Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007729.1 Hibiscus syriacus cultivar Beakdansim tig00109980_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: 1111098
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 7
Found at i:187422 original size:20 final size:20
Alignment explanation
Indices: 187397--187463 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 20
187387 TTTTCCCAAT
187397 TCGCAATGCAAATAAGTAAA
1 TCGCAATGCAAATAAGTAAA
* * ** *
187417 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGC-AAATAAGTAAA
187438 TCGCAATGCAAATAAGTAAA
1 TCGCAATGCAAATAAGTAAA
187458 TCGCAA
1 TCGCAA
187464 CGCGAATTGG
Statistics
Matches: 36, Mismatches: 10, Indels: 2
0.75 0.21 0.04
Matches are distributed among these distances:
20 21 0.58
21 15 0.42
ACGTcount: A:0.45, C:0.18, G:0.19, T:0.18
Consensus pattern (20 bp):
TCGCAATGCAAATAAGTAAA
Found at i:187440 original size:21 final size:21
Alignment explanation
Indices: 187414--187489 Score: 91
Period size: 21 Copynumber: 3.7 Consensus size: 21
187404 GCAAATAAGT
187414 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
* * ** *
187435 AAATCGCAATGC-AAATAAGT
1 AAATCGCAACGCGAATTGGGA
187455 AAATCGCAACGCGAATTGGGA
1 AAATCGCAACGCGAATTGGGA
*
187476 AAATCGCAATGCGA
1 AAATCGCAACGCGA
187490 TACTGACTAT
Statistics
Matches: 43, Mismatches: 11, Indels: 2
0.77 0.20 0.04
Matches are distributed among these distances:
20 15 0.35
21 28 0.65
ACGTcount: A:0.42, C:0.18, G:0.24, T:0.16
Consensus pattern (21 bp):
AAATCGCAACGCGAATTGGGA
Found at i:187454 original size:41 final size:41
Alignment explanation
Indices: 187397--187487 Score: 182
Period size: 41 Copynumber: 2.2 Consensus size: 41
187387 TTTTCCCAAT
187397 TCGCAATGCAAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCAAATAAGTAAATCGCAACGCGAATTGGGAAAA
187438 TCGCAATGCAAATAAGTAAATCGCAACGCGAATTGGGAAAA
1 TCGCAATGCAAATAAGTAAATCGCAACGCGAATTGGGAAAA
187479 TCGCAATGC
1 TCGCAATGC
187488 GATACTGACT
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.42, C:0.19, G:0.22, T:0.18
Consensus pattern (41 bp):
TCGCAATGCAAATAAGTAAATCGCAACGCGAATTGGGAAAA
Found at i:187502 original size:41 final size:41
Alignment explanation
Indices: 187416--187550 Score: 123
Period size: 41 Copynumber: 3.3 Consensus size: 41
187406 AAATAAGTAA
* * *
187416 ATCGCAACGCGAATTGGGAAAATCGCAATGCAAATA-AGTA-A
1 ATCGCAACGCGAATTGGGAAAATCGCAATGC-GATACTG-ACT
187457 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
1 ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
* * ** * * *
187498 ATCGCAATGCGATAAT-ACAAAATCGCAACGAGATACTTACT
1 ATCGCAACGCGA-ATTGGGAAAATCGCAATGCGATACTGACT
*
187539 TTCGCAACGCGA
1 ATCGCAACGCGA
187551 TACTGACTTT
Statistics
Matches: 79, Mismatches: 12, Indels: 6
0.81 0.12 0.06
Matches are distributed among these distances:
40 4 0.05
41 73 0.92
42 2 0.03
ACGTcount: A:0.39, C:0.21, G:0.21, T:0.19
Consensus pattern (41 bp):
ATCGCAACGCGAATTGGGAAAATCGCAATGCGATACTGACT
Found at i:187503 original size:20 final size:19
Alignment explanation
Indices: 187478--187592 Score: 86
Period size: 20 Copynumber: 5.7 Consensus size: 19
187468 AATTGGGAAA
*
187478 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACT-ACT
* * *
187498 ATCGCAATGCGATAATACAAA
1 ATCGCAACGCGATACTAC--T
*
187519 ATCGCAACGAGATACTTACT
1 ATCGCAACGCGATAC-TACT
*
187539 TTCGCAACGCGATACTGACT
1 ATCGCAACGCGATACT-ACT
* *
187559 TTCGCAACGCGATAATACAT
1 ATCGCAACGCGATACTAC-T
*
187579 AATCGCAATGCGAT
1 -ATCGCAACGCGAT
187593 TTTCAAAGCG
Statistics
Matches: 78, Mismatches: 11, Indels: 11
0.78 0.11 0.11
Matches are distributed among these distances:
19 5 0.06
20 47 0.60
21 23 0.29
22 3 0.04
ACGTcount: A:0.35, C:0.24, G:0.17, T:0.23
Consensus pattern (19 bp):
ATCGCAACGCGATACTACT
Found at i:187788 original size:22 final size:22
Alignment explanation
Indices: 187760--187803 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
187750 CACTCTCTCA
187760 CCCATCTCCGACGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
*
187782 CCCATCTCCGGCGAAATCCGTC
1 CCCATCTCCGACGAAATCCGTC
187804 TATCTCCATC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.20, C:0.45, G:0.16, T:0.18
Consensus pattern (22 bp):
CCCATCTCCGACGAAATCCGTC
Found at i:188119 original size:20 final size:20
Alignment explanation
Indices: 188065--188123 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
188055 GCGATTATCT
**
188065 CGTTGCGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
188085 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
* **
188105 TGTTGCGATTTTCATTTTC
1 CGTTGCGATAGTCATTTTC
188124 AGAAACTATT
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 34 1.00
ACGTcount: A:0.17, C:0.19, G:0.22, T:0.42
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:189463 original size:18 final size:18
Alignment explanation
Indices: 189442--189486 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
189432 TCCACTTCGG
*
189442 GAGCCATCACCTCGCCCA
1 GAGCCATCACCTCACCCA
*
189460 GAGCTATCACCTCACCCA
1 GAGCCATCACCTCACCCA
189478 GAGCCATCA
1 GAGCCATCA
189487 TTTGATCGAC
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 24 1.00
ACGTcount: A:0.27, C:0.44, G:0.16, T:0.13
Consensus pattern (18 bp):
GAGCCATCACCTCACCCA
Found at i:190025 original size:14 final size:14
Alignment explanation
Indices: 190008--190065 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
189998 ATGCAAAATG
*
190008 AAAATCGCAACGAC
1 AAAATCGCAACGAA
190022 AAAATCGCAATGCGAA
1 AAAATCGCAA--CGAA
190038 ATGAAATCGCAACGAA
1 A--AAATCGCAACGAA
190054 AAAATCGCAACG
1 AAAATCGCAACG
190066 CGAAATGAAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
14 21 0.54
16 9 0.23
18 9 0.23
ACGTcount: A:0.50, C:0.22, G:0.17, T:0.10
Consensus pattern (14 bp):
AAAATCGCAACGAA
Found at i:190050 original size:32 final size:33
Alignment explanation
Indices: 189992--190082 Score: 148
Period size: 32 Copynumber: 2.8 Consensus size: 33
189982 GGAAATGGCT
* *
189992 ATCGCAATGCAAAATGAAAATCGCAACGACAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
190025 ATCGCAATGCGAAATG-AAATCGCAACGAAAAA
1 ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
*
190057 ATCGCAACGCGAAATGAAAATCGCAA
1 ATCGCAATGCGAAATGAAAATCGCAA
190083 TGCGATTTGT
Statistics
Matches: 54, Mismatches: 3, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
32 30 0.56
33 24 0.44
ACGTcount: A:0.49, C:0.21, G:0.18, T:0.12
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAAAAA
Found at i:191357 original size:19 final size:19
Alignment explanation
Indices: 191335--191465 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
191325 GGAAATTACT
191335 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
191354 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
191368 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
* *
191387 ATCGCAA--CG--CT-AAT
1 ATCGCAATGCGAAATGAAA
*
191401 TTCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
**
191420 ATCGCAA--CG--A-GGGA
1 ATCGCAATGCGAAATGAAA
*
191434 ATAGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
191453 ATCGCAACGCGAA
1 ATCGCAATGCGAA
191466 TTTAATTTCG
Statistics
Matches: 82, Mismatches: 15, Indels: 30
0.65 0.12 0.24
Matches are distributed among these distances:
14 26 0.32
15 3 0.04
16 6 0.07
17 6 0.07
18 3 0.04
19 38 0.46
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:191377 original size:33 final size:33
Alignment explanation
Indices: 191335--191461 Score: 193
Period size: 33 Copynumber: 3.8 Consensus size: 33
191325 GGAAATTACT
191335 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
**
191368 ATCGCAATGCGAAATGAAAATCGCAACGCTA-A
1 ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
* *
191400 TTTCGCAATGCGAAATGAAAATCGCAACGAGGGA
1 -ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
*
191434 ATAGCAATGCGAAATGAAAATCGCAACG
1 ATCGCAATGCGAAATGAAAATCGCAACG
191462 CGAATTTAAT
Statistics
Matches: 84, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
32 1 0.01
33 82 0.98
34 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.23, T:0.15
Consensus pattern (33 bp):
ATCGCAATGCGAAATGAAAATCGCAACGAGAGA
Found at i:191442 original size:66 final size:66
Alignment explanation
Indices: 191336--191468 Score: 239
Period size: 66 Copynumber: 2.0 Consensus size: 66
191326 GAAATTACTA
* *
191336 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCGCAACGCTAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATAGCAATGCGAAATGAAAATCGCAACGCGAAT
191401 T
66 T
*
191402 TCGCAATGCGAAATGAAAATCGCAACGAGGGAATAGCAATGCGAAATGAAAATCGCAACGCGAAT
1 TCGCAATGCGAAATGAAAATCGCAACGAGAGAATAGCAATGCGAAATGAAAATCGCAACGCGAAT
191467 T
66 T
191468 T
1 T
191469 AATTTCGCGT
Statistics
Matches: 64, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.42, C:0.19, G:0.23, T:0.17
Consensus pattern (66 bp):
TCGCAATGCGAAATGAAAATCGCAACGAGAGAATAGCAATGCGAAATGAAAATCGCAACGCGAAT
T
Found at i:191643 original size:14 final size:14
Alignment explanation
Indices: 191624--191660 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
191614 CATCAATTAA
191624 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
191638 ACAAATCACCTTTT
1 ACAAATCAACTTTT
191652 ACAAATCAA
1 ACAAATCAA
191661 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.24, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:193083 original size:21 final size:21
Alignment explanation
Indices: 193017--193083 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
193007 GTGAATCGGG
*
193017 CTCTTGAATGGTGGGA-GGGA
1 CTCTTGAACGGTGGGAGGGGA
* * ** * *
193037 CCTCTTCAACGATGACAGTGGC
1 -CTCTTGAACGGTGGGAGGGGA
193059 CTCTTGAACGGTGGGAGGGGA
1 CTCTTGAACGGTGGGAGGGGA
193080 CTCT
1 CTCT
193084 CGAGGAATGA
Statistics
Matches: 32, Mismatches: 13, Indels: 2
0.68 0.28 0.04
Matches are distributed among these distances:
21 30 0.94
22 2 0.06
ACGTcount: A:0.19, C:0.21, G:0.36, T:0.24
Consensus pattern (21 bp):
CTCTTGAACGGTGGGAGGGGA
Found at i:193102 original size:42 final size:41
Alignment explanation
Indices: 193017--193139 Score: 113
Period size: 42 Copynumber: 2.9 Consensus size: 41
193007 GTGAATCGGG
* * * *
193017 CTCTTGAATGGTGGGA-GGGACCTCTTCAACGATGACAGTGGC
1 CTCTTGAACGGTGGGAGGGGA-CTC-TCGAGGATGACAGGGGC
*
193059 CTCTTGAACGGTGGGAGGGGACTCTCGAGGAATGATAGGGGC
1 CTCTTGAACGGTGGGAGGGGACTCTCGAGG-ATGACAGGGGC
* * * * *
193101 CTCTTCAACGATAGGAGTGGACTCTTGAGGGATGACAGG
1 CTCTTGAACGGTGGGAGGGGACTCTCGA-GGATGACAGG
193140 CGAGTCGGGC
Statistics
Matches: 67, Mismatches: 11, Indels: 6
0.80 0.13 0.07
Matches are distributed among these distances:
