Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr04 ID=Chr04-JGI_221_v2.0
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: 62178258
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 912357 characters in sequence are not A, C, G, or T
File 63 of 198
Found at i:19427847 original size:62 final size:61
Alignment explanation
Indices: 19427770--19427917 Score: 171
Period size: 57 Copynumber: 2.5 Consensus size: 61
19427760 AATTGACGGT
19427770 AAAAACGATCTAGCCCGGACGGGTGATCCTATCCTGATATAGCCCTCCCAAAGAATATGTGTG
1 AAAAA-GATCTAGCCCGGACGGGTGATCCTATCCTGATATAGCCCTCCCAAAGAATATGTG-G
* * **
19427833 AAAAAGATCTAGCCCGGA-GGG-G-T--TATCTTGATATAGCCCTTCTGAAGAATATGTGG
1 AAAAAGATCTAGCCCGGACGGGTGATCCTATCCTGATATAGCCCTCCCAAAGAATATGTGG
* * *
19427889 AAAATGGATTTAGCCCGGACGGGTAATCC
1 AAAA-AGATCTAGCCCGGACGGGTGATCC
19427918 GAATTAGGGT
Statistics
Matches: 72, Mismatches: 7, Indels: 13
0.78 0.08 0.14
Matches are distributed among these distances:
56 5 0.07
57 40 0.56
58 3 0.04
59 1 0.01
60 2 0.03
61 3 0.04
62 13 0.18
63 5 0.07
ACGTcount: A:0.30, C:0.21, G:0.25, T:0.24
Consensus pattern (61 bp):
AAAAAGATCTAGCCCGGACGGGTGATCCTATCCTGATATAGCCCTCCCAAAGAATATGTGG
Found at i:19431956 original size:37 final size:39
Alignment explanation
Indices: 19431859--19431957 Score: 114
Period size: 38 Copynumber: 2.6 Consensus size: 39
19431849 CCAACACACC
* * *
19431859 AATTTGGCACCTAGTGCCTCAT-TGGATAAATCCGAAGT
1 AATTTTGCACCTAGTGCCTCATCAGGATAAATCCAAAGT
* * *
19431897 AAGTTTGACACCTAGTGTCTCATCAGTAT-AA-CCAAAGT
1 AATTTTG-CACCTAGTGCCTCATCAGGATAAATCCAAAGT
19431935 AATTTTGCACCTAGTGCCTCATC
1 AATTTTGCACCTAGTGCCTCATC
19431958 GACTGATAAG
Statistics
Matches: 51, Mismatches: 8, Indels: 5
0.80 0.12 0.08
Matches are distributed among these distances:
37 15 0.29
38 17 0.33
39 16 0.31
40 3 0.06
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.30
Consensus pattern (39 bp):
AATTTTGCACCTAGTGCCTCATCAGGATAAATCCAAAGT
Found at i:19438595 original size:70 final size:70
Alignment explanation
Indices: 19438482--19438620 Score: 244
Period size: 70 Copynumber: 2.0 Consensus size: 70
19438472 GGTAGTGTTG
*
19438482 TGACACCACATCCCCATGTCGTGACATTGCACTTCGAACCTAAAAACTTCTCAAAT-TCCATCCA
1 TGACACCACATCCCCATGTCGTGACAATGCACTTCGAACCTAAAAACTTCTCAAATGT-CATCCA
19438546 ATGTCA
65 ATGTCA
*
19438552 TGACACCACATCCCCATGTCGTGACAATGCACTTCGAACCTAAAAACTTCTCAAATGTCATCCAG
1 TGACACCACATCCCCATGTCGTGACAATGCACTTCGAACCTAAAAACTTCTCAAATGTCATCCAA
19438617 TGTC
66 TGTC
19438621 GCGAAATTGA
Statistics
Matches: 66, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
70 65 0.98
71 1 0.02
ACGTcount: A:0.31, C:0.32, G:0.12, T:0.25
Consensus pattern (70 bp):
TGACACCACATCCCCATGTCGTGACAATGCACTTCGAACCTAAAAACTTCTCAAATGTCATCCAA
TGTCA
Found at i:19457400 original size:36 final size:36
Alignment explanation
Indices: 19457360--19457428 Score: 120
Period size: 36 Copynumber: 1.9 Consensus size: 36
19457350 AGTTGCTACT
* *
19457360 AGGGTGCCGCTTGGGCAGGAGGAAACAATAACCTCG
1 AGGGTGCCGCTTAGGCAGGAGGAAACAACAACCTCG
19457396 AGGGTGCCGCTTAGGCAGGAGGAAACAACAACC
1 AGGGTGCCGCTTAGGCAGGAGGAAACAACAACC
19457429 CTTGGCCGGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
36 31 1.00
ACGTcount: A:0.30, C:0.23, G:0.35, T:0.12
Consensus pattern (36 bp):
AGGGTGCCGCTTAGGCAGGAGGAAACAACAACCTCG
Found at i:19470569 original size:16 final size:16
Alignment explanation
Indices: 19470548--19470589 Score: 52
Period size: 15 Copynumber: 2.7 Consensus size: 16
19470538 TTATTAAATT
*
19470548 ATATATTTTAATTATA
1 ATATATTTTAATAATA
19470564 ATATA-TTTAATAATA
1 ATATATTTTAATAATA
19470579 AT-TATGTTTAA
1 ATATAT-TTTAA
19470590 ATATGATTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
14 2 0.09
15 11 0.48
16 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.52
Consensus pattern (16 bp):
ATATATTTTAATAATA
Found at i:19470574 original size:15 final size:15
Alignment explanation
Indices: 19470539--19470580 Score: 52
Period size: 15 Copynumber: 2.9 Consensus size: 15
19470529 TTAAGAATTT
*
19470539 TATTAAATTAT-ATA
1 TATTTAATTATAATA
19470553 T-TTTAATTATAATA
1 TATTTAATTATAATA
*
19470567 TATTTAATAATAAT
1 TATTTAATTATAAT
19470581 TATGTTTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
13 8 0.33
14 5 0.21
15 11 0.46
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (15 bp):
TATTTAATTATAATA
Found at i:19470583 original size:120 final size:120
Alignment explanation
Indices: 19470370--19470586 Score: 389
Period size: 120 Copynumber: 1.8 Consensus size: 120
19470360 NNNNNNNNNN
* *
19470370 TATTATGATTTGAGTAAATTCATATAAGATTATTAATTATTAAGAATTTTATTAAATTATAGATT
1 TATTATGATTTGAGTAAATTCATATAAGAATATTAACTATTAAGAATTTTATTAAATTATAGATT
19470435 TTAATTATAACATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCATA
66 TTAATTATAACATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCATA
* *
19470490 TATTATGATTTGAGTAAATTCATATAAGAATATTGACTATTAAGAATTTTATTAAATTATATATT
1 TATTATGATTTGAGTAAATTCATATAAGAATATTAACTATTAAGAATTTTATTAAATTATAGATT
*
19470555 TTAATTATAATATATTTAATAATAATTATGTT
66 TTAATTATAACATATTTAATAATAATTATGTT
19470587 TAAATATGAT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
120 92 1.00
ACGTcount: A:0.42, C:0.02, G:0.07, T:0.49
Consensus pattern (120 bp):
TATTATGATTTGAGTAAATTCATATAAGAATATTAACTATTAAGAATTTTATTAAATTATAGATT
TTAATTATAACATATTTAATAATAATTATGTTAATTTATATTTTATAGTATCATA
Found at i:19470821 original size:16 final size:16
Alignment explanation
Indices: 19470800--19470830 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
19470790 TTGATTTGCT
19470800 ATTACGCATCTATTCC
1 ATTACGCATCTATTCC
*
19470816 ATTACGCCTCTATTC
1 ATTACGCATCTATTC
19470831 TAATACAGCG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.23, C:0.32, G:0.06, T:0.39
Consensus pattern (16 bp):
ATTACGCATCTATTCC
Found at i:19471996 original size:41 final size:41
Alignment explanation
Indices: 19471911--19472031 Score: 174
Period size: 41 Copynumber: 3.0 Consensus size: 41
19471901 TGCTATTCAG
* * *
19471911 GGGTACTGAAGAACAAACAGGGG-ACGTATGTGTAATTCAG
1 GGGTACTGAAGTACAAACAGGGGCACGTATGTGTAATTTAA
19471951 GGGTA-TCGAAGTACAAACAGGGGCACGTATGTGTAATTTAA
1 GGGTACT-GAAGTACAAACAGGGGCACGTATGTGTAATTTAA
* *
19471992 GGGTACTGAAGTACAAATAAGGGCACGTATGTGTAATTTA
1 GGGTACTGAAGTACAAACAGGGGCACGTATGTGTAATTTA
19472032 GGGAATAATT
Statistics
Matches: 73, Mismatches: 5, Indels: 5
0.88 0.06 0.06
Matches are distributed among these distances:
39 1 0.01
40 20 0.27
41 51 0.70
42 1 0.01
ACGTcount: A:0.35, C:0.12, G:0.30, T:0.24
Consensus pattern (41 bp):
GGGTACTGAAGTACAAACAGGGGCACGTATGTGTAATTTAA
Found at i:19474371 original size:26 final size:26
Alignment explanation
Indices: 19474342--19474391 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
19474332 TCTCATCCCT
19474342 ATTTTACCCAAAATAAAATTTTGATG
1 ATTTTACCCAAAATAAAATTTTGATG
** *
19474368 ATTTTACCCCTAGTAAAATTTTGA
1 ATTTTACCCAAAATAAAATTTTGA
19474392 CAATTTTAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.40
Consensus pattern (26 bp):
ATTTTACCCAAAATAAAATTTTGATG
Found at i:19474410 original size:26 final size:25
Alignment explanation
Indices: 19474354--19474414 Score: 61
Period size: 26 Copynumber: 2.4 Consensus size: 25
19474344 TTTACCCAAA
** * *
19474354 ATAAAATTTTGATGATTTTACCCCT
1 ATAAAATTTTGACAATTTTAACCAT
19474379 AGTAAAATTTTGACAATTTTAACCAT
1 A-TAAAATTTTGACAATTTTAACCAT
19474405 GAT-AAATTTT
1 -ATAAAATTTT
19474415 CAGGAAAATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
25 8 0.27
26 21 0.70
27 1 0.03
ACGTcount: A:0.38, C:0.11, G:0.08, T:0.43
Consensus pattern (25 bp):
ATAAAATTTTGACAATTTTAACCAT
Found at i:19481251 original size:43 final size:43
Alignment explanation
Indices: 19481188--19481349 Score: 216
Period size: 43 Copynumber: 3.8 Consensus size: 43
19481178 GTGGAAAAAT
*
19481188 GCCGCTAAAGAACATGACCTTTAGAGGTGCTTTCCCCACAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGGTGCTTTCCCCACAAAC
* * * *
19481231 GTCGCTAAAGAACAGGACCTTTAGCGGCGCGTTCCCCACAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGGTGCTTTCCCCACAAAC
* *
19481274 GCCACTAAAGAACATGACATTTAGCGGTGCTTTCCCCACAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGGTGCTTTCCCCACAAAC
** ** *
19481317 GCCGCTAAATTACATGTTCTTTAGCAGTGCTTT
1 GCCGCTAAAGAACATGACCTTTAGCGGTGCTTT
19481350 TCCTAAAAAT
Statistics
Matches: 101, Mismatches: 18, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
43 101 1.00
ACGTcount: A:0.28, C:0.29, G:0.19, T:0.23
Consensus pattern (43 bp):
GCCGCTAAAGAACATGACCTTTAGCGGTGCTTTCCCCACAAAC
Found at i:19481369 original size:86 final size:86
Alignment explanation
Indices: 19481182--19481369 Score: 216
Period size: 86 Copynumber: 2.2 Consensus size: 86
19481172 ATTTATGTGG
* *
19481182 AAAAATGCC-GCTAAAGAACATGACCTTTAGAGGTGCTTTCCCCACAAACGTCGCTAAAGAACAG
1 AAAAATGCCAG-TAAAGAACATGACATTTAGAGGTGCTTTCCCCACAAACGCCGCTAAAGAACAG
*
19481246 GACCTTTAGCGGCGCGTTCCCC
65 GACCTTTAGCAGCGCGTTCCCC
* * * * ** *
19481268 ACAAACGCCACTAAAGAACATGACATTTAGCGGTGCTTTCCCCACAAACGCCGCTAAATTACATG
1 AAAAATGCCAGTAAAGAACATGACATTTAGAGGTGCTTTCCCCACAAACGCCGCTAAAGAACAGG
** * * * *
19481333 TTCTTTAGCAGTGCTTTTCCT
66 ACCTTTAGCAGCGCGTTCCCC
19481354 AAAAATGCCAGTAAAG
1 AAAAATGCCAGTAAAG
19481370 GTCAACGGCA
Statistics
Matches: 82, Mismatches: 19, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
86 82 1.00
ACGTcount: A:0.32, C:0.27, G:0.18, T:0.23
Consensus pattern (86 bp):
AAAAATGCCAGTAAAGAACATGACATTTAGAGGTGCTTTCCCCACAAACGCCGCTAAAGAACAGG
ACCTTTAGCAGCGCGTTCCCC
Found at i:19487565 original size:14 final size:14
Alignment explanation
Indices: 19487546--19487572 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
19487536 TTAATGATTC
19487546 ACACGTCTGCATCT
1 ACACGTCTGCATCT
19487560 ACACGTCTGCATC
1 ACACGTCTGCATC
19487573 CATTTCCATA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.37, G:0.15, T:0.26
Consensus pattern (14 bp):
ACACGTCTGCATCT
Found at i:19489043 original size:27 final size:27
Alignment explanation
Indices: 19489013--19489083 Score: 97
Period size: 27 Copynumber: 2.6 Consensus size: 27
19489003 TAGTGAACTT
* *
19489013 CCCCGTGTTTATTATCCTGGCAAGCTA
1 CCCCGTGTTTACTATCCTGACAAGCTA
* **
19489040 CCCCGTGTTTACTACCCTGACGGGCTA
1 CCCCGTGTTTACTATCCTGACAAGCTA
19489067 CCCCGTGTTTACTATCC
1 CCCCGTGTTTACTATCC
19489084 CAGTGGACTC
Statistics
Matches: 38, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.15, C:0.35, G:0.18, T:0.31
Consensus pattern (27 bp):
CCCCGTGTTTACTATCCTGACAAGCTA
Found at i:19490952 original size:38 final size:37
Alignment explanation
Indices: 19490908--19491006 Score: 126
Period size: 38 Copynumber: 2.6 Consensus size: 37
19490898 GAAATCCTTG
** *
19490908 TTATAATTATTGTAATTATAATTTAGGATTGAATATTA
1 TTATAATTATTGTAATTATAATTTAGG-TCAAACATTA
* *
19490946 TTATAATTATTGTAATTGTAATTTTTGGTCAAACATTA
1 TTATAATTATTGTAATTATAA-TTTAGGTCAAACATTA
*
19490984 TTATAATTATGGTAATTATAATT
