Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D12
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: 63843421
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1690000 characters in sequence are not A, C, G, or T
File 167 of 214
Found at i:49313014 original size:84 final size:84
Alignment explanation
Indices: 49312880--49313054 Score: 289
Period size: 84 Copynumber: 2.1 Consensus size: 84
49312870 TGGATTTACT
* * *
49312880 GGCGTTTTTATGTATGCGCCGCTATTGGTTTGGGGTGATAGTGGCGTGTTTTGGTCAATCGCCAC
1 GGCGTTTCTATGTATGCGCCGCTATTGGATTGGGGGGATAGTGGCGTGTTTTGGTCAATCGCCAC
49312945 TAATGTTAAGGTATTTAGC
66 TAATGTTAAGGTATTTAGC
*
49312964 GGCGTTTCTAT-TATAGCGCCGCTATTTGATTGGGGGGATAGTGGCGTGTTTTGGTCAATCGCCA
1 GGCGTTTCTATGTAT-GCGCCGCTATTGGATTGGGGGGATAGTGGCGTGTTTTGGTCAATCGCCA
*
49313028 CTAATGTTAATGTATTTAGC
65 CTAATGTTAAGGTATTTAGC
49313048 GGCGTTT
1 GGCGTTT
49313055 GGTTTTAAAG
Statistics
Matches: 85, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
83 3 0.04
84 82 0.96
ACGTcount: A:0.17, C:0.15, G:0.30, T:0.38
Consensus pattern (84 bp):
GGCGTTTCTATGTATGCGCCGCTATTGGATTGGGGGGATAGTGGCGTGTTTTGGTCAATCGCCAC
TAATGTTAAGGTATTTAGC
Found at i:49314117 original size:28 final size:28
Alignment explanation
Indices: 49314085--49314221 Score: 113
Period size: 28 Copynumber: 4.9 Consensus size: 28
49314075 GTATGGATTA
49314085 GGGTTTGGGATTAAGGTTTATGGGTTTG
1 GGGTTTGGGATTAAGGTTTATGGGTTTG
** * *
49314113 GGGTTACGG-TCT-AGGTTTAGGGGTTAG
1 GGGTTTGGGAT-TAAGGTTTATGGGTTTG
* * *
49314140 GGGTTAGGGGTTAAGGATT-TGGGTTTTG
1 GGGTTTGGGATTAAGGTTTATGGG-TTTG
* *
49314168 GGGTTTGGGGTT-TGTGATTTA-GGGTTTG
1 GGGTTTGGGATTAAG-G-TTTATGGGTTTG
*
49314196 GGGTTTGGGATTAAAGTTTATGGGTT
1 GGGTTTGGGATTAAGGTTTATGGGTT
49314222 AAGGACTTAT
Statistics
Matches: 86, Mismatches: 14, Indels: 18
0.73 0.12 0.15
Matches are distributed among these distances:
27 31 0.36
28 50 0.58
29 5 0.06
ACGTcount: A:0.14, C:0.01, G:0.44, T:0.41
Consensus pattern (28 bp):
GGGTTTGGGATTAAGGTTTATGGGTTTG
Found at i:49314181 original size:21 final size:21
Alignment explanation
Indices: 49314157--49314207 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
49314147 GGGTTAAGGA
* *
49314157 TTTGGGTTTTGGGGTTTGGGG
1 TTTGGGATTTAGGGTTTGGGG
*
49314178 TTTGTGATTTAGGGTTTGGGG
1 TTTGGGATTTAGGGTTTGGGG
49314199 TTTGGGATT
1 TTTGGGATT
49314208 AAAGTTTATG
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.06, C:0.00, G:0.45, T:0.49
Consensus pattern (21 bp):
TTTGGGATTTAGGGTTTGGGG
Found at i:49314202 original size:7 final size:7
Alignment explanation
Indices: 49314126--49314204 Score: 68
Period size: 7 Copynumber: 11.1 Consensus size: 7
49314116 TTACGGTCTA
49314126 GGTTTAGG
1 GGTTT-GG
*
49314134 GGTTAGG
1 GGTTTGG
*
49314141 GGTTAGG
1 GGTTTGG
**
49314148 GGTTAAG
1 GGTTTGG
*
49314155 GATTTGG
1 GGTTTGG
*
49314162 GTTTTGG
1 GGTTTGG
49314169 GGTTTGG
1 GGTTTGG
*
49314176 GGTTTGT
1 GGTTTGG
* *
49314183 GATTTAG
1 GGTTTGG
49314190 GGTTTGG
1 GGTTTGG
49314197 GGTTTGG
1 GGTTTGG
49314204 G
1 G
49314205 ATTAAAGTTT
Statistics
Matches: 58, Mismatches: 13, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
7 54 0.93
8 4 0.07
ACGTcount: A:0.10, C:0.00, G:0.49, T:0.41
Consensus pattern (7 bp):
GGTTTGG
Found at i:49315098 original size:23 final size:24
Alignment explanation
Indices: 49315072--49315128 Score: 71
Period size: 23 Copynumber: 2.4 Consensus size: 24
49315062 CACTTAGCCG
49315072 AAATTCCCCCCAAATTAT-CCCCA
1 AAATTCCCCCCAAATTATCCCCCA
* * *
49315095 AAATTCCCCCCGATTTTTCCCCCA
1 AAATTCCCCCCAAATTATCCCCCA
*
49315119 AAAATCCCCC
1 AAATTCCCCC
49315129 AATTCTAGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
23 15 0.52
24 14 0.48
ACGTcount: A:0.30, C:0.46, G:0.02, T:0.23
Consensus pattern (24 bp):
AAATTCCCCCCAAATTATCCCCCA
Found at i:49315616 original size:12 final size:12
Alignment explanation
Indices: 49315601--49315640 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
49315591 TGTAATACTG
49315601 TTTGTTCATAAT
1 TTTGTTCATAAT
49315613 TTTGTT-ACTAAT
1 TTTGTTCA-TAAT
*
49315625 TTTGTTCATAAG
1 TTTGTTCATAAT
49315637 TTTG
1 TTTG
49315641 AAACTATTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
11 1 0.04
12 23 0.92
13 1 0.04
ACGTcount: A:0.23, C:0.07, G:0.12, T:0.57
Consensus pattern (12 bp):
TTTGTTCATAAT
Found at i:49315646 original size:24 final size:24
Alignment explanation
Indices: 49315601--49315646 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
49315591 TGTAATACTG
* **
49315601 TTTGTTCATAATTTTGTTACTAAT
1 TTTGTTCATAAGTTTGAAACTAAT
49315625 TTTGTTCATAAGTTTGAAACTA
1 TTTGTTCATAAGTTTGAAACTA
49315647 TTTGTATTAC
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.28, C:0.09, G:0.11, T:0.52
Consensus pattern (24 bp):
TTTGTTCATAAGTTTGAAACTAAT
Found at i:49315929 original size:18 final size:18
Alignment explanation
Indices: 49315906--49315943 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
49315896 GCAATTCGTA
49315906 TAGTTTATATCCTGTTTG
1 TAGTTTATATCCTGTTTG
49315924 TAGTTTATATCCTGTTTG
1 TAGTTTATATCCTGTTTG
49315942 TA
1 TA
49315944 TCCTATTTGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.18, C:0.11, G:0.16, T:0.55
Consensus pattern (18 bp):
TAGTTTATATCCTGTTTG
Found at i:49316835 original size:24 final size:23
Alignment explanation
Indices: 49316808--49316905 Score: 55
Period size: 24 Copynumber: 4.2 Consensus size: 23
49316798 AAATTTTATA
49316808 ATTTTAGAAATAATTGTAAATGTT
1 ATTTTAGAAATAATT-TAAATGTT
** *
49316832 ATTTTCTAAAT-A-TTAACATATAT
1 ATTTTAGAAATAATTTAA-ATGT-T
*
49316855 ATTTTCA-ATAATAAATTT---TGTA
1 ATTTT-AGA-AAT-AATTTAAATGTT
49316877 ATTTTAGAAATAATTGTAAATGTT
1 ATTTTAGAAATAATT-TAAATGTT
49316901 ATTTT
1 ATTTT
49316906 TCTAAATATG
Statistics
Matches: 55, Mismatches: 7, Indels: 24
0.64 0.08 0.28
Matches are distributed among these distances:
20 4 0.07
21 8 0.15
22 10 0.18
23 10 0.18
24 20 0.36
26 1 0.02
27 2 0.04
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (23 bp):
ATTTTAGAAATAATTTAAATGTT
Found at i:49316852 original size:69 final size:69
Alignment explanation
Indices: 49316739--49317526 Score: 1326
Period size: 69 Copynumber: 11.3 Consensus size: 69
49316729 TTCTAGAAAT
* * *
49316739 TTTTA-AAACTAATTATACATGTTATTTTTCTAAATATTAACATATATATTTTCAGTAATAAATT
1 TTTTAGAAA-TAATTGTAAATGTTA-TTTTCTAAATATTAACATATATATTTTCAATAATAAATT
49316803 TTATAA
64 TTATAA
49316809 TTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAACATATATATTTTCAATAATAAATTTT
1 TTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAACATATATATTTTCAATAATAAATTTT
*
49316874 GTAA
66 ATAA
*
49316878 TTTTAGAAATAATTGTAAATGTTATTTTTCTAAATATGAACATATATATTTTCAATAATAAATTT
1 TTTTAGAAATAATTGTAAATGTTA-TTTTCTAAATATTAACATATATATTTTCAATAATAAATTT
*
49316943 TGTAA
65 TATAA
*
49316948 TTTTAGAAATAATTGTAAATGTTATTTTTCTAAATATGAACATATATATTTTCAATAATAAATTT
1 TTTTAGAAATAATTGTAAATGTTA-TTTTCTAAATATTAACATATATATTTTCAATAATAAATTT
49317013 TATAA
65 TATAA
49317018 TTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAACATATATATTTTCAATAATAAATTTT
1 TTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAACATATATATTTTCAATAATAAATTTT
*
49317083 GTAA
66 ATAA
*
49317087 TTTTAGAAATAATTGTAAATGTTATTTTTCTAAATATGAACATATATATTTTCAATAATAAATTT
1 TTTTAGAAATAATTGTAAATGTTA-TTTTCTAAATATTAACATATATATTTTCAATAATAAATTT
*
49317152 TGTAA
65 TATAA
*
49317157 TTTTAGAAATAATTGTAAATGTTATTTTTCTAAATATGAACATATATATTTTCAATAATAAATTT
1 TTTTAGAAATAATTGTAAATGTTA-TTTTCTAAATATTAACATATATATTTTCAATAATAAATTT
49317222 TATAA
65 TATAA
* * *
49317227 TATTAGAAATAATTGTAAATGTTATTTTCTAAATATTAACATCTATATTTTCAATAATAAATTCT
1 TTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAACATATATATTTTCAATAATAAATTTT
*
49317292 ATGA
66 ATAA
*
49317296 TTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAACATCTATATTTTCAATAATAAATTTT
1 TTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAACATATATATTTTCAATAATAAATTTT
*
49317361 GTAA
66 ATAA
*
49317365 TTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAACATCTATATTTTCAATAATAAATTTT
1 TTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAACATATATATTTTCAATAATAAATTTT
49317430 ATAA
66 ATAA
* *
49317434 TTTTAGAAATAATTGTAAATGTTATTTTCTAAATATGAACATCTATATTTTCAATAATAAATTTT
1 TTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAACATATATATTTTCAATAATAAATTTT
49317499 ATAA
66 ATAA
*
49317503 TTTTAGAAAGAATTGTAAATGTTA
1 TTTTAGAAATAATTGTAAATGTTA
49317527 CATAATTCAA
Statistics
Matches: 693, Mismatches: 22, Indels: 7
0.96 0.03 0.01
Matches are distributed among these distances:
69 399 0.58
70 291 0.42
71 3 0.00
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (69 bp):
TTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAACATATATATTTTCAATAATAAATTTT
ATAA
Found at i:49317016 original size:21 final size:21
Alignment explanation
Indices: 49316783--49317507 Score: 97
Period size: 21 Copynumber: 31.4 Consensus size: 21
49316773 TATTAACATA
* *
49316783 TATATTTTCAGTAATAAATTT
1 TATATTTTAAATAATAAATTT
*
49316804 TATAATTTTAGAAATAATTGTAAATGT
1 TAT-ATTTT--AAATAA---TAAATTT
* *
49316831 TAT-TTTCTAAATATTAACA-TA
1 TATATTT-TAAATAATAA-ATTT
*
49316852 TATATTTTCAATAATAAATTT
1 TATATTTTAAATAATAAATTT
* *
49316873 TGTAATTTTAGAAATAATTGTAAATGT
1 TAT-ATTTT--AAATAA---TAAATTT
* *
49316900 TATTTTTCTAAAT-ATGAACA-TA
1 TATATTT-TAAATAAT-AA-ATTT
*
49316922 TATATTTTCAATAATAAATTT
1 TATATTTTAAATAATAAATTT
* *
49316943 TGTAATTTTAGAAATAATTGTAAATGT
1 TAT-ATTTT--AAATAA---TAAATTT
* *
49316970 TATTTTTCTAAAT-ATGAACA-TA
1 TATATTT-TAAATAAT-AA-ATTT
*
49316992 TATATTTTCAATAATAAATTT
1 TATATTTTAAATAATAAATTT
*
49317013 TATAATTTTAGAAATAATTGTAAATGT
1 TAT-ATTTT--AAATAA---TAAATTT
* *
49317040 TAT-TTTCTAAATATTAACA-TA
1 TATATTT-TAAATAATAA-ATTT
*
49317061 TATATTTTCAATAATAAATTT
1 TATATTTTAAATAATAAATTT
* *
49317082 TGTAATTTTAGAAATAATTGTAAATGT
1 TAT-ATTTT--AAATAA---TAAATTT
* *
49317109 TATTTTTCTAAAT-ATGAACA-TA
1 TATATTT-TAAATAAT-AA-ATTT
*
49317131 TATATTTTCAATAATAAATTT
1 TATATTTTAAATAATAAATTT
* *
49317152 TGTAATTTTAGAAATAATTGTAAATGT
1 TAT-ATTTT--AAATAA---TAAATTT
* *
49317179 TATTTTTCTAAAT-ATGAACA-TA
1 TATATTT-TAAATAAT-AA-ATTT
*
49317201 TATATTTTCAATAATAAATTT
1 TATATTTTAAATAATAAATTT
* *
49317222 TATAATATTAGAAATAATTGTAAATGT
1 TAT-AT-TT-TAAATAA---TAAATTT
* *
49317249 TAT-TTTCTAAATATTAACA-TC
1 TATATTT-TAAATAATAA-ATTT
* *
49317270 TATATTTTCAATAATAAATTC
1 TATATTTTAAATAATAAATTT
*
49317291 TATGATTTTAGAAATAATTGTAAATGT
1 TAT-ATTTT--AAATAA---TAAATTT
* *
49317318 TAT-TTTCTAAATATTAACA-TC
1 TATATTT-TAAATAATAA-ATTT
*
49317339 TATATTTTCAATAATAAATTT
1 TATATTTTAAATAATAAATTT
* *
49317360 TGTAATTTTAGAAATAATTGTAAATGT
1 TAT-ATTTT--AAATAA---TAAATTT
* *
49317387 TAT-TTTCTAAATATTAACA-TC
1 TATATTT-TAAATAATAA-ATTT
*
49317408 TATATTTTCAATAATAAATTT
1 TATATTTTAAATAATAAATTT
*
49317429 TATAATTTTAGAAATAATTGTAAATGT
1 TAT-ATTTT--AAATAA---TAAATTT
*
49317456 TAT-TTTCTAAAT-ATGAACA-TC
1 TATATTT-TAAATAAT-AA-ATTT
*
49317477 TATATTTTCAATAATAAATTT
1 TATATTTTAAATAATAAATTT
49317498 TATAATTTTA
1 TAT-ATTTTA
49317508 GAAAGAATTG
Statistics
Matches: 505, Mismatches: 93, Indels: 211
0.62 0.11 0.26
Matches are distributed among these distances:
20 11 0.02
21 148 0.29
22 118 0.23
23 7 0.01
24 84 0.17
25 32 0.06
26 17 0.03
27 88 0.17
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (21 bp):
TATATTTTAAATAATAAATTT
Found at i:49317044 original size:24 final size:23
Alignment explanation
Indices: 49317017--49317114 Score: 55
Period size: 24 Copynumber: 4.2 Consensus size: 23
49317007 AAATTTTATA
49317017 ATTTTAGAAATAATTGTAAATGTT
1 ATTTTAGAAATAATT-TAAATGTT
** *
49317041 ATTTTCTAAAT-A-TTAACATATAT
1 ATTTTAGAAATAATTTAA-ATGT-T
*
49317064 ATTTTCA-ATAATAAATTT---TGTA
1 ATTTT-AGA-AAT-AATTTAAATGTT
49317086 ATTTTAGAAATAATTGTAAATGTT
1 ATTTTAGAAATAATT-TAAATGTT
49317110 ATTTT
1 ATTTT
49317115 TCTAAATATG
Statistics
Matches: 55, Mismatches: 7, Indels: 24
0.64 0.08 0.28
Matches are distributed among these distances:
20 4 0.07
21 8 0.15
22 10 0.18
23 10 0.18
24 20 0.36
26 1 0.02
27 2 0.04
ACGTcount: A:0.41, C:0.03, G:0.07, T:0.49
Consensus pattern (23 bp):
ATTTTAGAAATAATTTAAATGTT
Found at i:49317117 original size:209 final size:209
Alignment explanation
Indices: 49316739--49317526 Score: 1393
Period size: 209 Copynumber: 3.8 Consensus size: 209
49316729 TTCTAGAAAT
* * * *
49316739 TTTTA-AAACTAATTATACATGTTATTTTTCTAAATATTAACATATATATTTTCAGTAATAAATT
1 TTTTAGAAA-TAATTGTAAATGTTATTTTTCTAAATATGAACATATATATTTTCAATAATAAATT
49316803 TTATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAACATATATATTTTCAATAATA
