Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008470.1 Hibiscus syriacus cultivar Beakdansim tig00111294_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: 393165
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:220066 original size:108 final size:108
Alignment explanation
Indices: 219893--220150 Score: 338
Period size: 108 Copynumber: 2.4 Consensus size: 108
219883 CTAACACGGT
* *** * * *
219893 AATTCACAAACTCATTATGAATTACATGGGGTTGCACACATAGTGCTAATACGAAAATTCATAAA
1 AATTCACAAACTCATTATGAATTTC-TTAAGTTGCACACACAGTACCAATACGAAAATTCATAAA
* * *
219958 CTTATTATGAATTTCTTAAGTTGCACACACAGTCCCAATACA-TA
65 CATATAATGAATTTCTTAAGTTGCACACACAGTCCCAATA-AGGA
*
220002 AATTCACAAACTCATTATGAATTTCTTAAGTTGCACACACAGTACCAATACGGAAATTCATAAAC
1 AATTCACAAACTCATTATGAATTTCTTAAGTTGCACACACAGTACCAATACGAAAATTCATAAAC
* ***
220067 ATATAATGAATTTCTTAAGTTGTACACACAGTGGTAATAAGGA
66 ATATAATGAATTTCTTAAGTTGCACACACAGTCCCAATAAGGA
* *
220110 AATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACA
1 AATTCACAAACTCATTATGAATTTCTTAAGTTGCACACACA
220151 ATGCCCATTC
Statistics
Matches: 131, Mismatches: 17, Indels: 3
0.87 0.11 0.02
Matches are distributed among these distances:
107 1 0.01
108 106 0.81
109 24 0.18
ACGTcount: A:0.40, C:0.18, G:0.12, T:0.31
Consensus pattern (108 bp):
AATTCACAAACTCATTATGAATTTCTTAAGTTGCACACACAGTACCAATACGAAAATTCATAAAC
ATATAATGAATTTCTTAAGTTGCACACACAGTCCCAATAAGGA
Found at i:231091 original size:17 final size:18
Alignment explanation
Indices: 231052--231098 Score: 69
Period size: 18 Copynumber: 2.7 Consensus size: 18
231042 TGTTTCTGAG
*
231052 GGAATTGGAATTTGTGAA
1 GGAATTGGAATCTGTGAA
*
231070 GGAATTGGAATCTGT-CA
1 GGAATTGGAATCTGTGAA
231087 GGAATTGGAATC
1 GGAATTGGAATC
231099 CAATTCCATA
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
17 13 0.48
18 14 0.52
ACGTcount: A:0.32, C:0.06, G:0.32, T:0.30
Consensus pattern (18 bp):
GGAATTGGAATCTGTGAA
Found at i:231824 original size:244 final size:247
Alignment explanation
Indices: 231405--232142 Score: 994
Period size: 244 Copynumber: 2.9 Consensus size: 247
231395 CTCCATCCGA
*
231405 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGACCTGAATATATGAATTAGAAACCCGAC
1 GACCCGACCCGACCAAAATAAAGTTTCACCCGA--C--CC-GAATATATGAATTAGAAATCCGAC
*
231470 CCGACCTGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAATA
61 CCGACCAGAAAT-A-AAAAAAA-TA--TTTATTCAATAAAAACAGTGACTTAATTGAAAAAAAT-
* * *
231535 TATATAGAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTTTATAT-TTTTTG
120 TATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTCG
*
231599 GGTCGGGTATTTTTCACCCTAAACTCGAACCCAACCCGACCCGAATATCACACTTTAAAAAAACT
185 GGTCGGGTATTTTTCACCCTAAACTCGAACCCGACCCGACCCGAATATCACAC-TTAAAAAAA-T
231664 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGAATATATGAATTA-AAATCCGACCCGAC
1 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGAATATATGAATTAGAAATCCGACCCGAC
* * *
231728 CAGAAATAAAAAAAA-A-TTGTTCAATAAAAAGAGTGAGTTAATTG-AAAAAATTATATATAGAG
66 CAGAAATAAAAAAAATATTTATTCAATAAAAACAGTGACTTAATTGAAAAAAATTATATATAGAG
231790 GGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTCGGGTCGGGTATT
131 GGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTCGGGTCGGGTATT
* * *
231855 TTTCACCCTAAACTCAAACTCGACCCGACCCGAATATTACACTTAAAAAAAT
196 TTTCACCCTAAACTCGAACCCGACCCGACCCGAATATCACACTTAAAAAAAT
* *
231907 ----CGACCCAACCAAAATAAAGTTTCACCCGACCCGACCCAAATAGATGAATTAGAAATCCGAC
1 GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCG-----AATATATGAATTAGAAATCCGAC
* * *
231968 CCGACCCGACCCAAAATAATAATAAAATATTTTTATTTAATAAAAATAGTGACTTAATTGAAAAA
61 CCGA-CC-A---GAAATAA-AA-AAAATA--TTTATTCAATAAAAACAGTGACTTAATTGAAAAA
232033 AATTATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGT-AAATTATATATATTT
117 AATTATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTT
*
232097 TCGGGTCGGGTATTTTTCACCCTAAACCCGAA-CCGACCCGACCCGA
182 TCGGGTCGGGTATTTTTCACCCTAAACTCGAACCCGACCCGACCCGA
232143 CCAAAATAAA
Statistics
Matches: 438, Mismatches: 22, Indels: 42
0.87 0.04 0.08
Matches are distributed among these distances:
239 32 0.07
243 1 0.00
244 77 0.18
245 74 0.17
246 27 0.06
247 1 0.00
249 1 0.00
250 6 0.01
251 9 0.02
252 5 0.01
253 20 0.05
254 14 0.03
255 15 0.03
256 69 0.16
257 54 0.12
259 33 0.08
ACGTcount: A:0.40, C:0.19, G:0.13, T:0.28
Consensus pattern (247 bp):
GACCCGACCCGACCAAAATAAAGTTTCACCCGACCCGAATATATGAATTAGAAATCCGACCCGAC
CAGAAATAAAAAAAATATTTATTCAATAAAAACAGTGACTTAATTGAAAAAAATTATATATAGAG
GGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATATTTTCGGGTCGGGTATT
TTTCACCCTAAACTCGAACCCGACCCGACCCGAATATCACACTTAAAAAAAT
Found at i:243203 original size:2 final size:2
Alignment explanation
Indices: 243196--243235 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
243186 TAAATTTACT
243196 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
243236 TATATATATA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:248927 original size:25 final size:24
Alignment explanation
Indices: 248887--248937 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 24
248877 TGGTGGTTGG
248887 TTTAATGGATGTTTTAAACTTTATT
1 TTTAATGGATGTTTT-AACTTTATT
*
248912 TTTAATGGTATG-TTTAAGTTTATT
1 TTTAATGG-ATGTTTTAACTTTATT
248936 TT
1 TT
248938 GGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
24 10 0.42
25 11 0.46
26 3 0.12
ACGTcount: A:0.25, C:0.02, G:0.14, T:0.59
Consensus pattern (24 bp):
TTTAATGGATGTTTTAACTTTATT
Found at i:254328 original size:24 final size:24
Alignment explanation
Indices: 254283--254332 Score: 75
Period size: 24 Copynumber: 2.1 Consensus size: 24
254273 TGGTGGTTGG
254283 TTTAATGGATGTTTAAACTTTATT
1 TTTAATGGATGTTTAAACTTTATT
*
254307 TTTAATGGTATGTTT-AAGTTTATT
1 TTTAATGG-ATGTTTAAACTTTATT
254331 TT
1 TT
254333 GGTTCTTTAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
24 18 0.75
25 6 0.25
ACGTcount: A:0.26, C:0.02, G:0.14, T:0.58
Consensus pattern (24 bp):
TTTAATGGATGTTTAAACTTTATT
Found at i:254833 original size:16 final size:16
Alignment explanation
Indices: 254809--254855 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
254799 CACGTGAGGA
*
254809 TTATCTTCTTTTTATT
1 TTATTTTCTTTTTATT
*
254825 TTATTTTCTATTTATT
1 TTATTTTCTTTTTATT
254841 TACTATTTT-TTTTTA
1 T--TATTTTCTTTTTA
254856 CCATTTTCCT
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
16 15 0.58
17 5 0.19
18 6 0.23
ACGTcount: A:0.17, C:0.09, G:0.00, T:0.74
Consensus pattern (16 bp):
TTATTTTCTTTTTATT
Found at i:264202 original size:24 final size:24
Alignment explanation
Indices: 264174--264236 Score: 126
Period size: 24 Copynumber: 2.6 Consensus size: 24
264164 GGGTAATGAT
264174 ATTTTTTACAGTAATGGAAATATA
1 ATTTTTTACAGTAATGGAAATATA
264198 ATTTTTTACAGTAATGGAAATATA
1 ATTTTTTACAGTAATGGAAATATA
264222 ATTTTTTACAGTAAT
1 ATTTTTTACAGTAAT
264237 ATGCCCCACT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.40, C:0.05, G:0.11, T:0.44
Consensus pattern (24 bp):
ATTTTTTACAGTAATGGAAATATA
