Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004679.1 Hibiscus syriacus cultivar Beakdansim tig00010492_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: 63626
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1645 original size:29 final size:29
Alignment explanation
Indices: 1603--1661 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
1593 ATTTTCACCT
1603 AACTAAACTAATGTAAGCAATGACATCAA
1 AACTAAACTAATGTAAGCAATGACATCAA
* *
1632 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAACTAATGTAAGCAATGACATCAA
1661 A
1 A
1662 TAATTTAGGT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 28 1.00
ACGTcount: A:0.51, C:0.15, G:0.12, T:0.22
Consensus pattern (29 bp):
AACTAAACTAATGTAAGCAATGACATCAA
Found at i:10760 original size:2 final size:2
Alignment explanation
Indices: 10753--10792 Score: 80
Period size: 2 Copynumber: 20.0 Consensus size: 2
10743 TTTTCAAACT
10753 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
10793 GACCTTTTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11144 original size:2 final size:2
Alignment explanation
Indices: 11137--11197 Score: 122
Period size: 2 Copynumber: 30.5 Consensus size: 2
11127 TAATTAACCA
11137 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
11179 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
11198 CCAAGCCAAA
Statistics
Matches: 59, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 59 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:17530 original size:89 final size:90
Alignment explanation
Indices: 17377--17572 Score: 236
Period size: 89 Copynumber: 2.2 Consensus size: 90
17367 CCATAACTAC
* * * * * **
17377 GTCCGTAGGGCTTCCCCTAAGCACGCAACAAAAGGGAGCTAACCTAAGGATATTTCATGGGGCCT
1 GTCCGTAGGGCTTACCCTAAGCACGAAACAAAAGAGAACCAACCTAAGGATATGCCATGGGGCCT
17442 ATCGGCCTACCCAAGGGTATCCTTAG
66 AT-GGCCTACCCAAGGGTATCCTTAG
*
17468 GTCCGTAGGG-TTACCCTAAGCA-GAAA-ACAAAGAGAACCAACCTAAGGATATGCCTTGGGGCC
1 GTCCGTAGGGCTTACCCTAAGCACGAAACA-AAAGAGAACCAACCTAAGGATATGCCATGGGGCC
* * *
17530 TATGGTCTTCCCAAGGGTATCCTTTG
65 TATGGCCTACCCAAGGGTATCCTTAG
*
17556 GTTCGTAGGGACTTACC
1 GTCCGTAGGG-CTTACC
17573 AGCTGGATCA
Statistics
Matches: 90, Mismatches: 12, Indels: 7
0.83 0.11 0.06
Matches are distributed among these distances:
88 30 0.33
89 34 0.38
90 16 0.18
91 10 0.11
ACGTcount: A:0.27, C:0.26, G:0.26, T:0.22
Consensus pattern (90 bp):
GTCCGTAGGGCTTACCCTAAGCACGAAACAAAAGAGAACCAACCTAAGGATATGCCATGGGGCCT
ATGGCCTACCCAAGGGTATCCTTAG
Found at i:20247 original size:18 final size:19
Alignment explanation
Indices: 20209--20249 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
20199 TTAAAGTCAA
* *
20209 CGGCTCAGTCGGCTTGGCT
1 CGGCTCAGTCGGCTCGACT
20228 CGGCTCAGT-GGCTCGACT
1 CGGCTCAGTCGGCTCGACT
20246 CGGC
1 CGGC
20250 GGGGCGGCTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 11 0.55
19 9 0.45
