Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005120.1 Hibiscus syriacus cultivar Beakdansim tig00011518_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: 60237
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:1196 original size:31 final size:31
Alignment explanation
Indices: 1148--1334 Score: 286
Period size: 31 Copynumber: 6.0 Consensus size: 31
1138 CCCGAATGAC
* *
1148 CAGTCCATA-GATTCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
1179 CAGTCTATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
1210 AAGTCCATATGTCCCGAAGAATATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
* *
1241 CAGTCTATATGTCCCGAAGAACATCGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
*
1272 CAGTCCATATATCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1303 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1334 C
1 C
1335 CCTCGACCCT
Statistics
Matches: 141, Mismatches: 14, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
31 140 0.99
32 1 0.01
ACGTcount: A:0.39, C:0.21, G:0.19, T:0.21
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:2170 original size:64 final size:64
Alignment explanation
Indices: 2054--2178 Score: 164
Period size: 64 Copynumber: 2.0 Consensus size: 64
2044 TATTATTGAG
* * *
2054 ATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGGATTCATCGATGCACTATTT
1 ATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAGATGCATCGATGCACTATTT
** *
2118 ATGCATCGATGCATGAATTGCATTCGATGTCTTTATT-TTAAA-AGAGTGCATCGATGCACTA
1 ATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAAAGAGA-TGCATCGATGCACTA
2179 CCAATGCATC
Statistics
Matches: 53, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
63 2 0.04
64 46 0.87
65 5 0.09
ACGTcount: A:0.28, C:0.18, G:0.18, T:0.36
Consensus pattern (64 bp):
ATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAGATGCATCGATGCACTATTT
Found at i:2186 original size:64 final size:64
Alignment explanation
Indices: 2054--2195 Score: 162
Period size: 64 Copynumber: 2.2 Consensus size: 64
2044 TATTATTGAG
* * * ***
2054 ATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGGATTCATCGATGCACTATTT
1 ATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAGATGCATCGATGCACTACCA
** *
2118 ATGCATCGATGCATGAATTGCATTCGATGTCTTTATT-TTAAA-AGAGTGCATCGATGCACTACC
1 ATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAAAGAGA-TGCATCGATGCACTACC
2181 A
64 A
*
2182 ATGCATCGGTGCAC
1 ATGCATCGATGCAC
2196 ATTCAAACAA
Statistics
Matches: 65, Mismatches: 11, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
63 2 0.03
64 58 0.89
65 5 0.08
ACGTcount: A:0.27, C:0.20, G:0.19, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAGATGCATCGATGCACTACCA
Found at i:3305 original size:60 final size:60
Alignment explanation
Indices: 3208--3341 Score: 144
Period size: 60 Copynumber: 2.2 Consensus size: 60
3198 AAAAATTTAA
** * ** *
3208 AAAAGTTTGGGGACAAAATTAGAATGAAGATCGTAGTTTGGGGATGAAAATGAAATGTTT
1 AAAAGTTTAAGGACAAAATTAGAATGAAGATCATAGTTTAAGGATGAAAATGAAATATTT
* * * * *
3268 AGAAGTTTAAGGACTAAATTAGAATGATA-ATTATAGTTTAAGGATGAGATTGAAATATTT
1 AAAAGTTTAAGGACAAAATTAGAATGA-AGATCATAGTTTAAGGATGAAAATGAAATATTT
*
3328 AAAAGTTTAGGGAC
1 AAAAGTTTAAGGAC
3342 CAATTTAAAA
Statistics
Matches: 60, Mismatches: 13, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
60 59 0.98
61 1 0.02
ACGTcount: A:0.42, C:0.03, G:0.25, T:0.31
Consensus pattern (60 bp):
AAAAGTTTAAGGACAAAATTAGAATGAAGATCATAGTTTAAGGATGAAAATGAAATATTT
Found at i:4105 original size:20 final size:19
Alignment explanation
Indices: 4076--4114 Score: 51
Period size: 20 Copynumber: 2.0 Consensus size: 19
4066 TATTTGGGTT
*
4076 AATTTAAATTCATATTTAAA
1 AATTTAAATTAAT-TTTAAA
*
4096 AATTTTAATTAATTTTAAA
1 AATTTAAATTAATTTTAAA
4115 TCTATAAACT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (19 bp):
AATTTAAATTAATTTTAAA
Found at i:5198 original size:8 final size:7
