Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007514.1 Hibiscus syriacus cultivar Beakdansim tig00020898_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: 57409
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:238 original size:29 final size:30
Alignment explanation
Indices: 208--269 Score: 85
Period size: 29 Copynumber: 2.2 Consensus size: 30
198 TTTTAGATCT
*
208 TTTAA-TTTCTATTTTTGTT-TTTTGGTCC
1 TTTAAGTTTCTATATTTGTTATTTTGGTCC
*
236 TTTAAGTTTCTGTATTTGTTATTTTGGT-C
1 TTTAAGTTTCTATATTTGTTATTTTGGTCC
265 TTTAA
1 TTTAA
270 CTTTATGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
28 5 0.17
29 18 0.60
30 7 0.23
ACGTcount: A:0.15, C:0.08, G:0.13, T:0.65
Consensus pattern (30 bp):
TTTAAGTTTCTATATTTGTTATTTTGGTCC
Found at i:278 original size:29 final size:29
Alignment explanation
Indices: 221--280 Score: 86
Period size: 29 Copynumber: 2.1 Consensus size: 29
211 AATTTCTATT
* *
221 TTTGTTTTTTGGTCCTTTAAGTTTCTGTA
1 TTTGTTTTTTGGTCCTTTAACTTTATGTA
250 TTTGTTATTTTGGT-CTTTAACTTTATGTA
1 TTTGTT-TTTTGGTCCTTTAACTTTATGTA
279 TT
1 TT
281 ACTATTTAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
29 21 0.75
30 7 0.25
ACGTcount: A:0.13, C:0.08, G:0.15, T:0.63
Consensus pattern (29 bp):
TTTGTTTTTTGGTCCTTTAACTTTATGTA
Found at i:5447 original size:32 final size:32
Alignment explanation
Indices: 5405--5468 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
5395 AAGAAACGAT
*
5405 GAATGATGGGGTATCATTGGAGATTCAACATC
1 GAATGATGGGGCATCATTGGAGATTCAACATC
* * *
5437 GAATGTTGGGGCATCTTTGGGGATTCAACATC
1 GAATGATGGGGCATCATTGGAGATTCAACATC
5469 TTGATGTGAA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
32 28 1.00
ACGTcount: A:0.27, C:0.14, G:0.30, T:0.30
Consensus pattern (32 bp):
GAATGATGGGGCATCATTGGAGATTCAACATC
Found at i:5826 original size:30 final size:32
Alignment explanation
Indices: 5772--5830 Score: 95
Period size: 30 Copynumber: 1.9 Consensus size: 32
5762 GAAACGCAAA
*
5772 ATCTTTGAGTTTGTTTCTCTTGAAACAAAACC
1 ATCTTTGAGTTCGTTTCTCTTGAAACAAAACC
5804 ATCTTTGAG-TCGTTTC-CTTGAAACAAA
1 ATCTTTGAGTTCGTTTCTCTTGAAACAAA
5831 TTTTGTCTCT
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
30 11 0.42
31 6 0.23
32 9 0.35
ACGTcount: A:0.29, C:0.19, G:0.14, T:0.39
Consensus pattern (32 bp):
ATCTTTGAGTTCGTTTCTCTTGAAACAAAACC
Found at i:6262 original size:135 final size:130
Alignment explanation
Indices: 5929--6236 Score: 372
Period size: 130 Copynumber: 2.3 Consensus size: 130
5919 CCTCATCGTA
* *
5929 TAGGAACCA-TGTCATCCCCTGACTAGACCTCCTCATCACGTAGGAGCTGTGTCACCCCTA-ATA
1 TAGGAA-CAGTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGC-GTGTCACCCCTAGATA
