Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003997.1 Hibiscus syriacus cultivar Beakdansim tig00008711_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: 64253
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:7761 original size:23 final size:23
Alignment explanation
Indices: 7735--7778 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
7725 CATTCACAAT
*
7735 AGATATTGGATCTGATTATATTC
1 AGATATTGAATCTGATTATATTC
7758 AGATATTGAATCTGATTATAT
1 AGATATTGAATCTGATTATAT
7779 CTTTATAATG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.34, C:0.07, G:0.16, T:0.43
Consensus pattern (23 bp):
AGATATTGAATCTGATTATATTC
Found at i:8769 original size:32 final size:32
Alignment explanation
Indices: 8733--8831 Score: 135
Period size: 32 Copynumber: 3.1 Consensus size: 32
8723 TGCCAACCTT
* * *
8733 AGGGAATATCTTGGGGCATGAGAGCCTACCCA
1 AGGGAATACCTTGGGGCCTCAGAGCCTACCCA
* *
8765 AGGGAGTACCTTGGGGCCTTAGAGCCTACCCA
1 AGGGAATACCTTGGGGCCTCAGAGCCTACCCA
* *
8797 AGGAAATGCCTTGGGGCCTCAGAGCCTACCCA
1 AGGGAATACCTTGGGGCCTCAGAGCCTACCCA
8829 AGG
1 AGG
8832 TAACCTTAGG
Statistics
Matches: 59, Mismatches: 8, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 59 1.00
ACGTcount: A:0.25, C:0.26, G:0.31, T:0.17
Consensus pattern (32 bp):
AGGGAATACCTTGGGGCCTCAGAGCCTACCCA
Found at i:9589 original size:21 final size:24
Alignment explanation
Indices: 9514--9599 Score: 85
Period size: 24 Copynumber: 3.8 Consensus size: 24
9504 CTGCTAACAT
9514 AATTTG-CACCGAAGTG-CCACATAG
1 AATTTGTC-CCGAAG-GACCACATAG
* * *
9538 AATTTCTCCCGAAGGACCGCGTAG
1 AATTTGTCCCGAAGGACCACATAG
9562 AATTTGTCCCG-A-GACCACATAG
1 AATTTGTCCCGAAGGACCACATAG
9584 -ATTTGTCCC-AAGGACC
1 AATTTGTCCCGAAGGACC
9600 GCGTAAAACC
Statistics
Matches: 52, Mismatches: 6, Indels: 10
0.76 0.09 0.15
Matches are distributed among these distances:
21 10 0.19
22 12 0.23
23 2 0.04
24 27 0.52
25 1 0.02
ACGTcount: A:0.29, C:0.28, G:0.21, T:0.22
Consensus pattern (24 bp):
AATTTGTCCCGAAGGACCACATAG
Found at i:12171 original size:18 final size:19
Alignment explanation
Indices: 12148--12194 Score: 71
Period size: 19 Copynumber: 2.5 Consensus size: 19
12138 AATAATTGAA
12148 CATCGAATGCA-ATT-AGTG
1 CATCG-ATGCATATTGAGTG
12166 CATCGATGCATATTGAGTG
1 CATCGATGCATATTGAGTG
12185 CATCGATGCA
1 CATCGATGCA
12195 CCCCCTTAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
17 5 0.19
18 8 0.30
19 14 0.52
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (19 bp):
CATCGATGCATATTGAGTG
Found at i:13063 original size:18 final size:18
Alignment explanation
Indices: 13042--13082 Score: 73
Period size: 18 Copynumber: 2.3 Consensus size: 18
13032 TGGACCTTCA
13042 GGACATAGTGGTCATTCG
1 GGACATAGTGGTCATTCG
*
13060 GGACATAGTGGTCCTTCG
1 GGACATAGTGGTCATTCG
13078 GGACA
1 GGACA
13083 AATATACAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.22, C:0.20, G:0.34, T:0.24
Consensus pattern (18 bp):
GGACATAGTGGTCATTCG
Found at i:13501 original size:21 final size:21
Alignment explanation
