Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008056.1 Hibiscus syriacus cultivar Beakdansim tig00110551_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: 2370532
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 13
Found at i:222900 original size:21 final size:21
Alignment explanation
Indices: 222836--222910 Score: 100
Period size: 20 Copynumber: 3.7 Consensus size: 21
222826 TGCAGAAGAG
*
222836 TCGCAACGAGATAAA-GAAAA
1 TCGCAACGAGAGAAATGAAAA
***
222856 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGAAAA
222876 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
222897 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
222911 TCGCAACGCG
Statistics
Matches: 46, Mismatches: 7, Indels: 3
0.82 0.12 0.05
Matches are distributed among these distances:
19 2 0.04
20 25 0.54
21 19 0.41
ACGTcount: A:0.47, C:0.17, G:0.25, T:0.11
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:222903 original size:41 final size:40
Alignment explanation
Indices: 222835--222911 Score: 136
Period size: 41 Copynumber: 1.9 Consensus size: 40
222825 TTGCAGAAGA
*
222835 GTCGCAACGAGATAAAGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAAGAAAATCGCAACGAGAGAATGACT
222875 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAA-GAAAATCGCAACGAGAGAAT
222912 CGCAACGCGA
Statistics
Matches: 35, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
40 15 0.43
41 20 0.57
ACGTcount: A:0.45, C:0.17, G:0.26, T:0.12
Consensus pattern (40 bp):
GTCGCAACGAGAGAAAGAAAATCGCAACGAGAGAATGACT
Found at i:222944 original size:31 final size:32
Alignment explanation
Indices: 222887--222966 Score: 126
Period size: 31 Copynumber: 2.5 Consensus size: 32
222877 CGCAACGAGA
222887 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAAC-AGAGAATCGCAACGC
222920 GAAATGAAAATCGCAAC-GAGAATCGCAACGC
1 GAAATGAAAATCGCAACAGAGAATCGCAACGC
**
222951 GAAACCAAAATCGCAA
1 GAAATGAAAATCGCAA
222967 TGCGATTTTG
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
31 28 0.62
33 17 0.38
ACGTcount: A:0.47, C:0.23, G:0.21, T:0.09
Consensus pattern (32 bp):
GAAATGAAAATCGCAACAGAGAATCGCAACGC
Found at i:223002 original size:14 final size:14
Alignment explanation
Indices: 222983--223072 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
222973 TTTGGTTTCG
222983 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
222997 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
223016 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
223030 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
223049 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
223063 CGTTGCGATT
1 CGTTGCGATT
223073 TTCATTTCAA
Statistics
Matches: 62, Mismatches: 4, Indels: 20
0.72 0.05 0.23
Matches are distributed among these distances:
14 30 0.48
16 6 0.10
17 6 0.10
19 20 0.32
ACGTcount: A:0.09, C:0.24, G:0.22, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:223015 original size:33 final size:33
Alignment explanation
Indices: 222967--223080 Score: 210
Period size: 33 Copynumber: 3.5 Consensus size: 33
222957 AAAATCGCAA
**
222967 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
223000 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
223033 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
223066 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
223081 AACCAAAAGA
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
33 79 1.00
ACGTcount: A:0.09, C:0.23, G:0.22, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:223021 original size:19 final size:19
Alignment explanation
Indices: 222997--223058 Score: 80
Period size: 19 Copynumber: 3.5 Consensus size: 19
222987 GCGATTCTCT
222997 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
*
223016 CGTTGCGA--TTC---TCT
1 CGTTGCGATTTTCATTTCG
223030 CGTTGCGATTTTCATTTCG
1 CGTTGCGATTTTCATTTCG
223049 CGTTGCGATT
1 CGTTGCGATT
223059 CTCTCGTTGC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 10 0.28
16 3 0.08
17 3 0.08
19 20 0.56
ACGTcount: A:0.10, C:0.23, G:0.23, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTCATTTCG
Found at i:224930 original size:93 final size:93
Alignment explanation
Indices: 224768--225143 Score: 727
Period size: 93 Copynumber: 4.1 Consensus size: 93
224758 TAGATTGCTT
*
224768 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTT
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
224833 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
224861 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
224926 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
224954 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
*
225019 TTTGTCTTTGTTTTTTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
225047 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
225112 TTTGTCTTTGTTTTGTCTTTTGGTTG-A
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
225139 AGTAA
1 AGTAA
225144 TGCAATCCAT
Statistics
Matches: 280, Mismatches: 3, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
92 6 0.02
93 274 0.98
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.47
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:225311 original size:19 final size:19
Alignment explanation
Indices: 225207--225305 Score: 136
Period size: 19 Copynumber: 5.5 Consensus size: 19
225197 CACGAAACTT
225207 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
**
225226 AAAATCGCAACGCGAAATG
1 AAAATCGCAACGCGAAACC
225245 AAAATCGCAA--CG--A-C
1 AAAATCGCAACGCGAAACC
*
225259 AGAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
225278 AAAATCGCAACGCGAAACC
1 AAAATCGCAACGCGAAACC
225297 AAAATCGCA
1 AAAATCGCA
225306 TTGCGATTTT
Statistics
Matches: 70, Mismatches: 5, Indels: 10
0.82 0.06 0.12
Matches are distributed among these distances:
14 9 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 55 0.79
ACGTcount: A:0.47, C:0.28, G:0.17, T:0.07
Consensus pattern (19 bp):
AAAATCGCAACGCGAAACC
Found at i:225323 original size:19 final size:17
Alignment explanation
Indices: 225301--225398 Score: 91
Period size: 16 Copynumber: 5.8 Consensus size: 17
225291 GAAACCAAAA
225301 TCGCATTGCGATTTTCATT
1 TCGC-TTGCGA-TTTCATT
225320 TCGCGTTGCGA-TTC-TT
1 TCGC-TTGCGATTTCATT
225336 TCG-TTGCGATTTTCATT
1 TCGCTTGCGA-TTTCATT
*
225353 TCGCATTGCGA-TTC-TG
1 TCGC-TTGCGATTTCATT
225369 TCG-TTGCGATTTCATT
1 TCGCTTGCGATTTCATT
225385 TCGCGTTGCGATTT
1 TCGC-TTGCGATTT
225399 TAAGTTTCGT
Statistics
Matches: 67, Mismatches: 3, Indels: 19
0.75 0.03 0.21
Matches are distributed among these distances:
14 12 0.18
15 3 0.04
16 16 0.24
17 11 0.16
18 9 0.13
19 16 0.24
ACGTcount: A:0.11, C:0.21, G:0.21, T:0.46
Consensus pattern (17 bp):
TCGCTTGCGATTTCATT
Found at i:225342 original size:14 final size:14
Alignment explanation
Indices: 225323--225379 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
225313 TTTCATTTCG
225323 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
225337 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
225354 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
225370 CGTTGCGATT
1 CGTTGCGATT
225380 TCATTTCGCG
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:225387 original size:32 final size:33
Alignment explanation
Indices: 225306--225397 Score: 159
Period size: 33 Copynumber: 2.8 Consensus size: 33
225296 CAAAATCGCA
*
225306 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
225339 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
225372 TTGCGA-TTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
225398 TTAAGTTTCG
Statistics
Matches: 56, Mismatches: 3, Indels: 1
0.93 0.05 0.02
Matches are distributed among these distances:
32 19 0.34
33 37 0.66
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:225412 original size:20 final size:18
Alignment explanation
Indices: 225301--225415 Score: 57
Period size: 19 Copynumber: 6.6 Consensus size: 18
225291 GAAACCAAAA
* *
225301 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGA-TTTAATT
*
225320 TCGCGTTGCGA-TT-CTT
1 TCGCGTTGCGATTTAATT
*
225336 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGA-TTTAATT
* * *
225353 TCGCATTGCGA-TT-CTG
1 TCGCGTTGCGATTTAATT
*
225369 T--CGTTGCGATTTCATT
1 TCGCGTTGCGATTTAATT
225385 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGA-TTTAA-TT
*
225405 TCGTGTTGCGA
1 TCGCGTTGCGA
225416 AAGTAAACTA
Statistics
Matches: 74, Mismatches: 11, Indels: 21
0.70 0.10 0.20
Matches are distributed among these distances:
14 15 0.20
15 2 0.03
16 9 0.12
17 7 0.09
18 8 0.11
19 21 0.28
20 12 0.16
ACGTcount: A:0.12, C:0.20, G:0.23, T:0.45
Consensus pattern (18 bp):
TCGCGTTGCGATTTAATT
Found at i:225872 original size:44 final size:44
Alignment explanation
Indices: 225809--225894 Score: 118
Period size: 44 Copynumber: 2.0 Consensus size: 44
225799 GCCCGACTCG
* * *
225809 CCTATCATCCCTCAAGAGTCCACTCCTATCGTTGAAGAGGCCCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCC
* * *
225853 CCTATCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCC
1 CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCC
225895 ACTGTCATCA
Statistics
Matches: 36, Mismatches: 6, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
44 36 1.00
ACGTcount: A:0.21, C:0.41, G:0.16, T:0.22
Consensus pattern (44 bp):
CCTATCATCCCTCAAGAGTCCACTCCCACCGTTCAAGAGGCCCC
Found at i:227352 original size:14 final size:14
Alignment explanation
Indices: 227333--227368 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
227323 ATTGTTTAAT
227333 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
227347 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
227361 TGATTTGT
1 TGATTTGT
227369 GTAATTGATG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.33, C:0.00, G:0.22, T:0.44
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:227499 original size:19 final size:19
Alignment explanation
Indices: 227475--227572 Score: 143
Period size: 19 Copynumber: 5.4 Consensus size: 19
227465 AAAATTGACT
227475 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
227494 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
227513 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
227527 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
227546 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
227566 ATCGCAA
1 ATCGCAA
227573 CGGGAGAATC
Statistics
Matches: 71, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 39 0.55
20 16 0.23
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.14
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:227604 original size:53 final size:53
Alignment explanation
Indices: 227475--227591 Score: 218
Period size: 53 Copynumber: 2.2 Consensus size: 53
227465 AAAATTGACT
227475 ATCGCAATGCGAAATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
*
227527 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGGGAGA
1 ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