41 4 0.06
42 57 0.85
43 6 0.09
ACGTcount: A:0.23, C:0.19, G:0.37, T:0.22
Consensus pattern (41 bp):
CTCTTGAACGGTGGGAGGGGACTCTCGAGGATGACAGGGGC
Found at i:194287 original size:21 final size:22
Alignment explanation
Indices: 194245--194287 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
194235 AATAACAAAC
*
194245 ATTAGTAATTGTTAAATAATTA
1 ATTAGTAATTGTTAAAAAATTA
194267 ATTA-TAATT-TTAAAAACATTA
1 ATTAGTAATTGTTAAAAA-ATTA
194288 TATAGAAATT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
20 6 0.32
21 9 0.47
22 4 0.21
ACGTcount: A:0.49, C:0.02, G:0.05, T:0.44
Consensus pattern (22 bp):
ATTAGTAATTGTTAAAAAATTA
Found at i:195224 original size:33 final size:33
Alignment explanation
Indices: 195167--195265 Score: 135
Period size: 33 Copynumber: 3.0 Consensus size: 33
195157 ACGAGATAAT
*
195167 GAGAATCGCAACGCGGAAATGACTATCGCAACGA
1 GAGAATCGCAACGC-GAAATGACTATCGCAACCA
* *
195201 TAGAATCGCAACGCGAAATGACTATCGCGACCA
1 GAGAATCGCAACGCGAAATGACTATCGCAACCA
* **
195234 GACAATCGCAACGCGAAATGAAAATCGCAACC
1 GAGAATCGCAACGCGAAATGACTATCGCAACC
195266 GCGAAATAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
33 44 0.77
34 13 0.23
ACGTcount: A:0.39, C:0.26, G:0.22, T:0.12
Consensus pattern (33 bp):
GAGAATCGCAACGCGAAATGACTATCGCAACCA
Found at i:195259 original size:19 final size:19
Alignment explanation
Indices: 195142--195307 Score: 118
Period size: 20 Copynumber: 9.1 Consensus size: 19
195132 TCTTTTGGTT
*
195142 GAAATGAAAATCGCAACGA
1 GAAATGAAAATCGCAACGC
*
195161 GATAATGAGAATCGCAACGC
1 GA-AATGAAAATCGCAACGC
**
195181 GGAAATGACTATCGCAA--C
1 -GAAATGAAAATCGCAACGC
*
195199 G--AT-AGAATCGCAACGC
1 GAAATGAAAATCGCAACGC
** *
195215 GAAATGACTATCGCGAC-C
1 GAAATGAAAATCGCAACGC
*
195233 ---A-GACAATCGCAACGC
1 GAAATGAAAATCGCAACGC
195248 GAAATGAAAATCGCAACCGC
1 GAAATGAAAATCGCAA-CGC
* * *
195268 GAAATAAAAATCGTAACTC
1 GAAATGAAAATCGCAACGC
*
195287 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAACGC
195306 GA
1 GA
195308 TTTTTGTTTC
Statistics
Matches: 115, Mismatches: 19, Indels: 26
0.72 0.12 0.16
Matches are distributed among these distances:
14 18 0.16
15 4 0.03
16 2 0.02
17 1 0.01
18 5 0.04
19 39 0.34
20 44 0.38
21 2 0.02
ACGTcount: A:0.43, C:0.22, G:0.21, T:0.14
Consensus pattern (19 bp):
GAAATGAAAATCGCAACGC
Found at i:195330 original size:19 final size:19
Alignment explanation
Indices: 195303--195369 Score: 71
Period size: 19 Copynumber: 3.5 Consensus size: 19
195293 AAAATCGCAA
*
195303 TGCGATTTTTGTTTCACGT
1 TGCGATTTTTATTTCACGT
* *
195322 TGCGTTTTTTATTTCTCGT
1 TGCGATTTTTATTTCACGT
** *
195341 TGCGATAGTTATTTCCGCGT
1 TGCGATTTTTATTT-CACGT
195361 TGCGATTTT
1 TGCGATTTT
195370 CATTCTCGAA
Statistics
Matches: 38, Mismatches: 9, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
19 27 0.71
20 11 0.29
ACGTcount: A:0.10, C:0.16, G:0.21, T:0.52
Consensus pattern (19 bp):
TGCGATTTTTATTTCACGT
Found at i:195974 original size:20 final size:20
Alignment explanation
Indices: 195889--196002 Score: 120
Period size: 20 Copynumber: 5.7 Consensus size: 20
195879 CGCTATGTAA
* * *
195889 ATCGCGTTGCGAAAGTCAGA
1 ATCGCATTGCGATAGTCAGT
*
195909 ATCGCATTGCGAAAGTCAGT
1 ATCGCATTGCGATAGTCAGT
* * ** * *
195929 ATCTCGTTGCGATTTTATATT
1 ATCGCATTGCGATAGT-CAGT
*
195950 ATCGCATTGCGATAGTAAGT
1 ATCGCATTGCGATAGTCAGT
195970 ATCGCATTGCGATAGTCAGT
1 ATCGCATTGCGATAGTCAGT
195990 ATCGCATTGCGAT
1 ATCGCATTGCGAT
196003 TTTCCCAATT
Statistics
Matches: 77, Mismatches: 16, Indels: 2
0.81 0.17 0.02
Matches are distributed among these distances:
20 63 0.82
21 14 0.18
ACGTcount: A:0.26, C:0.18, G:0.24, T:0.32
Consensus pattern (20 bp):
ATCGCATTGCGATAGTCAGT
Found at i:195987 original size:61 final size:61
Alignment explanation
Indices: 195889--196005 Score: 171
Period size: 61 Copynumber: 1.9 Consensus size: 61
195879 CGCTATGTAA
* * * *
195889 ATCGCGTTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCTCGTTGCGATTTTATATT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTATATT
* * *
195950 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTT
1 ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT
196006 CCCAATTCGC
Statistics
Matches: 49, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
61 49 1.00
ACGTcount: A:0.26, C:0.18, G:0.23, T:0.33
Consensus pattern (61 bp):
ATCGCATTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTATATT
Found at i:196021 original size:61 final size:61
Alignment explanation
Indices: 195889--196023 Score: 164
Period size: 61 Copynumber: 2.2 Consensus size: 61
195879 CGCTATGTAA
* * * * *
195889 ATCGCGTTGCGAAAGTCAGAATCGCATTGCGAAAGTCAGTATCTCGTTGCGATTTTATATT
1 ATCGCGTTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTACAAT
* * * * *
195950 ATCGCATTGCGATAGTAAGTATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 ATCGCGTTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTT-ACAAT
196012 -TCGCGTTGCGAA
1 ATCGCGTTGCGAA
196024 TTGGGAAATC
Statistics
Matches: 61, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
61 59 0.97
62 2 0.03
ACGTcount: A:0.25, C:0.20, G:0.23, T:0.32
Consensus pattern (61 bp):
ATCGCGTTGCGAAAGTAAGAATCGCATTGCGAAAGTCAGTATCGCATTGCGATTTTACAAT
Found at i:196737 original size:25 final size:25
Alignment explanation
Indices: 196709--196760 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
196699 TTTCAAGGGC
196709 TTAAAATATAATTAAATCATAAAAG
1 TTAAAATATAATTAAATCATAAAAG
196734 TTAAAATATAATTAAATCATAAAAG
1 TTAAAATATAATTAAATCATAAAAG
196759 TT
1 TT
196761 GCGATGGGTC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.35
Consensus pattern (25 bp):
TTAAAATATAATTAAATCATAAAAG
Found at i:198052 original size:21 final size:21
Alignment explanation
Indices: 198000--198046 Score: 94
Period size: 21 Copynumber: 2.2 Consensus size: 21
197990 GTTTCCAGAT
198000 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
198021 TCGCAACGCGAACTTCGACTA
1 TCGCAACGCGAACTTCGACTA
198042 TCGCA
1 TCGCA
198047 TTGCGATTTA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.28, C:0.34, G:0.19, T:0.19
Consensus pattern (21 bp):
TCGCAACGCGAACTTCGACTA
Found at i:198091 original size:21 final size:21
Alignment explanation
Indices: 198061--198130 Score: 90
Period size: 21 Copynumber: 3.4 Consensus size: 21
198051 GATTTACATA
*
198061 TTCGCATTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
** *
198082 TTCGCGTTGCGATTTTCCAAA
1 TTCGCGTTGCGATAGTCCAAG
198103 TT--CGTTGCGATAGTCCAAG
1 TTCGCGTTGCGATAGTCCAAG
198122 TTCGCGTTG
1 TTCGCGTTG
198131 TGATTTATTA
Statistics
Matches: 40, Mismatches: 7, Indels: 4
0.78 0.14 0.08
Matches are distributed among these distances:
19 16 0.40
21 24 0.60
ACGTcount: A:0.19, C:0.23, G:0.24, T:0.34
Consensus pattern (21 bp):
TTCGCGTTGCGATAGTCCAAG
Found at i:198146 original size:42 final size:40
Alignment explanation
Indices: 198042--198167 Score: 164
Period size: 42 Copynumber: 3.1 Consensus size: 40
198032 ACTTCGACTA
* *
198042 TCGCATTGCGA-TTTACATATTCGCATTGCGATAGTCCAAGT
1 TCGCGTTGCGATTTTACAAATTCG--TTGCGATAGTCCAAGT
*
198083 TCGCGTTGCGATTTTCCAAATTCGTTGCGATAGTCCAAGT
1 TCGCGTTGCGATTTTACAAATTCGTTGCGATAGTCCAAGT
* *
198123 TCGCGTTGTGATTTATTACAAATTCGTTGCGGTAGTCCAAGT
1 TCGCGTTGCGA-TT-TTACAAATTCGTTGCGATAGTCCAAGT
198165 TCG
1 TCG
198168 TATCGCAACG
Statistics
Matches: 76, Mismatches: 6, Indels: 5
0.87 0.07 0.06
Matches are distributed among these distances:
40 26 0.34
41 12 0.16
42 38 0.50
ACGTcount: A:0.21, C:0.21, G:0.22, T:0.36
Consensus pattern (40 bp):
TCGCGTTGCGATTTTACAAATTCGTTGCGATAGTCCAAGT
Found at i:199092 original size:42 final size:42
Alignment explanation
Indices: 199030--199131 Score: 195
Period size: 42 Copynumber: 2.4 Consensus size: 42
199020 TGCGATTTTG
*
199030 GACTATCGCAACGAATTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
199072 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
1 GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
199114 GACTATCGCAACGAACTT
1 GACTATCGCAACGAACTT
199132 CGACTATCGC
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 59 1.00
ACGTcount: A:0.35, C:0.25, G:0.19, T:0.21
Consensus pattern (42 bp):
GACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTC
Found at i:199137 original size:61 final size:61
Alignment explanation
Indices: 199055--199186 Score: 219
Period size: 61 Copynumber: 2.1 Consensus size: 61
199045 TTTGGAATAA
*
199055 ATCGCAACGCGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACT
1 ATCGCAA--CGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCAAACTTCGACT
* *
199118 ATCGCAACGAACTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCAAACTTGGACT
1 ATCGCAACGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCAAACTTCGACT
199179 ATCGCAAC
1 ATCGCAAC
199187 AAATTTGGAA
Statistics
Matches: 66, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
61 59 0.89
63 7 0.11
ACGTcount: A:0.35, C:0.27, G:0.18, T:0.20
Consensus pattern (61 bp):
ATCGCAACGAACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCAAACTTCGACT
Found at i:199185 original size:42 final size:38
Alignment explanation
Indices: 199118--199203 Score: 118
Period size: 42 Copynumber: 2.2 Consensus size: 38
199108 AACTTCGACT
*
199118 ATCGCAACGAACTTCGACTATCGCAACGAATTTGGAATAA
1 ATCGCAACGAACTTCGACTATCGCAACAAATTTGG-A-AA
*
199158 ATCGCAACGCAAACTTGGACTATCGCAACAAATTTGGAAA
1 ATCGCAACG--AACTTCGACTATCGCAACAAATTTGGAAA
199198 ATCGCA
1 ATCGCA
199204 TTGCGATAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
40 17 0.40
41 1 0.02
42 24 0.57
ACGTcount: A:0.38, C:0.23, G:0.17, T:0.21
Consensus pattern (38 bp):
ATCGCAACGAACTTCGACTATCGCAACAAATTTGGAAA
Found at i:199201 original size:19 final size:19
Alignment explanation
Indices: 199137--199203 Score: 62
Period size: 19 Copynumber: 3.3 Consensus size: 19
199127 AACTTCGACT
*
199137 ATCGCAACGAATTTGGAATAA
1 ATCGCAACAAATTTGG-A-AA
* **
199158 ATCGCAACGCAAACTTGGACT
1 ATCGCAA--CAAATTTGGAAA
199179 ATCGCAACAAATTTGGAAA
1 ATCGCAACAAATTTGGAAA
199198 ATCGCA
1 ATCGCA
199204 TTGCGATAGT
Statistics
Matches: 37, Mismatches: 7, Indels: 6
0.74 0.14 0.12
Matches are distributed among these distances:
19 15 0.41
21 14 0.38
22 1 0.03
23 7 0.19
ACGTcount: A:0.40, C:0.21, G:0.18, T:0.21
Consensus pattern (19 bp):
ATCGCAACAAATTTGGAAA
Found at i:199202 original size:61 final size:61
Alignment explanation
Indices: 199066--199203 Score: 186
Period size: 61 Copynumber: 2.3 Consensus size: 61
199056 TCGCAACGCG
** * *
199066 AACTTCGACTATCGCAACGAACTTGGAATAAATCGCAACGCGAACTTCGACTATCGCAACG
