Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005918.1 Hibiscus syriacus cultivar Beakdansim tig00013896_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: 68784
ACGTcount: A:0.33, C:0.16, G:0.18, T:0.33
Found at i:981 original size:24 final size:24
Alignment explanation
Indices: 954--1011 Score: 89
Period size: 24 Copynumber: 2.4 Consensus size: 24
944 TAGTTAATGC
* *
954 ATCGATGCACATATTACTGAGTGT
1 ATCGATGCACATACTACAGAGTGT
978 ATCGATGCACATACTACAGAGTGT
1 ATCGATGCACATACTACAGAGTGT
*
1002 ACCGATGCAC
1 ATCGATGCAC
1012 TTCAAGGAAA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (24 bp):
ATCGATGCACATACTACAGAGTGT
Found at i:2045 original size:2 final size:2
Alignment explanation
Indices: 2038--2074 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
2028 TAGGAATTTG
2038 TA TA TA TA TA TA 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 TA TA TA TA TA TA T
2075 GTGTGTGTGT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:10653 original size:32 final size:32
Alignment explanation
Indices: 10617--10681 Score: 85
Period size: 32 Copynumber: 2.0 Consensus size: 32
10607 CAGGTCAATA
*
10617 TTGGGTCAAGTCAAGACCGGATCAGTTGATTT
1 TTGGGTCAAGTCAAGACCAGATCAGTTGATTT
* * * *
10649 TTGGGTCAGGTTAATACCAGATCGGTTGATTT
1 TTGGGTCAAGTCAAGACCAGATCAGTTGATTT
10681 T
1 T
10682 CGGTTTAGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.23, C:0.14, G:0.28, T:0.35
Consensus pattern (32 bp):
TTGGGTCAAGTCAAGACCAGATCAGTTGATTT
Found at i:11139 original size:18 final size:19
Alignment explanation
Indices: 11103--11141 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
11093 AAGTAAACTT
*
11103 TATATTATTTTTATTATAAA
1 TATAATATTTTTA-TATAAA
11123 TATAATATTTTTA-ATAAA
1 TATAATATTTTTATATAAA
11141 T
1 T
11142 TATCAATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 6 0.33
20 12 0.67
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (19 bp):
TATAATATTTTTATATAAA
Found at i:11253 original size:16 final size:16
Alignment explanation
Indices: 11234--11283 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
11224 TGCTTTTGGG
11234 TCGGGTTAAATTCGGT
1 TCGGGTTAAATTCGGT
** *
11250 TCGGGTTACTTTCGGA
1 TCGGGTTAAATTCGGT
*
11266 TCGAGTTAAAATTCGGT
1 TCGGGTT-AAATTCGGT
11283 T
1 T
11284 TGAGTTTCTT
Statistics
Matches: 26, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
16 19 0.73
17 7 0.27
ACGTcount: A:0.20, C:0.14, G:0.28, T:0.38
Consensus pattern (16 bp):
TCGGGTTAAATTCGGT
Found at i:11336 original size:16 final size:16
Alignment explanation
Indices: 11317--11396 Score: 70
Period size: 16 Copynumber: 5.0 Consensus size: 16
11307 TTTTTGGTTC
11317 GGGTTAATTTCAGTTT
1 GGGTTAATTTCAGTTT
** * *
11333 GGGTTGCTTTCGGTTC
1 GGGTTAATTTCAGTTT
*
11349 GGGTTATTTTCAGTTT