227580 ATCGCAATGCGA
1 ATCGCAATGCGA
227592 TTTTAATTTC
Statistics
Matches: 63, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
52 29 0.46
53 34 0.54
ACGTcount: A:0.44, C:0.18, G:0.25, T:0.14
Consensus pattern (53 bp):
ATCGCAATGCGAAATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGA
Found at i:227609 original size:19 final size:19
Alignment explanation
Indices: 227581--227782 Score: 194
Period size: 19 Copynumber: 11.7 Consensus size: 19
227571 AACGGGAGAA
* *
227581 TCGCAATGCGATTTTAATT
1 TCGCATTGCGATTTTCATT
*
227600 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
227616 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
227633 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
227652 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
227668 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
227685 TCGCATTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
*
227704 TCGCATTGCGA--TTC-TC
1 TCGCATTGCGATTTTCATT
227720 TCG--TTGCGATTTTCATT
1 TCGCATTGCGATTTTCATT
227737 TCCGCATTGCGA-TTTCA--
1 T-CGCATTGCGATTTTCATT
*
227754 T-G--TTGGGATTTTCATT
1 TCGCATTGCGATTTTCATT
227770 TCGCATTGCGATT
1 TCGCATTGCGATT
227783 CTCTCGTTGC
Statistics
Matches: 151, Mismatches: 10, Indels: 44
0.74 0.05 0.21
Matches are distributed among these distances:
13 5 0.03
14 23 0.15
15 1 0.01
16 22 0.15
17 20 0.13
18 2 0.01
19 72 0.48
20 6 0.04
ACGTcount: A:0.15, C:0.22, G:0.18, T:0.45
Consensus pattern (19 bp):
TCGCATTGCGATTTTCATT
Found at i:227624 original size:33 final size:33
Alignment explanation
Indices: 227587--227796 Score: 223
Period size: 33 Copynumber: 6.2 Consensus size: 33
227577 AGAATCGCAA
*
227587 TGCGATTTTAATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
*
227620 TGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCAT
1 TGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--T
* * * * *
227658 TGCGATTCTCTCGTTGCG-ATTTTC-ATT-TCGCAT
1 TGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCGT
227691 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
227724 TGCGATTTTCATTTCCGCATTGCGATT-TCAT-GT
1 TGCGATTTTCATTT-CGCATTGCGATTCTC-TCGT
*
227757 TGGGATTTTCATTTCGCATTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
227790 TGCGATT
1 TGCGATT
227797 GTAATTTCCG
Statistics
Matches: 147, Mismatches: 15, Indels: 30
0.77 0.08 0.16
Matches are distributed among these distances:
31 9 0.06
32 18 0.12
33 76 0.52
34 13 0.09
35 5 0.03
36 4 0.03
37 2 0.01
38 8 0.05
39 3 0.02
40 9 0.06
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.46
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCATTGCGATTCTCTCGT
Found at i:227782 original size:52 final size:52
Alignment explanation
Indices: 227581--227751 Score: 315
Period size: 52 Copynumber: 3.3 Consensus size: 52
227571 AACGGGAGAA
* *
227581 TCGCAATGCGATTTTAATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
227633 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
227685 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
1 TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
227737 TCCGCATTGCGATTT
1 T-CGCATTGCGATTT
227752 CATGTTGGGA
Statistics
Matches: 116, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
52 103 0.89
53 13 0.11
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.45
Consensus pattern (52 bp):
TCGCATTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATT
Found at i:230308 original size:24 final size:24
Alignment explanation
Indices: 230274--230320 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
230264 CTGAAACATC
230274 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
230298 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
230321 GACCAAATTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 1 0.05
24 20 0.95
ACGTcount: A:0.38, C:0.21, G:0.15, T:0.26
Consensus pattern (24 bp):
ATCAAAATCCGGATATTGACCAAT
Found at i:231030 original size:20 final size:20
Alignment explanation
Indices: 231002--231211 Score: 249
Period size: 20 Copynumber: 10.4 Consensus size: 20
230992 AAATTTCAGT
* *
231002 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
231022 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
*
231042 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
* *
231062 GTTGCGATTTACGAATTATC
1 GTTGCGATTTACGGATTCTC
*
231082 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATTCTC
*
231102 GTTGCGATTTACGGATTATC
1 GTTGCGATTTACGGATTCTC
* *
231122 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
231142 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATTCTC
* * *
231162 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATTCTC
*
231182 GTTGCGATTTTTACGGATACTC
1 GTTGCGA--TTTACGGATTCTC
231204 GTTGCGAT
1 GTTGCGAT
231212 AGTAAGAATC
Statistics
Matches: 167, Mismatches: 21, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
20 148 0.89
22 19 0.11
ACGTcount: A:0.21, C:0.18, G:0.24, T:0.37
Consensus pattern (20 bp):
GTTGCGATTTACGGATTCTC
Found at i:231062 original size:40 final size:40
Alignment explanation
Indices: 231002--231272 Score: 282
Period size: 40 Copynumber: 6.7 Consensus size: 40
230992 AAATTTCAGT
* *
231002 GTTGTGATTTACAGATTCTCGTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
* *
231042 GTTGCGATTTACAGATTCTCGTTGCGATTTACGAATTATC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
*
231082 GTTGCGATTTACAGATTCTCGTTGCGATTTACGGATTATC
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
* * *
231122 GTTGCGATTTACGGATACGCGTTGCGATATACGGA-TA-C
1 GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
* *
231160 GCATTGCGATTTACGGATACGCGTTGCGATTTTTACGGA-TACTC
1 G--TTGCGATTTACAGATTCGCGTTGCGA--TTTACGGATTA-TC
* * * **
231204 GTTGCGATAGTA-AGAATCGCGTTGCGATTTATGTG-TTCGC
1 GTTGCGAT-TTACAGATTCGCGTTGCGATTTACG-GATTATC
* * *
231244 ATTGCGATTTTCATATTCGCGTTGCGATT
1 GTTGCGATTTACAGATTCGCGTTGCGATT
231273 CTAGAAAATC
Statistics
Matches: 201, Mismatches: 20, Indels: 20
0.83 0.08 0.08
Matches are distributed among these distances:
38 2 0.01
39 3 0.01
40 162 0.81
41 2 0.01
42 28 0.14
43 2 0.01
44 2 0.01
ACGTcount: A:0.21, C:0.17, G:0.24, T:0.38
Consensus pattern (40 bp):
GTTGCGATTTACAGATTCGCGTTGCGATTTACGGATTATC
Found at i:231243 original size:20 final size:20
Alignment explanation
Indices: 231220--231272 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 20
231210 ATAGTAAGAA
* *
231220 TCGCGTTGCGATTTAT-GTGT
1 TCGCGTTGCGATTT-TCATAT
*
231240 TCGCATTGCGATTTTCATAT
1 TCGCGTTGCGATTTTCATAT
231260 TCGCGTTGCGATT
1 TCGCGTTGCGATT
231273 CTAGAAAATC
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
19 1 0.04
20 27 0.96
ACGTcount: A:0.13, C:0.19, G:0.25, T:0.43
Consensus pattern (20 bp):
TCGCGTTGCGATTTTCATAT
Found at i:231249 original size:62 final size:62
Alignment explanation
Indices: 231103--231254 Score: 163
Period size: 62 Copynumber: 2.5 Consensus size: 62
231093 CAGATTCTCG
* *
231103 TTGCGATTTACGGATTATCG--TTGCGA--TTTACGGATACGCGTTGCGATATACGGATACGCA
1 TTGCGATTTACGGA-TA-CGCATTGCGATTTTTACGGATACGCGTTGCGATATAAGAATACGCA
* * *
231163 TTGCGATTTACGGATACGCGTTGCGATTTTTACGGATACTCGTTGCGATAGTAAGAAT-CGCG
1 TTGCGATTTACGGATACGCATTGCGATTTTTACGGATACGCGTTGCGATA-TAAGAATACGCA
* *
231225 TTGCGATTTATGTG-TTCGCATTGCGATTTT
1 TTGCGATTTACG-GATACGCATTGCGATTTT
231255 CATATTCGCG
Statistics
Matches: 79, Mismatches: 7, Indels: 10
0.82 0.07 0.10
Matches are distributed among these distances:
58 2 0.03
59 2 0.03
60 20 0.25
62 49 0.62
63 6 0.08
ACGTcount: A:0.21, C:0.17, G:0.26, T:0.36
Consensus pattern (62 bp):
TTGCGATTTACGGATACGCATTGCGATTTTTACGGATACGCGTTGCGATATAAGAATACGCA
Found at i:231325 original size:21 final size:21
Alignment explanation
Indices: 231240--231337 Score: 65
Period size: 21 Copynumber: 4.7 Consensus size: 21
231230 ATTTATGTGT
* *
231240 TCGCATTGCGATTTTC-ATAT
1 TCGCATTGCGATTTTCAAAAA
* *
231260 TCGCGTTGCGATTCT-AGAAAA
1 TCGCATTGCGATTTTCA-AAAA
* * ** **
231281 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTCAAAAA
*
231302 TCGCATTGCGATTTTCAAGAA
1 TCGCATTGCGATTTTCAAAAA
*
231323 TCGCGTTGCGATTTT
1 TCGCATTGCGATTTT
231338 GGAAACTGAT
Statistics
Matches: 57, Mismatches: 18, Indels: 5
0.71 0.22 0.06
Matches are distributed among these distances:
20 13 0.23
21 44 0.77
ACGTcount: A:0.23, C:0.19, G:0.20, T:0.37
Consensus pattern (21 bp):
TCGCATTGCGATTTTCAAAAA
Found at i:232220 original size:37 final size:37
Alignment explanation
Indices: 232150--232224 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
232140 TATTAAACCT
*
232150 TTTTATATTTTAAATTTTGTAAAAAAAATTATATAAA
1 TTTTATAATTTAAATTTTGTAAAAAAAATTATATAAA
* * *
232187 TTTTATGAATTTAAATTTTTTTAAGAAAA-TATATAAA
1 TTTTAT-AATTTAAATTTTGTAAAAAAAATTATATAAA
232224 T
1 T
232225 ATTTTCTAAC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 15 0.45
38 18 0.55
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (37 bp):
TTTTATAATTTAAATTTTGTAAAAAAAATTATATAAA
Found at i:236391 original size:55 final size:54
Alignment explanation
Indices: 236329--236820 Score: 510
Period size: 55 Copynumber: 9.0 Consensus size: 54
236319 AAATGCGAGC
* *
236329 TCGCTCCCTATTCCTTCAGGGAGTATATG-ACTCGAA-AAACATTCGACAAACAGGT
1 TCGCTCCCTATTCCTTCAGGGAGTATA-GAACTCGAACAATC-TTCAACAAAC-GGT
* *
236384 TCGCTCCCTATTCCTTCAGGGAGTATAGAACTCGAATAATCTTCTAA-AAGCGGGT
1 TCGCTCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTC-AACAAAC-GGT
* * * ** * *
236439 TCGCTCCCTATTTCTTCAGGGAGTACAGAACTCAAATTATCTTTAGCAAACGTGT
1 TCGCTCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACG-GT
* * *
236494 AT-GCTCCTTATTCGTTCAGGGAGTATA-AGACTCGAACAATCTTCAATAAACGGGT
1 -TCGCTCCCTATTCCTTCAGGGAGTATAGA-ACTCGAACAATCTTCAACAAAC-GGT
* * *
236549 CCGCTCCCTATTCGTTCAGGGAGTATAGAACTCGAACAATCTTTAACAAACGTGT
1 TCGCTCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACG-GT
* * * *
236604 AT-TCTCTCTATTCCTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGG
1 -TCGCTCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGGT
* * *
236658 TCTGCTCTCTATTCTTTCAGAGAGTATAGAACTCGAACAATCTTCAACAAACGGGT
1 TC-GCTCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAAC-GGT
* * * * * **
236714 CCGCTCTCTATTCTTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAACGCA
1 TCGCTCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGGT
* * *
236768 TCTGCTCCCTATTCCTTCAGAGAGTATAGGACTTGAACAATCTTCAACAAACG
1 TC-GCTCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACG
236821 TGTTTGCTTC
Statistics
Matches: 376, Mismatches: 45, Indels: 32
0.83 0.10 0.07
Matches are distributed among these distances:
53 1 0.00
54 8 0.02
55 357 0.95
56 10 0.03
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (54 bp):
TCGCTCCCTATTCCTTCAGGGAGTATAGAACTCGAACAATCTTCAACAAACGGT
Found at i:236636 original size:165 final size:163
Alignment explanation
Indices: 236331--236820 Score: 563
Period size: 165 Copynumber: 3.0 Consensus size: 163
236321 ATGCGAGCTC
* * * * * *