1 AACTTCGAAAATCGCAACGAACTTGGAATAAATCGCAACGCAAACTTCGACTATCGCAACA
** * *
199127 AACTTCGACTATCGCAACGAATTTGGAATAAATCGCAACGCAAACTTGGACTATCGCAACA
1 AACTTCGAAAATCGCAACGAACTTGGAATAAATCGCAACGCAAACTTCGACTATCGCAACA
* *
199188 AATTTGGAAAATCGCA
1 AACTTCGAAAATCGCA
199204 TTGCGATAGT
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
61 69 1.00
ACGTcount: A:0.37, C:0.25, G:0.17, T:0.21
Consensus pattern (61 bp):
AACTTCGAAAATCGCAACGAACTTGGAATAAATCGCAACGCAAACTTCGACTATCGCAACA
Found at i:199227 original size:20 final size:20
Alignment explanation
Indices: 199199--199236 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
199189 ATTTGGAAAA
199199 TCGCATTGCGATAGTCGAGT
1 TCGCATTGCGATAGTCGAGT
* *
199219 TCGCGTTGCGATATTCGA
1 TCGCATTGCGATAGTCGA
199237 TGTTTGCGAT
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:0.18, C:0.21, G:0.29, T:0.32
Consensus pattern (20 bp):
TCGCATTGCGATAGTCGAGT
Found at i:200090 original size:45 final size:42
Alignment explanation
Indices: 200024--200128 Score: 104
Period size: 45 Copynumber: 2.4 Consensus size: 42
200014 TCTCCTCAAT
* * * *
200024 TTTAGATAAATAATTTATTTTT-TTAATAATTTTAATTTTATACT
1 TTTAAATAAATTATTGATTTTTATTAATAA-TTTAA-TTTATA-A
200068 TGTTAAATAAATTATTGATTTTTAAATTAATAATTTAATTTATAA
1 T-TTAAATAAATTATTGATTTTT--ATTAATAATTTAATTTATAA
200113 TTTAAATAATATTATT
1 TTTAAATAA-ATTATT
200129 TGATCAAATT
Statistics
Matches: 52, Mismatches: 4, Indels: 9
0.80 0.06 0.14
Matches are distributed among these distances:
44 9 0.17
45 25 0.48
46 6 0.12
47 5 0.10
48 7 0.13
ACGTcount: A:0.41, C:0.01, G:0.03, T:0.55
Consensus pattern (42 bp):
TTTAAATAAATTATTGATTTTTATTAATAATTTAATTTATAA
Found at i:200816 original size:2 final size:2
Alignment explanation
Indices: 200809--200846 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
200799 TTAATATTGA
200809 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
200847 TTGAGAAATA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:201717 original size:20 final size:21
Alignment explanation
Indices: 201649--201741 Score: 63
Period size: 20 Copynumber: 4.6 Consensus size: 21
201639 AAATGACCAA
*
201649 CAAATTCGCAACACAG-GT-T
1 CAAATTCGCAACACAGAATGT
* *
201668 CCAAATTAGCAACGC-GAATTTGT
1 -CAAATTCGCAACACAGAA--TGT
201691 -AAA-TCGCAACACAGAA-GT
1 CAAATTCGCAACACAGAATGT
* *
201709 CAAATTCGCAACACGGAATTT
1 CAAATTCGCAACACAGAATGT
*
201730 CAAATTCACAAC
1 CAAATTCGCAAC
201742 GCGAATTTAT
Statistics
Matches: 57, Mismatches: 8, Indels: 15
0.71 0.10 0.19
Matches are distributed among these distances:
18 2 0.04
19 4 0.07
20 31 0.54
21 18 0.32
22 1 0.02
23 1 0.02
ACGTcount: A:0.41, C:0.25, G:0.14, T:0.20
Consensus pattern (21 bp):
CAAATTCGCAACACAGAATGT
Found at i:201820 original size:40 final size:40
Alignment explanation
Indices: 201771--201861 Score: 119
Period size: 40 Copynumber: 2.3 Consensus size: 40
201761 ACAAGTTTCC
*
201771 TTTTCGCAACAAGATTTTCTAAATCGCAACACAAATTTTG
1 TTTTCGCAACAAGATTTTCGAAATCGCAACACAAATTTTG
* ** * *
201811 TTTTTGCAACTCGATTTTCGAATTCGCAACACAAATTTTA
1 TTTTCGCAACAAGATTTTCGAAATCGCAACACAAATTTTG
*
201851 ATTTCGCAACA
1 TTTTCGCAACA
201862 GCTTTTATTT
Statistics
Matches: 42, Mismatches: 9, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
40 42 1.00
ACGTcount: A:0.33, C:0.21, G:0.10, T:0.36
Consensus pattern (40 bp):
TTTTCGCAACAAGATTTTCGAAATCGCAACACAAATTTTG
Found at i:201856 original size:20 final size:20
Alignment explanation
Indices: 201794--201884 Score: 66
Period size: 20 Copynumber: 4.7 Consensus size: 20
201784 ATTTTCTAAA
**
201794 TCGCAACACAAATTTTGTTT
1 TCGCAACACAAATTTTAATT
* * *
201814 TTGCAACTC-GATTTTCGAA-T
1 TCGCAACACAAATTTT--AATT
201834 TCGCAACACAAATTTTAATT
1 TCGCAACACAAATTTTAATT
*
201854 TCGCAACAGC---TTTTATTT
1 TCGCAACA-CAAATTTTAATT
201872 TCGCAACACAAAT
1 TCGCAACACAAAT
201885 GTTTTGGGTA
Statistics
Matches: 54, Mismatches: 9, Indels: 16
0.68 0.11 0.20
Matches are distributed among these distances:
17 1 0.02
18 15 0.28
19 7 0.13
20 25 0.46
21 6 0.11
ACGTcount: A:0.32, C:0.22, G:0.10, T:0.36
Consensus pattern (20 bp):
TCGCAACACAAATTTTAATT
Found at i:202037 original size:14 final size:15
Alignment explanation
Indices: 202018--202055 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
202008 TCCCCATCTC
202018 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
202032 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
202048 TAATTTTT
1 TAATTTTT
202056 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:202821 original size:24 final size:24
Alignment explanation
Indices: 202794--202847 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
202784 GTATTCGAAA
202794 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
202818 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
202842 TTTGAT
1 TTTGAT
202848 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:205115 original size:18 final size:18
Alignment explanation
Indices: 205081--205116 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
205071 AAGCAAAAGG
**
205081 AAATCAAAATCGTAATCA
1 AAATCAAAATCCCAATCA
205099 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
205117 CAACCGACTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.56, C:0.22, G:0.03, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:205545 original size:60 final size:59
Alignment explanation
Indices: 205438--205566 Score: 145
Period size: 60 Copynumber: 2.2 Consensus size: 59
205428 AAAATCGCAA
* * * *
205438 TGCGAATTTAACTATCGCGTTGCGAATTTGACCTTCGCGTAGCGAATTTGACTTTCGCGT
1 TGCGAATTTAACTATCACATTACGAATTTGACCTTC-CGTAGCGAATTTGACTTTCGAGT
* *
205498 TGCGAATTTAACTATCACATTACGAATTTGA-CTAT-CGTAACGTGAATTTGACTTTTGAGT
1 TGCGAATTTAACTATCACATTACGAATTTGACCT-TCCGT-A-GCGAATTTGACTTTCGAGT
*
205558 AGCGAATTT
1 TGCGAATTT
205567 GACTTTCGCG
Statistics
Matches: 59, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
58 3 0.05
59 3 0.05
60 53 0.90
ACGTcount: A:0.26, C:0.18, G:0.20, T:0.36
Consensus pattern (59 bp):
TGCGAATTTAACTATCACATTACGAATTTGACCTTCCGTAGCGAATTTGACTTTCGAGT
Found at i:205582 original size:20 final size:20
Alignment explanation
Indices: 205438--205583 Score: 130
Period size: 20 Copynumber: 7.3 Consensus size: 20
205428 AAAATCGCAA
* *
205438 TGCGAATTTAACTATCGCGT
1 TGCGAATTTGACTTTCGCGT
*
205458 TGCGAATTTGACCTTCGCGT
1 TGCGAATTTGACTTTCGCGT
*
205478 AGCGAATTTGACTTTCGCGT
1 TGCGAATTTGACTTTCGCGT
* * * *
205498 TGCGAATTTAACTATCACAT
1 TGCGAATTTGACTTTCGCGT
* * ***
205518 TACGAATTTGACTATCGTAA
1 TGCGAATTTGACTTTCGCGT
* * * *
205538 CGTGAATTTGACTTTTGAGT
1 TGCGAATTTGACTTTCGCGT
*
205558 AGCGAATTTGACTTTCGCGT
1 TGCGAATTTGACTTTCGCGT
205578 TGCGAA
1 TGCGAA
205584 AGTGTACCTT
Statistics
Matches: 98, Mismatches: 28, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
20 98 1.00
ACGTcount: A:0.25, C:0.18, G:0.21, T:0.36
Consensus pattern (20 bp):
TGCGAATTTGACTTTCGCGT
Found at i:207263 original size:4 final size:4
Alignment explanation
Indices: 207242--207279 Score: 58
Period size: 4 Copynumber: 9.5 Consensus size: 4
207232 GGGCCGTTAA
* *
207242 AAAT AAAT TAAT ACAT AAAT AAAT AAAT AAAT AAAT AA
1 AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AAAT AA
207280 TGCCGAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (4 bp):
AAAT
Found at i:207455 original size:20 final size:21
Alignment explanation
Indices: 207403--207455 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
207393 AGTAGATACC
*
207403 TCACCACGTAAAACATAATTT
1 TCACCACGTAAAACATAATTA
* * *
207424 TCATCGCGTAAAACATCA-TA
1 TCACCACGTAAAACATAATTA
207444 TCACCACGTAAA
1 TCACCACGTAAA
207456 GACCATACTT
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.42, C:0.26, G:0.08, T:0.25
Consensus pattern (21 bp):
TCACCACGTAAAACATAATTA
Found at i:207513 original size:21 final size:21
Alignment explanation
Indices: 207489--207538 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 21
207479 ACCATTTTCG
**
207489 TCACGTAAAGTACCGACCTCA
1 TCACGTAAAACACCGACCTCA
*
207510 TCACGTAAAACACTGACCTCA
1 TCACGTAAAACACCGACCTCA
207531 TCACGTAA
1 TCACGTAA
207539 CTCCCCTAAC
Statistics
Matches: 26, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.36, C:0.32, G:0.12, T:0.20
Consensus pattern (21 bp):
TCACGTAAAACACCGACCTCA
Found at i:209207 original size:20 final size:20
Alignment explanation
Indices: 209182--209225 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
209172 GAAACTTAAA
*
209182 CGAAAATGAAATTCACAATG
1 CGAAAATGAAATTCACAACG
*
209202 CGAAAATGAAATTCGCAACG
1 CGAAAATGAAATTCACAACG
209222 CGAA
1 CGAA
209226 GCTAAAATCG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.48, C:0.18, G:0.18, T:0.16
Consensus pattern (20 bp):
CGAAAATGAAATTCACAACG
Found at i:209823 original size:20 final size:20
Alignment explanation
Indices: 209798--209836 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
209788 ACGCGCTTTG
* *
209798 CGAATTTGACTTCTGTGTTA
1 CGAATTTAACTTATGTGTTA
209818 CGAATTTAACTTATGTGTT
1 CGAATTTAACTTATGTGTT
209837 GCGATTTACA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (20 bp):
CGAATTTAACTTATGTGTTA
Found at i:210421 original size:25 final size:26
Alignment explanation
Indices: 210374--210422 Score: 73
Period size: 25 Copynumber: 1.9 Consensus size: 26
210364 TGATTATGAT
* *
210374 TATAATTATTATATTATATAAAATCA
1 TATAATTAATATATTATAAAAAATCA
210400 TATAATTAAT-TATTATAAAAAAT
1 TATAATTAATATATTATAAAAAAT
210423 ATTTCTCATG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 12 0.57
26 9 0.43
ACGTcount: A:0.53, C:0.02, G:0.00, T:0.45
Consensus pattern (26 bp):
TATAATTAATATATTATAAAAAATCA
Found at i:211394 original size:60 final size:60
Alignment explanation
Indices: 211271--211405 Score: 155
Period size: 60 Copynumber: 2.2 Consensus size: 60
211261 ATAGTCGAGT
* * * * * * *
211271 GACTATTTTATAACTTTTAATAGTCAAGGGACTGAACAAAGTAATTCTCTATAGCCAGAG
1 GACTATTTTGTAACTTTTAATAATCAAGAGACTCAACAAAATAATTATCTATAACCAGAG
* ** *
211331 GACTATTTTGTAACTTTTAATAATCAAGAGACTCAATAAAAT-ATTATCATATAATTAGGG
1 GACTATTTTGTAACTTTTAATAATCAAGAGACTCAACAAAATAATTATC-TATAACCAGAG
211391 GACTATTTTGTAACT
1 GACTATTTTGTAACT
211406 CTAAAACTTT
Statistics
Matches: 63, Mismatches: 11, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
59 5 0.08
60 58 0.92
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.36
Consensus pattern (60 bp):
GACTATTTTGTAACTTTTAATAATCAAGAGACTCAACAAAATAATTATCTATAACCAGAG
Found at i:221490 original size:3 final size:3
Alignment explanation
Indices: 221482--221567 Score: 145
Period size: 3 Copynumber: 28.0 Consensus size: 3
221472 AATATTTATT
*