ACGTcount: A:0.07, C:0.34, G:0.37, T:0.22
Consensus pattern (19 bp):
CGGCTCAGTCGGCTCGACT
Found at i:24825 original size:21 final size:21
Alignment explanation
Indices: 24800--24840 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
24790 TGGGGCTTCT
24800 TTGTATAAGTGGACATTCTCC
1 TTGTATAAGTGGACATTCTCC
*
24821 TTGTATAGGTGGACATTCTC
1 TTGTATAAGTGGACATTCTC
24841 GTATGCGTGT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.22, C:0.17, G:0.22, T:0.39
Consensus pattern (21 bp):
TTGTATAAGTGGACATTCTCC
Found at i:31932 original size:29 final size:29
Alignment explanation
Indices: 31890--32114 Score: 181
Period size: 29 Copynumber: 7.8 Consensus size: 29
31880 AGAAATGTGA
* *
31890 TTATTGTAATTTCTATGAAGTTTTTTATT
1 TTATTGTAATTTCTATAAAGTTTTGTATT
*
31919 TTATTGTAATTTCTATGAAGTTTTGTATT
1 TTATTGTAATTTCTATAAAGTTTTGTATT
* * *
31948 TTATTGTAATTTATA-AAATATTTTGTACT
1 TTATTGTAATTTCTATAAA-GTTTTGTATT
* *
31977 TTATTGTAAATTCTAAAAAGTTTTGTATT
1 TTATTGTAATTTCTATAAAGTTTTGTATT
* * *
32006 TTATTGTAAATTCCAAAAAGTTTTGTCA-T
1 TTATTGTAATTTCTATAAAGTTTTGT-ATT
* * * * **
32035 TTATTGTAAATTCCAAAAAGTTTTATCCT
1 TTATTGTAATTTCTATAAAGTTTTGTATT
* * *
32064 TTATTGTAAATTACAAT-TAGTTTTGT-TCT
1 TTATTGT-AATTTCTATAAAGTTTTGTAT-T
*
32093 TTATTGTAAATTTC-AAAAAGTT
1 TTATTGT-AATTTCTATAAAGTT
32115 ATCCTTTATT
Statistics
Matches: 167, Mismatches: 22, Indels: 14
0.82 0.11 0.07
Matches are distributed among these distances:
28 3 0.02
29 155 0.93
30 9 0.05
ACGTcount: A:0.32, C:0.06, G:0.10, T:0.52
Consensus pattern (29 bp):
TTATTGTAATTTCTATAAAGTTTTGTATT
Found at i:31980 original size:58 final size:57
Alignment explanation
Indices: 31918--32114 Score: 220
Period size: 58 Copynumber: 3.4 Consensus size: 57
31908 AGTTTTTTAT
* ** *
31918 TTTATTGTAATTTCTATGAAGTTTTGTATTTTATTGTAATTTATAAAATA-TTTTGTAC
1 TTTATTGTAAATTCTAAAAAGTTTTGTATTTTATTGTAAATTA-AAAATAGTTTTGT-C
*
31976 TTTATTGTAAATTCTAAAAAGTTTTGTATTTTATTGTAAATTCCAAAA-AGTTTTGTC
1 TTTATTGTAAATTCTAAAAAGTTTTGTATTTTATTGTAAATT-AAAAATAGTTTTGTC
* * ** * *
32033 ATTTATTGTAAATTCCAAAAAGTTTTATCCTTTATTGTAAATTACAATTAGTTTTGTTC
1 -TTTATTGTAAATTCTAAAAAGTTTTGTATTTTATTGTAAATTAAAAATAGTTTTG-TC
32092 TTTATTGTAAATT-TCAAAAAGTT
1 TTTATTGTAAATTCT-AAAAAGTT
32115 ATCCTTTATT
Statistics
Matches: 120, Mismatches: 13, Indels: 12
0.83 0.09 0.08
Matches are distributed among these distances:
57 4 0.03
58 114 0.95
59 2 0.02
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.51
Consensus pattern (57 bp):
TTTATTGTAAATTCTAAAAAGTTTTGTATTTTATTGTAAATTAAAAATAGTTTTGTC
Found at i:32038 original size:87 final size:87
Alignment explanation
Indices: 31890--32141 Score: 246
Period size: 87 Copynumber: 2.9 Consensus size: 87
31880 AGAAATGTGA
* ** * * * **
31890 TTATTGTAATTTCTATGAAGTTTTTTATTTTATTGTAATTTCTATGAAGTTTTGTATTTTATTGT
1 TTATTGTAAATTCTAAAAAGTTTTGTATTTTATTGTAAATTCCAAAAAGTTTTGTATTTTATTGT
