Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004667.1 Hibiscus syriacus cultivar Beakdansim tig00010466_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: 157313
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:5539 original size:70 final size:70
Alignment explanation
Indices: 5456--5651 Score: 239
Period size: 70 Copynumber: 2.8 Consensus size: 70
5446 CTATAATGCT
* * * *
5456 AGGATATGAATTATACAGGTATATAGTTATACCTAGTTAGCAGGGTATGGTTCGATCAACCTATA
1 AGGATATGGATTATACAGGAATATAGTTGTACCTAATTAGCAGGGTATGGTTCGATCAACCTATA
*
5521 GTGTC
66 CTGTC
** * * * * * *
5526 AGGATATGGATTATGTAGGGATATAGATGTACCTAATTAGTAGGGTATGGTTGGATCAACTTGTA
1 AGGATATGGATTATACAGGAATATAGTTGTACCTAATTAGCAGGGTATGGTTCGATCAACCTATA
5591 CTGTC
66 CTGTC
* * * *
5596 AGGATATGGATTACACAGGAATATAATTGTACCTAATAAGCAGGGCATGGTTCGAT
1 AGGATATGGATTATACAGGAATATAGTTGTACCTAATTAGCAGGGTATGGTTCGAT
5652 TCGTGATTGC
Statistics
Matches: 104, Mismatches: 22, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
70 104 1.00
ACGTcount: A:0.32, C:0.11, G:0.26, T:0.32
Consensus pattern (70 bp):
AGGATATGGATTATACAGGAATATAGTTGTACCTAATTAGCAGGGTATGGTTCGATCAACCTATA
CTGTC
Found at i:6227 original size:24 final size:22
Alignment explanation
Indices: 6200--6279 Score: 70
Period size: 25 Copynumber: 3.4 Consensus size: 22
6190 GTATAAATAC
* *
6200 TTAAATTCACAATATTTTTATATA
1 TTAAATTAAAAATATTTTT-T-TA
*
6224 TTAACTTAAAAATATTTTTTTA
1 TTAAATTAAAAATATTTTTTTA
* *
6246 TTAACTTATTAAATATATTTTATTA
1 TTAA---ATTAAAAATATTTTTTTA
6271 TTAAATTAA
1 TTAAATTAA
6280 TTTAAAAAAT
Statistics
Matches: 47, Mismatches: 6, Indels: 8
0.77 0.10 0.13
Matches are distributed among these distances:
22 11 0.23
23 1 0.02
24 16 0.34
25 19 0.40
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (22 bp):
TTAAATTAAAAATATTTTTTTA
Found at i:6257 original size:25 final size:27
Alignment explanation
Indices: 6214--6348 Score: 89
Period size: 25 Copynumber: 5.0 Consensus size: 27
6204 ATTCACAATA
* *
6214 TTTTTA-TATATTAACTTAAAAATATT
1 TTTTTATTAAATTAATTTAAAAATATT
* *
6240 TTTTTATTAACTT-A-TTAAATATATT
1 TTTTTATTAAATTAATTTAAAAATATT
*
6265 TTATTATTAAATTAATTTAAAAAATATT
1 TTTTTATTAAATTAATTT-AAAAATATT
* ** *
6293 TATTT-TTATTTTCATTTAGAAATATATAT
1 TTTTTATTAAATTAATTTA-AAA-ATAT-T
* * *
6322 TTTATGTTAAAATTTATTTAAAAATAT
1 TTTTTATT-AAATTAATTTAAAAATAT
6349 GACTAAATTG
Statistics
Matches: 84, Mismatches: 16, Indels: 15
0.73 0.14 0.13
Matches are distributed among these distances:
25 21 0.25
26 9 0.11
27 18 0.21
28 15 0.18
29 8 0.10
30 5 0.06
31 8 0.10
ACGTcount: A:0.41, C:0.02, G:0.01, T:0.55
Consensus pattern (27 bp):
TTTTTATTAAATTAATTTAAAAATATT
Found at i:6290 original size:30 final size:30
Alignment explanation
Indices: 6256--6345 Score: 73
Period size: 30 Copynumber: 3.1 Consensus size: 30
6246 TTAACTTATT
6256 AAATATATTTTATTATTAAATTAATTTAAA
1 AAATATATTTTATTATTAAATTAATTTAAA
* *
6286 AAATAT-TTATTTTTATT---TTCATTTAGAA
1 AAATATATT-TTATTATTAAATTAATTTA-AA
* * *
6314 ATATATATTTTATGT-TAAAATTTATTTAAA
1 AAATATATTTTAT-TATTAAATTAATTTAAA
6344 AA
1 AA
6346 TATGACTAAA
Statistics
Matches: 46, Mismatches: 7, Indels: 14
0.69 0.10 0.21
Matches are distributed among these distances:
27 7 0.15
28 11 0.24
29 5 0.11
30 16 0.35
31 7 0.15
ACGTcount: A:0.44, C:0.01, G:0.02, T:0.52
Consensus pattern (30 bp):
AAATATATTTTATTATTAAATTAATTTAAA
Found at i:6572 original size:3 final size:3
Alignment explanation
Indices: 6564--6638 Score: 111
Period size: 3 Copynumber: 25.3 Consensus size: 3
6554 TAGTTAACCC
6564 TTA TTA TTA TTA TTA TT- 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
6611 TTA TTA -TA TT- TTA TTA GTTCA TTA TTA T
1 TTA TTA TTA TTA TTA TTA -TT-A TTA TTA T
6639 AAACACTTTA
Statistics
Matches: 67, Mismatches: 0, Indels: 10
0.87 0.00 0.13
Matches are distributed among these distances:
2 6 0.09
3 56 0.84
4 4 0.06
5 1 0.01
ACGTcount: A:0.31, C:0.01, G:0.01, T:0.67
Consensus pattern (3 bp):
TTA
Found at i:7412 original size:44 final size:44
Alignment explanation
Indices: 7331--7455 Score: 119
Period size: 44 Copynumber: 2.8 Consensus size: 44
7321 TGAGAACAAA
* * * * * *
7331 AAACGCCGCAAAAGGTCGAGCTCTATAGCGACATTTTTT-TATAC
1 AAACACCGCAAAAGG-CAAGATATATAGCGGCATTTTTTGGATAC
* * * *
7375 AAACGCCGTAAAAGGTC-AGATATATAGTGGCGTTTTTTGGATAC
1 AAACACCGCAAAAGG-CAAGATATATAGCGGCATTTTTTGGATAC
*
7419 AAACACCGCAAAAGGCAAGATCTATAGCGGCATTTTT
1 AAACACCGCAAAAGGCAAGATATATAGCGGCATTTTT
7456 GGAATAAATG
Statistics
Matches: 67, Mismatches: 12, Indels: 4
0.81 0.14 0.05
Matches are distributed among these distances:
43 17 0.25
44 50 0.75
ACGTcount: A:0.34, C:0.19, G:0.21, T:0.26
Consensus pattern (44 bp):
AAACACCGCAAAAGGCAAGATATATAGCGGCATTTTTTGGATAC
Found at i:7483 original size:43 final size:44
Alignment explanation
Indices: 7331--7515 Score: 180
Period size: 43 Copynumber: 4.3 Consensus size: 44
7321 TGAGAACAAA
* * **
7331 AAACGCCGCAAAAGGTCGAGCTCTATAGCGACATTTTTTTATAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCATTTTTGGATAC
* * * *
7375 AAACGCCGTAAAAGGTC-AGATATATAGTGGCGTTTTTTGGATAC
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGC-ATTTTTGGATAC
* * *
7419 AAACACCGCAAAAGG-CAAGATCTATAGCGGCATTTTTGGA-AT
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCATTTTTGGATAC
* * * * *
7461 AAATGCCACAAAAGGTCGAGATCTATACCGGCATTTTCGGA-AT
1 AAACGCCGCAAAAGGTCGAGATCTATAGCGGCATTTTTGGATAC
*
7504 AAATGCCGCAAA
1 AAACGCCGCAAA
7516 TTATCTAAAA
Statistics
Matches: 117, Mismatches: 21, Indels: 7
0.81 0.14 0.05
Matches are distributed among these distances:
42 13 0.11
43 54 0.46
44 50 0.43
ACGTcount: A:0.35, C:0.19, G:0.21, T:0.24
Consensus pattern (44 bp):
AAACGCCGCAAAAGGTCGAGATCTATAGCGGCATTTTTGGATAC
Found at i:10746 original size:45 final size:45
Alignment explanation
Indices: 10666--10905 Score: 317
Period size: 45 Copynumber: 5.3 Consensus size: 45
10656 TGGTATATGG
* * * * *
10666 TTATGGAAT-AATGGCAAGTGTATTGGTAAACTCAGCTTACGAGC
1 TTATGGAATAAATGGTAAGTATATTTGTAAAATAAGCTTACGAGC
* * *
10710 TTATCGAACAAATGGTAAGTATATTTGTAAAATCAGCTTACGAGC
1 TTATGGAATAAATGGTAAGTATATTTGTAAAATAAGCTTACGAGC
10755 TTATGGAATAAATGGTAAGTATA-TTGATAAAATAAGCTTACGAGC
1 TTATGGAATAAATGGTAAGTATATTTG-TAAAATAAGCTTACGAGC
*
10800 TTATGGAATAAATGGTAAGTAT-TTTGGTAAAATAAGCTTACTAGC
1 TTATGGAATAAATGGTAAGTATATTT-GTAAAATAAGCTTACGAGC
*
10845 TTATGGGATTAAATGGTAAGTAT-TTTGGTAAAATAAGCTTACGAGC
1 TTAT-GGAATAAATGGTAAGTATATTT-GTAAAATAAGCTTACGAGC
*
10891 TTATGGGATAAATGG
1 TTATGGAATAAATGG
10906 CAAGAGATTT
Statistics
Matches: 177, Mismatches: 14, Indels: 9
0.88 0.07 0.05
Matches are distributed among these distances:
44 10 0.06
45 123 0.69
46 44 0.25
ACGTcount: A:0.37, C:0.09, G:0.22, T:0.33
Consensus pattern (45 bp):
TTATGGAATAAATGGTAAGTATATTTGTAAAATAAGCTTACGAGC
Found at i:11393 original size:20 final size:21
Alignment explanation
Indices: 11356--11397 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
11346 ATTTCCAGAA
*
11356 TGCTACAGGGTACTGATACCC
1 TGCTACAGGGTACCGATACCC
11377 TGCTACA-GGTACCGATACCC
