Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007711.1 Hibiscus syriacus cultivar Beakdansim tig00109926_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: 1768490
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
File 2 of 8
Found at i:215650 original size:37 final size:37
Alignment explanation
Indices: 215583--215676 Score: 127
Period size: 37 Copynumber: 2.5 Consensus size: 37
215573 GGATCATATC
* * *
215583 TTTAGGAGTTT-AAATCATAGTAGAACTCTATCCTATT
1 TTTAGGAGTTTGAATTC-TAGCAAAACTCTATCCTATT
*
215620 TTTAGGAGTTTGAATTCTAGCAAAATTCTATCCTATT
1 TTTAGGAGTTTGAATTCTAGCAAAACTCTATCCTATT
*
215657 TTTAGGAGTTTGAATCCTAG
1 TTTAGGAGTTTGAATTCTAG
215677 TAGGACGAAA
Statistics
Matches: 51, Mismatches: 5, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
37 47 0.92
38 4 0.08
ACGTcount: A:0.30, C:0.13, G:0.16, T:0.41
Consensus pattern (37 bp):
TTTAGGAGTTTGAATTCTAGCAAAACTCTATCCTATT
Found at i:216046 original size:19 final size:20
Alignment explanation
Indices: 216009--216047 Score: 53
Period size: 20 Copynumber: 2.0 Consensus size: 20
215999 CATTGTATTT
*
216009 TTAATTTTTTAATTTACTCA
1 TTAATTTTTTAATTCACTCA
*
216029 TTAATTTTTTTA-TCACTCA
1 TTAATTTTTTAATTCACTCA
216048 CCCGTTAACT
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:0.28, C:0.13, G:0.00, T:0.59
Consensus pattern (20 bp):
TTAATTTTTTAATTCACTCA
Found at i:216188 original size:16 final size:17
Alignment explanation
Indices: 216162--216198 Score: 67
Period size: 16 Copynumber: 2.2 Consensus size: 17
216152 TATTTATTTT
216162 TTCTCATTCCATACTTC
1 TTCTCATTCCATACTTC
216179 TTCT-ATTCCATACTTC
1 TTCTCATTCCATACTTC
216195 TTCT
1 TTCT
216199 TCTTAAATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 16 0.80
17 4 0.20
ACGTcount: A:0.16, C:0.32, G:0.00, T:0.51
Consensus pattern (17 bp):
TTCTCATTCCATACTTC
Found at i:218718 original size:22 final size:24
Alignment explanation
Indices: 218693--218747 Score: 62
Period size: 22 Copynumber: 2.4 Consensus size: 24
218683 TTTTCACATA
*
218693 TTTTCAC-ATACTTTT-TGATACG
1 TTTTCACTATACTTTTGTGACACG
*
218715 TTTT-ACTCTACTTTTGTGACACG
1 TTTTCACTATACTTTTGTGACACG
*
218738 TTTTCTCTAT
1 TTTTCACTAT
218748 TTTTTGGCAT
Statistics
Matches: 26, Mismatches: 4, Indels: 4
0.76 0.12 0.12
Matches are distributed among these distances:
21 2 0.08
22 11 0.42
23 10 0.38
24 3 0.12
ACGTcount: A:0.18, C:0.20, G:0.09, T:0.53
Consensus pattern (24 bp):
TTTTCACTATACTTTTGTGACACG
Found at i:218751 original size:22 final size:22
Alignment explanation
Indices: 218701--218753 Score: 72
Period size: 22 Copynumber: 2.4 Consensus size: 22
218691 TATTTTCACA
*
218701 TACTTTTTGATACGTTTTACTC
1 TACTTTTTGACACGTTTTACTC
218723 TACTTTTGTGACACGTTTT-CTC
1 TACTTTT-TGACACGTTTTACTC
*
218745 TATTTTTTG
1 TACTTTTTG
218754 GCATATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 2 0.07
22 16 0.57
23 10 0.36
ACGTcount: A:0.15, C:0.17, G:0.11, T:0.57
Consensus pattern (22 bp):
TACTTTTTGACACGTTTTACTC
Found at i:221107 original size:42 final size:42
Alignment explanation
Indices: 221060--221146 Score: 156
Period size: 42 Copynumber: 2.1 Consensus size: 42
221050 GCTTGTTCCC
*
221060 AGATAATATAACTACCATCAAATTGAATGTCTCATAGCAAAA
1 AGATAATATAACTACCATCAAATTGAACGTCTCATAGCAAAA
*
221102 AGATAATATAACTACTATCAAATTGAACGTCTCATAGCAAAA
1 AGATAATATAACTACCATCAAATTGAACGTCTCATAGCAAAA
221144 AGA
1 AGA
221147 AGGTAACTTT
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.48, C:0.16, G:0.10, T:0.25
Consensus pattern (42 bp):
AGATAATATAACTACCATCAAATTGAACGTCTCATAGCAAAA
Found at i:227019 original size:2 final size:2
Alignment explanation
Indices: 227012--227036 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
227002 TAGTGTCATG
227012 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 T
227037 TGGAAATGGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:232457 original size:56 final size:54
Alignment explanation
Indices: 232378--232484 Score: 142
Period size: 56 Copynumber: 1.9 Consensus size: 54
232368 CAAAATATAC
* *
232378 CTAAAACATTCCCTGGGAATCACAAGAATCACACTGTAAACGAACCAAAAATCCAT
1 CTAAAACATTCCCTGAGAATCACAAGAAT--CACTGTAAACGAACAAAAAATCCAT
* * * *
232434 CTAAAATATTCCCTGAGATTCACAAGCATCACTGTAAAGGAACAAAAAATC
1 CTAAAACATTCCCTGAGAATCACAAGAATCACTGTAAACGAACAAAAAATC
232485 TACCTGGATT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
54 20 0.44
56 25 0.56
ACGTcount: A:0.45, C:0.24, G:0.11, T:0.20
Consensus pattern (54 bp):
CTAAAACATTCCCTGAGAATCACAAGAATCACTGTAAACGAACAAAAAATCCAT
Found at i:236600 original size:20 final size:21
Alignment explanation
Indices: 236575--236626 Score: 61
Period size: 21 Copynumber: 2.5 Consensus size: 21
236565 TTTTCCCAAT
*
236575 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
* **
236595 TCGCAACGCGAATTGGGAAAA
1 TCGCAATGCGAATTAAGAAAA
236616 TCGCAATGCGA
1 TCGCAATGCGA
236627 TACTGACTAT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
20 11 0.42
21 15 0.58
ACGTcount: A:0.38, C:0.19, G:0.25, T:0.17
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:236640 original size:20 final size:20
Alignment explanation
Indices: 236615--236708 Score: 82
Period size: 20 Copynumber: 4.7 Consensus size: 20
236605 AATTGGGAAA
*
236615 ATCGCAATGCGATACTGACT
1 ATCGCAACGCGATACTGACT
* * *
236635 ATCGCAATGCGATAAT-ACAAA
1 ATCGCAACGCGATACTGAC--T
* *
236656 ATCGTAACGAGATACTGACT
1 ATCGCAACGCGATACTGACT
* *
236676 TTCGCAACGCGATTCTGACT
1 ATCGCAACGCGATACTGACT
*
236696 TTCGCAACGCGAT
1 ATCGCAACGCGAT
236709 TTACATAGTG
Statistics
Matches: 60, Mismatches: 11, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
19 2 0.03
20 44 0.73
21 12 0.20
22 2 0.03
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.24
Consensus pattern (20 bp):
ATCGCAACGCGATACTGACT
Found at i:237311 original size:19 final size:19
Alignment explanation
Indices: 237264--237305 Score: 66
Period size: 19 Copynumber: 2.2 Consensus size: 19
237254 ACGAGAGAAT
*
237264 CGCAACGCGAAATAAAAAA
1 CGCAACGCGAAACAAAAAA
*
237283 CGCAACGCGAAACAAAAAT
1 CGCAACGCGAAACAAAAAA
237302 CGCA
1 CGCA
237306 TTGCGATTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.52, C:0.26, G:0.17, T:0.05
Consensus pattern (19 bp):
CGCAACGCGAAACAAAAAA
Found at i:237323 original size:19 final size:19
Alignment explanation
Indices: 237301--237390 Score: 153
Period size: 19 Copynumber: 4.7 Consensus size: 19
237291 GAAACAAAAA
*
237301 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
237320 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
*
237339 TCGCGTTGCGATTTTTATT
1 TCGCGTTGCGATTTTCATT
237358 TCGCGGTTGCGATTTTCATT
1 TCGC-GTTGCGATTTTCATT
237378 TCGCGTTGCGATT
1 TCGCGTTGCGATT
237391 GTCTGGTCGC
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
19 49 0.73
20 18 0.27
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:237378 original size:39 final size:38
Alignment explanation
Indices: 237301--237390 Score: 153
Period size: 39 Copynumber: 2.3 Consensus size: 38
237291 GAAACAAAAA
*
237301 TCGCATTGCGATTTTCATTTCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
*
237339 TCGCGTTGCGATTTTTATTTCGCGGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATTTCGC-GTTGCGATTTTCATT
237378 TCGCGTTGCGATT
1 TCGCGTTGCGATT
237391 GTCTGGTCGC
Statistics
Matches: 49, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
38 21 0.43
39 28 0.57
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (38 bp):
TCGCGTTGCGATTTTCATTTCGCGTTGCGATTTTCATT
Found at i:237401 original size:39 final size:39
Alignment explanation
Indices: 237320--237401 Score: 114
Period size: 39 Copynumber: 2.1 Consensus size: 39
237310 GATTTTCATT
* **
237320 TCGC-GTTGCGATTTTCATTTCGCGTTGCGATTTTTATT
1 TCGCGGTTGCGATTTTCATTTCGCGTTGCGATTTCTAGG
237358 TCGCGGTTGCGATTTTCATTTCGCGTTGCGATTGTCT-GG
1 TCGCGGTTGCGATTTTCATTTCGCGTTGCGATT-TCTAGG
237397 TCGCG
1 TCGCG
237402 ATGTCATTTC
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
38 4 0.10
39 33 0.85
40 2 0.05
ACGTcount: A:0.09, C:0.21, G:0.27, T:0.44
Consensus pattern (39 bp):
TCGCGGTTGCGATTTTCATTTCGCGTTGCGATTTCTAGG
Found at i:237435 original size:32 final size:32
Alignment explanation
Indices: 237363--237435 Score: 92
Period size: 32 Copynumber: 2.2 Consensus size: 32
237353 TTATTTCGCG
* * *
237363 GTTGCGATTTTCATTTCGCGTTGCGATTGTCTG
1 GTTGCGA-TGTCATTTCGCGTTGCGATTCTCTC
* *
237396 GTCGCGATGTCATTTCGCGTTGTGATTCTCTC
1 GTTGCGATGTCATTTCGCGTTGCGATTCTCTC
237428 GTTGCGAT
1 GTTGCGAT
237436 TCTCTCGTTG
Statistics
Matches: 34, Mismatches: 6, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
32 28 0.82
33 6 0.18
ACGTcount: A:0.10, C:0.21, G:0.27, T:0.42
Consensus pattern (32 bp):
GTTGCGATGTCATTTCGCGTTGCGATTCTCTC
Found at i:237436 original size:14 final size:14
Alignment explanation
Indices: 237413--237449 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
237403 TGTCATTTCG
*
237413 CGTTGTGATTCTCT
1 CGTTGCGATTCTCT
237427 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
237441 CGTTGCGAT
1 CGTTGCGAT
237450 AGTCATTTCC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.08, C:0.24, G:0.24, T:0.43
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:237449 original size:46 final size:48
Alignment explanation
Indices: 237381--237473 Score: 136
