTATAGATTCTGTTATTTGGTTATTGTGTTTGCTGCAT
*
5496128 TCCTTGTACATACCTCAAAGTTAATTGTCCCCCATCCTGGAACTGTATTTTGTGCCTTAGACTGT
261 TCCTTGTACATATCTCAAAGTTAATTGTCCCCCATCCTGGAACTGTATTTTGTGCCTTAGACTGT
5496193 CTATGTTCTTCCCTCTCTAGCAATTCTGCATCCTCAAAAATAAGCTTAAAATTATCTATTTGTTA
326 CTATGTTCTTCCCTCTCTAGCAATTCTGCATCCTCAAAAATAAGCTTAAAATTATCTATTTGTTA
* *
5496258 ACAGTAGTATCATGTTGCAGGTGTAAAAAATA
391 ACAGTAGTATCATGTTGCACGTGTAAAATATA
5496290 TATA
1 TATA
5496294 TTTAGTTCCA
Statistics
Matches: 840, Mismatches: 8, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
422 840 1.00
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (422 bp):
TATAAAGGTAATCTGTGTCATACCACTGTGGCTATAAAGATGTTGCATTCTAATAGCTTGCAAGG
TCCATCGGAATTTCAACAAGAGGTATAGTCCCCTAAGTATTGTTTTATTTATTGTTTGGATGGAC
TTCATGTTACATTGAGTTGAACATATTATTAGTGGTATCCGTGTCATAAATTCAGAGCCTATGAT
ATATCCAGAAAAAGCCCAAGGAGTTAATTATAGATTCTGTTATTTGGTTATTGTGTTTGCTGCAT
TCCTTGTACATATCTCAAAGTTAATTGTCCCCCATCCTGGAACTGTATTTTGTGCCTTAGACTGT
CTATGTTCTTCCCTCTCTAGCAATTCTGCATCCTCAAAAATAAGCTTAAAATTATCTATTTGTTA
ACAGTAGTATCATGTTGCACGTGTAAAATATA
Found at i:5498186 original size:15 final size:15
Alignment explanation
Indices: 5498166--5498195 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
5498156 GAAAATTACA
5498166 ATTATATTGATAAAT
1 ATTATATTGATAAAT
5498181 ATTATATTGATAAAT
1 ATTATATTGATAAAT
5498196 TTAATTTGAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.00, G:0.07, T:0.47
Consensus pattern (15 bp):
ATTATATTGATAAAT
Found at i:5499250 original size:26 final size:25
Alignment explanation
Indices: 5499210--5499259 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 25
5499200 AAATTTAATT
*
5499210 AATTAATAATCAAAATTTATTCTCTA
1 AATTAATAATCAAAA-ATATTCTCTA
* *
5499236 AATTAATTATGAAAAATATTCTCT
1 AATTAATAATCAAAAATATTCTCT
5499260 TTAATATTAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.46, C:0.10, G:0.02, T:0.42
Consensus pattern (25 bp):
AATTAATAATCAAAAATATTCTCTA
Found at i:5505050 original size:27 final size:27
Alignment explanation
Indices: 5505019--5505196 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
5505009 TAAATTGTAC
5505019 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
5505046 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
5505072 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
5505100 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
5505128 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
5505155 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
5505182 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
5505197 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:5505133 original size:82 final size:81
Alignment explanation
Indices: 5505020--5505175 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
5505010 AAATTGTACA
* *
5505020 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
5505084 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
5505101 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
5505166 TGCGAGTTGA
65 TGCGAATTGA
5505176 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:5505187 original size:82 final size:81
Alignment explanation
Indices: 5505016--5505196 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
5505006 GATTAAATTG
* *
5505016 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
