Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: A07
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: 93829987
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 4250000 characters in sequence are not A, C, G, or T
File 70 of 295
Found at i:20278580 original size:17 final size:17
Alignment explanation
Indices: 20278558--20278590 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
20278548 GCCTCTCCTT
20278558 TTTTTTCCTTTTTATTC
1 TTTTTTCCTTTTTATTC
*
20278575 TTTTTTCTTTTTTATT
1 TTTTTTCCTTTTTATT
20278591 ATACGAAGTA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.06, C:0.12, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTCCTTTTTATTC
Found at i:20279552 original size:80 final size:79
Alignment explanation
Indices: 20279449--20279598 Score: 187
Period size: 80 Copynumber: 1.9 Consensus size: 79
20279439 AAAGAATATT
* * * * *
20279449 CCAAAGAATAAATAAATCGAAGAATAGTTAT-TTTATGGTATGGTCATGAATGAAGAATAAAAGA
1 CCAAAGAACAAATAAATCGAAGAATAATTATCTGTATAGTATGATCATGAATG-A-AATAAAAGA
20279513 ATATTTGAAAGAAAGC
64 ATATTTGAAAGAAAGC
* * *
20279529 CCAAAGAACAAA-AGAATCTAAGAATAATTGTCTGTATAGTATGATTATGAATGAAATAAAAGAA
1 CCAAAGAACAAATA-AATCGAAGAATAATTATCTGTATAGTATGATCATGAATGAAATAAAAGAA
20279593 TATTTG
65 TATTTG
20279599 CTCAAAATGA
Statistics
Matches: 60, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
79 17 0.28
80 26 0.43
81 17 0.28
ACGTcount: A:0.49, C:0.07, G:0.17, T:0.27
Consensus pattern (79 bp):
CCAAAGAACAAATAAATCGAAGAATAATTATCTGTATAGTATGATCATGAATGAAATAAAAGAAT
ATTTGAAAGAAAGC
Found at i:20280764 original size:501 final size:501
Alignment explanation
Indices: 20279822--20280826 Score: 1920
Period size: 501 Copynumber: 2.0 Consensus size: 501
20279812 CGATTTTTTC
20279822 TTCGGATACGTCGTCAAGGTCCAGATTGCTCGATATTTCCTCCAGGCTTCTTTTTCAAGGGATTG
1 TTCGGATACGTCGTCAAGGTCCAGATTGCTCGATATTTCCTCCAGGCTTCTTTTTCAAGGGATTG
20279887 CAACTCTCTTGCCATCCCCTTCAGTTATCACATTTACTGTCTCATCGAGGCGGTTAGGTTCTGAT
66 CAACTCTCTTGCCATCCCCTTCAGTTATCACATTTACTGTCTCATCGAGGCGGTTAGGTTCTGAT
* *
20279952 TAATCGTCAAACTTCATGATTCCCACTTTAATGAGCCTTTCGATCAACTTTTTAAATATAATACA
131 TAATCATCAAACTTCATGATTCCCACTTTAATGAGCCTTTCGATCAACTTTTTAAACATAATACA
* *
20280017 GTTTTCGATTGAGTGTCCCGTTACTCCTGCGTGATACTCACATGGGTATTCACATCATACCATTT
196 GTTTTCGATTGAGTGCCCCGTTACTCCTGCGTAATACTCACATGGGTATTCACATCATACCATTT
20280082 TGGGAATGGAGGTTGCACGGGTTCCGAGTAGAATTGGGACACCACATGCGCATCAAAAAAATTCT
261 TGGGAATGGAGGTTGCACGGGTTCCGAGTAGAATTGGGACACCACATGCGCATCAAAAAAATTCT
*
20280147 GATACAGTTCTTTATACGTCATCAGGATGGGTGTAAACTTGAGTTTTTCTGTATTTGGTCTCGAG
326 GATACAGTTCTTTATACGTCATCAGGATGGGTGTAAACTTGAGTTTTTCTATATTTGGTCTCGAG
*
20280212 TTGGAGTCTTGCCTTTAGGTTCCTTGATAGTTGGTGGTCATGGCCCTCGGCTGGCTTACAGTGAC
391 TTGGAGTCTTGCCTTGAGGTTCCTTGATAGTTGGTGGTCATGGCCCTCGGCTGGCTTACAGTGAC
20280277 CGATCTGAAATACCTATTGCCCACATTATTCACCTCATTTTTATTT
456 CGATCTGAAATACCTATTGCCCACATTATTCACCTCATTTTTATTT
20280323 TTCGGATACGTCGTCAAGGTCCAGATTGCTCGATATTTCCTCCAGGCTTCTTTTTCAAGGGATTG
1 TTCGGATACGTCGTCAAGGTCCAGATTGCTCGATATTTCCTCCAGGCTTCTTTTTCAAGGGATTG
20280388 CAACTCTCTTGCCATCCCCTTCAGTTATCACATTTACTGTCTCATCGAGGCGGTTAGGTTCTGAT
66 CAACTCTCTTGCCATCCCCTTCAGTTATCACATTTACTGTCTCATCGAGGCGGTTAGGTTCTGAT
*
20280453 TAATCATCAAACTTCATGATTCCCACTTTAATGAGCCTTTCGATCAACTTTTTAAACATAATGCA
131 TAATCATCAAACTTCATGATTCCCACTTTAATGAGCCTTTCGATCAACTTTTTAAACATAATACA
20280518 GTTTTCGATTGAGTGCCCCGTTACTCCTGCGTAATACTCACATGGGTATTCACATCATACCATTT
196 GTTTTCGATTGAGTGCCCCGTTACTCCTGCGTAATACTCACATGGGTATTCACATCATACCATTT
* *
20280583 TGGGAATGGAGGTTGCACGGGTTCCGAGTAGATTTGGGACACCACATGCGTATCAAAAAAATTCT
261 TGGGAATGGAGGTTGCACGGGTTCCGAGTAGAATTGGGACACCACATGCGCATCAAAAAAATTCT
*
20280648 GATACAGTTCTTTATACGTCATCAGGATGGGTGTGAACTTGAGTTTTTCTATATTTGGTCTCGAG
326 GATACAGTTCTTTATACGTCATCAGGATGGGTGTAAACTTGAGTTTTTCTATATTTGGTCTCGAG
20280713 TTGGAGTCTTGCCTTGAGGTTCCTTGATAGTTGGTGGTCATGGCCCTCGGCTGGCTTACAGTGAC
391 TTGGAGTCTTGCCTTGAGGTTCCTTGATAGTTGGTGGTCATGGCCCTCGGCTGGCTTACAGTGAC
20280778 CGATCTGAAATACCTATTGCCCACATTATTCACCTCATTTTTATTT
456 CGATCTGAAATACCTATTGCCCACATTATTCACCTCATTTTTATTT
20280824 TTC
1 TTC
20280827 TTCGGGGTTA
Statistics
Matches: 494, Mismatches: 10, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
501 494 1.00
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.35
Consensus pattern (501 bp):
TTCGGATACGTCGTCAAGGTCCAGATTGCTCGATATTTCCTCCAGGCTTCTTTTTCAAGGGATTG
CAACTCTCTTGCCATCCCCTTCAGTTATCACATTTACTGTCTCATCGAGGCGGTTAGGTTCTGAT
TAATCATCAAACTTCATGATTCCCACTTTAATGAGCCTTTCGATCAACTTTTTAAACATAATACA
GTTTTCGATTGAGTGCCCCGTTACTCCTGCGTAATACTCACATGGGTATTCACATCATACCATTT
TGGGAATGGAGGTTGCACGGGTTCCGAGTAGAATTGGGACACCACATGCGCATCAAAAAAATTCT
GATACAGTTCTTTATACGTCATCAGGATGGGTGTAAACTTGAGTTTTTCTATATTTGGTCTCGAG
TTGGAGTCTTGCCTTGAGGTTCCTTGATAGTTGGTGGTCATGGCCCTCGGCTGGCTTACAGTGAC
CGATCTGAAATACCTATTGCCCACATTATTCACCTCATTTTTATTT
Found at i:20287281 original size:27 final size:24
Alignment explanation
Indices: 20287230--20287288 Score: 66
Period size: 25 Copynumber: 2.3 Consensus size: 24
20287220 GTAAAATGGG
20287230 TTTAAAATAAGGTATATAAAATAA
1 TTTAAAATAAGGTATATAAAATAA
*
20287254 TTTTAAAATAA-GTAATATATAAGTTAA
1 -TTTAAAATAAGGT-ATATA-AA-ATAA
20287281 TTTAAAAT
1 TTTAAAAT
20287289 GTTATATAAC
Statistics
Matches: 30, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
24 2 0.07
25 15 0.50
26 10 0.33
27 3 0.10
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (24 bp):
TTTAAAATAAGGTATATAAAATAA
Found at i:20287314 original size:20 final size:19
Alignment explanation
Indices: 20287291--20287330 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
20287281 TTTAAAATGT
20287291 TATATAACAAGTTAAAAAAA
1 TATATAACAAG-TAAAAAAA
* *
20287311 TATATAATATGTAAAAAAA
1 TATATAACAAGTAAAAAAA
20287330 T
1 T
20287331 TAAAAAAAGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 9 0.50
20 9 0.50
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (19 bp):
TATATAACAAGTAAAAAAA
Found at i:20289901 original size:16 final size:17
Alignment explanation
Indices: 20289880--20289912 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
20289870 TTTAATTATA
20289880 TAAAAATAATAA-AAAT
1 TAAAAATAATAATAAAT
*
20289896 TAAAAATGATAATAAAT
1 TAAAAATAATAATAAAT
20289913 ATTTAATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (17 bp):
TAAAAATAATAATAAAT
Found at i:20289975 original size:13 final size:13
Alignment explanation
Indices: 20289957--20289989 Score: 50
Period size: 12 Copynumber: 2.5 Consensus size: 13
20289947 ATATACAAAA
20289957 TAAATTTAAAATT
1 TAAATTTAAAATT
20289970 TAAA-TTAAAATT
1 TAAATTTAAAATT
20289982 TCAAATTT
1 T-AAATTT
20289990 TCTTCATTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
12 9 0.50
13 7 0.39
14 2 0.11
ACGTcount: A:0.52, C:0.03, G:0.00, T:0.45
Consensus pattern (13 bp):
TAAATTTAAAATT
Found at i:20294967 original size:3 final size:3
Alignment explanation
Indices: 20294922--20294947 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
20294912 AATAAAAGGT
20294922 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
20294948 GTTAAGCAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:20295138 original size:21 final size:21
Alignment explanation
Indices: 20295082--20295128 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
20295072 TAACAAACGT
*
20295082 AATAG-TATAATATTATGATAAC
1 AATAGTTATAATA--ATAATAAC
20295104 AATAGTTATAATAATAATAAC
1 AATAGTTATAATAATAATAAC
20295125 AATA
1 AATA
20295129 TTTTATATAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
21 11 0.48
22 5 0.22
23 7 0.30
ACGTcount: A:0.55, C:0.04, G:0.06, T:0.34
Consensus pattern (21 bp):
AATAGTTATAATAATAATAAC
Found at i:20295194 original size:3 final size:3
Alignment explanation
Indices: 20295188--20295425 Score: 132
Period size: 3 Copynumber: 80.7 Consensus size: 3
20295178 CCTTAGTAAG
* * * * * *
20295188 AAT AAT AGT AGT AAT AAT AAA AAC AAT AGT AGT AA- ATAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT
* * *
20295233 AAT AAC AAT AAT AAT AAT AAT AAT AAT AAT -AT AGTT AAA AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A-AT AAT AAT AAT
* * * * * * *
20295278 AAT AAT AGT AAT AGT GAT AAT GAT AAT AA- AAA AAT AGT AAT AAT AGT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
** * * * * *
20295325 -AT GTT AAAT AAT AAT AGT AA- AA- AAT AGT AAT AGT AAT AAT TAC
1 AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
* * * * *
20295368 AAA AAT GAT AAT GAA- CAT AA- AAT GAT AAT AAT ACT AAT AAT AAT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
20295412 AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AA
20295426 ATTATAGGAA
Statistics
Matches: 176, Mismatches: 48, Indels: 22
0.72 0.20 0.09
Matches are distributed among these distances:
2 13 0.07
3 157 0.89
4 6 0.03
ACGTcount: A:0.61, C:0.02, G:0.08, T:0.30
Consensus pattern (3 bp):
AAT
Found at i:20295320 original size:38 final size:36
Alignment explanation
Indices: 20295269--20295356 Score: 106
Period size: 38 Copynumber: 2.4 Consensus size: 36
20295259 TAATATAGTT
* *
20295269 AAAAATAATAATAATAGTAATAGTGATAATGATAATA-A
1 AAAAATAGTAATAATAGT-AT-GTGA-AATAATAATAGA
*
20295307 AAAAATAGTAATAATAGTATGTTAAATAATAATAGTA
1 AAAAATAGTAATAATAGTATGTGAAATAATAATAG-A
20295344 AAAAATAGTAATA
1 AAAAATAGTAATA
20295357 GTAATAATTA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
35 9 0.20
36 3 0.07
37 16 0.36
38 17 0.38
ACGTcount: A:0.60, C:0.00, G:0.10, T:0.30
Consensus pattern (36 bp):
AAAAATAGTAATAATAGTATGTGAAATAATAATAGA
Found at i:20297107 original size:88 final size:88
Alignment explanation
Indices: 20296982--20297356 Score: 452
Period size: 88 Copynumber: 4.3 Consensus size: 88
20296972 GTTCCACTGC
* ** * * ** *
20296982 AACTTCAGGGAGATAAGGTTTAGTGGCTTC-AATCGCTCCAATATCATTTCAGGAAGAAGATATT
1 AACTTCAAGGAGATAAGAATT-GTGGCTTCGAACCGCTCCAGTGCCATTTCAGGAAGAAGAGATT
* *
20297046 TGTAACTTCGATCT-CATCCGCTGG
65 TGTAGCTTCGATCTAC-TCCGCTGA
*
20297070 AACTTCAAGGAGATAAGAATTGTGGCTTCGAGCCGCTCCAGTGCCATTTCAAGG-AGAAGAGATT
1 AACTTCAAGGAGATAAGAATTGTGGCTTCGAACCGCTCCAGTGCCATTTC-AGGAAGAAGAGATT