65 TTATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAACATATATATTTTCAATAATA
*
49316868 AATTTTGTAATTTTAGAAATAATTGTAAATGTTATTTTTCTAAATATGAACATATATATTTTCAA
130 AATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTTCTAAATATGAACATATATATTTTCAA
49316933 TAATAAATTTTGTAA
195 TAATAAATTTTGTAA
49316948 TTTTAGAAATAATTGTAAATGTTATTTTTCTAAATATGAACATATATATTTTCAATAATAAATTT
1 TTTTAGAAATAATTGTAAATGTTATTTTTCTAAATATGAACATATATATTTTCAATAATAAATTT
49317013 TATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAACATATATATTTTCAATAATAA
66 TATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAACATATATATTTTCAATAATAA
*
49317078 ATTTTGTAATTTTAGAAATAATTGTAAATGTTATTTTTCTAAATATGAACATATATATTTTCAAT
131 ATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTTCTAAATATGAACATATATATTTTCAAT
49317143 AATAAATTTTGTAA
196 AATAAATTTTGTAA
49317157 TTTTAGAAATAATTGTAAATGTTATTTTTCTAAATATGAACATATATATTTTCAATAATAAATTT
1 TTTTAGAAATAATTGTAAATGTTATTTTTCTAAATATGAACATATATATTTTCAATAATAAATTT
* *
49317222 TATAATATTAGAAATAATTGTAAATGTTATTTTCTAAATATTAACATCTATATTTTCAATAATAA
66 TATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAACATATATATTTTCAATAATAA
* * * *
49317287 ATTCTATGATTTTAGAAATAATTGTAAATGTTA-TTTTCTAAATATTAACATCTATATTTTCAAT
131 ATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTTCTAAATATGAACATATATATTTTCAAT
49317351 AATAAATTTTGTAA
196 AATAAATTTTGTAA
* *
49317365 TTTTAGAAATAATTGTAAATGTTA-TTTTCTAAATATTAACATCTATATTTTCAATAATAAATTT
1 TTTTAGAAATAATTGTAAATGTTATTTTTCTAAATATGAACATATATATTTTCAATAATAAATTT
* *
49317429 TATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATGAACATCTATATTTTCAATAATAA
66 TATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAACATATATATTTTCAATAATAA
*
49317494 ATTTTATAATTTTAGAAAGAATTGTAAATGTTA
131 ATTTTATAATTTTAGAAATAATTGTAAATGTTA
49317527 CATAATTCAA
Statistics
Matches: 560, Mismatches: 18, Indels: 4
0.96 0.03 0.01
Matches are distributed among these distances:
207 131 0.23
208 67 0.12
209 359 0.64
210 3 0.01
ACGTcount: A:0.42, C:0.05, G:0.06, T:0.47
Consensus pattern (209 bp):
TTTTAGAAATAATTGTAAATGTTATTTTTCTAAATATGAACATATATATTTTCAATAATAAATTT
TATAATTTTAGAAATAATTGTAAATGTTATTTTCTAAATATTAACATATATATTTTCAATAATAA
ATTTTATAATTTTAGAAATAATTGTAAATGTTATTTTTCTAAATATGAACATATATATTTTCAAT
AATAAATTTTGTAA
Found at i:49317660 original size:19 final size:19
Alignment explanation
Indices: 49317636--49317672 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
49317626 ATATAAACTT
49317636 ACATAATACATAACTTATG
1 ACATAATACATAACTTATG
49317655 ACATAATACATAACTTAT
1 ACATAATACATAACTTAT
49317673 ATATAAACTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.49, C:0.16, G:0.03, T:0.32
Consensus pattern (19 bp):
ACATAATACATAACTTATG
Found at i:49317670 original size:47 final size:47
Alignment explanation
Indices: 49317619--49317709 Score: 173
Period size: 47 Copynumber: 1.9 Consensus size: 47
49317609 ATTATATAAC
49317619 AACTTATATATAAACTTACATAATACATAACTTATGACATAATACAT
1 AACTTATATATAAACTTACATAATACATAACTTATGACATAATACAT
*
49317666 AACTTATATATAAACTTACATAATACATAACTTATTACATAATA
1 AACTTATATATAAACTTACATAATACATAACTTATGACATAATA
49317710 AGTTACGTAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
47 43 1.00
ACGTcount: A:0.49, C:0.14, G:0.01, T:0.35
Consensus pattern (47 bp):
AACTTATATATAAACTTACATAATACATAACTTATGACATAATACAT
Found at i:49317824 original size:16 final size:16
Alignment explanation
Indices: 49317801--49317854 Score: 81
Period size: 16 Copynumber: 3.3 Consensus size: 16
49317791 GTCGGACTTG
*
49317801 CATAACTTATATAATA
1 CATAACTTACATAATA
*
49317817 CTTAACTTACATAATA
1 CATAACTTACATAATA
49317833 CATAACTTACATAATAA
1 CATAACTTACATAAT-A
49317850 CATAA
1 CATAA
49317855 TAAGTTACAT
Statistics
Matches: 34, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
16 28 0.82
17 6 0.18
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (16 bp):
CATAACTTACATAATA
Found at i:49317940 original size:9 final size:9
Alignment explanation
Indices: 49317922--49317998 Score: 69
Period size: 9 Copynumber: 9.3 Consensus size: 9
49317912 AACTTGTCGG
*
49317922 ACTTGCATA
1 ACTTACATA
*
49317931 ACTTATATA
1 ACTTACATA
*
49317940 A--TACTTA
1 ACTTACATA
49317947 ACTTACATA
1 ACTTACATA
49317956 ACTTACATA
1 ACTTACATA
49317965 A--TACATA
1 ACTTACATA
*
49317972 ACTTACGT-
1 ACTTACATA
49317980 A--TACATA
1 ACTTACATA
49317987 ACTTACATA
1 ACTTACATA
49317996 ACT
1 ACT
49317999 GATATATACT
Statistics
Matches: 54, Mismatches: 7, Indels: 14
0.72 0.09 0.19
Matches are distributed among these distances:
6 4 0.07
7 13 0.24
8 1 0.02
9 36 0.67
ACGTcount: A:0.43, C:0.19, G:0.03, T:0.35
Consensus pattern (9 bp):
ACTTACATA
Found at i:49317956 original size:25 final size:25
Alignment explanation
Indices: 49317922--49317977 Score: 85
Period size: 25 Copynumber: 2.2 Consensus size: 25
49317912 AACTTGTCGG
* * *
49317922 ACTTGCATAACTTATATAATACTTA
1 ACTTACATAACTTACATAATACATA
49317947 ACTTACATAACTTACATAATACATA
1 ACTTACATAACTTACATAATACATA
49317972 ACTTAC
1 ACTTAC
49317978 GTATACATAA
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 28 1.00
ACGTcount: A:0.43, C:0.20, G:0.02, T:0.36
Consensus pattern (25 bp):
ACTTACATAACTTACATAATACATA
Found at i:49317985 original size:15 final size:16
Alignment explanation
Indices: 49317950--49317996 Score: 78
Period size: 15 Copynumber: 3.0 Consensus size: 16
49317940 ATACTTAACT
49317950 TACATAACTTACATAA
1 TACATAACTTACATAA
*
49317966 TACATAACTTACGT-A
1 TACATAACTTACATAA
49317981 TACATAACTTACATAA
1 TACATAACTTACATAA
49317997 CTGATATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
15 14 0.50
16 14 0.50
ACGTcount: A:0.47, C:0.19, G:0.02, T:0.32
Consensus pattern (16 bp):
TACATAACTTACATAA
Found at i:49323624 original size:19 final size:18
Alignment explanation
Indices: 49323591--49323636 Score: 65
Period size: 19 Copynumber: 2.5 Consensus size: 18
49323581 GACTATCGTG
*
49323591 TAACTTTTTTTATCATTT
1 TAACTTTTATTATCATTT
49323609 TAACTTTATATTATCATTT
1 TAACTTT-TATTATCATTT
*
49323628 TACCTTTTA
1 TAACTTTTA
49323637 ACATATTTGT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
18 9 0.36
19 16 0.64
ACGTcount: A:0.26, C:0.13, G:0.00, T:0.61
Consensus pattern (18 bp):
TAACTTTTATTATCATTT
Found at i:49324087 original size:43 final size:42
Alignment explanation
Indices: 49323819--49324196 Score: 226
Period size: 43 Copynumber: 8.8 Consensus size: 42
49323809 AGCTGCTCAA
* * * * * * **
49323819 TTTAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGGTTAATGCA
1 TTTAGCGGCGTTTGT-AGTAAAGCGCCGCTAAAAGTCAAGGTT
* * * *
49323862 TTTAGCGGCGTTTTTATGAAAAGCGTCGCTAAAAGTCAAGTTCT
1 TTTAGCGGCGTTTGTA-GTAAAGCGCCGCTAAAAGTCAAGGT-T
* * * * ***
49323906 TTTAGCCGCGTTTGTGAGAAAATCGTCGCTAAAAGGGTAGGTCT
1 TTTAGCGGCGTTTGT-AGTAAAGCGCCGCTAAAAGTCAAGGT-T
* * ** *
49323950 TCTAGCGGCGTTTGT-GCCTAAAGCGCCGCTAAAGGTCAACATA
1 TTTAGCGGCGTTTGTAG--TAAAGCGCCGCTAAAAGTCAAGGTT
* * * * * *
49323993 TCTAGTGGCGTTTGTAAATAAAGCGCCGCT-ATAGGCTAATGTAT
1 TTTAGCGGCGTTTGT-AGTAAAGCGCCGCTAAAAGTC-AAGGT-T
*
49324037 TTT-GCGGCGTTTGTAGTGAAAGCGCCGCTAAAAGTCAGGGTT
1 TTTAGCGGCGTTTGTAGT-AAAGCGCCGCTAAAAGTCAAGGTT
* * *
49324079 TTTAGCGGCGTTTGTTGTTTAAGCGCCGCTAAAGGTCAAGGTT
1 TTTAGCGGCGTTTGTAG-TAAAGCGCCGCTAAAAGTCAAGGTT
* * * *
49324122 TATAGTGGCGTTTGTAGTAAAAGCGCCGCT-AAAGCTCAAGCTC
1 TTTAGCGGCGTTTGTAGT-AAAGCGCCGCTAAAAG-TCAAGGTT
* *
49324165 TTTAGCGGCGTTTAG-ATTAAAGCACCGCTAAA
1 TTTAGCGGCGTTT-GTAGTAAAGCGCCGCTAAA
49324197 GATAATAACC
Statistics
Matches: 259, Mismatches: 59, Indels: 34
0.74 0.17 0.10
Matches are distributed among these distances:
42 24 0.09
43 163 0.63
44 71 0.27
45 1 0.00
ACGTcount: A:0.25, C:0.18, G:0.28, T:0.29
Consensus pattern (42 bp):
TTTAGCGGCGTTTGTAGTAAAGCGCCGCTAAAAGTCAAGGTT
Found at i:49324089 original size:86 final size:86
Alignment explanation
Indices: 49323819--49324177 Score: 270
Period size: 86 Copynumber: 4.2 Consensus size: 86
49323809 AGCTGCTCAA
* * * * *
49323819 TTTAGCGGCGTTTGTGGGAAAAGTGCCGCTAAAGGTTAATGCATT-TAGCGGCGTTTTTA-TGAA
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGG-TAAGGTATTATAGCGGCGTTTGTAGTG-A
* *
49323882 AAGCGTCGCTAAAAGTCAAGTTCT
64 AAGCGCCGCTAAAAGTCAAGAT-T
* * * * *
49323906 TTTAGCCGCGTTTGTGAGAAAATCGTCGCTAAAAGGGT-AGGTCTTCTAGCGGCGTTTGT-GCCT
1 TTTAGCGGCGTTTGTGAGAAAAGCGCCGCT-AAA-GGTAAGGTATTATAGCGGCGTTTGTAG--T
* * *
49323969 -AAAGCGCCGCTAAAGGTCAACATA
62 GAAAGCGCCGCTAAAAGTCAAGATT
* * * * * *
49323993 TCTAGTGGCGTTTGT-AAATAAAGCGCCGCTATAGGCTAATGTATT-TTGCGGCGTTTGTAGTGA
1 TTTAGCGGCGTTTGTGAGA-AAAGCGCCGCTAAAGG-TAAGGTATTATAGCGGCGTTTGTAGTGA
* *
49324056 AAGCGCCGCTAAAAGTCAGGGTT
64 AAGCGCCGCTAAAAGTCAAGATT
*** * *
49324079 TTTAGCGGCGTTTGTTG-TTTAAGCGCCGCTAAAGGTCAAGGT-TTATAGTGGCGTTTGTAGTAA
1 TTTAGCGGCGTTTG-TGAGAAAAGCGCCGCTAAAGGT-AAGGTATTATAGCGGCGTTTGTAGTGA
* *
49324142 AAGCGCCGCT-AAAGCTCAAGCTC
64 AAGCGCCGCTAAAAG-TCAAGATT
49324165 TTTAGCGGCGTTT
1 TTTAGCGGCGTTT
49324178 AGATTAAAGC
Statistics
Matches: 214, Mismatches: 42, Indels: 33
0.74 0.15 0.11
Matches are distributed among these distances:
85 10 0.05
86 109 0.51
87 57 0.27
88 35 0.16
89 2 0.01
90 1 0.00
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (86 bp):
TTTAGCGGCGTTTGTGAGAAAAGCGCCGCTAAAGGTAAGGTATTATAGCGGCGTTTGTAGTGAAA
GCGCCGCTAAAAGTCAAGATT
Found at i:49324745 original size:16 final size:16
Alignment explanation
Indices: 49324714--49324743 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
49324704 TTTAAAATAT
49324714 ATATTTATATTATTTA
1 ATATTTATATTATTTA
49324730 ATATTTA-ATTATTT
1 ATATTTATATTATTT
49324744 TATTTATTAA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (16 bp):
ATATTTATATTATTTA
Found at i:49328267 original size:9 final size:9
Alignment explanation
Indices: 49328253--49328328 Score: 91
Period size: 9 Copynumber: 8.4 Consensus size: 9
49328243 GTAGTTATTC
49328253 AATTCGGTT
1 AATTCGGTT
49328262 AATTCGGTT
1 AATTCGGTT
* *
49328271 AATTTGATT
1 AATTCGGTT
* *
49328280 AATTTGGCT
1 AATTCGGTT
49328289 AATTCAGG-T
1 AATTC-GGTT
*
49328298 AATTAGGTT
1 AATTCGGTT
49328307 AATTCGGTT
1 AATTCGGTT
49328316 AATTCGGTT
1 AATTCGGTT
49328325 AATT
1 AATT
49328329 TTTAACCAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
8 2 0.03
9 54 0.93
10 2 0.03
ACGTcount: A:0.28, C:0.08, G:0.20, T:0.45
Consensus pattern (9 bp):
AATTCGGTT
Found at i:49330241 original size:39 final size:39
Alignment explanation
Indices: 49330198--49330278 Score: 144
Period size: 39 Copynumber: 2.1 Consensus size: 39
49330188 ATATAGTTTG
*
49330198 GTTTTGGTATAGTATTCACCTTATTGATTTTTGTGACAT
1 GTTTTGGTATAGTAGTCACCTTATTGATTTTTGTGACAT
*
49330237 GTTTTGGTATAGTAGTCACTTTATTGATTTTTGTGACAT
1 GTTTTGGTATAGTAGTCACCTTATTGATTTTTGTGACAT
49330276 GTT
1 GTT
49330279 ATGTTAGCCA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.20, C:0.09, G:0.20, T:0.52
Consensus pattern (39 bp):
GTTTTGGTATAGTAGTCACCTTATTGATTTTTGTGACAT
Found at i:49336444 original size:25 final size:25
Alignment explanation
Indices: 49336342--49336461 Score: 84
Period size: 25 Copynumber: 4.9 Consensus size: 25
49336332 TGGATTTTCG
* * **
49336342 GAGCTACCTGCTAT-TGGCTCGCAT
1 GAGCTTCCTGTTATATGGCTCATAT
* * * *
49336366 GAGCTCCCTG-AATAGGGCTCTTAT
1 GAGCTTCCTGTTATATGGCTCATAT
* * * *
49336390 GAGCTTCCTATTATACAGCCTGA-AT
1 GAGCTTCCTGTTATA-TGGCTCATAT
*
49336415 AAGCTTCCTGTTATATGGCTCATAT
1 GAGCTTCCTGTTATATGGCTCATAT
*
49336440 GAGCTTCTTGTTATATGGCTCA
1 GAGCTTCCTGTTATATGGCTCA
49336462 AGAGAGGGCT
Statistics
Matches: 73, Mismatches: 19, Indels: 7
0.74 0.19 0.07
Matches are distributed among these distances:
23 2 0.03
24 28 0.38
25 40 0.55
26 3 0.04
ACGTcount: A:0.22, C:0.23, G:0.21, T:0.34
Consensus pattern (25 bp):
GAGCTTCCTGTTATATGGCTCATAT
Found at i:49338516 original size:83 final size:82
Alignment explanation
Indices: 49338393--49338557 Score: 276
Period size: 83 Copynumber: 2.0 Consensus size: 82
49338383 GAAATGTCTA
* * *
49338393 TTCGGAGAGTTGATTGATGAAACGACAAGACTACCGTATATTGTGATAGTCAAAGTGTCATACAT
1 TTCGGAGAGCTAATTGATGAAACGACAAGACTACCATATATTGTGATAGTCAAAGTGTCATACAT
*
49338458 CTTACGAAAGTACAAAG
66 CTCACGAAAGTACAAAG
*
49338475 TTCGGAGAGCTAATTGATAGAAATGACAAGACTACCATATATTGTGATAGTCAAAGTGTCATACA
1 TTCGGAGAGCTAATTGAT-GAAACGACAAGACTACCATATATTGTGATAGTCAAAGTGTCATACA
49338540 TCTCACGAAAGTACAAAG
65 TCTCACGAAAGTACAAAG
49338558 CACTCTAGCT
Statistics
Matches: 77, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
82 16 0.21
83 61 0.79
ACGTcount: A:0.38, C:0.15, G:0.21, T:0.26
Consensus pattern (82 bp):
TTCGGAGAGCTAATTGATGAAACGACAAGACTACCATATATTGTGATAGTCAAAGTGTCATACAT
CTCACGAAAGTACAAAG