1 TTATAATTATTGTAATTATAATT
19491007 ATTATATTTA
Statistics
Matches: 53, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
37 2 0.04
38 46 0.87
39 5 0.09
ACGTcount: A:0.37, C:0.02, G:0.10, T:0.51
Consensus pattern (37 bp):
TTATAATTATTGTAATTATAATTTAGGTCAAACATTA
Found at i:19492273 original size:15 final size:15
Alignment explanation
Indices: 19492255--19492303 Score: 50
Period size: 15 Copynumber: 3.3 Consensus size: 15
19492245 ACTTATTACC
19492255 TTTCGCTAATTCCAT
1 TTTCGCTAATTCCAT
*
19492270 TTTCGGC-ACTTACC-T
1 TTTC-GCTAATT-CCAT
19492285 TTT-GCTAATTCCAT
1 TTTCGCTAATTCCAT
19492299 TTTCG
1 TTTCG
19492304 GCACTTAGTA
Statistics
Matches: 27, Mismatches: 2, Indels: 10
0.69 0.05 0.26
Matches are distributed among these distances:
13 4 0.15
14 7 0.26
15 12 0.44
16 4 0.15
ACGTcount: A:0.16, C:0.27, G:0.10, T:0.47
Consensus pattern (15 bp):
TTTCGCTAATTCCAT
Found at i:19492291 original size:29 final size:29
Alignment explanation
Indices: 19492250--19492310 Score: 113
Period size: 29 Copynumber: 2.1 Consensus size: 29
19492240 TTATTACTTA
19492250 TTACCTTTCGCTAATTCCATTTTCGGCAC
1 TTACCTTTCGCTAATTCCATTTTCGGCAC
*
19492279 TTACCTTTTGCTAATTCCATTTTCGGCAC
1 TTACCTTTCGCTAATTCCATTTTCGGCAC
19492308 TTA
1 TTA
19492311 GTACTTGAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.18, C:0.28, G:0.10, T:0.44
Consensus pattern (29 bp):
TTACCTTTCGCTAATTCCATTTTCGGCAC
Found at i:19492323 original size:29 final size:29
Alignment explanation
Indices: 19492262--19492323 Score: 72
Period size: 29 Copynumber: 2.1 Consensus size: 29
19492252 ACCTTTCGCT
* **
19492262 AATTCCATTTTCGGCACTTACCTTTTGCT
1 AATTCCATTTTCGGCACTTACCTCTTGAA
*
19492291 AATTCCATTTTCGGCACTTA-GTACTTGAA
1 AATTCCATTTTCGGCACTTACCT-CTTGAA
19492320 AATT
1 AATT
19492324 TTCATAATCC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
28 1 0.04
29 27 0.96
ACGTcount: A:0.24, C:0.23, G:0.11, T:0.42
Consensus pattern (29 bp):
AATTCCATTTTCGGCACTTACCTCTTGAA
Found at i:19496416 original size:42 final size:42
Alignment explanation
Indices: 19496369--19496460 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
19496359 ATATTCTAGG
** *
19496369 ATTATTTTATTTTATCTTTTAGTAGTTGATTAGAATAAGGTA
1 ATTATTTTACCTTATCTTTTAGTAGTTGATTAGAATAAGGGA
* *
19496411 ATTATTTTCCCTTATCTTTTAGTAGTTTATTAGAATAAGGGA
1 ATTATTTTACCTTATCTTTTAGTAGTTGATTAGAATAAGGGA
19496453 ATTATTTT
1 ATTATTTT
19496461 TCCAATTAGG
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.29, C:0.05, G:0.13, T:0.52
Consensus pattern (42 bp):
ATTATTTTACCTTATCTTTTAGTAGTTGATTAGAATAAGGGA
Found at i:19502900 original size:24 final size:24
Alignment explanation
Indices: 19502879--19502926 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
19502869 AAAATTTAGT
19502879 ATTTATTAGTATAATATATTTAAC
1 ATTTATTAGTATAATATATTTAAC
*
19502903 ATTTATTAGTATAATTTATTTAAC
1 ATTTATTAGTATAATATATTTAAC
19502927 CTACGAATTT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.52
Consensus pattern (24 bp):
ATTTATTAGTATAATATATTTAAC
Found at i:19505379 original size:12 final size:12
Alignment explanation
Indices: 19505362--19505387 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
19505352 CACCCTCTTC
19505362 CTCTCCTCTTTT
1 CTCTCCTCTTTT
19505374 CTCTCCTCTTTT
1 CTCTCCTCTTTT
19505386 CT
1 CT
19505388 TTCTTTCTCC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.00, C:0.42, G:0.00, T:0.58
Consensus pattern (12 bp):
CTCTCCTCTTTT
Found at i:19509572 original size:23 final size:23
Alignment explanation
Indices: 19509528--19509573 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
19509518 TAAGTTTATT
* **
19509528 TTCTTGTCACCTAACTGTGAAAA
1 TTCTAGTCACCTAACTAAGAAAA
19509551 TTCTAGTCACCTAACTAAGAAAA
1 TTCTAGTCACCTAACTAAGAAAA
19509574 GTTAAAAAAT
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:0.37, C:0.22, G:0.11, T:0.30
Consensus pattern (23 bp):
TTCTAGTCACCTAACTAAGAAAA
Found at i:19509738 original size:216 final size:216
Alignment explanation
Indices: 19509364--19509759 Score: 792
Period size: 216 Copynumber: 1.8 Consensus size: 216
19509354 CATTCCGTTG
19509364 AAATTATAACATAAGAAATGACCCAATGCTACTTCTTAGCGAAAATTCTAAAGCCCTGATGGGTT
1 AAATTATAACATAAGAAATGACCCAATGCTACTTCTTAGCGAAAATTCTAAAGCCCTGATGGGTT
19509429 TTATAAGTATCTCTAACTTTAAAATAATTACATAAATTATCTTATACTAATTATTGGTTAAACTA
66 TTATAAGTATCTCTAACTTTAAAATAATTACATAAATTATCTTATACTAATTATTGGTTAAACTA
19509494 CACTAGTAGTCACCCAATTATTAGTAAGTTTATTTTCTTGTCACCTAACTGTGAAAATTCTAGTC
131 CACTAGTAGTCACCCAATTATTAGTAAGTTTATTTTCTTGTCACCTAACTGTGAAAATTCTAGTC
19509559 ACCTAACTAAGAAAAGTTAAA
196 ACCTAACTAAGAAAAGTTAAA
19509580 AAATTATAACATAAGAAATGACCCAATGCTACTTCTTAGCGAAAATTCTAAAGCCCTGATGGGTT
1 AAATTATAACATAAGAAATGACCCAATGCTACTTCTTAGCGAAAATTCTAAAGCCCTGATGGGTT
19509645 TTATAAGTATCTCTAACTTTAAAATAATTACATAAATTATCTTATACTAATTATTGGTTAAACTA
66 TTATAAGTATCTCTAACTTTAAAATAATTACATAAATTATCTTATACTAATTATTGGTTAAACTA
19509710 CACTAGTAGTCACCCAATTATTAGTAAGTTTATTTTCTTGTCACCTAACT
131 CACTAGTAGTCACCCAATTATTAGTAAGTTTATTTTCTTGTCACCTAACT
19509760 AAGAAAAGTT
Statistics
Matches: 180, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
216 180 1.00
ACGTcount: A:0.38, C:0.16, G:0.10, T:0.36
Consensus pattern (216 bp):
AAATTATAACATAAGAAATGACCCAATGCTACTTCTTAGCGAAAATTCTAAAGCCCTGATGGGTT
TTATAAGTATCTCTAACTTTAAAATAATTACATAAATTATCTTATACTAATTATTGGTTAAACTA
CACTAGTAGTCACCCAATTATTAGTAAGTTTATTTTCTTGTCACCTAACTGTGAAAATTCTAGTC
ACCTAACTAAGAAAAGTTAAA
Found at i:19513221 original size:59 final size:58
Alignment explanation
Indices: 19513156--19513284 Score: 149
Period size: 59 Copynumber: 2.2 Consensus size: 58
19513146 ACCACTTTAA
* * *
19513156 TATTAAATTAATATAATATTTA-T-TAAGATAAATATTAGATTAAATTTAATATTAAATCT
1 TATTAAAATAATAGAATATTTACTATAAGATAAACATT---TTAAATTTAATATTAAATCT
*
19513215 TATTAAAATAATAGAATATTTATCTATAAGATAAACATTTTTAATTTAATATTAAA-C-
1 TATTAAAATAATAGAATATTTA-CTATAAGATAAACATTTTAAATTTAATATTAAATCT
*
19513272 TAATAAAATAATA
1 TATTAAAATAATA
19513285 TTATTTTTAG
Statistics
Matches: 62, Mismatches: 5, Indels: 8
0.83 0.07 0.11
Matches are distributed among these distances:
57 12 0.19
58 1 0.02
59 36 0.58
61 1 0.02
62 12 0.19
ACGTcount: A:0.51, C:0.03, G:0.03, T:0.43
Consensus pattern (58 bp):
TATTAAAATAATAGAATATTTACTATAAGATAAACATTTTAAATTTAATATTAAATCT
Found at i:19513791 original size:22 final size:20
Alignment explanation
Indices: 19513751--19513791 Score: 55
Period size: 20 Copynumber: 1.9 Consensus size: 20
19513741 CAAAAATAAT
*
19513751 TTTTCCAAAAATAATTTAAA
1 TTTTCCAAAAAAAATTTAAA
19513771 TTTTCCAAATTAAAAATTTAA
1 TTTTCCAAA--AAAAATTTAA
19513792 GAAAATTCTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 9 0.50
22 9 0.50
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (20 bp):
TTTTCCAAAAAAAATTTAAA
Found at i:19514924 original size:15 final size:15
Alignment explanation
Indices: 19514900--19514931 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
19514890 TATGCATGCA
*
19514900 AAATATAAAAGACAT
1 AAATACAAAAGACAT
19514915 AAATACAAAAGACAT
1 AAATACAAAAGACAT
19514930 AA
1 AA
19514932 TAGTGAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATACAAAAGACAT
Found at i:19519802 original size:27 final size:27
Alignment explanation
Indices: 19519755--19519809 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
19519745 ACACTTGAAT
* *
19519755 TCATTTCATGTTTCACATCTCATTTCA
1 TCATTTCATATTTCACATCTCATGTCA
**
19519782 TCATTTCATATTTCATTTCTCATGTCA
1 TCATTTCATATTTCACATCTCATGTCA
19519809 T
1 T
19519810 ATTCATTTCT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.22, C:0.24, G:0.04, T:0.51
Consensus pattern (27 bp):
TCATTTCATATTTCACATCTCATGTCA
Found at i:19519809 original size:19 final size:18
Alignment explanation
Indices: 19519774--19519822 Score: 71
Period size: 18 Copynumber: 2.6 Consensus size: 18
19519764 GTTTCACATC
*
19519774 TCATTTCATCATTTCATATT
1 TCATTTC-TCATGTCATA-T
19519794 TCATTTCTCATGTCATAT
1 TCATTTCTCATGTCATAT
19519812 TCATTTCTCAT
1 TCATTTCTCAT
19519823 CTTTTCCATT
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
18 12 0.43
19 9 0.32
20 7 0.25
ACGTcount: A:0.22, C:0.22, G:0.02, T:0.53
Consensus pattern (18 bp):
TCATTTCTCATGTCATAT
Found at i:19528318 original size:11 final size:12
Alignment explanation
Indices: 19528302--19528348 Score: 50
Period size: 11 Copynumber: 4.3 Consensus size: 12
19528292 TTTAATCATT
19528302 TTAATATTAA-A
1 TTAATATTAAGA
19528313 TTAATA-TAAGA
1 TTAATATTAAGA
19528324 TT--TATTAAGA
1 TTAATATTAAGA
*
19528334 TAAATATT-AGA
1 TTAATATTAAGA
19528345 TTAA
1 TTAA
19528349 ATTTAATATT
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
9 2 0.07
10 9 0.30
11 15 0.50
12 4 0.13
ACGTcount: A:0.51, C:0.00, G:0.06, T:0.43
Consensus pattern (12 bp):
TTAATATTAAGA
Found at i:19528345 original size:21 final size:20
Alignment explanation
Indices: 19528306--19528346 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 20
19528296 ATCATTTTAA
*
19528306 TATTAAATTAATATAAGATT
1 TATTAAATAAATATAAGATT
*
19528326 TATTAAGATAAATATTAGATT
1 TATTAA-ATAAATATAAGATT
19528347 AAATTTAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.49, C:0.00, G:0.07, T:0.44
Consensus pattern (20 bp):
TATTAAATAAATATAAGATT
Found at i:19528448 original size:20 final size:18
Alignment explanation
Indices: 19528401--19528507 Score: 52
Period size: 17 Copynumber: 6.2 Consensus size: 18
19528391 CAAGATAAAC
*
19528401 ATTAAATTAA-AATTATT
1 ATTAAATTAATAATTAAT
19528418 ATTAAGA-TAATAATTTTAAT
1 ATTAA-ATTAATAA--TTAAT
19528438 ATTAAATTAATAA--AAT
1 ATTAAATTAATAATTAAT
* *
19528454 ACT--ATTAA-GA-TAAGT
1 ATTAAATTAATAATTAA-T
*
19528469 ATTAAATTAA-ATTTAAT
1 ATTAAATTAATAATTAAT
* * *
19528486 ATTAAACTATTAAATAAT
1 ATTAAATTAATAATTAAT
19528504 ATTA
1 ATTA
19528508 TTTTCGAAAT
Statistics
Matches: 69, Mismatches: 10, Indels: 21
0.69 0.10 0.21
Matches are distributed among these distances:
13 1 0.01
14 7 0.10
15 3 0.04
16 5 0.07
17 22 0.32
18 15 0.22
19 1 0.01
20 15 0.22
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (18 bp):
ATTAAATTAATAATTAAT
Found at i:19528495 original size:37 final size:35
Alignment explanation
Indices: 19528426--19528507 Score: 96
Period size: 37 Copynumber: 2.3 Consensus size: 35
19528416 TTATTAAGAT
*
19528426 AATAATTTTAATATTAAATTAATAAAATACTATTA
1 AATAATATTAATATTAAATTAATAAAATACTATTA
*
19528461 AGATAAGTATTAA-ATTAAATTTAATATTAA-ACTATTA
1 A-ATAA-TATTAATATTAAA-TTAATA-AAATACTATTA
19528498 AATAATATTA
1 AATAATATTA
19528508 TTTTCGAAAT
Statistics
Matches: 41, Mismatches: 2, Indels: 8
0.80 0.04 0.16
Matches are distributed among these distances:
35 6 0.15
36 14 0.34
37 19 0.46
38 2 0.05
ACGTcount: A:0.54, C:0.02, G:0.02, T:0.41
Consensus pattern (35 bp):
AATAATATTAATATTAAATTAATAAAATACTATTA
Found at i:19537234 original size:50 final size:50
Alignment explanation
Indices: 19537159--19537349 Score: 184
Period size: 50 Copynumber: 3.7 Consensus size: 50
