Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr9
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: 91122320
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.32
Warning! 2661692 characters in sequence are not A, C, G, or T
File 125 of 279
Found at i:39667695 original size:15 final size:15
Alignment explanation
Indices: 39667671--39667704 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
39667661 AACAATTACG
* *
39667671 ATAATGCGAGTAAAA
1 ATAATACGAGCAAAA
39667686 ATAATACGAGCAAAA
1 ATAATACGAGCAAAA
39667701 ATAA
1 ATAA
39667705 CAAAAAGTAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.09, G:0.15, T:0.18
Consensus pattern (15 bp):
ATAATACGAGCAAAA
Found at i:39669204 original size:16 final size:17
Alignment explanation
Indices: 39669183--39669227 Score: 56
Period size: 19 Copynumber: 2.6 Consensus size: 17
39669173 TACATAAAAT
*
39669183 AAATGATAAAT-ATAGG
1 AAATGAAAAATAATAGG
39669199 AAATGAAAAAATAGATAGG
1 AAATG-AAAAATA-ATAGG
39669218 AAATGAAAAA
1 AAATGAAAAA
39669228 AAATGAAACC
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
16 5 0.20
17 5 0.20
18 5 0.20
19 10 0.40
ACGTcount: A:0.64, C:0.00, G:0.18, T:0.18
Consensus pattern (17 bp):
AAATGAAAAATAATAGG
Found at i:39670172 original size:88 final size:89
Alignment explanation
Indices: 39670026--39670345 Score: 214
Period size: 86 Copynumber: 3.7 Consensus size: 89
39670016 GCCTACTCCA
* * * * * *
39670026 CTACTGCTTAGGGAGATAGGGTCTACAATTTCTAGCCTGTTACCTTATTGCTTAAGGGG-TTAAG
1 CTACTGCTTAGGGAGATAAGATCTAAAATTTCTAGCCTATTACCCTACTGCTTAAGGGGTTTAAG
*
39670090 GCTCGTCGTCTTCGATCTATTTCC
66 GCCCGTCGTCTTCGATCTATTTCC
* *
39670114 CTACTGCTTAGGGTGATAAGATCTATAAATTT-TCAGCCTATTACCCTACTG-TTTAGGGGTTTA
1 CTACTGCTTAGGGAGATAAGATCTA-AAATTTCT-AGCCTATTACCCTACTGCTTAAGGGGTTTA
* * **
39670177 AGGCCCTTCGTCTTTGATCT-GCTCC
64 AGGCCCGTCGTCTTCGATCTATTTCC
*** ** * * ** * * *
39670202 ACTACAATTTCAGGGAGGCAAAATTTGCAA-TT-TGGTCTGTTACCCTACCT-CTT-A-GGGTTT
1 -CTACTGCTT-AGGGAGATAAGATCTAAAATTTCTAGCCTATTACCCTA-CTGCTTAAGGGGTTT
* * *
39670262 AAGACCCTTCGTCTTCGATCTGTTTCC
63 AAGGCCCGTCGTCTTCGATCTATTTCC
* * * *
39670289 CTACTGCTTAGGGGGTTAAGATCTGGAAA-TTC-AGCCTATTACCCTACTG-TTTAGGGG
1 CTACTGCTTAGGGAGATAAGATCT-AAAATTTCTAGCCTATTACCCTACTGCTTAAGGGG
39670346 AACAGGATGG
Statistics
Matches: 177, Mismatches: 42, Indels: 27
0.72 0.17 0.11
Matches are distributed among these distances:
85 14 0.08
86 48 0.27
87 18 0.10
88 40 0.23
89 47 0.27
90 10 0.06
ACGTcount: A:0.21, C:0.22, G:0.21, T:0.36
Consensus pattern (89 bp):
CTACTGCTTAGGGAGATAAGATCTAAAATTTCTAGCCTATTACCCTACTGCTTAAGGGGTTTAAG
GCCCGTCGTCTTCGATCTATTTCC
Found at i:39670331 original size:86 final size:87
Alignment explanation
Indices: 39670095--39670345 Score: 217
Period size: 86 Copynumber: 2.9 Consensus size: 87
39670085 TTAAGGCTCG
* * *
39670095 TCGTCTTCGATCTATTTCCCTACTGCTTAGGGTGATAAGATCTATAAATTTTCAGCCTATTACCC
1 TCGTCTTCGATCTGTTTCCCTACTGCTTAGGG-GGTAAGATCTAGAAA--TTCAGCCTATTACCC
* *
39670160 TA-CTGTTTAGGGGTTTAAGGCCCT
63 TACCTGCTTAGGGGTTTAAGACCCT
* * *** * * * * ** * *
39670184 TCGTCTTTGATCTG-CTCCACTACAATTTCAGGGAGGCAAAAT-TTGCAATTTGGTCTGTTACCC
1 TCGTCTTCGATCTGTTTCC-CTACTGCTT-AGGG-GGTAAGATCTAGAAATTCAGCCTATTACCC
39670247 TACCT-CTTA-GGGTTTAAGACCCT
63 TACCTGCTTAGGGGTTTAAGACCCT
*
39670270 TCGTCTTCGATCTGTTTCCCTACTGCTTAGGGGGTTAAGATCTGGAAATTCAGCCTATTACCCTA
1 TCGTCTTCGATCTGTTTCCCTACTGCTTAGGGGG-TAAGATCTAGAAATTCAGCCTATTACCCTA
*
39670335 -CTGTTTAGGGG
65 CCTGCTTAGGGG
39670346 AACAGGATGG
Statistics
Matches: 121, Mismatches: 33, Indels: 18
0.70 0.19 0.10
Matches are distributed among these distances:
84 2 0.02
85 10 0.08
86 52 0.43
87 22 0.18
88 5 0.04
89 21 0.17
90 9 0.07
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (87 bp):
TCGTCTTCGATCTGTTTCCCTACTGCTTAGGGGGTAAGATCTAGAAATTCAGCCTATTACCCTAC
CTGCTTAGGGGTTTAAGACCCT
Found at i:39678484 original size:19 final size:20
Alignment explanation
Indices: 39678448--39678489 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
39678438 GTCTTTTTGC
* *
39678448 GAAATTTAATACACATG-AT
1 GAAATGTAATACAAATGAAT
*
39678467 GAAATGTAATGCAAATGAAT
1 GAAATGTAATACAAATGAAT
39678487 GAA
1 GAA
39678490 TGCAAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.26
Consensus pattern (20 bp):
GAAATGTAATACAAATGAAT
Found at i:39678561 original size:19 final size:20
Alignment explanation
Indices: 39678525--39678566 Score: 50
Period size: 19 Copynumber: 2.1 Consensus size: 20
39678515 TTCTTTTCAA
* *
39678525 GAAATTTAATACACATG-AT
1 GAAATGTAATACAAATGAAT
*
39678544 GAAATGTAATGCAAATGAAT
1 GAAATGTAATACAAATGAAT
39678564 GAA
1 GAA
39678567 TGCAAAAAAA
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.50, C:0.07, G:0.17, T:0.26
Consensus pattern (20 bp):
GAAATGTAATACAAATGAAT
Found at i:39678566 original size:77 final size:78
Alignment explanation
Indices: 39678448--39678591 Score: 281
Period size: 77 Copynumber: 1.9 Consensus size: 78
39678438 GTCTTTTTGC
39678448 GAAATTTAATACACATGATGAAATGTAATGCAAATGAATGAATGC-AAAAAAAGAGGCGTTGATT
1 GAAATTTAATACACATGATGAAATGTAATGCAAATGAATGAATGCAAAAAAAAGAGGCGTTGATT
39678512 CCGTTCTTTTCAA
66 CCGTTCTTTTCAA
39678525 GAAATTTAATACACATGATGAAATGTAATGCAAATGAATGAATGCAAAAAAAAGAGGCGTTGATT
1 GAAATTTAATACACATGATGAAATGTAATGCAAATGAATGAATGCAAAAAAAAGAGGCGTTGATT
39678590 CC
66 CC
39678592 AATTCAATTT
Statistics
Matches: 66, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
77 45 0.68
78 21 0.32
ACGTcount: A:0.44, C:0.11, G:0.19, T:0.26
Consensus pattern (78 bp):
GAAATTTAATACACATGATGAAATGTAATGCAAATGAATGAATGCAAAAAAAAGAGGCGTTGATT
CCGTTCTTTTCAA
Found at i:39681397 original size:26 final size:26
Alignment explanation
Indices: 39681367--39681429 Score: 90
Period size: 26 Copynumber: 2.4 Consensus size: 26
39681357 TATAAAATAA
39681367 AAGTTTTAAAGTATTTCATATTTATG
1 AAGTTTTAAAGTATTTCATATTTATG
* *
39681393 AAGTTATAAAGTTTTTCATATTTATG
1 AAGTTTTAAAGTATTTCATATTTATG
*
39681419 AAATTATTAAA
1 AAGTT-TTAAA
39681430 AAGTAAGGAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 28 0.88
27 4 0.12
ACGTcount: A:0.40, C:0.03, G:0.10, T:0.48
Consensus pattern (26 bp):
AAGTTTTAAAGTATTTCATATTTATG
Found at i:39681583 original size:60 final size:59
Alignment explanation
Indices: 39681455--39681586 Score: 187
Period size: 60 Copynumber: 2.2 Consensus size: 59
39681445 TCACTAATAC
39681455 TCACCCAACTATTAATAAATTTATTTTTGGTCACTCAACTATGAAAAGTTACAAAATGA
1 TCACCCAACTATTAATAAATTTATTTTTGGTCACTCAACTATGAAAAGTTACAAAATGA
* * * *
39681514 TCTCTCAACTATTAGTAAATTTATTTTTTGGTCACTTAACTATGAAAAGTTATC-AAATGGA
1 TCACCCAACTATTAATAAATTTA-TTTTTGGTCACTCAACTATGAAAAGTTA-CAAAAT-GA
39681575 -CACCCAACTATT
1 TCACCCAACTATT
39681587 CAATTTCTTC
Statistics
Matches: 64, Mismatches: 6, Indels: 5
0.85 0.08 0.07
Matches are distributed among these distances:
59 20 0.31
60 41 0.64
61 3 0.05
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.36
Consensus pattern (59 bp):
TCACCCAACTATTAATAAATTTATTTTTGGTCACTCAACTATGAAAAGTTACAAAATGA
Found at i:39690446 original size:17 final size:19
Alignment explanation
Indices: 39690426--39690475 Score: 50
Period size: 19 Copynumber: 2.6 Consensus size: 19
39690416 TTTAATTTTT
39690426 TATTAAATATAATAA-A-A
1 TATTAAATATAATAATAGA
*
39690443 TATTTAATATTTAATAATAGA
1 TA-TTAA-ATATAATAATAGA
*
39690464 TATTAAAGATAA
1 TATTAAATATAA
39690476 AGATATTTTA
Statistics
Matches: 26, Mismatches: 3, Indels: 6
0.74 0.09 0.17
Matches are distributed among these distances:
17 2 0.08
18 4 0.15
19 12 0.46
20 5 0.19
21 3 0.12
ACGTcount: A:0.56, C:0.00, G:0.04, T:0.40
Consensus pattern (19 bp):
TATTAAATATAATAATAGA
Found at i:39697109 original size:21 final size:21
Alignment explanation
Indices: 39697083--39697123 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
39697073 ATCTGCTCAA
* *
39697083 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
39697104 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
39697124 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:39701069 original size:16 final size:17
Alignment explanation
Indices: 39701025--39701069 Score: 51
Period size: 16 Copynumber: 2.8 Consensus size: 17
39701015 TAAAATTTTA
*
39701025 AAATTTAAATA-AATTT
1 AAATTAAAATATAATTT
*
39701041 ACATTAAAA-ATAA-TT
1 AAATTAAAATATAATTT
39701056 AAATTAAAATATAA
1 AAATTAAAATATAA
39701070 AGAATTAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 11 0.46
16 13 0.54
ACGTcount: A:0.62, C:0.02, G:0.00, T:0.36
Consensus pattern (17 bp):
AAATTAAAATATAATTT
Found at i:39701397 original size:13 final size:13
Alignment explanation
Indices: 39701379--39701405 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
39701369 TTCTTTTCTC
39701379 TCTTTTTTGTTTT
1 TCTTTTTTGTTTT
39701392 TCTTTTTTGTTTT
1 TCTTTTTTGTTTT
39701405 T
1 T
39701406 TTAATGAATA
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:0.00, C:0.07, G:0.07, T:0.85
Consensus pattern (13 bp):
TCTTTTTTGTTTT
Found at i:39701561 original size:28 final size:28
Alignment explanation
Indices: 39701512--39701566 Score: 83
