Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004822.1 Hibiscus syriacus cultivar Beakdansim tig00010867_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: 272678
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
File 2 of 2
Found at i:187410 original size:106 final size:105
Alignment explanation
Indices: 187226--187427 Score: 386
Period size: 106 Copynumber: 1.9 Consensus size: 105
187216 TTAAAATGAA
187226 CCATAAAACCCAATAACCCTATTCATTCAAAGTTTAATATCCCAATTAAAATCAATAATCAGAAT
1 CCATAAAACCCAATAACCCTATTCATTCAAAGTTTAATATCCCAATTAAAATCAATAATCAGAAT
187291 CGCACCCGCTTAAAATATATTAGTATTTAATACCATAAAC
66 CGCACCCGCTTAAAATATATTAGTATTTAATACCATAAAC
*
187331 CCATATAACCCAATAACCCATATTCATTCAAAGTTTAATATCCCAATTAAAATCAATAATCAGAA
1 CCATAAAACCCAATAACCC-TATTCATTCAAAGTTTAATATCCCAATTAAAATCAATAATCAGAA
187396 TCGCACCCGCTTAAAATATATTAGTATTTAAT
65 TCGCACCCGCTTAAAATATATTAGTATTTAAT
187428 TTTTTTTCAT
Statistics
Matches: 95, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
105 18 0.19
106 77 0.81
ACGTcount: A:0.43, C:0.22, G:0.05, T:0.30
Consensus pattern (105 bp):
CCATAAAACCCAATAACCCTATTCATTCAAAGTTTAATATCCCAATTAAAATCAATAATCAGAAT
CGCACCCGCTTAAAATATATTAGTATTTAATACCATAAAC
Found at i:190303 original size:14 final size:14
Alignment explanation
Indices: 190265--190305 Score: 50
Period size: 14 Copynumber: 2.9 Consensus size: 14
190255 TATTTAATTA
190265 TTTATTTTAT-TAT
1 TTTATTTTATCTAT
190278 TTTATTCTTATCT-T
1 TTTATT-TTATCTAT
190292 TTTATCTTTATCTA
1 TTTAT-TTTATCTA
190306 AAATTTTATC
Statistics
Matches: 24, Mismatches: 0, Indels: 6
0.80 0.00 0.20
Matches are distributed among these distances:
13 6 0.25
14 16 0.67
15 2 0.08
ACGTcount: A:0.20, C:0.10, G:0.00, T:0.71
Consensus pattern (14 bp):
TTTATTTTATCTAT
Found at i:192181 original size:24 final size:25
Alignment explanation
Indices: 192146--192201 Score: 78
Period size: 24 Copynumber: 2.3 Consensus size: 25
192136 GAAAAAATAA
* *
192146 AAAAAAATTGTTCATTGTTTCGAAC
1 AAAAAAATTGTTCACTATTTCGAAC
*
192171 AAAAAAA-TGTTTACTATTTCGAAC
1 AAAAAAATTGTTCACTATTTCGAAC
192195 AAAAAAA
1 AAAAAAA
192202 AGAAGGAAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
24 21 0.75
25 7 0.25
ACGTcount: A:0.50, C:0.11, G:0.09, T:0.30
Consensus pattern (25 bp):
AAAAAAATTGTTCACTATTTCGAAC
Found at i:193120 original size:44 final size:43
Alignment explanation
Indices: 193040--193122 Score: 105
Period size: 44 Copynumber: 1.9 Consensus size: 43
193030 ATTAAACTCA
* **
193040 TGTTTTAGGATATTATTTTAAATATTTTATTTTATTTTATCTT
1 TGTTTTAGGATATTAGTTTAAATATTTTATAGTATTTTATCTT
*
193083 TGTTTTAGGTATTTTAGTTTAAATAGTTTTA-AGTATTTTA
1 TGTTTTAGG-ATATTAGTTTAAATA-TTTTATAGTATTTTA
193123 ATTAGGATTT
Statistics
Matches: 34, Mismatches: 4, Indels: 3
0.83 0.10 0.07
Matches are distributed among these distances:
43 9 0.26
44 20 0.59
45 5 0.15
ACGTcount: A:0.27, C:0.01, G:0.11, T:0.61
Consensus pattern (43 bp):
TGTTTTAGGATATTAGTTTAAATATTTTATAGTATTTTATCTT
Found at i:193142 original size:20 final size:22
Alignment explanation
Indices: 193119--193158 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
193109 TTTTAAGTAT
193119 TTTAAT-TAGGATT-TATTTTC
1 TTTAATCTAGGATTATATTTTC
*
193139 TTTATTCTAGGATTATATTT
1 TTTAATCTAGGATTATATTT
193159 ACCTTGTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 7 0.41
22 5 0.29
ACGTcount: A:0.25, C:0.05, G:0.10, T:0.60
Consensus pattern (22 bp):
TTTAATCTAGGATTATATTTTC
Found at i:194066 original size:12 final size:12
Alignment explanation
Indices: 194049--194073 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
194039 AAACGATTTA
