Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002324.1 Hibiscus syriacus cultivar Beakdansim tig00004740_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: 84601
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:6571 original size:29 final size:29
Alignment explanation
Indices: 6502--6617 Score: 92
Period size: 29 Copynumber: 4.0 Consensus size: 29
6492 GAAATAGAAT
*
6502 GGGGATATAATCCTATGTAGAATCAGGAC
1 GGGGATATAATCCCATGTAGAATCAGGAC
* * *
6531 AGTGATATAATCCCATGTAGAATCAGGAG
1 GGGGATATAATCCCATGTAGAATCAGGAC
* * *
6560 GGGGA-ATAAATCTCATGCA-TATCAGGAC
1 GGGGATAT-AATCCCATGTAGAATCAGGAC
* * * * * *
6588 AGAGAAAAAATCTCATGCAGAATCAGGAC
1 GGGGATATAATCCCATGTAGAATCAGGAC
6617 G
1 G
6618 AGACTAAGCT
Statistics
Matches: 69, Mismatches: 15, Indels: 6
0.77 0.17 0.07
Matches are distributed among these distances:
28 23 0.33
29 46 0.67
ACGTcount: A:0.39, C:0.16, G:0.25, T:0.21
Consensus pattern (29 bp):
GGGGATATAATCCCATGTAGAATCAGGAC
Found at i:6584 original size:28 final size:29
Alignment explanation
Indices: 6520--6620 Score: 98
Period size: 29 Copynumber: 3.6 Consensus size: 29
6510 AATCCTATGT
* * * * *
6520 AGAATCAGGACAGTGATATAATCCCATGT
1 AGAATCAGGACAGAGAAAAAATCTCATGC
** * *
6549 AGAATCAGGAGGGGGAATAAATCTCATGC
1 AGAATCAGGACAGAGAAAAAATCTCATGC
*
6578 A-TATCAGGACAGAGAAAAAATCTCATGC
1 AGAATCAGGACAGAGAAAAAATCTCATGC
6606 AGAATCAGGAC-GAGA
1 AGAATCAGGACAGAGA
6621 CTAAGCTATA
Statistics
Matches: 57, Mismatches: 14, Indels: 3
0.77 0.19 0.04
Matches are distributed among these distances:
28 27 0.47
29 30 0.53
ACGTcount: A:0.42, C:0.16, G:0.25, T:0.18
Consensus pattern (29 bp):
AGAATCAGGACAGAGAAAAAATCTCATGC
Found at i:8176 original size:54 final size:54
Alignment explanation
Indices: 8119--8762 Score: 923
Period size: 54 Copynumber: 11.9 Consensus size: 54
8109 TGAATATTAC
* * * * *
8119 AACTCATTATAAATTCCATGGTTTTGCACACATAGCGTCGATACGGTAATTCAC-
1 AACTCATTATGAATTACGTGG-GTTGCACACATAGTGTCGATACGGTAATTCACA
*
8173 AACTCATTATGAATTACGTGGTTTTGCACACATAGTGTCGATACGGTAATTCACA
1 AACTCATTATGAATTACGTGG-GTTGCACACATAGTGTCGATACGGTAATTCACA
* *
8228 AACTCATTATGAATTACGTGGGTTGCAAATATAGTGTCGATACGGTAATTCACA
1 AACTCATTATGAATTACGTGGGTTGCACACATAGTGTCGATACGGTAATTCACA
8282 AACTCATTATGAATTACGTGGGTTGCACACATAGTGTCGATACGGTAATTCACA
1 AACTCATTATGAATTACGTGGGTTGCACACATAGTGTCGATACGGTAATTCACA
* * * *
8336 AACTCATTATGAATTATGTGGGTTGTACACATAATGTCGATACGATAATTCACA
1 AACTCATTATGAATTACGTGGGTTGCACACATAGTGTCGATACGGTAATTCACA
* * * *
8390 AACTCATTATGAATTACGTGGGTTGAATACATAGT-ACTAATACGGTAATTCACA
1 AACTCATTATGAATTACGTGGGTTGCACACATAGTGTC-GATACGGTAATTCACA
*
8444 AACTCATTATGAATTACGTGGGTTGCACACATAGTGCCGATACGGTAATTCACA
1 AACTCATTATGAATTACGTGGGTTGCACACATAGTGTCGATACGGTAATTCACA
**
8498 AACTCATTATGAATTACGTGGGTTGCACACATAGTACCGATACGGTAATTCACA
1 AACTCATTATGAATTACGTGGGTTGCACACATAGTGTCGATACGGTAATTCACA
* ** *
8552 AACTCATTATGAATTACGTGGGTTGCACACATATTCCCGATACGATAATTCACA
1 AACTCATTATGAATTACGTGGGTTGCACACATAGTGTCGATACGGTAATTCACA
* * * **
8606 AACTCATTATGAATTACGTAGGTTGCACACATAGTGCCGATACGATAATTTGCA
1 AACTCATTATGAATTACGTGGGTTGCACACATAGTGTCGATACGGTAATTCACA
* * * * *
8660 AACTCAATATGAATTATGTGGGTTGCACACATAGTGACAATACAGTAATTCACA
1 AACTCATTATGAATTACGTGGGTTGCACACATAGTGTCGATACGGTAATTCACA
* * *
8714 AACTCATTATGAATTACATGGGTTGCATACATAGTATCGATACGGTAAT
1 AACTCATTATGAATTACGTGGGTTGCACACATAGTGTCGATACGGTAAT
8763 GCAACATATG
Statistics
Matches: 537, Mismatches: 50, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
53 1 0.00
54 514 0.96
55 22 0.04
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Consensus pattern (54 bp):
AACTCATTATGAATTACGTGGGTTGCACACATAGTGTCGATACGGTAATTCACA
