Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr12 ID=Chr12-JGI_221_v2.0
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 35429946
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 509281 characters in sequence are not A, C, G, or T
File 14 of 120
Found at i:4082842 original size:16 final size:16
Alignment explanation
Indices: 4082823--4082901 Score: 56
Period size: 16 Copynumber: 4.9 Consensus size: 16
4082813 ATATAATAAT
4082823 TTATATTAATAATTTA
1 TTATATTAATAATTTA
* *
4082839 TTATTTTAATAAATTA
1 TTATATTAATAATTTA
*
4082855 TTTAATATTAA-ATTTTA
1 -TT-ATATTAATAATTTA
*
4082872 TT-TAATAATAAATTT-
1 TTATATTAAT-AATTTA
* *
4082887 TTAAAATAATAATTT
1 TTATATTAATAATTT
4082902 TAAATAATAT
Statistics
Matches: 50, Mismatches: 8, Indels: 11
0.72 0.12 0.16
Matches are distributed among these distances:
14 5 0.10
15 7 0.14
16 26 0.52
17 6 0.12
18 6 0.12
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (16 bp):
TTATATTAATAATTTA
Found at i:4082872 original size:17 final size:17
Alignment explanation
Indices: 4082852--4082887 Score: 63
Period size: 17 Copynumber: 2.1 Consensus size: 17
4082842 TTTTAATAAA
*
4082852 TTATTTAATATTAAATT
1 TTATTTAATAATAAATT
4082869 TTATTTAATAATAAATT
1 TTATTTAATAATAAATT
4082886 TT
1 TT
4082888 TAAAATAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTATTTAATAATAAATT
Found at i:4082901 original size:32 final size:31
Alignment explanation
Indices: 4082829--4082903 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 31
4082819 TAATTTATAT
*
4082829 TAATAATTTATTATTTTAATAAATTATTTAATA
1 TAATAA-TT-TTATTTTAATAAATTATTTAAAA
*
4082862 TTA-AATTTTATTTAATAATAAATT-TTTAAAA
1 TAATAATTTTATTT--TAATAAATTATTTAAAA
4082893 TAATAATTTTA
1 TAATAATTTTA
4082904 AATAATATTA
Statistics
Matches: 36, Mismatches: 3, Indels: 7
0.78 0.07 0.15
Matches are distributed among these distances:
30 6 0.17
31 10 0.28
32 18 0.50
33 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (31 bp):
TAATAATTTTATTTTAATAAATTATTTAAAA
Found at i:4082910 original size:16 final size:17
Alignment explanation
Indices: 4082857--4082910 Score: 58
Period size: 17 Copynumber: 3.3 Consensus size: 17
4082847 ATAAATTATT
* **
4082857 TAATATTAAATTTTATT
1 TAATAATAAATTTTAAA
*
4082874 TAATAATAAATTTTTAA
1 TAATAATAAATTTTAAA
4082891 -AATAAT-AATTTTAAA
1 TAATAATAAATTTTAAA
4082906 TAATA
1 TAATA
4082911 TTATATTATT
Statistics
Matches: 31, Mismatches: 5, Indels: 3
0.79 0.13 0.08
Matches are distributed among these distances:
15 8 0.26
16 10 0.32
17 13 0.42
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TAATAATAAATTTTAAA
Found at i:4082910 original size:32 final size:32
Alignment explanation
Indices: 4082845--4082920 Score: 82
Period size: 32 Copynumber: 2.4 Consensus size: 32
4082835 TTTATTATTT
* * **
4082845 TAATAAATTATTTAATATTAAATTTTATTTAA
1 TAATAAATTATTTAAAATAAAATTTTAAATAA
4082877 TAATAAATT-TTTAAAATAATAATTTTAAATAA
1 TAATAAATTATTTAAAATAA-AATTTTAAATAA
* *
4082909 TATTATATTATT
1 TAATAAATTATT
4082921 AGAAATATTC
Statistics
Matches: 36, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
31 8 0.22
32 26 0.72
33 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (32 bp):
TAATAAATTATTTAAAATAAAATTTTAAATAA
Found at i:4085183 original size:2 final size:2
Alignment explanation
Indices: 4085176--4085200 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4085166 TTAGGGTGTT
4085176 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
4085201 TAATTGGATG
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:4089005 original size:23 final size:23
Alignment explanation
Indices: 4088970--4089020 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
4088960 ACCTACTTTC
* *
4088970 TTACTGTAATAATTTTCGGGGTA
1 TTACAGTAATAATTTTCGGGATA
* *
4088993 TTACAGTAGTAATTTTTGGGATA
1 TTACAGTAATAATTTTCGGGATA
4089016 TTACA
1 TTACA
4089021 TGTGGAGACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.29, C:0.08, G:0.20, T:0.43
Consensus pattern (23 bp):
TTACAGTAATAATTTTCGGGATA
Found at i:4090836 original size:88 final size:89
Alignment explanation
Indices: 4090735--4090908 Score: 228
Period size: 88 Copynumber: 2.0 Consensus size: 89
4090725 ACAAATGCCA
*
4090735 AGTTCAAGAACTAACTTGAAAAAAAAAAGTTCAAGCCCCAATG-GAGGAATAATTATCT-AGTTC
1 AGTTCAAGAACTAACTTGAAAAAAAAAAGTTCAAGCCCCAATGTGA-GAACAATTATCTAAGTTC
4090798 ATGCCCTAATGT-GGAACAATTGTCG
65 A-GCCCTAATGTGGGAACAATTGTCG
* * * * * * *
4090823 AGTTCAAGGACTAACTTGGACAAAAAAAGTTCAAGCCCGAATGTGAGAACAATTGTCTAATTTGA
1 AGTTCAAGAACTAACTTGAAAAAAAAAAGTTCAAGCCCCAATGTGAGAACAATTATCTAAGTTCA
*
4090888 GCCCTAGTGTGGGAACAATTG
66 GCCCTAATGTGGGAACAATTG
4090909 CCTAATTCAG
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
88 58 0.78
89 16 0.22
ACGTcount: A:0.38, C:0.17, G:0.21, T:0.25
Consensus pattern (89 bp):
AGTTCAAGAACTAACTTGAAAAAAAAAAGTTCAAGCCCCAATGTGAGAACAATTATCTAAGTTCA
GCCCTAATGTGGGAACAATTGTCG
Found at i:4090891 original size:31 final size:31
Alignment explanation
Indices: 4090856--4090915 Score: 84
Period size: 31 Copynumber: 1.9 Consensus size: 31
4090846 AAAAAGTTCA
*
4090856 AGCCCGAATGTGAGAACAATTGTCTAATTTG
1 AGCCCGAATGTGAGAACAATTGCCTAATTTG
* * *
4090887 AGCCCTAGTGTGGGAACAATTGCCTAATT
1 AGCCCGAATGTGAGAACAATTGCCTAATT
4090916 CAGGCCTTAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 25 1.00
ACGTcount: A:0.30, C:0.18, G:0.23, T:0.28
Consensus pattern (31 bp):
AGCCCGAATGTGAGAACAATTGCCTAATTTG
Found at i:4097669 original size:16 final size:16
Alignment explanation
Indices: 4097648--4097681 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
4097638 GCAATACACA
4097648 TTTTGAAGAGATAAAT
1 TTTTGAAGAGATAAAT
4097664 TTTTGAAGAGATAAAT
1 TTTTGAAGAGATAAAT
4097680 TT
1 TT
4097682 CTGTAACTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.41, C:0.00, G:0.18, T:0.41
Consensus pattern (16 bp):
TTTTGAAGAGATAAAT
Found at i:4100033 original size:3 final size:3
Alignment explanation
Indices: 4100016--4100069 Score: 85
Period size: 3 Copynumber: 18.7 Consensus size: 3
4100006 TTAACAAAAT
*
4100016 TTC TTC TTG TT- TTC TTC -TC TTC TTC TTC TTC TTC TTC TTC TTC TTC
1 TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC TTC
4100062 TTC TTC TT
1 TTC TTC TT
4100070 TTTTATGAAT
Statistics
Matches: 48, Mismatches: 1, Indels: 4
0.91 0.02 0.08
Matches are distributed among these distances:
2 4 0.08
3 44 0.92
ACGTcount: A:0.00, C:0.30, G:0.02, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:4103850 original size:7 final size:7
Alignment explanation
Indices: 4103838--4103870 Score: 66
Period size: 7 Copynumber: 4.7 Consensus size: 7
4103828 TGTTAGAGTT
4103838 AAGGGTA
1 AAGGGTA
4103845 AAGGGTA
1 AAGGGTA
4103852 AAGGGTA
1 AAGGGTA
4103859 AAGGGTA
1 AAGGGTA
4103866 AAGGG
1 AAGGG
4103871 GTTTGTGAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 26 1.00
ACGTcount: A:0.42, C:0.00, G:0.45, T:0.12
Consensus pattern (7 bp):
AAGGGTA
Found at i:4106000 original size:27 final size:27
Alignment explanation
Indices: 4105969--4106031 Score: 117
Period size: 27 Copynumber: 2.3 Consensus size: 27
4105959 TAATATAGAT
4105969 GGTGCAATTTCGCTTAGCTCTTACTTG
1 GGTGCAATTTCGCTTAGCTCTTACTTG
4105996 GGTGCAATTTCGCTTAGCTCTTACTTG
1 GGTGCAATTTCGCTTAGCTCTTACTTG
*
4106023 GCTGCAATT
1 GGTGCAATT
4106032 GGGGGAGTCA
Statistics
Matches: 35, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.16, C:0.22, G:0.22, T:0.40
Consensus pattern (27 bp):
GGTGCAATTTCGCTTAGCTCTTACTTG
Found at i:4108204 original size:40 final size:40
Alignment explanation
Indices: 4108151--4108262 Score: 138
Period size: 40 Copynumber: 2.8 Consensus size: 40
4108141 ATAAATATTT
*
4108151 TATTTTTTT--ATTTTTTTAATTTTAAAATACTTTTCAAA
1 TATTTTTTTAAATTTTTTTAATTTTAAAATACTTTTAAAA
*
4108189 TATTTTTTTAAATTTTTTTAATTTTAAAATATTTTTAAAA
1 TATTTTTTTAAATTTTTTTAATTTTAAAATACTTTTAAAA
**
4108229 TACTTTTTAAAAATTTTATTTTAATTTTTAAAAT
1 TA-TTTTTTTAAA-TTT-TTTTAA-TTTTAAAAT
4108263 GAATTTTTGG
Statistics
Matches: 64, Mismatches: 4, Indels: 6
0.86 0.05 0.08
Matches are distributed among these distances:
38 9 0.14
40 29 0.45
41 8 0.12
42 3 0.05
43 6 0.09
44 9 0.14
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.62
Consensus pattern (40 bp):
TATTTTTTTAAATTTTTTTAATTTTAAAATACTTTTAAAA
Found at i:4108218 original size:17 final size:17
Alignment explanation
Indices: 4108193--4108226 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
4108183 TTCAAATATT
* *
4108193 TTTTTAAATTTTTTTAA
1 TTTTAAAATATTTTTAA
4108210 TTTTAAAATATTTTTAA
1 TTTTAAAATATTTTTAA
4108227 AATACTTTTT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTTTAAAATATTTTTAA
Found at i:4108235 original size:29 final size:29
Alignment explanation
Indices: 4108181--4108238 Score: 73
Period size: 29 Copynumber: 2.0 Consensus size: 29
4108171 TTTAAAATAC
* * *
4108181 TTTTCAAATATTTTTTTAAATTTTTTTAA
1 TTTTAAAATATTTTTTAAAATCTTTTTAA
4108210 TTTTAAAATA-TTTTTAAAATACTTTTTAA
1 TTTTAAAATATTTTTTAAAAT-CTTTTTAA
4108239 AAATTTTATT
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 9 0.36
29 16 0.64
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.60
Consensus pattern (29 bp):
TTTTAAAATATTTTTTAAAATCTTTTTAA
