Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003913.1 Hibiscus syriacus cultivar Beakdansim tig00008462_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: 52216
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Found at i:4450 original size:199 final size:199
Alignment explanation
Indices: 4076--4546 Score: 473
Period size: 199 Copynumber: 2.5 Consensus size: 199
4066 TTTTTTACTC
* * * *
4076 TCACGGAAGCTGCTCTCAACCTGGTGTTTGGGCAGCCTACTATCTTACCTCCCCCTTACCCCATT
1 TCACGGAAGCTGCTCTCAACCTGGCGTTTGGGCAGCCTACTACCTTACCTCCCCCTCAACCCATT
* * * * *
4141 ACATATGGGAATAAGGGTTAGCTAATTTTGAATTGCCCGTCCAGCTCAATTGGTAGAGCGCAAGG
66 ACATATGGGAATAAGGGTCAGCTAATTTAGAATTGACCATCCAGCTCAATTGGTAGAGCACAAGG
* * **
4206 TTATTAACCTTGTGGTCATGGGATCGAGTCCCACGTGGGTAATTCATAATTCTGACTGCCAGAGG
131 TTATTAACATTGGGGTCATGGGATCGAGTCCCACGTGCATAATTCATAATTCTGACTGCCAGAGG
4271 TCTT
196 TCTT
*
4275 TCACGGAAGCTGCTCTCAACCTGGCG-TTGGGACAGCCTACTACCTTACCTCCCCCTCAACCTAT
1 TCACGGAAGCTGCTCTCAACCTGGCGTTTGGG-CAGCCTACTACCTTACCTCCCCCTCAACCCAT
* *
4339 TACATAT-GGAAT-ATGGTCAGCT-ATTTAAGAA-TGACCATCCAGCTCAGTTGGTAGAGCACAA
65 TACATATGGGAATAAGGGTCAGCTAATTT-AGAATTGACCATCCAGCTCAATTGGTAGAGCACAA
* * ** * ** *
4400 GGTTCTTAATATTGGGGTTGTGGGATCCCA--CGGA-GGGCAT--TTCATAA---T---T--CAG
129 GGTTATTAACATTGGGGTCATGGGAT-CGAGTCCCACGTGCATAATTCATAATTCTGACTGCCAG
4452 A-GTC-T
193 AGGTCTT
* * * * *
4457 CCTACGGAAGCTGCTCTCAACCTGACGTTGGGGCAGCCTACTATCC-TACCT-CCCCTTACCCCA
1 TC-ACGGAAGCTGCTCTCAACCTGGCGTTTGGGCAGCCTACTA-CCTTACCTCCCCCTCAACCCA
*
4520 TTACATATGGGAATAAGGTTCAGCTAA
64 TTACATATGGGAATAAGGGTCAGCTAA
4547 AAATATCCTA
Statistics
Matches: 231, Mismatches: 32, Indels: 32
0.78 0.11 0.11
Matches are distributed among these distances:
182 19 0.08
183 46 0.20
184 18 0.08
185 1 0.00
186 1 0.00
189 1 0.00
192 7 0.03
194 3 0.01
195 2 0.01
196 50 0.22
197 13 0.06
198 10 0.04
199 60 0.26
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (199 bp):
TCACGGAAGCTGCTCTCAACCTGGCGTTTGGGCAGCCTACTACCTTACCTCCCCCTCAACCCATT
ACATATGGGAATAAGGGTCAGCTAATTTAGAATTGACCATCCAGCTCAATTGGTAGAGCACAAGG
TTATTAACATTGGGGTCATGGGATCGAGTCCCACGTGCATAATTCATAATTCTGACTGCCAGAGG
TCTT
Found at i:5321 original size:29 final size:29
Alignment explanation
Indices: 5289--5351 Score: 81
Period size: 29 Copynumber: 2.2 Consensus size: 29
5279 ATCCCTGTCC
*
5289 TGATTCTACATGAGATCATATCTCTATCA
1 TGATTCTACATGAGATCATATCTCCATCA
* * * *
5318 TGATTCTACTTGGGATTATATCTCCATCT
1 TGATTCTACATGAGATCATATCTCCATCA
5347 TGATT
1 TGATT
5352 TGCATGGAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.25, C:0.19, G:0.13, T:0.43
Consensus pattern (29 bp):
TGATTCTACATGAGATCATATCTCCATCA
Found at i:13207 original size:27 final size:27
Alignment explanation
Indices: 13149--13214 Score: 105
Period size: 27 Copynumber: 2.4 Consensus size: 27
13139 GATAATGGCT
* *
13149 TTGAATAATTCAGAATGTACTTCTGTG
1 TTGAATCATTCAGAATGTACTTCTGTA
*
13176 CTGAATCATTCAGAATGTACTTCTGTA
1 TTGAATCATTCAGAATGTACTTCTGTA
13203 TTGAATCATTCA
1 TTGAATCATTCA
13215 ACACTGTTTT
Statistics
Matches: 35, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.39
Consensus pattern (27 bp):
TTGAATCATTCAGAATGTACTTCTGTA
Found at i:17274 original size:34 final size:33
Alignment explanation
Indices: 17202--17298 Score: 99
Period size: 34 Copynumber: 2.9 Consensus size: 33
17192 TTTTTCCTAC
* *
17202 TTTATT-ATTCTTGTTATATATGCATAT-TATTT
1 TTTATTAATT-TTATTATATATGTATATATATTT
* *
17234 TCTATTAATTTTATTATATATGTATATATGTTTT
1 TTTATTAATTTTATTATATATGTATATAT-ATTT
* * *
17268 TTTATTAGTGTTATTATATATATATATATAT
1 TTTATTAATTTTATTATATATGTATATATAT
17299 ATATTATTTA
Statistics
Matches: 53, Mismatches: 9, Indels: 5
0.79 0.13 0.07
Matches are distributed among these distances:
32 20 0.38
33 5 0.09
34 28 0.53
ACGTcount: A:0.30, C:0.03, G:0.06, T:0.61
Consensus pattern (33 bp):
TTTATTAATTTTATTATATATGTATATATATTT
Found at i:17432 original size:2 final size:2