5505081 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
5505097 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
5505161 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
5505179 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
5505197 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:5512900 original size:25 final size:25
Alignment explanation
Indices: 5512835--5512900 Score: 64
Period size: 25 Copynumber: 2.6 Consensus size: 25
5512825 TCTCAAAAAT
* *
5512835 TTAATTAAA-TAAAAATTATTAATGA
1 TTAAATAAATTAAAAATTA-TAATAA
*
5512860 TTCAATAAATTGAAAAATTA-AATAA
1 TTAAATAAATT-AAAAATTATAATAA
5512885 TTAAATAAAATTAAAA
1 TTAAAT-AAATTAAAA
5512901 GTTTAGGAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
25 20 0.59
26 6 0.18
27 8 0.24
ACGTcount: A:0.61, C:0.02, G:0.03, T:0.35
Consensus pattern (25 bp):
TTAAATAAATTAAAAATTATAATAA
Found at i:5513704 original size:30 final size:29
Alignment explanation
Indices: 5513647--5513704 Score: 80
Period size: 29 Copynumber: 2.0 Consensus size: 29
5513637 CTTTTGAAAA
* * *
5513647 TATTTACAAAAAAGGCATCTAATTTTTAT
1 TATTTACAAAAAAGGCAACCAAATTTTAT
5513676 TATTTACAAAAAAGAGCAACCAAATTTTA
1 TATTTACAAAAAAG-GCAACCAAATTTTA
5513705 AAAAAATTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 14 0.56
30 11 0.44
ACGTcount: A:0.47, C:0.12, G:0.07, T:0.34
Consensus pattern (29 bp):
TATTTACAAAAAAGGCAACCAAATTTTAT
Found at i:5516094 original size:323 final size:323
Alignment explanation
Indices: 5515506--5516147 Score: 1257
Period size: 323 Copynumber: 2.0 Consensus size: 323
5515496 AGTGGTCCAT
5515506 ATAGACAGTCACTTTGGTACCTACAAGATAAGATCGAAACTTGTGACAGCCTAAAATTGACCCTA
1 ATAGACAGTCACTTTGGTACCTACAAGATAAGATCGAAACTTGTGACAGCCTAAAATTGACCCTA
5515571 GTCGGGAAGTGGTTTCGGGACCACAAAACCGAGTCATAATAATAATTAGCCATCATATTTGATGC
66 GTCGGGAAGTGGTTTCGGGACCACAAAACCGAGTCATAATAATAATTAGCCATCATATTTGATGC
5515636 TTATTATATGTATATATGCATGTGTGAAAATTTCATGTTTGAATTTTGTTAATTGTAAGTGAATT
131 TTATTATATGTATATATGCATGTGTGAAAATTTCATGTTTGAATTTTGTTAATTGTAAGTGAATT
*
5515701 TTATTAAATAGGACTTATGTGAGAAAATTTGGAAATGTGCTAGGCAAATCTGAAGTGGCCTATTA
196 TTATTAAATAGGACTTATGTGAGAAAATTTAGAAATGTGCTAGGCAAATCTGAAGTGGCCTATTA
*
5515766 ATGCATGTTATGAAAATGATGGGTTTGCATGTCAAATTACCCAAAATTTGAGCTAGTGGTCGG
261 ATGCATGTTATGAAAATGATGGATTTGCATGTCAAATTACCCAAAATTTGAGCTAGTGGTCGG
5515829 ATAGACAGTCACTTTGGTACCTACAAGATAAGATCGAAACTTGTGACAGCCTAAAATTGACCCTA
1 ATAGACAGTCACTTTGGTACCTACAAGATAAGATCGAAACTTGTGACAGCCTAAAATTGACCCTA
5515894 GTCGGGAAGTGGTTTCGGGACCACAAAACCGAGTCATAATAATAATTAGCCATCATATTTGATGC
66 GTCGGGAAGTGGTTTCGGGACCACAAAACCGAGTCATAATAATAATTAGCCATCATATTTGATGC
5515959 TTATTATATGTATATATGCATGTGTGAAAATTTCATGTTTGAATTTTGTTAATTGTAAGTGAATT
131 TTATTATATGTATATATGCATGTGTGAAAATTTCATGTTTGAATTTTGTTAATTGTAAGTGAATT
*
5516024 TTATTAAATAGGACTTATGTGAGAAAATTTAGAAATGTGCTAGGCAAATGTGAAGTGGCCTATTA
196 TTATTAAATAGGACTTATGTGAGAAAATTTAGAAATGTGCTAGGCAAATCTGAAGTGGCCTATTA
5516089 ATGCATGTTATGAAAATGATGGATTTGCATGTCAAATTACCCAAAATTTGAGCTAGTGG
261 ATGCATGTTATGAAAATGATGGATTTGCATGTCAAATTACCCAAAATTTGAGCTAGTGG
5516148 CCGGCCATGC
Statistics
Matches: 316, Mismatches: 3, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
323 316 1.00
ACGTcount: A:0.34, C:0.13, G:0.21, T:0.33
Consensus pattern (323 bp):
ATAGACAGTCACTTTGGTACCTACAAGATAAGATCGAAACTTGTGACAGCCTAAAATTGACCCTA
