Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003663.1 Hibiscus syriacus cultivar Beakdansim tig00007823_pilon, 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: 87280
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2723 original size:26 final size:28
Alignment explanation
Indices: 2662--2725 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
2652 GAGACCAGAT
**
2662 GTTTGAAAGATCGGTGCAGTAAGGAGAG
1 GTTTGAAAGATCGGCACAGTAAGGAGAG
2690 GTTTGAAAGATCGGCACAGTAA-G-GAG
1 GTTTGAAAGATCGGCACAGTAAGGAGAG
2716 GTTTGAAAGA
1 GTTTGAAAGA
2726 AAAAAATTAT
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
26 13 0.38
27 1 0.03
28 20 0.59
ACGTcount: A:0.34, C:0.08, G:0.36, T:0.22
Consensus pattern (28 bp):
GTTTGAAAGATCGGCACAGTAAGGAGAG
Found at i:9272 original size:113 final size:113
Alignment explanation
Indices: 9059--9494 Score: 513
Period size: 113 Copynumber: 3.9 Consensus size: 113
9049 AGACCACAAT
* * *
9059 ATCTGATTTTCCCTTCAAAGTAAGCGGAACATGTCTCTC-TTTTCTAAGATTTGATATTCCCTTT
1 ATCTGATTTTCCCTTCAGAGTAAGCGGAACATGTATCTCTTTTTC-AAGATTTGATATTCCCTTC
* * * * *
9123 AGAGTAAGCGGAATAAATCTACCCCGATTTAATGGATCAACTCCCCTAA
65 AGAGTAAGAGGAACAAATCTACCCCGATTCAATGGATAAACTCCCCTAG
* *
9172 AT-TCAATTTTCCCTTCAGAGTAAGCGGAACATGTATCTCTTTTTCAATATTTGATATTCCCTTC
1 ATCT-GATTTTCCCTTCAGAGTAAGCGGAACATGTATCTCTTTTTCAAGATTTGATATTCCCTTC
* * * * *
9236 AGAGTAAGAGGAACAAGTCTGCCCCAATTCATTGGATTAACTCCCCTAG
65 AGAGTAAGAGGAACAAATCTACCCCGATTCAATGGATAAACTCCCCTAG
* *
9285 ATCTGATTTTCCCTTCAGAGTAAGCGGAACA-G-ATCTCTCTTTTCCAAGATTTGTTATTCCTTT
1 ATCTGATTTTCCCTTCAGAGTAAGCGGAACATGTATCTCT-TTTT-CAAGATTTGATATTCCCTT
* * *
9348 CAGAGTAAGCGGAACAAATCTACCCTGATTCAATGGATAAACTCCCCCAG
64 CAGAGTAAGAGGAACAAATCTACCCCGATTCAATGGATAAACTCCCCTAG
* * * * * * * * *
9398 ATCTGATTTTCCCTTCAGAGTAAGCGAAATAGGTCTCACTTTTCCAAGTTTTGATTTTCCTTTCA
1 ATCTGATTTTCCCTTCAGAGTAAGCGGAACATGTATCTCTTTTTCAAGATTTGATATTCCCTTCA
* *
9463 GAGTAAGCA-GAACAAGTCTGCCCCGATTCAAT
66 GAGTAAG-AGGAACAAATCTACCCCGATTCAAT
9495 CTTCCCTGGG
Statistics
Matches: 277, Mismatches: 38, Indels: 16
0.84 0.11 0.05
Matches are distributed among these distances:
111 6 0.02
112 6 0.02
113 251 0.91
114 10 0.04
115 4 0.01
ACGTcount: A:0.28, C:0.23, G:0.15, T:0.33
Consensus pattern (113 bp):
ATCTGATTTTCCCTTCAGAGTAAGCGGAACATGTATCTCTTTTTCAAGATTTGATATTCCCTTCA
GAGTAAGAGGAACAAATCTACCCCGATTCAATGGATAAACTCCCCTAG
Found at i:9465 original size:226 final size:226
Alignment explanation
Indices: 9059--9492 Score: 617
Period size: 226 Copynumber: 1.9 Consensus size: 226
9049 AGACCACAAT
*
9059 ATCTGATTTTCCCTTCAAAGTAAGCGGAACATGTCTCTCTTTTCTAAGATTTGATATTCCCTTTA
1 ATCTGATTTTCCCTTCAAAGTAAGCGGAACATGTCTCTCTTTTCCAAGATTTGATATTCCCTTTA
* * * *
9124 GAGTAAGCGGAATAAATCTACCCCGATTTAATGGATCAACTCCCCTAAATTCAATTTTCCCTTCA
66 GAGTAAGCGGAACAAATCTACCCCGATTCAATGGATAAACTCCCCCAAATTCAATTTTCCCTTCA
* * * *
9189 GAGTAAGCGGAACATGTATCTCTTTTTCAATATTTGATATTCCCTTCAGAGTAAG-AGGAACAAG
131 GAGTAAGCGAAACAGGTATCACTTTTCCAATATTTGATATTCCCTTCAGAGTAAGCA-GAACAAG
9253 TCTGCCCCAATTCATTGGATTAACTCCCCTAG
195 TCTGCCCCAATTCATTGGATTAACTCCCCTAG
* *
9285 ATCTGATTTTCCCTTCAGAGTAAGCGGAACA-GATCTCTCTTTTCCAAGATTTGTTATT-CCTTT
1 ATCTGATTTTCCCTTCAAAGTAAGCGGAACATG-TCTCTCTTTTCCAAGATTTGATATTCCCTTT
* * *
9348 CAGAGTAAGCGGAACAAATCTACCCTGATTCAATGGATAAACTCCCCCAGA-TCTGATTTTCCCT
65 -AGAGTAAGCGGAACAAATCTACCCCGATTCAATGGATAAACTCCCCCAAATTC-AATTTTCCCT
* * * *
9412 TCAGAGTAAGCGAAATAGGTCTCACTTTTCCAAGT-TTTGATTTTCCTTTCAGAGTAAGCAGAAC
128 TCAGAGTAAGCGAAACAGGTATCACTTTTCCAA-TATTTGATATTCCCTTCAGAGTAAGCAGAAC
*
9476 AAGTCTGCCCCGATTCA
192 AAGTCTGCCCCAATTCA
9493 ATCTTCCCTG
Statistics
Matches: 184, Mismatches: 19, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
225 8 0.04
226 174 0.95
227 2 0.01
ACGTcount: A:0.28, C:0.24, G:0.15, T:0.33
Consensus pattern (226 bp):
ATCTGATTTTCCCTTCAAAGTAAGCGGAACATGTCTCTCTTTTCCAAGATTTGATATTCCCTTTA
GAGTAAGCGGAACAAATCTACCCCGATTCAATGGATAAACTCCCCCAAATTCAATTTTCCCTTCA
GAGTAAGCGAAACAGGTATCACTTTTCCAATATTTGATATTCCCTTCAGAGTAAGCAGAACAAGT
CTGCCCCAATTCATTGGATTAACTCCCCTAG
Found at i:9576 original size:136 final size:135
Alignment explanation
Indices: 9379--9766 Score: 389
Period size: 136 Copynumber: 2.9 Consensus size: 135
9369 ACCCTGATTC
* * * * * *
9379 AATGGAT-AAACTCCCCCAGATCTGATTTTCCCTTCAGAGTAAGCGAAATAGGTCTCACTTTTCC
1 AATGGATCAACCTCCTCCAGATCTGATATTCCCTTCAAAGTAAGCGAAACAGGTCTCTCTTTTCC
* * *
9443 AAGTTTTGATTTTCCTTTCAGAGTAAGCAGAACAAGTCTGCCCCGATTCAATCTTCCCTG-GGTG
66 AAGTTTTGATTTTCCTTT-AGAGTAAGCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAAG-A
*
9507 ACAGTGA
129 ACAGAGA
* * *
9514 AATGGATCAACCTCCTCCAGATCTGATATTCCCTTCAAAGTAAGGGGAAGAGGTCTCTCTTTTCC
1 AATGGATCAACCTCCTCCAGATCTGATATTCCCTTCAAAGTAAGCGAAACAGGTCTCTCTTTTCC
* * ** *
9579 AAGTTTTGATTTTCC-TTAGTG-ACAGCGGAACAAGTCTACCTTGATTCAAACTTCCCTGAAGAA
66 AAGTTTTGATTTTCCTTTAGAGTA-AGCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAAGAA
*
9642 CAGAGG
130 CAGAGA
* * *
9648 AATGAATC-ACGTATCCTCTCAGATCTGATATTCCCTTC-AAGATAAGC-ATAACAGATC-CATC
1 AATGGATCAAC--CTCCTC-CAGATCTGATATTCCCTTCAAAG-TAAGCGA-AACAGGTCTC-TC
* * *
9709 TCCTT-CAAGATTTGATATTACCTTTAGAGTAAGCGGAACAAGTCTGCCCCGATTCAAT
60 T-TTTCCAAGTTTTGAT-TTTCCTTTAGAGTAAGCGGAACAAGTCTGCCCCGATTCAAT
9767 GGATCAACTC
Statistics
Matches: 208, Mismatches: 32, Indels: 23
0.79 0.12 0.09
Matches are distributed among these distances:
133 3 0.01
134 45 0.22
135 19 0.09
136 106 0.51
137 6 0.03
138 28 0.13
139 1 0.00
ACGTcount: A:0.29, C:0.24, G:0.18, T:0.30
Consensus pattern (135 bp):
AATGGATCAACCTCCTCCAGATCTGATATTCCCTTCAAAGTAAGCGAAACAGGTCTCTCTTTTCC
AAGTTTTGATTTTCCTTTAGAGTAAGCGGAACAAGTCTGCCCCGATTCAATCTTCCCTGAAGAAC
AGAGA
Found at i:9966 original size:48 final size:49
Alignment explanation
Indices: 9894--10015 Score: 140
Period size: 49 Copynumber: 2.5 Consensus size: 49
9884 CAACTCCCTC
* * * *
9894 AGATCTGATTTTCCCTTCGGAGTAAG-CATAACATGTCTC-TCTTTTCCA
1 AGATTTGATATTCCCTTCAGAGTAAGTCA-AACAGGTCTCTTCTTTTCCA
* * * *
9942 AGATTTGATATTCCCTTCAGAGTAAGTGAAATAGGTCTCTTTTTTTTCA
1 AGATTTGATATTCCCTTCAGAGTAAGTCAAACAGGTCTCTTCTTTTCCA
*
9991 AGATTTGATATTCTCTTCAGAGTAA
1 AGATTTGATATTCCCTTCAGAGTAA
10016 TCGGAACAAA
Statistics
Matches: 63, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
