Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 129486693
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: 129486693
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 305 characters in sequence are not A, C, G, or T
File 19 of 444
Found at i:5377387 original size:18 final size:18
Alignment explanation
Indices: 5377364--5377419 Score: 76
Period size: 18 Copynumber: 3.1 Consensus size: 18
5377354 CAATCCCAAC
*
5377364 TACTGTATACGTGAACAG
1 TACTGTATACGTAAACAG
*
5377382 TACTGTATACGTAAATAG
1 TACTGTATACGTAAACAG
* *
5377400 TACCGTATACGTAAATAG
1 TACTGTATACGTAAACAG
5377418 TA
1 TA
5377420 TCGTATACAT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 35 1.00
ACGTcount: A:0.38, C:0.14, G:0.18, T:0.30
Consensus pattern (18 bp):
TACTGTATACGTAAACAG
Found at i:5377426 original size:36 final size:36
Alignment explanation
Indices: 5377368--5377442 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 36
5377358 CCCAACTACT
* *
5377368 GTATACGTGAACAGTACTGTATACGTAAATAGTACC
1 GTATACGTAAACAGTACTGTATACATAAATAGTACC
* * *
5377404 GTATACGTAAATAGTA-TCGTATACATGAATAGTGCC
1 GTATACGTAAACAGTACT-GTATACATAAATAGTACC
5377440 GTA
1 GTA
5377443 AATGGTCGTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
35 1 0.03
36 32 0.97
ACGTcount: A:0.36, C:0.15, G:0.20, T:0.29
Consensus pattern (36 bp):
GTATACGTAAACAGTACTGTATACATAAATAGTACC
Found at i:5377436 original size:18 final size:17
Alignment explanation
Indices: 5377368--5377427 Score: 75
Period size: 18 Copynumber: 3.4 Consensus size: 17
5377358 CCCAACTACT
* *
5377368 GTATACGTGAACAGTAC
1 GTATACGTAAATAGTAC
5377385 TGTATACGTAAATAGTACC
1 -GTATACGTAAATAGTA-C
5377404 GTATACGTAAATAGTATC
1 GTATACGTAAATAGTA-C
5377422 GTATAC
1 GTATAC
5377428 ATGAATAGTG
Statistics
Matches: 38, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
18 37 0.97
19 1 0.03
ACGTcount: A:0.37, C:0.15, G:0.18, T:0.30
Consensus pattern (17 bp):
GTATACGTAAATAGTAC
Found at i:5377442 original size:18 final size:18
Alignment explanation
Indices: 5377380--5377442 Score: 72
Period size: 18 Copynumber: 3.5 Consensus size: 18
5377370 ATACGTGAAC
* *
5377380 AGTACTGTATACGTAAAT
1 AGTACCGTATACATAAAT
*
5377398 AGTACCGTATACGTAAAT
1 AGTACCGTATACATAAAT
* *
5377416 AGTATCGTATACATGAAT
1 AGTACCGTATACATAAAT
*
5377434 AGTGCCGTA
1 AGTACCGTA
5377443 AATGGTCGTA
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 39 1.00
ACGTcount: A:0.37, C:0.14, G:0.19, T:0.30
Consensus pattern (18 bp):
AGTACCGTATACATAAAT
Found at i:5380675 original size:2 final size:2
Alignment explanation
Indices: 5380668--5380706 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
5380658 TTAAACCAAT
*
5380668 TA TA TA TA TA TA TA TA TA CA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
5380707 TTAAAAATCT
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Found at i:5380762 original size:2 final size:2
Alignment explanation
Indices: 5380755--5380779 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
5380745 CATATCCTAT
5380755 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
5380780 TTAGAACCTT
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:5381377 original size:2 final size:2
Alignment explanation
Indices: 5381370--5381395 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
5381360 TTTTCACACT
5381370 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
5381396 CATCCAAATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5382100 original size:26 final size:26
Alignment explanation
Indices: 5382063--5382198 Score: 236
Period size: 26 Copynumber: 5.2 Consensus size: 26
5382053 TGATACAAAT
* *
5382063 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
5382089 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
* *
5382115 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
5382141 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
5382167 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
5382193 TGATAA
1 TGATAA
5382199 GAATATCATG
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 104 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:5384228 original size:136 final size:137
Alignment explanation
Indices: 5383983--5384268 Score: 502
Period size: 136 Copynumber: 2.1 Consensus size: 137
5383973 GAGTAGTCTC
5383983 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
* *
5384048 TGTTATCTAAATAAAGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTTTGGCCCAGTATC
66 TGTTATCTAAATAAAGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
5384113 ACTGTTA
131 ACTGTTA
*
5384120 CCCAAATGGGCTTGCATATG-TTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
* *
5384184 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTAAATAAAGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
5384249 ACTGTTA
131 ACTGTTA
**
5384256 CCTGAATGGGCTT
1 CCCAAATGGGCTT
5384269 AGGCCCAATG
Statistics
Matches: 142, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
136 122 0.86
137 20 0.14
ACGTcount: A:0.25, C:0.18, G:0.24, T:0.32
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTAAATAAAGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
ACTGTTA
Found at i:5385363 original size:127 final size:127
Alignment explanation
Indices: 5385074--5385368 Score: 358
Period size: 127 Copynumber: 2.3 Consensus size: 127
5385064 GCAATGCTTG
* * * *
5385074 ATGTTTGGAAATTCGAGGAATCGTGTCCTATCGTGCCGGGTTTCAATTTCCCGTTTGTTTAAAAT
1 ATGTTTGGAAATTCGAGGAATCGTGCCCTATCGTGCTGGGTTTCAATTTCCCGTTTGCTCAAAAT
*
5385139 AATCAAATATTCCTTTAGAATTTCACTCATGTCTTCAAAATGCTAAGACAAGGCAATATTCA
66 AATCAAATATTCCTTTAGAATTTCACTCATATCTTCAAAATGCTAAGACAAGGCAATATTCA
* * * * * * *
5385201 ACGCTTGGAAATTTGGGGAATCGTGCCCAATCGTGCTGGGTTTCGATTTCCGGTTTGCTCAAAAT
1 ATGTTTGGAAATTCGAGGAATCGTGCCCTATCGTGCTGGGTTTCAATTTCCCGTTTGCTCAAAAT
* *** * * * *
5385266 AGTTGGATATTCCTTTAGAATTTCATTCATATTTTCTAAATGCT-AGAGCGAGGCAATATTCA
66 AATCAAATATTCCTTTAGAATTTCACTCATATCTTCAAAATGCTAAGA-CAAGGCAATATTCA
* * * *
5385328 ATGTTTGAAAATTCGATGAAACGTGCCCTACCGTGCTGGGT
1 ATGTTTGGAAATTCGAGGAATCGTGCCCTATCGTGCTGGGT
5385369 GTCGGTTTTT
Statistics
Matches: 138, Mismatches: 29, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
126 3 0.02
127 135 0.98
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (127 bp):
ATGTTTGGAAATTCGAGGAATCGTGCCCTATCGTGCTGGGTTTCAATTTCCCGTTTGCTCAAAAT
AATCAAATATTCCTTTAGAATTTCACTCATATCTTCAAAATGCTAAGACAAGGCAATATTCA
Found at i:5389883 original size:28 final size:29
Alignment explanation
Indices: 5389837--5389892 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 29
5389827 TAATGTTATT
* *
5389837 TTTTTATTAATTAACTATTATTCTATTCA
1 TTTTTATTAATCAACTATTATTATATTCA
* *
5389866 TTTTTATT-ATCATCTATTTTTATATTC
1 TTTTTATTAATCAACTATTATTATATTC
5389893 GGAATAATAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 15 0.65
29 8 0.35
ACGTcount: A:0.27, C:0.11, G:0.00, T:0.62
Consensus pattern (29 bp):
TTTTTATTAATCAACTATTATTATATTCA
Found at i:5392250 original size:24 final size:22
Alignment explanation
Indices: 5392223--5392272 Score: 68
Period size: 21 Copynumber: 2.3 Consensus size: 22
5392213 GTAAGTTTTC
5392223 AGTTTCTTCTTTATTTAAACTCGA
1 AGTTT-TTCTTTATTTAAACTC-A
5392247 AG--TTTCTTTATTTAAACTCA
1 AGTTTTTCTTTATTTAAACTCA
5392267 AGTTTT
1 AGTTTT
5392273 CACTTATATC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
20 3 0.12
21 16 0.67
22 3 0.12
24 2 0.08
ACGTcount: A:0.26, C:0.14, G:0.08, T:0.52
Consensus pattern (22 bp):
AGTTTTTCTTTATTTAAACTCA
Found at i:5392273 original size:21 final size:21
Alignment explanation
Indices: 5392229--5392271 Score: 79
Period size: 21 Copynumber: 2.1 Consensus size: 21
5392219 TTTCAGTTTC
5392229 TTCTTTATTTAAACTCGAAGT
1 TTCTTTATTTAAACTCGAAGT
5392250 TTCTTTATTTAAACTC-AAGT
1 TTCTTTATTTAAACTCGAAGT
5392270 TT
1 TT
5392272 TCACTTATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.28, C:0.14, G:0.07, T:0.51
Consensus pattern (21 bp):
TTCTTTATTTAAACTCGAAGT
Found at i:5396415 original size:4 final size:4
Alignment explanation
Indices: 5396406--5396430 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
5396396 ATTTTAATCC
5396406 ATTT ATTT ATTT ATTT ATTT ATTT A
1 ATTT ATTT ATTT ATTT ATTT ATTT A
5396431 CTTGCTTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (4 bp):
ATTT
Found at i:5399055 original size:22 final size:22
Alignment explanation
Indices: 5399027--5399071 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
5399017 TCCAAACTCT
5399027 TAATTTTGTTAAGCCTTGAGAA
1 TAATTTTGTTAAGCCTTGAGAA
5399049 TAATTTTGTTAAGCCTTGAGAA
1 TAATTTTGTTAAGCCTTGAGAA
5399071 T
1 T
5399072 GTTGATGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (22 bp):
TAATTTTGTTAAGCCTTGAGAA
Found at i:5401203 original size:31 final size:31
Alignment explanation
Indices: 5401167--5401228 Score: 81
Period size: 31 Copynumber: 2.0 Consensus size: 31
5401157 GAAATTTAGT
*
5401167 TTTTATATTTTA-ATTTCAAGAATTTTAGTCC
1 TTTTATATTTTAGATTTCAA-AATTTAAGTCC
* *
5401198 TTTTATTTTTTAGATTTTAAAATTTAAGTCC
1 TTTTATATTTTAGATTTCAAAATTTAAGTCC
5401229 AATTATTAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
31 21 0.78
32 6 0.22
ACGTcount: A:0.29, C:0.08, G:0.06, T:0.56
Consensus pattern (31 bp):
TTTTATATTTTAGATTTCAAAATTTAAGTCC
Found at i:5401235 original size:31 final size:31
Alignment explanation
Indices: 5401169--5401235 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 31
5401159 AATTTAGTTT
* * **
5401169 TTATATTTTAATTTCAAGAATTTTAGTCCTT
1 TTATTTTTTAATTTCAAGAATTTAAGTCCAA
*
5401200 TTATTTTTTAGATTTTAA-AATTTAAGTCCAA
1 TTATTTTTTA-ATTTCAAGAATTTAAGTCCAA
5401231 TTATT
1 TTATT
5401236 AACACAATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
31 24 0.80
32 6 0.20
ACGTcount: A:0.31, C:0.07, G:0.06, T:0.55
Consensus pattern (31 bp):
TTATTTTTTAATTTCAAGAATTTAAGTCCAA
Found at i:5403480 original size:11 final size:12
Alignment explanation
Indices: 5403430--5403480 Score: 63
Period size: 11 Copynumber: 4.4 Consensus size: 12
5403420 ATCCTCCCAA
*
5403430 TTTTTAGTGTCT
1 TTTTTAGTGTAT
5403442 TTTTTA-TGTAT
1 TTTTTAGTGTAT
