Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007848.1 Hibiscus syriacus cultivar Beakdansim tig00110205_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: 84188
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:6808 original size:38 final size:38
Alignment explanation
Indices: 6748--6821 Score: 112
Period size: 38 Copynumber: 1.9 Consensus size: 38
6738 AATTGCGTAC
* *
6748 GAAGACGGCAAAAACAATGCTATCGTAAATTACTATCT
1 GAAGACGGCAAAAACAACGCTATCGTAAAATACTATCT
* *
6786 GAAGACGGCAAACACAACGCTATCTTAAAATACTAT
1 GAAGACGGCAAAAACAACGCTATCGTAAAATACTAT
6822 ATTAGGTAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
38 32 1.00
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (38 bp):
GAAGACGGCAAAAACAACGCTATCGTAAAATACTATCT
Found at i:9997 original size:18 final size:18
Alignment explanation
Indices: 9974--10008 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
9964 ATGTGTAATA
*
9974 TCCCTTAAGTAATATTAG
1 TCCCTTAAGTAAAATTAG
9992 TCCCTTAAGTAAAATTA
1 TCCCTTAAGTAAAATTA
10009 TCTCATATTG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.37, C:0.17, G:0.09, T:0.37
Consensus pattern (18 bp):
TCCCTTAAGTAAAATTAG
Found at i:10361 original size:29 final size:29
Alignment explanation
Indices: 10335--10390 Score: 76
Period size: 29 Copynumber: 1.9 Consensus size: 29
10325 AAGATTACAG
* *
10335 TGTTTGGCTGAAGGAATATAAAATTACGA
1 TGTTTGACTAAAGGAATATAAAATTACGA
* *
10364 TGTTTGATTAAAGGAATATAATATTAC
1 TGTTTGACTAAAGGAATATAAAATTAC
10391 TTAGATGTAT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 23 1.00
ACGTcount: A:0.39, C:0.05, G:0.20, T:0.36
Consensus pattern (29 bp):
TGTTTGACTAAAGGAATATAAAATTACGA
Found at i:12053 original size:27 final size:26
Alignment explanation
Indices: 12023--12077 Score: 67
Period size: 26 Copynumber: 2.1 Consensus size: 26
12013 CTTCAACCTA
12023 TTTCCCATCTTCTTCAC-TTTACTTCTT
1 TTTCCCATC-TCTTCACTTTTA-TTCTT
**
12050 TTTCCTTTCTCTTCACTTTTATTCTT
1 TTTCCCATCTCTTCACTTTTATTCTT
12076 TT
1 TT
12078 CCTCTTATCA
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 14 0.56
27 11 0.44
ACGTcount: A:0.09, C:0.29, G:0.00, T:0.62
Consensus pattern (26 bp):
TTTCCCATCTCTTCACTTTTATTCTT
Found at i:12872 original size:14 final size:14
Alignment explanation
Indices: 12840--12879 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
12830 AAAGAAAAGT
12840 GAAGAAAAG-AG-A
1 GAAGAAAAGAAGAA
12852 -AAG-AAAGAAGAA
1 GAAGAAAAGAAGAA
12864 GAAGAAAAGAAGAA
1 GAAGAAAAGAAGAA
12878 GA
1 GA
12880 TGGGGAATGG
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
10 4 0.17
11 5 0.21
12 1 0.04
13 3 0.12
14 11 0.46
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (14 bp):
GAAGAAAAGAAGAA
Found at i:20252 original size:24 final size:24
Alignment explanation
Indices: 20207--20253 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
20197 ACGACTCGTC
** *
20207 TGGAAGAAACAGTTATGTCAGCAA
1 TGGAAGAAACAGCCATGGCAGCAA
*
20231 TGGAAGAAGCAGCCATGGCAGCA
1 TGGAAGAAACAGCCATGGCAGCA
20254 CAATTACACT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.38, C:0.17, G:0.30, T:0.15
Consensus pattern (24 bp):
TGGAAGAAACAGCCATGGCAGCAA
Found at i:22858 original size:21 final size:20
Alignment explanation
Indices: 22824--22865 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
22814 TTAATTTAAA
* *
22824 ATATATTTTTATTTTTATTT
1 ATATATTATTATTTGTATTT
22844 ATATCATTATTATTTGTATTT
1 ATAT-ATTATTATTTGTATTT
22865 A
1 A
22866 GTTATGAAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.29, C:0.02, G:0.02, T:0.67
Consensus pattern (20 bp):
ATATATTATTATTTGTATTT
Found at i:30475 original size:23 final size:22
Alignment explanation
Indices: 30444--30519 Score: 73
Period size: 23 Copynumber: 3.4 Consensus size: 22
30434 TGATATAGAT
30444 TATATATATGTGTATGTGTG-A
1 TATATATATGTGTATGTGTGTA
* *
30465 TATTCATATATGAGTTTAGTGTGTA
1 TA-T-ATATATGTGTAT-GTGTGTA
* *
30490 TATATATATGTATATGTTTGTA
1 TATATATATGTGTATGTGTGTA
*
30512 TGTATATA
1 TATATATA
30520 ACATAAAACT
Statistics
Matches: 44, Mismatches: 7, Indels: 7
0.76 0.12 0.12
Matches are distributed among these distances:
21 2 0.05
22 14 0.32
23 19 0.43
24 6 0.14
25 3 0.07
ACGTcount: A:0.30, C:0.01, G:0.18, T:0.50
Consensus pattern (22 bp):
TATATATATGTGTATGTGTGTA
Found at i:31219 original size:32 final size:32
