Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000678.1 Hibiscus syriacus cultivar Beakdansim tig00001316_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: 73149
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:2669 original size:17 final size:17
Alignment explanation
Indices: 2649--2704 Score: 53
Period size: 17 Copynumber: 3.3 Consensus size: 17
2639 TTGAAAATAC
2649 ATTTACTGTTGACATCA
1 ATTTACTGTTGACATCA
* *
2666 ATTTA-TTTTGAAAAT-A
1 ATTTACTGTTG-ACATCA
2682 CATTTACTGTTGACATCA
1 -ATTTACTGTTGACATCA
*
2700 TTTTA
1 ATTTA
2705 ATAACTTGTA
Statistics
Matches: 30, Mismatches: 5, Indels: 8
0.70 0.12 0.19
Matches are distributed among these distances:
16 5 0.17
17 20 0.67
18 5 0.17
ACGTcount: A:0.32, C:0.12, G:0.09, T:0.46
Consensus pattern (17 bp):
ATTTACTGTTGACATCA
Found at i:2669 original size:34 final size:34
Alignment explanation
Indices: 2626--2704 Score: 149
Period size: 34 Copynumber: 2.3 Consensus size: 34
2616 ACAAATTATA
2626 ACATCAATTTATTTTGAAAATACATTTACTGTTG
1 ACATCAATTTATTTTGAAAATACATTTACTGTTG
2660 ACATCAATTTATTTTGAAAATACATTTACTGTTG
1 ACATCAATTTATTTTGAAAATACATTTACTGTTG
*
2694 ACATCATTTTA
1 ACATCAATTTA
2705 ATAACTTGTA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
34 44 1.00
ACGTcount: A:0.35, C:0.13, G:0.08, T:0.44
Consensus pattern (34 bp):
ACATCAATTTATTTTGAAAATACATTTACTGTTG
Found at i:4509 original size:2 final size:2
Alignment explanation
Indices: 4502--4532 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
4492 TGAACTAGCA
4502 AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
4533 TGCATAGTGA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:16350 original size:31 final size:30
Alignment explanation
Indices: 16315--16389 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
16305 GATCTAGGGA
16315 TTAAATTAATATTTAATATAAAATATAATG-G
1 TTAAATTAATATTTAAT-TAAAATATAA-GAG
* * * * *
16346 TTAAATTAGTATTTTATTTAAATTTTAGAG
1 TTAAATTAATATTTAATTAAAATATAAGAG
16376 TTAAATTAATATTT
1 TTAAATTAATATTT
16390 CGTCTAAAAC
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
29 1 0.03
30 21 0.57
31 15 0.41
ACGTcount: A:0.44, C:0.00, G:0.07, T:0.49
Consensus pattern (30 bp):
TTAAATTAATATTTAATTAAAATATAAGAG
Found at i:23877 original size:20 final size:20
Alignment explanation
Indices: 23849--23900 Score: 59
Period size: 20 Copynumber: 2.6 Consensus size: 20
23839 TATAACTTTG
* * *
23849 ATAATATTTTATGTAATTTT
1 ATAAAATTTTATCTAATTAT
23869 ATAAAATTTTATCTAATTAT
1 ATAAAATTTTATCTAATTAT
* *
23889 AAAAAATCTTAT
1 ATAAAATTTTAT
23901 TTGATATGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 27 1.00
ACGTcount: A:0.44, C:0.04, G:0.02, T:0.50
Consensus pattern (20 bp):
ATAAAATTTTATCTAATTAT
Found at i:24269 original size:60 final size:59
Alignment explanation
Indices: 24195--24308 Score: 174
Period size: 59 Copynumber: 1.9 Consensus size: 59
24185 ACATCCTTAA
* * * *
24195 ATTATGTCTCTCATTCTAAATTGATCCCCTAACTATTGAATATTTCAAATTCATCACTAT
1 ATTATGGCTCTCATTCTAAATTGAT-CCCAAACTATTGAACATTCCAAATTCATCACTAT
*
24255 ATTATGGCTCTCATTCTAAATTGATCCCAAACTTTTGAACATTCCAAATTCATC
1 ATTATGGCTCTCATTCTAAATTGATCCCAAACTATTGAACATTCCAAATTCATC
24309 CTGACCCTCA
Statistics
Matches: 49, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
59 25 0.51
60 24 0.49
ACGTcount: A:0.32, C:0.23, G:0.06, T:0.39
Consensus pattern (59 bp):