* * *
31955 AATTTATAAAATA-TTTTGTACT
66 AAATTACAAAA-AGTTTTATACT
31977 TTATTGTAAATTCTAAAAAGTTTTGTATTTTATTGTAAATTCCAAAAAGTTTTGTCA-TTTATTG
1 TTATTGTAAATTCTAAAAAGTTTTGTATTTTATTGTAAATTCCAAAAAGTTTTGT-ATTTTATTG
* *
32041 TAAATTCCAAAAAGTTTTATCCT
65 TAAATTACAAAAAGTTTTATACT
** * * **
32064 TTATTGTAAATTAC-AATTAGTTTTGT-TCTTTATTGTAAATTTCAAAAAG--TTATCCTTTATT
1 TTATTGTAAATT-CTAAAAAGTTTTGTAT-TTTATTGTAAATTCCAAAAAGTTTTGTATTTTATT
*
32125 GTAAATTTCAAAAAGTT
64 GTAAATTACAAAAAGTT
32142 ATGCCTTTTA
Statistics
Matches: 141, Mismatches: 19, Indels: 12
0.82 0.11 0.07
Matches are distributed among these distances:
85 25 0.18
86 2 0.01
87 112 0.79
88 2 0.01
ACGTcount: A:0.32, C:0.07, G:0.10, T:0.52
Consensus pattern (87 bp):
TTATTGTAAATTCTAAAAAGTTTTGTATTTTATTGTAAATTCCAAAAAGTTTTGTATTTTATTGT
AAATTACAAAAAGTTTTATACT
Found at i:32160 original size:28 final size:27
Alignment explanation
Indices: 32005--32149 Score: 146
Period size: 29 Copynumber: 5.1 Consensus size: 27
31995 AGTTTTGTAT
* * *
32005 TTTATTGTAAATTCCAAAAAGTTTTGTCA
1 TTTATTGTAAATTTCAAAAAG--TTATCC
*
32034 TTTATTGTAAATTCCAAAAAGTTTTATCC
1 TTTATTGTAAATTTCAAAAAG--TTATCC
* ** * *
32063 TTTATTGTAAATTACAATTAGTTTTGTTC
1 TTTATTGTAAATTTCAAAAAG--TTATCC
32092 TTTATTGTAAATTTCAAAAAGTTATCC
1 TTTATTGTAAATTTCAAAAAGTTATCC
32119 TTTATTGTAAATTTCAAAAAGTTATGCC
1 TTTATTGTAAATTTCAAAAAGTTAT-CC
32147 TTT
1 TTT
32150 TATAGTAATT
Statistics
Matches: 103, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
27 29 0.28
28 5 0.05
29 69 0.67
ACGTcount: A:0.33, C:0.10, G:0.09, T:0.48
Consensus pattern (27 bp):
TTTATTGTAAATTTCAAAAAGTTATCC
Found at i:33518 original size:13 final size:13
Alignment explanation
Indices: 33494--33534 Score: 54
Period size: 10 Copynumber: 3.5 Consensus size: 13
33484 CTTTACTAAC
33494 TAAATT-AAGAAT
1 TAAATTAAAGAAT
33506 TAAATTAAAGAAT
1 TAAATTAAAGAAT
33519 T-AA--AAAGAAT
1 TAAATTAAAGAAT
33529 TAAATT
1 TAAATT
33535 CGAAAATGCT
Statistics
Matches: 25, Mismatches: 0, Indels: 7
0.78 0.00 0.22
Matches are distributed among these distances:
10 8 0.32
11 2 0.08
12 8 0.32
13 7 0.28
ACGTcount: A:0.61, C:0.00, G:0.07, T:0.32
Consensus pattern (13 bp):
TAAATTAAAGAAT
Found at i:33522 original size:25 final size:25
Alignment explanation
Indices: 33466--33534 Score: 72
Period size: 25 Copynumber: 2.8 Consensus size: 25
33456 ATTATGAATA
* **
33466 AATTAAATTAA-AATTAAACTTTACT
1 AATTAAATTAAGAATTAAA-TTAAAG
*
33491 AACTAAATTAAGAATTAAATTAAAG
1 AATTAAATTAAGAATTAAATTAAAG
33516 AATTAAA--AAGAATTAAATT
1 AATTAAATTAAGAATTAAATT
33535 CGAAAATGCT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
23 12 0.32
25 19 0.50
26 7 0.18
ACGTcount: A:0.58, C:0.04, G:0.04, T:0.33
Consensus pattern (25 bp):
AATTAAATTAAGAATTAAATTAAAG
Found at i:34851 original size:27 final size:27
Alignment explanation
Indices: 34811--34875 Score: 121