1 TGCTACAGGGTACCGATACCC
11397 T
1 T
11398 CACTGTTCAC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 13 0.65
21 7 0.35
ACGTcount: A:0.24, C:0.31, G:0.21, T:0.24
Consensus pattern (21 bp):
TGCTACAGGGTACCGATACCC
Found at i:13723 original size:18 final size:17
Alignment explanation
Indices: 13687--13742 Score: 53
Period size: 16 Copynumber: 3.2 Consensus size: 17
13677 AAAAAATATT
13687 AAAAGAAAAATA-AAAA-
1 AAAAGAAAAA-AGAAAAG
**
13703 AAATTAAAAAAGAAAAG
1 AAAAGAAAAAAGAAAAG
13720 AAAAGAAAAAGAGAAAGAG
1 AAAAGAAAAA-AGAAA-AG
13739 AAAA
1 AAAA
13743 AAATGATAGA
Statistics
Matches: 32, Mismatches: 4, Indels: 5
0.78 0.10 0.12
Matches are distributed among these distances:
15 1 0.03
16 12 0.38
17 8 0.25
18 5 0.16
19 6 0.19
ACGTcount: A:0.80, C:0.00, G:0.14, T:0.05
Consensus pattern (17 bp):
AAAAGAAAAAAGAAAAG
Found at i:16434 original size:21 final size:22
Alignment explanation
Indices: 16410--16450 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
16400 TGATTGTTGC
16410 ATATG-ATGTTATCATGAATAT
1 ATATGAATGTTATCATGAATAT
*
16431 ATATGAATTTTATCATGAAT
1 ATATGAATGTTATCATGAAT
16451 GTTATTTCAG
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:0.39, C:0.05, G:0.12, T:0.44
Consensus pattern (22 bp):
ATATGAATGTTATCATGAATAT
Found at i:16815 original size:45 final size:45
Alignment explanation
Indices: 16746--16985 Score: 349
Period size: 45 Copynumber: 5.3 Consensus size: 45
16736 GGTATATTTG
* * * *
16746 TTATGGAAT-AATGGCAAGTGTATTGGGAAAATCAGCTTACGAGC
1 TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
* *
16790 TTATGGAACAAATGGTAAGTATATTGGTAAAATCAGCTTACGAGC
1 TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
16835 TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
1 TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
* * *
16880 ATATGGAATAAATGGTAAGTATTTTGGTAAAATAAGCTTACGAAC
1 TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
* *
16925 TTATGGGATTAAATGGTAAGTATTTTGGTAAAATAAGCTTACGAGC
1 TTAT-GGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
16971 TTAT-GAGATAAATGG
1 TTATGGA-ATAAATGG
16986 CAAGAGATTT
Statistics
Matches: 180, Mismatches: 13, Indels: 5
0.91 0.07 0.03
Matches are distributed among these distances:
44 10 0.06
45 127 0.71
46 43 0.24
ACGTcount: A:0.38, C:0.08, G:0.23, T:0.31
Consensus pattern (45 bp):
TTATGGAATAAATGGTAAGTATATTGGTAAAATAAGCTTACGAGC
Found at i:17458 original size:20 final size:21
Alignment explanation
Indices: 17425--17466 Score: 77
Period size: 20 Copynumber: 2.0 Consensus size: 21
17415 ATTTCCAGAA
17425 TGCTACAGGGTACCGATACCC
1 TGCTACAGGGTACCGATACCC
17446 TGCTACA-GGTACCGATACCC
1 TGCTACAGGGTACCGATACCC
17466 T
1 T
17467 CACTAGTCAC
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 14 0.67
21 7 0.33
ACGTcount: A:0.24, C:0.33, G:0.21, T:0.21
Consensus pattern (21 bp):
TGCTACAGGGTACCGATACCC
Found at i:25113 original size:41 final size:40
Alignment explanation
Indices: 24989--25113 Score: 110
Period size: 41 Copynumber: 3.0 Consensus size: 40
24979 GCGTTTGTGA
* *
24989 TTAAAAAGATGTCACTAAAGTACGAGTTTATAGCGGCG-TTT
1 TTAAAAA-ATGCCACTAAAGTACGAGTTT-TAGCAGCGTTTT
* * * *
25030 ATATAAAAACGCCACTAAAGTATGAGTATTTA-CAGACTTTTT
1 TTA-AAAAATGCCACTAAAGTACGAGT-TTTAGCAG-CGTTTT
* *
25072 TTAAAAAATGCCACTAAAATACGGGTGTTTAGCAGCGTTTT
1 TTAAAAAATGCCACTAAAGTACGAGT-TTTAGCAGCGTTTT
25113 T
1 T
25114 AGAATAAACG
Statistics
Matches: 66, Mismatches: 13, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
40 2 0.03
41 50 0.76
42 14 0.21
ACGTcount: A:0.36, C:0.14, G:0.18, T:0.33
Consensus pattern (40 bp):
TTAAAAAATGCCACTAAAGTACGAGTTTTAGCAGCGTTTT
Found at i:27992 original size:42 final size:41
Alignment explanation
Indices: 27861--28080 Score: 139
Period size: 42 Copynumber: 5.3 Consensus size: 41
27851 AGAAGAAAAT
* *
27861 CCACTAAAGTACGAGTCTTTCGCGGCGTTTATGCTT-AAAACG
1 CCACTAAAGTACAAGTCTTTAGCGGCGTTT-TG-TTAAAAACG
* * * *
27903 CCACTACA-TCACGAA-TCTATAGCGGCGTTTT-TATACAAACA
1 CCACTAAAGT-AC-AAGTCTTTAGCGGCGTTTTGT-TAAAAACG
* *
27944 CCACTAAAGTACAAGTATTTAGCGGCATTTATGTTAAAAACG
1 CCACTAAAGTACAAGTCTTTAGCGGCGTTT-TGTTAAAAACG
* * * *
27986 CCACTAATA-TACGAGTCTTTAACGGC-ATTTGTATAAAAATG
1 CCACTAA-AGTACAAGTCTTTAGCGGCGTTTTGT-TAAAAACG
* * * * * *
28027 CCATTAAAATACAGGTATGTAGTGGCGTTTGTGCTT-AAAACG
1 CCACTAAAGTACAAGTCTTTAGCGGCGTTT-TG-TTAAAAACG
28069 CCACTAAAGTAC
1 CCACTAAAGTAC
28081 GACCGTTACC
Statistics
Matches: 136, Mismatches: 28, Indels: 28
0.71 0.15 0.15
Matches are distributed among these distances:
39 1 0.01
40 7 0.05
41 53 0.39
42 68 0.50
43 6 0.04
44 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.17, T:0.29
Consensus pattern (41 bp):
CCACTAAAGTACAAGTCTTTAGCGGCGTTTTGTTAAAAACG
Found at i:30196 original size:24 final size:24
Alignment explanation
Indices: 30166--30212 Score: 94
Period size: 24 Copynumber: 2.0 Consensus size: 24
30156 CAGTACATTA
30166 TTTTTAGATAATCTTAAATGATTT
1 TTTTTAGATAATCTTAAATGATTT
30190 TTTTTAGATAATCTTAAATGATT
1 TTTTTAGATAATCTTAAATGATT
30213 ATAAAATAGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 23 1.00
ACGTcount: A:0.34, C:0.04, G:0.09, T:0.53
Consensus pattern (24 bp):
TTTTTAGATAATCTTAAATGATTT
Found at i:41731 original size:22 final size:22
Alignment explanation
Indices: 41706--41761 Score: 103
Period size: 22 Copynumber: 2.5 Consensus size: 22
41696 CATTTCATGG
41706 CACGTATATGATATGTTGTCTA
1 CACGTATATGATATGTTGTCTA
*
41728 CACGTATATGATATGTTGTCTG
1 CACGTATATGATATGTTGTCTA
41750 CACGTATATGAT
1 CACGTATATGAT
41762 GTTGGTGCGA
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 33 1.00
ACGTcount: A:0.27, C:0.14, G:0.20, T:0.39
Consensus pattern (22 bp):
CACGTATATGATATGTTGTCTA
Found at i:47015 original size:16 final size:17
Alignment explanation
Indices: 46989--47022 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
46979 TTCATATATT
*
46989 TATTCATATTTTTTTGC
1 TATTCATATTTTATTGC
47006 TATT-ATATTTTATTGC
1 TATTCATATTTTATTGC
47022 T
1 T
47023 TTGTTCCCAG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 12 0.75
17 4 0.25
ACGTcount: A:0.21, C:0.09, G:0.06, T:0.65
Consensus pattern (17 bp):
TATTCATATTTTATTGC
Found at i:59507 original size:19 final size:19
Alignment explanation
Indices: 59447--59507 Score: 59
Period size: 22 Copynumber: 2.9 Consensus size: 19
59437 CATAATATTA
*
59447 AAAAAATTATTTTATTACTTT
1 AAAAAATAATTTTATT--TTT
59468 AAAATAATAATATTATATTTTT
1 AAAA-AATAAT-TT-TATTTTT
*
59490 AATAAATAATTTTATTTT
1 AAAAAATAATTTTATTTT
59508 ATTATATTCA
Statistics
Matches: 35, Mismatches: 2, Indels: 8
0.78 0.04 0.18
Matches are distributed among these distances:
19 6 0.17
20 2 0.06
21 10 0.29
22 11 0.31
23 2 0.06
24 4 0.11
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (19 bp):
AAAAAATAATTTTATTTTT
Found at i:65446 original size:17 final size:17
Alignment explanation
Indices: 65405--65449 Score: 54
Period size: 17 Copynumber: 2.6 Consensus size: 17
65395 AACTACTTGA
65405 TTAAATATTTAATAAAT
1 TTAAATATTTAATAAAT