194049 TATTTAATTATT
1 TATTTAATTATT
194061 TATTTAATTATT
1 TATTTAATTATT
194073 T
1 T
194074 TTTTCTTATC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (12 bp):
TATTTAATTATT
Found at i:194708 original size:26 final size:25
Alignment explanation
Indices: 194620--194717 Score: 96
Period size: 24 Copynumber: 3.8 Consensus size: 25
194610 ATATAAATAC
* *
194620 TTAACTTAAATTCATAATATTATATATA
1 TTAACTT-AATT-AAAATATT-TTTATA
194648 TTAACTTAA--AAAATATTTTTATA
1 TTAACTTAATTAAAATATTTTTATA
194671 TTAACTT-ATTAAATATATTTTT-TA
1 TTAACTTAATTAAA-ATATTTTTATA
194695 TTAACTTAATTTAAAATTATTTT
1 TTAACTTAA-TTAAAA-TATTTT
194718 ATTTTTACTT
Statistics
Matches: 62, Mismatches: 2, Indels: 14
0.79 0.03 0.18
Matches are distributed among these distances:
22 1 0.02
23 12 0.19
24 19 0.31
25 10 0.16
26 11 0.18
27 2 0.03
28 7 0.11
ACGTcount: A:0.43, C:0.05, G:0.00, T:0.52
Consensus pattern (25 bp):
TTAACTTAATTAAAATATTTTTATA
Found at i:194727 original size:26 final size:28
Alignment explanation
Indices: 194648--194737 Score: 77
Period size: 27 Copynumber: 3.4 Consensus size: 28
194638 ATTATATATA
* *
194648 TTAACTTAAAAAATATTTTTATATTAAC-
1 TTAATTTAAAATATATTTTT-TATTAACT
194676 TT-A-TT-AAATATATTTTTTATTAAC-
1 TTAATTTAAAATATATTTTTTATTAACT
*
194700 TTAATTTAAAAT-TATTTTATT-TTTACT
1 TTAATTTAAAATATATTTT-TTATTAACT
*
194727 TTTATTTAAAA
1 TTAATTTAAAA
194738 ATGTATATTT
Statistics
Matches: 54, Mismatches: 3, Indels: 11
0.79 0.04 0.16
Matches are distributed among these distances:
24 9 0.17
25 12 0.22
26 14 0.26
27 17 0.31
28 2 0.04
ACGTcount: A:0.40, C:0.04, G:0.00, T:0.56
Consensus pattern (28 bp):
TTAATTTAAAATATATTTTTTATTAACT
Found at i:194816 original size:25 final size:24
Alignment explanation
Indices: 194774--194839 Score: 78
Period size: 25 Copynumber: 2.7 Consensus size: 24
194764 GAAATTAAGA
**
194774 TAAGAATAAAATATATTTAATAATT
1 TAAG-ATAAAATATATTTAATAAAG
* *
194799 TAATATAATAATATATTTAGTAAAG
1 TAAGATAA-AATATATTTAATAAAG
194824 TAAGATAAAATATATT
1 TAAGATAAAATATATT
194840 CTTTAAAAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
24 12 0.34
25 23 0.66
ACGTcount: A:0.55, C:0.00, G:0.06, T:0.39
Consensus pattern (24 bp):
TAAGATAAAATATATTTAATAAAG
Found at i:194908 original size:33 final size:33
Alignment explanation
Indices: 194819--194911 Score: 104
Period size: 31 Copynumber: 2.9 Consensus size: 33
194809 ATATATTTAG
*
194819 TAAAGTAAG-ATAAAATATAT-TCTTTAAAAAGTT
1 TAAA-TAAGAATAAAATATATAT-TTTTAAAAGTT
* * *
194852 CAAATAATAA-CAAA-ATATATTTTTAAAAGTT
1 TAAATAAGAATAAAATATATATTTTTAAAAGTT
194883 TAAATAAGAATAAAATATATATTTTTAAA
1 TAAATAAGAATAAAATATATATTTTTAAA
194912 TCCAGCGGTA
Statistics
Matches: 49, Mismatches: 7, Indels: 8
0.77 0.11 0.12
Matches are distributed among these distances:
31 22 0.45
32 10 0.20
33 17 0.35
ACGTcount: A:0.55, C:0.03, G:0.05, T:0.37
Consensus pattern (33 bp):
TAAATAAGAATAAAATATATATTTTTAAAAGTT
Found at i:202615 original size:24 final size:24
Alignment explanation
Indices: 202588--202633 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
202578 TATAACAAAC
202588 TATAACTGTCTA-ACAATCATCAGT
1 TATAACTGTCTATACAA-CATCAGT
* *
202612 TATAATTGTTTATACAACATCA
1 TATAACTGTCTATACAACATCA
202634 AACTGCAGCT
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 15 0.79
25 4 0.21
ACGTcount: A:0.39, C:0.17, G:0.07, T:0.37
Consensus pattern (24 bp):
TATAACTGTCTATACAACATCAGT
Found at i:207117 original size:35 final size:35
Alignment explanation
Indices: 207054--207153 Score: 119
Period size: 35 Copynumber: 2.7 Consensus size: 35
207044 TTTCGTCCTA
*
207054 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
