Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005781.1 Hibiscus syriacus cultivar Beakdansim tig00013540_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: 116125
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:69 original size:18 final size:18
Alignment explanation
Indices: 38--72 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
28 TCCATTTTTT
* *
38 TTTATTTTTTAAATAATA
1 TTTATATTTAAAATAATA
56 TTTATATTTAAAATAAT
1 TTTATATTTAAAATAAT
73 CAAGAATAAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (18 bp):
TTTATATTTAAAATAATA
Found at i:386 original size:16 final size:17
Alignment explanation
Indices: 349--389 Score: 50
Period size: 16 Copynumber: 2.5 Consensus size: 17
339 TTAAATTTAA
*
349 AAAATATATTTAATATTT
1 AAAAT-TATCTAATATTT
367 -AAATTATCTAAT-TTT
1 AAAATTATCTAATATTT
382 AAAATTAT
1 AAAATTAT
390 TAAGATCCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
15 3 0.14
16 14 0.67
17 4 0.19
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (17 bp):
AAAATTATCTAATATTT
Found at i:2322 original size:20 final size:20
Alignment explanation
Indices: 2297--2561 Score: 241
Period size: 20 Copynumber: 13.8 Consensus size: 20
2287 TTACACATTC
* *
2297 ATTTGAATATCGCAACGCAA
1 ATTTGACTATCGCAACGCGA
2317 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * * *
2337 ATTTGATTATTGTAACTC-A
1 ATTTGACTATCGCAACGCGA
*
2356 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
2371 ATTTGACTATCGCAACACGA
1 ATTTGACTATCGCAACGCGA
*
2391 ATATGACTATCGCAACGC-A
1 ATTTGACTATCGCAACGCGA
*
2410 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
2425 ATTTGTCTATCGCAACTCGA
1 ATTTGACTATCGCAACGCGA
* *
2445 ATTTGACTATCGCAATG-GCT
1 ATTTGACTATCGCAACGCG-A
* *
2465 ATTTGACAATCGCAACGCAA
1 ATTTGACTATCGCAACGCGA
*
2485 ATTTGAGTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
2505 ATTTGAGTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* * *
2525 ATTTGATTATCGCAACGGGT
1 ATTTGACTATCGCAACGCGA
2545 ATTTGACTATCGCAACG
1 ATTTGACTATCGCAACG
2562 AGAAAATTGC
Statistics
Matches: 198, Mismatches: 33, Indels: 28
0.76 0.13 0.11
Matches are distributed among these distances:
14 17 0.09
15 6 0.03
19 6 0.03
20 169 0.85
ACGTcount: A:0.33, C:0.22, G:0.18, T:0.26
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:2374 original size:54 final size:54
Alignment explanation
Indices: 2305--2522 Score: 247
Period size: 54 Copynumber: 3.9 Consensus size: 54
2295 TCATTTGAAT
* * * * * *
2305 ATCGCAACGCAAATTTGACTATCGCAACGCGAATTTGATTATTGTAACTCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACACGAATTTGACTATCGCAACGCAAAA
*
2359 ATCGCAACGCGAATTTGACTATCGCAACACGAATATGACTATCGCAACGCAAAA
1 ATCGCAACGCGAATTTGACTATCGCAACACGAATTTGACTATCGCAACGCAAAA
* * * *
2413 ATCGCAACGCGAATTTGTCTATCGCAACTCGAATTTGACTATCGCAATGGCTATTTGACA
1 ATCGCAACGCGAATTTGACTATCGCAACACGAATTTGACTATCGCAA-CGC-A----AAA
* * * *
2473 ATCGCAACGCAAATTTGAGTATCGCAACGCGAATTTGAGTATCGCAACGC
1 ATCGCAACGCGAATTTGACTATCGCAACACGAATTTGACTATCGCAACGC
2523 GAATTTGATT
Statistics
Matches: 140, Mismatches: 18, Indels: 7
0.85 0.11 0.04
Matches are distributed among these distances:
54 91 0.65
55 2 0.01
56 1 0.01
59 2 0.01
60 44 0.31
ACGTcount: A:0.34, C:0.23, G:0.18, T:0.25
Consensus pattern (54 bp):
ATCGCAACGCGAATTTGACTATCGCAACACGAATTTGACTATCGCAACGCAAAA
Found at i:2655 original size:20 final size:20
Alignment explanation
Indices: 2600--2657 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
2590 GCAACGCGAA
2600 TTGACTTTCA-CGTTGCGATT
1 TTGACTTT-AGCGTTGCGATT
* * *
2620 TTGTCTTTCGCATTGCGATT
1 TTGACTTTAGCGTTGCGATT
*
2640 TTGAGTTTAGCGTTGCGA
1 TTGACTTTAGCGTTGCGA
2658 AAGCGTACCT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.14, C:0.17, G:0.24, T:0.45
Consensus pattern (20 bp):
TTGACTTTAGCGTTGCGATT
Found at i:2816 original size:14 final size:14
Alignment explanation
Indices: 2756--2817 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
2746 CACAAATAAG
*
2756 AATTATTTACACATC
1 AATT-TTTACAAATC
**
2771 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
2786 AACTTTTACAAATC
1 AATTTTTACAAATC
*
2800 AATTTTTATAAATC
1 AATTTTTACAAATC
2814 AATT
1 AATT
2818 AAACAAGCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 12 0.32
16 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:4312 original size:42 final size:42
Alignment explanation
Indices: 4233--4323 Score: 103
Period size: 42 Copynumber: 2.2 Consensus size: 42
4223 CCTCTTCAAC
* * *
4233 GATGACAGTGGCCTCTTGAACGGTGGGAGGGGACTCTTGAGG
1 GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
* * **
4275 GATGATAGGGGCCTCTTGAACGATAGGG-GAGGCCTCTTGAAT
1 GATGACAGGGGCCTCTTGAACGAT-GGGAGAGGACTCTTGAGG
4317 GATGACA
1 GATGACA
4324 TGTGAGTCGG
Statistics
Matches: 40, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
42 37 0.93
43 3 0.08
ACGTcount: A:0.23, C:0.16, G:0.38, T:0.22
Consensus pattern (42 bp):
GATGACAGGGGCCTCTTGAACGATGGGAGAGGACTCTTGAGG
Found at i:4847 original size:20 final size:20
Alignment explanation
Indices: 4822--4897 Score: 125