Found at i:12794 original size:15 final size:15
Alignment explanation
Indices: 12774--12812 Score: 78
Period size: 15 Copynumber: 2.6 Consensus size: 15
12764 TTAACTCAGT
12774 TGGAGCCATTTGATA
1 TGGAGCCATTTGATA
12789 TGGAGCCATTTGATA
1 TGGAGCCATTTGATA
12804 TGGAGCCAT
1 TGGAGCCAT
12813 AGAAACAGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.26, C:0.15, G:0.28, T:0.31
Consensus pattern (15 bp):
TGGAGCCATTTGATA
Found at i:15442 original size:54 final size:54
Alignment explanation
Indices: 15305--15865 Score: 758
Period size: 54 Copynumber: 10.5 Consensus size: 54
15295 TTCCATGGTT
** * * *
15305 TTGCACACATAGTGCATAAACGGTAATTCACAAACTCGTTATAAATTACGTGGG
1 TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
* *
15359 TTTGCACACATAGTGTCGATACGGTAATTCACAAACTTATTATGAATTACGTGGG
1 -TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
*
15414 TTGCACACATAGTGCCGATACTGTAATTCACAAACTCATTATGAATTACGTGGG
1 TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
* *
15468 TTGTACAC--AGTGTCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
1 TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
* * * * * *
15520 TT-CACACATAGTGCTGATATGGTAATTCAAAAACTCGTTATAAATTACGTGGA
1 TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
* * * *
15573 TTGCACAAATAGTGTCGATACGATAATTGACAAACTCATTATGAATTACGTGGG
1 TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
** * *
15627 TTGCACACATAGTATCGATACGGTAATTCACAAACTTATTATGAATTACATGGG
1 TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
*
15681 TT---CACATAGTGCTGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
1 TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
* * * *
15732 TTACACACATAGTGCCGATACAGTAATTCACAAACTC-GTATAAATTACGTGGG
1 TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
* * *
15785 TTGCACACAAAGTGTCGATACGGTAATTCACAAACTCATTATGAATTACGTGAG
1 TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
* *
15839 TTGCACAGATAGTGCAGATACGGTAAT
1 TTGCACACATAGTGCCGATACGGTAAT
15866 GCAACATATG
Statistics
Matches: 442, Mismatches: 57, Indels: 15
0.86 0.11 0.03
Matches are distributed among these distances:
51 50 0.11
52 44 0.10
53 86 0.19
54 215 0.49
55 47 0.11
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (54 bp):
TTGCACACATAGTGCCGATACGGTAATTCACAAACTCATTATGAATTACGTGGG
Found at i:15615 original size:159 final size:161
Alignment explanation
Indices: 15324--15865 Score: 778
Period size: 159 Copynumber: 3.4 Consensus size: 161
15314 TAGTGCATAA
* *
15324 ACGGTAATTCACAAACTCGTTATAAATTACGTGGGTTTGCACACATAGTG-TCGATACGGTAATT
1 ACGGTAATTCACAAACTCATTATGAATTACGTGGG-TTGCACACATAGTGCT-GATACGGTAATT
*
15388 CACAAACTTATTATGAATTACGTGGGTTGCACACATAGTGCCGATACTG-TAATTCACAAACTCA
64 CACAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCGATAC-GATAATTCACAAACTCA
*
15452 TTATGAATTACGTGGGTTGTACAC-AGTGTCGAT
128 TTATGAATTACGTGGGTTGCACACAAGTGTCGAT
*
15485 ACGGTAATTCACAAACTCATTATGAATTACGTGGGTT-CACACATAGTGCTGATATGGTAATTCA
1 ACGGTAATTCACAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCTGATACGGTAATTCA
* * * * * * *
15549 AAAACTCGTTATAAATTACGTGGATTGCACAAATAGTGTCGATACGATAATTGACAAACTCATTA
66 CAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCGATACGATAATTCACAAACTCATTA
*
15614 TGAATTACGTGGGTTGCACACATAGTATCGAT
131 TGAATTACGTGGGTTGCACACA-AGTGTCGAT
* *
15646 ACGGTAATTCACAAACTTATTATGAATTACATGGGTT---CACATAGTGCTGATACGGTAATTCA
1 ACGGTAATTCACAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCTGATACGGTAATTCA
* *
15708 CAAACTCATTATGAATTACGTGGGTTACACACATAGTGCCGATAC-AGTAATTCACAAACTC-GT
66 CAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCGATACGA-TAATTCACAAACTCATT
