Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004512.1 Hibiscus syriacus cultivar Beakdansim tig00009951_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: 52172
ACGTcount: A:0.33, C:0.16, G:0.19, T:0.32
Found at i:5260 original size:54 final size:55
Alignment explanation
Indices: 5106--5325 Score: 259
Period size: 55 Copynumber: 4.0 Consensus size: 55
5096 ATTACCAAAT
*
5106 GGCACT-GAGTGTGCAAAAAGCTAAGAAATTCATACTAAGTGTATGAATTTCCGTATA
1 GGCACTAG-GTGTGC-AAAA-CTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
* * *
5163 AGCACTATGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCTGTATG
1 GGCACTAGGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
5218 GGCACTAGGTGTGC-AAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
1 GGCACTAGGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
* * ** * * * *
5272 GGAAATATATGTACAAATA-TAAGAAGTTCATAATAAGT-TGGTGAATTTCCGTAT
1 GGCACTAGGTGTGCAAA-ACTAAGAAATTCATACTAAGTGT-ATGAATTTCCGTAT
5326 TGGTGTTGGG
Statistics
Matches: 144, Mismatches: 15, Indels: 10
0.85 0.09 0.06
Matches are distributed among these distances:
54 49 0.34
55 79 0.55
56 5 0.03
57 11 0.08
ACGTcount: A:0.37, C:0.12, G:0.20, T:0.31
Consensus pattern (55 bp):
GGCACTAGGTGTGCAAAACTAAGAAATTCATACTAAGTGTATGAATTTCCGTATG
Found at i:5317 original size:109 final size:109
Alignment explanation
Indices: 5126--5325 Score: 278
Period size: 109 Copynumber: 1.8 Consensus size: 109
5116 GTGCAAAAAG
* * * *
5126 CTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAAGCACTATGTGTGCAAAACTAAGAAATT
1 CTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAAGAAATATATGTACAAAACTAAGAAATT
* *
5191 CATACTAAGTGTATGAATTTCTGTATGGGCACTAGGTGTGCAAA
66 CATAATAAGTGTATGAATTTCCGTATGGGCACTAGGTGTGCAAA
** *
5235 CTAAGAAATTCATACTAAGTGTATGAATTTCCGTATGGGAAATATATGTACAAATA-TAAGAAGT
1 CTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAAGAAATATATGTACAAA-ACTAAGAAAT
*
5299 TCATAATAAGT-TGGTGAATTTCCGTAT
65 TCATAATAAGTGT-ATGAATTTCCGTAT
5326 TGGTGTTGGG
Statistics
Matches: 79, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
108 1 0.01
109 77 0.97
110 1 0.01
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.33
Consensus pattern (109 bp):
CTAAGAAATTCATACTAAGTGTATGAATTTCCGTATAAGAAATATATGTACAAAACTAAGAAATT
CATAATAAGTGTATGAATTTCCGTATGGGCACTAGGTGTGCAAA
Found at i:5611 original size:81 final size:81
Alignment explanation
Indices: 5474--6124 Score: 953
Period size: 81 Copynumber: 8.0 Consensus size: 81
5464 ATTCTAAAGT
* * * *
5474 TAAAAGATTAATGTCCAAGCTGTGCATTTGACAGAAAGATGTCAATTATGCTAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
5539 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* *
5555 TAAAATATTAATGACCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
5620 GTTAAATACATTTGAG
66 GTTAAATACCTTTGAG
* *
5636 TAAAAGATTAATGGCCTAGTTGTGCATTTAACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
5701 GTTAAATACATTTGAG
66 GTTAAATACCTTTGAG
* * * * * * *
5717 TAAAAGATTAATGGCCTAGCTATGCATTTGACTGAAAGGCGTCAATAATGCTA-TCAGATGAAAT
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
5781 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * *
5797 TAAAAGATTAATGGCCTATCTGTGCATTTGACCGAAAGGTATCAATTATGCCAGTTAGATGAATG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