Period size: 28 Copynumber: 2.0 Consensus size: 28
39701502 ATTATCAACC
39701512 CCATAAGTTATAAAACTCTTCCTATACT
1 CCATAAGTTATAAAACTCTTCCTATACT
* * *
39701540 CCATAAGTTATGAGACTTTTCCTATAC
1 CCATAAGTTATAAAACTCTTCCTATAC
39701567 CCTATTAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.33, C:0.24, G:0.07, T:0.36
Consensus pattern (28 bp):
CCATAAGTTATAAAACTCTTCCTATACT
Found at i:39707983 original size:39 final size:39
Alignment explanation
Indices: 39707888--39707976 Score: 151
Period size: 39 Copynumber: 2.3 Consensus size: 39
39707878 GCTCTGATGA
*
39707888 GCTTCAGTTAGCCTTCGGGCTTCCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGACTTCCGTTTAGCACTTATGT
* *
39707927 GCTTCAATTAGCCTTCGGACTTTCGTTTAGCACTTATGT
1 GCTTCAGTTAGCCTTCGGACTTCCGTTTAGCACTTATGT
39707966 GCTTCAGTTAG
1 GCTTCAGTTAG
39707977 ATTTCGGGTT
Statistics
Matches: 46, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 46 1.00
ACGTcount: A:0.16, C:0.24, G:0.21, T:0.39
Consensus pattern (39 bp):
GCTTCAGTTAGCCTTCGGACTTCCGTTTAGCACTTATGT
Found at i:39709662 original size:28 final size:28
Alignment explanation
Indices: 39709622--39709684 Score: 99
Period size: 28 Copynumber: 2.2 Consensus size: 28
39709612 GTCATTATCA
39709622 ACCCCATAAGTTATAAAACTCTTCCTAT
1 ACCCCATAAGTTATAAAACTCTTCCTAT
* * *
39709650 ACCCCATAAGTTATGAAGCTTTTCCTAT
1 ACCCCATAAGTTATAAAACTCTTCCTAT
39709678 ACCCCAT
1 ACCCCAT
39709685 TAATATGGGA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.32, C:0.30, G:0.06, T:0.32
Consensus pattern (28 bp):
ACCCCATAAGTTATAAAACTCTTCCTAT
Found at i:39721770 original size:52 final size:52
Alignment explanation
Indices: 39721691--39721796 Score: 176
Period size: 52 Copynumber: 2.0 Consensus size: 52
39721681 GAAAGAAAAA
*
39721691 AACCTTTTCCTCTAGATATATTCAATAAATTTGATAAATTGAGTCTTAACTT
1 AACCTTTTCCTCTAAATATATTCAATAAATTTGATAAATTGAGTCTTAACTT
* * *
39721743 AACCTTTTTCTTTAAATATATTTAATAAATTTGATAAATTGAGTCTTAACTT
1 AACCTTTTCCTCTAAATATATTCAATAAATTTGATAAATTGAGTCTTAACTT
39721795 AA
1 AA
39721797 TTTATATCAC
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 50 1.00
ACGTcount: A:0.37, C:0.12, G:0.07, T:0.44
Consensus pattern (52 bp):
AACCTTTTCCTCTAAATATATTCAATAAATTTGATAAATTGAGTCTTAACTT
Found at i:39740063 original size:8 final size:8
Alignment explanation
Indices: 39740052--39740090 Score: 51
Period size: 8 Copynumber: 4.8 Consensus size: 8
39740042 AGTTTTTTTT
39740052 TTTTTTAC
1 TTTTTTAC
*
39740060 TTTTTTAA
1 TTTTTTAC
39740068 TTTTTTGAC
1 TTTTTT-AC
*
39740077 TTTTGTAC
1 TTTTTTAC
39740085 TTTTTT
1 TTTTTT
39740091 TACTCTTCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
8 20 0.77
9 6 0.23
ACGTcount: A:0.13, C:0.08, G:0.05, T:0.74
Consensus pattern (8 bp):
TTTTTTAC
Found at i:39740071 original size:17 final size:17
Alignment explanation
Indices: 39740051--39740094 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
39740041 CAGTTTTTTT
*
39740051 TTTTTTTACTTTTTTAA
1 TTTTTTTACTTTTGTAA
* *
39740068 TTTTTTGACTTTTGTAC
1 TTTTTTTACTTTTGTAA
39740085 TTTTTTTACT
1 TTTTTTTACT
39740095 CTTCTTTATT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.14, C:0.09, G:0.05, T:0.73
Consensus pattern (17 bp):
TTTTTTTACTTTTGTAA
Found at i:39740195 original size:21 final size:21
Alignment explanation
Indices: 39740136--39740207 Score: 81
Period size: 21 Copynumber: 3.3 Consensus size: 21
39740126 TTAACTTTAA
* *
39740136 AAAATTTGAAATATATATTTG
1 AAAATTTTAAATATATATTTT
39740157 AAATATTTTATTAATATATATTTT
1 AAA-ATTTTA--AATATATATTTT
*
39740181 TAAATTTTAAATATATATTTT
1 AAAATTTTAAATATATATTTT
*
39740202 GAAATT
1 AAAATT
39740208 ACTTTTTTAA
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
21 20 0.45
22 5 0.11
23 6 0.14
24 13 0.30
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.51
Consensus pattern (21 bp):
AAAATTTTAAATATATATTTT
Found at i:39740233 original size:33 final size:33
Alignment explanation
Indices: 39740177--39740245 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 33
39740167 TTAATATATA
39740177 TTTTTAAATTTTAAATATATATTTTGAAATTACT
1 TTTTTAAATTTTAAATATATATTTTGAAATTA-T
39740211 TTTTTAAATTTTAAATAT-TATTTTGAAATTAT
1 TTTTTAAATTTTAAATATATATTTTGAAATTAT
39740243 TTT
1 TTT
39740246 ATTTTGTTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
32 4 0.11
33 13 0.37
34 18 0.51
ACGTcount: A:0.36, C:0.01, G:0.03, T:0.59
Consensus pattern (33 bp):
TTTTTAAATTTTAAATATATATTTTGAAATTAT
Found at i:39740278 original size:22 final size:21
Alignment explanation
Indices: 39740243--39740284 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
39740233 TTGAAATTAT
*
39740243 TTTATTTTGTTTATTTATTTA
1 TTTATTTTGTTTATTAATTTA
*
39740264 TTTATTTTTTGTTATTAATTT
1 TTTATTTTGT-TTATTAATTT
39740285 TAAAAAAATT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.19, C:0.00, G:0.05, T:0.76
Consensus pattern (21 bp):
TTTATTTTGTTTATTAATTTA
Found at i:39740312 original size:152 final size:153
Alignment explanation
Indices: 39740099--39740386 Score: 431
Period size: 152 Copynumber: 1.9 Consensus size: 153
39740089 TTTACTCTTC
* *
39740099 TTTATTTATTTATTTTATTTATTATTATTAACTTTAAAAAATTTGAAATATATATTTGAAATATT
1 TTTATTTATTTATTTTATTTATTATTATTAACTTTAAAAAAATTAAAATATATATTTGAAATATT
39740164 TTATTAATATATAT-T-TTT-AAATTTTAAATATATATTTTGAAATTACTTTTTTAAATTTTAAA
66 TTA-TAATATATATGTATTTAAAATTTTAAATAT-TATTTT-AAATTACTTTTTTAAATTTTAAA
39740226 TATTATTTTGAAATTATTTTATTTTG
128 TATTATTTTGAAATTATTTTATTTTG
* * * * *
39740252 TTTATTTATTTA-TTTATTTTTTGTTATTAATTTTAAAAAAATTAAAATGTATATTTGAAATTTT
1 TTTATTTATTTATTTTATTTATTATTATTAACTTTAAAAAAATTAAAATATATATTTGAAATATT
* * *
39740316 TTATAATATATATGTATTTAAAATTTTAAATATTATTTTAAATTATTTTTTTTAATTTTTAATAT
66 TTATAATATATATGTATTTAAAATTTTAAATATTATTTTAAATTACTTTTTTAAATTTTAAATAT
39740381 TATTTT
131 TATTTT
39740387 TTAAACATTA
Statistics
Matches: 122, Mismatches: 10, Indels: 7
0.88 0.07 0.05
Matches are distributed among these distances:
151 10 0.08
152 78 0.64
153 21 0.17
154 13 0.11
ACGTcount: A:0.37, C:0.01, G:0.03, T:0.59
Consensus pattern (153 bp):
TTTATTTATTTATTTTATTTATTATTATTAACTTTAAAAAAATTAAAATATATATTTGAAATATT
TTATAATATATATGTATTTAAAATTTTAAATATTATTTTAAATTACTTTTTTAAATTTTAAATAT
TATTTTGAAATTATTTTATTTTG
Found at i:39740729 original size:20 final size:20
Alignment explanation
Indices: 39740674--39740729 Score: 60
Period size: 20 Copynumber: 2.8 Consensus size: 20
39740664 TGACCAATTA
39740674 TAATATATATTTTTAATTTTT
1 TAATATATATTTTT-ATTTTT
* *
39740695 T-ATTTAATTTTTTTATTTTT
1 TAATAT-ATATTTTTATTTTT
*
39740715 TAATATATATATTTA
1 TAATATATATTTTTA
39740730 AATTCATTTT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
20 17 0.61
21 11 0.39
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (20 bp):
TAATATATATTTTTATTTTT
Found at i:39741003 original size:21 final size:21
Alignment explanation
Indices: 39740979--39741024 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
39740969 TTATAATACT
*
39740979 AAAAAAATATTTAATATTTAA
1 AAAAAAATATTTAAAATTTAA
*
39741000 AAAATAATATTTAAAATTTAA
1 AAAAAAATATTTAAAATTTAA
39741021 AAAA
1 AAAA
39741025 GTAATTTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (21 bp):
AAAAAAATATTTAAAATTTAA
Found at i:39741036 original size:21 final size:19
Alignment explanation
Indices: 39740980--39741037 Score: 64
Period size: 21 Copynumber: 2.9 Consensus size: 19
39740970 TATAATACTA
*
39740980 AAAAAAT-ATTTAATATTT
1 AAAAAATAATTTAAAATTT
39740998 AAAAAATAATATTTAAAATTT
1 AAAAAAT-A-ATTTAAAATTT
39741019 AAAAAAGTAATTTCAAAAT
1 AAAAAA-TAATTT-AAAAT
39741038 ATATATTTAA
Statistics
Matches: 34, Mismatches: 1, Indels: 7
0.81 0.02 0.17
Matches are distributed among these distances:
18 7 0.21
20 4 0.12
21 22 0.65
22 1 0.03
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (19 bp):
AAAAAATAATTTAAAATTT
Found at i:39741089 original size:24 final size:24
Alignment explanation
Indices: 39741028--39741098 Score: 85
Period size: 24 Copynumber: 3.0 Consensus size: 24
39741018 TAAAAAAGTA
39741028 ATTTCAAAATATATATT--TAAAAT
1 ATTTC-AAATATATATTAATAAAAT
*
39741051 -TTTAAAAAATATATATTAATAAAAT
1 ATTT--CAAATATATATTAATAAAAT
39741076 ATTTCAAATATATATTAATAAAA
1 ATTTCAAATATATATTAATAAAA
39741099 AAGATTTATT
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
22 3 0.07
23 11 0.27
24 18 0.44
25 6 0.15
26 3 0.07
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (24 bp):
ATTTCAAATATATATTAATAAAAT
Found at i:39741149 original size:16 final size:15
Alignment explanation
Indices: 39741130--39741184 Score: 53
Period size: 16 Copynumber: 3.8 Consensus size: 15
39741120 GAATTTAATT
*
39741130 AAAAATATAAATATTA
1 AAAAATAAAAAT-TTA
39741146 AAAAATAAAAATTT-
1 AAAAATAAAAATTTA
*
39741160 -AAATTAAAAA-TTA
1 AAAAATAAAAATTTA
*
39741173 AAAATTAAAAAT
1 AAAAATAAAAAT
39741185 ACATATTATA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
12 2 0.06
13 9 0.26
14 10 0.29
15 2 0.06
16 11 0.32
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (15 bp):
AAAAATAAAAATTTA
Found at i:39741155 original size:6 final size:7
