Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002989.1 Hibiscus syriacus cultivar Beakdansim tig00006178_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: 56375
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Found at i:2558 original size:32 final size:32
Alignment explanation
Indices: 2480--2696 Score: 260
Period size: 32 Copynumber: 6.8 Consensus size: 32
2470 ATGACCTATC
* * *
2480 CATATGTTCTGAAAAACATAGGTAA-C-TGTC
1 CATATGTTCCGAAGAACATAGGTAATCATGTT
* * *
2510 CATATGTTCTGGAGAACATAGGTAATCTTGTT
1 CATATGTTCCGAAGAACATAGGTAATCATGTT
*
2542 CATATGTTCCGAAGAACATAGGTAATCATGTC
1 CATATGTTCCGAAGAACATAGGTAATCATGTT
* * * *
2574 CATATGCTCTGAAGAACATATGTAATC-TTTT
1 CATATGTTCCGAAGAACATAGGTAATCATGTT
* * *
2605 CCATATGTTCCAAAGAACATAAGTAAGCATGTT
1 -CATATGTTCCGAAGAACATAGGTAATCATGTT
* *
2638 CATATGTTCCGAAGAACATAAGTAAGCATGTT
1 CATATGTTCCGAAGAACATAGGTAATCATGTT
2670 CATATGTTCCGAAGAACATAGGTAATC
1 CATATGTTCCGAAGAACATAGGTAATC
2697 CTCGACTCTT
Statistics
Matches: 162, Mismatches: 21, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
30 23 0.14
31 3 0.02
32 133 0.82
33 3 0.02
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.31
Consensus pattern (32 bp):
CATATGTTCCGAAGAACATAGGTAATCATGTT
Found at i:2599 original size:64 final size:64
Alignment explanation
Indices: 2480--2696 Score: 287
Period size: 64 Copynumber: 3.4 Consensus size: 64
2470 ATGACCTATC
* * * *
2480 CATATGTTCTGAAAAACATAGGTAA-C-TGTCCATATGTTCTGGAGAACATAGGTAATCTTGTT
1 CATATGTTCCGAAGAACATAGGTAATCATGTCCATATGTTCTGAAGAACATAAGTAATCTTGTT
* *
2542 CATATGTTCCGAAGAACATAGGTAATCATGTCCATATGCTCTGAAGAACATATGTAATCTT-TT
1 CATATGTTCCGAAGAACATAGGTAATCATGTCCATATGTTCTGAAGAACATAAGTAATCTTGTT
* * * * * * *
2605 CCATATGTTCCAAAGAACATAAGTAAGCATGTTCATATGTTCCGAAGAACATAAGTAAGCATGTT
1 -CATATGTTCCGAAGAACATAGGTAATCATGTCCATATGTTCTGAAGAACATAAGTAATCTTGTT
2670 CATATGTTCCGAAGAACATAGGTAATC
1 CATATGTTCCGAAGAACATAGGTAATC
2697 CTCGACTCTT
Statistics
Matches: 134, Mismatches: 17, Indels: 6
0.85 0.11 0.04
Matches are distributed among these distances:
62 23 0.17
63 3 0.02
64 106 0.79
65 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.31
Consensus pattern (64 bp):
CATATGTTCCGAAGAACATAGGTAATCATGTCCATATGTTCTGAAGAACATAAGTAATCTTGTT
Found at i:2640 original size:96 final size:95
Alignment explanation
Indices: 2478--2696 Score: 296
Period size: 96 Copynumber: 2.3 Consensus size: 95
2468 GAATGACCTA
* *** * * *
2478 TCCATATGTTCTGAAAAACATAGGTAA-CTGTCCATATGTTCTGGAGAACATAGGTAATCTTGTT
1 TCCATATGTTCTGAAGAACATAGGTAATCTGTCCATATGTTCCAAAGAACATAAGTAAGCATGTT
* *
2542 CATATGTTCCGAAGAACATAGGTAATCATG
66 CATATGTTCCGAAGAACATAAGTAAGCATG
* * *
