Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001060.1 Hibiscus syriacus cultivar Beakdansim tig00002095_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: 83074
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:1735 original size:18 final size:18
Alignment explanation
Indices: 1712--1749 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
1702 TAAAACAAAC
* *
1712 TATGAATGTTAAATAAGT
1 TATGAATATGAAATAAGT
1730 TATGAATATGAAATAAGT
1 TATGAATATGAAATAAGT
1748 TA
1 TA
1750 GGAGTCTGAG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.47, C:0.00, G:0.16, T:0.37
Consensus pattern (18 bp):
TATGAATATGAAATAAGT
Found at i:1931 original size:39 final size:39
Alignment explanation
Indices: 1872--1954 Score: 130
Period size: 39 Copynumber: 2.1 Consensus size: 39
1862 AAAAATAATA
* *
1872 TGATATGACTATTATATATGATATTGTTTATCATTGCTT
1 TGATATGACTATTATATATGATATTATTTATCATGGCTT
* *
1911 TGATATGACTATTATGTATGATATTATTTATCATGGTTT
1 TGATATGACTATTATATATGATATTATTTATCATGGCTT
1950 TGATA
1 TGATA
1955 AAATCATGAG
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.29, C:0.06, G:0.14, T:0.51
Consensus pattern (39 bp):
TGATATGACTATTATATATGATATTATTTATCATGGCTT
Found at i:1934 original size:18 final size:18
Alignment explanation
Indices: 1870--1934 Score: 58
Period size: 18 Copynumber: 3.4 Consensus size: 18
1860 TGAAAAATAA
*
1870 TATGATATGACTATTATA
1 TATGATATGACTATTATG
** *
1888 TATGATATTGTTTATCATTG
1 TATGATA-TGACTATTA-TG
*
1908 CTTTGATATGACTATTATG
1 -TATGATATGACTATTATG
1927 TATGATAT
1 TATGATAT
1935 TATTTATCAT
Statistics
Matches: 35, Mismatches: 9, Indels: 6
0.70 0.18 0.12
Matches are distributed among these distances:
18 14 0.40
19 8 0.23
20 7 0.20
21 6 0.17
ACGTcount: A:0.31, C:0.06, G:0.14, T:0.49
Consensus pattern (18 bp):
TATGATATGACTATTATG
Found at i:11592 original size:4 final size:4
Alignment explanation
Indices: 11583--11713 Score: 172
Period size: 4 Copynumber: 32.8 Consensus size: 4
11573 AATGCTCTAA
* * *
11583 AATG AATG AATG AATG AATG AACG AACG AATG AATG AATG AACG AATG
1 AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG
* * * * *
11631 AACG AATG AATG AATG AATG AACG AATG AACG AATG AACG AATG AACG
1 AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG AATG
* *
11679 AATG AACG AATG AACG AATG AATG AATG AATG AAT
1 AATG AATG AATG AATG AATG AATG AATG AATG AAT
11714 ATTTATGTTG
Statistics
Matches: 109, Mismatches: 18, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
4 109 1.00
ACGTcount: A:0.50, C:0.08, G:0.24, T:0.18
Consensus pattern (4 bp):
AATG
Found at i:12048 original size:65 final size:66
Alignment explanation
Indices: 11813--12092 Score: 411
Period size: 66 Copynumber: 4.3 Consensus size: 66
11803 GGTGCACTTT
* * *
11813 GGCATAAAAGGTGCCACTAATGAAAATTATCGATCAATTTTGATTAATGAATAATGGTGCATTAT
1 GGCATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCATAACGGTGCATTAT
11878 C
66 C
* * *
11879 GGCATAAAAGGTACCACTAATGAAAATTATCGATTGATTTTGATTAATGCATAACGATGCATTAT
1 GGCATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCATAACGGTGCATTAT
11944 C
66 C
* * * *
11945 AGCATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGTATAACAGTGTATTAT
1 GGCATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCATAACGGTGCATTAT
12010 C
66 C
* * *
12011 GGCAT-AAAGGTGCCACTAATGAAAATTATCAATCGATTTTGTTTAATACATAACGGTGCATTAT
1 GGCATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCATAACGGTGCATTAT
12075 C
66 C
* *
12076 AGCAT-AAAGGTGTCACT
1 GGCATAAAAGGTGCCACT
12093 CATGGTATTC
Statistics
Matches: 192, Mismatches: 22, Indels: 1
0.89 0.10 0.00
Matches are distributed among these distances:
65 69 0.36
66 123 0.64
ACGTcount: A:0.37, C:0.14, G:0.17, T:0.32
Consensus pattern (66 bp):
GGCATAAAAGGTGCCACTAATGAAAATTATCGATCGATTTTGATTAATGCATAACGGTGCATTAT
C
Found at i:18847 original size:4 final size:4
Alignment explanation
Indices: 18838--18864 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
18828 ATTGCTCTAA
18838 AATG AATG AATG AATG AATG AATG AAT
1 AATG AATG AATG AATG AATG AATG AAT
18865 ATTGATGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.22, T:0.26
Consensus pattern (4 bp):
AATG
Found at i:19065 original size:65 final size:65
Alignment explanation
Indices: 18972--19247 Score: 428
Period size: 65 Copynumber: 4.2 Consensus size: 65
18962 GTGCACTTTG
* * *
18972 GCATAAAAGGTGCCACTAATGAAAATTATCGATCGAATTTGATTAATTCATAAGGGTGCATTAT-
1 GCATAAAAGGTGCCACTAATGAAAATTATCGATC-ATTTTGATTAATGCATAACGGTGCATTATC
19036 A
65 A
* * *
19037 GCATAAATGGTGCCATTAATGAAAATTATCGATCATTTTGATTAATGCATAACAGTGCATTATCA
1 GCATAAAAGGTGCCACTAATGAAAATTATCGATCATTTTGATTAATGCATAACGGTGCATTATCA
*
19102 GCATAAAAGGTGCCACTAATGAAAATTATCGATCATTTTGATTAATGCATAACGGTGCATTATCG
1 GCATAAAAGGTGCCACTAATGAAAATTATCGATCATTTTGATTAATGCATAACGGTGCATTATCA
* * *
19167 GCATAAAAGGTGCCACTAATGAAAATTATCAATCGATTTTGTTTAATGCATAACGGTGCATTATT
1 GCATAAAAGGTGCCACTAATGAAAATTATCGATC-ATTTTGATTAATGCATAACGGTGCATTATC
*
19232 G
65 A
19233 GCATAAAAGGTGCCA
1 GCATAAAAGGTGCCA
19248 GTCATGATAT
Statistics
Matches: 196, Mismatches: 13, Indels: 3
0.92 0.06 0.01
Matches are distributed among these distances:
64 25 0.13
65 127 0.65
66 44 0.22
ACGTcount: A:0.37, C:0.14, G:0.18, T:0.31
Consensus pattern (65 bp):
GCATAAAAGGTGCCACTAATGAAAATTATCGATCATTTTGATTAATGCATAACGGTGCATTATCA
Found at i:21207 original size:6 final size:6
Alignment explanation
Indices: 21192--21307 Score: 142
Period size: 6 Copynumber: 19.3 Consensus size: 6
21182 TGTAAGGTAA
* * *
21192 TCTCTC TCTCTT TCTCTC TCTCTC TCCCTC TCTCTT TCTCTC TCTCTC
1 TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC
* * * * *
21240 TCCCTC TCTCTC CCTCCC TCTCTC TCCCTC TCTCTC TCTCCC TCTCTC
1 TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC TCTCTC
* *
21288 TCTCTC TCCCTC TCCCTC TC
1 TCTCTC TCTCTC TCTCTC TC
21308 CTTGTTCCTC
Statistics
Matches: 93, Mismatches: 17, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
6 93 1.00
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (6 bp):
TCTCTC
Found at i:21209 original size:8 final size:8
Alignment explanation
Indices: 21192--21307 Score: 142
Period size: 8 Copynumber: 14.5 Consensus size: 8
21182 TGTAAGGTAA
21192 TCTCTCTC
1 TCTCTCTC
*
21200 TCTTTCTC
1 TCTCTCTC
21208 TCTCTCTC
1 TCTCTCTC
*
21216 TCCCTCTC
1 TCTCTCTC
*
21224 TCTTTCTC
1 TCTCTCTC
21232 TCTCTCTC
1 TCTCTCTC
*
21240 TCCCTCTC
1 TCTCTCTC
*
21248 TCTCCCTC
1 TCTCTCTC
*
21256 CCTCTCTC
1 TCTCTCTC
*
21264 TCCCTCTC
1 TCTCTCTC
21272 TCTCTCTC
1 TCTCTCTC
*
21280 CCTCTCTC
1 TCTCTCTC
21288 TCTCTCTC
1 TCTCTCTC
* *