Alignment explanation
Indices: 39741126--39741184 Score: 75
Period size: 7 Copynumber: 8.4 Consensus size: 7
39741116 AAATGAATTT
39741126 AATTAAA
1 AATTAAA
39741133 AATATAAA
1 AAT-TAAA
*
39741141 TATTAAA
1 AATTAAA
*
39741148 AAATAAA
1 AATTAAA
*
39741155 AATT-TA
1 AATTAAA
39741161 AATTAAA
1 AATTAAA
39741168 AATTAAA
1 AATTAAA
39741175 AATTAAA
1 AATTAAA
39741182 AAT
1 AAT
39741185 ACATATTATA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
6 5 0.11
7 33 0.75
8 6 0.14
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (7 bp):
AATTAAA
Found at i:39741172 original size:27 final size:28
Alignment explanation
Indices: 39741132--39741184 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
39741122 ATTTAATTAA
*
39741132 AAATATAAATATTAAAAAATAAAAATTT
1 AAATATAAAAATTAAAAAATAAAAATTT
*
39741160 AAAT-TAAAAATTAAAAATTAAAAAT
1 AAATATAAAAATTAAAAAATAAAAAT
39741185 ACATATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 19 0.83
28 4 0.17
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (28 bp):
AAATATAAAAATTAAAAAATAAAAATTT
Found at i:39741192 original size:27 final size:27
Alignment explanation
Indices: 39741132--39741192 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
39741122 ATTTAATTAA
* **
39741132 AAATATAAATATTAAAAAATAAAAATTT
1 AAAT-TAAAAATTAAAAAATAAAAATAC
*
39741160 AAATTAAAAATTAAAAATTAAAAATAC
1 AAATTAAAAATTAAAAAATAAAAATAC
*
39741187 ATATTA
1 AAATTA
39741193 TAACTGGTCA
Statistics
Matches: 28, Mismatches: 5, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
27 24 0.86
28 4 0.14
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (27 bp):
AAATTAAAAATTAAAAAATAAAAATAC
Found at i:39741247 original size:15 final size:15
Alignment explanation
Indices: 39741207--39741251 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 15
39741197 TGGTCACATC
39741207 ATATTTTTTTAACAA
1 ATATTTTTTTAACAA
39741222 ATAAATCTTTTTTTAACAA
1 AT--A--TTTTTTTAACAA
39741241 ATATTTTTTTA
1 ATATTTTTTTA
39741252 TTTTTTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
15 10 0.38
17 2 0.08
19 14 0.54
ACGTcount: A:0.38, C:0.07, G:0.00, T:0.56
Consensus pattern (15 bp):
ATATTTTTTTAACAA
Found at i:39741473 original size:23 final size:21
Alignment explanation
Indices: 39741444--39741511 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
39741434 AAAATATTTA
39741444 AATATTTTATATTATTAAAAAT
1 AATATTTTATATT-TTAAAAAT
* * * *
39741466 ATATATTTAATGTTTAAAAAAC
1 A-ATATTTTATATTTTAAAAAT
*
39741488 AATATTTTAAATTTTAAAAAT
1 AATATTTTATATTTTAAAAAT
39741509 AAT
1 AAT
39741512 TTAAAATAAT
Statistics
Matches: 36, Mismatches: 9, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
21 18 0.50
22 8 0.22
23 10 0.28
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (21 bp):
AATATTTTATATTTTAAAAAT
Found at i:39741485 original size:22 final size:22
Alignment explanation
Indices: 39741444--39741507 Score: 62
Period size: 22 Copynumber: 2.9 Consensus size: 22
39741434 AAAATATTTA
*
39741444 AATATTTTATATTATT-AAAAA-
1 AATATTTTAAATT-TTAAAAAAC
*
39741465 TATATATTT-AATGTTTAAAAAAC
1 AATAT-TTTAAAT-TTTAAAAAAC
39741488 AATATTTTAAATTTTAAAAA
1 AATATTTTAAATTTTAAAAA
39741508 TAATTTAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 9
0.74 0.06 0.19
Matches are distributed among these distances:
21 8 0.23
22 20 0.57
23 7 0.20
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.45
Consensus pattern (22 bp):
AATATTTTAAATTTTAAAAAAC
Found at i:39741623 original size:18 final size:17
Alignment explanation
Indices: 39741582--39741625 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
39741572 TTAAATTTTT
*
39741582 TAAAATTAATAACAAAA
1 TAAAATAAATAACAAAA
*
39741599 AATAAATAAATAAACAAAA
1 TA-AAATAAAT-AACAAAA
39741618 TAAAATAA
1 TAAAATAA
39741626 TTTCAAAATA
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 1 0.05
18 13 0.59
19 8 0.36
ACGTcount: A:0.75, C:0.05, G:0.00, T:0.20
Consensus pattern (17 bp):
TAAAATAAATAACAAAA
Found at i:39741667 original size:49 final size:50
Alignment explanation
Indices: 39741613--39741718 Score: 178
Period size: 50 Copynumber: 2.1 Consensus size: 50
39741603 AATAAATAAA
*
39741613 CAAAATAAAATAATTT-CAAAATAATATTTAAAATTTAAAAAAGTAATTT
1 CAAAATAAAATAATTTAAAAAATAATATTTAAAATTTAAAAAAGTAATTT
*
39741662 CAAAATAAAATAATTTAAAAAATAATATTTAAAATTTTAAAAAGTAATTT
1 CAAAATAAAATAATTTAAAAAATAATATTTAAAATTTAAAAAAGTAATTT
*
39741712 CAGAATA
1 CAAAATA
39741719 TATATTTAAA
Statistics
Matches: 53, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
49 16 0.30
50 37 0.70
ACGTcount: A:0.59, C:0.04, G:0.03, T:0.34
Consensus pattern (50 bp):
CAAAATAAAATAATTTAAAAAATAATATTTAAAATTTAAAAAAGTAATTT
Found at i:39741702 original size:22 final size:22
Alignment explanation
Indices: 39741630--39741709 Score: 65
Period size: 22 Copynumber: 3.4 Consensus size: 22
39741620 AAATAATTTC
39741630 AAAATAATATTTAAAA-TTTAA
1 AAAATAATATTTAAAATTTTAA
39741651 AAAAGTAAT-TTCAAAATAAAATAATTTAA
1 AAAA-TAATATT-----TAAAAT--TTTAA
39741680 AAAATAATATTTAAAATTTTAA
1 AAAATAATATTTAAAATTTTAA
*
39741702 AAAGTAAT
1 AAAATAAT
39741710 TTCAGAATAT
Statistics
Matches: 48, Mismatches: 1, Indels: 19
0.71 0.01 0.28
Matches are distributed among these distances:
21 6 0.12
22 16 0.33
24 6 0.12
26 5 0.10
28 4 0.08
29 11 0.23
ACGTcount: A:0.61, C:0.01, G:0.03, T:0.35
Consensus pattern (22 bp):
AAAATAATATTTAAAATTTTAA
Found at i:39741753 original size:83 final size:78
Alignment explanation
Indices: 39741619--39741772 Score: 177
Period size: 83 Copynumber: 1.9 Consensus size: 78
39741609 TAAACAAAAT
*
39741619 AAAATAATTTCAAAATAATATTTAAAATTTAAAAAAGTAATTTCAAAATAAAATAATTTAAAAAA
1 AAAATAATTTCAAAATAATATTTAAAATTTAAAAAAGTAAATT--AAATAAAAT-ATTTAAAAAA
39741684 TAATATTTAAAATTTTA
63 T-ATATTTAAAATTTTA
* *
39741701 AAAAGTAATTTCAGAATATATATTTAAAATTTTAAAAAA-TATAGATT-AATAAAATATTTCAAA
1 AAAA-TAATTTCAAAATA-ATATTTAAAA-TTTAAAAAAGTA-A-ATTAAATAAAATATTTAAAA
*
39741764 TATATATTT
61 AATATATTT
39741773 CAATTTTTTT
Statistics
Matches: 63, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
81 6 0.10
82 13 0.21
83 20 0.32
84 12 0.19
85 10 0.16
86 2 0.03
ACGTcount: A:0.56, C:0.03, G:0.03, T:0.38
Consensus pattern (78 bp):
AAAATAATTTCAAAATAATATTTAAAATTTAAAAAAGTAAATTAAATAAAATATTTAAAAAATAT
ATTTAAAATTTTA
Found at i:39741758 original size:34 final size:33
Alignment explanation
Indices: 39741668--39741764 Score: 88
Period size: 34 Copynumber: 2.8 Consensus size: 33
39741658 ATTTCAAAAT
* *
39741668 AAAATAATTTAAAAAATAATATTTAAAATTTTAA
1 AAAATAAATT-AAGAATAATATTTAAAATTTTAA
* * *
39741702 AAAGTAATTTCAGAATATATATTTAAAATTTTAA
1 AAAATAAATTAAGAATA-ATATTTAAAATTTTAA
* *
39741736 AAAATATAGATTAATAA-AATATTTCAAAT
1 AAAATA-A-ATTAAGAATAATATTTAAAAT
39741765 ATATATTTCA
Statistics
Matches: 52, Mismatches: 8, Indels: 6
0.79 0.12 0.09
Matches are distributed among these distances:
33 5 0.10
34 40 0.77
35 2 0.04
36 5 0.10
ACGTcount: A:0.57, C:0.02, G:0.03, T:0.38
Consensus pattern (33 bp):
AAAATAAATTAAGAATAATATTTAAAATTTTAA
Found at i:39741833 original size:14 final size:14
Alignment explanation
Indices: 39741798--39741849 Score: 54
Period size: 14 Copynumber: 3.7 Consensus size: 14
39741788 TAATAATAAT
*
39741798 AAATAAAATAAAATA
1 AAATAAAA-AAAGTA
*
39741813 AAATAAAGAAAG-A
1 AAATAAAAAAAGTA
39741826 AAAGTAAAAAAAGTA
1 AAA-TAAAAAAAGTA
39741841 AAA-AAAAAA
1 AAATAAAAAA
39741850 GAAACTGACA
Statistics
Matches: 32, Mismatches: 3, Indels: 6
0.78 0.07 0.15
Matches are distributed among these distances:
13 10 0.31
14 11 0.34
15 11 0.34
ACGTcount: A:0.81, C:0.00, G:0.08, T:0.12
Consensus pattern (14 bp):
AAATAAAAAAAGTA
Found at i:39742340 original size:28 final size:28
Alignment explanation
Indices: 39742307--39742401 Score: 90
Period size: 27 Copynumber: 3.4 Consensus size: 28
39742297 AGTGCAAATA
39742307 ACGATAAGCACCGAAATGCAAAATAATT
1 ACGATAAGCACCGAAATGCAAAATAATT
* *
39742335 ACGATAAGCACC-AAA-GTACAAAT-TTT
1 ACGATAAGCACCGAAATGCA-AAATAATT
* *
39742361 ACAATGATAAGCACCGAAGTGCGAAATAA-T
1 AC---GATAAGCACCGAAATGCAAAATAATT
39742391 ACGATAAGCAC
1 ACGATAAGCAC
39742402 ACTAATTTTT
Statistics
Matches: 54, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
26 6 0.11
27 16 0.30
28 12 0.22
29 10 0.19
30 9 0.17
31 1 0.02
ACGTcount: A:0.47, C:0.19, G:0.16, T:0.18
Consensus pattern (28 bp):
ACGATAAGCACCGAAATGCAAAATAATT
Found at i:39744764 original size:46 final size:44
Alignment explanation
Indices: 39744660--39744767 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
39744650 TGTCTTTGAC
** * * *
39744660 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
39744704 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
39744750 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
39744768 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:39745658 original size:9 final size:9
Alignment explanation
Indices: 39745644--39745678 Score: 52
Period size: 9 Copynumber: 3.9 Consensus size: 9
39745634 TTCTATTCTG
39745644 TTTCTTTTC
1 TTTCTTTTC
*
39745653 TTTCTTTTT
1 TTTCTTTTC
*
39745662 TTTCTATTC