** **
65422 TTTTATATTTTTTAAAT
1 TTAAATATTTAATAAAT
65439 TTAAATATTTA
1 TTAAATATTTA
65450 CTTTTACCTA
Statistics
Matches: 21, Mismatches: 7, Indels: 0
0.75 0.25 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.58
Consensus pattern (17 bp):
TTAAATATTTAATAAAT
Found at i:65492 original size:2 final size:2
Alignment explanation
Indices: 65485--65532 Score: 89
Period size: 2 Copynumber: 24.5 Consensus size: 2
65475 AAATCAAAAT
65485 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
65526 TA TA TA T
1 TA TA TA T
65533 TGAAAAGACT
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 44 0.98
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:67835 original size:20 final size:21
Alignment explanation
Indices: 67810--67879 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
67800 TATTATTTCA
67810 AATTAATT-AAATATATATTT
1 AATTAATTAAAATATATATTT
* * *
67830 AATTAATTGAAATTAAATATTC
1 AATTAATT-AAAATATATATTT
*
67852 AGGATT-ATTAAAACATATATTT
1 A--ATTAATTAAAATATATATTT
67874 AATTAA
1 AATTAA
67880 CTCTAGATAT
Statistics
Matches: 38, Mismatches: 7, Indels: 9
0.70 0.13 0.17
Matches are distributed among these distances:
20 11 0.29
21 1 0.03
22 20 0.53
23 3 0.08
24 3 0.08
ACGTcount: A:0.50, C:0.03, G:0.04, T:0.43
Consensus pattern (21 bp):
AATTAATTAAAATATATATTT
Found at i:67841 original size:90 final size:87
Alignment explanation
Indices: 67685--67848 Score: 265
Period size: 90 Copynumber: 1.9 Consensus size: 87
67675 CTTTTATAGC
* *
67685 CAAGTTACCATAATCATATTAGGGTTTATTATTTCATATAATTAAATCTATATTTAATTAATTGA
1 CAAGTTACCATAATCATATTAGGGTTTATTATTTCAAATAATTAAATATATATTTAATTAATTGA
*
67750 AATTTAATAATCCTCTTATATT
66 AATTAAATAATCCTCTTATATT
*
67772 CAAGTTACCCTAATCATATTAGGGATTTTATTATTTCAAATTAATTAAATATATATTTAATTAAT
1 CAAGTTACCATAATCATATTAGGG--TTTATTATTTCAAA-TAATTAAATATATATTTAATTAAT
67837 TGAAATTAAATA
63 TGAAATTAAATA
67849 TTCAGGATTA
Statistics
Matches: 70, Mismatches: 4, Indels: 3
0.91 0.05 0.04
Matches are distributed among these distances:
87 23 0.33
89 13 0.19
90 34 0.49
ACGTcount: A:0.40, C:0.09, G:0.06, T:0.45
Consensus pattern (87 bp):
CAAGTTACCATAATCATATTAGGGTTTATTATTTCAAATAATTAAATATATATTTAATTAATTGA
AATTAAATAATCCTCTTATATT
Found at i:72187 original size:128 final size:128
Alignment explanation
Indices: 71942--72224 Score: 343
Period size: 128 Copynumber: 2.2 Consensus size: 128
71932 TATCGAAACA
* * *
71942 TTTTTGGAACAAACACCACAAAAGGTCGATATATAAAGCGGCGTTTTTGGAACAAATGACGCAAA
1 TTTTTGGAACAAACACCGCAAAAGGTCGAGATATAAAGCGGCGTTTTTGGAACAAACGACGCAAA
* * *
72007 AGGTTAAGATCTATAGCAGCGTTTTCAGAATAAACGCCGCAAAAGGTCAGATCTATAGCGGTG
66 AAGTTAAGATCTATAGCAGCGTTTTCAGAACAAACGACGCAAAAGGTCAGATCTATAGCGGTG
* * * * * *
72070 TTTTTGGAACAAACACCGCAAAAGGTTGAGATCTATAGCGTCGTTTTTGGAACAAACGCCGTAAA
1 TTTTTGGAACAAACACCGCAAAAGGTCGAGATATAAAGCGGCGTTTTTGGAACAAACGACGCAAA
* * * ** * *
72135 AAG-TCATATCTATAGCGGCGTTTTTGGAACAAACGACGCAAAAGGTTGAGATCTATAGTGGTG
66 AAGTTAAGATCTATAGCAGCGTTTTCAGAACAAACGACGCAAAAGG-TCAGATCTATAGCGGTG
** * *
72198 TTTTCCGAATAAACTCCGCAAAAGGTC
1 TTTTTGGAACAAACACCGCAAAAGGTC
72225 ATATCTATAA
Statistics
Matches: 130, Mismatches: 24, Indels: 2
0.83 0.15 0.01
Matches are distributed among these distances:
127 35 0.27
128 95 0.73
ACGTcount: A:0.35, C:0.18, G:0.23, T:0.25
Consensus pattern (128 bp):
TTTTTGGAACAAACACCGCAAAAGGTCGAGATATAAAGCGGCGTTTTTGGAACAAACGACGCAAA
AAGTTAAGATCTATAGCAGCGTTTTCAGAACAAACGACGCAAAAGGTCAGATCTATAGCGGTG
Found at i:72250 original size:42 final size:42
Alignment explanation
Indices: 71942--72257 Score: 301
Period size: 43 Copynumber: 7.4 Consensus size: 42
71932 TATCGAAACA
* * *
71942 TTTTTGGAACAAACACCACAAAAGGTC-GATATATAAAGCGGCG
1 TTTTTGGAACAAACGCCGCAAAAGGTCAGATCTAT--AGCGGCG
* * * *
71985 TTTTTGGAACAAATGACGCAAAAGGTTAAGATCTATAGCAGCG
1 TTTTTGGAACAAACGCCGCAAAAGG-TCAGATCTATAGCGGCG
** * *
72028 TTTTCAGAATAAACGCCGCAAAAGGTCAGATCTATAGCGGTG
1 TTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCG
* * *
72070 TTTTTGGAACAAACACCGCAAAAGGTTGAGATCTATAGCGTCG
1 TTTTTGGAACAAACGCCGCAAAAGG-TCAGATCTATAGCGGCG
* * *
72113 TTTTTGGAACAAACGCCGTAAAAAGTCATATCTATAGCGGCG
1 TTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCG
* * * *
72155 TTTTTGGAACAAACGACGCAAAAGGTTGAGATCTATAGTGGTG
1 TTTTTGGAACAAACGCCGCAAAAGG-TCAGATCTATAGCGGCG
** * * * ** *
72198 TTTTCCGAATAAACTCCGCAAAAGGTCATATCTATAATGGCA
1 TTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCG
* *
72240 TTTTTTGAATAAACGCCG
1 TTTTTGGAACAAACGCCG
72258 GAAATGTGTG
Statistics
Matches: 221, Mismatches: 48, Indels: 9
0.79 0.17 0.03
Matches are distributed among these distances:
42 98 0.44
43 116 0.52
44 1 0.00
45 6 0.03
ACGTcount: A:0.34, C:0.17, G:0.22, T:0.26
Consensus pattern (42 bp):
TTTTTGGAACAAACGCCGCAAAAGGTCAGATCTATAGCGGCG
Found at i:72254 original size:85 final size:84
Alignment explanation
Indices: 71960--72233 Score: 352
Period size: 85 Copynumber: 3.2 Consensus size: 84
71950 ACAAACACCA
* * * *
71960 CAAAAGGTCGATATATAAAGCGGCGTTTTTGGAACAAATGACGCAAAAGGTTAAGATCTATAGCA
1 CAAAAGGTC-ATATCTATAGCGGCGTTTTTGGAACAAACGACGCAAAAGGTTGAGATCTATAG-A
*
72025 GCGTTTTCAGAATAAACGCCG
64 GTGTTTTCAGAATAAACGCCG
* * *
72046 CAAAAGGTCAGATCTATAGCGGTGTTTTTGGAACAAAC-ACCGCAAAAGGTTGAGATCTATAGCG
1 CAAAAGGTCATATCTATAGCGGCGTTTTTGGAACAAACGA-CGCAAAAGGTTGAGATCTATAGAG
** *
72110 TCGTTTTTGGAACAAACGCCG
65 T-GTTTTCAGAATAAACGCCG
* * *
72131 TAAAAAGTCATATCTATAGCGGCGTTTTTGGAACAAACGACGCAAAAGGTTGAGATCTATAGTGG
1 CAAAAGGTCATATCTATAGCGGCGTTTTTGGAACAAACGACGCAAAAGGTTGAGATCTATAG-AG
* *
72196 TGTTTTCCGAATAAACTCCG
65 TGTTTTCAGAATAAACGCCG
72216 CAAAAGGTCATATCTATA
1 CAAAAGGTCATATCTATA
72234 ATGGCATTTT
Statistics
Matches: 162, Mismatches: 22, Indels: 9
0.84 0.11 0.05
Matches are distributed among these distances:
84 2 0.01
85 148 0.91
86 12 0.07
ACGTcount: A:0.35, C:0.17, G:0.23, T:0.26
Consensus pattern (84 bp):
CAAAAGGTCATATCTATAGCGGCGTTTTTGGAACAAACGACGCAAAAGGTTGAGATCTATAGAGT
GTTTTCAGAATAAACGCCG
Found at i:75080 original size:80 final size:83
Alignment explanation
Indices: 74905--75104 Score: 218
Period size: 80 Copynumber: 2.5 Consensus size: 83
74895 ACATACCAAA
* *
74905 CTATTGCGGCGTTTGTATTAAAATGCCGCTAAA-A-TACTACTATGTTGCGGCGTTTGTTAATAA
1 CTATTGCGGCGTTTGTA-TAAAATACCGCTAAAGATTACTACTATGTTACGGCGTTTGTTAATAA
* *
74968 ATGCCACTATATATGAACC
65 AGGCCACTATAGATGAACC
* * * *
74987 ATATTGTGGCGTTTGTATAAAATACCGCTAAAGATTACT-CT-T-TTACGGCATTTTTTTAA-AA
1 CTATTGCGGCGTTTGTATAAAATACCGCTAAAGATTACTACTATGTTACGGC-GTTTGTTAATAA
*
75048 AGGCCACTATAGATTAACC
65 AGGCCACTATAGATGAACC
*
75067 CTATTGCGACGTTTGTATAAAA-ACGCCGCTAAAG-TTAC
1 CTATTGCGGCGTTTGTATAAAATA--CCGCTAAAGATTAC
75105 CATTTTGGCG
Statistics
Matches: 101, Mismatches: 12, Indels: 12
0.81 0.10 0.10
Matches are distributed among these distances:
79 1 0.01
80 47 0.47
81 31 0.31
82 18 0.18
83 4 0.04
ACGTcount: A:0.31, C:0.18, G:0.17, T:0.34
Consensus pattern (83 bp):
CTATTGCGGCGTTTGTATAAAATACCGCTAAAGATTACTACTATGTTACGGCGTTTGTTAATAAA
GGCCACTATAGATGAACC
