Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004140.1 Hibiscus syriacus cultivar Beakdansim tig00009054_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: 61970
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:35 original size:20 final size:20
Alignment explanation
Indices: 9--279 Score: 339
Period size: 20 Copynumber: 13.7 Consensus size: 20
1 CAAATTCA
* *
9 CGTTGCGAATTTGACTTTTG
1 CGTTGCGAATTTGACTATCG
* * *
29 TGTTGCGAATTTGACTTTTG
1 CGTTGCGAATTTGACTATCG
* *
49 TGTTGTGAATTTGACTATCG
1 CGTTGCGAATTTGACTATCG
*
69 CGTTGCGAATTTGACTATTG
1 CGTTGCGAATTTGACTATCG
* * *
89 CGTTGCGAAATTGAAT-TTG
1 CGTTGCGAATTTGACTATCG
*
108 TGTTGCGAATTTGACTATCG
1 CGTTGCGAATTTGACTATCG
*
128 CGTTGCGAATTTGACTATCA
1 CGTTGCGAATTTGACTATCG
148 CGTTGCGAATTTGACTATCG
1 CGTTGCGAATTTGACTATCG
* * *
168 TGTTGCGAATTTGACTTTTG
1 CGTTGCGAATTTGACTATCG
*
188 CGTTGCGAATTTGACTTTCG
1 CGTTGCGAATTTGACTATCG
*
208 CGTTGCGAATTTGACT-TTG
1 CGTTGCGAATTTGACTATCG
*
227 TGTTGCGAATTTGACTATCG
1 CGTTGCGAATTTGACTATCG
247 CGTTGCGAATTTGACTATCG
1 CGTTGCGAATTTGACTATCG
* *
267 CATTGTGAATTTG
1 CGTTGCGAATTTG
280 GCTTATGTGT
Statistics
Matches: 222, Mismatches: 27, Indels: 4
0.88 0.11 0.02
Matches are distributed among these distances:
19 33 0.15
20 189 0.85
ACGTcount: A:0.19, C:0.15, G:0.25, T:0.41
Consensus pattern (20 bp):
CGTTGCGAATTTGACTATCG
Found at i:181 original size:99 final size:99
Alignment explanation
Indices: 9--279 Score: 391
Period size: 99 Copynumber: 2.7 Consensus size: 99
1 CAAATTCA
* * * *
9 CGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTTTTGTGTTGTGAATTTGACTATCGCGTTG
1 CGTTGCGAATTTGAC-TTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATCGCGTTG
74 CGAATTTGACTATTGCGTTGCGAAATTGAATTT-G
65 CGAATTTGACTATTGCGTTGCGAAATTGAATTTCG
* * * * *
108 TGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATCACGTTGCGAATTTGACTATCGTGTTG
1 CGTTGCGAATTTGACT-TTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATCGCGTTG
* * *
173 CGAATTTGACTTTTGCGTTGCGAATTTGACTTTCG
65 CGAATTTGACTATTGCGTTGCGAAATTGAATTTCG
* *
208 CGTTGCGAATTTGACTTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATCGCATTGT
1 CGTTGCGAATTTGACTTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATCGCGTTGC
273 GAATTTG
66 GAATTTG
280 GCTTATGTGT
Statistics
Matches: 151, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
98 1 0.01
99 134 0.89
100 16 0.11
ACGTcount: A:0.19, C:0.15, G:0.25, T:0.41
Consensus pattern (99 bp):
CGTTGCGAATTTGACTTTGTGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATCGCGTTGC
GAATTTGACTATTGCGTTGCGAAATTGAATTTCG
Found at i:227 original size:119 final size:118
Alignment explanation
Indices: 9--378 Score: 421
Period size: 119 Copynumber: 3.1 Consensus size: 118
1 CAAATTCA
* * * * *
9 CGTTGCGAATTTGACTTTTGTGTTGCGAATTTGACTTTTGTGTTGTGAATTTGACTATCGCGTTG
1 CGTTGCGAATTTGACTATCGCGTTGCGAATTTGAC-TATGTGTTGCGAATTTGACTATCGCGTTG
