Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009422.1 Hibiscus syriacus cultivar Beakdansim tig00113396_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: 48853
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:959 original size:20 final size:21
Alignment explanation
Indices: 934--984 Score: 77
Period size: 20 Copynumber: 2.5 Consensus size: 21
924 TTAAAACAAG
934 ATTATAATATCATAT-ATATT
1 ATTATAATATCATATCATATT
954 ATTATAATATCATATCATATT
1 ATTATAATATCATATCATATT
* *
975 GTTATGATAT
1 ATTATAATAT
985 TAAAAATATA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
20 15 0.54
21 13 0.46
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.49
Consensus pattern (21 bp):
ATTATAATATCATATCATATT
Found at i:997 original size:29 final size:31
Alignment explanation
Indices: 949--1026 Score: 79
Period size: 30 Copynumber: 2.5 Consensus size: 31
939 AATATCATAT
* * **
949 ATATTATTATAATATCATATCATATTGTT-ATG
1 ATATTAATA-AATAT-ATATCATATTATTAAAA
*
981 ATATTAA-AAATATATATTATATTATTAAAA
1 ATATTAATAAATATATATCATATTATTAAAA
1011 ATATTAATAAATATAT
1 ATATTAATAAATATAT
1027 TTTAATTATT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
29 11 0.28
30 13 0.33
31 9 0.23
32 6 0.15
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (31 bp):
ATATTAATAAATATATATCATATTATTAAAA
Found at i:1027 original size:21 final size:22
Alignment explanation
Indices: 981--1027 Score: 62
Period size: 21 Copynumber: 2.2 Consensus size: 22
971 TATTGTTATG
* *
981 ATATTAAAAATATATATTATAT
1 ATATTAAAAATATATAATAAAT
1003 -TATTAAAAATAT-TAATAAAT
1 ATATTAAAAATATATAATAAAT
1023 ATATT
1 ATATT
1028 TTAATTATTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 6 0.27
21 16 0.73
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (22 bp):
ATATTAAAAATATATAATAAAT
Found at i:1051 original size:29 final size:31
Alignment explanation
Indices: 981--1038 Score: 93
Period size: 30 Copynumber: 1.9 Consensus size: 31
971 TATTGTTATG
981 ATATTAA-AAATATATATTATATTATTAAAA
1 ATATTAATAAATATATATTATATTATTAAAA
*
1011 ATATTAATAAATATATTTTA-ATTATTAA
1 ATATTAATAAATATATATTATATTATTAA
1039 TATTTTATTA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 15 0.58
31 11 0.42
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (31 bp):
ATATTAATAAATATATATTATATTATTAAAA
Found at i:3301 original size:21 final size:21
Alignment explanation
Indices: 3275--3322 Score: 78
Period size: 21 Copynumber: 2.3 Consensus size: 21
3265 TACCTCGGAT
* *
3275 CATCAAATGACATCCTTGCTG
1 CATCAAAGGACATCCTGGCTG
3296 CATCAAAGGACATCCTGGCTG
1 CATCAAAGGACATCCTGGCTG
3317 CATCAA
1 CATCAA
3323 GGGAAAACCT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.31, C:0.29, G:0.17, T:0.23
Consensus pattern (21 bp):
CATCAAAGGACATCCTGGCTG
Found at i:4343 original size:20 final size:20
Alignment explanation
Indices: 4306--4343 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
4296 GAGTGAGAGA
*
4306 AAAATGAATAAAATAAAAAG
1 AAAATGAAGAAAATAAAAAG
4326 AAAATGAGAGAAAA-AAAA
1 AAAATGA-AGAAAATAAAA
4344 TGAGTGTCGA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
20 11 0.69
21 5 0.31
ACGTcount: A:0.76, C:0.00, G:0.13, T:0.11
Consensus pattern (20 bp):
AAAATGAAGAAAATAAAAAG
Found at i:5822 original size:22 final size:22
Alignment explanation
Indices: 5795--5878 Score: 66
Period size: 22 Copynumber: 3.8 Consensus size: 22
5785 ATACAATAAA
5795 TAATATTATTTATTATAAAATT
1 TAATATTATTTATTATAAAATT
*
5817 TAATATTA-TTATTTTTAAAATAT
1 TAATATTATTTA-TTATAAAAT-T
* * **
5840 TAAAATAATTTATT-TATTATT
1 TAATATTATTTATTATAAAATT
*
5861 AAAATATTATTT-TTATAA
1 -TAATATTATTTATTATAA
5879 TTTTATTAAT
Statistics
Matches: 48, Mismatches: 9, Indels: 10
0.72 0.13 0.15
Matches are distributed among these distances:
21 6 0.12
22 30 0.62
23 9 0.19
24 3 0.06
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (22 bp):
TAATATTATTTATTATAAAATT
Found at i:5875 original size:20 final size:20
Alignment explanation
Indices: 5823--5876 Score: 56
Period size: 20 Copynumber: 2.6 Consensus size: 20
5813 AATTTAATAT
*
5823 TATTATTTTTAAAATATTAAAA
1 TATTATTTTT--ATTATTAAAA
*
5845 TAATT-TATTTATTATTAAAA
1 T-ATTATTTTTATTATTAAAA
5865 TATTATTTTTAT
1 TATTATTTTTAT
5877 AATTTTATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 6
0.75 0.08 0.17
Matches are distributed among these distances:
19 3 0.11
20 16 0.59
22 5 0.19
23 3 0.11
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (20 bp):
TATTATTTTTATTATTAAAA
Found at i:6064 original size:26 final size:26
Alignment explanation
Indices: 6033--6114 Score: 71
Period size: 26 Copynumber: 3.2 Consensus size: 26
6023 ATTAGACTAT
6033 TATATTAATATTAAATATATAAATAA
1 TATATTAATATTAAATATATAAATAA
* * *
6059 TATATTCAT-TTTAATA-ATTTAATAA
1 TATATTAATATTAAATATA-TAAATAA
* *
6084 TATTATTTATATGAAAT-TAATAAATAA
1 TA-TATTAATATTAAATAT-ATAAATAA
6111 TATA
1 TATA
6115 AATTTATTAA
Statistics
Matches: 44, Mismatches: 7, Indels: 10
0.72 0.11 0.16
Matches are distributed among these distances:
24 1 0.02
25 14 0.32
26 16 0.36
27 12 0.27
28 1 0.02
ACGTcount: A:0.51, C:0.01, G:0.01, T:0.46
Consensus pattern (26 bp):
TATATTAATATTAAATATATAAATAA
Found at i:6159 original size:31 final size:32