5403453 ATTTTTAGTGT-T
1 -TTTTTAGTGTAT
5403465 TTTTTA-TGTAT
1 TTTTTAGTGTAT
5403476 TTTTT
1 TTTTT
5403481 TTAAAATTTA
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
10 3 0.09
11 16 0.46
12 13 0.37
13 3 0.09
ACGTcount: A:0.14, C:0.02, G:0.12, T:0.73
Consensus pattern (12 bp):
TTTTTAGTGTAT
Found at i:5403483 original size:13 final size:12
Alignment explanation
Indices: 5403441--5403481 Score: 57
Period size: 12 Copynumber: 3.5 Consensus size: 12
5403431 TTTTAGTGTC
5403441 TTTTTTATGTAT
1 TTTTTTATGTAT
* *
5403453 ATTTTTA-GTGT
1 TTTTTTATGTAT
5403464 TTTTTTATGTAT
1 TTTTTTATGTAT
5403476 TTTTTT
1 TTTTTT
5403482 TAAAATTTAT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
11 9 0.38
12 15 0.62
ACGTcount: A:0.15, C:0.00, G:0.10, T:0.76
Consensus pattern (12 bp):
TTTTTTATGTAT
Found at i:5403483 original size:24 final size:24
Alignment explanation
Indices: 5403429--5403481 Score: 90
Period size: 23 Copynumber: 2.2 Consensus size: 24
5403419 AATCCTCCCA
5403429 ATTTTTAGTGTCTTTTTTATGTAT
1 ATTTTTAGTGTCTTTTTTATGTAT
5403453 ATTTTTAGTGT-TTTTTTATGTAT
1 ATTTTTAGTGTCTTTTTTATGTAT
*
5403476 TTTTTT
1 ATTTTT
5403482 TAAAATTTAT
Statistics
Matches: 28, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
23 17 0.61
24 11 0.39
ACGTcount: A:0.15, C:0.02, G:0.11, T:0.72
Consensus pattern (24 bp):
ATTTTTAGTGTCTTTTTTATGTAT
Found at i:5408918 original size:13 final size:14
Alignment explanation
Indices: 5408902--5408937 Score: 51
Period size: 13 Copynumber: 2.8 Consensus size: 14
5408892 CAATCTCATA
5408902 TCTCAATTTCAA-T
1 TCTCAATTTCAATT
5408915 TCTCAA-TTCAATT
1 TCTCAATTTCAATT
5408928 TCTC-ATTTCA
1 TCTCAATTTCA
5408938 TTCCAATAGC
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.28, C:0.25, G:0.00, T:0.47
Consensus pattern (14 bp):
TCTCAATTTCAATT
Found at i:5408927 original size:18 final size:19
Alignment explanation
Indices: 5408889--5408929 Score: 59
Period size: 18 Copynumber: 2.2 Consensus size: 19
5408879 TGGTTCATGT
5408889 TTTCAATCTCATATCTCAA
1 TTTCAATCTCATATCTCAA
5408908 TTTCAATTCTCA-AT-TCAA
1 TTTCAA-TCTCATATCTCAA
5408926 TTTC
1 TTTC
5408930 TCATTTCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 8 0.38
19 8 0.38
20 5 0.24
ACGTcount: A:0.29, C:0.24, G:0.00, T:0.46
Consensus pattern (19 bp):
TTTCAATCTCATATCTCAA
Found at i:5409052 original size:23 final size:23
Alignment explanation
Indices: 5409022--5409070 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
5409012 TCTGATAGAT
5409022 ACCAGAATATCCAACCCAAACAC
1 ACCAGAATATCCAACCCAAACAC
*
5409045 ACCAGAATATCCAATCCAAACAC
1 ACCAGAATATCCAACCCAAACAC
5409068 ACC
1 ACC
5409071 CGGAATATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.47, C:0.39, G:0.04, T:0.10
Consensus pattern (23 bp):
ACCAGAATATCCAACCCAAACAC
Found at i:5409464 original size:15 final size:15
Alignment explanation
Indices: 5409446--5409492 Score: 67
Period size: 15 Copynumber: 3.1 Consensus size: 15
5409436 TATATTATAT
5409446 TTCAATCAATATAAA
1 TTCAATCAATATAAA
* * *
5409461 TTCAATCAAAATGAT
1 TTCAATCAATATAAA
5409476 TTCAATCAATATAAA
1 TTCAATCAATATAAA
5409491 TT
1 TT
5409493 TGATAAATTC
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.49, C:0.13, G:0.02, T:0.36
Consensus pattern (15 bp):
TTCAATCAATATAAA
Found at i:5410239 original size:25 final size:25
Alignment explanation
Indices: 5410206--5410256 Score: 59
Period size: 25 Copynumber: 2.0 Consensus size: 25
5410196 CTTCCCCTGC
5410206 TTTTCGTTTGCCTAT-TCTGTTTCTT
1 TTTTCGTTT-CCTATCTCTGTTTCTT
* * *
5410231 TTTTTGTTTCCTTTCTCTTTTTCTT
1 TTTTCGTTTCCTATCTCTGTTTCTT
5410256 T
1 T
5410257 ATTTATTTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
24 4 0.18
25 18 0.82
ACGTcount: A:0.02, C:0.20, G:0.08, T:0.71
Consensus pattern (25 bp):
TTTTCGTTTCCTATCTCTGTTTCTT
Found at i:5410452 original size:31 final size:32
Alignment explanation
Indices: 5410397--5410458 Score: 83
Period size: 31 Copynumber: 2.0 Consensus size: 32
5410387 ACATTTGTCA
*
5410397 TAATTTAATATATTTATTACATAAAAATCTCG
1 TAATATAATATATTTATTACATAAAAATCTCG
*
5410429 TAATATAAT-TATTTAATTA-ATAAATATCTC
1 TAATATAATATATTT-ATTACATAAAAATCTC
5410459 ATTTAATATT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
31 15 0.56
32 12 0.44
ACGTcount: A:0.45, C:0.08, G:0.02, T:0.45
Consensus pattern (32 bp):
TAATATAATATATTTATTACATAAAAATCTCG
Found at i:5411350 original size:25 final size:26
Alignment explanation
Indices: 5411288--5411420 Score: 218
Period size: 25 Copynumber: 5.2 Consensus size: 26
5411278 TGATACAAAT
5411288 TGATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
5411314 TAATAATAGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
5411340 T-ATAATAGGTTAGGT-AATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
5411364 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
5411390 TGATAAT-GGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
5411415 TGATAA
1 TGATAA
5411421 GAATTTCATG
Statistics
Matches: 102, Mismatches: 3, Indels: 5
0.93 0.03 0.05
Matches are distributed among these distances:
24 9 0.09
25 51 0.50
26 42 0.41
ACGTcount: A:0.35, C:0.05, G:0.22, T:0.38
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:5412956 original size:25 final size:25
Alignment explanation
Indices: 5412908--5412956 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
5412898 ACAGTTTTAC
5412908 CCCTAGGAGATAAATTACCGAAATA
1 CCCTAGGAGATAAATTACCGAAATA
* *
5412933 CCCTAGG-GTTAAATTGACCTAAAT
1 CCCTAGGAGATAAATT-ACCGAAAT
5412957 GCATGTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.24
Consensus pattern (25 bp):
CCCTAGGAGATAAATTACCGAAATA
Found at i:5413449 original size:136 final size:137
Alignment explanation
Indices: 5413204--5413489 Score: 529
Period size: 136 Copynumber: 2.1 Consensus size: 137
5413194 GAGTAGTCTC
5413204 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
5413269 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
5413334 ACTGTTA
131 ACTGTTA
*
5413341 CCCAAATGGGCTTGCATATG-TTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
*
5413405 TGTTATTTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
5413470 ACTGTTA
131 ACTGTTA
**
5413477 CCTGAATGGGCTT
1 CCCAAATGGGCTT
5413490 AGGCCCAATG
Statistics
Matches: 145, Mismatches: 4, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
136 125 0.86
137 20 0.14
ACGTcount: A:0.24, C:0.19, G:0.25, T:0.32
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
ACTGTTA
Found at i:5414727 original size:12 final size:12
Alignment explanation
Indices: 5414710--5414740 Score: 62
Period size: 12 Copynumber: 2.6 Consensus size: 12
5414700 ACTCGGGGAA
5414710 GAGGCCGTGGTC
1 GAGGCCGTGGTC
5414722 GAGGCCGTGGTC
1 GAGGCCGTGGTC
5414734 GAGGCCG
1 GAGGCCG
5414741 AGGTAGTACT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.10, C:0.26, G:0.52, T:0.13
Consensus pattern (12 bp):
GAGGCCGTGGTC
Found at i:5419675 original size:24 final size:24
Alignment explanation
Indices: 5419612--5419738 Score: 197
Period size: 24 Copynumber: 5.2 Consensus size: 24
5419602 TGATACAAAT
5419612 TGATAATAGGTTAGGTAAATGTTCA
1 TGATAAT-GGTTAGGTAAATGTTCA
5419637 T-ATAATGGTTAGGTAAATGTTCA
1 TGATAATGGTTAGGTAAATGTTCA
5419660 T-ATAATAGGTTAGGT-AATGTTCCA
1 TGATAAT-GGTTAGGTAAATGTT-CA
5419684 TGATAATGGTTAGGTAAATGTTCA
1 TGATAATGGTTAGGTAAATGTTCA
5419708 TGATAATGGTTAGGTAAATGTTTCA
1 TGATAATGGTTAGGTAAATG-TTCA
5419733 TGATAA
1 TGATAA
5419739 GAATTTCATG
Statistics
Matches: 97, Mismatches: 0, Indels: 10
0.91 0.00 0.09
Matches are distributed among these distances:
23 29 0.30
24 46 0.47
25 22 0.23
ACGTcount: A:0.35, C:0.05, G:0.23, T:0.38
Consensus pattern (24 bp):
TGATAATGGTTAGGTAAATGTTCA
Found at i:5421269 original size:25 final size:25
Alignment explanation
Indices: 5421221--5421269 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
5421211 ACAGTTTTAC
5421221 CCCTAGGAGATAAATTACCGAAATA
1 CCCTAGGAGATAAATTACCGAAATA
* *
5421246 CCCTAGG-GTTAAATTGACCTAAAT
1 CCCTAGGAGATAAATT-ACCGAAAT
5421270 GCATGTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.24
Consensus pattern (25 bp):
CCCTAGGAGATAAATTACCGAAATA
Found at i:5421769 original size:135 final size:137
Alignment explanation
Indices: 5421517--5421801 Score: 529
Period size: 135 Copynumber: 2.1 Consensus size: 137
5421507 GAGTAGTCTC
5421517 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
5421582 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
5421647 ACTGTTA
131 ACTGTTA
*
5421654 CCCAAATGGGCTTGCATATG-TTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
5421718 TGTTAT-TGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
5421782 ACTGTTA
131 ACTGTTA
**
5421789 CCTGAATGGGCTT
1 CCCAAATGGGCTT
5421802 AGGCCCAATG
Statistics
Matches: 145, Mismatches: 3, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
135 76 0.52
136 49 0.34
137 20 0.14
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.32
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
ACTGTTA
Found at i:5422533 original size:13 final size:14
Alignment explanation
Indices: 5422515--5422543 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5422505 GATTAACTTC
5422515 ATAAATATTTT-TA
1 ATAAATATTTTCTA
5422528 ATAAATATTTTCTA
1 ATAAATATTTTCTA
5422542 AT
1 AT
5422544 CCATTTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAAATATTTTCTA
Found at i:5424811 original size:13 final size:13
Alignment explanation
Indices: 5424776--5424853 Score: 58
Period size: 12 Copynumber: 6.1 Consensus size: 13
5424766 TATATATTAT
5424776 ATAAT-TTATATAA
1 ATAATATTA-ATAA
* *
5424789 CATAAAATTAATAT
1 -ATAATATTAATAA
*
5424803 ATAATATT-ATAGT
1 ATAATATTAATA-A
5424816 ATAAATATTAA-AA
1 AT-AATATTAATAA
5424829 AT-ATATTAATAA
1 ATAATATTAATAA
5424841 ATAAT-TTAATAA
1 ATAATATTAATAA
5424853 A
1 A
5424854 AGAAAAAACA
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
11 7 0.13
12 15 0.28
13 14 0.26
14 14 0.26
15 4 0.07
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (13 bp):
ATAATATTAATAA
Found at i:5426251 original size:14 final size:13
Alignment explanation