Found at i:266560 original size:18 final size:18
Alignment explanation
Indices: 266531--266575 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 18
266521 ATATAAATAT
* *
266531 AAATGTAAATGAATATTAA
1 AAATG-AAATGAAAATGAA
*
266550 TAATGAAATGAAAATGAA
1 AAATGAAATGAAAATGAA
266568 AAATGAAA
1 AAATGAAA
266576 AAATGCATGA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 18 0.82
19 4 0.18
ACGTcount: A:0.62, C:0.00, G:0.13, T:0.24
Consensus pattern (18 bp):
AAATGAAATGAAAATGAA
Found at i:266564 original size:24 final size:22
Alignment explanation
Indices: 266515--266567 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
266505 AAGCTTTAAT
* *
266515 AAATTAATATAAATATAAATGT
1 AAATGAATATAAATATAAATGA
*
266537 AAATGAATATTAATAATGAAATGA
1 AAATGAATATAAAT-AT-AAATGA
266561 AAATGAA
1 AAATGAA
266568 AAATGAAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 12 0.46
23 2 0.08
24 12 0.46
ACGTcount: A:0.60, C:0.00, G:0.09, T:0.30
Consensus pattern (22 bp):
AAATGAATATAAATATAAATGA
Found at i:267872 original size:20 final size:18
Alignment explanation
Indices: 267825--267878 Score: 74
Period size: 18 Copynumber: 2.9 Consensus size: 18
267815 GGAAGACGAA
267825 CCTC-ACCCATTTGTTTT
1 CCTCAACCCATTTGTTTT
267842 CCTCAACCCATTTGTTTT
1 CCTCAACCCATTTGTTTT
*
267860 CCTCGTGACCCATTTGTTT
1 CCTC--AACCCATTTGTTT
267879 CTTCCATAGG
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
17 4 0.12
18 17 0.52
20 12 0.36
ACGTcount: A:0.13, C:0.33, G:0.09, T:0.44
Consensus pattern (18 bp):
CCTCAACCCATTTGTTTT
Found at i:268788 original size:20 final size:20
Alignment explanation
Indices: 268763--268829 Score: 134
Period size: 20 Copynumber: 3.4 Consensus size: 20
268753 GTTTGATCGA
268763 CTTGGAGTAAACTCGGTTCT
1 CTTGGAGTAAACTCGGTTCT
268783 CTTGGAGTAAACTCGGTTCT
1 CTTGGAGTAAACTCGGTTCT
268803 CTTGGAGTAAACTCGGTTCT
1 CTTGGAGTAAACTCGGTTCT
268823 CTTGGAG
1 CTTGGAG
268830 CCCTCAATTA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 47 1.00
ACGTcount: A:0.19, C:0.19, G:0.27, T:0.34
Consensus pattern (20 bp):
CTTGGAGTAAACTCGGTTCT
Found at i:272622 original size:80 final size:79
Alignment explanation
Indices: 272400--272689 Score: 395
Period size: 80 Copynumber: 3.6 Consensus size: 79
272390 AAAAGGGGAG
* * * *
272400 CCAACCTAAGGATATACCTT-GGATCTACCCAAGGACATCCTTAGATCCGTAGGGTTACCTTAAG
1 CCAACCTAAGGATATACCTTGGGACCTACCCAA-GATATCCTTAGGTCCGTAGGGTTACCTTATG
* *
272464 TACACAACTAAGGTAA
65 CACACAACAAAGG-AA
* * *
272480 CCAGCCTAAGGATGTACCTTGGG-CCTATCCAAGATATCCTTAGGTCCGTAGGGTTACCTTATGC
1 CCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCTTATGC
*
272544 ACATAACAAAGGAA
66 ACACAACAAAGGAA
* *
272558 GCCAAACTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACATTATG
1 -CCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCTTATG
*
272623 CACGCAACAAAGGGAA
65 CACACAACAAA-GGAA
* *
272639 CTAACCTAAGGATATACCTTGGGGCCTACCCAAGATATCCTTAGGTCCGTA
1 CCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTA
272690 AGGACTTACA
Statistics
Matches: 186, Mismatches: 20, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
78 2 0.01
79 58 0.31
80 120 0.65
81 6 0.03
ACGTcount: A:0.31, C:0.25, G:0.20, T:0.23
Consensus pattern (79 bp):
CCAACCTAAGGATATACCTTGGGACCTACCCAAGATATCCTTAGGTCCGTAGGGTTACCTTATGC
ACACAACAAAGGAA
Found at i:275685 original size:18 final size:17
Alignment explanation
Indices: 275655--275707 Score: 61
Period size: 18 Copynumber: 3.0 Consensus size: 17
275645 GGTCAACACC
*
275655 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCA
*
275672 GGTCAACGGGTCGGGTTA
1 GGTCAAC-GGTCGGGTCA
*
275690 GGTCAACAGATCGGGTCA
1 GGTCAAC-GGTCGGGTCA
275708 AACTGGTTCA
Statistics
Matches: 30, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
17 7 0.23
18 23 0.77
ACGTcount: A:0.19, C:0.21, G:0.42, T:0.19
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCA
Found at i:279509 original size:43 final size:44
Alignment explanation
Indices: 279450--279707 Score: 316
Period size: 43 Copynumber: 5.9 Consensus size: 44
279440 GGTAACCAGC
*
279450 AAATAAGC-TACGAGCTTATGGAATAATGGCAAGTA-ATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAATGGTAAGTATATTGGTA
*
279492 AAATAAGCTTACGAGCTTATGGTATAATGGTAAGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAATAATGGTAAGTATATTGGTA
* *
279536 AAACAAGC-TACGAGCTTATGGAATAAATGGTATGGTATATTGGTA
1 AAATAAGCTTACGAGCTTATGGAAT-AATGGTA-AGTATATTGGTA
*
279581 AAATAAGCTTACGAGCTTATGGAACAAATGGTAAGTATA-TGGT-
1 AAATAAGCTTACGAGCTTATGGAA-TAATGGTAAGTATATTGGTA
* * * *
279624 AAATAAGCTTACGAGCTTATGAAACATATGGTAAGTATGTTGATA
1 AAATAAGCTTACGAGCTTATGGAATA-ATGGTAAGTATATTGGTA
* *
279669 AAATAAGCTTACGAG-ATA-GG-ATAAATGGTAAATATATTG
1 AAATAAGCTTACGAGCTTATGGAAT-AATGGTAAGTATATTG
279708 ATAAGAAATG
Statistics
Matches: 189, Mismatches: 17, Indels: 20
0.84 0.08 0.09
Matches are distributed among these distances:
42 23 0.12
43 76 0.40
44 30 0.16
45 38 0.20
46 22 0.12
ACGTcount: A:0.40, C:0.08, G:0.22, T:0.29
Consensus pattern (44 bp):
AAATAAGCTTACGAGCTTATGGAATAATGGTAAGTATATTGGTA
Found at i:279595 original size:89 final size:86
Alignment explanation
Indices: 279454--279707 Score: 311
Period size: 89 Copynumber: 2.9 Consensus size: 86
279444 ACCAGCAAAT
*
279454 AAGCTACGAGCTTATGGAAT-AATGGCAAGTA-ATTGGTAAAATAAGCTTACGAGCTTATGGTAT
1 AAGCTACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGG-AT
279517 AATGGTAAGTATATTGGTAAAAC
65 AATGGTAAGTATATTGGT-AAAC
*
279540 AAGCTACGAGCTTATGGAATAAATGGTATGGTATATTGGTAAAATAAGCTTACGAGCTTATGGAA
1 AAGCTACGAGCTTATGGAATAAATGGTA-AGTATATTGGTAAAATAAGCTTACGAGCTTATGG-A
* *
279605 CAAATGGTAAGTATA-TGGTAAAT
64 -TAATGGTAAGTATATTGGTAAAC
* * * * * *
279628 AAGCTTACGAGCTTATGAAACATATGGTAAGTATGTTGATAAAATAAGCTTACGAG-ATA-GGAT
1 AAGC-TACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGAT
*
279691 AAATGGTAAATATATTG
65 -AATGGTAAGTATATTG
279708 ATAAGAAATG
Statistics
Matches: 147, Mismatches: 14, Indels: 14
0.84 0.08 0.08
Matches are distributed among these distances:
85 13 0.09
86 24 0.16
87 8 0.05
88 34 0.23
89 55 0.37
90 13 0.09
ACGTcount: A:0.39, C:0.08, G:0.23, T:0.30
Consensus pattern (86 bp):
AAGCTACGAGCTTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGCTTATGGATA
ATGGTAAGTATATTGGTAAAC
Found at i:279633 original size:132 final size:130
Alignment explanation
Indices: 279450--279698 Score: 335
Period size: 132 Copynumber: 1.9 Consensus size: 130
279440 GGTAACCAGC
* **
279450 AAATAAGCTACGAGCTTATGGAATAATGGCAAGTAATTGGTAAAATAAGCTTACGAGCTTATGGT
1 AAATAAGCTACGAGCTTATGGAAAAATGGCAAGTAATTGGTAAAATAAGCTTACGAGCTTATGAA
* * *
279515 ATA-ATGGTAAGTATATTGGTAAAACAAGC-TACGAGCTTATGGAATAAATGGTATGGTATATTG
66 ACATATGGTAAGTATATTGATAAAACAAGCTTACGAG-ATA-GG-ATAAATGGTATGGTATATTG
279578 GTA
128 GTA
*
279581 AAATAAGCTTACGAGCTTATGGAACAAATGGTAAGT-ATATGGT-AAATAAGCTTACGAGCTTAT
1 AAATAAGC-TACGAGCTTATGGAA-AAATGGCAAGTAAT-TGGTAAAATAAGCTTACGAGCTTAT
* *
279644 GAAACATATGGTAAGTATGTTGATAAAATAAGCTTACGAGATAGGATAAATGGTA