Alignment explanation
Indices: 5172--5196 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
5162 GACACTCTCA
5172 TTTTATT
1 TTTTATT
5179 TTTTATT
1 TTTTATT
5186 TTTTATT
1 TTTTATT
5193 TTTT
1 TTTT
5197 TAAAGTTTAT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.12, C:0.00, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTATT
Found at i:5246 original size:19 final size:18
Alignment explanation
Indices: 5206--5247 Score: 50
Period size: 19 Copynumber: 2.3 Consensus size: 18
5196 TTAAAGTTTA
*
5206 TAAA-TTTAAAATTAATT
1 TAAATTTTAAAATGAATT
*
5223 AAAATTTTAAATATGAATT
1 TAAATTTTAAA-ATGAATT
5242 TAAATT
1 TAAATT
5248 GACTCAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
17 3 0.15
18 6 0.30
19 11 0.55
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (18 bp):
TAAATTTTAAAATGAATT
Found at i:10283 original size:54 final size:54
Alignment explanation
Indices: 10201--10463 Score: 445
Period size: 54 Copynumber: 4.9 Consensus size: 54
10191 ACCAAATAGG
* *
10201 CACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAATCGTTTCGA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCATTTCGA
* * * * * *
10255 CACTAAGTGTGCATTTCATGGAATTCATCATATGTGGATGAATAATCGTTTCGG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCATTTCGA
10309 CACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCATTTCGA
1 CACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCATTTCGA
*
10363 CACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCATTTCGG
1 CACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCATTTCGA
10417 CACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACC
1 CACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACC
10464 GTACATGCAC
Statistics
Matches: 198, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
54 198 1.00
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.31
Consensus pattern (54 bp):
CACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCATTTCGA
Found at i:10474 original size:54 final size:53
Alignment explanation
Indices: 10200--10535 Score: 381
Period size: 54 Copynumber: 6.2 Consensus size: 53
10190 TACCAAATAG
* *
10200 GCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAATCGT-TT
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCGTACT
* * * * * *
10252 CGACACTAAGTGTGCATTTCATGGAATTCATCATATGTGGATGAATAATCGTTTCG
1 -G-CACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCG-TACT
* *
10308 GCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCAT-TT
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCGTACT
* * *
10360 CGACACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCATTTCG
1 -G-CACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACC-GTACT
10416 GCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCGTACAT
1 GCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCGTAC-T
* * * * * *
10470 GCACTATGTGGGCAAATCCACGGAATTCATCAT-GAGTTGATGAATAACCGTACAT
1 GCACTAAGTGTGC-ATTTCACGGAATTCATCCTAG-GTGGATGAATAACCGTAC-T
*
10525 GCACTATGTGT
1 GCACTAAGTGT
10536 ACAAATCCAT
Statistics
Matches: 248, Mismatches: 25, Indels: 18
0.85 0.09 0.06
Matches are distributed among these distances:
53 5 0.02
54 194 0.78
55 49 0.20
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (53 bp):
GCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCGTACT
Found at i:10475 original size:108 final size:109
Alignment explanation
Indices: 10199--10518 Score: 461
Period size: 108 Copynumber: 3.0 Consensus size: 109
10189 TTACCAAATA
*
10199 GGCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAATCGT-TTCGACACTAAGT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCGTATTCGACACTAAGT
* * * *
10263 GTGCATTTCATGGAATTCATCATATGTGGATGAATAATCGTTTC
66 GTGCATTTCACGGAATTCATCATAGGTGGATGAATAACCATTTC
*
10307 GGCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCAT-TTCGACACTAAGT
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCGTATTCGACACTAAGT
