Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr03 135709677
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: 135709677
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Warning! 350 characters in sequence are not A, C, G, or T
File 333 of 438
Found at i:104390061 original size:58 final size:58
Alignment explanation
Indices: 104389940--104390129 Score: 179
Period size: 58 Copynumber: 3.3 Consensus size: 58
104389930 TACTCGATTT
* * * *** *
104389940 CGCACACTTAGTGCCACGTA-ATTT-AAGCCCGCACACACAGTGCCATA-CCCTCCGAGCT
1 CGCACACTTAGTG-C-CGTATATTTCCAGCACGCACACATAGTGCCATATATTTCC-AGCA
** * ** * *
104389998 CGCACACCCAGTGCCGTATTTTTCCAGCTTGCACACATAGTGTCATATTTTTCCAGCA
1 CGCACACTTAGTGCCGTATATTTCCAGCACGCACACATAGTGCCATATATTTCCAGCA
* * *
104390056 TGCACACTTAGTGCCTTATATTTCCAGCACGCACACTTAGTGCCATATATTTCCAGCA
1 CGCACACTTAGTGCCGTATATTTCCAGCACGCACACATAGTGCCATATATTTCCAGCA
104390114 CGCACACTTAGTGCCG
1 CGCACACTTAGTGCCG
104390130 ATCTCGTCAC
Statistics
Matches: 105, Mismatches: 24, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
56 4 0.04
57 4 0.04
58 94 0.90
59 3 0.03
ACGTcount: A:0.24, C:0.33, G:0.16, T:0.26
Consensus pattern (58 bp):
CGCACACTTAGTGCCGTATATTTCCAGCACGCACACATAGTGCCATATATTTCCAGCA
Found at i:104392068 original size:22 final size:21
Alignment explanation
Indices: 104392043--104392101 Score: 55
Period size: 22 Copynumber: 2.8 Consensus size: 21
104392033 TTTTTTAGAC
*
104392043 TTTAGTTTTTAGGATTTTATTT
1 TTTAATTTTTAGGATTTTA-TT
* ** **
104392065 TTTATTTTTTATTACATTATT
1 TTTAATTTTTAGGATTTTATT
104392086 TTTAATTTTTAGGATT
1 TTTAATTTTTAGGATT
104392102 GGGTTGGATT
Statistics
Matches: 27, Mismatches: 10, Indels: 1
0.71 0.26 0.03
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.22, C:0.02, G:0.08, T:0.68
Consensus pattern (21 bp):
TTTAATTTTTAGGATTTTATT
Found at i:104393800 original size:26 final size:27
Alignment explanation
Indices: 104393771--104393821 Score: 68
Period size: 26 Copynumber: 1.9 Consensus size: 27
104393761 TATTATATAA
*
104393771 TATTTGAATTGTTT-AATAAATTAATG
1 TATTTGAATTATTTAAATAAATTAATG
* *
104393797 TATTTTAATTATTTAAATAATTTAA
1 TATTTGAATTATTTAAATAAATTAA
104393822 ATAATAAATA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
26 12 0.57
27 9 0.43
ACGTcount: A:0.41, C:0.00, G:0.06, T:0.53
Consensus pattern (27 bp):
TATTTGAATTATTTAAATAAATTAATG
Found at i:104404721 original size:17 final size:17
Alignment explanation
Indices: 104404699--104404731 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
104404689 CATTCAAAAG
*
104404699 ATGTAGTAAAAAATGTT
1 ATGTAGCAAAAAATGTT
104404716 ATGTAGCAAAAAATGT
1 ATGTAGCAAAAAATGT
104404732 AATTTTTAAA
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:0.48, C:0.03, G:0.18, T:0.30
Consensus pattern (17 bp):
ATGTAGCAAAAAATGTT
Found at i:104405156 original size:97 final size:96
Alignment explanation
Indices: 104405048--104405244 Score: 238
Period size: 97 Copynumber: 2.0 Consensus size: 96
104405038 TTAATTCATC
* *
104405048 TTTTTAATTAAT-AACTCTTTTATATATATAAATAAAATAA-AGA-AATGTAATAATATAATAAA
1 TTTTTAATTAATAAATTC-TTTATATATATAAATAAAATAATA-ATAATATAATAATATAAT-AA
104405110 ATATAATTTTTATATATATCATTATGTTAAAAATA
63 AT-TAATTTTTATATATATCATTATGTTAAAAATA
* * * * *
104405145 TTTTTAATTAATAAATTCTTTATTTATTTAAATAAATTAATAATTATATAATTATATAATAAATT
1 TTTTTAATTAATAAATTCTTTATATATATAAATAAAATAATAATAATATAATAATATAATAAATT
** * *
104405210 TTTTTTTATATTTATCATTATGTTGAAAATA
66 AATTTTTATATATATCATTATGTTAAAAATA
104405241 TTTT
1 TTTT
104405245 ATTTCTTAAA
Statistics
Matches: 86, Mismatches: 11, Indels: 7
0.83 0.11 0.07
Matches are distributed among these distances:
96 32 0.37
97 36 0.42
98 18 0.21
ACGTcount: A:0.45, C:0.03, G:0.03, T:0.50
Consensus pattern (96 bp):
TTTTTAATTAATAAATTCTTTATATATATAAATAAAATAATAATAATATAATAATATAATAAATT
AATTTTTATATATATCATTATGTTAAAAATA
Found at i:104410816 original size:2 final size:2
Alignment explanation
Indices: 104410809--104410847 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
104410799 TTTGTCAACT
104410809 TA TA TA 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 TA TA TA T
104410848 TGTATGATCA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:104415185 original size:29 final size:28
Alignment explanation
Indices: 104415153--104415212 Score: 66
Period size: 29 Copynumber: 2.1 Consensus size: 28
104415143 AAATTTATTT
104415153 AAACCTACAAAAATTATAAAAATTCATAA
1 AAACCTACAAAAATTATAAAAATT-ATAA
* * * * *
104415182 AAACTTATAAATATTTTATAAATTATAA
1 AAACCTACAAAAATTATAAAAATTATAA
104415210 AAA
1 AAA
104415213 TAATTATAAA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
28 7 0.27
29 19 0.73
ACGTcount: A:0.60, C:0.08, G:0.00, T:0.32
Consensus pattern (28 bp):
AAACCTACAAAAATTATAAAAATTATAA
Found at i:104415207 original size:18 final size:19
Alignment explanation
Indices: 104415161--104415213 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
104415151 TTAAACCTAC
104415161 AAAAATTATAAAAATTCAT
1 AAAAATTATAAAAATTCAT
* *
104415180 AAAAACTTATAAATATT-TT
1 AAAAA-TTATAAAAATTCAT
*
104415199 ATAAATTATAAAAAT
1 AAAAATTATAAAAAT
104415214 AATTATAAAA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
18 9 0.31
19 10 0.34
20 10 0.34
ACGTcount: A:0.60, C:0.04, G:0.00, T:0.36
Consensus pattern (19 bp):
AAAAATTATAAAAATTCAT
Found at i:104415219 original size:12 final size:12
Alignment explanation
Indices: 104415202--104415253 Score: 50
Period size: 12 Copynumber: 3.9 Consensus size: 12
104415192 ATATTTTATA
104415202 AATTATAAAAAT
1 AATTATAAAAAT
104415214 AATTATAAAAAAT
1 AATTAT-AAAAAT
*
104415227 AAAACATATTAAAAAT
1 --AA-TTA-TAAAAAT
104415243 AATTATAAAAA
1 AATTATAAAAA
104415254 ATTATAATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 10
0.73 0.04 0.22
Matches are distributed among these distances:
12 12 0.36
13 8 0.24
14 2 0.06
15 2 0.06
16 8 0.24
17 1 0.03
ACGTcount: A:0.69, C:0.02, G:0.00, T:0.29
Consensus pattern (12 bp):
AATTATAAAAAT
Found at i:104415258 original size:10 final size:10
Alignment explanation
Indices: 104415161--104415289 Score: 74
Period size: 10 Copynumber: 13.1 Consensus size: 10
104415151 TTAAACCTAC
104415161 AAAAATTAT-
1 AAAAATTATA
104415170 AAAAATTCATA
1 AAAAATT-ATA
*
104415181 AAAACTTAT-
1 AAAAATTATA
* *
104415190 AAATATT-TT
1 AAAAATTATA
*
104415199 ATAAATTATAA
1 AAAAATTAT-A
104415210 AAATAATTATA
1 AAA-AATTATA
104415221 AAAAA-TA-A
1 AAAAATTATA
*
104415229 AACATATTA-A
1 AA-AAATTATA
104415239 AAATAATTATA
1 AAA-AATTATA
104415250 AAAAATTATA
1 AAAAATTATA
* * *
104415260 ATAAGTTCTA
1 AAAAATTATA
*
104415270 ATAAATTAT-
1 AAAAATTATA
*
104415279 ATAAATTATA
1 AAAAATTATA
104415289 A
1 A
104415290 TTTTTAATAA
Statistics
Matches: 95, Mismatches: 14, Indels: 21
0.73 0.11 0.16
Matches are distributed among these distances:
8 4 0.04
9 31 0.33
10 38 0.40
11 16 0.17
12 6 0.06
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (10 bp):
AAAAATTATA
Found at i:104416801 original size:21 final size:21
Alignment explanation
Indices: 104416780--104416818 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
104416770 TTTTATGTTA
*
104416780 AATAA-GGTTATAATAATATT
1 AATAATGGTTAAAATAATATT
104416800 AATAATGGTTAAAATAATA
1 AATAATGGTTAAAATAATA
104416819 AAACATAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.54, C:0.00, G:0.10, T:0.36
Consensus pattern (21 bp):
AATAATGGTTAAAATAATATT
Found at i:104430025 original size:2 final size:2
Alignment explanation
Indices: 104430018--104430051 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
104430008 CTGATCTGTG
104430018 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
104430052 GAAATTGCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:104434847 original size:18 final size:18
Alignment explanation
Indices: 104434824--104434858 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
104434814 TACGCCCGCT
104434824 ACTCCCAAGGCGGAGACC
1 ACTCCCAAGGCGGAGACC
*
104434842 ACTCCCACGGCGGAGAC
1 ACTCCCAAGGCGGAGAC
104434859 GGTAAGCGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.26, C:0.40, G:0.29, T:0.06
Consensus pattern (18 bp):
ACTCCCAAGGCGGAGACC
Found at i:104435343 original size:2 final size:2
Alignment explanation
Indices: 104435338--104435364 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
104435328 TTTGATAAAT
104435338 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
104435365 TGTTTGACTA
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:104441850 original size:41 final size:43
Alignment explanation
Indices: 104441771--104441850 Score: 103
Period size: 41 Copynumber: 1.9 Consensus size: 43
104441761 TATAATAATA
* *
104441771 TTTCGTGCAAATATAACTTAAAATAACAACATAAATAAACAAT
1 TTTCATGCAAATATAACTAAAAATAACAACATAAATAAACAAT
*
104441814 TTTCATGCAAATAT-A-TAAAAATAATAA-ATAACATAAA
1 TTTCATGCAAATATAACTAAAAATAACAACATAA-ATAAA
104441851 AATAACAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
40 4 0.12
41 15 0.45
42 1 0.03
43 13 0.39
ACGTcount: A:0.56, C:0.11, G:0.04, T:0.29
Consensus pattern (43 bp):
TTTCATGCAAATATAACTAAAAATAACAACATAAATAAACAAT
Found at i:104441851 original size:18 final size:18
Alignment explanation
Indices: 104441828--104441862 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
104441818 ATGCAAATAT
*
104441828 ATAAAAATAATAAATAAC
1 ATAAAAATAACAAATAAC
104441846 ATAAAAATAACAAATAA
1 ATAAAAATAACAAATAA
104441863 TTTATGAGAT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.74, C:0.06, G:0.00, T:0.20
Consensus pattern (18 bp):
ATAAAAATAACAAATAAC
Found at i:104441861 original size:25 final size:25
Alignment explanation
Indices: 104441828--104441919 Score: 66
Period size: 25 Copynumber: 3.8 Consensus size: 25
104441818 ATGCAAATAT
104441828 ATAA-AAATAATAAATAACATAAAA
1 ATAACAAATAATAAATAACATAAAA
** * *
104441852 ATAACAAATAATTTATGAGATAAAA
1 ATAACAAATAATAAATAACATAAAA
* * * *
104441877 TTAACATACTAACACAAT-ACAAAAAA
1 ATAACA-AATAATA-AATAACATAAAA
104441903 AT-ACAAA-AATAAATAAC
1 ATAACAAATAATAAATAAC
104441920 CAATTATGAA
Statistics
Matches: 50, Mismatches: 14, Indels: 9
0.68 0.19 0.12
Matches are distributed among these distances:
22 3 0.06
23 5 0.10
24 5 0.10
25 24 0.48
26 11 0.22
27 2 0.04
ACGTcount: A:0.66, C:0.10, G:0.02, T:0.22
Consensus pattern (25 bp):
ATAACAAATAATAAATAACATAAAA
Found at i:104441980 original size:22 final size:22
Alignment explanation
Indices: 104441946--104442016 Score: 74