1 CTAGGATTC-AACTC-CTAAAATAGGATAGAATTCTG
*
207091 CTAGGATTCAACTCCTAAAATAGGATAGAATTTTG
1 CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
** *
207126 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTA-GGATTCAACTCCTAAA-ATAGGAT
207154 CCACAAGTAC
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 22 0.39
36 18 0.32
37 16 0.29
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (35 bp):
CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
Found at i:209870 original size:18 final size:18
Alignment explanation
Indices: 209847--209886 Score: 80
Period size: 18 Copynumber: 2.2 Consensus size: 18
209837 TTCCTTCAAG
209847 TCTGGATTCACATCCACT
1 TCTGGATTCACATCCACT
209865 TCTGGATTCACATCCACT
1 TCTGGATTCACATCCACT
209883 TCTG
1 TCTG
209887 AAAGACTAAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.20, C:0.33, G:0.12, T:0.35
Consensus pattern (18 bp):
TCTGGATTCACATCCACT
Found at i:210420 original size:8 final size:8
Alignment explanation
Indices: 210407--210445 Score: 53
Period size: 8 Copynumber: 5.0 Consensus size: 8
210397 GAACATTTCA
*
210407 TGCATTCT
1 TGCATTTT
210415 TGCA-TTT
1 TGCATTTT
210422 TGCATTTT
1 TGCATTTT
*
210430 TGCCTTTT
1 TGCATTTT
210438 TGCATTTT
1 TGCATTTT
210446 CATCTACATT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
7 6 0.22
8 21 0.78
ACGTcount: A:0.10, C:0.18, G:0.13, T:0.59
Consensus pattern (8 bp):
TGCATTTT
Found at i:211596 original size:22 final size:22
Alignment explanation
Indices: 211573--211634 Score: 72
Period size: 23 Copynumber: 2.7 Consensus size: 22
211563 CAAAAAGGGC
211573 AAAAAGAAAAAAGAAAAGAAGCA
1 AAAAAGAAAAAA-AAAAGAAGCA
* *
211596 AAAAAGGAAAAAACAAGAA-CA
1 AAAAAGAAAAAAAAAAGAAGCA
211617 AAAAAGAAAGAACAAAAA
1 AAAAAGAAA-AA-AAAAA
211635 TAAAAAAAAG
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 10 0.30
22 8 0.24
23 15 0.45
ACGTcount: A:0.79, C:0.06, G:0.15, T:0.00
Consensus pattern (22 bp):
AAAAAGAAAAAAAAAAGAAGCA
Found at i:211625 original size:20 final size:20
Alignment explanation
Indices: 211573--211641 Score: 66
Period size: 20 Copynumber: 3.2 Consensus size: 20
211563 CAAAAAGGGC
*
211573 AAAAAGAAAAAAGAAAAGAAGCA
1 AAAAAG-AAAAA-ACAAGAA-CA
211596 AAAAAGGAAAAAACAAGAACA
1 AAAAA-GAAAAAACAAGAACA
* * *
211617 AAAAAGAAAGAACAAAAATA
1 AAAAAGAAAAAACAAGAACA
211637 AAAAA
1 AAAAA
211642 AAGGGACAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
20 17 0.41
21 7 0.17
22 6 0.15
23 10 0.24
24 1 0.02
ACGTcount: A:0.80, C:0.06, G:0.13, T:0.01
Consensus pattern (20 bp):
AAAAAGAAAAAACAAGAACA
Found at i:212276 original size:22 final size:22
Alignment explanation
Indices: 212248--212298 Score: 93
Period size: 22 Copynumber: 2.3 Consensus size: 22
212238 CCCCATCAAT
212248 CCTTTGAGCATCAAATACCAAA
1 CCTTTGAGCATCAAATACCAAA
*
212270 CCTTTGAGCATCAAATGCCAAA
1 CCTTTGAGCATCAAATACCAAA
212292 CCTTTGA
1 CCTTTGA
212299 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:212718 original size:18 final size:18
Alignment explanation
Indices: 212695--212730 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
212685 TCAACATCAA
* *
212695 ATATTGGGGCATTTTTGG
1 ATATTGAGGCATCTTTGG
212713 ATATTGAGGCATCTTTGG
1 ATATTGAGGCATCTTTGG
212731 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):
ATATTGAGGCATCTTTGG
Found at i:213261 original size:21 final size:21
Alignment explanation
Indices: 213235--213281 Score: 67
Period size: 21 Copynumber: 2.2 Consensus size: 21
213225 GATAGTTTCC
* * *
213235 CTTGAAATAAATTTTGTCTCT
1 CTTGAAACAAATTTCGTCTAT
213256 CTTGAAACAAATTTCGTCTAT
1 CTTGAAACAAATTTCGTCTAT
213277 CTTGA
