Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold106
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: 4928209
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Warning! 8888 characters in sequence are not A, C, G, or T
File 13 of 27
Found at i:2075258 original size:29 final size:28
Alignment explanation
Indices: 2075209--2075264 Score: 103
Period size: 28 Copynumber: 2.0 Consensus size: 28
2075199 TTAAATTACC
*
2075209 TTTTTTTCATTTTATTCAAAAATATTTA
1 TTTTTTTAATTTTATTCAAAAATATTTA
2075237 TTTTTTTAATTTTATTCAAAAATATTTA
1 TTTTTTTAATTTTATTCAAAAATATTTA
2075265 GAATAATATA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (28 bp):
TTTTTTTAATTTTATTCAAAAATATTTA
Found at i:2076211 original size:28 final size:26
Alignment explanation
Indices: 2076172--2076247 Score: 80
Period size: 29 Copynumber: 2.7 Consensus size: 26
2076162 ATGTTAATAA
2076172 TTTGTTTTATATTAATTTTGATACTTT
1 TTTGTTTTATATTAATTTTGATA-TTT
*
2076199 TTTGTATTTATATTATATTCTTGTTATTT
1 TTTGT-TTTATATTA-ATT-TTGATATTT
* *
2076228 TTATGTTATATTTTAATTTT
1 TT-TGTTTTATATTAATTTT
2076248 TTTCATGTTA
Statistics
Matches: 42, Mismatches: 3, Indels: 8
0.79 0.06 0.15
Matches are distributed among these distances:
27 7 0.17
28 12 0.29
29 15 0.36
30 8 0.19
ACGTcount: A:0.22, C:0.03, G:0.07, T:0.68
Consensus pattern (26 bp):
TTTGTTTTATATTAATTTTGATATTT
Found at i:2077633 original size:16 final size:16
Alignment explanation
Indices: 2077587--2077635 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
2077577 ACAACTTGAT
2077587 ATATATTTAAATATA-A
1 ATAT-TTTAAATATATA
* * *
2077603 AAATTATAAAAATATA
1 ATATTTTAAATATATA
2077619 ATATTTTAAATATATA
1 ATATTTTAAATATATA
2077635 A
1 A
2077636 AAAAATTTAA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
15 8 0.31
16 18 0.69
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
ATATTTTAAATATATA
Found at i:2080281 original size:45 final size:45
Alignment explanation
Indices: 2080197--2080282 Score: 102
Period size: 45 Copynumber: 1.9 Consensus size: 45
2080187 TTTATCTATA
* * **
2080197 ATATATATATATATGTATAAATACATTTTTGTTACTTATAAAAAT
1 ATATATATATATATATATAAATACAATTTTGAAACTTATAAAAAT
* *
2080242 ATATATATATATATATGTAAATACAGATTTT-AAATTTATAA
1 ATATATATATATATATATAAATACA-ATTTTGAAACTTATAA
2080283 GTATTTATTC
Statistics
Matches: 34, Mismatches: 6, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
45 30 0.88
46 4 0.12
ACGTcount: A:0.47, C:0.03, G:0.05, T:0.45
Consensus pattern (45 bp):
ATATATATATATATATATAAATACAATTTTGAAACTTATAAAAAT
Found at i:2081104 original size:17 final size:17
Alignment explanation
Indices: 2081084--2081125 Score: 84
Period size: 17 Copynumber: 2.5 Consensus size: 17
2081074 GTTGGAATAT
2081084 ATATATATATATTAATG
1 ATATATATATATTAATG
2081101 ATATATATATATTAATG
1 ATATATATATATTAATG
2081118 ATATATAT
1 ATATATAT
2081126 TTTTTGGCAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.05, T:0.48
Consensus pattern (17 bp):
ATATATATATATTAATG
Found at i:2082080 original size:2 final size:2
Alignment explanation
Indices: 2082073--2082097 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2082063 AAAGAATCCT
2082073 TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC T
2082098 ATATATATAT
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:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:2082102 original size:2 final size:2
Alignment explanation
Indices: 2082097--2082137 Score: 73
Period size: 2 Copynumber: 20.5 Consensus size: 2
2082087 TCTCTCTCTC
*
2082097 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2082138 GTACACACAC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2084204 original size:6 final size:6
Alignment explanation
Indices: 2084179--2084216 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
2084169 ATAATGTAAC
*
2084179 ATATTT A-ATAT ATA-TT ATATTT ATATTT ATATTT ATAT
1 ATATTT ATATTT ATATTT ATATTT ATATTT ATATTT ATAT
2084217 AATTAATAGA
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 8 0.29
6 20 0.71
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (6 bp):
ATATTT
Found at i:2084357 original size:10 final size:10
Alignment explanation
Indices: 2084342--2084366 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
2084332 CGACAAAAAT
2084342 AAAAAAATAA
1 AAAAAAATAA
2084352 AAAAAAATAA
1 AAAAAAATAA
2084362 AAAAA
1 AAAAA
2084367 GAAAAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.92, C:0.00, G:0.00, T:0.08
Consensus pattern (10 bp):
AAAAAAATAA
Found at i:2084359 original size:18 final size:18
Alignment explanation
Indices: 2084336--2084378 Score: 68
Period size: 18 Copynumber: 2.3 Consensus size: 18
2084326 AAAGAACGAC
*
2084336 AAAAATAAAAAAATAAAA
1 AAAAATAAAAAAAGAAAA
2084354 AAAAATAAAAAAAGAAAA
1 AAAAATAAAAAAAGAAAA
2084372 AGAAAAT
1 A-AAAAT
2084379 GAAGAGATGA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
18 18 0.78
19 5 0.22
ACGTcount: A:0.86, C:0.00, G:0.05, T:0.09
Consensus pattern (18 bp):
AAAAATAAAAAAAGAAAA
Found at i:2085681 original size:22 final size:22
Alignment explanation
Indices: 2085623--2085675 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 22
2085613 AATTTGATTC
* *
2085623 ATATAAATT-AAATATTAATTA
1 ATATAATTTAAAATTTTAATTA
*
2085644 ATATATTTTAAAATTTTAATTA
1 ATATAATTTAAAATTTTAATTA
*
2085666 ATTTAATTTA
1 ATATAATTTA
2085676 TTATTTAATA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 7 0.27
22 19 0.73
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (22 bp):
ATATAATTTAAAATTTTAATTA
Found at i:2085761 original size:27 final size:27
Alignment explanation
Indices: 2085706--2085784 Score: 76
Period size: 27 Copynumber: 3.0 Consensus size: 27
2085696 TTTAATTTGA
*
2085706 ATTA-TAAAATATAAAAT-AATTATTAAT
1 ATTATTAAAATATAATATAAATT-TT-AT
*
2085733 ATTATTAAAAAATAATATAAATTTTAT
1 ATTATTAAAATATAATATAAATTTTAT
*
2085760 ATTAATT-TAATATAAT-TAAATTTTA
1 ATT-ATTAAAATATAATATAAATTTTA
2085785 AAAAAATCGA
Statistics
Matches: 45, Mismatches: 4, Indels: 7
0.80 0.07 0.12
Matches are distributed among these distances:
26 9 0.20
27 16 0.36
28 16 0.36
29 4 0.09
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (27 bp):
ATTATTAAAATATAATATAAATTTTAT
Found at i:2086809 original size:17 final size:18
Alignment explanation
Indices: 2086777--2086812 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
2086767 AGTTTCAGAA
2086777 ATATTTTTTTAAAATTTTT
1 ATATTTTTTT-AAATTTTT
2086796 ATATTTTTTT-AATTTTT
1 ATATTTTTTTAAATTTTT
2086813 GAATAAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 7 0.41
19 10 0.59
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (18 bp):
ATATTTTTTTAAATTTTT
Found at i:2087086 original size:21 final size:22
Alignment explanation
Indices: 2087057--2087097 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
2087047 TTTATTAATT
2087057 CAAAATAAA-TATTTCTTTAAA
1 CAAAATAAATTATTTCTTTAAA
*
2087078 CAAATTAAATTATTTCTTTA
1 CAAAATAAATTATTTCTTTA
2087098 CGAAACAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 8 0.44
22 10 0.56
ACGTcount: A:0.46, C:0.10, G:0.00, T:0.44
Consensus pattern (22 bp):
CAAAATAAATTATTTCTTTAAA
Found at i:2092774 original size:338 final size:336
Alignment explanation
Indices: 2091955--2092947 Score: 1782
Period size: 328 Copynumber: 3.0 Consensus size: 336
2091945 TACCAATTGA
*
2091955 CATTGTGTCCGAAGTCATACACATTGATAGAGGGCTAATGATTGTCGTTTTGTTTATTAAAATTA
1 CATTGTGTCCGAAGTCATACACATTGATCGAGGGCTAATGATTGTCGTTTTGTTTATTAAAATTA
2092020 ATATAATCTTTCGATAAAATTTTAATCATAAAATTAGATTCTCAATGATTTTATTTATGTCTAAA
66 ATATAATCTTTCGATAAAATTTTAATCATAAAATTAGATTCTCAATGATTTTATTTATGTCTAAA
2092085 AGAGTTGCTAATTAAGTTATAAAATATTTATAAATTTAAATTAAATTATAATTTTAATAATAATT
131 AGAGTTGCTAATTAAGTTATAAAATATTTATAAATTTAAATTAAATTATAATTTTAATAATAATT
*
2092150 TTACAATTAATTTATAAAAATTTATAAATATTAATATAAAAATAATA-TTTAATGTTATTATAAA
196 TTAAAATTAATTTATAAAAATTTATAAATATTAATATAAAAATAATATTTTAATGTTATTATAAA
2092214 TAATAAACTAAAATTTTATATTAAATTTTAATTAAAAATTTAAATAATGA-TTGATTAA-TTTTG
261 TAATAAACTAAAATTTTATATTAAATTTTAATTAAAAATTTAAATAATGATTTGATTAATTTTTG
2092277 -AT-AATAAAT
326 AATAAATAAAT