1 GGGTTAATTTCAGTTT
** ** *
11365 GGGTTGCTTTTGGTTC
1 GGGTTAATTTCAGTTT
11381 GGGTTAATTTCAGTTT
1 GGGTTAATTTCAGTTT
11397 CGATTCGAGT
Statistics
Matches: 46, Mismatches: 18, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
16 46 1.00
ACGTcount: A:0.10, C:0.10, G:0.30, T:0.50
Consensus pattern (16 bp):
GGGTTAATTTCAGTTT
Found at i:11348 original size:32 final size:32
Alignment explanation
Indices: 11302--11396 Score: 163
Period size: 32 Copynumber: 3.0 Consensus size: 32
11292 TTTCGGTTCA
*
11302 GGTTGTTTTTGGTTCGGGTTAATTTCAGTTTG
1 GGTTGCTTTTGGTTCGGGTTAATTTCAGTTTG
* *
11334 GGTTGCTTTCGGTTCGGGTTATTTTCAGTTTG
1 GGTTGCTTTTGGTTCGGGTTAATTTCAGTTTG
11366 GGTTGCTTTTGGTTCGGGTTAATTTCAGTTT
1 GGTTGCTTTTGGTTCGGGTTAATTTCAGTTT
11397 CGATTCGAGT
Statistics
Matches: 58, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
32 58 1.00
ACGTcount: A:0.08, C:0.09, G:0.31, T:0.52
Consensus pattern (32 bp):
GGTTGCTTTTGGTTCGGGTTAATTTCAGTTTG
Found at i:11369 original size:48 final size:49
Alignment explanation
Indices: 11244--11369 Score: 137
Period size: 48 Copynumber: 2.6 Consensus size: 49
11234 TCGGGTTAAA
* * * * *
11244 TTCGGTTCGGGTTACTTTCGGATCGAGTTAAAATTCGGTTTGAGTTTCT
1 TTCGGTTCGGGTTATTTTCGGTTCGGGTTAAAATTCAGTTTGAGTTGCT
* * * * *
11293 TTCGGTTCAGGTTGTTTTTGGTTCGGGTT-AATTTCAGTTTGGGTTGCT
1 TTCGGTTCGGGTTATTTTCGGTTCGGGTTAAAATTCAGTTTGAGTTGCT
* *
11341 TTCGGTTCGGGTTATTTTCAGTTTGGGTT
1 TTCGGTTCGGGTTATTTTCGGTTCGGGTT
11370 GCTTTTGGTT
Statistics
Matches: 62, Mismatches: 15, Indels: 1
0.79 0.19 0.01
Matches are distributed among these distances:
48 39 0.63
49 23 0.37
ACGTcount: A:0.11, C:0.12, G:0.29, T:0.48
Consensus pattern (49 bp):
TTCGGTTCGGGTTATTTTCGGTTCGGGTTAAAATTCAGTTTGAGTTGCT
Found at i:16035 original size:24 final size:24
Alignment explanation
Indices: 15995--16042 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
15985 TCATGGATTA
15995 ATTTAATTATAAATTAAAAAATAT
1 ATTTAATTATAAATTAAAAAATAT
*
16019 ATTTATTTA-AAATTTAAAAAATAT
1 ATTTAATTATAAA-TTAAAAAATAT
16043 TAAATCAATG
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 3 0.14
24 19 0.86
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (24 bp):
ATTTAATTATAAATTAAAAAATAT
Found at i:20522 original size:20 final size:22
Alignment explanation
Indices: 20480--20521 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 22
20470 AAGAGTACAA
*
20480 ATATAGAAATAATTTAAATTTT
1 ATATAGAAATAATATAAATTTT
*
20502 ATATA-AAATTATATAAATTT
1 ATATAGAAATAATATAAATTT
20522 AAAAAACGGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 13 0.72
22 5 0.28
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.45
Consensus pattern (22 bp):
ATATAGAAATAATATAAATTTT
Found at i:20989 original size:25 final size:25
Alignment explanation