21296 CCTCTCCC
1 TCTCTCTC
21304 TCTC
1 TCTC
21308 CTTGTTCCTC
Statistics
Matches: 89, Mismatches: 19, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
8 89 1.00
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (8 bp):
TCTCTCTC
Found at i:21209 original size:10 final size:10
Alignment explanation
Indices: 21192--21307 Score: 142
Period size: 10 Copynumber: 11.6 Consensus size: 10
21182 TGTAAGGTAA
21192 TCTCTCTCTC
1 TCTCTCTCTC
*
21202 TTTCTCTCTC
1 TCTCTCTCTC
*
21212 TCTCTCCCTC
1 TCTCTCTCTC
*
21222 TCTCTTTCTC
1 TCTCTCTCTC
21232 TCTCTCTCTC
1 TCTCTCTCTC
*
21242 CCTCTCTCTC
1 TCTCTCTCTC
* *
21252 CCTCCCTCTC
1 TCTCTCTCTC
*
21262 TCTCCCTCTC
1 TCTCTCTCTC
*
21272 TCTCTCTCCC
1 TCTCTCTCTC
21282 TCTCTCTCTC
1 TCTCTCTCTC
*
21292 TCTCCCTCTC
1 TCTCTCTCTC
*
21302 CCTCTC
1 TCTCTC
21308 CTTGTTCCTC
Statistics
Matches: 91, Mismatches: 15, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
10 91 1.00
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (10 bp):
TCTCTCTCTC
Found at i:21211 original size:14 final size:14
Alignment explanation
Indices: 21192--21307 Score: 142
Period size: 14 Copynumber: 8.3 Consensus size: 14
21182 TGTAAGGTAA
*
21192 TCTCTCTCTCTTTC
1 TCTCTCTCTCTCTC
*
21206 TCTCTCTCTCTCCC
1 TCTCTCTCTCTCTC
*
21220 TCTCTCTTTCTCTC
1 TCTCTCTCTCTCTC
*
21234 TCTCTCTCCCTCTC
1 TCTCTCTCTCTCTC
* *
21248 TCTCCCTCCCTCTC
1 TCTCTCTCTCTCTC
*
21262 TCTCCCTCTCTCTC
1 TCTCTCTCTCTCTC
*
21276 TCTCCCTCTCTCTC
1 TCTCTCTCTCTCTC
* *
21290 TCTCTCCCTCTCCC
1 TCTCTCTCTCTCTC
21304 TCTC
1 TCTC
21308 CTTGTTCCTC
Statistics
Matches: 91, Mismatches: 11, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
14 91 1.00
ACGTcount: A:0.00, C:0.55, G:0.00, T:0.45
Consensus pattern (14 bp):
TCTCTCTCTCTCTC
Found at i:21227 original size:24 final size:24
Alignment explanation
Indices: 21195--21307 Score: 158
Period size: 24 Copynumber: 4.8 Consensus size: 24
21185 AAGGTAATCT
* *
21195 CTCTCTCTTTCTCTCTCTCTCTCC
1 CTCTCTCTCTCTCCCTCTCTCTCC
* *
21219 CTCTCTCTTTCTCTCTCTCTCTCC
1 CTCTCTCTCTCTCCCTCTCTCTCC
*
21243 CTCTCTCTCCCTCCCTCTCTCTCC
1 CTCTCTCTCTCTCCCTCTCTCTCC
21267 CTCTCTCTCTCTCCCTCTCTCT--
1 CTCTCTCTCTCTCCCTCTCTCTCC
*
21289 CTCTCTCCCTCTCCCTCTC
1 CTCTCTCTCTCTCCCTCTC
21308 CTTGTTCCTC
Statistics
Matches: 84, Mismatches: 5, Indels: 2
0.92 0.05 0.02
Matches are distributed among these distances:
22 18 0.21
24 66 0.79
ACGTcount: A:0.00, C:0.56, G:0.00, T:0.44
Consensus pattern (24 bp):
CTCTCTCTCTCTCCCTCTCTCTCC
Found at i:23553 original size:24 final size:24
Alignment explanation
Indices: 23526--23571 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 24
23516 AGATATAGAA
* *
23526 TTTTTATATTTGT-AGTTATGTAT
1 TTTTTTTATTTCTAAGTTATGTAT
*
23549 TTTTTTTCTTTCTAAGTTATGTA
1 TTTTTTTATTTCTAAGTTATGTA
23572 AAATGAACAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
23 10 0.53
24 9 0.47
ACGTcount: A:0.20, C:0.04, G:0.11, T:0.65
Consensus pattern (24 bp):
TTTTTTTATTTCTAAGTTATGTAT
Found at i:23754 original size:19 final size:20
Alignment explanation
Indices: 23710--23754 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 20
23700 ATTTGTTTTT
*
23710 AATAAATTTTTATCTATGAA
1 AATAAATTTTTATCTATCAA
* *
23730 ATTAAATTTTTAT-TTTCAA
1 AATAAATTTTTATCTATCAA
23749 AATAAA
1 AATAAA
23755 ATATTAAAAG
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 9 0.43
20 12 0.57
ACGTcount: A:0.47, C:0.04, G:0.02, T:0.47
Consensus pattern (20 bp):
AATAAATTTTTATCTATCAA
Found at i:24395 original size:37 final size:37
Alignment explanation
Indices: 24354--24429 Score: 143
Period size: 37 Copynumber: 2.1 Consensus size: 37
24344 ACCACAAAAG
*
24354 CTGAACAGCACCCACGTTCAAGCGGCGGAAAAGTATT
1 CTGAACAGCACCCACGTTCAAGAGGCGGAAAAGTATT
24391 CTGAACAGCACCCACGTTCAAGAGGCGGAAAAGTATT
1 CTGAACAGCACCCACGTTCAAGAGGCGGAAAAGTATT
24428 CT
1 CT
24430 CTGCATTCTG
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.33, C:0.26, G:0.24, T:0.17
Consensus pattern (37 bp):
CTGAACAGCACCCACGTTCAAGAGGCGGAAAAGTATT
Found at i:28779 original size:76 final size:77
Alignment explanation
Indices: 28670--28843 Score: 187
Period size: 76 Copynumber: 2.2 Consensus size: 77
28660 TATACACCTA
* * *
28670 GATTCATGCATTATACAACTTAAATTAATGCCTTAA-TCCCA-TCCATTAATGCGGCTCGTGT-A
1 GATTCATGCATTATACAACTTAAATTAAAGCCTTAACT-CCAGT-CATTAACGCGGCTCAT-TCA
28732 TTCACACTTCACTG-
63 TTCACACTTCACTGT
* * * * *
28746 GATTCATGCACTATAC-AGTCTAGATTAAAGCCTTAACTCCAGTCATTAACGTGGCTCATTCGTT
1 GATTCATGCATTATACAACT-TAAATTAAAGCCTTAACTCCAGTCATTAACGCGGCTCATTCATT
28810 CACACTTCACTGTT
65 CACACTTCACTG-T
28824 GAATTCATGCATTATACAAC
1 G-ATTCATGCATTATACAAC
28844 AAAGAATGTG
Statistics
Matches: 80, Mismatches: 10, Indels: 12
0.78 0.10 0.12
Matches are distributed among these distances:
75 3 0.04
76 59 0.74
77 2 0.03
78 1 0.01
79 14 0.17
80 1 0.01
ACGTcount: A:0.29, C:0.25, G:0.13, T:0.33
Consensus pattern (77 bp):
GATTCATGCATTATACAACTTAAATTAAAGCCTTAACTCCAGTCATTAACGCGGCTCATTCATTC
ACACTTCACTGT
Found at i:29408 original size:12 final size:13
Alignment explanation
Indices: 29393--29425 Score: 50
Period size: 12 Copynumber: 2.6 Consensus size: 13
29383 TTTATTTTAT
29393 TTTTTAAAATA-A
1 TTTTTAAAATATA
29405 TTTTTAAAATATA
1 TTTTTAAAATATA
*
29418 ATTTTAAA
1 TTTTTAAA
29426 GAATATATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
12 11 0.58
13 8 0.42
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (13 bp):
TTTTTAAAATATA
Found at i:29418 original size:14 final size:14
Alignment explanation
Indices: 29391--29432 Score: 50
Period size: 14 Copynumber: 3.0 Consensus size: 14
29381 TATTTATTTT
*
29391 ATTTTTTAAA-ATA
1 ATTTTTAAAATATA
29404 ATTTTTAAAATATA
1 ATTTTTAAAATATA
*
29418 ATTTTAAAGAATATA
1 ATTTTTAA-AATATA
29433 TTAATTTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
13 9 0.36
14 10 0.40
15 6 0.24
ACGTcount: A:0.50, C:0.00, G:0.02, T:0.48
Consensus pattern (14 bp):
ATTTTTAAAATATA
Found at i:31677 original size:9 final size:9
Alignment explanation
Indices: 31665--31780 Score: 53
Period size: 9 Copynumber: 12.6 Consensus size: 9
31655 TTGAAACAAT
31665 TATAATATA
1 TATAATATA
31674 TATACACTATA
1 TATA-A-TATA
*
31685 TATGAACTACA
1 TAT-AA-TATA
* *
31696 TATATTATG
1 TATAATATA
31705 TATAACTATA
1 TATAA-TATA
31715 TAGT-ATATA
1 TA-TAATATA
31724 TATAA-AGTA
1 TATAATA-TA
*
31733 TATAATTTA
1 TATAATATA
*
31742 TAT-TTATA
1 TATAATATA
*
31750 T-TATTATA
1 TATAATATA
31758 TACT-ATATA
1 TA-TAATATA
* *
31767 TATATTATG
1 TATAATATA
31776 TATAA
1 TATAA
31781 ACTATATAGT
Statistics
Matches: 82, Mismatches: 13, Indels: 24
0.69 0.11 0.20
