Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001041.1 Hibiscus syriacus cultivar Beakdansim tig00002069_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: 59828
ACGTcount: A:0.35, C:0.18, G:0.16, T:0.32
Found at i:1476 original size:13 final size:14
Alignment explanation
Indices: 1458--1488 Score: 55
Period size: 13 Copynumber: 2.3 Consensus size: 14
1448 ATCTCTCCTT
1458 TCCTACTTCTT-AA
1 TCCTACTTCTTAAA
1471 TCCTACTTCTTAAA
1 TCCTACTTCTTAAA
1485 TCCT
1 TCCT
1489 TTCTTCTTCG
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 11 0.65
14 6 0.35
ACGTcount: A:0.23, C:0.32, G:0.00, T:0.45
Consensus pattern (14 bp):
TCCTACTTCTTAAA
Found at i:6284 original size:39 final size:39
Alignment explanation
Indices: 6239--6326 Score: 128
Period size: 39 Copynumber: 2.3 Consensus size: 39
6229 GGAAAATTAT
6239 GAATTAGGGATTG-AGATGCG-AAGGAGAAATGAAAAA-GGG
1 GAATTAGGGATTGAAG-TGCGAAAGG-GAAAT-AAAAATGGG
6278 GAATTAGGGATTGAAGTGCGAAAGGGAAATAAAAATGGG
1 GAATTAGGGATTGAAGTGCGAAAGGGAAATAAAAATGGG
6317 GAATTAGGGA
1 GAATTAGGGA
6327 ATAATTAAAA
Statistics
Matches: 46, Mismatches: 0, Indels: 6
0.88 0.00 0.12
Matches are distributed among these distances:
38 5 0.11
39 35 0.76
40 6 0.13
ACGTcount: A:0.43, C:0.02, G:0.38, T:0.17
Consensus pattern (39 bp):
GAATTAGGGATTGAAGTGCGAAAGGGAAATAAAAATGGG
Found at i:24783 original size:22 final size:22
Alignment explanation
Indices: 24758--24799 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
24748 TTTCATGTAT
24758 ATATATAGAAAGAGAGAGGGAG
1 ATATATAGAAAGAGAGAGGGAG
* *
24780 ATATATATATAGAGAGAGGG
1 ATATATAGAAAGAGAGAGGG
24800 GGGAGAGTGA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.48, C:0.00, G:0.33, T:0.19
Consensus pattern (22 bp):
ATATATAGAAAGAGAGAGGGAG
Found at i:24790 original size:26 final size:25
Alignment explanation
Indices: 24755--24805 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
24745 ATGTTTCATG
24755 TATATATATAGAAAGAGAGAGGGAGA
1 TATATATATAGAAAGAG-GAGGGAGA
* *
24781 TATATATATAGAGAGAGGGGGGAGA
1 TATATATATAGAAAGAGGAGGGAGA
24806 GTGAGAGAGG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
25 7 0.30
26 16 0.70
ACGTcount: A:0.45, C:0.00, G:0.35, T:0.20
Consensus pattern (25 bp):
TATATATATAGAAAGAGGAGGGAGA
Found at i:35579 original size:16 final size:17
Alignment explanation
Indices: 35548--35581 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
35538 TGAGACATTT
*
35548 TTATTATTTATTTTAAA
1 TTATTATTTATATTAAA
35565 TTATT-TTTATATTAAA
1 TTATTATTTATATTAAA
35581 T
1 T
35582 AATAAAAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 11 0.69
17 5 0.31
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (17 bp):
TTATTATTTATATTAAA
Found at i:42002 original size:25 final size:24
Alignment explanation
Indices: 41954--41999 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
41944 GGATGAGGGA
41954 TTAAATTGAAATAATTATAAAATG
1 TTAAATTGAAATAATTATAAAATG
*
41978 TTAAGTTGAAATTAA-TATAAAA
1 TTAAATTGAAA-TAATTATAAAA
42000 ATGGATAAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
24 17 0.85
25 3 0.15
ACGTcount: A:0.54, C:0.00, G:0.09, T:0.37
Consensus pattern (24 bp):
TTAAATTGAAATAATTATAAAATG
Found at i:42664 original size:2 final size:2
Alignment explanation
Indices: 42657--42732 Score: 152
Period size: 2 Copynumber: 38.0 Consensus size: 2
42647 TATAAGTTTA
42657 AT AT 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 AT AT
42699 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
42733 GCAAAAGGTA
Statistics
Matches: 74, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 74 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:43124 original size:54 final size:56