221482 TAA TAA TAAA TAA TAA TAA TAA TAA TAA TAA TGTA TAA TAA TAA TAA
1 TAA TAA T-AA TAA TAA TAA TAA TAA TAA TAA T-AA TAA TAA TAA TAA
221529 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
221568 AAACAAACTG
Statistics
Matches: 79, Mismatches: 2, Indels: 4
0.93 0.02 0.05
Matches are distributed among these distances:
3 74 0.94
4 5 0.06
ACGTcount: A:0.65, C:0.00, G:0.01, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:221830 original size:25 final size:24
Alignment explanation
Indices: 221802--221875 Score: 59
Period size: 25 Copynumber: 3.2 Consensus size: 24
221792 AAAAGCTCCC
221802 GAAGGTTTTAAAAACATCATGCACT
1 GAAGGTTTT-AAAACATCATGCACT
** * *
221827 GAAGGGCTT---ACA-GATG-ACC
1 GAAGGTTTTAAAACATCATGCACT
221846 GAAGGTTTTGAAAACATCATGCACT
1 GAAGGTTTT-AAAACATCATGCACT
221871 GAAGG
1 GAAGG
221876 GCTTACAGAT
Statistics
Matches: 35, Mismatches: 8, Indels: 12
0.64 0.15 0.22
Matches are distributed among these distances:
19 9 0.26
20 3 0.09
21 3 0.09
23 3 0.09
24 3 0.09
25 14 0.40
ACGTcount: A:0.36, C:0.16, G:0.24, T:0.23
Consensus pattern (24 bp):
GAAGGTTTTAAAACATCATGCACT
Found at i:222030 original size:46 final size:46
Alignment explanation
Indices: 221799--222391 Score: 914
Period size: 46 Copynumber: 13.0 Consensus size: 46
221789 TCAAAAAGCT
*
221799 CCCGAAGG-TTTTAAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
221844 -CCGAAGG-TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
221888 CCCAAAGG-TTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
* *
221933 CCCGAAGGTTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGG-TTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
* *
221980 -CCGAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
222025 CCCGAAGG-TTTTGAAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTTG-AAAACATCATGCACTGAAGGGCTTACAGATGA
* * * *
222071 CCCGGAGGTTTTTGATAACATCATGCACTAAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
222117 CCTGAAGGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
222163 CCCAAAGG-TTTTGAAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTTG-AAAACATCATGCACTGAAGGGCTTACAGATGA
**
222209 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGAACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
* * *
222255 CCCAAAGGTTTTTGATAACATCATGCACTGAAGGACTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
*
222301 CTCGAAGGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
1 CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
* *
222347 CCTGATGG-TTTTGAAAAACATCATGCACTGAAGGGCTTACAGATG
1 CCCGAAGGTTTTTG-AAAACATCATGCACTGAAGGGCTTACAGATG
222392 TGGGAAATAG
Statistics
Matches: 508, Mismatches: 31, Indels: 17
0.91 0.06 0.03
Matches are distributed among these distances:
44 43 0.08
45 103 0.20
46 317 0.62
47 45 0.09
ACGTcount: A:0.34, C:0.19, G:0.22, T:0.25
Consensus pattern (46 bp):
CCCGAAGGTTTTTGAAAACATCATGCACTGAAGGGCTTACAGATGA
Found at i:223094 original size:22 final size:22
Alignment explanation
Indices: 223066--223177 Score: 172
Period size: 22 Copynumber: 5.1 Consensus size: 22
223056 TATTTGAAAA
* *
223066 AGAGAATTTATCATCTTTAAAG
1 AGAGAATCTATCATCTTTGAAG
223088 AGAGAATCTATCATCTTTTG-AG
1 AGAGAATCTATCATC-TTTGAAG
*
223110 AGAGAATCTATCATCTTTGGAG
1 AGAGAATCTATCATCTTTGAAG
*
223132 AGAGAATCTATCATCCTTGAAG
1 AGAGAATCTATCATCTTTGAAG
223154 AGAGAATCTATCATCTTTGAAG
1 AGAGAATCTATCATCTTTGAAG
223176 AG
1 AG
223178 TGTAGATGTA
Statistics
Matches: 83, Mismatches: 5, Indels: 4
0.90 0.05 0.04
Matches are distributed among these distances:
21 4 0.05
22 76 0.92
23 3 0.04
ACGTcount: A:0.36, C:0.13, G:0.19, T:0.32
Consensus pattern (22 bp):
AGAGAATCTATCATCTTTGAAG
Found at i:227889 original size:15 final size:15
Alignment explanation
Indices: 227869--227902 Score: 61
Period size: 14 Copynumber: 2.3 Consensus size: 15
227859 GACTGCCAAA
227869 TTTTTTTTCTTTT-C
1 TTTTTTTTCTTTTCC
227883 TTTTTTTTCTTTTCC
1 TTTTTTTTCTTTTCC
227898 TTTTT
1 TTTTT
227903 CCTTTTTTTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
14 13 0.68
15 6 0.32
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (15 bp):
TTTTTTTTCTTTTCC
Found at i:227895 original size:21 final size:21
Alignment explanation
Indices: 227869--227912 Score: 58
Period size: 22 Copynumber: 2.2 Consensus size: 21
227859 GACTGCCAAA
227869 TTTT-TTTTC-TTTT-CTTTT
1 TTTTCTTTTCTTTTTCCTTTT
227887 TTTTCTTTTCCTTTTTCCTTTT
1 TTTTCTTTT-CTTTTTCCTTTT
227909 TTTT
1 TTTT
227913 TCAAGTATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
18 4 0.18
19 4 0.18
20 1 0.05
21 4 0.18
22 9 0.41
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (21 bp):
TTTTCTTTTCTTTTTCCTTTT
Found at i:230878 original size:38 final size:39
Alignment explanation
Indices: 230805--230878 Score: 105
Period size: 38 Copynumber: 1.9 Consensus size: 39
230795 TGCATCAAAC
* *
230805 AAAACTTTTACATGTAGGGGACAACTTTCAGTCCTATCT
1 AAAACTTTTACATATAGGGGACAACTTTCACTCCTATCT
* *
230844 AAAAC-TTTACATATAGGGGATAACTTTCCCTCCTA
1 AAAACTTTTACATATAGGGGACAACTTTCACTCCTA
230879 ACTTCTCTAA
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
38 26 0.84
39 5 0.16
ACGTcount: A:0.32, C:0.22, G:0.14, T:0.32
Consensus pattern (39 bp):
AAAACTTTTACATATAGGGGACAACTTTCACTCCTATCT
Found at i:232854 original size:2 final size:2
Alignment explanation
Indices: 232847--232906 Score: 58
Period size: 2 Copynumber: 32.5 Consensus size: 2
232837 AACCATATTA
* *
232847 AT AT AT AT AT AT AT AT AT AT -T AT A- AT A- AA AC AT AT -T A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
232884 AT AT AT AT AT AT AT AT AT TT AT A
1 AT AT AT AT AT AT AT AT AT AT AT A
232907 AATAAGATAT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
1 5 0.10
2 44 0.90
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:232911 original size:37 final size:37
Alignment explanation
Indices: 232823--232907 Score: 129
Period size: 37 Copynumber: 2.4 Consensus size: 37
232813 AAATTTATTA
* * *
232823 ATATA-ATTTTAAGAAACCATATTAATATATATATAT
1 ATATATATTATAATAAAACATATTAATATATATATAT
232859 ATATATATTATAATAAAACATATTAATATATATATAT
1 ATATATATTATAATAAAACATATTAATATATATATAT
232896 ATATAT-TTATAA
1 ATATATATTATAA
232908 ATAAGATATT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
36 11 0.24
37 34 0.76
ACGTcount: A:0.52, C:0.04, G:0.01, T:0.44
Consensus pattern (37 bp):
ATATATATTATAATAAAACATATTAATATATATATAT
Found at i:234198 original size:19 final size:19
Alignment explanation
Indices: 234174--234211 Score: 60
Period size: 19 Copynumber: 2.0 Consensus size: 19
234164 GATGTGTTCA
234174 TTGTT-GTTGTGTCTCCTCT
1 TTGTTGGTTGT-TCTCCTCT
234193 TTGTTGGTTGTTCTCCTCT
1 TTGTTGGTTGTTCTCCTCT
234212 GTTCTCTATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.00, C:0.21, G:0.21, T:0.58
Consensus pattern (19 bp):
TTGTTGGTTGTTCTCCTCT
Found at i:236572 original size:40 final size:40
Alignment explanation
Indices: 236527--236606 Score: 160
Period size: 40 Copynumber: 2.0 Consensus size: 40
236517 TGATGTATAA
236527 GAGGATAATATTAAATATGTTCCAATGGTTCCACTTCCAT
1 GAGGATAATATTAAATATGTTCCAATGGTTCCACTTCCAT
236567 GAGGATAATATTAAATATGTTCCAATGGTTCCACTTCCAT
1 GAGGATAATATTAAATATGTTCCAATGGTTCCACTTCCAT
236607 CGATTGGAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.17, G:0.15, T:0.35
Consensus pattern (40 bp):
GAGGATAATATTAAATATGTTCCAATGGTTCCACTTCCAT
Found at i:236738 original size:15 final size:15
Alignment explanation
Indices: 236718--236751 Score: 59
Period size: 15 Copynumber: 2.3 Consensus size: 15
236708 TTGGATTGCT
236718 TTTGTAATCCATATG
1 TTTGTAATCCATATG
*
236733 TTTGTAATCTATATG
1 TTTGTAATCCATATG
236748 TTTG
1 TTTG
236752 AAAATGAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 18 1.00
ACGTcount: A:0.24, C:0.09, G:0.15, T:0.53
Consensus pattern (15 bp):
TTTGTAATCCATATG
Found at i:239607 original size:19 final size:20
Alignment explanation
Indices: 239583--239624 Score: 68
Period size: 19 Copynumber: 2.1 Consensus size: 20
239573 CATGTTTATA
239583 AAATTATAAAGAT-AAAAAT
1 AAATTATAAAGATAAAAAAT
*
239602 AAATTATAAATATAAAAAAT
1 AAATTATAAAGATAAAAAAT
239622 AAA
1 AAA
239625 AAATAAATTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
19 12 0.57
20 9 0.43
ACGTcount: A:0.71, C:0.00, G:0.02, T:0.26
Consensus pattern (20 bp):
AAATTATAAAGATAAAAAAT
Found at i:239608 original size:27 final size:28
Alignment explanation
Indices: 239578--239636 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 28
239568 AAAACCATGT
*
239578 TTATAAAAT-TATAAAGAT-AAAAATAAA
1 TTATAAAATATA-AAAAATAAAAAATAAA
239605 TTAT-AAATATAAAAAATAAAAAATAAA
1 TTATAAAATATAAAAAATAAAAAATAAA
239632 TTATA
1 TTATA
239637 TAAAAGATTA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
26 9 0.32
27 19 0.68
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (28 bp):
TTATAAAATATAAAAAATAAAAAATAAA
Found at i:239991 original size:36 final size:36
Alignment explanation
Indices: 239944--240020 Score: 109
Period size: 36 Copynumber: 2.1 Consensus size: 36
239934 CACAATCATT
* *
239944 AATTATATTCTAAACCCCAAATTCAAAAAATGCTTC
1 AATTACATTCTAAACCCCAAATTCAAAAAATACTTC
* * *
239980 AATTACATTCTAAACCTCAAATTCCAAAAATACTTT
1 AATTACATTCTAAACCCCAAATTCAAAAAATACTTC
240016 AATTA
1 AATTA
240021 TATGACCAAC
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.45, C:0.21, G:0.01, T:0.32
Consensus pattern (36 bp):
AATTACATTCTAAACCCCAAATTCAAAAAATACTTC
Found at i:240037 original size:36 final size:36
Alignment explanation
Indices: 239944--240040 Score: 97
Period size: 36 Copynumber: 2.7 Consensus size: 36
239934 CACAATCATT
* * *
239944 AATTATATTCTAAACCCCAAATTCAAAAAATGCTTC
1 AATTACATACTAAACCCCAAATTCAAAAAATACTTC
* * * *
239980 AATTACATTCTAAACCTCAAATTCCAAAAATACTTT
1 AATTACATACTAAACCCCAAATTCAAAAAATACTTC
* *
240016 AATTATATGAC-CAACCCCAAATTCA
1 AATTACAT-ACTAAACCCCAAATTCA
240041 TAATATATCC
Statistics
Matches: 50, Mismatches: 10, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
36 49 0.98
37 1 0.02
ACGTcount: A:0.44, C:0.24, G:0.02, T:0.30
Consensus pattern (36 bp):
AATTACATACTAAACCCCAAATTCAAAAAATACTTC
Found at i:240798 original size:148 final size:148
Alignment explanation
Indices: 240523--240817 Score: 484
Period size: 148 Copynumber: 2.0 Consensus size: 148
240513 AAAAATTATT
* * * *
240523 TAAATTTGAATAAAATAATATTATAGTATTATAAATATTTATAATTAAATTTATACAGAAACTCA
1 TAAATTAGAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCA
240588 AAAATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAAGTTCGAGTCAA
66 AAAATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAAGTTCGAGTCAA
240653 CTATTTTATAAACTGAAC
131 CTATTTTATAAACTGAAC
* *
240671 TAAATTAGAATCAAATGATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACT-A
1 TAAATTAGAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCA
* *
240735 GAAAATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAATTTTGAGTCA
66 -AAAATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAAGTTCGAGTCA
* *
240800 GCTATTTTATAAATTGAA
130 ACTATTTTATAAACTGAA
240818 TTGAGTATTT
Statistics
Matches: 136, Mismatches: 10, Indels: 2
0.92 0.07 0.01
Matches are distributed among these distances:
147 1 0.01
148 135 0.99
ACGTcount: A:0.47, C:0.09, G:0.07, T:0.37
Consensus pattern (148 bp):
TAAATTAGAATAAAATAATATTATAATATGATAAATATTTATAATTAAATTTAAACAGAAACTCA
AAAATTCAATTCAATTCGACTTGATTTAAATTTTATAAACTCAAATCGAAAAAAGTTCGAGTCAA
CTATTTTATAAACTGAAC
Found at i:241035 original size:35 final size:35
Alignment explanation
Indices: 240980--241075 Score: 104
Period size: 35 Copynumber: 2.7 Consensus size: 35
240970 AATGGATTGT
* *
240980 GAATTTG-GGGTTAGACATGTAATTGAAGTATGTTG
1 GAATTTGAGGTTTAGA-ATGTAATTGAAGCATGTTG
* * *
241015 GAATTTGATGTTTAGAATGTAATTGAAGCATTTTT
1 GAATTTGAGGTTTAGAATGTAATTGAAGCATGTTG
* * *
241050 TATTTTGGGGTTTAGAATGTAATTGA
1 GAATTTGAGGTTTAGAATGTAATTGA
241076 TGAATGTGTT
Statistics
Matches: 51, Mismatches: 9, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
35 45 0.88
36 6 0.12
ACGTcount: A:0.29, C:0.02, G:0.26, T:0.43
Consensus pattern (35 bp):
GAATTTGAGGTTTAGAATGTAATTGAAGCATGTTG
Found at i:241858 original size:22 final size:22
Alignment explanation
Indices: 241833--241886 Score: 81
Period size: 22 Copynumber: 2.5 Consensus size: 22
241823 TCACTCTCTA
* *
241833 CGACGACATCCGTCCCTATCTC
1 CGACGAAATCCGTCCCCATCTC
241855 CGACGAAATCCGTCCCCATCTC
1 CGACGAAATCCGTCCCCATCTC
*
241877 CGGCGAAATC
1 CGACGAAATC
241887 TGTCTATCTC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 29 1.00
ACGTcount: A:0.22, C:0.43, G:0.17, T:0.19
Consensus pattern (22 bp):
CGACGAAATCCGTCCCCATCTC
Found at i:242302 original size:19 final size:20
Alignment explanation
Indices: 242278--242316 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
242268 ATCGCAACGT
*
242278 GATTTT-AGTTTCGTGTTGC
1 GATTTTCAGTTTCGCGTTGC
*
242297 GATTTTCATTTTCGCGTTGC
1 GATTTTCAGTTTCGCGTTGC
242317 AAATTTAAGT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.10, C:0.15, G:0.23, T:0.51
Consensus pattern (20 bp):
GATTTTCAGTTTCGCGTTGC
Found at i:244513 original size:42 final size:42
Alignment explanation
Indices: 244466--244584 Score: 159
Period size: 42 Copynumber: 2.8 Consensus size: 42
244456 TGATTCACCT
* * * * *
244466 TCATCGTTCAAGAGGCGCCTCCTATCGTTCAAGAGGCTCTTC
1 TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTC
*
244508 TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTG
1 TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTC
*
244550 TCATCGTTCAATG-GGTCCCTCCCACCGTTCAAGAG
1 TCATCGTTCAA-GAGGCCCCTCCCACCGTTCAAGAG
244585 CCCAATTCAC
Statistics
Matches: 69, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
42 68 0.99
43 1 0.01
ACGTcount: A:0.19, C:0.35, G:0.21, T:0.24
Consensus pattern (42 bp):
TCATCGTTCAAGAGGCCCCTCCCACCGTTCAAGAGGCCCCTC
Found at i:244547 original size:21 final size:21
Alignment explanation
Indices: 244467--244584 Score: 130
Period size: 21 Copynumber: 5.6 Consensus size: 21
244457 GATTCACCTT
*
244467 CATCGTTCAAGAGGCGCCTCC
1 CATCGTTCAAGAGGCCCCTCC
* * * *
244488 TATCGTTCAAGAGGCTCTTCT
1 CATCGTTCAAGAGGCCCCTCC
244509 CATCGTTCAAGAGGCCCCTCC
1 CATCGTTCAAGAGGCCCCTCC
* **
244530 CACCGTTCAAGAGGCCCCTGT
1 CATCGTTCAAGAGGCCCCTCC
*
244551 CATCGTTCAATG-GGTCCCTCC
1 CATCGTTCAA-GAGGCCCCTCC
*
244572 CACCGTTCAAGAG
1 CATCGTTCAAGAG
244585 CCCAATTCAC
Statistics
Matches: 79, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
20 1 0.01
21 77 0.97
22 1 0.01
ACGTcount: A:0.19, C:0.36, G:0.21, T:0.24
Consensus pattern (21 bp):
CATCGTTCAAGAGGCCCCTCC
Found at i:245989 original size:70 final size:66
Alignment explanation
Indices: 245906--246081 Score: 234
Period size: 66 Copynumber: 2.6 Consensus size: 66
245896 TGGGGTACAC
245906 TTTTTTTCTTGTTTAATTGAATTT-TACATTGAAAGTTGATTTGTTTAA-TTGATGAGGAAATAA
1 TTTTTTTCTTGTTTAATTGAATTTGT--A---AAAGTTGATTTGTTTAATTTGATGAGGAAATAA
245969 GAATTA
61 GAATTA
* * *
245975 TTTTTTTGCTTGTTTAATTG-ATTTGTAAAATTTGATTTGTTTAATTTGATGTGTAAATAAGAAT
1 TTTTTTT-CTTGTTTAATTGAATTTGTAAAAGTTGATTTGTTTAATTTGATGAGGAAATAAGAAT
246039 TA
65 TA
246041 TTTTTTCTCTTGTTTAATTG-ATTTGTAAAAGTTGATTTGTT
1 TTTTTT-TCTTGTTTAATTGAATTTGTAAAAGTTGATTTGTT
246082 GTTTTAAATT
Statistics
Matches: 99, Mismatches: 4, Indels: 11
0.87 0.04 0.10
Matches are distributed among these distances:
65 16 0.16
66 57 0.58
67 1 0.01
68 1 0.01
69 11 0.11
70 13 0.13
ACGTcount: A:0.28, C:0.03, G:0.15, T:0.54
Consensus pattern (66 bp):
TTTTTTTCTTGTTTAATTGAATTTGTAAAAGTTGATTTGTTTAATTTGATGAGGAAATAAGAATT
A
Found at i:246011 original size:14 final size:14
Alignment explanation
Indices: 245992--246031 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
245982 GCTTGTTTAA
245992 TTGATTTGTAAAAT
1 TTGATTTGTAAAAT
**
246006 TTGATTTGTTTAAT
1 TTGATTTGTAAAAT
*
246020 TTGATGTGTAAA
1 TTGATTTGTAAA
246032 TAAGAATTAT
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.30, C:0.00, G:0.17, T:0.53
Consensus pattern (14 bp):
TTGATTTGTAAAAT
Found at i:246041 original size:66 final size:65
Alignment explanation
Indices: 245937--246081 Score: 238
Period size: 66 Copynumber: 2.2 Consensus size: 65
245927 TTTTACATTG
245937 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTT-TGCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTCT-CTTGTTTAATTGATTTGT
246001 A
65 A
* * *
246002 AAATTTGATTTGTTTAATTTGATGTGTAAATAAGAATTATTTTTTCTCTTGTTTAATTGATTTGT
1 AAAGTTGATTTGTTTAA-TTGATGAGGAAATAAGAATTATTTTTTCTCTTGTTTAATTGATTTGT
246067 A
65 A
246068 AAAGTTGATTTGTT
1 AAAGTTGATTTGTT
246082 GTTTTAAATT
Statistics
Matches: 74, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
65 16 0.22
66 57 0.77
67 1 0.01
ACGTcount: A:0.30, C:0.02, G:0.17, T:0.52
Consensus pattern (65 bp):
AAAGTTGATTTGTTTAATTGATGAGGAAATAAGAATTATTTTTTCTCTTGTTTAATTGATTTGTA
Found at i:246473 original size:18 final size:18
Alignment explanation
Indices: 246450--246485 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
246440 AAGCCGGTTG
* *
246450 TGATTGGGATTTTGATTT
1 TGATTGCGATTTTAATTT
246468 TGATTGCGATTTTAATTT
1 TGATTGCGATTTTAATTT
246486 CCTTTTGCTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.03, G:0.22, T:0.56
Consensus pattern (18 bp):
TGATTGCGATTTTAATTT
Found at i:248689 original size:24 final size:24
Alignment explanation
Indices: 248662--248715 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
248652 TTGAAACATC
*
248662 ATCAAAATCTGAGTATTGAACAAG
1 ATCAAAATCCGAGTATTGAACAAG
** * *
248686 ATCAAGGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGAACAAG
248710 ATCAAA
1 ATCAAA
248716 TTTCGAATAC
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.41, C:0.17, G:0.20, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGAACAAG
Found at i:249713 original size:19 final size:20
Alignment explanation
Indices: 249653--249857 Score: 99
Period size: 20 Copynumber: 10.3 Consensus size: 20
249643 ACTAAAACCT
* *
249653 GTTGCGAAATT-AAATTCGT
1 GTTGCGAATTTGAAATTCGA
* * *
249672 GTTGTGAATTCGAAAATCGA
1 GTTGCGAATTTGAAATTCGA
249692 GTTGCGAATTTGAAATTC-A
1 GTTGCGAATTTGAAATTCGA
* *
249711 GTTGCGAATTTG-ACTATCGC
1 GTTGCGAATTTGAAAT-TCGA
* * *
249731 GTTGCGAATTTG-ACTTATGT
1 GTTGCGAATTTGAAATT-CGA
* *
249751 GTTGCGAATTTG-ACTTCTGT
1 GTTGCGAATTTGAAATTC-GA
*
249771 GTTGCG-ATTT-ACAGATTCGC
1 GTTGCGAATTTGA-A-ATTCGA
*
249791 GTTGCG-ATTT-ACAGATTCGC
1 GTTGCGAATTTGA-A-ATTCGA
* *
249811 GTTGCGAATTTG-ACTTCTGT
1 GTTGCGAATTTGAAATTC-GA
*
249831 GTTGCG-ATTTACAAATTCGA
1 GTTGCGAATTT-GAAATTCGA
249851 GTTGCGA
1 GTTGCGA
249858 TTTACAGATT
Statistics
Matches: 152, Mismatches: 20, Indels: 26
0.77 0.10 0.13
Matches are distributed among these distances:
18 2 0.01
19 35 0.23
20 104 0.68
21 11 0.07
ACGTcount: A:0.23, C:0.15, G:0.24, T:0.38
Consensus pattern (20 bp):
GTTGCGAATTTGAAATTCGA
Found at i:249720 original size:39 final size:40
Alignment explanation
Indices: 249653--249743 Score: 105
Period size: 39 Copynumber: 2.3 Consensus size: 40
249643 ACTAAAACCT
* * *
249653 GTTGCGAAATT-AAATTCGTGTTGTGAATTCGAAAATCGA
1 GTTGCGAATTTGAAATTCGAGTTGCGAATTCGAAAATCGA
* ** *
249692 GTTGCGAATTTGAAATTC-AGTTGCGAATTTGACTATCGC
1 GTTGCGAATTTGAAATTCGAGTTGCGAATTCGAAAATCGA
249731 GTTGCGAATTTGA
1 GTTGCGAATTTGA
249744 CTTATGTGTT
Statistics
Matches: 44, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
39 38 0.86
40 6 0.14
ACGTcount: A:0.29, C:0.12, G:0.24, T:0.35
Consensus pattern (40 bp):
GTTGCGAATTTGAAATTCGAGTTGCGAATTCGAAAATCGA
Found at i:249744 original size:20 final size:21
Alignment explanation
Indices: 249687--249824 Score: 107
Period size: 20 Copynumber: 6.9 Consensus size: 21
249677 GAATTCGAAA
* *
249687 ATCGAGTTGCGAATTTGAAAT
1 ATCGCGTTGCGAATTTGACAT
*
249708 -TC-AGTTGCGAATTTGAC-T
1 ATCGCGTTGCGAATTTGACAT
*
249726 ATCGCGTTGCGAATTTGACTT
1 ATCGCGTTGCGAATTTGACAT
*
249747 AT-GTGTTGCGAATTTGAC-T
1 ATCGCGTTGCGAATTTGACAT
* *
249766 -TCTGTGTTGCG-ATTT-ACAG
1 ATC-GCGTTGCGAATTTGACAT
*
249785 ATTCGCGTTGCG-ATTT-ACAG
1 A-TCGCGTTGCGAATTTGACAT
249805 ATTCGCGTTGCGAATTTGAC
1 A-TCGCGTTGCGAATTTGAC
249825 TTCTGTGTTG
Statistics
Matches: 102, Mismatches: 5, Indels: 19
0.81 0.04 0.15
Matches are distributed among these distances:
18 4 0.04
19 21 0.21
20 66 0.65
21 9 0.09
22 2 0.02
ACGTcount: A:0.22, C:0.16, G:0.25, T:0.38
Consensus pattern (21 bp):
ATCGCGTTGCGAATTTGACAT
Found at i:249763 original size:40 final size:40
Alignment explanation
Indices: 249711--249837 Score: 120
Period size: 40 Copynumber: 3.2 Consensus size: 40
249701 TTGAAATTCA
249711 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATGT
1 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATGT
* ** *
249751 GTTGCGAATTTGACT-TCTGTGTTGCG-ATTT-ACAGATTCGC
1 GTTGCGAATTTGACTATC-GCGTTGCGAATTTGACTTA-T-GT
* *
249791 GTTGCG-ATTT-ACAGATTCGCGTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGAC-TA-TCGCGTTGCGAATTTGACTTATGT
249831 GTTGCGA
1 GTTGCGA
249838 TTTACAAATT
Statistics
Matches: 68, Mismatches: 10, Indels: 17
0.72 0.11 0.18
Matches are distributed among these distances:
38 5 0.07
39 11 0.16
40 43 0.63
41 7 0.10
42 2 0.03
ACGTcount: A:0.18, C:0.17, G:0.26, T:0.39
Consensus pattern (40 bp):
GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTATGT
Found at i:249797 original size:60 final size:61
Alignment explanation
Indices: 249751--249879 Score: 217
Period size: 60 Copynumber: 2.1 Consensus size: 61
249741 TGACTTATGT
*
249751 GTTGCGAATTTGACTTCTGTGTTGCGATTTACAGATTCGCGTTGCG-ATTTACAGATTCGC
1 GTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGCGAATTTACAGATTCGC
*
249811 GTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTCGAGTTGCG-ATTTACAGATTCGC
1 GTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGCGAATTTACAGATTCGC
*
249871 ATTGCGAAT
1 GTTGCGAAT
249880 CTGGAAAATC
Statistics
Matches: 66, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
60 66 1.00
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (61 bp):
GTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGCGAATTTACAGATTCGC
Found at i:249817 original size:80 final size:78
Alignment explanation
Indices: 249727--249877 Score: 223
Period size: 80 Copynumber: 1.9 Consensus size: 78
249717 AATTTGACTA
*
249727 TCGCGTTGCGAATTTGACTTATGTGTTGCGAATTTGAC-TTCTGTGTTGCGATTTACAGATTCGC
1 TCGCGTTGCGAATTTGACTTATGTGTTGCG-ATTT-ACATTC-GAGTTGCGATTTACAGATTCGC
*
249791 GTTGCGATTTACAGAT
63 ATTGCGATTTACAGAT
*
249807 TCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTCGAGTTGCGATTTACAGATTCGCA
1 TCGCGTTGCGAATTTGACTTATGTGTTGCGATTTAC--ATTCGAGTTGCGATTTACAGATTCGCA
249872 TTGCGA
64 TTGCGA
249878 ATCTGGAAAA
Statistics
Matches: 65, Mismatches: 3, Indels: 6
0.88 0.04 0.08
Matches are distributed among these distances:
78 2 0.03
79 4 0.06
80 56 0.86
81 3 0.05
ACGTcount: A:0.20, C:0.17, G:0.25, T:0.38
Consensus pattern (78 bp):
TCGCGTTGCGAATTTGACTTATGTGTTGCGATTTACATTCGAGTTGCGATTTACAGATTCGCATT
GCGATTTACAGAT
Found at i:249838 original size:40 final size:40
Alignment explanation
Indices: 249727--249857 Score: 121
Period size: 40 Copynumber: 3.3 Consensus size: 40
249717 AATTTGACTA
*
249727 TCGCGTTGCGAATTTGACTTATGTGTTGCGAATTT---GACT
1 TCGCGTTGCGAATTTGACTTCTGTGTTGCG-ATTTACAGA-T
* *
249766 TCTGTGTTGCG-ATTT-ACAGATTC-GCGTTGCGATTTACAGAT
1 TC-GCGTTGCGAATTTGAC---TTCTGTGTTGCGATTTACAGAT
*
249807 TCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACAAAT
1 TCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACAGAT
*
249847 TCGAGTTGCGA
1 TCGCGTTGCGA
249858 TTTACAGATT
Statistics
Matches: 75, Mismatches: 7, Indels: 19
0.74 0.07 0.19
Matches are distributed among these distances:
38 2 0.03
39 13 0.17
40 47 0.63
41 9 0.12
42 4 0.05
ACGTcount: A:0.19, C:0.17, G:0.25, T:0.39
Consensus pattern (40 bp):
TCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACAGAT
Found at i:249854 original size:20 final size:20
Alignment explanation
Indices: 249831--249877 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
249821 TGACTTCTGT
* *
249831 GTTGCGATTTACAAATTCGA
1 GTTGCGATTTACAGATTCGC
249851 GTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAGATTCGC
*
249871 ATTGCGA
1 GTTGCGA
249878 ATCTGGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.26, C:0.17, G:0.23, T:0.34
Consensus pattern (20 bp):
GTTGCGATTTACAGATTCGC
Found at i:249876 original size:40 final size:40
Alignment explanation
Indices: 249771--249877 Score: 130
Period size: 40 Copynumber: 2.7 Consensus size: 40
249761 TGACTTCTGT
* *
249771 GTTGCGATTTACAGATTCGCGTTGCGATTTACAGATTCGC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACAAATTCGA
*
249811 GTTGCGAATTT---GACTTCTGTGTTGCGATTTACAAATTCGA
1 GTTGCG-ATTTACAGA-TTC-GCGTTGCGATTTACAAATTCGA
*
249851 GTTGCGATTTACAGATTCGCATTGCGA
1 GTTGCGATTTACAGATTCGCGTTGCGA
249878 ATCTGGAAAA
Statistics
Matches: 56, Mismatches: 5, Indels: 12
0.77 0.07 0.16
Matches are distributed among these distances:
38 2 0.04
39 7 0.12
40 38 0.68
41 7 0.12
42 2 0.04
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.36
Consensus pattern (40 bp):
GTTGCGATTTACAGATTCGCGTTGCGATTTACAAATTCGA
Found at i:249900 original size:21 final size:21
Alignment explanation
Indices: 249874--249919 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 21
249864 GATTCGCATT
*
249874 GCGAATCTGGAAAATCTCAAC
1 GCGAATCTGGAAAATCGCAAC
* *
249895 GCGAATTTGGAAAATCGCAAT
1 GCGAATCTGGAAAATCGCAAC
249916 GCGA
1 GCGA
249920 TTTATATATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.37, C:0.20, G:0.24, T:0.20
Consensus pattern (21 bp):
GCGAATCTGGAAAATCGCAAC
Found at i:251216 original size:19 final size:20
Alignment explanation
Indices: 251192--251230 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
251182 TCGCCCCAAG
*
251192 GCCCC-ATTCGAATCAATCT
1 GCCCCAATTCGAACCAATCT
*
251211 GCCCCAATTGGAACCAATCT
1 GCCCCAATTCGAACCAATCT
251231 CCAACTATAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.28, C:0.36, G:0.13, T:0.23
Consensus pattern (20 bp):
GCCCCAATTCGAACCAATCT
Found at i:254496 original size:7 final size:7
Alignment explanation
Indices: 254484--254516 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
254474 TTTTTTTATC
254484 CATTTGT
1 CATTTGT
254491 CATTTGT
1 CATTTGT
254498 CATTTGT
1 CATTTGT
254505 CATTTGT
1 CATTTGT
*
254512 TATTT
1 CATTT
254517 ATTATTATTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
7 25 1.00
ACGTcount: A:0.15, C:0.12, G:0.12, T:0.61
Consensus pattern (7 bp):
CATTTGT
Found at i:254523 original size:3 final size:3
Alignment explanation
Indices: 254515--254570 Score: 78
Period size: 3 Copynumber: 18.3 Consensus size: 3
254505 CATTTGTTAT
*
254515 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -AA TATA TATA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA T-TA T-TA
254561 TTA TTA TTA T
1 TTA TTA TTA T
254571 ATTTCAGACC
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
2 1 0.02
3 42 0.86
4 6 0.12
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:256902 original size:20 final size:21
Alignment explanation
Indices: 256868--256917 Score: 59
Period size: 20 Copynumber: 2.4 Consensus size: 21
256858 TATATGTATT
256868 TATTATTTTCATAAT-ATTTA
1 TATTATTTTCATAATGATTTA
*
256888 TATTATTTT-ATTAATGTTTTA
1 TATTATTTTCA-TAATGATTTA
*
256909 TTTTATTTT
1 TATTATTTT
256918 TCAAGTATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 1 0.04
20 13 0.50
21 12 0.46
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.68
Consensus pattern (21 bp):
TATTATTTTCATAATGATTTA
Found at i:259276 original size:10 final size:10
Alignment explanation
Indices: 259270--259397 Score: 52
Period size: 10 Copynumber: 12.4 Consensus size: 10
259260 CTAAAAACAT
259270 AATAAAAATA
1 AATAAAAATA
259280 AAT--AAAT-
1 AATAAAAATA
* *
259287 AGTATAAATAA
1 AATAAAAAT-A
259298 AATAAAAATA
1 AATAAAAATA
*
259308 TATAAAAATA
1 AATAAAAATA
*
259318 TATAAAAAT-
1 AATAAAAATA
*
259327 -ATAAAAATG
1 AATAAAAATA
* * *
259336 TATGTATAATAA
1 AAT-AAAAAT-A
259348 AATAAAATACTA
1 AATAAAA-A-TA
259360 AATAGTAACAAT-
1 AATA--AA-AATA
259372 AATAATAAATA
1 AATAA-AAATA
259383 AATGAAAAATA
1 AAT-AAAAATA
259394 AATA
1 AATA
259398 TACATATAAT
Statistics
Matches: 92, Mismatches: 10, Indels: 32
0.69 0.07 0.24
Matches are distributed among these distances:
7 2 0.02
8 12 0.13
9 4 0.04
10 29 0.32
11 25 0.27
12 14 0.15
13 2 0.02
14 3 0.03
15 1 0.01
ACGTcount: A:0.68, C:0.02, G:0.04, T:0.27
Consensus pattern (10 bp):
AATAAAAATA
Found at i:259281 original size:17 final size:16
Alignment explanation
Indices: 259255--259334 Score: 58
Period size: 18 Copynumber: 4.8 Consensus size: 16
259245 ATAAGAGCAA
259255 AAAAACTAAAAACATAAT
1 AAAAA-TAAAAA-ATAAT
*
259273 AAAAATAAATAAATAGT
1 AAAAATAAA-AAATAAT
*
259290 ATAAAT--AAAATAA-
1 AAAAATAAAAAATAAT
*
259303 AAATATATAAAAATATAT
1 AAAAATA-AAAAATA-AT
259321 AAAAATATAAAAAT
1 AAAAATA-AAAAAT
259335 GTATGTATAA
Statistics
Matches: 50, Mismatches: 6, Indels: 12
0.74 0.09 0.18
Matches are distributed among these distances:
13 4 0.08
14 5 0.10
15 1 0.02
16 6 0.12
17 14 0.28
18 20 0.40
ACGTcount: A:0.72, C:0.03, G:0.01, T:0.24
Consensus pattern (16 bp):
AAAAATAAAAAATAAT
Found at i:259306 original size:28 final size:28
Alignment explanation
Indices: 259270--259334 Score: 80
Period size: 28 Copynumber: 2.3 Consensus size: 28
259260 CTAAAAACAT
*
259270 AATAAAAATA-A-ATAAATAGTATAAATAA
1 AATAAAAATATATAAAAATA-TATAAA-AA
259298 AATAAAAATATATAAAAATATATAAAAA
1 AATAAAAATATATAAAAATATATAAAAA
*
259326 TATAAAAAT
1 AATAAAAAT
259335 GTATGTATAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
28 20 0.61
29 7 0.21
30 6 0.18
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (28 bp):
AATAAAAATATATAAAAATATATAAAAA
Found at i:259530 original size:2 final size:2
Alignment explanation
Indices: 259525--259561 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
259515 ATAAAAAATA
259525 AT 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 AT A
259562 ATAGGAAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:259580 original size:8 final size:9
Alignment explanation
Indices: 259522--259564 Score: 61
Period size: 10 Copynumber: 4.7 Consensus size: 9
259512 TAGATAAAAA
259522 ATAATATAT
1 ATAATATAT
259531 AT-ATATAT
1 ATAATATAT
259539 ATATATATAT
1 ATA-ATATAT
259549 ATATATATAT
1 ATA-ATATAT
259559 ATAATA
1 ATAATA
259565 GGAAAATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
8 8 0.25
9 5 0.16
10 19 0.59
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (9 bp):
ATAATATAT
Found at i:261078 original size:106 final size:106
Alignment explanation
Indices: 260894--262169 Score: 1958
Period size: 106 Copynumber: 12.0 Consensus size: 106
260884 GCATTGTTCC
* * * * * ** *
260894 GAGTCCAATATCCTCCGTCGTGAATTTGAAATTGGCTCTGGAATCGAAAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
** * * * *
260959 CCAGCCATCCCTTCGTTGTGAAGTTGAACTTGTGTTGCCTC
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
261000 GAGTCCAATATCCTTTGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
261065 CCAGCGGTCCCTTCATCTTGAAGTTGAACTTGCGTTATCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
261106 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
261171 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * * *
261212 TAGTCCAATATCCTTCGCTATTAAGTTGAAATTGGCTCCGAAATTGGGAAATTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
261277 CCTGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * *
261318 GAGTCCAATATCCTTCGCTGTGAAGTTAAAATTGGCTCTGAAATTGTGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
261383 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
261424 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTATTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