1 TTTCTTTTC
39745671 TTTCTTTT
1 TTTCTTTT
39745679 GTTTTATGTA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 22 1.00
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (9 bp):
TTTCTTTTC
Found at i:39745671 original size:18 final size:19
Alignment explanation
Indices: 39745644--39745683 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
39745634 TTCTATTCTG
*
39745644 TTTCTTTTCTTTCTTTT-T
1 TTTCTATTCTTTCTTTTGT
39745662 TTTCTATTCTTTCTTTTGT
1 TTTCTATTCTTTCTTTTGT
39745681 TTT
1 TTT
39745684 ATGTATATAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
18 16 0.80
19 4 0.20
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.80
Consensus pattern (19 bp):
TTTCTATTCTTTCTTTTGT
Found at i:39745700 original size:5 final size:5
Alignment explanation
Indices: 39745687--39745759 Score: 64
Period size: 5 Copynumber: 14.6 Consensus size: 5
39745677 TTGTTTTATG
39745687 TATATA TATAA TATAA TATAA TAT-A T-TAA TAATAA TATAA TATAA -A-AA
1 TATA-A TATAA TATAA TATAA TATAA TATAA T-ATAA TATAA TATAA TATAA
* *
39745735 CATAA TCATTAC TATAA TATAA TAT
1 TATAA T-A-TAA TATAA TATAA TAT
39745760 TTTTTTAACA
Statistics
Matches: 57, Mismatches: 3, Indels: 15
0.76 0.04 0.20
Matches are distributed among these distances:
3 3 0.05
4 6 0.11
5 35 0.61
6 10 0.18
7 3 0.05
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (5 bp):
TATAA
Found at i:39745712 original size:19 final size:19
Alignment explanation
Indices: 39745688--39745730 Score: 70
Period size: 19 Copynumber: 2.3 Consensus size: 19
39745678 TGTTTTATGT
39745688 ATATATATAAT-ATAATATA
1 ATATAT-TAATAATAATATA
39745707 ATATATTAATAATAATATA
1 ATATATTAATAATAATATA
39745726 ATATA
1 ATATA
39745731 AAAACATAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
18 4 0.17
19 19 0.83
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (19 bp):
ATATATTAATAATAATATA
Found at i:39745740 original size:24 final size:25
Alignment explanation
Indices: 39745694--39745758 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 25
39745684 ATGTATATAT
* *
39745694 ATAATATAATATAATATATTAAT-A
1 ATAATATAATATAATAAAATAATCA
39745718 ATAATATAATATAA-AAACATAATCA
1 ATAATATAATATAATAAA-ATAATCA
* *
39745743 TTACTATAATATAATA
1 ATAATATAATATAATA
39745759 TTTTTTTAAC
Statistics
Matches: 34, Mismatches: 4, Indels: 4
0.81 0.10 0.10
Matches are distributed among these distances:
23 2 0.06
24 18 0.53
25 13 0.38
26 1 0.03
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (25 bp):
ATAATATAATATAATAAAATAATCA
Found at i:39750913 original size:46 final size:44
Alignment explanation
Indices: 39750809--39750916 Score: 144
Period size: 44 Copynumber: 2.4 Consensus size: 44
39750799 TGTCTTTGAC
** * * *
39750809 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
*
39750853 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATTTCTAAT
1 ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATA--TATAAT
39750899 ATGGACTTACATGGCTCA
1 ATGGACTTACATGGCTCA
39750917 TTTCTGTTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
44 33 0.59
46 23 0.41
ACGTcount: A:0.30, C:0.23, G:0.14, T:0.33
Consensus pattern (44 bp):
ATGGACTTACATGGCTCAATCCTGTCTCCAAAGCCATATATAAT
Found at i:39763222 original size:15 final size:13
Alignment explanation
Indices: 39763188--39763218 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
39763178 TTTCTGAAAG
39763188 TTTTTATATTTTC
1 TTTTTATATTTTC
*
39763201 TTTTTATATTTTA
1 TTTTTATATTTTC
39763214 TTTTT
1 TTTTT
39763219 TTATGAATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.16, C:0.03, G:0.00, T:0.81
Consensus pattern (13 bp):
TTTTTATATTTTC
Found at i:39763423 original size:3 final size:3
Alignment explanation
Indices: 39763415--39763447 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
39763405 TCATTATATC
39763415 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
39763448 GCTTTGTAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:39768352 original size:21 final size:21
Alignment explanation
Indices: 39768326--39768366 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
39768316 ATCTGCTCAA
* *
39768326 ACTCCACCTGTTTTGGAGTAC
1 ACTCCACCTGCTGTGGAGTAC
39768347 ACTCCACCTGCTGTGGAGTA
1 ACTCCACCTGCTGTGGAGTA
39768367 TTGCTCGTCT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.20, C:0.29, G:0.22, T:0.29
Consensus pattern (21 bp):
ACTCCACCTGCTGTGGAGTAC
Found at i:39775126 original size:16 final size:16
Alignment explanation
Indices: 39775105--39775145 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
39775095 AAAATTATAG
*
39775105 AAAAGTTAAAATAATT
1 AAAAGTTAAAAAAATT
*
39775121 AAAAGTAAAAAAAATT
1 AAAAGTTAAAAAAATT
*
39775137 AAAAATTAA
1 AAAAGTTAA
39775146 TTTAAAATAT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.71, C:0.00, G:0.05, T:0.24
Consensus pattern (16 bp):
AAAAGTTAAAAAAATT
Found at i:39778407 original size:16 final size:16
Alignment explanation
Indices: 39778386--39778457 Score: 63
Period size: 16 Copynumber: 4.2 Consensus size: 16
39778376 TAAATATTTT
39778386 TAAAAATATATAAAAA
1 TAAAAATATATAAAAA
* **
39778402 TAAAAATATTGTTAGCAA
1 TAAAAATA-T-ATAAAAA
**
39778420 TAAATAATATATACAATT
1 TAAA-AATATATA-AAAA
39778438 TAAAAATATATAAAAA
1 TAAAAATATATAAAAA
39778454 TAAA
1 TAAA
39778458 TAAATGTTTT
Statistics
Matches: 42, Mismatches: 10, Indels: 8
0.70 0.17 0.13
Matches are distributed among these distances:
16 14 0.33
17 11 0.26
18 13 0.31
19 4 0.10
ACGTcount: A:0.64, C:0.03, G:0.03, T:0.31
Consensus pattern (16 bp):
TAAAAATATATAAAAA
Found at i:39780542 original size:26 final size:24
Alignment explanation
Indices: 39780497--39780556 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 24
39780487 GAAAATATAT
* *
39780497 ATATATACACAATATAGTATTTAAAA
1 ATATATACATAAGATAGTA--TAAAA
*
39780523 ATATATACATAAGATGGTATAAAA
1 ATATATACATAAGATAGTATAAAA
*
39780547 ATATGTACAT
1 ATATATACAT
39780557 GGAAATGTAT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
24 14 0.47
26 16 0.53
ACGTcount: A:0.52, C:0.07, G:0.08, T:0.33
Consensus pattern (24 bp):
ATATATACATAAGATAGTATAAAA
Found at i:39780739 original size:21 final size:22
Alignment explanation
Indices: 39780702--39780804 Score: 106
Period size: 21 Copynumber: 4.8 Consensus size: 22
39780692 ACACATATAT
*
39780702 ATATA-AATAATAGTATTAGAA
1 ATATACAATAATAATATTAGAA
39780723 ATATACAAT-ATAATATTAGAA
1 ATATACAATAATAATATTAGAA
* * *
39780744 ATATACATATAATAGTATAAAAA
1 ATATACA-ATAATAATATTAGAA
*
39780767 ATATATAACTAATAATATTA-AA
1 ATATACAA-TAATAATATTAGAA
*
39780789 ATATA-TATAATAATAT
1 ATATACAATAATAATAT
39780805 ATATAATATA
Statistics
Matches: 70, Mismatches: 8, Indels: 9
0.80 0.09 0.10
Matches are distributed among these distances:
20 9 0.13
21 24 0.34
22 13 0.19
23 24 0.34
ACGTcount: A:0.58, C:0.03, G:0.04, T:0.35
Consensus pattern (22 bp):
ATATACAATAATAATATTAGAA
Found at i:39780779 original size:23 final size:22
Alignment explanation
Indices: 39780700--39780810 Score: 89
Period size: 23 Copynumber: 4.9 Consensus size: 22
39780690 TTACACATAT
* * *
39780700 ATATATAAATAATAGTATTAGAA
1 ATATAT-AATAATAATATAAAAA
* * *
39780723 ATATACAAT-ATAATATTAGAA
1 ATATATAATAATAATATAAAAA
* *
39780744 ATATACATATAATAGTATAAAAA
1 ATATATA-ATAATAATATAAAAA
*
39780767 ATATATAACTAATAATATTAAAAT
1 ATATATAA-TAATAATA-TAAAAA
39780791 ATATATAATAATATATATAA
1 ATATATAATAATA-ATATAA
39780811 TATAATATTA
Statistics
Matches: 75, Mismatches: 8, Indels: 10
0.81 0.09 0.11
Matches are distributed among these distances:
21 18 0.24
22 6 0.08
23 35 0.47
24 16 0.21
ACGTcount: A:0.59, C:0.03, G:0.04, T:0.35
Consensus pattern (22 bp):
ATATATAATAATAATATAAAAA
Found at i:39780784 original size:12 final size:12
Alignment explanation
Indices: 39780743--39780812 Score: 62
Period size: 12 Copynumber: 6.1 Consensus size: 12
39780733 TAATATTAGA
*
39780743 AATATACAT-AT
1 AATATATATAAT
39780754 AATAGTATA-AA-
1 AATA-TATATAAT
39780765 AA-ATATATAACT
1 AATATATATAA-T
39780777 AATA-ATATTAA-
1 AATATATA-TAAT
39780788 AATATATATAAT
1 AATATATATAAT
39780800 AATATATATAAT
1 AATATATATAAT
39780812 A
1 A
39780813 TAATATTAAA
Statistics
Matches: 49, Mismatches: 1, Indels: 17
0.73 0.01 0.25
Matches are distributed among these distances:
9 4 0.08
10 3 0.06
11 13 0.27
12 25 0.51
13 4 0.08
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (12 bp):
AATATATATAAT
Found at i:39780816 original size:34 final size:35
Alignment explanation
Indices: 39780759--39780824 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
39780749 CATATAATAG
39780759 TATAAAAAATATATAACTAATAATATTAAAATATA
1 TATAAAAAATATATAACTAATAATATTAAAATATA
*
39780794 TATAATAATATATATAA-T-ATAATATTAAAAT
1 TATAA-AAAATATATAACTAATAATATTAAAAT
39780825 TTTATTTACA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
34 13 0.45
35 6 0.21
36 10 0.34
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.38
Consensus pattern (35 bp):
TATAAAAAATATATAACTAATAATATTAAAATATA
Found at i:39780818 original size:12 final size:12
Alignment explanation
Indices: 39780696--39780818 Score: 61