Found at i:4108237 original size:12 final size:11
Alignment explanation
Indices: 4108210--4108245 Score: 56
Period size: 11 Copynumber: 3.3 Consensus size: 11
4108200 ATTTTTTTAA
4108210 TTTTAAAATAT
1 TTTTAAAATAT
4108221 TTTTAAAATACT
1 TTTTAAAATA-T
4108233 TTTTAAAA-AT
1 TTTTAAAATAT
4108243 TTT
1 TTT
4108246 ATTTTAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
10 4 0.17
11 11 0.46
12 9 0.38
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.56
Consensus pattern (11 bp):
TTTTAAAATAT
Found at i:4110414 original size:26 final size:25
Alignment explanation
Indices: 4110385--4110439 Score: 67
Period size: 28 Copynumber: 2.1 Consensus size: 25
4110375 TATTTTTTAT
*
4110385 ATAC-TTTATAATTTATATATTCATAC
1 ATACATTTATAATATATATA-T-ATAC
4110411 ATACATTTTATAATATATATATATAC
1 ATACA-TTTATAATATATATATATAC
4110437 ATA
1 ATA
4110440 TACGTGTACA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
26 11 0.42
27 1 0.04
28 14 0.54
ACGTcount: A:0.44, C:0.09, G:0.00, T:0.47
Consensus pattern (25 bp):
ATACATTTATAATATATATATATAC
Found at i:4121174 original size:305 final size:305
Alignment explanation
Indices: 4120623--4121233 Score: 1222
Period size: 305 Copynumber: 2.0 Consensus size: 305
4120613 AATGATTAAA
4120623 CCAAGTTTTTGAAATTTCACAAAATATGGGGGATAATTAACTAAATTGAGTGTTGTTTAACATTA
1 CCAAGTTTTTGAAATTTCACAAAATATGGGGGATAATTAACTAAATTGAGTGTTGTTTAACATTA
4120688 TTTTATAATCATTATTAATTGTAAAAAAATGTTGATTTGGTTGTTATTGTTACCCCTACGTGTGT
66 TTTTATAATCATTATTAATTGTAAAAAAATGTTGATTTGGTTGTTATTGTTACCCCTACGTGTGT
4120753 TACGGTTCAGTCCAAATGACAACCCAACTGGAGAAACTTGAATATGACGACCCGACTTGGAAACT
131 TACGGTTCAGTCCAAATGACAACCCAACTGGAGAAACTTGAATATGACGACCCGACTTGGAAACT
4120818 CAAACAGCTCGCTTTCCTCTGCGTCCATAGCTCACCATCCCTTGTCCGCTTGATGGTCACAGTTC
196 CAAACAGCTCGCTTTCCTCTGCGTCCATAGCTCACCATCCCTTGTCCGCTTGATGGTCACAGTTC
4120883 GTCATCTCCTTATTCGTACCATTTCACCAGCTCGCCACTCCGTTC
261 GTCATCTCCTTATTCGTACCATTTCACCAGCTCGCCACTCCGTTC
4120928 CCAAGTTTTTGAAATTTCACAAAATATGGGGGATAATTAACTAAATTGAGTGTTGTTTAACATTA
1 CCAAGTTTTTGAAATTTCACAAAATATGGGGGATAATTAACTAAATTGAGTGTTGTTTAACATTA
4120993 TTTTATAATCATTATTAATTGTAAAAAAATGTTGATTTGGTTGTTATTGTTACCCCTACGTGTGT
66 TTTTATAATCATTATTAATTGTAAAAAAATGTTGATTTGGTTGTTATTGTTACCCCTACGTGTGT
4121058 TACGGTTCAGTCCAAATGACAACCCAACTGGAGAAACTTGAATATGACGACCCGACTTGGAAACT
131 TACGGTTCAGTCCAAATGACAACCCAACTGGAGAAACTTGAATATGACGACCCGACTTGGAAACT
4121123 CAAACAGCTCGCTTTCCTCTGCGTCCATAGCTCACCATCCCTTGTCCGCTTGATGGTCACAGTTC
196 CAAACAGCTCGCTTTCCTCTGCGTCCATAGCTCACCATCCCTTGTCCGCTTGATGGTCACAGTTC
4121188 GTCATCTCCTTATTCGTACCATTTCACCAGCTCGCCACTCCGTTC
261 GTCATCTCCTTATTCGTACCATTTCACCAGCTCGCCACTCCGTTC
4121233 C
1 C
4121234 TAGCTTTTCA
Statistics
Matches: 306, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
305 306 1.00
ACGTcount: A:0.27, C:0.23, G:0.16, T:0.33
Consensus pattern (305 bp):
CCAAGTTTTTGAAATTTCACAAAATATGGGGGATAATTAACTAAATTGAGTGTTGTTTAACATTA
TTTTATAATCATTATTAATTGTAAAAAAATGTTGATTTGGTTGTTATTGTTACCCCTACGTGTGT
TACGGTTCAGTCCAAATGACAACCCAACTGGAGAAACTTGAATATGACGACCCGACTTGGAAACT
CAAACAGCTCGCTTTCCTCTGCGTCCATAGCTCACCATCCCTTGTCCGCTTGATGGTCACAGTTC
GTCATCTCCTTATTCGTACCATTTCACCAGCTCGCCACTCCGTTC
Found at i:4121546 original size:21 final size:21
Alignment explanation
Indices: 4121522--4121604 Score: 98
Period size: 21 Copynumber: 4.0 Consensus size: 21
4121512 TAATAAATAC
*
4121522 TAAAAAAATTATTTTAAAAAT
1 TAAAAAAAGTATTTTAAAAAT
4121543 TAAAAAAAGTATTTTAAAAAT
1 TAAAAAAAGTATTTTAAAAAT
*** *
4121564 ATTTTAAAA-T-TTTAAAAAAT
1 -TAAAAAAAGTATTTTAAAAAT
4121584 TAAAAAAAGTATTTTAAAAAT
1 TAAAAAAAGTATTTTAAAAAT
4121605 ATTTTAAAAT
Statistics
Matches: 50, Mismatches: 9, Indels: 6
0.77 0.14 0.09
Matches are distributed among these distances:
19 5 0.10
20 10 0.20
21 30 0.60
22 5 0.10
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.37
Consensus pattern (21 bp):
TAAAAAAAGTATTTTAAAAAT
Found at i:4121587 original size:41 final size:41
Alignment explanation
Indices: 4121532--4121629 Score: 166
Period size: 41 Copynumber: 2.5 Consensus size: 41
4121522 TAAAAAAATT
4121532 ATTTT-AAAAATTAAAAAAAGTATTTTAAAAATATTTTAAA
1 ATTTTAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAA
4121572 ATTTTAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAA
1 ATTTTAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAA
*
4121613 A--TTAAAAAATTTAAAAA
1 ATTTTAAAAAATTAAAAAA
4121630 TAAATATATT
Statistics
Matches: 56, Mismatches: 1, Indels: 3
0.93 0.02 0.05
Matches are distributed among these distances:
39 15 0.27
40 5 0.09
41 36 0.64
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (41 bp):
ATTTTAAAAAATTAAAAAAAGTATTTTAAAAATATTTTAAA
Found at i:4121624 original size:16 final size:17
Alignment explanation
Indices: 4121597--4121641 Score: 58
Period size: 16 Copynumber: 2.8 Consensus size: 17
4121587 AAAAAGTATT
*
4121597 TTAAAAATATTTTAAAA
1 TTAAAAATATTTAAAAA
4121614 TTAAAAA-ATTTAAAAA
1 TTAAAAATATTTAAAAA
*
4121630 -TAAATATATTTA
1 TTAAAAATATTTA
4121642 TTATATCGGG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 5 0.20
16 13 0.52
17 7 0.28
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (17 bp):
TTAAAAATATTTAAAAA
Found at i:4131297 original size:20 final size:20
Alignment explanation
Indices: 4131246--4131297 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 20
4131236 AATCTTGATT
*
4131246 CTATCAATACTCAACAAAAA
1 CTATCAATACTTAACAAAAA
* *
4131266 CTATCGATACTTGACAAAAA
1 CTATCAATACTTAACAAAAA
*
4131286 GTATCAATACTT
1 CTATCAATACTT
4131298 TTTAGCCTGG
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.46, C:0.21, G:0.06, T:0.27
Consensus pattern (20 bp):
CTATCAATACTTAACAAAAA
Found at i:4131479 original size:21 final size:20
Alignment explanation
Indices: 4131450--4131489 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
4131440 GTTTAAAAAT
* *
4131450 ATTTTTTATTTAAAACATAAC
1 ATTTGTTATATAAAA-ATAAC
4131471 ATTTGTTATATAAAAATAA
1 ATTTGTTATATAAAAATAA
4131490 TATGCCAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.47, C:0.05, G:0.03, T:0.45
Consensus pattern (20 bp):
ATTTGTTATATAAAAATAAC
Found at i:4131640 original size:20 final size:19
Alignment explanation
Indices: 4131615--4131670 Score: 67
Period size: 19 Copynumber: 2.9 Consensus size: 19
4131605 AGCCTTAGAC
4131615 AAATTTGTCATTCATTACAA
1 AAATTTGTCATTCATT-CAA
* * *
4131635 AAATTTGGCATTCATTTAT
1 AAATTTGTCATTCATTCAA
*
4131654 AAATTGGTCATTCATTC
1 AAATTTGTCATTCATTC
4131671 TCAGTTAAAG
Statistics
Matches: 30, Mismatches: 6, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
19 15 0.50
20 15 0.50
ACGTcount: A:0.34, C:0.14, G:0.09, T:0.43
Consensus pattern (19 bp):
AAATTTGTCATTCATTCAA
Found at i:4138935 original size:14 final size:14
Alignment explanation
Indices: 4138916--4138946 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
4138906 TGCTACCATT
4138916 TTACTATTATGTTG
1 TTACTATTATGTTG
*
4138930 TTACTATTTTGTTG
1 TTACTATTATGTTG
4138944 TTA
1 TTA
4138947 TTGTTTGTAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.06, G:0.13, T:0.61
Consensus pattern (14 bp):
TTACTATTATGTTG
Found at i:4139509 original size:33 final size:32
Alignment explanation
Indices: 4139448--4139526 Score: 108
Period size: 33 Copynumber: 2.5 Consensus size: 32
4139438 AATTTAGAAC
* *
4139448 TTAGTATCTATTC--TTGTTTTTTTGAGAAAT
1 TTAGTATCTATTCTTTTGTTTTTTTAAGAAAA
*
4139478 TTAGTATCTATTCTTTTCTTTTTTTTAAGAAAA
1 TTAGTATCTATTCTTTT-GTTTTTTTAAGAAAA
4139511 TTAGTATCTATTCTTT
1 TTAGTATCTATTCTTT
4139527 AATGGGATAT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
30 13 0.30
32 2 0.05
33 28 0.65
ACGTcount: A:0.24, C:0.09, G:0.09, T:0.58
Consensus pattern (32 bp):
TTAGTATCTATTCTTTTGTTTTTTTAAGAAAA
Found at i:4141617 original size:13 final size:12
Alignment explanation
Indices: 4141601--4141642 Score: 59
Period size: 13 Copynumber: 3.4 Consensus size: 12
4141591 GTTTTTAAGA
4141601 TTTTTGTTTAGGG
1 TTTTTGTTTA-GG
4141614 TTTTTGTTTTAGG
1 TTTTTG-TTTAGG
4141627 TTTTT-TTTAGG
1 TTTTTGTTTAGG
4141638 TTTTT
1 TTTTT
4141643 TAATTTTAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
11 11 0.39
13 13 0.46
14 4 0.14
ACGTcount: A:0.07, C:0.00, G:0.21, T:0.71
Consensus pattern (12 bp):
TTTTTGTTTAGG
Found at i:4141641 original size:10 final size:11
Alignment explanation
Indices: 4141601--4141643 Score: 50
Period size: 11 Copynumber: 3.5 Consensus size: 11
4141591 GTTTTTAAGA
4141601 TTTTTGTTTAGGG
1 TTTTT-TTTA-GG
4141614 TTTTTGTTTTAGG
1 -TTTT-TTTTAGG
4141627 TTTTTTTTAGG
1 TTTTTTTTAGG
4141638 TTTTTT
1 TTTTTT
4141644 AATTTTAATT
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
11 13 0.46
12 4 0.14
13 2 0.07
14 8 0.29
15 1 0.04
ACGTcount: A:0.07, C:0.00, G:0.21, T:0.72
Consensus pattern (11 bp):
TTTTTTTTAGG
Found at i:4141655 original size:25 final size:26
Alignment explanation
Indices: 4141593--4141656 Score: 69
Period size: 25 Copynumber: 2.5 Consensus size: 26
4141583 GATTTAGGGT
*
4141593 TTTTAAGATTTTTGTTTAGGGTTTTTG
1 TTTT-AGATTTTTGTTTAGGGTTTTTA
* *
4141620 TTTTAGGTTTTT-TTTAGGTTTTTTAA
1 TTTTAGATTTTTGTTTAGGGTTTTT-A
4141646 TTTTA-ATTTTT
1 TTTTAGATTTTT