*
15771 ATAAATTACGTGGGTTGCACACAAAGTGTCGAT
130 ATGAATTACGTGGGTTGCACAC-AAGTGTCGAT
* * *
15804 ACGGTAATTCACAAACTCATTATGAATTACGTGAGTTGCACAGATAGTGCAGATACGGTAAT
1 ACGGTAATTCACAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCTGATACGGTAAT
15866 GCAACATATG
Statistics
Matches: 340, Mismatches: 32, Indels: 18
0.87 0.08 0.05
Matches are distributed among these distances:
158 66 0.19
159 175 0.51
160 3 0.01
161 96 0.28
ACGTcount: A:0.34, C:0.17, G:0.19, T:0.30
Consensus pattern (161 bp):
ACGGTAATTCACAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCTGATACGGTAATTCA
CAAACTCATTATGAATTACGTGGGTTGCACACATAGTGCCGATACGATAATTCACAAACTCATTA
TGAATTACGTGGGTTGCACACAAGTGTCGAT
Found at i:15824 original size:212 final size:212
Alignment explanation
Indices: 15308--15865 Score: 836
Period size: 212 Copynumber: 2.6 Consensus size: 212
15298 CATGGTTTTG
* * *
15308 CACACATAGTGCATAAACGGTAATTCACAAACTCGTTATAAATTACGTGGGTTTGCACACATAGT
1 CACACATAGTGCAGATACGGTAATTCACAAACTCGTTATAAATTACGTGGG-TTGCACACAAAGT
* *
15373 GTCGATACGGTAATTCACAAACTTATTATGAATTACGTGGGTTGCACACATAGTGCCGATACTGT
65 GTCGATACGGTAATTCACAAACTCATTATGAATTACGTGGGTTGCACACATAGT-CCGATACGGT
* *
15438 AATTCACAAACTCATTATGAATTACGTGGGTTGTACACAGTGTCGATACGGTAATTCACAAACTC
129 AATTCACAAACTCATTATGAATTACATGGGTTGCACACAGTGTCGATACGGTAATTCACAAACTC
15503 ATTATGAATTACGTGGGTT
194 ATTATGAATTACGTGGGTT
* * * *
15522 CACACATAGTGCTGATATGGTAATTCAAAAACTCGTTATAAATTACGTGGATTGCACA-AATAGT
1 CACACATAGTGCAGATACGGTAATTCACAAACTCGTTATAAATTACGTGGGTTGCACACAA-AGT
* * *
15586 GTCGATACGATAATTGACAAACTCATTATGAATTACGTGGGTTGCACACATAGTATCGATACGGT
65 GTCGATACGGTAATTCACAAACTCATTATGAATTACGTGGGTTGCACACATAGT-CCGATACGGT
* *
15651 AATTCACAAACTTATTATGAATTACATGGGTT-CACATAGTG-CTGATACGGTAATTCACAAACT
129 AATTCACAAACTCATTATGAATTACATGGGTTGCACACAGTGTC-GATACGGTAATTCACAAACT
15714 CATTATGAATTACGTGGGTT
193 CATTATGAATTACGTGGGTT
* *
15734 ACACACATAGTGCCGATACAGTAATTCACAAACTCG-TATAAATTACGTGGGTTGCACACAAAGT
1 -CACACATAGTGCAGATACGGTAATTCACAAACTCGTTATAAATTACGTGGGTTGCACACAAAGT
* * *
15798 GTCGATACGGTAATTCACAAACTCATTATGAATTACGTGAGTTGCACAGATAGTGCAGATACGGT
65 GTCGATACGGTAATTCACAAACTCATTATGAATTACGTGGGTTGCACACATAGT-CCGATACGGT
15863 AAT
129 AAT
15866 GCAACATATG
Statistics
Matches: 311, Mismatches: 29, Indels: 10
0.89 0.08 0.03
Matches are distributed among these distances:
211 1 0.00
212 133 0.43
213 132 0.42
214 45 0.14
ACGTcount: A:0.34, C:0.18, G:0.19, T:0.30
Consensus pattern (212 bp):
CACACATAGTGCAGATACGGTAATTCACAAACTCGTTATAAATTACGTGGGTTGCACACAAAGTG
TCGATACGGTAATTCACAAACTCATTATGAATTACGTGGGTTGCACACATAGTCCGATACGGTAA
TTCACAAACTCATTATGAATTACATGGGTTGCACACAGTGTCGATACGGTAATTCACAAACTCAT
TATGAATTACGTGGGTT
Found at i:16304 original size:20 final size:21
Alignment explanation
Indices: 16281--16330 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
16271 CTTCCTCTTG
*
16281 GTATCGATAC-CCCCACATCA
1 GTATCGATACTACCCACATCA
**
16301 GTATCGATACTACTTACATCA
1 GTATCGATACTACCCACATCA
16322 GTATCGATA
1 GTATCGATA
16331 TTGTTCCTCG
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
20 10 0.38
21 16 0.62
ACGTcount: A:0.32, C:0.28, G:0.12, T:0.28
Consensus pattern (21 bp):
GTATCGATACTACCCACATCA
Found at i:22061 original size:2 final size:2
Alignment explanation
Indices: 22056--22092 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
22046 AAAAATCAAT
22056 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
22093 TCATTATTCA
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:23490 original size:23 final size:23
Alignment explanation
Indices: 23438--23498 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 23
