Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004081.1 Hibiscus syriacus cultivar Beakdansim tig00008932_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: 181177
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3375 original size:17 final size:17
Alignment explanation
Indices: 3351--3391 Score: 73
Period size: 17 Copynumber: 2.4 Consensus size: 17
3341 CATTTAAATT
3351 AATGATCAGATTGATAA
1 AATGATCAGATTGATAA
*
3368 AGTGATCAGATTGATAA
1 AATGATCAGATTGATAA
3385 AATGATC
1 AATGATC
3392 TAACCTACAC
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.44, C:0.07, G:0.20, T:0.29
Consensus pattern (17 bp):
AATGATCAGATTGATAA
Found at i:4497 original size:24 final size:24
Alignment explanation
Indices: 4470--4534 Score: 78
Period size: 24 Copynumber: 2.7 Consensus size: 24
4460 AATTTAAAGT
**
4470 ATATATAAATTATATATTTTTAAA
1 ATATATAAATTATATATTAATAAA
*
4494 ATATA-AAATTAAATAATTAATAAA
1 ATATATAAATTATAT-ATTAATAAA
*
4518 ATATCTAAATTATATAT
1 ATATATAAATTATATAT
4535 AAATTTAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 4
0.79 0.12 0.09
Matches are distributed among these distances:
23 8 0.24
24 18 0.53
25 8 0.24
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (24 bp):
ATATATAAATTATATATTAATAAA
Found at i:9751 original size:38 final size:37
Alignment explanation
Indices: 9662--9751 Score: 119
Period size: 38 Copynumber: 2.4 Consensus size: 37
9652 TCAGGTCGGG
9662 TATATATATAT-ATTTAAATTAAATATATAAATATTA
1 TATATATATATAATTTAAATTAAATATATAAATATTA
* * * *
9698 TATATATTTTTTAATTTAAATTAAATTTATTAATATTA
1 TATATA-TATATAATTTAAATTAAATATATAAATATTA
9736 TATATATATAATAATT
1 TATATATAT-ATAATT
9752 ATTTTTAATA
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
36 6 0.13
37 5 0.11
38 34 0.76
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (37 bp):
TATATATATATAATTTAAATTAAATATATAAATATTA
Found at i:11539 original size:25 final size:25
Alignment explanation
Indices: 11471--11551 Score: 90
Period size: 25 Copynumber: 3.2 Consensus size: 25
11461 GATAAGTTCA
* * *
11471 GTTCGGGTTGGACCAGTACGGTTCG
1 GTTCGGGCTGGACCAGTTCGGTTTG
* **
11496 ATTCGGGCTGGATAAGTTCGGTTTG
1 GTTCGGGCTGGACCAGTTCGGTTTG
* *
11521 GTTCGGGCTGGACCGGTTCAGTTTG
1 GTTCGGGCTGGACCAGTTCGGTTTG
11546 GTTCGG
1 GTTCGG
11552 ACGAGTTTGG
Statistics
Matches: 45, Mismatches: 11, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
25 45 1.00
ACGTcount: A:0.11, C:0.17, G:0.40, T:0.32
Consensus pattern (25 bp):
GTTCGGGCTGGACCAGTTCGGTTTG
Found at i:14243 original size:29 final size:29
Alignment explanation
Indices: 14197--14275 Score: 124
Period size: 29 Copynumber: 2.7 Consensus size: 29
14187 TACTGCTACG
14197 GGTGTTAGATCGAG-AAATATAATCTCACC
1 GGTGTTAGATCG-GTAAATATAATCTCACC
*
14226 GGTGTTAGATCGGTAAATATAATCTGACC
1 GGTGTTAGATCGGTAAATATAATCTCACC
*
14255 AGTGTTAGATCGGTAAATATA
1 GGTGTTAGATCGGTAAATATA
14276 CCGATCACCG
Statistics
Matches: 47, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
28 1 0.02
29 46 0.98
ACGTcount: A:0.34, C:0.13, G:0.23, T:0.30
Consensus pattern (29 bp):
GGTGTTAGATCGGTAAATATAATCTCACC
Found at i:28147 original size:17 final size:17
Alignment explanation
Indices: 28123--28170 Score: 55
Period size: 16 Copynumber: 2.9 Consensus size: 17
28113 ATTTCGGTTG
28123 TAAATGACTTATTGTAA
1 TAAATGACTTATTGTAA
* *
28140 TTAATGACCTCA--GTAA
1 TAAATGA-CTTATTGTAA
28156 TAAATGACTTATTGT
1 TAAATGACTTATTGT
28171 TAACATCTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 6
0.71 0.12 0.18
Matches are distributed among these distances:
15 3 0.12
16 10 0.42
17 8 0.33
18 3 0.12
ACGTcount: A:0.38, C:0.10, G:0.12, T:0.40
Consensus pattern (17 bp):
TAAATGACTTATTGTAA
Found at i:37833 original size:2 final size:2
Alignment explanation
Indices: 37826--37873 Score: 96
Period size: 2 Copynumber: 24.0 Consensus size: 2
37816 CCGACCCGAT
37826 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
37868 TA TA TA
1 TA TA TA
37874 CACTATTTTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 46 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:37904 original size:34 final size:34
Alignment explanation
Indices: 37866--37950 Score: 125
Period size: 34 Copynumber: 2.5 Consensus size: 34
37856 TATATATATA
* *
37866 TATATATACACTATTTTATACTTTTTATACTAAT
1 TATATATAAAATATTTTATACTTTTTATACTAAT
* * *
37900 TATATATATAATATTTTATATTTTTTATATTAAT
1 TATATATAAAATATTTTATACTTTTTATACTAAT
37934 TATATATAAAATATTTT
1 TATATATAAAATATTTT
37951 CGGGTTCGGG
Statistics
Matches: 46, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
34 46 1.00
ACGTcount: A:0.39, C:0.05, G:0.00, T:0.56
Consensus pattern (34 bp):
TATATATAAAATATTTTATACTTTTTATACTAAT
Found at i:38836 original size:30 final size:30
Alignment explanation
Indices: 38745--38843 Score: 117
Period size: 30 Copynumber: 3.3 Consensus size: 30
38735 CTAAGTTGTA
* * * *
38745 ATTTGATTATAATAATTGATAAATTGAATA
1 ATTTAATTATAATAATTAATAAATTAAATG
* *
38775 ATTTAATTATTATAATTAATAAATTAGATG
1 ATTTAATTATAATAATTAATAAATTAAATG
* *
38805 ATTTAGTTATCATAATTAATAAATTAAATG
1 ATTTAATTATAATAATTAATAAATTAAATG
*
38835 ATCTAATTA
1 ATTTAATTA
38844 ATATATTTTT
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
30 58 1.00
ACGTcount: A:0.46, C:0.02, G:0.07, T:0.44
Consensus pattern (30 bp):
ATTTAATTATAATAATTAATAAATTAAATG
Found at i:42762 original size:3 final size:3
Alignment explanation
Indices: 42754--42838 Score: 163
Period size: 3 Copynumber: 28.7 Consensus size: 3
42744 GAAAACAATG
42754 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