4141657 ATATATTCTT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
25 16 0.50
26 12 0.38
27 4 0.12
ACGTcount: A:0.16, C:0.00, G:0.16, T:0.69
Consensus pattern (26 bp):
TTTTAGATTTTTGTTTAGGGTTTTTA
Found at i:4144484 original size:23 final size:23
Alignment explanation
Indices: 4144442--4144487 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
4144432 ATTTGCAACT
*
4144442 TTTATCATAAAGCAAAGCTCAAA
1 TTTATCATAAAACAAAGCTCAAA
* *
4144465 TTTATCATAAAACGATGCTCAAA
1 TTTATCATAAAACAAAGCTCAAA
4144488 ACCAGCAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.46, C:0.17, G:0.09, T:0.28
Consensus pattern (23 bp):
TTTATCATAAAACAAAGCTCAAA
Found at i:4146255 original size:69 final size:70
Alignment explanation
Indices: 4146174--4146355 Score: 201
Period size: 69 Copynumber: 2.6 Consensus size: 70
4146164 AGTGATAATT
* *
4146174 TCTTCACTATTTTTGTTAAAAAGTTAATTTTAATCT-CACGTTAACTA-AAAATTACTCTTATAG
1 TCTTCACTATTTTTATTAAAAAGTTAATTTTAATCTCCACGTTAACTAGAAAA-TACTCATATAG
* *
4146237 CTCACA
65 CTAAAA
* * * * *
4146243 TCTTCACTATTTTCATTAAAAAATTAATTTTAAT-TCCATGTTGACTAGAGAATACTCATATAGC
1 TCTTCACTATTTTTATTAAAAAGTTAATTTTAATCTCCACGTTAACTAGAAAATACTCATATAGC
4146307 TAAAA
66 TAAAA
4146312 TCTTCACTATTTTCATTAAATTAAAAAGTTAATTTTAATC-CCAC
1 TCTTCACTA-TTT--TT--ATTAAAAAGTTAATTTTAATCTCCAC
4146356 ATTGATTAGA
Statistics
Matches: 93, Mismatches: 12, Indels: 11
0.80 0.10 0.09
Matches are distributed among these distances:
68 1 0.01
69 63 0.68
70 6 0.06
72 1 0.01
74 22 0.24
ACGTcount: A:0.37, C:0.16, G:0.05, T:0.41
Consensus pattern (70 bp):
TCTTCACTATTTTTATTAAAAAGTTAATTTTAATCTCCACGTTAACTAGAAAATACTCATATAGC
TAAAA
Found at i:4146851 original size:141 final size:142
Alignment explanation
Indices: 4146598--4146866 Score: 348
Period size: 141 Copynumber: 1.9 Consensus size: 142
4146588 TAAAAAATAA
* * * * *
4146598 TTTTAATCTCATATTAGCTAGAGAACACTCGCATACTCGCTATTTTCATAAGCTCTTTAGAGTTT
1 TTTTAATCCCATATTAACTAGAGAACAATCCCATACTCGCTATTTTCATAAACTCTTTAGAGTTT
* * * *
4146663 CTTCCTCTAAAGAAACTTATGAGAGAGAACTTCTAGTTTAAAGTTATTTATATATTATTGATATG
66 CTTCCTCTAAAGAAACTTACGAGAAAGAACTTCTAGCTTAAAGTTATTTATATATTATCGATATG
4146728 AACGATGATGAT
131 AACGATGATGAT
* * *
4146740 TTTTAATCCCATTTTAACTAGAGAACAATCCCATGCTCAG-TATTTTCATAAACT-TTTCGAGTT
1 TTTTAATCCCATATTAACTAGAGAACAATCCCATACTC-GCTATTTTCATAAACTCTTTAGAGTT
* * *
4146803 TCTTCCTTTAAAGAAA-TTCACGAGAAAGAGC-TCATAGCTTGAAGTTATTTATATATTATCGAT
65 TCTTCCTCTAAAGAAACTT-ACGAGAAAGAACTTC-TAGCTTAAAGTTATTTATATATTATCGAT
4146866 A
128 A
4146867 CGAATGGAGG
Statistics
Matches: 109, Mismatches: 15, Indels: 7
0.83 0.11 0.05
Matches are distributed among these distances:
140 4 0.04
141 59 0.54
142 45 0.41
143 1 0.01
ACGTcount: A:0.33, C:0.16, G:0.13, T:0.38
Consensus pattern (142 bp):
TTTTAATCCCATATTAACTAGAGAACAATCCCATACTCGCTATTTTCATAAACTCTTTAGAGTTT
CTTCCTCTAAAGAAACTTACGAGAAAGAACTTCTAGCTTAAAGTTATTTATATATTATCGATATG
AACGATGATGAT
Found at i:4147638 original size:21 final size:20
Alignment explanation
Indices: 4147611--4147658 Score: 62
Period size: 21 Copynumber: 2.4 Consensus size: 20
4147601 ATTTTATGTT
4147611 TTAAAAAAAT-TATAAAAAAA
1 TTAAAAAAATATAT-AAAAAA
*
4147631 TCTAAAAATATATATAAAAAA
1 T-TAAAAAAATATATAAAAAA
4147652 TTAAAAA
1 TTAAAAA
4147659 TTTTAAAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
20 7 0.28
21 15 0.60
22 3 0.12
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (20 bp):
TTAAAAAAATATATAAAAAA
Found at i:4147644 original size:20 final size:19
Alignment explanation
Indices: 4147615--4147660 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
4147605 TATGTTTTAA
4147615 AAAAATTATA-AAAAAATCT
1 AAAAATTATATAAAAAAT-T
4147634 AAAAATATATATAAAAAATT
1 AAAAAT-TATATAAAAAATT
4147654 AAAAATT
1 AAAAATT
4147661 TTAAAATTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.28
20 11 0.44
21 7 0.28
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAAATTATATAAAAAATT
Found at i:4149962 original size:18 final size:20
Alignment explanation
Indices: 4149925--4149965 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
4149915 TAATGTCACA
4149925 TTAATAATTTTATTTTTAATT
1 TTAATAATTTTA-TTTTAATT
4149946 TTAA-AATTTTA-TTTAATT
1 TTAATAATTTTATTTTAATT
4149964 TT
1 TT
4149966 GATTTTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
18 9 0.45
20 7 0.35
21 4 0.20
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (20 bp):
TTAATAATTTTATTTTAATT
Found at i:4154934 original size:28 final size:29
Alignment explanation
Indices: 4154898--4154968 Score: 99
Period size: 28 Copynumber: 2.5 Consensus size: 29
4154888 TTTTAATTGA
*
4154898 TAATATTTTATTTTGAAATAATAGTCA-T
1 TAATCTTTTATTTTGAAATAATAGTCATT
*
4154926 TAATCTTTTATTTTGAAGTAATAGTCATT
1 TAATCTTTTATTTTGAAATAATAGTCATT
* *
4154955 TACTCTTTTTTTTT
1 TAATCTTTTATTTT
4154969 TTTCATTTAA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
28 25 0.66
29 13 0.34
ACGTcount: A:0.30, C:0.07, G:0.07, T:0.56
Consensus pattern (29 bp):
TAATCTTTTATTTTGAAATAATAGTCATT
Found at i:4167842 original size:60 final size:61
Alignment explanation
Indices: 4167733--4167861 Score: 136
Period size: 60 Copynumber: 2.1 Consensus size: 61
4167723 GAATAATAAT
* * **
4167733 AAATTTAGCCCTCATATGTTTATAGATTATAACAATTTGGTCCTAATTCTAAAAAAATCAA
1 AAATTTAACCCTCATATCTTTATAGATTATAACAATTTAATCCTAATTCTAAAAAAATCAA
* * * * * *
4167794 CAAATTTAACCCTCA-A-CTTTATATATTATGACAATTTAATCTTGATTCTTAAAAATTCAA
1 -AAATTTAACCCTCATATCTTTATAGATTATAACAATTTAATCCTAATTCTAAAAAAATCAA
*
4167854 AATTTTAA
1 AAATTTAA
4167862 AAACTTAAAA
Statistics
Matches: 56, Mismatches: 11, Indels: 3
0.80 0.16 0.04
Matches are distributed among these distances:
59 7 0.12
60 35 0.62
61 1 0.02
62 13 0.23
ACGTcount: A:0.41, C:0.15, G:0.05, T:0.39
Consensus pattern (61 bp):
AAATTTAACCCTCATATCTTTATAGATTATAACAATTTAATCCTAATTCTAAAAAAATCAA
Found at i:4175485 original size:24 final size:24
Alignment explanation
Indices: 4175453--4175500 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
4175443 AATAGGTGCC
4175453 ATCACTTACTTGCTGTTAACTAAG
1 ATCACTTACTTGCTGTTAACTAAG
4175477 ATCACTTACTTGCTGTTAACTAAG
1 ATCACTTACTTGCTGTTAACTAAG
4175501 GAGCCTGCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.38
Consensus pattern (24 bp):
ATCACTTACTTGCTGTTAACTAAG
Found at i:4179046 original size:11 final size:11
Alignment explanation
Indices: 4179030--4179089 Score: 61
Period size: 11 Copynumber: 5.2 Consensus size: 11
4179020 TTCAAATAAA
4179030 AATTAAAAATT
1 AATTAAAAATT
4179041 AATT-AAAA-T
1 AATTAAAAATT
4179050 AATTAAAAATAT
1 AATTAAAAAT-T
4179062 ATTATTTACAAAATT
1 A--A-TTA-AAAATT
4179077 AATTAAAAATT
1 AATTAAAAATT
4179088 AA
1 AA
4179090 ACGTGTAAAA
Statistics
Matches: 42, Mismatches: 0, Indels: 14
0.75 0.00 0.25
Matches are distributed among these distances:
9 5 0.12
10 8 0.19
11 12 0.29
12 5 0.12
13 1 0.02
14 1 0.02
15 5 0.12
16 5 0.12
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.37
Consensus pattern (11 bp):
AATTAAAAATT
Found at i:4188065 original size:20 final size:20
Alignment explanation
Indices: 4188040--4188091 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 20
4188030 ATTATAAATG
*
4188040 TTGAATTTTTTATAAATATT
1 TTGAATTTTTTAAAAATATT
*
4188060 TTGAATTTTTAAAAAATATT
1 TTGAATTTTTTAAAAATATT
4188080 TTGAATTCTTTT
1 TTGAATT-TTTT
4188092 TTGTATTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
20 25 0.89
21 3 0.11
ACGTcount: A:0.35, C:0.02, G:0.06, T:0.58
Consensus pattern (20 bp):
TTGAATTTTTTAAAAATATT
Found at i:4188426 original size:2 final size:2
Alignment explanation
Indices: 4188421--4188492 Score: 144
Period size: 2 Copynumber: 36.0 Consensus size: 2
4188411 AACTGGTATC
4188421 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
4188463 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
4188493 NNNNNNNNNN
Statistics
Matches: 70, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 70 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:4191023 original size:22 final size:21
Alignment explanation
Indices: 4190987--4191027 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
4190977 AGATTGTTGT
4190987 TTTTCTTATTGTTTTCTTACTA
1 TTTTCTTATTGTTTT-TTACTA
* *
4191009 TTTTCTTGTTTTTTTTTAC
1 TTTTCTTATTGTTTTTTAC
4191028 ACTATTTTGC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 4 0.24
22 13 0.76
ACGTcount: A:0.10, C:0.12, G:0.05, T:0.73
Consensus pattern (21 bp):
TTTTCTTATTGTTTTTTACTA
Found at i:4193138 original size:2 final size:2
Alignment explanation
Indices: 4193133--4193157 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
4193123 ATTTTTTATC
4193133 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
4193158 GTTATATTAT
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:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:4198752 original size:18 final size:18
Alignment explanation
Indices: 4198729--4198763 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
4198719 GGCAATGAAG
4198729 TAAGTGTTCGTGCACAGT
1 TAAGTGTTCGTGCACAGT
4198747 TAAGTGTTCGTGCACAG
1 TAAGTGTTCGTGCACAG
4198764 ATGCACATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.17, G:0.29, T:0.31
Consensus pattern (18 bp):
TAAGTGTTCGTGCACAGT
