Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr05 97880472
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: 97880472
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 192 characters in sequence are not A, C, G, or T
File 97 of 335
Found at i:31044757 original size:3 final size:3
Alignment explanation
Indices: 31044749--31044821 Score: 146
Period size: 3 Copynumber: 24.3 Consensus size: 3
31044739 TTCTCGCCCA
31044749 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
31044797 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
31044822 TACTTTGTTT
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 70 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:31050283 original size:3 final size:3
Alignment explanation
Indices: 31050268--31050365 Score: 187
Period size: 3 Copynumber: 32.7 Consensus size: 3
31050258 CCACAACTCG
*
31050268 TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
31050316 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
31050364 TT
1 TT
31050366 TACTTTGTTT
Statistics
Matches: 93, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
3 93 1.00
ACGTcount: A:0.33, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:31054050 original size:6 final size:6
Alignment explanation
Indices: 31054041--31054067 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
31054031 GATTTCAATT
31054041 TTTAGA TTTAGA TTTAGA TTTAGA TTT
1 TTTAGA TTTAGA TTTAGA TTTAGA TTT
31054068 TTTTTTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.15, T:0.56
Consensus pattern (6 bp):
TTTAGA
Found at i:31054131 original size:19 final size:19
Alignment explanation
Indices: 31054109--31054170 Score: 58
Period size: 18 Copynumber: 3.3 Consensus size: 19
31054099 TTTAGAAAAT
31054109 TTTTAAATATTTTCATTAA
1 TTTTAAATATTTTCATTAA
* *
31054128 TTTTAAAT-TTATTTA-TAT
1 TTTTAAATATT-TTCATTAA
31054146 TTTTAAA-ATTTTCATAATAA
1 TTTTAAATATTTTCAT--TAA
31054166 TTTTA
1 TTTTA
31054171 GGTGATGATA
Statistics
Matches: 34, Mismatches: 4, Indels: 9
0.72 0.09 0.19
Matches are distributed among these distances:
17 3 0.09
18 13 0.38
19 11 0.32
20 7 0.21
ACGTcount: A:0.37, C:0.03, G:0.00, T:0.60
Consensus pattern (19 bp):
TTTTAAATATTTTCATTAA
Found at i:31054132 original size:38 final size:38
Alignment explanation
Indices: 31054084--31054171 Score: 92
Period size: 38 Copynumber: 2.3 Consensus size: 38
31054074 TAAAAAAACT
*
31054084 ATATATTTTTAGAATTT-TAGAAAATTTTTAAATATTTTC
1 ATATAATTTTAGAATTTAT-GAAAATTTTTAAA-ATTTTC
** *
31054123 AT-TAATTTTA-AATTTATTTATATTTTTAAAATTTTC
1 ATATAATTTTAGAATTTATGAAAATTTTTAAAATTTTC
31054159 ATAATAATTTTAG
1 AT-ATAATTTTAG
31054172 GTGATGATAT
Statistics
Matches: 41, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
36 8 0.20
37 15 0.37
38 16 0.39
39 2 0.05
ACGTcount: A:0.39, C:0.02, G:0.03, T:0.56
Consensus pattern (38 bp):
ATATAATTTTAGAATTTATGAAAATTTTTAAAATTTTC
Found at i:31058381 original size:26 final size:26
Alignment explanation
Indices: 31058346--31058397 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
31058336 CGATGAATAT
31058346 TTTAGATTAGGTCCGGAATTCAAACA
1 TTTAGATTAGGTCCGGAATTCAAACA
31058372 TTTAGATTAGGTCCGGAATTCAAACA
1 TTTAGATTAGGTCCGGAATTCAAACA
31058398 CCTTTCATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.35, C:0.15, G:0.19, T:0.31
Consensus pattern (26 bp):
TTTAGATTAGGTCCGGAATTCAAACA
Found at i:31063224 original size:28 final size:30
Alignment explanation
Indices: 31063185--31063242 Score: 77
Period size: 28 Copynumber: 2.0 Consensus size: 30
31063175 GTGGAATAAA
31063185 AAAATATATTATAAA-TATAT-TAAAAATT
1 AAAATATATTATAAATTATATATAAAAATT
*
31063213 AAAATGAT-TTATAAATTATATATAATAATT
1 AAAAT-ATATTATAAATTATATATAAAAATT
31063243 TATTTGAAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
28 12 0.46
29 7 0.27
30 7 0.27
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (30 bp):
AAAATATATTATAAATTATATATAAAAATT
Found at i:31069618 original size:44 final size:45
Alignment explanation
Indices: 31069554--31070147 Score: 298
Period size: 45 Copynumber: 12.9 Consensus size: 45
31069544 AATATGCTCC
* * *
31069554 ACTTCAGTCTACTCCACTGCAACTTCAGGAAGATAAGACTTG-TA
1 ACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTA
* * * *
31069598 GCTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTCTGTAATTTCTA
1 ACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA-----G-ACTTGCTA
* * * * * *
31069649 GCTTCAATCTACTCCACTGTAACTCCAAGGAGATAATA-TTCGCTA
1 ACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GCTA
* * *
31069694 TCTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTTG-TA
1 ACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTA
* ** *
31069738 ACTTCAACCTGCTCCACTGCAACTTCAGGGAGATAAGGTTTGTGATTTCCA
1 ACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA-GACT-TG----CTA
31069789 ACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTCGCTA
1 ACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GCTA
* * * * * *
31069834 TCTTCAGTCTACTCCACTGCAACTTTAGGAAGATAAAAC-T--T-
1 ACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTA
* ** * * * **
31069875 ATTTTGATCTGCTCTATTGCAACTTCAGAGAGATAAGATCTGTAATTTA
1 ACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-T--GCTA
* * * *
31069924 TATCCTT-AATCTGTTCAATTGCAACTTCA-GGACGATAAGATTTGCTA
1 -A--CTTCAATCTGCTCCACTGCAACTTCAGGGA-GATAAGACTTGCTA
* * ** * *
31069971 TCTTTAGCCTGCTCCATTGCAACTTCAAGGAGATAAGACTTG-T-
1 ACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTA
** * * * **
31070014 --TTTGATCTGCTCTACTGCAACTTTAGAGAGATAAGATCTGTAATTTA
1 ACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-T--GCTA
* * * * *
31070061 TAGCTTCAATCTGTTCTACTACAACTTCAGGGAAATAAGATTTGCTA
1 -A-CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTA
* ** *
31070108 TCTTCAGCCTGTTCCACTGCAACTTCAGGGAGATAAGACT
1 ACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACT
31070148 GTGAATTTAC
Statistics
Matches: 418, Mismatches: 90, Indels: 83
0.71 0.15 0.14
Matches are distributed among these distances:
41 54 0.13
42 4 0.01
43 1 0.00
44 72 0.17
45 133 0.32
46 8 0.02
47 4 0.01
48 2 0.00
49 5 0.01
50 9 0.02
51 124 0.30
52 2 0.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.32
Consensus pattern (45 bp):
ACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTA
Found at i:31069724 original size:96 final size:95
Alignment explanation
Indices: 31069555--31069730 Score: 239
Period size: 96 Copynumber: 1.8 Consensus size: 95
31069545 ATATGCTCCA
* *
31069555 CTTCAGTCTACTCCACTGCAACTTCAGGAAGATAAGACTTGTAGCTTCAACCTGCTCCACTGCAA
1 CTTCAATCTACTCCACTGCAACTCCAGGAAGATAAGACTTGTAGCTTCAACCTGCTCCACTGCAA
31069620 CTTCAGGGAGATAAGGTCTGTAATTTCTAG
66 CTTCAGGGAGATAAGGTCTGTAATTTCTAG
* * * **
31069650 CTTCAATCTACTCCACTGTAACTCCAAGG-AGATAATA-TTCGCTATCTTCAGTCTGCTCCACTG
1 CTTCAATCTACTCCACTGCAACTCC-AGGAAGATAAGACTT-G-TAGCTTCAACCTGCTCCACTG
*
31069713 CAACTTTAGGGAGATAAG
63 CAACTTCAGGGAGATAAG
31069731 ACTTGTAACT
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
94 2 0.03
95 30 0.43
96 38 0.54
ACGTcount: A:0.28, C:0.26, G:0.18, T:0.29
Consensus pattern (95 bp):
CTTCAATCTACTCCACTGCAACTCCAGGAAGATAAGACTTGTAGCTTCAACCTGCTCCACTGCAA
CTTCAGGGAGATAAGGTCTGTAATTTCTAG
Found at i:31069819 original size:95 final size:96
Alignment explanation
Indices: 31069695--31069869 Score: 255
Period size: 95 Copynumber: 1.8 Consensus size: 96
31069685 TATTCGCTAT
* * *
31069695 CTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTT-G-TAACTTCAACCTGCTCCACTGC
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTCGCTAACTTCAACCTACTCCACTGC
*
31069758 AACTTCAGGGAGATAAGGTTTGTGATTTCCAA
65 AACTTCAGGAAGATAAGGTTTGTGATTTCCAA
* **
31069790 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTATCTTCAGTCTACTCCACTGCA
1 CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTAACTTCAACCTACTCCACTGCA
*
31069855 ACTTTAGGAAGATAA
66 ACTTCAGGAAGATAA
31069870 AACTTATTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 3
0.86 0.10 0.04
Matches are distributed among these distances:
94 2 0.03
95 36 0.51
96 32 0.46
ACGTcount: A:0.27, C:0.25, G:0.18, T:0.29
Consensus pattern (96 bp):
CTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGATTCGCTAACTTCAACCTACTCCACTGCA
ACTTCAGGAAGATAAGGTTTGTGATTTCCAA
Found at i:31069963 original size:137 final size:139
Alignment explanation
Indices: 31069555--31070147 Score: 660
Period size: 137 Copynumber: 4.3 Consensus size: 139
31069545 ATATGCTCCA
*
31069555 CTTCAGTCTACTCCACTGCAACTTCAGGAAGATAAGACTTGTAGCTTCAACCTGCTCCACTGCAA
1 CTTCAGTCTGCTCCACTGCAACTTCAGGAAGATAAGACTTGTA-CTTCAACCTGCTCCACTGCAA
* * * * * * *
31069620 CTTCAGGGAGATAAGGTCTGTAATTTCTAGCTTCAATCTACTCCACTGTAACTCCAAGGAGATAA
65 CTTCAGAGAGATAAGATCTGTAATTTATAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA
*
31069685 TATTCGCTAT
130 GATTCGCTAT
* *
31069695 CTTCAGTCTGCTCCACTGCAACTTTAGGGAGATAAGACTTGTAACTTCAACCTGCTCCACTGCAA
1 CTTCAGTCTGCTCCACTGCAACTTCAGGAAGATAAGACTTGT-ACTTCAACCTGCTCCACTGCAA
* * * * ** *
31069760 CTTCAGGGAGATAAGGTTTGTGATTTCCAACTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA
65 CTTCAGAGAGATAAGATCTGTAATTTATAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA
31069825 GATTCGCTAT
130 GATTCGCTAT
* * * * ** * * *
31069835 CTTCAGTCTACTCCACTGCAACTTTAGGAAGATAAAAC-T-TATTTTGATCTGCTCTATTGCAAC
1 CTTCAGTCTGCTCCACTGCAACTTCAGGAAGATAAGACTTGTACTTCAACCTGCTCCACTGCAAC
* * * *
31069898 TTCAGAGAGATAAGATCTGTAATTTATATCCTT-AATCTGTTCAATTGCAACTTCA-GGACGATA
66 TTCAGAGAGATAAGATCTGTAATTTATA-GCTTCAATCTGCTCCACTGCAACTTCAGGGA-GATA
*
31069961 AGATTTGCTAT
129 AGATTCGCTAT
* * * ** * *
31069972 CTTTAGCCTGCTCCATTGCAACTTCAAGG-AGATAAGACTTGT--TTTGATCTGCTCTACTGCAA
1 CTTCAGTCTGCTCCACTGCAACTTC-AGGAAGATAAGACTTGTACTTCAACCTGCTCCACTGCAA
* * * * *
31070034 CTTTAGAGAGATAAGATCTGTAATTTATAGCTTCAATCTGTTCTACTACAACTTCAGGGAAATAA
65 CTTCAGAGAGATAAGATCTGTAATTTATAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAA
*
31070099 GATTTGCTAT
130 GATTCGCTAT
* * *
31070109 CTTCAGCCTGTTCCACTGCAACTTCAGGGAGATAAGACT
1 CTTCAGTCTGCTCCACTGCAACTTCAGGAAGATAAGACT
31070148 GTGAATTTAC
Statistics
Matches: 396, Mismatches: 48, Indels: 21
0.85 0.10 0.05
Matches are distributed among these distances:
136 9 0.02
137 212 0.54
138 11 0.03
139 2 0.01
140 161 0.41
141 1 0.00
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Consensus pattern (139 bp):
CTTCAGTCTGCTCCACTGCAACTTCAGGAAGATAAGACTTGTACTTCAACCTGCTCCACTGCAAC
TTCAGAGAGATAAGATCTGTAATTTATAGCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAG
ATTCGCTAT
Found at i:31077806 original size:19 final size:20
Alignment explanation
Indices: 31077773--31077816 Score: 54
Period size: 19 Copynumber: 2.2 Consensus size: 20
31077763 GGGCCTTTTC
* * *
31077773 ATGAAATTTAGTGCATATG-
1 ATGAAATGTAATGCAAATGA
31077792 ATGAAATGTAATGCAAATGA
1 ATGAAATGTAATGCAAATGA