*
10371 GTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCATTTC
66 GTGCATTTCACGGAATTCATCATAGGTGGATGAATAACCATTTC
* *
10415 GGCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCGTACAT-G-CACTATG
1 GGCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCGTA-TTCGACACTAAG
* * * *
10478 TGGGCAAATCCACGGAATTCATCAT-GAGTTGATGAATAACC
65 TGTGC-ATTTCACGGAATTCATCATAG-GTGGATGAATAACC
10519 GTACATGCAC
Statistics
Matches: 193, Mismatches: 15, Indels: 7
0.90 0.07 0.03
Matches are distributed among these distances:
108 162 0.84
109 30 0.16
110 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.30
Consensus pattern (109 bp):
GGCACTAAGTGTGCATTTCACGGAATTCATCCTAGGTGGATGAATAACCGTATTCGACACTAAGT
GTGCATTTCACGGAATTCATCATAGGTGGATGAATAACCATTTC
Found at i:10517 original size:55 final size:55
Alignment explanation
Indices: 10433--10802 Score: 401
Period size: 55 Copynumber: 6.8 Consensus size: 55
10423 GTGTGCATTT
* * * * *
10433 CACGGAATTCATCCT-AGGTGGATGAATAACCGTACATGCACTATGTGGGCAAATC
1 CACGGAATTCATCATGA-GTTGATGAATAACCGTACAGGCACTATGTGTGCAAACC
* * *
10488 CACGGAATTCATCATGAGTTGATGAATAACCGTACATGCACTATGTGTACAAATC
1 CACGGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAACC
* * ** * * * *
10543 CATGAAATTCATCATGAGTTGATGAATAACCGTACAAACATTTTGTATGCAAATC
1 CACGGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAACC
* * * * * *
10598 CACGAAATTCATCATGAGTTGATGAATACCCGTATAGGCACGATGTATG-TAACC
1 CACGGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAACC
* * * *
10652 CACAGAATTCATCATGAGTTAATGAAT-ACACGTACAAGCACGATGTGTGC-AACC
1 CACGGAATTCATCATGAGTTGATGAATAAC-CGTACAGGCACTATGTGTGCAAACC
* * *
10706 CACGAAATTCATCATGAGTTGATGAATACCCGTACAGGCACGATGTGTGC-AACC
1 CACGGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAACC
*
10760 CACGGAATTCATCATGAGTTGATGAACT-ACCGTATAGGCACTA
1 CACGGAATTCATCATGAGTTGATGAA-TAACCGTACAGGCACTA
10803 CATGTGCATC
Statistics
Matches: 272, Mismatches: 38, Indels: 11
0.85 0.12 0.03
Matches are distributed among these distances:
53 1 0.00
54 131 0.48
55 139 0.51
56 1 0.00
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (55 bp):
CACGGAATTCATCATGAGTTGATGAATAACCGTACAGGCACTATGTGTGCAAACC
Found at i:10738 original size:108 final size:109
Alignment explanation
Indices: 10453--10802 Score: 429
Period size: 108 Copynumber: 3.2 Consensus size: 109
10443 ATCCTAGGTG
* * * *
10453 GATGAATAACCGTACATGCACTATGTGGGCAAATCCACGGAATTCATCATGAGTTGATGAATAAC
1 GATGAATAACCGTACAAGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATACC
* * * * *
10518 CGTACATGCACTATGTGTACAAATCCA-TGAAATTCATCATGAGTT
66 CGTACAGGCACGATGTGT-GAAACCCACAG-AATTCATCATGAGTT
* * * *
10563 GATGAATAACCGTACAAACATTTTGTATGCAAATCCACGAAATTCATCATGAGTTGATGAATACC
1 GATGAATAACCGTACAAGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATACC
* * *
10628 CGTATAGGCACGATGTATGTAACCCACAGAATTCATCATGAGTT
66 CGTACAGGCACGATGTGTGAAACCCACAGAATTCATCATGAGTT
* * *
10672 AATGAAT-ACACGTACAAGCACGATGTGTGC-AACCCACGAAATTCATCATGAGTTGATGAATAC
1 GATGAATAAC-CGTACAAGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATAC
* *
10735 CCGTACAGGCACGATGTGTGCAACCCACGGAATTCATCATGAGTT
65 CCGTACAGGCACGATGTGTGAAACCCACAGAATTCATCATGAGTT
* *
10780 GATGAACT-ACCGTATAGGCACTA
1 GATGAA-TAACCGTACAAGCACTA
10803 CATGTGCATC
Statistics
Matches: 206, Mismatches: 31, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
108 90 0.44
109 44 0.21
110 72 0.35
ACGTcount: A:0.35, C:0.21, G:0.19, T:0.25
Consensus pattern (109 bp):
GATGAATAACCGTACAAGCACTATGTGTGCAAATCCACGAAATTCATCATGAGTTGATGAATACC
CGTACAGGCACGATGTGTGAAACCCACAGAATTCATCATGAGTT
Found at i:10810 original size:54 final size:53
Alignment explanation
Indices: 10453--10800 Score: 374
Period size: 54 Copynumber: 6.4 Consensus size: 53
10443 ATCCTAGGTG
* * * * *
10453 GATGAATAACCGTACATGCACTATGTGGGCAAATCCACGGAATTCATCATGAGTT