74 CGAATTTGACTATTGCGTTGCGAAATTGAATTTGTGTTGCGAATTTGACTATCG
65 CGAATTTGACTATTGCGTTGCGAAATTGAATTTGTGTTGCGAATTTGACTATCG
* * *
128 CGTTGCGAATTTGACTATCACGTTGCGAATTTGACTATCGTGTTGCGAATTTGACTTTTGCGTTG
1 CGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTAT-GTGTTGCGAATTTGACTATCGCGTTG
* *
193 CGAATTTGACT-TTCGCGTTGCGAATTTGACTTTGTGTTGCGAATTTGACTATCG
65 CGAATTTGACTATT-GCGTTGCGAAATTGAATTTGTGTTGCGAATTTGACTATCG
* * * *
247 CGTTGCGAATTTGACTATCGCATTGTGAATTTGGCTTATGTGTTGCG-ATTT-ACAAATTCGCGT
1 CGTTGCGAATTTGACTATCGCGTTGCGAATTTGAC-TATGTGTTGCGAATTTGAC-TA-TCGCGT
* ** * * *
310 TGCG-A-TT-ACAGATTCGCGTTGCGAAATTGGAAACTGGGTTGCGAAATTGGAGT-TCG
63 TGCGAATTTGAC-TATT-GCGTTGCGAAATT-GAATTTGTGTTGCG-AATTTGACTATCG
366 CGTTGCGAATTTG
1 CGTTGCGAATTTG
379 TTGGTCATTT
Statistics
Matches: 217, Mismatches: 25, Indels: 18
0.83 0.10 0.07
Matches are distributed among these distances:
116 2 0.01
117 4 0.02
118 24 0.11
119 177 0.82
120 10 0.05
ACGTcount: A:0.20, C:0.15, G:0.26, T:0.39
Consensus pattern (118 bp):
CGTTGCGAATTTGACTATCGCGTTGCGAATTTGACTATGTGTTGCGAATTTGACTATCGCGTTGC
GAATTTGACTATTGCGTTGCGAAATTGAATTTGTGTTGCGAATTTGACTATCG
Found at i:324 original size:19 final size:20
Alignment explanation
Indices: 288--333 Score: 76
Period size: 19 Copynumber: 2.4 Consensus size: 20
278 TGGCTTATGT
288 GTTGCGATTTACAAATTCGC
1 GTTGCGATTTACAAATTCGC
*
308 GTTGCGA-TTACAGATTCGC
1 GTTGCGATTTACAAATTCGC
327 GTTGCGA
1 GTTGCGA
334 AATTGGAAAC
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.33
Consensus pattern (20 bp):
GTTGCGATTTACAAATTCGC
Found at i:370 original size:20 final size:19
Alignment explanation
Indices: 320--374 Score: 65
Period size: 20 Copynumber: 2.8 Consensus size: 19
310 TGCGATTACA
320 GATTCGCGTTGCGAAATTG
1 GATTCGCGTTGCGAAATTG
** *
339 GAAACTGGGTTGCGAAATTG
1 GATTC-GCGTTGCGAAATTG
359 GAGTTCGCGTTGCGAA
1 GA-TTCGCGTTGCGAA
375 TTTGTTGGTC
Statistics
Matches: 28, Mismatches: 6, Indels: 3
0.76 0.16 0.08
Matches are distributed among these distances:
19 3 0.11
20 24 0.86
21 1 0.04
ACGTcount: A:0.24, C:0.15, G:0.35, T:0.27
Consensus pattern (19 bp):
GATTCGCGTTGCGAAATTG
Found at i:7121 original size:30 final size:30
Alignment explanation
Indices: 7051--7123 Score: 110
Period size: 30 Copynumber: 2.4 Consensus size: 30
7041 GGTTCTTCGG
* *
7051 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
**
7081 GACCTCTGGATAGTTATTGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
7111 GACCTCTGGATAG
1 GACCTCTGGATAG
7124 GTCCTTCGGG
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 39 1.00
ACGTcount: A:0.25, C:0.18, G:0.25, T:0.33
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:9773 original size:2 final size:2
Alignment explanation
Indices: 9766--9825 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
9756 AGTTTGGGGA
9766 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