ATTATGGCTCTCATTCTAAATTGATCCCAAACTATTGAACATTCCAAATTCATCACTAT
Found at i:26294 original size:19 final size:18
Alignment explanation
Indices: 26256--26294 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
26246 TATTTTTTAA
* *
26256 AAAAAATATATAAATTTT
1 AAAAAATAAATAAATATT
26274 AAAAAATAAAATAAATATT
1 AAAAAAT-AAATAAATATT
26293 AA
1 AA
26295 CCAGTATTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 7 0.39
19 11 0.61
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (18 bp):
AAAAAATAAATAAATATT
Found at i:26463 original size:2 final size:2
Alignment explanation
Indices: 26456--26486 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
26446 AAATTTGACT
26456 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
26487 TATGTTAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28171 original size:24 final size:24
Alignment explanation
Indices: 28089--28185 Score: 79
Period size: 24 Copynumber: 4.0 Consensus size: 24
28079 CAGAAAACAA
28089 AACATAATTCAGATCAGATATCAG
1 AACATAATTCAGATCAGATATCAG
** * *
28113 AGTATAATCCAGGTCAGGA-ATCAG
1 AACATAATTCAGATCA-GATATCAG
* * * *
28137 AACAGATTTCAGATTAGATGTCAG
1 AACATAATTCAGATCAGATATCAG
* * *
28161 AACATAATTCAAATCGGAAATCAG
1 AACATAATTCAGATCAGATATCAG
28185 A
1 A
28186 TAAAATATTC
Statistics
Matches: 52, Mismatches: 19, Indels: 4
0.69 0.25 0.05
Matches are distributed among these distances:
23 2 0.04
24 48 0.92
25 2 0.04
ACGTcount: A:0.43, C:0.15, G:0.18, T:0.24
Consensus pattern (24 bp):
AACATAATTCAGATCAGATATCAG
Found at i:30335 original size:21 final size:22
Alignment explanation
Indices: 30286--30332 Score: 78
Period size: 22 Copynumber: 2.2 Consensus size: 22
30276 TTCGGGTTCG
30286 AATTTGG-AAAACATACTTCAA
1 AATTTGGAAAAACATACTTCAA
*
30307 AATTTGGAAAAACATACTTCAG
1 AATTTGGAAAAACATACTTCAA
30329 AATT
1 AATT
30333 GGACCCAAGA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 7 0.29
22 17 0.71
ACGTcount: A:0.47, C:0.13, G:0.11, T:0.30
Consensus pattern (22 bp):
AATTTGGAAAAACATACTTCAA
Found at i:30809 original size:239 final size:239
Alignment explanation
Indices: 30374--30856 Score: 824
Period size: 239 Copynumber: 2.0 Consensus size: 239
30364 ACTTTCAAAA
30374 AATTTAACTTTTTGTCAAAGTCAACGATCAACAGTAAACGGGTCGAGTCGGGTCAAGCCGGGTCA
1 AATTTAACTTTTTGTCAAAGTCAACGATCAACAGTAAACGGGTCGAGTCGGGT--A--CGGGTCA
*
30439 ACTGCCCCCAATTGTTTTCGAACCTCCCCACGCGCAAGGGCGGCGCTGGGGGGCATGAACAGTGA
62 ACTGCCCCCAATTGTTTTCGAACCTCCCCACGCGCAAGGCCGGCGCTGGGGGGCATGAACAGTGA
* * * *
30504 TATGGTGTCTGAAAATTTTCAAAAAATATTTTATGGCATTTTGAGACACTTACCAAGCTCGGTTC
127 TACGGTGTCCGAAAAATTTCAAAAAATATTTTATGGCAATTTGAGACACTTACCAAGCTCGGTTC
*
30569 ACAATTTTGAACGGTGGAGAGCTCGATTCCGAAACATCGGAAACTTTG
192 ACAATTTTGAACGGTGGAGAGCTCGATTCCGAAACATCGAAAACTTTG
* *
30617 AATTTAACTTTTTGTCAAAGTCAATGGTCAACAGTAAACGGGTCGAGTCGGGT-CGGGTCAACTG
1 AATTTAACTTTTTGTCAAAGTCAACGATCAACAGTAAACGGGTCGAGTCGGGTACGGGTCAACTG
*
30681 CCCCCAATTGTTTTCGAACCTCCCCACGCGCAAGGCCGGCGCTGGGGGCGCATGAACAGTGCTAC
66 CCCCCAATTGTTTTCGAACCTCCCCACGCGCAAGGCCGGCGCTGGGGG-GCATGAACAGTGATAC
*
30746 GGTGTCCGAAAAATTTCAAAAAATATTTTATGGCAATTTGAGACACTTACCAAGCTTGGTTCACA
130 GGTGTCCGAAAAATTTCAAAAAATATTTTATGGCAATTTGAGACACTTACCAAGCTCGGTTCACA
30811 ATTTTGAACGGTGGAGAGCTCGATTCCGAAACATCGAAAACTTTG
195 ATTTTGAACGGTGGAGAGCTCGATTCCGAAACATCGAAAACTTTG
30856 A
1 A
30857 CTTCCTCACT
Statistics
Matches: 229, Mismatches: 10, Indels: 6
0.93 0.04 0.02