Alignment explanation
Indices: 43038--43159 Score: 155
Period size: 54 Copynumber: 2.2 Consensus size: 56
43028 CCTTAAGCCA
* * *
43038 TATATATATATATATATATATATATATAATATAAGTACATAGACA-ATATATATAAG
1 TATATATATATAGATATATATATATATAATATAAGTACACACACATATATATA-AAG
43094 TATATATAT-TAGA-ATATATATGATAT-ATATAAGTACACACACATATATATAAAG
1 TATATATATATAGATATATATAT-ATATAATATAAGTACACACACATATATATAAAG
43148 TATA-AGTATATA
1 TATATA-TATATA
43160 AACTATAAAG
Statistics
Matches: 59, Mismatches: 3, Indels: 9
0.83 0.04 0.13
Matches are distributed among these distances:
53 1 0.02
54 33 0.56
55 16 0.27
56 9 0.15
ACGTcount: A:0.51, C:0.05, G:0.07, T:0.38
Consensus pattern (56 bp):
TATATATATATAGATATATATATATATAATATAAGTACACACACATATATATAAAG
Found at i:43144 original size:2 final size:2
Alignment explanation
Indices: 43037--43124 Score: 71
Period size: 2 Copynumber: 45.5 Consensus size: 2
43027 CCCTTAAGCC
*
43037 AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A- AGT AC AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A-T AT AT
* * *
43078 AG AC A- AT AT AT AT A- AGT AT AT AT AT -T AG A- AT AT AT AT GAT
1 AT AT AT AT AT AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT -AT
43118 AT AT AT A
1 AT AT AT A
43125 AGTACACACA
Statistics
Matches: 72, Mismatches: 5, Indels: 18
0.76 0.05 0.19
Matches are distributed among these distances:
1 6 0.08
2 62 0.86
3 4 0.06
ACGTcount: A:0.51, C:0.02, G:0.06, T:0.41
Consensus pattern (2 bp):
AT
Found at i:43189 original size:14 final size:14
Alignment explanation
Indices: 43040--43246 Score: 67
Period size: 14 Copynumber: 14.7 Consensus size: 14
43030 TTAAGCCATA
43040 TATATATATATATA-
1 TATATATATATA-AG
43054 TATATATATATAA-
1 TATATATATATAAG
*
43067 TATA-AGTACAT-AG
1 TATATA-TATATAAG
*
43080 -ACAATATATATAAG
1 TA-TATATATATAAG
43094 TATATATATTAGAATATA-
1 TATATATA-T---ATA-AG
43112 TATGATATATATAAG
1 TAT-ATATATATAAG
* * * *
43127 TACACACACAT-A-
1 TATATATATATAAG
*
43139 TATATAAAGTATAAG
1 TATATATA-TATAAG
*
43154 TATATAAACTATAAAG
1 TATATATA-TAT-AAG
*
43170 TTTATATATATAAG
1 TATATATATATAAG
* * *
43184 --TGTATACATAAT
1 TATATATATATAAG
* *
43196 TATATATGTATGA-
1 TATATATATATAAG
* * *
43209 TGTATGTACATAAG
1 TATATATATATAAG
*
43223 TATATATATAAAAG
1 TATATATATATAAG
43237 TATATATATA
1 TATATATATA
43247 ATATGTAAGC
Statistics
Matches: 142, Mismatches: 31, Indels: 40
0.67 0.15 0.19
Matches are distributed among these distances:
12 17 0.12
13 25 0.18
14 57 0.40
15 21 0.15
16 9 0.06
18 7 0.05
19 6 0.04
ACGTcount: A:0.49, C:0.04, G:0.08, T:0.39
Consensus pattern (14 bp):
TATATATATATAAG
Found at i:43424 original size:2 final size:2
Alignment explanation
Indices: 43370--43406 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
43360 TATACAATTT
43370 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 T
43407 CATTGATCAA
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:43519 original size:2 final size:2
Alignment explanation
Indices: 43512--43595 Score: 84
Period size: 2 Copynumber: 42.0 Consensus size: 2
43502 AATATAAGTT
* *
43512 TA TA TA TA TA AA GTA TA TA AA CTA 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
* *
43556 TA TA TA TA TA TA TA -A GTA TA TA CA TA -A T- TA TA TA TG TA TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA
43596 ATGTATGTAC
Statistics
Matches: 68, Mismatches: 8, Indels: 12
0.77 0.09 0.14
Matches are distributed among these distances:
1 3 0.04
2 62 0.91
3 3 0.04
ACGTcount: A:0.50, C:0.02, G:0.04, T:0.44
Consensus pattern (2 bp):
TA
Found at i:43830 original size:40 final size:40