Indices: 20949--20997 Score: 71
Period size: 25 Copynumber: 2.0 Consensus size: 25
20939 GATATTATTT
*
20949 TTTTCTACCCGATATTAGGGTTCTC
1 TTTTCTACCCGATATTAAGGTTCTC
* *
20974 TTTTCTACTCGGTATTAAGGTTCT
1 TTTTCTACCCGATATTAAGGTTCT
20998 TTGCCGCCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 21 1.00
ACGTcount: A:0.16, C:0.20, G:0.16, T:0.47
Consensus pattern (25 bp):
TTTTCTACCCGATATTAAGGTTCTC
Found at i:22199 original size:55 final size:55
Alignment explanation
Indices: 22131--22589 Score: 659
Period size: 55 Copynumber: 8.3 Consensus size: 55
22121 TTTCGTGGGT
* *
22131 TGCACAC-ATAGTGCATGTATGGTGATTCATCCACTCAGGATGAATTCCGTGAATA
1 TGCACACGA-AGTGCCTGTACGGTGATTCATCCACTCAGGATGAATTCCGTGAATA
* * * *
22186 TGCACACGAAGTGCCTATACAGTGATTTATCCACTCAGGATGAATTCCGTTAATA
1 TGCACACGAAGTGCCTGTACGGTGATTCATCCACTCAGGATGAATTCCGTGAATA
* * *
22241 TGCACACGAAGTACCTGTACGGTGATTCATCCACTCAGGATGAATTTCATGAATA
1 TGCACACGAAGTGCCTGTACGGTGATTCATCCACTCAGGATGAATTCCGTGAATA
*
22296 TGCAAACGAAGTGCCTGTACGGTGATTCATCCACTCAGGATGAATTCCGTGAATA
1 TGCACACGAAGTGCCTGTACGGTGATTCATCCACTCAGGATGAATTCCGTGAATA
* * * *
22351 TGCACATGAAGTGCCTGTACGGTGATTTATCCACTTAGGATGAATTCCATGAATA
1 TGCACACGAAGTGCCTGTACGGTGATTCATCCACTCAGGATGAATTCCGTGAATA
* * * *
22406 TGCACACAAAGTGCCTATACGTTGATTCATCCACTCAGGATGAATTTCGTGAATA
1 TGCACACGAAGTGCCTGTACGGTGATTCATCCACTCAGGATGAATTCCGTGAATA
* * * **
22461 TGCACACGAAGTGCATCTACGGTGATTCATCCACTCATGATGAATTTTGTGAATA
1 TGCACACGAAGTGCCTGTACGGTGATTCATCCACTCAGGATGAATTCCGTGAATA
* *
22516 TGCATACGAAGTGCCTGTATGGTGATTCATCCACTCAGGATGAATTCCGTGAATA
1 TGCACACGAAGTGCCTGTACGGTGATTCATCCACTCAGGATGAATTCCGTGAATA
* *
22571 TGCACACAAAGTGCATGTA
1 TGCACACGAAGTGCCTGTA
22590 GTACACATAG
Statistics
Matches: 357, Mismatches: 46, Indels: 2
0.88 0.11 0.00
Matches are distributed among these distances:
55 356 1.00
56 1 0.00
ACGTcount: A:0.30, C:0.21, G:0.21, T:0.29
Consensus pattern (55 bp):
TGCACACGAAGTGCCTGTACGGTGATTCATCCACTCAGGATGAATTCCGTGAATA
Found at i:24473 original size:183 final size:182
Alignment explanation
Indices: 24163--24523 Score: 679
Period size: 183 Copynumber: 2.0 Consensus size: 182
24153 ATAAATCTAA
24163 GGATTCTATGTTATTTTTGTTGGATTTAGGCTATTGGAAGTATTCTAATCCTTATTTTCATTACA
1 GGATTCTATGTTATTTTTG-TGGATTTAGGCTATTGGAAGTATTCTAATCCTTATTTTCATTACA
*
24228 TAGATTATTTAGAAACTTCTCTTTTTTATCTTTATTAGTGAAAGAAGTGGGTGAAGCCTCCAAGA
65 TAGATTATTTAGAAACTTCTCTTTTTTATCTTTATTAGTGAAAGAAGTGGGTGAAACCTCCAAGA
24293 TAAAGGGGAAGGAAAAATCTTTCATTGAGTGAGTTGGAGCTTTGTTTTTTGTT
130 TAAAGGGGAAGGAAAAATCTTTCATTGAGTGAGTTGGAGCTTTGTTTTTTGTT
24346 GGATTCTATGTTATTTTTG-GGAGGTTTAGGCTATTGGAAGTATTCTAATCCTTATTTTCATTAC
1 GGATTCTATGTTATTTTTGTGGA--TTTAGGCTATTGGAAGTATTCTAATCCTTATTTTCATTAC
24410 ATAGATTATTTAGAAACTTCTCTTTTTTATCTTTATTAGTGAAAGAAGTGGGTGAAACCTCCAAG
