Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008885.1 Hibiscus syriacus cultivar Beakdansim tig00112131_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: 671647
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 3
Found at i:93 original size:55 final size:55
Alignment explanation
Indices: 1--220 Score: 370
Period size: 55 Copynumber: 4.0 Consensus size: 55
* *
1 CAATCGTGTCTGCTCCCT-TTTCTTCAGAGAGAGATAAGACTCGAACAATCTTCAA
1 CAATCGCGTCTGCTCCCTATTTCTTCAGAGAG-TATAAGACTCGAACAATCTTCAA
* *
56 CAATCGCGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAAAAATTTTCAA
1 CAATCGCGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAA
*
111 CAATCGTGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAA
1 CAATCGCGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAA
*
166 CAATCGCGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGATCAATCTTCAA
1 CAATCGCGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAA
221 TTATCGTTGG
Statistics
Matches: 155, Mismatches: 9, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
55 142 0.92
56 13 0.08
ACGTcount: A:0.29, C:0.25, G:0.15, T:0.30
Consensus pattern (55 bp):
CAATCGCGTCTGCTCCCTATTTCTTCAGAGAGTATAAGACTCGAACAATCTTCAA
Found at i:1233 original size:7 final size:8
Alignment explanation
Indices: 1204--1257 Score: 54
Period size: 8 Copynumber: 6.2 Consensus size: 8
1194 TGAACCGTCA
1204 TTTTTCAT
1 TTTTTCAT
1212 TTTTTCATT
1 TTTTTCA-T
*
1221 CCTTTTTTATT
1 --TTTTTCA-T
*
1232 TTTTTTAT
1 TTTTTCAT
1240 TTTTTCAT
1 TTTTTCAT
1248 TTTTTCAT
1 TTTTTCAT
1256 TT
1 TT
1258 CACTCATTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
8 25 0.61
9 8 0.20
11 8 0.20
ACGTcount: A:0.11, C:0.11, G:0.00, T:0.78
Consensus pattern (8 bp):
TTTTTCAT
Found at i:1279 original size:36 final size:36
Alignment explanation
Indices: 1204--1281 Score: 86
Period size: 36 Copynumber: 2.1 Consensus size: 36
1194 TGAACCGTCA
** * *
1204 TTTTTCATTTTTTCATTCCTTTTTTATTTTTTTTAT
1 TTTTTCATTTTTTCATTCCTCATTTATTTCTTCTAT
*
1240 TTTTTCATTTTTTCATTTCACTCATTT-TTTCTTCTTT
1 TTTTTCATTTTTTCA-TTC-CTCATTTATTTCTTCTAT
1277 TTTTT
1 TTTTT
1282 TTTTCTTCAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
36 15 0.43
37 15 0.43
38 5 0.14
ACGTcount: A:0.10, C:0.14, G:0.00, T:0.76
Consensus pattern (36 bp):
TTTTTCATTTTTTCATTCCTCATTTATTTCTTCTAT
Found at i:4740 original size:8 final size:8
Alignment explanation
Indices: 4727--4752 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
4717 GAAAAAGAAG
4727 ATATACAT
1 ATATACAT
4735 ATATACAT
1 ATATACAT
4743 ATATACAT
1 ATATACAT
4751 AT
1 AT
4753 GGGAGAATCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.50, C:0.12, G:0.00, T:0.38
Consensus pattern (8 bp):
ATATACAT
Found at i:14226 original size:17 final size:17
Alignment explanation
Indices: 14206--14248 Score: 77
Period size: 17 Copynumber: 2.5 Consensus size: 17
14196 TGTGCTTGCA
14206 GGTCACGGGTGCGAGCT
1 GGTCACGGGTGCGAGCT
*
14223 GGTCACGAGTGCGAGCT
1 GGTCACGGGTGCGAGCT
14240 GGTCACGGG
1 GGTCACGGG
14249 CTTCAGGGAG
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:0.14, C:0.23, G:0.47, T:0.16
Consensus pattern (17 bp):
GGTCACGGGTGCGAGCT
Found at i:14859 original size:21 final size:23
Alignment explanation
Indices: 14835--14884 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 23
14825 CGAAAATATT
* *
14835 CATTTTA-GGTAG-CAAAATTAA
1 CATTTTATGGTAGAAAAAAATAA
14856 CA-TTTATGGTAGAAAAAAATAA
1 CATTTTATGGTAGAAAAAAATAA
14878 CATTTTA
1 CATTTTA
14885 AGTAACGCTC
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
20 4 0.17
21 7 0.29
22 9 0.38
23 4 0.17
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.34
Consensus pattern (23 bp):
CATTTTATGGTAGAAAAAAATAA
Found at i:15268 original size:12 final size:13
Alignment explanation
Indices: 15243--15280 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
15233 TTATTTTTAT
15243 TTAAATTAAAAAA
1 TTAAATTAAAAAA
15256 TTAAATT-AAAAA
1 TTAAATTAAAAAA
**
15268 TTATTTTAAAAAA
1 TTAAATTAAAAAA
15281 CACCCAAAAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 10 0.45
13 12 0.55
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (13 bp):
TTAAATTAAAAAA
Found at i:21665 original size:25 final size:29
Alignment explanation
Indices: 21601--21674 Score: 66
Period size: 32 Copynumber: 2.6 Consensus size: 29
21591 AAATATAAAA
*
21601 TTTATTAATTAAAAATTTCAACTAGATTTT
1 TTTATTAATTAAAAATATCAACTA-ATTTT
21631 TATTATTTAATTAAAAATAT-AA-T-A-TTT
1 T-TTA-TTAATTAAAAATATCAACTAATTTT
* *
21658 TTTATTAAATATAAATA
1 TTTATTAATTAAAAATA
21675 ATAAATTAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
25 11 0.28
26 3 0.08
27 4 0.10
28 1 0.03
30 2 0.05
31 5 0.13
32 13 0.33
ACGTcount: A:0.46, C:0.03, G:0.01, T:0.50
Consensus pattern (29 bp):
TTTATTAATTAAAAATATCAACTAATTTT
Found at i:32137 original size:19 final size:19
Alignment explanation
Indices: 32094--32147 Score: 63
Period size: 19 Copynumber: 2.8 Consensus size: 19
32084 AAATAACCAA
* * *
32094 CAAATTCGCAACGCGATCT
1 CAAATTCGCAACACAAACT
32113 CAAATTCGCAACACAAACT
1 CAAATTCGCAACACAAACT
*
32132 CCAATTTCGCAACACA
1 -CAAATTCGCAACACA
32148 GTTGCGAATT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
19 16 0.53
20 14 0.47
ACGTcount: A:0.39, C:0.33, G:0.09, T:0.19
Consensus pattern (19 bp):
CAAATTCGCAACACAAACT
Found at i:32354 original size:22 final size:22
Alignment explanation
Indices: 32329--32376 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
32319 CTCTCTACGA
* *
32329 CGACATCCGTCCCCTTCTCCGG
1 CGACATCCGTCCCCATATCCGG
32351 CGACATCCGTCCCCATATCCGG
1 CGACATCCGTCCCCATATCCGG
32373 CGAC
1 CGAC
32377 CCCCCTCCAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.15, C:0.48, G:0.19, T:0.19
Consensus pattern (22 bp):
CGACATCCGTCCCCATATCCGG
Found at i:32787 original size:20 final size:20
Alignment explanation
Indices: 32719--32787 Score: 69
Period size: 20 Copynumber: 3.8 Consensus size: 20
32709 CTTGAATCTT
*
32719 AAATTCGCAACTCGAAAATG
1 AAATTCGCAACGCGAAAATG
32739 AAATTCGCAA--C----ATG
1 AAATTCGCAACGCGAAAATG
* *
32753 AAAATCGCAATGCGAAAATG
1 AAATTCGCAACGCGAAAATG
32773 AAATTCGCAACGCGA
1 AAATTCGCAACGCGA
32788 TTTTAGTTTT
Statistics
Matches: 40, Mismatches: 3, Indels: 12
0.73 0.05 0.22
Matches are distributed among these distances:
14 12 0.30
16 1 0.03
18 1 0.03
20 26 0.65
ACGTcount: A:0.45, C:0.20, G:0.17, T:0.17
Consensus pattern (20 bp):
AAATTCGCAACGCGAAAATG
Found at i:32858 original size:34 final size:34
Alignment explanation
Indices: 32794--32859 Score: 80
Period size: 34 Copynumber: 1.9 Consensus size: 34
32784 GCGATTTTAG
* * **
32794 TTTTCGCGTTGCGAATTTCGTGTTTTGAATTTCA
1 TTTTCGAGTTGCGAATTTCATGTTGCGAATTTCA
32828 TTTTCGAGTTGC-AATTTTCATGTTGCGAATTT
1 TTTTCGAGTTGCGAA-TTTCATGTTGCGAATTT
32860 AAGTTTGAAG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
33 2 0.07
34 25 0.93
ACGTcount: A:0.17, C:0.14, G:0.20, T:0.50
Consensus pattern (34 bp):
TTTTCGAGTTGCGAATTTCATGTTGCGAATTTCA
Found at i:34425 original size:42 final size:42
Alignment explanation
Indices: 34366--34518 Score: 209
Period size: 42 Copynumber: 3.6 Consensus size: 42
34356 ATGAGCACCC
*
34366 CCACTCCGACACAGAGAGCCATCACCTCATCGAGCCTCTTCT
1 CCACTCCGACACCGAGAGCCATCACCTCATCGAGCCTCTTCT
34408 CCACTCCGACACCGAGAGCCATCACCTCATCGAGCCTCTTCT
1 CCACTCCGACACCGAGAGCCATCACCTCATCGAGCCTCTTCT
* * * * * **
34450 CTACTTCGACACCGAGAGCTATCACCTGATAGAGCCGATTCT
1 CCACTCCGACACCGAGAGCCATCACCTCATCGAGCCTCTTCT
*
34492 ACAC-CTCGACACCGAGAGCCATCACCT
1 CCACTC-CGACACCGAGAGCCATCACCT
34519 ATTTCATCAC
Statistics
Matches: 98, Mismatches: 12, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
42 98 1.00
ACGTcount: A:0.25, C:0.41, G:0.16, T:0.19
Consensus pattern (42 bp):
CCACTCCGACACCGAGAGCCATCACCTCATCGAGCCTCTTCT
Found at i:34711 original size:21 final size:21
Alignment explanation
Indices: 34650--34702 Score: 97
Period size: 21 Copynumber: 2.5 Consensus size: 21
34640 GTTAGGGGAG
34650 TTACGTGATGAGGTCGGTGCT
1 TTACGTGATGAGGTCGGTGCT
*
34671 TTACGTAATGAGGTCGGTGCT
1 TTACGTGATGAGGTCGGTGCT
34692 TTACGTGATGA
1 TTACGTGATGA
34703 CAACGGTGCA
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.19, C:0.13, G:0.34, T:0.34
Consensus pattern (21 bp):
TTACGTGATGAGGTCGGTGCT
Found at i:34962 original size:21 final size:21
Alignment explanation
Indices: 34938--34986 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
34928 ATTCACTTGT
34938 CATCGTTCAAGAAGCCCCTTC
1 CATCGTTCAAGAAGCCCCTTC
* *
34959 CATCATTCAAGAGGCCCCTTC
1 CATCGTTCAAGAAGCCCCTTC
*
34980 TATCGTT
1 CATCGTT
34987 AAGGATCCAC
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.22, C:0.35, G:0.14, T:0.29
Consensus pattern (21 bp):
CATCGTTCAAGAAGCCCCTTC
Found at i:36436 original size:20 final size:20
Alignment explanation
Indices: 36373--36439 Score: 80
Period size: 20 Copynumber: 3.4 Consensus size: 20
36363 TTGTGTTGAA
* *
36373 AATTTTATTTTCACGTTGCG
1 AATTTGATTTTCGCGTTGCG
** *
36393 AATACGATTTTCGCATTGCG
1 AATTTGATTTTCGCGTTGCG
*
36413 AATTTGATTTTTGCGTTGCG
1 AATTTGATTTTCGCGTTGCG
36433 AATTTGA
1 AATTTGA
36440 GTTACGAATC
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 38 1.00
ACGTcount: A:0.22, C:0.13, G:0.19, T:0.45
Consensus pattern (20 bp):
AATTTGATTTTCGCGTTGCG
Found at i:36702 original size:6 final size:6
Alignment explanation
Indices: 36693--36727 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
36683 TTGTGATTGG
*
36693 GATTTT GATTTT GATTTT GATTTC GATTTT GATTT
1 GATTTT GATTTT GATTTT GATTTT GATTTT GATTT
36728 CCTTTTGCTT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
6 27 1.00
ACGTcount: A:0.17, C:0.03, G:0.17, T:0.63
Consensus pattern (6 bp):
GATTTT
Found at i:38281 original size:25 final size:25
Alignment explanation
Indices: 38247--38298 Score: 104
Period size: 25 Copynumber: 2.1 Consensus size: 25
38237 GCTTCTGGCG
38247 ACCCCCTCAATAATTCCAAGGCATA
1 ACCCCCTCAATAATTCCAAGGCATA
38272 ACCCCCTCAATAATTCCAAGGCATA
1 ACCCCCTCAATAATTCCAAGGCATA
38297 AC
1 AC
38299 ATTTGGCTCT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.37, C:0.37, G:0.08, T:0.19
Consensus pattern (25 bp):