63 GAAACATATGGTAAGTATATTGATAAAACAAGCTTACGAGATAGGATAAATGGTA
279699 AATATATTGA
Statistics
Matches: 104, Mismatches: 9, Indels: 10
0.85 0.07 0.08
Matches are distributed among these distances:
131 18 0.17
132 42 0.40
133 38 0.37
134 6 0.06
ACGTcount: A:0.40, C:0.08, G:0.23, T:0.29
Consensus pattern (130 bp):
AAATAAGCTACGAGCTTATGGAAAAATGGCAAGTAATTGGTAAAATAAGCTTACGAGCTTATGAA
ACATATGGTAAGTATATTGATAAAACAAGCTTACGAGATAGGATAAATGGTATGGTATATTGGTA
Found at i:281042 original size:21 final size:21
Alignment explanation
Indices: 280977--281045 Score: 56
Period size: 21 Copynumber: 3.4 Consensus size: 21
280967 CGAGCCATCA
*
280977 AAGTCTTTTGAGCAAGATGATT
1 AAGTCTTTCGAGCAAGATGA-T
* * *
280999 AAATC-TTCGGATC-ATATG-T
1 AAGTCTTTC-GAGCAAGATGAT
281018 -AGTCTTTCGAGCAAGATGAT
1 AAGTCTTTCGAGCAAGATGAT
281038 AAGTCTTT
1 AAGTCTTT
281046 GGGCCATCTA
Statistics
Matches: 35, Mismatches: 7, Indels: 11
0.66 0.13 0.21
Matches are distributed among these distances:
18 6 0.17
19 8 0.23
20 1 0.03
21 13 0.37
22 7 0.20
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.36
Consensus pattern (21 bp):
AAGTCTTTCGAGCAAGATGAT
Found at i:283591 original size:13 final size:14
Alignment explanation
Indices: 283573--283608 Score: 56
Period size: 13 Copynumber: 2.6 Consensus size: 14
283563 ATTTCCCTTA
283573 TTTTAATTTTTG-T
1 TTTTAATTTTTGTT
*
283586 TTTTAATTATTGTT
1 TTTTAATTTTTGTT
283600 TTTTAATTT
1 TTTTAATTT
283609 ATGGTTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.19, C:0.00, G:0.06, T:0.75
Consensus pattern (14 bp):
TTTTAATTTTTGTT
Found at i:284020 original size:15 final size:15
Alignment explanation
Indices: 283997--284039 Score: 70
Period size: 15 Copynumber: 2.9 Consensus size: 15
283987 ACATTTATAC
283997 CCTTT-AATTTCAGT
1 CCTTTAAATTTCAGT
284011 CCTTTAAATTTCAGT
1 CCTTTAAATTTCAGT
*
284026 CCTTTAATTTTCAG
1 CCTTTAAATTTCAG
284040 CATTTTAAGT
Statistics
Matches: 27, Mismatches: 1, Indels: 1
0.93 0.03 0.03
Matches are distributed among these distances:
14 5 0.19
15 22 0.81
ACGTcount: A:0.23, C:0.21, G:0.07, T:0.49
Consensus pattern (15 bp):
CCTTTAAATTTCAGT
Found at i:285757 original size:3 final size:3
Alignment explanation
Indices: 285749--285789 Score: 57
Period size: 3 Copynumber: 13.3 Consensus size: 3
285739 TGGCCTTTGC
285749 ATA ATA ATA ATA ATTA ATA A-A CATA ATA ATA ATA ATA ATA A
1 ATA ATA ATA ATA A-TA ATA ATA -ATA ATA ATA ATA ATA ATA A
285790 ATAAAAAAAA
Statistics
Matches: 35, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 1 0.03
3 30 0.86
4 4 0.11
ACGTcount: A:0.66, C:0.02, G:0.00, T:0.32
Consensus pattern (3 bp):
ATA
Found at i:285801 original size:25 final size:25
Alignment explanation
Indices: 285749--285802 Score: 81
Period size: 25 Copynumber: 2.2 Consensus size: 25
285739 TGGCCTTTGC
* * *
285749 ATAATAATAATAATTAATAAACATA
1 ATAATAATAATAATAAATAAAAAAA
285774 ATAATAATAATAATAAATAAAAAAA
1 ATAATAATAATAATAAATAAAAAAA
285799 ATAA
1 ATAA
285803 AAAAAGACCG
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 26 1.00
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (25 bp):
ATAATAATAATAATAAATAAAAAAA
Found at i:286285 original size:29 final size:29
Alignment explanation
Indices: 286209--286286 Score: 93
Period size: 29 Copynumber: 2.7 Consensus size: 29
286199 CATCTTTAGG
* *
286209 GATAATGGTTTCAAGAGAAACTGACTCAAA
1 GATAAT-GTTTCAAGAGAAACAGACCCAAA
*
286239 GATAATGTTTCAAAAGAAACAGACCCAAA
1 GATAATGTTTCAAGAGAAACAGACCCAAA
* * *
286268 GATGATTTTTTAAGAGAAA
1 GATAATGTTTCAAGAGAAA
286287 TTGTCTCAAG
Statistics
Matches: 41, Mismatches: 7, Indels: 1
0.84 0.14 0.02
Matches are distributed among these distances:
29 35 0.85
30 6 0.15
ACGTcount: A:0.46, C:0.12, G:0.18, T:0.24
Consensus pattern (29 bp):
GATAATGTTTCAAGAGAAACAGACCCAAA
Found at i:286371 original size:30 final size:30
Alignment explanation
Indices: 286337--286395 Score: 82
Period size: 30 Copynumber: 2.0 Consensus size: 30
286327 CTCAAGATTG
* * *
286337 TTTTGTTTTAATAGAAACAGACTCAAAGAC
1 TTTTGTTTCAAGAGAAACAAACTCAAAGAC
*
286367 TTTTGTTTCAAGATAAACAAACTCAAAGA
1 TTTTGTTTCAAGAGAAACAAACTCAAAGA
286396 TAATGTCTCA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 25 1.00
ACGTcount: A:0.42, C:0.14, G:0.12, T:0.32
Consensus pattern (30 bp):
TTTTGTTTCAAGAGAAACAAACTCAAAGAC
Found at i:287604 original size:203 final size:203
Alignment explanation
Indices: 287240--287644 Score: 760
Period size: 203 Copynumber: 2.0 Consensus size: 203
287230 TGATAATTTA
287240 TTTCTTTGCCCCATCAAAATTTACCAAAAAATTTGTCTTTCTTAACCCAACTTCGATCTTGAGCT
1 TTTCTTTGCCCCATCAAAATTTACCAAAAAATTTGTCTTTCTTAACCCAACTTCGATCTTGAGCT
287305 TCAGAGAGATTTTCGTTGAATTCCAAGATACTTCTAGAGAACTTATCTTGTTTGAAAGAAAATTT
66 TCAGAGAGATTTTCGTTGAATTCCAAGATACTTCTAGAGAACTTATCTTGTTTGAAAGAAAATTT
287370 CTCCTTTGGATTTTCAAAATTTTGAAAAAAA-ATCAAAAGGGATTTTC-AAAATATTGCCTCATT
131 CTCCTTTGGATTTTCAAAATTTTGAAAAAAATATCAAAAGGGATTTTCAAAAATATTGCCTCATT
287433 CTAGGTAT
196 CTAGGTAT
287441 TTTCTTTGCCCCATCAAAATTTACCCAAAAAATTTGTCTTTTCTTAACCCAACTTCGATCTTGAG
1 TTTCTTTGCCCCATCAAAATTTA-CCAAAAAATTTGTC-TTTCTTAACCCAACTTCGATCTTGAG
*
287506 CTTCAGAGAGATTTTTGTTGAATTCCAAGATACTTCTAGAGAACTTATCTTGTTTGAAAGAAAAT
64 CTTCAGAGAGATTTTCGTTGAATTCCAAGATACTTCTAGAGAACTTATCTTGTTTGAAAGAAAAT
287571 TTCTTCCTTTGGATTTTCAAAATTTTGAAAAAAATATCAAAAGGGATTTTCAAAAATATTGCCTC
129 TTC-TCCTTTGGATTTTCAAAATTTTGAAAAAAATATCAAAAGGGATTTTCAAAAATATTGCCTC
287636 ATTCTAGGT
193 ATTCTAGGT
287645 TTCACAATTG
Statistics
Matches: 198, Mismatches: 1, Indels: 5
0.97 0.00 0.02
Matches are distributed among these distances:
201 23 0.12
202 14 0.07
203 93 0.47
204 30 0.15
205 16 0.08
206 22 0.11
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (203 bp):
TTTCTTTGCCCCATCAAAATTTACCAAAAAATTTGTCTTTCTTAACCCAACTTCGATCTTGAGCT
TCAGAGAGATTTTCGTTGAATTCCAAGATACTTCTAGAGAACTTATCTTGTTTGAAAGAAAATTT
CTCCTTTGGATTTTCAAAATTTTGAAAAAAATATCAAAAGGGATTTTCAAAAATATTGCCTCATT
CTAGGTAT
Found at i:288342 original size:2 final size:2
Alignment explanation
Indices: 288335--288372 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
288325 TCAGATTTAT
288335 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
288373 TATGGGTATA
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:293400 original size:3 final size:3
Alignment explanation
Indices: 293392--293434 Score: 52
Period size: 3 Copynumber: 13.7 Consensus size: 3
293382 ATATTTGTAT
293392 TAA TAA TAA TAA TTAA TAA TAA TAA TATA TAAA TAA -AA TAA TA
1 TAA TAA TAA TAA -TAA TAA TAA TAA TA-A T-AA TAA TAA TAA TA
293435 TAAAAAAAAT
Statistics
Matches: 36, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
2 2 0.06
3 26 0.72
4 7 0.19
5 1 0.03
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:293408 original size:13 final size:13
Alignment explanation
Indices: 293390--293417 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
293380 GTATATTTGT
293390 ATTAATAATAATA
1 ATTAATAATAATA
293403 ATTAATAATAATA