Found at i:76805 original size:84 final size:84
Alignment explanation
Indices: 76656--76848 Score: 287
Period size: 84 Copynumber: 2.3 Consensus size: 84
76646 GTGAATCTTC
* *
76656 AAGCAAAGATTTTGTGAGTTTAGGTTAAAAACTCAAAAAATTTAGGGTTTTGTTAGGGAAAAAAA
1 AAGCAAAGATTTTGTGAGTTTGGGTTAAAAACTCAAAAAATTTAAGGTTTTGTTAGGGAAAAAAA
*
76721 GGAGAATTTTAGAATATGT
66 GGACAATTTTAGAATATGT
* *** * *
76740 AAGCAAAGATTTTGTGAGATTGGGTTAAAAACTCAAATTTTTTAAGGTTTTGTTATGGAAGAAAA
1 AAGCAAAGATTTTGTGAGTTTGGGTTAAAAACTCAAAAAATTTAAGGTTTTGTTAGGGAAAAAAA
*
76805 GGACAATTTTAGAATCTGT
66 GGACAATTTTAGAATATGT
*
76824 AAGCAAAGATTTTGTAAGTTTGGGT
1 AAGCAAAGATTTTGTGAGTTTGGGT
76849 GTGGGATTTA
Statistics
Matches: 97, Mismatches: 12, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
84 97 1.00
ACGTcount: A:0.38, C:0.05, G:0.23, T:0.34
Consensus pattern (84 bp):
AAGCAAAGATTTTGTGAGTTTGGGTTAAAAACTCAAAAAATTTAAGGTTTTGTTAGGGAAAAAAA
GGACAATTTTAGAATATGT
Found at i:81503 original size:9 final size:9
Alignment explanation
Indices: 81469--81506 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
81459 TTTACTAAAT
81469 TTTATTTATA
1 TTTA-TTATA
81479 TTTATT-TA
1 TTTATTATA
*
81487 TCTATTATA
1 TTTATTATA
81496 TTTATTATA
1 TTTATTATA
81505 TT
1 TT
81507 AATTTTTCTT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
8 7 0.28
9 14 0.56
10 4 0.16
ACGTcount: A:0.29, C:0.03, G:0.00, T:0.68
Consensus pattern (9 bp):
TTTATTATA
Found at i:83349 original size:19 final size:19
Alignment explanation
Indices: 83322--83367 Score: 83
Period size: 19 Copynumber: 2.4 Consensus size: 19
83312 ATTTAGACAT
*
83322 TTTGTATTTTGTTATTTTC
1 TTTGCATTTTGTTATTTTC
83341 TTTGCATTTTGTTATTTTC
1 TTTGCATTTTGTTATTTTC
83360 TTTGCATT
1 TTTGCATT
83368 CACATTAACT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 26 1.00
ACGTcount: A:0.11, C:0.09, G:0.11, T:0.70
Consensus pattern (19 bp):
TTTGCATTTTGTTATTTTC
Found at i:87117 original size:167 final size:166
Alignment explanation
Indices: 86746--87633 Score: 1043
Period size: 167 Copynumber: 5.3 Consensus size: 166
86736 CTATTTGCCT
* * * * *
86746 ACCAAATACCTTCGAGTTCGACTACGTTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGT
* * * *** * * * * *
86811 CGATAAGGGCTATCTG-C--C-AAAGACCCCCGAGTTCGATTACACTCAGCTTTGAGGGCATATC
66 CTAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGC--TCAAGGCACATC
*
86872 ATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGTC
129 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTC
* * * *
86910 TCCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAACACAACTTAAG
1 ACC-AAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAG
* * *
86975 TCTAAAAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGTACATC
65 TCTAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAA-GGCACATC
* *
87040 ATTTACAGCTTGACTCAAGGCTAGAAGGGTTATCTGTC
129 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTC
* * *
87078 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGT
* * * * *
87143 CTAGAAGGGTTGTCTGGCAACACAATACCTTTGAGTTTGACTACGCTCAGCTCAACGGCACATCA
66 CTAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAA-GGCACATCA
* * * * * *
87208 TTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG--
130 TTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTC
** * * * * * * * * *
87243 -CCAAAGACCCCCGATTTCGATTACACTCAGCTTCGAGGGAACATTATTTGCAACATAACTTAAG
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGC-TCCAAGGCACATCATTTACAGCATAACTTAAG
* *
87307 TCGAGAAGGGTTATCTGCCAACCAAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATC
65 TCTAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAAGGCACATC
*
87372 ATTTACAGCATAACTCAAGGTTAGAAGGGTTATCTGTC
129 ATTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTC
* *
87410 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGG
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGT
* * * * *
87475 CTAGAAGGGTTATATGTCACCAAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCACATCA
66 CTAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCT-CAAGGCACATCA
*** *
87540 TTTGTGGCATAACTCAAGGCTAGAAGGGTTATCTGCC
130 TTTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTC
* **
87577 AACAAAGACCTTCGAGTTCGACTACGCTCAGCTCTTAGGCACATCATTTACAGCATA
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATA
87634 GCCCAAGGCA
Statistics
Matches: 617, Mismatches: 96, Indels: 19
0.84 0.13 0.03
Matches are distributed among these distances:
164 28 0.05
165 174 0.28
166 4 0.01
167 317 0.51
168 70 0.11
169 24 0.04
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.25
Consensus pattern (166 bp):
ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTTAAGT
CTAGAAGGGTTATCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAAGGCACATCAT
TTACAGCATAACTCAAGGCTAGAAGGGTTATCTGTC
Found at i:87503 original size:416 final size:415
Alignment explanation
Indices: 86720--87635 Score: 1302
Period size: 416 Copynumber: 2.2 Consensus size: 415
86710 TGCAATATAG
* * * * * *
86720 CTCAAGACAAGAAGGGCTATTTGCCTACCAAATACCTTCGAGTTCGACTACGTTCAGCTCTAAGG
1 CTCAAGGCTAGAAGGGTTATCTGCC-AACAAATACCTTCGAGTTCGACTACGCTCAGCTCTAAGG
*
86785 CACATCATTTGCAGCATAGCTTAAGTCGATAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTA
65 CACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTA
* * * ** * * *
86850 CACTCAGCTTTGAGGGCATATCATTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGTCTCCAA
130 CACTCAGCTTCGAGGGAACATCATTTACAACATAACTCAAGGCGAGAAGGGTTATCTGCCACCAA
* *
86915 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTACAACACAACTTAAGTCTAA
195 AAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAACACAACTCAAGTCTAA
* * *
86980 AAGGGTTGTCTGCCAACAAAAGACCTTTGAGTTCGACTACGCTCAGCTCAACGGTACATCATTTA
260 AAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTA
* * *
87045 CAGCTTGACTCAAGGCTAGAAGGGTTATCTGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGC
325 CAGCATAACTCAAGGCTAGAAGGGTTATATGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGC
*
87110 TCCAAGGCATATCATTTGCAGCACAA
390 TCCAAGGCACATCATTTGCAGCACAA
* * * * * *
87136 CTTAAGTCTAGAAGGGTTGTCTGGCAACACAATACCTTTGAGTTTGACTACGCTCAGCTC-AACG
1 CTCAAGGCTAGAAGGGTTATCTGCCAACA-AATACCTTCGAGTTCGACTACGCTCAGCTCTAA-G
*
87200 GCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGATTTCGATT
64 GCACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATT
* * * *
87265 ACACTCAGCTTCGAGGGAACATTATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTGCCAACC
129 ACACTCAGCTTCGAGGGAACATCATTTACAACATAACTCAAGGCGAGAAGGGTTATCTGCC-ACC
* * *
87330 -AAAGACCTTTGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGGT-
193 AAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAACACAACTCAA-GTC
* * *
87393 TAGAAGGGTTATCTGTC-ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAA-GGCACATCA
257 TAAAAGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCT-CAACGGCACATCA
*
87456 TTTACAGCATAACTCAAGGCTAGAAGGGTTATATGTCACCAAAAGACCTTCGAGTTCGACTACGT
321 TTTACAGCATAACTCAAGGCTAGAAGGGTTATATGTCACC-AAAGACCTTCGAGTTCGACTACGC
