Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005505.1 Hibiscus syriacus cultivar Beakdansim tig00012689_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: 120325
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:5928 original size:8 final size:8
Alignment explanation
Indices: 5915--5940 Score: 52
Period size: 8 Copynumber: 3.2 Consensus size: 8
5905 AGATTCTCCC
5915 ATATGTAT
1 ATATGTAT
5923 ATATGTAT
1 ATATGTAT
5931 ATATGTAT
1 ATATGTAT
5939 AT
1 AT
5941 GTATATCTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 18 1.00
ACGTcount: A:0.38, C:0.00, G:0.12, T:0.50
Consensus pattern (8 bp):
ATATGTAT
Found at i:9477 original size:7 final size:8
Alignment explanation
Indices: 9450--9476 Score: 54
Period size: 8 Copynumber: 3.4 Consensus size: 8
9440 AAAATGAGTG
9450 AAAATAAA
1 AAAATAAA
9458 AAAATAAA
1 AAAATAAA
9466 AAAATAAA
1 AAAATAAA
9474 AAA
1 AAA
9477 TGGAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 19 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (8 bp):
AAAATAAA
Found at i:10503 original size:55 final size:54
Alignment explanation
Indices: 10423--10716 Score: 303
Period size: 54 Copynumber: 5.4 Consensus size: 54
10413 TTGAAGATTG
* * * * * **
10423 TTCGAG-TCTCATACTCTCTGAAGAAATAGGGGAGCAGACACGATTGTTGAAGATA
1 TTCGAGTTCT-ATTCTCCCTGAAGAAAGA-GGGAGCAGACCCGTTTGAAGAAGATA
*
10478 TTCGAGTTCTATTCTCCCT-AGAGAAAGAGGGAGCAAACCCGTTTGAAGAAGATA
1 TTCGAGTTCTATTCTCCCTGA-AGAAAGAGGGAGCAGACCCGTTTGAAGAAGATA
10532 TTCGAGTTCTATTCTCCCTGAAGAAAGAGGGAGC-GAACCCGTTTGAAGAAGATA
1 TTCGAGTTCTATTCTCCCTGAAGAAAGAGGGAGCAG-ACCCGTTTGAAGAAGATA
* * * *
10586 TTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGC-GAACCAGTTAGCAGAAGAT-
1 TTCGAGTTCTATTCTCCCTGAAGAAAGAGGGAGCAG-ACCCGTTTGAAGAAGATA
* * * * * *
10639 TCTTGAGTTCTATACTCCCTGAA-ACAATAGGGAGCGGACCCGTTAGCAGAAGATTA
1 T-TCGAGTTCTATTCTCCCTGAAGA-AAGAGGGAGCAGACCCGTTTGAAGAAGA-TA
*
10695 TTCGAGTTCTATACTCCCTGAA
1 TTCGAGTTCTATTCTCCCTGAA
10717 ACATAGGGAG
Statistics
Matches: 213, Mismatches: 17, Indels: 18
0.86 0.07 0.07
Matches are distributed among these distances:
53 2 0.01
54 165 0.77
55 42 0.20
56 4 0.02
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Consensus pattern (54 bp):
TTCGAGTTCTATTCTCCCTGAAGAAAGAGGGAGCAGACCCGTTTGAAGAAGATA
Found at i:10743 original size:54 final size:53
Alignment explanation
Indices: 10471--10789 Score: 345
Period size: 54 Copynumber: 5.9 Consensus size: 53
10461 CACGATTGTT
* * * *
10471 GAAGATATTCGAGTTCTATTCTCCCTAGAGAA-AGAGGGAGCAAACCCGTTTGAA
1 GAAGATATTCGAGTTCTATACTCCCT-GA-AACAGAGGGAGCGAACCCGTTAGCA
* * * *
10525 GAAGATATTCGAGTTCTATTCTCCCTGAAGAAAGAGGGAGCGAACCCGTTTGAA
1 GAAGATATTCGAGTTCTATACTCCCTGAA-ACAGAGGGAGCGAACCCGTTAGCA
* *
10579 GAAGATATTCGAGTTCTATACTCCCTGAAGAAAGAGGGAGCGAACCAGTTAGCA
1 GAAGATATTCGAGTTCTATACTCCCTGAA-ACAGAGGGAGCGAACCCGTTAGCA
* * *
10633 GAAGAT-TCTTGAGTTCTATACTCCCTGAAACAATAGGGAGCGGACCCGTTAGCA
1 GAAGATAT-TCGAGTTCTATACTCCCTGAAAC-AGAGGGAGCGAACCCGTTAGCA
* ***
10687 GAAGATTATTCGAGTTCTATACTCCCTGAAACATAGGGAGCGAACCCGTCCCCA
1 GAAGA-TATTCGAGTTCTATACTCCCTGAAACAGAGGGAGCGAACCCGTTAGCA
* * ** *
10741 GAAGATTCTTCAAGTTCTATGTTCCCTGAAACGATAGGGAGCGAACCCG
1 GAAGA-TATTCGAGTTCTATACTCCCTGAAAC-AGAGGGAGCGAACCCG
10790 ATTTTGAAGA
Statistics
Matches: 239, Mismatches: 19, Indels: 13
0.88 0.07 0.05
Matches are distributed among these distances:
52 1 0.00
53 5 0.02
54 193 0.81
55 39 0.16
56 1 0.00
ACGTcount: A:0.31, C:0.21, G:0.24, T:0.23
Consensus pattern (53 bp):
GAAGATATTCGAGTTCTATACTCCCTGAAACAGAGGGAGCGAACCCGTTAGCA
Found at i:21926 original size:18 final size:18
Alignment explanation
Indices: 21903--21947 Score: 90
Period size: 18 Copynumber: 2.5 Consensus size: 18
21893 CTCACCCTCA
21903 CATCAACAAACAGTGTCT
1 CATCAACAAACAGTGTCT
21921 CATCAACAAACAGTGTCT
1 CATCAACAAACAGTGTCT
21939 CATCAACAA
1 CATCAACAA
21948 TCTCATCCCC
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 27 1.00
ACGTcount: A:0.42, C:0.29, G:0.09, T:0.20
Consensus pattern (18 bp):
CATCAACAAACAGTGTCT
Found at i:28749 original size:6 final size:6
Alignment explanation
Indices: 28733--28850 Score: 71
Period size: 6 Copynumber: 18.8 Consensus size: 6
28723 AAATCAAAGA
* * * *
28733 AAAACAT AAAAAT AAAAAT AAGAAAT AATAAT AATAAC AAGAAT --AAAT
1 AAAA-AT AAAAAT AAAAAT AA-AAAT AAAAAT AAAAAT AAAAAT AAAAAT
* * *
28781 CAAAAGAA AAAAAT -AAAAT AAATAAA AACAAAT CAAAGAAA AAAAAT
1 -AAAA-AT AAAAAT AAAAAT AAA-AAT AA-AAAT -AAA-AAT AAAAAT
*
28828 AAAAAT AAAGAT AAAAAT AAAAA
1 AAAAAT AAAAAT AAAAAT AAAAA
28851 ATGAATAAAA
Statistics
Matches: 88, Mismatches: 13, Indels: 21
0.72 0.11 0.17
Matches are distributed among these distances:
4 3 0.03
5 5 0.06
6 48 0.55
7 26 0.30
8 6 0.07
ACGTcount: A:0.77, C:0.04, G:0.04, T:0.14
Consensus pattern (6 bp):
AAAAAT
Found at i:28801 original size:32 final size:33
Alignment explanation
Indices: 28759--28836 Score: 88
Period size: 33 Copynumber: 2.3 Consensus size: 33
28749 AATAAGAAAT
* *
28759 AATAATAAT-AACAAGAATAAATCAAA-AGAAAAA
1 AATAA-AATAAACAAAAACAAATCAAAGA-AAAAA
*
28792 AATAAAATAAATAAAAACAAATCAAAGAAAAAA
1 AATAAAATAAACAAAAACAAATCAAAGAAAAAA
28825 AATAAAAATAAA
1 AAT-AAAATAAA
28837 GATAAAAATA
Statistics
Matches: 39, Mismatches: 3, Indels: 5
0.83 0.06 0.11
Matches are distributed among these distances:
32 3 0.08
33 27 0.69
34 9 0.23
ACGTcount: A:0.77, C:0.05, G:0.04, T:0.14
Consensus pattern (33 bp):
AATAAAATAAACAAAAACAAATCAAAGAAAAAA
Found at i:28851 original size:19 final size:18
Alignment explanation
Indices: 28782--28852 Score: 72
Period size: 19 Copynumber: 3.7 Consensus size: 18
28772 AGAATAAATC
28782 AAAAGAAAAAAATAAA-AT
1 AAAA-AAAAAAATAAAGAT
*
28800 AAATAAAAACAAATCAAAGAA
1 AAA-AAAAA-AAAT-AAAGAT
28821 AAAAAATAAAAATAAAGAT
1 AAAAAA-AAAAATAAAGAT
28840 AAAAATAAAAAAT
1 AAAAA-AAAAAAT
28853 GAATAAAAAA
Statistics
Matches: 45, Mismatches: 2, Indels: 11
0.78 0.03 0.19
Matches are distributed among these distances:
18 7 0.16
19 21 0.47
20 11 0.24
21 6 0.13
ACGTcount: A:0.80, C:0.03, G:0.04, T:0.13
Consensus pattern (18 bp):
AAAAAAAAAAATAAAGAT
Found at i:28862 original size:18 final size:17
Alignment explanation
Indices: 28740--28850 Score: 56
Period size: 16 Copynumber: 6.6 Consensus size: 17
28730 AGAAAAACAT
28740 AAAAATAAAAAT-AAGA
1 AAAAATAAAAATAAAGA
* *
28756 AATAATAATAATAACAAGA
1 AAAAATAAAAAT-A-AAGA
* * *
28775 ATAAATCAAAAGAAA-A
1 AAAAATAAAAATAAAGA
28791 AAATAA-AATAAATAAA-A
1 AAA-AATAA-AAATAAAGA
* * *
28808 ACAAAT-CAAA-GAA-A
1 AAAAATAAAAATAAAGA
28822 AAAAATAAAAATAAAGA
1 AAAAATAAAAATAAAGA
28839 TAAAAATAAAAA
1 -AAAAATAAAAA
28851 ATGAATAAAA
Statistics
Matches: 69, Mismatches: 16, Indels: 18
0.67 0.16 0.17
Matches are distributed among these distances:
14 8 0.12
15 6 0.09
16 18 0.26
17 14 0.20
18 12 0.17
19 11 0.16
ACGTcount: A:0.77, C:0.04, G:0.05, T:0.14
Consensus pattern (17 bp):
AAAAATAAAAATAAAGA
Found at i:28862 original size:39 final size:38
Alignment explanation
Indices: 28740--28862 Score: 101
Period size: 39 Copynumber: 3.1 Consensus size: 38
28730 AGAAAAACAT
*
28740 AAAAATAAAAATAAGAAATAATAATAATAACAA-GAATAAATCA
1 AAAAATAAAAAT-A-AAATAAAAATAA-AA-AATGAATAAA--A
*
28783 AAAGAA-AAAAATAAAATAAATAA-AAACAAATCAA-AGAAA
1 AAA-AATAAAAATAAAATAAA-AATAAA-AAATGAATA-AAA
28822 AAAAATAAAAATAAAGATAAAAATAAAAAATGAATAAAA
1 AAAAATAAAAATAAA-ATAAAAATAAAAAATGAATAAAA
28861 AA
1 AA
28863 GATAAATTGA
Statistics
Matches: 68, Mismatches: 3, Indels: 22
0.73 0.03 0.24
Matches are distributed among these distances:
38 2 0.03
39 26 0.38
40 13 0.19
41 13 0.19
42 3 0.04
43 9 0.13
44 2 0.03
ACGTcount: A:0.77, C:0.03, G:0.05, T:0.15
Consensus pattern (38 bp):
AAAAATAAAAATAAAATAAAAATAAAAAATGAATAAAA
Found at i:28890 original size:88 final size:86
Alignment explanation
Indices: 28699--28869 Score: 204
Period size: 88 Copynumber: 2.0 Consensus size: 86
28689 AATGTTAGAT
* * * * *
28699 AAAAACAATAAATAAATATTAAATAAATCAAAGAAAAACATAAAAATAAAAATAAGAAATAATAA
1 AAAAAAAATAAATAAATATAAAACAAATCAAAGAAAAAAATAAAAATAAAAATAAGAAATAAAAA
*
28764 TAATAACAAGAATAAATCAAA
66 TAATAAAAAGAATAAATCAAA
*
28785 AGAAAAAAATAAAATAAATA-AAAACAAATCAAAGAAAAAAAATAAAAATAAAGATAA-AAATAA
1 A-AAAAAAAT-AAATAAATATAAAACAAATCAAAG-AAAAAAATAAAAATAAAAATAAGAAAT-A
28848 AAAATGAATAAAAA-AGATAAAT
62 AAAAT-AATAAAAAGA-ATAAAT
28870 TGAACAAAAA
Statistics
Matches: 72, Mismatches: 7, Indels: 9
0.82 0.08 0.10
Matches are distributed among these distances:
86 1 0.01
87 23 0.32
88 35 0.49
89 13 0.18
ACGTcount: A:0.75, C:0.04, G:0.05, T:0.16
Consensus pattern (86 bp):
AAAAAAAATAAATAAATATAAAACAAATCAAAGAAAAAAATAAAAATAAAAATAAGAAATAAAAA
TAATAAAAAGAATAAATCAAA
Found at i:30281 original size:36 final size:37
Alignment explanation
Indices: 30241--30589 Score: 301
Period size: 36 Copynumber: 9.8 Consensus size: 37
30231 AATTGATTTC
* * *
30241 AAAACCATATAATATAAAATATTTTCAAAATATTTT-
1 AAAACTATATAATATAATATATTTTCAAAATGTTTTA
* * *
30277 AAAACTATATATTAT-ATATTTTTTCAAAAATATTTTA
1 AAAACTATATAATATAATATATTTTC-AAAATGTTTTA
*
30314 AAAACTATAT--TCA-AA-AT-GTTTCATAAA----TT-
1 AAAACTATATAAT-ATAATATATTTTCA-AAATGTTTTA
* *
30343 ---A-TATATTATAT-ATATATTTTCAAAATGTTTTG
1 AAAACTATATAATATAATATATTTTCAAAATGTTTTA
* * *
30375 AAAACTATATATTAT-ATATATTTTAAAAATGTTTTG
1 AAAACTATATAATATAATATATTTTCAAAATGTTTTA
*
30411 AAAACTATATATTATATATATATTTTCAAAATGTTTTA
1 AAAACTATATAATATA-ATATATTTTCAAAATGTTTTA
* * *
30449 AAAACTAAATATTAT-ATATATTTTTAAAATGTTTTA
1 AAAACTATATAATATAATATATTTTCAAAATGTTTTA
*
30485 AAAACTATATATTATATATATATATATTCAAAATGTTTTA
1 AAAACTATATA--ATATA-ATATATTTTCAAAATGTTTTA
*
30525 AAAACTATATATTAT-ATA-AGTTTTCAAAATGTTTTA
1 AAAACTATATAATATAATATA-TTTTCAAAATGTTTTA
*
30561 AAAACTATATATTAT-ATATATTTTCAAAA
1 AAAACTATATAATATAATATATTTTCAAAA
30590 ATCATACTAC
Statistics
Matches: 267, Mismatches: 19, Indels: 54
0.79 0.06 0.16
Matches are distributed among these distances:
25 5 0.02
26 3 0.01
27 6 0.02
28 5 0.02
30 2 0.01
31 2 0.01
33 1 0.00
34 7 0.03
35 13 0.05
36 143 0.54
37 11 0.04
38 39 0.15
40 30 0.11
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.45
Consensus pattern (37 bp):
AAAACTATATAATATAATATATTTTCAAAATGTTTTA
Found at i:30370 original size:38 final size:38
Alignment explanation
Indices: 30323--30589 Score: 388
Period size: 36 Copynumber: 7.2 Consensus size: 38
30313 AAAAACTATA
* * *
30323 TTCAAAATGTTTCATAAATTATATATTATATATATATT
1 TTCAAAATGTTTTAAAAACTATATATTATATATATATT
*
30361 TTCAAAATGTTTTGAAAACTATATA-T-TATATATATT
1 TTCAAAATGTTTTAAAAACTATATATTATATATATATT
* *
30397 TTAAAAATGTTTTGAAAACTATATATTATATATATATT
1 TTCAAAATGTTTTAAAAACTATATATTATATATATATT
*
30435 TTCAAAATGTTTTAAAAACTAAATATTATATATAT-TT
1 TTCAAAATGTTTTAAAAACTATATATTATATATATATT
30472 TT-AAAATGTTTTAAAAACTATATATTATATATATATAT
1 TTCAAAATGTTTTAAAAACTATATATTATATATATAT-T
*
30510 ATTCAAAATGTTTTAAAAACTATATATTATATA-A-GTT
1 -TTCAAAATGTTTTAAAAACTATATATTATATATATATT
30547 TTCAAAATGTTTTAAAAACTATATA-T-TATATATATT
1 TTCAAAATGTTTTAAAAACTATATATTATATATATATT
30583 TTCAAAA
1 TTCAAAA
30590 ATCATACTAC
Statistics
Matches: 210, Mismatches: 11, Indels: 18
0.88 0.05 0.08
Matches are distributed among these distances:
34 4 0.02
35 2 0.01
36 99 0.47
37 8 0.04
38 65 0.31
39 3 0.01
40 29 0.14
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (38 bp):
TTCAAAATGTTTTAAAAACTATATATTATATATATATT
Found at i:30504 original size:76 final size:74
Alignment explanation
Indices: 30326--30589 Score: 408
Period size: 74 Copynumber: 3.6 Consensus size: 74
30316 AACTATATTC
* * * *
30326 AAAATGTTTCATAAATTATATATTATATATATATTTTCAAAATGTTTTGAAAACTATATATTATA
1 AAAATGTTTTAAAAACTATATATTATATATATATTTTCAAAATGTTTTAAAAACTATATATTATA
30391 TATATTTTA
66 TATATTTTA
* *
30400 AAAATGTTTTGAAAACTATATATTATATATATATTTTCAAAATGTTTTAAAAACTAAATATTATA
1 AAAATGTTTTAAAAACTATATATTATATATATATTTTCAAAATGTTTTAAAAACTATATATTATA
*
30465 TATATTTTT
66 TATATTTTA
30474 AAAATGTTTTAAAAACTATATATTATATATATATATATTCAAAATGTTTTAAAAACTATATATTA
1 AAAATGTTTTAAAAACTATATATTATATATATAT-T-TTCAAAATGTTTTAAAAACTATATATTA
*
30539 TATA-AGTTTTC
64 TATATA-TTTTA
30550 AAAATGTTTTAAAAACTATATA-T-TATATATATTTTCAAAA
1 AAAATGTTTTAAAAACTATATATTATATATATATTTTCAAAA
30590 ATCATACTAC
Statistics
Matches: 177, Mismatches: 10, Indels: 8
0.91 0.05 0.04
Matches are distributed among these distances:
72 7 0.04
73 1 0.01
74 109 0.62
75 3 0.02
76 57 0.32
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (74 bp):
AAAATGTTTTAAAAACTATATATTATATATATATTTTCAAAATGTTTTAAAAACTATATATTATA
TATATTTTA
Found at i:30611 original size:2 final size:2
Alignment explanation
Indices: 30604--30631 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
30594 TACTACATTA
30604 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
30632 GTAAAAAAAT
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:31502 original size:85 final size:84
Alignment explanation
Indices: 31368--31952 Score: 778
Period size: 85 Copynumber: 6.9 Consensus size: 84
31358 TGATGTCTCA
* * * * * * * *
31368 TTGAGTTGAATGAAATCGAACTCAAAGGTATTTGTTGACACATAACCCTTCTCTCCTTGAGTTAT
1 TTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTAT
*
31433 GATGTAAATTTGATATGTCC
66 GCTGTAAATTTGATATG-CC
*
31453 TTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGATGACAGATAGCCCTTCTCACCTTGAGCTAT
1 TTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTAT
31518 GCTGTAAATTTGATATGCC
66 GCTGTAAATTTGATATGCC
* * * * * * *
31537 TTTGGGTTGATTGTAATCGAACTCAAAGGTATTTGTTGACAGATAACCCTTATCACCTTGAGCTA