2572 TCCATATGCTCTGAAGAACATATGTAATCTTTTCCATATGTTCCAAAGAACATAAGTAAGCATGT
1 TCCATATGTTCTGAAGAACATAGGTAATC-TGTCCATATGTTCCAAAGAACATAAGTAAGCATGT
2637 TCATATGTTCCGAAGAACATAAGTAAGCATG
65 TCATATGTTCCGAAGAACATAAGTAAGCATG
* *
2668 TTCATATGTTCCGAAGAACATAGGTAATC
1 TCCATATGTTCTGAAGAACATAGGTAATC
2697 CTCGACTCTT
Statistics
Matches: 107, Mismatches: 16, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
94 24 0.22
95 1 0.01
96 82 0.77
ACGTcount: A:0.35, C:0.17, G:0.17, T:0.31
Consensus pattern (95 bp):
TCCATATGTTCTGAAGAACATAGGTAATCTGTCCATATGTTCCAAAGAACATAAGTAAGCATGTT
CATATGTTCCGAAGAACATAAGTAAGCATG
Found at i:3206 original size:2 final size:2
Alignment explanation
Indices: 3199--3223 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
3189 TTATCACATT
3199 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 T
3224 TTACACAATT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:7390 original size:32 final size:32
Alignment explanation
Indices: 7322--7424 Score: 174
Period size: 32 Copynumber: 3.3 Consensus size: 32
7312 GAAGGACCTA
* *
7322 TCCATATGTTCCGAAGAACATAGGTAA--CTG
1 TCCATATGTTCTGGAGAACATAGGTAATCCTG
7352 TCCATATGTTCTGGAGAACATAGGTAATCCTG
1 TCCATATGTTCTGGAGAACATAGGTAATCCTG
7384 TCCATATGTTCTGGAGAACATAGGTAATCCTG
1 TCCATATGTTCTGGAGAACATAGGTAATCCTG
7416 TCCATATGT
1 TCCATATGT
7425 CCAACTATAC
Statistics
Matches: 69, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
30 25 0.36
32 44 0.64
ACGTcount: A:0.29, C:0.19, G:0.20, T:0.31
Consensus pattern (32 bp):
TCCATATGTTCTGGAGAACATAGGTAATCCTG
Found at i:9744 original size:3 final size:3
Alignment explanation
Indices: 9725--9779 Score: 69
Period size: 3 Copynumber: 18.7 Consensus size: 3
9715 TAAAATTAAA
* *
9725 AAT AAT ACT AAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT -AT AGT
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
9770 AAT -AT AAT AA
1 AAT AAT AAT AA
9780 AAACTCAGAC
Statistics
Matches: 45, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
2 4 0.09
3 38 0.84
4 3 0.07
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:10462 original size:134 final size:134
Alignment explanation
Indices: 10008--10595 Score: 770
Period size: 133 Copynumber: 4.4 Consensus size: 134
9998 TCTTCCGGGG
* * * *
10008 AGATTGAATCGGAATCGACTTGTTTCACTGCTTTTCAGGAAGACCAAATATGAAAGAAGAAGAAT
1 AGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATATGAAAGAAGAAGAAT
* * * * * * * *
10073 ATGTTCCACTACCCTTTAGAGGAGATCAGACTCGAAAAAAGTTTGAT-TATTTCACTATTCTTCA
66 ATGCTCCACTACTCTTTAGGGGAGATCAAACTCGAGAAAACTTTGATCCACTTCACTATTCTTCA
10137 T-AGA
131 TGA-A
* * **
10141 AGATTGAATCAGAATCGATTTGCTTCACTGCTCTTTAGGAAGACCAAATCTGAAAGAAGAAGCGT
