Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008354.1 Hibiscus syriacus cultivar Beakdansim tig00111091_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: 54563
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:2762 original size:20 final size:20
Alignment explanation
Indices: 2710--2770 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
2700 AGAACCCCAG
* *
2710 GGGGGTATCGATTCCCCTTCAAA
1 GGGGGAATCGATT-CCC-TC-AT
*
2733 GGGGGAATCGGTTCCCTCAT
1 GGGGGAATCGATTCCCTCAT
*
2753 GGGGGGATCGATTCCCTC
1 GGGGGAATCGATTCCCTC
2771 TGCACAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
20 17 0.52
21 2 0.06
22 3 0.09
23 11 0.33
ACGTcount: A:0.16, C:0.26, G:0.33, T:0.25
Consensus pattern (20 bp):
GGGGGAATCGATTCCCTCAT
Found at i:10400 original size:18 final size:18
Alignment explanation
Indices: 10373--10408 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
10363 AGCTGCCTAG
10373 ACCAAGGGGTCGGTACTC
1 ACCAAGGGGTCGGTACTC
*
10391 ACCAATGGGTCGGTACTC
1 ACCAAGGGGTCGGTACTC
10409 CTAAAGGGAG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.22, C:0.28, G:0.31, T:0.19
Consensus pattern (18 bp):
ACCAAGGGGTCGGTACTC
Found at i:13729 original size:7 final size:7
Alignment explanation
Indices: 13717--13744 Score: 56
Period size: 7 Copynumber: 4.0 Consensus size: 7
13707 TGTACATGTG
13717 CATGCAT
1 CATGCAT
13724 CATGCAT
1 CATGCAT
13731 CATGCAT
1 CATGCAT
13738 CATGCAT
1 CATGCAT
13745 GAAATTGAAC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 21 1.00
ACGTcount: A:0.29, C:0.29, G:0.14, T:0.29
Consensus pattern (7 bp):
CATGCAT
Found at i:15286 original size:15 final size:15
Alignment explanation
Indices: 15266--15297 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
15256 GAGAATGATG
15266 TAATTATTTAATAAT
1 TAATTATTTAATAAT
15281 TAATTATTTAATAAT
1 TAATTATTTAATAAT
15296 TA
1 TA
15298 GCATAATAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (15 bp):
TAATTATTTAATAAT
Found at i:19397 original size:6 final size:6
Alignment explanation
Indices: 19378--19419 Score: 50
Period size: 6 Copynumber: 7.2 Consensus size: 6
19368 GATGGAAGTC
* * *
19378 TAAA-T TAAAGT TAAATT TAAGTT TAAATT CAAATT TAAATT T
1 TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT TAAATT T
19420 TATGTACATA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
5 4 0.13
6 27 0.87
ACGTcount: A:0.48, C:0.02, G:0.05, T:0.45
Consensus pattern (6 bp):
TAAATT
Found at i:19444 original size:22 final size:22
Alignment explanation
Indices: 19419--19463 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
19409 AATTTAAATT
*
19419 TTATGTACATAAAAATATTATA
1 TTATGTACATAAAAATAATATA
* **
19441 TTATTTTTATAAAAATAATATA
1 TTATGTACATAAAAATAATATA
19463 T
1 T
19464 AAATATTAAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (22 bp):
TTATGTACATAAAAATAATATA
Found at i:26522 original size:17 final size:18
Alignment explanation
Indices: 26496--26535 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
26486 ATTATATGGA
26496 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
26512 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
26530 TATTAT
1 TATTAT
26536 ACGTGTATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:26800 original size:14 final size:16
Alignment explanation
Indices: 26776--26825 Score: 52
Period size: 16 Copynumber: 3.2 Consensus size: 16
26766 TATTTACGTA
*
26776 ATATATTTATAACT-TT
1 ATATATATAT-ACTATT
*
26792 ATATATATATATTATT
1 ATATATATATACTATT
26808 ATATATATAT--TATT
1 ATATATATATACTATT
26822 ATAT
1 ATAT
26826 TATTTTTTTT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
14 8 0.26
