Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002972.1 Hibiscus syriacus cultivar Beakdansim tig00006148_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: 103718
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.33
Found at i:708 original size:34 final size:35
Alignment explanation
Indices: 645--713 Score: 95
Period size: 34 Copynumber: 2.0 Consensus size: 35
635 ATGCAGAACA
* *
645 AAAAACCATTTAGACGCTACTGAACATTATAGCTC
1 AAAAACCATTTAGACACTACTGAAAATTATAGCTC
* *
680 AAAAACCA-TTGGACACTTCTGAAAATTATAGCTC
1 AAAAACCATTTAGACACTACTGAAAATTATAGCTC
714 TGTCTTTCAG
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
34 22 0.73
35 8 0.27
ACGTcount: A:0.41, C:0.22, G:0.12, T:0.26
Consensus pattern (35 bp):
AAAAACCATTTAGACACTACTGAAAATTATAGCTC
Found at i:6437 original size:28 final size:28
Alignment explanation
Indices: 6398--6461 Score: 128
Period size: 28 Copynumber: 2.3 Consensus size: 28
6388 TCGAAGTAAT
6398 TTTCTTTTCAACAATTCTCACTTGCTGA
1 TTTCTTTTCAACAATTCTCACTTGCTGA
6426 TTTCTTTTCAACAATTCTCACTTGCTGA
1 TTTCTTTTCAACAATTCTCACTTGCTGA
6454 TTTCTTTT
1 TTTCTTTT
6462 GTTTCATTTC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.19, C:0.23, G:0.06, T:0.52
Consensus pattern (28 bp):
TTTCTTTTCAACAATTCTCACTTGCTGA
Found at i:6809 original size:24 final size:24
Alignment explanation
Indices: 6778--6825 Score: 87
Period size: 24 Copynumber: 2.0 Consensus size: 24
6768 TCGTGTCGTA
*
6778 AAACCGAGTAATTAGATCATTGTT
1 AAACCGAGTAAATAGATCATTGTT
6802 AAACCGAGTAAATAGATCATTGTT
1 AAACCGAGTAAATAGATCATTGTT
6826 TATTCGATAT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.40, C:0.12, G:0.17, T:0.31
Consensus pattern (24 bp):
AAACCGAGTAAATAGATCATTGTT
Found at i:11040 original size:29 final size:30
Alignment explanation
Indices: 10984--11041 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 30
10974 AAAACAATCG
* **
10984 AGTGAGCAAAATGATTCGATTGTAAAGTTC
1 AGTGAGCAAAATGAATAAATTGTAAAGTTC
*
11014 AGTGAGCAAATTGAATAAATTG-AAAGTT
1 AGTGAGCAAAATGAATAAATTGTAAAGTT
11042 GGATGAGAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 6 0.25
30 18 0.75
ACGTcount: A:0.41, C:0.07, G:0.22, T:0.29
Consensus pattern (30 bp):
AGTGAGCAAAATGAATAAATTGTAAAGTTC
Found at i:25327 original size:7 final size:7
Alignment explanation
Indices: 25315--25341 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
25305 ATATTATACA
25315 AAATTTG
1 AAATTTG
25322 AAATTTG
1 AAATTTG
25329 AAATTTG
1 AAATTTG
25336 AAATTT
1 AAATTT
25342 TTATATTTAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.44, C:0.00, G:0.11, T:0.44
Consensus pattern (7 bp):
AAATTTG
Found at i:25366 original size:26 final size:26
Alignment explanation
Indices: 25337--25411 Score: 70
Period size: 26 Copynumber: 3.0 Consensus size: 26
25327 TGAAATTTGA
*
25337 AATTTTTATA-TTTAA-TATTGTAAAAT
1 AATTTATATATTTTAATTATT-T-AAAT
25363 AATTTATATATTTTAATTATTTAAAT
1 AATTTATATATTTTAATTATTTAAAT
*
25389 AA--TAT-TATTTTAAATTAATTAAA
1 AATTTATATATTTT-AATTATTTAAA
25412 ATGTTTGATA
Statistics
Matches: 44, Mismatches: 2, Indels: 8
0.81 0.04 0.15
Matches are distributed among these distances:
23 6 0.14
24 13 0.30
26 15 0.34
27 6 0.14
28 4 0.09
ACGTcount: A:0.45, C:0.00, G:0.01, T:0.53
Consensus pattern (26 bp):
AATTTATATATTTTAATTATTTAAAT
Found at i:26237 original size:50 final size:50
Alignment explanation
Indices: 26160--26256 Score: 167
Period size: 50 Copynumber: 1.9 Consensus size: 50
26150 ATCTTCTTTC
* *
26160 AAATCCCAACATTGGGAAGGTCGAGGAGAAAGCGAGTTGTATATCTCACG
1 AAATCCCAACACTGGGAAGGTCAAGGAGAAAGCGAGTTGTATATCTCACG
*
26210 AAATCCCAACACTGGGAAGGTTAAGGAGAAAGCGAGTTGTATATCTC
1 AAATCCCAACACTGGGAAGGTCAAGGAGAAAGCGAGTTGTATATCTC
26257 TTGATTCCAC
Statistics
Matches: 44, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
50 44 1.00
ACGTcount: A:0.35, C:0.18, G:0.27, T:0.21
Consensus pattern (50 bp):
AAATCCCAACACTGGGAAGGTCAAGGAGAAAGCGAGTTGTATATCTCACG
Found at i:37045 original size:2 final size:2
Alignment explanation
Indices: 37038--37100 Score: 126
Period size: 2 Copynumber: 31.5 Consensus size: 2
37028 CCATAGGCAT
37038 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
37080 TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA T
37101 GGAAAGTGAG
Statistics
Matches: 61, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 61 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:38500 original size:23 final size:23
Alignment explanation
Indices: 38467--38602 Score: 236
Period size: 23 Copynumber: 5.9 Consensus size: 23
38457 ATAAACGAAC
* *
38467 ATAAATGAACATAAACGAATATA
1 ATAAATGAACATAAACGAACACA
*
38490 ATAAATAAACATAAACGAACACA
1 ATAAATGAACATAAACGAACACA
*
38513 ATAAATGAACATAAACGAACATA
1 ATAAATGAACATAAACGAACACA
38536 ATAAATGAACATAAACGAACACA
1 ATAAATGAACATAAACGAACACA
38559 ATAAATGAACATAAACGAACACA
1 ATAAATGAACATAAACGAACACA
38582 ATAAATGAACATAAACGAACA
1 ATAAATGAACATAAACGAACA
38603 ACACAAACAT
Statistics