42802 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA -AA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
42839 CCGGTTGTTA
Statistics
Matches: 81, Mismatches: 0, Indels: 2
0.98 0.00 0.02
Matches are distributed among these distances:
2 2 0.02
3 79 0.98
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:43210 original size:50 final size:50
Alignment explanation
Indices: 43152--43252 Score: 202
Period size: 50 Copynumber: 2.0 Consensus size: 50
43142 TTTAGTCCCT
43152 AACTCCACTATATTGAAAAAGATATAAGGAAAATGAGAACCGGGTAAGCG
1 AACTCCACTATATTGAAAAAGATATAAGGAAAATGAGAACCGGGTAAGCG
43202 AACTCCACTATATTGAAAAAGATATAAGGAAAATGAGAACCGGGTAAGCG
1 AACTCCACTATATTGAAAAAGATATAAGGAAAATGAGAACCGGGTAAGCG
43252 A
1 A
43253 TCTTATAAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 51 1.00
ACGTcount: A:0.47, C:0.14, G:0.22, T:0.18
Consensus pattern (50 bp):
AACTCCACTATATTGAAAAAGATATAAGGAAAATGAGAACCGGGTAAGCG
Found at i:46621 original size:13 final size:13
Alignment explanation
Indices: 46603--46629 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
46593 AAGAGAAAAC
46603 GTAGAAGAAAGAA
1 GTAGAAGAAAGAA
46616 GTAGAAGAAAGAA
1 GTAGAAGAAAGAA
46629 G
1 G
46630 CCAAATAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.59, C:0.00, G:0.33, T:0.07
Consensus pattern (13 bp):
GTAGAAGAAAGAA
Found at i:50988 original size:2 final size:2
Alignment explanation
Indices: 50975--51032 Score: 89
Period size: 2 Copynumber: 29.0 Consensus size: 2
50965 TGTAAATAAT
* * *
50975 TA TA TA TG TA TA TA TA TA TA TA TG TT 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
51017 TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA
51033 AATTTAAATG
Statistics
Matches: 51, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
2 51 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:51895 original size:59 final size:58
Alignment explanation
Indices: 51786--51900 Score: 135
Period size: 59 Copynumber: 2.0 Consensus size: 58
51776 ATTGAAAGAC
* * * * *
51786 TATTTTATAACTTTTAATAATTTAAGAACTTGACAAAATAATTTTCTATAATAGAAAAA
1 TATTTTATAACATTTAATAATTTAAAAAATTAACAAAATAAGTTTCTATAAT-GAAAAA
*
51845 TATTTTATAACATTTAATAA-TTAAAAAATTCAATAAAATAACGTTT-TATAATGAAA
1 TATTTTATAACATTTAATAATTTAAAAAATT-AACAAAATAA-GTTTCTATAATGAAA
51901 TAAAAAAAGT
Statistics
Matches: 48, Mismatches: 6, Indels: 5
0.81 0.10 0.08
Matches are distributed among these distances:
58 12 0.25
59 33 0.69
60 3 0.06
ACGTcount: A:0.50, C:0.06, G:0.04, T:0.40
Consensus pattern (58 bp):
TATTTTATAACATTTAATAATTTAAAAAATTAACAAAATAAGTTTCTATAATGAAAAA
Found at i:52416 original size:2 final size:2
Alignment explanation
Indices: 52405--52433 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
52395 AATATAAAAC
52405 AT AT -T 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
52434 TATGTGTTAT
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:53652 original size:15 final size:16
Alignment explanation
Indices: 53634--53663 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
53624 ATATTAATAA
53634 TTTTTTTAT-TATTCT
1 TTTTTTTATATATTCT
53649 TTTTTTTATATATTC
1 TTTTTTTATATATTC
53664 AATTTTATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.17, C:0.07, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTTTTTATATATTCT
Found at i:53655 original size:16 final size:17
Alignment explanation
Indices: 53634--53678 Score: 51
Period size: 15 Copynumber: 2.7 Consensus size: 17
53624 ATATTAATAA
53634 TTTTTTTAT-TATTC-T
1 TTTTTTTATATATTCAT
53649 TTTTTTTATATATTCAAT
1 TTTTTTTATATATTC-AT
53667 TTTATTTT-TATA
1 TTT-TTTTATATA
53679 ATCTAATATT
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 9 0.35
16 5 0.19
18 8 0.31
19 4 0.15
ACGTcount: A:0.22, C:0.04, G:0.00, T:0.73
Consensus pattern (17 bp):
TTTTTTTATATATTCAT
Found at i:68421 original size:6 final size:6
Alignment explanation
Indices: 68368--68401 Score: 68
Period size: 6 Copynumber: 5.7 Consensus size: 6
68358 TCTGTCATAC
68368 ATACAT ATACAT ATACAT ATACAT ATACAT ATAC
1 ATACAT ATACAT ATACAT ATACAT ATACAT ATAC
68402 TTCTATATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 28 1.00
ACGTcount: A:0.50, C:0.18, G:0.00, T:0.32
Consensus pattern (6 bp):
ATACAT
Found at i:74474 original size:17 final size:17
Alignment explanation
Indices: 74441--74498 Score: 57
Period size: 17 Copynumber: 3.4 Consensus size: 17
74431 GGGTTCGAGC
*
74441 TATAATATTAACA-ATAT
1 TATAATTTTAA-ATATAT
74458 TATAATTTTAAATATAT
1 TATAATTTTAAATATAT
*
74475 TTTAATTTATAAAT-TAT
1 TATAATTT-TAAATATAT
*
74492 GATAATT
1 TATAATT
74499 AATATCTAAA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
16 1 0.03
17 29 0.83
18 5 0.14
ACGTcount: A:0.47, C:0.02, G:0.02, T:0.50
Consensus pattern (17 bp):
TATAATTTTAAATATAT
Found at i:76378 original size:2 final size:2
Alignment explanation
Indices: 76371--76415 Score: 90
Period size: 2 Copynumber: 22.5 Consensus size: 2
76361 AAAAACTTTA
76371 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
76413 AT A
1 AT A
76416 CTTCATTTTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:91352 original size:2 final size:2
Alignment explanation
Indices: 91345--91372 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
91335 TTAAATTGAA
91345 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
91373 GGGGTATTAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:94057 original size:423 final size:423
Alignment explanation
Indices: 92799--94060 Score: 2382
Period size: 423 Copynumber: 3.0 Consensus size: 423
92789 TTTAGTTCGA