1 ATTAATAATAATA
293416 AT
1 AT
293418 ATATAAATAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (13 bp):
ATTAATAATAATA
Found at i:293413 original size:16 final size:17
Alignment explanation
Indices: 293392--293446 Score: 69
Period size: 16 Copynumber: 3.4 Consensus size: 17
293382 ATATTTGTAT
*
293392 TAATAATAATA-ATTAA
1 TAATAATAATATATAAA
293408 TAATAATAATATATAAA
1 TAATAATAATATATAAA
*
293425 TAA-AATAATATAAAAA
1 TAATAATAATATATAAA
*
293441 AAATAA
1 TAATAA
293447 ATAAAAAGAC
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
16 25 0.74
17 9 0.26
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
TAATAATAATATATAAA
Found at i:293435 original size:14 final size:14
Alignment explanation
Indices: 293409--293451 Score: 54
Period size: 14 Copynumber: 3.1 Consensus size: 14
293399 AATAATTAAT
293409 AATAATAAT-ATATA
1 AATAA-AATAATATA
293423 AATAAAATAATATA
1 AATAAAATAATATA
*
293437 AAAAAAATAA-ATA
1 AATAAAATAATATA
293450 AA
1 AA
293452 AAGACCAGGA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
13 8 0.30
14 19 0.70
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (14 bp):
AATAAAATAATATA
Found at i:293899 original size:17 final size:18
Alignment explanation
Indices: 293869--293920 Score: 52
Period size: 17 Copynumber: 2.9 Consensus size: 18
293859 TTTCAATAAT
293869 AAAAATAAAAATAA-ATA
1 AAAAATAAAAATAATATA
* *
293886 AAAAATATATATAATATA
1 AAAAATAAAAATAATATA
**
293904 ATGAATATAAAATAATA
1 AAAAATA-AAAATAATA
293921 AATACAAAAC
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
17 12 0.44
18 8 0.30
19 7 0.26
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.27
Consensus pattern (18 bp):
AAAAATAAAAATAATATA
Found at i:293913 original size:14 final size:14
Alignment explanation
Indices: 293863--293929 Score: 54
Period size: 14 Copynumber: 5.1 Consensus size: 14
293853 ATATATTTTC
*
293863 AATAATAAAAAT-A
1 AATAATAAATATAA
293876 AA-AAT-AA-ATAA
1 AATAATAAATATAA
*
293887 AA-AATATATATAA
1 AATAATAAATATAA
* *
293900 TATAATGAATATAA
1 AATAATAAATATAA
*
293914 AATAATAAATACAA
1 AATAATAAATATAA
293928 AA
1 AA
293930 CGAAAAAATA
Statistics
Matches: 43, Mismatches: 7, Indels: 7
0.75 0.12 0.12
Matches are distributed among these distances:
10 2 0.05
11 8 0.19
12 4 0.09
13 7 0.16
14 22 0.51
ACGTcount: A:0.72, C:0.01, G:0.01, T:0.25
Consensus pattern (14 bp):
AATAATAAATATAA
Found at i:294417 original size:159 final size:159
Alignment explanation
Indices: 294119--294420 Score: 387
Period size: 159 Copynumber: 1.9 Consensus size: 159
294109 TGAAAAAATT
* * * *
294119 TTCTCATTATTAACTTCTTCTCCCTCATTGGATGAATTCTTCTCATTACGAACCTTTCCATTGGA
1 TTCTCATTATGAACTTCTTCTCCCTCATCGGATGAATTCTTCTCATTACGAACCTCTCCA-TAGA
* * * * *
294184 AATTTTGATCCACCTGCTTCTGTGATGGATTCAAACAAAGTGATGATGCTGATCCAATTCCATAT
65 AATATTGATCCACCTGCTTCTGTGATGGAGTCAAACAAAGTGATCATGCTGACCCAACTCCATAT
*
294249 GCGATGGATGAGCTAAGGTTAAACAAGTTC
130 GCGAAGGATGAGCTAAGGTTAAACAAGTTC
** * *
294279 TTCTCATTATGAACTTCTTCTTTCTCATCGGAT-AAGTTCTTCTTATTATGAACTCTCTCC-TAG
1 TTCTCATTATGAACTTCTTCTCCCTCATCGGATGAA-TTCTTCTCATTACGAAC-CTCTCCATAG
* *
294342 AAATATTGATTCATCT-CTTTCTGTGATGGAGTCAAACAAAGTGATCATGCT-ACCCAACTCCAT
64 AAATATTGATCCACCTGC-TTCTGTGATGGAGTCAAACAAAGTGATCATGCTGACCCAACTCCAT
294405 ATGCGGAAGGATGAGC
128 ATGC-GAAGGATGAGC
294421 AAAGTGTTGA
Statistics
Matches: 122, Mismatches: 16, Indels: 9
0.83 0.11 0.06
Matches are distributed among these distances:
158 15 0.12
159 58 0.48
160 44 0.36
161 5 0.04
ACGTcount: A:0.27, C:0.22, G:0.16, T:0.36
Consensus pattern (159 bp):
TTCTCATTATGAACTTCTTCTCCCTCATCGGATGAATTCTTCTCATTACGAACCTCTCCATAGAA
ATATTGATCCACCTGCTTCTGTGATGGAGTCAAACAAAGTGATCATGCTGACCCAACTCCATATG
CGAAGGATGAGCTAAGGTTAAACAAGTTC
Found at i:294577 original size:13 final size:13
Alignment explanation
Indices: 294559--294595 Score: 74
Period size: 13 Copynumber: 2.8 Consensus size: 13
294549 ACCTTCTTTT
294559 GTGATGGAATGAA
1 GTGATGGAATGAA
294572 GTGATGGAATGAA
1 GTGATGGAATGAA
294585 GTGATGGAATG
1 GTGATGGAATG
294596 GAGCTAAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.35, C:0.00, G:0.41, T:0.24
Consensus pattern (13 bp):
GTGATGGAATGAA
Found at i:295784 original size:5 final size:5
Alignment explanation
Indices: 295766--295826 Score: 59
Period size: 5 Copynumber: 11.0 Consensus size: 5
295756 CATTAATTTC
*
295766 CTTTT CTTTCT CTTTT CTTTT CTTTT CATTGTTT CTTTT CTTCT CTTTATT
1 CTTTT CTTT-T CTTTT CTTTT CTTTT C--T-TTT CTTTT CTTTT C-TT-TT
295817 CTTTT CTTTT
1 CTTTT CTTTT
295827 TCTTCTCTAA
Statistics
Matches: 48, Mismatches: 2, Indels: 12
0.77 0.03 0.19
Matches are distributed among these distances:
5 31 0.65
6 10 0.21
7 3 0.06
8 4 0.08
ACGTcount: A:0.03, C:0.21, G:0.02, T:0.74
Consensus pattern (5 bp):
CTTTT
Found at i:295802 original size:18 final size:16
Alignment explanation
Indices: 295766--295826 Score: 70
Period size: 17 Copynumber: 3.6 Consensus size: 16
295756 CATTAATTTC
295766 CTTTTC-TTTCTCTTTT
1 CTTTTCTTTTCT-TTTT
295782 CTTTTCTTTTCATTGTTT
1 CTTTTCTTTTC-TT-TTT
*
295800 CTTTTCTTCTCTTTATT
1 CTTTTCTTTTCTTT-TT
295817 CTTTTCTTTT
1 CTTTTCTTTT
295827 TCTTCTCTAA
Statistics
Matches: 39, Mismatches: 2, Indels: 7
0.81 0.04 0.15
Matches are distributed among these distances:
16 7 0.18
17 18 0.46
18 14 0.36
ACGTcount: A:0.03, C:0.21, G:0.02, T:0.74
Consensus pattern (16 bp):
CTTTTCTTTTCTTTTT
Found at i:295822 original size:35 final size:36
Alignment explanation
Indices: 295752--295826 Score: 102
Period size: 35 Copynumber: 2.1 Consensus size: 36
295742 CTCATTTCCA
295752 TTTTCATTAATTTCCTTTTCTTTCTCTTTTCTTTTC
1 TTTTCATTAATTTCCTTTTCTTTCTCTTTTCTTTTC
*
295788 TTTTCATT-GTTT-CTTTTC-TTCTCTTTATTCTTTTC
1 TTTTCATTAATTTCCTTTTCTTTCTC-TT-TTCTTTTC
295823 TTTT
1 TTTT
295827 TCTTCTCTAA
Statistics
Matches: 36, Mismatches: 1, Indels: 5
0.86 0.02 0.12
Matches are distributed among these distances:
33 5 0.14
34 8 0.22
35 15 0.42
36 8 0.22
ACGTcount: A:0.07, C:0.20, G:0.01, T:0.72
Consensus pattern (36 bp):
TTTTCATTAATTTCCTTTTCTTTCTCTTTTCTTTTC
Found at i:295824 original size:12 final size:11
Alignment explanation
Indices: 295801--295834 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
295791 TCATTGTTTC
295801 TTTTCTTCTCT
1 TTTTCTTCTCT
*
295812 TTATTCTTTTCT
1 TT-TTCTTCTCT
295824 TTTTCTTCTCT
1 TTTTCTTCTCT
295835 AATATTTCTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
11 10 0.50
12 10 0.50
ACGTcount: A:0.03, C:0.24, G:0.00, T:0.74
Consensus pattern (11 bp):
TTTTCTTCTCT
Found at i:304250 original size:3 final size:3
Alignment explanation
Indices: 304235--304274 Score: 55
Period size: 3 Copynumber: 13.7 Consensus size: 3
304225 AATTAAAAAA
* *
304235 TAT TAT TA- AAT TAT TAT TAT TAT TAT TAT TAG TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
304275 AGTGTGTTTA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
2 1 0.03
3 31 0.97
ACGTcount: A:0.38, C:0.00, G:0.03, T:0.60
Consensus pattern (3 bp):
TAT