Matches: 107, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 107 1.00
ACGTcount: A:0.62, C:0.15, G:0.08, T:0.15
Consensus pattern (23 bp):
ATAAATGAACATAAACGAACACA
Found at i:38516 original size:13 final size:13
Alignment explanation
Indices: 38500--38592 Score: 78
Period size: 13 Copynumber: 7.8 Consensus size: 13
38490 ATAAATAAAC
38500 ATAAACGAACACA
1 ATAAACGAACACA
*
38513 ATAAATG-A-AC-
1 ATAAACGAACACA
*
38523 ATAAACGAACATA
1 ATAAACGAACACA
*
38536 ATAAATG-A-AC-
1 ATAAACGAACACA
38546 ATAAACGAACACA
1 ATAAACGAACACA
*
38559 ATAAATG-A-AC-
1 ATAAACGAACACA
38569 ATAAACGAACACA
1 ATAAACGAACACA
*
38582 ATAAATGAACA
1 ATAAACGAACA
38593 TAAACGAACA
Statistics
Matches: 62, Mismatches: 9, Indels: 18
0.70 0.10 0.20
Matches are distributed among these distances:
10 18 0.29
11 8 0.13
12 8 0.13
13 28 0.45
ACGTcount: A:0.61, C:0.16, G:0.09, T:0.14
Consensus pattern (13 bp):
ATAAACGAACACA
Found at i:46838 original size:37 final size:38
Alignment explanation
Indices: 46759--46851 Score: 152
Period size: 37 Copynumber: 2.4 Consensus size: 38
46749 TTCACCCTAA
*
46759 ACCCGAACCCGACCCGAATATCACACTTAAAAAAACTCG
1 ACCCG-ACCCGACCCGAATATCACACTTAAAAAAACCCG
*
46798 ACCCGACCCGACACGAATATCACACTT-AAAAAACCCG
1 ACCCGACCCGACCCGAATATCACACTTAAAAAAACCCG
46835 ACCCGACCCGACCCGAA
1 ACCCGACCCGACCCGAA
46852 CAAAATAAAG
Statistics
Matches: 51, Mismatches: 3, Indels: 2
0.91 0.05 0.04
Matches are distributed among these distances:
37 25 0.49
38 21 0.41
39 5 0.10
ACGTcount: A:0.39, C:0.40, G:0.12, T:0.10
Consensus pattern (38 bp):
ACCCGACCCGACCCGAATATCACACTTAAAAAAACCCG
Found at i:47190 original size:221 final size:215
Alignment explanation
Indices: 46840--47287 Score: 770
Period size: 221 Copynumber: 2.1 Consensus size: 215
46830 ACCCGACCCG
* * *
46840 ACCCGACCCGAACAAAATAAAGTTTCATCCGACCCGACCCGAATATATGAATTAGAAATCCGACC
1 ACCCGACCCGAACAAAATAAAGTTTCATCCGACCCAACCCGAATATATGAATTAGAAATCCAAAC
*
46905 CGACCCGACCTGAAATAATAAAAAATTATTTTTACTTAATAAAAACAGTGACTTAATCCGACCCG
66 CGACCCGACCCGAAATAATAAAAAATTATTTTTACTTAATAAAAACAGTGACTTAATCCGACCCG
*
46970 ACCCGAATTATATATATTTTCGGGTCGGTCCGGTTTTTTTCACCCTAAACCCGAACCCGACCCGA
131 ACCCGAATTATATATATTTTCGGGTCGGTCCGATTTTTTTCACCCT--A----AACCCGACCCGA
47035 CCCGACCCGAATATCACACTTAAAAA
190 CCCGACCCGAATATCACACTTAAAAA
47061 ACCCGACCCGAACAAAATAAAGTTTCATCCGACCCAACCCGAATATATGAATTAGAAATCCAAAC
1 ACCCGACCCGAACAAAATAAAGTTTCATCCGACCCAACCCGAATATATGAATTAGAAATCCAAAC
* *
47126 CGACCCGACCCGAAATAATAAAAAATTATTTTTATTTAATAAAAACAGTGACTTAATTCGACCCG
66 CGACCCGACCCGAAATAATAAAAAATTATTTTTACTTAATAAAAACAGTGACTTAATCCGACCCG
*
47191 ACCTGAATTATATATATTTTCGGGTCGGTCCGATTTTTTTCACCCTAAACCCGACCCGACCCGAC
131 ACCCGAATTATATATATTTTCGGGTCGGTCCGATTTTTTTCACCCTAAACCCGACCCGACCCGAC
47256 CCGAATATCACACTTAAAAA
196 CCGAATATCACACTTAAAAA
47276 ACCCGACCCGAA
1 ACCCGACCCGAA
47288 ATAAAAAAAA
Statistics
Matches: 219, Mismatches: 8, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
215 50 0.23
219 1 0.00
221 168 0.77
ACGTcount: A:0.36, C:0.28, G:0.12, T:0.23
Consensus pattern (215 bp):
ACCCGACCCGAACAAAATAAAGTTTCATCCGACCCAACCCGAATATATGAATTAGAAATCCAAAC
CGACCCGACCCGAAATAATAAAAAATTATTTTTACTTAATAAAAACAGTGACTTAATCCGACCCG
ACCCGAATTATATATATTTTCGGGTCGGTCCGATTTTTTTCACCCTAAACCCGACCCGACCCGAC
CCGAATATCACACTTAAAAA
Found at i:55834 original size:21 final size:20
Alignment explanation
Indices: 55748--55905 Score: 86
Period size: 21 Copynumber: 7.8 Consensus size: 20
55738 AAATGACCAA
**
55748 CAAAATCGCAACGCGA-AAT
1 CAAAATCGCAACGCGATTTT
* ***
55767 AAAAATCGCAACGCGATCCC
1 CAAAATCGCAACGCGATTTT
* ** *
55787 CAGAATCGCAAATC-AGTTTC
1 CAAAATCGCAACGCGA-TTTT
55807 CAAAATCGCAACGCGATTCTT
1 CAAAATCGCAACGCGATT-TT
* * * *
55828 GAAAATCGCAATGCGATAGTA
1 CAAAATCGCAACGCGAT-TTT
* **
55849 CAAATTCGCATTGCGATTTT
1 CAAAATCGCAACGCGATTTT
* *
55869 CCAAAATCGCAACGCGAATAT
1 -CAAAATCGCAACGCGATTTT
*
55890 GAAAATCGCAACGCGA
1 CAAAATCGCAACGCGA
55906 ACACATAAAT
Statistics
Matches: 104, Mismatches: 29, Indels: 11
0.72 0.20 0.08
Matches are distributed among these distances:
19 16 0.15
20 41 0.39
21 47 0.45
ACGTcount: A:0.39, C:0.25, G:0.17, T:0.19
Consensus pattern (20 bp):
CAAAATCGCAACGCGATTTT
Found at i:55934 original size:20 final size:20
Alignment explanation
Indices: 55872--56042 Score: 177
Period size: 20 Copynumber: 8.5 Consensus size: 20
55862 CGATTTTCCA
* ** *
55872 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
55892 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
55912 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
55932 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
55952 TAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
55972 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
55992 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
*
56013 AAATCGCAACG-ATAATCCGT
1 AAATCGCAACGCGT-ATCCGT
56033 AAATCGCAAC
1 AAATCGCAAC
56043 ACGGAAATTA
Statistics
Matches: 127, Mismatches: 18, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