Found at i:4200811 original size:13 final size:13
Alignment explanation
Indices: 4200793--4200819 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
4200783 GAGTGTTCAA
4200793 ATCGGCGAATTCT
1 ATCGGCGAATTCT
4200806 ATCGGCGAATTCT
1 ATCGGCGAATTCT
4200819 A
1 A
4200820 GGCTTATCCA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.26, C:0.22, G:0.22, T:0.30
Consensus pattern (13 bp):
ATCGGCGAATTCT
Found at i:4204433 original size:21 final size:21
Alignment explanation
Indices: 4204383--4204433 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
4204373 AGATTCAGGA
* *
4204383 TTCATTGTTATGGGTTTGGGG
1 TTCATGGTTATGAGTTTGGGG
*
4204404 TT-ACGGGTTATGAGTTTGGGG
1 TTCA-TGGTTATGAGTTTGGGG
4204425 TTCATGGTT
1 TTCATGGTT
4204434 TAAAGATTCG
Statistics
Matches: 24, Mismatches: 4, Indels: 4
0.75 0.12 0.12
Matches are distributed among these distances:
20 1 0.04
21 22 0.92
22 1 0.04
ACGTcount: A:0.12, C:0.06, G:0.37, T:0.45
Consensus pattern (21 bp):
TTCATGGTTATGAGTTTGGGG
Found at i:4204956 original size:26 final size:27
Alignment explanation
Indices: 4204905--4204958 Score: 92
Period size: 26 Copynumber: 2.0 Consensus size: 27
4204895 TTACTTGAAT
4204905 TATATATAAAATAACTGAAATTTATGG
1 TATATATAAAATAACTGAAATTTATGG
*
4204932 TATATATAAAAT-ATTGAAATTTATGG
1 TATATATAAAATAACTGAAATTTATGG
4204958 T
1 T
4204959 TACTATTTTT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
26 14 0.54
27 12 0.46
ACGTcount: A:0.46, C:0.02, G:0.11, T:0.41
Consensus pattern (27 bp):
TATATATAAAATAACTGAAATTTATGG
Found at i:4214174 original size:11 final size:11
Alignment explanation
Indices: 4214147--4214199 Score: 54
Period size: 11 Copynumber: 4.7 Consensus size: 11
4214137 GTCTTTAAGA
4214147 TTTTTAGATTAT
1 TTTTTA-ATTAT
*
4214159 ATTTTAATTATT
1 TTTTTAATTA-T
*
4214171 TTTTTAA-AAT
1 TTTTTAATTAT
*
4214181 TTTTTAACTAT
1 TTTTTAATTAT
4214192 TTTTTAAT
1 TTTTTAAT
4214200 ACAATTTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 5
0.77 0.11 0.11
Matches are distributed among these distances:
10 8 0.24
11 14 0.41
12 12 0.35
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.66
Consensus pattern (11 bp):
TTTTTAATTAT
Found at i:4216050 original size:18 final size:17
Alignment explanation
Indices: 4216027--4216069 Score: 50
Period size: 18 Copynumber: 2.5 Consensus size: 17
4216017 TTATAATCCC
4216027 TTTAATTATATTAGAATT
1 TTTAATTATATTA-AATT
* * *
4216045 TTTAATAATTTTATATT
1 TTTAATTATATTAAATT
4216062 TTTAATTA
1 TTTAATTA
4216070 ATTTCTGTCA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
17 10 0.48
18 11 0.52
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
TTTAATTATATTAAATT
Found at i:4227040 original size:23 final size:23
Alignment explanation
Indices: 4227001--4227045 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
4226991 GTATTAAAAT
* *
4227001 AAATATATTAATTATATTATATC
1 AAATATATTAATAATATAATATC
4227024 AAATAATATTAA-AATATAATAT
1 AAAT-ATATTAATAATATAATAT
4227046 ATTAATTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
23 12 0.63
24 7 0.37
ACGTcount: A:0.56, C:0.02, G:0.00, T:0.42
Consensus pattern (23 bp):
AAATATATTAATAATATAATATC
Found at i:4227068 original size:39 final size:37
Alignment explanation
Indices: 4226992--4227076 Score: 91
Period size: 39 Copynumber: 2.2 Consensus size: 37
4226982 GGCTAACAAG
**
4226992 TATTAAAATAAATATATTAATTATATTATATCAAATAA
1 TATTAAAATAAATATATTAATTATAAAATAT-AAATAA
*
4227030 TATTAAAATATAATATATTAATTTTAAAA-ACTATAATAA
1 TATTAAAATA-AATATATTAATTATAAAATA-TA-AATAA
*
4227069 TTTTAAAA
1 TATTAAAA
4227077 GTTCAAGCAA
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
38 12 0.30
39 28 0.70
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.42
Consensus pattern (37 bp):
TATTAAAATAAATATATTAATTATAAAATATAAATAA
Found at i:4228507 original size:11 final size:11
Alignment explanation
Indices: 4228491--4228518 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
4228481 TACCAATGAT
4228491 AATTAGTTTAA
1 AATTAGTTTAA
4228502 AATTAGTTTAA
1 AATTAGTTTAA
4228513 AATTAG
1 AATTAG
4228519 AAGGGAATGC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.46, C:0.00, G:0.11, T:0.43
Consensus pattern (11 bp):
AATTAGTTTAA
Found at i:4231408 original size:91 final size:89
Alignment explanation
Indices: 4231237--4231409 Score: 211
Period size: 91 Copynumber: 1.9 Consensus size: 89
4231227 ATCAAATGGC
* * * * * ** * *
4231237 CTTTTTGATGCATTTTGATAGTTCAAGTATCCAATTAAGTGCAAAAAAATTCAGGAGCTTAATTG
1 CTTTTTGATGCATTTTGAAAGTTCAAGTAGCCAACTAAATGAAAAAAAAAACAGAAGCATAATTG
4231302 TTTTTTTTAAAAAAAAGTTTAAAGAT
66 TTTTTTTT--AAAAAAGTTTAAAGAT
*
4231328 CTTTTTGATGCATTTTGAAAGTTCAAGTAGCTAACTAAATGTAAAAAAGAAAACAGAAGCATAAT
1 CTTTTTGATGCATTTTGAAAGTTCAAGTAGCCAACTAAATG-AAAAAA-AAAACAGAAGCATAAT
4231393 TGCTTTTTTTTAAAAAA
64 TG-TTTTTTTTAAAAAA
4231410 AATTAAGAAT
Statistics
Matches: 69, Mismatches: 10, Indels: 5
0.82 0.12 0.06
Matches are distributed among these distances:
91 36 0.52
92 11 0.16
93 14 0.20
94 8 0.12
ACGTcount: A:0.40, C:0.09, G:0.14, T:0.37
Consensus pattern (89 bp):
CTTTTTGATGCATTTTGAAAGTTCAAGTAGCCAACTAAATGAAAAAAAAAACAGAAGCATAATTG
TTTTTTTTAAAAAAGTTTAAAGAT
Found at i:4232553 original size:21 final size:23
Alignment explanation
Indices: 4232513--4232570 Score: 66
Period size: 22 Copynumber: 2.5 Consensus size: 23
4232503 ATGTTTTAAA
*
4232513 AACATTTATTTTATTTTAATAT-TT
1 AACA-TTATTTTA-TATAATATCTT
*
4232537 AATATT-TTTTATATAATATCTT
1 AACATTATTTTATATAATATCTT
4232559 AACATTATTTTA
1 AACATTATTTTA
4232571 ATATTTATAT
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
21 7 0.24
22 12 0.41
23 7 0.24
24 3 0.10
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.59
Consensus pattern (23 bp):
AACATTATTTTATATAATATCTT
Found at i:4238774 original size:20 final size:20
Alignment explanation
Indices: 4238731--4238774 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
4238721 ATAATTTAAT
* *
4238731 TATATCAAACTATAATATAT
1 TATATCAAACTATAATAAAA
* *
4238751 TATATCAAATTATATTAAAA
1 TATATCAAACTATAATAAAA
4238771 TATA
1 TATA
4238775 ATATATTGAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.52, C:0.07, G:0.00, T:0.41
Consensus pattern (20 bp):
TATATCAAACTATAATAAAA
Found at i:4241321 original size:18 final size:18
Alignment explanation
Indices: 4241294--4241333 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
4241284 TAGGTGCGTA
*
4241294 TCCTAGCCCTTATATGTG
1 TCCTAACCCTTATATGTG
*
4241312 TCCTAACCCTTATATGTT
1 TCCTAACCCTTATATGTG
4241330 TCCT
1 TCCT
4241334 TTTCCCAGTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.17, C:0.30, G:0.10, T:0.42
Consensus pattern (18 bp):
TCCTAACCCTTATATGTG
Found at i:4242139 original size:46 final size:46
Alignment explanation
Indices: 4242038--4242199 Score: 269
Period size: 46 Copynumber: 3.6 Consensus size: 46
4242028 TACTTATGAT
*
4242038 CACTTATCAC-TTGTC-CCTGATCAGATAAGTGTAGCT-A-GACTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATG-CTAC
*
4242081 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGTTAATGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATGCTAC
4242127 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATGCTAC
1 CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATGCTAC
4242173 CACTTATCACTTTGTCACTTGATCAGA
1 CACTTATCACTTTGTCACTTGATCAGA
4242200 AGTACTCAAA
Statistics
Matches: 112, Mismatches: 3, Indels: 5
0.93 0.03 0.04
Matches are distributed among these distances:
43 10 0.09
44 5 0.04
45 19 0.17
46 77 0.69
47 1 0.01
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.35
Consensus pattern (46 bp):
CACTTATCACTTTGTCACTTGATCAGATAAGTGTAGCTAATGCTAC
Found at i:4244491 original size:8 final size:10
Alignment explanation
Indices: 4244465--4244490 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
4244455 TACAAACTAT
4244465 TTTTATATTG
1 TTTTATATTG
4244475 TTTTATATTG
1 TTTTATATTG
4244485 TTTTAT
1 TTTTAT
4244491 TTAATAAAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.19, C:0.00, G:0.08, T:0.73
Consensus pattern (10 bp):
TTTTATATTG
Found at i:4244740 original size:34 final size:33
Alignment explanation
Indices: 4244690--4244817 Score: 134
Period size: 34 Copynumber: 3.8 Consensus size: 33
4244680 AAAATTATTT
4244690 TTTTTTAAAAA--CTAAACCCTAATTTAATTAA
1 TTTTTTAAAAACTCTAAACCCTAATTTAATTAA
* *
4244721 TTTTCTTAAAAACTTTAAACCTTAATTTAATTAA
1 TTTT-TTAAAAACTCTAAACCCTAATTTAATTAA
* * * * *
4244755 TTAATTTAATACCGCTAAAACCTAATTTAATTAA
1 TT-TTTTAAAAACTCTAAACCCTAATTTAATTAA
**
4244789 TTTTAAAAAAAACTCTAAACCCTAATTTA
1 TTTT-TTAAAAACTCTAAACCCTAATTTA
4244818 TTTTTTAAAA
Statistics
Matches: 76, Mismatches: 16, Indels: 7
0.77 0.16 0.07
Matches are distributed among these distances:
31 4 0.05
32 7 0.09
33 1 0.01
34 63 0.83
35 1 0.01
ACGTcount: A:0.45, C:0.14, G:0.01, T:0.41
Consensus pattern (33 bp):
TTTTTTAAAAACTCTAAACCCTAATTTAATTAA
Found at i:4245665 original size:6 final size:6
Alignment explanation
Indices: 4245650--4245679 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
4245640 TTGAATTAAG
4245650 TTTT-T TTTTGT TTTTGT TTTTGT TTTTGT T
1 TTTTGT TTTTGT TTTTGT TTTTGT TTTTGT T