Found at i:305619 original size:14 final size:16
Alignment explanation
Indices: 305595--305627 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
305585 GTTTATTTTG
305595 TTTTAAGTATTT-TAT
1 TTTTAAGTATTTATAT
305610 TTTTAA-TATTTATAT
1 TTTTAAGTATTTATAT
305625 TTT
1 TTT
305628 AGTCACACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (16 bp):
TTTTAAGTATTTATAT
Found at i:317378 original size:8 final size:8
Alignment explanation
Indices: 317346--317448 Score: 103
Period size: 8 Copynumber: 13.5 Consensus size: 8
317336 GCTTGAAGAA
*
317346 AAAAAAGG
1 AAAAAATG
*
317354 AACAAAT-
1 AAAAAATG
317361 AAAAAGATG
1 AAAAA-ATG
317370 AAAAAATG
1 AAAAAATG
317378 AAAAAATG
1 AAAAAATG
317386 AAAAAATG
1 AAAAAATG
*
317394 AAAAAGA-A
1 AAAAA-ATG
317402 AAAAAATG
1 AAAAAATG
317410 -AAAAATG
1 AAAAAATG
317417 -AAAAATG
1 AAAAAATG
317424 -AAAAA--
1 AAAAAATG
*
317429 AAGAAATG
1 AAAAAATG
317437 AAAAAATG
1 AAAAAATG
317445 AAAA
1 AAAA
317449 GAGAAAAAGG
Statistics
Matches: 81, Mismatches: 7, Indels: 14
0.79 0.07 0.14
Matches are distributed among these distances:
6 4 0.05
7 24 0.30
8 47 0.58
9 6 0.07
ACGTcount: A:0.76, C:0.01, G:0.14, T:0.10
Consensus pattern (8 bp):
AAAAAATG
Found at i:317455 original size:13 final size:13
Alignment explanation
Indices: 317369--317456 Score: 58
Period size: 13 Copynumber: 6.5 Consensus size: 13
317359 ATAAAAAGAT
317369 GAAAAAATGAAAAAA
1 GAAAAAATG--AAAA
317384 TGAAAAAATGAAAA
1 -GAAAAAATGAAAA
*
317398 -AGAAAAA--AAAT
1 GA-AAAAATGAAAA
317409 G-AAAAATGAAAAA
1 GAAAAAATG-AAAA
* *
317422 TGAAAAAAAGAAAT
1 -GAAAAAATGAAAA
317436 GAAAAAATGAAAA
1 GAAAAAATGAAAA
317449 GAGAAAAA
1 GA-AAAAA
317457 GGAGGGTTTG
Statistics
Matches: 58, Mismatches: 6, Indels: 18
0.71 0.07 0.22
Matches are distributed among these distances:
10 5 0.09
11 3 0.05
12 1 0.02
13 21 0.36
14 13 0.22
15 6 0.10
16 9 0.16
ACGTcount: A:0.76, C:0.00, G:0.15, T:0.09
Consensus pattern (13 bp):
GAAAAAATGAAAA
Found at i:318904 original size:105 final size:105
Alignment explanation
Indices: 318684--318977 Score: 331
Period size: 105 Copynumber: 2.8 Consensus size: 105
318674 CTCACTTGAG
*
318684 GGATCGACATTTCCAATTAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAA
1 GGATCAACATTTCCAA--AAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAA
* * * *
318749 TGAGAAAAACTTGTTCCTTTCAAATTCACCACAGATGGAGGT
64 TGAGAAAAACATGTTCCTTTCAAAGTCACCACAAAAGGAGGT
* * * * * *
318791 GAACCAACATTTCCAGAAGATTTCATAATGAGAAGAACTCGTCCTAAAGGAGAAAGTTCATAATG
1 GGATCAACATTTCCAAAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAATG
* ** **
318856 AGAAAAACATGTT-CTTTCTAAGTCAACCGTAAAAGGATTT
66 AGAAAAACATGTTCCTTTCAAAGTC-ACCACAAAAGGAGGT
* *
318896 GGATCAACATTTCCAAAAGAGTTCATAATGAGAAGAACTCATTCACGAGAAAGA-AGAAGTTCAT
1 GGATCAACATTTCCAAAAGAGTTCATAATGAGAAGAACTCA-TCA-TA-AAGGAGA-AAGTTCAT
* *
318960 AATGAGAAGAACTTGTTC
62 AATGAGAAAAACATGTTC
318978 AATCTAACGA
Statistics
Matches: 155, Mismatches: 26, Indels: 10
0.81 0.14 0.05
Matches are distributed among these distances:
104 9 0.06
105 103 0.66
106 2 0.01
107 14 0.09
108 27 0.17
ACGTcount: A:0.41, C:0.16, G:0.18, T:0.25
Consensus pattern (105 bp):
GGATCAACATTTCCAAAAGAGTTCATAATGAGAAGAACTCATCATAAAGGAGAAAGTTCATAATG
AGAAAAACATGTTCCTTTCAAAGTCACCACAAAAGGAGGT
Found at i:319118 original size:3 final size:3
Alignment explanation
Indices: 319103--319154 Score: 79
Period size: 3 Copynumber: 17.7 Consensus size: 3
319093 GAATTAAAAA
* *
319103 TAT TAT TA- AAT TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
319150 TAT TA
1 TAT TA
319155 AGTGTGTTTA
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
2 1 0.02
3 43 0.98
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TAT
Found at i:320511 original size:14 final size:16
Alignment explanation
Indices: 320487--320519 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
320477 GTTTATTTTG
320487 TTTTAAGTATTT-TAT
1 TTTTAAGTATTTATAT
320502 TTTTAA-TATTTATAT
1 TTTTAAGTATTTATAT
320517 TTT
1 TTT
320520 AGTCACATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 12 0.71
ACGTcount: A:0.27, C:0.00, G:0.03, T:0.70
Consensus pattern (16 bp):
TTTTAAGTATTTATAT
Found at i:326281 original size:22 final size:22
Alignment explanation
Indices: 326266--326307 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
326256 AATAATAATA
326266 ATAA-AATAAATAAATAAAAAT
1 ATAATAATAAATAAATAAAAAT
326287 ATAATAATAAATAATATAAAA
1 ATAATAATAAATAA-ATAAAA
326308 CGAAAAAATA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
21 4 0.21
22 9 0.47
23 6 0.32
ACGTcount: A:0.74, C:0.00, G:0.00, T:0.26
Consensus pattern (22 bp):
ATAATAATAAATAAATAAAAAT
Found at i:326292 original size:15 final size:14
Alignment explanation
Indices: 326260--326305 Score: 60
Period size: 14 Copynumber: 3.3 Consensus size: 14
326250 TATTTTAATA
326260 ATAATAAT-AAAAT
1 ATAATAATAAAAAT
326273 A-AATAAATAAAAAT
1 ATAAT-AATAAAAAT
326287 ATAATAATAAATAAT
1 ATAATAATAAA-AAT
326302 ATAA
1 ATAA
326306 AACGAAAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
12 3 0.10
13 4 0.14
14 12 0.41
15 10 0.34
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
ATAATAATAAAAAT
Found at i:326317 original size:15 final size:14
Alignment explanation
Indices: 326281--326330 Score: 55
Period size: 15 Copynumber: 3.4 Consensus size: 14
326271 ATAAATAAAT
*
326281 AAAAATATAATAATA
1 AAAAATATAA-AAGA
*
326296 AATAATATAAAACGA
1 AAAAATATAAAA-GA
326311 AAAAATATAAAATGA
1 AAAAATATAAAA-GA
326326 AAAAA
1 AAAAA
326331 ATGGTGATTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
14 2 0.07
15 28 0.93
ACGTcount: A:0.74, C:0.02, G:0.04, T:0.20
Consensus pattern (14 bp):
AAAAATATAAAAGA
Found at i:326317 original size:22 final size:22
Alignment explanation
Indices: 326268--326317 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
326258 TAATAATAAT
*
326268 AAAATAAATAAATAAAAATATA
1 AAAATAAATAAATAAAAAGATA
* *
326290 ATAATAAATAATATAAAACGA-A
1 AAAATAAATAA-ATAAAAAGATA
326312 AAAATA
1 AAAATA
326318 TAAAATGAAA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 16 0.70
23 7 0.30
ACGTcount: A:0.74, C:0.02, G:0.02, T:0.22
Consensus pattern (22 bp):
AAAATAAATAAATAAAAAGATA
Found at i:326729 original size:73 final size:74
Alignment explanation
Indices: 326575--326777 Score: 243
Period size: 73 Copynumber: 2.8 Consensus size: 74
326565 ATTGTTGCGT
**** * * * *
326575 TCAATATTTTAACTTTCGATCTTAAAATCAACTTTTTTCAATAATTAAAAGTATCAATCATTACC
1 TCAATATTTTAACTTTCGATCTTGTCTTCAACTTTTTTCAATATTTAAAAGTATCGATCATCACA
*
326640 GCATACGTA
66 GCATAAGTA
** *
326649 TTGATATTTTAACTTTCGATCTTGTCTTCAACTTTTTT-AATATTTAAAAGTATCGATCATCATA
1 TCAATATTTTAACTTTCGATCTTGTCTTCAACTTTTTTCAATATTTAAAAGTATCGATCATCACA
326713 G-ATTAAGTA
66 GCA-TAAGTA
* *
326722 TCAATATTTTAACTTTCGATCTTGTCTT-AA-TTTTTTCAGTATTTAAATGTATCGAT
1 TCAATATTTTAACTTTCGATCTTGTCTTCAACTTTTTTCAATATTTAAAAGTATCGAT
326778 ATTTAAAATG
Statistics
Matches: 111, Mismatches: 16, Indels: 6
0.83 0.12 0.05
