Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000544.1 Hibiscus syriacus cultivar Beakdansim tig00001055_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: 84706
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:4061 original size:10 final size:10
Alignment explanation
Indices: 4046--4096 Score: 60
Period size: 10 Copynumber: 5.7 Consensus size: 10
4036 AAGTGTTATG
4046 TTATTATATA
1 TTATTATATA
4056 TTATTATATA
1 TTATTATATA
4066 -TATTA-ATA
1 TTATTATATA
4074 -TA-TA-A-A
1 TTATTATATA
4080 TTATTATATA
1 TTATTATATA
4090 TTATTAT
1 TTATTAT
4097 TACAAATGGA
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
6 1 0.03
7 5 0.14
8 7 0.19
9 6 0.16
10 18 0.49
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (10 bp):
TTATTATATA
Found at i:4067 original size:12 final size:12
Alignment explanation
Indices: 4050--4098 Score: 71
Period size: 12 Copynumber: 4.0 Consensus size: 12
4040 GTTATGTTAT
4050 TATATATTATTA
1 TATATATTATTA
*
4062 TATATATTAATA
1 TATATATTATTA
*
4074 TATAAATTATTA
1 TATATATTATTA
4086 TATATTATTATTA
1 TATA-TATTATTA
4099 CAAATGGAGG
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
12 25 0.78
13 7 0.22
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (12 bp):
TATATATTATTA
Found at i:12138 original size:20 final size:20
Alignment explanation
Indices: 12113--12274 Score: 198
Period size: 20 Copynumber: 8.1 Consensus size: 20
12103 TTTTCCATGA
*
12113 ATTTGTAAAGCCTTCGGGTC
1 ATTTGTAAATCCTTCGGGTC
*
12133 ATTTGTAAAGCCTTCGGGTC
1 ATTTGTAAATCCTTCGGGTC
*
12153 ATTTGTAAAGCCTTCGGGTC
1 ATTTGTAAATCCTTCGGGTC
* * *
12173 CTTTGTAAATTCTTCGGGTA
1 ATTTGTAAATCCTTCGGGTC
* *
12193 ATTTTTAAATCCTTCAGGTC
1 ATTTGTAAATCCTTCGGGTC
* *
12213 ATTTGTAAATTCTTCGGGTA
1 ATTTGTAAATCCTTCGGGTC
*
12233 ATTTGTAAATCCTTCGGGTA
1 ATTTGTAAATCCTTCGGGTC
* * *
12253 ATTTATAAATCTTTTGGGTC
1 ATTTGTAAATCCTTCGGGTC
12273 AT
1 AT
12275 CTGTTAGTCT
Statistics
Matches: 124, Mismatches: 18, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 124 1.00
ACGTcount: A:0.23, C:0.16, G:0.20, T:0.41
Consensus pattern (20 bp):
ATTTGTAAATCCTTCGGGTC
Found at i:12670 original size:190 final size:189
Alignment explanation
Indices: 12323--12789 Score: 609
Period size: 190 Copynumber: 2.4 Consensus size: 189
12313 AATCAAAATC
* *
12323 CACGGAAGAGTAGTGGAAGTAAATCCAACTTTGAATCTGATCTTCACAGAAGAGTAGTGAAATTA
1 CACGGAAGAGTAGT-GAAGT-AATCCAA-TTTGAATCTAATCTTCACGGAAGAGTAGTGAAATTA
* *
12388 GATTCTTATCAAGTTAGTCATT-TCAGCCTTCACAGAAGAGCAGTGAAGCAAAAGCAAGAGCAAG
63 GATTCTTATCAAGTTAATCATTCTCAGCCTTCACAGAAGAACAGTGAAGCAAAAGCAAGAGCAAG
* * *
12452 ATTAAAATTCACTCTCCACAAAAGAGTAGTGGAATGGATATTTT-AGCAAAGTATGTAATCTT
128 ATTAAAATTCACTCTCCACAAAAGAGTAGTGGAA-CGAAATTTTCAGCAAAGTATGAAATCTT