Alignment explanation
Indices: 6124--6207 Score: 79
Period size: 31 Copynumber: 2.8 Consensus size: 32
6114 AAATTTATTA
6124 ATAATTTATTATATATTATTAAAATAA-CAAT
1 ATAATTTATTATATATTATTAAAATAATCAAT
* * * *
6155 ATAATATCTTATATTATTA-TAATATAATTAAT
1 ATAATTTATTATA-TATTATTAAAATAATCAAT
*
6187 -TATTTTATTATA-A-TATTAAAA
1 ATAATTTATTATATATTATTAAAA
6208 ATATTATATT
Statistics
Matches: 42, Mismatches: 8, Indels: 8
0.72 0.14 0.14
Matches are distributed among these distances:
28 2 0.05
29 5 0.12
31 27 0.64
32 8 0.19
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (32 bp):
ATAATTTATTATATATTATTAAAATAATCAAT
Found at i:6182 original size:23 final size:23
Alignment explanation
Indices: 6152--6227 Score: 84
Period size: 23 Copynumber: 3.3 Consensus size: 23
6142 TTAAAATAAC
*
6152 AATATAATATCTTATATTATTAT
1 AATATAATATATTATATTATTAT
*
6175 AATATAAT-TAATTATTTTATTAT
1 AATATAATAT-ATTATATTATTAT
*
6198 AATATTAAAAATATTATATTATTA-
1 AATA-T-AATATATTATATTATTAT
6222 AATATA
1 AATATA
6228 TCTAAATATT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
22 2 0.04
23 24 0.53
24 5 0.11
25 13 0.29
26 1 0.02
ACGTcount: A:0.49, C:0.01, G:0.00, T:0.50
Consensus pattern (23 bp):
AATATAATATATTATATTATTAT
Found at i:6188 original size:18 final size:19
Alignment explanation
Indices: 6154--6200 Score: 53
Period size: 18 Copynumber: 2.6 Consensus size: 19
6144 AAAATAACAA
*
6154 TATAATAT-CTTATATTAT
1 TATAATATAATTATATTAT
6172 TATAATATAATTA-ATTAT
1 TATAATATAATTATATTAT
* *
6190 TTTATTATAAT
1 TATAATATAAT
6201 ATTAAAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
18 22 0.88
19 3 0.12
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
TATAATATAATTATATTAT
Found at i:6214 original size:17 final size:17
Alignment explanation
Indices: 6192--6237 Score: 58
Period size: 17 Copynumber: 2.7 Consensus size: 17
6182 TTAATTATTT
6192 TATTATAATATTAAAAA
1 TATTATAATATTAAAAA
* *
6209 TATTATATTATTAAATA
1 TATTATAATATTAAAAA
6226 TATCTA-AATATT
1 TAT-TATAATATT
6238 TTAATAATTA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
17 23 0.92
18 2 0.08
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (17 bp):
TATTATAATATTAAAAA
Found at i:6582 original size:17 final size:17
Alignment explanation
Indices: 6560--6592 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
6550 AATGAGAGAG
6560 ACATA-GGATACGCGTAC
1 ACATAGGGAT-CGCGTAC
6577 ACATAGGGATCGCGTA
1 ACATAGGGATCGCGTA
6593 GACTTACGTG
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.33, C:0.21, G:0.27, T:0.18
Consensus pattern (17 bp):
ACATAGGGATCGCGTAC
Found at i:8651 original size:32 final size:32
Alignment explanation
Indices: 8597--8668 Score: 83
Period size: 32 Copynumber: 2.2 Consensus size: 32
8587 TCCTACGATT
** * *
8597 TACCCAAGTGAGTGTCTTGGGGCCT-GAGAGCC
1 TACCCAAGAAAGTGTCTCGGGGCATCG-GAGCC
*
8629 TACCCAAGAAAGTTTCTCGGGGCATCGGAGCC
1 TACCCAAGAAAGTGTCTCGGGGCATCGGAGCC
8661 TACCCAAG
1 TACCCAAG
8669 GGTCAACTTA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
32 33 0.97
33 1 0.03
ACGTcount: A:0.24, C:0.28, G:0.29, T:0.19
Consensus pattern (32 bp):
TACCCAAGAAAGTGTCTCGGGGCATCGGAGCC
Found at i:13962 original size:21 final size:20
Alignment explanation
Indices: 13876--14033 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
13866 AAATGACCAA
**
13876 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
13895 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* **
13915 CAGAATCGCAAATC-ATTTT
1 CAAAATCGCAACGCGATTTT
13934 CCAAAATCGCAACGCGATTCTT
1 -CAAAATCGCAACGCGATT-TT
* * * * *
13956 GAAAATCGCGATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
13977 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
13997 CAATAATCGCAACGCGAATAT
1 CAA-AATCGCAACGCGATTTT
*
14018 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
14034 ACACTTAAAT
Statistics
Matches: 102, Mismatches: 31, Indels: 11
0.71 0.22 0.08
Matches are distributed among these distances:
19 17 0.17
20 38 0.37
21 45 0.44
22 2 0.02
ACGTcount: A:0.38, C:0.25, G:0.17, T:0.20
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:14062 original size:20 final size:20
Alignment explanation
Indices: 14001--14390 Score: 457
Period size: 20 Copynumber: 19.4 Consensus size: 20
13991 GATTTTCAAT
* ** *
14001 AATCGCAACGCGAATATGAA
1 AATCGCAACGCGTATCCGTA
* *
14021 AATCGCAACGCG-AACACTTA
1 AATCGCAACGCGTATC-CGTA
14041 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
14061 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
**
14081 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGTATCCGTA
*
14101 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
14121 TATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
* * *
14141 AATCGCAACG-ATAATACATAA
1 AATCGCAACGCGT-ATCCGT-A
14162 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
14182 AATCGCAACGTGTATCCGTA
1 AATCGCAACGCGTATCCGTA
14202 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
14222 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
14242 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
14262 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
14282 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTA
*
14302 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
14322 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
14342 AATCGCAACG-ATAATCCGTA
1 AATCGCAACGCGT-ATCCGTA
* * *
14362 AATCGCAACGAGAATCTGTA
1 AATCGCAACGCGTATCCGTA
*
14382 AATCACAAC
1 AATCGCAAC
14391 ACTGAAATTT
Statistics
Matches: 319, Mismatches: 40, Indels: 22
0.84 0.10 0.06
Matches are distributed among these distances:
19 4 0.01
20 296 0.93
21 18 0.06
22 1 0.00
ACGTcount: A:0.35, C:0.26, G:0.18, T:0.21
Consensus pattern (20 bp):
AATCGCAACGCGTATCCGTA
Found at i:15106 original size:24 final size:24
Alignment explanation
Indices: 15067--15113 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
15057 AAATTTGGTC
15067 TTGGTCAATATCCGGACTTTGATA
1 TTGGTCAATATCCGGACTTTGATA
*
15091 TTGGTCAATA-CACGGATTTTGAT
1 TTGGTCAATATC-CGGACTTTGAT
15114 GATGTTTCAG
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:0.26, C:0.15, G:0.21, T:0.38
Consensus pattern (24 bp):
TTGGTCAATATCCGGACTTTGATA
Found at i:15305 original size:12 final size:12
Alignment explanation
Indices: 15288--15312 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
15278 ATATAATCCT
15288 GAAGAAGAAAAA
1 GAAGAAGAAAAA
15300 GAAGAAGAAAAA
1 GAAGAAGAAAAA
15312 G
1 G
15313 TCCCCGAAGA
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:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (12 bp):
GAAGAAGAAAAA
Found at i:17615 original size:19 final size:19
Alignment explanation
Indices: 17593--17865 Score: 345
Period size: 19 Copynumber: 15.4 Consensus size: 19
17583 CGGAAAATAC
*
17593 AATCGCAACGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
17612 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
17626 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
17646 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
17660 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
17679 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
17698 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
17712 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
17731 AATCGCAATGCGAAATG-A
1 AATCGCAATGCGAAATGAA
*
17749 AATCGCAATGCGAAATGGA
1 AATCGCAATGCGAAATGAA
17768 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
17787 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
17806 AATCGCAA--CGAAA-G--
1 AATCGCAATGCGAAATGAA
17820 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
17839 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
17858 AATCGCAA
1 AATCGCAA
17866 CGAGATAATC
Statistics
Matches: 225, Mismatches: 7, Indels: 44
0.82 0.03 0.16
Matches are distributed among these distances:
14 40 0.18
15 2 0.01
16 11 0.05
17 10 0.04
18 21 0.09
19 128 0.57
20 13 0.06
ACGTcount: A:0.47, C:0.18, G:0.22, T:0.14
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:17645 original size:34 final size:33
Alignment explanation
Indices: 17593--17887 Score: 160
Period size: 33 Copynumber: 8.5 Consensus size: 33
17583 CGGAAAATAC
*
17593 AATCGCAACGCGAAATGAAAATCCCAAC-ATGAA
1 AATCGCAATGCGAAATGAAAATCCCAACGA-GAA
* *
17626 AATCGCAATGCGGAAATGAAAATCGCAACGAGAG
1 AATCGCAATGC-GAAATGAAAATCCCAACGAGAA
*
17660 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--CG--A-GAA
* * * * *
17698 AATCGCAACGAGAGAATCG-CAATGCGAA--ATGAA
1 AATCGCAATGCGA-AAT-GAAAATCCCAACGA-GAA
* *
17731 AATCGCAATGCGAAATG-AAATCGCAATGCGAAATGGA
1 AATCGCAATGCGAAATGAAAATCCCAA--CG--A-GAA
*
17768 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--CG--A-GAA
*
17806 AATCGCAA--CGAAA-G--AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAAAATCCCAA--CG--A-GAA
* *
17839 AATCGCAATGCGAAATGAAAATCGCAACGAGAT
1 AATCGCAATGCGAAATGAAAATCCCAACGAGAA
17872 AATCGCAATGCGAAAT
1 AATCGCAATGCGAAAT
17888 TATAAACGCA
Statistics
Matches: 222, Mismatches: 19, Indels: 42
0.78 0.07 0.15
Matches are distributed among these distances:
31 6 0.03
32 3 0.01
33 87 0.39
34 30 0.14
35 9 0.04
36 8 0.04
37 22 0.10
38 48 0.22
39 8 0.04
40 1 0.00
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (33 bp):
AATCGCAATGCGAAATGAAAATCCCAACGAGAA
Found at i:17903 original size:52 final size:52
Alignment explanation
Indices: 17621--17887 Score: 446
Period size: 52 Copynumber: 5.0 Consensus size: 52
17611 AAATCCCAAC
17621 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
17674 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
17726 ATGAAAATCGCAATGCGAAATG-AAATCGCAATGCGAAATGGAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CGAGA--G-AATCGCAATGCGAA
*
17782 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAAAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
17834 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGATAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
17886 AT
1 AT
17888 TATAAACGCA
Statistics
Matches: 205, Mismatches: 3, Indels: 13
0.93 0.01 0.06
Matches are distributed among these distances:
51 9 0.04
52 124 0.60
53 21 0.10
55 6 0.03
56 36 0.18
57 9 0.04
ACGTcount: A:0.46, C:0.17, G:0.22, T:0.15
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:17984 original size:19 final size:19
Alignment explanation