Indices: 13475--13514 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
13465 TTAATTATGG
13475 AAAAGG-TATATAAACAAGTAT
1 AAAAGGATAT-TAAACAAGTAT
*
13496 AAAAGGATATTAAATAAGT
1 AAAAGGATATTAAACAAGT
13515 TGTGTAGGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 14 0.82
22 3 0.18
ACGTcount: A:0.57, C:0.03, G:0.15, T:0.25
Consensus pattern (21 bp):
AAAAGGATATTAAACAAGTAT
Found at i:13948 original size:4 final size:4
Alignment explanation
Indices: 13939--13963 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
13929 AAAAGGTTTG
13939 TGTA TGTA TGTA TGTA TGTA TGTA T
1 TGTA TGTA TGTA TGTA TGTA TGTA T
13964 TCATTTGATG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.52
Consensus pattern (4 bp):
TGTA
Found at i:15211 original size:27 final size:28
Alignment explanation
Indices: 15153--15215 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 28
15143 CATGACTTTG
*
15153 GGGTATTTTAGGTCATTTCTCACTTCAG
1 GGGTATTTTAGGTCATTTCTCACTTCAA
* *
15181 GGGTATTTT-GGTCATTT-TATAGTTCAA
1 GGGTATTTTAGGTCATTTCT-CACTTCAA
15208 GGGTATTT
1 GGGTATTT
15216 CAGTATTTTC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
26 1 0.03
27 21 0.68
28 9 0.29
ACGTcount: A:0.19, C:0.11, G:0.24, T:0.46
Consensus pattern (28 bp):
GGGTATTTTAGGTCATTTCTCACTTCAA
Found at i:24301 original size:15 final size:17
Alignment explanation
Indices: 24267--24299 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
24257 CGATTATATT
*
24267 ATATTATTCAATTAAAA
1 ATATTATTCAAGTAAAA
24284 ATATTA-TCAAGTAAAA
1 ATATTATTCAAGTAAAA
24300 TAACAAATTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.55, C:0.06, G:0.03, T:0.36
Consensus pattern (17 bp):
ATATTATTCAAGTAAAA
Found at i:24432 original size:87 final size:87
Alignment explanation
Indices: 24286--24506 Score: 298
Period size: 87 Copynumber: 2.5 Consensus size: 87
24276 AATTAAAAAT
* * * * * * *
24286 ATTATCAAGTAAAATAACAAATTAGATAACGTTTATATAATTTAATAGGTAGCATTTATATAATA
1 ATTATCAAGCACAACAACATATTAGGTAACGTTTATATAATGTAATAGGTAGCACTTATATAATA
*
24351 AAATAGATTAATTACTAGAAAC
66 AAATAGATTAATTACAAGAAAC
* ** *
24373 ATTATCAAGCACAATAGTATATTAGGTAACGTTTATATAATGTAATAGGTAGCCCTTATATAATA
1 ATTATCAAGCACAACAACATATTAGGTAACGTTTATATAATGTAATAGGTAGCACTTATATAATA
*
24438 AAATAGGTTAATTACAAGAAAC
66 AAATAGATTAATTACAAGAAAC
** *
24460 ATTATCAAGCACAACAACATATTAGGTAGTGCTTATATAATGTAATA
1 ATTATCAAGCACAACAACATATTAGGTAACGTTTATATAATGTAATA
24507 TGTAACGTTT
Statistics
Matches: 117, Mismatches: 17, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
87 117 1.00
ACGTcount: A:0.46, C:0.10, G:0.12, T:0.33
Consensus pattern (87 bp):
ATTATCAAGCACAACAACATATTAGGTAACGTTTATATAATGTAATAGGTAGCACTTATATAATA
AAATAGATTAATTACAAGAAAC
Found at i:24728 original size:24 final size:25
Alignment explanation
Indices: 24660--24728 Score: 76
Period size: 24 Copynumber: 2.9 Consensus size: 25
24650 TAGATAATAT
*
24660 TAAATAA-ATTATTCTAATATT-TTAA
1 TAAATAATATTA-T-TATTATTGTTAA
24685 -AAATAATATTATTATT-TTGTTAA
1 TAAATAATATTATTATTATTGTTAA
24708 TAAATAATATTATT-TTATTGT