Alignment explanation
Indices: 31181--31255 Score: 141
Period size: 32 Copynumber: 2.3 Consensus size: 32
31171 TGGTCGGTTC
31181 ATTTAAATAATACTTTAAGTACTTAGAAAATG
1 ATTTAAATAATACTTTAAGTACTTAGAAAATG
31213 ATTTAAATAATACTTTAAGTACTTAGAAAATG
1 ATTTAAATAATACTTTAAGTACTTAGAAAATG
*
31245 ATTTTAATAAT
1 ATTTAAATAAT
31256 TAATAATAAC
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
32 42 1.00
ACGTcount: A:0.47, C:0.05, G:0.08, T:0.40
Consensus pattern (32 bp):
ATTTAAATAATACTTTAAGTACTTAGAAAATG
Found at i:36098 original size:24 final size:24
Alignment explanation
Indices: 36071--36116 Score: 76
Period size: 24 Copynumber: 1.9 Consensus size: 24
36061 GTTCAAATTA
36071 TTGTGTTCGTTTA-TGTTCGTTTGT
1 TTGTGTTCGTTTACT-TTCGTTTGT
36095 TTGTGTTCGTTTACTTTCGTTT
1 TTGTGTTCGTTTACTTTCGTTT
36117 ATCATTTAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
24 20 0.95
25 1 0.05
ACGTcount: A:0.04, C:0.11, G:0.22, T:0.63
Consensus pattern (24 bp):
TTGTGTTCGTTTACTTTCGTTTGT
Found at i:36449 original size:20 final size:20
Alignment explanation
Indices: 36426--36477 Score: 95
Period size: 20 Copynumber: 2.6 Consensus size: 20
36416 AACGCGATCC
36426 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
36446 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATCAGTTT
*
36466 CCAAAATCGCAA
1 CCAGAATCGCAA
36478 CGCGATTCTT
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.38, C:0.27, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATCAGTTT
Found at i:36494 original size:21 final size:20
Alignment explanation
Indices: 36467--36565 Score: 72
Period size: 21 Copynumber: 4.8 Consensus size: 20
36457 AATCAGTTTC
36467 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * * *
36488 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
36509 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
36529 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
36550 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
36566 ACACATAAAT
Statistics
Matches: 59, Mismatches: 17, Indels: 5
0.73 0.21 0.06
Matches are distributed among these distances:
20 16 0.27
21 43 0.73
ACGTcount: A:0.36, C:0.23, G:0.19, T:0.21
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:36594 original size:20 final size:20
Alignment explanation
Indices: 36532--36725 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
36522 CGATTTTCCA
* ** *
36532 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
36552 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
36572 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
36592 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
36612 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
36632 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
36652 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
36672 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
36692 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
36713 AAATCGCAACGCG
1 AAATCGCAACGCG
36726 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:36616 original size:60 final size:60
Alignment explanation
Indices: 36532--36725 Score: 253
Period size: 60 Copynumber: 3.2 Consensus size: 60
36522 CGATTTTCCA
* ** * *
36532 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* * *** *
36592 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
* **
36652 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGT
36713 AAATCGCAACGCG
1 AAATCGCAACGCG
36726 ATATTTAAAG
Statistics
Matches: 112, Mismatches: 21, Indels: 1
0.84 0.16 0.01
Matches are distributed among these distances:
60 81 0.72
61 31 0.28
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGT
Found at i:37149 original size:33 final size:33
Alignment explanation
Indices: 37107--37177 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
37097 TTCACTTAGA
*
37107 TTTCATTTCGCGTTACGATTATGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTATCTCGTTGCGAT
* * *
37140 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTATCTCGTTGCGAT
37173 TTTCA
1 TTTCA
37178 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.13, C:0.21, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTATCTCGTTGCGAT
Found at i:37317 original size:14 final size:14
Alignment explanation
