Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000296.1 Hibiscus syriacus cultivar Beakdansim tig00000545_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: 216456
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 2 of 2
Found at i:191847 original size:108 final size:108
Alignment explanation
Indices: 191685--192204 Score: 692
Period size: 108 Copynumber: 4.9 Consensus size: 108
191675 CAACCTCGAG
* * * * *
191685 CTTAGCCTACATGGAAGAGTAGTGAAGTAAAGCCATCTTAGCCTCTACAGAAGAGTAGTGAAGCA
1 CTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCCATCTTAGCCTCCACGGAAGAGTAGTGAAGCA
*
191750 AAGCAATCTTATCCTCCACGGAAGAGTAGTGAAGCAAAGCAAT
66 AAGCAATCTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAAT
* * * * *
191793 CTTAACCTCGACGGAAGAGTAATGAAGCAAATCAATCTTAGCCTCCACGGAAGAGTAGTGAAGCA
1 CTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCCATCTTAGCCTCCACGGAAGAGTAGTGAAGCA
*
191858 AAGCAATCTTAGCCTCCACGGAAGAGTAGTGAAGCAAAACAAT
66 AAGCAATCTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAAT
* *
191901 CTTAGCCTCCACGAAAGAGTAGTGAAGCAAAGCAATCTTAGCCTCCACGGAAGAGTAGTGAAGCA
1 CTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCCATCTTAGCCTCCACGGAAGAGTAGTGAAGCA
* * *
191966 AAACAATCTTAGCCTCCATGAAAGAGTAGTGAAGCAAAGCAAT
66 AAGCAATCTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAAT
* * *
192009 CTTAGCCTTCACAGAAGAGTAGTGAAGCAAAGCCACCTTAGCCTCCACGGAAGAGTAGTGAAG--
1 CTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCCATCTTAGCCTCCACGGAAGAGTAGTGAAGCA
* *
192072 -A--AA----AGGCT--A---AAGAGTAGTGAAGCAAAGCCAT
66 AAGCAATCTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAAT
* * *
192103 TTTAGCCTCCACGGAAGAGTATTG-AGACAAAGCCATCTTAGCCTCCACGAAAGAGTAGTGAAGC
1 CTTAGCCTCCACGGAAGAGTAGTGAAG-CAAAGCCATCTTAGCCTCCACGGAAGAGTAGTGAAGC
*
192167 AAAGCCATCTTAGCCTCCACGGAAGAGTAGTGAAGCAA
65 AAAGCAATCTTAGCCTCCACGGAAGAGTAGTGAAGCAA
192205 GAACAGATTA
Statistics
Matches: 361, Mismatches: 36, Indels: 30
0.85 0.08 0.07
Matches are distributed among these distances:
93 2 0.01
94 75 0.21
97 2 0.01
99 5 0.01
103 6 0.02
105 2 0.01
108 269 0.75
ACGTcount: A:0.38, C:0.21, G:0.23, T:0.18
Consensus pattern (108 bp):
CTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCCATCTTAGCCTCCACGGAAGAGTAGTGAAGCA
AAGCAATCTTAGCCTCCACGGAAGAGTAGTGAAGCAAAGCAAT
Found at i:192134 original size:36 final size:36
Alignment explanation
Indices: 192081--192204 Score: 205
Period size: 36 Copynumber: 3.4 Consensus size: 36
192071 GAAAAGGCTA
*
192081 AAGAGTAGTGAAGCAAAGCCATTTTAGCCTCCACGG
1 AAGAGTAGTGAAGCAAAGCCATCTTAGCCTCCACGG
* *
192117 AAGAGTATTG-AGACAAAGCCATCTTAGCCTCCACGA
1 AAGAGTAGTGAAG-CAAAGCCATCTTAGCCTCCACGG
192153 AAGAGTAGTGAAGCAAAGCCATCTTAGCCTCCACGG
1 AAGAGTAGTGAAGCAAAGCCATCTTAGCCTCCACGG
192189 AAGAGTAGTGAAGCAA
1 AAGAGTAGTGAAGCAA
192205 GAACAGATTA
Statistics
Matches: 81, Mismatches: 5, Indels: 4
0.90 0.06 0.04