Matches are distributed among these distances:
238 58 0.25
239 120 0.52
243 51 0.22
ACGTcount: A:0.28, C:0.22, G:0.24, T:0.26
Consensus pattern (239 bp):
AATTTAACTTTTTGTCAAAGTCAACGATCAACAGTAAACGGGTCGAGTCGGGTACGGGTCAACTG
CCCCCAATTGTTTTCGAACCTCCCCACGCGCAAGGCCGGCGCTGGGGGGCATGAACAGTGATACG
GTGTCCGAAAAATTTCAAAAAATATTTTATGGCAATTTGAGACACTTACCAAGCTCGGTTCACAA
TTTTGAACGGTGGAGAGCTCGATTCCGAAACATCGAAAACTTTG
Found at i:31898 original size:37 final size:36
Alignment explanation
Indices: 31830--31900 Score: 88
Period size: 37 Copynumber: 1.9 Consensus size: 36
31820 CATTTTGAAG
* **
31830 TTAAAAGAAATAATTTAGATTATTATGGTGAAATAA
1 TTAAAAGAAATAATTTAGAATATTACAGTGAAATAA
* *
31866 TTAAATAGTAATAATTTAGAATGTTACAGTGAAAT
1 TTAAA-AGAAATAATTTAGAATATTACAGTGAAAT
31901 GATTTAAGAA
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
36 5 0.17
37 24 0.83
ACGTcount: A:0.48, C:0.01, G:0.14, T:0.37
Consensus pattern (36 bp):
TTAAAAGAAATAATTTAGAATATTACAGTGAAATAA
Found at i:31984 original size:21 final size:24
Alignment explanation
Indices: 31958--32003 Score: 69
Period size: 22 Copynumber: 2.0 Consensus size: 24
31948 AATTAGGAAT
*
31958 AAAAAATCTA-ATATAA-AATAAA
1 AAAAAATATATATATAATAATAAA
31980 AAAAAATATATATATAATAATAAA
1 AAAAAATATATATATAATAATAAA
32004 CATGGTACTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
22 9 0.43
23 6 0.29
24 6 0.29
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (24 bp):
AAAAAATATATATATAATAATAAA
Found at i:32224 original size:2 final size:2
Alignment explanation
Indices: 32217--32259 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
32207 TTATTAATTG
32217 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
32259 A
1 A
32260 CTATTATTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:34178 original size:14 final size:15
Alignment explanation
Indices: 34161--34197 Score: 51
Period size: 14 Copynumber: 2.6 Consensus size: 15
34151 GATTGGGTTA
*
34161 AACATAAAT-AAATG
1 AACATAAATCAAACG
34175 AACAT-AATCAAACG
1 AACATAAATCAAACG
34189 AACATAAAT
1 AACATAAAT
34198 GAACATAACC
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
13 3 0.15
14 14 0.70
15 3 0.15
ACGTcount: A:0.62, C:0.14, G:0.05, T:0.19
Consensus pattern (15 bp):
AACATAAATCAAACG
Found at i:40047 original size:2 final size:2
Alignment explanation
Indices: 40040--40075 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
40030 TTTGTATTAG
40040 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
40076 TTTGTAATTA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42193 original size:18 final size:19
Alignment explanation
Indices: 42160--42195 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
42150 GTATAAGCAT
*
42160 AAAATATTATAATAATTAC
1 AAAATAGTATAATAATTAC
42179 AAAATAGTA-AATAATTA
1 AAAATAGTATAATAATTA
42196 GCATCAAAGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 8 0.50
19 8 0.50
ACGTcount: A:0.61, C:0.03, G:0.03, T:0.33
Consensus pattern (19 bp):
AAAATAGTATAATAATTAC
Found at i:44069 original size:21 final size:21
Alignment explanation
Indices: 44045--44154 Score: 61
Period size: 21 Copynumber: 5.3 Consensus size: 21
44035 GAAGTTCGCA
44045 TTGCGATTTATTCCAAATTCG
1 TTGCGATTTATTCCAAATTCG
** * *
44066 TTGCGA--TAGGCGAAGTTCGTG
1 TTGCGATTTATTCCAAATTC--G
*
44087 TTGCGATTCATTCCAAA-TCG
1 TTGCGATTTATTCCAAATTCG
* * *
44107 TTGCGA--TAGTCGAAGTTCGCG
1 TTGCGATTTATTCCAAATT--CG
