Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001114.1 Hibiscus syriacus cultivar Beakdansim tig00002198_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: 109882
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:131 original size:24 final size:24
Alignment explanation
Indices: 91--136 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
81 GGCTATTGGT
91 ATATATTATAGATGTTTTGAAAAC
1 ATATATTATAGATGTTTTGAAAAC
*
115 ATATA-TATATATGGTTTTGAAA
1 ATATATTATAGAT-GTTTTGAAA
137 GTATTTTCGA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 6 0.30
24 14 0.70
ACGTcount: A:0.41, C:0.02, G:0.13, T:0.43
Consensus pattern (24 bp):
ATATATTATAGATGTTTTGAAAAC
Found at i:1263 original size:19 final size:17
Alignment explanation
Indices: 1239--1281 Score: 59
Period size: 19 Copynumber: 2.4 Consensus size: 17
1229 CATTAAATTA
*
1239 TTTATTTAATTATTTTCTT
1 TTTATTTAATT-TTATC-T
1258 TTTATTTAATTTTATCT
1 TTTATTTAATTTTATCT
1275 TTTATTT
1 TTTATTT
1282 TAAAAACAAC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
17 8 0.35
18 4 0.17
19 11 0.48
ACGTcount: A:0.21, C:0.05, G:0.00, T:0.74
Consensus pattern (17 bp):
TTTATTTAATTTTATCT
Found at i:1283 original size:18 final size:19
Alignment explanation
Indices: 1239--1284 Score: 53
Period size: 18 Copynumber: 2.5 Consensus size: 19
1229 CATTAAATTA
*
1239 TTTA-TTTAATTATTTTCT
1 TTTATTTTAATTATTATCT
1257 TTT-TATTTAATT-TTATCT
1 TTTAT-TTTAATTATTATCT
1275 TTTATTTTAA
1 TTTATTTTAA
1285 AAACAACTTT
Statistics
Matches: 24, Mismatches: 1, Indels: 6
0.77 0.03 0.19
Matches are distributed among these distances:
18 16 0.67
19 8 0.33
ACGTcount: A:0.24, C:0.04, G:0.00, T:0.72
Consensus pattern (19 bp):
TTTATTTTAATTATTATCT
Found at i:1385 original size:28 final size:27
Alignment explanation
Indices: 1322--1396 Score: 71
Period size: 28 Copynumber: 2.7 Consensus size: 27
1312 TTTACTACTA
* *
1322 TTATTTATTATTTTATTATATTTCCCT
1 TTATTTATTATTTTTTTATATTACCCT
*
1349 TTATATTATTATTTTTTTATA-TACCTT
1 TTAT-TTATTATTTTTTTATATTACCCT
* *
1376 TTCAATTTATTACTATTTTAT
1 TT--ATTTATTATTTTTTTAT
1397 GTTTATTTTA
Statistics
Matches: 40, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
27 10 0.25
28 28 0.70
29 2 0.05
ACGTcount: A:0.25, C:0.09, G:0.00, T:0.65
Consensus pattern (27 bp):
TTATTTATTATTTTTTTATATTACCCT
Found at i:1513 original size:36 final size:36
Alignment explanation
Indices: 1473--1541 Score: 129
Period size: 36 Copynumber: 1.9 Consensus size: 36
1463 AAAATTTAAA
*
1473 CACTTCTTTTTTTATTTTGTTTTATTTTTATTTTCC
1 CACTTCTTTATTTATTTTGTTTTATTTTTATTTTCC
1509 CACTTCTTTATTTATTTTGTTTTATTTTTATTT
1 CACTTCTTTATTTATTTTGTTTTATTTTTATTT
1542 CTATTTTAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
36 32 1.00
ACGTcount: A:0.13, C:0.12, G:0.03, T:0.72
Consensus pattern (36 bp):
CACTTCTTTATTTATTTTGTTTTATTTTTATTTTCC
Found at i:1561 original size:27 final size:26
Alignment explanation
Indices: 1531--1590 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 26
1521 TATTTTGTTT
* *
1531 TATTTTTATTTCTATTTTAAAATTTTA
1 TATTTTTATTTCT-TTCTAAAATTTAA
*
1558 TATTTATTATTTCTTTCTGAAATTTAA
1 TATTT-TTATTTCTTTCTAAAATTTAA
1585 TATTTT
1 TATTTT
1591 CTCATTTTTT
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
26 1 0.03
27 20 0.69
28 8 0.28
ACGTcount: A:0.28, C:0.05, G:0.02, T:0.65
Consensus pattern (26 bp):
TATTTTTATTTCTTTCTAAAATTTAA
Found at i:3269 original size:27 final size:27
Alignment explanation
Indices: 3231--3285 Score: 85
Period size: 27 Copynumber: 2.0 Consensus size: 27
3221 ATAAATTTCA
3231 CCTTAAGTGTAAAATGA-CCAAAATAC
1 CCTTAAGTGTAAAATGACCCAAAATAC
*
3257 CCTTGAAGTGTAAAATGACCCAAAGTAC
1 CCTT-AAGTGTAAAATGACCCAAAATAC
3285 C
1 C
3286 TCCAAGCCCG
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
26 4 0.15
27 13 0.50
28 9 0.35
ACGTcount: A:0.42, C:0.22, G:0.15, T:0.22
Consensus pattern (27 bp):
CCTTAAGTGTAAAATGACCCAAAATAC
Found at i:13975 original size:22 final size:22
Alignment explanation
Indices: 13949--13994 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
13939 GTAAATTTCT
**
13949 AAAATAAATATTATTAAAATAA
1 AAAATAAATAAAATTAAAATAA
* *
13971 AAAATATATAAAATTACAATAA
1 AAAATAAATAAAATTAAAATAA
13993 AA
1 AA
13995 TTTTAAATAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.70, C:0.02, G:0.00, T:0.28
Consensus pattern (22 bp):
AAAATAAATAAAATTAAAATAA
Found at i:14075 original size:29 final size:28
Alignment explanation
Indices: 14008--14130 Score: 96
Period size: 29 Copynumber: 4.4 Consensus size: 28
13998 TAAATATTTA
*
14008 TATAAATTACAATAAA-AGTC--AACTTT
1 TATAAATTACAATAAATA-CCAAAACTTT
14034 T-TAATATTACAATAAATACCAAAACTATT
1 TATAA-ATTACAATAAATACCAAAACT-TT
* *
14063 TATAAATTACAATCAATGA-AAAAACTTCT
1 TATAAATTACAATAAAT-ACCAAAACTT-T
* * *
14092 CATAAATTACAAT-AATACCTATAATTTT
1 TATAAATTACAATAAATACC-AAAACTTT
14120 TATAAATTACA
1 TATAAATTACA
14131 TGAAAAGGTC
Statistics
Matches: 79, Mismatches: 8, Indels: 18
0.75 0.08 0.17
Matches are distributed among these distances:
25 3 0.04
26 13 0.16
27 2 0.03
28 19 0.24
29 38 0.48
30 4 0.05
ACGTcount: A:0.50, C:0.13, G:0.02, T:0.35
Consensus pattern (28 bp):
TATAAATTACAATAAATACCAAAACTTT
Found at i:15667 original size:22 final size:22
Alignment explanation
Indices: 15610--15668 Score: 75
Period size: 21 Copynumber: 2.7 Consensus size: 22
15600 ACGCGATTCT
15610 GACTATCGCATTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
* * *
15632 AAAT-TCGCGTTGCGATTTTCC
1 GACTATCGCATTGCGATTTTCC
*
15653 GACTATCGCAATGCGA
1 GACTATCGCATTGCGA
15669 ATATGTAAAT
Statistics
Matches: 29, Mismatches: 7, Indels: 2
0.76 0.18 0.05
Matches are distributed among these distances:
21 18 0.62
22 11 0.38
ACGTcount: A:0.22, C:0.25, G:0.20, T:0.32
Consensus pattern (22 bp):
GACTATCGCATTGCGATTTTCC
Found at i:15682 original size:20 final size:20
Alignment explanation
Indices: 15657--15708 Score: 86
Period size: 20 Copynumber: 2.6 Consensus size: 20
15647 TTTTCCGACT
15657 ATCGCAATGCGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
15677 ATCGCAATACGAATATGTAA