GTCGGGAAGTGGTTTCGGGACCACAAAACCGAGTCATAATAATAATTAGCCATCATATTTGATGC
TTATTATATGTATATATGCATGTGTGAAAATTTCATGTTTGAATTTTGTTAATTGTAAGTGAATT
TTATTAAATAGGACTTATGTGAGAAAATTTAGAAATGTGCTAGGCAAATCTGAAGTGGCCTATTA
ATGCATGTTATGAAAATGATGGATTTGCATGTCAAATTACCCAAAATTTGAGCTAGTGGTCGG
Found at i:5525165 original size:97 final size:91
Alignment explanation
Indices: 5524987--5525173 Score: 320
Period size: 97 Copynumber: 2.0 Consensus size: 91
5524977 AATGAAAAGG
5524987 GAGGGGTGATGAAAACAAAGTTGTCTCATCCATCCCCCCCCTCCATTTGCCGTAACTAGACAAAG
1 GAGGGGTGATGAAAACAAAGTTGTCTCATCCATCCCCCCCCTCCATTTGCCGTAACTAGACAAAG
5525052 AAAAGAGAAAAAAAAAAGAGTGTGTA
66 AAAAGAGAAAAAAAAAAGAGTGTGTA
5525078 GAGGGGTGATGAAAACAAAGTTGTCTCATCCATCCCCCCCTCCATTTGCCATTTGCCGTAACTAG
1 GAGGGGTGATGAAAACAAAGTTGTCTCATCCAT-CCCCCC-CC---T-CCATTTGCCGTAACTAG
5525143 ACAAAGAAAAGAGAAAAAAAAAAGAGTGTGT
60 ACAAAGAAAAGAGAAAAAAAAAAGAGTGTGT
5525174 TCATCTTCCT
Statistics
Matches: 90, Mismatches: 0, Indels: 6
0.94 0.00 0.06
Matches are distributed among these distances:
91 33 0.37
92 6 0.07
93 2 0.02
96 1 0.01
97 48 0.53
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.20
Consensus pattern (91 bp):
GAGGGGTGATGAAAACAAAGTTGTCTCATCCATCCCCCCCCTCCATTTGCCGTAACTAGACAAAG
AAAAGAGAAAAAAAAAAGAGTGTGTA
Found at i:5526418 original size:89 final size:90
Alignment explanation
Indices: 5526267--5526447 Score: 301
Period size: 89 Copynumber: 2.0 Consensus size: 90
5526257 TAATTTAAAT
* *
5526267 GGTCATAACGTCTATGTAATGATGCTGAATGGAATGATAAATATATATATATACAT-GTATGTAT
1 GGTCATAACATCTATGTAATGATGCTGAATGGAATGATAAATATATATATATACATACTATGTAT
5526331 GTGGTGATGAAAGTGTTGAATGAAC
66 GTGGTGATGAAAGTGTTGAATGAAC
*
5526356 GGTCATAACATCTATGTAATGATGCTGAATGGAATGATAAATATATATATATATATACATGTATG
1 GGTCATAACATCTATGTAATGATGCTGAATGGAATGATAAATATATATATATACATAC---TATG
5526421 TATGTGGTGATGAAAGTGTTGAATGAA
63 TATGTGGTGATGAAAGTGTTGAATGAA
5526448 AAGAAAAGAG
Statistics
Matches: 85, Mismatches: 3, Indels: 4
0.92 0.03 0.04
Matches are distributed among these distances:
89 54 0.64
93 31 0.36
ACGTcount: A:0.37, C:0.06, G:0.23, T:0.34
Consensus pattern (90 bp):
GGTCATAACATCTATGTAATGATGCTGAATGGAATGATAAATATATATATATACATACTATGTAT
GTGGTGATGAAAGTGTTGAATGAAC
Found at i:5526621 original size:56 final size:56
Alignment explanation
Indices: 5526530--5526652 Score: 176
Period size: 55 Copynumber: 2.2 Consensus size: 56
5526520 GAGATTGGCG
* * *
5526530 CTAAGTGTGCGGGTTTAAATTGTACAGCACTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAG-TTGATTATATAGCA
* *
5526587 CTAAGTGTGCGAGTTT-GATTATATAGCACTAAGTGTGCGAGTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTGATTATATAGCA
*
5526642 CTGAGTGTGCG
1 CTAAGTGTGCG
5526653 GACTTAATAT
Statistics
Matches: 60, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
55 23 0.38
56 22 0.37
57 15 0.25
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.33
Consensus pattern (56 bp):
CTAAGTGTGCGAGTTTAAATTATACAGCACTAAGTGTGCGAGTTGATTATATAGCA
Found at i:5526639 original size:27 final size:28
Alignment explanation
Indices: 5526530--5526652 Score: 176
Period size: 28 Copynumber: 4.4 Consensus size: 28
5526520 GAGATTGGCG
* * * *
5526530 CTAAGTGTGCGGGTTTAAATTGTACAGCA
1 CTAAGTGTGCGAGTTT-GATTATATAGCA
*
5526559 CTAAGTGTGCGAGTTTGATTATGTAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
5526587 CTAAGTGTGCGAGTTTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
5526615 CTAAGTGTGCGAG-TTGATTATATAGCA
1 CTAAGTGTGCGAGTTTGATTATATAGCA
*
5526642 CTGAGTGTGCG
1 CTAAGTGTGCG
5526653 GACTTAATAT
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
27 24 0.28
28 48 0.55
29 15 0.17
ACGTcount: A:0.26, C:0.12, G:0.28, T:0.33
Consensus pattern (28 bp):
CTAAGTGTGCGAGTTTGATTATATAGCA
Found at i:5526663 original size:27 final size:27
Alignment explanation
Indices: 5526555--5526665 Score: 116
Period size: 28 Copynumber: 4.0 Consensus size: 27
5526545 TAAATTGTAC
* * *
5526555 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
5526583 AGCACTAAGTGTGCGAGTTTGATTATAT
1 AGCACTAAGTGTGCGA-CTTGAATATAT
* *
5526611 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGACTTGAATATAT
*
5526638 AGCACTGAGTGTGCGGACTT-AATATAT
1 AGCACTAAGTGTGC-GACTTGAATATAT
5526665 A
1 A
5526666 CTTTTGAATC
Statistics
Matches: 77, Mismatches: 5, Indels: 3
0.91 0.06 0.04
Matches are distributed among these distances:
27 30 0.39
28 47 0.61
ACGTcount: A:0.29, C:0.12, G:0.26, T:0.33
Consensus pattern (27 bp):
AGCACTAAGTGTGCGACTTGAATATAT
Found at i:5527292 original size:48 final size:48
Alignment explanation
Indices: 5527221--5527316 Score: 183
Period size: 48 Copynumber: 2.0 Consensus size: 48
5527211 TTCTTAGTCG
*
5527221 GCTTAGGAGAACATTTCGGCATGTATAGGCTATTATGTTGTGTTTGAA
1 GCTTAGGAGAACATTTCGACATGTATAGGCTATTATGTTGTGTTTGAA
5527269 GCTTAGGAGAACATTTCGACATGTATAGGCTATTATGTTGTGTTTGAA
1 GCTTAGGAGAACATTTCGACATGTATAGGCTATTATGTTGTGTTTGAA
5527317 CTTTGGTATG
Statistics
Matches: 47, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 47 1.00
ACGTcount: A:0.26, C:0.10, G:0.26, T:0.38
Consensus pattern (48 bp):
GCTTAGGAGAACATTTCGACATGTATAGGCTATTATGTTGTGTTTGAA
Found at i:5527482 original size:99 final size:100
Alignment explanation
Indices: 5527355--5527553 Score: 373
Period size: 99 Copynumber: 2.0 Consensus size: 100
5527345 AAAATGGCAT
* *
5527355 AAATGTTTGGTTGGGTTTGGTTTTATAACGTTAGGTCGTAAGTTTTGGTAATTCGAC-TTTTTTT
1 AAATGTTCGGTTGGGTTTGGTTTTATAACGTTAGGTCGTAAGTCTTGGTAATTCGACTTTTTTTT
5527419 TATGCCATATGTCATGGTTGATTATTTTTTTGGTG
66 TATGCCATATGTCATGGTTGATTATTTTTTTGGTG
5527454 AAATGTTCGGTTGGGTTTGGTTTTATAACGTTAGGTCGTAAGTCTTGGTAATTCGACTTTTTTTT
1 AAATGTTCGGTTGGGTTTGGTTTTATAACGTTAGGTCGTAAGTCTTGGTAATTCGACTTTTTTTT
5527519 TATGCCATATGTCATGGTTGATTATTTTTTTGGTG
66 TATGCCATATGTCATGGTTGATTATTTTTTTGGTG
5527554 TATTCGACTT
Statistics
Matches: 97, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
99 55 0.57
100 42 0.43
ACGTcount: A:0.18, C:0.08, G:0.24, T:0.50
Consensus pattern (100 bp):
AAATGTTCGGTTGGGTTTGGTTTTATAACGTTAGGTCGTAAGTCTTGGTAATTCGACTTTTTTTT
TATGCCATATGTCATGGTTGATTATTTTTTTGGTG
Found at i:5527596 original size:28 final size:28
Alignment explanation
Indices: 5527515--5527597 Score: 72
Period size: 28 Copynumber: 3.2 Consensus size: 28
5527505 TTCGACTTTT
5527515 TTTTTATGCCATATGTCATGGTTGATTA
1 TTTTTATGCCATATGTCATGGTTGATTA
* * * *
5527543 TTTTTTTG----GTGT-AT--TCGACTTT
1 TTTTTATGCCATATGTCATGGTTGA-TTA
5527565 TTTTTATGCCATATGTCATGGTTGATTA
1 TTTTTATGCCATATGTCATGGTTGATTA
5527593 TTTTT
1 TTTTT
5527598 TTGGTGTTAA
Statistics
Matches: 39, Mismatches: 8, Indels: 16
0.62 0.13 0.25
Matches are distributed among these distances:
21 3 0.08