Matches are distributed among these distances:
7 1 0.01
8 13 0.16
9 42 0.51
10 9 0.11
11 16 0.20
12 1 0.01
ACGTcount: A:0.45, C:0.05, G:0.04, T:0.46
Consensus pattern (9 bp):
TATAATATA
Found at i:31787 original size:52 final size:50
Alignment explanation
Indices: 31696--31794 Score: 130
Period size: 50 Copynumber: 1.9 Consensus size: 50
31686 ATGAACTACA
*
31696 TATATTATGTATAACTATATAGTATATATATAAAGTATATAATTTATATT
1 TATATTATGTATAACTATATAGTATATATATAAACTATATAATTTATATT
*
31746 TATATTAT-TATATACTATATA-TATATTATGTATAAACTATATAGTTTAT
1 TATATTATGTATA-ACTATATAGTATA-TA--TATAAACTATATAATTTAT
31795 TAATATGAAC
Statistics
Matches: 43, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
49 8 0.19
50 18 0.42
52 17 0.40
ACGTcount: A:0.42, C:0.03, G:0.05, T:0.49
Consensus pattern (50 bp):
TATATTATGTATAACTATATAGTATATATATAAACTATATAATTTATATT
Found at i:32038 original size:2 final size:2
Alignment explanation
Indices: 32033--32183 Score: 59
Period size: 2 Copynumber: 75.5 Consensus size: 2
32023 TTATATAGTG
* * *
32033 TA TA TA TA AA GTA TA TA TA T- TA TA TA TA TA AA CTA TG 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
* *
32076 AA CTA TA TA GTT TA TA -A T- TA TA T- TA T- TA TA TA CTA TA TA
1 TA -TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA
* * * * *
32115 TA AA CTC TA TA TA T- TA TG TA TA AA CTA TA TA -A TT TA T- TA -A
1 TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
*
32155 TA TA TA CTA TA TA TA AA CTA TA TA TA TA T
1 TA TA TA -TA TA TA TA TA -TA TA TA TA TA T
32184 TATGTATAAA
Statistics
Matches: 109, Mismatches: 22, Indels: 36
0.65 0.13 0.22
Matches are distributed among these distances:
1 9 0.08
2 90 0.83
3 10 0.09
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:32049 original size:13 final size:13
Alignment explanation
Indices: 32033--32128 Score: 60
Period size: 13 Copynumber: 7.5 Consensus size: 13
32023 TTATATAGTG
*
32033 TATATATAAAGTA
1 TATATATAAACTA
32046 TATATAT----TA
1 TATATATAAACTA
32055 TATATATAAACTA
1 TATATATAAACTA
*
32068 TGTATATAAACTA
1 TATATATAAACTA
* *
32081 TATAGTTTATAATTA
1 TATA-TATA-AACTA
*
32096 TAT-TATTATA-TA
1 TATATA-TAAACTA
*
32108 CTATATATAAACTC
1 -TATATATAAACTA
32122 TATATAT
1 TATATAT
32129 TATGTATAAA
Statistics
Matches: 65, Mismatches: 8, Indels: 20
0.70 0.09 0.22
Matches are distributed among these distances:
9 9 0.14
12 2 0.03
13 39 0.60
14 8 0.12
15 7 0.11
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (13 bp):
TATATATAAACTA
Found at i:32056 original size:20 final size:19
Alignment explanation
Indices: 32033--32562 Score: 152
Period size: 20 Copynumber: 27.3 Consensus size: 19
32023 TTATATAGTG
32033 TATATATAAAGTATATATAT
1 TATATATAAA-TATATATAT
32053 TATATAT--ATA-A-ACTAT
1 TATATATAAATATATA-TAT
*
32069 GTATATA-AACTATATAGT-T
1 -TATATATAAATATATA-TAT
* *
32088 TATA-ATTATATTATTATATAC
1 TATATA-TA-AATA-TATATAT
*
32109 TATATATAAACTCTATATAT
1 TATATATAAA-TATATATAT
*
32129 TATGTATAAACTATATA-AT
1 TATATATAAA-TATATATAT
32148 T-TAT-T-AATATATACTA-
1 TATATATAAATATATA-TAT
32164 TATATA-AACTATATATATAT
1 TATATATAA--ATATATATAT
* *
32184 TATGTATAAACTAT-TCATAC
1 TATATATAAA-TATAT-ATAT
* * *
32204 CATGTATAAACTATAGAGT-T
1 TATATATAAA-TATATA-TAT
*
32224 TATATATGAACTAT-TGA-AT
1 TATATAT-AAATATAT-ATAT
32243 TATATATAAACTATATAGT-T
1 TATATATAAA-TATATA-TAT
32263 TATTAATATAAAT-TATATAGTT
1 TA-T-ATATAAATATATATA--T
*
32285 TATATGTAAATTATATATGAAT
1 TATATATAAA-TATATAT--AT
* *
32307 TATATTTAAATATATACAACT
1 TATATATAAATATATA-TA-T
* ** *
32328 TATATTTATTTATTATGTAT
1 TATATATAAATA-TATATAT
* *
32348 AAT-TATAAATTATATATAC
1 TATATATAAA-TATATATAT
*
32367 TATGTATAAA-ATATATAGTT
1 TATATATAAATATATATA--T
*
32387 TAAATATAAAGTATATA-AGT
1 TATATATAAA-TATATATA-T
32407 ATATATATAAACTATA-A-AT
1 -TATATATAAA-TATATATAT
* * * *
32426 TATACATATACATATATAA
1 TATATATAAATATATATAT
32445 TA-ATATAAAGTATATATAT
1 TATATATAAA-TATATATAT
32464 ATATATATAAATATATA-A-
1 -TATATATAAATATATATAT
* **
32482 -AGACTA-ACGTATATAGTA-
1 TATA-TATAAATATATA-TAT
*
32500 TATA-ATATATATATATA-
1 TATATATAAATATATATAT
*
32517 TATATATATATATATATAT
1 TATATATAAATATATATAT
* *
32536 TATATACTTATATATTTATAT
1 TATATA--TAAATATATATAT
32557 TATATA
1 TATATA
32563 CTTATATACT
Statistics
Matches: 389, Mismatches: 55, Indels: 131
0.68 0.10 0.23
Matches are distributed among these distances:
15 7 0.02
16 16 0.04
17 26 0.07
18 54 0.14
19 53 0.14
20 121 0.31
21 77 0.20
22 34 0.09
24 1 0.00
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.44
Consensus pattern (19 bp):
TATATATAAATATATATAT
Found at i:32062 original size:11 final size:11
Alignment explanation
Indices: 32044--32191 Score: 60
Period size: 11 Copynumber: 13.5 Consensus size: 11
32034 ATATATAAAG
32044 TATATATATTA
1 TATATATATTA
*
32055 TATATATA-AA
1 TATATATATTA
*
32065 CTATGTATA-TA
1 -TATATATATTA
*
32076 AACTATATAGTT-
1 TA-TATATA-TTA
32088 TATAATTATATTA
1 TAT-A-TATATTA
*
32101 T-TATATACTA
1 TATATATATTA
32111 TATATA-A--A
1 TATATATATTA
*
32119 CTCTATATATTA
1 -TATATATATTA
* * *
32131 TGTATAAACTA
1 TATATATATTA
*
32142 TATAATTTATTA
1 TAT-ATATATTA
*
32154 -ATATATACTA
1 TATATATATTA
* *
32164 TATATAAACTA
1 TATATATATTA
32175 TATATATATTA
1 TATATATATTA
*
32186 TGTATA
1 TATATA
32192 AACTATTCAT
Statistics
Matches: 102, Mismatches: 21, Indels: 28
0.68 0.14 0.19
Matches are distributed among these distances:
8 1 0.01
9 5 0.05
10 17 0.17
11 62 0.61
12 11 0.11
13 6 0.06
ACGTcount: A:0.45, C:0.05, G:0.03, T:0.47
Consensus pattern (11 bp):
TATATATATTA
Found at i:32074 original size:22 final size:22
Alignment explanation
Indices: 32024--32578 Score: 88
Period size: 22 Copynumber: 26.6 Consensus size: 22
32014 CTAATTTATT
* * *
32024 TATATAGTGTATATATAAAGTA
1 TATATATTATATATATAAACTA
32046 TATATATTATATATATAAACTA
1 TATATATTATATATATAAACTA
* * * *
32068 TGTATA-TA-A-ACTATATAGTT
1 TATATATTATATA-TATAAACTA
*
32088 TATA-ATTATATTATTATATACTA
1 TATATATTATA-TA-TATAAACTA
* * * *
32111 TATATA-AACTCTATATATTA-TG
1 TATATATTA-TATATATA-AACTA
* * ** *
32133 TATAAACTATATA-ATTTATTA
1 TATATATTATATATATAAACTA
32154 -ATATA-TACTATATATAAACTA
1 TATATATTA-TATATATAAACTA
*
32175 TATATA-TATTATGTATAAACTA
1 TATATATTA-TATATATAAACTA
** *
32197 T-TCATA--CCATGTATAAACTA
1 TAT-ATATTATATATATAAACTA
* * *
32217 TAGA-GTT-TATATATGAACTA
1 TATATATTATATATATAAACTA
32237 T-TGA-A-T-TATATATAAACTA
1 TAT-ATATTATATATATAAACTA
32256 TATAGT-TTAT-TAATATAAA-T-
1 TATA-TATTATAT-ATATAAACTA
* *
32276 TATATAGTT-TATATGTAAATTA
1 TATATA-TTATATATATAAACTA
32298 TATATGAATTATAT-T-TAAA-TA
1 TATAT--ATTATATATATAAACTA
* * **
32319 TATACAACTTATATTTATTTA-T-
1 TATA-TA-TTATATATATAAACTA