261489 CCAGCGGTCCCTTCGTCGTGAAGTTAAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
261530 GAGTCCAATATCATTCGTTGTGAAGTTGAAATTAGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
261595 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTTTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
261636 GAGTCCAATATTCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTTGGAAGTTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
261701 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * * * *
261742 GAGTCCAATATCATACGATGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
*
261807 CCAGCGATCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
261848 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTCGTTTGTTGATAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
** * *
261913 CCAGCGGTCCCTTCGTTATGAAGTTTAACTTGCATTGTCTG
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
* * *
261954 GAGTCCAATATCCTTCGCTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATTGTTTATTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
262019 CCAACGGTCCTTTCGTCGTGAAGTTGAACTTGCGTTGTCTA
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
*
262060 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAA
1 GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
* * *
262125 CCAGCGGTCCCTTCGTTGTGAAGTTGAACTTGTGTTGTCTT
66 CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
262166 GAGT
1 GAGT
262170 GGCACGATAT
Statistics
Matches: 1063, Mismatches: 107, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
106 1063 1.00
ACGTcount: A:0.23, C:0.18, G:0.24, T:0.35
Consensus pattern (106 bp):
GAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGGGAAGTTGTTTGTTGACAA
CCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTG
Found at i:263003 original size:22 final size:22
Alignment explanation
Indices: 262978--263051 Score: 105
Period size: 22 Copynumber: 3.4 Consensus size: 22
262968 GTTTGGTCAA
262978 AGGTTTGACATTTGATGCTCAT
1 AGGTTTGACATTTGATGCTCAT
**
263000 AGGTTTGGTATTTGATGCTCAT
1 AGGTTTGACATTTGATGCTCAT
*
263022 AGGTTTGGCATTTGATGCTCA-
1 AGGTTTGACATTTGATGCTCAT
263043 ACGGTTTGA
1 A-GGTTTGA
263052 TGGGGTAGCT
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
21 1 0.02
22 46 0.98
ACGTcount: A:0.20, C:0.12, G:0.27, T:0.41
Consensus pattern (22 bp):
AGGTTTGACATTTGATGCTCAT
Found at i:263770 original size:172 final size:165
Alignment explanation
Indices: 263446--263776 Score: 488
Period size: 167 Copynumber: 2.0 Consensus size: 165
263436 TAAATAGGCC
* *
263446 CAAATAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTCTGATGCCTTCAATCATGTCCTG
1 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAA-CA-GTCCTG
263511 CTCAAAATGTCTCTCTCTTGATACTCTATGATCTTCGAGTGAAGTGATTTGGGAATGATTGTGCT
64 CTCAAAATGTCTCTCTCTTGATACTCTATGATCTTCGAGTGAAGTGATTTGGGAATGATTGTGCT
263576 TGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
129 TGATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
*
263613 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGTCTTC-A-A-TCCTGCT
1 CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAACAGTCCTGCT
* *
263675 CAAAATGTTTTTCTCTCTTGATGCTCTATGATCTTCGAGTGAAGTGATTCAGTGATTCGGGAATG
66 CAAAATG--TCTCTCTCTTGATACTCTATGATCTTCGAGTGAAGTG----A-T--TT-GGGAATG
263740 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATG
121 ATTGTGCTTGATCAATCTCATAGTTTGAAGCTTGATG
263777 CACCATTTGT
Statistics
Matches: 149, Mismatches: 5, Indels: 15
0.88 0.03 0.09
Matches are distributed among these distances:
162 14 0.09
164 36 0.24
166 1 0.01
167 50 0.34
168 1 0.01
169 1 0.01
171 2 0.01
172 44 0.30
ACGTcount: A:0.25, C:0.17, G:0.21, T:0.37
Consensus pattern (165 bp):
CAAACAAGTGTTTCAGGGTGTTGAACCAAGGATCAATTCATTATGATGCCTTCAACAGTCCTGCT
CAAAATGTCTCTCTCTTGATACTCTATGATCTTCGAGTGAAGTGATTTGGGAATGATTGTGCTTG
ATCAATCTCATAGTTTGAAGCTTGATGTGCCATTT
Found at i:263832 original size:7 final size:7
Alignment explanation
Indices: 263820--263884 Score: 60
Period size: 7 Copynumber: 8.7 Consensus size: 7
263810 TTTTTGTCCC
263820 TTTTTCT
1 TTTTTCT
263827 TTTTTCTT
1 TTTTTC-T
263835 TTTGTTCT
1 TTT-TTCT
263843 TGTTTCTCT
1 T-TTT-TCT
263852 TTTTTCT
1 TTTTTCT
*
263859 TTGTT-T
1 TTTTTCT
*
263865 TTTTGCT
1 TTTTTCT
263872 TTTTTGCT
1 TTTTT-CT
263880 TTTTT
1 TTTTT
263885 GCTTCTTTTA
Statistics
Matches: 48, Mismatches: 4, Indels: 11
0.76 0.06 0.17
Matches are distributed among these distances:
6 4 0.08
7 18 0.38
8 17 0.35
9 9 0.19
ACGTcount: A:0.00, C:0.12, G:0.08, T:0.80
Consensus pattern (7 bp):
TTTTTCT
Found at i:263842 original size:16 final size:16
Alignment explanation
Indices: 263823--263900 Score: 65
Period size: 16 Copynumber: 4.8 Consensus size: 16
263813 TTGTCCCTTT
263823 TTCTTTTTTCTTTTTG
1 TTCTTTTTTCTTTTTG
*
263839 TTCTTGTTTCTCTTTT-
1 TTCTTTTTTCT-TTTTG
*
263855 TTCTTTGTT-TTTTTG
1 TTCTTTTTTCTTTTTG
263870 --CTTTTTTGCTTTTTTG
1 TTCTTTTTT-C-TTTTTG
263886 CTTCTTTTATTCTTT
1 -TTCTTTT-TTCTTT
263901 ATTCTTGATT
Statistics
Matches: 49, Mismatches: 4, Indels: 16
0.71 0.06 0.23
Matches are distributed among these distances:
13 6 0.12
14 4 0.08
15 1 0.02
16 23 0.47
17 4 0.08
18 3 0.06
19 6 0.12
20 2 0.04
ACGTcount: A:0.01, C:0.14, G:0.08, T:0.77
Consensus pattern (16 bp):
TTCTTTTTTCTTTTTG
Found at i:263874 original size:8 final size:8
Alignment explanation
Indices: 263858--263893 Score: 54
Period size: 8 Copynumber: 4.4 Consensus size: 8
263848 CTCTTTTTTC
*
263858 TTTGTTTT
1 TTTGCTTT
263866 TTTGCTTT
1 TTTGCTTT
263874 TTTGCTTT
1 TTTGCTTT
263882 TTTGCTTCT
1 TTTGCTT-T
263891 TTT
1 TTT
263894 ATTCTTTATT
Statistics
Matches: 26, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
8 22 0.85
9 4 0.15
ACGTcount: A:0.00, C:0.11, G:0.11, T:0.78
Consensus pattern (8 bp):
TTTGCTTT
Found at i:267351 original size:19 final size:20
Alignment explanation
Indices: 267323--267360 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
267313 TGCAGATGAT
*
267323 GGAAATAAAAT-AAAAGAGA
1 GGAAAAAAAATGAAAAGAGA
267342 GGAAAAAAAATGAAAAGAG
1 GGAAAAAAAATGAAAAGAG
267361 TTAGTAAGGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 10 0.59
20 7 0.41
ACGTcount: A:0.68, C:0.00, G:0.24, T:0.08
Consensus pattern (20 bp):
GGAAAAAAAATGAAAAGAGA
Found at i:268694 original size:12 final size:12
Alignment explanation
Indices: 268664--268705 Score: 52
Period size: 12 Copynumber: 3.6 Consensus size: 12
268654 CATAATGAAA
*
268664 ATAAATAAATAGT
1 ATAAAAAAATA-T
268677 AT-AAAAAATA-
1 ATAAAAAAATAT
268687 ATAAAAAAATAT
1 ATAAAAAAATAT
268699 ATAAAAA
1 ATAAAAA
268706 TATAAAAATG
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
10 2 0.08
11 8 0.31
12 14 0.54
13 2 0.08
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (12 bp):
ATAAAAAAATAT
Found at i:268699 original size:20 final size:20
Alignment explanation
Indices: 268664--268713 Score: 64
Period size: 23 Copynumber: 2.4 Consensus size: 20
268654 CATAATGAAA
*
268664 ATAAATAAATAGTATAAAAAAT
1 ATAAAAAAATA-TAT-AAAAAT
268686 AATAAAAAAATATATAAAAAT
1 -ATAAAAAAATATATAAAAAT
268707 ATAAAAA
1 ATAAAAA
268714 TGTATGTATA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 7 0.27
21 6 0.23
22 3 0.12
23 10 0.38
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.24
Consensus pattern (20 bp):
ATAAAAAAATATATAAAAAT
Found at i:268881 original size:14 final size:14
Alignment explanation
Indices: 268859--268907 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 14
268849 TAACGTTAGG
*
268859 AAAATATAGTAAAA
1 AAAACATAGTAAAA
268873 AAAACATAGTAAATA
1 AAAACATAGTAAA-A
268888 AGTAAACATAGATAAAA
1 A--AAACATAG-TAAAA
268905 AAA
1 AAA
268908 TAATATATAT
Statistics
Matches: 30, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
14 12 0.40
15 4 0.13
17 10 0.33
18 4 0.13
ACGTcount: A:0.69, C:0.04, G:0.08, T:0.18
Consensus pattern (14 bp):
AAAACATAGTAAAA
Found at i:274835 original size:8 final size:9
Alignment explanation
Indices: 274808--274838 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
274798 AAATGGCAAT
274808 CATTCTTTA
1 CATTCTTTA
274817 CATTCTTTA
1 CATTCTTTA
274826 CATT-TTTA
1 CATTCTTTA
274834 CATTC
1 CATTC
274839 ATTATTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.55
Consensus pattern (9 bp):
CATTCTTTA
Found at i:275298 original size:8 final size:9
Alignment explanation
Indices: 275271--275301 Score: 55
Period size: 9 Copynumber: 3.6 Consensus size: 9
275261 AAATGGCAAT
275271 CATTCTTTA
1 CATTCTTTA
275280 CATTCTTTA
1 CATTCTTTA
275289 CATT-TTTA
1 CATTCTTTA
275297 CATTC
1 CATTC
275302 ATTATTTTTC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
8 8 0.38
9 13 0.62
ACGTcount: A:0.23, C:0.23, G:0.00, T:0.55
Consensus pattern (9 bp):
CATTCTTTA
Found at i:275318 original size:463 final size:463
Alignment explanation
Indices: 274453--275384 Score: 1846
Period size: 463 Copynumber: 2.0 Consensus size: 463
274443 AAGAGGAACG
274453 GTTAATGTAGAACAACAGCTTGTTGAGGCCTTTAAAGAAGAAAAATTGACAAAATATCAAAGCAT
1 GTTAATGTAGAACAACAGCTTGTTGAGGCCTTTAAAGAAGAAAAATTGACAAAATATCAAAGCAT
274518 AGTTGAAGAAGATATGGAAGGATTATTTGTCAACATGATCATGAATAACAACAAGACTGGCAAAT
66 AGTTGAAGAAGATATGGAAGGATTATTTGTCAACATGATCATGAATAACAACAAGACTGGCAAAT
*
274583 ACTTGGCTAAGATTCGCCCTTGTTTTCCTGGAGAAACATTCAACAATTGGACTGCTGAAGACCTC
131 ACTTGGCTAAGATTCGCCCTTGTTTTCCTGGAGAAACACTCAACAATTGGACTGCTGAAGACCTC
274648 CCTGTAGTTTTTAGTATTAACATAGAGTAATACTCATAACTAATCTTTTATGCTTTAGCCTAGGA
196 CCTGTAGTTTTTAGTATTAACATAGAGTAATACTCATAACTAATCTTTTATGCTTTAGCCTAGGA
274713 ATACGAAAACTTTTTGTTATCTTGTAAATGAAATTATGTTAAGTTCACCTAATATCAAATATAAG
261 ATACGAAAACTTTTTGTTATCTTGTAAATGAAATTATGTTAAGTTCACCTAATATCAAATATAAG
274778 AAGTTTTCATTAAAATTCTCAAATGGCAATCATTCTTTACATTCTTTACATTTTTACATTCATTA
326 AAGTTTTCATTAAAATTCTCAAATGGCAATCATTCTTTACATTCTTTACATTTTTACATTCATTA
274843 TTTTTCATTTATTTCATAAATTTACTATATTCTTTCAGAAATATGTCCGACTTAAATTTGCAGGT
391 TTTTTCATTTATTTCATAAATTTACTATATTCTTTCAGAAATATGTCCGACTTAAATTTGCAGGT
274908 GTCACAAT
456 GTCACAAT
274916 GTTAATGTAGAACAACAGCTTGTTGAGGCCTTTAAAGAAGAAAAATTGACAAAATATCAAAGCAT
1 GTTAATGTAGAACAACAGCTTGTTGAGGCCTTTAAAGAAGAAAAATTGACAAAATATCAAAGCAT
274981 AGTTGAAGAAGATATGGAAGGATTATTTGTCAACATGATCATGAATAACAACAAGACTGGCAAAT
66 AGTTGAAGAAGATATGGAAGGATTATTTGTCAACATGATCATGAATAACAACAAGACTGGCAAAT
275046 ACTTGGCTAAGATTCGCCCTTGTTTTCCTGGAGAAACACTCAACAATTGGACTGCTGAAGACCTC
131 ACTTGGCTAAGATTCGCCCTTGTTTTCCTGGAGAAACACTCAACAATTGGACTGCTGAAGACCTC
275111 CCTGTAGTTTTTAGTATTAACATAGAGTAATACTCATAACTAATCTTTTATGCTTTAGCCTAGGA
196 CCTGTAGTTTTTAGTATTAACATAGAGTAATACTCATAACTAATCTTTTATGCTTTAGCCTAGGA