64 ATAGATTATTTAGAAACTTCTCTTTTTTATCTTTATTAGTGAAAGAAGTGGGTGAAACCTCCAAG
24475 ATAAAGGGGAAGGAAAAATCTTTCATTGAGTGAGTTGGAGCTTTGTTTT
129 ATAAAGGGGAAGGAAAAATCTTTCATTGAGTGAGTTGGAGCTTTGTTTT
24524 AGCCTATAAA
Statistics
Matches: 175, Mismatches: 1, Indels: 4
0.97 0.01 0.02
Matches are distributed among these distances:
181 3 0.02
183 172 0.98
ACGTcount: A:0.27, C:0.10, G:0.21, T:0.42
Consensus pattern (182 bp):
GGATTCTATGTTATTTTTGTGGATTTAGGCTATTGGAAGTATTCTAATCCTTATTTTCATTACAT
AGATTATTTAGAAACTTCTCTTTTTTATCTTTATTAGTGAAAGAAGTGGGTGAAACCTCCAAGAT
AAAGGGGAAGGAAAAATCTTTCATTGAGTGAGTTGGAGCTTTGTTTTTTGTT
Found at i:27451 original size:7 final size:7
Alignment explanation
Indices: 27439--27485 Score: 67
Period size: 7 Copynumber: 6.7 Consensus size: 7
27429 CCAGAACCAT
*
27439 TTCTTCC
1 TTCTTCA
27446 TTCTTCA
1 TTCTTCA
27453 TTCTTCA
1 TTCTTCA
27460 TTCTTCA
1 TTCTTCA
*
27467 TTCTTCC
1 TTCTTCA
*
27474 TTCTTCC
1 TTCTTCA
27481 TTCTT
1 TTCTT
27486 ACTCCCGTTG
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
7 38 1.00
ACGTcount: A:0.06, C:0.34, G:0.00, T:0.60
Consensus pattern (7 bp):
TTCTTCA
Found at i:27458 original size:14 final size:14
Alignment explanation
Indices: 27439--27485 Score: 76
Period size: 14 Copynumber: 3.4 Consensus size: 14
27429 CCAGAACCAT
27439 TTCTTCCTTCTTCA
1 TTCTTCCTTCTTCA
*
27453 TTCTTCATTCTTCA
1 TTCTTCCTTCTTCA
*
27467 TTCTTCCTTCTTCC
1 TTCTTCCTTCTTCA
27481 TTCTT
1 TTCTT
27486 ACTCCCGTTG
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 30 1.00
ACGTcount: A:0.06, C:0.34, G:0.00, T:0.60
Consensus pattern (14 bp):
TTCTTCCTTCTTCA
Found at i:28944 original size:30 final size:30
Alignment explanation
Indices: 28908--28965 Score: 82
Period size: 30 Copynumber: 1.9 Consensus size: 30
28898 AGAATCGAGG
*
28908 GTTACCTTTGTCCTTCTGG-ACATATGGACA
1 GTTACCTATGTCCTT-TGGAACATATGGACA
*
28938 GTTACCTATGTTCTTTGGAACATATGGA
1 GTTACCTATGTCCTTTGGAACATATGGA
28966 TAGTGGTCCT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 3 0.12
30 22 0.88
ACGTcount: A:0.22, C:0.19, G:0.21, T:0.38
Consensus pattern (30 bp):
GTTACCTATGTCCTTTGGAACATATGGACA
Found at i:41496 original size:12 final size:11
Alignment explanation
Indices: 41452--41499 Score: 55
Period size: 12 Copynumber: 4.4 Consensus size: 11
41442 GTTTTGTCGG
41452 TTATAAA-TAT
1 TTATAAATTAT
*
41462 TTATAATATTAA
1 TTATAA-ATTAT
41474 TTA-AAATTAT
1 TTATAAATTAT
41484 TTATAACATTAT
1 TTATAA-ATTAT
41496 TTAT
1 TTAT
41500 GATAGAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
10 13 0.41
11 5 0.16
12 14 0.44
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (11 bp):
TTATAAATTAT
Found at i:41873 original size:72 final size:72
Alignment explanation
Indices: 41756--41901 Score: 292