31077812 ATGAA
1 ATGAA
31077817 TGCAAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
19 16 0.76
20 5 0.24
ACGTcount: A:0.45, C:0.05, G:0.20, T:0.30
Consensus pattern (20 bp):
ATGAAATGTAATGCAAATGA
Found at i:31081950 original size:18 final size:19
Alignment explanation
Indices: 31081929--31081964 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
31081919 AATTAATGAT
31081929 AATAGTAATGATA-ATATC
1 AATAGTAATGATATATATC
*
31081947 AATAGTGATGATATATAT
1 AATAGTAATGATATATAT
31081965 ATAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 12 0.75
19 4 0.25
ACGTcount: A:0.47, C:0.03, G:0.14, T:0.36
Consensus pattern (19 bp):
AATAGTAATGATATATATC
Found at i:31082007 original size:21 final size:22
Alignment explanation
Indices: 31081977--31082017 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
31081967 AATAATAAAA
* *
31081977 TAAAATAAAATAAATGTGTTTT
1 TAAAATAAAAGAAATATGTTTT
31081999 TAAAA-AAAAGAAATATGTT
1 TAAAATAAAAGAAATATGTT
31082018 AACTCGTTTA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 12 0.71
22 5 0.29
ACGTcount: A:0.56, C:0.00, G:0.10, T:0.34
Consensus pattern (22 bp):
TAAAATAAAAGAAATATGTTTT
Found at i:31083336 original size:19 final size:20
Alignment explanation
Indices: 31083312--31083351 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
31083302 TTGCTACTGT
31083312 TTTGC-TTCGTTTCTGCTTC
1 TTTGCTTTCGTTTCTGCTTC
* *
31083331 TTTGCTTTCTTTTCTGTTTC
1 TTTGCTTTCGTTTCTGCTTC
31083351 T
1 T
31083352 ATTTTGTAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 5 0.28
20 13 0.72
ACGTcount: A:0.00, C:0.23, G:0.12, T:0.65
Consensus pattern (20 bp):
TTTGCTTTCGTTTCTGCTTC
Found at i:31088157 original size:20 final size:20
Alignment explanation
Indices: 31088134--31088172 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
31088124 ATATATATAT
31088134 ATATTAT-ATTATATAATTGA
1 ATATTATAATTAT-TAATTGA
31088154 ATATTATAATTATTAATTG
1 ATATTATAATTATTAATTG
31088173 TTATGGTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.44, C:0.00, G:0.05, T:0.51
Consensus pattern (20 bp):
ATATTATAATTATTAATTGA
Found at i:31089775 original size:45 final size:45
Alignment explanation
Indices: 31089725--31089819 Score: 158
Period size: 45 Copynumber: 2.1 Consensus size: 45
31089715 CGACTACTGT
31089725 TACTGTTATCGTTACTGTTATCA-ATTC-GACACTTTGTGTGTTGAA
1 TACTGTTATCGTTACTGTTA-CAGATTCAG-CACTTTGTGTGTTGAA
31089770 TACTGTTATCGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAA
1 TACTGTTATCGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAA
31089815 TACTG
1 TACTG
31089820 CTACTGTTAC
Statistics
Matches: 48, Mismatches: 0, Indels: 4
0.92 0.00 0.08
Matches are distributed among these distances:
44 2 0.04
45 45 0.94
46 1 0.02
ACGTcount: A:0.22, C:0.16, G:0.19, T:0.43
Consensus pattern (45 bp):
TACTGTTATCGTTACTGTTACAGATTCAGCACTTTGTGTGTTGAA
Found at i:31089829 original size:45 final size:45
Alignment explanation
Indices: 31089725--31089831 Score: 148
Period size: 45 Copynumber: 2.4 Consensus size: 45
31089715 CGACTACTGT
*
31089725 TACTGTTATCGTTACTGTTATCAATTCGACACTTTGTGTGTTGAA
1 TACTGCTATCGTTACTGTTATCAATTCGACACTTTGTGTGTTGAA
*
31089770 TACTGTTATCGTTACTGTTA-CAGATTC-AGCACTTTGTGTGTTGAA
1 TACTGCTATCGTTACTGTTATCA-ATTCGA-CACTTTGTGTGTTGAA
31089815 TACTGCTA-CTGTTACTG
1 TACTGCTATC-GTTACTG
31089832 CTACTGTTAC
Statistics
Matches: 58, Mismatches: 1, Indels: 6
0.89 0.02 0.09
Matches are distributed among these distances:
44 4 0.07
45 54 0.93
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.43
Consensus pattern (45 bp):
TACTGCTATCGTTACTGTTATCAATTCGACACTTTGTGTGTTGAA
Found at i:31089832 original size:12 final size:12
Alignment explanation
Indices: 31089815--31089847 Score: 66
Period size: 12 Copynumber: 2.8 Consensus size: 12
31089805 GTGTGTTGAA
31089815 TACTGCTACTGT
1 TACTGCTACTGT
31089827 TACTGCTACTGT
1 TACTGCTACTGT
31089839 TACTGCTAC
1 TACTGCTAC
31089848 CGTTTCTGAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.18, C:0.27, G:0.15, T:0.39
Consensus pattern (12 bp):
TACTGCTACTGT
Found at i:31089862 original size:24 final size:24
Alignment explanation
Indices: 31089815--31089863 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
31089805 GTGTGTTGAA
* *
31089815 TACTGCTACTGTTACTGCTACTGT
1 TACTGCTACCGTTACTGATACTGT
* *
31089839 TACTGCTACCGTTTCTGATTCTGT
1 TACTGCTACCGTTACTGATACTGT
31089863 T
1 T
31089864 TAGGTATTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.14, C:0.24, G:0.16, T:0.45
Consensus pattern (24 bp):
TACTGCTACCGTTACTGATACTGT
Found at i:31107493 original size:9 final size:9
Alignment explanation
Indices: 31107471--31107516 Score: 58
Period size: 9 Copynumber: 5.2 Consensus size: 9
31107461 AATTAAATTT
31107471 TTAAAAAT-
1 TTAAAAATA
*
31107479 TAAAAAATA
1 TTAAAAATA
*
31107488 TTAAAAAAA
1 TTAAAAATA
*
31107497 TTAAAAACA
1 TTAAAAATA
31107506 TTAAAAATA
1 TTAAAAATA
31107515 TT
1 TT
31107517 TTTTAATATT
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
8 7 0.22
9 25 0.78
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (9 bp):
TTAAAAATA
Found at i:31107552 original size:28 final size:29
Alignment explanation
Indices: 31107459--31107554 Score: 85
Period size: 28 Copynumber: 3.4 Consensus size: 29
31107449 ACATAATCAT
* *
31107459 TTAATTAAATTTTTAAAAATTAAAAAATA
1 TTAATTAAATATTTAAAAATTTAAAAATA
* *
31107488 TTAA--AAA-AATTAAAAACATTAAAAATA
1 TTAATTAAATATTTAAAAA-TTTAAAAATA
* * *
31107515 TT-TTTTAATATTTAAAATTTTAAAAA-A
1 TTAATTAAATATTTAAAAATTTAAAAATA
31107542 TTAATTAAATATT
1 TTAATTAAATATT
31107555 GACATGTCAT
Statistics
Matches: 51, Mismatches: 11, Indels: 11
0.70 0.15 0.15
Matches are distributed among these distances:
26 7 0.14
27 16 0.31
28 17 0.33
29 11 0.22
ACGTcount: A:0.57, C:0.01, G:0.00, T:0.42
Consensus pattern (29 bp):
TTAATTAAATATTTAAAAATTTAAAAATA
Found at i:31108116 original size:22 final size:20
Alignment explanation
Indices: 31108079--31108118 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
31108069 TTAAAATATT
*
31108079 TTTTTATTCATTAAACTTAA
1 TTTTTATTCATAAAACTTAA
31108099 TTTTTATTCTATCAAAACTT
1 TTTTTATTC-AT-AAAACTT
31108119 GTAAGAGTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 9 0.53
21 2 0.12
22 6 0.35
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTTATTCATAAAACTTAA
Found at i:31110046 original size:21 final size:21
Alignment explanation
Indices: 31110020--31110066 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
31110010 TGTTGGTAGC
* * *
31110020 GAGATTAGTTATTGTAGTTGT
1 GAGATTAGATACTGTAATTGT
31110041 GAGATTAGATACTGTAATTGT
1 GAGATTAGATACTGTAATTGT
31110062 GAGAT
1 GAGAT
31110067 CAAAGTCATT
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.02, G:0.28, T:0.40
Consensus pattern (21 bp):
GAGATTAGATACTGTAATTGT
Found at i:31131146 original size:10 final size:10
Alignment explanation
Indices: 31131131--31131181 Score: 57
Period size: 10 Copynumber: 5.0 Consensus size: 10
31131121 TAATTTTAGG
31131131 ATTTATTTTT
1 ATTTATTTTT
*
31131141 ATTTATCTTT
1 ATTTATTTTT
*
31131151 ATTTATCTTT
1 ATTTATTTTT
* *
31131161 AATTATTTGT
1 ATTTATTTTT
31131171 ATTTATCTTTT
1 ATTTAT-TTTT
31131182 GAAATTTAAG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
10 31 0.91
11 3 0.09
ACGTcount: A:0.22, C:0.06, G:0.02, T:0.71
Consensus pattern (10 bp):
ATTTATTTTT
Found at i:31131156 original size:20 final size:20
Alignment explanation
Indices: 31131131--31131180 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
31131121 TAATTTTAGG
* * *
31131131 ATTTATTTTTATTTATCTTT
1 ATTTATCTTTAATTATCTGT
*
31131151 ATTTATCTTTAATTATTTGT
1 ATTTATCTTTAATTATCTGT
31131171 ATTTATCTTT
1 ATTTATCTTT
31131181 TGAAATTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.22, C:0.06, G:0.02, T:0.70
Consensus pattern (20 bp):
ATTTATCTTTAATTATCTGT
Found at i:31132560 original size:15 final size:16
Alignment explanation
Indices: 31132542--31132572 Score: 55
Period size: 15 Copynumber: 2.0 Consensus size: 16
31132532 TTAGTGTTCC
31132542 CTCCAAAGTTT-AAAA
1 CTCCAAAGTTTGAAAA
31132557 CTCCAAAGTTTGAAAA
1 CTCCAAAGTTTGAAAA
31132573 GTATAATGGG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.73
16 4 0.27
ACGTcount: A:0.45, C:0.19, G:0.10, T:0.26
Consensus pattern (16 bp):
CTCCAAAGTTTGAAAA
Found at i:31137872 original size:24 final size:24
Alignment explanation
Indices: 31137839--31137888 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
31137829 AAGTCTGTCT
31137839 GGAGAAGATTTAGGAGCTGATAAG
1 GGAGAAGATTTAGGAGCTGATAAG
* *
31137863 GGAGAGGATTTAGGAGCTGATTAG
1 GGAGAAGATTTAGGAGCTGATAAG
31137887 GG
1 GG
31137889 TGACCTGTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.32, C:0.04, G:0.42, T:0.22
Consensus pattern (24 bp):
GGAGAAGATTTAGGAGCTGATAAG
Found at i:31139367 original size:27 final size:26
Alignment explanation
Indices: 31139328--31139429 Score: 114
Period size: 27 Copynumber: 3.8 Consensus size: 26
31139318 CTAGTGTCTA
31139328 TGCCACAATTATCTGATCTGGTGGCTC
1 TGCCAC-ATTATCTGATCTGGTGGCTC
* * *
31139355 TGCCACATATATCTGTTCTGGTGGTTT
1 TGCCACAT-TATCTGATCTGGTGGCTC
*
31139382 TGCCACGATTATCTGTATCTGGTGACTC
1 TGCCAC-ATTATCTG-ATCTGGTGGCTC
* *
31139410 TGTCACATTATCTGTTCTGG
1 TGCCACATTATCTGATCTGG
31139430 CAGCCATGCT
Statistics
Matches: 63, Mismatches: 9, Indels: 7
0.80 0.11 0.09
Matches are distributed among these distances:
26 7 0.11
27 41 0.65
28 15 0.24
ACGTcount: A:0.17, C:0.23, G:0.22, T:0.39
Consensus pattern (26 bp):
TGCCACATTATCTGATCTGGTGGCTC
Found at i:31142007 original size:45 final size:44
Alignment explanation
Indices: 31141715--31142280 Score: 352
Period size: 44 Copynumber: 12.5 Consensus size: 44
31141705 GATAATGGCG
* * *
31141715 AATCTCATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGATAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATA-CA
* * * * * * *
31141760 AATCTTATCTCTCTGAAATTACAATAGAGCAGATTAAAGCTATA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACA
* * * * *
31141804 AATCTTATCTCCCTGAAGTTGTAAG-GGGGCAGGTTGAAGTTACA
1 AATCTTATCTCCCTGAAGTTG-CAGTGGAGCAGATTAAAGATACA
* * * * *
31141848 AGTCTTATCTCCCTAAAGTTGAAGTGGAGCAGACTAAAGATAGCG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATA-CA
* * * * *
31141893 AGTTTTATTTCCCTGAAATTGCAGTGGAAC-GATTAAAGCTACAAATTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG------A-TACA
* * * *
31141943 AATCTAATCTCCCTGAAGTTGCAGTCGAGTAGATTGAAGATAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATA-CA
* * * * * * *
31141988 AATCTTATCTCTCTAAAGTTGCATTAGAGTAGATTAAAGCTATA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACA
* * * * * *
31142032 AACCTTATCTCTCTTAAGTTGCAGTGGGGCAGGTTAAAGTTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACA
* * *
31142076 AGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAA-ATAACG
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGA-TTAAAGAT-ACA