Found at i:49340240 original size:34 final size:34
Alignment explanation
Indices: 49340196--49340261 Score: 98
Period size: 34 Copynumber: 1.9 Consensus size: 34
49340186 CGGTAAAATA
*
49340196 TTTTCCGTAAAATGATTT-CTAGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACT-GAAAATATTTTAC
*
49340230 TTTTCTGTAAAATGATTTACTGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGAAAATATTTT
49340262 TTGGTGTTTG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
34 27 0.93
35 2 0.07
ACGTcount: A:0.33, C:0.09, G:0.11, T:0.47
Consensus pattern (34 bp):
TTTTCCGTAAAATGATTTACTGAAAATATTTTAC
Found at i:49340376 original size:18 final size:18
Alignment explanation
Indices: 49340349--49340392 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
49340339 TTTTTACATA
49340349 TATATATT-AATAAATTTT
1 TATATATTAAAT-AATTTT
* *
49340367 TATATTTTAAATTATTTT
1 TATATATTAAATAATTTT
49340385 TATATATT
1 TATATATT
49340393 GTTTTTACAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 19 0.86
19 3 0.14
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (18 bp):
TATATATTAAATAATTTT
Found at i:49340539 original size:34 final size:34
Alignment explanation
Indices: 49340496--49340560 Score: 114
Period size: 34 Copynumber: 1.9 Consensus size: 34
49340486 ACAACTAAAA
49340496 TCAATATTTGTAATTGTGTTAAAA-TAATAATAC
1 TCAATATTTGTAATTGTGTTAAAAGTAATAATAC
49340529 TCAATTATTTGTAATTGTGTTAAAAGTAATAA
1 TCAA-TATTTGTAATTGTGTTAAAAGTAATAA
49340561 AAAACAAGGA
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
33 4 0.13
34 20 0.67
35 6 0.20
ACGTcount: A:0.42, C:0.05, G:0.11, T:0.43
Consensus pattern (34 bp):
TCAATATTTGTAATTGTGTTAAAAGTAATAATAC
Found at i:49341223 original size:19 final size:19
Alignment explanation
Indices: 49341199--49341251 Score: 52
Period size: 21 Copynumber: 2.7 Consensus size: 19
49341189 CATATAGGAT
49341199 TTCAGCAAATAAACACATC
1 TTCAGCAAATAAACACATC
***
49341218 TTCAGCTTCTTAGAACACATC
1 TTCAGC-AAATA-AACACATC
*
49341239 TTCAGGAAATAAA
1 TTCAGCAAATAAA
49341252 TCATTAAAAA
Statistics
Matches: 25, Mismatches: 7, Indels: 4
0.69 0.19 0.11
Matches are distributed among these distances:
19 8 0.32
20 4 0.16
21 13 0.52
ACGTcount: A:0.42, C:0.23, G:0.09, T:0.26
Consensus pattern (19 bp):
TTCAGCAAATAAACACATC
Found at i:49342845 original size:24 final size:25
Alignment explanation
Indices: 49342813--49342859 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
49342803 TTAAGGTGAA
*
49342813 ATTTGATTT-TTTTTTGTTATTTTCT
1 ATTTGATTTCTTTTAT-TTATTTTCT
49342838 ATTT-ATTTCTTTTATTTATTTT
1 ATTTGATTTCTTTTATTTATTTT
49342860 TTTTCGTTTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
24 11 0.55
25 9 0.45
ACGTcount: A:0.15, C:0.04, G:0.04, T:0.77
Consensus pattern (25 bp):
ATTTGATTTCTTTTATTTATTTTCT
Found at i:49347418 original size:20 final size:20
Alignment explanation
Indices: 49347393--49347432 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
49347383 TTCACCTCAT
49347393 GCATCGCATCATATGCATTA
1 GCATCGCATCATATGCATTA
*
49347413 GCATCGTATCATATGCATTA
1 GCATCGCATCATATGCATTA
49347433 AAGACCTTTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.30, C:0.23, G:0.15, T:0.33
Consensus pattern (20 bp):
GCATCGCATCATATGCATTA
Found at i:49355519 original size:45 final size:45
Alignment explanation
Indices: 49355446--49355681 Score: 185
Period size: 45 Copynumber: 5.3 Consensus size: 45
49355436 AAAAAGTAGT
* * * * * * * *
49355446 AGATCATGTCTTCCTATATTGGTAGCGAAGTGGATCGAATATACC
1 AGATCTTGTCTTCCCATACTAGTGGCGAAGTAGATCGAAGAAACC
* * *
49355491 AGATCTTGCCTTCCCATACTAGTGGCGAAGCAGATCGAAGAAAGC
1 AGATCTTGTCTTCCCATACTAGTGGCGAAGTAGATCGAAGAAACC
* * * *
49355536 AGATCTTATCTT--CAT-GTACTGGCGTAAAGTAGATC-AGAGATACC
1 AGATCTTGTCTTCCCATACTAGTGGCG--AAGTAGATCGA-AGAAACC
* * * *
49355580 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATC-AAAAAAAC
1 AGATCTTGTCTTCCCATACTAGTGGCGAAGTAGATCGAAGAAACC
* * * * *
49355624 AGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATCGAAGAAAGC
1 AGATCTTGTCTTCCCATACTAGTGGCGAAGTAGATCGAAGAAACC
*
49355669 AGATCTTATCTTC
1 AGATCTTGTCTTC
49355682 ATGTACTGGC
Statistics
Matches: 152, Mismatches: 32, Indels: 14
0.77 0.16 0.07
Matches are distributed among these distances:
42 7 0.05
43 4 0.03
44 62 0.41
45 71 0.47
46 3 0.02
47 5 0.03
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.28
Consensus pattern (45 bp):
AGATCTTGTCTTCCCATACTAGTGGCGAAGTAGATCGAAGAAACC
Found at i:49355583 original size:44 final size:45
Alignment explanation
Indices: 49355529--49355704 Score: 153
Period size: 44 Copynumber: 4.0 Consensus size: 45
49355519 AGCAGATCGA
* ** *
49355529 AGAAAGCAGATCTTATCTTCATGTACTGG-CGTAAAGTAGATCAG
1 AGAAAACAGATCTTATCTTCACATACTGGTCGTGAAGTAGATCAG
* * * * *
49355573 AGATACCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCA-
1 AGAAAACAGATCTTATCTTCACATACTGGTCGTGAAGTAGATCAG
* * * * * *
49355617 AAAAAACAGATCTTGTCTCCCCATACTGGTGGTGGAGTAGATC-G
1 AGAAAACAGATCTTATCTTCACATACTGGTCGTGAAGTAGATCAG
* **
49355661 AAGAAAGCAGATCTTATCTTCATGTACTGG-CGTGAAGTAGATCA
1 -AGAAAACAGATCTTATCTTCACATACTGGTCGTGAAGTAGATCA
49355705 AAGATAGTAG
Statistics
Matches: 106, Mismatches: 22, Indels: 7
0.79 0.16 0.05
Matches are distributed among these distances:
44 72 0.68
45 34 0.32
ACGTcount: A:0.31, C:0.18, G:0.23, T:0.27
Consensus pattern (45 bp):
AGAAAACAGATCTTATCTTCACATACTGGTCGTGAAGTAGATCAG
Found at i:49355656 original size:89 final size:88
Alignment explanation
Indices: 49355473--49355706 Score: 220
Period size: 89 Copynumber: 2.6 Consensus size: 88
49355463 ATTGGTAGCG
* * * * * * * *
49355473 AAGTGGATCGAATATACCAGATCTTGCCTTCCCATACTAGTGGCGAAGCAGATCGAAGAAAGCAG
1 AAGTAGATCGAAGATACCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATC-AAAAAAACAG
* **
49355538 ATCTTATCTTCATGTACTGGCGTA
65 ATCTTATCTCCACATACTGGCGTA
49355562 AAGTAGATC-AGAGATACCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCAAAAAAACAG
1 AAGTAGATCGA-AGATACCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCAAAAAAACAG
* * * *
49355626 ATCTTGTCTCCCCATACTGGTGGTG
65 ATCTTATCTCCACATACTGG-CGTA
* * * * *** *
49355651 GAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTACTGG-CGTGAAGTAGATCAAA
1 AAGTAGATCGAAGATACCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCAAA
49355707 GATAGTAGGT
Statistics
Matches: 119, Mismatches: 23, Indels: 7
0.80 0.15 0.05
Matches are distributed among these distances:
88 39 0.33
89 79 0.66
90 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.23, T:0.26
Consensus pattern (88 bp):
AAGTAGATCGAAGATACCAGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCAAAAAAACAGA
TCTTATCTCCACATACTGGCGTA
Found at i:49355773 original size:133 final size:133
Alignment explanation
Indices: 49355438--49355791 Score: 397
Period size: 133 Copynumber: 2.7 Consensus size: 133
49355428 AGCAGGTTAA
* *
49355438 AAAG-TAGTAGATCATGTCTTCCTATATTGGTAGCGAAGTGGATCGAATATACCAGATCTTGCCT
1 AAAGATAGTAGATCATGTCTTCCTATATCGGTAGCGAAGTGGATCGAATATA-CAGATCTTGTCT
*
49355502 TCCCATACTAGTGGCGAAGCAGATCGAAGAAAGCAGATCTTATCTTCATGTACTGGCGTAAAGTA
65 TCCCATACTGGTGGCGAAGCAGATCGAAGAAAGCAGATCTTATCTTCATGTACTGGCGTAAAGTA
49355567 GATC
130 GATC
* ** * * * * * * * *
49355571 AGAGATACCAGATCTTGTCTTCCCATA-CTGGTGGTGAAGTAGATCAAAAAAACAGATCTTGTCT
1 AAAGATAGTAGATCATGTCTTCCTATATC-GGTAGCGAAGTGGATCGAATATACAGATCTTGTCT
* * * * *
49355635 CCCCATACTGGTGGTGGAGTAGATCGAAGAAAGCAGATCTTATCTTCATGTACTGGCGTGAAGTA
65 TCCCATACTGGTGGCGAAGCAGATCGAAGAAAGCAGATCTTATCTTCATGTACTGGCGTAAAGTA
49355700 GATC
130 GATC
* * * * ** * * * *
49355704 AAAGATAGTAGGTCCTGTCTTCATATATCGGTAACGGGGTGGATCGAATATATATATTTTATCTT
1 AAAGATAGTAGATCATGTCTTCCTATATCGGTAGCGAAGTGGATCGAATATACAGATCTTGTCTT
* *
49355769 CCCATACTGGTGGCAAAGTAGAT
66 CCCATACTGGTGGCGAAGCAGAT
49355792 TGAAAATTAC
Statistics
Matches: 175, Mismatches: 43, Indels: 6
0.78 0.19 0.03
Matches are distributed among these distances:
133 139 0.79
134 36 0.21
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.29
Consensus pattern (133 bp):
AAAGATAGTAGATCATGTCTTCCTATATCGGTAGCGAAGTGGATCGAATATACAGATCTTGTCTT
CCCATACTGGTGGCGAAGCAGATCGAAGAAAGCAGATCTTATCTTCATGTACTGGCGTAAAGTAG
ATC
Found at i:49355982 original size:44 final size:45
Alignment explanation
Indices: 49355934--49356018 Score: 118
Period size: 44 Copynumber: 1.9 Consensus size: 45
49355924 CGGAAAAAGC
** *
49355934 AGATCTTGTCTTCATGTATTGG-CGTGAAGTAGATCGAAGAAAAT
1 AGATCTTGTCTTCACATACTGGTCGTGAAGTAGATCGAAGAAAAT
* *
49355978 AGATCTTGTCTTCCCATACTGGTGGTGAAGTAGATCGAAGA
1 AGATCTTGTCTTCACATACTGGTCGTGAAGTAGATCGAAGA
49356019 CACAAGTCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
44 18 0.51
45 17 0.49
ACGTcount: A:0.29, C:0.14, G:0.26, T:0.31
Consensus pattern (45 bp):
AGATCTTGTCTTCACATACTGGTCGTGAAGTAGATCGAAGAAAAT
Found at i:49356941 original size:24 final size:23
Alignment explanation
Indices: 49356914--49356972 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 23
49356904 TTAAGGTGAA
49356914 ATTTGATTTTTTTTTCTTTT-TGTT
1 ATTT-ATTTTTTTTTCTTTTAT-TT
*
49356938 ATTT-TCTATTTATTTCTTTTATTT
1 ATTTAT-T-TTTTTTTCTTTTATTT
49356962 ATTTATTTTTT
1 ATTTATTTTTT
49356973 CGTTTTAAAT
Statistics
Matches: 29, Mismatches: 2, Indels: 9
0.73 0.05 0.22
Matches are distributed among these distances:
22 1 0.03
23 4 0.14
24 22 0.76
25 2 0.07
ACGTcount: A:0.14, C:0.05, G:0.03, T:0.78
Consensus pattern (23 bp):
ATTTATTTTTTTTTCTTTTATTT
Found at i:49359955 original size:7 final size:7
Alignment explanation
Indices: 49359943--49359971 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
49359933 GGGGAGGATG
49359943 ACATGAA
1 ACATGAA
49359950 ACATGAA
1 ACATGAA
49359957 ACATGAA
1 ACATGAA
49359964 ACATGAA
1 ACATGAA
49359971 A
1 A
49359972 ATCAACCTCG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.59, C:0.14, G:0.14, T:0.14
Consensus pattern (7 bp):
ACATGAA
Found at i:49364527 original size:15 final size:17
Alignment explanation
Indices: 49364497--49364528 Score: 50
Period size: 15 Copynumber: 2.0 Consensus size: 17
49364487 TAAAAAGTGT
49364497 TTTTTATTCTAAAAATA
1 TTTTTATTCTAAAAATA
49364514 TTTTT-TTC-AAAAATA
1 TTTTTATTCTAAAAATA
49364529 CTTCTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 7 0.47
16 3 0.20
17 5 0.33
ACGTcount: A:0.41, C:0.06, G:0.00, T:0.53
Consensus pattern (17 bp):
TTTTTATTCTAAAAATA
Found at i:49377296 original size:7 final size:7
Alignment explanation
Indices: 49377278--49377307 Score: 51
Period size: 7 Copynumber: 4.1 Consensus size: 7
49377268 TATTAATATT
49377278 TTTAATAA
1 TTTAA-AA
49377286 TTTAAAA
1 TTTAAAA
49377293 TTTAAAA
1 TTTAAAA
49377300 TTTAAAA
1 TTTAAAA
49377307 T
1 T
49377308 GATATTTTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 17 0.77
8 5 0.23
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (7 bp):
TTTAAAA
Found at i:49386931 original size:19 final size:19
Alignment explanation
Indices: 49386907--49386951 Score: 81
Period size: 19 Copynumber: 2.4 Consensus size: 19
49386897 ATTGCGATAG
49386907 GATGTTACTTGCCATATAC
1 GATGTTACTTGCCATATAC
49386926 GATGTTACTTGCCATATAC
1 GATGTTACTTGCCATATAC
*
49386945 GAAGTTA
1 GATGTTA
49386952 ACAATTTATG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.36
Consensus pattern (19 bp):
GATGTTACTTGCCATATAC
Found at i:49388483 original size:22 final size:22
Alignment explanation
Indices: 49388453--49388506 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 22
49388443 AAGTTATGAA
*
49388453 ATATATAAAAAAATATATATGT
1 ATATATAAAAAAATATATATAT
* * *
49388475 ATGTATAAATATATATATATAT
1 ATATATAAAAAAATATATATAT
49388497 ATATATAAAA
1 ATATATAAAA
49388507 CATTAAATAT
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.57, C:0.00, G:0.04, T:0.39
Consensus pattern (22 bp):
ATATATAAAAAAATATATATAT
Found at i:49388518 original size:2 final size:2
Alignment explanation
Indices: 49388465--49388503 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
49388455 ATATAAAAAA
* * *
49388465 AT AT AT AT GT AT GT AT AA 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 AT A
49388504 AAACATTAAA
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.49, C:0.00, G:0.05, T:0.46
Consensus pattern (2 bp):
AT
Found at i:49388577 original size:27 final size:25
Alignment explanation
Indices: 49388545--49388603 Score: 73
Period size: 25 Copynumber: 2.3 Consensus size: 25
49388535 AAAAATGTGT
*
49388545 ATGTATGTGCAGGTATGCATTATAAAA
1 ATGTATGTGCA--TATACATTATAAAA
* *
49388572 ATGTATGTGTATATATATTATAAAA
1 ATGTATGTGCATATACATTATAAAA
49388597 ATGTATG
1 ATGTATG
49388604 AATGTATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 19 0.66
