Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01009613.1 Kokia drynarioides strain JFW-HI SEQ_124329, whole genome shotgun sequence
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: 123871
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:1209 original size:17 final size:17
Alignment explanation
Indices: 1184--1315 Score: 78
Period size: 17 Copynumber: 7.8 Consensus size: 17
1174 GACCTTTTAA
* **
1184 TTAAGTTTTAAATCCAT
1 TTAAATTTTAAATAAAT
*
1201 TTAAATTTTAATTAAAT
1 TTAAATTTTAAATAAAT
*
1218 TTAAA-TTTAAA-AGA-
1 TTAAATTTTAAATAAAT
1232 -TAAA-TTTAAATTTAAAT
1 TTAAATTTTAAA--TAAAT
***
1249 TTAAAAGATAAATTTAAAT
1 TTAAATTTTAAA--TAAAT
*
1268 TTAAATTTAAAATAAAT
1 TTAAATTTTAAATAAAT
*
1285 TTAAATTTAAAAGATAAAT
1 TTAAATTT-TAA-ATAAAT
1304 TTAAA-TTTAAAT
1 TTAAATTTTAAAT
1316 TTAAAATAAA
Statistics
Matches: 93, Mismatches: 14, Indels: 17
0.75 0.11 0.14
Matches are distributed among these distances:
13 10 0.11
15 2 0.02
16 9 0.10
17 33 0.35
18 9 0.10
19 30 0.32
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.43
Consensus pattern (17 bp):
TTAAATTTTAAATAAAT
Found at i:1213 original size:6 final size:6
Alignment explanation
Indices: 1199--1337 Score: 149
Period size: 6 Copynumber: 23.2 Consensus size: 6
1189 TTTTAAATCC
* **
1199 ATTTAA ATTTTA A-TTAA ATTTAA ATTTAAA AGATAA ATTTAA ATTTAA
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA ATTTAA ATTTAA ATTTAA
** *
1247 ATTTAAA AGATAA ATTTAA ATTTAA ATTTAA A-ATAA ATTTAA ATTTAAA
1 ATTT-AA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTT-AA
** *
1296 AGATAA ATTTAA ATTTAA ATTTAA A-ATAA ATTTAA ATTTAA A
1 ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA ATTTAA A
1338 AATAAATTTG
Statistics
Matches: 109, Mismatches: 18, Indels: 12
0.78 0.13 0.09
Matches are distributed among these distances:
5 12 0.11
6 85 0.78
7 12 0.11
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.42
Consensus pattern (6 bp):
ATTTAA
Found at i:1243 original size:25 final size:25
Alignment explanation
Indices: 1212--1337 Score: 182
Period size: 25 Copynumber: 5.4 Consensus size: 25
1202 TAAATTTTAA
1212 TTAAATTTAAATTTAAAAGATAAAT
1 TTAAATTTAAATTTAAAAGATAAAT
1237 TTAAATTTAAATTTAAAAGATAAAT
1 TTAAATTTAAATTTAAAAGATAAAT
1262 TTAAATTTAAATTT-----A-AAA-
1 TTAAATTTAAATTTAAAAGATAAAT
1280 -TAAATTTAAATTTAAAAGATAAAT
1 TTAAATTTAAATTTAAAAGATAAAT
1304 TTAAATTTAAATTT-AAA-ATAAAT
1 TTAAATTTAAATTTAAAAGATAAAT
1327 TTAAATTTAAA
1 TTAAATTTAAA
1338 AATAAATTTG
Statistics
Matches: 93, Mismatches: 0, Indels: 18
0.84 0.00 0.16
Matches are distributed among these distances:
17 13 0.14
19 3 0.03
20 1 0.01
22 1 0.01
23 20 0.22
24 3 0.03
25 52 0.56
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (25 bp):
TTAAATTTAAATTTAAAAGATAAAT
Found at i:1272 original size:67 final size:65
Alignment explanation
Indices: 1199--1337 Score: 242
Period size: 67 Copynumber: 2.1 Consensus size: 65
1189 TTTTAAATCC
* *
1199 ATTTAAATTTTAATTAAATTTAAATTTAAAAGATAAATTTAAATTTAAATTTAAAAGATAAATTT
1 ATTTAAATTTAAAATAAATTTAAATTTAAAAGATAAATTTAAATTTAAATTT-AAA-ATAAATTT
1264 AA
64 AA
1266 ATTTAAATTTAAAATAAATTTAAATTTAAAAGATAAATTTAAATTTAAATTTAAAATAAATTTAA
1 ATTTAAATTTAAAATAAATTTAAATTTAAAAGATAAATTTAAATTTAAATTTAAAATAAATTTAA
1331 ATTTAAA
1 ATTTAAA
1338 AATAAATTTG
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
65 17 0.24
66 3 0.04
67 50 0.71
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.42
Consensus pattern (65 bp):
ATTTAAATTTAAAATAAATTTAAATTTAAAAGATAAATTTAAATTTAAATTTAAAATAAATTTAA
Found at i:2091 original size:51 final size:51
Alignment explanation
Indices: 2015--2119 Score: 192
Period size: 51 Copynumber: 2.1 Consensus size: 51
2005 GTGTAAAATG
*
2015 TATCTTAACAAAATTTAGAATATGTAAACATCTAATTTTTATTTGAGGTTT
1 TATCTTAACAAAAGTTAGAATATGTAAACATCTAATTTTTATTTGAGGTTT
*
2066 TATCTTAACAAAAGTTAGAATATGTAAACATCTAATTTTTCTTTGAGGTTT
1 TATCTTAACAAAAGTTAGAATATGTAAACATCTAATTTTTATTTGAGGTTT
2117 TAT
1 TAT
2120 GTTGTATGGT
Statistics
Matches: 52, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.36, C:0.09, G:0.10, T:0.45
Consensus pattern (51 bp):
TATCTTAACAAAAGTTAGAATATGTAAACATCTAATTTTTATTTGAGGTTT
Found at i:2547 original size:42 final size:41
Alignment explanation
Indices: 2473--2555 Score: 98
Period size: 42 Copynumber: 2.0 Consensus size: 41
2463 TATATTTTTA
* *
2473 TTTAATTTAGAGTTTTTTTAAGAAGAGAAAATTGATTTTTGG
1 TTTAAGTTAGAGTTTTTTTAAGAAGAGAAAATT-ATATTTGG
*
2515 TTTAAGTTATGAGTTTTGTTTAAGAA-TG-AAATTATATTTGG
1 TTTAAGTTA-GAGTTTT-TTTAAGAAGAGAAAATTATATTTGG
2556 GTAAGATAAA
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
41 7 0.19
42 13 0.36
43 8 0.22
44 8 0.22
ACGTcount: A:0.33, C:0.00, G:0.19, T:0.48
Consensus pattern (41 bp):
TTTAAGTTAGAGTTTTTTTAAGAAGAGAAAATTATATTTGG
Found at i:2995 original size:17 final size:17
Alignment explanation
Indices: 2972--3015 Score: 63
Period size: 17 Copynumber: 2.6 Consensus size: 17
2962 CCGGGCCCTT
2972 TTTAAATTTATTTTAAGA
1 TTTAAATTTATTTTAA-A
*
2990 -TTAAATTTGTTTTAAA
1 TTTAAATTTATTTTAAA
3006 TTTAAATTTA
1 TTTAAATTTA
3016 AAATTATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
16 1 0.04
17 22 0.96
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.57
Consensus pattern (17 bp):
TTTAAATTTATTTTAAA
Found at i:3046 original size:23 final size:23
Alignment explanation
Indices: 3002--3046 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
2992 AAATTTGTTT
* *
3002 TAAATTTAAATTTAAAATTATTA
1 TAAATTTAAATTAAAAAATATTA
3025 TAAATTTAAA-TAAATAAATATT
1 TAAATTTAAATTAAA-AAATATT
3047 CAATTACAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 3 0.16
23 16 0.84
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (23 bp):
TAAATTTAAATTAAAAAATATTA
Found at i:3760 original size:3 final size:3
Alignment explanation
Indices: 3752--3851 Score: 80
Period size: 3 Copynumber: 33.3 Consensus size: 3
3742 GGTCATAAAT
* * * *
3752 TAA TAA TAA TAA -AA -AA TAA TAT TAA TAA TAAA TAA TAT TAG TAT
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
* * * *
3796 TAA TAT TAA TAA CAC TAAA TAA TAA T-A TAG TAA TTAA TAA TAA TAA
1 TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA TAA -TAA TAA TAA TAA
3842 TAA TAA TAA T
1 TAA TAA TAA T
3852 GAAAATAAAA
Statistics
Matches: 78, Mismatches: 14, Indels: 10
0.76 0.14 0.10
Matches are distributed among these distances:
2 6 0.08
3 64 0.82
4 8 0.10
ACGTcount: A:0.60, C:0.02, G:0.02, T:0.36
Consensus pattern (3 bp):
TAA
Found at i:3777 original size:16 final size:16
Alignment explanation
Indices: 3752--3791 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
3742 GGTCATAAAT
*
3752 TAATAATAATAAAAAA
1 TAATATTAATAAAAAA
*
3768 TAATATTAATAATAAA
1 TAATATTAATAAAAAA
3784 TAATATTA
1 TAATATTA
3792 GTATTAATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (16 bp):
TAATATTAATAAAAAA
Found at i:4903 original size:29 final size:27
Alignment explanation
Indices: 4840--5206 Score: 135
Period size: 29 Copynumber: 12.6 Consensus size: 27
4830 TTAAACTGTA
* *
4840 CAAAAATTATATTTAACCCCTAAACTTC
1 CAAAAATTACATTTTACCCCT-AACTTC
* *
4868 TCCAAAATTATATTTTGACCCCCTAACTTC
1 -CAAAAATTACATTTT-A-CCCCTAACTTC
* * *
4898 CAAAAAATACATTTTTACCCTCGAACTTT
1 CAAAAATTACA-TTTTACCC-CTAACTTC
** * * **
4927 CTGACATTACATATTTGACCCCGATTTTTC
1 CAAAAATTACAT-TTT-ACCCCTA-ACTTC
4957 CAAAAATTACCATTTTACCCCTAAACTTC
1 CAAAAATTA-CATTTTACCCCT-AACTTC
* * * *
4986 TAAAAATTCCATTTTTA-ACCTCAATTTTTC
1 CAAAAATTACA-TTTTACCCCT-AA--CTTC
5016 CAAAAATTATCATTTTACCCCTAAACTTC
1 CAAAAATTA-CATTTTACCCCT-AACTTC
* * * *
5045 CCAAAGTTCCATTTTACCCCCAAACTTCC
1 CAAAAATTACATTTTA-CCCCTAACTT-C
* * * * **
5074 CAAAAATTATATTTTTGATCTCGATTTTTC
1 CAAAAATTACA-TTTT-ACCCCTA-ACTTC
*
5104 CAAAAATTACCATTTTACCCCTAAAATTC
1 CAAAAATTA-CATTTTACCCCT-AACTTC
* * * * *
5133 CCAAAATTCCATTTTTA-ACCTCGATTTC
1 CAAAAATTACA-TTTTACCCCT-AACTTC
*
5161 TCTAAAAATTACCATTTTACCCTCGAACTTC
1 -C-AAAAATTA-CATTTTACCC-CTAACTTC