1 GATGAAT-ACCGTACAGGCACGATGTGTGC-AACCCACGAAATTCATCATGAGTT
* * * * *
10508 GATGAATAACCGTACATGCACTATGTGTACAAATCCATGAAATTCATCATGAGTT
1 GATGAAT-ACCGTACAGGCACGATGTGTGC-AACCCACGAAATTCATCATGAGTT
** *** * *
10563 GATGAATAACCGTACAAACATTTTGTATGCAAATCCACGAAATTCATCATGAGTT
1 GATGAAT-ACCGTACAGGCACGATGTGTGC-AACCCACGAAATTCATCATGAGTT
* * *
10618 GATGAATACCCGTATAGGCACGATGTATGTAACCCAC-AGAATTCATCATGAGTT
1 GATGAATA-CCGTACAGGCACGATGTGTGCAACCCACGA-AATTCATCATGAGTT
* *
10672 AATGAATACACGTACAAGCACGATGTGTGCAACCCACGAAATTCATCATGAGTT
1 GATGAATAC-CGTACAGGCACGATGTGTGCAACCCACGAAATTCATCATGAGTT
*
10726 GATGAATACCCGTACAGGCACGATGTGTGCAACCCACGGAATTCATCATGAGTT
1 GATGAATA-CCGTACAGGCACGATGTGTGCAACCCACGAAATTCATCATGAGTT
*
10780 GATGAACTACCGTATAGGCAC
1 GATGAA-TACCGTACAGGCAC
10801 TACATGTGCA
Statistics
Matches: 259, Mismatches: 28, Indels: 13
0.86 0.09 0.04
Matches are distributed among these distances:
53 2 0.01
54 133 0.51
55 124 0.48
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (53 bp):
GATGAATACCGTACAGGCACGATGTGTGCAACCCACGAAATTCATCATGAGTT
Found at i:11143 original size:46 final size:45
Alignment explanation
Indices: 11075--11177 Score: 134
Period size: 45 Copynumber: 2.3 Consensus size: 45
11065 AAAATAGGGC
* * *
11075 ATGAAATGTATTATAGCATATAAAAGGGAATGAAATGATGACATAA
1 ATGAAATGTATAATAGCATATAAAA-GGAATAAAAGGATGACATAA
* * *
11121 ATGAAATGTATAATAGCGTATAAAAGGCATAAAAGGATGCCATAA
1 ATGAAATGTATAATAGCATATAAAAGGAATAAAAGGATGACATAA
*
11166 ATAAAATGTATA
1 ATGAAATGTATA
11178 TGGGTGCATT
Statistics
Matches: 50, Mismatches: 7, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
45 27 0.54
46 23 0.46
ACGTcount: A:0.50, C:0.06, G:0.18, T:0.25
Consensus pattern (45 bp):
ATGAAATGTATAATAGCATATAAAAGGAATAAAAGGATGACATAA
Found at i:11280 original size:46 final size:46
Alignment explanation
Indices: 11147--11309 Score: 167
Period size: 45 Copynumber: 3.6 Consensus size: 46
11137 CGTATAAAAG
* *
11147 GCAT-AAAAGGATGCCATAAAT-AAAATGTATATGGGTGCATTATTG
1 GCATGAAAA-GATGCCATAAATGAAAATGCATATGGGTGCATTATTA
* *
11192 GCATGAAAGGATGCCATAAGTG-AAATGCATATGGGTGCATTATTA
1 GCATGAAAAGATGCCATAAATGAAAATGCATATGGGTGCATTATTA
* *
11237 GCATGAAATAG-TGTCATAAATGAAAATGCATAAT-GGTGCATTATAA
1 GCATGAAA-AGATGCCATAAATGAAAATGCAT-ATGGGTGCATTATTA
* * *
11283 GTATGAATAGATGCTC-TCAATGAAAAT
1 GCATGAAAAGATGC-CATAAATGAAAAT
11310 AAAGAATAAT
Statistics
Matches: 99, Mismatches: 12, Indels: 13
0.80 0.10 0.10
Matches are distributed among these distances:
45 55 0.56
46 41 0.41
47 3 0.03
ACGTcount: A:0.40, C:0.10, G:0.22, T:0.28
Consensus pattern (46 bp):
GCATGAAAAGATGCCATAAATGAAAATGCATATGGGTGCATTATTA
Found at i:13315 original size:59 final size:59
Alignment explanation
Indices: 13221--13344 Score: 160
Period size: 59 Copynumber: 2.1 Consensus size: 59
13211 CACCAGGCTG
* * * * *
13221 CATATTCGGGTTAGTACTAAAGGATACCTAATGCAGATAGTGGGCACGACCTTCTGTTT
1 CATATTCGGGTTAGCACTAAAGGATACCTAATGCAGATAGTGGGCACAACATTATGTGT
* * *
13280 CATATTCGGGTTAGCACTAAATGATA-CTGAGTGCAGATGGTGGGCACAACATTATGTGT
1 CATATTCGGGTTAGCACTAAAGGATACCT-AATGCAGATAGTGGGCACAACATTATGTGT
13339 CATATT
1 CATATT
13345 GAGTTTAGCA
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
58 2 0.04
59 54 0.96
ACGTcount: A:0.28, C:0.17, G:0.24, T:0.31
Consensus pattern (59 bp):
CATATTCGGGTTAGCACTAAAGGATACCTAATGCAGATAGTGGGCACAACATTATGTGT
Found at i:13722 original size:32 final size:32
Alignment explanation
Indices: 13642--13726 Score: 125
Period size: 32 Copynumber: 2.7 Consensus size: 32
13632 ATTTGTAGTC
* * *
13642 AATAAAGTTTCCAGGTATCTTTACCCAAAGTA
1 AATAAAGTTTCCAGATTTTTTTACCCAAAGTA
**
13674 AATAAAGTTTCCAGATTTTTTTACCCAGGGTA
1 AATAAAGTTTCCAGATTTTTTTACCCAAAGTA
13706 AATAAAGTTTCCAGATTTTTT
1 AATAAAGTTTCCAGATTTTTT
13727 ATAAAAAATA
Statistics
Matches: 48, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
32 48 1.00
ACGTcount: A:0.34, C:0.15, G:0.13, T:0.38
Consensus pattern (32 bp):
AATAAAGTTTCCAGATTTTTTTACCCAAAGTA