Period size: 46 Copynumber: 2.0 Consensus size: 48
237371 TTTCATTTCG
* * *
237381 CGTTGCGATTGTCTGGTCGCGAT-GTCATTT-CGCGTTGTGATTCTCT
1 CGTTGCGATTCTCTCGTCGCGATAGTCATTTCCGCGTTGCGATTCTCT
*
237427 CGTTGCGATTCTCTCGTTGCGATAGTCATTTCCGCGTTGCGATTCTC
1 CGTTGCGATTCTCTCGTCGCGATAGTCATTTCCGCGTTGCGATTCTC
237474 ATTATCTCGT
Statistics
Matches: 41, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
46 20 0.49
47 7 0.17
48 14 0.34
ACGTcount: A:0.10, C:0.25, G:0.26, T:0.40
Consensus pattern (48 bp):
CGTTGCGATTCTCTCGTCGCGATAGTCATTTCCGCGTTGCGATTCTCT
Found at i:237475 original size:20 final size:20
Alignment explanation
Indices: 237441--237498 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
237431 GCGATTCTCT
**
237441 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTCTCATTTCCG
*
237461 CGTTGCGATTCTCATTAT-CT
1 CGTTGCGATTCTCATT-TCCG
*
237481 CGTTGCGATTTTCATTTC
1 CGTTGCGATTCTCATTTC
237499 AACCAAAAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
19 1 0.03
20 30 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.43
Consensus pattern (20 bp):
CGTTGCGATTCTCATTTCCG
Found at i:239582 original size:42 final size:42
Alignment explanation
Indices: 239506--239585 Score: 106
Period size: 42 Copynumber: 1.9 Consensus size: 42
239496 GACTCGCCTG
* * *
239506 TCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCCTA
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
* * *
239548 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
239586 ACTGTTATCG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
42 32 1.00
ACGTcount: A:0.21, C:0.39, G:0.17, T:0.23
Consensus pattern (42 bp):
TCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCCTA
Found at i:241001 original size:14 final size:14
Alignment explanation
Indices: 240982--241017 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
240972 ATTGTTTAAT
240982 TGATTTGTAAAAGG
1 TGATTTGTAAAAGG
* *
240996 TGATTTATAAAAGT
1 TGATTTGTAAAAGG
241010 TGATTTGT
1 TGATTTGT
241018 TTAATTGATG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGG
Found at i:241198 original size:19 final size:19
Alignment explanation
Indices: 241176--241306 Score: 85
Period size: 19 Copynumber: 7.7 Consensus size: 19
241166 CGAAATTAAA
*
241176 TTCGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
241195 TTCGCATTGCGA--TTC--
1 TTCGCATTGCGATTTTCAT
* *
241210 -CCTCATTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
241228 TTCGCATTGCGA-----AA
1 TTCGCATTGCGATTTTCAT
* *
241242 TTAGCGTTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
241261 TTCGCATTGCGA--TTC-T
1 TTCGCATTGCGATTTTCAT
*
241277 CTCG--TTGCGATTTTCAT
1 TTCGCATTGCGATTTTCAT
*
241294 TTTGCATTGCGAT
1 TTCGCATTGCGAT
241307 AGTAATTTCC
Statistics
Matches: 83, Mismatches: 14, Indels: 30
0.65 0.11 0.24
Matches are distributed among these distances:
14 26 0.31
16 10 0.12
17 9 0.11
19 38 0.46
ACGTcount: A:0.15, C:0.22, G:0.19, T:0.44
Consensus pattern (19 bp):
TTCGCATTGCGATTTTCAT
Found at i:241224 original size:33 final size:32
Alignment explanation
Indices: 241180--241306 Score: 175
Period size: 33 Copynumber: 3.9 Consensus size: 32
241170 ATTAAATTCG
241180 CGTTGCGATTTTCATTTCGCATTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATT-CCT
* **
241213 CATTGCGATTTTCATTTCGCATTGCGAAATT-AG
1 CGTTGCGATTTTCATTTCGCATTGCG--ATTCCT
241246 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTC-CT
*
241279 CGTTGCGATTTTCATTTTGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
241307 AGTAATTTCC
Statistics
Matches: 83, Mismatches: 7, Indels: 8
0.85 0.07 0.08
Matches are distributed among these distances:
31 3 0.04
33 77 0.93
35 3 0.04
ACGTcount: A:0.16, C:0.22, G:0.19, T:0.43
Consensus pattern (32 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCCT
Found at i:241263 original size:66 final size:66
Alignment explanation
Indices: 241173--241305 Score: 230
Period size: 66 Copynumber: 2.0 Consensus size: 66
241163 ACGCGAAATT
*
241173 AAATTCGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCATTGCGATTTTCATTTCGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCATTGCGATTTTCATTTCGCATTGC
241238 G
66 G
* * *
241239 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTTGCATTGC
1 AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCATTGCGATTTTCATTTCGCATTGC
241304 G
66 G
241305 A
1 A
241306 TAGTAATTTC
Statistics
Matches: 63, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
66 63 1.00
ACGTcount: A:0.17, C:0.22, G:0.19, T:0.42
Consensus pattern (66 bp):
AAATTAGCGTTGCGATTTTCATTTCGCATTGCGATTCCCTCATTGCGATTTTCATTTCGCATTGC
G
Found at i:243616 original size:12 final size:12
Alignment explanation
Indices: 243599--243623 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
243589 TCTTCGGGGA
243599 CTTTTTCTTCTT
1 CTTTTTCTTCTT
243611 CTTTTTCTTCTT
1 CTTTTTCTTCTT
243623 C
1 C
243624 AGGATTATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.00, C:0.28, G:0.00, T:0.72
Consensus pattern (12 bp):
CTTTTTCTTCTT
Found at i:243832 original size:24 final size:24
Alignment explanation
Indices: 243798--243851 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
243788 CTGAAACATC
* *
243798 ATCAAAATCCGTGTATTGACCAAT
1 ATCAAAATCCGGGTATTGACCAAG
*
243822 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGGGTATTGACCAAG
243846 ATCAAA
1 ATCAAA
243852 TTTCGAATAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.39, C:0.20, G:0.17, T:0.24
Consensus pattern (24 bp):
ATCAAAATCCGGGTATTGACCAAG
Found at i:244933 original size:20 final size:20
Alignment explanation
Indices: 244908--244965 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
244898 ATTCATTTGA
244908 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
244928 CTATCGCAACGCGAAAATGG
1 CTATCGCAACGCGAAAATGG
* *
244948 CTATTGCAACGAGAAAAT
1 CTATCGCAACGCGAAAAT
244966 CGCAATGCGA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.38, C:0.22, G:0.22, T:0.17
Consensus pattern (20 bp):
CTATCGCAACGCGAAAATGG
Found at i:245029 original size:19 final size:19
Alignment explanation
Indices: 245007--245051 Score: 90
Period size: 19 Copynumber: 2.4 Consensus size: 19
244997 TTCTTGTTGT
245007 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
245026 GATTTTCATTTCGCATTGC
1 GATTTTCATTTCGCATTGC
245045 GATTTTC
1 GATTTTC
245052 TCGTTGCGAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.16, C:0.20, G:0.16, T:0.49
Consensus pattern (19 bp):
GATTTTCATTTCGCATTGC
Found at i:245187 original size:14 final size:14
Alignment explanation
Indices: 245168--245204 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
245158 CATCAATTAA
245168 ACAAATCAACATTT
1 ACAAATCAACATTT
* *
245182 ACAAATCATCTTTT
1 ACAAATCAACATTT
245196 ACAAATCAA
1 ACAAATCAA
245205 TTAAACAATC
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.49, C:0.22, G:0.00, T:0.30
Consensus pattern (14 bp):
ACAAATCAACATTT
Found at i:247143 original size:14 final size:14
Alignment explanation
Indices: 247124--247181 Score: 71
Period size: 14 Copynumber: 3.9 Consensus size: 14
247114 TTTCATTTCA
247124 CGTTGCGATTTTGT
1 CGTTGCGATTTTGT
*
247138 CGTTGCGATTTCATTT
1 CGTTGCGATTT--TGT
247154 CGCATTGCGATTTTGT
1 CG--TTGCGATTTTGT
247170 CGTTGCGATTTT
1 CGTTGCGATTTT
247182 CATTTCGCAT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
14 21 0.55
16 8 0.21
18 9 0.24
ACGTcount: A:0.10, C:0.17, G:0.24, T:0.48
Consensus pattern (14 bp):
CGTTGCGATTTTGT
Found at i:247188 original size:33 final size:33
Alignment explanation
Indices: 247107--247197 Score: 157
Period size: 32 Copynumber: 2.8 Consensus size: 33
247097 CAACGCAGAA
* *
247107 TTGCGATTTTCATTTCACGTTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
247140 TTGCGA-TTTCATTTCGCATTGCGATTTTGTCG
1 TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
247172 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
247198 AGCCATTTCT
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
32 30 0.55
33 25 0.45
ACGTcount: A:0.13, C:0.19, G:0.21, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCATTGCGATTTTGTCG
Found at i:247236 original size:20 final size:20
Alignment explanation
Indices: 247182--247225 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
247172 TTGCGATTTT
*
247182 CATTTC-GCATTGCGATAGC
1 CATTTCTGCGTTGCGATAGC
*
247201 CATTTCTGCGTTGCGATAGT
1 CATTTCTGCGTTGCGATAGC
247221 CATTT
1 CATTT
247226 TCGTGTTGCG
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 6 0.27
20 16 0.73
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (20 bp):
CATTTCTGCGTTGCGATAGC
Found at i:247744 original size:18 final size:18
Alignment explanation
Indices: 247718--247762 Score: 72
Period size: 18 Copynumber: 2.5 Consensus size: 18
247708 GTCGATCAGA
*
247718 TGATGGCTCTGGGTGAGG
1 TGATGGCTCTGGGCGAGG
*
247736 TGATAGCTCTGGGCGAGG
1 TGATGGCTCTGGGCGAGG
247754 TGATGGCTC
1 TGATGGCTC
247763 CCGAAGTGGA
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:0.13, C:0.16, G:0.44, T:0.27
Consensus pattern (18 bp):
TGATGGCTCTGGGCGAGG
Found at i:249130 original size:20 final size:20
Alignment explanation
Indices: 249082--249140 Score: 73
Period size: 20 Copynumber: 3.0 Consensus size: 20
249072 AATAGTTTCT
** *
249082 GAAAATGAAAATCGCAACAC
1 GAAAATGACTATCGCAACGC