236331 GCTCCCTATTCCTTCAGGGAGTATATGACTCGAA-AAACATTCGACAAACAGGTTCGCTCCCTAT
1 GCTCCTTATTCCTTCAGGGAGTATAAGACTCGAACAATC-TTCAACAAACGGGTCCGCTCCCTAT
* * * * *
236395 TCCTTCAGGGAGTATAGAACTCGAATAATCTTCTAAAAGCGGGTTCGCTCCCTATTTCTTCAGGG
65 TCCTTCAGGGAGTATAGAACTCGAACAATCTT-TAAAAACGCGTT-GCTCCCTATTCCTTCAGAG
* ** * * *
236460 AGTACAGAACTCAAATTATCTTTAGCAAACGTGTAT
128 AGTATAGAACTCAAACAATCTTCAACAAACGGGTAT
* *
236496 GCTCCTTATTCGTTCAGGGAGTATAAGACTCGAACAATCTTCAATAAACGGGTCCGCTCCCTATT
1 GCTCCTTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGGGTCCGCTCCCTATT
* * * *
236561 CGTTCAGGGAGTATAGAACTCGAACAATCTTTAACAAACGTGTATTCTCTCTATTCCTTCAGAGA
66 CCTTCAGGGAGTATAGAACTCGAACAATCTTTAA-AAACGCGT-TGCTCCCTATTCCTTCAGAGA
* *
236626 GTATAGAACTCGAACAATCTTCAACAAACGGGTCT
129 GTATAGAACTCAAACAATCTTCAACAAACGGGTAT
* * *
236661 GCT-CTCTATTCTTTCAGAGAGTAT-AGAACTCGAACAATCTTCAACAAACGGGTCCGCTCTCTA
1 GCTCCT-TATTCCTTCAGGGAGTATAAG-ACTCGAACAATCTTCAACAAACGGGTCCGCTCCCTA
* * * *
236724 TTCTTTCAGAGAGTATAGAACTCGAACAATCTTCAATAAACGCATCTGCTCCCTATTCCTTCAGA
64 TTCCTTCAGGGAGTATAGAACTCGAACAATCTTTAA-AAACGCGT-TGCTCCCTATTCCTTCAGA
* **
236789 GAGTATAGGACTTGAACAATCTTCAACAAACG
127 GAGTATAGAACTCAAACAATCTTCAACAAACG
236821 TGTTTGCTTC
Statistics
Matches: 281, Mismatches: 39, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
164 7 0.02
165 270 0.96
166 4 0.01
ACGTcount: A:0.30, C:0.24, G:0.17, T:0.29
Consensus pattern (163 bp):
GCTCCTTATTCCTTCAGGGAGTATAAGACTCGAACAATCTTCAACAAACGGGTCCGCTCCCTATT
CCTTCAGGGAGTATAGAACTCGAACAATCTTTAAAAACGCGTTGCTCCCTATTCCTTCAGAGAGT
ATAGAACTCAAACAATCTTCAACAAACGGGTAT
Found at i:236931 original size:37 final size:37
Alignment explanation
Indices: 236824--236933 Score: 168
Period size: 37 Copynumber: 3.0 Consensus size: 37
236814 ACAAACGTGT
* *
236824 TTGCTTCACTACTCCTCCGTGAAGGCTTATAGA-TGAT
1 TTGCTTCACTACTCTTCCGTGAAGGCTTA-AGATTGAA
236861 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAA
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAA
* *
236898 TTGCTTCACTGCTCTTTCGTGAAGGCTTAAGATTGA
1 TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGA
236934 CTTGTTTCGA
Statistics
Matches: 68, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
36 3 0.04
37 65 0.96
ACGTcount: A:0.22, C:0.22, G:0.20, T:0.36
Consensus pattern (37 bp):
TTGCTTCACTACTCTTCCGTGAAGGCTTAAGATTGAA
Found at i:238385 original size:25 final size:23
Alignment explanation
Indices: 238363--238437 Score: 96
Period size: 24 Copynumber: 3.1 Consensus size: 23
238353 CATCGAAGTT
*
238363 CCGCGTAGAAATTTGTCCCGAAGGA
1 CCGCGCAG-AATTTGTCCCGAA-GA
*
238388 CCGCACAGAATTTGTCCCGAAAGA
1 CCGCGCAGAATTTGTCCCG-AAGA
238412 CCGCGCAGAATTTGTCCCGAATGA
1 CCGCGCAGAATTTGTCCCGAA-GA
238436 CC
1 CC
238438 ACATAGAAAA
Statistics
Matches: 45, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
23 2 0.04
24 35 0.78
25 8 0.18
ACGTcount: A:0.28, C:0.29, G:0.24, T:0.19
Consensus pattern (23 bp):
CCGCGCAGAATTTGTCCCGAAGA
Found at i:238445 original size:24 final size:24
Alignment explanation
Indices: 238372--238437 Score: 105
Period size: 24 Copynumber: 2.8 Consensus size: 24
238362 TCCGCGTAGA
*
238372 AATTTGTCCCGAAGGACCGCACAG
1 AATTTGTCCCGAAAGACCGCACAG
*
238396 AATTTGTCCCGAAAGACCGCGCAG
1 AATTTGTCCCGAAAGACCGCACAG
*
238420 AATTTGTCCCGAATGACC
1 AATTTGTCCCGAAAGACC
238438 ACATAGAAAA
Statistics
Matches: 39, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 39 1.00
ACGTcount: A:0.29, C:0.29, G:0.23, T:0.20
Consensus pattern (24 bp):
AATTTGTCCCGAAAGACCGCACAG
Found at i:240174 original size:21 final size:21
Alignment explanation
Indices: 240148--240215 Score: 84
Period size: 21 Copynumber: 3.2 Consensus size: 21
240138 GTATCGGTTC
240148 CCCCTTGAATGGTTACCGATT
1 CCCCTTGAATGGTTACCGATT
* * *
240169 CCCCTTGAATGGGTATCAATT
1 CCCCTTGAATGGTTACCGATT
*
240190 CCCATTGAAT-GTGTACCGATT
1 CCCCTTGAATGGT-TACCGATT
240211 CCCCT
1 CCCCT
240216 AGCCCAGAAA
Statistics
Matches: 38, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
20 1 0.03
21 37 0.97
ACGTcount: A:0.21, C:0.29, G:0.18, T:0.32
Consensus pattern (21 bp):
CCCCTTGAATGGTTACCGATT
Found at i:241658 original size:11 final size:11
Alignment explanation
Indices: 241639--241706 Score: 70
Period size: 11 Copynumber: 6.4 Consensus size: 11
241629 TCGAACCCCC
*
241639 TTTTATTTCTT
1 TTTTCTTTCTT
*
241650 TTTTCTTTCTC
1 TTTTCTTTCTT
*
241661 TTTT-TTTCATC
1 TTTTCTTTC-TT
*
241672 ATTT-TTTCTT
1 TTTTCTTTCTT
241682 TTTTCTTT-TT
1 TTTTCTTTCTT
241692 TTTTCTTTCTT
1 TTTTCTTTCTT
241703 TTTT
1 TTTT
241707 TTCATTTTTC
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
10 18 0.37
11 31 0.63
ACGTcount: A:0.04, C:0.15, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTTCTTTCTT
Found at i:241695 original size:28 final size:31
Alignment explanation
Indices: 241655--241729 Score: 84
Period size: 28 Copynumber: 2.5 Consensus size: 31
241645 TTCTTTTTTC
*
241655 TTTCTCTTTTTTTC-ATC-ATTTTTTC-TTT
1 TTTCTTTTTTTTTCTATCTATTTTTTCATTT
* *
241683 TTTCTTTTTTTTTCTTTCTTTTTTTTCATTT
1 TTTCTTTTTTTTTCTATCTATTTTTTCATTT
*
241714 TTCTCTTTTTATTTCT
1 TT-TCTTTTTTTTTCT
241730 TCTTCAAGCG
Statistics
Matches: 39, Mismatches: 4, Indels: 4
0.83 0.09 0.09
Matches are distributed among these distances:
28 13 0.33
29 2 0.05
30 7 0.18
31 5 0.13
32 12 0.31
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.79
Consensus pattern (31 bp):
TTTCTTTTTTTTTCTATCTATTTTTTCATTT
Found at i:241705 original size:38 final size:40
Alignment explanation
Indices: 241644--241723 Score: 114
Period size: 39 Copynumber: 2.0 Consensus size: 40
241634 CCCCCTTTTA
241644 TTTCTTTTTTCTTTCTCTTTTTTTCATCATTTTT-TCTTT
1 TTTCTTTTTTCTTTCTCTTTTTTTCATCATTTTTCTCTTT
241683 TTTCTTTTTT-TTTCTTTCTTTTTTT--TCATTTTTCTCTTT
1 TTTCTTTTTTCTTTC--TCTTTTTTTCATCATTTTTCTCTTT
241722 TT
1 TT
241724 ATTTCTTCTT
Statistics
Matches: 38, Mismatches: 0, Indels: 6
0.86 0.00 0.14
Matches are distributed among these distances:
38 12 0.32
39 17 0.45
40 9 0.24
ACGTcount: A:0.04, C:0.16, G:0.00, T:0.80
Consensus pattern (40 bp):
TTTCTTTTTTCTTTCTCTTTTTTTCATCATTTTTCTCTTT
Found at i:241715 original size:11 final size:10
Alignment explanation
Indices: 241639--241730 Score: 64
Period size: 10 Copynumber: 9.1 Consensus size: 10
241629 TCGAACCCCC
*
241639 TTTTATTTCT
1 TTTTTTTTCT
241649 TTTTTCTTTCT
1 TTTTT-TTTCT
*
241660 CTTTTTTTCAT
1 TTTTTTTTC-T
**
241671 CATTTTTTCT
1 TTTTTTTTCT
241681 TTTTTCTTT-T
1 TTTTT-TTTCT
241691 TTTTTCTTTC-
1 TTTTT-TTTCT
241701 TTTTTTTTC-
1 TTTTTTTTCT
* *
241710 ATTTTTCTCT
1 TTTTTTTTCT
*
241720 TTTTATTTCT
1 TTTTTTTTCT
241730 T
1 T
241731 CTTCAAGCGA
Statistics
Matches: 67, Mismatches: 10, Indels: 10
0.77 0.11 0.11
Matches are distributed among these distances:
9 11 0.16
10 35 0.52
11 21 0.31
ACGTcount: A:0.05, C:0.15, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTTTTTTCT
Found at i:241729 original size:42 final size:40
Alignment explanation
Indices: 241638--241730 Score: 113
Period size: 38 Copynumber: 2.3 Consensus size: 40
241628 CTCGAACCCC
241638 CTTTTATTTCTTTTTTCTTTCTCTTTTTTTCATCATTTTTT
1 CTTTTATTTCTTTTTTCTTTCTCTTTTTTT-ATCATTTTTT
241679 C-TTT-TTTCTTTTTT-TTTCTTTCTTTTTTT-TCATTTTTCT
1 CTTTTATTTCTTTTTTCTTTC--TCTTTTTTTATCATTTTT-T
241718 CTTTTTATTTCTT
1 C-TTTTATTTCTT
241731 CTTCAAGCGA
Statistics
Matches: 46, Mismatches: 0, Indels: 11
0.81 0.00 0.19
Matches are distributed among these distances:
38 12 0.26
39 12 0.26
40 12 0.26
41 4 0.09
42 6 0.13
ACGTcount: A:0.05, C:0.16, G:0.00, T:0.78
Consensus pattern (40 bp):
CTTTTATTTCTTTTTTCTTTCTCTTTTTTTATCATTTTTT
Found at i:246782 original size:24 final size:24
Alignment explanation
Indices: 246755--246809 Score: 101
Period size: 24 Copynumber: 2.3 Consensus size: 24
246745 ATCTGCACAT
*
246755 CAACCTTTTTCCCCTTATCAACCG
1 CAACCTTGTTCCCCTTATCAACCG
246779 CAACCTTGTTCCCCTTATCAACCG
1 CAACCTTGTTCCCCTTATCAACCG
246803 CAACCTT
1 CAACCTT
246810 CTTCTCAGAC
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 30 1.00
ACGTcount: A:0.22, C:0.42, G:0.05, T:0.31
Consensus pattern (24 bp):
CAACCTTGTTCCCCTTATCAACCG
Found at i:261785 original size:24 final size:24
Alignment explanation
Indices: 261758--261804 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
261748 ACTAATGCTA
261758 AACAA-AATAAATAAATAAAATATT
1 AACAATAATAAA-AAATAAAATATT
* *
261782 AACAATAATTAAAATTAAAATAT
1 AACAATAATAAAAAATAAAATAT
261805 AATTTAAAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
24 15 0.75
25 5 0.25
ACGTcount: A:0.68, C:0.04, G:0.00, T:0.28
Consensus pattern (24 bp):
AACAATAATAAAAAATAAAATATT
Found at i:264157 original size:43 final size:43
Alignment explanation
Indices: 264061--264173 Score: 113
Period size: 43 Copynumber: 2.6 Consensus size: 43
264051 ATGATATGTC
* * * * *
264061 ATATAGTGGCGTTTGTGAATGTA-AAACGCCGCTATTGACTACGT
1 ATATAGTGGCATTT-T-ATTGTACAAACGCCGATATTAACTAAGT
* *
264105 ATATAGTGGCGTTTTATTTTACAAACGCCGATATTAACTAAGT
1 ATATAGTGGCATTTTATTGTACAAACGCCGATATTAACTAAGT
*
264148 A-ATTTGTGGCATTTTATTGTACAAAC
1 ATA-TAGTGGCATTTTATTGTACAAAC
264174 TCCGCTAATT
Statistics
Matches: 59, Mismatches: 8, Indels: 5
0.82 0.11 0.07
Matches are distributed among these distances:
42 5 0.08
43 40 0.68
44 14 0.24
ACGTcount: A:0.30, C:0.14, G:0.19, T:0.36
Consensus pattern (43 bp):
ATATAGTGGCATTTTATTGTACAAACGCCGATATTAACTAAGT
Found at i:267846 original size:3 final size:3
Alignment explanation
Indices: 267838--267885 Score: 96
Period size: 3 Copynumber: 16.0 Consensus size: 3
267828 AATAAATGAG
267838 TAA TAA TAA 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 TAA TAA TAA
267886 ATATAAATAT
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 45 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:268937 original size:21 final size:20
Alignment explanation
Indices: 268904--268952 Score: 64
Period size: 21 Copynumber: 2.5 Consensus size: 20
268894 AAAAAAGGAA
*
268904 AAAATAATTAAAAGAAGAAT
1 AAAATAATAAAAAGAAGAAT
*
268924 AAAATAAATAAAAAGAATAAT
1 AAAAT-AATAAAAAGAAGAAT
268945 -AAATAATA
1 AAAATAATA
268953 TATAAATAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 4 0.15
20 9 0.35
21 13 0.50
ACGTcount: A:0.73, C:0.00, G:0.06, T:0.20
Consensus pattern (20 bp):
AAAATAATAAAAAGAAGAAT
Found at i:269075 original size:36 final size:36
Alignment explanation
Indices: 269028--269283 Score: 201
Period size: 38 Copynumber: 6.6 Consensus size: 36
269018 AGTATTTTCG
269028 AAACTATATTATATATATATATT-AAAATATTTTCAA
1 AAACTATATTATATATATATATTCAAAATATTTT-AA
*
269064 AAACTATATTATATATATATATATATATATTCAAAATGTTTTTAA
1 AAAC-------TATAT-TATATATATATATTCAAAAT-ATTTTAA
* * *
269109 AAACTATA-TATTAAATATAAGTTTTCAAAATGTTTTAA
1 AAACTATATTA-TATATAT-A-TATTCAAAATATTTTAA
* * *
269147 AAACTATATAATATATAAATGTTTTCAAAATATTTTAA
1 AAACTATAT--TATATATATATATTCAAAATATTTTAA
*
269185 AAACTATATTATATATATATATTCAAAATGTTTTAA
1 AAACTATATTATATATATATATTCAAAATATTTTAA
* * * *
269221 AAACTATATAATATATATTTTTTTCAAAAATGTTTTAAAA
1 AAACTATATTATATATA-TATATTC-AAAATATTTT--AA
* *