48 31 0.49
49 32 0.51
ACGTcount: A:0.26, C:0.18, G:0.16, T:0.40
Consensus pattern (49 bp):
AGATTTGATATTCCCTTCAGAGTAAGTCAAACAGGTCTCTTCTTTTCCA
Found at i:9991 original size:113 final size:113
Alignment explanation
Indices: 9714--9967 Score: 364
Period size: 113 Copynumber: 2.2 Consensus size: 113
9704 CCATCTCCTT
* * ** * * *
9714 CAAGATTTGATATTACCTTTAGAGTAAGCGGAACAAGTCTGCCCCGATTCAATGGATCAACTCCC
1 CAAGATTTGATATTCCCTTCAGAGTAAGCAAAAAAAGTATACCCCGATTCAATGGATCAACTCCC
*
9779 CCAGATCTGATTTTCCATTCAAAGTAAGCGGAACAAGTCTCTCTTTTC
66 CCAGATCTGATTTTCCATTCAAAGTAAGCAGAACAAGTCTCTCTTTTC
* *
9827 CAAGATTTGATATTCTCTTCGGAGTAAGCAAAAAAAGTATACCCCGATTCAATGGATCAACTCCC
1 CAAGATTTGATATTCCCTTCAGAGTAAGCAAAAAAAGTATACCCCGATTCAATGGATCAACTCCC
* * ** * *
9892 TCAGATCTGATTTTCCCTTCGGAGTAAGCATAACATGTCTCTCTTTTC
66 CCAGATCTGATTTTCCATTCAAAGTAAGCAGAACAAGTCTCTCTTTTC
9940 CAAGATTTGATATTCCCTTCAGAGTAAG
1 CAAGATTTGATATTCCCTTCAGAGTAAG
9968 TGAAATAGGT
Statistics
Matches: 123, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
113 123 1.00
ACGTcount: A:0.30, C:0.24, G:0.16, T:0.31
Consensus pattern (113 bp):
CAAGATTTGATATTCCCTTCAGAGTAAGCAAAAAAAGTATACCCCGATTCAATGGATCAACTCCC
CCAGATCTGATTTTCCATTCAAAGTAAGCAGAACAAGTCTCTCTTTTC
Found at i:10093 original size:161 final size:162
Alignment explanation
Indices: 9822--10128 Score: 467
Period size: 161 Copynumber: 1.9 Consensus size: 162
9812 CAAGTCTCTC
*
9822 TTTTCCAAGATTTGATATTCTCTTCGGAGTAAGCAAAAAAAGTATACCCCGATTCAATGGATCAA
1 TTTTCCAAGATTTGATATTCTCTTCAGAGTAAGCAAAAAAAGTATACCCCGATTCAATGGATCAA
* *
9887 CTCCCTCAGATCTGATTTTCCCTTCGGAGTAAGCATAACATGTCTCTCTTTTCCAAGATTTGATA
66 CTCCCTCAGATCTGATTTTCCCTTCAGAGTAAGCAGAACATGTCTCTCTTTTCCAAGATTTGATA
9952 TTCCCTTCAGAGTAAGTGAAATAGGTCTCTTT
131 TTCCCTTCAGAGTAAGTGAAATAGGTCTCTTT
* * * * * **
9984 TTTTTCAAGATTTGATATTCTCTTCAGAGTAATCGGAACAAA-TCTGGCCCGATTCAATGGAT-A
1 TTTTCCAAGATTTGATATTCTCTTCAGAGTAAGC-AAAAAAAGTATACCCCGATTCAATGGATCA
*
10047 GACTCCC-CAGATCTGATTTTCCCTTCAGAGTAAGCAGAACATGTCTCTCTTTTCTAAGATTTGA
65 -ACTCCCTCAGATCTGATTTTCCCTTCAGAGTAAGCAGAACATGTCTCTCTTTTCCAAGATTTGA
*
10111 TATTCCCTTTAGAGTAAG
129 TATTCCCTTCAGAGTAAG
10129 CGGAATAAAT
Statistics
Matches: 131, Mismatches: 12, Indels: 5
0.89 0.08 0.03
Matches are distributed among these distances:
161 72 0.55
162 54 0.41
163 5 0.04
ACGTcount: A:0.28, C:0.21, G:0.16, T:0.35
Consensus pattern (162 bp):
TTTTCCAAGATTTGATATTCTCTTCAGAGTAAGCAAAAAAAGTATACCCCGATTCAATGGATCAA
CTCCCTCAGATCTGATTTTCCCTTCAGAGTAAGCAGAACATGTCTCTCTTTTCCAAGATTTGATA
TTCCCTTCAGAGTAAGTGAAATAGGTCTCTTT
Found at i:10150 original size:112 final size:113
Alignment explanation
Indices: 9942--10265 Score: 431
Period size: 112 Copynumber: 2.9 Consensus size: 113
9932 CTCTTTTCCA
* * * * * *
9942 AGATTTGATATTCCCTTCAGAGTAAG-TGAA-ATAGGTCTCTTTTTTTTCAAGATTTGATATTCT
1 AGATCTGATTTTCCCTTCAGAGTAAGCAGAACAT--GTCTCTCTTTTCT-AAGATTTGATATTCC
* * * * *
10005 CTTCAGAGTAATCGGAACAAATCTGGCCCGATTCAATGGATAGACT-CCCC
63 CTTTAGAGTAAGCGGAATAAATCTGCCCCGATTCAATGGATAAACTCCCCC
10055 AGATCTGATTTTCCCTTCAGAGTAAGCAGAACATGTCTCTCTTTTCTAAGATTTGATATTCCCTT
1 AGATCTGATTTTCCCTTCAGAGTAAGCAGAACATGTCTCTCTTTTCTAAGATTTGATATTCCCTT
*
10120 TAGAGTAAGCGGAATAAATCTTCCCCGATTCAATGGATAAACTCCCCC
66 TAGAGTAAGCGGAATAAATCTGCCCCGATTCAATGGATAAACTCCCCC
* * * * *
10168 AGATCTGA-TTTCCCTTCAGAGTAAGCGGAACATGTCTCACTTTTCCAAGATTTGATTTTCCTTT
1 AGATCTGATTTTCCCTTCAGAGTAAGCAGAACATGTCTCTCTTTTCTAAGATTTGATATTCCCTT
*
10232 TAGAGTAAGCGGAATAATTCTGCCCCGATTCAAT
66 TAGAGTAAGCGGAATAAATCTGCCCCGATTCAAT
10266 TTTCCGTGGT
Statistics
Matches: 189, Mismatches: 19, Indels: 7
0.88 0.09 0.03
Matches are distributed among these distances:
112 137 0.72
113 47 0.25
114 3 0.02
115 2 0.01
ACGTcount: A:0.28, C:0.22, G:0.17, T:0.34
Consensus pattern (113 bp):
AGATCTGATTTTCCCTTCAGAGTAAGCAGAACATGTCTCTCTTTTCTAAGATTTGATATTCCCTT
TAGAGTAAGCGGAATAAATCTGCCCCGATTCAATGGATAAACTCCCCC
Found at i:13923 original size:19 final size:19
Alignment explanation
Indices: 13899--13937 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
13889 ACACGAAAAG
13899 AAAGGAAAAGAGAGAGAAA
1 AAAGGAAAAGAGAGAGAAA
*
13918 AAAGGAAAATAGAGAGAAA
1 AAAGGAAAAGAGAGAGAAA
13937 A
1 A
13938 GAAAACAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.28, T:0.03
Consensus pattern (19 bp):
AAAGGAAAAGAGAGAGAAA
Found at i:13925 original size:29 final size:29
Alignment explanation
Indices: 13893--14006 Score: 83
Period size: 29 Copynumber: 3.9 Consensus size: 29
13883 AAAAACACAC
*
13893 GAAAAGAAAGGAAAAGAGAGAGAAAAA-AG
1 GAAAAGAAAGGAAAAGA-AAAGAAAAAGAG
* * * *
13922 GAAAATAGAGAGAAAAGAAAACAAAAAGATA
1 GAAAAGAAAG-GAAAAGAAAAGAAAAAGA-G
* *
13953 GAAAAGAAAAG-AAAGAAGAGAAAAAGAG
1 GAAAAGAAAGGAAAAGAAAAGAAAAAGAG
*
13981 GAACAA-AAA-TAAAAGAAAAAGAAAAA
1 GAA-AAGAAAGGAAAAG-AAAAGAAAAA
14007 AGAAATAAAG
Statistics
Matches: 66, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
28 10 0.15
29 40 0.61
30 9 0.14
31 7 0.11
ACGTcount: A:0.73, C:0.02, G:0.23, T:0.03
Consensus pattern (29 bp):
GAAAAGAAAGGAAAAGAAAAGAAAAAGAG
Found at i:13957 original size:20 final size:20
Alignment explanation
Indices: 13904--13989 Score: 77
Period size: 20 Copynumber: 4.2 Consensus size: 20
13894 AAAAGAAAGG
**
13904 AAAAGAGAGAGAAA-AAAGGA
1 AAAAGAGAGA-AAAGAAAACA
13924 AAATAGAGAGAAAAGAAAACA
1 AAA-AGAGAGAAAAGAAAACA
* *
13945 AAAAGATAGAAAAGAAAAGA
1 AAAAGAGAGAAAAGAAAACA
*
13965 AAGAAGAGA-AAAAGAGGAACA
1 AA-AAGAGAGAAAAGA-AAACA
13986 AAAA
1 AAAA
13990 TAAAAGAAAA
Statistics
Matches: 55, Mismatches: 7, Indels: 8
0.79 0.10 0.11
Matches are distributed among these distances:
20 31 0.56
21 24 0.44
ACGTcount: A:0.72, C:0.02, G:0.23, T:0.02
Consensus pattern (20 bp):
AAAAGAGAGAAAAGAAAACA
Found at i:13964 original size:14 final size:14
Alignment explanation
Indices: 13893--14036 Score: 52
Period size: 14 Copynumber: 10.0 Consensus size: 14
13883 AAAAACACAC
13893 GAAAAGAAAGGAAAA
1 GAAAAGAAA-GAAAA
* *
13908 GAGAGAGAAA-AAAG
1 GA-AAAGAAAGAAAA
*
13922 GAAAATAGAGAGAAAA
1 G-AAA-AGAAAGAAAA
*
13938 GAAAACAAA-AAGATA
1 GAAAAGAAAGAA-A-A
13953 GAAAAGAAA-AGAAA
1 GAAAAGAAAGA-AAA
* *
13967 GAAGAGAAA-AAGAG
1 GAAAAGAAAGAA-AA
*
13981 GAACAA-AAATAAAA
1 GAA-AAGAAAGAAAA
13995 GAAAA-AGAA-AAAA
1 GAAAAGA-AAGAAAA