*
5192 CAAAAATTCCATTTT
1 CAAAAATTACATTTT
5207 TTATCTCGAT
Statistics
Matches: 249, Mismatches: 62, Indels: 55
0.68 0.17 0.15
Matches are distributed among these distances:
28 38 0.15
29 108 0.43
30 76 0.31
31 26 0.10
32 1 0.00
ACGTcount: A:0.34, C:0.27, G:0.03, T:0.37
Consensus pattern (27 bp):
CAAAAATTACATTTTACCCCTAACTTC
Found at i:4984 original size:59 final size:59
Alignment explanation
Indices: 4840--5043 Score: 161
Period size: 59 Copynumber: 3.5 Consensus size: 59
4830 TTAAACTGTA
* * * * * *
4840 CAAAAATTATATTTAACCCCTAAAC-TTCTCCAAAATTATAT-TTTGACCCCCTAA--CTTC
1 CAAAAATTACATTTTACCCCTAAACTTTCT-AAAAATTACATATTT-AACCCC-AATTTTTC
* * * * * *
4898 CAAAAAATACATTTTTA-CCCTCGAACTTTCT-GACATTACATATTTGACCCCGATTTTTC
1 CAAAAATTACA-TTTTACCCCT-AAACTTTCTAAAAATTACATATTTAACCCCAATTTTTC
* * *
4957 CAAAAATTACCATTTTACCCCTAAAC-TTCTAAAAATTCCATTTTTAACCTCAATTTTTC
1 CAAAAATTA-CATTTTACCCCTAAACTTTCTAAAAATTACATATTTAACCCCAATTTTTC
5016 CAAAAATTATCATTTTACCCCTAAACTT
1 CAAAAATTA-CATTTTACCCCTAAACTT
5044 CCCAAAGTTC
Statistics
Matches: 115, Mismatches: 21, Indels: 18
0.75 0.14 0.12
Matches are distributed among these distances:
57 1 0.01
58 28 0.24
59 75 0.65
60 11 0.10
ACGTcount: A:0.35, C:0.26, G:0.02, T:0.37
Consensus pattern (59 bp):
CAAAAATTACATTTTACCCCTAAACTTTCTAAAAATTACATATTTAACCCCAATTTTTC
Found at i:5036 original size:88 final size:89
Alignment explanation
Indices: 4939--5329 Score: 259
Period size: 88 Copynumber: 4.4 Consensus size: 89
4929 GACATTACAT
* **
4939 ATTTGACCCCGATTTTTCCAAAAATTACCATTTTACCCCTAAACTTCTAAAAATTCCATTTTTAA
1 ATTTTACCCCGAAATTTCCAAAAATTACCATTTTACCCCTAAACTTCTAAAAATTCCATTTTTAA
*
5004 CCTC-AATTTTTCCAAAAATTATC
66 CCTCAAATTTTTCCAAAAATTACC
* * * * * * ** *
5027 ATTTTACCCCTAAACTTCCCAAAGTT-CCATTTTACCCCCAAACTTCCCAAAAATTATATTTTTG
1 ATTTTACCCCGAAATTTCCAAAAATTACCATTTTACCCCTAAACTT-CTAAAAATTCCATTTTTA
* *
5091 ATCTC-GATTTTTCCAAAAATTACC
65 ACCTCAAATTTTTCCAAAAATTACC
* * * * * **
5115 ATTTTACCCCTAAAATTCCCAAAATT-CCATTTTTA-ACCTCGATTTCTCTAAAAATTACCA-TT
1 ATTTTACCCCGAAATTTCCAAAAATTACCA-TTTTACCCCT-AAACT-TCTAAAAATT-CCATTT
* * *
5177 TTACCCTCGAA--CTTCCAAAAATT-CC
62 TTAACCTCAAATTTTTCCAAAAATTACC
* * ** * * * * **
5202 ATTTTTTATCTCGATTTTTCTAAAAATTATCATTTTACCCC-GAACTTCTAGAAATTTTATTTTT
1 A--TTTTACCCCGAAATTTCCAAAAATTACCATTTTACCCCTAAACTTCTAAAAATTCCATTTTT
* *
5266 GACCTCAAACTTTTCC-AAAATTACC
64 AACCTCAAATTTTTCCAAAAATTACC
* * *
5291 ATTTTACCCTCG-AGTGTCC-AAAATTACCATTTTGCCCCT
1 ATTTTACCC-CGAAATTTCCAAAAATTACCATTTTACCCCT
5330 CGGTATACAA
Statistics
Matches: 230, Mismatches: 57, Indels: 33
0.72 0.18 0.10
Matches are distributed among these distances:
86 18 0.08
87 49 0.21
88 105 0.46
89 51 0.22
90 7 0.03
ACGTcount: A:0.31, C:0.26, G:0.04, T:0.39
Consensus pattern (89 bp):
ATTTTACCCCGAAATTTCCAAAAATTACCATTTTACCCCTAAACTTCTAAAAATTCCATTTTTAA
CCTCAAATTTTTCCAAAAATTACC
Found at i:5091 original size:147 final size:147
Alignment explanation
Indices: 4940--5206 Score: 410
Period size: 147 Copynumber: 1.8 Consensus size: 147
4930 ACATTACATA
* *
4940 TTTGACCCCGATTTTTCCAAAAATTACCATTTTACCCCTAAACTTCTAAAAATTCCATTTTTAAC
1 TTTGACCCCGATTTTTCCAAAAATTACCATTTTACCCCTAAAATTCCAAAAATTCCATTTTTAAC
* * * *
5005 CTCAATTTTTCCAAAAATTATCATTTTACCC-CTAAACTTCCCAAAGTTCCATTTTACCCCCAAA
66 CTCAATTTCTCCAAAAATTACCATTTTACCCTC-AAACTTCCAAAAATTCCATTTTACCCCCAAA
5069 CTTCCCAAAAATTATATT
130 CTTCCCAAAAATTATATT
* * *
5087 TTTGATCTCGATTTTTCCAAAAATTACCATTTTACCCCTAAAATTCCCAAAATTCCATTTTTAAC
1 TTTGACCCCGATTTTTCCAAAAATTACCATTTTACCCCTAAAATTCCAAAAATTCCATTTTTAAC
* * *
5152 CTCGATTTCTCTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATTCCATTTT
66 CTCAATTTCTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTT
5207 TTATCTCGAT
Statistics
Matches: 107, Mismatches: 12, Indels: 2
0.88 0.10 0.02
Matches are distributed among these distances:
147 106 0.99
148 1 0.01
ACGTcount: A:0.33, C:0.27, G:0.03, T:0.38
Consensus pattern (147 bp):
TTTGACCCCGATTTTTCCAAAAATTACCATTTTACCCCTAAAATTCCAAAAATTCCATTTTTAAC
CTCAATTTCTCCAAAAATTACCATTTTACCCTCAAACTTCCAAAAATTCCATTTTACCCCCAAAC
TTCCCAAAAATTATATT
Found at i:5107 original size:58 final size:58
Alignment explanation
Indices: 5045--5299 Score: 244
Period size: 59 Copynumber: 4.3 Consensus size: 58
5035 CCTAAACTTC
* ** *
5045 CCAAAGTT-CCATTTTACCCCCAAACTTCCCAAAAATTATATTTTTGATCTCGATTTTT
1 CCAAAATTACCATTTTACCCCCAAACTT-CCAAAAATTCCATTTTTGACCTCGATTTTT
* * * * *
5103 CCAAAAATTACCATTTTACCCCTAAAATTCCCAAAATTCCATTTTTAACCTCGATTTCT
1 CC-AAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCTCGATTTTT
* * * * *
5162 CTAAAAATTACCATTTTACCCTCGAACTTCCAAAAATTCCATTTTTTATCTCGATTTTT
1 C-CAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCTCGATTTTT
* * * * * ** * *
5221 CTAAAAATTATCATTTTA-CCCCGAACTTCTAGAAATTTTATTTTTGACCTCAAACTTTT
1 C-CAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCTC-GATTTTT
5280 CCAAAATTACCATTTTACCC
1 CCAAAATTACCATTTTACCC
5300 TCGAGTGTCC
Statistics
Matches: 162, Mismatches: 30, Indels: 9
0.81 0.15 0.04
Matches are distributed among these distances:
58 42 0.26
59 103 0.64
60 17 0.10
ACGTcount: A:0.32, C:0.25, G:0.04, T:0.39
Consensus pattern (58 bp):
CCAAAATTACCATTTTACCCCCAAACTTCCAAAAATTCCATTTTTGACCTCGATTTTT
Found at i:5137 original size:118 final size:118
Alignment explanation
Indices: 5053--5299 Score: 284
Period size: 118 Copynumber: 2.1 Consensus size: 118
5043 TCCCAAAGTT
*
5053 CCATTTTACCCCCAAACTTCCCAAAAATTATATTTTTGATCTCGATTTTTCCAAAAATTACCATT
1 CCATTTTACCCCCAAACTT-CCAAAAATTACATTTTTGATCTCGATTTTTCCAAAAATTACCATT
** *
5118 TTACCCCTAAAATTCCCAAAATTCCATTTTTAACCTCGATTTCTCTAAAAATTA
65 TTACCCCTAAAATTCCCAAAATTCCATTTTTAACCTAAACTTCTCTAAAAATTA
* * * * * *
5172 CCATTTTACCCTCGAACTTCCAAAAATTCCATTTTTTATCTCGATTTTTCTAAAAATTATCATTT
1 CCATTTTACCCCCAAACTTCCAAAAATTACATTTTTGATCTCGATTTTTCCAAAAATTACCATTT
* * * ** * * *
5237 TACCCC-GAACTT-CTAGAAATTTTATTTTTGACCTCAAACTTTTC-CAAAATTA
66 TACCCCTAAAATTCCCA-AAATTCCATTTTTAACCT-AAACTTCTCTAAAAATTA
5289 CCATTTTACCC
1 CCATTTTACCC
5300 TCGAGTGTCC
Statistics
Matches: 108, Mismatches: 18, Indels: 6
0.82 0.14 0.05
Matches are distributed among these distances:
116 2 0.02
117 37 0.34
118 52 0.48
119 17 0.16
ACGTcount: A:0.32, C:0.26, G:0.03, T:0.40
Consensus pattern (118 bp):
CCATTTTACCCCCAAACTTCCAAAAATTACATTTTTGATCTCGATTTTTCCAAAAATTACCATTT
TACCCCTAAAATTCCCAAAATTCCATTTTTAACCTAAACTTCTCTAAAAATTA
Found at i:5168 original size:59 final size:59
Alignment explanation
Indices: 5053--5242 Score: 247
Period size: 59 Copynumber: 3.2 Consensus size: 59
5043 TCCCAAAGTT
* ** * *
5053 CCATTTTACCCCCAAACTTCCCAAAAATTATATTTTTGATCTCGATTTTTCCAAAAATTA
1 CCATTTTACCCCTAAACTTCCC-AAAATTCCATTTTTAATCTCGATTTTTCTAAAAATTA
* * *
5113 CCATTTTACCCCTAAAATTCCCAAAATTCCATTTTTAACCTCGATTTCTCTAAAAATTA
1 CCATTTTACCCCTAAACTTCCCAAAATTCCATTTTTAATCTCGATTTTTCTAAAAATTA
* * *
5172 CCATTTTA-CCCTCGAACTTCCAAAAATTCCATTTTTTATCTCGATTTTTCTAAAAATTA
1 CCATTTTACCCCT-AAACTTCCCAAAATTCCATTTTTAATCTCGATTTTTCTAAAAATTA
*
5231 TCATTTTACCCC
1 CCATTTTACCCC
5243 GAACTTCTAG
Statistics
Matches: 113, Mismatches: 15, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
58 4 0.04
59 86 0.76
60 23 0.20
ACGTcount: A:0.32, C:0.26, G:0.03, T:0.39
Consensus pattern (59 bp):
CCATTTTACCCCTAAACTTCCCAAAATTCCATTTTTAATCTCGATTTTTCTAAAAATTA
Found at i:5227 original size:30 final size:30
Alignment explanation
Indices: 5135--5229 Score: 97
Period size: 30 Copynumber: 3.2 Consensus size: 30
5125 TAAAATTCCC
* *
5135 AAAATTCCATTTTTAACCTCGATTTCTCTA
1 AAAATTCCATTTTTTACCTCGATTTTTCTA
** *
5165 AAAATTACCA--TTTTACCCTCGA-ACTTCCA
1 AAAATT-CCATTTTTTA-CCTCGATTTTTCTA
*
5194 AAAATTCCATTTTTTATCTCGATTTTTCTA
1 AAAATTCCATTTTTTACCTCGATTTTTCTA
5224 AAAATT
1 AAAATT
5230 ATCATTTTAC
Statistics
Matches: 51, Mismatches: 9, Indels: 10
0.73 0.13 0.14
Matches are distributed among these distances:
28 3 0.06
29 18 0.35
30 27 0.53
31 3 0.06
ACGTcount: A:0.33, C:0.22, G:0.03, T:0.42