269261 AAACTATATAATATATATCTATT
1 AAACTATATTATATATATATATT
269284 TTCAAAAACC
Statistics
Matches: 183, Mismatches: 17, Indels: 37
0.77 0.07 0.16
Matches are distributed among these distances:
36 45 0.25
37 11 0.06
38 54 0.30
39 13 0.07
40 24 0.13
41 2 0.01
43 5 0.03
44 14 0.08
45 11 0.06
46 4 0.02
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.44
Consensus pattern (36 bp):
AAACTATATTATATATATATATTCAAAATATTTTAA
Found at i:269082 original size:34 final size:36
Alignment explanation
Indices: 269015--269085 Score: 117
Period size: 36 Copynumber: 2.0 Consensus size: 36
269005 ACGTTTTCAA
*
269015 AAAAGTATTTTCGAAACTATATTATATATATATATT
1 AAAAGTATTTTCAAAACTATATTATATATATATATT
269051 AAAA-TATTTTCAAAAACTATATTATATATATATAT
1 AAAAGTATTTTC-AAAACTATATTATATATATATAT
269086 ATATATATTC
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
35 7 0.21
36 26 0.79
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.44
Consensus pattern (36 bp):
AAAAGTATTTTCAAAACTATATTATATATATATATT
Found at i:269097 original size:34 final size:36
Alignment explanation
Indices: 269028--269099 Score: 112
Period size: 36 Copynumber: 2.1 Consensus size: 36
269018 AGTATTTTCG
*
269028 AAACTATATTATATATATATATTAAAATATTTTCAA
1 AAACTATATTATATATATATATTAAAATATATTCAA
*
269064 AAACTATATTATATATATATA-T-ATATATATTCAA
1 AAACTATATTATATATATATATTAAAATATATTCAA
269098 AA
1 AA
269100 TGTTTTTAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
34 12 0.35
35 1 0.03
36 21 0.62
ACGTcount: A:0.51, C:0.06, G:0.00, T:0.43
Consensus pattern (36 bp):
AAACTATATTATATATATATATTAAAATATATTCAA
Found at i:269117 original size:38 final size:37
Alignment explanation
Indices: 269075--269290 Score: 258
Period size: 38 Copynumber: 5.7 Consensus size: 37
269065 AACTATATTA
*
269075 TATATATATATATATATATTCAAAATGTTTTTAAAAAC
1 TATATATATATATATATTTTCAAAATG-TTTTAAAAAC
*
269113 TATATAT-TAAATATAAGTTTTCAAAATGTTTTAAAAAC
1 TATATATATATATAT-A-TTTTCAAAATGTTTTAAAAAC
* * *
269151 TATATAATATATAAATGTTTTCAAAATATTTTAAAAAC
1 TATAT-ATATATATATATTTTCAAAATGTTTTAAAAAC
*
269189 TATAT-TATATATATATATTCAAAATGTTTTAAAAAC
1 TATATATATATATATATTTTCAAAATGTTTTAAAAAC
*
269225 TATATA-ATATATATTTTTTTCAAAAATGTTTTAAAAAAAC
1 TATATATATATATA-TATTTTC-AAAATGTTTT--AAAAAC
*
269265 TATATAATATATATCTATTTTCAAAA
1 TATAT-ATATATATATATTTTCAAAA
269291 ACCGATTTTT
Statistics
Matches: 153, Mismatches: 14, Indels: 20
0.82 0.07 0.11
Matches are distributed among these distances:
36 39 0.25
37 11 0.07
38 58 0.38
39 12 0.08
40 20 0.13
41 7 0.05
42 6 0.04
ACGTcount: A:0.48, C:0.06, G:0.03, T:0.44
Consensus pattern (37 bp):
TATATATATATATATATTTTCAAAATGTTTTAAAAAC
Found at i:270312 original size:41 final size:41
Alignment explanation
Indices: 270238--270580 Score: 192
Period size: 41 Copynumber: 8.2 Consensus size: 41
270228 AAGTATGAGA
* * *
270238 CTTTAGCGGCATTTGCATAAAAACACCGCTAAAGTACAAGT
1 CTTTAGCGGCATTTGTATAAAAACGCCACTAAAGTACAAGT
* * *
270279 CTTTAGCGGCATTTGTATATAAACGCCATTAAAGCACAAGT
1 CTTTAGCGGCATTTGTATAAAAACGCCACTAAAGTACAAGT
* * *
270320 CTTTAGCAACATTTTTGTGGCGTTTGTATAAAAACGCCGCTAAAATACGAA-T
1 CTTTAG---C--------GGCATTTGTATAAAAACGCCACTAAAGTAC-AAGT
* * * * *
270372 CTATAGCGGCGTCTGTATAAAAATGCCACTAAAGTACGAGT
1 CTTTAGCGGCATTTGTATAAAAACGCCACTAAAGTACAAGT
* * * *
270413 CTTTAGCGGCATTTTTATATAAACGCCACTAAAGTGCGAGT
1 CTTTAGCGGCATTTGTATAAAAACGCCACTAAAGTACAAGT
** * * * * **
270454 CTTTAGCAACATTT-TATACAAATGTCGCTAAAGTATGAGT
1 CTTTAGCGGCATTTGTATAAAAACGCCACTAAAGTACAAGT
** * * *
270494 CTACAACGGC-GTT-TATATAAACGCCACTAAAGTAC-AGT
1 CTTTAGCGGCATTTGTATAAAAACGCCACTAAAGTACAAGT
** * * * * *
270532 CTTTAGCAACGTTTATATAAAAACACCACCAAAGTACGAGT
1 CTTTAGCGGCATTTGTATAAAAACGCCACTAAAGTACAAGT
*
270573 ATTTAGCG
1 CTTTAGCG
270581 ATGTTTGTTA
Statistics
Matches: 231, Mismatches: 55, Indels: 32
0.73 0.17 0.10
Matches are distributed among these distances:
38 8 0.03
39 21 0.09
40 45 0.19
41 123 0.53
44 1 0.00
49 1 0.00
52 30 0.13
53 2 0.01
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.29
Consensus pattern (41 bp):
CTTTAGCGGCATTTGTATAAAAACGCCACTAAAGTACAAGT
Found at i:270414 original size:93 final size:93
Alignment explanation
Indices: 270249--270428 Score: 227
Period size: 93 Copynumber: 1.9 Consensus size: 93
270239 TTTAGCGGCA
* * * * *
270249 TTTGCATAAAAACACCGCTAAAGTACAAGTCTTTAGCGGCATTTGTATATAAACGCCATTAAAGC
1 TTTGCATAAAAACACCGCTAAAATACAAGTCTATAGCGGCATCTGTATAAAAACGCCACTAAAGC
270314 ACAAGTCTTTAGCAACATTTTTGTGGCG
66 ACAAGTCTTTAGCAACATTTTTGTGGCG
* * * *
270342 TTTGTATAAAAACGCCGCTAAAATACGAA-TCTATAGCGGCGTCTGTATAAAAATGCCACTAAAG
1 TTTGCATAAAAACACCGCTAAAATAC-AAGTCTATAGCGGCATCTGTATAAAAACGCCACTAAAG
* * **
270406 TACGAGTCTTTAGCGGCATTTTT
65 CACAAGTCTTTAGCAACATTTTT
270429 ATATAAACGC
Statistics
Matches: 73, Mismatches: 13, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
93 71 0.97
94 2 0.03
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (93 bp):
TTTGCATAAAAACACCGCTAAAATACAAGTCTATAGCGGCATCTGTATAAAAACGCCACTAAAGC
ACAAGTCTTTAGCAACATTTTTGTGGCG
Found at i:270485 original size:40 final size:41
Alignment explanation
Indices: 270387--270579 Score: 162
Period size: 40 Copynumber: 4.8 Consensus size: 41
270377 GCGGCGTCTG
* * **
270387 TATAAAAATGCCACTAAAGTACGAGTCTTTAGCGGCATTTT
1 TATACAAACGCCACTAAAGTACGAGTCTTTAGCAACATTTT
* *
270428 TATATAAACGCCACTAAAGTGCGAGTCTTTAGCAACA-TTT
1 TATACAAACGCCACTAAAGTACGAGTCTTTAGCAACATTTT
* * * * ***
270468 TATACAAATGTCGCTAAAGTATGAGTC--TA-CAACGGCGTT
1 TATACAAACGCCACTAAAGTACGAGTCTTTAGCAAC-ATTTT
* * *
270507 TATATAAACGCCACTAAAGTAC-AGTCTTTAGCAACGTTTA
1 TATACAAACGCCACTAAAGTACGAGTCTTTAGCAACATTTT
* * * *
270547 TATAAAAACACCACCAAAGTACGAGTATTTAGC
1 TATACAAACGCCACTAAAGTACGAGTCTTTAGC
270580 GATGTTTGTT
Statistics
Matches: 121, Mismatches: 25, Indels: 12
0.77 0.16 0.08
Matches are distributed among these distances:
37 4 0.03
38 6 0.05
39 19 0.16
40 47 0.39
41 45 0.37
ACGTcount: A:0.37, C:0.19, G:0.16, T:0.28
Consensus pattern (41 bp):
TATACAAACGCCACTAAAGTACGAGTCTTTAGCAACATTTT
Found at i:270566 original size:79 final size:79
Alignment explanation
Indices: 270426--270572 Score: 197
Period size: 79 Copynumber: 1.9 Consensus size: 79
270416 TAGCGGCATT
* * *** * * *
270426 TTTATATAAACGCCACTAAAGTGCGAGTCTTTAGCAACATTTTATACAAATGTCGCTAAAGTATG
1 TTTATATAAACGCCACTAAAGTACGAGTCTTTAGCAACATTTTATAAAAACACCACCAAAGTACG
270491 AGTCTACAACGGCG
66 AGTCTACAACGGCG
*
270505 TTTATATAAACGCCACTAAAGTAC-AGTCTTTAGCAACGTTTATATAAAAACACCACCAAAGTAC
1 TTTATATAAACGCCACTAAAGTACGAGTCTTTAGCAACATTT-TATAAAAACACCACCAAAGTAC
270569 GAGT
65 GAGT
270573 ATTTAGCGAT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
78 16 0.28
79 42 0.72
ACGTcount: A:0.37, C:0.20, G:0.15, T:0.28
Consensus pattern (79 bp):
TTTATATAAACGCCACTAAAGTACGAGTCTTTAGCAACATTTTATAAAAACACCACCAAAGTACG
AGTCTACAACGGCG
Found at i:273698 original size:19 final size:18
Alignment explanation
Indices: 273655--273703 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 18
273645 TTTGCTTGAG
*
273655 ATGTTATCC-TCCGTGAA
1 ATGTTATCCTTCAGTGAA
273672 ATAAGTTATCCTTCAAGTGAA
1 AT--GTTATCCTTC-AGTGAA
273693 ATGTTATCCTT
1 ATGTTATCCTT
273704 TTTGAGAAAT
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
17 2 0.07
19 16 0.59
20 2 0.07
21 7 0.26
ACGTcount: A:0.29, C:0.18, G:0.14, T:0.39
Consensus pattern (18 bp):
ATGTTATCCTTCAGTGAA
Found at i:281222 original size:20 final size:21
Alignment explanation
Indices: 281175--281227 Score: 65
Period size: 20 Copynumber: 2.6 Consensus size: 21
281165 TAGATGAACA
*
281175 ATATCGATACT-AATGCAAGT
1 ATATCGATACTAAAAGCAAGT
*
281195 AGTATCGATACTAAAAGGAAG-
1 A-TATCGATACTAAAAGCAAGT
281216 ATATCGATACTA
1 ATATCGATACTA
281228 TGGATTTCAG
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
20 12 0.41
21 11 0.38
22 6 0.21
ACGTcount: A:0.43, C:0.13, G:0.17, T:0.26
Consensus pattern (21 bp):
ATATCGATACTAAAAGCAAGT
Found at i:281797 original size:230 final size:231
Alignment explanation
Indices: 281382--281844 Score: 796
Period size: 230 Copynumber: 2.0 Consensus size: 231
281372 CTTTTTAAGT
281382 ATTATCAAAAGATAAATGTTAGAAAGTATAATAACATTGTATGGTATGTTTAATAATGGATGCTT
1 ATTATCAAAAGATAAATGTTAGAAAGTATAATAACATTGTATGGTATGTTTAATAATGGATGCTT
281447 GTGTAGATCGTAACCAAGCTCCAGAGCAAGCAAGAAAAAAGGGCAAAGATAAAGTTGTCGAATAG
66 GTGTAGATCGTAACCAAGCTCCAGAGCAAGCAAG--AAAAGGGCAAAGATAAAGTTGTCGAATAG
*
281512 TTGGACATCCTTAAAGCATACTAGTGAGGCATCATGTGAGTGCATTTATTGTACTTATATGAGAT
129 TTGGACATCCTTAAAGCATACTAGTGAGGCATCACGTGAGTGCATTTATTGTACTTATATGAGAT
281577 GAGGAAGACT-C-ATGAGTCAACCTCGAAGGTTTTGTTAA
194 --GGAAGACTCCGATGAGTCAACCTCGAAGGTTTTGTTAA
281615 ATTATCAAAAGAATAAATGTTAGAAAGTATAATAACATTGT-TGGTATGTTTAATAATGGATGCT
1 ATTATCAAAAG-ATAAATGTTAGAAAGTATAATAACATTGTATGGTATGTTTAATAATGGATGCT
281679 TGTGTAGATCGTAACCAAGCTCCAGAGTCAAG-AAG-AAAGGGCAAAGATAAAGTTGTCGAATAG
65 TGTGTAGATCGTAACCAAGCTCCAGAG-CAAGCAAGAAAAGGGCAAAGATAAAGTTGTCGAATAG
281742 TTGGACATCCTTAAAGCATACTA-TGAGGCATATCACGTGAGTGCA-TTATTGTACTTATATGAG
129 TTGGACATCCTTAAAGCATACTAGTGAGGC--ATCACGTGAGTGCATTTATTGTACTTATATGAG
281805 ATGGAAGACTCCGATGAGTCAACCTCGAAGGTTTTGTTAA
192 ATGGAAGACTCCGATGAGTCAACCTCGAAGGTTTTGTTAA
281845 TGTATGTTTT
Statistics
Matches: 223, Mismatches: 1, Indels: 15
0.93 0.00 0.06
Matches are distributed among these distances:
228 8 0.04
229 7 0.03
230 98 0.44
231 13 0.06
233 64 0.29
234 33 0.15
ACGTcount: A:0.37, C:0.12, G:0.22, T:0.29
Consensus pattern (231 bp):
ATTATCAAAAGATAAATGTTAGAAAGTATAATAACATTGTATGGTATGTTTAATAATGGATGCTT
GTGTAGATCGTAACCAAGCTCCAGAGCAAGCAAGAAAAGGGCAAAGATAAAGTTGTCGAATAGTT
GGACATCCTTAAAGCATACTAGTGAGGCATCACGTGAGTGCATTTATTGTACTTATATGAGATGG
AAGACTCCGATGAGTCAACCTCGAAGGTTTTGTTAA
Found at i:282175 original size:112 final size:111
Alignment explanation
Indices: 282043--282271 Score: 352
Period size: 112 Copynumber: 2.1 Consensus size: 111
282033 GTCATAGGTG
* * * * *
282043 CATTTCGACATACTTTGTGTATGATAG-TATCGATCGATTTTGTTTAATGCATAACGGTGCATTT
1 CATTTCAACATACTTCGTGTATGAAAGTTATCGATCAATTTTGCTTAATGCATAACGGTGCATTT
** * *
282107 TTGGCATAAAAGGTGTTCACCCATGGTATTCATGATGAGGTGAATTAC
66 TCAGCATAAAAGGTG-CCACCCATGGTATTCATAATGAGGTG-ATTAC
282155 CATTTCAACATACTTCGTGTATGAAAGTTATCGATCAATTTTGCTTAATGCATAACGGTGCATTT
1 CATTTCAACATACTTCGTGTATGAAAGTTATCGATCAATTTTGCTTAATGCATAACGGTGCATTT
282220 TCAGCATAAAAGGTGCCACCCATGGTATTCATAATGAGGTGATTAC
66 TCAGCATAAAAGGTGCCACCCATGGTATTCATAATGAGGTGATTAC
282266 CATTTC
1 CATTTC
282272 CGCACTTCGG
Statistics
Matches: 107, Mismatches: 9, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
111 11 0.10
112 48 0.45
113 48 0.45
ACGTcount: A:0.28, C:0.17, G:0.19, T:0.36
Consensus pattern (111 bp):
CATTTCAACATACTTCGTGTATGAAAGTTATCGATCAATTTTGCTTAATGCATAACGGTGCATTT
TCAGCATAAAAGGTGCCACCCATGGTATTCATAATGAGGTGATTAC
Found at i:283243 original size:30 final size:29
Alignment explanation
Indices: 283207--283373 Score: 106
Period size: 30 Copynumber: 5.5 Consensus size: 29
283197 CCGAAATTTG
283207 TTTGGTTCGGTTAATAATTTTCAAATAAGT