Period size: 20 Copynumber: 3.8 Consensus size: 20
4812 TCGCAACACG
*
4822 AATGACTATCGCAACTCGAA
1 AATGACTATCGCAACGCGAA
4842 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
4862 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
**
4882 TTTGACTATCGCAACG
1 AATGACTATCGCAACG
4898 AGATAATAGC
Statistics
Matches: 53, Mismatches: 3, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 53 1.00
ACGTcount: A:0.37, C:0.25, G:0.18, T:0.20
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:4968 original size:20 final size:20
Alignment explanation
Indices: 4940--5005 Score: 96
Period size: 20 Copynumber: 3.3 Consensus size: 20
4930 GCGATTCTTT
* **
4940 CGTTACGATAGTCAAATTCG
1 CGTTGCGATAGTCATTTTCG
*
4960 CGTTGCGATAGTCATTTTTG
1 CGTTGCGATAGTCATTTTCG
4980 CGTTGCGATAGTCATTTTCG
1 CGTTGCGATAGTCATTTTCG
5000 CGTTGC
1 CGTTGC
5006 AAAAGTAAAC
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.18, C:0.20, G:0.24, T:0.38
Consensus pattern (20 bp):
CGTTGCGATAGTCATTTTCG
Found at i:5562 original size:18 final size:18
Alignment explanation
Indices: 5539--5587 Score: 89
Period size: 18 Copynumber: 2.7 Consensus size: 18
5529 CGGGTCGATC
*
5539 AGGTGATTGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
5557 AGGTGATGGCTCTGGGTG
1 AGGTGATGGCTCTGGGTG
5575 AGGTGATGGCTCT
1 AGGTGATGGCTCT
5588 TGAAGTGGAG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.12, C:0.12, G:0.45, T:0.31
Consensus pattern (18 bp):
AGGTGATGGCTCTGGGTG
Found at i:6945 original size:20 final size:20
Alignment explanation
Indices: 6922--7028 Score: 110
Period size: 20 Copynumber: 5.5 Consensus size: 20
6912 TCTGAAACTT
*
6922 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
*
6942 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
** **
6962 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACGCGAAAATG
** *
6982 ACTATCGCATCGC-AAAATG
1 AAAATCGCAACGCGAAAATG
*
7001 AAAATCGCAACGCGAAACT-
1 AAAATCGCAACGCGAAAATG
7020 AAAATCGCA
1 AAAATCGCA
7029 TTGCGATTCT
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
19 23 0.31
20 51 0.69
ACGTcount: A:0.46, C:0.23, G:0.16, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:7646 original size:20 final size:20
Alignment explanation
Indices: 7609--7707 Score: 144
Period size: 20 Copynumber: 5.0 Consensus size: 20
7599 GCGCTTTGAA
* *
7609 AATCGCATTGTGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
* *
7629 CATCGCGTTGCGACAGTCAG
1 AATCGCGTTGCGATAGTCAG
7649 AATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
7669 AATCTCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
7689 AATCACGTTGCGATAGTCA
1 AATCGCGTTGCGATAGTCA
7708 TACTCACATT
Statistics
Matches: 71, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 71 1.00
ACGTcount: A:0.26, C:0.21, G:0.26, T:0.26
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:7714 original size:20 final size:20
Alignment explanation
Indices: 7620--7722 Score: 134
Period size: 20 Copynumber: 5.2 Consensus size: 20
7610 ATCGCATTGT
* *
7620 GATAGTCAGCATCGCGTTGC
1 GATAGTCAGAATCACGTTGC
* *
7640 GACAGTCAGAATCGCGTTGC
1 GATAGTCAGAATCACGTTGC
*
7660 GATAGTCAGAATCTCGTTGC
1 GATAGTCAGAATCACGTTGC
7680 GATAGTCAGAATCACGTTGC
1 GATAGTCAGAATCACGTTGC
* * *
7700 GATAGTCATACTCACATTGC
1 GATAGTCAGAATCACGTTGC
7720 GAT
1 GAT
7723 TTACATATTC
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 75 1.00
ACGTcount: A:0.26, C:0.22, G:0.25, T:0.26
Consensus pattern (20 bp):
GATAGTCAGAATCACGTTGC
Found at i:28437 original size:14 final size:14
Alignment explanation
Indices: 28418--28451 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
28408 GAACATAGTG
*
28418 AACTGTCATATCAA
1 AACTGTAATATCAA
*
28432 AACTGTAATATCAG
1 AACTGTAATATCAA
28446 AACTGT
1 AACTGT
28452 GATAATTAAC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.41, C:0.18, G:0.12, T:0.29
Consensus pattern (14 bp):
AACTGTAATATCAA
Found at i:30859 original size:21 final size:21
Alignment explanation
Indices: 30818--30859 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
30808 TATTTTGAAT
* *
30818 TAAATCATCATTTAGAGACAA
1 TAAATCATAATTTAGACACAA
30839 TAAATCGATAATTT-GACACAA
1 TAAATC-ATAATTTAGACACAA
30860 ATACGATACT
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 12 0.67
22 6 0.33
ACGTcount: A:0.48, C:0.14, G:0.10, T:0.29
Consensus pattern (21 bp):
TAAATCATAATTTAGACACAA
Found at i:31255 original size:18 final size:18
Alignment explanation
Indices: 31207--31259 Score: 54
Period size: 18 Copynumber: 2.9 Consensus size: 18
31197 ATTTTCTATT
31207 ATTTTATTATAAATCTAACA
1 ATTTTATT-TAAAT-TAACA
* * *
31227 TTTTTA-ATAAATTATCA
1 ATTTTATTTAAATTAACA
31244 ATTTTATTTAAATTAA
1 ATTTTATTTAAATTAA
31260 TTTATTATTG
Statistics
Matches: 26, Mismatches: 6, Indels: 4
0.72 0.17 0.11
Matches are distributed among these distances:
17 9 0.35
18 12 0.46
20 5 0.19
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (18 bp):
ATTTTATTTAAATTAACA
Found at i:33432 original size:12 final size:12
Alignment explanation
Indices: 33415--33444 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