Indices: 37298--37352 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
37288 AGAATGACTG
37298 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
37312 TCGCAACGCGAAATGGAAA
1 TCGCAA--CGAGA--G-AA
37331 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
37345 TCGCAACG
1 TCGCAACG
37353 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 16 0.47
15 1 0.03
16 4 0.12
17 4 0.12
18 1 0.03
19 8 0.24
ACGTcount: A:0.40, C:0.24, G:0.27, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:37365 original size:33 final size:33
Alignment explanation
Indices: 37298--37368 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
37288 AGAATGACTG
***
37298 TCGCAACGAGAGAATCGCAACGCGAAATGGAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
37331 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
37364 TCGCA
1 TCGCA
37369 TTGCGATTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.42, C:0.25, G:0.24, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:37386 original size:19 final size:19
Alignment explanation
Indices: 37364--37461 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
37354 GAAACCAAAA
*
37364 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
37383 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
37397 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
37416 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
37430 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
37449 TCGCGTTGCGATT
1 TCGCGTTGCGATT
37462 CTCTCGTTGC
Statistics
Matches: 63, Mismatches: 6, Indels: 20
0.71 0.07 0.22
Matches are distributed among these distances:
14 20 0.32
16 5 0.08
17 6 0.10
19 32 0.51
ACGTcount: A:0.10, C:0.24, G:0.22, T:0.43
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:37405 original size:14 final size:14
Alignment explanation
Indices: 37386--37475 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
37376 TTTCATTTCG
37386 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
37400 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
37419 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
37433 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
37450 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
37466 CGTTGCGATT
1 CGTTGCGATT
37476 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:37411 original size:33 final size:33
Alignment explanation
Indices: 37369--37483 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
37359 CAAAATCGCA
37369 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
37402 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
37435 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
37468 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
37484 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:39409 original size:185 final size:186
Alignment explanation
Indices: 39180--39645 Score: 876
Period size: 185 Copynumber: 2.5 Consensus size: 186
39170 TAGATTGCTT
39180 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
39245 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
39310 GTGTATTCTTTAACACTGTGAAATA-TATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
39365 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
39430 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
39495 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
131 GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
39551 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAAC--TG---TCTTTAACACTGTG-AA-AGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
39609 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTT
39646 ATCCATTCAA
Statistics
Matches: 280, Mismatches: 0, Indels: 8
0.97 0.00 0.03
Matches are distributed among these distances:
179 41 0.15
180 2 0.01
181 14 0.05
184 2 0.01
185 155 0.55
186 66 0.24
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (186 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAAAGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACT
GTGTATTCTTTAACACTGTGAAATAGTATTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:39494 original size:93 final size:93
Alignment explanation
Indices: 39180--39645 Score: 876
Period size: 93 Copynumber: 5.1 Consensus size: 93
39170 TAGATTGCTT