92799 ACAAAAAAGATAACATTCACTAAAGCTATAGAAATACAATACAATCCAACAACCTAGGATTTGAG
1 ACAAAAAAGATAACATTCACTAAAGCTATAGAAATACAATACAATCCAACAACCTAGGATTTGAG
*
92864 TAACCCTAAAATCATGCAAGTAACCTGAAATATATATAAAAAGAAATCGAGATTGGAAAACAGAA
66 TAACCCTAAAATCATGCAAGTAACCTGAAATATAT-GAAAAAGAAATCGAGATTGGAAAACAGAA
*
92929 CAAGAAACAGCTAAACAATGGAGAAGATGAGATGGAAACAACACATGTGGTAGAGTTAGTTACTT
130 CAAGAAACAGCTAAACAATGGAGAAGATGAGATGGCAACAACACATGTGGTAGAGTTAGTTACTT
* *
92994 GCAATTAGAATGAGCTAAAACGTTTTACTTAACCAAATCAACACTATATTCAAATATGTGCATTT
195 GCAATTAGAATGAGCTAAAACGTGTTACTTAACCAAATCAACACTATATTCAAATATGTGCATTC
93059 GAGTGGGTTTTCAAACATAATCATCCAAAGCAAATGCAATATAATTCGAGATGAGTGGTAACGAT
260 GAGTGGGTTTTCAAACATAATCATCCAAAGCAAATGCAATATAATTCGAGATGAGTGGTAACGAT
*
93124 ATACAATTTATGACAACAACAACATCGAAATAAG-AAAGTACAAGATCAACTTTAGCTCAGTGAG
325 ATACAATTTATGACAACAACAACATCGAAAGAAGAAAAGTACAAGATCAACTTTAGCTCAGTGAG
93188 ATATGTTACAAAAATTTCCAGAAGTTATAGAAAT
390 ATATGTTACAAAAATTTCCAGAAGTTATAGAAAT
*
93222 ACAAAAAAGATAACATTCACTAAAGCTATAGAAATACAATGCAATCCAACAACCTAGGATTTGAG
1 ACAAAAAAGATAACATTCACTAAAGCTATAGAAATACAATACAATCCAACAACCTAGGATTTGAG
*
93287 TAACCCTAAATTCATGCAAGTAACCTGAAATATATGAAAAAGAAATCGAGATTGGAAAACAGAAC
66 TAACCCTAAAATCATGCAAGTAACCTGAAATATATGAAAAAGAAATCGAGATTGGAAAACAGAAC
93352 AAGAAACAGCTAAACAATGGAGAAGATGAGATGGCAACAACACATGTGGTAGAGTTAGTTACTTG
131 AAGAAACAGCTAAACAATGGAGAAGATGAGATGGCAACAACACATGTGGTAGAGTTAGTTACTTG
93417 CAATTAGAATGAGCTAAAACGTGTTACTTAACCAAATCAACACTATATTCAAATATGTGCATTCG
196 CAATTAGAATGAGCTAAAACGTGTTACTTAACCAAATCAACACTATATTCAAATATGTGCATTCG
*
93482 AGTGGGTTTTCAAACATAATCATCCAAAGCAAATGCAATATAATTCGAGATGTGTGGTAACGATA
261 AGTGGGTTTTCAAACATAATCATCCAAAGCAAATGCAATATAATTCGAGATGAGTGGTAACGATA
*
93547 TACAATTTATGACAACAACAACATCAAAAGAAGAAAAGTACAAGATCAACTTTAGCTCAGTGAGA
326 TACAATTTATGACAACAACAACATCGAAAGAAGAAAAGTACAAGATCAACTTTAGCTCAGTGAGA
93612 TATGTTACAAAAATTTCCAGAAGTTATAGAAAT
391 TATGTTACAAAAATTTCCAGAAGTTATAGAAAT
*
93645 ACAAAAAAGATAACATTCACTAAAGCAATAGAAATACAATACAATCCAACAACCTAGGATTTGAG
1 ACAAAAAAGATAACATTCACTAAAGCTATAGAAATACAATACAATCCAACAACCTAGGATTTGAG
93710 TAACCCTAAAATCATGCAAGTAACCTGAAATATATGAAAAAGAAATCGAGATTGGAAAACAGAAC
66 TAACCCTAAAATCATGCAAGTAACCTGAAATATATGAAAAAGAAATCGAGATTGGAAAACAGAAC
93775 AAGAAACAGCTAAACAATGGAGAAGATGAGATGGCAACAACACATGTGGTAGAGTTAGTTACTTG
131 AAGAAACAGCTAAACAATGGAGAAGATGAGATGGCAACAACACATGTGGTAGAGTTAGTTACTTG
93840 CAATTAGAATGAGCTAAAACGTGTTACTTAACCAAATCAACACTATATTCAAATATGTGCATTCG
196 CAATTAGAATGAGCTAAAACGTGTTACTTAACCAAATCAACACTATATTCAAATATGTGCATTCG
* *
93905 AGTGGGTTTTCAAACATAATCATCCAAAGCAAATGCAATATACTTCGAGATGAGTGGCAACGATA
261 AGTGGGTTTTCAAACATAATCATCCAAAGCAAATGCAATATAATTCGAGATGAGTGGTAACGATA
*
93970 TACAATTTATGACAACAACATCATCGAAAGAAGAAAAGTACAAGATCAACTTTAGCTCAGTGAGA
326 TACAATTTATGACAACAACAACATCGAAAGAAGAAAAGTACAAGATCAACTTTAGCTCAGTGAGA
*
94035 TATGATACAAAAATTTCCAGAAGTTA
391 TATGTTACAAAAATTTCCAGAAGTTA
94061 AACAAATAAC
Statistics
Matches: 820, Mismatches: 18, Indels: 2
0.98 0.02 0.00
Matches are distributed among these distances:
422 251 0.31
423 569 0.69
ACGTcount: A:0.45, C:0.15, G:0.16, T:0.23
Consensus pattern (423 bp):
ACAAAAAAGATAACATTCACTAAAGCTATAGAAATACAATACAATCCAACAACCTAGGATTTGAG
TAACCCTAAAATCATGCAAGTAACCTGAAATATATGAAAAAGAAATCGAGATTGGAAAACAGAAC
AAGAAACAGCTAAACAATGGAGAAGATGAGATGGCAACAACACATGTGGTAGAGTTAGTTACTTG
CAATTAGAATGAGCTAAAACGTGTTACTTAACCAAATCAACACTATATTCAAATATGTGCATTCG
AGTGGGTTTTCAAACATAATCATCCAAAGCAAATGCAATATAATTCGAGATGAGTGGTAACGATA
TACAATTTATGACAACAACAACATCGAAAGAAGAAAAGTACAAGATCAACTTTAGCTCAGTGAGA
TATGTTACAAAAATTTCCAGAAGTTATAGAAAT
Found at i:95831 original size:34 final size:32
Alignment explanation
Indices: 95771--95840 Score: 86
Period size: 34 Copynumber: 2.1 Consensus size: 32
95761 CCTTATAAAC
* * *
95771 TCCCTAGTTTTTCCAGGCTAAACTAGAACCTT
1 TCCCTAGCTTTTACAGGCTAAACTAGAACATT
*
95803 TCCCTAGCTTTTACACGTGCTAAGCTAGAACATT
1 TCCCTAGCTTTTACA-G-GCTAAACTAGAACATT
95837 TCCC
1 TCCC
95841 CTTTACAAAA
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
32 13 0.41
33 1 0.03
34 18 0.56
ACGTcount: A:0.24, C:0.30, G:0.13, T:0.33
Consensus pattern (32 bp):
TCCCTAGCTTTTACAGGCTAAACTAGAACATT
Found at i:96148 original size:21 final size:21
Alignment explanation
Indices: 96124--96165 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
96114 CCAGAATGGG
*
96124 GGGAATCGGTACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
96145 GGGAATCGATACCCCTTCATA
1 GGGAATCGATACCCCTTCATA
96166 ATATTCAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.26, C:0.29, G:0.21, T:0.24
Consensus pattern (21 bp):
GGGAATCGATACCCCTTCATA
Found at i:96320 original size:19 final size:19
Alignment explanation
Indices: 96270--96328 Score: 82
Period size: 19 Copynumber: 3.1 Consensus size: 19
96260 GAGCCTCGGG
* *
96270 TTACTGTTCAAACAGTGAT
1 TTACTGTTCAAATAGTAAT
*
96289 TTATTGTTCAAATAGTAAT
1 TTACTGTTCAAATAGTAAT
96308 TTACTGTTCAAATAGTTAAT
1 TTACTGTTCAAATAG-TAAT
96328 T
1 T
96329 ACTATTCATA
Statistics
Matches: 35, Mismatches: 4, Indels: 1
0.88 0.10 0.03
Matches are distributed among these distances:
19 30 0.86
20 5 0.14
ACGTcount: A:0.34, C:0.10, G:0.12, T:0.44
Consensus pattern (19 bp):
TTACTGTTCAAATAGTAAT
Found at i:96330 original size:19 final size:19
Alignment explanation
Indices: 96270--96336 Score: 73
Period size: 19 Copynumber: 3.5 Consensus size: 19
96260 GAGCCTCGGG
* * *
96270 TTACTGTTCAAACAGTGAT
1 TTACTGTTCAAATAGTTAA
*
96289 TTATTGTTCAAATAG-TAA
1 TTACTGTTCAAATAGTTAA
96307 TTTACTGTTCAAATAGTTAA
1 -TTACTGTTCAAATAGTTAA
*
96327 TTACTATTCA
1 TTACTGTTCA