*
14008 G-AAATAAAGAATAA
1 GAAAAGAAAGAA-AA
14022 GAACAAGAAAGAAAA
1 GAA-AAGAAAGAAAA
14037 CAGATCAAAC
Statistics
Matches: 100, Mismatches: 13, Indels: 32
0.69 0.09 0.22
Matches are distributed among these distances:
12 5 0.05
13 14 0.14
14 35 0.35
15 27 0.27
16 19 0.19
ACGTcount: A:0.73, C:0.02, G:0.22, T:0.03
Consensus pattern (14 bp):
GAAAAGAAAGAAAA
Found at i:16156 original size:52 final size:52
Alignment explanation
Indices: 16086--16390 Score: 224
Period size: 52 Copynumber: 5.7 Consensus size: 52
16076 AACTTTTAAA
* * * *
16086 AGAAGCTAAGCCTAATTTTTAGAGGCTTCTTGATGTTTGTAAATGAGTTTTT
1 AGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTGTAAATGAATTTTT
* * * * ** *
16138 AGAAACTAAGGCTGATTTTCAAGGGTACCTTGATGATTATTTCCAAA-GAATTTTT
1 AGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATG-TT-TGT--AAATGAATTTTT
* * * *
16193 AAATAAGCAAAGCCTAATTTTTAGGGGTTTCTTGATATTT-TCAAATGAGTTTTT
1 AGA-AA-CTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTGT-AAATGAATTTTT
* * * * *
16247 AGAAAATAAGTCTGAA-TTTCAGGGTTTTCTTGATG-ATGATTACTAATGAATTTTT
1 AGAAACTAAGCCT-AATTTTTAGGGGTTTCTTGATGTTTG--TA--AATGAATTTTT
* * *
16302 AAAAGAAATTAAGCCT-ATTTTTAGGGGGTTCTTGATGTTTTTAAATGAATTTTT
1 ---AGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTGTAAATGAATTTTT
*
16356 ATAAACTAAGCCTAATTTTTAGGGGTTTCTTGATG
1 AGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATG
16391 AAAACTGAAA
Statistics
Matches: 194, Mismatches: 40, Indels: 38
0.71 0.15 0.14
Matches are distributed among these distances:
51 12 0.06
52 67 0.35
53 11 0.06
54 24 0.12
55 20 0.10
56 10 0.05
57 38 0.20
58 12 0.06
ACGTcount: A:0.31, C:0.09, G:0.19, T:0.41
Consensus pattern (52 bp):
AGAAACTAAGCCTAATTTTTAGGGGTTTCTTGATGTTTGTAAATGAATTTTT
Found at i:16385 original size:109 final size:110
Alignment explanation
Indices: 16079--16391 Score: 371
Period size: 109 Copynumber: 2.9 Consensus size: 110
16069 TCAAATAAAC
* *
16079 TTTTAAAAGAAGCTAAGCCTAATTTTTAGAGGCTTCTTGATGTTTGTAAATGAGTTTTTAGAAAC
1 TTTTAAAAGAAGCTAAGCCTAATTTTTAGGGGCTTCTTGATGTTTTTAAATGAGTTTTTAGAAAC
* * * ** * *
16144 TAAGGCTGATTTTCAAGGGTACCTTGATGATTATTTCCAAAGAAT
66 TAAGCCTAATTTTCAGGGGTTTCTTGATGATGATTACCAAAGAAT
* * * * * *
16189 TTTT-AAATAAGCAAAGCCTAATTTTTAGGGGTTTCTTGATATTTTCAAATGAGTTTTTAGAAAA
1 TTTTAAAAGAAGCTAAGCCTAATTTTTAGGGGCTTCTTGATGTTTTTAAATGAGTTTTTAGAAAC
* * * *
16253 TAAGTCTGAA-TTTCAGGGTTTTCTTGATGATGATTACTAATGAAT
66 TAAGCCT-AATTTTCAGGGGTTTCTTGATGATGATTACCAAAGAAT
** * * *
16298 TTTTAAAAGAAATTAAGCCT-ATTTTTAGGGGGTTCTTGATGTTTTTAAATGAATTTTTATAAAC
1 TTTTAAAAGAAGCTAAGCCTAATTTTTAGGGGCTTCTTGATGTTTTTAAATGAGTTTTTAGAAAC
*
16362 TAAGCCTAATTTTTAGGGGTTTCTTGATGA
66 TAAGCCTAATTTTCAGGGGTTTCTTGATGA
16392 AAACTGAAAA
Statistics
Matches: 169, Mismatches: 31, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
108 2 0.01
109 151 0.89
110 16 0.09
ACGTcount: A:0.31, C:0.09, G:0.18, T:0.42
Consensus pattern (110 bp):
TTTTAAAAGAAGCTAAGCCTAATTTTTAGGGGCTTCTTGATGTTTTTAAATGAGTTTTTAGAAAC
TAAGCCTAATTTTCAGGGGTTTCTTGATGATGATTACCAAAGAAT
Found at i:16738 original size:38 final size:39
Alignment explanation
Indices: 16641--17323 Score: 777
Period size: 40 Copynumber: 17.5 Consensus size: 39
16631 AAGGATAAAC
* ** *
16641 ATCTCGCTTGAGATAGTTTCACTCAAAACAGAAGACCATC
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTTT
*
16681 ATCTCTCTTGAGATAGTTTCACTCGAAACAGAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* * * *
16719 ATCTTGCTTGAGATAGTTTCATTTGAAACAAAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* * *
16757 ATCTCGCTTGAGATAGTTTCATTCGAAAGAGAGGATTTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTTT
* *
16797 ATCTCACTTGAGATAGTTTCACTCGAAACATAAGATTTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTTT
* * *
16837 GTCTCGCTTGAGATAGTTTCACTCGAATCAAAAGATTTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTTT
* *
16877 ATCTCGCTTGAGATAGTTTCACCCGAAACATAAGATTTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTTT
* *
16917 GTCTCGCTTGAGATAGTTTCACTCGAATCAGAAGATTTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTTT
** *
16957 ATCTCGCTTGAGATAGTTTCAAACGAAACAAAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* * *
16996 ATTTAGCTTGAGATATTTTCACTCGAAACAGAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
*
17034 ATCTCGCTTGAGATAGTTTCACTTGAAACAGAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* *
17072 ATCTCGCTTGAGATTGTTTCACTTGAAACAGAAGATTTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTTT
*
17112 ATCTCACTTGAGATAGTTTCACTCGAAACA-ACAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGA-AGATTTT
* * ** *
17151 ATATCGCTTGATATAGTTTCGTTCGAAACAG-ATATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* * * * ** * *
17189 ATATCTCTTAAGATATTTTTGCTCGAAAAAGAATATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* *
17228 ATCTCGCTTAAGATAGTTTCGCTCGAAACAGAAGATTTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
* * *
17267 ATCTTGCTTGAGCTAGTTTCACTCGAAACATAAGA-TTT
1 ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
** *
17305 ATCTCAATTGAGATTGTTT
1 ATCTCGCTTGAGATAGTTT
17324 TCCTTAAAGA
Statistics
Matches: 557, Mismatches: 79, Indels: 16
0.85 0.12 0.02
Matches are distributed among these distances:
38 182 0.33
39 133 0.24
40 242 0.43
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.36
Consensus pattern (39 bp):
ATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTT
Found at i:17122 original size:155 final size:156
Alignment explanation
Indices: 16641--17304 Score: 780
Period size: 155 Copynumber: 4.2 Consensus size: 156
16631 AAGGATAAAC
* * * ** * * *
16641 ATCTCGCTTGAGATAGTTTCACTCAAAACAGAAGACCATCATCTCTCTTGAGATAGTTTCACTCG
1 ATCTCACTTGAGATAGTTTCACTCGAAACAAAAGA-TTTTATTTCGCTTGAGATAGTTTCACTCG
* * * *
16706 AAACAGAAGATTTATCTTGCTTGAGATAGTTTCATTTGAAACAAAAGA-TTTATCTCGCTTGAGA
65 AAACAGAAGATTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGA
* * *
16770 TAGTTTCATTCGAAAGAGAGGATTTTT
130 TAGTTTCACTCGAAACAGAAGATTTTT
*
16797 ATCTCACTTGAGATAGTTTCACTCGAAACATAAGATTTT-TGTCTCGCTTGAGATAGTTTCACTC
1 ATCTCACTTGAGATAGTTTCACTCGAAACAAAAGATTTTAT-T-TCGCTTGAGATAGTTTCACTC
* * * * *
16861 GAATCAAAAGATTTTTATCTCGCTTGAGATAGTTTCACCCGAAACATAAGATTTTTGTCTCGCTT
