Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004336.1 Hibiscus syriacus cultivar Beakdansim tig00009505_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: 72871
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:2178 original size:23 final size:23
Alignment explanation
Indices: 2113--2181 Score: 93
Period size: 23 Copynumber: 3.0 Consensus size: 23
2103 CACCACAGCT
* * *
2113 CGTATAAATGCATCGAAGTACCA
1 CGTAGAAATGCACCGAAGTGCCA
* *
2136 CGTAGAATTGCACCGAAGTGCCG
1 CGTAGAAATGCACCGAAGTGCCA
2159 CGTAGAAATGCACCGAAGTGCCA
1 CGTAGAAATGCACCGAAGTGCCA
2182 TATAAGATGT
Statistics
Matches: 39, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 39 1.00
ACGTcount: A:0.33, C:0.25, G:0.25, T:0.17
Consensus pattern (23 bp):
CGTAGAAATGCACCGAAGTGCCA
Found at i:2698 original size:2 final size:2
Alignment explanation
Indices: 2693--2730 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
2683 ACATGTAGTC
2693 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
2731 TCTTTCATAA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:14772 original size:36 final size:36
Alignment explanation
Indices: 14722--14797 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
14712 TTATAGCAAA
*
14722 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
14758 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
14794 AAAA
1 AAAA
14798 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:19275 original size:15 final size:15
Alignment explanation
Indices: 19257--19286 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
19247 CCACGGTGTT
19257 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
19272 CCCGGAATCCTGCGC
1 CCCGGAATCCTGCGC
19287 GATTGTGATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.13, C:0.47, G:0.27, T:0.13
Consensus pattern (15 bp):
CCCGGAATCCTGCGC
Found at i:19759 original size:36 final size:36
Alignment explanation
Indices: 19709--19784 Score: 143
Period size: 36 Copynumber: 2.1 Consensus size: 36
19699 TTATAGCAAA
*
19709 AAAAATCGTCTTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
19745 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
1 AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
19781 AAAA
1 AAAA
19785 TCCCGAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
36 39 1.00
ACGTcount: A:0.43, C:0.14, G:0.11, T:0.32
Consensus pattern (36 bp):
AAAAATCGTATTTATTCGAATTTTGCCAAAAATAGC
Found at i:20587 original size:35 final size:37
Alignment explanation
Indices: 20524--20592 Score: 115
Period size: 35 Copynumber: 1.9 Consensus size: 37
20514 TTTCGTCCTA
20524 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
1 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
*
20561 CTAGGATTC-AACTC-CTAAAATAGGATAGAATT
1 CTAGGATTCAAACTCTCAAAAATAGGATAGAATT
20593 TTACTATGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 17 0.55
36 5 0.16
37 9 0.29
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (37 bp):
CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
Found at i:21004 original size:12 final size:12
Alignment explanation
Indices: 20977--21013 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
20967 ATTATATGGA
20977 TATTTTATTCATT
1 TATTTTATT-ATT
20990 TATTTTATTATT
1 TATTTTATTATT
*
21002 TATGTTATTATT
1 TATTTTATTATT