1 -TTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTA
31602 TGCTGTAAATTTGATATGCC
65 TGCTGTAAATTTGATATGCC
* *
31622 TTTGAGCTGAATGTAATCAAACTCGAAGGTCTTTGTTGACAGATAAG-CCTTCTCACCTTGAGCT
1 -TTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGAT-AGCCCTTCTCACCTTGAGCT
31686 ATGCTGTAAATTTGATATGCCC
64 ATGCTGTAAATTTGATATG-CC
* * * * **
31708 TTGAGCTGAATGTAATCGAACTCAAAGGTCTTTGTTGACAAATAACCCTTCTCGTCTTGAGCTAT
1 TTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTAT
31773 GCTGTAAATTTGATATGCTC
66 GCTGTAAATTTGATATGC-C
* * * *
31793 TTGAGCGGAATGTAATCGAAATCGAAGGTTTTTGTTGACAGATAGCCCTTCTTACCTTGAGTTAT
1 TTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTAT
31858 GCTGTAAATTTGATATGCCC
66 GCTGTAAATTTGATATG-CC
* * *
31878 TTGAGCTGAATATAATCGAACTCGAAGGTTTGTTGCTGGA-AGATAGCCCTTCTCGCCTTGAGCT
1 TTGAGCTGAATGTAATCGAACTCGAAGGTTT-TTG-TTGACAGATAGCCCTTCTCACCTTGAGCT
*
31942 ATTCTGTAAAT
64 ATGCTGTAAAT
31953 AGGCTGGGAG
Statistics
Matches: 442, Mismatches: 50, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
84 4 0.01
85 397 0.90
86 38 0.09
87 3 0.01
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (84 bp):
TTGAGCTGAATGTAATCGAACTCGAAGGTTTTTGTTGACAGATAGCCCTTCTCACCTTGAGCTAT
GCTGTAAATTTGATATGCC
Found at i:34337 original size:21 final size:21
Alignment explanation
Indices: 34313--34353 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
34303 TTAAGATCAA
34313 AATAAAA-AAATAAATAAAATG
1 AATAAAAGAAA-AAATAAAATG
*
34334 AATAAAAGAAAATATAAAAT
1 AATAAAAGAAAAAATAAAAT
34354 AAGAAATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.76, C:0.00, G:0.05, T:0.20
Consensus pattern (21 bp):
AATAAAAGAAAAAATAAAATG
Found at i:36469 original size:85 final size:85
Alignment explanation
Indices: 36372--36731 Score: 434
Period size: 85 Copynumber: 4.2 Consensus size: 85
36362 ATTTTTATTA
* * ** * * *
36372 ACAGATAGCCCTTCTTGCCTTGAGCTATACTGTAAATTTGATATGCCTCTGAGCTGAATGTAATC
1 ACAGATAACCCTTCTCGCCTTGAGCTATGTTGTAAATTTAATATGCCTTTGAGCTGAATATAATC
*
36437 GAACTCGAAGGTCTTTAATG
66 GAACTCGAAGGTCTTTGATG
* * * * * *
36457 ACATATAACCCTTCTTGCCTTGAGTTATGTTATAAATTTGATATGCATTTGAGCTGAATATAATC
1 ACAGATAACCCTTCTCGCCTTGAGCTATGTTGTAAATTTAATATGCCTTTGAGCTGAATATAATC
* ** *
36522 AAACTAAAAGGACTTTGATG
66 GAACTCGAAGGTCTTTGATG
* * * * * * *
36542 ACAGAAAACACTTCTCGCTTTGAGTTATGTTGTAAATTTAATATGCCTTTAAGCTGAGTGTAATC
1 ACAGATAACCCTTCTCGCCTTGAGCTATGTTGTAAATTTAATATGCCTTTGAGCTGAATATAATC
* *
36607 GAACTCGAAGGTCTTGGTTG
66 GAACTCGAAGGTCTTTGATG
* * * *
36627 ATAGAT-GCCCTTCTCGCCTTGAGCTATGTTGTAAATTTAATATCCCTTTGAGCTGAGTATAATC
1 ACAGATAACCCTTCTCGCCTTGAGCTATGTTGTAAATTTAATATGCCTTTGAGCTGAATATAATC
36691 GAACTCGAAGGTCTTTGATG
66 GAACTCGAAGGTCTTTGATG
36711 ACAGATAACCCTTCTCGCCTT
1 ACAGATAACCCTTCTCGCCTT
36732 TAGTTATGCT
Statistics
Matches: 230, Mismatches: 44, Indels: 2
0.83 0.16 0.01
Matches are distributed among these distances:
84 74 0.32
85 156 0.68
ACGTcount: A:0.28, C:0.18, G:0.19, T:0.35
Consensus pattern (85 bp):
ACAGATAACCCTTCTCGCCTTGAGCTATGTTGTAAATTTAATATGCCTTTGAGCTGAATATAATC
GAACTCGAAGGTCTTTGATG
Found at i:36690 original size:169 final size:170
Alignment explanation
Indices: 36402--36739 Score: 446
Period size: 169 Copynumber: 2.0 Consensus size: 170
36392 TGAGCTATAC
* * * *
36402 TGTAAATTTGATATGCCTCTGAGCTGAATGTAATCGAACTCGAAGGTCTTTAATGACATATAACC
1 TGTAAATTTAATATGCCTCTAAGCTGAATGTAATCGAACTCGAAGGTCTTGAATGACAGATAACC
* * * *
36467 CTTCTTGCCTTGAGTTATGTTATAAATTTGATATGCATTTGAGCTGAATATAATCAAACTAAAAG
66 CTTCTCGCCTTGAGCTATGTTATAAATTTAATATCCATTTGAGCTGAATATAATCAAACTAAAAG
36532 GACTTTGATGACAGAAAACACTTCTCG-CTTTGAGTTATGT
131 GACTTTGATGACAGAAAACACTTCTCGCCTTT-AGTTATGT
* * ** * *
36572 TGTAAATTTAATATGCCTTTAAGCTGAGTGTAATCGAACTCGAAGGTCTTGGTTGATAGAT-GCC
1 TGTAAATTTAATATGCCTCTAAGCTGAATGTAATCGAACTCGAAGGTCTTGAATGACAGATAACC
* * * * **
36636 CTTCTCGCCTTGAGCTATGTTGTAAATTTAATATCCCTTTGAGCTGAGTATAATCGAACTCGAAG
66 CTTCTCGCCTTGAGCTATGTTATAAATTTAATATCCATTTGAGCTGAATATAATCAAACTAAAAG
* * *
36701 GTCTTTGATGACAGATAACCCTTCTCGCCTTTAGTTATG
131 GACTTTGATGACAGAAAACACTTCTCGCCTTTAGTTATG
36740 CTGCACTGGG
Statistics
Matches: 144, Mismatches: 23, Indels: 3
0.85 0.14 0.02
Matches are distributed among these distances:
169 88 0.61
170 56 0.39
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.36
Consensus pattern (170 bp):
TGTAAATTTAATATGCCTCTAAGCTGAATGTAATCGAACTCGAAGGTCTTGAATGACAGATAACC
CTTCTCGCCTTGAGCTATGTTATAAATTTAATATCCATTTGAGCTGAATATAATCAAACTAAAAG
GACTTTGATGACAGAAAACACTTCTCGCCTTTAGTTATGT
Found at i:36991 original size:57 final size:59
Alignment explanation
Indices: 36854--37004 Score: 191
Period size: 57 Copynumber: 2.6 Consensus size: 59
36844 TCGTTGAGCA
* **
36854 TTGAGTTAGATATCCTTCATTGTGAAGTTGAAATCCAAGTATTGTTTCACGAAATTGGCT
1 TTGAGTTGGATATCCTTCATTGTGAAGTTGAAATCCAAGTATTGAATCACG-AATTGGCT
* * * * *
36914 TTGAGTTGGATATCGTTCATTGTGAAGTTGAAATCCAA-TCTTGAAT-ATTG-TTTTGCT
1 TTGAGTTGGATATCCTTCATTGTGAAGTTGAAATCCAAGTATTGAATCA-CGAATTGGCT
36971 TTGAGTTGGATATCCTTCATTGTGAAGTTGAAAT
1 TTGAGTTGGATATCCTTCATTGTGAAGTTGAAAT
37005 TTAATATTTT
Statistics
Matches: 81, Mismatches: 9, Indels: 5
0.85 0.09 0.05
Matches are distributed among these distances:
57 38 0.47
58 1 0.01
59 6 0.07
60 36 0.44
ACGTcount: A:0.26, C:0.11, G:0.21, T:0.41
Consensus pattern (59 bp):
TTGAGTTGGATATCCTTCATTGTGAAGTTGAAATCCAAGTATTGAATCACGAATTGGCT
Found at i:37253 original size:156 final size:156
Alignment explanation
Indices: 36969--37255 Score: 405
Period size: 156 Copynumber: 1.8 Consensus size: 156
36959 TATTGTTTTG
* * * ** *
36969 CTTTGAGTTGGATATCCTTCATTGTGAAGTTGAAATTTAATATTTTATAAGTTGTGTCGATTCGA
1 CTTTGAATTGGATATCATTCATTGTGAAGTTAAAATCCAATATTGTATAAGTTGTGTCGATTCGA
* * * * *
37034 GTTCAATATCCTTCGCTGTGAAGTTGAAATTGACTCTGAATGAAACTGAAAAGTTATTTGTTGAC
66 ATCCAATATCCTTCACTGTGAAGTTAAAATTGACTCTAAATGAAACTGAAAAGTTATTTGTTGAC
37099 ATACGCTAATTCACTGTGAAGTTGAA
131 ATACGCTAATTCACTGTGAAGTTGAA
* * * *
37125 CTTTGAATTGGATATCATT-AGTTGTGAAGTTAAAATCCAATCTTGTGTAAGTTGTGTTGTTTCG
1 CTTTGAATTGGATATCATTCA-TTGTGAAGTTAAAATCCAATATTGTATAAGTTGTGTCGATTCG
* *
37189 AATCCAATATCCTTCACTGTGAAGTTAAAATTGACTCTAAATGAAACTGGAAAGTTGTTTGTTGA
65 AATCCAATATCCTTCACTGTGAAGTTAAAATTGACTCTAAATGAAACTGAAAAGTTATTTGTTGA
37254 CA
130 CA
37256 GACAGCTTTT
Statistics
Matches: 113, Mismatches: 17, Indels: 2
0.86 0.13 0.02
Matches are distributed among these distances:
155 1 0.01
156 112 0.99
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (156 bp):
CTTTGAATTGGATATCATTCATTGTGAAGTTAAAATCCAATATTGTATAAGTTGTGTCGATTCGA
ATCCAATATCCTTCACTGTGAAGTTAAAATTGACTCTAAATGAAACTGAAAAGTTATTTGTTGAC
ATACGCTAATTCACTGTGAAGTTGAA
Found at i:42289 original size:30 final size:30
Alignment explanation