Matches are distributed among these distances:
35 2 0.02
36 77 0.95
37 2 0.02
ACGTcount: A:0.36, C:0.22, G:0.24, T:0.18
Consensus pattern (36 bp):
AAGAGTAGTGAAGCAAAGCCATCTTAGCCTCCACGG
Found at i:192147 original size:94 final size:94
Alignment explanation
Indices: 191986--192170 Score: 282
Period size: 94 Copynumber: 2.0 Consensus size: 94
191976 AGCCTCCATG
*
191986 AAAGAGTAGTGAAGCAAAGCAATCTTAGCCTTCACAGAAGAGTAGTGAAGCAAAGCCACCTTAGC
1 AAAGAGTAGTGAAGCAAAGCAATCTTAGCCTCCACAGAAGAGTAGTGAAGCAAAGCCACCTTAGC
*
192051 CTCCACGGAAGAGTAGTGAAGAAAAGGCT
66 CTCCACGAAAGAGTAGTGAAGAAAAGGCT
* * * * *
192080 AAAGAGTAGTGAAGCAAAGCCATTTTAGCCTCCACGGAAGAGTATTG-AGACAAAGCCATCTTAG
1 AAAGAGTAGTGAAGCAAAGCAATCTTAGCCTCCACAGAAGAGTAGTGAAG-CAAAGCCACCTTAG
*
192144 CCTCCACGAAAGAGTAGTGAAGCAAAG
65 CCTCCACGAAAGAGTAGTGAAGAAAAG
192171 CCATCTTAGC
Statistics
Matches: 82, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
93 2 0.02
94 80 0.98
ACGTcount: A:0.39, C:0.19, G:0.25, T:0.17
Consensus pattern (94 bp):
AAAGAGTAGTGAAGCAAAGCAATCTTAGCCTCCACAGAAGAGTAGTGAAGCAAAGCCACCTTAGC
CTCCACGAAAGAGTAGTGAAGAAAAGGCT
Found at i:192184 original size:130 final size:130
Alignment explanation
Indices: 191951--192201 Score: 389
Period size: 130 Copynumber: 1.9 Consensus size: 130
191941 GCCTCCACGG
*
191951 AAGAGTAGTGAAGCAAAACAATCTTAGCCTCCATGAAAGAGTAGTGAAGCAAAGCAATCTTAGCC
1 AAGAGTAGTGAAGCAAAACAATCTTAGCCTCCACGAAAGAGTAGTGAAGCAAAGCAATCTTAGCC
*
192016 TTCACAGAAGAGTAGTGAAGCAAAGCCACCTTAGCCTCCACGGAAGAGTAGTGAAGAAAAGGCTA
66 TCCACAGAAGAGTAGTGAAGCAAAGCCACCTTAGCCTCCACGGAAGAGTAGTGAAGAAAAGGCTA
* * * * * *
192081 AAGAGTAGTGAAGCAAAGCCATTTTAGCCTCCACGGAAGAGTATTG-AGACAAAGCCATCTTAGC
1 AAGAGTAGTGAAGCAAAACAATCTTAGCCTCCACGAAAGAGTAGTGAAG-CAAAGCAATCTTAGC
*
192145 CTCCAC-GAAAGAGTAGTGAAGCAAAGCCATCTTAGCCTCCACGGAAGAGTAGTGAAG
65 CTCCACAG-AAGAGTAGTGAAGCAAAGCCACCTTAGCCTCCACGGAAGAGTAGTGAAG
192202 CAAGAACAGA
Statistics
Matches: 110, Mismatches: 9, Indels: 4
0.89 0.07 0.03
Matches are distributed among these distances:
129 3 0.03
130 107 0.97
ACGTcount: A:0.38, C:0.20, G:0.24, T:0.18
Consensus pattern (130 bp):
AAGAGTAGTGAAGCAAAACAATCTTAGCCTCCACGAAAGAGTAGTGAAGCAAAGCAATCTTAGCC
TCCACAGAAGAGTAGTGAAGCAAAGCCACCTTAGCCTCCACGGAAGAGTAGTGAAGAAAAGGCTA
Found at i:196472 original size:17 final size:18
Alignment explanation
Indices: 196450--196484 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
196440 ACACACTAAA
196450 TCGGTT-TCGGTTTTTTT
1 TCGGTTATCGGTTTTTTT
196467 TCGGTTATCGGTTTTTTT
1 TCGGTTATCGGTTTTTTT
196485 AGATCAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 6 0.35
18 11 0.65
ACGTcount: A:0.03, C:0.11, G:0.23, T:0.63
Consensus pattern (18 bp):
TCGGTTATCGGTTTTTTT
Found at i:201119 original size:28 final size:28
Alignment explanation
Indices: 201082--201136 Score: 101
Period size: 28 Copynumber: 2.0 Consensus size: 28
201072 CTATAATACA
201082 TGTTAGAATTTGTTATCAAAATTTTATG
1 TGTTAGAATTTGTTATCAAAATTTTATG