1 CTTGA
213282 GACAGTTTCC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.30, C:0.17, G:0.11, T:0.43
Consensus pattern (21 bp):
CTTGAAACAAATTTCGTCTAT
Found at i:213385 original size:37 final size:36
Alignment explanation
Indices: 213317--213435 Score: 127
Period size: 36 Copynumber: 3.3 Consensus size: 36
213307 TTGAATATGT
* * * *
213317 TTTCT-TTGAAACAAATTTCATCTCCCTTGAGACAG
1 TTTCTCTTGAATCAATTTTCGTCTCTCTTGAGACAG
*
213352 TTTCTTTTGGAA-CTAAGTTTT-GTCTCTCTTGAGACAG
1 TTTCTCTT-GAATC-AA-TTTTCGTCTCTCTTGAGACAG
*
213389 TTTCTCTTGAATCAATTTTCGTCTATCTTGAGACAG
1 TTTCTCTTGAATCAATTTTCGTCTCTCTTGAGACAG
*
213425 TTACTCTTGAA
1 TTTCTCTTGAA
213436 ACACAAAATC
Statistics
Matches: 72, Mismatches: 6, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
35 9 0.12
36 33 0.46
37 27 0.38
38 3 0.04
ACGTcount: A:0.24, C:0.19, G:0.14, T:0.43
Consensus pattern (36 bp):
TTTCTCTTGAATCAATTTTCGTCTCTCTTGAGACAG
Found at i:214609 original size:106 final size:105
Alignment explanation
Indices: 214108--214770 Score: 620
Period size: 109 Copynumber: 6.3 Consensus size: 105
214098 GGGCCATCCG
* * * * * *
214108 CAATTTCAACTTCACAACGAAGGATATTGGACCCAAGACAGCACAAGCTCAACTTCACAGCGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
* ** * * *
214173 GGGCGGCTGACTGT---C-GACAA---GCAATTTCGGAGC
66 GGACGGCTGGTTGTCAACAAACAATTTTCAATTTCAGAGC
* *
214206 CAATCTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAGCGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
* *
214271 GGACGGCTGGTTGTCAACAAACAATTTCCCAATTCCAGAGC
66 GGACGGCTGGTTGTCAACAAACAATTT-TCAATTTCAGAGC
* * * *
214312 CGATTTCAACTCCAC-GACGGAGGATATCGTG-CTACCTGAGACAACACAAGTTCAACTTCACAA
1 CAATTTCAACTTCACAG-CGAAGGATATTG-GACT--C-GAGACAACACAAGTTCAACTTCACAA
* * **
214375 CGAAGGGACGGCTGGTTGTCAACGAACAACTTTTCAGTTTCA-TCC
61 CGAAGGGACGGCTGGTTGTCAACAAACAA-TTTTCAATTTCAGAGC
* * * * *
214420 GCGATTTCAACTCCAC-GACGGAGGATATCGTGCCACTCGAGACAACACAAATTCAACTTCACAA
1 -CAATTTCAACTTCACAG-CGAAGGATAT--TG-GACTCGAGACAACACAAGTTCAACTTCACAA
* *
214484 CGAAGGGACGGTTGGTTGTCAACAAACATTTTTCAAATTTCAGAGC
61 CGAAGGGACGGCTGGTTGTCAACAAACAATTTTC-AATTTCAGAGC
**
214530 CAATTTCAACTTCGTAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
* * * *
214595 GGACGGCTGATTGTCAAC-AA-GA-TTTC--GTTCAGAGT
66 GGACGGCTGGTTGTCAACAAACAATTTTCAATTTCAGAGC
* * * * * *
214630 CAATTTCATCTTCACAGCGAAGGATATTAGACTCGAGACAGCACAAGCTCAACTTCACAGCAAAG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
* * ** * * * *
214695 GGGCGACTGACTGTCAACAAACAATTTCCCAGTTCCAGAAC
66 GGACGGCTGGTTGTCAACAAACAATTT-TCAATTTCAGAGC
*
214736 CAATTTCAACTTCACAGCGGAGGATATTGGACTCG
1 CAATTTCAACTTCACAGCGAAGGATATTGGACTCG
214771 GAACAATATT
Statistics
Matches: 470, Mismatches: 68, Indels: 46
0.80 0.12 0.08
Matches are distributed among these distances:
98 70 0.15
100 79 0.17
101 3 0.01
102 5 0.01
103 6 0.01
104 1 0.00
105 3 0.01
106 121 0.26
107 3 0.01
108 7 0.01
109 163 0.35
110 6 0.01
111 1 0.00
112 2 0.00
ACGTcount: A:0.33, C:0.25, G:0.21, T:0.21
Consensus pattern (105 bp):
CAATTTCAACTTCACAGCGAAGGATATTGGACTCGAGACAACACAAGTTCAACTTCACAACGAAG
GGACGGCTGGTTGTCAACAAACAATTTTCAATTTCAGAGC
Found at i:215294 original size:35 final size:35
Alignment explanation
Indices: 215231--215330 Score: 119
Period size: 35 Copynumber: 2.7 Consensus size: 35
215221 TTTCGTCCTA
*
215231 CTAGGATTCAAACTCTCAAAAATAGGATAGAATTCTG
1 CTAGGATTC-AACTC-CTAAAATAGGATAGAATTCTG
*
215268 CTAGGATTCAACTCCTAAAATAGGATAGAATTTTG
1 CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
** *
215303 CTATGTTTTAAACTCCTAAAGATAGGAT
1 CTA-GGATTCAACTCCTAAA-ATAGGAT
215331 CCACAAGCAC