Period size: 22 Copynumber: 3.2 Consensus size: 22
104441936 AAAATAAGTC
104441946 AAAAAGATAAAAACTAA-ATAAAT
1 AAAAA-ATAAAAA-TAATATAAAT
* *
104441969 TAAAAATAAAAATAATATTAAT
1 AAAAAATAAAAATAATATAAAT
*
104441991 AAAAAATAAATAATAAT-TTAAT
1 AAAAAATAAA-AATAATATAAAT
104442013 AAAA
1 AAAA
104442017 TATATATATA
Statistics
Matches: 43, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
21 3 0.07
22 30 0.70
23 10 0.23
ACGTcount: A:0.72, C:0.01, G:0.01, T:0.25
Consensus pattern (22 bp):
AAAAAATAAAAATAATATAAAT
Found at i:104442029 original size:23 final size:23
Alignment explanation
Indices: 104441980--104442064 Score: 68
Period size: 21 Copynumber: 3.7 Consensus size: 23
104441970 AAAAATAAAA
* *
104441980 ATAATATTAATAAAAAATAAATA-
1 ATAAT-TTAATAAAATATATATAT
104442003 ATAATTTAATAAAATATATATAT
1 ATAATTTAATAAAATATATATAT
* *
104442026 ATAA--TACTAATATATATATAT
1 ATAATTTAATAAAATATATATAT
* **
104442047 TTAAAATAATAATAATAT
1 ATAATTTAATAA-AATAT
104442065 GTTAAATAGG
Statistics
Matches: 51, Mismatches: 7, Indels: 7
0.78 0.11 0.11
Matches are distributed among these distances:
21 18 0.35
22 15 0.29
23 14 0.27
24 4 0.08
ACGTcount: A:0.60, C:0.01, G:0.00, T:0.39
Consensus pattern (23 bp):
ATAATTTAATAAAATATATATAT
Found at i:104442030 original size:26 final size:23
Alignment explanation
Indices: 104441970--104442037 Score: 86
Period size: 22 Copynumber: 3.0 Consensus size: 23
104441960 TAAATAAATT
104441970 AAAAATAAA-AATAATATTAATA
1 AAAAATAAATAATAATATTAATA
104441992 AAAAATAAATAATAAT-TTAATA
1 AAAAATAAATAATAATATTAATA
* * *
104442014 AAATATATATATATAATACTAATA
1 AAAAATAAATA-ATAATATTAATA
104442038 TATATATATT
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
22 24 0.60
23 11 0.28
24 5 0.12
ACGTcount: A:0.66, C:0.01, G:0.00, T:0.32
Consensus pattern (23 bp):
AAAAATAAATAATAATATTAATA
Found at i:104442182 original size:14 final size:14
Alignment explanation
Indices: 104442163--104442204 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
104442153 ATTTTAAAAT
104442163 TATACATAATATAA
1 TATACATAATATAA
*
104442177 TATAC--AATAAAA
1 TATACATAATATAA
*
104442189 TATAAATAATATAA
1 TATACATAATATAA
104442203 TA
1 TA
104442205 GATAATACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
12 10 0.43
14 13 0.57
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (14 bp):
TATACATAATATAA
Found at i:104442211 original size:26 final size:27
Alignment explanation
Indices: 104442157--104442211 Score: 76
Period size: 26 Copynumber: 2.1 Consensus size: 27
104442147 TTACAAATTT
* *
104442157 TAAAATTATACATAATATAATATACAA
1 TAAAATTATAAATAATATAATAGACAA
*
104442184 TAAAA-TATAAATAATATAATAGATAA
1 TAAAATTATAAATAATATAATAGACAA
104442210 TA
1 TA
104442212 CAAAAAAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
26 20 0.80
27 5 0.20
ACGTcount: A:0.62, C:0.04, G:0.02, T:0.33
Consensus pattern (27 bp):
TAAAATTATAAATAATATAATAGACAA
Found at i:104442299 original size:29 final size:30
Alignment explanation
Indices: 104442243--104442303 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 30
104442233 ATAAATAAAG
*
104442243 TTTAAAGTAAAATAAATAATATACAAAATA
1 TTTAAAATAAAATAAATAATATACAAAATA
104442273 TTTAAAAT-AAATAAATAAATTATA-AAAATA
1 TTTAAAATAAAATAAAT-AA-TATACAAAATA
104442303 T
1 T
104442304 GTATATATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
29 8 0.29
30 16 0.57
31 4 0.14
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (30 bp):
TTTAAAATAAAATAAATAATATACAAAATA
Found at i:104442847 original size:8 final size:8
Alignment explanation
Indices: 104442834--104442865 Score: 55
Period size: 8 Copynumber: 4.0 Consensus size: 8
104442824 TACCGGGCTG
104442834 CACGCGCC
1 CACGCGCC
104442842 CACGCGCC
1 CACGCGCC
*
104442850 CACGCGCT
1 CACGCGCC
104442858 CACGCGCC
1 CACGCGCC
104442866 ATACGCGCCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
8 22 1.00
ACGTcount: A:0.12, C:0.59, G:0.25, T:0.03
Consensus pattern (8 bp):
CACGCGCC
Found at i:104443863 original size:45 final size:45
Alignment explanation
Indices: 104443813--104444042 Score: 131
Period size: 45 Copynumber: 5.1 Consensus size: 45
104443803 TAATATCATT
104443813 GATCTGCTCCTCGTCAAATACAGAGACTCTAAATCTGCTATCTTC
1 GATCTGCTCCTCGTCAAATACAGAGACTCTAAATCTGCTATCTTC
* * * *
104443858 GATCTGCT--TCGATGTAAACACACGA-A-TGTCAGATCTGCTATCTTC
1 GATCTGCTCCTCG-T-CAAATACA-GAGACTCT-AAATCTGCTATCTTC
* * * * *
104443903 AATCTGCTCCCTC-TCTAATACAGAGACGCCAAATCTG-TCATCTTT
1 GATCTGCT-CCTCGTCAAATACAGAGACTCTAAATCTGCT-ATCTTC
* * *
104443948 GATCTGCT--TCGATGTAAACACACGA-A-TGTCAAATCTGCTATCTTC
1 GATCTGCTCCTCG-T-CAAATACA-GAGACTCT-AAATCTGCTATCTTC
* * * * *
104443993 GATCTGCTCCCCATCTAATACAGAGACGCCAAATCTG-TCATCTTC
1 GATCTGCTCCTCGTCAAATACAGAGACTCTAAATCTGCT-ATCTTC
104444038 GATCT
1 GATCT
104444043 ACTTCGATGT
Statistics
Matches: 135, Mismatches: 29, Indels: 42
0.66 0.14 0.20
Matches are distributed among these distances:
42 2 0.01
43 3 0.02
44 10 0.07
45 110 0.81
46 7 0.05
47 1 0.01
48 2 0.01
ACGTcount: A:0.27, C:0.28, G:0.14, T:0.30
Consensus pattern (45 bp):
GATCTGCTCCTCGTCAAATACAGAGACTCTAAATCTGCTATCTTC
Found at i:104443967 original size:90 final size:90
Alignment explanation
Indices: 104443813--104444309 Score: 730
Period size: 90 Copynumber: 5.5 Consensus size: 90
104443803 TAATATCATT
* * * *
104443813 GATCTGCTCCTCGTCAAATACAGAGACTCTAAATCTG-CTATCTTCGATCTGCTTCGATGTAAAC
1 GATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTC-ATCTTCGATCTGCTTCGATGTAAAC
104443877 ACACGAATGTCAGATCTGCTATCTTC
65 ACACGAATGTCAGATCTGCTATCTTC
* *
104443903 AATCTGCTCCCTC-TCTAATACAGAGACGCCAAATCTGTCATCTTTGATCTGCTTCGATGTAAAC
1 GATCTGCTCCC-CGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAAC
*
104443967 ACACGAATGTCAAATCTGCTATCTTC
65 ACACGAATGTCAGATCTGCTATCTTC
* *
104443993 GATCTGCTCCCCATCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTACTTCGATGTAAACA
1 GATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACA
*
104444058 CACGAATGTCAGATCTGCTATATTC
66 CACGAATGTCAGATCTGCTATCTTC
* * * *
104444083 GATCTGCTCCCCATCTAATACGGAGACGCCAAATCTGTCATCTTCGATCTACTTTGATGTAAACA
1 GATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACA
* * * *
104444148 TACAAATGTTAGATCTTCTATCTTC
66 CACGAATGTCAGATCTGCTATCTTC
* *
104444173 GATTTGCTCCCCGTCTAATACGGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACA
1 GATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACA
104444238 CACGAATGTCAGATCTGCTATCTTC
66 CACGAATGTCAGATCTGCTATCTTC
* * * * *
104444263 GATCTGCTCCCCGTTTAATACAAAGATGCCAAATTTG-CTTCTTCGAT
1 GATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGAT
104444310 TTGTTCTCTG
Statistics
Matches: 370, Mismatches: 34, Indels: 7
0.90 0.08 0.02
Matches are distributed among these distances:
89 10 0.03
90 358 0.97
91 2 0.01
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (90 bp):
GATCTGCTCCCCGTCTAATACAGAGACGCCAAATCTGTCATCTTCGATCTGCTTCGATGTAAACA
CACGAATGTCAGATCTGCTATCTTC
Found at i:104444074 original size:45 final size:46
Alignment explanation
Indices: 104443843--104444270 Score: 282
Period size: 45 Copynumber: 9.5 Consensus size: 46
104443833 CAGAGACTCT
104443843 AAATCTG-CTATCTTCGATCTGCTTCGATGTAAACACACGAATGTC
1 AAATCTGTCTATCTTCGATCTGCTTCGATGTAAACACACGAATGTC
* * ** * * * * *
104443888 AGATCTG-CTATCTTCAATCTGC-TCCCTCTCTAATACA-GAGACGCC
1 AAATCTGTCTATCTTCGATCTGCTTCGATGT-AAACACACGA-ATGTC
*
104443933 AAATCTGTC-ATCTTTGATCTGCTTCGATGTAAACACACGAATGTC
1 AAATCTGTCTATCTTCGATCTGCTTCGATGTAAACACACGAATGTC
* * * * * *
104443978 AAATCTG-CTATCTTCGATCTGCTCCCCATCT-AATACA-GAGACGCC
1 AAATCTGTCTATCTTCGATCTGCT-TCGATGTAAACACACGA-ATGTC
*
104444023 AAATCTGTC-ATCTTCGATCTACTTCGATGTAAACACACGAATGTC
1 AAATCTGTCTATCTTCGATCTGCTTCGATGTAAACACACGAATGTC
* * * * * * * * *
104444068 AGATCTG-CTATATTCGATCTGCTCCCCATCT-AATAC-GGAGACGCC
1 AAATCTGTCTATCTTCGATCTGCT-TCGATGTAAACACACGA-ATGTC
* * * * *
104444113 AAATCTGTC-ATCTTCGATCTACTTTGATGTAAACATACAAATGTT
1 AAATCTGTCTATCTTCGATCTGCTTCGATGTAAACACACGAATGTC
* * * * * * * *
104444158 AGATCT-TCTATCTTCGATTTGCTCCCCG-TCT-AATAC-GGAGACGCC
1 AAATCTGTCTATCTTCGATCTGCT--TCGATGTAAACACACGA-ATGTC
104444203 AAATCTGTC-ATCTTCGATCTGCTTCGATGTAAACACACGAATGTC
1 AAATCTGTCTATCTTCGATCTGCTTCGATGTAAACACACGAATGTC
*
104444248 AGATCTG-CTATCTTCGATCTGCT
1 AAATCTGTCTATCTTCGATCTGCT
104444271 CCCCGTTTAA
Statistics
Matches: 278, Mismatches: 79, Indels: 52
0.68 0.19 0.13
Matches are distributed among these distances:
43 2 0.01
44 25 0.09
45 224 0.81
46 26 0.09
47 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.15, T:0.31
Consensus pattern (46 bp):
AAATCTGTCTATCTTCGATCTGCTTCGATGTAAACACACGAATGTC
Found at i:104456756 original size:31 final size:27
Alignment explanation
Indices: 104456720--104456791 Score: 72
Period size: 31 Copynumber: 2.4 Consensus size: 27
104456710 AAAACCAAAG
*
104456720 GTTCATGTATACATATGAACCACAATTCAA
1 GTTCATGTATA-AT-TGAACCA-AATTAAA
*
104456750 GTTTCATGTGTATAATTGCACCAAATTAAA
1 G-TTCA--TGTATAATTGAACCAAATTAAA
104456780 GTTCATGTATAA
1 GTTCATGTATAA
104456792 ATTAAAGTGT
Statistics
Matches: 37, Mismatches: 2, Indels: 9
0.77 0.04 0.19
Matches are distributed among these distances:
27 7 0.19
29 4 0.11
30 8 0.22
31 10 0.27
32 2 0.05
33 6 0.16
ACGTcount: A:0.38, C:0.15, G:0.12, T:0.35
Consensus pattern (27 bp):
GTTCATGTATAATTGAACCAAATTAAA
Found at i:104456814 original size:19 final size:18
Alignment explanation
Indices: 104456772--104456815 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
104456762 TAATTGCACC
*
104456772 AAATTAAAGTTCATGTAT
1 AAATTAAAGTTCATATAT
104456790 AAATTAAAGTGTGCATATA-
1 AAATTAAAGT-T-CATATAT
104456809 AAATTAA
1 AAATTAA
104456816 TATTTATCCC
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 10 0.43
19 8 0.35
20 5 0.22
ACGTcount: A:0.50, C:0.05, G:0.11, T:0.34
Consensus pattern (18 bp):
AAATTAAAGTTCATATAT
Found at i:104456944 original size:30 final size:30
Alignment explanation
Indices: 104456910--104456972 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
104456900 AAAGATACTA
104456910 ATATATATCAAACAATTTTCATATAACCGT
1 ATATATATCAAACAATTTTCATATAACCGT
* *
104456940 ATATATATCAAACAATTTTTATTTAACCGT
1 ATATATATCAAACAATTTTCATATAACCGT
104456970 ATA
1 ATA
104456973 AATTTTGTAA
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.43, C:0.14, G:0.03, T:0.40
Consensus pattern (30 bp):
ATATATATCAAACAATTTTCATATAACCGT
Found at i:104458338 original size:3 final size:3