ACCCCCTCAATAATTCCAAGGCATA
Found at i:39831 original size:14 final size:15
Alignment explanation
Indices: 39795--39832 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
39785 GAAATCATTG
39795 AAAAATTATATAGAA
1 AAAAATTATATAGAA
*
39810 ATAAAATTATGTA-AA
1 A-AAAATTATATAGAA
39825 AAAAATTA
1 AAAAATTA
39833 GAGATGGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.66, C:0.00, G:0.05, T:0.29
Consensus pattern (15 bp):
AAAAATTATATAGAA
Found at i:40014 original size:20 final size:19
Alignment explanation
Indices: 39970--40017 Score: 62
Period size: 18 Copynumber: 2.5 Consensus size: 19
39960 CAAAATATTT
39970 GTGTTGCGAAAATAAAAGC
1 GTGTTGCGAAAATAAAAGC
* *
39989 -TGTTGCGAAATTAAAATTC
1 GTGTTGCGAAAATAAAA-GC
40008 GTGTTGCGAA
1 GTGTTGCGAA
40018 TTCAGAAATC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
18 15 0.60
19 1 0.04
20 9 0.36
ACGTcount: A:0.35, C:0.10, G:0.25, T:0.29
Consensus pattern (19 bp):
GTGTTGCGAAAATAAAAGC
Found at i:40155 original size:20 final size:21
Alignment explanation
Indices: 40120--40248 Score: 86
Period size: 20 Copynumber: 6.3 Consensus size: 21
40110 TTGCTAAAAA
*
40120 GAAATTCGCCTTGCGAATTTG
1 GAAATTCGCGTTGCGAATTTG
*
40141 GAAATT-GCGTTGCGAAATTG
1 GAAATTCGCGTTGCGAATTTG
* **
40161 G-AGTTCGCGTTGCGAA-AAG
1 GAAATTCGCGTTGCGAATTTG
* * *
40180 GAAATTTGAGTTGCGAATTTC
1 GAAATTCGCGTTGCGAATTTG
* * * **
40201 AAAACT-GAGTTATGAATTTTG
1 GAAATTCGCGTTGCGAA-TTTG
* *
40222 GAAATTCACGTTGTGAATTTG
1 GAAATTCGCGTTGCGAATTTG
40243 GAAATT
1 GAAATT
40249 ATATTGCGAA
Statistics
Matches: 82, Mismatches: 21, Indels: 10
0.73 0.19 0.09
Matches are distributed among these distances:
19 5 0.06
20 43 0.52
21 27 0.33
22 7 0.09
ACGTcount: A:0.30, C:0.11, G:0.26, T:0.33
Consensus pattern (21 bp):
GAAATTCGCGTTGCGAATTTG
Found at i:49034 original size:4 final size:4
Alignment explanation
Indices: 49025--49054 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
49015 CCTCATTTGT
49025 ATTC ATTC ATTC ATTC ATTC ATTC ATTC AT
1 ATTC ATTC ATTC ATTC ATTC ATTC ATTC AT
49055 CAATTCTCTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.27, C:0.23, G:0.00, T:0.50
Consensus pattern (4 bp):
ATTC
Found at i:55952 original size:21 final size:20
Alignment explanation
Indices: 55912--55953 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 20
55902 ACTGTATCAT
55912 AATAAATTCATTCAATATTA
1 AATAAATTCATTCAATATTA
55932 AATAATATTCAATTCAA-ATTA
1 AATAA-ATTC-ATTCAATATTA
55953 A
1 A
55954 CCTATAAATG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 5 0.25
21 9 0.45
22 6 0.30
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.38
Consensus pattern (20 bp):
AATAAATTCATTCAATATTA
Found at i:58961 original size:313 final size:303
Alignment explanation
Indices: 58403--59020 Score: 1119
Period size: 313 Copynumber: 2.0 Consensus size: 303
58393 GGTTCCAGAG
58403 AACTATTCACTATAGTGAAATAGTGGGAGCTATCCGTAAAAGAAGTTATGGCAACGAAATTTGAT
1 AACTATTCACTATAGTGAAATAGTGGGAGCTATCCGTAAAAGAAGTTATGGCAACGAAATTTGAT
*
58468 ATTGAAAAATTCAATGGGAGAAATTTCTCATTGTGGAAATTGAAGATGAAGGCCATCCTAAGGAA
66 ATTGAAAAATTCAATGGGAGAAATTTCTCATTGTGGAAATTCAAGATGAAGGCCATCCTAAGGAA
58533 AGACGGGTGTCTAGCGGCTATCAATGAAAGGTCGGTGGATTTCGCAGATGACATCAAATGGAACG
131 AGACGGGTGTCTAGCGGCTATCAATGAAAGGTCGGTGGATTTCGCAGATGACATCAAATGGAACG
58598 AGATGGATGGGAATGCTATGGCAAACTTTCATCTAGCATTAGCAGATGAAGTATTGTCAAGCATC
196 AGATGGATGGGAATGCTATGGCAAACTTTCATCTAGCATTAGCAGATGAAGTATTGTCAAGCATC
58663 GAGGAGAAGAAGACAGCTAAGGAGATATGAGATCATCTCACCA
261 GAGGAGAAGAAGACAGCTAAGGAGATATGAGATCATCTCACCA
58706 AACTATTCACTATAGTGAAATAGTGGGAGCTATCCGTAAAAGAAGTTATGGCAACGAAATTTGAT
1 AACTATTCACTATAGTGAAATAGTGGGAGCTATCCGTAAAAGAAGTTATGGCAACGAAATTTGAT
58771 ATTGAAAAATTCAATGGGAGATTCAAGATGAAATTTCTCATTGTGGAAATTCAAGATGAAGGCCA
66 ATTGAAAAATTCAAT--G-G------GA-GAAATTTCTCATTGTGGAAATTCAAGATGAAGGCCA
58836 TCCTAAGGAAAGACGGGTGTCTAGCGGCTATCAATGAAAGGTCGGTGGATTTCGCAGATGACATC
121 TCCTAAGGAAAGACGGGTGTCTAGCGGCTATCAATGAAAGGTCGGTGGATTTCGCAGATGACATC
* *
58901 AAATGGAACGAGATGGATGGGAATGCTATGGCAAGCTTTCATCTAGCATTAGTAGATGAAGTATT
186 AAATGGAACGAGATGGATGGGAATGCTATGGCAAACTTTCATCTAGCATTAGCAGATGAAGTATT
58966 GTCAAGCATCGAGGAGAAGAAGACAGCTAAGGAGATATGAGATCATCTCACCA
251 GTCAAGCATCGAGGAGAAGAAGACAGCTAAGGAGATATGAGATCATCTCACCA
59019 AA
1 AA
59021 TTGTACTAGG
Statistics
Matches: 302, Mismatches: 3, Indels: 10
0.96 0.01 0.03
Matches are distributed among these distances:
303 80 0.26
305 1 0.00
306 1 0.00
312 2 0.01
313 218 0.72
ACGTcount: A:0.36, C:0.14, G:0.26, T:0.24
Consensus pattern (303 bp):
AACTATTCACTATAGTGAAATAGTGGGAGCTATCCGTAAAAGAAGTTATGGCAACGAAATTTGAT
ATTGAAAAATTCAATGGGAGAAATTTCTCATTGTGGAAATTCAAGATGAAGGCCATCCTAAGGAA
AGACGGGTGTCTAGCGGCTATCAATGAAAGGTCGGTGGATTTCGCAGATGACATCAAATGGAACG
AGATGGATGGGAATGCTATGGCAAACTTTCATCTAGCATTAGCAGATGAAGTATTGTCAAGCATC
GAGGAGAAGAAGACAGCTAAGGAGATATGAGATCATCTCACCA
Found at i:70550 original size:39 final size:35
Alignment explanation
Indices: 70502--70579 Score: 95
Period size: 35 Copynumber: 2.1 Consensus size: 35
70492 TGCATCCAAA
70502 TAATCTTATATTCCT-CTAACCATACACAACCAAACAATG
1 TAATCTTATATTCCTGCT-A--A-ACA-AACCAAACAATG
*
70541 TAATTTTATATTCCTGCTAAACAAACCAAACAATG
1 TAATCTTATATTCCTGCTAAACAAACCAAACAATG
70576 TAAT
1 TAAT
70580 ACAACATTCT
Statistics
Matches: 37, Mismatches: 1, Indels: 6
0.84 0.02 0.14
Matches are distributed among these distances:
35 16 0.43
36 3 0.08
37 1 0.03
39 15 0.41
40 2 0.05
ACGTcount: A:0.42, C:0.23, G:0.04, T:0.31
Consensus pattern (35 bp):
TAATCTTATATTCCTGCTAAACAAACCAAACAATG
Found at i:70820 original size:2 final size:2
Alignment explanation
Indices: 70813--70868 Score: 69
Period size: 2 Copynumber: 28.0 Consensus size: 2
70803 TACTTGATGT
* * *
70813 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA CA CA CA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
70855 TA TA T- TA TGA TA TA
1 TA TA TA TA T-A TA TA
70869 CTACGTATGT
Statistics
Matches: 50, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
1 1 0.02
2 47 0.94
3 2 0.04
ACGTcount: A:0.48, C:0.05, G:0.02, T:0.45
Consensus pattern (2 bp):
TA
Found at i:71069 original size:25 final size:23
Alignment explanation
Indices: 71022--71074 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 23
71012 TTAACTAATT
71022 ATTTTTACTTATTATATAATTAAA
1 ATTTTTACTTATTATATAATT-AA
*
71046 ATTTTTACTATATTA-ATATCTTAA
1 ATTTTTACT-TATTATATA-ATTAA
71070 ATTTT
1 ATTTT
71075 AATGATTAGC
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
24 19 0.73
25 7 0.27
ACGTcount: A:0.38, C:0.06, G:0.00, T:0.57
Consensus pattern (23 bp):
ATTTTTACTTATTATATAATTAA
Found at i:71109 original size:14 final size:14
Alignment explanation
Indices: 71092--71139 Score: 59
Period size: 14 Copynumber: 3.7 Consensus size: 14
71082 AGCTAATTAC
71092 ATAATTTTAATTTA
1 ATAATTTTAATTTA
71106 ATAATTTT--TTT-
1 ATAATTTTAATTTA
*
71117 A-ACTTTTAATTTA
1 ATAATTTTAATTTA
71130 ATAATTTTAA
1 ATAATTTTAA
71140 AATCTTAAAA
Statistics
Matches: 28, Mismatches: 2, Indels: 8
0.74 0.05 0.21
Matches are distributed among these distances:
10 5 0.18
11 1 0.04
12 6 0.21
13 1 0.04
14 15 0.54
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.58
Consensus pattern (14 bp):
ATAATTTTAATTTA
Found at i:74127 original size:3 final size:3
Alignment explanation
Indices: 74119--74159 Score: 55
Period size: 3 Copynumber: 13.0 Consensus size: 3
74109 TGTAACAATA
*
74119 AAT AAT AAT AAT AAT AAT AAT AAAT AAT GAT ATAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT -AAT AAT AAT A-AT AAT AAT
74160 TAAAAAAATT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
3 28 0.82
4 6 0.18
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:74144 original size:13 final size:13
Alignment explanation
Indices: 74119--74159 Score: 50
Period size: 13 Copynumber: 3.2 Consensus size: 13
74109 TGTAACAATA
74119 AATAATAAT-AAT
1 AATAATAATAAAT
74131 AATAATAATAAAT
1 AATAATAATAAAT
*
74144 AATGAT-ATATAAT
1 AATAATAATA-AAT
74157 AAT
1 AAT
74160 TAAAAAAATT
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
12 12 0.46
13 14 0.54
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (13 bp):
AATAATAATAAAT
Found at i:74670 original size:135 final size:131
Alignment explanation
Indices: 74364--74803 Score: 560
Period size: 135 Copynumber: 3.3 Consensus size: 131
74354 GAGGTCTTCG
* * *
74364 TCTAAGGGTGACACGGCTCCTATGTGATGAGGAGATCTGGCCGGGGGATGACACTG-CTCATACT
1 TCTAAGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACAC-GACTCATA-T
* * * *
74428 TGATGAAGAGTTCTTGGCCATCTTTAGGAACGATAACACAGTTCCTATGCGATGAGGATGACTGG
64 TGATGAAGAGTTCTTGGCCATCTTTAGGAATGATAACACGGTTCCTACGCGATGAGGATGGCTGG
74493 TTA
129 TTA
* * * *
74496 TTTAGGGGTGACACGACTCTTACATGATGAGGAGATCTGGTCGGGGGATGACACGACTCATATGT
1 TCTAAGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGACTCATAT-T
* * *
74561 GATGAAGAGTTCTTGGCTATCTTTAGGAAGGGTGATAATATGGTTCCTACGCGATGAGGATGGCT
65 GATGAAGAGTTCTTGGCCATCTTTAGGAA---TGATAACACGGTTCCTACGCGATGAGGATGGCT
74626 GGTTA
127 GGTTA
* * * * * *
74631 TCTAGGGGTGACACGACTCCTATGTGATAAGGAGGTCTGGTCGGTGGATGACACGACTCATACAT
1 TCTAAGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGACTCATA-TT
* * * *
74696 GATGAAGAGTTC-TGGCCATCTTTAGGAATGATAACACGGTTCCTACGTGATAAGGACGGTTGGT
65 GATGAAGAGTTCTTGGCCATCTTTAGGAATGATAACACGGTTCCTACGCGATGAGGATGGCTGGT
74760 TA
130 TA
* * *
74762 TCTAAGGTTGACACGGCTCCTACGTGATGAGGAGGTCTGGTC
1 TCTAAGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTC
74804 AAGAGACGAA
Statistics
Matches: 268, Mismatches: 34, Indels: 13
0.85 0.11 0.04
Matches are distributed among these distances:
131 71 0.26
132 82 0.31
134 15 0.06
135 100 0.37
ACGTcount: A:0.25, C:0.17, G:0.31, T:0.27
Consensus pattern (131 bp):
TCTAAGGGTGACACGACTCCTACGTGATGAGGAGATCTGGTCGGGGGATGACACGACTCATATTG
ATGAAGAGTTCTTGGCCATCTTTAGGAATGATAACACGGTTCCTACGCGATGAGGATGGCTGGTT
A
Found at i:74900 original size:28 final size:28
Alignment explanation
Indices: 74860--74925 Score: 96
Period size: 28 Copynumber: 2.4 Consensus size: 28
74850 AGGGATTATG
* *
74860 GTTTCAAGAGAAACCGACCCAAAGATTT
1 GTTTCAAAAGAAACAGACCCAAAGATTT