Indices: 17894--17976 Score: 113
Period size: 20 Copynumber: 4.6 Consensus size: 19
17884 AAATTATAAA
17894 CGCATTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
17913 CCGCATTGCGATTTTCATTT
1 -CGCATTGCGATTTTCATTT
*
17933 CGCATTGCGA--TTC-TCT
1 CGCATTGCGATTTTCATTT
17949 CG--TTGCGATTTTCATTT
1 CGCATTGCGATTTTCATTT
17966 CGCATTGCGAT
1 CGCATTGCGAT
17977 AGTCATTTTG
Statistics
Matches: 56, Mismatches: 2, Indels: 11
0.81 0.03 0.16
Matches are distributed among these distances:
14 6 0.11
16 7 0.12
17 7 0.12
19 17 0.30
20 19 0.34
ACGTcount: A:0.14, C:0.24, G:0.18, T:0.43
Consensus pattern (19 bp):
CGCATTGCGATTTTCATTT
Found at i:18100 original size:14 final size:14
Alignment explanation
Indices: 18081--18117 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
18071 CATCAATTAC
18081 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
18095 ACAAATCATCTTTT
1 ACAAATCAACTTTT
18109 ACAAATCAA
1 ACAAATCAA
18118 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:20084 original size:14 final size:14
Alignment explanation
Indices: 20065--20121 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
20055 GCGAAATGAA
*
20065 AATCGCAACGACAG
1 AATCGCAACGAAAG
20079 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
20096 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
20112 AATCGCAACG
1 AATCGCAACG
20122 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:20092 original size:33 final size:33
Alignment explanation
Indices: 20046--20138 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
20036 GCGAAACCAA
*
20046 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
20079 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
20112 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
20139 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:20103 original size:19 final size:19
Alignment explanation
Indices: 20009--20143 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
19999 TAGTTTACTT
* *
20009 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
20029 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
20048 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
20067 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
20081 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
20100 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
20114 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
20133 TCGCAATGCGA
1 TCGCAACGCGA
20144 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:20155 original size:19 final size:19
Alignment explanation
Indices: 20139--20253 Score: 141
Period size: 19 Copynumber: 6.3 Consensus size: 19
20129 AAAATCGCAA
20139 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
20158 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
20172 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
**
20191 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
20210 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
20229 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
20249 TGCGA
1 TGCGA
20254 AAGTAAACTA
Statistics
Matches: 82, Mismatches: 8, Indels: 11
0.81 0.08 0.11
Matches are distributed among these distances:
14 11 0.13
15 1 0.01
16 1 0.01
17 1 0.01
18 1 0.01
19 54 0.66
20 13 0.16
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:20467 original size:92 final size:93
Alignment explanation
Indices: 20297--20675 Score: 735
Period size: 92 Copynumber: 4.1 Consensus size: 93
20287 TTGAATGGAT
20297 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
20362 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
20390 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
20454 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
20482 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
20546 AGTTTAGCAGAATTGGCAGCAACCGAAC
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
20574 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
*
20639 AGTTTAGCAGAATTGGCAGCAACCGAAT
66 AGTTTAGCAGAATTGGCAGCAACCGAAC
20667 AAATTTACT
1 AAATTTACT
20676 AAGCAATCTA
Statistics
Matches: 284, Mismatches: 1, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
92 184 0.65
93 100 0.35
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (93 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:20626 original size:185 final size:185
Alignment explanation
Indices: 20297--20675 Score: 733
Period size: 185 Copynumber: 2.0 Consensus size: 185
20287 TTGAATGGAT
20297 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
20362 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
20427 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
131 TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
20482 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATA-TATTTCACAGTGTTAAAGAATACAC
1 AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
20546 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
66 AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
*
20611 TACTATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAT
131 TA-TATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
20667 AAATTTACT