* * * *
5992 ACCAGCCGTCCTCATCATGTAGGAATCGTGTTATCATCCCTAAAGATGGCATATCATCCTCATCA
64 ACCAGCCGTCCTCATCACGTAGGAATCGTGTTATCACCCCTAAAGATGGCAGAACATCCTCATCA
6057 CG
129 CG
* * *
6059 TAGGAACCGTGTCATCCACCGACCAGACCTCATCATCACGTAGGAGACGTGTCACCCCTAGATAA
1 TAGGAACAGTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAG-CGTGTCACCCCTAGATAA
* *
6124 CCAGCCGTCCTCATCGCGTAGGAA-CTGTGTTATCACCCTCTTTAAAGATGGCCAAGAAC-TCTT
65 CCAGCCGTCCTCATCACGTAGGAATC-GTGTTATCACCC-C--TAAAGATGG-C-AGAACATCCT
6187 CATCACG
124 CATCACG
* * * *
6194 TATGAGCAGTGTCATCCCCCGACGAGATCTCCTCATCACGTAG
1 TAGGAACAGTGTCATCCCCCGACCAGACCTCCTCATCACGTAG
6237 AAGTCGTATC
Statistics
Matches: 151, Mismatches: 18, Indels: 13
0.83 0.10 0.07
Matches are distributed among these distances:
129 1 0.01
130 52 0.34
131 38 0.25
132 1 0.01
134 9 0.06
135 47 0.31
136 3 0.02
ACGTcount: A:0.26, C:0.32, G:0.19, T:0.24
Consensus pattern (130 bp):
TAGGAACAGTGTCATCCCCCGACCAGACCTCCTCATCACGTAGGAGCGTGTCACCCCTAGATAAC
CAGCCGTCCTCATCACGTAGGAATCGTGTTATCACCCCTAAAGATGGCAGAACATCCTCATCACG
Found at i:6460 original size:3 final size:3
Alignment explanation
Indices: 6446--6504 Score: 102
Period size: 3 Copynumber: 20.0 Consensus size: 3
6436 TCTACAAAAA
*
6446 ATT ATT -TT ATT ATT ATT ATT ATT ATT ACT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
6493 ATT ATT ATT ATT
1 ATT ATT ATT ATT
6505 TACATACTTA
Statistics
Matches: 53, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
2 2 0.04
3 51 0.96
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
ATT
Found at i:7385 original size:30 final size:29
Alignment explanation
Indices: 7340--7474 Score: 96
Period size: 29 Copynumber: 4.5 Consensus size: 29
7330 TGTTAATACC
* *
7340 ATTTTAGACCCTTTAAGATTCTATTTTTATT
1 ATTTTAG-TCCTTTAA-ATTCTATTTTTACT
*
7371 ATTTTAGTCCTTTAAATATCTA-TTTTGCT
1 ATTTTAGTCCTTTAAAT-TCTATTTTTACT
* * *
7400 ATTTTAATCCCTTAAATGTCTTTTTTTTACT
1 ATTTTAGTCCTTTAAAT-TC-TATTTTTACT
* * *
7431 ATTTTAGACCTTTTAAATTTTTATTTTT-GT
1 ATTTTAGTCC-TTTAAA-TTCTATTTTTACT
*
7461 -TTTTGGTCCTTTAA
1 ATTTTAGTCCTTTAA
7475 GTTTCTGTAT
Statistics
Matches: 83, Mismatches: 16, Indels: 13
0.74 0.14 0.12
Matches are distributed among these distances:
28 5 0.06
29 31 0.37
30 13 0.16
31 27 0.33
32 6 0.07
33 1 0.01
ACGTcount: A:0.23, C:0.13, G:0.07, T:0.58
Consensus pattern (29 bp):
ATTTTAGTCCTTTAAATTCTATTTTTACT
Found at i:7458 original size:31 final size:30
Alignment explanation
Indices: 7340--7458 Score: 100
Period size: 31 Copynumber: 3.9 Consensus size: 30
7330 TGTTAATACC
*
7340 ATTTTAGACCCTTTAAGA-TTCTATTTTTATT
1 ATTTTAGA-CCTTTAA-ATTTCTATTTTTACT
* * *