*
44128 TTGCGATTCATTCCAAA-TCG
1 TTGCGATTTATTCCAAATTCG
44148 TTGCGAT
1 TTGCGAT
44155 AGGCGAAGTT
Statistics
Matches: 63, Mismatches: 17, Indels: 19
0.64 0.17 0.19
Matches are distributed among these distances:
18 5 0.08
19 9 0.14
20 16 0.25
21 21 0.33
22 3 0.05
23 9 0.14
ACGTcount: A:0.22, C:0.20, G:0.24, T:0.35
Consensus pattern (21 bp):
TTGCGATTTATTCCAAATTCG
Found at i:44111 original size:20 final size:20
Alignment explanation
Indices: 44086--44154 Score: 70
Period size: 20 Copynumber: 3.4 Consensus size: 20
44076 CGAAGTTCGT
44086 GTTGCGATTCATTCCAAATC
1 GTTGCGATTCATTCCAAATC
* * *
44106 GTTGCGA-T-AGTCGAAGTTCGC
1 GTTGCGATTCATTCCAA-AT--C
44127 GTTGCGATTCATTCCAAATC
1 GTTGCGATTCATTCCAAATC
44147 GTTGCGAT
1 GTTGCGAT
44155 AGGCGAAGTT
Statistics
Matches: 38, Mismatches: 6, Indels: 10
0.70 0.11 0.19
Matches are distributed among these distances:
18 5 0.13
19 2 0.05
20 16 0.42
21 8 0.21
22 2 0.05
23 5 0.13
ACGTcount: A:0.22, C:0.22, G:0.23, T:0.33
Consensus pattern (20 bp):
GTTGCGATTCATTCCAAATC
Found at i:44121 original size:41 final size:41
Alignment explanation
Indices: 44029--44267 Score: 390
Period size: 41 Copynumber: 5.8 Consensus size: 41
44019 TCGCAACGCA
* * *
44029 ATAGTCGAAGTTCGCATTGCGATTTATTCCAAATTCGTTGCG
1 ATAGGCGAAGTTCGCGTTGCGATTCATTCCAAA-TCGTTGCG
*
44071 ATAGGCGAAGTTCGTGTTGCGATTCATTCCAAATCGTTGCG
1 ATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTTGCG
*
44112 ATAGTCGAAGTTCGCGTTGCGATTCATTCCAAATCGTTGCG
1 ATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTTGCG
*
44153 ATAGGCGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCG
1 ATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTTGCG
*
44194 ATAGGCGAAGTTCGCGTTGCGATTCATTCCAATTCGTTGCG
1 ATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTTGCG
*
44235 ATAGGCGAAGTTCGCGTTGCGATTC-GTCCAAAT
1 ATAGGCGAAGTTCGCGTTGCGATTCATTCCAAAT
44268 ATTGCATTTG
Statistics
Matches: 187, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
40 6 0.03
41 152 0.81
42 29 0.16
ACGTcount: A:0.22, C:0.21, G:0.26, T:0.32
Consensus pattern (41 bp):
ATAGGCGAAGTTCGCGTTGCGATTCATTCCAAATCGTTGCG
Found at i:44172 original size:21 final size:21
Alignment explanation
Indices: 44146--44257 Score: 92
Period size: 21 Copynumber: 5.4 Consensus size: 21
44136 CATTCCAAAT
44146 CGTTGCGATAGGCGAAGTTCG
1 CGTTGCGATAGGCGAAGTTCG
** *
44167 CGTTGCGATTCATTCCAA-TT--
1 CGTTGCGA-T-AGGCGAAGTTCG
44187 CGTTGCGATAGGCGAAGTTCG
1 CGTTGCGATAGGCGAAGTTCG
** *
44208 CGTTGCGATTCATTCCAA-TT--
1 CGTTGCGA-T-AGGCGAAGTTCG
44228 CGTTGCGATAGGCGAAGTTCG
1 CGTTGCGATAGGCGAAGTTCG
44249 CGTTGCGAT
1 CGTTGCGAT
44258 TCGTCCAAAT
Statistics
Matches: 69, Mismatches: 12, Indels: 20
0.68 0.12 0.20
Matches are distributed among these distances:
18 8 0.12
19 6 0.09
20 16 0.23
21 25 0.36
22 6 0.09
23 8 0.12
ACGTcount: A:0.19, C:0.21, G:0.29, T:0.30
Consensus pattern (21 bp):
CGTTGCGATAGGCGAAGTTCG
Found at i:45060 original size:6 final size:6
Alignment explanation
Indices: 45049--45088 Score: 62
Period size: 6 Copynumber: 6.7 Consensus size: 6
45039 GTCGTGTCAT
* *
45049 GTCGTG GTCGTG GTCGTG GTCATG GTCATG GTCGTG GTCG
1 GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCGTG GTCG
45089 CAACGAATTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.05, C:0.17, G:0.45, T:0.33
Consensus pattern (6 bp):
GTCGTG
Found at i:45150 original size:41 final size:41