Found at i:13741 original size:33 final size:32
Alignment explanation
Indices: 13668--13748 Score: 83
Period size: 32 Copynumber: 2.5 Consensus size: 32
13658 ATCTTTACCC
**
13668 AAAG-TAAATAAAGTTTCCAGATTTTTTTACC
1 AAAGATAAATAAAGTTTCCAGATTTTTTTAAA
* * *
13699 CAGGGTAAATAAAGTTTCCAGATTTTTTATAAA
1 AAAGATAAATAAAGTTTCCAGATTTTTT-TAAA
* *
13732 AAATATAAATGAAGTTT
1 AAAGATAAATAAAGTTT
13749 TTAAGTTCTA
Statistics
Matches: 39, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
31 2 0.05
32 23 0.59
33 14 0.36
ACGTcount: A:0.42, C:0.09, G:0.12, T:0.37
Consensus pattern (32 bp):
AAAGATAAATAAAGTTTCCAGATTTTTTTAAA
Found at i:19184 original size:18 final size:18
Alignment explanation
Indices: 19161--19206 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
19151 GAAGACACGT
* *
19161 ACTACCACTATCACTACC
1 ACTACCACGATCACGACC
19179 ACTACCACGATCACGACC
1 ACTACCACGATCACGACC
*
19197 ACGACCACGA
1 ACTACCACGA
19207 CCCGACCCGA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.35, C:0.43, G:0.09, T:0.13
Consensus pattern (18 bp):
ACTACCACGATCACGACC
Found at i:19216 original size:5 final size:6
Alignment explanation
Indices: 19176--19213 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
19166 CACTATCACT
* *
19176 ACCACT ACCACG ATCACG ACCACG ACCACG ACC-CG ACC
1 ACCACG ACCACG ACCACG ACCACG ACCACG ACCACG ACC
19214 CGAGACGGGA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.32, C:0.50, G:0.13, T:0.05
Consensus pattern (6 bp):
ACCACG
Found at i:20938 original size:29 final size:28
Alignment explanation
Indices: 20858--20938 Score: 76
Period size: 27 Copynumber: 2.9 Consensus size: 28
20848 ACCCCTAATC
* *
20858 ACTACATAAAATGTACATACGAAT-ACT
1 ACTAAATAAAATGTACATATGAATAACT
* * * *
20885 ATTAAA-AAAATTGTATATGTGAATAATT
1 ACTAAATAAAA-TGTACATATGAATAACT
20913 ACTAAATTAAAATGTACATATGAATA
1 ACTAAA-TAAAATGTACATATGAATA
20939 GTTTATTTAC
Statistics
Matches: 41, Mismatches: 9, Indels: 6
0.73 0.16 0.11
Matches are distributed among these distances:
26 4 0.10
27 14 0.34
28 7 0.17
29 12 0.29
30 4 0.10
ACGTcount: A:0.51, C:0.09, G:0.09, T:0.32
Consensus pattern (28 bp):
ACTAAATAAAATGTACATATGAATAACT
Found at i:21316 original size:19 final size:19
Alignment explanation
Indices: 21274--21317 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
21264 ATTAGTAGAA
*
21274 TAAAAATAAAAATTTAATT
1 TAAAAATAAAAATATAATT
*
21293 AAAAAATAAAAA-ATAATT
1 TAAAAATAAAAATATAATT
*
21311 TTAAAAT
1 TAAAAAT
21318 TTTAGAAAAA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 10 0.48
19 11 0.52
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (19 bp):
TAAAAATAAAAATATAATT
Found at i:21317 original size:18 final size:19
Alignment explanation
Indices: 21275--21310 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
21265 TTAGTAGAAT
*
21275 AAAAATAAAAATTTAATTA
1 AAAAATAAAAATATAATTA
21294 AAAAATAAAAA-ATAATT
1 AAAAATAAAAATATAATT
21311 TTAAAATTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (19 bp):
AAAAATAAAAATATAATTA
Found at i:23197 original size:2 final size:2
Alignment explanation
Indices: 23192--23217 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
23182 TTTTTTTATT
23192 TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA
23218 AGAAAACACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:36983 original size:14 final size:15
Alignment explanation
Indices: 36959--36992 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
36949 CAAAAAAATG
36959 AAACC-TTT-AAACC
1 AAACCGTTTAAAACC
36972 AAACCGTTTAAAACC
1 AAACCGTTTAAAACC
36987 AAACCG
1 AAACCG
36993 AACTGAACCG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.26
14 3 0.16
15 11 0.58
ACGTcount: A:0.47, C:0.29, G:0.06, T:0.18
Consensus pattern (15 bp):
AAACCGTTTAAAACC
Found at i:47698 original size:13 final size:13
Alignment explanation
Indices: 47680--47715 Score: 56
Period size: 12 Copynumber: 2.8 Consensus size: 13