* * * *
31142121 AATCTTATTTCCCCGAAGTTGCAGTGGAACAAATTAAAGCTATAAATTACA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAG------A-TACA
* * * * * *
31142172 AATCTTATCTCTCTGAAATTGCAGTAGAGTAGATTAAAGCTATA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACA
* * * * **
31142216 AATCTTATCTCCATGAAGTCGCAAGTGGAGCAGATTGAAGTTATT
1 AATCTTATCTCCCTGAAGTTGC-AGTGGAGCAGATTAAAGATACA
31142261 AA---TATCTCCCTGAAGTTGCA
1 AATCTTATCTCCCTGAAGTTGCA
31142281 ATAGAGTAGA
Statistics
Matches: 398, Mismatches: 100, Indels: 50
0.73 0.18 0.09
Matches are distributed among these distances:
41 1 0.00
42 15 0.04
43 3 0.01
44 161 0.40
45 150 0.38
50 24 0.06
51 43 0.11
52 1 0.00
ACGTcount: A:0.34, C:0.17, G:0.20, T:0.30
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGATACA
Found at i:31142074 original size:228 final size:229
Alignment explanation
Indices: 31141715--31142226 Score: 728
Period size: 228 Copynumber: 2.2 Consensus size: 229
31141705 GATAATGGCG
* *
31141715 AATCTCATCTCCCTGAAGTTGCAGTGGAGTAGATTGAAGATAGCAAATCTTATCTCTCTGAAATT
1 AATCTAATCTCCCTGAAGTTGCAGTAGAGTAGATTGAAGATAGCAAATCTTATCTCTCTGAAATT
* *
31141780 ACAATAGAGCAGATTAAAGCTATAAATCTTATCTCCCTGAAGTTGTAAGGGGGCAGGTTGAAGTT
66 ACAATAGAGCAGATTAAAGCTATAAACCTTATCTCCCTGAAGTTGTAAGGGGGCAGGTTAAAGTT
* * * *
31141845 ACAAGTCTTATCTCCCTAAAGTTGAAGTGGAGCAGACT-AAAGATAGCGAGTTTTATTTCCCTGA
131 ACAAGTCTTATCTCCCTAAAGTTGAAGTGGAGCAGACTGAAA-ATAACGAATCTTATTTCCCCGA
*
31141909 AATTGCAGTGGAAC-GATTAAAGCTACAAATTACA
195 AATTGCAGTGGAACAAATTAAAGCTACAAATTACA
*
31141943 AATCTAATCTCCCTGAAGTTGCAGTCGAGTAGATTGAAGATAGCAAATCTTATCTCTCT-AAAGT
1 AATCTAATCTCCCTGAAGTTGCAGTAGAGTAGATTGAAGATAGCAAATCTTATCTCTCTGAAA-T
* * * * * *
31142007 TGCATTAGAGTAGATTAAAGCTATAAACCTTATCTCTCTTAAGTTG-CAGTGGGGCAGGTTAAAG
65 TACAATAGAGCAGATTAAAGCTATAAACCTTATCTCCCTGAAGTTGTAAG-GGGGCAGGTTAAAG
* *
31142071 TTACAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAAATAACGAATCTTATTTCCCCG
129 TTACAAGTCTTATCTCCCTAAAGTTGAAGTGGAGCAGACTGAAAATAACGAATCTTATTTCCCCG
* *
31142136 AAGTTGCAGTGGAACAAATTAAAGCTATAAATTACA
194 AAATTGCAGTGGAACAAATTAAAGCTACAAATTACA
* * * * * *
31142172 AATCTTATCTCTCTGAAATTGCAGTAGAGTAGATTAAAGCTA-TAAATCTTATCTC
1 AATCTAATCTCCCTGAAGTTGCAGTAGAGTAGATTGAAGATAGCAAATCTTATCTC
31142227 CATGAAGTCG
Statistics
Matches: 254, Mismatches: 26, Indels: 8
0.88 0.09 0.03
Matches are distributed among these distances:
227 5 0.02
228 192 0.76
229 57 0.22
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (229 bp):
AATCTAATCTCCCTGAAGTTGCAGTAGAGTAGATTGAAGATAGCAAATCTTATCTCTCTGAAATT
ACAATAGAGCAGATTAAAGCTATAAACCTTATCTCCCTGAAGTTGTAAGGGGGCAGGTTAAAGTT
ACAAGTCTTATCTCCCTAAAGTTGAAGTGGAGCAGACTGAAAATAACGAATCTTATTTCCCCGAA
ATTGCAGTGGAACAAATTAAAGCTACAAATTACA
Found at i:31143190 original size:20 final size:20
Alignment explanation
Indices: 31143162--31143199 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
31143152 CGGTGGCGCC
*
31143162 GTCATCGGCGACCGACGGCT
1 GTCACCGGCGACCGACGGCT
*
31143182 GTCACCGGCGATCGACGG
1 GTCACCGGCGACCGACGG
31143200 TAGCCACGGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.16, C:0.34, G:0.37, T:0.13
Consensus pattern (20 bp):
GTCACCGGCGACCGACGGCT
Found at i:31143840 original size:14 final size:14
Alignment explanation
Indices: 31143823--31143854 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
31143813 CTACTGCGCA
31143823 TTTTATTCTTATTT
1 TTTTATTCTTATTT
*
31143837 TTTTATTTTTATTT
1 TTTTATTCTTATTT
31143851 TTTT
1 TTTT
31143855 CTATTAATAT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.12, C:0.03, G:0.00, T:0.84
Consensus pattern (14 bp):
TTTTATTCTTATTT
Found at i:31143987 original size:14 final size:15
Alignment explanation
Indices: 31143961--31144001 Score: 66
Period size: 14 Copynumber: 2.8 Consensus size: 15
31143951 CTTGCACATT
*
31143961 TTATTAGTATTACCA
1 TTATTATTATTACCA
31143976 TT-TTATTATTACCA
1 TTATTATTATTACCA
31143990 TTATTATTATTA
1 TTATTATTATTA
31144002 TTGTTTAATT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
14 13 0.54
15 11 0.46
ACGTcount: A:0.32, C:0.10, G:0.02, T:0.56
Consensus pattern (15 bp):
TTATTATTATTACCA
Found at i:31144082 original size:17 final size:17
Alignment explanation
Indices: 31144060--31144092 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
31144050 TTATTTGGTG
31144060 TTTTATTATTATTATAA
1 TTTTATTATTATTATAA
31144077 TTTTATTATTATTATA
1 TTTTATTATTATTATA
31144093 TCATTCCTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTATTATTATTATAA
Found at i:31145804 original size:15 final size:14
Alignment explanation
Indices: 31145784--31145821 Score: 60
Period size: 15 Copynumber: 2.7 Consensus size: 14
31145774 AGCAAACGTG
31145784 AGAAAGAAAGAAGAA
1 AGAAAGAAAGAA-AA
31145799 AGAAAGAAAGAAAA
1 AGAAAGAAAGAAAA
31145813 AGAAA-AAAG
1 AGAAAGAAAG
31145822 GGAAATTTGA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 4 0.17
14 7 0.30
15 12 0.52
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (14 bp):
AGAAAGAAAGAAAA
Found at i:31153030 original size:4 final size:4
Alignment explanation
Indices: 31153021--31153053 Score: 66
Period size: 4 Copynumber: 8.2 Consensus size: 4
31153011 AGCAAACGTG
31153021 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA A
31153054 AAGGGAAATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 29 1.00
ACGTcount: A:0.76, C:0.00, G:0.24, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:31159257 original size:20 final size:20
Alignment explanation
Indices: 31159215--31159261 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
31159205 AAAATTACAA
* *
31159215 AAAAAATTCAATATAATTTT
1 AAAAAATTCAAAATAATTAT
31159235 AAAAAATTCAAAAT-ATTCAT
1 AAAAAATTCAAAATAATT-AT
31159255 AAAAAAT
1 AAAAAAT
31159262 CTAAAATTTA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 3 0.12
20 21 0.88
ACGTcount: A:0.62, C:0.06, G:0.00, T:0.32
Consensus pattern (20 bp):
AAAAAATTCAAAATAATTAT
Found at i:31160305 original size:17 final size:18
Alignment explanation
Indices: 31160272--31160306 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
31160262 GATTTGCATG
31160272 AAATATTTAAGAATAAAA
1 AAATATTTAAGAATAAAA
31160290 AAATATTTAA-AATAAAA
1 AAATATTTAAGAATAAAA
31160307 TTTTATATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.41
18 10 0.59
ACGTcount: A:0.69, C:0.00, G:0.03, T:0.29
Consensus pattern (18 bp):
AAATATTTAAGAATAAAA
Found at i:31160959 original size:13 final size:13
Alignment explanation
Indices: 31160941--31161006 Score: 69
Period size: 13 Copynumber: 5.1 Consensus size: 13
31160931 AGTTTGGCAA
31160941 TACTTTTAAAAAG
1 TACTTTTAAAAAG
*
31160954 TACTTTTCAAAAG
1 TACTTTTAAAAAG
* * *
31160967 TGCTGTGAAAAAG
1 TACTTTTAAAAAG
* *
31160980 TACTTTTGATAAG
1 TACTTTTAAAAAG
*
31160993 TACTTTTGAAAAG
1 TACTTTTAAAAAG
31161006 T
1 T
31161007 TTGGTTTAAA
Statistics
Matches: 42, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 42 1.00
ACGTcount: A:0.38, C:0.09, G:0.15, T:0.38
Consensus pattern (13 bp):
TACTTTTAAAAAG
Found at i:31161493 original size:13 final size:13
Alignment explanation
Indices: 31161477--31161501 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31161467 TTAGCTTTTC
31161477 CTTTTTAAAAGTG
1 CTTTTTAAAAGTG
31161490 CTTTTTAAAAGT
1 CTTTTTAAAAGT
31161502 ACTTCTAAAA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.12, T:0.48
Consensus pattern (13 bp):
CTTTTTAAAAGTG
Found at i:31169513 original size:18 final size:18
Alignment explanation
Indices: 31169470--31169513 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
31169460 TTGTGGAGTT
*
31169470 TATTT-ATGAGTATTTTA
1 TATTTGATGAATATTTTA
31169487 TATAATTGATGAATATTTTA
1 TAT--TTGATGAATATTTTA
31169507 TATTTGA
1 TATTTGA
31169514 AATTTATTCA
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
17 3 0.13
18 4 0.17
19 2 0.09
20 14 0.61
ACGTcount: A:0.34, C:0.00, G:0.11, T:0.55
Consensus pattern (18 bp):
TATTTGATGAATATTTTA
Found at i:31182875 original size:29 final size:31
Alignment explanation
Indices: 31182808--31182879 Score: 80
Period size: 28 Copynumber: 2.5 Consensus size: 31
31182798 TTACATTTAA
*
31182808 ATATTTAAAATAAATCTTTAACTTTTAATTT
1 ATATTTAAAATAAAGCTTTAACTTTTAATTT
* * *
31182839 ATA-GTAAAAT-AAGC-TTCACTTTTTATTT
1 ATATTTAAAATAAAGCTTTAACTTTTAATTT
31182867 ATATTT-AAATAAA
1 ATATTTAAAATAAA
31182880 TTATTAATAA
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
28 19 0.56
29 6 0.18
30 6 0.18
31 3 0.09
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (31 bp):
ATATTTAAAATAAAGCTTTAACTTTTAATTT
Found at i:31183586 original size:3 final size:3
Alignment explanation
Indices: 31183578--31183625 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
31183568 GAGCCAATGG
31183578 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
31183626 ATAGTATGAC
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:31185180 original size:20 final size:20
Alignment explanation
Indices: 31185126--31185190 Score: 73
Period size: 20 Copynumber: 3.3 Consensus size: 20
31185116 AAACAAGCAA
*
31185126 AAAGAAAA-AA-GAACAAGG
1 AAAGAAAAGAAGGAAGAAGG
31185144 AAAGAAAAGAAAGGAAGAAGG
1 AAAGAAAAG-AAGGAAGAAGG
*
31185165 AACAGAAAAG-AGGAAGAAGA
1 AA-AGAAAAGAAGGAAGAAGG
31185185 AAAGAA
1 AAAGAA
31185191 CTAACGTGAA
Statistics
Matches: 41, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
18 8 0.20
19 4 0.10
20 13 0.32
21 9 0.22
22 7 0.17
ACGTcount: A:0.69, C:0.03, G:0.28, T:0.00
Consensus pattern (20 bp):
AAAGAAAAGAAGGAAGAAGG
Found at i:31185985 original size:16 final size:18
Alignment explanation
Indices: 31185953--31185985 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
31185943 ATTAAGAGAA
31185953 TGAATTTAGTGTTAATTG
1 TGAATTTAGTGTTAATTG
31185971 TGAATTT-GT-TTAATT
1 TGAATTTAGTGTTAATT
31185986 TTATGTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 6 0.40
17 2 0.13
18 7 0.47
ACGTcount: A:0.27, C:0.00, G:0.18, T:0.55
Consensus pattern (18 bp):
TGAATTTAGTGTTAATTG
Found at i:31186879 original size:10 final size:10
Alignment explanation
Indices: 31186861--31187063 Score: 58
Period size: 10 Copynumber: 20.9 Consensus size: 10
31186851 TAAATATTAA
*
31186861 ATATTAAAAT
1 ATATAAAAAT
31186871 ATATAAAAAT
1 ATATAAAAAT
*
31186881 -TGATATAAACT
1 AT-ATA-AAAAT
31186892 -TATAAAAAT
1 ATATAAAAAT
* *
31186901 TTATAAGAAT
1 ATATAAAAAT
*
31186911 -TGTAAAAGAT
1 ATATAAAA-AT
* *
31186921 GTA-AAAAAA
1 ATATAAAAAT
*
31186930 ATCTAACAAAT
1 ATATAA-AAAT
*
31186941 -TATAAAAGT
1 ATATAAAAAT
**
31186950 A-ACCAAAAT
1 ATATAAAAAT
*
31186959 AT-TTAAAAT
1 ATATAAAAAT
*
31186968 ATTATAAAAAC
1 A-TATAAAAAT
*
31186979 ATATTAAAATT
1 ATA-TAAAAAT
*
31186990 CTATAAAAAT
1 ATATAAAAAT
31187000 CATA-AAAAAT
1 -ATATAAAAAT
31187010 A-A-AAAAA-
1 ATATAAAAAT
*
31187017 AGTATTAAAAT
1 A-TATAAAAAT
*
31187028 -TGATATAAAT
1 AT-ATAAAAAT
*
31187038 -TATAAAATT
1 ATATAAAAAT