** *
20297134 TGTAGCTTCGATCTACTCCATTAA
65 TGTAGCTTCGATCTACTCCGCTGA
* * ** *
20297158 AACTTCAAGGAGATACGAATTGTGGCTTCGAGCTACTCCAGTGCCATTTCAGGGAGAAGAGATTT
1 AACTTCAAGGAGATAAGAATTGTGGCTTCGAACCGCTCCAGTGCCATTTCAGGAAGAAGAGATTT
*
20297223 GTAGCTTTGATCTACTCCGCTGA
66 GTAGCTTCGATCTACTCCGCTGA
* * * *
20297246 AACTTCAAGGAGATACGAATTGTGGCTTCGAACTGCTCTAGTGTCATTTCAGGAAGAAGAGATTT
1 AACTTCAAGGAGATAAGAATTGTGGCTTCGAACCGCTCCAGTGCCATTTCAGGAAGAAGAGATTT
*
20297311 GTAGCTTCGATCTATTCCGCCTG-
66 GTAGCTTCGATCTACTCCG-CTGA
*
20297334 AACTTCAAGAAGATAAGAATTGT
1 AACTTCAAGGAGATAAGAATTGT
20297357 AATTTTTAGC
Statistics
Matches: 252, Mismatches: 30, Indels: 10
0.86 0.10 0.03
Matches are distributed among these distances:
87 11 0.04
88 234 0.93
89 7 0.03
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (88 bp):
AACTTCAAGGAGATAAGAATTGTGGCTTCGAACCGCTCCAGTGCCATTTCAGGAAGAAGAGATTT
GTAGCTTCGATCTACTCCGCTGA
Found at i:20297121 original size:44 final size:44
Alignment explanation
Indices: 20297073--20297356 Score: 186
Period size: 44 Copynumber: 6.5 Consensus size: 44
20297063 CCGCTGGAAC
** *
20297073 TTCAAGGAGATAAGAATTGTGGCTTCGAGCCGCTCCAGTGCCAT
1 TTCAAGGAGATAAGAATTGTGGCTTCGAGCTACTCCAGTGACAT
* * * * * * *
20297117 TTCAAGGAGA-AGAGATTTGTAGCTTCGATCTACTCCATTAAAAC
1 TTCAAGGAGATA-AGAATTGTGGCTTCGAGCTACTCCAGTGACAT
* *
20297161 TTCAAGGAGATACGAATTGTGGCTTCGAGCTACTCCAGTGCCAT
1 TTCAAGGAGATAAGAATTGTGGCTTCGAGCTACTCCAGTGACAT
* * * * * * *
20297205 TTCAGGGAGA-AGAGATTTGTAGCTTTGATCTACTCC-GCTGAAAC
1 TTCAAGGAGATA-AGAATTGTGGCTTCGAGCTACTCCAG-TGACAT
* * * * *
20297249 TTCAAGGAGATACGAATTGTGGCTTCGAACTGCTCTAGTGTCAT
1 TTCAAGGAGATAAGAATTGTGGCTTCGAGCTACTCCAGTGACAT
* * * * *
20297293 TTC-AGGAAGA-AGAGATTTGTAGCTTCGATCTATTCC-GCCTGA-AC
1 TTCAAGG-AGATA-AGAATTGTGGCTTCGAGCTACTCCAG--TGACAT
*
20297337 TTCAAGAAGATAAGAATTGT
1 TTCAAGGAGATAAGAATTGT
20297357 AATTTTTAGC
Statistics
Matches: 178, Mismatches: 50, Indels: 24
0.71 0.20 0.10
Matches are distributed among these distances:
43 8 0.04
44 162 0.91
45 8 0.04
ACGTcount: A:0.29, C:0.19, G:0.24, T:0.29
Consensus pattern (44 bp):
TTCAAGGAGATAAGAATTGTGGCTTCGAGCTACTCCAGTGACAT
Found at i:20297598 original size:44 final size:44
Alignment explanation
Indices: 20297375--20297606 Score: 131
Period size: 44 Copynumber: 5.3 Consensus size: 44
20297365 GCCTGTTACC
* *
20297375 CTACTGCTTTGGGGGTTAAGGCTCACCATCTTCGATCTGCTCCA
1 CTACTGCTTAGGGGGTTAAGGTTCACCATCTTCGATCTGCTCCA
* * * * * * *
20297419 CTACTGTTTAGGGAGATAAGATCTGTA--ATTTTCAGA-CTGTTACCA
1 CTACTGCTTAGGGGGTTAAGGT-T-CACCATCTTC-GATCTGCT-CCA
* *
20297464 -TACTGCTTA-GGGGTTAAGGCTCACCGTCTTCGATCTGCTCCA
1 CTACTGCTTAGGGGGTTAAGGTTCACCATCTTCGATCTGCTCCA
* * * * * ** * **
20297506 CTACTGCTTAAGGAGATAAGATCTGTA--AT-TTTTAGCCTATTACC-
1 CTACTGCTTAGGGGGTTAAGGT-T-CACCATCTTCGA-TCTGCT-CCA
*
20297550 CTACTGCTTAGGGGGTTAAGGTTCACCGTCTTCGATCTGCTCCA
1 CTACTGCTTAGGGGGTTAAGGTTCACCATCTTCGATCTGCTCCA
20297594 CTACTGCTTAGGG
1 CTACTGCTTAGGG
20297607 AGATAAGATC
Statistics
Matches: 131, Mismatches: 40, Indels: 34
0.64 0.20 0.17
Matches are distributed among these distances:
41 1 0.01
42 7 0.05
43 30 0.23
44 79 0.60
45 12 0.09
46 2 0.02
ACGTcount: A:0.21, C:0.24, G:0.22, T:0.33
Consensus pattern (44 bp):
CTACTGCTTAGGGGGTTAAGGTTCACCATCTTCGATCTGCTCCA
Found at i:20297600 original size:88 final size:88
Alignment explanation
Indices: 20297344--20297624 Score: 449
Period size: 88 Copynumber: 3.2 Consensus size: 88
20297334 AACTTCAAGA
* *
20297344 AGATAAGAAT-TGTAATTTTTAGCCTGTTACCCTACTGCTTTGGGGGTTAAGGCTCACCATCTTC
1 AGATAAG-ATCTGTAATTTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTC
*
20297408 GATCTGCTCCACTACTGTTTAGGG
65 GATCTGCTCCACTACTGCTTAGGG
* * *
20297432 AGATAAGATCTGTAATTTTCAGACTGTTACCATACTGCTTA-GGGGTTAAGGCTCACCGTCTTCG
1 AGATAAGATCTGTAATTTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCG
*
20297496 ATCTGCTCCACTACTGCTTAAGG
66 ATCTGCTCCACTACTGCTTAGGG
* *
20297519 AGATAAGATCTGTAATTTTTAGCCTATTACCCTACTGCTTAGGGGGTTAAGGTTCACCGTCTTCG
1 AGATAAGATCTGTAATTTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCG
20297584 ATCTGCTCCACTACTGCTTAGGG
66 ATCTGCTCCACTACTGCTTAGGG
20297607 AGATAAGATCTGTGAATT
1 AGATAAGATCTGT-AATT
20297625 CACCGACGTT
Statistics
Matches: 177, Mismatches: 13, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
87 82 0.46
88 91 0.51
89 4 0.02
ACGTcount: A:0.23, C:0.21, G:0.21, T:0.34
Consensus pattern (88 bp):
AGATAAGATCTGTAATTTTTAGCCTGTTACCCTACTGCTTAGGGGGTTAAGGCTCACCGTCTTCG
ATCTGCTCCACTACTGCTTAGGG
Found at i:20302265 original size:28 final size:28
Alignment explanation
Indices: 20302204--20302266 Score: 90
Period size: 28 Copynumber: 2.2 Consensus size: 28
20302194 TCGATATTTT
* *
20302204 GCACATTAAGTGTCATTCTCAATATCTC
1 GCACACTAAGTGCCATTCTCAATATCTC
*
20302232 GCACACTAAGTGCCATTCTCAATATTTC
1 GCACACTAAGTGCCATTCTCAATATCTC
*
20302260 GTACACT
1 GCACACT
20302267 GAGTACTATA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 31 1.00
ACGTcount: A:0.29, C:0.27, G:0.11, T:0.33
Consensus pattern (28 bp):
GCACACTAAGTGCCATTCTCAATATCTC
Found at i:20306371 original size:3 final size:3
Alignment explanation
Indices: 20306363--20306638 Score: 113
Period size: 3 Copynumber: 93.3 Consensus size: 3
20306353 AACAATAGTT
* * * * *
20306363 ATA ATA ATA AAA ATA ATA GTA GTA A-A TATA ATA ACA ATA ACA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA
* * * * * *
20306408 ACA ATA ACA ATA ACA ATA ACA ATA ATA ATA AT- ATA GTTA AAA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA
* * * * *
20306453 ATA ATA ATA GTA ATA GTG ATA ATG ATA ATA A-A A-A ATA GTA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * *
20306499 GT- ATG TTAA ATA ATA ATA GTA A-A A-A ATA GTA ATA GTA ATA ATT
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * * * * *
20306542 ACA AAA ATG ATA ATGA A-C ATA A-A ATC ATA ATA ATA CTA ATG TTA
1 ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * *
20306586 ATA GTA ATAA ATA AGA ATA GTA ATA ATA GTA A-A TATA ATA ATA ATA
1 ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA
20306632 ATA ATA A
1 ATA ATA A
20306639 ATTATAGGAA
Statistics
Matches: 193, Mismatches: 66, Indels: 28
0.67 0.23 0.10
Matches are distributed among these distances:
2 16 0.08
3 167 0.87
4 10 0.05
ACGTcount: A:0.60, C:0.04, G:0.07, T:0.29
Consensus pattern (3 bp):
ATA
Found at i:20306401 original size:21 final size:20
Alignment explanation
Indices: 20306334--20306401 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 20
20306324 TAACAAACGT
*
20306334 AATAGTATAATATTATGATAAC
1 AATAGTATAA-A-TATAATAAC
* *
20306356 AATAGT-TATAATAATAAAAAT
1 AATAGTATA-AAT-ATAATAAC
20306377 AATAGTAGTAAATATAATAAC
1 AATAGTA-TAAATATAATAAC
20306398 AATA
1 AATA
20306402 ACAATAACAA
Statistics
Matches: 37, Mismatches: 5, Indels: 9
0.73 0.10 0.18
Matches are distributed among these distances:
20 1 0.03
21 24 0.65
22 10 0.27
23 2 0.05
ACGTcount: A:0.57, C:0.03, G:0.07, T:0.32
Consensus pattern (20 bp):
AATAGTATAAATATAATAAC
Found at i:20306495 original size:37 final size:37
Alignment explanation
Indices: 20306431--20306640 Score: 110
Period size: 37 Copynumber: 5.5 Consensus size: 37
20306421 CAATAACAAT
* *
20306431 AATAATAATATAGTTAAAAATAATAATAATAGTAATAG-T-
1 AATAATAATA-A-TAAAAAATAGTAATAATAGT-AT-GTTA
* *
20306470 GATAATGATAATAAAAAATAGTAATAATAGTATGTTA
1 AATAATAATAATAAAAAATAGTAATAATAGTATGTTA
* * * *
20306507 AATAATAATAGTAAAAAATAGTAATAGTAATA-ATTA
1 AATAATAATAATAAAAAATAGTAATAATAGTATGTTA
* * *
20306543 CAAAAATGATAATGAACATAAAATCA-TAATAATACTAATGTT-
1 -AATAATAATAAT--A-A-AAAAT-AGTAATAATAGT-ATGTTA
* * **
20306585 AATAGTAATAA-ATAAGAATAGTAATAATAGTA-AATA
1 AATAATAATAATA-AAAAATAGTAATAATAGTATGTTA
*
20306621 TAATAATAATAATAATAAAT
1 -AATAATAATAATAAAAAAT
20306641 TATAGGAATT
Statistics
Matches: 130, Mismatches: 27, Indels: 30
0.70 0.14 0.16
Matches are distributed among these distances:
35 2 0.02
36 8 0.06
37 81 0.62
38 4 0.03
39 9 0.07
40 1 0.01
41 21 0.16
42 2 0.02
43 2 0.02
ACGTcount: A:0.59, C:0.02, G:0.09, T:0.31
Consensus pattern (37 bp):
AATAATAATAATAAAAAATAGTAATAATAGTATGTTA
Found at i:20306531 original size:16 final size:16
Alignment explanation
Indices: 20306506--20306536 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20306496 ATAGTATGTT
20306506 AAATAATAATAGTAAA
1 AAATAATAATAGTAAA
*
20306522 AAATAGTAATAGTAA
1 AAATAATAATAGTAA
20306537 TAATTACAAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.65, C:0.00, G:0.10, T:0.26
Consensus pattern (16 bp):
AAATAATAATAGTAAA
Found at i:20309005 original size:87 final size:86
Alignment explanation
Indices: 20308848--20309008 Score: 216
Period size: 87 Copynumber: 1.9 Consensus size: 86
20308838 TACATGCATA
* * * **
20308848 AGGTTGAGTTCTTACTCTTAATGAATTCATATCTTAGGTTTTAGGTGGTCTTATTGAGACGGACT
1 AGGTTGAGTTCTTACTCTTAATGAATTCATATCTCAGATTTTAGGTGGTCCTATTGAGAAAGACT
20308913 AGATGAATTCATTGACATGTG
66 AGATGAATTCATTGACATGTG
* * *
20308934 AGGTTGAGTTTCTTACTCTTAATGAGTTCATAT-TCCAGATTTTGGGTGGTCCTATTTAGAAAGA
1 AGGTTGAG-TTCTTACTCTTAATGAATTCATATCT-CAGATTTTAGGTGGTCCTATTGAGAAAGA
*
20308998 CTTGATGAATT
64 CTAGATGAATT
20309009 AACGAATTTA
Statistics
Matches: 64, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
86 9 0.14
87 55 0.86
ACGTcount: A:0.25, C:0.12, G:0.22, T:0.40
Consensus pattern (86 bp):
AGGTTGAGTTCTTACTCTTAATGAATTCATATCTCAGATTTTAGGTGGTCCTATTGAGAAAGACT
AGATGAATTCATTGACATGTG
Found at i:20310836 original size:28 final size:28
Alignment explanation
Indices: 20310804--20310863 Score: 84
Period size: 28 Copynumber: 2.1 Consensus size: 28
20310794 TTTATAATTC
* * * *
20310804 ATAATTTTTTATATTATTAATTTTTTTT
1 ATAATTCTCTATATAATAAATTTTTTTT
20310832 ATAATTCTCTATATAATAAATTTTTTTT
1 ATAATTCTCTATATAATAAATTTTTTTT
20310860 ATAA
1 ATAA
20310864 ATAATTACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (28 bp):
ATAATTCTCTATATAATAAATTTTTTTT
Found at i:20311868 original size:3 final size:3
Alignment explanation
Indices: 20311860--20311888 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
20311850 TATTAATAAA