Alignment explanation
Indices: 17382--17412 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
17372 TATTATTATT
17382 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
17413 GTTTTTACTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:20699 original size:21 final size:22
Alignment explanation
Indices: 20677--20737 Score: 79
Period size: 22 Copynumber: 2.7 Consensus size: 22
20667 CAAAAAGGGC
20677 AAAAAGAAAAAAAAAAGAAGCA
1 AAAAAGAAAAAAAAAAGAAGCA
* *
20699 AAAAAGGAAAAAACAAGAA-CA
1 AAAAAGAAAAAAAAAAGAAGCA
20720 AAAAAGAAAGAACAAAAA
1 AAAAAGAAA-AA-AAAAA
20738 TAAAAAAGGG
Statistics
Matches: 33, Mismatches: 4, Indels: 3
0.82 0.10 0.08
Matches are distributed among these distances:
21 10 0.30
22 19 0.58
23 4 0.12
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAAAAAAAAGAAGCA
Found at i:20709 original size:22 final size:21
Alignment explanation
Indices: 20677--20745 Score: 77
Period size: 22 Copynumber: 3.3 Consensus size: 21
20667 CAAAAAGGGC
20677 AAAAAGAAAAAAAAAAGAAGCA
1 AAAAAGAAAAAAAAAAGAA-CA
* *
20699 AAAAAGGAAAAAACAAGAACA
1 AAAAAGAAAAAAAAAAGAACA
* * *
20720 AAAAAGAAAGAACAAA-AATA
1 AAAAAGAAAAAAAAAAGAACA
20740 AAAAAG
1 AAAAAG
20746 GGAACAAAAA
Statistics
Matches: 40, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
20 9 0.22
21 14 0.35
22 17 0.43
ACGTcount: A:0.80, C:0.06, G:0.13, T:0.01
Consensus pattern (21 bp):
AAAAAGAAAAAAAAAAGAACA
Found at i:20742 original size:20 final size:20
Alignment explanation
Indices: 20677--20745 Score: 75
Period size: 20 Copynumber: 3.3 Consensus size: 20
20667 CAAAAAGGGC
*
20677 AAAAAGAAAAAAAAAAGAAGCA
1 AAAAAGAAAAAACAAA-AA-CA
*
20699 AAAAAGGAAAAAACAAGAACA
1 AAAAA-GAAAAAACAAAAACA
* *
20720 AAAAAGAAAGAACAAAAATA
1 AAAAAGAAAAAACAAAAACA
20740 AAAAAG
1 AAAAAG
20746 GGAACAAAAA
Statistics
Matches: 41, Mismatches: 5, Indels: 4
0.82 0.10 0.08
Matches are distributed among these distances:
20 18 0.44
21 7 0.17
22 7 0.17
23 9 0.22
ACGTcount: A:0.80, C:0.06, G:0.13, T:0.01
Consensus pattern (20 bp):
AAAAAGAAAAAACAAAAACA
Found at i:21391 original size:22 final size:22
Alignment explanation
Indices: 21366--21414 Score: 80
Period size: 22 Copynumber: 2.2 Consensus size: 22
21356 CCATCAATCT
* *
21366 TTTGAGCATCCAATGTCAAACC
1 TTTGAGCATCAAATGCCAAACC
21388 TTTGAGCATCAAATGCCAAACC
1 TTTGAGCATCAAATGCCAAACC
21410 TTTGA
1 TTTGA
21415 CCAAACACAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.33, C:0.24, G:0.14, T:0.29
Consensus pattern (22 bp):
TTTGAGCATCAAATGCCAAACC
Found at i:22386 original size:36 final size:36
Alignment explanation
Indices: 22346--22628 Score: 278
Period size: 36 Copynumber: 8.0 Consensus size: 36
22336 CTAGAAGAGT
22346 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* *
22382 TTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * * * *
22418 TTTCGTCTATCTTGAGATAGTTTCCATTGAAATAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
22454 TTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
1 -TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
* * * * *
22491 ------ATAT-TTGA-ATATGTTTTCTTTGAAACAAA
1 TTTTGTCTCTCTTGAGACA-GTTTCCCTTGAAACAAA
** * ** * *
22520 TTCCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAA
*
22557 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAAC-AA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
*
22592 TTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAA
1 TTTT-GTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
22629 ACCTTTGAAT
Statistics
Matches: 201, Mismatches: 33, Indels: 25
0.78 0.13 0.10
Matches are distributed among these distances:
28 2 0.01
29 19 0.09
30 2 0.01
35 6 0.03
36 107 0.53
37 65 0.32
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (36 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA
Found at i:22563 original size:102 final size:104
