Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005181.1 Hibiscus syriacus cultivar Beakdansim tig00011695_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: 63470
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:2428 original size:38 final size:38
Alignment explanation
Indices: 2386--2460 Score: 123
Period size: 38 Copynumber: 2.0 Consensus size: 38
2376 TTATTTATAT
2386 ATTATATGTAAATTTCGGTTAATCGATAGAATTAATTG
1 ATTATATGTAAATTTCGGTTAATCGATAGAATTAATTG
* * *
2424 ATTATTTTTAAATTTCGGTTAATCGATCGAATTAATT
1 ATTATATGTAAATTTCGGTTAATCGATAGAATTAATT
2461 AAAATTTTCG
Statistics
Matches: 34, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
38 34 1.00
ACGTcount: A:0.35, C:0.07, G:0.13, T:0.45
Consensus pattern (38 bp):
ATTATATGTAAATTTCGGTTAATCGATAGAATTAATTG
Found at i:4019 original size:60 final size:60
Alignment explanation
Indices: 3926--4041 Score: 178
Period size: 60 Copynumber: 1.9 Consensus size: 60
3916 AACGTAGTTA
* * * *
3926 AAAGCCTAATTATCGATTTAGGTAATCGTTGTTACTTAGAGAAATTTAGGTAATCGCATG
1 AAAGCCTAATTACCGATATAGGTAATAGTTGTTACTTAGAGAAATTTAGATAATCGCATG
* *
3986 AAAGCCTAATTACCGATATAGGTAATATTTGTTACTTAGGGAAATTTAGATAATCG
1 AAAGCCTAATTACCGATATAGGTAATAGTTGTTACTTAGAGAAATTTAGATAATCG
4042 TTGTTCGGAG
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 50 1.00
ACGTcount: A:0.35, C:0.11, G:0.19, T:0.34
Consensus pattern (60 bp):
AAAGCCTAATTACCGATATAGGTAATAGTTGTTACTTAGAGAAATTTAGATAATCGCATG
Found at i:6332 original size:31 final size:31
Alignment explanation
Indices: 6297--6363 Score: 116
Period size: 31 Copynumber: 2.2 Consensus size: 31
6287 GATAAATTGG
*
6297 TCACTAACGTTATCGATTTATAACAAAATGC
1 TCACTAACATTATCGATTTATAACAAAATGC
*
6328 TCACTAACATTATCGATTTATAACAAAATGG
1 TCACTAACATTATCGATTTATAACAAAATGC
6359 TCACT
1 TCACT
6364 CTACCATCAT
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
31 34 1.00
ACGTcount: A:0.39, C:0.19, G:0.09, T:0.33
Consensus pattern (31 bp):
TCACTAACATTATCGATTTATAACAAAATGC
Found at i:8515 original size:18 final size:19
Alignment explanation
Indices: 8477--8515 Score: 62
Period size: 20 Copynumber: 2.1 Consensus size: 19
8467 CGAAATATCT
8477 ATGCATCGATGCACCCCTTA
1 ATGCATCGATGCA-CCCTTA
8497 ATGCATCGATGCA-CCTTA
1 ATGCATCGATGCACCCTTA
8515 A
1 A
8516 AAATTGTCTT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 6 0.32
20 13 0.68
ACGTcount: A:0.28, C:0.31, G:0.15, T:0.26
Consensus pattern (19 bp):
ATGCATCGATGCACCCTTA
Found at i:9571 original size:30 final size:27
Alignment explanation
Indices: 9506--9561 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
9496 GAGGCCAAGA
9506 GATACAAAAAACAACAAACAAAACAAT
1 GATACAAAAAACAACAAACAAAACAAT
9533 GATACAAAAAACAACAAACAAAACAAT
1 GATACAAAAAACAACAAACAAAACAAT
9560 GA
1 GA
9562 AGCTTCAAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.70, C:0.18, G:0.05, T:0.07
Consensus pattern (27 bp):
GATACAAAAAACAACAAACAAAACAAT
Found at i:12071 original size:20 final size:20
Alignment explanation
Indices: 12046--12091 Score: 92
Period size: 20 Copynumber: 2.3 Consensus size: 20
12036 ATAAGTCGAG