1 TAAATAATATTATTATTATTGT
24729 ATTTGATGTT
Statistics
Matches: 39, Mismatches: 1, Indels: 9
0.80 0.02 0.18
Matches are distributed among these distances:
22 2 0.05
23 9 0.23
24 24 0.62
25 4 0.10
ACGTcount: A:0.43, C:0.01, G:0.03, T:0.52
Consensus pattern (25 bp):
TAAATAATATTATTATTATTGTTAA
Found at i:25008 original size:11 final size:12
Alignment explanation
Indices: 24992--25024 Score: 52
Period size: 11 Copynumber: 2.9 Consensus size: 12
24982 TATTGTTGGG
24992 CATAAAAAAT-C
1 CATAAAAAATAC
25003 CATAAAAAATAC
1 CATAAAAAATAC
25015 C-TAAAAAATA
1 CATAAAAAATA
25025 TTATTTCTAC
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
11 19 0.90
12 2 0.10
ACGTcount: A:0.67, C:0.15, G:0.00, T:0.18
Consensus pattern (12 bp):
CATAAAAAATAC
Found at i:25102 original size:21 final size:21
Alignment explanation
Indices: 25067--25117 Score: 77
Period size: 21 Copynumber: 2.5 Consensus size: 21
25057 CATTTTCGGT
*
25067 AAAACCAGT-AAAAAAATAAC
1 AAAACCGGTAAAAAAAATAAC
*
25087 AAAATCGGTAAAAAAAATAAC
1 AAAACCGGTAAAAAAAATAAC
25108 AAAACCGGTA
1 AAAACCGGTA
25118 GCGCTTTACC
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 7 0.26
21 20 0.74
ACGTcount: A:0.65, C:0.14, G:0.10, T:0.12
Consensus pattern (21 bp):
AAAACCGGTAAAAAAAATAAC
Found at i:25192 original size:86 final size:86
Alignment explanation
Indices: 25092--25256 Score: 303
Period size: 86 Copynumber: 1.9 Consensus size: 86
25082 ATAACAAAAT
*
25092 CGGTAAAAAAAATAACAAAACCGGTAGCGCTTTACCTAATATATTGAAAGTATCGATCTTTTTAT
1 CGGTAAAAAAAATAACAAAACCGGTAGCGCTTTACCTAATATATTGAAAGTATCGATCCTTTTAT
*
25157 AAAAATGATCGATAATATAAC
66 AAAAAGGATCGATAATATAAC
*
25178 CGGTAAAAAAAATAACAAAACCGGTAGCGCTTTACCTGATATATTGAAAGTATCGATCCTTTTAT
1 CGGTAAAAAAAATAACAAAACCGGTAGCGCTTTACCTAATATATTGAAAGTATCGATCCTTTTAT
25243 AAAAAGGATCGATA
66 AAAAAGGATCGATA
25257 CTTTACAATA
Statistics
Matches: 76, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
86 76 1.00
ACGTcount: A:0.43, C:0.15, G:0.15, T:0.28
Consensus pattern (86 bp):
CGGTAAAAAAAATAACAAAACCGGTAGCGCTTTACCTAATATATTGAAAGTATCGATCCTTTTAT
AAAAAGGATCGATAATATAAC
Found at i:25298 original size:20 final size:20
Alignment explanation
Indices: 25273--25315 Score: 77
Period size: 20 Copynumber: 2.1 Consensus size: 20
25263 AATATAACAT
*
25273 GTAAAAAAATAACAAAATCG
1 GTAAAAAAATAACAAAACCG
25293 GTAAAAAAATAACAAAACCG
1 GTAAAAAAATAACAAAACCG
25313 GTA
1 GTA
25316 GCGCTTTACC
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.63, C:0.12, G:0.12, T:0.14
Consensus pattern (20 bp):
GTAAAAAAATAACAAAACCG
Found at i:25305 original size:112 final size:113
Alignment explanation
Indices: 25178--25595 Score: 576
Period size: 112 Copynumber: 3.7 Consensus size: 113
25168 ATAATATAAC
*
25178 CGGTAAAAAAAATAACAAAACCGGTAGCGCTTTACCTGATATATTGAAAGTATCGATCCTTTTAT
1 CGGTAAAAAAAATAACAAAACCGATAGCGCTTTACCTGATATATTGAAAGTATCGATCCTTTTAT
*
25243 AAAAAGGATCGATACTTTACAATATAACATGTAAAAAAATAACAAAAT
66 AAAAAGGATCGATACTTTACAATATAACAGGTAAAAAAATAACAAAAT
* *