20311860 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT AT
20311889 AAGTGTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:20312287 original size:16 final size:16
Alignment explanation
Indices: 20312268--20312298 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
20312258 CTTTCTAATT
20312268 TTTTTACTATTTTTAA
1 TTTTTACTATTTTTAA
*
20312284 TTTTTACTTTTTTTA
1 TTTTTACTATTTTTA
20312299 TTTATTTCAA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.74
Consensus pattern (16 bp):
TTTTTACTATTTTTAA
Found at i:20313427 original size:25 final size:27
Alignment explanation
Indices: 20313390--20313442 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
20313380 TCAAACATGC
20313390 ATTTAGGTCAATTTAAC-CCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
* *
20313416 ATTTCGGT-AATTTATCTCCTAGGGGT
1 ATTTAGGTCAATTTAACTCCTAGGGGT
20313442 A
1 A
20313443 AAACTGTAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
25 7 0.29
26 17 0.71
ACGTcount: A:0.25, C:0.15, G:0.23, T:0.38
Consensus pattern (27 bp):
ATTTAGGTCAATTTAACTCCTAGGGGT
Found at i:20314957 original size:32 final size:32
Alignment explanation
Indices: 20314916--20314980 Score: 130
Period size: 32 Copynumber: 2.0 Consensus size: 32
20314906 TAATCTTACC
20314916 ATGCCCATCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
20314948 ATGCCCATCATCCATTAACTATTAAAATGCTA
1 ATGCCCATCATCCATTAACTATTAAAATGCTA
20314980 A
1 A
20314981 AATGCATACA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.38, C:0.25, G:0.06, T:0.31
Consensus pattern (32 bp):
ATGCCCATCATCCATTAACTATTAAAATGCTA
Found at i:20320704 original size:26 final size:24
Alignment explanation
Indices: 20320674--20320723 Score: 73
Period size: 26 Copynumber: 2.0 Consensus size: 24
20320664 AAATAAAAAA
*
20320674 ATTTAAAAATATAATAAATCAAATAT
1 ATTTAAAAACATAA-AAA-CAAATAT
20320700 ATTTAAAAACATAAAAACAAATAT
1 ATTTAAAAACATAAAAACAAATAT
20320724 TAAAACAAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 7 0.30
25 3 0.13
26 13 0.57
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.30
Consensus pattern (24 bp):
ATTTAAAAACATAAAAACAAATAT
Found at i:20320743 original size:21 final size:21
Alignment explanation
Indices: 20320694--20320752 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
20320684 ATAATAAATC
*
20320694 AAAT-ATATTTAAAA-ACATAA
1 AAATAATA-TTAAAACAAATAA
*
20320714 AAACAAATATTAAAACAAATAA
1 AAA-TAATATTAAAACAAATAA
*
20320736 AAATAATACTAAAACAA
1 AAATAATATTAAAACAA
20320753 TTCTTAAAAC
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
20 3 0.09
21 18 0.56
22 11 0.34
ACGTcount: A:0.69, C:0.08, G:0.00, T:0.22
Consensus pattern (21 bp):
AAATAATATTAAAACAAATAA
Found at i:20321211 original size:32 final size:32
Alignment explanation
Indices: 20321174--20321235 Score: 124
Period size: 32 Copynumber: 1.9 Consensus size: 32
20321164 GCTTATCATA
20321174 CCCATCATCCATTAACTATTAAAATGCTAATG
1 CCCATCATCCATTAACTATTAAAATGCTAATG
20321206 CCCATCATCCATTAACTATTAAAATGCTAA
1 CCCATCATCCATTAACTATTAAAATGCTAA
20321236 AATGCATACA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.39, C:0.26, G:0.05, T:0.31
Consensus pattern (32 bp):
CCCATCATCCATTAACTATTAAAATGCTAATG
Found at i:20322609 original size:27 final size:27
Alignment explanation
Indices: 20322537--20322640 Score: 95
Period size: 27 Copynumber: 3.9 Consensus size: 27
20322527 AAGTCCTTAT
* *
20322537 TACAGAATATGCCACAAAGG-TGTTCCA
1 TACAGAGTATGCCACAAAGGCTATT-CA
* ** *
20322564 TATAGAGTACACCATAAAGGCTATAT-A
1 TACAGAGTATGCCACAAAGGCTAT-TCA
*
20322591 TACAGAGTATGCCACAAAGGCGATTCA
1 TACAGAGTATGCCACAAAGGCTATTCA
* *
20322618 TTCAGTGTATGCCACAAAGGCTA
1 TACAGAGTATGCCACAAAGGCTA
20322641 ACAGGATCCC
Statistics
Matches: 60, Mismatches: 14, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
26 1 0.02
27 56 0.93
28 2 0.03
29 1 0.02
ACGTcount: A:0.38, C:0.20, G:0.19, T:0.23
Consensus pattern (27 bp):
TACAGAGTATGCCACAAAGGCTATTCA
Found at i:20324440 original size:71 final size:71
Alignment explanation
Indices: 20324324--20324489 Score: 289
Period size: 71 Copynumber: 2.4 Consensus size: 71
20324314 ATGCTTTATG
* * *
20324324 AAATTAGTGTTACTTTGTTAGATTTTAAGTTTAGACATGAAAAAACAAGACTAATTTATAATAAA
1 AAATTGGTGTTAATTTGTTAGATTTTAAGCTTAGACATGAAAAAACAAGACTAATTTATAATAAA
20324389 AGGACT
66 AGGACT
20324395 AAATTGGTGTTAATTTGTTAGATTTTAAGCTTAGACATGAAAAAACAAGACTAATTTATAATAAA
1 AAATTGGTGTTAATTTGTTAGATTTTAAGCTTAGACATGAAAAAACAAGACTAATTTATAATAAA
*
20324460 GGGACT
66 AGGACT
20324466 AAATTGGTGTT-ATTTGTTAGATTT
1 AAATTGGTGTTAATTTGTTAGATTT
20324490 CAAGACAAAT
Statistics
Matches: 91, Mismatches: 4, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
70 13 0.14
71 78 0.86
ACGTcount: A:0.40, C:0.06, G:0.16, T:0.37
Consensus pattern (71 bp):
AAATTGGTGTTAATTTGTTAGATTTTAAGCTTAGACATGAAAAAACAAGACTAATTTATAATAAA
AGGACT
Found at i:20327229 original size:38 final size:38
Alignment explanation
Indices: 20327178--20327279 Score: 136
Period size: 38 Copynumber: 2.7 Consensus size: 38
20327168 GTTATATCGT
* *
20327178 TATTCAAGCTTTGTGCCTA-CTAGGCTTAGTGCTAGTGA
1 TATTCAGGCTTTGTGCCTAGC-AGGCTTAGTGCCAGTGA
* *
20327216 TATTCAGGCTTTGTGCCTAGCATGCTTAGTGCCAGTGT
1 TATTCAGGCTTTGTGCCTAGCAGGCTTAGTGCCAGTGA
*
20327254 TATTCAGG-TTAGTGCCTAGCAGGCTT
1 TATTCAGGCTTTGTGCCTAGCAGGCTT
20327280 CTTACCGGTG
Statistics
Matches: 57, Mismatches: 6, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
37 16 0.28
38 40 0.70
39 1 0.02
ACGTcount: A:0.19, C:0.20, G:0.25, T:0.36
Consensus pattern (38 bp):
TATTCAGGCTTTGTGCCTAGCAGGCTTAGTGCCAGTGA
Found at i:20328326 original size:15 final size:16
Alignment explanation
Indices: 20328291--20328333 Score: 54
Period size: 15 Copynumber: 2.8 Consensus size: 16
20328281 TCGAGGACTC
20328291 GATTTAGGTATGATAT
1 GATTTAGGTATGATAT
*
20328307 G-TTTATGTATGAT-T
1 GATTTAGGTATGATAT
20328321 GATTTAGGATATG
1 GATTTAGG-TATG
20328334 TCTAGGATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
14 2 0.09
15 16 0.70
16 5 0.22
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.47
Consensus pattern (16 bp):
GATTTAGGTATGATAT
Found at i:20331908 original size:17 final size:17
Alignment explanation
Indices: 20331881--20331922 Score: 66
Period size: 17 Copynumber: 2.5 Consensus size: 17
20331871 TTATACCATG
*
20331881 CATATCATGTAAATTTT
1 CATACCATGTAAATTTT
*
20331898 CCTACCATGTAAATTTT
1 CATACCATGTAAATTTT
20331915 CATACCAT
1 CATACCAT
20331923 TTCATTAGTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.33, C:0.21, G:0.05, T:0.40
Consensus pattern (17 bp):
CATACCATGTAAATTTT
Found at i:20332395 original size:19 final size:19
Alignment explanation
Indices: 20332351--20332401 Score: 59
Period size: 19 Copynumber: 2.6 Consensus size: 19
20332341 GTTCATGCTT
*
20332351 TCTATTCACATTTTCATAT
1 TCTATTCACATTTTCATAA
*
20332370 TCGATTCACATTTTCA-AA
1 TCTATTCACATTTTCATAA
20332388 TCATATTCCACATT
1 TC-TATT-CACATT
20332402 CACATTTCTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
18 3 0.11
19 18 0.67
20 6 0.22
ACGTcount: A:0.29, C:0.24, G:0.02, T:0.45
Consensus pattern (19 bp):
TCTATTCACATTTTCATAA
Found at i:20333126 original size:17 final size:18
Alignment explanation
Indices: 20333092--20333127 Score: 56
Period size: 18 Copynumber: 2.1 Consensus size: 18
20333082 TGAATTTCTA
20333092 TCCAATTTATACCCTAAT
1 TCCAATTTATACCCTAAT
*
20333110 TCCAATTTA-ATCCTAAT
1 TCCAATTTATACCCTAAT
20333127 T
1 T
20333128 AACTTATTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 8 0.47
18 9 0.53
ACGTcount: A:0.33, C:0.25, G:0.00, T:0.42
Consensus pattern (18 bp):
TCCAATTTATACCCTAAT
Found at i:20333589 original size:22 final size:20
Alignment explanation
Indices: 20333557--20333597 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 20
20333547 TTCTGTTTCT
20333557 TTTTAGCTTTGTTTCTTTTG
1 TTTTAGCTTTGTTTCTTTTG
20333577 TTTTATGCTTTTGTTTCTTTT
1 TTTTA-GC-TTTGTTTCTTTT
20333598 ATTTCATTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.26
21 2 0.11
22 12 0.63
ACGTcount: A:0.05, C:0.10, G:0.12, T:0.73
Consensus pattern (20 bp):
TTTTAGCTTTGTTTCTTTTG
Found at i:20335961 original size:18 final size:19
Alignment explanation
Indices: 20335930--20335965 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
20335920 TTTTTTTTAC
*
20335930 TTTTAATATTTGTTTAAAT
1 TTTTAATATATGTTTAAAT
20335949 TTTTAATA-ATGTTTAAA
1 TTTTAATATATGTTTAAA
20335966 GCTTCAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.36, C:0.00, G:0.06, T:0.58
Consensus pattern (19 bp):
TTTTAATATATGTTTAAAT
Found at i:20342453 original size:90 final size:90
Alignment explanation
Indices: 20342300--20342480 Score: 362
Period size: 90 Copynumber: 2.0 Consensus size: 90
20342290 ACGAACATGT
20342300 TGCAGACTACCTTGGGTGTGGCTTATGAGAGACCCAAAGGAAGAAATAATAAAAAAAGAGTAGAA
1 TGCAGACTACCTTGGGTGTGGCTTATGAGAGACCCAAAGGAAGAAATAATAAAAAAAGAGTAGAA
20342365 AAAGATAACCAGATGAAAGCTTTGC
66 AAAGATAACCAGATGAAAGCTTTGC
20342390 TGCAGACTACCTTGGGTGTGGCTTATGAGAGACCCAAAGGAAGAAATAATAAAAAAAGAGTAGAA
1 TGCAGACTACCTTGGGTGTGGCTTATGAGAGACCCAAAGGAAGAAATAATAAAAAAAGAGTAGAA
20342455 AAAGATAACCAGATGAAAGCTTTGC
66 AAAGATAACCAGATGAAAGCTTTGC
20342480 T
1 T
20342481 TGTCAAAAGT
Statistics
Matches: 91, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
90 91 1.00
ACGTcount: A:0.43, C:0.13, G:0.24, T:0.19
Consensus pattern (90 bp):
TGCAGACTACCTTGGGTGTGGCTTATGAGAGACCCAAAGGAAGAAATAATAAAAAAAGAGTAGAA
AAAGATAACCAGATGAAAGCTTTGC
Found at i:20345025 original size:126 final size:125
Alignment explanation
Indices: 20344801--20345090 Score: 422
Period size: 126 Copynumber: 2.3 Consensus size: 125
20344791 TAATTTAAAA
* * *
20344801 AAGCTTCTACGTGGACGCTCTTTTGCTACAGTAGTCTCTGAAAATTAAATTTGAGAAGACGTGTC
1 AAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGTCTCTAAAAAATAAATTTGAGAAGACGTGTC
*
20344866 TGCGTAAATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACT-GAAAG
66 TGCGCAAATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTAG-AAG
*
20344926 AAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGTCTCTAAAAAAATAATTTTGAGAAGACGTGT