** *
87521 TCAGCTCCAAGGCACATCATTTGTGGCATAA
385 TCAGCTCCAAGGCACATCATTTGCAGCACAA
* *
87552 CTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACGCTCAGCTCTTAGGC
1 CTCAAGGCTAGAAGGGTTATCTGCCAACAAATACCTTCGAGTTCGACTACGCTCAGCTCTAAGGC
*
87617 ACATCATTTACAGCATAGC
66 ACATCATTTGCAGCATAGC
87636 CCAAGGCAAT
Statistics
Matches: 440, Mismatches: 53, Indels: 15
0.87 0.10 0.03
Matches are distributed among these distances:
415 129 0.29
416 307 0.70
417 4 0.01
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.25
Consensus pattern (415 bp):
CTCAAGGCTAGAAGGGTTATCTGCCAACAAATACCTTCGAGTTCGACTACGCTCAGCTCTAAGGC
ACATCATTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTGCCAAAGACCCCCGAGTTCGATTAC
ACTCAGCTTCGAGGGAACATCATTTACAACATAACTCAAGGCGAGAAGGGTTATCTGCCACCAAA
AGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAACACAACTCAAGTCTAAA
AGGGTTATCTGCCAACAAAAGACCTTCGAGTTCGACTACGCTCAGCTCAACGGCACATCATTTAC
AGCATAACTCAAGGCTAGAAGGGTTATATGTCACCAAAGACCTTCGAGTTCGACTACGCTCAGCT
CCAAGGCACATCATTTGCAGCACAA
Found at i:87692 original size:332 final size:328
Alignment explanation
Indices: 86746--87633 Score: 1027
Period size: 332 Copynumber: 2.7 Consensus size: 328
86736 CTATTTGCCT
* * * *
86746 ACCAAATACCTTCGAGTTCGACTACGTTCAGCTCTAAGGCACATCATTTGCAGCATAGCTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGT
* * * ** * * * * *
86811 CGATAAGGGCTATCTG--CC-AAAGACCCCCGAGTTCGATTACACTCAGCTTTGAGGGCATATCA
66 CTAGAAGGGTTATCTGCACCAAAAGACCTTCGAGTTCGACTACGCTCAGC--TCAAGGCACATCA
* *
86873 TTTACAGTATAACTCAAGGCTAGAAGGGTTATCTGTCTC-CAAAAGACCTTCGAGTTCGACTACG
129 TTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTG-C-CAC-AAAGACCTTCGAGTTCGACTACG
* * * *
86937 CTCAGCTCCAAGGCATATCATTTACAACACAACTTAAGTCTAAAAGGGTTGTCTGCCAACAAAAG
191 CTCAGCTCTAAGGCACATCATTTACAACATAACTTAAGTC-AAAAGGGTTATCTGCCAACAAAAG
* * *
87002 ACCTTTGAGTTCGACTACGCTCAGCT-CAACGGTACATCATTTACAGCTTGACTCAAGGCTAGAA
255 ---TTTGAGTTCGACTACGCTCAGCTCCAACGGCACATCATTTACAGCATAACTCAAGGCTAGAA
87066 GGGTTATCTGTC
317 GGGTTATCTGTC
* *
87078 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCATATCATTTGCAGCACAACTTAAGT
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGT
* * * * * *
87143 CTAGAAGGGTTGTCTGGCAACACAATACCTTTGAGTTTGACTACGCTCAGCTCAACGGCACATCA
66 CTAGAAGGGTTATCT-GCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCAA-GGCACATCA
* * * * * ** * * *
87208 TTTGCAGCATAGCTTAAGTCGAGAAGGGCTATCTG-C-CAAAGACCCCCGATTTCGATTACACTC
129 TTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACAAAGACCTTCGAGTTCGACTACGCTC
* * * * * *
87271 AGCTTCGAGGGAACATTATTTGCAACATAACTTAAGTCGAGAAGGGTTATCTGCCAACCAAAGAC
194 AGC-TCTAAGGCACATCATTTACAACATAACTTAAGTC-AAAAGGGTTATCTGCCAA-CAAA-A-
* *
87336 CTTTGAGTTCGACTACGCTCAGCTCCAA-GGCACATCATTTACAGCATAACTCAAGGTTAGAAGG
254 GTTTGAGTTCGACTACGCTCAGCTCCAACGGCACATCATTTACAGCATAACTCAAGGCTAGAAGG
87400 GTTATCTGTC
319 GTTATCTGTC
* * *
87410 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTACAGCATAACTCAAGG
1 ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGT
* *
87475 CTAGAAGGGTTATATGTCACCAAAAGACCTTCGAGTTCGACTACGTTCAGCTCCAAGGCACATCA
66 CTAGAAGGGTTATCTG-CACCAAAAGACCTTCGAGTTCGACTACGCTCAGCT-CAAGGCACATCA
**
87540 TTTGTGGCATAACTCAAGGCTAGAAGGGTTATCTGCCAACAAAGACCTTCGAGTTCGACTACGCT
129 TTTGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCC-ACAAAGACCTTCGAGTTCGACTACGCT
* *
87605 CAGCTCTTAGGCACATCATTTACAGCATA
193 CAGCTCTAAGGCACATCATTTACAACATA
87634 GCCCAAGGCA
Statistics
Matches: 460, Mismatches: 81, Indels: 28
0.81 0.14 0.05
Matches are distributed among these distances:
331 25 0.05
332 319 0.69
333 12 0.03
334 21 0.05
335 62 0.13
336 21 0.05
ACGTcount: A:0.30, C:0.26, G:0.20, T:0.25
Consensus pattern (328 bp):
ACCAAAGACCTTCGAGTTCGACTACGCTCAGCTCCAAGGCACATCATTTGCAGCATAACTTAAGT
CTAGAAGGGTTATCTGCACCAAAAGACCTTCGAGTTCGACTACGCTCAGCTCAAGGCACATCATT
TGCAGCATAACTCAAGGCTAGAAGGGTTATCTGCCACAAAGACCTTCGAGTTCGACTACGCTCAG
CTCTAAGGCACATCATTTACAACATAACTTAAGTCAAAAGGGTTATCTGCCAACAAAAGTTTGAG
TTCGACTACGCTCAGCTCCAACGGCACATCATTTACAGCATAACTCAAGGCTAGAAGGGTTATCT
GTC
Found at i:88359 original size:37 final size:37
Alignment explanation
Indices: 88235--88599 Score: 218
Period size: 39 Copynumber: 9.7 Consensus size: 37
88225 TTGCAAATAG
* * *
88235 TTTTTGAAAATACAGGTATAATATATAGTTTTCAAAATA
1 TTTTTGAAAATATA--TATAATATATAGTTTTTAAAACA
* *
88274 TTTTTGAAAATGTATATATTATATAGTTTTTAAAAAACA
1 TTTTTGAAAATATATATAATATATAGTTTTT--AAAACA
*
88313 TTTTTGAAAAT-TATATAATAAATAGATTTTTAAAACA
1 TTTTTGAAAATATATATAATATATAG-TTTTTAAAACA
* ** *
88350 TTTTAGAAAATATATATAATATATATAGTTTAGAAAATA
1 TTTTTGAAAATATATAT-A-ATATATAGTTTTTAAAACA
* * *
88389 ATTTTGAAAGTATATATAATATATAATTTTTGAAAAAAAAACA
1 TTTTTGAAAATATATATAATATATAGTTTTT------AAAACA
* *
88432 TTTTT-AAAA-ACATAT-A-ATATAG-TTTTAAAACG
1 TTTTTGAAAATATATATAATATATAGTTTTTAAAACA
* * **
88464 TTTTTGAAAA-CTATATAACATATAG-TTCGAAAACA
1 TTTTTGAAAATATATATAATATATAGTTTTTAAAACA
* * **
88499 TCTTTT-AAAAT-TAAATAATAT-TA-TTTTGGAAATATTT
1 T-TTTTGAAAATATATATAATATATAGTTTT-TAAA-A-CA
*
88536 TATTTTG-AAATATATATTATATATAG-TTTTAAAACAA
1 T-TTTTGAAAATATATATAATATATAGTTTTTAAAAC-A
*
88573 TATTTTTAAAATATATATATATATATA
1 T-TTTTGAAAATATATATA-ATATATA
88600 TATATATATA
Statistics
Matches: 256, Mismatches: 42, Indels: 56
0.72 0.12 0.16
Matches are distributed among these distances:
32 10 0.04
33 8 0.03
34 5 0.02
35 30 0.12
36 5 0.02
37 57 0.22
38 43 0.17
39 73 0.29
40 8 0.03
41 5 0.02
42 3 0.01
43 9 0.04
ACGTcount: A:0.47, C:0.04, G:0.07, T:0.43
Consensus pattern (37 bp):
TTTTTGAAAATATATATAATATATAGTTTTTAAAACA
Found at i:88487 original size:115 final size:113
Alignment explanation
Indices: 88255--88480 Score: 269
Period size: 115 Copynumber: 2.0 Consensus size: 113
88245 TACAGGTATA
* * * * *
88255 ATATATAGTTTTCAAAATATTTTTGAAAATGTATATATTATATAGTTTTTAAAAAACATTTTTGA
1 ATATATAGTTTACAAAATAATTTTGAAAATATATATAATATATAATTTTTAAAAAACATTTTTGA
**
88320 AAATTATATAATAAATAGATTTTTAAAACATTTTAGAAAATATATATAAT
66 AAAACATATAAT-AATAGA-TTTTAAAACATTTTAGAAAATATATATAAT
* *
88370 ATATATAGTTTAGAAAATAATTTTGAAAGTATATATAATATATAATTTTTGAAAAAAAAACATTT
1 ATATATAGTTTACAAAATAATTTTGAAAATATATATAATATATAATTTTT----AAAAAACATTT
* *
88435 TT-AAAAACATATAAT-ATAG-TTTTAAAACGTTTTTGAAAACTATATA
62 TTGAAAAACATATAATAATAGATTTTAAAACATTTTAGAAAA-TATATA
88481 ACATATAGTT
Statistics
Matches: 95, Mismatches: 11, Indels: 10
0.82 0.09 0.09
Matches are distributed among these distances:
114 18 0.19
115 49 0.52
116 4 0.04
118 11 0.12
119 13 0.14
ACGTcount: A:0.48, C:0.03, G:0.07, T:0.42
Consensus pattern (113 bp):
ATATATAGTTTACAAAATAATTTTGAAAATATATATAATATATAATTTTTAAAAAACATTTTTGA
AAAACATATAATAATAGATTTTAAAACATTTTAGAAAATATATATAAT
Found at i:88497 original size:35 final size:32
Alignment explanation
Indices: 88426--88508 Score: 94
Period size: 32 Copynumber: 2.5 Consensus size: 32
88416 TTTTGAAAAA
**
88426 AAAACATTTTTAAAAACATATAATATAGTTTT
1 AAAACATTTTTAAAAACATATAATATAGTTCG
* *
88458 AAAACGTTTTTGAAAACTATATAACATATAGTTCG