33405 TGGGAACCTC
33415 GGCGATTCAGCT
1 GGCGATTCAGCT
33427 GGCGATTCAGCT
1 GGCGATTCAGCT
33439 GGCGAT
1 GGCGAT
33445 CGTACTCTAG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.17, C:0.23, G:0.37, T:0.23
Consensus pattern (12 bp):
GGCGATTCAGCT
Found at i:34950 original size:28 final size:27
Alignment explanation
Indices: 34885--34951 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 27
34875 TTTAAATTCA
* *
34885 CCAAAAATACCCTAAATTCCATAAAAT
1 CCAAAAAAACCCCAAATTCCATAAAAT
*
34912 CTCAAAGAAACCCCAAATT-CATAAAAATT
1 C-CAAAAAAACCCCAAATTCCAT-AAAA-T
34941 CCAAAAAAACC
1 CCAAAAAAACC
34952 ATAAACGCTA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
27 4 0.12
28 27 0.82
29 2 0.06
ACGTcount: A:0.54, C:0.27, G:0.01, T:0.18
Consensus pattern (27 bp):
CCAAAAAAACCCCAAATTCCATAAAAT
Found at i:39206 original size:38 final size:38
Alignment explanation
Indices: 39134--39210 Score: 100
Period size: 38 Copynumber: 2.0 Consensus size: 38
39124 TAATTGTAGG
****
39134 TTAACCTATTACAATTATTTGTCAAATTTTTTTATAAT
1 TTAACCTATTACAATTATTTGTCAAAAAAATTTATAAT
* *
39172 TTAACTTATTACACTTATTTGTCAAAAAAATTTATAAT
1 TTAACCTATTACAATTATTTGTCAAAAAAATTTATAAT
39210 T
1 T
39211 AACACTAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
38 33 1.00
ACGTcount: A:0.38, C:0.10, G:0.03, T:0.49
Consensus pattern (38 bp):
TTAACCTATTACAATTATTTGTCAAAAAAATTTATAAT
Found at i:39525 original size:65 final size:63
Alignment explanation
Indices: 39397--39526 Score: 147
Period size: 65 Copynumber: 2.0 Consensus size: 63
39387 AAAATAAAAA
* * * * * * *
39397 AAATTAAAATAATAAAAATATTTATTAAGTTATTTGTGTACAAATTTTATTAAATATATATAT
1 AAATTAAAATAATAAAAAAATATATTAAATTATTTGTGTACAAATTATAATAAATAGAAATAT
39460 AAATTAGAAATAATAAAAAAAATATATTAAATTATTTGTGTA-AAGA-TATAATAAATTAGAAAT
1 AAATTA-AAATAAT-AAAAAAATATATTAAATTATTTGTGTACAA-ATTATAATAAA-TAGAAAT
39523 AT
62 AT
39525 AA
1 AA
39527 TCGTAAATTT
Statistics
Matches: 56, Mismatches: 7, Indels: 6
0.81 0.10 0.09
Matches are distributed among these distances:
63 6 0.11
64 16 0.29
65 34 0.61
ACGTcount: A:0.55, C:0.01, G:0.06, T:0.38
Consensus pattern (63 bp):
AAATTAAAATAATAAAAAAATATATTAAATTATTTGTGTACAAATTATAATAAATAGAAATAT
Found at i:53452 original size:2 final size:2
Alignment explanation
Indices: 53445--53480 Score: 72
Period size: 2 Copynumber: 18.0 Consensus size: 2
53435 ATCGTATACA
53445 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
53481 TTGTATTTTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 34 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:54404 original size:60 final size:59
Alignment explanation
Indices: 54289--54439 Score: 203
Period size: 60 Copynumber: 2.5 Consensus size: 59
54279 AAAAAAAATG
* * * *
54289 AAGTCTCTCGACTATTAAAAGTTACATAAATGGTCCTCCGACTTAGGATACTGCTTTGTT
1 AAGTCTCTCGACTATTAAAAGTTATA-AAATGGTCCTACAACTTAGAATACTGCTTTGTT
* **
54349 AAGTCCCTCGACTATTAAAAGTTATAAAATGGTCCTACAACTATAGAATGTTGCTTTGTT
1 AAGTCTCTCGACTATTAAAAGTTATAAAATGGTCCTACAACT-TAGAATACTGCTTTGTT
* *
54409 AAGTCTCTTGGCTATTAAAAGTTATAAAATG
1 AAGTCTCTCGACTATTAAAAGTTATAAAATG
54440 ATCACTCAAT
Statistics
Matches: 80, Mismatches: 10, Indels: 2
0.87 0.11 0.02
Matches are distributed among these distances:
59 14 0.17
60 66 0.82
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.35
Consensus pattern (59 bp):
AAGTCTCTCGACTATTAAAAGTTATAAAATGGTCCTACAACTTAGAATACTGCTTTGTT
Found at i:54662 original size:60 final size:60
Alignment explanation
Indices: 54555--54696 Score: 151
Period size: 60 Copynumber: 2.4 Consensus size: 60
54545 TTGGAACATA
* * * * *
54555 ATTA-ATAGTCGGATGATCATTTTGTAACTTTTAATAGTCGACGGACTTAACAAAACAAC
1 ATTATATAGTCGAAGGATCATTTTATAACTTTTAATAGTCAACAGACTTAACAAAACAAC
* * ** *
54614 ATTATATAGTCGAAGGATCATTTTATAATTTTTAATAGTCAATAGACTTAATGAAACAAT
1 ATTATATAGTCGAAGGATCATTTTATAACTTTTAATAGTCAACAGACTTAACAAAACAAC
* * * *
54674 ATCATATATTCGAGGGACCATTT
1 ATTATATAGTCGAAGGATCATTT
54697 ATGTACTTTA
Statistics
Matches: 68, Mismatches: 14, Indels: 1
0.82 0.17 0.01
Matches are distributed among these distances:
59 4 0.06
60 64 0.94
ACGTcount: A:0.38, C:0.13, G:0.14, T:0.35
Consensus pattern (60 bp):
ATTATATAGTCGAAGGATCATTTTATAACTTTTAATAGTCAACAGACTTAACAAAACAAC
Found at i:55098 original size:39 final size:40
Alignment explanation
Indices: 55050--55125 Score: 102
Period size: 39 Copynumber: 1.9 Consensus size: 40
55040 AATAATTTAT
*
55050 TTTAGTTATAATTTAAATCT-TTATAATTCACATATAATAA
1 TTTAGTTATAATTTAAAT-TGGTATAATTCACATATAATAA
* *
55090 TTTA-TTATAGTTTAAATTGGTATAATTCATATATAA
1 TTTAGTTATAATTTAAATTGGTATAATTCACATATAA
55126 GTGTAAATAT
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
38 1 0.03
39 27 0.84
40 4 0.12
ACGTcount: A:0.41, C:0.05, G:0.05, T:0.49
Consensus pattern (40 bp):
TTTAGTTATAATTTAAATTGGTATAATTCACATATAATAA
Found at i:58857 original size:71 final size:71
Alignment explanation
Indices: 58718--58857 Score: 181
Period size: 71 Copynumber: 2.0 Consensus size: 71
58708 TTTTTTCAAT
* * * * ***