Indices: 5426225--5426250 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5426215 GCCCAATACC
5426225 TAAAACAAAAAAA
1 TAAAACAAAAAAA
5426238 TAAAACAAAAAAA
1 TAAAACAAAAAAA
5426251 AAGAAAAATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.85, C:0.08, G:0.00, T:0.08
Consensus pattern (13 bp):
TAAAACAAAAAAA
Found at i:5427356 original size:3 final size:3
Alignment explanation
Indices: 5427350--5427398 Score: 53
Period size: 3 Copynumber: 16.0 Consensus size: 3
5427340 TGTATTTCAA
* * * *
5427350 TAT TAT TAC TAT TAT TAT TAT TAT TAA TAT TAG TAT ATAT TTT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT
5427396 TAT
1 TAT
5427399 ATATGTATAT
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
3 34 0.92
4 3 0.08
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:5427386 original size:145 final size:143
Alignment explanation
Indices: 5427217--5427515 Score: 483
Period size: 145 Copynumber: 2.1 Consensus size: 143
5427207 TTATTTTTTA
* *
5427217 TATTATTATTATAAATTAGTGTATATTTTTTTATTATATACGTATATGTATTTATATTTTTACAT
1 TATTATTATTATAAATTAG-GTATATATTTTTATTATATACGTATATGTATTTATATTTATACAT
* * * *
5427282 AGTATTATTTTTTAATTACTTTATTTTAATATTTTTATTATATTATATTTTCTTTTTTTGTATTT
65 AGTATTATTTTTTAATTACTTTACTTTAATATTTTTATTATATTACATTTGC-CTTTTTGTATTT
5427347 CAATATTATTACTAT
129 CAATATTATTACTAT
*
5427362 TATTATTATTATTAATATTA-GTATATATTTTTATTATATATGTATATGTATTTATATTTATACA
1 TATTATTATTA-TAA-ATTAGGTATATATTTTTATTATATACGTATATGTATTTATATTTATACA
5427426 TAGTATTATTTTTTAATTACTTTACTTTAATATTTTTATTATATTACATTTGCCTTTTTGTATTT
64 TAGTATTATTTTTTAATTACTTTACTTTAATATTTTTATTATATTACATTTGCCTTTTTGTATTT
*
5427491 CAATATTATTATTAT
129 CAATATTATTACTAT
5427506 TATTATTATT
1 TATTATTATT
5427516 GTAACGCCCC
Statistics
Matches: 144, Mismatches: 8, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
144 35 0.24
145 102 0.71
146 3 0.02
147 4 0.03
ACGTcount: A:0.30, C:0.04, G:0.04, T:0.61
Consensus pattern (143 bp):
TATTATTATTATAAATTAGGTATATATTTTTATTATATACGTATATGTATTTATATTTATACATA
GTATTATTTTTTAATTACTTTACTTTAATATTTTTATTATATTACATTTGCCTTTTTGTATTTCA
ATATTATTACTAT
Found at i:5427885 original size:26 final size:26
Alignment explanation
Indices: 5427848--5427931 Score: 150
Period size: 26 Copynumber: 3.2 Consensus size: 26
5427838 TGATACAAAT
* *
5427848 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTTCA
5427874 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
5427900 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATGGGTTAGGTAAATGTTTCA
5427926 TGATAA
1 TGATAA
5427932 GAATTTCATG
Statistics
Matches: 56, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
26 56 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTTCA
Found at i:5429465 original size:25 final size:25
Alignment explanation
Indices: 5429417--5429465 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
5429407 ACAGTTTTAC
5429417 CCCTAGGAGATAAATTACCGAAATA
1 CCCTAGGAGATAAATTACCGAAATA
* *
5429442 CCCTAGG-GTTAAATTGACCTAAAT
1 CCCTAGGAGATAAATT-ACCGAAAT
5429466 GCATGTTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 7 0.33
25 14 0.67
ACGTcount: A:0.39, C:0.20, G:0.16, T:0.24
Consensus pattern (25 bp):
CCCTAGGAGATAAATTACCGAAATA
Found at i:5430582 original size:3 final size:3
Alignment explanation
Indices: 5430574--5430620 Score: 60
Period size: 3 Copynumber: 15.7 Consensus size: 3
5430564 GGGTGCTACA
* *
5430574 ATT ATT ATT ATT ATT ATT ATT ATT AAT ATT AGT ATAT ATT -TT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT AT-T ATT ATT ATT
5430619 AT
1 AT
5430621 ATATGTATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
2 2 0.05
3 33 0.87
4 3 0.08
ACGTcount: A:0.36, C:0.00, G:0.02, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:5430854 original size:119 final size:121
Alignment explanation
Indices: 5430630--5430865 Score: 316
Period size: 119 Copynumber: 1.9 Consensus size: 121
5430620 TATATGTATA
* * * * * *
5430630 TGTATTTATATTTATACATAGTATTATTTTTTAATTACTTTATTTTAATATTTTTATTATATTAC
1 TGTATATATATTTATACATAATACTATTCTTTAATTACTTTATTTTAACATTATTATTATATTAC
*
5430695 ATTTGCTTTTTGTATTTCAATATTATTACTATTATTATTATCATTATTATTAATATTAG
66 --TT-CTTTTTGTATTTCAATATTATTACTAGTATTATTATCATTATTATTAATATTAG
*
5430754 TGTATATATATTTATATATAATACTA-TCTTTAATTACTTTATTTTAACATTATTATTATATTTA
1 TGTATATATATTTATACATAATACTATTCTTTAATTACTTTATTTTAACATTATTATTATA-TTA
* * *
5430818 C-T-TTTTTGTATTTCATTATTATTGCTAGTATTATTATTATTATTATTA
65 CTTCTTTTTGTATTTCAATATTATTACTAGTATTATTATCATTATTATTA
5430866 GTGTATGTTT
Statistics
Matches: 100, Mismatches: 11, Indels: 7
0.85 0.09 0.06
Matches are distributed among these distances:
119 42 0.42
121 1 0.01
123 31 0.31
124 26 0.26
ACGTcount: A:0.31, C:0.06, G:0.04, T:0.59
Consensus pattern (121 bp):
TGTATATATATTTATACATAATACTATTCTTTAATTACTTTATTTTAACATTATTATTATATTAC
TTCTTTTTGTATTTCAATATTATTACTAGTATTATTATCATTATTATTAATATTAG
Found at i:5430857 original size:6 final size:6
Alignment explanation
Indices: 5430832--5431153 Score: 74
Period size: 6 Copynumber: 53.2 Consensus size: 6
5430822 TTTGTATTTC
** *
5430832 ATTATT ATTGCT AGTATT ATTATT ATTATT ATTAGTGT ATGT-TT -TTATT
1 ATTATT ATTATT ATTATT ATTATT ATTATT ATTA-T-T AT-TATT ATTATT
* *
5430881 ATATAGGT A-TATAT ATATATT -TATATAT AGTATT ATT-TT -TTAATT
1 AT-TA-TT ATTAT-T AT-TATT AT-TAT-T ATTATT ATTATT ATT-ATT
* * *
5430926 ATT-TT ATT-TT AATATT ATTATT A-TATT ATGT-TT -TTTTGT ATT-TC
1 ATTATT ATTATT ATTATT ATTATT ATTATT AT-TATT ATTAT-T ATTATT
* * *
5430970 ATTATT ATT-TCT AGTATT ATTATT ATTATT ATTATT AATATT AGTA-T
1 ATTATT ATTAT-T ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT
* * *
5431017 ATGTTTT ATTATAT ATGTATAT ATATATT -TATATAT AGTATT ATTTTT
1 AT-TATT ATTAT-T AT-TAT-T AT-TATT AT-TAT-T ATTATT ATTATT
* * *
5431065 AATTACT -TTATT -TTAAT ATTATT ATTA-T ATTA-T ATTTACTT -TTTTGT
1 -ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT A-TTA-TT ATTAT-T
* * * * * *
5431112 ATT-TC ATTACT ATTGTT AGTATT ATTATC ATTATT AATATT A
1 ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT ATTATT A
5431154 GTGTATGTTT
Statistics
Matches: 236, Mismatches: 42, Indels: 76
0.67 0.12 0.21
Matches are distributed among these distances:
4 4 0.02
5 46 0.19
6 134 0.57
7 32 0.14
8 19 0.08
9 1 0.00
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (6 bp):
ATTATT
Found at i:5430928 original size:14 final size:14
Alignment explanation
Indices: 5430911--5431006 Score: 54
Period size: 14 Copynumber: 6.6 Consensus size: 14
5430901 TTATATATAG
5430911 TATTATT-TTTTAA
1 TATTATTATTTTAA
5430924 TTATT-TTATTTTAA
1 -TATTATTATTTTAA
* *
5430938 TATTATTATTATAT
1 TATTATTATTTTAA
* *
5430952 TATGT-TTTTTTGTATT
1 TAT-TATTATTT-TA-A
*
5430968 TCATTATTATTTCTAG
1 T-ATTATTATTT-TAA
*
5430984 TATTATTATTATTAT
1 TATTATTATT-TTAA
5430999 TATTATTA
1 TATTATTA
5431007 ATATTAGTAT
Statistics
Matches: 66, Mismatches: 8, Indels: 15
0.74 0.09 0.17
Matches are distributed among these distances:
13 6 0.09
14 24 0.36
15 22 0.33
16 5 0.08
17 9 0.14
ACGTcount: A:0.28, C:0.02, G:0.03, T:0.67
Consensus pattern (14 bp):
TATTATTATTTTAA
Found at i:5430988 original size:138 final size:136
Alignment explanation
Indices: 5430857--5431241 Score: 506
Period size: 142 Copynumber: 2.7 Consensus size: 136
5430847 ATTATTATTA
*
5430857 TTATTATTAGTGTATGTTTTTATTATATAGGTATATATATATATTTATATATAGTATTATTTTTT
1 TTATTATTAGTGTATGTTTTTATTATATA-GTGTATATATATATTTATATATAGTATTA-TTTTT
* *
5430922 AATTATTTTATTTTAATATTATTATTATATTATGTTTTTTTGTATTTCATTATTATTTCTAGTAT
64 AATTACTTTATTTTAATATTATTATTATATTATATTTTTTTGTATTTCATTATTATTTCTAG---
5430987 TATTATTATTA
126 TATTATTATTA
* *
5430998 TTATTATTAATATTAGTATATGTTTTATTATATA-TGTATATATATATTTATATATAGTATTATT
1 TTATTA-T--TAGT-GTATGT-TTTTATTATATAGTGTATATATATATTTATATATAGTATTATT
*
5431062 TTTAATTACTTTATTTTAATATTATTATTATATTATATTTACTTTTTTGTATTTCATTACTATTG
61 TTTAATTACTTTATTTTAATATTATTATTATATTATA--T--TTTTTTGTATTTCATTATTATT-
5431127 T-TAGTATTATTATCATTA
121 TCTAGTATTA-T-T-ATTA
* * *
5431145 TTAATATTAGTGTATGTTTTTATTATAT-GTGTGTATATATATTTATATACAGTATTATTTTTAA
1 TTATTATTAGTGTATGTTTTTATTATATAGTGTATATATATATTTATATATAGTATTATTTTTAA
5431209 TTACTTTATTTTAATATTATTATTATATTATAT
66 TTACTTTATTTTAATATTATTATTATATTATAT
5431242 GCCTTCCTTT
Statistics
Matches: 219, Mismatches: 11, Indels: 29
0.85 0.04 0.11
Matches are distributed among these distances:
140 1 0.00
141 6 0.03
142 77 0.35
143 42 0.19
144 38 0.17
145 7 0.03
146 14 0.06
147 33 0.15
148 1 0.00
ACGTcount: A:0.31, C:0.02, G:0.06, T:0.61
Consensus pattern (136 bp):
TTATTATTAGTGTATGTTTTTATTATATAGTGTATATATATATTTATATATAGTATTATTTTTAA
TTACTTTATTTTAATATTATTATTATATTATATTTTTTTGTATTTCATTATTATTTCTAGTATTA
TTATTA
Found at i:5437571 original size:46 final size:44
Alignment explanation
Indices: 5437512--5437626 Score: 149
Period size: 44 Copynumber: 2.6 Consensus size: 44
5437502 ACAGGACAGA
* *
5437512 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATT--AAATATGGCATTGGAG
* *
5437558 ACAGGATTGAGCCATGTAAGTCCATATTATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
* **
5437602 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
5437627 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
44 35 0.57
46 26 0.43
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAATATGGCATTGGAG
Found at i:5437607 original size:44 final size:45
Alignment explanation
Indices: 5437512--5437645 Score: 153
Period size: 46 Copynumber: 3.0 Consensus size: 45
5437502 ACAGGACAGA
* *
5437512 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTTTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCATTGGAG
* *
5437558 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCATTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
* ** * * *
5437602 ACAGGAATAATTCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAA-ATATGGCATTGG
5437646 CAGGATATTG
Statistics
Matches: 74, Mismatches: 12, Indels: 4
0.82 0.13 0.04
Matches are distributed among these distances:
44 36 0.49
45 1 0.01
46 37 0.50
ACGTcount: A:0.35, C:0.14, G:0.24, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCATTGGAG
Found at i:5439215 original size:21 final size:21
Alignment explanation
Indices: 5439191--5439232 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
5439181 CGATATCGCT
5439191 CACCTCCAAACTT-TTATTATC
1 CACC-CCAAACTTCTTATTATC
*
5439212 CACCCCAAAGTTCTTATTATC
1 CACCCCAAACTTCTTATTATC
5439233 AAGCACCTCC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.29, C:0.33, G:0.02, T:0.36
Consensus pattern (21 bp):
CACCCCAAACTTCTTATTATC
Found at i:5446258 original size:77 final size:77
Alignment explanation
Indices: 5446131--5446419 Score: 445
Period size: 77 Copynumber: 3.7 Consensus size: 77
5446121 CATAAAAAAT
* *
5446131 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTAGGGTCACACGCTGAGGTATCTTTAGT
1 AAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATCTTTAGT
5446196 TCCTATTTTTCA
66 TCCTATTTTTCA
* *
5446208 AAAAAATCAACTCATATTGCGAGAGGTGAGTTGAGCCTCGGGTCACACGCTAAGGTATCTTTAGT
1 AAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATCTTTAGT
5446273 TCCTATTTTTCA
66 TCCTATTTTTCA
** *
5446285 AAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCTAGTCACACGTTGAGGTAT-TTTCAG
1 AAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATCTTT-AG
*
5446349 TTTCTATTTTTTCAA
65 TTCCTA-TTTTTC-A
* **
5446364 AAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCAGGTCACATACTGAGGT
1 AAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGT
5446420 GTTTTCAATT
Statistics
Matches: 196, Mismatches: 13, Indels: 4
0.92 0.06 0.02
Matches are distributed among these distances:
76 3 0.02
77 135 0.69
78 6 0.03
79 52 0.27
ACGTcount: A:0.30, C:0.18, G:0.21, T:0.31
Consensus pattern (77 bp):
AAAAAATCAACTCATATTACGAGAGGTGAGTTGAGCCTCGGGTCACACGCTGAGGTATCTTTAGT
TCCTATTTTTCA
Found at i:5446770 original size:28 final size:28
Alignment explanation
Indices: 5446727--5446783 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
5446717 AGTTGCATGA
5446727 AGTGGACCGAAACAACAAGACGCAGTGG
1 AGTGGACCGAAACAACAAGACGCAGTGG
* *
5446755 AGTGGACCGAAGCAACCAGACGCAGTGG
1 AGTGGACCGAAACAACAAGACGCAGTGG
5446783 A
1 A
5446784 CTAGAACGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.37, C:0.23, G:0.33, T:0.07
Consensus pattern (28 bp):
AGTGGACCGAAACAACAAGACGCAGTGG
Found at i:5447134 original size:13 final size:13
Alignment explanation
Indices: 5447116--5447140 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
5447106 CCCTATACCT
5447116 AAAACAAAAAAAC
1 AAAACAAAAAAAC
5447129 AAAACAAAAAAA
1 AAAACAAAAAAA
5447141 AAGAAAAACC
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:0.88, C:0.12, G:0.00, T:0.00
Consensus pattern (13 bp):
AAAACAAAAAAAC
Found at i:5447546 original size:7 final size:8
Alignment explanation
Indices: 5447531--5447557 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
5447521 TATTAAAAGT
5447531 ATAAAAAA
1 ATAAAAAA
5447539 ATAAAAAA
1 ATAAAAAA
5447547 ATAAAAAA
1 ATAAAAAA
5447555 ATA
1 ATA
5447558 TACGGTGGCC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.85, C:0.00, G:0.00, T:0.15
Consensus pattern (8 bp):
ATAAAAAA
Found at i:5448092 original size:3 final size:3
Alignment explanation
Indices: 5448068--5448118 Score: 54
Period size: 3 Copynumber: 17.7 Consensus size: 3
5448058 TGTCTAACAC
* *
5448068 TAT TAT TTT TAT T-T T-T TA- TAT TAT TAT TAT TAC TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5448113 ATAT TA
1 -TAT TA
5448119 GTGTATATTT
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
2 6 0.15
3 32 0.78
4 3 0.07
ACGTcount: A:0.31, C:0.02, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:5448246 original size:3 final size:3
Alignment explanation
Indices: 5448231--5448623 Score: 213
Period size: 3 Copynumber: 133.0 Consensus size: 3
5448221 TGTATTTCAA
*
5448231 TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
5448279 TAT TAT TAT TAT TAT TAG TAT ATAT TTT TAT TAT ATAT GTA- TAT GTAT
1 TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT -TAT -TAT TAT -TAT
* * * *
5448327 T-T ATAT TTT TACA TAG TAT TAT T-T T-T TAAT TAC T-T TAT T-T TGA-
1 TAT -TAT TAT TA-T TAT TAT TAT TAT TAT T-AT TAT TAT TAT TAT T-AT
* ** * * * *
5448370 TAT TTT TAT TA- TAT TA- TAT T-T GCT TTT TTT GTAT T-T CAA TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT TAT TAT TAT
* *
5448412 TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAG TAT ATAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT -TAT
* * *
5448458 TTT TAT TAT ATAT GTA- TAT GTAT T-T ATAT T-T ATACA TAG TAT TAT
1 TAT TAT TAT -TAT -TAT TAT -TAT TAT -TAT TAT -TA-T TAT TAT TAT
* * * *
5448503 T-T T-T TAAT TAC T-T TAT T-T TAA TAT TTT TAT TA- TAT TA- CAT
1 TAT TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
** * *
5448543 T-T GCT T-T T-T GTAT T-T CAA TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT -TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5448585 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
5448624 ATTCGTATAT
Statistics
Matches: 305, Mismatches: 48, Indels: 74
0.71 0.11 0.17
Matches are distributed among these distances:
2 36 0.12
3 234 0.77
4 35 0.11
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.63
Consensus pattern (3 bp):
TAT
Found at i:5448353 original size:154 final size:157
Alignment explanation
Indices: 5448195--5448935 Score: 552
Period size: 154 Copynumber: 4.7 Consensus size: 157
5448185 TATTTTAATA
*
5448195 TTTTT-ATTA-TATTATATTTGCTTTTTTGTATTTCAATATTA-TTACTATTATTATTATTATTA
1 TTTTTAATTATTATTATATTTGCTTTTTTGTATTTCATTATTATTTACTATTATTATTATTATTA
5448257 TTATTATTATTATTATTATTATTATTATTATTATTATTAGTATATATTTTTATTATATATGTATA
66 TTATTATTATTATTATTATTATTATTATTATTATTATTAGTATATATTTTTATTATATATGTATA
5448322 TGTATTTATATTTTTACATAGTATTAT
131 TGTATTTATATTTTTACATAGTATTAT
* * * * *
5448349 TTTTTAATTACT-TTAT-TTTGATATTTT-TATTAT-ATTA-TATTTGCT-TT-TTTTGTATTTC
1 TTTTTAATTATTATTATATTTGCTTTTTTGTATT-TCATTATTATTTACTATTATTAT-TA-TT-
* *
5448407 AATATTATTACTATTATTATTATTATTATTATTATTATTATTAGTATATATTTTTATTATATATG
62 ATTATTATTATTATTATTATTATTATTATTATTATTATTATTAGTATATATTTTTATTATATATG
*
5448472 TATATGTATTTATATTTATACATAGTATTAT
127 TATATGTATTTATATTTTTACATAGTATTAT
* ** * * *
5448503 TTTTTAATTACTTTATTTTAATATTT-TTATTATATTACATTTGCTTTTTGTATTTCAATATTAT
1 TTTTTAATTA--TTA--TT-ATATTTGCT-TT-T-TTGTATTT-CATTAT-TATTT-ACTATTAT
* **
5448567 TATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATATTCGTAT
55 TATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTAGTA-TATATTTTTAT
* * * *
5448632 ATATATATTTATATATA-ATACTATTTTTA-ATTACT-TTA-
119 -TATATATGTATATGTATTTA-TATTTTTACA-TAGTATTAT
* * * * *
5448670 TTTTAACATTATTATTATATTTACTTTTTTGTATTTCATTATTA-TTGCTAGTACTATTATTATT
1 TTTTTA-ATTATTATTATATTTGCTTTTTTGTATTTCATTATTATTTACTATTATTATTATTATT
* * * * * *
5448734 ATTA--A-TACTAGT-GTATGT-TT-TTATTA-TA-TA--GGTATATATATATATT-TATA--TA
65 ATTATTATTATTATTATTAT-TATTATTATTATTATTATTAGTATATATTTTTATTATATATGTA
5448786 TA-GTA-TTAT-TTTTTA-AT--TACTT-T
129 TATGTATTTATATTTTTACATAGTA-TTAT
* * *
5448809 ATTTTAA-TATTATTATATTATGTTTTTTTTGTATTTCATTATTATTTCAAGTATTATTATTATT
1 TTTTTAATTATTATTATATT-TG-CTTTTTTGTATTTCATTATTATTT--ACTATTATTATTATT
* *
5448873 ATTAATATTAGTATATGTTTTATTATATATGTATATATATATT-TATATATAGTAT-TATTTTTA
62 ATTATTATTA-T-TAT-TATTATTAT-TAT-TAT-TAT-TATTAT-TAT-TAGTATATATTTTTA
5448936 ATTACTTTAT
Statistics
Matches: 465, Mismatches: 64, Indels: 112
0.73 0.10 0.17
Matches are distributed among these distances:
137 13 0.03
138 2 0.00
139 27 0.06
140 9 0.02
141 1 0.00
142 21 0.05
143 4 0.01
144 1 0.00
145 4 0.01
146 1 0.00
147 10 0.02
148 4 0.01
149 4 0.01
150 3 0.01
151 6 0.01
152 13 0.03
153 21 0.05
154 126 0.27
155 10 0.02
156 4 0.01
157 18 0.04
158 8 0.02
159 8 0.02
160 7 0.02
161 10 0.02
162 2 0.00
163 11 0.02
164 6 0.01
165 2 0.00
166 3 0.01
167 53 0.11
168 22 0.05
169 28 0.06
170 3 0.01
ACGTcount: A:0.31, C:0.03, G:0.04, T:0.61
Consensus pattern (157 bp):
TTTTTAATTATTATTATATTTGCTTTTTTGTATTTCATTATTATTTACTATTATTATTATTATTA
TTATTATTATTATTATTATTATTATTATTATTATTATTAGTATATATTTTTATTATATATGTATA
TGTATTTATATTTTTACATAGTATTAT
Found at i:5448409 original size:178 final size:178
Alignment explanation
Indices: 5448068--5448492 Score: 695
Period size: 177 Copynumber: 2.4 Consensus size: 178
5448058 TGTCTAACAC
* * *
5448068 TATTATTTTTATT-TT-TTA-TATTATTATTATTACTATTATTATTATATATTAGTGTATATTTT
1 TATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATATATTAGTATATATTTT
5448130 TATTATATACGTATATGTATTTATATTTTTACATAGTATTATTTTTTAATTACTTTATTTTAATA
66 TATTATATACGTATATGTATTTATATTTTTACATAGTATTATTTTTTAATTACTTTATTTTAATA
5448195 TTTTTATTATATTATATTTGCTTTTTTGTATTTCAATATTATTACTAT
131 TTTTTATTATATTATATTTGCTTTTTTGTATTTCAATATTATTACTAT
5448243 TATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTAT-TATTAGTATATATTTT
1 TATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATATATTAGTATATATTTT
* *
5448307 TATTATATATGTATATGTATTTATATTTTTACATAGTATTATTTTTTAATTACTTTATTTTGATA
66 TATTATATACGTATATGTATTTATATTTTTACATAGTATTATTTTTTAATTACTTTATTTTAATA
5448372 TTTTTATTATATTATATTTGCTTTTTTTGTATTTCAATATTATTACTAT
131 TTTTTATTATATTATATTTGC-TTTTTTGTATTTCAATATTATTACTAT
* * *
5448421 TATTATTATTATTATTATTATTATTATTAGTA-TA-TATTTTTATTATATATGTA-TATGTATTT
1 TATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATATAT-TAGTATATATTT
*
5448483 ATATT-TATAC
65 TTATTATATAC
5448493 ATAGTATTAT
Statistics
Matches: 234, Mismatches: 10, Indels: 11
0.92 0.04 0.04
Matches are distributed among these distances:
175 12 0.05
176 17 0.07
177 119 0.51
178 86 0.37
ACGTcount: A:0.30, C:0.03, G:0.04, T:0.63
Consensus pattern (178 bp):
TATTATTATTATTATTATTATTATTATTATTATTATTATTATTATTATATATTAGTATATATTTT
TATTATATACGTATATGTATTTATATTTTTACATAGTATTATTTTTTAATTACTTTATTTTAATA
TTTTTATTATATTATATTTGCTTTTTTGTATTTCAATATTATTACTAT
Found at i:5448908 original size:124 final size:129
Alignment explanation
Indices: 5448772--5449063 Score: 335
Period size: 142 Copynumber: 2.2 Consensus size: 129
5448762 TAGGTATATA
*
5448772 TATATATTTATATATAGTAT-TATTTTTTAATTACTTTATTTTAA-TATTATTATA-T-TATGT-
1 TATATATGTATATATA-TATATATTTTTTAATTACTTTATTTTAATTATTATTATATTATATGTA
* *