22 9 0.23
23 2 0.05
24 3 0.08
26 3 0.08
27 2 0.05
28 14 0.36
29 3 0.08
ACGTcount: A:0.17, C:0.10, G:0.17, T:0.57
Consensus pattern (28 bp):
TTTTTATGCCATATGTCATGGTTGATTA
Found at i:5527598 original size:51 final size:51
Alignment explanation
Indices: 5527504--5527604 Score: 195
Period size: 50 Copynumber: 2.0 Consensus size: 51
5527494 AGTCTTGGTA
5527504 ATTCGACTTTTTTTTTATGCCATATGTCATGGTTGATTATTTTTTTGGTGT
1 ATTCGACTTTTTTTTTATGCCATATGTCATGGTTGATTATTTTTTTGGTGT
5527555 ATTCGAC-TTTTTTTTATGCCATATGTCATGGTTGATTATTTTTTTGGTGT
1 ATTCGACTTTTTTTTTATGCCATATGTCATGGTTGATTATTTTTTTGGTGT
5527605 TAAAATTCAT
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
50 43 0.86
51 7 0.14
ACGTcount: A:0.16, C:0.10, G:0.18, T:0.56
Consensus pattern (51 bp):
ATTCGACTTTTTTTTTATGCCATATGTCATGGTTGATTATTTTTTTGGTGT
Found at i:5532263 original size:123 final size:118
Alignment explanation
Indices: 5531947--5532304 Score: 478
Period size: 112 Copynumber: 3.0 Consensus size: 118
5531937 TTCTGCACAT
* *
5531947 CAATAAGGGTCCTTCCGGTTGCTAAGAATGGTCTTCCTAAGATAATTGACACTTCTTTGTCTGCT
1 CAATAAGGGTCCTTCCGGTTTCTAAGAATGGTTTTCCTAAGATAATTGACACTTCTTTGTCTGCT
5532012 TCAAAGTGTAAGATAACAAAATCAGCAGGGAAGATAAATTTATCTACACGTAC
66 TCAAAGTGTAAGATAACAAAATCAGCAGGGAAGATAAATTTATCTACACGTAC
* * ***** * * * *
5532065 CAATACA---TCC-T-CGATTTTTCCTTTTGGATGTGCTAAG--GATTGACACTTCTTTGTCTGC
1 CAATA-AGGGTCCTTCCGGTTTCTAAGAATGGTTTTCCTAAGATAATTGACACTTCTTTGTCTGC
*
5532123 TTCAAAGTGTAAGATAACAAAATCAGTAGGGAAGATAACACTTCTTTATCTACACGTAC
65 TTCAAAGTGTAAGATAACAAAATCAGCAGGGAAGATAA-A----TTTATCTACACGTAC
5532182 CAATAAGGGTCCTTCCGGTTTCTAAGAATGGTTTTCCTAAGATAATTGACACTTCTTTGTCTGCT
1 CAATAAGGGTCCTTCCGGTTTCTAAGAATGGTTTTCCTAAGATAATTGACACTTCTTTGTCTGCT
*
5532247 TCAAAGTGTAAGATAACAAAATCAGCAGGGAAGATAAATTTATCTACACATAC
66 TCAAAGTGTAAGATAACAAAATCAGCAGGGAAGATAAATTTATCTACACGTAC
5532300 CAATA
1 CAATA
5532305 CATCCTCGAT
Statistics
Matches: 200, Mismatches: 27, Indels: 26
0.79 0.11 0.10
Matches are distributed among these distances:
112 57 0.28
113 1 0.00
114 14 0.07
115 1 0.00
116 4 0.02
117 20 0.10
118 24 0.12
119 4 0.02
120 1 0.00
121 16 0.08
122 1 0.00
123 57 0.28
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.32
Consensus pattern (118 bp):
CAATAAGGGTCCTTCCGGTTTCTAAGAATGGTTTTCCTAAGATAATTGACACTTCTTTGTCTGCT
TCAAAGTGTAAGATAACAAAATCAGCAGGGAAGATAAATTTATCTACACGTAC
Found at i:5536377 original size:22 final size:20
Alignment explanation
Indices: 5536332--5536377 Score: 51
Period size: 18 Copynumber: 2.3 Consensus size: 20
5536322 TTAAGTGCAC
5536332 TTTAATTATTTTATAAAAAA
1 TTTAATTATTTTATAAAAAA
*
5536352 --TAATTATTTTTTGACAAAAA
1 TTTAATTATTTTAT-A-AAAAA
5536372 TTTAAT
1 TTTAAT
5536378 CGAATTCGCA
Statistics
Matches: 21, Mismatches: 1, Indels: 6
0.75 0.04 0.21
Matches are distributed among these distances:
18 11 0.52
19 1 0.05
20 5 0.24
22 4 0.19
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (20 bp):
TTTAATTATTTTATAAAAAA
Found at i:5536599 original size:19 final size:19
Alignment explanation
Indices: 5536575--5536613 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
5536565 AATAAATTAC
5536575 TCATCTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
5536594 TCATCTTAGTTAATTAAGT
1 TCATCTTAGTTAATTAAGT
5536613 T
1 T
5536614 GTTGGAATAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.31, C:0.10, G:0.10, T:0.49