39180 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
39245 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
39273 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
39337 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
39365 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
39430 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
39458 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
39523 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
39551 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAAC--TG---TCTTTAACACTGTG-AA-AGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
39609 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
39637 AGTAAATTT
1 AGTAAATTT
39646 ATCCATTCAA
Statistics
Matches: 372, Mismatches: 0, Indels: 9
0.98 0.00 0.02
Matches are distributed among these distances:
86 41 0.11
87 2 0.01
88 14 0.04
91 2 0.01
92 92 0.25
93 221 0.59
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:39729 original size:19 final size:19
Alignment explanation
Indices: 39689--39817 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
39679 TAGTTTACTT
* *
39689 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
39709 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
39728 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
39747 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
39761 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
39780 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
39794 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
39813 TCGCA
1 TCGCA
39818 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:39768 original size:33 final size:32
Alignment explanation
Indices: 39725--39817 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
39715 CGCGAAACCA
**
39725 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
39757 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
39790 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
39818 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:39815 original size:52 final size:52
Alignment explanation
Indices: 39689--39817 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
39679 TAGTTTACTT
**
39689 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
39741 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
39794 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
39818 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:39835 original size:19 final size:19
Alignment explanation
Indices: 39813--39946 Score: 119
Period size: 19 Copynumber: 7.6 Consensus size: 19
39803 GAAACCAAAA
*
39813 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
39832 TCGCGTTGCGA--TTC--T
1 TCGCGTTGCGATTTTCATT
39847 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
39864 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
39880 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
39897 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGATTTTCATT
*
39916 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
39936 TCGTGTTGCGA
1 TCGCGTTGCGA
39947 AAGTAAACTA
Statistics
Matches: 93, Mismatches: 10, Indels: 23
0.74 0.08 0.18
Matches are distributed among these distances:
13 8 0.09
14 7 0.08
15 5 0.05
16 5 0.05
17 10 0.11
19 46 0.49
20 12 0.13
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:39859 original size:32 final size:33
Alignment explanation
Indices: 39818--39909 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
39808 CAAAATCGCA
39818 TTGCGATTTTCATTTCGCGTTGCGATTCT-TCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
39850 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
39883 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
39910 TTGGTTTCGC
Statistics
Matches: 57, Mismatches: 2, Indels: 1
0.95 0.03 0.02
Matches are distributed among these distances:
32 28 0.49
33 29 0.51
ACGTcount: A:0.11, C:0.21, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:41867 original size:14 final size:14
Alignment explanation
Indices: 41848--41883 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
41838 ATTGTTTAAT
41848 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
*
41862 TGATTTGTAAAAGT
1 TGATTTGTAAAAGA
41876 TGATTTGT
1 TGATTTGT