27 10 0.34
ACGTcount: A:0.39, C:0.03, G:0.19, T:0.39
Consensus pattern (25 bp):
ATGTATGTGCATATACATTATAAAA
Found at i:49388596 original size:25 final size:26
Alignment explanation
Indices: 49388563--49388616 Score: 92
Period size: 25 Copynumber: 2.1 Consensus size: 26
49388553 GCAGGTATGC
49388563 ATTATAAAAATGTATG-TGTATATAT
1 ATTATAAAAATGTATGATGTATATAT
49388588 ATTATAAAAATGTATGAATGTATATAT
1 ATTATAAAAATGTATG-ATGTATATAT
49388615 AT
1 AT
49388617 AACAAAATTT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 16 0.59
27 11 0.41
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (26 bp):
ATTATAAAAATGTATGATGTATATAT
Found at i:49388623 original size:27 final size:25
Alignment explanation
Indices: 49388568--49388623 Score: 76
Period size: 27 Copynumber: 2.2 Consensus size: 25
49388558 TATGCATTAT
* *
49388568 AAAAATGTATGTGTATATATATTAT
1 AAAAATGTATGTGTATATATATAAC
49388593 AAAAATGTATGAATGTATATATATAAC
1 AAAAATGTATG--TGTATATATATAAC
49388620 AAAA
1 AAAA
49388624 TTTGAAATTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
25 11 0.41
27 16 0.59
ACGTcount: A:0.52, C:0.02, G:0.11, T:0.36
Consensus pattern (25 bp):
AAAAATGTATGTGTATATATATAAC
Found at i:49388674 original size:11 final size:11
Alignment explanation
Indices: 49388652--49388681 Score: 51
Period size: 11 Copynumber: 2.6 Consensus size: 11
49388642 TAAATGAGTA
49388652 AATAATAATAAT
1 AATAA-AATAAT
49388664 AATAAAATAAT
1 AATAAAATAAT
49388675 AATAAAA
1 AATAAAA
49388682 GAACAAAATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 13 0.72
12 5 0.28
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (11 bp):
AATAAAATAAT
Found at i:49390261 original size:44 final size:43
Alignment explanation
Indices: 49390213--49390435 Score: 125
Period size: 44 Copynumber: 5.0 Consensus size: 43
49390203 GGGATGAGGT
* *
49390213 TTGTAGTTTTAGTCTGTTCCACTGCAACTTCAGGGAGATAAGA
1 TTGTAGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA
* * * * *
49390256 CTTGTA-TCTTCAACCTACTCCACTACAACTTCAGGGAGATAAGGT
1 -TTGTAGT-TTTAATCTGCTCCACTGCAACTTCAGGGAGATAA-GA
* * * *
49390301 TTGATATGATAATATCTAAT-T-CAACCTACTGCAACTTTAGAGG-TATATGA
1 TTG-TA-G-T--T-T-TAATCTGC-TCC-ACTGCAACTTCAG-GGAGATAAGA
* * * *
49390351 TTCATCGTTTTAATCCGCTCCACTGCAACTTCAGGGAGATAGGA
1 TT-GTAGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA
* *
49390395 TTG--GTTTCAGTCTGCTCCACTGCAACTTCAGGGAGATAAGA
1 TTGTAGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA
49390436 CTCGTTATCT
Statistics
Matches: 135, Mismatches: 28, Indels: 35
0.68 0.14 0.18
Matches are distributed among these distances:
41 34 0.25
43 3 0.02
44 59 0.44
45 6 0.04
46 2 0.01
48 2 0.01
49 3 0.02
50 8 0.06
51 16 0.12
52 2 0.01
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.32
Consensus pattern (43 bp):
TTGTAGTTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGA
Found at i:49390706 original size:81 final size:81
Alignment explanation
Indices: 49390590--49390745 Score: 224
Period size: 81 Copynumber: 1.9 Consensus size: 81
49390580 AACTTCAGGG
* * * * *
49390590 AGATAAGATTGGATACGATCTGCTCTATTGTAACTTCAAAGAGATAATATTTGTGGTTTTAATTC
1 AGATAAGATTGGATACGATCTGCTCTACTGCAACTTCAAAGAGATAAGATCTGTGGTTTTAATCC
49390655 GCTCCACTGCTTAGGA
66 GCTCCACTGCTTAGGA
* * *
49390671 AGATAAGACTT-GATGCGATCTGCTCTACTGCAACTTTAGAGAGATAAGATCTGTGGTTTTAATC
1 AGATAAGA-TTGGATACGATCTGCTCTACTGCAACTTCAAAGAGATAAGATCTGTGGTTTTAATC
49390735 CGCTCCACTGC
65 CGCTCCACTGC
49390746 AACTTCAGAG
Statistics
Matches: 66, Mismatches: 8, Indels: 2
0.87 0.11 0.03
Matches are distributed among these distances:
81 64 0.97
82 2 0.03
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (81 bp):
AGATAAGATTGGATACGATCTGCTCTACTGCAACTTCAAAGAGATAAGATCTGTGGTTTTAATCC
GCTCCACTGCTTAGGA
Found at i:49390716 original size:41 final size:41
Alignment explanation
Indices: 49390566--49390848 Score: 138
Period size: 41 Copynumber: 6.8 Consensus size: 41
49390556 GGTTTCTTCA
* *
49390566 ATCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTGGATACG
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGACTT-GATGCG
* * * * * *
49390607 ATCTGCTCTATTGTAACTTCAAAGAGATAATATTTG-TG-G
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGATGCG
49390646 TTTTAAT-TCGCTCCACTG---CTT-AG-GAAGATAAGACTTGATGCG
1 -----ATCT-GCTCCACTGCAACTTCAGAG-AGATAAGACTTGATGCG
* * * ***
49390688 ATCTGCTCTACTGCAACTTTAGAGAGATAAGATCTGTGGTTTTA
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGA-CT-T-GATGCG
* * ** *
49390732 ATCCGCTCCACTGCAACTTCAGAGAGATAGGATTGGCTTTTTCCG
1 ATCTGCTCCACTGCAACTTCAGAGAGATA--A--GACTTGATGCG
* * *
49390777 -TCTGCTCCACTGCAACTTCAGGGAGATAAGACTGGATGTG
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGATGCG
*
49390817 ATCTG-TCCTACTACAACTTCAGAGAGATAAGA
1 ATCTGCTCC-ACTGCAACTTCAGAGAGATAAGA
49390849 TCTGTGGTTT
Statistics
Matches: 182, Mismatches: 35, Indels: 50
0.68 0.13 0.19
Matches are distributed among these distances:
37 10 0.05
38 1 0.01
39 2 0.01
40 23 0.13
41 67 0.37
42 7 0.04
43 2 0.01
44 63 0.35
45 2 0.01
46 2 0.01
47 2 0.01
48 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.22, T:0.30
Consensus pattern (41 bp):
ATCTGCTCCACTGCAACTTCAGAGAGATAAGACTTGATGCG
Found at i:49390746 original size:210 final size:210
Alignment explanation
Indices: 49390471--49390868 Score: 586
Period size: 210 Copynumber: 1.9 Consensus size: 210
49390461 GCATAAAGTC
* * *
49390471 TGATGTGATCTGCTCTATTGCAACTTTAGAGAGATAAGATCTATCATTTTAATCCGCTTCACTGC
1 TGATGCGATCTGCTCTACTGCAACTTTAGAGAGATAAGATCTATCATTTTAATCCGCTCCACTGC
*
49390536 AACTTCAG-GAAGATAGGATTGG-TTTCTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAT
66 AACTTCAGAG-AGATAGGATTGGCTTT-TTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGAC
* ** * * *
49390599 TGGATACGATCTG-CTCTATTGTAACTTCAAAGAGATAATATTTGTGGTTTTAATTCGCTCCACT
129 TGGATACGATCTGTC-CTACTACAACTTCAAAGAGATAAGATCTGTGGTTTTAATCCGCTCCACT
49390663 GCTTAGGAAGATAAGACT
193 GCTTAGGAAGATAAGACT
* **
49390681 TGATGCGATCTGCTCTACTGCAACTTTAGAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGC
1 TGATGCGATCTGCTCTACTGCAACTTTAGAGAGATAAGATCTATCATTTTAATCCGCTCCACTGC
**
49390746 AACTTCAGAGAGATAGGATTGGCTTTTTCCGTCTGCTCCACTGCAACTTCAGGGAGATAAGACTG
66 AACTTCAGAGAGATAGGATTGGCTTTTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTG
** *
49390811 GATGTGATCTGTCCTACTACAACTTCAGAGAGATAAGATCTGTGGTTTTAATCCGCTC
131 GATACGATCTGTCCTACTACAACTTCAAAGAGATAAGATCTGTGGTTTTAATCCGCTC
49390869 TACTACAACT
Statistics
Matches: 167, Mismatches: 18, Indels: 6
0.87 0.09 0.03
Matches are distributed among these distances:
210 162 0.97
211 5 0.03
ACGTcount: A:0.27, C:0.20, G:0.21, T:0.32
Consensus pattern (210 bp):
TGATGCGATCTGCTCTACTGCAACTTTAGAGAGATAAGATCTATCATTTTAATCCGCTCCACTGC
AACTTCAGAGAGATAGGATTGGCTTTTTCAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTG
GATACGATCTGTCCTACTACAACTTCAAAGAGATAAGATCTGTGGTTTTAATCCGCTCCACTGCT
TAGGAAGATAAGACT
Found at i:49390748 original size:44 final size:44
Alignment explanation
Indices: 49390478--49390889 Score: 236
Period size: 44 Copynumber: 9.7 Consensus size: 44
49390468 GTCTGATGTG
* * * * **
49390478 ATCTGCTCTATTGCAACTTTAGAGAGATAAGATCTATCATTTTA
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTA
* * * *
49390522 ATCCGCTTCACTGCAACTTCAG-GAAGATAGGAT-TG-GTTTCTTCA
1 ATCTGCTCCACTGCAACTTCAGAG-AGATAAGATCTGTGGTT-TT-A
* * ***
49390566 ATCTGCTCCACTGCAACTTCAGGGAGATAAGA--T-TGGATACG
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTA
* * * * * *
49390607 ATCTGCTCTATTGTAACTTCAAAGAGATAATATTTGTGGTTTTA
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTA
* ***
49390651 AT-TCGCTCCACTG---CTT-AG-GAAGATAAGA-CT-T-GATGCG
1 ATCT-GCTCCACTGCAACTTCAGAG-AGATAAGATCTGTGGTTTTA
* *
49390688 ATCTGCTCTACTGCAACTTTAGAGAGATAAGATCTGTGGTTTTA
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTA
* * * *
49390732 ATCCGCTCCACTGCAACTTCAGAGAGATAGGAT-TG-GCTTTTTCC
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTG-GTTTT-A
* * * * *
49390776 GTCTGCTCCACTGCAACTTCAGGGAGATAAGA-C--TGGATGTG
1 ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTA
*
49390817 ATCTG-TCCTACTACAACTTCAGAGAGATAAGATCTGTGGTTTTA
1 ATCTGCTCC-ACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTA
* * * *
49390861 ATCCGCTCTACTACAACTTCAGGGAGATA
1 ATCTGCTCCACTGCAACTTCAGAGAGATA
49390890 GGATTGGCTT
Statistics
Matches: 276, Mismatches: 64, Indels: 56
0.70 0.16 0.14
Matches are distributed among these distances:
37 12 0.04
38 2 0.01
39 2 0.01
40 14 0.05
41 64 0.23
42 9 0.03
43 17 0.06
44 153 0.55
45 3 0.01
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (44 bp):
ATCTGCTCCACTGCAACTTCAGAGAGATAAGATCTGTGGTTTTA
Found at i:49390834 original size:129 final size:129
Alignment explanation
Indices: 49390671--49390917 Score: 390
Period size: 129 Copynumber: 1.9 Consensus size: 129
49390661 CTGCTTAGGA
* * *
49390671 AGATAAGACTTGATGCGATCTGCTCTACTGCAACTTTAGAGAGATAAGATCTGTGGTTTTAATCC
1 AGATAAGACTGGATGCGATCTGCTCTACTACAACTTCAGAGAGATAAGATCTGTGGTTTTAATCC
*
49390736 GCTCCACTGCAACTTCAGAGAGATAGGATTGGCTT-TTTCCGTCTGCTCCACTGCAACTTCAGGG
66 GCTCCACTACAACTTCAGAGAGATAGGATTGGCTTCTTT-CGTCTGCTCCACTGCAACTTCAGGG
*
49390800 AGATAAGACTGGATGTGATCTG-TCCTACTACAACTTCAGAGAGATAAGATCTGTGGTTTTAATC
1 AGATAAGACTGGATGCGATCTGCT-CTACTACAACTTCAGAGAGATAAGATCTGTGGTTTTAATC
* * *
49390864 CGCTCTACTACAACTTCAGGGAGATAGGATTGGCTTCTTTTGTCTGCTCCACTG
65 CGCTCCACTACAACTTCAGAGAGATAGGATTGGCTTCTTTCGTCTGCTCCACTG
49390918 TACCACCAGG
Statistics
Matches: 108, Mismatches: 8, Indels: 4
0.90 0.07 0.03
Matches are distributed among these distances:
128 1 0.01
129 104 0.96
130 3 0.03
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.31
Consensus pattern (129 bp):
AGATAAGACTGGATGCGATCTGCTCTACTACAACTTCAGAGAGATAAGATCTGTGGTTTTAATCC
GCTCCACTACAACTTCAGAGAGATAGGATTGGCTTCTTTCGTCTGCTCCACTGCAACTTCAGGG
Found at i:49390987 original size:50 final size:50
Alignment explanation
Indices: 49390924--49391516 Score: 457
Period size: 50 Copynumber: 11.9 Consensus size: 50
49390914 ACTGTACCAC
* * *
49390924 CAGGGAAGTAAGATTCACCGTTGTGGCTTCAATCTTTTTAATTGCAATGT
1 CAGGGAAGTAAGATTCGCCGTCGTAGCTTCAATCTTTTTAATTGCAATGT
* * *
49390974 CGGGGAAGCAAGATTCGCCGTCGCAGCTTCAATCTTTTTAATTGCAATGT
1 CAGGGAAGTAAGATTCGCCGTCGTAGCTTCAATCTTTTTAATTGCAATGT
* * * * * * ** * ****
49391024 CGGGGAAGCAAGATTCGCCATCGTAACTTTAATCTGTTCCACTGCACCAC
1 CAGGGAAGTAAGATTCGCCGTCGTAGCTTCAATCTTTTTAATTGCAATGT
* * *
49391074 CAGGGAAGTAAGATTCGCTGTCGTGGCTTCAATATTTTTAATTGCAATGT
1 CAGGGAAGTAAGATTCGCCGTCGTAGCTTCAATCTTTTTAATTGCAATGT
* * * ** * *
49391124 CAGGGAA-CAAGATTCGCCGTTGTAGCTTCAATCTGTTCCACTGC-ATCGC
1 CAGGGAAGTAAGATTCGCCGTCGTAGCTTCAATCTTTTTAATTGCAAT-GT
** * * *
49391173 CAGGGAAGTAAGATTCGTTGTCGTGGCTTCAATCTTTTTAATTGTAATAT
1 CAGGGAAGTAAGATTCGCCGTCGTAGCTTCAATCTTTTTAATTGCAATGT
* * ** * *
49391223 CGGGGAA-TAAGATTCGCCGTTGTAGCTTCAAT-TTATTCCACTGC-ATCGC
1 CAGGGAAGTAAGATTCGCCGTCGTAGCTTCAATCTT-TTTAATTGCAAT-GT
* *
49391272 CAGGGAAGTAAGATTCACCGTCGTGGCTTCAATCTTTTTAATTGCAATGT
1 CAGGGAAGTAAGATTCGCCGTCGTAGCTTCAATCTTTTTAATTGCAATGT
* * * * * * ** * *
49391322 CGGGGAA-CAAGATTCGTCGTTGTAGTTTCAATCTGTTCCACTGC-ATCGC
1 CAGGGAAGTAAGATTCGCCGTCGTAGCTTCAATCTTTTTAATTGCAAT-GT
* * * *
49391371 CAGGGAAGTAAGATTTGCCATTGTGGCTTCAATCTTTTTAATTGCAATGT
1 CAGGGAAGTAAGATTCGCCGTCGTAGCTTCAATCTTTTTAATTGCAATGT
** * * * * * ** * *
49391421 TGGGGAA-CAAGATTCACCATTGTAGCTTCAATCTATTCCACTGC-ATCGC
1 CAGGGAAGTAAGATTCGCCGTCGTAGCTTCAATCTTTTTAATTGCAAT-GT
* *
49391470 CAGGGAAGTAAGATTCGTCGTCGTGGCTTCAATCTTTTTAATTGCAA
1 CAGGGAAGTAAGATTCGCCGTCGTAGCTTCAATCTTTTTAATTGCAA
49391517 CCTCAGGGGT
Statistics
Matches: 407, Mismatches: 122, Indels: 27
0.73 0.22 0.05
Matches are distributed among these distances:
48 10 0.02
49 137 0.34
50 251 0.62
51 9 0.02
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (50 bp):
CAGGGAAGTAAGATTCGCCGTCGTAGCTTCAATCTTTTTAATTGCAATGT
Found at i:49391183 original size:99 final size:99
Alignment explanation
Indices: 49390976--49391516 Score: 803
Period size: 99 Copynumber: 5.5 Consensus size: 99
49390966 TGCAATGTCG
* **
49390976 GGGAAGCAAGATTCGCCGTCGCAGCTTCAATCTTTTTAATTGCAATGTCGGGGAAGCAAGATTCG
1 GGGAAGTAAGATTCGCCGTCGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAA-CAAGATTCG
* * * * * *
49391041 CCATCGTAACTTTAATCTGTTCCACTGCACCACCA
65 CCGTTGTAGCTTCAATCTGTTCCACTGCATCGCCA
* * *
49391076 GGGAAGTAAGATTCGCTGTCGTGGCTTCAATATTTTTAATTGCAATGTCAGGGAACAAGATTCGC
1 GGGAAGTAAGATTCGCCGTCGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAACAAGATTCGC
49391141 CGTTGTAGCTTCAATCTGTTCCACTGCATCGCCA