249102 GAAAATGACTATCGCAACGC
1 GAAAATGACTATCGCAACGC
**
249122 GAATTTGACTATCGCAACG
1 GAAAATGACTATCGCAACG
249141 AGATAATCGC
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:0.42, C:0.22, G:0.19, T:0.17
Consensus pattern (20 bp):
GAAAATGACTATCGCAACGC
Found at i:249429 original size:22 final size:22
Alignment explanation
Indices: 249402--249445 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
249392 GATGGAGATA
249402 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
249424 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
249446 TGAGAGAGTG
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:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:249747 original size:20 final size:20
Alignment explanation
Indices: 249633--249746 Score: 113
Period size: 20 Copynumber: 5.7 Consensus size: 20
249623 GATTATGTAT
249633 TATCGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* *
249653 AATTGCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
249673 TATCGCGTTGCGAAAGTAAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
249693 TATCTCGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
* *
249714 TATCGCATTGCGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
*
249734 TATCGCATTGCGA
1 TATCGCGTTGCGA
249747 TTTTCCCAAT
Statistics
Matches: 78, Mismatches: 13, Indels: 6
0.80 0.13 0.06
Matches are distributed among these distances:
19 3 0.04
20 61 0.78
21 12 0.15
22 2 0.03
ACGTcount: A:0.25, C:0.18, G:0.26, T:0.32
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:249750 original size:41 final size:41
Alignment explanation
Indices: 249617--249748 Score: 142
Period size: 41 Copynumber: 3.2 Consensus size: 41
249607 TTGAAAATCA
* *
249617 CATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGAATTG
1 CATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATCG
* * * * *
249658 CGTTGCGA--AAGTCAGTATCGCGTTGCGAAAGTAAGTATCT
1 CATTGCGATTATGT-ATTATCGCGTTGCGAAAGTCAGTATCG
* * * *
249698 CGTTGCGATTTTGTATTATCGCATTGCGATAGTCAGTATCG
1 CATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATCG
249739 CATTGCGATT
1 CATTGCGATT
249749 TTCCCAATTC
Statistics
Matches: 73, Mismatches: 15, Indels: 6
0.78 0.16 0.06
Matches are distributed among these distances:
39 3 0.04
40 30 0.41
41 38 0.52
42 2 0.03
ACGTcount: A:0.24, C:0.17, G:0.25, T:0.34
Consensus pattern (41 bp):
CATTGCGATTATGTATTATCGCGTTGCGAAAGTCAGTATCG
Found at i:249765 original size:21 final size:21
Alignment explanation
Indices: 249736--249828 Score: 91
Period size: 20 Copynumber: 4.5 Consensus size: 21
249726 ATAGTCAGTA
*
249736 TCGCATTGCGATTTTCCCAAT
1 TCGCATTGCGATTTTACCAAT
* **
249757 TCGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACCAAT
*
249777 TCGCATTGCGATTTTTCCAAT
1 TCGCATTGCGATTTTACCAAT
* * **
249798 TTGCGTTGCGA-TTTACTTAT
1 TCGCATTGCGATTTTACCAAT
249818 TCGCATTGCGA
1 TCGCATTGCGA
249829 ATTGGGAAAA
Statistics
Matches: 56, Mismatches: 15, Indels: 3
0.76 0.20 0.04
Matches are distributed among these distances:
20 31 0.55
21 25 0.45
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.42
Consensus pattern (21 bp):
TCGCATTGCGATTTTACCAAT
Found at i:249766 original size:41 final size:40
Alignment explanation
Indices: 249675--249809 Score: 119
Period size: 41 Copynumber: 3.3 Consensus size: 40
249665 AAAGTCAGTA
* * * ** *
249675 TCGCGTTGCGAAAGTAAGTATCTCGTTGCGATTTTGTATT
1 TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
* *
249715 ATCGCATTGCGATAGTCAGTATCGCATTGCGATTTTCCCAAT
1 -TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTT-CCAAT
* **
249757 TCGCGTTGCGAT-TTACTTATTCGCATTGCGATTTTTCCAAT
1 TCGCGTTGCGATAGTAAGTA-TCGCATTGCGA-TTTTCCAAT
*
249798 TTGCGTTGCGAT
1 TCGCGTTGCGAT
249810 TTACTTATTC
Statistics
Matches: 77, Mismatches: 14, Indels: 6
0.79 0.14 0.06
Matches are distributed among these distances:
40 3 0.04
41 68 0.88
42 6 0.08
ACGTcount: A:0.19, C:0.20, G:0.21, T:0.39
Consensus pattern (40 bp):
TCGCGTTGCGATAGTAAGTATCGCATTGCGATTTTCCAAT
Found at i:249810 original size:41 final size:41
Alignment explanation
Indices: 249736--249828 Score: 168
Period size: 41 Copynumber: 2.3 Consensus size: 41
249726 ATAGTCAGTA
249736 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
* *
249777 TCGCATTGCGATTTTTCCAATTTGCGTTGCGATTTACTTAT
1 TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
249818 TCGCATTGCGA
1 TCGCATTGCGA
249829 ATTGGGAAAA
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 50 1.00
ACGTcount: A:0.17, C:0.23, G:0.18, T:0.42
Consensus pattern (41 bp):
TCGCATTGCGATTTTCCCAATTCGCGTTGCGATTTACTTAT
Found at i:251387 original size:3 final size:3
Alignment explanation
Indices: 251379--251406 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
251369 TGATTTGTTA
251379 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT T
251407 GAATTATGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:254197 original size:7 final size:7
Alignment explanation
Indices: 254185--254222 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
254175 GTCAAAGAAA
254185 GTCAACG
1 GTCAACG
254192 GTCAACG
1 GTCAACG
254199 GTCAACG
1 GTCAACG
254206 GTCAACG
1 GTCAACG
254213 GTCAACG
1 GTCAACG
254220 GTC
1 GTC
254223 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:254229 original size:5 final size:5
Alignment explanation
Indices: 254219--254276 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
254209 AACGGTCAAC
* *
254219 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTCAAC GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGTC--G GGTCG
254268 GGTCG GGTC
1 GGTCG GGTC
254277 AGACCGGTCA
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.07, C:0.22, G:0.52, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:254240 original size:22 final size:22
Alignment explanation
Indices: 254212--254276 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
254202 AACGGTCAAC
254212 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
254234 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
254256 GGTCAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
254277 AGACCGGTCA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.09, C:0.23, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:254296 original size:19 final size:18
Alignment explanation
Indices: 254273--254351 Score: 88
Period size: 19 Copynumber: 4.2 Consensus size: 18
254263 GGTCGGGTCG
254273 GGTCAGACCGGTCAAACC
1 GGTCAGACCGGTCAAACC
254291 GAGTCAGACCGGTCAAACC
1 G-GTCAGACCGGTCAAACC
*
254310 GGTTC-GAACCGGTTGAAACC
1 GG-TCAG-ACCGG-TCAAACC
*
254330 GGTCAAACCGGTCAGAACC
1 GGTCAGACCGGTCA-AACC
254349 GGT
1 GGT
254352 TGAAAACCGG
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
18 5 0.10
19 39 0.75
20 8 0.15
ACGTcount: A:0.28, C:0.29, G:0.29, T:0.14
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACC
Found at i:254330 original size:29 final size:31
Alignment explanation
Indices: 254298--254372 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
254288 ACCGAGTCAG
254298 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
254327 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
254357 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
254373 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:254372 original size:9 final size:9
Alignment explanation
Indices: 254273--254371 Score: 90
Period size: 9 Copynumber: 10.3 Consensus size: 9
254263 GGTCGGGTCG
*
254273 GGTCAGACC
1 GGTCAAACC
254282 GGTCAAACC
1 GGTCAAACC
*
254291 GAGTCAGACC
1 G-GTCAAACC
254301 GGTCAAACC
1 GGTCAAACC
*
254310 GGTTCGAACC
1 GG-TCAAACC
*
254320 GGTTGAAACC
1 GG-TCAAACC
254330 GGTCAAACC
1 GGTCAAACC
254339 GGTCAGAACC
1 GGTCA-AACC
*
254349 GGTTGAAAACC
1 GG-T-CAAACC
*
254360 GGTTAAACC
1 GGTCAAACC
254369 GGT
1 GGT
254372 TTCCAGCAGC
Statistics
Matches: 76, Mismatches: 9, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
9 37 0.49
10 31 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.28, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:261544 original size:7 final size:7
Alignment explanation
Indices: 261532--261569 Score: 76
Period size: 7 Copynumber: 5.4 Consensus size: 7
261522 GTCAAAGAAA
261532 GTCAACG
1 GTCAACG
261539 GTCAACG
1 GTCAACG
261546 GTCAACG
1 GTCAACG
261553 GTCAACG
1 GTCAACG
261560 GTCAACG
1 GTCAACG
261567 GTC
1 GTC
261570 GGGTCGGGTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 31 1.00
ACGTcount: A:0.26, C:0.29, G:0.29, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:261576 original size:5 final size:5
Alignment explanation
Indices: 261566--261623 Score: 55
Period size: 5 Copynumber: 10.8 Consensus size: 5
261556 AACGGTCAAC
*
261566 GGTCG GGTCG GGTCG GGTCAAC GGTCG GGTCG GGTCG GGTAAAC- GGTCG
1 GGTCG GGTCG GGTCG GGTC--G GGTCG GGTCG GGTCG GGT---CG GGTCG
261615 GGTCG GGTC
1 GGTCG GGTC
261624 AGACCGGTCA
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
4 1 0.02
5 36 0.80
7 7 0.16
8 1 0.02
ACGTcount: A:0.09, C:0.21, G:0.52, T:0.19
Consensus pattern (5 bp):
GGTCG
Found at i:261587 original size:22 final size:22
Alignment explanation
Indices: 261559--261623 Score: 121
Period size: 22 Copynumber: 3.0 Consensus size: 22
261549 AACGGTCAAC