58718 AAACGTCACTATAGATTGACCTATTGCGACGTTTTTAAAAAAACACCACTATTATTGCGGCTTTA
1 AAACGTCACTATAGATGGACCTATCGCGACGTTTATAAAAAAACACCACTATTATTGCCGCGAAA
58783 TTGATA
66 TTGATA
* * * *
58789 AAACGTCATTATAGATGGATCTATCGCGACGTTTATAAAAAAACGCCACTATTATTGCCTCGAAA
1 AAACGTCACTATAGATGGACCTATCGCGACGTTTATAAAAAAACACCACTATTATTGCCGCGAAA
58854 TTGA
66 TTGA
58858 ATATATCTAA
Statistics
Matches: 58, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
71 58 1.00
ACGTcount: A:0.35, C:0.19, G:0.15, T:0.31
Consensus pattern (71 bp):
AAACGTCACTATAGATGGACCTATCGCGACGTTTATAAAAAAACACCACTATTATTGCCGCGAAA
TTGATA
Found at i:59469 original size:18 final size:18
Alignment explanation
Indices: 59448--59486 Score: 51
Period size: 18 Copynumber: 2.2 Consensus size: 18
59438 GTTTTTAGTA
59448 AAAATACATAAAAATTAT
1 AAAATACATAAAAATTAT
* * *
59466 AAAATATATAATAATTTT
1 AAAATACATAAAAATTAT
59484 AAA
1 AAA
59487 TTTTCAAAAG
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (18 bp):
AAAATACATAAAAATTAT
Found at i:66762 original size:3 final size:3
Alignment explanation
Indices: 66754--66798 Score: 90
Period size: 3 Copynumber: 15.0 Consensus size: 3
66744 TGTGTATATG
66754 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
66799 AGATAATGTT
Statistics
Matches: 42, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 42 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
TAA
Found at i:66875 original size:53 final size:54
Alignment explanation
Indices: 66794--66984 Score: 172
Period size: 53 Copynumber: 3.5 Consensus size: 54
66784 TAATAATAAT
** * * * *
66794 AATAAAGATAATGTTGCATTAACCTTTGTATCACACTTTCTAAATATACATAAAA
1 AATAAAGAT-ATGTTATATTAACATTTGTATTACAATTTCTAAATATATATAAAA
** *
66849 AATAAAGATAT-TTATATTAACATTTGTATTACAATTT-TTTAT-TATATGAAA
1 AATAAAGATATGTTATATTAACATTTGTATTACAATTTCTAAATATATATAAAA
* ** * *
66900 AATAAAGATAATGTTATGTTGGCTTTTTTATTACAATTTCTAAATATATATATAAAAA
1 AATAAAGAT-ATGTTATATTAACATTTGTATTACAATTTCT-AA-ATATATAT-AAAA
*
66958 AATAAAGACAATGTTATATTAACATTT
1 AATAAAGA-TATGTTATATTAACATTT
66985 CAAAAATGTT
Statistics
Matches: 106, Mismatches: 22, Indels: 13
0.75 0.16 0.09
Matches are distributed among these distances:
51 16 0.15
52 5 0.05
53 42 0.40
54 3 0.03
55 9 0.08
56 2 0.02
57 5 0.05
58 24 0.23
ACGTcount: A:0.44, C:0.08, G:0.07, T:0.41
Consensus pattern (54 bp):
AATAAAGATATGTTATATTAACATTTGTATTACAATTTCTAAATATATATAAAA
Found at i:76735 original size:5 final size:5
Alignment explanation
Indices: 76725--76768 Score: 52
Period size: 5 Copynumber: 8.2 Consensus size: 5
76715 TACGTTTAAA
*
76725 TATTT TATTT TATTTT TAGTT TATTCT TATTCT TATTT TATTT T
1 TATTT TATTT TA-TTT TATTT TATT-T TATT-T TATTT TATTT T
76769 TTCACTAACA
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
5 19 0.54
6 16 0.46
ACGTcount: A:0.18, C:0.05, G:0.02, T:0.75
Consensus pattern (5 bp):
TATTT
Found at i:76747 original size:11 final size:11
Alignment explanation
Indices: 76727--76768 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
76717 CGTTTAAATA
76727 TTTTATTTTAT
1 TTTTATTTTAT
*
76738 TTTTAGTTTAT
1 TTTTATTTTAT
*
76749 TCTTATTCTTA-
1 TTTTATT-TTAT
76760 TTTTATTTT
1 TTTTATTTT
76769 TTCACTAACA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
10 2 0.08
11 21 0.81
12 3 0.12
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (11 bp):
TTTTATTTTAT
Found at i:79916 original size:23 final size:22
Alignment explanation
Indices: 79874--79963 Score: 65
Period size: 23 Copynumber: 3.9 Consensus size: 22
79864 AATCAAGAAC
*
79874 AAAAAAGAAAAGAAGTAAAAAAG
1 AAAAAAGAAAA-AAGAAAAAAAG
*
79897 CAAAAAA-AAACAAAGAAAAAGAG
1 -AAAAAAGAAA-AAAGAAAAAAAG
*
79920 AAACAAGAACAAAAGGAAAAAAGAG
1 AAAAAAGAA-AAAA-GAAAAAA-AG
* **
79945 CAAAAATCAAAAAGAAAAA
1 AAAAAAGAAAAAAGAAAAA
79964 GGGATAAAAA
Statistics
Matches: 53, Mismatches: 8, Indels: 11
0.74 0.11 0.15
Matches are distributed among these distances:
22 5 0.09
23 23 0.43
24 18 0.34
25 7 0.13
ACGTcount: A:0.77, C:0.07, G:0.14, T:0.02
Consensus pattern (22 bp):
AAAAAAGAAAAAAGAAAAAAAG
Found at i:81933 original size:106 final size:106
Alignment explanation
Indices: 81805--82336 Score: 829
Period size: 106 Copynumber: 5.0 Consensus size: 106
81795 ATATCGTGCC
* * *
81805 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAACTTCCC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
81870 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
*
81911 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAAC---TTCCC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* *
81973 AATTTCAGAGCCAATTTCAACTTCACAACGAAAGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * *
82014 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGATGTCAATAAACAATTTCCC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* *
82079 AATTTCAGATCCAATTTCAACTTCACATCGAAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
82120 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
* *
82185 AATTTCGGAGCCAATTTCAACTTCACAGCGAAGGATATTAG
66 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
* * * * *