Matches are distributed among these distances:
71 6 0.05
72 20 0.18
73 53 0.48
74 32 0.29
ACGTcount: A:0.33, C:0.14, G:0.08, T:0.45
Consensus pattern (74 bp):
TCAATATTTTAACTTTCGATCTTGTCTTCAACTTTTTTCAATATTTAAAAGTATCGATCATCACA
GCATAAGTA
Found at i:327585 original size:3 final size:3
Alignment explanation
Indices: 327577--327638 Score: 124
Period size: 3 Copynumber: 20.7 Consensus size: 3
327567 GTGAATTCAC
327577 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
327625 TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TT
327639 TTAACAGTAT
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 59 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TTA
Found at i:328244 original size:18 final size:19
Alignment explanation
Indices: 328217--328254 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
328207 TTTTAAAAAG
*
328217 AAAACAC-AAATTTTGAAA
1 AAAACACAAAACTTTGAAA
*
328235 AAAACTCAAAACTTTGAAA
1 AAAACACAAAACTTTGAAA
328254 A
1 A
328255 CCTTCATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.61, C:0.13, G:0.05, T:0.21
Consensus pattern (19 bp):
AAAACACAAAACTTTGAAA
Found at i:333005 original size:34 final size:34
Alignment explanation
Indices: 332963--333044 Score: 96
Period size: 36 Copynumber: 2.4 Consensus size: 34
332953 AATATATTTA
*
332963 TTGCTCGACTCG-ACTCGTAAAGCTCGTTAAAATT
1 TTGCTCGACTCGTACTCGTAAAGCTCGAT-AAATT
* *
332997 TTGCTCGACTCGTTGCTCGTTAAGCTCGATAAATT
1 TTGCTCGACTCG-TACTCGTAAAGCTCGATAAATT
333032 TTGCTTC-ACTCGT
1 TTGC-TCGACTCGT
333045 GCTAGTTAAG
Statistics
Matches: 42, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
34 13 0.31
35 14 0.33
36 15 0.36
ACGTcount: A:0.21, C:0.24, G:0.18, T:0.37
Consensus pattern (34 bp):
TTGCTCGACTCGTACTCGTAAAGCTCGATAAATT
Found at i:333043 original size:35 final size:35
Alignment explanation
Indices: 332963--333054 Score: 109
Period size: 34 Copynumber: 2.7 Consensus size: 35
332953 AATATATTTA
* * *
332963 TTGCTCGACTCG-ACTCGTAAAGCTCGTTAAAATT
1 TTGCTCGACTCGTGCTCGTTAAGCTCGATAAAATT
332997 TTGCTCGACTCGTTGCTCGTTAAGCTCGAT-AAATT
1 TTGCTCGACTCG-TGCTCGTTAAGCTCGATAAAATT
*
333032 TTGCTTC-ACTCGTGCTAGTTAAG
1 TTGC-TCGACTCGTGCTCGTTAAG
333055 AAATTTTGTC
Statistics
Matches: 51, Mismatches: 4, Indels: 6
0.84 0.07 0.10
Matches are distributed among these distances:
34 22 0.43
35 14 0.27
36 15 0.29
ACGTcount: A:0.22, C:0.23, G:0.20, T:0.36
Consensus pattern (35 bp):
TTGCTCGACTCGTGCTCGTTAAGCTCGATAAAATT
Found at i:346007 original size:16 final size:16
Alignment explanation
Indices: 345977--346016 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
345967 CGTAAAAATA
* *
345977 AATATAAATATATAATT
1 AATA-AAATAAATAATG
345994 AATAAAATAAATAATG
1 AATAAAATAAATAATG
346010 AATAAAA
1 AATAAAA
346017 AATTAAATTT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 17 0.81
17 4 0.19
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.30
Consensus pattern (16 bp):
AATAAAATAAATAATG
Found at i:346013 original size:27 final size:26
Alignment explanation
Indices: 345971--346022 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 26
345961 AAAATACGTA
* *
345971 AAAATAAATATAAATATATAATTAAT
1 AAAATAAATATAAATAAAAAATTAAT
*
345997 AAAATAAATAATGAATAAAAAATTAA
1 AAAATAAAT-ATAAATAAAAAATTAA
346023 ATTTTAAGAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (26 bp):
AAAATAAATATAAATAAAAAATTAAT
Found at i:346475 original size:32 final size:33
Alignment explanation
Indices: 346439--346508 Score: 124
Period size: 32 Copynumber: 2.2 Consensus size: 33
346429 TTATAAAAAA
*
346439 TTAAAATTCTAAATGATTCAATAGTT-AAAATT
1 TTAAAATTCTAAATAATTCAATAGTTAAAAATT
346471 TTAAAATTCTAAATAATTCAATAGTTAAAAATT
1 TTAAAATTCTAAATAATTCAATAGTTAAAAATT
346504 TTAAA
1 TTAAA
346509 GTAAATTATT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
32 25 0.69
33 11 0.31
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (33 bp):
TTAAAATTCTAAATAATTCAATAGTTAAAAATT
Found at i:347031 original size:29 final size:28
Alignment explanation
Indices: 346938--347031 Score: 89
Period size: 29 Copynumber: 3.2 Consensus size: 28
346928 ATTCACATAT
*
346938 TAAATTAAAATATATTTTTAAATTAAAA
1 TAAAATAAAATATATTTTTAAATTAAAA
**
346966 TAAGAATAAAATATATTTTTAGGTTACGAAAA
1 TAA-AATAAAATATATTTTTAAATT---AAAA
* * *
346998 GAAAATAAAATATATTTAATAAATTAAGA
1 TAAAATAAAATATATTT-TTAAATTAAAA
347027 TAAAA
1 TAAAA
347032 GAATATTTTT
Statistics
Matches: 52, Mismatches: 9, Indels: 9
0.74 0.13 0.13
Matches are distributed among these distances:
28 3 0.06
29 25 0.48
31 14 0.27
32 10 0.19
ACGTcount: A:0.57, C:0.01, G:0.06, T:0.35
Consensus pattern (28 bp):
TAAAATAAAATATATTTTTAAATTAAAA
Found at i:347328 original size:16 final size:16
Alignment explanation
Indices: 347307--347341 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
347297 AGTTGTTGAG
* *
347307 AAAAATATATTAAACT
1 AAAAATAAATTAAAAT
347323 AAAAATAAATTAAAAT
1 AAAAATAAATTAAAAT
347339 AAA
1 AAA
347342 TTTATTCATC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (16 bp):
AAAAATAAATTAAAAT
Found at i:348545 original size:35 final size:35
Alignment explanation
Indices: 348499--348636 Score: 179
Period size: 35 Copynumber: 3.9 Consensus size: 35
348489 GATGAACAAC
* *
348499 TGAATCGAAAGTGCTGAAGCTTCCTTCCGTTCACT
1 TGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACT
* * *
348534 TGAATTGAAAGTGCCGATGCTTCCTTTCGTT-ATTCA
1 TGAATCGAAAGTGCCGATGCTTCCTTCCGTTCA--CT
* *
348570 TGAATCGAAAGTGTCGATGCTTTCTTCCGTTCACT
1 TGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACT
*
348605 TGAATCGAAAGTGCCGATGCTTCCTTTCGTTC
1 TGAATCGAAAGTGCCGATGCTTCCTTCCGTTC
348637 TTCTTATTCA
Statistics
Matches: 87, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
34 1 0.01
35 57 0.66
36 28 0.32
37 1 0.01
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (35 bp):
TGAATCGAAAGTGCCGATGCTTCCTTCCGTTCACT
Found at i:348615 original size:71 final size:71
Alignment explanation
Indices: 348499--348635 Score: 231
Period size: 71 Copynumber: 1.9 Consensus size: 71
348489 GATGAACAAC
*
348499 TGAATCGAAAGTGCTGAAGCTTCCTTCCGTTCACTTGAATTGAAAGTGCCGATGCTTCCTTTCGT
1 TGAATCGAAAGTGCTGAAGCTTCCTTCCGTTCACTTGAATCGAAAGTGCCGATGCTTCCTTTCGT
348564 TATTCA
66 TATTCA
* *
348570 TGAATCGAAAGTG-TCGATGCTTTCTTCCGTTCACTTGAATCGAAAGTGCCGATGCTTCCTTTCG
1 TGAATCGAAAGTGCT-GAAGCTTCCTTCCGTTCACTTGAATCGAAAGTGCCGATGCTTCCTTTCG
348634 TT
65 TT
348636 CTTCTTATTC
Statistics
Matches: 62, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
70 1 0.02
71 61 0.98
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (71 bp):
TGAATCGAAAGTGCTGAAGCTTCCTTCCGTTCACTTGAATCGAAAGTGCCGATGCTTCCTTTCGT
TATTCA
Found at i:355882 original size:21 final size:21
Alignment explanation
Indices: 355856--355895 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
355846 CCCCCTTTGA
*
355856 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
355877 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