31187047 ATA-AAAAAT
1 ATATAAAAAT
31187056 -TATAAAAA
1 ATATAAAAA
31187064 CTTAAATTAG
Statistics
Matches: 142, Mismatches: 31, Indels: 41
0.66 0.14 0.19
Matches are distributed among these distances:
7 1 0.01
8 8 0.06
9 46 0.32
10 63 0.44
11 24 0.17
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.31
Consensus pattern (10 bp):
ATATAAAAAT
Found at i:31186986 original size:21 final size:22
Alignment explanation
Indices: 31186954--31187003 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
31186944 AAAAGTAACC
31186954 AAAAT-AT-TTAAAATAT-TATA
1 AAAATCATATTAAAAT-TCTATA
31186974 AAAA-CATATTAAAATTCTATA
1 AAAATCATATTAAAATTCTATA
31186995 AAAATCATA
1 AAAATCATA
31187004 AAAAATAAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
20 7 0.27
21 15 0.58
22 4 0.15
ACGTcount: A:0.60, C:0.06, G:0.00, T:0.34
Consensus pattern (22 bp):
AAAATCATATTAAAATTCTATA
Found at i:31187008 original size:21 final size:21
Alignment explanation
Indices: 31186970--31187009 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
31186960 TTTAAAATAT
*
31186970 TATAAAAACATATTAAAATTC
1 TATAAAAACATATAAAAATTC
31186991 TATAAAAATCATA-AAAAAT
1 TATAAAAA-CATATAAAAAT
31187010 AAAAAAAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 13 0.76
22 4 0.24
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.30
Consensus pattern (21 bp):
TATAAAAACATATAAAAATTC
Found at i:31187043 original size:18 final size:18
Alignment explanation
Indices: 31186968--31187062 Score: 68
Period size: 19 Copynumber: 5.1 Consensus size: 18
31186958 TATTTAAAAT
31186968 ATTATAAAAACA-TATTAAA
1 ATTATAAAAA-ATTA-TAAA
* *
31186987 ATTCTATAAAAATCATAAAA
1 ATTATA-AAAAATTAT-AAA
* * *
31187007 AATAAAAAAAAGTATTAAA
1 ATTATAAAAAATTA-TAAA
*
31187026 ATTGAT-ATAAATTATAAA
1 ATT-ATAAAAAATTATAAA
31187044 ATTATAAAAAATTATAAA
1 ATTATAAAAAATTATAAA
31187062 A
1 A
31187063 ACTTAAATTA
Statistics
Matches: 58, Mismatches: 12, Indels: 13
0.70 0.14 0.16
Matches are distributed among these distances:
17 2 0.03
18 19 0.33
19 24 0.41
20 13 0.22
ACGTcount: A:0.64, C:0.03, G:0.02, T:0.31
Consensus pattern (18 bp):
ATTATAAAAAATTATAAA
Found at i:31187043 original size:38 final size:40
Alignment explanation
Indices: 31186962--31187054 Score: 102
Period size: 39 Copynumber: 2.4 Consensus size: 40
31186952 CCAAAATATT
* * *
31186962 TAAAATATTATAAAAACA-TATTAAAATTCTATAAAAATCA
1 TAAAATAATA-AAAAAAAGTATTAAAATTCGATAAAAATCA
* *
31187002 TAAAA-AATAAAAAAAAGTATTAAAATT-GATATAAATTA
1 TAAAATAATAAAAAAAAGTATTAAAATTCGATAAAAATCA
*
31187040 TAAAATTATAAAAAA
1 TAAAATAATAAAAAA
31187055 TTATAAAAAC
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
38 19 0.42
39 21 0.47
40 5 0.11
ACGTcount: A:0.65, C:0.03, G:0.02, T:0.30
Consensus pattern (40 bp):
TAAAATAATAAAAAAAAGTATTAAAATTCGATAAAAATCA
Found at i:31191763 original size:15 final size:15
Alignment explanation
Indices: 31191740--31191778 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
31191730 GTTTAGTCCC
* * *
31191740 TAGGATTTTTTGGTT
1 TAGGGTTTTTAGGGT
31191755 TAGGGTTTTTAGGGT
1 TAGGGTTTTTAGGGT
31191770 TAGGGTTTT
1 TAGGGTTTT
31191779 GCTAAAATAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.13, C:0.00, G:0.33, T:0.54
Consensus pattern (15 bp):
TAGGGTTTTTAGGGT
Found at i:31191943 original size:34 final size:33
Alignment explanation
Indices: 31191857--31191987 Score: 106
Period size: 34 Copynumber: 3.9 Consensus size: 33
31191847 TAGTGTTCTT
* * * *
31191857 TTTTAAA-AATTAATTAAATTAAGGTTTATGAT
1 TTTTAAATAAATAATTAAATTAGGGTTTAAGAG
* *
31191889 TTTTAAATAAATTAAGTAAATTAGGGTTTAAGGG
1 TTTTAAATAAA-TAATTAAATTAGGGTTTAAGAG
* *
31191923 TTTTAAATAAATACATTAAATTAGAGATT-AGAG
1 TTTTAAATAAATA-ATTAAATTAGGGTTTAAGAG
*
31191956 -TTTAAGGTTAAAGTTAATTAAATTAGGGTTTA
1 TTTTAA--ATAAA--TAATTAAATTAGGGTTTA
31191988 GTTTTTTCAA
Statistics
Matches: 78, Mismatches: 13, Indels: 12
0.76 0.13 0.12
Matches are distributed among these distances:
32 12 0.15
33 7 0.09
34 44 0.56
35 13 0.17
36 2 0.03
ACGTcount: A:0.43, C:0.01, G:0.15, T:0.41
Consensus pattern (33 bp):
TTTTAAATAAATAATTAAATTAGGGTTTAAGAG
Found at i:31192356 original size:127 final size:126
Alignment explanation
Indices: 31192048--31192410 Score: 484
Period size: 125 Copynumber: 2.9 Consensus size: 126
31192038 TTTTTACCCC
* *
31192048 AAAAAATAATTTTGAGAAGACGTTTCTAAACAAATAGTGTCAAAAAT-GCTTTAAGTAGGATGCA
1 AAAAAATAATTTTGAGAAGATGTTTCTAAACAAATAGTGTCAAAAATCGCTTTAAGCAGGATGCA
* * * *
31192112 CTATCAACAAAATTACTAAAAAAAGCTACCACATGGACGCTCTTTTTCTATAGTAGTTCCT
66 CTATCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTATAGTAGTTCCT
* * *
31192173 GAAAAATAATTTTAAGAAGATGTTTCTGAACAAATAGTGTCAAAAA-CGCTTTAAGCAGGATGCA
1 AAAAAATAATTTTGAGAAGATGTTTCTAAACAAATAGTGTCAAAAATCGCTTTAAGCAGGATGCA
* * * *
31192237 CTGTCAGCAAAAGTACTGAAAAATGCTCCCACGTGGACGCAAT-TTTTTTTACT-GTAGTTCCT
66 CTATCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGC--TCTTTTTCTA-TAGTAGTTCCT
* *
31192299 AAAAAAATAATTTTGAGAAGATGTTTCTAAACAAATAGTGT-AAAAATCACTTCAAGCAGGATGC
1 -AAAAAATAATTTTGAGAAGATGTTTCTAAACAAATAGTGTCAAAAATCGCTTTAAGCAGGATGC
* * * *
31192363 ACTATCAGTAAAATTACTGAAAAAAGCTCTCATGTGGATGCTCTTTTT
65 ACTATCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTT
31192411 TTACAATAGT
Statistics
Matches: 206, Mismatches: 25, Indels: 13
0.84 0.10 0.05
Matches are distributed among these distances:
125 92 0.45
126 26 0.13
127 88 0.43
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (126 bp):
AAAAAATAATTTTGAGAAGATGTTTCTAAACAAATAGTGTCAAAAATCGCTTTAAGCAGGATGCA
CTATCAGCAAAATTACTGAAAAAAGCTCCCACGTGGACGCTCTTTTTCTATAGTAGTTCCT
Found at i:31192411 original size:127 final size:126
Alignment explanation
Indices: 31192048--31192412 Score: 479
Period size: 127 Copynumber: 2.9 Consensus size: 126
31192038 TTTTTACCCC
* *
31192048 AAAAAATAATTTTGAGAAGACGTTTCTAAACAAATAGTGTCAAAAAT-GCTTTAAGTAGGATGCA
1 AAAAAATAATTTTGAGAAGATGTTTCTAAACAAATAGTGTCAAAAATCGCTTTAAGCAGGATGCA
* * * *
31192112 CTATCAACAAAATTACTAAAAAAAGCTACCACATGGACGCTC-TTTTTCTATAGTAGTTCCT
66 CTATCAGCAAAATTACTGAAAAAAGCT-CCACGTGGACGCTCTTTTTTTTATAGTAGTTCCT
* * *
31192173 GAAAAATAATTTTAAGAAGATGTTTCTGAACAAATAGTGTCAAAAA-CGCTTTAAGCAGGATGCA
1 AAAAAATAATTTTGAGAAGATGTTTCTAAACAAATAGTGTCAAAAATCGCTTTAAGCAGGATGCA
* * * **
31192237 CTGTCAGCAAAAGTACTGAAAAATGCTCCCACGTGGACGCAATTTTTTTTACT-GTAGTTCCT
66 CTATCAGCAAAATTACTGAAAAAAGCT-CCACGTGGACGCTCTTTTTTTTA-TAGTAGTTCCT
* *
31192299 AAAAAAATAATTTTGAGAAGATGTTTCTAAACAAATAGTGT-AAAAATCACTTCAAGCAGGATGC
1 -AAAAAATAATTTTGAGAAGATGTTTCTAAACAAATAGTGTCAAAAATCGCTTTAAGCAGGATGC
* * *
31192363 ACTATCAGTAAAATTACTGAAAAAAGCTCTCATGTGGATGCTCTTTTTTT
65 ACTATCAGCAAAATTACTGAAAAAAGCTC-CACGTGGACGCTCTTTTTTT
31192413 ACAATAGTTC
Statistics
Matches: 206, Mismatches: 28, Indels: 10
0.84 0.11 0.04
Matches are distributed among these distances:
125 91 0.44
126 22 0.11
127 93 0.45
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (126 bp):
AAAAAATAATTTTGAGAAGATGTTTCTAAACAAATAGTGTCAAAAATCGCTTTAAGCAGGATGCA
CTATCAGCAAAATTACTGAAAAAAGCTCCACGTGGACGCTCTTTTTTTTATAGTAGTTCCT
Found at i:31194285 original size:18 final size:18
Alignment explanation
Indices: 31194259--31194301 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
31194249 GACTGGGAAA
* * *
31194259 AGGAAACATATAAGGGTT
1 AGGATACATATAAAGGCT
31194277 AGGATACATATAAAGGCT
1 AGGATACATATAAAGGCT
31194295 AGGATAC
1 AGGATAC
31194302 GCACCTGACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.44, C:0.09, G:0.26, T:0.21
Consensus pattern (18 bp):
AGGATACATATAAAGGCT
Found at i:31194894 original size:7 final size:7
Alignment explanation
Indices: 31194884--31194908 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
31194874 TTATATACAT
31194884 AATACTA
1 AATACTA
31194891 AATACTA
1 AATACTA
31194898 AATACTA
1 AATACTA
31194905 AATA
1 AATA
31194909 TGAAATGACT
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:31198532 original size:15 final size:15
Alignment explanation
Indices: 31198509--31198551 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 15
31198499 AATTTAGCAA
**
31198509 TTAAATTTTTCGTAT
1 TTAAATTTTTAATAT
*
31198524 TTAACTTTTTAATAT
1 TTAAATTTTTAATAT
31198539 TTAAATTTTTAAT
1 TTAAATTTTTAAT
31198552 TTACCAAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (15 bp):
TTAAATTTTTAATAT
Found at i:31199714 original size:30 final size:30
Alignment explanation
Indices: 31199680--31199743 Score: 87
Period size: 30 Copynumber: 2.1 Consensus size: 30
31199670 AAATATCGAA
31199680 TCTTCCCAAGC-TCTTAAATGCA-ATATTAAG
1 TCTTCCCAAGCTTC-TAAATG-AGATATTAAG
*
31199710 TCTTCCCAAGCTTCTGAATGAGATATTAAG
1 TCTTCCCAAGCTTCTAAATGAGATATTAAG
31199740 TCTT
1 TCTT
31199744 ATCAATCCCA
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
29 1 0.03
30 28 0.90
31 2 0.06
ACGTcount: A:0.30, C:0.22, G:0.12, T:0.36
Consensus pattern (30 bp):
TCTTCCCAAGCTTCTAAATGAGATATTAAG
Found at i:31202427 original size:33 final size:34
Alignment explanation
Indices: 31202379--31202442 Score: 96
Period size: 33 Copynumber: 1.9 Consensus size: 34
31202369 AATAGATGTA
31202379 TTAACTATAAAAAATAA-TTACAAATAATTATCAT
1 TTAACTATAAAAAATAATTTA-AAATAATTATCAT
*
31202413 TTAA-TATAATAAATAATTTAAAATAATTAT
1 TTAACTATAAAAAATAATTTAAAATAATTAT
31202443 ATAATTAATT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 21 0.75
34 7 0.25
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.39
Consensus pattern (34 bp):
TTAACTATAAAAAATAATTTAAAATAATTATCAT
Found at i:31202448 original size:18 final size:17
Alignment explanation
Indices: 31202385--31202439 Score: 51
Period size: 17 Copynumber: 3.3 Consensus size: 17
31202375 TGTATTAACT
*
31202385 ATAAAAAATAA-TTACAA
1 ATAATAAATAATTTA-AA
* * *
31202402 ATAAT-TATCATTTAAT
1 ATAATAAATAATTTAAA
31202418 ATAATAAATAATTTAAA
1 ATAATAAATAATTTAAA
31202435 ATAAT
1 ATAAT
31202440 TATATAATTA
Statistics
Matches: 29, Mismatches: 7, Indels: 4
0.73 0.17 0.10
Matches are distributed among these distances:
16 9 0.31
17 20 0.69
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (17 bp):
ATAATAAATAATTTAAA
Found at i:31202450 original size:17 final size:17
Alignment explanation
Indices: 31202392--31202450 Score: 52
Period size: 17 Copynumber: 3.5 Consensus size: 17
31202382 ACTATAAAAA
31202392 ATAATTACAAATAATTAT
1 ATAATTA-AAATAATTAT
* *
31202410 CAT--TTAATATAA-TAA
1 -ATAATTAAAATAATTAT
31202425 ATAATTTAAAATAATTAT
1 ATAA-TTAAAATAATTAT
31202443 ATAATTAA
1 ATAATTAA
31202451 TTAGAATATT
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
14 2 0.06
15 2 0.06
16 5 0.16
17 15 0.47
18 6 0.19
19 2 0.06
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (17 bp):
ATAATTAAAATAATTAT
Found at i:31204244 original size:42 final size:42
Alignment explanation
Indices: 31204187--31204269 Score: 141
Period size: 42 Copynumber: 2.0 Consensus size: 42
31204177 TAAAAGTTAT
*