1 AAATTTACT
20676 AAGCAATCTA
Statistics
Matches: 192, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
184 92 0.48
185 100 0.52
ACGTcount: A:0.46, C:0.18, G:0.13, T:0.22
Consensus pattern (185 bp):
AAATTTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACAC
AGTTTAGCAGAATTGGCAGCAACCGAACAAATTTACTTTCAACCAAAAGACAAAACAAAGACAAA
TATATTTCACAGTGTTAAAGAATACACAGTTTAGCAGAATTGGCAGCAACCGAAC
Found at i:22416 original size:19 final size:18
Alignment explanation
Indices: 22392--22489 Score: 86
Period size: 19 Copynumber: 5.7 Consensus size: 18
22382 CGCACGAGAG
22392 AATCGCAACGCGAGATGA
1 AATCGCAACGCGAGATGA
22410 CAATCGCAA--CGAGA-G-
1 -AATCGCAACGCGAGATGA
*
22425 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAGATG-A
22444 AATCGCAA--CGAGA-G-
1 AATCGCAACGCGAGATGA
*
22458 AATCGCAACGCGAAATGAA
1 AATCGCAACGCGAGATG-A
*
22477 AATCGCAATGCGA
1 AATCGCAACGCGA
22490 TTTTGGTTTC
Statistics
Matches: 65, Mismatches: 4, Indels: 20
0.73 0.04 0.22
Matches are distributed among these distances:
14 16 0.25
16 10 0.15
17 11 0.17
19 28 0.43
ACGTcount: A:0.43, C:0.22, G:0.24, T:0.10
Consensus pattern (18 bp):
AATCGCAACGCGAGATGA
Found at i:22424 original size:33 final size:33
Alignment explanation
Indices: 22371--22484 Score: 203
Period size: 33 Copynumber: 3.5 Consensus size: 33
22361 TCTTTTGGTT
22371 GAAATGAAAATCGC-ACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* *
22403 GAGATGACAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
22436 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
22469 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
22485 TGCGATTTTG
Statistics
Matches: 77, Mismatches: 4, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
32 12 0.16
33 65 0.84
ACGTcount: A:0.45, C:0.21, G:0.25, T:0.10
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:22430 original size:14 final size:14
Alignment explanation
Indices: 22379--22467 Score: 72
Period size: 14 Copynumber: 5.7 Consensus size: 14
22369 TTGAAATGAA
22379 AATCGC-ACGAGAG
1 AATCGCAACGAGAG
22392 AATCGCAACGCGAGATG
1 AATCGCAA--CGAGA-G
22409 ACAATCGCAACGAGAG
1 --AATCGCAACGAGAG
*
22425 AATCGCAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
22444 AATCGCAACGAGAG
1 AATCGCAACGAGAG
22458 AATCGCAACG
1 AATCGCAACG
22468 CGAAATGAAA
Statistics
Matches: 63, Mismatches: 2, Indels: 21
0.73 0.02 0.24
Matches are distributed among these distances:
13 6 0.10
14 21 0.33
15 1 0.02
16 8 0.13
17 8 0.13
18 1 0.02
19 18 0.29
ACGTcount: A:0.42, C:0.24, G:0.26, T:0.09
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:22520 original size:14 final size:14
Alignment explanation
Indices: 22501--22555 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
22491 TTTGGTTTCG
22501 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
22515 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
22534 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
22548 CGTTGCGA
1 CGTTGCGA
22556 CAGTCATTCT
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
16 3 0.09
17 3 0.09
19 10 0.29
ACGTcount: A:0.09, C:0.25, G:0.24, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:22533 original size:33 final size:33
Alignment explanation
Indices: 22485--22555 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
22475 AAAATCGCAA
**
22485 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
22518 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
22551 TGCGA
1 TGCGA
22556 CAGTCATTCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 36 1.00
ACGTcount: A:0.08, C:0.23, G:0.25, T:0.44
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:22563 original size:33 final size:33
Alignment explanation
Indices: 22496--22577 Score: 119
Period size: 33 Copynumber: 2.5 Consensus size: 33
22486 GCGATTTTGG
***
22496 TTTCGCGTTGCGATTCTCTCGTTGCGATTTTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
22529 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
1 TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
*
22562 TTCTCTCGTTGCGATT
1 TT-TCGCGTTGCGATT
22578 TTCATTTATC
Statistics
Matches: 44, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.73
34 12 0.27
ACGTcount: A:0.10, C:0.26, G:0.22, T:0.43
Consensus pattern (33 bp):
TTTCGCGTTGCGATTCTCTCGTTGCGACAGTCA
Found at i:22582 original size:20 final size:20
Alignment explanation
Indices: 22508--22596 Score: 75
Period size: 20 Copynumber: 4.8 Consensus size: 20
22498 TCGCGTTGCG
22508 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
22528 ATT-TCGCGTTGCG------
1 ATTCTCTCGTTGCGATTTTC
***
22541 ATTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTC
22561 ATTCTCTCGTTGCGATTTTC
1 ATTCTCTCGTTGCGATTTTC
*
22581 ATTTATCTCGTTGCGA
1 A-TTCTCTCGTTGCGA
22597 CTCTTCTGCA
Statistics
Matches: 55, Mismatches: 6, Indels: 15
0.72 0.08 0.20
Matches are distributed among these distances:
13 3 0.05
14 9 0.16
19 9 0.16
20 21 0.38
21 13 0.24
ACGTcount: A:0.12, C:0.25, G:0.19, T:0.44
Consensus pattern (20 bp):
ATTCTCTCGTTGCGATTTTC
Found at i:22717 original size:31 final size:32
Alignment explanation
Indices: 22679--22746 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 32
