Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002945.1 Hibiscus syriacus cultivar Beakdansim tig00006077_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: 68103
ACGTcount: A:0.31, C:0.19, G:0.16, T:0.34
Found at i:3700 original size:15 final size:16
Alignment explanation
Indices: 3662--3711 Score: 61
Period size: 15 Copynumber: 3.3 Consensus size: 16
3652 CGTTCATTTA
3662 ATAAAT-AA-ACGAAC
1 ATAAATGAACACGAAC
* *
3676 ACAAACGAACAC-AAC
1 ATAAATGAACACGAAC
3691 ATAAATGAACACGAAC
1 ATAAATGAACACGAAC
3707 ATAAA
1 ATAAA
3712 CATTGGAGAC
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
14 4 0.14
15 15 0.52
16 10 0.34
ACGTcount: A:0.62, C:0.20, G:0.08, T:0.10
Consensus pattern (16 bp):
ATAAATGAACACGAAC
Found at i:3878 original size:12 final size:12
Alignment explanation
Indices: 3861--3889 Score: 58
Period size: 12 Copynumber: 2.4 Consensus size: 12
3851 AATATATTAA
3861 AGCTCGATTCTG
1 AGCTCGATTCTG
3873 AGCTCGATTCTG
1 AGCTCGATTCTG
3885 AGCTC
1 AGCTC
3890 AACATTACCC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.17, C:0.28, G:0.24, T:0.31
Consensus pattern (12 bp):
AGCTCGATTCTG
Found at i:7853 original size:12 final size:11
Alignment explanation
Indices: 7813--7858 Score: 58
Period size: 11 Copynumber: 4.1 Consensus size: 11
7803 TTGCAATTCC
7813 TTTATCTT-TT
1 TTTATCTTGTT
7823 CTTTATCTTGTT
1 -TTTATCTTGTT
*
7835 TTAATCTTAGTT
1 TTTATCTT-GTT
7847 TTTATCTTGTT
1 TTTATCTTGTT
7858 T
1 T
7859 CCAGCACCAA
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
11 19 0.61
12 12 0.39
ACGTcount: A:0.13, C:0.11, G:0.07, T:0.70
Consensus pattern (11 bp):
TTTATCTTGTT
Found at i:12414 original size:23 final size:22
Alignment explanation
Indices: 12376--12418 Score: 68
Period size: 23 Copynumber: 1.9 Consensus size: 22
12366 CAATTCCTTT
12376 ATCTTTTCTTTATCTTGTTTTA
1 ATCTTTTCTTTATCTTGTTTTA
*
12398 ATCTTATTTTTTATCTTGTTT
1 ATCTT-TTCTTTATCTTGTTT
12419 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 5 0.26
23 14 0.74
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.70
Consensus pattern (22 bp):
ATCTTTTCTTTATCTTGTTTTA
Found at i:15144 original size:21 final size:21
Alignment explanation
Indices: 15120--15162 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
15110 TGCTATTGTC
*
15120 GCTATCACTGCTGCTGTCATT
1 GCTATCACTGATGCTGTCATT
*
15141 GCTATCACTGATGTTGTCATT
1 GCTATCACTGATGCTGTCATT
15162 G
1 G
15163 TTGTCATCGT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.16, C:0.23, G:0.21, T:0.40
Consensus pattern (21 bp):
GCTATCACTGATGCTGTCATT
Found at i:18331 original size:23 final size:23
Alignment explanation
Indices: 18305--18371 Score: 89
Period size: 23 Copynumber: 2.9 Consensus size: 23
18295 CCACAACACA
18305 TATAAATGCACCGAAGTGCCACG
1 TATAAATGCACCGAAGTGCCACG
* * * *
18328 TATAACTGCACCGTAGTGTCGCG
1 TATAAATGCACCGAAGTGCCACG
*
18351 TAGAAATGCACCGAAGTGCCA
1 TATAAATGCACCGAAGTGCCA
18372 TATAAGGTTG
Statistics
Matches: 35, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
23 35 1.00
ACGTcount: A:0.31, C:0.25, G:0.24, T:0.19
Consensus pattern (23 bp):
TATAAATGCACCGAAGTGCCACG
Found at i:18769 original size:2 final size:2
Alignment explanation
Indices: 18762--18797 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