Alignment explanation
Indices: 22346--22591 Score: 286
Period size: 102 Copynumber: 2.3 Consensus size: 104
22336 CTAGAAGAGT
* *
22346 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCTCTTG
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA-----TATATCTTGAGATAGTTTCTCTTG
* * * *
22411 AAACAAATTTCGTCTATCTTGAGATAGTTTCCATTGAAATAAAT
61 AAACAAATTCCGTCTACCTTGAGACAGTTTCCATTGAAATAAAG
22455 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAA-ATAT-TTGA-ATATGTTT-TCTTTGAAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATATATCTTGAGATA-GTTTCTC-TTGAAA
* ** *
22516 CAAATTCCGTCTCCCTTGAGACAGTTTCTTTTGGAACT-AAG
64 CAAATTCCGTCTACCTTGAGACAGTTTCCATT-GAAATAAAG
*
22557 TTTTGTCTCTCTTGAGACAGTTTCTCTTGAAACAA
1 TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAA
22592 TTTTCGTCTA
Statistics
Matches: 123, Mismatches: 11, Indels: 13
0.84 0.07 0.09
Matches are distributed among these distances:
101 5 0.04
102 76 0.62
103 6 0.05
109 36 0.29
ACGTcount: A:0.26, C:0.18, G:0.14, T:0.41
Consensus pattern (104 bp):
TTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAATATATCTTGAGATAGTTTCTCTTGAAACA
AATTCCGTCTACCTTGAGACAGTTTCCATTGAAATAAAG
Found at i:22594 original size:138 final size:138
Alignment explanation
Indices: 22366--22691 Score: 413
Period size: 138 Copynumber: 2.4 Consensus size: 138
22356 CTTGAGACAG
* *
22366 TTTCCCTTGAAACAAATTTTGTCTCTCTTGAGATAGTTTCTCTTGAAACAAATTTCGTCTATCTT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
* * * *
22431 GAGATAGTTTCCATTGAAATAAATTTTTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATATT
66 GAGACAGTTTCCATTGAAATAAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACATT
*
22496 TGAATATG
131 TGAATATA
* * ** * * * * *
22504 TTTTCTTTGAAACAAATTCCGTCTCCCTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCTCT
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAAC-AAATTTCGTCTATCT
* *
22569 TGAGACAGTTTCTC-TTGAAA-CAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACC
65 TGAGACAGTTTC-CATTGAAATAAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACA
*
22632 TTTGAATTTA
129 TTTGAATATA
* * * *
22642 TTTCCCCTAAAACAAATTTTATCTCCCTTGAGACAGTTACTCTTGAAACA
1 TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACA
22692 CAAAATCTTC
Statistics
Matches: 157, Mismatches: 29, Indels: 5
0.82 0.15 0.03
Matches are distributed among these distances:
137 1 0.01
138 126 0.80
139 29 0.18
140 1 0.01
ACGTcount: A:0.28, C:0.20, G:0.13, T:0.40
Consensus pattern (138 bp):
TTTCCCTTGAAACAAATTTTGTCTCCCTTGAGACAGTTTCTCTTGAAACAAATTTCGTCTATCTT
GAGACAGTTTCCATTGAAATAAATTTTCGTCTATCTTGAGACAGTTTCCCTTGAAACAAAACATT
TGAATATA
Found at i:23602 original size:105 final size:106
Alignment explanation
Indices: 23403--23814 Score: 579
Period size: 105 Copynumber: 4.0 Consensus size: 106
23393 GCACTCGAGG
* *
23403 CAACACAAGTTCAACTTCACAACGAAGGGA-CGACTGGTTGTCAACAAACAATTTCTCAATTTCA
1 CAACACAAGTTCAACTTCACAACGAAGGGACCG-CTGGTTGTCAACAAACAATTTCCCAATTCCA
23467 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
65 GAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * * *
23509 CAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGTTTGTCAAC-AACAACTTCCCAATCCCAG
1 CAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTCCAG
*
23573 AGCCAATTTCAACTTCACAACGAAAGATATTGGACTCCAGA
66 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* * * *
23614 CAACGCAAGTTCAACTTCACGACGAATGGACCGCTGCTTGTCAAC-AA-AATTT--C-ATT-CAG
1 CAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTCCAG
** *
23673 ATTCAATTTCAACTTCACAACGAAGGATATTGGACTCGAGA
66 AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
* **
23714 CAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCCGGTTCCAG
1 CAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTCCAG
* *
23779 AGCCAATTTCAACTTCACTACGGAGGATATTGGACT
66 AGCCAATTTCAACTTCACAACGAAGGATATTGGACT
23815 TGGAACAATG