Consensus pattern (30 bp):
AAAATTCCATTTTTTACCTCGATTTTTCTA
Found at i:5237 original size:29 final size:30
Alignment explanation
Indices: 5093--5241 Score: 83
Period size: 29 Copynumber: 5.0 Consensus size: 30
5083 TATTTTTGAT
* *
5093 CTCGATTTTTCCAAAAATTACCATTTTACC
1 CTCGATTTTTCTAAAAATTATCATTTTACC
* *** ** * *
5123 C-CTAAAATTCCCAAAATT-CCATTTTTAAC
1 CTCGATTTTTCTAAAAATTATCA-TTTTACC
* *
5152 CTCGATTTCTCTAAAAATTACCATTTTACC
1 CTCGATTTTTCTAAAAATTATCATTTTACC
** * * *
5182 CTCGA-ACTTCCAAAAATTCCAT-TTTTTA-T
1 CTCGATTTTTCTAAAAATT--ATCATTTTACC
5211 CTCGATTTTTCTAAAAATTATCATTTTACC
1 CTCGATTTTTCTAAAAATTATCATTTTACC
5241 C
1 C
5242 CGAACTTCTA
Statistics
Matches: 85, Mismatches: 26, Indels: 16
0.67 0.20 0.13
Matches are distributed among these distances:
28 5 0.06
29 38 0.45
30 38 0.45
31 4 0.05
ACGTcount: A:0.32, C:0.26, G:0.03, T:0.40
Consensus pattern (30 bp):
CTCGATTTTTCTAAAAATTATCATTTTACC
Found at i:5321 original size:117 final size:119
Alignment explanation
Indices: 5053--5323 Score: 306
Period size: 117 Copynumber: 2.3 Consensus size: 119
5043 TCCCAAAGTT
* * *
5053 CCATTTTACCCCCAAACTTCCCAAAAATTA-TATTTTTGATCTCGATTTTTCCAAAAATTACCAT
1 CCATTTTACCCTCGAACTT-CCAAAAATTACCATTTTTGATCTCGATTTTTCCAAAAATTACCAT
*
5117 TTTACCCCTAAAATTCCCAAAATTCCATTTTTAACCTCGATTTCTCTAAAAATTA
65 TTTACCCCTAAAATTCCCAAAATTCCATTTTTAACCTCAATTTCTCTAAAAATTA
* * *
5172 CCATTTTACCCTCGAACTTCCAAAAATT-CCATTTTTTATCTCGATTTTTCTAAAAATTATCATT
1 CCATTTTACCCTCGAACTTCCAAAAATTACCATTTTTGATCTCGATTTTTCCAAAAATTACCATT
* * * ** * *
5236 TTACCCC-GAACTT-CTAGAAATTTTATTTTTGACCTCAAACTTT-TC-CAAAATTA
66 TTACCCCTAAAATTCCCA-AAATTCCATTTTTAACCTC-AA-TTTCTCTAAAAATTA
*
5289 CCATTTTACCCTCG-AGTGTCC-AAAATTACCATTTT
1 CCATTTTACCCTCGAACT-TCCAAAAATTACCATTTT
5324 GCCCCTCGGT
Statistics
Matches: 131, Mismatches: 15, Indels: 14
0.82 0.09 0.09
Matches are distributed among these distances:
116 10 0.08
117 51 0.39
118 50 0.38
119 20 0.15
ACGTcount: A:0.31, C:0.25, G:0.04, T:0.39
Consensus pattern (119 bp):
CCATTTTACCCTCGAACTTCCAAAAATTACCATTTTTGATCTCGATTTTTCCAAAAATTACCATT
TTACCCCTAAAATTCCCAAAATTCCATTTTTAACCTCAATTTCTCTAAAAATTA
Found at i:5340 original size:28 final size:28
Alignment explanation
Indices: 5281--5341 Score: 79
Period size: 28 Copynumber: 2.2 Consensus size: 28
5271 CAAACTTTTC
* *
5281 CAAAATTACCATTTTACCCTCGAGTGTC
1 CAAAATTACCATTTTACCCTCGAGTATA
*
5309 CAAAATTACCATTTTGCCCCTCG-GTATA
1 CAAAATTACCATTTT-ACCCTCGAGTATA
5337 CAAAA
1 CAAAA
5342 ATCACATTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 23 0.79
29 6 0.21
ACGTcount: A:0.33, C:0.28, G:0.10, T:0.30
Consensus pattern (28 bp):
CAAAATTACCATTTTACCCTCGAGTATA
Found at i:5342 original size:29 final size:28
Alignment explanation
Indices: 5282--5351 Score: 72
Period size: 28 Copynumber: 2.5 Consensus size: 28
5272 AAACTTTTCC
* *
5282 AAAATTACCATTTTACCCTCGAGTGTCC
1 AAAATTACCATTTTACCCTCGAGTATCA
*
5310 AAAATTACCATTTTGCCCCTCG-GTATACA
1 AAAATTACCATTTT-ACCCTCGAGTAT-CA
*
5339 AAAATCA-CATTTT
1 AAAATTACCATTTT
5352 CAAACCCCAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
28 23 0.64
29 13 0.36
ACGTcount: A:0.33, C:0.26, G:0.09, T:0.33
Consensus pattern (28 bp):
AAAATTACCATTTTACCCTCGAGTATCA
Found at i:6840 original size:24 final size:24
Alignment explanation
Indices: 6772--6842 Score: 97
Period size: 24 Copynumber: 3.0 Consensus size: 24
6762 ATAAATAATC
* * *
6772 TTTCAGTTAAACTTTGTTTAATTG
1 TTTCAATTAAACTATGTTTATTTG
* *
6796 TTTCAATTAAACTCTATTTATTTG
1 TTTCAATTAAACTATGTTTATTTG
6820 TTTCAATTAAACTATGTTTATTT
1 TTTCAATTAAACTATGTTTATTT
6843 ATTCGAGTCA
Statistics
Matches: 41, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 41 1.00
ACGTcount: A:0.28, C:0.10, G:0.07, T:0.55
Consensus pattern (24 bp):
TTTCAATTAAACTATGTTTATTTG
Found at i:8657 original size:12 final size:12
Alignment explanation
Indices: 8636--8674 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
8626 ATGTTTCTAA
8636 AAATGAAAATGG
1 AAATGAAAATGG
* *
8648 AAATGGAAATGA
1 AAATGAAAATGG
8660 AAAT-AAAATGG
1 AAATGAAAATGG
8671 AAAT
1 AAAT
8675 AATCCATTCG
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
11 9 0.39
12 14 0.61
ACGTcount: A:0.62, C:0.00, G:0.21, T:0.18
Consensus pattern (12 bp):
AAATGAAAATGG
Found at i:11223 original size:28 final size:27
Alignment explanation
Indices: 11159--11310 Score: 142
Period size: 28 Copynumber: 5.5 Consensus size: 27
11149 TGTTACTAAT
* * * *
11159 TTTTCATATTGTATAGTTTTACCACTA
1 TTTTCAGATTTTATAATTTTGCCACTA
* * *
11186 TTTTCAGATTTCAGATTTTTGCCACTA
1 TTTTCAGATTTTATAATTTTGCCACTA
*
11213 CTTTTCAGATTTTATAGTTTTGCCACTA
1 -TTTTCAGATTTTATAATTTTGCCACTA
* * *
11241 TGTTTTAGATTTTATACTTTTGCCACTGC
1 T-TTTCAGATTTTATAATTTTGCCACT-A
* *
11270 TTTTCAAATTTTACAATTTTGCCACTA
1 TTTTCAGATTTTATAATTTTGCCACTA
*
11297 GTTTTCAAATTTTA
1 -TTTTCAGATTTTA
11311 CAGTTCAGCC
Statistics
Matches: 104, Mismatches: 17, Indels: 7
0.81 0.13 0.05
Matches are distributed among these distances:
27 22 0.21
28 81 0.78
29 1 0.01
ACGTcount: A:0.24, C:0.16, G:0.09, T:0.51
Consensus pattern (27 bp):
TTTTCAGATTTTATAATTTTGCCACTA
Found at i:11229 original size:55 final size:55
Alignment explanation
Indices: 11159--11308 Score: 174
Period size: 56 Copynumber: 2.7 Consensus size: 55
11149 TGTTACTAAT
* * * *
11159 TTTTCATATTGTATAGTTTTACCACTATTTTCAGATTTCAGATTTTTGCCACTAC
1 TTTTCAAATTTTATAGTTTTGCCACTATTTTCAGATTTCAGACTTTTGCCACTAC
* * * * *
11214 TTTTCAGATTTTATAGTTTTGCCACTATGTTTTAGATTTTATACTTTTGCCACTGC
1 TTTTCAAATTTTATAGTTTTGCCACTAT-TTTCAGATTTCAGACTTTTGCCACTAC
* * *
11270 TTTTCAAATTTTACAATTTTGCCACTAGTTTTCAAATTT
1 TTTTCAAATTTTATAGTTTTGCCACTA-TTTTCAGATTT
11309 TACAGTTCAG
Statistics
Matches: 80, Mismatches: 13, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
55 25 0.31
56 54 0.68
57 1 0.01
ACGTcount: A:0.23, C:0.17, G:0.09, T:0.51
Consensus pattern (55 bp):
TTTTCAAATTTTATAGTTTTGCCACTATTTTCAGATTTCAGACTTTTGCCACTAC
Found at i:11311 original size:28 final size:28
Alignment explanation
Indices: 11175--11345 Score: 132
Period size: 28 Copynumber: 6.1 Consensus size: 28
11165 TATTGTATAG
* * * * *
11175 TTTTACCACTA-TTTTCAGATTTCAGAT
1 TTTTGCCACTAGTTTTCAAATTTTACAA
* * * *
11202 TTTTGCCACTACTTTTCAGATTTTATAG
1 TTTTGCCACTAGTTTTCAAATTTTACAA
* * *
11230 TTTTGCCACTATGTTTT-AGATTTTATAC
1 TTTTGCCACTA-GTTTTCAAATTTTACAA
11258 TTTTGCCACT-GCTTTTCAAATTTTACAA
1 TTTTGCCACTAG-TTTTCAAATTTTACAA
*
11286 TTTTGCCACTAGTTTTCAAATTTTACAG
1 TTTTGCCACTAGTTTTCAAATTTTACAA
** * * * *
11314 TTCAGCCATTAATTATCAAAATTTACAA
1 TTTTGCCACTAGTTTTCAAATTTTACAA
11342 TTTT
1 TTTT
11346 TTCCCAAAAT
Statistics
Matches: 120, Mismatches: 19, Indels: 9
0.81 0.13 0.06
Matches are distributed among these distances:
26 1 0.01
27 14 0.12
28 100 0.83
29 5 0.04
ACGTcount: A:0.26, C:0.18, G:0.08, T:0.48
Consensus pattern (28 bp):
TTTTGCCACTAGTTTTCAAATTTTACAA
Found at i:12474 original size:2 final size:2
Alignment explanation
Indices: 12469--12500 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
12459 ATTTTGATTA
12469 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
12501 TTAAAAAATA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12798 original size:30 final size:30
Alignment explanation
Indices: 12762--12825 Score: 85
Period size: 30 Copynumber: 2.1 Consensus size: 30
12752 AAAAAATTTG
12762 GGGGCCAAAACAT-AATTTTTGGAAAGTTTA
1 GGGGCC-AAACATGAATTTTTGGAAAGTTTA
** *
12792 GGGGCCAAATTTGAATTTTTGGAAAGTTTG
1 GGGGCCAAACATGAATTTTTGGAAAGTTTA
12822 GGGG
1 GGGG
12826 TTAAAAATGG
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
29 4 0.13
30 26 0.87
ACGTcount: A:0.30, C:0.08, G:0.31, T:0.31
Consensus pattern (30 bp):
GGGGCCAAACATGAATTTTTGGAAAGTTTA
Found at i:14169 original size:17 final size:17
Alignment explanation
Indices: 14144--14181 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
14134 TTTTGGATAT
14144 TTTTAAATTAAAAACAAA
1 TTTTAAATTAAAAA-AAA
*