18752 ATGTCTTATC
18762 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
18798 CACATGTTCA
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:18865 original size:2 final size:2
Alignment explanation
Indices: 18858--18885 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
18848 ATTCATCTTC
18858 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
18886 CATTTTTCCT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:20094 original size:64 final size:64
Alignment explanation
Indices: 19985--20122 Score: 156
Period size: 64 Copynumber: 2.2 Consensus size: 64
19975 TTCCCTTGAA
* *
19985 GTGCATTGATGCACTACCCATGCATCGATACACAAATCACCTTCGATGTTTTC-A-TTTTAAGGG
1 GTGCATCGATGCACTACCCATGCATCGATACACAAATCACATTCGATG-TTTCAATTTTTAA-GG
20048 G
64 G
* * * ** *
20049 GTGCATCGATGCACT-CCTTATGCATCGATGCACTAATTGCATTCGATGTTTCAATTTTTAATGG
1 GTGCATCGATGCACTACC-CATGCATCGATACACAAATCACATTCGATGTTTCAATTTTTAAGGG
20113 GTGCATCGAT
1 GTGCATCGAT
20123 ACACACTGAA
Statistics
Matches: 63, Mismatches: 8, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
63 6 0.10
64 51 0.81
65 6 0.10
ACGTcount: A:0.25, C:0.22, G:0.20, T:0.34
Consensus pattern (64 bp):
GTGCATCGATGCACTACCCATGCATCGATACACAAATCACATTCGATGTTTCAATTTTTAAGGG
Found at i:23589 original size:23 final size:23
Alignment explanation
Indices: 23545--23604 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
23535 CAGCTCATAT
*
23545 AAATGCACCGAAGTGCCACGTAG
1 AAATGCACCGAAGTACCACGTAG
* * *
23568 AATTGCACCGTAGTACCGCGTAG
1 AAATGCACCGAAGTACCACGTAG
23591 AAATGCACCGAAGT
1 AAATGCACCGAAGT
23605 GCCATATAAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 31 1.00
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.17
Consensus pattern (23 bp):
AAATGCACCGAAGTACCACGTAG
Found at i:24006 original size:2 final size:2
Alignment explanation
Indices: 23999--24038 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
23989 ATGTCTTATC
23999 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
24039 CACATGTTCA
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:24105 original size:2 final size:2
Alignment explanation
Indices: 24098--24137 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
24088 AATCATCTTC
24098 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
24138 CATTTTTCCT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26655 original size:19 final size:19
Alignment explanation
Indices: 26633--26669 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
26623 ATTTAGTTGC
26633 CTAAATTATAGCCTAATTA
1 CTAAATTATAGCCTAATTA
26652 CTAAATTATAGCCTAATT
1 CTAAATTATAGCCTAATT
26670 GTTAGGATTG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.41, C:0.16, G:0.05, T:0.38
Consensus pattern (19 bp):
CTAAATTATAGCCTAATTA
Found at i:31531 original size:25 final size:25
Alignment explanation
Indices: 31497--31549 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
31487 TTGTAACACC
*
31497 CTAATCCAGTCCGACCTGAAGATCG
1 CTAATCCAGTCCGACCCGAAGATCG
31522 CTAATCCAGTCCGACCCGAAGATCG
1 CTAATCCAGTCCGACCCGAAGATCG
31547 CTA
1 CTA
31550 GATCATGATG
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.28, C:0.34, G:0.19, T:0.19
Consensus pattern (25 bp):
CTAATCCAGTCCGACCCGAAGATCG