*
201110 TGTTAGAATTTGTTATCAAATTTTTAT
1 TGTTAGAATTTGTTATCAAAATTTTAT
201137 ATTAATCTCG
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.31, C:0.04, G:0.13, T:0.53
Consensus pattern (28 bp):
TGTTAGAATTTGTTATCAAAATTTTATG
Found at i:201775 original size:10 final size:10
Alignment explanation
Indices: 201760--201786 Score: 54
Period size: 10 Copynumber: 2.7 Consensus size: 10
201750 AATTGTCACT
201760 TAGCTCCTGC
1 TAGCTCCTGC
201770 TAGCTCCTGC
1 TAGCTCCTGC
201780 TAGCTCC
1 TAGCTCC
201787 AACTGTTGTG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 17 1.00
ACGTcount: A:0.11, C:0.41, G:0.19, T:0.30
Consensus pattern (10 bp):
TAGCTCCTGC
Found at i:202180 original size:32 final size:32
Alignment explanation
Indices: 202130--202231 Score: 96
Period size: 32 Copynumber: 3.2 Consensus size: 32
202120 TCCATTCGAA
* * *
202130 TTAATTTCTATTTGGGTTGCTTTCGGATAGGG
1 TTAAATTCGATTTAGGTTGCTTTCGGATAGGG
* * *
202162 TTAAATTCGATTTAGGTTGCTTTCAGATCGGT
1 TTAAATTCGATTTAGGTTGCTTTCGGATAGGG
* * * * *
202194 TTAAATTTGGTTCAGGTTTCTTTCGGTTAGGTG
1 TTAAATTCGATTTAGGTTGCTTTCGGATAGG-G
202227 TTAAA
1 TTAAA
202232 ATTTGGTTCG
Statistics
Matches: 55, Mismatches: 14, Indels: 1
0.79 0.20 0.01
Matches are distributed among these distances:
32 50 0.91
33 5 0.09
ACGTcount: A:0.20, C:0.10, G:0.25, T:0.46
Consensus pattern (32 bp):
TTAAATTCGATTTAGGTTGCTTTCGGATAGGG
Found at i:202295 original size:32 final size:33
Alignment explanation
Indices: 202259--202343 Score: 120
Period size: 32 Copynumber: 2.6 Consensus size: 33
202249 TTCAGTTCGA
202259 GTTGCTTTCGGTTCAGGTTAGC-TTAGGTTTAG
1 GTTGCTTTCGGTTCAGGTTAGCTTTAGGTTTAG
* *
202291 GTTGCTTTCGGTTCAGGTT-GCTTTCGGTTTGG
1 GTTGCTTTCGGTTCAGGTTAGCTTTAGGTTTAG
* *
202323 GTTGCTTTCGCTTCGGGTTAG
1 GTTGCTTTCGGTTCAGGTTAG
202344 TTTCGATTTT
Statistics
Matches: 47, Mismatches: 4, Indels: 3
0.87 0.07 0.06
Matches are distributed among these distances:
31 2 0.04
32 44 0.94
33 1 0.02
ACGTcount: A:0.07, C:0.15, G:0.33, T:0.45
Consensus pattern (33 bp):
GTTGCTTTCGGTTCAGGTTAGCTTTAGGTTTAG
Found at i:202340 original size:16 final size:16
Alignment explanation
Indices: 202236--202341 Score: 97
Period size: 16 Copynumber: 6.6 Consensus size: 16
202226 GTTAAAATTT
* *
202236 GGTTCGAGTTTCTTTC
1 GGTTCGGGTTGCTTTC
* *
202252 AGTTCGAGTTGCTTTC
1 GGTTCGGGTTGCTTTC
* *
202268 GGTTCAGGTTAGC-TTA
1 GGTTCGGGTT-GCTTTC
**
202284 GGTTTAGGTTGCTTTC
1 GGTTCGGGTTGCTTTC
*
202300 GGTTCAGGTTGCTTTC
1 GGTTCGGGTTGCTTTC
*
202316 GGTTTGGGTTGCTTTC
1 GGTTCGGGTTGCTTTC
*
202332 GCTTCGGGTT
1 GGTTCGGGTT
202342 AGTTTCGATT
Statistics
Matches: 75, Mismatches: 13, Indels: 4
0.82 0.14 0.04
Matches are distributed among these distances:
15 2 0.03
16 71 0.95
17 2 0.03
ACGTcount: A:0.08, C:0.16, G:0.31, T:0.45
Consensus pattern (16 bp):
GGTTCGGGTTGCTTTC
Found at i:202348 original size:32 final size:32
Alignment explanation