21014 ATTATGTATA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 14 0.61
13 9 0.39
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.70
Consensus pattern (12 bp):
TATTTTATTATT
Found at i:21504 original size:9 final size:9
Alignment explanation
Indices: 21483--21516 Score: 52
Period size: 9 Copynumber: 3.8 Consensus size: 9
21473 ATTTTTTTCC
21483 TTTATCTTA-
1 TTTAT-TTAT
21492 TTTATTTAT
1 TTTATTTAT
21501 TTTATTTAT
1 TTTATTTAT
21510 TTTATTT
1 TTTATTT
21517 TTCCCTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
8 3 0.12
9 21 0.88
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (9 bp):
TTTATTTAT
Found at i:21505 original size:13 final size:14
Alignment explanation
Indices: 21483--21517 Score: 54
Period size: 13 Copynumber: 2.6 Consensus size: 14
21473 ATTTTTTTCC
*
21483 TTTATCTTATTTA-
1 TTTATTTTATTTAT
21496 TTTATTTTATTTAT
1 TTTATTTTATTTAT
21510 TTTATTTT
1 TTTATTTT
21518 TCCCTTTTAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 12 0.60
14 8 0.40
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (14 bp):
TTTATTTTATTTAT
Found at i:24530 original size:7 final size:7
Alignment explanation
Indices: 24518--24569 Score: 52
Period size: 7 Copynumber: 7.3 Consensus size: 7
24508 CAAAAAGGGC
24518 AAAAAGA
1 AAAAAGA
24525 AAAAAGA
1 AAAAAGA
*
24532 AAGAAGCA
1 AAAAAG-A
24540 AAAAAGA
1 AAAAAGA
24547 AAAAA-A
1 AAAAAGA
* *
24553 CAAGAACA
1 -AAAAAGA
24561 AAAAAGA
1 AAAAAGA
24568 AA
1 AA
24570 GAACAAAAAT
Statistics
Matches: 37, Mismatches: 5, Indels: 6
0.77 0.10 0.12
Matches are distributed among these distances:
6 1 0.03
7 29 0.78
8 7 0.19
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (7 bp):
AAAAAGA
Found at i:24540 original size:21 final size:22
Alignment explanation
Indices: 24518--24569 Score: 81
Period size: 22 Copynumber: 2.4 Consensus size: 22
24508 CAAAAAGGGC
24518 AAAAAGAAAAAAGA-AAGAAGCA
1 AAAAAGAAAAAA-ACAAGAAGCA
24540 AAAAAGAAAAAAACAAGAA-CA
1 AAAAAGAAAAAAACAAGAAGCA
24561 AAAAAGAAA
1 AAAAAGAAA
24570 GAACAAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
21 12 0.41
22 17 0.59
ACGTcount: A:0.81, C:0.06, G:0.13, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAAAAACAAGAAGCA
Found at i:24546 original size:22 final size:21
Alignment explanation
Indices: 24518--24586 Score: 79
Period size: 20 Copynumber: 3.3 Consensus size: 21
24508 CAAAAAGGGC
24518 AAAAAGAAAAAAGA-AAGAAGCA
1 AAAAAGAAAAAA-ACAAGAA-CA
24540 AAAAAGAAAAAAACAAGAACA
1 AAAAAGAAAAAAACAAGAACA
* * *
24561 AAAAAG-AAAGAACAAAAATA
1 AAAAAGAAAAAAACAAGAACA
24581 AAAAAG
1 AAAAAG
24587 GGAACAAAAA
Statistics
Matches: 43, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
20 17 0.40
21 9 0.21
22 17 0.40
ACGTcount: A:0.80, C:0.06, G:0.13, T:0.01
Consensus pattern (21 bp):
AAAAAGAAAAAAACAAGAACA
Found at i:24565 original size:14 final size:14
Alignment explanation
Indices: 24518--24578 Score: 52
Period size: 14 Copynumber: 4.3 Consensus size: 14
24508 CAAAAAGGGC
* *
24518 AAAAAGAAAAAAGA
1 AAAAAGAAAGAACA
* * *
24532 AAGAAGCAAAAAAGA
1 AAAAAG-AAAGAACA
24547 AAAAA-ACAAGAACA
1 AAAAAGA-AAGAACA
24561 AAAAAGAAAGAACA
1 AAAAAGAAAGAACA
24575 AAAA
1 AAAA
24579 TAAAAAAGGG
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
13 1 0.03
14 26 0.65
15 13 0.32
ACGTcount: A:0.80, C:0.07, G:0.13, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAGAACA
Found at i:24584 original size:32 final size:35
Alignment explanation
Indices: 24524--24597 Score: 84
Period size: 32 Copynumber: 2.2 Consensus size: 35
24514 GGGCAAAAAG
24524 AAAAAAGAAAGAAGCAAAAAAGAAAAAAACA-AGAAC
1 AAAAAAGAAAGAAGC-AAAAAGAAAAAAA-AGAGAAC
* *
24560 AAAAAAGAAAGAA-C-AAAA-ATAAAAAAGGGAAC
1 AAAAAAGAAAGAAGCAAAAAGAAAAAAAAGAGAAC
24592 AAAAAA
1 AAAAAA
24598 CACATGCAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
31 1 0.03
32 16 0.46
33 4 0.11
35 1 0.03
36 13 0.37
ACGTcount: A:0.78, C:0.07, G:0.14, T:0.01
Consensus pattern (35 bp):
AAAAAAGAAAGAAGCAAAAAGAAAAAAAAGAGAAC
Found at i:25224 original size:22 final size:22
Alignment explanation
Indices: 25196--25246 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
25186 CCCCATCAAT
25196 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
*
25218 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATACCAAA
25240 CCTTTGA
1 CCTTTGA
25247 CCAAACACAA
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:0.35, C:0.27, G:0.12, T:0.25
Consensus pattern (22 bp):
CCTTTGAGCATCAAATACCAAA
Found at i:26152 original size:36 final size:36
Alignment explanation
Indices: 26105--26209 Score: 165
Period size: 36 Copynumber: 2.9 Consensus size: 36
26095 GTGCTCATCA
26105 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
*
26141 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
* * *
26178 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACA
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA
26210 TAAACATTGA
Statistics
Matches: 64, Mismatches: 4, Indels: 2
0.91 0.06 0.03
Matches are distributed among these distances:
36 32 0.50
37 32 0.50
ACGTcount: A:0.25, C:0.24, G:0.13, T:0.38
Consensus pattern (36 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAACT
Found at i:26199 original size:37 final size:37
Alignment explanation
Indices: 26105--26214 Score: 168
Period size: 37 Copynumber: 3.0 Consensus size: 37
26095 GTGCTCATCA
26105 TTGTCTCTCTTGAGACAGTTTCCCTTGAAAC-AAACT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
*
26141 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAATT
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
* * *
26178 TTTTCTCCCTTGAGACAGTTTCTCTTGAAACATAAAC
1 TTGTCTCTCTTGAGACAGTTTCCCTTGAAACA-AAAC
26215 ATTGAAAACA
Statistics
Matches: 67, Mismatches: 5, Indels: 2
0.91 0.07 0.03
Matches are distributed among these distances:
36 31 0.46
37 33 0.49
38 3 0.04
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (37 bp):
TTGTCTCTCTTGAGACAGTTTCCCTTGAAACAAAACT
Found at i:26398 original size:35 final size:36
Alignment explanation
Indices: 26316--26412 Score: 133
Period size: 35 Copynumber: 2.7 Consensus size: 36
26306 TACCATTTCC
* * * *
26316 CTTGAGACAGTTTCTTTTGGAACTAAGTTTTGTCTCT
1 CTTGAGACAGTTTCTCTTGAAAC-AAGTTTCGTCTAT
26353 CTTGAGACAGTTTCTCTTGAAACAA-TTTCGTCTAT
1 CTTGAGACAGTTTCTCTTGAAACAAGTTTCGTCTAT
*
26388 CTTGAGACAGTTTCCCTTGAAACAA
1 CTTGAGACAGTTTCTCTTGAAACAA
26413 AATCTTTGAA
Statistics
Matches: 55, Mismatches: 5, Indels: 2
0.89 0.08 0.03
Matches are distributed among these distances:
35 32 0.58
36 2 0.04
37 21 0.38
ACGTcount: A:0.25, C:0.20, G:0.16, T:0.39
Consensus pattern (36 bp):
CTTGAGACAGTTTCTCTTGAAACAAGTTTCGTCTAT
Found at i:26472 original size:63 final size:67