*
2092286 C--TATGTCCG-AGTCATACACATTGATCGAGGGCTAATGATTGTCGTTTTGTTTATTAAAATTA
1 CATTGTGTCCGAAGTCATACACATTGATCGAGGGCTAATGATTGTCGTTTTGTTTATTAAAATTA
*
2092348 ATATAATCTTTCGATAAAATTTTAACCATAAAATTAGATTCTCAATGATTTTATTTATGTCTAAA
66 ATATAATCTTTCGATAAAATTTTAATCATAAAATTAGATTCTCAATGATTTTATTTATGTCTAAA
2092413 AGAGTTGCTAATTAAGTTATAAAATATTTATAAATTTAAATTAAATTATAATTTTAATAATAATT
131 AGAGTTGCTAATTAAGTTATAAAATATTTATAAATTTAAATTAAATTATAATTTTAATAATAATT
*
2092478 TGAAAATTAATTTATAAAAATTTATAAATATTAATATAAAAATAATATTTTAATGTTATTATAAA
196 TTAAAATTAATTTATAAAAATTTATAAATATTAATATAAAAATAATATTTTAATGTTATTATAAA
*
2092543 TAATAAACTAAAATTTTATATTAAATTTTAATTAAAAATTTAAATAATAATTTGATTCAATTTTT
261 TAATAAACTAAAATTTTATATTAAATTTTAATTAAAAATTTAAATAATGATTTGATT-AATTTTT
2092608 GAATAAATAAAAT
325 GAATAAAT-AAAT
2092621 CATTGTGTCCGAAGTCATACACATTGATCGAGGGCTAATGATTGTCGTTTTGTTTATTAAAATTA
1 CATTGTGTCCGAAGTCATACACATTGATCGAGGGCTAATGATTGTCGTTTTGTTTATTAAAATTA
2092686 ATATAATCTTTCGATAAAATTTTAATCATAAAATTAGATTCTCAATGATTTTATTTATGTCTAAA
66 ATATAATCTTTCGATAAAATTTTAATCATAAAATTAGATTCTCAATGATTTTATTTATGTCTAAA
2092751 AGAGTTGCTAATTAAGTTATAAAATATTTATAAATTTAAATTAAATTATAATTTTAATAATAATT
131 AGAGTTGCTAATTAAGTTATAAAATATTTATAAATTTAAATTAAATTATAATTTTAATAATAATT
2092816 TTAAAATTAATTTATAAAAATTT-TAAATATTAATATAAAAATAATATTTTAA--TTATTATAAA
196 TTAAAATTAATTTATAAAAATTTATAAATATTAATATAAAAATAATATTTTAATGTTATTATAAA
*
2092878 TAAT-AA--AAAATTTTATATTAAATTTTAATTAAAAATTTAAATAATGATGTAT-TTTAATTTT
261 TAATAAACTAAAATTTTATATTAAATTTTAATTAAAAATTTAAATAATGAT-T-TGATTAATTTT
2092939 TGAATAAAT
324 TGAATAAAT
2092948 TTAGAGTATT
Statistics
Matches: 639, Mismatches: 11, Indels: 23
0.95 0.02 0.03
Matches are distributed among these distances:
328 226 0.35
329 73 0.11
330 6 0.01
331 3 0.00
332 61 0.10
333 5 0.01
334 6 0.01
335 19 0.03
337 36 0.06
338 204 0.32
ACGTcount: A:0.44, C:0.05, G:0.07, T:0.43
Consensus pattern (336 bp):
CATTGTGTCCGAAGTCATACACATTGATCGAGGGCTAATGATTGTCGTTTTGTTTATTAAAATTA
ATATAATCTTTCGATAAAATTTTAATCATAAAATTAGATTCTCAATGATTTTATTTATGTCTAAA
AGAGTTGCTAATTAAGTTATAAAATATTTATAAATTTAAATTAAATTATAATTTTAATAATAATT
TTAAAATTAATTTATAAAAATTTATAAATATTAATATAAAAATAATATTTTAATGTTATTATAAA
TAATAAACTAAAATTTTATATTAAATTTTAATTAAAAATTTAAATAATGATTTGATTAATTTTTG
AATAAATAAAT
Found at i:2092829 original size:23 final size:24
Alignment explanation
Indices: 2092803--2092860 Score: 75
Period size: 22 Copynumber: 2.5 Consensus size: 24
2092793 AAATTATAAT
2092803 TTTAATAATAATTTTAAA-ATTAA
1 TTTAATAATAATTTTAAATATTAA
*
2092826 TTT-ATAAAAATTTTAAATATTAA
1 TTTAATAATAATTTTAAATATTAA
* *
2092849 TATAAAAATAAT
1 TTTAATAATAAT
2092861 ATTTTAATTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 13 0.45
23 10 0.34
24 6 0.21
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
TTTAATAATAATTTTAAATATTAA
Found at i:2092890 original size:26 final size:24
Alignment explanation
Indices: 2092831--2092897 Score: 71
Period size: 26 Copynumber: 2.6 Consensus size: 24
2092821 ATTAATTTAT
* *
2092831 AAAAATTTTAAATATTAATATAAA
1 AAAAATTTTAATTATTAAAATAAA
2092855 AATAATATTTTAATTATTATAAATAATA
1 AA-AA-ATTTTAATTATTA-AAATAA-A
2092883 AAAAATTTTATATTA
1 AAAAATTTTA-ATTA
2092898 AATTTTAATT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
24 2 0.06
25 2 0.06
26 18 0.50
27 11 0.31
28 3 0.08
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (24 bp):
AAAAATTTTAATTATTAAAATAAA
Found at i:2093275 original size:9 final size:9
Alignment explanation
Indices: 2093261--2093291 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
2093251 TTATATTATA
2093261 TTTATAAAT
1 TTTATAAAT
2093270 TTTATAAAT
1 TTTATAAAT
2093279 TTT-TAAAT
1 TTTATAAAT
2093287 TTTAT
1 TTTAT
2093292 TTCACTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (9 bp):
TTTATAAAT
Found at i:2095906 original size:16 final size:16
Alignment explanation
Indices: 2095882--2095932 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
2095872 TTAAATATTT
*
2095882 ATATGATTATAATAAA
1 ATATTATTATAATAAA
2095898 ATATTATTATAAATTAAA
1 ATATTATTAT-AA-TAAA
*
2095916 ATA-TATTA-AATATA
1 ATATTATTATAATAAA
2095930 ATA
1 ATA
2095933 AAAAATAATT
Statistics
Matches: 31, Mismatches: 2, Indels: 6
0.79 0.05 0.15
Matches are distributed among these distances:
14 6 0.19
15 2 0.06
16 9 0.29
17 7 0.23
18 7 0.23
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (16 bp):
ATATTATTATAATAAA
Found at i:2096263 original size:17 final size:15
Alignment explanation
Indices: 2096232--2096267 Score: 54
Period size: 17 Copynumber: 2.3 Consensus size: 15
2096222 ATCGGAATTC
2096232 GAAAAAAAAAAAAAA
1 GAAAAAAAAAAAAAA
2096247 GAAAAAGAAAAAGAAAA
1 GAAAAA-AAAAA-AAAA
2096264 GAAA
1 GAAA
2096268 GGAAGGAAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 6 0.32
16 5 0.26
17 8 0.42
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (15 bp):
GAAAAAAAAAAAAAA
Found at i:2096928 original size:17 final size:16
Alignment explanation
Indices: 2096895--2096940 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
2096885 ATAAAATTAA
* *
2096895 TAAAATAAAATATATT
1 TAAAAAAAAATTTATT
2096911 TAAAAAAAAATTTAATT
1 TAAAAAAAAATTT-ATT
2096928 TAAAAAATAAATT
1 TAAAAAA-AAATT
2096941 AAACATATTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
16 11 0.42
17 10 0.38
18 5 0.19
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TAAAAAAAAATTTATT
Found at i:2096942 original size:17 final size:17
Alignment explanation
Indices: 2096891--2096942 Score: 61
Period size: 17 Copynumber: 2.9 Consensus size: 17
2096881 GTAAATAAAA
*
2096891 TTAATAAAATAAAATATAT
1 TTAA-AAAATAAATTA-AT
2096910 TTAAAAAA-AAATTTAAT
1 TTAAAAAATAAA-TTAAT
2096927 TTAAAAAATAAATTAA
1 TTAAAAAATAAATTAA
2096943 ACATATTTCA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
17 17 0.57
18 9 0.30
19 4 0.13
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (17 bp):
TTAAAAAATAAATTAAT
Found at i:2101084 original size:2 final size:2
Alignment explanation
Indices: 2101077--2101104 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2101067 CGCCATGAAA
2101077 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG
2101105 CCTAACCTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2101587 original size:2 final size:2
Alignment explanation
Indices: 2101580--2101618 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
2101570 ACTTCTCTGA
2101580 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
2101619 CCTCAACTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:2101938 original size:3 final size:3
Alignment explanation
Indices: 2101930--2101967 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
2101920 AAACTCTTTC
2101930 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
2101968 GAAATTAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2102391 original size:54 final size:54
Alignment explanation
Indices: 2102327--2102435 Score: 218
Period size: 54 Copynumber: 2.0 Consensus size: 54
2102317 ATAGGCCACC
2102327 GGCGACCTCTAGTTGTAGACTTGTAGTCATTGGTTTTAAAAGGATAAATTCGTT
1 GGCGACCTCTAGTTGTAGACTTGTAGTCATTGGTTTTAAAAGGATAAATTCGTT
2102381 GGCGACCTCTAGTTGTAGACTTGTAGTCATTGGTTTTAAAAGGATAAATTCGTT
1 GGCGACCTCTAGTTGTAGACTTGTAGTCATTGGTTTTAAAAGGATAAATTCGTT
2102435 G
1 G
2102436 ACAGTTTAGA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
54 55 1.00
ACGTcount: A:0.26, C:0.13, G:0.25, T:0.37
Consensus pattern (54 bp):
GGCGACCTCTAGTTGTAGACTTGTAGTCATTGGTTTTAAAAGGATAAATTCGTT
Found at i:2109066 original size:2 final size:2
Alignment explanation
Indices: 2109059--2109086 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
2109049 TACCACATTG
2109059 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
2109087 TGTTTTTGTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2109228 original size:2 final size:2
Alignment explanation
Indices: 2109221--2109245 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2109211 TAATTTTTAT
2109221 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
2109246 GTAAATATAG
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:2111605 original size:3 final size:3