5448832 TTTTTTTGTATTTCATTATTATT-TCAAGTATTATTATTATTATTAATATTAGTATATGTTTTAT
65 TTTTTTTGTATTTCATTACTATTGT-AAGTATTATTATCATTATTAATATTAGTATATG-TTT-T
5448896 TAT
127 TAT
*
5448899 ATATGTATATATATATTTATATATAGTATTATTTTTAATTACTTTATTTTAATATTATTATTATA
1 -TA--TATATGTATA--TATATATA-TA-T-TTTTTAATTACTTTATTTT-A-ATTATTATTATA
* * *
5448964 TTATATTTACTTTTTTTGTATTTCATTACTATTGTTAGTATTATTATCATTATTAATATTAGTGT
56 TTATATGTA-TTTTTTTGTATTTCATTACTATTGTAAGTATTATTATCATTATTAATATTAGTAT
5449029 ATGTTTTTAT
120 ATGTTTTTAT
*
5449039 TATATGTGTATATATATATATATTT
1 TATATATGTATATATATATATATTT
5449064 ATATATAGTA
Statistics
Matches: 140, Mismatches: 8, Indels: 28
0.80 0.05 0.16
Matches are distributed among these distances:
128 2 0.01
130 9 0.06
131 3 0.02
132 6 0.04
133 3 0.02
134 3 0.02
135 27 0.19
136 1 0.01
137 9 0.06
138 10 0.07
139 3 0.02
140 8 0.06
141 3 0.02
142 52 0.37
143 1 0.01
ACGTcount: A:0.31, C:0.03, G:0.05, T:0.61
Consensus pattern (129 bp):
TATATATGTATATATATATATATTTTTTAATTACTTTATTTTAATTATTATTATATTATATGTAT
TTTTTTGTATTTCATTACTATTGTAAGTATTATTATCATTATTAATATTAGTATATGTTTTTAT
Found at i:5451462 original size:12 final size:12
Alignment explanation
Indices: 5451445--5451471 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
5451435 TTGGTAGACT
5451445 AATTCATTGGCA
1 AATTCATTGGCA
5451457 AATTCATTGGCA
1 AATTCATTGGCA
5451469 AAT
1 AAT
5451472 GCTGGACTGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.37, C:0.15, G:0.15, T:0.33
Consensus pattern (12 bp):
AATTCATTGGCA
Found at i:5455347 original size:18 final size:18
Alignment explanation
Indices: 5455328--5455396 Score: 93
Period size: 18 Copynumber: 3.8 Consensus size: 18
5455318 CCCAACTACT
* *
5455328 GTATACGTGAACAGTACT
1 GTATACGTGAATAGTACC
* *
5455346 GTATATGTAAATAGTACC
1 GTATACGTGAATAGTACC
*
5455364 GTATACATGAATAGTACC
1 GTATACGTGAATAGTACC
5455382 GTATACGTGAATAGT
1 GTATACGTGAATAGT
5455397 GTCATAAATG
Statistics
Matches: 43, Mismatches: 8, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
18 43 1.00
ACGTcount: A:0.36, C:0.13, G:0.20, T:0.30
Consensus pattern (18 bp):
GTATACGTGAATAGTACC
Found at i:5461021 original size:2 final size:2
Alignment explanation
Indices: 5461014--5461043 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
5461004 ATGTATACAT
*
5461014 TA TA TA TA TA TA TA TA TG TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5461044 CTATGTGCAT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5461390 original size:2 final size:2
Alignment explanation
Indices: 5461335--5461377 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
5461325 TATTGTACTA
5461335 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5461376 AT
1 AT
5461378 TTCTTTCATA
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 39 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:5464302 original size:44 final size:45
Alignment explanation
Indices: 5464219--5464341 Score: 149
Period size: 44 Copynumber: 2.7 Consensus size: 45
5464209 CAGAAATGAG
* * *
5464219 CCATGTAAGTCCATATTAGAAATATGGCTTTGGAGACAGGATTGAT
1 CCATGTAAGTCCATATTA-AAATATGGCATTGGAGACAGGAATAAT
*
5464265 CCATGTAAGTCCATATT-ATATATGGCATTGGAGACAGGAATAAT
1 CCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGGAATAAT
* * * *
5464309 TCATGTAAGTCCATGTCAAAGACATGGCATTGG
1 CCATGTAAGTCCATATTAAA-ATATGGCATTGG
5464342 CAGGATATTG
Statistics
Matches: 66, Mismatches: 9, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
44 37 0.56
45 1 0.02
46 28 0.42
ACGTcount: A:0.33, C:0.15, G:0.23, T:0.29
Consensus pattern (45 bp):
CCATGTAAGTCCATATTAAAATATGGCATTGGAGACAGGAATAAT
Found at i:5467883 original size:18 final size:18
Alignment explanation
Indices: 5467860--5467902 Score: 61
Period size: 18 Copynumber: 2.3 Consensus size: 18
5467850 CAATGTTTTT
5467860 TTGCATTCATTGCATC-CA
1 TTGCATTCA-TGCATCACA
5467878 TTGCATTCATGCATCAGCA
1 TTGCATTCATGCATCA-CA
5467897 TTGCAT
1 TTGCAT
5467903 CATACGCACT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 6 0.26
18 9 0.39
19 8 0.35
ACGTcount: A:0.23, C:0.26, G:0.14, T:0.37
Consensus pattern (18 bp):
TTGCATTCATGCATCACA
Found at i:5474757 original size:26 final size:25
Alignment explanation
Indices: 5474721--5474830 Score: 157
Period size: 26 Copynumber: 4.2 Consensus size: 25
5474711 TGATACAAAT
5474721 TGATAATAGGTTAGGTAAATGTTCAA
1 TGATAATAGGTTAGGTAAATGTTC-A
5474747 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTT-CA
*
5474773 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATG-TTCA
*
5474799 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATG-TTCA
*
5474825 TTATAA
1 TGATAA
5474831 GAATTTCATG
Statistics
Matches: 80, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
26 77 0.96
27 3 0.04
ACGTcount: A:0.35, C:0.05, G:0.24, T:0.37
Consensus pattern (25 bp):
TGATAATAGGTTAGGTAAATGTTCA
Found at i:5476316 original size:28 final size:26
Alignment explanation
Indices: 5476274--5476348 Score: 87
Period size: 26 Copynumber: 2.8 Consensus size: 26
5476264 AAAAGTAGCT
* *
5476274 AAATTACTATAATACCCCTATGTATGGA
1 AAATTACTGTTATACCCCTA-G-ATGGA
* *
5476302 AAATTACTGTTATACCCCTAGGTGTA
1 AAATTACTGTTATACCCCTAGATGGA
*
5476328 AAATTACCGTTATACCCCTAG
1 AAATTACTGTTATACCCCTAG
5476349 GGTTAATTTT
Statistics
Matches: 42, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
26 23 0.55
27 1 0.02
28 18 0.43
ACGTcount: A:0.35, C:0.21, G:0.12, T:0.32
Consensus pattern (26 bp):
AAATTACTGTTATACCCCTAGATGGA
Found at i:5476493 original size:27 final size:27
Alignment explanation
Indices: 5476452--5476591 Score: 156
Period size: 27 Copynumber: 5.2 Consensus size: 27
5476442 GAGGAAGCGT
*
5476452 TCTGGTGGCTATGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
*
5476479 TCTGATGGCTCTGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
5476506 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* * * *
5476533 TCTGGTGGCCCTACCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
5476561 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
5476587 TCTGG
1 TCTGG
5476592 CAGCCATGCT
Statistics
Matches: 96, Mismatches: 16, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
26 5 0.05
27 78 0.81
28 13 0.14
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.34
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:5476557 original size:54 final size:55
Alignment explanation
Indices: 5476452--5476591 Score: 176
Period size: 54 Copynumber: 2.6 Consensus size: 55
5476442 GAGGAAGCGT
* * * * * *
5476452 TCTGGTGGCTATGCCACAAATATCTGATCTGATGGCTCTGCCACAAATATCTG-A
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCCCTACCACAAATATCTGTA
* *
5476506 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCCCTACCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCCCTACCACAAATATCTGTA
* *
5476561 TCTGGTGACTCTGTCACAT-TATCTGTTCTGG
1 TCTGGTGGCTCTGCCACATATATCTGTTCTGG
5476592 CAGCCATGCT
Statistics
Matches: 75, Mismatches: 10, Indels: 2
0.86 0.11 0.02
Matches are distributed among these distances:
54 57 0.76
55 18 0.24
ACGTcount: A:0.19, C:0.25, G:0.21, T:0.34
Consensus pattern (55 bp):
TCTGGTGGCTCTGCCACATATATCTGTTCTGGTGGCCCTACCACAAATATCTGTA
Found at i:5479149 original size:43 final size:43
Alignment explanation
Indices: 5479102--5479257 Score: 140
Period size: 43 Copynumber: 3.6 Consensus size: 43
5479092 TTACAGATCT
*
5479102 TAAACCCCTAAGCAGTAAGGAAACAGATCGAAGATGGT-GAGCC
1 TAAACCCCTAAGCAGTAGGGAAACAGATCGAAGAT-GTAGAGCC
* * * *
5479145 TAAACCCCTAAGCAGTAGGGTAACAG-GCTGAAGATGTACAGATCT
1 TAAACCCCTAAGCAGTAGGGAAACAGATC-GAAGATGT--AGAGCC
* * *
5479190 TAACCCCCTAAGCAGTAGGGAAACAGATCGAA-A-GTAACAAGCT
1 TAAACCCCTAAGCAGTAGGGAAACAGATCGAAGATGT-A-GAGCC
* *
5479233 TTAACCCCTAAGCAGTAGGGTAACA
1 TAAACCCCTAAGCAGTAGGGAAACA
5479258 AGCTGAATTT
Statistics
Matches: 93, Mismatches: 14, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
42 4 0.04
43 57 0.61
44 1 0.01
45 30 0.32
46 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.23, T:0.17
Consensus pattern (43 bp):
TAAACCCCTAAGCAGTAGGGAAACAGATCGAAGATGTAGAGCC
Found at i:5479212 original size:88 final size:87
Alignment explanation
Indices: 5479064--5479298 Score: 303
Period size: 88 Copynumber: 2.7 Consensus size: 87
5479054 GGCTTTAACG
* *
5479064 CCCTAAGCAGTAGGGTAACAAGCTG-AATTTACAGATCTTAAACCCCTAAGCAGTAAGGAAACAG
1 CCCTAAGCAGTAGGGTAACAAGCTGAAATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAG
****
5479128 ATCG-AAGATGGTGAGCCTAAAC
66 ATCGAAAG-TAACAAGCCTAAAC
* *
5479150 CCCTAAGCAGTAGGGTAACAGGCTGAAGATGTACAGATCTTAACCCCCTAAGCAGTAGGGAAACA
1 CCCTAAGCAGTAGGGTAACAAGCTGAA-ATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACA
* *
5479215 GATCGAAAGTAACAAGCTTTAAC
65 GATCGAAAGTAACAAGCCTAAAC
* * * * *
5479238 CCCTAAGCAGTAGGGTAACAAGCTGAATTTTAAAGATTTTATCACCCTAAGCAGTAGGGAA
1 CCCTAAGCAGTAGGGTAACAAGCTGAAATTTACAGATCTTAACCCCCTAAGCAGTAGGGAA
5479299 GTAGATCAAA
Statistics
Matches: 129, Mismatches: 17, Indels: 5
0.85 0.11 0.03
Matches are distributed among these distances:
86 24 0.19
87 29 0.22
88 73 0.57
89 3 0.02
ACGTcount: A:0.37, C:0.20, G:0.22, T:0.20
Consensus pattern (87 bp):
CCCTAAGCAGTAGGGTAACAAGCTGAAATTTACAGATCTTAACCCCCTAAGCAGTAGGGAAACAG
ATCGAAAGTAACAAGCCTAAAC
Found at i:5479475 original size:88 final size:88
Alignment explanation
Indices: 5479366--5479527 Score: 218
Period size: 88 Copynumber: 1.8 Consensus size: 88
5479356 CCACCAAACC
* * * * * *
5479366 TTAAACCCCTAAGCAGTAGGGTAAC-AGGTTAAATTTACAATATCTTAACCCCCTAAGCAGTAGG
1 TTAAACCCCTAAGAAGCAGGGTAACAAGCTGAAATTTA-AAGATCTTAACACCCTAAGCAGTAGG
5479430 GAAACAGATCGAAGGCAACAAGCT
65 GAAACAGATCGAAGGCAACAAGCT
* * *
5479454 TTAACCCCCTAAGAAGCAGGGTAACAAGCTGAATTTTAAAGATCTTATCACCCTAAGCAGTAGGG
1 TTAAACCCCTAAGAAGCAGGGTAACAAGCTGAAATTTAAAGATCTTAACACCCTAAGCAGTAGGG
*
5479519 AAGCAGATC
66 AAACAGATC
5479528 AAAAGAAGGT
Statistics
Matches: 63, Mismatches: 10, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
88 54 0.86
89 9 0.14
ACGTcount: A:0.38, C:0.22, G:0.20, T:0.21
Consensus pattern (88 bp):
TTAAACCCCTAAGAAGCAGGGTAACAAGCTGAAATTTAAAGATCTTAACACCCTAAGCAGTAGGG
AAACAGATCGAAGGCAACAAGCT