1 AAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGTCTCT-AAAAAATAAATTTGAGAAGACGTGT
* * * *
20344991 CTGTGCAAATAGTGGT-AAAAACGCTTTAAGCAGGATGCATTTTCAGCAAAATTACTAGAAG
65 CTGCGCAAATAGT-GTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTAGAAG
* * * *
20345052 AAACTCCCACGTTGACGCTCTTTTGCTACAGTGGTCTCT
1 AAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGTCTCT
20345091 GAAATAACTT
Statistics
Matches: 149, Mismatches: 13, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
125 38 0.26
126 108 0.72
127 3 0.02
ACGTcount: A:0.31, C:0.19, G:0.21, T:0.29
Consensus pattern (125 bp):
AAGCTTCCACGTGGACGCTCTTTTGCTACAGTAGTCTCTAAAAAATAAATTTGAGAAGACGTGTC
TGCGCAAATAGTGTCAAAAACGCTTCAAGCAGGATGCATTGTCAGCAAAAGTACTAGAAG
Found at i:20348289 original size:116 final size:116
Alignment explanation
Indices: 20348113--20348609 Score: 850
Period size: 116 Copynumber: 4.3 Consensus size: 116
20348103 TTTATATTTT
* *** *
20348113 ATTACATGAAATAATATAAAAATATTTCAAAATATTGTTTTATTTAAAATAATTTTCATTTTATT
1 ATTACATGAAATAATATAAAAATA-TTCAAAATGTTGCCCTATTTAAAATAATTTCCATTTTATT
* * *
20348178 AAAAATATAAAAGTAAATTATAATTACTTTATTTAAAACAACCTTTTATATT
65 AAAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
* * *
20348230 ATCACATGAAATAATATAAAAATATTCAAAATGTTACCTTATTTAAAATAATTTCCATTTTATTA
1 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCCTATTTAAAATAATTTCCATTTTATTA
*
20348295 AAAATATAAAAGTAAATTGCAATTACTTTATTTAAAACAACCTTTTATCTA
66 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
* * *
20348346 ATTACCTGAAATAATATAAAAATATTCAAAATGTTGCCCTATTTAAAATAATTTCAATTTTATAA
1 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCCTATTTAAAATAATTTCCATTTTATTA
20348411 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
66 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
20348462 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCCTATTTAAAATAATTTCCATTTTATTA
1 ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCCTATTTAAAATAATTTCCATTTTATTA
20348527 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
66 AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
20348578 ATTACATGAAATAATATAAAAATATTCAAAAT
1 ATTACATGAAATAATATAAAAATATTCAAAAT
20348610 ATTTGTACAA
Statistics
Matches: 360, Mismatches: 20, Indels: 1
0.94 0.05 0.00
Matches are distributed among these distances:
116 337 0.94
117 23 0.06
ACGTcount: A:0.48, C:0.10, G:0.03, T:0.39
Consensus pattern (116 bp):
ATTACATGAAATAATATAAAAATATTCAAAATGTTGCCCTATTTAAAATAATTTCCATTTTATTA
AAAATATAAAAGTAAATTACAATTACTTTATTTAAAACAACCTTTTATCTA
Found at i:20349031 original size:18 final size:18
Alignment explanation
Indices: 20349004--20349041 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
20348994 GAAAAAGGAA
*
20349004 ACATATAAGGGCTACGAT
1 ACATAAAAGGGCTACGAT
*
20349022 ACATAAAAGGGCTAGGAT
1 ACATAAAAGGGCTACGAT
20349040 AC
1 AC
20349042 GTACCTGGCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.42, C:0.16, G:0.24, T:0.18
Consensus pattern (18 bp):
ACATAAAAGGGCTACGAT
Found at i:20350797 original size:15 final size:15
Alignment explanation
Indices: 20350779--20350809 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
20350769 TTTTTATTTT
*
20350779 AAAAAATAAATTTAG
1 AAAAAATAAAATTAG
20350794 AAAAAATAAAATTAG
1 AAAAAATAAAATTAG
20350809 A
1 A
20350810 GCTTTTTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (15 bp):
AAAAAATAAAATTAG
Found at i:20350848 original size:22 final size:22
Alignment explanation
Indices: 20350836--20350885 Score: 77
Period size: 20 Copynumber: 2.4 Consensus size: 22
20350826 TAATGAGAGT
20350836 TTTGAGAGGAATTTAAGAGAAA
1 TTTGAGAGGAATTTAAGAGAAA
*
20350858 TTTGAGA-G-ATTTCAGAGAAA
1 TTTGAGAGGAATTTAAGAGAAA
20350878 TTTGAGAG
1 TTTGAGAG
20350886 AATATTGAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 18 0.69
21 1 0.04
22 7 0.27
ACGTcount: A:0.40, C:0.02, G:0.28, T:0.30
Consensus pattern (22 bp):
TTTGAGAGGAATTTAAGAGAAA
Found at i:20350880 original size:31 final size:31
Alignment explanation
Indices: 20350829--20350887 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
20350819 AAACAATTAA
* * *
20350829 TGAGAGTTTTGAGAGGAATTTAAGAGAAATT
1 TGAGAGATTTCAGAGAAATTTAAGAGAAATT
*
20350860 TGAGAGATTTCAGAGAAATTTGAGAGAA
1 TGAGAGATTTCAGAGAAATTTAAGAGAA
20350888 TATTGAAAGA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.41, C:0.02, G:0.29, T:0.29
Consensus pattern (31 bp):
TGAGAGATTTCAGAGAAATTTAAGAGAAATT
Found at i:20350899 original size:31 final size:31
Alignment explanation
Indices: 20350840--20350899 Score: 77
Period size: 31 Copynumber: 1.9 Consensus size: 31
20350830 GAGAGTTTTG
* *
20350840 AGAGGAATTTAAGAGAAATTTGAGAGATTTC
1 AGAGAAATTTAAGAGAAATTTGAAAGATTTC
*
20350871 AGAGAAATTTGAGAG-AATATTGAAAGATT
1 AGAGAAATTTAAGAGAAAT-TTGAAAGATT
20350900 GAAGATTGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 3 0.12
31 22 0.88
ACGTcount: A:0.45, C:0.02, G:0.25, T:0.28
Consensus pattern (31 bp):
AGAGAAATTTAAGAGAAATTTGAAAGATTTC
Found at i:20353941 original size:11 final size:11
Alignment explanation
Indices: 20353901--20353976 Score: 61
Period size: 11 Copynumber: 6.8 Consensus size: 11
20353891 ATTCCAAAAA
*
20353901 TAATATTATTT
1 TAATATTAATT
20353912 TAATAGTTTAATAT
1 TAATA--TTAAT-T
20353926 TAATATTAATT
1 TAATATTAATT
20353937 TAATACTT-ATCT
1 TAATA-TTAAT-T
*
20353949 TAATAAT-ATT
1 TAATATTAATT
20353959 T--TATTAATT
1 TAATATTAATT
20353968 TAATATTAA
1 TAATATTAA
20353977 AATAATTATC
Statistics
Matches: 54, Mismatches: 3, Indels: 16
0.74 0.04 0.22
Matches are distributed among these distances:
8 3 0.06
9 4 0.07
10 2 0.04
11 22 0.41
12 13 0.24
13 4 0.07
14 6 0.11
ACGTcount: A:0.42, C:0.03, G:0.01, T:0.54
Consensus pattern (11 bp):
TAATATTAATT
Found at i:20354074 original size:24 final size:21
Alignment explanation
Indices: 20354032--20354075 Score: 61
Period size: 24 Copynumber: 2.0 Consensus size: 21
20354022 ATAAATAATT
20354032 TATTATTTTAATAATATTTAA
1 TATTATTTTAATAATATTTAA
20354053 TATTAATTTTAATCTAATATTTA
1 TATT-ATTTTAA--TAATATTTA
20354076 TCTTGATAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
21 4 0.20
22 7 0.35
24 9 0.45
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (21 bp):
TATTATTTTAATAATATTTAA
Found at i:20361590 original size:18 final size:16
Alignment explanation
Indices: 20361566--20361620 Score: 65
Period size: 16 Copynumber: 3.3 Consensus size: 16
20361556 CTCTTATAAC
20361566 ATATAATCCATGTAAA
1 ATATAATCCATGTAAA
*
20361582 ATTTATAATCCATGTAAC
1 A--TATAATCCATGTAAA
*
20361600 ATATAATTCATGTAAA
1 ATATAATCCATGTAAA
*
20361616 GTATA
1 ATATA
20361621 TTATTCATGT
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 18 0.55
18 15 0.45
ACGTcount: A:0.45, C:0.11, G:0.07, T:0.36
Consensus pattern (16 bp):
ATATAATCCATGTAAA
Found at i:20361606 original size:16 final size:16
Alignment explanation
Indices: 20361562--20361614 Score: 70
Period size: 16 Copynumber: 3.2 Consensus size: 16
20361552 TGTACTCTTA
20361562 TAACATATAATCCATG
1 TAACATATAATCCATG
*
20361578 TAAAATTTATAATCCATG
1 TAACA--TATAATCCATG
*
20361596 TAACATATAATTCATG
1 TAACATATAATCCATG
20361612 TAA
1 TAA
20361615 AGTATATTAT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
16 17 0.53
18 15 0.47
ACGTcount: A:0.45, C:0.13, G:0.06, T:0.36
Consensus pattern (16 bp):
TAACATATAATCCATG
Found at i:20361620 original size:16 final size:16
Alignment explanation
Indices: 20361562--20361635 Score: 69
Period size: 18 Copynumber: 4.4 Consensus size: 16
20361552 TGTACTCTTA
*
20361562 TAACATATAATCCATG
1 TAACATATAATTCATG
* *
20361578 TAAAATTTATAATCCATG
1 TAACA--TATAATTCATG
20361596 TAACATATAATTCATG
1 TAACATATAATTCATG
20361612 TAA-AGTATATTATTCATG
1 TAACA-TATA--ATTCATG
20361630 TAACAT
1 TAACAT
20361636 GTACTTCATA
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
15 1 0.02
16 21 0.43
18 26 0.53
19 1 0.02
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (16 bp):
TAACATATAATTCATG
Found at i:20361644 original size:34 final size:34
Alignment explanation
Indices: 20361562--20361644 Score: 103
Period size: 34 Copynumber: 2.4 Consensus size: 34
20361552 TGTACTCTTA
* *
20361562 TAACATATAATCCATGTAAAATTTATAATCCATG
1 TAACATATAATTCATGTAAAATATATAATCCATG
* * *
20361596 TAACATATAATTCATGTAAAGTATATTATTCATG
1 TAACATATAATTCATGTAAAATATATAATCCATG
* *
20361630 TAACATGTACTTCAT
1 TAACATATAATTCAT
20361645 ATTTCATATC
Statistics
Matches: 42, Mismatches: 7, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
34 42 1.00
ACGTcount: A:0.41, C:0.13, G:0.07, T:0.39
Consensus pattern (34 bp):
TAACATATAATTCATGTAAAATATATAATCCATG
Found at i:20362805 original size:23 final size:21
Alignment explanation
Indices: 20362753--20362848 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
20362743 CCTGATCAGT
** * *
20362753 ATACGACACATAAAGTGCCTA
1 ATACGACACACGAGGTGCCTG
*
20362774 AAACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
20362795 ATACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
20362816 ATACGACACACGAGGTGCCTG
1 ATACGACACACGAGGTGCCTG
20362837 AAATACGACACA
1 --ATACGACACA
20362849 TAAAGTGCCT
Statistics
Matches: 67, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
21 57 0.85
23 10 0.15
ACGTcount: A:0.36, C:0.27, G:0.23, T:0.14
Consensus pattern (21 bp):
ATACGACACACGAGGTGCCTG
Found at i:20362813 original size:42 final size:43
Alignment explanation
Indices: 20362753--20362858 Score: 142
Period size: 42 Copynumber: 2.5 Consensus size: 43
20362743 CCTGATCAGT
*
20362753 ATACGACACATAAAGTGCCTAAAACGACACACGAGGTGCCTG-
1 ATACGACACACAAAGTGCCTAAAACGACACACGAGGTGCCTGA
* * * *
20362795 ATACGACACACGAGGTGCCTGATACGACACACGAGGTGCCTGAA
1 ATACGACACACAAAGTGCCTAAAACGACACACGAGGTGCCTG-A
*
20362839 ATACGACACATAAAGTGCCT
1 ATACGACACACAAAGTGCCT
20362859 GATCGATAAA
Statistics
Matches: 54, Mismatches: 8, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
42 37 0.69
44 17 0.31
ACGTcount: A:0.36, C:0.26, G:0.23, T:0.15
Consensus pattern (43 bp):
ATACGACACACAAAGTGCCTAAAACGACACACGAGGTGCCTGA
Found at i:20375868 original size:23 final size:22
Alignment explanation