5862 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * *
5878 TAAAAGATTAATGGCCTAGATGTGCATTTGACAAAAAGATGTGAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
5943 GTTAAATACCTTTGCG
66 GTTAAATACCTTTGAG
* *
5959 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAT
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
*
6024 GTTAAATGCCTTTGAG
66 GTTAAATACCTTTGAG
* * * ** *
6040 TAAAAGATTAATGGCCTAGCTGTGCATTTGGCATAAATGTGTCAATTATGTAAATTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
* * *
6105 GATAAATGCCTTTGGG
66 GTTAAATACCTTTGAG
6121 TAAA
1 TAAA
6125 GACTAAAGGA
Statistics
Matches: 514, Mismatches: 55, Indels: 2
0.90 0.10 0.00
Matches are distributed among these distances:
80 70 0.14
81 444 0.86
ACGTcount: A:0.36, C:0.12, G:0.22, T:0.31
Consensus pattern (81 bp):
TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:6068 original size:323 final size:323
Alignment explanation
Indices: 5474--6069 Score: 985
Period size: 323 Copynumber: 1.8 Consensus size: 323
5464 ATTCTAAAGT
* * *
5474 TAAAAGATTAATGTCCAAGCTGTGCATTTGACAGAAAGATGTCAATTATGCTAGTTAGATGAAAG
1 TAAAAGATTAATGGCCAAGCTGTGCATTTGACAGAAAGATATCAATTATGCCAGTTAGATGAAAG
* * * *
5539 GTTAAATACCTTTGAGTAAAATATTAATGACCTAGCTGTGCATTTGACAGAAAGGTGTCAATTAT
66 GTTAAATACCTTTGAGTAAAAGATTAATGACCTAGATGTGCATTTGACAAAAAGATGTCAATTAT
*
5604 GCCAGTTAGATGAAAGGTTAAATACATTTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTAACA
131 GCCAGTTAGATGAAAGGTTAAATACATTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTAACA
5669 GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACATTTGAGTAAAAGATTAATGGCCT
196 GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACATTTGAGTAAAAGATTAATGGCCT
5734 AGCTATGCATTTGACTGAAAGGCGTCAATAATGCTATCAGATGAAATGTTAAATACCTTTGAG
261 AGCTATGCATTTGACTGAAAGGCGTCAATAATGCTATCAGATGAAATGTTAAATACCTTTGAG
* * * * *
5797 TAAAAGATTAATGGCCTATCTGTGCATTTGACCGAAAGGTATCAATTATGCCAGTTAGATGAATG
1 TAAAAGATTAATGGCCAAGCTGTGCATTTGACAGAAAGATATCAATTATGCCAGTTAGATGAAAG
* *
5862 GTTAAATACCTTTGAGTAAAAGATTAATGGCCTAGATGTGCATTTGACAAAAAGATGTGAATTAT
66 GTTAAATACCTTTGAGTAAAAGATTAATGACCTAGATGTGCATTTGACAAAAAGATGTCAATTAT
* * *
5927 GCCAGTTAGATGAAAGGTTAAATACCTTTGCGTAAAAGATTAATGGCCTAGCTGTGCATTTGACA
131 GCCAGTTAGATGAAAGGTTAAATACATTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTAACA
* * * *
5992 GAAATGTGTCAATTATGCCAGTTAGATGAAATGTTAAATGCCTTTGAGTAAAAGATTAATGGCCT
196 GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACATTTGAGTAAAAGATTAATGGCCT
*
6057 AGCTGTGCATTTG
261 AGCTATGCATTTG
6070 GCATAAATGT
Statistics
Matches: 250, Mismatches: 23, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
323 250 1.00
ACGTcount: A:0.36, C:0.12, G:0.21, T:0.31
Consensus pattern (323 bp):
TAAAAGATTAATGGCCAAGCTGTGCATTTGACAGAAAGATATCAATTATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAGTAAAAGATTAATGACCTAGATGTGCATTTGACAAAAAGATGTCAATTAT
GCCAGTTAGATGAAAGGTTAAATACATTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTAACA
GAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAATACATTTGAGTAAAAGATTAATGGCCT
AGCTATGCATTTGACTGAAAGGCGTCAATAATGCTATCAGATGAAATGTTAAATACCTTTGAG
Found at i:6148 original size:323 final size:323
Alignment explanation
Indices: 5496--6148 Score: 927