Period size: 72 Copynumber: 2.0 Consensus size: 72
41746 TGAGAGGATT
41756 GCTAAGTAATATCTCTTCTAAAAGAATCTTATTCAATTTGTATGTCAATTTTCAATGGAGAGGGG
1 GCTAAGTAATATCTCTTCTAAAAGAATCTTATTCAATTTGTATGTCAATTTTCAATGGAGAGGGG
41821 TGGAGAG
66 TGGAGAG
41828 GCTAAGTAATATCTCTTCTAAAAGAATCTTATTCAATTTGTATGTCAATTTTCAATGGAGAGGGG
1 GCTAAGTAATATCTCTTCTAAAAGAATCTTATTCAATTTGTATGTCAATTTTCAATGGAGAGGGG
41893 TGGAGAG
66 TGGAGAG
41900 GC
1 GC
41902 AGAGTTTCAA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 74 1.00
ACGTcount: A:0.32, C:0.12, G:0.23, T:0.34
Consensus pattern (72 bp):
GCTAAGTAATATCTCTTCTAAAAGAATCTTATTCAATTTGTATGTCAATTTTCAATGGAGAGGGG
TGGAGAG
Found at i:42124 original size:129 final size:130
Alignment explanation
Indices: 41882--42150 Score: 389
Period size: 129 Copynumber: 2.1 Consensus size: 130
41872 TCAATTTTCA
* * * * * * *
41882 ATGGAGAGGGGTGGAGAGGC-AGAGTTTCAATCCAAGCAGGAACTATCGTCGGTGTTTAGGCGTC
1 ATGGA-AGGGGTGGAGCGGCGA-AATTTTAACCCAGGCAGGAACTATCGTCGGTGTTCAAGCGTC
**
41946 TCAGTTTTTGTGGACAATGTTAGTAGGAGAATCCATCACCAGATGCTCAAGGAATCTTTTCTGAT
64 TCAGTTTTTGTGGACAATGTTAGTAGGAGAATCCATCACCAGAAACTCAAGGAATCTTTTCTGAT
42011 GT
129 GT
*
42013 AT-GAAGGGGTGGAGCGGCGAAATTTTAACCCAGGCAGGAGCTATCGTCGGTGTTCAAGCGTCTC
1 ATGGAAGGGGTGGAGCGGCGAAATTTTAACCCAGGCAGGAACTATCGTCGGTGTTCAAGCGTCTC
* * *
42077 AGTTTTTGTGGACATTGTTAGTAGGAGAATCCATCACCGGAAACTCAAGGAATCTTTTCTGATTT
66 AGTTTTTGTGGACAATGTTAGTAGGAGAATCCATCACCAGAAACTCAAGGAATCTTTTCTGATGT
42142 ATGGAAGGG
1 ATGGAAGGG
42151 TCTTAGACAC
Statistics
Matches: 123, Mismatches: 13, Indels: 5
0.87 0.09 0.04
Matches are distributed among these distances:
129 112 0.91
130 9 0.07
131 2 0.02
ACGTcount: A:0.26, C:0.16, G:0.30, T:0.28
Consensus pattern (130 bp):
ATGGAAGGGGTGGAGCGGCGAAATTTTAACCCAGGCAGGAACTATCGTCGGTGTTCAAGCGTCTC
AGTTTTTGTGGACAATGTTAGTAGGAGAATCCATCACCAGAAACTCAAGGAATCTTTTCTGATGT
Found at i:43665 original size:29 final size:29
Alignment explanation
Indices: 43623--43680 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
43613 AGTGGAGTTG
43623 TTTTGTCGACCAGACAACTGTCAAATTGC
1 TTTTGTCGACCAGACAACTGTCAAATTGC
43652 TTTTGTCGACCAGACAACTGTCAAATTGC
1 TTTTGTCGACCAGACAACTGTCAAATTGC
43681 AAAAGACTAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.24, G:0.17, T:0.31
Consensus pattern (29 bp):
TTTTGTCGACCAGACAACTGTCAAATTGC
Found at i:55278 original size:26 final size:26
Alignment explanation
Indices: 55248--55301 Score: 72
Period size: 26 Copynumber: 2.1 Consensus size: 26
55238 GTCATGCAAC
*
55248 AACAAAACCTAGAAAAGATAAACAAA
1 AACAAAAACTAGAAAAGATAAACAAA
* * *
55274 AACAAAAACTAGTAAAGCTATACAAA
1 AACAAAAACTAGAAAAGATAAACAAA
55300 AA
1 AA
55302 TAAAGAAGTA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.67, C:0.15, G:0.07, T:0.11
Consensus pattern (26 bp):