1 AGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATATGAAAGAAGAAGAAT
*
10206 ATGCTCCACTAATCTTTAGGGGAGATCAAACTCGAG-AAACTTTGATCCACTTCACTATTCTTCA
66 ATGCTCCACTACTCTTTAGGGGAGATCAAACTCGAGAAAACTTTGATCCACTTCACTATTCTTCA
* *
10270 AGGA
131 TGAA
* * * * **
10274 AGATTGAATCATAATCAATTTGCTTCACTGCTCTTCATGAAGACCAAATCTGAAAGAAGAAGCGT
1 AGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATATGAAAGAAGAAGAAT
* *
10339 CTGCTCCACTACTCTTTAGGGGAGATCAAACTCGAGAAAACTTTGATCCACTTCACTATTATTCA
66 ATGCTCCACTACTCTTTAGGGGAGATCAAACTCGAGAAAACTTTGATCCACTTCACTATTCTTCA
10404 TGAA
131 TGAA
** * *
10408 AGATTGAATTGGAATCGATTTGCTTCACTGCTCTTCAGGAAGAGCAAATATGAAAGAAGAATAAT
1 AGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATATGAAAGAAGAAGAAT
* * *
10473 ATGCTCCATTACTCTTTAAGGGAGATCAGACTCGAGAAAACTTTGATCCACTTCACTATTCTTCA
66 ATGCTCCACTACTCTTTAGGGGAGATCAAACTCGAGAAAACTTTGATCCACTTCACTATTCTTCA
*
10538 TGGA
131 TGAA
* * * * * *
10542 AGATTGAATCAGAATTGATTTG-TTCATTACTCTCCAGGAAGACCACATCTGAAA
1 AGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATATGAAA
10596 ATCAAACATT
Statistics
Matches: 399, Mismatches: 53, Indels: 6
0.87 0.12 0.01
Matches are distributed among these distances:
132 9 0.02
133 224 0.56
134 166 0.42
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (134 bp):
AGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACCAAATATGAAAGAAGAAGAAT
ATGCTCCACTACTCTTTAGGGGAGATCAAACTCGAGAAAACTTTGATCCACTTCACTATTCTTCA
TGAA
Found at i:10478 original size:267 final size:266
Alignment explanation
Indices: 9990--10595 Score: 793
Period size: 267 Copynumber: 2.3 Consensus size: 266
9980 TTTTATTCAT
* ** * * * *
9990 TTCACTACTCTTCCGGGGAGATTGAATCGGAATCGACTTGTTTCACTGCTTTTCAGGAAGACCAA
1 TTCACTATTCTTCAAGGAAGATTGAATCAGAATCGATTTG-TTCACTGCTCTTCAGGAAGACCAA
* * * *
10055 ATATGAAAGAAGAAGAATATGTTCCACTACCCTTTAGAGGAGATCAGACTCGAAAAAAGTTTGAT
65 ATCTGAAAGAAGAAGAATATGCTCCACTACCCTTTAGAGGAGATCAAACTCGAAAAAACTTTGAT
* * * *
10120 TATTTCACTATTCTTCATAGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTTAGGAAGAC
130 CACTTCACTATTATTCATAGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGAC
* ** *
10185 CAAATCTGAAAGAAGAAGCGTATGCTCCACTAATCTTTAGGGGAGATCAAACTCGAG-AAACTTT
195 CAAATATGAAAGAAGAAGAATATGCTCCACTAATCTTTAAGGGAGATCAAACTCGAGAAAACTTT
10249 GATCCAC
260 GATCCAC
* * *
10256 TTCACTATTCTTCAAGGAAGATTGAATCATAATCAATTTGCTTCACTGCTCTTCATGAAGACCAA
1 TTCACTATTCTTCAAGGAAGATTGAATCAGAATCGATTTG-TTCACTGCTCTTCAGGAAGACCAA
** * * * *
10321 ATCTGAAAGAAGAAGCGTCTGCTCCACTACTCTTTAGGGGAGATCAAACTCGAGAAAACTTTGAT
65 ATCTGAAAGAAGAAGAATATGCTCCACTACCCTTTAGAGGAGATCAAACTCGAAAAAACTTTGAT
**
10386 CCACTTCACTATTATTCAT-GAAAGATTGAATTGGAATCGATTTGCTTCACTGCTCTTCAGGAAG