1 AAAACATTTTTAAAAAC-ATAT-A-ATATAGTTCG
88493 AAAACATCTTTTAAAA
1 AAAACAT-TTTTAAAA
88509 TTAAATAATA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
32 15 0.37
33 4 0.10
34 1 0.02
35 14 0.34
36 7 0.17
ACGTcount: A:0.48, C:0.10, G:0.06, T:0.36
Consensus pattern (32 bp):
AAAACATTTTTAAAAACATATAATATAGTTCG
Found at i:88547 original size:15 final size:16
Alignment explanation
Indices: 88519--88548 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
88509 TTAAATAATA
88519 TTATTTTGGAAATATT
1 TTATTTTGGAAATATT
88535 TTATTTT-GAAATAT
1 TTATTTTGGAAATAT
88549 ATATTATATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 7 0.50
16 7 0.50
ACGTcount: A:0.33, C:0.00, G:0.10, T:0.57
Consensus pattern (16 bp):
TTATTTTGGAAATATT
Found at i:88550 original size:17 final size:16
Alignment explanation
Indices: 88511--88555 Score: 54
Period size: 16 Copynumber: 2.7 Consensus size: 16
88501 TTTTAAAATT
*
88511 AAATAATATTATTTTGG
1 AAAT-ATATTATTTTGA
*
88528 AAATATTTTATTTTGA
1 AAATATATTATTTTGA
88544 AATATATATTAT
1 AA-ATATATTAT
88556 ATATAGTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
16 12 0.50
17 12 0.50
ACGTcount: A:0.42, C:0.00, G:0.07, T:0.51
Consensus pattern (16 bp):
AAATATATTATTTTGA
Found at i:88590 original size:2 final size:2
Alignment explanation
Indices: 88583--88620 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
88573 TATTTTTAAA
88583 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
88621 GTTTTTATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:90182 original size:21 final size:21
Alignment explanation
Indices: 90158--90228 Score: 60
Period size: 21 Copynumber: 3.5 Consensus size: 21
90148 ATTTTATTTA
*
90158 TATTTATT-TATCTGTTATATT
1 TATTTATTATAT-TATTATATT
90179 TATTTATTATATTATTATATT
1 TATTTATTATATTATTATATT
* * *
90200 AATTT-TTCT-TTTTTCATATT
1 TATTTATTATATTATT-ATATT
90220 TATTT-TTAT
1 TATTTATTAT
90229 TGTACATTCT
Statistics
Matches: 42, Mismatches: 6, Indels: 5
0.79 0.11 0.09
Matches are distributed among these distances:
19 4 0.10
20 15 0.36
21 20 0.48
22 3 0.07
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.69
Consensus pattern (21 bp):
TATTTATTATATTATTATATT
Found at i:90199 original size:13 final size:13
Alignment explanation
Indices: 90150--90228 Score: 54
Period size: 13 Copynumber: 5.9 Consensus size: 13
90140 TTTACTAAAT
*
90150 TTTATTTATATTTA
1 TTTATTTAT-TATA
* *
90164 TTTATCTGTTATA
1 TTTATTTATTATA
90177 TTTATTTATTATA
1 TTTATTTATTATA
*
90190 -TTATTATATTAATT
1 TTTATT-TATT-ATA
* *
90204 TTTCTTTTTTCATA
1 TTTATTTATT-ATA
90218 TTTATTT-TTAT
1 TTTATTTATTAT
90229 TGTACATTCT
Statistics
Matches: 51, Mismatches: 11, Indels: 8
0.73 0.16 0.11
Matches are distributed among these distances:
12 7 0.14
13 20 0.39
14 20 0.39
15 4 0.08
ACGTcount: A:0.25, C:0.04, G:0.01, T:0.70
Consensus pattern (13 bp):
TTTATTTATTATA
Found at i:91329 original size:16 final size:16
Alignment explanation
Indices: 91308--91339 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
91298 AAAGCCTTGA
91308 GTACATGCTCAGGTGC
1 GTACATGCTCAGGTGC
91324 GTACATGCTCAGGTGC
1 GTACATGCTCAGGTGC
91340 TATTGTTCGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.19, C:0.25, G:0.31, T:0.25
Consensus pattern (16 bp):
GTACATGCTCAGGTGC
Found at i:91813 original size:3 final size:3
Alignment explanation
Indices: 91797--91850 Score: 69
Period size: 3 Copynumber: 18.3 Consensus size: 3
91787 TCTACAAAAA
91797 TAT T-T TAT TA- TAT TAT TAT TATT TAT TAT TAT TAT TAT TATT TAT
1 TAT TAT TAT TAT TAT TAT TAT TA-T TAT TAT TAT TAT TAT TA-T TAT
91842 T-T TAT TAT T
1 TAT TAT TAT T
91851 TTTGCAGGCC
Statistics
Matches: 46, Mismatches: 0, Indels: 10
0.82 0.00 0.18
Matches are distributed among these distances:
2 6 0.13
3 34 0.74
4 6 0.13
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (3 bp):
TAT
Found at i:91826 original size:16 final size:16
Alignment explanation
Indices: 91797--91850 Score: 69
Period size: 16 Copynumber: 3.4 Consensus size: 16
91787 TCTACAAAAA
91797 TATT-TTATTATATTAT
1 TATTATTATT-TATTAT
91813 TATTATT-TATTATTAT
1 TATTATTAT-TTATTAT
91829 TATTATTATTTATT-T
1 TATTATTATTTATTAT
91844 TATTATT
1 TATTATT
91851 TTTGCAGGCC
Statistics
Matches: 35, Mismatches: 0, Indels: 7
0.83 0.00 0.17
Matches are distributed among these distances:
15 8 0.23
16 23 0.66
17 4 0.11
ACGTcount: A:0.30, C:0.00, G:0.00, T:0.70
Consensus pattern (16 bp):
TATTATTATTTATTAT
Found at i:91829 original size:19 final size:19
Alignment explanation
Indices: 91800--91850 Score: 88
Period size: 19 Copynumber: 2.8 Consensus size: 19
91790 ACAAAAATAT
91800 TTTATTA-TATTATTATTA
1 TTTATTATTATTATTATTA
91818 TTTATTATTATTATTATTA
1 TTTATTATTATTATTATTA
91837 TTTATT-TTATTATT
1 TTTATTATTATTATT
91851 TTTGCAGGCC
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
18 15 0.47
19 17 0.53
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (19 bp):
TTTATTATTATTATTATTA
Found at i:92278 original size:14 final size:14
Alignment explanation
Indices: 92226--92284 Score: 57
Period size: 14 Copynumber: 4.0 Consensus size: 14
92216 TTTTAGCATT
92226 TTTTATTATTATTTA
1 TTTTATTATT-TTTA
*
92241 TTTTATGT-TCTTTA
1 TTTTAT-TATTTTTA
92255 CTTCTTATTATTTTTA
1 -TT-TTATTATTTTTA
*
92271 TTTTATTACTTTTA
1 TTTTATTATTTTTA
92285 GAATTTAACC
Statistics
Matches: 37, Mismatches: 3, Indels: 9
0.76 0.06 0.18
Matches are distributed among these distances:
14 15 0.41
15 12 0.32
16 10 0.27
ACGTcount: A:0.20, C:0.07, G:0.02, T:0.71
Consensus pattern (14 bp):
TTTTATTATTTTTA
Found at i:93803 original size:16 final size:16
Alignment explanation
Indices: 93782--93825 Score: 79
Period size: 16 Copynumber: 2.8 Consensus size: 16
93772 ACGAACATAA
93782 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
93798 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
93814 ACGAACATAAAC
1 ACGAACATAAAC
93826 ATTGGAGACC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 26 1.00
ACGTcount: A:0.57, C:0.23, G:0.11, T:0.09
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:93814 original size:10 final size:10
Alignment explanation
Indices: 93768--93798 Score: 62
Period size: 10 Copynumber: 3.1 Consensus size: 10
93758 CATTTAATAA
93768 ATAAACGAAC
1 ATAAACGAAC
93778 ATAAACGAAC
1 ATAAACGAAC
93788 ATAAACGAAC
1 ATAAACGAAC
93798 A
1 A
93799 CGAACATAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 21 1.00
ACGTcount: A:0.61, C:0.19, G:0.10, T:0.10
Consensus pattern (10 bp):
ATAAACGAAC
Found at i:95769 original size:75 final size:76
Alignment explanation
Indices: 95651--95798 Score: 226
Period size: 75 Copynumber: 2.0 Consensus size: 76
95641 AGGAAACATA
* * * *
95651 AAAGTTGTTGATTTTTTCAAATGAATAATTTAAATGAGATAATTTTAAAACACAAAAGGTACAAA
1 AAAGTTGTTGATTTTTTCAAATAAACAATTTAAACGAGATAATTTTAAAACACAAAAGGGACAAA
95716 TTTAAAGGAAT
66 TTTAAAGGAAT
* * *
95727 AAAGTTGTTGATTTTTT-AAATAAACCATTTAAACGAGGTAATTTTAAAACACAAAAGGGATAAA
1 AAAGTTGTTGATTTTTTCAAATAAACAATTTAAACGAGATAATTTTAAAACACAAAAGGGACAAA
95791 TTTAAAGG