Alignment explanation
Indices: 2111592--2111628 Score: 56
Period size: 3 Copynumber: 12.0 Consensus size: 3
2111582 TTTGGATTTA
*
2111592 AAT ATAT AAT AAT AAT AAT AAT TAT AAT AAT AAT AAT
1 AAT A-AT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
2111629 TATTATTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
3 28 0.90
4 3 0.10
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
AAT
Found at i:2111617 original size:18 final size:18
Alignment explanation
Indices: 2111596--2111634 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
2111586 GATTTAAATA
2111596 TATAATAATAATAATAAT
1 TATAATAATAATAATAAT
*
2111614 TATAATAATAATAATTAT
1 TATAATAATAATAATAAT
2111632 TAT
1 TAT
2111635 TATTATTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TATAATAATAATAATAAT
Found at i:2111620 original size:15 final size:15
Alignment explanation
Indices: 2111600--2111631 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
2111590 TAAATATATA
2111600 ATAATAATAATAATT
1 ATAATAATAATAATT
2111615 ATAATAATAATAATT
1 ATAATAATAATAATT
2111630 AT
1 AT
2111632 TATTATTATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (15 bp):
ATAATAATAATAATT
Found at i:2112906 original size:23 final size:23
Alignment explanation
Indices: 2112854--2112911 Score: 59
Period size: 22 Copynumber: 2.5 Consensus size: 23
2112844 TTTAGTTTTA
*
2112854 TAATGTTTATATTTTTTATCATGT
1 TAAT-TTTATATTTTTTATCATAT
2112878 TAATTTTA-ATTTTTT-TCGATAT
1 TAATTTTATATTTTTTATC-ATAT
2112900 T-ATATTTATATT
1 TAAT-TTTATATT
2112912 GTATGATATT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
21 4 0.13
22 15 0.50
23 7 0.23
24 4 0.13
ACGTcount: A:0.28, C:0.03, G:0.05, T:0.64
Consensus pattern (23 bp):
TAATTTTATATTTTTTATCATAT
Found at i:2115275 original size:23 final size:22
Alignment explanation
Indices: 2115230--2115287 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
2115220 TAATAAATTT
*
2115230 TTATTTAAATATAATTATAAATA
1 TTATATAAA-ATAATTATAAATA
* *
2115253 TTAATATAAAATAATTTTTAATA
1 TT-ATATAAAATAATTATAAATA
*
2115276 TTATTTAAAATA
1 TTATATAAAATA
2115288 GTGAAAAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
22 9 0.30
23 15 0.50
24 6 0.20
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TTATATAAAATAATTATAAATA
Found at i:2115506 original size:28 final size:29
Alignment explanation
Indices: 2115474--2115540 Score: 70
Period size: 28 Copynumber: 2.4 Consensus size: 29
2115464 ATTAAAATTT
*
2115474 TAAAAAATATATGATGTTATA-TAA-TATA
1 TAAAAAATATAT-ATATTATATTAACTATA
*
2115502 TAAAAATTA-ATATATTATATTAACTATA
1 TAAAAAATATATATATTATATTAACTATA
*
2115530 T-TAAAATATAT
1 TAAAAAATATAT
2115541 TAATTACATC
Statistics
Matches: 32, Mismatches: 4, Indels: 6
0.76 0.10 0.14
Matches are distributed among these distances:
26 7 0.22
27 10 0.31
28 15 0.47
ACGTcount: A:0.54, C:0.01, G:0.03, T:0.42
Consensus pattern (29 bp):
TAAAAAATATATATATTATATTAACTATA
Found at i:2115546 original size:28 final size:26
Alignment explanation
Indices: 2115456--2115536 Score: 69
Period size: 28 Copynumber: 3.1 Consensus size: 26
2115446 AATAATAATT
*
2115456 ATTAATATATTA-A-AAT-TTTAAAA
1 ATTAATATATTATATAATATATAAAA
* *
2115479 AATATATGATGTTATATAATATATAAAA
1 ATTA-AT-ATATTATATAATATATAAAA
*
2115507 ATTAATATATTATATTAACTATATTAAA
1 ATTAATATATTATA-TAA-TATATAAAA
2115535 AT
1 AT
2115537 ATATTAATTA
Statistics
Matches: 45, Mismatches: 6, Indels: 9
0.75 0.10 0.15
Matches are distributed among these distances:
23 3 0.07
24 2 0.04
25 5 0.11
26 8 0.18
27 8 0.18
28 19 0.42
ACGTcount: A:0.53, C:0.01, G:0.02, T:0.43
Consensus pattern (26 bp):
ATTAATATATTATATAATATATAAAA
Found at i:2115839 original size:23 final size:24
Alignment explanation
Indices: 2115808--2115869 Score: 63
Period size: 24 Copynumber: 2.6 Consensus size: 24
2115798 CCCACTAAGC
* * *
2115808 TTTTTTAATTTTAATTTTA-TTTA
1 TTTTATAATTTTAAATTAATTTTA
*
2115831 TTTTATAATTTAAAATTAATTTTA
1 TTTTATAATTTTAAATTAATTTTA
* *
2115855 TTTAAAAATTTTAAA
1 TTTTATAATTTTAAA
2115870 ATATATTTAA
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
23 15 0.48
24 16 0.52
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (24 bp):
TTTTATAATTTTAAATTAATTTTA
Found at i:2115878 original size:24 final size:22
Alignment explanation
Indices: 2115824--2115878 Score: 56
Period size: 24 Copynumber: 2.3 Consensus size: 22
2115814 AATTTTAATT
* *
2115824 TTATTTATTTTATAATTTAAAA
1 TTATTTATTTAAAAATTTAAAA
2115846 TTAATTTTATTTAAAAATTTTAAAA
1 TT-A-TTTATTTAAAAA-TTTAAAA
2115871 TATATTTA
1 T-TATTTA
2115879 AAAACAACTT
Statistics
Matches: 27, Mismatches: 2, Indels: 6
0.77 0.06 0.17
Matches are distributed among these distances:
22 2 0.07
23 1 0.04
24 14 0.52
25 9 0.33
26 1 0.04
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (22 bp):
TTATTTATTTAAAAATTTAAAA
Found at i:2133346 original size:23 final size:25
Alignment explanation
Indices: 2133318--2133374 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 25
2133308 CAATTAATTT
2133318 ATTATTTTGAAATAAT-ATT-TATA
1 ATTATTTTGAAATAATGATTATATA
**
2133341 ATTATTTCAAAATAATGATTATATA
1 ATTATTTTGAAATAATGATTATATA
* *
2133366 TTTTTTTTG
1 ATTATTTTG
2133375 TTAAACTGAT
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
23 14 0.54
24 3 0.12
25 9 0.35
ACGTcount: A:0.39, C:0.02, G:0.05, T:0.54
Consensus pattern (25 bp):
ATTATTTTGAAATAATGATTATATA
Found at i:2137029 original size:2 final size:2
Alignment explanation
Indices: 2137022--2137059 Score: 67
Period size: 2 Copynumber: 19.0 Consensus size: 2
2137012 ACGAATCATC
*
2137022 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2137060 TTACAAGCCA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
AT
Found at i:2137372 original size:2 final size:2
Alignment explanation
Indices: 2137367--2137395 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2137357 TGGAAAAGAA
2137367 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 A
2137396 AGGTATCATC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:2140841 original size:22 final size:23
Alignment explanation
Indices: 2140816--2140862 Score: 78
Period size: 22 Copynumber: 2.1 Consensus size: 23
2140806 TATAAATAAT
2140816 TATAAAAAAATAAAATTTT-AAA
1 TATAAAAAAATAAAATTTTGAAA
*
2140838 TATAAAAAATTAAAATTTTGAAA
1 TATAAAAAAATAAAATTTTGAAA
2140861 TA
1 TA
2140863 ACCTATATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 18 0.78
23 5 0.22
ACGTcount: A:0.64, C:0.00, G:0.02, T:0.34
Consensus pattern (23 bp):
TATAAAAAAATAAAATTTTGAAA
Found at i:2142218 original size:31 final size:32
Alignment explanation
Indices: 2142160--2142220 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
2142150 TAATTACACT
2142160 TTTAATCCTTAACGTTTAATAAGTTTTTCACA
1 TTTAATCCTTAACGTTTAATAAGTTTTTCACA
* *
2142192 TTTAAT-CTTAAACTTTTAA-AATTTTTTCA
1 TTTAATCCTT-AACGTTTAATAAGTTTTTCA
2142221 TCAATTTTAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
31 12 0.46
32 14 0.54
ACGTcount: A:0.33, C:0.13, G:0.03, T:0.51
Consensus pattern (32 bp):
TTTAATCCTTAACGTTTAATAAGTTTTTCACA
Found at i:2143388 original size:21 final size:24
Alignment explanation
Indices: 2143364--2143413 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
2143354 ATAAGTTTGC
2143364 AAAAGG-AAAT-C-AAGAAAAAAA
1 AAAAGGAAAATCCAAAGAAAAAAA
2143385 AAAAGGAAAATCCAAAGAAAAAAA
1 AAAAGGAAAATCCAAAGAAAAAAA
2143409 AAAAG
1 AAAAG
2143414 AGTCAAGAAG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
21 6 0.23
22 4 0.15
23 1 0.04
24 15 0.58
ACGTcount: A:0.76, C:0.06, G:0.14, T:0.04
Consensus pattern (24 bp):
AAAAGGAAAATCCAAAGAAAAAAA
Found at i:2143733 original size:20 final size:22
Alignment explanation
Indices: 2143696--2143740 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
2143686 GATCCCAATG
*
2143696 TTTAAAAAAAATCTTAATGT-T
1 TTTAAAAAAAAACTTAATGTAT
2143717 TTTAAAAAAAAAC-TAATGTAT
1 TTTAAAAAAAAACTTAATGTAT
2143738 TTT
1 TTT
2143741 TATATATTAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.49, C:0.04, G:0.04, T:0.42
Consensus pattern (22 bp):
TTTAAAAAAAAACTTAATGTAT
Found at i:2143931 original size:19 final size:19
Alignment explanation