261559 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
261581 GGTCAACGGTCGGGTCGGGTCG
1 GGTCAACGGTCGGGTCGGGTCG
*
261603 GGTAAACGGTCGGGTCGGGTC
1 GGTCAACGGTCGGGTCGGGTC
261624 AGACCGGTCA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
22 42 1.00
ACGTcount: A:0.11, C:0.22, G:0.49, T:0.18
Consensus pattern (22 bp):
GGTCAACGGTCGGGTCGGGTCG
Found at i:261643 original size:19 final size:18
Alignment explanation
Indices: 261620--261698 Score: 88
Period size: 19 Copynumber: 4.2 Consensus size: 18
261610 GGTCGGGTCG
261620 GGTCAGACCGGTCAAACC
1 GGTCAGACCGGTCAAACC
261638 GAGTCAGACCGGTCAAACC
1 G-GTCAGACCGGTCAAACC
*
261657 GGTTC-GAACCGGTTGAAACC
1 GG-TCAG-ACCGG-TCAAACC
*
261677 GGTCAAACCGGTCAGAACC
1 GGTCAGACCGGTCA-AACC
261696 GGT
1 GGT
261699 TGAAAACCGG
Statistics
Matches: 52, Mismatches: 3, Indels: 11
0.79 0.05 0.17
Matches are distributed among these distances:
18 5 0.10
19 39 0.75
20 8 0.15
ACGTcount: A:0.28, C:0.29, G:0.29, T:0.14
Consensus pattern (18 bp):
GGTCAGACCGGTCAAACC
Found at i:261677 original size:29 final size:31
Alignment explanation
Indices: 261645--261719 Score: 120
Period size: 29 Copynumber: 2.5 Consensus size: 31
261635 ACCGAGTCAG
261645 ACCGGTCAAACCGGTTC-GAACCGGTTG-AA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
261674 ACCGGTCAAACCGG-TCAGAACCGGTTGAAA
1 ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
*
261704 ACCGGTTAAACCGGTT
1 ACCGGTCAAACCGGTT
261720 TCCAGCAGCC
Statistics
Matches: 42, Mismatches: 1, Indels: 4
0.89 0.02 0.09
Matches are distributed among these distances:
28 2 0.05
29 24 0.57
30 15 0.36
31 1 0.02
ACGTcount: A:0.29, C:0.27, G:0.27, T:0.17
Consensus pattern (31 bp):
ACCGGTCAAACCGGTTCAGAACCGGTTGAAA
Found at i:261719 original size:9 final size:9
Alignment explanation
Indices: 261620--261718 Score: 90
Period size: 9 Copynumber: 10.3 Consensus size: 9
261610 GGTCGGGTCG
*
261620 GGTCAGACC
1 GGTCAAACC
261629 GGTCAAACC
1 GGTCAAACC
*
261638 GAGTCAGACC
1 G-GTCAAACC
261648 GGTCAAACC
1 GGTCAAACC
*
261657 GGTTCGAACC
1 GG-TCAAACC
*
261667 GGTTGAAACC
1 GG-TCAAACC
261677 GGTCAAACC
1 GGTCAAACC
261686 GGTCAGAACC
1 GGTCA-AACC
*
261696 GGTTGAAAACC
1 GG-T-CAAACC
*
261707 GGTTAAACC
1 GGTCAAACC
261716 GGT
1 GGT
261719 TTCCAGCAGC
Statistics
Matches: 76, Mismatches: 9, Indels: 10
0.80 0.09 0.11
Matches are distributed among these distances:
9 37 0.49
10 31 0.41
11 7 0.09
12 1 0.01
ACGTcount: A:0.29, C:0.27, G:0.28, T:0.15
Consensus pattern (9 bp):
GGTCAAACC
Found at i:264717 original size:21 final size:22
Alignment explanation
Indices: 264693--264741 Score: 64
Period size: 22 Copynumber: 2.3 Consensus size: 22
264683 ATAGAAAATA
*
264693 TTAAAAAAAT-TTGATACCAAT
1 TTAAAAAAATATCGATACCAAT
* *
264714 TTAAAAGAATATCGATACCACT
1 TTAAAAAAATATCGATACCAAT
264736 TTAAAA
1 TTAAAA
264742 GGAGAATTAC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 9 0.38
22 15 0.62
ACGTcount: A:0.51, C:0.12, G:0.06, T:0.31
Consensus pattern (22 bp):
TTAAAAAAATATCGATACCAAT
Found at i:268672 original size:18 final size:18
Alignment explanation
Indices: 268638--268698 Score: 61
Period size: 18 Copynumber: 3.4 Consensus size: 18
268628 TATTTTTAAC
*
268638 TTATTTTGATATTTAAATT
1 TTATTTT-ATTTTTAAATT
268657 TTATTTTATTTTTAAATT
1 TTATTTTATTTTTAAATT
* ** *
268675 ATACCTTA-TTTTAATTT
1 TTATTTTATTTTTAAATT
268692 TTATTTT
1 TTATTTT
268699 TCATAAAATA
Statistics
Matches: 34, Mismatches: 8, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
17 12 0.35
18 15 0.44
19 7 0.21
ACGTcount: A:0.28, C:0.03, G:0.02, T:0.67
Consensus pattern (18 bp):
TTATTTTATTTTTAAATT
Found at i:268950 original size:37 final size:34
Alignment explanation
Indices: 268883--268952 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 34
268873 CCAGTCCAAC
*
268883 ACCCTTCTTTCCCCTTAAACCTCACCCATGTTAA
1 ACCCTTCTTTCCCCTAAAACCTCACCCATGTTAA
*
268917 ACCCTTCTTTCCCCTCAAACAACCTCAGCCATGTTA
1 ACCCTTCTTTCCCCT--AA-AACCTCACCCATGTTA
268953 CTGCTTCTCC
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
34 15 0.48
36 1 0.03
37 15 0.48
ACGTcount: A:0.24, C:0.41, G:0.04, T:0.30
Consensus pattern (34 bp):
ACCCTTCTTTCCCCTAAAACCTCACCCATGTTAA
Found at i:288792 original size:21 final size:23
Alignment explanation
Indices: 288762--288812 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
288752 TTGAGTATAT
288762 TATT-ATATTAT-TAATTAAAAA
1 TATTAATATTATGTAATTAAAAA
* *
288783 TA-TAATATTATGTTATTAAAAT
1 TATTAATATTATGTAATTAAAAA
288805 TATTAATA
1 TATTAATA
288813 AATAATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
20 1 0.04
21 9 0.36
22 10 0.40
23 5 0.20
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (23 bp):
TATTAATATTATGTAATTAAAAA
Found at i:289890 original size:21 final size:20
Alignment explanation
Indices: 289789--289880 Score: 123
Period size: 20 Copynumber: 4.5 Consensus size: 20
289779 TCGACTATCA
289789 CATTGCGATTTACATATTCG
1 CATTGCGATTTACATATTCG
289809 CATTGCGATTTACATATTCG
1 CATTGCGATTTACATATTCG
**
289829 CATTGCGATTTACATATTTT
1 CATTGCGATTTACATATTCG
* *
289849 CATTGCGATAGTCCA-AGTTCG
1 CATTGCGAT-TTACATA-TTCG
289870 CATTGCGATTT
1 CATTGCGATTT
289881 TCCAAATTCG
Statistics
Matches: 63, Mismatches: 7, Indels: 4
0.85 0.09 0.05
Matches are distributed among these distances:
20 49 0.78
21 14 0.22
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (20 bp):
CATTGCGATTTACATATTCG
Found at i:289945 original size:21 final size:21
Alignment explanation
Indices: 289921--289990 Score: 72
Period size: 21 Copynumber: 3.3 Consensus size: 21
289911 GACTATCGCA
289921 TTGCGATTTATTCCAAATTCG
1 TTGCGATTTATTCCAAATTCG
* * *
289942 TTGCGA--TAGTCGAAGTTCGCG
1 TTGCGATTTATTCCAAATT--CG
*
289963 TTGCGATTTATTTCAAATTCG
1 TTGCGATTTATTCCAAATTCG
289984 TTGCGAT
1 TTGCGAT
289991 AGTCCAAAAT
Statistics
Matches: 38, Mismatches: 7, Indels: 8
0.72 0.13 0.15
Matches are distributed among these distances:
19 8 0.21
21 23 0.61
23 7 0.18
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.40
Consensus pattern (21 bp):
TTGCGATTTATTCCAAATTCG
Found at i:290108 original size:6 final size:6
Alignment explanation
Indices: 290099--290131 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
290089 CATTACCATT
*
290099 ACCACG ACCACG ACCACG AGCACG ACCACG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACC
290132 CGAGACGAGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.33, C:0.48, G:0.18, T:0.00
Consensus pattern (6 bp):
ACCACG
Found at i:290627 original size:9 final size:9
Alignment explanation
Indices: 290613--290640 Score: 56
Period size: 9 Copynumber: 3.1 Consensus size: 9
290603 GACTCTCGCG
290613 CGCCGCCGT
1 CGCCGCCGT
290622 CGCCGCCGT
1 CGCCGCCGT
290631 CGCCGCCGT
1 CGCCGCCGT
290640 C
1 C
290641 CTGTCTCGTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 19 1.00
ACGTcount: A:0.00, C:0.57, G:0.32, T:0.11
Consensus pattern (9 bp):
CGCCGCCGT
Found at i:290782 original size:21 final size:21
Alignment explanation
Indices: 290757--290828 Score: 126
Period size: 21 Copynumber: 3.4 Consensus size: 21
290747 ATTTTGGACT
*
290757 ATCGCAACGAATTTGAAATAA
1 ATCGCAACGAATTTGGAATAA
*
290778 ATCGCAATGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
290799 ATCGCAACGAATTTGGAATAA
1 ATCGCAACGAATTTGGAATAA
290820 ATCGCAACG
1 ATCGCAACG
290829 CGAACTTGGA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 48 1.00
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.24
Consensus pattern (21 bp):
ATCGCAACGAATTTGGAATAA
Found at i:290845 original size:42 final size:40
Alignment explanation
Indices: 290750--290847 Score: 124
Period size: 42 Copynumber: 2.4 Consensus size: 40
290740 CGTTGCAATT
* *
290750 TTGGACTATCGCAACGAATTTGAAATAAATCGCAATGAAT
1 TTGGACTATCGCAACGAATTTGAAATAAATCGCAACGAAC
* *
290790 TTGGAATAAATCGCAACGAATTTGGAATAAATCGCAACGCGAAC
1 TTGGACT--ATCGCAACGAATTTGAAATAAATCGCAA--CGAAC
290834 TTGGACTATCGCAA
1 TTGGACTATCGCAA
290848 TACGAATATG
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
40 6 0.12
42 34 0.69
44 9 0.18
ACGTcount: A:0.39, C:0.17, G:0.19, T:0.24
Consensus pattern (40 bp):
TTGGACTATCGCAACGAATTTGAAATAAATCGCAACGAAC
Found at i:294366 original size:30 final size:30
Alignment explanation
Indices: 294323--294380 Score: 91
Period size: 30 Copynumber: 1.9 Consensus size: 30
294313 GTTAGAAATA
*
294323 AACTTAAATTTATAAAATTTTAAGGGGAAG
1 AACTTAAATTTATAAAATTATAAGGGGAAG
294353 AACTTGAAA-TTATAAAATTATAAGGGGA
1 AACTT-AAATTTATAAAATTATAAGGGGA
294381 CGAAAACAAT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 23 0.88
31 3 0.12
ACGTcount: A:0.48, C:0.03, G:0.17, T:0.31
Consensus pattern (30 bp):
AACTTAAATTTATAAAATTATAAGGGGAAG
Found at i:294440 original size:24 final size:23
Alignment explanation
Indices: 294388--294434 Score: 64
Period size: 20 Copynumber: 2.1 Consensus size: 23
294378 GGACGAAAAC
294388 AATTTTTTTTAATAGAAAATATAT
1 AATTTTTTTT-ATAGAAAATATAT
294412 AATTTTTTTT-T--AAAATATAT
1 AATTTTTTTTATAGAAAATATAT
294432 AAT
1 AAT
294435 AAATTTAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
20 12 0.52
22 1 0.04
24 10 0.43
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (23 bp):
AATTTTTTTTATAGAAAATATAT
Found at i:305228 original size:13 final size:13
Alignment explanation
Indices: 305206--305249 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