1 ATCGCAATGCGAATATGTAA
*
15697 ATTGCAATGCGA
1 ATCGCAATGCGA
15709 TTCTGACTAT
Statistics
Matches: 29, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 29 1.00
ACGTcount: A:0.40, C:0.15, G:0.19, T:0.25
Consensus pattern (20 bp):
ATCGCAATGCGAATATGTAA
Found at i:15723 original size:20 final size:20
Alignment explanation
Indices: 15700--15796 Score: 131
Period size: 20 Copynumber: 4.8 Consensus size: 20
15690 TATGTAAATT
15700 GCAATGCGATTCTGACTATC
1 GCAATGCGATTCTGACTATC
*
15720 GCAATGCAATTCTGACTATC
1 GCAATGCGATTCTGACTATC
15740 GCAATGCGATTCTGACTATC
1 GCAATGCGATTCTGACTATC
*** *
15760 GCAACATGATTCTGACTGTC
1 GCAATGCGATTCTGACTATC
* *
15780 GCAAAGTGATTCTGACT
1 GCAATGCGATTCTGACT
15797 GTTGCAACAC
Statistics
Matches: 69, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 69 1.00
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.30
Consensus pattern (20 bp):
GCAATGCGATTCTGACTATC
Found at i:16657 original size:24 final size:24
Alignment explanation
Indices: 16625--16678 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
16615 GTATTCGAAA
16625 TTTGATCTTGGTCAATACCCGGAC
1 TTTGATCTTGGTCAATACCCGGAC
* *
16649 TTTGATCTTGGTCAATACTCGGAT
1 TTTGATCTTGGTCAATACCCGGAC
16673 TTTGAT
1 TTTGAT
16679 GATGTTTCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.41
Consensus pattern (24 bp):
TTTGATCTTGGTCAATACCCGGAC
Found at i:16897 original size:14 final size:14
Alignment explanation
Indices: 16868--16904 Score: 56
Period size: 14 Copynumber: 2.6 Consensus size: 14
16858 AGAAAAAGAA
16868 GAAGAAGAAATCCCC
1 GAAGAA-AAATCCCC
*
16883 GAAGAAAAGTCCCC
1 GAAGAAAAATCCCC
16897 GAAGAAAA
1 GAAGAAAA
16905 TGCCACGGGA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
14 15 0.71
15 6 0.29
ACGTcount: A:0.51, C:0.22, G:0.22, T:0.05
Consensus pattern (14 bp):
GAAGAAAAATCCCC
Found at i:18966 original size:18 final size:18
Alignment explanation
Indices: 18943--18977 Score: 61
Period size: 18 Copynumber: 1.9 Consensus size: 18
18933 AGAAAAAGGC
*
18943 AATCAAAATCGCAATCAA
1 AATCAAAATCCCAATCAA
18961 AATCAAAATCCCAATCA
1 AATCAAAATCCCAATCA
18978 CAACCGGCTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.54, C:0.26, G:0.03, T:0.17
Consensus pattern (18 bp):
AATCAAAATCCCAATCAA
Found at i:19289 original size:140 final size:140
Alignment explanation
Indices: 19037--19306 Score: 504
Period size: 140 Copynumber: 1.9 Consensus size: 140
19027 AAACGTTGTA
*
19037 TTATGTGTAAACTTTTAATATTTTCAGCTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGCTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
* *
19102 TGATATGTTCAGTTGTTATCACTTATTACGCATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATCTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
19167 TATGTGTATT
131 TATGTGTATT
*
19177 TTATGTGTAAACTTTTAACATTTTCAGTTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
1 TTATGTGTAAACTTTTAACATTTTCAGCTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
19242 TGATATCTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
66 TGATATCTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
19307 CATAACACGA
Statistics
Matches: 126, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
140 126 1.00
ACGTcount: A:0.29, C:0.14, G:0.16, T:0.42
Consensus pattern (140 bp):
TTATGTGTAAACTTTTAACATTTTCAGCTAGGCATGTATTAGTAACTTGAGTTTGAACATTGCTA
TGATATCTTCAGTTGTTATCACTTATTACACATTCATTTGAATATCGCAACGCGAATTTGACTAT
TATGTGTATT
Found at i:19302 original size:20 final size:20
Alignment explanation
Indices: 19277--19570 Score: 171
Period size: 20 Copynumber: 15.7 Consensus size: 20
19267 TTACACATTC
*
19277 ATTTGAATATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
** *
19297 ATTTGACTATCATAACACGA
1 ATTTGACTATCGCAACGCGA
* * *
19317 ATATGACTATCGTAATGC-A
1 ATTTGACTATCGCAACGCGA
*
19336 A----A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
19351 ATTTGTCTATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
19371 ATTTGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
* *
19391 ATTTGATTATCGCAACG-GCT
1 ATTTGACTATCGCAACGCG-A
* *
19411 ATTTGACTAGCGCAA--TG-
1 ATTTGACTATCGCAACGCGA
* *
19428 A-GT-A-AATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
19445 ATTTGACTATCGCAATGCGA
1 ATTTGACTATCGCAACGCGA
* *
19465 AATTGAGTATC-CTAACGCGA
1 ATTTGACTATCGC-AACGCGA
* * * *
19485 ATTTGATTATCGCAATGGGT
1 ATTTGACTATCGCAACGCGA
*
19505 ATTTGACTATCGCAACGAGA
1 ATTTGACTATCGCAACGCGA
* *
19525 A----A--ATCGCAAAGCGT
1 ATTTGACTATCGCAACGCGA
*
19539 ATTAGACTATCGCAACGCGA
1 ATTTGACTATCGCAACGCGA
*
19559 A-TTGACTTTCGC
1 ATTTGACTATCGC
19571 GTTGCGATTT
Statistics
Matches: 206, Mismatches: 46, Indels: 45
0.69 0.15 0.15
Matches are distributed among these distances:
14 24 0.12
15 4 0.02
16 3 0.01
17 2 0.01
18 2 0.01
19 15 0.07
20 155 0.75
21 1 0.00
ACGTcount: A:0.33, C:0.20, G:0.20, T:0.27
Consensus pattern (20 bp):
ATTTGACTATCGCAACGCGA
Found at i:19438 original size:94 final size:94
Alignment explanation
Indices: 19336--19570 Score: 330
Period size: 94 Copynumber: 2.5 Consensus size: 94
19326 TCGTAATGCA
*
19336 AAAATCGCAACGCGAATTTGTCTATCGCAATGCGAATTTGACTATCGC-AACGCGAATTTGATTA
1 AAAATCGCAACGCGAATTTGACTATCGCAATGCGAA-TTGACTATCGCTAACGCGAATTTGATTA
*
19400 TCGCAACGGCTATTTGACTAGCGCAATGAG
65 TCGCAACGGCTATTTGACTAGCGCAACGAG
* *
19430 TAAATCGCAACGCGAATTTGACTATCGCAATGCGAAATTGAGTATC-CTAACGCGAATTTGATTA
1 AAAATCGCAACGCGAATTTGACTATCGCAATGCG-AATTGACTATCGCTAACGCGAATTTGATTA
* * *
19494 TCGCAATGGGTATTTGACTATCGCAACGAG
65 TCGCAACGGCTATTTGACTAGCGCAACGAG
* * * * *
19524 AAAATCGCAAAGCGTATTAGACTATCGCAACGCGAATTGACTTTCGC
1 AAAATCGCAACGCGAATTTGACTATCGCAATGCGAATTGACTATCGC
19571 GTTGCGATTT
Statistics
Matches: 124, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
93 10 0.08
94 112 0.90
95 2 0.02
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.26
Consensus pattern (94 bp):
AAAATCGCAACGCGAATTTGACTATCGCAATGCGAATTGACTATCGCTAACGCGAATTTGATTAT
CGCAACGGCTATTTGACTAGCGCAACGAG
Found at i:19489 original size:74 final size:74
Alignment explanation
Indices: 19359--19501 Score: 191