Statistics
Matches: 56, Mismatches: 5, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
35 22 0.39
36 18 0.32
37 16 0.29
ACGTcount: A:0.38, C:0.15, G:0.16, T:0.31
Consensus pattern (35 bp):
CTAGGATTCAACTCCTAAAATAGGATAGAATTCTG
Found at i:215760 original size:2 final size:2
Alignment explanation
Indices: 215755--215799 Score: 81
Period size: 2 Copynumber: 22.5 Consensus size: 2
215745 TTAGTGTTAT
*
215755 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TT TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
215797 TA T
1 TA T
215800 TTCCTATTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:215886 original size:20 final size:20
Alignment explanation
Indices: 215861--215898 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
215851 ATTATTATTA
215861 TTTTACTTATATATATATGC
1 TTTTACTTATATATATATGC
* *
215881 TTTTACTTTTTTATATAT
1 TTTTACTTATATATATAT
215899 TTTACTCATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.26, C:0.08, G:0.03, T:0.63
Consensus pattern (20 bp):
TTTTACTTATATATATATGC
Found at i:215930 original size:16 final size:18
Alignment explanation
Indices: 215909--215943 Score: 56
Period size: 16 Copynumber: 2.1 Consensus size: 18
215899 TTTACTCATT
215909 TATTTAT-CTAT-TTTTA
1 TATTTATCCTATATTTTA
215925 TATTTATCCTATATTTTA
1 TATTTATCCTATATTTTA
215943 T
1 T
215944 GTTTTTATAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 7 0.41
17 4 0.24
18 6 0.35
ACGTcount: A:0.26, C:0.09, G:0.00, T:0.66
Consensus pattern (18 bp):
TATTTATCCTATATTTTA
Found at i:216720 original size:34 final size:33
Alignment explanation
Indices: 216673--216736 Score: 101
Period size: 34 Copynumber: 1.9 Consensus size: 33
216663 AACCACCTAG
*
216673 CTATAACGTCTAACAACCATCAGTTATAACAAA
1 CTATAACGTCTAACAACCATCAGCTATAACAAA
*
216706 CTATAACTGTCTAACAATCATCAGCTATAAC
1 CTATAAC-GTCTAACAACCATCAGCTATAAC
216737 TGTTTATACA
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
33 7 0.25
34 21 0.75
ACGTcount: A:0.42, C:0.25, G:0.06, T:0.27
Consensus pattern (33 bp):
CTATAACGTCTAACAACCATCAGCTATAACAAA
Found at i:216733 original size:24 final size:24
Alignment explanation
Indices: 216706--216752 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
216696 TTATAACAAA
216706 CTATAACTGTCTA-ACAATCATCAG
1 CTATAACTGTCTATACAA-CATCAG
*
216730 CTATAACTGTTTATACAACATCA
1 CTATAACTGTCTATACAACATCA
216753 CACTGCAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.38, C:0.23, G:0.06, T:0.32
Consensus pattern (24 bp):
CTATAACTGTCTATACAACATCAG
Found at i:219762 original size:239 final size:238
Alignment explanation
Indices: 219319--219764 Score: 720
Period size: 239 Copynumber: 1.9 Consensus size: 238
219309 CTCCATCCAA
* *
219319 GACCTGACCTACCAAAATAAAGTTTCACCTGACCTGACCCGACCCGAATATATGAATTAGAAACC
1 GACCCGACCGACCAAAATAAAGTTTCACC--ACCTGACCCGACCCGAATATATGAATTAGAAACC
* *
219384 CGACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATACAAACAGTGACTTAATTGAAAAA
64 CGACCCGACCCAAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAA
219449 AAATATATATAGAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTT
129 AAATATATATAGAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTT
219514 TTGGGGTCGGGTCGGGTCGGGTATTTTTCACCCTAAACCGAACCC
194 TTGGGGTCGGGTCGGGTCGGGTATTTTTCACCCTAAACCGAACCC
*
219559 GACCCGACCGACCAAAATAAAGTTTCA-C-CC-GACCCGACCCGAATATATGAATTAGAAATCCG
1 GACCCGACCGACCAAAATAAAGTTTCACCACCTGACCCGACCCGAATATATGAATTAGAAACCCG
*
219621 ACCCGACCGACCCAAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGTAA
66 A--C--CCGACCCAAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAA
* *
