Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006009.1 Hibiscus syriacus cultivar Beakdansim tig00014175_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: 85162
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:444 original size:14 final size:14
Alignment explanation
Indices: 425--461 Score: 58
Period size: 14 Copynumber: 2.6 Consensus size: 14
415 AGTCAACGTT
425 TGAGTCAACT-TGTC
1 TGAGTCAACTCT-TC
439 TGAGTCAACTCTTC
1 TGAGTCAACTCTTC
453 TGAGTCAAC
1 TGAGTCAAC
462 CCATTGACTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
14 21 0.95
15 1 0.05
ACGTcount: A:0.24, C:0.24, G:0.19, T:0.32
Consensus pattern (14 bp):
TGAGTCAACTCTTC
Found at i:3400 original size:27 final size:27
Alignment explanation
Indices: 3369--3424 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
3359 TTCCATCAAT
* *
3369 CAGCTTGTTTCATACAAAATAAAAGAC
1 CAGCTTGTTGCATACAAAACAAAAGAC
3396 CAGCTTGTTGCATACAAAACAAAAGAC
1 CAGCTTGTTGCATACAAAACAAAAGAC
3423 CA
1 CA
3425 AAATACAAAA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.45, C:0.21, G:0.12, T:0.21
Consensus pattern (27 bp):
CAGCTTGTTGCATACAAAACAAAAGAC
Found at i:4100 original size:18 final size:19
Alignment explanation
Indices: 4074--4110 Score: 67
Period size: 18 Copynumber: 2.0 Consensus size: 19
4064 AATTGGCTTA
4074 TTTCAAACATTTCCAATAT
1 TTTCAAACATTTCCAATAT
4093 TTTC-AACATTTCCAATAT
1 TTTCAAACATTTCCAATAT
4111 AGGCGTGTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 14 0.78
19 4 0.22
ACGTcount: A:0.35, C:0.22, G:0.00, T:0.43
Consensus pattern (19 bp):
TTTCAAACATTTCCAATAT
Found at i:6306 original size:55 final size:55
Alignment explanation
Indices: 6210--6549 Score: 441
Period size: 54 Copynumber: 6.3 Consensus size: 55
6200 TTACCGAAAG
*
6210 GGCACTA-GTGTGCAACCTTACA-AAATTCATAATGAGTTTATGAATTTCTGTATT
1 GGCACTATGTGTGCAACCTTA-AGAAATTCATAATAAGTTTATGAATTTCTGTATT
* *
6264 GGAACTATGTGTACAACCTTAAGAAATTCATAATAAGTTTATGAATTT-TCGTATT
1 GGCACTATGTGTGCAACCTTAAGAAATTCATAATAAGTTTATGAATTTCT-GTATT
**
6319 GGCACTATGTGTGCAACC-TAAGAAATTCATAATAAGTTTATGAATTTCCCTATT
1 GGCACTATGTGTGCAACCTTAAGAAATTCATAATAAGTTTATGAATTTCTGTATT
* * **
6373 GGAACTGTGTGTGCAA-CTTAAGAAGCTCATAATAAG-TTATGAATTT-TCGTATT
1 GGCACTATGTGTGCAACCTTAAGAAATTCATAATAAGTTTATGAATTTCT-GTATT
* * *
6426 GGCACTATGTGTGCAAAC-TAAGAAATTCATAATAATTTTATGAATTTCCGTATT
1 GGCACTATGTGTGCAACCTTAAGAAATTCATAATAAGTTTATGAATTTCTGTATT
* *
6480 GGCAC--TGTGTG-AAACTTAAGAAGTTCATAATAAGTTTATGAATTTCTGTATT
1 GGCACTATGTGTGCAACCTTAAGAAATTCATAATAAGTTTATGAATTTCTGTATT
*
6532 GGCACTATGGGTGCAACC
1 GGCACTATGTGTGCAACC
6550 CCACGTGATT
Statistics
Matches: 249, Mismatches: 24, Indels: 25
0.84 0.08 0.08
Matches are distributed among these distances:
51 4 0.02
52 44 0.18
53 44 0.18
54 97 0.39
55 60 0.24
ACGTcount: A:0.33, C:0.14, G:0.18, T:0.36
Consensus pattern (55 bp):
GGCACTATGTGTGCAACCTTAAGAAATTCATAATAAGTTTATGAATTTCTGTATT
Found at i:6447 original size:107 final size:107
Alignment explanation
Indices: 6210--6585 Score: 492
Period size: 107 Copynumber: 3.5 Consensus size: 107
6200 TTACCGAAAG
* *
6210 GGCACTA-GTGTGCAACCTTACA-AAATTCATAATGAGTTTATGAATTTCTGTATTGGAACTATG
1 GGCACTATGTGTGCAACC-TA-AGAAATTCATAATAAGTTTATGAATTTCCGTATTGGAACT-TG
* *
6273 TGTACAACCTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATT
63 TGTGCAA-CTTAAGAAGTTCATAATAAGTTTATGAATTTTCGTATT
*
6319 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCCTATTGGAACTGTGTG
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGAACT-TGTG
*
6384 TGCAACTTAAGAAGCTCATAATAAG-TTATGAATTTTCGTATT
65 TGCAACTTAAGAAGTTCATAATAAGTTTATGAATTTTCGTATT
* * *
6426 GGCACTATGTGTGCAAACTAAGAAATTCATAATAATTTTATGAATTTCCGTATTGGCAC-TGTGT
1 GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGAACTTGTGT
*
6490 GAAACTTAAGAAGTTCATAATAAGTTTATGAA-TTTCTGTATT
66 GCAACTTAAGAAGTTCATAATAAGTTTATGAATTTTC-GTATT
* * * ** * * *
6532 GGCACTATGGGTGCAACCCCACGTGATTCATAATGAGTTTGTGAATTACCGTAT
1 GGCACTATGTGTGCAA-CCTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
6586 CGGCACAATA
Statistics
Matches: 239, Mismatches: 23, Indels: 12
0.87 0.08 0.04
Matches are distributed among these distances:
105 31 0.13
106 27 0.11
107 100 0.42
108 19 0.08
109 52 0.22
110 10 0.04
ACGTcount: A:0.32, C:0.14, G:0.18, T:0.36
Consensus pattern (107 bp):
GGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGAACTTGTGT
GCAACTTAAGAAGTTCATAATAAGTTTATGAATTTTCGTATT
Found at i:10197 original size:60 final size:60
Alignment explanation
Indices: 10011--10315 Score: 353
Period size: 60 Copynumber: 5.1 Consensus size: 60
10001 CATTGTTTTT
* ** * * *
10011 TCATCTAACTAGCATTAGTGGCACCTTAATGCCAAAAATGC-TCATTAGGCATTTAAATTTT
1 TCATCTAACTTGCATTAGTGGCACCTTTCTGCC-AAAATGCACCATTAGGCATTT-AACTTA