Found at i:5479531 original size:222 final size:222
Alignment explanation
Indices: 5479145--5479658 Score: 816
Period size: 222 Copynumber: 2.3 Consensus size: 222
5479135 ATGGTGAGCC
5479145 TAAACCCCTAAGCAGTAGGGTAACAGGCTGAAGATGTACAGATCTTAACCCCCTAAGCAGTAGGG
1 TAAACCCCTAAGCAGTAGGGTAACAGGCTGAAGATGTACAGATCTTAACCCCCTAAGCAGTAGGG
* * *
5479210 AAACAGATCGAAAGTAACAAGCTTTAACCCCTAAGCAGTAGGGTAACAAGCTGAATTTTAAAGAT
66 AAACAGATCGAAAGCAACAAGCTTTAACCCCTAAGAAGCAGGGTAACAAGCTGAATTTTAAAGAT
* * *
5479275 TTTATCACCCTAAGCAGTAGGGAAGTAGATCAAAAGACGGTGAATCTTGCCCTCCTGAAATTGCA
131 CTTATCACCCTAAGCAGTAGGGAAGCAGATCAAAAGAAGGTGAATCTTGCCCTCCTGAAATTGCA
5479340 GTGAAGCAGATTCAAACCACCAAACCT
196 GTGAAGCAGATTCAAACCACCAAACCT
* * *
5479367 TAAACCCCTAAGCAGTAGGGTAACAGG-TTAA-ATTTACAATATCTTAACCCCCTAAGCAGTAGG
1 TAAACCCCTAAGCAGTAGGGTAACAGGCTGAAGATGTAC-AGATCTTAACCCCCTAAGCAGTAGG
*
5479430 GAAACAGATCGAAGGCAACAAGCTTTAACCCCCTAAGAAGCAGGGTAACAAGCTGAATTTTAAAG
65 GAAACAGATCGAAAGCAACAAGCTTTAA-CCCCTAAGAAGCAGGGTAACAAGCTGAATTTTAAAG
*
5479495 ATCTTATCACCCTAAGCAGTAGGGAAGCAGATCAAAAGAAGGTGAATCTTGCCCTCCTGAAGTTG
129 ATCTTATCACCCTAAGCAGTAGGGAAGCAGATCAAAAGAAGGTGAATCTTGCCCTCCTGAAATTG
* *
5479560 CAGTGAAGTAGATTCAAACCACCAAGCCT
194 CAGTGAAGCAGATTCAAACCACCAAACCT
* * * * * *
5479589 TAACCCCCTAAGCAGTAGGGAAACAGGCTGAAGATCTACAGATCTTATCACCCTAAACAGTAGGG
1 TAAACCCCTAAGCAGTAGGGTAACAGGCTGAAGATGTACAGATCTTAACCCCCTAAGCAGTAGGG
*
5479654 TAACA
66 AAACA
5479659 AGCCAAATTT
Statistics
Matches: 266, Mismatches: 22, Indels: 7
0.90 0.07 0.02
Matches are distributed among these distances:
220 5 0.02
221 53 0.20
222 174 0.65
223 29 0.11
224 5 0.02
ACGTcount: A:0.37, C:0.22, G:0.20, T:0.20
Consensus pattern (222 bp):
TAAACCCCTAAGCAGTAGGGTAACAGGCTGAAGATGTACAGATCTTAACCCCCTAAGCAGTAGGG
AAACAGATCGAAAGCAACAAGCTTTAACCCCTAAGAAGCAGGGTAACAAGCTGAATTTTAAAGAT
CTTATCACCCTAAGCAGTAGGGAAGCAGATCAAAAGAAGGTGAATCTTGCCCTCCTGAAATTGCA
GTGAAGCAGATTCAAACCACCAAACCT
Found at i:5479686 original size:43 final size:45
Alignment explanation
Indices: 5479586--5479699 Score: 126
Period size: 43 Copynumber: 2.6 Consensus size: 45
5479576 AACCACCAAG
* * * *
5479586 CCTTAACCCCCTAAGCAGTAGGGAAACAGGCTGAAGATCTACAGA
1 CCTTAAACCCCTAAGCAGTAGGGTAACAAGCTCAAGATCTACAGA
* * * *
5479631 TCTT-ATCACCCTAAACAGTAGGGTAACAAGC-CAA-ATTTACAGA
1 CCTTAAAC-CCCTAAGCAGTAGGGTAACAAGCTCAAGATCTACAGA
5479674 CCTTAAACCCCTAAGCAGTAGGGTAA
1 CCTTAAACCCCTAAGCAGTAGGGTAA
5479700 TAGGCTAAAA
Statistics
Matches: 57, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
43 28 0.49
44 6 0.11
45 23 0.40
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.19
Consensus pattern (45 bp):
CCTTAAACCCCTAAGCAGTAGGGTAACAAGCTCAAGATCTACAGA
Found at i:5481561 original size:2 final size:2
Alignment explanation
Indices: 5481556--5481601 Score: 60
Period size: 2 Copynumber: 24.0 Consensus size: 2
5481546 ATATATTTTT
* *
5481556 TA TA TA T- TA TG TA TA CA T- TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5481596 TA TA TA
1 TA TA TA
5481602 CTATGTGCAT
Statistics
Matches: 38, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
1 2 0.05
2 36 0.95
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (2 bp):
TA
Found at i:5481570 original size:11 final size:11
Alignment explanation
Indices: 5481545--5481601 Score: 64
Period size: 11 Copynumber: 5.4 Consensus size: 11
5481535 TATATGCATG
* *
5481545 TATATATTTTT
1 TATATATTATA
*
5481556 TATATATTATG
1 TATATATTATA
*
5481567 TATACATTATA
1 TATATATTATA
5481578 TATATA-TATA
1 TATATATTATA
5481588 TATATA-TATA
1 TATATATTATA
5481598 TATA
1 TATA
5481602 CTATGTGCAT
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
10 18 0.44
11 23 0.56
ACGTcount: A:0.42, C:0.02, G:0.02, T:0.54
Consensus pattern (11 bp):
TATATATTATA
Found at i:5493200 original size:26 final size:26
Alignment explanation
Indices: 5493164--5493299 Score: 229
Period size: 26 Copynumber: 5.2 Consensus size: 26
5493154 CATGATATTC
5493164 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
5493190 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
* *
5493216 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGAAACATTTACCTAACCCA
5493242 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGAAACATTTACCTAACCCA
*
5493268 TTATCAT-AGAACATTTACCTAACCTA
1 TTATCATGA-AACATTTACCTAACCCA
5493294 TTATCA
1 TTATCA
5493300 ATTTGTATCA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
25 1 0.01
26 103 0.99
ACGTcount: A:0.38, C:0.25, G:0.04, T:0.33
Consensus pattern (26 bp):
TTATCATGAAACATTTACCTAACCCA
Found at i:5494571 original size:12 final size:12
Alignment explanation
Indices: 5494554--5494578 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
5494544 CACAACATGC
5494554 ATGGTATTAAAA
1 ATGGTATTAAAA
5494566 ATGGTATTAAAA
1 ATGGTATTAAAA
5494578 A
1 A
5494579 AACATAATAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.16, T:0.32
Consensus pattern (12 bp):
ATGGTATTAAAA
Found at i:5494750 original size:3 final size:3
Alignment explanation
Indices: 5494744--5494798 Score: 110
Period size: 3 Copynumber: 18.3 Consensus size: 3
5494734 ACACTACTAT
5494744 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
5494792 ATA ATA A
1 ATA ATA A
5494799 AGAAATACAA
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 52 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5495114 original size:19 final size:20
Alignment explanation
Indices: 5495087--5495124 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
5495077 AGTATTAGAA
5495087 TAAAAATAA-AAAATAAATG
1 TAAAAATAATAAAATAAATG
* *
5495106 TAAACATAATAATATAAAT
1 TAAAAATAATAAAATAAAT
5495125 AAGATAAATA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (20 bp):
TAAAAATAATAAAATAAATG
Found at i:5497832 original size:13 final size:14
Alignment explanation
Indices: 5497814--5497842 Score: 51
Period size: 13 Copynumber: 2.1 Consensus size: 14
5497804 GATTAACTTC
5497814 ATAAATATTTT-TA
1 ATAAATATTTTCTA
5497827 ATAAATATTTTCTA
1 ATAAATATTTTCTA
5497841 AT
1 AT
5497843 CCATTTTTCA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.73
14 4 0.27
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.52
Consensus pattern (14 bp):
ATAAATATTTTCTA
Found at i:5500115 original size:13 final size:13
Alignment explanation
Indices: 5500080--5500157 Score: 58
Period size: 12 Copynumber: 6.1 Consensus size: 13
5500070 TATATATTAT
5500080 ATAAT-TTATATAA
1 ATAATATTA-ATAA
* *
5500093 CATAAAATTAATAT
1 -ATAATATTAATAA
*
5500107 ATAATATT-ATAGT
1 ATAATATTAATA-A
5500120 ATAAATATTAA-AA
1 AT-AATATTAATAA
5500133 AT-ATATTAATAA
1 ATAATATTAATAA
5500145 ATAAT-TTAATAA
1 ATAATATTAATAA
5500157 A
1 A
5500158 AGAAAAAACA
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
11 7 0.13
12 15 0.28
13 14 0.26
14 14 0.26
15 4 0.07
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (13 bp):
ATAATATTAATAA
Found at i:5500196 original size:26 final size:29
Alignment explanation
Indices: 5500167--5500226 Score: 90
Period size: 26 Copynumber: 2.2 Consensus size: 29
5500157 AAGAAAAAAC
*
5500167 ATATAAAATTATT-AA-AT-TTAAATTTA
1 ATATAAAATTATTAAACATATAAAATTTA
5500193 ATATAAAATTATTAAACATATAAAATTTA
1 ATATAAAATTATTAAACATATAAAATTTA
5500222 ATATA
1 ATATA
5500227 TAATATTTGC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 13 0.43
27 2 0.07
28 2 0.07
29 13 0.43
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (29 bp):
ATATAAAATTATTAAACATATAAAATTTA
Found at i:5503627 original size:2 final size:2
Alignment explanation
Indices: 5503620--5503651 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
5503610 ACACCACCTA
5503620 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5503652 GTTTTTAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:5505571 original size:21 final size:21
Alignment explanation
Indices: 5505547--5505589 Score: 52
Period size: 21 Copynumber: 2.0 Consensus size: 21
5505537 AATAAAAATG
*
5505547 ATAATCATGAG-AATAATATAA
1 ATAAT-ATGAGAAATAAAATAA
*
5505568 ATAATATTAGAAATAAAATAA
1 ATAATATGAGAAATAAAATAA
5505589 A
1 A
5505590 ATAGCAAGGA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.63, C:0.02, G:0.07, T:0.28
Consensus pattern (21 bp):
ATAATATGAGAAATAAAATAA
Found at i:5515606 original size:26 final size:26
Alignment explanation
Indices: 5515570--5515679 Score: 177
Period size: 26 Copynumber: 4.2 Consensus size: 26
5515560 TGATACAAAT
5515570 TGATAATAGGTTAGGTAAATG-TTCAA
1 TGATAATAGGTTAGGTAAATGTTTC-A
*
5515596 TGATAATAGGTTAGGTAAATGTTCCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
5515622 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
*
5515648 TGATAATGGGTTAGGTAAATGTTTCA
1 TGATAATAGGTTAGGTAAATGTTTCA
5515674 TGATAA
1 TGATAA
5515680 GAATTTCATG
Statistics
Matches: 80, Mismatches: 3, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
26 78 0.98
27 2 0.03
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.36
Consensus pattern (26 bp):
TGATAATAGGTTAGGTAAATGTTTCA
Found at i:5517337 original size:27 final size:27
Alignment explanation
Indices: 5517299--5517411 Score: 138
Period size: 27 Copynumber: 4.2 Consensus size: 27
5517289 GAGGAAGCGT
5517299 TCTGGTGGCTCTGCCACAAATATCTGA
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
5517326 TCTGGTGGCTCTGCCACATATATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
* *
5517353 TCTGGTGGCTCTGCCACGATTATCTGTA
1 TCTGGTGGCTCTGCCACAAATATCTG-A
* * * *
5517381 TCTGGTGACTCTGTCAC-ATTATCTGT
1 TCTGGTGGCTCTGCCACAAATATCTGA
5517407 TCTGG
1 TCTGG
5517412 CAGCCATGCT
Statistics
Matches: 76, Mismatches: 9, Indels: 3
0.86 0.10 0.03
Matches are distributed among these distances:
26 5 0.07
27 56 0.74
28 15 0.20
ACGTcount: A:0.16, C:0.25, G:0.23, T:0.36
Consensus pattern (27 bp):
TCTGGTGGCTCTGCCACAAATATCTGA
Found at i:5517404 original size:54 final size:54
Alignment explanation
Indices: 5517297--5517411 Score: 178
Period size: 54 Copynumber: 2.1 Consensus size: 54
5517287 TGGAGGAAGC
*
5517297 GTTCTGGTGGCTCTGCCACAAATATCTGATCTGGTGGCTCTGCCACATATATCT
1 GTTCTGGTGGCTCTGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
* * *