66 TTTAAAGG
95799 GTCAAAGGGA
Statistics
Matches: 65, Mismatches: 7, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
75 48 0.74
76 17 0.26
ACGTcount: A:0.47, C:0.06, G:0.14, T:0.33
Consensus pattern (76 bp):
AAAGTTGTTGATTTTTTCAAATAAACAATTTAAACGAGATAATTTTAAAACACAAAAGGGACAAA
TTTAAAGGAAT
Found at i:98260 original size:20 final size:21
Alignment explanation
Indices: 98237--98275 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
98227 TATGTTTTCT
*
98237 TCCTTTTTTC-TTAATTTTAG
1 TCCTTTTTACTTTAATTTTAG
98257 TCCTTTTTACTTTAATTTT
1 TCCTTTTTACTTTAATTTT
98276 TGAAATAAGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.15, C:0.15, G:0.03, T:0.67
Consensus pattern (21 bp):
TCCTTTTTACTTTAATTTTAG
Found at i:105626 original size:21 final size:23
Alignment explanation
Indices: 105602--105645 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
105592 TAAAAATTTG
*
105602 TTTAA-TTTTAAAAC-ATTTTAT
1 TTTAACTTTAAAAACTATTTTAT
105623 TTTAACTTTAAAAACTATTTTAT
1 TTTAACTTTAAAAACTATTTTAT
105646 GAATATCTCA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 5 0.25
22 8 0.40
23 7 0.35
ACGTcount: A:0.39, C:0.07, G:0.00, T:0.55
Consensus pattern (23 bp):
TTTAACTTTAAAAACTATTTTAT
Found at i:106390 original size:24 final size:24
Alignment explanation
Indices: 106354--106449 Score: 122
Period size: 24 Copynumber: 4.0 Consensus size: 24
106344 ACACTCGTAC
*
106354 ATTCTATGCGGCACTTTATGTGCA
1 ATTCTATGTGGCACTTTATGTGCA
* *
106378 ATTCTACGTGGCACTTTATGCGCA
1 ATTCTATGTGGCACTTTATGTGCA
**
106402 ATTCTATGTGGCACTAAATGTGCA
1 ATTCTATGTGGCACTTTATGTGCA
*
106426 ATTCTATGTGGAACTATT-TGTGCA
1 ATTCTATGTGGCACT-TTATGTGCA
106450 TTCAGGAAAT
Statistics
Matches: 61, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
24 61 1.00
ACGTcount: A:0.24, C:0.19, G:0.21, T:0.36
Consensus pattern (24 bp):
ATTCTATGTGGCACTTTATGTGCA
Found at i:114614 original size:2 final size:2
Alignment explanation
Indices: 114607--114644 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
114597 TGAAATAAGG
114607 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
114645 GCGCATGCGC
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:114845 original size:65 final size:66
Alignment explanation
Indices: 114727--114858 Score: 239
Period size: 65 Copynumber: 2.0 Consensus size: 66
114717 TTATTTATTC
*
114727 TCTTATTTTATTCAATATATTTTTATTTTTTTCAATTTAATCACTAAACTTTATTCATTGAAATA
1 TCTTATTTTATTCAATATATTTTAATTTTTTTCAATTTAATCACTAAACTTTATTCATTGAAATA
114792 T
66 T
*
114793 TCTTATTTTATTCAATATATTTTAATTTTTTT-AATTTAATCACTAAATTTTATTCATTGAAATA
1 TCTTATTTTATTCAATATATTTTAATTTTTTTCAATTTAATCACTAAACTTTATTCATTGAAATA
114857 T
66 T
114858 T
1 T
114859 TTTGGTCATT
Statistics
Matches: 64, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
65 33 0.52
66 31 0.48
ACGTcount: A:0.33, C:0.09, G:0.02, T:0.57
Consensus pattern (66 bp):
TCTTATTTTATTCAATATATTTTAATTTTTTTCAATTTAATCACTAAACTTTATTCATTGAAATA
T
Found at i:130377 original size:3 final size:3
Alignment explanation
Indices: 130371--130483 Score: 199
Period size: 3 Copynumber: 37.7 Consensus size: 3
130361 TTTTTATCCA
*
130371 TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
130419 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAC TAT TAT TAT TAT CAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
130467 TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TA
130484 AATACATATT
Statistics
Matches: 104, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
3 104 1.00
ACGTcount: A:0.34, C:0.03, G:0.00, T:0.64
Consensus pattern (3 bp):
TAT
Found at i:130510 original size:12 final size:11
Alignment explanation
Indices: 130479--130514 Score: 54
Period size: 11 Copynumber: 3.2 Consensus size: 11
130469 TTATTATTAT
*
130479 TATTAAATACA
1 TATTAAATAAA
130490 TATTAAATAAA
1 TATTAAATAAA
130501 TATATAAATAAA
1 TAT-TAAATAAA
130513 TA
1 TA
130515 ATTACAGACC
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 13 0.57
12 10 0.43
ACGTcount: A:0.61, C:0.03, G:0.00, T:0.36
Consensus pattern (11 bp):
TATTAAATAAA
Found at i:131860 original size:18 final size:19
Alignment explanation
Indices: 131820--131861 Score: 50
Period size: 18 Copynumber: 2.3 Consensus size: 19
131810 TTTAGTCAGT
**
131820 TATTTTATATGTTTTCATT
1 TATTTTATATGTTTTCAAA
*
131839 TATTTTAT-TGTTTTTAAA
1 TATTTTATATGTTTTCAAA
131857 TATTT
1 TATTT
131862 GTTTTAGTAG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.24, C:0.02, G:0.05, T:0.69
Consensus pattern (19 bp):
TATTTTATATGTTTTCAAA
Found at i:143146 original size:9 final size:8
Alignment explanation
Indices: 143120--143184 Score: 82
Period size: 8 Copynumber: 8.1 Consensus size: 8
143110 TATTATGCTT
143120 AAAG-AAA
1 AAAGAAAA
143127 AAAGAAAA
1 AAAGAAAA
143135 AAAGAAAGA
1 AAAGAAA-A
143144 AAAG-AAA
1 AAAGAAAA
143151 AAAGAGAAA
1 AAAGA-AAA
143160 AAAGAAAA
1 AAAGAAAA
143168 AAA-AGAAA
1 AAAGA-AAA
143176 AAAGAAAA
1 AAAGAAAA
143184 A
1 A
143185 GGGGGGTCAA
Statistics
Matches: 52, Mismatches: 0, Indels: 11
0.83 0.00 0.17
Matches are distributed among these distances:
7 10 0.19
8 28 0.54
9 14 0.27
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (8 bp):
AAAGAAAA
Found at i:143153 original size:16 final size:15
Alignment explanation
Indices: 143120--143184 Score: 94
Period size: 17 Copynumber: 4.1 Consensus size: 15
143110 TATTATGCTT
143120 AAAGAAAAAAGAAAA
1 AAAGAAAAAAGAAAA
143135 AAAGAAAGAAAAGAAAA
1 AAAG-AA-AAAAGAAAA
143152 AAGAGAAAAAAGAAAAA
1 AA-AGAAAAAAG-AAAA
143169 AAAGAAAAAAGAAAA
1 AAAGAAAAAAGAAAA
143184 A
1 A
143185 GGGGGGTCAA
Statistics
Matches: 46, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
15 9 0.20
16 16 0.35
17 19 0.41
18 2 0.04
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (15 bp):
AAAGAAAAAAGAAAA
Found at i:143523 original size:16 final size:16
Alignment explanation
Indices: 143497--143541 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
143487 TTTGAATACA
*
143497 ATTCTATTTATTTCAAG
1 ATTCAATTTATTT-AAG
*
143514 -TTCAATTTATTTGAG
1 ATTCAATTTATTTAAG
143529 ATTCAATTTATTT
1 ATTCAATTTATTT
143542 TTGGAAATTC
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 2 0.08
16 23 0.92
ACGTcount: A:0.29, C:0.09, G:0.07, T:0.56
Consensus pattern (16 bp):
ATTCAATTTATTTAAG
Found at i:144424 original size:83 final size:83
Alignment explanation
Indices: 144322--144669 Score: 626
Period size: 83 Copynumber: 4.2 Consensus size: 83
144312 AATGGAACAA
*
144322 ATGAAGGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
144387 AATCATTGAATTTGGAAG
66 AATCATTGAATTTGGAAG
144405 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
144470 AATCATTGAATTTGGAAG
66 AATCATTGAATTTGGAAG
*
144488 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAAAACC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
*
144553 AATCATTGAATTTAGAAG
66 AATCATTGAATTTGGAAG
* *
144571 ATGAATTTGTTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGG-TTGGACAGAAC
1 ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGG-CAGAAC