Alignment explanation
Indices: 104458332--104458436 Score: 83
Period size: 3 Copynumber: 35.3 Consensus size: 3
104458322 TTTTCTTACG
* * * **
104458332 ATT ATT ATTT ATT ATC AAT ATT ATT ATT ATC ATT GCT ATT -TT -TT
1 ATT ATT A-TT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
104458376 ATT -TGT ATT ACT ATT ATT ATT ATT -TT ACT AGT ATT ATT ATT ATTT
1 ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A-TT
104458421 ATT ATT ATT ATT ATT A
1 ATT ATT ATT ATT ATT A
104458437 CTGTTATTTT
Statistics
Matches: 81, Mismatches: 15, Indels: 12
0.75 0.14 0.11
Matches are distributed among these distances:
2 7 0.09
3 67 0.83
4 7 0.09
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:104458429 original size:19 final size:19
Alignment explanation
Indices: 104458332--104458436 Score: 90
Period size: 19 Copynumber: 5.4 Consensus size: 19
104458322 TTTTCTTACG
104458332 ATTATTATTTATTATCAATATT
1 ATTATTATTTATTA-C--TATT
* *
104458354 ATTATTA-TCATTGCTATT
1 ATTATTATTTATTACTATT
104458372 -TT-TTATTTGTATTACTATT
1 ATTATTA-TT-TATTACTATT
* *
104458391 ATTATTATTTTACTAGTATT
1 ATTATTA-TTTATTACTATT
*
104458411 ATTATTATTTATTATTATT
1 ATTATTATTTATTACTATT
104458430 ATTATTA
1 ATTATTA
104458437 CTGTTATTTT
Statistics
Matches: 70, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
16 3 0.04
17 2 0.03
18 5 0.07
19 25 0.36
20 18 0.26
21 10 0.14
22 7 0.10
ACGTcount: A:0.30, C:0.05, G:0.03, T:0.62
Consensus pattern (19 bp):
ATTATTATTTATTACTATT
Found at i:104466681 original size:18 final size:18
Alignment explanation
Indices: 104466654--104466689 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
104466644 TTCAGCTATT
*
104466654 GTAAGTTTTGATAACCTA
1 GTAAGGTTTGATAACCTA
104466672 GTAAGGTTTGATAACCTA
1 GTAAGGTTTGATAACCTA
104466690 ATTGTAAGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.33, C:0.11, G:0.19, T:0.36
Consensus pattern (18 bp):
GTAAGGTTTGATAACCTA
Found at i:104468650 original size:151 final size:151
Alignment explanation
Indices: 104468376--104468671 Score: 592
Period size: 151 Copynumber: 2.0 Consensus size: 151
104468366 ATCCTCCTCC
104468376 CACTGTAATTTGTGACACTAGTAAATGGTTATTAAATGTTTATGGTGACCTTTTCAAAATCCTAT
1 CACTGTAATTTGTGACACTAGTAAATGGTTATTAAATGTTTATGGTGACCTTTTCAAAATCCTAT
104468441 CTATATCCATGACATGAAAAATTGAAATAAAAATCTTTTTTCTCCCAAATCTCGAATTTGAACAC
66 CTATATCCATGACATGAAAAATTGAAATAAAAATCTTTTTTCTCCCAAATCTCGAATTTGAACAC
104468506 CCTAAACATGATGTCCTACCT
131 CCTAAACATGATGTCCTACCT
104468527 CACTGTAATTTGTGACACTAGTAAATGGTTATTAAATGTTTATGGTGACCTTTTCAAAATCCTAT
1 CACTGTAATTTGTGACACTAGTAAATGGTTATTAAATGTTTATGGTGACCTTTTCAAAATCCTAT
104468592 CTATATCCATGACATGAAAAATTGAAATAAAAATCTTTTTTCTCCCAAATCTCGAATTTGAACAC
66 CTATATCCATGACATGAAAAATTGAAATAAAAATCTTTTTTCTCCCAAATCTCGAATTTGAACAC
104468657 CCTAAACATGATGTC
131 CCTAAACATGATGTC
104468672 ATAAATTTGT
Statistics
Matches: 145, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
151 145 1.00
ACGTcount: A:0.35, C:0.19, G:0.11, T:0.35
Consensus pattern (151 bp):
CACTGTAATTTGTGACACTAGTAAATGGTTATTAAATGTTTATGGTGACCTTTTCAAAATCCTAT
CTATATCCATGACATGAAAAATTGAAATAAAAATCTTTTTTCTCCCAAATCTCGAATTTGAACAC
CCTAAACATGATGTCCTACCT
Found at i:104471386 original size:39 final size:39
Alignment explanation
Indices: 104471342--104471498 Score: 217
Period size: 39 Copynumber: 4.0 Consensus size: 39
104471332 GATGTGTATG
104471342 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCA
1 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCA
104471381 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCA
1 AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCA
* * *
104471420 ATTGTGCGAGA-TATGATATCCGGGCTAAGCCCGAAGGCG
1 AATGTGCGA-ATTGTGATATCCGGGCTAAGCCCGAAGGCA
* * * * *
104471459 ATTGTGCGAGTTGTGATATCCGAGTTAAGTCTCGAAGGCA
1 AATGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGCA
104471499 TTTGTGCGGG
Statistics
Matches: 106, Mismatches: 9, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
39 97 0.92
40 9 0.08
ACGTcount: A:0.27, C:0.19, G:0.31, T:0.23
Consensus pattern (39 bp):
AATGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCA
Found at i:104471473 original size:78 final size:79
Alignment explanation
Indices: 104471355--104471538 Score: 244
Period size: 78 Copynumber: 2.3 Consensus size: 79
104471345 GTGCGAATTG
* *
104471355 TGATATCCGGGCTAAGCCCGAAGGCAAATGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCGAATGTGCGAATTGTGATATCCGAGCTAAGTCCCGAAGGC
104471419 AATTGTGCGAGATA
66 AATTGTGCGAGATA
* * * *
104471433 TGATATCCGGGCTAAGCCCGAAGGCGATTGTGCGAGTTGTGATATCCGAGTTAAGTCTCGAAGGC
1 TGATATCCGGGCTAAGCCCGAAGGCGAATGTGCGAATTGTGATATCCGAGCTAAGTCCCGAAGGC
* * *
104471498 ATTTGTGCGGGTTA
66 AATTGTGCGAGATA
* * *
104471512 TCATAACCGGGCTATGTCCCGAAGGCG
1 TGATATCCGGGCTAAG-CCCGAAGGCG
104471539 TTTGAACGAG
Statistics
Matches: 92, Mismatches: 12, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
78 50 0.54
79 32 0.35
80 10 0.11
ACGTcount: A:0.24, C:0.21, G:0.32, T:0.23
Consensus pattern (79 bp):
TGATATCCGGGCTAAGCCCGAAGGCGAATGTGCGAATTGTGATATCCGAGCTAAGTCCCGAAGGC
AATTGTGCGAGATA
Found at i:104471535 original size:40 final size:39
Alignment explanation
Indices: 104471344--104471542 Score: 211
Period size: 39 Copynumber: 5.1 Consensus size: 39
104471334 TGTGTATGAA
* * **
104471344 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAA
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCATT
* * *
104471383 TGTGCGAATTGTGATATCCGGGCTAAGCCCGAAGGCAAT
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCATT
*
104471422 TGTGCGAGATATGATATCCGGGCTAAGCCCGAAGGCGA-T
1 TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGC-ATT
* * * *
104471461 TGTGCGAGTTGTGATATCCGAGTTAAGTCTCGAAGGCATT
1 TGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGGCATT
* * * * *
104471501 TGTGCGGGTTATCATAACCGGGCTATGTCCCGAAGGCGTT
1 TGTGCGAGTTATGATATCCGGGCTAAG-CCCGAAGGCATT
104471541 TG
1 TG
104471543 AACGAGTAGC
Statistics
Matches: 139, Mismatches: 18, Indels: 5
0.86 0.11 0.03
Matches are distributed among these distances:
39 96 0.69
40 43 0.31
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.25
Consensus pattern (39 bp):
TGTGCGAGTTATGATATCCGGGCTAAGCCCGAAGGCATT
Found at i:104471565 original size:79 final size:79
Alignment explanation
Indices: 104471361--104471565 Score: 200
Period size: 78 Copynumber: 2.6 Consensus size: 79
104471351 ATTGTGATAT
* * ** * * * * *
104471361 CCGGGCTAAGCCCGAAGGCAAATGTGCGAATTGTGATATCCGGGCTAAG-CCCGAAGGCAATTGT
1 CCGGGCTAAGCCCGAAGGCGATTGAACGAGTAGTGATATCCGAGTTAAGTCTCGAAGGCAATTGT
* *
104471425 GCGAGATATGATAT
66 GCGAGATATCATAA
** * *
104471439 CCGGGCTAAGCCCGAAGGCGATTGTGCGAGTTGTGATATCCGAGTTAAGTCTCGAAGGCATTTGT
1 CCGGGCTAAGCCCGAAGGCGATTGAACGAGTAGTGATATCCGAGTTAAGTCTCGAAGGCAATTGT
* *
104471504 GCGGGTTATCATAA
66 GCGAGATATCATAA
* *
104471518 CCGGGCTATGTCCCGAAGGCGTTTGAACGAGTAGCT-ATATCCG-GTTAA
1 CCGGGCTAAG-CCCGAAGGCGATTGAACGAGTAG-TGATATCCGAGTTAA
104471566 ACTCCGAAGG
Statistics
Matches: 108, Mismatches: 16, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
78 44 0.41
79 37 0.34
80 26 0.24
81 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.31, T:0.24
Consensus pattern (79 bp):
CCGGGCTAAGCCCGAAGGCGATTGAACGAGTAGTGATATCCGAGTTAAGTCTCGAAGGCAATTGT
GCGAGATATCATAA
Found at i:104473025 original size:18 final size:18
Alignment explanation
Indices: 104472989--104473048 Score: 95
Period size: 18 Copynumber: 3.3 Consensus size: 18
104472979 TATATGCAAC
104472989 CTTAGATATGA-TACAAT
1 CTTAGATATGATTACAAT
*
104473006 CTTAGATATGATTGCAAT
1 CTTAGATATGATTACAAT
104473024 CTTAGATATGATATACAAT
1 CTTAGATATGAT-TACAAT
104473043 CTTAGA
1 CTTAGA
104473049 AGATATGATT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
17 11 0.28
18 17 0.44
19 11 0.28
ACGTcount: A:0.38, C:0.12, G:0.13, T:0.37
Consensus pattern (18 bp):
CTTAGATATGATTACAAT
Found at i:104473579 original size:15 final size:16
Alignment explanation
Indices: 104473536--104473594 Score: 50
Period size: 16 Copynumber: 3.5 Consensus size: 16
104473526 CAATATATTT
*
104473536 TATATATTTTATATAA
1 TATATTTTTTATATAA
104473552 T-TATTATTCTTATA-AA
1 TATATT-TT-TTATATAA
104473568 TATATTTTTTATTATATA
1 TATATTTTTTA-TATA-A
104473586 TTATATTTT
1 -TATATTTT
104473595 AAATTAATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
15 6 0.17
16 10 0.29
17 10 0.29
18 1 0.03
19 8 0.23
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.63
Consensus pattern (16 bp):
TATATTTTTTATATAA
Found at i:104476841 original size:17 final size:18
Alignment explanation
Indices: 104476805--104476842 Score: 51
Period size: 20 Copynumber: 2.1 Consensus size: 18
104476795 CCACATATGT
104476805 AATCTATTTTCATGTAAAAA
1 AATCTATTTTCA--TAAAAA
104476825 AATCTATTTTC-TAAAAA
1 AATCTATTTTCATAAAAA
104476842 A
1 A
104476843 GTTATTCTAA
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 7 0.39
20 11 0.61
ACGTcount: A:0.47, C:0.11, G:0.03, T:0.39
Consensus pattern (18 bp):
AATCTATTTTCATAAAAA
Found at i:104478995 original size:44 final size:45
Alignment explanation
Indices: 104478900--104479014 Score: 144
Period size: 44 Copynumber: 2.6 Consensus size: 45
104478890 ACAGGACAGA
*
104478900 ACAGAAATGAGCCATGTAAGTCCATATTAGAAATATGGCTCTGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTA-AAATATGGCTCTGGAG
* *
104478946 ACAGGATTGAGCCATGTAAGTCCATATT-ATATATGGCAT-TGGAG
1 ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGC-TCTGGAG
* **
104478990 ACAGGAATAATTCATGTAAGTCCAT
1 ACAGGAATGAGCCATGTAAGTCCAT
104479015 GTCAAAGACA
Statistics
Matches: 61, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
44 34 0.56
45 1 0.02
46 26 0.43
ACGTcount: A:0.36, C:0.15, G:0.23, T:0.27
Consensus pattern (45 bp):
ACAGGAATGAGCCATGTAAGTCCATATTAAAATATGGCTCTGGAG
Found at i:104482127 original size:9 final size:9
Alignment explanation
Indices: 104482112--104482202 Score: 71
Period size: 9 Copynumber: 9.6 Consensus size: 9
104482102 TCTATTTTAA
104482112 AAAAAAAAG
1 AAAAAAAAG
*
104482121 GAAAAAAAG
1 AAAAAAAAG
104482130 AAAAGAAAAAG
1 -AAA-AAAAAG
104482141 AAAAAAAAG
1 AAAAAAAAG
*
104482150 --AAAAAGG
1 AAAAAAAAG
104482157 AAAAAGAAAG
1 AAAAA-AAAG
104482167 AAAAGAAAAAGG
1 -AAA-AAAAA-G
104482179 AAAAATAAA-
1 AAAAA-AAAG
104482188 AAAGAAAAAG
1 AAA-AAAAAG
104482198 AAAAA
1 AAAAA
104482203 TGGAGAGGCG
Statistics
Matches: 67, Mismatches: 4, Indels: 22
0.72 0.04 0.24