*
74888 GTTTCAAAAGAAACAGACTCAAAGATTT
1 GTTTCAAAAGAAACAGACCCAAAGATTT
*
74916 CTTTCAAAAG
1 GTTTCAAAAG
74926 CAACTGTCTC
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 34 1.00
ACGTcount: A:0.42, C:0.18, G:0.15, T:0.24
Consensus pattern (28 bp):
GTTTCAAAAGAAACAGACCCAAAGATTT
Found at i:75130 original size:35 final size:36
Alignment explanation
Indices: 75082--75178 Score: 110
Period size: 36 Copynumber: 2.7 Consensus size: 36
75072 GAGAAAATTC
* **
75082 GTTTCAAGAGAAAC-GATTTCAAAGATG-TTTATTTT
1 GTTTCAAGAGAAACAGA-CTCAAAGATGATAAATTTT
*
75117 GTTTCAAGGGAAACAGACTCAAAGATGATAAATTTT
1 GTTTCAAGAGAAACAGACTCAAAGATGATAAATTTT
*
75153 GTTTCCAA-ATAAACAGACTCAAAGAT
1 GTTT-CAAGAGAAACAGACTCAAAGAT
75179 TTTTCTCAAA
Statistics
Matches: 53, Mismatches: 6, Indels: 5
0.83 0.09 0.08
Matches are distributed among these distances:
35 22 0.42
36 28 0.53
37 3 0.06
ACGTcount: A:0.40, C:0.12, G:0.16, T:0.31
Consensus pattern (36 bp):
GTTTCAAGAGAAACAGACTCAAAGATGATAAATTTT
Found at i:77758 original size:16 final size:16
Alignment explanation
Indices: 77737--77769 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
77727 TATATTATTC
*
77737 AAATAAATATTTTTTT
1 AAATAAATATGTTTTT
77753 AAATAAATATGTTTTT
1 AAATAAATATGTTTTT
77769 A
1 A
77770 TTTAATAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (16 bp):
AAATAAATATGTTTTT
Found at i:77773 original size:20 final size:19
Alignment explanation
Indices: 77746--77783 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
77736 CAAATAAATA
77746 TTTTTTTAA-ATAAATATGT
1 TTTTTTTAATA-AAATATGT
77765 TTTTATTTAATAAAATATG
1 TTTT-TTTAATAAAATATG
77784 GGCCATTTCT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 4 0.24
20 12 0.71
21 1 0.06
ACGTcount: A:0.39, C:0.00, G:0.05, T:0.55
Consensus pattern (19 bp):
TTTTTTTAATAAAATATGT
Found at i:81311 original size:95 final size:95
Alignment explanation
Indices: 81149--81321 Score: 310
Period size: 95 Copynumber: 1.8 Consensus size: 95
81139 TTTTTTTTTC
* *
81149 TTTTCTTTTCTTTCTAGCCTAAGAGCCGTTTGTTTAATGCTTTTGTGTGGTTTTCACTTTCTGAG
1 TTTTCTTTTCTTCCTAGCCTAAGAGCCGTTAGTTTAATGCTTTTGTGTGGTTTTCACTTTCTGAG
*
81214 TCACCGGTTAAGATTAGATTTTCTAATAGT
66 TCACAGGTTAAGATTAGATTTTCTAATAGT
*
81244 TTTTCTTTTCTTCCTAGCCTAAGAGCTGTTAGTTTAATGCTTTTGTGTGGTTTTCACTTTCTGAG
1 TTTTCTTTTCTTCCTAGCCTAAGAGCCGTTAGTTTAATGCTTTTGTGTGGTTTTCACTTTCTGAG
81309 TCACAGGTTAAGA
66 TCACAGGTTAAGA
81322 GAATGAGTAC
Statistics
Matches: 74, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
95 74 1.00
ACGTcount: A:0.18, C:0.16, G:0.18, T:0.47
Consensus pattern (95 bp):
TTTTCTTTTCTTCCTAGCCTAAGAGCCGTTAGTTTAATGCTTTTGTGTGGTTTTCACTTTCTGAG
TCACAGGTTAAGATTAGATTTTCTAATAGT
Found at i:96907 original size:25 final size:23
Alignment explanation
Indices: 96877--96944 Score: 59
Period size: 25 Copynumber: 2.9 Consensus size: 23
96867 TTTATGCATT
96877 TATATATATATAATACTTTAGAAA
1 TATATATATATAATACTTTA-AAA
* *
96901 TAT-TATAACAATTATACATTTAAAA
1 TATATAT-A-TATAATAC-TTTAAAA
*
96926 TATAT-TATATATTACTTTA
1 TATATATATATAATACTTTA
96945 TTTATACCTT
Statistics
Matches: 35, Mismatches: 5, Indels: 10
0.70 0.10 0.20
Matches are distributed among these distances:
22 4 0.11
23 8 0.23
24 5 0.14
25 13 0.37
26 5 0.14
ACGTcount: A:0.47, C:0.06, G:0.01, T:0.46
Consensus pattern (23 bp):
TATATATATATAATACTTTAAAA
Found at i:97251 original size:15 final size:12
Alignment explanation
Indices: 97189--97245 Score: 51
Period size: 12 Copynumber: 4.6 Consensus size: 12
97179 AATCTGTACG
97189 ATATATGTATAT
1 ATATATGTATAT
* * *
97201 CACATATATAAAT
1 -ATATATGTATAT
* *
97214 AAATATATATAT
1 ATATATGTATAT
97226 ATATATGTATAT
1 ATATATGTATAT
97238 CATATATG
1 -ATATATG
97246 GTTATAAAAA
Statistics
Matches: 36, Mismatches: 7, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
12 20 0.56
13 16 0.44
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.42
Consensus pattern (12 bp):
ATATATGTATAT
Found at i:103728 original size:17 final size:17
Alignment explanation
Indices: 103706--103757 Score: 52
Period size: 17 Copynumber: 3.0 Consensus size: 17
103696 AACAATGACC
103706 AAAATAAAATAAATTAA
1 AAAATAAAATAAATTAA
* *
103723 AAAATAATATTAATTTATA
1 AAAATAA-AATAAATTA-A
*
103742 AAAAT-ATATAAATTAA
1 AAAATAAAATAAATTAA
103758 TAGCCCTAAT
Statistics
Matches: 28, Mismatches: 5, Indels: 5
0.74 0.13 0.13
Matches are distributed among these distances:
16 1 0.04
17 13 0.46
18 8 0.29
19 6 0.21
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAATAAAATAAATTAA
Found at i:104933 original size:12 final size:12
Alignment explanation
Indices: 104916--104941 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
104906 TTTATTAATT
104916 AATAATAATATA
1 AATAATAATATA
104928 AATAATAATATA
1 AATAATAATATA
104940 AA
1 AA
104942 AAGGATGGGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (12 bp):
AATAATAATATA
Found at i:116495 original size:82 final size:82
Alignment explanation
Indices: 116319--116617 Score: 429
Period size: 82 Copynumber: 3.6 Consensus size: 82
116309 ATACACATCC
* *
116319 TTTGTTTTTCATTGACATATCACATCAACTCAGATAAATTGAAATAATTATTTAGAGAATCATAG
1 TTTGCTTTTCATTGACATATCACATCAACTCAGATAAATTGAAAT-A--ATTTAGAGAATCAGAG
*
116384 AATCTAAACTATTCACGTCA
63 AATCTATACTATTCACGTCA
* * *
116404 TTTGCTTTTCATTGACATATCACATCAACTTAGATAAACTGAAATAATTTAGAGAATCGGAGAAT
1 TTTGCTTTTCATTGACATATCACATCAACTCAGATAAATTGAAATAATTTAGAGAATCAGAGAAT
*
116469 CTATACTATTCATGTCA
66 CTATACTATTCACGTCA
* * *
116486 TTTGCTTTTCATTGACATATCACATCAATTCAGATAAATTGAAATAATTTAGAGAATTAGATAAT
1 TTTGCTTTTCATTGACATATCACATCAACTCAGATAAATTGAAATAATTTAGAGAATCAGAGAAT
* *
116551 CTATATTATTCACATCA
66 CTATACTATTCACGTCA
* *
116568 TTTGCATTTT-ATTGACATATCACATCAAATCAGAGAAATTGAAATAATTT
1 TTTGC-TTTTCATTGACATATCACATCAACTCAGATAAATTGAAATAATTT
116618 CCATTCAAAT
Statistics
Matches: 195, Mismatches: 18, Indels: 5
0.89 0.08 0.02
Matches are distributed among these distances:
82 148 0.76
83 4 0.02
84 1 0.01
85 42 0.22
ACGTcount: A:0.38, C:0.14, G:0.10, T:0.37
Consensus pattern (82 bp):
TTTGCTTTTCATTGACATATCACATCAACTCAGATAAATTGAAATAATTTAGAGAATCAGAGAAT
CTATACTATTCACGTCA
Found at i:116828 original size:21 final size:20
Alignment explanation
Indices: 116799--116837 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
116789 TAACTTCTTC
116799 TTTTTA-TTTTAATAATTTTT
1 TTTTTATTTTTAA-AATTTTT
116819 TTTTTAATTTTTAAAATTT
1 TTTTT-ATTTTTAAAATTT
116838 GAAATTTTTC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 5 0.29
21 6 0.35
22 6 0.35
ACGTcount: A:0.28, C:0.00, G:0.00, T:0.72
Consensus pattern (20 bp):
TTTTTATTTTTAAAATTTTT
Found at i:122020 original size:18 final size:18
Alignment explanation
Indices: 121997--122076 Score: 83
Period size: 18 Copynumber: 4.3 Consensus size: 18
121987 TTTACTTAAT
121997 TTATTATTATTAAAATTA
1 TTATTATTATTAAAATTA
122015 TTATTATTATTATAAA-TA
1 TTATTATTATTA-AAATTA
* *
122033 TTATTATTATATTATATATA
1 TTATTATTAT-TAAAAT-TA
*
122053 TATATTATTATT-AAATAA
1 T-TATTATTATTAAAATTA
122071 TTATTA
1 TTATTA
122077 CAAGCCCAGA
Statistics
Matches: 53, Mismatches: 4, Indels: 11
0.78 0.06 0.16
Matches are distributed among these distances:
17 5 0.09
18 28 0.53
19 7 0.13
20 4 0.08
21 9 0.17
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTATTATTATTAAAATTA
Found at i:122038 original size:24 final size:24
Alignment explanation
Indices: 122011--122065 Score: 85
Period size: 24 Copynumber: 2.3 Consensus size: 24
122001 TATTATTAAA
122011 ATTATTATTATTAT-TATAAATATT
1 ATTATTA-TATTATATATAAATATT
*
122035 ATTATTATATTATATATATATATT
1 ATTATTATATTATATATAAATATT
122059 ATTATTA
1 ATTATTA
122066 AATAATTATT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
23 6 0.21
24 23 0.79
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (24 bp):
ATTATTATATTATATATAAATATT
Found at i:122076 original size:3 final size:3
Alignment explanation
Indices: 121997--122065 Score: 70
Period size: 3 Copynumber: 23.0 Consensus size: 3
121987 TTTACTTAAT
** * *
121997 TTA TTA TTA TTA AAA TTA TTA TTA TTA TTA TAA ATA TTA TTA TTA -TA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
122044 TTA -TA TATA TATA TTA TTA TTA
1 TTA TTA T-TA T-TA TTA TTA TTA
122066 AATAATTATT
Statistics
Matches: 55, Mismatches: 8, Indels: 6
0.80 0.12 0.09
Matches are distributed among these distances:
2 4 0.07
3 44 0.80
4 7 0.13
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (3 bp):
TTA
Found at i:123564 original size:2 final size:2
Alignment explanation
Indices: 123551--123594 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
123541 TATTTTAGTC
*
123551 AT AT AA 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
123593 AT
1 AT
123595 TTGTTTAATT
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:124014 original size:22 final size:22
Alignment explanation
Indices: 123989--124042 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
123979 AAAATAGATA
*
123989 TTAATATATTAT-ATTAATAAAT
1 TTAATATATCATGATT-ATAAAT
* *
124011 TTAAAATAACATGATTATAAAT
1 TTAATATATCATGATTATAAAT
*
124033 TAAATATATC
1 TTAATATATC
124043 TTTGAACTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
22 22 0.88
23 3 0.12
ACGTcount: A:0.52, C:0.04, G:0.02, T:0.43
Consensus pattern (22 bp):
TTAATATATCATGATTATAAAT
Found at i:129852 original size:16 final size:15
Alignment explanation
Indices: 129829--129871 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
129819 GATGAAGATG
129829 AAAA-AAAAAGATGAA
1 AAAAGAAAAAGA-GAA
*
129844 AAAGGAAAAATGAGAA
1 AAAAGAAAAA-GAGAA
129860 AAAAGAAAAAGA
1 AAAAGAAAAAGA
129872 AAGGGGAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
15 5 0.21
16 17 0.71
17 2 0.08
ACGTcount: A:0.77, C:0.00, G:0.19, T:0.05
Consensus pattern (15 bp):
AAAAGAAAAAGAGAA
Found at i:129852 original size:17 final size:16
Alignment explanation
Indices: 129832--129892 Score: 50
Period size: 16 Copynumber: 3.6 Consensus size: 16
129822 GAAGATGAAA
*
129832 AAAAAAGATGAAAAAGG
1 AAAAAAGA-GAAAAAAG
*
129849 AAAAATGAGAAAAAAG
1 AAAAAAGAGAAAAAAG
* *
129865 AAAAAGAAAGGGGAAAAAG
1 --AAA-AAAGAGAAAAAAG
129884 AAAAAAGAG
1 AAAAAAGAG
129893 GAGAAATTGA