Consensus pattern (19 bp):
TCATCTTAGTTAATTAAGT
Found at i:5536734 original size:9 final size:9
Alignment explanation
Indices: 5536720--5536756 Score: 56
Period size: 9 Copynumber: 4.0 Consensus size: 9
5536710 TATGTGTCTA
5536720 AATGTGTTT
1 AATGTGTTT
5536729 AATGTGTTT
1 AATGTGTTT
*
5536738 AATGAGTTTT
1 AATGTG-TTT
5536748 AATGTGTTT
1 AATGTGTTT
5536757 GTTTGTAGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.24, C:0.00, G:0.22, T:0.54
Consensus pattern (9 bp):
AATGTGTTT
Found at i:5536735 original size:19 final size:19
Alignment explanation
Indices: 5536711--5536755 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
5536701 TAAGTCTAAT
*
5536711 ATGTGTCTAAATGTG-TTTA
1 ATGTGT-TAAATGAGTTTTA
*
5536730 ATGTGTTTAATGAGTTTTA
1 ATGTGTTAAATGAGTTTTA
5536749 ATGTGTT
1 ATGTGTT
5536756 TGTTTGTAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
18 6 0.26
19 17 0.74
ACGTcount: A:0.24, C:0.02, G:0.22, T:0.51
Consensus pattern (19 bp):
ATGTGTTAAATGAGTTTTA
Found at i:5543765 original size:33 final size:33
Alignment explanation
Indices: 5543722--5543798 Score: 109
Period size: 33 Copynumber: 2.3 Consensus size: 33
5543712 AGTGAATAAC
*
5543722 ACAGTATCAGTACACTCTGGGCCAAAGCCCTAT
1 ACAGTATCAGTACACTCTAGGCCAAAGCCCTAT
* * *
5543755 TCAGTATCAGTACAGTCTAGGCCTAAGCCCTAT
1 ACAGTATCAGTACACTCTAGGCCAAAGCCCTAT
*
5543788 ACAGTAGCAGT
1 ACAGTATCAGT
5543799 GCAGGCCTAG
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.30, C:0.27, G:0.19, T:0.23
Consensus pattern (33 bp):
ACAGTATCAGTACACTCTAGGCCAAAGCCCTAT
Found at i:5544280 original size:27 final size:28
Alignment explanation
Indices: 5544208--5544263 Score: 82
Period size: 27 Copynumber: 2.1 Consensus size: 28
5544198 GGGCATAATC
*
5544208 GTCA-TTTACCATACA-GGGCAATTACG
1 GTCACTTTACCCTACAGGGGCAATTACG
5544234 GTCACTTTACCCTACAGGGGC-ATTACG
1 GTCACTTTACCCTACAGGGGCAATTACG
5544261 GTC
1 GTC
5544264 TTTTTACCTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
26 4 0.15
27 19 0.70
28 4 0.15
ACGTcount: A:0.25, C:0.27, G:0.21, T:0.27
Consensus pattern (28 bp):
GTCACTTTACCCTACAGGGGCAATTACG
Found at i:5544354 original size:27 final size:27
Alignment explanation
Indices: 5544324--5544638 Score: 204
Period size: 27 Copynumber: 11.6 Consensus size: 27
5544314 AGTAAATCTA
* *
5544324 CAAACCAAGGGTATTTCAGTAATTTTT
1 CAAATCAAGGGTATTTCGGTAATTTTT
* * * **
5544351 CAAACCAATGGTATATCTATAATTTTTT
1 CAAATCAAGGGTATTTCGGTAA-TTTTT
* **
5544379 GAAAGTCAAGGGTATTTCTATAATTTTGT
1 CAAA-TCAAGGGTATTTCGGTAATTTT-T
* * * *
5544408 -AAATTAGGGGTATTTCTGTAATTTTC
1 CAAATCAAGGGTATTTCGGTAATTTTT
* * * *
5544434 CAATTTAAGGGTATTTCGATAATTTTC
1 CAAATCAAGGGTATTTCGGTAATTTTT
* * * *
5544461 CAAATTAGGGGTATTTTGGTAATTTTA
1 CAAATCAAGGGTATTTCGGTAATTTTT
* *
5544488 CAAATTAAGGGTATTTCGGTAATTTTA
1 CAAATCAAGGGTATTTCGGTAATTTTT
*
5544515 CAAATCGAGGGTATTTCGGTAATTTTAT
1 CAAATCAAGGGTATTTCGGTAATTTT-T
** *** * **
5544543 -AGGTTGGGGGTATTTCGATAATTTCA
1 CAAATCAAGGGTATTTCGGTAATTTTT
* * *
5544569 CAAACCAAGGGTATTTTGGTAATTTTA
1 CAAATCAAGGGTATTTCGGTAATTTTT
* * *
5544596 CAAACCAGGGGTATTTTGGTAATTTTGT
1 CAAATCAAGGGTATTTCGGTAATTTT-T
*
5544624 -AAACCAAGGGTATTT
1 CAAATCAAGGGTATTT
5544639 AGTAATTCTA
Statistics
Matches: 236, Mismatches: 45, Indels: 14
0.80 0.15 0.05