Alignment explanation
Indices: 43700--43834 Score: 100
Period size: 40 Copynumber: 3.4 Consensus size: 40
43690 AATTTATTAA
* *
43700 TATAAGCTCATTTGTATTACAAAATACATAA-CTCAATACT
1 TATAAACTCATTTGTATTACAAAATACATAAGC-CAATATT
* * *** * *
43740 TAAAAACTCATTTCTAAGCCCAATATACAATTAAG----TATA
1 TATAAACTCATTTGT-ATTACAAAATAC-A-TAAGCCAATATT
**
43779 TATAAGTTCATTTGTATTACAAAATACATAAGCCAATATT
1 TATAAACTCATTTGTATTACAAAATACATAAGCCAATATT
43819 TATAAACTCATTTGTA
1 TATAAACTCATTTGTA
43835 AGCCCAATAT
Statistics
Matches: 67, Mismatches: 20, Indels: 16
0.65 0.19 0.16
Matches are distributed among these distances:
36 4 0.06
37 1 0.01
38 8 0.12
39 13 0.19
40 29 0.43
41 8 0.12
42 1 0.01
43 3 0.04
ACGTcount: A:0.43, C:0.16, G:0.06, T:0.36
Consensus pattern (40 bp):
TATAAACTCATTTGTATTACAAAATACATAAGCCAATATT
Found at i:43830 original size:79 final size:79
Alignment explanation
Indices: 43699--43861 Score: 265
Period size: 79 Copynumber: 2.1 Consensus size: 79
43689 AAATTTATTA
43699 ATATAAGCTCATTTGTATTACAAAATACATAACTCAATACTTAAAAACTCATTTCTAAGCCCAAT
1 ATATAAGCTCATTTGTATTACAAAATACATAACTCAATACTTAAAAACTCATTTCTAAGCCCAAT
43764 ATACAATTAAGTAT
66 ATACAATTAAGTAT
* * * *
43778 ATATAAGTTCATTTGTATTACAAAATACATAAGC-CAATATTTATAAACTCATTTGTAAGCCCAA
1 ATATAAGCTCATTTGTATTACAAAATACATAA-CTCAATACTTAAAAACTCATTTCTAAGCCCAA
43842 TATACAATTAAGTAT
65 TATACAATTAAGTAT
*
43857 TTATA
1 ATATA
43862 TATATATATA
Statistics
Matches: 78, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
79 77 0.99
80 1 0.01
ACGTcount: A:0.44, C:0.15, G:0.06, T:0.35
Consensus pattern (79 bp):
ATATAAGCTCATTTGTATTACAAAATACATAACTCAATACTTAAAAACTCATTTCTAAGCCCAAT
ATACAATTAAGTAT
Found at i:43933 original size:2 final size:2
Alignment explanation
Indices: 43926--44115 Score: 164
Period size: 2 Copynumber: 96.5 Consensus size: 2
43916 TACAAGTTTA
43926 AT AT 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 AT AT
*
43968 AT A- AGT AT AT AT AT AT AT A- AGT AT A- AGT AT AT AA AT -T AT
1 AT AT A-T AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT
* *
44007 AT A- AT AT A- AT AT AT A- ACC AT AT AGT GT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT A-T AT AT A-T AT AT AT AT AT AT AT AT
* * * * *
44048 AT AT AT AT AT AT AT AT GT AT AT GT CT AA AT AT GT AT AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
44089 AGT AT A- AA AT AT AT AC AT AC AT AT AT A
1 A-T AT AT AT AT AT AT AT AT AT AT AT AT A
44116 CATACATACA
Statistics
Matches: 154, Mismatches: 19, Indels: 30
0.76 0.09 0.15
Matches are distributed among these distances:
1 9 0.06
2 139 0.90
3 6 0.04
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (2 bp):
AT
Found at i:44120 original size:4 final size:4
Alignment explanation
Indices: 44101--45685 Score: 3112
Period size: 4 Copynumber: 398.0 Consensus size: 4
44091 TATAAAATAT
*
44101 ATAC ATAC ATAT ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44149 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT-- ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44195 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44243 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44291 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44339 ATAC ATAC ATAC ATAC --AC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44385 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44433 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44481 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44529 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44577 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44625 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44673 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44721 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44769 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44817 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44865 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44913 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