25291 CGGT-AAAAAAATAACAAAACCGGTAGCGCTTTACCTGATATATTAAAAGTATCGATCCTTTTAT
1 CGGTAAAAAAAATAACAAAACCGATAGCGCTTTACCTGATATATTGAAAGTATCGATCCTTTTAT
* *
25355 AAAAAGGATTGATACTTTACAATATAACAGGTAAAAAAATAACAAAAC
66 AAAAAGGATCGATACTTTACAATATAACAGGTAAAAAAATAACAAAAT
25403 CGGTAAAAAAAATAACAAAACCGATAGCGCTTTACCTGATATATT-AAAGTATCGATCCTTTTAT
1 CGGTAAAAAAAATAACAAAACCGATAGCGCTTTACCTGATATATTGAAAGTATCGATCCTTTTAT
* * *
25467 AAAAAGGATAGATACTTTCCAATATAACAGGT-AAAAAATGACAAAAT
66 AAAAAGGATCGATACTTTACAATATAACAGGTAAAAAAATAACAAAAT
* *** ** * *** * * * *
25514 CAGT-TTTATTATGACAAAACCGATA-AAATTTACCTGATATGTTGAAAGTATAGATACTTTTTG
1 CGGTAAAAAAAATAACAAAACCGATAGCGCTTTACCTGATATATTGAAAGTATCGAT-CCTTTTA
*
25577 TAAAAAGAATCGATACTTT
65 TAAAAAGGATCGATACTTT
25596 TTTTAAAGTT
Statistics
Matches: 277, Mismatches: 25, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
109 14 0.05
110 25 0.09
111 38 0.14
112 157 0.57
113 43 0.16
ACGTcount: A:0.45, C:0.14, G:0.13, T:0.28
Consensus pattern (113 bp):
CGGTAAAAAAAATAACAAAACCGATAGCGCTTTACCTGATATATTGAAAGTATCGATCCTTTTAT
AAAAAGGATCGATACTTTACAATATAACAGGTAAAAAAATAACAAAAT
Found at i:25504 original size:113 final size:113
Alignment explanation
Indices: 25175--25512 Score: 583
Period size: 112 Copynumber: 3.0 Consensus size: 113
25165 TCGATAATAT
*
25175 AACCGGTAAAAAAAATAACAAAACCGGTAGCGCTTTACCTGATATATTGAAAGTATCGATCCTTT
1 AACCGGTAAAAAAAATAACAAAACCGGTAGCGCTTTACCTGATATATTAAAAGTATCGATCCTTT
* *
25240 TATAAAAAGGATCGATACTTTACAATATAACATGTAAAAAAATAACAA
66 TATAAAAAGGATAGATACTTTACAATATAACAGGTAAAAAAATAACAA
*
25288 AATCGGT-AAAAAAATAACAAAACCGGTAGCGCTTTACCTGATATATTAAAAGTATCGATCCTTT
1 AACCGGTAAAAAAAATAACAAAACCGGTAGCGCTTTACCTGATATATTAAAAGTATCGATCCTTT
*
25352 TATAAAAAGGATTGATACTTTACAATATAACAGGTAAAAAAATAACAA
66 TATAAAAAGGATAGATACTTTACAATATAACAGGTAAAAAAATAACAA
*
25400 AACCGGTAAAAAAAATAACAAAACCGATAGCGCTTTACCTGATATATT-AAAGTATCGATCCTTT
1 AACCGGTAAAAAAAATAACAAAACCGGTAGCGCTTTACCTGATATATTAAAAGTATCGATCCTTT
* *
25464 TATAAAAAGGATAGATACTTTCCAATATAACAGGT-AAAAAATGACAA
66 TATAAAAAGGATAGATACTTTACAATATAACAGGTAAAAAAATAACAA
25511 AA
1 AA
25513 TCAGTTTTAT
Statistics
Matches: 215, Mismatches: 9, Indels: 4
0.94 0.04 0.02
Matches are distributed among these distances:
111 13 0.06
112 157 0.73
113 45 0.21
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.26
Consensus pattern (113 bp):
AACCGGTAAAAAAAATAACAAAACCGGTAGCGCTTTACCTGATATATTAAAAGTATCGATCCTTT
TATAAAAAGGATAGATACTTTACAATATAACAGGTAAAAAAATAACAA
Found at i:28956 original size:183 final size:184
Alignment explanation
Indices: 28626--28973 Score: 646
Period size: 183 Copynumber: 1.9 Consensus size: 184
28616 GCGTTACTTA
28626 AAAGTATGGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTCTCATAAAACCGG
1 AAAGTATGGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTCTCATAAAACCGG
*
28691 TATATTTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGATGTTTTT
66 TATATCTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGATGTTTTT
28756 TCAATCGACACTTTTTGAAAAGGTATCGACACTTTTTTCATCCATTCTGGACAT