* * * *
10072 TAATCTAACTTGCATTAGTGGCACCTTTCTGTCAAAAATGCACCTTTAGTCATTTAACTTA
1 TCATCTAACTTGCATTAGTGGCACCTTTCTG-CCAAAATGCACCATTAGGCATTTAACTTA
* * * *
10133 TCATCTAACTTGCATTAATGACACTTTTCTGCCAAAATGCACCATTAGACATTTAACTTA
1 TCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACCATTAGGCATTTAACTTA
* *** * *
10193 TCATCTAACTAGCATTAGTGGCACCTTTCTGCCAAAATGCAATGTTAGCCATTTATCTTA
1 TCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACCATTAGGCATTTAACTTA
* * * *
10253 TCATCTAACTTGCATTAGTGACACATTTCTGCCAAAATGCACCGTCAGGCATTTAACTT-
1 TCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACCATTAGGCATTTAACTTA
10312 TCAT
1 TCAT
10316 TTTAGAGCAT
Statistics
Matches: 208, Mismatches: 34, Indels: 6
0.84 0.14 0.02
Matches are distributed among these distances:
59 4 0.02
60 128 0.62
61 65 0.31
62 11 0.05
ACGTcount: A:0.30, C:0.23, G:0.12, T:0.35
Consensus pattern (60 bp):
TCATCTAACTTGCATTAGTGGCACCTTTCTGCCAAAATGCACCATTAGGCATTTAACTTA
Found at i:10754 original size:22 final size:22
Alignment explanation
Indices: 10724--10784 Score: 97
Period size: 22 Copynumber: 2.8 Consensus size: 22
10714 ATCGTACCTC
*
10724 TACTGTGGTATCGATACTTCTA
1 TACTATGGTATCGATACTTCTA
10746 TACTATGGTATCGATACTTCTA
1 TACTATGGTATCGATACTTCTA
*
10768 TAATATGGTA-CGATACT
1 TACTATGGTATCGATACT
10785 CCCTTGCAGT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
21 7 0.19
22 30 0.81
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.39
Consensus pattern (22 bp):
TACTATGGTATCGATACTTCTA
Found at i:10868 original size:18 final size:19
Alignment explanation
Indices: 10826--10873 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 19
10816 GGAATCCACG
* *
10826 GTATCGATACCTACCTCATA
1 GTATCGATACCCACATCA-A
10846 GTATCGATACCCACATC-A
1 GTATCGATACCCACATCAA
10864 GTATCGATAC
1 GTATCGATAC
10874 TAACTGCATC
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
18 11 0.42
20 15 0.58
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.27
Consensus pattern (19 bp):
GTATCGATACCCACATCAA
Found at i:15370 original size:54 final size:55
Alignment explanation
Indices: 15305--15759 Score: 611
Period size: 54 Copynumber: 8.4 Consensus size: 55
15295 TCATAATGAG
** * *
15305 TTTCAGTATTGGCGTTATG-GTGCAACCTTAAGAAATTCAAAATAATTTTATGAAT
1 TTTC-GTATTGGCACTATGTGTGCAACCTTAAGAAATTCATAATAAGTTTATGAAT
15360 TTTCGTATTGGCACTATGTGTGCAACC-TAAGAAATTCATAATAAGTTTATGAAT
1 TTTCGTATTGGCACTATGTGTGCAACCTTAAGAAATTCATAATAAGTTTATGAAT
* *
15414 TTTCGTATTGGCAATGTGTGTGCAA-CTTAAGAAATTCATAATAAGTTTATGAAT
1 TTTCGTATTGGCACTATGTGTGCAACCTTAAGAAATTCATAATAAGTTTATGAAT
* *
15468 TTTCGTATTAGCACTATGTGTGCAACC-TAAGAAATTCATAATAAGGTTATGAAT
1 TTTCGTATTGGCACTATGTGTGCAACCTTAAGAAATTCATAATAAGTTTATGAAT
* * * * *
15522 TTCCCTATTGGAACTGTGTGTGCAA-CTTAAGAAGTTCATAATAAGTTTATGAAT
1 TTTCGTATTGGCACTATGTGTGCAACCTTAAGAAATTCATAATAAGTTTATGAAT
15576 TTTCGTATTGGCACTATGTGTGCAACC-TAAGAAATTCATAATAAGTTTATGAAT
1 TTTCGTATTGGCACTATGTGTGCAACCTTAAGAAATTCATAATAAGTTTATGAAT
* * *
15630 TTCCGTATTGGCACTGTGTGTGCAA-CTTAAGAAGTTCATAATAAGTTTATGAAT
1 TTTCGTATTGGCACTATGTGTGCAACCTTAAGAAATTCATAATAAGTTTATGAAT
* * * * *
15684 TTTTGTATTGGCACTATGTGTGCAACC-CAACGTAATTCATAATGAGTTTGTGAAT
1 TTTCGTATTGGCACTATGTGTGCAACCTTAA-GAAATTCATAATAAGTTTATGAAT
** * *
15739 TACCGTATCGGCACTACGTGT
1 TTTCGTATTGGCACTATGTGT
15760 ACGAAAACCA
Statistics
Matches: 354, Mismatches: 38, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
53 3 0.01
54 300 0.85
55 51 0.14
ACGTcount: A:0.32, C:0.13, G:0.18, T:0.37
Consensus pattern (55 bp):
TTTCGTATTGGCACTATGTGTGCAACCTTAAGAAATTCATAATAAGTTTATGAAT
Found at i:15457 original size:108 final size:108
Alignment explanation
Indices: 15324--15751 Score: 678
Period size: 108 Copynumber: 3.9 Consensus size: 108
15314 TGGCGTTATG
* *
15324 GTGCAACCTTAAGAAATTCAAAATAATTTTATGAATTTTCGTATTGGCACTATGTGTGCAACCTA
1 GTGCAA-CTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACCTA
*
15389 AGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCAATGTGT
65 AGAAATTCATAATAAGTTTATGAATTTCCGTATTGGCAATGTGT
*
15433 GTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTAGCACTATGTGTGCAACCTAA
1 GTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACCTAA
* *
15498 GAAATTCATAATAAGGTTATGAATTTCCCTATTGG-AACTGTGT
66 GAAATTCATAATAAGTTTATGAATTTCCGTATTGGCAA-TGTGT
*
15541 GTGCAACTTAAGAAGTTCATAATAAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACCTAA
1 GTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACCTAA
*
15606 GAAATTCATAATAAGTTTATGAATTTCCGTATTGGCACTGTGT
66 GAAATTCATAATAAGTTTATGAATTTCCGTATTGGCAATGTGT
* * *
15649 GTGCAACTTAAGAAGTTCATAATAAGTTTATGAATTTTTGTATTGGCACTATGTGTGCAACCCAA
1 GTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACCTAA
* * * * *
15714 CGTAATTCATAATGAGTTTGTGAATTACCGTATCGGCA
66 -GAAATTCATAATAAGTTTATGAATTTCCGTATTGGCA
15752 CTACGTGTAC
Statistics
Matches: 298, Mismatches: 18, Indels: 6
0.93 0.06 0.02
Matches are distributed among these distances:
107 2 0.01
108 257 0.86
109 39 0.13
ACGTcount: A:0.33, C:0.13, G:0.18, T:0.36
Consensus pattern (108 bp):
GTGCAACTTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGCACTATGTGTGCAACCTAA
GAAATTCATAATAAGTTTATGAATTTCCGTATTGGCAATGTGT
Found at i:17663 original size:15 final size:15
Alignment explanation
Indices: 17643--17677 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
17633 TTCGTTTACT
17643 ACATCTTCTTCCACA
1 ACATCTTCTTCCACA
17658 ACATCTTCTTCCACA
1 ACATCTTCTTCCACA
17673 ACATC
1 ACATC
17678 CTCTCCAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.29, C:0.40, G:0.00, T:0.31
Consensus pattern (15 bp):
ACATCTTCTTCCACA
Found at i:18182 original size:36 final size:36
Alignment explanation
Indices: 18119--18188 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
18109 CTAACCCAAA
** * *
18119 TACACCAGCAGGCCCAATCAGTTCATCATTTGCCTC
1 TACACCAGCAGGCCCAAAAACTCCATCATTTGCCTC
*
18155 TACAGCAGCAGGCCCAAAAACTCCATCATTTGCC
1 TACACCAGCAGGCCCAAAAACTCCATCATTTGCC
18189 CTTAACCCAT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
36 29 1.00
ACGTcount: A:0.29, C:0.36, G:0.14, T:0.21
Consensus pattern (36 bp):
TACACCAGCAGGCCCAAAAACTCCATCATTTGCCTC
Found at i:18318 original size:21 final size:21
Alignment explanation
Indices: 18293--18336 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
18283 CACAATTATC
* *
18293 ACACCATCAACAATCTTATTA
1 ACACCATCAACAACCTTAGTA
*
18314 ACACCCTCAACAACCTTAGTA
1 ACACCATCAACAACCTTAGTA
18335 AC
1 AC
18337 TTATTCACAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.41, C:0.34, G:0.02, T:0.23
Consensus pattern (21 bp):
ACACCATCAACAACCTTAGTA
Found at i:18901 original size:47 final size:48
Alignment explanation
Indices: 18840--18950 Score: 156
Period size: 49 Copynumber: 2.3 Consensus size: 48
18830 TCATGATGTA
18840 AAAGACAAAAATAAA-CTTAAAT-AA-CACATGCTAACAAACAAAACTAT
1 AAAGA-AAAAATAAATC-TAAATGAACCACATGCTAACAAACAAAACTAT
*
18887 AAAGAAAAAGATAAATCTACATGAACCACATGCTAACAAACAAAACTAT
1 AAAGAAAAA-ATAAATCTAAATGAACCACATGCTAACAAACAAAACTAT
*
18936 AAAGAAAATATAAAT
1 AAAGAAAAAATAAAT
18951 ACAAGTACAC
Statistics
Matches: 58, Mismatches: 2, Indels: 7
0.87 0.03 0.10
Matches are distributed among these distances:
46 4 0.07
47 14 0.24
48 9 0.16
49 31 0.53
ACGTcount: A:0.61, C:0.15, G:0.06, T:0.17
Consensus pattern (48 bp):
AAAGAAAAAATAAATCTAAATGAACCACATGCTAACAAACAAAACTAT
Found at i:18968 original size:48 final size:48
Alignment explanation
Indices: 18840--18969 Score: 153
Period size: 49 Copynumber: 2.7 Consensus size: 48
18830 TCATGATGTA
*
18840 AAAGACAAAA-ATAAACTTA-AATAA-CACATGCTAACAAACAAAACTAT
1 AAAGA-AAAAGATAAAC-TACAAGAACCACATGCTAACAAACAAAACTAT
*
18887 AAAGAAAAAGATAAATCTACATGAACCACATGCTAACAAACAAAACTAT
1 AAAGAAAAAGATAAA-CTACAAGAACCACATGCTAACAAACAAAACTAT
*
18936 AAAG-AAAATATAAA-TACAAGTACACCACATGCTA
1 AAAGAAAAAGATAAACTACAAG-A-ACCACATGCTA
18970 CCTCAAATCA
Statistics
Matches: 73, Mismatches: 4, Indels: 11
0.83 0.05 0.12
Matches are distributed among these distances:
46 9 0.12
47 13 0.18
48 24 0.33
49 27 0.37
ACGTcount: A:0.58, C:0.18, G:0.07, T:0.17
Consensus pattern (48 bp):
AAAGAAAAAGATAAACTACAAGAACCACATGCTAACAAACAAAACTAT
Found at i:19085 original size:16 final size:16
Alignment explanation
Indices: 19064--19123 Score: 70
Period size: 16 Copynumber: 3.8 Consensus size: 16
19054 CTCTTAAACT
*
19064 AAACAATATGTTATAG
1 AAACAATATATTATAG
*
19080 AAACAATATATTATAT
1 AAACAATATATTATAG
*
19096 AAACAACTATA--ATTG
1 AAACAA-TATATTATAG
19111 AAACAATATATTA
1 AAACAATATATTA
19124 AACCGTGAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 6
0.79 0.09 0.13
Matches are distributed among these distances:
14 4 0.11
15 8 0.22
16 21 0.57
17 4 0.11
ACGTcount: A:0.55, C:0.08, G:0.05, T:0.32
Consensus pattern (16 bp):
AAACAATATATTATAG
Found at i:24428 original size:3 final size:3
Alignment explanation
Indices: 24416--24475 Score: 68
Period size: 3 Copynumber: 20.0 Consensus size: 3
24406 ACCCATTTTT
* *
24416 TTA TTG TTA TTA TAA TTA TTA TT- TTA TTTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
**
24461 AAA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA
24476 CAAACAAGCT
Statistics
Matches: 47, Mismatches: 8, Indels: 4
0.80 0.14 0.07
Matches are distributed among these distances:
2 2 0.04
3 42 0.89
4 3 0.06
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (3 bp):
TTA
Found at i:26310 original size:11 final size:13
Alignment explanation