41884 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:42006 original size:19 final size:19
Alignment explanation
Indices: 41990--42091 Score: 151
Period size: 19 Copynumber: 5.6 Consensus size: 19
41980 AAAAATGACT
41990 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
42009 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
42028 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
42042 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
42061 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
42081 ATCGCAATGCG
1 ATCGCAATGCG
42092 TTTATAATTT
Statistics
Matches: 75, Mismatches: 2, Indels: 12
0.84 0.02 0.13
Matches are distributed among these distances:
14 10 0.13
15 1 0.01
16 2 0.03
17 2 0.03
18 1 0.01
19 40 0.53
20 19 0.25
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:42144 original size:19 final size:19
Alignment explanation
Indices: 42120--42397 Score: 346
Period size: 19 Copynumber: 15.7 Consensus size: 19
42110 GATTATCTCG
42120 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
42139 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
42158 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
42172 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
42191 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
42210 TTGCGA-TTTCATTTCGTA
1 TTGCGATTTTCATTTCGCA
*
42228 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
* *
42247 TTGCGA--TT-ATGTCG-G
1 TTGCGATTTTCATTTCGCA
42262 TT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
42280 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
42299 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
42313 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
42332 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
42351 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
42365 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
42385 TTGCGATTTTCAT
1 TTGCGATTTTCAT
42398 GTTGGGATTT
Statistics
Matches: 226, Mismatches: 11, Indels: 43
0.81 0.04 0.15
Matches are distributed among these distances:
14 21 0.09
15 2 0.01
16 29 0.13
17 27 0.12
18 21 0.09
19 113 0.50
20 13 0.06
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:42278 original size:141 final size:137
Alignment explanation
Indices: 42088--42424 Score: 511
Period size: 141 Copynumber: 2.4 Consensus size: 137
42078 AAAATCGCAA
42088 TGCG-TTTATAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
1 TGCGATTT-TAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCAT
*
42152 TTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
65 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-
*
42217 TTCATTTCGTAT
129 TTC-TCTCG--T
*
42229 TGCGATTTTAATTTCGCATTGCGATTATGTCGGTT-CGATTTTCATTTCGCATTGCGATTTTCAT
1 TGCGATTTTAATTTCGCATTGCGATTATCTC-GTTGCGATTTTCATTTCGCATTGCGATTTTCAT
42293 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
65 TTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGAT
42358 TCTCTCGT
130 TCTCTCGT
* * * *
42366 TGCGATTTTCATTTCCGCATTGCGATTTTCAT-GTTGGGATTTTCA-TTCGCGTTGCGATT
1 TGCGATTTTAATTT-CGCATTGCGATTATC-TCGTTGCGATTTTCATTTCGCATTGCGATT
42425 GTATTTCCGT
Statistics
Matches: 183, Mismatches: 8, Indels: 14
0.89 0.04 0.07
Matches are distributed among these distances:
137 30 0.16
138 21 0.11
139 5 0.03
140 3 0.02
141 118 0.64
142 6 0.03
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (137 bp):
TGCGATTTTAATTTCGCATTGCGATTATCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATT
TCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGATT
CTCTCGT
Found at i:42424 original size:52 final size:52
Alignment explanation
Indices: 42120--42397 Score: 345
Period size: 52 Copynumber: 5.2 Consensus size: 52
42110 GATTATCTCG
*
42120 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* *
42172 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTTCATTTCGTA
1 TTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCGCA
* * *
42228 TTGCGATTTTAATTTCGCATTGCGATTATGTCGGTT-CGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTC-GTTGCGATTTTCATTTCGCA
42280 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
42332 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTT-CGCA
42385 TTGCGATTTTCAT
1 TTGCGATTTTCAT
42398 GTTGGGATTT