* *
32341 TATGTA-TA-AT-TATAAATTA
1 TATATATTATATATATAAACTA
* *
32360 TATATACTATGTATA-AAA-TA
1 TATATATTATATATATAAACTA
*
32380 TATAGT-TTA-A-ATATAAAGTA
1 TATA-TATTATATATATAAACTA
*
32400 TATA-AGTATATATATAAACTA
1 TATATATTATATATATAAACTA
*
32421 TA-A-ATTATACATAT--AC-A
1 TATATATTATATATATAAACTA
*
32438 TATATA--ATA-ATATAAAGTA
1 TATATATTATATATATAAACTA
32457 TATATA-TATATATATAAA-TA
1 TATATATTATATATATAAACTA
** * *
32477 TATA-AAGACTA-ACGTATATAGTA
1 TATATATTA-TATA--TATAAACTA
*
32500 TATA-ATATATATATATATA-TA
1 TATATAT-TATATATATAAACTA
*
32521 TATATATATATATATTATATACT-
1 TATATAT-TATATA-TATAAACTA
*
32544 TATATATT-TATATTATATACT-
1 TATATATTATATA-TATAAACTA
32565 TATATACTT-TATAT
1 TATATA-TTATATAT
32579 TATATGCTTA
Statistics
Matches: 412, Mismatches: 56, Indels: 131
0.69 0.09 0.22
Matches are distributed among these distances:
16 4 0.01
17 10 0.02
18 10 0.02
19 41 0.10
20 99 0.24
21 83 0.20
22 110 0.27
23 46 0.11
24 9 0.02
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.45
Consensus pattern (22 bp):
TATATATTATATATATAAACTA
Found at i:32173 original size:53 final size:55
Alignment explanation
Indices: 32088--32197 Score: 179
Period size: 53 Copynumber: 2.0 Consensus size: 55
32078 CTATATAGTT
* *
32088 TATAATTATATTATTATATACTATATATAAAC-TCTATATATTATGTATAAACTA
1 TATAATTATATTAATATATACTATATATAAACATATATATATTATGTATAAACTA
32142 TATAATT-TATTAATATATACTATATATAAACTATATATATATTATGTATAAACTA
1 TATAATTATATTAATATATACTATATATAAAC-ATATATATATTATGTATAAACTA
32197 T
1 T
32198 TCATACCATG
Statistics
Matches: 52, Mismatches: 2, Indels: 3
0.91 0.04 0.05
Matches are distributed among these distances:
53 23 0.44
54 7 0.13
55 22 0.42
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.46
Consensus pattern (55 bp):
TATAATTATATTAATATATACTATATATAAACATATATATATTATGTATAAACTA
Found at i:32193 original size:55 final size:54
Alignment explanation
Indices: 32047--32197 Score: 180
Period size: 54 Copynumber: 2.8 Consensus size: 54
32037 TATAAAGTAT
* * ** * * *
32047 ATATATTA-TATATATAAACTATGTATATAAACTATATAGTTTATAATTATATTA
1 ATATA-TACTATATATAAACTATATATATTATGTATAAACTATATAATTATATTA
* *
32101 TTATATACTATATATAAACTCTATATATTATGTATAAACTATATAATT-TATTA
1 ATATATACTATATATAAACTATATATATTATGTATAAACTATATAATTATATTA
32154 ATATATACTATATATAAACTATATATATATTATGTATAAACTAT
1 ATATATACTATATATAAAC--TATATATATTATGTATAAACTAT
32198 TCATACCATG
Statistics
Matches: 83, Mismatches: 11, Indels: 5
0.84 0.11 0.05
Matches are distributed among these distances:
53 25 0.30
54 36 0.43
55 22 0.27
ACGTcount: A:0.46, C:0.06, G:0.03, T:0.46
Consensus pattern (54 bp):
ATATATACTATATATAAACTATATATATTATGTATAAACTATATAATTATATTA
Found at i:32217 original size:53 final size:50
Alignment explanation
Indices: 32100--32218 Score: 123
Period size: 55 Copynumber: 2.3 Consensus size: 50
32090 TAATTATATT
* * **
32100 ATTATATACTATATATAAACTCTATATATTATGTATAAACTATATAATTT
1 ATTATAAACTATATATAAACTATATATATTATGTATAAACTATATAATCC
*
32150 ATTAATATATACTATATATAAACTATATATATATTATGTATAAACTAT-TCATACC
1 ATT-ATA-A-ACTATATATAAAC--TATATATATTATGTATAAACTATATAAT-CC
32205 ATGTATAAACTATA
1 AT-TATAAACTATA
32219 GAGTTTATAT
Statistics
Matches: 57, Mismatches: 5, Indels: 11
0.78 0.07 0.15
Matches are distributed among these distances:
50 3 0.05
51 3 0.05
53 19 0.33
54 4 0.07
55 27 0.47
56 1 0.02
ACGTcount: A:0.45, C:0.09, G:0.03, T:0.43
Consensus pattern (50 bp):
ATTATAAACTATATATAAACTATATATATTATGTATAAACTATATAATCC
Found at i:32300 original size:11 final size:11
Alignment explanation
Indices: 32240--32332 Score: 61
Period size: 11 Copynumber: 8.7 Consensus size: 11
32230 TGAACTATTG
32240 AATTATATATA
1 AATTATATATA
* *
32251 AACTATATAGTT
1 AATTATATA-TA
*
32263 TATTA-ATATA
1 AATTATATATA
32273 AATTATATAGT-
1 AATTATATA-TA
*
32284 --TTATATGTA
1 AATTATATATA
*
32293 AATTATATATG
1 AATTATATATA
*
32304 AATTATATTTA
1 AATTATATATA
*
32315 AA-TATATACA
1 AATTATATATA
*
32325 ACTTATAT
1 AATTATAT
32333 TTATTTATTA
Statistics
Matches: 61, Mismatches: 14, Indels: 14
0.69 0.16 0.16
Matches are distributed among these distances:
8 1 0.02
9 6 0.10
10 12 0.20
11 37 0.61
12 5 0.08
ACGTcount: A:0.46, C:0.03, G:0.04, T:0.46
Consensus pattern (11 bp):
AATTATATATA
Found at i:32322 original size:21 final size:22
Alignment explanation
Indices: 32284--32335 Score: 63
Period size: 21 Copynumber: 2.4 Consensus size: 22
32274 ATTATATAGT
* *
32284 TTATATGTAAATTATATATGAA-
1 TTATATTTAAATTATATA-CAAC
32306 TTATATTTAAA-TATATACAAC
1 TTATATTTAAATTATATACAAC
32327 TTATATTTA
1 TTATATTTA
32336 TTTATTATGT
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
20 2 0.07
21 15 0.56
22 10 0.37
ACGTcount: A:0.44, C:0.04, G:0.04, T:0.48
Consensus pattern (22 bp):
TTATATTTAAATTATATACAAC
Found at i:32738 original size:8 final size:8
Alignment explanation
Indices: 32727--32787 Score: 51
Period size: 8 Copynumber: 8.2 Consensus size: 8
32717 TATATATTAA
32727 ATATAAGT
1 ATATAAGT
32735 ATATAAGT
1 ATATAAGT
*
32743 ACATAAGT
1 ATATAAGT
* *
32751 ACAAAAGT
1 ATATAAGT
32759 ATAT-A--
1 ATATAAGT
32764 ATATAAGT
1 ATATAAGT
*
32772 AT-TAAAT
1 ATATAAGT
32779 ATA-AAGT
1 ATATAAGT
32786 AT
1 AT
32788 TAATAATCAT
Statistics
Matches: 43, Mismatches: 6, Indels: 9
0.74 0.10 0.16
Matches are distributed among these distances:
5 4 0.09
6 1 0.02
7 12 0.28
8 26 0.60
ACGTcount: A:0.54, C:0.03, G:0.10, T:0.33
Consensus pattern (8 bp):
ATATAAGT
Found at i:32739 original size:2 final size:2
Alignment explanation
Indices: 32358--32723 Score: 146
Period size: 2 Copynumber: 184.5 Consensus size: 2
32348 AATTATAAAT
* * * * *
32358 TA TA TA TA CTA TG TA TA -A AA TA TA TA GTT TA AA TA TA AA GTA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA -TA
* * * *
32400 TA TA -A GTA TA TA TA TA AA CTA TA AA T- TA TA CA TA TA CA TA TA
1 TA TA TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA
* * *
32442 TA -A TA -A TA TA AA GTA TA TA TA TA TA TA TA TA AA TA TA TA AA
1 TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* **
32483 GA CTA -A CG TA TA TA GTA TA TA -A TA TA TA TA TA TA TA TA TA TA
1 TA -TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
32525 TA TA TA TA TA T- TA TA TA CT- TA TA TA TT TA TA T- TA TA TA CT-
1 TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA
* * * * *
32565 TA TA TA CTT TA TA T- TA TA TGC T- TA TA TA T- TT TA GTT TT TA
1 TA TA TA -TA TA TA TA TA TA T-A TA TA TA TA TA TA TA -TA TA TA
* * *
32605 TA -A T- TA TA CTT TA CA TA TA TA TA -A TA TA CT- TA TA CTT TA
1 TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA
* * * * *