64 GAAACAGAAGA--TTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGA-TTTTATCTCGCTT
*
16926 GAGATAGTTTCACTCGAATCAGAAGATTTTT
126 GAGATAGTTTCACTCGAAACAGAAGATTTTT
* ** * *
16957 ATCTCGCTTGAGATAGTTTCAAACGAAACAAAAGATTTTATTTAGCTTGAGATATTTTCACTCGA
1 ATCTCACTTGAGATAGTTTCACTCGAAACAAAAGATTTTATTTCGCTTGAGATAGTTTCACTCGA
*
17022 AACAGAAGATTTATCTCGCTTGAGATAGTTTCACTTGAAACAGAAGA-TTTATCTCGCTTGAGAT
66 AACAGAAGATTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGAT
* *
17086 TGTTTCACTTGAAACAGAAGATTTTT
131 AGTTTCACTCGAAACAGAAGATTTTT
* * * **
17112 ATCTCACTTGAGATAGTTTCACTCGAAACAACAGATTTTATATCGCTTGATATAGTTTCGTTCGA
1 ATCTCACTTGAGATAGTTTCACTCGAAACAAAAGATTTTATTTCGCTTGAGATAGTTTCACTCGA
* * * * * ** * * *
17177 AACAGATA-TTTTATATCTCTTAAGATATTTTTGCTCGAAAAAGAATATTTTATCTCGCTTAAGA
66 AACAGA-AGATTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGA
*
17241 TAGTTTCGCTCGAAACAGAAGA-TTTT
130 TAGTTTCACTCGAAACAGAAGATTTTT
** * *
17267 ATCTTGCTTGAGCTAGTTTCACTCGAAACATAAGATTT
1 ATCTCACTTGAGATAGTTTCACTCGAAACAAAAGATTT
17305 ATCTCAATTG
Statistics
Matches: 435, Mismatches: 64, Indels: 19
0.84 0.12 0.04
Matches are distributed among these distances:
154 1 0.00
155 167 0.38
156 96 0.22
157 35 0.08
158 33 0.08
159 28 0.06
160 74 0.17
161 1 0.00
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.36
Consensus pattern (156 bp):
ATCTCACTTGAGATAGTTTCACTCGAAACAAAAGATTTTATTTCGCTTGAGATAGTTTCACTCGA
AACAGAAGATTTATCTCGCTTGAGATAGTTTCACTCGAAACAGAAGATTTTATCTCGCTTGAGAT
AGTTTCACTCGAAACAGAAGATTTTT
Found at i:17240 original size:20 final size:20
Alignment explanation
Indices: 17182--17240 Score: 50
Period size: 20 Copynumber: 3.0 Consensus size: 20
17172 TTCGAAACAG
* *
17182 ATATTTTATATCTCTTAAG-
1 ATATTTTATCTCGCTTAAGA
***
17201 ATATTTT-TGCTCGAAAAAGA
1 ATATTTTAT-CTCGCTTAAGA
17221 ATATTTTATCTCGCTTAAGA
1 ATATTTTATCTCGCTTAAGA
17241 TAGTTTCGCT
Statistics
Matches: 29, Mismatches: 8, Indels: 5
0.69 0.19 0.12
Matches are distributed among these distances:
18 1 0.03
19 12 0.41
20 15 0.52
21 1 0.03
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (20 bp):
ATATTTTATCTCGCTTAAGA
Found at i:17433 original size:59 final size:59
Alignment explanation
Indices: 17341--17484 Score: 189
Period size: 59 Copynumber: 2.4 Consensus size: 59
17331 AGAAAACTAT
* * * * *
17341 GCCTCACTCGAGGGATTAACATTTCGTTTGCTCGATTCATAACACTTCAAATCAGTAAC
1 GCCTCACTTGAGGGATCAACATTTCCTTTGCTCGATTCACAACACTTCAAATCAGCAAC
* * * *
17400 GCCTCACTTGAAGGATCAACATTTCCTTTGCTCGATTCACAACACTTCGAATCAGCGAT
1 GCCTCACTTGAGGGATCAACATTTCCTTTGCTCGATTCACAACACTTCAAATCAGCAAC
* *
17459 GCCTCACATGAGGGACCAACATTTCC
1 GCCTCACTTGAGGGATCAACATTTCC
17485 AGAAGAGGAT
Statistics
Matches: 73, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
59 73 1.00
ACGTcount: A:0.28, C:0.28, G:0.16, T:0.28
Consensus pattern (59 bp):
GCCTCACTTGAGGGATCAACATTTCCTTTGCTCGATTCACAACACTTCAAATCAGCAAC
Found at i:17662 original size:90 final size:88
Alignment explanation
Indices: 17421--17671 Score: 281
Period size: 92 Copynumber: 2.8 Consensus size: 88
17411 AGGATCAACA
*
17421 TTTCCTTTGCTCGATTCACAACACTTCGAATCAGCGATGCCTCACATGAGGGACCAACATTTCCA
1 TTTCATTTGCTCGATTCACAACACTTCGAATCAGCGATGCCTCACATGAGGGA-CAACATTTCCA
* * * *
17486 GAAGAGGATTCATGAGAAGAACTT
65 GTAGAGAACTCATAAGAAGAACTT
* *
17510 ATTCAATCTTGGCTCGATTCACAACACTTCGAATCAGCGACGCCTCACATGAGGGACTAACATTT
1 TTTC-AT-TT-GCTCGATTCACAACACTTCGAATCAGCGATGCCTCACATGAGGGAC-AACATTT
*
17575 CCAGTAGAGAACTCATAATGAAGAGCTT
62 CCAGTAGAGAACTCATAA-GAAGAACTT
* * * * * *
17603 GTTTCATTTGCTCGATTCACGACATTTCAAATCAACAATG-CTCAC-TAGAGGGATCAACATTTA
1 -TTTCATTTGCTCGATTCACAACACTTCGAATCAGCGATGCCTCACAT-GAGGGA-CAACATTTC
17666 CAGTAG
63 CAGTAG
17672 GAAGATCACG
Statistics
Matches: 138, Mismatches: 16, Indels: 15
0.82 0.09 0.09
Matches are distributed among these distances:
89 4 0.03
90 25 0.18
91 29 0.21
92 67 0.49
93 10 0.07
94 3 0.02
ACGTcount: A:0.31, C:0.24, G:0.18, T:0.27
Consensus pattern (88 bp):
TTTCATTTGCTCGATTCACAACACTTCGAATCAGCGATGCCTCACATGAGGGACAACATTTCCAG
TAGAGAACTCATAAGAAGAACTT
Found at i:18783 original size:110 final size:111
Alignment explanation
Indices: 18666--19005 Score: 415
Period size: 110 Copynumber: 3.1 Consensus size: 111
18656 CTAAATTCTC
* * * **
18666 TCGTGTTTTTACAAAATGGTTACTCGAAGGGCATT-TTTT-ATAATTTTTCCCATTTTACTATAT
1 TCGTGTTTTTGCAAAATAGTCACTCTTAGGG-ATTGTTTTCATAATTTTTCCCATTTTACTATAT
*
18729 GCATTGTATTTTTTGGTAAAATATCATTCAAGGTCCCCCAAACTTTG
65 GCTTTGTATTTTTTGGTAAAATATCATTCAAGGTCCCCCAAACTTTG
* *
18776 TCATGTTTTTGCAAAATAGTCAC-CTTTAGGGATTGTTTTCATAA-TTTTCCTATTTTACTATAT
1 TCGTGTTTTTGCAAAATAGTCACTC-TTAGGGATTGTTTTCATAATTTTTCCCATTTTACTATAT
* * *
18839 GCTTTGTATTTTTTGGTAAAATATCATTCCAGAT-CCCCAAACTTTA
65 GCTTTGTATTTTTTGGTAAAATATCATTCAAGGTCCCCCAAACTTTG
* * * * * *
18885 CCGTGTTTATTGTAAAATAGCCACTTTTAGAGATTGTTTTCATAATTTTT-CCATTTTACTGTAT
1 TCGTGTTT-TTGCAAAATAGTCACTCTTAGGGATTGTTTTCATAATTTTTCCCATTTTACTATAT
** *
18949 G-TTTCGTATTTTTTGGTAAAATATCATTCTTGGTCCCCAAAACTTTG
65 GCTTT-GTATTTTTTGGTAAAATATCATTCAAGGTCCCCCAAACTTTG
18996 TCGTGTTTTT
1 TCGTGTTTTT
19006 TGCATTTTGG
Statistics
Matches: 197, Mismatches: 25, Indels: 16
0.83 0.11 0.07
Matches are distributed among these distances:
109 24 0.12
110 148 0.75
111 25 0.13
ACGTcount: A:0.25, C:0.16, G:0.13, T:0.46
Consensus pattern (111 bp):
TCGTGTTTTTGCAAAATAGTCACTCTTAGGGATTGTTTTCATAATTTTTCCCATTTTACTATATG
CTTTGTATTTTTTGGTAAAATATCATTCAAGGTCCCCCAAACTTTG
Found at i:22761 original size:25 final size:22
Alignment explanation
Indices: 22742--22787 Score: 74
Period size: 22 Copynumber: 2.1 Consensus size: 22
22732 ATTGTATACC
22742 AACCTCATCAAATATGTTGTTA
1 AACCTCATCAAATATGTTGTTA
* *
22764 AATCTTATCAAATATGTTGTTA
1 AACCTCATCAAATATGTTGTTA
22786 AA
1 AA
22788 TCTTGAAGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.39, C:0.13, G:0.09, T:0.39
Consensus pattern (22 bp):
AACCTCATCAAATATGTTGTTA
Found at i:22803 original size:25 final size:22
Alignment explanation
Indices: 22748--22791 Score: 88
Period size: 22 Copynumber: 2.0 Consensus size: 22
22738 TACCAACCTC
22748 ATCAAATATGTTGTTAAATCTT
1 ATCAAATATGTTGTTAAATCTT
22770 ATCAAATATGTTGTTAAATCTT
1 ATCAAATATGTTGTTAAATCTT
22792 GAAGTAGAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 22 1.00