130 -CACTTCACTATTATTCATAG-AAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAG
* * * * *
10450 AGCAAATATGAAAGAAGAATAATATGCTCCATTACTCTTTAAGGGAGATCAGACTCGAGAAAACT
193 ACCAAATATGAAAGAAGAAGAATATGCTCCACTAATCTTTAAGGGAGATCAAACTCGAGAAAACT
10515 TTGATCCAC
258 TTGATCCAC
* * * * * *
10524 TTCACTATTCTTCATGGAAGATTGAATCAGAATTGATTTGTTCATTACTCTCCAGGAAGACCACA
1 TTCACTATTCTTCAAGGAAGATTGAATCAGAATCGATTTGTTCACTGCTCTTCAGGAAGACCAAA
10589 TCTGAAA
66 TCTGAAA
10596 ATCAAACATT
Statistics
Matches: 292, Mismatches: 45, Indels: 5
0.85 0.13 0.01
Matches are distributed among these distances:
266 110 0.38
267 132 0.45
268 50 0.17
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.29
Consensus pattern (266 bp):
TTCACTATTCTTCAAGGAAGATTGAATCAGAATCGATTTGTTCACTGCTCTTCAGGAAGACCAAA
TCTGAAAGAAGAAGAATATGCTCCACTACCCTTTAGAGGAGATCAAACTCGAAAAAACTTTGATC
ACTTCACTATTATTCATAGAAGATTGAATCAGAATCGATTTGCTTCACTGCTCTTCAGGAAGACC
AAATATGAAAGAAGAAGAATATGCTCCACTAATCTTTAAGGGAGATCAAACTCGAGAAAACTTTG
ATCCAC
Found at i:28308 original size:31 final size:31
Alignment explanation
Indices: 28270--28394 Score: 207
Period size: 31 Copynumber: 4.0 Consensus size: 31
28260 CCCGAATGAC
* * *
28270 CAGTCCATA-GATTCCGAAGAACCTAGGTAAT
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
28301 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
28332 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
28363 CAGTCCATATGTCCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
28394 C
1 C
28395 CCTCGACCCT
Statistics
Matches: 90, Mismatches: 3, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
31 89 0.99
32 1 0.01
ACGTcount: A:0.38, C:0.23, G:0.19, T:0.20
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:34117 original size:24 final size:24
Alignment explanation
Indices: 34090--34141 Score: 61
Period size: 24 Copynumber: 2.2 Consensus size: 24
34080 TATATCAAAA
34090 ATCAAAACATAAATCAT-GTCAAGT
1 ATCAAAACA-AAATCATGGTCAAGT
* * *
34114 ATCATATCAAAATCCTGGTCAAGT
1 ATCAAAACAAAATCATGGTCAAGT
34138 ATCA
1 ATCA
34142 GATCAGAATC
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 6 0.25
24 18 0.75
ACGTcount: A:0.44, C:0.19, G:0.10, T:0.27
Consensus pattern (24 bp):
ATCAAAACAAAATCATGGTCAAGT
Found at i:34146 original size:24 final size:23
Alignment explanation
Indices: 34101--34222 Score: 129
Period size: 24 Copynumber: 5.1 Consensus size: 23
34091 TCAAAACATA
* * *
34101 AATCATGTCAAGTATCATATCAA
1 AATCCTGTCAAGTATCAGATCAG
34124 AATCCTGGTCAAGTATCAGATCAG
1 AATCCT-GTCAAGTATCAGATCAG
*
34148 AATCCAAGTCAAGTATCAGATCAG
1 AATCC-TGTCAAGTATCAGATCAG
* *
34172 AATCTATGTC-AGATATCATATCAG
1 AATC-CTGTCAAG-TATCAGATCAG