7371 ATTTTAGTCCTTTAAATATCTA-TTTTGCT
1 ATTTTAGACCTTTAAATTTCTATTTTTACT
* * *
7400 ATTTTA-ATCCCTTAAATGTCTTTTTTTTACT
1 ATTTTAGA-CCTTTAAATTTC-TATTTTTACT
*
7431 ATTTTAGACCTTTTAAATTTTTATTTTT
1 ATTTTAGACC-TTTAAATTTCTATTTTT
7459 GTTTTTGGTC
Statistics
Matches: 69, Mismatches: 13, Indels: 12
0.73 0.14 0.13
Matches are distributed among these distances:
29 22 0.32
30 12 0.17
31 27 0.39
32 8 0.12
ACGTcount: A:0.24, C:0.13, G:0.05, T:0.58
Consensus pattern (30 bp):
ATTTTAGACCTTTAAATTTCTATTTTTACT
Found at i:10447 original size:6 final size:6
Alignment explanation
Indices: 10436--10476 Score: 64
Period size: 6 Copynumber: 6.8 Consensus size: 6
10426 TCCTTTCAAA
* *
10436 TATATG TATATG TATATG TATATG TATATA TATATA TATAT
1 TATATG TATATG TATATG TATATG TATATG TATATG TATAT
10477 CCCTTATTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.39, C:0.00, G:0.10, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:10789 original size:26 final size:24
Alignment explanation
Indices: 10759--10817 Score: 73
Period size: 26 Copynumber: 2.3 Consensus size: 24
10749 TAAAAAAGAT
*
10759 AGAAAAGAAAGAAAAAAATAGAAAA
1 AGAAAA-AAAGAAAAAAAAAGAAAA
*
10784 ATGAAACAAATGAAAAAAAAAGAAAA
1 A-GAAA-AAAAGAAAAAAAAAGAAAA
10810 AGAAAAAA
1 AGAAAAAA
10818 TGAGAGAAAA
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 3 0.10
25 5 0.17
26 21 0.70
27 1 0.03
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.05
Consensus pattern (24 bp):
AGAAAAAAAGAAAAAAAAAGAAAA
Found at i:10794 original size:17 final size:16
Alignment explanation
Indices: 10735--10800 Score: 53
Period size: 17 Copynumber: 3.9 Consensus size: 16
10725 GAAAAGATAT
*
10735 AAAAAAATGAAACAT-
1 AAAAAAATGAAAAATG
*
10750 AAAAAAGATAGAAAAGAAAG
1 AAAAAA-AT-G-AAA-AATG
10770 AAAAAAATAGAAAAATG
1 AAAAAAAT-GAAAAATG
*
10787 AAACAAATGAAAAA
1 AAAAAAATGAAAAA
10801 AAAAGAAAAA
Statistics
Matches: 42, Mismatches: 4, Indels: 9
0.76 0.07 0.16
Matches are distributed among these distances:
15 6 0.14
16 8 0.19
17 11 0.26
18 6 0.14
19 5 0.12
20 6 0.14
ACGTcount: A:0.76, C:0.03, G:0.12, T:0.09
Consensus pattern (16 bp):
AAAAAAATGAAAAATG
Found at i:10799 original size:35 final size:35
Alignment explanation
Indices: 10719--10816 Score: 91
Period size: 35 Copynumber: 2.9 Consensus size: 35
10709 ACACAGAGAG
* *
10719 AAAGA-AGAAAAGATATAAAAAAAT-GAAACATAAA
1 AAAGATAGAAAAGA-AAAAAAAAATAGAAAAATAAA
10753 AAAGATAGAAAAGAAAGAAAAAAATAGAAAAATGAAA
1 AAAGATAGAAAAGAAA-AAAAAAATAGAAAAAT-AAA
* *
10790 CAA-AT-GAAAA-AAAAAGAAAA-AGAAAAA
1 AAAGATAGAAAAGAAAAAAAAAATAGAAAAA
10817 ATGAGAGAAA
Statistics
Matches: 56, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