Period size: 74 Copynumber: 1.9 Consensus size: 74
19349 GAATTTGTCT
* * * *
19359 ATCGCAATGCGAATTTGACTATCGCAACGCGAATTTGATTATCGCAACGGCTATTTGACTAGCGC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAAATTGAGTATCGCAACGGCAATTTGACTAGCGC
19424 AATGAGTAA
66 AATGAGTAA
* * *
19433 ATCGCAACGCGAATTTGACTATCGCAATGCGAAATTGAGTATC-CTAAC-GCGAATTTGATTATC
1 ATCGCAACGCGAATTTGACTATCGCAACGCGAAATTGAGTATCGC-AACGGC-AATTTGACTAGC
19496 GCAATG
64 GCAATG
19502 GGTATTTGAC
Statistics
Matches: 60, Mismatches: 7, Indels: 4
0.85 0.10 0.06
Matches are distributed among these distances:
73 3 0.05
74 57 0.95
ACGTcount: A:0.31, C:0.20, G:0.21, T:0.27
Consensus pattern (74 bp):
ATCGCAACGCGAATTTGACTATCGCAACGCGAAATTGAGTATCGCAACGGCAATTTGACTAGCGC
AATGAGTAA
Found at i:19615 original size:20 final size:20
Alignment explanation
Indices: 19560--19617 Score: 71
Period size: 20 Copynumber: 2.9 Consensus size: 20
19550 GCAACGCGAA
*
19560 TTGACTTTCGCGTTGCGATT
1 TTGACTTTAGCGTTGCGATT
* * *
19580 TTGTCTTTTGCATTGCGATT
1 TTGACTTTAGCGTTGCGATT
*
19600 TTGAGTTTAGCGTTGCGA
1 TTGACTTTAGCGTTGCGA
19618 AAGTGTACCT
Statistics
Matches: 31, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.12, C:0.16, G:0.26, T:0.47
Consensus pattern (20 bp):
TTGACTTTAGCGTTGCGATT
Found at i:19776 original size:14 final size:14
Alignment explanation
Indices: 19716--19777 Score: 61
Period size: 14 Copynumber: 4.3 Consensus size: 14
19706 CACAAATAAG
*
19716 AATTATTTACACATC
1 AATT-TTTACAAATC
**
19731 AATATTAAACAAATC
1 AAT-TTTTACAAATC
*
19746 AACTTTTACAAATC
1 AATTTTTACAAATC
*
19760 AATTTTTATAAATC
1 AATTTTTACAAATC
19774 AATT
1 AATT
19778 AAACAAGCAA
Statistics
Matches: 38, Mismatches: 8, Indels: 3
0.78 0.16 0.06
Matches are distributed among these distances:
14 25 0.66
15 12 0.32
16 1 0.03
ACGTcount: A:0.47, C:0.15, G:0.00, T:0.39
Consensus pattern (14 bp):
AATTTTTACAAATC
Found at i:21784 original size:20 final size:20
Alignment explanation
Indices: 21759--21829 Score: 115
Period size: 20 Copynumber: 3.5 Consensus size: 20
21749 TTGCAACACG
*
21759 AATGACTATCGCAACGTGAA
1 AATGACTATCGCAACGCGAA
21779 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
21799 AATGACTATCGCAACGCGAA
1 AATGACTATCGCAACGCGAA
**
21819 TTTGACTATCG
1 AATGACTATCG
21830 TAATGAGAGA
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 48 1.00
ACGTcount: A:0.37, C:0.23, G:0.20, T:0.21
Consensus pattern (20 bp):
AATGACTATCGCAACGCGAA
Found at i:23839 original size:20 final size:20
Alignment explanation
Indices: 23816--23922 Score: 110
Period size: 20 Copynumber: 5.5 Consensus size: 20
23806 TCTGAAACTT
*
23816 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
*
23836 AAAATCGCAACACGAAAATG
1 AAAATCGCAACGCGAAAATG
** **
23856 ACTATCGCAACGCGAATTTG
1 AAAATCGCAACGCGAAAATG
**
23876 ACTATCGCAACGCG-AAATG
1 AAAATCGCAACGCGAAAATG
* *
23895 AAAATCGTAACGCGAAACT-
1 AAAATCGCAACGCGAAAATG
23914 AAAATCGCA
1 AAAATCGCA
23923 TTGCGATTCT
Statistics
Matches: 74, Mismatches: 12, Indels: 3
0.83 0.13 0.03
Matches are distributed among these distances:
19 22 0.30
20 52 0.70
ACGTcount: A:0.46, C:0.22, G:0.17, T:0.15
Consensus pattern (20 bp):
AAAATCGCAACGCGAAAATG
Found at i:23959 original size:19 final size:20
Alignment explanation
Indices: 23935--23973 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
23925 GCGATTCTGT
*
23935 CGTTGCGATTTTC-ATTTCA
1 CGTTGCGATTCTCGATTTCA
23954 CGTTGCGATTCTCGATTTCA
1 CGTTGCGATTCTCGATTTCA
23974 AATACTAAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.15, C:0.23, G:0.18, T:0.44
Consensus pattern (20 bp):
CGTTGCGATTCTCGATTTCA
Found at i:24554 original size:20 final size:20
Alignment explanation
Indices: 24524--24637 Score: 165
Period size: 20 Copynumber: 5.7 Consensus size: 20
24514 GCGCTTTGAA
*
24524 AATCGCATTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
24544 CATCGCGTTGCGATAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
24564 AATCGCGTTGCGACAGTCAG
1 AATCGCGTTGCGATAGTCAG
* *
24584 AATCGCGTTGCAACAGTCAG
1 AATCGCGTTGCGATAGTCAG
*
24604 AATCGCGTTGCGATAGTCAT
1 AATCGCGTTGCGATAGTCAG
*
24624 AATCGCATTGCGAT
1 AATCGCGTTGCGAT
24638 TTACATATTC
Statistics
Matches: 85, Mismatches: 9, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 85 1.00
ACGTcount: A:0.26, C:0.23, G:0.26, T:0.25
Consensus pattern (20 bp):
AATCGCGTTGCGATAGTCAG
Found at i:26386 original size:2 final size:2
Alignment explanation
Indices: 26336--26366 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
26326 GACTTTTTGA
26336 AT AT -T 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
26367 TAAAAAACTC
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
1 1 0.04
2 27 0.96
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:29152 original size:2 final size:2
Alignment explanation
Indices: 29094--29132 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
29084 GACTTTTTGA
29094 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
29133 TAAAAAACTC
Statistics
Matches: 36, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 35 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:30780 original size:35 final size:35
Alignment explanation
Indices: 30734--30802 Score: 129
Period size: 35 Copynumber: 2.0 Consensus size: 35
30724 ATTTTTCACT
*
30734 TGGAAAGAAGAGGGTAAGAACTCAATGGAAGTATA
1 TGGAAAGAAGAGGGTAAGAAATCAATGGAAGTATA
30769 TGGAAAGAAGAGGGTAAGAAATCAATGGAAGTAT
1 TGGAAAGAAGAGGGTAAGAAATCAATGGAAGTAT
30803 TGTTGGACTT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.46, C:0.04, G:0.32, T:0.17
Consensus pattern (35 bp):
TGGAAAGAAGAGGGTAAGAAATCAATGGAAGTATA
Found at i:32309 original size:2 final size:2
Alignment explanation
Indices: 32258--32289 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
32248 GACTTTTTGA
32258 AT AT -T AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
32290 AAAAACTCTT
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:33936 original size:35 final size:35
Alignment explanation
Indices: 33890--33958 Score: 138