Matches are distributed among these distances:
7 6 0.09
9 25 0.37
10 15 0.22
11 18 0.27
12 3 0.04
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.01
Consensus pattern (9 bp):
AAAAAAAAG
Found at i:104482147 original size:22 final size:21
Alignment explanation
Indices: 104482111--104482202 Score: 62
Period size: 22 Copynumber: 4.1 Consensus size: 21
104482101 TTCTATTTTA
104482111 AAAAAAAAAGGAA-AAAAAGAAA
1 AAAAAAAAA--AAGAAAAAGAAA
* *
104482133 AGAAAAAGAAA-AAAAAGAAA
1 AAAAAAAAAAAGAAAAAGAAA
* *
104482153 AAGGAAAAAGAAAGAAAAGAAAAA
1 AA--AAAAAAAAAGAAAA-AGAAA
104482177 GGAAAAATAAAAAAGAAAAAGAAA
1 --AAAAA-AAAAAAGAAAAAGAAA
104482201 AA
1 AA
104482203 TGGAGAGGCG
Statistics
Matches: 57, Mismatches: 6, Indels: 14
0.74 0.08 0.18
Matches are distributed among these distances:
20 12 0.21
22 18 0.32
23 4 0.07
24 11 0.19
25 10 0.18
26 2 0.04
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.01
Consensus pattern (21 bp):
AAAAAAAAAAAGAAAAAGAAA
Found at i:104482171 original size:42 final size:41
Alignment explanation
Indices: 104482122--104482202 Score: 87
Period size: 42 Copynumber: 2.0 Consensus size: 41
104482112 AAAAAAAAGG
*
104482122 AAAAAAAG-AAAAGAAAAAGAAAAAAAAGAAAAAGGAAAAAGA
1 AAAAAAAGAAAAAGAAAAAGGAAAAAAAGAAAAA-GAAAAA-A
* *
104482164 AAGAAAAGAAAAAGGAAAAA--TAAAAAAGAAAAAGAAAAA
1 AAAAAAAGAAAAA-GAAAAAGGAAAAAAAGAAAAAGAAAAA
104482203 TGGAGAGGCG
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
41 6 0.17
42 19 0.54
43 4 0.11
44 6 0.17
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.01
Consensus pattern (41 bp):
AAAAAAAGAAAAAGAAAAAGGAAAAAAAGAAAAAGAAAAAA
Found at i:104482188 original size:6 final size:6
Alignment explanation
Indices: 104482110--104482202 Score: 74
Period size: 6 Copynumber: 15.8 Consensus size: 6
104482100 CTTCTATTTT
*
104482110 AAAAA- AAAAAGG AAAAAA AGAAAAG AAAAAG --AAA- AAAAAG AAAAAGG
1 AAAAAG AAAAA-G AAAAAG A-AAAAG AAAAAG AAAAAG AAAAAG AAAAA-G
*
104482157 AAAAAG --AAAG -AAAAG AAAAAGG AAAAATA AAAAAG AAAAAG AAAAA
1 AAAAAG AAAAAG AAAAAG AAAAA-G AAAAA-G AAAAAG AAAAAG AAAAA
104482203 TGGAGAGGCG
Statistics
Matches: 73, Mismatches: 5, Indels: 19
0.75 0.05 0.20
Matches are distributed among these distances:
4 7 0.10
5 12 0.16
6 27 0.37
7 27 0.37
ACGTcount: A:0.83, C:0.00, G:0.16, T:0.01
Consensus pattern (6 bp):
AAAAAG
Found at i:104483176 original size:44 final size:44
Alignment explanation
Indices: 104483115--104483296 Score: 181
Period size: 44 Copynumber: 4.1 Consensus size: 44
104483105 CAAAGAAACA
* *
104483115 AGATTTGGCATCCCTGTGTTTATAGGGAATAGATCGAAGATAGC
1 AGATCTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGC
* ** * * * * **
104483159 AGATCTGACATTTCTGTGCTTACAGCGAAGCAGATTGAAGATTTC
1 AGATCTGGCATCCCTGTGTTTATAGGGAA-CAGATCGAAGATAGC
* *
104483204 AG--CATGGCATCCCTGTGTTCATAGGGAAC-GAGTTGAAGATAGC
1 AGATC-TGGCATCCCTGTGTTTATAGGGAACAGA-TCGAAGATAGC
* *
104483247 AGATTTGGCATCCCTGTATTTATAGGGAACAGATCGAAGATAGC
1 AGATCTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGC
104483291 AGATCT
1 AGATCT
104483297 AACCTTTAGA
Statistics
Matches: 107, Mismatches: 25, Indels: 12
0.74 0.17 0.08
Matches are distributed among these distances:
42 2 0.02
43 13 0.12
44 77 0.72
45 15 0.14
ACGTcount: A:0.30, C:0.16, G:0.26, T:0.28
Consensus pattern (44 bp):
AGATCTGGCATCCCTGTGTTTATAGGGAACAGATCGAAGATAGC
Found at i:104483548 original size:83 final size:83
Alignment explanation
Indices: 104483405--104483996 Score: 990
Period size: 83 Copynumber: 7.1 Consensus size: 83
104483395 GTTCTTAGAC
* * * * *
104483405 ACATAGCAGATTAGACTCTCAGATGTTTTTAAACAGACTCAAGATGGTTTAGCGTCCTTGTGCTT
1 ACATAGCAGATTAGACTCTCAGATGTTCTCAAACAGACTCAAGATGGTTTGGCATTCTTGTGCTT
104483470 ACAAGGAACAAATCGAGG
66 ACAAGGAACAAATCGAGG
104483488 ACATAGCAGATTAGACTCTCAGATGTTCTCAAACAGACTCAAGATGGTTTGGCATTCTTGTGCTT
1 ACATAGCAGATTAGACTCTCAGATGTTCTCAAACAGACTCAAGATGGTTTGGCATTCTTGTGCTT
104483553 ACAAGGAACAAATCGAGG
66 ACAAGGAACAAATCGAGG
*
104483571 ACATAACAGATTAGACTCTCAGATGTTCTCAAACAGACTCAAGATGGTTTGGCATTCTTGTGCTT
1 ACATAGCAGATTAGACTCTCAGATGTTCTCAAACAGACTCAAGATGGTTTGGCATTCTTGTGCTT
104483636 ACAAGGAACAAATCGAGG
66 ACAAGGAACAAATCGAGG
104483654 ACATAGCAGATTAGACTCTCAGATGTTCTCAAACAGACTCAAGATGGTTTGGCATTCTTGTGCTT
1 ACATAGCAGATTAGACTCTCAGATGTTCTCAAACAGACTCAAGATGGTTTGGCATTCTTGTGCTT
104483719 ACAAGGAACAAATCGAGG
66 ACAAGGAACAAATCGAGG
104483737 ACATAGCAGATTAGACTCTCAGATGTTCTCAAACAGACTCAAGATGGTTTGGCATTCTTGTGCTT
1 ACATAGCAGATTAGACTCTCAGATGTTCTCAAACAGACTCAAGATGGTTTGGCATTCTTGTGCTT
*
104483802 ACCAGGAACAAATCGAGG
66 ACAAGGAACAAATCGAGG
* * * * *
104483820 ACATAGCAGATTTGACTCTCAGATGTTCTTAAACAGACTCAAGATGATTTGGTATTCTTGTGTTT
1 ACATAGCAGATTAGACTCTCAGATGTTCTCAAACAGACTCAAGATGGTTTGGCATTCTTGTGCTT
*
104483885 ACCAA-AAACAAATCGAGG
66 A-CAAGGAACAAATCGAGG
* * * *
104483903 ACATAGCAGATTTGACTCTCAGATGTTCTCAAACAGACTTAAGATGATTTGGCATCCTTGTGCTT
1 ACATAGCAGATTAGACTCTCAGATGTTCTCAAACAGACTCAAGATGGTTTGGCATTCTTGTGCTT
*
104483968 ACAAGAAACAAATCGA-G
66 ACAAGGAACAAATCGAGG
*
104483985 ACATAGCTGATT
1 ACATAGCAGATT
104483997 TGGCTTTCAC
Statistics
Matches: 486, Mismatches: 21, Indels: 5
0.95 0.04 0.01
Matches are distributed among these distances:
82 15 0.03
83 469 0.97
84 2 0.00
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (83 bp):
ACATAGCAGATTAGACTCTCAGATGTTCTCAAACAGACTCAAGATGGTTTGGCATTCTTGTGCTT
ACAAGGAACAAATCGAGG
Found at i:104484777 original size:17 final size:17
Alignment explanation
Indices: 104484768--104484867 Score: 155
Period size: 17 Copynumber: 5.8 Consensus size: 17
104484758 CTTCAATGAT
104484768 ATGCAATCTTAGATATG
1 ATGCAATCTTAGATATG
104484785 ATGCAATCTTAGATATG
1 ATGCAATCTTAGATATG
*
104484802 ATACAATCTTAGATATG
1 ATGCAATCTTAGATATG
*
104484819 ATTGCAATATTAGATATG
1 A-TGCAATCTTAGATATG
*
104484837 ATACAATCTTAGATATG
1 ATGCAATCTTAGATATG
104484854 ATTGCAATCTTAGA
1 A-TGCAATCTTAGA
104484868 AGATATGATG
Statistics
Matches: 75, Mismatches: 6, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
17 49 0.65
18 26 0.35
ACGTcount: A:0.38, C:0.11, G:0.15, T:0.36
Consensus pattern (17 bp):
ATGCAATCTTAGATATG
Found at i:104484826 original size:52 final size:54
Alignment explanation
Indices: 104484763--104484874 Score: 169
Period size: 52 Copynumber: 2.1 Consensus size: 54
104484753 ATAATCTTCA
* *
104484763 ATGATATGCAATCTTAGATATGATGCAATCTTAGATATGA-TACAATCTTAGAT
1 ATGATATGCAATATTAGATATGATACAATCTTAGATATGATTACAATCTTAGAT
*
104484816 ATGAT-TGCAATATTAGATATGATACAATCTTAGATATGATTGCAATCTTAGA-
1 ATGATATGCAATATTAGATATGATACAATCTTAGATATGATTACAATCTTAGAT
104484868 A-GATATG
1 ATGATATG
104484875 ATGTAATCTT
Statistics
Matches: 54, Mismatches: 3, Indels: 5
0.87 0.05 0.08
Matches are distributed among these distances:
51 3 0.06
52 35 0.65
53 16 0.30
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (54 bp):
ATGATATGCAATATTAGATATGATACAATCTTAGATATGATTACAATCTTAGAT
Found at i:104484832 original size:35 final size:35
Alignment explanation
Indices: 104484771--104484867 Score: 178
Period size: 35 Copynumber: 2.8 Consensus size: 35
104484761 CAATGATATG
104484771 CAATCTTAGATATGA-TGCAATCTTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
*
104484805 CAATCTTAGATATGATTGCAATATTAGATATGATA
1 CAATCTTAGATATGATTGCAATCTTAGATATGATA
104484840 CAATCTTAGATATGATTGCAATCTTAGA
1 CAATCTTAGATATGATTGCAATCTTAGA
104484868 AGATATGATG
Statistics
Matches: 60, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
34 15 0.25
35 45 0.75
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.36
Consensus pattern (35 bp):
CAATCTTAGATATGATTGCAATCTTAGATATGATA
Found at i:104485394 original size:15 final size:16
Alignment explanation
Indices: 104485351--104485409 Score: 50
Period size: 16 Copynumber: 3.5 Consensus size: 16
104485341 CAATATATTT
*
104485351 TATATATTTTATATAA
1 TATATTTTTTATATAA
104485367 T-TATTATTCTTATA-AA
1 TATATT-TT-TTATATAA
104485383 TATATTTTTTATTATACA
1 TATATTTTTTA-TATA-A
104485401 TTATATTTT
1 -TATATTTT
104485410 AAATTTATTA
Statistics
Matches: 35, Mismatches: 1, Indels: 11
0.74 0.02 0.23
Matches are distributed among these distances:
15 6 0.17
16 10 0.29
17 10 0.29
18 1 0.03
19 8 0.23
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (16 bp):
TATATTTTTTATATAA
Found at i:104486893 original size:2 final size:2
Alignment explanation
Indices: 104486886--104486927 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
104486876 GGATCCAGGA
104486886 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
104486928 TAGTTTTTAC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:104490990 original size:28 final size:28
Alignment explanation
Indices: 104490950--104491009 Score: 120
Period size: 28 Copynumber: 2.1 Consensus size: 28
104490940 ACTCTTAAGC
104490950 TTAAACATATATTAGCTTGTTTAGAGAA
1 TTAAACATATATTAGCTTGTTTAGAGAA
104490978 TTAAACATATATTAGCTTGTTTAGAGAA
1 TTAAACATATATTAGCTTGTTTAGAGAA
104491006 TTAA
1 TTAA
104491010 GTTCTTTATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 32 1.00
ACGTcount: A:0.40, C:0.07, G:0.13, T:0.40
Consensus pattern (28 bp):
TTAAACATATATTAGCTTGTTTAGAGAA
Found at i:104493580 original size:118 final size:118
Alignment explanation
Indices: 104493377--104493594 Score: 312
Period size: 118 Copynumber: 1.8 Consensus size: 118
104493367 ATTATATAAT
* * *
104493377 ATATTAATAATTTATATATATGCATCGATGATTAAACATTATAATATCATATAATATTATATCTT
1 ATATTAATAATTTATATATATGCATCAATGACTAAACATTATAATATCATATAATACTATATCTT
*
104493442 TTATTATAATCTATATTATAATAATAGTTATATATGTATTAATATTTTTAGTA
66 TTATTATAACCTATATTATAATAATAGTTATATATGTATTAATATTTTTAGTA
* * * * * * * *
104493495 ATATTAATAGTTTATATATGTGTATCAATTACTAAACATTATAATCTTATGTAATACTGTATCTT
1 ATATTAATAATTTATATATATGCATCAATGACTAAACATTATAATATCATATAATACTATATCTT
104493560 TTATTATAACCTAT-TGTATAATAATAGTTATATAT
66 TTATTATAACCTATAT-TATAATAATAGTTATATAT
104493595 TATAGTAGTA
Statistics
Matches: 87, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
117 1 0.01
118 86 0.99
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (118 bp):
ATATTAATAATTTATATATATGCATCAATGACTAAACATTATAATATCATATAATACTATATCTT
TTATTATAACCTATATTATAATAATAGTTATATATGTATTAATATTTTTAGTA
Found at i:104493628 original size:17 final size:17
Alignment explanation
Indices: 104493606--104493642 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
104493596 ATAGTAGTAC
104493606 ATTATATATTA-CATATT
1 ATTATATATTATC-TATT
104493623 ATTATATATTATCTATT