47670 TCAATTATTA
47680 AATTACAAAATTT
1 AATTACAAAATTT
47693 AATTACAAAA-TT
1 AATTACAAAATTT
*
47705 AATTATAAAAT
1 AATTACAAAAT
47716 AAATTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
12 11 0.52
13 10 0.48
ACGTcount: A:0.58, C:0.06, G:0.00, T:0.36
Consensus pattern (13 bp):
AATTACAAAATTT
Found at i:47708 original size:12 final size:12
Alignment explanation
Indices: 47680--47720 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
47670 TCAATTATTA
47680 AATTACAAAATTT
1 AATTACAAAA-TT
47693 AATTACAAAATT
1 AATTACAAAATT
* *
47705 AATTATAAAATA
1 AATTACAAAATT
47717 AATT
1 AATT
47721 TAAAATATTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 16 0.62
13 10 0.38
ACGTcount: A:0.59, C:0.05, G:0.00, T:0.37
Consensus pattern (12 bp):
AATTACAAAATT
Found at i:48865 original size:30 final size:30
Alignment explanation
Indices: 48829--48885 Score: 105
Period size: 30 Copynumber: 1.9 Consensus size: 30
48819 AATTTTAAAA
*
48829 GTAACAAATTGATCACTAATGTTATCGCTT
1 GTAACAAATTAATCACTAATGTTATCGCTT
48859 GTAACAAATTAATCACTAATGTTATCG
1 GTAACAAATTAATCACTAATGTTATCG
48886 ATTTATAACA
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
30 26 1.00
ACGTcount: A:0.37, C:0.16, G:0.12, T:0.35
Consensus pattern (30 bp):
GTAACAAATTAATCACTAATGTTATCGCTT
Found at i:48906 original size:31 final size:30
Alignment explanation
Indices: 48830--48898 Score: 102
Period size: 30 Copynumber: 2.3 Consensus size: 30
48820 ATTTTAAAAG
*
48830 TAACAAATTGATCACTAATGTTATCGCTTG
1 TAACAAATTGATCACTAATGTTATCGCTTA
* *
48860 TAACAAATTAATCACTAATGTTATCGATTTA
1 TAACAAATTGATCACTAATGTTATCG-CTTA
48891 TAACAAAT
1 TAACAAAT
48899 CGGTCACTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
30 25 0.71
31 10 0.29
ACGTcount: A:0.41, C:0.14, G:0.09, T:0.36
Consensus pattern (30 bp):
TAACAAATTGATCACTAATGTTATCGCTTA
Found at i:51363 original size:27 final size:30
Alignment explanation
Indices: 51333--51410 Score: 90
Period size: 32 Copynumber: 2.6 Consensus size: 30
51323 AAATAATTTA
51333 TTTATTAAT-AAATATT-ATTTTTATA-AT
1 TTTATTAATAAAATATTAATTTTTATATAT
*
51360 TTTATTAATAAAAATATTAATTTTTGTATAT
1 TTTATTAAT-AAAATATTAATTTTTATATAT
*
51391 TTTAGTGAAATAAAATATTA
1 TTTA-T-TAATAAAATATTA
51411 TAAATTATAT
Statistics
Matches: 43, Mismatches: 2, Indels: 7
0.83 0.04 0.13
Matches are distributed among these distances:
27 9 0.21
29 7 0.16
30 8 0.19
31 6 0.14
32 10 0.23
33 3 0.07
ACGTcount: A:0.44, C:0.00, G:0.04, T:0.53
Consensus pattern (30 bp):
TTTATTAATAAAATATTAATTTTTATATAT
Found at i:51364 original size:31 final size:30
Alignment explanation
Indices: 51333--51394 Score: 85
Period size: 27 Copynumber: 2.1 Consensus size: 30
51323 AAATAATTTA
51333 TTTATTAAT--AAATATT-ATTTTTATAAT
1 TTTATTAATAAAAATATTAATTTTTATAAT
*
51360 TTTATTAATAAAAATATTAATTTTTGTATAT
1 TTTATTAATAAAAATATTAATTTTTATA-AT
51391 TTTA
1 TTTA
51395 GTGAAATAAA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
27 9 0.30
29 7 0.23
30 8 0.27
31 6 0.20
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (30 bp):
TTTATTAATAAAAATATTAATTTTTATAAT
Found at i:51501 original size:23 final size:23
Alignment explanation
Indices: 51452--51502 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
51442 GTGTTATATT
**
51452 ATATTTTAAAAATATTAATTAGT
1 ATATTTTAAAAATATTAATTAAA
* * *
51475 ATATTTTAAATATCTTTATTAAA
1 ATATTTTAAAAATATTAATTAAA
51498 ATATT
1 ATATT
51503 ATTTAAACAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (23 bp):
ATATTTTAAAAATATTAATTAAA
Found at i:51542 original size:28 final size:26
Alignment explanation
Indices: 51499--51653 Score: 79
Period size: 28 Copynumber: 5.8 Consensus size: 26
51489 TTTATTAAAA
*
51499 TATTATTTAAACATATAAATAATATTAT
1 TATTA-TTAAAAATATAAATAAT-TTAT
*
51527 TCATTATTAAAAATATAAAAAATTTAT
1 T-ATTATTAAAAATATAAATAATTTAT
* **
51554 TATATATTATTAAAATAAAAATAAACATAT
1 TAT-TATTA--AAAATATAAAT-AATTTAT
* * *