Period size: 35 Copynumber: 2.0 Consensus size: 35
33880 ATTTTTCACT
33890 TGGAAAGAAGAGGGTAAGAACTCAATGGAAGTATA
1 TGGAAAGAAGAGGGTAAGAACTCAATGGAAGTATA
33925 TGGAAAGAAGAGGGTAAGAACTCAATGGAAGTAT
1 TGGAAAGAAGAGGGTAAGAACTCAATGGAAGTAT
33959 TGCTGGACTT
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.45, C:0.06, G:0.32, T:0.17
Consensus pattern (35 bp):
TGGAAAGAAGAGGGTAAGAACTCAATGGAAGTATA
Found at i:38933 original size:24 final size:24
Alignment explanation
Indices: 38879--38933 Score: 67
Period size: 24 Copynumber: 2.3 Consensus size: 24
38869 TTTTATCTAA
* *
38879 ATTT-TGATTTGAATTCTATTCTG
1 ATTTCTGATCTGAATTCAATTCTG
**
38902 ATACCTGATCTGAATTCAATTCTG
1 ATTTCTGATCTGAATTCAATTCTG
38926 ATTTCTGA
1 ATTTCTGA
38934 CCTGGATTTT
Statistics
Matches: 25, Mismatches: 6, Indels: 1
0.78 0.19 0.03
Matches are distributed among these distances:
23 2 0.08
24 23 0.92
ACGTcount: A:0.25, C:0.15, G:0.13, T:0.47
Consensus pattern (24 bp):
ATTTCTGATCTGAATTCAATTCTG
Found at i:40487 original size:2 final size:2
Alignment explanation
Indices: 40480--40509 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
40470 TTGATTTTAA
40480 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
40510 TAATTAAGAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:42950 original size:60 final size:60
Alignment explanation
Indices: 42843--42960 Score: 150
Period size: 60 Copynumber: 2.0 Consensus size: 60
42833 TAAAGTACAC
* *
42843 AAATGGTCTCCCGACTATATGACAATGCTCTGTTGAGTCTCTAGACTATTAAAAGTTATA
1 AAATGGTCTCCCGACTATAGGACAATGCTCTGTTAAGTCTCTAGACTATTAAAAGTTATA
* * * *
42903 AAATGGTC-CACCGACTATAGGACACTGCTTTGTTAAGTC-CTCCGACTATTAATAGTTA
1 AAATGGTCTC-CCGACTATAGGACAATGCTCTGTTAAGTCTCT-AGACTATTAAAAGTTA
42961 CAATTTGATC
Statistics
Matches: 50, Mismatches: 6, Indels: 4
0.83 0.10 0.07
Matches are distributed among these distances:
59 3 0.06
60 47 0.94
ACGTcount: A:0.31, C:0.20, G:0.17, T:0.32
Consensus pattern (60 bp):
AAATGGTCTCCCGACTATAGGACAATGCTCTGTTAAGTCTCTAGACTATTAAAAGTTATA
Found at i:43754 original size:4 final size:4
Alignment explanation
Indices: 43745--43817 Score: 58
Period size: 4 Copynumber: 18.5 Consensus size: 4
43735 ATTTTCTCAT
* * * * *
43745 TATA TATA TATA TGTA T-TA TATA TATG TATG TATA TGTA TATC TATA
1 TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA TATA
* * * *
43792 TGTA TATG TATA TGTA TATG TATA TA
1 TATA TATA TATA TATA TATA TATA TA
43818 AATCCTGATT
Statistics
Matches: 53, Mismatches: 15, Indels: 2
0.76 0.21 0.03
Matches are distributed among these distances:
3 3 0.06
4 50 0.94
ACGTcount: A:0.37, C:0.01, G:0.11, T:0.51
Consensus pattern (4 bp):
TATA
Found at i:43756 original size:6 final size:6
Alignment explanation
Indices: 43747--43816 Score: 90
Period size: 6 Copynumber: 11.8 Consensus size: 6
43737 TTTCTCATTA
* * *
43747 TATATA TATATG TATTATA TATATG --TATG TATATG TATATC TATATG
1 TATATG TATATG TA-TATG TATATG TATATG TATATG TATATG TATATG
43794 TATATG TATATG TATATG TATAT
1 TATATG TATATG TATATG TATAT
43817 AAATCCTGAT
Statistics
Matches: 56, Mismatches: 5, Indels: 6
0.84 0.07 0.09
Matches are distributed among these distances:
4 4 0.07
6 47 0.84
7 5 0.09
ACGTcount: A:0.36, C:0.01, G:0.11, T:0.51
Consensus pattern (6 bp):
TATATG
Found at i:47548 original size:60 final size:60
Alignment explanation
Indices: 47440--47554 Score: 144
Period size: 60 Copynumber: 1.9 Consensus size: 60
47430 ATAGTTGAGT
***
47440 GACCATTTTATAACTTTTAATAGTCAAGGAACTCAACAATGTTGTGTCCTATAGTCGGGA
1 GACCATTTTATAACTTTTAATAGTCAAGGAACTCAACAAACATGTGTCCTATAGTCGGGA
* **
47500 GACCATGTTTGTAACTTTTAATAGT-TGGGAACTCAACAAAACAT-TGTCCTATAGT
1 GACCAT-TTTATAACTTTTAATAGTCAAGGAACTCAAC-AAACATGTGTCCTATAGT
47555 TTGGGATCAT
Statistics
Matches: 47, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
60 27 0.57
61 20 0.43
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Consensus pattern (60 bp):
GACCATTTTATAACTTTTAATAGTCAAGGAACTCAACAAACATGTGTCCTATAGTCGGGA
Found at i:49409 original size:59 final size:60
Alignment explanation
Indices: 49337--49469 Score: 137
Period size: 60 Copynumber: 2.2 Consensus size: 60
49327 AATATAGGAT
* * *
49337 AAAA-TACACAAATGATACCCCAATTATAGGATATT-TTTTATTGAGTCCGC-AGAATATTA
1 AAAATTACA-AAATGATACCCCAACTATAGGACATTGCTTTATTGAGTCC-CTAGAATATTA
* * * * * * *
49396 AAAGTTACAAAATGGTCCCCCGACTATAGGACATTGCTTTGTTGAGTCCCTTGACTATTA
1 AAAATTACAAAATGATACCCCAACTATAGGACATTGCTTTATTGAGTCCCTAGAATATTA
49456 AAAATTACAAAATG
1 AAAATTACAAAATG
49470 GTCACCTGAC
Statistics
Matches: 60, Mismatches: 11, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
59 25 0.42
60 35 0.58
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.31
Consensus pattern (60 bp):
AAAATTACAAAATGATACCCCAACTATAGGACATTGCTTTATTGAGTCCCTAGAATATTA
Found at i:49816 original size:60 final size:60
Alignment explanation
Indices: 49682--49816 Score: 180
Period size: 60 Copynumber: 2.2 Consensus size: 60
49672 TAATGAATTT
* * * * *
49682 TTGGGTGACCATTTTGTAATTTTTACTAGTTGAGGGACTCAACAAAGCAACATTCTATAG
1 TTGGGGGACCATTTTATAACTTTTAATAGTTGAGGGACTCAACAAAGCAACATCCTATAG
** * * *
49742 TTGGGGGAATATTTTATAACTTTTAATAGTTGGGGGACTCAACAAAGGAATATCCTATAG
1 TTGGGGGACCATTTTATAACTTTTAATAGTTGAGGGACTCAACAAAGCAACATCCTATAG
49802 TTGGGGGACCATTTT
1 TTGGGGGACCATTTT
49817 TGCATTTTTC
Statistics
Matches: 63, Mismatches: 12, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
60 63 1.00
ACGTcount: A:0.30, C:0.13, G:0.23, T:0.35
Consensus pattern (60 bp):
TTGGGGGACCATTTTATAACTTTTAATAGTTGAGGGACTCAACAAAGCAACATCCTATAG
Found at i:50037 original size:38 final size:38
Alignment explanation
Indices: 49986--50062 Score: 129
Period size: 38 Copynumber: 2.0 Consensus size: 38
49976 GTTTTGGCCC
49986 ATTAGATCCCATGGTTTTATTCACAGAA-AGCAACATAG
1 ATTAGATCCCATGGTTTTATTCACA-AATAGCAACATAG
*
50024 ATTAGATCCCATGGTTTTATTCACAAATAGCAACTTAG
1 ATTAGATCCCATGGTTTTATTCACAAATAGCAACATAG
50062 A
1 A
50063 AATTGAAGGG
Statistics
Matches: 37, Mismatches: 1, Indels: 2
0.93 0.03 0.05
Matches are distributed among these distances:
37 2 0.05
38 35 0.95