19537149 TCCTGTACTA
* * * * **
19537159 CCAATGCCATATTCTAGATATGGTCTTACATGGGAGTTCTCATATCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG
* * ** *
19537209 CCCATGCCAAGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG
* * * *
19537259 CCAACGCGATGTCCCAGACATGGTCTTACGTGGGACCTCTCATAATCTCAATGATG
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GGTG
*
19537315 CCAATTCCATGTCCCAGACATGGTCTTACATGGGA
1 CCAATGCCATGTCCCAGACATGGTCTTACATGGGA
19537350 TCTAATCCTC
Statistics
Matches: 113, Mismatches: 22, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
50 77 0.68
53 2 0.02
56 34 0.30
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.27
Consensus pattern (50 bp):
CCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG
Found at i:19550008 original size:51 final size:51
Alignment explanation
Indices: 19549808--19550002 Score: 225
Period size: 51 Copynumber: 3.8 Consensus size: 51
19549798 TGAAAGTGAA
* * * *
19549808 AGTGATGGTCACGTGTGTGGTATTATGTGCAGGCTACTACGTGTACCAGA-
1 AGTGATGGTCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAT
* * * *
19549858 A-TGATAGGTCGCATGTGTAGTACTATGTGTAGGCTACTATGCGTACCGGAT
1 AGTGAT-GGTCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAT
* ** * *
19549909 AGCT-TTCATCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGAT
1 AG-TGATGGTCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAT
*
19549960 AGTGATGGTCACGTGTGTAGTACCATGTGCAGGCTACTATGTG
1 AGTGATGGTCACGTGTGTAGTACTATGTGCAGGCTACTATGTG
19550003 AATCGGTATC
Statistics
Matches: 118, Mismatches: 22, Indels: 9
0.79 0.15 0.06
Matches are distributed among these distances:
49 4 0.03
50 38 0.32
51 74 0.63
52 1 0.01
53 1 0.01
ACGTcount: A:0.22, C:0.17, G:0.30, T:0.31
Consensus pattern (51 bp):
AGTGATGGTCACGTGTGTAGTACTATGTGCAGGCTACTATGTGTACCGGAT
Found at i:19550245 original size:16 final size:16
Alignment explanation
Indices: 19550224--19550255 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
19550214 TGATTGAAAG
*
19550224 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
19550240 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
19550256 GCAACAAAAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:19556419 original size:19 final size:19
Alignment explanation
Indices: 19556395--19556432 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
19556385 TTGATAAGTA
19556395 TTTATTGTCATTGCATTTT
1 TTTATTGTCATTGCATTTT
*
19556414 TTTATTGTCATTTCATTTT
1 TTTATTGTCATTGCATTTT
19556433 CATATTAGTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.16, C:0.11, G:0.08, T:0.66
Consensus pattern (19 bp):
TTTATTGTCATTGCATTTT
Found at i:19556438 original size:19 final size:19
Alignment explanation
Indices: 19556397--19556438 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
19556387 GATAAGTATT
**
19556397 TATTGTCATTGCATTTTTT
1 TATTGTCATTGCATTTTCA
*
19556416 TATTGTCATTTCATTTTCA
1 TATTGTCATTGCATTTTCA
19556435 TATT
1 TATT
19556439 AGTGCGTTGG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.19, C:0.12, G:0.07, T:0.62
Consensus pattern (19 bp):
TATTGTCATTGCATTTTCA
Found at i:19561101 original size:15 final size:15
Alignment explanation
Indices: 19561062--19561093 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
19561052 TATGCATGCA
19561062 AAATATAAAAGACAT
1 AAATATAAAAGACAT
*
19561077 AAATACAAAAGACAT
1 AAATATAAAAGACAT
19561092 AA
1 AA
19561094 TAGTAAAATG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.69, C:0.09, G:0.06, T:0.16
Consensus pattern (15 bp):
AAATATAAAAGACAT
Found at i:19574741 original size:29 final size:29
Alignment explanation
Indices: 19574704--19574905 Score: 235
Period size: 29 Copynumber: 6.9 Consensus size: 29
19574694 ACGCCTATCA
* *
19574704 AATAAGAAAAGAGATGGTTTCGACCATCG
1 AATATGAAAAGGGATGGTTTCGACCATCG
** * *
19574733 AATATGAAAAGGGATGGTGACAATCATCG
1 AATATGAAAAGGGATGGTTTCGACCATCG
**
19574762 AATATGAAAAGGGATGGTGACGACCATCG
1 AATATGAAAAGGGATGGTTTCGACCATCG
*
19574791 AATATGAAAAGGGATGGTTTCAACCATCG
1 AATATGAAAAGGGATGGTTTCGACCATCG
*
19574820 AATATGAAATGGGATGGTTTCGACCATCG
1 AATATGAAAAGGGATGGTTTCGACCATCG
* ** *
19574849 ATTTATGAAAAGGGATGGTAACTACCATC-
1 A-ATATGAAAAGGGATGGTTTCGACCATCG
*
19574878 AATTAATGAAAGGGGATGGTTTCGACCA
1 AA-T-ATGAAAAGGGATGGTTTCGACCA
19574906 ACATTTATGA
Statistics
Matches: 147, Mismatches: 23, Indels: 5
0.84 0.13 0.03
Matches are distributed among these distances:
29 106 0.72
30 41 0.28
ACGTcount: A:0.38, C:0.13, G:0.26, T:0.23
Consensus pattern (29 bp):
AATATGAAAAGGGATGGTTTCGACCATCG
Found at i:19574912 original size:59 final size:58
Alignment explanation
Indices: 19574704--19574967 Score: 262
Period size: 58 Copynumber: 4.5 Consensus size: 58
19574694 ACGCCTATCA
* * *
19574704 AATAAGAAAAGAGATGGTTTCGACCATCGAATATGAAAAGGGATGGTGACAATCATCG
1 AATATGAAAAGGGATGGTTTCGACCATCGAATATGAAAAGGGATGGTGACAACCATCG
** **
19574762 AATATGAAAAGGGATGGTGACGACCATCGAATATGAAAAGGGATGGTTTCAACCATCG
1 AATATGAAAAGGGATGGTTTCGACCATCGAATATGAAAAGGGATGGTGACAACCATCG
* * * *
19574820 AATATGAAATGGGATGGTTTCGACCATCGATTTATGAAAAGGGATGGTAACTACCATC-
1 AATATGAAAAGGGATGGTTTCGACCATCGA-ATATGAAAAGGGATGGTGACAACCATCG
* * * * * * **
19574878 AATTAATGAAAGGGGATGGTTTCGACCAAC-ATTTATGAGAATGGATGGTGACGACCATTT
1 AA-T-ATGAAAAGGGATGGTTTCGACCATCGA-ATATGAAAAGGGATGGTGACAACCATCG
* * **
19574938 ATTAAAGAAAAGGGACAGTTTCGACCATCG
1 AAT-ATGAAAAGGGATGGTTTCGACCATCG
19574968 TTTAGCACAC
Statistics
Matches: 174, Mismatches: 27, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
58 80 0.46
59 70 0.40
60 24 0.14
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.24
Consensus pattern (58 bp):
AATATGAAAAGGGATGGTTTCGACCATCGAATATGAAAAGGGATGGTGACAACCATCG
Found at i:19574915 original size:29 final size:30
Alignment explanation
Indices: 19574709--19574971 Score: 214
Period size: 29 Copynumber: 9.0 Consensus size: 30
19574699 TATCAAATAA
* *
19574709 GAAAAGAGATGGTTTCGACCATCGA-ATAT
1 GAAAAGGGATGGTTTCGACCATCGATTTAT
** * * *
19574738 GAAAAGGGATGGTGACAATCATCGA-ATAT
1 GAAAAGGGATGGTTTCGACCATCGATTTAT
** *
19574767 GAAAAGGGATGGTGACGACCATCGA-ATAT
1 GAAAAGGGATGGTTTCGACCATCGATTTAT
* *
19574796 GAAAAGGGATGGTTTCAACCATCGA-ATAT
1 GAAAAGGGATGGTTTCGACCATCGATTTAT
*
19574825 GAAATGGGATGGTTTCGACCATCGATTTAT
1 GAAAAGGGATGGTTTCGACCATCGATTTAT
** * * *
19574855 GAAAAGGGATGGTAACTACCATCAATTAAT
1 GAAAAGGGATGGTTTCGACCATCGATTTAT
* *
19574885 GAAAGGGGATGGTTTCGACCAAC-ATTTAT
1 GAAAAGGGATGGTTTCGACCATCGATTTAT
* * ** ** * *
19574914 GAGAATGGATGGTGACGACCATTTATTAAA
1 GAAAAGGGATGGTTTCGACCATCGATTTAT
**
19574944 GAAAAGGGACAGTTTCGACCATCG-TTTA
1 GAAAAGGGATGGTTTCGACCATCGATTTA
19574972 GCACACTTGT
Statistics
Matches: 189, Mismatches: 43, Indels: 4
0.80 0.18 0.02
Matches are distributed among these distances:
29 124 0.66
30 65 0.34
ACGTcount: A:0.36, C:0.13, G:0.26, T:0.25
Consensus pattern (30 bp):
GAAAAGGGATGGTTTCGACCATCGATTTAT
Found at i:19576741 original size:14 final size:15
Alignment explanation
Indices: 19576715--19576743 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
19576705 TATTGGTTGA
19576715 ATGGAATTTGGTCAT
1 ATGGAATTTGGTCAT
19576730 ATGGAA-TTGGTCAT
1 ATGGAATTTGGTCAT
19576744 TTTATGCATG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 8 0.57
15 6 0.43
ACGTcount: A:0.28, C:0.07, G:0.28, T:0.38
Consensus pattern (15 bp):
ATGGAATTTGGTCAT
Found at i:19580520 original size:50 final size:50
Alignment explanation
Indices: 19580399--19580638 Score: 236
Period size: 50 Copynumber: 4.7 Consensus size: 50
19580389 ACATGCTAAA
* * *
19580399 GCCATGTCCCAGACATGGTCTTACATGGGATG-TTTCATGTAC--TGTCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGA-GCTCTCATAT-CGGTGCCAAT
* * * * *
19580448 GCCATATCTCAGATATGGTCTTACATGGGAGTTCTCATATCGGTGCCCAT
1 GCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATATCGGTGCCAAT
* * * *
19580498 GCCATGTCCCAGACATGGTCTTAC-GGGGGGCCTCTCATCTCGTTGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGAG-CTCTCATATCGGTGCCAAT
*
19580548 GCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATGATCTCAAGGATGCCAAT
1 GCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCAT-A--TC--GG-TGCCAAT
* *
19580604 GCCATGTCCCAGAGATGGTCTTACATGGGATCTCT
1 GCCATGTCCCAGACATGGTCTTACATGGGAGCTCT
19580639 TTACCCAAAT
Statistics
Matches: 157, Mismatches: 23, Indels: 15
0.81 0.12 0.08
Matches are distributed among these distances:
48 2 0.01
49 37 0.24
50 72 0.46
51 3 0.02
53 2 0.01
55 1 0.01
56 40 0.25
ACGTcount: A:0.21, C:0.27, G:0.23, T:0.29
Consensus pattern (50 bp):
GCCATGTCCCAGACATGGTCTTACATGGGAGCTCTCATATCGGTGCCAAT
Found at i:19589568 original size:63 final size:63
Alignment explanation
Indices: 19589464--19589585 Score: 181
Period size: 63 Copynumber: 1.9 Consensus size: 63
19589454 TCAGGCCGTG
* *
19589464 TAACTCACTGTTTTGAAATTAGAGTCACACGGGCTAAAGACACCGGCGTGTATCCAAGCTTTA
1 TAACTCACTGTTTTGAAATTAAAGTCAAACGGGCTAAAGACACCGGCGTGTATCCAAGCTTTA
* * * * *
19589527 TAACTCATTGTTTTGGAATTAAAGTCAAACGGGCTAGAGACACGGGTGTGTATCCAAGC
1 TAACTCACTGTTTTGAAATTAAAGTCAAACGGGCTAAAGACACCGGCGTGTATCCAAGC
19589586 CATGTGAGAG
Statistics
Matches: 52, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
63 52 1.00
ACGTcount: A:0.30, C:0.20, G:0.23, T:0.27
Consensus pattern (63 bp):
TAACTCACTGTTTTGAAATTAAAGTCAAACGGGCTAAAGACACCGGCGTGTATCCAAGCTTTA
Found at i:19590209 original size:22 final size:22
Alignment explanation
Indices: 19590178--19590232 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
19590168 TAGGAATCTA
*
19590178 CATCTGTATCTAATCTGTTCTG
1 CATCTGTATCTAATATGTTCTG
* *
19590200 CATCTATATCTATTATGTTCTG
1 CATCTGTATCTAATATGTTCTG
*
19590222 CAACTGTATCT
1 CATCTGTATCT
19590233 TGTATCTTGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.22, C:0.22, G:0.11, T:0.45
Consensus pattern (22 bp):
CATCTGTATCTAATATGTTCTG
Found at i:19593335 original size:21 final size:21
Alignment explanation
Indices: 19593309--19593382 Score: 130
Period size: 21 Copynumber: 3.5 Consensus size: 21
19593299 CCTGTCCCAG
*
19593309 GTCTCGAGACATACGAAATAT
1 GTCTCGAGACATACAAAATAT
19593330 GTCTCGAGACATACAAAATAT
1 GTCTCGAGACATACAAAATAT
19593351 GTCTCGAGACATACAAAATAT
1 GTCTCGAGACATACAAAATAT
*
19593372 GTCTTGAGACA
1 GTCTCGAGACA
19593383 CAAGAACTTT
Statistics
Matches: 51, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 51 1.00
ACGTcount: A:0.39, C:0.19, G:0.18, T:0.24
Consensus pattern (21 bp):
GTCTCGAGACATACAAAATAT
Found at i:19597729 original size:50 final size:49
Alignment explanation
Indices: 19597660--19597852 Score: 215
Period size: 50 Copynumber: 3.9 Consensus size: 49
19597650 ACTATTATCA
* * *
19597660 TTCGATACATGTAGTAGCCTTCACATAGTACTACACACGTGATCAAACT
1 TTCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGATCAAACT
*
19597709 TTCTGGTTCACGTAGTAGCCTGCACATAGTACTACACACGTGATCAAAGCT
1 TTC-GGTACACGTAGTAGCCTGCACATAGTACTACACACGTGATCAAA-CT
* * * * * ***