Indices: 202259--202357 Score: 119
Period size: 32 Copynumber: 3.1 Consensus size: 32
202249 TTCAGTTCGA
* *
202259 GTTGCTTTCGGTTCAGGTTAGCTTAGGTTTAG
1 GTTGCTTTCGGTTCAGGTTAGTTTCGGTTTAG
*
202291 GTTGCTTTCGGTTCAGGTT-GCTTTCGGTTTGG
1 GTTGCTTTCGGTTCAGGTTAG-TTTCGGTTTAG
* * * *
202323 GTTGCTTTCGCTTCGGGTTAGTTTCGATTTTG
1 GTTGCTTTCGGTTCAGGTTAGTTTCGGTTTAG
202355 GTT
1 GTT
202358 TGGGTTAATT
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
31 1 0.02
32 56 0.97
33 1 0.02
ACGTcount: A:0.07, C:0.14, G:0.31, T:0.47
Consensus pattern (32 bp):
GTTGCTTTCGGTTCAGGTTAGTTTCGGTTTAG
Found at i:202358 original size:38 final size:39
Alignment explanation
Indices: 202316--202391 Score: 102
Period size: 38 Copynumber: 2.0 Consensus size: 39
202306 GGTTGCTTTC
** *
202316 GGTTTGGGTTGCTTTC-GCTTCGGGTTAGTTTC-GATTTT
1 GGTTTGGGTTAATTTCTG-TTCGGGTTACTTTCAGATTTT
202354 GGTTTGGGTTAATTTCTGTTCGGGTTACTTTCAGATTT
1 GGTTTGGGTTAATTTCTGTTCGGGTTACTTTCAGATTT
202392 GCTAAATTTT
Statistics
Matches: 33, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
38 27 0.82
39 6 0.18
ACGTcount: A:0.09, C:0.12, G:0.29, T:0.50
Consensus pattern (39 bp):
GGTTTGGGTTAATTTCTGTTCGGGTTACTTTCAGATTTT
Found at i:203737 original size:32 final size:32
Alignment explanation
Indices: 203698--203760 Score: 117
Period size: 32 Copynumber: 2.0 Consensus size: 32
203688 TCTATTGTAC
203698 TGGATTGATGCAATTATACATGCATAACTGAT
1 TGGATTGATGCAATTATACATGCATAACTGAT
*
203730 TGGATTGATGCAATTTTACATGCATAACTGA
1 TGGATTGATGCAATTATACATGCATAACTGA
203761 GGGCCCTAAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 30 1.00
ACGTcount: A:0.33, C:0.13, G:0.19, T:0.35
Consensus pattern (32 bp):
TGGATTGATGCAATTATACATGCATAACTGAT
Found at i:204706 original size:54 final size:54
Alignment explanation
Indices: 204673--205143 Score: 653
Period size: 54 Copynumber: 8.8 Consensus size: 54
204663 AATACGGTCG
* * ** ** * *
204673 TTCATAAACACATTATGAATTTCGTGGGTTGCACACTTAATGACAATACGAAAA
1 TTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAA
* *
204727 TTCATAAACTCATTATGAATTTTTTAAGTTGCACACACAGTGCCAATACGGAAA
1 TTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAA
* * *
204781 TTCATAAACTTATTATGAATTTCTTAAGTTGCACATATAGTGCCAATACGAAAA
1 TTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAA
* *
204835 TTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAGTTCCAATAC--AAA
1 TTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAA
*
204887 TTCATAAACTCATTATGAATTTCTTAAGTTTCACACACAGTGCCAATAC-ATAAA
1 TTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGA-AAA
* * * *
204941 TTAATAAACTTATTATGAATTTCTTAAGTTGCACACAGAGTGTCAATACGAAAA
1 TTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAA
* * *
204995 TTCATAAACTTATTATGAATTTCTTATGTTGCACACACAGTGCCAATACGGAAA
1 TTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAA
**
205049 TTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTATCAATACG-AAA