Alignment explanation
Indices: 26388--26525 Score: 178
Period size: 65 Copynumber: 2.1 Consensus size: 67
26378 TTTCGTCTAT
* * **
26388 CTTGAGACAGTTTCCCTTG-AA-ACAAAATCTTTGAATTTATTT-CCTCTAAAACA-AATTT-TC
1 CTTGAGACAATTACCCTTGAAACACAAAATCTTCAAATTTATTTCCCT-TAAAACATAATTTGTC
26448 TCC
65 TCC
* *
26451 CTTGAGACAATTACTCTTGAAACACAAAATCTTCAAATTTATTTCCCTTAAAACATAATTTGTTT
1 CTTGAGACAATTACCCTTGAAACACAAAATCTTCAAATTTATTTCCCTTAAAACATAATTTGTCT
26516 CC
66 CC
26518 CTTGAGAC
1 CTTGAGAC
26526 CGTTCTCATG
Statistics
Matches: 64, Mismatches: 6, Indels: 6
0.84 0.08 0.08
Matches are distributed among these distances:
63 16 0.25
64 2 0.03
65 26 0.41
66 8 0.12
67 12 0.19
ACGTcount: A:0.33, C:0.22, G:0.08, T:0.37
Consensus pattern (67 bp):
CTTGAGACAATTACCCTTGAAACACAAAATCTTCAAATTTATTTCCCTTAAAACATAATTTGTCT
CC
Found at i:27491 original size:212 final size:215
Alignment explanation
Indices: 27142--27527 Score: 645
Period size: 212 Copynumber: 1.8 Consensus size: 215
27132 GCCATCCGCG
* *
27142 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTCCACGACGAAGGATATC-TGGCACTCCAGACAACACAAGTTCAACTTCACAACGAA
* * *
27207 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCAATTTCAACTTCACAACGAAGG
65 GGGACCGCTGGTTGTCAACAAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGG
27272 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
130 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACA
27337 ATTTTCCCAATTTCAGAGCCA
195 ATTTTCCCAATTTCAGAGCCA
* * *
27358 ATTTCAACTTCAC-AGCGAAGGATAT-TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
1 ATTTCAACTCCACGA-CGAAGGATATCTGGCACTCCAGACAACACAAGTTCAACTTCACAACGAA
27420 GGGACCGCTGGTTGTCAAC-AACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGG
65 GGGACCGCTGGTTGTCAACAAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGG
*
27484 ATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
130 ATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
27528 GCCCTGTACG
Statistics
Matches: 160, Mismatches: 9, Indels: 6
0.91 0.05 0.03
Matches are distributed among these distances:
212 86 0.54
213 49 0.31
214 3 0.02
215 1 0.01
216 21 0.13
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (215 bp):
ATTTCAACTCCACGACGAAGGATATCTGGCACTCCAGACAACACAAGTTCAACTTCACAACGAAG
GGACCGCTGGTTGTCAACAAACAACTTCCCAATCTCAGAGCCAATTTCAACTTCACAACGAAGGA
TATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAA
TTTTCCCAATTTCAGAGCCA
Found at i:27512 original size:105 final size:105
Alignment explanation
Indices: 27142--27527 Score: 601
Period size: 107 Copynumber: 3.6 Consensus size: 105
27132 GCCATCCGCG
* * * * * *
27142 ATTTCAACTCCACGACGGAGGATATCGTGGCACTCGAGACAACACAAGTTCAACTTCACAACGAA
1 ATTTCAACTTCACAACGAAGGATAT--TGG-ACTCCAGACAACGCAAGTTCAACTTCACGACGAA
* *
27207 GGGACGGCTGGTTGTCAACAAACAACTTCTCAATTTCAGAGCCA
63 GGGACCGCTGGTTGTCAAC-AACAACTTCCCAATTTCAGAGCCA
27251 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
* *
27316 ACCGCTGGTTGTCAATAAACAATTTTCCCAATTTCAGAGCCA
66 ACCGCTGGTTGTCAA-CAACAA-CTTCCCAATTTCAGAGCCA
*
27358 ATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
*
27423 ACCGCTGGTTGTCAACAACAACTTCCCAATCTCAGAGCCA
66 ACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCA
*
27463 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAATGCAAGTTCAACTTCACGACGAAGGG