19597760 ATTCGGTACGCATAGTAGCCTGCACATAGTACTACACATGGGACCTTTCAT
1 -TTCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGATCAAAC-T
* * *
19597811 TCCAGTACACGTAGTAGCCTACACATAGTACTACACACGTGA
1 TTCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGA
19597853 CCATCACTTT
Statistics
Matches: 120, Mismatches: 20, Indels: 7
0.82 0.14 0.05
Matches are distributed among these distances:
49 3 0.03
50 76 0.63
51 38 0.32
52 3 0.03
ACGTcount: A:0.30, C:0.26, G:0.18, T:0.26
Consensus pattern (49 bp):
TTCGGTACACGTAGTAGCCTGCACATAGTACTACACACGTGATCAAACT
Found at i:19605112 original size:24 final size:23
Alignment explanation
Indices: 19605024--19605113 Score: 58
Period size: 24 Copynumber: 3.6 Consensus size: 23
19605014 TCTTTTTCTC
*
19605024 TCTTTTTCTTTTTATAACTCATTT
1 TCTTTTTCTTTTTTTAACT-ATTT
*
19605048 TCTTTTTCCTCACTTGTTTTCAACT-CTT
1 TCTTTTT-CT---TT-TTTT-AACTATTT
19605076 TCTTTCCTT-TTTTTTTGAACTATTT
1 TCTTT--TTCTTTTTTT-AACTATTT
19605101 TCTTTTTCTTTTT
1 TCTTTTTCTTTTT
19605114 CGTTTTCATT
Statistics
Matches: 52, Mismatches: 4, Indels: 20
0.68 0.05 0.26
Matches are distributed among these distances:
23 2 0.04
24 20 0.38
25 11 0.21
28 10 0.19
29 3 0.06
30 6 0.12
ACGTcount: A:0.11, C:0.20, G:0.02, T:0.67
Consensus pattern (23 bp):
TCTTTTTCTTTTTTTAACTATTT
Found at i:19605132 original size:18 final size:18
Alignment explanation
Indices: 19605098--19605142 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
19605088 TTTTGAACTA
19605098 TTTTC-TTTTTCTTTTTC
1 TTTTCATTTTTCTTTTTC
19605115 GTTTTCATTTTTC-TTTTC
1 -TTTTCATTTTTCTTTTTC
19605133 TTGTTCATTT
1 TT-TTCATTT
19605143 GCTCTCGCAC
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 2 0.08
18 17 0.68
19 6 0.24
ACGTcount: A:0.04, C:0.16, G:0.04, T:0.76
Consensus pattern (18 bp):
TTTTCATTTTTCTTTTTC
Found at i:19605134 original size:5 final size:6
Alignment explanation
Indices: 19605098--19605131 Score: 50
Period size: 6 Copynumber: 5.5 Consensus size: 6
19605088 TTTTGAACTA
*
19605098 TTTTCT TTTTCT TTTTCG TTTTCAT TTTTCT TTT
1 TTTTCT TTTTCT TTTTCT TTTTC-T TTTTCT TTT
19605132 CTTGTTCATT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 20 0.80
7 5 0.20
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (6 bp):
TTTTCT
Found at i:19613883 original size:22 final size:21
Alignment explanation
Indices: 19613858--19613901 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 21
19613848 TGATAAACTT
19613858 TAATATATA-ATTATATTATTTA
1 TAATATATATATTA-ATT-TTTA
*
19613880 TAATTTATATATTAATTTTTA
1 TAATATATATATTAATTTTTA
19613901 T
1 T
19613902 CAACTTAGCT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
21 5 0.25
22 11 0.55
23 4 0.20
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (21 bp):
TAATATATATATTAATTTTTA
Found at i:19614730 original size:24 final size:24
Alignment explanation
Indices: 19614703--19614750 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
19614693 AGAAGTATGA
19614703 AATGCTCTAAAAATTGTAGTACAT
1 AATGCTCTAAAAATTGTAGTACAT
19614727 AATGCTCTAAAAATTGTAGTACAT
1 AATGCTCTAAAAATTGTAGTACAT
19614751 GCAGTAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.42, C:0.12, G:0.12, T:0.33
Consensus pattern (24 bp):
AATGCTCTAAAAATTGTAGTACAT
Found at i:19614758 original size:21 final size:22
Alignment explanation
Indices: 19614703--19614759 Score: 62
Period size: 24 Copynumber: 2.5 Consensus size: 22
19614693 AGAAGTATGA
*
19614703 AATGCTCTAAAAATTGTAGTAC
1 AATGCACTAAAAATTGTAGTAC
*
19614725 ATAATGCTCTAAAAATTGTAGTAC
1 --AATGCACTAAAAATTGTAGTAC
*
19614749 -ATGCAGTAAAA
1 AATGCACTAAAA
19614760 TTCTCGAGAA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
21 9 0.29
24 22 0.71
ACGTcount: A:0.44, C:0.12, G:0.14, T:0.30
Consensus pattern (22 bp):
AATGCACTAAAAATTGTAGTAC
Found at i:19622733 original size:25 final size:26
Alignment explanation
Indices: 19622688--19622750 Score: 76
Period size: 25 Copynumber: 2.5 Consensus size: 26
19622678 TCGTTTTCTT
*
19622688 TTTCCTCACTTTTTTTCAACTC-TTTC
1 TTTCCTC-TTTTTTTTCAACTCTTTTC
*
19622714 TTTCCTCTTTTTTTTGAACTCTTTTC
1 TTTCCTCTTTTTTTTCAACTCTTTTC
*
19622740 TTT-TTCTTTTT
1 TTTCCTCTTTTT
19622751 CTTTTTCTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
25 19 0.58
26 14 0.42
ACGTcount: A:0.08, C:0.24, G:0.02, T:0.67
Consensus pattern (26 bp):
TTTCCTCTTTTTTTTCAACTCTTTTC
Found at i:19622746 original size:6 final size:6
Alignment explanation
Indices: 19622735--19622788 Score: 83
Period size: 6 Copynumber: 9.0 Consensus size: 6
19622725 TTTTGAACTC
*
19622735 TTTTCT TTTTCT TTTTCT TTTTCT TTTTCAT TTTTC- TTTTCT TTTTCA
1 TTTTCT TTTTCT TTTTCT TTTTCT TTTTC-T TTTTCT TTTTCT TTTTCT
19622783 TTTTCT
1 TTTTCT
19622789 CTCGTACTCT
Statistics
Matches: 44, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
5 5 0.11
6 33 0.75
7 6 0.14
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTCT
Found at i:19628002 original size:43 final size:43
Alignment explanation
Indices: 19627951--19628036 Score: 172
Period size: 43 Copynumber: 2.0 Consensus size: 43
19627941 TTAGATGTTA
19627951 ACATAAATTTGCACTTTGCCCCTCAAGATTGGTAAATTTTCAG
1 ACATAAATTTGCACTTTGCCCCTCAAGATTGGTAAATTTTCAG
19627994 ACATAAATTTGCACTTTGCCCCTCAAGATTGGTAAATTTTCAG
1 ACATAAATTTGCACTTTGCCCCTCAAGATTGGTAAATTTTCAG
19628037 TCTAATCCTA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
43 43 1.00
ACGTcount: A:0.30, C:0.21, G:0.14, T:0.35
Consensus pattern (43 bp):
ACATAAATTTGCACTTTGCCCCTCAAGATTGGTAAATTTTCAG
Found at i:19629827 original size:2 final size:2
Alignment explanation
Indices: 19629816--19629858 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
19629806 ATTCAAGTCT
19629816 TC TC -C TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
19629857 TC
1 TC
19629859 GTAGCGAAGC
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
TC
Found at i:19633623 original size:125 final size:124
Alignment explanation
Indices: 19633435--19633772 Score: 541
Period size: 125 Copynumber: 2.7 Consensus size: 124
19633425 AGTTTATGAT
* * * * *
19633435 CAAATAGTATAAAATCACTTCTACCAGGATGTTATTTGAGAAGAATTTGTGAAATCACGCCCTCG
1 CAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTCG
19633500 TGGAAGCGCTTTTGCTACAGTAGGTCATAGAAGAAATAATTTTTTTTTGACGATTCTAAG
66 TGGAAGCGCTTTTGCTACAGTAGGTCATAGAAGAAATAA-TTTTTTTTGACGATTCTAAG
*
19633560 CAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTAAAATCGCACCCTCG
1 CAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTCG
* * * * *
19633625 TGGACGCGCTTTTGCTACAGTCGGTCATGGAAGAAATAATTTTTTTTGACGTTTCTGAG
66 TGGAAGCGCTTTTGCTACAGTAGGTCATAGAAGAAATAATTTTTTTTGACGATTCTAAG
*
19633684 CAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAAATCGCGCTCTC
1 CAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGT-AAAATCGCGCCCTC
*
19633749 GTGGATGCGCTTTTGCTACAGTAG
65 GTGGAAGCGCTTTTGCTACAGTAG
19633773 CATGTTTGGG
Statistics
Matches: 197, Mismatches: 15, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
124 68 0.35
125 129 0.65
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.32
Consensus pattern (124 bp):
CAAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTAAAATCGCGCCCTCG
TGGAAGCGCTTTTGCTACAGTAGGTCATAGAAGAAATAATTTTTTTTGACGATTCTAAG
Found at i:19636987 original size:116 final size:116
Alignment explanation
Indices: 19636783--19637026 Score: 418
Period size: 116 Copynumber: 2.1 Consensus size: 116
19636773 TAAGTTTGTG
* *
19636783 AAATTATTAATTGATAAATTGTATTAATGGTTAGTAAAAATTATCAATTTATATAAAATTATTAA
1 AAATTATTAATTGATAAATTGTATTAATGATTAGTAAAAATTATCAAATTATATAAAATTATTAA
** *
19636848 TTGTTAGTACCAGTCAAAATATTTTTCCAAATCTAACATTATGTGAATGTA
66 TTGTTAGTACCAGAAAAAATATTTTTCCAAATCTAACATTATGTGAAAGTA
*
19636899 AAATTATTAATTGATAAATTGTATTAATGATTAGT-AAAATTATCAAATTATATAAAATTATTAC
1 AAATTATTAATTGATAAATTGTATTAATGATTAGTAAAAATTATCAAATTATATAAAATTATTAA
19636963 TTGTTAGTACCAAGAAAAAATATTTTTCCAAATCTAACATTATGTGAAAGTA
66 TTGTTAGTACC-AGAAAAAATATTTTTCCAAATCTAACATTATGTGAAAGTA
19637015 AAATTATTAATT
1 AAATTATTAATT
19637027 TAGTTTAGGG
Statistics
Matches: 121, Mismatches: 6, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
115 38 0.31
116 83 0.69
ACGTcount: A:0.44, C:0.07, G:0.09, T:0.41
Consensus pattern (116 bp):
AAATTATTAATTGATAAATTGTATTAATGATTAGTAAAAATTATCAAATTATATAAAATTATTAA
TTGTTAGTACCAGAAAAAATATTTTTCCAAATCTAACATTATGTGAAAGTA
Found at i:19637057 original size:23 final size:23
Alignment explanation
Indices: 19637020--19637592 Score: 350
Period size: 23 Copynumber: 25.1 Consensus size: 23
19637010 AAGTAAAATT
* *
19637020 ATTAATTTAGTTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
*
19637043 ATTAAATTATGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
* *
19637066 ATTTAATTAGGTTAGTGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
**
19637089 AGTTAAA-GGGGTTAGGGTTTTTA
1 A-TTAAATTAGGTTAGGGTTTTTA
* *
19637112 AGT---TTAGGGTT---TTTAATTTA
1 ATTAAATTA-GGTTAGGGTT--TTTA
**
19637132 ATTAGGTTA-G---G-GTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
*
19637150 AGTT-AATTAGGTTAGGGCTTTTA
1 A-TTAAATTAGGTTAGGGTTTTTA
***
19637173 AGTT-AAGGGGGTTAGGGTTTTTA
1 A-TTAAATTAGGTTAGGGTTTTTA
* *
19637196 AGT---TTAGGGTTTAAGGTTTTTA
1 ATTAAATTA-GG-TTAGGGTTTTTA
19637218 ATTAAATTAGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
* *
19637241 AGT---TTAGGGTTTAGAGTTTTTA
1 ATTAAATTA-GG-TTAGGGTTTTTA
*
19637263 AATAAATTAGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
*
19637286 ATTTAAA-TAGGTTA-GGATTTTA
1 A-TTAAATTAGGTTAGGGTTTTTA
19637308 AGTT-AATTAGGTTA-GGTTTTTA
1 A-TTAAATTAGGTTAGGGTTTTTA
***
19637330 AGTT-AAGGGGGTTAGGGTTTTTA
1 A-TTAAATTAGGTTAGGGTTTTTA
*
19637353 AGT---TTAGGGTTTAGGGTTTTTA
1 ATTAAATTA-GG-TTAGGGTTTTTA
*
19637375 ATTTAATTAGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
* *
19637398 ATTTAATTAGGTTAAGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
*
19637421 AGT---TTAGGGTTTAGGGTTTTTA
1 ATTAAATTA-GG-TTAGGGTTTTTA
19637443 ATTAAATTAGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
19637466 AGTT-AATTAGGTTAGGGTTTTTA
1 A-TTAAATTAGGTTAGGGTTTTTA
19637489 AGTT-AATTAGGTTAGGGTTTTTA
1 A-TTAAATTAGGTTAGGGTTTTTA
***
19637512 AGTT-AAGGGGGTTAGGGTTTTTA
1 A-TTAAATTAGGTTAGGGTTTTTA
*
19637535 AGTTAATTTAAGTTTAGGGTTTAAGGTTTTTA
1 A-TT-A---AA--TTA-GG-TTAGGGTTTTTA
19637567 ATTAAATTAGGTTAGGGTTTTTA
1 ATTAAATTAGGTTAGGGTTTTTA
19637590 ATT
1 ATT
19637593 TAAGGGTATT
Statistics
Matches: 444, Mismatches: 58, Indels: 96
0.74 0.10 0.16
Matches are distributed among these distances:
18 10 0.02
19 3 0.01
20 14 0.03
21 15 0.03
22 92 0.21
23 254 0.57
24 20 0.05
25 15 0.03
27 2 0.00
28 2 0.00
30 1 0.00
31 4 0.01
32 12 0.03
ACGTcount: A:0.26, C:0.00, G:0.25, T:0.48
Consensus pattern (23 bp):
ATTAAATTAGGTTAGGGTTTTTA
Found at i:19637131 original size:14 final size:15
Alignment explanation
Indices: 19637100--19637131 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
19637090 GTTAAAGGGG
19637100 TTAGGGTTTTTAAGT