Indices: 26273--26312 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 13
26263 TGTTTAATAA
26273 AATATA-TATATT
1 AATATATTATATT
*
26285 AATATATTATCTT
1 AATATATTATATT
26298 AA-A-ATTATATT
1 AATATATTATATT
26309 AATA
1 AATA
26313 AACTTTACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 8 0.33
13 7 0.29
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
AATATATTATATT
Found at i:28419 original size:12 final size:13
Alignment explanation
Indices: 28402--28430 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
28392 ACATTCACAT
28402 ATTTACA-TTTGC
1 ATTTACATTTTGC
28414 ATTTACATTTTGC
1 ATTTACATTTTGC
28427 ATTT
1 ATTT
28431 TTTCCATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 7 0.44
13 9 0.56
ACGTcount: A:0.24, C:0.14, G:0.07, T:0.55
Consensus pattern (13 bp):
ATTTACATTTTGC
Found at i:30429 original size:25 final size:25
Alignment explanation
Indices: 30396--30472 Score: 106
Period size: 25 Copynumber: 3.2 Consensus size: 25
30386 CTATACTCAT
*
30396 AAAAAAAAGGAAAAAAGAAAAAGGA
1 AAAAAAAAGGAAAAAAGAAAAAAGA
30421 AAAAAAAAGGAAAAAAGAAAAAAGA
1 AAAAAAAAGGAAAAAAGAAAAAAGA
*
30446 AAAAAGAAA--AAAGAA-AAAAAAGA
1 AAAAA-AAAGGAAAAAAGAAAAAAGA
30469 AAAA
1 AAAA
30473 TTGAATCAAG
Statistics
Matches: 49, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
23 12 0.24
24 5 0.10
25 29 0.59
26 3 0.06
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (25 bp):
AAAAAAAAGGAAAAAAGAAAAAAGA
Found at i:30471 original size:14 final size:13
Alignment explanation
Indices: 30396--30471 Score: 82
Period size: 14 Copynumber: 5.7 Consensus size: 13
30386 CTATACTCAT
*
30396 AAAAAAAAGGAAA
1 AAAAAAAAAGAAA
* *
30409 AAAGAAAAAG-GA
1 AAAAAAAAAGAAA
*
30421 AAAAAAAAGGAAA
1 AAAAAAAAAGAAA
30434 AAAGAAAAAAGAAA
1 AAA-AAAAAAGAAA
30448 AAAGAAAAAAGAAA
1 AAA-AAAAAAGAAA
30462 AAAAAGAAAA
1 AAAAA-AAAA
30472 ATTGAATCAA
Statistics
Matches: 53, Mismatches: 7, Indels: 5
0.82 0.11 0.08
Matches are distributed among these distances:
12 9 0.17
13 14 0.26
14 30 0.57
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (13 bp):
AAAAAAAAAGAAA
Found at i:30472 original size:7 final size:7
Alignment explanation
Indices: 30398--30464 Score: 86
Period size: 7 Copynumber: 9.9 Consensus size: 7
30388 ATACTCATAA
30398 AAAAAAGG
1 AAAAAA-G
30406 AAAAAAG
1 AAAAAAG
30413 -AAAAAG
1 AAAAAAG
*
30419 -GAAAA-
1 AAAAAAG
*
30424 AAAAAGG
1 AAAAAAG
30431 AAAAAAG
1 AAAAAAG
30438 AAAAAAG
1 AAAAAAG
30445 AAAAAAG
1 AAAAAAG
30452 AAAAAAG
1 AAAAAAG
30459 AAAAAA
1 AAAAAA
30465 AAGAAAAATT
Statistics
Matches: 53, Mismatches: 4, Indels: 5
0.85 0.06 0.08
Matches are distributed among these distances:
6 13 0.25
7 34 0.64
8 6 0.11
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (7 bp):
AAAAAAG
Found at i:35867 original size:112 final size:112
Alignment explanation
Indices: 35619--36200 Score: 606
Period size: 112 Copynumber: 5.1 Consensus size: 112
35609 GCAAAGATTT
* * * *
35619 AAATCCATCACTTGATGGATCAATATTTCTAGACGAGTTCATAATGAGAAGAACTCATCTGAAGA
1 AAATTCATCACTTGATGGATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGA
* * *
35684 AGGAATAAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGCTC
66 AGGAA-GAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* *
35732 AAATCCATCACTTGATGGATCAACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGA
1 AAATTCATCACTTGATGGATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGA
* *
35797 AGGAAGAAGAAGTTCATAATGAGAAGAACTTGTTTAACCTTTTGCTC
66 AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * **
35844 GAATTCATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTGTCTGAA-
1 AAATTCATCACTTGATGGATCAACATTTCCAGA-AGAGTTCATAATGAGAAGAACTCATCTGAAG
* * *
35908 TAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTT
65 AAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
* * * *
35956 AAATTCATCACTTGATGGATCAACTTTTCCATAGAA-AGTTCATAATGAAAAGAACTCTTTTGAA
1 AAATTCATCACTTGATGGATCAACATTTCC--AGAAGAGTTCATAATGAGAAGAACTCATCTGAA
* * ** *
36020 GAAAGAAGAAAAAAGTTCATAATGAGAAGAGCTTGTTCGACCTTTTACATGACTTTGTCAC
64 GAAGGAAG-AAGAAGTTCATAATGAGAAGAATTTGTTCAACC-TTT---TG-C----T--C
*** * * * * *
36081 AGAAGGAGAT-A-TATCAT-CATCAACATTTCCAGAAGTGTTCATAATAAGAAGAACTCATTTGA
1 A-AA-TTCATCACT-TGATGGATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGA
36143 AG-AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACC--TTGC-C
63 AGAAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
36189 ATAATTCATCAC
1 A-AATTCATCAC
36201 ATATGAAACC
Statistics
Matches: 396, Mismatches: 51, Indels: 48
0.80 0.10 0.10
Matches are distributed among these distances:
107 2 0.01
108 5 0.01
112 165 0.42
113 98 0.25
114 31 0.08
115 4 0.01
116 2 0.01
118 2 0.01
119 2 0.01
122 29 0.07