5517351 GTTCTGGTGGCTCTGCCACGATTATCTGTATCTGGTGACTCTGTCACAT-TATCT
1 GTTCTGGTGGCTCTGCCACAAATATCTG-ATCTGGTGACTCTGCCACATATATCT
5517405 GTTCTGG
1 GTTCTGG
5517412 CAGCCATGCT
Statistics
Matches: 56, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
54 38 0.68
55 18 0.32
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (54 bp):
GTTCTGGTGGCTCTGCCACAAATATCTGATCTGGTGACTCTGCCACATATATCT
Found at i:5528070 original size:13 final size:13
Alignment explanation
Indices: 5528035--5528112 Score: 58
Period size: 12 Copynumber: 6.1 Consensus size: 13
5528025 TATATATTAT
5528035 ATAAT-TTATATAA
1 ATAATATTA-ATAA
* *
5528048 CATAAAATTAATAT
1 -ATAATATTAATAA
*
5528062 ATAATATT-ATAGT
1 ATAATATTAATA-A
5528075 ATAAATATTAA-AA
1 AT-AATATTAATAA
5528088 AT-ATATTAATAA
1 ATAATATTAATAA
5528100 ATAAT-TTAATAA
1 ATAATATTAATAA
5528112 A
1 A
5528113 AGAAAAAACA
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
11 7 0.13
12 15 0.28
13 14 0.26
14 14 0.26
15 4 0.07
ACGTcount: A:0.58, C:0.01, G:0.01, T:0.40
Consensus pattern (13 bp):
ATAATATTAATAA
Found at i:5528151 original size:26 final size:29
Alignment explanation
Indices: 5528122--5528181 Score: 90
Period size: 26 Copynumber: 2.2 Consensus size: 29
5528112 AAGAAAAAAC
*
5528122 ATATAAAATTATT-AA-AT-TTAAATTTA
1 ATATAAAATTATTAAACATATAAAATTTA
5528148 ATATAAAATTATTAAACATATAAAATTTA
1 ATATAAAATTATTAAACATATAAAATTTA
5528177 ATATA
1 ATATA
5528182 TAATATTTGC
Statistics
Matches: 30, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
26 13 0.43
27 2 0.07
28 2 0.07
29 13 0.43
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (29 bp):
ATATAAAATTATTAAACATATAAAATTTA
Found at i:5531582 original size:2 final size:2
Alignment explanation
Indices: 5531575--5531623 Score: 98
Period size: 2 Copynumber: 24.5 Consensus size: 2
5531565 CAACACCACC
5531575 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5531617 TA TA TA T
1 TA TA TA T
5531624 TTTTTAAAAT
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 47 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5533314 original size:2 final size:2
Alignment explanation
Indices: 5533307--5533349 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
5533297 ATAGTATGAA
5533307 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5533349 A
1 A
5533350 GTGTTAGAAT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:5539444 original size:14 final size:15
Alignment explanation
Indices: 5539425--5539457 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
5539415 GATATTTGTA
5539425 TTTCTTTTT-TTCTT
1 TTTCTTTTTCTTCTT
*
5539439 TTTCTTTTTCTTTTT
1 TTTCTTTTTCTTCTT
5539454 TTTC
1 TTTC
5539458 CTTCTTTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 9 0.53
15 8 0.47
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTCTTTTTCTTCTT
Found at i:5540190 original size:21 final size:22
Alignment explanation
Indices: 5540155--5540198 Score: 56
Period size: 21 Copynumber: 2.0 Consensus size: 22
5540145 TATATATTAA
5540155 ATTAAAATTAAATTAATCT-TTTT
1 ATTAAAA-TAAATT-ATCTATTTT
5540178 ATTAAAA-AAATTATCTATTTT
1 ATTAAAATAAATTATCTATTTT
5540199 TACTTTTAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
20 4 0.20
21 9 0.45
23 7 0.35
ACGTcount: A:0.45, C:0.05, G:0.00, T:0.50
Consensus pattern (22 bp):
ATTAAAATAAATTATCTATTTT
Found at i:5541270 original size:3 final size:3
Alignment explanation
Indices: 5541258--5541317 Score: 59
Period size: 3 Copynumber: 20.3 Consensus size: 3
5541248 TCTTGGACCT
* * * *
5541258 ATC A-C ATC ATC ATC ACC ATC CTC ATC ATG TTC ATC ATC ATC ATC ATC
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC
* *
5541305 AAC ACC ATC ATC A
1 ATC ATC ATC ATC A
5541318 AAGGGCTTGA
Statistics
Matches: 45, Mismatches: 11, Indels: 2
0.78 0.19 0.03
Matches are distributed among these distances:
2 2 0.04
3 43 0.96
ACGTcount: A:0.33, C:0.37, G:0.02, T:0.28
Consensus pattern (3 bp):
ATC
Found at i:5549338 original size:38 final size:38
Alignment explanation
Indices: 5549288--5549364 Score: 154
Period size: 38 Copynumber: 2.0 Consensus size: 38
5549278 GAAAGCATCG
5549288 TCGTCTCCCATGGAAGAAGTGGAAAAATGTTGTAGAGA
1 TCGTCTCCCATGGAAGAAGTGGAAAAATGTTGTAGAGA
5549326 TCGTCTCCCATGGAAGAAGTGGAAAAATGTTGTAGAGA
1 TCGTCTCCCATGGAAGAAGTGGAAAAATGTTGTAGAGA
5549364 T
1 T
5549365 TTGAATAGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
38 39 1.00
ACGTcount: A:0.34, C:0.13, G:0.29, T:0.25
Consensus pattern (38 bp):
TCGTCTCCCATGGAAGAAGTGGAAAAATGTTGTAGAGA
Found at i:5555618 original size:3 final size:3
Alignment explanation
Indices: 5555610--5555910 Score: 84
Period size: 3 Copynumber: 98.3 Consensus size: 3
5555600 TGGGTAAAAT
* * *
5555610 ATA ATA ATA ATA ATA AT- ATA ATA GTA GTA ATA ATA GTA ATA ATA AGGTA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A--TA
* * * * * *
5555659 ACAA ATA ATA ATG ACA ATA GTA ATC ATA ATA ATA AT- ATA AGTC ATA
1 A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A-TA ATA
** * * *
5555705 AT- ATA AGTAA ATA CGGA GAGA AT- ATGT ATA ATA A-C ATA ATA ATA
1 ATA ATA A-T-A ATA -ATA -ATA ATA AT-A ATA ATA ATA ATA ATA ATA
* * * * * *
5555749 ACTA TATA A-A TTA ATTA AT- CTA ATA A-A ATG ATG ATA ATA CTA GTA
1 A-TA -ATA ATA ATA A-TA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
* * * * *
5555794 ATA ATA ATA A-A GTGGA A-A ACA ATA ATA ATA ATA CATTA GTA AGA AGA
1 ATA ATA ATA ATA AT--A ATA ATA ATA ATA ATA ATA -A-TA ATA ATA ATA
* * * * **
5555841 AAA ACA AT- ATA TTT ATA ATA ACG ATAA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA
*
5555886 ATA ATA ATA ATA ATA ATA ATG ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA A
5555911 GTTAAACTAA
Statistics
Matches: 219, Mismatches: 53, Indels: 52
0.68 0.16 0.16
Matches are distributed among these distances:
2 18 0.08
3 171 0.78
4 21 0.10
5 9 0.04
ACGTcount: A:0.57, C:0.04, G:0.08, T:0.30
Consensus pattern (3 bp):
ATA
Found at i:5555946 original size:8 final size:7
Alignment explanation
Indices: 5555864--5555942 Score: 55
Period size: 6 Copynumber: 12.1 Consensus size: 7
5555854 TATAATAACG
*
5555864 ATAAATA
1 ATAAGTA
5555871 ATAA-TA
1 ATAAGTA
5555877 ATAA-TA
1 ATAAGTA
5555883 ATAA-TA
1 ATAAGTA
5555889 ATAA-TA
1 ATAAGTA
5555895 ATAA-TA
1 ATAAGTA
*
5555901 ATAA-TG
1 ATAAGTA
*
5555907 ATAAGTT
1 ATAAGTA
*
5555914 A-AACTA
1 ATAAGTA
*
5555920 ATTAGTA
1 ATAAGTA
5555927 ATGAAGTA
1 AT-AAGTA
5555935 ATAAGTA
1 ATAAGTA
5555942 A
1 A
5555943 ATAAATAGAA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
6 39 0.63
7 17 0.27
8 6 0.10
ACGTcount: A:0.59, C:0.01, G:0.08, T:0.32
Consensus pattern (7 bp):
ATAAGTA
Found at i:5556271 original size:3 final size:3
Alignment explanation
Indices: 5556195--5556251 Score: 98
Period size: 3 Copynumber: 19.0 Consensus size: 3
5556185 ATGTATAAAT
5556195 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA TATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA -ATA ATA ATA ATA
5556241 ATA ATA A-A ATA
1 ATA ATA ATA ATA
5556252 GAGCAACCAA
Statistics
Matches: 52, Mismatches: 0, Indels: 4
0.93 0.00 0.07
Matches are distributed among these distances:
2 2 0.04
3 47 0.90
4 3 0.06
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:5556395 original size:3 final size:3
Alignment explanation
Indices: 5556387--5556413 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
5556377 AGCAAACTAG
5556387 TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA
5556414 GCTTAATAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:5557057 original size:2 final size:2
Alignment explanation
Indices: 5557050--5557092 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
5557040 AATATGTATT
5557050 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
5557092 T
1 T
5557093 GTGTGTGTGT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:5557349 original size:6 final size:6
Alignment explanation
Indices: 5557338--5557364 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
5557328 AAATATTACA
5557338 TTTGAT TTTGAT TTTGAT TTTGAT TTT
1 TTTGAT TTTGAT TTTGAT TTTGAT TTT
5557365 TCTTTCTTAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.15, C:0.00, G:0.15, T:0.70
Consensus pattern (6 bp):
TTTGAT
Found at i:5558598 original size:37 final size:35
Alignment explanation
Indices: 5558557--5558645 Score: 81
Period size: 39 Copynumber: 2.4 Consensus size: 35
5558547 TTCTAAACAT
*
5558557 TAAAAATATTTATATTAAAAA-ACTACCATAGATATAA
1 TAAAAAT-TTTATATTAAAAACACTA--ATAAATATAA
*
5558594 TAAAATGTTTTATTATATTAAAAACACTAATAAATATAA
1 TAAAA---ATT-TTATATTAAAAACACTAATAAATATAA
*
5558633 TAAATATTTTATA
1 TAAAAATTTTATA
5558646 GTATTAAATA
Statistics
Matches: 43, Mismatches: 4, Indels: 12
0.73 0.07 0.20
Matches are distributed among these distances:
35 5 0.12
36 2 0.05
37 5 0.12
39 14 0.33
40 13 0.30
41 4 0.09
ACGTcount: A:0.54, C:0.06, G:0.02, T:0.38
Consensus pattern (35 bp):
TAAAAATTTTATATTAAAAACACTAATAAATATAA
Found at i:5558652 original size:38 final size:39
Alignment explanation
Indices: 5558566--5558653 Score: 110
Period size: 38 Copynumber: 2.3 Consensus size: 39
5558556 TTAAAAATAT
* *
5558566 TTATATTAAAAAACTACCATAGATATAATAAAATGTTTTA
1 TTATATTAAAAAACTA-CATAAATATAATAAAATATTTTA
5558606 TTATATTAAAAACACTA-ATAAATATAAT-AAATATTTTA
1 TTATATTAAAAA-ACTACATAAATATAATAAAATATTTTA
5558644 -TAGTATTAAA
1 TTA-TATTAAA
5558654 TATAATTTTT
Statistics
Matches: 44, Mismatches: 2, Indels: 6
0.85 0.04 0.12
Matches are distributed among these distances:
37 2 0.05
38 16 0.36
39 10 0.23
40 12 0.27
41 4 0.09
ACGTcount: A:0.52, C:0.06, G:0.03, T:0.39
Consensus pattern (39 bp):
TTATATTAAAAAACTACATAAATATAATAAAATATTTTA
Found at i:5560233 original size:22 final size:23
Alignment explanation
Indices: 5560186--5560233 Score: 62
Period size: 22 Copynumber: 2.1 Consensus size: 23
5560176 TATATTAATA
* * *
5560186 TTACATTACATATATTTGTTTTT
1 TTACATTACATATATATATTTGT
5560209 TTACA-TACATATATATATTTGT
1 TTACATTACATATATATATTTGT
5560231 TTA
1 TTA
5560234 TGTATATACT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
22 17 0.77
23 5 0.23