1 TTAGGGTTTTTAAGT
19637115 TTAGGGTTTTTAA-T
1 TTAGGGTTTTTAAGT
19637129 TTA
1 TTA
19637132 ATTAGGTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.24
15 13 0.76
ACGTcount: A:0.22, C:0.00, G:0.22, T:0.56
Consensus pattern (15 bp):
TTAGGGTTTTTAAGT
Found at i:19637178 original size:28 final size:23
Alignment explanation
Indices: 19637115--19637556 Score: 466
Period size: 23 Copynumber: 19.4 Consensus size: 23
19637105 GTTTTTAAGT
*
19637115 TTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAAGTTAATTAGG
19637138 TTAGGGTTTTTAAGTTAATTAGG
1 TTAGGGTTTTTAAGTTAATTAGG
* ***
19637161 TTAGGGCTTTTAAGTTAAGGGGG
1 TTAGGGTTTTTAAGTTAATTAGG
19637184 TTAGGGTTTTTAAG-T--TTAGGG
1 TTAGGGTTTTTAAGTTAATTA-GG
*
19637205 TTTAAGGTTTTTAA-TTAAATTAGG
1 -TTAGGGTTTTTAAGTT-AATTAGG
19637229 TTAGGGTTTTTAAG-T--TTAGGG
1 TTAGGGTTTTTAAGTTAATTA-GG
* * *
19637250 TTTAGAGTTTTTAAATAAATTAGG
1 -TTAGGGTTTTTAAGTTAATTAGG
* *
19637274 TTAGGGTTTTTAATTTAAATAGG
1 TTAGGGTTTTTAAGTTAATTAGG
*
19637297 TTA-GGATTTTAAGTTAATTAGG
1 TTAGGGTTTTTAAGTTAATTAGG
***
19637319 TTA-GGTTTTTAAGTTAAGGGGG
1 TTAGGGTTTTTAAGTTAATTAGG
19637341 TTAGGGTTTTTAAG-T--TTAGGG
1 TTAGGGTTTTTAAGTTAATTA-GG
*
19637362 TTTAGGGTTTTTAATTTAATTAGG
1 -TTAGGGTTTTTAAGTTAATTAGG
*
19637386 TTAGGGTTTTTAATTTAATTAGG
1 TTAGGGTTTTTAAGTTAATTAGG
*
19637409 TTAAGGTTTTTAAG-T--TTAGGG
1 TTAGGGTTTTTAAGTTAATTA-GG
19637430 TTTAGGGTTTTTAA-TTAAATTAGG
1 -TTAGGGTTTTTAAGTT-AATTAGG
19637454 TTAGGGTTTTTAAGTTAATTAGG
1 TTAGGGTTTTTAAGTTAATTAGG
19637477 TTAGGGTTTTTAAGTTAATTAGG
1 TTAGGGTTTTTAAGTTAATTAGG
***
19637500 TTAGGGTTTTTAAGTTAAGGGGG
1 TTAGGGTTTTTAAGTTAATTAGG
*
19637523 TTAGGGTTTTTAAGTTAATTTAAGT
1 TTAGGGTTTTTAAGTTAA-TT-AGG
19637548 TTAGGGTTT
1 TTAGGGTTT
19637557 AAGGTTTTTA
Statistics
Matches: 353, Mismatches: 39, Indels: 52
0.80 0.09 0.12
Matches are distributed among these distances:
20 6 0.02
21 8 0.02
22 91 0.26
23 216 0.61
24 10 0.03
25 22 0.06
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (23 bp):
TTAGGGTTTTTAAGTTAATTAGG
Found at i:19637226 original size:68 final size:66
Alignment explanation
Indices: 19637115--19637538 Score: 368
Period size: 68 Copynumber: 6.2 Consensus size: 66
19637105 GTTTTTAAGT
* * *
19637115 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGCTTTTAAGTTAAG
1 TTAGGGTTTTTAA-GT--TTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAAT
*
19637180 GGGG
63 GAGG
* *
19637184 TTAGGGTTTTTAAGTTTAGGGTTTAAGGTTTTTAA-TTAAATTAGGTTAGGGTTTTTAAGTTTA-
1 TTAGGGTTTTTAAGTTTA-GG-TTAGGGTTTTTAAGTT-AATTAGGTTAGGGTTTTTAAGTTAAT
19637247 G-GG
63 GAGG
* * * * *
19637250 TTTAGAGTTTTTAAATAAATTAGGTTAGGGTTTTTAATTTAAATAGGTTA-GGATTTTAAGTTAA
1 -TTAGGGTTTTTAAGT---TTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAA
*
19637314 TTAGG
62 TGAGG
* *
19637319 TTA-GGTTTTTAAGTTAAGGGGGTTAGGGTTTTTAAG-T--TTAGGGTTTAGGGTTTTTAATTTA
1 TTAGGGTTTTTAAGTTTA---GGTTAGGGTTTTTAAGTTAATTA-GG-TTAGGGTTTTTAAGTTA
*
19637380 ATTAGG
61 ATGAGG
* *
19637386 TTAGGGTTTTTAATTTAATTAGGTTAAGGTTTTTAAG-T--TTAGGGTTTAGGGTTTTTAA-TTA
1 TTAGGGTTTTTAA-GT--TTAGGTTAGGGTTTTTAAGTTAATTA-GG-TTAGGGTTTTTAAGTT-
*
19637447 AATTAGG
60 AATGAGG
*
19637454 TTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAAG
1 TTAGGGTTTTTAAG-T--TTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAAT
*
19637519 GGGG
63 GAGG
19637523 TTAGGGTTTTTAAGTT
1 TTAGGGTTTTTAAGTT
19637539 AATTTAAGTT
Statistics
Matches: 303, Mismatches: 26, Indels: 55
0.79 0.07 0.14
Matches are distributed among these distances:
64 4 0.01
65 2 0.01
66 10 0.03
67 76 0.25
68 147 0.49
69 52 0.17
70 7 0.02
71 5 0.02
ACGTcount: A:0.26, C:0.00, G:0.27, T:0.47
Consensus pattern (66 bp):
TTAGGGTTTTTAAGTTTAGGTTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAATGAG
G
Found at i:19637232 original size:45 final size:43
Alignment explanation
Indices: 19637031--19637556 Score: 425
Period size: 45 Copynumber: 11.7 Consensus size: 43
19637021 TTAATTTAGT
* *
19637031 TTAGGGTTTTTAATTAAATTATGTTAGGGTTTTTAA-TTTAATTAGG
1 TTAGGGTTTTTAATT-AATTAGGTTAGGGTTTTTAAGTTT-A--GGG
* ***
19637077 TTAGTGTTTTTAAGTTAAAGGGGTTAGGGTTTTTAAG--T----
1 TTAGGGTTTTTAA-TTAATTAGGTTAGGGTTTTTAAGTTTAGGG
19637115 TTAGGGTTTTTAATTTAATTAGGTTAGGGTTTTTAAGTTAATTA-GG
1 TTAGGGTTTTTAA-TTAATTAGGTTAGGGTTTTTAAG-T--TTAGGG
* ***
19637161 TTAGGGCTTTTAAGTTAAGGGGGTTAGGGTTTTTAAGTTTAGGG
1 TTAGGGTTTTTAA-TTAATTAGGTTAGGGTTTTTAAGTTTAGGG
*
19637205 TTTAAGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTTAGGG
1 -TTAGGGTTTTTAATT-AATTAGGTTAGGGTTTTTAAGTTTAGGG
* * *
19637250 TTTAGAGTTTTTAAATAAATTAGGTTAGGGTTTTTAA-TTTAAATAGG
1 -TTAGGGTTTTT-AATTAATTAGGTTAGGGTTTTTAAGTTT--A-GGG
* *
19637297 TTA-GGATTTTAAGTTAATTAGGTTA-GGTTTTTAAGTTAAGGGGG
1 TTAGGGTTTTTAA-TTAATTAGGTTAGGGTTTTTAAGTTTA--GGG
* *
19637341 TTAGGGTTTTTAAGT--TTAGGGTTTAGGGTTTTTAA-TTTAATTAGG
1 TTAGGGTTTTTAATTAATTA-GG-TTAGGGTTTTTAAGTTT-A--GGG
*
19637386 TTAGGGTTTTTAATTTAATTAGGTTAAGGTTTTTAAGTTTAGGG
1 TTAGGGTTTTTAA-TTAATTAGGTTAGGGTTTTTAAGTTTAGGG
19637430 TTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAAGTTAATTA-GG
1 -TTAGGGTTTTTAATT-AATTAGGTTAGGGTTTTTAAG-T--TTAGGG
*
19637477 TTAGGGTTTTTAAGTTAATTAGGTTAGGGTTTTTAAGTTAAGGGGG
1 TTAGGGTTTTTAA-TTAATTAGGTTAGGGTTTTTAAGTTTA--GGG
*
19637523 TTAGGGTTTTTAAGTTAATTTAAGTTTAGGGTTT
1 TTAGGGTTTTTAA-TTAA-TT-AGGTTAGGGTTT
19637557 AAGGTTTTTA
Statistics
Matches: 398, Mismatches: 42, Indels: 78
0.77 0.08 0.15
Matches are distributed among these distances:
38 32 0.08
42 3 0.01
43 9 0.02
44 33 0.08
45 153 0.38
46 136 0.34
47 15 0.04
48 17 0.04
ACGTcount: A:0.26, C:0.00, G:0.26, T:0.48
Consensus pattern (43 bp):
TTAGGGTTTTTAATTAATTAGGTTAGGGTTTTTAAGTTTAGGG
Found at i:19637590 original size:32 final size:32
Alignment explanation
Indices: 19637527--19637586 Score: 88
Period size: 30 Copynumber: 1.9 Consensus size: 32
19637517 AGGGGGTTAG
* *
19637527 GGTTTTTAAGTTAATTTAAGTTTAGGGTTTAA
1 GGTTTTTAAGTTAAATTAAGGTTAGGGTTTAA
19637559 GGTTTTTAA-TTAAATT-AGGTTAGGGTTT
1 GGTTTTTAAGTTAAATTAAGGTTAGGGTTT
19637587 TTAATTTAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
30 11 0.42
31 6 0.23
32 9 0.35
ACGTcount: A:0.27, C:0.00, G:0.23, T:0.50
Consensus pattern (32 bp):
GGTTTTTAAGTTAAATTAAGGTTAGGGTTTAA
Found at i:19638141 original size:18 final size:18
Alignment explanation
Indices: 19638118--19638153 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
19638108 CGGAAAAGGG
*
19638118 TACATATAAGGGTTAGGA
1 TACATATAAGGGCTAGGA
19638136 TACATATAAGGGCTAGGA
1 TACATATAAGGGCTAGGA
19638154 AACGCCCCTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.08, G:0.28, T:0.25
Consensus pattern (18 bp):
TACATATAAGGGCTAGGA
Found at i:19638814 original size:7 final size:7
Alignment explanation
Indices: 19638804--19638828 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
19638794 TTATATACAT
19638804 AATACTA
1 AATACTA
19638811 AATACTA
1 AATACTA
19638818 AATACTA
1 AATACTA
19638825 AATA
1 AATA
19638829 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:19639036 original size:20 final size:20
Alignment explanation
Indices: 19638999--19639036 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
19638989 TTTATTTTTA
*
19638999 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
19639019 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
19639037 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:19639947 original size:11 final size:11
Alignment explanation
Indices: 19639931--19639961 Score: 53
Period size: 11 Copynumber: 2.8 Consensus size: 11
19639921 AAAAAGGGAG
19639931 TTAAGAGAAAC
1 TTAAGAGAAAC
*
19639942 TTAAGAGGAAC
1 TTAAGAGAAAC
19639953 TTAAGAGAA
1 TTAAGAGAA
19639962 TTTTTGAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.52, C:0.06, G:0.23, T:0.19
Consensus pattern (11 bp):
TTAAGAGAAAC
Found at i:19640569 original size:5 final size:5
Alignment explanation
Indices: 19640559--19640589 Score: 62
Period size: 5 Copynumber: 6.2 Consensus size: 5
19640549 TAATTATATT
19640559 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA T
1 TTAAA TTAAA TTAAA TTAAA TTAAA TTAAA T
19640590 CCAAAGATTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 26 1.00
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (5 bp):
TTAAA
Found at i:19644947 original size:38 final size:37
Alignment explanation
Indices: 19644903--19645043 Score: 108
Period size: 38 Copynumber: 3.6 Consensus size: 37
19644893 AATAATTATT
*
19644903 TTAAATTATATTATATAGTATTATATATTATGATTTTA
1 TTAAATTATA-TATATAATATTATATATTATGATTTTA
* *
19644941 TTAAATTCATATA-AGAATATT-TAATATTAAGAATTTTA
1 TTAAATT-ATATATATAATATTAT-ATATTATG-ATTTTA
** *
19644979 TTAAATTATATATATTTTTATTAAATTATATAT-ATTTTTA
1 TTAAATTATATATA-TAATATTATA-TAT-TATGA-TTTTA
*
19645019 TTAAATTATATTTAATAATAATTAT
1 TTAAATTATATAT-ATAAT-ATTAT
19645044 GTTAAATTAT
Statistics
Matches: 80, Mismatches: 12, Indels: 19
0.72 0.11 0.17
Matches are distributed among these distances:
36 1 0.01
37 18 0.22
38 23 0.29
39 9 0.11
40 22 0.28
41 7 0.09
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (37 bp):
TTAAATTATATATATAATATTATATATTATGATTTTA
Found at i:19644963 original size:73 final size:72
Alignment explanation
Indices: 19644884--19645108 Score: 246
Period size: 73 Copynumber: 3.1 Consensus size: 72
19644874 TTATTAAATT
19644884 ATATTTAATAATAATTATTTTAAATTATATTATATAGTATTATATATTATGATTTTATTAAATTC
1 ATATTTAATAATAATTATTTTAAATTATATTATATAGTATTATATATTATGATTTTA-TAAATTC
19644949 ATATAAGA
65 ATATAAGA
* ** * * * * * **
19644957 ATATTTAATATTAAGAATTTT--ATTAAATTATATA-TATT-TTTATTA-AATTATATATATTTT
1 ATATTTAATAATAATTATTTTAAATTATATTATATAGTATTATATATTATGATTTTATAAATTCA
19645017 TATTAA-A
66 TA-TAAGA
* * *
19645024 TTATATTTAATAATAATTATGTTAAATTATATTTTATAGTATTATATATTATGATTTTAGAAAAT
1 --ATATTTAATAATAATTATTTTAAATTATATTATATAGTATTATATATTATGATTTTA-TAAAT
19645089 TCATATAAGA
63 TCATATAAGA
19645099 ATATTTAATA
1 ATATTTAATA
19645109 TTAAGAATTT
Statistics
Matches: 119, Mismatches: 23, Indels: 20
0.73 0.14 0.12
Matches are distributed among these distances:
67 8 0.07
68 8 0.07
69 23 0.19
70 4 0.03
71 23 0.19
72 4 0.03
73 34 0.29
74 8 0.07
75 7 0.06
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.52
Consensus pattern (72 bp):
ATATTTAATAATAATTATTTTAAATTATATTATATAGTATTATATATTATGATTTTATAAATTCA
TATAAGA
Found at i:19644989 original size:59 final size:56
Alignment explanation
Indices: 19644806--19645010 Score: 200
Period size: 57 Copynumber: 3.4 Consensus size: 56
19644796 TATAGTATTA
*
19644806 TATATTATGATTTTAGTAAATTCATATAAGAATATTTAATTTTAAGAATTTTATTAAAT
1 TATA-TAT-ATTTTATTAAATT-ATATAAGAATATTTAATTTTAAGAATTTTATTAAAT
* * * *
19644865 TATATAT-TTTTATTAAATTATATTTAATAATAATT-ATTTTAA-ATTATATTATATAGTATT
1 TATATATATTTTATTAAATTATA--TAAGAATATTTAATTTTAAGA--ATTTTAT-TA--AAT
*
19644925 ATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAAT
1 -TATA-TAT-ATTTTATTAAATT-ATATAAGAATATTTAATTTTAAGAATTTTATTAAAT