12046 AGATGTAGGGAAATAGAAAT
1 AGATGTAGGGAAATAGAAAT
12066 AGATGTAGGGAAATAGAAAT
1 AGATGTAGGGAAATAGAAAT
12086 AGATGT
1 AGATGT
12092 TTATAAAGAG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.48, C:0.00, G:0.30, T:0.22
Consensus pattern (20 bp):
AGATGTAGGGAAATAGAAAT
Found at i:13087 original size:103 final size:103
Alignment explanation
Indices: 12908--13116 Score: 364
Period size: 103 Copynumber: 2.0 Consensus size: 103
12898 GGTCTACGTT
* *
12908 GTCCTTCGGGACATATATGTATTCTTTGGAACATGTGTGAAGTCTGGTGAGACACATACTTGATC
1 GTCCTTCGGGACATATATGTATTCTTTAGAACATATGTGAAGTCTGGTGAGACACATACTTGATC
* *
12973 ATTGGCATATGTATATGATTCTTAAGGAATGATATGTG
66 ACTAGCATATGTATATGATTCTTAAGGAATGATATGTG
13011 GTCCTTCGGGACATATATGTATTCTTTAGAACATATGTGAAGTCTGGTGAGACACATACTTGATC
1 GTCCTTCGGGACATATATGTATTCTTTAGAACATATGTGAAGTCTGGTGAGACACATACTTGATC
* *
13076 CCTAGTATATGTATATGATTCTTAAGGAATGATATGTG
66 ACTAGCATATGTATATGATTCTTAAGGAATGATATGTG
13114 GTC
1 GTC
13117 TTTATGGACA
Statistics
Matches: 100, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
103 100 1.00
ACGTcount: A:0.28, C:0.13, G:0.23, T:0.36
Consensus pattern (103 bp):
GTCCTTCGGGACATATATGTATTCTTTAGAACATATGTGAAGTCTGGTGAGACACATACTTGATC
ACTAGCATATGTATATGATTCTTAAGGAATGATATGTG
Found at i:13169 original size:23 final size:23
Alignment explanation
Indices: 13136--13203 Score: 91
Period size: 23 Copynumber: 3.0 Consensus size: 23
13126 ATTATTATAT
*
13136 GGCACTACGGTGTAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
13159 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
13182 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
13204 AGCTGTGGTT
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 40 1.00
ACGTcount: A:0.21, C:0.26, G:0.26, T:0.26
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:17327 original size:20 final size:20
Alignment explanation
Indices: 17298--17343 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
17288 ATAAGTCGAG
*
17298 AGATGCAGGGAAATAGAAAT
1 AGATGTAGGGAAATAGAAAT
17318 AGATGTAGGGAAATAGAAAT
1 AGATGTAGGGAAATAGAAAT
*
17338 ATATGT
1 AGATGT
17344 TTATAAAGAG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.48, C:0.02, G:0.28, T:0.22
Consensus pattern (20 bp):
AGATGTAGGGAAATAGAAAT
Found at i:18337 original size:103 final size:103
Alignment explanation
Indices: 18158--18369 Score: 388
Period size: 103 Copynumber: 2.1 Consensus size: 103
18148 GGTCTACGTT
18158 GTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATACTTGATC
1 GTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATACTTGATC
* *
18223 CTTGGCATATGTATATGATTCGTAAGGAATGATATGTG
66 CCTAGCATATGTATATGATTCGTAAGGAATGATATGTG
18261 GTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATACTTGATC
1 GTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATACTTGATC
* *
18326 CCTAGTATATGTATATGATTCTTAAGGAATGATATGTG
66 CCTAGCATATGTATATGATTCGTAAGGAATGATATGTG
18364 GTCCTT
1 GTCCTT
18370 ATGGACATTA
Statistics
Matches: 105, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
103 105 1.00
ACGTcount: A:0.27, C:0.14, G:0.23, T:0.36
Consensus pattern (103 bp):