Period size: 27 Copynumber: 2.4 Consensus size: 27
34801 ACACCTAATG
34811 AAGATTGCTTTCAACTTCATGGCTAAGA
1 AAGA-TGCTTTCAACTTCATGGCTAAGA
34839 AAGATGCTTTCAACTTCATGGCTAAGA
1 AAGATGCTTTCAACTTCATGGCTAAGA
34866 AAGATGCTTT
1 AAGATGCTTT
34876 ATGGGTACGC
Statistics
Matches: 37, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
27 33 0.89
28 4 0.11
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Consensus pattern (27 bp):
AAGATGCTTTCAACTTCATGGCTAAGA
Found at i:37763 original size:23 final size:22
Alignment explanation
Indices: 37721--37763 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
37711 ACTAATTTAT
*
37721 AATAATTATATTTAAATAAATA
1 AATAATTAAATTTAAATAAATA
*
37743 AATAACTTAAATTTAATTAAA
1 AATAA-TTAAATTTAAATAAA
37764 ATTTATATTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
22 5 0.28
23 13 0.72
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (22 bp):
AATAATTAAATTTAAATAAATA
Found at i:37887 original size:21 final size:21
Alignment explanation
Indices: 37865--37940 Score: 75
Period size: 21 Copynumber: 3.7 Consensus size: 21
37855 TACCTCATAT
* *
37865 CTCAAACCCTAAATCTTAAAT
1 CTCAAACCCTAAATCATAAAC
* * * *
37886 CTTAAATCCTCAATCCTAAAC
1 CTCAAACCCTAAATCATAAAC
37907 CTCAAACCCT-AATCATAAAC
1 CTCAAACCCTAAATCATAAAC
*
37927 CT-AAACCTTAAATC
1 CTCAAACCCTAAATC
37941 CTAACCCTAA
Statistics
Matches: 45, Mismatches: 9, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
19 6 0.13
20 15 0.33
21 24 0.53
ACGTcount: A:0.42, C:0.32, G:0.00, T:0.26
Consensus pattern (21 bp):
CTCAAACCCTAAATCATAAAC
Found at i:37917 original size:14 final size:14
Alignment explanation
Indices: 37865--37944 Score: 58
Period size: 14 Copynumber: 5.9 Consensus size: 14
37855 TACCTCATAT
* *
37865 CTCAAACCCTAAAT
1 CTCAAATCCTAAAC
* *
37879 CTTAAATCTTAAATC
1 CTCAAATCCTAAA-C
37894 CTC-AATCCTAAAC
1 CTCAAATCCTAAAC
* *
37907 CTCAAACCCTAATC
1 CTCAAATCCTAAAC
*
37921 AT-AAA-CCTAAAC
1 CTCAAATCCTAAAC
*
37933 CTTAAATCCTAA
1 CTCAAATCCTAA
37945 CCCTAACAAG
Statistics
Matches: 51, Mismatches: 11, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
12 7 0.14
13 10 0.20
14 32 0.63
15 2 0.04
ACGTcount: A:0.42, C:0.31, G:0.00, T:0.26
Consensus pattern (14 bp):
CTCAAATCCTAAAC
Found at i:37940 original size:20 final size:19
Alignment explanation
Indices: 37868--37950 Score: 67
Period size: 20 Copynumber: 4.1 Consensus size: 19
37858 CTCATATCTC
* *
37868 AAACCCTAAATCTTAAATCTT
1 AAACCCT-AATCCTAAA-CCT
*
37889 AAATCCTCAATCCTAAACCT
1 AAACCCT-AATCCTAAACCT
*
37909 CAAACCCTAATCATAAACCT
1 -AAACCCTAATCCTAAACCT
* *
37929 AAACCTTAAATCCTAACCCT
1 AAACCCT-AATCCTAAACCT
37949 AA
1 AA
37951 CAAGAAAAAA
Statistics
Matches: 51, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
19 6 0.12
20 25 0.49
21 20 0.39
ACGTcount: A:0.43, C:0.31, G:0.00, T:0.25
Consensus pattern (19 bp):
AAACCCTAATCCTAAACCT