** * *
12514 CACGGAAGAGTAGTGAAGTAATCTGATTTCGAGTCTAATCCTCACGGAAGAGTAGTGAAATTAGA
1 CACGGAAGAGTAGTGAAGTAATCCAATTT-GAATCTAATCTTCACGGAAGAGTAGTGAAATTAGA
* * * * *
12579 TTCTTATCAAGTTAATCATTCTCAGTCTTCACGGACGAATAGTGAAGCAAGAGC-AGAAGCAA-A
65 TTCTTATCAAGTTAATCATTCTCAGCCTTCACAGAAGAACAGTGAAGCAAAAGCAAG-AGCAAGA
* * **
12642 GTTAGAATTCGCTCTCCACGGAAGAGTAGTGGAACGAAATTTTCAGCAAAGTATGAAATCTT
129 -TTAAAATTCACTCTCCACAAAAGAGTAGTGGAACGAAATTTTCAGCAAAGTATGAAATCTT
* * *
12704 CACGGAAGAGTAGTGAAGTAATCCAATTGTGACTATAATCTTCACGAAAGAGTAGTGAAATTAGA
1 CACGGAAGAGTAGTGAAGTAATCCAATT-TGAATCTAATCTTCACGGAAGAGTAGTGAAATTAGA
* *
12769 TTCCTATTAAGTTAATCATTC
65 TTCTTATCAAGTTAATCATTC
12790 AATTTTTTCG
Statistics
Matches: 242, Mismatches: 28, Indels: 13
0.86 0.10 0.05
Matches are distributed among these distances:
188 3 0.01
189 65 0.27
190 159 0.66
191 15 0.06
ACGTcount: A:0.37, C:0.15, G:0.21, T:0.27
Consensus pattern (189 bp):
CACGGAAGAGTAGTGAAGTAATCCAATTTGAATCTAATCTTCACGGAAGAGTAGTGAAATTAGAT
TCTTATCAAGTTAATCATTCTCAGCCTTCACAGAAGAACAGTGAAGCAAAAGCAAGAGCAAGATT
AAAATTCACTCTCCACAAAAGAGTAGTGGAACGAAATTTTCAGCAAAGTATGAAATCTT
Found at i:13104 original size:10 final size:10
Alignment explanation
Indices: 13089--13143 Score: 53
Period size: 10 Copynumber: 5.7 Consensus size: 10
13079 GAGAGTTATG
13089 TTATTATATA
1 TTATTATATA
13099 TTATTATATA
1 TTATTATATA
13109 -TA-TATAT-
1 TTATTATATA
* *
13116 TAATATATAAA
1 TTAT-TATATA
13127 TTATTATATA
1 TTATTATATA
*
13137 ATATTAT
1 TTATTAT
13144 TACAAATAGA
Statistics
Matches: 36, Mismatches: 5, Indels: 8
0.73 0.10 0.16
Matches are distributed among these distances:
8 6 0.17
9 2 0.06
10 25 0.69
11 3 0.08
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (10 bp):
TTATTATATA
Found at i:34716 original size:102 final size:102
Alignment explanation
Indices: 34530--34716 Score: 232
Period size: 102 Copynumber: 1.8 Consensus size: 102
34520 TTGATAGAAC
* * *
34530 AATATGTTCAAAAACTATATGACACTATGCCTTCAAGTTCAAAGGGAATGAATTTATCTGCAAAC
1 AATATGTTCAAAAACCATATGACACTATACCTTCAAGTTCAAAGGGAATGAATTCATCTGCAAAC
*** *
34595 TTATTCGTCCTCAATATCGAGATGTCATCTACACAAT
66 TTATTAAACCTCAACATCGAGATGTCATCTACACAAT
* * * *
34632 AATATGTTTAAAACCCATATGACACTATATCTTCAAGTTCAAAGGGAA-GACATTCATCTGCCAA
1 AATATGTTCAAAAACCATATGACACTATACCTTCAAGTTCAAAGGGAATGA-ATTCATCTGCAAA
* * *
34696 CTTGTTAAACCTTAGCATCGA
65 CTTATTAAACCTCAACATCGA
34717 ATTGGAGACT
Statistics
Matches: 70, Mismatches: 14, Indels: 2
0.81 0.16 0.02
Matches are distributed among these distances:
101 2 0.03
102 68 0.97
ACGTcount: A:0.36, C:0.20, G:0.13, T:0.30
Consensus pattern (102 bp):
AATATGTTCAAAAACCATATGACACTATACCTTCAAGTTCAAAGGGAATGAATTCATCTGCAAAC
TTATTAAACCTCAACATCGAGATGTCATCTACACAAT
Found at i:42207 original size:22 final size:21