66 CGTTGTAGCTTCAATCTGTTCCACTGCATCGCCA
** * * *
49391175 GGGAAGTAAGATTCGTTGTCGTGGCTTCAATCTTTTTAATTGTAATATCGGGGAATAAGATTCGC
1 GGGAAGTAAGATTCGCCGTCGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAACAAGATTCGC
* *
49391240 CGTTGTAGCTTCAATTTATTCCACTGCATCGCCA
66 CGTTGTAGCTTCAATCTGTTCCACTGCATCGCCA
* *
49391274 GGGAAGTAAGATTCACCGTCGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAACAAGATTCGT
1 GGGAAGTAAGATTCGCCGTCGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAACAAGATTCGC
*
49391339 CGTTGTAGTTTCAATCTGTTCCACTGCATCGCCA
66 CGTTGTAGCTTCAATCTGTTCCACTGCATCGCCA
* * * * *
49391373 GGGAAGTAAGATTTGCCATTGTGGCTTCAATCTTTTTAATTGCAATGTTGGGGAACAAGATTCAC
1 GGGAAGTAAGATTCGCCGTCGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAACAAGATTCGC
* *
49391438 CATTGTAGCTTCAATCTATTCCACTGCATCGCCA
66 CGTTGTAGCTTCAATCTGTTCCACTGCATCGCCA
*
49391472 GGGAAGTAAGATTCGTCGTCGTGGCTTCAATCTTTTTAATTGCAA
1 GGGAAGTAAGATTCGCCGTCGTGGCTTCAATCTTTTTAATTGCAA
49391517 CCTCAGGGGT
Statistics
Matches: 397, Mismatches: 44, Indels: 1
0.90 0.10 0.00
Matches are distributed among these distances:
99 348 0.88
100 49 0.12
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (99 bp):
GGGAAGTAAGATTCGCCGTCGTGGCTTCAATCTTTTTAATTGCAATGTCGGGGAACAAGATTCGC
CGTTGTAGCTTCAATCTGTTCCACTGCATCGCCA
Found at i:49392869 original size:17 final size:16
Alignment explanation
Indices: 49392843--49392880 Score: 67
Period size: 17 Copynumber: 2.3 Consensus size: 16
49392833 CCGGTAGAGG
49392843 TTTTTTTGTTTTATTT
1 TTTTTTTGTTTTATTT
49392859 TTTTGTTTGTTTTATTT
1 TTTT-TTTGTTTTATTT
49392876 TTTTT
1 TTTTT
49392881 GTACCGTTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 5 0.24
17 16 0.76
ACGTcount: A:0.05, C:0.00, G:0.08, T:0.87
Consensus pattern (16 bp):
TTTTTTTGTTTTATTT
Found at i:49397149 original size:25 final size:26
Alignment explanation
Indices: 49397120--49397177 Score: 84
Period size: 25 Copynumber: 2.3 Consensus size: 26
49397110 GCAGGTATGC
*
49397120 ATTATAAAAATGTATG-TGTATATAT
1 ATTATAAAAATCTATGATGTATATAT
49397145 ATTATAAAAATCTATGAATGTATATAT
1 ATTATAAAAATCTATG-ATGTATATAT
49397172 A-TATAA
1 ATTATAA
49397178 CAAAATTTGA
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
25 15 0.50
26 5 0.17
27 10 0.33
ACGTcount: A:0.48, C:0.02, G:0.09, T:0.41
Consensus pattern (26 bp):
ATTATAAAAATCTATGATGTATATAT
Found at i:49401822 original size:35 final size:34
Alignment explanation
Indices: 49401743--49401823 Score: 101
Period size: 35 Copynumber: 2.3 Consensus size: 34
49401733 ATGTGGATAC
*
49401743 ATATATATGTATATGAATTGTAAAATATACGAAAA
1 ATATATATGTATATGAATTATAAAATATAC-AAAA
*
49401778 ATATGTATGTATTTATGAATTATAAAATATA-AAAA
1 ATATATATGTA--TATGAATTATAAAATATACAAAA
*
49401813 CTATATATGTA
1 ATATATATGTA
49401824 AAAGAGGTGT
Statistics
Matches: 40, Mismatches: 4, Indels: 4
0.83 0.08 0.08
Matches are distributed among these distances:
35 23 0.57
37 17 0.43
ACGTcount: A:0.49, C:0.02, G:0.10, T:0.38
Consensus pattern (34 bp):
ATATATATGTATATGAATTATAAAATATACAAAA
Found at i:49402252 original size:23 final size:23
Alignment explanation
Indices: 49402224--49402267 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
49402214 CAAGCAAGAA
* *
49402224 AATTAATAATAATAAACAAAAGC
1 AATTAAAAAAAATAAACAAAAGC
*
49402247 AATTAAAAAAAATACACAAAA
1 AATTAAAAAAAATAAACAAAA
49402268 AAAACTTATG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.70, C:0.09, G:0.02, T:0.18
Consensus pattern (23 bp):
AATTAAAAAAAATAAACAAAAGC
Found at i:49407357 original size:65 final size:66
Alignment explanation
Indices: 49407276--49407407 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
49407266 CTTCTTTCAA
* *
49407276 AAATTTTATATGCCTTCAAGATATAACAAAG-CCTCAATATTTTAAACAGAACAATAAAAATGAC
1 AAATTTTATATGCCTTCAAAATATAACAAAGCCCTCAACATTTTAAACAGAACAATAAAAATGAC
49407340 T
66 T
*
49407341 AAATTTTATATGCCTTCAAAATATAACAAAGCCCTCAACATTTTAAATAGAACAATAAAAATGAC
1 AAATTTTATATGCCTTCAAAATATAACAAAGCCCTCAACATTTTAAACAGAACAATAAAAATGAC
49407406 T
66 T
49407407 A
1 A
49407408 CGGACATTTA
Statistics
Matches: 63, Mismatches: 3, Indels: 1
0.94 0.04 0.01
Matches are distributed among these distances:
65 30 0.48
66 33 0.52
ACGTcount: A:0.48, C:0.16, G:0.07, T:0.29
Consensus pattern (66 bp):
AAATTTTATATGCCTTCAAAATATAACAAAGCCCTCAACATTTTAAACAGAACAATAAAAATGAC
T
Found at i:49409276 original size:8 final size:8
Alignment explanation
Indices: 49409263--49409298 Score: 58
Period size: 8 Copynumber: 4.8 Consensus size: 8
49409253 TAATAAATAA
49409263 AAATTATT
1 AAATTATT
49409271 AAATTATT
1 AAATTATT
49409279 AAA-TATT
1 AAATTATT
49409286 -AATTATT
1 AAATTATT
49409293 AAATTA
1 AAATTA
49409299 AAAATATGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
6 2 0.08
7 8 0.31
8 16 0.62
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (8 bp):
AAATTATT
Found at i:49409397 original size:18 final size:19
Alignment explanation
Indices: 49409351--49409398 Score: 57
Period size: 18 Copynumber: 2.7 Consensus size: 19
49409341 AATAGACTTA
49409351 AAATATTCTATA-AAATTG
1 AAATATTCTATATAAATTG
* *
49409369 AGAGATT-TATATAAATT-
1 AAATATTCTATATAAATTG
49409386 AAATATTCTATAT
1 AAATATTCTATAT
49409399 TTTTCGTACA
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
17 9 0.38
18 15 0.62
ACGTcount: A:0.48, C:0.04, G:0.06, T:0.42
Consensus pattern (19 bp):
AAATATTCTATATAAATTG
Found at i:49420211 original size:29 final size:29
Alignment explanation
Indices: 49420111--49420214 Score: 77
Period size: 29 Copynumber: 3.5 Consensus size: 29
49420101 TTTTCTTTTT
*
49420111 TGGTCACTCAATTATGAAAAGTTACAAAA
1 TGGTCACTCAACTATGAAAAGTTACAAAA
* * * ****
49420140 TGGTCACCCAACTATAAGTAAACTT-CTTTTT
1 TGGTCACTCAACTAT--GAAAAGTTAC-AAAA
*
49420171 TGGTTAAC-CAACTATGAAAAGTTACAAAA
1 TGG-TCACTCAACTATGAAAAGTTACAAAA
49420200 TGGTCACTCAACTAT
1 TGGTCACTCAACTAT
49420215 TCAATTTTGT
Statistics
Matches: 53, Mismatches: 16, Indels: 12
0.65 0.20 0.15
Matches are distributed among these distances:
28 3 0.06
29 29 0.55
30 2 0.04
31 16 0.30
32 3 0.06
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.31
Consensus pattern (29 bp):
TGGTCACTCAACTATGAAAAGTTACAAAA
Found at i:49420228 original size:60 final size:58
Alignment explanation
Indices: 49420100--49420232 Score: 153
Period size: 60 Copynumber: 2.2 Consensus size: 58
49420090 TCCAATTATT
* *
49420100 TTTTTCTTTTTTGGTCACTCAATTATGAAAAGTTACAAAATGGTCACCCAACTATAAG
1 TTTTTCTTTTTTGGTAACTCAACTATGAAAAGTTACAAAATGGTCACCCAACTATAAG
** *
49420158 TAAACTTCTTTTTTGGTTAAC-CAACTATGAAAAGTTACAAAATGGTCACTCAACTATTCAA-
1 T--TTTTCTTTTTTGG-TAACTCAACTATGAAAAGTTACAAAATGGTCACCCAACTA-T-AAG
49420219 TTTTGTCTTTTTTG
1 TTTT-TCTTTTTTG
49420233 TAATGTCTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 10
0.78 0.09 0.13
Matches are distributed among these distances:
58 1 0.02
59 1 0.02
60 53 0.85
61 5 0.08
62 2 0.03
ACGTcount: A:0.32, C:0.17, G:0.11, T:0.41
Consensus pattern (58 bp):
TTTTTCTTTTTTGGTAACTCAACTATGAAAAGTTACAAAATGGTCACCCAACTATAAG
Found at i:49424873 original size:18 final size:18
Alignment explanation
Indices: 49424846--49424880 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
49424836 ATAAATAAAC
49424846 ATAATAACTTACAATATT
1 ATAATAACTTACAATATT
* *
49424864 ATAATCACTTATAATAT
1 ATAATAACTTACAATAT
49424881 ATCATCTCAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.49, C:0.11, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAATAACTTACAATATT
Found at i:49426988 original size:25 final size:25
Alignment explanation
Indices: 49426960--49427015 Score: 60
Period size: 25 Copynumber: 2.2 Consensus size: 25
49426950 CTGTTATTTA
*
49426960 GCTCTTATGGGCATCCCGA-TATATG
1 GCTCTTATGAGCATCCCGATTA-ATG
** *
49426985 GCTCACATGAGCTTCCCGATTAATG
1 GCTCTTATGAGCATCCCGATTAATG
49427010 GCTCTT
1 GCTCTT
49427016 CGAAGCTTCT
Statistics
Matches: 24, Mismatches: 6, Indels: 2
0.75 0.19 0.06
Matches are distributed among these distances:
25 22 0.92
26 2 0.08
ACGTcount: A:0.20, C:0.27, G:0.21, T:0.32
Consensus pattern (25 bp):
GCTCTTATGAGCATCCCGATTAATG
Found at i:49427118 original size:25 final size:24
Alignment explanation
Indices: 49427090--49427172 Score: 80
Period size: 25 Copynumber: 3.3 Consensus size: 24
49427080 TGGCTCGTAT
*
49427090 GAGCTTCTCGATAATTGGCTCACAA
1 GAGCTTC-CCATAATTGGCTCACAA
*
49427115 GAGCTTCCCATTACA-TGGCTCACAT
1 GAGCTTCCCA-TA-ATTGGCTCACAA
*
49427140 GAGCTTCCCATTATATGGCTCGA-AA
1 GAGCTTCCCATAAT-TGGCTC-ACAA
49427165 GAGCTTCC
1 GAGCTTCC
49427173 TGATTACATG
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
23 1 0.02
24 3 0.06
25 43 0.88
26 2 0.04
ACGTcount: A:0.25, C:0.28, G:0.19, T:0.28
Consensus pattern (24 bp):
GAGCTTCCCATAATTGGCTCACAA
Found at i:49427167 original size:50 final size:51
Alignment explanation
Indices: 49427079--49427182 Score: 124
Period size: 50 Copynumber: 2.1 Consensus size: 51
49427069 CTGCCCGTTT
** *
49427079 ATGGCTCGTATGAGCTTCTCGATAATTGGCTCACAAGAGCTTCC-CATTAC
1 ATGGCTCACATGAGCTTCTCCATAATTGGCTCACAAGAGCTTCCTCATTAC
* *
49427129 ATGGCTCACATGAGCTTC-CCATTATATGGCTCGA-AAGAGCTTCCTGATTAC
1 ATGGCTCACATGAGCTTCTCCATAAT-TGGCTC-ACAAGAGCTTCCTCATTAC
49427180 ATG
1 ATG
49427183 CTTGCACGGG
Statistics
Matches: 46, Mismatches: 5, Indels: 5
0.82 0.09 0.09
Matches are distributed among these distances:
49 5 0.11
50 32 0.70
51 9 0.20
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (51 bp):
ATGGCTCACATGAGCTTCTCCATAATTGGCTCACAAGAGCTTCCTCATTAC
Found at i:49428623 original size:105 final size:101
Alignment explanation
Indices: 49428477--49428706 Score: 241
Period size: 105 Copynumber: 2.2 Consensus size: 101
49428467 ACACATACAT
** * ** * *
49428477 TGCCATGGCCCTGCCATGGTCTTACATTTGTAGTGCCATAACCTAGTTATGGTCTTATT-ATCAG
1 TGCCATGGCCCAACCATGGTCTTACAGTTCAAGTGCCATAACCCAGTTATGGTCTT-TTCATCAA
* * *
49428541 AATGT-CATAGCCCAGATATGGTCTTACACATGTATATATAC
65 AAT-TCCATAGCCCAGATATAGTCTT--ACAT-T-TAAACAC
* *
49428582 TGCCATGGCCCAACCATGGTCTTAC-GTTCAAGATGTCATAACCCAGTTATGGTCTTTTCATTAA
1 TGCCATGGCCCAACCATGGTCTTACAGTTCAAG-TGCCATAACCCAGTTATGGTCTTTTCATCAA
* *
49428646 AATTCCATAGCTCAGCTATAGTCTTACATTTAAACAC
65 AATTCCATAGCCCAGATATAGTCTTACATTTAAACAC
*
49428683 TGCCATGGTCCAACCATGGTCTTA
1 TGCCATGGCCCAACCATGGTCTTA
49428707 TCCGTCAATT
Statistics
Matches: 107, Mismatches: 15, Indels: 10
0.81 0.11 0.08
Matches are distributed among these distances:
101 28 0.26
102 1 0.01
103 4 0.04
104 7 0.07
105 67 0.63
ACGTcount: A:0.27, C:0.24, G:0.17, T:0.33
Consensus pattern (101 bp):
TGCCATGGCCCAACCATGGTCTTACAGTTCAAGTGCCATAACCCAGTTATGGTCTTTTCATCAAA
ATTCCATAGCCCAGATATAGTCTTACATTTAAACAC
Found at i:49434412 original size:17 final size:17
Alignment explanation
Indices: 49434378--49434415 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
49434368 AAAACTAATT
**
49434378 TTTTTTAGTTTATTCAG
1 TTTTTTAGTTTAACCAG
49434395 TTTTTTAGTTTAACCAG
1 TTTTTTAGTTTAACCAG
49434412 TTTT
1 TTTT
49434416 CATGTTCGGT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.18, C:0.08, G:0.11, T:0.63
Consensus pattern (17 bp):
TTTTTTAGTTTAACCAG
Found at i:49440787 original size:20 final size:20
Alignment explanation
Indices: 49440762--49440811 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
49440752 TGGCTTAAAA
49440762 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
49440782 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
49440799 GTGGTAGTGGATT
1 TTGGTAGTGGATT
49440812 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:49445427 original size:20 final size:20
Alignment explanation
Indices: 49445402--49445451 Score: 70
Period size: 17 Copynumber: 2.6 Consensus size: 20
49445392 TGGCTTAAAA
49445402 TTGGTAGTGGATTGTTGTTG
1 TTGGTAGTGGATTGTTGTTG
49445422 TTGGTAGTGG---GTTGTTG
1 TTGGTAGTGGATTGTTGTTG
*
49445439 GTGGTAGTGGATT
1 TTGGTAGTGGATT
49445452 AGTGGATGGT
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 16 0.62
20 10 0.38
ACGTcount: A:0.10, C:0.00, G:0.44, T:0.46
Consensus pattern (20 bp):
TTGGTAGTGGATTGTTGTTG
Found at i:49449750 original size:31 final size:29
Alignment explanation
Indices: 49449707--49449768 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 29
49449697 TTTTATAAAT
*
49449707 AATTAATATTTAT-TAATTAAAAATATTTAC
1 AATTAATATTTATAT-ATT-AAAATATTAAC
*
49449737 AATTTATATTTTATATATTAAAATATTAAC
1 AATTAATA-TTTATATATTAAAATATTAAC
49449767 AA
1 AA
49449769 CAAGTTATAA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
30 19 0.68
31 8 0.29
32 1 0.04
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (29 bp):
AATTAATATTTATATATTAAAATATTAAC