1 ATTATATATTATCTATT
104493640 ATT
1 ATT
104493643 GTTTATTATT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 18 0.95
18 1 0.05
ACGTcount: A:0.38, C:0.05, G:0.00, T:0.57
Consensus pattern (17 bp):
ATTATATATTATCTATT
Found at i:104493628 original size:118 final size:116
Alignment explanation
Indices: 104493375--104493631 Score: 286
Period size: 118 Copynumber: 2.2 Consensus size: 116
104493365 ATATTATATA
* * *
104493375 ATATATTAATAATTTATATATATGCATCGATGATTAAACATTATAATATCATATAATATTATATC
1 ATATATTAATAATTTATATATATGCATCAATGACTAAACATTATAATATCATATAATACTATATC
* **
104493440 TTTTATTATAATCTATATTATAATAATAGTTATATATGTATTAATATTTTT
66 TTTTATTATAACCTATATTATAATAATAGTTATATATGTATTAATATCATT
* * * * * * * *
104493491 AGTAATATTAATAGTTTATATATGTGTATCAATTACTAAACATTATAATCTTATGTAATACTGTA
1 A-T-ATATTAATAATTTATATATATGCATCAATGACTAAACATTATAATATCATATAATACTATA
*
104493556 TCTTTTATTATAACCTAT-TGTATAATAATAGTTATATAT-TA-TAGTAGTACATT
64 TCTTTTATTATAACCTATAT-TATAATAATAGTTATATATGTATTAATA-T-CATT
*
104493609 ATATATTACATATTATTATATAT
1 ATATATTA-ATAAT-TTATATAT
104493632 TATCTATTAT
Statistics
Matches: 118, Mismatches: 16, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
116 11 0.09
117 10 0.08
118 97 0.82
ACGTcount: A:0.40, C:0.06, G:0.06, T:0.48
Consensus pattern (116 bp):
ATATATTAATAATTTATATATATGCATCAATGACTAAACATTATAATATCATATAATACTATATC
TTTTATTATAACCTATATTATAATAATAGTTATATATGTATTAATATCATT
Found at i:104496037 original size:43 final size:43
Alignment explanation
Indices: 104495987--104496137 Score: 198
Period size: 43 Copynumber: 3.5 Consensus size: 43
104495977 TATCCCAGAT
* * *
104495987 ATGGTCTTACATTTTATCACATATCGATGCCACTGTCCTAGAC
1 ATGGTCTTACATGTAATCACATATCGATGCCAATGTCCTAGAC
* * * *
104496030 AGGGTCTTACACGTAATCGA-TTAACGATGCCAATGTCCTAGAC
1 ATGGTCTTACATGTAATC-ACATATCGATGCCAATGTCCTAGAC
*
104496073 ATGGTCTTACATGTAATCACA-ATACAATGCCAATGTCCTAGAC
1 ATGGTCTTACATGTAATCACATAT-CGATGCCAATGTCCTAGAC
104496116 ATGGTCTTACATGTAATCACAT
1 ATGGTCTTACATGTAATCACAT
104496138 CTCAGTAACC
Statistics
Matches: 92, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
42 2 0.02
43 89 0.97
44 1 0.01
ACGTcount: A:0.30, C:0.23, G:0.16, T:0.30
Consensus pattern (43 bp):
ATGGTCTTACATGTAATCACATATCGATGCCAATGTCCTAGAC
Found at i:104502103 original size:17 final size:17
Alignment explanation
Indices: 104502081--104502113 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
104502071 TGTGTATGTG
104502081 AATGAATGTTAATTGAT
1 AATGAATGTTAATTGAT
*
104502098 AATGAATGTTTATTGA
1 AATGAATGTTAATTGA
104502114 GTTGTGAAAT
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:0.39, C:0.00, G:0.18, T:0.42
Consensus pattern (17 bp):
AATGAATGTTAATTGAT
Found at i:104509622 original size:19 final size:19
Alignment explanation
Indices: 104509592--104509662 Score: 74
Period size: 19 Copynumber: 3.7 Consensus size: 19
104509582 AAAAATACAA
104509592 ATTTTAGAATTTTTATAAA-T
1 ATTTT-GAATTTTTA-AAATT
*
104509612 ATTTTGAATTTTAAAAATT
1 ATTTTGAATTTTTAAAATT
**
104509631 ATTTTTTATTTTTGAAAATT
1 ATTTTGAATTTTT-AAAATT
104509651 ATTTTG-ATTTTT
1 ATTTTGAATTTTT
104509663 TTTTTGTAAT
Statistics
Matches: 44, Mismatches: 5, Indels: 5
0.81 0.09 0.09
Matches are distributed among these distances:
18 3 0.07
19 25 0.57
20 16 0.36
ACGTcount: A:0.34, C:0.00, G:0.06, T:0.61
Consensus pattern (19 bp):
ATTTTGAATTTTTAAAATT
Found at i:104509623 original size:18 final size:21
Alignment explanation
Indices: 104509592--104509663 Score: 64
Period size: 20 Copynumber: 3.7 Consensus size: 21
104509582 AAAAATACAA
*
104509592 ATTTTAGAATTTTTATAAA-T
1 ATTTTAGAATTTTTAAAAATT
104509612 ATTTT-GAA-TTTTAAAAATT
1 ATTTTAGAATTTTTAAAAATT
** *
104509631 ATTTT-TTATTTTTGAAAATT
1 ATTTTAGAATTTTTAAAAATT
*
104509651 ATTTT-GATTTTTT
1 ATTTTAGAATTTTT
104509664 TTTTGTAATT
Statistics
Matches: 43, Mismatches: 7, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
18 8 0.19
19 10 0.23
20 25 0.58
ACGTcount: A:0.33, C:0.00, G:0.06, T:0.61
Consensus pattern (21 bp):
ATTTTAGAATTTTTAAAAATT
Found at i:104512018 original size:26 final size:26
Alignment explanation
Indices: 104511989--104512096 Score: 189
Period size: 26 Copynumber: 4.2 Consensus size: 26
104511979 TGATACAAAT
104511989 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
* *
104512015 TGATAATGGATTAGGTAAATATTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
104512041 TGATAATGGGTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
*
104512067 TGATAATGGTTTAGGTAAATGTTCCA
1 TGATAATGGGTTAGGTAAATGTTCCA
104512093 TGAT
1 TGAT
104512097 GGGCATTTCA
Statistics
Matches: 77, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
26 77 1.00
ACGTcount: A:0.32, C:0.07, G:0.24, T:0.36
Consensus pattern (26 bp):
TGATAATGGGTTAGGTAAATGTTCCA
Found at i:104515199 original size:16 final size:16
Alignment explanation
Indices: 104515178--104515213 Score: 72
Period size: 16 Copynumber: 2.2 Consensus size: 16
104515168 ATCACTAAAA
104515178 GCATTAGCACATACAT
1 GCATTAGCACATACAT
104515194 GCATTAGCACATACAT
1 GCATTAGCACATACAT
104515210 GCAT
1 GCAT
104515214 ATAAATAGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.36, C:0.25, G:0.14, T:0.25
Consensus pattern (16 bp):
GCATTAGCACATACAT
Found at i:104519634 original size:22 final size:22
Alignment explanation
Indices: 104519609--104519660 Score: 86
Period size: 22 Copynumber: 2.4 Consensus size: 22
104519599 CACACGGCCG
104519609 TGTGCCTCCCTTCACACAGGCA
1 TGTGCCTCCCTTCACACAGGCA
* *
104519631 TGTGCCTCCTTTCACACAGGTA
1 TGTGCCTCCCTTCACACAGGCA
104519653 TGTGCCTC
1 TGTGCCTC
104519661 TATCACATGG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.15, C:0.37, G:0.19, T:0.29
Consensus pattern (22 bp):
TGTGCCTCCCTTCACACAGGCA
Found at i:104519676 original size:21 final size:22
Alignment explanation
Indices: 104519609--104519676 Score: 77
Period size: 22 Copynumber: 3.1 Consensus size: 22
104519599 CACACGGCCG
104519609 TGTGCCTCCCT-TCACACAGGCA
1 TGTGCCT-CCTATCACACAGGCA
* *
104519631 TGTGCCTCCTTTCACACAGGTA
1 TGTGCCTCCTATCACACAGGCA
**
104519653 TGTGCCT-CTATCACATGGGCA
1 TGTGCCTCCTATCACACAGGCA
104519674 TGT
1 TGT
104519677 TGACCCTCCC
Statistics
Matches: 40, Mismatches: 5, Indels: 3
0.83 0.10 0.06
Matches are distributed among these distances:
21 16 0.40
22 24 0.60
ACGTcount: A:0.18, C:0.32, G:0.21, T:0.29
Consensus pattern (22 bp):
TGTGCCTCCTATCACACAGGCA
Found at i:104521836 original size:15 final size:15
Alignment explanation
Indices: 104521827--104521875 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 15
104521817 TTTTTAAATT
104521827 TAAAAATTTTAAAAA
1 TAAAAATTTTAAAAA
104521842 TAAAAATTATTAAAAA
1 TAAAAATT-TTAAAAA
* *
104521858 TATAAAATATAAAAAA
1 TA-AAAATTTTAAAAA
104521874 TA
1 TA
104521876 TGATATTTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
15 8 0.27
16 17 0.57
17 5 0.17
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (15 bp):
TAAAAATTTTAAAAA
Found at i:104521836 original size:16 final size:16
Alignment explanation
Indices: 104521817--104521865 Score: 55
Period size: 15 Copynumber: 3.1 Consensus size: 16
104521807 TAATTAATTT
**
104521817 TTTTTAAATTTAAAAA
1 TTTTTAAAAATAAAAA
104521833 -TTTTAAAAATAAAAA
1 TTTTTAAAAATAAAAA
*
104521848 TTATTAAAAATATAAAA
1 TTTTTAAAAATA-AAAA
104521865 T
1 T
104521866 ATAAAAAATA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
15 13 0.46
16 10 0.36
17 5 0.18
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (16 bp):
TTTTTAAAAATAAAAA
Found at i:104540628 original size:22 final size:21
Alignment explanation
Indices: 104540603--104540655 Score: 54
Period size: 23 Copynumber: 2.4 Consensus size: 21
104540593 AATAAAATAT
104540603 AAATTAAAAATGCTATAA-CTTG
1 AAATTAAAAA-GCT-TAATCTTG
104540625 AAATTTTAAAAAGCTTAATCTTG
1 AAA--TTAAAAAGCTTAATCTTG
*
104540648 GAATTAAA
1 AAATTAAA
104540656 CCAAAGCTTT
Statistics
Matches: 27, Mismatches: 1, Indels: 7
0.77 0.03 0.20
Matches are distributed among these distances:
21 5 0.19
22 6 0.22
23 9 0.33
24 7 0.26
ACGTcount: A:0.49, C:0.08, G:0.09, T:0.34
Consensus pattern (21 bp):
AAATTAAAAAGCTTAATCTTG
Found at i:104540635 original size:23 final size:23
Alignment explanation
Indices: 104540606--104540652 Score: 60
Period size: 23 Copynumber: 2.0 Consensus size: 23
104540596 AAAATATAAA
104540606 TTAAAAATGCTATAA-CTTGAAATT
1 TTAAAAA-GCT-TAATCTTGAAATT
*
104540630 TTAAAAAGCTTAATCTTGGAATT
1 TTAAAAAGCTTAATCTTGAAATT
104540653 AAACCAAAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
22 3 0.14
23 11 0.52
24 7 0.33
ACGTcount: A:0.43, C:0.09, G:0.11, T:0.38
Consensus pattern (23 bp):
TTAAAAAGCTTAATCTTGAAATT
Found at i:104541766 original size:13 final size:13
Alignment explanation
Indices: 104541722--104541782 Score: 50
Period size: 13 Copynumber: 4.7 Consensus size: 13
104541712 TGTAAATCAA
**
104541722 ACTTTTCAAAAGT
1 ACTTTTCAAAAAC
**
104541735 ACTTTTCAAAATT
1 ACTTTTCAAAAAC
* *
104541748 ATTTTTCCAAAAC
1 ACTTTTCAAAAAC
*
104541761 ACTTTTTAAAAAC
1 ACTTTTCAAAAAC
*
104541774 ACTTCTCAA
1 ACTTTTCAA
104541783 TAGCAATGAT
Statistics
Matches: 38, Mismatches: 10, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 38 1.00
ACGTcount: A:0.39, C:0.20, G:0.02, T:0.39
Consensus pattern (13 bp):
ACTTTTCAAAAAC
Found at i:104550838 original size:21 final size:21
Alignment explanation
Indices: 104550795--104550840 Score: 56
Period size: 21 Copynumber: 2.2 Consensus size: 21
104550785 AACACACTCA
*
104550795 TGTGGCTACCCCACATGCCTG
1 TGTGGCTACCCCACACGCCTG
** *
104550816 TGTGGCTACCTTACACGCTTG
1 TGTGGCTACCCCACACGCCTG
104550837 TGTG
1 TGTG
104550841 CTCAGACCGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.13, C:0.30, G:0.26, T:0.30
Consensus pattern (21 bp):
TGTGGCTACCCCACACGCCTG
Found at i:104553161 original size:22 final size:22
Alignment explanation
Indices: 104553135--104553198 Score: 112
Period size: 22 Copynumber: 2.9 Consensus size: 22
104553125 ATGAAAACTA
104553135 GAAAATTAAC-AATTAAGAAAAT
1 GAAAATTAACTAA-TAAGAAAAT
104553157 GAAAATTAACTAATAAGAAAAT
1 GAAAATTAACTAATAAGAAAAT
104553179 GAAAATTAACTAATAAGAAA
1 GAAAATTAACTAATAAGAAA
104553199 CAATTTTTGA
Statistics
Matches: 41, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
22 39 0.95
23 2 0.05
ACGTcount: A:0.64, C:0.05, G:0.09, T:0.22
Consensus pattern (22 bp):
GAAAATTAACTAATAAGAAAAT
Found at i:104553165 original size:15 final size:15
Alignment explanation