31204187 GACCTTTAGCGGCGCTTTTC-CTACAAACGCCGCTAAAAAATG
1 GACCTTTAGCAGCGCTTTTCTC-ACAAACGCCGCTAAAAAATG
31204229 GACCTTTAGCAGCGCTTTTCTCACAAACGCCGCTAAAAAAT
1 GACCTTTAGCAGCGCTTTTCTCACAAACGCCGCTAAAAAAT
31204270 ATTACCTTTA
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
42 38 0.97
43 1 0.03
ACGTcount: A:0.30, C:0.29, G:0.17, T:0.24
Consensus pattern (42 bp):
GACCTTTAGCAGCGCTTTTCTCACAAACGCCGCTAAAAAATG
Found at i:31207260 original size:41 final size:41
Alignment explanation
Indices: 31207216--31207312 Score: 124
Period size: 41 Copynumber: 2.4 Consensus size: 41
31207206 GAGTGAAAGT
* *
31207216 TTTTTGCGGCATTTTTA-CAAAAACACCACTATATCTTAAC
1 TTTTTGCGGCATTTTTACCAAAAACACCACTATAGCTCAAC
* * * *
31207256 TTTTTGCAGCGTTTTCACCAAAAATACCACTATAGCTCAAC
1 TTTTTGCGGCATTTTTACCAAAAACACCACTATAGCTCAAC
*
31207297 TTTTTACGGCATTTTT
1 TTTTTGCGGCATTTTT
31207313 TGGAAAAAAC
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
40 14 0.30
41 32 0.70
ACGTcount: A:0.29, C:0.23, G:0.09, T:0.39
Consensus pattern (41 bp):
TTTTTGCGGCATTTTTACCAAAAACACCACTATAGCTCAAC
Found at i:31207494 original size:8 final size:8
Alignment explanation
Indices: 31207483--31207530 Score: 64
Period size: 8 Copynumber: 6.2 Consensus size: 8
31207473 AATATTAAAA
31207483 TTTTAATT
1 TTTTAATT
*
31207491 TTTTAAGT
1 TTTTAATT
31207499 TTTTAA-T
1 TTTTAATT
31207506 TTTTAA-T
1 TTTTAATT
31207513 TTTTAATT
1 TTTTAATT
*
31207521 TTTTTATT
1 TTTTAATT
31207529 TT
1 TT
31207531 AAAATTTTCA
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
7 14 0.38
8 23 0.62
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.75
Consensus pattern (8 bp):
TTTTAATT
Found at i:31207496 original size:23 final size:23
Alignment explanation
Indices: 31207470--31207516 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
31207460 GACTAAAAAA
31207470 TTAAATATTAAAATTTTAATTTT
1 TTAAATATTAAAATTTTAATTTT
* * * *
31207493 TTAAGTTTTTAATTTTTAATTTT
1 TTAAATATTAAAATTTTAATTTT
31207516 T
1 T
31207517 AATTTTTTTA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.34, C:0.00, G:0.02, T:0.64
Consensus pattern (23 bp):
TTAAATATTAAAATTTTAATTTT
Found at i:31207524 original size:23 final size:22
Alignment explanation
Indices: 31207483--31207548 Score: 78
Period size: 23 Copynumber: 2.9 Consensus size: 22
31207473 AATATTAAAA
* *
31207483 TTTTAATTTTTTAAGTTTTTAAT
1 TTTTAA-TTTTTAATTTTTTTAT
31207506 TTTTAATTTTTAATTTTTTTAT
1 TTTTAATTTTTAATTTTTTTAT
* *
31207528 TTTAAAATTTTCAATTTTTTT
1 TTT-TAATTTTTAATTTTTTT
31207549 TGAAGATTTT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
22 17 0.45
23 21 0.55
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.71
Consensus pattern (22 bp):
TTTTAATTTTTAATTTTTTTAT
Found at i:31207529 original size:15 final size:15
Alignment explanation
Indices: 31207483--31207546 Score: 76
Period size: 15 Copynumber: 4.3 Consensus size: 15
31207473 AATATTAAAA
31207483 TTTTAATTTTTTAAGT
1 TTTTAATTTTTTAA-T
31207499 TTTTAA-TTTTTAAT
1 TTTTAATTTTTTAAT
*
31207513 TTTTAATTTTTTTAT
1 TTTTAATTTTTTAAT
* * *
31207528 TTTAAAATTTTCAAT
1 TTTTAATTTTTTAAT
31207543 TTTT
1 TTTT
31207547 TTTGAAGATT
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
14 7 0.17
15 28 0.68
16 6 0.15
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (15 bp):
TTTTAATTTTTTAAT
Found at i:31207546 original size:8 final size:7
Alignment explanation
Indices: 31207483--31207546 Score: 65
Period size: 7 Copynumber: 8.6 Consensus size: 7
31207473 AATATTAAAA
31207483 TTTTAATT
1 TTTTAA-T
31207491 TTTTAAGT
1 TTTTAA-T
31207499 TTTTAAT
1 TTTTAAT
31207506 TTTTAAT
1 TTTTAAT
31207513 TTTTAATT
1 TTTTAA-T
*
31207521 TTTTTAT
1 TTTTAAT
*
31207528 TTTAAAAT
1 TTT-TAAT
*
31207536 TTTCAAT
1 TTTTAAT
31207543 TTTT
1 TTTT
31207547 TTTGAAGATT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
7 24 0.50
8 24 0.50
ACGTcount: A:0.27, C:0.02, G:0.02, T:0.70
Consensus pattern (7 bp):
TTTTAAT
Found at i:31209065 original size:18 final size:18
Alignment explanation
Indices: 31208998--31209155 Score: 223
Period size: 18 Copynumber: 8.8 Consensus size: 18
31208988 ATAATCTTCA
31208998 ATGATATGCAATCTTAGAT
1 ATGAT-TGCAATCTTAGAT
31209017 ATGATATGCAATCTTAGAT
1 ATGAT-TGCAATCTTAGAT
*
31209036 ATGA-TACAATCTTAGAT
1 ATGATTGCAATCTTAGAT
31209053 ATGATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGAT
31209071 ATGATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGAT
*
31209089 ATGA-TACAATCTTAGAT
1 ATGATTGCAATCTTAGAT
*
31209106 ATGATTGCAATATTAGAT
1 ATGATTGCAATCTTAGAT
*
31209124 ATGA-TACAATCTTAGAT
1 ATGATTGCAATCTTAGAT
* *
31209141 ATAATTGTAATCTTA
1 ATGATTGCAATCTTA
31209156 ATTAGATATG
Statistics
Matches: 126, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
17 46 0.37
18 57 0.45
19 23 0.18
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (18 bp):
ATGATTGCAATCTTAGAT
Found at i:31209069 original size:35 final size:35
Alignment explanation
Indices: 31208998--31209155 Score: 228
Period size: 35 Copynumber: 4.4 Consensus size: 35
31208988 ATAATCTTCA
31208998 ATGATATGCAATCTTAGATATGATATGCAATCTTAGAT
1 ATGAT-TGCAATCTTAGATATGATA--CAATCTTAGAT
* *
31209036 ATGA-TACAATCTTAGATATGATTGCAATCTTAGAT
1 ATGATTGCAATCTTAGATATGA-TACAATCTTAGAT
31209071 ATGATTGCAATCTTAGATATGATACAATCTTAGAT
1 ATGATTGCAATCTTAGATATGATACAATCTTAGAT
*
31209106 ATGATTGCAATATTAGATATGATACAATCTTAGAT
1 ATGATTGCAATCTTAGATATGATACAATCTTAGAT
* *
31209141 ATAATTGTAATCTTA
1 ATGATTGCAATCTTA
31209156 ATTAGATATG
Statistics
Matches: 110, Mismatches: 8, Indels: 7
0.88 0.06 0.06
Matches are distributed among these distances:
35 73 0.66
36 32 0.29
37 1 0.01
38 4 0.04
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.38
Consensus pattern (35 bp):
ATGATTGCAATCTTAGATATGATACAATCTTAGAT
Found at i:31209085 original size:53 final size:53
Alignment explanation
Indices: 31208998--31209142 Score: 247
Period size: 53 Copynumber: 2.7 Consensus size: 53
31208988 ATAATCTTCA
31208998 ATGATATGCAATCTTAGATATGATATGCAATCTTAGATATGATACAATCTTAGAT
1 ATGAT-TGCAATCTTAGATATGAT-TGCAATCTTAGATATGATACAATCTTAGAT
31209053 ATGATTGCAATCTTAGATATGATTGCAATCTTAGATATGATACAATCTTAGAT
1 ATGATTGCAATCTTAGATATGATTGCAATCTTAGATATGATACAATCTTAGAT
* *
31209106 ATGATTGCAATATTAGATATGA-TACAATCTTAGATAT
1 ATGATTGCAATCTTAGATATGATTGCAATCTTAGATAT
31209143 AATTGTAATC
Statistics
Matches: 88, Mismatches: 2, Indels: 3
0.95 0.02 0.03
Matches are distributed among these distances:
52 14 0.16
53 51 0.58
54 18 0.20
55 5 0.06
ACGTcount: A:0.38, C:0.10, G:0.14, T:0.37
Consensus pattern (53 bp):
ATGATTGCAATCTTAGATATGATTGCAATCTTAGATATGATACAATCTTAGAT
Found at i:31209689 original size:18 final size:17
Alignment explanation
Indices: 31209665--31209724 Score: 63
Period size: 17 Copynumber: 3.5 Consensus size: 17
31209655 CCAATATATT
31209665 TTATATTTTTTATATAA
1 TTATATTTTTTATATAA
*
31209682 TTAT-TATTCTTATA-AA
1 TTATAT-TTTTTATATAA
31209698 -TATATTTTTTATTATATA
1 TTATATTTTTTA-TATA-A
31209716 TTATATTTT
1 TTATATTTT
31209725 AAATTTATTA
Statistics
Matches: 35, Mismatches: 2, Indels: 10
0.74 0.04 0.21
Matches are distributed among these distances:
15 8 0.23
16 6 0.17
17 12 0.34
18 1 0.03
19 8 0.23
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATATTTTTTATATAA
Found at i:31209709 original size:15 final size:16
Alignment explanation
Indices: 31209666--31209724 Score: 59
Period size: 16 Copynumber: 3.5 Consensus size: 16
31209656 CAATATATTT
31209666 TATATTTTTTATATAA
1 TATATTTTTTATATAA
31209682 T-TATTATTCTTATA-AA
1 TATATT-TT-TTATATAA
31209698 TATATTTTTTATTATATA
1 TATATTTTTTA-TATA-A
31209716 TTATATTTT
1 -TATATTTT
31209725 AAATTTATTA
Statistics
Matches: 36, Mismatches: 0, Indels: 11
0.77 0.00 0.23
Matches are distributed among these distances:
15 7 0.19
16 10 0.28
17 10 0.28
18 1 0.03
19 8 0.22
ACGTcount: A:0.34, C:0.02, G:0.00, T:0.64
Consensus pattern (16 bp):
TATATTTTTTATATAA
Found at i:31209735 original size:26 final size:26
Alignment explanation
Indices: 31209701--31209750 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
31209691 TTATAAATAT
* * *
31209701 ATTTTTTATTATATATTATATTTTAA
1 ATTTATTATTAAATATCATATTTTAA
31209727 ATTTATTATTAAATATCATATTTT
1 ATTTATTATTAAATATCATATTTT
31209751 TTTATATGCT
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:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (26 bp):
ATTTATTATTAAATATCATATTTTAA
Found at i:31211180 original size:7 final size:7
Alignment explanation
Indices: 31211168--31211219 Score: 50
Period size: 7 Copynumber: 7.4 Consensus size: 7
31211158 AATTAACTCC
*
31211168 TAAACCT
1 TAAACCA
31211175 TAAACCA
1 TAAACCA
31211182 TAAACCA
1 TAAACCA
* * *
31211189 TATATCT
1 TAAACCA
31211196 TAAACCA
1 TAAACCA
*
31211203 TAAACCT
1 TAAACCA
*
31211210 TAAACTA
1 TAAACCA
31211217 TAA
1 TAA
31211220 TGATAATTAA
Statistics
Matches: 35, Mismatches: 10, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
7 35 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (7 bp):
TAAACCA
Found at i:31211185 original size:14 final size:14
Alignment explanation
Indices: 31211168--31211219 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
31211158 AATTAACTCC
* *
31211168 TAAACCTTAAACCA
1 TAAACCATAAACCT
* *
31211182 TAAACCATATATCT
1 TAAACCATAAACCT
31211196 TAAACCATAAACCT
1 TAAACCATAAACCT
*
31211210 TAAACTATAA
1 TAAACCATAA
31211220 TGATAATTAA
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
14 31 1.00
ACGTcount: A:0.50, C:0.23, G:0.00, T:0.27
Consensus pattern (14 bp):
TAAACCATAAACCT
Found at i:31211446 original size:41 final size:41
Alignment explanation
Indices: 31211385--31211604 Score: 221
Period size: 41 Copynumber: 5.4 Consensus size: 41
31211375 GTTATATGAC
* *
31211385 TTTT-AGCGGCATTTTACCGAAAGCGCCGCTAATGCTCTGG
1 TTTTAAGCGGCGTTTTACCGAAAGCACCGCTAATGCTCTGG
* *
31211425 TATTAAGCGGCGTTTTACCGAAAGCACCGCTAATGCTCTAGT
1 TTTTAAGCGGCGTTTTACCGAAAGCACCGCTAATGCTCT-GG
* **
31211467 TTTTAA-TGGCGTTTTATAGAAAGCACCGCTAATGCTCTGG
1 TTTTAAGCGGCGTTTTACCGAAAGCACCGCTAATGCTCTGG
* * ** *
31211507 TTTTTAGTGGCGTTTTAATGAAAGCGCCGCTAATGCTCTGG
1 TTTTAAGCGGCGTTTTACCGAAAGCACCGCTAATGCTCTGG
* ** * * **
31211548 TTTTTAGCGGCGTTTTAGCATAAAACACCGCTATTGCTCTAT
1 TTTTAAGCGGCGTTTTA-CCGAAAGCACCGCTAATGCTCTGG
*
31211590 TTTTAA-CAGCGTTTT
1 TTTTAAGCGGCGTTTT
31211605 TGGTAAAATG
Statistics
Matches: 152, Mismatches: 24, Indels: 7
0.83 0.13 0.04
Matches are distributed among these distances:
40 9 0.06
41 116 0.76
42 27 0.18
ACGTcount: A:0.23, C:0.20, G:0.22, T:0.35
Consensus pattern (41 bp):
TTTTAAGCGGCGTTTTACCGAAAGCACCGCTAATGCTCTGG
Found at i:31211626 original size:123 final size:124
Alignment explanation
Indices: 31211385--31211634 Score: 299
Period size: 123 Copynumber: 2.0 Consensus size: 124
31211375 GTTATATGAC
* * *
31211385 TTTTAGCGGCATTTTACCGAAAGCGCCGCTAATGCTCTGGTATTAAGCGGCGTTTTACCGAAAGC