Matches are distributed among these distances:
27 205 0.87
28 15 0.06
29 16 0.07
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.40
Consensus pattern (27 bp):
CAAATCAAGGGTATTTCGGTAATTTTT
Found at i:5544504 original size:81 final size:81
Alignment explanation
Indices: 5544330--5544621 Score: 244
Period size: 81 Copynumber: 3.6 Consensus size: 81
5544320 TCTACAAACC
* * * * * * ** * *
5544330 AAGGGTATTTCAGTAATTTTTCAAACCAATGGTATATCTATAATTTTTTGAAAGTCAAGGGTATT
1 AAGGGTATTTCTGTAATTTTACAAATCAAGGGTATTTCGATAA-TTTTACAAA-TTAGGGGTATT
* **
5544395 TCTATAATTTTGTAAATT
64 TCGATAATTTTACAAATT
* * * * * *
5544413 AGGGGTATTTCTGTAATTTTCCAATTTAAGGGTATTTCGATAATTTTCCAAATTAGGGGTATTTT
1 AAGGGTATTTCTGTAATTTTACAAATCAAGGGTATTTCGATAATTTTACAAATTAGGGGTATTTC
*
5544478 GGTAATTTTACAAATT
66 GATAATTTTACAAATT
* * * * ** *
5544494 AAGGGTATTTCGGTAATTTTACAAATCGAGGGTATTTCGGTAATTTTATAGGTTGGGGGTATTTC
1 AAGGGTATTTCTGTAATTTTACAAATCAAGGGTATTTCGATAATTTTACAAATTAGGGGTATTTC
* **
5544559 GATAATTTCACAAACC
66 GATAATTTTACAAATT
* * * *
5544575 AAGGGTATTT-TGGTAATTTTACAAACCAGGGGTATTTTGGTAATTTT
1 AAGGGTATTTCT-GTAATTTTACAAATCAAGGGTATTTCGATAATTTT
5544622 GTAAACCAAG
Statistics
Matches: 168, Mismatches: 40, Indels: 4
0.79 0.19 0.02
Matches are distributed among these distances:
81 127 0.76
82 7 0.04
83 34 0.20
ACGTcount: A:0.30, C:0.09, G:0.20, T:0.42
Consensus pattern (81 bp):
AAGGGTATTTCTGTAATTTTACAAATCAAGGGTATTTCGATAATTTTACAAATTAGGGGTATTTC
GATAATTTTACAAATT
Found at i:5544685 original size:26 final size:27
Alignment explanation
Indices: 5544628--5544698 Score: 92
Period size: 27 Copynumber: 2.7 Consensus size: 27
5544618 TTTTGTAAAC
*
5544628 CAAGGGTATTT-AGTAATTCTACTCTA
1 CAAGGGCATTTCAGTAATTCTACTCTA
5544654 CAAGGGCATTTCAGTAATTCTAC-CATA
1 CAAGGGCATTTCAGTAATTCTACTC-TA
* *
5544681 CAGGGGCAATTCAGTAAT
1 CAAGGGCATTTCAGTAAT
5544699 ACTAGCCTAC
Statistics
Matches: 40, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
26 11 0.28
27 29 0.73
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.31
Consensus pattern (27 bp):
CAAGGGCATTTCAGTAATTCTACTCTA
Found at i:5544709 original size:27 final size:26
Alignment explanation
Indices: 5544639--5544710 Score: 81
Period size: 27 Copynumber: 2.7 Consensus size: 26
5544629 AAGGGTATTT
* * *
5544639 AGTAATTCTACTCTACAAGGGCATTTC
1 AGTAATACTAC-CTACAGGGGCAATTC
*
5544666 AGTAATTCTACCATACAGGGGCAATTC
1 AGTAATACTACC-TACAGGGGCAATTC
5544693 AGTAATACTAGCCTACAG
1 AGTAATACTA-CCTACAG
5544711 ATATGAGATT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
26 1 0.03
27 37 0.93
28 2 0.05
ACGTcount: A:0.33, C:0.22, G:0.17, T:0.28
Consensus pattern (26 bp):
AGTAATACTACCTACAGGGGCAATTC
Found at i:5545921 original size:50 final size:50
Alignment explanation
Indices: 5545862--5546003 Score: 275
Period size: 50 Copynumber: 2.8 Consensus size: 50
5545852 TAATCAGCAG
*
5545862 CAAAGTGATTAATGCAGCTATTCAAGTTGGGATTGGTTACATGGCTGTTA
1 CAAAGTGATTAATACAGCTATTCAAGTTGGGATTGGTTACATGGCTGTTA
5545912 CAAAGTGATTAATACAGCTATTCAAGTTGGGATTGGTTACATGGCTGTTA
1 CAAAGTGATTAATACAGCTATTCAAGTTGGGATTGGTTACATGGCTGTTA
5545962 CAAAGTGATTAATACAGCTATTCAAGTTGGGATTGGTTACAT
1 CAAAGTGATTAATACAGCTATTCAAGTTGGGATTGGTTACAT
5546004 ACAAAGCCTT
Statistics
Matches: 91, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
50 91 1.00
ACGTcount: A:0.30, C:0.12, G:0.24, T:0.34