9808 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
9826 CTGTGATTAG
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12296 original size:30 final size:30
Alignment explanation
Indices: 12235--12331 Score: 115
Period size: 30 Copynumber: 3.2 Consensus size: 30
12225 CTAAGTAACA
* * *
12235 TATGGACAGTTTACCTAGGTTCTTCGA-GACC
1 TATGGACAG-TTACCGAGGATCTT-TATGACC
12266 TATGGACAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
* *
12296 TCTGGATAGTTACCGAGGATCTTTATGACC
1 TATGGACAGTTACCGAGGATCTTTATGACC
*
12326 TCTGGA
1 TATGGA
12332 TAGGTCCTTC
Statistics
Matches: 60, Mismatches: 5, Indels: 3
0.88 0.07 0.04
Matches are distributed among these distances:
29 1 0.02
30 50 0.83
31 9 0.15
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.32
Consensus pattern (30 bp):
TATGGACAGTTACCGAGGATCTTTATGACC
Found at i:12332 original size:30 final size:30
Alignment explanation
Indices: 12262--12334 Score: 128
Period size: 30 Copynumber: 2.4 Consensus size: 30
12252 GGTTCTTCGA
* *
12262 GACCTATGGACAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
12292 GACCTCTGGATAGTTACCGAGGATCTTTAT
1 GACCTCTGGATAGTTACCGAGGATCTTTAT
12322 GACCTCTGGATAG
1 GACCTCTGGATAG
12335 GTCCTTCGGG
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
30 41 1.00
ACGTcount: A:0.25, C:0.21, G:0.25, T:0.30
Consensus pattern (30 bp):
GACCTCTGGATAGTTACCGAGGATCTTTAT
Found at i:15907 original size:23 final size:23
Alignment explanation
Indices: 15877--15940 Score: 110
Period size: 23 Copynumber: 2.8 Consensus size: 23
15867 ACGTCTTATA
15877 TGGCACTTCGGTGCATTTCTACG
1 TGGCACTTCGGTGCATTTCTACG
*
15900 TGGCACTTCGGTGCAATTCTACG
1 TGGCACTTCGGTGCATTTCTACG
*
15923 TGGCACTTCAGTGCATTT
1 TGGCACTTCGGTGCATTT
15941 ATATGAGCTG
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
23 38 1.00
ACGTcount: A:0.16, C:0.25, G:0.25, T:0.34
Consensus pattern (23 bp):
TGGCACTTCGGTGCATTTCTACG
Found at i:23445 original size:20 final size:20
Alignment explanation
Indices: 23420--23467 Score: 60
Period size: 20 Copynumber: 2.4 Consensus size: 20
23410 GTCAGAGTGT
*
23420 GGCGGCGGACGGCTGACGGC
1 GGCGGCGGACGGCGGACGGC
* *
23440 GGCGGCAGACGGCGGGCGGC
1 GGCGGCGGACGGCGGACGGC
*
23460 GGCAGCGG
1 GGCGGCGG
23468 CCAGCGGGCA
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 23 1.00
ACGTcount: A:0.10, C:0.29, G:0.58, T:0.02
Consensus pattern (20 bp):
GGCGGCGGACGGCGGACGGC
Found at i:23457 original size:17 final size:16
Alignment explanation
Indices: 23437--23468 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
23427 GACGGCTGAC
23437 GGCGGCGGCAGACGGCG
1 GGCGGCGGCAG-CGGCG
23454 GGCGGCGGCAGCGGC
1 GGCGGCGGCAGCGGC
23469 CAGCGGGCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.09, C:0.31, G:0.59, T:0.00
Consensus pattern (16 bp):
GGCGGCGGCAGCGGCG
Found at i:25294 original size:39 final size:39
Alignment explanation
Indices: 25240--25323 Score: 143