23428 TTGAAACTTT
* **
23438 ATAAATAATAATATTTTTTTACA
1 ATAAATAATAATAATTTAATACA
23461 ATAAATAATAATAATTTAATATCA
1 ATAAATAATAATAATTTAATA-CA
23485 AT-AATAAT-ATAATT
1 ATAAATAATAATAATT
23499 CTGTAGACTT
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
22 6 0.18
23 24 0.71
24 4 0.12
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (23 bp):
ATAAATAATAATAATTTAATACA
Found at i:24052 original size:48 final size:48
Alignment explanation
Indices: 23997--24100 Score: 199
Period size: 48 Copynumber: 2.2 Consensus size: 48
23987 TTGTAACAAA
23997 AAGTAAATAAAAGAGGGGAGTTTGATAGAGTAAGAATTGAAGAGAATT
1 AAGTAAATAAAAGAGGGGAGTTTGATAGAGTAAGAATTGAAGAGAATT
*
24045 AAGTAAATATAAGAGGGGAGTTTGATAGAGTAAGAATTGAAGAGAATT
1 AAGTAAATAAAAGAGGGGAGTTTGATAGAGTAAGAATTGAAGAGAATT
24093 AAGTAAAT
1 AAGTAAAT
24101 GCAAACAGTG
Statistics
Matches: 55, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
48 55 1.00
ACGTcount: A:0.48, C:0.00, G:0.28, T:0.24
Consensus pattern (48 bp):
AAGTAAATAAAAGAGGGGAGTTTGATAGAGTAAGAATTGAAGAGAATT
Found at i:27195 original size:20 final size:20
Alignment explanation
Indices: 27168--27224 Score: 98
Period size: 20 Copynumber: 2.9 Consensus size: 20
27158 ATGGATATTT
27168 AATC-TTCGGTATGGAGACC
1 AATCTTTCGGTATGGAGACC
27187 AATCTTTCGGTATGGAGACC
1 AATCTTTCGGTATGGAGACC
*
27207 AATCTTTCGGTATAGAGA
1 AATCTTTCGGTATGGAGA
27225 TCAACTGTCT
Statistics
Matches: 36, Mismatches: 1, Indels: 1
0.95 0.03 0.03
Matches are distributed among these distances:
19 4 0.11
20 32 0.89
ACGTcount: A:0.28, C:0.18, G:0.25, T:0.30
Consensus pattern (20 bp):
AATCTTTCGGTATGGAGACC
Found at i:32619 original size:26 final size:27
Alignment explanation
Indices: 32559--32622 Score: 69
Period size: 26 Copynumber: 2.4 Consensus size: 27
32549 AGAAAGAAAT
*
32559 AATAAAAAAAACAATAATAAAAGGTTA
1 AATAAAAAAAACAATAATAAAAGGTAA
* * *
32586 AGTTAAAAAAA-AATATTTAAAA-GTAA
1 AATAAAAAAAACAATA-ATAAAAGGTAA
32612 AATAAAAAAAA
1 AATAAAAAAAA
32623 TAAAGATAAA
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
26 16 0.53
27 14 0.47
ACGTcount: A:0.72, C:0.02, G:0.06, T:0.20
Consensus pattern (27 bp):
AATAAAAAAAACAATAATAAAAGGTAA
Found at i:33900 original size:3 final size:3
Alignment explanation
Indices: 33892--33935 Score: 79
Period size: 3 Copynumber: 14.3 Consensus size: 3
33882 AATGAAAAGA
33892 AAT AAT AAT AAT AAAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT -AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
33936 TAGCGTATAT
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:34026 original size:69 final size:67
Alignment explanation
Indices: 33963--34187 Score: 222
Period size: 67 Copynumber: 3.3 Consensus size: 67
33953 AAAAAATATT
* * * * *
33963 TTTTAAAACTATATATTATACTTAAAAACGTTTTCAAAGCTATATATTATATAGTTTTCAAAAAT
1 TTTTAAAACTATATATTATATTTCAAAATGTTTTCAAAACTATATATTATATAATTTTCAAAAAT
34028 GA
66 GA
* * *
34030 TTTTAAAA-TATAATATAAGTTTTTCAAAATGTTTTTTAAAACTATATATTATATAAATTTTTCA
1 TTTTAAAACTAT-ATATTA-TATTTCAAAATG-TTTTCAAAACTATATATTATAT-AA-TTTTCA
*
34094 AAAATGTTT
61 AAAATG--A
* * * *
34103 TTTTAAAAACTATACATTATATTTTCAAAATGATTTCAAAAATATATATTATATAACTTTC-AAA
1 TTTT-AAAACTATATATTATA-TTTCAAAATGTTTTCAAAACTATATATTATATAATTTTCAAAA
34167 AT-A
64 ATGA
34170 TTTTAAAACTTATATATT
1 TTTTAAAAC-TATATATT
34188 GTATATAAGT
Statistics
Matches: 129, Mismatches: 18, Indels: 22
0.76 0.11 0.13
Matches are distributed among these distances:
66 8 0.06
67 24 0.19
68 8 0.06
69 20 0.16
70 6 0.05
71 16 0.12
72 2 0.02
73 24 0.19
74 18 0.14
75 3 0.02
ACGTcount: A:0.44, C:0.07, G:0.04, T:0.45
Consensus pattern (67 bp):
TTTTAAAACTATATATTATATTTCAAAATGTTTTCAAAACTATATATTATATAATTTTCAAAAAT