Statistics
Matches: 273, Mismatches: 26, Indels: 14
0.87 0.08 0.04
Matches are distributed among these distances:
100 80 0.29
101 4 0.01
102 6 0.02
104 5 0.02
105 102 0.37
106 74 0.27
107 2 0.01
ACGTcount: A:0.34, C:0.26, G:0.17, T:0.23
Consensus pattern (106 bp):
CAACACAAGTTCAACTTCACAACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTCCAG
AGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGA
Found at i:24993 original size:24 final size:23
Alignment explanation
Indices: 24940--24994 Score: 60
Period size: 24 Copynumber: 2.4 Consensus size: 23
24930 TTTGATTTTC
24940 TTTTTAT-TATTATTATTTTACT
1 TTTTTATATATTATTATTTTACT
* *
24962 TATATATATATATATGT-TTTTACT
1 TTTTTATATAT-TAT-TATTTTACT
24986 TTTTTATAT
1 TTTTTATAT
24995 TTTACTCATT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
22 5 0.19
23 3 0.12
24 17 0.65
25 1 0.04
ACGTcount: A:0.27, C:0.04, G:0.02, T:0.67
Consensus pattern (23 bp):
TTTTTATATATTATTATTTTACT
Found at i:25023 original size:15 final size:17
Alignment explanation
Indices: 25005--25037 Score: 52
Period size: 15 Copynumber: 2.1 Consensus size: 17
24995 TTTACTCATT
25005 TATTTAT-CTAT-TTTA
1 TATTTATCCTATATTTA
25020 TATTTATCCTATATTTA
1 TATTTATCCTATATTTA
25037 T
1 T
25038 GTTTTTATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 7 0.44
16 4 0.25
17 5 0.31
ACGTcount: A:0.27, C:0.09, G:0.00, T:0.64
Consensus pattern (17 bp):
TATTTATCCTATATTTA
Found at i:29762 original size:216 final size:216
Alignment explanation
Indices: 29098--29919 Score: 1338
Period size: 216 Copynumber: 3.8 Consensus size: 216
29088 ATTTATGAAT
*
29098 TAAATTGAACAAATATGAAATTACAAATAAAAAATTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
* *
29163 AGATCAAATCAAAATAATTTTAAATTGTGA-GATTGAAATTAATACAAAAAAGTACTAAATTATA
66 GGATCAAATCGAAATAATTTTAAATTGTGATG-TTGAAATTAATACAAAAAAGTACTAAATTATA
* * * * * *
29227 TCCATTTAAAAAGTAATGGGCCAATTAAAAAAATAGAATTAAGTAATAAGTATGGATTAATTTCA
130 CCCATTTAAAAAGTTATGGGCCAATT-TAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCA
*
29292 TATGCAAATAAAATTTAGAGGAC
194 TATGCAAATAAAATTTGGAGGAC
29315 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
*
29380 GGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATAAATAC-AAAAAGTACTAAATTATAC
66 GGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATAC
*
29444 CCATTTAAAAAGTTACGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCATA
131 CCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCATA
29509 TGCAAATAAAATTTGGAGGAC
196 TGCAAATAAAATTTGGAGGAC
* *
29530 TAAATTAAAAAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
29595 GGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATAC
66 GGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATAC
* * *
29660 CCATTTAAAAAGTTATGAGCCAATTTAAAAATAGAAATAAATAATAAGTATGGGTCAATTTCAGA
131 CCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCATA
*
29725 TGCAAATAAAATTTGGAGGAA
196 TGCAAATAAAATTTGGAGGAC
29746 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACA-A---A--AG
1 TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
* *
29805 GGATCAAAATCGAAATAATTTTAAATTTTGAGGTTGAAATTAATACAAAAAAGTACTAAATTATA
66 GGATC-AAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATA
* * *
29870 CTCATTTAAAAAGTTATGGGTCAA-TTAATAAATAGAATTAAGTAATAAGT
130 CCCATTTAAAAAGTTATGGGCCAATTTAA-AAATAGAAATAAGTAATAAGT
29920 TGAGAAAAAA
Statistics
Matches: 572, Mismatches: 29, Indels: 14
0.93 0.05 0.02
Matches are distributed among these distances:
210 11 0.02
211 97 0.17
212 1 0.00
215 164 0.29
216 194 0.34
217 104 0.18
218 1 0.00
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.29
Consensus pattern (216 bp):
TAAATTGAACAAATATGAAATTACAAATAAAAATTTAAATAAATTAAACAACACACATTGATGAG
GGATCAAATCGAAATAATTTTAAATTGTGATGTTGAAATTAATACAAAAAAGTACTAAATTATAC
CCATTTAAAAAGTTATGGGCCAATTTAAAAATAGAAATAAGTAATAAGTATGGGTCAATTTCATA
TGCAAATAAAATTTGGAGGAC