305196 TAATTGGCAT
305206 GTTAAGATTTTAA
1 GTTAAGATTTTAA
*
305219 GTTAAAATTTATTAAA
1 GTTAAGA-TT-TT-AA
305235 GTTAAGATTTTAA
1 GTTAAGATTTTAA
305248 GT
1 GT
305250 ATGTGAATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 10 0.38
14 4 0.15
15 4 0.15
16 8 0.31
ACGTcount: A:0.41, C:0.00, G:0.14, T:0.45
Consensus pattern (13 bp):
GTTAAGATTTTAA
Found at i:305868 original size:7 final size:7
Alignment explanation
Indices: 305856--305897 Score: 75
Period size: 7 Copynumber: 5.9 Consensus size: 7
305846 AAGAAGAGAA
305856 GGGAAAG
1 GGGAAAG
305863 GGGAAAG
1 GGGAAAG
305870 GGGAAAG
1 GGGAAAG
305877 GGGAAAG
1 GGGAAAG
305884 GGGAAAG
1 GGGAAAG
305891 GGCGAAA
1 GG-GAAA
305898 ATGCCGAAGA
Statistics
Matches: 34, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
7 30 0.88
8 4 0.12
ACGTcount: A:0.43, C:0.02, G:0.55, T:0.00
Consensus pattern (7 bp):
GGGAAAG
Found at i:309678 original size:33 final size:32
Alignment explanation
Indices: 309635--309734 Score: 128
Period size: 34 Copynumber: 3.0 Consensus size: 32
309625 CTAAGTACAT
* *
309635 CTTTAGCGTGATCGAAATGAGTGTCGTTTAAAGC
1 CTTTA-CGTGA-CGAAATGAGCGTCATTTAAAGC
309669 CTTTACGTGACTGAAATGAGCGTCATTTAAAGC
1 CTTTACGTGAC-GAAATGAGCGTCATTTAAAGC
*
309702 CTTATATGTGACCGAAATGAGCGTCATTTAAAG
1 CTT-TACGTGA-CGAAATGAGCGTCATTTAAAG
309735 ATCGAAATGA
Statistics
Matches: 60, Mismatches: 3, Indels: 6
0.87 0.04 0.09
Matches are distributed among these distances:
32 1 0.02
33 27 0.45
34 31 0.52
35 1 0.02
ACGTcount: A:0.30, C:0.16, G:0.23, T:0.31
Consensus pattern (32 bp):
CTTTACGTGACGAAATGAGCGTCATTTAAAGC
Found at i:317389 original size:11 final size:12
Alignment explanation
Indices: 317359--317400 Score: 59
Period size: 12 Copynumber: 3.6 Consensus size: 12
317349 GTTATTTAAA
317359 CGGGTATTGGGC
1 CGGGTATTGGGC
*
317371 CGGGTATTGGGT
1 CGGGTATTGGGC
*
317383 C-GGTATTAGGC
1 CGGGTATTGGGC
317394 CGGGTAT
1 CGGGTAT
317401 ATATATATAT
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
11 9 0.35
12 17 0.65
ACGTcount: A:0.12, C:0.14, G:0.45, T:0.29
Consensus pattern (12 bp):
CGGGTATTGGGC
Found at i:317460 original size:24 final size:25
Alignment explanation
Indices: 317398--317460 Score: 71
Period size: 24 Copynumber: 2.6 Consensus size: 25
317388 TTAGGCCGGG
317398 TATATA-TATATATATTTAAATTAAA
1 TATATATTATAT-TATTTAAATTAAA
*
317423 TATATATT-TTTTATTTAAATTAAA
1 TATATATTATATTATTTAAATTAAA
317447 T-T-TATTAATATTAT
1 TATATATT-ATATTAT
317461 ATATATATAT
Statistics
Matches: 33, Mismatches: 2, Indels: 7
0.79 0.05 0.17
Matches are distributed among these distances:
22 4 0.12
23 1 0.03
24 19 0.58
25 8 0.24
26 1 0.03
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (25 bp):
TATATATTATATTATTTAAATTAAA
Found at i:320566 original size:25 final size:24
Alignment explanation
Indices: 320530--320576 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 24
320520 GAAAACAAGA
*
320530 TCTTTTAGGTTTTTG-ATTTAAAT
1 TCTTTTAGGTTTTAGTATTTAAAT
320553 TCTTCTTAGGGTTTTAGTATTTAA
1 TCTT-TTA-GGTTTTAGTATTTAA
320577 TGTCCTTTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 3 0.15
25 7 0.35
26 6 0.30
ACGTcount: A:0.21, C:0.06, G:0.15, T:0.57
Consensus pattern (24 bp):
TCTTTTAGGTTTTAGTATTTAAAT
Found at i:324649 original size:23 final size:23
Alignment explanation
Indices: 324614--324659 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
324604 TTTAAAAATT
*
324614 TTATATAAATTTTAAAAATAAAA
1 TTATATAAATTTTAAAAAGAAAA
**
324637 TTATATATTTTTTAAAAAGAAAA
1 TTATATAAATTTTAAAAAGAAAA
324660 CACATAAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (23 bp):
TTATATAAATTTTAAAAAGAAAA
Found at i:326171 original size:60 final size:59
Alignment explanation
Indices: 326067--326209 Score: 144
Period size: 60 Copynumber: 2.4 Consensus size: 59
326057 AACACAATGA
** * * * * * * *
326067 ATAGTCAAATGATCATTGTGTAACTTTTAATAGTCGAGTGACTCAACAAAGCAATGTCCT
1 ATAGTCAAGGGATCATTTTATAAATTTTAATAGTCAAGTGACTCAACAAA-AAATATACT
* *
326127 ATAGTCATGGGATCATTTTATAAATTTTAATAGTCAA-TGTACTCAATAAAAAATATACT
1 ATAGTCAAGGGATCATTTTATAAATTTTAATAGTCAAGTG-ACTCAACAAAAAATATACT
*
326186 ATAGTCAAGGAATCATTTGTATAA
1 ATAGTCAAGGGATCATTT-TATAA
326210 TTTACCCTAA
Statistics
Matches: 68, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
59 24 0.35
60 44 0.65
ACGTcount: A:0.39, C:0.13, G:0.14, T:0.34
Consensus pattern (59 bp):
ATAGTCAAGGGATCATTTTATAAATTTTAATAGTCAAGTGACTCAACAAAAAATATACT
Found at i:332110 original size:20 final size:21
Alignment explanation
Indices: 332085--332257 Score: 107
Period size: 19 Copynumber: 8.8 Consensus size: 21
332075 AATTTGTAAA
332085 TCGCAACACAGAA-GTCAAAT
1 TCGCAACACAGAATGTCAAAT
*
332105 TCGCAACACA-AAAGTCAAAT
1 TCGCAACACAGAATGTCAAAT
* * * *
332125 TCACAACGCGGAATTTCAAAT
1 TCGCAACACAGAATGTCAAAT
* * *
332146 TCACAACACGGAATTTCAAAT
1 TCGCAACACAGAATGTCAAAT
* *
332167 TCGC-A-ACTGAATTTCAAAT
1 TCGCAACACAGAATGTCAAAT
* *
332186 TCGC-A-ACTGAATTTCAAAT
1 TCGCAACACAGAATGTCAAAT
* * *
332205 CCGC-A-ACTGAATTTCAAAT
1 TCGCAACACAGAATGTCAAAT
* **
332224 TCGCAACACA-AAT-TTAGTT
1 TCGCAACACAGAATGTCAAAT
332243 TCGCAACACA-AATGT
1 TCGCAACACAGAATGT
332258 TTTGGGTATA
Statistics
Matches: 134, Mismatches: 14, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
19 71 0.53
20 30 0.22
21 33 0.25
ACGTcount: A:0.40, C:0.24, G:0.12, T:0.24
Consensus pattern (21 bp):
TCGCAACACAGAATGTCAAAT
Found at i:332180 original size:19 final size:19
Alignment explanation
Indices: 332135--332230 Score: 147
Period size: 19 Copynumber: 4.9 Consensus size: 19
332125 TCACAACGCG
* *
332135 GAATTTCAAATTCACAACACG
1 GAATTTCAAATTCGC-A-ACT
332156 GAATTTCAAATTCGCAACT
1 GAATTTCAAATTCGCAACT
332175 GAATTTCAAATTCGCAACT
1 GAATTTCAAATTCGCAACT
*
332194 GAATTTCAAATCCGCAACT
1 GAATTTCAAATTCGCAACT
332213 GAATTTCAAATTCGCAAC
1 GAATTTCAAATTCGCAAC
332231 ACAAATTTAG
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
19 56 0.79
20 1 0.01
21 14 0.20
ACGTcount: A:0.39, C:0.23, G:0.10, T:0.28
Consensus pattern (19 bp):
GAATTTCAAATTCGCAACT
Found at i:332249 original size:38 final size:39
Alignment explanation
Indices: 332099--332238 Score: 165
Period size: 38 Copynumber: 3.5 Consensus size: 39
332089 AACACAGAAG
* ** * *
332099 TCAAATTCGCAACACAAAAGTCAAATTCACAACGCGGAATT
1 TCAAATTCGCAACACGAATTTCAAATTCGCAA--CTGAATT
*
332140 TCAAATTCACAACACGGAATTTCAAATTCGCAACTGAATT
1 TCAAATTCGCAACAC-GAATTTCAAATTCGCAACTGAATT
* *
332180 TCAAATTCGCAAC-TGAATTTCAAATCCGCAACTGAATT
1 TCAAATTCGCAACACGAATTTCAAATTCGCAACTGAATT
*
332218 TCAAATTCGCAACACAAATTT
1 TCAAATTCGCAACACGAATTT
332239 AGTTTCGCAA
Statistics
Matches: 86, Mismatches: 11, Indels: 6
0.83 0.11 0.06
Matches are distributed among these distances:
38 36 0.42
39 5 0.06
40 18 0.21
41 14 0.16
42 13 0.15
ACGTcount: A:0.41, C:0.24, G:0.10, T:0.26
Consensus pattern (39 bp):
TCAAATTCGCAACACGAATTTCAAATTCGCAACTGAATT
Found at i:332409 original size:16 final size:16
Alignment explanation
Indices: 332388--332427 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
332378 TCTCCATCTC
*
332388 TAATTTTTTTTTTACA
1 TAATTTTTTTTCTACA
* *
332404 TAATTTTATTTCTATA
1 TAATTTTTTTTCTACA
332420 TAATTTTT
1 TAATTTTT
332428 CAATTATTTC
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.28, C:0.05, G:0.00, T:0.68
Consensus pattern (16 bp):
TAATTTTTTTTCTACA
Found at i:333171 original size:24 final size:24
Alignment explanation
Indices: 333139--333216 Score: 129
Period size: 24 Copynumber: 3.2 Consensus size: 24
333129 GTATTCGAAA
*
333139 TTTGATCTTGGTCAATACTCAGAC
1 TTTGATCTTGGTCAATACTCGGAC
*
333163 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACTCGGAC
*
333187 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACTCGGAC
333211 TTTGAT
1 TTTGAT
333217 GATGTGATGG
Statistics
Matches: 50, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 50 1.00
ACGTcount: A:0.22, C:0.19, G:0.19, T:0.40
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACTCGGAC
Found at i:335773 original size:14 final size:14
Alignment explanation
Indices: 335754--335790 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
335744 ATCAAATTAA
335754 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
335768 ATAAATCAACTTTT
1 ACAAATCAACTTTT
335782 ACAAATCAA
1 ACAAATCAA
335791 TTAATCAAAA
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:0.49, C:0.19, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:337270 original size:42 final size:42
Alignment explanation
Indices: 337214--337316 Score: 116
Period size: 42 Copynumber: 2.5 Consensus size: 42
337204 GCGGGCGGGA
* * * * *
337214 CCTCTTGAACGATGATAGGGCCCTCTTGAACGGTAGGAGGGG
1 CCTCTTAAATGATGATAGGGCACTCTTGAACGATAGGAGGCG
* ** * *
337256 CTTCTTCGATGATGAGAGGGGACTCTTGAACGATAGGAGGCG
1 CCTCTTAAATGATGATAGGGCACTCTTGAACGATAGGAGGCG
337298 CCTCTTAAATGATGATAGG
1 CCTCTTAAATGATGATAGG
337317 TGCATCGAGC
Statistics
Matches: 48, Mismatches: 13, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
42 48 1.00
ACGTcount: A:0.24, C:0.18, G:0.33, T:0.24
Consensus pattern (42 bp):
CCTCTTAAATGATGATAGGGCACTCTTGAACGATAGGAGGCG
Found at i:337302 original size:21 final size:21
Alignment explanation
Indices: 337214--337312 Score: 69
Period size: 21 Copynumber: 4.7 Consensus size: 21