Indices: 2143889--2143944 Score: 55
Period size: 19 Copynumber: 3.1 Consensus size: 19
2143879 GATAAATTAT
* *
2143889 TTATATATTAATAA-TAT-
1 TTATATATTAAAAATTTTA
2143906 TTA-ATATTAAAAATTTTA
1 TTATATATTAAAAATTTTA
**
2143924 TTATATATTAACTATTTTA
1 TTATATATTAAAAATTTTA
2143943 TT
1 TT
2143945 TAATCAACTA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
16 9 0.28
17 5 0.16
18 3 0.09
19 15 0.47
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
TTATATATTAAAAATTTTA
Found at i:2144027 original size:32 final size:33
Alignment explanation
Indices: 2143991--2144062 Score: 121
Period size: 32 Copynumber: 2.2 Consensus size: 33
2143981 TATTCTATTA
2143991 AATAAAATATAAATATATTAAATATTACCTTT-
1 AATAAAATATAAATATATTAAATATTACCTTTG
*
2144023 AATAAAAAATAAATATATTAAATATTACCTTTG
1 AATAAAATATAAATATATTAAATATTACCTTTG
2144056 AA-AAAAT
1 AATAAAAT
2144063 TCAAATTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
32 35 0.95
33 2 0.05
ACGTcount: A:0.57, C:0.06, G:0.01, T:0.36
Consensus pattern (33 bp):
AATAAAATATAAATATATTAAATATTACCTTTG
Found at i:2145275 original size:2 final size:2
Alignment explanation
Indices: 2145268--2145306 Score: 62
Period size: 2 Copynumber: 20.0 Consensus size: 2
2145258 ACGAGAAGGA
*
2145268 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
2145307 TGGTAAAGAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
1 1 0.03
2 33 0.97
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:2147886 original size:18 final size:17
Alignment explanation
Indices: 2147837--2147901 Score: 68
Period size: 16 Copynumber: 4.0 Consensus size: 17
2147827 ATAAATATTT
2147837 TAAAATTTATAT-AATA
1 TAAAATTTATATAAATA
2147853 T-AAA-TTAT-TAACATA
1 TAAAATTTATATAA-ATA
2147868 TTAAAATTTATATAAATA
1 -TAAAATTTATATAAATA
*
2147886 TAAAATAT-TATAAATA
1 TAAAATTTATATAAATA
2147902 AAATTATAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 12
0.76 0.02 0.22
Matches are distributed among these distances:
13 1 0.02
14 5 0.12
15 6 0.14
16 10 0.24
17 10 0.24
18 7 0.17
19 3 0.07
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
TAAAATTTATATAAATA
Found at i:2147909 original size:12 final size:11
Alignment explanation
Indices: 2147896--2147938 Score: 50
Period size: 12 Copynumber: 3.6 Consensus size: 11
2147886 TAAAATATTA
2147896 TAAATAAAATT
1 TAAATAAAATT
*
2147907 ATAAATATAATT
1 -TAAATAAAATT
2147919 TAAATATATAATT
1 TAAATA-A-AATT
2147932 TAAATAA
1 TAAATAA
2147939 CAAAATTAAC
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
11 6 0.22
12 11 0.41
13 10 0.37
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
TAAATAAAATT
Found at i:2147915 original size:18 final size:18
Alignment explanation
Indices: 2147877--2147938 Score: 51
Period size: 18 Copynumber: 3.6 Consensus size: 18
2147867 ATTAAAATTT
2147877 ATATAAATATAAA-ATAT-
1 ATATAAATA-AAATATATA
2147894 -TATAAATAAAAT-TATAA
1 ATATAAATAAAATATAT-A
* *
2147911 ATATAATTTAAATATATA
1 ATATAAATAAAATATATA
*
2147929 ATTTAAATAA
1 ATATAAATAA
2147939 CAAAATTAAC
Statistics
Matches: 35, Mismatches: 5, Indels: 9
0.71 0.10 0.18
Matches are distributed among these distances:
15 6 0.17
16 8 0.23
18 18 0.51
19 3 0.09
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (18 bp):
ATATAAATAAAATATATA
Found at i:2147929 original size:13 final size:13
Alignment explanation
Indices: 2147911--2147937 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
2147901 AAAATTATAA
2147911 ATATAATTTAAAT
1 ATATAATTTAAAT
2147924 ATATAATTTAAAT
1 ATATAATTTAAAT
2147937 A
1 A
2147938 ACAAAATTAA
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:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (13 bp):
ATATAATTTAAAT
Found at i:2148261 original size:6 final size:6
Alignment explanation
Indices: 2148250--2148285 Score: 72
Period size: 6 Copynumber: 6.0 Consensus size: 6
2148240 TCTTTAAATA
2148250 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
1 AATTTT AATTTT AATTTT AATTTT AATTTT AATTTT
2148286 TAATCCAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 30 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
AATTTT
Found at i:2149820 original size:2 final size:2
Alignment explanation
Indices: 2149813--2149837 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2149803 TGATTCTTTA
2149813 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
2149838 AAGTGAAGTG
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:2150147 original size:19 final size:19
Alignment explanation
Indices: 2150123--2150160 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
2150113 AATTTGGATT
2150123 GATCTAGATCAAACTTATC
1 GATCTAGATCAAACTTATC
*
2150142 GATCTAGATTAAACTTATC
1 GATCTAGATCAAACTTATC
2150161 AATCCACTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.37, C:0.18, G:0.11, T:0.34
Consensus pattern (19 bp):
GATCTAGATCAAACTTATC
Found at i:2151562 original size:19 final size:19
Alignment explanation
Indices: 2151540--2151579 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
2151530 TTAAAATAAA
2151540 AATAAATATTTTTATAATT
1 AATAAATATTTTTATAATT
* *
2151559 AATATATTTTTTTATAATT
1 AATAAATATTTTTATAATT
2151578 AA
1 AA
2151580 ATTTGATTAA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (19 bp):
AATAAATATTTTTATAATT
Found at i:2152063 original size:247 final size:246
Alignment explanation
Indices: 2151625--2152119 Score: 663
Period size: 247 Copynumber: 2.0 Consensus size: 246
2151615 TCTGATTAAT
* * *
2151625 TTAAATTAATAAAAATTTATCTTAAATCTTATTATATCAACTTAAATCATTAAATTTATCTTAAA
1 TTAAATTAATAAAAATTTATCTCAAATCTTATTAAATCAACTCAAATCATTAAATTTATCTTAAA
* * ** * * *
2151690 TCTATTCTAATTAAATTCAAATCTATAAATTAAAAAATAATTTAAATTATTAAAGAATCTAATTA
66 CCTAATCTAAAAAAATTCAAAACTATAAATTAAAAAATAATTCAAATTATTAAAGAATCTAATCA
* * * *
2151755 CCGCTTAACACCTGAATTAAGTAAGTGCAAAATCATGGGTTTATACTTTAGACCGCCAAATTGAA
131 CCGCTTAACACCTGAATCAAGTAAGTACAAAATCATGGGTTTATACTTCAGACCACCAAATTGAA
* * *
2151820 TACCTCAATTACTTTCATTGGGCCCTTGGTTGAGAATATTATGTGGGTTTA
196 TACCTCAATTACTTTCATTGCGCCCTTAGTCGAGAATATTATGTGGGTTTA
* * *
2151871 TTAAATTATTAAAAATTTATCTCAAATTTTATTAAATCAAC-CAAATCATTAAATTTAT-TTCAG
1 TTAAATTAATAAAAATTTATCTCAAATCTTATTAAATCAACTCAAATCATTAAATTTATCTT-AA
* * *
2151934 ACCTAATCTAACAAAAATTTAAAACTGTAAATTAAAAGAATAATTCAAATTATTAATA-AATTTA
65 ACCTAATCTAA-AAAAATTCAAAACTATAAATTAAAA-AATAATTCAAATTATTAA-AGAATCTA
* * * *
2151998 ATCATCGTTTAACATCTGCATCAAGTAAGTACAAAATCATGGGTTTATACTTCAGACCACCAAAT
127 ATCACCGCTTAACACCTGAATCAAGTAAGTACAAAATCATGGGTTTATACTTCAGACCACCAAAT
** *
2152063 TGAATACCTCAATTGGTTTCATTGCGCCCTTAGTCGAGAATATTTTGTGGGTTTA
192 TGAATACCTCAATTACTTTCATTGCGCCCTTAGTCGAGAATATTATGTGGGTTTA
2152118 TT
1 TT
2152120 GAAGCTGCCT
Statistics
Matches: 215, Mismatches: 30, Indels: 7
0.85 0.12 0.03
Matches are distributed among these distances:
244 2 0.01
245 26 0.12
246 57 0.27
247 129 0.60
248 1 0.00
ACGTcount: A:0.40, C:0.14, G:0.09, T:0.37
Consensus pattern (246 bp):
TTAAATTAATAAAAATTTATCTCAAATCTTATTAAATCAACTCAAATCATTAAATTTATCTTAAA
CCTAATCTAAAAAAATTCAAAACTATAAATTAAAAAATAATTCAAATTATTAAAGAATCTAATCA
CCGCTTAACACCTGAATCAAGTAAGTACAAAATCATGGGTTTATACTTCAGACCACCAAATTGAA
TACCTCAATTACTTTCATTGCGCCCTTAGTCGAGAATATTATGTGGGTTTA
Found at i:2155313 original size:18 final size:20
Alignment explanation
Indices: 2155274--2155315 Score: 59
Period size: 20 Copynumber: 2.1 Consensus size: 20
2155264 CAATCATATT
2155274 TAAAATATTATATATTTATA
1 TAAAATATTATATATTTATA
*
2155294 TAAAAT-TTAATATGTTTATA
1 TAAAATATT-ATATATTTATA
2155314 TA
1 TA
2155316 TTCATATTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (20 bp):
TAAAATATTATATATTTATA
Found at i:2155328 original size:22 final size:22
Alignment explanation
Indices: 2155298--2155343 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
2155288 TTTATATAAA
2155298 ATTTAATATGTTTATATATTCAT
1 ATTTAATATGTTTATATATT-AT
* *
2155321 ATTT-ATATTTTTTTATATTAT
1 ATTTAATATGTTTATATATTAT
2155342 AT
1 AT
2155344 CATACTATAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
21 4 0.19
22 13 0.62
23 4 0.19
ACGTcount: A:0.33, C:0.02, G:0.02, T:0.63