275176 ATACGAAAACTTTTTGTTATCTTGTAAATGAAATTATGTTAAGTTCACCTAATATCAAATATAAG
261 ATACGAAAACTTTTTGTTATCTTGTAAATGAAATTATGTTAAGTTCACCTAATATCAAATATAAG
275241 AAGTTTTCATTAAAATTCTCAAATGGCAATCATTCTTTACATTCTTTACATTTTTACATTCATTA
326 AAGTTTTCATTAAAATTCTCAAATGGCAATCATTCTTTACATTCTTTACATTTTTACATTCATTA
*
275306 TTTTTCATTTATTTCATAAATTTACTATATTCTTTCGGAAATATGTCCGACTTAAATTTGCAGGT
391 TTTTTCATTTATTTCATAAATTTACTATATTCTTTCAGAAATATGTCCGACTTAAATTTGCAGGT
275371 GTCACAAT
456 GTCACAAT
275379 GTTAAT
1 GTTAAT
275385 AGCATGCTTA
Statistics
Matches: 467, Mismatches: 2, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
463 467 1.00
ACGTcount: A:0.35, C:0.15, G:0.14, T:0.36
Consensus pattern (463 bp):
GTTAATGTAGAACAACAGCTTGTTGAGGCCTTTAAAGAAGAAAAATTGACAAAATATCAAAGCAT
AGTTGAAGAAGATATGGAAGGATTATTTGTCAACATGATCATGAATAACAACAAGACTGGCAAAT
ACTTGGCTAAGATTCGCCCTTGTTTTCCTGGAGAAACACTCAACAATTGGACTGCTGAAGACCTC
CCTGTAGTTTTTAGTATTAACATAGAGTAATACTCATAACTAATCTTTTATGCTTTAGCCTAGGA
ATACGAAAACTTTTTGTTATCTTGTAAATGAAATTATGTTAAGTTCACCTAATATCAAATATAAG
AAGTTTTCATTAAAATTCTCAAATGGCAATCATTCTTTACATTCTTTACATTTTTACATTCATTA
TTTTTCATTTATTTCATAAATTTACTATATTCTTTCAGAAATATGTCCGACTTAAATTTGCAGGT
GTCACAAT
Found at i:278846 original size:9 final size:9
Alignment explanation
Indices: 278830--278864 Score: 54
Period size: 9 Copynumber: 4.0 Consensus size: 9
278820 TATTATGCTT
278830 GAAAAAAAA
1 GAAAAAAAA
*
278839 -AGAAAAAA
1 GAAAAAAAA
278847 GAAAAAAAA
1 GAAAAAAAA
278856 GAAAAAAAA
1 GAAAAAAAA
278865 ATGTTGAAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
8 7 0.30
9 16 0.70
ACGTcount: A:0.89, C:0.00, G:0.11, T:0.00
Consensus pattern (9 bp):
GAAAAAAAA
Found at i:278853 original size:16 final size:16
Alignment explanation
Indices: 278832--278862 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
278822 TTATGCTTGA
278832 AAAAAAAAGAAAAAAG
1 AAAAAAAAGAAAAAAG
278848 AAAAAAAAGAAAAAA
1 AAAAAAAAGAAAAAA
278863 AAATGTTGAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.90, C:0.00, G:0.10, T:0.00
Consensus pattern (16 bp):
AAAAAAAAGAAAAAAG
Found at i:279271 original size:20 final size:20
Alignment explanation
Indices: 279245--279300 Score: 80
Period size: 18 Copynumber: 2.9 Consensus size: 20
279235 AGTTTCTCTG
279245 AATTCAATTTATTTTTTTGA
1 AATTCAATTTATTTTTTTGA
*
279265 GATTCAATTTA--TTTTTGA
1 AATTCAATTTATTTTTTTGA
279283 AATTCAATTTATTCTTTT
1 AATTCAATTTATT-TTTT
279301 ATTTTGTAAA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
18 17 0.55
20 10 0.32
21 4 0.13
ACGTcount: A:0.29, C:0.07, G:0.05, T:0.59
Consensus pattern (20 bp):
AATTCAATTTATTTTTTTGA
Found at i:280591 original size:113 final size:114
Alignment explanation
Indices: 280441--280649 Score: 341
Period size: 114 Copynumber: 1.8 Consensus size: 114
280431 TTAGCAAAGA
* *
280441 TTTGAATCCATCATTCGATGGATCAACATTTCCAGAG-AAGTTCATAATGAGAAGAACTCATTTG
1 TTTGAATCCATCACTCGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
280505 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACTTTTTG
66 AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACTTTTTG
* *
280554 TTTGAATTCATCACTCGATGGATCAA-ATTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCT
1 TTTGAATCCATCACTCGATGGATCAACA-TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCT
* *
280618 GAAGAGGGAAGAAGAAGTTCATAATGAGAAGA
65 GAAGAAGGAAGAAGAAATTCATAATGAGAAGA
280650 GCTTGTTTAA
Statistics
Matches: 88, Mismatches: 6, Indels: 3
0.91 0.06 0.03
Matches are distributed among these distances:
112 1 0.01
113 33 0.38
114 54 0.61
ACGTcount: A:0.40, C:0.12, G:0.20, T:0.28
Consensus pattern (114 bp):
TTTGAATCCATCACTCGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTG
AAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACTTTTTG
Found at i:280640 original size:114 final size:113
Alignment explanation
Indices: 280441--280786 Score: 340
Period size: 114 Copynumber: 3.0 Consensus size: 113
280431 TTAGCAAAGA
* *
280441 TTTGAATCCATCATTCGATGGATCAACATTTCCAGAGAAGTTCATAATGAGAAGAACTCATTTGA
1 TTTGAATCCATCACTCGATGGATCAACATTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGA
280506 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACTTTTTG
66 AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACTTTTTG
* *
280554 TTTGAATTCATCACTCGATGGATCAA-ATTTTCCAGAGAAAGTTCATAATGAGAAGAACTTATCT
1 TTTGAATCCATCACTCGATGGATCAACA-TTTCCAGAG-AAGTTCATAATGAGAAGAACTCATCT
* * ** * *
280618 GAAGAGGGAAGAAGAAGTTCATAATGAGAAGAGCTTGTT-TAACCTTTTG
64 GAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACTTTTTG
** * * * ** *
280667 CATGACTCTATCACAGAAGGAGATAGATCATCATCAACACTTCCAGA-AAGTTCATAATGAGAAG
1 TTTGAATCCATCAC---------TCGAT--GGATCAACATTTCCAGAGAAGTTCATAATGAGAAG
* * * * *
280731 AACTTATCTGAAGAA-GAAGAATAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT
55 AACTCATCTGAAGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACTTTT
280787 GCATGATTCT
Statistics
Matches: 193, Mismatches: 25, Indels: 21
0.81 0.10 0.09
Matches are distributed among these distances:
112 1 0.01
113 50 0.26
114 59 0.31
121 30 0.16
122 40 0.21
124 12 0.06
125 1 0.01
ACGTcount: A:0.39, C:0.14, G:0.19, T:0.29
Consensus pattern (113 bp):
TTTGAATCCATCACTCGATGGATCAACATTTCCAGAGAAGTTCATAATGAGAAGAACTCATCTGA
AGAAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAAACTTTTTG
Found at i:280778 original size:20 final size:20
Alignment explanation
Indices: 280716--280779 Score: 55
Period size: 20 Copynumber: 3.2 Consensus size: 20
280706 CTTCCAGAAA
280716 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
* *
280736 -ATC-TGAA-GAAGAAGAA-TAA
1 GTTCAT-AATG-AGAAGAACT-T
280755 GTTCATAATGAGAAGAACTT
1 GTTCATAATGAGAAGAACTT
280775 GTTCA
1 GTTCA
280780 ACCTTTTGCA
Statistics
Matches: 33, Mismatches: 4, Indels: 14
0.65 0.08 0.27
Matches are distributed among these distances:
18 3 0.09
19 11 0.33
20 16 0.48
21 3 0.09
ACGTcount: A:0.44, C:0.09, G:0.20, T:0.27
Consensus pattern (20 bp):
GTTCATAATGAGAAGAACTT
Found at i:280853 original size:122 final size:121
Alignment explanation
Indices: 280589--280906 Score: 494
Period size: 122 Copynumber: 2.6 Consensus size: 121
280579 AATTTTCCAG
* *
280589 AGAAAGTTCATAATGAGAAGAACTTATCTGAAGAGGGAAGAAGAAGTTCATAATGAGAAGAGCTT
1 AGAAAGTTCATAATGAGAAGAACTTATCTGAAGA-AGAAGAAGAAGTTCATAATGAGAAGAACTT
* * *
280654 GTTTAACCTTTTGCATGACTCTATCACAGAAGGAGATAGATCATCATCAACACTTCC
65 GTTCAACCTTTTGCATGACTCTATCACAGAAAGAGATAGATCAACATCAACACTTCC
*
280711 AGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAGAATAAGTTCATAATGAGAAGAACTTG
1 AGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTG
* * *
280776 TTCAACCTTTTGCATGATTCTATCACAGAAAGAGATATATCAACATCAACATTTCC
66 TTCAACCTTTTGCATGACTCTATCACAGAAAGAGATAGATCAACATCAACACTTCC
* * *
280832 AGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA-AAGAAGTTCATAATGAGAAAAACT
1 AGAA-AGTTCATAATGAGAAGAACTTATCTGAAGAA-GAAGAAGAAGTTCATAATGAGAAGAACT
280896 TGTTCAACCTT
64 TGTTCAACCTT
280907 GCCTTAATTC
Statistics
Matches: 181, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
121 82 0.45
122 96 0.53
123 3 0.02
ACGTcount: A:0.41, C:0.14, G:0.19, T:0.26
Consensus pattern (121 bp):
AGAAAGTTCATAATGAGAAGAACTTATCTGAAGAAGAAGAAGAAGTTCATAATGAGAAGAACTTG
TTCAACCTTTTGCATGACTCTATCACAGAAAGAGATAGATCAACATCAACACTTCC
Found at i:281334 original size:3 final size:3
Alignment explanation
Indices: 281276--281317 Score: 75
Period size: 3 Copynumber: 14.0 Consensus size: 3
281266 CATTTGTTAT
*
281276 TTA TTA TTA TTA TTA TTA TTA TTA TTA TCA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
281318 AAAATATATT
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 37 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.64
Consensus pattern (3 bp):
TTA
Found at i:281817 original size:25 final size:24
Alignment explanation
Indices: 281767--281818 Score: 61
Period size: 24 Copynumber: 2.1 Consensus size: 24
281757 AGCCCTCTGC
* *
281767 CAACAAAAAAAAAAGAACAGGAAG
1 CAACAAAAAAAAAAGAAAAAGAAG
281791 CAACAAAAAGAAAAA-AAAAAGATAG
1 CAACAAAAA-AAAAAGAAAAAGA-AG
281816 CAA
1 CAA
281819 ACATTTACAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.73, C:0.12, G:0.13, T:0.02
Consensus pattern (24 bp):
CAACAAAAAAAAAAGAAAAAGAAG
Found at i:282967 original size:42 final size:42
Alignment explanation
Indices: 282916--283191 Score: 393
Period size: 42 Copynumber: 6.7 Consensus size: 42
282906 CATATTCGAA
*
282916 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
282958 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
*
283000 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
** * *
283042 TTGCGATAGTTGAAGTTCGCATTGCAATTTATTCCAAATTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
* *
283084 TTGCGATAGTCGAAGTTCGCGTTGCGATTTATTCCAAGTTCG
1 TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
* *
283126 TTGCGATATTCCCAAATT--CGTTGCGA--TATTCCCAAATTCG
1 TTGCGATAGT-CCAAGTTCGCGTTGCGATTTATT-CCAAATTCG
283166 TTGCGATAGTCCAAGTT--CGTTGCGAT
1 TTGCGATAGTCCAAGTTCGCGTTGCGAT
283192 AGTCCAAAAT
Statistics
Matches: 212, Mismatches: 19, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
39 18 0.08
40 17 0.08
41 8 0.04
42 164 0.77
43 5 0.02
ACGTcount: A:0.21, C:0.20, G:0.22, T:0.36
Consensus pattern (42 bp):
TTGCGATAGTCCAAGTTCGCGTTGCGATTTATTCCAAATTCG
Found at i:283145 original size:20 final size:19
Alignment explanation
Indices: 282916--283199 Score: 183
Period size: 21 Copynumber: 13.8 Consensus size: 19
282906 CATATTCGAA
* *
282916 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATATTCCAAATT--CG
*
282937 TTGCGATTTATTCCAAGTTCG
1 TTGCGA--TATTCCAAATTCG
* * *
282958 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATATTCCAAATT--CG
282979 TTGCGATTTATTCCAAATTCG
1 TTGCGA--TATTCCAAATTCG
* *
283000 TTGCGATAGTCCAAGTTCGCG
1 TTGCGATATTCCAAATT--CG
*
283021 TTGCGATTTATTCCAAGTTCG
1 TTGCGA--TATTCCAAATTCG
* *
283042 TTGCGATAGTT-GAAGTTCG
1 TTGCGATA-TTCCAAATTCG
*
283061 CATTGCAATTTATTCCAAATTCG
1 --TTGCGA--TATTCCAAATTCG
* * *
283084 TTGCGATAGTCGAAGTTCGCG
1 TTGCGATATTCCAAATT--CG
*
283105 TTGCGATTTATTCCAAGTTCG
1 TTGCGA--TATTCCAAATTCG
283126 TTGCGATATTCCCAAATTCG
1 TTGCGATATT-CCAAATTCG
283146 TTGCGATATTCCCAAATTCG
1 TTGCGATATT-CCAAATTCG
* *
283166 TTGCGATAGTCCAAGTTCG
1 TTGCGATATTCCAAATTCG
*
283185 TTGCGATAGTCCAAA
1 TTGCGATATTCCAAA
283200 ATCGCAACGA
Statistics
Matches: 219, Mismatches: 23, Indels: 44
0.77 0.08 0.15
Matches are distributed among these distances:
19 61 0.28
20 39 0.18
21 72 0.33
22 2 0.01
23 45 0.21
ACGTcount: A:0.22, C:0.20, G:0.22, T:0.35
Consensus pattern (19 bp):
TTGCGATATTCCAAATTCG
Done.