19 3 0.02
20 106 0.83
21 17 0.13
22 1 0.01
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:56016 original size:81 final size:80
Alignment explanation
Indices: 55872--56042 Score: 236
Period size: 81 Copynumber: 2.1 Consensus size: 80
55862 CGATTTTCCA
* *
55872 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTAAATC
1 AAATCGCAACGCGAATACGAAAATCGCAACGAGAACACATAAATCGCAACGCGTATCCGTAAATC
*
55937 GCAACG-TGTATCCGT
66 GCAACGAT-AATCCGT
* * * * * *
55952 TAATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTAAAT
1 AAATCGCAACGCGAATACGAAAATCGCAACGAGAACACAT-AAATCGCAACGCGTATCCGTAAAT
56017 CGCAACGATAATCCGT
65 CGCAACGATAATCCGT
56033 AAATCGCAAC
1 AAATCGCAAC
56043 ACGGAAATTA
Statistics
Matches: 79, Mismatches: 10, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
80 32 0.41
81 46 0.58
82 1 0.01
ACGTcount: A:0.38, C:0.26, G:0.17, T:0.19
Consensus pattern (80 bp):
AAATCGCAACGCGAATACGAAAATCGCAACGAGAACACATAAATCGCAACGCGTATCCGTAAATC
GCAACGATAATCCGT
Found at i:56058 original size:81 final size:80
Alignment explanation
Indices: 55872--56066 Score: 223
Period size: 81 Copynumber: 2.4 Consensus size: 80
55862 CGATTTTCCA
* * * * *
55872 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGTAAATC
1 AAATCGCAACACGGATAAGTAAATCGCAACGAGAACACATAAATCGCAACGCGTATCCGTAAATC
*
55937 GCAACGTGTATCCGT
66 GCAACGTGAATCCGT
* * * ** * *
55952 TAATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGTAAAT
1 AAATCGCAACACGGATAAGTAAATCGCAACGAGAACACAT-AAATCGCAACGCGTATCCGTAAAT
56017 CGCAACGAT-AATCCGT
65 CGCAACG-TGAATCCGT
*
56033 AAATCGCAACACGGA-AATTACAATCGCAACGAGA
1 AAATCGCAACACGGATAAGTA-AATCGCAACGAGA
56067 GAATCGCAAT
Statistics
Matches: 96, Mismatches: 16, Indels: 5
0.82 0.14 0.04
Matches are distributed among these distances:
80 34 0.35
81 61 0.64
82 1 0.01
ACGTcount: A:0.39, C:0.26, G:0.17, T:0.18
Consensus pattern (80 bp):
AAATCGCAACACGGATAAGTAAATCGCAACGAGAACACATAAATCGCAACGCGTATCCGTAAATC
GCAACGTGAATCCGT
Found at i:56105 original size:33 final size:34
Alignment explanation
Indices: 56054--56302 Score: 242
Period size: 33 Copynumber: 7.2 Consensus size: 34
56044 CGGAAATTAC
* *
56054 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
*
56087 AATCCCAAC-ATGAAAATCGCAATGCGGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGC-GAAATGAA
* *
56121 AATCGCAACGA-GAGAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
* * *
56154 AATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCG-C
1 AATCGCAA--C--AATGAAAATCGCAATGCGA-AAT-GAA
*
56193 AAT-GCGA-AATGAAAATCGCAATGCGAAATGAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
56225 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--C--AATGAAAATCGCAATGCGAAATGAA
* * *
56263 AATCGCAACGA-GAGAATCGCAATGCGAAATTAA
1 AATCGCAACAATGAAAATCGCAATGCGAAATGAA
56296 AATCGCA
1 AATCGCA
56303 TTGCGATTCT
Statistics
Matches: 182, Mismatches: 17, Indels: 34
0.78 0.07 0.15
Matches are distributed among these distances:
31 1 0.01
32 7 0.04
33 84 0.46
34 30 0.16
35 2 0.01
36 1 0.01
37 1 0.01
38 49 0.27
39 6 0.03
40 1 0.01
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.14
Consensus pattern (34 bp):
AATCGCAACAATGAAAATCGCAATGCGAAATGAA
Found at i:56159 original size:19 final size:19
Alignment explanation
Indices: 56068--56308 Score: 279
Period size: 19 Copynumber: 13.7 Consensus size: 19
56058 GCAACGAGAG
56068 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
56087 AATCCCAA--C---ATGAA
1 AATCGCAATGCGAAATGAA
56101 AATCGCAATGCGGAAATGAA
1 AATCGCAATGC-GAAATGAA
*
56121 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
56135 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
56154 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
56173 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
56187 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
56206 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
56225 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
56244 AATCGCAATGCGAAATGAA
1 AATCGCAATGCGAAATGAA
*
56263 AATCGCAA--CG--A-GAG
1 AATCGCAATGCGAAATGAA
*
56277 AATCGCAATGCGAAATTAA
1 AATCGCAATGCGAAATGAA
*
56296 AATCGCATTGCGA
1 AATCGCAATGCGA
56309 TTCTCCCGTT
Statistics
Matches: 191, Mismatches: 10, Indels: 42
0.79 0.04 0.17
Matches are distributed among these distances:
14 42 0.22
15 3 0.02
16 7 0.04
17 6 0.03
18 4 0.02
19 116 0.61
20 13 0.07
ACGTcount: A:0.46, C:0.18, G:0.22, T:0.15
Consensus pattern (19 bp):
AATCGCAATGCGAAATGAA
Found at i:56181 original size:52 final size:52
Alignment explanation
Indices: 56096--56270 Score: 287
Period size: 52 Copynumber: 3.2 Consensus size: 52
56086 AAATCCCAAC
56096 ATGAAAATCGCAATGCGGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGC-GAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
56149 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
*
56201 ATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAAATGAAAATCGCAA--CG--A-GAGAATCGCAATGCGAA