ACGTcount: A:0.36, C:0.18, G:0.14, T:0.31
Consensus pattern (38 bp):
ATTAGATCCCATGGTTTTATTCACAAATAGCAACATAG
Found at i:52368 original size:21 final size:20
Alignment explanation
Indices: 52339--52450 Score: 59
Period size: 20 Copynumber: 5.5 Consensus size: 20
52329 TTCCAGATTT
*
52339 GCAACGCGAATATGAATAATC
1 GCAATGCGAATATGAA-AATC
52360 GCAATGCG-ATA-GTACAAATTC
1 GCAATGCGAATATG-A-AAA-TC
* * * * *
52381 GCATTGCGATTTTCCATAATC
1 GCAATGCGAATAT-GAAAATC
* *
52402 GCAACGCGAATATGCAAATC
1 GCAATGCGAATATGAAAATC
*
52422 GCAATGCGAACAT-ATAAATC
1 GCAATGCGAATATGA-AAATC
*
52442 GCAACGCGA
1 GCAATGCGA
52451 TTCTGACTAT
Statistics
Matches: 67, Mismatches: 17, Indels: 15
0.68 0.17 0.15
Matches are distributed among these distances:
19 1 0.01
20 34 0.51
21 28 0.42
22 3 0.04
23 1 0.01
ACGTcount: A:0.38, C:0.22, G:0.19, T:0.21
Consensus pattern (20 bp):
GCAATGCGAATATGAAAATC
Found at i:52423 original size:20 final size:20
Alignment explanation
Indices: 52398--52673 Score: 229
Period size: 20 Copynumber: 13.7 Consensus size: 20
52388 GATTTTCCAT
* *
52398 AATCGCAACGCGAATATGCA
1 AATCGCAACGCGAATACGTA
* * **
52418 AATCGCAATGCGAACATATA
1 AATCGCAACGCGAATACGTA
*
52438 AATCGCAACGCG-ATTC-TGA
1 AATCGCAACGCGAATACGT-A
* * * *
52457 CTATCGCAACGAGTATCCGTAA
1 -AATCGCAACGCGAATACGT-A
* *
52479 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
52499 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACGT-A
* *
52520 AATCGCAACGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
*
52540 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
*
52560 AATCGCAACGCGTAT-CTGTA
1 AATCGCAACGCGAATAC-GTA
*
52580 AATCGCAACGAGAATACGTA
1 AATCGCAACGCGAATACGTA
* * *
52600 AATCGCAATGCGTATCCGTA
1 AATCGCAACGCGAATACGTA
52620 AATCGCAACGAC-AATACGTAA
1 AATCGCAACG-CGAATACGT-A
* * *
52641 AATCGCAACGCGTATCCATA
1 AATCGCAACGCGAATACGTA
52661 AATCGCAACGCGA
1 AATCGCAACGCGA
52674 TTTTTAAAGC
Statistics
Matches: 208, Mismatches: 36, Indels: 24
0.78 0.13 0.09
Matches are distributed among these distances:
18 1 0.00
19 3 0.01
20 148 0.71
21 54 0.26
22 2 0.01
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (20 bp):
AATCGCAACGCGAATACGTA
Found at i:52486 original size:81 final size:81
Alignment explanation
Indices: 52398--52670 Score: 313
Period size: 81 Copynumber: 3.4 Consensus size: 81
52388 GATTTTCCAT
* * * * * * *
52398 AATCGCAACGCGAATATGCAAATCGCAATG-CGA-ACATATAAATCGCAACGCG-ATTC-TGACT
1 AATCGCAACGCGTATCTGTAAATCGCAACGACAATACATA-AAATCGCAACGCGTATCCGT-A-A
* *
52459 ATCGCAACGAGTATCCGTAA
63 ATCGCAACGAGAATACGT-A
* *
52479 AATCGCAACGCGTATCCGTAAATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAAATC
1 AATCGCAACGCGTATCTGTAAATCGCAACGACAATACATAAAATCGCAACGCGTATCCGTAAATC
52544 GCAACGAGAATACGTA
66 GCAACGAGAATACGTA
* * *
52560 AATCGCAACGCGTATCTGTAAATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAAATC
1 AATCGCAACGCGTATCTGTAAATCGCAACGACAATACATAAAATCGCAACGCGTATCCGTAAATC
*
52624 GCAACGACAATACGTAA
66 GCAACGAGAATACGT-A
**
52641 AATCGCAACGCGTATCCATAAATCGCAACG
1 AATCGCAACGCGTATCTGTAAATCGCAACG
52671 CGATTTTTAA
Statistics
Matches: 170, Mismatches: 17, Indels: 10
0.86 0.09 0.05
Matches are distributed among these distances:
80 38 0.22
81 92 0.54
82 31 0.18
83 8 0.05
84 1 0.01
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.19
Consensus pattern (81 bp):
AATCGCAACGCGTATCTGTAAATCGCAACGACAATACATAAAATCGCAACGCGTATCCGTAAATC
GCAACGAGAATACGTA
Found at i:52574 original size:40 final size:41
Alignment explanation
Indices: 52459--52670 Score: 347
Period size: 41 Copynumber: 5.2 Consensus size: 41
52449 GATTCTGACT
* *
52459 ATCGCAACGAGTATCCGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
52500 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
52541 ATCGCAACGAGAATACGT-AAATCGCAACGCGTATCTGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
*
52581 ATCGCAACGAGAATACGT-AAATCGCAATGCGTATCCGTAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
* *
52621 ATCGCAACGACAATACGTAAAATCGCAACGCGTATCCATAA
1 ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
52662 ATCGCAACG
1 ATCGCAACG
52671 CGATTTTTAA
Statistics
Matches: 160, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
40 76 0.47
41 84 0.52
ACGTcount: A:0.38, C:0.25, G:0.18, T:0.18
Consensus pattern (41 bp):
ATCGCAACGAGAATACGTAAAATCGCAACGCGTATCCGTAA
Found at i:53996 original size:14 final size:14
Alignment explanation
Indices: 53977--54012 Score: 54
Period size: 14 Copynumber: 2.6 Consensus size: 14
53967 ATTGTTTAAT
53977 TGATTTGTAAAAGA
1 TGATTTGTAAAAGA
* *
53991 TGATTTGTAAATGT
1 TGATTTGTAAAAGA
54005 TGATTTGT
1 TGATTTGT
54013 TTAATTGATG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
14 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.22, T:0.47
Consensus pattern (14 bp):
TGATTTGTAAAAGA
Found at i:54200 original size:20 final size:19
Alignment explanation
Indices: 54114--54161 Score: 69
Period size: 19 Copynumber: 2.5 Consensus size: 19
54104 AAAACAGACT
54114 ATCGCAACGCGGAAATGAAA
1 ATCGCAACGC-GAAATGAAA
* *
54134 ATCGTAATGCGAAATGAAA
1 ATCGCAACGCGAAATGAAA
54153 ATCGCAACG
1 ATCGCAACG
54162 AGTGAATCGC
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 16 0.67
20 8 0.33
ACGTcount: A:0.44, C:0.19, G:0.23, T:0.15
Consensus pattern (19 bp):
ATCGCAACGCGAAATGAAA
Found at i:54268 original size:33 final size:33
Alignment explanation
Indices: 54210--54294 Score: 125
Period size: 33 Copynumber: 2.5 Consensus size: 33
54200 ATTAGTTTCG
54210 CGTTGCGATTTTCATTTTCGCATTGCGATTCACT
1 CGTTGCGATTTTCA-TTTCGCATTGCGATTCACT
* *
54244 CGTTGCGATTTTCATTTCGTATTGCGATTCTCT
1 CGTTGCGATTTTCATTTCGCATTGCGATTCACT
**
54277 CGTTGCGATAGTCATTTC
1 CGTTGCGATTTTCATTTC
54295 CACGTTGCGA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 33 0.70
34 14 0.30
ACGTcount: A:0.14, C:0.22, G:0.19, T:0.45
Consensus pattern (33 bp):
CGTTGCGATTTTCATTTCGCATTGCGATTCACT
Found at i:54302 original size:20 final size:20
Alignment explanation
Indices: 54277--54331 Score: 74
Period size: 20 Copynumber: 2.8 Consensus size: 20