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
16 12 0.34
17 10 0.29
18 3 0.09
19 10 0.29
ACGTcount: A:0.72, C:0.00, G:0.25, T:0.03
Consensus pattern (16 bp):
AAAAAAGAGAAAAAAG
Found at i:129852 original size:19 final size:19
Alignment explanation
Indices: 129801--129889 Score: 74
Period size: 19 Copynumber: 4.7 Consensus size: 19
129791 ATCCAACAAA
129801 GAAAGAAGAAGAAAAAAAGAT
1 GAAA-AAGAA-AAAAAAAGAT
* *
129822 GAAGATGAAAAAAAAAGAT
1 GAAAAAGAAAAAAAAAGAT
* **
129841 GAAAAAGGAAAAATGAGA-
1 GAAAAAGAAAAAAAAAGAT
* **
129859 -AAAAAGAAAAAGAAAGGG
1 GAAAAAGAAAAAAAAAGAT
129877 GAAAAAGAAAAAA
1 GAAAAAGAAAAAA
129890 GAGGAGAAAT
Statistics
Matches: 53, Mismatches: 13, Indels: 6
0.74 0.18 0.08
Matches are distributed among these distances:
17 12 0.23
19 34 0.64
20 4 0.08
21 3 0.06
ACGTcount: A:0.72, C:0.00, G:0.24, T:0.04
Consensus pattern (19 bp):
GAAAAAGAAAAAAAAAGAT
Found at i:129873 original size:29 final size:28
Alignment explanation
Indices: 129823--129889 Score: 66
Period size: 29 Copynumber: 2.4 Consensus size: 28
129813 AAAAAAGATG
*
129823 AAGATGAAAAAAAAAGATGAAAAAGGAAA
1 AAGA-GAAAAAAAAAGAAGAAAAAGGAAA
**
129852 AATGAGAAAAAAGAAA-AAGAAAGGGGAAA
1 AA-GAGAAAAAA-AAAGAAGAAAAAGGAAA
129881 AAGA-AAAAA
1 AAGAGAAAAA
129890 GAGGAGAAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
27 5 0.15
28 2 0.06
29 21 0.64
30 5 0.15
ACGTcount: A:0.73, C:0.00, G:0.22, T:0.04
Consensus pattern (28 bp):
AAGAGAAAAAAAAAGAAGAAAAAGGAAA
Found at i:132202 original size:15 final size:15
Alignment explanation
Indices: 132182--132239 Score: 66
Period size: 15 Copynumber: 3.9 Consensus size: 15
132172 TTCTCTTTTA
132182 CAGAAAAGTATATTC
1 CAGAAAAGTATATTC
**
132197 CAG-AAA-TAGCCTTC
1 CAGAAAAGTA-TATTC
132211 ACAGAAAAGTATATTC
1 -CAGAAAAGTATATTC
132227 CAGAAAAGTATAT
1 CAGAAAAGTATAT
132240 GTACCAAGCT
Statistics
Matches: 35, Mismatches: 4, Indels: 8
0.74 0.09 0.17
Matches are distributed among these distances:
13 2 0.06
14 6 0.17
15 19 0.54
16 6 0.17
17 2 0.06
ACGTcount: A:0.47, C:0.16, G:0.14, T:0.24
Consensus pattern (15 bp):
CAGAAAAGTATATTC
Found at i:133808 original size:50 final size:50
Alignment explanation
Indices: 133733--133874 Score: 266
Period size: 50 Copynumber: 2.8 Consensus size: 50
133723 AAATCTTGGC
133733 AGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACATCTAAGT
1 AGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACATCTAAGT
133783 AGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACATCTAAGT
1 AGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACATCTAAGT
* *
133833 AGAAACCACATGAAATGATGAATGTGTTGTCAAATGTTTTAC
1 AGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTAC
133875 GAACCAGTTA
Statistics
Matches: 90, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 90 1.00
ACGTcount: A:0.38, C:0.12, G:0.21, T:0.29
Consensus pattern (50 bp):
AGAAACCACAGGAAAGGATGAATGTGTTGTCAAATGTTTTACATCTAAGT
Found at i:134309 original size:22 final size:22
Alignment explanation
Indices: 134239--134313 Score: 120
Period size: 21 Copynumber: 3.5 Consensus size: 22
134229 CTACATACAC
134239 TTCAAAGATGATAGATTCTC-T
1 TTCAAAGATGATAGATTCTCTT
134260 TTCAAAGATGATAGATATCT-TT
1 TTCAAAGATGATAGAT-TCTCTT
134282 TT-AAAGATGATAGATTCTCTT
1 TTCAAAGATGATAGATTCTCTT
134303 TTCAAAGATGA
1 TTCAAAGATGA
134314 AAGCTTTATT
Statistics
Matches: 50, Mismatches: 0, Indels: 7
0.88 0.00 0.12
Matches are distributed among these distances:
20 3 0.06
21 33 0.66
22 14 0.28
ACGTcount: A:0.36, C:0.11, G:0.15, T:0.39
Consensus pattern (22 bp):
TTCAAAGATGATAGATTCTCTT
Found at i:135114 original size:76 final size:76
Alignment explanation
Indices: 134988--135732 Score: 1356
Period size: 76 Copynumber: 9.9 Consensus size: 76
134978 CTATTTCCCA
*
134988 CATCTGTAACTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
*
135053 AACCTTAGGGT
66 AGCCTTAGGGT
135064 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
135129 AGCCTTAGGGT
66 AGCCTTAGGGT
135140 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
135205 AGCCTTAGGGT
66 AGCCTTAGGGT
135216 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
135281 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
135292 CATATGTAAGTCCTACAAT-CATGATGTTTCCAAAAAGCCTTCGGGAG-TTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
135355 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
135366 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGAGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
135431 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
135442 CATCTGTAAGTTCTACAGTGCATGATGTTTCCAAAAAGCCTTC-GGAGC-TTTTGATATTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
135505 AGCCTTA-GGT
66 AGCCTTAGGGT
*
135515 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTTAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
135580 AGCCTTAGGGT
66 AGCCTTAGGGT
135591 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
135656 AGCCTTAGGGT
66 AGCCTTAGGGT
* *
135667 CATCTGTAAGTCCTACAGTGCATGATGTTTTCAAAAAGCCTTTGGGAGCTTTTTGATGTTTTCAA
1 CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
135732 A
66 A
135733 ACATATTATT
Statistics
Matches: 646, Mismatches: 18, Indels: 10
0.96 0.03 0.01
Matches are distributed among these distances:
73 45 0.07
74 69 0.11
75 79 0.12
76 453 0.70
ACGTcount: A:0.25, C:0.19, G:0.21, T:0.35
Consensus pattern (76 bp):
CATCTGTAAGTCCTACAGTGCATGATGTTTCCAAAAAGCCTTCGGGAGCTTTTTGATGTTTTCAA
AGCCTTAGGGT
Found at i:149644 original size:31 final size:31
Alignment explanation
Indices: 149609--149675 Score: 73
Period size: 31 Copynumber: 2.2 Consensus size: 31
149599 TTAAAACTTA
* *
149609 CAATACAATCCCCTAACATTTA-TTTCGTTTG
1 CAATACAATCCCCCAACATTTAGTCT-GTTTG
***
149640 CAATATGGTCCCCCAACATTTAGTCTGTTTG
1 CAATACAATCCCCCAACATTTAGTCTGTTTG
149671 CAATA
1 CAATA
149676 TGGTCCCTGA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.28, C:0.25, G:0.10, T:0.36
Consensus pattern (31 bp):
CAATACAATCCCCCAACATTTAGTCTGTTTG
Found at i:149676 original size:31 final size:31
Alignment explanation
Indices: 149617--149682 Score: 98
Period size: 31 Copynumber: 2.1 Consensus size: 31
149607 TACAATACAA
* *
149617 TCCCCTAACATTTATTTCGTTTGCAATATGG
1 TCCCCCAACATTTATCTCGTTTGCAATATGG
149648 TCCCCCAACATTTAGTCT-GTTTGCAATATGG
1 TCCCCCAACATTTA-TCTCGTTTGCAATATGG
149679 TCCC
1 TCCC
149683 TGATCGTTTG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
31 30 0.94
32 2 0.06
ACGTcount: A:0.21, C:0.27, G:0.14, T:0.38
Consensus pattern (31 bp):
TCCCCCAACATTTATCTCGTTTGCAATATGG
Found at i:152656 original size:36 final size:36
Alignment explanation
Indices: 152610--152683 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
152600 TGAATTCTGA
* *
152610 AAAATGAATTATATTTTCTGGAAAATGTTTTCCAGG
1 AAAATGAATTACATTTTATGGAAAATGTTTTCCAGG
152646 AAAATGAATTACATTTTATGGAAAATGTTTTCCAGG
1 AAAATGAATTACATTTTATGGAAAATGTTTTCCAGG
152682 AA
1 AA
152684 TTTTCTGGAA
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.39, C:0.08, G:0.16, T:0.36
Consensus pattern (36 bp):
AAAATGAATTACATTTTATGGAAAATGTTTTCCAGG
Found at i:152929 original size:26 final size:27
Alignment explanation
Indices: 152878--152929 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
152868 TTATTAATAA
* * *
152878 AAATAAAAATATTGGTATATTTTATTG
1 AAATAAAAATATTGATAAATTATATTG
152905 AAATAAAAATATT-ATAAATTATATT
1 AAATAAAAATATTGATAAATTATATT
152930 AATTATTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
26 9 0.41
27 13 0.59
ACGTcount: A:0.52, C:0.00, G:0.06, T:0.42
Consensus pattern (27 bp):
AAATAAAAATATTGATAAATTATATTG
Found at i:152972 original size:23 final size:23
Alignment explanation
Indices: 152957--153009 Score: 61
Period size: 23 Copynumber: 2.3 Consensus size: 23
152947 ATATTGTTAT
152957 ATATATTTTAAAAATATTAATTA
1 ATATATTTTAAAAATATTAATTA
* * * *
152980 GTATATTTTAAATATCTTTATTA
1 ATATATTTTAAAAATATTAATTA
*
153003 AAATATT
1 ATATATT
153010 ATTAGATTAT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATATTTTAAAAATATTAATTA
Found at i:152975 original size:34 final size:35
Alignment explanation
Indices: 152937--153010 Score: 82
Period size: 34 Copynumber: 2.1 Consensus size: 35
152927 ATTAATTATT
*
152937 TATTAAATTA-ATATTGTTATATATATTT-TAAAAA
1 TATTAAATTAGATATT-TTAAATATATTTATAAAAA
* *
152971 TATT-AATTAGTATATTTTAAATATCTTTATTAAAA
1 TATTAAATTAG-ATATTTTAAATATATTTATAAAAA
153006 TATTA
1 TATTA
153011 TTAGATTATT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
33 5 0.15
34 14 0.42
35 14 0.42
ACGTcount: A:0.45, C:0.01, G:0.03, T:0.51
Consensus pattern (35 bp):
TATTAAATTAGATATTTTAAATATATTTATAAAAA
Found at i:153065 original size:19 final size:19
Alignment explanation
Indices: 152997--153077 Score: 64
Period size: 19 Copynumber: 4.3 Consensus size: 19
152987 TTAAATATCT
152997 TTATTAA-AATATTATTAGA
1 TTATTAATAATATTATTA-A
153016 TTATTATATTAATATTA--AA
1 TTATTA-A-TAATATTATTAA
* *
153035 TATATAAATAATATTATTCA
1 T-TATTAATAATATTATTAA
*
153055 TTATTAATAAT-TTAATAA
1 TTATTAATAATATTATTAA
153073 -TATTA
1 TTATTA
153078 TTAGACGCGC
Statistics
Matches: 51, Mismatches: 5, Indels: 14
0.73 0.07 0.20
Matches are distributed among these distances:
17 5 0.10
18 13 0.25
19 18 0.35
20 8 0.16
22 7 0.14
ACGTcount: A:0.48, C:0.01, G:0.01, T:0.49
Consensus pattern (19 bp):
TTATTAATAATATTATTAA
Found at i:153450 original size:32 final size:32
Alignment explanation
Indices: 153383--153452 Score: 81
Period size: 32 Copynumber: 2.2 Consensus size: 32
153373 ATATTATTAT
* * *
153383 AATATAATTGATTATTTTATTATAATATTAAA
1 AATATAATTGATTATATTATTAGAAGATTAAA
153415 AATATAA-T-ATTATATTATTAGGAAGATTAATA
1 AATATAATTGATTATATTATTA-GAAGATTAA-A
153447 AATATA
1 AATATA
153453 TTTTAAATAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 11 0.33
31 8 0.24
32 14 0.42
ACGTcount: A:0.50, C:0.00, G:0.06, T:0.44
Consensus pattern (32 bp):
AATATAATTGATTATATTATTAGAAGATTAAA
Found at i:154500 original size:20 final size:20
Alignment explanation
Indices: 154477--154528 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
154467 AACGCGATCC
*
154477 CCAGAATCGCAAATCAGTTT