*
34196 AATCCATATCAAGTATCAGATCAG
1 AATCC-TGTCAAGTATCAGATCAG
34220 AAT
1 AAT
34223 TCAAATCGAA
Statistics
Matches: 83, Mismatches: 10, Indels: 11
0.80 0.10 0.11
Matches are distributed among these distances:
23 7 0.08
24 74 0.89
25 2 0.02
ACGTcount: A:0.40, C:0.19, G:0.14, T:0.27
Consensus pattern (23 bp):
AATCCTGTCAAGTATCAGATCAG
Found at i:34189 original size:48 final size:49
Alignment explanation
Indices: 34107--34222 Score: 150
Period size: 48 Copynumber: 2.4 Consensus size: 49
34097 CATAAATCAT
* *
34107 GTCAAGTATCATATCAAAATCCTGGTCAAGTATCAGATCAGAATCCA-A
1 GTCAAGTATCAGATCAGAATCCTGGTCAAGTATCAGATCAGAATCCATA
* *
34155 GTCAAGTATCAGATCAGAAT-CTATGTC-AGATATCATATCAGAATCCATA
1 GTCAAGTATCAGATCAGAATCCT-GGTCAAG-TATCAGATCAGAATCCATA
34204 -TCAAGTATCAGATCAGAAT
1 GTCAAGTATCAGATCAGAAT
34223 TCAAATCGAA
Statistics
Matches: 61, Mismatches: 4, Indels: 6
0.86 0.06 0.08
Matches are distributed among these distances:
47 4 0.07
48 56 0.92
49 1 0.02
ACGTcount: A:0.40, C:0.19, G:0.15, T:0.27
Consensus pattern (49 bp):
GTCAAGTATCAGATCAGAATCCTGGTCAAGTATCAGATCAGAATCCATA
Found at i:34238 original size:72 final size:71
Alignment explanation
Indices: 34101--34240 Score: 178
Period size: 72 Copynumber: 2.0 Consensus size: 71
34091 TCAAAACATA
* * *
34101 AATCATGTCAAGTATCATATCAAAATCCTGGTCAAGTATCAGATCAGAATCCAAGTCAAGTATCA
1 AATCATGTCAAGTATCATATCAAAATCCTGATCAAGTATCAGATCAGAATCCAAATCAAGAATCA
34166 GATCAG
66 GATCAG
* *
34172 AATCTATGTC-AGATATCATATCAGAATCCAT-ATCAAGTATCAGATCAGAATTCAAATCGAA-A
1 AATC-ATGTCAAG-TATCATATCAAAATCC-TGATCAAGTATCAGATCAGAATCCAAATC-AAGA
34234 ATCAGAT
62 ATCAGAT
34241 AAAATATTCA
Statistics
Matches: 60, Mismatches: 5, Indels: 7
0.83 0.07 0.10
Matches are distributed among these distances:
71 6 0.10
72 51 0.85
73 3 0.05
ACGTcount: A:0.41, C:0.19, G:0.14, T:0.26
Consensus pattern (71 bp):
AATCATGTCAAGTATCATATCAAAATCCTGATCAAGTATCAGATCAGAATCCAAATCAAGAATCA
GATCAG
Found at i:35263 original size:18 final size:18
Alignment explanation
Indices: 35242--35277 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
35232 CTTCCATCCG
*
35242 ATCTTATTATTTAATTCA
1 ATCTTATCATTTAATTCA
*
35260 ATCTTATCATTTACTTCA
1 ATCTTATCATTTAATTCA
35278 GTCCTTTCGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.31, C:0.17, G:0.00, T:0.53
Consensus pattern (18 bp):
ATCTTATCATTTAATTCA
Found at i:36631 original size:18 final size:18
Alignment explanation
Indices: 36605--36645 Score: 64
Period size: 18 Copynumber: 2.3 Consensus size: 18
36595 CGGTCAACGG
*
36605 GTCGAGTCAACGGGTCGA
1 GTCGGGTCAACGGGTCGA
*
36623 GTCGGGTCAACGGGTCGG
1 GTCGGGTCAACGGGTCGA
36641 GTCGG
1 GTCGG