96337 TAAAAACATT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
18 1 0.03
19 36 0.90
20 3 0.08
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.43
Consensus pattern (19 bp):
TTACTGTTCAAATAGTTAA
Found at i:96436 original size:29 final size:31
Alignment explanation
Indices: 96402--96460 Score: 86
Period size: 29 Copynumber: 2.0 Consensus size: 31
96392 AAATTTTGAA
* *
96402 TAAATTCAATT-AAGTCCAAATA-CATTTTG
1 TAAATTCAATTCAAATCCAAAAACCATTTTG
96431 TAAATTCAATTCAAATCCAAAAACCATTTT
1 TAAATTCAATTCAAATCCAAAAACCATTTT
96461 ACCTTAAATT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 11 0.42
30 9 0.35
31 6 0.23
ACGTcount: A:0.44, C:0.17, G:0.03, T:0.36
Consensus pattern (31 bp):
TAAATTCAATTCAAATCCAAAAACCATTTTG
Found at i:104438 original size:37 final size:36
Alignment explanation
Indices: 104337--104440 Score: 93
Period size: 41 Copynumber: 2.8 Consensus size: 36
104327 AAATGAATTG
* *
104337 AATATAAATATTTTTAAAAATAAATAATAAACAAAA
1 AATATAAATATCTTTAAAAATAAATAACAAACAAAA
* * *
104373 AATATAAATGTGACATTAAAAATTTAAATGAACAAA-AAATG
1 AATATAAATAT--CTTTAAAAA--TAAAT-AACAAACAAA-A
*
104414 ATTATAAATATCTTTAAAAATAAATAA
1 AATATAAATATCTTTAAAAATAAATAA
104441 ATAAACACAA
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
36 12 0.22
37 5 0.09
38 7 0.13
39 8 0.15
40 8 0.15
41 14 0.26
ACGTcount: A:0.62, C:0.04, G:0.04, T:0.31
Consensus pattern (36 bp):
AATATAAATATCTTTAAAAATAAATAACAAACAAAA
Found at i:106509 original size:31 final size:31
Alignment explanation
Indices: 106474--106539 Score: 96
Period size: 31 Copynumber: 2.1 Consensus size: 31
106464 TTCAATGACC
*
106474 ATTTTACAACAATTGGATAAATTTAATGATA
1 ATTTTACAACAATTCGATAAATTTAATGATA
* * *
106505 ATTTTATAATAATTCGATAAATTTAATGATT
1 ATTTTACAACAATTCGATAAATTTAATGATA
106536 ATTT
1 ATTT
106540 GTAACATTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.42, C:0.05, G:0.08, T:0.45
Consensus pattern (31 bp):
ATTTTACAACAATTCGATAAATTTAATGATA
Found at i:111438 original size:19 final size:19
Alignment explanation
Indices: 111410--111458 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 19
111400 ATACGTTTTC
111410 ATGAACAGTACTATATAGT
1 ATGAACAGTACTATATAGT
* * *
111429 ATGAATAGTATTATATTGT
1 ATGAACAGTACTATATAGT
*
111448 ATTAACAGTAC
1 ATGAACAGTAC
111459 CGTTAACAGT
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
19 24 1.00
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.37
Consensus pattern (19 bp):
ATGAACAGTACTATATAGT
Found at i:120696 original size:234 final size:231
Alignment explanation
Indices: 120237--120697 Score: 698
Period size: 234 Copynumber: 2.0 Consensus size: 231
120227 ATTTTTATTC
*
120237 AATATATGAATTAGAAACCCGACCCGACACGACACAAAATAATAAAAAATTATTTTTATTCAATA
1 AATATATGAATTAGAAACCAGACCCGACACGACACAAAATAATAAAAAATTATTTTTATTCAATA
* *
120302 AAAACATTGACTTAATTGAAAAAATTATATATAGAGGGGTATTATTGTAATTATTCCTAAATATA
66 AAAACAATGACTTAATTGAAAAAATTATATATAGAGGGGTATTATTATAATTATTCCTAAATATA
* * * *
120367 TAAGGTAAAATTATATATTTTTTTCGGGTCGGACCGATTTTTTTTACCCTAAACCCGAACTTGAC
131 TAAGGTAAAATTATATA-TTATTTCGGGTCGGA-CGA-TATTTTCACCCTAAACCCGAACTCGAC
*
120432 CCGACCCGAATATCACACTTAAAAACCCGACCCGACCCG
193 CCGAACCGAATATCACACTTAAAAACCCGACCCGACCCG
* * * * *
120471 AATATATGAATTAGAAATCAGACCTGACTCGACCCGAAATAATAAAAAATTATTTTTATTCAATA
1 AATATATGAATTAGAAACCAGACCCGACACGACACAAAATAATAAAAAATTATTTTTATTCAATA
*
120536 AAAACAATGACTTAATTGGAAAAA-TATATATAGAGATGGGTATTATTATAATTATTCCTAAATA
66 AAAACAATGACTTAATTGAAAAAATTATATATAGAG--GGGTATTATTATAATTATTCCTAAATA
120600 TATAAGGTAAAATTATATA-TATTTCGGGTC-GA-G-TATTTTCACCCTAAACCCGAACTCGACC
129 TATAAGGTAAAATTATATATTATTTCGGGTCGGACGATATTTTCACCCTAAACCCGAACTCGACC
*
120661 CGAACCGAATATCACACTTAAAAAAACCGACCCGACC
194 CGAACCGAATATCACACTT-AAAAACCCGACCCGACC
120698 AAAATAAAGT
Statistics
Matches: 209, Mismatches: 15, Indels: 11
0.89 0.06 0.05
Matches are distributed among these distances:
228 43 0.21
229 16 0.08
230 1 0.00
232 2 0.01
233 21 0.10
234 81 0.39
235 45 0.22
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (231 bp):
AATATATGAATTAGAAACCAGACCCGACACGACACAAAATAATAAAAAATTATTTTTATTCAATA
AAAACAATGACTTAATTGAAAAAATTATATATAGAGGGGTATTATTATAATTATTCCTAAATATA
TAAGGTAAAATTATATATTATTTCGGGTCGGACGATATTTTCACCCTAAACCCGAACTCGACCCG
AACCGAATATCACACTTAAAAACCCGACCCGACCCG
Found at i:121524 original size:101 final size:96
Alignment explanation
Indices: 121405--121623 Score: 260
Period size: 101 Copynumber: 2.2 Consensus size: 96
121395 ACACAATTTT
* * * * * *
121405 AATATTAGGTGCAACCTAATATGTTGATAATCTTTAAGTAATTATTTACCTATTTTTTTATTATC
1 AATATTAGGCGCTACCTAATATGTTGATAATCTTTAAGTAATCA---ACATATTTTGTTATCATC
* * * *
121470 GGATTTCTAAGGCTCC-ATCTGCTTAAACATTGGTAA
63 GGATTTCCAAGAC-CCTATCAGCTT-AA-AGTGGTAA
*
121506 AATATTAGGCGCTACCTAATATGTTGATAATCTTTAAGTAATCAACATATTTTGTTATCGTCGGA
1 AATATTAGGCGCTACCTAATATGTTGATAATCTTTAAGTAATCAACATATTTTGTTATCATCGGA
121571 TTTCCAAGACCCTATCAGCTTAAAGTGGTAA
66 TTTCCAAGACCCTATCAGCTTAAAGTGGTAA
* *
121602 CATATTAGGCGTTACCTAATAT
1 AATATTAGGCGCTACCTAATAT
121624 ATTATTAATA
Statistics
Matches: 104, Mismatches: 13, Indels: 7
0.84 0.10 0.06
Matches are distributed among these distances:
96 27 0.26
97 4 0.04
98 32 0.31
101 41 0.39
ACGTcount: A:0.32, C:0.16, G:0.14, T:0.39
Consensus pattern (96 bp):
AATATTAGGCGCTACCTAATATGTTGATAATCTTTAAGTAATCAACATATTTTGTTATCATCGGA
TTTCCAAGACCCTATCAGCTTAAAGTGGTAA
Found at i:121960 original size:108 final size:108
Alignment explanation
Indices: 121647--121961 Score: 425
Period size: 108 Copynumber: 2.9 Consensus size: 108
121637 TCCAAGGCCT