219686 AAAAAT-TATATATAGAGGGGTATTATTTTAATTATTCCTAAATATATAAGGTAAAATTATATAT
127 AAAAATATATATAGAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATAT
*
219750 ATTTTTGGGTCGGGT
192 -TTTTGGGGTCGGGT
219765 ATTTTTCACC
Statistics
Matches: 192, Mismatches: 9, Indels: 11
0.91 0.04 0.05
Matches are distributed among these distances:
235 32 0.17
236 2 0.01
237 1 0.01
238 56 0.29
239 76 0.40
240 25 0.13
ACGTcount: A:0.39, C:0.17, G:0.15, T:0.29
Consensus pattern (238 bp):
GACCCGACCGACCAAAATAAAGTTTCACCACCTGACCCGACCCGAATATATGAATTAGAAACCCG
ACCCGACCCAAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAAAA
ATATATATAGAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATTTTT
GGGGTCGGGTCGGGTCGGGTATTTTTCACCCTAAACCGAACCC
Found at i:219876 original size:268 final size:263
Alignment explanation
Indices: 219558--220191 Score: 998
Period size: 269 Copynumber: 2.4 Consensus size: 263
219548 AAACCGAACC
*
219558 CGACCCGA-CCGACCAAAATAAAGTTTCACCCGACCCGACCCGAATATATGAATTAGAAATCCGA
1 CGACCCGACCCGACCAAAATAAAGTTTCA-CCGA-CCGACCCGAATATATGAATTAGAAATCTGA
*
219622 CCCGA-CCGACCCAAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGTAA
64 CCCGACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTG-AA
*
219686 AAAAA-T-TATATATAGAGGGGTATTATTTTAATTATTCCTAAATATATAAGGTAAAATTATATA
128 AAAAATTATATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATA
*
219749 TATTTTTGGGTCGGGTATTTTTCACCCTAAACCCGAACTCGACCCGACCCGACCTGAATATCACA
193 TATTTTTGGGTCAGGTATTTTTCACCCTAAACCCGAACT-----CGACCCGACCTGAATATCACA
219814 CTTAAAAAAAT
253 CTTAAAAAAAT
* *
219825 CGACCCGACCCAACCAAAATAAAGTTTCACTCGAACCTACCCGAATATATGAATTAGAAATCTGA
1 CGACCCGACCCGACCAAAATAAAGTTTCAC-CG-ACCGACCCGAATATATGAATTAGAAATCTGA
* * *
219890 CCCGACCCGACCCGAAATAATAAAAATATTATTTTTATTCAAT-AAAACAGTTATTTAATTGAAA
64 CCCGACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAA
*
219954 AAAATTATATATATAGAGGGGTATTATTGTAATTATTCCTAACTATATAAGGTAAAATTATATAT
129 AAAATTATATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATAT
*
220019 ATTTTTGGGTCAGGTATTTTTCACCCTAAACCCGAACTCGACCCGACCTGAATATCACACTTAAG
194 ATTTTTGGGTCAGGTATTTTTCACCCTAAACCCGAACTCGACCCGACCTGAATATCACACTTAAA
220084 AAAAT
259 AAAAT
*
220089 CGACCCTACCCGACCAAAATAAAGTTTCA-C--CCGACCCGAATATATGAATTAGAAATCTGACC
1 CGACCCGACCCGACCAAAATAAAGTTTCACCGACCGACCCGAATATATGAATTAGAAATCTGACC
*
220151 CGACCCGGCCCGAAATAATAAAAAAA-TATTTTTATTCAATA
66 CGACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATA
220192 TATGAATAAG
Statistics
Matches: 344, Mismatches: 16, Indels: 22
0.90 0.04 0.06
Matches are distributed among these distances:
258 14 0.04
259 55 0.16
262 1 0.00
264 58 0.17
267 16 0.05
268 71 0.21
269 129 0.38
ACGTcount: A:0.40, C:0.21, G:0.12, T:0.28
Consensus pattern (263 bp):
CGACCCGACCCGACCAAAATAAAGTTTCACCGACCGACCCGAATATATGAATTAGAAATCTGACC
CGACCCGACCCGAAATAATAAAAAAATTATTTTTATTCAATAAAAACAGTGACTTAATTGAAAAA
AATTATATATATAGAGGGGTATTATTGTAATTATTCCTAAATATATAAGGTAAAATTATATATAT
TTTTGGGTCAGGTATTTTTCACCCTAAACCCGAACTCGACCCGACCTGAATATCACACTTAAAAA
AAT
Found at i:224498 original size:21 final size:21
Alignment explanation
Indices: 224481--224549 Score: 120
Period size: 21 Copynumber: 3.3 Consensus size: 21
224471 AGAAGTATTA
*
224481 ATACTCTTATCTCGAGTACCG
1 ATACTCTTATCCCGAGTACCG
224502 ATACTCTTATCCCGAGTACCG
1 ATACTCTTATCCCGAGTACCG
224523 ATACTCTTATCCCGAGTACCG
1 ATACTCTTATCCCGAGTACCG
*
224544 ACACTC
1 ATACTC
224550 CTTGGTCTGG
Statistics
Matches: 46, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 46 1.00
ACGTcount: A:0.25, C:0.33, G:0.13, T:0.29
Consensus pattern (21 bp):
ATACTCTTATCCCGAGTACCG