Period size: 39 Copynumber: 2.2 Consensus size: 39
25230 ATTTAGAAAA
* *
25240 TAAA-AAGATAGAGTTATAGTTAATCTAAACTACTAAAT
1 TAAATAAGATAGAGTTATAGGTAATCTAAACAACTAAAT
25278 TAAATAAGATAGAGTTATAGGTAATCTAAACAACTAAAT
1 TAAATAAGATAGAGTTATAGGTAATCTAAACAACTAAAT
25317 TAAATAA
1 TAAATAA
25324 TTTACTACAA
Statistics
Matches: 43, Mismatches: 2, Indels: 1
0.93 0.04 0.02
Matches are distributed among these distances:
38 4 0.09
39 39 0.91
ACGTcount: A:0.52, C:0.07, G:0.11, T:0.30
Consensus pattern (39 bp):
TAAATAAGATAGAGTTATAGGTAATCTAAACAACTAAAT
Found at i:27038 original size:81 final size:81
Alignment explanation
Indices: 26903--27061 Score: 291
Period size: 81 Copynumber: 2.0 Consensus size: 81
26893 GGAACTGGTG
*
26903 TACTATCAACACTTGTTGTGAAAGCCTTGAAAGCAGGCGTCAAATGGTTATAAGCAACATGCTTT
1 TACTATCAACACTTGTTGTGAAAGCCTTGAAAGCAGGCGTCAAATGGTTATAAGCAACATACTTT
26968 TGTATGGGATGAGCAA
66 TGTATGGGATGAGCAA
* *
26984 TACTATCAACACTTGTTGTGAAAGCCTTGAAAGTAGGCTTCAAATGGTTATAAGCAACATACTTT
1 TACTATCAACACTTGTTGTGAAAGCCTTGAAAGCAGGCGTCAAATGGTTATAAGCAACATACTTT
27049 TGTATGGGATGAG
66 TGTATGGGATGAG
27062 AAGTACACTT
Statistics
Matches: 75, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
81 75 1.00
ACGTcount: A:0.32, C:0.15, G:0.23, T:0.30
Consensus pattern (81 bp):
TACTATCAACACTTGTTGTGAAAGCCTTGAAAGCAGGCGTCAAATGGTTATAAGCAACATACTTT
TGTATGGGATGAGCAA
Found at i:27421 original size:42 final size:42
Alignment explanation
Indices: 27360--27440 Score: 117
Period size: 42 Copynumber: 1.9 Consensus size: 42
27350 TAAGTGGAGG
* *
27360 AGGAGGTTCAAAAGATAATATTGGTTAAGATGTAGGATTTAA
1 AGGAGGTTCAAAAGATAATATCGGTTAAGATGTAAGATTTAA
* * *
27402 AGGAGGTTCAATAGCTAATATCGGTTGAGATGTAAGATT
1 AGGAGGTTCAAAAGATAATATCGGTTAAGATGTAAGATT
27441 AGAAGGCAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.37, C:0.05, G:0.27, T:0.31
Consensus pattern (42 bp):
AGGAGGTTCAAAAGATAATATCGGTTAAGATGTAAGATTTAA
Found at i:29088 original size:20 final size:19
Alignment explanation
Indices: 29061--29154 Score: 76
Period size: 20 Copynumber: 5.1 Consensus size: 19
29051 TTAGCAACAG
29061 AATAAAAATGATTCTATCT
1 AATAAAAATGATTCTATCT
*
29080 AATTAAAAATGATCCTATCT
1 AA-TAAAAATGATTCTATCT
*
29100 AATAACTAATAGA----A--T
1 AATAA-AAAT-GATTCTATCT
*
29115 AA-AAAACTGATTCTATCT
1 AATAAAAATGATTCTATCT
29133 AATTAAAAATGATTCTATCT
1 AA-TAAAAATGATTCTATCT
29153 AA
1 AA
29155 AAACTAATAG
Statistics
Matches: 59, Mismatches: 5, Indels: 21
0.69 0.06 0.25
Matches are distributed among these distances:
12 2 0.03
13 2 0.03
14 2 0.03
15 3 0.05
16 1 0.02
17 1 0.02
18 3 0.05
19 5 0.08
20 38 0.64
21 2 0.03
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.34
Consensus pattern (19 bp):
AATAAAAATGATTCTATCT
Found at i:29137 original size:53 final size:52
Alignment explanation
Indices: 29059--29187 Score: 224
Period size: 53 Copynumber: 2.5 Consensus size: 52