36646 ATTGTGACCA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.15, C:0.22, G:0.46, T:0.17
Consensus pattern (18 bp):
GTCGGGTCAACGGGTCGA
Found at i:36643 original size:13 final size:13
Alignment explanation
Indices: 36597--36625 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
36587 CCGGTCAACG
36597 GTCAACGGGTCGA
1 GTCAACGGGTCGA
36610 GTCAACGGGTCGA
1 GTCAACGGGTCGA
36623 GTC
1 GTC
36626 GGGTCAACGG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.21, C:0.24, G:0.38, T:0.17
Consensus pattern (13 bp):
GTCAACGGGTCGA
Found at i:39863 original size:31 final size:32
Alignment explanation
Indices: 39802--39869 Score: 88
Period size: 32 Copynumber: 2.2 Consensus size: 32
39792 ATTTTTGTTT
39802 AAAAAAATTAAAGATGTTATTATATATTTTAA
1 AAAAAAATTAAAGATGTTATTATATATTTTAA
*
39834 AAAAAAATTCAAA-ATTTCTATTAT-T-TTTTAA
1 AAAAAAATT-AAAGATGT-TATTATATATTTTAA
39865 AAAAA
1 AAAAA
39870 TCCAAAATAC
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
31 11 0.33
32 13 0.39
33 9 0.27
ACGTcount: A:0.54, C:0.03, G:0.03, T:0.40
Consensus pattern (32 bp):
AAAAAAATTAAAGATGTTATTATATATTTTAA
Found at i:40016 original size:16 final size:16
Alignment explanation
Indices: 39995--40043 Score: 62
Period size: 16 Copynumber: 3.1 Consensus size: 16
39985 AGGGCATGGA
*
39995 TAACAAATATTTAATT
1 TAACAAATATTTAAAT
40011 TAACAAATATTTAAAT
1 TAACAAATATTTAAAT
* * *
40027 TAATAAGTATTAAAAT
1 TAACAAATATTTAAAT
40043 T
1 T
40044 GGCATTAGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 29 1.00
ACGTcount: A:0.53, C:0.04, G:0.02, T:0.41
Consensus pattern (16 bp):
TAACAAATATTTAAAT
Found at i:46285 original size:32 final size:32
Alignment explanation
Indices: 46249--46310 Score: 97
Period size: 32 Copynumber: 1.9 Consensus size: 32
46239 CATAAGAAGA
* * *
46249 TAAAATATAATTAATCATATAAAATGAGGGAG
1 TAAAATATAAATAAGCATAGAAAATGAGGGAG
46281 TAAAATATAAATAAGCATAGAAAATGAGGG
1 TAAAATATAAATAAGCATAGAAAATGAGGG
46311 GACAAAATTA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
32 27 1.00
ACGTcount: A:0.55, C:0.03, G:0.18, T:0.24
Consensus pattern (32 bp):
TAAAATATAAATAAGCATAGAAAATGAGGGAG
Found at i:46326 original size:32 final size:32
Alignment explanation
Indices: 46250--46322 Score: 87
Period size: 32 Copynumber: 2.3 Consensus size: 32
46240 ATAAGAAGAT
* * * *
46250 AAAATATAATTAATCATATAAAATGAGGGAGT
1 AAAATATAAATAAGCATAGAAAATGAGGGAGC
46282 AAAATATAAATAAGCATAGAAAATGAGGG-GAC
1 AAAATATAAATAAGCATAGAAAATGAGGGAG-C
46314 AAAAT-TAAA
1 AAAATATAAA
46323 ATAAATTAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
31 5 0.14
32 31 0.86
ACGTcount: A:0.58, C:0.04, G:0.16, T:0.22
Consensus pattern (32 bp):
AAAATATAAATAAGCATAGAAAATGAGGGAGC
Done.