Indices: 42210--42321 Score: 84
Period size: 30 Copynumber: 3.7 Consensus size: 30
42200 AAAAAGAAAA
* * * *
42210 AGAAATTTAAAGTACCAAAATAGCACAAAC
1 AGAAAATTAAAGGACTAAAATAGTACAAAC
* *
42240 AGAAAATTAAAGGATTAAAATAGTATAAAC
1 AGAAAATTAAAGGACTAAAATAGTACAAAC
* * * *
42270 AGAAAGTTAAGAGG-CTAAAACAGTAAAAAT
1 AGAAAATTAA-AGGACTAAAATAGTACAAAC
* *
42300 A-AAAATTTAAAAGACCAAAATA
1 AGAAAA-TTAAAGGACTAAAATA
42322 AAATAACAGT
Statistics
Matches: 64, Mismatches: 15, Indels: 6
0.75 0.18 0.07
Matches are distributed among these distances:
29 5 0.08
30 56 0.88
31 3 0.05
ACGTcount: A:0.60, C:0.09, G:0.12, T:0.19
Consensus pattern (30 bp):
AGAAAATTAAAGGACTAAAATAGTACAAAC
Found at i:45531 original size:14 final size:14
Alignment explanation
Indices: 45497--45533 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
45487 ACCAAAAAAC
*
45497 AATAAAAAAAAGTA
1 AATAAATAAAAGTA
*
45511 AATAAATAAAATTA
1 AATAAATAAAAGTA
45525 AATAAATAA
1 AATAAATAA
45534 TAATATAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.03, T:0.22
Consensus pattern (14 bp):
AATAAATAAAAGTA
Found at i:45538 original size:24 final size:25
Alignment explanation
Indices: 45511--45582 Score: 75
Period size: 24 Copynumber: 3.0 Consensus size: 25
45501 AAAAAAAGTA
45511 AATAAATAAAATTAAATA-AATA-AT
1 AATAAA-AAAATTAAATATAATATAT
45535 AATATAAAAATATT-AATATAATATAT
1 AATA-AAAAA-ATTAAATATAATATAT
45561 AAT-AAAAAATTAAAT-T-ATATAT
1 AATAAAAAAATTAAATATAATATAT
45583 CATATATGCG
Statistics
Matches: 43, Mismatches: 0, Indels: 12
0.78 0.00 0.22
Matches are distributed among these distances:
22 6 0.14
23 4 0.09
24 19 0.44
25 9 0.21
26 5 0.12
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (25 bp):
AATAAAAAAATTAAATATAATATAT
Found at i:45545 original size:14 final size:15
Alignment explanation
Indices: 45511--45565 Score: 62
Period size: 14 Copynumber: 3.8 Consensus size: 15
45501 AAAAAAAGTA
45511 AATAAATAA-AAT-T
1 AATAAATAATAATAT
45524 AAATAAATAATAATAT
1 -AATAAATAATAATAT
*
45540 AA-AAATATTAATAT
1 AATAAATAATAATAT
*
45554 AATATATAATAA
1 AATAAATAATAA
45566 AAAATTAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 5
0.81 0.07 0.12
Matches are distributed among these distances:
14 22 0.63
15 12 0.34
16 1 0.03
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (15 bp):
AATAAATAATAATAT
Found at i:45652 original size:36 final size:35
Alignment explanation
Indices: 45609--45920 Score: 201
Period size: 36 Copynumber: 8.9 Consensus size: 35
45599 AAATAATTAT
*
45609 TTTCAAAATCATATAATATAATATATTTTCAAAATA
1 TTTCAAAA-CATATATTATAATATATTTTCAAAATA
*
45645 TTTCAAAACTATATATTATATATATATATTCAAAATA
1 TTTCAAAAC-ATATATTATA-ATATATTTTCAAAATA
* * *
45682 TTTTAAAA-ACTATATTCA-AA-AT-GTTTCGAAA-A
1 TTTCAAAACA-TATATT-ATAATATATTTTCAAAATA
* *
45714 -TT------ATATATTATATATATTTTTTCAAAATGT
1 TTTCAAAACATATATTATA-ATATATTTTCAAAAT-A
*
45744 TTTAAAAACTATATATTAT-ATATATTTTCAAAATGA
1 TTTCAAAAC-ATATATTATAATATATTTTCAAAAT-A
* *
45780 TTTGAAAACTATATATTAT-ATATATTTTCAAAATGT
1 TTTCAAAAC-ATATATTATAATATATTTTCAAAAT-A
* * *
45816 TTTGAAAAC-TATATTATATATATATATATCAAAATGT
1 TTTCAAAACATATATTATA-ATATAT-TTTCAAAAT-A
* *
45853 TTTAAAAACTATATATTAT-ATA-AGTTTTCAAAATT
1 TTTCAAAAC-ATATATTATAATATA-TTTTCAAAATA
*
45888 TTTAAAAACTATATATTAT-ATATATTTTCAAAA
1 TTTCAAAAC-ATATATTATAATATATTTTCAAAA
45921 AATATACTAC
Statistics
Matches: 235, Mismatches: 16, Indels: 51
0.78 0.05 0.17
Matches are distributed among these distances:
24 1 0.00
25 7 0.03
26 2 0.01
27 2 0.01
28 7 0.03
31 4 0.02
32 1 0.00
33 6 0.03
34 10 0.04
35 35 0.15
36 98 0.42
37 45 0.19
38 9 0.04
39 8 0.03
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.45
Consensus pattern (35 bp):
TTTCAAAACATATATTATAATATATTTTCAAAATA
Found at i:45713 original size:23 final size:23
Alignment explanation
Indices: 45669--45719 Score: 66
Period size: 23 Copynumber: 2.2 Consensus size: 23
45659 ATTATATATA
*
45669 TATATTCAAAATATTTTAAAAAC
1 TATATTCAAAATATTTCAAAAAC
* * *
45692 TATATTCAAAATGTTTCGAAAAT
1 TATATTCAAAATATTTCAAAAAC
45715 TATAT
1 TATAT
45720 ATTATATATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.47, C:0.08, G:0.04, T:0.41
Consensus pattern (23 bp):
TATATTCAAAATATTTCAAAAAC
Found at i:45720 original size:25 final size:23
Alignment explanation
Indices: 45666--45722 Score: 62
Period size: 23 Copynumber: 2.4 Consensus size: 23
45656 TATATTATAT
*
45666 ATATATATTCAAAATATTTTAAA
1 ATATATATTCAAAATATTTGAAA
*
45689 A-ACTATATTCAAAATGTTTCGAAA
1 ATA-TATATTCAAAATATTT-GAAA
45713 ATTATATATT
1 A-TATATATT
45723 ATATATATTT
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
22 1 0.04
23 16 0.57
24 4 0.14
25 6 0.21
26 1 0.04
ACGTcount: A:0.47, C:0.07, G:0.04, T:0.42
Consensus pattern (23 bp):
ATATATATTCAAAATATTTGAAA
Found at i:45727 original size:61 final size:60
Alignment explanation
Indices: 45636--45757 Score: 190
Period size: 61 Copynumber: 2.0 Consensus size: 60
45626 ATAATATATT
45636 TTCAAAATATTTCAAAACTATATATTATATATATATATTCAAAATATTTTAAAAACTATA
1 TTCAAAATATTTCAAAACTATATATTATATATATATATTCAAAATATTTTAAAAACTATA
* * * * *
45696 TTCAAAATGTTTCGAAAATTATATATTATATATATTTTTTCAAAATGTTTTAAAAACTATA
1 TTCAAAATATTTC-AAAACTATATATTATATATATATATTCAAAATATTTTAAAAACTATA
45757 T
1 T
45758 ATTATATATA
Statistics
Matches: 56, Mismatches: 5, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
60 12 0.21
61 44 0.79
ACGTcount: A:0.46, C:0.07, G:0.02, T:0.44
Consensus pattern (60 bp):
TTCAAAATATTTCAAAACTATATATTATATATATATATTCAAAATATTTTAAAAACTATA
Found at i:45793 original size:72 final size:72
Alignment explanation
Indices: 45696--45920 Score: 314
Period size: 72 Copynumber: 3.1 Consensus size: 72
45686 AAAAACTATA
* *
45696 TTCAAAATG-TTTCGAAAATTATATATTATATATATTTTTTCAAAATGTTTTAAAAACTATATAT
1 TTCAAAATGATTT-AAAAACTATATATTATATATA--TTTTCAAAATGTTTTAAAAACTATATAT
45760 TATATATATT
63 TATATATATT
* *
45770 TTCAAAATGATTTGAAAACTATATATTATATATATTTTCAAAATGTTTTGAAAACTATAT-TATA
1 TTCAAAATGATTTAAAAACTATATATTATATATATTTTCAAAATGTTTTAAAAACTATATAT-TA
45834 TATATATAT
65 TATATAT-T
* *
45843 ATCAAAATGTTTTAAAAACTATATATTATATA-AGTTTTCAAAAT-TTTTAAAAACTATATATTA
1 TTCAAAATGATTTAAAAACTATATATTATATATA-TTTTCAAAATGTTTTAAAAACTATATATTA
45906 TATATATT
65 TATATATT
45914 TTCAAAA
1 TTCAAAA
45921 AATATACTAC
Statistics
Matches: 139, Mismatches: 7, Indels: 13
0.87 0.04 0.08
Matches are distributed among these distances:
71 8 0.06
72 58 0.42
73 41 0.29
74 29 0.21
75 3 0.02
ACGTcount: A:0.44, C:0.06, G:0.04, T:0.46
Consensus pattern (72 bp):
TTCAAAATGATTTAAAAACTATATATTATATATATTTTCAAAATGTTTTAAAAACTATATATTAT
ATATATT
Found at i:46740 original size:17 final size:17
Alignment explanation
Indices: 46712--46745 Score: 52
Period size: 16 Copynumber: 2.0 Consensus size: 17