56258 ATGAAAATCGCAA
1 ATGAAAATCGCAA
56271 CGAGAGAATC
Statistics
Matches: 116, Mismatches: 1, Indels: 6
0.94 0.01 0.05
Matches are distributed among these distances:
52 68 0.59
53 16 0.14
54 2 0.02
56 1 0.01
57 29 0.25
ACGTcount: A:0.47, C:0.17, G:0.22, T:0.14
Consensus pattern (52 bp):
ATGAAAATCGCAATGCGAAATGAAAATCGCAACGAGAGAATCGCAATGCGAA
Found at i:56281 original size:52 final size:51
Alignment explanation
Indices: 56054--56308 Score: 197
Period size: 52 Copynumber: 4.9 Consensus size: 51
56044 CGGAAATTAC
*
56054 AATCGCAACGAGAGAATCGCAATGCGAAATGAAAATCCCAA--C---ATGAA
1 AATCGCAACGAGA-AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
* * *
56101 AATCGCAATGCG-GAAAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAA--CGAGAAATCG-CAATGCGAAATGA-A-AATCGCAATGCGAAATGAA
* * * * *
56154 AATCGCAATGCGAAAT-GAAAAT-CGCAACGAGAGAATCGCAATGCGAAATGAA
1 AATCGCAACGAGAAATCG-CAATGCGAAATGA-A-AATCGCAATGCGAAATGAA
56206 AATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
1 AATCGCAA--CG--A-G-AAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
* *
56263 AATCGCAACGAGAGAATCGCAATGCGAAATTAAAATCGCATTGCGA
1 AATCGCAACGAGA-AATCGCAATGCGAAATGAAAATCGCAATGCGA
56309 TTCTCCCGTT
Statistics
Matches: 176, Mismatches: 12, Indels: 35
0.79 0.05 0.16
Matches are distributed among these distances:
46 7 0.04
47 15 0.09
48 9 0.05
49 2 0.01
50 1 0.01
51 2 0.01
52 80 0.45
53 14 0.08
54 1 0.01
55 2 0.01
57 28 0.16
58 8 0.05
59 7 0.04
ACGTcount: A:0.45, C:0.18, G:0.22, T:0.15
Consensus pattern (51 bp):
AATCGCAACGAGAAATCGCAATGCGAAATGAAAATCGCAATGCGAAATGAA
Found at i:56377 original size:19 final size:19
Alignment explanation
Indices: 56317--56453 Score: 212
Period size: 19 Copynumber: 7.4 Consensus size: 19
56307 GATTCTCCCG
56317 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
56337 TTGCGATTTTCATTTCCGCA
1 TTGCGATTTTCATTT-CGCA
56357 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
56376 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
*
56395 TTGCGA--TTC-TCTCG--
1 TTGCGATTTTCATTTCGCA
56409 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
56428 TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCA
56447 TTGCGAT
1 TTGCGAT
56454 AGTCAATTTT
Statistics
Matches: 110, Mismatches: 2, Indels: 11
0.89 0.02 0.09
Matches are distributed among these distances:
14 6 0.05
16 7 0.06
17 7 0.06
19 55 0.50
20 35 0.32
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.46
Consensus pattern (19 bp):
TTGCGATTTTCATTTCGCA
Found at i:56418 original size:33 final size:35
Alignment explanation
Indices: 56336--56453 Score: 141
Period size: 33 Copynumber: 3.2 Consensus size: 35
56326 TCATTTCCGC
*
56336 ATTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCG
1 ATTGCGATTTTCATTT-CGCATTGCGA--TTCATCTCG
56374 CATTGCGATTTTCATTTCGCATTGCGATTC-TCTCG
1 -ATTGCGATTTTCATTTCGCATTGCGATTCATCTCG
*
56409 -TTGCGATTTTCATTTCGCATTGCGATTTTCATTTCG
1 ATTGCGATTTTCATTTCGCATTGCGA--TTCATCTCG
56445 CATTGCGAT
1 -ATTGCGAT
56454 AGTCAATTTT
Statistics
Matches: 72, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
33 25 0.35
35 7 0.10
36 7 0.10
38 17 0.24
39 16 0.22
ACGTcount: A:0.15, C:0.22, G:0.17, T:0.46
Consensus pattern (35 bp):
ATTGCGATTTTCATTTCGCATTGCGATTCATCTCG
Found at i:56435 original size:52 final size:55
Alignment explanation
Indices: 56317--56453 Score: 208
Period size: 52 Copynumber: 2.5 Consensus size: 55
56307 GATTCTCCCG
*
56317 TTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCCGCATTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTT-CGCATTGCGA--TTCATCTCCG-ATTGCGATTTTCATTTCGCA
56376 TTGCGATTTTCATTTCGCATTGCGATTC-TCT-CG-TTGCGATTTTCATTTCGCA
1 TTGCGATTTTCATTTCGCATTGCGATTCATCTCCGATTGCGATTTTCATTTCGCA
56428 TTGCGATTTTCATTTCGCATTGCGAT
1 TTGCGATTTTCATTTCGCATTGCGAT
56454 AGTCAATTTT
Statistics
Matches: 77, Mismatches: 1, Indels: 7
0.91 0.01 0.08
Matches are distributed among these distances:
52 45 0.58
54 2 0.03
55 2 0.03
56 3 0.04
58 10 0.13
59 15 0.19
ACGTcount: A:0.15, C:0.23, G:0.17, T:0.46
Consensus pattern (55 bp):
TTGCGATTTTCATTTCGCATTGCGATTCATCTCCGATTGCGATTTTCATTTCGCA
Found at i:56579 original size:14 final size:14
Alignment explanation
Indices: 56560--56596 Score: 65
Period size: 14 Copynumber: 2.6 Consensus size: 14
56550 CATCAATTAC
56560 ACAAATCAACTTTT
1 ACAAATCAACTTTT
*
56574 ACAAATCATCTTTT
1 ACAAATCAACTTTT
56588 ACAAATCAA
1 ACAAATCAA
56597 TTAAACAATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.22, G:0.00, T:0.32
Consensus pattern (14 bp):
ACAAATCAACTTTT
Found at i:58592 original size:14 final size:14
Alignment explanation
Indices: 58573--58629 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
58563 GCGAAATGAA
*
58573 AATCGCAACGACAG
1 AATCGCAACGAAAG
58587 AATCGCAATGCGAAATG
1 AATCGCAA--CGAAA-G
58604 AAAATCGCAACGAAAG
1 --AATCGCAACGAAAG
58620 AATCGCAACG
1 AATCGCAACG