1 CCAGAATCGCAAATAAGTTT
154497 CCAGAATCGCAAATAAGTTT
1 CCAGAATCGCAAATAAGTTT
*
154517 CCAAAATCGCAA
1 CCAGAATCGCAA
154529 CGCGATTCTT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.40, C:0.25, G:0.13, T:0.21
Consensus pattern (20 bp):
CCAGAATCGCAAATAAGTTT
Found at i:154609 original size:20 final size:20
Alignment explanation
Indices: 154584--154777 Score: 76
Period size: 20 Copynumber: 9.7 Consensus size: 20
154574 GATTTTCCAT
* *
154584 AATCGCAACGCGAATATGA-A
1 AATCGCAACGCGAACA-CATA
154604 AATCGCAACGCGAACACATA
1 AATCGCAACGCGAACACATA
* *
154624 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
154644 AATCGCAACGTGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* ****
154664 AATCGCAACGCGTATGGGTA
1 AATCGCAACGCGAACACATA
* * *
154684 AATCGCAATGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
* * *
154704 TATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
** *
154724 AATCGCAACGATAATACATAA
1 AATCGCAACGCGAACACAT-A
* *
154745 AATCGCAACGCGTATC-CGTA
1 AATCGCAACGCG-AACACATA
154765 AATCGCAACGCGA
1 AATCGCAACGCGA
154778 TATTTAAAGC
Statistics
Matches: 139, Mismatches: 28, Indels: 15
0.76 0.15 0.08
Matches are distributed among these distances:
19 3 0.02
20 120 0.86
21 15 0.11
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AATCGCAACGCGAACACATA
Found at i:154629 original size:40 final size:39
Alignment explanation
Indices: 154580--154777 Score: 200
Period size: 40 Copynumber: 5.0 Consensus size: 39
154570 TTGCGATTTT
* ** *
154580 CCAT-AATCGCAACGCGAATATGAAAATCGCAACGCGAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
* *
154618 CACATAAATCGCAACGCGTATCCGTAAATCGCAACGTGTAT
1 C-CATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* ** * *
154659 CCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTAT
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCG-AA
* * **
154699 CCGTATATCGCAACGCGTATCCGTAAATCGCAACGATAA
1 CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
*
154738 TACATAAAATCGCAACGCGTATCCGTAAATCGCAACGCGA
1 -CCAT-AAATCGCAACGCGTATCCGTAAATCGCAACGCGA
154778 TATTTAAAGC
Statistics
Matches: 132, Mismatches: 23, Indels: 7
0.81 0.14 0.04
Matches are distributed among these distances:
38 1 0.01
39 4 0.03
40 94 0.71
41 33 0.25
ACGTcount: A:0.35, C:0.26, G:0.19, T:0.19
Consensus pattern (39 bp):
CCATAAATCGCAACGCGTATCCGTAAATCGCAACGCGAA
Found at i:154667 original size:60 final size:60
Alignment explanation
Indices: 154584--154776 Score: 251
Period size: 60 Copynumber: 3.2 Consensus size: 60
154574 GATTTTCCAT
* ** * *
154584 AATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* * *** *
154644 AATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
* **
154704 TATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTA
1 AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACAT-AAATCGCAACGCGTATCCGTA
154765 AATCGCAACGCG
1 AATCGCAACGCG
154777 ATATTTAAAG
Statistics
Matches: 111, Mismatches: 21, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
60 80 0.72
61 31 0.28
ACGTcount: A:0.35, C:0.26, G:0.20, T:0.19
Consensus pattern (60 bp):
AATCGCAACGCGTATCCGTAAATCGCAACGCGAATACATAAATCGCAACGCGTATCCGTA
Found at i:155198 original size:33 final size:33
Alignment explanation
Indices: 155159--155229 Score: 115
Period size: 33 Copynumber: 2.2 Consensus size: 33
155149 TTCACTTAGA
*
155159 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
* *
155192 TTTCATTTCGCGTTGCTATTCTCTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
155225 TTTCA
1 TTTCA
155230 AGTTAGTATT
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:0.11, C:0.23, G:0.18, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTGCGAT
Found at i:155369 original size:14 final size:14
Alignment explanation
Indices: 155350--155404 Score: 56
Period size: 14 Copynumber: 3.6 Consensus size: 14
155340 AGAATGACTG
155350 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
*
155364 TCGCAACGCGAAATGAAAA
1 TCGCAA--CG--A-GAGAA
155383 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
155397 TCGCAACG
1 TCGCAACG
155405 CGAAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 10
0.74 0.04 0.22
Matches are distributed among these distances:
14 18 0.53
15 1 0.03
16 2 0.06
17 2 0.06
18 1 0.03
19 10 0.29
ACGTcount: A:0.42, C:0.24, G:0.25, T:0.09
Consensus pattern (14 bp):
TCGCAACGAGAGAA
Found at i:155387 original size:33 final size:33
Alignment explanation
Indices: 155350--155420 Score: 124
Period size: 33 Copynumber: 2.2 Consensus size: 33
155340 AGAATGACTG
**
155350 TCGCAACGAGAGAATCGCAACGCGAAATGAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
155383 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
1 TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
155416 TCGCA
1 TCGCA
155421 TTGCGATTTT
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:0.44, C:0.25, G:0.23, T:0.08
Consensus pattern (33 bp):
TCGCAACGAGAGAATCGCAACGCGAAACCAAAA
Found at i:155438 original size:19 final size:19
Alignment explanation
Indices: 155416--155513 Score: 81
Period size: 19 Copynumber: 5.7 Consensus size: 19
155406 GAAACCAAAA
*
155416 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
155435 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
*
155449 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
155468 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* * *
155482 TCTCGTTGCGATTGTCATC
1 TCGCGTTGCGATTTTCATT
155501 TCGCGTTGCGATT
1 TCGCGTTGCGATT
155514 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:155457 original size:14 final size:14
Alignment explanation
Indices: 155438--155527 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
155428 TTTCATTTCG
155438 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
155452 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
155471 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
155485 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
155502 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
155518 CGTTGCGATT
1 CGTTGCGATT
155528 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:155463 original size:33 final size:33
Alignment explanation
Indices: 155421--155535 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
155411 CAAAATCGCA
155421 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
155454 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
155487 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
155520 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
155536 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:157435 original size:92 final size:93
Alignment explanation
Indices: 157229--157515 Score: 558
Period size: 93 Copynumber: 3.1 Consensus size: 93
157219 TAGATTGCTT
*
157229 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
157294 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
157322 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATA-TA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
157386 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
157414 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
157479 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
157507 AGTAAATTT
1 AGTAAATTT
157516 ATCCATTCAA
Statistics
Matches: 192, Mismatches: 1, Indels: 2
0.98 0.01 0.01
Matches are distributed among these distances:
92 92 0.48
93 100 0.52
ACGTcount: A:0.23, C:0.13, G:0.18, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:157599 original size:19 final size:19
Alignment explanation
Indices: 157559--157687 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
157549 TAGTTTACTT
* *
157559 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
157579 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
157598 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
157617 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
157631 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
157650 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
157664 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
157683 TCGCA
1 TCGCA
157688 TTGCGATTTC
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:157638 original size:33 final size:32
Alignment explanation
Indices: 157595--157687 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
157585 CGCGAAACCA
**
157595 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
157627 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
157660 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
157688 TTGCGATTTC
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:157685 original size:52 final size:52
Alignment explanation
Indices: 157559--157687 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
157549 TAGTTTACTT
**
157559 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
157611 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
157664 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
157688 TTGCGATTTC
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:157723 original size:14 final size:14
Alignment explanation
Indices: 157704--157759 Score: 67
Period size: 14 Copynumber: 3.7 Consensus size: 14
157694 TTTCATTTTG
157704 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
157718 CGTTGCGATTTCATTT
1 CGTTGCGA-TTC-TTT
*
157734 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
157750 CGTTGCGATT
1 CGTTGCGATT
157760 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 8
0.80 0.02 0.17
Matches are distributed among these distances:
14 16 0.43
15 3 0.08
16 9 0.24
17 3 0.08
18 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.45
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:157768 original size:33 final size:32
Alignment explanation
Indices: 157688--157778 Score: 146
Period size: 32 Copynumber: 2.8 Consensus size: 32
157678 CAAAATCGCA
* *
157688 TTGCGATTTCATTTTGCGTTGCGATTCTTTCG
1 TTGCGATTTCATTTCGCGTTGCGATTCTGTCG
*
157720 TTGCGATTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTCATTTCGCGTTGCGATTCTGTCG