AACAAAAACTAGAAAAGATAAACAAA
Found at i:61080 original size:10 final size:10
Alignment explanation
Indices: 61057--61094 Score: 58
Period size: 11 Copynumber: 3.6 Consensus size: 10
61047 GACTATTATC
61057 TTTTATGAGTT
1 TTTTATGAG-T
61068 TTTTATGAGT
1 TTTTATGAGT
61078 TTTTATGAGGT
1 TTTTATGA-GT
61089 TTTTAT
1 TTTTAT
61095 CATCCGTGCA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
10 9 0.35
11 17 0.65
ACGTcount: A:0.18, C:0.00, G:0.18, T:0.63
Consensus pattern (10 bp):
TTTTATGAGT
Found at i:62036 original size:30 final size:31
Alignment explanation
Indices: 61993--62052 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
61983 ATTTATATTA
*
61993 GGGAGCAATCTTGAACACT-TAAAATTTTAGT
1 GGGAGCAAACTTGAAC-CTATAAAATTTTAGT
*
62024 GGGA-CAAACTTGAACTTATAAAATTTTAG
1 GGGAGCAAACTTGAACCTATAAAATTTTAG
62053 AAAGATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 1 0.04
30 21 0.81
31 4 0.15
ACGTcount: A:0.38, C:0.12, G:0.18, T:0.32
Consensus pattern (31 bp):
GGGAGCAAACTTGAACCTATAAAATTTTAGT
Found at i:66972 original size:20 final size:20
Alignment explanation
Indices: 66886--67136 Score: 122
Period size: 20 Copynumber: 12.6 Consensus size: 20
66876 AATGACCAAC
* *
66886 AAATTCGCAACGCG-ATCTC
1 AAATTCGCAACGCGAATTTT
* * **
66905 AAATTTGCAACGCGAACTCC
1 AAATTCGCAACGCGAATTTT
* * **
66925 AATTTCGCAACTC-AACTTCC
1 AAATTCGCAACGCGAA-TTTT
66945 AAATTCGCAACGCGAATTTGT
1 AAATTCGCAACGCGAATTT-T
* *
66966 AAA-TCGCAACGTGAATCTGT
1 AAATTCGCAACGCGAAT-TTT
* *
66986 AAA-TCGCAACGAG-ATTTCC
1 AAATTCGCAACGCGAATTT-T
67005 AAATTCGCAACGCG-ATTTT
1 AAATTCGCAACGCGAATTTT
*
67024 CAAATTCGCAACACTGAATTTT
1 -AAATTCGCAACGC-GAATTTT
*
67046 AAATTCGCAACTCG-ATTTCT
1 AAATTCGCAACGCGAATTT-T
* * *
67066 GAATTTGTAACGCGAATTTT
1 AAATTCGCAACGCGAATTTT
*** *
67086 GTTTTCGCAACTCG-ATTTT
1 AAATTCGCAACGCGAATTTT
* ** *
67105 CTAATTCGCAATACAAATTTT
1 -AAATTCGCAACGCGAATTTT
*
67126 AATTTCGCAAC
1 AAATTCGCAAC
67137 AGGTTTTAGT
Statistics
Matches: 179, Mismatches: 39, Indels: 27
0.73 0.16 0.11
Matches are distributed among these distances:
18 1 0.01
19 29 0.16
20 116 0.65
21 28 0.16
22 5 0.03
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.31
Consensus pattern (20 bp):
AAATTCGCAACGCGAATTTT
Found at i:67005 original size:60 final size:62
Alignment explanation
Indices: 66941--67085 Score: 165
Period size: 60 Copynumber: 2.4 Consensus size: 62
66931 GCAACTCAAC
*
66941 TTCCAAATTCGCAACGCGAATTTGT-AAA-TCGCAAC-GTGAATCTGTAAA-TCGCAACGAGAT
1 TTCCAAATTCGCAACGCGAATTT-TCAAATTCGCAACACTGAAT-TGTAAATTCGCAACGAGAT
* **
67001 TTCCAAATTCGCAACGCG-ATTTTCAAATTCGCAACACTGAATTTTAAATTCGCAACTCGAT
1 TTCCAAATTCGCAACGCGAATTTTCAAATTCGCAACACTGAATTGTAAATTCGCAACGAGAT
** * *
67062 TTCTGAATTTGTAACGCGAATTTT
1 TTCCAAATTCGCAACGCGAATTTT
67086 GTTTTCGCAA