15 2 0.06
16 21 0.68
ACGTcount: A:0.42, C:0.02, G:0.00, T:0.56
Consensus pattern (16 bp):
ATATATATATACTATT
Found at i:26809 original size:16 final size:17
Alignment explanation
Indices: 26790--26823 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
26780 ATTTATAACT
26790 TTATATATATA-TATTA
1 TTATATATATATTATTA
26806 TTATATATATATTATTA
1 TTATATATATATTATTA
26823 T
1 T
26824 ATTATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (17 bp):
TTATATATATATTATTA
Found at i:26826 original size:8 final size:8
Alignment explanation
Indices: 26790--26829 Score: 50
Period size: 8 Copynumber: 5.2 Consensus size: 8
26780 ATTTATAACT
26790 TTATA-TA
1 TTATATTA
26797 TATATATTA
1 T-TATATTA
26806 TTATA-TA
1 TTATATTA
26813 -TATATTA
1 TTATATTA
26820 TTATATTA
1 TTATATTA
26828 TT
1 TT
26830 TTTTTTTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
6 4 0.14
7 5 0.17
8 17 0.59
9 3 0.10
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (8 bp):
TTATATTA
Found at i:27015 original size:2 final size:2
Alignment explanation
Indices: 27008--27038 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
26998 ATATTTGTTG
27008 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 T
27039 TTTCCTTTTT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:31535 original size:16 final size:16
Alignment explanation
Indices: 31514--31569 Score: 58
Period size: 18 Copynumber: 3.2 Consensus size: 16
31504 AATCAAGAAT
*
31514 AAAAAAGAAAAGAAGC
1 AAAAAAGAAAACAAGC
31530 AAAAAAGAAAAAACAAGAAC
1 AAAAAAG--AAAACAAG--C
*
31550 AAAAAAGAAAATAAGC
1 AAAAAAGAAAACAAGC
31566 AAAA
1 AAAA
31570 TTAAAAAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 8
0.77 0.05 0.18
Matches are distributed among these distances:
16 12 0.35
18 14 0.41
20 8 0.24
ACGTcount: A:0.79, C:0.07, G:0.12, T:0.02
Consensus pattern (16 bp):
AAAAAAGAAAACAAGC
Found at i:32627 original size:18 final size:18
Alignment explanation
Indices: 32604--32639 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
32594 TCAATATCAA
*
32604 ATATTGGGACATTTTTGG
1 ATATTGGGACATCTTTGG
*
32622 ATATTGGGGCATCTTTGG
1 ATATTGGGACATCTTTGG
32640 GGATTCAACA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.19, C:0.08, G:0.31, T:0.42
Consensus pattern (18 bp):
ATATTGGGACATCTTTGG
Found at i:33172 original size:34 final size:35
Alignment explanation
Indices: 33129--33195 Score: 118
Period size: 34 Copynumber: 1.9 Consensus size: 35
33119 CTCACCATTG
*
33129 TCTCTCTTGAGACAGTTTCCCTT-GAAACAAACTT
1 TCTCTCTTGAGACAGTTTCCCTTGGAAAAAAACTT
33163 TCTCTCTTGAGACAGTTTCCCTTGGAAAAAAAC
1 TCTCTCTTGAGACAGTTTCCCTTGGAAAAAAAC
33196 CTTTGAAATT
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 23 0.74
35 8 0.26
ACGTcount: A:0.28, C:0.25, G:0.13, T:0.33
Consensus pattern (35 bp):
TCTCTCTTGAGACAGTTTCCCTTGGAAAAAAACTT
Found at i:33442 original size:37 final size:37
Alignment explanation
Indices: 33372--33443 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
33362 TGGAACTAAG
* *
33372 TTTTGTCTCTCTTGAGACAGATTTTCTTAAAACAAAA
1 TTTTGTCTCCCTTGAGACAGATTTTCATAAAACAAAA
* *
33409 TTTTGTCTCCCTTGAGACCG-TTTCTCATGAAACAA
1 TTTTGTCTCCCTTGAGACAGATTT-TCATAAAACAA
33444 CAGATATCTT
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
36 3 0.10
37 27 0.90
ACGTcount: A:0.28, C:0.21, G:0.12, T:0.39
Consensus pattern (37 bp):
TTTTGTCTCCCTTGAGACAGATTTTCATAAAACAAAA
Found at i:34929 original size:106 final size:106
Alignment explanation
Indices: 33960--34928 Score: 1363
Period size: 106 Copynumber: 9.0 Consensus size: 106
33950 ATATCGCGCC
* * * * *
33960 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGGCAGCTGGTTGTCAACAAACCACTTT-T