Consensus pattern (50 bp):
CAAAGTGATTAATACAGCTATTCAAGTTGGGATTGGTTACATGGCTGTTA
Found at i:5553584 original size:20 final size:20
Alignment explanation
Indices: 5553559--5553599 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
5553549 TTCCTCAACA
*
5553559 TAATTCACAAGTGGCTTACT
1 TAATTCACAAGTAGCTTACT
*
5553579 TAATTCACTAGTAGCTTACT
1 TAATTCACAAGTAGCTTACT
5553599 T
1 T
5553600 TGAGCATCAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.29, C:0.20, G:0.12, T:0.39
Consensus pattern (20 bp):
TAATTCACAAGTAGCTTACT
Found at i:5571498 original size:23 final size:23
Alignment explanation
Indices: 5571453--5571498 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
5571443 ACAATTTAGG
* **
5571453 TGTAGGGGACACACGGCTGGATC
1 TGTAGGGAACACACGGCAAGATC
5571476 TGTAGGGAACACACGGCAAGATC
1 TGTAGGGAACACACGGCAAGATC
5571499 ACACGCCCAT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.28, C:0.22, G:0.35, T:0.15
Consensus pattern (23 bp):
TGTAGGGAACACACGGCAAGATC
Found at i:5571529 original size:28 final size:28
Alignment explanation
Indices: 5571484--5571539 Score: 78
Period size: 28 Copynumber: 2.0 Consensus size: 28
5571474 TCTGTAGGGA
5571484 ACACACGGCAAGATCACACGCCCATGTG
1 ACACACGGCAAGATCACACGCCCATGTG
* *
5571512 ACACACGGCCTAGA-CACACGCCCGTGTG
1 ACACACGG-CAAGATCACACGCCCATGTG
5571540 TCTACCCATG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
28 21 0.84
29 4 0.16
ACGTcount: A:0.29, C:0.38, G:0.23, T:0.11
Consensus pattern (28 bp):
ACACACGGCAAGATCACACGCCCATGTG
Found at i:5573240 original size:59 final size:59
Alignment explanation
Indices: 5573148--5573268 Score: 233
Period size: 59 Copynumber: 2.1 Consensus size: 59
5573138 CACTGTACCG
*
5573148 AATCTCTATTGGTCATTTCTGTAGCACCATACTCAATAATATTCACATTTCATTTCAAT
1 AATCTCTATTGGTCATTTCCGTAGCACCATACTCAATAATATTCACATTTCATTTCAAT
5573207 AATCTCTATTGGTCATTTCCGTAGCACCATACTCAATAATATTCACATTTCATTTCAAT
1 AATCTCTATTGGTCATTTCCGTAGCACCATACTCAATAATATTCACATTTCATTTCAAT
5573266 AAT
1 AAT
5573269 ATAGCAGTTA
Statistics
Matches: 61, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 61 1.00
ACGTcount: A:0.31, C:0.22, G:0.07, T:0.40
Consensus pattern (59 bp):
AATCTCTATTGGTCATTTCCGTAGCACCATACTCAATAATATTCACATTTCATTTCAAT
Found at i:5581022 original size:39 final size:39
Alignment explanation
Indices: 5580950--5581026 Score: 111
Period size: 39 Copynumber: 2.0 Consensus size: 39
5580940 AATTATTTTC
* * *
5580950 ACTTTAGATTTGTTGTCCTGAAATCACTCTTCCGATTTG
1 ACTTTAGATTTGTTGTCCCGAAACCACTATTCCGATTTG
5580989 ACTTTAGATTT-TTGGTCCCGAAACCACTATTCCGATTT
1 ACTTTAGATTTGTT-GTCCCGAAACCACTATTCCGATTT
5581027 AACTAAAAAT
Statistics
Matches: 34, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
38 2 0.06
39 32 0.94
ACGTcount: A:0.22, C:0.22, G:0.14, T:0.42
Consensus pattern (39 bp):
ACTTTAGATTTGTTGTCCCGAAACCACTATTCCGATTTG
Found at i:5581757 original size:27 final size:27
Alignment explanation
Indices: 5581716--5581769 Score: 99
Period size: 27 Copynumber: 2.0 Consensus size: 27
5581706 AATTAGAAGG
5581716 TATTTAAATTAAATTTGATAGTTCATA
1 TATTTAAATTAAATTTGATAGTTCATA
*
5581743 TATTTAAATTCAATTTGATAGTTCATA
1 TATTTAAATTAAATTTGATAGTTCATA
5581770 ACCAAATTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.39, C:0.06, G:0.07, T:0.48
Consensus pattern (27 bp):
TATTTAAATTAAATTTGATAGTTCATA
Done.