Statistics
Matches: 211, Mismatches: 7, Indels: 15
0.91 0.03 0.06
Matches are distributed among these distances:
51 6 0.03
52 150 0.71
53 23 0.11
54 8 0.04
56 24 0.11
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (52 bp):
TTGCGATTTTCATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCA
Found at i:44739 original size:12 final size:12
Alignment explanation
Indices: 44722--44746 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
44712 TCTTCGGGGA
44722 CTTTTTCTTCTT
1 CTTTTTCTTCTT
44734 CTTTTTCTTCTT
1 CTTTTTCTTCTT
44746 C
1 C
44747 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:44955 original size:24 final size:24
Alignment explanation
Indices: 44921--44967 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
44911 CTGAAACATC
44921 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
44945 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
44968 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:45664 original size:20 final size:20
Alignment explanation
Indices: 45636--46004 Score: 458
Period size: 20 Copynumber: 18.4 Consensus size: 20
45626 AAATTTCAGT
* * * *
45636 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
45656 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
45676 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
45696 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
45716 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
45736 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
45756 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
45776 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
45796 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
45816 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
45836 GTTGCGGTTTACGGATACGC
1 GTTGCGATTTACGGATACGC
45856 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
45876 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
45896 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
45916 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
45936 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
45956 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
45976 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
45996 GTTGCGATT
1 GTTGCGATT
46005 ATGGAAAATC
Statistics
Matches: 309, Mismatches: 32, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
19 5 0.02
20 299 0.97
21 5 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:53500 original size:21 final size:19
Alignment explanation
Indices: 53463--53503 Score: 55
Period size: 21 Copynumber: 2.1 Consensus size: 19
53453 TAATATAATA
*
53463 TTTTTATATTTTTTCTTAT
1 TTTTTATATTTTGTCTTAT
53482 TTTTTAATAATTTTGTCTTAT
1 TTTTT-AT-ATTTTGTCTTAT
53503 T
1 T
53504 ACACGTTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
19 5 0.26
20 2 0.11
21 12 0.63
ACGTcount: A:0.20, C:0.05, G:0.02, T:0.73
Consensus pattern (19 bp):
TTTTTATATTTTGTCTTAT
Found at i:54794 original size:7 final size:7
Alignment explanation
Indices: 54784--54809 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
54774 TTTTTCTATT
54784 TTCTGAC
1 TTCTGAC
54791 TTCTGAC
1 TTCTGAC
54798 TTCTGAC
1 TTCTGAC
54805 TTCTG
1 TTCTG
54810 CTTTTAGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.12, C:0.27, G:0.15, T:0.46
Consensus pattern (7 bp):
TTCTGAC
Found at i:61326 original size:32 final size:33
Alignment explanation
Indices: 61279--61346 Score: 111
Period size: 32 Copynumber: 2.1 Consensus size: 33
61269 AAAAACAAAC
*
61279 GAAAGAAAGACGACACCAGCGTTTCACTGGAGG
1 GAAAGAAAGACGACACCAACGTTTCACTGGAGG
*
61312 GAAAGACA-ACGACACCAACGTTTCACTGGAGG
1 GAAAGAAAGACGACACCAACGTTTCACTGGAGG
61344 GAA
1 GAA
61347 TTGGTTTTTA
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
32 26 0.79
33 7 0.21
ACGTcount: A:0.38, C:0.22, G:0.28, T:0.12
Consensus pattern (33 bp):
GAAAGAAAGACGACACCAACGTTTCACTGGAGG
Found at i:70435 original size:25 final size:25
Alignment explanation
Indices: 70388--70435 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
70378 AGAATTTATG
*
70388 TTTTTTATAATATGATTTCTTTTAA
1 TTTTTTATAATATGATTTATTTTAA
* **
70413 TTTTTTATAGTATTTTTTATTTT
1 TTTTTTATAATATGATTTATTTT
70436 TGATATATAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.23, C:0.02, G:0.04, T:0.71