Found at i:38093 original size:2 final size:2
Alignment explanation
Indices: 38082--38149 Score: 129
Period size: 2 Copynumber: 34.5 Consensus size: 2
38072 TTAATTTTAC
38082 AT AT -T 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
38123 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
38150 ACGGTTAACA
Statistics
Matches: 65, Mismatches: 0, Indels: 2
0.97 0.00 0.03
Matches are distributed among these distances:
1 1 0.02
2 64 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:38537 original size:13 final size:13
Alignment explanation
Indices: 38497--38542 Score: 58
Period size: 13 Copynumber: 3.5 Consensus size: 13
38487 AATAAATTCA
38497 ATTATAAATAAAT
1 ATTATAAATAAAT
*
38510 AATT-TAAATTGAAT
1 -ATTATAAA-TAAAT
38524 ATTATAAATAAAT
1 ATTATAAATAAAT
38537 ATTATA
1 ATTATA
38543 TACATATTAT
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
13 17 0.61
14 11 0.39
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (13 bp):
ATTATAAATAAAT
Found at i:38683 original size:2 final size:2
Alignment explanation
Indices: 38676--38733 Score: 116
Period size: 2 Copynumber: 29.0 Consensus size: 2
38666 TATCCCATGT
38676 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
38718 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
38734 ATTTTGTTGA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 56 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:40249 original size:20 final size:21
Alignment explanation
Indices: 40211--40250 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
40201 CCGTTAAACA
40211 GGGGGGAATCGGTACTCCCTTG
1 GGGGGGAATCGGTA-TCCCTTG
40233 GGGGGGAATCGGT-TCCCT
1 GGGGGGAATCGGTATCCCT
40251 CCGAGCATTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
20 5 0.28
22 13 0.72
ACGTcount: A:0.12, C:0.23, G:0.42, T:0.23
Consensus pattern (21 bp):
GGGGGGAATCGGTATCCCTTG
Found at i:41323 original size:18 final size:18
Alignment explanation
Indices: 41300--41345 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
41290 AGGCATTTGA
41300 TCCTCTGGCT-GTGCTTGT
1 TCCTCT-GCTAGTGCTTGT
*
41318 TCCTCTGCTATTGCTTGT
1 TCCTCTGCTAGTGCTTGT
41336 TCCTCGTGCT
1 TCCTC-TGCT
41346 GTTCTGGTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 3 0.12
18 18 0.72
19 4 0.16
ACGTcount: A:0.02, C:0.30, G:0.22, T:0.46
Consensus pattern (18 bp):
TCCTCTGCTAGTGCTTGT
Found at i:41355 original size:18 final size:19
Alignment explanation
Indices: 41311--41360 Score: 50
Period size: 18 Copynumber: 2.7 Consensus size: 19
41301 CCTCTGGCTG
*
41311 TGCTTGTTCCTC-TGCTAT
1 TGCTGGTTCCTCGTGCTAT
* *
41329 TGCTTGTTCCTCGTGCTGT
1 TGCTGGTTCCTCGTGCTAT
*
41348 T-CTGGTTCATCGT
1 TGCTGGTTCCTCGT
41361 CGGAGTCGTC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 22 0.79
19 6 0.21
ACGTcount: A:0.04, C:0.26, G:0.22, T:0.48
Consensus pattern (19 bp):
TGCTGGTTCCTCGTGCTAT
Found at i:42936 original size:21 final size:21