Found at i:32154 original size:273 final size:272
Alignment explanation
Indices: 31667--32459 Score: 837
Period size: 273 Copynumber: 2.9 Consensus size: 272
31657 CATTTAAGTT
* * * * * * * **
31667 TTTTGTAAAAATAAGGAATTTTTAGAAGATTTTCTCTTTGCTCTTTCT-ATAGAGTCTGGAAAGT
1 TTTTGTAAAACTAAGGAATTTTCAAAAGATTTTATGTTTGCT-TTTCTCAAACAGTCCAG-AAGT
* * * * * * * * * * *
31731 CACCAGTTCC-TATC-CACCACTCACGCCACCATTGTCATCGTCTCTGGCCGCTATTGCTAGAAA
64 CAGCAG-TCCATATCAC-CCACTCATGTCATCATCGTCATCATCTTTGACCGCTATCGCCAAAAA
* * * * * *
31794 ATATTGAAGGCTTGTCTAGGCTTCTTGATCACTATTCTAATGTTGTATTCGCTGAAAAATATTAA
127 ATATCGAAGGCTTGTCTCGGCTTCTTGATCACTATTTTGATGTTGCATTCGCTAAAAAATATTAA
* * * *
31859 AGGTCTCGTTTGAACATCAACTTAGATTAGGTATCTCATTCTTGTAATTGCTATTTCTT-TCGTG
192 AAGTCTCGTTTGAGCATCAACTTAGATTAAGTATCTCATTCTTGTAATTGTTATTTCTTCTC-TG
31923 TCTTTACATTTCTTTCA
256 TCTTTACATTTCTTTCA
* * **
31940 TTTTGTAAAACTAATGAATTTTCAAAAGATTTTATGTTTTCTCTTTCT-AAACAGTCTGGAAGTC
1 TTTTGTAAAACTAAGGAATTTTCAAAAGATTTTATGTTTGCT-TTTCTCAAACAGTCCAGAAGTC
* * * * * ** * *
32004 AGC-GATTCATGT-ACTCAGCTCATGTCGTCATCGTCATCGTCTTTGGTCGTTATCGCCGAAAAA
65 AGCAG-TCCATATCACCCA-CTCATGTCATCATCGTCATCATCTTTGACCGCTATCGCCAAAAAA
* *
32067 TATCGAAGGCTTGTCTCGGCTTCTTGATCGCTATTTTGATGTTGCATTCGCCAAAAAATATTAAA
128 TATCGAAGGCTTGTCTCGGCTTCTTGATCACTATTTTGATGTTGCATTCGCTAAAAAATATT-AA
* *
32132 AAGTCTCGTTTGAGCTTCAACTTAGATTAAGTATCTCATTCTTGTAATTGTTATTTCTTCTCTTT
192 AAGTCTCGTTTGAGCATCAACTTAGATTAAGTATCTCATTCTTGTAATTGTTATTTCTTCTCTGT
**
32197 CTTTACATTTCTTTTG
257 CTTTACATTTCTTTCA
* * * *
32213 TTTTGTTAAACTAAGGAATTTTCAGAAGATTTTCTGTTTGCTTTTTTCAAACAGTCCAGAAGTCA
1 TTTTGTAAAACTAAGGAATTTTCAAAAGATTTTATGTTTGCTTTTCTCAAACAGTCCAGAAGTCA
* * * * * *
32278 GCAGTCCCTATCCCCCACTCATGTTATCGTTGTCATCATCTTTGACCGCTATCGTCAAAACAATA
66 GCAGTCCATATCACCCACTCATGTCATCATCGTCATCATCTTTGACCGCTATCGCCAAAA-AATA
* ** * *
32343 TCGAAGTCTTGTCTCAACTTCTTGATCACTATTTTGATGTTGCATTCGCTAGAAAATATTGAAAG
130 TCGAAGGCTTGTCTCGGCTTCTTGATCACTATTTTGATGTTGCATTCGCTAAAAAATATTAAAAG
* *
32408 TCTCGTTTGAGCATCAACTCAGATTATGTATCTCATT-TTCGTAATTGTTATT
195 TCTCGTTTGAGCATCAACTTAGATTAAGTATCTCATTCTT-GTAATTGTTATT
32460 ATTTCTTTTG
Statistics
Matches: 435, Mismatches: 75, Indels: 20
0.82 0.14 0.04
Matches are distributed among these distances:
271 5 0.01
272 103 0.24
273 263 0.60
274 64 0.15
ACGTcount: A:0.25, C:0.19, G:0.15, T:0.40
Consensus pattern (272 bp):
TTTTGTAAAACTAAGGAATTTTCAAAAGATTTTATGTTTGCTTTTCTCAAACAGTCCAGAAGTCA
GCAGTCCATATCACCCACTCATGTCATCATCGTCATCATCTTTGACCGCTATCGCCAAAAAATAT
CGAAGGCTTGTCTCGGCTTCTTGATCACTATTTTGATGTTGCATTCGCTAAAAAATATTAAAAGT
CTCGTTTGAGCATCAACTTAGATTAAGTATCTCATTCTTGTAATTGTTATTTCTTCTCTGTCTTT
ACATTTCTTTCA
Found at i:33075 original size:19 final size:19
Alignment explanation
Indices: 33051--33100 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
33041 TACTCAAATC
33051 AATATTATTTTATGTA-TTT
1 AATATTATTTTAT-TATTTT
* *
33070 AATATTAATATATTATTTT
1 AATATTATTTTATTATTTT
*
33089 AATACTATTTTA
1 AATATTATTTTA
33101 GTAAAAATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
18 2 0.08
19 23 0.92
ACGTcount: A:0.38, C:0.02, G:0.02, T:0.58
Consensus pattern (19 bp):
AATATTATTTTATTATTTT
Found at i:33289 original size:32 final size:31
Alignment explanation