51584 TATTA-TAATATAAT-TGATTATTTTAT
1 TATTATTAA-A-AATATAAATAATTTAT
*
51610 ATAATATTAAAAATAT-AAT-A-TTA-
1 -TATTATTAAAAATATAAATAATTTAT
* *
51633 TATTATTATAAATATTAATAA
1 TATTATTAAAAATATAAATAA
51654 ATAAATAAAT
Statistics
Matches: 98, Mismatches: 17, Indels: 28
0.69 0.12 0.20
Matches are distributed among these distances:
22 13 0.13
23 3 0.03
24 4 0.04
26 12 0.12
27 19 0.19
28 24 0.24
29 15 0.15
30 8 0.08
ACGTcount: A:0.53, C:0.02, G:0.01, T:0.45
Consensus pattern (26 bp):
TATTATTAAAAATATAAATAATTTAT
Found at i:51563 original size:30 final size:30
Alignment explanation
Indices: 51489--51568 Score: 85
Period size: 30 Copynumber: 2.7 Consensus size: 30
51479 TTTAAATATC
* * *
51489 TTTATTAAAATATTATTTAAACATATAAATAA
1 TTTATT-ATATATTA-TTAAAAATATAAAAAA
51521 --TATTAT-TCATTATTAAAAATATAAAAAA
1 TTTATTATAT-ATTATTAAAAATATAAAAAA
51549 TTTATTATATATTATTAAAA
1 TTTATTATATATTATTAAAA
51569 TAAAAATAAA
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
28 15 0.37
29 5 0.12
30 20 0.49
31 1 0.02
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (30 bp):
TTTATTATATATTATTAAAAATATAAAAAA
Found at i:51585 original size:30 final size:30
Alignment explanation
Indices: 51520--51587 Score: 77
Period size: 30 Copynumber: 2.3 Consensus size: 30
51510 CATATAAATA
* *
51520 ATATTATTCATTATTAAAAATATAAAAAAT
1 ATATTATTCATTATTAAAAATAAAAAAAAC
*
51550 TTATTATAT-ATTATT-AAAATAAAAATAAAC
1 ATATTAT-TCATTATTAAAAATAAAAA-AAAC
51580 ATATTATT
1 ATATTATT
51588 ATAATATAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
29 10 0.31
30 21 0.66
31 1 0.03
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (30 bp):
ATATTATTCATTATTAAAAATAAAAAAAAC
Found at i:51634 original size:22 final size:23
Alignment explanation
Indices: 51609--51652 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 23
51599 GATTATTTTA
51609 TATAATATTAAAAATA-TAATAT
1 TATAATATTAAAAATATTAATAT
* *
51631 TATATTATTATAAATATTAATA
1 TATAATATTAAAAATATTAATA
51653 AATAAATAAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 14 0.74
23 5 0.26
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (23 bp):
TATAATATTAAAAATATTAATAT
Found at i:52153 original size:30 final size:31
Alignment explanation
Indices: 52119--52185 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
52109 TTTCTAGTCA
* *
52119 TTTTTAACGTCTAATAATGTTTTCGGTC-TT
1 TTTTTAACGCCTAATAATGTTTCCGGTCATT
**
52149 TTTTTAGTGCCTAATAATGTTTCCGGTCATT
1 TTTTTAACGCCTAATAATGTTTCCGGTCATT
52180 TTTTTA
1 TTTTTA
52186 CCGGTTTTAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 24 0.75
31 8 0.25
ACGTcount: A:0.19, C:0.13, G:0.13, T:0.54
Consensus pattern (31 bp):
TTTTTAACGCCTAATAATGTTTCCGGTCATT
Found at i:52841 original size:30 final size:28
Alignment explanation
Indices: 52799--52904 Score: 99
Period size: 28 Copynumber: 3.6 Consensus size: 28
52789 CTTTTACATT
52799 TAAGTACTTAAAGTATTTTTTTAGT-AGAAA
1 TAAGTAC-TAAAGTATTTTTTT-GTCA-AAA
*
52829 TAAGTATCTAAAGTTACGTTTTTTGTCAAAA
1 TAAGTA-CTAAAG-TA-TTTTTTTGTCAAAA
* *
52860 TAGGTACCTAAAGTA-TTTTTGGTCAAAA
1 TAAGTA-CTAAAGTATTTTTTTGTCAAAA
52888 TAAGTACTTAAAGTATT
1 TAAGTAC-TAAAGTATT
52905 CAATTTTTTT
Statistics
Matches: 65, Mismatches: 5, Indels: 13
0.78 0.06 0.16
Matches are distributed among these distances:
27 1 0.02
28 24 0.37
29 1 0.02
30 13 0.20
31 19 0.29
32 7 0.11
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.41
Consensus pattern (28 bp):
TAAGTACTAAAGTATTTTTTTGTCAAAA
Found at i:59821 original size:14 final size:14
Alignment explanation
Indices: 59802--59834 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
59792 ACATTCGTGA
59802 ATGTTCGTTCATTT
1 ATGTTCGTTCATTT
*
59816 ATGTTCGTTCGTTT
1 ATGTTCGTTCATTT
59830 ATGTT
1 ATGTT
59835 AATTTATGTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.12, C:0.12, G:0.18, T:0.58
Consensus pattern (14 bp):
ATGTTCGTTCATTT
Found at i:59839 original size:24 final size:25