58630 CGAAATGAAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 18 0.49
16 5 0.14
17 6 0.16
19 8 0.22
ACGTcount: A:0.46, C:0.23, G:0.21, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAAAG
Found at i:58600 original size:33 final size:33
Alignment explanation
Indices: 58554--58646 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
58544 GCGAAACCAA
*
58554 AATCGCAACGCGAAATGAAAATCGCAACGACAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
*
58587 AATCGCAATGCGAAATGAAAATCGCAACGAAAG
1 AATCGCAACGCGAAATGAAAATCGCAACGAAAG
58620 AATCGCAACGCGAAATGAAAATCGCAA
1 AATCGCAACGCGAAATGAAAATCGCAA
58647 TGCGATTTTG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.47, C:0.22, G:0.20, T:0.11
Consensus pattern (33 bp):
AATCGCAACGCGAAATGAAAATCGCAACGAAAG
Found at i:58611 original size:19 final size:19
Alignment explanation
Indices: 58517--58651 Score: 128
Period size: 19 Copynumber: 7.6 Consensus size: 19
58507 TAGTTTACTT
* *
58517 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAA-TGAAAA
**
58537 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAATGAAAA
58556 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
58575 TCGCAA--CGACA-G--AA
1 TCGCAACGCGAAATGAAAA
*
58589 TCGCAATGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
58608 TCGCAA--CGAAA-G--AA
1 TCGCAACGCGAAATGAAAA
58622 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAATGAAAA
*
58641 TCGCAATGCGA
1 TCGCAACGCGA
58652 TTTTGGTTTC
Statistics
Matches: 97, Mismatches: 8, Indels: 21
0.77 0.06 0.17
Matches are distributed among these distances:
14 16 0.16
16 11 0.11
17 11 0.11
19 47 0.48
20 12 0.12
ACGTcount: A:0.46, C:0.24, G:0.19, T:0.11
Consensus pattern (19 bp):
TCGCAACGCGAAATGAAAA
Found at i:58669 original size:19 final size:19
Alignment explanation
Indices: 58647--58775 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
58637 AAAATCGCAA
58647 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
58666 TGCGATCTT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
58680 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
*
58699 TGCGATTCT-G--T--CGT
1 TGCGATTTTGGTTTCGCGT
**
58713 TGCGATTTTCATTTCGCGT
1 TGCGATTTTGGTTTCGCGT
58732 TGCGATTTTGGTTTCGCGT
1 TGCGATTTTGGTTTCGCGT
* *
58751 TGCGATTTTAAGTTTCGTGT
1 TGCGATTTT-GGTTTCGCGT
58771 TGCGA
1 TGCGA
58776 AAGTAAACTA
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 22 0.24
15 1 0.01
16 2 0.02
17 2 0.02
18 2 0.02
19 48 0.53
20 13 0.14
ACGTcount: A:0.09, C:0.17, G:0.29, T:0.46
Consensus pattern (19 bp):
TGCGATTTTGGTTTCGCGT
Found at i:58689 original size:33 final size:33
Alignment explanation
Indices: 58647--58738 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 33
58637 AAAATCGCAA
58647 TGCGATTTTGGTTTCGCGTTGCGA-TCTTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTC-TGTCGT
58680 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
1 TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
**
58713 TGCGATTTTCATTTCGCGTTGCGATT
1 TGCGATTTTGGTTTCGCGTTGCGATT
58739 TTGGTTTCGC
Statistics
Matches: 56, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
33 54 0.96
34 2 0.04
ACGTcount: A:0.08, C:0.18, G:0.28, T:0.46
Consensus pattern (33 bp):
TGCGATTTTGGTTTCGCGTTGCGATTCTGTCGT
Found at i:58982 original size:93 final size:93
Alignment explanation
Indices: 58823--59292 Score: 895
Period size: 93 Copynumber: 5.1 Consensus size: 93
58813 ATGGATTGCA
58823 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
58888 TAGCAGAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
58916 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
58981 TAGCAGAATTGACAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
*
59009 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCATAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
59074 TAGCAGAATTGACAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
59102 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
59167 TAGCATAATTGGCAGCAACCGAACAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
59195 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
1 TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
*
59260 TAGCAGAATTGGCAGCAACCGAATAAAT
66 TAGCAGAATTGGCAGCAACCGAACAAAT
59288 TTACT
1 TTACT
59293 AAGCAATCTA
Statistics
Matches: 370, Mismatches: 7, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
93 370 1.00
ACGTcount: A:0.46, C:0.19, G:0.12, T:0.23
Consensus pattern (93 bp):
TTACTTTCAACCAAAAGACAAAACAAAGACAAATACTATTTCACAGTGTTAAAGAATACACAGTT
TAGCAGAATTGGCAGCAACCGAACAAAT
Found at i:61018 original size:14 final size:14
Alignment explanation
Indices: 60999--61088 Score: 54
Period size: 14 Copynumber: 5.7 Consensus size: 14
60989 TTGAAATGAA
60999 AATCGCAACGAGAG
1 AATCGCAACGAGAG
*
61013 AATCGCAAAGCGAAATGAC
1 AATCGC-AA-CG--A-GAG
*
61032 AATCGCAACGAGAT
1 AATCGCAACGAGAG
* *
61046 AATCGTAACGCGAAATGAA
1 AATCGCAA--CG--A-GAG
61065 AATCGCAACGAGAG
1 AATCGCAACGAGAG