32644 TA T- TA T- TA CA TA TG TA TA TA CTT TA AA CTA -A AA CT- TA TA
1 TA TA TA TA TA TA TA TA TA TA TA -TA TA TA -TA TA TA -TA TA TA
32683 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
32724 TAAATATAAG
Statistics
Matches: 273, Mismatches: 50, Indels: 82
0.67 0.12 0.20
Matches are distributed among these distances:
1 22 0.08
2 231 0.85
3 20 0.07
ACGTcount: A:0.46, C:0.05, G:0.03, T:0.46
Consensus pattern (2 bp):
TA
Found at i:32773 original size:13 final size:13
Alignment explanation
Indices: 32754--32792 Score: 53
Period size: 13 Copynumber: 2.9 Consensus size: 13
32744 CATAAGTACA
32754 AAAGTATATAATAT
1 AAAGTAT-TAATAT
32768 -AAGTATTAAATAT
1 AAAGTATT-AATAT
32781 AAAGTATTAATA
1 AAAGTATTAATA
32793 ATCATAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
12 1 0.04
13 15 0.65
14 7 0.30
ACGTcount: A:0.56, C:0.00, G:0.08, T:0.36
Consensus pattern (13 bp):
AAAGTATTAATAT
Found at i:32787 original size:14 final size:14
Alignment explanation
Indices: 32754--32790 Score: 51
Period size: 14 Copynumber: 2.7 Consensus size: 14
32744 CATAAGTACA
32754 AAAGTA-TATAATAT
1 AAAGTATTA-AATAT
32768 -AAGTATTAAATAT
1 AAAGTATTAAATAT
32781 AAAGTATTAA
1 AAAGTATTAA
32791 TAATCATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 4
0.84 0.00 0.16
Matches are distributed among these distances:
13 10 0.48
14 11 0.52
ACGTcount: A:0.57, C:0.00, G:0.08, T:0.35
Consensus pattern (14 bp):
AAAGTATTAAATAT
Found at i:33919 original size:15 final size:15
Alignment explanation
Indices: 33901--33939 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
33891 TTAAAGGACA
33901 GAAAAATAAAGTACT
1 GAAAAATAAAGTACT
* *
33916 G-AAATTAAAGTGCT
1 GAAAAATAAAGTACT
33930 GAAAAATAAA
1 GAAAAATAAA
33940 TAAATAAACA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.59, C:0.05, G:0.15, T:0.21
Consensus pattern (15 bp):
GAAAAATAAAGTACT
Found at i:34756 original size:25 final size:25
Alignment explanation
Indices: 34721--34770 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
34711 ACAAGGTAAT
* *
34721 GTGCTGGTGAGTGGAGCATGGGCTG
1 GTGCTGATGAGCGGAGCATGGGCTG
34746 GTGCTGATGAGCGGAGCATGGGCTG
1 GTGCTGATGAGCGGAGCATGGGCTG
34771 ATGACAGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.14, C:0.14, G:0.50, T:0.22
Consensus pattern (25 bp):
GTGCTGATGAGCGGAGCATGGGCTG
Found at i:35422 original size:182 final size:182
Alignment explanation
Indices: 35115--35754 Score: 1023
Period size: 182 Copynumber: 3.5 Consensus size: 182
35105 ATCAGAAGAT
* * *
35115 AATTTGGGGACAATACGGTTCCTTCATGATGAGGAAGTCTGATTGTCTCAAGGTGACACTGCTCC
1 AATTTGGGGACAATACGGTTCCTTCGTGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCC
* * * *
35180 TTCGTGATGAGCAGATCGGGTCGGTTTGATGTTGAAGATGACACTGCTCATCCACGATGAAGAGA
66 TTCGTGATGAGGAGATCTGGTCGGTTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGA
* * ** *
35245 TCGAGTCATTTTTTATTATGACGTTGTTCCTTCATGATGAGGAAATGGAGTC
131 TCGGGTCGTTTTCGATTATGACGTTGTTCCTTCGTGATGAGGAAATGGAGTC
*
35297 AATTTGGGGACAATACGATTCCTTCGTGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCC
1 AATTTGGGGACAATACGGTTCCTTCGTGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCC
* * *
35362 TTCGTGATGAGGAGATATGGTCGATTTGATGTTGAAGACGACAATGCTCATCCGCGATGAAGAGA
66 TTCGTGATGAGGAGATCTGGTCGGTTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGA
* * *
35427 TCGGGTCGTTTTCGATTATGACGTTGTTCTTTCGTGATGAGTAAAT-CAGGTC
131 TCGGGTCGTTTTCGATTATGACGTTGTTCCTTCGTGATGAGGAAATGGA-GTC
* * *
35479 AATCTGGGGACAATACGGTTCATTCGTGATGAGGAAGTATGATTGTCTGAGGGTGACACTGCTCC
1 AATTTGGGGACAATACGGTTCCTTCGTGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCC
35544 TTCGTGATGAGGAGATCTGGTCGGTTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGA
66 TTCGTGATGAGGAGATCTGGTCGGTTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGA
*
35609 TCGGGTCGTTTTCGATTATGACGATGTTCCTTCGTGATGAGGAAATCGG-GTC
131 TCGGGTCGTTTTCGATTATGACGTTGTTCCTTCGTGATGAGGAAAT-GGAGTC
*
35661 AATTTGGGGACAATACGGTTCCTTCGTGATGAGGAAGTCTGATTTTCTGAGGGTGACACTGCTCC
1 AATTTGGGGACAATACGGTTCCTTCGTGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCC
*
35726 TTTGTGATGAGGAGATCTGGTCGGTTTGA
66 TTCGTGATGAGGAGATCTGGTCGGTTTGA
35755 AAATTTAATT
Statistics
Matches: 420, Mismatches: 35, Indels: 6
0.91 0.08 0.01
Matches are distributed among these distances:
181 1 0.00
182 419 1.00
ACGTcount: A:0.23, C:0.16, G:0.30, T:0.31
Consensus pattern (182 bp):
AATTTGGGGACAATACGGTTCCTTCGTGATGAGGAAGTCTGATTGTCTGAGGGTGACACTGCTCC
TTCGTGATGAGGAGATCTGGTCGGTTTGATGTTGAAGACGACACTGCTCATCCGCGATGAAGAGA
TCGGGTCGTTTTCGATTATGACGTTGTTCCTTCGTGATGAGGAAATGGAGTC
Found at i:35975 original size:84 final size:84
Alignment explanation
Indices: 35867--36023 Score: 235
Period size: 84 Copynumber: 1.9 Consensus size: 84
35857 ATTTGACATG
* *
35867 TCCTTAAGCTGAATGGAATCGAACTCGAAGG-TTTGTGTTGACATATAACCCTTCTCACCTTGAG
1 TCCTTAAGCTGAATGGAATCGAACTCGAAGGTTTTG-GTTAACAGATAACCCTTCTCACCTTGAG
*
35931 TTATGCTATGAATTTGGTTT
65 TTATACTATGAATTTGGTTT
* * * *
35951 TCCTTGAGCTGAATGGAATTGAACTCGAAGGTTTTGGTTAACAGATTACCCTTCTCGCCTTGAGT
1 TCCTTAAGCTGAATGGAATCGAACTCGAAGGTTTTGGTTAACAGATAACCCTTCTCACCTTGAGT
36016 TATACTAT
66 TATACTAT
36024 AAAATTGATA
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
84 61 0.94
85 4 0.06
ACGTcount: A:0.25, C:0.18, G:0.20, T:0.36
Consensus pattern (84 bp):
TCCTTAAGCTGAATGGAATCGAACTCGAAGGTTTTGGTTAACAGATAACCCTTCTCACCTTGAGT
TATACTATGAATTTGGTTT
Found at i:36187 original size:84 final size:84
Alignment explanation
Indices: 36038--36437 Score: 454
Period size: 84 Copynumber: 4.8 Consensus size: 84
36028 TTGATATGCT
* * * * *
36038 TGTAATCAAACTCAAAGGTCTCTTGCTGACAGATAACCCTTCTCA-CCTTGAGTTATGCTACAAA
1 TGTAATCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCT-AGCCTTGAGTTATGCTGCAAA
36102 TGATGTGCCTTTGAGCTGAG
65 TGATGTGCCTTTGAGCTGAG
* * * *
36122 TATAATTGAACTCAAAGGTCTTTTGTTGGCATATAACTCTTCTAGCCTTGAGTTATGCTGCAAAT
1 TGTAATCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAAT
36187 GATGTGCCTTTGAGCTGAG
66 GATGTGCCTTTGAGCTGAG
* * * * *
36206 TGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAAACCTTCTTGCCTTGAGTTAAGCTGCAAAT
1 TGTAATCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAAT
**
36271 GATGCACCTTTGAGCTGAG
66 GATGTGCCTTTGAGCTGAG
* * * * * * * *
36290 TGTAATCAAACTCGAAGGTC-TTTGTTGACAAATAACTCTTTTAGCCTTGAGTTATGTTGTAAAA
1 TGTAATCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTG-CAAA
* *
36354 CGATGTGTCTTTGAGCTGAG
65 TGATGTGCCTTTGAGCTGAG
* * * *
36374 TGTAATCGAACTCGAAA-GTC---T-TTGGCATATAACCCTTCTTGTCTTGAGCTATGCTGCAAA