Period size: 12 Copynumber: 10.8 Consensus size: 12
39780686 ATACTTACAC
39780696 ATAT-ATATATA
1 ATATAATATATA
*
39780707 A-ATAATAGTATT
1 ATATAATA-TATA
* *
39780719 AGA-AATATACA
1 ATATAATATATA
39780730 ATATAATAT-T-
1 ATATAATATATA
* *
39780740 AGA-AATATA-C
1 ATATAATATATA
39780750 ATATAATAGTATA
1 ATATAATA-TATA
*
39780763 A-AAAATATATA
1 ATATAATATATA
39780774 ACTAATAATAT-TA
1 A-T-ATAATATATA
*
39780787 AAAT-ATATATA
1 ATATAATATATA
39780798 ATA-ATATATATA
1 ATATA-ATATATA
39780810 ATATAATAT
1 ATATAATAT
39780819 TAAAATTTTA
Statistics
Matches: 84, Mismatches: 12, Indels: 31
0.66 0.09 0.24
Matches are distributed among these distances:
9 5 0.06
10 10 0.12
11 23 0.27
12 34 0.40
13 6 0.07
14 6 0.07
ACGTcount: A:0.58, C:0.02, G:0.03, T:0.37
Consensus pattern (12 bp):
ATATAATATATA
Found at i:39781096 original size:3 final size:3
Alignment explanation
Indices: 39781088--39781117 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
39781078 ATGTACTATG
39781088 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
39781118 TTGATATATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:39783693 original size:21 final size:21
Alignment explanation
Indices: 39783644--39783698 Score: 51
Period size: 21 Copynumber: 2.6 Consensus size: 21
39783634 TATATTCACA
*
39783644 AATATAAATATACATATAAAT
1 AATATAAATATACAAATAAAT
*
39783665 AATCTAAAT-TA-AAATCAAAT
1 AATATAAATATACAAAT-AAAT
39783685 CAATATAAAATATA
1 -AATAT-AAATATA
39783699 ACTAATGAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
19 3 0.11
20 6 0.22
21 12 0.44
22 4 0.15
23 2 0.07
ACGTcount: A:0.62, C:0.07, G:0.00, T:0.31
Consensus pattern (21 bp):
AATATAAATATACAAATAAAT
Found at i:39793773 original size:31 final size:31
Alignment explanation
Indices: 39793737--39793801 Score: 103
Period size: 31 Copynumber: 2.1 Consensus size: 31
39793727 AATAGTCTAG
* *
39793737 TGACTTAAATAAAAACTTTCGACTAGTTCAA
1 TGACTTAAATAAAAAATTTCGAATAGTTCAA
*
39793768 TGACTTAAATAAAAAATTTTGAATAGTTCAA
1 TGACTTAAATAAAAAATTTCGAATAGTTCAA
39793799 TGA
1 TGA
39793802 TTGTTTTGTA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.45, C:0.11, G:0.11, T:0.34
Consensus pattern (31 bp):
TGACTTAAATAAAAAATTTCGAATAGTTCAA
Found at i:39805412 original size:28 final size:29
Alignment explanation
Indices: 39805354--39805412 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
39805344 CTGGTGACCA
* *
39805354 AACTATCAATTTTTTTAATTTAGTCATCC
1 AACTATCAACTTTTTTAATTGAGTCATCC
39805383 AACTATCAACTTTTTTAACTTGA-TCA-CC
1 AACTATCAACTTTTTTAA-TTGAGTCATCC
39805411 AA
1 AA
39805413 ATTAATGGAG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 4 0.15
29 20 0.74
30 3 0.11
ACGTcount: A:0.34, C:0.20, G:0.03, T:0.42
Consensus pattern (29 bp):
AACTATCAACTTTTTTAATTGAGTCATCC
Found at i:39808216 original size:9 final size:9
Alignment explanation
Indices: 39808199--39808272 Score: 59
Period size: 9 Copynumber: 8.6 Consensus size: 9
39808189 TTTTAAAAAA
39808199 TTTATTAATT
1 TTTA-TAATT
39808209 TTTATAATT
1 TTTATAATT
39808218 TTTA-AA-T
1 TTTATAATT
39808225 TTTA-AATT
1 TTTATAATT
*
39808233 TTTATCATT
1 TTTATAATT
**
39808242 TGAAT-ATT
1 TTTATAATT
*
39808250 TTTATAAAT
1 TTTATAATT
39808259 TTTA-AATT
1 TTTATAATT
39808267 ATTTAT
1 -TTTAT
39808273 TGATGCGACA
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
7 7 0.13
8 16 0.31
9 25 0.48
10 4 0.08
ACGTcount: A:0.35, C:0.01, G:0.01, T:0.62
Consensus pattern (9 bp):
TTTATAATT
Found at i:39814591 original size:25 final size:27
Alignment explanation
Indices: 39814540--39814593 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 27
39814530 TATTGTTTTC
* **
39814540 TTTATATTTTATTTTTCACATGTTATT
1 TTTATATTTTATTTTTCAAATCATATT
39814567 TTTAT-TTTTATTTTT-AAATCATATT
1 TTTATATTTTATTTTTCAAATCATATT
39814592 TT
1 TT
39814594 AAAAATCTAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
25 9 0.38
26 10 0.42
27 5 0.21
ACGTcount: A:0.24, C:0.06, G:0.02, T:0.69
Consensus pattern (27 bp):
TTTATATTTTATTTTTCAAATCATATT
Found at i:39819214 original size:24 final size:24
Alignment explanation
Indices: 39819185--39819232 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
39819175 CTACTTTCTT
39819185 AGTCCAAATTATCTGCCTACTTCC
1 AGTCCAAATTATCTGCCTACTTCC
39819209 AGTCCAAATTATCTGCCTACTTCC
1 AGTCCAAATTATCTGCCTACTTCC
39819233 TTCCCCATGA
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:0.25, C:0.33, G:0.08, T:0.33
Consensus pattern (24 bp):
AGTCCAAATTATCTGCCTACTTCC
Found at i:39823291 original size:29 final size:29
Alignment explanation
Indices: 39823246--39823301 Score: 103
Period size: 29 Copynumber: 1.9 Consensus size: 29
39823236 TCTAGGCCAG
39823246 ATAAGAGAATAACAAATACCATATTCTGT
1 ATAAGAGAATAACAAATACCATATTCTGT
*
39823275 ATAAGAGAATAATAAATACCATATTCT
1 ATAAGAGAATAACAAATACCATATTCT
39823302 ATCTCTCTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.50, C:0.12, G:0.09, T:0.29
Consensus pattern (29 bp):
ATAAGAGAATAACAAATACCATATTCTGT
Found at i:39824909 original size:16 final size:16
Alignment explanation
Indices: 39824900--39824929 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
39824890 TTTATATATT
39824900 TTTTATTTTATTAATA
1 TTTTATTTTATTAATA
39824916 TTTTATTTT-TTAAT
1 TTTTATTTTATTAAT
39824930 CTCAAATCTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.27, C:0.00, G:0.00, T:0.73
Consensus pattern (16 bp):
TTTTATTTTATTAATA
Found at i:39824916 original size:20 final size:21
Alignment explanation
Indices: 39824873--39824916 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
39824863 TAATACTTTC
*
39824873 TATATTTTATTAGTATATTTA
1 TATATTTTATTAGTATATTAA
* *
39824894 TATATTTT-TTATTTTATTAA
1 TATATTTTATTAGTATATTAA
39824914 TAT
1 TAT
39824917 TTTATTTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 12 0.60
21 8 0.40
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (21 bp):
TATATTTTATTAGTATATTAA
Found at i:39847247 original size:18 final size:18
Alignment explanation
Indices: 39847224--39847264 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
39847214 GATGTTAATA
*
39847224 TAGGAGTAAATCATTGGT
1 TAGGAGTAAATCATTGAT
*
39847242 TAGGAGTAAATCCTTGAT
1 TAGGAGTAAATCATTGAT
39847260 TAGGA
1 TAGGA
39847265 TTTATCTGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.34, C:0.07, G:0.27, T:0.32
Consensus pattern (18 bp):
TAGGAGTAAATCATTGAT
Found at i:39848035 original size:15 final size:15
Alignment explanation
Indices: 39848015--39848044 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39848005 AACCTAAAAA
*
39848015 TTCTATTTCTGTTTT
1 TTCTATTTCTATTTT
39848030 TTCTATTTCTATTTT
1 TTCTATTTCTATTTT
39848045 CTTAGGACTC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.10, C:0.13, G:0.03, T:0.73
Consensus pattern (15 bp):
TTCTATTTCTATTTT
Found at i:39854065 original size:15 final size:15
Alignment explanation
Indices: 39854045--39854074 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
39854035 TATGAAAAAC
*
39854045 TAAATAAAAATAAAT
1 TAAATAAAAACAAAT
39854060 TAAATAAAAACAAAT
1 TAAATAAAAACAAAT
39854075 AACTAAGCAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.23
Consensus pattern (15 bp):
TAAATAAAAACAAAT
Found at i:39855032 original size:264 final size:265
Alignment explanation
Indices: 39854534--39855068 Score: 817
Period size: 264 Copynumber: 2.0 Consensus size: 265
39854524 CTATTAAGGC
* * *
39854534 GAATATCTTTAAAACTCAATAAATTTTTTTTTAGATTTAGTTGAAAATAAAGTATCATCAATGAC
1 GAATATCTTTAAAACTCAATAAATTTTCTTTTAGATTTAGTAGAAAATAAAGCATCATCAATGAC
*
39854599 AATTTTTATCCCTTTAGATAATAATATAATAGCTCTTTCAGAGCTTTCAATAATTTGAATTACCT
66 AATTTCTATCCCTTTAGATAATAATATAATAGCTCTTTCAGAGCTTTCAATAATTTGAATTACCT
* * * * *
39854664 GATATTGTATTAATATAAGCATCACTCTTTGTCAAATAAGAAGAATATATATATATTATTTTAGT
131 GATATGGTATTAATATAAGCATCACTCATTATCAAATAAGAAAAATATATATATATTATTTTAAT
*
39854729 ATAGCATGTATTGTTCCACTATTTGCAAAACACATGTTTCCATCGATCTTGGATCTAATAAAATT
196 ATAGCATGTATTGTACCACTATTTGCAAAACACATGTTTCCATCGATCTTGGATCTAATAAAATT
39854794 AT-AGT
261 ATGA-T
*
39854799 GAATATCTTTAAAACTCAATAAA-TTTCTTTTAGATTTAGTAGAAAATAAAGCATCATCAGTGAC
1 GAATATCTTTAAAACTCAATAAATTTTCTTTTAGATTTAGTAGAAAATAAAGCATCATCAATGAC
* * * *
39854863 AATTTCTGTCCCTTTGGATAATAATATATTAGCTCTTTCGGAGCTTTCAATAAGTTTTGAATTAC
66 AATTTCTATCCCTTTAGATAATAATATAATAGCTCTTTCAGAGCTTTCAATAA--TTTGAATTAC
* * *
39854928 CTGATATGGTATTAATATAAGCATCACTCATTATCAAATGAGAAAAATATTTTTA-ATT-TTTTA
129 CTGATATGGTATTAATATAAGCATCACTCATTATCAAATAAGAAAAATATATATATATTATTTTA
* * * *
39854991 ATATAGTATGTATTGTAGCATTATTTGCAAGACACATGTTTCCATCGATCTTGGATCTAATAAAA
194 ATATAGCATGTATTGTACCACTATTTGCAAAACACATGTTTCCATCGATCTTGGATCTAATAAAA
39855056 TTATGAT
259 TTATGAT
39855063 GAATAT
1 GAATAT
39855069 TCATGTTTTT
Statistics
Matches: 245, Mismatches: 22, Indels: 7
0.89 0.08 0.03
Matches are distributed among these distances:
264 160 0.65
265 27 0.11
266 58 0.24
ACGTcount: A:0.36, C:0.12, G:0.11, T:0.40
Consensus pattern (265 bp):
GAATATCTTTAAAACTCAATAAATTTTCTTTTAGATTTAGTAGAAAATAAAGCATCATCAATGAC
AATTTCTATCCCTTTAGATAATAATATAATAGCTCTTTCAGAGCTTTCAATAATTTGAATTACCT