54267 GCGATTCTCT
*
54277 CGTTGCGATAGTCATTTCCA
1 CGTTGCGATAGTCAATTCCA
*
54297 CGTTGCGATAGTCAATTCCG
1 CGTTGCGATAGTCAATTCCA
* *
54317 CATTGTGATAGTCAA
1 CGTTGCGATAGTCAA
54332 ATGAATGTCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.33
Consensus pattern (20 bp):
CGTTGCGATAGTCAATTCCA
Found at i:54572 original size:19 final size:19
Alignment explanation
Indices: 54548--54585 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
54538 AGAGGAAAAG
54548 ATGAAAATCGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
*
54567 ATGAAAATTGCAATGCGAA
1 ATGAAAATCGCAATGCGAA
54586 CTCGTTGCGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.47, C:0.13, G:0.21, T:0.18
Consensus pattern (19 bp):
ATGAAAATCGCAATGCGAA
Found at i:54617 original size:19 final size:19
Alignment explanation
Indices: 54590--54631 Score: 75
Period size: 19 Copynumber: 2.2 Consensus size: 19
54580 TGCGAACTCG
*
54590 TTGCGATTTTCATTTCGCA
1 TTGCAATTTTCATTTCGCA
54609 TTGCAATTTTCATTTCGCA
1 TTGCAATTTTCATTTCGCA
54628 TTGC
1 TTGC
54632 GATTCTCTCA
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.17, C:0.21, G:0.14, T:0.48
Consensus pattern (19 bp):
TTGCAATTTTCATTTCGCA
Found at i:54667 original size:20 final size:20
Alignment explanation
Indices: 54640--54694 Score: 83
Period size: 20 Copynumber: 2.8 Consensus size: 20
54630 GCGATTCTCT
* *
54640 CATTGCGATAGTCATTTCTG
1 CATTGCGATAGTCAATTCCG
*
54660 CGTTGCGATAGTCAATTCCG
1 CATTGCGATAGTCAATTCCG
54680 CATTGCGATAGTCAA
1 CATTGCGATAGTCAA
54695 ATGAATATCT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 31 1.00
ACGTcount: A:0.24, C:0.22, G:0.22, T:0.33
Consensus pattern (20 bp):
CATTGCGATAGTCAATTCCG
Found at i:57144 original size:24 final size:24
Alignment explanation
Indices: 57110--57163 Score: 90
Period size: 24 Copynumber: 2.2 Consensus size: 24
57100 CTGAAAAATC
57110 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
* *
57134 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAATCCGAGTATTGACCAAG
57158 ATCAAA
1 ATCAAA
57164 TTTCGAATAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.41, C:0.20, G:0.19, T:0.20
Consensus pattern (24 bp):
ATCAAAATCCGAGTATTGACCAAG
Found at i:57177 original size:24 final size:24
Alignment explanation
Indices: 57110--57177 Score: 64
Period size: 24 Copynumber: 2.8 Consensus size: 24
57100 CTGAAAAATC
* * *
57110 ATCAAAATCCGAGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
** *
57134 ATCAAAGTCCGGGTATTGACCAAG
1 ATCAAAGTCCGAATACTGACCAAG
* *
57158 ATCAAATTTCGAATACTGAC
1 ATCAAAGTCCGAATACTGAC
57178 TAGTACTCAC
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
24 37 1.00
ACGTcount: A:0.38, C:0.21, G:0.18, T:0.24
Consensus pattern (24 bp):
ATCAAAGTCCGAATACTGACCAAG
Found at i:58031 original size:20 final size:18
Alignment explanation
Indices: 58012--58226 Score: 101
Period size: 20 Copynumber: 10.7 Consensus size: 18
58002 GATAGTCAGA
58012 ATCTCGTTGCGATTTACAG
1 ATCTCGTTGCGATTTAC-G
* *
58031 ATTTGCATTGCGATTTACG
1 ATCT-CGTTGCGATTTACG
58050 TAT-TCGCATTGCGATTTACG
1 -ATCTCG--TTGCGATTTACG
58070 TAT-TCGCATTGCGATTTACGG
1 -ATCTCG--TTGCGATTTAC-G
* * *
58091 ATACGCATTGTGATTTACG
1 AT-CTCGTTGCGATTTACG
58110 TATTCTCGTTGCGATTTACAG
1 -A-TCTCGTTGCGATTTAC-G
* *
58131 ATACGCGTTGCGATTTATGG
1 AT-CTCGTTGCGATTTA-CG
* *
58151 ATACGCATTGCGATTTTACG
1 AT-CTCGTTGCGA-TTTACG
*
58171 TATTGTCGTTGCGATTTACGG
1 -A-TCTCGTTGCGATTTAC-G
*
58192 ATACGCGTTGCGATTTTACGG
1 AT-CTCGTTGCGA-TTTAC-G
58213 ATACTCGTTGCGAT
1 AT-CTCGTTGCGAT
58227 AATTAGAATC
Statistics
Matches: 159, Mismatches: 19, Indels: 35
0.75 0.09 0.16
Matches are distributed among these distances:
18 1 0.01
19 8 0.05
20 113 0.71
21 35 0.22
22 2 0.01
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.38
Consensus pattern (18 bp):
ATCTCGTTGCGATTTACG
Found at i:58082 original size:60 final size:59
Alignment explanation
Indices: 58016--58226 Score: 262
Period size: 60 Copynumber: 3.5 Consensus size: 59
58006 GTCAGAATCT
* ** * *
58016 CGTTGCGATTTACAGATTTGCATTGCGATTTACGTATTCGCATTGCGATTTACGTATTCG
1 CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCGCGTTGCGATTTACG-ATACG
* * *
58076 CATTGCGATTTACGGATACGCATTGTGATTTACGTATTCTCGTTGCGATTTACAGATACG
1 CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCGCGTTGCGATTTAC-GATACG
*
58136 CGTTGCGATTTATGGATACGCATTGCGATTTTACGTATT-GTCGTTGCGATTTACGGATACG
1 CGTTGCGATTTACGGATACGCATTGCGA-TTTACGTATTCG-CGTTGCGATTTAC-GATACG
* *
58197 CGTTGCGATTTTACGGATACTCGTTGCGAT
1 CGTTGCGA-TTTACGGATACGCATTGCGAT
58227 AATTAGAATC
Statistics
Matches: 131, Mismatches: 16, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
60 75 0.57
61 39 0.30
62 17 0.13
ACGTcount: A:0.20, C:0.18, G:0.24, T:0.38
Consensus pattern (59 bp):
CGTTGCGATTTACGGATACGCATTGCGATTTACGTATTCGCGTTGCGATTTACGATACG
Found at i:58181 original size:41 final size:41
Alignment explanation
Indices: 58014--58226 Score: 198
Period size: 40 Copynumber: 5.3 Consensus size: 41
58004 TAGTCAGAAT
* ** * *
58014 CTCGTTGCGATTTACAGATTTGCATTGCGA-TTTACGTATT
1 CTCGTTGCGATTTACGGATACGCATTGCGATTTTACGGATA
* * * *
58054 CGCATTGCGATTTACGTATTCGCATTGCGA-TTTACGGATA
1 CTCGTTGCGATTTACGGATACGCATTGCGATTTTACGGATA
* * * * * * * *
58094 CGCATTGTGATTTACGTATTCTCGTTGCGA-TTTACAGATA
1 CTCGTTGCGATTTACGGATACGCATTGCGATTTTACGGATA
* * * *
58134 CGCGTTGCGATTTATGGATACGCATTGCGATTTTACGTATT
1 CTCGTTGCGATTTACGGATACGCATTGCGATTTTACGGATA
* *
58175 GTCGTTGCGATTTACGGATACGCGTTGCGATTTTACGGATA
1 CTCGTTGCGATTTACGGATACGCATTGCGATTTTACGGATA
58216 CTCGTTGCGAT
1 CTCGTTGCGAT
58227 AATTAGAATC
Statistics
Matches: 144, Mismatches: 28, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
40 92 0.64
41 52 0.36
ACGTcount: A:0.20, C:0.18, G:0.23, T:0.38
Consensus pattern (41 bp):
CTCGTTGCGATTTACGGATACGCATTGCGATTTTACGGATA
Found at i:58386 original size:20 final size:20
Alignment explanation
Indices: 58340--58390 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
58330 CTTCATAATA
58340 GCGTTGCGATTCTGGGAACT
1 GCGTTGCGATTCTGGGAACT
** *
58360 GATTTGCGATTCTGGAGATC-