Found at i:30010 original size:22 final size:21
Alignment explanation
Indices: 29961--30023 Score: 85
Period size: 20 Copynumber: 3.0 Consensus size: 21
29951 TATATAACAT
29961 AAACTATATAGTTTATATAT-
1 AAACTATATAGTTTATATATA
*
29981 AAAGTATAT-GTATTATATATAA
1 AAACTATATAGT-TTATATAT-A
30003 AAACTATATAGTTTATATATA
1 AAACTATATAGTTTATATATA
30024 TATATTATGT
Statistics
Matches: 37, Mismatches: 2, Indels: 7
0.80 0.04 0.15
Matches are distributed among these distances:
19 2 0.05
20 16 0.43
21 1 0.03
22 16 0.43
23 2 0.05
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.43
Consensus pattern (21 bp):
AAACTATATAGTTTATATATA
Found at i:30045 original size:18 final size:18
Alignment explanation
Indices: 29959--30070 Score: 59
Period size: 20 Copynumber: 5.9 Consensus size: 18
29949 TATATATAAC
*
29959 ATAAACTATATAGTTTATAT
1 ATAAACTATATA--TTATGT
* *
29979 ATAAAGTATATGTATTATAT
1 ATAAACTATA--TATTATGT
*
29999 ATAAAAACTATATAGT-T-T
1 AT--AAACTATATATTATGT
*
30017 ATATA-TATATATTATGT
1 ATAAACTATATATTATGT
* *
30034 GTAAACTATATATACCATGT
1 ATAAACTATATAT--TATGT
30054 ATAAACTATAATATTAT
1 ATAAACTAT-ATATTAT
30071 ATAGTTTATA
Statistics
Matches: 72, Mismatches: 10, Indels: 21
0.70 0.10 0.20
Matches are distributed among these distances:
15 7 0.10
16 3 0.04
17 4 0.06
18 10 0.14
19 3 0.04
20 32 0.44
21 4 0.06
22 9 0.12
ACGTcount: A:0.46, C:0.05, G:0.06, T:0.43
Consensus pattern (18 bp):
ATAAACTATATATTATGT
Found at i:30129 original size:11 final size:11
Alignment explanation
Indices: 30115--30152 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
30105 ACTACATAGT
30115 TTATATATAAA
1 TTATATATAAA
*
30126 TTATATATGAA
1 TTATATATAAA
30137 TTATATATAAA
1 TTATATATAAA
*
30148 CTATA
1 TTATA
30153 CAATTTATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (11 bp):
TTATATATAAA
Found at i:30178 original size:17 final size:17
Alignment explanation
Indices: 30158--30209 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
30148 CTATACAATT
* *
30158 TATATTTATATATTATG
1 TATATTTATAAATTATA
* *
30175 TATAATTATAAATAATA
1 TATATTTATAAATTATA
30192 TATATTGTATAAATTATA
1 TATATT-TATAAATTATA
30210 CAGTTTATTA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
17 18 0.64
18 10 0.36
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (17 bp):
TATATTTATAAATTATA
Found at i:30231 original size:22 final size:24
Alignment explanation
Indices: 30190--30248 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 24
30180 TTATAAATAA
* *
30190 TATATATTGTATAAATTATACAGTT
1 TATATA-TATATAAACTATACAGTT
*
30215 TAT-TA-ATATAAACTATATAGTT
1 TATATATATATAAACTATACAGTT
30237 TATATATATATA
1 TATATATATATA
30249 TATATATATA
Statistics
Matches: 29, Mismatches: 3, Indels: 5
0.78 0.08 0.14
Matches are distributed among these distances:
22 17 0.59
23 2 0.07
24 7 0.24
25 3 0.10
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.47
Consensus pattern (24 bp):
TATATATATATAAACTATACAGTT
Found at i:30242 original size:2 final size:2
Alignment explanation
Indices: 30237--30263 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
30227 CTATATAGTT
30237 TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA T
30264 GGGTTAGGGT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30279 original size:7 final size:7
Alignment explanation
Indices: 30267--30291 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
30257 TATATATGGG
30267 TTAGGGT
1 TTAGGGT
30274 TTAGGGT
1 TTAGGGT
30281 TTAGGGT
1 TTAGGGT
30288 TTAG
1 TTAG
30292 AAATATATAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.16, C:0.00, G:0.40, T:0.44
Consensus pattern (7 bp):
TTAGGGT
Found at i:30391 original size:41 final size:43
Alignment explanation
Indices: 29951--30379 Score: 130
Period size: 42 Copynumber: 9.7 Consensus size: 43
29941 CTAATATATA
*
29951 TATATAACATAAACTATATAGTTTATATATAAAGTATATGTAT