1 TGTAATCGAACTC-AAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAA
36434 TGAT
65 TGAT
36438 TCCTTTAATC
Statistics
Matches: 266, Mismatches: 47, Indels: 10
0.82 0.15 0.03
Matches are distributed among these distances:
80 6 0.02
81 27 0.10
82 1 0.00
83 31 0.12
84 199 0.75
85 2 0.01
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34
Consensus pattern (84 bp):
TGTAATCGAACTCAAAGGTCTTTTGTTGGCAGATAACCCTTCTAGCCTTGAGTTATGCTGCAAAT
GATGTGCCTTTGAGCTGAG
Found at i:36272 original size:168 final size:167
Alignment explanation
Indices: 36038--36437 Score: 511
Period size: 168 Copynumber: 2.4 Consensus size: 167
36028 TTGATATGCT
* * * * ** *
36038 TGTAATCAAACTCAAAGGTCTCTTGCTGACAGATAACCCTTCTCACCTTGAGTTATGCTACAAAT
1 TGTAATCGAACTCGAAGGTCT-TTGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAAT
** ** * *
36103 GATGTGCCTTTGAGCTGAGTATAATTGAACTCAAAGGTCTTTTGTTGGCATATAACTCTTCTAGC
65 GATGCACCTTTGAGCTGAGTATAATCAAACTCAAAGGTC-TTTGTTGACAAATAACTCTTCTAGC
* *
36168 CTTGAGTTATGCTG-CAAATGATGTGCCTTTGAGCTGAG
129 CTTGAGTTATGCTGTAAAACGATGTGCCTTTGAGCTGAG
* *
36206 TGTAATCGAACTCGAAGGTCTTTGGTTGGCAGATAAACCTTCTTGCCTTGAGTTAAGCTGCAAAT
1 TGTAATCGAACTCGAAGGTCTTT-GTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAAT
* * *
36271 GATGCACCTTTGAGCTGAGTGTAATCAAACTCGAAGGTCTTTGTTGACAAATAACTCTTTTAGCC
65 GATGCACCTTTGAGCTGAGTATAATCAAACTCAAAGGTCTTTGTTGACAAATAACTCTTCTAGCC
* *
36336 TTGAGTTATGTTGTAAAACGATGTGTCTTTGAGCTGAG
130 TTGAGTTATGCTGTAAAACGATGTGCCTTTGAGCTGAG
* * * *
36374 TGTAATCGAACTCGAAAGTC--T-TTGGCATATAACCCTTCTTGTCTTGAGCTATGCTGCAAATG
1 TGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATG
36436 AT
66 AT
36438 TCCTTTAATC
Statistics
Matches: 202, Mismatches: 28, Indels: 8
0.85 0.12 0.03
Matches are distributed among these distances:
164 38 0.19
166 1 0.00
167 37 0.18
168 126 0.62
ACGTcount: A:0.26, C:0.18, G:0.21, T:0.34
Consensus pattern (167 bp):
TGTAATCGAACTCGAAGGTCTTTGTTGGCAGATAACCCTTCTTGCCTTGAGTTATGCTGCAAATG
ATGCACCTTTGAGCTGAGTATAATCAAACTCAAAGGTCTTTGTTGACAAATAACTCTTCTAGCCT
TGAGTTATGCTGTAAAACGATGTGCCTTTGAGCTGAG
Found at i:38542 original size:21 final size:21
Alignment explanation
Indices: 38524--38564 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
38514 ATTTTCAAAG
38524 GCATGCACCGATGCATCAATA
1 GCATGCACCGATGCATCAATA
* *
38545 TCATGCATCGATGCATCAAT
1 GCATGCACCGATGCATCAAT
38565 GAATAAATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.32, C:0.27, G:0.17, T:0.24
Consensus pattern (21 bp):
GCATGCACCGATGCATCAATA
Found at i:38614 original size:19 final size:19
Alignment explanation
Indices: 38590--38628 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
38580 TCGAATGCAT
38590 TCCATGCACCGATGCACTC
1 TCCATGCACCGATGCACTC
*
38609 TCCATGCATCGATGCACTC
1 TCCATGCACCGATGCACTC
38628 T
1 T
38629 GATTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.21, C:0.38, G:0.15, T:0.26
Consensus pattern (19 bp):
TCCATGCACCGATGCACTC
Found at i:38652 original size:64 final size:64
Alignment explanation
Indices: 38546--38754 Score: 205
Period size: 64 Copynumber: 3.2 Consensus size: 64
38536 GCATCAATAT
* * * *
38546 CATGCATCGATGCA-TCAATGAATAAATTGAAACATCGAATGCATTCCATGCACCGATGCACTCT
1 CATGCATCGATGCACTC-ATGATTTAATTAAAACATCGAATGCATT-CATGCATCGATGCACTCT
38610 C
64 C
* **
38611 CATGCATCGATGCACTC-TGATTTAATTAAAACATCGAATGCATTTGATGCATCGATGCACAATC
1 CATGCATCGATGCACTCATGATTTAATTAAAACATCGAATGCA-TTCATGCATCGATGCACTCTC
* * *
38675 CATGCATCGATACAC-CAGGCTATTT--TTCAAACATCGAATGCACTTCATGCATCGATGCACTC
1 CATGCATCGATGCACTCATG--ATTTAATTAAAACATCGAATGCA-TTCATGCATCGATGCACTC
38737 T-
63 TC
* *
38738 TAGTGCACCGATGCACT
1 CA-TGCATCGATGCACT
38755 AGGAGTCTAA
Statistics
Matches: 120, Mismatches: 17, Indels: 14
0.79 0.11 0.09
Matches are distributed among these distances:
63 2 0.02
64 96 0.80
65 16 0.13
66 6 0.05
ACGTcount: A:0.31, C:0.26, G:0.16, T:0.27
Consensus pattern (64 bp):
CATGCATCGATGCACTCATGATTTAATTAAAACATCGAATGCATTCATGCATCGATGCACTCTC
Found at i:38734 original size:17 final size:19
Alignment explanation
Indices: 38706--38754 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
38696 ATTTTTCAAA
38706 CATCGAATGCACT-TCA-TG
1 CATCG-ATGCACTCTCAGTG
*
38724 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTCAGTG
*
38743 CACCGATGCACT
1 CATCGATGCACT
38755 AGGAGTCTAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.31, G:0.18, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTCAGTG
Found at i:44571 original size:24 final size:22
Alignment explanation
Indices: 44543--44622 Score: 92
Period size: 24 Copynumber: 3.5 Consensus size: 22
44533 CATTTAACAA
44543 TGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCAT-CC-TTGAATG
*
44567 TGCATCGATGCAT-C-TGCATG
1 TGCATCGATGCATCCTTGAATG
*
44587 ATGCACCGATGCATGCCTTGAATG
1 -TGCATCGATGCAT-CCTTGAATG
44611 TGCATCGATGCA
1 TGCATCGATGCA
44623 CAAGACCATG
Statistics
Matches: 48, Mismatches: 4, Indels: 9
0.79 0.07 0.15
Matches are distributed among these distances:
20 5 0.10
21 12 0.25
22 1 0.02
23 12 0.25
24 18 0.38
ACGTcount: A:0.23, C:0.25, G:0.24, T:0.29
Consensus pattern (22 bp):
TGCATCGATGCATCCTTGAATG
Found at i:44578 original size:44 final size:43
Alignment explanation
Indices: 44523--44645 Score: 133
Period size: 44 Copynumber: 2.8 Consensus size: 43
44513 TTGTGCTTAA
* *
44523 TGCACCGATGCATTTAACAATGCATCGATGCATCCCTTTGAATG
1 TGCATCGATGCATCTAACAATGCATCGATGCATCCC-TTGAATG
* * *
44567 TGCATCGATGCATCT-GCATGATGCACCGATGCATGCCTTGAATG
1 TGCATCGATGCATCTAACA--ATGCATCGATGCATCCCTTGAATG
* *
44611 TGCATCGATGCA-CAAGACCATGCATCGATGCATCC
1 TGCATCGATGCATCTA-ACAATGCATCGATGCATCC
44646 GTCAGGTTTT
Statistics
Matches: 65, Mismatches: 10, Indels: 9
0.77 0.12 0.11
Matches are distributed among these distances:
43 17 0.26
44 32 0.49
45 16 0.25
ACGTcount: A:0.26, C:0.27, G:0.21, T:0.26
Consensus pattern (43 bp):
TGCATCGATGCATCTAACAATGCATCGATGCATCCCTTGAATG
Found at i:47146 original size:21 final size:21
Alignment explanation
Indices: 47122--47161 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
47112 TTTTCAAAGG
47122 CATGCACCGATGCATCAATAT
1 CATGCACCGATGCATCAATAT
*
47143 CATGCATCGATGCATCAAT
1 CATGCACCGATGCATCAAT
47162 GAATAAATTG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.33, C:0.28, G:0.15, T:0.25
Consensus pattern (21 bp):
CATGCACCGATGCATCAATAT
Found at i:49625 original size:14 final size:14
Alignment explanation
Indices: 49606--49680 Score: 68
Period size: 14 Copynumber: 5.5 Consensus size: 14
49596 TTTGTCCTGG
*
49606 TTATAAATATTATA
1 TTATAATTATTATA
49620 TTATAATTATTACTA
1 TTATAATTATTA-TA
49635 TTAT-ATTA-T-TA