123 10 0.03
124 25 0.06
125 13 0.03
126 6 0.02
127 2 0.01
ACGTcount: A:0.39, C:0.15, G:0.18, T:0.29
Consensus pattern (112 bp):
AAATTCATCACTTGATGGATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGA
AGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTTTTGCTC
Found at i:36170 original size:236 final size:223
Alignment explanation
Indices: 35624--36185 Score: 644
Period size: 226 Copynumber: 2.4 Consensus size: 223
35614 GATTTAAATC
* * * *
35624 CATCACTTGATGGATCAATATTTCTAGACGAGTTCATAATGAGAAGAACTCATCTGAAGAAGGAA
1 CATCACTTGATGCATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAG-AGGAA
* *
35689 TAAAGAAATTCATAATGAGAAGAATTTGTTTAACCTTTTGCTCAAATCCATCACTTGATGGATCA
65 -GAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCA
* * * *
35754 ACATTTCCAGAAGTGTTCATAATGAGAAGAACTCATCTGAAGAAGGAAGAAGAAGTTCATAATGA
129 ACATTTCCAGAAGAGTTCATAATGAAAAGAACTCATCTGAAGAAAGAAGAAAAAGTTCATAATGA
* *
35819 GAAGAACTTGTTTAACCTTTTGCTCGAATT
194 GAAGAACTTGTTCAACCTTTTACTCGAATT
* * ** *
35849 CATCACTTGATGGATCAACATTTCCAGAGAAAGTTCATAATGAGAAGAACTTGTCTGAATAGGAA
1 CATCACTTGATGCATCAACATTTCCAGA-AGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAA
* *
35914 GAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTTAAATTCATCACTTGATGGATCAA
65 GAAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAA
* * *
35979 CTTTTCCATAGAA-AGTTCATAATGAAAAGAACTCTTTTGAAGAAAGAAGAAAAAAGTTCATAAT
130 CATTTCC--AGAAGAGTTCATAATGAAAAGAACTCATCTGAAGAAAGAAG-AAAAAGTTCATAAT
* * *
36043 GAGAAGAGCTTGTTCGACCTTTTACAT-GACTT
192 GAGAAGAACTTGTTCAACCTTTTAC-TCGAATT
** * * *
36075 TGTCACAGAAGGAGATAT-ATCATCATCAACATTTCCAGAAGTGTTCATAATAAGAAGAACTCAT
1 CATCAC---------T-TGAT--GCATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCAT
* *
36139 TTGAAGAGGAAGAAGAAGTTCATAATGAGAAGAATTTGTTCAACCTT
54 CTGAAGAGGAAGAAGAAATTCATAATGAGAAGAATTTGTTCAACCTT
36186 GCCATAATTC
Statistics
Matches: 285, Mismatches: 35, Indels: 23
0.83 0.10 0.07
Matches are distributed among these distances:
224 67 0.24
225 62 0.22
226 72 0.25
227 1 0.00
235 3 0.01
236 65 0.23
237 15 0.05
ACGTcount: A:0.39, C:0.14, G:0.18, T:0.29
Consensus pattern (223 bp):
CATCACTTGATGCATCAACATTTCCAGAAGAGTTCATAATGAGAAGAACTCATCTGAAGAGGAAG
AAGAAATTCATAATGAGAAGAATTTGTTCAACCTTTTGCTCAAATCCATCACTTGATGGATCAAC
ATTTCCAGAAGAGTTCATAATGAAAAGAACTCATCTGAAGAAAGAAGAAAAAGTTCATAATGAGA
AGAACTTGTTCAACCTTTTACTCGAATT
Found at i:36557 original size:3 final size:3
Alignment explanation
Indices: 36543--36605 Score: 83
Period size: 3 Copynumber: 21.0 Consensus size: 3
36533 ACCCAATTTT
*
36543 TTA TTG TTA TTA TTA TTA TTA TT- TTA TTTA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA TTA TTA
**
36588 TTA AAA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA
36606 CAAACAGGCT
Statistics
Matches: 52, Mismatches: 6, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
2 2 0.04
3 47 0.90
4 3 0.06
ACGTcount: A:0.33, C:0.00, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:38017 original size:16 final size:16
Alignment explanation
Indices: 37996--38026 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
37986 TTTTACTTTC
*
37996 ATATATTTATGATTAT
1 ATATATTTATCATTAT
38012 ATATATTTATCATTA
1 ATATATTTATCATTA
38027 GTATTACTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.39, C:0.03, G:0.03, T:0.55
Consensus pattern (16 bp):
ATATATTTATCATTAT
Found at i:38082 original size:38 final size:36
Alignment explanation
Indices: 38040--38124 Score: 95
Period size: 34 Copynumber: 2.3 Consensus size: 36
38030 TTACTATTAT
*
38040 TATTTATTATTTATGTCAATATATATATATATAAATAA
1 TATTTATTATTTA-GTC-ATATAAATATATATAAATAA
*
38078 TATTTATCTA---AGTCTTATAAATATATATAAATAA
1 TATTTAT-TATTTAGTCATATAAATATATATAAATAA
38112 TATTTATTTATTT
1 TATTTA-TTATTT
38125 TATGAAAATC
Statistics
Matches: 40, Mismatches: 2, Indels: 11
0.75 0.04 0.21
Matches are distributed among these distances:
34 26 0.65
35 4 0.10
36 1 0.03
38 7 0.17
39 2 0.05
ACGTcount: A:0.42, C:0.04, G:0.02, T:0.52
Consensus pattern (36 bp):
TATTTATTATTTAGTCATATAAATATATATAAATAA
Found at i:38440 original size:11 final size:13
Alignment explanation
Indices: 38403--38442 Score: 50
Period size: 11 Copynumber: 3.3 Consensus size: 13
38393 TGTTTAATAA
38403 AATATA-TATATT
1 AATATATTATATT
*
38415 AATATATTATCTT
1 AATATATTATATT
38428 AA-A-ATTATATT
1 AATATATTATATT
38439 AATA
1 AATA
38443 AACTTTACAG
Statistics
Matches: 24, Mismatches: 2, Indels: 4
0.80 0.07 0.13
Matches are distributed among these distances:
11 9 0.38
12 8 0.33
13 7 0.29
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (13 bp):
AATATATTATATT
Found at i:44417 original size:18 final size:18
Alignment explanation
Indices: 44396--44431 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