Alignment explanation
Indices: 42910--42991 Score: 83
Period size: 22 Copynumber: 3.8 Consensus size: 21
42900 AGAACCCCAG
42910 GGGGGTATCGATTCCCCTACA
1 GGGGGTATCGATTCCCCTACA
* * *
42931 GGGGGTATTGGTTCCCCTTCAAA
1 GGGGGTATCGATTCCCC-T-ACA
* * *
42954 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGTATCGATTCCCCTAC-A
42976 GGGGGTATCGATTCCC
1 GGGGGTATCGATTCCC
42992 TCTGCACTAA
Statistics
Matches: 49, Mismatches: 9, Indels: 5
0.78 0.14 0.08
Matches are distributed among these distances:
21 15 0.31
22 17 0.35
23 17 0.35
ACGTcount: A:0.17, C:0.26, G:0.32, T:0.26
Consensus pattern (21 bp):
GGGGGTATCGATTCCCCTACA
Found at i:42992 original size:21 final size:22
Alignment explanation
Indices: 42910--42991 Score: 103
Period size: 23 Copynumber: 3.7 Consensus size: 22
42900 AGAACCCCAG
*
42910 GGGGGTATCGATTCCCCTAC-A
1 GGGGGTATCGATTCCCCTTCAA
* *
42931 GGGGGTATTGGTTCCCCTTCAAA
1 GGGGGTATCGATTCCCCTTC-AA
* *
42954 GGGGGAATCGGTTCCCCTTCAA
1 GGGGGTATCGATTCCCCTTCAA
42976 GGGGGTATCGATTCCC
1 GGGGGTATCGATTCCC
42992 TCTGCACTAA
Statistics
Matches: 52, Mismatches: 7, Indels: 3
0.84 0.11 0.05
Matches are distributed among these distances:
21 17 0.33
22 16 0.31
23 19 0.37
ACGTcount: A:0.17, C:0.26, G:0.32, T:0.26
Consensus pattern (22 bp):
GGGGGTATCGATTCCCCTTCAA
Found at i:49493 original size:25 final size:23
Alignment explanation
Indices: 49446--49520 Score: 78
Period size: 25 Copynumber: 3.1 Consensus size: 23
49436 AAGAAAGGGT
*
49446 AATAAAAAATAAGGAAAATAAATA
1 AATAAAAAAAAAGGAAAA-AAATA
49470 AATAAAATAAAAAGGAAGAAAAATA
1 AATAAAA-AAAAAGGAA-AAAAATA
* * *
49495 AATACAAGAAAAACGAAATAAATA
1 AATA-AAAAAAAAGGAAAAAAATA
49519 AA
1 AA
49521 CAAAGTATAG
Statistics
Matches: 44, Mismatches: 4, Indels: 6
0.81 0.07 0.11
Matches are distributed among these distances:
24 15 0.34
25 25 0.57
26 4 0.09
ACGTcount: A:0.75, C:0.03, G:0.09, T:0.13
Consensus pattern (23 bp):
AATAAAAAAAAAGGAAAAAAATA
Found at i:49648 original size:2 final size:2
Alignment explanation
Indices: 49641--49676 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
49631 AAGTATAATG
49641 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
49677 AAACAATGAT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:49799 original size:24 final size:24
Alignment explanation
Indices: 49770--49818 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
49760 AAAGGAAAAA
*
49770 TAAAAAATAAAAAATATATATATAT
1 TAAAAAA-ATAAAATATATATATAT
* *
49795 TAAAAAAATTAAATATGTATATAT
1 TAAAAAAATAAAATATATATATAT
49819 AGTAAAATAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 14 0.67
25 7 0.33
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.35
Consensus pattern (24 bp):
TAAAAAAATAAAATATATATATAT
Found at i:49800 original size:26 final size:26
Alignment explanation
Indices: 49771--49825 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