ACGTcount: A:0.36, C:0.09, G:0.09, T:0.45
Consensus pattern (22 bp):
ATCAAATATGTTGTTAAATCTT
Found at i:24463 original size:20 final size:20
Alignment explanation
Indices: 24434--24484 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
24424 CTCAGAAGGA
* *
24434 GTATCAATACTACAGGATTG
1 GTATCGATACTACAGGAGTG
* * *
24454 GTATCGATACTCCTGGGGTG
1 GTATCGATACTACAGGAGTG
24474 GTATCGATACT
1 GTATCGATACT
24485 CGAAAAACAT
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.31
Consensus pattern (20 bp):
GTATCGATACTACAGGAGTG
Found at i:28299 original size:26 final size:26
Alignment explanation
Indices: 28263--28312 Score: 82
Period size: 26 Copynumber: 1.9 Consensus size: 26
28253 CCGACGTGGT
28263 AGTTTCTAGAAGATCCAATCAGCGGC
1 AGTTTCTAGAAGATCCAATCAGCGGC
* *
28289 AGTTTCTAGAAGATCTAGTCAGCG
1 AGTTTCTAGAAGATCCAATCAGCG
28313 CTCCTTCTGG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 22 1.00
ACGTcount: A:0.30, C:0.20, G:0.24, T:0.26
Consensus pattern (26 bp):
AGTTTCTAGAAGATCCAATCAGCGGC
Found at i:28544 original size:26 final size:25
Alignment explanation
Indices: 28515--28571 Score: 62
Period size: 27 Copynumber: 2.2 Consensus size: 25
28505 GGTTTTATAA
*
28515 AAGTTCTC-TTCTTTATTTTATTTTT
1 AAGTTCTCATT-TTTACTTTATTTTT
*
28540 CAAGTTTTCGATTTTTACTTTATTTTT
1 -AAGTTCTC-ATTTTTACTTTATTTTT
28567 AAGTT
1 AAGTT
28572 TTGAGGGATT
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
26 12 0.44
27 13 0.48
28 2 0.07
ACGTcount: A:0.19, C:0.11, G:0.07, T:0.63
Consensus pattern (25 bp):
AAGTTCTCATTTTTACTTTATTTTT
Found at i:28804 original size:3 final size:3
Alignment explanation
Indices: 28796--28824 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
28786 GAATAGGGTT
28796 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
28825 TTAAGCTTTG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:29484 original size:16 final size:17
Alignment explanation
Indices: 29463--29496 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
29453 CTTTAATTGC
29463 CTTTTT-TATTTAATCT
1 CTTTTTATATTTAATCT
29479 CTTTTTACTATTTAATCT
1 CTTTTTA-TATTTAATCT
29497 TATTTTACCA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
18 10 0.62
ACGTcount: A:0.21, C:0.15, G:0.00, T:0.65
Consensus pattern (17 bp):
CTTTTTATATTTAATCT
Found at i:31378 original size:3 final size:3
Alignment explanation
Indices: 31370--31397 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
31360 TGTTAAGTTC
31370 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
31398 ATAAAATGGA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:31578 original size:25 final size:25
Alignment explanation
Indices: 31486--31578 Score: 68
Period size: 25 Copynumber: 3.8 Consensus size: 25
31476 TTGAAAATTA
*
31486 ATTTT-TAATATTTTATCAATAATAA
1 ATTTTATAATATTTTAT-AATAATAT
* *
31511 ATTTTATATATAATGTAT-AT-ATAT
1 ATTTTATA-ATATTTTATAATAATAT
* ***
31535 ATATTAATAA-ATCAGATAATAATAT
1 AT-TTTATAATATTTTATAATAATAT
31560 ATTTTATAATATTTTATAA
1 ATTTTATAATATTTTATAA
31579 ATTAAATTTA
Statistics
Matches: 50, Mismatches: 12, Indels: 12
0.68 0.16 0.16
Matches are distributed among these distances:
23 3 0.06
24 14 0.28
25 24 0.48
26 2 0.04
27 7 0.14
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.49
Consensus pattern (25 bp):
ATTTTATAATATTTTATAATAATAT
Found at i:31594 original size:34 final size:34
Alignment explanation
Indices: 31486--31594 Score: 78
Period size: 34 Copynumber: 3.0 Consensus size: 34
31476 TTGAAAATTA
*
31486 ATTTT-TAATATTTTATCAATAATAAATTTTATATAT
1 ATTTTATAATATTTTAT-AA-ATTAAA-TTTATATAT
* * * * *
31522 AATGTATATATATATATTAATAAATCAGA-TAATAATAT
1 -AT-TTTATA-ATAT-TTTATAAATTAAATTTAT-ATAT
31560 ATTTTATAATATTTTATAAATTAAATTTATATAT
1 ATTTTATAATATTTTATAAATTAAATTTATATAT
31594 A
1 A
31595 ATATATTTTT
Statistics
Matches: 55, Mismatches: 11, Indels: 15
0.68 0.14 0.19
Matches are distributed among these distances:
34 15 0.27
35 7 0.13
36 5 0.09
37 7 0.13
38 6 0.11
39 5 0.09
40 6 0.11
41 4 0.07
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (34 bp):
ATTTTATAATATTTTATAAATTAAATTTATATAT
Found at i:34936 original size:59 final size:60
Alignment explanation
Indices: 34825--34947 Score: 212
Period size: 59 Copynumber: 2.0 Consensus size: 60
34815 CGATCGCCTG
34825 AAACTTAGCCTGCCTCCTTTGAGCTTACTTGTTCTTTATGTTGATATGTGTGGTAAAGGAACT
1 AAACTTAGCCTGCCTCCTTTGAG--T-CTTGTTCTTTATGTTGATATGTGTGGTAAAGGAACT
34888 AAACTTAGCCTGCCTCCTTTGAG-CTTGTTCTTTATGTTGATATGTGTGGTAAAGGAACT
1 AAACTTAGCCTGCCTCCTTTGAGTCTTGTTCTTTATGTTGATATGTGTGGTAAAGGAACT
34947 A
1 A
34948 TCTACTTTTG
Statistics
Matches: 60, Mismatches: 0, Indels: 4
0.94 0.00 0.06
Matches are distributed among these distances:
59 37 0.62
63 23 0.38
ACGTcount: A:0.23, C:0.17, G:0.21, T:0.39
Consensus pattern (60 bp):
AAACTTAGCCTGCCTCCTTTGAGTCTTGTTCTTTATGTTGATATGTGTGGTAAAGGAACT
Found at i:37087 original size:3 final size:3
Alignment explanation
Indices: 37079--37110 Score: 55
Period size: 3 Copynumber: 10.7 Consensus size: 3
37069 TAAATAGGGG
*
37079 TTA TTA TTA TTA TTG TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
37111 CCGATATGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:39924 original size:32 final size:31
Alignment explanation
Indices: 39888--39963 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
39878 CGGGGCCGTG
*
39888 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
39920 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
39951 GAGCCTACCTAAG
1 GGGCCTACCTAAG
39964 TGTCACATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.26, C:0.32, G:0.28, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:39947 original size:63 final size:63
Alignment explanation
Indices: 39841--39963 Score: 151
Period size: 63 Copynumber: 2.0 Consensus size: 63
39831 ACCTAAGGGA
* * ** *
39841 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
39904 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAG
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAG
39964 TGTCACATTA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.25, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:41473 original size:18 final size:18
Alignment explanation