Indices: 33220--33317 Score: 96
Period size: 31 Copynumber: 3.2 Consensus size: 31
33210 TATTGCATGT
*
33220 ATATTTTTATTTTA-ATAATTAATAA-TTTA
1 ATATTTTTATTTTATAAAATTAATAATTTTA
*
33249 ATATTTTTATTTTAGTAAAATATAATAATTTTC
1 ATATTTTTATTTTA-TAAAAT-TAATAATTTTA
**
33282 ATA-TTTTA-TTTATAAAACTTTAATAATAATA
1 ATATTTTTATTTTATAAAA--TTAATAATTTTA
33313 ATATT
1 ATATT
33318 GACATAAATA
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
29 14 0.25
30 5 0.09
31 19 0.33
32 13 0.23
33 6 0.11
ACGTcount: A:0.43, C:0.02, G:0.01, T:0.54
Consensus pattern (31 bp):
ATATTTTTATTTTATAAAATTAATAATTTTA
Found at i:43034 original size:6 final size:6
Alignment explanation
Indices: 43023--43071 Score: 59
Period size: 6 Copynumber: 8.7 Consensus size: 6
43013 GAACCCACTT
* *
43023 TTTTTC TTTTTC TTTTTC -TTTTC TTTTTC ATCTTC -TTTT- TTTTTC
1 TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC TTTTTC
43068 TTTT
1 TTTT
43072 CTTCTTTTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 6
0.80 0.07 0.13
Matches are distributed among these distances:
5 12 0.32
6 25 0.68
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (6 bp):
TTTTTC
Found at i:43046 original size:17 final size:17
Alignment explanation
Indices: 43024--43071 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 17
43014 AACCCACTTT
43024 TTTTCTTTTTCTTTTTC
1 TTTTCTTTTTCTTTTTC
* *
43041 TTTTCTTTTTCATCTTC
1 TTTTCTTTTTCTTTTTC
43058 TTTT-TTTTTCTTTT
1 TTTTCTTTTTCTTTT
43072 CTTCTTTTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
16 8 0.30
17 19 0.70
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (17 bp):
TTTTCTTTTTCTTTTTC
Found at i:43058 original size:23 final size:22
Alignment explanation
Indices: 43023--43071 Score: 71
Period size: 23 Copynumber: 2.2 Consensus size: 22
43013 GAACCCACTT
* *
43023 TTTTTCTTTTTCTTTTTCTTTTC
1 TTTTTCATCTTCTTTTT-TTTTC
43046 TTTTTCATCTTCTTTTTTTTTC
1 TTTTTCATCTTCTTTTTTTTTC
43068 TTTT
1 TTTT
43072 CTTCTTTTTT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
22 9 0.38
23 15 0.62
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (22 bp):
TTTTTCATCTTCTTTTTTTTTC
Found at i:43079 original size:17 final size:17
Alignment explanation
Indices: 43021--43081 Score: 52
Period size: 18 Copynumber: 3.3 Consensus size: 17
43011 TTGAACCCAC
43021 TTTTTTTCTTTTTCTT-T
1 TTTTTTTC-TTTTCTTCT
*
43038 TTCTTTTCTTTTTCATCTTCTT
1 TT-TTTT-TCTTT--TCTTC-T
43060 TTTTTTTCTTTTCTTCT
1 TTTTTTTCTTTTCTTCT
43077 TTTTT
1 TTTTT
43082 CAATTTAGGA
Statistics
Matches: 36, Mismatches: 2, Indels: 12
0.72 0.04 0.24
Matches are distributed among these distances:
17 8 0.22
18 12 0.33
19 1 0.03
20 8 0.22
21 4 0.11
22 3 0.08
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (17 bp):
TTTTTTTCTTTTCTTCT
Found at i:43151 original size:6 final size:7
Alignment explanation
Indices: 43119--43150 Score: 57
Period size: 7 Copynumber: 4.7 Consensus size: 7
43109 ACCCTAAATA
43119 TTTTTTC
1 TTTTTTC
43126 -TTTTTC
1 TTTTTTC
43132 TTTTTTC
1 TTTTTTC
43139 TTTTTTC
1 TTTTTTC
43146 TTTTT
1 TTTTT
43151 CGACTTAGGA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.25
7 18 0.75
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (7 bp):
TTTTTTC
Found at i:43178 original size:69 final size:71