14162 TTTT-AATTTAAAAAAA
1 TTTTAAATTAAAAAAAA
14178 TTTT
1 TTTT
14182 TGGGTTGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
16 7 0.37
17 8 0.42
18 4 0.21
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (17 bp):
TTTTAAATTAAAAAAAA
Found at i:14182 original size:17 final size:18
Alignment explanation
Indices: 14142--14182 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
14132 AATTTTGGAT
14142 ATTTTTAAATTAAAAACA
1 ATTTTTAAATTAAAAACA
* *
14160 AATTTTAATTTAAAAA-A
1 ATTTTTAAATTAAAAACA
14177 ATTTTT
1 ATTTTT
14183 GGGTTGTTTT
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
17 6 0.30
18 14 0.70
ACGTcount: A:0.51, C:0.02, G:0.00, T:0.46
Consensus pattern (18 bp):
ATTTTTAAATTAAAAACA
Found at i:14649 original size:48 final size:48
Alignment explanation
Indices: 14557--14650 Score: 154
Period size: 48 Copynumber: 2.0 Consensus size: 48
14547 TATTGAGCTC
* *
14557 CGCTTCATTGTTTTGGTCCACTTCTCTGTATCTCATAAGGAAGATGAT
1 CGCTTCATTGTTTTGATCCACTTCTCTGTATCTCATAAGAAAGATGAT
14605 CGCTTCATTGTTTTGATCCACTTCTCTGTATCTCATCAA-AAAGATG
1 CGCTTCATTGTTTTGATCCACTTCTCTGTATCTCAT-AAGAAAGATG
14651 GGGTTTGAAG
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
48 41 0.95
49 2 0.05
ACGTcount: A:0.22, C:0.22, G:0.16, T:0.39
Consensus pattern (48 bp):
CGCTTCATTGTTTTGATCCACTTCTCTGTATCTCATAAGAAAGATGAT
Found at i:14732 original size:123 final size:123
Alignment explanation
Indices: 14491--15142 Score: 1011
Period size: 123 Copynumber: 5.3 Consensus size: 123
14481 CAGCTTAATC
* * * *
14491 TTTTGGTCCACTTCTCTGTATCACATCAGGAAGATGGGGTTTGAAGTTCCACTCCCTATTGAGCT
1 TTTTGATCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCAC-ATTGAGCT
* *
14556 CCGCTTCATTGTTTTGGTCCACTTCTCTGTATCTCAT-AAGGAAGATGATCGCTTCATTG
65 TCGCTTCATTGTTTTGGTCCACTTCTCTGTATCTCATCAA-GAAGATGACCGCTTCATTG
**
14615 TTTTGATCCACTTCTCTGTATCTCATCAAAAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTT
1 TTTTGATCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTT
* * * * *
14680 CGCTTCATTATTTTGGTTCACTTCTCTGTATCTCATCAGGAATATGACCGCTTAATTG
66 CGCTTCATTGTTTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTG
* *
14738 TTTTAATCCACTGCTCTGTATC-CTATCAGGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCT
1 TTTTGATCCACTTCTCTGTATCTC-ATCAGGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCT
*
14802 TCGCTTCATTGTTTTGGTCCACTTCTTTGTATCTCATCAAGAAGATGACCGCTTCATTG
65 TCGCTTCATTGTTTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTG
*
14861 TTTTGATCCACTTCTCTATATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTT
1 TTTTGATCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTT
**
14926 CGCTTCATTGTTTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACTACTTCATTG
66 CGCTTCATTGTTTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTG
* * *
14984 TTTTGATCCACTTCTCTGTATCTAATCAGGAAGATGGGGTTTTAAGTTTCACTCACATTGAACTT
1 TTTTGATCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTT
* *
15049 TGCTTCATTGTTTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACCTCTTCATTG
66 CGCTTCATTGTTTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTG
* * * *
15107 TTTTTATCCACTTCTTTGTATCTCATTAAGAAGATG
1 TTTTGATCCACTTCTCTGTATCTCATCAGGAAGATG
15143 ATCGCTTCAT
Statistics
Matches: 484, Mismatches: 41, Indels: 7
0.91 0.08 0.01
Matches are distributed among these distances:
122 1 0.00
123 431 0.89
124 52 0.11
ACGTcount: A:0.22, C:0.22, G:0.17, T:0.39
Consensus pattern (123 bp):
TTTTGATCCACTTCTCTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTT
CGCTTCATTGTTTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACCGCTTCATTG
Found at i:14874 original size:48 final size:48
Alignment explanation
Indices: 14803--14896 Score: 152
Period size: 48 Copynumber: 2.0 Consensus size: 48
14793 CATTGAGCTT
* * *
14803 CGCTTCATTGTTTTGGTCCACTTCTTTGTATCTCATCAAGAAGATGAC
1 CGCTTCATTGTTTTGATCCACTTCTCTATATCTCATCAAGAAGATGAC
*
14851 CGCTTCATTGTTTTGATCCACTTCTCTATATCTCATCAGGAAGATG
1 CGCTTCATTGTTTTGATCCACTTCTCTATATCTCATCAAGAAGATG
14897 GGGTTTGAAG
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.21, C:0.23, G:0.16, T:0.39
Consensus pattern (48 bp):
CGCTTCATTGTTTTGATCCACTTCTCTATATCTCATCAAGAAGATGAC
Found at i:14999 original size:48 final size:48
Alignment explanation
Indices: 14928--15019 Score: 157
Period size: 48 Copynumber: 1.9 Consensus size: 48
14918 TTGAGCTTCG
* *
14928 CTTCATTGTTTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACTA
1 CTTCATTGTTTTGATCCACTTCTCTGTATCTAATCAAGAAGATGACTA
*
14976 CTTCATTGTTTTGATCCACTTCTCTGTATCTAATCAGGAAGATG
1 CTTCATTGTTTTGATCCACTTCTCTGTATCTAATCAAGAAGATG
15020 GGGTTTTAAG
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.23, C:0.22, G:0.15, T:0.40
Consensus pattern (48 bp):
CTTCATTGTTTTGATCCACTTCTCTGTATCTAATCAAGAAGATGACTA
Found at i:15189 original size:48 final size:48
Alignment explanation
Indices: 15050--15179 Score: 188
Period size: 48 Copynumber: 2.7 Consensus size: 48
15040 ATTGAACTTT
* *
15050 GCTTCATTGTTTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACC
1 GCTTCATTGTTTTGATCCACTTCTATGTATCTCATCAAGAAGATGACC
* * * * *
15098 TCTTCATTGTTTTTATCCACTTCTTTGTATCTCATTAAGAAGATGATC
1 GCTTCATTGTTTTGATCCACTTCTATGTATCTCATCAAGAAGATGACC
*
15146 GCTTCATTGTTTTGATCTACTTCTATGTATCTCA
1 GCTTCATTGTTTTGATCCACTTCTATGTATCTCA
15180 ACGGGAAGAT
Statistics
Matches: 72, Mismatches: 10, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
48 72 1.00
ACGTcount: A:0.21, C:0.22, G:0.13, T:0.45
Consensus pattern (48 bp):
GCTTCATTGTTTTGATCCACTTCTATGTATCTCATCAAGAAGATGACC
Found at i:15278 original size:172 final size:171
Alignment explanation
Indices: 14928--15314 Score: 530
Period size: 172 Copynumber: 2.3 Consensus size: 171
14918 TTGAGCTTCG
* *
14928 CTTCATTGTTTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACTACTTCATTGTTTTGATCC
1 CTTCATTGTTTTGATCCACTTCTTTGTATCTCATCAAGAAGATGACTACTTCATTGTTTTGATCC
* * *
14993 ACTTCTCTGTATCTAATCAGGAAGATGGGGTTTTAAGTTTCACTCACATTGAACTTTGCTTCATT
66 ACTTCTATGTATCTAATCAGGAAGATGGGGTTTGAAGTTTCACTCACATTGAACTTCGCTTCATT
*
15058 GTTTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACCT
131 GTTTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGAACT
* * *
15099 CTTCATTGTTTTTATCCACTTCTTTGTATCTCATTAAGAAGATGA-TCGCTTCATTGTTTTGATC
1 CTTCATTGTTTTGATCCACTTCTTTGTATCTCATCAAGAAGATGACT-ACTTCATTGTTTTGATC
* * *
15163 TACTTCTATGTATCTCAA-CGGGAAGATAGGGGTTTGAAGTTTCACTCACTTTGAACTTCGCTTC
65 CACTTCTATGTATCT-AATCAGGAAGAT-GGGGTTTGAAGTTTCACTCACATTGAACTTCGCTTC
* * * *
15227 ATTGTTTTGGTTCACTTCTCTGTATCTCATCAGGATGAT-AATT
128 ATTGTTTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGAACT
* * *
15270 GTTTCATTGTTTTGATCTACTTCTTTGTATGTCATC-AGAAAGATG
1 -CTTCATTGTTTTGATCCACTTCTTTGTATCTCATCAAG-AAGATG
15315 GGGTTTGAAG
Statistics
Matches: 190, Mismatches: 21, Indels: 9
0.86 0.10 0.04
Matches are distributed among these distances:
170 1 0.01
171 82 0.43
172 107 0.56
ACGTcount: A:0.22, C:0.19, G:0.16, T:0.42
Consensus pattern (171 bp):
CTTCATTGTTTTGATCCACTTCTTTGTATCTCATCAAGAAGATGACTACTTCATTGTTTTGATCC
ACTTCTATGTATCTAATCAGGAAGATGGGGTTTGAAGTTTCACTCACATTGAACTTCGCTTCATT
GTTTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGAACT
Found at i:15351 original size:295 final size:294
Alignment explanation
Indices: 14804--15437 Score: 964
Period size: 295 Copynumber: 2.2 Consensus size: 294
14794 ATTGAGCTTC
*
14804 GCTTCATTGTTTTGGTCCACTTCTTTGTATCTCATCAAGAAGATGACCGCTTCATTGTTTTGATC
1 GCTTCATTGTTTTGATCCACTTCTTTGTATCTCATCAAGAAGATGACCGCTTCATTGTTTTGATC
* * *
14869 CACTTCTCTATATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACATTGAGCTTCGCTTCAT
66 CACTTCTATATATCTCAACAGGAAGATGGGGTTTGAAGTTTCACTCACATTGAACTTCGCTTCAT
*
14934 TGTTTTGGTCCACTTCTCTGTATCTCATCAAGAAGATGACTACTTCATTGTTTTGATCCACTTCT
131 TGTTTTGGTCCACTTCTCTGTATCTCATCAAGAAGATAACTACTTCATTGTTTTGATCCACTTCT
* * *
14999 CTGTATCTAATCAGGAAGATGGGGTTTTAAGTTTCACTCACATTGAACTTTGCTTCATTGTTTTG