Period size: 323 Copynumber: 2.0 Consensus size: 323
5486 GTCCAAGCTG
* * *
5496 TGCATTTGACAGAAAGATGTCAATTATGCTAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAT
1 TGCATTTGACAGAAAGATATCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAG
* * *
5561 ATTAATGACCTAGCTGTGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAGGTTAAA
66 ATTAATGACCTAGATGTGCATTTGACAAAAAGATGTCAATTATGCCAGTTAGATGAAAGGTTAAA
*
5626 TACATTTGAGTAAAAGATTAATGGCCTAGTTGTGCATTTAACAGAAAGGTGTCAATTATGCCAGT
131 TACATTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTAACAGAAAGGTGTCAATTATGCCAGT
5691 TAGATGAAAGGTTAAATACATTTGAGTAAAAGATTAATGGCCTAGCTATGCATTTGACTGAAAGG
196 TAGATGAAAGGTTAAATACATTTGAGTAAAAGATTAATGGCCTAGCTATGCATTTGACTGAAAGG
* * * * * **
5756 CGTCAATAATGCTATCAGATGAAATGTTAAATACCTTTGAGTAAAAGATTAATGGCCTATCTG
261 CGTCAATAATGCTATCAGATGAAAGGATAAATACCTTTGAGTAAAAGACTAAAGGACTATCAA
* * *
5819 TGCATTTGACCGAAAGGTATCAATTATGCCAGTTAGATGAATGGTTAAATACCTTTGAGTAAAAG
1 TGCATTTGACAGAAAGATATCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAG
* *
5884 ATTAATGGCCTAGATGTGCATTTGACAAAAAGATGTGAATTATGCCAGTTAGATGAAAGGTTAAA
66 ATTAATGACCTAGATGTGCATTTGACAAAAAGATGTCAATTATGCCAGTTAGATGAAAGGTTAAA
* * * *
5949 TACCTTTGCGTAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGT
131 TACATTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTAACAGAAAGGTGTCAATTATGCCAGT
* * * * * *
6014 TAGATGAAATGTTAAATGCCTTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTGGCAT-AAAT
196 TAGATGAAAGGTTAAATACATTTGAGTAAAAGATTAATGGCCTAGCTATGCATTTGAC-TGAAAG
* * * * * *
6078 GTGTCAATTATG-TAAATTAGATGAAAGGATAAATGCCTTTGGGT-AAAGACTAAAGGAATTAT-
260 GCGTCAATAATGCT--ATCAGATGAAAGGATAAATACCTTTGAGTAAAAGACTAAAGG-ACTATC
6140 AA
322 AA
6142 TGCATTT
1 TGCATTT
6149 TTTATAAACA
Statistics
Matches: 291, Mismatches: 35, Indels: 8
0.87 0.10 0.02
Matches are distributed among these distances:
322 1 0.00
323 262 0.90
324 28 0.10
ACGTcount: A:0.36, C:0.11, G:0.21, T:0.31
Consensus pattern (323 bp):
TGCATTTGACAGAAAGATATCAATTATGCCAGTTAGATGAAAGGTTAAATACCTTTGAGTAAAAG
ATTAATGACCTAGATGTGCATTTGACAAAAAGATGTCAATTATGCCAGTTAGATGAAAGGTTAAA
TACATTTGAGTAAAAGATTAATGGCCTAGCTGTGCATTTAACAGAAAGGTGTCAATTATGCCAGT
TAGATGAAAGGTTAAATACATTTGAGTAAAAGATTAATGGCCTAGCTATGCATTTGACTGAAAGG
CGTCAATAATGCTATCAGATGAAAGGATAAATACCTTTGAGTAAAAGACTAAAGGACTATCAA
Found at i:23572 original size:18 final size:19
Alignment explanation
Indices: 23551--23600 Score: 61
Period size: 17 Copynumber: 2.8 Consensus size: 19
23541 TTAACTTCAC
*
23551 TTTTTCTTTTCTTTTCT-T
1 TTTTTCTTTTCTTTTCTGA
23569 TTTTTC-TTT-TTTTCTGA
1 TTTTTCTTTTCTTTTCTGA
*
23586 TTTTTCTCTTCTTTT
1 TTTTTCTTTTCTTTT
23601 TGCACTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
16 6 0.22
17 9 0.33
18 8 0.30
19 4 0.15
ACGTcount: A:0.02, C:0.16, G:0.02, T:0.80
Consensus pattern (19 bp):
TTTTTCTTTTCTTTTCTGA
Found at i:25259 original size:23 final size:25
Alignment explanation
Indices: 25213--25260 Score: 73
Period size: 23 Copynumber: 2.0 Consensus size: 25
25203 ATAGGTATAA
25213 TATACATATATGAAAATAACTATCT
1 TATACATATATGAAAATAACTATCT
*
25238 TATA-ATATATG-AAATAAGTATCT
1 TATACATATATGAAAATAACTATCT
25261 ATAGGTATAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 11 0.50
24 7 0.32
25 4 0.18
ACGTcount: A:0.48, C:0.08, G:0.06, T:0.38