Alignment explanation
Indices: 43053--43184 Score: 171
Period size: 69 Copynumber: 1.9 Consensus size: 71
43043 TTCTTTTTCA
* * * *
43053 TCTTCTTTTTTTTTCTTTTCTTCTTTTTTCAATTTAGGACGCCCTTTCGGGATTTCACCCTAAAT
1 TCTTCTTTTTTTTTCTTTTCTTCTTTTTTCAACTTAGGACGCCATCTCGCGATTTCACCCTAAAT
43118 ATTTTT
66 ATTTTT
* * *
43124 TCTT-TTTCTTTTTTCTTTT-TTC-TTTTTCGACTTAGGACGCCATCTCGCGTTTTCATCCTAA
1 TCTTCTTT-TTTTTTCTTTTCTTCTTTTTTCAACTTAGGACGCCATCTCGCGATTTCACCCTAA
43185 GCGAAGTACT
Statistics
Matches: 53, Mismatches: 7, Indels: 4
0.83 0.11 0.06
Matches are distributed among these distances:
69 32 0.60
70 6 0.11
71 15 0.28
ACGTcount: A:0.13, C:0.23, G:0.09, T:0.55
Consensus pattern (71 bp):
TCTTCTTTTTTTTTCTTTTCTTCTTTTTTCAACTTAGGACGCCATCTCGCGATTTCACCCTAAAT
ATTTTT
Found at i:49442 original size:23 final size:20
Alignment explanation
Indices: 49419--49456 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
49409 ATAAATGTAA
49419 AAACATGGAAAATATAAAAAT
1 AAACAT-GAAAATATAAAAAT
49440 AAACATGAAAA-ATAAAA
1 AAACATGAAAATATAAAA
49457 TGCAAAGGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
19 6 0.35
20 5 0.29
21 6 0.35
ACGTcount: A:0.71, C:0.05, G:0.08, T:0.16
Consensus pattern (20 bp):
AAACATGAAAATATAAAAAT
Found at i:52777 original size:29 final size:29
Alignment explanation
Indices: 52738--52815 Score: 88
Period size: 29 Copynumber: 2.7 Consensus size: 29
52728 TAAAGTAATG
* *
52738 AAAAATAAATAAAT-AAAATACAAAAAATC
1 AAAAAGAAATAAATCAAAAAACAAAAAA-C
*
52767 AAAAAGAAATAAATCAAAAAACCAAAAAC
1 AAAAAGAAATAAATCAAAAAACAAAAAAC
**
52796 AAAAATCAA-AAATCAAAAAA
1 AAAAAGAAATAAATCAAAAAA
52816 AATAATAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
28 11 0.26
29 21 0.49
30 11 0.26
ACGTcount: A:0.77, C:0.10, G:0.01, T:0.12
Consensus pattern (29 bp):
AAAAAGAAATAAATCAAAAAACAAAAAAC
Found at i:52780 original size:15 final size:15
Alignment explanation
Indices: 52738--52820 Score: 63
Period size: 14 Copynumber: 5.8 Consensus size: 15
52728 TAAAGTAATG
*
52738 AAAAATAAATAAAT-
1 AAAAACAAATAAATC
52752 AAAATACAAA-AAATC
1 AAAA-ACAAATAAATC
*
52767 AAAAAGAAATAAATC
1 AAAAACAAATAAATC
*
52782 AAAAAACCAA-AAA-C
1 -AAAAACAAATAAATC
52796 AAAAATC-AA-AAATC
1 AAAAA-CAAATAAATC
52810 AAAAA-AAATAA
1 AAAAACAAATAA
52821 TAAAAGAATA
Statistics
Matches: 57, Mismatches: 4, Indels: 16
0.74 0.05 0.21
Matches are distributed among these distances:
13 12 0.21
14 22 0.39
15 16 0.28
16 7 0.12
ACGTcount: A:0.77, C:0.10, G:0.01, T:0.12
Consensus pattern (15 bp):
AAAAACAAATAAATC
Found at i:52798 original size:6 final size:7
Alignment explanation
Indices: 52760--52814 Score: 58
Period size: 7 Copynumber: 7.7 Consensus size: 7
52750 ATAAAATACA
52760 AAAAATC
1 AAAAATC
**
52767 AAAAAGA
1 AAAAATC
52774 AATAAATC
1 AA-AAATC
*
52782 AAAAAACC
1 -AAAAATC
52790 AAAAA-C
1 AAAAATC
52796 AAAAATC
1 AAAAATC
52803 AAAAATC
1 AAAAATC
52810 AAAAA
1 AAAAA
52815 AAATAATAAA
Statistics
Matches: 40, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
6 6 0.15
7 25 0.62
8 7 0.17
9 2 0.05
ACGTcount: A:0.76, C:0.13, G:0.02, T:0.09
Consensus pattern (7 bp):
AAAAATC
Found at i:52798 original size:14 final size:15
Alignment explanation
Indices: 52760--52815 Score: 57
Period size: 15 Copynumber: 3.9 Consensus size: 15