22669 ACTAACTTGA
*
22679 AAATCGCAAC-AGAGAATAGCAACGCGAAATG
1 AAATCGCAACGACAGAATAGCAACGCGAAATG
* *
22710 AAATCGCAACGACAGAATCGTAACGCGAAATG
1 AAATCGCAACGACAGAATAGCAACGCGAAATG
22742 AAATC
1 AAATC
22747 TAAGTGAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
31 10 0.30
32 23 0.70
ACGTcount: A:0.47, C:0.21, G:0.21, T:0.12
Consensus pattern (32 bp):
AAATCGCAACGACAGAATAGCAACGCGAAATG
Found at i:22720 original size:18 final size:18
Alignment explanation
Indices: 22697--22746 Score: 54
Period size: 16 Copynumber: 3.0 Consensus size: 18
22687 ACAGAGAATA
22697 GCAACGCGAAATGAAATC
1 GCAACGCGAAATGAAATC
*
22715 GCAA--CGACA-G-AATC
1 GCAACGCGAAATGAAATC
*
22729 GTAACGCGAAATGAAATC
1 GCAACGCGAAATGAAATC
22747 TAAGTGAAAT
Statistics
Matches: 25, Mismatches: 3, Indels: 8
0.69 0.08 0.22
Matches are distributed among these distances:
14 7 0.28
15 1 0.04
16 8 0.32
17 1 0.04
18 8 0.32
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (18 bp):
GCAACGCGAAATGAAATC
Found at i:22976 original size:22 final size:21
Alignment explanation
Indices: 22925--22978 Score: 63
Period size: 22 Copynumber: 2.5 Consensus size: 21
22915 TGGTTGTGAG
**
22925 GGATTTCGCCGGAGATGGGAC
1 GGATTTCTTCGGAGATGGGAC
**
22946 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGAT-GGGAC
22968 GGATTTCTTCG
1 GGATTTCTTCG
22979 CCGTAGAGAG
Statistics
Matches: 26, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
21 12 0.46
22 14 0.54
ACGTcount: A:0.20, C:0.17, G:0.39, T:0.24
Consensus pattern (21 bp):
GGATTTCTTCGGAGATGGGAC
Found at i:23149 original size:20 final size:20
Alignment explanation
Indices: 23124--23316 Score: 219
Period size: 20 Copynumber: 9.6 Consensus size: 20
23114 CTTTAAATAT
23124 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
23144 CGCGTTGCGATTTTATGTATTA
1 CGCGTTGCGA-TTTACGGA-TA
*
23166 -TCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
23185 CGCGTTGCGATATACGGATA
1 CGCGTTGCGATTTACGGATA
* **
23205 CGCATTGCGATTTACCCATA
1 CGCGTTGCGATTTACGGATA
23225 CGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
*
23245 CACGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATA
* *
23265 CGCGTTGCGATTTATGTG-TT
1 CGCGTTGCGATTTACG-GATA
* ** *
23285 CGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATA
23305 CGCGTTGCGATT
1 CGCGTTGCGATT
23317 ATTGAAAATC
Statistics
Matches: 146, Mismatches: 22, Indels: 10
0.82 0.12 0.06
Matches are distributed among these distances:
19 2 0.01
20 127 0.87
21 15 0.10
22 2 0.01
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (20 bp):
CGCGTTGCGATTTACGGATA
Found at i:23311 original size:60 final size:60
Alignment explanation
Indices: 23124--23316 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
23114 CTTTAAATAT
**
23124 CGCGTTGCGATTTACGGATACGCGTTGCGATTTTATGTATTATCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTATTCGCGTTGCGATTTACGGATA
* * *** *
23185 CGCGTTGCGATATACGGATACGCATTGCGATTTACCCATACGCGTTGCGATTTACGGATA
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
* * * ** *
23245 CACGTTGCGATTTACGGATACGCGTTGCGATTTATGTGTTCGCGTTGCGATTTTCATATT
1 CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
23305 CGCGTTGCGATT
1 CGCGTTGCGATT
23317 ATTGAAAATC
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 83 0.75
61 28 0.25
ACGTcount: A:0.19, C:0.20, G:0.26, T:0.35
Consensus pattern (60 bp):
CGCGTTGCGATTTACGGATACGCGTTGCGATTTATGTATTCGCGTTGCGATTTACGGATA
Found at i:25665 original size:2 final size:2
Alignment explanation
Indices: 25660--25689 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
25650 TTCTTTTTTG
25660 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
25690 GGTTGTAAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:25995 original size:17 final size:17
Alignment explanation
Indices: 25973--26015 Score: 68
Period size: 17 Copynumber: 2.5 Consensus size: 17
25963 ATTCGAGTTT
*
25973 GAGTTCGAGCTTGAATC
1 GAGTTCGAGCATGAATC
25990 GAGTTCGAGCATGAATC
1 GAGTTCGAGCATGAATC
*
26007 GAGCTCGAG
1 GAGTTCGAG
26016 TCTCGAGCTT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.26, C:0.19, G:0.33, T:0.23
Consensus pattern (17 bp):
GAGTTCGAGCATGAATC
Found at i:26023 original size:24 final size:23
Alignment explanation
Indices: 25988--26036 Score: 71
Period size: 24 Copynumber: 2.1 Consensus size: 23
25978 CGAGCTTGAA
*
25988 TCGAGTTCGAGCATGAATCGAGC
1 TCGAGTTCGAGCATCAATCGAGC
*
26011 TCGAGTCTCGAGCTTCAATCGAGC
1 TCGAGT-TCGAGCATCAATCGAGC
26035 TC
1 TC
26037 CTAAATTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 6 0.26
24 17 0.74
ACGTcount: A:0.22, C:0.27, G:0.27, T:0.24
Consensus pattern (23 bp):
TCGAGTTCGAGCATCAATCGAGC
Found at i:34628 original size:9 final size:9
Alignment explanation
Indices: 34614--34665 Score: 54
Period size: 9 Copynumber: 5.8 Consensus size: 9
34604 TTAATATTCT
34614 TTTATTTTA
1 TTTATTTTA
34623 TTTATTTTA
1 TTTATTTTA
34632 -TTATTTT-
1 TTTATTTTA
* *
34639 TTCATTTGA
1 TTTATTTTA
34648 TTTATTTAATA
1 TTTATTT--TA
34659 TTTATTT
1 TTTATTT
34666 ATTATTCTCA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
8 12 0.34
9 15 0.43
11 8 0.23
ACGTcount: A:0.23, C:0.02, G:0.02, T:0.73