4245680 ATTCAAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
5 4 0.17
6 20 0.83
ACGTcount: A:0.00, C:0.00, G:0.13, T:0.87
Consensus pattern (6 bp):
TTTTGT
Found at i:4248155 original size:31 final size:31
Alignment explanation
Indices: 4248120--4248179 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
4248110 TTCACAAGCC
*
4248120 AATTCATAACCCTTAAATCCAGCCAAAAATT
1 AATTCATAACCCTTAAATCCAACCAAAAATT
4248151 AATTCATAACCCTTAAATCCAACCAAAAA
1 AATTCATAACCCTTAAATCCAACCAAAAA
4248180 CTAAGTCTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.48, C:0.27, G:0.02, T:0.23
Consensus pattern (31 bp):
AATTCATAACCCTTAAATCCAACCAAAAATT
Found at i:4249203 original size:22 final size:22
Alignment explanation
Indices: 4249177--4249221 Score: 90
Period size: 22 Copynumber: 2.0 Consensus size: 22
4249167 AACAAAAAGT
4249177 TCATAAGAGCTAATAACGGGAC
1 TCATAAGAGCTAATAACGGGAC
4249199 TCATAAGAGCTAATAACGGGAC
1 TCATAAGAGCTAATAACGGGAC
4249221 T
1 T
4249222 GTCTTTCGAG
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:0.40, C:0.18, G:0.22, T:0.20
Consensus pattern (22 bp):
TCATAAGAGCTAATAACGGGAC
Found at i:4260774 original size:2 final size:2
Alignment explanation
Indices: 4260767--4260803 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
4260757 CAAATCATTC
4260767 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
4260804 ATTTTCCTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:4261747 original size:41 final size:41
Alignment explanation
Indices: 4261604--4261803 Score: 249
Period size: 41 Copynumber: 4.9 Consensus size: 41
4261594 TAACCGTTAC
* *** * *
4261604 TCGGTGGAATCAGCACTTAGCAACCACCTTTAGAATCAATAAT
1 TCGG-GGAATCTGCACTTAGCAACC-CCTTTTTCATCAGTGAT
* * * *
4261647 TCAGAGAATCTGCACTTAGCAACCCCTTTTT-ATCAGAGTT
1 TCGGGGAATCTGCACTTAGCAACCCCTTTTTCATCAGTGAT
*
4261687 TCGGGGAATCTGCACTTAGCAACCCCTTTTTCATTAGTGAT
1 TCGGGGAATCTGCACTTAGCAACCCCTTTTTCATCAGTGAT
* *
4261728 TCTGGGAATCTGCACTTAGCAACTCCTTTTTCATCAGTGAT
1 TCGGGGAATCTGCACTTAGCAACCCCTTTTTCATCAGTGAT
*
4261769 TCGGGGAATTTGCACTTAGCAACCCCTTTTTCATC
1 TCGGGGAATCTGCACTTAGCAACCCCTTTTTCATC
4261804 TAATGAATCT
Statistics
Matches: 136, Mismatches: 20, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
40 34 0.25
41 81 0.60
42 18 0.13
43 3 0.02
ACGTcount: A:0.26, C:0.25, G:0.17, T:0.33
Consensus pattern (41 bp):
TCGGGGAATCTGCACTTAGCAACCCCTTTTTCATCAGTGAT
Found at i:4265135 original size:13 final size:13
Alignment explanation
Indices: 4265096--4265137 Score: 54
Period size: 13 Copynumber: 3.4 Consensus size: 13
4265086 GTTATGTTTG
4265096 AATATATTGATGT
1 AATATATTGATGT
4265109 AATAT-TAT-AT-T
1 AATATAT-TGATGT
4265120 AATATATTGATGT
1 AATATATTGATGT
4265133 AATAT
1 AATAT
4265138 TGAAGAGTTA
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
11 7 0.28
12 6 0.24
13 12 0.48
ACGTcount: A:0.43, C:0.00, G:0.10, T:0.48
Consensus pattern (13 bp):
AATATATTGATGT
Found at i:4265748 original size:19 final size:21
Alignment explanation
Indices: 4265712--4265751 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
4265702 TTTTATAATA
*
4265712 TTATTAGTGAGTTTAAATATT
1 TTATTAGTGAGTTAAAATATT
4265733 TTATTA-TGA-TTAAAATATT
1 TTATTAGTGAGTTAAAATATT
4265752 AATGTGAAGT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 9 0.50
20 3 0.17
21 6 0.33
ACGTcount: A:0.38, C:0.00, G:0.10, T:0.53
Consensus pattern (21 bp):
TTATTAGTGAGTTAAAATATT
Found at i:4265763 original size:38 final size:39
Alignment explanation
Indices: 4265690--4265768 Score: 90
Period size: 38 Copynumber: 2.1 Consensus size: 39
4265680 TATAAAGAAT
** * *
4265690 TATTTTATTATTTTTTATAATATTATTAGTGAGTTTAAA
1 TATTTTATTATTGATTAAAATATTAATAGTGAGTTTAAA
*
4265729 TATTTTATTA-TGATTAAAATATTAAT-GTGAAGTTTTAA
1 TATTTTATTATTGATTAAAATATTAATAGTG-AGTTTAAA
4265767 TA
1 TA
4265769 CCGTTAAAAT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
37 3 0.09
38 21 0.62
39 10 0.29
ACGTcount: A:0.37, C:0.00, G:0.09, T:0.54
Consensus pattern (39 bp):
TATTTTATTATTGATTAAAATATTAATAGTGAGTTTAAA
Found at i:4266591 original size:94 final size:94
Alignment explanation
Indices: 4266482--4266657 Score: 352
Period size: 94 Copynumber: 1.9 Consensus size: 94
4266472 AATTGGTACC
4266482 AAATTGATTGTTTAATATCTTGGTGCCGAAAATTTGAAAAGATTTTAAAAGAAAACTTTTTATCT
1 AAATTGATTGTTTAATATCTTGGTGCCGAAAATTTGAAAAGATTTTAAAAGAAAACTTTTTATCT
4266547 TGAATGAATTAAAAATATCTTGGTGCCCA
66 TGAATGAATTAAAAATATCTTGGTGCCCA
4266576 AAATTGATTGTTTAATATCTTGGTGCCGAAAATTTGAAAAGATTTTAAAAGAAAACTTTTTATCT
1 AAATTGATTGTTTAATATCTTGGTGCCGAAAATTTGAAAAGATTTTAAAAGAAAACTTTTTATCT
4266641 TGAATGAATTAAAAATA
66 TGAATGAATTAAAAATA
4266658 ACAAAACATT
Statistics
Matches: 82, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
94 82 1.00
ACGTcount: A:0.40, C:0.08, G:0.14, T:0.38
Consensus pattern (94 bp):
AAATTGATTGTTTAATATCTTGGTGCCGAAAATTTGAAAAGATTTTAAAAGAAAACTTTTTATCT
TGAATGAATTAAAAATATCTTGGTGCCCA
Found at i:4267366 original size:19 final size:19
Alignment explanation
Indices: 4267325--4267371 Score: 51
Period size: 19 Copynumber: 2.5 Consensus size: 19
4267315 GTGGCTTAAT
* *
4267325 GATAATAATAATAATAAAT
1 GATAATAATAATAACAAAC
4267344 GATAATAA-AATAACAATAC
1 GATAATAATAATAACAA-AC
*
4267363 GATATTAAT
1 GATAATAAT
4267372 GATGCAATAT
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
18 7 0.30
19 16 0.70
ACGTcount: A:0.60, C:0.04, G:0.06, T:0.30
Consensus pattern (19 bp):
GATAATAATAATAACAAAC
Found at i:4269178 original size:11 final size:11
Alignment explanation
Indices: 4269161--4269219 Score: 57
Period size: 12 Copynumber: 5.2 Consensus size: 11
4269151 TTTAAAAAAA
4269161 TTAAAAAGTATT
1 TTAAAAA-TATT
4269173 TTAAAAATATT
1 TTAAAAATATT
**
4269184 TT-AAAATAAAA
1 TTAAAAAT-ATT
*
4269195 ATAAAAAGTATT
1 TTAAAAA-TATT
4269207 TTAAAAATATT
1 TTAAAAATATT
4269218 TT
1 TT
4269220 TTATTTTTAA
Statistics
Matches: 38, Mismatches: 6, Indels: 7
0.75 0.12 0.14
Matches are distributed among these distances:
10 5 0.13
11 14 0.37
12 18 0.47
13 1 0.03
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (11 bp):
TTAAAAATATT
Found at i:4269201 original size:52 final size:50
Alignment explanation
Indices: 4269144--4269254 Score: 123
Period size: 52 Copynumber: 2.1 Consensus size: 50
4269134 AATAAACACC
*
4269144 AAAAAAATTTAAAAAAATTAAAAAGTATTTTAAAAATATTTTAAAATAAAAAT
1 AAAAAATTTTAAAAAAATT---AAGTATTTTAAAAATATTTTAAAATAAAAAT
* *** *
4269197 AAAAAGTATTTTAAAAATATTTTTTATTTTTAAAATATTTTAAAATAAAAAT
1 AAAAA--ATTTTAAAAAAATTAAGTATTTTAAAAATATTTTAAAATAAAAAT
4269249 AAAAAA
1 AAAAAA
4269255 ATATTTATTA
Statistics
Matches: 50, Mismatches: 6, Indels: 7
0.79 0.10 0.11
Matches are distributed among these distances:
50 1 0.02
52 32 0.64
53 5 0.10
55 12 0.24
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (50 bp):
AAAAAATTTTAAAAAAATTAAGTATTTTAAAAATATTTTAAAATAAAAAT
Found at i:4269224 original size:18 final size:18
Alignment explanation
Indices: 4269203--4269237 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
4269193 AAATAAAAAG
4269203 TATTTTAAAAATATTTTT
1 TATTTTAAAAATATTTTT
*
4269221 TATTTTTAAAATATTTT
1 TATTTTAAAAATATTTT
4269238 AAAATAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TATTTTAAAAATATTTTT
Found at i:4269656 original size:15 final size:17
Alignment explanation
Indices: 4269638--4269675 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
4269628 AAGTTTATAC
4269638 TATTTTATAT-T-ATGT
1 TATTTTATATATGATGT
4269653 TATTTTTATATATGATGT
1 TA-TTTTATATATGATGT
4269671 TATTT
1 TATTT
4269676 AGAGCACATT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
15 2 0.10
16 8 0.40
17 4 0.20
18 6 0.30
ACGTcount: A:0.26, C:0.00, G:0.08, T:0.66
Consensus pattern (17 bp):
TATTTTATATATGATGT
Found at i:4269659 original size:16 final size:18
Alignment explanation
Indices: 4269640--4269675 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
4269630 GTTTATACTA
4269640 TTTTATAT-T-ATGTTAT
1 TTTTATATATGATGTTAT
4269656 TTTTATATATGATGTTAT
1 TTTTATATATGATGTTAT
4269674 TT
1 TT
4269676 AGAGCACATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
17 1 0.06
18 9 0.50
ACGTcount: A:0.25, C:0.00, G:0.08, T:0.67
Consensus pattern (18 bp):
TTTTATATATGATGTTAT
Found at i:4271104 original size:69 final size:69
Alignment explanation
Indices: 4270991--4271121 Score: 208
Period size: 69 Copynumber: 1.9 Consensus size: 69
4270981 GTGCGGAAGT
* *
4270991 CTCTTTGGGCAAAGGCAAATCTAACTTTTGTCGGAAATCCAAAGCAACATTTGGGCAGCAACTTT
1 CTCTTTGGACAAAGACAAATCTAACTTTTGTCGGAAATCCAAAGCAACATTTGGGCAGCAACTTT
4271056 TAGG
66 TAGG
* ** *
4271060 CTCTTTGGACAAAGACAAATCTACCTTTTGTCGGAAATTTAAAGCAACGTTTGGGCAGCAAC
1 CTCTTTGGACAAAGACAAATCTAACTTTTGTCGGAAATCCAAAGCAACATTTGGGCAGCAAC
4271122 AGCTTAATCT
Statistics
Matches: 56, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
69 56 1.00
ACGTcount: A:0.31, C:0.21, G:0.21, T:0.27
Consensus pattern (69 bp):
CTCTTTGGACAAAGACAAATCTAACTTTTGTCGGAAATCCAAAGCAACATTTGGGCAGCAACTTT
TAGG
Found at i:4272895 original size:25 final size:26
Alignment explanation
Indices: 4272867--4272917 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
4272857 TATAATATAT
4272867 TATATCAAA-TA-ATATTAAATTTTAA
1 TATATCAAACTATATATT-AATTTTAA