337204 GCGGGCGGGA
* *
337214 CCTCTTGAACGATGATAGGGC
1 CCTCTTGAACGATGAGAGGGG
*
337235 CCTCTTGAACGGT-AGGAGGGG
1 CCTCTTGAACGATGA-GAGGGG
* *
337256 CTTCTTCG-ATGATGAGAGGGG
1 CCTCTT-GAACGATGAGAGGGG
* *
337277 ACTCTTGAACGAT-AGGAGGCG
1 CCTCTTGAACGATGA-GAGGGG
* *
337298 CCTCTTAAATGATGA
1 CCTCTTGAACGATGA
337313 TAGGTGCATC
Statistics
Matches: 59, Mismatches: 13, Indels: 11
0.71 0.16 0.13
Matches are distributed among these distances:
20 3 0.05
21 53 0.90
22 3 0.05
ACGTcount: A:0.24, C:0.19, G:0.32, T:0.24
Consensus pattern (21 bp):
CCTCTTGAACGATGAGAGGGG
Found at i:339408 original size:19 final size:19
Alignment explanation
Indices: 339357--339410 Score: 72
Period size: 20 Copynumber: 2.7 Consensus size: 19
339347 AGAAGTTTCT
*
339357 GAAACTTAAATTCGCAACGC
1 GAAAC-TAAAATCGCAACGC
*
339377 GAAAATGAAAATCGCAACGC
1 GAAACT-AAAATCGCAACGC
339397 GAAACTAAAATCGC
1 GAAACTAAAATCGC
339411 GTTGCGATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
19 9 0.30
20 21 0.70
ACGTcount: A:0.46, C:0.22, G:0.17, T:0.15
Consensus pattern (19 bp):
GAAACTAAAATCGCAACGC
Found at i:342578 original size:48 final size:48
Alignment explanation
Indices: 342522--342615 Score: 118
Period size: 48 Copynumber: 2.0 Consensus size: 48
342512 AAGACTCGAC
* * *
342522 CAATCTTCAGCAAAC-GTGTCTGCTCCCTACTCATTCAGGGAGTATATT
1 CAATCTTCAACAAACAG-GTCCGCTCCCTACTCATTCAGAGAGTATATT
* * *
342570 CAATCTTCAACAAACAGGTCCGCTCTCTATTCCTTCAGAGAGTATA
1 CAATCTTCAACAAACAGGTCCGCTCCCTACTCATTCAGAGAGTATA
342616 GAACTCGAAC
Statistics
Matches: 39, Mismatches: 6, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
48 38 0.97
49 1 0.03
ACGTcount: A:0.28, C:0.28, G:0.15, T:0.30
Consensus pattern (48 bp):
CAATCTTCAACAAACAGGTCCGCTCCCTACTCATTCAGAGAGTATATT
Found at i:342654 original size:55 final size:55
Alignment explanation
Indices: 342570--342839 Score: 367
Period size: 55 Copynumber: 5.0 Consensus size: 55
342560 GGAGTATATT
342570 CAATCTTCAACAAAC-AGGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAA
1 CAATCTTCAACAAACGA-GTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAA
* *
342625 CAATCTTCATA-AAACGGGTCCGCTCTCTATTTCTTCAGAGAGTATAGAACTCGAA
1 CAATCTTCA-ACAAACGAGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAA
*
342680 CAATCTTCAACAAACGAGTCCGTTCTCTATTCCTTCAGAGAGTATAGAACTCGAA
1 CAATCTTCAACAAACGAGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAA
* *
342735 CAATCTTCAACAAACAAGTCCGCTCTCTATTCTTTCAGAGAGTATATG-ACTCG--
1 CAATCTTCAACAAACGAGTCCGCTCTCTATTCCTTCAGAGAGTATA-GAACTCGAA
* * * *
342788 --ATCTTCATA-AAATGTGTCCTCTCCCTATTCCTTCAGAGAGTATAGAACTCGA
1 CAATCTTCA-ACAAACGAGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGA
342840 TCTTCATAAA
Statistics
Matches: 194, Mismatches: 14, Indels: 17
0.86 0.06 0.08
Matches are distributed among these distances:
50 1 0.01
51 41 0.21
52 1 0.01
54 1 0.01
55 148 0.76
56 2 0.01
ACGTcount: A:0.31, C:0.26, G:0.14, T:0.29
Consensus pattern (55 bp):
CAATCTTCAACAAACGAGTCCGCTCTCTATTCCTTCAGAGAGTATAGAACTCGAA
Found at i:342718 original size:110 final size:108
Alignment explanation
Indices: 342493--342839 Score: 362
Period size: 110 Copynumber: 3.3 Consensus size: 108
342483 GGTCTGCTCC
* * * * ** * * * *
342493 CTATCCCTTCAGGGAGTATA-AGACTCGACCAATCTTCAGCAAACGTGTCTGCTCCCTACTCATT
1 CTATTCCTTCAGAGAGTATAGA-ACTCGAACAATCTTCAACAAACAAGTCCGCTCTCTATTCTTT
* *
342557 CAGGGAGTATAT---T--CAATCTTCAACAAAC-AGGTCCGCTCT
65 CAGAGAGTATATGACTCGCAATCTTCAACAAACGA-GTCCGTTCT
**
342596 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCATA-AAACGGGTCCGCTCTCTATT-TCT
1 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCA-ACAAACAAGTCCGCTCTCTATTCT-T
342659 TCAGAGAGTATA-GAACTCGAACAATCTTCAACAAACGAGTCCGTTCT
64 TCAGAGAGTATATG-ACTCG--CAATCTTCAACAAACGAGTCCGTTCT
342706 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACAAGTCCGCTCTCTATTCTTTC
1 CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACAAGTCCGCTCTCTATTCTTTC
* * *
342771 AGAGAGTATATGACTCG--ATCTTCATA-AAATGTGTCC-TCTCC
66 AGAGAGTATATGACTCGCAATCTTCA-ACAAACGAGTCCGT-TCT
342812 CTATTCCTTCAGAGAGTATAGAACTCGA
1 CTATTCCTTCAGAGAGTATAGAACTCGA
342840 TCTTCATAAA
Statistics
Matches: 211, Mismatches: 16, Indels: 31
0.82 0.06 0.12
Matches are distributed among these distances:
103 61 0.29
104 1 0.00
105 1 0.00
106 46 0.22
107 1 0.00
109 1 0.00
110 97 0.46
111 3 0.01
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.29
Consensus pattern (108 bp):
CTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACAAGTCCGCTCTCTATTCTTTC
AGAGAGTATATGACTCGCAATCTTCAACAAACGAGTCCGTTCT
Found at i:342895 original size:37 final size:36
Alignment explanation
Indices: 342854--342925 Score: 117
Period size: 37 Copynumber: 2.0 Consensus size: 36
342844 CATAAAATGA
**
342854 GTTTGCTTCACTGTTCTTCCGTGAAGGCTTACAGATG
1 GTTTGCTTCACTACTCTTCCGTGAAGGCTTA-AGATG
342891 GTTTGCTTCACTACTCTTCCGTGAAGGCTTAAGAT
1 GTTTGCTTCACTACTCTTCCGTGAAGGCTTAAGAT
342926 TGACCTGTTT
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
36 4 0.12
37 29 0.88
ACGTcount: A:0.18, C:0.22, G:0.22, T:0.38
Consensus pattern (36 bp):
GTTTGCTTCACTACTCTTCCGTGAAGGCTTAAGATG
Found at i:344233 original size:15 final size:16
Alignment explanation
Indices: 344207--344382 Score: 67
Period size: 17 Copynumber: 10.3 Consensus size: 16
344197 CCTCCTTTTA
344207 TTTCTCTTTTTTTCATT
1 TTTCTC-TTTTTTCATT
344224 TTTCTCTTTTTTCA-T
1 TTTCTCTTTTTTCATT
344239 TTTC-CATTTTTTC-TT
1 TTTCTC-TTTTTTCATT
* *
344254 CTTTTTCTTCTTTTCGTTT
1 -TTTCTCTT-TTTTC-ATT
* *
344273 TTTCCATCATTTTTCTTTT
1 TTT-C-TCTTTTTTC-ATT
344292 TTTCTCATTTTTTTCTTATT
1 TTTCTC--TTTTTTC--ATT
* *
344312 TTTCT-TCTTCTCATT
1 TTTCTCTTTTTTCATT
* * *
344327 TTTATTTTTATTATTATT
1 TTTCTCTTT-TT-TCATT
344345 TTT-TCATTTTTTCATT
1 TTTCTC-TTTTTTCATT
*
344361 TTTTTCTCTTTTT-ATT
1 TTTCTCT-TTTTTCATT
344377 TCTTCT
1 T-TTCT
344383 TCAAGAGAAA
Statistics
Matches: 125, Mismatches: 15, Indels: 38
0.70 0.08 0.21
Matches are distributed among these distances:
14 1 0.01
15 20 0.16
16 27 0.22
17 33 0.26
18 14 0.11
19 19 0.15
20 11 0.09
ACGTcount: A:0.09, C:0.17, G:0.01, T:0.74
Consensus pattern (16 bp):
TTTCTCTTTTTTCATT
Found at i:344234 original size:9 final size:9
Alignment explanation
Indices: 344207--344373 Score: 51
Period size: 9 Copynumber: 19.2 Consensus size: 9
344197 CCTCCTTTTA
344207 TTTCTCTTT
1 TTTCTCTTT
*
344216 TTT-TCATT
1 TTTCTCTTT
344224 TTTCTC-TT
1 TTTCTCTTT
*
344232 TTT-TC-AT
1 TTTCTCTTT
344239 TTTC-CATTT
1 TTTCTC-TTT
344248 TTTCT-TCTT
1 TTTCTCT-TT
*
344257 TTTCT-TCT
1 TTTCTCTTT
344265 TTTCGT-TTT
1 TTTC-TCTTT
* *
344274 TTCCATCATT
1 TTTC-TCTTT
344284 TTTCT-TTT
1 TTTCTCTTT
344292 TTTCTCATTT
1 TTTCTC-TTT
344302 TTT-TCTTAT
1 TTTCTCTT-T
344311 TTT-TC-TT
1 TTTCTCTTT
* *
344318 CTTCTCATT
1 TTTCTCTTT
*
344327 TTTAT-TTT
1 TTTCTCTTT
*
344335 TATTAT-TATT
1 T-TTCTCT-TT
344345 TTT-TCATTT
1 TTTCTC-TTT
344354 TTTCAT-TTT
1 TTTC-TCTTT
344363 TTTCTCTTT
1 TTTCTCTTT
344372 TT
1 TT
344374 ATTTCTTCTT
Statistics
Matches: 124, Mismatches: 14, Indels: 40
0.70 0.08 0.22
Matches are distributed among these distances:
7 10 0.08
8 35 0.28
9 63 0.51
10 15 0.12
11 1 0.01
ACGTcount: A:0.08, C:0.17, G:0.01, T:0.74
Consensus pattern (9 bp):
TTTCTCTTT
Found at i:344305 original size:20 final size:19
Alignment explanation
Indices: 344264--344316 Score: 54
Period size: 19 Copynumber: 2.7 Consensus size: 19
344254 CTTTTTCTTC
*
344264 TTTTCGTTTTTTC-CATCAT
1 TTTTCTTTTTTTCTCA-CAT
**
344283 TTTTCTTTTTTTCTCATTT
1 TTTTCTTTTTTTCTCACAT
344302 TTTTCTTATTTTTCT
1 TTTTCTT-TTTTTCT
344317 TCTTCTCATT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
19 20 0.69
20 9 0.31
ACGTcount: A:0.08, C:0.17, G:0.02, T:0.74
Consensus pattern (19 bp):
TTTTCTTTTTTTCTCACAT
Found at i:344355 original size:8 final size:8
Alignment explanation
Indices: 344214--344364 Score: 70
Period size: 8 Copynumber: 18.8 Consensus size: 8
344204 TTATTTCTCT
344214 TTTTTTCA
1 TTTTTTCA
344222 TTTTTCTC-
1 TTTTT-TCA
344230 TTTTTTCA
1 TTTTTTCA
*
344238 -TTTTCCA
1 TTTTTTCA
*
344245 TTTTTTCT
1 TTTTTTCA
344253 TCTTTTTC-
1 T-TTTTTCA
*
344261 TTCTTTTCG
1 TT-TTTTCA
344270 TTTTTTCCA
1 TTTTTT-CA
*
344279 TCATTTTTCTT
1 T--TTTTTC-A
344290 TTTTTCTCA
1 TTTTT-TCA
*
344299 TTTTTTTCT
1 -TTTTTTCA
344308 TATTTTTC-
1 T-TTTTTCA
*
344316 TTCTTCTCA
1 TT-TTTTCA
344325 -TTTTT-A
1 TTTTTTCA
344331 -TTTTT-A
1 TTTTTTCA
*
344337 -TTATT-A
1 TTTTTTCA
344343 TTTTTTCA
1 TTTTTTCA
344351 TTTTTTCA
1 TTTTTTCA
344359 TTTTTT
1 TTTTTT
344365 TCTCTTTTTA
Statistics
Matches: 115, Mismatches: 11, Indels: 34
0.72 0.07 0.21
Matches are distributed among these distances:
6 12 0.10
7 17 0.15
8 48 0.42
9 24 0.21
10 8 0.07
11 6 0.05
ACGTcount: A:0.09, C:0.16, G:0.01, T:0.74
Consensus pattern (8 bp):
TTTTTTCA
Found at i:344380 original size:10 final size:9
Alignment explanation
Indices: 344245--344380 Score: 51
Period size: 10 Copynumber: 14.0 Consensus size: 9
344235 TCATTTTCCA
344245 TTTTTTCTT
1 TTTTTTCTT
*
344254 CTTTTTC-T
1 TTTTTTCTT
* *
344262 TCTTTTCGT
1 TTTTTTCTT
* *
344271 TTTTTCCATC
1 TTTTTTC-TT
*
344281 ATTTTTCTT
1 TTTTTTCTT
*
344290 TTTTTCTCAT
1 TTTTT-TCTT
344300 TTTTTTCTTAT
1 TTTTTTC-T-T
344311 TTTTCTTCTT
1 TTTT-TTCTT
*
344321 CTCATTTTTATT
1 -T--TTTTTCTT
* *
344333 TTTATTATT