32 7 0.12
33 6 0.11
34 9 0.16
35 21 0.38
36 8 0.14
37 5 0.09
ACGTcount: A:0.77, C:0.02, G:0.13, T:0.08
Consensus pattern (35 bp):
AAAGATAGAAAAGAAAAAAAAAATAGAAAAATAAA
Found at i:10817 original size:43 final size:41
Alignment explanation
Indices: 10717--10817 Score: 96
Period size: 43 Copynumber: 2.3 Consensus size: 41
10707 CGACACAGAG
* * *
10717 AGAAAGAAGAAAAGATATAAAAAAATGAAACATAAAAAAGAT
1 AGAAA-AAGAAAAAAAATAAAAAAATGAAACATAAAAAAGAA
* *
10759 AGAAAAGAAAGAAAAAAATAGAAAAATGAAACAAATGAAAAAA-AA
1 AGAAAA-AGA-AAAAAAATAAAAAAATGAAAC--AT-AAAAAAGAA
10804 AGAAAAAGAAAAAA
1 AGAAAAAGAAAAAA
10818 TGAGAGAAAA
Statistics
Matches: 48, Mismatches: 6, Indels: 9
0.76 0.10 0.14
Matches are distributed among these distances:
41 1 0.02
42 7 0.15
43 23 0.48
44 2 0.04
45 9 0.19
46 6 0.12
ACGTcount: A:0.76, C:0.02, G:0.14, T:0.08
Consensus pattern (41 bp):
AGAAAAAGAAAAAAAATAAAAAAATGAAACATAAAAAAGAA
Found at i:10827 original size:26 final size:27
Alignment explanation
Indices: 10770--10829 Score: 81
Period size: 26 Copynumber: 2.3 Consensus size: 27
10760 GAAAAGAAAG
10770 AAAAAAATAGAAAAATGAAACAAATGA
1 AAAAAAATAGAAAAATGAAACAAATGA
10797 AAAAAAA-AGAAAAA-GAAA-AAATGA
1 AAAAAAATAGAAAAATGAAACAAATGA
10821 GAGAAAAAA
1 -A-AAAAAA
10830 GGGGAAAAAA
Statistics
Matches: 31, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
24 6 0.19
25 5 0.16
26 13 0.42
27 7 0.23
ACGTcount: A:0.78, C:0.02, G:0.13, T:0.07
Consensus pattern (27 bp):
AAAAAAATAGAAAAATGAAACAAATGA
Found at i:11545 original size:28 final size:28
Alignment explanation
Indices: 11505--11613 Score: 155
Period size: 28 Copynumber: 3.9 Consensus size: 28
11495 GCAAGAATCC
*
11505 AACCTGTAACACATTACCTCCCCAAATT
1 AACCTGAAACACATTACCTCCCCAAATT
*
11533 AACCTGAAACACATTACCTCACCAAATT
1 AACCTGAAACACATTACCTCCCCAAATT
* *
11561 AACCTGAAACACATTACCACCCCAAAAT
1 AACCTGAAACACATTACCTCCCCAAATT
* * *
11589 AACATGAAGCACATTACCTTCCCAA
1 AACCTGAAACACATTACCTCCCCAA
11614 GACAGCCTAA
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
28 72 1.00
ACGTcount: A:0.41, C:0.34, G:0.05, T:0.20
Consensus pattern (28 bp):
AACCTGAAACACATTACCTCCCCAAATT
Found at i:13120 original size:42 final size:42
Alignment explanation
Indices: 13042--13123 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
13032 ATGGGTTTCT
* *
13042 TGATGCGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGGA
1 TGATGCGTAAATCCTTCGGGCCATCAGTAAGCCTTTCGAGGA
* * *
13084 TGATGCTTAAATCCTTTGGGTCATCTA-TAAGCCTTTCGAG
1 TGATGCGTAAATCCTTCGGGCCATC-AGTAAGCCTTTCGAG
13124 CAAGATGATA
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
42 33 0.97
43 1 0.03