29049 AATTAGCAAC
*
29059 AGAATAAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAAAAACTAAT
*
29110 AGAATAAAAAACTGATTCTATCTAATTAAAAATGATTCTATCTAAAAACTAAT
1 AGAAT-AAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAAAAACTAAT
29163 AGAATAAAAACTGATTCTATCTAAT
1 AGAATAAAAACTGATTCTATCTAAT
29188 ATTTAATTTA
Statistics
Matches: 74, Mismatches: 2, Indels: 3
0.94 0.03 0.04
Matches are distributed among these distances:
51 5 0.07
52 25 0.34
53 44 0.59
ACGTcount: A:0.50, C:0.12, G:0.06, T:0.33
Consensus pattern (52 bp):
AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAAAAACTAAT
Found at i:33782 original size:20 final size:20
Alignment explanation
Indices: 33757--33796 Score: 71
Period size: 20 Copynumber: 2.0 Consensus size: 20
33747 AGCAACAGAA
*
33757 TAAAAATGATTCTATCTAAT
1 TAAAAATGATCCTATCTAAT
33777 TAAAAATGATCCTATCTAAT
1 TAAAAATGATCCTATCTAAT
33797 AACTAATAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.45, C:0.12, G:0.05, T:0.38
Consensus pattern (20 bp):
TAAAAATGATCCTATCTAAT
Found at i:33825 original size:53 final size:52
Alignment explanation
Indices: 33753--33881 Score: 233
Period size: 53 Copynumber: 2.5 Consensus size: 52
33743 AATTAGCAAC
33753 AGAATAAAAA-TGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
33804 AGAATAAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
1 AGAAT-AAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
*
33857 ATAATAAAAACTGATTCTATCTAAT
1 AGAATAAAAACTGATTCTATCTAAT
33882 ATTTAATTTA
Statistics
Matches: 75, Mismatches: 1, Indels: 3
0.95 0.01 0.04
Matches are distributed among these distances:
51 5 0.07
52 25 0.33
53 45 0.60
ACGTcount: A:0.49, C:0.12, G:0.05, T:0.33
Consensus pattern (52 bp):
AGAATAAAAACTGATTCTATCTAATTAAAAATGATCCTATCTAATAACTAAT
Found at i:33839 original size:20 final size:21
Alignment explanation
Indices: 33810--33849 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
33800 TAATAGAATA
*
33810 AAAAACTGATTCTATCTAATT
1 AAAAACTGATCCTATCTAATT
33831 AAAAA-TGATCCTATCTAAT
1 AAAAACTGATCCTATCTAAT
33850 AACTAATATA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (21 bp):
AAAAACTGATCCTATCTAATT
Found at i:39987 original size:34 final size:34
Alignment explanation
Indices: 39910--40055 Score: 256
Period size: 34 Copynumber: 4.3 Consensus size: 34
39900 ATCCTCGGTT
39910 GGGGATGAAATTGGCACTGCTGTTTCAGTTTCAGG
1 GGGGATGAAATTGGCACTGCTGTTTCAGTTTCA-G
*
39945 GGGGATGAAATTGGCACTGCTGTTTCAATTTCAG
1 GGGGATGAAATTGGCACTGCTGTTTCAGTTTCAG
*
39979 GGGGATGAAATTGGCACTACTGTTTCAGTTTCAG
1 GGGGATGAAATTGGCACTGCTGTTTCAGTTTCAG
40013 GGGGATGAAATTGGCACTGCTGTTTCAGTTTCAG
1 GGGGATGAAATTGGCACTGCTGTTTCAGTTTCAG
*
40047 GAGGATGAA
1 GGGGATGAA
40056 GTCGTCGAGA
Statistics
Matches: 106, Mismatches: 5, Indels: 1
0.95 0.04 0.01
Matches are distributed among these distances:
34 74 0.70
35 32 0.30
ACGTcount: A:0.23, C:0.14, G:0.32, T:0.31