82226 ACTCGAGACAACACAAGTTCAACTTCACAATGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
** * *
82291 GGTTCCAGAGCCAATTTCAACTTCAC-GACGGAGGATATTGG
66 AATTTCAGAGCCAATTTCAACTTCACAG-CGAAGGATATTGG
82332 ACTCA
1 ACTCA
82337 GAACAATGCT
Statistics
Matches: 393, Mismatches: 29, Indels: 8
0.91 0.07 0.02
Matches are distributed among these distances:
103 99 0.25
105 1 0.00
106 293 0.75
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.22
Consensus pattern (106 bp):
ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGG
Found at i:82170 original size:209 final size:209
Alignment explanation
Indices: 81805--82336 Score: 832
Period size: 209 Copynumber: 2.5 Consensus size: 209
81795 ATATCGTGCC
* *
81805 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAATAACTTCCC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
81870 AATTTCAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGACTCCAGACAACGCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACA-CGAAGGATATTGGACTCAAGACAACGCAAGTTCAACT
81935 TCACGACGAAGGGACCGCTGGTTGTCAACAAAC-TTCCCAATTTCAGAGCCAATTTCAACTTCAC
130 TCACGACGAAGGGACCGCTGGTTGTCAACAAACATTCCCAATTTCAGAGCCAATTTCAACTTCAC
*
81999 AACGAAAGATATTGG
195 AACGAAAGATATTAG
* *
82014 ACTCCAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGATGTCAATAAACAATTTCCC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
*
82079 AATTTCAGATCCAATTTCAACTTCACATCGAAGGATATTGGACTCAAGACAACGCAAGTTCAACT
66 AATTTCAGAGCCAATTTCAACTTCACA-CGAAGGATATTGGACTCAAGACAACGCAAGTTCAACT
*
82144 TCACGACGAAGGGACCGCTGGTTGTCAACAAACAATTTCCCAATTTCGGAGCCAATTTCAACTTC
130 TCACGACGAAGGGACCGCTGGTTGTCAACAAAC-A-TTCCCAATTTCAGAGCCAATTTCAACTTC
* *
82209 ACAGCGAAGGATATTAG
193 ACAACGAAAGATATTAG
* * * * * *
82226 ACTCGAGACAACACAAGTTCAACTTCACAATGAAGGGACGGCTGGTTGTCAACAAACAATTTCCC
1 ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
** * *
82291 GGTTCCAGAGCCAATTTCAACTTCACGACGGAGGATATTGGACTCA
66 AATTTCAGAGCCAATTTCAACTTCAC-ACGAAGGATATTGGACTCA
82337 GAACAATGCT
Statistics
Matches: 296, Mismatches: 23, Indels: 5
0.91 0.07 0.02
Matches are distributed among these distances:
209 156 0.53
212 139 0.47
213 1 0.00
ACGTcount: A:0.34, C:0.26, G:0.19, T:0.22
Consensus pattern (209 bp):
ACTCAAGACAACGCAAGTTCAACTTCACGACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCC
AATTTCAGAGCCAATTTCAACTTCACACGAAGGATATTGGACTCAAGACAACGCAAGTTCAACTT
CACGACGAAGGGACCGCTGGTTGTCAACAAACATTCCCAATTTCAGAGCCAATTTCAACTTCACA
ACGAAAGATATTAG
Found at i:83863 original size:5 final size:5
Alignment explanation
Indices: 83853--83894 Score: 50
Period size: 5 Copynumber: 8.2 Consensus size: 5
83843 TACGTTTAAA
*
83853 TATTT TATTT T-TTT TAGTT TATTCT TATTCT TATTT TATTT T
1 TATTT TATTT TATTT TATTT TATT-T TATT-T TATTT TATTT T
83895 TTCACTAACC
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
4 4 0.12
5 18 0.55
6 11 0.33
ACGTcount: A:0.17, C:0.05, G:0.02, T:0.76
Consensus pattern (5 bp):
TATTT
Found at i:85869 original size:19 final size:22
Alignment explanation
Indices: 85834--85879 Score: 62
Period size: 19 Copynumber: 2.2 Consensus size: 22
85824 AATTAAATCC
85834 TATTTTTCTTGAATAAAAATA-
1 TATTTTTCTTGAATAAAAATAT
*
85855 TATTTTT-TT-AATAAATATAT
1 TATTTTTCTTGAATAAAAATAT
85875 TATTT
1 TATTT
85880 CAAGTCGGGT
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
19 9 0.39
20 7 0.30
21 7 0.30
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (22 bp):
TATTTTTCTTGAATAAAAATAT
Found at i:87937 original size:26 final size:28
Alignment explanation
Indices: 87876--87937 Score: 65
Period size: 31 Copynumber: 2.2 Consensus size: 28
87866 GAGTATTGCT
* *
87876 GAGCTCGACTCGACTCGAAAACTCTGAAAT
1 GAGCTCAACTCGACTCGAAAACTCTG--AC
87906 GAAGCTCAACTCGACTCGAAAACTC-G-C
1 G-AGCTCAACTCGACTCGAAAACTCTGAC
87933 GAGCT
1 GAGCT
87938 TAAAATTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 6
0.78 0.05 0.16
Matches are distributed among these distances:
26 4 0.14
27 1 0.03
30 2 0.07
31 22 0.76
ACGTcount: A:0.32, C:0.29, G:0.21, T:0.18
Consensus pattern (28 bp):
GAGCTCAACTCGACTCGAAAACTCTGAC
Found at i:88862 original size:59 final size:59
Alignment explanation
Indices: 88738--88865 Score: 143
Period size: 59 Copynumber: 2.2 Consensus size: 59
88728 GAATAGTCGA
* * *
88738 GAGACCATTTTATAACTCCTAATAGTTGAGGGACTCAACAAAGCAACATCCTATAGTCG
1 GAGACCATTTTATAACTCCTAATAGTCGAGGGACTCAACAAAACAACATCCTATAGCCG
* * * **
88797 GAGACCATTTTATAACT-TTCAATAGTCGAGGGACTCAATAAAATATTATCCTATA-CCGG
1 GAGACCATTTTATAACTCCT-AATAGTCGAGGGACTCAACAAAACAACATCCTATAGCC-G
*
88856 GGGACCATTT
1 GAGACCATTT
88866 GTGTACTTTA
Statistics
Matches: 58, Mismatches: 9, Indels: 4
0.82 0.13 0.06
Matches are distributed among these distances:
58 2 0.03
59 56 0.97
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.28
Consensus pattern (59 bp):
GAGACCATTTTATAACTCCTAATAGTCGAGGGACTCAACAAAACAACATCCTATAGCCG
Found at i:90103 original size:24 final size:24
Alignment explanation
Indices: 90071--90119 Score: 89
Period size: 24 Copynumber: 2.0 Consensus size: 24
90061 AACATATAAA
*