ACGTcount: A:0.22, C:0.21, G:0.24, T:0.33
Consensus pattern (42 bp):
TGATGCGTAAATCCTTCGGGCCATCAGTAAGCCTTTCGAGGA
Found at i:13410 original size:278 final size:278
Alignment explanation
Indices: 12884--13712 Score: 1179
Period size: 278 Copynumber: 3.0 Consensus size: 278
12874 AGCTAAACAA
* * * *
12884 CATGAT-ATTTTCAAAAGAATTTTTAAAGAAACTAAGTCTGATTTTCAGGGGTTTCTTGATGATG
1 CATGATGA-TTTCAAATGAGTTTTT-AA-AAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATT
* * * ** *
12948 ATTTTCAATGAGTTTTTAAAAAGGAAGCTAATTCAAATTTTTAGGGGTTCCTTGATGACAACTAA
63 ATATCCAAAGAGTTTTT-AAAAGGAAGCTAAGCCTAATTTTTAGGGGTTCCTTGATGACAACTAA
* * *
13013 GAAACTAAGCTTGATTTTTATGGGTTTCTTGATGCGTAAGTCCTTCGGGCCATCAGTAAGTCTTT
127 GAAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTTT
* * * *
13078 CGAGGATGATGCTTAAATCCTTTGGGTCATCTATAAGCCTTTCGAGCAAGATGATAAGT-CTTCC
192 CGAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTT-A
*
13142 GGGCCATCAATAAGACCTTCTG-G
256 GGGCCATCCATAAGACCTTC-GAG
13165 C-TGGATGATTTCAAATGAGTTTTTAAAAACTAAGCCTGATTTAT-AGGGGTTTTCTTGATGATT
1 CAT-GATGATTTCAAATGAGTTTTTAAAAACTAAGCCTGATTT-TCAGGGG-TTTCTTGATGATT
* *
13228 ATATCCAAAGAGTTTTTAAAAGGAAACTAAGCCTAATTTTTAGGGGTTCCTTGATGAAAACTAAG
63 ATATCCAAAGAGTTTTTAAAAGGAAGCTAAGCCTAATTTTTAGGGGTTCCTTGATGACAACTAAG
* *
13293 AAACT-AGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCGTGTCATCAGTAAGTCTTTC
128 AAACTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTC
*
13357 GACCATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTAGG
193 GAGCATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTAGG
13422 GCCATCCATAAGACCTTCGAG
258 GCCATCCATAAGACCTTCGAG
* * *
13443 CATGATGATTTCAAATAAGTTTTTAGAAACTAAGCCTTATTTTCA-GGGTTTCTTGATGATTATA
1 CATGATGATTTCAAATGAGTTTTTAAAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTATA
* * * *
13507 TCCAAAGAGTTTTTAAAAGGAAGTTAAGCCTAACTTTTAGGGGTTCCTTAATGACAACTAAGAAG
66 TCCAAAGAGTTTTTAAAAGGAAGCTAAGCCTAATTTTTAGGGGTTCCTTGATGACAACTAAGAAA
*
13572 CTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCAAG
131 CTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAG
* * * * * *
13637 CATGATG-TGTAAGTCTTTCGGGCCATCTATAAGTATTTCGAACAAGATGATAAGTCCTTTGGGC
196 CATGATGCT-TAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTAGGGC
13701 CATCCATAAGAC
260 CATCCATAAGAC
13713 ATCTGGGTAG
Statistics
Matches: 496, Mismatches: 42, Indels: 24
0.88 0.07 0.04
Matches are distributed among these distances:
276 78 0.16
277 131 0.26
278 166 0.33
279 72 0.15
280 30 0.06
281 18 0.04
282 1 0.00
ACGTcount: A:0.29, C:0.16, G:0.20, T:0.34
Consensus pattern (278 bp):