Consensus pattern (22 bp):
ATTTAATATGTTTATATATTAT
Found at i:2156460 original size:3 final size:3
Alignment explanation
Indices: 2156452--2156481 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
2156442 AAAAAATTTT
2156452 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2156482 TGTAACGTCT
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:2160377 original size:20 final size:20
Alignment explanation
Indices: 2160354--2160392 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
2160344 CTAATGCTTA
2160354 ATTTATTA-GTATAATAAATT
1 ATTTATTAGGTAT-ATAAATT
2160374 ATTTATTAGGTATATAAAT
1 ATTTATTAGGTATATAAAT
2160393 AAATAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (20 bp):
ATTTATTAGGTATATAAATT
Found at i:2160625 original size:21 final size:21
Alignment explanation
Indices: 2160599--2160652 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
2160589 AATAAAAATT
2160599 TTAATTTTAT-AATTATAATAA
1 TTAATTTTATCAA-TATAATAA
* *
2160620 TTAATTGTATCAATATAGTAA
1 TTAATTTTATCAATATAATAA
*
2160641 TTAATATTATCA
1 TTAATTTTATCA
2160653 TCATCGCACT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (21 bp):
TTAATTTTATCAATATAATAA
Found at i:2160862 original size:34 final size:33
Alignment explanation
Indices: 2160799--2160863 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 33
2160789 GGATGATCGA
2160799 ATTTAAATTATAATTTAATTAATAAAAATATTTT
1 ATTTAAATTATAATTTAA-TAATAAAAATATTTT
2160833 ATTTAAATT-TAATTATAA-AATATATAAATAT
1 ATTTAAATTATAATT-TAATAATA-A-AAATAT
2160864 AAATATTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
32 4 0.14
33 6 0.21
34 18 0.64
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (33 bp):
ATTTAAATTATAATTTAATAATAAAAATATTTT
Found at i:2163942 original size:81 final size:81
Alignment explanation
Indices: 2163758--2164001 Score: 407
Period size: 81 Copynumber: 3.0 Consensus size: 81
2163748 CTGAAAGTGA
* * *
2163758 AGATTGATATTGTCACACAGTGAGCATAATTTTCAGATGCTGCTCCTATAATCCTCTCTACTCCT
1 AGATTGATACTGTCACACAATGAGCATAATTTTCAGATGCTGCTCCTATAATCCCCTCTACTCC-
2163823 TTTTCTTTTTGGTTAAT
65 TTTTCTTTTTGGTTAAT
* * * *
2163840 AGATTGATACTGTCACACAATGAGCATAATTTCCGGATGCTGTTCCTATAACCCCCTCTACTCCT
1 AGATTGATACTGTCACACAATGAGCATAATTTTCAGATGCTGCTCCTATAATCCCCTCTACTCCT
*
2163905 ATTCTTTTTGGTTAAT
66 TTTCTTTTTGGTTAAT
2163921 AGATTGATACTGTCACACAATGAGCATAATTTTCAGATGCTGCTCCTATAATCCCCTCTACTCCT
1 AGATTGATACTGTCACACAATGAGCATAATTTTCAGATGCTGCTCCTATAATCCCCTCTACTCCT
2163986 TTTCTTTTTGGTTAAT
66 TTTCTTTTTGGTTAAT
2164002 CTTTGTTTGT
Statistics
Matches: 149, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
81 92 0.62
82 57 0.38
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.40
Consensus pattern (81 bp):
AGATTGATACTGTCACACAATGAGCATAATTTTCAGATGCTGCTCCTATAATCCCCTCTACTCCT
TTTCTTTTTGGTTAAT
Found at i:2168145 original size:14 final size:14
Alignment explanation
Indices: 2168107--2168157 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
2168097 TATAGTAAAA
*
2168107 AATATTTTAATTTT
1 AATATTTTAAATTT
* *
2168121 TAGATTATTAAATTT
1 AATATT-TTAAATTT
2168136 AATATTTT-AATTT
1 AATATTTTAAATTT
2168149 ATATATTTT
1 A-ATATTTT
2168158 TAAAATTATA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
13 6 0.20
14 13 0.43
15 11 0.37
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (14 bp):
AATATTTTAAATTT
Found at i:2168191 original size:18 final size:17
Alignment explanation
Indices: 2168160--2168193 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2168150 TATATTTTTA
2168160 AAATTATAACAAATAAG
1 AAATTATAACAAATAAG
*
2168177 AAATTAATAATAAATAA
1 AAATT-ATAACAAATAA
2168194 AATTTTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (17 bp):
AAATTATAACAAATAAG
Found at i:2168909 original size:3 final size:3
Alignment explanation
Indices: 2168901--2168940 Score: 80
Period size: 3 Copynumber: 13.3 Consensus size: 3
2168891 TTGCAGACTT
2168901 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2168941 GACAAAAGAA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2169462 original size:2 final size:2
Alignment explanation
Indices: 2169455--2169481 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
2169445 TTTGTTTTCT
2169455 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
2169482 CTTTTGCAAT
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:2169979 original size:14 final size:14
Alignment explanation
Indices: 2169960--2170009 Score: 54
Period size: 12 Copynumber: 3.9 Consensus size: 14
2169950 CTTACCAATT
*
2169960 ATCTATAATCTATA
1 ATCTATAATATATA
2169974 ATCTATAATATAT-
1 ATCTATAATATATA
*
2169987 ATATAT-ATATAT-
1 ATCTATAATATATA
2169999 AT-TATAATATA
1 ATCTATAATATA
2170010 AAAAAATTTG
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
11 3 0.09
12 13 0.39
13 5 0.15
14 12 0.36
ACGTcount: A:0.48, C:0.06, G:0.00, T:0.46
Consensus pattern (14 bp):
ATCTATAATATATA
Found at i:2170240 original size:16 final size:16
Alignment explanation
Indices: 2170219--2170250 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2170209 ATATTATAAG
2170219 TTTAAAATTATAATTT
1 TTTAAAATTATAATTT
*
2170235 TTTAAAATTATTATTT
1 TTTAAAATTATAATTT
2170251 AAATATTGAT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTAAAATTATAATTT
Found at i:2170420 original size:20 final size:19
Alignment explanation
Indices: 2170358--2170423 Score: 78
Period size: 20 Copynumber: 3.4 Consensus size: 19
2170348 AAGCTTAATA
* *
2170358 TAATATTAAATATATTATAT
1 TAATATTAAATTTATGAT-T
* *
2170378 TATTATTAAATTTATGTTT
1 TAATATTAAATTTATGATT
2170397 TAATATTAAATTTATGAATT
1 TAATATTAAATTTATG-ATT
2170417 TAATATT
1 TAATATT
2170424 CAATATTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
19 16 0.41
20 23 0.59
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
TAATATTAAATTTATGATT
Found at i:2170901 original size:14 final size:13
Alignment explanation
Indices: 2170879--2170915 Score: 51
Period size: 13 Copynumber: 2.9 Consensus size: 13
2170869 TAAAAAAAAT
2170879 TAAATTAATATTA
1 TAAATTAATATTA
2170892 TAATATTAATA-TA
1 TAA-ATTAATATTA
2170905 TAAA-TAATATT
1 TAAATTAATATT
2170916 TTTAAAAATT
Statistics
Matches: 22, Mismatches: 0, Indels: 5
0.81 0.00 0.19
Matches are distributed among these distances:
11 5 0.23
12 2 0.09
13 8 0.36
14 7 0.32
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (13 bp):
TAAATTAATATTA
Found at i:2171653 original size:6 final size:6
Alignment explanation
Indices: 2171643--2171680 Score: 67
Period size: 6 Copynumber: 6.3 Consensus size: 6
2171633 TTAAAGCCGA
*
2171643 AAACCA AAACCC AAACCC AAACCC AAACCC AAACCC AA
1 AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AA
2171681 CTTCCCCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.55, C:0.45, G:0.00, T:0.00
Consensus pattern (6 bp):
AAACCC
Found at i:2173742 original size:32 final size:32
Alignment explanation
Indices: 2173706--2173768 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
2173696 ATAGTAATAA
2173706 ATATAATATAAA-TATATAAAATATTAAAATTT
1 ATATAATATAAATTAT-TAAAATATTAAAATTT
**
2173738 ATATAATATAAATTATTAATTTATTAAAATT
1 ATATAATATAAATTATTAAAATATTAAAATT
2173769 ATTTTTAATT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 25 0.89
33 3 0.11
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
ATATAATATAAATTATTAAAATATTAAAATTT
Found at i:2175958 original size:20 final size:20
Alignment explanation
Indices: 2175930--2175967 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2175920 ACACAAGCCC
2175930 ATTAAAA-CCAAACAAACCGT
1 ATTAAAACCCAAA-AAACCGT
*
2175950 ATTAGAACCCAAAAAACC
1 ATTAAAACCCAAAAAACC
2175968 TTCAATGCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.55, C:0.26, G:0.05, T:0.13
Consensus pattern (20 bp):
ATTAAAACCCAAAAAACCGT
Found at i:2182202 original size:85 final size:84
Alignment explanation
Indices: 2182075--2182259 Score: 218
Period size: 85 Copynumber: 2.2 Consensus size: 84
2182065 CACTCCTTTT
* *
2182075 TTTCTTTTTGGTTAATAGATTGATACTTTCCACCAAATTGAGATTTAATTTCCGGATGCTG-TTC
1 TTTCTTTTTGGTTAATAGATTGATACTGTCCACCAAATTGAGA--TAATTTCCAGATGCTGCTTC
2182139 CTATA-ACCCCCTCTAAC-TCTA