44961 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
45009 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
45057 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
45105 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
45153 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
45201 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
45249 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
45297 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
45345 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
45393 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
45441 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
45489 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC -TAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
45536 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC --AC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
45582 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
45630 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC
45678 ATAC ATAC
1 ATAC ATAC
45686 GGTTTAATTT
Statistics
Matches: 1572, Mismatches: 2, Indels: 14
0.99 0.00 0.01
Matches are distributed among these distances:
2 6 0.00
3 3 0.00
4 1563 0.99
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ATAC
Found at i:49119 original size:14 final size:13
Alignment explanation
Indices: 49092--49130 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
49082 TATACCCTAC
49092 CCCTAACATA-AAA
1 CCCTAA-ATATAAA
49105 CCCTAAATTATAAA
1 CCCTAAA-TATAAA
49119 CCCTAAATATAA
1 CCCTAAATATAA
49131 CCCCCTCAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
12 1 0.04
13 13 0.54
14 10 0.42
ACGTcount: A:0.51, C:0.26, G:0.00, T:0.23
Consensus pattern (13 bp):
CCCTAAATATAAA
Found at i:49136 original size:14 final size:14
Alignment explanation
Indices: 49102--49130 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
49092 CCCTAACATA
49102 AAACCCTAAATTAT
1 AAACCCTAAATTAT
49116 AAACCCTAAA-TAT
1 AAACCCTAAATTAT
49129 AA
1 AA
49131 CCCCCTCAGA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.55, C:0.21, G:0.00, T:0.24
Consensus pattern (14 bp):
AAACCCTAAATTAT
Found at i:58444 original size:13 final size:14
Alignment explanation
Indices: 58426--58459 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
58416 TATACCCTAC
*
58426 CCCTAACTTA-AAA
1 CCCTAAATTATAAA
58439 CCCTAAATTATAAA
1 CCCTAAATTATAAA
58453 CCCTAAA
1 CCCTAAA
58460 CTCTAACCAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.47
14 10 0.53
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (14 bp):
CCCTAAATTATAAA
Found at i:58806 original size:2 final size:2
Alignment explanation
Indices: 58667--58797 Score: 171
Period size: 2 Copynumber: 65.5 Consensus size: 2
58657 CTAAAGCCAA
58667 AT AT 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 AT AT
58709 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT A-
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * *
58749 AGT AC AT AT AT AT AA AGT AT A- AGT AT AT AA ACT AT A- AT AT AT
1 A-T AT AT AT AT AT AT A-T AT AT A-T AT AT AT A-T AT AT AT AT AT
58791 AT AT AT A
1 AT AT AT A
58798 AAGTATATAA
Statistics