* **
121647 CATCAACTTAAACTTTGGTAACATATTAAACCCTACCTAATATGTTGATAATATTATCAACAAAA
1 CATCAACTTAAACTTTGGTAACATTTTAGGCCCTACCTAATATGTTGATAATATTATCAACAAAA
* * * *
121712 TAAATAATTTCCCTATTTTTTTATCGTCAGATTTCTAAGACTC
66 TAAGTAATTTACCTATTTTGTTATCGTCGGATTTCTAAGACTC
* * * * * * *
121755 AATCAGCTTAAACTTTAGTAACACTTTAGGCGCTACTTAATATGTTGATAGTATTATCAACAAAA
1 CATCAACTTAAACTTTGGTAACATTTTAGGCCCTACCTAATATGTTGATAATATTATCAACAAAA
* *
121820 TAAGTAATTTACCTATTTTGTAATTGTCGGATTTCTAAGACTC
66 TAAGTAATTTACCTATTTTGTTATCGTCGGATTTCTAAGACTC
* * * *
121863 CATCAACTTAAACTTTGGTAACATTTTAGGCTCTACCTAGTATGTTGATATTATTAAT-AACATA
1 CATCAACTTAAACTTTGGTAACATTTTAGGCCCTACCTAATATGTTGATAATATT-ATCAACAAA
*
121927 ATAAGTAATTTACCTATTTTGTTATCGTTGGATTT
65 ATAAGTAATTTACCTATTTTGTTATCGTCGGATTT
121962 TCTGATTGCA
Statistics
Matches: 178, Mismatches: 28, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
108 176 0.99
109 2 0.01
ACGTcount: A:0.34, C:0.16, G:0.10, T:0.40
Consensus pattern (108 bp):
CATCAACTTAAACTTTGGTAACATTTTAGGCCCTACCTAATATGTTGATAATATTATCAACAAAA
TAAGTAATTTACCTATTTTGTTATCGTCGGATTTCTAAGACTC
Found at i:122689 original size:31 final size:31
Alignment explanation
Indices: 122654--122715 Score: 124
Period size: 31 Copynumber: 2.0 Consensus size: 31
122644 TTATTGAGTG
122654 ACATTAATGATTAAAAGAATAATATTTTTAT
1 ACATTAATGATTAAAAGAATAATATTTTTAT
122685 ACATTAATGATTAAAAGAATAATATTTTTAT
1 ACATTAATGATTAAAAGAATAATATTTTTAT
122716 TTGAGGTTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 31 1.00
ACGTcount: A:0.48, C:0.03, G:0.06, T:0.42
Consensus pattern (31 bp):
ACATTAATGATTAAAAGAATAATATTTTTAT
Found at i:137565 original size:2 final size:2
Alignment explanation
Indices: 137554--137644 Score: 53
Period size: 2 Copynumber: 51.5 Consensus size: 2
137544 GAACCCAAAA
* * *
137554 AT AT -T AT AT AT AT A- AT -T A- AT AT AA AA AT AT A- AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* *
137591 -T AT AT AT AT A- AT -T A- AT AT A- AA AT AT AT A- AA AT AT -T
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
137626 AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT A
137645 ATCGGGGCGG
Statistics
Matches: 72, Mismatches: 5, Indels: 24
0.71 0.05 0.24
Matches are distributed among these distances:
1 12 0.17
2 60 0.83
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (2 bp):
AT
Found at i:137575 original size:9 final size:8
Alignment explanation
Indices: 137553--137646 Score: 57
Period size: 9 Copynumber: 11.0 Consensus size: 8
137543 CGAACCCAAA
*
137553 AATATTAT
1 AATATAAT
137561 ATATATAATT
1 A-ATATAA-T
*
137571 AATATAAA
1 AATATAAT
137579 AATATAA-
1 AATATAAT
*
137586 AATATTAT
1 AATATAAT
137594 ATATATAATT
1 A-ATATAA-T
137604 AATATAA-
1 AATATAAT
*
137611 AATATATAA
1 AATATA-AT
*
137620 AATATTAT
1 AATATAAT
137628 ATATATATAT
1 A-ATATA-AT
137638 ATATATAAT
1 A-ATATAAT
137647 CGGGGCGGGG
Statistics
Matches: 70, Mismatches: 7, Indels: 17
0.74 0.07 0.18
Matches are distributed among these distances:
7 12 0.17
8 12 0.17
9 33 0.47
10 13 0.19
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (8 bp):
AATATAAT
Found at i:137593 original size:33 final size:34
Alignment explanation
Indices: 137551--137634 Score: 161
Period size: 33 Copynumber: 2.5 Consensus size: 34
137541 CCCGAACCCA
137551 AAAATATTATATATATAATTAATATAAAA-ATAT
1 AAAATATTATATATATAATTAATATAAAATATAT
137584 AAAATATTATATATATAATTAATATAAAATATAT
1 AAAATATTATATATATAATTAATATAAAATATAT
137618 AAAATATTATATATATA
1 AAAATATTATATATATA
137635 TATATATATA
Statistics
Matches: 50, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
33 29 0.58
34 21 0.42
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (34 bp):
AAAATATTATATATATAATTAATATAAAATATAT
Found at i:143595 original size:15 final size:15
Alignment explanation
Indices: 143575--143611 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
143565 TGAGACATTA
*
143575 CCCGCCCCGCATCCG
1 CCCGCCCCACATCCG
143590 CCCGCCCCACATCCG
1 CCCGCCCCACATCCG
*
143605 TCCGCCC
1 CCCGCCC
143612 AGTTAAATAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.08, C:0.68, G:0.16, T:0.08
Consensus pattern (15 bp):
CCCGCCCCACATCCG
Found at i:145578 original size:18 final size:18
Alignment explanation
Indices: 145555--145589 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
145545 TAATCTCAGC
145555 TATTAGCTTAGACTTTCA
1 TATTAGCTTAGACTTTCA
145573 TATTAGCTTAGACTTTC
1 TATTAGCTTAGACTTTC
145590 TTTTTTCCTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.26, C:0.17, G:0.11, T:0.46
Consensus pattern (18 bp):
TATTAGCTTAGACTTTCA
Found at i:147768 original size:30 final size:30
Alignment explanation
Indices: 147734--147794 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 30
147724 GAGGGGGTAA
** *
147734 AGTATAATTAATTATAAAAATGAGGGACAC
1 AGTATAATTAACCATAAAAACGAGGGACAC
*
147764 AGTATAATTAACCATAGAAACGAGGGACAC
1 AGTATAATTAACCATAAAAACGAGGGACAC
147794 A
1 A
147795 ATCAAAATAA
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.49, C:0.11, G:0.18, T:0.21
Consensus pattern (30 bp):
AGTATAATTAACCATAAAAACGAGGGACAC
Found at i:151233 original size:29 final size:29
Alignment explanation
Indices: 151190--151272 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
151180 CTCACCTAAC
151190 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
151220 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
151249 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
151273 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:155995 original size:29 final size:29
Alignment explanation