44386 TATGTACCCT
*
44396 TATTATGATATATATTTA
1 TATTATGATATAGATTTA
44414 TATTATGATATAGATTTA
1 TATTATGATATAGATTTA
44432 GTTTTTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.39, C:0.00, G:0.08, T:0.53
Consensus pattern (18 bp):
TATTATGATATAGATTTA
Found at i:44884 original size:31 final size:31
Alignment explanation
Indices: 44849--44940 Score: 130
Period size: 31 Copynumber: 3.0 Consensus size: 31
44839 TTAACAGCCT
44849 AATGACCAAAATATAATGAATCGATAATATA
1 AATGACCAAAATATAATGAATCGATAATATA
* *
44880 AATGACCAAAATATAATAAATCAATAATATA
1 AATGACCAAAATATAATGAATCGATAATATA
* * * *
44911 AGTGACTAAAATGTAATGAATTGATAATAT
1 AATGACCAAAATATAATGAATCGATAATAT
44941 TAATAAGATG
Statistics
Matches: 53, Mismatches: 8, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
31 53 1.00
ACGTcount: A:0.54, C:0.08, G:0.10, T:0.28
Consensus pattern (31 bp):
AATGACCAAAATATAATGAATCGATAATATA
Found at i:53126 original size:21 final size:21
Alignment explanation
Indices: 53102--53145 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
53092 AGTAAATTTA
*
53102 TAAATATTATTT-ATATATTAT
1 TAAATAATATTTAATATA-TAT
53123 TAAATAATATTTAATATATAT
1 TAAATAATATTTAATATATAT
53144 TA
1 TA
53146 TTTATATGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 16 0.76
22 5 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (21 bp):
TAAATAATATTTAATATATAT
Found at i:65693 original size:19 final size:21
Alignment explanation
Indices: 65651--65701 Score: 70
Period size: 19 Copynumber: 2.5 Consensus size: 21
65641 GGAGTCTTTG
*
65651 TCCTTTGACCGTAAAATGTTT
1 TCCTTTGACCATAAAATGTTT
65672 TCCTTTGACCAT-AAAT-TTT
1 TCCTTTGACCATAAAATGTTT
*
65691 TCCTTTAACCA
1 TCCTTTGACCA
65702 AATATGGGAA
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 13 0.46
20 4 0.14
21 11 0.39
ACGTcount: A:0.25, C:0.24, G:0.08, T:0.43
Consensus pattern (21 bp):
TCCTTTGACCATAAAATGTTT
Found at i:68303 original size:18 final size:18
Alignment explanation
Indices: 68267--68304 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
68257 ATCCAACATC
* *
68267 GGGAGGGAAAACCCCTTG
1 GGGAGGGAAAAACCATTG
68285 GGGAGGGAAAAACCATTG
1 GGGAGGGAAAAACCATTG
68303 GG
1 GG
68305 AAGGTTATTT
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:0.32, C:0.16, G:0.42, T:0.11
Consensus pattern (18 bp):
GGGAGGGAAAAACCATTG
Found at i:71097 original size:68 final size:69
Alignment explanation
Indices: 71004--71141 Score: 190
Period size: 70 Copynumber: 2.0 Consensus size: 69
70994 GAATTATTCA
* * *
71004 TTAATATTCAAACTCTAAAATGATAATATA-TTTTAATTTGCAATATTCAAAAAGATATTGATAT
1 TTAATATTCAAACTCTAAAAAGATAAAATACTTTTAATTTGCAATATTAAAAAAGATATTGATAT
71068 CTTT
66 CTTT
* * *
71072 TTAATATTCAAA-TTTAAAAAAGATAAAATACTTTTTAATTTGGAATATTAAAAAAGATGTTGAT
1 TTAATATTCAAACTCT-AAAAAGATAAAATAC-TTTTAATTTGCAATATTAAAAAAGATATTGAT
71136 ATCTTT
64 ATCTTT
71142 AATATATTTT
Statistics
Matches: 61, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
67 2 0.03
68 24 0.39
70 35 0.57
ACGTcount: A:0.44, C:0.07, G:0.07, T:0.42
Consensus pattern (69 bp):
TTAATATTCAAACTCTAAAAAGATAAAATACTTTTAATTTGCAATATTAAAAAAGATATTGATAT
CTTT
Found at i:71123 original size:34 final size:36
Alignment explanation
Indices: 71034--71129 Score: 108
Period size: 34 Copynumber: 2.7 Consensus size: 36
71024 TGATAATATA
* * **
71034 TTTTAATTTGCAATATTCAAAAAGATATTGATATCT
1 TTTTAATTTGAAATATTAAAAAAGATATAAATATCT
*
71070 TTTTAATATTCAAAT-TTAAAAAAGATA-AAATA-CT
1 TTTTAAT-TTGAAATATTAAAAAAGATATAAATATCT
*
71104 TTTTAATTTGGAATATTAAAAAAGAT
1 TTTTAATTTGAAATATTAAAAAAGAT
71130 GTTGATATCT
Statistics
Matches: 51, Mismatches: 7, Indels: 6
0.80 0.11 0.09
Matches are distributed among these distances:
33 5 0.10
34 20 0.39
35 3 0.06
36 18 0.35
37 5 0.10
ACGTcount: A:0.46, C:0.05, G:0.07, T:0.42
Consensus pattern (36 bp):
TTTTAATTTGAAATATTAAAAAAGATATAAATATCT
Found at i:71143 original size:34 final size:33
Alignment explanation
Indices: 71031--71144 Score: 88
Period size: 34 Copynumber: 3.3 Consensus size: 33
71021 AAATGATAAT
* *
71031 ATAT-TTTAATTTGCAATATTCAAAAAGATATTG
1 ATATCTTTAATTTGAAATATTAAAAAAGAT-TTG
* ***
71064 ATATCTTTTTAATATTCAAAT-TTAAAAAAGATAAA
1 ATATC--TTTAAT-TTGAAATATTAAAAAAGATTTG
* *
71099 ATACTTTTTAATTTGGAATATTAAAAAAGATGTTG
1 ATA-TCTTTAATTTGAAATATTAAAAAAGAT-TTG
71134 ATATCTTTAAT
1 ATATCTTTAAT
71145 ATATTTTTAA
Statistics
Matches: 61, Mismatches: 13, Indels: 13
0.70 0.15 0.15
Matches are distributed among these distances:
33 9 0.15
34 24 0.39
35 6 0.10
36 17 0.28
37 5 0.08
ACGTcount: A:0.44, C:0.05, G:0.08, T:0.43
Consensus pattern (33 bp):
ATATCTTTAATTTGAAATATTAAAAAAGATTTG
Found at i:71144 original size:68 final size:67
Alignment explanation