GATATGGTATTAATATAAGCATCACTCATTATCAAATAAGAAAAATATATATATATTATTTTAAT
ATAGCATGTATTGTACCACTATTTGCAAAACACATGTTTCCATCGATCTTGGATCTAATAAAATT
ATGAT
Found at i:39858952 original size:66 final size:66
Alignment explanation
Indices: 39858846--39858971 Score: 207
Period size: 66 Copynumber: 1.9 Consensus size: 66
39858836 CAACAGAAGC
*
39858846 TTTCCCTTGCCTCAAGAAACTATCCATCATGAATTGTCCACTCTTAAAAACAATGCCATCCTTTG
1 TTTCCCTTGCCTCAAGAAACTATCCATCATGAAATGTCCACTCTTAAAAACAATGCCATCCTTTG
39858911 G
66 G
* ** *
39858912 TTTCCCTTGCCTCAAGAGACTATCGGTCATGAAATGTCCACTCTTAAAGACAATGCCATC
1 TTTCCCTTGCCTCAAGAAACTATCCATCATGAAATGTCCACTCTTAAAAACAATGCCATC
39858972 GTTTCCAACT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
66 55 1.00
ACGTcount: A:0.29, C:0.29, G:0.13, T:0.30
Consensus pattern (66 bp):
TTTCCCTTGCCTCAAGAAACTATCCATCATGAAATGTCCACTCTTAAAAACAATGCCATCCTTTG
G
Found at i:39871395 original size:19 final size:18
Alignment explanation
Indices: 39871367--39871406 Score: 53
Period size: 19 Copynumber: 2.2 Consensus size: 18
39871357 GTGCATGAAG
39871367 GCAAGCATTTTGATTGTGT
1 GCAAGCATTTTGATTGT-T
* *
39871386 GCAAGGATTTTGCTTGTT
1 GCAAGCATTTTGATTGTT
39871404 GCA
1 GCA
39871407 TGGTGGCCCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 4 0.21
19 15 0.79
ACGTcount: A:0.20, C:0.12, G:0.28, T:0.40
Consensus pattern (18 bp):
GCAAGCATTTTGATTGTT
Found at i:39872700 original size:14 final size:12
Alignment explanation
Indices: 39872674--39872698 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
39872664 CTTAGTAATA
39872674 TATATATACGTG
1 TATATATACGTG
39872686 TATATATACGTG
1 TATATATACGTG
39872698 T
1 T
39872699 GTGTGTGTGT
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:0.32, C:0.08, G:0.16, T:0.44
Consensus pattern (12 bp):
TATATATACGTG
Found at i:39873212 original size:12 final size:12
Alignment explanation
Indices: 39873195--39873221 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
39873185 TAGAGATTGT
39873195 AATGATTTTGAC
1 AATGATTTTGAC
39873207 AATGATTTTGAC
1 AATGATTTTGAC
39873219 AAT
1 AAT
39873222 CAACTATTAA
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:0.07, G:0.15, T:0.41
Consensus pattern (12 bp):
AATGATTTTGAC
Found at i:39899027 original size:14 final size:15
Alignment explanation
Indices: 39899001--39899030 Score: 53
Period size: 14 Copynumber: 2.1 Consensus size: 15
39898991 TTGTAATAAA
39899001 TATATAGGGGATACT
1 TATATAGGGGATACT
39899016 TATATA-GGGATACT
1 TATATAGGGGATACT
39899030 T
1 T
39899031 TTGGAAAAAG
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 9 0.60
15 6 0.40
ACGTcount: A:0.33, C:0.07, G:0.23, T:0.37
Consensus pattern (15 bp):
TATATAGGGGATACT
Found at i:39907180 original size:20 final size:21
Alignment explanation
Indices: 39907143--39907181 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
39907133 GCATAACATT
* *
39907143 TTTTTTTTGGTGTCAATGAAA
1 TTTTGTTTGGTATCAATGAAA
39907164 TTTTGTTTGGTAT-AATGA
1 TTTTGTTTGGTATCAATGA
39907182 TAATGGACAA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 5 0.31
21 11 0.69
ACGTcount: A:0.23, C:0.03, G:0.21, T:0.54
Consensus pattern (21 bp):
TTTTGTTTGGTATCAATGAAA
Found at i:39921693 original size:30 final size:30
Alignment explanation
Indices: 39921657--39921717 Score: 113
Period size: 30 Copynumber: 2.0 Consensus size: 30
39921647 AAAAAGCCAC
39921657 AAAGAGGGAGTTAAAAGCTATTCAGAACTT
1 AAAGAGGGAGTTAAAAGCTATTCAGAACTT
*
39921687 AAAGAGGGAGTTAAAAGCTATTCAGATCTT
1 AAAGAGGGAGTTAAAAGCTATTCAGAACTT
39921717 A
1 A
39921718 GTTTTGAGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 30 1.00
ACGTcount: A:0.43, C:0.10, G:0.23, T:0.25
Consensus pattern (30 bp):
AAAGAGGGAGTTAAAAGCTATTCAGAACTT
Found at i:39932817 original size:15 final size:15
Alignment explanation
Indices: 39932797--39932825 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
39932787 TGCCATCAAT
39932797 TACTTTTGTCAGTAG
1 TACTTTTGTCAGTAG
39932812 TACTTTTGTCAGTA
1 TACTTTTGTCAGTA
39932826 ATCGAAGTGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.14, G:0.17, T:0.48
Consensus pattern (15 bp):
TACTTTTGTCAGTAG
Found at i:39936579 original size:3 final size:3
Alignment explanation
Indices: 39936571--39936595 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
39936561 ATAAAGAGTA
39936571 AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT A
39936596 GTAAAGAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:39936712 original size:2 final size:2
Alignment explanation
Indices: 39936705--39936731 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
39936695 TATCATATTT
39936705 TA 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 TA T
39936732 TCAATTATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:39937539 original size:9 final size:9
Alignment explanation
Indices: 39937525--39937562 Score: 51
Period size: 9 Copynumber: 4.1 Consensus size: 9
39937515 AAACTAAATA
39937525 TAAAATATT
1 TAAAATATT
39937534 TAAAATA-T
1 TAAAATATT
39937542 TAAAATTATGT
1 TAAAA-TAT-T
39937553 TAAAATATT
1 TAAAATATT
39937562 T
1 T
39937563 TTATAAATAA
Statistics
Matches: 26, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
8 6 0.23
9 11 0.42
10 3 0.12
11 6 0.23
ACGTcount: A:0.53, C:0.00, G:0.03, T:0.45
Consensus pattern (9 bp):
TAAAATATT
Found at i:39937557 original size:19 final size:17
Alignment explanation
Indices: 39937520--39937561 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 17
39937510 AATTAAAACT
39937520 AAATA-TAAAATATTTA
1 AAATATTAAAATATTTA
39937536 AAATATTAAAATTATGTTA
1 AAATATTAAAA-TAT-TTA
39937555 AAATATT
1 AAATATT
39937562 TTTATAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.22
17 5 0.22
18 3 0.13
19 10 0.43
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.40
Consensus pattern (17 bp):
AAATATTAAAATATTTA
Found at i:39937580 original size:13 final size:13
Alignment explanation
Indices: 39937564--39937588 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
39937554 AAAATATTTT
39937564 TATAAATAAAAAA
1 TATAAATAAAAAA
39937577 TATAAATAAAAA
1 TATAAATAAAAA
39937589 TTTTCCAAAA
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:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (13 bp):
TATAAATAAAAAA
Found at i:39951971 original size:78 final size:78
Alignment explanation
Indices: 39951870--39952032 Score: 238
Period size: 78 Copynumber: 2.1 Consensus size: 78
39951860 GTCTCTCTCT
* * * *
39951870 AACTCATAAATAGAAAAATAAGACTTTCAGTATATTTGAATTTACGTCCTTTTATATTGATACAA
1 AACTAATAAATAGAAAAATAAGACTTTCAGTATACTCGAATTCACGTCCTTTTATATTGATA-AA
39951935 -TTAAGACTCAATC
65 GTTAAGACTCAATC
* *
39951948 AACTAATAAATAGAAGAATAAGACTTTCAGTATACTCGAATTCACGTCTTTTTATATTGATAAAG
1 AACTAATAAATAGAAAAATAAGACTTTCAGTATACTCGAATTCACGTCCTTTTATATTGATAAAG
*
39952013 TTAAGATTCAATC
66 TTAAGACTCAATC
*
39952026 GACTAAT
1 AACTAAT
39952033 TATGATAAAG
Statistics
Matches: 76, Mismatches: 8, Indels: 2
0.88 0.09 0.02
Matches are distributed among these distances:
77 2 0.03
78 74 0.97
ACGTcount: A:0.41, C:0.13, G:0.10, T:0.35
Consensus pattern (78 bp):
AACTAATAAATAGAAAAATAAGACTTTCAGTATACTCGAATTCACGTCCTTTTATATTGATAAAG
TTAAGACTCAATC
Found at i:39954483 original size:28 final size:28
Alignment explanation
Indices: 39954416--39954483 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
39954406 CTTTTATGAG
*
39954416 TAAAAAC--TATAAGTTAAGGGCTTATT
1 TAAAAACAATATAGGTTAAGGGCTTATT
*
39954442 TAACTAAA-AA-ATAGGTTAAGGGCTTGTT
1 TAA--AAACAATATAGGTTAAGGGCTTATT
39954470 TAAAAACAATATAG
1 TAAAAACAATATAG
39954484 TGGGTTGAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
26 6 0.18
27 2 0.06
28 26 0.76
ACGTcount: A:0.46, C:0.07, G:0.16, T:0.31
Consensus pattern (28 bp):
TAAAAACAATATAGGTTAAGGGCTTATT
Found at i:39954919 original size:16 final size:16
Alignment explanation
Indices: 39954876--39954919 Score: 61
Period size: 16 Copynumber: 2.8 Consensus size: 16
39954866 TGTAATTTCT
39954876 ATTGTTAATATTAAAA
1 ATTGTTAATATTAAAA
** *
39954892 ATAATTAGTATTAAAA
1 ATTGTTAATATTAAAA
39954908 ATTGTTAATATT
1 ATTGTTAATATT
39954920 CTAAACATAA
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.48, C:0.00, G:0.07, T:0.45
Consensus pattern (16 bp):
ATTGTTAATATTAAAA
Found at i:39954972 original size:18 final size:18
Alignment explanation
Indices: 39954937--39954973 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
39954927 TAAGTGAAAA
39954937 TTTTACAATCTTTATTTT
1 TTTTACAATCTTTATTTT
*
39954955 TTTTATAAT-TTT-TTTT
1 TTTTACAATCTTTATTTT
39954971 TTT
1 TTT
39954974 AGTTTTGCAC
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
16 7 0.39
17 3 0.17
18 8 0.44
ACGTcount: A:0.19, C:0.05, G:0.00, T:0.76
Consensus pattern (18 bp):
TTTTACAATCTTTATTTT
Found at i:39956090 original size:19 final size:22
Alignment explanation
Indices: 39956044--39956090 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 22
39956034 GTTGTGTGTT
39956044 TAATTAGACTTTAATTAAGTAA
1 TAATTAGACTTTAATTAAGTAA
*
39956066 -ATTTAG-C-TTAATTAAG-AA