CATGATGATTTCAAATGAGTTTTTAAAAACTAAGCCTGATTTTCAGGGGTTTCTTGATGATTATA
TCCAAAGAGTTTTTAAAAGGAAGCTAAGCCTAATTTTTAGGGGTTCCTTGATGACAACTAAGAAA
CTAAGCTTGATTTTCAAGGGTTTCTTGATGAGTAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAG
CATGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCAAGATGATAAGTCCTTAGGGCC
ATCCATAAGACCTTCGAG
Found at i:13433 original size:41 final size:41
Alignment explanation
Indices: 13320--13451 Score: 140
Period size: 42 Copynumber: 3.2 Consensus size: 41
13310 AAGGGTTTCT
* *
13320 TGATGAGTAAGTCCTTCGTGTCAT-CAGTAAGTCTTTCGACCA
1 TGATGA-TAAGTCCTTCGGGTCATCCA-TAAGTCTTTCGAGCA
* * *
13362 TGATGCTTAAATCCTTCGGGTCATCTATAAGTCTTTCGAGCA
1 TGATG-ATAAGTCCTTCGGGTCATCCATAAGTCTTTCGAGCA
* * * * *
13404 AGATGATAAGTCCTTAGGGCCATCCATAAGACCTTCGAGCA
1 TGATGATAAGTCCTTCGGGTCATCCATAAGTCTTTCGAGCA
13445 TGATGAT
1 TGATGAT
13452 TTCAAATAAG
Statistics
Matches: 74, Mismatches: 14, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
41 35 0.47
42 38 0.51
43 1 0.01
ACGTcount: A:0.27, C:0.21, G:0.21, T:0.31
Consensus pattern (41 bp):
TGATGATAAGTCCTTCGGGTCATCCATAAGTCTTTCGAGCA
Found at i:13657 original size:42 final size:41
Alignment explanation
Indices: 13597--13710 Score: 117
Period size: 42 Copynumber: 2.7 Consensus size: 41
13587 AAGGGTTTCT
* *
13597 TGATGAGTAAGTCCTTCGGGCCATC-AGTAAGTCTTTC-AAGCA
1 TGATG-GTAAGTCTTTCGGGCCATCTA-TAAGTATTTCGAA-CA
13639 TGATGTGTAAGTCTTTCGGGCCATCTATAAGTATTTCGAACA
1 TGATG-GTAAGTCTTTCGGGCCATCTATAAGTATTTCGAACA
* * *
13681 AGATGATAAGTCCTTT-GGGCCATCCATAAG
1 TGATGGTAAGT-CTTTCGGGCCATCTATAAG
13711 ACATCTGGGT
Statistics
Matches: 63, Mismatches: 6, Indels: 7
0.83 0.08 0.09
Matches are distributed among these distances:
41 18 0.29
42 42 0.67
43 3 0.05
ACGTcount: A:0.27, C:0.19, G:0.23, T:0.31
Consensus pattern (41 bp):
TGATGGTAAGTCTTTCGGGCCATCTATAAGTATTTCGAACA
Found at i:15417 original size:31 final size:29
Alignment explanation
Indices: 15349--15422 Score: 71
Period size: 31 Copynumber: 2.5 Consensus size: 29
15339 TCACTAGTAG
*
15349 TTTGT-TTTTATTTTATTTTGAATTCGCC
1 TTTGTATTTTAATTTATTTTGAATTCGCC
**
15377 TTTAAATTTTAATTTATTTT-AATTTAGCGCC
1 TTTGTATTTTAATTTATTTTGAA-TT--CGCC
*
15408 TTTGTATTTTTATTT
1 TTTGTATTTTAATTT
15423 TAACTTTAGT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
28 5 0.14
29 15 0.42
31 16 0.44
ACGTcount: A:0.20, C:0.08, G:0.08, T:0.64
Consensus pattern (29 bp):
TTTGTATTTTAATTTATTTTGAATTCGCC
Found at i:15512 original size:17 final size:15
Alignment explanation
Indices: 15471--15513 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
15461 GTACTTGTGT
*
15471 TTATTTTATTTTTTA
1 TTATTTTATTTATTA
15486 TTATTGTTATTCTATTA