Indices: 104553122--104553165 Score: 54
Period size: 15 Copynumber: 2.9 Consensus size: 15
104553112 AAATTTCATA
*
104553122 AAAATGAAAACT-AG
1 AAAATGAAAATTAAG
*
104553136 AAAATTAACAATTAAG
1 AAAATGAA-AATTAAG
104553152 AAAATGAAAATTAA
1 AAAATGAAAATTAA
104553166 CTAATAAGAA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
14 7 0.28
15 9 0.36
16 9 0.36
ACGTcount: A:0.66, C:0.05, G:0.09, T:0.20
Consensus pattern (15 bp):
AAAATGAAAATTAAG
Found at i:104553526 original size:37 final size:37
Alignment explanation
Indices: 104553485--104553559 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
104553475 ACCTTAACTC
104553485 AGATTAATTATGCCCACTTCAATTAACCAAACTCCCT
1 AGATTAATTATGCCCACTTCAATTAACCAAACTCCCT
104553522 AGATTAATTATGCCCACTTCAATTAACCAAACTCCCT
1 AGATTAATTATGCCCACTTCAATTAACCAAACTCCCT
104553559 A
1 A
104553560 AGGATTTAGT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.36, C:0.29, G:0.05, T:0.29
Consensus pattern (37 bp):
AGATTAATTATGCCCACTTCAATTAACCAAACTCCCT
Found at i:104559325 original size:136 final size:136
Alignment explanation
Indices: 104559081--104559326 Score: 330
Period size: 136 Copynumber: 1.8 Consensus size: 136
104559071 ATGGGCCTAT
* **
104559081 TCACACAAGTTGTCGGTCGGAACGTAGCTACACGGTGCTGCTCCGTAAGCTGTCGAGTATCCACA
1 TCACACAAGCTGTCGGTCGGAACGTAGCTACACGGTGCTGCTCCACAAGCTGTCGAGTATCCACA
* * *
104559146 AAAAATGCCAAAACTTAGCCACCGGTAGGATATTCAAAACCAGCACCCGAAATATGGTAACCTAG
66 AAAAATGCCAAAACTCAGCCACCAGTAGGACATTCAAAACCAGCACCCGAAATATGGTAACCTAG
104559211 GTTTGC
131 GTTTGC
* * * * * **
104559217 TCACACATGCTGTTGGTCGGAATGTAGCTACACGGTGCTGCTTCACAAGCTGTCGAGTATTCGTA
1 TCACACAAGCTGTCGGTCGGAACGTAGCTACACGGTGCTGCTCCACAAGCTGTCGAGTATCCACA
* * * * *
104559282 ACAAATGTCAGAACTCAGCCAGCAGTAGGACATTCAAGACCAGCA
66 AAAAATGCCAAAACTCAGCCACCAGTAGGACATTCAAAACCAGCA
104559327 TCCAAAACAT
Statistics
Matches: 92, Mismatches: 18, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
136 92 1.00
ACGTcount: A:0.30, C:0.25, G:0.23, T:0.22
Consensus pattern (136 bp):
TCACACAAGCTGTCGGTCGGAACGTAGCTACACGGTGCTGCTCCACAAGCTGTCGAGTATCCACA
AAAAATGCCAAAACTCAGCCACCAGTAGGACATTCAAAACCAGCACCCGAAATATGGTAACCTAG
GTTTGC
Found at i:104562387 original size:29 final size:29
Alignment explanation
Indices: 104562345--104562417 Score: 146
Period size: 29 Copynumber: 2.5 Consensus size: 29
104562335 GTGACAAGAT
104562345 TGGCACTAAGTGTGCAAGCTTGAAAAGTA
1 TGGCACTAAGTGTGCAAGCTTGAAAAGTA
104562374 TGGCACTAAGTGTGCAAGCTTGAAAAGTA
1 TGGCACTAAGTGTGCAAGCTTGAAAAGTA
104562403 TGGCACTAAGTGTGC
1 TGGCACTAAGTGTGC
104562418 GAATTTAAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 44 1.00
ACGTcount: A:0.32, C:0.15, G:0.29, T:0.25
Consensus pattern (29 bp):
TGGCACTAAGTGTGCAAGCTTGAAAAGTA
Found at i:104562436 original size:29 final size:29
Alignment explanation
Indices: 104562404--104562476 Score: 92
Period size: 29 Copynumber: 2.5 Consensus size: 29
104562394 TGAAAAGTAT
* * *
104562404 GGCACTAAGTGTGCGAATTTAAATTATAC
1 GGCACTAAGTGTGCGAACTTAAATCACAC
* * *
104562433 GGCACTATGTGTGCGAGCTTAAATCACAT
1 GGCACTAAGTGTGCGAACTTAAATCACAC
104562462 GGCACTAAGTGTGCG
1 GGCACTAAGTGTGCG
104562477 TGATCGATTA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
29 37 1.00
ACGTcount: A:0.29, C:0.18, G:0.26, T:0.27
Consensus pattern (29 bp):
GGCACTAAGTGTGCGAACTTAAATCACAC
Found at i:104570268 original size:21 final size:21
Alignment explanation
Indices: 104570242--104570287 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 21
104570232 CAAAAAATAC
*
104570242 AAAAAAATACAAAAT-TATTTT
1 AAAAAAATA-AAAATAAATTTT
*
104570263 AAAAAATTAAAAATAAATTTT
1 AAAAAAATAAAAATAAATTTT
104570284 AAAA
1 AAAA
104570288 TTCGAAACAT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 5 0.23
21 17 0.77
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.30
Consensus pattern (21 bp):
AAAAAAATAAAAATAAATTTT
Found at i:104570339 original size:25 final size:26
Alignment explanation
Indices: 104570297--104570345 Score: 66
Period size: 25 Copynumber: 1.9 Consensus size: 26
104570287 ATTCGAAACA
*
104570297 TTTATAAAAATTTCAAAATTTATATT
1 TTTATAAAAATTTCAAAAATTATATT
104570323 TTTA-AAAAATTAT-AAAAATTATA
1 TTTATAAAAATT-TCAAAAATTATA
104570346 AAAAATTCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
TTTATAAAAATTTCAAAAATTATATT
Found at i:104570340 original size:10 final size:10
Alignment explanation
Indices: 104570325--104570371 Score: 60
Period size: 10 Copynumber: 4.7 Consensus size: 10
104570315 TTTATATTTT
104570325 TAAAAAATTA
1 TAAAAAATTA
104570335 T-AAAAATTA
1 TAAAAAATTA
*
104570344 TAAAAAATTC
1 TAAAAAATTA
*
104570354 TAAAGAATATA
1 TAAAAAAT-TA
104570365 TAAAAAA
1 TAAAAAA
104570372 GTTAATAATT
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
9 9 0.29
10 15 0.48
11 7 0.23
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (10 bp):
TAAAAAATTA
Found at i:104570349 original size:19 final size:21
Alignment explanation
Indices: 104570325--104570371 Score: 71
Period size: 19 Copynumber: 2.3 Consensus size: 21
104570315 TTTATATTTT
104570325 TAAAAAATTATAAA-AAT-TA
1 TAAAAAATTATAAAGAATATA
*
104570344 TAAAAAATTCTAAAGAATATA
1 TAAAAAATTATAAAGAATATA
104570365 TAAAAAA
1 TAAAAAA
104570372 GTTAATAATT
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 13 0.52
20 3 0.12
21 9 0.36
ACGTcount: A:0.68, C:0.02, G:0.02, T:0.28
Consensus pattern (21 bp):
TAAAAAATTATAAAGAATATA
Found at i:104582530 original size:33 final size:33
Alignment explanation
Indices: 104582482--104582621 Score: 174
Period size: 33 Copynumber: 4.3 Consensus size: 33
104582472 CTTGACGAAA
* * *
104582482 TATCTTTATTCTGTGTTTACTATCCCAGTGGAC
1 TATCTCTATTATGTGTTTACTATCCCAGCGGAC
**
104582515 TATCTCTATTATGTGTTTACTAT-CTTGCGGAC
1 TATCTCTATTATGTGTTTACTATCCCAGCGGAC
* *
104582547 TATCTCTATTATGTGTTTATTGTCCCAGCGGAC
1 TATCTCTATTATGTGTTTACTATCCCAGCGGAC
* * * *
104582580 TATCTCTGTTCTATGTTTACTATCCCAGCGAAC
1 TATCTCTATTATGTGTTTACTATCCCAGCGGAC
104582613 TATCTCTAT
1 TATCTCTAT
104582622 GGATGCCATG
Statistics
Matches: 90, Mismatches: 16, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
32 27 0.30
33 63 0.70
ACGTcount: A:0.19, C:0.22, G:0.14, T:0.44
Consensus pattern (33 bp):
TATCTCTATTATGTGTTTACTATCCCAGCGGAC
Found at i:104582564 original size:65 final size:66
Alignment explanation
Indices: 104582477--104582621 Score: 175
Period size: 65 Copynumber: 2.2 Consensus size: 66
104582467 ATTGTCTTGA
* * * * * **
104582477 CGAAATATCTTTATTCTGTGTTTACTATCCCAGTGGACTATCTCTATTATGTGTTTACTAT-CTT
1 CGAACTATCTCTATTATGTGTTTACTATCCCAGCGGACTATCTCTATTATATGTTTACTATCCCA
104582541 G
66 G
* * * * *
104582542 CGGACTATCTCTATTATGTGTTTATTGTCCCAGCGGACTATCTCTGTTCTATGTTTACTATCCCA
1 CGAACTATCTCTATTATGTGTTTACTATCCCAGCGGACTATCTCTATTATATGTTTACTATCCCA
104582607 G
66 G
104582608 CGAACTATCTCTAT
1 CGAACTATCTCTAT
104582622 GGATGCCATG
Statistics
Matches: 66, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
65 51 0.77
66 15 0.23
ACGTcount: A:0.21, C:0.22, G:0.14, T:0.43
Consensus pattern (66 bp):
CGAACTATCTCTATTATGTGTTTACTATCCCAGCGGACTATCTCTATTATATGTTTACTATCCCA
G
Found at i:104584089 original size:21 final size:21
Alignment explanation
Indices: 104584028--104584089 Score: 53
Period size: 21 Copynumber: 3.0 Consensus size: 21
104584018 CAAGATCAAG
104584028 ATAGCTTCGGCTATATATGGTAC
1 ATAGCTTCGGCTATATAT-G-AC
*
104584051 TTAG--T-GTGCTAT-T-TGAC
1 ATAGCTTCG-GCTATATATGAC
104584068 ATAGCTTCGGCTATATATGAC
1 ATAGCTTCGGCTATATATGAC
104584089 A
1 A
104584090 CTTAGTGTGC
Statistics
Matches: 31, Mismatches: 2, Indels: 14
0.66 0.04 0.30
Matches are distributed among these distances:
17 5 0.16
18 1 0.03
19 7 0.23
20 4 0.13
21 11 0.35
23 3 0.10
ACGTcount: A:0.26, C:0.16, G:0.21, T:0.37
Consensus pattern (21 bp):
ATAGCTTCGGCTATATATGAC
Found at i:104584091 original size:81 final size:81
Alignment explanation
Indices: 104583951--104584179 Score: 280
Period size: 81 Copynumber: 2.8 Consensus size: 81
104583941 GACGACATAA
* * * *
104583951 CTTCGGTTATATATGGCACTTAGTATGCGATTCGACATAG-TGTTGGCTATATATAACACTTAGT
1 CTTCGGCTATATATGGCACTTAGTGTGCGATTCGACATAGCT-TCGGCTATATATGACACTTAGT
104584015 GTACAAGATCAAGATAG
65 GTACAAGATCAAGATAG
* * *
104584032 CTTCGGCTATATATGGTACTTAGTGTGCTATTTGACATAGCTTCGGCTATATATGACACTTAGTG
1 CTTCGGCTATATATGGCACTTAGTGTGCGATTCGACATAGCTTCGGCTATATATGACACTTAGTG
* * *
104584097 TGCGAGATCGAGATAG
66 TACAAGATCAAGATAG
* ** * * * *
104584113 CTTCGACTATATATTACACTTAATGTGCGAGGTCGAGATAGCTTCGGCTATATATGGCACTTAGT
1 CTTCGGCTATATATGGCACTTAGTGTGCGA-TTCGACATAGCTTCGGCTATATATGACACTTAGT
104584178 GT
65 GT
104584180 GCGTTTTGAG
Statistics
Matches: 126, Mismatches: 20, Indels: 3
0.85 0.13 0.02
Matches are distributed among these distances:
81 93 0.74
82 33 0.26
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (81 bp):
CTTCGGCTATATATGGCACTTAGTGTGCGATTCGACATAGCTTCGGCTATATATGACACTTAGTG
TACAAGATCAAGATAG
Found at i:104584165 original size:122 final size:122
Alignment explanation
Indices: 104583944--104584226 Score: 349
Period size: 122 Copynumber: 2.3 Consensus size: 122
104583934 CATGTTCGAC
* * * * * *
104583944 GACATAACTTCGGTTATATATGGCACTTAGTATGCGA-TTCGACATAGTGTTGGCTATATATAAC
1 GACATAGCTTCGGCTATATATGGCACTTAGTGTGCGAGATCGACATAGTGTCGACTATATATAAC
* *
104584008 ACTTAGTGTACAAGATCAAGATAGCTTCGGCTATATATGGTACTTAGTGTGC-TATTT
66 ACTTAATGTACAAGATCAAGATAGCTTCGGCTATATATGGCACTTAGTGTGCGT-TTT
* * *
104584065 GACATAGCTTCGGCTATATATGACACTTAGTGTGCGAGATCGAGATAGCT-TCGACTATATATTA
1 GACATAGCTTCGGCTATATATGGCACTTAGTGTGCGAGATCGACATAG-TGTCGACTATATATAA
* * * *
104584129 CACTTAATGTGCGAGGTCGAGATAGCTTCGGCTATATATGGCACTTAGTGTGCGTTTT
65 CACTTAATGTACAAGATCAAGATAGCTTCGGCTATATATGGCACTTAGTGTGCGTTTT
* **
104584187 GAGATAGCTTCCACTA-AGTATGGCACTTAGTGTGCGAGAT
1 GACATAGCTTCGGCTATA-TATGGCACTTAGTGTGCGAGAT
104584227 ACCTAGTATT
Statistics
Matches: 139, Mismatches: 19, Indels: 7
0.84 0.12 0.04
Matches are distributed among these distances:
121 34 0.24
122 103 0.74
123 2 0.01
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.33
Consensus pattern (122 bp):
GACATAGCTTCGGCTATATATGGCACTTAGTGTGCGAGATCGACATAGTGTCGACTATATATAAC
ACTTAATGTACAAGATCAAGATAGCTTCGGCTATATATGGCACTTAGTGTGCGTTTT
Found at i:104584209 original size:40 final size:41
Alignment explanation
Indices: 104583951--104584224 Score: 270
Period size: 41 Copynumber: 6.8 Consensus size: 41
104583941 GACGACATAA
* * *