ACGTcount: A:0.31, C:0.08, G:0.04, T:0.56
Consensus pattern (23 bp):
TTACATTACATATATATATTTGT
Found at i:5560719 original size:21 final size:18
Alignment explanation
Indices: 5560695--5560739 Score: 56
Period size: 17 Copynumber: 2.4 Consensus size: 18
5560685 ATATTATGTG
5560695 TATGTATTTCTAATACTATAT
1 TATGTATTTC--ATA-TATAT
5560716 TATGT-TTTCATATATAT
1 TATGTATTTCATATATAT
5560733 TATGTAT
1 TATGTAT
5560740 ATACTTTAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 10 0.43
18 4 0.17
20 4 0.17
21 5 0.22
ACGTcount: A:0.31, C:0.07, G:0.07, T:0.56
Consensus pattern (18 bp):
TATGTATTTCATATATAT
Found at i:5561351 original size:26 final size:26
Alignment explanation
Indices: 5561313--5561423 Score: 204
Period size: 26 Copynumber: 4.3 Consensus size: 26
5561303 ATTGATACAA
5561313 ATGATAATGGGTTAGGTAAATGTTTC
1 ATGATAATGGGTTAGGTAAATGTTTC
* *
5561339 ATGATAATAGGTTAGGTAAATGTTCC
1 ATGATAATGGGTTAGGTAAATGTTTC
5561365 ATGATAATGGGTTAGGTAAATGTTTC
1 ATGATAATGGGTTAGGTAAATGTTTC
5561391 ATGATAATGGGTTAGGTAAATGTTTC
1 ATGATAATGGGTTAGGTAAATGTTTC
5561417 ATGATAA
1 ATGATAA
5561424 GAATATCATG
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
26 81 1.00
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
ATGATAATGGGTTAGGTAAATGTTTC
Found at i:5562611 original size:8 final size:8
Alignment explanation
Indices: 5562598--5562633 Score: 54
Period size: 8 Copynumber: 4.5 Consensus size: 8
5562588 CTAGATCGGC
5562598 AAAAGCCG
1 AAAAGCCG
5562606 AAAAGCCG
1 AAAAGCCG
*
5562614 AAATGCCG
1 AAAAGCCG
*
5562622 AAATGCCG
1 AAAAGCCG
5562630 AAAA
1 AAAA
5562634 CTGGTATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
8 26 1.00
ACGTcount: A:0.50, C:0.22, G:0.22, T:0.06
Consensus pattern (8 bp):
AAAAGCCG
Found at i:5563454 original size:135 final size:137
Alignment explanation
Indices: 5563211--5563495 Score: 520
Period size: 135 Copynumber: 2.1 Consensus size: 137
5563201 GAGTAGTCTC
5563211 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
*
5563276 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCT-TGGCCCAGTATC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
5563340 ACTGTTA
131 ACTGTTA
*
5563347 CCCAAATGGGCTTGCATATG-TTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
5563411 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
5563476 ACTGTTA
131 ACTGTTA
**
5563483 CCTGAATGGGCTT
1 CCCAAATGGGCTT
5563496 AGGCCCAATG
Statistics
Matches: 144, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
135 95 0.66
136 49 0.34
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.32
Consensus pattern (137 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
TGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
ACTGTTA
Found at i:5567306 original size:26 final size:26
Alignment explanation
Indices: 5567265--5567426 Score: 281
Period size: 26 Copynumber: 6.3 Consensus size: 26
5567255 ATTGATACAA
5567265 ATGATAAT-GGTTAGGTAAATGTTTC
1 ATGATAATGGGTTAGGTAAATGTTTC
* *
5567290 ATGATAATAGGTTAGGTAAATGTTCC
1 ATGATAATGGGTTAGGTAAATGTTTC
5567316 ATGATAATGGGTTAGGTAAATGTTTC
1 ATGATAATGGGTTAGGTAAATGTTTC
* *
5567342 ATGATAATAGGTTAGGTAAATGTTCC
1 ATGATAATGGGTTAGGTAAATGTTTC
5567368 ATGATAATGGGTTAGGTAAATGTTTC
1 ATGATAATGGGTTAGGTAAATGTTTC
5567394 ATGATAATGGGTTAGGTAAATGTTTC
1 ATGATAATGGGTTAGGTAAATGTTTC
5567420 ATGATAA
1 ATGATAA
5567427 GAATATCATG
Statistics
Matches: 129, Mismatches: 7, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
25 8 0.06
26 121 0.94
ACGTcount: A:0.33, C:0.05, G:0.25, T:0.37
Consensus pattern (26 bp):
ATGATAATGGGTTAGGTAAATGTTTC
Found at i:5569490 original size:136 final size:136
Alignment explanation
Indices: 5569210--5569483 Score: 487
Period size: 135 Copynumber: 2.0 Consensus size: 136
5569200 GAGTAGTCTC
5569210 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
* * *
5569275 CGTTATCTGAATAAGGGGCTAAGGCCCAGTTTATTGTAATTGAAAAGGGCTTTGGCCCAGTATCA
66 CGTTATCTGAATAAGAGGCTAAGGCCCAGTTTATTGTAATTGAAAAGGGCTCTGGCCCAGTACCA
5569340 CTGTTA
131 CTGTTA
*
5569346 CCCAAATGGGCTTGCATATG-TTATTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
1 CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
*
5569410 TGTTATCTGAATAAGAGGCTAAGGCCCAGTTTATTGTAATCTGAAAAGGGCTCTGGCCCAGTACC
66 CGTTATCTGAATAAGAGGCTAAGGCCCAGTTTATTGTAAT-TGAAAAGGGCTCTGGCCCAGTACC
5569475 ACTGTTA
130 ACTGTTA
5569482 CC
1 CC
5569484 TGAATGGACT
Statistics
Matches: 132, Mismatches: 5, Indels: 2
0.95 0.04 0.01
Matches are distributed among these distances:
135 81 0.61
136 51 0.39
ACGTcount: A:0.25, C:0.19, G:0.24, T:0.32
Consensus pattern (136 bp):
CCCAAATGGGCTTGCATATGTTTACTGATGTTGCATGTATTTTGAAATGGGCCTATGGGCCATAC
CGTTATCTGAATAAGAGGCTAAGGCCCAGTTTATTGTAATTGAAAAGGGCTCTGGCCCAGTACCA
CTGTTA
Found at i:5572417 original size:21 final size:20
Alignment explanation
Indices: 5572393--5572434 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
5572383 AAAATTATAT
*
5572393 TATATTATAATTTATAATTTA
1 TATATTATAATTT-TAAATTA
*
5572414 TATATTATTATTTTAAATTA
1 TATATTATAATTTTAAATTA
5572434 T
1 T
5572435 TTAAATTTCA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 7 0.37
21 12 0.63
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TATATTATAATTTTAAATTA
Found at i:5573218 original size:22 final size:24
Alignment explanation
Indices: 5573166--5573219 Score: 58
Period size: 22 Copynumber: 2.3 Consensus size: 24
5573156 TTTTTTATGA
5573166 TTAAATTATTGTTATTAAATATGCT
1 TTAAATTATTGTTATT-AATATGCT
* **
5573191 TGAAATTATTG-TATT-ATATTTT
1 TTAAATTATTGTTATTAATATGCT
5573213 TTAAATT
1 TTAAATT
5573220 GAATTTATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
22 11 0.44
24 4 0.16
25 10 0.40
ACGTcount: A:0.35, C:0.02, G:0.07, T:0.56
Consensus pattern (24 bp):
TTAAATTATTGTTATTAATATGCT
Found at i:5580058 original size:26 final size:26
Alignment explanation
Indices: 5579930--5580064 Score: 227
Period size: 26 Copynumber: 5.2 Consensus size: 26
5579920 CATGAAATTC
* *
5579930 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTA
* *
5579956 TTATCATGAAACATTTACCTAACCCA
1 TTATCATGGAACATTTACCTAACCTA
5579982 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
5580008 TTATCATGGAACATTTACCTAACCTA
1 TTATCATGGAACATTTACCTAACCTA
5580034 TTATCATGGAACATTTACCTAACCT-
1 TTATCATGGAACATTTACCTAACCTA
5580059 TTATCA
1 TTATCA
5580065 ATTTGTATCA
Statistics
Matches: 107, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
25 6 0.06
26 101 0.94
ACGTcount: A:0.36, C:0.24, G:0.06, T:0.34
Consensus pattern (26 bp):
TTATCATGGAACATTTACCTAACCTA
Found at i:5580804 original size:13 final size:13
Alignment explanation
Indices: 5580757--5580805 Score: 55
Period size: 13 Copynumber: 3.8 Consensus size: 13
5580747 CTTAATCAAA
* *
5580757 ATTTAATATATCA
1 ATTTAATATCTCT
*
5580770 ATATAATATCTCT
1 ATTTAATATCTCT
*
5580783 -TTAAATATCTCT
1 ATTTAATATCTCT
5580795 ATTTAATATCT
1 ATTTAATATCT
5580806 ACGGACTCGA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
12 10 0.34
13 19 0.66
ACGTcount: A:0.39, C:0.12, G:0.00, T:0.49
Consensus pattern (13 bp):
ATTTAATATCTCT
Found at i:5581368 original size:16 final size:16
Alignment explanation
Indices: 5581347--5581378 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
5581337 ACTAACGGAA
5581347 ATATAAATTTTTTATC
1 ATATAAATTTTTTATC
5581363 ATATAAATTTTTTATC
1 ATATAAATTTTTTATC
5581379 GTATTACTGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.56
Consensus pattern (16 bp):
ATATAAATTTTTTATC
Found at i:5582405 original size:12 final size:12
Alignment explanation
Indices: 5582388--5582423 Score: 56
Period size: 11 Copynumber: 3.0 Consensus size: 12
5582378 TATAAGTAAT
5582388 TAAAATTTAAAA
1 TAAAATTTAAAA
5582400 TAAAA-TTAAAA
1 TAAAATTTAAAA
5582411 TAAAATCTTAAAA
1 TAAAAT-TTAAAA
5582424 ACAATAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.50
12 5 0.23
13 6 0.27
ACGTcount: A:0.67, C:0.03, G:0.00, T:0.31
Consensus pattern (12 bp):
TAAAATTTAAAA
Found at i:5582470 original size:20 final size:21
Alignment explanation
Indices: 5582439--5582478 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
5582429 AAATTAAATC
*
5582439 TAATATTTATTTTTCGTTATA
1 TAATATTTATTTTTCATTATA
5582460 TAATA-TTATTTTTCATTAT
1 TAATATTTATTTTTCATTAT
5582479 TTTGATTAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (21 bp):
TAATATTTATTTTTCATTATA
Found at i:5582499 original size:21 final size:20
Alignment explanation
Indices: 5582467--5582506 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
5582457 ATATAATATT
* *
5582467 ATTTTTCATTATTTTGATTA
1 ATTTTTAATTATATTGATTA
5582487 ATTTTTAATTTATATTGATT
1 ATTTTTAA-TTATATTGATT
5582507 TATCAATTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 7 0.41
21 10 0.59
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.65
Consensus pattern (20 bp):
ATTTTTAATTATATTGATTA
Found at i:5587549 original size:26 final size:26
Alignment explanation
Indices: 5587497--5587549 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 26
5587487 TCTTAATTTT
*
5587497 AAAATTGAGTAAATTAACTCCTCTCAA
1 AAAATTGAGTAAATTAAC-CCTATCAA
*
5587524 AAAATTGGAGTAATTTAA-CCTATCAA
1 AAAATT-GAGTAAATTAACCCTATCAA
5587550 TTTTGAAAGT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
26 7 0.30
27 6 0.26
28 10 0.43
ACGTcount: A:0.45, C:0.15, G:0.09, T:0.30
Consensus pattern (26 bp):
AAAATTGAGTAAATTAACCCTATCAA
Found at i:5588327 original size:17 final size:17
Alignment explanation
Indices: 5588295--5588327 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
5588285 ATTTTTTGAA
*
5588295 TTTTGAATTTTTTTATT
1 TTTTGAATATTTTTATT
5588312 TTTTGAATATTTTTAT
1 TTTTGAATATTTTTAT
5588328 AAATTTTAAA
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:0.21, C:0.00, G:0.06, T:0.73
Consensus pattern (17 bp):
TTTTGAATATTTTTATT
Found at i:5589062 original size:2 final size:2
Alignment explanation
Indices: 5589055--5589082 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
5589045 AATCCACTTC
5589055 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5589083 TCATGGCTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.