Indices: 41450--41484 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
41440 TTCCATCCGG
*
41450 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
41468 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
41485 GTCCTTCGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:42837 original size:14 final size:14
Alignment explanation
Indices: 42837--42903 Score: 71
Period size: 14 Copynumber: 4.4 Consensus size: 14
42827 TCAAACGGCT
42837 CGGCTCAGCTCAAA
1 CGGCTCAGCTCAAA
42851 CGGCTCGGCTCAGCTCAAA
1 CGG--C---TCAGCTCAAA
*
42870 CGGCTCGGCTCAAA
1 CGGCTCAGCTCAAA
*
42884 CGGCTCGGCTCAAA
1 CGGCTCAGCTCAAA
42898 CGGCTC
1 CGGCTC
42904 CTCATGCTTC
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
14 32 0.68
16 1 0.02
17 1 0.02
19 13 0.28
ACGTcount: A:0.21, C:0.37, G:0.27, T:0.15
Consensus pattern (14 bp):
CGGCTCAGCTCAAA
Found at i:42862 original size:33 final size:33
Alignment explanation
Indices: 42818--42903 Score: 95
Period size: 33 Copynumber: 2.6 Consensus size: 33
42808 CGGCTCGGCT
*
42818 CGGCTCAGCTCAAACGGCTCGGCTCAGCTCAAA
1 CGGCTCGGCTCAAACGGCTCGGCTCAGCTCAAA
* * * *
42851 CGGCTCGGCTC-AGC-TCAAACGGCTCGGCTCAAA
1 CGGCTCGGCTCAAACGGC--TCGGCTCAGCTCAAA
42884 CGGCTCGGCTCAAACGGCTC
1 CGGCTCGGCTCAAACGGCTC
42904 CTCATGCTTC
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
31 1 0.02
32 2 0.05
33 35 0.85
34 2 0.05
35 1 0.02
ACGTcount: A:0.21, C:0.37, G:0.27, T:0.15
Consensus pattern (33 bp):
CGGCTCGGCTCAAACGGCTCGGCTCAGCTCAAA
Found at i:42893 original size:38 final size:38
Alignment explanation
Indices: 42791--42894 Score: 124
Period size: 38 Copynumber: 2.7 Consensus size: 38
42781 GGTCAACAGT
*
42791 AAACGGCTCGG-TCTAGGCGGCTCGGCTCGGCTCAGCTC
1 AAACGGCTCGGCTC-AAGCGGCTCGGCTCGGCTCAGCTC
* *
42829 AAACGGCTCGGCTC-AGC-TCAAACGGCTCGGCTCAGCTC
1 AAACGGCTCGGCTCAAGCGGC--TCGGCTCGGCTCAGCTC
*
42867 AAACGGCTCGGCTCAAACGGCTCGGCTC
1 AAACGGCTCGGCTCAAGCGGCTCGGCTC
42895 AAACGGCTCC
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
36 1 0.02
37 2 0.04
38 47 0.85
39 4 0.07
40 1 0.02
ACGTcount: A:0.18, C:0.36, G:0.30, T:0.16
Consensus pattern (38 bp):
AAACGGCTCGGCTCAAGCGGCTCGGCTCGGCTCAGCTC
Found at i:42894 original size:19 final size:19
Alignment explanation
Indices: 42813--42881 Score: 138
Period size: 19 Copynumber: 3.6 Consensus size: 19
42803 CTAGGCGGCT
42813 CGGCTCGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
42832 CGGCTCGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
42851 CGGCTCGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
42870 CGGCTCGGCTCA
1 CGGCTCGGCTCA
42882 AACGGCTCGG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.19, C:0.38, G:0.28, T:0.16
Consensus pattern (19 bp):
CGGCTCGGCTCAGCTCAAA
Found at i:45004 original size:32 final size:31
Alignment explanation
Indices: 44968--45043 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
44958 CGGGGCCGTG
*
44968 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
45000 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
45031 GAGCCTACCTAAG
1 GGGCCTACCTAAG
45044 TGTCACATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.26, C:0.32, G:0.28, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:45027 original size:63 final size:63
Alignment explanation
Indices: 44921--45043 Score: 151
Period size: 63 Copynumber: 2.0 Consensus size: 63
44911 ACCTAAGGGA
* * ** *
44921 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
44984 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAG
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAG
45044 TGTCACATTA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.25, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:46554 original size:18 final size:18
Alignment explanation
Indices: 46531--46565 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
46521 TTCCATCCGG
*
46531 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
46549 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
46566 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:47919 original size:14 final size:14
Alignment explanation
Indices: 47919--47985 Score: 71
Period size: 14 Copynumber: 4.4 Consensus size: 14
47909 TCAAACGGCT
47919 CGGCTCAGCTCAAA
1 CGGCTCAGCTCAAA
47933 CGGCTCGGCTCAGCTCAAA
1 CGG--C---TCAGCTCAAA
*
47952 CGGCTCGGCTCAAA
1 CGGCTCAGCTCAAA
*
47966 CGGCTCGGCTCAAA
1 CGGCTCAGCTCAAA
47980 CGGCTC
1 CGGCTC
47986 CTCATGCTTC
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
14 32 0.68
16 1 0.02
17 1 0.02
19 13 0.28
ACGTcount: A:0.21, C:0.37, G:0.27, T:0.15
Consensus pattern (14 bp):
CGGCTCAGCTCAAA
Found at i:47944 original size:33 final size:33
Alignment explanation
Indices: 47900--47985 Score: 95
Period size: 33 Copynumber: 2.6 Consensus size: 33
47890 CGGCTCGGCT
*
47900 CGGCTCAGCTCAAACGGCTCGGCTCAGCTCAAA
1 CGGCTCGGCTCAAACGGCTCGGCTCAGCTCAAA
* * * *
47933 CGGCTCGGCTC-AGC-TCAAACGGCTCGGCTCAAA
1 CGGCTCGGCTCAAACGGC--TCGGCTCAGCTCAAA
47966 CGGCTCGGCTCAAACGGCTC
1 CGGCTCGGCTCAAACGGCTC
47986 CTCATGCTTC
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
31 1 0.02
32 2 0.05
33 35 0.85
34 2 0.05
35 1 0.02
ACGTcount: A:0.21, C:0.37, G:0.27, T:0.15
Consensus pattern (33 bp):
CGGCTCGGCTCAAACGGCTCGGCTCAGCTCAAA
Found at i:47975 original size:38 final size:38
Alignment explanation
Indices: 47873--47976 Score: 124
Period size: 38 Copynumber: 2.7 Consensus size: 38
47863 GGTCAACAGT
*
47873 AAACGGCTCGG-TCTAGGCGGCTCGGCTCGGCTCAGCTC
1 AAACGGCTCGGCTC-AAGCGGCTCGGCTCGGCTCAGCTC
* *
47911 AAACGGCTCGGCTC-AGC-TCAAACGGCTCGGCTCAGCTC
1 AAACGGCTCGGCTCAAGCGGC--TCGGCTCGGCTCAGCTC
*
47949 AAACGGCTCGGCTCAAACGGCTCGGCTC
1 AAACGGCTCGGCTCAAGCGGCTCGGCTC
47977 AAACGGCTCC
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
36 1 0.02
37 2 0.04
38 47 0.85
39 4 0.07
40 1 0.02
ACGTcount: A:0.18, C:0.36, G:0.30, T:0.16
Consensus pattern (38 bp):
AAACGGCTCGGCTCAAGCGGCTCGGCTCGGCTCAGCTC
Found at i:47976 original size:19 final size:19
Alignment explanation
Indices: 47895--47963 Score: 138
Period size: 19 Copynumber: 3.6 Consensus size: 19
47885 CTAGGCGGCT
47895 CGGCTCGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
47914 CGGCTCGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