196 CTGTATCTAATCAGAAAGATGGGGTTTGAAGTTTCACTCACATTGAACTTCGCTTCATTGTTTTG
15064 GTCCACTTCTCTGTATCTCATCAAGAAGATGACCT
261 GTCCACTTCTCTGTATCTCATCAAGAAGATGA-CT
* * *
15099 -CTTCATTGTTTTTATCCACTTCTTTGTATCTCATTAAGAAGATGATCGCTTCATTGTTTTGATC
1 GCTTCATTGTTTTGATCCACTTCTTTGTATCTCATCAAGAAGATGACCGCTTCATTGTTTTGATC
* * * *
15163 TACTTCTATGTATCTCAACGGGAAGATAGGGGTTTGAAGTTTCACTCACTTTGAACTTCGCTTCA
66 CACTTCTATATATCTCAACAGGAAGAT-GGGGTTTGAAGTTTCACTCACATTGAACTTCGCTTCA
* * * * ** *
15228 TTGTTTTGGTTCACTTCTCTGTATCTCATCAGGATGATAATTGTTTCATTGTTTTGATCTACTTC
130 TTGTTTTGGTCCACTTCTCTGTATCTCATCAAGAAGATAACTACTTCATTGTTTTGATCCACTTC
* * * * *
15293 TTTGTATGTCATCAGAAAGATGGGGTTTGAAGTTTCACTCGCATTGAGCTTCGCTTCATTGTTTT
195 TCTGTATCTAATCAGAAAGATGGGGTTTGAAGTTTCACTCACATTGAACTTCGCTTCATTGTTTT
* *
15358 GGTCCACTTCTCTGTATCTCATCAGGAAGATGATT
260 GGTCCACTTCTCTGTATCTCATCAAGAAGATGACT
* *
15393 GCTTCATTGTTTTGATTCACTTCTTTGTATCTCATCAGGAAGATG
1 GCTTCATTGTTTTGATCCACTTCTTTGTATCTCATCAAGAAGATG
15438 GGGTTTGATC
Statistics
Matches: 304, Mismatches: 33, Indels: 4
0.89 0.10 0.01
Matches are distributed among these distances:
294 83 0.27
295 221 0.73
ACGTcount: A:0.21, C:0.20, G:0.18, T:0.41
Consensus pattern (294 bp):
GCTTCATTGTTTTGATCCACTTCTTTGTATCTCATCAAGAAGATGACCGCTTCATTGTTTTGATC
CACTTCTATATATCTCAACAGGAAGATGGGGTTTGAAGTTTCACTCACATTGAACTTCGCTTCAT
TGTTTTGGTCCACTTCTCTGTATCTCATCAAGAAGATAACTACTTCATTGTTTTGATCCACTTCT
CTGTATCTAATCAGAAAGATGGGGTTTGAAGTTTCACTCACATTGAACTTCGCTTCATTGTTTTG
GTCCACTTCTCTGTATCTCATCAAGAAGATGACT
Found at i:15369 original size:123 final size:123
Alignment explanation
Indices: 15099--15445 Score: 507
Period size: 123 Copynumber: 2.8 Consensus size: 123
15089 AAGATGACCT
** * * * *
15099 CTTCATTGTTTTTATCCACTTCTTTGTATCTCATTAAGAAGATGATCGCTTCATTGTTTTGATCT
1 CTTCATTGTTTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGATTGCTTCATTGTTTTGATCT
* * * *
15164 ACTTCTATGTATCTCAACGGGAAGATAGGGGTTTGAAGTTTCACTCACTTTGAACTTCG
66 ACTTCTTTGTATCTCATCAGGAAGAT-GGGGTTTGAAGTTTCACTCACATTGAACTTCG
* * * *
15223 CTTCATTGTTTTGGTTCACTTCTCTGTATCTCATCAGGATGATAATTGTTTCATTGTTTTGATCT
1 CTTCATTGTTTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGATTGCTTCATTGTTTTGATCT
* * * *
15288 ACTTCTTTGTATGTCATCAGAAAGATGGGGTTTGAAGTTTCACTCGCATTGAGCTTCG
66 ACTTCTTTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACATTGAACTTCG
15346 CTTCATTGTTTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGATTGCTTCATTGTTTTGAT-T
1 CTTCATTGTTTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGATTGCTTCATTGTTTTGATCT
15410 CACTTCTTTGTATCTCATCAGGAAGATGGGGTTTGA
66 -ACTTCTTTGTATCTCATCAGGAAGATGGGGTTTGA
15446 TCTGACCCAC
Statistics
Matches: 198, Mismatches: 24, Indels: 3
0.88 0.11 0.01
Matches are distributed among these distances:
122 1 0.01
123 121 0.61
124 76 0.38
ACGTcount: A:0.20, C:0.18, G:0.19, T:0.43
Consensus pattern (123 bp):
CTTCATTGTTTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGATTGCTTCATTGTTTTGATCT
ACTTCTTTGTATCTCATCAGGAAGATGGGGTTTGAAGTTTCACTCACATTGAACTTCG
Found at i:15416 original size:48 final size:48
Alignment explanation
Indices: 15345--15437 Score: 159
Period size: 48 Copynumber: 1.9 Consensus size: 48
15335 ATTGAGCTTC
*
15345 GCTTCATTGTTTTGGTCCACTTCTCTGTATCTCATCAGGAAGATGATT
1 GCTTCATTGTTTTGATCCACTTCTCTGTATCTCATCAGGAAGATGATT
* *
15393 GCTTCATTGTTTTGATTCACTTCTTTGTATCTCATCAGGAAGATG
1 GCTTCATTGTTTTGATCCACTTCTCTGTATCTCATCAGGAAGATG
15438 GGGTTTGATC
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
48 42 1.00
ACGTcount: A:0.19, C:0.19, G:0.18, T:0.43
Consensus pattern (48 bp):
GCTTCATTGTTTTGATCCACTTCTCTGTATCTCATCAGGAAGATGATT
Found at i:16328 original size:36 final size:38
Alignment explanation
Indices: 16251--16331 Score: 101
Period size: 37 Copynumber: 2.2 Consensus size: 38
16241 ACGTGTCTTT
* *
16251 TTTTTTGAGACGCCCTTTACGGGTTTTCATCTTGATCC
1 TTTTTTGAGACGCCCTTTACGGGTTTACATCTCGATCC
* * * *
16289 TTTTTT-AGATGCCTTTTGCGGGTTTACATCTCGATCT
1 TTTTTTGAGACGCCCTTTACGGGTTTACATCTCGATCC
16326 TTTTTT
1 TTTTTT
16332 TAGGCGAAAC
Statistics
Matches: 37, Mismatches: 6, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
37 31 0.84
38 6 0.16
ACGTcount: A:0.12, C:0.20, G:0.17, T:0.51
Consensus pattern (38 bp):
TTTTTTGAGACGCCCTTTACGGGTTTACATCTCGATCC
Found at i:27236 original size:42 final size:42
Alignment explanation
Indices: 27183--27275 Score: 186
Period size: 42 Copynumber: 2.2 Consensus size: 42
27173 CAAAATTATT
27183 TATATTTTTGAAGAAAATCAAAAAACAATTTTGATTAAAATA
1 TATATTTTTGAAGAAAATCAAAAAACAATTTTGATTAAAATA
27225 TATATTTTTGAAGAAAATCAAAAAACAATTTTGATTAAAATA
1 TATATTTTTGAAGAAAATCAAAAAACAATTTTGATTAAAATA
27267 TATATTTTT
1 TATATTTTT
27276 TTAAAATGAG
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 51 1.00
ACGTcount: A:0.49, C:0.04, G:0.06, T:0.40
Consensus pattern (42 bp):
TATATTTTTGAAGAAAATCAAAAAACAATTTTGATTAAAATA
Found at i:27571 original size:29 final size:28
Alignment explanation
Indices: 27538--27649 Score: 111
Period size: 30 Copynumber: 3.9 Consensus size: 28
27528 GAAACAGGGT
*
27538 CCAAAACA-AAATTTTGGAAAGTTATGGG
1 CCAAAACATAATTTTTGGAAAGTT-TGGG
* *
27566 ACCAAATTCA-ATTTTTTGGAAAGTTTAGAGG
1 -CCAAA-ACATAATTTTTGGAAAGTTT-G-GG
*
27597 CCAAAACATAATTTTTGGAAAGGTTGGGG
1 CCAAAACATAATTTTTGGAAA-GTTTGGG
*
27626 CCAAAACATAATTTTTAGAAAGTT
1 CCAAAACATAATTTTTGGAAAGTT
27650 CGAGGGTAAA
Statistics
Matches: 71, Mismatches: 7, Indels: 11
0.80 0.08 0.12
Matches are distributed among these distances:
28 3 0.04
29 30 0.42
30 33 0.46
31 5 0.07
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (28 bp):
CCAAAACATAATTTTTGGAAAGTTTGGG
Found at i:27641 original size:59 final size:59
Alignment explanation
Indices: 27538--27649 Score: 138
Period size: 59 Copynumber: 1.9 Consensus size: 59
27528 GAAACAGGGT
* * * *
27538 CCAAAACAAAATTTTGGAAAGTTATGGGACCAAATTCAATTTTTTGGAAAGTTTAGAGG
1 CCAAAACAAAATTTTGGAAAGGTATGGGACCAAATACAAATTTTTAGAAAGTTTAGAGG
* *
27597 CCAAAACATAATTTTTGGAAAGGT-TGGGGCCAAA-ACATAATTTTTAGAAAGTT
1 CCAAAACA-AAATTTTGGAAAGGTATGGGACCAAATACA-AATTTTTAGAAAGTT
27650 CGAGGGTAAA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
58 2 0.04
59 30 0.67
60 13 0.29
ACGTcount: A:0.39, C:0.11, G:0.20, T:0.30
Consensus pattern (59 bp):
CCAAAACAAAATTTTGGAAAGGTATGGGACCAAATACAAATTTTTAGAAAGTTTAGAGG
Found at i:29838 original size:91 final size:85
Alignment explanation
Indices: 29689--29892 Score: 275
Period size: 88 Copynumber: 2.3 Consensus size: 85
29679 AAAAACTCTT
* * * *
29689 AAACTTTTTCAAAAAAAGTAATTAAGTC-TATTTTTTTTTGCACTCAATTAGGTACTTGAACTGT
1 AAACTTTTTCAAAAAAGGAAATTAAG-CATATTTTTATTTGCACTCAATTAGATACTTGAACTGT
29753 CAAAATGCATCAAACAGACCCTA
65 C-AAATGCATCAAA-AGACCCTA
29776 AAACTTTTTTCAAAAAAGGAAATTAAGCATATGCATTTTATTTGCACTCAATTAGATACTTGAAC
1 AAAC-TTTTTCAAAAAAGGAAATTAAGCATAT---TTTTATTTGCACTCAATTAGATACTTGAAC
* *
29841 TTTCAAATGCATCAAAAGACCCTC
62 TGTCAAATGCATCAAAAGACCCTA
*
29865 AAACTTTTTCAAAAAAGAAAATTAAGCA
1 AAACTTTTTCAAAAAAGGAAATTAAGCA
29893 CCAGTTTTTT
Statistics
Matches: 105, Mismatches: 7, Indels: 9
0.87 0.06 0.07
Matches are distributed among these distances:
87 5 0.05
88 46 0.44
89 11 0.10
90 12 0.11
91 31 0.30
ACGTcount: A:0.41, C:0.17, G:0.10, T:0.32
Consensus pattern (85 bp):
AAACTTTTTCAAAAAAGGAAATTAAGCATATTTTTATTTGCACTCAATTAGATACTTGAACTGTC
AAATGCATCAAAAGACCCTA
Found at i:30052 original size:29 final size:29
Alignment explanation
Indices: 30015--30090 Score: 100
Period size: 29 Copynumber: 2.6 Consensus size: 29
30005 AAATAAAAAA
*
30015 TAATGAAAATTATAAAAATGA-TTAAATTT
1 TAATAAAAATTATAAAAAT-ATTTAAATTT
*
30044 TAATAAAAACTATAAAAATATTTAAATTT
1 TAATAAAAATTATAAAAATATTTAAATTT
* *
30073 TATTAAAAATTAGAAAAA
1 TAATAAAAATTATAAAAA
30091 AAAAATATAA
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
28 1 0.02
29 40 0.98
ACGTcount: A:0.59, C:0.01, G:0.04, T:0.36
Consensus pattern (29 bp):
TAATAAAAATTATAAAAATATTTAAATTT