GTCCTTCGGGACATATATGTATTCTTTGAAACATGTGTGAAGTCTGGTGAGACACATACTTGATC
CCTAGCATATGTATATGATTCGTAAGGAATGATATGTG
Found at i:18419 original size:23 final size:23
Alignment explanation
Indices: 18386--18453 Score: 100
Period size: 23 Copynumber: 3.0 Consensus size: 23
18376 ATTATTATAT
18386 GGCACTACGGTGCAATTCTACGC
1 GGCACTACGGTGCAATTCTACGC
* *
18409 GGCACTCCGGTGCAATTCTACGT
1 GGCACTACGGTGCAATTCTACGC
* *
18432 GGCACTTCGGTGCAATTATACG
1 GGCACTACGGTGCAATTCTACG
18454 AGCTGTGGTG
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.21, C:0.28, G:0.26, T:0.25
Consensus pattern (23 bp):
GGCACTACGGTGCAATTCTACGC
Found at i:22042 original size:2 final size:2
Alignment explanation
Indices: 22035--22064 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
22025 AATTCTAATA
22035 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
22065 TTTTTTATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:26428 original size:19 final size:19
Alignment explanation
Indices: 26404--26492 Score: 126
Period size: 19 Copynumber: 4.7 Consensus size: 19
26394 AACGCGAAAG
26404 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
26423 TCAAATTCGCAACTGAATT
1 TCAAATTCGCAACTGAATT
**
26442 TCAAATTCATAACTGAATT
1 TCAAATTCGCAACTGAATT
*
26461 TCAAATTCGCAACGCGAATT
1 TCAAATTCGCAAC-TGAATT
*
26481 T-AATTTCGCAAC
1 TCAAATTCGCAAC
26493 ATGTTTTAGT
Statistics
Matches: 63, Mismatches: 6, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
19 57 0.90
20 6 0.10
ACGTcount: A:0.37, C:0.21, G:0.10, T:0.31
Consensus pattern (19 bp):
TCAAATTCGCAACTGAATT
Found at i:26449 original size:38 final size:39
Alignment explanation
Indices: 26304--26492 Score: 145
Period size: 38 Copynumber: 4.8 Consensus size: 39
26294 AAATGACCAA
** * * * *
26304 CAAATTCGCAATACGAATTCCAATTTCGCAACTCAGTTT
1 CAAATTCGCAACGCGAATTTCAAATTCGCAACTGAATTT
* * *
26343 CCAATTTCGCAACGCGAATATGT-AAA-TCGC-ATTGCGATTTT
1 -CAAATTCGCAACGCGAAT-T-TCAAATTCGCAACT--GAATTT
* **
26384 CCAAATTCGTAACGCGAAAGTCAAATTCGCAACTGAATTT
1 -CAAATTCGCAACGCGAATTTCAAATTCGCAACTGAATTT
* **
26424 CAAATTCGCAAC-TGAATTTCAAATTCATAACTGAATTT
1 CAAATTCGCAACGCGAATTTCAAATTCGCAACTGAATTT
*
26462 CAAATTCGCAACGCGAATTT-AATTTCGCAAC
1 CAAATTCGCAACGCGAATTTCAAATTCGCAAC
26493 ATGTTTTAGT
Statistics
Matches: 117, Mismatches: 24, Indels: 18
0.74 0.15 0.11
Matches are distributed among these distances:
38 41 0.35
39 20 0.17
40 27 0.23
41 27 0.23
42 2 0.02
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.30
Consensus pattern (39 bp):
CAAATTCGCAACGCGAATTTCAAATTCGCAACTGAATTT
Found at i:26481 original size:20 final size:20
Alignment explanation
Indices: 26304--26492 Score: 122
Period size: 19 Copynumber: 9.6 Consensus size: 20
26294 AAATGACCAA
** *
26304 CAAATTCGCAATACGAATTC
1 CAAATTCGCAACGCGAATTT
* * *
26324 CAATTTCGCAACTC-AGTTT
1 CAAATTCGCAACGCGAATTT
*
26343 CCAATTTCGCAACGCGAATATGT
1 -CAAATTCGCAACGCGAAT-T-T
** *
26366 -AAA-TCGCATTGCGATTTT
1 CAAATTCGCAACGCGAATTT
* **
26384 CCAAATTCGTAACGCGAAAGT
1 -CAAATTCGCAACGCGAATTT
*
26405 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAATTT
*
26424 CAAATTCGCAAC-TGAATTT
1 CAAATTCGCAACGCGAATTT
** *
26443 CAAATTCATAAC-TGAATTT
1 CAAATTCGCAACGCGAATTT
26462 CAAATTCGCAACGCGAATTT
1 CAAATTCGCAACGCGAATTT
*
26482 -AATTTCGCAAC
1 CAAATTCGCAAC
26493 ATGTTTTAGT
Statistics
Matches: 134, Mismatches: 27, Indels: 17
0.75 0.15 0.10
Matches are distributed among these distances:
18 1 0.01
19 64 0.48
20 54 0.40
21 13 0.10
22 1 0.01
23 1 0.01
ACGTcount: A:0.35, C:0.23, G:0.13, T:0.30
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTT
Found at i:29741 original size:18 final size:18
Alignment explanation
Indices: 29718--29753 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
29708 AAGTAAAAGG
*
29718 AAATCAAAATCGCAATCA
1 AAATCAAAATCCCAATCA
29736 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
29754 CAACCGGCTT
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:0.56, C:0.25, G:0.03, T:0.17
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:30086 original size:20 final size:20
Alignment explanation
Indices: 30041--30079 Score: 78
Period size: 20 Copynumber: 1.9 Consensus size: 20
30031 TGCGATCAAT
30041 GCGAAAGTCAAATTCGCAAC
1 GCGAAAGTCAAATTCGCAAC
30061 GCGAAAGTCAAATTCGCAA
1 GCGAAAGTCAAATTCGCAA
30080 ACCGAAAATC
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.41, C:0.23, G:0.21, T:0.15
Consensus pattern (20 bp):
GCGAAAGTCAAATTCGCAAC
Found at i:30113 original size:20 final size:20
Alignment explanation
Indices: 30088--30126 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
30078 AAACCGAAAA
*
30088 TCGCGTTGCGAATTTGACTT
1 TCGCGTTGCAAATTTGACTT
30108 TCGCGTTGCAAATTTGACT
1 TCGCGTTGCAAATTTGACT
30127 ATCACAACGC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.18, C:0.21, G:0.23, T:0.38
Consensus pattern (20 bp):
TCGCGTTGCAAATTTGACTT
Found at i:30347 original size:61 final size:63
Alignment explanation
Indices: 30216--30356 Score: 162
Period size: 61 Copynumber: 2.2 Consensus size: 63
30206 TTTTAGAGAC
* *
30216 AACAAATCAACTTTTACAAATGAATTAAACAAGCAAAAAAATAATTCTTATTTACAAATCAAATT
1 AACAAATCAACTTTTACAAATCAATT--A-AAGCAAAAAAATAAATCTTATTTACAAATCAAATT
30281 A
63 A
* * ** *
30282 AACAAATCAACTTTTACAAATCAATT-AATC-AAAAAATAAATCTTATTTCCTCATC-AATTGT
1 AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTTACAAATCAAATT-A
30343 AACAAATCAACTTT
1 AACAAATCAACTTT
30357 CAATGTAAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 7
0.83 0.09 0.09
Matches are distributed among these distances:
60 4 0.06
61 35 0.52
62 3 0.04
66 25 0.37
ACGTcount: A:0.50, C:0.16, G:0.02, T:0.31
Consensus pattern (63 bp):
AACAAATCAACTTTTACAAATCAATTAAAGCAAAAAAATAAATCTTATTTACAAATCAAATTA
Found at i:34039 original size:13 final size:13
Alignment explanation
Indices: 34021--34052 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
34011 GGGTTTCTTC
34021 AACAAAAAGACAA
1 AACAAAAAGACAA
*
34034 AACAAAAAGATAA
1 AACAAAAAGACAA
34047 AACAAA
1 AACAAA
34053 GACAAATACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.78, C:0.12, G:0.06, T:0.03
Consensus pattern (13 bp):
AACAAAAAGACAA
Found at i:34297 original size:22 final size:22