Matches: 115, Mismatches: 6, Indels: 16
0.84 0.04 0.12
Matches are distributed among these distances:
1 4 0.03
2 107 0.93
3 4 0.03
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (2 bp):
AT
Found at i:58826 original size:29 final size:29
Alignment explanation
Indices: 58666--58814 Score: 121
Period size: 28 Copynumber: 5.1 Consensus size: 29
58656 CCTAAAGCCA
* *
58666 AATATATATATATATA-TATATATA-TAT
1 AATATATATATATAAAGTATATAAACTAT
* *
58693 ATATATATATATATATA-TATATATA-TAT
1 A-ATATATATATATAAAGTATATAAACTAT
*
58721 ATATATATATATATATA-TATATAATA-TAAGT
1 A-ATATATATATATAAAGTATATAA-ACT-A-T
*
58752 ACATATATATAAAGTATAAGTATATAAACTAT
1 A-ATATATATATA-TA-AAGTATATAAACTAT
*
58784 AATATATATATATAAAGTATATAAGCTAT
1 AATATATATATATAAAGTATATAAACTAT
58813 AA
1 AA
58815 AGTGTGTATA
Statistics
Matches: 108, Mismatches: 6, Indels: 14
0.84 0.05 0.11
Matches are distributed among these distances:
27 1 0.01
28 49 0.45
29 18 0.17
30 3 0.03
31 22 0.20
32 4 0.04
33 3 0.03
34 8 0.07
ACGTcount: A:0.52, C:0.02, G:0.03, T:0.42
Consensus pattern (29 bp):
AATATATATATATAAAGTATATAAACTAT
Found at i:59102 original size:19 final size:19
Alignment explanation
Indices: 59074--59119 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
59064 AGTATGATCA
* *
59074 ATGATATATGTACTTATGT
1 ATGATATATGTACATAAGT
*
59093 ATGATGTATGTACATAAGT
1 ATGATATATGTACATAAGT
59112 ATGA-ATAT
1 ATGATATAT
59120 AAGTTTAATA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
18 3 0.13
19 20 0.87
ACGTcount: A:0.37, C:0.04, G:0.17, T:0.41
Consensus pattern (19 bp):
ATGATATATGTACATAAGT
Found at i:59190 original size:21 final size:20
Alignment explanation
Indices: 59160--59203 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 20
59150 TGATCAATGA
* *
59160 TGTATGTATACATGTATGATG
1 TGTATATATACATATATG-TG
*
59181 TGTATATATATATATATGTG
1 TGTATATATACATATATGTG
59201 TGT
1 TGT
59204 GTGTAAAGTA
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 5 0.25
21 15 0.75
ACGTcount: A:0.30, C:0.02, G:0.20, T:0.48
Consensus pattern (20 bp):
TGTATATATACATATATGTG
Found at i:59194 original size:25 final size:25
Alignment explanation
Indices: 59161--59217 Score: 62
Period size: 25 Copynumber: 2.3 Consensus size: 25
59151 GATCAATGAT
* *
59161 GTATGTATACATGTATGATGTGTATA
1 GTATATATACATGTATG-TGTGTAAA
* *
59187 -TATATATATATGTGTGTGTGTAAA
1 GTATATATACATGTATGTGTGTAAA
59211 GTATATA
1 GTATATA
59218 AACTATAAAG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
24 7 0.27
25 19 0.73
ACGTcount: A:0.33, C:0.02, G:0.21, T:0.44
Consensus pattern (25 bp):
GTATATATACATGTATGTGTGTAAA
Found at i:59228 original size:16 final size:17
Alignment explanation
Indices: 59207--59251 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 17
59197 TGTGTGTGTG
59207 TAAAGTATATA-A-ACTA
1 TAAAGTATATATATA-TA
59223 TAAAGTATATATATATA
1 TAAAGTATATATATATA
59240 TATAAGTATATA
1 TA-AAGTATATA
59252 CATAATTATA
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
16 11 0.42
17 5 0.19
18 10 0.38
ACGTcount: A:0.53, C:0.02, G:0.07, T:0.38
Consensus pattern (17 bp):
TAAAGTATATATATATA
Found at i:59235 original size:18 final size:18
Alignment explanation
Indices: 59212--59307 Score: 58
Period size: 18 Copynumber: 5.4 Consensus size: 18
59202 GTGTGTAAAG
59212 TATATAAACTATA-AAGTA
1 TATATAAA-TATATAAGTA
*
59230 TATATATATATATAAGTA
1 TATATAAATATATAAGTA
* *
59248 TATACATAATTATATATGTA
1 TAT--ATAAATATATAAGTA
* ** *
59268 TGATGTATGTACATAAGTA
1 T-ATATAAATATATAAGTA
59287 TATAT--ATA-A-AAGTA
1 TATATAAATATATAAGTA
59301 TATATAA
1 TATATAA
59308 TATGTAGCAT
Statistics
Matches: 61, Mismatches: 11, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