Found at i:30437 original size:19 final size:19
Alignment explanation
Indices: 30413--30505 Score: 91
Period size: 19 Copynumber: 4.8 Consensus size: 19
30403 TTTTTGATGC
*
30413 ATTTTATAATTTTTATAAA
1 ATTTAATAATTTTTATAAA
*
30432 AGTTTACA-ATTTTTTATAAA
1 A-TTTA-ATAATTTTTATAAA
*
30452 ATTTCAT-ATTTTTATTAAA
1 ATTTAATAATTTTTA-TAAA
30471 ATTTAATAATTTTTATAAA
1 ATTTAATAATTTTTATAAA
* * *
30490 TTTTATTTATTTTTAT
1 ATTTAATAATTTTTAT
30506 TTTTTATAGT
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
18 7 0.11
19 31 0.51
20 22 0.36
21 1 0.02
ACGTcount: A:0.38, C:0.02, G:0.01, T:0.59
Consensus pattern (19 bp):
ATTTAATAATTTTTATAAA
Found at i:30823 original size:95 final size:91
Alignment explanation
Indices: 30610--30828 Score: 235
Period size: 95 Copynumber: 2.4 Consensus size: 91
30600 TTTTGATACA
* * * * ***
30610 TTTGACAGTTCAAGTTCCCAATTGAGTG-AAAAAAATCAAGGGTTTAATTGTTTTTTTTTTTTTT
1 TTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAGCAAGGGCTTAATTGTTTTTTTTTTTGAA
* *
30674 TAAGTTTGAGGGTCCTTGTGATGCAT
66 AAAATTTGAGGGTCCTTGTGATGCAT
* *
30700 TTTGAAAGTTTAAGCACCCAATTGAGTGCCAAAAAAAGGC-AGGAGCTTAATTGTTTTTTTTTTT
1 TTTGAAAGTTCAAGTACCCAATTGAGTG-CAAAAAAA-GCAAGG-GCTTAATTGTTTTTTTTTTT
* * *
30764 GAAAAAATTTGAGGGTCTTTTTTTTATGCAT
63 GAAAAAATTTGAGGGTC--CTTGTGATGCAT
* *
30795 TTTGATAGTTCAAATACCCAATTGAGTGCAAAAA
1 TTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAA
30829 GAAAACACGA
Statistics
Matches: 105, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
90 24 0.23
92 10 0.10
93 32 0.30
94 6 0.06
95 33 0.31
ACGTcount: A:0.30, C:0.11, G:0.19, T:0.40
Consensus pattern (91 bp):
TTTGAAAGTTCAAGTACCCAATTGAGTGCAAAAAAAGCAAGGGCTTAATTGTTTTTTTTTTTGAA
AAAATTTGAGGGTCCTTGTGATGCAT
Found at i:30841 original size:95 final size:89
Alignment explanation
Indices: 30694--30874 Score: 211
Period size: 95 Copynumber: 2.0 Consensus size: 89
30684 GGTCCTTGTG
* * ** *
30694 ATGCATTTTGAAAGTTTAAGCACCCAATTGAGTGCCAAAAAAAGGCAGGAGCTTAATTGTTTTTT
1 ATGCATTTTGAAAGTTCAAACACCCAATTGAGTGCCAAAAAAAAACACGAGC----TT-TTTTTT
*
30759 TTTTTGAAAAAATTTGAGGGTCTTTTTTTT
61 TTTTTGAAAAAATTTGAGAG-CTTTTTTTT
* *
30789 ATGCATTTTGATAGTTCAAATACCCAATTGAGTG-CAAAAAGAAAACACGAGCTTTTTTTTTTTT
1 ATGCATTTTGAAAGTTCAAACACCCAATTGAGTGCCAAAAA-AAAACACGAGCTTTTTTTTTTTT
*
30853 TGAAAAAGTTTGAGAGCTTTTT
65 TGAAAAAATTTGAGAGCTTTTT
30875 ACGCTTTTAA
Statistics
Matches: 76, Mismatches: 9, Indels: 8
0.82 0.10 0.09
Matches are distributed among these distances:
89 6 0.08
90 24 0.32
91 2 0.03
94 6 0.08
95 38 0.50
ACGTcount: A:0.32, C:0.11, G:0.18, T:0.39
Consensus pattern (89 bp):
ATGCATTTTGAAAGTTCAAACACCCAATTGAGTGCCAAAAAAAAACACGAGCTTTTTTTTTTTTT
GAAAAAATTTGAGAGCTTTTTTTT
Found at i:35460 original size:36 final size:36
Alignment explanation
Indices: 35420--35497 Score: 111
Period size: 36 Copynumber: 2.2 Consensus size: 36
35410 AACATAATTA
* *
35420 GTCACATGACATGAAGAACATACCCACATATTTTCT
1 GTCACAGGACATGAAGAACATACCCACATATTTACT
* *
35456 GTCACAGGGCATGAATAACATACCCACATATTTACT
1 GTCACAGGACATGAAGAACATACCCACATATTTACT
*
35492 TTCACA
1 GTCACA
35498 ACAGTCATCA
Statistics
Matches: 37, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.36, C:0.26, G:0.12, T:0.27
Consensus pattern (36 bp):
GTCACAGGACATGAAGAACATACCCACATATTTACT
Found at i:48950 original size:37 final size:37
Alignment explanation
Indices: 48900--48973 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
48890 TATATTGGCT
48900 GTCATTACATTTGATTTGAAATTTTCCTATGTTCTGG
1 GTCATTACATTTGATTTGAAATTTTCCTATGTTCTGG
48937 GTCATTACATTTGATTTGAAATTTTCCTATGTTCTGG
1 GTCATTACATTTGATTTGAAATTTTCCTATGTTCTGG
48974 CTAGTTGGGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.22, C:0.14, G:0.16, T:0.49
Consensus pattern (37 bp):
GTCATTACATTTGATTTGAAATTTTCCTATGTTCTGG
Found at i:49706 original size:32 final size:32
Alignment explanation
Indices: 49669--49743 Score: 107
Period size: 32 Copynumber: 2.3 Consensus size: 32
49659 TTGGTTTATT
49669 GATATTGAAATTATTATGTTTTAAAG-TTGTTG
1 GATATTGAAATTATTATG-TTTAAAGCTTGTTG
* *
49701 GATATTGAATTTATTATGTTTCAAGCTTGTTG
1 GATATTGAAATTATTATGTTTAAAGCTTGTTG
*
49733 GATATTTAAAT
1 GATATTGAAAT
49744 GATTGACAAT
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
31 6 0.16
32 32 0.84
ACGTcount: A:0.31, C:0.03, G:0.17, T:0.49
Consensus pattern (32 bp):
GATATTGAAATTATTATGTTTAAAGCTTGTTG
Found at i:51640 original size:29 final size:29
Alignment explanation
Indices: 51608--51760 Score: 123
Period size: 29 Copynumber: 5.2 Consensus size: 29
51598 GACTTCGGGA
* * *
51608 AAGTTCGAGGTCAAAATGTGATTTTTTG-G
1 AAGTTCGAGGGCAAAATAT-AATTTTTGAG
* * * *
51637 AAGTACGGGGGTAATAATATATTTTTTGAG
1 AAGTTCGAGGGCAA-AATATAATTTTTGAG
51667 AAGTTC-AGGGGCAAAATATAATTTTTG-G
1 AAGTTCGA-GGGCAAAATATAATTTTTGAG
* *
51695 AAATTCGAGGGCAAAAATGTAATTTTTGAG
1 AAGTTCGAGGGC-AAAATATAATTTTTGAG
** * *
51725 AAGTTTAAGGGGTAAAATGTAATTTTTGAG
1 AAGTTCGA-GGGCAAAATATAATTTTTGAG
51755 AAGTTC
1 AAGTTC
51761 AAAAGTAAAA
Statistics
Matches: 101, Mismatches: 16, Indels: 13
0.78 0.12 0.10
Matches are distributed among these distances:
28 10 0.10
29 45 0.45
30 43 0.43
31 3 0.03
ACGTcount: A:0.35, C:0.05, G:0.25, T:0.35
Consensus pattern (29 bp):
AAGTTCGAGGGCAAAATATAATTTTTGAG
Found at i:51670 original size:30 final size:29
Alignment explanation
Indices: 51630--51758 Score: 104
Period size: 30 Copynumber: 4.4 Consensus size: 29
51620 AAAATGTGAT
* * *
51630 TTTTTG-GAAGTACGGGGGTAATAATATAT
1 TTTTTGAGAAGTACAGGGGCAA-AATATAA
*
51659 TTTTTGAGAAGTTCAGGGGCAAAATATAA
1 TTTTTGAGAAGTACAGGGGCAAAATATAA
* * *
51688 TTTTTG-GAAATTC-GAGGGCAAAAATGTAA
1 TTTTTGAGAAGTACAG-GGGC-AAAATATAA
* *
51717 TTTTTGAGAAGTTTA-AGGGGTAAAATGTAA
1 TTTTTGAGAAG--TACAGGGGCAAAATATAA
51747 TTTTTGAGAAGT
1 TTTTTGAGAAGT
51759 TCAAAAGTAA
Statistics
Matches: 84, Mismatches: 9, Indels: 15
0.78 0.08 0.14
Matches are distributed among these distances:
27 1 0.01
28 11 0.13
29 32 0.38
30 35 0.42
31 3 0.04
32 2 0.02
ACGTcount: A:0.35, C:0.04, G:0.26, T:0.36
Consensus pattern (29 bp):
TTTTTGAGAAGTACAGGGGCAAAATATAA
Found at i:51759 original size:30 final size:30
Alignment explanation
Indices: 51644--51791 Score: 131
Period size: 30 Copynumber: 5.0 Consensus size: 30
51634 TGGAAGTACG
* * *
51644 GGGGTAATAATATATTTTTTGAGAAG-TTCA
1 GGGGTAA-AATGTAATTTTTGAGAAGTTTAA
* * * **
51674 GGGGCAAAATATAATTTTTG-GAAATTCGA
1 GGGGTAAAATGTAATTTTTGAGAAGTTTAA
**
51703 GGGCAAAAATGTAATTTTTGAGAAGTTTAA
1 GGGGTAAAATGTAATTTTTGAGAAGTTTAA
*
51733 GGGGTAAAATGTAATTTTTGAGAAGTTCAA
1 GGGGTAAAATGTAATTTTTGAGAAGTTTAA
** *
51763 -AAGTAAAATTGTAATTTTTGGGAAGTTTA
1 GGGGTAAAA-TGTAATTTTTGAGAAGTTTA
51792 GGGCCAAAAC
Statistics
Matches: 97, Mismatches: 18, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
28 3 0.03
29 37 0.38
30 57 0.59
ACGTcount: A:0.37, C:0.03, G:0.24, T:0.36
Consensus pattern (30 bp):
GGGGTAAAATGTAATTTTTGAGAAGTTTAA
Found at i:52908 original size:26 final size:25
Alignment explanation
Indices: 52872--52922 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
52862 AATAAACTAT
* *
52872 TAATAATTATATTAATATATAATAAA
1 TAATAAATATATTAACATAT-ATAAA
52898 TAATAAATATATTAACATATATAAA
1 TAATAAATATATTAACATATATAAA
52923 AACGCCTAGA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 5 0.22
26 18 0.78
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.39
Consensus pattern (25 bp):
TAATAAATATATTAACATATATAAA
Found at i:56825 original size:31 final size:29
Alignment explanation
Indices: 56756--56826 Score: 88
Period size: 29 Copynumber: 2.4 Consensus size: 29
56746 ACAAAATAAT
**
56756 AACATAAGTGACTAAAACGTAACATTTCA
1 AACATAAGTGACTAAAACGTAACAAGTCA
*
56785 AACATAAGTGACTAAAATGTAAACTAAGTCA
1 AACATAAGTGACTAAAACGT-AAC-AAGTCA
*
56816 AACAAAAGTGA
1 AACATAAGTGA
56827 TTATTTTTAT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
29 19 0.53
30 3 0.08
31 14 0.39
ACGTcount: A:0.52, C:0.14, G:0.13, T:0.21
Consensus pattern (29 bp):
AACATAAGTGACTAAAACGTAACAAGTCA