52750 ATAAAATACA
52760 AAAAATCAAAAAGA--
1 AAAAATCAAAAA-ACC
52774 AATAAATCAAAAAACC
1 AA-AAATCAAAAAACC
*
52790 AAAAA-C-AAAAATC
1 AAAAATCAAAAAACC
52803 AAAAATCAAAAAA
1 AAAAATCAAAAAA
52816 AATAATAAAA
Statistics
Matches: 36, Mismatches: 1, Indels: 9
0.78 0.02 0.20
Matches are distributed among these distances:
13 11 0.31
14 5 0.14
15 18 0.50
16 2 0.06
ACGTcount: A:0.77, C:0.12, G:0.02, T:0.09
Consensus pattern (15 bp):
AAAAATCAAAAAACC
Found at i:52805 original size:13 final size:14
Alignment explanation
Indices: 52760--52814 Score: 58
Period size: 13 Copynumber: 3.9 Consensus size: 14
52750 ATAAAATACA
**
52760 AAAAATCAAAAAGA
1 AAAAATCAAAAACC
52774 AATAAATCAAAAAACC
1 AA-AAATC-AAAAACC
*
52790 AAAAA-CAAAAATC
1 AAAAATCAAAAACC
52803 AAAAATCAAAAA
1 AAAAATCAAAAA
52815 AAATAATAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
13 11 0.31
14 9 0.26
15 8 0.23
16 7 0.20
ACGTcount: A:0.76, C:0.13, G:0.02, T:0.09
Consensus pattern (14 bp):
AAAAATCAAAAACC
Found at i:52815 original size:8 final size:8
Alignment explanation
Indices: 52752--52815 Score: 50
Period size: 7 Copynumber: 8.5 Consensus size: 8
52742 ATAAATAAAT
52752 AAAATACAA
1 AAAAT-CAA
52761 AAAATCAA
1 AAAATCAA
52769 AAAGA--AA
1 AAA-ATCAA
*
52776 TAAATCAA
1 AAAATCAA
*
52784 AAAA-CCA
1 AAAATCAA
52791 AAAA-C-A
1 AAAATCAA
52797 AAAATC-A
1 AAAATCAA
52804 AAAATCAA
1 AAAATCAA
52812 AAAA
1 AAAA
52816 AATAATAAAA
Statistics
Matches: 47, Mismatches: 3, Indels: 11
0.77 0.05 0.18
Matches are distributed among these distances:
6 6 0.13
7 19 0.40
8 16 0.34
9 6 0.13
ACGTcount: A:0.77, C:0.12, G:0.02, T:0.09
Consensus pattern (8 bp):
AAAATCAA
Found at i:52929 original size:34 final size:34
Alignment explanation
Indices: 52886--52951 Score: 132
Period size: 34 Copynumber: 1.9 Consensus size: 34
52876 TGTAATTGGT
52886 TTTCTGGAAAACCAATTCCAGAAAACCAATTATA
1 TTTCTGGAAAACCAATTCCAGAAAACCAATTATA
52920 TTTCTGGAAAACCAATTCCAGAAAACCAATTA
1 TTTCTGGAAAACCAATTCCAGAAAACCAATTA
52952 CGTTGTTTGT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.44, C:0.21, G:0.09, T:0.26
Consensus pattern (34 bp):
TTTCTGGAAAACCAATTCCAGAAAACCAATTATA
Found at i:55334 original size:33 final size:33
Alignment explanation
Indices: 55245--55336 Score: 139
Period size: 33 Copynumber: 2.8 Consensus size: 33
55235 AAATTATATA
* * *
55245 TTCAATGTCTAACAATCTAAAAAAAATTTCAAT
1 TTCAATATCCAACAATCTAAAAACAATTTCAAT
*
55278 TTCAATATCCAACAATCTAAAAACATTTTCAAT
1 TTCAATATCCAACAATCTAAAAACAATTTCAAT
*
55311 TTCAATATCCAACAAACTAAAAACAA
1 TTCAATATCCAACAATCTAAAAACAA
55337 CAATATTCAA
Statistics
Matches: 53, Mismatches: 6, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 53 1.00
ACGTcount: A:0.50, C:0.20, G:0.01, T:0.29
Consensus pattern (33 bp):
TTCAATATCCAACAATCTAAAAACAATTTCAAT
Found at i:57154 original size:13 final size:13
Alignment explanation
Indices: 57136--57173 Score: 67
Period size: 13 Copynumber: 2.9 Consensus size: 13
57126 CAATTCTAAA
*
57136 CAATTTTATTTTT
1 CAATTTTATTTCT
57149 CAATTTTATTTCT
1 CAATTTTATTTCT
57162 CAATTTTATTTC
1 CAATTTTATTTC
57174 ATAAGTATTA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
13 24 1.00
ACGTcount: A:0.24, C:0.13, G:0.00, T:0.63
Consensus pattern (13 bp):