Found at i:49449954 original size:13 final size:13
Alignment explanation
Indices: 49449938--49449988 Score: 59
Period size: 13 Copynumber: 3.9 Consensus size: 13
49449928 TTTAAACCAA
49449938 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
* *
49449951 ACTTCTCAAAATC
1 ACTTTTCAAAAGC
*
49449964 ACTTTTCCACAA-C
1 ACTTTT-CAAAAGC
49449977 ACTTTTCAAAAG
1 ACTTTTCAAAAG
49449989 TAATTAAGAA
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
12 4 0.13
13 23 0.74
14 4 0.13
ACGTcount: A:0.37, C:0.27, G:0.04, T:0.31
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:49451966 original size:7 final size:7
Alignment explanation
Indices: 49451954--49451979 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
49451944 ATTGAGTAAA
49451954 AATATTC
1 AATATTC
49451961 AATATTC
1 AATATTC
49451968 AATATTC
1 AATATTC
49451975 AATAT
1 AATAT
49451980 GAAATTGAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.46, C:0.12, G:0.00, T:0.42
Consensus pattern (7 bp):
AATATTC
Found at i:49455519 original size:14 final size:14
Alignment explanation
Indices: 49455500--49455527 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
49455490 TATATTTTTA
49455500 CTTAGTTTTTAATC
1 CTTAGTTTTTAATC
49455514 CTTAGTTTTTAATC
1 CTTAGTTTTTAATC
49455528 ATTTTTAAAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.07, T:0.57
Consensus pattern (14 bp):
CTTAGTTTTTAATC
Found at i:49457485 original size:20 final size:21
Alignment explanation
Indices: 49457448--49457489 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
49457438 AGAGTTGATT
49457448 TAATGAAAATGTAAAATTAAC
1 TAATGAAAATGTAAAATTAAC
* *
49457469 TAAT-AAAATTTACAATTAAC
1 TAATGAAAATGTAAAATTAAC
49457489 T
1 T
49457490 TTCATCAAAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 15 0.79
21 4 0.21
ACGTcount: A:0.55, C:0.07, G:0.05, T:0.33
Consensus pattern (21 bp):
TAATGAAAATGTAAAATTAAC
Found at i:49465022 original size:3 final size:3
Alignment explanation
Indices: 49465014--49465048 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
49465004 AGAAGGATGA
49465014 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
49465049 GCTTTTGCTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:49465220 original size:3 final size:3
Alignment explanation
Indices: 49465212--49465269 Score: 116
Period size: 3 Copynumber: 19.3 Consensus size: 3
49465202 TTTGTTTGTG
49465212 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
49465260 TTC TTC TTC T
1 TTC TTC TTC T
49465270 CGTGTACTGT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 55 1.00
ACGTcount: A:0.00, C:0.33, G:0.00, T:0.67
Consensus pattern (3 bp):
TTC
Found at i:49470459 original size:25 final size:25
Alignment explanation
Indices: 49470326--49470459 Score: 105
Period size: 25 Copynumber: 5.4 Consensus size: 25
49470316 AGCTCTTGCC
* *
49470326 AGCCAATTATCGGGAAGCTCAT-ACG
1 AGCCAAATAACGGGAAGCTCATGA-G
* * * *
49470351 AGCCATA-AACGAGAAGCTCAAGAA
1 AGCCAAATAACGGGAAGCTCATGAG
*
49470375 AGCCATTAATTA--GGAAGCTCATGAG
1 AGCCA--AATAACGGGAAGCTCATGAG
*
49470400 AGCCAAATATCGGGAAGCTCATGAG
1 AGCCAAATAACGGGAAGCTCATGAG
* * *
49470425 AGCCATATAACGGGATGCTCATAAG
1 AGCCAAATAACGGGAAGCTCATGAG
*
49470450 AGCTAAATAA
1 AGCCAAATAA
49470460 TGGAACGCTT
Statistics
Matches: 84, Mismatches: 19, Indels: 12
0.73 0.17 0.10
Matches are distributed among these distances:
23 3 0.04
24 16 0.19
25 63 0.75
26 1 0.01
27 1 0.01
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.18
Consensus pattern (25 bp):
AGCCAAATAACGGGAAGCTCATGAG
Found at i:49473672 original size:30 final size:29
Alignment explanation
Indices: 49473631--49473786 Score: 136
Period size: 30 Copynumber: 5.2 Consensus size: 29
49473621 AGTTTTTTTG
* *
49473631 CATTTTAACCCCTATACTTTTCAAAATTTA
1 CATTTTGACCCCTAAACTTTTCAAAA-TTA
*
49473661 CATTTTGACCCC-AAAATTTTCTAAAATTTA
1 CATTTTGACCCCTAAACTTTTC-AAAA-TTA
* *
49473691 CATTTTGACCGCAAAAC-TTTCTAAAATTA
1 CATTTTGACCCCTAAACTTTTC-AAAATTA
* **
49473720 CATTTTGACCCTTAGGCTTTCTCAAAATTA
1 CATTTTGACCCCTAAACTTT-TCAAAATTA
* * * *
49473750 CACTTTAACCCCTAAACTCTTAAGAAATTA
1 CATTTTGACCCCTAAACTTTTCA-AAATTA
49473780 CATTTTG
1 CATTTTG
49473787 GCCCATATTT
Statistics
Matches: 102, Mismatches: 19, Indels: 10
0.78 0.15 0.08
Matches are distributed among these distances:
29 24 0.24
30 73 0.72
31 5 0.05
ACGTcount: A:0.34, C:0.22, G:0.05, T:0.38
Consensus pattern (29 bp):
CATTTTGACCCCTAAACTTTTCAAAATTA
Found at i:49473739 original size:29 final size:28
Alignment explanation
Indices: 49473649--49473820 Score: 116
Period size: 30 Copynumber: 5.9 Consensus size: 28
49473639 CCCCTATACT
*
49473649 TTTC-AAAATTTACATTTTGACCCCAAAAT
1 TTTCTAAAA-TTACATTTTGA-CCCAAAAC
49473678 TTTCTAAAATTTACATTTTGACCGCAAAAC
1 TTTCTAAAA-TTACATTTTGACC-CAAAAC
* **
49473708 TTTCTAAAATTACATTTTGACCCTTAGGC
1 TTTCTAAAATTACATTTTGACCC-AAAAC
* * *
49473737 TTTCTCAAAATTACACTTTAACCCCTAAAC
1 TTTCT-AAAATTACATTTTGA-CCCAAAAC
* * * *
49473767 TCTT-AAGAAATTACATTTTGGCCC-ATAT
1 T-TTCTA-AAATTACATTTTGACCCAAAAC
*
49473795 TTTGCTAAAATTACACTTTTGCCCCA
1 TTT-CTAAAATTACA-TTTTGACCCA
49473821 GAAGCTTTAC
Statistics
Matches: 116, Mismatches: 16, Indels: 21
0.76 0.10 0.14
Matches are distributed among these distances:
27 2 0.02
28 12 0.10
29 39 0.34
30 58 0.50
31 5 0.04
ACGTcount: A:0.33, C:0.23, G:0.06, T:0.38
Consensus pattern (28 bp):
TTTCTAAAATTACATTTTGACCCAAAAC
Found at i:49474346 original size:11 final size:11
Alignment explanation
Indices: 49474330--49474388 Score: 82
Period size: 11 Copynumber: 5.3 Consensus size: 11
49474320 GAGCGACCCG
49474330 AAAAAGAAGGA
1 AAAAAGAAGGA
*
49474341 AAAAAGAAAGA
1 AAAAAGAAGGA
*
49474352 AAAAAGAAGTA
1 AAAAAGAAGGA
49474363 GAAAAAGAAGGA
1 -AAAAAGAAGGA
*
49474375 AAAAAGAAAGA
1 AAAAAGAAGGA
49474386 AAA
1 AAA
49474389 GAAAAGAAAA
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
11 32 0.76
12 10 0.24
ACGTcount: A:0.76, C:0.00, G:0.22, T:0.02
Consensus pattern (11 bp):
AAAAAGAAGGA
Found at i:49474355 original size:12 final size:11
Alignment explanation
Indices: 49474330--49474399 Score: 63
Period size: 11 Copynumber: 6.3 Consensus size: 11
49474320 GAGCGACCCG
*
49474330 AAAAAGAAGGA
1 AAAAAGAAGAA
49474341 AAAAAGAA-AGA
1 AAAAAGAAGA-A
*
49474352 AAAAAGAAGTAG
1 AAAAAGAAG-AA
*
49474364 AAAAAGAAGGA
1 AAAAAGAAGAA
49474375 AAAAAGAAAGAA
1 AAAAAG-AAGAA
*
49474387 AAGAA-AAGAA
1 AAAAAGAAGAA
49474397 AAA
1 AAA
49474400 GAAAAATCAA
Statistics
Matches: 48, Mismatches: 7, Indels: 9
0.75 0.11 0.14
Matches are distributed among these distances:
10 7 0.15
11 23 0.48
12 17 0.35
13 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.01
Consensus pattern (11 bp):
AAAAAGAAGAA
Found at i:49474357 original size:22 final size:22
Alignment explanation
Indices: 49474330--49474399 Score: 88
Period size: 23 Copynumber: 3.2 Consensus size: 22
49474320 GAGCGACCCG
49474330 AAAAAGAAGGAAAAAAGAAAGA
1 AAAAAGAAGGAAAAAAGAAAGA
* *
49474352 AAAAAGAAGTAGAAAAAGAAGGA
1 AAAAAGAAGGA-AAAAAGAAAGA
* *
49474375 AAAAAGAAAGAAAAGA-AAAGA
1 AAAAAGAAGGAAAAAAGAAAGA
49474396 AAAA
1 AAAA
49474400 GAAAAATCAA
Statistics
Matches: 41, Mismatches: 6, Indels: 3
0.82 0.12 0.06
Matches are distributed among these distances:
21 8 0.20
22 14 0.34
23 19 0.46
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.01
Consensus pattern (22 bp):
AAAAAGAAGGAAAAAAGAAAGA
Found at i:49474534 original size:11 final size:11
Alignment explanation
Indices: 49474503--49474556 Score: 56
Period size: 11 Copynumber: 4.7 Consensus size: 11
49474493 AGCAGCTCAA
49474503 AAAAAAAACA-
1 AAAAAAAACAG
*
49474513 AACAAAAACAG
1 AAAAAAAACAG
49474524 AAAAAAAACAG
1 AAAAAAAACAG
*
49474535 CAGAAAAAAAAAG
1 -A-AAAAAAACAG
49474548 AGAAAAAAA
1 A-AAAAAAA
49474557 ACAAAGCAGG
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
10 9 0.24
11 10 0.26
12 10 0.26
13 9 0.24
ACGTcount: A:0.81, C:0.09, G:0.09, T:0.00
Consensus pattern (11 bp):
AAAAAAAACAG
Found at i:49474538 original size:14 final size:14
Alignment explanation
Indices: 49474521--49474559 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
49474511 CAAACAAAAA
49474521 CAGAAAAAAAACAG
1 CAGAAAAAAAACAG
49474535 CAGAAAAAAAA-AG
1 CAGAAAAAAAACAG
49474548 -AGAAAAAAAACA
1 CAGAAAAAAAACA
49474560 AAGCAGGCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
12 10 0.42
13 3 0.12
14 11 0.46
ACGTcount: A:0.77, C:0.10, G:0.13, T:0.00
Consensus pattern (14 bp):
CAGAAAAAAAACAG
Found at i:49474557 original size:11 final size:12
Alignment explanation
Indices: 49474501--49474557 Score: 62
Period size: 12 Copynumber: 4.7 Consensus size: 12
49474491 AAAGCAGCTC
*
49474501 AAAAAAAAA-AC
1 AAAAAAAAAGAG
* *
49474512 AAACAAAAACAG
1 AAAAAAAAAGAG
49474524 AAAAAAAACAGCAG
1 AAAAAAAA-AG-AG
49474538 AAAAAAAAAGAG
1 AAAAAAAAAGAG
49474550 AAAAAAAA
1 AAAAAAAA
49474558 CAAAGCAGGC
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
11 8 0.21
12 18 0.46
13 3 0.08
14 10 0.26
ACGTcount: A:0.82, C:0.09, G:0.09, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAGAG
Found at i:49475276 original size:18 final size:17
Alignment explanation
Indices: 49475242--49475604 Score: 170
Period size: 17 Copynumber: 20.2 Consensus size: 17
49475232 AAAAAGAAGA
49475242 AAAAATTCTCGTG-TTTC
1 AAAAATT-TCGTGTTTTC
49475259 AAAGAATTTCGTGTTTTC
1 AAA-AATTTCGTGTTTTC
49475277 AAAAAATTCTCGTGTTTT-
1 -AAAAATT-TCGTGTTTTC
49475295 AAAAATTTTCGTGTTTTC
1 AAAAA-TTTCGTGTTTTC
* *
49475313 AAAAATTT-TTTTGTTTC
1 AAAAATTTCGTGT-TTTC
*
49475330 AAAAATCCTCGTGTTTTC
1 AAAAAT-TTCGTGTTTTC
** *
49475348 AAAAATCCCG-GTGCTTC
1 AAAAATTTCGTGT-TTTC
* *
49475365 AAAAAAATTTTGTGTTCTC
1 --AAAAATTTCGTGTTTTC
* * *
49475384 AAAAATTCCAATG--ATC
1 AAAAATTTC-GTGTTTTC
49475400 AAAAATTTTTTTTCGTGTTTTC
1 AAAAA-----TTTCGTGTTTTC
*
49475422 TAAAAAAATTCCGTG-TTTC
1 ---AAAAATTTCGTGTTTTC
49475441 AAAAATTTTCGTGTTTTTC
1 AAAAA-TTTCGTG-TTTTC
* *
49475460 AACAATTCTCGT-ATTTC
1 AAAAATT-TCGTGTTTTC
*
49475477 AAAAATTTTCGCG-TTTC
1 AAAAA-TTTCGTGTTTTC
** **
49475494 AAAAAAAATATTGTTTTC
1 -AAAAATTTCGTGTTTTC
*
49475512 AAAAATTGTCGTGTTCTC
1 AAAAATT-TCGTGTTTTC
*
49475530 AAAAATATTCGTGTTTTT
1 AAAAAT-TTCGTGTTTTC
* *
49475548 AAGAATTTTCGTG-TCTC
1 AA-AAATTTCGTGTTTTC
* *
49475565 TAAAATTCTCGTGTTTTAA
1 AAAAATT-TCGTGTTTT-C
49475584 AAAAATTTCGTGTTTTC
1 AAAAATTTCGTGTTTTC
49475601 AAAA
1 AAAA
49475605 TAAAATTTGT
Statistics
Matches: 262, Mismatches: 46, Indels: 76
0.68 0.12 0.20
Matches are distributed among these distances:
16 20 0.08
17 88 0.34
18 85 0.32
19 49 0.19
20 10 0.04
21 3 0.01
22 2 0.01
25 5 0.02
ACGTcount: A:0.32, C:0.14, G:0.11, T:0.43
Consensus pattern (17 bp):
AAAAATTTCGTGTTTTC
Found at i:49475281 original size:35 final size:35
Alignment explanation
Indices: 49475242--49475640 Score: 262
Period size: 35 Copynumber: 11.1 Consensus size: 35
49475232 AAAAAGAAGA
49475242 AAAAATTCTCGTGTTTCAAAGAA-TTTCGTGTTTTC
1 AAAAATTCTCGTGTTTCAAA-AATTTTCGTGTTTTC
*
49475277 AAAAAATTCTCGTGTTTTAAAAATTTTCGTGTTTTC
1 -AAAAATTCTCGTGTTTCAAAAATTTTCGTGTTTTC
* ** **
49475313 AAAAATTTTTTTGTTTCAAAAATCCTCGTGTTTTC
1 AAAAATTCTCGTGTTTCAAAAATTTTCGTGTTTTC
* * *
49475348 AAAAA-TCCCGGTGCTTCAAAAAAATTTT-GTGTTCTC
1 AAAAATTCTC-GTGTTTC--AAAAATTTTCGTGTTTTC
* *
49475384 AAAAATTC-CAATG-ATCAAAAATTTTTTTTCGTGTTTTC
1 AAAAATTCTC-GTGTTTCAAAAA----TTTTCGTGTTTTC
49475422 TAAAAAAATTC-CGTGTTTCAAAAATTTTCGTGTTTTTC
1 ---AAAAATTCTCGTGTTTCAAAAATTTTCGTG-TTTTC
* * *
49475460 AACAATTCTCGTATTTCAAAAATTTTCGCG-TTTC
1 AAAAATTCTCGTGTTTCAAAAATTTTCGTGTTTTC
* * * * *
49475494 AAAAAAAATATTGT-TTTCAAAAATTGTCGTGTTCTC
1 --AAAAATTCTCGTGTTTCAAAAATTTTCGTGTTTTC
* * *
49475530 AAAAATAT-TCGTGTTTTTAAGAATTTTCGTG-TCTC
1 AAAAAT-TCTCGTG-TTTCAAAAATTTTCGTGTTTTC
* * *
49475565 TAAAATTCTCGTGTTTTAAAAAAATTTCGTGTTTTC
1 AAAAATTCTCGTG-TTTCAAAAATTTTCGTGTTTTC
*** * * *
49475601 AAAATAAAAT-TTGTTTCAAAAATCTTCGTGTTTTA
1 AAAA-ATTCTCGTGTTTCAAAAATTTTCGTGTTTTC
49475636 AAAAA
1 AAAAA
49475641 ATTGTATTTT
Statistics
Matches: 288, Mismatches: 50, Indels: 52
0.74 0.13 0.13
Matches are distributed among these distances:
33 5 0.02
34 15 0.05
35 117 0.41
36 98 0.34
37 23 0.08
38 12 0.04
40 2 0.01
41 16 0.06
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (35 bp):
AAAAATTCTCGTGTTTCAAAAATTTTCGTGTTTTC
Found at i:49475623 original size:53 final size:53
Alignment explanation
Indices: 49475456--49475643 Score: 151
Period size: 53 Copynumber: 3.6 Consensus size: 53
49475446 TTTTCGTGTT
* * * * *
49475456 TTTCAACAATTCTCGT-ATTTCAAAAATTTTCGCG-TTTCAAAA-AAAATATTG
1 TTTCAAAAATTCTCGTGTTTTAAAAAAATTTCGTGTTTTCAAAATAAAAT-TTG