*
4272892 TATATTAAACTATATATTAATTTTAA
1 TATATCAAACTATATATTAATTTTAA
4272918 AACTATGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 8 0.35
26 10 0.43
27 5 0.22
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (26 bp):
TATATCAAACTATATATTAATTTTAA
Found at i:4274226 original size:51 final size:49
Alignment explanation
Indices: 4274158--4274315 Score: 218
Period size: 51 Copynumber: 3.2 Consensus size: 49
4274148 ATCACATTTA
4274158 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCACTT
1 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCA-TT
* *
4274208 GTCACTTGTCACTGATCAGATAAGTGTTGCTGAAGCTACCAC-T-T-A--
1 -TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCATT
*
4274253 TCACTTGTCACTGATCAGATAAGTTTAGCTAAAGCTACCACTTATCTATT
1 TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATC-ATT
4274303 ATCACTTGTCACT
1 -TCACTTGTCACT
4274316 TGTCACTGAC
Statistics
Matches: 95, Mismatches: 5, Indels: 14
0.83 0.04 0.12
Matches are distributed among these distances:
44 38 0.40
45 1 0.01
46 1 0.01
48 2 0.02
49 1 0.01
50 1 0.01
51 51 0.54
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.34
Consensus pattern (49 bp):
TCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCACTTATCATT
Found at i:4274251 original size:44 final size:44
Alignment explanation
Indices: 4274155--4274298 Score: 191
Period size: 44 Copynumber: 3.1 Consensus size: 44
4274145 CGGATCACAT
*
4274155 TTATCACTTGTCACTGATCAGATAAGTGTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTGATCAGATAAGTTTAGCTAAAGCTACCAC
*
4274199 TTATCACTTGTCACTTGTCACTGATCAGATAAGTGTT-GCTGAAGCTACCAC
1 -T-T-A----TCACTTGTCACTGATCAGATAAGT-TTAGCTAAAGCTACCAC
4274250 TTATCACTTGTCACTGATCAGATAAGTTTAGCTAAAGCTACCAC
1 TTATCACTTGTCACTGATCAGATAAGTTTAGCTAAAGCTACCAC
4274294 TTATC
1 TTATC
4274299 TATTATCACT
Statistics
Matches: 88, Mismatches: 3, Indels: 17
0.81 0.03 0.16
Matches are distributed among these distances:
43 2 0.02
44 42 0.48
45 1 0.01
46 1 0.01
47 1 0.01
48 1 0.01
49 1 0.01
50 1 0.01
51 37 0.42
52 1 0.01
ACGTcount: A:0.29, C:0.23, G:0.15, T:0.33
Consensus pattern (44 bp):
TTATCACTTGTCACTGATCAGATAAGTTTAGCTAAAGCTACCAC
Found at i:4276273 original size:3 final size:3
Alignment explanation
Indices: 4276260--4276333 Score: 139
Period size: 3 Copynumber: 24.3 Consensus size: 3
4276250 TATCCTTGTC
4276260 TAT TCAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT T-AT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
4276306 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
4276334 TATATCCTTT
Statistics
Matches: 70, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
3 67 0.96
4 3 0.04
ACGTcount: A:0.32, C:0.01, G:0.00, T:0.66
Consensus pattern (3 bp):
TAT
Found at i:4279327 original size:29 final size:31
Alignment explanation
Indices: 4279261--4279327 Score: 75
Period size: 31 Copynumber: 2.2 Consensus size: 31
4279251 TATTGGGCTG
* * * *
4279261 TACATATATATCTTTATATATTTTTTTAATT
1 TACATATATATATATATATACTTTTTTAATC
*
4279292 TATATATATATATATATAT-CTTTTTT-ATC
1 TACATATATATATATATATACTTTTTTAATC
4279321 TACATAT
1 TACATAT
4279328 CTTTACATAC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
29 8 0.27
30 6 0.20
31 16 0.53
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.58
Consensus pattern (31 bp):
TACATATATATATATATATACTTTTTTAATC
Found at i:4279403 original size:6 final size:6
Alignment explanation
Indices: 4279392--4279421 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
4279382 TACATACTTT
4279392 ATATAC ATATAC ATATAC ATATAC ATATAC
1 ATATAC ATATAC ATATAC ATATAC ATATAC
4279422 CCTTTTGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.50, C:0.17, G:0.00, T:0.33
Consensus pattern (6 bp):
ATATAC
Found at i:4283880 original size:1 final size:1
Alignment explanation
Indices: 4283876--4283955 Score: 52
Period size: 1 Copynumber: 80.0 Consensus size: 1
4283866 TTCAAAAACC
* * * * * * * * * *
4283876 AAAAAAAAAAGAAAAAAGAACAAAAAAGAAAAAATAACAAAAAAGAAAAGAAAAAAAGAAAAATA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
* *
4283941 AAAGAAAAAGAAAAA
1 AAAAAAAAAAAAAAA
4283956 GGAGAGGCCA
Statistics
Matches: 55, Mismatches: 24, Indels: 0
0.70 0.30 0.00
Matches are distributed among these distances:
1 55 1.00
ACGTcount: A:0.85, C:0.03, G:0.10, T:0.03
Consensus pattern (1 bp):
A
Found at i:4283900 original size:17 final size:16
Alignment explanation
Indices: 4283878--4283955 Score: 83
Period size: 17 Copynumber: 4.9 Consensus size: 16
4283868 CAAAAACCAA
4283878 AAAAAAAAGAAAAAAG
1 AAAAAAAAGAAAAAAG
*
4283894 AACAAAAAAGAAAAAAT
1 AA-AAAAAAGAAAAAAG
4283911 AACAAAAAAG--AAAAG
1 AA-AAAAAAGAAAAAAG
4283926 -AAAAAAAGAAAAATA-
1 AAAAAAAAGAAAAA-AG
4283941 AAAGAAAAAGAAAAA
1 AAA-AAAAAGAAAAA
4283956 GGAGAGGCCA
Statistics
Matches: 54, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
13 7 0.13
14 1 0.02
15 7 0.13
16 5 0.09
17 34 0.63
ACGTcount: A:0.85, C:0.03, G:0.10, T:0.03
Consensus pattern (16 bp):
AAAAAAAAGAAAAAAG
Found at i:4283929 original size:11 final size:10
Alignment explanation
Indices: 4283876--4283954 Score: 72
Period size: 10 Copynumber: 7.8 Consensus size: 10
4283866 TTCAAAAACC
4283876 AAAAAAAA-A
1 AAAAAAAAGA
*
4283885 AGAAAAAAGA
1 AAAAAAAAGA
*
4283895 ACAAAAAAGA
1 AAAAAAAAGA
* *
4283905 AAAAATAACA
1 AAAAAAAAGA
4283915 AAAAAGAAA-A
1 AAAAA-AAAGA
*
4283925 GAAAAAAAGA
1 AAAAAAAAGA
4283935 AAAATAAAAGA
1 AAAA-AAAAGA
4283946 AAAAGAAAA
1 AAAA-AAAA
4283955 AGGAGAGGCC
Statistics
Matches: 57, Mismatches: 9, Indels: 6
0.79 0.12 0.08
Matches are distributed among these distances:
9 10 0.18
10 31 0.54
11 16 0.28
ACGTcount: A:0.85, C:0.03, G:0.10, T:0.03
Consensus pattern (10 bp):
AAAAAAAAGA
Found at i:4283933 original size:30 final size:30
Alignment explanation
Indices: 4283876--4283954 Score: 92
Period size: 29 Copynumber: 2.7 Consensus size: 30
4283866 TTCAAAAACC
* * *
4283876 AAAAAAAAAAGAAAAA-AGAA-CAAAAAAG
1 AAAAATAAAAGAAAAAGAAAAGAAAAAAAG
*
4283904 AAAAAATAACA-AAAAAGAAAAGAAAAAAAG
1 -AAAAATAAAAGAAAAAGAAAAGAAAAAAAG
4283934 AAAAATAAAAGAAAAAGAAAA
1 AAAAATAAAAGAAAAAGAAAA
4283955 AGGAGAGGCC
Statistics
Matches: 42, Mismatches: 5, Indels: 5
0.81 0.10 0.10
Matches are distributed among these distances:
28 5 0.12
29 20 0.48
30 17 0.40
ACGTcount: A:0.85, C:0.03, G:0.10, T:0.03
Consensus pattern (30 bp):
AAAAATAAAAGAAAAAGAAAAGAAAAAAAG
Found at i:4288689 original size:54 final size:54
Alignment explanation
Indices: 4288629--4288740 Score: 224
Period size: 54 Copynumber: 2.1 Consensus size: 54
4288619 GTTAAGATAC
4288629 AAAAGGAATTTAATTCCTTCTGTGTACGTCCATTTGCGACCCACCCGCCCCCCA
1 AAAAGGAATTTAATTCCTTCTGTGTACGTCCATTTGCGACCCACCCGCCCCCCA
4288683 AAAAGGAATTTAATTCCTTCTGTGTACGTCCATTTGCGACCCACCCGCCCCCCA
1 AAAAGGAATTTAATTCCTTCTGTGTACGTCCATTTGCGACCCACCCGCCCCCCA
4288737 AAAA
1 AAAA
4288741 ATATGGTTGA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 58 1.00
ACGTcount: A:0.27, C:0.34, G:0.14, T:0.25
Consensus pattern (54 bp):
AAAAGGAATTTAATTCCTTCTGTGTACGTCCATTTGCGACCCACCCGCCCCCCA
Found at i:4289502 original size:15 final size:17
Alignment explanation
Indices: 4289476--4289507 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
4289466 AAAGTTCGAG
4289476 GGGAGAGAAAAA-TAAA
1 GGGAGAGAAAAAGTAAA
4289492 GGGAG-GAAAAAGTAAA
1 GGGAGAGAAAAAGTAAA
4289508 AAGGATAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 6 0.40
16 9 0.60
ACGTcount: A:0.59, C:0.00, G:0.34, T:0.06
Consensus pattern (17 bp):
GGGAGAGAAAAAGTAAA
Found at i:4291735 original size:22 final size:22
Alignment explanation
Indices: 4291685--4291738 Score: 65
Period size: 22 Copynumber: 2.5 Consensus size: 22
4291675 AATTTAAAAC
* *
4291685 TTAAAAATAAAAACTAAATTAT
1 TTAAAAATAAAAACTAAATGAA
*
4291707 TTTAAAATAAAAA-TAAATAGAA
1 TTAAAAATAAAAACTAAAT-GAA
4291729 TTAAAAATAA
1 TTAAAAATAA
4291739 TATAAAACAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 5 0.19
22 22 0.81
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (22 bp):
TTAAAAATAAAAACTAAATGAA
Found at i:4292464 original size:35 final size:35
Alignment explanation
Indices: 4292424--4292543 Score: 177
Period size: 35 Copynumber: 3.3 Consensus size: 35
4292414 TGTTCCCGGC
*
4292424 CCCAACCCAAGCAAGTTGAACTCTCCTCTTTCATT
1 CCCAACCCAAGCAAGCTGAACTCTCCTCTTTCATT
*
4292459 CCCAACCCAAGCAAGCAAGCCGAACTCTCCTCTTTCATT
1 CCCAA-CC---CAAGCAAGCTGAACTCTCCTCTTTCATT
*
4292498 CCCAACCCAAGCAAGCTAAACTCTCCTCTTTCATT
1 CCCAACCCAAGCAAGCTGAACTCTCCTCTTTCATT
4292533 CCCAACCCAAG
1 CCCAACCCAAG
4292544 AAAAAAGGAG
Statistics
Matches: 77, Mismatches: 4, Indels: 8
0.87 0.04 0.09
Matches are distributed among these distances:
35 42 0.55
36 2 0.03
38 2 0.03
39 31 0.40
ACGTcount: A:0.28, C:0.41, G:0.08, T:0.23
Consensus pattern (35 bp):
CCCAACCCAAGCAAGCTGAACTCTCCTCTTTCATT
Found at i:4292474 original size:39 final size:38
Alignment explanation
Indices: 4292431--4292543 Score: 169
Period size: 39 Copynumber: 3.0 Consensus size: 38
4292421 GGCCCCAACC
4292431 CAAGCAAGTTGAACTCTCCTCTTTCATTCCCAACCCAAG
1 CAAGCAAG-TGAACTCTCCTCTTTCATTCCCAACCCAAG
*
4292470 CAAGCAAGCCGAACTCTCCTCTTTCATTCCCAACCCAAG