46702 TTTTTTTAGT
46712 AATTTATTTAATTATTTA
1 AATTTATTTAA-TATTTA
46730 AATTT-TTTAATATTTA
1 AATTTATTTAATATTTA
46746 TTTAATTAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 6 0.38
17 5 0.31
18 5 0.31
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (17 bp):
AATTTATTTAATATTTA
Found at i:46743 original size:24 final size:24
Alignment explanation
Indices: 46716--46761 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
46706 TTTAGTAATT
*
46716 TATTTAATTATTTAAATTTTTTAA
1 TATTTAATTAATTAAATTTTTTAA
* *
46740 TATTTATTTAATTAATTTTTTT
1 TATTTAATTAATTAAATTTTTT
46762 TGCAGATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (24 bp):
TATTTAATTAATTAAATTTTTTAA
Found at i:49060 original size:33 final size:34
Alignment explanation
Indices: 49023--49105 Score: 107
Period size: 33 Copynumber: 2.5 Consensus size: 34
49013 AAATACTTAC
49023 TTTATTTTGTTAATTTGGTTGGA-TTTTT-TAAAA
1 TTTATTTTGTTAATTTGGTTGGACTTTTTCT-AAA
* * *
49056 TTTATTTTGTTTATTTTGTTGGACTTTTTCTTAA
1 TTTATTTTGTTAATTTGGTTGGACTTTTTCTAAA
*
49090 TTTATTTTGATAATTT
1 TTTATTTTGTTAATTT
49106 TGTTTATTAC
Statistics
Matches: 43, Mismatches: 5, Indels: 3
0.84 0.10 0.06
Matches are distributed among these distances:
33 21 0.49
34 21 0.49
35 1 0.02
ACGTcount: A:0.20, C:0.02, G:0.12, T:0.65
Consensus pattern (34 bp):
TTTATTTTGTTAATTTGGTTGGACTTTTTCTAAA
Found at i:49092 original size:34 final size:33
Alignment explanation
Indices: 49018--49109 Score: 114
Period size: 34 Copynumber: 2.8 Consensus size: 33
49008 TCATTAAATA
* *
49018 CTTACTTTATTTTGTTAATTTGGTTGGATTTTT
1 CTTAATTTATTTTGTTAATTTTGTTGGATTTTT
* *
49051 -TAAAATTTATTTTGTTTATTTTGTTGGACTTTTT
1 CT-TAATTTATTTTGTTAATTTTGTTGGA-TTTTT
*
49085 CTTAATTTATTTTGATAATTTTGTT
1 CTTAATTTATTTTGTTAATTTTGTT
49110 TATTACCATT
Statistics
Matches: 49, Mismatches: 7, Indels: 5
0.80 0.11 0.08
Matches are distributed among these distances:
32 1 0.02
33 22 0.45
34 25 0.51
35 1 0.02
ACGTcount: A:0.20, C:0.04, G:0.12, T:0.64
Consensus pattern (33 bp):
CTTAATTTATTTTGTTAATTTTGTTGGATTTTT
Found at i:63060 original size:17 final size:17
Alignment explanation
Indices: 63040--63078 Score: 51
Period size: 17 Copynumber: 2.3 Consensus size: 17
63030 TTATTAATAA
63040 AAAATATAAAAAAAATT
1 AAAATATAAAAAAAATT
* * *
63057 AAAATATATAATAATTT
1 AAAATATAAAAAAAATT
63074 AAAAT
1 AAAAT
63079 TTTCAAGGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (17 bp):
AAAATATAAAAAAAATT
Found at i:63479 original size:24 final size:25
Alignment explanation
Indices: 63452--63498 Score: 62
Period size: 24 Copynumber: 1.9 Consensus size: 25
63442 TAAAATAATA
63452 TAAATTCATAA-AAATA-AAAAACTC
1 TAAATT-ATAATAAATATAAAAACTC
*
63476 TAAATTTTAATAAATATAAAAAC
1 TAAATTATAATAAATATAAAAAC
63499 GTTTTGAGTT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 3 0.15
24 11 0.55
25 6 0.30
ACGTcount: A:0.62, C:0.09, G:0.00, T:0.30
Consensus pattern (25 bp):
TAAATTATAATAAATATAAAAACTC
Found at i:68684 original size:53 final size:53
Alignment explanation
Indices: 68583--68949 Score: 426
Period size: 53 Copynumber: 7.0 Consensus size: 53
68573 ATCTTCAAAT
* * * ***
68583 TACGGGTCCGCTCCCTCTTG-TTCAGGGATTAAGGAACTCGAACAATCTTCTAAA
1 TACGGGTTCGCTCCCTCTTGCTTCAAGGAGT-A-GAACTCGAACAATCTTCTGCC
* * * * * *
68637 AATGGGTTCGCTCCCTATTGCTTCAAGGAGTAGAACTCGAATAATCTTTTGCT
1 TACGGGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTGCC
* * *
68690 TATGAGTTCGCTCCCTCTTGCTTGAGAGG-GTAGAACTCGAACAATCTTCTGCC
1 TACGGGTTCGCTCCCTCTTGCTTCA-AGGAGTAGAACTCGAACAATCTTCTGCC
* *
68743 TACGGGTTCACTCCCTCTTTCTTCAAGGAGTAGAACTCGAACAATCTTCTGCC
1 TACGGGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTGCC
*
68796 TACGAGTTCGCTCCCTCTTGCTTC-AGGAAGTAGAACTCGAACAATCTTCTGCC
1 TACGGGTTCGCTCCCTCTTGCTTCAAGG-AGTAGAACTCGAACAATCTTCTGCC
*
68849 TACGGGTTCGCTCCCTCTTACTTC-AGGTAGTAGAACTCGAACAATCTTCTGCC
1 TACGGGTTCGCTCCCTCTTGCTTCAAGG-AGTAGAACTCGAACAATCTTCTGCC
* * *
68902 TAC-AG-TC-CTCCATCTTGCTTC-AGGAAGTAAAACTCGAACAATCTTCTG
1 TACGGGTTCGCTCCCTCTTGCTTCAAGG-AGTAGAACTCGAACAATCTTCTG
68950 GTGTGATTCT
Statistics
Matches: 275, Mismatches: 34, Indels: 12
0.86 0.11 0.04
Matches are distributed among these distances:
50 37 0.13
51 2 0.01
52 7 0.03
53 201 0.73
54 20 0.07
55 8 0.03
ACGTcount: A:0.24, C:0.27, G:0.19, T:0.30
Consensus pattern (53 bp):
TACGGGTTCGCTCCCTCTTGCTTCAAGGAGTAGAACTCGAACAATCTTCTGCC
Found at i:69562 original size:93 final size:93
Alignment explanation
Indices: 69416--69588 Score: 271
Period size: 93 Copynumber: 1.9 Consensus size: 93
69406 TATTGATGAA
*
69416 TTTGCTTCATTACTCTTCGGTGAAGGATTACAAATTACCTGAAGTATTTAATCATCATGCT-TGA
1 TTTGCTTCATTACTCTTCGGTGAAGGATTACAAATTACCTAAAGTATTTAATCATCATGCTCT-A
69480 AAGACTTACTAATGGCACTTACTGATTGG
65 AAGACTTACTAATGGCACTTACTGATTGG
*
69509 TTTGCTTCATTACTCTTTC-GTGAAGGCTTACAAATTAGCCTAAAG-ATTTAATCATCATGCTCT
1 TTTGCTTCATTACTC-TTCGGTGAAGGATTACAAATTA-CCTAAAGTATTTAATCATCATGCTCT
*
69572 AAAGACTTATTAATGGC
64 AAAGACTTACTAATGGC
69589 CCTAAGGATT
Statistics
Matches: 74, Mismatches: 3, Indels: 6
0.89 0.04 0.07
Matches are distributed among these distances:
93 64 0.86
94 10 0.14
ACGTcount: A:0.29, C:0.18, G:0.16, T:0.37
Consensus pattern (93 bp):
TTTGCTTCATTACTCTTCGGTGAAGGATTACAAATTACCTAAAGTATTTAATCATCATGCTCTAA
AGACTTACTAATGGCACTTACTGATTGG
Found at i:69576 original size:22 final size:22
Alignment explanation
Indices: 69548--69618 Score: 58
Period size: 22 Copynumber: 3.3 Consensus size: 22
69538 ACAAATTAGC
69548 CTAAAGATTTAATCATCATGCT
1 CTAAAGATTTAATCATCATGCT
* * *
69570 CTAAAGACTT-AT--TAATGGCC
1 CTAAAGATTTAATCATCAT-GCT
* *
69590 CTAAGGATTTAAGCATCATGCT
1 CTAAAGATTTAATCATCATGCT
*
69612 CAAAAGA
1 CTAAAGA
69619 CTTATTGATG
Statistics
Matches: 35, Mismatches: 10, Indels: 8
0.66 0.19 0.15
Matches are distributed among these distances:
19 3 0.09
20 10 0.29
21 3 0.09
22 16 0.46
23 3 0.09
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (22 bp):
CTAAAGATTTAATCATCATGCT
Found at i:69607 original size:42 final size:42
Alignment explanation
Indices: 69547--69638 Score: 139
Period size: 42 Copynumber: 2.2 Consensus size: 42
69537 TACAAATTAG
* * *
69547 CCTAAAGATTTAATCATCATGCTCTAAAGACTTATTAATGGC
1 CCTAAGGATTTAAGCATCATGCTCAAAAGACTTATTAATGGC
*
69589 CCTAAGGATTTAAGCATCATGCTCAAAAGACTTATTGATGGC
1 CCTAAGGATTTAAGCATCATGCTCAAAAGACTTATTAATGGC
*
69631 CCGAAGGA
1 CCTAAGGA
69639 CTTACTAAGT
Statistics
Matches: 45, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 45 1.00
ACGTcount: A:0.35, C:0.20, G:0.17, T:0.28
Consensus pattern (42 bp):
CCTAAGGATTTAAGCATCATGCTCAAAAGACTTATTAATGGC
Found at i:73142 original size:28 final size:28
Alignment explanation
Indices: 73102--73158 Score: 114