64 CTA-ACACCCCCTCTAACTTC-A
* *
2182160 TTTCTTTTTGGTTAATAGATTGATACATGT-CACACACA-TGAGATAATTTTCAGATGCTGCTTC
1 TTTCTTTTTGGTTAATAGATTGATAC-TGTCCAC-CAAATTGAGATAATTTCCAGATGCTGCTTC
* * *
2182223 CTAACTCCCCCTCTACCTTCC
64 CTAACACCCCCTCTAACTTCA
2182244 TTTCTTTTTGGTTAAT
1 TTTCTTTTTGGTTAAT
2182260 CTTTGTTGTA
Statistics
Matches: 88, Mismatches: 7, Indels: 11
0.83 0.07 0.10
Matches are distributed among these distances:
83 15 0.17
84 32 0.36
85 36 0.41
86 5 0.06
ACGTcount: A:0.23, C:0.23, G:0.12, T:0.42
Consensus pattern (84 bp):
TTTCTTTTTGGTTAATAGATTGATACTGTCCACCAAATTGAGATAATTTCCAGATGCTGCTTCCT
AACACCCCCTCTAACTTCA
Found at i:2187255 original size:7 final size:6
Alignment explanation
Indices: 2187240--2187283 Score: 52
Period size: 7 Copynumber: 6.8 Consensus size: 6
2187230 CGACTTTATA
*
2187240 AATACT AATAACT AATAATT AATAAT AATAAT AATACAT AATAA
1 AATAAT AATAA-T AATAA-T AATAAT AATAAT AATA-AT AATAA
2187284 GACAAAAAGA
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
6 16 0.47
7 18 0.53
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (6 bp):
AATAAT
Found at i:2187258 original size:10 final size:9
Alignment explanation
Indices: 2187240--2187283 Score: 52
Period size: 10 Copynumber: 4.6 Consensus size: 9
2187230 CGACTTTATA
*
2187240 AATACTAAT
1 AATAATAAT
2187249 AACTAATAATT
1 AA-TAATAA-T
2187260 AATAATAAT
1 AATAATAAT
2187269 AATAATACAT
1 AATAATA-AT
2187279 AATAA
1 AATAA
2187284 GACAAAAAGA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
9 10 0.32
10 18 0.58
11 3 0.10
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (9 bp):
AATAATAAT
Found at i:2187265 original size:3 final size:3
Alignment explanation
Indices: 2187240--2187283 Score: 52
Period size: 3 Copynumber: 13.7 Consensus size: 3
2187230 CGACTTTATA
*
2187240 AAT ACT AAT AACT AAT AATT AAT AAT AAT AAT AAT ACAT AAT AA
1 AAT AAT AAT AA-T AAT AA-T AAT AAT AAT AAT AAT A-AT AAT AA
2187284 GACAAAAAGA
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
3 27 0.75
4 9 0.25
ACGTcount: A:0.61, C:0.07, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:2190080 original size:7 final size:7
Alignment explanation
Indices: 2190070--2190102 Score: 50
Period size: 7 Copynumber: 4.9 Consensus size: 7
2190060 CGTAAAACCA
2190070 AAACCCC
1 AAACCCC
2190077 AAA-CCC
1 AAACCCC
2190083 AAACCCC
1 AAACCCC
*
2190090 AAAACCC
1 AAACCCC
2190097 AAACCC
1 AAACCC
2190103 AACTTTCCCC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
6 6 0.26
7 17 0.74
ACGTcount: A:0.48, C:0.52, G:0.00, T:0.00
Consensus pattern (7 bp):
AAACCCC
Found at i:2190094 original size:14 final size:14
Alignment explanation
Indices: 2190063--2190102 Score: 64
Period size: 13 Copynumber: 2.9 Consensus size: 14
2190053 TTTAAAGCGT
*
2190063 AAAACCAAAACCCC
1 AAAACCCAAACCCC
2190077 -AAACCCAAACCCC
1 AAAACCCAAACCCC
2190090 AAAACCCAAACCC
1 AAAACCCAAACCC
2190103 AACTTTCCCC
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
13 12 0.50
14 12 0.50
ACGTcount: A:0.53, C:0.47, G:0.00, T:0.00
Consensus pattern (14 bp):
AAAACCCAAACCCC
Found at i:2192973 original size:3 final size:3
Alignment explanation
Indices: 2192965--2192997 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
2192955 AAAAAATTTT
2192965 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
2192998 TGTAACGTCT
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):
ATA
Found at i:2196881 original size:20 final size:20
Alignment explanation
Indices: 2196858--2196896 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
2196848 CTAATGCTTA
2196858 ATTTATTA-GTATAATAAATT
1 ATTTATTAGGTAT-ATAAATT
2196878 ATTTATTAGGTATATAAAT
1 ATTTATTAGGTATATAAAT
2196897 AAATAAATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 14 0.78
21 4 0.22
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.49
Consensus pattern (20 bp):
ATTTATTAGGTATATAAATT
Found at i:2197129 original size:21 final size:21
Alignment explanation
Indices: 2197103--2197156 Score: 65
Period size: 21 Copynumber: 2.6 Consensus size: 21
2197093 AATAAAAATT
2197103 TTAATTTTAT-AATTATAATAA
1 TTAATTTTATCAA-TATAATAA
* *
2197124 TTAATTGTATCAATATAGTAA
1 TTAATTTTATCAATATAATAA
*
2197145 TTAATATTATCA
1 TTAATTTTATCA
2197157 TCATCGCACT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 26 0.93
22 2 0.07
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (21 bp):
TTAATTTTATCAATATAATAA
Found at i:2197364 original size:34 final size:33
Alignment explanation
Indices: 2197301--2197365 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 33
2197291 GGATGATCGA
2197301 ATTTAAATTATAATTTAATTAATAAAAATATTTT
1 ATTTAAATTATAATTTAA-TAATAAAAATATTTT
2197335 ATTTAAATT-TAATTATAA-AATATATAAATAT
1 ATTTAAATTATAATT-TAATAATA-A-AAATAT
2197366 AAATATTTAC
Statistics
Matches: 28, Mismatches: 0, Indels: 6
0.82 0.00 0.18
Matches are distributed among these distances:
32 4 0.14
33 6 0.21
34 18 0.64
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (33 bp):
ATTTAAATTATAATTTAATAATAAAAATATTTT
Found at i:2200445 original size:81 final size:81
Alignment explanation
Indices: 2200261--2200504 Score: 407
Period size: 81 Copynumber: 3.0 Consensus size: 81
2200251 CTGAAAGTGA
* * *
2200261 AGATTGATATTGTCACACAGTGAGCATAATTTTCAGATGCTGCTCCTATAATCCTCTCTACTCCT
1 AGATTGATACTGTCACACAATGAGCATAATTTTCAGATGCTGCTCCTATAATCCCCTCTACTCC-
2200326 TTTTCTTTTTGGTTAAT
65 TTTTCTTTTTGGTTAAT
* * * *
2200343 AGATTGATACTGTCACACAATGAGCATAATTTCCGGATGCTGTTCCTATAACCCCCTCTACTCCT
1 AGATTGATACTGTCACACAATGAGCATAATTTTCAGATGCTGCTCCTATAATCCCCTCTACTCCT
*
2200408 ATTCTTTTTGGTTAAT
66 TTTCTTTTTGGTTAAT
2200424 AGATTGATACTGTCACACAATGAGCATAATTTTCAGATGCTGCTCCTATAATCCCCTCTACTCCT
1 AGATTGATACTGTCACACAATGAGCATAATTTTCAGATGCTGCTCCTATAATCCCCTCTACTCCT
2200489 TTTCTTTTTGGTTAAT
66 TTTCTTTTTGGTTAAT
2200505 CTTTGTTTGT
Statistics
Matches: 149, Mismatches: 13, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
81 92 0.62
82 57 0.38
ACGTcount: A:0.24, C:0.23, G:0.13, T:0.40
Consensus pattern (81 bp):
AGATTGATACTGTCACACAATGAGCATAATTTTCAGATGCTGCTCCTATAATCCCCTCTACTCCT
TTTCTTTTTGGTTAAT
Found at i:2204647 original size:14 final size:14
Alignment explanation
Indices: 2204609--2204659 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
2204599 TATAGTAAAA
*
2204609 AATATTTTAATTTT
1 AATATTTTAAATTT
* *
2204623 TAGATTATTAAATTT
1 AATATT-TTAAATTT
2204638 AATATTTT-AATTT
1 AATATTTTAAATTT
2204651 ATATATTTT
1 A-ATATTTT
2204660 TAAAATTATA
Statistics
Matches: 30, Mismatches: 5, Indels: 4
0.77 0.13 0.10
Matches are distributed among these distances:
13 6 0.20
14 13 0.43
15 11 0.37
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (14 bp):
AATATTTTAAATTT
Found at i:2204693 original size:18 final size:17
Alignment explanation
Indices: 2204662--2204695 Score: 50
Period size: 18 Copynumber: 1.9 Consensus size: 17
2204652 TATATTTTTA
2204662 AAATTATAACAAATAAG
1 AAATTATAACAAATAAG
*
2204679 AAATTAATAATAAATAA
1 AAATT-ATAACAAATAA
2204696 AATTTTAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 5 0.33
18 10 0.67
ACGTcount: A:0.68, C:0.03, G:0.03, T:0.26
Consensus pattern (17 bp):
AAATTATAACAAATAAG
Found at i:2205416 original size:3 final size:3
Alignment explanation
Indices: 2205408--2205450 Score: 86
Period size: 3 Copynumber: 14.3 Consensus size: 3
2205398 TTGCAGACTT
2205408 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA A
2205451 GACAAAAGAA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 40 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:2205975 original size:2 final size:2
Alignment explanation
Indices: 2205968--2205996 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
2205958 TTTGTTTTCT
2205968 TA 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 TA T
2205997 CTTTTGCAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2206501 original size:14 final size:14
Alignment explanation
Indices: 2206482--2206532 Score: 51
Period size: 14 Copynumber: 4.1 Consensus size: 14
2206472 CTTACCAATT
*
2206482 ATCTATAATCTATA
1 ATCTATAATATATA
2206496 ATCTATAATATAT-
1 ATCTATAATATATA