Alignment explanation
Indices: 45085--45329 Score: 400
Period size: 41 Copynumber: 5.9 Consensus size: 41
45075 CATGGTCGTG
45085 GTCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCT
1 GTCGCAACGAA-TTGGAATGAATCGCAACGCGAACTTCGCCT
* * *
45127 GTCGCAACGAATTGGAATGAATCGGAATGCGAACTTCGCAT
1 GTCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGCCT
45168 GTCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCT
1 GTCGCAACGAA-TTGGAATGAATCGCAACGCGAACTTCGCCT
*
45210 GTCGCAACGAATTGGAATGAATCGCAATGCGAACTTCGCCT
1 GTCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGCCT
* * *
45251 GTCGCAACAAATTGGAATGAATCGCAATGCGAACTTCACCT
1 GTCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGCCT
*
45292 GTCGCAACGATTTGGAATGAATCGCAACGCGAACTTCG
1 GTCGCAACGAATTGGAATGAATCGCAACGCGAACTTCG
45330 ACTATCGCGT
Statistics
Matches: 189, Mismatches: 13, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
41 140 0.74
42 49 0.26
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (41 bp):
GTCGCAACGAATTGGAATGAATCGCAACGCGAACTTCGCCT
Found at i:45224 original size:83 final size:83
Alignment explanation
Indices: 45085--45329 Score: 420
Period size: 83 Copynumber: 3.0 Consensus size: 83
45075 CATGGTCGTG
45085 GTCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTGTCGCAACGAATTGGAATGAATC
1 GTCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTGTCGCAACGAATTGGAATGAATC
*
45150 GGAATGCGAACTTCGCAT
66 GCAATGCGAACTTCGCAT
45168 GTCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTGTCGCAACGAATTGGAATGAATC
1 GTCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTGTCGCAACGAATTGGAATGAATC
*
45233 GCAATGCGAACTTCGCCT
66 GCAATGCGAACTTCGCAT
* * * *
45251 GTCGCAAC-AAATTGGAATGAATCGCAATGCGAACTTCACCTGTCGCAACGATTTGGAATGAATC
1 GTCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTGTCGCAACGAATTGGAATGAATC
*
45315 GCAACGCGAACTTCG
66 GCAATGCGAACTTCG
45330 ACTATCGCGT
Statistics
Matches: 155, Mismatches: 7, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
82 66 0.43
83 89 0.57
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (83 bp):
GTCGCAACGAATTTGGAATGAATCGCAACGCGAACTTCGCCTGTCGCAACGAATTGGAATGAATC
GCAATGCGAACTTCGCAT
Found at i:52858 original size:14 final size:14
Alignment explanation
Indices: 52839--52866 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
52829 TTCATCTTTT
52839 TAGAGAGTGAAAAG
1 TAGAGAGTGAAAAG
52853 TAGAGAGTGAAAAG
1 TAGAGAGTGAAAAG
52867 ACTTGCACTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.00, G:0.36, T:0.14
Consensus pattern (14 bp):
TAGAGAGTGAAAAG
Found at i:60822 original size:13 final size:13
Alignment explanation
Indices: 60806--60831 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
60796 TCTTTATTTT
60806 CTCCTATTACATG
1 CTCCTATTACATG
60819 CTCCTATTACATG
1 CTCCTATTACATG
60832 TGTTAAGGTT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.08, T:0.38
Consensus pattern (13 bp):
CTCCTATTACATG
Found at i:66105 original size:18 final size:18
Alignment explanation
Indices: 66082--66118 Score: 74
Period size: 18 Copynumber: 2.1 Consensus size: 18
66072 AAAGGAATAC
66082 TAACAATAGGGTAAGAGA
1 TAACAATAGGGTAAGAGA
66100 TAACAATAGGGTAAGAGA
1 TAACAATAGGGTAAGAGA
66118 T
1 T
66119 TATCTTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.49, C:0.05, G:0.27, T:0.19
Consensus pattern (18 bp):
TAACAATAGGGTAAGAGA
Done.