131 TCAATCGACACTTTTTGAAAAGGTATCGACACTTTTTTCATCCATTCTGGACAT
28810 AAAGTA-GCGACACAATATT-AAAAGTGTCGATATAGGTTGTAGACCTATTCTCTCATAAAACCG
1 AAAGTATG-GACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTCTCATAAAACCG
*
28873 GTATATCTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGGTGTTTT
65 GTATATCTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGATGTTTT
*
28938 TTCAATCGACATTTTTTGAAAAGGTATCGACACTTT
130 TTCAATCGACACTTTTTGAAAAGGTATCGACACTTT
28974 ATGCTGATAT
Statistics
Matches: 160, Mismatches: 3, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
183 143 0.89
184 17 0.11
ACGTcount: A:0.33, C:0.16, G:0.15, T:0.36
Consensus pattern (184 bp):
AAAGTATGGACACAATATTAAAAAGTGTCGATATAGGTTGTAGACCTATTCTCTCATAAAACCGG
TATATCTATACCGGTTATATTACAAAATTACCTATTACATTATAATTATGGGTTCCGATGTTTTT
TCAATCGACACTTTTTGAAAAGGTATCGACACTTTTTTCATCCATTCTGGACAT
Found at i:32220 original size:200 final size:200
Alignment explanation
Indices: 31873--32658 Score: 1340
Period size: 200 Copynumber: 3.9 Consensus size: 200
31863 ATATTTAAAT
* * * **
31873 TAGTATCGACACAAAATTAAAAAGTGTCGATACATA-TATTACACCTATTATCTCATAAAATTTG
1 TAGTATCGACACAAAATTAAAAAGTGTCGATACATATTA-TATACCTAATCTCTCATAAAATCGG
*
31937 TATACTTATACCGGTTAGATTGAAAAATTATCTATTACATTATACTTATGGGTTTCGATGTTTCT
65 TATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCT
** *
32002 GGGATCGACATTTTTTATATATGGATCGACACTTTATGGTTGCACCATGTTTGCCATTCATTCTG
130 GGGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTG
32067 GACCAA
195 GACCAA
* *
32073 TAGTATCGACACAAAATTAAAAAGTGTCGATACATATTATATACCTAATCTCTCATAAAACCGAT
1 TAGTATCGACACAAAATTAAAAAGTGTCGATACATATTATATACCTAATCTCTCATAAAATCGGT
* *
32138 ATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTAAACTTATGGGTTTCGATGTTTCTA
66 ATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
* * *
32203 GGATTGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTATTTGCCATTCATTTTGG
131 GGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGG
32268 ACCAA
196 ACCAA
32273 TAGTATCGACACAAAATTAAAAAGTGTCGATACATATTATATACCTAATCTCTCATAAAATCGGT
1 TAGTATCGACACAAAATTAAAAAGTGTCGATACATATTATATACCTAATCTCTCATAAAATCGGT
*
32338 ATACTTATACCGGTTAGATTGAAAAATTACCTATTATATTATACTTATGGGTTTCGATGTTTCTG
66 ATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
* *
32403 GGATCAACACCTTTTATATATGGATCGACACTTTATGGTTGGACCCTGTTTGCCATTCATTCTGG
131 GGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGG
32468 ACCAA
196 ACCAA
* *
32473 TAGTATCGACATAAAATTAAAAAGTGTTGATACATATTATATACCTAATCTCTCATAAAATCGGT
1 TAGTATCGACACAAAATTAAAAAGTGTCGATACATATTATATACCTAATCTCTCATAAAATCGGT
* *
32538 ATACTTATACCGGTTATATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTATG
66 ATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
*
32603 GGATCGACACTTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCAT
131 GGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCAT
32659 ATTGTAAATT
Statistics
Matches: 551, Mismatches: 34, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