1 GCGTTGCGATTCTGG-GAACT
58380 GCGTTGCGATT
1 GCGTTGCGATT
58391 TTTATTTCGC
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
20 22 0.88
21 3 0.12
ACGTcount: A:0.16, C:0.18, G:0.33, T:0.33
Consensus pattern (20 bp):
GCGTTGCGATTCTGGGAACT
Found at i:62542 original size:11 final size:11
Alignment explanation
Indices: 62523--62564 Score: 50
Period size: 11 Copynumber: 3.8 Consensus size: 11
62513 CTCTAACTTC
*
62523 TTTCATTTCTT
1 TTTCTTTTCTT
62534 TTTCTTTTCTT
1 TTTCTTTTCTT
62545 TTT-TTTCTCTT
1 TTTCTTT-TCTT
*
62556 TTTTTTTTC
1 TTTCTTTTC
62565 ATTGTTACGA
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 3 0.11
11 22 0.79
12 3 0.11
ACGTcount: A:0.02, C:0.17, G:0.00, T:0.81
Consensus pattern (11 bp):
TTTCTTTTCTT
Found at i:62545 original size:20 final size:19
Alignment explanation
Indices: 62520--62567 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 19
62510 TTACTCTAAC
*
62520 TTCTTTCATTTCTTTTTCTT
1 TTCTTTCATTTCTCTTT-TT
**
62540 TTCTTTTTTTTCTCTTTTT
1 TTCTTTCATTTCTCTTTTT
62559 TT-TTTCATT
1 TTCTTTCATT
62568 GTTACGAGGG
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 5 0.22
19 4 0.17
20 14 0.61
ACGTcount: A:0.04, C:0.17, G:0.00, T:0.79
Consensus pattern (19 bp):
TTCTTTCATTTCTCTTTTT
Found at i:67265 original size:64 final size:63
Alignment explanation
Indices: 67174--67431 Score: 196
Period size: 64 Copynumber: 4.2 Consensus size: 63
67164 CACTTTATTC
* *
67174 ATTTCATAGCATGTACCATTAAC----TTCATTTATTTCATAGCATGTACCACTCATTTGTTTT
1 ATTTCATAGCATGTATCATTCACTTTATTCATTTATTTCATAGCATGTACCACTCATTT-TTTT
* ** *** * *
67234 ATTTCATAACATGTATCATTCACTTTATTCATTTCATAACA-AATTTGTGCC-TTCCATTTTATT
1 ATTTCATAGCATGTATCATTCACTTTATTCATTT-ATTTCATAGCATGTACCACT-CATTTT-TT
67297 T
63 T
* * * *
67298 ATTTCATAGCATGTACCACTCA-TTT-TT-TTTTATTTCTTAGCATGTACCACTCATTTTTTT
1 ATTTCATAGCATGTATCATTCACTTTATTCATTTATTTCATAGCATGTACCACTCATTTTTTT
** * * **
67358 ATTTCA-ATGCATGTATCATTCACTTTATTCATTTCATAGCA-AACTTGTACCTTTCATTTTATT
1 ATTTCATA-GCATGTATCATTCACTTTATTCATTT-ATTTCATAGCATGTACCACTCATTTT-TT
67421 T
63 T
67422 ATTTCATAGC
1 ATTTCATAGC
67432 CCATTGTAAA
Statistics
Matches: 150, Mismatches: 32, Indels: 28
0.71 0.15 0.13
Matches are distributed among these distances:
59 1 0.01
60 44 0.29
61 18 0.12
62 5 0.03
63 23 0.15
64 54 0.36
65 5 0.03
ACGTcount: A:0.26, C:0.19, G:0.07, T:0.48
Consensus pattern (63 bp):
ATTTCATAGCATGTATCATTCACTTTATTCATTTATTTCATAGCATGTACCACTCATTTTTTT
Found at i:67295 original size:124 final size:124
Alignment explanation
Indices: 67139--67431 Score: 419
Period size: 124 Copynumber: 2.4 Consensus size: 124
67129 AGCACATTTC
* * * * *
67139 CATTTCATATCAAACCTGTGCCTTTCACTTTATTCATTTCATAGCATGTACCA-TTAACTTCATT
1 CATTTCATAACAAACTTGTGCCTTTCATTTTATTTATTTCATAGCATGTACCACTCAACTTCATT
67203 TATTTCATAGCATGTACCACTCATTTGTTTTATTTC-ATAACATGTATCATTCACTTTATT
66 TATTTCATAGCATGTACCACTCATTT-TTTTATTTCAAT-ACATGTATCATTCACTTTATT
* * ** **
67263 CATTTCATAACAAATTTGTGCCTTCCATTTTATTTATTTCATAGCATGTACCACTCATTTTTTTT
1 CATTTCATAACAAACTTGTGCCTTTCATTTTATTTATTTCATAGCATGTACCACTCAACTTCATT
* *
67328 TATTTCTTAGCATGTACCACTCATTTTTTTATTTCAATGCATGTATCATTCACTTTATT
66 TATTTCATAGCATGTACCACTCATTTTTTTATTTCAATACATGTATCATTCACTTTATT
* *
67387 CATTTCATAGCAAACTTGTACCTTTCATTTTATTTATTTCATAGC
1 CATTTCATAACAAACTTGTGCCTTTCATTTTATTTATTTCATAGC
67432 CCATTGTAAA
Statistics
Matches: 150, Mismatches: 17, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
124 117 0.78
125 33 0.22
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.47
Consensus pattern (124 bp):
CATTTCATAACAAACTTGTGCCTTTCATTTTATTTATTTCATAGCATGTACCACTCAACTTCATT
TATTTCATAGCATGTACCACTCATTTTTTTATTTCAATACATGTATCATTCACTTTATT
Found at i:67426 original size:34 final size:30
Alignment explanation
Indices: 67162--67431 Score: 224
Period size: 30 Copynumber: 8.7 Consensus size: 30
67152 ACCTGTGCCT
* *
67162 TTCACTTTATTCATTTCATAGCATGTACCA
1 TTCATTTTATTTATTTCATAGCATGTACCA
* * *
67192 TTAACTTCATTTATTTCATAGCATGTACCA
1 TTCATTTTATTTATTTCATAGCATGTACCA
* * *
67222 CTCATTTGT-TTTATTTCATAACATGTATCA
1 TTCATTT-TATTTATTTCATAGCATGTACCA
* * * *
67252 TTCACTTTATTCATTTCATAACAAATTTGTGCC-
1 TTCATTTTATTTATTTCATAGC--A--TGTACCA
67285 TTCCATTTTATTTATTTCATAGCATGTACCA
1 TT-CATTTTATTTATTTCATAGCATGTACCA
* * *
67316 CTCATTTTTTTTTATTTCTTAGCATGTACCA
1 TTCA-TTTTATTTATTTCATAGCATGTACCA
* *
67347 CTCATTTT-TTTATTTCA-ATGCATGTATCA
1 TTCATTTTATTTATTTCATA-GCATGTACCA
* * *
67376 TTCACTTTATTCATTTCATAGCAAACTTGTACCT
1 TTCATTTTATTTATTTCATAGC--A--TGTACCA
67410 TTCATTTTATTTATTTCATAGC
1 TTCATTTTATTTATTTCATAGC
67432 CCATTGTAAA
Statistics
Matches: 194, Mismatches: 30, Indels: 28
0.77 0.12 0.11
Matches are distributed among these distances:
28 1 0.01
29 24 0.12
30 88 0.45
31 30 0.15
32 3 0.02
33 2 0.01
34 46 0.24
ACGTcount: A:0.26, C:0.20, G:0.06, T:0.49
Consensus pattern (30 bp):
TTCATTTTATTTATTTCATAGCATGTACCA
Found at i:72793 original size:33 final size:31
Alignment explanation
Indices: 72614--72864 Score: 169
Period size: 30 Copynumber: 8.0 Consensus size: 31
72604 TCATATCAGA
* * *
72614 CATGTTCCTTTCAC-TTTATTCATTTCATAG
1 CATGTACCATTCACTTTTATTTATTTCATAG
** *
72644 CATGTACCATT-AAATTCATTTATTTCATAG
1 CATGTACCATTCACTTTTATTTATTTCATAG
* *
72674 CATGTTCCACTCACTTCTT-TTTATTTCATAG
1 CATGTACCATTCACTT-TTATTTATTTCATAG
*
72705 CATGTATCATTCAC-TTTATTTATTTCA-AG
1 CATGTACCATTCACTTTTATTTATTTCATAG
* *
72734 CAAACTTGTGCCTTTCA-TTTTATTTATTTCATAG
1 C--A--TGTACCATTCACTTTTATTTATTTCATAG
* *
72768 CATGTACCACTCACTTTTTTTTTTATTTCATAG
1 CATGTACCATTCAC--TTTTATTTATTTCATAG
* * *
72801 -ACTGTATCATTCAC-TTTATTCATTTCTTAG
1 CA-TGTACCATTCACTTTTATTTATTTCATAG
* *
72831 CAAACTTGTGCCTTTCA-TTTTATTTATTTCATAG
1 C--A--TGTACCATTCACTTTTATTTATTTCATAG
72865 GCCAATGTAA
Statistics
Matches: 171, Mismatches: 31, Indels: 34
0.72 0.13 0.14
Matches are distributed among these distances:
29 6 0.04
30 63 0.37
31 26 0.15
32 3 0.02
33 48 0.28
34 25 0.15
ACGTcount: A:0.24, C:0.20, G:0.07, T:0.49
Consensus pattern (31 bp):
CATGTACCATTCACTTTTATTTATTTCATAG