Found at i:228547 original size:14 final size:14
Alignment explanation
Indices: 228528--228567 Score: 62
Period size: 14 Copynumber: 2.9 Consensus size: 14
228518 ATAGTGAGGG
228528 TGTATCGATACATA
1 TGTATCGATACATA
*
228542 TGTATCCATACATA
1 TGTATCGATACATA
*
228556 TATATCGATACA
1 TGTATCGATACA
228568 CTGTGCACAA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.38, C:0.17, G:0.10, T:0.35
Consensus pattern (14 bp):
TGTATCGATACATA
Found at i:234325 original size:19 final size:19
Alignment explanation
Indices: 234301--234352 Score: 104
Period size: 19 Copynumber: 2.7 Consensus size: 19
234291 GGTTGACTTA
234301 GTGTATCGGTACAACCCAT
1 GTGTATCGGTACAACCCAT
234320 GTGTATCGGTACAACCCAT
1 GTGTATCGGTACAACCCAT
234339 GTGTATCGGTACAA
1 GTGTATCGGTACAA
234353 TAATTAGGTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 33 1.00
ACGTcount: A:0.27, C:0.23, G:0.23, T:0.27
Consensus pattern (19 bp):
GTGTATCGGTACAACCCAT
Found at i:237414 original size:20 final size:20
Alignment explanation
Indices: 237353--237420 Score: 61
Period size: 20 Copynumber: 3.4 Consensus size: 20
237343 CAGTATACAA
237353 TATCGATATCGCATGAATAG
1 TATCGATATCGCATGAATAG
* * *
237373 TA-CTGATATTGTTCTTG--CAG
1 TATC-GATATCG--CATGAATAG
237393 TATCGATATCGCATGAATAG
1 TATCGATATCGCATGAATAG
237413 TATCGATA
1 TATCGATA
237421 CCCAAGGTAA
Statistics
Matches: 36, Mismatches: 6, Indels: 12
0.67 0.11 0.22
Matches are distributed among these distances:
18 3 0.08
19 1 0.03
20 28 0.78
21 1 0.03
22 3 0.08
ACGTcount: A:0.31, C:0.15, G:0.19, T:0.35
Consensus pattern (20 bp):
TATCGATATCGCATGAATAG
Found at i:239802 original size:20 final size:20
Alignment explanation
Indices: 239777--239832 Score: 112
Period size: 20 Copynumber: 2.8 Consensus size: 20
239767 CTTCATGGTA
239777 GTATCGGTACTACCTTGATG
1 GTATCGGTACTACCTTGATG
239797 GTATCGGTACTACCTTGATG
1 GTATCGGTACTACCTTGATG
239817 GTATCGGTACTACCTT
1 GTATCGGTACTACCTT
239833 TGCCTATGGT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 36 1.00
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (20 bp):
GTATCGGTACTACCTTGATG
Found at i:241009 original size:2 final size:2
Alignment explanation
Indices: 241004--241032 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
240994 TATATTAAGC
241004 AT AT AT -T 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
241033 TATTATTACA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 25 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:242268 original size:2 final size:2
Alignment explanation
Indices: 242259--242300 Score: 77
Period size: 2 Copynumber: 21.5 Consensus size: 2
242249 TATTTTTTGT
242259 TA TA -A 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
242300 T
1 T
242301 TTCTTGTTTT
Statistics
Matches: 39, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 38 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:242463 original size:16 final size:16
Alignment explanation
Indices: 242444--242476 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
242434 GTGATCTTTA
242444 TTTATTTGTTTTATTT
1 TTTATTTGTTTTATTT
242460 TTTATTTGTTTTATTT
1 TTTATTTGTTTTATTT
242476 T
1 T
242477 CTTTTAATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.82
Consensus pattern (16 bp):
TTTATTTGTTTTATTT
Found at i:252954 original size:13 final size:13
Alignment explanation
Indices: 252936--252977 Score: 59
Period size: 13 Copynumber: 3.2 Consensus size: 13
252926 TAAGTCGAAT
252936 AAGAAAAAGAAAA
1 AAGAAAAAGAAAA
252949 AAGAAAAAGAAAA
1 AAGAAAAAGAAAA
252962 TAA-AAAAAGAGAAA
1 -AAGAAAAAGA-AAA
252976 AA
1 AA
252978 ACATTTAGGG