1 ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
27528 GCCCTGTACG
Statistics
Matches: 259, Mismatches: 16, Indels: 8
0.92 0.06 0.03
Matches are distributed among these distances:
105 80 0.31
106 58 0.22
107 99 0.38
109 22 0.08
ACGTcount: A:0.33, C:0.26, G:0.19, T:0.21
Consensus pattern (105 bp):
ATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGG
ACCGCTGGTTGTCAACAACAACTTCCCAATTTCAGAGCCA
Found at i:27981 original size:35 final size:37
Alignment explanation
Indices: 27918--27986 Score: 115
Period size: 35 Copynumber: 1.9 Consensus size: 37
27908 TTTCGTCCTA
27918 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
1 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
*
27955 CTAGGATTC-AACTC-CTAAAATAGGATAGAATT
1 CTAGGATTCAAACTCTCAAAAATAGGATAGAATT
27987 TTACTATGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
35 17 0.55
36 5 0.16
37 9 0.29
ACGTcount: A:0.41, C:0.16, G:0.16, T:0.28
Consensus pattern (37 bp):
CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
Found at i:28401 original size:12 final size:12
Alignment explanation
Indices: 28374--28410 Score: 56
Period size: 12 Copynumber: 3.0 Consensus size: 12
28364 ATTATATGGA
28374 TATTTTATTCATT
1 TATTTTATT-ATT
28387 TATTTTATTATT
1 TATTTTATTATT
*
28399 TATGTTATTATT
1 TATTTTATTATT
28411 ATTATATGTA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
12 14 0.61
13 9 0.39
ACGTcount: A:0.24, C:0.03, G:0.03, T:0.70
Consensus pattern (12 bp):
TATTTTATTATT
Found at i:28817 original size:2 final size:2
Alignment explanation
Indices: 28810--28834 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28800 TACTTTGATG
28810 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 T
28835 TCCTTTTTCA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:28901 original size:9 final size:9
Alignment explanation
Indices: 28883--28912 Score: 51
Period size: 9 Copynumber: 3.3 Consensus size: 9
28873 TTTTTTTTCC
*
28883 TTTATCTTA
1 TTTATTTTA
28892 TTTATTTTA
1 TTTATTTTA
28901 TTTATTTTA
1 TTTATTTTA
28910 TTT
1 TTT
28913 TTCCCTTTTA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.20, C:0.03, G:0.00, T:0.77
Consensus pattern (9 bp):
TTTATTTTA
Found at i:37778 original size:2 final size:2
Alignment explanation
Indices: 37773--37809 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
37763 AGAGTGTGTA
37773 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
37810 ACCTCAAGGA
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:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:39175 original size:22 final size:22
Alignment explanation
Indices: 39150--39197 Score: 87
Period size: 22 Copynumber: 2.2 Consensus size: 22
39140 GACAGTTATC
*
39150 AACAACGGCGGAATAGGTACCA
1 AACAACGGCGGAACAGGTACCA
39172 AACAACGGCGGAACAGGTACCA
1 AACAACGGCGGAACAGGTACCA
39194 AACA
1 AACA
39198 GTGGAATGGG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
22 25 1.00
ACGTcount: A:0.44, C:0.25, G:0.25, T:0.06
Consensus pattern (22 bp):
AACAACGGCGGAACAGGTACCA
Found at i:43129 original size:30 final size:30
Alignment explanation
Indices: 43093--43184 Score: 121
Period size: 30 Copynumber: 3.1 Consensus size: 30
43083 GAGAGGAGAA
* *
43093 TCTAATTTGATTGGCGGTGATGGATCTAAG
1 TCTAATTTGATCGGCGGTGATGGAACTAAG
* *
43123 TTTAATTTGATGGGCGGTGATGGAACTAAG