61079 AATCGCAACG
1 AATCGCAACG
61089 CGAAATGAAA
Statistics
Matches: 60, Mismatches: 6, Indels: 20
0.70 0.07 0.23
Matches are distributed among these distances:
14 27 0.45
15 4 0.07
16 4 0.07
17 4 0.07
18 4 0.07
19 17 0.28
ACGTcount: A:0.44, C:0.21, G:0.23, T:0.11
Consensus pattern (14 bp):
AATCGCAACGAGAG
Found at i:61036 original size:33 final size:33
Alignment explanation
Indices: 60991--61105 Score: 194
Period size: 33 Copynumber: 3.5 Consensus size: 33
60981 TCTTTTGGTT
*
60991 GAAATGAAAATCGCAACGAGAGAATCGCAAAGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
* * *
61024 GAAATGACAATCGCAACGAGATAATCGTAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
61057 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
1 GAAATGAAAATCGCAACGAGAGAATCGCAACGC
61090 GAAATGAAAATCGCAA
1 GAAATGAAAATCGCAA
61106 TGCGATTTTG
Statistics
Matches: 75, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 75 1.00
ACGTcount: A:0.47, C:0.19, G:0.23, T:0.11
Consensus pattern (33 bp):
GAAATGAAAATCGCAACGAGAGAATCGCAACGC
Found at i:61074 original size:19 final size:18
Alignment explanation
Indices: 60991--61110 Score: 75
Period size: 19 Copynumber: 7.1 Consensus size: 18
60981 TCTTTTGGTT
60991 GAAATGAAAATCGCAA-C
1 GAAATGAAAATCGCAAGC
*
61008 G--A-GAGAATCGCAAAGC
1 GAAATGAAAATCGC-AAGC
*
61024 GAAATGACAATCGCAA-C
1 GAAATGAAAATCGCAAGC
* *
61041 G--A-GATAATCGTAACGC
1 GAAATGAAAATCGCAA-GC
61057 GAAATGAAAATCGCAA-C
1 GAAATGAAAATCGCAAGC
*
61074 G--A-GAGAATCGCAACGC
1 GAAATGAAAATCGCAA-GC
61090 GAAATGAAAATCGCAATGC
1 GAAATGAAAATCGCAA-GC
61109 GA
1 GA
61111 TTTTGGTTTC
Statistics
Matches: 79, Mismatches: 9, Indels: 28
0.68 0.08 0.24
Matches are distributed among these distances:
14 27 0.34
15 5 0.06
16 6 0.08
17 5 0.06
18 5 0.06
19 31 0.39
ACGTcount: A:0.46, C:0.19, G:0.23, T:0.12
Consensus pattern (18 bp):
GAAATGAAAATCGCAAGC
Found at i:61141 original size:14 final size:14
Alignment explanation
Indices: 61122--61178 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
61112 TTTGGTTTCG
61122 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
61136 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
61155 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
61169 CGTTGCGATT
1 CGTTGCGATT
61179 TTCATTTCTC
Statistics
Matches: 36, Mismatches: 2, Indels: 10
0.75 0.04 0.21
Matches are distributed among these distances:
14 20 0.56
16 3 0.08
17 3 0.08
19 10 0.28
ACGTcount: A:0.09, C:0.25, G:0.23, T:0.44
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:61154 original size:33 final size:33
Alignment explanation
Indices: 61106--61186 Score: 144
Period size: 33 Copynumber: 2.5 Consensus size: 33
61096 AAAATCGCAA
**
61106 TGCGATTTTGGTTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
61139 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
1 TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
61172 TGCGATTTTCATTTC
1 TGCGATTTTCATTTC
61187 TCTCGTTGCG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
33 46 1.00
ACGTcount: A:0.09, C:0.22, G:0.22, T:0.47
Consensus pattern (33 bp):
TGCGATTTTCATTTCGCGTTGCGATTCTCTCGT
Found at i:61189 original size:21 final size:21
Alignment explanation
Indices: 61163--61238 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
61153 CGCGTTGCGA
61163 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
***
61184 TTCTCTCGTTGCGACAGTCA-
1 TTCTCTCGTTGCGATTTTCAT
61204 TTCTCTCGTTGCGATTTTCAT
1 TTCTCTCGTTGCGATTTTCAT
*
61225 TTATCTCGTTGCGA
1 TTCTCTCGTTGCGA
61239 CTCTTCTGCA
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.12, C:0.25, G:0.17, T:0.46
Consensus pattern (21 bp):
TTCTCTCGTTGCGATTTTCAT
Found at i:61219 original size:41 final size:41
Alignment explanation
Indices: 61162--61239 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
61152 TCGCGTTGCG
*
61162 ATTCTCTCGTTGCGATTTTCATTTCTCTCGTTGCGACAGTC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
61203 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
1 ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGAC
61240 TCTTCTGCAA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.13, C:0.26, G:0.17, T:0.45
Consensus pattern (41 bp):
ATTCTCTCGTTGCGATTTTCATTTATCTCGTTGCGACAGTC
Found at i:61363 original size:33 final size:33
Alignment explanation
Indices: 61318--61388 Score: 97
Period size: 33 Copynumber: 2.2 Consensus size: 33
61308 AATACTAACT
* *
61318 TGAAAATCGCAACGAGAGAATAGCAACGCGAAA
1 TGAAAATAGCAACGACAGAATAGCAACGCGAAA
* * *
61351 TGAAAATAGCAACGACAGAATCGTAACGTGAAA
1 TGAAAATAGCAACGACAGAATAGCAACGCGAAA
61384 TGAAA
1 TGAAA
61389 TCTAAGTGAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.49, C:0.15, G:0.23, T:0.13
Consensus pattern (33 bp):
TGAAAATAGCAACGACAGAATAGCAACGCGAAA
Found at i:61622 original size:22 final size:22
Alignment explanation
Indices: 61570--61624 Score: 83
Period size: 22 Copynumber: 2.5 Consensus size: 22
61560 TGGTTGTGAG