1 TTTTTTCTT
*
344342 ATTTTTTC-A
1 -TTTTTTCTT
344351 TTTTTTCATT
1 TTTTTTC-TT
344361 TTTTTCTCTT
1 TTTTT-TCTT
344371 TTTATTTCTT
1 TTT-TTTCTT
344381 CTTCAAGAGA
Statistics
Matches: 94, Mismatches: 19, Indels: 27
0.67 0.14 0.19
Matches are distributed among these distances:
8 13 0.14
9 26 0.28
10 33 0.35
11 12 0.13
12 7 0.07
13 3 0.03
ACGTcount: A:0.09, C:0.15, G:0.01, T:0.75
Consensus pattern (9 bp):
TTTTTTCTT
Found at i:347736 original size:17 final size:17
Alignment explanation
Indices: 347714--347746 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
347704 TACAACAAAG
347714 AATGAAT-GAATGAATGA
1 AATGAATAGAAT-AATGA
347731 AATGAATAGAATAATG
1 AATGAATAGAATAATG
347747 TTTGCCATTT
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.55, C:0.00, G:0.21, T:0.24
Consensus pattern (17 bp):
AATGAATAGAATAATGA
Found at i:352512 original size:20 final size:20
Alignment explanation
Indices: 352487--352614 Score: 138
Period size: 20 Copynumber: 6.5 Consensus size: 20
352477 GCGTAAAAAC
352487 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
352507 ATTTGAC-TTCTGTGTTGCG-
1 ATTTGACTTTC-GCGTTGCGA
*
352526 ATTT-ACAAATTCGCGTTGCGA
1 ATTTGAC--TTTCGCGTTGCGA
* * *
352547 ATTTGACTATCGCTTTACGA
1 ATTTGACTTTCGCGTTGCGA
*
352567 ATTTGACTTT-GTGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
*
352586 ATTTGACTATCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
352606 ATTTGACTT
1 ATTTGACTT
352615 CTGTGTTGCG
Statistics
Matches: 88, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
18 2 0.02
19 22 0.25
20 55 0.62
21 7 0.08
22 2 0.02
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.41
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:352594 original size:39 final size:40
Alignment explanation
Indices: 352540--352625 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 40
352530 ACAAATTCGC
*
352540 GTTGCGAATTTGACTATCGCTTTACGAATTTGACTT-TGT
1 GTTGCGAATTTGACTATCGCGTTACGAATTTGACTTCTGT
*
352579 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACTATCGCGTTACGAATTTGACTTCTGT
352619 GTTGCGA
1 GTTGCGA
352626 TTTACAAATT
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
39 34 0.77
40 10 0.23
ACGTcount: A:0.19, C:0.16, G:0.24, T:0.41
Consensus pattern (40 bp):
GTTGCGAATTTGACTATCGCGTTACGAATTTGACTTCTGT
Found at i:352604 original size:59 final size:60
Alignment explanation
Indices: 352487--352613 Score: 179
Period size: 60 Copynumber: 2.1 Consensus size: 60
352477 GCGTAAAAAC
* *
352487 ATTTGACTTTCGCGTTGCGAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGCGA
1 ATTTGACTATCGCGTTACGAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGCGA
* *
352547 ATTTGACTATCGCTTTACGAATTTGACTT-TGTGTTGCGAATTTGAC-TA-TCGCGTTGCGA
1 ATTTGACTATCGCGTTACGAATTTGACTTCTGTGTTGCG-ATTT-ACAAATTCGCGTTGCGA
352606 ATTTGACT
1 ATTTGACT
352614 TCTGTGTTGC
Statistics
Matches: 61, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
59 28 0.46
60 31 0.51
61 2 0.03
ACGTcount: A:0.20, C:0.17, G:0.22, T:0.41
Consensus pattern (60 bp):
ATTTGACTATCGCGTTACGAATTTGACTTCTGTGTTGCGATTTACAAATTCGCGTTGCGA
Found at i:352642 original size:20 final size:20
Alignment explanation
Indices: 352619--352665 Score: 69
Period size: 20 Copynumber: 2.4 Consensus size: 20
352609 TGACTTCTGT
352619 GTTGCGATTTACAA-ATTCAC
1 GTTGCGATTTA-AATATTCAC
*
352639 GTTGCGATTTAAATATTCGC
1 GTTGCGATTTAAATATTCAC
352659 GTTGCGA
1 GTTGCGA
352666 AATTGGAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 2 0.08
20 23 0.92
ACGTcount: A:0.26, C:0.17, G:0.21, T:0.36
Consensus pattern (20 bp):
GTTGCGATTTAAATATTCAC
Found at i:352642 original size:40 final size:39
Alignment explanation
Indices: 352540--352645 Score: 117
Period size: 39 Copynumber: 2.7 Consensus size: 39
352530 ACAAATTCGC
* * * *
352540 GTTGCGAATTTGACTATCGCTTTACGAATTTGACTTTGT
1 GTTGCGAATTTGACAATCACGTTGCGAATTTGACTTTGT
* *
352579 GTTGCGAATTTGACTATCGCGTTGCGAATTTGACTTCTGT
1 GTTGCGAATTTGACAATCACGTTGCGAATTTGACTT-TGT
352619 GTTGCG-ATTT-ACAAATTCACGTTGCGA
1 GTTGCGAATTTGAC-AA-TCACGTTGCGA
352646 TTTAAATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
38 2 0.03
39 39 0.65
40 19 0.32
ACGTcount: A:0.21, C:0.17, G:0.23, T:0.40
Consensus pattern (39 bp):
GTTGCGAATTTGACAATCACGTTGCGAATTTGACTTTGT
Found at i:353516 original size:23 final size:22
Alignment explanation
Indices: 353488--353565 Score: 68
Period size: 23 Copynumber: 3.4 Consensus size: 22
353478 TTATTTAAAT
*
353488 AATAAACGAACATAATAAACAA
1 AATAAATGAACATAATAAACAA
* *
353510 ACGTAAATGAATACA-AACAAACAA
1 A-ATAAATG-A-ACATAATAAACAA
*
353534 AATAAATGAACATAATTAAACAC
1 AATAAATGAACATAA-TAAACAA
*
353557 AATATATGA
1 AATAAATGA
353566 TTGTAAACAA
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
21 3 0.07
22 4 0.09
23 24 0.55
24 10 0.23
25 3 0.07
ACGTcount: A:0.63, C:0.13, G:0.06, T:0.18
Consensus pattern (22 bp):
AATAAATGAACATAATAAACAA
Found at i:354709 original size:16 final size:16
Alignment explanation
Indices: 354688--354720 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
354678 TAATAAATAG
354688 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
354704 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
354720 A
1 A
354721 AATTTTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:354802 original size:10 final size:10
Alignment explanation
Indices: 354787--354859 Score: 66
Period size: 10 Copynumber: 7.5 Consensus size: 10
354777 TTTAATAAAC
354787 AAACGAACAT
1 AAACGAACAT
354797 AAACGAAC--
1 AAACGAACAT
354805 --ACGAACAT
1 AAACGAACAT
*
354813 AAACGAACAC
1 AAACGAACAT
*
354823 AAAC-ATAAAT
1 AAACGA-ACAT
354833 GAACACGAACAT
1 -AA-ACGAACAT
354845 AAACGAACAT
1 AAACGAACAT
354855 AAACG
1 AAACG
354860 TTGGAGACCC
Statistics
Matches: 51, Mismatches: 4, Indels: 16
0.72 0.06 0.23
Matches are distributed among these distances:
6 6 0.12
9 1 0.02
10 34 0.67
11 4 0.08
12 5 0.10
13 1 0.02
ACGTcount: A:0.59, C:0.22, G:0.11, T:0.08
Consensus pattern (10 bp):
AAACGAACAT
Found at i:354810 original size:16 final size:16
Alignment explanation
Indices: 354781--354853 Score: 114
Period size: 16 Copynumber: 4.7 Consensus size: 16
354771 CGTTCATTTA
354781 ATAAAC-AA-ACGAAC
1 ATAAACGAACACGAAC
354795 ATAAACGAACACGAAC
1 ATAAACGAACACGAAC
*
354811 ATAAACGAACACAAAC
1 ATAAACGAACACGAAC
*
354827 ATAAATGAACACGAAC
1 ATAAACGAACACGAAC
354843 ATAAACGAACA
1 ATAAACGAACA
354854 TAAACGTTGG
Statistics
Matches: 53, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
14 6 0.11
15 2 0.04
16 45 0.85
ACGTcount: A:0.60, C:0.22, G:0.10, T:0.08
Consensus pattern (16 bp):
ATAAACGAACACGAAC
Found at i:355623 original size:14 final size:14
Alignment explanation
Indices: 355606--355661 Score: 75
Period size: 14 Copynumber: 4.3 Consensus size: 14
355596 AATGAACATA
355606 AACGAACATAATCG
1 AACGAACATAATCG
355620 AACGAACAT-A---
1 AACGAACATAATCG
*
355630 AACGAACATAACCG
1 AACGAACATAATCG
355644 AACGAACATAATCG
1 AACGAACATAATCG
355658 AACG
1 AACG
355662 TTCACGAACG
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
10 9 0.24
11 1 0.03
13 1 0.03
14 26 0.70
ACGTcount: A:0.52, C:0.23, G:0.14, T:0.11
Consensus pattern (14 bp):
AACGAACATAATCG
Found at i:355626 original size:24 final size:24
Alignment explanation
Indices: 355586--355660 Score: 107
Period size: 24 Copynumber: 3.1 Consensus size: 24
355576 GATTGGGTTA
*
355586 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
355610 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
* *
355634 AACATAACCGAACGAACATAATCG
1 AACATAATCGAACGAACATAAACG
355658 AAC
1 AAC
355661 GTTCACGAAC
Statistics
Matches: 47, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
23 3 0.06
24 44 0.94
ACGTcount: A:0.55, C:0.20, G:0.12, T:0.13
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:355660 original size:10 final size:10
Alignment explanation
Indices: 355599--355646 Score: 51
Period size: 10 Copynumber: 4.4 Consensus size: 10
355589 ATAAATGAAT
355599 GAACATAAAC
1 GAACATAAAC
355609 GAACATAATCGAAC
1 GAACAT-A---AAC
355623 GAACATAAAC
1 GAACATAAAC
*
355633 GAACATAACC
1 GAACATAAAC
355643 GAAC
1 GAAC
355647 GAACATAATC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
10 22 0.67
11 1 0.03
13 1 0.03
14 9 0.27
ACGTcount: A:0.54, C:0.23, G:0.12, T:0.10
Consensus pattern (10 bp):
GAACATAAAC
Found at i:366772 original size:40 final size:40
Alignment explanation
Indices: 366710--366791 Score: 146
Period size: 40 Copynumber: 2.0 Consensus size: 40
366700 ATGTGTGGTC
*
366710 TTAATAGTTTATTGTCGACTCGTGCACATCAACTGGGAAA
1 TTAATAGTTTATTCTCGACTCGTGCACATCAACTGGGAAA
*
366750 TTAATAGTTTATTCTCGGCTCGTGCACATCAACTGGGAAA
1 TTAATAGTTTATTCTCGACTCGTGCACATCAACTGGGAAA
366790 TT
1 TT
366792 TTGATGAATG
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.28, C:0.18, G:0.20, T:0.34
Consensus pattern (40 bp):
TTAATAGTTTATTCTCGACTCGTGCACATCAACTGGGAAA
Found at i:378068 original size:32 final size:31
Alignment explanation
Indices: 377963--378068 Score: 108
Period size: 32 Copynumber: 3.4 Consensus size: 31
377953 AAGTTTTATA
377963 TGTTACAAAATAGTCATT-AAACTTATCAAAT
1 TGTTACAAAATA-TCATTAAAACTTATCAAAT
* * *
377994 TATTATAAAATGATCATTAAAATTTATCAAACT
1 TGTTACAAAAT-ATCATTAAAACTTATCAAA-T
* * *
378027 AG-TAAAAAATATTCATTAAAACTTATTAAAT