CAATTTTATTTCT
Found at i:57227 original size:36 final size:36
Alignment explanation
Indices: 57181--57312 Score: 223
Period size: 36 Copynumber: 3.7 Consensus size: 36
57171 TTCATAAGTA
57181 TTAAGCTTTTACCTAAAGCTAAAGTTCATATTACGT
1 TTAAGCTTTTACCTAAAGCTAAAGTTCATATTACGT
* *
57217 ATT-ATCTTTTACCTAAAGATAAAGTTCATATTACGT
1 -TTAAGCTTTTACCTAAAGCTAAAGTTCATATTACGT
57253 TTAAGCTTTTACCTAAAGCTAAAGTTCATATTACGT
1 TTAAGCTTTTACCTAAAGCTAAAGTTCATATTACGT
57289 TTAAGCTTTTACCT-AAGCTAAAGT
1 TTAAGCTTTTACCTAAAGCTAAAGT
57313 GGATGTAATT
Statistics
Matches: 90, Mismatches: 4, Indels: 4
0.92 0.04 0.04
Matches are distributed among these distances:
35 12 0.13
36 76 0.84
37 2 0.02
ACGTcount: A:0.34, C:0.16, G:0.11, T:0.39
Consensus pattern (36 bp):
TTAAGCTTTTACCTAAAGCTAAAGTTCATATTACGT
Found at i:58135 original size:34 final size:34
Alignment explanation
Indices: 58114--58192 Score: 122
Period size: 34 Copynumber: 2.3 Consensus size: 34
58104 ATATAACAGA
*
58114 GAAATATTAATCGATGAGAACAAATTGAAAATAC
1 GAAATATTAATCGATGAGAACAAATTGAAAAGAC
* * *
58148 GAAATATTAATCTATGAGAACAAATTGAGAATAC
1 GAAATATTAATCGATGAGAACAAATTGAAAAGAC
58182 GAAATATTAAT
1 GAAATATTAAT
58193 TTTTGCGGAA
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
34 43 1.00
ACGTcount: A:0.52, C:0.08, G:0.14, T:0.27
Consensus pattern (34 bp):
GAAATATTAATCGATGAGAACAAATTGAAAAGAC
Found at i:59333 original size:14 final size:14
Alignment explanation
Indices: 59314--59343 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
59304 GAATCTGACG
59314 AATGGTAATATGGA
1 AATGGTAATATGGA
*
59328 AATGGTAATCTGGA
1 AATGGTAATATGGA
59342 AA
1 AA
59344 AGTTGAGTTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.43, C:0.03, G:0.27, T:0.27
Consensus pattern (14 bp):
AATGGTAATATGGA
Found at i:59985 original size:2 final size:2
Alignment explanation
Indices: 59980--60005 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
59970 GAAAAAACTA
59980 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
60006 TAATGTAAAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:62367 original size:2 final size:2
Alignment explanation
Indices: 62360--62452 Score: 159
Period size: 2 Copynumber: 46.5 Consensus size: 2
62350 GATGTTTTTA
62360 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
* * *
62402 AT AT AT AT AT AT AT AT AT AT AT AT AT AC AC AC 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
62444 AT AT AT AT A
1 AT AT AT AT A
62453 CACACACACA
Statistics
Matches: 89, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
2 89 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:63569 original size:14 final size:15
Alignment explanation
Indices: 63538--63578 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 15
63528 TCAAACATTA
63538 TAAAT-TTTAAAATG
1 TAAATATTTAAAATG
*
63552 TAAATATTTAATAT-
1 TAAATATTTAAAATG
*
63566 TAAATAATTAAAA
1 TAAATATTTAAAA
63579 ATTATTTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
14 16 0.70
15 7 0.30
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.41
Consensus pattern (15 bp):
TAAATATTTAAAATG
Found at i:65975 original size:25 final size:24
Alignment explanation
Indices: 65922--65975 Score: 56
Period size: 25 Copynumber: 2.2 Consensus size: 24