355896 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:359848 original size:19 final size:19
Alignment explanation
Indices: 359824--359890 Score: 116
Period size: 19 Copynumber: 3.5 Consensus size: 19
359814 AACTAATCGT
* *
359824 TAACAGTCTTAACTGTTGC
1 TAACAGCCTTAACTGCTGC
359843 TAACAGCCTTAACTGCTGC
1 TAACAGCCTTAACTGCTGC
359862 TAACAGCCTTAACTGCTGC
1 TAACAGCCTTAACTGCTGC
359881 TAACAGCCTT
1 TAACAGCCTT
359891 CTAGAACCTA
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 46 1.00
ACGTcount: A:0.27, C:0.28, G:0.15, T:0.30
Consensus pattern (19 bp):
TAACAGCCTTAACTGCTGC
Found at i:366259 original size:233 final size:227
Alignment explanation
Indices: 365804--366282 Score: 646
Period size: 233 Copynumber: 2.1 Consensus size: 227
365794 TGAATTAGAA
365804 ACCCGACCCGACCCGAAATAATAAAAAAACTATTTTTATTCAATAAAAACAGTGACTTAATTGGA
1 ACCCGACCCGACCCGAAATAATAAAAAAACTATTTTTATTCAATAAAAACAGTGACTTAATTGGA
*
365869 AAAACAATATATATAGATGGGTATTATTGTAATTATTCCTAAATATATATAAGGTAAAATTATAC
66 AAAACAATATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATATAAGGTAAAATTATA-
* *
365934 ATTTTTTGGTTCGAGTGGGGTCGGGTATTTTTCACCCTAAACCCGAACCCGACCCGAATATCACA
130 ATATATT-GTTC----GGGGTCGGGTATTTTTCACCCTAAACCCGAACCCGACCCGAATATCACA
* * *
365999 CTTAAAAAAATGACCTGACCTGACCAAAATAAAGTTTC
190 CTTAAAAAAACGACCCGACCCGACCAAAATAAAGTTTC
*
366037 ACCCGACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGGA
1 ACCCGACCCGACCCGAAATAATAAAAAAACTATTTTTATTCAATAAAAACAGTGACTTAATTGGA
* *
366102 AAAA-ATTATATATAGAGGGGTATTATTGTAATTATTCCT-GA-ATATATAAGGTAAAATTAT-A
66 AAAACAATATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATATAAGGTAAAATTATAA
366163 TATATT-TTC-GGGTCGGGTATTTTTCACCCTAAACCCGAACTCGACCCGACCCGACCCAAATAT
131 TATATTGTTCGGGGTCGGGTATTTTTCACCCTAAACCCG-A----ACCCGACCCG-----AATAT
***
366226 TTTACTTTAAAAAAACCGACCCGACCCGACCAAAATAAAGTTTC
186 CACAC-TTAAAAAAA-CGACCCGACCCGACCAAAATAAAGTTTC
366270 ACCCGACCCGACC
1 ACCCGACCCGACC
366283 TGAATATATG
Statistics
Matches: 222, Mismatches: 12, Indels: 24
0.86 0.05 0.09
Matches are distributed among these distances:
221 28 0.13
222 1 0.00
226 13 0.06
228 5 0.02
230 19 0.09
231 8 0.04
232 42 0.19
233 106 0.48
ACGTcount: A:0.38, C:0.20, G:0.13, T:0.28
Consensus pattern (227 bp):
ACCCGACCCGACCCGAAATAATAAAAAAACTATTTTTATTCAATAAAAACAGTGACTTAATTGGA
AAAACAATATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATATAAGGTAAAATTATAA
TATATTGTTCGGGGTCGGGTATTTTTCACCCTAAACCCGAACCCGACCCGAATATCACACTTAAA
AAAACGACCCGACCCGACCAAAATAAAGTTTC
Found at i:371148 original size:173 final size:173
Alignment explanation
Indices: 370852--371194 Score: 569
Period size: 173 Copynumber: 2.0 Consensus size: 173
370842 TTGATCACTT
370852 TTTAAGTGTTCATCTGGTTATGGCATCGTGAAGAGAAGCCCTCAGTCTATTCGATAACATTGATG
1 TTTAAGTGTTCATCTGGTTATGGCATCGTGAAGAGAAGCCCTCAGTCTATTCGATAACATTGATG
* * * *
370917 ATTAGTGACACCAGAGTGAAACCATTCGATATTAAGATTTTGTCATGAAGAGAGCCATGAGTACC
66 ATTAGTGACACCAGAGTGAAACCATTCGAGATTAAGATTTTGGCATAAAAAGAGCCATGAGTACC
* * *
370982 CATATTGGGGCATTACCTAAACCAGATGTCGTTAAGATCACGA
131 CACATTGGAGCATTACCTAAACCAGATGTCATTAAGATCACGA
* * * *
371025 TTTAAGTGTTCATTTGGTTATGTCATCGTGAAGAGAAGCCCTTAGTCTATTCGATAACATTGCTG
1 TTTAAGTGTTCATCTGGTTATGGCATCGTGAAGAGAAGCCCTCAGTCTATTCGATAACATTGATG
*
371090 ATTAGTGACACCAGAGTGAAACCATTCGAGATTAAGATTTTGGCATAAAAATAGCCATGAGTACC
66 ATTAGTGACACCAGAGTGAAACCATTCGAGATTAAGATTTTGGCATAAAAAGAGCCATGAGTACC
*
371155 CACATTGGAGCATTATCTAAACCAGATGTCATTAAGATCA
131 CACATTGGAGCATTACCTAAACCAGATGTCATTAAGATCA
371195 TGAGATTTAA
Statistics
Matches: 157, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
173 157 1.00
ACGTcount: A:0.32, C:0.17, G:0.21, T:0.30
Consensus pattern (173 bp):
TTTAAGTGTTCATCTGGTTATGGCATCGTGAAGAGAAGCCCTCAGTCTATTCGATAACATTGATG
ATTAGTGACACCAGAGTGAAACCATTCGAGATTAAGATTTTGGCATAAAAAGAGCCATGAGTACC
CACATTGGAGCATTACCTAAACCAGATGTCATTAAGATCACGA
Found at i:372222 original size:58 final size:57
Alignment explanation
Indices: 372081--372224 Score: 171
Period size: 57 Copynumber: 2.5 Consensus size: 57
372071 TTTAGGAACC
** *
372081 AAGCATGATTTTCAAGGGTTTCTTGATGATTATCTCCAAAGAATTTTTAAAGAAACT
1 AAGCATGATTTTCAAGGGTTTCTTGATGACGATCTCCAAAGAATTTTTAAAGAAAAT
* * * * * *
372138 AAGCCTAATTTTCAGGGGTTTCTTGATGACGATTTTCAATGAATTTTTATAAGAAAAT
1 AAGCATGATTTTCAAGGGTTTCTTGATGACGATCTCCAAAGAATTTTTA-AAGAAAAT
* * *
372196 AAGCTTGATTTTCAAGGTTTTATTGATGA
1 AAGCATGATTTTCAAGGGTTTCTTGATGA
372225 GTAATTTCTT
Statistics
Matches: 72, Mismatches: 14, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
57 41 0.57
58 31 0.43
ACGTcount: A:0.33, C:0.10, G:0.17, T:0.40
Consensus pattern (57 bp):
AAGCATGATTTTCAAGGGTTTCTTGATGACGATCTCCAAAGAATTTTTAAAGAAAAT
Found at i:372613 original size:2 final size:2
Alignment explanation
Indices: 372606--372634 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
372596 TTTTGTAAAT
372606 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
372635 TGTAGATTGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:377169 original size:42 final size:40
Alignment explanation
Indices: 377106--377219 Score: 131
Period size: 42 Copynumber: 2.7 Consensus size: 40
377096 AACGGTTTCT
377106 TGATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCA
1 TGATG-GTAAGTCCTTCGGGCCATCA-TAAGTCTTTCGAGCA
* *
377148 TGATGTGTAAGTCCTAT-GGGCCATTTATAAGTCTTTCGAGTA
1 TGATG-GTAAGTCCT-TCGGGCCA-TCATAAGTCTTTCGAGCA
* *
377190 AGATGATAAGTCCTTCGGGCCATCCATAAG
1 TGATGGTAAGTCCTTCGGGCCAT-CATAAG
377220 ACCTTCGGGC
Statistics
Matches: 62, Mismatches: 6, Indels: 9
0.81 0.08 0.12
Matches are distributed among these distances:
40 2 0.03
41 19 0.31
42 38 0.61
43 3 0.05
ACGTcount: A:0.25, C:0.19, G:0.25, T:0.31
Consensus pattern (40 bp):
TGATGGTAAGTCCTTCGGGCCATCATAAGTCTTTCGAGCA
Found at i:377452 original size:257 final size:256
Alignment explanation
Indices: 376924--377461 Score: 768
Period size: 257 Copynumber: 2.1 Consensus size: 256
376914 TCTTGTAGTG
*
376924 TTTCGAGCAAGATGATAAAACCTTCGAGCCATCCATAAGACCTTCGGGCAGGATGTTTTCAACAT
1 TTTCGAGCAAGATGATAAGACCTTCGAGCCATCCATAAGACCTTCGGGCAGGATGTTTTCAACAT
*
376989 TTTTCGTACTCGATTCATCACATATGGAGTTGAATCAACAACACCTCACTCGAGGGACCAACATA
66 TTTTCGTACTCGATTAATCACATATGGAGTTGAATCAACAACACCTCACTCGAGGGACCAACATA
*
377054 ATATGTAGGGGTTCCTTGATGACAAAACTAAGCTTAATTTTCAACGGTTTCTTGATGAGTAAGTC
131 ATATGTAGGGGTTCCTTGATGACAAAACTAAGCTTAATTTTCAAAGGTTTCTTGATGAGTAAGT-
* * ** *
377119 CTTCGGGCCATCAGTAAGTCTTTCGAGCATGATGTGTAAGTCCTATGGGCCATTTATAAGTC
195 CTCCGGGCCATCAGTAAGTCTTCCGAGCATGATACGTAAGTCCTATGGGCCATTTATAAATC
* * *
377181 TTTCGAGTAAGATGATAAGTCCTTCGGGCCATCCATAAGACCTTCGGGCA-GAT-TTTTCAACAT
1 TTTCGAGCAAGATGATAAGACCTTCGAGCCATCCATAAGACCTTCGGGCAGGATGTTTTCAACAT
* *
377244 TTTAT-GTACTCGATTAATCATATATGGAGTTGAATCAACAATACCTCACTCGAGGGACCAACAT
66 TTT-TCGTACTCGATTAATCACATATGGAGTTGAATCAACAACACCTCACTCGAGGGACCAACAT
* *
377308 AATATGTAGGGGTTCCTTGATGACAACTAAGAAACTAAGCTTGATTTTTAAAGGTTTCTTGATGA
130 AATATGTAGGGGTTCCTTGATG---AC--A-AAACTAAGCTTAATTTTCAAAGGTTTCTTGATGA