1 TTTTAGCGGCATTTTAACGAAAGCGCCGCTAATGCTCTGGTATTAAGCGGCGTTTTACAGAAAAC
** * *
31211450 ACCGCTAATGCTCTAGTTTTTAATGGCGTTTTATAGAAAGCACCGCTAATGCTCTG-GT
66 ACCGCTAATGCTCTAGTTTTTAACAGCGTTTTATAGAAAACACCACTAATGCTCTGTGT
* * * * * *
31211508 TTTTAGTGGCGTTTTAATGAAAGCGCCGCTAATGCTCTGGTTTTTAGCGGCGTTTTAGCATAAAA
1 TTTTAGCGGCATTTTAACGAAAGCGCCGCTAATGCTCTGGTATTAAGCGGCGTTTTA-CAGAAAA
* * ** *
31211573 CACCGCTATTGCTCTA-TTTTTAACAGCGTTTT-TGGTAAAATGCCACTATTGCTCTGTGT
65 CACCGCTAATGCTCTAGTTTTTAACAGCGTTTTATAG-AAAACACCACTAATGCTCTGTGT
31211632 TTT
1 TTT
31211635 ACATTTTTTG
Statistics
Matches: 106, Mismatches: 18, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
122 2 0.02
123 80 0.75
124 24 0.23
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.36
Consensus pattern (124 bp):
TTTTAGCGGCATTTTAACGAAAGCGCCGCTAATGCTCTGGTATTAAGCGGCGTTTTACAGAAAAC
ACCGCTAATGCTCTAGTTTTTAACAGCGTTTTATAGAAAACACCACTAATGCTCTGTGT
Found at i:31214345 original size:26 final size:26
Alignment explanation
Indices: 31214314--31214421 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
31214304 TGAAATTCCC
*
31214314 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
31214340 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
31214366 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
31214392 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
31214418 ATCA
1 ATCA
31214422 ATTTATATCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:31215690 original size:22 final size:22
Alignment explanation
Indices: 31215665--31215714 Score: 75
Period size: 21 Copynumber: 2.3 Consensus size: 22
31215655 ATAGTCCAAT
*
31215665 CCAAACAAACTCAAAACAAAAC
1 CCAAACAAACCCAAAACAAAAC
*
31215687 CC-AACAAACCCAAAACAGAAC
1 CCAAACAAACCCAAAACAAAAC
31215708 CCAAACA
1 CCAAACA
31215715 CGAATGGCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 19 0.76
22 6 0.24
ACGTcount: A:0.60, C:0.36, G:0.02, T:0.02
Consensus pattern (22 bp):
CCAAACAAACCCAAAACAAAAC
Found at i:31215710 original size:12 final size:11
Alignment explanation
Indices: 31215667--31215712 Score: 51
Period size: 12 Copynumber: 4.2 Consensus size: 11
31215657 AGTCCAATCC
*
31215667 AAACAAACTCA
1 AAACAAACCCA
31215678 AAACAAAACCC-
1 AAAC-AAACCCA
31215689 -AACAAACCCA
1 AAACAAACCCA
31215699 AAACAGAACCCA
1 AAACA-AACCCA
31215711 AA
1 AA
31215713 CACGAATGGC
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
9 6 0.20
10 3 0.10
11 8 0.27
12 13 0.43
ACGTcount: A:0.63, C:0.33, G:0.02, T:0.02
Consensus pattern (11 bp):
AAACAAACCCA
Found at i:31216976 original size:244 final size:244
Alignment explanation
Indices: 31216533--31217036 Score: 936
Period size: 244 Copynumber: 2.1 Consensus size: 244
31216523 AGGTTTTTCT
* *
31216533 TTATTTTTAATTATTACCACATACTTTATTTCAATCACATTTTAGTCCTCATGGGAACGACGTCA
1 TTATTATT-ATTATTACCACATACTTTATTTCAATCACATTTTAGTCCTCATGGGAACGACATCA
* *
31216598 TTTTGGAGGAGAAGGGAGAATTCCCCTTTTAGTCCCTCCATATTATTCGCGTGTTCGGATAGGTC
65 TTTTGGAGGAGAAGGGAGAATTCCCCTTTTAATCCCTCAATATTATTCGCGTGTTCGGATAGGTC
*
31216663 CTCCCCTTTCCTTTTTATTTCAAATTTGCCCCAATTTTCTATTTTGAGTTCAATTTTAGTCATTT
130 CTCCCCTTTCCTTTTTATTTCAAATTTGCCCCAATTTTCTATTTTGAGTTCAATTTTAGTCAGTT
31216728 TTTGGTTATTTTTGCTATCTTATTTTTAAATTAATTAATTTAACATTGTA
195 TTTGGTTATTTTTGCTATCTTATTTTTAAATTAATTAATTTAACATTGTA
*
31216778 TTATTATTATTATTACCACATACTTTATTTCGATCACATTTTAGTCCTCATGGGAACGACATCAT
1 TTATTATTATTATTACCACATACTTTATTTCAATCACATTTTAGTCCTCATGGGAACGACATCAT
31216843 TTTGGAGGAGAAGGGAGAATTCCCCTTTTAATCCCTCAATATTATTCGCGTGTTCGGATAGGTCC
66 TTTGGAGGAGAAGGGAGAATTCCCCTTTTAATCCCTCAATATTATTCGCGTGTTCGGATAGGTCC
*
31216908 TCCCTTTTCCTTTTTATTTCAAATTTGCCCCAATTTTCTATTTTGAGTTCAATTTTAGTCAGTTT
131 TCCCCTTTCCTTTTTATTTCAAATTTGCCCCAATTTTCTATTTTGAGTTCAATTTTAGTCAGTTT
31216973 TTGGTTATTTTTGCTATCTTATTTTTAAATTAATTAATTTAACATTGTA
196 TTGGTTATTTTTGCTATCTTATTTTTAAATTAATTAATTTAACATTGTA
31217022 TTATTATTATTATTA
1 TTATTATTATTATTA
31217037 TCATTACTAT
Statistics
Matches: 252, Mismatches: 7, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
244 245 0.97
245 7 0.03
ACGTcount: A:0.24, C:0.17, G:0.12, T:0.46
Consensus pattern (244 bp):
TTATTATTATTATTACCACATACTTTATTTCAATCACATTTTAGTCCTCATGGGAACGACATCAT
TTTGGAGGAGAAGGGAGAATTCCCCTTTTAATCCCTCAATATTATTCGCGTGTTCGGATAGGTCC
TCCCCTTTCCTTTTTATTTCAAATTTGCCCCAATTTTCTATTTTGAGTTCAATTTTAGTCAGTTT
TTGGTTATTTTTGCTATCTTATTTTTAAATTAATTAATTTAACATTGTA
Found at i:31217028 original size:3 final size:3
Alignment explanation
Indices: 31217020--31217091 Score: 90
Period size: 3 Copynumber: 24.0 Consensus size: 3
31217010 TTTAACATTG
* * * * *
31217020 TAT TAT TAT TAT TAT TAT CAT TAC TAT TAT CAT TAC TAT TAT TAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
31217068 TAT TAT TAT TAT TAC TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT
31217092 ATTTCTTTTT
Statistics
Matches: 57, Mismatches: 12, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
3 57 1.00
ACGTcount: A:0.33, C:0.08, G:0.00, T:0.58
Consensus pattern (3 bp):
TAT
Found at i:31217450 original size:16 final size:16
Alignment explanation
Indices: 31217424--31217457 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 16
31217414 CTTTTTATTA
31217424 ATTTTTTACGCAT-TT
1 ATTTTTTACGCATGTT
31217439 ATTTTATTACGCATGTT
1 ATTTT-TTACGCATGTT
31217456 AT
1 AT
31217458 CATCGTGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 8 0.47
17 4 0.24
ACGTcount: A:0.24, C:0.12, G:0.09, T:0.56
Consensus pattern (16 bp):
ATTTTTTACGCATGTT
Found at i:31219468 original size:12 final size:12
Alignment explanation
Indices: 31219437--31219471 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
31219427 TCTGTGTACC
*
31219437 GCTACTGCTACT
1 GCTACTGTTACT
31219449 GCTACTGTTACT
1 GCTACTGTTACT
*
31219461 GTTACTGTTAC
1 GCTACTGTTAC
31219472 GGTGTATTCC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 21 1.00
ACGTcount: A:0.17, C:0.26, G:0.17, T:0.40
Consensus pattern (12 bp):
GCTACTGTTACT
Found at i:31219993 original size:23 final size:24
Alignment explanation
Indices: 31219950--31219997 Score: 89
Period size: 23 Copynumber: 2.0 Consensus size: 24
31219940 AGGTTAATCT
31219950 ATATAAGCAAAATTTATGTTTATA
1 ATATAAGCAAAATTTATGTTTATA
31219974 ATATAAGCAAAA-TTATGTTTATA
1 ATATAAGCAAAATTTATGTTTATA
31219997 A
1 A
31219998 AATAGTCACT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
23 12 0.50
24 12 0.50
ACGTcount: A:0.48, C:0.04, G:0.08, T:0.40
Consensus pattern (24 bp):
ATATAAGCAAAATTTATGTTTATA
Found at i:31222025 original size:44 final size:46
Alignment explanation
Indices: 31221916--31222029 Score: 137
Period size: 44 Copynumber: 2.5 Consensus size: 46
31221906 GAGTGCCAGA
* *
31221916 GTAAGACATGTCTGAGACATGCATCGGCCTCAACAGAGATAGTCAGT
1 GTAAGACATGTCTGGGACATGCACCGGCCT-AACAGAGATAGTCAGT
* *
31221963 GTAAGACATGTCTAGGACATGCACCGG-CT-A-AGAG-TTGTGCTAGT
1 GTAAGACATGTCTGGGACATGCACCGGCCTAACAGAGATAGT-C-AGT
31222007 GTAAGACATGTCTGGGACATGCA
1 GTAAGACATGTCTGGGACATGCA
31222030 TCATCACGCA
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
42 3 0.05
43 5 0.08
44 26 0.43
46 2 0.03
47 24 0.40
ACGTcount: A:0.30, C:0.19, G:0.28, T:0.23
Consensus pattern (46 bp):
GTAAGACATGTCTGGGACATGCACCGGCCTAACAGAGATAGTCAGT
Found at i:31235514 original size:140 final size:140
Alignment explanation
Indices: 31235262--31235949 Score: 701
Period size: 140 Copynumber: 5.0 Consensus size: 140
31235252 ATGCTTACTG
** * *
31235262 CGACACTTTTGAGG-CGACACTTTTTTAAATGTTGGGATAGACTTGTCGACATACGTTTTGGCCA
1 CGACACTTTTG-GGCCGACACTTTCCTAAGTGTTGGGATAGACTTGTCGACATACGCTTTGGCCA
*
31235326 ACTATTTGTATAAGAGTTGGGATATGCATGCCTAAGGCAACACTTAAATAAGAGTCGGCTTTGTT
65 ACTCTTTGTATAAGAGTTGGGATATGCATGCCTAAGGCAACACTTAAATAAGAGTCGGCTTTGTT
*
31235391 CAACATTATGC
130 CAACACTATGC
* * * *
31235402 CGACACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAGACTTATCAATATACACTTTGGCCAA
1 CGACACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAGACTTGTCGACATACGCTTTGGCCAA
* * * * * *
31235467 -TCCTTTATATAAGAGTTGGGATATGTATGCCTAGGGCAACGCTTAAATAAGAGTTGACTTT-TT
66 CT-CTTTGTATAAGAGTTGGGATATGCATGCCTAAGGCAACACTTAAATAAGAGTCGGCTTTGTT
31235530 CCAACACTATGC
130 -CAACACTATGC
* * * * * ** * *
31235542 TGAAACTTTTGGGCCGAAACTTTTCCTAAGTGTTGGGATAAACTTGTTGATGTACACTTTGTCCA
1 CGACACTTTTGGGCCGACAC-TTTCCTAAGTGTTGGGATAGACTTGTCGACATACGCTTTGGCCA
* * ** * * *
31235607 ACCCTTTGTATAAGAGTTGGGATATGCATGCCTAAGACAATGCTTATATAAGATTAGGCTTTGTT
65 ACTCTTTGTATAAGAGTTGGGATATGCATGCCTAAGGCAACACTTAAATAAGAGTCGGCTTTGTT
31235672 CAACACTAT--
130 CAACACTATGC
* * * * * * * *
31235681 -G-C-C------G--G-CACTTTTCTAAGTGCTGGGGTAAACTGGTCGGCATACGTTTTGGTCAA
1 CGACACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAGACTTGTCGACATACGCTTTGGCCAA
* * * ** *
31235734 CTCTTTGTATAAGAGTTGGAATATGCATACCAAAGGCAACACTTAAATAAGAGTTAGCTTTGTCC
66 CTCTTTGTATAAGAGTTGGGATATGCATGCCTAAGGCAACACTTAAATAAGAGTCGGCTTTGTTC
31235799 AACACTATGC
131 AACACTATGC
* * * *
31235809 CGACACTTTTGGGCCAACACTTTCCTAAGTGTTGGGATAGACTTGCCAACATATGCTTTGGCCAA
1 CGACACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAGACTTGTCGACATACGCTTTGGCCAA
** * * * *
31235874 CTCTTTGTATAAG-GATCAGGATATGCATGCCTAAGGTAACACTTAAATAAGAGTCAGTTTTGTC
66 CTCTTTGTATAAGAG-TTGGGATATGCATGCCTAAGGCAACACTTAAATAAGAGTCGGCTTTGTT
31235938 CAACACTATGC
130 CAACACTATGC
31235949 C
1 C
31235950 AACTTGTGTT
Statistics
Matches: 446, Mismatches: 81, Indels: 42
0.78 0.14 0.07
Matches are distributed among these distances:
126 94 0.21
127 2 0.00
128 1 0.00
129 1 0.00
130 2 0.00
131 1 0.00
136 1 0.00
137 1 0.00
138 1 0.00
139 6 0.01
140 236 0.53
141 98 0.22
142 2 0.00
ACGTcount: A:0.28, C:0.19, G:0.21, T:0.32
Consensus pattern (140 bp):
CGACACTTTTGGGCCGACACTTTCCTAAGTGTTGGGATAGACTTGTCGACATACGCTTTGGCCAA
CTCTTTGTATAAGAGTTGGGATATGCATGCCTAAGGCAACACTTAAATAAGAGTCGGCTTTGTTC
AACACTATGC
Found at i:31236954 original size:21 final size:21
Alignment explanation
Indices: 31236930--31236976 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
31236920 TATCTAATTA
*
31236930 ATTTAGAGTTTAAAGTTTATG
1 ATTTAGAGTTTAAAGTTTAGG
* *
31236951 ATTTAGGGTTTATAGTTTAGG
1 ATTTAGAGTTTAAAGTTTAGG
31236972 ATTTA
1 ATTTA
31236977 ATGATTATGG
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.00, G:0.21, T:0.49
Consensus pattern (21 bp):
ATTTAGAGTTTAAAGTTTAGG
Found at i:31236996 original size:28 final size:27
Alignment explanation
Indices: 31236965--31237054 Score: 76
Period size: 28 Copynumber: 3.2 Consensus size: 27
31236955 AGGGTTTATA
31236965 GTTTAGGATTTAATGATTATGGTTTAGG
1 GTTTAGGATTTAA-GATTATGGTTTAGG
* * *
31236993 GTTTAGAAATTTAAG-TTTTGGGTTTTGG
1 GTTTAG-GATTTAAGATTAT-GGTTTAGG
* *
31237021 GTTTAGGGTTTTAGATGTACT-GTTTAGG
1 GTTTAGGATTTAAGAT-TA-TGGTTTAGG
31237049 GTTTAG
1 GTTTAG
31237055 AAAAGATTAA
Statistics
Matches: 49, Mismatches: 8, Indels: 10
0.73 0.12 0.15
Matches are distributed among these distances:
27 8 0.16
28 33 0.67
29 7 0.14
30 1 0.02
ACGTcount: A:0.21, C:0.01, G:0.30, T:0.48
Consensus pattern (27 bp):
GTTTAGGATTTAAGATTATGGTTTAGG
Found at i:31237266 original size:111 final size:111
Alignment explanation
Indices: 31237065--31237287 Score: 374
Period size: 111 Copynumber: 2.0 Consensus size: 111
31237055 AAAAGATTAA
31237065 ATGAAGACGAGAGTGAAGGAGAGACCAATGCTACTAAAGAACAGTTTAGTCAGCGAATCAATTAA
1 ATGAAGACGAGAGTGAAGGAGAGACCAATGCTACTAAAGAACAGTTTAGTCAGCGAATCAATTAA
* *
31237130 CCGATGTCAACCGGAACAGAGCTATTTTTAATCAAGTTTTTTTTTC
66 CCGATGTCAACCAGAACAGAACTATTTTTAATCAAGTTTTTTTTTC
* * * * *
31237176 ATGAAGACGGGAGTGAATGAGAGACCAATGCTACTAAAGAACGGTTTAGTCAGTGAATCAGTTAA
1 ATGAAGACGAGAGTGAAGGAGAGACCAATGCTACTAAAGAACAGTTTAGTCAGCGAATCAATTAA
*
31237241 CCGATGTCAACCAGAATAGAACTATTTTTAATCAAGTTTTTTTTTC
66 CCGATGTCAACCAGAACAGAACTATTTTTAATCAAGTTTTTTTTTC
31237287 A
1 A
31237288 CCTTTATTTG
Statistics
Matches: 104, Mismatches: 8, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
111 104 1.00
ACGTcount: A:0.36, C:0.15, G:0.21, T:0.28
Consensus pattern (111 bp):
ATGAAGACGAGAGTGAAGGAGAGACCAATGCTACTAAAGAACAGTTTAGTCAGCGAATCAATTAA
CCGATGTCAACCAGAACAGAACTATTTTTAATCAAGTTTTTTTTTC
Found at i:31238605 original size:15 final size:15
Alignment explanation
Indices: 31238585--31238616 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
31238575 GGCTCGGATG
31238585 TAAGGTAGGTGCTCT
1 TAAGGTAGGTGCTCT
31238600 TAAGGTAGGTGCTCT
1 TAAGGTAGGTGCTCT
31238615 TA
1 TA
31238617 GGGTCTTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.22, C:0.12, G:0.31, T:0.34
Consensus pattern (15 bp):
TAAGGTAGGTGCTCT
Found at i:31241091 original size:37 final size:37
Alignment explanation
Indices: 31240939--31241388 Score: 169
Period size: 35 Copynumber: 12.4 Consensus size: 37
31240929 GGTTTATTCC
* * *
31240939 AACC-TTTTAAAGGCTGTCGTAGAC-GGGTCTATCCT
1 AACCTTTTTAAAGGTTGTCTTAGACACGGTCTATCCT
* * * * * *
31240974 AACTTTTTTAAAGGTTGTCTTAGGCAAGGTATGTCTT
1 AACCTTTTTAAAGGTTGTCTTAGACACGGTCTATCCT
* * *
31241011 AACCTTTTTAAA-ATTGTATTAG--ACGGCTTTAT-CT
1 AACCTTTTTAAAGGTTGTCTTAGACACGG-TCTATCCT
** *
31241045 CAATTTTTTTAAAGGTTGTCTTAGACACGGTTTATCCT
1 -AACCTTTTTAAAGGTTGTCTTAGACACGGTCTATCCT
* *
31241083 AGCCTTTTT-AGGGTTG-CTTTAG--ACGAGTCTATCCT
1 AACCTTTTTAAAGGTTGTC-TTAGACACG-GTCTATCCT
* * **
31241118 AACCTTTTTTAAGGGTTGCCTTAGACAATGTCTATCC-
1 AACC-TTTTTAAAGGTTGTCTTAGACACGGTCTATCCT
*
31241155 AACCTTTTT-AAGGTTGCCTTA-A-ACGAGTCTAT-CT
1 AACCTTTTTAAAGGTTGTCTTAGACACG-GTCTATCCT
* * ** * * * *
31241189 CAACCTTTTTCAAGAATTACCTTAGATAAGGTTTATCCC
1 -AACCTTTTTAAAG-GTTGTCTTAGACACGGTCTATCCT
* * * *
31241228 AACCTTTTT-GAGTTTGCCTTA-A-ACGAGTCGAT-CT
1 AACCTTTTTAAAGGTTGTCTTAGACACG-GTCTATCCT
* * * *
31241262 CAACCTTTTTTAAGGGTTGCCTCAGACTGAC--T-TATCCC
1 -AACC-TTTTTAAAGGTTGTCTTAGAC--ACGGTCTATCCT
* **
31241300 AACCTTTTT-AAGGTTGTCTTATA-TGGGTCTATCCT
1 AACCTTTTTAAAGGTTGTCTTAGACACGGTCTATCCT
* * *
31241335 AACCTTTTTCAAAGATTGGCCTT-GACTA-GGTCTATCCC
1 AACCTTTTT-AAAGGTT-GTCTTAGAC-ACGGTCTATCCT
31241373 AACCTTTTTTAAAGGT
1 AACC-TTTTTAAAGGT
31241389 CGGCATTGAC
Statistics
Matches: 313, Mismatches: 61, Indels: 79
0.69 0.13 0.17
Matches are distributed among these distances:
33 2 0.01
34 18 0.06
35 81 0.26
36 73 0.23
37 73 0.23
38 55 0.18
39 9 0.03
41 2 0.01
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.39
Consensus pattern (37 bp):
AACCTTTTTAAAGGTTGTCTTAGACACGGTCTATCCT
Found at i:31241143 original size:73 final size:73
Alignment explanation
Indices: 31240929--31241381 Score: 330
Period size: 72 Copynumber: 6.3 Consensus size: 73
31240919 GTCTTAAATG
* * * * * * * * *
31240929 GGTTTATTCCAACCTTTTAAAGGCTGTCGTAGACGGGTCTATC-CTAA-CTTTTTTAAAGGTTGT
1 GGTTTATCCCAACCTTTTTAAGGTTGCCTTAAACGAGTCTATCTC-AACCTTTTTTAAGGGTTGC
*
31240992 CTTAGGCAA
65 CTTAGACAA
* * ** ** ** * * * * *
31241001 GGTATGTCTTAACCTTTTTAAAATTGTATTAGACG-GCTTTATCTCAA-TTTTTTTAAAGGTTGT
1 GGTTTATCCCAACCTTTTTAAGGTTGCCTTAAACGAG-TCTATCTCAACCTTTTTTAAGGGTTGC
*
31241064 CTTAGACAC
65 CTTAGACAA
* * * * *
31241073 GGTTTATCCTAGCCTTTTTAGGGTTGCTTTAGACGAGTCTATC-CTAACCTTTTTTAAGGGTTGC
1 GGTTTATCCCAACCTTTTTAAGGTTGCCTTAAACGAGTCTATCTC-AACCTTTTTTAAGGGTTGC
31241137 CTTAGACAA
65 CTTAGACAA
* * * ** *
31241146 TGTCTAT-CCAACCTTTTTAAGGTTGCCTTAAACGAGTCTATCTCAACCTTTTTCAAGAATTACC
1 GGTTTATCCCAACCTTTTTAAGGTTGCCTTAAACGAGTCTATCTCAACCTTTTTTAAGGGTTGCC
*
31241210 TTAGATAA
66 TTAGACAA
* * *
31241218 GGTTTATCCCAACCTTTTTGAGTTTGCCTTAAACGAGTCGATCTCAACCTTTTTTAAGGGTTGCC
1 GGTTTATCCCAACCTTTTTAAGGTTGCCTTAAACGAGTCTATCTCAACCTTTTTTAAGGGTTGCC
* *
31241283 TCAGAC-T
66 TTAGACAA
** * * * * * * *
31241290 GACTTATCCCAACCTTTTTAAGGTTGTCTTATATGGGTCTATC-CTAACCTTTTTCAAAGATTGG
1 GGTTTATCCCAACCTTTTTAAGGTTGCCTTAAACGAGTCTATCTC-AACCTTTTTTAAGGGTT-G
*
31241354 CCTT-GACTA
64 CCTTAGACAA
*
31241363 GGTCTATCCCAACCTTTTT
1 GGTTTATCCCAACCTTTTT
31241382 TAAAGGTCGG
Statistics
Matches: 301, Mismatches: 70, Indels: 19
0.77 0.18 0.05
Matches are distributed among these distances:
71 3 0.01
72 195 0.65
73 103 0.34
ACGTcount: A:0.24, C:0.20, G:0.17, T:0.40
Consensus pattern (73 bp):
GGTTTATCCCAACCTTTTTAAGGTTGCCTTAAACGAGTCTATCTCAACCTTTTTTAAGGGTTGCC
TTAGACAA
Found at i:31241234 original size:145 final size:146
Alignment explanation
Indices: 31241064--31241381 Score: 366
Period size: 145 Copynumber: 2.2 Consensus size: 146
31241054 TAAAGGTTGT
* * * * * * *
31241064 CTTAGACACGGTTTATCCTAGCCTTTTT-AGGGTTGCTTTAGACGAGTCTATC-CTAACCTTTTT
1 CTTAGATAAGGTTTATCCCAACCTTTTTGA-GGTTGCCTTAAACGAGTCGATCTC-AACCTTTTT
* *
31241127 TAAGGGTTGCCTTAGACAATGTC-TAT-CCAACCTTTTTAAGGTTGCCTTAAACGAGTCTAT-CT
64 TAAGGGTTGCCTCAGAC--TGACTTATCCCAACCTTTTTAAGGTTGCCTTAAACGAGTCTATCCT
31241189 CAACCTTTTTC-AAGAATT-AC
127 -AACCTTTTTCAAAG-ATTGAC
*
31241209 CTTAGATAAGGTTTATCCCAACCTTTTTGAGTTTGCCTTAAACGAGTCGATCTCAACCTTTTTTA
1 CTTAGATAAGGTTTATCCCAACCTTTTTGAGGTTGCCTTAAACGAGTCGATCTCAACCTTTTTTA
* * * *
31241274 AGGGTTGCCTCAGACTGACTTATCCCAACCTTTTTAAGGTTGTCTTATATGGGTCTATCCTAACC
66 AGGGTTGCCTCAGACTGACTTATCCCAACCTTTTTAAGGTTGCCTTAAACGAGTCTATCCTAACC
*
31241339 TTTTTCAAAGATTGGC
131 TTTTTCAAAGATTGAC
*
31241355 CTT-GACT-AGGTCTATCCCAACCTTTTT
1 CTTAGA-TAAGGTTTATCCCAACCTTTTT
31241382 TAAAGGTCGG
Statistics
Matches: 149, Mismatches: 16, Indels: 16
0.82 0.09 0.09
Matches are distributed among these distances:
143 3 0.02
144 3 0.02
145 131 0.88
146 12 0.08
ACGTcount: A:0.23, C:0.23, G:0.16, T:0.38
Consensus pattern (146 bp):
CTTAGATAAGGTTTATCCCAACCTTTTTGAGGTTGCCTTAAACGAGTCGATCTCAACCTTTTTTA
AGGGTTGCCTCAGACTGACTTATCCCAACCTTTTTAAGGTTGCCTTAAACGAGTCTATCCTAACC
TTTTTCAAAGATTGAC
Found at i:31241377 original size:38 final size:38
Alignment explanation
Indices: 31241325--31241400 Score: 107
Period size: 38 Copynumber: 2.0 Consensus size: 38
31241315 GTCTTATATG
* * *
31241325 GGTCTATCCTAACCTTTTTCAAAGATTGGCCTTGACTA
1 GGTCTATCCCAACCTTTTTCAAAGATCGGCATTGACTA
* *
31241363 GGTCTATCCCAACCTTTTTTAAAGGTCGGCATTGACTA
1 GGTCTATCCCAACCTTTTTCAAAGATCGGCATTGACTA
31241401 ATTTTTTCAC
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.24, C:0.24, G:0.17, T:0.36
Consensus pattern (38 bp):
GGTCTATCCCAACCTTTTTCAAAGATCGGCATTGACTA
Found at i:31242111 original size:44 final size:44
Alignment explanation
Indices: 31242042--31242142 Score: 148
Period size: 44 Copynumber: 2.3 Consensus size: 44
31242032 GATAGCGAAT
* * *
31242042 CTTATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTATAGAC
1 CTTATCTCCTTGAAGTTACAATGGAGCAGATTAAAGCTATAGAC
* * *
31242086 CTTATCTCCTTGAAGTTACAATGGAGCAGATTGAAGTTATAGAT
1 CTTATCTCCTTGAAGTTACAATGGAGCAGATTAAAGCTATAGAC
31242130 CTTATCTCCTTGA
1 CTTATCTCCTTGA
31242143 TGTTGTGATG
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
44 51 1.00
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.33
Consensus pattern (44 bp):
CTTATCTCCTTGAAGTTACAATGGAGCAGATTAAAGCTATAGAC
Found at i:31242154 original size:44 final size:43
Alignment explanation
Indices: 31241999--31242165 Score: 138
Period size: 44 Copynumber: 3.8 Consensus size: 43
31241989 TAGCAAACAC
* * * **
31241999 TATCTCCCTGAAGTTGTAGTGGAGCA-AGTTGAAGATAGCGAATCT
1 TATCTCCTTGAAGTTG-AATGGAGCAGA-TTGAAGCTATAG-ATCT
* * * *
31242044 TATCTCCCTGAAGTTGCAGTGGAGCAGATTAAAGCTATAGACCT
1 TATCTCCTTGAAGTTG-AATGGAGCAGATTGAAGCTATAGATCT
* *
31242088 TATCTCCTTGAAGTTACAATGGAGCAGATTGAAGTTATAGATCT
1 TATCTCCTTGAAGTT-GAATGGAGCAGATTGAAGCTATAGATCT
* * * *
31242132 TATCTCCTTGATGTTGTGATGGAGTAGATCGAAG
1 TATCTCCTTGAAGTTG-AATGGAGCAGATTGAAG
31242166 ATAGCAAATC
Statistics
Matches: 102, Mismatches: 17, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
44 68 0.67
45 33 0.32
46 1 0.01
ACGTcount: A:0.29, C:0.16, G:0.25, T:0.31
Consensus pattern (43 bp):
TATCTCCTTGAAGTTGAATGGAGCAGATTGAAGCTATAGATCT
Found at i:31242288 original size:133 final size:133
Alignment explanation
Indices: 31241999--31242298 Score: 286
Period size: 133 Copynumber: 2.3 Consensus size: 133
31241989 TAGCAAACAC
* * * * *
31241999 TATCTCCCTGAAGTTGT-AGTGGAGCA-AGTTGAAGATAGCGAATCTTATCTCCCTGAAGTTGCA
1 TATCACCCTAAAGTTGTGA-TGGAGCAGA-TCGAAGATAGCAAATCTTATCTCCCTAAAGTTGCA
* * * * * * * *
31242062 GTGGAGCAGATTAAAGCTATAGACCTTATCTCCTTGAAGTTACAATGGAGCAGATTGAAGTTATA
64 ATAGAACAGATTAAAGCCATAGACCTTATCTCCCTGAAGTTACAACGGAGCAGATTGAAGATACA
31242127 GATCT
129 GATCT
* * * * * * *
31242132 TATCTCCTTGATGTTGTGATGGAGTAGATCGAAGATAGCAAATCTTATCTCTCTAAAGTTTCAAT
1 TATCACCCTAAAGTTGTGATGGAGCAGATCGAAGATAGCAAATCTTATCTCCCTAAAGTTGCAAT
* * * *
31242197 AGAATAGATTAAAGCCATA-AGCCTTATCTCCCTGAAGTTGCAGCGGAGCAGGTTGAAGATACCA
66 AGAACAGATTAAAGCCATAGA-CCTTATCTCCCTGAAGTTACAACGGAGCAGATTGAAGATA-CA
31242261 -ATCT
129 GATCT
* *
31242265 TGTCACCCTAAAGTTGCTG-TGGAGCAGATTGAAG
1 TATCACCCTAAAGTTG-TGATGGAGCAGATCGAAG
31242299 CTACTAATTC
Statistics
Matches: 135, Mismatches: 27, Indels: 10
0.78 0.16 0.06
Matches are distributed among these distances:
132 1 0.01
133 129 0.96
134 5 0.04
ACGTcount: A:0.30, C:0.17, G:0.23, T:0.30
Consensus pattern (133 bp):
TATCACCCTAAAGTTGTGATGGAGCAGATCGAAGATAGCAAATCTTATCTCCCTAAAGTTGCAAT
AGAACAGATTAAAGCCATAGACCTTATCTCCCTGAAGTTACAACGGAGCAGATTGAAGATACAGA
TCT
Found at i:31243014 original size:13 final size:13
Alignment explanation
Indices: 31242998--31243041 Score: 54
Period size: 13 Copynumber: 3.2 Consensus size: 13
31242988 TATATTTACT
31242998 TATTATATAAATA
1 TATTATATAAATA
31243011 TATTAT-TAAATTA
1 TATTATATAAA-TA
31243024 TATTATTATAATATA
1 TATTA-TATAA-ATA
31243039 TAT
1 TAT
31243042 AAAGTAAATG
Statistics
Matches: 27, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
12 4 0.15
13 13 0.48
14 1 0.04
15 8 0.30
16 1 0.04
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TATTATATAAATA
Found at i:31244327 original size:44 final size:44
Alignment explanation
Indices: 31244278--31244369 Score: 123
Period size: 44 Copynumber: 2.1 Consensus size: 44