Alignment explanation
Indices: 42171--42211 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
42161 TATTGATACC
*
42171 AGTAGGGGGTATCGATACCGT
1 AGTAGGGAGTATCGATACCGT
42192 AGTAGGGTAGTATCGATACC
1 AGTAGGG-AGTATCGATACC
42212 ATGGAAAGGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.27, C:0.15, G:0.34, T:0.24
Consensus pattern (21 bp):
AGTAGGGAGTATCGATACCGT
Found at i:42240 original size:95 final size:93
Alignment explanation
Indices: 42086--42264 Score: 238
Period size: 95 Copynumber: 1.9 Consensus size: 93
42076 GATTCAATCA
* * * *
42086 GTATCGATACCTATGGGGTAGTATTGATACCATGATAAGGGGTATTGATACCAATAACATCGAAT
1 GTATCGATACCTATAGGGTAGTATCGATACCATGATAAGGGGTATCGATACCAATAACATCGAAC
*
42151 CTAATTTTGGTATTGATACCAGTAGGGG
66 CTAATTTTGGTATCGATACCAGTAGGGG
42179 GTATCGATACCGTAGTAGGGTAGTATCGATACCATGGA-AA-GGGTATCGATACCAGGA-AACAT
1 GTATCGATACC-TA-TAGGGTAGTATCGATACCAT-GATAAGGGGTATCGATACCA--ATAACAT
*
42241 CGAACCTATTTTTGGTATCGATAC
61 CGAACCTAATTTTGGTATCGATAC
42265 TATAGTATAG
Statistics
Matches: 75, Mismatches: 6, Indels: 8
0.84 0.07 0.09
Matches are distributed among these distances:
93 11 0.15
94 15 0.20
95 46 0.61
96 3 0.04
ACGTcount: A:0.31, C:0.15, G:0.25, T:0.29
Consensus pattern (93 bp):
GTATCGATACCTATAGGGTAGTATCGATACCATGATAAGGGGTATCGATACCAATAACATCGAAC
CTAATTTTGGTATCGATACCAGTAGGGG
Found at i:42705 original size:55 final size:55
Alignment explanation
Indices: 42639--42850 Score: 325
Period size: 55 Copynumber: 3.9 Consensus size: 55
42629 TACTACAGGC
* *
42639 ACTTCGTGTGCACATTCACATAATTCATCATGAGTGGATGAATCACCGTATAGGA
1 ACTTCGTGTGCATATTCACAGAATTCATCATGAGTGGATGAATCACCGTATAGGA
* * * *
42694 ACTTCGTGTGCATATTCACAGAATTCATCCTAAGTGGATAAATCACCGTACAGGA
1 ACTTCGTGTGCATATTCACAGAATTCATCATGAGTGGATGAATCACCGTATAGGA
* * *
42749 ACTTCATGTGCATATTCACAGAATTCATCCTGAGTGGATGAATCACCGTATAGGC
1 ACTTCGTGTGCATATTCACAGAATTCATCATGAGTGGATGAATCACCGTATAGGA
* *
42804 ACTTCGTGTGCATATTTACGGAATTCATCATGAGTGGATGAATCACC
1 ACTTCGTGTGCATATTCACAGAATTCATCATGAGTGGATGAATCACC
42851 ATACAGACAC
Statistics
Matches: 142, Mismatches: 15, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
55 142 1.00
ACGTcount: A:0.30, C:0.21, G:0.20, T:0.29
Consensus pattern (55 bp):
ACTTCGTGTGCATATTCACAGAATTCATCATGAGTGGATGAATCACCGTATAGGA
Found at i:42924 original size:54 final size:54
Alignment explanation
Indices: 42769--42900 Score: 138
Period size: 55 Copynumber: 2.4 Consensus size: 54
42759 CATATTCACA
* * * * ** * ***
42769 GAATTCATCCTGAGTGGATGAATCACCGTATAGGCACTTCGTGTGCATATTTACG
1 GAATTCATCATGAGTGGATGAATCACCATACAGACACTAAGTGTGTA-ACCCACG
*
42824 GAATTCATCATGAGTGGATGAATCACCATACAGACACTATGTGTGTAACCCACG
1 GAATTCATCATGAGTGGATGAATCACCATACAGACACTAAGTGTGTAACCCACG
* *
42878 GAATTCATCATGTGTTGATGAAT
1 GAATTCATCATGAGTGGATGAAT