49761 AAGGAAAAAT
*
49771 AAAAAATAAAAAATATATATATATTA
1 AAAAAATAAAAAATATATATATAGTA
* * *
49797 AAAAAATTAAATATGTATATATAGTA
1 AAAAAATAAAAAATATATATATAGTA
49823 AAA
1 AAA
49826 TATAATATAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.65, C:0.00, G:0.04, T:0.31
Consensus pattern (26 bp):
AAAAAATAAAAAATATATATATAGTA
Found at i:50991 original size:12 final size:12
Alignment explanation
Indices: 50974--51008 Score: 54
Period size: 12 Copynumber: 2.9 Consensus size: 12
50964 TGTGCAATAA
50974 AATATATTATAT
1 AATATATTATAT
50986 AATATAATT-TAT
1 AATAT-ATTATAT
50998 AATATATTATA
1 AATATATTATA
51009 ATATTAAAGG
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
11 3 0.14
12 15 0.71
13 3 0.14
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (12 bp):
AATATATTATAT
Found at i:51940 original size:43 final size:43
Alignment explanation
Indices: 51827--51946 Score: 123
Period size: 43 Copynumber: 2.8 Consensus size: 43
51817 CTTGTGTAGA
* * * * * * *
51827 TGGGCATGATATCCTTCATTGTGAAGTTGAAACCGTGGATTTG
1 TGGGCACGATATCCTTCGTTGTGGAGTTGAAATCATAGATGTG
* * *
51870 TGGGCACGATATCCTCCGTCGTAGAGTTGAAATCATAGATGTG
1 TGGGCACGATATCCTTCGTTGTGGAGTTGAAATCATAGATGTG
* * *
51913 TGGGTACGATATCCTTCGTTATGGAGTTAAAATC
1 TGGGCACGATATCCTTCGTTGTGGAGTTGAAATC
51947 GTGGAAGCCC
Statistics
Matches: 61, Mismatches: 16, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
43 61 1.00
ACGTcount: A:0.25, C:0.16, G:0.27, T:0.33
Consensus pattern (43 bp):
TGGGCACGATATCCTTCGTTGTGGAGTTGAAATCATAGATGTG
Found at i:52901 original size:6 final size:6
Alignment explanation
Indices: 52890--52932 Score: 61
Period size: 6 Copynumber: 7.0 Consensus size: 6
52880 ACCCACCTTA
52890 TTTTTC TTTTTC -TTTTC TCTTTTC TTTTTTC TTTTTC TTTTTC
1 TTTTTC TTTTTC TTTTTC T-TTTTC -TTTTTC TTTTTC TTTTTC
52933 AATTTAGGGC
Statistics
Matches: 34, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
5 5 0.15
6 18 0.53
7 10 0.29
8 1 0.03
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (6 bp):
TTTTTC
Found at i:62078 original size:12 final size:12
Alignment explanation
Indices: 62052--62083 Score: 55
Period size: 13 Copynumber: 2.6 Consensus size: 12
62042 AATAATAAAT
62052 AAATAAAAGGAA
1 AAATAAAAGGAA
62064 AAATAGAAAGGAA
1 AAATA-AAAGGAA
62077 AAATAAA
1 AAATAAA
62084 TAAAATAAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
12 7 0.37
13 12 0.63
ACGTcount: A:0.75, C:0.00, G:0.16, T:0.09
Consensus pattern (12 bp):
AAATAAAAGGAA
Found at i:62093 original size:13 final size:13
Alignment explanation
Indices: 62077--62111 Score: 52
Period size: 13 Copynumber: 2.7 Consensus size: 13
62067 TAGAAAGGAA
62077 AAATAAATAAAAT
1 AAATAAATAAAAT
* *
62090 AAATATATTAAAT
1 AAATAAATAAAAT
62103 AAATAAATA
1 AAATAAATA
62112 TGTATATATA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (13 bp):
AAATAAATAAAAT
Done.