Consensus pattern (25 bp):
TTTTTTATAATATGATTTATTTTAA
Found at i:70546 original size:22 final size:22
Alignment explanation
Indices: 70504--70547 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
70494 TAATGTTTGA
* *
70504 ATTTTTTATATTTTTTTAAAAT
1 ATTTTTTATATTTTATAAAAAT
70526 ATTTTTTAT-TTTTAATAAAAAT
1 ATTTTTTATATTTT-ATAAAAAT
70548 TAAATAAGTT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 4 0.21
22 15 0.79
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (22 bp):
ATTTTTTATATTTTATAAAAAT
Found at i:71038 original size:18 final size:19
Alignment explanation
Indices: 71015--71058 Score: 54
Period size: 18 Copynumber: 2.4 Consensus size: 19
71005 ATCATTACAT
* *
71015 ATTATTATAATTTA-ATTA
1 ATTATTAAAATTAATATTA
71033 ATTATTAAAATTAATATTA
1 ATTATTAAAATTAATATTA
*
71052 AGTATTA
1 ATTATTA
71059 GATTTTTTAG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
18 12 0.55
19 10 0.45
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (19 bp):
ATTATTAAAATTAATATTA
Found at i:74155 original size:72 final size:72
Alignment explanation
Indices: 74038--74185 Score: 244
Period size: 72 Copynumber: 2.1 Consensus size: 72
74028 TGGGCATCAC
* * *
74038 CAAAATATGTTTTGGTATACAATATCATGTATCTATTTCGGTTGCTCATAGAATCTAAGATTTGT
1 CAAAATATGTTTTGGTATACAATATCATGTAGCTATTTAGGTTGCTCATAGAATCTAAGATATGT
74103 TCAGTTG
66 TCAGTTG
*
74110 CAAAATAT-TGTTTGGTATACAATATCATGTAGCTATTTATGTTGCTCATAGAATCTAAGATATG
1 CAAAATATGT-TTTGGTATACAATATCATGTAGCTATTTAGGTTGCTCATAGAATCTAAGATATG
74174 TTCAGTTG
65 TTCAGTTG
74182 CAAA
1 CAAA
74186 GTTCTAATTC
Statistics
Matches: 71, Mismatches: 4, Indels: 2
0.92 0.05 0.03
Matches are distributed among these distances:
71 1 0.01
72 70 0.99
ACGTcount: A:0.32, C:0.12, G:0.16, T:0.40
Consensus pattern (72 bp):
CAAAATATGTTTTGGTATACAATATCATGTAGCTATTTAGGTTGCTCATAGAATCTAAGATATGT
TCAGTTG
Found at i:74202 original size:72 final size:72
Alignment explanation
Indices: 74054--74203 Score: 194
Period size: 72 Copynumber: 2.1 Consensus size: 72
74044 ATGTTTTGGT
* * *
74054 ATACAATATCATGTATCTATTTCGGTTGCTCATAGAATCTAAGATTTGTTCAGTTGCAAAATATT
1 ATACAATATCATGTAGCTATTTAGGTTGCTCATAGAATCTAAGATATGTTCAGTTGCAAAATATT
** ***
74119 GTTTGGT
66 AATTCCA
* *
74126 ATACAATATCATGTAGCTATTTATGTTGCTCATAGAATCTAAGATATGTTCAGTTGCAAAGT-TC
1 ATACAATATCATGTAGCTATTTAGGTTGCTCATAGAATCTAAGATATGTTCAGTTGCAAAATAT-
74190 TAATTCCA
65 TAATTCCA
74198 ATACAA
1 ATACAA
74204 CATCCAATAT
Statistics
Matches: 67, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
71 1 0.01
72 66 0.99
ACGTcount: A:0.33, C:0.14, G:0.15, T:0.39
Consensus pattern (72 bp):
ATACAATATCATGTAGCTATTTAGGTTGCTCATAGAATCTAAGATATGTTCAGTTGCAAAATATT
AATTCCA
Found at i:77940 original size:2 final size:2
Alignment explanation
Indices: 77935--77979 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
77925 TAAAAAAAAC
77935 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
77977 AT A
1 AT A
77980 ATTAAATTGA
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:80342 original size:146 final size:144
Alignment explanation
Indices: 80076--80342 Score: 376
Period size: 146 Copynumber: 1.8 Consensus size: 144
80066 AATGAACTTA
* * *
80076 CTCTCAGCAAGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGGGTGACCCGGGTTC
1 CTCTCAACAAGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGAGTGAACCGGGTTC
* * *
80141 GATCCCCGGCAACGGCGCTAGCTGTTATTTTTCGCTCCTTTTCTATCTAAAAAAAAATAACAATT
66 GATCCCCGGCAACAGCGCTAGC-GTAATTTTTCCCTCCTTTTCTATCTAAAAAAAAATAACAATT
80206 GTAAAATAAAAATTG
130 GTAAAATAAAAATTG
* * * *
80221 CTCTCAACAAAGTTGTTGTAGTATAGTTGTAAGTATTCTCGCCTGTCACGCGAGTGAACCGTGTT
1 CTCTCAAC-AAGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGAGTGAACCGGGTT
* *
80286 CGATCCCCGGCAACAGCG-TAAG-GTAATTTTTTCCCTCCTTTTCTCTCTAAAGAAAAA
65 CGATCCCCGGCAACAGCGCT-AGCGTAA-TTTTTCCCTCCTTTTCTATCTAAAAAAAAA
80343 GTAAAAGCTA
Statistics
Matches: 107, Mismatches: 12, Indels: 6
0.86 0.10 0.05
Matches are distributed among these distances:
144 3 0.03
145 35 0.33
146 69 0.64
ACGTcount: A:0.26, C:0.23, G:0.20, T:0.31
Consensus pattern (144 bp):
CTCTCAACAAGTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGTCACGCGAGTGAACCGGGTTC
GATCCCCGGCAACAGCGCTAGCGTAATTTTTCCCTCCTTTTCTATCTAAAAAAAAATAACAATTG
TAAAATAAAAATTG
Done.