Indices: 155952--156034 Score: 139
Period size: 29 Copynumber: 2.8 Consensus size: 29
155942 CTCACCTAAC
155952 TAAATTGATGTAAGCAATGACATCATTAAT
1 TAAA-TGATGTAAGCAATGACATCATTAAT
*
155982 TAAATGATGTAAGCAATGACATCTTTAAT
1 TAAATGATGTAAGCAATGACATCATTAAT
*
156011 TAAATGATGTAAGTAATGACATCA
1 TAAATGATGTAAGCAATGACATCA
156035 ATTTAGTTTG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
29 46 0.92
30 4 0.08
ACGTcount: A:0.43, C:0.10, G:0.14, T:0.33
Consensus pattern (29 bp):
TAAATGATGTAAGCAATGACATCATTAAT
Found at i:159772 original size:2 final size:2
Alignment explanation
Indices: 159765--159790 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
159755 TTTTCCATTC
159765 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
159791 TATGTTTATA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:174255 original size:19 final size:20
Alignment explanation
Indices: 174217--174255 Score: 53
Period size: 19 Copynumber: 2.0 Consensus size: 20
174207 TTTGAAGATT
* *
174217 TTATTTTTTCAAATAAATTA
1 TTATATTTTCAAAAAAATTA
174237 TTATATTTT-AAAAAAATTA
1 TTATATTTTCAAAAAAATTA
174256 AAAAAATTCA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (20 bp):
TTATATTTTCAAAAAAATTA
Found at i:175232 original size:34 final size:36
Alignment explanation
Indices: 175160--175232 Score: 89
Period size: 36 Copynumber: 2.1 Consensus size: 36
175150 TTTTTATATT
*
175160 TTTAATTTTGTAAAAAAATTATATAAATATTATGAA
1 TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
* *
175196 TTTAATTTTTTAAAGAAAA-TATA-AAATTTTA-CAA
1 TTTAATTTTGTAAA-AAAATTATATAAATATTATCAA
175230 TTT
1 TTT
175233 GTATTATTAT
Statistics
Matches: 33, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
34 5 0.15
35 7 0.21
36 17 0.52
37 4 0.12
ACGTcount: A:0.48, C:0.01, G:0.04, T:0.47
Consensus pattern (36 bp):
TTTAATTTTGTAAAAAAATTATATAAATATTATCAA
Found at i:175413 original size:20 final size:20
Alignment explanation
Indices: 175377--175414 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
175367 ATCTTATTCC
**
175377 CTGGTAATCTTTTATTCCCA
1 CTGGTAATCTTACATTCCCA
175397 CTGGTAATCTTACATTCC
1 CTGGTAATCTTACATTCC
175415 GTGAACCAAA
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:0.21, C:0.26, G:0.11, T:0.42
Consensus pattern (20 bp):
CTGGTAATCTTACATTCCCA
Found at i:176618 original size:20 final size:21
Alignment explanation
Indices: 176591--176706 Score: 78
Period size: 20 Copynumber: 5.7 Consensus size: 21
176581 ACGCGAAATA
176591 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGAGTCCCC
* ** **
176611 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGAGTCCCC
* ***
176631 AAAATCGCAACGCGATTCTTG
1 AAAATCGCAACGCGAGTCCCC
176652 AAAATCGCAACGCGA-TCCCC
1 AAAATCGCAACGCGAGTCCCC
* ** **
176672 AGAATCGCAAATC-AGTTTCC
1 AAAATCGCAACGCGAGTCCCC
176692 AAAATCGCAACGCGA
1 AAAATCGCAACGCGA
176707 ATATGAAAAT
Statistics
Matches: 69, Mismatches: 23, Indels: 7
0.70 0.23 0.07
Matches are distributed among these distances:
19 2 0.03
20 48 0.70
21 19 0.28
ACGTcount: A:0.36, C:0.30, G:0.16, T:0.17
Consensus pattern (21 bp):
AAAATCGCAACGCGAGTCCCC
Found at i:176667 original size:61 final size:60
Alignment explanation
Indices: 176571--176726 Score: 269
Period size: 61 Copynumber: 2.6 Consensus size: 60
176561 AAATGACCAA
*
176571 CAAAATCGCAACGCGAA-ATAAAAATCGCAACGCGATCCCCAGAATCGCAAATCAGTTTC
1 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGATCCCCAGAATCGCAAATCAGTTTC
* *
176630 CAAAATCGCAACGCGATTCTTGAAAATCGCAACGCGATCCCCAGAATCGCAAATCAGTTTC
1 CAAAATCGCAACGCGAAT-ATGAAAATCGCAACGCGATCCCCAGAATCGCAAATCAGTTTC
176691 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGA
1 CAAAATCGCAACGCGAATATGAAAATCGCAACGCGA
176727 ACACATAAAT
Statistics
Matches: 90, Mismatches: 5, Indels: 3
0.92 0.05 0.03
Matches are distributed among these distances:
59 16 0.18
60 17 0.19
61 57 0.63
ACGTcount: A:0.39, C:0.28, G:0.17, T:0.16
Consensus pattern (60 bp):
CAAAATCGCAACGCGAATATGAAAATCGCAACGCGATCCCCAGAATCGCAAATCAGTTTC
Found at i:176755 original size:20 final size:20
Alignment explanation
Indices: 176693--176886 Score: 221
Period size: 20 Copynumber: 9.7 Consensus size: 20
176683 TCAGTTTCCA
* ** *
176693 AAATCGCAACGCGAATATGA
1 AAATCGCAACGCGTATCCGT
* *
176713 AAATCGCAACGCG-AACACAT
1 AAATCGCAACGCGTATC-CGT
176733 AAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
176753 AAATCGCAACGTGTATCCGT
1 AAATCGCAACGCGTATCCGT
**
176773 AAATCGCAACGCGTATGGGT
1 AAATCGCAACGCGTATCCGT
*
176793 AAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
*
176813 ATATCGCAACGCGTATCCGT
1 AAATCGCAACGCGTATCCGT
* * *
176833 AAATCGCAACG-ATAATACAT
1 AAATCGCAACGCGT-ATCCGT
176853 AAAATCGCAACGCGTATCCGT
1 -AAATCGCAACGCGTATCCGT
176874 AAATCGCAACGCG
1 AAATCGCAACGCG
176887 ATATTTAAAG
Statistics
Matches: 146, Mismatches: 23, Indels: 10
0.82 0.13 0.06
Matches are distributed among these distances:
19 2 0.01
20 126 0.86
21 17 0.12
22 1 0.01
ACGTcount: A:0.36, C:0.26, G:0.20, T:0.19
Consensus pattern (20 bp):
AAATCGCAACGCGTATCCGT
Found at i:176757 original size:60 final size:60
Alignment explanation
Indices: 176573--176887 Score: 217
Period size: 60 Copynumber: 5.2 Consensus size: 60
176563 ATGACCAACA
* * * * * * *
176573 AAATCGCAACGCGAA-ATAAAAATCGCAACGCGATCCCCA-GAATCGCAAATCAGTTTCC-A
1 AAATCGCAACGCGAATATGAAAATCGCAACGCGA-ACACATAAATCGCAAAGC-GTATCCGT
* * * * * * * *
176632 AAATCGCAACGCGATTCTTGAAAATCGCAACGCGATCCCCA-GAATCGCAAATCAGTTTCC-A
1 AAATCGCAACGCGAAT-ATGAAAATCGCAACGCGA-ACACATAAATCGCAAAGC-GTATCCGT
*