Indices: 20375815--20375871 Score: 78
Period size: 22 Copynumber: 2.5 Consensus size: 22
20375805 CTTGAGCCGA
*
20375815 TAAACAGTAAGCTCAATTGAGC
1 TAAACGGTAAGCTCAATTGAGC
**
20375837 TAAACGGTAAGCTCCGTTGAGC
1 TAAACGGTAAGCTCAATTGAGC
20375859 TGAAACGGTAAGC
1 T-AAACGGTAAGC
20375872 CCCTAAGGAC
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
22 20 0.65
23 11 0.35
ACGTcount: A:0.35, C:0.19, G:0.25, T:0.21
Consensus pattern (22 bp):
TAAACGGTAAGCTCAATTGAGC
Found at i:20375927 original size:22 final size:23
Alignment explanation
Indices: 20375884--20375944 Score: 63
Period size: 22 Copynumber: 2.7 Consensus size: 23
20375874 CTAAGGACTG
*
20375884 AAACAGTAAGCTC-TAAAAAGCT-
1 AAACGGTAAGCTCAT-AAAAGCTA
* * *
20375906 GAATGGTAAGCTCATAAGAGCTA
1 AAACGGTAAGCTCATAAAAGCTA
20375929 AAACGGTAAGCTCATA
1 AAACGGTAAGCTCATA
20375945 CGAACTGTGG
Statistics
Matches: 31, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
22 16 0.52
23 15 0.48
ACGTcount: A:0.44, C:0.16, G:0.20, T:0.20
Consensus pattern (23 bp):
AAACGGTAAGCTCATAAAAGCTA
Found at i:20375940 original size:23 final size:22
Alignment explanation
Indices: 20375815--20375944 Score: 79
Period size: 23 Copynumber: 5.8 Consensus size: 22
20375805 CTTGAGCCGA
* *
20375815 TAAACAGTAAGCTCA-ATTGAGC
1 TAAACGGTAAGCTCATA-AGAGC
* *
20375837 TAAACGGTAAGCTCCGT-TGAGC
1 TAAACGGTAAGCT-CATAAGAGC
* *
20375859 TGAAACGGTAAGCCCCTAAG-GAC
1 T-AAACGGTAAGCTCATAAGAG-C
* *
20375882 TGAAACAGTAAGCTC-TAAAAAGC
1 T-AAACGGTAAGCTCAT-AAGAGC
* *
20375905 TGAATGGTAAGCTCATAAGAGC
1 TAAACGGTAAGCTCATAAGAGC
20375927 TAAAACGGTAAGCTCATA
1 T-AAACGGTAAGCTCATA
20375945 CGAACTGTGG
Statistics
Matches: 85, Mismatches: 14, Indels: 17
0.73 0.12 0.15
Matches are distributed among these distances:
22 38 0.45
23 46 0.54
24 1 0.01
ACGTcount: A:0.38, C:0.19, G:0.22, T:0.20
Consensus pattern (22 bp):
TAAACGGTAAGCTCATAAGAGC
Found at i:20386351 original size:2 final size:2
Alignment explanation
Indices: 20386344--20386368 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
20386334 ATATAGAAGT
20386344 TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA T
20386369 TAGATGTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20388914 original size:19 final size:18
Alignment explanation
Indices: 20388885--20388920 Score: 63
Period size: 19 Copynumber: 1.9 Consensus size: 18
20388875 AGTCAAAATA
20388885 CAAAAATGGTATTGATAT
1 CAAAAATGGTATTGATAT
20388903 CAAAAGATGGTATTGATA
1 CAAAA-ATGGTATTGATA
20388921 AAAATACAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 5 0.29
19 12 0.71
ACGTcount: A:0.44, C:0.06, G:0.19, T:0.31
Consensus pattern (18 bp):
CAAAAATGGTATTGATAT
Found at i:20388924 original size:17 final size:17
Alignment explanation
Indices: 20388882--20388924 Score: 61
Period size: 19 Copynumber: 2.5 Consensus size: 17
20388872 TCAAGTCAAA
20388882 ATACAAAAATGGTATTG
1 ATACAAAAATGGTATTG
20388899 ATATCAAAAGATGGTATTG
1 ATA-CAAAA-ATGGTATTG
20388918 ATA-AAAA
1 ATACAAAA
20388925 TACAATAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.29
18 5 0.21
19 12 0.50
ACGTcount: A:0.51, C:0.05, G:0.16, T:0.28
Consensus pattern (17 bp):
ATACAAAAATGGTATTG
Found at i:20391088 original size:12 final size:11
Alignment explanation
Indices: 20391055--20391093 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
20391045 AAACATAATT
20391055 TTCAACAAATAA
1 TTCAACAAA-AA
**
20391067 TTTGACAAAAA
1 TTCAACAAAAA
20391078 TTCAACAAAAA
1 TTCAACAAAAA
20391089 TTCAA
1 TTCAA
20391094 AATGAGAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
11 16 0.70
12 7 0.30
ACGTcount: A:0.56, C:0.15, G:0.03, T:0.26
Consensus pattern (11 bp):
TTCAACAAAAA
Found at i:20392749 original size:64 final size:64
Alignment explanation
Indices: 20392618--20392749 Score: 147
Period size: 64 Copynumber: 2.1 Consensus size: 64
20392608 GAGCATCCCA
* * * * * * ** * *
20392618 ATCGGTATTGATCCTGCATGTGTTGCGGACATACCGCAGCCCTTTGTGAGCGTCTTGTTATATG
1 ATCGGTATTGATCCTGCATGTATTACGGACAAACCGCAGCCCTTTATAAGCATCCCGATATAGG
* * *
20392682 ATCGGTATTGATCCTGCATGTATTACGGATAAACTGCAGCTCTTTATAAGCATCCCGATATAGG
1 ATCGGTATTGATCCTGCATGTATTACGGACAAACCGCAGCCCTTTATAAGCATCCCGATATAGG
20392746 ATCG
1 ATCG
20392750 CTTGAACTTC
Statistics
Matches: 55, Mismatches: 13, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
64 55 1.00
ACGTcount: A:0.23, C:0.21, G:0.23, T:0.33
Consensus pattern (64 bp):
ATCGGTATTGATCCTGCATGTATTACGGACAAACCGCAGCCCTTTATAAGCATCCCGATATAGG
Found at i:20399337 original size:11 final size:11
Alignment explanation
Indices: 20399321--20399361 Score: 55
Period size: 11 Copynumber: 3.6 Consensus size: 11
20399311 GTGAAATAAA
20399321 AAAAATAAATT
1 AAAAATAAATT
20399332 AAAAATAAATT
1 AAAAATAAATT
*
20399343 AAAAAATCAATT
1 -AAAAATAAATT
*
20399355 TAAAATA
1 AAAAATA
20399362 TTAATAAACT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 16 0.62
12 10 0.38
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (11 bp):
AAAAATAAATT
Found at i:20399346 original size:24 final size:23
Alignment explanation
Indices: 20399314--20399361 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
20399304 AAATTACGTG
20399314 AAATAAAAAAAATAAATTAAAAAT
1 AAAT-AAAAAAATAAATTAAAAAT
* * *
20399338 AAATTAAAAAATCAATTTAAAAT
1 AAATAAAAAAATAAATTAAAAAT
20399361 A
1 A
20399362 TTAATAAACT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 17 0.81
24 4 0.19
ACGTcount: A:0.73, C:0.02, G:0.00, T:0.25
Consensus pattern (23 bp):
AAATAAAAAAATAAATTAAAAAT
Found at i:20400460 original size:5 final size:5
Alignment explanation
Indices: 20400450--20400500 Score: 59
Period size: 5 Copynumber: 10.0 Consensus size: 5
20400440 TTTGTTTTAG
* *
20400450 ATTTT ATTTT ATTTT ATTTTT ATTTG ATTTT -TTATT TTTTT ATTTT ATTTT
1 ATTTT ATTTT ATTTT A-TTTT ATTTT ATTTT ATT-TT ATTTT ATTTT ATTTT
20400501 TGGAAGTTAC
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
4 2 0.05
5 31 0.77
6 7 0.17
ACGTcount: A:0.18, C:0.00, G:0.02, T:0.80
Consensus pattern (5 bp):
ATTTT
Found at i:20401176 original size:21 final size:20
Alignment explanation
Indices: 20401148--20401202 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 20
20401138 GGTTACACAA
20401148 CCTA-TTCACACGGCCGTGTC
1 CCTACTTCACACGG-CGTGTC
20401168 CCTACTTCACACAGGCGTGTC
1 CCTACTTCACAC-GGCGTGTC
20401189 CCT-CTGTCACACGG
1 CCTACT-TCACACGG
20401203 TCATGTGCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
20 8 0.25
21 22 0.69
22 2 0.06
ACGTcount: A:0.16, C:0.40, G:0.20, T:0.24
Consensus pattern (20 bp):
CCTACTTCACACGGCGTGTC
Found at i:20403376 original size:22 final size:21
Alignment explanation
Indices: 20403330--20403373 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
20403320 TTTAAAACCC
20403330 AATGAGTATCAATACTTTTTA
1 AATGAGTATCAATACTTTTTA
*
20403351 AATGAGTATCAATATTTTTTA
1 AATGAGTATCAATACTTTTTA
20403372 AA
1 AA
20403374 ATGTATCGAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.41, C:0.07, G:0.09, T:0.43
Consensus pattern (21 bp):
AATGAGTATCAATACTTTTTA
Found at i:20404976 original size:22 final size:22
Alignment explanation
Indices: 20404950--20404996 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 22
20404940 GGTTTTCTTG
20404950 TTTAT-TTCTGTTT-TTGTTTTAT
1 TTTATCTTCT-TTTATT-TTTTAT
20404972 TTTATCTTCTTTTATTTTTTAT
1 TTTATCTTCTTTTATTTTTTAT
20404994 TTT
1 TTT
20404997 TTTTAACTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 17 0.74
23 6 0.26
ACGTcount: A:0.11, C:0.06, G:0.04, T:0.79
Consensus pattern (22 bp):
TTTATCTTCTTTTATTTTTTAT
Found at i:20404991 original size:27 final size:27
Alignment explanation
Indices: 20404960--20405012 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
20404950 TTTATTTCTG
* *
20404960 TTTTTGTTTTATTTTATCTT-CTTTTAT
1 TTTTTATTTT-TTTTAACTTACTTTTAT
20404987 TTTTTATTTTTTTTAACTTACTTTTA
1 TTTTTATTTTTTTTAACTTACTTTTA
20405013 AACATAAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 8 0.35
27 15 0.65
ACGTcount: A:0.15, C:0.08, G:0.02, T:0.75
Consensus pattern (27 bp):
TTTTTATTTTTTTTAACTTACTTTTAT
Found at i:20406623 original size:5 final size:5
Alignment explanation
Indices: 20406613--20406639 Score: 54
Period size: 5 Copynumber: 5.4 Consensus size: 5
20406603 CTCTCCAAAT
20406613 TTATA TTATA TTATA TTATA TTATA TT
1 TTATA TTATA TTATA TTATA TTATA TT
20406640 TAATATTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 22 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (5 bp):
TTATA
Found at i:20407319 original size:16 final size:17
Alignment explanation
Indices: 20407284--20407318 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
20407274 CGCATAATAT
*
20407284 AATAAGCATTTTTAAAA
1 AATAAACATTTTTAAAA
20407301 AATAAACATTTTTAAAA
1 AATAAACATTTTTAAAA
20407318 A
1 A
20407319 TTTAATTTTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.57, C:0.06, G:0.03, T:0.34
Consensus pattern (17 bp):
AATAAACATTTTTAAAA
Found at i:20436658 original size:17 final size:18
Alignment explanation
Indices: 20436636--20436675 Score: 66
Period size: 17 Copynumber: 2.3 Consensus size: 18
20436626 CAAAACGTGT
20436636 TTTTTAATAATTTTAT-A
1 TTTTTAATAATTTTATAA
20436653 TTTTT-ATAATTTTATAA
1 TTTTTAATAATTTTATAA
20436670 TTTTTA
1 TTTTTA
20436676 TTTCTTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.68
Consensus pattern (18 bp):
TTTTTAATAATTTTATAA
Found at i:20436659 original size:8 final size:8
Alignment explanation
Indices: 20436636--20436708 Score: 69
Period size: 8 Copynumber: 9.0 Consensus size: 8
20436626 CAAAACGTGT
20436636 TTTTTAATA
1 TTTTT-ATA
*
20436645 ATTTTATA
1 TTTTTATA
20436653 TTTTTATA
1 TTTTTATA
*
20436661 ATTTTATAA
1 TTTTTAT-A
20436670 TTTTTAT-
1 TTTTTATA
20436677 TTCTTTATA
1 TT-TTTATA
* *
20436686 TTTATATT
1 TTTTTATA
20436694 TTTTTAT-
1 TTTTTATA
20436701 TTTTTATA
1 TTTTTATA
20436709 AATGTATATA
Statistics
Matches: 53, Mismatches: 7, Indels: 9
0.77 0.10 0.13
Matches are distributed among these distances:
7 9 0.17
8 31 0.58
9 13 0.25
ACGTcount: A:0.27, C:0.01, G:0.00, T:0.71
Consensus pattern (8 bp):
TTTTTATA