200 549 1.00
201 2 0.00
ACGTcount: A:0.32, C:0.17, G:0.14, T:0.37
Consensus pattern (200 bp):
TAGTATCGACACAAAATTAAAAAGTGTCGATACATATTATATACCTAATCTCTCATAAAATCGGT
ATACTTATACCGGTTAGATTGAAAAATTACCTATTACATTATACTTATGGGTTTCGATGTTTCTG
GGATCGACACCTTTTATATATGGATCGACACTTTATGGTTGCACCCTGTTTGCCATTCATTCTGG
ACCAA
Found at i:32912 original size:19 final size:19
Alignment explanation
Indices: 32888--32936 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
32878 TTACATTCAC
32888 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
32907 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
32926 ATACAAAATTA
1 ATACAAAATTA
32937 ACCCCACATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:34545 original size:30 final size:30
Alignment explanation
Indices: 34493--34559 Score: 109
Period size: 30 Copynumber: 2.3 Consensus size: 30
34483 CATCGACTTC
34493 CTTCCT-CCTCATTTCTTCCATCTCTTCTT
1 CTTCCTCCCTCATTTCTTCCATCTCTTCTT
* *
34522 CTTCCTCCCTCTTTTCTTTCATCTCTTCTT
1 CTTCCTCCCTCATTTCTTCCATCTCTTCTT
34552 CTTCCTCC
1 CTTCCTCC
34560 TCCCTCTTTT
Statistics
Matches: 35, Mismatches: 2, Indels: 1
0.92 0.05 0.03
Matches are distributed among these distances:
29 6 0.17
30 29 0.83
ACGTcount: A:0.04, C:0.43, G:0.00, T:0.52
Consensus pattern (30 bp):
CTTCCTCCCTCATTTCTTCCATCTCTTCTT
Found at i:34585 original size:16 final size:16
Alignment explanation
Indices: 34566--34606 Score: 55
Period size: 18 Copynumber: 2.4 Consensus size: 16
34556 CTCCTCCCTC
*
34566 TTTTCTTCTTCATATT
1 TTTTCTTCATCATATT
34582 TTTTCAGTTCATCATATT
1 TTTTC--TTCATCATATT
34600 TTTTCTT
1 TTTTCTT
34607 TACATAGCTC
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
16 7 0.32
18 15 0.68
ACGTcount: A:0.15, C:0.17, G:0.02, T:0.66
Consensus pattern (16 bp):
TTTTCTTCATCATATT
Found at i:34807 original size:33 final size:33
Alignment explanation
Indices: 34761--34826 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
34751 CATCTTAAGA
*
34761 TCACCCCTTAACACCTCAACTTATTTCACCACT
1 TCACCCCTCAACACCTCAACTTATTTCACCACT
* *
34794 TCACCCCTCAACACCTCTACTTCTTTCACCACT
1 TCACCCCTCAACACCTCAACTTATTTCACCACT
34827 CCATCTATTT
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.24, C:0.45, G:0.00, T:0.30
Consensus pattern (33 bp):
TCACCCCTCAACACCTCAACTTATTTCACCACT
Found at i:34900 original size:21 final size:21
Alignment explanation
Indices: 34876--34924 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
34866 AGTGTATATT
* *
34876 CGACTCTCTCAAGTTTTTCTC
1 CGACTCTATCAAGTTTCTCTC
*
34897 CGACTCTATCAAGTTTCTCTT
1 CGACTCTATCAAGTTTCTCTC
34918 CGACTCT
1 CGACTCT
34925 TGATTGTCTT
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.16, C:0.33, G:0.10, T:0.41
Consensus pattern (21 bp):
CGACTCTATCAAGTTTCTCTC
Found at i:37232 original size:20 final size:19
Alignment explanation
Indices: 37177--37223 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 19
37167 TCCGGTAGCG
37177 TTTTACCGGTTTTATCATT
1 TTTTACCGGTTTTATCATT
*
37196 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTTATCAT-T