GA
Found at i:34046 original size:31 final size:33
Alignment explanation
Indices: 34004--34075 Score: 85
Period size: 33 Copynumber: 2.2 Consensus size: 33
33994 TTTCAAAGCT
*
34004 ATATATTATATAG-TTTTCAAAAATG-ATTTTAAA
1 ATATAATATA-AGTTTTTC-AAAATGTATTTTAAA
*
34037 ATATAATATAAGTTTTTCAAAATGTTTTTTAAA
1 ATATAATATAAGTTTTTCAAAATGTATTTTAAA
34070 ACTATA
1 A-TATA
34076 TATTATATAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
32 8 0.24
33 22 0.65
34 4 0.12
ACGTcount: A:0.44, C:0.04, G:0.06, T:0.46
Consensus pattern (33 bp):
ATATAATATAAGTTTTTCAAAATGTATTTTAAA
Found at i:34122 original size:41 final size:38
Alignment explanation
Indices: 34042--34124 Score: 121
Period size: 41 Copynumber: 2.1 Consensus size: 38
34032 TTAAAATATA
* *
34042 ATATAAGTTTTTCAAAATGTTTTTTAAAACTATATATT
1 ATATAAATTTTTCAAAATGTTTTTTAAAACTATACATT
34080 ATATAAATTTTTCAAAAATGTTTTTTTAAAAACTATACATT
1 ATATAAATTTTTC-AAAATG-TTTTTT-AAAACTATACATT
34121 ATAT
1 ATAT
34125 TTTCAAAATG
Statistics
Matches: 40, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
38 12 0.30
39 6 0.15
40 6 0.15
41 16 0.40
ACGTcount: A:0.42, C:0.06, G:0.04, T:0.48
Consensus pattern (38 bp):
ATATAAATTTTTCAAAATGTTTTTTAAAACTATACATT
Found at i:34164 original size:35 final size:35
Alignment explanation
Indices: 34003--34205 Score: 152
Period size: 35 Copynumber: 5.7 Consensus size: 35
33993 TTTTCAAAGC
*
34003 TATATATTATATAGTTTTCAAAAATGATTTT-AAAA
1 TATATATTATATAATTTTC-AAAATGATTTTAAAAA
* * *
34038 TATA-A-TATA-AGTTTTTCAAAATGTTTTTTAAAAC
1 TATATATTATATA-ATTTTCAAAATG-ATTTTAAAAA
*
34072 TATATATTATATAAATTTTTCAAAAATGTTTTTTTAAAAA
1 TATATATTATAT-AA-TTTTC-AAAATG--ATTTTAAAAA
* *
34112 CTATACA-T-TAT-ATTTTCAAAATGATTTCAAAAA
1 -TATATATTATATAATTTTCAAAATGATTTTAAAAA
* *
34145 TATATATTATATAACTTTCAAAAT-ATTTTAAAACT
1 TATATATTATATAATTTTCAAAATGATTTTAAAA-A
34180 TATATATTGTATATAAGTTTTCAAAA
1 TATATA-T-TATATAA-TTTTCAAAA
34206 ACATTAACTA
Statistics
Matches: 137, Mismatches: 13, Indels: 33
0.75 0.07 0.18
Matches are distributed among these distances:
32 12 0.09
33 22 0.16
34 19 0.14
35 27 0.20
36 10 0.07
37 8 0.06
38 14 0.10
39 9 0.07
40 11 0.08
41 5 0.04
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (35 bp):
TATATATTATATAATTTTCAAAATGATTTTAAAAA
Found at i:34164 original size:71 final size:68
Alignment explanation
Indices: 33954--34167 Score: 211
Period size: 73 Copynumber: 3.1 Consensus size: 68
33944 ATAATATATA
* * * * * *
33954 AAAAATATTTTTTAAAACTATATATTATA-CTTAAAAACGTTTTCAAAGCTATATATTATATAGT
1 AAAAATGTTTTTTAAAACTATA-ATTATATTTTCAAAATGTTTTCAAAACTATATATTATATAAT
34018 TTTC
65 TTTC
* *
34022 AAAAATG-ATTTTAAAA-TATAA-TATAAGTTTTTCAAAATGTTTTTTAAAACTATATATTATAT
1 AAAAATGTTTTTTAAAACTATAATTAT-A--TTTTCAAAATG-TTTTCAAAACTATATATTATAT
34084 AAATTTTTC
62 -AA-TTTTC
* *
34093 AAAAATGTTTTTTTAAAAACTATACATTATATTTTCAAAATGATTTCAAAAATATATATTATATA
1 AAAAATG-TTTTTT-AAAACTATA-ATTATATTTTCAAAATGTTTTCAAAACTATATATTATATA
*
34158 ACTTTC
63 ATTTTC
34164 AAAA
1 AAAA
34168 TATTTTAAAA
Statistics
Matches: 120, Mismatches: 13, Indels: 23
0.77 0.08 0.15
Matches are distributed among these distances:
64 3 0.03
65 2 0.02
66 4 0.03
67 8 0.07
68 13 0.11
69 20 0.17
70 1 0.01
71 20 0.17
72 2 0.02
73 23 0.19
74 15 0.12
75 4 0.03
76 2 0.02
77 3 0.03
ACGTcount: A:0.45, C:0.07, G:0.04, T:0.44
Consensus pattern (68 bp):
AAAAATGTTTTTTAAAACTATAATTATATTTTCAAAATGTTTTCAAAACTATATATTATATAATT
TTC
Found at i:34956 original size:84 final size:86
Alignment explanation
Indices: 34827--35007 Score: 267
Period size: 84 Copynumber: 2.1 Consensus size: 86
34817 CTAAATGGAA
* * *