19644985 TATATATATTTTTATTAAATTATATA
1 TATATATA-TTTTATTAAATTATATA
19645011 TATTTTTATT
Statistics
Matches: 121, Mismatches: 10, Indels: 32
0.74 0.06 0.20
Matches are distributed among these distances:
55 4 0.03
56 18 0.15
57 21 0.17
58 20 0.17
59 8 0.07
60 4 0.03
61 4 0.03
62 5 0.04
63 15 0.12
64 18 0.15
65 4 0.03
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (56 bp):
TATATATATTTTATTAAATTATATAAGAATATTTAATTTTAAGAATTTTATTAAAT
Found at i:19644999 original size:20 final size:20
Alignment explanation
Indices: 19644974--19645029 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
19644964 ATATTAAGAA
19644974 TTTTATTAAATTATATATAT
1 TTTTATTAAATTATATATAT
19644994 TTTTATTAAATTATATATAT
1 TTTTATTAAATTATATATAT
19645014 TTTTATTAAATTATAT
1 TTTTATTAAATTATAT
19645030 TTAATAATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (20 bp):
TTTTATTAAATTATATATAT
Found at i:19645029 original size:142 final size:140
Alignment explanation
Indices: 19644854--19645149 Score: 524
Period size: 142 Copynumber: 2.1 Consensus size: 140
19644844 ATTTTAAGAA
*
19644854 TTTTATTAAA-T-TATATATTTTTATTAAATTATATTTAATAATAATTATTTTAAATTATATTAT
1 TTTTATTAAATTATATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTAT
**
19644917 ATAGTATTATATATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTA
66 ATAGTATTATATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTA
19644982 AATTATATATAT
131 AA-T-TATATAT
*
19644994 TTTTATTAAATTATATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTTT
1 TTTTATTAAATTATATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTAT
19645059 ATAGTATTATATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTA
66 ATAGTATTATATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTA
19645124 AATTATATAT
131 AATTATATAT
19645134 TTTTATTAAATTATAT
1 TTTTATTAAATTATAT
19645150 TTAATAATAA
Statistics
Matches: 150, Mismatches: 4, Indels: 4
0.95 0.03 0.03
Matches are distributed among these distances:
140 33 0.22
141 2 0.01
142 115 0.77
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.53
Consensus pattern (140 bp):
TTTTATTAAATTATATATATTTTTATTAAATTATATTTAATAATAATTATGTTAAATTATATTAT
ATAGTATTATATATTATGATTTTAGAAAATTCATATAAGAATATTTAATATTAAGAATTTTATTA
AATTATATAT
Found at i:19645053 original size:120 final size:120
Alignment explanation
Indices: 19644809--19645177 Score: 351
Period size: 120 Copynumber: 3.1 Consensus size: 120
19644799 AGTATTATAT
* *
19644809 ATTATGATTTTAGTAAATTCATATAAGAATATTTAATTTTAAGAATTTTATTAAA-T-TATATAT
1 ATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATAT
* *
19644872 TTTTATTAAATTATATTTAATAATAATTATT-TTAAATTATA-TT-AT-AT-AGTAT-TATAT
66 TTTTATTAAATTATA--T-AT-AT--TT-TTATTAAATTATATTTAATAATAATTATGT-TAA
19644929 ATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATAT
1 ATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATAT
19644994 TTTTATTAAATTATATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
66 TTTTATTAAATTATATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
* * * * *
19645049 ATTAT-ATTTTATAGTATTATATATTATGATTTTAGAA-AATTCATA-TAAGAATATTTA--ATA
1 ATTATGATTTTAT--TA--A-AT-TCAT-A--TAAGAATATTTAATATTAAGAAT-TTTATTAAA
*
19645109 TTA-AGA-A-TTTTATTAAA-T-TATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
56 TTATATATATTTTTATTAAATTATATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
*
19645169 AATATGATT
1 ATTATGATT
19645178 AAATTATTTA
Statistics
Matches: 219, Mismatches: 11, Indels: 37
0.82 0.04 0.14
Matches are distributed among these distances:
115 2 0.01
116 12 0.05
117 2 0.01
118 4 0.02
119 11 0.05
120 111 0.51
121 8 0.04
122 32 0.15
123 2 0.01
124 4 0.02
125 8 0.04
126 8 0.04
127 10 0.05
128 5 0.02
ACGTcount: A:0.43, C:0.01, G:0.04, T:0.52
Consensus pattern (120 bp):
ATTATGATTTTATTAAATTCATATAAGAATATTTAATATTAAGAATTTTATTAAATTATATATAT
TTTTATTAAATTATATATATTTTTATTAAATTATATTTAATAATAATTATGTTAA
Found at i:19645375 original size:44 final size:46
Alignment explanation
Indices: 19645308--19645400 Score: 145
Period size: 44 Copynumber: 2.1 Consensus size: 46
19645298 TTACACCTCT
* *
19645308 ATTCCATTCAACCAAACACAAGAA-TACC-ATTACGCCTCTATTCC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTATATTCC
*
19645352 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTATATTTC
1 ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTATATTCC
19645398 ATT
1 ATT
19645401 ACGCATCTAT
Statistics
Matches: 44, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
44 23 0.52
45 4 0.09
46 17 0.39
ACGTcount: A:0.38, C:0.29, G:0.04, T:0.29
Consensus pattern (46 bp):
ATTCCATTCAACCAAACAAAAGAATTACCTATTACGCCTATATTCC
Found at i:19645403 original size:16 final size:16
Alignment explanation
Indices: 19645382--19645434 Score: 70
Period size: 16 Copynumber: 3.3 Consensus size: 16
19645372 AGAATTACCT
* *
19645382 ATTACGCCTATATTTC
1 ATTACGCCTCTATTCC
*
19645398 ATTACGCATCTATTCC
1 ATTACGCCTCTATTCC
*
19645414 ATTACACCTCTATTCC
1 ATTACGCCTCTATTCC
19645430 ATTAC
1 ATTAC
19645435 AGCGAACCAA
Statistics
Matches: 32, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
16 32 1.00
ACGTcount: A:0.26, C:0.30, G:0.04, T:0.40
Consensus pattern (16 bp):
ATTACGCCTCTATTCC
Found at i:19645624 original size:17 final size:17
Alignment explanation
Indices: 19645599--19645632 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
19645589 CTACTTTTTA
* *
19645599 ACAATATCTAGTATTGT
1 ACAAAATCTACTATTGT
19645616 ACAAAATCTACTATTGT
1 ACAAAATCTACTATTGT
19645633 TTTCATCAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (17 bp):
ACAAAATCTACTATTGT
Found at i:19651371 original size:21 final size:21
Alignment explanation
Indices: 19651347--19651409 Score: 74
Period size: 21 Copynumber: 3.0 Consensus size: 21
19651337 ATTGAGCTTT
19651347 CGTTCAACCCTTATGGGTTTC
1 CGTTCAACCCTTATGGGTTTC
* * *
19651368 CGTTCAGCTCTTATGAGCTTT-
1 CGTTCAACCCTTATG-GGTTTC
*
19651389 CGTTCAACGCTTATGGGTTTC
1 CGTTCAACCCTTATGGGTTTC
19651410 TATTTAGCTC
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 4 0.12
21 26 0.76
22 4 0.12
ACGTcount: A:0.14, C:0.25, G:0.21, T:0.40
Consensus pattern (21 bp):
CGTTCAACCCTTATGGGTTTC
Found at i:19651436 original size:42 final size:42
Alignment explanation
Indices: 19651339--19651429 Score: 137
Period size: 42 Copynumber: 2.2 Consensus size: 42
19651329 TCACCTTTAT
* *
19651339 TGAGCTTTCGTTCAACCCTTATGGGTTTCCGTTCAGCTCTTA
1 TGAGCTTTCGTTCAACCCTTATGGGTTTCCATTCAGCTCTCA
* * *
19651381 TGAGCTTTCGTTCAACGCTTATGGGTTTCTATTTAGCTCTCA
1 TGAGCTTTCGTTCAACCCTTATGGGTTTCCATTCAGCTCTCA
19651423 TGAGCTT
1 TGAGCTT
19651430 CTGTTCAGCC
Statistics
Matches: 44, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 44 1.00
ACGTcount: A:0.15, C:0.23, G:0.20, T:0.42
Consensus pattern (42 bp):
TGAGCTTTCGTTCAACCCTTATGGGTTTCCATTCAGCTCTCA
Found at i:19659388 original size:14 final size:12
Alignment explanation
Indices: 19659351--19659393 Score: 59
Period size: 12 Copynumber: 3.4 Consensus size: 12
19659341 TAAGTATTCG
*
19659351 AAAAAATTTCAA
1 AAAAAATTTGAA
19659363 AAAAAATTTGAA
1 AAAAAATTTGAA
19659375 AAAAAATTCGTGAA
1 AAAAAATT--TGAA
19659389 AAAAA
1 AAAAA
19659394 TAATATAAGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
12 19 0.68
14 9 0.32
ACGTcount: A:0.67, C:0.05, G:0.07, T:0.21
Consensus pattern (12 bp):
AAAAAATTTGAA
Found at i:19662564 original size:52 final size:51
Alignment explanation
Indices: 19662435--19662566 Score: 176
Period size: 50 Copynumber: 2.6 Consensus size: 51
19662425 ATGTATTATG
* * * *
19662435 CATTTAATAAAGTCATGCATTATGTAACTCTCATGTTAGTTAAGTTTCCAT
1 CATTAAATTAAGTCATGCATTATGTAACTCCCATGTTAGTTAAGTCTCCAT
* * *
19662486 CA-TAAATTATGACATGCATTATGTAACTCCCATGTTAGTTTAAGTCTGCAT
1 CATTAAATTAAGTCATGCATTATGTAACTCCCATGTTAG-TTAAGTCTCCAT
*
19662537 CATTAAATTAAGTCATGCATTAAGTAACTC
1 CATTAAATTAAGTCATGCATTATGTAACTC
19662567 ATTTGTTCAT
Statistics
Matches: 69, Mismatches: 10, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
50 31 0.45
51 14 0.20
52 24 0.35
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (51 bp):
CATTAAATTAAGTCATGCATTATGTAACTCCCATGTTAGTTAAGTCTCCAT
Found at i:19670636 original size:15 final size:15
Alignment explanation
Indices: 19670617--19670651 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
19670607 TTATATATAG
19670617 AAAAATTTA-AAATA
1 AAAAATTTAGAAATA
19670631 ATAAAATTTAGAAATA
1 A-AAAATTTAGAAATA
19670647 AAAAA
1 AAAAA
19670652 AATATCGTAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
14 1 0.05
15 12 0.63
16 6 0.32
ACGTcount: A:0.71, C:0.00, G:0.03, T:0.26
Consensus pattern (15 bp):
AAAAATTTAGAAATA
Found at i:19670652 original size:16 final size:15
Alignment explanation
Indices: 19670617--19670652 Score: 54
Period size: 16 Copynumber: 2.3 Consensus size: 15
19670607 TTATATATAG
19670617 AAAAATTTAAAATAA
1 AAAAATTTAAAATAA
*
19670632 TAAAATTTAGAAATAA
1 AAAAATTTA-AAATAA
19670648 AAAAA
1 AAAAA
19670653 ATATCGTAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
15 8 0.44
16 10 0.56
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.25
Consensus pattern (15 bp):
AAAAATTTAAAATAA
Found at i:19670652 original size:31 final size:31
Alignment explanation
Indices: 19670591--19670652 Score: 72
Period size: 31 Copynumber: 2.0 Consensus size: 31
19670581 TAATTCAATT
* * *
19670591 TTTAAAAAAATTAAAATTATATATAGAAAAA
1 TTTAAAAAAATTAAAATTAGAAATAAAAAAA
*
19670622 TTTAAAATAA-TAAAATTTAGAAATAAAAAAA
1 TTTAAAAAAATTAAAA-TTAGAAATAAAAAAA
19670653 ATATCGTAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
30 5 0.19
31 21 0.81
ACGTcount: A:0.66, C:0.00, G:0.03, T:0.31
Consensus pattern (31 bp):
TTTAAAAAAATTAAAATTAGAAATAAAAAAA
Found at i:19672394 original size:32 final size:32
Alignment explanation
Indices: 19672353--19672417 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
19672343 CATTATATTA
*
19672353 AATTATTTAAGTACTTTTCAAATTAATTTTTT
1 AATTATTTAAATACTTTTCAAATTAATTTTTT
19672385 AATTATTTAAATACTTTTCAAATTAATTTTTT
1 AATTATTTAAATACTTTTCAAATTAATTTTTT
19672417 A
1 A
19672418 CTTTCTAACA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.37, C:0.06, G:0.02, T:0.55
Consensus pattern (32 bp):
AATTATTTAAATACTTTTCAAATTAATTTTTT
Found at i:19694305 original size:32 final size:32
Alignment explanation
Indices: 19694267--19694351 Score: 170
Period size: 32 Copynumber: 2.7 Consensus size: 32
19694257 GTATATGTTT
19694267 TATATATTGCCGAATTGATTTAAATAGAGATA
1 TATATATTGCCGAATTGATTTAAATAGAGATA
19694299 TATATATTGCCGAATTGATTTAAATAGAGATA
1 TATATATTGCCGAATTGATTTAAATAGAGATA
19694331 TATATATTGCCGAATTGATTT
1 TATATATTGCCGAATTGATTT
19694352 GAGTATTGGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 53 1.00
ACGTcount: A:0.38, C:0.07, G:0.15, T:0.40
Consensus pattern (32 bp):
TATATATTGCCGAATTGATTTAAATAGAGATA
Found at i:19698998 original size:12 final size:12
Alignment explanation