* * * *
49475507 TTTTCAAAAATTGTCGTGTTCT-CAAAAATATTCGTGTTTTTAAGAAT----TTTCG
1 -TTTCAAAAATTCTCGTGTTTTAAAAAAAT-TTCGTGTTTTCAA-AATAAAATTT-G
*
49475559 TGTCTCTAAAATTCTCGTGTTTTAAAAAAATTTCGTGTTTTCAAAATAAAATTTG
1 T-T-TCAAAAATTCTCGTGTTTTAAAAAAATTTCGTGTTTTCAAAATAAAATTTG
49475614 TTTCAAAAA-TCTTCGTGTTTTAAAAAAATT
1 TTTCAAAAATTC-TCGTGTTTTAAAAAAATT
49475644 GTATTTTGAT
Statistics
Matches: 108, Mismatches: 14, Indels: 27
0.72 0.09 0.18
Matches are distributed among these distances:
51 3 0.03
52 27 0.25
53 59 0.55
54 12 0.11
55 4 0.04
56 3 0.03
ACGTcount: A:0.35, C:0.12, G:0.10, T:0.43
Consensus pattern (53 bp):
TTTCAAAAATTCTCGTGTTTTAAAAAAATTTCGTGTTTTCAAAATAAAATTTG
Found at i:49475632 original size:17 final size:16
Alignment explanation
Indices: 49475242--49475639 Score: 149
Period size: 18 Copynumber: 22.3 Consensus size: 16
49475232 AAAAAGAAGA
49475242 AAAAATTCTCGTGTTTC
1 AAAAATT-TCGTGTTTC
49475259 AAAGAATTTCGTGTTTTC
1 AAA-AATTTCGTG-TTTC
*
49475277 AAAAAATTCTCGTGTTTT
1 -AAAAATT-TCGTGTTTC
49475295 AAAAATTTTCGTGTTTTC
1 AAAAA-TTTCGTG-TTTC
**
49475313 AAAAATTTTTTTGTTTC
1 AAAAA-TTTCGTGTTTC
*
49475330 AAAAATCCTCGTGTTTTC
1 AAAAAT-TTCGTG-TTTC
** *
49475348 AAAAATCCCGGTGCTTC
1 AAAAATTTC-GTGTTTC
*
49475365 AAAAAAATTTTGTGTTCTC
1 --AAAAATTTCGTGTT-TC
* * *
49475384 AAAAATTCCAATG-ATC
1 AAAAATTTC-GTGTTTC
49475400 AAAAATTTTTTTTCGTGTTTTC
1 AAAAA-----TTTCGTG-TTTC
*
49475422 TAAAAAAATTCCGTGTTTC
1 ---AAAAATTTCGTGTTTC
49475441 AAAAATTTTCGTGTTTTTC
1 AAAAA-TTTCGTG--TTTC
* *
49475460 AACAATTCTCGTATTTC
1 AAAAATT-TCGTGTTTC
*
49475477 AAAAATTTTCGCGTTTC
1 AAAAA-TTTCGTGTTTC
49475494 AAAAAAAATATT-GT-TTTC
1 ---AAAAAT-TTCGTGTTTC
49475512 AAAAATTGTCGTGTTCTC
1 AAAAATT-TCGTGTT-TC
*
49475530 AAAAATATTCGTGTTTTT
1 AAAAAT-TTCGTG-TTTC
* *
49475548 AAGAATTTTCGTGTCTC
1 AA-AAATTTCGTGTTTC
* *
49475565 TAAAATTCTCGTGTTTTAA
1 AAAAATT-TCGTG-TTT-C
49475584 AAAAATTTCGTGTTTTC
1 AAAAATTTCGTG-TTTC
*
49475601 AAAATAAAATT--TGTTTC
1 --AA-AAATTTCGTGTTTC
*
49475618 AAAAATCTTCGTGTTTT
1 AAAAAT-TTCGTGTTTC
49475635 AAAAA
1 AAAAA
49475640 AATTGTATTT
Statistics
Matches: 292, Mismatches: 41, Indels: 96
0.68 0.10 0.22
Matches are distributed among these distances:
14 4 0.01
15 11 0.04
16 19 0.07
17 87 0.30
18 93 0.32
19 48 0.16
20 20 0.07
21 3 0.01
22 2 0.01
25 5 0.02
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (16 bp):
AAAAATTTCGTGTTTC
Found at i:49482993 original size:10 final size:10
Alignment explanation
Indices: 49482972--49483000 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
49482962 TCCTTTTCCA
49482972 TCATAT-ATC
1 TCATATCATC
49482981 TCATATCATC
1 TCATATCATC
49482991 TCATATCATC
1 TCATATCATC
49483001 ATGTGTTGAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 6 0.32
10 13 0.68
ACGTcount: A:0.31, C:0.28, G:0.00, T:0.41
Consensus pattern (10 bp):
TCATATCATC
Found at i:49486508 original size:11 final size:11
Alignment explanation
Indices: 49486486--49486533 Score: 73
Period size: 11 Copynumber: 4.5 Consensus size: 11
49486476 TTATGCCTGA
49486486 AAAAAAACAAC
1 AAAAAAACAAC
49486497 AACAAAAA-AAC
1 AA-AAAAACAAC
49486508 AAAAAAACAAC
1 AAAAAAACAAC
49486519 AAAAAAACAA-
1 AAAAAAACAAC
49486529 AAAAA
1 AAAAA
49486534 GAAAAAAGAA
Statistics
Matches: 35, Mismatches: 0, Indels: 5
0.88 0.00 0.12
Matches are distributed among these distances:
10 10 0.29
11 20 0.57
12 5 0.14
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (11 bp):
AAAAAAACAAC
Found at i:49486510 original size:8 final size:8
Alignment explanation
Indices: 49486497--49486540 Score: 52
Period size: 8 Copynumber: 5.1 Consensus size: 8
49486487 AAAAAACAAC
49486497 AACAAAAA
1 AACAAAAA
49486505 AACAAAAAAA
1 AAC--AAAAA
49486515 CAACAAAAA
1 -AACAAAAA
49486524 AACAAAAA
1 AACAAAAA
*
49486532 AAGAAAAA
1 AACAAAAA
49486540 A
1 A
49486541 GAAAAATCAA
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
8 19 0.59
9 5 0.16
10 5 0.16
11 3 0.09
ACGTcount: A:0.86, C:0.11, G:0.02, T:0.00
Consensus pattern (8 bp):
AACAAAAA
Found at i:49486516 original size:19 final size:19
Alignment explanation
Indices: 49486488--49486533 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
49486478 ATGCCTGAAA
49486488 AAAAACAACAACAAAAAAAC
1 AAAAA-AACAACAAAAAAAC
49486508 AAAAAAACAACAAAAAAAC
1 AAAAAAACAACAAAAAAAC
49486527 AAAAAAA
1 AAAAAAA
49486534 GAAAAAAGAA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 21 0.81
20 5 0.19
ACGTcount: A:0.85, C:0.15, G:0.00, T:0.00
Consensus pattern (19 bp):
AAAAAAACAACAAAAAAAC
Found at i:49488649 original size:76 final size:76
Alignment explanation
Indices: 49487421--49489117 Score: 2030
Period size: 76 Copynumber: 21.6 Consensus size: 76
49487411 TCTGTGTTTT
* * *
49487421 TTTTTCAAAAATTAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTCTT
1 TTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTCTT
49487486 TTAAATTTCTG
66 TTAAATTTCTG
* *
49487497 TTTTTC-AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTTCTT
1 TTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTCTT
49487561 TTAAATTTCTG
66 TTAAATTTCTG
*
49487572 TTTTTCAAAAAAAATCAACTCATAATGCGAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
1 TTTTTC---AAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
49487637 T-TTTTAAATTTCTG
62 TCTTTTAAATTTCTG
* *
49487651 TTTTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGGTATTT
1 ---TTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
*
49487716 CTTTTAAATTTTTG
63 CTTTTAAATTTCTG
* * *
49487730 TTTTTC-AAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCCGAGATATTTCTT
1 TTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTCTT
*
49487794 TTAAATTTTTG
66 TTAAATTTCTG
* * *
49487805 TTTTTAAAAAAAAAATCAACTCATAATGCGATAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTAT
1 TTTTT----CAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTAT
*
49487870 TT-TTTTTAATTTCTG
61 TTCTTTTAAATTTCTG
49487885 TTTTTTTTCAAAAATTCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
1 ---TTTTTCAAAAA-TCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATT
49487950 T-TTTTAAATTTCTG
62 TCTTTTAAATTTCTG
49487964 TTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
1 --TTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
49488029 -TTTTAATTTAATTTCTG
63 CTTTT-A---AATTTCTG
49488046 CTTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTATT
1 -TTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGG---TATT
*
49488111 TTTAATTTAATTAATTTCTG
62 TCT--TTT-A--AATTTCTG
49488131 CTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
1 --TTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
49488196 -TTTTAATTTAATTTCTG
63 CTTTT-A---AATTTCTG
49488213 CTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
1 --TTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTA---
*
49488278 TTTTTTAAATTTAATTAATTTCTG
60 -TTTCT---TTT-A--AATTTCTG
*
49488302 CTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTTGGGTCACGCTGAGGTATTT
1 --TTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
* *
49488367 TTTTTTAATTTCTG
63 CTTTTAAATTTCTG
*
49488381 CTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCAGGTCACGCTGAGGTA-TT
1 --TTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
49488445 -TTTTAAATTTCTG
63 CTTTTAAATTTCTG
*
49488458 TTTTTTTCAAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTAAGGTATTT
1 --TTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
49488523 -TTTTAAATTTCTG
63 CTTTTAAATTTCTG
* * * * *
49488536 TTTTTTTCAAAAAATTAACTCATAATACAGAGGTGAGTTGAGTCACGGGTCATGCCGAGGTATTT
1 --TTTTTC-AAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTT
*
49488601 CTTTTAAATTTCCG
63 CTTTTAAATTTCTG
* * *
49488615 TTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAACCTCGGGTCATGCCGAGGTATTTCTT
1 TTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTCTT
49488680 TTAAATTT-TCG
66 TTAAATTTCT-G
* * * *
49488691 TTTTTCAAAAATCAACTCATAATACGGAGGTGAGTTGAGCCTCGGGTCATGCCGAGTTATTTCTT
1 TTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTCTT
49488756 TTAAATTTCTG
66 TTAAATTTCTG
*
49488767 TTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCATGCTGAGGTATTTCTT
1 TTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTCTT
49488832 TTAAATTTCTG
66 TTAAATTTCTG
* * * ** ** *
49488843 TTTTTCAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTTGGACCATACCGAGGTATTTCT
1 TTTTTCAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTCT
49488908 TTTAAATTTCTG
65 TTTAAATTTCTG
* * *
49488920 TTTTTCAAAAATCAACTCATAATGCGAGAGATGAGTTGAGCCTCGGGTCACGCCGAGGTA--T-T
1 TTTTTCAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTCT
*
49488982 TTTCAA-TTCATG
65 TTTAAATTTC-TG
* * ** *
49488994 TTTTTCAAAAATTAACTCATATTGTTAGAGGTGAGTTGAGCCTCGGGGCACATG-TCGAGGTA--
1 TTTTTCAAAAATCAACTCATAAT-ACAGAGGTGAGTTGAGCCTCGGGTCAC--GCT-GAGGTATT
** *
49489056 --TTTTCGATTTTTG
62 TCTTTTAAATTTCTG
* * * * *
49489069 TTTTGCGAAGATCAACTCATAATCCAAGAGGTGAGTTGAGTCTCGGGTC
1 TTTTTCAAAAATCAACTCATAATAC-AGAGGTGAGTTGAGCCTCGGGTC
49489118 GCACGCCGAG
Statistics
Matches: 1486, Mismatches: 82, Indels: 107
0.89 0.05 0.06
Matches are distributed among these distances:
73 3 0.00
74 52 0.03
75 195 0.13
76 252 0.17
77 177 0.12
78 174 0.12
79 199 0.13
80 127 0.09
81 44 0.03
82 89 0.06
83 11 0.01
84 6 0.00
85 15 0.01
86 14 0.01
87 52 0.03
89 71 0.05
90 5 0.00
ACGTcount: A:0.28, C:0.16, G:0.20, T:0.37
Consensus pattern (76 bp):
TTTTTCAAAAATCAACTCATAATACAGAGGTGAGTTGAGCCTCGGGTCACGCTGAGGTATTTCTT
TTAAATTTCTG
Found at i:49489356 original size:30 final size:31
Alignment explanation
Indices: 49489315--49489451 Score: 142
Period size: 30 Copynumber: 4.6 Consensus size: 31
49489305 GTTTTTTTTG
* *
49489315 CATTTTAACCCCTATACTTTTC-AAAATTTA
1 CATTTTGACCCCTAAACTTTTCTAAAATTTA
49489345 CATTTTGACCCC-AAACTTTTCTAAAATTTA
1 CATTTTGACCCCTAAACTTTTCTAAAATTTA
*
49489375 CATTTTGACCCCAAAAC-TTTCTAAAA-TTA
1 CATTTTGACCCCTAAACTTTTCTAAAATTTA
* * * *
49489404 CATTTCGACCCTTAGACTTTT-TCAAAA-TTG
1 CATTTTGACCCCTAAACTTTTCT-AAAATTTA
* *
49489434 CACTTTGACCCTTAAACT
1 CATTTTGACCCCTAAACT
49489452 CTTAAGAAAT
Statistics
Matches: 93, Mismatches: 10, Indels: 8
0.84 0.09 0.07
Matches are distributed among these distances:
29 25 0.27
30 64 0.69
31 4 0.04
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.39
Consensus pattern (31 bp):
CATTTTGACCCCTAAACTTTTCTAAAATTTA
Found at i:49489422 original size:29 final size:28
Alignment explanation
Indices: 49489333--49489468 Score: 98
Period size: 30 Copynumber: 4.6 Consensus size: 28
49489323 CCCCTATACT
*
49489333 TTTC-AAAATTTACATTTTGACCC-CAAAC
1 TTTCTAAAA-TTACA-TTTGACCCTTAAAC
**
49489361 TTTTCTAAAATTTACATTTTGACCCCAAAAC
1 -TTTCTAAAA-TTACA-TTTGACCCTTAAAC
*
49489392 TTTCTAAAATTACATTTCGACCCTTAGAC
1 TTTCTAAAATTACATTT-GACCCTTAAAC
* *
49489421 TTTTTCAAAATTGCACTTTGACCCTTAAAC
1 TTTCT-AAAATTACA-TTTGACCCTTAAAC
*
49489451 TCTT-AAGAAATTACATTT
1 T-TTCTA-AAATTACATTT
49489469 TGGCCCATAT
Statistics
Matches: 91, Mismatches: 9, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
28 3 0.03
29 25 0.27
30 54 0.59
31 9 0.10
ACGTcount: A:0.34, C:0.22, G:0.05, T:0.39
Consensus pattern (28 bp):
TTTCTAAAATTACATTTGACCCTTAAAC
Found at i:49489843 original size:20 final size:20
Alignment explanation
Indices: 49489813--49489852 Score: 64
Period size: 19 Copynumber: 2.0 Consensus size: 20
49489803 CTACACTTAG
49489813 CAAAGCAAGCAAGAATCCAAA
1 CAAAGCAAGCAA-AATCCAAA
49489834 CAAA-CAAGCAAAATCCAAA
1 CAAAGCAAGCAAAATCCAAA
49489853 AGAAAAGAGA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 8 0.42
20 7 0.37
21 4 0.21
ACGTcount: A:0.60, C:0.25, G:0.10, T:0.05
Consensus pattern (20 bp):
CAAAGCAAGCAAAATCCAAA
Found at i:49489880 original size:20 final size:21
Alignment explanation
Indices: 49489843--49489882 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
49489833 ACAAACAAGC
*
49489843 AAAATCCAAAAGAAAAGAGAG
1 AAAACCCAAAAGAAAAGAGAG
49489864 AAAACCCAAAA-AAAAGAGA
1 AAAACCCAAAAGAAAAGAGA
49489883 CAAAGAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 8 0.44
21 10 0.56
ACGTcount: A:0.70, C:0.12, G:0.15, T:0.03
Consensus pattern (21 bp):
AAAACCCAAAAGAAAAGAGAG
Found at i:49490036 original size:11 final size:11
Alignment explanation
Indices: 49490016--49490111 Score: 99
Period size: 11 Copynumber: 8.5 Consensus size: 11
49490006 CGACCCGAAG
*
49490016 AAGAAGGAAAA
1 AAGAAAGAAAA
49490027 AAGAAAGAAAA
1 AAGAAAGAAAA
49490038 AAG-AAGTAGAAA
1 AAGAAAG-A-AAA
*
49490050 AAGAAGGAAAA
1 AAGAAAGAAAA
49490061 AAGAAAGAAAA
1 AAGAAAGAAAA
49490072 AAG-AAGAAGAAA