Period size: 28 Copynumber: 2.0 Consensus size: 28
73092 AAGATCCTTG
73102 AAGTTATTCGTCGACTTTCCCAGCATTA
1 AAGTTATTCGTCGACTTTCCCAGCATTA
73130 AAGTTATTCGTCGACTTTCCCAGCATTA
1 AAGTTATTCGTCGACTTTCCCAGCATTA
73158 A
1 A
73159 CTCAAAGAAA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.26, C:0.25, G:0.14, T:0.35
Consensus pattern (28 bp):
AAGTTATTCGTCGACTTTCCCAGCATTA
Found at i:79900 original size:46 final size:48
Alignment explanation
Indices: 79809--79900 Score: 109
Period size: 46 Copynumber: 2.0 Consensus size: 48
79799 TTATTATTAT
* * ** *
79809 TTTTTTTTCTTTTTTCCTTCTGATTTATTTAATTTTTTTGTTTTTTTG
1 TTTTTTTTCTTTTTTCCTTCTCATTTATTTAAATTAATTGATTTTTTG
79857 TTTTTTTTC-TTTTTCCTT-TCATTTATTTAACATTAATT-ATTTTT
1 TTTTTTTTCTTTTTTCCTTCTCATTTATTTAA-ATTAATTGATTTTT
79901 CTTATCTAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 4
0.81 0.11 0.09
Matches are distributed among these distances:
46 16 0.42
47 13 0.34
48 9 0.24
ACGTcount: A:0.13, C:0.10, G:0.03, T:0.74
Consensus pattern (48 bp):
TTTTTTTTCTTTTTTCCTTCTCATTTATTTAAATTAATTGATTTTTTG
Found at i:79900 original size:47 final size:48
Alignment explanation
Indices: 79809--79900 Score: 116
Period size: 47 Copynumber: 1.9 Consensus size: 48
79799 TTATTATTAT
* * ** *
79809 TTTTTTTTCTTTTTTCCTTCTGATTTATTTAATTTTTTTGTTTTTTTG
1 TTTTTTTTCTTTTTTCCTTCTCATTTATTTAAATTAATTATTTTTTTG
79857 TTTTTTTTC-TTTTTCCTT-TCATTTATTTAACATTAATTATTTTT
1 TTTTTTTTCTTTTTTCCTTCTCATTTATTTAA-ATTAATTATTTTT
79901 CTTATCTAAT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
46 11 0.29
47 18 0.47
48 9 0.24
ACGTcount: A:0.13, C:0.10, G:0.03, T:0.74
Consensus pattern (48 bp):
TTTTTTTTCTTTTTTCCTTCTCATTTATTTAAATTAATTATTTTTTTG
Found at i:92109 original size:27 final size:27
Alignment explanation
Indices: 92067--92128 Score: 76
Period size: 27 Copynumber: 2.3 Consensus size: 27
92057 GTATTTCGCT
92067 TGAAAAAAAAATGAAAAAGACAA-AAAA
1 TGAAAAAAAAATGAAAAAGA-AAGAAAA
*
92094 TGAAAAATAAAA-GAAAGAGAAAGAAAA
1 TGAAAAA-AAAATGAAAAAGAAAGAAAA
92121 -GAAAAAAA
1 TGAAAAAAA
92129 TAAAAGGAGG
Statistics
Matches: 32, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
25 2 0.06
26 8 0.25
27 18 0.56
28 4 0.12
ACGTcount: A:0.77, C:0.02, G:0.15, T:0.06
Consensus pattern (27 bp):
TGAAAAAAAAATGAAAAAGAAAGAAAA
Found at i:93340 original size:48 final size:48
Alignment explanation
Indices: 93264--93534 Score: 358
Period size: 48 Copynumber: 5.8 Consensus size: 48
93254 CAACTCCCCC
*
93264 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCA
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTCTCCA
* * *
93312 AGATTTGATATTCCCTTTAGAGTAAGTGGAACAAG----TC-T-GCC-
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTCTCCA
* * * *
93353 AGATCCGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAA
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTCTCCA
* * *
93401 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCTATCTTCTCCA
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTCTCCA
* * *
93449 AGATCTGATATTTCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCA
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTCTCCA
*
93497 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAGTCT
1 AGATCTGATATTCCCTTCAGAGTAAGTGGAACAAGTCT
93535 GCTTCGATTC
Statistics
Matches: 188, Mismatches: 28, Indels: 14
0.82 0.12 0.06
Matches are distributed among these distances:
41 30 0.16
42 2 0.01
43 1 0.01
44 2 0.01
45 2 0.01
46 1 0.01
47 1 0.01
48 149 0.79
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.31
Consensus pattern (48 bp):
AGATCTGATATTCCCTTCAGAGTAAGTGGAACAAGTCTCTCTTCTCCA
Found at i:93413 original size:89 final size:89
Alignment explanation
Indices: 93262--93536 Score: 424
Period size: 89 Copynumber: 3.0 Consensus size: 89
93252 ATCAACTCCC
*
93262 CCAGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCC
1 CCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCC
*
93327 TTTAGAGTAAGTGGAACAAGTCTG
66 TTCAGAGTAAGTGGAACAAGTCTG
* *
93351 CCAGATCCGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAAAGATTTGATATTCCC
1 CCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCC
* *
93416 TTCAGAGTAAGTGGAACAAATCTATCTTCT
66 TTCAGAGTAAGTGGAAC-AA---GTC-T-G
*
93446 CCAAGATCTGATATTTCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCC
1 CC-AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCC
93511 CTTCAGAGTAAGTGGAACAAGTCTG
65 CTTCAGAGTAAGTGGAACAAGTCTG
93536 C
1 C
93537 TTCGATTCAA
Statistics
Matches: 168, Mismatches: 11, Indels: 13
0.88 0.06 0.07
Matches are distributed among these distances:
89 78 0.46
90 3 0.02
91 1 0.01
92 2 0.01
93 2 0.01
94 1 0.01
95 4 0.02
96 77 0.46
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.31
Consensus pattern (89 bp):
CCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCC
TTCAGAGTAAGTGGAACAAGTCTG
Found at i:93487 original size:96 final size:90
Alignment explanation
Indices: 93262--93530 Score: 414
Period size: 96 Copynumber: 2.9 Consensus size: 90
93252 ATCAACTCCC
*
93262 CCAGATCTGATATTCCCTTCAGAGTAAGTGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCC
1 CCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCC
* *
93327 TTTAGAGTAAGTGGAAC-AAGTCTG
66 TTCAGAGTAAGTGGAACAAAATCTG
* *
93351 CCAGATCCGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCAAAGATTTGATATTCCC
1 CCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCC
*
93416 TTCAGAGTAAGTGGAACAAATCTATCTTCT
66 TTCAGAGTAAGTGGAACAAA---ATC-T-G
*
93446 CCAAGATCTGATATTTCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCC
1 CC-AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCC
93511 CTTCAGAGTAAGTGGAACAA
65 CTTCAGAGTAAGTGGAACAA
93531 GTCTGCTTCG
Statistics
Matches: 164, Mismatches: 9, Indels: 7
0.91 0.05 0.04
Matches are distributed among these distances:
89 78 0.48
90 2 0.01
93 2 0.01
94 1 0.01
95 2 0.01
96 79 0.48
ACGTcount: A:0.28, C:0.23, G:0.19, T:0.30
Consensus pattern (90 bp):
CCAGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCC
TTCAGAGTAAGTGGAACAAAATCTG
Found at i:93659 original size:113 final size:112
Alignment explanation
Indices: 93449--93652 Score: 313
Period size: 113 Copynumber: 1.8 Consensus size: 112
93439 ATCTTCTCCA
*
93449 AGATCTGATATTTCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCCTT
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCCTT
* * *
93514 CAGAGTAAGTGGAACAAGTCTGCTTCGATTCAATGGATCAACTCCCTC
66 CAGAGTAAGCGGAACAAATCTCCTTC-ATTCAATGGATCAACTCCCTC
*
93562 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTTCCAAGATTTGATATTCCCTT
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCCTT
93627 CAGAAAAG-AAGCGGAACAAATC-CCTT
66 CAG---AGTAAGCGGAACAAATCTCCTT
93653 TCTTCAAGAT