1 TTATT-TTATT-TATTA
15503 TTATGTTTATT
1 TTAT-TTTATT
15514 AATTGTTTTG
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
15 5 0.21
16 5 0.21
17 13 0.54
18 1 0.04
ACGTcount: A:0.21, C:0.02, G:0.05, T:0.72
Consensus pattern (15 bp):
TTATTTTATTTATTA
Found at i:22200 original size:9 final size:9
Alignment explanation
Indices: 22186--22211 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
22176 AATGATGAGA
22186 AAATAAAGT
1 AAATAAAGT
22195 AAATAAAGT
1 AAATAAAGT
22204 AAATAAAG
1 AAATAAAG
22212 AAGAATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.69, C:0.00, G:0.12, T:0.19
Consensus pattern (9 bp):
AAATAAAGT
Found at i:23572 original size:13 final size:14
Alignment explanation
Indices: 23543--23575 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
23533 ACATCACACC
*
23543 ATCATAGTAACAAT
1 ATCATAGCAACAAT
23557 ATCATAGCAA-AAT
1 ATCATAGCAACAAT
23570 ATCATA
1 ATCATA
23576 ATTAGTCCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.52, C:0.15, G:0.06, T:0.27
Consensus pattern (14 bp):
ATCATAGCAACAAT
Found at i:40101 original size:21 final size:21
Alignment explanation
Indices: 40068--40121 Score: 58
Period size: 21 Copynumber: 2.6 Consensus size: 21
40058 ACTTTGGTTC
* *
40068 AAAA-TCAACATTTCA-ACTT
1 AAAAGTCAGCATTTCATAATT
*
40087 AAAATTTCAGCATTTCATAATT
1 AAAA-GTCAGCATTTCATAATT
40109 AAAAGTCAGCATT
1 AAAAGTCAGCATT
40122 GAATACCCCA
Statistics
Matches: 29, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 4 0.14
21 18 0.62
22 7 0.24
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (21 bp):
AAAAGTCAGCATTTCATAATT
Found at i:56403 original size:19 final size:20
Alignment explanation
Indices: 56362--56434 Score: 71
Period size: 19 Copynumber: 3.6 Consensus size: 20
56352 ATCTAATGTT
*
56362 GGTATCGATACCGATA--AGG
1 GGTATCGATACC-ATAGTAAG
*
56381 GGTATCGATACCCTAGTAAG
1 GGTATCGATACCATAGTAAG
*
56401 GTAGTATCGATACCATGGTAA-
1 G--GTATCGATACCATAGTAAG
56422 GGTATCGATACCA
1 GGTATCGATACCA
56435 GGCAACATCG
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
18 2 0.04
19 24 0.52
20 3 0.07
21 1 0.02
22 16 0.35
ACGTcount: A:0.32, C:0.18, G:0.26, T:0.25
Consensus pattern (20 bp):
GGTATCGATACCATAGTAAG
Found at i:56410 original size:22 final size:22
Alignment explanation
Indices: 56382--56425 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
56372 CCGATAAGGG
*
56382 GTATCGATACCCTAGTAAGGTA
1 GTATCGATACCATAGTAAGGTA
*
56404 GTATCGATACCATGGTAAGGTA
1 GTATCGATACCATAGTAAGGTA
56426 TCGATACCAG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.32, C:0.16, G:0.25, T:0.27
Consensus pattern (22 bp):
GTATCGATACCATAGTAAGGTA
Done.