2206509 A--TAT-ATATATA
1 ATCTATAATATATA
2206520 AT-TATAA-ATATA
1 ATCTATAATATATA
2206532 A
1 A
2206533 AAAAATTTGA
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 6 0.18
11 4 0.12
12 9 0.27
13 2 0.06
14 12 0.36
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (14 bp):
ATCTATAATATATA
Found at i:2206766 original size:16 final size:16
Alignment explanation
Indices: 2206745--2206776 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
2206735 ATATTATAAG
2206745 TTTAAAATTATAATTT
1 TTTAAAATTATAATTT
*
2206761 TTTAAAATTATTATTT
1 TTTAAAATTATAATTT
2206777 AAATATTTGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (16 bp):
TTTAAAATTATAATTT
Found at i:2206947 original size:20 final size:19
Alignment explanation
Indices: 2206885--2206950 Score: 78
Period size: 20 Copynumber: 3.4 Consensus size: 19
2206875 AAGCTTAATA
* *
2206885 TAATATTAAATATATTATAT
1 TAATATTAAATTTATGAT-T
* *
2206905 TATTATTAAATTTATGTTT
1 TAATATTAAATTTATGATT
2206924 TAATATTAAATTTATGAATT
1 TAATATTAAATTTATG-ATT
2206944 TAATATT
1 TAATATT
2206951 CAATATTTTT
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
19 16 0.41
20 23 0.59
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (19 bp):
TAATATTAAATTTATGATT
Found at i:2208187 original size:6 final size:6
Alignment explanation
Indices: 2208177--2208216 Score: 71
Period size: 6 Copynumber: 6.7 Consensus size: 6
2208167 TTAAAGCCGA
*
2208177 AAACCA AAACCC AAACCC AAACCC AAACCC AAACCC AAAC
1 AAACCC AAACCC AAACCC AAACCC AAACCC AAACCC AAAC
2208217 TTCCCCAAAA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.55, C:0.45, G:0.00, T:0.00
Consensus pattern (6 bp):
AAACCC
Found at i:2210279 original size:18 final size:20
Alignment explanation
Indices: 2210226--2210287 Score: 60
Period size: 18 Copynumber: 3.3 Consensus size: 20
2210216 TATAATCATG
*
2210226 ATATAATAT-AGTA-ATAAA
1 ATATAATATAAATATATAAA
2210244 ATATAATATAAATATATAAA
1 ATATAATATAAATATATAAA
* * *
2210264 A-ATATTA-AAATTTATATA
1 ATATAATATAAATATATAAA
2210282 ATATAA
1 ATATAA
2210288 ATTATTAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 5
0.78 0.11 0.11
Matches are distributed among these distances:
18 19 0.53
19 11 0.31
20 6 0.17
ACGTcount: A:0.61, C:0.00, G:0.02, T:0.37
Consensus pattern (20 bp):
ATATAATATAAATATATAAA
Found at i:2210286 original size:33 final size:32
Alignment explanation
Indices: 2210244--2210307 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
2210234 TAGTAATAAA
2210244 ATATAATATAAATATATAAAAATATTAAAATTT
1 ATATAATATAAAT-TATAAAAATATTAAAATTT
* **
2210277 ATATAATATAAATTATTAATTTATTAAAATT
1 ATATAATATAAATTATAAAAATATTAAAATT
2210308 ATTTTTAAAT
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
32 15 0.54
33 13 0.46
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (32 bp):
ATATAATATAAATTATAAAAATATTAAAATTT
Found at i:2212493 original size:20 final size:20
Alignment explanation
Indices: 2212465--2212502 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
2212455 ACACAAGCCC
2212465 ATTAAAA-CCAAACAAACCGT
1 ATTAAAACCCAAA-AAACCGT
*
2212485 ATTAGAACCCAAAAAACC
1 ATTAAAACCCAAAAAACC
2212503 TTCAATGCCC
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.55, C:0.26, G:0.05, T:0.13
Consensus pattern (20 bp):
ATTAAAACCCAAAAAACCGT
Found at i:2213651 original size:61 final size:61
Alignment explanation
Indices: 2213565--2213685 Score: 161
Period size: 61 Copynumber: 2.0 Consensus size: 61
2213555 CGGGTATGCG
* * **
2213565 TTAAACATAGATATATTTTAGTTTTTTTAAGTTTTTTTATATATTTAGAGGATCGTATCTA
1 TTAAACATAGACATATTTAAGTTTTTTTAAGTTTTTCCATATATTTAGAGGATCGTATCTA
* * * * *
2213626 TTAAACATGGACATGTTTAAGTTTTTTTGAGTTTTTCCATATATTTGGAGGATTGTATCT
1 TTAAACATAGACATATTTAAGTTTTTTTAAGTTTTTCCATATATTTAGAGGATCGTATCT
2213686 CCAAACCTAT
Statistics
Matches: 51, Mismatches: 9, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
61 51 1.00
ACGTcount: A:0.28, C:0.07, G:0.15, T:0.50
Consensus pattern (61 bp):
TTAAACATAGACATATTTAAGTTTTTTTAAGTTTTTCCATATATTTAGAGGATCGTATCTA
Found at i:2214339 original size:83 final size:83
Alignment explanation
Indices: 2214200--2214362 Score: 317
Period size: 83 Copynumber: 2.0 Consensus size: 83
2214190 GGTGCTCTAA
2214200 TGCTCACAACTTGCATCAGTTACTTATCTCATGCACAGGTGAAAAGTATATGTCTATTATGAATT
1 TGCTCACAACTTGCATCAGTTACTTATCTCATGCACAGGTGAAAAGTATATGTCTATTATGAATT
2214265 TATCTGAAAATCCTTGAG
66 TATCTGAAAATCCTTGAG
2214283 TGCTCACAACTTGCATCAGTTACTTATCTCATGCACAGGTGAAAAGTATATGTCTATTATGAATT
1 TGCTCACAACTTGCATCAGTTACTTATCTCATGCACAGGTGAAAAGTATATGTCTATTATGAATT
*
2214348 TCTCTGAAAATCCTT
66 TATCTGAAAATCCTT
2214363 CAGGGCAGAA
Statistics
Matches: 79, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
83 79 1.00
ACGTcount: A:0.31, C:0.19, G:0.15, T:0.36
Consensus pattern (83 bp):
TGCTCACAACTTGCATCAGTTACTTATCTCATGCACAGGTGAAAAGTATATGTCTATTATGAATT
TATCTGAAAATCCTTGAG
Found at i:2219249 original size:2 final size:2
Alignment explanation
Indices: 2219242--2219266 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
2219232 AAGTCGCCAT
2219242 GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA G
2219267 GGGTAGGGGA
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:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:2219832 original size:20 final size:21
Alignment explanation
Indices: 2219791--2219836 Score: 60
Period size: 20 Copynumber: 2.2 Consensus size: 21
2219781 AATATCAAAT
2219791 ATAAATAAACATACATTTATA
1 ATAAATAAACATACATTTATA
*
2219812 ATAAGTAAA-ATAC-TTTAATA
1 ATAAATAAACATACATTT-ATA
2219832 ATAAA
1 ATAAA
2219837 ATTTAAAATA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
19 3 0.14
20 11 0.50
21 8 0.36
ACGTcount: A:0.59, C:0.07, G:0.02, T:0.33
Consensus pattern (21 bp):
ATAAATAAACATACATTTATA
Found at i:2219853 original size:22 final size:20
Alignment explanation
Indices: 2219817--2219867 Score: 66
Period size: 20 Copynumber: 2.4 Consensus size: 20
2219807 TTATAATAAG
2219817 TAAAATACTTTAATAATAAAATT
1 TAAAATA-TTTAAT-A-AAAATT
2219840 TAAAATATTTAATAAAAATT
1 TAAAATATTTAATAAAAATT
*
2219860 AAAAATAT
1 TAAAATAT
2219868 CATATTTTAT
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 13 0.48
21 1 0.04
22 6 0.22
23 7 0.26
ACGTcount: A:0.61, C:0.02, G:0.00, T:0.37
Consensus pattern (20 bp):
TAAAATATTTAATAAAAATT
Found at i:2220149 original size:17 final size:18
Alignment explanation
Indices: 2220107--2220154 Score: 55
Period size: 17 Copynumber: 2.6 Consensus size: 18
2220097 AAAATATATT
2220107 TATATATTTGTATAAAGATA
1 TATATATTTG-AT-AAGATA
2220127 -AGTATATTTGAT-AGATA
1 TA-TATATTTGATAAGATA
2220144 TATATATTTGA
1 TATATATTTGA
2220155 GAATTTTTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
17 14 0.54
18 1 0.04
19 3 0.12
20 8 0.31
ACGTcount: A:0.42, C:0.00, G:0.12, T:0.46
Consensus pattern (18 bp):
TATATATTTGATAAGATA
Found at i:2220281 original size:12 final size:12
Alignment explanation
Indices: 2220264--2220288 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
2220254 TTAATATTTG
2220264 ATTTTTTAATTA
1 ATTTTTTAATTA
2220276 ATTTTTTAATTA
1 ATTTTTTAATTA
2220288 A
1 A
2220289 ATCAATATAT
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:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (12 bp):
ATTTTTTAATTA
Found at i:2221029 original size:27 final size:28
Alignment explanation
Indices: 2220976--2221030 Score: 69
Period size: 27 Copynumber: 2.0 Consensus size: 28
2220966 TTAATCATCT
* *
2220976 TTATCTTAAATAAATTCTTATATTTTTA
1 TTATATTAAATAAAGTCTTATATTTTTA
2221004 TTATATTAAAT-AAGTCTT-TATCTTTTA
1 TTATATTAAATAAAGTCTTATAT-TTTTA
2221031 ACATGTACTC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 3 0.12
27 11 0.46
28 10 0.42
ACGTcount: A:0.35, C:0.07, G:0.02, T:0.56
Consensus pattern (28 bp):
TTATATTAAATAAAGTCTTATATTTTTA
Found at i:2221091 original size:23 final size:24
Alignment explanation
Indices: 2221065--2221127 Score: 67
Period size: 24 Copynumber: 2.6 Consensus size: 24
2221055 TTAATTAATT
2221065 TAAATTTAAATAAATT-TTTAAAA
1 TAAATTTAAATAAATTATTTAAAA
* *
2221088 TAAATATAAAT-ATTTCATTTAAAA