1 TTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAA
* * *
205102 TTCATAAACTTATTATGAATTTCTTAAATTGCACACATAGTG
1 TTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTG
205144 TCCATTTGGT
Statistics
Matches: 375, Mismatches: 39, Indels: 7
0.89 0.09 0.02
Matches are distributed among these distances:
52 49 0.13
53 41 0.11
54 284 0.76
55 1 0.00
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (54 bp):
TTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAA
Found at i:204928 original size:160 final size:160
Alignment explanation
Indices: 204648--205143 Score: 715
Period size: 160 Copynumber: 3.1 Consensus size: 160
204638 TTCTCTGGGC
* **** ** * ** ** *
204648 TGCACACGTAGTGCCAATACGGTCGTTCATAAACACATTATGAATTTCGTGGGTTGCACACTTAA
1 TGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAG
* *
204713 TGACAATACGAAAATTCATAAACTCATTATGAATTTTTTAAGTTGCACACACAGTGCCAATACGG
66 TGCCAATACG-AAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTGCCAATAC-G
204778 AAATTCATAAACTTATTATGAATTTCTTAAGT
129 AAATTCATAAACTTATTATGAATTTCTTAAGT
*
204810 TGCACATATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAG
1 TGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAG
* * *
204875 TTCCAATAC-AAATTCATAAACTCATTATGAATTTCTTAAGTTTCACACACAGTGCCAATACATA
66 TGCCAATACGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTGCCAATAC-GA
*
204939 AATTAATAAACTTATTATGAATTTCTTAAGT
130 AATTCATAAACTTATTATGAATTTCTTAAGT
* * *
204970 TGCACACAGAGTGTCAATACGAAAATTCATAAACTTATTATGAATTTCTTATGTTGCACACACAG
1 TGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAG
**
205035 TGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTATCAATACGA
66 TGCCAATAC-GAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGA
*
205100 AATTCATAAACTTATTATGAATTTCTTAAAT
130 AATTCATAAACTTATTATGAATTTCTTAAGT
205131 TGCACACATAGTG
1 TGCACACATAGTG
205144 TCCATTTGGT
Statistics
Matches: 299, Mismatches: 33, Indels: 5
0.89 0.10 0.01
Matches are distributed among these distances:
160 150 0.50
161 42 0.14
162 107 0.36
ACGTcount: A:0.38, C:0.18, G:0.12, T:0.33
Consensus pattern (160 bp):
TGCACACATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCACACACAG
TGCCAATACGAAATTCATAAACTCATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAA
ATTCATAAACTTATTATGAATTTCTTAAGT
Found at i:205042 original size:214 final size:215
Alignment explanation
Indices: 204673--205143 Score: 705
Period size: 214 Copynumber: 2.2 Consensus size: 215
204663 AATACGGTCG
* * ** * * *
204673 TTCATAAACACATTATGAATTTCGTGGGTTGCACACTTAATGACAATACGAAAATTCATAAACTC
1 TTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGACAATACGAAAATTAATAAACTC
* *
204738 ATTATGAATTTTTTAAGTTGCACACACAGTGCCAATACGGAAATTCATAAACTTATTATGAATTT
66 ATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTT
* * *
204803 CTTAAGTTGCACATATAGTGCCAATACGAAAATTCATAAACTTATTATGAATTTCTTAAGTTGCA
131 CTTAAGTTGCACACACAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCA
204868 CACACAGT-TCCAATAC-AAA
196 CACACAGTAT-CAATACGAAA
* * *
204887 TTCATAAACTCATTATGAATTTCTTAAGTTTCACACACAGTGCCAATAC-ATAAATTAATAAACT
1 TTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGACAATACGA-AAATTAATAAACT
* * *
204951 TATTATGAATTTCTTAAGTTGCACACAGAGTGTCAATACGAAAATTCATAAACTTATTATGAATT
65 CATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATT
* *
205016 TCTTATGTTGCACACACAGTGCCAATACGGAAATTCATAAACTCATTATGAATTTCTTAAGTTGC
130 TCTTAAGTTGCACACACAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGC
205081 ACACACAGTATCAATACGAAA
195 ACACACAGTATCAATACGAAA
* *
205102 TTCATAAACTTATTATGAATTTCTTAAATTGCACACATAGTG
1 TTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTG
205144 TCCATTTGGT
Statistics
Matches: 230, Mismatches: 24, Indels: 5
0.89 0.09 0.02
Matches are distributed among these distances:
213 1 0.00
214 187 0.81
215 42 0.18
ACGTcount: A:0.38, C:0.17, G:0.11, T:0.34
Consensus pattern (215 bp):
TTCATAAACTCATTATGAATTTCTTAAGTTGCACACATAGTGACAATACGAAAATTAATAAACTC
ATTATGAATTTCTTAAGTTGCACACACAGTGCCAATACGAAAATTCATAAACTTATTATGAATTT
CTTAAGTTGCACACACAGTGCCAATACGAAAATTCATAAACTCATTATGAATTTCTTAAGTTGCA
CACACAGTATCAATACGAAA
Found at i:205581 original size:26 final size:26
Alignment explanation
Indices: 205552--205658 Score: 184
Period size: 26 Copynumber: 4.2 Consensus size: 26
205542 TTCTGAATCT
205552 ATGATATCGATACCTTCCTCATAGTA
1 ATGATATCGATACCTTCCTCATAGTA
*
205578 ATGATATCGAGACCTTCCTCATAGTA
1 ATGATATCGATACCTTCCTCATAGTA
205604 ATGATATCGATACCTTCCTCATAGTA
1 ATGATATCGATACCTTCCTCATAGTA
205630 ATGATAT-GATACCTTCCTCATA--A
1 ATGATATCGATACCTTCCTCATAGTA
205653 ATGATA
1 ATGATA
205659 CCCATAGTAA
Statistics
Matches: 79, Mismatches: 2, Indels: 3
0.94 0.02 0.04
Matches are distributed among these distances:
23 7 0.09
25 15 0.19
26 57 0.72
ACGTcount: A:0.33, C:0.21, G:0.12, T:0.34
Consensus pattern (26 bp):
ATGATATCGATACCTTCCTCATAGTA
Found at i:205688 original size:16 final size:15
Alignment explanation
Indices: 205652--205690 Score: 51
Period size: 15 Copynumber: 2.5 Consensus size: 15
205642 CTTCCTCATA
*
205652 AATGATACCCATAGT
1 AATGATACCCACAGT
205667 AATGATACCCACCAGT
1 AATGATACCCA-CAGT
*
205683 ATTGATAC
1 AATGATAC
205691 TAATTACATC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.38, C:0.23, G:0.13, T:0.26
Consensus pattern (15 bp):
AATGATACCCACAGT
Found at i:208197 original size:25 final size:25
Alignment explanation
Indices: 208158--208206 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
208148 ATCAAACATT
208158 TAAAATATTTTTATT-CAAAATCAG
1 TAAAATATTTTTATTGCAAAATCAG
* *
208182 TAAAATTTTGTTTATTGTAAAATCA
1 TAAAATATT-TTTATTGCAAAATCA
208207 TTAATTTTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 8 0.38
25 6 0.29
26 7 0.33
ACGTcount: A:0.43, C:0.06, G:0.06, T:0.45
Consensus pattern (25 bp):
TAAAATATTTTTATTGCAAAATCAG
Done.