42901 TTCCGTATAG
Statistics
Matches: 65, Mismatches: 12, Indels: 1
0.83 0.15 0.01
Matches are distributed among these distances:
54 25 0.38
55 40 0.62
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.30
Consensus pattern (54 bp):
GAATTCATCATGAGTGGATGAATCACCATACAGACACTAAGTGTGTAACCCACG
Found at i:49065 original size:19 final size:21
Alignment explanation
Indices: 49041--49092 Score: 72
Period size: 22 Copynumber: 2.5 Consensus size: 21
49031 TCTAATTTTG
*
49041 GTATCGATACC-GGTAGGG-A
1 GTATCGATACCTAGTAGGGTA
49060 GTATCGATACCCTAGTAGGGTA
1 GTATCGATA-CCTAGTAGGGTA
49082 GTATCGATACC
1 GTATCGATACC
49093 ATGGAAAGGG
Statistics
Matches: 29, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
19 9 0.31
20 2 0.07
21 8 0.28
22 10 0.34
ACGTcount: A:0.27, C:0.19, G:0.29, T:0.25
Consensus pattern (21 bp):
GTATCGATACCTAGTAGGGTA
Found at i:49180 original size:95 final size:95
Alignment explanation
Indices: 49007--49182 Score: 228
Period size: 95 Copynumber: 1.9 Consensus size: 95
48997 CCTATGGTTA
* * * * * *
49007 GTATCGATACCAAGAAACATCGAATCTAATTTTGGTATCGATACCGGTAGGGAGTATCGATACCC
1 GTATCGATACCAAGAAACATCGAACCTAATTTTAGTATCAATACCCGAAGGGAGTATCGATACCA
* *
49072 TAGTAGGGTAGTATCGATACCATGGAAAGG
66 TAGTAGAGAAGTATCGATACCATGGAAAGG
* * *
49102 GTATCGATACCAAGCAACATCGAACCTATTTTTAGTATCAATACCCGAAGGG-GATATCGGTACC
1 GTATCGATACCAAGAAACATCGAACCTAATTTTAGTATCAATACCCGAAGGGAG-TATCGATACC
*
49166 ATAGTATAGAAGTATCG
65 ATAGTAGAGAAGTATCG
49183 GTACTAGGGT
Statistics
Matches: 68, Mismatches: 12, Indels: 2
0.83 0.15 0.02
Matches are distributed among these distances:
94 1 0.01
95 67 0.99
ACGTcount: A:0.34, C:0.18, G:0.23, T:0.26
Consensus pattern (95 bp):
GTATCGATACCAAGAAACATCGAACCTAATTTTAGTATCAATACCCGAAGGGAGTATCGATACCA
TAGTAGAGAAGTATCGATACCATGGAAAGG
Found at i:49201 original size:95 final size:96
Alignment explanation
Indices: 49005--49206 Score: 221
Period size: 95 Copynumber: 2.1 Consensus size: 96
48995 TACCTATGGT
* * * * *
49005 TAGTATCGATACCAAGAAACATCGAATCTAATTTTGGTATCGATACCGGTAGGGAGTATCGATAC
1 TAGTATCGATACCAAGAAACATCGAACCTAATTTTAGTATCAATACCCGAAGGGAGTATCGATAC
* * *
49070 CCTAGTAGGGTAGTATCGATACCATGGAAAG
66 CATAGTAGAGAAGTATCGATACCATGGAAAG
* * * *
49101 -GGTATCGATACCAAGCAACATCGAACCTATTTTTAGTATCAATACCCGAAGGG-GATATCGGTA
1 TAGTATCGATACCAAGAAACATCGAACCTAATTTTAGTATCAATACCCGAAGGGAG-TATCGATA
* * * **
49164 CCATAGTATAGAAGTATCGGTACTA-GGGTAG
65 CCATAGTAGAGAAGTATCGATACCATGGAAAG
49195 TAGTATCGATAC
1 TAGTATCGATAC
49207 TATGGAGCCA
Statistics
Matches: 86, Mismatches: 18, Indels: 5
0.79 0.17 0.05
Matches are distributed among these distances:
94 5 0.06
95 81 0.94
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.26
Consensus pattern (96 bp):