1 TTATAATTATTATA
*
49646 TTAT-ATTATTGTTA
1 TTATAATTATT-ATA
**
49660 TTATAACAATTATA
1 TTATAATTATTATA
49674 TTATAAT
1 TTATAAT
49681 AAATATTAGT
Statistics
Matches: 51, Mismatches: 5, Indels: 10
0.77 0.08 0.15
Matches are distributed among these distances:
11 10 0.20
12 1 0.02
13 1 0.02
14 29 0.57
15 10 0.20
ACGTcount: A:0.41, C:0.03, G:0.01, T:0.55
Consensus pattern (14 bp):
TTATAATTATTATA
Found at i:49641 original size:11 final size:11
Alignment explanation
Indices: 49613--49676 Score: 51
Period size: 11 Copynumber: 5.9 Consensus size: 11
49603 TGGTTATAAA
49613 TATTATATTA-
1 TATTATATTAC
*
49623 TAAT-TATTAC
1 TATTATATTAC
*
49633 TATTATATTAT
1 TATTATATTAC
*
49644 TATTATATTAT
1 TATTATATTAC
* *
49655 TGTTATTATAAC
1 TATTA-TATTAC
*
49667 AATTATATTA
1 TATTATATTA
49677 TAATAAATAT
Statistics
Matches: 42, Mismatches: 9, Indels: 5
0.75 0.16 0.09
Matches are distributed among these distances:
9 5 0.12
10 6 0.14
11 24 0.57
12 7 0.17
ACGTcount: A:0.39, C:0.03, G:0.02, T:0.56
Consensus pattern (11 bp):
TATTATATTAC
Found at i:49644 original size:3 final size:3
Alignment explanation
Indices: 49613--49700 Score: 58
Period size: 3 Copynumber: 30.7 Consensus size: 3
49603 TGGTTATAAA
* * *
49613 TAT TA- TAT TAT AAT TAT TAC TAT TA- TAT TAT TAT TA- TAT TAT TGT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
* * * * * * *
49658 TAT TAT AAC AAT TA- TAT TAT AAT AAA TAT TAG TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TA
49701 ATATCATTTA
Statistics
Matches: 65, Mismatches: 16, Indels: 8
0.73 0.18 0.09
Matches are distributed among these distances:
2 8 0.12
3 57 0.88
ACGTcount: A:0.41, C:0.02, G:0.02, T:0.55
Consensus pattern (3 bp):
TAT
Found at i:60590 original size:55 final size:55
Alignment explanation
Indices: 60523--60984 Score: 755
Period size: 55 Copynumber: 8.4 Consensus size: 55
60513 TTAAAGCATC
* * *
60523 AAGATTTTTCGAGTCTTATACTCTCTGAAGGAATAAGGAGCAGACATGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
** *
60578 AAGATTGTTCGAGTCTTATACTCTCTTCAGGAATAGGGACCAGACACGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
* *
60633 AAGATTGTTCGAGTCTTATACTCTCTAAAGGAATAGGGAGCAGACACGATTGTTT
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
* *
60688 AAGATTGTTCGAGTCTTATACTCTTTGAAGGAATAGGGAGCAGACATGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
* *
60743 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGTAGACACGATTATTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
*
60798 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGGCACGATTGTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
*
60853 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTTTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
* * *
60908 AATATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACATGATTTTTG
1 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
*
60963 AAGA-TGTTCGAGTTTTATACTC
1 AAGATTGTTCGAGTCTTATACTC
60985 CCTAAAGAAA
Statistics
Matches: 380, Mismatches: 27, Indels: 1
0.93 0.07 0.00
Matches are distributed among these distances:
54 17 0.04
55 363 0.96
ACGTcount: A:0.29, C:0.14, G:0.25, T:0.32
Consensus pattern (55 bp):
AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
Found at i:61056 original size:110 final size:110
Alignment explanation
Indices: 60523--61058 Score: 535
Period size: 110 Copynumber: 4.9 Consensus size: 110
60513 TTAAAGCATC
* * * * * * * * **
60523 AAGATTTTTCGAGTCTTATACTCTCTGAAGGAATAAGGAG-CAGACATGATTGTTGAAGATTGTT
1 AAGATTGTTCGAGTCTTATACTCCCTAAAGAAAGAGGGAGTGAGACACGA-TGAAGAAGATTGTT
** *
60587 CGAGTCTTATACTCTCTTCAGGAATAGGGACCAGACACGATTGTTG
65 CGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
* * * * ***
60633 AAGATTGTTCGAGTCTTATACTCTCTAAAGGAATAGGGAG-CAGACACGATTGTTTAAGATTGTT
1 AAGATTGTTCGAGTCTTATACTCCCTAAAGAAAGAGGGAGTGAGACACGA-TGAAGAAGATTGTT
* *
60697 CGAGTCTTATACTCTTTGAAGGAATAGGGAGCAGACATGATTGTTG
65 CGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
* * * * * *
60743 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAGT-AGACACGATTATTGAAGATTGTT
1 AAGATTGTTCGAGTCTTATACTCCCTAAAGAAAGAGGGAGTGAGACACGATGA-AGAAGATTGTT
*
60807 CGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGGCACGATTGTTG
65 CGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
* * * * * *** *
60853 AAGATTGTTCGAGTCTTATACTCTCTGAAGGAATAGGGAG-CAGACACGATTTTTGAATATTGTT
1 AAGATTGTTCGAGTCTTATACTCCCTAAAGAAAGAGGGAGTGAGACACGA-TGAAGAAGATTGTT
* *
60917 CGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACATGATTTTTG
65 CGAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
* * * * *
60963 AAGA-TGTTCGAGTTTTATACTCCCTAAAGAAAGAGGGGGTGA-ACCCGTAGGAAGAAGATTATT
1 AAGATTGTTCGAGTCTTATACTCCCTAAAGAAAGAGGGAGTGAGACACG-ATGAAGAAGATTGTT
* * * *
61026 CGAGTTTTGTACTCCCTGAAAGAATGAGGGAGC
65 CGAGTCTTATACTCTCTGAAGGAAT-AGGGAGC
61059 GAACCCGTTA
Statistics
Matches: 379, Mismatches: 40, Indels: 14
0.88 0.09 0.03
Matches are distributed among these distances:
109 63 0.17
110 314 0.83
111 2 0.01
ACGTcount: A:0.30, C:0.14, G:0.26, T:0.30
Consensus pattern (110 bp):
AAGATTGTTCGAGTCTTATACTCCCTAAAGAAAGAGGGAGTGAGACACGATGAAGAAGATTGTTC
GAGTCTTATACTCTCTGAAGGAATAGGGAGCAGACACGATTGTTG
Found at i:61416 original size:56 final size:56
Alignment explanation
Indices: 60969--61399 Score: 550
Period size: 56 Copynumber: 7.8 Consensus size: 56
60959 TTTGAAGATG
* * * *
60969 TTCGAGTTTTATACTCCCT-AAAGAAAGAGGGGGTGAACCCG-TAGGAAGAAGATTA
1 TTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTA-GCAGAAGATTA
* * * *
61024 TTCGAGTTTTGTACTCCCTGAAAGAATGAGGGAGCGAACCCGTTAGCAGGAGATTA
1 TTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTAGCAGAAGATTA
*
61080 TTTGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTAGCAGAAGATTA
1 TTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTAGCAGAAGATTA
* *
61136 TTCGAGTTCTATACTCCCTGAGAGAAAGAGAGAGCGAACCCG-TAGACAGAAGATTA
1 TTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTAG-CAGAAGATTA
* * * **
61192 TTCGAGTTCTATACTCCCAGAAAGAAAGAGGGATCAAACCTATTAGCAGAAGATTA
1 TTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTAGCAGAAGATTA
* * *
61248 TTCGAGTTTTATACTCCCTGAAAGAAAGAGGGAGCGAACCCG-TAGGCATAAGATTG
1 TTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTA-GCAGAAGATTA
* * * * *
61304 TTCGAGTTC-CTACTCCCT-AAAGAAAGAAGGAGCGAACCTGTTGGCAGAAGATTG
1 TTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTAGCAGAAGATTA
* * *
61358 TTCGAGTTCCATACTCCCTGAAAGCAAGAGAGAGCGAACCCG
1 TTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCG
61400 CTGATTGAAG
Statistics