157752 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGA-TTTCATTTCGCGTTGCGATT
157779 TTGGTTTCGC
Statistics
Matches: 54, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
32 35 0.65
33 19 0.35
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (32 bp):
TTGCGATTTCATTTCGCGTTGCGATTCTGTCG
Found at i:157774 original size:19 final size:18
Alignment explanation
Indices: 157683--157798 Score: 104
Period size: 19 Copynumber: 6.8 Consensus size: 18
157673 GAAACCAAAA
*
157683 TCGCATTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
*
157701 TTGCGTTGCGA-TTC-TT
1 TCGCGTTGCGATTTCATT
157717 T--CGTTGCGATTTCATT
1 TCGCGTTGCGATTTCATT
* *
157733 TCGCATTGCGA-TTC-TG
1 TCGCGTTGCGATTTCATT
157749 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGA-TTTCATT
**
157766 TCGCGTTGCGATTTTGGTT
1 TCGCGTTGCGA-TTTCATT
157785 TCGCGTTGCGATTT
1 TCGCGTTGCGATTT
157799 TAAGTTTCGT
Statistics
Matches: 81, Mismatches: 8, Indels: 18
0.76 0.07 0.17
Matches are distributed among these distances:
14 15 0.19
15 3 0.04
16 11 0.14
17 8 0.10
18 19 0.23
19 25 0.31
ACGTcount: A:0.10, C:0.20, G:0.23, T:0.47
Consensus pattern (18 bp):
TCGCGTTGCGATTTCATT
Found at i:157807 original size:20 final size:19
Alignment explanation
Indices: 157750--157815 Score: 89
Period size: 19 Copynumber: 3.4 Consensus size: 19
157740 GCGATTCTGT
157750 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTT-AGTTTCG
*
157769 CGTTGCGATTTTGGTTTCG
1 CGTTGCGATTTTAGTTTCG
157788 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTT-AGTTTCG
*
157808 TGTTGCGA
1 CGTTGCGA
157816 AAGTAAACTA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
19 29 0.69
20 13 0.31
ACGTcount: A:0.11, C:0.17, G:0.27, T:0.45
Consensus pattern (19 bp):
CGTTGCGATTTTAGTTTCG
Found at i:159708 original size:13 final size:14
Alignment explanation
Indices: 159700--159736 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
159690 GATTGTTTAA
159700 TTGATTTGTAAAAG
1 TTGATTTGTAAAAG
*
159714 ATGATTTGTAAAAG
1 TTGATTTGTAAAAG
159728 TTGATTTGT
1 TTGATTTGT
159737 GTAATTGATG
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:0.32, C:0.00, G:0.22, T:0.46
Consensus pattern (14 bp):
TTGATTTGTAAAAG
Found at i:159858 original size:19 final size:19
Alignment explanation
Indices: 159842--159942 Score: 142
Period size: 19 Copynumber: 5.6 Consensus size: 19
159832 AAAAATGACT
159842 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
159861 ATCGCAATGCGAAATGAAA
1 ATCGCAATGCGAAATGAAA
*
159880 ATCGCAA--CG--A-GAGA
1 ATCGCAATGCGAAATGAAA
159894 ATCGCAATGCGAAATG-AA
1 ATCGCAATGCGAAATGAAA
159912 ATCGCAATGCGGAAATGAAA
1 ATCGCAATGC-GAAATGAAA
159932 ATCGCAATGCG
1 ATCGCAATGCG
159943 TTTATAATTT
Statistics
Matches: 73, Mismatches: 2, Indels: 14
0.82 0.02 0.16
Matches are distributed among these distances:
14 10 0.14
15 1 0.01
16 2 0.03
17 2 0.03
18 12 0.16
19 34 0.47
20 12 0.16
ACGTcount: A:0.44, C:0.18, G:0.24, T:0.15
Consensus pattern (19 bp):
ATCGCAATGCGAAATGAAA
Found at i:159989 original size:52 final size:52
Alignment explanation
Indices: 159949--160262 Score: 321
Period size: 52 Copynumber: 5.9 Consensus size: 52
159939 TGCGTTTATA
*
159949 ATTTCGCATTGCGATTCTCTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
160001 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
1 ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
160053 ATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTTC
1 ATTTCGCATTGCGA--TTC-TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
* *
160109 ATTTCGCATTGCGATTTTAATTTCGCATTGCGA--TT-ATGTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA--TT-CTTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
*
160161 ATTTCGCATTGCGATTTTCATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTC
1 ATTTCGCATTGCGA--TTC-TTTCG--TTGCGATTTTCATTTCGCATTGCGATTTTC
* *
160213 ATTTCCGCATTGCGA-T-TTTCATGTTGGGATTTTCATTTCGCGTTGCGATT
1 ATTT-CGCATTGCGATTCTTTC--GTTGCGATTTTCATTTCGCATTGCGATT
160263 GTATTTTCCG
Statistics
Matches: 238, Mismatches: 7, Indels: 33
0.86 0.03 0.12
Matches are distributed among these distances:
48 9 0.04
50 5 0.02
51 10 0.04
52 121 0.51
53 23 0.10
54 5 0.02
55 5 0.02
56 35 0.15
57 25 0.11
ACGTcount: A:0.15, C:0.21, G:0.18, T:0.46
Consensus pattern (52 bp):
ATTTCGCATTGCGATTCTTTCGTTGCGATTTTCATTTCGCATTGCGATTTTC
Found at i:159995 original size:19 final size:19
Alignment explanation
Indices: 159971--160262 Score: 383
Period size: 19 Copynumber: 16.4 Consensus size: 19
159961 GATTCTCTCG
159971 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
159990 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
160009 TTGCGA--TTC-TTTCG--
1 TTGCGATTTTCATTTCGCA
160023 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
160042 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
160061 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
160080 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
160099 TTGCGA-TTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
160117 TTGCGATTTTAATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
160136 TTGCGA--TT-ATGTCG--
1 TTGCGATTTTCATTTCGCA
160150 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
160169 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
160188 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
160202 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
160222 TTGCGATTTTCA--T-G--
1 TTGCGATTTTCATTTCGCA
* *
160236 TTGGGATTTTCATTTCGCG
1 TTGCGATTTTCATTTCGCA
160255 TTGCGATT
1 TTGCGATT
160263 GTATTTTCCG
Statistics
Matches: 244, Mismatches: 7, Indels: 44
0.83 0.02 0.15
Matches are distributed among these distances:
14 29 0.12
16 24 0.10
17 21 0.09
18 21 0.09
19 137 0.56
20 12 0.05
ACGTcount: A:0.15, C:0.20, G:0.18, T:0.47
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:160132 original size:127 final size:122
Alignment explanation
Indices: 159971--160231 Score: 170
Period size: 127 Copynumber: 2.1 Consensus size: 122
159961 GATTCTCTCG
* *
159971 TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCGCATTGCGA-TTC-TTTCG-TTGCGATTTT
1 TTGCGATTTTAATTTCGCATTGCGA--TT-ATGTCG--TTGCGATTTCATTTCGATTGCGATTTT
*
160033 CATTTCGCATTGCGATTTTCATTTCGCATTGCGATTTTCATTT-CGCATTGCGATTTTCATTTCG
61 CATTTCGCATTGCGA--TTC-TCTCG--TTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCG
160097 CA
121 CA
* * *
160099 TTGCGA-TTTCATTTCGCATTGCGATTTTAATTTCGCATTGCGA-TT-ATGTCG-TTGCGATTTT
1 TTGCGATTTTAATTTCGCATTGCGA--TT-ATGTCG--TTGCGATTTCATTTCGATTGCGATTTT
* * *
160160 CATTTCGCATTGCGATT-T-TCATTTCGCA-TTGCGATTCTCTCG--TTGCGATTTTCATTTCCG
61 CATTTCGCATTGCGATTCTCTCGTTGCG-ATTTTC-ATT-TC-CGCATTGCGATTTTCATTT-CG
160220 CA
121 CA
160222 TTGCGATTTT
1 TTGCGATTTT
160232 CATGTTGGGA
Statistics
Matches: 120, Mismatches: 5, Indels: 20
0.83 0.03 0.14
Matches are distributed among these distances:
120 7 0.06
121 4 0.03
122 18 0.15
123 11 0.09
124 5 0.04
125 2 0.02
127 67 0.56
128 6 0.05
ACGTcount: A:0.15, C:0.21, G:0.17, T:0.47
Consensus pattern (122 bp):
TTGCGATTTTAATTTCGCATTGCGATTATGTCGTTGCGATTTCATTTCGATTGCGATTTTCATTT
CGCATTGCGATTCTCTCGTTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCGCA
Found at i:162765 original size:24 final size:24
Alignment explanation
Indices: 162731--162777 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
162721 CTGAAACATC
162731 ATCAAAATCCGTG-TATTGACCAAT
1 ATCAAAATCCG-GATATTGACCAAT
*
162755 ATCAAAGTCCGGATATTGACCAA
1 ATCAAAATCCGGATATTGACCAA
162778 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:163485 original size:20 final size:20
Alignment explanation
Indices: 163457--163825 Score: 442
Period size: 20 Copynumber: 18.4 Consensus size: 20
163447 AAATTTAAGT
* * * *
163457 GTTGTGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
163477 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
* * *
163497 GTTGCGATTTACAGATTCTC
1 GTTGCGATTTACGGATACGC
*
163517 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
163537 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
163557 GTTGCGATTTACGGATTA-TC
1 GTTGCGATTTACGGA-TACGC
163577 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
163597 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
163617 ATTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
163637 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
*
163657 GTTGC-AGTTTACGGATATGC
1 GTTGCGA-TTTACGGATACGC
163677 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
*
163697 GTTGCGATATACGGATACGC
1 GTTGCGATTTACGGATACGC
* **
163717 ATTGCGATTTACCCATACGC
1 GTTGCGATTTACGGATACGC
*
163737 GTTGCGATTTACGGATACAC
1 GTTGCGATTTACGGATACGC
163757 GTTGCGATTTACGGATACGC
1 GTTGCGATTTACGGATACGC
* *
163777 GTTGCGATTTATGTG-TTCGC
1 GTTGCGATTTACG-GATACGC
* ** *
163797 GTTGCGATTTTCATATTCGC
1 GTTGCGATTTACGGATACGC
163817 GTTGCGATT
1 GTTGCGATT
163826 ATGGAAAATC
Statistics
Matches: 307, Mismatches: 32, Indels: 20
0.86 0.09 0.06
Matches are distributed among these distances:
19 6 0.02
20 295 0.96
21 6 0.02
ACGTcount: A:0.20, C:0.19, G:0.26, T:0.35
Consensus pattern (20 bp):
GTTGCGATTTACGGATACGC
Found at i:164451 original size:28 final size:30
Alignment explanation
Indices: 164419--164493 Score: 79
Period size: 29 Copynumber: 2.6 Consensus size: 30
164409 ATTTTAATAT
164419 ATAAAAATATCAAATTAAATTAT-A-AAAA
1 ATAAAAATATCAAATTAAATTATAATAAAA
*
164447 ATAAAAATA--AAAATATAATTATAATAAAA
1 ATAAAAATATCAAATTA-AATTATAATAAAA
* *
164476 ATATAAA-ATCAATTTAAA
1 ATAAAAATATCAAATTAAA
164494 AGTTTTTTTG
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
26 5 0.13
27 6 0.16
28 11 0.29
29 12 0.32
30 4 0.11
ACGTcount: A:0.68, C:0.03, G:0.00, T:0.29
Consensus pattern (30 bp):
ATAAAAATATCAAATTAAATTATAATAAAA
Found at i:164489 original size:23 final size:23
Alignment explanation
Indices: 164446--164489 Score: 63
Period size: 23 Copynumber: 1.9 Consensus size: 23
164436 AATTATAAAA
*
164446 AATAAAAATAAAAATATAATTAT
1 AATAAAAATAAAAATACAATTAT
164469 AATAAAAATATAAAAT-CAATT
1 AATAAAAATA-AAAATACAATT
164490 TAAAAGTTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
23 14 0.74