176693 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAAAGCGTATCCGT
* * ** * * **** *
176753 AAATCGCAACGTGTATCCGTAAATCGCAACGCGTATGGGTAAATCGCAATGCGTATCCGT
1 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAAAGCGTATCCGT
* * ** * ** * *
176813 ATATCGCAACGCGTATCCGTAAATCGCAACGATAATACATAAAATCGCAACGCGTATCCGT
1 AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACAT-AAATCGCAAAGCGTATCCGT
176874 AAATCGCAACGCGA
1 AAATCGCAACGCGA
176888 TATTTAAAGC
Statistics
Matches: 217, Mismatches: 34, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
59 22 0.10
60 107 0.49
61 88 0.41
ACGTcount: A:0.37, C:0.27, G:0.18, T:0.18
Consensus pattern (60 bp):
AAATCGCAACGCGAATATGAAAATCGCAACGCGAACACATAAATCGCAAAGCGTATCCGT
Found at i:177305 original size:33 final size:33
Alignment explanation
Indices: 177266--177336 Score: 106
Period size: 33 Copynumber: 2.2 Consensus size: 33
177256 TTCACTTAGA
* *
177266 TTTCATTTCGCGTTACGATTCTGTCGTTGCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
* *
177299 TTTCATTTCGCGTTGCTATTCTCTCGTTCCGAT
1 TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
177332 TTTCA
1 TTTCA
177337 AGTTAGTATT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 34 1.00
ACGTcount: A:0.11, C:0.24, G:0.17, T:0.48
Consensus pattern (33 bp):
TTTCATTTCGCGTTACGATTCTCTCGTTCCGAT
Found at i:177473 original size:41 final size:41
Alignment explanation
Indices: 177415--177492 Score: 147
Period size: 41 Copynumber: 1.9 Consensus size: 41
177405 TTGCAGAAGA
*
177415 GTCGCAACGAGATAAATGAAAATCGCAACGAGAGAATGACT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
177456 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
1 GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAAT
177493 CGCAACGCGA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.45, C:0.17, G:0.26, T:0.13
Consensus pattern (41 bp):
GTCGCAACGAGAGAAATGAAAATCGCAACGAGAGAATGACT
Found at i:177489 original size:21 final size:21
Alignment explanation
Indices: 177416--177491 Score: 109
Period size: 21 Copynumber: 3.7 Consensus size: 21
177406 TGCAGAAGAG
*
177416 TCGCAACGAGATAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
***
177437 TCGCAACGAGAG-AATGACTG
1 TCGCAACGAGAGAAATGAAAA
177457 TCGCAACGAGAGAAATGAAAA
1 TCGCAACGAGAGAAATGAAAA
177478 TCGCAACGAGAGAA
1 TCGCAACGAGAGAA
177492 TCGCAACGCG
Statistics
Matches: 47, Mismatches: 7, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
20 17 0.36
21 30 0.64
ACGTcount: A:0.46, C:0.17, G:0.25, T:0.12
Consensus pattern (21 bp):
TCGCAACGAGAGAAATGAAAA
Found at i:177537 original size:19 final size:18
Alignment explanation
Indices: 177510--177627 Score: 80
Period size: 14 Copynumber: 7.1 Consensus size: 18
177500 CGAAACCAAA
*
177510 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCA-T
177529 TCGCGTTGCGA--TTC--
1 TCGCGTTGCGATTTTCAT
*
177543 TCTCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCA-T
177562 TCGCGTTGCGA--TTC--
1 TCGCGTTGCGATTTTCAT
* *
177576 TCTCGTTGCGATTGTCAT
1 TCGCGTTGCGATTTTCAT
177594 CTCGCGTTGCGA--TTC--
1 -TCGCGTTGCGATTTTCAT
*
177609 TCTCGTTGCGATTTTCAT
1 TCGCGTTGCGATTTTCAT
177627 T
1 T
177628 TCAACCAAAA
Statistics
Matches: 77, Mismatches: 8, Indels: 29
0.68 0.07 0.25
Matches are distributed among these distances:
14 30 0.39
16 8 0.10
17 8 0.10
18 1 0.01
19 30 0.39
ACGTcount: A:0.10, C:0.25, G:0.21, T:0.44
Consensus pattern (18 bp):
TCGCGTTGCGATTTTCAT
Found at i:177551 original size:14 final size:14
Alignment explanation
Indices: 177532--177621 Score: 81
Period size: 14 Copynumber: 5.7 Consensus size: 14
177522 TTTCATTTCG
177532 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
*
177546 CGTTGCGATTTTCATTTCG
1 CGTTGCGA--TTC---TCT
177565 CGTTGCGATTCTCT
1 CGTTGCGATTCTCT
177579 CGTTGCGATTGTCATCT
1 CGTTGCGA-T-TC-TCT
177596 CGCGTTGCGATTCTCT
1 --CGTTGCGATTCTCT
177612 CGTTGCGATT
1 CGTTGCGATT
177622 TTCATTTCAA
Statistics
Matches: 64, Mismatches: 2, Indels: 20
0.74 0.02 0.23
Matches are distributed among these distances:
14 28 0.44
15 1 0.02
16 8 0.12
17 8 0.12
18 1 0.02
19 18 0.28
ACGTcount: A:0.09, C:0.26, G:0.23, T:0.42
Consensus pattern (14 bp):
CGTTGCGATTCTCT
Found at i:177557 original size:33 final size:33
Alignment explanation
Indices: 177515--177629 Score: 212
Period size: 33 Copynumber: 3.5 Consensus size: 33
177505 CCAAATCGCA
177515 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
177548 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
* *
177581 TTGCGATTGTCATCTCGCGTTGCGATTCTCTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
177614 TTGCGATTTTCATTTC
1 TTGCGATTTTCATTTC
177630 AACCAAAAGA
Statistics
Matches: 78, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 78 1.00
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTCTCG
Found at i:179483 original size:93 final size:93
Alignment explanation
Indices: 179324--179704 Score: 735
Period size: 93 Copynumber: 4.1 Consensus size: 93
179314 TAGATTGCTT
*
179324 AGTAAATTTATTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
179389 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
179417 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
179482 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
179510 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTATAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
179575 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
*
179603 AGTAAATTTGTTCAGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
1 AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