Consensus pattern (25 bp):
TATACATATATGAAAATAACTATCT
Found at i:28439 original size:81 final size:81
Alignment explanation
Indices: 28351--28769 Score: 660
Period size: 81 Copynumber: 5.2 Consensus size: 81
28341 ATTCTAAAGT
* * * *
28351 TAAAAGATTAATGACCTAGCTTTGCATTTGACAGAAATGTGTCAATTATGCAAATTAAATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCAAGTTAGATGAAAG
28416 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* *
28432 TAAAAGATTAATGGCCTAACTGTGCATTTGACAGAAAAGTGTCAATTATGCAAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCAAGTTAGATGAAAG
*
28497 GTTAAATACCGTTGAG
66 GTTAAATACCTTTGAG
*
28513 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCTAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCAAGTTAGATGAAAG
28578 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * *
28594 TAAAAGATTAATGGCATAGCTGTGAATTTGACAGAAATGTTTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCAAGTTAGATGAAAG
*
28659 GTTAAATGCCTTTGAG
66 GTTAAATACCTTTGAG
* *
28675 TAAAAGATTAATAGG-CTAGCTGTGCATTTGACAGAAATGTGTCAATTATGTAAATTAGATGAAA
1 TAAAAGATTAAT-GGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCAAGTTAGATGAAA
* *
28739 GGCTAAATACCTTTGCG
65 GGTTAAATACCTTTGAG
*
28756 TAAAAGACTAATGG
1 TAAAAGATTAATGG
28770 AATTATAATG
Statistics
Matches: 311, Mismatches: 26, Indels: 3
0.91 0.08 0.01
Matches are distributed among these distances:
80 2 0.01
81 307 0.99
82 2 0.01
ACGTcount: A:0.37, C:0.11, G:0.21, T:0.31
Consensus pattern (81 bp):
TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCAAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:34084 original size:18 final size:18
Alignment explanation
Indices: 34043--34085 Score: 54
Period size: 19 Copynumber: 2.4 Consensus size: 18
34033 AAATAAAGAG
34043 AATT-AATTAAAGTAATA
1 AATTAAATTAAAGTAATA
34060 AATTTAAATTAAAGATAA-A
1 AA-TTAAATTAAAG-TAATA
34079 AATTAAA
1 AATTAAA
34086 AACAATTTGT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
17 2 0.09
18 7 0.30
19 11 0.48
20 3 0.13
ACGTcount: A:0.63, C:0.00, G:0.05, T:0.33
Consensus pattern (18 bp):
AATTAAATTAAAGTAATA
Found at i:35492 original size:54 final size:55
Alignment explanation
Indices: 35354--35505 Score: 225
Period size: 55 Copynumber: 2.8 Consensus size: 55
35344 GAGTGTGCGA
* * * *
35354 AAAACTAAGAAATTTATACCAAGTGTATGAATTTTCGTATAGGCACTATGTCTGC
1 AAAACTAAGAAATTCATACCAAGTGTATGAATTTTTGTATGGGCACTAGGTCTGC
* * *
35409 AAAACTAAGAAATTCATACTAAGTATATGAATTTTTGTATGGGCACTAGGTGTGC
1 AAAACTAAGAAATTCATACCAAGTGTATGAATTTTTGTATGGGCACTAGGTCTGC
*
35464 -AAACTAAGAAATTCATACCAAGTGTATGAATTTCTGTATGGG
1 AAAACTAAGAAATTCATACCAAGTGTATGAATTTTTGTATGGG
35506 AAATATATCT
Statistics
Matches: 87, Mismatches: 10, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
54 39 0.45
55 48 0.55
ACGTcount: A:0.37, C:0.12, G:0.18, T:0.32
Consensus pattern (55 bp):
AAAACTAAGAAATTCATACCAAGTGTATGAATTTTTGTATGGGCACTAGGTCTGC
Found at i:35549 original size:109 final size:109
Alignment explanation
Indices: 35355--35551 Score: 263
Period size: 109 Copynumber: 1.8 Consensus size: 109
35345 AGTGTGCGAA
* * * * *
35355 AAACTAAGAAATTTATACCAAGTGTATGAATTTTCGTATAGGCACTATGTCTGCAAAACTAAGAA
1 AAACTAAGAAATTCATACCAAGTGTATGAATTTTCGTATAGGAAATATATCTACAAAACTAAGAA
* *