1 TTTGGTTCGGTTAATAATTTTCAAATAA-T
* * ****
283237 TTTGGTTCGATTAACCGAATTTTTGCTTCAA-
1 TTTGGTTCGGTTAA--TAATTTTCAAAT-AAT
** *
283268 -TTAATTCGGTTAATAATTTTCAAAAAAAT
1 TTTGGTTCGGTTAATAATTTTC-AAATAAT
283297 TCGATTGAGTTCGGTTAATAATTTTCAAATTAA-
1 T---TTG-GTTCGGTTAATAATTTTCAAA-TAAT
* *
283330 TTCGGTTCAGTTAATAATTTTCAAATAAAT
1 TTTGGTTCGGTTAATAATTTTCAAAT-AAT
*
283360 TTTGGTTCGATTAA
1 TTTGGTTCGGTTAA
283374 CCAAACCGAA
Statistics
Matches: 101, Mismatches: 23, Indels: 26
0.67 0.15 0.17
Matches are distributed among these distances:
28 9 0.09
29 22 0.22
30 36 0.36
32 7 0.07
33 8 0.08
34 19 0.19
ACGTcount: A:0.32, C:0.10, G:0.14, T:0.44
Consensus pattern (29 bp):
TTTGGTTCGGTTAATAATTTTCAAATAAT
Found at i:283332 original size:34 final size:29
Alignment explanation
Indices: 283272--283360 Score: 106
Period size: 29 Copynumber: 2.9 Consensus size: 29
283262 CTTCAATTAA
*
283272 TTCGGTTAATAATTTTCAAAAAAATTCGATTGAG
1 TTCGGTTAATAATTTTCAAATAAATTC----G-G
*
283306 TTCGGTTAATAATTTTCAAATTAATTCGG
1 TTCGGTTAATAATTTTCAAATAAATTCGG
*
283335 TTCAGTTAATAATTTTCAAATAAATT
1 TTCGGTTAATAATTTTCAAATAAATT
283361 TTGGTTCGAT
Statistics
Matches: 51, Mismatches: 4, Indels: 5
0.85 0.07 0.08
Matches are distributed among these distances:
29 25 0.49
30 1 0.02
34 25 0.49
ACGTcount: A:0.37, C:0.09, G:0.11, T:0.43
Consensus pattern (29 bp):
TTCGGTTAATAATTTTCAAATAAATTCGG
Found at i:291501 original size:19 final size:20
Alignment explanation
Indices: 291477--291529 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
291467 CTTAGCATAT
291477 TAAAAATAAAAACTT-AAAA
1 TAAAAATAAAAACTTGAAAA
*
291496 TAAAAATGAAAACTTGAAAA
1 TAAAAATAAAAACTTGAAAA
*
291516 TAAAGA-AAAAACTT
1 TAAAAATAAAAACTT
291530 TATAAAACCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
19 21 0.70
20 9 0.30
ACGTcount: A:0.68, C:0.06, G:0.06, T:0.21
Consensus pattern (20 bp):
TAAAAATAAAAACTTGAAAA
Found at i:295188 original size:22 final size:23
Alignment explanation
Indices: 295161--295222 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
295151 CGATTCCCCT
295161 AGGGGGAATCGGTTCCCCTTCAA
1 AGGGGGAATCGGTTCCCCTTCAA
*
295184 AGGGGGAATCAGTTCCCCTTC-A
1 AGGGGGAATCGGTTCCCCTTCAA
* *
295206 AGGGGGTATCGATTCCC
1 AGGGGGAATCGGTTCCC
295223 TCTGCCCTAT
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
22 15 0.43
23 20 0.57
ACGTcount: A:0.21, C:0.26, G:0.31, T:0.23
Consensus pattern (23 bp):
AGGGGGAATCGGTTCCCCTTCAA
Found at i:303968 original size:4 final size:4
Alignment explanation
Indices: 303959--303993 Score: 52
Period size: 4 Copynumber: 8.5 Consensus size: 4
303949 TCAGTTTTGT
*
303959 AATA AATA AAGTA AATA AATG AATA AATA AATA AA
1 AATA AATA AA-TA AATA AATA AATA AATA AATA AA
303994 ATATTTATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
4 24 0.86
5 4 0.14
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (4 bp):
AATA
Found at i:306470 original size:15 final size:15
Alignment explanation
Indices: 306450--306486 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
306440 TGAGACCTTA
* *
306450 CCCGCCCCGCTTCCG
1 CCCGCCCCACATCCG
306465 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
306480 CCCGCCC
1 CCCGCCC
306487 ACTAAGTATC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.05, C:0.70, G:0.16, T:0.08
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:308108 original size:42 final size:41
Alignment explanation
Indices: 308002--308158 Score: 117
Period size: 42 Copynumber: 3.8 Consensus size: 41
307992 AATTAATACT
* * *
308002 TTAGCGGCGTTTTTTCCACAAACGCCGCAATAGAGTATAAA
1 TTAGTGGCGTTTTTACCACAAACGCCGCAATAAAGTATAAA
* * * *
308043 TT--TTGCGGTGATTTAGCCA-AAACGCCGTAATAAAGTGGTAAA
1 TTAGTGGC-GT-TTTTA-CCACAAACGCCGCAATAAAGT-ATAAA
* * * *
308085 TTAGTGGCGTTTTTACCACAAACGCCGCAATATATTACACA
1 TTAGTGGCGTTTTTACCACAAACGCCGCAATAAAGTATAAA
308126 TATAGTGGCGTTTGTT-CCTA-AAACGCCGCAATA
1 T-TAGTGGCGTTT-TTACC-ACAAACGCCGCAATA
308159 GTGTTAATCA
Statistics
Matches: 91, Mismatches: 15, Indels: 19
0.73 0.12 0.15
Matches are distributed among these distances:
39 2 0.02
40 2 0.02
41 26 0.29
42 53 0.58
43 5 0.05
44 3 0.03
ACGTcount: A:0.31, C:0.20, G:0.20, T:0.29
Consensus pattern (41 bp):
TTAGTGGCGTTTTTACCACAAACGCCGCAATAAAGTATAAA
Found at i:308206 original size:41 final size:41
Alignment explanation
Indices: 308086--308345 Score: 280
Period size: 41 Copynumber: 6.3 Consensus size: 41
308076 AGTGGTAAAT
** * *
308086 TAGTGGCGTTTTTACCACAAACGCCGCAATA-TATTACA-CATA
1 TAGTGGCGTTTTT-GTACAAACGCCACAATAGTGTTA-ATCA-A
* *
308128 TAGTGGCGTTTGTTCCTA-AAACGCCGCAATAGTGTTAATCAA
1 TAGTGGCGTTT-TT-GTACAAACGCCACAATAGTGTTAATCAA
*
308170 TAGTGGCGTTTTTGTACAAACTCCACAATAGTGTTAATCAA
1 TAGTGGCGTTTTTGTACAAACGCCACAATAGTGTTAATCAA
* *
308211 TAGTGGCGTTTTTATACAAACGTCACAATAGTGTTAATCAA
1 TAGTGGCGTTTTTGTACAAACGCCACAATAGTGTTAATCAA
* *
308252 TAGTGGCGTTTTTAG-ACAAACGCCGCAATAGTGTTAAACAA
1 TAGTGGCGTTTTT-GTACAAACGCCACAATAGTGTTAATCAA
* * *
308293 TAGTGGCATTTAT-TAGCAAACGCCACAATAATG-TAATCAA
1 TAGTGGCGTTTTTGTA-CAAACGCCACAATAGTGTTAATCAA
*
308333 AAGTGGCGTTTTT
1 TAGTGGCGTTTTT
308346 TTGTATAAAC
Statistics
Matches: 190, Mismatches: 21, Indels: 16
0.84 0.09 0.07
Matches are distributed among these distances:
40 19 0.10
41 124 0.65
42 37 0.19
43 10 0.05
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (41 bp):
TAGTGGCGTTTTTGTACAAACGCCACAATAGTGTTAATCAA
Found at i:308313 original size:123 final size:124
Alignment explanation
Indices: 308086--308345 Score: 325
Period size: 123 Copynumber: 2.1 Consensus size: 124
308076 AGTGGTAAAT
* **
308086 TAGTGGCGTTTTTACCACAAACGCCGCAATATATTACACATATAGTGGCGTTTGTTCCTAAAACG
1 TAGTGGCGTTTTTACCACAAACGCCACAATATATTACACATATAGTGGCGTTTGTTCAGAAAACG
* * * * *
308151 CCGCAATAGTGTTAATCAATAGTGGCGTTTTTGTACAAACTCCACAATAGTGTTAATCAA
66 CCGCAATAGTGTTAAACAATAGTGGCATTTATGTACAAACGCCACAATAATG-TAATCAA
* * *
308211 TAGTGGCGTTTTTA-TACAAACGTCACAATAGTGTTA-ATCA-ATAGTGGCGTTT-TT-AGACAA
1 TAGTGGCGTTTTTACCACAAACGCCACAATA-TATTACA-CATATAGTGGCGTTTGTTCAGA-AA
308271 ACGCCGCAATAGTGTTAAACAATAGTGGCATTTAT-TAGCAAACGCCACAATAATGTAATCAA
63 ACGCCGCAATAGTGTTAAACAATAGTGGCATTTATGTA-CAAACGCCACAATAATGTAATCAA
*
308333 AAGTGGCGTTTTT
1 TAGTGGCGTTTTT
308346 TTGTATAAAC
Statistics
Matches: 119, Mismatches: 12, Indels: 11
0.84 0.08 0.08
Matches are distributed among these distances:
122 22 0.18
123 51 0.43
124 26 0.22
125 20 0.17
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Consensus pattern (124 bp):
TAGTGGCGTTTTTACCACAAACGCCACAATATATTACACATATAGTGGCGTTTGTTCAGAAAACG
CCGCAATAGTGTTAAACAATAGTGGCATTTATGTACAAACGCCACAATAATGTAATCAA
Found at i:308346 original size:82 final size:82
Alignment explanation
Indices: 308086--308371 Score: 314
Period size: 82 Copynumber: 3.5 Consensus size: 82
308076 AGTGGTAAAT
** * * *
308086 TAGTGGCGTTTTTACCACAAACGCCGCAATA-TATTACACATATAGTGGCGTTTGTT-CCTAAAA
1 TAGTGGCGTTTTTAGTACAAACGCCGCAATAGTGTTAAACA-ATAGTGGCGTTT-TTAAC--AAA
*
308149 CGCCGCAATAGTGTTAATCAA
62 CGCCACAATAGTGTTAATCAA
* * * *
308170 TAGTGGCGTTTTT-GTACAAACTCCACAATAGTGTTAATCAATAGTGGCGTTTTTATACAAACGT
1 TAGTGGCGTTTTTAGTACAAACGCCGCAATAGTGTTAAACAATAGTGGCGTTTTTA-ACAAACGC
308234 CACAATAGTGTTAATCAA
65 CACAATAGTGTTAATCAA
* *
308252 TAGTGGCGTTTTTAG-ACAAACGCCGCAATAGTGTTAAACAATAGTGGCATTTATTAGCAAACGC
1 TAGTGGCGTTTTTAGTACAAACGCCGCAATAGTGTTAAACAATAGTGGCGTTT-TTAACAAACGC
*
308316 CACAATAATG-TAATCAA
65 CACAATAGTGTTAATCAA
* * * *
308333 AAGTGGCGTTTTTTTGTATAAACGCCGCAA-AATGTTAAA
1 TAGTGGCG-TTTTTAGTACAAACGCCGCAATAGTGTTAAA
308372 TATATAGTCC
Statistics
Matches: 174, Mismatches: 21, Indels: 16
0.82 0.10 0.08
Matches are distributed among these distances:
81 14 0.08
82 99 0.57
83 41 0.24
84 20 0.11
ACGTcount: A:0.34, C:0.17, G:0.18, T:0.31
Consensus pattern (82 bp):
TAGTGGCGTTTTTAGTACAAACGCCGCAATAGTGTTAAACAATAGTGGCGTTTTTAACAAACGCC
ACAATAGTGTTAATCAA
Found at i:311696 original size:21 final size:21
Alignment explanation
Indices: 311656--311721 Score: 73
Period size: 21 Copynumber: 3.1 Consensus size: 21
311646 AGTGAAAAAT
311656 GAAGCAAG-GGAAGC-CGAGAGA
1 GAAGC-AGTGGAAGCAC-AGAGA
* *
311677 GCAGCAGTGGAAGCATAGAGA
1 GAAGCAGTGGAAGCACAGAGA
*
311698 GAAGCAGTGGCAGCACAGAGA
1 GAAGCAGTGGAAGCACAGAGA
311719 GAA
1 GAA
311722 TCAACATATC
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
20 2 0.05
21 36 0.95
ACGTcount: A:0.41, C:0.15, G:0.39, T:0.05
Consensus pattern (21 bp):
GAAGCAGTGGAAGCACAGAGA
Found at i:312141 original size:43 final size:43
Alignment explanation
Indices: 312041--312158 Score: 136
Period size: 42 Copynumber: 2.8 Consensus size: 43
312031 ATTCTGTGTT
* *
312041 ATTTAGCGGCGTTTGTA-ACAAAAACGCCGTAATATACCATAC
1 ATTTAGCGGCGTTTGTATATAAAAACGCCCTAATATACCATAC
* *
312083 ATTTAGCGGCGTTTGTATCATAAAAACGCCACT-ATATACGA-AT
1 ATTTAGCGGCGTTTGTAT-ATAAAAACGCC-CTAATATACCATAC
*
312126 TTTTAGCGGCGTTTGTAT-TAAAAACGCCGCTAA
1 ATTTAGCGGCGTTTGTATATAAAAACGCC-CTAA
312159 ACCTCAACGC
Statistics
Matches: 66, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
41 12 0.18
42 18 0.27
43 18 0.27
44 17 0.26
45 1 0.02
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (43 bp):
ATTTAGCGGCGTTTGTATATAAAAACGCCCTAATATACCATAC
Found at i:312178 original size:43 final size:42
Alignment explanation
Indices: 312131--312261 Score: 145
Period size: 43 Copynumber: 3.0 Consensus size: 42
312121 CGAATTTTTA
* * * *
312131 GCGGCGTTTGTATTAAAAACGCCGCTAAACCTCAACGCCTATT
1 GCGGCGTTT-TACTAAAAACGCCGCTAAATCTCAACACATATT
* *
312174 GCGGCATTTTAGCTAAAAACGTCGCTAAATCTCAACACATATT
1 GCGGCGTTTTA-CTAAAAACGCCGCTAAATCTCAACACATATT
* * * *
312217 ACGGCGTTTTCGCTAAAAATGCCGCTAAATCTCAAGACATATT
1 GCGGCGTTTT-ACTAAAAACGCCGCTAAATCTCAACACATATT
312260 GC
1 GC
312262 AACATTTGTG
Statistics
Matches: 73, Mismatches: 13, Indels: 4
0.81 0.14 0.04
Matches are distributed among these distances:
42 2 0.03
43 71 0.97
ACGTcount: A:0.31, C:0.25, G:0.17, T:0.27
Consensus pattern (42 bp):
GCGGCGTTTTACTAAAAACGCCGCTAAATCTCAACACATATT
Found at i:320070 original size:2 final size:2
Alignment explanation
Indices: 320063--320102 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
320053 TTATTTCTTA
*
320063 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
320103 TCGATATGAC
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:322552 original size:22 final size:20
Alignment explanation
Indices: 322527--322597 Score: 63
Period size: 21 Copynumber: 3.3 Consensus size: 20
322517 CACCACAACT
322527 CACATAATTTGCATCGAAGTAC
1 CACATAATTTGC-TCGAAG-AC
*
322549 CACAT-ATTTGTCCCGAAGGAC
1 CACATAATTTG-CTCGAA-GAC
*
322570 CACATAGATTTGTTCCGAAGAC
1 CACATA-ATTTGCT-CGAAGAC
322592 CACATA
1 CACATA
322598 GAACCCTCGA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
21 16 0.39
22 16 0.39
23 9 0.22
ACGTcount: A:0.34, C:0.25, G:0.15, T:0.25
Consensus pattern (20 bp):
CACATAATTTGCTCGAAGAC
Found at i:322587 original size:23 final size:23
Alignment explanation
Indices: 322541--322599 Score: 79
Period size: 21 Copynumber: 2.7 Consensus size: 23