Consensus pattern (9 bp):
TTTATTTTA
Found at i:34645 original size:25 final size:25
Alignment explanation
Indices: 34603--34668 Score: 75
Period size: 25 Copynumber: 2.7 Consensus size: 25
34593 CTTTTAAAAC
*
34603 TTTAATATTCTTTTATTTTATTTAT
1 TTTAATATTCTTTTATTTGATTTAT
*
34628 TTTATTATT-TTTTCATTTGATTTA-
1 TTTAATATTCTTTT-ATTTGATTTAT
34652 TTTAATATT-TATTTATT
1 TTTAATATTCT-TTTATT
34669 ATTCTCATCT
Statistics
Matches: 36, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
24 16 0.44
25 20 0.56
ACGTcount: A:0.24, C:0.03, G:0.02, T:0.71
Consensus pattern (25 bp):
TTTAATATTCTTTTATTTGATTTAT
Found at i:38478 original size:21 final size:21
Alignment explanation
Indices: 38445--38489 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
38435 ATCAAGTACA
*
38445 ATAATATATTAGGTAGCGCTT
1 ATAATATAATAGGTAGCGCTT
* *
38466 ATAATGTAATAGGTAGCGTTT
1 ATAATATAATAGGTAGCGCTT
38487 ATA
1 ATA
38490 TTGACATATT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.36, C:0.07, G:0.20, T:0.38
Consensus pattern (21 bp):
ATAATATAATAGGTAGCGCTT
Found at i:39322 original size:111 final size:111
Alignment explanation
Indices: 39120--39409 Score: 456
Period size: 111 Copynumber: 2.6 Consensus size: 111
39110 TGGTATCTCT
* * *
39120 ACCGGTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCAA
1 ACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATC-ATATATTTTTATAAAGTATCGA
* * *
39185 CACTTTCAATATATCCGGTAGTGCTTTACTTGTTTTGTCATTTATAG
65 CACTTTCAATATATCCGGTAGCGCTTTACCTATTTTGTCATTTATAG
* * *
39232 ATCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATAGATCA-ATATATTTTATAAAGTATCGT
1 ACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCATATAT-TTTTATAAAGTATCGA
39296 CACTTTCAATATATCCGGTAGCGCTTTACCTATTTTGTCATTTATAG
65 CACTTTCAATATATCCGGTAGCGCTTTACCTATTTTGTCATTTATAG
* *
39343 ACCGGTTTTATCATTTGTTTACCTGTTATATTGTTATGGATCATATATTTTTATAAAGTATCGAC
1 ACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCATATATTTTTATAAAGTATCGAC
39408 AC
66 AC
39410 AAACCGACAA
Statistics
Matches: 162, Mismatches: 14, Indels: 5
0.90 0.08 0.03
Matches are distributed among these distances:
110 3 0.02
111 116 0.72
112 43 0.27
ACGTcount: A:0.26, C:0.14, G:0.13, T:0.47
Consensus pattern (111 bp):
ACCGGTTTTGTCATTTTTTTACCTGTTATATTGTTATGGATCATATATTTTTATAAAGTATCGAC
ACTTTCAATATATCCGGTAGCGCTTTACCTATTTTGTCATTTATAG
Found at i:42035 original size:21 final size:22
Alignment explanation
Indices: 41998--42042 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
41988 TAATTATACA
41998 TTTTATCATATATA-TTTAATT
1 TTTTATCATATATATTTTAATT
*
42019 TTTTATCA-ATTTAATTTTAATT
1 TTTTATCATATAT-ATTTTAATT
42041 TT
1 TT
42043 AATTTAATTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
20 3 0.14
21 9 0.43
22 9 0.43
ACGTcount: A:0.31, C:0.04, G:0.00, T:0.64
Consensus pattern (22 bp):
TTTTATCATATATATTTTAATT
Found at i:44268 original size:20 final size:19
Alignment explanation
Indices: 44231--44277 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
44221 ACCGTATCCT
*
44231 TAAAATTTTTTTTTTAATA
1 TAAAATTTTTTCTTTAATA
44250 TAAAATTTATTTCTTTAATA
1 TAAAATTT-TTTCTTTAATA
44270 T-AAATTTT
1 TAAAATTTT
44278 GTATTCGTTC
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
18 1 0.04
19 14 0.54
20 11 0.42
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (19 bp):
TAAAATTTTTTCTTTAATA
Found at i:46883 original size:19 final size:20
Alignment explanation
Indices: 46859--46908 Score: 84
Period size: 19 Copynumber: 2.5 Consensus size: 20
46849 GATTTTCCAG
*
46859 AATCGCAACGCGAATAT-TA
1 AATCGCAACGCGAACATATA
46878 AATCGCAACGCGAACATATA
1 AATCGCAACGCGAACATATA
46898 AATCGCAACGC
1 AATCGCAACGC
46909 AATTCTGACT
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
19 16 0.55
20 13 0.45
ACGTcount: A:0.42, C:0.26, G:0.16, T:0.16
Consensus pattern (20 bp):
AATCGCAACGCGAACATATA
Found at i:46964 original size:20 final size:20
Alignment explanation
Indices: 46919--47209 Score: 230
Period size: 20 Copynumber: 14.3 Consensus size: 20
46909 AATTCTGACT
*
46919 ATCGCAACGAGTACCCGTAAAA
1 ATCGCAACGAGTATCCGT--AA
*
46941 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
** *
46961 ATCGCAACGAAAATACGTAAA
1 ATCGCAACGAGTATCCGT-AA
*
46982 ATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
* * *
47002 ATCACAACGAGAATACGTAA
1 ATCGCAACGAGTATCCGTAA
* * *
47022 ATCGCAACGCG-ATTC-TGATT
1 ATCGCAACGAGTATCCGT-A-A
* * *
47042 ATCGCAACGAGAATACGTTA
1 ATCGCAACGAGTATCCGTAA
* *
47062 ATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGTATCCGTAA
* * *
47082 ATCGCAACGAGAATACATAAA
1 ATCGCAACGAGTATCCGT-AA
* * *
47103 ATCGTAACGCGTATCTGTAA
1 ATCGCAACGAGTATCCGTAA
* * *
47123 ATCGCAAAGAGAATCTGTAA
1 ATCGCAACGAGTATCCGTAA
47143 ATCGCAACGA-TAATCCGTAA
1 ATCGCAACGAGT-ATCCGTAA
47163 ATCGCAACGA-TAATCCGTAA
1 ATCGCAACGAGT-ATCCGTAA
* *
47183 ATCGCAACGAGAATCTGTAA
1 ATCGCAACGAGTATCCGTAA
47203 ATCGCAA
1 ATCGCAA
47210 TACTGAAATT
Statistics
Matches: 214, Mismatches: 47, Indels: 18
0.77 0.17 0.06
Matches are distributed among these distances:
18 1 0.00
19 4 0.02
20 159 0.74
21 33 0.15
22 17 0.08
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (20 bp):