Alignment explanation
Indices: 59812--59867 Score: 80
Period size: 24 Copynumber: 2.3 Consensus size: 25
59802 ATGTTCGTTC
59812 ATTTATGTTC-GTTCGTTTATGTTA
1 ATTTATGTTCTGTTCGTTTATGTTA
* *
59836 ATTTATG-TCTTTTCGTTTATGTTC
1 ATTTATGTTCTGTTCGTTTATGTTA
59860 ATTTATGT
1 ATTTATGT
59868 GTACTCATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 2 0.07
24 26 0.93
ACGTcount: A:0.16, C:0.09, G:0.14, T:0.61
Consensus pattern (25 bp):
ATTTATGTTCTGTTCGTTTATGTTA
Found at i:59878 original size:24 final size:24
Alignment explanation
Indices: 59827--59882 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
59817 TGTTCGTTCG
** *
59827 TTTATGTTAATTTATGTCTTTTCG
1 TTTATGTTAATTTATGTCTACTCA
* *
59851 TTTATGTTCATTTATGTGTACTCA
1 TTTATGTTAATTTATGTCTACTCA
59875 TTTATGTT
1 TTTATGTT
59883 TATCCCAATC
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 27 1.00
ACGTcount: A:0.18, C:0.09, G:0.12, T:0.61
Consensus pattern (24 bp):
TTTATGTTAATTTATGTCTACTCA
Found at i:60145 original size:37 final size:33
Alignment explanation
Indices: 60093--60194 Score: 98
Period size: 37 Copynumber: 3.0 Consensus size: 33
60083 CATTTATTGT
*
60093 GTTCGTTTACGTTCGTTCATTTGTGTTCATTTAC
1 GTTCGTTTATGTTCGTTCATTT-TGTTCATTTAC
* * ** *
60127 GTTCGTTTATTGTTTTCGTTTATGTTTGTTTACATCC
1 GTTCGTTTA-TG--TTCGTTCAT-TTTGTTCATTTAC
60164 GTTCGTTTATGTTCG-TCATTTTGTTCATTTA
1 GTTCGTTTATGTTCGTTCATTTTGTTCATTTA
60195 TCATTTAAAT
Statistics
Matches: 53, Mismatches: 11, Indels: 10
0.72 0.15 0.14
Matches are distributed among these distances:
32 8 0.15
33 3 0.06
34 13 0.25
35 1 0.02
36 2 0.04
37 24 0.45
38 2 0.04
ACGTcount: A:0.12, C:0.15, G:0.17, T:0.57
Consensus pattern (33 bp):
GTTCGTTTATGTTCGTTCATTTTGTTCATTTAC
Found at i:60157 original size:23 final size:23
Alignment explanation
Indices: 60070--60158 Score: 97
Period size: 23 Copynumber: 3.8 Consensus size: 23
60060 GTTCGTTTAC
** *
60070 GTTCGTTTATATTCATTTATTGT
1 GTTCGTTTACGTTCGTTTATTGT
*
60093 GTTCGTTTACGTTCGTTCATTTGT
1 GTTCGTTTACGTTCGTTTA-TTGT
*
60117 GTTCATTTACGTTCGTTTATTGT
1 GTTCGTTTACGTTCGTTTATTGT
* * *
60140 TTTCGTTTATGTTTGTTTA
1 GTTCGTTTACGTTCGTTTA
60159 CATCCGTTCG
Statistics
Matches: 55, Mismatches: 10, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
23 34 0.62
24 21 0.38
ACGTcount: A:0.12, C:0.11, G:0.17, T:0.60
Consensus pattern (23 bp):
GTTCGTTTACGTTCGTTTATTGT
Found at i:60177 original size:10 final size:10
Alignment explanation
Indices: 60056--60179 Score: 50
Period size: 10 Copynumber: 11.0 Consensus size: 10
60046 CTATTTTCAG
60056 TTATGTTCGT
1 TTATGTTCGT
*
60066 TTACGTTCGT
1 TTATGTTCGT
* *
60076 TTATATTCAT
1 TTATGTTCGT
60086 TTATTGTGTTCGT
1 TTA---TGTTCGT
*
60099 TTACGTTCGTTCAT
1 TTA---T-GTTCGT
* *
60113 TTGTGTTCAT
1 TTATGTTCGT
*
60123 TTACGTTCGT
1 TTATGTTCGT
60133 TTATTGTTTTCGT
1 TTA-TG--TTCGT
*
60146 TTATGTTTGT
1 TTATGTTCGT
60156 TTACATCCGTTCGT
1 TT--AT--GTTCGT
60170 TTATGTTCGT
1 TTATGTTCGT
60180 CATTTTGTTC
Statistics
Matches: 86, Mismatches: 17, Indels: 22
0.69 0.14 0.18
Matches are distributed among these distances:
10 47 0.55
11 2 0.02
12 6 0.07
13 17 0.20
14 14 0.16
ACGTcount: A:0.12, C:0.14, G:0.17, T:0.57
Consensus pattern (10 bp):
TTATGTTCGT
Found at i:60178 original size:47 final size:47
Alignment explanation
Indices: 60069--60179 Score: 114
Period size: 47 Copynumber: 2.4 Consensus size: 47
60059 TGTTCGTTTA
* * ** *
60069 CGTTCGTTTATATTCATTTATTGTGTTCGTTTACGTTCGTTCATTTG
1 CGTTCGTTTATGTTCGTTTATTGTGTTCGTTTACGTTCGTTCACATC
* * * * * * *
60116 TGTTCATTTACGTTCGTTTATTGTTTTCGTTTATGTTTGTTTACATC
1 CGTTCGTTTATGTTCGTTTATTGTGTTCGTTTACGTTCGTTCACATC
60163 CGTTCGTTTATGTTCGT
1 CGTTCGTTTATGTTCGT
60180 CATTTTGTTC
Statistics
Matches: 49, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
47 49 1.00
ACGTcount: A:0.12, C:0.14, G:0.17, T:0.57
Consensus pattern (47 bp):
CGTTCGTTTATGTTCGTTTATTGTGTTCGTTTACGTTCGTTCACATC
Done.