Found at i:20436699 original size:33 final size:31
Alignment explanation
Indices: 20436647--20436707 Score: 77
Period size: 33 Copynumber: 1.9 Consensus size: 31
20436637 TTTTAATAAT
*
20436647 TTTATATTTTTATAATTTTATAATTTTTATTTC
1 TTTATATTTATATAATTTTAT--TTTTTATTTC
**
20436680 TTTATATTTATATTTTTTTATTTTTTAT
1 TTTATATTTATATAATTTTATTTTTTAT
20436708 AAATGTATAT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
31 7 0.28
33 18 0.72
ACGTcount: A:0.25, C:0.02, G:0.00, T:0.74
Consensus pattern (31 bp):
TTTATATTTATATAATTTTATTTTTTATTTC
Found at i:20436781 original size:58 final size:59
Alignment explanation
Indices: 20436700--20436820 Score: 228
Period size: 58 Copynumber: 2.1 Consensus size: 59
20436690 TATTTTTTTA
20436700 TTTT-TTATAAATGTATATATTATATTTTTCTTTCAAAATATTATA-TTTTTTATATAT
1 TTTTATTATAAATGTATATATTATATTTTTCTTTCAAAATATTATATTTTTTTATATAT
20436757 TTTTATTATAAATGTATATATTATATTTTTCTTTCAAAATATTATATTTTTTTATATAT
1 TTTTATTATAAATGTATATATTATATTTTTCTTTCAAAATATTATATTTTTTTATATAT
20436816 TTTTA
1 TTTTA
20436821 ATTCTACTTA
Statistics
Matches: 62, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
57 4 0.06
58 41 0.66
59 17 0.27
ACGTcount: A:0.33, C:0.03, G:0.02, T:0.62
Consensus pattern (59 bp):
TTTTATTATAAATGTATATATTATATTTTTCTTTCAAAATATTATATTTTTTTATATAT
Found at i:20436813 original size:10 final size:10
Alignment explanation
Indices: 20436798--20436879 Score: 57
Period size: 10 Copynumber: 8.3 Consensus size: 10
20436788 TTTCAAAATA
*
20436798 TTATATTTTT
1 TTATATATTT
20436808 TTATATATTT
1 TTATATATTT
* *
20436818 TTAATTCTACTTAC
1 TT-A-TATA-TT-T
20436832 TT-TATATTT
1 TTATATATTT
*
20436841 TTATA-A-AT
1 TTATATATTT
20436849 TTATAT-TTT
1 TTATATATTT
20436858 TTATAT-TTT
1 TTATATATTT
20436867 TTATATATTT
1 TTATATATTT
20436877 TTA
1 TTA
20436880 ATTCTACTTA
Statistics
Matches: 57, Mismatches: 7, Indels: 16
0.71 0.09 0.20
Matches are distributed among these distances:
8 6 0.11
9 19 0.33
10 21 0.37
11 4 0.07
12 3 0.05
13 2 0.04
14 2 0.04
ACGTcount: A:0.28, C:0.04, G:0.00, T:0.68
Consensus pattern (10 bp):
TTATATATTT
Found at i:20436862 original size:9 final size:9
Alignment explanation
Indices: 20436848--20436879 Score: 55
Period size: 9 Copynumber: 3.4 Consensus size: 9
20436838 TTTTTATAAA
20436848 TTTATATTT
1 TTTATATTT
20436857 TTTATATTT
1 TTTATATTT
20436866 TTTATATATT
1 TTTATAT-TT
20436876 TTTA
1 TTTA
20436880 ATTCTACTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 16 0.73
10 6 0.27
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (9 bp):
TTTATATTT
Found at i:20436867 original size:59 final size:59
Alignment explanation
Indices: 20436798--20436926 Score: 213
Period size: 59 Copynumber: 2.2 Consensus size: 59
20436788 TTTCAAAATA
* **
20436798 TTATATTTTTTTATATATTTTTAATTCTACTTACTTTATATTTTTATAAATTTATATTTT
1 TTATA-TTTTTTATATATTTTTAATTCTACTTACTTTATATTTGTATAAATGCATATTTT
20436858 TTATATTTTTTATATATTTTTAATTCTACTTACTTTATATTTGTATAAATGCATATTTT
1 TTATATTTTTTATATATTTTTAATTCTACTTACTTTATATTTGTATAAATGCATATTTT
*
20436917 ATATATTTTT
1 TTATATTTTT
20436927 CAAAATAATA
Statistics
Matches: 65, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
59 60 0.92
60 5 0.08
ACGTcount: A:0.29, C:0.05, G:0.02, T:0.64
Consensus pattern (59 bp):
TTATATTTTTTATATATTTTTAATTCTACTTACTTTATATTTGTATAAATGCATATTTT
Found at i:20439506 original size:137 final size:137
Alignment explanation
Indices: 20439258--20439544 Score: 520
Period size: 137 Copynumber: 2.1 Consensus size: 137
20439248 CATTGGGCCT
** *
20439258 AAGCCCATTCAGGTAATAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTGGGCCTT
1 AAGCCCATTTGGGTAATAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTAGGCCTT
20439323 AGACCCTTATTCAGATAACAGTATGGCCCATAGGCCCATCTCAAAATACATGCAACATCAGTAAA
66 AGACCCTTATTCAGATAACAGTATGGCCCATAGGCCCATCTCAAAATACATGCAACATCAGTAAA
20439388 CATATGC
131 CATATGC
20439395 AAGCCCATTTGGGTAATAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTAGGCCTT
1 AAGCCCATTTGGGTAATAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTAGGCCTT
* * *
20439460 AGCCCCTTATTCAGATAACAGTATGGCCCATAGGCCCATTTTAAAATACATGCAACATCAGTAAA
66 AGACCCTTATTCAGATAACAGTATGGCCCATAGGCCCATCTCAAAATACATGCAACATCAGTAAA
20439525 CATATGC
131 CATATGC
20439532 AAGCCCATTTGGG
1 AAGCCCATTTGGG
20439545 GAGACTACTC
Statistics
Matches: 144, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
137 144 1.00
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.25
Consensus pattern (137 bp):
AAGCCCATTTGGGTAATAGTGGTACTGGGCCAGAGCCCTTTTCAGATTACAATAAACTAGGCCTT
AGACCCTTATTCAGATAACAGTATGGCCCATAGGCCCATCTCAAAATACATGCAACATCAGTAAA
CATATGC
Found at i:20441357 original size:26 final size:26
Alignment explanation
Indices: 20441326--20441433 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
20441316 TGAAATGCCC
*
20441326 ATCATGGAACATTTACCTAAACCATT
1 ATCATGGAACATTTACCTAACCCATT
20441352 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
* *
20441378 ATCATGGAATATTTACCTAATCCATT
1 ATCATGGAACATTTACCTAACCCATT
20441404 ATCATGGAACATTTACCTAACCCATT
1 ATCATGGAACATTTACCTAACCCATT
20441430 ATCA
1 ATCA
20441434 ATTTGTACCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.36, C:0.24, G:0.07, T:0.32
Consensus pattern (26 bp):
ATCATGGAACATTTACCTAACCCATT
Found at i:20443650 original size:30 final size:30
Alignment explanation
Indices: 20443614--20443677 Score: 92
Period size: 30 Copynumber: 2.1 Consensus size: 30
20443604 TCAATTAGAC
**
20443614 TAAGGACATGTGTAGGTTTGTCTACTAATA
1 TAAGGACATGTGTAGGTTCATCTACTAATA
* *
20443644 TAAGGACATGTTTAGGTTCATTTACTAATA
1 TAAGGACATGTGTAGGTTCATCTACTAATA
20443674 TAAG
1 TAAG
20443678 TTGTCTCTTT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.33, C:0.09, G:0.20, T:0.38
Consensus pattern (30 bp):
TAAGGACATGTGTAGGTTCATCTACTAATA
Found at i:20446804 original size:38 final size:38
Alignment explanation
Indices: 20446753--20446831 Score: 158
Period size: 38 Copynumber: 2.1 Consensus size: 38
20446743 GAATTAAGGC
20446753 TTAGTGCCTAACCCTTCTTAGTCCCTTGTTTTTTCACT
1 TTAGTGCCTAACCCTTCTTAGTCCCTTGTTTTTTCACT
20446791 TTAGTGCCTAACCCTTCTTAGTCCCTTGTTTTTTCACT
1 TTAGTGCCTAACCCTTCTTAGTCCCTTGTTTTTTCACT
20446829 TTA
1 TTA
20446832 AGTATTCAGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 41 1.00
ACGTcount: A:0.14, C:0.28, G:0.10, T:0.48
Consensus pattern (38 bp):
TTAGTGCCTAACCCTTCTTAGTCCCTTGTTTTTTCACT
Found at i:20452148 original size:30 final size:29
Alignment explanation
Indices: 20452114--20452184 Score: 83
Period size: 28 Copynumber: 2.4 Consensus size: 29
20452104 TAAAATCTAT
* *
20452114 TAATTTTTTATTTATGAAATCTATTTGTAA
1 TAATTTTTTATTTAT-AAAACTATTTATAA
*
20452144 TAATTTTTT-TTTATAAAACTCTTTATAA
1 TAATTTTTTATTTATAAAACTATTTATAA
20452172 -AATTTGTTTATTT
1 TAATTT-TTTATTT
20452185 TTTTTTAGAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
27 5 0.14
28 14 0.39
29 8 0.22
30 9 0.25
ACGTcount: A:0.32, C:0.04, G:0.04, T:0.59
Consensus pattern (29 bp):
TAATTTTTTATTTATAAAACTATTTATAA
Found at i:20457811 original size:17 final size:17
Alignment explanation
Indices: 20457789--20457822 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
20457779 GCTACAAAAT
*
20457789 CAAATCTTCTAATATTA
1 CAAATCTTCTAAGATTA
20457806 CAAATCTTCTAAGATTA
1 CAAATCTTCTAAGATTA
20457823 GTTTTCATAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.41, C:0.18, G:0.03, T:0.38
Consensus pattern (17 bp):
CAAATCTTCTAAGATTA
Found at i:20458623 original size:21 final size:21
Alignment explanation
Indices: 20458581--20458623 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
20458571 ACAAACACAA
* **
20458581 CTCTGCCTCTGTCACCTGCGC
1 CTCTGCCTCTGCCACCAACGC
*
20458602 CTCTTCCTCTGCCACCAACGC
1 CTCTGCCTCTGCCACCAACGC
20458623 C
1 C
20458624 ACGCCTGTTT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.09, C:0.51, G:0.14, T:0.26
Consensus pattern (21 bp):
CTCTGCCTCTGCCACCAACGC
Found at i:20460937 original size:4 final size:4
Alignment explanation
Indices: 20460928--20460961 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
20460918 TATGACGTAG
20460928 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AG
1 AGAA AGAA AGAA AGAA AGAA AGAA AGAA AGAA AG
20460962 GTTGCTTCGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (4 bp):
AGAA
Found at i:20461841 original size:43 final size:43
Alignment explanation
Indices: 20461726--20461844 Score: 166
Period size: 43 Copynumber: 2.8 Consensus size: 43
20461716 TTATCTGAAA
* *
20461726 AAACGCCGCTAAAGAACATGAGCTTTAGCCGCACTTTAACCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTAACCAC
* ** *
20461769 AAACGCCGCTAAAGTACATGACCTTTAGCGGTGCTTTCACCAC
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTAACCAC
* *
20461812 AAACGCTGTTAAAGAACATGACCTTTAGCGGCA
1 AAACGCCGCTAAAGAACATGACCTTTAGCGGCA
20461845 AACGCCGCTA
Statistics
Matches: 65, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
43 65 1.00
ACGTcount: A:0.33, C:0.28, G:0.18, T:0.21
Consensus pattern (43 bp):
AAACGCCGCTAAAGAACATGACCTTTAGCGGCACTTTAACCAC
Found at i:20461857 original size:32 final size:32
Alignment explanation
Indices: 20461811--20461871 Score: 95
Period size: 32 Copynumber: 1.9 Consensus size: 32
20461801 GCTTTCACCA
* * *
20461811 CAAACGCTGTTAAAGAACATGACCTTTAGCGG
1 CAAACGCCGCTAAAGAACATCACCTTTAGCGG
20461843 CAAACGCCGCTAAAGAACATCACCTTTAG
1 CAAACGCCGCTAAAGAACATCACCTTTAG
20461872 TGGCGTTTTC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 26 1.00
ACGTcount: A:0.36, C:0.26, G:0.18, T:0.20
Consensus pattern (32 bp):
CAAACGCCGCTAAAGAACATCACCTTTAGCGG
Found at i:20462648 original size:13 final size:14
Alignment explanation
Indices: 20462622--20462650 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
20462612 ACTAATGACA
20462622 AATTAAACCATTAT
1 AATTAAACCATTAT
20462636 AATTAAA-CATTAT
1 AATTAAACCATTAT
20462649 AA
1 AA
20462651 ATATTTAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.53
14 7 0.47
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.34
Consensus pattern (14 bp):
AATTAAACCATTAT
Found at i:20463796 original size:31 final size:31