* * *
377373 GTTA-T-TCCGGG-CATCAGTATGTCTTCCGAGCATGATACGTAAGT-CTTTCGGGCCATTTATA
189 GTAAGTCTCCGGGCCATCAGTAAGTCTTCCGAGCATGATACGTAAGTCCTAT-GGGCCATTTATA
377434 ACAT-
253 A-ATC
377438 TTTCGAGCAAGATGATAAGACCTT
1 TTTCGAGCAAGATGATAAGACCTT
377462 TTTATGGTAC
Statistics
Matches: 252, Mismatches: 20, Indels: 18
0.87 0.07 0.06
Matches are distributed among these distances:
255 91 0.36
256 7 0.03
257 110 0.44
258 8 0.03
260 2 0.01
261 34 0.13
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Consensus pattern (256 bp):
TTTCGAGCAAGATGATAAGACCTTCGAGCCATCCATAAGACCTTCGGGCAGGATGTTTTCAACAT
TTTTCGTACTCGATTAATCACATATGGAGTTGAATCAACAACACCTCACTCGAGGGACCAACATA
ATATGTAGGGGTTCCTTGATGACAAAACTAAGCTTAATTTTCAAAGGTTTCTTGATGAGTAAGTC
TCCGGGCCATCAGTAAGTCTTCCGAGCATGATACGTAAGTCCTATGGGCCATTTATAAATC
Found at i:379080 original size:23 final size:23
Alignment explanation
Indices: 379037--379080 Score: 54
Period size: 23 Copynumber: 1.9 Consensus size: 23
379027 TTGAGCTCCT
*
379037 GTTATTTTAATTTTTGCATTTTG
1 GTTATTTTAATTTCTGCATTTTG
*
379060 GTTATTGTTTATTTCTG-ATTT
1 GTTATT-TTAATTTCTGCATTT
379081 AGTTGCTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
23 10 0.56
24 8 0.44
ACGTcount: A:0.16, C:0.05, G:0.14, T:0.66
Consensus pattern (23 bp):
GTTATTTTAATTTCTGCATTTTG
Found at i:379285 original size:11 final size:11
Alignment explanation
Indices: 379269--379302 Score: 50
Period size: 11 Copynumber: 3.0 Consensus size: 11
379259 TATTTACTTT
*
379269 TTTTATTTTCA
1 TTTTATTTTAA
379280 TTTTATTTTAA
1 TTTTATTTTAA
379291 TTTTATATTTAA
1 TTTTAT-TTTAA
379303 GTAATTAGGT
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
11 16 0.76
12 5 0.24
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (11 bp):
TTTTATTTTAA
Found at i:379346 original size:5 final size:5
Alignment explanation
Indices: 379327--379391 Score: 60
Period size: 5 Copynumber: 12.6 Consensus size: 5
379317 ATATTTTAAG
* * * *
379327 TTTAT TTTAA TTTAT TTTAT GTTGT CTTTAT TTTACT TTT-T TTATTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT -TTTAT TTTA-T TTTAT TT-TAT
379374 TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTT
379392 TAAATTGTTT
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
4 3 0.06
5 36 0.73
6 10 0.20
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.77
Consensus pattern (5 bp):
TTTAT
Found at i:379356 original size:26 final size:22
Alignment explanation
Indices: 379327--379391 Score: 69
Period size: 21 Copynumber: 2.8 Consensus size: 22
379317 ATATTTTAAG
379327 TTTATTTTAATTTATTTTATGTTGT
1 TTTATTTTAATTTATTTTA--TT-T
*
379352 CTTTATTTTACTTT-TTTTATTT
1 -TTTATTTTAATTTATTTTATTT
*
379374 TTTATTTTATTTTATTTT
1 TTTATTTTAATTTATTTT
379392 TAAATTGTTT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
21 12 0.33
22 5 0.14
23 2 0.06
25 5 0.14
26 12 0.33
ACGTcount: A:0.17, C:0.03, G:0.03, T:0.77
Consensus pattern (22 bp):
TTTATTTTAATTTATTTTATTT
Found at i:379370 original size:81 final size:81
Alignment explanation
Indices: 379207--379380 Score: 225
Period size: 81 Copynumber: 2.2 Consensus size: 81
379197 TTTAGCTTGG
**
379207 TAATTTTATATTTAAGTAATTAGGTCCTCATATTTAAGTTTATTTATGTCTTTATTTACTTTTTT
1 TAATTTTATATTTAAGTAATTAGGTCCTCATATTTAAGTTTATTTATGAATTTATTTACTTTTTT
*
379272 TATTTTCATTTTATTT
66 TATTTTCACTTTATTT
379288 TAATTTTATATTTAAGTAATTAGGTCCTCATATTTTAAGTTTATTT-T-AATTTATTTTA-TGTT
1 TAATTTTATATTTAAGTAATTAGGTCCTCATA-TTTAAGTTTATTTATGAATTTA-TTTACT-TT
379350 GTCTTTATTTT-ACTTT-TTT
63 -T-TTTATTTTCACTTTATTT
*
379369 T-ATTTTTTATTT
1 TAATTTTATATTT
379381 TATTTTATTT
Statistics
Matches: 84, Mismatches: 4, Indels: 11
0.85 0.04 0.11
Matches are distributed among these distances:
80 15 0.18
81 43 0.51
82 18 0.21
83 8 0.10
ACGTcount: A:0.24, C:0.06, G:0.06, T:0.63
Consensus pattern (81 bp):
TAATTTTATATTTAAGTAATTAGGTCCTCATATTTAAGTTTATTTATGAATTTATTTACTTTTTT
TATTTTCACTTTATTT
Found at i:379376 original size:16 final size:17
Alignment explanation
Indices: 379357--379392 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
379347 GTTGTCTTTA
379357 TTTTACTTT-TTTTATT
1 TTTTACTTTATTTTATT
*
379373 TTTTATTTTATTTTATT
1 TTTTACTTTATTTTATT
379390 TTT
1 TTT
379393 AAATTGTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 8 0.44
17 10 0.56
ACGTcount: A:0.14, C:0.03, G:0.00, T:0.83
Consensus pattern (17 bp):
TTTTACTTTATTTTATT
Found at i:380683 original size:42 final size:40
Alignment explanation
Indices: 380618--380738 Score: 118
Period size: 42 Copynumber: 2.9 Consensus size: 40
380608 ATCGGTTTCT
*
380618 TGATGAGTAAGTTCTTC-AGGCCATCAGTAAGTCTTTCGAGCA
1 TGATGA-TAAGTCCTTCGA-GCCATCA-TAAGTCTTTCGAGCA
* * * *
380660 TGATGCGTAAGTCCTTTGAGCCATTTATAAGTCTTTCGAGTA
1 TGATG-ATAAGTCCTTCGAGCCA-TCATAAGTCTTTCGAGCA
* *
380702 TGATGATAAGTCCTTCGGGCCATCCATAAGACTTTCG
1 TGATGATAAGTCCTTCGAGCCAT-CATAAGTCTTTCG
380739 GGTAGGATTT
Statistics
Matches: 65, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
40 1 0.02
41 25 0.38
42 36 0.55
43 3 0.05
ACGTcount: A:0.25, C:0.20, G:0.22, T:0.33
Consensus pattern (40 bp):
TGATGATAAGTCCTTCGAGCCATCATAAGTCTTTCGAGCA
Found at i:382800 original size:10 final size:9
Alignment explanation
Indices: 382785--382846 Score: 63
Period size: 10 Copynumber: 6.6 Consensus size: 9
382775 TAGGTTCTCA
382785 TATTTATGTT
1 TATTTAT-TT
*
382795 TATTTAATT
1 TATTTATTT
382804 TATTTATGTT
1 TATTTAT-TT
*
382814 GTCTTTATTT
1 -TATTTATTT
382824 TACTTTATTT
1 TA-TTTATTT
382834 TA-TTATTT
1 TATTTATTT
382842 TATTT
1 TATTT
382847 TTTAAATTGT
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
8 8 0.18
9 11 0.25
10 19 0.43
11 6 0.14
ACGTcount: A:0.21, C:0.03, G:0.05, T:0.71
Consensus pattern (9 bp):
TATTTATTT
Found at i:390422 original size:21 final size:21
Alignment explanation
Indices: 390396--390465 Score: 67
Period size: 21 Copynumber: 3.3 Consensus size: 21
390386 TAGGTCCTTA
390396 TATTTTATGTTTATTTTAATT
1 TATTTTATGTTTATTTTAATT
*
390417 TATTTTATG-TTATCTTTATTT
1 TATTTTATGTTTAT-TTTAATT
390438 TATTATT-TGTTTTATTATT-ATT
1 TATT-TTATG-TTTATT-TTAATT
390460 T-TTTTA
1 TATTTTA
390466 ATTGTTTAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 12
0.75 0.04 0.22
Matches are distributed among these distances:
20 6 0.15
21 23 0.56
22 6 0.15
23 6 0.15
ACGTcount: A:0.21, C:0.01, G:0.04, T:0.73
Consensus pattern (21 bp):
TATTTTATGTTTATTTTAATT
Found at i:390435 original size:6 final size:5
Alignment explanation
Indices: 390396--390461 Score: 60
Period size: 5 Copynumber: 12.2 Consensus size: 5
390386 TAGGTCCTTA
* *
390396 TATTT TATGTT TATTT TAATT TATTT TATGT TATCTT TATTT TATTATT
1 TATTT TAT-TT TATTT TATTT TATTT TATTT TAT-TT TATTT TA-T-TT
*
390445 TGTTT TATTAT TATTT T
1 TATTT TATT-T TATTT T
390462 TTTAATTGTT
Statistics
Matches: 50, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
5 31 0.62
6 16 0.32
7 3 0.06
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.73
Consensus pattern (5 bp):
TATTT
Done.