TAGTATCGATACCAAGAAACATCGAACCTAATTTTAGTATCAATACCCGAAGGGAGTATCGATAC
CATAGTAGAGAAGTATCGATACCATGGAAAG
Found at i:53585 original size:19 final size:18
Alignment explanation
Indices: 53558--53605 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
53548 GAGAAAAAGT
*
53558 AAAAGTTAAAATGAAATAA
1 AAAAATTAAAATGAAA-AA
53577 AAAAATTAAAGATGAAAAA
1 AAAAATTAAA-ATGAAAAA
*
53596 GAAAA-TAAAA
1 AAAAATTAAAA
53606 AGTTAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
17 1 0.04
18 4 0.15
19 15 0.58
20 6 0.23
ACGTcount: A:0.73, C:0.00, G:0.10, T:0.17
Consensus pattern (18 bp):
AAAAATTAAAATGAAAAA
Found at i:53600 original size:20 final size:19
Alignment explanation
Indices: 53550--53600 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 19
53540 AAATGAGAGA
*
53550 GAAAAAGTAAAAGTTAAAAT
1 GAAAAAG-AAAAATTAAAAT
53570 GAAATAA-AAAAATTAAAGAT
1 GAAA-AAGAAAAATTAAA-AT
53590 GAAAAAGAAAA
1 GAAAAAGAAAA
53601 TAAAAAGTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
19 11 0.41
20 14 0.52
21 2 0.07
ACGTcount: A:0.71, C:0.00, G:0.14, T:0.16
Consensus pattern (19 bp):
GAAAAAGAAAAATTAAAAT
Found at i:61487 original size:55 final size:55
Alignment explanation
Indices: 61393--61631 Score: 309
Period size: 55 Copynumber: 4.3 Consensus size: 55
61383 TTATGTGTAC
* *
61393 TACAGGCACTTCGTGTGCATATTCACGGAATTCAACCTAAGTGGATGAATCACCG
1 TACAGGCACTTCGTGTGCATATTCACAGAATTCATCCTAAGTGGATGAATCACCG
* * * * ** *
61448 TAGAGGAACTTCGTATGCATATTCACAAAATTTTTCCTAAGTGGATGAATCATCG
1 TACAGGCACTTCGTGTGCATATTCACAGAATTCATCCTAAGTGGATGAATCACCG
* * * *
61503 TACAGGCACTTCGTGTGCATATTCACGGAATTTATCCTGAGTGGATGAATGACCG
1 TACAGGCACTTCGTGTGCATATTCACAGAATTCATCCTAAGTGGATGAATCACCG
* * * *
61558 TACAGGCACTTCGTGTGCATAGTCACAGAATTCATCCTGAGTGGATAAATCATCG
1 TACAGGCACTTCGTGTGCATATTCACAGAATTCATCCTAAGTGGATGAATCACCG
61613 TACAGGCACTAT-GTGTGCA
1 TACAGGCACT-TCGTGTGCA
61632 ACCTACGGAA
Statistics
Matches: 159, Mismatches: 24, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
55 158 0.99
56 1 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.28
Consensus pattern (55 bp):
TACAGGCACTTCGTGTGCATATTCACAGAATTCATCCTAAGTGGATGAATCACCG
Found at i:61601 original size:110 final size:110
Alignment explanation
Indices: 61393--61661 Score: 355
Period size: 110 Copynumber: 2.5 Consensus size: 110
61383 TTATGTGTAC
* * *
61393 TACAGGCACTTCGTGTGCATATTCACGGAATTCAACCTAAGTGGATGAATCACCGTAGAGGAACT
1 TACAGGCACTTCGTGTGCATATTCACGGAATTCATCCTGAGTGGATGAATCACCGTACAGGAACT
* ** *
61458 TCGTATGCATATTCACAAAATTTTTCCTAAGTGGATGAATCATCG
66 TCGTATGCATAGTCACAAAATTCATCCTAAGTGGATAAATCATCG
* * *
61503 TACAGGCACTTCGTGTGCATATTCACGGAATTTATCCTGAGTGGATGAATGACCGTACAGGCACT
1 TACAGGCACTTCGTGTGCATATTCACGGAATTCATCCTGAGTGGATGAATCACCGTACAGGAACT
* * *