104583951 CTTCGGTTATATATGGCACTTAGTATGCGA-TTCGACATAG
1 CTTCGGCTATATATGGCACTTAGTGTGCGAGTTCGAGATAG
* ** * * * *
104583991 -TGTTGGCTATATATAACACTTAGTGTACAAGATCAAGATAG
1 CT-TCGGCTATATATGGCACTTAGTGTGCGAGTTCGAGATAG
* * * *
104584032 CTTCGGCTATATATGGTACTTAGTGTGCTA-TTTGACATAG
1 CTTCGGCTATATATGGCACTTAGTGTGCGAGTTCGAGATAG
* *
104584072 CTTCGGCTATATATGACACTTAGTGTGCGAGATCGAGATAG
1 CTTCGGCTATATATGGCACTTAGTGTGCGAGTTCGAGATAG
* ** * *
104584113 CTTCGACTATATATTACACTTAATGTGCGAGGTCGAGATAG
1 CTTCGGCTATATATGGCACTTAGTGTGCGAGTTCGAGATAG
* *
104584154 CTTCGGCTATATATGGCACTTAGTGTGCG-TTTTGAGATAG
1 CTTCGGCTATATATGGCACTTAGTGTGCGAGTTCGAGATAG
**
104584194 CTTCCACTA-AGTATGGCACTTAGTGTGCGAG
1 CTTCGGCTATA-TATGGCACTTAGTGTGCGAG
104584225 ATACCTAGTA
Statistics
Matches: 188, Mismatches: 40, Indels: 11
0.79 0.17 0.05
Matches are distributed among these distances:
39 2 0.01
40 87 0.46
41 98 0.52
42 1 0.01
ACGTcount: A:0.26, C:0.16, G:0.24, T:0.34
Consensus pattern (41 bp):
CTTCGGCTATATATGGCACTTAGTGTGCGAGTTCGAGATAG
Found at i:104589021 original size:21 final size:21
Alignment explanation
Indices: 104588995--104589040 Score: 92
Period size: 21 Copynumber: 2.2 Consensus size: 21
104588985 TAGTTAAAGG
104588995 ATTAAATTGATATAATATTAA
1 ATTAAATTGATATAATATTAA
104589016 ATTAAATTGATATAATATTAA
1 ATTAAATTGATATAATATTAA
104589037 ATTA
1 ATTA
104589041 GGCATGAAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.43
Consensus pattern (21 bp):
ATTAAATTGATATAATATTAA
Found at i:104592654 original size:18 final size:17
Alignment explanation
Indices: 104592624--104592657 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
104592614 ATGAAAAGTG
*
104592624 TAAATAAAAATAAAAAT
1 TAAAAAAAAATAAAAAT
104592641 TAAAAAAAATATAAAAA
1 TAAAAAAAA-ATAAAAA
104592658 CAAAAGGGAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (17 bp):
TAAAAAAAAATAAAAAT
Found at i:104594278 original size:18 final size:18
Alignment explanation
Indices: 104594257--104594293 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
104594247 AAATAAGAGT
*
104594257 AATATTAGTAATAATAAA
1 AATAATAGTAATAATAAA
104594275 AATAATAGTAATAATAAA
1 AATAATAGTAATAATAAA
104594293 A
1 A
104594294 TGATTAAAAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.05, T:0.30
Consensus pattern (18 bp):
AATAATAGTAATAATAAA
Found at i:104596013 original size:24 final size:24
Alignment explanation
Indices: 104595986--104596035 Score: 82
Period size: 24 Copynumber: 2.1 Consensus size: 24
104595976 AGTTTAGGAA
*
104595986 TTTTATAGCCCAAAATGCTTTATG
1 TTTTATAGCCCAAAATACTTTATG
*
104596010 TTTTATAGCTCAAAATACTTTATG
1 TTTTATAGCCCAAAATACTTTATG
104596034 TT
1 TT
104596036 CTAGTTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.30, C:0.14, G:0.10, T:0.46
Consensus pattern (24 bp):
TTTTATAGCCCAAAATACTTTATG
Found at i:104603568 original size:30 final size:30
Alignment explanation
Indices: 104603482--104603557 Score: 134
Period size: 30 Copynumber: 2.5 Consensus size: 30
104603472 CACGTCCATG
104603482 ACACATGGGCGTGTGGCCAGCCCGTGTGTC
1 ACACATGGGCGTGTGGCCAGCCCGTGTGTC
* *
104603512 ACACTTGGGCGTGTGGCCAGCCCGTGTTTC
1 ACACATGGGCGTGTGGCCAGCCCGTGTGTC
104603542 ACACATGGGCGTGTGG
1 ACACATGGGCGTGTGG
104603558 ATTACTCGTG
Statistics
Matches: 43, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
30 43 1.00
ACGTcount: A:0.13, C:0.28, G:0.37, T:0.22
Consensus pattern (30 bp):
ACACATGGGCGTGTGGCCAGCCCGTGTGTC
Found at i:104604348 original size:13 final size:13
Alignment explanation
Indices: 104604313--104604413 Score: 96
Period size: 13 Copynumber: 7.8 Consensus size: 13
104604303 GTTAAATTTG
104604313 TATATGAAATGAT
1 TATATGAAATGAT
* * * *
104604326 AAAATAAAATGTT
1 TATATGAAATGAT
*
104604339 TAGATGAAATG-T
1 TATATGAAATGAT
*
104604351 TATACGAAATGAT
1 TATATGAAATGAT
*
104604364 TATATGGAATGAT
1 TATATGAAATGAT
* *
104604377 TACATGAAATGCT
1 TATATGAAATGAT
*
104604390 TATATGAAATGGT
1 TATATGAAATGAT
104604403 TATATGGAAAT
1 TATAT-GAAAT
104604414 AGATGTATAA
Statistics
Matches: 70, Mismatches: 16, Indels: 3
0.79 0.18 0.03
Matches are distributed among these distances:
12 10 0.14
13 55 0.79
14 5 0.07
ACGTcount: A:0.45, C:0.03, G:0.18, T:0.35
Consensus pattern (13 bp):
TATATGAAATGAT
Found at i:104604406 original size:39 final size:38
Alignment explanation
Indices: 104604333--104604411 Score: 113
Period size: 39 Copynumber: 2.1 Consensus size: 38
104604323 GATAAAATAA
* *
104604333 AATGTTTAGATGAAATGTTATACGAAATGATTATATGG
1 AATGATTACATGAAATGTTATACGAAATGATTATATGG
* *
104604371 AATGATTACATGAAATGCTTATATGAAATGGTTATATGG
1 AATGATTACATGAAATG-TTATACGAAATGATTATATGG
104604410 AA
1 AA
104604412 ATAGATGTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
38 15 0.42
39 21 0.58
ACGTcount: A:0.41, C:0.04, G:0.20, T:0.35
Consensus pattern (38 bp):
AATGATTACATGAAATGTTATACGAAATGATTATATGG
Found at i:104605431 original size:38 final size:37
Alignment explanation
Indices: 104605344--104605538 Score: 201
Period size: 38 Copynumber: 5.0 Consensus size: 37
104605334 AAACCCAAAC
* * * * *
104605344 ATAACACCAGCACGAAGCCTACGGGACTTTAAACTCAGAT
1 ATAATACCAGCA-TAAGCCTGCGGGA-TTT-AACCCGGAT
*
104605384 ATAATACCAGCACTAGGCCTGCGGGATTTAACCCGGAT
1 ATAATACCAGCA-TAAGCCTGCGGGATTTAACCCGGAT
**
104605422 ATAATACCAGCATGAAGCCTGCAAGATTTAACCCGGAT
1 ATAATACCAGCAT-AAGCCTGCGGGATTTAACCCGGAT
* *
104605460 ATATTACCAGCATGAAGCCCGCGGGATTTAACCCGGAT
1 ATAATACCAGCAT-AAGCCTGCGGGATTTAACCCGGAT
* *
104605498 ATAATTCCAGCATATAGCCTGCGGGTCTTTAAGCCCGGAT
1 ATAATACCAGCATA-AGCCTGCGGG-ATTTAA-CCCGGAT
104605538 A
1 A
104605539 CACATCAAAT
Statistics
Matches: 134, Mismatches: 17, Indels: 8
0.84 0.11 0.05
Matches are distributed among these distances:
37 2 0.01
38 94 0.70
39 8 0.06
40 30 0.22
ACGTcount: A:0.32, C:0.26, G:0.21, T:0.22
Consensus pattern (37 bp):
ATAATACCAGCATAAGCCTGCGGGATTTAACCCGGAT
Found at i:104617515 original size:2 final size:2
Alignment explanation
Indices: 104617508--104617534 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
104617498 CATCATCTTC
104617508 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
104617535 GTTCTTTTGC
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:104619297 original size:10 final size:10
Alignment explanation
Indices: 104619282--104619313 Score: 57
Period size: 10 Copynumber: 3.3 Consensus size: 10
104619272 TAAATACATT
104619282 TAATTAAAGA
1 TAATTAAAGA
104619292 TAATTAAAGA
1 TAATTAAAGA
104619302 TAATTAAA-A
1 TAATTAAAGA
104619311 TAA
1 TAA
104619314 AATCCTAAAA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.18
10 18 0.82
ACGTcount: A:0.62, C:0.00, G:0.06, T:0.31
Consensus pattern (10 bp):
TAATTAAAGA
Found at i:104632673 original size:108 final size:110
Alignment explanation
Indices: 104632455--104632726 Score: 279
Period size: 108 Copynumber: 2.5 Consensus size: 110
104632445 TTGCTAACTA
* * * * *
104632455 GACTGACAA-ATCACGATATGAAGATATGCGTAAGTCTATGTGGTAGAGACCCATGACATTATAT
1 GACTGA-AAGATCACAACATGAAGAGATGTGTAAGTCTATGTGGTAGAGACCCATGACATAATAT
*
104632519 GACAATGAAAACACTCATGCTATTGCCTCCAGTGAGATGAAGACTG
65 GACAATGAAAACACTCATGCTATTGCCTCCAGTAAGATGAAGACTG
* * *
104632565 GACT-AGCAGATCACAACAT-AAG-GATGTGTAAGTCTATGTGGTTGAGACCCATGGCATAATAT
1 GACTGA-AAGATCACAACATGAAGAGATGTGTAAGTCTATGTGGTAGAGACCCATGACATAATAT
* * * * *
104632627 GATAAT-AAGAATACTCATGGTGA-TGCCTTCAGTAATATGTAA-ACTG
65 GACAATGAA-AACACTCATGCT-ATTGCCTCCAGTAAGATG-AAGACTG
* * * * *
104632673 GACTGAAAGATCACGACATGAAGATATGTGTAAGTCTATGAGGGAGAAACCCAT
1 GACTGAAAGATCACAACATGAAGAGATGTGTAAGTCTATGTGGTAGAGACCCAT
104632727 AGCACCTACT
Statistics
Matches: 133, Mismatches: 22, Indels: 14
0.79 0.13 0.08
Matches are distributed among these distances:
107 2 0.02
108 82 0.62
109 12 0.09
110 37 0.28
ACGTcount: A:0.36, C:0.16, G:0.23, T:0.25
Consensus pattern (110 bp):
GACTGAAAGATCACAACATGAAGAGATGTGTAAGTCTATGTGGTAGAGACCCATGACATAATATG
ACAATGAAAACACTCATGCTATTGCCTCCAGTAAGATGAAGACTG
Found at i:104632800 original size:59 final size:59
Alignment explanation
Indices: 104632735--104632899 Score: 213
Period size: 59 Copynumber: 2.8 Consensus size: 59
104632725 ATAGCACCTA
* * *
104632735 CTATGAAAGTCCGTTGGGACTGTAAACACATCATTCTGTGTGTTGCCCCATAACAACTT
1 CTATGAAAGTCCGTTGGGACAGTAAACACATGATTTTGTGTGTTGCCCCATAACAACTT
* * * *
104632794 CTATGAAAGTCTGTCGGGACAGTAAACACATGATTTTGTGTGTTGCCCCATGACACCTT
1 CTATGAAAGTCCGTTGGGACAGTAAACACATGATTTTGTGTGTTGCCCCATAACAACTT
* * * * * *
104632853 TTGTGAAAGTCCGCTGGGACAATAAACTCGTGATTTTGTGTGTTGCC
1 CTATGAAAGTCCGTTGGGACAGTAAACACATGATTTTGTGTGTTGCC
104632900 TATATGGCGT
Statistics
Matches: 91, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
59 91 1.00
ACGTcount: A:0.25, C:0.21, G:0.22, T:0.32
Consensus pattern (59 bp):
CTATGAAAGTCCGTTGGGACAGTAAACACATGATTTTGTGTGTTGCCCCATAACAACTT
Found at i:104633690 original size:2 final size:2
Alignment explanation
Indices: 104633683--104633722 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
104633673 AGAGAAAAGA
104633683 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
104633723 CATCTAGTAA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:104637433 original size:14 final size:14
Alignment explanation
Indices: 104637414--104637457 Score: 52
Period size: 14 Copynumber: 3.0 Consensus size: 14
104637404 ATTGTTTAAT
104637414 AAATTTATTTTTTA
1 AAATTTATTTTTTA
104637428 AAATTTAATTTTATTA
1 AAATTT-ATTTT-TTA
* *
104637444 ATATTTATATTTTA
1 AAATTTATTTTTTA
104637458 TTTTATCTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
14 9 0.35
15 9 0.35
16 8 0.31
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (14 bp):
AAATTTATTTTTTA
Found at i:104637470 original size:17 final size:17
Alignment explanation
Indices: 104637419--104637459 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
104637409 TTAATAAATT
*
104637419 TATTTT-TTAAAATTTA
1 TATTTTATTAATATTTA
104637435 -ATTTTATTAATATTTA
1 TATTTTATTAATATTTA
104637451 TATTTTATT
1 TATTTTATT
104637460 TTATCTTATA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
15 5 0.23
16 9 0.41
17 8 0.36
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTTTATTAATATTTA
Found at i:104638035 original size:9 final size:9
Alignment explanation
Indices: 104638009--104638130 Score: 68
Period size: 10 Copynumber: 12.7 Consensus size: 9
104637999 CTCTCTCAAC
*
104638009 AAAAATTATA
1 AAAAATT-TT
104638019 AAATAATTTT
1 AAA-AATTTT
104638029 AAAAATTTTT
1 AAAAA-TTTT
* *
104638039 AAAAAATTC