1 TGTTACAAAATA-TCATTAAAACTTATCAAAT
378058 TGTTACAAAAT
1 TGTTACAAAAT
378069 TGATCTTTCA
Statistics
Matches: 60, Mismatches: 10, Indels: 9
0.76 0.13 0.11
Matches are distributed among these distances:
31 17 0.28
32 42 0.70
33 1 0.02
ACGTcount: A:0.49, C:0.09, G:0.05, T:0.37
Consensus pattern (31 bp):
TGTTACAAAATATCATTAAAACTTATCAAAT
Found at i:378085 original size:64 final size:63
Alignment explanation
Indices: 377969--378088 Score: 152
Period size: 64 Copynumber: 1.9 Consensus size: 63
377959 TATATGTTAC
* *
377969 AAAATAGTCATTAAACTTATCAAATTATTATAAAATGATCATTAAAATTTATCAAACTAGTAA
1 AAAATAGTCATTAAACTTATCAAATTATTACAAAATGATCATTAAAACTTATCAAACTAGTAA
* * * **
378032 AAAATATTCATTAAAACTTATTAAATTGTTACAAAATTGATC-TTTCAACTTATCAAA
1 AAAATAGTCATT-AAACTTATCAAATTATTACAAAA-TGATCATTAAAACTTATCAAA
378089 ATCTATCATT
Statistics
Matches: 48, Mismatches: 7, Indels: 3
0.83 0.12 0.05
Matches are distributed among these distances:
63 11 0.23
64 32 0.67
65 5 0.10
ACGTcount: A:0.48, C:0.11, G:0.04, T:0.37
Consensus pattern (63 bp):
AAAATAGTCATTAAACTTATCAAATTATTACAAAATGATCATTAAAACTTATCAAACTAGTAA
Found at i:383590 original size:17 final size:16
Alignment explanation
Indices: 383567--383625 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 16
383557 CTTGAGCTTG
383567 TAGTATTCGACTCTTA
1 TAGTATTCGACTCTTA
*
383583 TCAGTATT-GCAGCTGTTGA
1 T-AGTATTCG-A-CTCTT-A
383602 TAGTATTCGACTCTTA
1 TAGTATTCGACTCTTA
383618 TTAGTATT
1 -TAGTATT
383626 GCATCTGTTG
Statistics
Matches: 35, Mismatches: 2, Indels: 11
0.73 0.04 0.23
Matches are distributed among these distances:
16 3 0.09
17 18 0.51
18 11 0.31
19 3 0.09
ACGTcount: A:0.24, C:0.15, G:0.17, T:0.44
Consensus pattern (16 bp):
TAGTATTCGACTCTTA
Found at i:383613 original size:35 final size:35
Alignment explanation
Indices: 383567--383671 Score: 174
Period size: 35 Copynumber: 3.0 Consensus size: 35
383557 CTTGAGCTTG
*
383567 TAGTATTCGACTCTTATCAGTATTGCAGCTGTTGA
1 TAGTATTCGACTCTTATTAGTATTGCAGCTGTTGA
*
383602 TAGTATTCGACTCTTATTAGTATTGCATCTGTTGA
1 TAGTATTCGACTCTTATTAGTATTGCAGCTGTTGA
* *
383637 TAGCATTTGACTCTTATTAGTATTGCAGCTGTTGA
1 TAGTATTCGACTCTTATTAGTATTGCAGCTGTTGA
383672 GATCTCCGAT
Statistics
Matches: 65, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 65 1.00
ACGTcount: A:0.23, C:0.15, G:0.19, T:0.43
Consensus pattern (35 bp):
TAGTATTCGACTCTTATTAGTATTGCAGCTGTTGA
Found at i:385406 original size:93 final size:93
Alignment explanation
Indices: 385303--385489 Score: 347
Period size: 93 Copynumber: 2.0 Consensus size: 93
385293 TAACTATCCT
385303 TACTTTTCTGAATCAGAAACCCTAAATCGATACCCTATCCCAGTTTGAATTCCCAATTGGATTTC
1 TACTTTTCTGAATCAGAAACCCTAAATCGATACCCTATCCCAGTTTGAATTCCCAATTGGATTTC
*
385368 GACAATGAAATTCAAATCGAATCCCGAA
66 GACAATGAAATCCAAATCGAATCCCGAA
*
385396 TACTTTTCTGAATCAGAAACCCTAAATCGATACCCTATCCCAGTTTGAATTCCCAATTGGGTTTC
1 TACTTTTCTGAATCAGAAACCCTAAATCGATACCCTATCCCAGTTTGAATTCCCAATTGGATTTC
*
385461 GACAATGAAATCCAAATCGGATCCCGAA
66 GACAATGAAATCCAAATCGAATCCCGAA
385489 T
1 T
385490 CCTCTTTGCC
Statistics
Matches: 91, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
93 91 1.00
ACGTcount: A:0.33, C:0.25, G:0.13, T:0.29
Consensus pattern (93 bp):
TACTTTTCTGAATCAGAAACCCTAAATCGATACCCTATCCCAGTTTGAATTCCCAATTGGATTTC
GACAATGAAATCCAAATCGAATCCCGAA
Found at i:389591 original size:155 final size:156
Alignment explanation
Indices: 389414--389730 Score: 448
Period size: 162 Copynumber: 2.0 Consensus size: 156
389404 CTTTTAATGT
389414 TCATGAATATGTTTGTTTAAATGTTTGCG-A-A-C-A-TGTTCGTTTATCGTTCGTAAACATGTT
1 TCATGAATATGTTTGTTTAAATGTTTGCGAACATCTAGTGTTCGTTTATCGTTCGTAAACATGTT
*
389474 TGTTTAGAATAAAAAAAAAGGGAAAAGAGAGCTATTCAAAATATAAAAAAAAAATAAACAAGCTT
66 TGTTTAGAAT-AAAAAAAAGGAAAAAGAGAGCTATTCAAAATAT---AAAAAAATAAACAAGCTT
*
389539 ATAAATGTA-CTTGTTCGTGAACATAAACGA
127 ATAAATG-AGCTTGTTCATGAACATAAACGA
389569 TCATGAATATGTTTGTTTAAATGTTTGCGAACATGTTCGTTTAGTGTTCGTTTATCGTTCGTAAA
1 TCATGAATATGTTTGTTTAAATGTTTGCGAACA---TC---TAGTGTTCGTTTATCGTTCGTAAA
*
389634 CATGTTTGTTTAGAATAAAAAAAAGGAAAAAGAGAGCTATTCAAAATATGAAAAAATAAACAAGC
60 CATGTTTGTTTAGAATAAAAAAAAGGAAAAAGAGAGCTATTCAAAATATAAAAAAATAAACAAGC
* *
389699 TTATAAATGAGTTTGTTCATTAACATAAACGA
125 TTATAAATGAGCTTGTTCATGAACATAAACGA
389731 ACCGAACATA
Statistics
Matches: 145, Mismatches: 5, Indels: 17
0.87 0.03 0.10
Matches are distributed among these distances:
155 29 0.20
156 1 0.01
157 1 0.01
161 2 0.01
162 42 0.29
165 33 0.23
166 37 0.26
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.33
Consensus pattern (156 bp):
TCATGAATATGTTTGTTTAAATGTTTGCGAACATCTAGTGTTCGTTTATCGTTCGTAAACATGTT
TGTTTAGAATAAAAAAAAGGAAAAAGAGAGCTATTCAAAATATAAAAAAATAAACAAGCTTATAA
ATGAGCTTGTTCATGAACATAAACGA
Found at i:389787 original size:31 final size:31
Alignment explanation
Indices: 389751--389811 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
389741 TCTCTGTTCA
389751 TTTTTGTTCGTTTATCAAATGAACATAAAAT
1 TTTTTGTTCGTTTATCAAATGAACATAAAAT
389782 TTTTTGTTCGTTTATCAAATGAACATAAAA
1 TTTTTGTTCGTTTATCAAATGAACATAAAA
389812 AAAGGAAAAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.36, C:0.10, G:0.10, T:0.44
Consensus pattern (31 bp):
TTTTTGTTCGTTTATCAAATGAACATAAAAT
Found at i:392167 original size:20 final size:20
Alignment explanation
Indices: 392142--392182 Score: 82
Period size: 20 Copynumber: 2.0 Consensus size: 20
392132 ATGTTAATTA
392142 TAAGTCCATATACTATGCTT
1 TAAGTCCATATACTATGCTT
392162 TAAGTCCATATACTATGCTT
1 TAAGTCCATATACTATGCTT
392182 T
1 T
392183 GGAATCTCTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.29, C:0.20, G:0.10, T:0.41
Consensus pattern (20 bp):
TAAGTCCATATACTATGCTT
Found at i:393031 original size:12 final size:12
Alignment explanation
Indices: 393016--393041 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
393006 TTCAAAAAAA
393016 TTAAAATTATAT
1 TTAAAATTATAT
393028 TTAAAATTATAT
1 TTAAAATTATAT
393040 TT
1 TT
393042 TTATTTTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TTAAAATTATAT
Found at i:394370 original size:36 final size:36
Alignment explanation
Indices: 394322--394401 Score: 115
Period size: 36 Copynumber: 2.2 Consensus size: 36
394312 AAATATATAA
*
394322 AATTTTATATCATTTTCACATAAATAATACATAAATT
1 AATTTT-TATCATTTTCACACAAATAATACATAAATT
* *
394359 AATTTTTATCATTTTCACGCAAATAATACATAGATT
1 AATTTTTATCATTTTCACACAAATAATACATAAATT
*
394395 AAGTTTT
1 AATTTTT
394402 GGTCACTCAC
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 33 0.85
37 6 0.15
ACGTcount: A:0.41, C:0.11, G:0.04, T:0.44
Consensus pattern (36 bp):
AATTTTTATCATTTTCACACAAATAATACATAAATT
Found at i:399593 original size:16 final size:16
Alignment explanation
Indices: 399572--399603 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
399562 AATTAAAATA
399572 GTTAATTTACCAAGTC
1 GTTAATTTACCAAGTC
399588 GTTAATTTACCAAGTC
1 GTTAATTTACCAAGTC
399604 ATCCTCCTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (16 bp):
GTTAATTTACCAAGTC
Found at i:399729 original size:15 final size:15
Alignment explanation
Indices: 399709--399737 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
399699 AGGGGGGGGG
399709 GGGAAACAATTAACA
1 GGGAAACAATTAACA
399724 GGGAAACAATTAAC
1 GGGAAACAATTAAC
399738 CTTGTAAAGG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.52, C:0.14, G:0.21, T:0.14
Consensus pattern (15 bp):
GGGAAACAATTAACA
Found at i:399931 original size:6 final size:6
Alignment explanation
Indices: 399914--399949 Score: 54
Period size: 6 Copynumber: 5.8 Consensus size: 6
399904 TTGGAATGAC
*
399914 CGGAAT CAGAAT CGGAAT CGGAAT CGGAAT GCGGAA
1 CGGAAT CGGAAT CGGAAT CGGAAT CGGAAT -CGGAA
399950 CGACGTCGTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
6 22 0.81
7 5 0.19
ACGTcount: A:0.36, C:0.17, G:0.33, T:0.14
Consensus pattern (6 bp):
CGGAAT
Found at i:405171 original size:3 final size:3
Alignment explanation
Indices: 405163--405188 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
405153 GAGGTTCGTT
405163 TTC TTC TTC TTC TTC TTC TTC TTC TT
1 TTC TTC TTC TTC TTC TTC TTC TTC TT
405189 GTTTATACAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.00, C:0.31, G:0.00, T:0.69
Consensus pattern (3 bp):
TTC
Found at i:410702 original size:12 final size:12
Alignment explanation
Indices: 410687--410732 Score: 56
Period size: 12 Copynumber: 3.6 Consensus size: 12
410677 CGGTTTTTTT
*
410687 ACCGGATAAAAA
1 ACCGGTTAAAAA
410699 ACCGGTTTGAAAAAA
1 ACCGG-TT--AAAAA
410714 ACCGGTTAAAAA
1 ACCGGTTAAAAA
410726 ACCGGTT
1 ACCGGTT
410733 TTTATCCGGA
Statistics
Matches: 30, Mismatches: 1, Indels: 6
0.81 0.03 0.16
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
14 2 0.07
15 10 0.33
ACGTcount: A:0.46, C:0.17, G:0.20, T:0.17
Consensus pattern (12 bp):
ACCGGTTAAAAA
Found at i:410714 original size:15 final size:13
Alignment explanation
Indices: 410693--410733 Score: 57
Period size: 12 Copynumber: 3.1 Consensus size: 13
410683 TTTTACCGGA
410693 TAAAAAACCGGTT
1 TAAAAAACCGGTT
410706 TGAAAAAAACCGG-T
1 T--AAAAAACCGGTT
410720 TAAAAAACCGGTT
1 TAAAAAACCGGTT
410733 T
1 T
410734 TTATCCGGAA
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
12 10 0.40
13 3 0.12
14 2 0.08
15 10 0.40
ACGTcount: A:0.46, C:0.15, G:0.17, T:0.22
Consensus pattern (13 bp):
TAAAAAACCGGTT
Done.