Alignment explanation
Indices: 34266--34322 Score: 87
Period size: 22 Copynumber: 2.6 Consensus size: 22
34256 GATGGAGATA
*
34266 GACGGATTTCGTCGGATATGGG
1 GACGGATTTCGTCGGAGATGGG
*
34288 GATGGATTTCGTCGGAGATGGG
1 GACGGATTTCGTCGGAGATGGG
*
34310 GACGGATGTCGTC
1 GACGGATTTCGTC
34323 ATAGAGAGTG
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 31 1.00
ACGTcount: A:0.18, C:0.14, G:0.42, T:0.26
Consensus pattern (22 bp):
GACGGATTTCGTCGGAGATGGG
Found at i:34469 original size:20 final size:20
Alignment explanation
Indices: 34444--34507 Score: 110
Period size: 20 Copynumber: 3.2 Consensus size: 20
34434 GCGTAAAAAC
34444 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
34464 ATTTGACTTTCGCGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
* *
34484 ATTTGACTATCGTGTTGCGA
1 ATTTGACTTTCGCGTTGCGA
34504 ATTT
1 ATTT
34508 AGAAAATCGC
Statistics
Matches: 42, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.17, C:0.17, G:0.23, T:0.42
Consensus pattern (20 bp):
ATTTGACTTTCGCGTTGCGA
Found at i:34524 original size:21 final size:21
Alignment explanation
Indices: 34500--34570 Score: 108
Period size: 21 Copynumber: 3.4 Consensus size: 21
34490 CTATCGTGTT
34500 GCGAATTTAGAAAATCGCAAC
1 GCGAATTTAGAAAATCGCAAC
*
34521 GCGAATTTGGAAAATCGCAAC
1 GCGAATTTAGAAAATCGCAAC
* *
34542 GCGAATTTGGAAAATCGCAAT
1 GCGAATTTAGAAAATCGCAAC
34563 GCG-ATTTA
1 GCGAATTTA
34571 CATATTCGCG
Statistics
Matches: 47, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 4 0.09
21 43 0.91
ACGTcount: A:0.38, C:0.17, G:0.23, T:0.23
Consensus pattern (21 bp):
GCGAATTTAGAAAATCGCAAC
Found at i:34623 original size:20 final size:20
Alignment explanation
Indices: 34574--34627 Score: 65
Period size: 20 Copynumber: 2.7 Consensus size: 20
34564 CGATTTACAT
34574 ATTCGCGTTGCGAAATTGGA
1 ATTCGCGTTGCGAAATTGGA
* *
34594 A-ACTGGGTTGCGAAATTGGA
1 ATTC-GCGTTGCGAAATTGGA
*
34614 ATTCGTGTTGCGAA
1 ATTCGCGTTGCGAA
34628 TTTGTTGGTC
Statistics
Matches: 28, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
19 1 0.04
20 26 0.93
21 1 0.04
ACGTcount: A:0.26, C:0.13, G:0.31, T:0.30
Consensus pattern (20 bp):
ATTCGCGTTGCGAAATTGGA
Found at i:40029 original size:2 final size:2
Alignment explanation
Indices: 40022--40075 Score: 101
Period size: 2 Copynumber: 27.5 Consensus size: 2
40012 CACTGAAAAT
40022 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
40064 TA TA TA TA -A TA T
1 TA TA TA TA TA TA T
40076 TTTATGTTTC
Statistics
Matches: 51, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 50 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:41906 original size:31 final size:31
Alignment explanation
Indices: 41868--41939 Score: 90
Period size: 31 Copynumber: 2.3 Consensus size: 31
41858 AATTATTATG
* * *
41868 TCACAAATTTGTGAAGGGTATACATATTCCA
1 TCACAAATTTGAGAAGAGTAGACATATTCCA
* *
41899 TCACAAATTTGAGATGAGTCGACATATTCCA
1 TCACAAATTTGAGAAGAGTAGACATATTCCA
*
41930 TCATAAATTT
1 TCACAAATTT
41940 AAAATACTTT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
31 35 1.00
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (31 bp):