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAA-CAATTTCC
*
34024 CAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAG--T--TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * *
34070 ACTCGAGACAACACAAGTTCAACTTCACAACGAATGGACGGCTGGTTGTCAACAAACCATTACCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
* *
34135 AATTTCAGAGCCAATTTCAACTTCACATCGAAGGATATTGG
66 AGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
34176 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAAACAAACCACTTT-
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTC-AACAAA-CAATTTC
* * *
34240 TCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAATGATATTGG
64 CCAG--T--TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
34287 ACTCAAGACAACACAAGTTTAACTTCACAACGAAGGGACAGCTGGTTGTCAACAAAACAATTTCT
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AAACAATTTCC
34352 CAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
34394 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAAACAATTTCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAAC-AAACAATTTCC
*
34459 CAGTTTCAGAGCCAATTTCAACTTTACAGCGAAGGATATTGG
65 CAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
34501 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGTTGGTTGTCAACAAACCACTTT-T
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAA-CAATTTCC
34565 CAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
65 CAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
34607 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAGCAAACAATTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
* * *
34672 AATTTCAGAG-CATATTTCAACTTCACAACGAATGATATTGG
66 AGTTTCAGAGCCA-ATTTCAACTTCACAGCGAAGGATATTGG
* * * *
34713 ACTCAAGACGACACAAGTTCAAATTCACAACGAAGGGACGACTGGTTCTCAACAAACAATTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
* *
34778 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGA
66 AGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
34819 ACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGGCTGGCTGTCAACAAACAATTTCCC
1 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
* * *
34884 AGTTCCGGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
66 AGTTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
34925 ACTC
1 ACTC
34929 GGAACAATAC
Statistics
Matches: 779, Mismatches: 66, Indels: 32
0.89 0.08 0.04
Matches are distributed among these distances:
105 8 0.01
106 407 0.52
107 204 0.26
108 4 0.01
109 5 0.01
110 63 0.08
111 88 0.11
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (106 bp):
ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
AGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:34968 original size:431 final size:428
Alignment explanation
Indices: 33960--34935 Score: 1409
Period size: 431 Copynumber: 2.3 Consensus size: 428
33950 ATATCGCGCC
* * *
33960 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGGCAGCTGGTTGTCAACAAACCACTTT-T
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGGCGGCTGGTTGTCAACAAA-CAATTTCC
*
34024 CAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGAC-AACACAAGT
65 CAG-TTC---CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGA-ACAAACACAAGT
*
34088 TCAACTTCACAACGAATGGACGGCTGGTTGTCAACAAACCATTACCCAATTTCAGAGCCAATTTC
125 TCAACTTCACAACGAAGGGACGGCTGGTTGTCAACAAACCATTACCCAATTTCAGAGCCAATTTC
* *
34153 AACTTCACATCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGACGAC
190 AACTTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGAC
* * * *
34218 TGGTTGTCAAACAAACCACTTTTCAGTTTCATTCAGAGTCAATTTCAACTTCACAGCGAATGATA