1 TCTAATTTGATCGGCGGTGATGGAACTAAG
* * *
43153 TCTACTTTGAACGGTGGTGATGGAACTAAG
1 TCTAATTTGATCGGCGGTGATGGAACTAAG
43183 TC
1 TC
43185 CTGGACTGTG
Statistics
Matches: 54, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 54 1.00
ACGTcount: A:0.25, C:0.11, G:0.30, T:0.34
Consensus pattern (30 bp):
TCTAATTTGATCGGCGGTGATGGAACTAAG
Found at i:44369 original size:17 final size:18
Alignment explanation
Indices: 44335--44367 Score: 52
Period size: 16 Copynumber: 1.9 Consensus size: 18
44325 TTTTGTTAGT
44335 AATTTATTTAACTATTTA
1 AATTTATTTAACTATTTA
44353 AATTT-TTTAA-TATTT
1 AATTTATTTAACTATTT
44368 TATTTAATTA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
16 5 0.33
17 5 0.33
18 5 0.33
ACGTcount: A:0.36, C:0.03, G:0.00, T:0.61
Consensus pattern (18 bp):
AATTTATTTAACTATTTA
Found at i:45977 original size:19 final size:19
Alignment explanation
Indices: 45934--45971 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
45924 ACCTTTCAGT
*
45934 GACGTCGATAGAGACGTGC
1 GACGTCGACAGAGACGTGC
45953 GACGTCGACAGAGACGTGC
1 GACGTCGACAGAGACGTGC
45972 ACCGTCACAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.26, C:0.24, G:0.37, T:0.13
Consensus pattern (19 bp):
GACGTCGACAGAGACGTGC
Found at i:46652 original size:13 final size:14
Alignment explanation
Indices: 46623--46656 Score: 59
Period size: 14 Copynumber: 2.4 Consensus size: 14
46613 TATTTAGTTG
46623 TTTATTGGAATTTT
1 TTTATTGGAATTTT
*
46637 TTTATTGTAATTTT
1 TTTATTGGAATTTT
46651 TTTATT
1 TTTATT
46657 ATTTATCATT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.21, C:0.00, G:0.09, T:0.71
Consensus pattern (14 bp):
TTTATTGGAATTTT
Found at i:46715 original size:34 final size:34
Alignment explanation
Indices: 46677--46765 Score: 115
Period size: 34 Copynumber: 2.6 Consensus size: 34
46667 TAATACTTAC
* * *
46677 TTTATTTTGTTAATTTAGTTTTATTTTTTAAAAA
1 TTTATTTTGTTAATTTTGTTTGACTTTTTAAAAA
* ***
46711 TTTATTTTGTTAATTTTGTTGGACTTTTTGTTAA
1 TTTATTTTGTTAATTTTGTTTGACTTTTTAAAAA
46745 TTTATTTTGTTAATTTTGTTT
1 TTTATTTTGTTAATTTTGTTT
46766 ATTACCATTT
Statistics
Matches: 47, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
34 47 1.00
ACGTcount: A:0.21, C:0.01, G:0.10, T:0.67
Consensus pattern (34 bp):
TTTATTTTGTTAATTTTGTTTGACTTTTTAAAAA
Found at i:46754 original size:13 final size:13
Alignment explanation
Indices: 46736--46760 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
46726 TTGTTGGACT
46736 TTTTGTTAATTTA
1 TTTTGTTAATTTA
46749 TTTTGTTAATTT
1 TTTTGTTAATTT
46761 TGTTTATTAC
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:0.20, C:0.00, G:0.08, T:0.72
Consensus pattern (13 bp):
TTTTGTTAATTTA
Found at i:46823 original size:35 final size:36
Alignment explanation
Indices: 46741--46841 Score: 108
Period size: 35 Copynumber: 2.9 Consensus size: 36
46731 GGACTTTTTG
*
46741 TTAAT-TTATT-TTGTTAATTTTGTT-TA-TTACCAT
1 TTAATATTATTATTG-TAAGTTTGTTATATTTACCAT
46774 TTAATATTAGTTATTGTAA-TTTGGTTATTATTTACCAT
1 TTAATATTA-TTATTGTAAGTTT-GTTA-TATTTACCAT
46812 TTAATA-T-TTATTGTAAGTTTGTTATATTTA
1 TTAATATTATTATTGTAAGTTTGTTATATTTA
46842 TAATTATATT
Statistics
Matches: 60, Mismatches: 0, Indels: 15
0.80 0.00 0.20
Matches are distributed among these distances:
33 5 0.08
34 12 0.20
35 21 0.35
36 6 0.10
37 3 0.05
38 13 0.22
ACGTcount: A:0.28, C:0.04, G:0.09, T:0.59