90071 ACGAGTCGGGTCAGTTTGAATTGG
1 ACGAGTCGGGTCAATTTGAATTGG
90095 ACGAGTCGGGTCAATTTGAATTGG
1 ACGAGTCGGGTCAATTTGAATTGG
90119 A
1 A
90120 TTTGAACCTT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.24, C:0.12, G:0.35, T:0.29
Consensus pattern (24 bp):
ACGAGTCGGGTCAATTTGAATTGG
Found at i:90918 original size:2 final size:2
Alignment explanation
Indices: 90911--90964 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
90901 TTGATCATTA
90911 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
90953 AT AT AT AT AT AT
1 AT AT AT AT AT AT
90965 GTCAAATTAT
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:92166 original size:16 final size:19
Alignment explanation
Indices: 92126--92169 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 19
92116 CACGGAATGG
92126 AAGATTACCAGTGAGAATGT
1 AAGATTACCAGTGAGAA-GT
92146 AAGATTACCAG-G-GAA-T
1 AAGATTACCAGTGAGAAGT
92162 AAGATTAC
1 AAGATTAC
92170 TGAGAATGTT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
16 9 0.38
18 3 0.12
19 1 0.04
20 11 0.46
ACGTcount: A:0.43, C:0.11, G:0.23, T:0.23
Consensus pattern (19 bp):
AAGATTACCAGTGAGAAGT
Found at i:93435 original size:23 final size:23
Alignment explanation
Indices: 93409--93458 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
93399 CAATATAATT
*
93409 TGATGAATTATA-AATATATAAAG
1 TGATGAATAATATAATAT-TAAAG
* *
93432 TGATTAATAATATAATATTAATG
1 TGATGAATAATATAATATTAAAG
93455 TGAT
1 TGAT
93459 ATATGTCACA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 18 0.78
24 5 0.22
ACGTcount: A:0.48, C:0.00, G:0.12, T:0.40
Consensus pattern (23 bp):
TGATGAATAATATAATATTAAAG
Found at i:97488 original size:29 final size:29
Alignment explanation
Indices: 97446--97502 Score: 96
Period size: 29 Copynumber: 2.0 Consensus size: 29
97436 ATGGGTTGTG
*
97446 ACCAAATTGTAAAATTTCAGAATTTAGTT
1 ACCAAATTATAAAATTTCAGAATTTAGTT
*
97475 ACCAAATTATAAAATTTTAGAATTTAGT
1 ACCAAATTATAAAATTTCAGAATTTAGT
97503 GACTAAAGTA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 26 1.00
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.39
Consensus pattern (29 bp):
ACCAAATTATAAAATTTCAGAATTTAGTT
Found at i:98372 original size:29 final size:29
Alignment explanation
Indices: 98330--98406 Score: 109
Period size: 29 Copynumber: 2.7 Consensus size: 29
98320 AAACTATGGG
* * *
98330 TTAGTGACCAAATTGTAAAATTTCATAAT
1 TTAGTGACTAAATTATAAAATTTCAGAAT
*
98359 TTAGTGACTAAATTATAAAATTTTAGAAT
1 TTAGTGACTAAATTATAAAATTTCAGAAT
*
98388 TTAGTGACTAAAGTATAAA
1 TTAGTGACTAAATTATAAA
98407 TAATTGAAAA
Statistics
Matches: 43, Mismatches: 5, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 43 1.00
ACGTcount: A:0.44, C:0.06, G:0.12, T:0.38
Consensus pattern (29 bp):
TTAGTGACTAAATTATAAAATTTCAGAAT
Found at i:98421 original size:30 final size:29
Alignment explanation
Indices: 98356--98421 Score: 87
Period size: 29 Copynumber: 2.2 Consensus size: 29
98346 AAAATTTCAT
* * * *
98356 AATTTAGTGACTAAATTATAAAATTTTAG
1 AATTTAGTGACTAAAGTATAAAAATTGAA
98385 AATTTAGTGACTAAAGTATAAATAATTGAA
1 AATTTAGTGACTAAAGTATAAA-AATTGAA
98415 AATTTAG
1 AATTTAG
98422 GGATTTATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 21 0.66
30 11 0.34
ACGTcount: A:0.47, C:0.03, G:0.12, T:0.38
Consensus pattern (29 bp):
AATTTAGTGACTAAAGTATAAAAATTGAA
Found at i:99105 original size:905 final size:888
Alignment explanation
Indices: 97355--99156 Score: 3158
Period size: 905 Copynumber: 2.0 Consensus size: 888
97345 TTTATATAAA
*
97355 TATCAATACTTTTAAACATTATGTTCTGTCTAGTTTCGATACTTTCTGGGAGTTTCAAAACTATG
1 TATCGATACTTTTAAACATTATGTTCTGTCTAGTTTCGATACTTTCTGGGAGTTTCAAAACTATG
* *
97420 TGTAATATCTCAAACTATGGGTTGTGACCAAATTGTAAAATTTCAGAATTTAGTTACCAAATTAT
66 TGTAACATCTCAAACTATGGGTTGTGACCAAATTGTAAAATTTCAGAATTTAGTGACCAAATTAT
97485 AAAATTTTAGAATTTAGTGACTAAAGTAGAAATAATTAAAAACTTTAGGGATTTATATGGAAATT
131 AAAATTTTAGAATTTAGTGACTAAAGTAGAAATAATTAAAAACTTTAGGGATTTATATGGAAATT
* *
97550 TTGGTGTAGGATTAAATTACAAAGAATGATGAATGGAATGGCAAAATGGTCATTTAACTTAGAAA
196 TTGGTATAGGATTAAATTACAAAGAATGATGAATGGAAGGGCAAAATGGTCATTTAACTTAGAAA
*
97615 TAAATTAAAATGTGATAGGGATGAGATATATACACGTGAGAAATGTGGAATAGGGAAAAGAAAGT
261 TAAATTAAAATGTGATAGGGATGAGATATATACACGTGAGAAATGTAGAATAGGGAAAAGAAAGT
97680 TTCCAGAGTTCTCATCCTTCTTTCTCTCCACCGTGAACCCAAAGTAGAAAAGGTGAGTTTTCTGG
326 TTCCAGAGTTCTCATCCTTCTTTCTCTCCACCGTGAACCCAAAGTAGAAAAGGTGAGTTTTCTGG
97745 TTAGTTAATTATTTGTTGATTTTAAGTATGGGTTTTGATCCTTAAGTGATACTTAAGCTTAAGTT
391 TTAGTTAATTATTTGTTGATTTTAAGTATGGGTTTTGATCCTTAAGTGATACTTAAGCTTAAGTT
97810 GTCTTATAATCAAAAGATGAAGAAGTTATAAGAGATTAAAGAGAAGGGGGCTTCTAAATGAAATT
456 GTCTTATAATCAAAAGATGAAGAAGTTATAAGAGATTAAAGAGAAGGGGGCTTCTAAATGAAATT
* *
97875 CTGAAAAAGAGTTAATAAATAAAGTTGGAGTCTGGAATTGACTTATTAGCAACTTAATTAAGAGA
521 CTGAAAAAGAGTTAATAAATAAAGTTGGAGTCTCGAATTGACTTATTAACAACTTAATTAAGAGA
97940 TATCAAGTGATAGAATTGAAATTAGAACATATTGAAAATTTGGTATGATTATCGAGTTTTATATG
586 TATCAAGTGATAGAATTGAAATTAGAACATATTGAAAATTTGGTATGATTATCGAGTTTTATATG
98005 AAAGATGGGATTTTGAGGTTAAGGATGTATTGAATGAATAGAAATTGGTTTAAGTATGTGTACTT