24 5 0.26
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (23 bp):
AATAAAAATAAAAATACAATTAT
Found at i:165199 original size:13 final size:14
Alignment explanation
Indices: 165179--165217 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 14
165169 CTTGGAAGTG
165179 TATAAATTAAATAA
1 TATAAATTAAATAA
*
165193 T-TAAATTAAAAAA
1 TATAAATTAAATAA
*
165206 TATAGATTAAAT
1 TATAAATTAAAT
165218 TCATAAATTA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
13 12 0.57
14 9 0.43
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.36
Consensus pattern (14 bp):
TATAAATTAAATAA
Found at i:165382 original size:60 final size:61
Alignment explanation
Indices: 165318--165470 Score: 156
Period size: 60 Copynumber: 2.5 Consensus size: 61
165308 ATCTCTAAAA
* * * *
165318 TTTTGAATATTCTAATTTCATCCTTAAATTAT-G-ATTATCATTCTAAATT-AGTCCTCAAAC-
1 TTTTGAACATTCTAATTTCATCCCTAAACTATAGCA-T-TCATTCTAAATTGA-TCCCCAAACT
* *
165378 TTTTGAACATT-TCAATTTTATCCCTAAACTATAGCATTCATTTTAAATTGATCCCCAAACT
1 TTTTGAACATTCT-AATTTCATCCCTAAACTATAGCATTCATTCTAAATTGATCCCCAAACT
* *
165439 TTTTGAACATTCGAATTTCATCCC-AGACTATA
1 TTTTGAACATTCTAATTTCATCCCTAAACTATA
165471 CGTATATACT
Statistics
Matches: 78, Mismatches: 9, Indels: 12
0.79 0.09 0.12
Matches are distributed among these distances:
59 1 0.01
60 52 0.67
61 24 0.31
62 1 0.01
ACGTcount: A:0.33, C:0.20, G:0.06, T:0.42
Consensus pattern (61 bp):
TTTTGAACATTCTAATTTCATCCCTAAACTATAGCATTCATTCTAAATTGATCCCCAAACT
Found at i:166055 original size:22 final size:23
Alignment explanation
Indices: 166021--166063 Score: 61
Period size: 22 Copynumber: 1.9 Consensus size: 23
166011 ATATAATAAA
*
166021 TAATATTATTTATTATAAAAACT
1 TAATATCATTTATTATAAAAACT
*
166044 TAATATCA-TTATTTTAAAAA
1 TAATATCATTTATTATAAAAA
166064 TATTAGAATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 11 0.61
23 7 0.39
ACGTcount: A:0.49, C:0.05, G:0.00, T:0.47
Consensus pattern (23 bp):
TAATATCATTTATTATAAAAACT
Found at i:166227 original size:21 final size:23
Alignment explanation
Indices: 166202--166248 Score: 62
Period size: 23 Copynumber: 2.1 Consensus size: 23
166192 TCTATAAAAA
*
166202 TAAAAATATT-AT-ATTATATTT
1 TAAAAATATTAATAAATATATTT
*
166223 TAAAATTATTAATAAATATATTT
1 TAAAAATATTAATAAATATATTT
166246 TAA
1 TAA
166249 GGAATTTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 9 0.41
22 2 0.09
23 11 0.50
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (23 bp):
TAAAAATATTAATAAATATATTT
Found at i:166263 original size:23 final size:22
Alignment explanation
Indices: 166202--166264 Score: 58
Period size: 23 Copynumber: 2.8 Consensus size: 22
166192 TCTATAAAAA
* *
166202 TAAAAATA-TTATATTATATTT
1 TAAAATTATTTATAATATATTT
*
166223 TAAAATTATTAATAAATATATTT
1 TAAAATTATTTAT-AATATATTT
166246 TAAGGAATT-TTTATAATAT
1 TAA--AATTATTTATAATAT
166265 TATTAGGCTA
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
21 7 0.21
22 3 0.09
23 16 0.47
24 4 0.12
25 4 0.12
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.49
Consensus pattern (22 bp):
TAAAATTATTTATAATATATTT
Found at i:167368 original size:65 final size:65
Alignment explanation
Indices: 167293--167455 Score: 220
Period size: 65 Copynumber: 2.5 Consensus size: 65
167283 ACACCCTATT
* *
167293 TCGAATGCATTTAGTGTACCGATGCACAAGACATGCATCGATGCACTCTTGAATATTTTGAAACA
1 TCGAATGCATTTAGTGTACCGATGCACAAGACATGCATCGATGCACTCATGAATATTTTAAAACA
* **
167358 TCGAATGCATTTAGTGTACCGATGCACATA-CCATGCATCGATGCACTCATGGCTATTTTAAAAC
1 TCGAATGCATTTAGTGTACCGATGCACA-AGACATGCATCGATGCACTCATGAATATTTTAAAAC
167422 A
65 A
* * * *
167423 ACAAATACAATTAGTGTACCGATGCACTAAGAC
1 TCGAATGCATTTAGTGTACCGATGCAC-AAGAC
167456 TTATAACTGT
Statistics
Matches: 85, Mismatches: 10, Indels: 5
0.85 0.10 0.05
Matches are distributed among these distances:
65 82 0.96
66 3 0.04
ACGTcount: A:0.34, C:0.21, G:0.17, T:0.28
Consensus pattern (65 bp):
TCGAATGCATTTAGTGTACCGATGCACAAGACATGCATCGATGCACTCATGAATATTTTAAAACA
Found at i:169219 original size:14 final size:13
Alignment explanation
Indices: 169189--169223 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
169179 TATTATTTTG
*
169189 ATTTTTTATAAAT
1 ATTTTTAATAAAT
169202 ATTTTTAATAAAT
1 ATTTTTAATAAAT
*
169215 AATTTTAAT
1 ATTTTTAAT
169224 GATTAAGACC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (13 bp):
ATTTTTAATAAAT
Found at i:174991 original size:17 final size:17
Alignment explanation
Indices: 174957--175008 Score: 54
Period size: 17 Copynumber: 3.2 Consensus size: 17
174947 ACCGGACAAA
* *
174957 TTTATTATTTTAGAGAG
1 TTTATTAATTTACAGAG
*
174974 TTTATTAATTTACTGAG
1 TTTATTAATTTACAGAG
*
174991 --TATTAATTTAAAGAG
1 TTTATTAATTTACAGAG
175006 TTT
1 TTT
175009 CTACTGTATA
Statistics
Matches: 28, Mismatches: 5, Indels: 4
0.76 0.14 0.11
Matches are distributed among these distances:
15 13 0.46
17 15 0.54
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.52
Consensus pattern (17 bp):
TTTATTAATTTACAGAG
Found at i:176624 original size:21 final size:21
Alignment explanation
Indices: 176573--176625 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
176563 ATTATGACTA
176573 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
176594 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
176615 TCGCAATGCGA
1 TCGCAATGCGA
176626 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:176640 original size:20 final size:21
Alignment explanation
Indices: 176615--176666 Score: 79
Period size: 21 Copynumber: 2.5 Consensus size: 21
176605 TTTTCCCAAT
*
176615 TCGCAATGCGAA-TAAGTAAA
1 TCGCAATGCGAATTAAGAAAA
*
176635 TCGCAATGCGAATTTAGAAAA
1 TCGCAATGCGAATTAAGAAAA
176656 TCGCAATGCGA
1 TCGCAATGCGA
176667 TACTTACTAG
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
20 12 0.41
21 17 0.59
ACGTcount: A:0.40, C:0.17, G:0.21, T:0.21
Consensus pattern (21 bp):
TCGCAATGCGAATTAAGAAAA
Found at i:176645 original size:41 final size:41
Alignment explanation
Indices: 176600--176852 Score: 158
Period size: 41 Copynumber: 6.2 Consensus size: 41
176590 AATTTCGCGT
* *
176600 TGCGATTTTCCCAATTCGCAATGCGAATAAGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATACGTAAATCGCAA
* *** * * * *
176641 TGCGAATTTAGAAAATCGCAATGCG-ATACTTACTAGCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATACGTA-AATCGCAA
* * * **
176682 TGCAATTTTCCTAATTCGCATTGC-AATTTACGT-ATTCGCGT
1 TGCGATTTTCCTAATTCGCAATGCGAA--TACGTAAATCGCAA
*
176723 TGCGATTTTCATAATTCGCAATGCGAATACGTAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATACGTAAATCGCAA
* *** * * *
176764 CGCGA-TTAAGTAAATCGCAATGCGAATTAGGAAAATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAA-TACGTAAATCGCAA
* * * * * *
176805 TGCGA-ATACGTAAATCGCAATGCGAAT-CTTACTATCGCAA
1 TGCGATTTTCCTAATTCGCAATGCGAATACGTA-AATCGCAA
176845 TGCGATTT
1 TGCGATTT
176853 ACATAGCGCC
Statistics
Matches: 160, Mismatches: 43, Indels: 18
0.72 0.19 0.08
Matches are distributed among these distances:
39 1 0.01
40 40 0.25
41 113 0.71
42 2 0.01
43 4 0.03
ACGTcount: A:0.33, C:0.20, G:0.18, T:0.28
Consensus pattern (41 bp):
TGCGATTTTCCTAATTCGCAATGCGAATACGTAAATCGCAA
Found at i:176706 original size:21 final size:21
Alignment explanation
Indices: 176677--176742 Score: 71
Period size: 21 Copynumber: 3.2 Consensus size: 21
176667 TACTTACTAG
* *
176677 CGCAATGCAATTTTCCTAATT
1 CGCATTGCAATTTTCATAATT
* *
176698 CGCATTGCAATTTACGT-ATT
1 CGCATTGCAATTTTCATAATT
* *
176718 CGCGTTGCGATTTTCATAATT
1 CGCATTGCAATTTTCATAATT
176739 CGCA
1 CGCA
176743 ATGCGAATAC
Statistics
Matches: 36, Mismatches: 8, Indels: 2
0.78 0.17 0.04
Matches are distributed among these distances:
20 16 0.44
21 20 0.56
ACGTcount: A:0.24, C:0.23, G:0.15, T:0.38
Consensus pattern (21 bp):
CGCATTGCAATTTTCATAATT
Found at i:176763 original size:20 final size:20
Alignment explanation
Indices: 176738--176849 Score: 136
Period size: 20 Copynumber: 5.5 Consensus size: 20
176728 TTTTCATAAT
176738 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* * *
176758 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATACGTAAA
* *
176778 TCGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TACGTAAA
176799 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATACGTAAA
* *
176819 TCGCAATGCGAAT-CTTACTA
1 TCGCAATGCGAATACGTA-AA
176839 TCGCAATGCGA
1 TCGCAATGCGA
176850 TTTACATAGC
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
19 3 0.04
20 58 0.73
21 18 0.23
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.21
Consensus pattern (20 bp):
TCGCAATGCGAATACGTAAA
Found at i:177405 original size:33 final size:33
Alignment explanation
Indices: 177368--177446 Score: 122
Period size: 33 Copynumber: 2.4 Consensus size: 33
177358 TAGTTTCGAG
177368 AATGAAAATCGCAACGAGAGAATCACAACGCGA
1 AATGAAAATCGCAACGAGAGAATCACAACGCGA
* *
177401 AATGAAAATCGCAACGAGATAATCGCAACGCGA
1 AATGAAAATCGCAACGAGAGAATCACAACGCGA
**
177434 AACCAAAATCGCA
1 AATGAAAATCGCA
177447 TTGCGATTTT
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 42 1.00
ACGTcount: A:0.48, C:0.23, G:0.19, T:0.10
Consensus pattern (33 bp):
AATGAAAATCGCAACGAGAGAATCACAACGCGA
Found at i:177483 original size:14 final size:14
Alignment explanation
Indices: 177464--177552 Score: 70
Period size: 14 Copynumber: 5.6 Consensus size: 14
177454 TTTCATTTCG
177464 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
177478 CGTTGCGATAGTCATTTCG
1 CGTTGCGAT--TC---TCT
177497 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
177511 CGTTGCGATAGTCATTTCG
1 CGTTGCGAT--TC---TCT
177530 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
177544 CGTTGCGAT
1 CGTTGCGAT
177553 AGTCATTTCC
Statistics
Matches: 61, Mismatches: 4, Indels: 20
0.72 0.05 0.24
Matches are distributed among these distances:
14 31 0.51
16 4 0.07
17 4 0.07
19 22 0.36
ACGTcount: A:0.11, C:0.25, G:0.25, T:0.39
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:177493 original size:33 final size:33
Alignment explanation
Indices: 177447--177573 Score: 227
Period size: 33 Copynumber: 3.8 Consensus size: 33
177437 CAAAATCGCA
**
177447 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
177480 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