35420 ATTCATACTAAGTATATGAATTTTTGTATGGGCACTAGGTGTGC
66 ATTCATAATAAGTAGATGAATTTTTGTATGGGCACTAGGTGTGC
* *
35464 AAACTAAGAAATTCATACCAAGTGTATGAA-TTTCTGTATGGGAAATATATCTACTAATA-TAAG
1 AAACTAAGAAATTCATACCAAGTGTATGAATTTTC-GTATAGGAAATATATCTAC-AAAACTAAG
* *
35527 AAGTTCATAATAAGTAGGTGAATTT
64 AAATTCATAATAAGTAGATGAATTT
35552 CCATATTGGT
Statistics
Matches: 75, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
108 4 0.05
109 68 0.91
110 3 0.04
ACGTcount: A:0.39, C:0.11, G:0.17, T:0.33
Consensus pattern (109 bp):
AAACTAAGAAATTCATACCAAGTGTATGAATTTTCGTATAGGAAATATATCTACAAAACTAAGAA
ATTCATAATAAGTAGATGAATTTTTGTATGGGCACTAGGTGTGC
Found at i:35844 original size:81 final size:81
Alignment explanation
Indices: 35706--37003 Score: 1797
Period size: 81 Copynumber: 16.1 Consensus size: 81
35696 ATTCTAAAGT
* *
35706 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAAGGTGTCATTTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
35771 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * **
35787 TATAAGATTATTGGCCTAGCTGTGCATTTGTTAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
*
35852 GTTAAATACCTTTGTG
66 GTTAAATACCTTTGAG
* *
35868 TAAAAGATTAATGGCCTAGTTGTGCATTTGACAGAAATGTGTCAATTATGTCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
35933 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * *
35949 TAAAAGATTAATGGCCTAACTATGCATTTGACAGAAAGGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
*
36014 GTTAAATACCTCTGAG
66 GTTAAATACCTTTGAG
* * * * *
36030 TATAAGATTAATGGTCAAGCTGTGTATTTGACAAAAATGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
*
36095 TTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * * *
36111 TAAAATATTAATGGCTTAGTTGTGCATTTGACAGAAAGGTGTCAGTTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
*
36176 GTTAAATACTTTTGAG
66 GTTAAATACCTTTGAG
* * * *
36192 TAAAAGATTAATGGCCTAGATGTTCATTTGACATAAA-GT-TACCAATTATGTCAGTTAGATGAA
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGT--CAATTATGCCAGTTAGATGAA
*
36255 AGGTTAAATACCATTGAG
64 AGGTTAAATACCTTTGAG
36273 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
36338 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * **
36354 TAAATGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATCATG-TTGTTTAGATGAAA
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAG-TTAGATGAAA
*
36418 GGTTAAATACTTTTGAG
65 GGTTAAATACCTTTGAG
* * *
36435 TAAAAGATTAATGACCTAACTATGCATTTGACAGAAA-GTTGTCAATTATGCCAGTTAGATGAAA
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATG-TGTCAATTATGCCAGTTAGATGAAA
*
36499 GATTAAATACCTTTGAG
65 GGTTAAATACCTTTGAG
*
36516 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATATGTCAATTATGCCAGTTAGATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
36581 GTTAAATACCTTTGAG
66 GTTAAATACCTTTGAG
* * * ** * * *
36597 TAAAAGATTAATGGCCTAGTTGTGCATTTGACTGAAAGGTGTCCCTTATGTCTGTTATATGAAAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
36662 GTT-AATACCTTTGAG
66 GTTAAATACCTTTGAG
*
36677 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAA-GTGTCAATTATGCCAGTTAGATGAAAT
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
* *
36741 GTTAAATACATATGAG
66 GTTAAATACCTTTGAG
* * * * *
36757 TAAAAGATTAATGGACTAGTTTTGCATTTGATAGAAA-GATGTCTATTATGCCAGTTAGATGAAA