651 AAAGATGGGATTTTGAGGTTAAGGATGTATTGAATGAATAGAAATTGGTTTAAGTATGTGTACTT
*
98070 GAGTTAATAATATAAAAGAGAATGAAACATGAAGAAATTAAGCTAACAATGATGAATTTTCGGGA
716 GAGTTAATAATATAAAAGAGAATGAAACATGAAGAAATTAAGCTAACAAGGATGAATTTTCGGGA
*
98135 TTAAAAAGTGATTTCTGGGCAAGGGGTATCGATACCCATTCATCAGGTACCGATACCTTAGGAGT
781 TTAAAAAGTGATTTCTGGGCAAGGGGTATCGATACCCATTCATCAGGTACCGATACCTCAGGAGT
98200 AAAATTTAGGAAGATACCTAGGGGTACCGATACCTTAAGGAAGG
846 AAAATTTAGGAAGATACCTAGGGGTACC-ATACCTTAAGGAAGG
**
98244 TATCGATACTTTTAAACATTATGTTCTGTCTAGTTTCGATACTTTCTGGGAGTTTTGAAACTATG
1 TATCGATACTTTTAAACATTATGTTCTGTCTAGTTTCGATACTTTCTGGGAGTTTCAAAACTATG
* *
98309 TGTAACATCTCAAACTATGGGTTAGTGACCAAATTGTAAAATTTCATAATTTAGTGACTAAATTA
66 TGTAACATCTCAAACTATGGGTT-GTGACCAAATTGTAAAATTTCAGAATTTAGTGACCAAATTA
* *
98374 TAAAATTTTAGAATTTAGTGACTAAAGTATAAATAATTGAAAA-TTTAGGGATTTATATGGAAAT
130 TAAAATTTTAGAATTTAGTGACTAAAGTAGAAATAATTAAAAACTTTAGGGATTTATATGGAAAT
* *
98438 TTTGGTATATGATTAAATTACAAAGAATGATGAATGGAAGGGCAAAATGGTCATTTGACTTAGAA
195 TTTGGTATAGGATTAAATTACAAAGAATGATGAATGGAAGGGCAAAATGGTCATTTAACTTAGAA
* *
98503 ATGAATTAAAATGTGATAGGGATGAGATATATACATGTGAGAAATGTAGAATAGGGAAAAGAAAG
260 ATAAATTAAAATGTGATAGGGATGAGATATATACACGTGAGAAATGTAGAATAGGGAAAAGAAAG
*
98568 TTTCCAGAGTTCTCTTCATTCTTCTTCTTTCTCTCCACCGTGAACCCAAAGTAGCAAAGGTGAGT
325 TTTCCAGAG-T-TC-TCA-TC--CTTCTTTCTCTCCACCGTGAACCCAAAGTAGAAAAGGTGAGT
* *
98633 TTTCTGGTTAGTTAATTATTTGTTGATTTTAAGTATGTGTTTTGATCCTTAGGTGATACTTAAGC
384 TTTCTGGTTAGTTAATTATTTGTTGATTTTAAGTATGGGTTTTGATCCTTAAGTGATACTTAAGC
98698 TTAAGGAAAGCTTAAGCTGTCTTATAATCAAAAGATGAAGAAGTTATAAGAGATTAAAGAGAA-G
449 TT-----AAG--T----TGTCTTATAATCAAAAGATGAAGAAGTTATAAGAGATTAAAGAGAAGG
*
98762 GGGTTTCTAAATGAAATTCTGAAAAAGAGTTAATAAATAAAGTTGGAGTCTCGAATTGACTTATT
503 GGGCTTCTAAATGAAATTCTGAAAAAGAGTTAATAAATAAAGTTGGAGTCTCGAATTGACTTATT
98827 AACAACTTAATTAAGAGATATCAAGTGATAGAATTGAAATTAGAACATATTGAAAATTTGGTATG
568 AACAACTTAATTAAGAGATATCAAGTGATAGAATTGAAATTAGAACATATTGAAAATTTGGTATG
*
98892 ATTATCGAGTTTTATATGAAAGATGGGATTTTGAGGTTAAGGATGTATTGAATGAGTAGAAATTG
633 ATTATCGAGTTTTATATGAAAGATGGGATTTTGAGGTTAAGGATGTATTGAATGAATAGAAATTG
*
98957 GTTTAAGTATGTGTACTTGAGTTAATAATATAAAAGAGAATGAAACATGAAGAAATTAAGCTGAC
698 GTTTAAGTATGTGTACTTGAGTTAATAATATAAAAGAGAATGAAACATGAAGAAATTAAGCTAAC
*
99022 AAGGATGAATTTTCGGGCTTAAAAAGTGATTTCTGGGCAAGGGGTATCGATACCCATTCATCAGG
763 AAGGATGAATTTTCGGGATTAAAAAGTGATTTCTGGGCAAGGGGTATCGATACCCATTCATCAGG
* *
99087 TACCGATGCCTCAGGAGTAAAATTTAGGAAGATACCTAGGGGTACCATATCTTAAGGAAGG
828 TACCGATACCTCAGGAGTAAAATTTAGGAAGATACCTAGGGGTACCATACCTTAAGGAAGG
99148 TATCGATAC
1 TATCGATAC
99157 CATCTTGAAC
Statistics
Matches: 866, Mismatches: 29, Indels: 21
0.95 0.03 0.02
Matches are distributed among these distances:
889 237 0.27
890 80 0.09
891 2 0.00
892 3 0.00
893 2 0.00
895 106 0.12
900 3 0.00
902 1 0.00
904 23 0.03
905 363 0.42
906 46 0.05
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.33
Consensus pattern (888 bp):
TATCGATACTTTTAAACATTATGTTCTGTCTAGTTTCGATACTTTCTGGGAGTTTCAAAACTATG
TGTAACATCTCAAACTATGGGTTGTGACCAAATTGTAAAATTTCAGAATTTAGTGACCAAATTAT
AAAATTTTAGAATTTAGTGACTAAAGTAGAAATAATTAAAAACTTTAGGGATTTATATGGAAATT
TTGGTATAGGATTAAATTACAAAGAATGATGAATGGAAGGGCAAAATGGTCATTTAACTTAGAAA
TAAATTAAAATGTGATAGGGATGAGATATATACACGTGAGAAATGTAGAATAGGGAAAAGAAAGT
TTCCAGAGTTCTCATCCTTCTTTCTCTCCACCGTGAACCCAAAGTAGAAAAGGTGAGTTTTCTGG
TTAGTTAATTATTTGTTGATTTTAAGTATGGGTTTTGATCCTTAAGTGATACTTAAGCTTAAGTT
GTCTTATAATCAAAAGATGAAGAAGTTATAAGAGATTAAAGAGAAGGGGGCTTCTAAATGAAATT
CTGAAAAAGAGTTAATAAATAAAGTTGGAGTCTCGAATTGACTTATTAACAACTTAATTAAGAGA
TATCAAGTGATAGAATTGAAATTAGAACATATTGAAAATTTGGTATGATTATCGAGTTTTATATG
AAAGATGGGATTTTGAGGTTAAGGATGTATTGAATGAATAGAAATTGGTTTAAGTATGTGTACTT
GAGTTAATAATATAAAAGAGAATGAAACATGAAGAAATTAAGCTAACAAGGATGAATTTTCGGGA
TTAAAAAGTGATTTCTGGGCAAGGGGTATCGATACCCATTCATCAGGTACCGATACCTCAGGAGT
AAAATTTAGGAAGATACCTAGGGGTACCATACCTTAAGGAAGG
Found at i:99286 original size:18 final size:20
Alignment explanation
Indices: 99240--99283 Score: 81
Period size: 19 Copynumber: 2.2 Consensus size: 20
99230 GGATGTATCA
99240 ATACCCTATGGGGGGTACCG
1 ATACCCTATGGGGGGTACCG
99260 ATACCCTAT-GGGGGTACCG
1 ATACCCTATGGGGGGTACCG
99279 ATACC
1 ATACC
99284 TATTTTATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
19 15 0.62
20 9 0.38
ACGTcount: A:0.23, C:0.27, G:0.30, T:0.20
Consensus pattern (20 bp):
ATACCCTATGGGGGGTACCG
Found at i:99810 original size:22 final size:22
Alignment explanation
Indices: 99784--99838 Score: 56
Period size: 22 Copynumber: 2.5 Consensus size: 22
99774 ATATAGGTCA
*
99784 TCGGGACATATACAGAGGTCCT
1 TCGGGACAAATACAGAGGTCCT
* * *
99806 TCGGGATAAATTCATAGGTCCT
1 TCGGGACAAATACAGAGGTCCT
* *
99828 TCAGAACAAAT
1 TCGGGACAAAT
99839 TTCACATGCC
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.33, C:0.20, G:0.22, T:0.25
Consensus pattern (22 bp):
TCGGGACAAATACAGAGGTCCT
Found at i:101773 original size:51 final size:51
Alignment explanation
Indices: 101714--101957 Score: 314
Period size: 51 Copynumber: 4.8 Consensus size: 51
101704 AGATGTACAT
* * * *