Indices: 19698978--19699010 Score: 57
Period size: 12 Copynumber: 2.8 Consensus size: 12
19698968 AAGCGTGATA
*
19698978 TTTCAAAATTTG
1 TTTCGAAATTTG
19698990 TTTCGAAATTTG
1 TTTCGAAATTTG
19699002 TTTCGAAAT
1 TTTCGAAAT
19699011 GTTTAATCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.30, C:0.09, G:0.12, T:0.48
Consensus pattern (12 bp):
TTTCGAAATTTG
Found at i:19710736 original size:45 final size:45
Alignment explanation
Indices: 19710663--19710783 Score: 134
Period size: 45 Copynumber: 2.7 Consensus size: 45
19710653 GCTAGTATGG
* * * *
19710663 TGTGGATGAACCACTCATTATTGCAGATAAAAACTACTAATACAA
1 TGTGGATAAACCACTCAATAGTGTAGATAAAAACTACTAATACAA
* ** * *
19710708 TGTGGATAAACCACTCAATAGTGTAGATACAAGTTGCTAATACAG
1 TGTGGATAAACCACTCAATAGTGTAGATAAAAACTACTAATACAA
* * *
19710753 TGTGGATAAATCACTCCATGGTGTAGATAAA
1 TGTGGATAAACCACTCAATAGTGTAGATAAA
19710784 CCACTCAAAT
Statistics
Matches: 63, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
45 63 1.00
ACGTcount: A:0.39, C:0.16, G:0.18, T:0.27
Consensus pattern (45 bp):
TGTGGATAAACCACTCAATAGTGTAGATAAAAACTACTAATACAA
Found at i:19710781 original size:21 final size:22
Alignment explanation
Indices: 19710752--19710798 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
19710742 TGCTAATACA
* * *
19710752 GTGTGGATAAATCACTC-CATG
1 GTGTAGATAAACCACTCAAATG
19710773 GTGTAGATAAACCACTCAAATG
1 GTGTAGATAAACCACTCAAATG
19710795 GTGT
1 GTGT
19710799 GCATGCAACC
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 15 0.68
22 7 0.32
ACGTcount: A:0.32, C:0.17, G:0.23, T:0.28
Consensus pattern (22 bp):
GTGTAGATAAACCACTCAAATG
Found at i:19711718 original size:11 final size:11
Alignment explanation
Indices: 19711676--19711730 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
19711666 AGAGAAAAAT
19711676 GAAATTTGAGTGA
1 GAAATTTGA--GA
*
19711689 GAAA-TTAAGA
1 GAAATTTGAGA
19711699 GGAAA-TTGAGA
1 -GAAATTTGAGA
19711710 GAAATTTGAGA
1 GAAATTTGAGA
*
19711721 GAGATTTGAG
1 GAAATTTGAG
19711731 GATTTGAGAA
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
10 6 0.16
11 24 0.65
12 3 0.08
13 4 0.11
ACGTcount: A:0.44, C:0.00, G:0.31, T:0.25
Consensus pattern (11 bp):
GAAATTTGAGA
Found at i:19718884 original size:45 final size:45
Alignment explanation
Indices: 19718739--19718960 Score: 259
Period size: 45 Copynumber: 5.0 Consensus size: 45
19718729 AATCGTTACA
* * * **
19718739 CGGTGG-ATCAACACATAGC-ACCACCCTTATAATCAATTATATT
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATACC
* * ** * ***
19718782 TGGTGGAATCAGCATATAGCAACCACCTTTATTTTTAATGATTTT
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATACC
* * *
19718827 CGATGGAGTCAGCACATAGCAACCACCTTTATAATCAATGGTACC
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATACC
* *
19718872 CGGTGGAATCAGCACATAGCAGCCACCTTTATAATCAATGGTACC
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATACC
*
19718917 CAGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATAC
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATAC
19718961 TCAATACACG
Statistics
Matches: 151, Mismatches: 26, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
43 5 0.03
44 11 0.07
45 135 0.89
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.27
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATACC
Found at i:19720264 original size:29 final size:28
Alignment explanation
Indices: 19720219--19720277 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 28
19720209 AATCAATTTA
*
19720219 ATCTCATATATCTCTTTTC-AATAAATAT
1 ATCTCATATATCTC-TTTCAAAAAAATAT
19720247 ATCTC-TATATCATACTTTCAAAAAAATAT
1 ATCTCATATATC-T-CTTTCAAAAAAATAT
19720276 AT
1 AT
19720278 ATTTTTTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
27 6 0.22
28 10 0.37
29 11 0.41
ACGTcount: A:0.41, C:0.17, G:0.00, T:0.42
Consensus pattern (28 bp):
ATCTCATATATCTCTTTCAAAAAAATAT
Found at i:19724177 original size:45 final size:45
Alignment explanation
Indices: 19724077--19724298 Score: 268
Period size: 45 Copynumber: 5.0 Consensus size: 45
19724067 AACCGTTACA
* * **
19724077 CGGTGG-ATCAGCACATAGC-ACCACCCTTATAATCAATTATATT
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATACC
* * ** ***
19724120 TGGTGGAATCAGCATATAGCAACCACCTTTATTTTCAATGATTTT
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATACC
* * * * * *
19724165 CGATGGAGTCAGCACTTAGCAACCACATTTATAATTAATGGTACC
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATACC
*
19724210 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGGTACC
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATACC
19724255 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATAC
1 CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATAC
19724299 TCAGTACACG
Statistics
Matches: 151, Mismatches: 26, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
43 5 0.03
44 12 0.08
45 134 0.89
ACGTcount: A:0.33, C:0.23, G:0.16, T:0.27
Consensus pattern (45 bp):
CGGTGGAATCAGCACATAGCAACCACCTTTATAATCAATGATACC
Found at i:19727330 original size:21 final size:21
Alignment explanation
Indices: 19727303--19727356 Score: 67
Period size: 21 Copynumber: 2.6 Consensus size: 21
19727293 CGTAAAGGTT
19727303 AAACAGAAGCTCA-ATAGAGTTG
1 AAACAGAAGCTCATAT-GAG-TG
*
19727325 -AACAGAAACTCATATGAGTG
1 AAACAGAAGCTCATATGAGTG
19727345 AAACAGAAGCTC
1 AAACAGAAGCTC
19727357 GTGAGAGCTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
20 2 0.07
21 24 0.86
22 2 0.07
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (21 bp):
AAACAGAAGCTCATATGAGTG
Found at i:19727937 original size:13 final size:13
Alignment explanation
Indices: 19727919--19727945 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
19727909 AGAATTTATA
19727919 TAAAAAAATAAAT
1 TAAAAAAATAAAT
19727932 TAAAAAAATAAAT
1 TAAAAAAATAAAT
19727945 T
1 T
19727946 TGGCCAAAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (13 bp):
TAAAAAAATAAAT
Found at i:19732345 original size:24 final size:24
Alignment explanation
Indices: 19732318--19732366 Score: 98
Period size: 24 Copynumber: 2.0 Consensus size: 24
19732308 AAAAAGAAAA
19732318 ATAACAGCAAAAGCTCGAAAATGG
1 ATAACAGCAAAAGCTCGAAAATGG
19732342 ATAACAGCAAAAGCTCGAAAATGG
1 ATAACAGCAAAAGCTCGAAAATGG
19732366 A
1 A
19732367 CTATGGAAAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.51, C:0.16, G:0.20, T:0.12
Consensus pattern (24 bp):
ATAACAGCAAAAGCTCGAAAATGG
Found at i:19736133 original size:31 final size:31
Alignment explanation
Indices: 19736095--19736155 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
19736085 CACTTCCCCC
19736095 ATTAAAGAAGAGTACACCAAACCTTACTAAT
1 ATTAAAGAAGAGTACACCAAACCTTACTAAT
*
19736126 ATTAAAGAAGAGTACTCCAAACCTTACTAA
1 ATTAAAGAAGAGTACACCAAACCTTACTAA
19736156 CATAATATTT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.48, C:0.20, G:0.10, T:0.23
Consensus pattern (31 bp):
ATTAAAGAAGAGTACACCAAACCTTACTAAT
Found at i:19736493 original size:22 final size:22
Alignment explanation
Indices: 19736463--19736505 Score: 77
Period size: 22 Copynumber: 2.0 Consensus size: 22
19736453 ACACCAAAAC
*
19736463 AGGCTTTTAGCGGCGCTTTTTT
1 AGGCCTTTAGCGGCGCTTTTTT
19736485 AGGCCTTTAGCGGCGCTTTTT
1 AGGCCTTTAGCGGCGCTTTTT
19736506 AGCGCCGCTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.09, C:0.21, G:0.28, T:0.42
Consensus pattern (22 bp):
AGGCCTTTAGCGGCGCTTTTTT
Found at i:19736703 original size:44 final size:43
Alignment explanation
Indices: 19736548--19736779 Score: 268
Period size: 43 Copynumber: 5.3 Consensus size: 43
19736538 AAGCGCCAGA
* * * *
19736548 AAAAACGCCGCTAAAGACCAAGACCTTTAGCAGTGCTTTACCC
1 AAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCAC
* * * *
19736591 ACAAACGCCGCTAAAGACCAAGACCTTTAACGGCGCTTTACCC
1 AAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCAC
* *
19736634 ACAAACGCCACTAAAGACCAAGACCTTTAGCGGCGCTTTTTCAC
1 AAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGC-TTTTCAC
* * *
19736678 AAAAACGCCGCTATAGACCATGACCTTTAGCGGCGCTTTTTC-G
1 AAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGC-TTTTCAC
* * * * *
19736721 GAAAACGCCGCTAAAGATCATGAAGCTTTAGCGGCGCTTCTCAC
1 AAAAACGCCGCTAAAGACCAAG-ACCTTTAGCGGCGCTTTTCAC
19736765 AAAAACGCCGCTAAA
1 AAAAACGCCGCTAAA
19736780 AATATAACCT
Statistics
Matches: 166, Mismatches: 20, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
43 96 0.58
44 70 0.42
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.19
Consensus pattern (43 bp):
AAAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCAC
Found at i:19736715 original size:87 final size:86
Alignment explanation
Indices: 19736549--19736779 Score: 284
Period size: 87 Copynumber: 2.7 Consensus size: 86
19736539 AGCGCCAGAA
* * * * *
19736549 AAAACGCCGCTAAAGACCAAGACCTTTAGCAGTGCTTTACCCACAAACGCCGCTAAAGACCAAGA
1 AAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCACAAAAACGCCGCTAAAGACCAAGA
19736614 CCTTTAACGGCGC-TTTACCC
66 CCTTTAACGGCGCTTTTACCC
* * *
19736634 ACAAACGCCACTAAAGACCAAGACCTTTAGCGGCGCTTTTTCACAAAAACGCCGCTATAGACCAT
1 A-AAACGCCGCTAAAGACCAAGACCTTTAGCGGCGC-TTTTCACAAAAACGCCGCTAAAGACCAA
* * **
19736699 GACCTTTAGCGGCGCTTTTTCGG
64 GACCTTTAACGGCGCTTTTACCC
* * * *
19736722 AAAACGCCGCTAAAGATCATGAAGCTTTAGCGGCGCTTCTCACAAAAACGCCGCTAAA
1 AAAACGCCGCTAAAGACCAAG-ACCTTTAGCGGCGCTTTTCACAAAAACGCCGCTAAA
19736780 AATATAACCT
Statistics
Matches: 124, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
85 1 0.01
86 31 0.25
87 74 0.60
88 18 0.15
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.19
Consensus pattern (86 bp):
AAAACGCCGCTAAAGACCAAGACCTTTAGCGGCGCTTTTCACAAAAACGCCGCTAAAGACCAAGA
CCTTTAACGGCGCTTTTACCC
Found at i:19739759 original size:142 final size:142
Alignment explanation
Indices: 19739499--19739866 Score: 691
Period size: 142 Copynumber: 2.6 Consensus size: 142
19739489 GGGAGGGGGT
*
19739499 AGGGAATTTAAAAAAATAGCGCTATTTTTTTAAAAGTAAATTTTATTTTGTGGCGTTTTTTATAA
1 AGGGAATTTAAAAAAATGGCGCTATTTTTTTAAAAGTAAATTTTATTTTGTGGCGTTTTTTATAA
*
19739564 AAACGCCGCTATTGCTTATCTATTGCGGCGTTTTTTACACAAACGTCGCAAAAAATTATTTTATT
66 AAACGCCGCTATTGCTTATCTATTGCGGCGTTTTTTACACAAACGCCGCAAAAAATTATTTTATT
19739629 TGGAATAAAACG
131 TGGAATAAAACG
*
19739641 AGGGAATTTAAGAAAATGGCGCTATTTTTTTAAAAGTAAATTTTATTTTGTGGCGTTTTTTATAA
1 AGGGAATTTAAAAAAATGGCGCTATTTTTTTAAAAGTAAATTTTATTTTGTGGCGTTTTTTATAA
*
19739706 AAACGCCGCTATTGCTTATCTATTGCGGCGTTTTTTACACAAACGCCGTAAAAAATTATTTTATT
66 AAACGCCGCTATTGCTTATCTATTGCGGCGTTTTTTACACAAACGCCGCAAAAAATTATTTTATT
19739771 TGGAATAAAACG
131 TGGAATAAAACG
*
19739783 AGGGAATTTAAAAAAATGGTGCTATTTTTTTAAAAGTAAATTTTATTTTGTGGCGTTTTTTATAA
1 AGGGAATTTAAAAAAATGGCGCTATTTTTTTAAAAGTAAATTTTATTTTGTGGCGTTTTTTATAA
19739848 AAACGCCGCTATTGCTTAT
66 AAACGCCGCTATTGCTTAT
19739867 AAAAAACGCC
Statistics
Matches: 220, Mismatches: 6, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
142 220 1.00
ACGTcount: A:0.33, C:0.11, G:0.16, T:0.40
Consensus pattern (142 bp):