255 TGGTTGTCAAACAAACCAATTTCCAG-AT-ATTCAGAGTCAATTTCAACTTCACAACGAATGATA
* * *
34283 TTGGACTCAAGACAACACAAGTTTAACTTCACAACGAAGGGACAGCTGGTTGTCAACAAAACAAT
318 TTGGACTCAAGACAACACAAGTTCAAATTCACAACGAAGGGACAGCTGGTTCTCAACAAAACAAT
* * *
34348 TTCTCAGTTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
383 TTCCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGA
* * *
34394 ACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTGTCAACAAAACAATTTCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGGCGGCTGGTTGTCAAC-AAACAATTTCC
* * *
34459 CAGTTTCAGAGCCAATTTCAACTTTACAGCGAAGGATATTGGACTC-AAGACAACACAAGTTCAA
65 CAGTTCCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAACA-AACACAAGTTCAA
* ** *
34523 CTTCACAACGAAGGGACGGTTGGTTGTCAACAAACCACTT-TTCAGTTTCAGAGCCAATTTCAAC
129 CTTCACAACGAAGGGACGGCTGGTTGTCAACAAACCA-TTACCCAATTTCAGAGCCAATTTCAAC
*
34587 TTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGGCTGG
193 TTCACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGG
*
34652 TTGTC-AGCAAA-CAATTTCCCA-AT-TTCAGAG-CATATTTCAACTTCACAACGAATGATATTG
258 TTGTCAAACAAACCAATTT-CCAGATATTCAGAGTCA-ATTTCAACTTCACAACGAATGATATTG
*
34712 GACTCAAGACGACACAAGTTCAAATTCACAACGAAGGGAC-GACTGGTTCTCAAC-AAACAATTT
321 GACTCAAGACAACACAAGTTCAAATTCACAACGAAGGGACAG-CTGGTTCTCAACAAAACAATTT
34775 CCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGA
385 CCCAATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGA
* * *
34819 ACTCGAGACAACACAAGCTCAACTTCACAGCGAAGGGGCGGCTGGCTGTCAACAAACAATTTCCC
1 ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGGCGGCTGGTTGTCAACAAACAATTTCCC
* *
34884 AGTTCCGGAGCCAATTTCAACTTCAC-GACGGAGGATATTGGACTCGGAACAA
66 AGTTCCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGGACTC-GAACAA
34936 TACTACCCGT
Statistics
Matches: 490, Mismatches: 41, Indels: 31
0.87 0.07 0.06
Matches are distributed among these distances:
423 1 0.00
424 51 0.10
425 101 0.21
426 84 0.17
428 1 0.00
429 6 0.01
430 8 0.02
431 174 0.36
432 2 0.00
434 56 0.11
435 6 0.01
ACGTcount: A:0.35, C:0.24, G:0.18, T:0.23
Consensus pattern (428 bp):
ACTCGAGACAACACAAGTTCAACTTCACAACGAAGGGGCGGCTGGTTGTCAACAAACAATTTCCC
AGTTCCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCGAACAAACACAAGTTCAACT
TCACAACGAAGGGACGGCTGGTTGTCAACAAACCATTACCCAATTTCAGAGCCAATTTCAACTTC
ACAGCGAAGGATATTGGACTCAAGACAACACAAGTTCAACTTCACAACGAAGGGACGACTGGTTG
TCAAACAAACCAATTTCCAGATATTCAGAGTCAATTTCAACTTCACAACGAATGATATTGGACTC
AAGACAACACAAGTTCAAATTCACAACGAAGGGACAGCTGGTTCTCAACAAAACAATTTCCCAAT
TTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGA
Found at i:36171 original size:17 final size:18
Alignment explanation
Indices: 36145--36184 Score: 57
Period size: 18 Copynumber: 2.3 Consensus size: 18
36135 ATTATATAGA
36145 TATT-TTATTCAT-TTAT
1 TATTATTATTCATGTTAT
*
36161 TTTTATTATTCATGTTAT
1 TATTATTATTCATGTTAT
36179 TATTAT
1 TATTAT
36185 ACGTATATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
16 3 0.15
17 8 0.40
18 9 0.45
ACGTcount: A:0.25, C:0.05, G:0.03, T:0.68
Consensus pattern (18 bp):
TATTATTATTCATGTTAT
Found at i:36723 original size:2 final size:2
Alignment explanation
Indices: 36716--36756 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
36706 TACTTTGATG
36716 TA TA 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 TA TA T
36757 TCCTTTTTCA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:36820 original size:21 final size:21
Alignment explanation
Indices: 36796--36847 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
36786 ATGACTTTAC
*
36796 TATTTTTTTCCTTATCTTATT
1 TATTTTTTTACTTATCTTATT
* * *
36817 TATTTATTTATTTATTTTATT