1 TAATTAGACTTTAATTAAGTAA
39956084 TAATTAG
1 TAATTAG
39956091 GGAAAAAGAC
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
18 2 0.09
19 14 0.64
20 1 0.05
21 5 0.23
ACGTcount: A:0.45, C:0.04, G:0.11, T:0.40
Consensus pattern (22 bp):
TAATTAGACTTTAATTAAGTAA
Found at i:39956605 original size:17 final size:19
Alignment explanation
Indices: 39956578--39956616 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 19
39956568 AGTAAATTAT
39956578 AAACATAAAAGAAT-AAAG
1 AAACATAAAAGAATAAAAG
39956596 AAAC-TAAAAGAATAAAAG
1 AAACATAAAAGAATAAAAG
39956614 AAA
1 AAA
39956617 GGAATGAAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 9 0.45
18 11 0.55
ACGTcount: A:0.74, C:0.05, G:0.10, T:0.10
Consensus pattern (19 bp):
AAACATAAAAGAATAAAAG
Found at i:39956760 original size:12 final size:12
Alignment explanation
Indices: 39956743--39956776 Score: 68
Period size: 12 Copynumber: 2.8 Consensus size: 12
39956733 AGAATCTGAG
39956743 GCATCGGCATTA
1 GCATCGGCATTA
39956755 GCATCGGCATTA
1 GCATCGGCATTA
39956767 GCATCGGCAT
1 GCATCGGCAT
39956777 CAAAAGGAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.24, C:0.26, G:0.26, T:0.24
Consensus pattern (12 bp):
GCATCGGCATTA
Found at i:39971484 original size:26 final size:26
Alignment explanation
Indices: 39971455--39971506 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
39971445 AATTTCAAAT
39971455 ATTT-AAAATTAAAAATATTTATAAAA
1 ATTTCAAAATTAAAAAT-TTTATAAAA
* *
39971481 ATTTCAAAATTTAAAATTTTCTAAAA
1 ATTTCAAAATTAAAAATTTTATAAAA
39971507 TAATAATTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 12 0.52
27 11 0.48
ACGTcount: A:0.56, C:0.04, G:0.00, T:0.40
Consensus pattern (26 bp):
ATTTCAAAATTAAAAATTTTATAAAA
Found at i:39973559 original size:26 final size:27
Alignment explanation
Indices: 39973515--39973567 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
39973505 AATCATTGCT
* *
39973515 TTGGTTTTTTTTTCCTTTTATGGATTA
1 TTGGTTTTTTTATCATTTTATGGATTA
*
39973542 TTGGTTTTTTTAT-ATTTTTTGGATTA
1 TTGGTTTTTTTATCATTTTATGGATTA
39973568 ATCATATATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
26 11 0.48
27 12 0.52
ACGTcount: A:0.13, C:0.04, G:0.15, T:0.68
Consensus pattern (27 bp):
TTGGTTTTTTTATCATTTTATGGATTA
Found at i:39990376 original size:38 final size:38
Alignment explanation
Indices: 39990298--39990525 Score: 402
Period size: 38 Copynumber: 6.0 Consensus size: 38
39990288 GAATTCAGTC
* *
39990298 ACCAGCACAAAGCCTGCGGGACTTTAACCCGGATAAATT
1 ACCAGCACGAAGCCTGCGGGAC-TTAACCCGGATATATT
*
39990337 ACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATT
1 ACCAGCACGAAGCCTGCGGGACTTAACCCGGATATATT
*
39990375 ACCAGCACGAAGCCTGCGGGATTTAACCCGGATATATT
1 ACCAGCACGAAGCCTGCGGGACTTAACCCGGATATATT
39990413 ACCAGCACGAAGCCTGCGGGACTTAACCCGGATATATT
1 ACCAGCACGAAGCCTGCGGGACTTAACCCGGATATATT
39990451 ACCAGCACGAAGCCTGCGGGACTTAACCCGGATATATT
1 ACCAGCACGAAGCCTGCGGGACTTAACCCGGATATATT
*
39990489 ACCAGCACGAAGCCTGCGAGACTTAACCCGGATATAT
1 ACCAGCACGAAGCCTGCGGGACTTAACCCGGATATAT
39990526 ATATCGAGTG
Statistics
Matches: 184, Mismatches: 5, Indels: 1
0.97 0.03 0.01
Matches are distributed among these distances:
38 164 0.89
39 20 0.11
ACGTcount: A:0.30, C:0.28, G:0.23, T:0.19
Consensus pattern (38 bp):
ACCAGCACGAAGCCTGCGGGACTTAACCCGGATATATT
Found at i:39995978 original size:26 final size:26
Alignment explanation
Indices: 39995943--39995994 Score: 95
Period size: 26 Copynumber: 2.0 Consensus size: 26
39995933 TTCGAAATAC
*
39995943 AAAAAAGGGGAATCAACAAGAGTGTA
1 AAAAAAGGGGAATAAACAAGAGTGTA
39995969 AAAAAAGGGGAATAAACAAGAGTGTA
1 AAAAAAGGGGAATAAACAAGAGTGTA
39995995 TCTACCTGCT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.56, C:0.06, G:0.27, T:0.12
Consensus pattern (26 bp):
AAAAAAGGGGAATAAACAAGAGTGTA
Found at i:40013760 original size:6 final size:7
Alignment explanation
Indices: 40013730--40013760 Score: 55
Period size: 7 Copynumber: 4.6 Consensus size: 7
40013720 ATCGTGATAA
40013730 ATTTAAT
1 ATTTAAT
40013737 ATTTAAT
1 ATTTAAT
40013744 ATTTAAT
1 ATTTAAT
40013751 ATTT-AT
1 ATTTAAT
40013757 ATTT
1 ATTT
40013761 TTATTAATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (7 bp):
ATTTAAT
Found at i:40013775 original size:15 final size:14
Alignment explanation
Indices: 40013731--40013779 Score: 62
Period size: 15 Copynumber: 3.4 Consensus size: 14
40013721 TCGTGATAAA
*
40013731 TTTAATATTTAATA
1 TTTAATATTTAATT
40013745 TTTAATATTTATATT
1 TTTAATATTTA-ATT
*
40013760 TTTATTAATTTAATT
1 TTTAAT-ATTTAATT
40013775 TTTAA
1 TTTAA
40013780 AAAATCAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
14 11 0.37
15 14 0.47
16 5 0.17
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (14 bp):
TTTAATATTTAATT
Found at i:40023128 original size:14 final size:14
Alignment explanation
Indices: 40023111--40023143 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
40023101 TAATTTCTTA
40023111 TATAATAAGTAAAT
1 TATAATAAGTAAAT
*
40023125 TATAATAATTAAAT
1 TATAATAAGTAAAT
40023139 TATAA
1 TATAA
40023144 GATTTTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.58, C:0.00, G:0.03, T:0.39
Consensus pattern (14 bp):
TATAATAAGTAAAT
Found at i:40023296 original size:22 final size:23
Alignment explanation
Indices: 40023245--40023287 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
40023235 AAAGTAATAT
*
40023245 AAAATA-ACTAAAAG-AAATAAG
1 AAAATAGAATAAAAGAAAATAAG
40023266 AAAATAGAATAAAAGAAAATAA
1 AAAATAGAATAAAAGAAAATAA
40023288 AAGAAAGAAG
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 6 0.32
22 7 0.37
23 6 0.32
ACGTcount: A:0.74, C:0.02, G:0.09, T:0.14
Consensus pattern (23 bp):
AAAATAGAATAAAAGAAAATAAG
Found at i:40023306 original size:17 final size:17
Alignment explanation
Indices: 40023286--40023318 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
40023276 AAAAGAAAAT
40023286 AAAAGAA-AGAAGAACAG
1 AAAAGAACA-AAGAACAG
40023303 AAAAGAACAAAGAACA
1 AAAAGAACAAAGAACA
40023319 AAACGAAAAC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 14 0.93
18 1 0.07
ACGTcount: A:0.73, C:0.09, G:0.18, T:0.00
Consensus pattern (17 bp):
AAAAGAACAAAGAACAG
Found at i:40023755 original size:17 final size:17
Alignment explanation
Indices: 40023735--40023767 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
40023725 TAAAATAGTT
*
40023735 AATTAGGATTAAATTGG
1 AATTAGGAATAAATTGG
40023752 AATTAGGAATAAATTG
1 AATTAGGAATAAATTG
40023768 AATAAAAATT
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:0.45, C:0.00, G:0.21, T:0.33
Consensus pattern (17 bp):
AATTAGGAATAAATTGG
Found at i:40024329 original size:29 final size:27
Alignment explanation
Indices: 40024268--40024339 Score: 99
Period size: 27 Copynumber: 2.7 Consensus size: 27
40024258 AATGCCTTAT
40024268 TGGTGTGTTAGGGAGGATATAATATAC
1 TGGTGTGTTAGGGAGGATATAATATAC
* * *
40024295 TGGTGTGTTTGGGAGGCTATATTATAC
1 TGGTGTGTTAGGGAGGATATAATATAC
* *
40024322 TAGTGTGTTATGGAGGAT
1 TGGTGTGTTAGGGAGGAT
40024340 TTATATTATT
Statistics
Matches: 38, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 38 1.00
ACGTcount: A:0.24, C:0.04, G:0.35, T:0.38
Consensus pattern (27 bp):
TGGTGTGTTAGGGAGGATATAATATAC
Found at i:40024344 original size:29 final size:27
Alignment explanation
Indices: 40024270--40024348 Score: 88
Period size: 27 Copynumber: 2.9 Consensus size: 27
40024260 TGCCTTATTG
* * *
40024270 GTGTGTTAGGGAGGATATAATATACTG
1 GTGTGTTATGGAGGATATATTATACTA
*
40024297 GTGTGTT-TGGGAGGCTATATTATACTA
1 GTGTGTTAT-GGAGGATATATTATACTA
40024324 GTGTGTTATGGAGGATTTATATTAT
1 GTGTGTTATGGAGGA--TATATTAT
40024349 TCCGGGTGTG
Statistics
Matches: 43, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
27 34 0.79
28 1 0.02
29 8 0.19
ACGTcount: A:0.25, C:0.04, G:0.30, T:0.41
Consensus pattern (27 bp):
GTGTGTTATGGAGGATATATTATACTA
Found at i:40027898 original size:16 final size:17
Alignment explanation
Indices: 40027869--40027906 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 17
40027859 TCTATTTAAC
* *
40027869 ATAAAAATATACAACAA
1 ATAAAAATAAACAAAAA
40027886 ATAAAAA-AAACAAAAA
1 ATAAAAATAAACAAAAA
40027902 ATAAA
1 ATAAA
40027907 TTTTTTACCT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
16 12 0.63
17 7 0.37
ACGTcount: A:0.79, C:0.08, G:0.00, T:0.13
Consensus pattern (17 bp):
ATAAAAATAAACAAAAA
Found at i:40028855 original size:38 final size:37
Alignment explanation
Indices: 40028771--40028864 Score: 95
Period size: 38 Copynumber: 2.5 Consensus size: 37
40028761 TATACATACT
40028771 TATACATACTTAAATATATTTTCCATATTTCATAATTC
1 TATACATACTTAAATATATTTTCCATATTT-ATAATTC
* * *
40028809 T-TATATACTTACATATATTTATGCATATTT-TACA-TC
1 TATACATACTTAAATATATTT-TCCATATTTATA-ATTC
*
40028845 ATATACATACTTATATATAT
1 -TATACATACTTAAATATAT
40028865 ATTCTCTTTA
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
36 4 0.09
37 19 0.40
38 24 0.51
ACGTcount: A:0.37, C:0.14, G:0.01, T:0.48
Consensus pattern (37 bp):
TATACATACTTAAATATATTTTCCATATTTATAATTC
Found at i:40033285 original size:15 final size:16
Alignment explanation