1 TAAATTTAAATAAATT-ATTTAAAA
*
2221112 TAAAATTAATATAAAT
1 TAAATTTAA-ATAAAT
2221128 CTAAAAATAA
Statistics
Matches: 31, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
22 3 0.10
23 10 0.32
24 14 0.45
25 2 0.06
26 2 0.06
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (24 bp):
TAAATTTAAATAAATTATTTAAAA
Found at i:2221149 original size:29 final size:30
Alignment explanation
Indices: 2221117--2221185 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
2221107 TAAAATAAAA
2221117 TTAATATAAATCTAAAAAT-AAAAATTT-AT
1 TTAATATAAAT-TAAAAATAAAAAATTTAAT
2221146 TTAA-ATACAA-TAAAAATAAAAAAATTTAAT
1 TTAATATA-AATTAAAAAT-AAAAAATTTAAT
2221176 TTAATA-AAAT
1 TTAATATAAAT
2221186 GACATAGTTC
Statistics
Matches: 34, Mismatches: 0, Indels: 11
0.76 0.00 0.24
Matches are distributed among these distances:
27 7 0.21
28 3 0.09
29 16 0.47
30 7 0.21
31 1 0.03
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (30 bp):
TTAATATAAATTAAAAATAAAAAATTTAAT
Found at i:2221150 original size:24 final size:26
Alignment explanation
Indices: 2221108--2221167 Score: 72
Period size: 24 Copynumber: 2.4 Consensus size: 26
2221098 TATTTCATTT
2221108 AAAAT-AAAATTAATATAAAT-C-TA
1 AAAATAAAAATTAATATAAATACATA
* *
2221131 AAAATAAAAATTTATTTAAATACAATA
1 AAAATAAAAATTAATATAAATAC-ATA
2221158 AAAATAAAAA
1 AAAATAAAAA
2221168 AATTTAATTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
23 5 0.16
24 13 0.42
25 1 0.03
27 12 0.39
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.28
Consensus pattern (26 bp):
AAAATAAAAATTAATATAAATACATA
Found at i:2221437 original size:13 final size:13
Alignment explanation
Indices: 2221419--2221444 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
2221409 TTATAATATT
2221419 ATAATATTTTTAA
1 ATAATATTTTTAA
2221432 ATAATATTTTTAA
1 ATAATATTTTTAA
2221445 TTAAATTAAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (13 bp):
ATAATATTTTTAA
Found at i:2226228 original size:2 final size:2
Alignment explanation
Indices: 2226221--2226263 Score: 59
Period size: 2 Copynumber: 21.5 Consensus size: 2
2226211 GATTTTCATC
* * *
2226221 TA TA TA TA TA TA TA TA TA TA TA TA TA TG TA TG TA TG TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2226263 T
1 T
2226264 TGACTTTATA
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (2 bp):
TA
Found at i:2227464 original size:4 final size:4
Alignment explanation
Indices: 2227457--2227490 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
2227447 ACATATGTAT
2227457 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
2227491 GCACACATGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:2228901 original size:28 final size:29
Alignment explanation
Indices: 2228846--2228901 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
2228836 TTAATGAAAT
* *
2228846 AAAATTAAAATTACATTTGTTAATAATAA
1 AAAATTAAAATTACATTTATTAAAAATAA
* *
2228875 AAAATTTAAATTA-TTTTATTAAAAATA
1 AAAATTAAAATTACATTTATTAAAAATA
2228902 TTAATTTGTA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 11 0.48
29 12 0.52
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.41
Consensus pattern (29 bp):
AAAATTAAAATTACATTTATTAAAAATAA
Found at i:2229103 original size:2 final size:2
Alignment explanation
Indices: 2229096--2229128 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
2229086 GATCAACGGC
2229096 TA TA TA 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 TA TA TA T
2229129 GGCCACTTTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:2229769 original size:14 final size:17
Alignment explanation
Indices: 2229736--2229772 Score: 53
Period size: 14 Copynumber: 2.4 Consensus size: 17
2229726 CTCTTTATTT
2229736 CTTTTTTGTTTTCTTGC
1 CTTTTTTGTTTTCTTGC
2229753 CTTTTTT-TTTT-TT-C
1 CTTTTTTGTTTTCTTGC
2229767 CTTTTT
1 CTTTTT
2229773 GAGATGTTTG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
14 7 0.35
15 2 0.10
16 4 0.20
17 7 0.35
ACGTcount: A:0.00, C:0.16, G:0.05, T:0.78
Consensus pattern (17 bp):
CTTTTTTGTTTTCTTGC
Found at i:2230806 original size:78 final size:75
Alignment explanation
Indices: 2230567--2230814 Score: 257
Period size: 75 Copynumber: 3.2 Consensus size: 75
2230557 AGTTTCGTTC
* *
2230567 TCTGATGTAAAAAGCCTAATCATGGAAGATAATTACGAGTCAACACCGGAGATTGCTTTGAAGCA
1 TCTGATGTAAAAAGCATAATCATGGAAGAT-A-T--GAGTCAACACCGGAGATTG-TTTGAACCA
2230632 GAAGAAGGTCTCATTT
61 GAAGAAGGTCTCA-TT
* * * * ** *
2230648 TCTGATGTCAAAAGCGTCATCATGGAAG--ATGAGCCAACACCGGAGATTGGTTCAAACCAAAAG
1 TCTGATGTAAAAAGCATAATCATGGAAGATATGAGTCAACACCGGAGATT-GTTTGAACCAGAAG
*
2230711 AAGGTTTCATT
65 AAGGTCTCATT
* * *
2230722 CTCTGATGTTAAAAGCATAATCATGGAAGATACTGAGTCAACTCCAGAGATTAGTTTGAACCAGA
1 -TCTGATGTAAAAAGCATAATCATGGAAGATA-TGAGTCAACACCGGAGATT-GTTTGAACCAGA
*
2230787 AGAAGGTGTCATT
63 AGAAGGTCTCATT
2230800 TGCTGATGTAAAAAG
1 T-CTGATGTAAAAAG
2230815 TACTGTCGCG
Statistics
Matches: 140, Mismatches: 21, Indels: 15
0.80 0.12 0.09
Matches are distributed among these distances:
74 2 0.01
75 59 0.42
76 1 0.01
77 3 0.02
78 50 0.36
81 25 0.18
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (75 bp):
TCTGATGTAAAAAGCATAATCATGGAAGATATGAGTCAACACCGGAGATTGTTTGAACCAGAAGA
AGGTCTCATT
Found at i:2239653 original size:2 final size:2
Alignment explanation
Indices: 2239641--2239672 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
2239631 CTTTGTAAAT
*
2239641 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
2239673 ATGGTTCGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2240356 original size:18 final size:17
Alignment explanation
Indices: 2240333--2240366 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
2240323 AGATCCGATC
2240333 CTTTTTTTTTTTCTTTTT
1 CTTTTTTTTTTT-TTTTT
2240351 CTTTTTTTTTTTTTTT
1 CTTTTTTTTTTTTTTT
2240367 AAATAGTTTG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 4 0.25
18 12 0.75
ACGTcount: A:0.00, C:0.09, G:0.00, T:0.91
Consensus pattern (17 bp):
CTTTTTTTTTTTTTTTT
Found at i:2242347 original size:9 final size:9
Alignment explanation
Indices: 2242335--2242396 Score: 58
Period size: 8 Copynumber: 6.8 Consensus size: 9
2242325 ATATACGAAA
2242335 TAATATATT
1 TAATATATT
2242344 TAATATATATTT
1 T-A-ATATA-TT
2242356 TAATTATATT
1 TAA-TATATT
*
2242366 TAAAAT-TT
1 TAATATATT
2242374 TAATATATT
1 TAATATATT
2242383 TAATA-ATT
1 TAATATATT
2242391 T-ATATA
1 TAATATA
2242397 ATATATATGG
Statistics
Matches: 45, Mismatches: 2, Indels: 13
0.75 0.03 0.22
Matches are distributed among these distances:
7 3 0.07
8 12 0.27
9 10 0.22
10 7 0.16
11 10 0.22
12 3 0.07
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (9 bp):
TAATATATT
Found at i:2242392 original size:17 final size:18
Alignment explanation
Indices: 2242335--2242391 Score: 71
Period size: 18 Copynumber: 3.0 Consensus size: 18
2242325 ATATACGAAA
2242335 TAATATATTTAATATATATTT
1 TAATATATTT-A-ATA-ATTT
2242356 TAATTATATTTAA-AATTT
1 TAA-TATATTTAATAATTT
2242374 TAATATATTTAATAATTT
1 TAATATATTTAATAATTT
2242392 ATATAATATA
Statistics
Matches: 34, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
17 9 0.26
18 12 0.35
19 1 0.03
20 1 0.03
21 4 0.12
22 7 0.21
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TAATATATTTAATAATTT
Found at i:2247708 original size:18 final size:19
Alignment explanation
Indices: 2247678--2247713 Score: 65
Period size: 18 Copynumber: 1.9 Consensus size: 19
2247668 ATTTTTAATT
2247678 AATTATATAAATATAAATA
1 AATTATATAAATATAAATA
2247697 AATTAT-TAAATATAAAT
1 AATTATATAAATATAAAT
2247714 TATTTAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
18 11 0.65
19 6 0.35
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (19 bp):
AATTATATAAATATAAATA
Found at i:2247713 original size:14 final size:15
Alignment explanation
Indices: 2247694--2247725 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
2247684 ATAAATATAA
2247694 ATAAATTA-TTAAAT
1 ATAAATTATTTAAAT
2247708 ATAAATTATTTAAAT
1 ATAAATTATTTAAAT
2247723 ATA
1 ATA
2247726 TTCTATAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.47
15 9 0.53
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (15 bp):
ATAAATTATTTAAAT
Done.