101714 ACTTACATCGGTGTAAGTATATGTTAAGTGCTACACTTTTTTATTTTGTTT
1 ACTTACATCGGTGTAAGTATGTGTTAAGTACTACACTTTTTTATTTTATTC
* * *
101765 ACTTACATCGTTGTAAGTATGTGTTAAATACTACATTTTTTTATTTTATTC
1 ACTTACATCGGTGTAAGTATGTGTTAAGTACTACACTTTTTTATTTTATTC
* * *
101816 ACTTA-GTTGGTGT-AGTATGTGTTAAGTACTACACTTTTTTGTTTTATTC
1 ACTTACATCGGTGTAAGTATGTGTTAAGTACTACACTTTTTTATTTTATTC
* * *
101865 ACTTACATCGGTGTAAGTTTGTATTAAGTGA-TACACTTGTTTATTTTATTC
1 ACTTACATCGGTGTAAGTATGTGTTAAGT-ACTACACTTTTTTATTTTATTC
* * *
101916 ACTTACACCGGTGTAAGTATGTGTTAAGTACTATATTTTTTT
1 ACTTACATCGGTGTAAGTATGTGTTAAGTACTACACTTTTTT
101958 TGTAATAATA
Statistics
Matches: 164, Mismatches: 25, Indels: 8
0.83 0.13 0.04
Matches are distributed among these distances:
49 38 0.23
50 12 0.07
51 113 0.69
52 1 0.01
ACGTcount: A:0.25, C:0.11, G:0.15, T:0.49
Consensus pattern (51 bp):
ACTTACATCGGTGTAAGTATGTGTTAAGTACTACACTTTTTTATTTTATTC
Found at i:101869 original size:100 final size:102
Alignment explanation
Indices: 101714--101957 Score: 305
Period size: 100 Copynumber: 2.4 Consensus size: 102
101704 AGATGTACAT
* * * * * *
101714 ACTTACATCGGTGTAAGTATATGTTAAGTGCTACACTTTTTTATTTTGTTTACTTACATCGTTGT
1 ACTTACACCGGTGTAAGTATGTGTTAAGTACTACACTTTTTTATTTTATTCACTTACATCGGTGT
* * *
101779 AAGTATGTGTTAAAT-ACTACATTTTTTTATTTTATTC
66 AAGTATGTATTAAATGA-TACACTTGTTTATTTTATTC
*** *
101816 ACTTA-GTTGGTGT-AGTATGTGTTAAGTACTACACTTTTTTGTTTTATTCACTTACATCGGTGT
1 ACTTACACCGGTGTAAGTATGTGTTAAGTACTACACTTTTTTATTTTATTCACTTACATCGGTGT
* *
101879 AAGTTTGTATTAAGTGATACACTTGTTTATTTTATTC
66 AAGTATGTATTAAATGATACACTTGTTTATTTTATTC
* *
101916 ACTTACACCGGTGTAAGTATGTGTTAAGTACTATATTTTTTT
1 ACTTACACCGGTGTAAGTATGTGTTAAGTACTACACTTTTTT
101958 TGTAATAATA
Statistics
Matches: 121, Mismatches: 18, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
100 79 0.65
101 12 0.10
102 30 0.25
ACGTcount: A:0.25, C:0.11, G:0.15, T:0.49
Consensus pattern (102 bp):
ACTTACACCGGTGTAAGTATGTGTTAAGTACTACACTTTTTTATTTTATTCACTTACATCGGTGT
AAGTATGTATTAAATGATACACTTGTTTATTTTATTC
Found at i:102014 original size:22 final size:21
Alignment explanation
Indices: 101960--102014 Score: 53
Period size: 18 Copynumber: 2.7 Consensus size: 21
101950 ATTTTTTTTG
*
101960 TAATAATAGGTTAACCGTAAGC
1 TAATAAT-GGTTAACCGGAAGC
*
101982 TAAT-AT-G-TAACCGGAACGT
1 TAATAATGGTTAACCGGAA-GC
102001 TAATAATGGTTAAC
1 TAATAATGGTTAAC
102015 AATTAGCGGT
Statistics
Matches: 27, Mismatches: 2, Indels: 8
0.73 0.05 0.22
Matches are distributed among these distances:
18 8 0.30
19 6 0.22
20 2 0.07
21 3 0.11
22 8 0.30
ACGTcount: A:0.40, C:0.13, G:0.18, T:0.29
Consensus pattern (21 bp):
TAATAATGGTTAACCGGAAGC
Found at i:102491 original size:20 final size:20
Alignment explanation
Indices: 102448--102491 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
102438 ACGCGATATC
* * *
102448 AAAATCGCAACGTTGAAAAG
1 AAAATCGCAACGGTAAAAAA
102468 AAAATCGCAACGGTAAAAAA
1 AAAATCGCAACGGTAAAAAA
102488 AAAA
1 AAAA
102492 ATCACAACGC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.59, C:0.14, G:0.16, T:0.11
Consensus pattern (20 bp):
AAAATCGCAACGGTAAAAAA
Found at i:102492 original size:21 final size:21
Alignment explanation
Indices: 102448--102500 Score: 63
Period size: 21 Copynumber: 2.6 Consensus size: 21
102438 ACGCGATATC
** *
102448 AAAATCGCAAC-GTTGAAAAG
1 AAAATCGCAACGGTAAAAAAA
102468 AAAATCGCAACGGTAAAAAAA
1 AAAATCGCAACGGTAAAAAAA
*
102489 AAAATCACAACG
1 AAAATCGCAACG
102501 CGATATTCCA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
20 11 0.39
21 17 0.61
ACGTcount: A:0.57, C:0.17, G:0.15, T:0.11
Consensus pattern (21 bp):
AAAATCGCAACGGTAAAAAAA
Found at i:102554 original size:12 final size:12
Alignment explanation
Indices: 102537--102564 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
102527 TAAGAGAATC
102537 GATCATTCGTTT
1 GATCATTCGTTT
102549 GATCATTCGTTT
1 GATCATTCGTTT
102561 GATC
1 GATC
102565 TAACTCAGCA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.46
Consensus pattern (12 bp):
GATCATTCGTTT
Found at i:109393 original size:29 final size:27
Alignment explanation
Indices: 109351--109416 Score: 69
Period size: 29 Copynumber: 2.3 Consensus size: 27
109341 TTATTTTTCT
109351 ATAATTTGATAAATGTAAGGATTAATTTA
1 ATAATTT-ATAAATGTAAGGA-TAATTTA
* * *
109380 ATAATTTATAAAATTTAATGATAGTTTA
1 ATAATTTAT-AAATGTAAGGATAATTTA
109408 ATAAATTTA
1 AT-AATTTA
109417 ATAATTATCT
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
28 10 0.31
29 22 0.69
ACGTcount: A:0.47, C:0.00, G:0.09, T:0.44
Consensus pattern (27 bp):
ATAATTTATAAATGTAAGGATAATTTA
Found at i:113811 original size:28 final size:28
Alignment explanation
Indices: 113771--113826 Score: 112
Period size: 28 Copynumber: 2.0 Consensus size: 28
113761 TGAAGATGTG
113771 CTTAAATTGAAGTTATTTCCGTATTCTT
1 CTTAAATTGAAGTTATTTCCGTATTCTT
113799 CTTAAATTGAAGTTATTTCCGTATTCTT
1 CTTAAATTGAAGTTATTTCCGTATTCTT
113827 TGAAAGATCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
28 28 1.00
ACGTcount: A:0.25, C:0.14, G:0.11, T:0.50
Consensus pattern (28 bp):
CTTAAATTGAAGTTATTTCCGTATTCTT
Done.