322531 TAATTTGCAT
*
322541 CGAAGTACCACAT--ATTTGTCC
1 CGAAGGACCACATAGATTTGTCC
*
322562 CGAAGGACCACATAGATTTGTTC
1 CGAAGGACCACATAGATTTGTCC
322585 CGAA-GACCACATAGA
1 CGAAGGACCACATAGA
322600 ACCCTCGACT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
21 12 0.35
22 11 0.32
23 11 0.32
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (23 bp):
CGAAGGACCACATAGATTTGTCC
Found at i:322598 original size:22 final size:22
Alignment explanation
Indices: 322541--322599 Score: 77
Period size: 22 Copynumber: 2.7 Consensus size: 22
322531 TAATTTGCAT
322541 CGAAGTACCACAT--ATTTGTCC
1 CGAAG-ACCACATAGATTTGTCC
*
322562 CGAAGGACCACATAGATTTGTTC
1 CGAA-GACCACATAGATTTGTCC
322585 CGAAGACCACATAGA
1 CGAAGACCACATAGA
322600 ACCCTCGACT
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
21 11 0.32
22 12 0.35
23 11 0.32
ACGTcount: A:0.34, C:0.25, G:0.19, T:0.22
Consensus pattern (22 bp):
CGAAGACCACATAGATTTGTCC
Found at i:327322 original size:21 final size:22
Alignment explanation
Indices: 327284--327339 Score: 60
Period size: 22 Copynumber: 2.5 Consensus size: 22
327274 TTACCACAAC
*
327284 TCACATAATTTGCACCGAAGTA
1 TCACATAATTTGCACCGAAGGA
* *
327306 TCACATATTTTTC-CCGAAGGA
1 TCACATAATTTGCACCGAAGGA
*
327327 CCACATAGATTTG
1 TCACATA-ATTTG
327340 TTCCGAAGAC
Statistics
Matches: 27, Mismatches: 6, Indels: 2
0.77 0.17 0.06
Matches are distributed among these distances:
21 13 0.48
22 14 0.52
ACGTcount: A:0.32, C:0.23, G:0.14, T:0.30
Consensus pattern (22 bp):
TCACATAATTTGCACCGAAGGA
Found at i:328098 original size:18 final size:18
Alignment explanation
Indices: 328049--328102 Score: 58
Period size: 18 Copynumber: 2.9 Consensus size: 18
328039 TTCATCTTTA
328049 CTTA-TAGTATCGATA-C
1 CTTACTAGTATCGATACC
*
328065 CTTACTGTTGGTATCGATACC
1 CTTAC---TAGTATCGATACC
328086 CTTACTAGTATCGATAC
1 CTTACTAGTATCGATAC
328103 TACTACCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
16 4 0.13
18 11 0.35
20 10 0.32
21 6 0.19
ACGTcount: A:0.26, C:0.22, G:0.15, T:0.37
Consensus pattern (18 bp):
CTTACTAGTATCGATACC
Found at i:332155 original size:22 final size:22
Alignment explanation
Indices: 332130--332196 Score: 70
Period size: 21 Copynumber: 3.1 Consensus size: 22
332120 CACCACAACT
332130 CACATAATTTG-CACCGAAGTG-C
1 CACATAATTTGTC-CCGAAG-GAC
332152 CACAT-ATTTGTCCCGAAGGAC
1 CACATAATTTGTCCCGAAGGAC
*
332173 CACATAGATTTGTTCCGAA-GAC
1 CACATA-ATTTGTCCCGAAGGAC
332195 CA
1 CA
332197 TATAGAACCT
Statistics
Matches: 40, Mismatches: 1, Indels: 8
0.82 0.02 0.16
Matches are distributed among these distances:
20 1 0.03
21 17 0.43
22 11 0.28
23 11 0.28
ACGTcount: A:0.31, C:0.27, G:0.18, T:0.24
Consensus pattern (22 bp):
CACATAATTTGTCCCGAAGGAC
Found at i:332190 original size:23 final size:22
Alignment explanation
Indices: 332157--332202 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 22
332147 AGTGCCACAT
332157 ATTTGTCCCGAAGGACCACATAG
1 ATTTGTCCCGAA-GACCACATAG
* *
332180 ATTTGTTCCGAAGACCATATAG
1 ATTTGTCCCGAAGACCACATAG
332202 A
1 A
332203 ACCTTGGGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 10 0.48
23 11 0.52
ACGTcount: A:0.33, C:0.22, G:0.20, T:0.26
Consensus pattern (22 bp):
ATTTGTCCCGAAGACCACATAG
Found at i:332874 original size:20 final size:21
Alignment explanation
Indices: 332851--332922 Score: 73
Period size: 18 Copynumber: 3.6 Consensus size: 21
332841 TCTTTACTTA
332851 TAGTATCGATA-CCTTACTAT
1 TAGTATCGATACCCTTACTAT
332871 TAGTATCGATACCCTTAC---
1 TAGTATCGATACCCTTACTAT
* *
332889 TAGTATCGATACGAC-TATTATT
1 TAGTATCGATAC-CCTTACTA-T
332911 TAGTATCGATAC
1 TAGTATCGATAC
332923 TGTTAATTCG
Statistics
Matches: 44, Mismatches: 2, Indels: 10
0.79 0.04 0.18
Matches are distributed among these distances:
18 14 0.32
19 1 0.02
20 11 0.25
21 6 0.14
22 12 0.27
ACGTcount: A:0.31, C:0.19, G:0.12, T:0.38
Consensus pattern (21 bp):
TAGTATCGATACCCTTACTAT
Found at i:332921 original size:40 final size:37
Alignment explanation
Indices: 332847--332922 Score: 100
Period size: 40 Copynumber: 2.0 Consensus size: 37
332837 TTCATCTTTA
332847 CTTATAGTATCGATACCTTACTATTAGTATCGATACC
1 CTTATAGTATCGATACCTTACTATTAGTATCGATACC
*
332884 CTTACTAGTATCGATACGAC-TATTATTTAGTATCGATAC
1 CTTA-TAGTATCGATAC--CTTACTA-TTAGTATCGATAC
332923 TGTTAATTCG
Statistics
Matches: 34, Mismatches: 1, Indels: 5
0.85 0.03 0.12
Matches are distributed among these distances:
37 4 0.12
38 12 0.35
39 4 0.12
40 14 0.41
ACGTcount: A:0.30, C:0.20, G:0.12, T:0.38
Consensus pattern (37 bp):
CTTATAGTATCGATACCTTACTATTAGTATCGATACC
Found at i:335564 original size:20 final size:19
Alignment explanation
Indices: 335539--335604 Score: 75
Period size: 20 Copynumber: 3.4 Consensus size: 19
335529 TTTGTCCTTT
335539 TTATTATTAATTATATATTA
1 TTATTA-TAATTATATATTA
335559 TTATTATAA-TATATATTTA
1 TTATTATAATTATATA-TTA
335578 TTATATATAA-TATATTATTA
1 TTAT-TATAATTATA-TATTA
335598 -TATTATA
1 TTATTATA
335605 TTTGTATTTA
Statistics
Matches: 43, Mismatches: 0, Indels: 8
0.84 0.00 0.16
Matches are distributed among these distances:
18 10 0.23
19 13 0.30
20 18 0.42
21 2 0.05
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (19 bp):
TTATTATAATTATATATTA
Found at i:335605 original size:20 final size:18
Alignment explanation
Indices: 335540--335605 Score: 81
Period size: 17 Copynumber: 3.9 Consensus size: 18
335530 TTGTCCTTTT
335540 TATTATTA-AT-TATATA
1 TATTATTATATATATATA
335556 TTATTATTATA-ATATATA
1 -TATTATTATATATATATA
335574 T-TTATTATATATA-ATA
1 TATTATTATATATATATA
335590 TATTATTATAT-TATAT
1 TATTATTATATATATAT
335606 TTGTATTTAC
Statistics
Matches: 44, Mismatches: 0, Indels: 10
0.81 0.00 0.19
Matches are distributed among these distances:
16 14 0.32
17 23 0.52
18 7 0.16
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (18 bp):
TATTATTATATATATATA
Found at i:343447 original size:42 final size:42
Alignment explanation
Indices: 343386--343467 Score: 119
Period size: 42 Copynumber: 2.0 Consensus size: 42
343376 CACGAATTTG
* *
343386 TAAATCCTTCGGGTCATCTGTAAGTCCTTCGAGCATGATGTT
1 TAAATCCTTCGGGTCATCTGTAAGTCCTTCAAGCAAGATGTT
* * *
343428 TAAATCCTTCGGGTTATCTGTTAGTCTTTCAAGCAAGATG
1 TAAATCCTTCGGGTCATCTGTAAGTCCTTCAAGCAAGATG
343468 ATAAGTCCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
42 35 1.00
ACGTcount: A:0.23, C:0.20, G:0.21, T:0.37
Consensus pattern (42 bp):
TAAATCCTTCGGGTCATCTGTAAGTCCTTCAAGCAAGATGTT
Found at i:343449 original size:22 final size:22
Alignment explanation
Indices: 343386--343449 Score: 62
Period size: 22 Copynumber: 3.0 Consensus size: 22
343376 CACGAATTTG
343386 TAAATCCTTCGGGTCATCTG--
1 TAAATCCTTCGGGTCATCTGTT
* * *
343406 TAAGTCCTTCGAG-CATGATGTT
1 TAAATCCTTCGGGTCAT-CTGTT
*
343428 TAAATCCTTCGGGTTATCTGTT
1 TAAATCCTTCGGGTCATCTGTT
343450 AGTCTTTCAA
Statistics
Matches: 33, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
19 3 0.09
20 13 0.39
22 15 0.45
23 2 0.06
ACGTcount: A:0.20, C:0.20, G:0.20, T:0.39
Consensus pattern (22 bp):
TAAATCCTTCGGGTCATCTGTT
Found at i:343683 original size:3 final size:3
Alignment explanation
Indices: 343675--343763 Score: 87
Period size: 3 Copynumber: 29.3 Consensus size: 3
343665 TTGTCCGTTT
343675 TTA TTA TTAA TTA -TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TT-A TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
* *
343720 -TA TTA CATA TTTA TTA TATA TAA TATA TTA TTA -TA TTA -TA TTA T
1 TTA TTA -TTA -TTA TTA T-TA TTA T-TA TTA TTA TTA TTA TTA TTA T
343764 ATTTACATTT
Statistics
Matches: 73, Mismatches: 5, Indels: 16
0.78 0.05 0.17
Matches are distributed among these distances:
2 8 0.11
3 53 0.73
4 12 0.16
ACGTcount: A:0.38, C:0.01, G:0.00, T:0.61
Consensus pattern (3 bp):
TTA
Found at i:343735 original size:16 final size:16
Alignment explanation
Indices: 343679--343757 Score: 83
Period size: 17 Copynumber: 4.8 Consensus size: 16
343669 CCGTTTTTAT
343679 TATTAATTATATT-AT-
1 TATT-ATTATATTAATA
*
343694 TATTATTATTATTATTA
1 TATTATTA-TATTAATA
343711 TTATTATTATATTACATA
1 -TATTATTATATTA-ATA
343729 T-TTATTATATATAATA
1 TATTATTATAT-TAATA
343745 TATTATTATATTA
1 TATTATTATATTA
343758 TATTATATTT
Statistics
Matches: 55, Mismatches: 2, Indels: 13
0.79 0.03 0.19
Matches are distributed among these distances:
14 4 0.07
15 8 0.15
16 16 0.29
17 17 0.31
18 10 0.18
ACGTcount: A:0.39, C:0.01, G:0.00, T:0.59
Consensus pattern (16 bp):
TATTATTATATTAATA
Found at i:343746 original size:25 final size:27
Alignment explanation
Indices: 343705--343765 Score: 74
Period size: 25 Copynumber: 2.3 Consensus size: 27
343695 ATTATTATTA
*
343705 TTATTAT-TATTATTATATTA-CATAT
1 TTATTATATATTAATATATTATCATAT
*
343730 TTATTATATA-TAATATATTATTATAT
1 TTATTATATATTAATATATTATCATAT
343756 TATATTATAT
1 T-TATTATAT
343766 TTACATTTAC
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
25 16 0.52
26 7 0.23
27 8 0.26
ACGTcount: A:0.39, C:0.02, G:0.00, T:0.59
Consensus pattern (27 bp):
TTATTATATATTAATATATTATCATAT
Found at i:343781 original size:36 final size:38
Alignment explanation
Indices: 343703--343791 Score: 96
Period size: 37 Copynumber: 2.3 Consensus size: 38
343693 TTATTATTAT
*
343703 TATTATTATTATTATTATATTACATATTTATTATATATAA
1 TATTATTATTA-TATTATATTA-ATATTTATTATACATAA
343743 TA-TATTATTATATTATATT-ATATTTACATT-TACA-AA
1 TATTATTATTATATTATATTAATATTT--ATTATACATAA
*
343779 TATTATAATTATA
1 TATTATTATTATA
343792 GCCCGGAGGC
Statistics
Matches: 44, Mismatches: 2, Indels: 9
0.80 0.04 0.16
Matches are distributed among these distances:
36 10 0.23
37 12 0.27
38 12 0.27
39 8 0.18
40 2 0.05
ACGTcount: A:0.42, C:0.03, G:0.00, T:0.55
Consensus pattern (38 bp):
TATTATTATTATATTATATTAATATTTATTATACATAA
Found at i:348503 original size:15 final size:15
Alignment explanation
Indices: 348483--348516 Score: 68
Period size: 15 Copynumber: 2.3 Consensus size: 15
348473 ACTAACAATT
348483 GCGGTGTTAGTATTA
1 GCGGTGTTAGTATTA
348498 GCGGTGTTAGTATTA
1 GCGGTGTTAGTATTA
348513 GCGG
1 GCGG
348517 CATTTTTTAC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.18, C:0.09, G:0.38, T:0.35
Consensus pattern (15 bp):
GCGGTGTTAGTATTA
Found at i:350867 original size:2 final size:2
Alignment explanation
Indices: 350862--350936 Score: 150
Period size: 2 Copynumber: 37.5 Consensus size: 2
350852 ATATCACATC
350862 AT AT 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 AT AT
350904 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 A
350937 CAAAGCACAT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 73 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:352041 original size:15 final size:15
Alignment explanation
Indices: 352021--352072 Score: 68
Period size: 15 Copynumber: 3.4 Consensus size: 15
352011 CCCGAAAATC
352021 GACCGATCTGATATT
1 GACCGATCTGATATT
* * *
352036 GACCGATCCGAAAATC
1 GACCGATCTG-ATATT
352052 GACCGATCTGATATT
1 GACCGATCTGATATT
352067 GACCGA
1 GACCGA
352073 CCCAAAAATC
Statistics
Matches: 30, Mismatches: 6, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