1 TATTTTTTTACTTATCTTATT
36838 TATTTATTTT
1 TATTT-TTTT
36848 TATTTTATTA
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.19, C:0.06, G:0.00, T:0.75
Consensus pattern (21 bp):
TATTTTTTTACTTATCTTATT
Found at i:36821 original size:4 final size:4
Alignment explanation
Indices: 36807--36846 Score: 62
Period size: 4 Copynumber: 9.5 Consensus size: 4
36797 ATTTTTTTCC
36807 TTAT CTTAT TTAT TTAT TTAT TTATT TTAT TTAT TTAT TT
1 TTAT -TTAT TTAT TTAT TTAT TTA-T TTAT TTAT TTAT TT
36847 TTATTTTATT
Statistics
Matches: 34, Mismatches: 0, Indels: 3
0.92 0.00 0.08
Matches are distributed among these distances:
4 26 0.76
5 8 0.24
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.75
Consensus pattern (4 bp):
TTAT
Found at i:37820 original size:10 final size:10
Alignment explanation
Indices: 37805--37833 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
37795 TTTCCATTAT
37805 TTTTTATTTA
1 TTTTTATTTA
37815 TTTTTATTTA
1 TTTTTATTTA
37825 TTTTTATTT
1 TTTTTATTT
37834 TACTAACTGT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (10 bp):
TTTTTATTTA
Found at i:49373 original size:18 final size:19
Alignment explanation
Indices: 49330--49373 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 19
49320 ATATTTAATT
*
49330 TCATAAAATCTCAAAAAAC
1 TCATAAAATCCCAAAAAAC
* *
49349 TCCTAAATTCCCAAAAAA-
1 TCATAAAATCCCAAAAAAC
49367 TCATAAA
1 TCATAAA
49374 CTTTAAATCG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
18 6 0.29
19 15 0.71
ACGTcount: A:0.55, C:0.23, G:0.00, T:0.23
Consensus pattern (19 bp):
TCATAAAATCCCAAAAAAC
Found at i:52421 original size:2 final size:2
Alignment explanation
Indices: 52414--52468 Score: 80
Period size: 2 Copynumber: 29.0 Consensus size: 2
52404 AAAATTAATA
*
52414 AT AT AT AT A- AT AT AT AT AT AT AT A- AA 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
52454 AT AT AT -T AT AT AT AT
1 AT AT AT AT AT AT AT AT
52469 TGGAACAAGT
Statistics
Matches: 49, Mismatches: 1, Indels: 6
0.88 0.02 0.11
Matches are distributed among these distances:
1 3 0.06
2 46 0.94
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:52436 original size:17 final size:17
Alignment explanation
Indices: 52414--52468 Score: 87
Period size: 17 Copynumber: 3.4 Consensus size: 17
52404 AAAATTAATA
52414 ATATATATAATATATAT
1 ATATATATAATATATAT
*
52431 ATATATAAAATATATAT
1 ATATATATAATATATAT
52448 ATATATAT-ATAT-TAT
1 ATATATATAATATATAT
52463 ATATAT
1 ATATAT
52469 TGGAACAAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
15 9 0.25
16 4 0.11
17 23 0.64
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
ATATATATAATATATAT
Found at i:52445 original size:19 final size:19
Alignment explanation
Indices: 52423--52468 Score: 74
Period size: 19 Copynumber: 2.4 Consensus size: 19
52413 AATATATATA
52423 ATATATATATATATAAAAT
1 ATATATATATATATAAAAT
* *
52442 ATATATATATATATATATT
1 ATATATATATATATAAAAT
52461 ATATATAT
1 ATATATAT
52469 TGGAACAAGT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
19 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (19 bp):
ATATATATATATATAAAAT
Found at i:52468 original size:15 final size:15
Alignment explanation
Indices: 52414--52467 Score: 83
Period size: 15 Copynumber: 3.6 Consensus size: 15
52404 AAAATTAATA
52414 ATATATATAATATAT
1 ATATATATAATATAT
*
52429 ATATATATAAAATAT
1 ATATATATAATATAT
52444 ATATATAT-ATATAT
1 ATATATATAATATAT
52458 ATTATATATA
1 A-TATATATA
52468 TTGGAACAAG
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
14 6 0.17
15 29 0.83
ACGTcount: A:0.54, C:0.00, G:0.00, T:0.46
Consensus pattern (15 bp):
ATATATATAATATAT
Done.