Alignment explanation
Indices: 20463758--20463820 Score: 126
Period size: 31 Copynumber: 2.0 Consensus size: 31
20463748 TGAACAATAC
20463758 TTAGATTTCGTAATCTTCTTCTAGGCATTTT
1 TTAGATTTCGTAATCTTCTTCTAGGCATTTT
20463789 TTAGATTTCGTAATCTTCTTCTAGGCATTTT
1 TTAGATTTCGTAATCTTCTTCTAGGCATTTT
20463820 T
1 T
20463821 CCTACAATAC
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 32 1.00
ACGTcount: A:0.19, C:0.16, G:0.13, T:0.52
Consensus pattern (31 bp):
TTAGATTTCGTAATCTTCTTCTAGGCATTTT
Found at i:20467743 original size:5 final size:5
Alignment explanation
Indices: 20467733--20467765 Score: 66
Period size: 5 Copynumber: 6.6 Consensus size: 5
20467723 TTATGTAAAT
20467733 TATGA TATGA TATGA TATGA TATGA TATGA TAT
1 TATGA TATGA TATGA TATGA TATGA TATGA TAT
20467766 CTATTTATGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 28 1.00
ACGTcount: A:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (5 bp):
TATGA
Found at i:20467791 original size:9 final size:9
Alignment explanation
Indices: 20467777--20467896 Score: 113
Period size: 9 Copynumber: 13.6 Consensus size: 9
20467767 TATTTATGTA
20467777 TTATGTAAG
1 TTATGTAAG
*
20467786 TTATGTGAG
1 TTATGTAAG
*
20467795 TTATGTAAC
1 TTATGTAAG
20467804 TTATGTAAG
1 TTATGTAAG
20467813 TTATGTAAG
1 TTATGTAAG
* *
20467822 TAATGTGAG
1 TTATGTAAG
20467831 TTATGTAAG
1 TTATGTAAG
20467840 TTATGGT--G
1 TTAT-GTAAG
* * *
20467848 TGATATATAT
1 TTATGTA-AG
*
20467858 TTATAT-A-
1 TTATGTAAG
20467865 TTATGTAAG
1 TTATGTAAG
*
20467874 TTATGTAAA
1 TTATGTAAG
20467883 TTATGTAAG
1 TTATGTAAG
20467892 TTATG
1 TTATG
20467897 AAATTTAAAC
Statistics
Matches: 90, Mismatches: 15, Indels: 12
0.77 0.13 0.10
Matches are distributed among these distances:
7 6 0.07
8 6 0.07
9 71 0.79
10 7 0.08
ACGTcount: A:0.33, C:0.01, G:0.21, T:0.46
Consensus pattern (9 bp):
TTATGTAAG
Found at i:20468001 original size:20 final size:20
Alignment explanation
Indices: 20467977--20468015 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
20467967 TCTATTTTGG
20467977 TTATA-ATATGTTT-TGAAT
1 TTATATATATGTTTATGAAT
*
20467995 TTATATATATTTTTATGAAT
1 TTATATATATGTTTATGAAT
20468015 T
1 T
20468016 AAATTTATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 5 0.28
19 7 0.39
20 6 0.33
ACGTcount: A:0.33, C:0.00, G:0.08, T:0.59
Consensus pattern (20 bp):
TTATATATATGTTTATGAAT
Found at i:20469392 original size:19 final size:19
Alignment explanation
Indices: 20469368--20469405 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
20469358 ATATTAGTAT
20469368 TAATTATACCAAATATATC
1 TAATTATACCAAATATATC
20469387 TAATTATACCAAATATATC
1 TAATTATACCAAATATATC
20469406 ATATAAATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.47, C:0.16, G:0.00, T:0.37
Consensus pattern (19 bp):
TAATTATACCAAATATATC
Found at i:20470098 original size:38 final size:39
Alignment explanation
Indices: 20470056--20470168 Score: 113
Period size: 38 Copynumber: 2.9 Consensus size: 39
20470046 TTAGATAGTT
*
20470056 CGAAGCAAAGTTGACACCCAGTGTCTCATCGGCT-TAGC
1 CGAAGTAAAGTTGACACCCAGTGTCTCATCGGCTCTAGC
** ** ** *
20470094 CGAAGTAAAG-TGGTACCCAGTACCTCATCGAATCTATC
1 CGAAGTAAAGTTGACACCCAGTGTCTCATCGGCTCTAGC
*
20470132 CGAAGTAATAGTATGACGCCCAGTGTCTCATCGGCTC
1 CGAAGTAA-AGT-TGACACCCAGTGTCTCATCGGCTC
20470169 GAGGTCGAAG
Statistics
Matches: 56, Mismatches: 15, Indels: 5
0.74 0.20 0.07
Matches are distributed among these distances:
37 17 0.30
38 20 0.36
39 2 0.04
41 17 0.30
ACGTcount: A:0.27, C:0.27, G:0.22, T:0.23
Consensus pattern (39 bp):
CGAAGTAAAGTTGACACCCAGTGTCTCATCGGCTCTAGC
Found at i:20470638 original size:19 final size:19
Alignment explanation
Indices: 20470612--20470675 Score: 67
Period size: 19 Copynumber: 3.4 Consensus size: 19
20470602 TTAATACTTA
20470612 ATAATAAATAACTTGAATT
1 ATAATAAATAACTTGAATT
* * ** *
20470631 ATAGTAAAAAAAAT-ACTT
1 ATAATAAATAACTTGAATT
20470649 AATAATAAATAACTTGAATT
1 -ATAATAAATAACTTGAATT
20470669 ATAATAA
1 ATAATAA
20470676 TACAAACCCG
Statistics
Matches: 33, Mismatches: 10, Indels: 4
0.70 0.21 0.09
Matches are distributed among these distances:
18 3 0.09
19 27 0.82
20 3 0.09
ACGTcount: A:0.58, C:0.05, G:0.05, T:0.33
Consensus pattern (19 bp):
ATAATAAATAACTTGAATT
Found at i:20471255 original size:12 final size:12
Alignment explanation
Indices: 20471240--20471270 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
20471230 TCTCTTTTAT
20471240 TTTTTCTTTCCC
1 TTTTTCTTTCCC
*
20471252 TTTTTCTTTCTC
1 TTTTTCTTTCCC
20471264 TTTTTCT
1 TTTTTCT
20471271 CCCCTACTTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.00, C:0.26, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTTTCTTTCCC
Found at i:20473183 original size:26 final size:26
Alignment explanation
Indices: 20473147--20473230 Score: 159
Period size: 26 Copynumber: 3.2 Consensus size: 26
20473137 TGATACAAAT
20473147 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
20473173 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
*
20473199 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTCCA
20473225 TGATAA
1 TGATAA
20473231 GAATTTCATG
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
26 57 1.00
ACGTcount: A:0.35, C:0.07, G:0.24, T:0.35
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTCCA
Found at i:20475966 original size:23 final size:23
Alignment explanation
Indices: 20475940--20475985 Score: 92
Period size: 23 Copynumber: 2.0 Consensus size: 23
20475930 TCCTATCATT
20475940 GGATTACATTGTCTTTAAGGCTA
1 GGATTACATTGTCTTTAAGGCTA
20475963 GGATTACATTGTCTTTAAGGCTA
1 GGATTACATTGTCTTTAAGGCTA
20475986 CCTACAATAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.26, C:0.13, G:0.22, T:0.39
Consensus pattern (23 bp):
GGATTACATTGTCTTTAAGGCTA
Found at i:20477651 original size:19 final size:18
Alignment explanation
Indices: 20477623--20477661 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 18
20477613 ACTATTAATT
*
20477623 TTTAAAAATTCAACAAAA
1 TTTAAAAATTCAAAAAAA
20477641 TTTATAAAATTCAAAAAAA
1 TTTA-AAAATTCAAAAAAA
20477660 TT
1 TT
20477662 GATCAAATTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.59, C:0.08, G:0.00, T:0.33
Consensus pattern (18 bp):
TTTAAAAATTCAAAAAAA
Found at i:20477669 original size:19 final size:19
Alignment explanation
Indices: 20477627--20477670 Score: 61
Period size: 19 Copynumber: 2.3 Consensus size: 19
20477617 TTAATTTTTA
* *
20477627 AAAATTCAACAAAATTTAT
1 AAAATTCAAAAAAATTGAT
20477646 AAAATTCAAAAAAATTGAT
1 AAAATTCAAAAAAATTGAT
*
20477665 CAAATT
1 AAAATT
20477671 GAAGTACACA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.59, C:0.09, G:0.02, T:0.30
Consensus pattern (19 bp):
AAAATTCAAAAAAATTGAT
Found at i:20478383 original size:41 final size:40
Alignment explanation
Indices: 20478319--20478425 Score: 153
Period size: 41 Copynumber: 2.6 Consensus size: 40
20478309 TTTTTTGTAG
*
20478319 CGTTTTTCAAAAAGCGCCGCTAATGCTCAATCTATAG-GTA
1 CGTTTTTCAAAAAGCACCGCTAATGCTCAATCTATAGCG-A
* * *
20478359 CGTTTTTTCAAAAAGCACCACTAATGCTCGATCTATAGCGG
1 CG-TTTTTCAAAAAGCACCGCTAATGCTCAATCTATAGCGA
20478400 CGTTTTTCAAAAAGCACCGCTAATGC
1 CGTTTTTCAAAAAGCACCGCTAATGC
20478426 CACTAAAGCT
Statistics
Matches: 60, Mismatches: 5, Indels: 4
0.87 0.07 0.06
Matches are distributed among these distances:
40 25 0.42
41 34 0.57
42 1 0.02
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (40 bp):
CGTTTTTCAAAAAGCACCGCTAATGCTCAATCTATAGCGA
Found at i:20478417 original size:40 final size:40
Alignment explanation
Indices: 20478318--20478579 Score: 175
Period size: 40 Copynumber: 6.7 Consensus size: 40
20478308 TTTTTTTGTA
*
20478318 GCGTTTTTCAAAAAGCGCCGCTAATGCTCAATCTATAG-G
1 GCGTTTTTCAAAAAGCACCGCTAATGCTCAATCTATAGCG
* * *
20478357 TACGTTTTTTCAAAAAGCACCACTAATGCTCGATCTATAGCG
1 -GCG-TTTTTCAAAAAGCACCGCTAATGCTCAATCTATAGCG
*
20478399 GCGTTTTTCAAAAAGCACCGCTAATGC-C-A-CTAAAGC-
1 GCGTTTTTCAAAAAGCACCGCTAATGCTCAATCTATAGCG
* **** * * ** * * * *
20478435 TC-AACAT-AAAACG-A-CGTGTTGTGCTTAATTTTTTTGCG
1 GCGTTTTTCAAAAAGCACCG-CTAATGCTCAA-TCTATAGCG
* *
20478473 GAGTTTTTCAAAAAG-AGCCGCTAATGCTCAATCTGTAGCG
1 GCGTTTTTCAAAAAGCA-CCGCTAATGCTCAATCTATAGCG
* * *
20478513 GCGTTTTTCAAAAAGCGCCACTAATGCTCGATCTATAGCG
1 GCGTTTTTCAAAAAGCACCGCTAATGCTCAATCTATAGCG
* * *
20478553 ACGTTTTTAAAAAAGCACTGCTAATGC
1 GCGTTTTTCAAAAAGCACCGCTAATGC
20478580 CACTAAAGCT
Statistics
Matches: 164, Mismatches: 45, Indels: 26
0.70 0.19 0.11
Matches are distributed among these distances:
32 2 0.01
33 5 0.03
34 5 0.03
35 2 0.01
36 1 0.01
37 9 0.05
38 1 0.01
39 2 0.01
40 93 0.57
41 41 0.25
42 3 0.02
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.29
Consensus pattern (40 bp):
GCGTTTTTCAAAAAGCACCGCTAATGCTCAATCTATAGCG
Found at i:20478579 original size:154 final size:152
Alignment explanation
Indices: 20478298--20478726 Score: 579
Period size: 147 Copynumber: 2.8 Consensus size: 152
20478288 AAATTGCGGC
* *
20478298 TTGTGCTTAATTTTTTTGTAGCGTTTTTCAAAAAGCGCCGCTAATGCTCAATCTATAG-GTACGT
1 TTGTGCTTAATTTTTTTG--G-GTTTTTCAAAAAGAGCCGCTAATGCTCAATCTATAGCG-GCG-
* *
20478362 TTTTTCAAAAAGCACCACTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCACCGCTAATGCC
61 TTTTTCAAAAAGCGCCACTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCACAGCTAATGCC
*
20478427 ACTAAAGCTCAACATAAAACGAC-GTG
126 ACTAAAGCTCAACATAAAACGACTGCG
*
20478453 TTGTGCTTAATTTTTTTGCGGAGTTTTTCAAAAAGAGCCGCTAATGCTCAATCTGTAGCGGCGTT
1 TTGTGCTTAATTTTTTT--GG-GTTTTTCAAAAAGAGCCGCTAATGCTCAATCTATAGCGGCGTT
* * *
20478518 TTTCAAAAAGCGCCACTAATGCTCGATCTATAGCGACGTTTTTAAAAAAGCACTGCTAATGCCAC
63 TTTCAAAAAGCGCCACTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCACAGCTAATGCCAC
20478583 TAAAGCTCAACATAAAACGACTGCG
128 TAAAGCTCAACATAAAACGACTGCG
* *
20478608 TTGTGCTTAA--TTTTT---TTTTGCAAAAA-ATGCCGCTAATGCTCAACCTATAGCGGCGTTTT
1 TTGTGCTTAATTTTTTTGGGTTTTTCAAAAAGA-GCCGCTAATGCTCAATCTATAGCGGCGTTTT
* * *
20478667 TCATAAAGCGCCGCTAATGCTCGATCCT-TAGCGGCGTTTTTCAAAAAGCGCAGCTAATGC
65 TCAAAAAGCGCCACTAATGCTCGAT-CTATAGCGGCGTTTTTCAAAAAGCACAGCTAATGC
20478727 TCGATCTATA
Statistics
Matches: 250, Mismatches: 18, Indels: 20