1 TATATAATATAAACTATATAGTTTATATATAAAGTATATGTAT
* * *
29994 TATAT-ATAAAAACTATATAGTTTATATATATATATTATGTGTAAACT
1 TATATAATATAAACTATATAGTTTATATATA-A-AGTATATGT--A-T
**
30041 ATATATACCATGTATAAACTATA-A-TATTATATAGTTTA-TATATGAACTAT
1 -TATATA--A--TATAAACTATATAGT-TTATATA-TAAAGTATATG---TAT
* * * * *
30091 TGA-ACTATATAGAAACTACATAGTTTATATATAAATTATATATGAA
1 T-ATA-TA-ATATAAACTATATAGTTTATATATAAAGTATATGT-AT
* * *
30137 T-TAT-ATATAAACTATACAATTTATAT-T-TA-TATAT-TAT
1 TATATAATATAAACTATATAGTTTATATATAAAGTATATGTAT
* * * * *
30174 GTATA-ATTATAAA-TA-ATA-TATATTGTATAAATTATACAGT-T
1 -TATATAATATAAACTATATAGTTTA-TATATAAAGTATA-TGTAT
* *
30215 TAT-TAATATAAACTATATAGTTTATATATATA-TATATATA-
1 TATATAATATAAACTATATAGTTTATATATAAAGTATATGTAT
**** * * *
30255 TATAT-ATATGGGTTAGGGTTTAGGGTTTAGGGTTTAGAAA-TATATAGTTTAT
1 TATATAATATAAACTA---TATA--GTTTA---TATATAAAGTATAT-G--TAT
30307 ATATATAATATAAACTATATAGTTTATATATAAAGTATATGTAT
1 -TATATAATATAAACTATATAGTTTATATATAAAGTATATGTAT
*
30351 TATAT-ATA-AAACTATATAGTTTTTATATA
1 TATATAATATAAACTATATAGTTTATATATA
30380 TATATTATGT
Statistics
Matches: 283, Mismatches: 50, Indels: 108
0.64 0.11 0.24
Matches are distributed among these distances:
36 3 0.01
37 5 0.02
38 5 0.02
39 14 0.05
40 25 0.09
41 29 0.10
42 54 0.19
43 17 0.06
44 11 0.04
45 7 0.02
46 10 0.04
47 17 0.06
48 28 0.10
49 9 0.03
50 9 0.03
51 9 0.03
52 8 0.03
53 17 0.06
54 6 0.02
ACGTcount: A:0.44, C:0.04, G:0.08, T:0.44
Consensus pattern (43 bp):
TATATAATATAAACTATATAGTTTATATATAAAGTATATGTAT
Found at i:30405 original size:41 final size:41
Alignment explanation
Indices: 30313--30410 Score: 112
Period size: 41 Copynumber: 2.4 Consensus size: 41
30303 TTATATATAT
30313 AATAT-AAACTATATAGTTTATATATAAAGTATATGTATTA
1 AATATAAAACTATATAGTTTATATATAAAGTATATGTATTA
* * *
30353 TATATAAAACTATATAGTTTTTATATATA-TATTATGTA-TA
1 AATATAAAACTATATAGTTTATATATAAAGTA-TATGTATTA
**
30393 AACTATTGAACTATATAG
1 AA-TATAAAACTATATAG
30411 AAACTACATA
Statistics
Matches: 49, Mismatches: 6, Indels: 5
0.82 0.10 0.08
Matches are distributed among these distances:
40 9 0.18
41 40 0.82
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (41 bp):
AATATAAAACTATATAGTTTATATATAAAGTATATGTATTA
Found at i:30426 original size:19 final size:21
Alignment explanation
Indices: 30404--30456 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 21
30394 ACTATTGAAC
*
30404 TATATAGAAACTACATA-G-T
1 TATATATAAACTACATATGAT
* *
30423 TATATATAAATTATATATGAT
1 TATATATAAACTACATATGAT
30444 TATATATAAACTA
1 TATATATAAACTA
30457 TACAATTTAT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 14 0.50
20 1 0.04
21 13 0.46
ACGTcount: A:0.49, C:0.06, G:0.06, T:0.40
Consensus pattern (21 bp):
TATATATAAACTACATATGAT
Found at i:30500 original size:92 final size:93
Alignment explanation
Indices: 30309--30501 Score: 230
Period size: 92 Copynumber: 2.1 Consensus size: 93
30299 TAGTTTATAT
* * * * * *
30309 ATATAATATAAACTATATAGTTTATATATAAAGTATATGTATTATATATAAAACTATATAGTTTT
1 ATAT-ATAGAAACTACATAGTTTATATATAAAGTATATATATTATATATAAAACTATACAATTTA
**
30374 TATATATATATTATGTATAAACTATTGAA
65 TATATATATATTATGTATAAACTATAAAA
* *
30403 CTATATAGAAACTACATAG-TTATATATAAATTATATATGATTATATAT-AAACTATACAATTTA
1 ATATATAGAAACTACATAGTTTATATATAAAGTATATAT-ATTATATATAAAACTATACAATTTA
* *
30466 TATTTATATATTATGTAT-AATTATAAATA
65 TATATATATATTATGTATAAACTATAAA-A
30495 ATATATA
1 ATATATA
30502 TTGTATATAT
Statistics
Matches: 84, Mismatches: 13, Indels: 6
0.82 0.13 0.06
Matches are distributed among these distances:
91 6 0.07
92 53 0.63
93 22 0.26
94 3 0.04
ACGTcount: A:0.47, C:0.04, G:0.05, T:0.44
Consensus pattern (93 bp):
ATATATAGAAACTACATAGTTTATATATAAAGTATATATATTATATATAAAACTATACAATTTAT
ATATATATATTATGTATAAACTATAAAA
Found at i:32026 original size:6 final size:6
Alignment explanation
Indices: 30521--32015 Score: 2383
Period size: 6 Copynumber: 259.0 Consensus size: 6
30511 TGGTTTAGGG