Indices: 71004--71146 Score: 182
Period size: 68 Copynumber: 2.1 Consensus size: 67
70994 GAATTATTCA
* * *
71004 TTAATATTCAAACTCTAAAATGATAATATATTTTAATTTGCAATATTCAAAAAGATATTGATATC
1 TTAATATTCAAACTCTAAAAAGATAAAATATTTTAATTTGCAATATTAAAAAAGATATTGATATC
71069 TTT
66 -TT
* * *
71072 TTAATATTCAAA-TTTAAAAAAGATAAAATACTTTTTAATTTGGAATATTAAAAAAGATGTTGAT
1 TTAATATTCAAACTCT-AAAAAGATAAAATA--TTTTAATTTGCAATATTAAAAAAGATATTGAT
71136 ATC-T
63 ATCTT
71140 TTAATAT
1 TTAATAT
71147 ATTTTTAATA
Statistics
Matches: 66, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
67 2 0.03
68 32 0.48
70 32 0.48
ACGTcount: A:0.45, C:0.06, G:0.07, T:0.42
Consensus pattern (67 bp):
TTAATATTCAAACTCTAAAAAGATAAAATATTTTAATTTGCAATATTAAAAAAGATATTGATATC
TT
Found at i:71189 original size:35 final size:34
Alignment explanation
Indices: 71141--71287 Score: 93
Period size: 35 Copynumber: 4.1 Consensus size: 34
71131 TTGATATCTT
*
71141 TAATATAT-TTTTAATATTTAAATTTAAAAAGTTTA
1 TAAT-TATCTTTTAATATTTAAATTTAAAAAG-ATA
* *
71176 TAATTATCTTTTAAT-TTGATATATTTAAAATGATA
1 TAATTATCTTTTAATATT--TAAATTTAAAAAGATA
* * * *
71211 TAATTATCTTACTAATATTCAAATGTAAAGAGATCA
1 TAATTATCTT-TTAATATTTAAATTTAAAAAGAT-A
* * * *
71247 TAAATGTATTTTAAT-TTAGAATATTTAAAAAGATA
1 TAATTATCTTTTAATATT-TAA-ATTTAAAAAGATA
71282 TGAATT
1 T-AATT
71288 TAATTTAATT
Statistics
Matches: 86, Mismatches: 17, Indels: 17
0.72 0.14 0.14
Matches are distributed among these distances:
34 7 0.08
35 41 0.48
36 36 0.42
37 2 0.02
ACGTcount: A:0.44, C:0.03, G:0.07, T:0.46
Consensus pattern (34 bp):
TAATTATCTTTTAATATTTAAATTTAAAAAGATA
Found at i:71229 original size:71 final size:72
Alignment explanation
Indices: 71152--71287 Score: 168
Period size: 71 Copynumber: 1.9 Consensus size: 72
71142 AATATATTTT
* * * * * * *
71152 TAATATTTAAATTTAAAAAGTTTATAATTATCTTTTAATTT-GATATATTTAAAATGATAT-AAT
1 TAATATTCAAATGTAAAAAGATCATAAATATATTTTAATTTAGA-ATATTTAAAAAGATATGAAT
71215 TATCTTAC
65 TATCTTAC
* *
71223 TAATATTCAAATGTAAAGAGATCATAAATGTATTTTAATTTAGAATATTTAAAAAGATATGAATT
1 TAATATTCAAATGTAAAAAGATCATAAATATATTTTAATTTAGAATATTTAAAAAGATATGAATT
71288 TAATTTAATT
Statistics
Matches: 54, Mismatches: 9, Indels: 3
0.82 0.14 0.05
Matches are distributed among these distances:
71 48 0.89
72 6 0.11
ACGTcount: A:0.45, C:0.04, G:0.07, T:0.44
Consensus pattern (72 bp):
TAATATTCAAATGTAAAAAGATCATAAATATATTTTAATTTAGAATATTTAAAAAGATATGAATT
ATCTTAC
Found at i:72649 original size:20 final size:20
Alignment explanation
Indices: 72600--72650 Score: 59
Period size: 21 Copynumber: 2.5 Consensus size: 20
72590 CGATCTCTTG
* *
72600 GTAAAAGGATTGATCCCTTT
1 GTAAAAGGATTGACCCCATT
72620 G-ACCAAAGGATTGACCCCATT
1 GTA--AAAGGATTGACCCCATT
72641 GTAAAAGGAT
1 GTAAAAGGAT
72651 CAATCCCTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
19 1 0.04
20 8 0.31
21 16 0.62
22 1 0.04
ACGTcount: A:0.35, C:0.18, G:0.22, T:0.25
Consensus pattern (20 bp):
GTAAAAGGATTGACCCCATT
Found at i:72703 original size:20 final size:21
Alignment explanation
Indices: 72677--72725 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
72667 AGAAAGTTTG
* *
72677 GGATCGATCTCTTCA-CAAAA
1 GGATCGATCCCTCCACCAAAA
*
72697 TGATCGATCCCTCCACCAAAA
1 GGATCGATCCCTCCACCAAAA
72718 GGATCGAT
1 GGATCGAT
72726 TCCTTCCCTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.22
Consensus pattern (21 bp):
GGATCGATCCCTCCACCAAAA
Found at i:72841 original size:41 final size:41
Alignment explanation
Indices: 72740--72860 Score: 155
Period size: 41 Copynumber: 3.1 Consensus size: 41
72730 TCCCTTAAAG
* * *
72740 GATCAATCCCTTTCTTGCAGCGGCCAAATTATTTG--AAAC
1 GATCAATCCCTTTCTTGCAACAGTCAAATTATTTGAAAAAC
*
72779 GAT-AA---CTTTCTTGCAACAGTCAAATTATTTGAAAAAT
1 GATCAATCCCTTTCTTGCAACAGTCAAATTATTTGAAAAAC
*
72816 GATCAATCCCTTTCTTGCAACAGTCAAATTATTTGAAAAAG
1 GATCAATCCCTTTCTTGCAACAGTCAAATTATTTGAAAAAC
72857 GATC
1 GATC
72861 GATATCTTAT
Statistics
Matches: 71, Mismatches: 5, Indels: 10
0.83 0.06 0.12
Matches are distributed among these distances:
35 23 0.32
37 6 0.08
38 4 0.06
39 3 0.04
41 35 0.49
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (41 bp):
GATCAATCCCTTTCTTGCAACAGTCAAATTATTTGAAAAAC
Found at i:75971 original size:59 final size:60
Alignment explanation
Indices: 75866--75985 Score: 138
Period size: 59 Copynumber: 2.0 Consensus size: 60
75856 CTCAAGGAAT
* * *
75866 AAATTCAAAGATTTAATTTCTTTTACAAAACAAAATCATATAAGA-TTCTATGAAAATAA
1 AAATTCAAAGATTTAATTTCTTTTACAAAACAAAATAATATAAGATTTCCAAGAAAATAA
** * *
75925 AAATTCAACA-ATTT-ATTTCTTTCTACAAAATGAAATAATTTTAGATTTCCAAGAAAATAA
1 AAATTCAA-AGATTTAATTTCTTT-TACAAAACAAAATAATATAAGATTTCCAAGAAAATAA
75985 A
1 A
75986 TTTGACGATT
Statistics
Matches: 51, Mismatches: 7, Indels: 5
0.81 0.11 0.08