AGGGAATTTAAAAAAATGGCGCTATTTTTTTAAAAGTAAATTTTATTTTGTGGCGTTTTTTATAA
AAACGCCGCTATTGCTTATCTATTGCGGCGTTTTTTACACAAACGCCGCAAAAAATTATTTTATT
TGGAATAAAACG
Found at i:19739885 original size:124 final size:123
Alignment explanation
Indices: 19739746--19739990 Score: 327
Period size: 124 Copynumber: 2.0 Consensus size: 123
19739736 TTTTTTACAC
* * *
19739746 AAACGCCGTAAAAAATTATTTTATTTGGAATAAAACG-AGGGAATT-TA-AAAAAATGGTGCTAT
1 AAACGCCGCAAAAAATTATTTTATTTGGAATAAAACGAACGGAATTCTATAAAAAATGGCGCTA-
*
19739808 TTTTTTAAAAGT-AAATTTTATTTTGTGGCGTTTTTTATAAAAACGCCGCTATTGCTTATAAA
65 -TTTTTAAAA-TAAAATTAT-TTTTGTGGCGTTTTTTA-AAAAACGCCGCTATTGCTTATAAA
* ** *
19739870 AAACGCCGCAAAAAATTATTTTATTTGGAATAAAACGACACTGTTTTGCTATATAAAATGGCGCT
1 AAACGCCGCAAAAAATTATTTTATTTGGAATAAAACGA-ACGGAATT-CTATAAAAAATGGCGCT
19739935 ATTTTTAAAATAAAATTATTTTTGTGGCGTTTTTTAAAAAACGCCGCTATTGCTTA
64 ATTTTTAAAATAAAATTATTTTTGTGGCGTTTTTTAAAAAACGCCGCTATTGCTTA
19739991 CCTTTTGCTA
Statistics
Matches: 107, Mismatches: 8, Indels: 11
0.85 0.06 0.09
Matches are distributed among these distances:
124 36 0.34
125 20 0.19
126 22 0.21
127 15 0.14
128 2 0.02
129 12 0.11
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.38
Consensus pattern (123 bp):
AAACGCCGCAAAAAATTATTTTATTTGGAATAAAACGAACGGAATTCTATAAAAAATGGCGCTAT
TTTTAAAATAAAATTATTTTTGTGGCGTTTTTTAAAAAACGCCGCTATTGCTTATAAA
Found at i:19741911 original size:41 final size:41
Alignment explanation
Indices: 19741854--19741967 Score: 219
Period size: 41 Copynumber: 2.8 Consensus size: 41
19741844 TTTTATTATT
19741854 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCAGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCAGAGC
*
19741895 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCCGAGC
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCAGAGC
19741936 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAA
1 ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAA
19741968 TGCCCCAAAA
Statistics
Matches: 72, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
41 72 1.00
ACGTcount: A:0.29, C:0.27, G:0.23, T:0.21
Consensus pattern (41 bp):
ATTAGCGGCGCTTTTTCAAAAACGCCGCTAAAGGCCAGAGC
Found at i:19742131 original size:40 final size:38
Alignment explanation
Indices: 19742008--19742140 Score: 126
Period size: 40 Copynumber: 3.4 Consensus size: 38
19741998 GGGCTTAGGC
*
19742008 TTTTT-GCGGCGCTTTTAAA-AAACGCCGCTAATGCTTA
1 TTTTTAGCGGCG-TTTTAAAGAAGCGCCGCTAATGCTTA
** * * *
19742045 TTTTTAGCGGCGGTTTCCAAGAAGCGCCGCTAGTTCTCGA
1 TTTTTAGCGGC-GTTTTAAAGAAGCGCCGCTAATGCT-TA
**
19742085 CCTTTAGCGGCGTTTTAATAGAAGCGCCGCTAATGCTTA
1 TTTTTAGCGGCGTTTTAA-AGAAGCGCCGCTAATGCTTA
*
19742124 TTTTTTAGTGGCGTTTT
1 -TTTTTAGCGGCGTTTT
19742141 TTGTCCAAAC
Statistics
Matches: 74, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
37 5 0.07
38 10 0.14
39 20 0.27
40 39 0.53
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (38 bp):
TTTTTAGCGGCGTTTTAAAGAAGCGCCGCTAATGCTTA
Found at i:19745692 original size:19 final size:20
Alignment explanation
Indices: 19745648--19745693 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
19745638 TATGATGTTT
*
19745648 AAATAAAATTATAAATTATG
1 AAATATAATTATAAATTATG
* *
19745668 -ATTATAATTAT-AATTTTG
1 AAATATAATTATAAATTATG
19745686 AAATATAA
1 AAATATAA
19745694 GATCTGTTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 3
0.75 0.14 0.11
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.54, C:0.00, G:0.04, T:0.41
Consensus pattern (20 bp):
AAATATAATTATAAATTATG
Found at i:19745879 original size:17 final size:18
Alignment explanation
Indices: 19745865--19745927 Score: 74
Period size: 19 Copynumber: 3.4 Consensus size: 18
19745855 ATAATCTTCG
19745865 AGGATATGCAATCTTAGA
1 AGGATATGCAATCTTAGA
*
19745883 TATGATATGCAATCTTAGA
1 -AGGATATGCAATCTTAGA
* *
19745902 TATGATATGTAATCTTAGA
1 -AGGATATGCAATCTTAGA
19745921 A-GATATG
1 AGGATATG
19745928 ATTTTGTAAT
Statistics
Matches: 42, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
17 6 0.14
18 1 0.02
19 35 0.83
ACGTcount: A:0.38, C:0.08, G:0.19, T:0.35
Consensus pattern (18 bp):
AGGATATGCAATCTTAGA
Found at i:19745891 original size:19 final size:19
Alignment explanation
Indices: 19745867--19745920 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
19745857 AATCTTCGAG
19745867 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
19745886 GATATGCAATCTTAGATAT
1 GATATGCAATCTTAGATAT
*
19745905 GATATGTAATCTTAGA
1 GATATGCAATCTTAGA
19745921 AGATATGATT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.37, C:0.09, G:0.17, T:0.37
Consensus pattern (19 bp):
GATATGCAATCTTAGATAT
Found at i:19745946 original size:22 final size:22
Alignment explanation
Indices: 19745880--19745943 Score: 80
Period size: 19 Copynumber: 3.0 Consensus size: 22
19745870 ATGCAATCTT
*
19745880 AGATATGATATGCAATCTT---
1 AGATATGATATGTAATCTTAGA
19745899 AGATATGATATGTAATCTTAGA
1 AGATATGATATGTAATCTTAGA
*
19745921 AGATATGATTTTGTAATCTTAGA
1 AGATATGA-TATGTAATCTTAGA
19745944 GATTTAATTT
Statistics
Matches: 39, Mismatches: 2, Indels: 4
0.87 0.04 0.09
Matches are distributed among these distances:
19 18 0.46
22 8 0.21
23 13 0.33
ACGTcount: A:0.38, C:0.06, G:0.17, T:0.39
Consensus pattern (22 bp):
AGATATGATATGTAATCTTAGA
Found at i:19745953 original size:22 final size:23
Alignment explanation
Indices: 19745909--19745953 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
19745899 AGATATGATA
*
19745909 TGTAATCTTAGAAGATATGATTT
1 TGTAATCTTAGAAGATATAATTT
*
19745932 TGTAATCTTAG-AGATTTAATTT
1 TGTAATCTTAGAAGATATAATTT
19745954 GTAGATACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.33, C:0.04, G:0.16, T:0.47
Consensus pattern (23 bp):
TGTAATCTTAGAAGATATAATTT
Found at i:19746143 original size:19 final size:21
Alignment explanation
Indices: 19746119--19746157 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 21
19746109 TGTTTTCTTT
*
19746119 TTTTTTTCTT-TTT-CGATTA
1 TTTTTTACTTATTTACGATTA
19746138 TTTTTTACTTATTTACGATT
1 TTTTTTACTTATTTACGATT
19746158 TTAAAAAAGG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
19 9 0.53
20 3 0.18
21 5 0.29
ACGTcount: A:0.15, C:0.10, G:0.05, T:0.69
Consensus pattern (21 bp):
TTTTTTACTTATTTACGATTA
Found at i:19747081 original size:19 final size:20
Alignment explanation
Indices: 19747035--19747081 Score: 51
Period size: 19 Copynumber: 2.4 Consensus size: 20
19747025 ACATTATTTC
* *
19747035 TATACCATTGTAATATTTAT
1 TATAGCATTGTAATATTTAA
*
19747055 TATTGCATTGT-ATATTTAA
1 TATAGCATTGTAATATTTAA
*
19747074 TGTAGCAT
1 TATAGCAT
19747082 CACATCATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 1
0.79 0.18 0.04
Matches are distributed among these distances:
19 13 0.59
20 9 0.41
ACGTcount: A:0.32, C:0.09, G:0.11, T:0.49
Consensus pattern (20 bp):
TATAGCATTGTAATATTTAA
Found at i:19752151 original size:29 final size:29
Alignment explanation
Indices: 19752119--19752208 Score: 96
Period size: 29 Copynumber: 3.1 Consensus size: 29
19752109 TTCGCCATAC
19752119 AGGCTTACCTTTCCTGAGTTTTGCCACAA
1 AGGCTTACCTTTCCTGAGTTTTGCCACAA
** * *
19752148 AGGCGTT--CTTAAACAGAG-GTTGCCACAA
1 AGGC-TTACCTT-TCCTGAGTTTTGCCACAA
*
19752176 AGGCTTACCTTTCCTGAGTTTTTCCACAA
1 AGGCTTACCTTTCCTGAGTTTTGCCACAA
19752205 AGGC
1 AGGC
19752209 ATCCTTTACA
Statistics
Matches: 47, Mismatches: 9, Indels: 10
0.71 0.14 0.15
Matches are distributed among these distances:
27 2 0.04
28 20 0.43
29 23 0.49
30 2 0.04
ACGTcount: A:0.24, C:0.26, G:0.20, T:0.30
Consensus pattern (29 bp):
AGGCTTACCTTTCCTGAGTTTTGCCACAA
Found at i:19752237 original size:31 final size:31
Alignment explanation
Indices: 19752200--19752270 Score: 97
Period size: 31 Copynumber: 2.3 Consensus size: 31
19752190 TGAGTTTTTC
*
19752200 CACAAAGGCATCCTTTACATCCAATACTCGA
1 CACAAAGGCAACCTTTACATCCAATACTCGA
* * * *
19752231 CACAAAGGCAACCTTTACATCTAGTAGTCGC
1 CACAAAGGCAACCTTTACATCCAATACTCGA
19752262 CACAAAGGC
1 CACAAAGGC
19752271 TTTCCTTTTC
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.35, C:0.31, G:0.14, T:0.20
Consensus pattern (31 bp):
CACAAAGGCAACCTTTACATCCAATACTCGA
Found at i:19752342 original size:28 final size:28
Alignment explanation
Indices: 19752310--19752369 Score: 93
Period size: 28 Copynumber: 2.1 Consensus size: 28
19752300 AACCTTTACA
*
19752310 TCCAGTACTCGCAACAAAAGCTTTCTTG
1 TCCAGTACTCCCAACAAAAGCTTTCTTG
* *
19752338 TCCAGTACTCCCCACAAAGGCTTTCTTG
1 TCCAGTACTCCCAACAAAAGCTTTCTTG
19752366 TCCA
1 TCCA
19752370 AATTTTTGCC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.25, C:0.33, G:0.13, T:0.28
Consensus pattern (28 bp):
TCCAGTACTCCCAACAAAAGCTTTCTTG
Found at i:19752421 original size:88 final size:88
Alignment explanation
Indices: 19752170--19752409 Score: 252
Period size: 91 Copynumber: 2.7 Consensus size: 88
19752160 ACAGAGGTTG
* ** * * *
19752170 CCACAAAGGCTTACCTTTCCTGAGTTTTTCCACAAAGGCATCCTTTACATCCAATACTCG-ACAC
1 CCACAAAGGCTTTCCTTTCCAAAGTTTTACCACAAAGGCAACCTTTACATCCAGTACTCGCA-AC
* *** * *
19752234 AAAGGCAACCTT-TACATCTAGTAGTCG
65 AAAAGCTTTCTTGT-C--C-AGTACTCC
*
19752261 CCACAAAGGCTTTCCTTTTCAAAGTTTTACCACAAAGGCAACCTTTACATCCAGTACTCGCAACA
1 CCACAAAGGCTTTCCTTTCCAAAGTTTTACCACAAAGGCAACCTTTACATCCAGTACTCGCAACA
19752326 AAAGCTTTCTTGTCCAGTACTCC
66 AAAGCTTTCTTGTCCAGTACTCC
* * * *
19752349 CCACAAAGGCTTT-CTTGTCCAAATTTTTGCCATAAAGGCATCCTTTACATCCAGTACTCGC
1 CCACAAAGGCTTTCCTT-TCCAAAGTTTTACCACAAAGGCAACCTTTACATCCAGTACTCGC
19752410 CACACAGGCT
Statistics
Matches: 128, Mismatches: 18, Indels: 9
0.83 0.12 0.06
Matches are distributed among these distances:
87 3 0.02
88 58 0.45
89 1 0.01
91 64 0.50
92 2 0.02
ACGTcount: A:0.29, C:0.30, G:0.12, T:0.29
Consensus pattern (88 bp):
CCACAAAGGCTTTCCTTTCCAAAGTTTTACCACAAAGGCAACCTTTACATCCAGTACTCGCAACA
AAAGCTTTCTTGTCCAGTACTCC
Found at i:19754284 original size:38 final size:38
Alignment explanation
Indices: 19754241--19754337 Score: 131
Period size: 38 Copynumber: 2.6 Consensus size: 38
19754231 GATACGCGGG
* *
19754241 AAATGCTCACATGAGTTGTGACTTTATCATGTAACCGT
1 AAATGCTCACACGAGTTGTGACTATATCATGTAACCGT
* * *
19754279 AAATGCTTACACAATTTGTGACTATATCATGTAACCGT
1 AAATGCTCACACGAGTTGTGACTATATCATGTAACCGT
* *
19754317 CAATGCTCACACGAGCTGTGA
1 AAATGCTCACACGAGTTGTGA
19754338 AATGGGTCTG
Statistics
Matches: 49, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
38 49 1.00
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (38 bp):
AAATGCTCACACGAGTTGTGACTATATCATGTAACCGT
Found at i:19775573 original size:16 final size:18
Alignment explanation
Indices: 19775554--19775588 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
19775544 TTTTGATGGC
19775554 TTTCTTTTT-TTTT-CTT
1 TTTCTTTTTCTTTTACTT
19775570 TTTCTTTTTCTTTTACTT
1 TTTCTTTTTCTTTTACTT
19775588 T
1 T
19775589 ATAAAACATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 9 0.53
17 4 0.24
18 4 0.24
ACGTcount: A:0.03, C:0.14, G:0.00, T:0.83
Consensus pattern (18 bp):
TTTCTTTTTCTTTTACTT
Done.