34827 TCGAACTCGAAAGGTCTTTGGTAGGCAGATAGCCCTTCTCGACTTAAGCTATGCTGCAAATGATG
1 TCGAACTCGAAAGGTCTTTGGTAGGCAGACAACCCTTCTAGACTTAAGCTATGCTGCAAATGATG
34892 TG-CCTTTGAGCTGACCGTAG
66 TGCCCTTTGAGCTGACCGTAG
* * * * *
34912 TCGAACTCGAAA-GTCTTTTGTTGGCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAGATGATG
1 TCGAACTCGAAAGGTCTTTGGTAGGCAGACAACCCTTCTAGACTTAAGCTATGCTGCAAATGATG
*
34976 TGCCCTTTGAGCTGAGCGTAG
66 TGCCCTTTGAGCTGACCGTAG
34997 TCGAACTCGAA
1 TCGAACTCGAA
35008 GGTATCGTGT
Statistics
Matches: 86, Mismatches: 9, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
84 46 0.53
85 40 0.47
ACGTcount: A:0.24, C:0.22, G:0.25, T:0.29
Consensus pattern (86 bp):
TCGAACTCGAAAGGTCTTTGGTAGGCAGACAACCCTTCTAGACTTAAGCTATGCTGCAAATGATG
TGCCCTTTGAGCTGACCGTAG
Found at i:35079 original size:27 final size:28
Alignment explanation
Indices: 35017--35085 Score: 113
Period size: 29 Copynumber: 2.5 Consensus size: 28
35007 AGGTATCGTG
*
35017 TTTCAAGAGAAACATTTTCAAAGGGGTTT
1 TTTCAAGAGAAACAATTTCAAA-GGGTTT
35046 TTTCAAGAGAAACAATTTCAAA-GGTTT
1 TTTCAAGAGAAACAATTTCAAAGGGTTT
35073 TTTCAAGAGAAAC
1 TTTCAAGAGAAAC
35086 TGTCTCAAGG
Statistics
Matches: 39, Mismatches: 1, Indels: 2
0.93 0.02 0.05
Matches are distributed among these distances:
27 18 0.46
29 21 0.54
ACGTcount: A:0.39, C:0.12, G:0.17, T:0.32
Consensus pattern (28 bp):
TTTCAAGAGAAACAATTTCAAAGGGTTT
Found at i:35189 original size:36 final size:36
Alignment explanation
Indices: 35073--35269 Score: 236
Period size: 36 Copynumber: 5.4 Consensus size: 36
35063 TCAAAGGTTT
*
35073 TTTCAAGAGAAACTGTCTCAAGGGAGACAAAATTTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAA-TTTG
* *
35110 TTTCAAGGGAAACTGTTTCAA-AGATTGACAAAAAATTTG
1 TTTCAAGAGAAACTGTCTCAAGAGA--GAC--AAAATTTG
* *
35149 TTTCAA-AGGAAACTGTCTCAAGGGAGACGAAATTTG
1 TTTCAAGA-GAAACTGTCTCAAGAGAGACAAAATTTG
*
35185 TTTCAAGTGAAACTGTCTCAAGAGAGACAAAATTTG
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
* * *
35221 TTTCAAGAGAATCTGTCTCAAGAGAGACAAATTTTA
1 TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
*
35257 TTTCAAGAAAAAC
1 TTTCAAGAGAAAC
35270 AATCTCAAAG
Statistics
Matches: 137, Mismatches: 16, Indels: 15
0.82 0.10 0.09
Matches are distributed among these distances:
36 84 0.61
37 19 0.14
38 6 0.04
39 22 0.16
40 6 0.04
ACGTcount: A:0.40, C:0.13, G:0.19, T:0.28
Consensus pattern (36 bp):
TTTCAAGAGAAACTGTCTCAAGAGAGACAAAATTTG
Found at i:35722 original size:164 final size:164
Alignment explanation
Indices: 35290--36269 Score: 1548
Period size: 164 Copynumber: 6.0 Consensus size: 164
35280 GTTTTTGTTG
* ** * * *
35290 ACAGATAACTCC-TCTAGCCTTGAGTTATGCTGTAAATGATGTGCCCTCGGAGCTGAGTGGAATC
1 ACAGATAAC-CCTTCTAGCCTTGAGTTATGCTGTAAATGTTACGCCCTTGAAGCTGAGTGTAATC
* * * *
35354 AAACTCAGGGGTCTTTGGCAGACAGCCCTTCTCGACTTAAGCTATACTGCAAATGATGTGCCTTG
65 GAACTCAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTG
* * * *
35419 GAGCTGAGCGTAGTCGAACTCAAAGGTATTTGGTTG
130 GAGCTGAGCGTAGTCGAACTCGAAGGTCTTT-GCTA
* * * * * * * ** *
35455 GCAGACAACCCTTCTAGACTTAAGTTGTGCTGCAAATGATGTGCCCTCGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTACGCCCTTGAAGCTGAGTGTAATCG
** * *
35520 AACTCGGGGGTCTTTGGCAGATAACCCTTCTTGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
66 AACTCAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
*
35585 AGCTGAGCGTAGTCGAACTCAAAGGTCTTTGCTA
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGCTA
* * * *
35619 ACAGATAACCCTTCTAGCTTTGAGTTATGCCGTAAAGGTTATGCCCTTGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTACGCCCTTGAAGCTGAGTGTAATCG
* *
35684 AACTCAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATGCTGCAAATGATGTGCCTTGG
66 AACTCAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
*
35749 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTCTA
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGCTA
35783 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTACGCCCTTGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTACGCCCTTGAAGCTGAGTGTAATCG
* *
35848 AACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGTTATTCTGCAAATGATGTGCCTTGG
66 AACTCAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
*
35913 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTCTA
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGCTA
35947 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTACGCCCTTGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTACGCCCTTGAAGCTGAGTGTAATCG
*
36012 AACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
66 AACTCAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
*
36077 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTTCTA
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGCTA
36111 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTACGCCCTTGAAGCTGAGTGTAATCG
1 ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTACGCCCTTGAAGCTGAGTGTAATCG
*
36176 AACTTAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
66 AACTCAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
*
36241 AGCTGAGCGTAGTTGAACTCGAAGGTCTT
131 AGCTGAGCGTAGTCGAACTCGAAGGTCTT
36270 GGTGGCAGGT
Statistics
Matches: 769, Mismatches: 45, Indels: 3
0.94 0.06 0.00
Matches are distributed among these distances:
164 627 0.82
165 142 0.18
ACGTcount: A:0.24, C:0.21, G:0.24, T:0.30
Consensus pattern (164 bp):
ACAGATAACCCTTCTAGCCTTGAGTTATGCTGTAAATGTTACGCCCTTGAAGCTGAGTGTAATCG
AACTCAAGGGTCTTTGGCAGATAGCCCTTCTCGACTTAAGCTATTCTGCAAATGATGTGCCTTGG
AGCTGAGCGTAGTCGAACTCGAAGGTCTTTGCTA
Found at i:39337 original size:18 final size:19
Alignment explanation
Indices: 39296--39340 Score: 65
Period size: 19 Copynumber: 2.4 Consensus size: 19
39286 AGTTAATGTG
*
39296 AATGCAAATAAAATAACAA
1 AATGCAAAGAAAATAACAA
*
39315 AATGCAAAGAAAATAA-GA
1 AATGCAAAGAAAATAACAA
39333 AATGCAAA
1 AATGCAAA
39341 ATGTCTAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
18 9 0.38
19 15 0.62
ACGTcount: A:0.67, C:0.09, G:0.11, T:0.13
Consensus pattern (19 bp):
AATGCAAAGAAAATAACAA
Found at i:41315 original size:24 final size:25
Alignment explanation
Indices: 41288--41341 Score: 58
Period size: 24 Copynumber: 2.2 Consensus size: 25
41278 CGAACGAACG
41288 TAAAAAAAAAT-AAAAAGACGAA-TA
1 TAAAAAAAAATGAAAAA-ACGAATTA
* * *
41312 TAAACAAATATGAACAAACGAATTA
1 TAAAAAAAAATGAAAAAACGAATTA
41337 TAAAA
1 TAAAA
41342 CGTTCACGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 3
0.77 0.13 0.10
Matches are distributed among these distances:
24 14 0.58
25 10 0.42
ACGTcount: A:0.69, C:0.07, G:0.07, T:0.17
Consensus pattern (25 bp):
TAAAAAAAAATGAAAAAACGAATTA
Found at i:42397 original size:2 final size:2
Alignment explanation
Indices: 42390--42439 Score: 100
Period size: 2 Copynumber: 25.0 Consensus size: 2
42380 ATTCTGGTGA
42390 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
42432 AT AT AT AT
1 AT AT AT AT
42440 CTAGAAAAAT
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 48 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:46004 original size:42 final size:42
Alignment explanation
Indices: 45945--46031 Score: 174
Period size: 42 Copynumber: 2.1 Consensus size: 42
45935 GGTACAGTCC
45945 AAAAGGTTAGCTATCTGCTAAGCAGGAAAACGAAACACATAA
1 AAAAGGTTAGCTATCTGCTAAGCAGGAAAACGAAACACATAA
45987 AAAAGGTTAGCTATCTGCTAAGCAGGAAAACGAAACACATAA