1 AAGAAAG-A-AAA
*
49490084 AAGAGAGAAAA
1 AAGAAAGAAAA
49490095 AAGAAA-AGAAA
1 AAGAAAGA-AAA
49490106 AAGAAA
1 AAGAAA
49490112 AATCAACAGT
Statistics
Matches: 73, Mismatches: 5, Indels: 14
0.79 0.05 0.15
Matches are distributed among these distances:
10 7 0.10
11 48 0.66
12 14 0.19
13 4 0.05
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.01
Consensus pattern (11 bp):
AAGAAAGAAAA
Found at i:49490054 original size:23 final size:22
Alignment explanation
Indices: 49490016--49490113 Score: 84
Period size: 21 Copynumber: 4.6 Consensus size: 22
49490006 CGACCCGAAG
49490016 AAGAAG-GAAAAAAGAAAGAAAA
1 AAGAAGAG-AAAAAGAAAGAAAA
*
49490038 AAGAAGTAGAAAAAGAAGGAAAA
1 AAGAAG-AGAAAAAGAAAGAAAA
*
49490061 AAGAA-AGAAAAA-AGAAGAAGA
1 AAGAAGAGAAAAAGA-AAGAAAA
*
49490082 AA-AAGAGAGAAA-AAAGAAAA
1 AAGAAGAGAAAAAGAAAGAAAA
49490102 GAA-AA-AGAAAAA
1 -AAGAAGAGAAAAA
49490114 TCAACAGTCG
Statistics
Matches: 65, Mismatches: 6, Indels: 12
0.78 0.07 0.14
Matches are distributed among these distances:
20 15 0.23
21 25 0.38
22 6 0.09
23 18 0.28
24 1 0.02
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (22 bp):
AAGAAGAGAAAAAGAAAGAAAA
Found at i:49490107 original size:45 final size:45
Alignment explanation
Indices: 49490016--49490113 Score: 116
Period size: 41 Copynumber: 2.3 Consensus size: 45
49490006 CGACCCGAAG
* *
49490016 AAGAAGGAAAAAAGAAAGAAAAAAGAAGTAGAAAAAGAAGGAAAA
1 AAGAAAGAAAAAAGAAAGAAAAAAGAAGTAGAAAAAGAAAGAAAA
* *
49490061 AAGAAAGAAAAAAG-AAGAAGAAA-AAG-AGAGAAA-AAAGAAAA
1 AAGAAAGAAAAAAGAAAGAAAAAAGAAGTAGAAAAAGAAAGAAAA
49490102 GAA-AAAGAAAAA
1 -AAGAAAGAAAAA
49490114 TCAACAGTCG
Statistics
Matches: 48, Mismatches: 4, Indels: 6
0.83 0.07 0.10
Matches are distributed among these distances:
41 16 0.33
42 8 0.17
43 3 0.06
44 8 0.17
45 13 0.27
ACGTcount: A:0.77, C:0.00, G:0.22, T:0.01
Consensus pattern (45 bp):
AAGAAAGAAAAAAGAAAGAAAAAAGAAGTAGAAAAAGAAAGAAAA
Found at i:49490110 original size:34 final size:34
Alignment explanation
Indices: 49490016--49490107 Score: 150
Period size: 34 Copynumber: 2.7 Consensus size: 34
49490006 CGACCCGAAG
*
49490016 AAGAAGGAAAAAAGAAAGAAAAAAGAAGTAGAAA
1 AAGAAGGAAAAAAGAAAGAAAAAAGAAGAAGAAA
49490050 AAGAAGGAAAAAAGAAAGAAAAAAGAAGAAGAAA
1 AAGAAGGAAAAAAGAAAGAAAAAAGAAGAAGAAA
49490084 AAG-AGAGAAAAAAGAAAAGAAAAA
1 AAGAAG-GAAAAAAG-AAAGAAAAA
49490108 GAAAAATCAA
Statistics
Matches: 55, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
33 2 0.04
34 44 0.80
35 9 0.16
ACGTcount: A:0.76, C:0.00, G:0.23, T:0.01
Consensus pattern (34 bp):
AAGAAGGAAAAAAGAAAGAAAAAAGAAGAAGAAA
Found at i:49490233 original size:14 final size:13
Alignment explanation
Indices: 49490209--49490263 Score: 53
Period size: 13 Copynumber: 4.4 Consensus size: 13
49490199 AAAGCAGCTC
49490209 AAAAAAA-A-AAA
1 AAAAAAACAGAAA
*
49490220 ACAAAAACAGAAA
1 AAAAAAACAGAAA
*
49490233 AAAAATAGCAG-AA
1 AAAAA-AACAGAAA
*
49490246 AAAAAAAGAGAAA
1 AAAAAAACAGAAA
49490259 AAAAA
1 AAAAA
49490264 CAAAGCAGGC
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
11 6 0.17
12 4 0.11
13 21 0.60
14 4 0.11
ACGTcount: A:0.84, C:0.05, G:0.09, T:0.02
Consensus pattern (13 bp):
AAAAAAACAGAAA
Found at i:49490925 original size:21 final size:21
Alignment explanation
Indices: 49490900--49490946 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
49490890 TCCCGTGGTC
*
49490900 AAAAATTTCGAGTTTT-A-AAA
1 AAAAAATT-GAGTTTTCACAAA
49490920 AAAAAATTGAGTTTTCACAAA
1 AAAAAATTGAGTTTTCACAAA
49490941 AAAAAA
1 AAAAAA
49490947 GAAGAAAAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
19 7 0.29
20 8 0.33
21 9 0.38
ACGTcount: A:0.57, C:0.06, G:0.09, T:0.28
Consensus pattern (21 bp):
AAAAAATTGAGTTTTCACAAA
Found at i:49490986 original size:18 final size:17
Alignment explanation
Indices: 49490952--49491313 Score: 143
Period size: 17 Copynumber: 20.2 Consensus size: 17
49490942 AAAAAGAAGA
49490952 AAAAATTCTCGTG-TTTC
1 AAAAATT-TCGTGTTTTC
49490969 AAAGAATTTCGTGTTTTC
1 AAA-AATTTCGTGTTTTC
*
49490987 AAAAAATTC-TCGTTTT-
1 AAAAATTTCGT-GTTTTC
*
49491003 AAAAATTTTCTTGTTTTC
1 AAAAA-TTTCGTGTTTTC
49491021 AAAAATTTTCGTG-TTTC
1 AAAAA-TTTCGTGTTTTC
*
49491038 AAAAATCCTCGTGTTTTC
1 AAAAAT-TTCGTGTTTTC
** *
49491056 AAAAATCCCG-GTGCTTC
1 AAAAATTTCGTGT-TTTC
* *
49491073 AAAAAAATTTTGTGTTCTC
1 --AAAAATTTCGTGTTTTC
* *
49491092 AAAAATTCCGATG--ATC
1 AAAAATTTCG-TGTTTTC
*
49491108 AAAATTTTTTTTTCGTGTTTTC
1 AAAA-----ATTTCGTGTTTTC
*
49491130 TAAAAAAATTCCGTG-TTTC
1 ---AAAAATTTCGTGTTTTC
49491149 AAAAATTTTCGTGTTTTTC
1 AAAAA-TTTCGTG-TTTTC
* *
49491168 AACAATTCTCGT-ATTTC
1 AAAAATT-TCGTGTTTTC
*
49491185 AAAAATTTTCGCG-TTTC
1 AAAAA-TTTCGTGTTTTC
** **
49491202 AAAAAAAAATATTGTTTTC
1 --AAAAATTTCGTGTTTTC
* *
49491221 AAAAATTGTCGTGTTCTA
1 AAAAATT-TCGTGTTTTC
*
49491239 AAAAATATTCGTGTTTTT
1 AAAAAT-TTCGTGTTTTC
* *
49491257 AAGAATTTTCGTG-TCTC
1 AA-AAATTTCGTGTTTTC
* * *
49491274 TAAAATTCTAGTGTTTTAA
1 AAAAATT-TCGTGTTTT-C
49491293 AAAAATTTCGTGTTTTC
1 AAAAATTTCGTGTTTTC
49491310 AAAA
1 AAAA
49491314 TAAAATTTGT
Statistics
Matches: 259, Mismatches: 48, Indels: 76
0.68 0.13 0.20
Matches are distributed among these distances:
16 24 0.09
17 91 0.35
18 80 0.31
19 44 0.17
20 10 0.04
21 4 0.02
22 2 0.01
25 4 0.02
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.43
Consensus pattern (17 bp):
AAAAATTTCGTGTTTTC
Found at i:49490991 original size:36 final size:35
Alignment explanation
Indices: 49490951--49491313 Score: 191
Period size: 36 Copynumber: 10.1 Consensus size: 35
49490941 AAAAAAGAAG
49490951 AAAAAATTCTCGTGTTTCAAAGAATTTCGTGTTTTC
1 AAAAAATTCTCGTGTTTCAAA-AATTTCGTGTTTTC
*
49490987 AAAAAATTCTCGT-TTT-AAAAATTTTCTTGTTTTC
1 AAAAAATTCTCGTGTTTCAAAAA-TTTCGTGTTTTC
* *
49491021 -AAAAATTTTCGTGTTTCAAAAATCCTCGTGTTTTC
1 AAAAAATTCTCGTGTTTCAAAAAT-TTCGTGTTTTC
* * * *
49491056 -AAAAA-TCCCGGTGCTTCAAAAAAATTTTGTGTTCTC
1 AAAAAATTCTC-GTGTTTC--AAAAATTTCGTGTTTTC
* *
49491092 -AAAAATTC-CGATG-ATCAAAATTTTTTTTTCGTGTTTTC
1 AAAAAATTCTCG-TGTTTCAAAA-----ATTTCGTGTTTTC
49491130 TAAAAAAATTC-CGTGTTTCAAAAATTTTCGTGTTTTTC
1 --AAAAAATTCTCGTGTTTCAAAAA-TTTCGTG-TTTTC
* * *
49491168 -AACAATTCTCGTATTTCAAAAATTTTCGCG-TTTC
1 AAAAAATTCTCGTGTTTCAAAAA-TTTCGTGTTTTC
* * * *
49491202 AAAAAAAAATATTGT-TTTCAAAAATTGTCGTGTTCT-
1 --AAAAAATTCTCGTGTTTCAAAAATT-TCGTGTTTTC
* * *
49491238 AAAAAATAT-TCGTGTTTTTAAGAATTTTCGTG-TCTC
1 AAAAAAT-TCTCGTG-TTTCAA-AAATTTCGTGTTTTC
* * *
49491274 -TAAAATTCTAGTGTTTTAAAAAAATTTCGTGTTTTC
1 AAAAAATTCTCGTG-TTT-CAAAAATTTCGTGTTTTC
49491310 AAAA
1 AAAA
49491314 TAAAATTTGT
Statistics
Matches: 257, Mismatches: 35, Indels: 69
0.71 0.10 0.19
Matches are distributed among these distances:
33 17 0.07
34 34 0.13
35 66 0.26
36 76 0.30
37 31 0.12
38 15 0.06
40 2 0.01
41 16 0.06
ACGTcount: A:0.33, C:0.13, G:0.11, T:0.43
Consensus pattern (35 bp):
AAAAAATTCTCGTGTTTCAAAAATTTCGTGTTTTC
Found at i:49491978 original size:25 final size:25
Alignment explanation
Indices: 49491927--49492006 Score: 61
Period size: 25 Copynumber: 3.2 Consensus size: 25
49491917 CCTCTCTCAT
* * * **
49491927 GCCATATAACAGGAAGCTCATGTGA
1 GCCATGTAACGGGAAGCTTATAAGA
* **
49491952 GCCATGTATCGGGAAGCTTATTCGA
1 GCCATGTAACGGGAAGCTTATAAGA
** *
49491977 GCTGTTTAACGGGAAGCTTATAAGA
1 GCCATGTAACGGGAAGCTTATAAGA
49492002 GCCAT
1 GCCAT
49492007 AATCAGAAAG
Statistics
Matches: 41, Mismatches: 14, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.30, C:0.19, G:0.26, T:0.25
Consensus pattern (25 bp):
GCCATGTAACGGGAAGCTTATAAGA
Found at i:49492075 original size:25 final size:25
Alignment explanation
Indices: 49492047--49492163 Score: 93
Period size: 25 Copynumber: 4.7 Consensus size: 25
49492037 GTAGCTCCGA
49492047 AGAGCCATTAATCAGGAAGCTTCAG
1 AGAGCCATTAATCAGGAAGCTTCAG
* *
49492072 AGAGCTA-TATATCGGGAAG-TTCA-
1 AGAGCCATTA-ATCAGGAAGCTTCAG
*
49492095 AGCAAGCCA-T-ATCGGGAAGCTTC-G
1 AG--AGCCATTAATCAGGAAGCTTCAG
* *
49492119 AAGAGCCATTAATCAGGAAGCTCACAA
1 -AGAGCCATTAATCAGGAAGCT-TCAG
*
49492146 AGAGCCTTTAATCAGGAA
1 AGAGCCATTAATCAGGAA
49492164 AATCACGAAG
Statistics
Matches: 75, Mismatches: 7, Indels: 19
0.74 0.07 0.19
Matches are distributed among these distances:
23 16 0.21
24 10 0.13
25 31 0.41
26 18 0.24
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.20
Consensus pattern (25 bp):
AGAGCCATTAATCAGGAAGCTTCAG
Found at i:49492125 original size:23 final size:22
Alignment explanation
Indices: 49492046--49492127 Score: 67
Period size: 23 Copynumber: 3.4 Consensus size: 22
49492036 GGTAGCTCCG
*
49492046 AAGAGCCATTAATCAGGAAGCTTC
1 AAGAGCCA-T-ATCGGGAAGCTTC
*
49492070 AGAGAGCTATATATCGGGAAG-TTC
1 A-AGAGC--CATATCGGGAAGCTTC
49492094 AAGCAAGCCATATCGGGAAGCTTC
1 AAG--AGCCATATCGGGAAGCTTC
49492118 GAAGAGCCAT
1 -AAGAGCCAT
49492128 TAATCAGGAA
Statistics
Matches: 48, Mismatches: 3, Indels: 15
0.73 0.05 0.23
Matches are distributed among these distances:
23 19 0.40
24 8 0.17
25 19 0.40
26 1 0.02
27 1 0.02
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.20
Consensus pattern (22 bp):
AAGAGCCATATCGGGAAGCTTC
Found at i:49492151 original size:26 final size:26
Alignment explanation
Indices: 49492119--49492179 Score: 86
Period size: 26 Copynumber: 2.3 Consensus size: 26
49492109 GGAAGCTTCG
**
49492119 AAGAGCCATTAATCAGGAAGCTCACA
1 AAGAGCCATTAATCAGGAAAATCACA
* *
49492145 AAGAGCCTTTAATCAGGAAAATCACG
1 AAGAGCCATTAATCAGGAAAATCACA
49492171 AAGAGCCAT
1 AAGAGCCAT
49492180 ATATCGAGAC
Statistics
Matches: 30, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 30 1.00
ACGTcount: A:0.43, C:0.21, G:0.20, T:0.16
Consensus pattern (26 bp):
AAGAGCCATTAATCAGGAAAATCACA
Found at i:49494825 original size:13 final size:13
Alignment explanation
Indices: 49494807--49494831 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
49494797 GAGCCCCCAA
49494807 CTAAGTTGGTGTC
1 CTAAGTTGGTGTC
49494820 CTAAGTTGGTGT
1 CTAAGTTGGTGT
49494832 AATGAGTTAA
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:0.16, C:0.12, G:0.32, T:0.40
Consensus pattern (13 bp):
CTAAGTTGGTGTC
Found at i:49502955 original size:23 final size:23
Alignment explanation
Indices: 49502920--49503028 Score: 148
Period size: 23 Copynumber: 4.7 Consensus size: 23
49502910 ACACTAATAT
* *
49502920 TAGCCGAAGCTACCACTGATATG
1 TAGCTGAAGCTACCACTGAAATG
49502943 TAGCTGTAA-CTACCACTGAAATG
1 TAGCTG-AAGCTACCACTGAAATG
* *
49502966 TAGCCGAAGCTACCACTGATATG
1 TAGCTGAAGCTACCACTGAAATG
* *
49502989 TAGCTGTAGCTACCATTGAAATG
1 TAGCTGAAGCTACCACTGAAATG
49503012 TAGCTGAAGCTACCACT
1 TAGCTGAAGCTACCACT
49503029 AATCAATAAC
Statistics
Matches: 74, Mismatches: 10, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
22 2 0.03
23 70 0.95
24 2 0.03
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (23 bp):
TAGCTGAAGCTACCACTGAAATG
Found at i:49502987 original size:46 final size:46
Alignment explanation
Indices: 49502920--49503028 Score: 191
Period size: 46 Copynumber: 2.4 Consensus size: 46
49502910 ACACTAATAT
49502920 TAGCCGAAGCTACCACTGATATGTAGCTGTAACTACCACTGAAATG
1 TAGCCGAAGCTACCACTGATATGTAGCTGTAACTACCACTGAAATG
* *
49502966 TAGCCGAAGCTACCACTGATATGTAGCTGTAGCTACCATTGAAATG
1 TAGCCGAAGCTACCACTGATATGTAGCTGTAACTACCACTGAAATG
*
49503012 TAGCTGAAGCTACCACT
1 TAGCCGAAGCTACCACT
49503029 AATCAATAAC
Statistics
Matches: 60, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 60 1.00
ACGTcount: A:0.31, C:0.24, G:0.20, T:0.25
Consensus pattern (46 bp):
TAGCCGAAGCTACCACTGATATGTAGCTGTAACTACCACTGAAATG
Found at i:49506846 original size:38 final size:38
Alignment explanation
Indices: 49506788--49506860 Score: 87
Period size: 36 Copynumber: 1.9 Consensus size: 38
49506778 ATTTAATCCA
*
49506788 TTTTTTAAAAAAACTTTTATTTTATT-TA-ATTATTAT
1 TTTTTTAAAAAAACTTTTATTATATTATATATTATTAT
* *
49506824 TTTTTTTAAAAAGCATTATTATTATATTATATATTAT
1 TTTTTTAAAAAAAC-TT-TTATTATATTATATATTAT
49506861 CATTATTACT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
36 12 0.40
37 2 0.07
38 9 0.30
39 2 0.07
40 5 0.17
ACGTcount: A:0.37, C:0.03, G:0.01, T:0.59
Consensus pattern (38 bp):
TTTTTTAAAAAAACTTTTATTATATTATATATTATTAT
Found at i:49506873 original size:12 final size:12
Alignment explanation
Indices: 49506837--49506878 Score: 59
Period size: 12 Copynumber: 3.5 Consensus size: 12
49506827 TTTTAAAAAG
49506837 CATTATTATTAT
1 CATTATTATTAT
49506849 -ATTATATATTAT
1 CATTAT-TATTAT
*
49506861 CATTATTACTAT
1 CATTATTATTAT
49506873 CATTAT
1 CATTAT
49506879 CTTTGTATTC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 5 0.19
12 17 0.63
13 5 0.19
ACGTcount: A:0.36, C:0.10, G:0.00, T:0.55
Consensus pattern (12 bp):
CATTATTATTAT
Done.