47933 CGGCTCGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
47952 CGGCTCGGCTCA
1 CGGCTCGGCTCA
47964 AACGGCTCGG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.19, C:0.38, G:0.28, T:0.16
Consensus pattern (19 bp):
CGGCTCGGCTCAGCTCAAA
Found at i:50074 original size:32 final size:31
Alignment explanation
Indices: 50038--50113 Score: 89
Period size: 31 Copynumber: 2.4 Consensus size: 31
50028 CGGGGCCGTG
*
50038 GGGCCTACCTAAGAACACATCTTAGGGCCGCA
1 GGGCCTACCTAAGAA-ACATCTCAGGGCCGCA
** **
50070 GGGCCTACCCGAGAATGATCTCAGGGCCGCA
1 GGGCCTACCTAAGAAACATCTCAGGGCCGCA
*
50101 GAGCCTACCTAAG
1 GGGCCTACCTAAG
50114 TGTCACATTA
Statistics
Matches: 36, Mismatches: 8, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
31 23 0.64
32 13 0.36
ACGTcount: A:0.26, C:0.32, G:0.28, T:0.14
Consensus pattern (31 bp):
GGGCCTACCTAAGAAACATCTCAGGGCCGCA
Found at i:50097 original size:63 final size:63
Alignment explanation
Indices: 49991--50113 Score: 151
Period size: 63 Copynumber: 2.0 Consensus size: 63
49981 ACCTAAGGGA
* * ** *
49991 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATTTCGGGGCCGTGGGGCCTACCTAAGAAC
1 ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
* *
50054 ACATCTTAGGGCC-GCAGGGCCTACCCGAGA-ATGATCTCAGGGCCGCAGAGCCTACCTAAG
1 ACATCTTAGGGCCTG-AGAGCCTACCCAAGATA-GATCTCAGGGCCGCAGAGCCTACCTAAG
50114 TGTCACATTA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
62 2 0.04
63 49 0.96
ACGTcount: A:0.25, C:0.29, G:0.28, T:0.17
Consensus pattern (63 bp):
ACATCTTAGGGCCTGAGAGCCTACCCAAGATAGATCTCAGGGCCGCAGAGCCTACCTAAGAAC
Found at i:51623 original size:18 final size:18
Alignment explanation
Indices: 51600--51634 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
51590 TTCCATCCGG
*
51600 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
51618 TCTTATCATTTACTTCA
1 TCTTATCATTTAATTCA
51635 GTCCTTTCGA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.29, C:0.17, G:0.00, T:0.54
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:52988 original size:14 final size:14
Alignment explanation
Indices: 52988--53054 Score: 71
Period size: 14 Copynumber: 4.4 Consensus size: 14
52978 TCAAACGGCT
52988 CGGCTCAGCTCAAA
1 CGGCTCAGCTCAAA
53002 CGGCTCGGCTCAGCTCAAA
1 CGG--C---TCAGCTCAAA
*
53021 CGGCTCGGCTCAAA
1 CGGCTCAGCTCAAA
*
53035 CGGCTCGGCTCAAA
1 CGGCTCAGCTCAAA
53049 CGGCTC
1 CGGCTC
53055 CTCATGCTTC
Statistics
Matches: 47, Mismatches: 1, Indels: 10
0.81 0.02 0.17
Matches are distributed among these distances:
14 32 0.68
16 1 0.02
17 1 0.02
19 13 0.28
ACGTcount: A:0.21, C:0.37, G:0.27, T:0.15
Consensus pattern (14 bp):
CGGCTCAGCTCAAA
Found at i:53013 original size:33 final size:33
Alignment explanation
Indices: 52969--53054 Score: 95
Period size: 33 Copynumber: 2.6 Consensus size: 33
52959 CGGCTCGGCT
*
52969 CGGCTCAGCTCAAACGGCTCGGCTCAGCTCAAA
1 CGGCTCGGCTCAAACGGCTCGGCTCAGCTCAAA
* * * *
53002 CGGCTCGGCTC-AGC-TCAAACGGCTCGGCTCAAA
1 CGGCTCGGCTCAAACGGC--TCGGCTCAGCTCAAA
53035 CGGCTCGGCTCAAACGGCTC
1 CGGCTCGGCTCAAACGGCTC
53055 CTCATGCTTC
Statistics
Matches: 41, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
31 1 0.02
32 2 0.05
33 35 0.85
34 2 0.05
35 1 0.02
ACGTcount: A:0.21, C:0.37, G:0.27, T:0.15
Consensus pattern (33 bp):
CGGCTCGGCTCAAACGGCTCGGCTCAGCTCAAA
Found at i:53044 original size:38 final size:38
Alignment explanation
Indices: 52942--53045 Score: 124
Period size: 38 Copynumber: 2.7 Consensus size: 38
52932 GGTCAACAGT
*
52942 AAACGGCTCGG-TCTAGGCGGCTCGGCTCGGCTCAGCTC
1 AAACGGCTCGGCTC-AAGCGGCTCGGCTCGGCTCAGCTC
* *
52980 AAACGGCTCGGCTC-AGC-TCAAACGGCTCGGCTCAGCTC
1 AAACGGCTCGGCTCAAGCGGC--TCGGCTCGGCTCAGCTC
*
53018 AAACGGCTCGGCTCAAACGGCTCGGCTC
1 AAACGGCTCGGCTCAAGCGGCTCGGCTC
53046 AAACGGCTCC
Statistics
Matches: 55, Mismatches: 6, Indels: 10
0.77 0.08 0.14
Matches are distributed among these distances:
36 1 0.02
37 2 0.04
38 47 0.85
39 4 0.07
40 1 0.02
ACGTcount: A:0.18, C:0.36, G:0.30, T:0.16
Consensus pattern (38 bp):
AAACGGCTCGGCTCAAGCGGCTCGGCTCGGCTCAGCTC
Found at i:53045 original size:19 final size:19
Alignment explanation
Indices: 52964--53032 Score: 138
Period size: 19 Copynumber: 3.6 Consensus size: 19
52954 CTAGGCGGCT
52964 CGGCTCGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
52983 CGGCTCGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
53002 CGGCTCGGCTCAGCTCAAA
1 CGGCTCGGCTCAGCTCAAA
53021 CGGCTCGGCTCA
1 CGGCTCGGCTCA
53033 AACGGCTCGG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 50 1.00
ACGTcount: A:0.19, C:0.38, G:0.28, T:0.16
Consensus pattern (19 bp):
CGGCTCGGCTCAGCTCAAA
Found at i:56616 original size:45 final size:45
Alignment explanation
Indices: 56567--56872 Score: 416
Period size: 45 Copynumber: 6.8 Consensus size: 45
56557 ATTATAACCT
* * ** * *
56567 CTTTTCTGTTGATAATGCACCCATATGCATTTCAATTACAATATA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACCATAGTATA
* *
56612 CTTTTTTGTTGATAATGTACCCATATATATTTCAACCATAGTATA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACCATAGTATA
*
56657 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTATA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACCATAGTATA
* * * *
56702 CTTTGCTGTTGATAATGCAACCATATGCATTTCAACCATAGTATA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACCATAGTATA
* * * *
56747 CTTTTATGTTGATAATGCACCCATATGCATTTCAACTC-TAGCATA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAAC-CATAGTATA
* *
56792 ATTTTCTGTTGATAATGTACCCATATACATTTCAACCATAGTATG
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACCATAGTATA
*
56837 TTTTTCTGTTGATAATGTACCCATATACATTTCAAC
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAAC
56873 TATGGCATCC
Statistics
Matches: 232, Mismatches: 27, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
44 1 0.00
45 230 0.99
46 1 0.00
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.41
Consensus pattern (45 bp):
CTTTTCTGTTGATAATGTACCCATATACATTTCAACCATAGTATA
Found at i:56897 original size:135 final size:135
Alignment explanation
Indices: 56623--56913 Score: 368
Period size: 135 Copynumber: 2.2 Consensus size: 135
56613 TTTTTTGTTG
* ** * *
56623 ATAATGTACCCATATATATTTCAACCATAGTATACTTTTCTGTTGATAATGTACCCATATACATT
1 ATAATGAACCCATATGCATTTCAACCATAGCATAATTTTCTGTTGATAATGTACCCATATACATT