Statistics
Matches: 83, Mismatches: 5, Indels: 5
0.89 0.05 0.05
Matches are distributed among these distances:
113 66 0.80
114 3 0.04
115 12 0.14
116 2 0.02
ACGTcount: A:0.28, C:0.24, G:0.18, T:0.30
Consensus pattern (112 bp):
AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCCTT
CAGAGTAAGCGGAACAAATCTCCTTCATTCAATGGATCAACTCCCTC
Found at i:93672 original size:49 final size:48
Alignment explanation
Indices: 93562--93674 Score: 133
Period size: 48 Copynumber: 2.3 Consensus size: 48
93552 CAACTCCCTC
* **
93562 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTTCCA
1 AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAATCTCTCTTTTCCA
*
93610 AGATTTGATATTCCCTTCAGAAAAG-AAGCGGAACAAATC-C-CTTTCTTCA
1 AGATTTGATATTCCCTTCAG---AGTAAGCGGAACAAATCTCTCTTT-TCCA
93659 AGATTTGATATTCCCT
1 AGATTTGATATTCCCT
93675 GAGTGACAGT
Statistics
Matches: 57, Mismatches: 4, Indels: 7
0.84 0.06 0.10
Matches are distributed among these distances:
48 23 0.40
49 20 0.35
50 12 0.21
51 2 0.04
ACGTcount: A:0.29, C:0.23, G:0.16, T:0.32
Consensus pattern (48 bp):
AGATTTGATATTCCCTTCAGAGTAAGCGGAACAAATCTCTCTTTTCCA
Found at i:93688 original size:161 final size:160
Alignment explanation
Indices: 93401--93695 Score: 400
Period size: 161 Copynumber: 1.8 Consensus size: 160
93391 CTCTTCTCAA
* * *
93401 AGATTTGATATTCCCTTCAGAGTAAGTGGAACAAATCTATCTTCTCCAAGATCTGATATTTCCTT
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAAATCTATCTTCTCCAAGATCTGATATTCCCTT
** *
93466 CAGAGTAAGCGGAACAGGTCTCTCTTCTCCAAGATTTGATATTCCCTTCAGAGTAAGTGGAACAA
66 CAGAGTAAGCGGAACAAATCCCTCTTCTCCAAGATTTGATATTCCCTT-AGAGTAAGTGGAACAA
93531 GTCTGCTTCGATTCAATGGATCAACTCCCTC
130 GTCTGCTTCGATTCAATGGATCAACTCCCTC
** * * *
93562 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAGGTCTCTCTTTTCCAAGATTTGATATTCCCTT
1 AGATCTGATATTCCCTTCAGAGTAAGCGGAACAAATCTATCTTCTCCAAGATCTGATATTCCCTT
*
93627 CAGAAAAG-AAGCGGAACAAATCCCT-TTCTTCAAGATTTGATATTCCC-T-GAGTGACAGTGGA
66 CAG---AGTAAGCGGAACAAATCCCTCTTCTCCAAGATTTGATATTCCCTTAGAGT-A-AGTGGA
93688 ACAAGTCT
126 ACAAGTCT
93696 ACCCCCGATT
Statistics
Matches: 117, Mismatches: 12, Indels: 10
0.84 0.09 0.07
Matches are distributed among these distances:
159 4 0.03
160 1 0.01
161 75 0.64
162 21 0.18
163 14 0.12
164 2 0.02
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.31
Consensus pattern (160 bp):
AGATCTGATATTCCCTTCAGAGTAAGCGGAACAAATCTATCTTCTCCAAGATCTGATATTCCCTT
CAGAGTAAGCGGAACAAATCCCTCTTCTCCAAGATTTGATATTCCCTTAGAGTAAGTGGAACAAG
TCTGCTTCGATTCAATGGATCAACTCCCTC
Found at i:96013 original size:3 final size:3
Alignment explanation
Indices: 95998--96063 Score: 123
Period size: 3 Copynumber: 22.0 Consensus size: 3
95988 AATTTTTAAT
*
95998 TTA TTA CTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
96046 TTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
96064 GTTTATATCT
Statistics
Matches: 61, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
3 61 1.00
ACGTcount: A:0.33, C:0.02, G:0.00, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:97505 original size:27 final size:27
Alignment explanation
Indices: 97475--97531 Score: 114
Period size: 27 Copynumber: 2.1 Consensus size: 27
97465 CGGTCGCATC
97475 TGATTTCCTTCGTTTTCTAGCCTTCAA
1 TGATTTCCTTCGTTTTCTAGCCTTCAA
97502 TGATTTCCTTCGTTTTCTAGCCTTCAA
1 TGATTTCCTTCGTTTTCTAGCCTTCAA
97529 TGA
1 TGA
97532 GGTTGTTTTT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 30 1.00
ACGTcount: A:0.16, C:0.25, G:0.12, T:0.47
Consensus pattern (27 bp):
TGATTTCCTTCGTTTTCTAGCCTTCAA
Found at i:99968 original size:60 final size:60
Alignment explanation
Indices: 99897--100088 Score: 207
Period size: 60 Copynumber: 3.2 Consensus size: 60
99887 CCCCTAGGCT
99897 ATAAGGACTTACCCAATGCACAAAGAAGAGGACCCACCCTAAGAAAGTACCTTAGGCTCC
1 ATAAGGACTTACCCAATGCACAAAGAAGAGGACCCACCCTAAGAAAGTACCTTAGGCTCC
** *** * * ** *
99957 ATAAGGACTTACCTTA-G-TTGAAG-CGCAGGAGCCCA-CCTGAGGGGAGTACCCCTAGGCT--
1 ATAAGGACTTACCCAATGCACAAAGAAG-AGGA-CCCACCCT-AAGAAAGTA-CCTTAGGCTCC
100015 ATAAGGACTTACCCAATGCACAAAGAAGAGGACCCACCCTAAGAAAGTACCTTAGGCTCC
1 ATAAGGACTTACCCAATGCACAAAGAAGAGGACCCACCCTAAGAAAGTACCTTAGGCTCC
*
100075 ATAAGGTCTTACCC
1 ATAAGGACTTACCC
100089 TAGGCCTAGT
Statistics
Matches: 101, Mismatches: 21, Indels: 20
0.71 0.15 0.14
Matches are distributed among these distances:
57 1 0.01
58 32 0.32
59 22 0.22
60 45 0.45
61 1 0.01
ACGTcount: A:0.34, C:0.28, G:0.21, T:0.17
Consensus pattern (60 bp):
ATAAGGACTTACCCAATGCACAAAGAAGAGGACCCACCCTAAGAAAGTACCTTAGGCTCC
Found at i:99987 original size:118 final size:118
Alignment explanation
Indices: 99837--100091 Score: 474
Period size: 118 Copynumber: 2.2 Consensus size: 118
99827 GCACCATGGA
99837 CCATAAGGACTTACCCTAGCTGAAGCGCAGGAGCCCACCTGAGAGGAGTACCCCTAGGCTATAAG
1 CCATAAGGACTTACCCTAGCTGAAGCGCAGGAGCCCACCTGAGAGGAGTACCCCTAGGCTATAAG
99902 GACTTACCCAATGCACAAAGAAGAGGACCCACCCTAAGAAAGTACCTTAGGCT
66 GACTTACCCAATGCACAAAGAAGAGGACCCACCCTAAGAAAGTACCTTAGGCT
* * *
99955 CCATAAGGACTTACCTTAGTTGAAGCGCAGGAGCCCACCTGAGGGGAGTACCCCTAGGCTATAAG
1 CCATAAGGACTTACCCTAGCTGAAGCGCAGGAGCCCACCTGAGAGGAGTACCCCTAGGCTATAAG
100020 GACTTACCCAATGCACAAAGAAGAGGACCCACCCTAAGAAAGTACCTTAGGCT
66 GACTTACCCAATGCACAAAGAAGAGGACCCACCCTAAGAAAGTACCTTAGGCT
*
100073 CCATAAGGTCTTACCCTAG
1 CCATAAGGACTTACCCTAG
100092 GCCTAGTATG
Statistics
Matches: 132, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
118 132 1.00
ACGTcount: A:0.32, C:0.28, G:0.23, T:0.17
Consensus pattern (118 bp):
CCATAAGGACTTACCCTAGCTGAAGCGCAGGAGCCCACCTGAGAGGAGTACCCCTAGGCTATAAG
GACTTACCCAATGCACAAAGAAGAGGACCCACCCTAAGAAAGTACCTTAGGCT
Found at i:101925 original size:32 final size:33
Alignment explanation
Indices: 101889--101971 Score: 80
Period size: 31 Copynumber: 2.5 Consensus size: 33
101879 TTGATCACTA
* * *
101889 AAATTTATTTTTTGTTTAGTTACT-TAACTTTC
1 AAATTTATTTTTTATTTAATCACTCTAACTTTC
* * *
101921 AAA-TTACTCTTAATTTAATCACTCTAACTTTC
1 AAATTTATTTTTTATTTAATCACTCTAACTTTC
101953 AAATTTATATTTTTTATTT
1 AAA-TT-TATTTTTTATTT
101972 TTAATTATAT
Statistics
Matches: 38, Mismatches: 9, Indels: 5
0.73 0.17 0.10
Matches are distributed among these distances:
31 14 0.37
32 14 0.37
34 1 0.03
35 9 0.24
ACGTcount: A:0.30, C:0.12, G:0.02, T:0.55
Consensus pattern (33 bp):
AAATTTATTTTTTATTTAATCACTCTAACTTTC
Found at i:104217 original size:28 final size:30
Alignment explanation
Indices: 104171--104232 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 30
104161 ATTTTATTAG
* *
104171 ATTAAATTTAGAATTTTAATAATTGTT-TT
1 ATTAAATTTAGAATATTAATAATTATTATT
*
104200 ATTAATTTTA-AATATTAATAATTATTATT
1 ATTAAATTTAGAATATTAATAATTATTATT
104229 ATTA
1 ATTA
104233 TTATTATTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 14 0.48