61568 TCGTGTGCATAGTCACAGAATTCATCCTGAGTGGATAAATCATCG
66 TCGTATGCATAGTCACAAAATTCATCCTAAGTGGATAAATCATCG
* * *
61613 TACAGGCACTAT-GTGTGCA-A-CCTACGGAATTCATCATGAGTTGATGAAT
1 TACAGGCACT-TCGTGTGCATATTC-ACGGAATTCATCCTGAGTGGATGAAT
61662 TTCTGTATAG
Statistics
Matches: 140, Mismatches: 17, Indels: 5
0.86 0.10 0.03
Matches are distributed among these distances:
108 1 0.01
109 24 0.17
110 114 0.81
111 1 0.01
ACGTcount: A:0.29, C:0.20, G:0.22, T:0.29
Consensus pattern (110 bp):
TACAGGCACTTCGTGTGCATATTCACGGAATTCATCCTGAGTGGATGAATCACCGTACAGGAACT
TCGTATGCATAGTCACAAAATTCATCCTAAGTGGATAAATCATCG
Found at i:66563 original size:20 final size:20
Alignment explanation
Indices: 66538--66589 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
66528 GATGCAATTA
66538 GTATCGATACTAAGAGAAAG
1 GTATCGATACTAAGAGAAAG
*
66558 GTATCGACACTAAGAGAAAG
1 GTATCGATACTAAGAGAAAG
*
66578 GTATTGATACTA
1 GTATCGATACTA
66590 TCGATCCAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.42, C:0.12, G:0.23, T:0.23
Consensus pattern (20 bp):
GTATCGATACTAAGAGAAAG
Found at i:67079 original size:54 final size:54
Alignment explanation
Indices: 66997--67388 Score: 464
Period size: 54 Copynumber: 7.2 Consensus size: 54
66987 TTGCAATTAC
*
66997 CGTATTGACACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTT
1 CGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTT
* * *
67051 CGTATTGGCACTATATGTGTAACCTAAGAAATTCATAATGAGTTTATGAATTTT
1 CGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTT
* * * *
67105 TGTATTGGCATTGTGTGTGCAACCTAAGAAATTCATAATAAGTTTACGAATTTT
1 CGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTT
* * * *
67159 TGTATTGGCACTGTATGTACAACCTAAGAAATTCATAATAAGTTTATGAA-TTT
1 CGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTT
* * * * *
67212 CTGTATTGGCATTATGTATGGAACCTAAAAAATTCGTAATAAGTTTATGAATTTT
1 C-GTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTT
* * * * * *
67267 CATATTTGCATTGTGTGTACAACCTAAGAAATTCATAATAAGTTTATGAATTTC
1 CGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTT
* ** * * * * *
67321 CATATTGGCACTAAATGTGCAACCCCACGTAATTCATAATAAGTTTGTGAA-TTA
1 CGTATTGGCACTATGTGTGCAA-CCTAAGAAATTCATAATAAGTTTATGAATTTT
67375 CTGTATTGGCACTA
1 C-GTATTGGCACTA
67389 CAGATGCAAA
Statistics
Matches: 289, Mismatches: 45, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
53 3 0.01
54 247 0.85
55 39 0.13
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.38
Consensus pattern (54 bp):
CGTATTGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTT
Found at i:67283 original size:162 final size:162
Alignment explanation
Indices: 66991--67388 Score: 537
Period size: 162 Copynumber: 2.5 Consensus size: 162
66981 TATGTATTGC
* * *
66991 AATTACCGTATTGACACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTT-TCGTA
1 AATTTCCGTATTGGCACTATATGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCT-GTA
* * * * **
67055 TTGGCACTATATGTGTAACCTAAGAAATTCATAATGAGTTTATGAATTTTTGTATTGGCATTGTG
65 TTGGCACTATATATGGAACCTAAAAAATTCATAATAAGTTTATGAATTTTCATATTGGCATTGTG
*
67120 TGTGCAACCTAAGAAATTCATAATAAGTTTACG
130 TGTACAACCTAAGAAATTCATAATAAGTTTACG
** * *
67153 AATTTTTGTATTGGCACTGTATGTACAACCTAAGAAATTCATAATAAGTTTATGAATTTCTGTAT
1 AATTTCCGTATTGGCACTATATGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCTGTAT
* * * *
67218 TGGCATTATGTATGGAACCTAAAAAATTCGTAATAAGTTTATGAATTTTCATATTTGCATTGTGT
66 TGGCACTATATATGGAACCTAAAAAATTCATAATAAGTTTATGAATTTTCATATTGGCATTGTGT
*
67283 GTACAACCTAAGAAATTCATAATAAGTTTATG
131 GTACAACCTAAGAAATTCATAATAAGTTTACG
* * * * * * *
67315 AATTTCCATATTGGCACTAAATGTGCAACCCCACGTAATTCATAATAAGTTTGTGAATTACTGTA
1 AATTTCCGTATTGGCACTATATGTGCAA-CCTAAGAAATTCATAATAAGTTTATGAATTTCTGTA
67380 TTGGCACTA
65 TTGGCACTA
67389 CAGATGCAAA
Statistics
Matches: 203, Mismatches: 31, Indels: 3
0.86 0.13 0.01
Matches are distributed among these distances:
162 163 0.80
163 40 0.20
ACGTcount: A:0.34, C:0.13, G:0.16, T:0.37
Consensus pattern (162 bp):
AATTTCCGTATTGGCACTATATGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCTGTAT
TGGCACTATATATGGAACCTAAAAAATTCATAATAAGTTTATGAATTTTCATATTGGCATTGTGT
GTACAACCTAAGAAATTCATAATAAGTTTACG
Found at i:69122 original size:20 final size:22
Alignment explanation
Indices: 69099--69139 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
69089 ATATTACCAT
69099 CATTTCAT-TT-CCACAACATC
1 CATTTCATCTTGCCACAACATC
69119 CATTTCATCTTGCCACAACAT
1 CATTTCATCTTGCCACAACAT
69140 TCTCATTTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 8 0.42
21 2 0.11
22 9 0.47
ACGTcount: A:0.29, C:0.34, G:0.02, T:0.34
Consensus pattern (22 bp):
CATTTCATCTTGCCACAACATC
Found at i:69420 original size:17 final size:17
Alignment explanation
Indices: 69374--69410 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
69364 GTAATTACTT
*
69374 AGCGTGTGTTAATTTCA
1 AGCGTGTATTAATTTCA
69391 AGCGTGTATTAATTTCA
1 AGCGTGTATTAATTTCA
69408 AGC
1 AGC
69411 AGGTTTTAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.27, C:0.14, G:0.22, T:0.38
Consensus pattern (17 bp):
AGCGTGTATTAATTTCA
Found at i:70393 original size:20 final size:20
Alignment explanation
Indices: 70370--70421 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
70360 CTAAATGCAA
*
70370 CTATATGCACCTAAAATGAC
1 CTATATGAACCTAAAATGAC
*
70390 CTATATAAACCTAAAATGAC
1 CTATATGAACCTAAAATGAC
70410 CTATATGAACCT
1 CTATATGAACCT
70422 TTAGACAAAC
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.42, C:0.23, G:0.08, T:0.27
Consensus pattern (20 bp):
CTATATGAACCTAAAATGAC