Consensus pattern (36 bp):
TTAATATTATTATTGTAAGTTTGTTATATTTACCAT
Found at i:49077 original size:20 final size:20
Alignment explanation
Indices: 49040--49078 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
49030 CAGAATGCTC
49040 GGAGGATACCGATACCCCCA
1 GGAGGATACCGATACCCCCA
49060 GGAGG-TACCGATACCCCCA
1 GGAGGATACCGATACCCCCA
49079 ATCTTATAAC
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.74
20 5 0.26
ACGTcount: A:0.28, C:0.36, G:0.26, T:0.10
Consensus pattern (20 bp):
GGAGGATACCGATACCCCCA
Found at i:50995 original size:21 final size:21
Alignment explanation
Indices: 50971--51010 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
50961 AAGAGTTTAT
50971 TTTCAAAATAAAAAAATGATA
1 TTTCAAAATAAAAAAATGATA
**
50992 TTTCAAAATTGAAAAATGA
1 TTTCAAAATAAAAAAATGA
51011 AAATATTCTT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.57, C:0.05, G:0.07, T:0.30
Consensus pattern (21 bp):
TTTCAAAATAAAAAAATGATA
Found at i:54838 original size:23 final size:23
Alignment explanation
Indices: 54812--54872 Score: 86
Period size: 23 Copynumber: 2.7 Consensus size: 23
54802 ATAAGCGCTA
* *
54812 GGTATCGATACCCCCTTTGCATG
1 GGTACCGATACCCCCTTTGAATG
*
54835 GGTACCGATACCCTCTTTGAATG
1 GGTACCGATACCCCCTTTGAATG
*
54858 GGTACCAATACCCCC
1 GGTACCGATACCCCC
54873 ACATGAGGGT
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.21, C:0.33, G:0.20, T:0.26
Consensus pattern (23 bp):
GGTACCGATACCCCCTTTGAATG
Found at i:56812 original size:19 final size:16
Alignment explanation
Indices: 56768--56818 Score: 66
Period size: 16 Copynumber: 3.0 Consensus size: 16
56758 ATGTTAGATG
*
56768 TTTGTGAATGTTTGAA
1 TTTGTGGATGTTTGAA
56784 TTTGTGGATGTTTGAA
1 TTTGTGGATGTTTGAA
56800 TTTGTTTTGGATGTTTGAA
1 TTTG---TGGATGTTTGAA
56819 CTTAAATGTT
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
16 19 0.61
19 12 0.39
ACGTcount: A:0.20, C:0.00, G:0.27, T:0.53
Consensus pattern (16 bp):
TTTGTGGATGTTTGAA
Found at i:57102 original size:15 final size:15
Alignment explanation
Indices: 57082--57112 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
57072 AGTAAGGGAG
57082 AGTAATAATTTTCTC
1 AGTAATAATTTTCTC
57097 AGTAATAATTTTCTC
1 AGTAATAATTTTCTC
57112 A
1 A
57113 AAATTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.45
Consensus pattern (15 bp):
AGTAATAATTTTCTC
Found at i:57123 original size:14 final size:14
Alignment explanation
Indices: 57085--57137 Score: 61
Period size: 14 Copynumber: 3.7 Consensus size: 14
57075 AAGGGAGAGT
*
57085 AATAATTTTCTCAGT
1 AATAATTTTCTCA-A
57100 AATAATTTTCTCAA
1 AATAATTTTCTCAA
* *
57114 AATTATTTTCTAAA
1 AATAATTTTCTCAA
*
57128 AATGATTTTC
1 AATAATTTTC
57138 AATAAGAAAA
Statistics
Matches: 34, Mismatches: 4, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
14 21 0.62
15 13 0.38
ACGTcount: A:0.38, C:0.11, G:0.04, T:0.47
Consensus pattern (14 bp):
AATAATTTTCTCAA
Found at i:57488 original size:20 final size:20
Alignment explanation
Indices: 57465--57505 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
57455 AGGGATATTA
*
57465 CCCAGAGGGCACTGATACCC
1 CCCAGAGGGCACCGATACCC
* *
57485 CCCATAGGGTACCGATACCC
1 CCCAGAGGGCACCGATACCC
57505 C
1 C
57506 TATGTAAGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.24, C:0.41, G:0.22, T:0.12
Consensus pattern (20 bp):
CCCAGAGGGCACCGATACCC
Done.