30521 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
30569 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATTTA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTA--TA
30619 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
30667 TATT-TA TATT-TA TTTATA -TTATA TTTATA TTTATA TTTATA TTTATA
1 T-TTATA T-TTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
30714 TTTATA TTTATA -TTATA -TT-TA TTT-TA TTT-TA TTT-TA TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
30756 TTTATA -TT-TA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
30802 TTTATA TTTATA TTTATA TTTATA -TT-TA TTTATA TTTATA TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
30848 TTTATA TATT-TA -TT-TA TTTATA TTTATA -TT-TA TTTATA TTTATA
1 TTTATA T-TTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
30892 TTTATA TTTATA TTTATA -TT-TA TTT-TA TTTATA TTTATA -TT-TA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
30935 TTTATA TTTATA TTTATA TTTATA -TT-TA TTTATA TTTATA TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
30981 TTT-TA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
31028 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA -TTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
31075 TTTATA TTTATTTA TTTATA TTTATTTA TTTATA -TTATA TTTATA TTTATA
1 TTTATA TTTA--TA TTTATA TTTA--TA TTTATA TTTATA TTTATA TTTATA
31126 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
31174 TTTATA TTTAT- TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
31221 -TTATA TTTATA -TT-TA TTTATA TTTATA TTTATA TTTATA TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
31266 TTTATA TTTATA TTTATA TTTATA TTTATA -TT-TA TTTATA TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
31312 -TTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
31359 -TTATA TTTATA TTTATA TTTATA -TT-TA TTT-TA TTTATA TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
31403 TTTATA TTTATA TTTATA TTTATA TTTATA -TTATA TTTATA -TTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
31449 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA -TT-TA TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
31495 -TTATA TTTATA TTTATA TTTATA TTTATA -TT-TA TTTATA TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
*
31540 TTTATA TTTTTA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
31588 TTTATA TTTAT- TTTATA TTTATA TTTATA -TTATA TTTATA TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
31634 TTTATA TTTATA -TT-TA TTTATA TTT-TA TTTATA TTTATA TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
31679 -TT-TA TTT-TA TTT-TA TTTATA -TTATA -TT-TA TTTAT- TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
31719 TTTATA TTTATA TTTATA -TT-TA TTTATA TTTATA TTTATA TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
31765 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
*
31813 TTTATA -TTATA TTATATT TATTATA TTTATA TTTATA TTTATA TTTATA
1 TTTATA TTTATA TT-TATA T-TTATA TTTATA TTTATA TTTATA TTTATA
31862 TTTATA TTTATA -TT-TA TTTATA TTTATA -TT-TA TTTATA TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
31906 TTTATA -TTATA TTTATA TTTATA TTTATA TTTATA TTTATA -TT-TA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
31951 TTTATA TTTATA TTTATA TTTATA TTTATA -TTATA TTTATA TTTATA
1 TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA TTTATA
31998 TTTATA TTTATA TTTATA
1 TTTATA TTTATA TTTATA
32016 AATATTTATA
Statistics
Matches: 1416, Mismatches: 4, Indels: 138
0.91 0.00 0.09
Matches are distributed among these distances:
4 42 0.03
5 215 0.15
6 1128 0.80
7 12 0.01
8 19 0.01
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (6 bp):
TTTATA
Found at i:32043 original size:11 final size:11
Alignment explanation
Indices: 32006--32045 Score: 53
Period size: 11 Copynumber: 3.5 Consensus size: 11
31996 TATTTATATT
*
32006 TATATTTATAAA
1 TATATATAT-AA
*