177513 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
177546 TTGCGATAGTCATTTCCGCGTTGCGATT
1 TTGCGATAGTCATTT-CGCGTTGCGATT
177574 TTCATTATCT
Statistics
Matches: 91, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
33 79 0.87
34 12 0.13
ACGTcount: A:0.12, C:0.24, G:0.24, T:0.41
Consensus pattern (33 bp):
TTGCGATAGTCATTTCGCGTTGCGATTCTCTCG
Found at i:177578 original size:20 final size:20
Alignment explanation
Indices: 177544--177601 Score: 73
Period size: 20 Copynumber: 2.9 Consensus size: 20
177534 GCGATTCTCT
**
177544 CGTTGCGATAGTCATTTCCG
1 CGTTGCGATTTTCATTTCCG
*
177564 CGTTGCGATTTTCATTAT-CT
1 CGTTGCGATTTTCATT-TCCG
177584 CGTTGCGATTTTCATTTC
1 CGTTGCGATTTTCATTTC
177602 AACCAAAAGA
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
19 1 0.03
20 31 0.94
21 1 0.03
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (20 bp):
CGTTGCGATTTTCATTTCCG
Found at i:179434 original size:94 final size:88
Alignment explanation
Indices: 179277--179455 Score: 254
Period size: 94 Copynumber: 2.0 Consensus size: 88
179267 ATTGCTTAGT
179277 AATTTATCGGTTGCTGCCAATACTGCTAAACTATTTATTAACAATGTGAAGTTAGTATTTGTCTT
1 AATTTATCGGTTGCTGCCAATACTGCTAAACTATTTATTAACAATGTGAAGTTAGTATTTGTC--
179342 TTTGTTTTGTCTTTTGGTTGAAGTA
64 TTTGTTTTGTCTTTTGGTTGAAGTA
* *
179367 AATTTATTCGGTTGCTGCCAAT-TTGCTAAACTGTGTATTCT-TTAACACTGTGAAGTTAGTATT
1 AATTTA-TCGGTTGCTGCCAATACTGCTAAAC----TATT-TATTAACAATGTGAAGTTAGTATT
179430 TGTCTTTGTTTTGTCTTTTGGTTGAA
60 TGTCTTTGTTTTGTCTTTTGGTTGAA
179456 AGTTTGAAAT
Statistics
Matches: 81, Mismatches: 2, Indels: 10
0.87 0.02 0.11
Matches are distributed among these distances:
90 14 0.17
91 15 0.19
92 22 0.27
94 29 0.36
95 1 0.01
ACGTcount: A:0.22, C:0.12, G:0.18, T:0.47
Consensus pattern (88 bp):
AATTTATCGGTTGCTGCCAATACTGCTAAACTATTTATTAACAATGTGAAGTTAGTATTTGTCTT
TGTTTTGTCTTTTGGTTGAAGTA
Found at i:179751 original size:21 final size:21
Alignment explanation
Indices: 179727--179793 Score: 55
Period size: 21 Copynumber: 3.2 Consensus size: 21
179717 TCATTCCTCG
179727 AGAGTCCCCTCCCACCGTTCA
1 AGAGTCCCCTCCCACCGTTCA
* * ** * *
179748 AGAGGCCACTGTCATCGTTGA
1 AGAGTCCCCTCCCACCGTTCA
*
179769 AGAGGT-CCCTCCCACCATTCA
1 AGA-GTCCCCTCCCACCGTTCA
179790 AGAG
1 AGAG
179794 CCCGATTCAC
Statistics
Matches: 32, Mismatches: 13, Indels: 3
0.67 0.27 0.06
Matches are distributed among these distances:
20 1 0.03
21 30 0.94
22 1 0.03
ACGTcount: A:0.24, C:0.36, G:0.21, T:0.19
Consensus pattern (21 bp):
AGAGTCCCCTCCCACCGTTCA
Found at i:179751 original size:42 final size:42
Alignment explanation
Indices: 179675--179793 Score: 107
Period size: 42 Copynumber: 2.8 Consensus size: 42
179665 GACTCGCCTG
* * * * * * *
179675 TCATCCCTCAAGAGTCCACTCCTATCGTTAAAGAGGCCCCTA
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
*
179717 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTG
1 TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
* * *
179759 TCA-TCGTTGAAGAGGT-CCCTCCCACCATTCAAGAG
1 TCATTCCTCG-AGA-GTCCCCTCCCACCGTTCAAGAG
179794 CCCGATTCAC
Statistics
Matches: 64, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
41 4 0.06
42 58 0.91
43 2 0.03
ACGTcount: A:0.24, C:0.36, G:0.18, T:0.23
Consensus pattern (42 bp):
TCATTCCTCGAGAGTCCCCTCCCACCGTTCAAGAGGCCACTA
Found at i:181165 original size:14 final size:13
Alignment explanation
Indices: 181131--181167 Score: 56
Period size: 14 Copynumber: 2.7 Consensus size: 13
181121 TTGATTGTTT
181131 AATTGATTTGTAA
1 AATTGATTTGTAA
181144 AATGTGATTTGTAA
1 AAT-TGATTTGTAA
181158 AAGTTGATTT
1 AA-TTGATTT
181168 TTTTAATTGA
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 3 0.14
14 18 0.82
15 1 0.05
ACGTcount: A:0.35, C:0.00, G:0.19, T:0.46
Consensus pattern (13 bp):
AATTGATTTGTAA
Found at i:181327 original size:33 final size:33
Alignment explanation
Indices: 181280--181388 Score: 146
Period size: 33 Copynumber: 3.3 Consensus size: 33
181270 ATTACTATCA
* *
181280 CAATACGAAATGAAAATCGCAACGAGATAATCG
1 CAATGCGAAATGAAAATCGCAACGAGAAAATCG
* *
181313 CAATGCGAAATGAAAATCGCAACTAGAGAATCG
1 CAATGCGAAATGAAAATCGCAACGAGAAAATCG
* * *
181346 CAATGCGAAATAAAAACCGCAACGACAAAATCG
1 CAATGCGAAATGAAAATCGCAACGAGAAAATCG
*
181379 CAACGCGAAA
1 CAATGCGAAA
181389 CTAAATTCGC
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
33 67 1.00
ACGTcount: A:0.49, C:0.21, G:0.18, T:0.12
Consensus pattern (33 bp):
CAATGCGAAATGAAAATCGCAACGAGAAAATCG
Found at i:181332 original size:19 final size:18
Alignment explanation
Indices: 181280--181334 Score: 55
Period size: 19 Copynumber: 3.2 Consensus size: 18
181270 ATTACTATCA
181280 CAATACGAAATGAAAATCG
1 CAAT-CGAAATGAAAATCG
*
181299 CAA-CG--A-GATAATCG
1 CAATCGAAATGAAAATCG
181313 CAATGCGAAATGAAAATCG
1 CAAT-CGAAATGAAAATCG
181332 CAA
1 CAA
181335 CTAGAGAATC
Statistics
Matches: 29, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
14 10 0.34
15 1 0.03
16 2 0.07
17 2 0.07
18 1 0.03
19 13 0.45
ACGTcount: A:0.49, C:0.18, G:0.18, T:0.15
Consensus pattern (18 bp):
CAATCGAAATGAAAATCG
Found at i:181416 original size:19 final size:19
Alignment explanation
Indices: 181394--181544 Score: 80
Period size: 19 Copynumber: 8.7 Consensus size: 19
181384 CGAAACTAAA
181394 TTCGCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
181413 TTCGCTTTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
* *
181428 -CCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
*
181446 TTCGCATTGCGA--TTC--
1 TTCGCGTTGCGATTTTCAT
*
181461 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
**
181479 TTCGTATTGCGA--TT-A-
1 TTCGCGTTGCGATTTTCAT
*
181494 -TCTCGTTGCGATTTTCAT
1 TTCGCGTTGCGATTTTCAT
* ** *
181512 TTCGCATTGCGATAGTAAT
1 TTCGCGTTGCGATTTTCAT
181531 TTCCGCGTTGCGAT
1 TT-CGCGTTGCGAT
181545 AGACATTAAG
Statistics
Matches: 95, Mismatches: 21, Indels: 31
0.65 0.14 0.21
Matches are distributed among these distances:
14 25 0.26
16 9 0.09
17 9 0.09
19 42 0.44
20 10 0.11
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (19 bp):
TTCGCGTTGCGATTTTCAT
Found at i:181440 original size:33 final size:33
Alignment explanation
Indices: 181398--181524 Score: 218
Period size: 33 Copynumber: 3.8 Consensus size: 33
181388 ACTAAATTCG
* *
181398 CGTTGCGATTTTCATTTCGCTTTGCGATTCCCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
181431 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
* *
181464 CGTTGCGATTTTCATTTCGTATTGCGATTATCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
181497 CGTTGCGATTTTCATTTCGCATTGCGAT
1 CGTTGCGATTTTCATTTCGCATTGCGAT
181525 AGTAATTTCC
Statistics
Matches: 89, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 89 1.00
ACGTcount: A:0.13, C:0.23, G:0.19, T:0.46
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCTCT
Found at i:181471 original size:14 final size:14
Alignment explanation
Indices: 181419--181506 Score: 50
Period size: 14 Copynumber: 5.6 Consensus size: 14
181409 TCATTTCGCT
*
181419 TTGCGATTCCCTCG
1 TTGCGATTCTCTCG
*
181433 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
181450 CATTGCGATTCTCTCG
1 --TTGCGATTCTCTCG
*
181466 TTGCGATTTTCATTTCG
1 TTGCGA--TTC-TCTCG
*
181483 TATTGCGATTATCTCG
1 --TTGCGATTCTCTCG
181499 TTGCGATT
1 TTGCGATT
181507 TTCATTTCGC
Statistics
Matches: 58, Mismatches: 6, Indels: 20
0.69 0.07 0.24
Matches are distributed among these distances:
14 20 0.34
16 14 0.24
17 12 0.21
19 12 0.21
ACGTcount: A:0.12, C:0.23, G:0.19, T:0.45
Consensus pattern (14 bp):
TTGCGATTCTCTCG
Found at i:184077 original size:24 final size:24
Alignment explanation
Indices: 184043--184096 Score: 72
Period size: 24 Copynumber: 2.2 Consensus size: 24
184033 CTGAAACATC
*
184043 ATCAAAATCCGAGTATTAACCAAT
1 ATCAAAATCCGAGTATTAACCAAG
* * *
184067 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTAACCAAG
184091 ATCAAA
1 ATCAAA
184097 TTTCGAATAC
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
24 26 1.00
ACGTcount: A:0.43, C:0.20, G:0.15, T:0.22
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTAACCAAG
Found at i:184990 original size:20 final size:20
Alignment explanation
Indices: 184957--185072 Score: 171
Period size: 20 Copynumber: 5.8 Consensus size: 20
184947 TAATACAAAA
*
184957 TCGCAACG-GATACTGACTT
1 TCGCAACGCGATTCTGACTT
*
184976 TCGCAACGCGATACTGACTT
1 TCGCAACGCGATTCTGACTT
184996 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
185016 TCGCAACGCGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
* *
185036 TCGCAATGAGATTCTGACTT
1 TCGCAACGCGATTCTGACTT
* *
185056 TCGCAATGAGATTCTGA
1 TCGCAACGCGATTCTGA
185073 AAATCGTAAT
Statistics
Matches: 93, Mismatches: 3, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
19 8 0.09
20 85 0.91
ACGTcount: A:0.24, C:0.26, G:0.21, T:0.29
Consensus pattern (20 bp):
TCGCAACGCGATTCTGACTT
Found at i:184990 original size:60 final size:60
Alignment explanation
Indices: 184923--185067 Score: 159
Period size: 60 Copynumber: 2.4 Consensus size: 60
184913 AAATCGTAAT
*
184923 GCGATACTGACTATCGCAATGAGATAAT-ACAAAATCGCAACG-GATACTGACTTTCGCAAC
1 GCGATACTGACTTTCGCAATGAGATAATGAC--AATCGCAACGCGATACTGACTTTCGCAAC
* * ** ** * *
184983 GCGATACTGACTTTCGCAACGCGATTCTGACTTTCGCAACGCGATTCTGACTTTCGCAAT
1 GCGATACTGACTTTCGCAATGAGATAATGACAATCGCAACGCGATACTGACTTTCGCAAC
* *
185043 GAGATTCTGACTTTCGCAATGAGAT
1 GCGATACTGACTTTCGCAATGAGAT
185068 TCTGAAAATC
Statistics
Matches: 70, Mismatches: 13, Indels: 4
0.80 0.15 0.05
Matches are distributed among these distances:
59 8 0.11
60 60 0.86
61 2 0.03
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (60 bp):
GCGATACTGACTTTCGCAATGAGATAATGACAATCGCAACGCGATACTGACTTTCGCAAC
Found at i:185319 original size:20 final size:20
Alignment explanation
Indices: 185294--185341 Score: 87
Period size: 20 Copynumber: 2.4 Consensus size: 20
185284 CAACGGGGAA
*
185294 ATCGCAACGCGTAAATGGCT
1 ATCGCAACGCGAAAATGGCT
185314 ATCGCAACGCGAAAATGGCT
1 ATCGCAACGCGAAAATGGCT
185334 ATCGCAAC
1 ATCGCAAC
185342 TAGAAAATCG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.33, C:0.27, G:0.23, T:0.17
Consensus pattern (20 bp):
ATCGCAACGCGAAAATGGCT
Done.