* * * *
56688 TCAACTATAGTATACTTTGCTGTTGATAATGCAACCATATGCATTTCAACCATAGTATACTTTTA
66 TCAACCATAGTATACTTTGCTGTTGATAATGCAACCATATACATTTCAACCATAGCATACTTTCA
***
56753 TGTTG
131 TGCCA
*
56758 ATAATGCACCCATATGCATTTCAACTC-TAGCATAATTTTCTGTTGATAATGTACCCATATACAT
1 ATAATGAACCCATATGCATTTCAAC-CATAGCATAATTTTCTGTTGATAATGTACCCATATACAT
** * * * * * *
56822 TTCAACCATAGTATGTTTTTCTGTTGATAATGTACCCATATACATTTCAACTATGGCATCCTTTC
65 TTCAACCATAGTATACTTTGCTGTTGATAATGCAACCATATACATTTCAACCATAGCATACTTTC
56887 ATGCCA
130 ATGCCA
*
56893 ATAATGAACCTATATGCATTT
1 ATAATGAACCCATATGCATTT
56914 GTATTTTCAT
Statistics
Matches: 133, Mismatches: 22, Indels: 2
0.85 0.14 0.01
Matches are distributed among these distances:
135 132 0.99
136 1 0.01
ACGTcount: A:0.31, C:0.20, G:0.10, T:0.39
Consensus pattern (135 bp):
ATAATGAACCCATATGCATTTCAACCATAGCATAATTTTCTGTTGATAATGTACCCATATACATT
TCAACCATAGTATACTTTGCTGTTGATAATGCAACCATATACATTTCAACCATAGCATACTTTCA
TGCCA
Found at i:56913 original size:90 final size:88
Alignment explanation
Indices: 56567--56913 Score: 397
Period size: 90 Copynumber: 3.9 Consensus size: 88
56557 ATTATAACCT
* * * * ** * *
56567 CTTTTCTGTTGATAATGCACCCATATGCATTTCAATTACAATATACTTTTTTGTTGATAATGTAC
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCATAC-TTTCTGTTGATAATG-AA
**
56632 CCATATATATTTCAACCATAGTATA
64 CCATATGCATTTCAACCATAGTATA
*
56657 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGTATACTTTGCTGTTGATAATGCAA
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCATACTTT-CTGTTGATAATG-AA
56722 CCATATGCATTTCAACCATAGTATA
64 CCATATGCATTTCAACCATAGTATA
* * * * * *
56747 CTTTTATGTTGATAATGCACCCATATGCATTTCAACTCTAGCATAATTTTCTGTTGATAATGTAC
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCAT-ACTTTCTGTTGATAATG-AA
* *
56812 CCATATACATTTCAACCATAGTATG
64 CCATATGCATTTCAACCATAGTATA
* * * ***
56837 TTTTTCTGTTGATAATGTACCCATATACATTTCAACTATGGCATCCTTTCATGCCAATAATGAAC
1 CTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCATACTTTC-TGTTGATAATGAAC
56902 CTATATGCATTT
65 C-ATATGCATTT
56914 GTATTTTCAT
Statistics
Matches: 220, Mismatches: 33, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
89 10 0.05
90 206 0.94
91 4 0.02
ACGTcount: A:0.30, C:0.19, G:0.10, T:0.40
Consensus pattern (88 bp):
CTTTTCTGTTGATAATGTACCCATATACATTTCAACTATAGCATACTTTCTGTTGATAATGAACC
ATATGCATTTCAACCATAGTATA
Found at i:57463 original size:22 final size:20
Alignment explanation
Indices: 57418--57463 Score: 56
Period size: 20 Copynumber: 2.2 Consensus size: 20
57408 GATGTTTCAT
*
57418 GGTATCGATACCCTTACCAT
1 GGTATCGATACCCTTACCAA
*
57438 GGTATCGATACTACCTTACTAA
1 GGTATCGATAC--CCTTACCAA
57460 GGTA
1 GGTA
57464 CCAATACCCC
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
20 11 0.50
22 11 0.50
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.30
Consensus pattern (20 bp):
GGTATCGATACCCTTACCAA
Found at i:57538 original size:20 final size:19
Alignment explanation
Indices: 57513--57563 Score: 68
Period size: 20 Copynumber: 2.6 Consensus size: 19
57503 GATGTTTGCT
57513 TGGTATCGATAC-CCTTACCA
1 TGGTATCGATACGCCTT--CA
57533 TGGTATCGATACTGCCTTCA
1 TGGTATCGATAC-GCCTTCA
57553 TGGTATCGATA
1 TGGTATCGATA
57564 TTAATTGAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
20 25 0.86
22 4 0.14
ACGTcount: A:0.24, C:0.24, G:0.20, T:0.33
Consensus pattern (19 bp):
TGGTATCGATACGCCTTCA
Found at i:60530 original size:14 final size:14
Alignment explanation
Indices: 60511--60538 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
60501 ATCGTTAACC
60511 GACCGTTGACCCTT
1 GACCGTTGACCCTT
60525 GACCGTTGACCCTT
1 GACCGTTGACCCTT
60539 AACTGACCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.14, C:0.36, G:0.21, T:0.29
Consensus pattern (14 bp):
GACCGTTGACCCTT
Found at i:61418 original size:39 final size:37
Alignment explanation
Indices: 61318--61419 Score: 89
Period size: 39 Copynumber: 2.6 Consensus size: 37
61308 GTCTATGACT
* **
61318 TGTAAGTCCTTACCGCAAGCTCATCGGCTTTGTGATAA
1 TGTAAGTCCTTACCG-AAGCTCCTCGAATTTGTGATAA
* * *
61356 TGGTAAGTCCTTGCC-ACAGGCTCCTCGAATTTGTGCTCAC
1 T-GTAAGTCCTTACCGA-A-GCTCCTCGAATTTGTGAT-AA
61396 TGTAAGTCCTTACCGAATGCTCCT
1 TGTAAGTCCTTACCGAA-GCTCCT
61420 TAGCTTTGTG
Statistics
Matches: 51, Mismatches: 8, Indels: 9
0.75 0.12 0.13
Matches are distributed among these distances:
37 1 0.02
38 2 0.04
39 45 0.88
40 3 0.06
ACGTcount: A:0.21, C:0.27, G:0.21, T:0.31
Consensus pattern (37 bp):
TGTAAGTCCTTACCGAAGCTCCTCGAATTTGTGATAA
Found at i:64526 original size:21 final size:21
Alignment explanation
Indices: 64500--64543 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
64490 AAAGACATGC
64500 TTGGTTTTCTCTTTTTTGTTT
1 TTGGTTTTCTCTTTTTTGTTT
64521 TTGGTTTTCTCTTTTTTGTTT
1 TTGGTTTTCTCTTTTTTGTTT
64542 TT
1 TT
64544 AGAGAAAGTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.00, C:0.09, G:0.14, T:0.77
Consensus pattern (21 bp):
TTGGTTTTCTCTTTTTTGTTT
Found at i:75283 original size:26 final size:25
Alignment explanation
Indices: 75252--75322 Score: 71
Period size: 21 Copynumber: 3.0 Consensus size: 25
75242 CCTCTTAAAT
75252 TTTTAACTTTTTCTTTTCTCTTTC-
1 TTTTAACTTTTTCTTTTCTCTTTCA
*
75276 -TTT-A-TTAATT-TTTTCTCTTTCA
1 TTTTAACTT-TTTCTTTTCTCTTTCA
*
75298 TTTTAACTTTTACTTTTTCTCTTTC
1 TTTTAACTTTTTC-TTTTCTCTTTC
75323 CTTCATTCAT
Statistics
Matches: 37, Mismatches: 3, Indels: 12
0.71 0.06 0.23
Matches are distributed among these distances:
21 13 0.35
22 3 0.08
23 6 0.16
24 2 0.05
25 2 0.05
26 11 0.30
ACGTcount: A:0.13, C:0.18, G:0.00, T:0.69
Consensus pattern (25 bp):
TTTTAACTTTTTCTTTTCTCTTTCA
Found at i:75342 original size:47 final size:46
Alignment explanation
Indices: 75252--75342 Score: 112
Period size: 47 Copynumber: 2.0 Consensus size: 46
75242 CCTCTTAAAT
* * * *
75252 TTTTAACTTTTTCTTTTCTCTTTCTTTATTAATTTTTTCTCTTTCA
1 TTTTAACTTTTACTTTTCTCTTTCTTCATTAATCTTCTCTCTTTCA
*
75298 TTTTAACTTTTACTTTTTCTCTTTCCTTCATTCATCTTCT-TCTTT
1 TTTTAACTTTTAC-TTTTCTCTTT-CTTCATTAATCTTCTCTCTTT
75343 TGTTATTCTC
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
46 12 0.32
47 15 0.39
48 11 0.29
ACGTcount: A:0.12, C:0.21, G:0.00, T:0.67
Consensus pattern (46 bp):
TTTTAACTTTTACTTTTCTCTTTCTTCATTAATCTTCTCTCTTTCA
Done.