ATCGCAACGAGTATCCGTAA
Found at i:47050 original size:40 final size:40
Alignment explanation
Indices: 46939--47209 Score: 316
Period size: 40 Copynumber: 6.7 Consensus size: 40
46929 GTACCCGTAA
*
46939 AAATCGCAACGCGTATCCGTAAATCGCAACGAAAATACGT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT
*
46979 AAAATCGCAACGCGTATCCGTAAATCACAACGAGAATACGT
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT
* *
47020 AAATCGCAACGCG-ATTC-TGATTATCGCAACGAGAATACGT
1 AAATCGCAACGCGTATCCGT-A-AATCGCAACGAGAATACGT
* * *
47060 TAATCGCAATGCGTATCCGTAAATCGCAACGAGAATACAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT
* * *
47100 AAAATCGTAACGCGTATCTGTAAATCGCAAAGAGAAT-CTGT
1 -AAATCGCAACGCGTATCCGTAAATCGCAACGAGAATAC-GT
* * *
47141 AAATCGCAACG-ATAATCCGTAAATCGCAACGATAATCCGT
1 AAATCGCAACGCGT-ATCCGTAAATCGCAACGAGAATACGT
* * *
47181 AAATCGCAACGAGAATCTGTAAATCGCAA
1 AAATCGCAACGCGTATCCGTAAATCGCAA
47210 TACTGAAATT
Statistics
Matches: 197, Mismatches: 24, Indels: 19
0.82 0.10 0.08
Matches are distributed among these distances:
38 1 0.01
39 5 0.03
40 115 0.58
41 75 0.38
42 1 0.01
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (40 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGAGAATACGT
Found at i:47105 original size:101 final size:101
Alignment explanation
Indices: 46939--47196 Score: 256
Period size: 101 Copynumber: 2.6 Consensus size: 101
46929 GTACCCGTAA
* * * * * * * * *
46939 AAATCGCAACGCGTATCCGTAAATCGCAACGAAAATACGTAAAATCGCAACGCGTATCCGT-AAA
1 AAATCGCAACGAGAATACGTAAATCGCAACGATAATCCGT-AAATCGCAACGAGAATACATAAAA
* * *
47003 TCACAACGAGAATAC-GTAAATCGCAACGCGATTCTG-
65 TCACAACGAGAAT-CTGTAAATCGCAAAGAGAATCTGT
* *
47039 ATTATCGCAACGAGAATACGTTAATCGCAATGCG-T-ATCCGTAAATCGCAACGAGAATACATAA
1 A-AATCGCAACGAGAATACGTAAATCGCAA--CGATAATCCGTAAATCGCAACGAGAATACATAA
** * *
47102 AATCGTAACGCGTATCTGTAAATCGCAAAGAGAATCTGT
63 AATCACAACGAGAATCTGTAAATCGCAAAGAGAATCTGT
* *
47141 AAATCGCAACGATAATCCGTAAATCGCAACGATAATCCGTAAATCGCAACGAGAAT
1 AAATCGCAACGAGAATACGTAAATCGCAACGATAATCCGTAAATCGCAACGAGAAT
47197 CTGTAAATCG
Statistics
Matches: 128, Mismatches: 22, Indels: 15
0.78 0.13 0.09
Matches are distributed among these distances:
99 2 0.02
100 19 0.15
101 104 0.81
102 1 0.01
103 2 0.02
ACGTcount: A:0.40, C:0.22, G:0.18, T:0.20
Consensus pattern (101 bp):
AAATCGCAACGAGAATACGTAAATCGCAACGATAATCCGTAAATCGCAACGAGAATACATAAAAT
CACAACGAGAATCTGTAAATCGCAAAGAGAATCTGT
Found at i:47106 original size:121 final size:122
Alignment explanation
Indices: 46896--47151 Score: 363
Period size: 121 Copynumber: 2.1 Consensus size: 122
46886 CGCGAACATA
* *
46896 TAAATCGCAACGCAATTCTGACTATCGCAACGAGTACCCGTAAAAATCGCAACGCGTATCCGTAA
1 TAAATCGCAACGCAATTCTGACTATCGCAACGAGAACACGT-AAAATCGCAACGCGTATCCGTAA
* *
46961 ATCGCAACGAAAATACGTAAAATCGCAACGCGTATCCGTAAATCACAACGAGAATAC-G
65 ATCGCAACGAAAATACATAAAATCGCAACGCGTATCCGTAAATCACAAAGAGAAT-CTG
* * * * *
47019 TAAATCGCAACGCGATTCTGATTATCGCAACGAGAATACGT-TAATCGCAATGCGTATCCGTAAA
1 TAAATCGCAACGCAATTCTGACTATCGCAACGAGAACACGTAAAATCGCAACGCGTATCCGTAAA
* * * *
47083 TCGCAACGAGAATACATAAAATCGTAACGCGTATCTGTAAATCGCAAAGAGAATCTG
66 TCGCAACGAAAATACATAAAATCGCAACGCGTATCCGTAAATCACAAAGAGAATCTG
47140 TAAATCGCAACG
1 TAAATCGCAACG
47152 ATAATCCGTA
Statistics
Matches: 119, Mismatches: 13, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
120 1 0.01
121 82 0.69
123 36 0.30
ACGTcount: A:0.38, C:0.23, G:0.18, T:0.20
Consensus pattern (122 bp):
TAAATCGCAACGCAATTCTGACTATCGCAACGAGAACACGTAAAATCGCAACGCGTATCCGTAAA
TCGCAACGAAAATACATAAAATCGCAACGCGTATCCGTAAATCACAAAGAGAATCTG
Found at i:47167 original size:121 final size:121
Alignment explanation
Indices: 46939--47209 Score: 348
Period size: 121 Copynumber: 2.2 Consensus size: 121
46929 GTACCCGTAA
*
46939 AAATCGCAACGCGTATCCGTAAATCGCAACGAAAATACGTAAAATCGCAACGCGTATCCGTAAAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGAAAATACATAAAATCGCAACGCGTATCCGTAAAT
* * * * *
47004 CACAACGAGAATACGTAAATCGCAACGCGATTCTGATTATCGCAACGAGAATACGT
66 CACAAAGAGAATACGTAAATCGCAACGAGAATCCGATAATCGCAACGAGAATACGT
* * * * *
47060 TAATCGCAATGCGTATCCGTAAATCGCAACGAGAATACATAAAATCGTAACGCGTATCTGTAAAT
1 AAATCGCAACGCGTATCCGTAAATCGCAACGAAAATACATAAAATCGCAACGCGTATCCGTAAAT
* * * *
47125 CGCAAAGAGAAT-CTGTAAATCGCAACGATAATCCG-TAAATCGCAACGATAATCCGT
66 CACAAAGAGAATAC-GTAAATCGCAACGAGAATCCGAT-AATCGCAACGAGAATACGT
* * *
47181 AAATCGCAACGAGAATCTGTAAATCGCAA
1 AAATCGCAACGCGTATCCGTAAATCGCAA
47210 TACTGAAATT
Statistics
Matches: 128, Mismatches: 20, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
120 2 0.02
121 126 0.98
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.20
Consensus pattern (121 bp):
AAATCGCAACGCGTATCCGTAAATCGCAACGAAAATACATAAAATCGCAACGCGTATCCGTAAAT
CACAAAGAGAATACGTAAATCGCAACGAGAATCCGATAATCGCAACGAGAATACGT
Found at i:48031 original size:24 final size:24
Alignment explanation
Indices: 48004--48057 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
47994 GTATTCGAAA
48004 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
48028 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
48052 TTTGAT
1 TTTGAT
48058 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Done.