Matches are distributed among these distances:
58 8 0.16
59 29 0.57
60 14 0.27
ACGTcount: A:0.49, C:0.11, G:0.05, T:0.35
Consensus pattern (60 bp):
AAATTCAAAGATTTAATTTCTTTTACAAAACAAAATAATATAAGATTTCCAAGAAAATAA
Found at i:75997 original size:58 final size:57
Alignment explanation
Indices: 75923--76115 Score: 160
Period size: 58 Copynumber: 3.4 Consensus size: 57
75913 CTATGAAAAT
* * **
75923 AAAAATTCAACAATTTATTT-CTTTCTACAAAAT-GAAATAATTTTAGATTTCC-AAGAA
1 AAAAATTCAACGATTTATTTCCCTT-TACAAAATAG-AATAATTCAAGA-TTCCTAAGAA
** *
75980 AATAAATTTGACGATTTATTTCCCTTTACAAAATAGAATCATTCAAGATTCCTAAGAA
1 AA-AAATTCAACGATTTATTTCCCTTTACAAAATAGAATAATTCAAGATTCCTAAGAA
** ** * *
76038 AAAAATTCAACGATTTATTTTTCTTCGCAAAATAGAATCACTT-AAGGTTCCTAAGAA
1 AAAAATTCAACGATTTATTTCCCTTTACAAAATAGAAT-AATTCAAGATTCCTAAGAA
* **
76095 ACTAAATTCAATAATTTATTT
1 A-AAAATTCAACGATTTATTT
76116 TTCCTATAAA
Statistics
Matches: 111, Mismatches: 19, Indels: 11
0.79 0.13 0.08
Matches are distributed among these distances:
57 50 0.45
58 57 0.51
59 4 0.04
ACGTcount: A:0.42, C:0.14, G:0.07, T:0.36
Consensus pattern (57 bp):
AAAAATTCAACGATTTATTTCCCTTTACAAAATAGAATAATTCAAGATTCCTAAGAA
Found at i:76069 original size:57 final size:56
Alignment explanation
Indices: 75791--76117 Score: 202
Period size: 57 Copynumber: 5.7 Consensus size: 56
75781 TACAAACATA
** * *
75791 TCAAGATTTGTAAGAAATAAATTCAACGATTTATTTCTTTTTACAAAATAGAATCAT
1 TCAAGATTCCTAAGAAAAAAATTCAACGATTTATTT-TTTTCACAAAATAGAATCAT
* *** * * * * *
75848 ACTTTATT-CTCAAGGAATAAATTCAAAGATTTAATTTCTTTT-ACAAAACAAAATCAT
1 TCAAGATTCCT-AAGAAAAAAATTCAACGATTT-ATTT-TTTTCACAAAATAGAATCAT
* * * *
75905 AT-AAGATT-CTATGAAAATAAAAATTCAACAATTTATTTCTTTCTACAAAAT-GAAATAAT
1 -TCAAGATTCCTA--AGAA-AAAAATTCAACGATTTATTTTTTTC-ACAAAATAG-AATCAT
** ** *
75964 TTTAGATTTCC-AAGAAAATAAATTTGACGATTTATTTCCCTTT-ACAAAATAGAATCAT
1 TCAAGA-TTCCTAAGAAAA-AAATTCAACGATTTATTT--TTTTCACAAAATAGAATCAT
*
76022 TCAAGATTCCTAAGAAAAAAATTCAACGATTTATTTTTCTTCGCAAAATAGAATCACT
1 TCAAGATTCCTAAGAAAAAAATTCAACGATTTATTTTT-TTCACAAAATAGAATCA-T
* * **
76080 T-AAGGTTCCTAAGAAACTAAATTCAATAATTTATTTTT
1 TCAAGATTCCTAAGAAA-AAAATTCAACGATTTATTTTT
76118 CCTATAAAGT
Statistics
Matches: 211, Mismatches: 38, Indels: 41
0.73 0.13 0.14
Matches are distributed among these distances:
55 1 0.00
56 4 0.02
57 93 0.44
58 77 0.36
59 28 0.13
60 7 0.03
61 1 0.00
ACGTcount: A:0.43, C:0.13, G:0.07, T:0.37
Consensus pattern (56 bp):
TCAAGATTCCTAAGAAAAAAATTCAACGATTTATTTTTTTCACAAAATAGAATCAT
Found at i:76132 original size:58 final size:57
Alignment explanation
Indices: 76007--76177 Score: 159
Period size: 58 Copynumber: 2.9 Consensus size: 57
75997 ATTTCCCTTT
* ** *
76007 ACAAAATAGAATCA-TTCAAGATTCCTAAGAAAAAAATTCAACGATTTATTTTTCTTC
1 ACAAAATAGAATCACTT-AAGATTCCTAAGAAATAAATTCAATAATTTATTTTTCCTC
* *
76064 GCAAAATAGAATCACTTAAGGTTCCTAAGAAACTAAATTCAATAATTTATTTTTCCT-
1 ACAAAATAGAATCACTTAAGATTCCTAAGAAA-TAAATTCAATAATTTATTTTTCCTC
* * * **
76121 ATAAAGTTAGAAGCAACGCAAGATT-CTAAGGTGAAATAAATTCAATAATTTATTTTT
1 ACAAA-ATAGAATC-ACTTAAGATTCCTAA---GAAATAAATTCAATAATTTATTTTT
76178 TTTTCAGTGT
Statistics
Matches: 94, Mismatches: 13, Indels: 11
0.80 0.11 0.09
Matches are distributed among these distances:
57 30 0.32
58 32 0.34
59 7 0.07
60 21 0.22
61 4 0.04
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (57 bp):
ACAAAATAGAATCACTTAAGATTCCTAAGAAATAAATTCAATAATTTATTTTTCCTC
Found at i:80013 original size:3 final size:3
Alignment explanation
Indices: 79997--80049 Score: 81
Period size: 3 Copynumber: 17.7 Consensus size: 3
79987 CGAGTGACAT
*
79997 TTA TTA -TA TATA TTA TTA TTA TTA TTA TTA TTA TTA TTC TTA TTA
1 TTA TTA TTA T-TA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
80042 TTA TTA TT
1 TTA TTA TT
80050 TACAAAGCCT
Statistics
Matches: 46, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
2 2 0.04
3 41 0.89
4 3 0.07
ACGTcount: A:0.32, C:0.02, G:0.00, T:0.66
Consensus pattern (3 bp):
TTA
Found at i:84827 original size:63 final size:65
Alignment explanation
Indices: 84707--84829 Score: 189
Period size: 64 Copynumber: 1.9 Consensus size: 65
84697 TGCACTAAGA
* * *
84707 GTGCATCGATGCATAAAATGCATTCGATGTTTTTAAACAAGCCTGAGTGCATCGATGCATGGTAT
1 GTGCATCGACGCATAAAATGCAATCGATGTTTTCAAACAAGCCTGAGTGCATCGATGCATGGTAT
84772 GTGCATCGACGCAT-AAATGCAATCGATGTTTTCATAA-AA-CCTGAGTGCATCGATGCAT
1 GTGCATCGACGCATAAAATGCAATCGATGTTTTCA-AACAAGCCTGAGTGCATCGATGCAT
84830 AAAATGCATT
Statistics
Matches: 54, Mismatches: 3, Indels: 4
0.89 0.05 0.07
Matches are distributed among these distances:
63 19 0.35
64 20 0.37
65 15 0.28
ACGTcount: A:0.30, C:0.19, G:0.22, T:0.29
Consensus pattern (65 bp):
GTGCATCGACGCATAAAATGCAATCGATGTTTTCAAACAAGCCTGAGTGCATCGATGCATGGTAT
Done.