37217 TTTTACC
1 TTTTACC
37224 TGTTATATCG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 2 0.08
20 19 0.79
21 3 0.12
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (19 bp):
TTTTACCGGTTTTATCATT
Found at i:37404 original size:20 final size:19
Alignment explanation
Indices: 37358--37404 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
37348 TCCGGTAGCG
37358 TTTTACCGGTTTCATCATT
1 TTTTACCGGTTTCATCATT
* *
37377 TTGATACCGGTTTTATCATAT
1 TT-TTACCGGTTTCATCAT-T
37398 TTTTACC
1 TTTTACC
37405 TGTTATATCG
Statistics
Matches: 23, Mismatches: 3, Indels: 3
0.79 0.10 0.10
Matches are distributed among these distances:
19 2 0.09
20 18 0.78
21 3 0.13
ACGTcount: A:0.19, C:0.19, G:0.11, T:0.51
Consensus pattern (19 bp):
TTTTACCGGTTTCATCATT
Found at i:37452 original size:181 final size:182
Alignment explanation
Indices: 37144--37616 Score: 734
Period size: 181 Copynumber: 2.6 Consensus size: 182
37134 CGTACTTACG
37144 AAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
37209 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTTTAAAGTATCGACACTTTAT
66 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTTTAAAGTATCGACACTTTAT
** * * *
37274 AGGCGCTATAACTGCTTCTCTTTTAAATTCACAAAGTGTCGATCCTTATA-T
131 AAACGCTAAAACTGCTTCTCTTTTAAATTAACAAAGTATCGATCCTTATATT
* *
37325 AAAGTATCGGCACTTTCAATATATCCGGTAGCGTTTTACCGGTTTCATCATTTTGATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
37390 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATATATTTTTTTAATGTAT-GAACACTTTA
66 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTTTAAAGTATCG-ACACTTTA
*
37454 TAAACGCTAAAACTGCTTCTCTTTTAAATTAACGAAGTATCGATCCTTATATT
130 TAAACGCTAAAACTGCTTCTCTTTTAAATTAACAAAGTATCGATCCTTATATT
* * * * * * * **
37507 AAAGTACCGACACTTTAAATATATCTGGTACCGCTTTATCGATTTTATCATTTCAATACCGGTTT
1 AAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
* *
37572 TGTCATAGTTTTACCTGTTATATCGTTGTGGATCGATACATTTTT
66 TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTT
37617 AATTTAGATC
Statistics
Matches: 266, Mismatches: 24, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
180 1 0.00
181 168 0.63
182 97 0.36
ACGTcount: A:0.26, C:0.17, G:0.14, T:0.42
Consensus pattern (182 bp):
AAAGTATCGACACTTTCAATATATCCGGTAGCGTTTTACCGGTTTTATCATTTTGATACCGGTTT
TATCATATTTTTACCTGTTATATCGTTGTGGATCGATACATTTTTTTAAAGTATCGACACTTTAT
AAACGCTAAAACTGCTTCTCTTTTAAATTAACAAAGTATCGATCCTTATATT
Found at i:43529 original size:36 final size:36
Alignment explanation
Indices: 43458--43578 Score: 165
Period size: 35 Copynumber: 3.3 Consensus size: 36
43448 ATCCCATTAT
* * *
43458 CATTTTTC-AACAAACATCTACCAAAATTTGAAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTG-AAAAC
*
43494 TATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
43530 CA-TTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
43565 CACTTTTTTCAAAG
1 CA--TTTTTCAAAG
43579 TTGGTTACCA
Statistics
Matches: 76, Mismatches: 5, Indels: 6
0.87 0.06 0.07
Matches are distributed among these distances:
35 35 0.46
36 13 0.17
37 19 0.25
38 9 0.12
ACGTcount: A:0.44, C:0.20, G:0.05, T:0.31
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
Found at i:48065 original size:37 final size:36
Alignment explanation
Indices: 48006--48125 Score: 154
Period size: 35 Copynumber: 3.3 Consensus size: 36
47996 ATCCCATTAT
* * *
48006 CATTTTTC-AACAAACATCTACCAAAATTTGAAAAA
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
*
48041 CTATTTTTCAAAGAAACATTTACCAAACTTTGAAAAC
1 C-ATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
* *
48078 CA-TTTTCAAAAAAACATTTACCAAACTTTGAAAAT
1 CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
48113 CATTTTTTCAAAG
1 CA-TTTTTCAAAG
48126 TTGGTTACCA
Statistics
Matches: 74, Mismatches: 7, Indels: 6
0.85 0.08 0.07
Matches are distributed among these distances:
35 34 0.46
36 8 0.11
37 32 0.43
ACGTcount: A:0.45, C:0.18, G:0.04, T:0.33
Consensus pattern (36 bp):
CATTTTTCAAAGAAACATTTACCAAACTTTGAAAAA
Found at i:48081 original size:21 final size:20
Alignment explanation
Indices: 48054--48117 Score: 59
Period size: 20 Copynumber: 3.4 Consensus size: 20
48044 TTTTTCAAAG
48054 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
*
48074 AAACCATTT-TCAAA-----A
1 AAA-CATTTACCAAACTTTGA
48089 AAACATTTACCAAACTTTGA
1 AAACATTTACCAAACTTTGA
48109 AAATCATTT
1 AAA-CATTT
48118 TTTCAAAGTT
Statistics
Matches: 34, Mismatches: 2, Indels: 15
0.67 0.04 0.29
Matches are distributed among these distances:
14 5 0.15
15 8 0.24
20 11 0.32
21 10 0.29
ACGTcount: A:0.47, C:0.19, G:0.03, T:0.31
Consensus pattern (20 bp):
AAACATTTACCAAACTTTGA
Found at i:50732 original size:28 final size:27
Alignment explanation
Indices: 50659--50734 Score: 93
Period size: 27 Copynumber: 2.7 Consensus size: 27
50649 TTATCAAAAG
50659 AAATATCATATTAA-ATATTAAAAAATAT
1 AAATAT-ATATTAATAT-TTAAAAAATAT
*
50687 AAATAT-TATATAATATTTCAAAAATAT
1 AAATATATAT-TAATATTTAAAAAATAT
50714 AAATATATATTCAATATTTAA
1 AAATATATATT-AATATTTAA
50735 TCAAAGTACA
Statistics
Matches: 42, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
26 3 0.07
27 20 0.48
28 19 0.45
ACGTcount: A:0.57, C:0.04, G:0.00, T:0.39
Consensus pattern (27 bp):
AAATATATATTAATATTTAAAAAATAT
Found at i:58561 original size:68 final size:68
Alignment explanation
Indices: 58481--58610 Score: 174
Period size: 68 Copynumber: 1.9 Consensus size: 68
58471 ACTTTCTGTT
* *
58481 GCTTGAATGATGAAGAAAGATTCTT-ATTTAAGGAA-AAATATGGCTAATCATTGTGCATTAATC
1 GCTTGAATGATGAAG-AAGATTCTTGATTTAAAGAACAAATATGCCTAATCATTGTGC-TTAATC
58544 ATGTC
64 ATGTC
* * * *
58549 GCTTGAATGATGAAGCAGATTCTTGTTTTAAAGAACAAGTATGCCTAATCATTTTGCTTAAT
1 GCTTGAATGATGAAGAAGATTCTTGATTTAAAGAACAAATATGCCTAATCATTGTGCTTAAT
58611 TATATTACCA
Statistics
Matches: 54, Mismatches: 6, Indels: 4
0.84 0.09 0.06
Matches are distributed among these distances:
67 8 0.15
68 28 0.52
69 18 0.33
ACGTcount: A:0.35, C:0.12, G:0.18, T:0.35
Consensus pattern (68 bp):
GCTTGAATGATGAAGAAGATTCTTGATTTAAAGAACAAATATGCCTAATCATTGTGCTTAATCAT
GTC
Done.