Found at i:70598 original size:23 final size:23
Alignment explanation
Indices: 70568--70617 Score: 77
Period size: 23 Copynumber: 2.2 Consensus size: 23
70558 CAAGGTTAAC
70568 ATTT-TAAGG-TTAATGATTTACG
1 ATTTATAAGGATTAATG-TTTACG
70590 ATTTATAAGGATTAATGTTTACG
1 ATTTATAAGGATTAATGTTTACG
70613 ATTTA
1 ATTTA
70618 GGTTAATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
22 4 0.15
23 16 0.62
24 6 0.23
ACGTcount: A:0.34, C:0.04, G:0.16, T:0.46
Consensus pattern (23 bp):
ATTTATAAGGATTAATGTTTACG
Found at i:75872 original size:27 final size:27
Alignment explanation
Indices: 75834--75886 Score: 106
Period size: 27 Copynumber: 2.0 Consensus size: 27
75824 CGGTTCTCAT
75834 TTGGTTTTCTGGTTCTTGTAAGGGGTG
1 TTGGTTTTCTGGTTCTTGTAAGGGGTG
75861 TTGGTTTTCTGGTTCTTGTAAGGGGT
1 TTGGTTTTCTGGTTCTTGTAAGGGGT
75887 ATTACTGAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.08, C:0.08, G:0.36, T:0.49
Consensus pattern (27 bp):
TTGGTTTTCTGGTTCTTGTAAGGGGTG
Found at i:81057 original size:48 final size:45
Alignment explanation
Indices: 80981--81090 Score: 132
Period size: 44 Copynumber: 2.4 Consensus size: 45
80971 TACACTAATA
* * *
80981 TAAGTATGCACATCTCCAACCTAAAAATAAATATATACTTACACCGGTG
1 TAAGTATGTATATCTCCAACCTAAAAAT-AA-ACATAC--ACACCGGTG
* *
81030 TAAGTATGTATATC-CCAACCTAAAAATAAGCATACACACCTGTG
1 TAAGTATGTATATCTCCAACCTAAAAATAAACATACACACCGGTG
81074 TAAGTATGTATATCTCC
1 TAAGTATGTATATCTCC
81091 CAATATTTTA
Statistics
Matches: 55, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
44 22 0.40
45 2 0.04
46 4 0.07
47 2 0.04
48 13 0.24
49 12 0.22
ACGTcount: A:0.39, C:0.22, G:0.11, T:0.28
Consensus pattern (45 bp):
TAAGTATGTATATCTCCAACCTAAAAATAAACATACACACCGGTG
Found at i:82348 original size:27 final size:28
Alignment explanation
Indices: 82318--82372 Score: 76
Period size: 28 Copynumber: 2.0 Consensus size: 28
82308 TACAAAAGAG
*
82318 CATATTAAATTA-TTTAACTACATAAAT
1 CATAATAAATTATTTTAACTACATAAAT
* *
82345 CATAATAACTTATTTTAATTACATAAAT
1 CATAATAAATTATTTTAACTACATAAAT
82373 GTTATATTAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
27 10 0.42
28 14 0.58
ACGTcount: A:0.47, C:0.11, G:0.00, T:0.42
Consensus pattern (28 bp):
CATAATAAATTATTTTAACTACATAAAT
Found at i:84069 original size:2 final size:2
Alignment explanation
Indices: 84062--84193 Score: 264
Period size: 2 Copynumber: 66.0 Consensus size: 2
84052 TATTTAAATG
84062 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
84104 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
84146 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
84188 AT AT AT
1 AT AT AT
84194 TATGATCAAG
Statistics
Matches: 130, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 130 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.