1 CAAGCAAG-TGAACTCTCCTCTTTCATTCCCAACCCAAG
*
4292509 CAAGC---TAAACTCTCCTCTTTCATTCCCAACCCAAG
1 CAAGCAAGTGAACTCTCCTCTTTCATTCCCAACCCAAG
4292544 AAAAAAGGAG
Statistics
Matches: 70, Mismatches: 4, Indels: 4
0.90 0.05 0.05
Matches are distributed among these distances:
35 28 0.40
39 42 0.60
ACGTcount: A:0.28, C:0.39, G:0.09, T:0.24
Consensus pattern (38 bp):
CAAGCAAGTGAACTCTCCTCTTTCATTCCCAACCCAAG
Found at i:4297464 original size:20 final size:19
Alignment explanation
Indices: 4297408--4297466 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
4297398 CAAATTTCTC
*
4297408 ATTAAGCCCGAAATATATT
1 ATTAAGCCCAAAATATATT
* ** * *
4297427 AATAATTCTAAAACATATAT
1 ATTAAGCCCAAAATATAT-T
4297447 ATTAAGCCCAAAATATATT
1 ATTAAGCCCAAAATATATT
4297466 A
1 A
4297467 ACAATTCAAA
Statistics
Matches: 28, Mismatches: 11, Indels: 2
0.68 0.27 0.05
Matches are distributed among these distances:
19 14 0.50
20 14 0.50
ACGTcount: A:0.49, C:0.14, G:0.05, T:0.32
Consensus pattern (19 bp):
ATTAAGCCCAAAATATATT
Found at i:4299649 original size:43 final size:43
Alignment explanation
Indices: 4299601--4299726 Score: 152
Period size: 43 Copynumber: 2.9 Consensus size: 43
4299591 GAAGCTCGTA
* * *
4299601 CAATGCCAACGTCCCAGACGTGGTCTTATATGTAATCACATA-T
1 CAATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACA-AGT
4299644 CAATGCC-ACTGTCCCAGACAG-GGTCTTACACGTAAACACAAGT
1 CAATGCCAAC-GTCCCAGAC-GTGGTCTTACACGTAAACACAAGT
*
4299687 CGATGCCAACGTCCCAGACGTGGTCTTACACG-ATAACACA
1 CAATGCCAACGTCCCAGACGTGGTCTTACACGTA-AACACA
4299727 TATCGGAAAT
Statistics
Matches: 73, Mismatches: 4, Indels: 12
0.82 0.04 0.13
Matches are distributed among these distances:
42 5 0.07
43 65 0.89
44 3 0.04
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.21
Consensus pattern (43 bp):
CAATGCCAACGTCCCAGACGTGGTCTTACACGTAAACACAAGT
Found at i:4301707 original size:23 final size:23
Alignment explanation
Indices: 4301671--4301964 Score: 345
Period size: 23 Copynumber: 12.7 Consensus size: 23
4301661 TCTACCTTGT
* *
4301671 TTGGACAGCTTTTATACATCAAA
1 TTGGACAGCATTTATACACCAAA
* * *
4301694 TCGGACAGCATTTATAGACCCAA
1 TTGGACAGCATTTATACACCAAA
* *
4301717 TTGGACAACATATATATATACCAAA
1 TTGGACAGCAT-T-TATACACCAAA
* * * *
4301742 TTGGGCAACATATAAACACCAAA
1 TTGGACAGCATTTATACACCAAA
4301765 TTGGACAGCATTTATACACCAAA
1 TTGGACAGCATTTATACACCAAA
* * *
4301788 TCGGACAGCATATATACACTAAA
1 TTGGACAGCATTTATACACCAAA
*
4301811 TTAGACAGCATTTATACACCAAA
1 TTGGACAGCATTTATACACCAAA
* *
4301834 TTGGACAGCATATATACACTAAA
1 TTGGACAGCATTTATACACCAAA
*
4301857 TTGGACAACATTTATACACCAAA
1 TTGGACAGCATTTATACACCAAA
*
4301880 TTGGACAGTATTTATACACCAAA
1 TTGGACAGCATTTATACACCAAA
* * *
4301903 TTGGAAAGCATATATACACTAAA
1 TTGGACAGCATTTATACACCAAA
* *
4301926 TTGAACAACATTTATACACCAAA
1 TTGGACAGCATTTATACACCAAA
*
4301949 TTGGACAGCATATATA
1 TTGGACAGCATTTATA
4301965 TATACCCAAT
Statistics
Matches: 225, Mismatches: 44, Indels: 4
0.82 0.16 0.01
Matches are distributed among these distances:
23 205 0.91
24 1 0.00
25 19 0.08
ACGTcount: A:0.43, C:0.19, G:0.12, T:0.26
Consensus pattern (23 bp):
TTGGACAGCATTTATACACCAAA
Found at i:4304849 original size:34 final size:33
Alignment explanation
Indices: 4304798--4304924 Score: 166
Period size: 34 Copynumber: 3.8 Consensus size: 33
4304788 CACAAAATTA
*
4304798 TTTTTAAAAA-ACTAAACCCTAATTTAATTAAT
1 TTTTTAAAAACTCTAAACCCTAATTTAATTAAT
4304830 TTTCTTAAAAACTCTAAACCCTAATTTAATTAAT
1 TTT-TTAAAAACTCTAAACCCTAATTTAATTAAT
* * * *
4304864 TAATTTAAAACCCCTAAAACCTAATTTAATTAAT
1 T-TTTTAAAAACTCTAAACCCTAATTTAATTAAT
* *
4304898 TTTTTAAAAACTTTAAACCCCAATTTA
1 TTTTTAAAAACTCTAAACCCTAATTTA
4304925 TTTTTTAAAA
Statistics
Matches: 81, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
32 3 0.04
33 27 0.33
34 50 0.62
35 1 0.01
ACGTcount: A:0.44, C:0.17, G:0.00, T:0.39
Consensus pattern (33 bp):
TTTTTAAAAACTCTAAACCCTAATTTAATTAAT
Found at i:4304929 original size:28 final size:28
Alignment explanation
Indices: 4304891--4304945 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
4304881 AACCTAATTT
4304891 AATTAATTTTTTAAAAACT-TTAAACCCC
1 AATTAATTTTTT-AAAACTCTTAAACCCC
*
4304919 AATTTATTTTTTAAAACTCTTAAACCC
1 AATTAATTTTTTAAAACTCTTAAACCC
4304946 TAAATAAATA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 6 0.24
28 19 0.76
ACGTcount: A:0.40, C:0.18, G:0.00, T:0.42
Consensus pattern (28 bp):
AATTAATTTTTTAAAACTCTTAAACCCC
Found at i:4309147 original size:18 final size:19
Alignment explanation
Indices: 4309102--4309150 Score: 66
Period size: 18 Copynumber: 2.7 Consensus size: 19
4309092 ACTTAAGTGC
* *
4309102 TTTAATTTTTATTTGTTTA
1 TTTACTTTTTATTTGTTGA
4309121 TTTAC-TTTTATTTGTTGA
1 TTTACTTTTTATTTGTTGA
4309139 TTT-CTTTTTATT
1 TTTACTTTTTATT
4309151 ATATATTTGC
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 1 0.04
18 22 0.81
19 4 0.15
ACGTcount: A:0.16, C:0.04, G:0.06, T:0.73
Consensus pattern (19 bp):
TTTACTTTTTATTTGTTGA
Found at i:4315792 original size:9 final size:9
Alignment explanation
Indices: 4315778--4315813 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
4315768 ATTATATATT
4315778 TTTTTTTAA
1 TTTTTTTAA
4315787 TTTTTTTAA
1 TTTTTTTAA
**
4315796 TTTTTTTGT
1 TTTTTTTAA
4315805 TTTTTTTAA
1 TTTTTTTAA
4315814 ATAAGAAAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 23 1.00
ACGTcount: A:0.17, C:0.00, G:0.03, T:0.81
Consensus pattern (9 bp):
TTTTTTTAA
Found at i:4316339 original size:4 final size:4
Alignment explanation
Indices: 4316310--4316358 Score: 66
Period size: 4 Copynumber: 12.2 Consensus size: 4
4316300 TGTCAACCAT
4316310 CATA CATAA CATA CACT- CAT- CATA CATA CATA CATA CATA CATA CATA
1 CATA CAT-A CATA CA-TA CATA CATA CATA CATA CATA CATA CATA CATA
4316358 C
1 C
4316359 CTTATCAACC
Statistics
Matches: 42, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
3 4 0.10
4 33 0.79
5 5 0.12
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (4 bp):
CATA
Found at i:4316358 original size:20 final size:19
Alignment explanation
Indices: 4316307--4316358 Score: 74
Period size: 16 Copynumber: 2.8 Consensus size: 19
4316297 ATTTGTCAAC
4316307 CATCATACATAACATACACT
1 CATCATACAT-ACATACACT
4316327 CATCATACATACATACA-T
1 CATCATACATACATACACT
4316345 -A-CATACATACATAC
1 CATCATACATACATAC
4316359 CTTATCAACC
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
16 13 0.41
17 1 0.03
18 1 0.03
19 7 0.22
20 10 0.31
ACGTcount: A:0.46, C:0.29, G:0.00, T:0.25
Consensus pattern (19 bp):
CATCATACATACATACACT
Found at i:4317060 original size:32 final size:32
Alignment explanation
Indices: 4317019--4317084 Score: 123
Period size: 32 Copynumber: 2.1 Consensus size: 32
4317009 AATACAGTAT
4317019 ATTATAAATATTGTGGTCATCATGACTTAACC
1 ATTATAAATATTGTGGTCATCATGACTTAACC
*
4317051 ATTATAAATATTGTGGTCATCATGATTTAACC
1 ATTATAAATATTGTGGTCATCATGACTTAACC
4317083 AT
1 AT
4317085 CTTAAAATAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.35, C:0.14, G:0.12, T:0.39
Consensus pattern (32 bp):
ATTATAAATATTGTGGTCATCATGACTTAACC
Found at i:4317773 original size:15 final size:15
Alignment explanation
Indices: 4317753--4317785 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
4317743 TGGTGGGGCA
4317753 CAAATCTCACCTTGT
1 CAAATCTCACCTTGT
*
4317768 CAAATCTCGCCTTGT
1 CAAATCTCACCTTGT
4317783 CAA
1 CAA
4317786 TCCATGGTCC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.27, C:0.33, G:0.09, T:0.30
Consensus pattern (15 bp):
CAAATCTCACCTTGT
Found at i:4321680 original size:28 final size:27
Alignment explanation
Indices: 4321615--4321688 Score: 78
Period size: 28 Copynumber: 2.6 Consensus size: 27
4321605 TATTATTTTG
4321615 TTTTCATAGTTTCTATATATATGTATATAC
1 TTTTCATA-TTT-TATA-ATATGTATATAC
* * *
4321645 ATTT-ATATTTTATAATATTTATATAGT
1 TTTTCATATTTTATAATATGTATATA-C
4321672 TTTTCATATTTTATAAT
1 TTTTCATATTTTATAAT
4321689 CCAAATATAT
Statistics
Matches: 38, Mismatches: 4, Indels: 6
0.79 0.08 0.12
Matches are distributed among these distances:
26 10 0.26
27 7 0.18
28 15 0.39
29 3 0.08
30 3 0.08
ACGTcount: A:0.32, C:0.05, G:0.04, T:0.58
Consensus pattern (27 bp):
TTTTCATATTTTATAATATGTATATAC
Found at i:4321755 original size:19 final size:19
Alignment explanation
Indices: 4321694--4321755 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
4321684 ATAATCCAAA
*
4321694 TATATATACATTTTTTTCT
1 TATATATACATATTTTTCT
*
4321713 TATATATACATA-TTTTCA
1 TATATATACATATTTTTCT
*
4321731 TATTATATTAGTATATTTTTCT
1 TA-TATA-TA-CATATTTTTCT
4321753 TAT
1 TAT
4321756 GTTTTTATTT
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
18 7 0.20
19 15 0.43
20 2 0.06
21 4 0.11
22 7 0.20
ACGTcount: A:0.31, C:0.08, G:0.02, T:0.60
Consensus pattern (19 bp):
TATATATACATATTTTTCT
Found at i:4344691 original size:16 final size:16
Alignment explanation
Indices: 4344670--4344702 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
4344660 GTAAGACTAC
4344670 ATACATAAGCAAAATT
1 ATACATAAGCAAAATT
4344686 ATACATAAGCAAAATT
1 ATACATAAGCAAAATT
4344702 A
1 A
4344703 AAAAGTGTAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.12, G:0.06, T:0.24
Consensus pattern (16 bp):
ATACATAAGCAAAATT
Found at i:4347128 original size:97 final size:98