Matches: 328, Mismatches: 40, Indels: 15
0.86 0.10 0.04
Matches are distributed among these distances:
54 39 0.12
55 40 0.12
56 244 0.74
57 5 0.02
ACGTcount: A:0.33, C:0.19, G:0.25, T:0.22
Consensus pattern (56 bp):
TTCGAGTTCTATACTCCCTGAAAGAAAGAGGGAGCGAACCCGTTAGCAGAAGATTA
Found at i:61590 original size:20 final size:20
Alignment explanation
Indices: 61565--61609 Score: 63
Period size: 20 Copynumber: 2.2 Consensus size: 20
61555 TTTGTCCTGG
61565 TTATAAATATTATATAATAA
1 TTATAAATATTATATAATAA
* * *
61585 TTATAATTATTATATTATTA
1 TTATAAATATTATATAATAA
61605 TTATA
1 TTATA
61610 TTATTGTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTATAAATATTATATAATAA
Found at i:61596 original size:3 final size:3
Alignment explanation
Indices: 61584--61655 Score: 51
Period size: 3 Copynumber: 25.0 Consensus size: 3
61574 TTATATAATA
* * * **
61584 ATT ATA ATT ATT A-T ATT ATT ATT A-T ATT ATT GTT ATT ATA ACA ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
* * *
61630 A-T ATT ATA ATA ATT ATT AGT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT
61656 TTTAATATCA
Statistics
Matches: 54, Mismatches: 12, Indels: 6
0.75 0.17 0.08
Matches are distributed among these distances:
2 6 0.11
3 48 0.89
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.56
Consensus pattern (3 bp):
ATT
Found at i:63269 original size:3 final size:3
Alignment explanation
Indices: 63261--63289 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
63251 GAATAGGGTA
63261 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TT
63290 TAATAAATAT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:64027 original size:18 final size:17
Alignment explanation
Indices: 64004--64042 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
63994 CGCATACCAC
64004 AAATTATCATTTTAATTA
1 AAATTAT-ATTTTAATTA
* *
64022 AAATTATGTTTTATTTA
1 AAATTATATTTTAATTA
64039 AAAT
1 AAAT
64043 GGAAAAACAT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 12 0.63
18 7 0.37
ACGTcount: A:0.44, C:0.03, G:0.03, T:0.51
Consensus pattern (17 bp):
AAATTATATTTTAATTA
Found at i:67638 original size:15 final size:15
Alignment explanation
Indices: 67620--67658 Score: 53
Period size: 14 Copynumber: 2.7 Consensus size: 15
67610 TTAATGGACA
67620 GAAAAATAAAGTACT
1 GAAAAATAAAGTACT
* *
67635 G-AAATTAAAGTGCT
1 GAAAAATAAAGTACT
67649 GAAAAATAAA
1 GAAAAATAAA
67659 TAAATAAATA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
14 12 0.60
15 8 0.40
ACGTcount: A:0.59, C:0.05, G:0.15, T:0.21
Consensus pattern (15 bp):
GAAAAATAAAGTACT
Found at i:68480 original size:25 final size:25
Alignment explanation
Indices: 68445--68494 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
68435 ACAAGGTAAT
*
68445 GTGCTGGTGAGTGGAGAATGGGCTG
1 GTGCTGATGAGTGGAGAATGGGCTG
*
68470 GTGCTGATGAGTGGAGCATGGGCTG
1 GTGCTGATGAGTGGAGAATGGGCTG
68495 ATGACAGGGT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.16, C:0.10, G:0.50, T:0.24
Consensus pattern (25 bp):
GTGCTGATGAGTGGAGAATGGGCTG
Found at i:69228 original size:6 final size:6
Alignment explanation
Indices: 69217--69257 Score: 50
Period size: 6 Copynumber: 7.0 Consensus size: 6
69207 GACTTCTTCT
*
69217 TTTTTC TTTTTC -TTTTC TTTTTTC TTTTTC -TTATC TTTTTC
1 TTTTTC TTTTTC TTTTTC -TTTTTC TTTTTC TTTTTC TTTTTC
69258 GTGAGCGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
5 9 0.30
6 16 0.53
7 5 0.17
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.80
Consensus pattern (6 bp):
TTTTTC
Found at i:69236 original size:18 final size:18
Alignment explanation
Indices: 69213--69256 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
69203 TCAAGACTTC
69213 TTCTTTTTTCTTTTTCTT
1 TTCTTTTTTCTTTTTCTT
69231 TTCTTTTTTCTTTTTCTT
1 TTCTTTTTTCTTTTTCTT
*
69249 ATCTTTTT
1 TTCTTTTT
69257 CGTGAGCGTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.02, C:0.16, G:0.00, T:0.82
Consensus pattern (18 bp):
TTCTTTTTTCTTTTTCTT
Found at i:70311 original size:15 final size:15
Alignment explanation
Indices: 70291--70321 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
70281 TTGGGCTAAA
70291 ATTTAATTTACTTGT
1 ATTTAATTTACTTGT
70306 ATTTAATTTACTTGT
1 ATTTAATTTACTTGT
70321 A
1 A
70322 ATTTTGTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.29, C:0.06, G:0.06, T:0.58
Consensus pattern (15 bp):
ATTTAATTTACTTGT
Found at i:76939 original size:65 final size:64
Alignment explanation
Indices: 76741--76942 Score: 216
Period size: 65 Copynumber: 3.1 Consensus size: 64
76731 TGCACTAAGA
* * * *
76741 GTGCATCGATGCATGAAATGCATTCGATGTTTCAAAATAAT-CATAGTGCATCGATGAATGGCTG
1 GTGCATCGATGCATGAAATGCATTCGATGTTTC-AATTAATCCATGGTGCATCGATGCATGGTTG
* * * * *
76805 GTGTATCGATGCATCAAATGCATTCGATGTTTTC-ATAAAACTC-TGAGTGCATCGATGCATAGT
1 GTGCATCGATGCATGAAATGCATTCGATG-TTTCAATTAATC-CATG-GTGCATCGATGCATGGT
76868 AT-
63 -TG
*
76870 GTGCATCGATGCATGAAATGCATTCGATG-TTCAATTTATTCCATGGTGCATCGATGCATGGATT
1 GTGCATCGATGCATGAAATGCATTCGATGTTTCAA-TTAATCCATGGTGCATCGATGCATGG-TT
76934 G
64 G
76935 GTGCATCG
1 GTGCATCG
76943 GTGTATCACT
Statistics
Matches: 113, Mismatches: 15, Indels: 19
0.77 0.10 0.13
Matches are distributed among these distances:
63 6 0.05
64 46 0.41
65 60 0.53
66 1 0.01
ACGTcount: A:0.28, C:0.17, G:0.23, T:0.32
Consensus pattern (64 bp):
GTGCATCGATGCATGAAATGCATTCGATGTTTCAATTAATCCATGGTGCATCGATGCATGGTTG
Found at i:77310 original size:21 final size:21
Alignment explanation
Indices: 77283--77348 Score: 61
Period size: 21 Copynumber: 3.4 Consensus size: 21
77273 AGTTTGAAAT
77283 TACTCCCCCTTACTTTAACAC
1 TACTCCCCCTTACTTTAACAC
* * *
77304 T-C-CTCCC---CTTTAAAAT
1 TACTCCCCCTTACTTTAACAC
77320 TACTCCCCCTTACTTTAACAC
1 TACTCCCCCTTACTTTAACAC
*
77341 TTCTCCCC
1 TACTCCCC
77349 TTTAAAACAT
Statistics
Matches: 33, Mismatches: 7, Indels: 10
0.66 0.14 0.20
Matches are distributed among these distances:
16 8 0.24
17 1 0.03
18 4 0.12
19 4 0.12
20 1 0.03
21 15 0.45
ACGTcount: A:0.21, C:0.44, G:0.00, T:0.35
Consensus pattern (21 bp):
TACTCCCCCTTACTTTAACAC
Found at i:77320 original size:37 final size:37
Alignment explanation
Indices: 77279--77355 Score: 145
Period size: 37 Copynumber: 2.1 Consensus size: 37
77269 ATTAAGTTTG
77279 AAATTACTCCCCCTTACTTTAACACTCCTCCCCTTTA
1 AAATTACTCCCCCTTACTTTAACACTCCTCCCCTTTA
*
77316 AAATTACTCCCCCTTACTTTAACACTTCTCCCCTTTA
1 AAATTACTCCCCCTTACTTTAACACTCCTCCCCTTTA
77353 AAA
1 AAA
77356 CATTTTAACA
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
37 39 1.00
ACGTcount: A:0.27, C:0.38, G:0.00, T:0.35
Consensus pattern (37 bp):
AAATTACTCCCCCTTACTTTAACACTCCTCCCCTTTA
Done.