65912 TGTCCGTTCG
* *
65922 ATTTTAAAAATATTTATTGTTTTA
1 ATTTTAAAAATATTTATTATTTCA
*
65946 TTTTTAGAAAATAATTT-TTATTTCA
1 ATTTTA-AAAAT-ATTTATTATTTCA
65971 ATTTT
1 ATTTT
65976 CTTTTGAAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
24 5 0.21
25 15 0.62
26 4 0.17
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (24 bp):
ATTTTAAAAATATTTATTATTTCA
Found at i:66272 original size:183 final size:183
Alignment explanation
Indices: 65927--66277 Score: 514
Period size: 183 Copynumber: 1.9 Consensus size: 183
65917 GTTCGATTTT
65927 AAAAATATTTATTGTTTTATTTTTAGAAAATAATTTTTATTTCAATTTTCTTTTGAAAATAAGAG
1 AAAAATATTTATTGTTTTATTTTTAGAAAATAATTTTTATTTCAATTTTCTTTTGAAAATAAGAG
65992 AATACGTTTGATTAATATAAATAAAAATTCAAATTCAGAAATAAAAAAACAAAAATATATTTAGT
66 AATACGTTTGATTAATATAAATAAAAATTCAAATTCAGAAAT-----AACAAAAATATATTTAGT
66057 ATCTAACTTTTTAAAATAGAAATAAATAAATAGTTATTTTAAGGGTCCATTCAGTTTA
126 ATCTAACTTTTTAAAATAGAAATAAATAAATAGTTATTTTAAGGGTCCATTCAGTTTA
* *
66115 AAAAATATTTATTGTTTTATTTTTAGAAAATAA-TTTTATTTCAATTTTGTTTTTTGAAAATTAG
1 AAAAATATTTATTGTTTTATTTTTAGAAAATAATTTTTATTTCAA-TTT-TCTTTTGAAAATAAG
* * *
66179 AGAATATGTTTGATTAATATAAATCAAAAATTTAAATTCA-ACAAT-A-AAAAGTATATTT-GAT
64 AGAATACGTTTGATTAATATAAAT-AAAAATTCAAATTCAGA-AATAACAAAAATATATTTAG-T
* *
66240 ATCTAACTTTTTAAAATGGAGATAAATAAATAGTTATT
126 ATCTAACTTTTTAAAATAGAAATAAATAAATAGTTATT
66278 AAATAATTAA
Statistics
Matches: 151, Mismatches: 7, Indels: 15
0.87 0.04 0.09
Matches are distributed among these distances:
182 1 0.01
183 48 0.32
184 1 0.01
187 11 0.07
188 36 0.24
189 37 0.25
190 17 0.11
ACGTcount: A:0.45, C:0.05, G:0.08, T:0.42
Consensus pattern (183 bp):
AAAAATATTTATTGTTTTATTTTTAGAAAATAATTTTTATTTCAATTTTCTTTTGAAAATAAGAG
AATACGTTTGATTAATATAAATAAAAATTCAAATTCAGAAATAACAAAAATATATTTAGTATCTA
ACTTTTTAAAATAGAAATAAATAAATAGTTATTTTAAGGGTCCATTCAGTTTA
Found at i:67886 original size:25 final size:24
Alignment explanation
Indices: 67798--67886 Score: 67
Period size: 25 Copynumber: 3.6 Consensus size: 24
67788 AATAATATTA
* * *
67798 TTTATTAATTAATATTAATAGATAT
1 TTTATTATTTATTA-TAATAAATAT
*
67823 TTTTTTATTT-TTAT-ATAAATAAT
1 TTTATTATTTATTATAATAAAT-AT
*
67846 ATTATTCA-TTATTTATAATAAATAT
1 TTTATT-ATTTA-TTATAATAAATAT
67871 TTTATATATTTATTAT
1 TTTAT-TATTTATTAT
67887 TAATTTATAA
Statistics
Matches: 50, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
22 5 0.10
23 9 0.18
24 3 0.06
25 23 0.46
26 10 0.20
ACGTcount: A:0.39, C:0.01, G:0.01, T:0.58
Consensus pattern (24 bp):
TTTATTATTTATTATAATAAATAT
Found at i:67973 original size:28 final size:29
Alignment explanation
Indices: 67882--67980 Score: 71
Period size: 28 Copynumber: 3.4 Consensus size: 29
67872 TTATATATTT
* *
67882 ATTATTAATTTATAATATTATATGTTAATA-A
1 ATTATTAATTTAT--TAATACATG-TAATATA
* * *
67913 AATATTAA-TTATTAAAACATTTCAA-ATA
1 ATTATTAATTTATTAATACATGT-AATATA
*
67941 TTTATTAATTTATTAATA-ATGTAATATA
1 ATTATTAATTTATTAATACATGTAATATA
*
67969 ATTATTATTTTA
1 ATTATTAATTTA
67981 ATATTGTACA
Statistics
Matches: 53, Mismatches: 11, Indels: 11
0.71 0.15 0.15
Matches are distributed among these distances:
27 4 0.08
28 30 0.57
29 8 0.15
30 4 0.08
31 7 0.13
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (29 bp):
ATTATTAATTTATTAATACATGTAATATA
Done.