Found at i:73702 original size:10 final size:10
Alignment explanation
Indices: 73687--73712 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
73677 TCATCATAGT
73687 CAAACATGAA
1 CAAACATGAA
73697 CAAACATGAA
1 CAAACATGAA
73707 CAAACA
1 CAAACA
73713 ATTTATCATC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.62, C:0.23, G:0.08, T:0.08
Consensus pattern (10 bp):
CAAACATGAA
Found at i:78109 original size:2 final size:2
Alignment explanation
Indices: 78102--78131 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
78092 TTTCATATCA
78102 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
78132 TACTTAAATA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:78226 original size:2 final size:2
Alignment explanation
Indices: 78213--78251 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
78203 TTATGCAAGC
*
78213 AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
78252 CATTAAAGTC
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.03, G:0.00, T:0.46
Consensus pattern (2 bp):
AT
Found at i:82236 original size:34 final size:34
Alignment explanation
Indices: 82172--82239 Score: 93
Period size: 34 Copynumber: 2.0 Consensus size: 34
82162 CAACTTCATG
* *
82172 GTGTATCGATACATCCAGGGATGTACCGATACCT
1 GTGTATCGATACATCCAGGCAGGTACCGATACCT
*
82206 GTGTATCGATACA-CACAGGCAGGTATCGATACCT
1 GTGTATCGATACATC-CAGGCAGGTACCGATACCT
82240 ATGAATTTCA
Statistics
Matches: 30, Mismatches: 3, Indels: 2
0.86 0.09 0.06
Matches are distributed among these distances:
33 1 0.03
34 29 0.97
ACGTcount: A:0.28, C:0.24, G:0.24, T:0.25
Consensus pattern (34 bp):
GTGTATCGATACATCCAGGCAGGTACCGATACCT
Found at i:89694 original size:23 final size:23
Alignment explanation
Indices: 89668--89730 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 23
89658 CATCTTATAT
*
89668 GGCACTTCGGTACATTTCTACCC
1 GGCACTTCGGTGCATTTCTACCC
* * ** **
89691 GGCATTTTGGTGCAAATCTACGT
1 GGCACTTCGGTGCATTTCTACCC
89714 GGCACTTCGGTGCATTT
1 GGCACTTCGGTGCATTT
89731 ATATGAGCTA
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
23 29 1.00
ACGTcount: A:0.17, C:0.25, G:0.24, T:0.33
Consensus pattern (23 bp):
GGCACTTCGGTGCATTTCTACCC
Found at i:97874 original size:37 final size:37
Alignment explanation
Indices: 97823--97908 Score: 145
Period size: 37 Copynumber: 2.3 Consensus size: 37
97813 ATGCTTAACT
*
97823 CTCTCGAACATTAAGCAAACAACTAAGTGATAGCCAA
1 CTCTCGAAGATTAAGCAAACAACTAAGTGATAGCCAA
*
97860 CTCTCGAAGGTTAAGCAAACAACTAAGTGATAGCCAA
1 CTCTCGAAGATTAAGCAAACAACTAAGTGATAGCCAA
*
97897 ATCTCGAAGATT
1 CTCTCGAAGATT
97909 TTCTCTTAAC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
37 45 1.00
ACGTcount: A:0.41, C:0.22, G:0.16, T:0.21
Consensus pattern (37 bp):
CTCTCGAAGATTAAGCAAACAACTAAGTGATAGCCAA
Found at i:100286 original size:57 final size:57
Alignment explanation
Indices: 100211--100412 Score: 291
Period size: 57 Copynumber: 3.5 Consensus size: 57
100201 GAATTTACCT
*
100211 ACTTATTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCATACGAAAATTCATAC
1 ACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCATACGAAAATTCATAC
* * *
100268 ACTTGGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCATATGGAAATTCATAC
1 ACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCATACGAAAATTCATAC
* *
100325 ACTTAGTATAAATTTCTTAGCTTTTTGCACACAAAGTGCCCATAC-AGAAATAT-ATAA
1 ACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCATACGA-AAAT-TCATAC
* * *
100382 ACTAATTATGAATTTCTTAACTTTTTGCACA
1 ACTTAGTATGAATTTCTTAGCTTTTTGCACA
100413 ATCAATGTCA
Statistics
Matches: 130, Mismatches: 13, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
57 129 0.99
58 1 0.01
ACGTcount: A:0.34, C:0.19, G:0.11, T:0.36
Consensus pattern (57 bp):
ACTTAGTATGAATTTCTTAGCTTTTTGCACACAAAGTGCCCATACGAAAATTCATAC
Found at i:100871 original size:20 final size:20
Alignment explanation
Indices: 100835--100884 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
100825 GATATCAATG
*
100835 GTATCGATAC-CTTCCTTATA
1 GTATCGATACTCTCCCTT-TA
100855 GTATCGATACTC-CCCTTTA
1 GTATCGATACTCTCCCTTTA
*
100874 GTGTCGATACT
1 GTATCGATACT
100885 GCTTGCATCA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
19 12 0.44
20 14 0.52
21 1 0.04
ACGTcount: A:0.22, C:0.26, G:0.14, T:0.38
Consensus pattern (20 bp):
GTATCGATACTCTCCCTTTA
Found at i:103546 original size:22 final size:22
Alignment explanation
Indices: 103521--103588 Score: 56
Period size: 22 Copynumber: 3.2 Consensus size: 22
103511 TTTAGCCATT
103521 ACAATTATTTCCAAAATAGTTA
1 ACAATTATTTCCAAAATAGTTA
**
103543 ACAAATTTAGTTT---AGCTA-TT-
1 AC-AA-TTA-TTTCCAAAATAGTTA
103563 ACAATTATTTCCAAAATAGTTA
1 ACAATTATTTCCAAAATAGTTA
103585 ACAA
1 ACAA
103589 AGCAACAAGA
Statistics
Matches: 34, Mismatches: 4, Indels: 16
0.63 0.07 0.30
Matches are distributed among these distances:
17 3 0.09
18 3 0.09
19 2 0.06
20 5 0.15
21 4 0.12
22 9 0.26
23 2 0.06
24 3 0.09
25 3 0.09
ACGTcount: A:0.44, C:0.13, G:0.06, T:0.37
Consensus pattern (22 bp):
ACAATTATTTCCAAAATAGTTA
Found at i:103551 original size:42 final size:42
Alignment explanation
Indices: 103504--103589 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
103494 AAAGTAAAAC
103504 AATTTAGTTTAGCCATTACAATTATTTCCAAAATAGTTAACA
1 AATTTAGTTTAGCCATTACAATTATTTCCAAAATAGTTAACA
*
103546 AATTTAGTTTAGCTATTACAATTATTTCCAAAATAGTTAACA
1 AATTTAGTTTAGCCATTACAATTATTTCCAAAATAGTTAACA
103588 AA
1 AA
103590 GCAACAAGAA
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.42, C:0.13, G:0.07, T:0.38
Consensus pattern (42 bp):
AATTTAGTTTAGCCATTACAATTATTTCCAAAATAGTTAACA
Found at i:104292 original size:23 final size:24
Alignment explanation
Indices: 104262--104309 Score: 80
Period size: 24 Copynumber: 2.0 Consensus size: 24
104252 AGTCTTCCTG
*
104262 ATGATGTA-AAAGCATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
104285 ATGATGTATAAAACATCTATGTAC
1 ATGATGTATAAAACATCTATGTAC
104309 A
1 A
104310 ATGTCATGCA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.42, C:0.12, G:0.15, T:0.31
Consensus pattern (24 bp):
ATGATGTATAAAACATCTATGTAC
Done.