179668 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
66 TTTGTCTTTGTTTTGTCTTTTGGTTGAA
179696 AGTAAATTT
1 AGTAAATTT
179705 ATCCATTCAA
Statistics
Matches: 284, Mismatches: 4, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 284 1.00
ACGTcount: A:0.23, C:0.13, G:0.19, T:0.46
Consensus pattern (93 bp):
AGTAAATTTGTTCGGTTGCTGCCAATTCTGCTAAACTGTGTATTCTTTAACACTGTGAAATAGTA
TTTGTCTTTGTTTTGTCTTTTGGTTGAA
Found at i:179787 original size:19 final size:19
Alignment explanation
Indices: 179747--179875 Score: 125
Period size: 19 Copynumber: 7.3 Consensus size: 19
179737 TAGTTTACTT
* *
179747 TCGCAACACGAAACTTAAAA
1 TCGCAACGCGAAAC-CAAAA
179767 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
**
179786 TCGCAACGCGAAATGAAAA
1 TCGCAACGCGAAACCAAAA
*
179805 TCGCAA--CG--A-CAGAA
1 TCGCAACGCGAAACCAAAA
179819 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
*
179838 TCGCAA--CG--A-CAAGA
1 TCGCAACGCGAAACCAAAA
179852 TCGCAACGCGAAACCAAAA
1 TCGCAACGCGAAACCAAAA
179871 TCGCA
1 TCGCA
179876 TTGCGATTTT
Statistics
Matches: 90, Mismatches: 9, Indels: 21
0.75 0.08 0.17
Matches are distributed among these distances:
14 19 0.21
15 2 0.02
16 4 0.04
17 4 0.04
18 2 0.02
19 46 0.51
20 13 0.14
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (19 bp):
TCGCAACGCGAAACCAAAA
Found at i:179826 original size:33 final size:32
Alignment explanation
Indices: 179783--179875 Score: 150
Period size: 33 Copynumber: 2.8 Consensus size: 32
179773 CGCGAAACCA
**
179783 AAATCGCAACGCGAAATGAAAATCGCAACGAC
1 AAATCGCAACGCGAAACCAAAATCGCAACGAC
179815 AGAATCGCAACGCGAAACCAAAATCGCAACGAC
1 A-AATCGCAACGCGAAACCAAAATCGCAACGAC
179848 AAGATCGCAACGCGAAACCAAAATCGCA
1 AA-ATCGCAACGCGAAACCAAAATCGCA
179876 TTGCGATTTT
Statistics
Matches: 57, Mismatches: 2, Indels: 3
0.92 0.03 0.05
Matches are distributed among these distances:
32 2 0.04
33 55 0.96
ACGTcount: A:0.46, C:0.28, G:0.18, T:0.08
Consensus pattern (32 bp):
AAATCGCAACGCGAAACCAAAATCGCAACGAC
Found at i:179873 original size:52 final size:52
Alignment explanation
Indices: 179747--179875 Score: 140
Period size: 52 Copynumber: 2.5 Consensus size: 52
179737 TAGTTTACTT
**
179747 TCGCAACACGAAACTTAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
1 TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
* * *
179799 T-G-AAAATCGCAACGACAGAATCGCAACGCGAAACCAAAATCGCAACGAC-AAGA
1 TCGCAACA-CGAAAC-ACAAAATCGCAACGCGAAACCAAAATCGCAACG-CGAA-A
*
179852 TCGCAACGCGAAAC-CAAAATCGCA
1 TCGCAACACGAAACACAAAATCGCA
179876 TTGCGATTTT
Statistics
Matches: 62, Mismatches: 9, Indels: 12
0.75 0.11 0.14
Matches are distributed among these distances:
50 3 0.05
51 6 0.10
52 42 0.68
53 3 0.05
54 6 0.10
55 2 0.03
ACGTcount: A:0.46, C:0.29, G:0.17, T:0.09
Consensus pattern (52 bp):
TCGCAACACGAAACACAAAATCGCAACGCGAAACCAAAATCGCAACGCGAAA
Found at i:179893 original size:19 final size:19
Alignment explanation
Indices: 179871--180006 Score: 121
Period size: 19 Copynumber: 7.6 Consensus size: 19
179861 GAAACCAAAA
*
179871 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
179890 TCGCGTTGCGA--TTC-TT
1 TCGCGTTGCGATTTTCATT
179906 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
* *
179923 TCGCATTGCGA--TTC-TG
1 TCGCGTTGCGATTTTCATT
179939 T--CGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
179956 TCGCGTTGCGATTTTTGGTT
1 TCGCGTTGCGA-TTTTCATT
*
179976 TCGCGTTGCGATTTTAAGTT
1 TCGCGTTGCGATTTTCA-TT
*
179996 TCGTGTTGCGA
1 TCGCGTTGCGA
180007 AAAGTAAACT
Statistics
Matches: 95, Mismatches: 10, Indels: 23
0.74 0.08 0.18
Matches are distributed among these distances:
14 15 0.16
16 11 0.12
17 11 0.12
19 29 0.31
20 29 0.31
ACGTcount: A:0.11, C:0.19, G:0.24, T:0.46
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:179912 original size:14 final size:14
Alignment explanation
Indices: 179893--179949 Score: 60
Period size: 14 Copynumber: 3.7 Consensus size: 14
179883 TTTCATTTCG
179893 CGTTGCGATTCTTT
1 CGTTGCGATTCTTT
179907 CGTTGCGATTTTCATTT
1 CGTTGCGA--TTC-TTT
*
179924 CGCATTGCGATTCTGT
1 CG--TTGCGATTCTTT
179940 CGTTGCGATT
1 CGTTGCGATT
179950 TTCATTTCGC
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
14 16 0.43
16 7 0.19
17 8 0.22
19 6 0.16
ACGTcount: A:0.11, C:0.21, G:0.23, T:0.46
Consensus pattern (14 bp):
CGTTGCGATTCTTT
Found at i:179918 original size:33 final size:33
Alignment explanation
Indices: 179876--179968 Score: 168
Period size: 33 Copynumber: 2.8 Consensus size: 33
179866 CAAAATCGCA
*
179876 TTGCGATTTTCATTTCGCGTTGCGATTCTTTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
*
179909 TTGCGATTTTCATTTCGCATTGCGATTCTGTCG
1 TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
179942 TTGCGATTTTCATTTCGCGTTGCGATT
1 TTGCGATTTTCATTTCGCGTTGCGATT
179969 TTTGGTTTCG
Statistics
Matches: 57, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 57 1.00
ACGTcount: A:0.11, C:0.20, G:0.22, T:0.47
Consensus pattern (33 bp):
TTGCGATTTTCATTTCGCGTTGCGATTCTGTCG
Found at i:179977 original size:20 final size:20
Alignment explanation
Indices: 179940--180006 Score: 91
Period size: 20 Copynumber: 3.4 Consensus size: 20
179930 GCGATTCTGT
*
179940 CGTTGCGATTTTCA-TTTCG
1 CGTTGCGATTTTTAGTTTCG
*
179959 CGTTGCGATTTTTGGTTTCG
1 CGTTGCGATTTTTAGTTTCG
*
179979 CGTTGCGATTTTAAGTTTCG
1 CGTTGCGATTTTTAGTTTCG
*
179999 TGTTGCGA
1 CGTTGCGA
180007 AAAGTAAACT
Statistics
Matches: 42, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
19 12 0.29
20 30 0.71
ACGTcount: A:0.10, C:0.16, G:0.27, T:0.46
Consensus pattern (20 bp):
CGTTGCGATTTTTAGTTTCG
Done.