Indices: 40033256--40033293 Score: 51
Period size: 16 Copynumber: 2.3 Consensus size: 16
40033246 AAAAATCATA
40033256 AAAAATCTTAAAAAAT
1 AAAAATCTTAAAAAAT
40033272 AAAAAT-TTAGAAAAAT
1 AAAAATCTTA-AAAAAT
40033288 ATAAAA
1 A-AAAA
40033294 ATATAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 3 0.15
16 13 0.65
17 4 0.20
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (16 bp):
AAAAATCTTAAAAAAT
Found at i:40033382 original size:9 final size:9
Alignment explanation
Indices: 40033244--40033494 Score: 75
Period size: 9 Copynumber: 27.8 Consensus size: 9
40033234 TATTTTTCCC
*
40033244 ATAAAAATC
1 ATAAAAATT
40033253 ATAAAAAATCT
1 AT-AAAAAT-T
40033264 -TAAAAA--
1 ATAAAAATT
40033270 ATAAAAATT
1 ATAAAAATT
*
40033279 -TAGAAAAAT
1 ATA-AAAATT
40033288 ATAAAAA-T
1 ATAAAAATT
40033296 ATAAAATATT
1 ATAAAA-ATT
40033306 -T--AAATT
1 ATAAAAATT
*
40033312 GATATAAACTT
1 -ATA-AAAATT
*
40033323 ATTAAAATT
1 ATAAAAATT
*
40033332 ATAAAAAATC
1 AT-AAAAATT
*
40033342 ATAAAAA-C
1 ATAAAAATT
40033350 A-AAAAATCT
1 ATAAAAAT-T
*
40033359 A-ATAAATT
1 ATAAAAATT
40033367 ATAAAAAATT
1 AT-AAAAATT
40033377 AT-AAAATT
1 ATAAAAATT
*
40033385 AATAAAACTT
1 -ATAAAAATT
*
40033395 ATTTAAATATT
1 A--TAAAAATT
40033406 -T-AAAATT
1 ATAAAAATT
* *
40033413 TTAAAAAAGT
1 AT-AAAAATT
* *
40033423 ATTAGAATCCT
1 ATAAAAAT--T
*
40033434 A-AAAAATA
1 ATAAAAATT
40033442 ATAAAAATT
1 ATAAAAATT
*
40033451 GTAAAAA-T
1 ATAAAAATT
*
40033459 ATTAAAATT
1 ATAAAAATT
*
40033468 GATATAAACTT
1 -ATA-AAAATT
*
40033479 ATTAAAATT
1 ATAAAAATT
40033488 ATAAAAA
1 ATAAAAA
40033495 AAATCATAAA
Statistics
Matches: 179, Mismatches: 31, Indels: 64
0.65 0.11 0.23
Matches are distributed among these distances:
6 3 0.02
7 18 0.10
8 29 0.16
9 66 0.37
10 46 0.26
11 17 0.09
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.32
Consensus pattern (9 bp):
ATAAAAATT
Found at i:40034018 original size:22 final size:22
Alignment explanation
Indices: 40033973--40034022 Score: 70
Period size: 21 Copynumber: 2.4 Consensus size: 22
40033963 TTACAATATT
*
40033973 TATGATTTTTACAGAAGTTTAA
1 TATGATTTTTACAAAAGTTTAA
40033995 TATG-TTTTTACAAAAGTTTAA
1 TATGATTTTTACAAAAGTTTAA
40034016 -AT-ATTTT
1 TATGATTTT
40034023 AAATATGTAT
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 6 0.23
21 16 0.62
22 4 0.15
ACGTcount: A:0.36, C:0.04, G:0.10, T:0.50
Consensus pattern (22 bp):
TATGATTTTTACAAAAGTTTAA
Found at i:40034049 original size:8 final size:8
Alignment explanation
Indices: 40034036--40034142 Score: 83
Period size: 8 Copynumber: 12.4 Consensus size: 8
40034026 TATGTATTAT
40034036 TAATTTTA
1 TAATTTTA
40034044 TAA-TTTA
1 TAATTTTA
40034051 TAATTATTA
1 TAATT-TTA
*
40034060 GAATTTTA
1 TAATTTTA
*
40034068 TATTTTTA
1 TAATTTTA
40034076 TAATATTTA
1 TAAT-TTTA
40034085 TAATTTTATA
1 TAA-TTT-TA
40034095 TCAATTTTCA
1 T-AATTTT-A
40034105 TATATTTT-
1 TA-ATTTTA
*
40034113 TATATTTAA
1 TA-ATTTTA
40034122 TAATTTTA
1 TAATTTTA
40034130 TAAATTTTTA
1 T-AA-TTTTA
40034140 TAA
1 TAA
40034143 CTTTCTGGTT
Statistics
Matches: 82, Mismatches: 6, Indels: 21
0.75 0.06 0.19
Matches are distributed among these distances:
7 7 0.09
8 29 0.35
9 24 0.29
10 20 0.24
11 2 0.02
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (8 bp):
TAATTTTA
Found at i:40034069 original size:17 final size:18
Alignment explanation
Indices: 40034046--40034089 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
40034036 TAATTTTATA
40034046 ATTTATAATTATTAGAAT
1 ATTTATAATTATTAGAAT
* *
40034064 -TTTAT-ATTTTTATAAT
1 ATTTATAATTATTAGAAT
40034080 ATTTATAATT
1 ATTTATAATT
40034090 TTATATCAAT
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
16 9 0.41
17 10 0.45
18 3 0.14
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (18 bp):
ATTTATAATTATTAGAAT
Found at i:40034075 original size:25 final size:25
Alignment explanation
Indices: 40034037--40034095 Score: 77
Period size: 25 Copynumber: 2.4 Consensus size: 25
40034027 ATGTATTATT
40034037 AATTTTATA-ATTTATAAT-TATTAG
1 AATTTTATATATTTATAATAT-TTAG
* *
40034061 AATTTTATATTTTTATAATATTTAT
1 AATTTTATATATTTATAATATTTAG
40034086 AATTTTATAT
1 AATTTTATAT
40034096 CAATTTTCAT
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
24 9 0.29
25 21 0.68
26 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (25 bp):
AATTTTATATATTTATAATATTTAG
Found at i:40034140 original size:10 final size:9
Alignment explanation
Indices: 40034039--40034142 Score: 78
Period size: 9 Copynumber: 11.9 Consensus size: 9
40034029 GTATTATTAA
40034039 TTTTATAA-
1 TTTTATAAT
40034047 -TTTATAAT
1 TTTTATAAT
* *
40034055 TATTAGAA-
1 TTTTATAAT
40034063 TTTTAT-AT
1 TTTTATAAT
40034071 TTTTATAAT
1 TTTTATAAT
*
40034080 ATTTATAAT
1 TTTTATAAT
40034089 TTTATATCAAT
1 TTT-TAT-AAT
*
40034100 TTTCATATAT
1 TTTTATA-AT
40034110 TTTTAT-A-
1 TTTTATAAT
*
40034117 TTTAATAA-
1 TTTTATAAT
40034125 TTTTATAAAT
1 TTTTAT-AAT
40034135 TTTTATAA
1 TTTTATAA
40034143 CTTTCTGGTT
Statistics
Matches: 76, Mismatches: 10, Indels: 19
0.72 0.10 0.18
Matches are distributed among these distances:
7 13 0.17
8 17 0.22
9 22 0.29
10 18 0.24
11 6 0.08
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.60
Consensus pattern (9 bp):
TTTTATAAT
Found at i:40034739 original size:33 final size:32
Alignment explanation
Indices: 40034702--40034768 Score: 82
Period size: 33 Copynumber: 2.1 Consensus size: 32
40034692 AGAAACTATG
* *
40034702 AAATTTAAAAT-TTTTAAGAATCTATAAAAATAA
1 AAATTGAAAATATTCTAA-AATCTATAAAAA-AA
*
40034735 AAATTGAAAATATTCTAAAATCTGTAAAAAAA
1 AAATTGAAAATATTCTAAAATCTATAAAAAAA
40034767 AA
1 AA
40034769 CTAAAAAAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
32 4 0.13
33 21 0.70
34 5 0.17
ACGTcount: A:0.60, C:0.04, G:0.04, T:0.31
Consensus pattern (32 bp):
AAATTGAAAATATTCTAAAATCTATAAAAAAA
Found at i:40040937 original size:6 final size:6
Alignment explanation
Indices: 40040920--40040952 Score: 57
Period size: 6 Copynumber: 5.3 Consensus size: 6
40040910 ATTTTCTTTC
40040920 AATGATA AATGAA AATGAA AATGAA AATGAA AA
1 AATGA-A AATGAA AATGAA AATGAA AATGAA AA
40040953 AAAAAAGAGA
Statistics
Matches: 26, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
6 21 0.81
7 5 0.19
ACGTcount: A:0.67, C:0.00, G:0.15, T:0.18
Consensus pattern (6 bp):
AATGAA
Found at i:40040958 original size:18 final size:19
Alignment explanation
Indices: 40040920--40040958 Score: 53
Period size: 18 Copynumber: 2.1 Consensus size: 19
40040910 ATTTTCTTTC
**
40040920 AATGATAAATGAAAATGAA
1 AATGATAAATGAAAAAAAA
40040939 AATGA-AAATGAAAAAAAA
1 AATGATAAATGAAAAAAAA
40040957 AA
1 AA
40040959 GAGAATCAAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 13 0.72
19 5 0.28
ACGTcount: A:0.72, C:0.00, G:0.13, T:0.15
Consensus pattern (19 bp):
AATGATAAATGAAAAAAAA
Found at i:40041838 original size:21 final size:21
Alignment explanation
Indices: 40041805--40041848 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
40041795 ATAAACACTA
*
40041805 AACACTAAACCCTTA-ACCCTT
1 AACACCAAACCCTTAGA-CCTT
*
40041826 AACACCAAGCCCTTAGACCTT
1 AACACCAAACCCTTAGACCTT
40041847 AA
1 AA
40041849 AGTCCAACCC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
21 19 0.95
22 1 0.05
ACGTcount: A:0.39, C:0.36, G:0.05, T:0.20
Consensus pattern (21 bp):
AACACCAAACCCTTAGACCTT
Found at i:40042012 original size:31 final size:32
Alignment explanation
Indices: 40041958--40042018 Score: 88
Period size: 31 Copynumber: 1.9 Consensus size: 32
40041948 CCATATATAT
*
40041958 TAAACCATATTTAACTCATAAACCCTAAACCC
1 TAAACCATATTAAACTCATAAACCCTAAACCC
* *
40041990 TAAACCATCTTAAAC-CATAAACCTTAAAC
1 TAAACCATATTAAACTCATAAACCCTAAAC
40042019 TATAATGATA
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
31 13 0.50
32 13 0.50
ACGTcount: A:0.46, C:0.30, G:0.00, T:0.25
Consensus pattern (32 bp):
TAAACCATATTAAACTCATAAACCCTAAACCC
Found at i:40042229 original size:41 final size:41
Alignment explanation
Indices: 40042181--40042430 Score: 306
Period size: 41 Copynumber: 6.1 Consensus size: 41
40042171 GTTATATGAC
*
40042181 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGTTCTAGT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTAGT
*
40042222 TTATAGCGGCGTTTTAT-CAAAAGCGCCGCTAATGCTCTAGT
1 TTTTAGCGGCGTTTT-TCCAAAAGCGCCGCTAATGCTCTAGT
* * *
40042263 TTTTAGCGGCGTTTTTTCAAAAGCGCAGCTAATGCTCTGGT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTAGT
* * * *
40042304 TTTTAGTGG-GTTTTACCAAAAGCGCCGCTAATGGTCTGGT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTAGT
* * * *
40042344 TTTTAGCGGTGTTTTACCAAAAGCGCCGCTATTGCTCTATT
1 TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTAGT
* * * *
40042385 TTTTAGCGGCGTTTTTTACTAAAGCACCGCTATTGCTCTATGT
1 TTTTAGCGGCG-TTTTTCCAAAAGCGCCGCTAATGCTCTA-GT
40042428 TTT
1 TTT
40042431 ACAATTTTTG
Statistics
Matches: 183, Mismatches: 21, Indels: 8
0.86 0.10 0.04
Matches are distributed among these distances:
40 36 0.20
41 118 0.64
42 25 0.14
43 4 0.02
ACGTcount: A:0.20, C:0.20, G:0.22, T:0.38
Consensus pattern (41 bp):
TTTTAGCGGCGTTTTTCCAAAAGCGCCGCTAATGCTCTAGT
Done.