Consensus pattern (34 bp):
GGGGATGAAATTGGCACTGCTGTTTCAGTTTCAG
Found at i:41948 original size:9 final size:10
Alignment explanation
Indices: 41921--41949 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
41911 TTATTATATT
41921 AGGGAGAAAA
1 AGGGAGAAAA
41931 AGGGAGAAAA
1 AGGGAGAAAA
41941 AGGG-GAAAA
1 AGGGAGAAAA
41950 GTTGAGAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
9 5 0.26
10 14 0.74
ACGTcount: A:0.59, C:0.00, G:0.41, T:0.00
Consensus pattern (10 bp):
AGGGAGAAAA
Found at i:43092 original size:54 final size:54
Alignment explanation
Indices: 43007--43240 Score: 360
Period size: 54 Copynumber: 4.3 Consensus size: 54
42997 TATGTGTACC
* * *
43007 ATCGGCACCAAGTGTGCAACTCACGGAATTCATAATAAGTCTATGAACGACTGT
1 ATCGGCACTAAGTGTGCAACTCACGGAATTCATAATAAGTTTATGAACGACCGT
*
43061 ATTGGCACTAAGTGTGCAACTCACGGAATTCATAATAAGTTTATGAACGACCGT
1 ATCGGCACTAAGTGTGCAACTCACGGAATTCATAATAAGTTTATGAACGACCGT
* * * **
43115 ATCCGCACTAAGAGTGCAACCCACGGAATTCATAATAAGTTTATGAACGATTGT
1 ATCGGCACTAAGTGTGCAACTCACGGAATTCATAATAAGTTTATGAACGACCGT
*
43169 ATCGGCACTAAGTGTGCAACACACGGAATTCATAATAAGTTTATGAACGACCGT
1 ATCGGCACTAAGTGTGCAACTCACGGAATTCATAATAAGTTTATGAACGACCGT
* *
43223 ATTGGCACTACGTGTGCA
1 ATCGGCACTAAGTGTGCA
43241 CCCCAAAGAA
Statistics
Matches: 163, Mismatches: 17, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
54 163 1.00
ACGTcount: A:0.33, C:0.21, G:0.21, T:0.26
Consensus pattern (54 bp):
ATCGGCACTAAGTGTGCAACTCACGGAATTCATAATAAGTTTATGAACGACCGT
Found at i:43099 original size:27 final size:27
Alignment explanation
Indices: 43016--43100 Score: 66
Period size: 27 Copynumber: 3.1 Consensus size: 27
43006 CATCGGCACC
43016 AAGTGTGCAACTCACGGAATTCATAAT
1 AAGTGTGCAACTCACGGAATTCATAAT
* * * * *** *
43043 AAGTCTATG-AAC-GACTGTATTGGCACT
1 AAG--TGTGCAACTCACGGAATTCATAAT
43070 AAGTGTGCAACTCACGGAATTCATAAT
1 AAGTGTGCAACTCACGGAATTCATAAT
43097 AAGT
1 AAGT
43101 TTATGAACGA
Statistics
Matches: 38, Mismatches: 16, Indels: 8
0.61 0.26 0.13
Matches are distributed among these distances:
25 3 0.08
26 3 0.08
27 26 0.68
28 3 0.08
29 3 0.08
ACGTcount: A:0.35, C:0.18, G:0.20, T:0.27
Consensus pattern (27 bp):
AAGTGTGCAACTCACGGAATTCATAAT
Found at i:55045 original size:61 final size:61
Alignment explanation
Indices: 54974--55094 Score: 197
Period size: 61 Copynumber: 2.0 Consensus size: 61
54964 TGTTGAGTAG
* * *
54974 AAGTGCAATGAAAAGTATGTTACATTCAGATGCAAATGGTTTTCATATAAATTTATCACTC
1 AAGTGAAATGAAAAGTATGTTACATTCAGATGCAAATGATTTGCATATAAATTTATCACTC
* *
55035 AAGTGAAATGAAAATTATGTTACATTCATATGCAAATGATTTGCATATAAATTTATCACT
1 AAGTGAAATGAAAAGTATGTTACATTCAGATGCAAATGATTTGCATATAAATTTATCACT
55095 TGTACAAGTT
Statistics
Matches: 55, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
61 55 1.00
ACGTcount: A:0.40, C:0.12, G:0.13, T:0.36
Consensus pattern (61 bp):
AAGTGAAATGAAAAGTATGTTACATTCAGATGCAAATGATTTGCATATAAATTTATCACTC
Done.