Found at i:57014 original size:36 final size:36
Alignment explanation
Indices: 56935--57055 Score: 120
Period size: 36 Copynumber: 3.4 Consensus size: 36
56925 CAAATAATCA
* *
56935 AAATAACAATC-AAAACAGCAGTAAAAATAACAGT-A
1 AAATAACAA-CAAAAACAACAATAAAAATAACAGTAA
* * * **
56970 AAATAACAATAAAAATAACAATAAAAATAGCAACAA
1 AAATAACAACAAAAACAACAATAAAAATAACAGTAA
**
57006 AAATAACAACAAAAACAGTAATAAAAATAACAGTAA
1 AAATAACAACAAAAACAACAATAAAAATAACAGTAA
* *
57042 AAACAACACCAAAA
1 AAATAACAACAAAA
57056 CAGTAAAAAA
Statistics
Matches: 68, Mismatches: 16, Indels: 3
0.78 0.18 0.03
Matches are distributed among these distances:
35 26 0.38
36 42 0.62
ACGTcount: A:0.69, C:0.14, G:0.05, T:0.12
Consensus pattern (36 bp):
AAATAACAACAAAAACAACAATAAAAATAACAGTAA
Found at i:57042 original size:12 final size:12
Alignment explanation
Indices: 56934--57049 Score: 108
Period size: 12 Copynumber: 9.8 Consensus size: 12
56924 TCAAATAATC
*
56934 AAAATAACAATC
1 AAAATAACAATA
* * *
56946 AAAACAGCAGTA
1 AAAATAACAATA
*
56958 AAAATAACAGT-
1 AAAATAACAATA
56969 AAAATAACAATA
1 AAAATAACAATA
56981 AAAATAACAATA
1 AAAATAACAATA
* *
56993 AAAATAGCAACA
1 AAAATAACAATA
*
57005 AAAATAACAACA
1 AAAATAACAATA
* **
57017 AAAACAGTAATA
1 AAAATAACAATA
*
57029 AAAATAACAGTA
1 AAAATAACAATA
*
57041 AAAACAACA
1 AAAATAACA
57050 CCAAAACAGT
Statistics
Matches: 84, Mismatches: 19, Indels: 2
0.80 0.18 0.02
Matches are distributed among these distances:
11 10 0.12
12 74 0.88
ACGTcount: A:0.69, C:0.13, G:0.05, T:0.13
Consensus pattern (12 bp):
AAAATAACAATA
Found at i:57055 original size:24 final size:24
Alignment explanation
Indices: 56934--57046 Score: 131
Period size: 24 Copynumber: 4.8 Consensus size: 24
56924 TCAAATAATC
* *
56934 AAAATAACAATCAAAACAGCAGTA
1 AAAATAACAATAAAAACAGCAATA
*
56958 AAAATAACAGTAAAATA-A-CAATA
1 AAAATAACAATAAAA-ACAGCAATA
* *
56981 AAAATAACAATAAAAATAGCAACA
1 AAAATAACAATAAAAACAGCAATA
* *
57005 AAAATAACAACAAAAACAGTAATA
1 AAAATAACAATAAAAACAGCAATA
*
57029 AAAATAACAGTAAAAACA
1 AAAATAACAATAAAAACA
57047 ACACCAAAAC
Statistics
Matches: 75, Mismatches: 11, Indels: 6
0.82 0.12 0.07
Matches are distributed among these distances:
22 1 0.01
23 19 0.25
24 54 0.72
25 1 0.01
ACGTcount: A:0.69, C:0.12, G:0.05, T:0.13
Consensus pattern (24 bp):
AAAATAACAATAAAAACAGCAATA
Found at i:57070 original size:21 final size:21
Alignment explanation
Indices: 57034--57098 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
57024 TAATAAAAAT
*
57034 AACAGT-AAAAACAACACCAA
1 AACAGTAAAAAATAACACCAA
57054 AACAGTAAAAAATAACACCAA
1 AACAGTAAAAAATAACACCAA
*
57075 AATAGTAAAAAAATAACACCAA
1 AACAGT-AAAAAATAACACCAA
57097 AA
1 AA
57099 TAATAATATA
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
20 6 0.15
21 18 0.44
22 17 0.41
ACGTcount: A:0.68, C:0.18, G:0.05, T:0.09
Consensus pattern (21 bp):
AACAGTAAAAAATAACACCAA
Found at i:57085 original size:22 final size:21
Alignment explanation
Indices: 57040--57100 Score: 95
Period size: 22 Copynumber: 2.9 Consensus size: 21
57030 AAATAACAGT
* *
57040 AAAAACAACACCAAAACAGTA
1 AAAAATAACACCAAAATAGTA
57061 AAAAATAACACCAAAATAGTAA
1 AAAAATAACACCAAAATAGT-A
57083 AAAAATAACACCAAAATA
1 AAAAATAACACCAAAATA
57101 ATAATATAAT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
21 18 0.49
22 19 0.51
ACGTcount: A:0.69, C:0.18, G:0.03, T:0.10
Consensus pattern (21 bp):
AAAAATAACACCAAAATAGTA
Found at i:61901 original size:31 final size:31
Alignment explanation
Indices: 61838--61903 Score: 82
Period size: 31 Copynumber: 2.1 Consensus size: 31
61828 AGGTCCACCC
*
61838 ATATTATTTTTTTAATTTTTTAAAAATATTT
1 ATATTATTTTTTTAATTATTTAAAAATATTT
*
61869 ATATTATATTATTTTAA-TATTTAATAAT-TTT
1 ATATTAT-TT-TTTTAATTATTTAAAAATATTT
61900 ATAT
1 ATAT
61904 ATTGTTTATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
31 14 0.45
32 11 0.35
33 6 0.19
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (31 bp):
ATATTATTTTTTTAATTATTTAAAAATATTT
Found at i:61905 original size:33 final size:32
Alignment explanation
Indices: 61838--61914 Score: 86
Period size: 32 Copynumber: 2.4 Consensus size: 32
61828 AGGTCCACCC
*
61838 ATATTATTT-TTTTAATTTTTTAAAAATATTT
1 ATATTATTTATTTTAATTATTTAAAAATATTT
* *
61869 ATATTATATTATTTTAA-TATTTAATAATTTTAT
1 ATATTAT-TTATTTTAATTATTTAAAAATATT-T
*
61902 ATATTGTTTATTT
1 ATATTATTTATTT
61915 ATTGAAATTT
Statistics
Matches: 39, Mismatches: 4, Indels: 5
0.81 0.08 0.10
Matches are distributed among these distances:
31 7 0.18
32 19 0.49
33 13 0.33
ACGTcount: A:0.35, C:0.00, G:0.01, T:0.64
Consensus pattern (32 bp):
ATATTATTTATTTTAATTATTTAAAAATATTT
Found at i:65294 original size:21 final size:21
Alignment explanation
Indices: 65256--65295 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
65246 ATGCTTTTGA
*
65256 TTTTCTTTATTTATTTTATAT
1 TTTTCTTTATTTACTTTATAT
65277 TTTTCTTTTATTT-CTTTAT
1 TTTTC-TTTATTTACTTTAT
65296 GGATTTGAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.15, C:0.07, G:0.00, T:0.78
Consensus pattern (21 bp):
TTTTCTTTATTTACTTTATAT
Found at i:70110 original size:44 final size:44
Alignment explanation
Indices: 70036--70120 Score: 125
Period size: 44 Copynumber: 1.9 Consensus size: 44
70026 TTGTTACTAG
* *
70036 TCTTTCAAACGTTGTGGTTGATAATACCTTTGATGTAATCACCC
1 TCTTTCAAACGTTGTGGTTGATAACACCTTTGATATAATCACCC
* * *
70080 TCTTTCAAACGTTGTGGTTGGTGACGCCTTTGATATAATCA
1 TCTTTCAAACGTTGTGGTTGATAACACCTTTGATATAATCA
70121 ACGTTCAATT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.24, C:0.19, G:0.19, T:0.39
Consensus pattern (44 bp):
TCTTTCAAACGTTGTGGTTGATAACACCTTTGATATAATCACCC
Found at i:71795 original size:18 final size:18
Alignment explanation
Indices: 71772--71808 Score: 65
Period size: 18 Copynumber: 2.1 Consensus size: 18
71762 TTTTTTTTGA
71772 TGAATTACAAGAGGAAAG
1 TGAATTACAAGAGGAAAG
*
71790 TGAATTAGAAGAGGAAAG
1 TGAATTACAAGAGGAAAG
71808 T
1 T
71809 AAAACCCTAA
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:0.49, C:0.03, G:0.30, T:0.19
Consensus pattern (18 bp):
TGAATTACAAGAGGAAAG
Found at i:73240 original size:27 final size:27
Alignment explanation
Indices: 73173--73240 Score: 66
Period size: 27 Copynumber: 2.5 Consensus size: 27
73163 AAAAAATTAC
* **
73173 AAAAATATAAAATTGTAAAAATTCTTT
1 AAAAATATAAAAATGTAAAAAAACTTT
* *
73200 AAAAACAAAAAAAAT-TAAAAAAACATTT
1 AAAAA-TATAAAAATGTAAAAAAAC-TTT
73228 AAAAATATAAAAA
1 AAAAATATAAAAA
73241 AATTTATTTA
Statistics
Matches: 32, Mismatches: 7, Indels: 4
0.74 0.16 0.09
Matches are distributed among these distances:
27 18 0.56
28 14 0.44
ACGTcount: A:0.69, C:0.04, G:0.01, T:0.25
Consensus pattern (27 bp):
AAAAATATAAAAATGTAAAAAAACTTT
Found at i:73973 original size:24 final size:24
Alignment explanation
Indices: 73925--73973 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
73915 TACACATGAA
**
73925 ACTTGAATTATGATTCGTATGTAT
1 ACTTGAATTATGATTCAAATGTAT
* *
73949 ACTTGAATTGTGATTCAAATTTAT
1 ACTTGAATTATGATTCAAATGTAT
73973 A
1 A
73974 AATGGATTGT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 21 1.00
ACGTcount: A:0.33, C:0.08, G:0.14, T:0.45
Consensus pattern (24 bp):
ACTTGAATTATGATTCAAATGTAT
Found at i:82469 original size:9 final size:9
Alignment explanation
Indices: 82443--82472 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
82433 GATTCATGTT
*
82443 ATTTTATTA
1 ATTTTATTG
82452 ATTTTATTG
1 ATTTTATTG
82461 ATTTTATTG
1 ATTTTATTG
82470 ATT
1 ATT
82473 ATGCTATTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.27, C:0.00, G:0.07, T:0.67
Consensus pattern (9 bp):
ATTTTATTG
Found at i:83084 original size:26 final size:25
Alignment explanation
Indices: 83048--83113 Score: 80
Period size: 25 Copynumber: 2.6 Consensus size: 25
83038 TTAATTAGTA
* *
83048 TAAAATATTAACAATTTAAAATAAAT
1 TAAAAAATTAACAAATT-AAATAAAT
* *
83074 TAAAAAGTTAATAAATTAAATAAAT
1 TAAAAAATTAACAAATTAAATAAAT
83099 TAAAAAATTAA-AAAT
1 TAAAAAATTAACAAAT
83114 AAAAATTTCT