*
61570 GGATTTCGTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
**
61592 GGAAATCTTCGGAGATGGGGAC
1 GGATTTCTTCGGAGATGGGGAC
61614 GGATTTCTTCG
1 GGATTTCTTCG
61625 CCGTAGAGAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.20, C:0.15, G:0.40, T:0.25
Consensus pattern (22 bp):
GGATTTCTTCGGAGATGGGGAC
Found at i:61796 original size:20 final size:20
Alignment explanation
Indices: 61766--61884 Score: 98
Period size: 20 Copynumber: 5.8 Consensus size: 20
61756 TGGCGCTTTA
61766 AATATCGCGTTGCGATTTACG
1 AATA-CGCGTTGCGATTTACG
*
61787 AATACGCGTTGCGATTTTATG
1 AATACGCGTTGCGA-TTTACG
* *
61808 TATTA-TCGTTGCGATTTACG
1 -AATACGCGTTGCGATTTACG
* *
61828 GATACGCGTTGCGATTTATG
1 AATACGCGTTGCGATTTACG
** * *
61848 TGTTCGCGTTGCGATTTTC-
1 AATACGCGTTGCGATTTACG
*
61867 ATATTCGCGTTGCGATTT
1 A-ATACGCGTTGCGATTT
61885 TGGAAAATCG
Statistics
Matches: 79, Mismatches: 15, Indels: 9
0.77 0.15 0.09
Matches are distributed among these distances:
19 2 0.03
20 57 0.72
21 17 0.22
22 3 0.04
ACGTcount: A:0.18, C:0.17, G:0.24, T:0.40
Consensus pattern (20 bp):
AATACGCGTTGCGATTTACG
Found at i:61827 original size:41 final size:41
Alignment explanation
Indices: 61772--61885 Score: 151
Period size: 40 Copynumber: 2.8 Consensus size: 41
61762 TTTAAATATC
61772 GCGTTGCGATTTACGAATACGCGTTGCGATTTTATGTATTA
1 GCGTTGCGATTTACGAATACGCGTTGCGATTTTATGTATTA
* * * *
61813 TCGTTGCGATTTACGGATACGCGTTGCGA-TTTATGTGTTC
1 GCGTTGCGATTTACGAATACGCGTTGCGATTTTATGTATTA
* *
61853 GCGTTGCGATTTTC-ATATTCGCGTTGCGATTTT
1 GCGTTGCGATTTACGA-ATACGCGTTGCGATTTT
61886 GGAAAATCGC
Statistics
Matches: 63, Mismatches: 8, Indels: 4
0.84 0.11 0.05
Matches are distributed among these distances:
40 33 0.52
41 30 0.48
ACGTcount: A:0.17, C:0.17, G:0.25, T:0.41
Consensus pattern (41 bp):
GCGTTGCGATTTACGAATACGCGTTGCGATTTTATGTATTA
Found at i:61901 original size:21 final size:21
Alignment explanation
Indices: 61871--61953 Score: 78
Period size: 21 Copynumber: 4.0 Consensus size: 21
61861 ATTTTCATAT
*
61871 TCGCGTTGCGATTTTGGAAAA
1 TCGCATTGCGATTTTGGAAAA
* * * **
61892 TCGCAATGCGAATTTGTACTA
1 TCGCATTGCGATTTTGGAAAA
*
61913 TCGCATTGCGATTTT-CAAGAA
1 TCGCATTGCGATTTTGGAA-AA
*
61934 TCGCGTTGCGATTTTGGAAA
1 TCGCATTGCGATTTTGGAAA
61954 CTGATTTGCG
Statistics
Matches: 47, Mismatches: 13, Indels: 4
0.73 0.20 0.06
Matches are distributed among these distances:
20 1 0.02
21 44 0.94
22 2 0.04
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (21 bp):
TCGCATTGCGATTTTGGAAAA
Found at i:61944 original size:42 final size:43
Alignment explanation
Indices: 61851--61949 Score: 100
Period size: 42 Copynumber: 2.4 Consensus size: 43
61841 ATTTATGTGT
* *
61851 TCGCGTTGCG-ATTT-TCATATTCGCGTTGCGATTTTGGAAAA
1 TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
**
61892 TCGCAATGCGAATTTGT-ACTA-TCGCATTGCGATTTT-CAAGAA
1 TCGCGTTGCGAATTTGTCA-TATTCGCATTGCGATTTTGCAA-AA
*
61934 TCGCGTTGCGATTTTG
1 TCGCGTTGCGAATTTG
61950 GAAACTGATT
Statistics
Matches: 47, Mismatches: 7, Indels: 7
0.77 0.11 0.11
Matches are distributed among these distances:
41 10 0.21
42 34 0.72
43 3 0.06
ACGTcount: A:0.21, C:0.18, G:0.23, T:0.37
Consensus pattern (43 bp):
TCGCGTTGCGAATTTGTCATATTCGCATTGCGATTTTGCAAAA
Found at i:68382 original size:17 final size:19
Alignment explanation
Indices: 68351--68390 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
68341 ATTAAATTCC
68351 TATTTTTATTGAATAAA-A
1 TATTTTTATTGAATAAATA
*
68369 TATTTTT-TTTAATAAATA
1 TATTTTTATTGAATAAATA
68387 TATT
1 TATT
68391 ATTTCGGGTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (19 bp):
TATTTTTATTGAATAAATA
Found at i:75863 original size:23 final size:23
Alignment explanation
Indices: 75837--75895 Score: 73
Period size: 23 Copynumber: 2.6 Consensus size: 23
75827 AACCATAAAG
* *
75837 AACGTGCCACAAGAGCAGAGAAA
1 AACGTGCCACAAAAACAGAGAAA
*
75860 AACGTGTCACAAAAACAGAGAAA
1 AACGTGCCACAAAAACAGAGAAA
**
75883 AACGAACCACAAA
1 AACGTGCCACAAA
75896 GACAAATATT
Statistics
Matches: 30, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 30 1.00
ACGTcount: A:0.54, C:0.22, G:0.19, T:0.05
Consensus pattern (23 bp):
AACGTGCCACAAAAACAGAGAAA
Found at i:78296 original size:81 final size:81
Alignment explanation
Indices: 78161--78322 Score: 306
Period size: 81 Copynumber: 2.0 Consensus size: 81
78151 GAGTTAGGAA
*
78161 CTGAATGGGAAAACTTTCATTACAGTAGTTTTTCATATGTTACATATCTAATATAAGTCTTACGT
1 CTGAATGGGAAAACTTTCATTACAATAGTTTTTCATATGTTACATATCTAATATAAGTCTTACGT
78226 TTTTTCTGTCGATGCT
66 TTTTTCTGTCGATGCT
78242 CTGAATGGGAAAACTTTCATTACAATAGTTTTTCATATGTTACATATCTAATATAAGTCTTACGT
1 CTGAATGGGAAAACTTTCATTACAATAGTTTTTCATATGTTACATATCTAATATAAGTCTTACGT
*
78307 TTTTTCTGTTGATGCT
66 TTTTTCTGTCGATGCT
78323 TGGGCATTGG
Statistics
Matches: 79, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
81 79 1.00
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.44
Consensus pattern (81 bp):
CTGAATGGGAAAACTTTCATTACAATAGTTTTTCATATGTTACATATCTAATATAAGTCTTACGT