Alignment explanation
Indices: 4347023--4347199 Score: 302
Period size: 97 Copynumber: 1.8 Consensus size: 98
4347013 TTTTAGGGGG
* *
4347023 TTTTAAGTGAAAGGATCACAAAGAAAAGAAAAATTGCAAAAAA-ATCCAATTACACAAATTTTGA
1 TTTTAAGTGAAAAGATCACAAAGAAAAGAAAAATTGCAAAAAAGATCAAATTACACAAATTTTGA
4347087 ATGTTGAAGGTTAGAATAATTTTATTTTTGGGA
66 ATGTTGAAGGTTAGAATAATTTTATTTTTGGGA
* * *
4347120 TTTTAAGTGAAAAGATTACAAAGAAAAGAAGAATTGCAAAAAAGATTAAATTACACAAATTTTGA
1 TTTTAAGTGAAAAGATCACAAAGAAAAGAAAAATTGCAAAAAAGATCAAATTACACAAATTTTGA
4347185 ATGTTGAAGGTTAGA
66 ATGTTGAAGGTTAGA
4347200 TTTTTATAAT
Statistics
Matches: 74, Mismatches: 5, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
97 40 0.54
98 34 0.46
ACGTcount: A:0.47, C:0.06, G:0.17, T:0.29
Consensus pattern (98 bp):
TTTTAAGTGAAAAGATCACAAAGAAAAGAAAAATTGCAAAAAAGATCAAATTACACAAATTTTGA
ATGTTGAAGGTTAGAATAATTTTATTTTTGGGA
Found at i:4357920 original size:15 final size:15
Alignment explanation
Indices: 4357900--4357930 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
4357890 CATTTTTAGA
4357900 ATTTTAGAATTATAT
1 ATTTTAGAATTATAT
*
4357915 ATTTTAGAATTTTAT
1 ATTTTAGAATTATAT
4357930 A
1 A
4357931 AAAAAATTCT
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:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (15 bp):
ATTTTAGAATTATAT
Found at i:4367231 original size:90 final size:90
Alignment explanation
Indices: 4367118--4367304 Score: 347
Period size: 90 Copynumber: 2.1 Consensus size: 90
4367108 TACCGGAATA
*
4367118 TACATTTATTAATGGTTAAATTCTATCGTCAATATTATGAGCAAGTTGTTGATTTAGTCAATGTG
1 TACATTTATTAATGGTTAAATTCTATCGTCAATATTATGAGCAAGTTGTTGATTTAGTCAATGTA
*
4367183 CTAATTTAATTATTTTTGATATTTG
66 CTAATTTAATTATTTTTAATATTTG
*
4367208 TACATTTATTAATGGTTAAATTCTATCTTCAATATTATGAGCAAGTTGTTGATTTAGTCAATGTA
1 TACATTTATTAATGGTTAAATTCTATCGTCAATATTATGAGCAAGTTGTTGATTTAGTCAATGTA
4367273 CTAATTTAATTATTTTTAATATTTG
66 CTAATTTAATTATTTTTAATATTTG
4367298 TACATTT
1 TACATTT
4367305 TATATTTTAA
Statistics
Matches: 94, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
90 94 1.00
ACGTcount: A:0.31, C:0.08, G:0.12, T:0.49
Consensus pattern (90 bp):
TACATTTATTAATGGTTAAATTCTATCGTCAATATTATGAGCAAGTTGTTGATTTAGTCAATGTA
CTAATTTAATTATTTTTAATATTTG
Found at i:4367717 original size:15 final size:18
Alignment explanation
Indices: 4367694--4367737 Score: 60
Period size: 15 Copynumber: 2.7 Consensus size: 18
4367684 GGACTTAGTT
4367694 GCGTT-GCGTTGGG-TTG
1 GCGTTGGCGTTGGGTTTG
4367710 G-G-TGGCGTTGGGTTTG
1 GCGTTGGCGTTGGGTTTG
4367726 GCGTTGGCGTTG
1 GCGTTGGCGTTG
4367738 ACCTCAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
14 1 0.04
15 9 0.38
16 5 0.21
17 1 0.04
18 8 0.33
ACGTcount: A:0.00, C:0.11, G:0.52, T:0.36
Consensus pattern (18 bp):
GCGTTGGCGTTGGGTTTG
Found at i:4372479 original size:17 final size:18
Alignment explanation
Indices: 4372457--4372496 Score: 73
Period size: 17 Copynumber: 2.3 Consensus size: 18
4372447 GGATATGGTG
4372457 ACCTTGTAATCAACCAA-
1 ACCTTGTAATCAACCAAC
4372474 ACCTTGTAATCAACCAAC
1 ACCTTGTAATCAACCAAC
4372492 ACCTT
1 ACCTT
4372497 TAGGCTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
17 17 0.77
18 5 0.23
ACGTcount: A:0.38, C:0.33, G:0.05, T:0.25
Consensus pattern (18 bp):
ACCTTGTAATCAACCAAC
Found at i:4388789 original size:97 final size:97
Alignment explanation
Indices: 4388623--4388817 Score: 286
Period size: 97 Copynumber: 2.0 Consensus size: 97
4388613 TATTTTATTT
* *
4388623 TAATAAAAATTAGGGTCACACAATTTCTAACATCACCGAAGAGAAACTGTTCCATCAACTATATT
1 TAATAAAAATTAGAGTCACACAACTTCTAACATCACCGAAGAGAAACTGTTCCATCAACTATATT
*
4388688 GCATGAATTAGATAATAGAGTTGTTGTTAACA
66 GCATGAATTAGATAATAGAGTTGCTGTTAACA
* * *
4388720 TAATAAAAATTTA-AGTCACAGAACTTCTAACGTCACCGAAGAGAAACTG-TCTCATCAATTATA
1 TAATAAAAA-TTAGAGTCACACAACTTCTAACATCACCGAAGAGAAACTGTTC-CATCAACTATA
* *
4388783 TTGCATGAATTAGATGATGGAGTTGCTGTTAACA
64 TTGCATGAATTAGATAATAGAGTTGCTGTTAACA
4388817 T
1 T
4388818 TTGTATATTT
Statistics
Matches: 88, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
96 2 0.02
97 83 0.94
98 3 0.03
ACGTcount: A:0.39, C:0.15, G:0.15, T:0.30
Consensus pattern (97 bp):
TAATAAAAATTAGAGTCACACAACTTCTAACATCACCGAAGAGAAACTGTTCCATCAACTATATT
GCATGAATTAGATAATAGAGTTGCTGTTAACA
Found at i:4390609 original size:26 final size:26
Alignment explanation
Indices: 4390554--4390610 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
4390544 TTTAATTCTT
*
4390554 TTAAATAATTTTATATTTAAAAAATA
1 TTAAATAATTTTATATTAAAAAAATA
* *
4390580 TTAAATAATTTTCTA-TAAAAAGAATC
1 TTAAATAATTTTATATTAAAAA-AATA
4390606 TTAAA
1 TTAAA
4390611 CAATCAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
25 5 0.19
26 22 0.81
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.42
Consensus pattern (26 bp):
TTAAATAATTTTATATTAAAAAAATA
Found at i:4401798 original size:67 final size:65
Alignment explanation
Indices: 4401661--4401834 Score: 149
Period size: 65 Copynumber: 2.6 Consensus size: 65
4401651 ATTACCTTTC
** *
4401661 GCTC-TCATGTTATTTTTGGATGCAACTACCATGTTGATTGTGGGTCTCATATATATGGAGCTTC
1 GCTCTTCATGTTATTTTTCAATGCAACTACCATGTTGATTGTGGGTCTCA-ATATATGAAGCTTC
4401725 G
65 G
* * * * *
4401726 GCTCTTTTCATGTTATTTTTCAAT-TAACTACTATGTTGATTTTGGGTCTC-ATATGTGAATCTT
1 GCTC--TTCATGTTATTTTTCAATGCAACTACCATGTTGATTGTGGGTCTCAATATATGAAGCTT
4401789 CG
64 CG
* * * * *
4401791 ACTCTCTTCATGTTGTTTTTGGAA-GCAACTATCATGTTAATTGT
1 --GCTCTTCATGTTATTTTT-CAATGCAACTACCATGTTGATTGT
4401835 AAGTATTGTT
Statistics
Matches: 86, Mismatches: 16, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
65 29 0.34
66 16 0.19
67 26 0.30
68 15 0.17
ACGTcount: A:0.21, C:0.16, G:0.18, T:0.45
Consensus pattern (65 bp):
GCTCTTCATGTTATTTTTCAATGCAACTACCATGTTGATTGTGGGTCTCAATATATGAAGCTTCG
Found at i:4406057 original size:23 final size:22
Alignment explanation
Indices: 4406008--4406058 Score: 84
Period size: 22 Copynumber: 2.3 Consensus size: 22
4405998 GTGAAAAGAG
*
4406008 TAAAAAAAATCGAAAACTATTC
1 TAAAAAAAATCGAAAACTATGC
4406030 TAAAAAAAATCGAAAACTATGC
1 TAAAAAAAATCGAAAACTATGC
*
4406052 TCAAAAA
1 TAAAAAA
4406059 TAGAAATCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.61, C:0.14, G:0.06, T:0.20
Consensus pattern (22 bp):
TAAAAAAAATCGAAAACTATGC
Found at i:4410247 original size:16 final size:16
Alignment explanation
Indices: 4410226--4410259 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
4410216 AAGCTCAAAT
4410226 TTGAAAGTTATGGCAA
1 TTGAAAGTTATGGCAA
4410242 TTGAAAGTTATGGCAA
1 TTGAAAGTTATGGCAA
4410258 TT
1 TT
4410260 TCGATTTTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.35, C:0.06, G:0.24, T:0.35
Consensus pattern (16 bp):
TTGAAAGTTATGGCAA
Found at i:4413716 original size:21 final size:21
Alignment explanation
Indices: 4413692--4413736 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 21
4413682 TTCACATTCG
*
4413692 TTTT-TACTAATTCAATATGGT
1 TTTTCTACTAATTAAATAT-GT
*
4413713 TTTTCTACTAGTTAAATATGT
1 TTTTCTACTAATTAAATATGT
4413734 TTT
1 TTT
4413737 AGACCAATAC
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 9 0.43
22 12 0.57
ACGTcount: A:0.27, C:0.09, G:0.09, T:0.56
Consensus pattern (21 bp):
TTTTCTACTAATTAAATATGT
Found at i:4415936 original size:16 final size:18
Alignment explanation
Indices: 4415894--4415936 Score: 54
Period size: 16 Copynumber: 2.5 Consensus size: 18
4415884 ACTCGATGGA
4415894 AAATATTAACTTATTTTT
1 AAATATTAACTTATTTTT
* *
4415912 ATATTTTAA-TTA-TTTT
1 AAATATTAACTTATTTTT
4415928 AAATATTAA
1 AAATATTAA
4415937 ATGGACTATA
Statistics
Matches: 21, Mismatches: 4, Indels: 2
0.78 0.15 0.07
Matches are distributed among these distances:
16 11 0.52
17 3 0.14
18 7 0.33
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (18 bp):
AAATATTAACTTATTTTT
Found at i:4416381 original size:32 final size:32
Alignment explanation
Indices: 4416340--4416404 Score: 112
Period size: 32 Copynumber: 2.0 Consensus size: 32
4416330 TTTTAATTGG
4416340 ATTATTATTAAATATAATTTAATAATAAAATA
1 ATTATTATTAAATATAATTTAATAATAAAATA
* *
4416372 ATTATTATTAAATATAATTTTATAATAATATA
1 ATTATTATTAAATATAATTTAATAATAAAATA
4416404 A
1 A
4416405 AATTTAATAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (32 bp):
ATTATTATTAAATATAATTTAATAATAAAATA
Found at i:4416465 original size:21 final size:23
Alignment explanation
Indices: 4416416--4416465 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 23
4416406 ATTTAATAAC
* * *
4416416 ATTTTTAATATAATTATGTTTTT
1 ATTTTTAATATAATCATGTTGTA
4416439 ATTTTTAATAT-ATCAT-TTGTA
1 ATTTTTAATATAATCATGTTGTA
4416460 ATTTTT
1 ATTTTT
4416466 TTTAAATTGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 9 0.38
22 4 0.17
23 11 0.46
ACGTcount: A:0.30, C:0.02, G:0.04, T:0.64
Consensus pattern (23 bp):
ATTTTTAATATAATCATGTTGTA
Found at i:4423656 original size:7 final size:7
Alignment explanation
Indices: 4423644--4423670 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
4423634 AAATTTTTGA
4423644 AAGAATC
1 AAGAATC
4423651 AAGAATC
1 AAGAATC
4423658 AAGAATC
1 AAGAATC
4423665 AAGAAT
1 AAGAAT
4423671 TAAAATCACT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.59, C:0.11, G:0.15, T:0.15
Consensus pattern (7 bp):
AAGAATC
Done.