TCACAAATTTGAGAAGAGTAGACATATTCCA
Found at i:43703 original size:46 final size:45
Alignment explanation
Indices: 43600--43705 Score: 124
Period size: 45 Copynumber: 2.3 Consensus size: 45
43590 GTGCACTAAG
* * * *
43600 AGTGCATCTATGCATCAAGTGTATTCGATGTTTCAAAATAGCCAG
1 AGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAC
* *
43645 AGTGCATCGATGCATCAAATGCATTCGATGTTTTCATAAA-ATCCTC
1 AGTGCATCGATGCATCAAATGCATTCGATG-TTTCA-AAATAGCCAC
*
43691 AGTGTATCGATGCAT
1 AGTGCATCGATGCAT
43706 GGTATGTGCA
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
45 27 0.52
46 22 0.42
47 3 0.06
ACGTcount: A:0.30, C:0.19, G:0.19, T:0.32
Consensus pattern (45 bp):
AGTGCATCGATGCATCAAATGCATTCGATGTTTCAAAATAGCCAC
Found at i:54309 original size:16 final size:17
Alignment explanation
Indices: 54288--54321 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
54278 TTTAAATTTG
*
54288 ATAAAAAA-TTTAAAAA
1 ATAAAAAAGTTGAAAAA
54304 ATAAAAAAGTTGAAAAA
1 ATAAAAAAGTTGAAAAA
54321 A
1 A
54322 AGACAAGAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 8 0.50
17 8 0.50
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.21
Consensus pattern (17 bp):
ATAAAAAAGTTGAAAAA
Found at i:55650 original size:16 final size:16
Alignment explanation
Indices: 55631--55664 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
55621 TAAATAATAT
* *
55631 AATAAATAAAAATAAA
1 AATAAAGAAAAAGAAA
55647 AATAAAGAAAAAGAAA
1 AATAAAGAAAAAGAAA
55663 AA
1 AA
55665 AATTAATTTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.82, C:0.00, G:0.06, T:0.12
Consensus pattern (16 bp):
AATAAAGAAAAAGAAA
Found at i:55687 original size:11 final size:12
Alignment explanation
Indices: 55661--55707 Score: 60
Period size: 13 Copynumber: 3.8 Consensus size: 12
55651 AAGAAAAAGA
55661 AAAAAATTAATTT
1 AAAAAATTAA-TT
55674 AAAAAATTAA-T
1 AAAAAATTAATT
55685 AAAAAATTAAAGTT
1 AAAAAATT-AA-TT
55699 AAAAAATTA
1 AAAAAATTA
55708 CCTTCCAACC
Statistics
Matches: 31, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
11 9 0.29
12 2 0.06
13 11 0.35
14 9 0.29
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (12 bp):
AAAAAATTAATT
Found at i:55688 original size:25 final size:25
Alignment explanation
Indices: 55661--55707 Score: 78
Period size: 25 Copynumber: 1.9 Consensus size: 25
55651 AAGAAAAAGA
*
55661 AAAAAATT-AATTTAAAAAATTAAT
1 AAAAAATTAAAGTTAAAAAATTAAT
55685 AAAAAATTAAAGTTAAAAAATTA
1 AAAAAATTAAAGTTAAAAAATTA
55708 CCTTCCAACC
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
24 8 0.38
25 13 0.62
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.30
Consensus pattern (25 bp):
AAAAAATTAAAGTTAAAAAATTAAT
Found at i:58396 original size:21 final size:21
Alignment explanation
Indices: 58372--58414 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
58362 TAATTTGATG
58372 ATACCTTTTTCCTGCATTTTT
1 ATACCTTTTTCCTGCATTTTT
*
58393 ATACCTTTTTCTTGCATTTTT
1 ATACCTTTTTCCTGCATTTTT
58414 A
1 A
58415 ACATTTGCAT
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.16, C:0.21, G:0.05, T:0.58
Consensus pattern (21 bp):
ATACCTTTTTCCTGCATTTTT
Done.