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATG-TGTCAATTATGCCAGTTAGATGAAA
36821 GGTT--ATACCTTTGAG
65 GGTTAAATACCTTTGAG
* * * ** * * *
36836 TAAAAGATTAATGGCCTAACCGTGCATATGACAGAAAAATGTTAATTATGCTAGTTAGATGATAG
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
* *
36901 GTTAAATGCATTTGAG
66 GTTAAATACCTTTGAG
* * * * ** *
36917 TAAAAGATTAATAGCCTAGCTGTGCATTTGGCAGAAAGGT-TCAATCATGTAAGTTAGATGAAAT
1 TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
* * *
36981 GCTAAATGCCTTTGGG
66 GTTAAATACCTTTGAG
36997 TAAAAGA
1 TAAAAGA
37004 CTAAAGGAAT
Statistics
Matches: 1072, Mismatches: 132, Indels: 27
0.87 0.11 0.02
Matches are distributed among these distances:
79 89 0.08
80 133 0.12
81 846 0.79
82 3 0.00
83 1 0.00
ACGTcount: A:0.35, C:0.11, G:0.21, T:0.33
Consensus pattern (81 bp):
TAAAAGATTAATGGCCTAGCTGTGCATTTGACAGAAATGTGTCAATTATGCCAGTTAGATGAAAG
GTTAAATACCTTTGAG
Found at i:39655 original size:42 final size:42
Alignment explanation
Indices: 39553--39709 Score: 136
Period size: 43 Copynumber: 3.7 Consensus size: 42
39543 ATATTGGCGT
* * * * *
39553 TGATTCAACTCCATGTGTAAAGAATCAAACAAAAGATTTTCAC
1 TGATCCAACTCCTTCTGTGAAGAATCAAATAAAAGATTTT-AC
* *
39596 TGATCCAACTTCTTCTGTGAAGAATCAAATGAAAGATTGTTA-
1 TGATCCAACTCCTTCTGTGAAGAATCAAATAAAAGATT-TTAC
* * * ** *
39638 TGATCCAACTCCTTCTGTGAAGGACCAAGTAAAATGATAAATAT
1 TGATCCAACTCCTTCTGTGAAGAATCAAATAAAA-GAT-TTTAC
* *
39682 TGATCTAACTCATTCTGTGAAGAATCAA
1 TGATCCAACTCCTTCTGTGAAGAATCAA
39710 GAAAAATGTC
Statistics
Matches: 92, Mismatches: 18, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
42 29 0.32
43 37 0.40
44 26 0.28
ACGTcount: A:0.38, C:0.17, G:0.15, T:0.30
Consensus pattern (42 bp):
TGATCCAACTCCTTCTGTGAAGAATCAAATAAAAGATTTTAC
Found at i:40031 original size:122 final size:117
Alignment explanation
Indices: 39737--40085 Score: 423
Period size: 122 Copynumber: 2.9 Consensus size: 117
39727 ATCTATTTTT
* * *
39737 TTCTATGATAGAATCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCTTCTT
1 TTCTGTGATAGAATCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCAT
* * * *
39802 TGGATGAGTTCTTCTCATTATGATCTCCCCATTAGAAATGTTGA-TTCATCTCA
66 CGGATGAGTTCTTCTCATTATGAACT--CTATTGGAAATGTTGATTTCATCTCA
* * * * *
39855 TTCTGTGATGGAATCAAAC-TAAGGTTGATCAAGTTCTTCTCATTATGAATTTCTTCTTCCTCAT
1 TTCTGTGATAGAATCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCAT
* *
39919 CGGATGAGTTCTTCTCATTATAAACTCTATTGGAAATGTTGATGCTTGTCTATCTCC
66 CGGATGAGTTCTTCTCATTATGAACTCTATTGGAAATGTTGA---TT-TC-ATCTCA
* * *
39976 TTCTGTGATAGAGTCGAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCAT
1 TTCTGTGATAGAATCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCAT
* * *
40041 CGAATGAGTTATTCTCATTATGAACTCTCCATTGAAAATGTTGAT
66 CGGATGAGTTCTTCTCATTATGAACTCT--ATTGGAAATGTTGAT
40086 CCCTCGAGTG
Statistics
Matches: 196, Mismatches: 26, Indels: 15
0.83 0.11 0.06
Matches are distributed among these distances:
115 14 0.07
117 63 0.32
118 16 0.08
119 1 0.01
120 2 0.01
121 21 0.11
122 66 0.34
124 13 0.07
ACGTcount: A:0.26, C:0.19, G:0.15, T:0.39
Consensus pattern (117 bp):
TTCTGTGATAGAATCAAGCAAAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTTCCTCAT
CGGATGAGTTCTTCTCATTATGAACTCTATTGGAAATGTTGATTTCATCTCA
Found at i:40575 original size:139 final size:139
Alignment explanation