15 18 0.60
16 12 0.40
ACGTcount: A:0.31, C:0.25, G:0.21, T:0.23
Consensus pattern (15 bp):
GACCGATCTGATATT
Found at i:352048 original size:31 final size:31
Alignment explanation
Indices: 352009--352109 Score: 148
Period size: 31 Copynumber: 3.2 Consensus size: 31
351999 TACTCGATTT
352009 GACCCGAAAATCGACCGATCTGATATTGACC
1 GACCCGAAAATCGACCGATCTGATATTGACC
*
352040 GATCCGAAAATCGACCGATCTGATATTGACC
1 GACCCGAAAATCGACCGATCTGATATTGACC
* * * *
352071 GACCCAAAAATCAAACGATCTGATTTTGACTC
1 GACCCGAAAATCGACCGATCTGATATTGAC-C
352103 GACCCGA
1 GACCCGA
352110 CCTAACTTGC
Statistics
Matches: 62, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
31 55 0.89
32 7 0.11
ACGTcount: A:0.34, C:0.28, G:0.18, T:0.21
Consensus pattern (31 bp):
GACCCGAAAATCGACCGATCTGATATTGACC
Found at i:352057 original size:16 final size:16
Alignment explanation
Indices: 352012--352059 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
352002 TCGATTTGAC
352012 CCGAAAATCGACCGAT
1 CCGAAAATCGACCGAT
* * *
352028 CTG-ATATTGACCGAT
1 CCGAAAATCGACCGAT
352043 CCGAAAATCGACCGAT
1 CCGAAAATCGACCGAT
352059 C
1 C
352060 TGATATTGAC
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
15 12 0.48
16 13 0.52
ACGTcount: A:0.33, C:0.29, G:0.19, T:0.19
Consensus pattern (16 bp):
CCGAAAATCGACCGAT
Found at i:356310 original size:14 final size:14
Alignment explanation
Indices: 356291--356322 Score: 64
Period size: 14 Copynumber: 2.3 Consensus size: 14
356281 CGTTCGTGAA
356291 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
356305 CGTTCGGTTATGTT
1 CGTTCGGTTATGTT
356319 CGTT
1 CGTT
356323 TATGTTCATT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.06, C:0.16, G:0.28, T:0.50
Consensus pattern (14 bp):
CGTTCGGTTATGTT
Found at i:356339 original size:24 final size:24
Alignment explanation
Indices: 356292--356342 Score: 66
Period size: 24 Copynumber: 2.1 Consensus size: 24
356282 GTTCGTGAAC
* *
356292 GTTCGGTTATGTTCGTTCGGTTAT
1 GTTCGGTTATGTTCATTCAGTTAT
* *
356316 GTTCGTTTATGTTCATTCATTTAT
1 GTTCGGTTATGTTCATTCAGTTAT
356340 GTT
1 GTT
356343 TAACCCAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.12, C:0.12, G:0.22, T:0.55
Consensus pattern (24 bp):
GTTCGGTTATGTTCATTCAGTTAT
Found at i:357373 original size:10 final size:10
Alignment explanation
Indices: 357358--357432 Score: 70
Period size: 10 Copynumber: 7.7 Consensus size: 10
357348 GGGTCTCCAA
357358 CGTTTATGTT
1 CGTTTATGTT
357368 CGTTTATGTT
1 CGTTTATGTT
357378 CGTGTTCAT-TT
1 CGT-TT-ATGTT
*
357389 ATGTTTATGTT
1 -CGTTTATGTT
357400 CGTTTATGTT
1 CGTTTATGTT
357410 CG----TGTT
1 CGTTTATGTT
*
357416 CATTTATGTT
1 CGTTTATGTT
357426 CGTTTAT
1 CGTTTAT
357433 TTATTAAATG
Statistics
Matches: 53, Mismatches: 4, Indels: 16
0.73 0.05 0.22
Matches are distributed among these distances:
6 5 0.09
10 36 0.68
11 8 0.15
12 4 0.08
ACGTcount: A:0.12, C:0.11, G:0.19, T:0.59
Consensus pattern (10 bp):
CGTTTATGTT
Found at i:357389 original size:16 final size:16
Alignment explanation
Indices: 357364--357436 Score: 96
Period size: 16 Copynumber: 4.7 Consensus size: 16
357354 CCAACGTTTA
*
357364 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
**
357380 TGTTCATTTATGTTTA
1 TGTTCATTTATGTTCG
*
357396 TGTTCGTTTATGTTCG
1 TGTTCATTTATGTTCG
357412 TGTTCATTTATGTTCG
1 TGTTCATTTATGTTCG
357428 T-TT-ATTTAT
1 TGTTCATTTAT
357437 TAAATGAACG
Statistics
Matches: 50, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
14 6 0.12
15 2 0.04
16 42 0.84
ACGTcount: A:0.12, C:0.10, G:0.18, T:0.60
Consensus pattern (16 bp):
TGTTCATTTATGTTCG
Found at i:357400 original size:32 final size:32
Alignment explanation
Indices: 357359--357425 Score: 134
Period size: 32 Copynumber: 2.1 Consensus size: 32
357349 GGTCTCCAAC
357359 GTTTATGTTCGTTTATGTTCGTGTTCATTTAT
1 GTTTATGTTCGTTTATGTTCGTGTTCATTTAT
357391 GTTTATGTTCGTTTATGTTCGTGTTCATTTAT
1 GTTTATGTTCGTTTATGTTCGTGTTCATTTAT
357423 GTT
1 GTT
357426 CGTTTATTTA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
32 35 1.00
ACGTcount: A:0.12, C:0.09, G:0.19, T:0.60
Consensus pattern (32 bp):
GTTTATGTTCGTTTATGTTCGTGTTCATTTAT
Found at i:360760 original size:19 final size:18
Alignment explanation
Indices: 360725--360766 Score: 57
Period size: 19 Copynumber: 2.3 Consensus size: 18
360715 GAAGTTCTAA
*
360725 TTTTCTTTCATCCTTTTAC
1 TTTTCTTTCATCATTTT-C
*
360744 TTTTCTTTCATTATTTTC
1 TTTTCTTTCATCATTTTC
360762 TTTTC
1 TTTTC
360767 ACAATGCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.10, C:0.21, G:0.00, T:0.69
Consensus pattern (18 bp):
TTTTCTTTCATCATTTTC
Found at i:361338 original size:17 final size:16
Alignment explanation
Indices: 361316--361348 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
361306 ATACCCCCAA
361316 CCCACATAATCGTAACC
1 CCCACATAATCG-AACC
361333 CCCACATAATCGAACC
1 CCCACATAATCGAACC
361349 TCCATACCTC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.36, C:0.42, G:0.06, T:0.15
Consensus pattern (16 bp):
CCCACATAATCGAACC
Found at i:364373 original size:46 final size:46
Alignment explanation
Indices: 364320--364426 Score: 164
Period size: 46 Copynumber: 2.3 Consensus size: 46
364310 ATGCACTGAC
364320 ATGCATCGATGCACT-CAGGATT-TTATGGAAACATCAAATGCAATTT
1 ATGCATCGATGCACTCCAGGATTGTT-T-GAAACATCAAATGCAATTT
* *
364366 ATGCATCGATGCACTCCAGGCTTGTTTGAAACATCAAATGCATTTT
1 ATGCATCGATGCACTCCAGGATTGTTTGAAACATCAAATGCAATTT
364412 ATGCATCGATGCACT
1 ATGCATCGATGCACT
364427 AAGTGTTCCA
Statistics
Matches: 57, Mismatches: 2, Indels: 4
0.90 0.03 0.06
Matches are distributed among these distances:
46 48 0.84
47 7 0.12
48 2 0.04
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.31
Consensus pattern (46 bp):
ATGCATCGATGCACTCCAGGATTGTTTGAAACATCAAATGCAATTT
Found at i:370200 original size:23 final size:22
Alignment explanation
Indices: 370171--370250 Score: 83
Period size: 23 Copynumber: 3.6 Consensus size: 22
370161 ACACTATCCA
370171 GTGCATCGATGCATCCTATGAAT
1 GTGCATCGATGCAT-CTATGAAT
* *
370194 GTGCATCGATACATC-ATGAAG
1 GTGCATCGATGCATCTATGAAT
* *
370215 GTGCACCAATGCACTGCT-TGAAT
1 GTGCATCGATGCA-T-CTATGAAT
370238 GTGCATCGATGCA
1 GTGCATCGATGCA
370251 CTCAGCAATG
Statistics
Matches: 46, Mismatches: 8, Indels: 6
0.77 0.13 0.10
Matches are distributed among these distances:
21 15 0.33
22 2 0.04
23 29 0.63
ACGTcount: A:0.28, C:0.23, G:0.24, T:0.26
Consensus pattern (22 bp):
GTGCATCGATGCATCTATGAAT
Found at i:372963 original size:46 final size:46
Alignment explanation
Indices: 372913--373018 Score: 137
Period size: 46 Copynumber: 2.3 Consensus size: 46
372903 ATGCACTGAC
372913 ATGCATCGATGCACT-CAGGATT-TTATGGAATA-ATCGAATGCACTTT
1 ATGCATCGATGCACTCCAGGATTGTT-T-GAA-ACATCGAATGCACTTT
* * *
372959 ATGCATCGATGCACTCCAGGCTTGTTTGAAACATCGAATGTATTTT
1 ATGCATCGATGCACTCCAGGATTGTTTGAAACATCGAATGCACTTT
373005 ATGCATCGATGCAC
1 ATGCATCGATGCAC
373019 CTTTAGTGCA
Statistics
Matches: 54, Mismatches: 3, Indels: 6
0.86 0.05 0.10
Matches are distributed among these distances:
45 1 0.02
46 44 0.81
47 7 0.13
48 2 0.04
ACGTcount: A:0.28, C:0.20, G:0.20, T:0.32
Consensus pattern (46 bp):
ATGCATCGATGCACTCCAGGATTGTTTGAAACATCGAATGCACTTT
Found at i:376622 original size:15 final size:15
Alignment explanation
Indices: 376602--376631 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
376592 TTATAAGTTC
376602 ATCTTCTAATATAAA
1 ATCTTCTAATATAAA
376617 ATCTTCTAATATAAA
1 ATCTTCTAATATAAA
376632 TTCATTCAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.47, C:0.13, G:0.00, T:0.40
Consensus pattern (15 bp):
ATCTTCTAATATAAA
Found at i:382102 original size:18 final size:18
Alignment explanation
Indices: 382075--382109 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
382065 CACCATTTCG
382075 TTTTTCTTTTGTTTGTTT
1 TTTTTCTTTTGTTTGTTT
* *
382093 TTTTTTTTTTTTTTGTT
1 TTTTTCTTTTGTTTGTT
382110 CAGATTGTGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.00, C:0.03, G:0.09, T:0.89
Consensus pattern (18 bp):
TTTTTCTTTTGTTTGTTT
Found at i:386243 original size:42 final size:40
Alignment explanation
Indices: 386197--386348 Score: 121
Period size: 42 Copynumber: 3.6 Consensus size: 40
386187 TAAATTAGCA
*
386197 GCGTTTATACCACAAACACCGCAATATATTACACATATAGTG
1 GCGTTTATACCA-AAACACCGCAATAGATTACA-ATATAGTG
* *
386239 GCGTTT-TAGCCAAAACACCTCAATAGAGTGGTA-AAT-TAGCG
1 GCGTTTATA-CCAAAACACCGCAATAGA-T--TACAATATAGTG
* * * *
386280 GCTTTTATACCACAAACGCTGTAATAGATTACATATATAGTG
1 GCGTTTATACCA-AAACACCGCAATAGATTACA-ATATAGTG
* *
386322 GCGTTTATTCTTAAAACACCGCAATAG
1 GCGTTTATAC-CAAAACACCGCAATAG
386349 TGATAATCAA
Statistics
Matches: 85, Mismatches: 15, Indels: 20
0.71 0.12 0.17
Matches are distributed among these distances:
39 2 0.02
40 1 0.01
41 30 0.35
42 48 0.56
43 2 0.02
44 2 0.02
ACGTcount: A:0.36, C:0.20, G:0.16, T:0.28
Consensus pattern (40 bp):
GCGTTTATACCAAAACACCGCAATAGATTACAATATAGTG
Found at i:386390 original size:41 final size:41
Alignment explanation
Indices: 386343--386493 Score: 209
Period size: 41 Copynumber: 3.7 Consensus size: 41
386333 TAAAACACCG
* *
386343 CAATAGTGATAATCAATAGTGGCATTTTTAGACAAACG-TA
1 CAATAGTGTTAATCAATAGTGGCATTTTTAGACAAACGCCA
* *
386383 GCAATAGTGTTAATCAATAGTGGCGTTTTTAGACAAATGCCA
1 -CAATAGTGTTAATCAATAGTGGCATTTTTAGACAAACGCCA
* *
386425 CAATAGTTTTAATCAATAGTGGCGTTTTTTA-ACAAACGCCA
1 CAATAGTGTTAATCAATAGTGGC-ATTTTTAGACAAACGCCA
386466 CAATAGTG-TAATCAATAGTGGCATTTTT
1 CAATAGTGTTAATCAATAGTGGCATTTTT
386494 TTTGTATAAA
Statistics
Matches: 99, Mismatches: 9, Indels: 6
0.87 0.08 0.05
Matches are distributed among these distances:
39 5 0.05
40 14 0.14
41 73 0.74
42 7 0.07
ACGTcount: A:0.35, C:0.14, G:0.18, T:0.33
Consensus pattern (41 bp):
CAATAGTGTTAATCAATAGTGGCATTTTTAGACAAACGCCA
Found at i:397991 original size:22 final size:23
Alignment explanation
Indices: 397949--397991 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
397939 CTGACGGGCA
*
397949 TCCAGTCATCAGCTTCCAGAAGG
1 TCCAGTCAACAGCTTCCAGAAGG
*
397972 TCCAGTCAACA-CTTCTAGAA
1 TCCAGTCAACAGCTTCCAGAA
397992 AGACGAACAA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 8 0.44
23 10 0.56
ACGTcount: A:0.30, C:0.30, G:0.16, T:0.23
Consensus pattern (23 bp):
TCCAGTCAACAGCTTCCAGAAGG
Found at i:399470 original size:15 final size:16
Alignment explanation
Indices: 399450--399482 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
399440 GAATACAATT
399450 AGTGCATCGATGC-TA
1 AGTGCATCGATGCATA
399465 AGTGCATCGATGCATA
1 AGTGCATCGATGCATA
399481 AG
1 AG
399483 GAGTACGTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.24
Consensus pattern (16 bp):
AGTGCATCGATGCATA
Found at i:400437 original size:18 final size:18
Alignment explanation
Indices: 400414--400462 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
400404 ATGGTTCTAC
400414 GTGGTCCTACGTGACATA
1 GTGGTCCTACGTGACATA
*
400432 GTGGTCCTACGGGACATA
1 GTGGTCCTACGTGACATA
*
400450 -TGTGTTCTACGTG
1 GTG-GTCCTACGTG
400463 GTCCTACAGG
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 2 0.07