1 AAAAGGTTAGCTATCTGCTAAGCAGGAAAACGAAACACATAA
46029 AAA
1 AAA
46032 GGATGGAGCG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.49, C:0.16, G:0.18, T:0.16
Consensus pattern (42 bp):
AAAAGGTTAGCTATCTGCTAAGCAGGAAAACGAAACACATAA
Found at i:56429 original size:17 final size:17
Alignment explanation
Indices: 56402--56440 Score: 71
Period size: 17 Copynumber: 2.4 Consensus size: 17
56392 AATTTACAAT
56402 TAATT-TAAATAATATC
1 TAATTATAAATAATATC
56418 TAATTATAAATAATATC
1 TAATTATAAATAATATC
56435 TAATTA
1 TAATTA
56441 ATTTGATTCA
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 5 0.23
17 17 0.77
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
TAATTATAAATAATATC
Found at i:57610 original size:2 final size:2
Alignment explanation
Indices: 57605--57645 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
57595 AACATTATCA
57605 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
57646 GTTTGTATCT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:60543 original size:15 final size:15
Alignment explanation
Indices: 60523--60564 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
60513 TTACCGTCAC
60523 CCAAAATCCCTAAAT
1 CCAAAATCCCTAAAT
*
60538 CCAAAATCCCAAAAT
1 CCAAAATCCCTAAAT
60553 CC-AAATCCCTAA
1 CCAAAATCCCTAA
60565 TTCTCAATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
14 9 0.36
15 16 0.64
ACGTcount: A:0.48, C:0.36, G:0.00, T:0.17
Consensus pattern (15 bp):
CCAAAATCCCTAAAT
Found at i:60557 original size:7 final size:8
Alignment explanation
Indices: 60522--60554 Score: 50
Period size: 8 Copynumber: 4.2 Consensus size: 8
60512 CTTACCGTCA
60522 CCCAAAAT
1 CCCAAAAT
*
60530 CCCTAAAT
1 CCCAAAAT
60538 -CCAAAAT
1 CCCAAAAT
60545 CCCAAAAT
1 CCCAAAAT
60553 CC
1 CC
60555 AAATCCCTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
7 6 0.27
8 16 0.73
ACGTcount: A:0.45, C:0.39, G:0.00, T:0.15
Consensus pattern (8 bp):
CCCAAAAT
Found at i:76570 original size:22 final size:22
Alignment explanation
Indices: 76545--76595 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
76535 TTTTTCTTGT
76545 CTGCCTCTATGAAGCCTTCTAG
1 CTGCCTCTATGAAGCCTTCTAG
76567 CTGCCTCTATGAAGCCTTCTAG
1 CTGCCTCTATGAAGCCTTCTAG
*
76589 CCGCCTC
1 CTGCCTC
76596 ATATAGATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.16, C:0.37, G:0.18, T:0.29
Consensus pattern (22 bp):
CTGCCTCTATGAAGCCTTCTAG
Found at i:78615 original size:15 final size:15
Alignment explanation
Indices: 78595--78627 Score: 57
Period size: 15 Copynumber: 2.2 Consensus size: 15
78585 AAAATCTTTC
*
78595 TTTCCCGTTCTTGAT
1 TTTCCCGTTCTGGAT
78610 TTTCCCGTTCTGGAT
1 TTTCCCGTTCTGGAT
78625 TTT
1 TTT
78628 GATCTGCCAC
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.06, C:0.24, G:0.15, T:0.55
Consensus pattern (15 bp):
TTTCCCGTTCTGGAT
Found at i:79388 original size:17 final size:18
Alignment explanation
Indices: 79361--79400 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
79351 CTCCGTCGAC
* *
79361 AAATTTGTATTGTTGACA
1 AAATTTGTATTATTCACA
79379 AAATTT-TATTATTCACA
1 AAATTTGTATTATTCACA
79396 AAATT
1 AAATT
79401 CACTATTCGC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 14 0.70
18 6 0.30
ACGTcount: A:0.40, C:0.07, G:0.07, T:0.45
Consensus pattern (18 bp):
AAATTTGTATTATTCACA
Found at i:79459 original size:13 final size:13
Alignment explanation
Indices: 79443--79467 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
79433 CTCGCAGAAA
79443 AACCACCAAAATT
1 AACCACCAAAATT
79456 AACCACCAAAAT
1 AACCACCAAAAT
79468 CTCTTATACC
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.56, C:0.32, G:0.00, T:0.12
Consensus pattern (13 bp):
AACCACCAAAATT
Done.