0.87 0.06 0.07
Matches are distributed among these distances:
146 1 0.00
147 90 0.36
148 2 0.01
153 5 0.02
154 84 0.34
155 66 0.26
156 1 0.00
157 1 0.00
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (152 bp):
TTGTGCTTAATTTTTTTGGGTTTTTCAAAAAGAGCCGCTAATGCTCAATCTATAGCGGCGTTTTT
CAAAAAGCGCCACTAATGCTCGATCTATAGCGGCGTTTTTCAAAAAGCACAGCTAATGCCACTAA
AGCTCAACATAAAACGACTGCG
Found at i:20478680 original size:40 final size:40
Alignment explanation
Indices: 20478622--20478747 Score: 164
Period size: 40 Copynumber: 3.1 Consensus size: 40
20478612 GCTTAATTTT
**
20478622 TTTTTGCAAAAAATGCCGCTAATGCTCAACCTATAGCGGCG
1 TTTTT-CAAAAAGCGCCGCTAATGCTCAACCTATAGCGGCG
* *
20478663 TTTTTCATAAAGCGCCGCTAATGCTCGATCCT-TAGCGGCG
1 TTTTTCAAAAAGCGCCGCTAATGCTC-AACCTATAGCGGCG
* * *
20478703 TTTTTCAAAAAGCGCAGCTAATGCTCGATCTATAGCGGCG
1 TTTTTCAAAAAGCGCCGCTAATGCTCAACCTATAGCGGCG
20478743 TTTTT
1 TTTTT
20478748 TATCCAGACG
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
39 2 0.03
40 63 0.85
41 9 0.12
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.31
Consensus pattern (40 bp):
TTTTTCAAAAAGCGCCGCTAATGCTCAACCTATAGCGGCG
Found at i:20478764 original size:41 final size:40
Alignment explanation
Indices: 20478636--20478747 Score: 172
Period size: 40 Copynumber: 2.8 Consensus size: 40
20478626 TGCAAAAAAT
* *
20478636 GCCGCTAATGCTCAACCTATAGCGGCGTTTTTCATAAAGC
1 GCCGCTAATGCTCGATCTATAGCGGCGTTTTTCATAAAGC
*
20478676 GCCGCTAATGCTCGATCCT-TAGCGGCGTTTTTCAAAAAGC
1 GCCGCTAATGCTCGAT-CTATAGCGGCGTTTTTCATAAAGC
*
20478716 GCAGCTAATGCTCGATCTATAGCGGCGTTTTT
1 GCCGCTAATGCTCGATCTATAGCGGCGTTTTT
20478748 TATCCAGACG
Statistics
Matches: 66, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
39 2 0.03
40 62 0.94
41 2 0.03
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.29
Consensus pattern (40 bp):
GCCGCTAATGCTCGATCTATAGCGGCGTTTTTCATAAAGC
Found at i:20480461 original size:22 final size:21
Alignment explanation
Indices: 20480436--20480478 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 21
20480426 TAAAGTATAT
20480436 ACATAATATATATGAAA-ACATA
1 ACATAATAT-TA-GAAATACATA
*
20480458 ACATAGTATTAGAAATACATA
1 ACATAATATTAGAAATACATA
20480479 TTAGAAATGT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 4 0.21
21 7 0.37
22 8 0.42
ACGTcount: A:0.56, C:0.09, G:0.07, T:0.28
Consensus pattern (21 bp):
ACATAATATTAGAAATACATA
Found at i:20480735 original size:3 final size:3
Alignment explanation
Indices: 20480717--20480750 Score: 52
Period size: 3 Copynumber: 11.3 Consensus size: 3
20480707 CTATACGTAT
20480717 ATA ATA A-A ATA TATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA -ATA ATA ATA ATA ATA ATA ATA A
20480751 GGATAATATA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
2 2 0.07
3 24 0.83
4 3 0.10
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:20480804 original size:25 final size:24
Alignment explanation
Indices: 20480760--20480838 Score: 70
Period size: 26 Copynumber: 3.1 Consensus size: 24
20480750 AGGATAATAT
*
20480760 AAATATATATACACGAAATAGTATAAA
1 AAATATATATA-AC-TAATA-TATAAA
20480787 AAATATATATAACTAATAATATTAAA
1 AAATATATATAACTAAT-ATA-TAAA
* * *
20480813 ATATATACATGA-TAATATATAAA
1 AAATATATATAACTAATATATAAA
20480836 AAA
1 AAA
20480839 AATAATATTA
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
23 6 0.13
24 3 0.07
25 9 0.20
26 16 0.36
27 11 0.24
ACGTcount: A:0.61, C:0.05, G:0.04, T:0.30
Consensus pattern (24 bp):
AAATATATATAACTAATATATAAA
Found at i:20480819 original size:22 final size:23
Alignment explanation
Indices: 20480756--20480909 Score: 90
Period size: 24 Copynumber: 6.6 Consensus size: 23
20480746 AATAAGGATA
**
20480756 ATATAAATATATATACACGA-AAT
1 ATATAAA-ATATATACATAATAAT
* *
20480779 AGTATAAAAAATATATATAACTAAT
1 A-TATAAAATATATACATAA-TAAT
*
20480804 AATATTAAAATATATACATGATAAT
1 -ATA-TAAAATATATACATAATAAT
20480829 ATATAAAA-A-A-A-ATAAT-AT
1 ATATAAAATATATACATAATAAT
*
20480847 -TAGAAAATATATGTACATAATATAT
1 ATATAAAATATA--TACATAATA-AT
*
20480872 ATATATAATATATACATAAT-AT
1 ATATAAAATATATACATAATAAT
*
20480894 AGTATTAAAAAATATA
1 A-TA-TAAAATATATA
20480910 ATATTAAAAT
Statistics
Matches: 102, Mismatches: 13, Indels: 31
0.70 0.09 0.21
Matches are distributed among these distances:
17 6 0.06
18 3 0.03
19 5 0.05
20 1 0.01
21 1 0.01
22 5 0.05
23 21 0.21
24 26 0.25
25 11 0.11
26 23 0.23
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.34
Consensus pattern (23 bp):
ATATAAAATATATACATAATAAT
Found at i:20480868 original size:13 final size:12
Alignment explanation
Indices: 20480852--20480894 Score: 52
Period size: 13 Copynumber: 3.5 Consensus size: 12
20480842 AATATTAGAA
20480852 AATATATGTACAT
1 AATATAT-TACAT
*
20480865 AATATATATATAT
1 AATATAT-TACAT
20480878 AATATA-TACAT
1 AATATATTACAT
20480889 AATATA
1 AATATA
20480895 GTATTAAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
11 10 0.37
13 17 0.63
ACGTcount: A:0.53, C:0.05, G:0.02, T:0.40
Consensus pattern (12 bp):
AATATATTACAT
Found at i:20480882 original size:11 final size:11
Alignment explanation
Indices: 20480868--20480983 Score: 70
Period size: 11 Copynumber: 9.8 Consensus size: 11
20480858 TGTACATAAT
20480868 ATATATATATA
1 ATATATATATA
*
20480879 ATATATACATA
1 ATATATATATA
*
20480890 ATATAGTATTAAA
1 ATATA-TA-TATA
*
20480903 AAATATAATATTA
1 ATATAT-ATA-TA
* *
20480916 AAATACATATA
1 ATATATATATA
* *
20480927 ATATATGTAAA
1 ATATATATATA
* *
20480938 ATATATACACA
1 ATATATATATA
*
20480949 ATATAGTATTAAA
1 ATATA-TA-TATA
20480962 ATATATATGCATA
1 ATATATAT--ATA
20480975 ATATATATA
1 ATATATATA
20480984 ACACATACAT
Statistics
Matches: 81, Mismatches: 16, Indels: 16
0.72 0.14 0.14
Matches are distributed among these distances:
11 39 0.48
12 12 0.15
13 30 0.37
ACGTcount: A:0.55, C:0.04, G:0.03, T:0.37
Consensus pattern (11 bp):
ATATATATATA
Found at i:20480927 original size:17 final size:15
Alignment explanation
Indices: 20480824--20480930 Score: 61
Period size: 16 Copynumber: 6.5 Consensus size: 15
20480814 TATATACATG
*
20480824 ATAATATATAAAAAAA
1 ATAATAT-TAAAAAAT
20480840 ATAATATTAGAAAATAT
1 ATAATATTA-AAAA-AT
* * *
20480857 ATGTACATAATATATATAT
1 A--TA-ATATTA-AAAAAT
* *
20480876 ATAATATATACATAAT
1 ATAATAT-TAAAAAAT
*
20480892 ATAGTATTAAAAAAT
1 ATAATATTAAAAAAT
20480907 ATAATATTAAAATACAT
1 ATAATATTAAAA-A-AT
20480924 ATAATAT
1 ATAATAT
20480931 ATGTAAAATA
Statistics
Matches: 69, Mismatches: 14, Indels: 15
0.70 0.14 0.15
Matches are distributed among these distances:
15 19 0.28
16 23 0.33
17 15 0.22
19 5 0.07
20 7 0.10
ACGTcount: A:0.59, C:0.03, G:0.03, T:0.36
Consensus pattern (15 bp):
ATAATATTAAAAAAT
Found at i:20481138 original size:19 final size:20
Alignment explanation
Indices: 20481092--20481139 Score: 53
Period size: 19 Copynumber: 2.5 Consensus size: 20
20481082 GAAATACTTA
**
20481092 ATATATAATATTTGAAATAT
1 ATATATAATATTAAAAATAT
**
20481112 ATGCATAATA-TAAAAATAT
1 ATATATAATATTAAAAATAT
20481131 ATATATAAT
1 ATATATAAT
20481140 GTAGTATTAA
Statistics
Matches: 22, Mismatches: 6, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
19 14 0.64
20 8 0.36
ACGTcount: A:0.54, C:0.02, G:0.04, T:0.40
Consensus pattern (20 bp):
ATATATAATATTAAAAATAT
Found at i:20482953 original size:15 final size:15
Alignment explanation
Indices: 20482933--20482966 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
20482923 TTCGGATACC
20482933 ATTTCATGAACCTTA
1 ATTTCATGAACCTTA
20482948 ATTTCATGAACCTTA
1 ATTTCATGAACCTTA
20482963 ATTT
1 ATTT
20482967 GAAAGAAAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.32, C:0.18, G:0.06, T:0.44
Consensus pattern (15 bp):
ATTTCATGAACCTTA
Found at i:20485016 original size:17 final size:17
Alignment explanation
Indices: 20484994--20485035 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
20484984 TTTCATCTTT
20484994 ATTTTTTTATCCATT-CA
1 ATTTTTTTAT-CATTCCA
*
20485011 A-TTTTTTATCTTTCCA
1 ATTTTTTTATCATTCCA
20485027 ATTTTTTTA
1 ATTTTTTTA
20485036 CACTGTACCA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 3 0.14
16 11 0.50
17 8 0.36
ACGTcount: A:0.21, C:0.14, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTTTTTATCATTCCA
Found at i:20485649 original size:35 final size:34
Alignment explanation
Indices: 20485582--20485649 Score: 84
Period size: 35 Copynumber: 2.0 Consensus size: 34
20485572 CTATTGAATT
*
20485582 AAATTTTAAATTATATTCTAATTTATTACATATG
1 AAATTTTAAATTATATTCTAATTTAATACATATG
* *
20485616 AAATATTTAAATTTTATTTTCAATTTAAT-CATAT
1 AAAT-TTTAAATTATATTCT-AATTTAATACATAT
20485650 ATTATTCAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
34 4 0.14
35 18 0.62
36 7 0.24
ACGTcount: A:0.41, C:0.06, G:0.01, T:0.51
Consensus pattern (34 bp):
AAATTTTAAATTATATTCTAATTTAATACATATG
Found at i:20494814 original size:22 final size:23
Alignment explanation
Indices: 20494786--20494834 Score: 64
Period size: 26 Copynumber: 2.0 Consensus size: 23
20494776 AAAAAACTTA
20494786 TTTTTAAT-TAAATTAATGTTAT
1 TTTTTAATATAAATTAATGTTAT
20494808 TTTTTAATAAAATAAATTAATGTTAT
1 TTTTTAAT---ATAAATTAATGTTAT
20494834 T
1 T
20494835 AAAAAAATAG
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 8 0.35
26 15 0.65
ACGTcount: A:0.41, C:0.00, G:0.04, T:0.55
Consensus pattern (23 bp):
TTTTTAATATAAATTAATGTTAT
Found at i:20497445 original size:13 final size:12
Alignment explanation
Indices: 20497427--20497454 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
20497417 AAAGGACATT
20497427 AAAAAAAAAAAG
1 AAAAAAAAAAAG
20497439 AAAAAAAAAAAG
1 AAAAAAAAAAAG
20497451 AAAA
1 AAAA
20497455 GAAGAAACCC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:20500274 original size:26 final size:26
Alignment explanation
Indices: 20500245--20500294 Score: 100
Period size: 26 Copynumber: 1.9 Consensus size: 26
20500235 TACATGATCG
20500245 TGCACAGCCCTGACTGATCCCTTTCA
1 TGCACAGCCCTGACTGATCCCTTTCA
20500271 TGCACAGCCCTGACTGATCCCTTT
1 TGCACAGCCCTGACTGATCCCTTT
20500295 TCTTCTTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.18, C:0.38, G:0.16, T:0.28
Consensus pattern (26 bp):
TGCACAGCCCTGACTGATCCCTTTCA
Done.