1 AAAAATTTT
104638048 AAATAATTTT
1 AAA-AATTTT
*
104638058 AAAAA-ATT
1 AAAAATTTT
104638066 AAAATATTTAT
1 AAAA-ATTT-T
*
104638077 AACAATTTT
1 AAAAATTTT
104638086 AAAAATATATAT
1 AAAAAT-T-T-T
*
104638098 AAAAAATTT
1 AAAAATTTT
*
104638107 -AAGATTTT
1 AAAAATTTT
*
104638115 TAAAATTTT
1 AAAAATTTT
104638124 CAAAAAT
1 -AAAAAT
104638131 AATAATTTTA
Statistics
Matches: 87, Mismatches: 14, Indels: 22
0.71 0.11 0.18
Matches are distributed among these distances:
8 12 0.14
9 24 0.28
10 35 0.40
11 10 0.11
12 6 0.07
ACGTcount: A:0.57, C:0.02, G:0.01, T:0.39
Consensus pattern (9 bp):
AAAAATTTT
Found at i:104638059 original size:19 final size:19
Alignment explanation
Indices: 104638035--104638071 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
104638025 TTTTAAAAAT
*
104638035 TTTTAAAAAATTCAAATAA
1 TTTTAAAAAATTAAAATAA
104638054 TTTTAAAAAATTAAAATA
1 TTTTAAAAAATTAAAATA
104638072 TTTATAACAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (19 bp):
TTTTAAAAAATTAAAATAA
Found at i:104638092 original size:40 final size:40
Alignment explanation
Indices: 104638015--104638134 Score: 108
Period size: 40 Copynumber: 3.0 Consensus size: 40
104638005 CAACAAAAAT
**
104638015 TATAAAATAATTTTAAAAATTTTTAAAAAATTC--AAATAAT-
1 TATAAAA-AA-TTT-AAAATTTTTAAAATTTTCAAAAATAATA
*
104638055 TTTAAAAAA-TTAAAATATTTATAACAATTTT-AAAAAT-ATA
1 TATAAAAAATTTAAAAT-TTT-TAA-AATTTTCAAAAATAATA
*
104638095 TATAAAAAATTTAAGATTTTTAAAATTTTCAAAAATAATA
1 TATAAAAAATTTAAAATTTTTAAAATTTTCAAAAATAATA
104638135 ATTTTAGAAC
Statistics
Matches: 66, Mismatches: 5, Indels: 18
0.74 0.06 0.20
Matches are distributed among these distances:
36 5 0.08
37 5 0.08
38 9 0.14
39 17 0.26
40 24 0.36
41 6 0.09
ACGTcount: A:0.57, C:0.03, G:0.01, T:0.40
Consensus pattern (40 bp):
TATAAAAAATTTAAAATTTTTAAAATTTTCAAAAATAATA
Found at i:104638480 original size:13 final size:13
Alignment explanation
Indices: 104638462--104638486 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
104638452 AGATGGTGCA
104638462 TATATGAAATATG
1 TATATGAAATATG
104638475 TATATGAAATAT
1 TATATGAAATAT
104638487 AAATGAGGAG
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:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (13 bp):
TATATGAAATATG
Found at i:104641613 original size:13 final size:14
Alignment explanation
Indices: 104641595--104641624 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
104641585 TTATTCATCG
104641595 ATCTCTTCCTC-AA
1 ATCTCTTCCTCGAA
104641608 ATCTCTTCCTCGAA
1 ATCTCTTCCTCGAA
104641622 ATC
1 ATC
104641625 AGCCTTTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.69
14 5 0.31
ACGTcount: A:0.23, C:0.37, G:0.03, T:0.37
Consensus pattern (14 bp):
ATCTCTTCCTCGAA
Found at i:104645398 original size:50 final size:50
Alignment explanation
Indices: 104645316--104645553 Score: 354
Period size: 50 Copynumber: 4.8 Consensus size: 50
104645306 GGGCGGTTAC
*
104645316 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTTGAGAT
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGAT
* * * *
104645366 ATGGGAGCTAGTGTAAGACCATGTCTGAGACATGGCATCGGTCTTGAGAT
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGAT
* *
104645416 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCAC-CGATAG
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGC-CTCGAGAT
* *
104645466 ATGAGAGCCAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGATAT
1 ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGAT
*
104645516 ACGAGAG-TCAGTGTAAGACCATGTCTGGGACATGGCAT
1 ATGAGAGCT-AGTGTAAGACCATGTCTGGGACATGGCAT
104645554 TGACTTTGAT
Statistics
Matches: 172, Mismatches: 13, Indels: 6
0.90 0.07 0.03
Matches are distributed among these distances:
49 1 0.01
50 170 0.99
51 1 0.01
ACGTcount: A:0.27, C:0.19, G:0.32, T:0.23
Consensus pattern (50 bp):
ATGAGAGCTAGTGTAAGACCATGTCTGGGACATGGCATCGGCCTCGAGAT
Found at i:104648250 original size:12 final size:12
Alignment explanation
Indices: 104648235--104648259 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
104648225 CATATCAAGT
104648235 TACATGTTCATA
1 TACATGTTCATA
104648247 TACATGTTCATA
1 TACATGTTCATA
104648259 T
1 T
104648260 TGCCATTTCC
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:0.16, G:0.08, T:0.44
Consensus pattern (12 bp):
TACATGTTCATA
Found at i:104649459 original size:17 final size:17
Alignment explanation
Indices: 104649433--104649466 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
104649423 TCAAAACAAC
*
104649433 ATAATAAACATTCAAAT
1 ATAATAAACATTAAAAT
*
104649450 ATAATTAACATTAAAAT
1 ATAATAAACATTAAAAT
104649467 GATTACGATT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.59, C:0.09, G:0.00, T:0.32
Consensus pattern (17 bp):
ATAATAAACATTAAAAT
Found at i:104657463 original size:39 final size:40
Alignment explanation
Indices: 104657409--104657500 Score: 132
Period size: 39 Copynumber: 2.3 Consensus size: 40
104657399 TGTTTGAATG
**
104657409 AAAAACGCCACTAAAGAATGAGCATTAGCGGCGC-TTTTT
1 AAAAACGCTGCTAAAGAATGAGCATTAGCGGCGCTTTTTT
* *
104657448 AAAAACGCTGCTAAAGATTGAGTATTAGCGGCGCTTTTTT
1 AAAAACGCTGCTAAAGAATGAGCATTAGCGGCGCTTTTTT
*
104657488 AAAAATGCTGCTA
1 AAAAACGCTGCTA
104657501 TATGTAGACC
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
39 30 0.64
40 17 0.36
ACGTcount: A:0.35, C:0.17, G:0.21, T:0.27
Consensus pattern (40 bp):
AAAAACGCTGCTAAAGAATGAGCATTAGCGGCGCTTTTTT
Found at i:104658062 original size:14 final size:14
Alignment explanation
Indices: 104658017--104658062 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
104658007 GGGTTAAGGG
*
104658017 TTTATGGTTCAGGA
1 TTTATGGTTTAGGA
* *
104658031 TTTATGTTTTAAGA
1 TTTATGGTTTAGGA
*
104658045 TTTATGGTTTAGGG
1 TTTATGGTTTAGGA
104658059 TTTA
1 TTTA
104658063 GAGATTAAAG
Statistics
Matches: 26, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 26 1.00
ACGTcount: A:0.22, C:0.02, G:0.24, T:0.52
Consensus pattern (14 bp):
TTTATGGTTTAGGA
Found at i:104658062 original size:21 final size:21
Alignment explanation
Indices: 104658038--104658087 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
104658028 GGATTTATGT
**
104658038 TTTAAGATTTATGGTTTAGGG
1 TTTAAGATTTAAAGTTTAGGG
104658059 TTTAGAGA-TTAAAGTTTAGGG
1 TTTA-AGATTTAAAGTTTAGGG
104658080 TTT-AGATT
1 TTTAAGATT
104658088 AATTAGTGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 5
0.78 0.06 0.16
Matches are distributed among these distances:
19 3 0.12
20 1 0.04
21 18 0.72
22 3 0.12
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.46
Consensus pattern (21 bp):
TTTAAGATTTAAAGTTTAGGG
Found at i:104658320 original size:29 final size:29
Alignment explanation
Indices: 104658282--104658369 Score: 72
Period size: 29 Copynumber: 3.1 Consensus size: 29
104658272 GGGTTGTGAT
104658282 TTAAG-GTTTAAGGGTTAGGGGTTTAGGG
1 TTAAGAGTTTAAGGGTTAGGGGTTTAGGG
* * ** **
104658310 TTAATAGTTTATGTTTTAGGATTTTAGGG
1 TTAAGAGTTTAAGGGTTAGGGGTTTAGGG
* * *
104658339 TTTAGAATTT-AGGGATTAGGGGTTTAAGG
1 TTAAGAGTTTAAGGG-TTAGGGGTTTAGGG
104658368 TT
1 TT
104658370 TAGATTAATT
Statistics
Matches: 43, Mismatches: 15, Indels: 3
0.70 0.25 0.05
Matches are distributed among these distances:
28 5 0.12
29 38 0.88
ACGTcount: A:0.24, C:0.00, G:0.33, T:0.43
Consensus pattern (29 bp):
TTAAGAGTTTAAGGGTTAGGGGTTTAGGG
Found at i:104658675 original size:19 final size:18
Alignment explanation
Indices: 104658648--104658696 Score: 62
Period size: 19 Copynumber: 2.7 Consensus size: 18
104658638 AAAAATATTG
*
104658648 ATAACAAATAAAAATAAA
1 ATAAAAAATAAAAATAAA
*
104658666 ATACAAAAATAAAAATGAA
1 ATA-AAAAATAAAAATAAA
*
104658685 ATATAAAATAAA
1 ATAAAAAATAAA
104658697 GATTAGTGGC
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
18 11 0.41
19 16 0.59
ACGTcount: A:0.76, C:0.04, G:0.02, T:0.18
Consensus pattern (18 bp):
ATAAAAAATAAAAATAAA
Found at i:104659259 original size:23 final size:23
Alignment explanation
Indices: 104659233--104659279 Score: 85
Period size: 23 Copynumber: 2.0 Consensus size: 23
104659223 TTGGTTGATA
*
104659233 TAATTTTCAGGTAGTTGTTTCTT
1 TAATTTTCAGGTAGTTGTTGCTT
104659256 TAATTTTCAGGTAGTTGTTGCTT
1 TAATTTTCAGGTAGTTGTTGCTT
104659279 T
1 T
104659280 TCTTTCTCTG
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.17, C:0.09, G:0.19, T:0.55
Consensus pattern (23 bp):
TAATTTTCAGGTAGTTGTTGCTT
Found at i:104663151 original size:9 final size:9
Alignment explanation
Indices: 104663133--104663163 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
104663123 TAACATGTTG
*
104663133 GTTTGTTTT
1 GTTTGATTT
104663142 GTTTGATTT
1 GTTTGATTT
104663151 GTTTGATTT
1 GTTTGATTT
104663160 GTTT
1 GTTT
104663164 CATTAAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 21 1.00
ACGTcount: A:0.06, C:0.00, G:0.23, T:0.71
Consensus pattern (9 bp):
GTTTGATTT
Found at i:104668358 original size:23 final size:23
Alignment explanation
Indices: 104668332--104668381 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
104668322 TGATTTTTAA
*
104668332 ATTTTA-ATTTATTTAGTGATAAT
1 ATTTTAGA-TTATTTAGTCATAAT
104668355 A-TTTAGGATTATTTAGTCATAAT
1 ATTTTA-GATTATTTAGTCATAAT
104668378 ATTT
1 ATTT
104668382 AGGAAAAATC
Statistics
Matches: 23, Mismatches: 1, Indels: 5
0.79 0.03 0.17
Matches are distributed among these distances:
22 4 0.17
23 16 0.70
24 3 0.13
ACGTcount: A:0.34, C:0.02, G:0.10, T:0.54
Consensus pattern (23 bp):
ATTTTAGATTATTTAGTCATAAT
Found at i:104668359 original size:13 final size:13
Alignment explanation
Indices: 104668341--104668383 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
104668331 AATTTTAATT
104668341 TATTTAGTGATAA
1 TATTTAGTGATAA
104668354 TATTTAG-GAT--
1 TATTTAGTGATAA
*
104668364 TATTTAGTCATAA
1 TATTTAGTGATAA
104668377 TATTTAG
1 TATTTAG
104668384 GAAAAATCTA
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
10 7 0.27
11 2 0.08
12 3 0.12
13 14 0.54
ACGTcount: A:0.35, C:0.02, G:0.14, T:0.49
Consensus pattern (13 bp):
TATTTAGTGATAA
Found at i:104668382 original size:23 final size:23
Alignment explanation
Indices: 104668340--104668385 Score: 83
Period size: 23 Copynumber: 2.0 Consensus size: 23
104668330 AAATTTTAAT
*
104668340 TTATTTAGTGATAATATTTAGGA
1 TTATTTAGTCATAATATTTAGGA
104668363 TTATTTAGTCATAATATTTAGGA
1 TTATTTAGTCATAATATTTAGGA
104668386 AAAATCTAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.35, C:0.02, G:0.15, T:0.48
Consensus pattern (23 bp):
TTATTTAGTCATAATATTTAGGA
Done.