31244268 TGTTCAAGGA
*
31244278 TACTTCAACCTTGAGTCGATGAGGCA-CTATAAGTGTCGTACTGT
1 TACTTCAACCTTAAGTCGATGAGGCACCT-TAAGTGTCGTACTGT
* * **
31244322 TACTTCGACTTTAAGTCGATGAGGCACCTTGTGTGTCGTACTGT
1 TACTTCAACCTTAAGTCGATGAGGCACCTTAAGTGTCGTACTGT
31244366 TACT
1 TACT
31244370 GTTACTTCGG
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
44 40 0.95
45 2 0.05
ACGTcount: A:0.22, C:0.21, G:0.23, T:0.35
Consensus pattern (44 bp):
TACTTCAACCTTAAGTCGATGAGGCACCTTAAGTGTCGTACTGT
Found at i:31244455 original size:47 final size:47
Alignment explanation
Indices: 31244353--31244463 Score: 118
Period size: 47 Copynumber: 2.4 Consensus size: 47
31244343 AGGCACCTTG
* ** * * * *
31244353 TGTGTCGTACTGTTACTGTTACTTCGGATTATTCCGATGATGTACTC
1 TGTGCCGTACTGTTACTGTTACTTCGGATTAGGCCAATGAGGCACTA
* *
31244400 TGTTCCGTACTGTTACTGTTTACTTCGGCTT-GGCCAATGAGGCACTA
1 TGTGCCGTACTGTTACTG-TTACTTCGGATTAGGCCAATGAGGCACTA
31244447 TGTGCCGTACTG-TACTG
1 TGTGCCGTACTGTTACTG
31244464 GTATGATGGT
Statistics
Matches: 53, Mismatches: 10, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
46 5 0.09
47 37 0.70
48 11 0.21
ACGTcount: A:0.16, C:0.22, G:0.23, T:0.39
Consensus pattern (47 bp):
TGTGCCGTACTGTTACTGTTACTTCGGATTAGGCCAATGAGGCACTA
Found at i:31244568 original size:36 final size:35
Alignment explanation
Indices: 31244528--31244639 Score: 125
Period size: 36 Copynumber: 3.1 Consensus size: 35
31244518 TAAATAAAAG
* * *
31244528 TACTGAATGACTGACTGTTACTGAATAATTGATCGT
1 TACTGAATAACTGATTGCTACTGAATAATTGAT-GT
* ** *
31244564 TACTGAATAATTGATTGCTACTGAGCAAATGATTGT
1 TACTGAATAACTGATTGCTACTGAATAATTGA-TGT
*
31244600 TACTGAATAACTAATTGCTACTGAATAATTGAATGT
1 TACTGAATAACTGATTGCTACTGAATAATTG-ATGT
31244636 TACT
1 TACT
31244640 AAATGAAGCT
Statistics
Matches: 62, Mismatches: 12, Indels: 4
0.79 0.15 0.05
Matches are distributed among these distances:
36 60 0.97
37 2 0.03
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (35 bp):
TACTGAATAACTGATTGCTACTGAATAATTGATGT
Found at i:31244639 original size:18 final size:18
Alignment explanation
Indices: 31244528--31244639 Score: 93
Period size: 18 Copynumber: 6.2 Consensus size: 18
31244518 TAAATAAAAG
* * *
31244528 TACTGAATGACTGACTGT
1 TACTGAATAATTGAATGT
31244546 TACTGAATAATTG-ATCGT
1 TACTGAATAATTGAAT-GT
* *
31244564 TACTGAATAATTGATTGC
1 TACTGAATAATTGAATGT
** * *
31244582 TACTGAGCAAATGATTGT
1 TACTGAATAATTGAATGT
* *
31244600 TACTGAATAACT-AATTGC
1 TACTGAATAATTGAA-TGT
31244618 TACTGAATAATTGAATGT
1 TACTGAATAATTGAATGT
31244636 TACT
1 TACT
31244640 AAATGAAGCT
Statistics
Matches: 74, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
17 2 0.03
18 69 0.93
19 3 0.04
ACGTcount: A:0.34, C:0.12, G:0.17, T:0.37
Consensus pattern (18 bp):
TACTGAATAATTGAATGT
Found at i:31246919 original size:39 final size:39
Alignment explanation
Indices: 31246865--31246942 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
31246855 TCGACCCGCT
31246865 CTAGCCTTAGGATTCGTGTGTTTTTGACGGAAGGGCTAA
1 CTAGCCTTAGGATTCGTGTGTTTTTGACGGAAGGGCTAA
31246904 CTAGCCTTAGGATTCGTGTGTTTTTGACGGAAGGGCTAA
1 CTAGCCTTAGGATTCGTGTGTTTTTGACGGAAGGGCTAA
31246943 TTGCACCTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.21, C:0.15, G:0.31, T:0.33
Consensus pattern (39 bp):
CTAGCCTTAGGATTCGTGTGTTTTTGACGGAAGGGCTAA
Found at i:31247252 original size:3 final size:3
Alignment explanation
Indices: 31247238--31247297 Score: 57
Period size: 3 Copynumber: 20.0 Consensus size: 3
31247228 TTTAACATTG
* * * * * *
31247238 TAT TAT TCT TAT TAT TAT TAT CAT TAC TAC TAC TAT TAT TAT TAT TAC
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
*
31247286 TAC TAT TAT TAT
1 TAT TAT TAT TAT
31247298 ATTTCTTTTT
Statistics
Matches: 49, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.57
Consensus pattern (3 bp):
TAT
Found at i:31247274 original size:21 final size:21
Alignment explanation
Indices: 31247250--31247297 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
31247240 TTATTCTTAT
31247250 TATTATTATCATTACTACTAC
1 TATTATTATCATTACTACTAC
* *
31247271 TATTATTATTATTACTACTAT
1 TATTATTATCATTACTACTAC
31247292 TATTAT
1 TATTAT
31247298 ATTTCTTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.33, C:0.12, G:0.00, T:0.54
Consensus pattern (21 bp):
TATTATTATCATTACTACTAC
Found at i:31247295 original size:18 final size:18
Alignment explanation
Indices: 31247238--31247297 Score: 75
Period size: 18 Copynumber: 3.3 Consensus size: 18
31247228 TTTAACATTG
* * *
31247238 TATTATTCTTATTATTAT
1 TATTATTATTACTACTAT
* *
31247256 TATCATTACTACTACTAT
1 TATTATTATTACTACTAT
31247274 TATTATTATTACTACTAT
1 TATTATTATTACTACTAT
31247292 TATTAT
1 TATTAT
31247298 ATTTCTTTTT
Statistics
Matches: 35, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.32, C:0.12, G:0.00, T:0.57
Consensus pattern (18 bp):
TATTATTATTACTACTAT
Found at i:31247653 original size:16 final size:17
Alignment explanation
Indices: 31247628--31247662 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
31247618 CTTTTTATTA
*
31247628 ATTTTTTTACGCAT-TT
1 ATTTTATTACGCATGTT
31247644 ATTTTATTACGCATGTT
1 ATTTTATTACGCATGTT
31247661 AT
1 AT
31247663 CATTGTGATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.23, C:0.11, G:0.09, T:0.57
Consensus pattern (17 bp):
ATTTTATTACGCATGTT
Found at i:31250663 original size:41 final size:41
Alignment explanation
Indices: 31250606--31250691 Score: 145
Period size: 41 Copynumber: 2.1 Consensus size: 41
31250596 TATGAGAATG
**
31250606 TGTTTACTTCTAATCAAGTTTGTTTTAAACATTATCTACTA
1 TGTTTACTTCTAATCAAGTTTGTCGTAAACATTATCTACTA
*
31250647 TGTTTACTTCTTATCAAGTTTGTCGTAAACATTATCTACTA
1 TGTTTACTTCTAATCAAGTTTGTCGTAAACATTATCTACTA
31250688 TGTT
1 TGTT
31250692 GATTTGGTGT
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
41 42 1.00
ACGTcount: A:0.27, C:0.15, G:0.09, T:0.49
Consensus pattern (41 bp):
TGTTTACTTCTAATCAAGTTTGTCGTAAACATTATCTACTA
Found at i:31266437 original size:29 final size:28
Alignment explanation
Indices: 31266386--31266448 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 28
31266376 TTACAGAACT
31266386 AAAATACAGGGCCAAACATAT-AATAAA
1 AAAATACAGGGCCAAACATATAAATAAA
31266413 AAAAGTACAGGAGCCAAAC-TGATAAATAAA
1 AAAA-TACAGG-GCCAAACAT-ATAAATAAA
*
31266443 ATAATA
1 AAAATA
31266449 TAAGTATTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 6
0.82 0.03 0.16
Matches are distributed among these distances:
27 4 0.13
28 7 0.23
29 11 0.35
30 9 0.29
ACGTcount: A:0.59, C:0.13, G:0.13, T:0.16
Consensus pattern (28 bp):
AAAATACAGGGCCAAACATATAAATAAA
Found at i:31266939 original size:3 final size:3
Alignment explanation
Indices: 31266931--31266963 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
31266921 TTTAAAGGAG
31266931 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
31266964 GTATTCATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:31275487 original size:108 final size:107
Alignment explanation
Indices: 31275317--31275525 Score: 244
Period size: 108 Copynumber: 1.9 Consensus size: 107
31275307 TTTGGGTTAA
** * * **
31275317 TATTTGGTATGTTGGTAGTGAACTTTTTTTATTTCACAAATAGTCTTACGAAATTATCATGTGTC
1 TATTTGGTACATTGATAGTGAACTTTTTTTATTTCACAAACAACCTTAC-AAATTATCATGTGTC
* ** * *
31275382 CCCTTTTTTTAAAAATATTTTGTT-ATATTTTACTATGGATAAG
65 CCATTTTTAAAAAAAT-TTTTCTTAACATTTTACTATGGATAAG
31275425 TATTTGGTACATTGATAGTGTAACTTTTTTTATTTCACAAACAACCTTA-AAATT-TGACATGTG
1 TATTTGGTACATTGATAGTG-AACTTTTTTTATTTCACAAACAACCTTACAAATTAT--CATGTG
*
31275488 TCTCATTTTTAAAAAAATTTTTCTTAACATTTTACTAT
63 TCCCATTTTTAAAAAAATTTTTCTTAACATTTTACTAT
31275526 TATAGGACAC
Statistics
Matches: 85, Mismatches: 12, Indels: 8
0.81 0.11 0.08
Matches are distributed among these distances:
106 1 0.01
107 11 0.13
108 48 0.56
109 25 0.29
ACGTcount: A:0.30, C:0.11, G:0.11, T:0.47
Consensus pattern (107 bp):
TATTTGGTACATTGATAGTGAACTTTTTTTATTTCACAAACAACCTTACAAATTATCATGTGTCC
CATTTTTAAAAAAATTTTTCTTAACATTTTACTATGGATAAG
Found at i:31279250 original size:19 final size:19
Alignment explanation
Indices: 31279211--31279269 Score: 57
Period size: 19 Copynumber: 3.1 Consensus size: 19
31279201 TTTTAAAAAA
*
31279211 TTGT-ATAATTTTTATTCTT
1 TTGTAATAATTTTTAAT-TT
31279230 TTGTAATAATTTTTAATTT
1 TTGTAATAATTTTTAATTT
** *
31279249 TTAAAATATTTTTTAAATTT
1 TTGTAATAATTTTT-AATTT
31279269 T
1 T
31279270 ATAAATTTTA
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
19 17 0.50
20 17 0.50
ACGTcount: A:0.31, C:0.02, G:0.03, T:0.64
Consensus pattern (19 bp):
TTGTAATAATTTTTAATTT
Found at i:31279270 original size:19 final size:20
Alignment explanation
Indices: 31279234--31279275 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
31279224 ATTCTTTTGT
*
31279234 AATAATTTTTAATTTTTA-A
1 AATAATTTTTAAATTTTATA
*
31279253 AATATTTTTTAAATTTTATA
1 AATAATTTTTAAATTTTATA
31279273 AAT
1 AAT
31279276 TTTAAAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
19 16 0.80
20 4 0.20
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
AATAATTTTTAAATTTTATA
Found at i:31279292 original size:28 final size:27
Alignment explanation
Indices: 31279237--31279292 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
31279227 CTTTTGTAAT
* * **
31279237 AATTTTTAATTTTTAAAATATTTTTTA
1 AATTTTTAAATTTTAAAAAATTAATTA
31279264 AATTTTATAAATTTTAAAAAATTAATTA
1 AATTTT-TAAATTTTAAAAAATTAATTA
31279292 A
1 A
31279293 TTACTAGCGT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 6 0.25
28 18 0.75
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (27 bp):
AATTTTTAAATTTTAAAAAATTAATTA
Found at i:31282745 original size:2 final size:2
Alignment explanation
Indices: 31282738--31282774 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
31282728 GAAAATTAAA
31282738 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
31282775 AAAGAAATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:31289971 original size:31 final size:31
Alignment explanation
Indices: 31289909--31289968 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
31289899 CAATGTTCAA
* *
31289909 TTAATTTTTTATATTTATCTTTATTTAAATT
1 TTAATTATTTATATTTATATTTATTTAAATT
31289940 TTAATTATTTAT-TTTATAATTATATTTAA
1 TTAATTATTTATATTTAT-ATT-TATTTAA
31289969 TTTCTCTTTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
30 5 0.20
31 13 0.52
32 7 0.28
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (31 bp):
TTAATTATTTATATTTATATTTATTTAAATT
Found at i:31292330 original size:23 final size:23
Alignment explanation
Indices: 31292282--31292331 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
31292272 TGCACGGTGG
**
31292282 CCGGTGCCGGCACCGGTGAAGGC
1 CCGGTGCCGGCACCGGTGAACCC
*
31292305 CCGGTGGCCGG-ACCGGTGACCCC
1 CCGGT-GCCGGCACCGGTGAACCC
31292328 CCGG
1 CCGG
31292332 CCGGAACCCC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.10, C:0.40, G:0.42, T:0.08
Consensus pattern (23 bp):
CCGGTGCCGGCACCGGTGAACCC
Done.