Statistics
Matches: 72, Mismatches: 8, Indels: 8
0.82 0.09 0.09
Matches are distributed among these distances:
58 1 0.01
59 7 0.10
60 30 0.42
61 29 0.40
62 5 0.07
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.31
Consensus pattern (62 bp):
TTCCAAATTCGCAACGCGAATTTTCAAATTCGCAACACTGAATTGTAAATTCGCAACGAGAT
Found at i:67056 original size:41 final size:40
Alignment explanation
Indices: 66886--67136 Score: 140
Period size: 40 Copynumber: 6.3 Consensus size: 40
66876 AATGACCAAC
* * * * * **
66886 AAATTCGCAACGCGA-TCTCAAATTTGCAACGCGAACTCC
1 AAATTCGCAACTCGATTTTCAAATTCGCAACACGAATTTT
* * * * *
66925 AATTTCGCAACTCAACTTCCAAATTCGCAACGCGAATTTGT
1 AAATTCGCAACTCGATTTTCAAATTCGCAACACGAATTT-T
* *
66966 AAA-TCGCAACGT-GAATCTGT-AAA-TCGC-A-ACGAGATTTCC
1 AAATTCGCAAC-TCG-AT-TTTCAAATTCGCAACACGA-ATTT-T
*
67005 AAATTCGCAACGCGATTTTCAAATTCGCAACACTGAATTTT
1 AAATTCGCAACTCGATTTTCAAATTCGCAACAC-GAATTTT
* * * *
67046 AAATTCGCAACTCGA-TTTCTGAATTTGTAACGCGAATTTT
1 AAATTCGCAACTCGATTTTC-AAATTCGCAACACGAATTTT
*** * * *
67086 GTTTTCGCAACTCGATTTTCTAATTCGCAATACAAATTTT
1 AAATTCGCAACTCGATTTTCAAATTCGCAACACGAATTTT
*
67126 AATTTCGCAAC
1 AAATTCGCAAC
67137 AGGTTTTAGT
Statistics
Matches: 161, Mismatches: 36, Indels: 29
0.71 0.16 0.13
Matches are distributed among these distances:
38 5 0.03
39 25 0.16
40 87 0.54
41 35 0.22
42 7 0.04
43 2 0.01
ACGTcount: A:0.32, C:0.24, G:0.14, T:0.31
Consensus pattern (40 bp):
AAATTCGCAACTCGATTTTCAAATTCGCAACACGAATTTT
Found at i:67124 original size:40 final size:40
Alignment explanation
Indices: 67008--67136 Score: 143
Period size: 40 Copynumber: 3.2 Consensus size: 40
66998 GATTTCCAAA
* * *
67008 TTCGCAACGCGATTTTCAAATTCGCAACACTGAATTTTAAA
1 TTCGCAACTCGATTTTCTAATTCGCAACAC-GAATTTTAAT
* * * **
67049 TTCGCAACTCGA-TTTCTGAATTTGTAACGCGAATTTTGTT
1 TTCGCAACTCGATTTTCT-AATTCGCAACACGAATTTTAAT
* *
67089 TTCGCAACTCGATTTTCTAATTCGCAATACAAATTTTAAT
1 TTCGCAACTCGATTTTCTAATTCGCAACACGAATTTTAAT
67129 TTCGCAAC
1 TTCGCAAC
67137 AGGTTTTAGT
Statistics
Matches: 71, Mismatches: 15, Indels: 5
0.78 0.16 0.05
Matches are distributed among these distances:
40 46 0.65
41 25 0.35
ACGTcount: A:0.29, C:0.21, G:0.12, T:0.37
Consensus pattern (40 bp):
TTCGCAACTCGATTTTCTAATTCGCAACACGAATTTTAAT
Found at i:68661 original size:20 final size:18
Alignment explanation
Indices: 68619--68670 Score: 59
Period size: 18 Copynumber: 2.8 Consensus size: 18
68609 TCTGAAACTT
*
68619 AAATCGCAACGCGAAATG
1 AAATCGCAATGCGAAATG
*
68637 AAATCGCAATGCGAATTTGG
1 AAATCGCAATGCGAA-AT-G
*
68657 AAATCACAATGCGA
1 AAATCGCAATGCGA
68671 TTTACATATT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 14 0.48
19 1 0.03
20 14 0.48
ACGTcount: A:0.42, C:0.19, G:0.21, T:0.17
Consensus pattern (18 bp):
AAATCGCAATGCGAAATG
Done.