29 15 0.52
ACGTcount: A:0.42, C:0.00, G:0.03, T:0.55
Consensus pattern (30 bp):
ATTAAATTTAGAATATTAATAATTATTATT
Found at i:104468 original size:22 final size:21
Alignment explanation
Indices: 104443--104483 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
104433 TTAATAAATT
104443 TATTTTTATTAAATATTTTTGG
1 TATTTTTATTAAAT-TTTTTGG
*
104465 TATTTTTATTTAATTTTTT
1 TATTTTTATTAAATTTTTT
104484 AAATAATTAT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 5 0.28
22 13 0.72
ACGTcount: A:0.24, C:0.00, G:0.05, T:0.71
Consensus pattern (21 bp):
TATTTTTATTAAATTTTTTGG
Found at i:105519 original size:22 final size:22
Alignment explanation
Indices: 105489--105567 Score: 131
Period size: 22 Copynumber: 3.6 Consensus size: 22
105479 TTGGCAGATA
*
105489 AAATCCAGGTTGAATCTTTATC
1 AAATACAGGTTGAATCTTTATC
105511 AAATACAGGTTGAATCTTTATC
1 AAATACAGGTTGAATCTTTATC
105533 AAATACAGGTTGAATCTTTATC
1 AAATACAGGTTGAATCTTTATC
* *
105555 AGATACAGATTGA
1 AAATACAGGTTGA
105568 GTTCAAATCG
Statistics
Matches: 54, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 54 1.00
ACGTcount: A:0.37, C:0.14, G:0.15, T:0.34
Consensus pattern (22 bp):
AAATACAGGTTGAATCTTTATC
Found at i:105887 original size:21 final size:21
Alignment explanation
Indices: 105863--105935 Score: 78
Period size: 23 Copynumber: 3.3 Consensus size: 21
105853 TAAATATATA
105863 TATATAAAGTATAAGTATAAG
1 TATATAAAGTATAAGTATAAG
105884 TATATAAAGTAT-A-TATAAG
1 TATATAAAGTATAAGTATAAG
105903 TATTTATATAAAGTATAAAGTATAAAG
1 ----TATATAAAGTAT-AAGTAT-AAG
105930 TATATA
1 TATATA
105936 TAAAATATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 14
0.76 0.00 0.24
Matches are distributed among these distances:
19 6 0.14
20 1 0.02
21 12 0.27
23 18 0.41
25 1 0.02
26 3 0.07
27 3 0.07
ACGTcount: A:0.52, C:0.00, G:0.11, T:0.37
Consensus pattern (21 bp):
TATATAAAGTATAAGTATAAG
Found at i:105893 original size:9 final size:9
Alignment explanation
Indices: 105863--105956 Score: 53
Period size: 9 Copynumber: 10.8 Consensus size: 9
105853 TAAATATATA
105863 TATATAAAG
1 TATATAAAG
105872 TATAAGTATAAG
1 TAT-A-TA-AAG
105884 TATATAAAG
1 TATATAAAG
105893 TATATATAAG
1 TATATA-AAG
105903 TAT-T----
1 TATATAAAG
105907 TATATAAAG
1 TATATAAAG
105916 --TATAAAG
1 TATATAAAG
105923 --TATAAAG
1 TATATAAAG
*
105930 TATATATAAAA
1 --TATATAAAG
*
105941 TATATAAGG
1 TATATAAAG
105950 TATATAA
1 TATATAA
105957 TATATATACT
Statistics
Matches: 69, Mismatches: 3, Indels: 26
0.70 0.03 0.27
Matches are distributed among these distances:
4 3 0.04
5 1 0.01
7 14 0.20
9 27 0.39
10 9 0.13
11 9 0.13
12 6 0.09
ACGTcount: A:0.53, C:0.00, G:0.11, T:0.36
Consensus pattern (9 bp):
TATATAAAG
Found at i:105900 original size:25 final size:24
Alignment explanation
Indices: 105872--105962 Score: 82
Period size: 23 Copynumber: 3.8 Consensus size: 24
105862 ATATATAAAG
105872 TATAAGTATAAGTATATAAAGTATA
1 TATAAGTATAAGTATATAAAG-ATA
*
105897 TATAAGTAT--TTATATAAAG-TA
1 TATAAGTATAAGTATATAAAGATA
*
105918 TA-AAGTATAAAGTATATATAAAATA
1 TATAAGTAT-AAGTATATA-AAGATA
*
105943 TATAAGGTATATAATATATA
1 TATAA-GTATA-AGTATATA
105963 TACTTTACAT
Statistics
Matches: 54, Mismatches: 4, Indels: 14
0.75 0.06 0.19
Matches are distributed among these distances:
20 6 0.11
21 4 0.07
23 15 0.28
24 2 0.04
25 13 0.24
26 3 0.06
27 11 0.20
ACGTcount: A:0.53, C:0.00, G:0.10, T:0.37
Consensus pattern (24 bp):
TATAAGTATAAGTATATAAAGATA
Found at i:105953 original size:7 final size:7
Alignment explanation
Indices: 105865--105933 Score: 54
Period size: 7 Copynumber: 9.6 Consensus size: 7
105855 AATATATATA
105865 TATAAAG
1 TATAAAG
105872 TAT-AAG
1 TATAAAG
105878 TAT-AAG
1 TATAAAG
105884 TATATAAAG
1 --TATAAAG
105893 TATATATAAG
1 --TATA-AAG
**
105903 TATTTA-
1 TATAAAG
105909 TATAAAG
1 TATAAAG
105916 TATAAAG
1 TATAAAG
105923 TATAAAG
1 TATAAAG
105930 TATA
1 TATA
105934 TATAAAATAT
Statistics
Matches: 53, Mismatches: 4, Indels: 10
0.79 0.06 0.15
Matches are distributed among these distances:
6 13 0.25
7 22 0.42
8 6 0.11
9 9 0.17
10 3 0.06
ACGTcount: A:0.52, C:0.00, G:0.12, T:0.36
Consensus pattern (7 bp):
TATAAAG
Found at i:107842 original size:19 final size:19
Alignment explanation
Indices: 107806--107842 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
107796 TGAAAATGAT
*
107806 TTGATTTTGAAAGCCAAAG
1 TTGATTTTGAAAACCAAAG
*
107825 TTGATTTTGAAAATCAAA
1 TTGATTTTGAAAACCAAA
107843 ATGAAATTTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.08, G:0.16, T:0.35
Consensus pattern (19 bp):
TTGATTTTGAAAACCAAAG
Found at i:110476 original size:20 final size:20
Alignment explanation
Indices: 110453--110497 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
110443 ATTTTATTTT
* * *
110453 ATATTGTTTGCTTCTGTTTG
1 ATATTGCTTGATTCTGCTTG
110473 ATATTGCTTGATTCTGCTTG
1 ATATTGCTTGATTCTGCTTG
110493 ATATT
1 ATATT
110498 TGTAAAGATT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.16, C:0.11, G:0.18, T:0.56
Consensus pattern (20 bp):
ATATTGCTTGATTCTGCTTG
Found at i:110497 original size:40 final size:40
Alignment explanation
Indices: 110417--110497 Score: 99
Period size: 40 Copynumber: 2.0 Consensus size: 40
110407 CAATAGCTGA
* * *
110417 TGTTTGATTCTGCTTGATATTGCATGATTTTATTTTATAT
1 TGTTTGATTCTGCTTGATATTGCATGATTCTACTTGATAT
* * * *
110457 TGTTTGCTTCTGTTTGATATTGCTTGATTCTGCTTGATAT
1 TGTTTGATTCTGCTTGATATTGCATGATTCTACTTGATAT
110497 T
1 T
110498 TGTAAAGATT
Statistics
Matches: 34, Mismatches: 7, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
40 34 1.00
ACGTcount: A:0.16, C:0.10, G:0.17, T:0.57
Consensus pattern (40 bp):
TGTTTGATTCTGCTTGATATTGCATGATTCTACTTGATAT
Found at i:110613 original size:23 final size:23
Alignment explanation
Indices: 110583--110639 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
110573 TGCTTTCTGA
*
110583 ATAC-ATGATGTTTGCTAAATTG
1 ATACAATGATGCTTGCTAAATTG
* *
110605 ATTCAATGATGCTTGCTGAATTG
1 ATACAATGATGCTTGCTAAATTG
*
110628 ATACAGTGATGC
1 ATACAATGATGC
110640 AAGGATGCTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
22 3 0.10
23 26 0.90
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (23 bp):
ATACAATGATGCTTGCTAAATTG
Found at i:116968 original size:23 final size:23
Alignment explanation
Indices: 116941--116993 Score: 65
Period size: 23 Copynumber: 2.3 Consensus size: 23
116931 TGTACCGAAA
*
116941 ACCACATT-GTTT-TCTCCCGAATG
1 ACCACATTAGTTTGTCT--CGAAGG
116964 ACCACATTAGTTTGTCTCGAAGG
1 ACCACATTAGTTTGTCTCGAAGG
116987 ACCACAT
1 ACCACAT
116994 AGAACCCTCG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
23 20 0.74
24 4 0.15
25 3 0.11
ACGTcount: A:0.26, C:0.28, G:0.15, T:0.30
Consensus pattern (23 bp):
ACCACATTAGTTTGTCTCGAAGG
Done.