TTTTTCTGTCGATGCT
Found at i:80082 original size:3 final size:3
Alignment explanation
Indices: 80074--80100 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
80064 TTAAAATATT
80074 ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA
80101 CATTAAAAAG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:87255 original size:2 final size:2
Alignment explanation
Indices: 87248--87307 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
87238 TATTTCAAAT
87248 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
87290 TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA
87308 ACCACTGAAT
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):
TA
Found at i:89263 original size:42 final size:42
Alignment explanation
Indices: 89206--89297 Score: 157
Period size: 42 Copynumber: 2.2 Consensus size: 42
89196 TGTTTCCCTG
*
89206 ATGAGAATGAGGAGATCATGTTGTGGAAAAATCTGATGATGA
1 ATGAGAATGAGGAGATCATGTTGTGGAAAAATCTGACGATGA
* *
89248 ATGAGAATGATGAGATCATGTTGTGGAAAAATGTGACGATGA
1 ATGAGAATGAGGAGATCATGTTGTGGAAAAATCTGACGATGA
89290 ATGAGAAT
1 ATGAGAAT
89298 TTGGTCGATT
Statistics
Matches: 47, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
42 47 1.00
ACGTcount: A:0.39, C:0.04, G:0.30, T:0.26
Consensus pattern (42 bp):
ATGAGAATGAGGAGATCATGTTGTGGAAAAATCTGACGATGA
Found at i:89715 original size:36 final size:35
Alignment explanation
Indices: 89638--89776 Score: 190
Period size: 36 Copynumber: 3.9 Consensus size: 35
89628 AAAAATGAAC
* * * *
89638 ACTTGAATTGAAAGTGCGACGCCTCATTCCGTTCG
1 ACTTGAATCGAAAGTGCGATGCTTCCTTCCGTTCG
*
89673 ACTTGAATCGAAAGTGCCGATGCTTCCTTCCATTCG
1 ACTTGAATCGAAAGTG-CGATGCTTCCTTCCGTTCG
*
89709 ACTTGAATCGGAAGTGTCGATGCTTCCTTCCGTTC-
1 ACTTGAATCGAAAGTG-CGATGCTTCCTTCCGTTCG
*
89744 ACTTGAATCGGAAGTGCGATGCTTCCTTCCGTT
1 ACTTGAATCGAAAGTGCGATGCTTCCTTCCGTT
89777 ATTCTTGTTC
Statistics
Matches: 95, Mismatches: 8, Indels: 3
0.90 0.08 0.03
Matches are distributed among these distances:
34 17 0.18
35 31 0.33
36 47 0.49
ACGTcount: A:0.20, C:0.26, G:0.22, T:0.32
Consensus pattern (35 bp):
ACTTGAATCGAAAGTGCGATGCTTCCTTCCGTTCG
Found at i:89724 original size:71 final size:70
Alignment explanation
Indices: 89638--89773 Score: 193
Period size: 71 Copynumber: 1.9 Consensus size: 70
89628 AAAAATGAAC
*
89638 ACTTGAATTGAAAGTG-CGACGCCTCATTCCGTTCGACTTGAATCGAAAGTGCCGATGCTTCCTT
1 ACTTGAATCGAAAGTGTCGACGCCTCATTCCGTTC-ACTTGAATCGAAAGTG-CGATGCTTCCTT
89702 CCATTCG
64 CCATTCG
* * * * *
89709 ACTTGAATCGGAAGTGTCGATGCTTCCTTCCGTTCACTTGAATCGGAAGTGCGATGCTTCCTTCC
1 ACTTGAATCGAAAGTGTCGACGCCTCATTCCGTTCACTTGAATCGAAAGTGCGATGCTTCCTTCC
89774 GTTATTCTTG
Statistics
Matches: 58, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
70 14 0.24
71 29 0.50
72 15 0.26
ACGTcount: A:0.21, C:0.26, G:0.22, T:0.31
Consensus pattern (70 bp):
ACTTGAATCGAAAGTGTCGACGCCTCATTCCGTTCACTTGAATCGAAAGTGCGATGCTTCCTTCC
ATTCG
Found at i:98000 original size:84 final size:84
Alignment explanation
Indices: 97871--98084 Score: 227
Period size: 84 Copynumber: 2.5 Consensus size: 84
97861 TCTTGCTTGG
* * * * * * * * *
97871 AACTGCTTGGGGCATCCTACAATGGATAGTTGGACAGATCGGAGTTGTTTCTCTTTTGAATGGAG
1 AACTGCTTCGTGCATCTTTCAATCGATATTTGGACCGAGCTGAGTTGTTTCTCTTTTGAATGGAG
97936 CTCTTCATCCTTTGC-TCC
66 CTCTTCATCCTTTGCTTCC
* *
97954 AAGCTGCTTCGTGCAT-TCTTCAATCGATATTTGGACC-ATGCTGAGTTTTTTCTCTTTTGAGTG
1 AA-CTGCTTCGTGCATCT-TTCAATCGATATTTGGACCGA-GCTGAGTTGTTTCTCTTTTGAATG
* *
98017 GAGCTCTTCTTCCTTTGCTTCG
63 GAGCTCTTCATCCTTTGCTTCC
* * * *
98039 AACTGTTTGGTGCATCTTTCTATTGATATTTGGACCGAGCTGAGTT
1 AACTGCTTCGTGCATCTTTCAATCGATATTTGGACCGAGCTGAGTT
98085 CTCTCTTTCG
Statistics
Matches: 108, Mismatches: 17, Indels: 11
0.79 0.12 0.08
Matches are distributed among these distances:
83 3 0.03
84 99 0.92
85 6 0.06
ACGTcount: A:0.17, C:0.21, G:0.22, T:0.40
Consensus pattern (84 bp):
AACTGCTTCGTGCATCTTTCAATCGATATTTGGACCGAGCTGAGTTGTTTCTCTTTTGAATGGAG
CTCTTCATCCTTTGCTTCC
Found at i:98396 original size:83 final size:83
Alignment explanation
Indices: 98257--98477 Score: 390
Period size: 83 Copynumber: 2.7 Consensus size: 83
98247 GATTGAGGCA
*
98257 AGCTCTTCCTCCTTTTCTTCGAGCTGCTTGGTGCATCCTTCTATCGAAATTTGGACCGACCGAGC
1 AGCTCTTTCTCCTTTTCTTCGAGCTGCTTGGTGCATCCTTCTATCGAAATTTGGACCGACCGAGC
98322 TGTTTCTCTGTCAAATGG
66 TGTTTCTCTGTCAAATGG
98340 AGCTCTTTCTCCTTTTCTTCGAGCTGCTTGGTGCATCCTTCTATCGAAATTTGGACCGACCGAGC
1 AGCTCTTTCTCCTTTTCTTCGAGCTGCTTGGTGCATCCTTCTATCGAAATTTGGACCGACCGAGC
98405 TGTTTCTCTGTCAAATGG
66 TGTTTCTCTGTCAAATGG
* * *
98423 AGCTCTTTCTCCTTTTCTTCGAGCTTCTTGGAGCATCCTT-TGATCGATATTTGGA
1 AGCTCTTTCTCCTTTTCTTCGAGCTGCTTGGTGCATCCTTCT-ATCGAAATTTGGA
98478 TCTAGTTGAG
Statistics
Matches: 133, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
82 1 0.01
83 132 0.99
ACGTcount: A:0.15, C:0.26, G:0.20, T:0.38
Consensus pattern (83 bp):
AGCTCTTTCTCCTTTTCTTCGAGCTGCTTGGTGCATCCTTCTATCGAAATTTGGACCGACCGAGC
TGTTTCTCTGTCAAATGG
Done.