18 25 0.93
ACGTcount: A:0.18, C:0.20, G:0.31, T:0.31
Consensus pattern (18 bp):
GTGGTCCTACGTGACATA
Found at i:400869 original size:24 final size:22
Alignment explanation
Indices: 400826--400870 Score: 54
Period size: 24 Copynumber: 2.0 Consensus size: 22
400816 TATGAACAAG
*
400826 ATAAGAGATAGAAAGGATAATC
1 ATAAGAGATAGAAAAGATAATC
*
400848 ATAAGAGTATGAGAAAATATAAT
1 ATAAGAG-AT-AGAAAAGATAAT
400871 GGTGACATGC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
22 7 0.37
23 2 0.11
24 10 0.53
ACGTcount: A:0.56, C:0.02, G:0.20, T:0.22
Consensus pattern (22 bp):
ATAAGAGATAGAAAAGATAATC
Found at i:404059 original size:21 final size:21
Alignment explanation
Indices: 404035--404095 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
404025 AGTCGACGGT
404035 TCTACGTGGTCCTACGGGACA
1 TCTACGTGGTCCTACGGGACA
**
404056 TCTACGTGGTCCTACTAGACA
1 TCTACGTGGTCCTACGGGACA
404077 --TA-GTGGTCCTACGGGACA
1 TCTACGTGGTCCTACGGGACA
404095 T
1 T
404096 ATGTGTTCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
18 14 0.40
19 2 0.06
21 19 0.54
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (21 bp):
TCTACGTGGTCCTACGGGACA
Found at i:404094 original size:18 final size:18
Alignment explanation
Indices: 404040--404163 Score: 77
Period size: 18 Copynumber: 7.0 Consensus size: 18
404030 ACGGTTCTAC
404040 GTGGTCCTACGGGACATCTA
1 GTGGTCCTACGGGACA--TA
**
404060 CGTGGTCCTACTAGACATA
1 -GTGGTCCTACGGGACATA
404079 GTGGTCCTACGGGACATA
1 GTGGTCCTACGGGACATA
*
404097 -TGTGT--T-C--TAC---
1 GTG-GTCCTACGGGACATA
404107 GTGGTCCTACGGGACATCTA
1 GTGGTCCTACGGGACA--TA
**
404127 CGTGGTCCTACTAGACATA
1 -GTGGTCCTACGGGACATA
404146 GTGGTCCTACGGGACATA
1 GTGGTCCTACGGGACATA
404164 TGTGTTCTAC
Statistics
Matches: 80, Mismatches: 10, Indels: 29
0.67 0.08 0.24
Matches are distributed among these distances:
10 2 0.03
11 2 0.03
12 1 0.01
13 3 0.04
15 3 0.04
16 1 0.01
17 2 0.03
18 34 0.43
19 4 0.05
21 28 0.35
ACGTcount: A:0.22, C:0.24, G:0.27, T:0.27
Consensus pattern (18 bp):
GTGGTCCTACGGGACATA
Found at i:404110 original size:28 final size:28
Alignment explanation
Indices: 404079--404189 Score: 114
Period size: 28 Copynumber: 3.6 Consensus size: 28
404069 ACTAGACATA
404079 GTGGTCCTACGGGACATATGTGTTCTAC
1 GTGGTCCTACGGGACATATGTGTTCTAC
*
404107 GTGGTCCTACGGGACATCTACGTGGTCCTACTAGAC
1 GTGGTCCTACGGGACA--TATGT-GT--T-CT--AC
404143 ATAGTGGTCCTACGGGACATATGTGTTCTAC
1 ---GTGGTCCTACGGGACATATGTGTTCTAC
404174 GTGGTCCTACGGGACA
1 GTGGTCCTACGGGACA
404190 AATTCTACGC
Statistics
Matches: 70, Mismatches: 2, Indels: 22
0.74 0.02 0.23
Matches are distributed among these distances:
28 32 0.46
30 4 0.06
31 4 0.06
33 3 0.04
34 3 0.04
36 4 0.06
37 4 0.06
39 16 0.23
ACGTcount: A:0.20, C:0.23, G:0.29, T:0.28
Consensus pattern (28 bp):
GTGGTCCTACGGGACATATGTGTTCTAC
Found at i:404128 original size:21 final size:21
Alignment explanation
Indices: 404102--404162 Score: 83
Period size: 21 Copynumber: 3.0 Consensus size: 21
404092 ACATATGTGT
404102 TCTACGTGGTCCTACGGGACA
1 TCTACGTGGTCCTACGGGACA
**
404123 TCTACGTGGTCCTACTAGACA
1 TCTACGTGGTCCTACGGGACA
404144 --TA-GTGGTCCTACGGGACA
1 TCTACGTGGTCCTACGGGACA
404162 T
1 T
404163 ATGTGTTCTA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
18 14 0.40
19 2 0.06
21 19 0.54
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (21 bp):
TCTACGTGGTCCTACGGGACA
Found at i:404141 original size:67 final size:67
Alignment explanation
Indices: 404033--404189 Score: 314
Period size: 67 Copynumber: 2.3 Consensus size: 67
404023 AAAGTCGACG
404033 GTTCTACGTGGTCCTACGGGACATCTACGTGGTCCTACTAGACATAGTGGTCCTACGGGACATAT
1 GTTCTACGTGGTCCTACGGGACATCTACGTGGTCCTACTAGACATAGTGGTCCTACGGGACATAT
404098 GT
66 GT
404100 GTTCTACGTGGTCCTACGGGACATCTACGTGGTCCTACTAGACATAGTGGTCCTACGGGACATAT
1 GTTCTACGTGGTCCTACGGGACATCTACGTGGTCCTACTAGACATAGTGGTCCTACGGGACATAT
404165 GT
66 GT
404167 GTTCTACGTGGTCCTACGGGACA
1 GTTCTACGTGGTCCTACGGGACA
404190 AATTCTACGC
Statistics
Matches: 90, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
67 90 1.00
ACGTcount: A:0.20, C:0.24, G:0.27, T:0.28
Consensus pattern (67 bp):
GTTCTACGTGGTCCTACGGGACATCTACGTGGTCCTACTAGACATAGTGGTCCTACGGGACATAT
GT
Found at i:426655 original size:24 final size:24
Alignment explanation
Indices: 426622--426696 Score: 89
Period size: 24 Copynumber: 3.1 Consensus size: 24
426612 GTTCGTGAAC
* * *
426622 GTTCGATTATGTTTGTTCGGTTAT
1 GTTCGTTTATGTTCGTTCGATTAT
*
426646 GTTTGTTTATGTTCGTTCGATTAT
1 GTTCGTTTATGTTCGTTCGATTAT
*
426670 GTTCGTTTATGTTCATTC-ATTTAT
1 GTTCGTTTATGTTCGTTCGA-TTAT
426694 GTT
1 GTT
426697 TAACTCAATC
Statistics
Matches: 44, Mismatches: 6, Indels: 2
0.85 0.12 0.04
Matches are distributed among these distances:
23 1 0.02
24 43 0.98
ACGTcount: A:0.13, C:0.09, G:0.20, T:0.57
Consensus pattern (24 bp):
GTTCGTTTATGTTCGTTCGATTAT
Found at i:426673 original size:14 final size:14
Alignment explanation
Indices: 426621--426676 Score: 57
Period size: 14 Copynumber: 4.3 Consensus size: 14
426611 CGTTCGTGAA
426621 CGTTCGATTATGTT
1 CGTTCGATTATGTT
* *
426635 TGTTCGGTTATG-T
1 CGTTCGATTATGTT
*
426648 --TT-GTTTATGTT
1 CGTTCGATTATGTT
426659 CGTTCGATTATGTT
1 CGTTCGATTATGTT
426673 CGTT
1 CGTT
426677 TATGTTCATT
Statistics
Matches: 34, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
10 6 0.18
11 3 0.09
13 3 0.09
14 22 0.65
ACGTcount: A:0.11, C:0.11, G:0.23, T:0.55
Consensus pattern (14 bp):
CGTTCGATTATGTT
Found at i:427448 original size:16 final size:16
Alignment explanation
Indices: 427427--427491 Score: 98
Period size: 16 Copynumber: 4.2 Consensus size: 16
427417 TTTATGTTCG
427427 TATGTTCGTGTTCATT
1 TATGTTCGTGTTCATT
*
427443 TATGTTCGTGTTCGTT
1 TATGTTCGTGTTCATT
*
427459 TATGTTCGTGTTCGTT
1 TATGTTCGTGTTCATT
427475 TATGTTCGT-TT-ATT
1 TATGTTCGTGTTCATT
427489 TAT
1 TAT
427492 TAAATGAACG
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
14 5 0.11
15 2 0.04
16 40 0.85
ACGTcount: A:0.11, C:0.11, G:0.20, T:0.58
Consensus pattern (16 bp):
TATGTTCGTGTTCATT
Found at i:427574 original size:16 final size:16
Alignment explanation
Indices: 427553--427585 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
427543 AAAAAAAATT
427553 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
427569 TGTTCGTTTATGTTCG
1 TGTTCGTTTATGTTCG
427585 T
1 T
427586 CTATTTATTA
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:0.06, C:0.12, G:0.24, T:0.58
Consensus pattern (16 bp):
TGTTCGTTTATGTTCG
Found at i:432199 original size:66 final size:66
Alignment explanation
Indices: 432112--432604 Score: 481
Period size: 66 Copynumber: 7.5 Consensus size: 66
432102 AGGGTTGATG
** * * * *
432112 GTTTCAAGAGAAACCGTCTCAAAAGAGACAAAACATGTTTCAAGGGAAAAAATCTCAAAGGTTGG
1 GTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACATGTTTCAAGGGAAAAGATCTCAAAGATTTG
432177 T
66 T
* * * *
432178 GTTTGAAGGGAAACTGTCTCAAGAGAGACAAAATTCA--TTTCAAGGGAAACGATCTCAAAGATT
1 GTTTCAAGAGAAATTGTCTCAAGAGAGACAAAA--CATGTTTCAAGGGAAAAGATCTCAAAGATT
432241 TGT
64 TGT
* * * ** *
432244 GTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTGTTTCAAGGGAAACAGAT-TCAAAGATTA
1 GTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACATGTTTCAAGGGAAA-AGATCTCAAAGATTT
432308 GT
65 GT
* * * *
432310 GTTTCAAGGGAAATTGTCTTAAGAGAGAGAAAATTCA--TTTCAAGGGAAACGATCTCAAAGATT
1 GTTTCAAGAGAAATTGTCTCAAGAGAGACAAAA--CATGTTTCAAGGGAAAAGATCTCAAAGATT
432373 TGT
64 TGT
* *
432376 GTTTCAAGAGAAATTGTCTCAATG-GATACAAAATC-TGTTTCAAGGGAAACAAAT-TCAAAGAT
1 GTTTCAAGAGAAATTGTCTCAA-GAGAGACAAAA-CATGTTTCAAGGGAAA-AGATCTCAAAGAT
*
432438 TGGT
63 TTGT
* * * * * *
432442 GTTTCAAGGGAAAATGTCTCAAGAAAGACAAAA-TTCGTTTCAAGGGAAACGATCTCAGAGACTT
1 GTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACAT-GTTTCAAGGGAAAAGATCTCAAAGA-TT
*
432506 TTT
64 TGT
* ** *
432509 GTTTCAAG-GAAATTGTCTCAAGGGAGACAAAATTTGTTCCAAGGGAAACAGA-CTCAAAGATTT
1 GTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACATGTTTCAAGGGAAA-AGATCTCAAAGATTT
432572 -T
65 GT
*
432573 -TTTTAAGAGAAATTGTCTCAAGAGAGACAAAA
1 GTTTCAAGAGAAATTGTCTCAAGAGAGACAAAA
432605 TTTGTTTTGA
Statistics
Matches: 358, Mismatches: 49, Indels: 42
0.80 0.11 0.09
Matches are distributed among these distances:
63 6 0.02
64 24 0.07
65 12 0.03
66 293 0.82
67 21 0.06
68 2 0.01
ACGTcount: A:0.40, C:0.13, G:0.22, T:0.26
Consensus pattern (66 bp):
GTTTCAAGAGAAATTGTCTCAAGAGAGACAAAACATGTTTCAAGGGAAAAGATCTCAAAGATTTG
T
Found at i:432249 original size:30 final size:31
Alignment explanation
Indices: 432215--432322 Score: 89
Period size: 30 Copynumber: 3.4 Consensus size: 31
432205 ACAAAATTCA
432215 TTTCAAGGGAAAC-GATCTCAAAGATTTGTG
1 TTTCAAGGGAAACAGATCTCAAAGATTTGTG
* * *
432245 TTTCAAGAGAAACTG-TCTCAAGGGAGAAAAAATT-TG
1 TTTCAAGGGAAACAGATCTCAA---AG----ATTTGTG
*
432281 TTTCAAGGGAAACAGAT-TCAAAGATTAGTG
1 TTTCAAGGGAAACAGATCTCAAAGATTTGTG
432311 TTTCAAGGGAAA
1 TTTCAAGGGAAA
432323 TTGTCTTAAG
Statistics
Matches: 62, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
29 2 0.03
30 32 0.52
31 1 0.02
33 4 0.06
36 19 0.31
37 4 0.06
ACGTcount: A:0.39, C:0.11, G:0.23, T:0.27
Consensus pattern (31 bp):
TTTCAAGGGAAACAGATCTCAAAGATTTGTG
Found at i:432349 original size:132 final size:132
Alignment explanation
Indices: 432112--432606 Score: 683
Period size: 132 Copynumber: 3.8 Consensus size: 132
432102 AGGGTTGATG
* ** ** *
432112 GTTTCAAGAGAAACCGTCTCAAAAGAGACAAAACATGTTTCAAGGGAAA-AAATCTCAAAGGTTG
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAAT-TCAAAGATTG
* *
432176 GTGTTTGAAGGGAAACTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATT
65 GTGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATT
432241 TGT
130 TGT
* * *
432244 GTTTCAAGAGAAACTGTCTCAAGGGAGAAAAAATTTGTTTCAAGGGAAACAGATTCAAAGATTAG
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTGG
* *
432309 TGTTTCAAGGGAAATTGTCTTAAGAGAGAGAAAATTCATTTCAAGGGAAACGATCTCAAAGATTT
66 TGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATTT
432374 GT
131 GT
* * * *
432376 GTTTCAAGAGAAATTGTCTCAATGGATACAAAATCTGTTTCAAGGGAAACAAATTCAAAGATTGG
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTGG
* * * *
432441 TGTTTCAAGGGAAAATGTCTCAAGAAAGACAAAATTCGTTTCAAGGGAAACGATCTCAGAGACTT
66 TGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGA-TT
*
432506 TTT
130 TGT
* * * *
432509 GTTTCAAG-GAAATTGTCTCAAGGGAGACAAAATTTGTTCCAAGGGAAACAGACTCAAAGATT--
1 GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTGG
* * *
432571 TTTTTTAAGAGAAATTGTCTCAAGAGAGACAAAATT
66 TGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATT
432607 TGTTTTGAGT
Statistics
Matches: 323, Mismatches: 38, Indels: 6
0.88 0.10 0.02
Matches are distributed among these distances:
130 31 0.10
132 277 0.86
133 15 0.05
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.26
Consensus pattern (132 bp):
GTTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTGTTTCAAGGGAAACAAATTCAAAGATTGG
TGTTTCAAGGGAAATTGTCTCAAGAGAGACAAAATTCATTTCAAGGGAAACGATCTCAAAGATTT
GT
Done.