Statistics
Matches: 35, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
24 4 0.11
25 18 0.51
26 13 0.37
ACGTcount: A:0.65, C:0.02, G:0.02, T:0.32
Consensus pattern (25 bp):
TAAAAAATTAACAAATTAAATAAAT
Found at i:83112 original size:9 final size:8
Alignment explanation
Indices: 83070--83112 Score: 59
Period size: 8 Copynumber: 5.2 Consensus size: 8
83060 AATTTAAAAT
83070 AAATTAAA
1 AAATTAAA
* *
83078 AAGTTAAT
1 AAATTAAA
83086 AAATTAAA
1 AAATTAAA
83094 TAAATTAAA
1 -AAATTAAA
83103 AAATTAAA
1 AAATTAAA
83111 AA
1 AA
83113 TAAAAATTTC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
8 22 0.73
9 8 0.27
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (8 bp):
AAATTAAA
Found at i:83119 original size:25 final size:25
Alignment explanation
Indices: 83064--83117 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
83054 ATTAACAATT
*
83064 TAAAATAAATTAAAAAGTTAATAAA
1 TAAAATAAATTAAAAAATTAATAAA
*
83089 TTAAATAAATTAAAAAATTAA-AAA
1 TAAAATAAATTAAAAAATTAATAAA
83113 TAAAA
1 TAAAA
83118 ATTTCTTACC
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.28
Consensus pattern (25 bp):
TAAAATAAATTAAAAAATTAATAAA
Found at i:83850 original size:15 final size:14
Alignment explanation
Indices: 83830--83865 Score: 63
Period size: 15 Copynumber: 2.5 Consensus size: 14
83820 CAAATTTTAA
83830 AAATAAAAATAAAT
1 AAATAAAAATAAAT
83844 AACATAAAAATAAAT
1 AA-ATAAAAATAAAT
83859 AAATAAA
1 AAATAAA
83866 TGAAAACATT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
14 7 0.33
15 14 0.67
ACGTcount: A:0.78, C:0.03, G:0.00, T:0.19
Consensus pattern (14 bp):
AAATAAAAATAAAT
Found at i:87877 original size:17 final size:16
Alignment explanation
Indices: 87855--87904 Score: 55
Period size: 17 Copynumber: 3.0 Consensus size: 16
87845 AGCTAAATTG
87855 AATGCAACGATAATTAA
1 AATGCAA-GATAATTAA
* *
87872 AATGCATGCATAATAAA
1 AATGCAAG-ATAATTAA
*
87889 AATGCAAGAAAATTAA
1 AATGCAAGATAATTAA
87905 CTAAAAAGGA
Statistics
Matches: 27, Mismatches: 5, Indels: 3
0.77 0.14 0.09
Matches are distributed among these distances:
16 7 0.26
17 20 0.74
ACGTcount: A:0.56, C:0.10, G:0.12, T:0.22
Consensus pattern (16 bp):
AATGCAAGATAATTAA
Found at i:103881 original size:5 final size:5
Alignment explanation
Indices: 103866--103939 Score: 51
Period size: 5 Copynumber: 13.6 Consensus size: 5
103856 TTCCCATTTC
*
103866 TTTATT TTTAT TTTAT TTTAT TATTGAT CTTTAT TTTATT ATTTAT TTAAT
1 TTTA-T TTTAT TTTAT TTTAT T-TT-AT -TTTAT TTTA-T -TTTAT TTTAT
* *
103917 TTCA- TTTAT GTTGAT TTTAT TTT
1 TTTAT TTTAT -TTTAT TTTAT TTT
103940 TATTACTTTT
Statistics
Matches: 56, Mismatches: 5, Indels: 15
0.74 0.07 0.20
Matches are distributed among these distances:
4 3 0.05
5 30 0.54
6 14 0.25
7 8 0.14
8 1 0.02
ACGTcount: A:0.22, C:0.03, G:0.04, T:0.72
Consensus pattern (5 bp):
TTTAT
Found at i:103912 original size:35 final size:37
Alignment explanation
Indices: 103866--103944 Score: 94
Period size: 38 Copynumber: 2.2 Consensus size: 37
103856 TTCCCATTTC
* *
103866 TTTATT-TTTATTTTATTTTA-TTA-TTGATCTTTA-T
1 TTTATTATTTATTTAATTTCATTTAGTTGAT-TTTATT
103900 TTTATTATTTATTTAATTTCATTTATGTTGATTTTATT
1 TTTATTATTTATTTAATTTCATTTA-GTTGATTTTATT
103938 TTTATTA
1 TTTATTA
103945 CTTTTTAGTA
Statistics
Matches: 38, Mismatches: 2, Indels: 6
0.83 0.04 0.13
Matches are distributed among these distances:
34 6 0.16
35 12 0.32
36 3 0.08
37 4 0.11
38 13 0.34
ACGTcount: A:0.23, C:0.03, G:0.04, T:0.71
Consensus pattern (37 bp):
TTTATTATTTATTTAATTTCATTTAGTTGATTTTATT
Found at i:104041 original size:18 final size:18
Alignment explanation
Indices: 104014--104051 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
104004 GTTGATTATA
*
104014 TTCATTCTATT-TTGATTT
1 TTCATACTATTATT-ATTT
104032 TTCATACTATTATTATTT
1 TTCATACTATTATTATTT
104050 TT
1 TT
104052 GTTTCAGGTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 16 0.89
19 2 0.11
ACGTcount: A:0.21, C:0.11, G:0.03, T:0.66
Consensus pattern (18 bp):
TTCATACTATTATTATTT
Found at i:113910 original size:15 final size:15
Alignment explanation
Indices: 113891--113930 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 15
113881 TAACCAGTAG
113891 AAAGAGAAGGAA-AA
1 AAAGAGAAGGAAGAA
113905 AGAAGAGAAGGAAGAA
1 A-AAGAGAAGGAAGAA
113921 AAAGAAGAAG
1 AAAG-AGAAG
113931 AGAATGAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
14 1 0.04
15 14 0.61
16 8 0.35
ACGTcount: A:0.68, C:0.00, G:0.33, T:0.00
Consensus pattern (15 bp):
AAAGAGAAGGAAGAA
Found at i:113939 original size:18 final size:17
Alignment explanation
Indices: 113892--113939 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 17
113882 AACCAGTAGA
113892 AAGAGAAGGAAAAAGAAG
1 AAGAGAA-GAAAAAGAAG
113910 -AGAAGGAAGAAAAAGAAG
1 AAG-A-GAAGAAAAAGAAG
113928 AAGAGAATGAAA
1 AAGAGAA-GAAA
113940 TGAAGGAACC
Statistics
Matches: 26, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
17 5 0.19
18 16 0.62
19 5 0.19
ACGTcount: A:0.67, C:0.00, G:0.31, T:0.02
Consensus pattern (17 bp):
AAGAGAAGAAAAAGAAG
Found at i:114306 original size:6 final size:6
Alignment explanation
Indices: 114295--114320 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
114285 GTGAGTGCCC
114295 AAAGAA AAAGAA AAAGAA AAAGAA AA
1 AAAGAA AAAGAA AAAGAA AAAGAA AA
114321 CAAAGACAAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAGAA
Found at i:116687 original size:12 final size:12
Alignment explanation
Indices: 116670--116697 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
116660 AATTGCGCTG
116670 ACATCTTCACTC
1 ACATCTTCACTC
116682 ACATCTTCACTC
1 ACATCTTCACTC
116694 ACAT
1 ACAT
116698 TTTCTCTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.29, C:0.39, G:0.00, T:0.32
Consensus pattern (12 bp):
ACATCTTCACTC
Found at i:118421 original size:13 final size:13
Alignment explanation
Indices: 118403--118428 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
118393 CATTTTATTC
118403 ATTAACCCATAAT
1 ATTAACCCATAAT
118416 ATTAACCCATAAT
1 ATTAACCCATAAT
118429 CCATATATGT
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:0.23, G:0.00, T:0.31
Consensus pattern (13 bp):
ATTAACCCATAAT
Found at i:119898 original size:16 final size:16
Alignment explanation
Indices: 119877--119927 Score: 93
Period size: 16 Copynumber: 3.2 Consensus size: 16
119867 AAGAAAGAGC
119877 AAATACGCTAGTAAAT
1 AAATACGCTAGTAAAT
119893 AAATACGCTAGTAAAT
1 AAATACGCTAGTAAAT
*
119909 AAACACGCTAGTAAAT
1 AAATACGCTAGTAAAT
119925 AAA
1 AAA
119928 ATACTAGAAA
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.53, C:0.14, G:0.12, T:0.22
Consensus pattern (16 bp):
AAATACGCTAGTAAAT
Found at i:123723 original size:11 final size:11
Alignment explanation
Indices: 123707--123742 Score: 54
Period size: 11 Copynumber: 3.3 Consensus size: 11
123697 TTTCTCCCTC
*
123707 TTCCCCCTTTT
1 TTCCCCCTTCT
*
123718 TTCCCCCCTCT
1 TTCCCCCTTCT
123729 TTCCCCCTTCT
1 TTCCCCCTTCT
123740 TTC
1 TTC
123743 ATTTGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
11 22 1.00
ACGTcount: A:0.00, C:0.53, G:0.00, T:0.47
Consensus pattern (11 bp):
TTCCCCCTTCT
Found at i:123735 original size:22 final size:21
Alignment explanation
Indices: 123702--123742 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
123692 CCCCCTTTCT
*
123702 CCCTCTTCCCCCTTTTTTCCC
1 CCCTCTTCCCCCTTCTTTCCC
123723 CCCTCTTTCCCCCTTCTTTC
1 CCCTC-TTCCCCCTTCTTTC
123743 ATTTGTTTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (21 bp):
CCCTCTTCCCCCTTCTTTCCC
Found at i:123759 original size:18 final size:18
Alignment explanation
Indices: 123736--123778 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
123726 TCTTTCCCCC
*
123736 TTCTTTCATTTGTTTATT
1 TTCTTTCATTTATTTATT
*
123754 TTCTTTCGTTTATTTATT
1 TTCTTTCATTTATTTATT
*
123772 TGCTTTC
1 TTCTTTC
123779 TTTTTATGCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.09, C:0.14, G:0.07, T:0.70
Consensus pattern (18 bp):
TTCTTTCATTTATTTATT
Done.