Indices: 39997--41035 Score: 1488
Period size: 138 Copynumber: 7.5 Consensus size: 139
39987 AGTCGAGCAA
* *
39997 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGAATGAGTTATTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTAT
* * *
40062 GAACTCTCCATTGAAAATGTTGATCCCTCGAGTGA-AGG--ACGTGATTCAACTCCATATGCGAT
66 GAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGGGTCAC-TGATTCAACTCCATATGCGAT
**
40124 GAATCGAATT
130 GAATCGAGCT
* * *
40134 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCTTCATCAGATGAGTTCTTCTCATTTT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTAT
* ** * * * * *
40199 GAAATCTCCACTAAAAATGTTGATCCCTTGAGTAAAGTGTCACTGATTTAACTCCATATGCGATG
66 GAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGGGTCACTGATTCAACTCCATATGCGATG
40264 AATCGAGCT
131 AATCGAGCT
* * *
40273 AAGGTTGAACAAGTTCTTCTCATTATGAACTTC-TCTCTCTCATCGGATGAGTTATTATCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTAT
*
40337 GAACTCTCCA-TAGGAAATGTTGATCACTCGAGTGAGGGGTCACT-ATTCAACTCCATATGCGAT
66 GAACTCTCCACT-GGAAATGTTGATCCCTCGAGTGAGGGGTCACTGATTCAACTCCATATGCGAT
*
40400 GAATCGAGCG
130 GAATCGAGCT
*
40410 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATTAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTAT
* * *
40475 GAACTATCCACTGGAAATGTTGATCCCTCGAGTGAGGGGTCATTGATTCAACTCGATATGCGATG
66 GAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGGGTCACTGATTCAACTCCATATGCGATG
40540 AATCGAGCT
131 AATCGAGCT
40549 AAGGTT-AATCAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATC-GATGAGTTCTTCTCATTA
1 AAGGTTGAA-CAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTA
* * * * * * * *
40612 TAAAATCTCCACTAGAAATATTGATCTCTCGAGTTAGGGGTC-GTCGATTCAACTCCATATGTGA
65 TGAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGGGTCACT-GATTCAACTCCATATGCGA
40676 TGAATCGAGCT
129 TGAATCGAGCT
*
40687 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTC-CCCTCATCGAATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTAT
* * * *
40751 GAACTCTCCACTGTAGATGTTGATCCCTCGAGTGAGGGGTCACTGATTCAACTCCATTTGCAATG
66 GAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGGGTCACTGATTCAACTCCATATGCGATG
40816 AATCGAGCT
131 AATCGAGCT
* *
40825 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTTTCCCTCACCGGATGAGTTCTTCTCATTAT
1 AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTAT
* * * *
40890 GAACTCTCCACTGGAAATATTGATCCCTCGAGTAAGGAGTCGCTGATTCAACTCCATATGCGATG
66 GAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGGGTCACTGATTCAACTCCATATGCGATG
40955 AATCGAGCT
131 AATCGAGCT
* * * * *
40964 AAGGTTGGAA-AAGTTATTCTCATTATAAACTTCTTCTTCCTTATCAGATGAGTTCTTCTCATTA
1 AAGGTT-GAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTA
*
41028 TAAACTCT
65 TGAACTCT
41036 ATATTGAAAT
Statistics
Matches: 805, Mismatches: 83, Indels: 26
0.88 0.09 0.03
Matches are distributed among these distances:
137 160 0.20
138 354 0.44
139 286 0.36
140 5 0.01
ACGTcount: A:0.27, C:0.22, G:0.17, T:0.34
Consensus pattern (139 bp):
AAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTCATTAT
GAACTCTCCACTGGAAATGTTGATCCCTCGAGTGAGGGGTCACTGATTCAACTCCATATGCGATG
AATCGAGCT
Found at i:42999 original size:23 final size:21
Alignment explanation
Indices: 42972--43046 Score: 75