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 22 0.81
14 5 0.19
ACGTcount: A:0.83, C:0.00, G:0.14, T:0.02
Consensus pattern (13 bp):
AAGAAAAAGAAAA
Found at i:252960 original size:19 final size:20
Alignment explanation
Indices: 252936--252976 Score: 59
Period size: 19 Copynumber: 2.1 Consensus size: 20
252926 TAAGTCGAAT
252936 AAGAAAA-AGAAAAAAGA-AA
1 AAGAAAATA-AAAAAAGAGAA
252955 AAGAAAATAAAAAAAGAGAA
1 AAGAAAATAAAAAAAGAGAA
252975 AA
1 AA
252977 AACATTTAGG
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
19 15 0.75
20 5 0.25
ACGTcount: A:0.83, C:0.00, G:0.15, T:0.02
Consensus pattern (20 bp):
AAGAAAATAAAAAAAGAGAA
Found at i:253998 original size:55 final size:56
Alignment explanation
Indices: 253848--253983 Score: 157
Period size: 60 Copynumber: 2.4 Consensus size: 56
253838 GACTTACTCG
* * * * *
253848 AGATTAGATTTTAACTTCACAACAAATGATATCCAACTCAAAGCCAATTTGGTGAAACAA
1 AGATTGGATTTCAACTTCACGACAAAAGATATCCAAC-C---GCCAATTTGATGAAACAA
* * *
253908 AGATTGGGTTTCAACTTCATGACAAAAGATATCCAACCGCCAATTTGATGAAGC-A
1 AGATTGGATTTCAACTTCACGACAAAAGATATCCAACCGCCAATTTGATGAAACAA
253963 AGATTGGATTTCAACTTCACG
1 AGATTGGATTTCAACTTCACG
253984 GTGAAGGATA
Statistics
Matches: 66, Mismatches: 10, Indels: 5
0.81 0.12 0.06
Matches are distributed among these distances:
55 20 0.30
56 14 0.21
59 1 0.02
60 31 0.47
ACGTcount: A:0.38, C:0.19, G:0.15, T:0.27
Consensus pattern (56 bp):
AGATTGGATTTCAACTTCACGACAAAAGATATCCAACCGCCAATTTGATGAAACAA
Found at i:254260 original size:124 final size:124
Alignment explanation
Indices: 253961--254272 Score: 416
Period size: 121 Copynumber: 2.5 Consensus size: 124
253951 TTTGATGAAG
** * * * * *
253961 CAAGATTGGATTTCAACTTCACGGTGAAGGATATCCAATTCAAGGCTTAACTTCACAATGAAGGG
1 CAAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGA
* *
254026 GCCATCCACGATTTCAACTTCACGACGAAGGATATCATACCCACAAGCAGCAATGCAAC
66 GCCATCCACGATTTCAACTTCACGACGAAGGATATCATACCCACAAGCAACAATACAAC
*
254085 C---CTTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGA
1 CAAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGA
* * * * *
254147 GCCATCCATGATTTCAACTTCACGATGAAGGCTATCGTGCCCACAAGCAAC-ATACAAC
66 GCCATCCACGATTTCAACTTCACGACGAAGGATATCATACCCACAAGCAACAATACAAC
* * * *
254205 TCAAGATTGGATATCAACTTCACGACGGAGGATATTCAATTCAAAGCTCAACTTCACAGCGAATG
1 -CAAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATG
254270 AGC
65 AGC
254273 TTTCCAGTTT
Statistics
Matches: 164, Mismatches: 20, Indels: 8
0.85 0.10 0.04
Matches are distributed among these distances:
120 6 0.04
121 99 0.60
124 59 0.36
ACGTcount: A:0.35, C:0.26, G:0.17, T:0.22
Consensus pattern (124 bp):
CAAGATTGGATTTCAACTTCACGACGAAGGATATCCAATTCAAAGCTCAACTTCACAACGAATGA
GCCATCCACGATTTCAACTTCACGACGAAGGATATCATACCCACAAGCAACAATACAAC
Found at i:256150 original size:2 final size:2
Alignment explanation
Indices: 256139--256172 Score: 61
Period size: 2 Copynumber: 17.5 Consensus size: 2
256129 TTATTTTTAT
256139 TA TA -A 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 T
256173 TTCTTGTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 30 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:258248 original size:25 final size:25
Alignment explanation
Indices: 258215--258262 Score: 69
Period size: 25 Copynumber: 1.9 Consensus size: 25
258205 CAGCTTTAAT
*
258215 TTTTTTTTTTGAAAAGTCAGCTTGG
1 TTTTATTTTTGAAAAGTCAGCTTGG
* *
258240 TTTTATTTTTGACAAGTTAGCTT
1 TTTTATTTTTGAAAAGTCAGCTT
258263 AAAAGGTTCG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.21, C:0.08, G:0.17, T:0.54
Consensus pattern (25 bp):
TTTTATTTTTGAAAAGTCAGCTTGG
Done.