144635 CAATCATTGAATTTGGAAG
65 CAATCATTGAATTTGGAAG
*
144654 ATGAATTTGCTCATAG
1 ATGAATGTGCTCATAG
144670 TAGAAATAAG
Statistics
Matches: 256, Mismatches: 8, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
82 4 0.02
83 252 0.98
ACGTcount: A:0.26, C:0.14, G:0.23, T:0.36
Consensus pattern (83 bp):
ATGAATGTGCTCATAGCATCTTCTGGAAGTGTTCTTTGAGTTATCTGATCTGGTTTGGCAGAACC
AATCATTGAATTTGGAAG
Found at i:145861 original size:114 final size:113
Alignment explanation
Indices: 145481--145904 Score: 591
Period size: 113 Copynumber: 3.7 Consensus size: 113
145471 ATGGATTATT
* *
145481 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTTATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGA
* * * *
145546 AGAATTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGATCAGCC
66 AGAACTTGTTCAACCTTTTATCTGAATTCATCAATTGATGGATCAACA
* *
145594 TTTCCAAAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGA
* * * * ***
145659 AGAATTTGTTCAACCTTTTATCTGAATTCATCACTGGATGGATTATTT
66 AGAACTTGTTCAACCTTTTATCTGAATTCATCAATTGATGGATCAACA
*
145707 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAGGAAGAAGTTCATAATGAGA
1 TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGA
* * * *
145772 AGAACTTGTTCAACTTTTTGGTTTGAATTCATCATTTGATGGATCAACA
66 AGAACTTGTTCAACCTTTT-ATCTGAATTCATCAATTGATGGATCAACA
* * *
145821 TTGCCAG-GAAGAGTTCATAATGAGAAGAACTCATCTGAAG-AAGAAAGAAGAAGTTCATGATAA
1 TTTCCAGAGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAAAG-AAGAAGAAGTTCATAATGA
*
145884 GAAGAACTTGTTCAACTTTTT
64 GAAGAACTTGTTCAACCTTTT
145905 TGCATAATTC
Statistics
Matches: 282, Mismatches: 26, Indels: 5
0.90 0.08 0.02
Matches are distributed among these distances:
113 189 0.67
114 93 0.33
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (113 bp):
TTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAAGAAGTTCATAATGAGA
AGAACTTGTTCAACCTTTTATCTGAATTCATCAATTGATGGATCAACA
Found at i:145889 original size:227 final size:225
Alignment explanation
Indices: 145465--145904 Score: 684
Period size: 227 Copynumber: 1.9 Consensus size: 225
145455 ATTTCAAATC
*
145465 CACTGGATGGATTATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAA
1 CACTGGATGGATTATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAA
* * * *
145530 GAAGTTTATAATGAGAAGAATTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGATCAGCCT
66 GAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGATCAACAT
* * *
145595 TTCCAAAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGAGAA
131 TGCCAAAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAAGAA
*
145660 GAATTTGTTCAACCTTTTATCTGAATTCAT
196 GAACTTGTTCAACCTTTTATCTGAATTCAT
*
145690 CACTGGATGGATTATTTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAGGA
1 CACTGGATGGATTA-TTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGA
* *** *
145755 AGAAGTTCATAATGAGAAGAACTTGTTCAACTTTTTGGTTTGAATTCATCATTTGATGGATCAAC
65 AGAAGTTCATAATGAGAAGAACTTGTTCAACCTTTT-ACCTGAATTCATCAATTGATGGATCAAC
* *
145820 ATTGCC-AGGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATGATAA
129 ATTGCCAAAGAA-AGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAA
*
145884 GAAGAACTTGTTCAACTTTTT
193 GAAGAACTTGTTCAACCTTTT
145905 TGCATAATTC
Statistics
Matches: 194, Mismatches: 18, Indels: 4
0.90 0.08 0.02
Matches are distributed among these distances:
225 14 0.07
226 85 0.44
227 95 0.49
ACGTcount: A:0.38, C:0.13, G:0.20, T:0.29
Consensus pattern (225 bp):
CACTGGATGGATTATTTTTCCAGAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAAGAAGAA
GAAGTTCATAATGAGAAGAACTTGTTCAACCTTTTACCTGAATTCATCAATTGATGGATCAACAT
TGCCAAAGAAAGTTCATAATGAGAAGAACTCATCTGAAGAAGAAAGAAGAAGTTCATAATAAGAA
GAACTTGTTCAACCTTTTATCTGAATTCAT
Found at i:146227 original size:3 final size:3
Alignment explanation
Indices: 146221--146313 Score: 136
Period size: 3 Copynumber: 31.7 Consensus size: 3
146211 TTTTTATCCA
* *
146221 TAT TAT TAT TAT TAC TAT TAC TAT TAT TAT TA- TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* *
146268 TAT TAT TAT TAT TAC TA- TAT TAT TAT CAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
146314 AACATATTAA
Statistics
Matches: 81, Mismatches: 7, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
2 4 0.05
3 77 0.95
ACGTcount: A:0.34, C:0.04, G:0.00, T:0.61
Consensus pattern (3 bp):
TAT
Found at i:146256 original size:32 final size:32
Alignment explanation
Indices: 146220--146313 Score: 152
Period size: 32 Copynumber: 2.9 Consensus size: 32
146210 TTTTTTATCC
* * *
146220 ATATTATTATTATTACTATTACTATTATTATT
1 ATATTATTATTATTATTATTATTATTATTACT
146252 ATATTATTATTATTATTATTATTATTATTACT
1 ATATTATTATTATTATTATTATTATTATTACT
*
146284 ATATTATTATCATTATTATTATTATTATTA
1 ATATTATTATTATTATTATTATTATTATTA
146314 AACATATTAA
Statistics
Matches: 58, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
32 58 1.00
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (32 bp):
ATATTATTATTATTATTATTATTATTATTACT
Found at i:146818 original size:23 final size:24
Alignment explanation
Indices: 146758--146819 Score: 67
Period size: 23 Copynumber: 2.6 Consensus size: 24
146748 GAAAAAAAAA
146758 AAAAAAAAACAG-GACAGAGACAG
1 AAAAAAAAACAGAGACAGAGACAG
* *
146781 AAAAAAAAGAGAGAGACA-A-ACCGG
1 AAAAAAAA-ACAGAGACAGAGA-CAG
146805 AAAAAAAAACAGAGA
1 AAAAAAAAACAGAGA
146820 AGATACAACT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
23 15 0.45
24 14 0.42
25 4 0.12
ACGTcount: A:0.68, C:0.11, G:0.21, T:0.00
Consensus pattern (24 bp):
AAAAAAAAACAGAGACAGAGACAG
Found at i:148670 original size:82 final size:82
Alignment explanation
Indices: 148577--148741 Score: 312
Period size: 82 Copynumber: 2.0 Consensus size: 82
148567 TACTCTAAAA
* *
148577 TTTATTCGAAATATCATTTACATAAACATTATAAAAACATATCAAAGTACTGTAAAACATGTTTT
1 TTTATTCGAAATATCATTTACATAAACATTATAAAAACATATCAAAGTACCGTAAAACATGCTTT
148642 ATCAAAACATTCGAGGT
66 ATCAAAACATTCGAGGT
148659 TTTATTCGAAATATCATTTACATAAACATTATAAAAACATATCAAAGTACCGTAAAACATGCTTT
1 TTTATTCGAAATATCATTTACATAAACATTATAAAAACATATCAAAGTACCGTAAAACATGCTTT
148724 ATCAAAACATTCGAGGT
66 ATCAAAACATTCGAGGT
148741 T
1 T
148742 GACTCGTCGC
Statistics
Matches: 81, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
82 81 1.00
ACGTcount: A:0.44, C:0.15, G:0.08, T:0.33
Consensus pattern (82 bp):
TTTATTCGAAATATCATTTACATAAACATTATAAAAACATATCAAAGTACCGTAAAACATGCTTT
ATCAAAACATTCGAGGT
Found at i:153156 original size:24 final size:23
Alignment explanation
Indices: 153093--153162 Score: 81
Period size: 24 Copynumber: 3.0 Consensus size: 23
153083 TCCCCTTGAA
*
153093 GTGCATCGATGCATTC-T-ACAT
1 GTGCATCGATGCATCCTTAACAT
*
153114 GTGTATCGATGCATCCCTTAACAT
1 GTGCATCGATGCAT-CCTTAACAT
153138 GTGCATCGATGCACTCCTTATACAT
1 GTGCATCGATGCA-TCCTTA-ACAT
153163 CGATGCACTA
Statistics
Matches: 41, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
21 13 0.32
22 1 0.02
23 1 0.02
24 21 0.51
25 5 0.12
ACGTcount: A:0.24, C:0.26, G:0.17, T:0.33
Consensus pattern (23 bp):
GTGCATCGATGCATCCTTAACAT
Done.