14 10 0.16
15 1 0.02
16 2 0.03
17 4 0.07
18 18 0.30
19 11 0.18
20 13 0.21
21 2 0.03
ACGTcount: A:0.49, C:0.03, G:0.08, T:0.40
Consensus pattern (18 bp):
TATATAAATATATAAGTA
Found at i:59249 original size:12 final size:12
Alignment explanation
Indices: 59234--59306 Score: 56
Period size: 12 Copynumber: 5.7 Consensus size: 12
59224 AAAGTATATA
59234 TATATATATAAG
1 TATATATATAAG
* *
59246 TATATACATAAT
1 TATATATATAAG
*
59258 TATATATGTATGATG
1 TATATA--TAT-AAG
* *
59273 TATGTACATAAG
1 TATATATATAAG
59285 TATATATATAAAAG
1 TATATATAT--AAG
59299 TATATATA
1 TATATATA
59307 ATATGTAGCA
Statistics
Matches: 46, Mismatches: 10, Indels: 8
0.72 0.16 0.12
Matches are distributed among these distances:
12 25 0.54
13 2 0.04
14 13 0.28
15 6 0.13
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.41
Consensus pattern (12 bp):
TATATATATAAG
Found at i:59423 original size:2 final size:2
Alignment explanation
Indices: 59416--59488 Score: 121
Period size: 2 Copynumber: 37.0 Consensus size: 2
59406 CCAATACAAT
* *
59416 TA TA TA TA GA -A TA TA TA TA TA TA TC 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
59457 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
59489 ATCATTGATC
Statistics
Matches: 67, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
1 1 0.01
2 66 0.99
ACGTcount: A:0.49, C:0.01, G:0.01, T:0.48
Consensus pattern (2 bp):
TA
Found at i:59589 original size:2 final size:2
Alignment explanation
Indices: 59582--59663 Score: 91
Period size: 2 Copynumber: 42.0 Consensus size: 2
59572 AATATAAGTT
* *
59582 TA TA TA TA TA AA GTA TA TA AA CTA 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
*
59626 TA TA TA TA TA TA TA T- TA T- TC TA TA TA TA TA -A TA -A TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
59664 CATAATTATA
Statistics
Matches: 69, Mismatches: 5, Indels: 12
0.80 0.06 0.14
Matches are distributed among these distances:
1 4 0.06
2 63 0.91
3 2 0.03
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.46
Consensus pattern (2 bp):
TA
Found at i:59638 original size:24 final size:24
Alignment explanation
Indices: 59582--59679 Score: 91
Period size: 24 Copynumber: 4.2 Consensus size: 24
59572 AATATAAGTT
* *
59582 TATATATATAAAGTATATAAACTATA
1 TATATATATATA-TATATATA-TATA
59608 TATATATATATATATATATATATA
1 TATATATATATATATATATATATA
*
59632 TATATATAT-TAT-TCTATATATA
1 TATATATATATATATATATATATA
*
59654 TA-ATA-ATATACATA-AT-TATA
1 TATATATATATATATATATATATA
*
59674 TGTATA
1 TATATA
59680 ATGTATGTAC
Statistics
Matches: 63, Mismatches: 6, Indels: 11
0.79 0.08 0.14
Matches are distributed among these distances:
20 7 0.11
21 10 0.16
22 12 0.19
23 3 0.05
24 13 0.21
25 7 0.11
26 11 0.17
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.46
Consensus pattern (24 bp):
TATATATATATATATATATATATA
Found at i:59680 original size:12 final size:12
Alignment explanation
Indices: 59581--59681 Score: 73
Period size: 14 Copynumber: 8.1 Consensus size: 12
59571 GAATATAAGT
59581 TTATATATATAA
1 TTATATATATAA
59593 --AGTATATA-AA
1 TTA-TATATATAA
*
59603 CTATATATATATA
1 TTATATATATA-A
59616 TATATATATATATA
1 T-TATATATATA-A
*
59630 TATATATATATTAT
1 T-TATATATA-TAA
59644 TCTATATATATAA
1 T-TATATATATAA
* *
59657 TAATATACATAA
1 TTATATATATAA
*
59669 TTATATGTATAA
1 TTATATATATAA
59681 T
1 T
59682 GTATGTACAT
Statistics
Matches: 73, Mismatches: 9, Indels: 14
0.76 0.09 0.15
Matches are distributed among these distances:
10 3 0.04
11 12 0.16
12 21 0.29
13 4 0.05
14 31 0.42
15 2 0.03
ACGTcount: A:0.49, C:0.03, G:0.02, T:0.47
Consensus pattern (12 bp):
TTATATATATAA
Done.