32018 TATTTATATAA
1 TATATATATAA
32029 TATATATATAA
1 TATATATATAA
32040 TATATA
1 TATATA
32046 ATGTATAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
11 18 0.72
12 7 0.28
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (11 bp):
TATATATATAA
Found at i:32062 original size:21 final size:21
Alignment explanation
Indices: 32036--32076 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
32026 TAATATATAT
32036 ATAATATATAATGTA-TAATAA
1 ATAATAT-TAATGTATTAATAA
*
32057 ATAATATTAATTTATTAATA
1 ATAATATTAATGTATTAATA
32077 TAAACATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 6 0.33
21 12 0.67
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.44
Consensus pattern (21 bp):
ATAATATTAATGTATTAATAA
Found at i:32203 original size:61 final size:61
Alignment explanation
Indices: 32122--32248 Score: 159
Period size: 61 Copynumber: 2.1 Consensus size: 61
32112 TATAAAGATC
* * * * *
32122 AAATTGAACAAATTTTAAATATGAAGCTTAAATTAATAAACTGTA-A-TATTAAATTTAGACT
1 AAATTGAAAAAAGTTGAAATATAAAACTTAAATTAATAAA-T-TACATTATTAAATTTAGACT
* *
32183 AAATTGAAAAAAGTTGAAATATAAAACTTAAATTAATATATTACATTATTAAATTTGGACT
1 AAATTGAAAAAAGTTGAAATATAAAACTTAAATTAATAAATTACATTATTAAATTTAGACT
32244 AAATT
1 AAATT
32249 AAACAAATTT
Statistics
Matches: 57, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
59 2 0.04
60 2 0.04
61 53 0.93
ACGTcount: A:0.50, C:0.06, G:0.08, T:0.36
Consensus pattern (61 bp):
AAATTGAAAAAAGTTGAAATATAAAACTTAAATTAATAAATTACATTATTAAATTTAGACT
Found at i:33301 original size:2 final size:2
Alignment explanation
Indices: 33294--33322 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
33284 TATATGTTTG
33294 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
33323 CTGGTTTATT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:33353 original size:26 final size:26
Alignment explanation
Indices: 33314--33367 Score: 83
Period size: 26 Copynumber: 2.1 Consensus size: 26
33304 ATATATATAT
33314 ATATATATACTGGTTTATT-ACTGTTG
1 ATATATATACTGGTTTATTGA-TGTTG
*
33340 ATATATATATTGGTTTATTGATGTTG
1 ATATATATACTGGTTTATTGATGTTG
33366 AT
1 AT
33368 GTAAATGTTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 25 0.96
27 1 0.04
ACGTcount: A:0.28, C:0.04, G:0.17, T:0.52
Consensus pattern (26 bp):
ATATATATACTGGTTTATTGATGTTG
Found at i:38930 original size:20 final size:20
Alignment explanation
Indices: 38901--38938 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
38891 CCCCTTCAAA
*
38901 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
38921 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
38939 TGCACCAAAT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.13, C:0.26, G:0.37, T:0.24
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:47750 original size:2 final size:2
Alignment explanation
Indices: 47743--47777 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
47733 TAGCAATTGG
47743 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
47778 AACTAACCGG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:49202 original size:18 final size:18
Alignment explanation
Indices: 49158--49202 Score: 54
Period size: 20 Copynumber: 2.4 Consensus size: 18
49148 ACAATAATCC
* *
49158 TATTCAATGATAATCTTT
1 TATTCATTGATAATCTTA
49176 TATTCTCATTGATAATCTTA
1 TA-T-TCATTGATAATCTTA
49196 TATTCAT
1 TATTCAT
49203 GAATTAAACG
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
18 6 0.26
19 2 0.09
20 15 0.65
ACGTcount: A:0.31, C:0.13, G:0.04, T:0.51
Consensus pattern (18 bp):
TATTCATTGATAATCTTA
Found at i:49922 original size:2 final size:2
Alignment explanation
Indices: 49915--49941 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
49905 TGGTAAACTC
49915 CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT C
49942 ACCTTTTTTT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.00, C:0.52, G:0.00, T:0.48
Consensus pattern (2 bp):
CT
Done.