Period size: 21 Copynumber: 3.6 Consensus size: 21
42962 CCATGCTATA
42972 TTTTTCTTCTCGTTCTTCTTCTC
1 TTTTTCTT-TC-TTCTTCTTCTC
*
42995 TTTTTCTTT-TTCTTTTTCT-
1 TTTTTCTTTCTTCTTCTTCTC
* *
43014 TTTTTCTTTCTTTTTTCTTTTC
1 TTTTTCTTTC-TTCTTCTTCTC
43036 -TTTTCTTTCTT
1 TTTTTCTTTCTT
43047 TTTTTTCTTT
Statistics
Matches: 45, Mismatches: 4, Indels: 9
0.78 0.07 0.16
Matches are distributed among these distances:
19 9 0.20
20 11 0.24
21 16 0.36
22 1 0.02
23 8 0.18
ACGTcount: A:0.00, C:0.21, G:0.01, T:0.77
Consensus pattern (21 bp):
TTTTTCTTTCTTCTTCTTCTC
Found at i:43016 original size:18 final size:18
Alignment explanation
Indices: 42993--43056 Score: 71
Period size: 17 Copynumber: 3.6 Consensus size: 18
42983 GTTCTTCTTC
42993 TCTTTTTCTTTTTCTTTT
1 TCTTTTTCTTTTTCTTTT
*
43011 TCTTTTT-TCTTTCTTTT
1 TCTTTTTCTTTTTCTTTT
43028 T-TCTTTTC-TTTTCTTTCT
1 TCT-TTTTCTTTTTCTTT-T
*
43046 TTTTTTTCTTT
1 TCTTTTTCTTT
43057 AAAAGAGCTA
Statistics
Matches: 39, Mismatches: 2, Indels: 9
0.78 0.04 0.18
Matches are distributed among these distances:
16 1 0.03
17 21 0.54
18 14 0.36
19 3 0.08
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (18 bp):
TCTTTTTCTTTTTCTTTT
Found at i:43050 original size:11 final size:11
Alignment explanation
Indices: 42997--43050 Score: 74
Period size: 11 Copynumber: 4.9 Consensus size: 11
42987 TTCTTCTCTT
*
42997 TTTCTTTTTCTT
1 TTTCTTTTT-TC
43009 TTTCTTTTTTC
1 TTTCTTTTTTC
43020 TTTCTTTTTTC
1 TTTCTTTTTTC
*
43031 TTT-TCTTTTC
1 TTTCTTTTTTC
43041 TTTCTTTTTT
1 TTTCTTTTTT
43051 TTCTTTAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
10 9 0.24
11 20 0.53
12 9 0.24
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (11 bp):
TTTCTTTTTTC
Found at i:43056 original size:23 final size:24
Alignment explanation
Indices: 42984--43055 Score: 84
Period size: 23 Copynumber: 3.2 Consensus size: 24
42974 TTTCTTCTCG
*
42984 TTCTTCTTCTCTT-TTTCTTTTTCT
1 TTCTTCTTCTTTTCTTTCTTTTT-T
43008 TT-TTCTT-TTTTCTTTC--TTTT
1 TTCTTCTTCTTTTCTTTCTTTTTT
43028 TTCTT-TTCTTTTCTTTCTTTTTT
1 TTCTTCTTCTTTTCTTTCTTTTTT
43051 TTCTT
1 TTCTT
43056 TAAAAGAGCT
Statistics
Matches: 42, Mismatches: 1, Indels: 11
0.78 0.02 0.20
Matches are distributed among these distances:
20 5 0.12
21 14 0.33
22 3 0.07
23 18 0.43
24 2 0.05
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (24 bp):
TTCTTCTTCTTTTCTTTCTTTTTT
Found at i:45545 original size:20 final size:20
Alignment explanation
Indices: 45520--45569 Score: 57
Period size: 20 Copynumber: 2.5 Consensus size: 20
45510 AGTTTTAAAC
* *
45520 AAAATGCAAAT-GAAATGTAA
1 AAAATGCAAATACAAACGT-A
*
45540 AAAATGAAAATACAAACGTA
1 AAAATGCAAATACAAACGTA
45560 AAAATGCAAA
1 AAAATGCAAA
45570 GGTGTGAATG
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
20 20 0.80
21 5 0.20
ACGTcount: A:0.64, C:0.08, G:0.12, T:0.16
Consensus pattern (20 bp):
AAAATGCAAATACAAACGTA
Found at i:45579 original size:14 final size:14
Alignment explanation
Indices: 45562--45597 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
45552 CAAACGTAAA
*
45562 AATGCAAAGGTGTG
1 AATGCAAAGGTGCG
*
45576 AATGCATAGGTGCG
1 AATGCAAAGGTGCG
45590 AATGCAAA
1 AATGCAAA
45598 TGCAACGGAG
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.39, C:0.11, G:0.31, T:0.19
Consensus pattern (14 bp):
AATGCAAAGGTGCG
Done.