Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007761.1 Hibiscus syriacus cultivar Beakdansim tig00110030_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: 1497221
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
File 1 of 7
Found at i:8670 original size:21 final size:20
Alignment explanation
Indices: 8636--8674 Score: 51
Period size: 21 Copynumber: 1.9 Consensus size: 20
8626 CATCAAGGTC
8636 TTTGTTGAACCCATGAAATCT
1 TTTGTTGAACCCAT-AAATCT
**
8657 TTTGTTGAGGCCATAAAT
1 TTTGTTGAACCCATAAAT
8675 TCTTGCAATG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.28, C:0.15, G:0.18, T:0.38
Consensus pattern (20 bp):
TTTGTTGAACCCATAAATCT
Found at i:11674 original size:10 final size:10
Alignment explanation
Indices: 11659--11683 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
11649 CAAATATAAC
11659 CTAAATGCAA
1 CTAAATGCAA
11669 CTAAATGCAA
1 CTAAATGCAA
11679 CTAAA
1 CTAAA
11684 ATGTTGTGCA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.52, C:0.20, G:0.08, T:0.20
Consensus pattern (10 bp):
CTAAATGCAA
Found at i:12009 original size:21 final size:21
Alignment explanation
Indices: 11983--12033 Score: 84
Period size: 21 Copynumber: 2.4 Consensus size: 21
11973 TCTGCAGCTG
* *
11983 CTATACTCTATGGCATGCTAA
1 CTATACCCTATGGCATGCCAA
12004 CTATACCCTATGGCATGCCAA
1 CTATACCCTATGGCATGCCAA
12025 CTATACCCT
1 CTATACCCT
12034 GTCCTTCAAC
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 28 1.00
ACGTcount: A:0.27, C:0.31, G:0.12, T:0.29
Consensus pattern (21 bp):
CTATACCCTATGGCATGCCAA
Found at i:22919 original size:15 final size:15
Alignment explanation
Indices: 22895--22924 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
22885 TATCACAATC
22895 GCGCAGGATTCCGGG
1 GCGCAGGATTCCGGG
*
22910 GCGCATGATTCCGGG
1 GCGCAGGATTCCGGG
22925 AGCACCGTGG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.13, C:0.27, G:0.43, T:0.17
Consensus pattern (15 bp):
GCGCAGGATTCCGGG
Found at i:28509 original size:20 final size:20
Alignment explanation
Indices: 28466--28509 Score: 52
Period size: 20 Copynumber: 2.2 Consensus size: 20
28456 TTTAAATATT
*
28466 AAAGTTGAAGTTTTAAAAAT
1 AAAGTTGAAGTTTTAAAAAG
* * *
28486 AAAGTTTAATTTTTTAAAAG
1 AAAGTTGAAGTTTTAAAAAG
28506 AAAG
1 AAAG
28510 AAACATTAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.50, C:0.00, G:0.14, T:0.36
Consensus pattern (20 bp):
AAAGTTGAAGTTTTAAAAAG
Found at i:29600 original size:17 final size:17
Alignment explanation
Indices: 29578--29616 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
29568 GACTTTGTAT
29578 ATACACTAAATTGTTAA
1 ATACACTAAATTGTTAA
29595 ATACACTAAATTGTTAA
1 ATACACTAAATTGTTAA
29612 ATACA
1 ATACA
29617 TCACTAATAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.49, C:0.13, G:0.05, T:0.33
Consensus pattern (17 bp):
ATACACTAAATTGTTAA
Found at i:31248 original size:3 final size:3
Alignment explanation
Indices: 31225--31282 Score: 68
Period size: 3 Copynumber: 20.3 Consensus size: 3
31215 TAAAAAACAA
* * *
31225 AAT AAT AA- AAT ATT AGT -AT AAT AAT AAT AAT AAT -AT AAT GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
31270 AAT AAT AAT AAT A
1 AAT AAT AAT AAT A
31283 GTGGACCCCA
Statistics
Matches: 47, Mismatches: 5, Indels: 6
0.81 0.09 0.10
Matches are distributed among these distances:
2 5 0.11
3 42 0.89
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (3 bp):
AAT
Found at i:31268 original size:23 final size:23
Alignment explanation
Indices: 31225--31282 Score: 84
Period size: 23 Copynumber: 2.6 Consensus size: 23
31215 TAAAAAACAA
*
31225 AATAATAA-AATATTAGTATAAT
1 AATAATAATAATATAAGTATAAT
31247 AATAATAATAATATAA-TGATAAT
1 AATAATAATAATATAAGT-ATAAT
31270 AATAATAATAATA
1 AATAATAATAATA
31283 GTGGACCCCA
Statistics
Matches: 33, Mismatches: 1, Indels: 3
0.89 0.03 0.08
Matches are distributed among these distances:
22 9 0.27
23 24 0.73
ACGTcount: A:0.62, C:0.00, G:0.03, T:0.34
Consensus pattern (23 bp):
AATAATAATAATATAAGTATAAT
Found at i:31770 original size:133 final size:132
Alignment explanation
Indices: 31472--31921 Score: 569
Period size: 133 Copynumber: 3.4 Consensus size: 132
31462 AGTATGGAAG
* * * * *
31472 AGATTTGGAAATATTGATTCATTCCACT-TCTCTACAAGAAAGATTGAATCGAGGAAGACTTGTT
1 AGATCTGGAAATATTGATTCATTCCACTGT-TCTTCAGGGAAGATTGAATCGAGGCAGACTTGTT
* *
31536 CCACTATTCCTCAGGGAAGATCAAATTTGAAAAAAGGGATTTGTTCTGTTGCTTCTTAAGGGAAT
65 CCACTATTCCTCAGGGAAGATCAAATTTGAAAAAAGGGATATGTTCTGTTGCTTCTTAAGGGAAA
*
31601 ATT
130 ATC
* * * * * *
31604 AGATCTGGTAATGTTGATTCATTCAAATGTTCTTCAGGGAAGATTGAATCGAGGCGGACTTGTTT
1 AGATCTGGAAATATTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTC
* * *
31669 CATTATTCCTCAGGGAAGATCAAATCTTGAAAAAAGGGATATGTTATGTTGCTTCTTAAGAGAAA
66 CACTATTCCTCAGGGAAGATCAAAT-TTGAAAAAAGGGATATGTTCTGTTGCTTCTTAAGGGAAA
31734 ATC
130 ATC
* * * * *
31737 AGGTCTAGAAATGTTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCATACATGTTC
1 AGATCTGGAAATATTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTC
** *** *
31802 CACTATTCCTCATAGAAGATCAAATTTGGAATAAATAGGGATATGTTCCCCTGCTTCTTGAGGGA
66 CACTATTCCTCAGGGAAGATCAAATTT-GAA-AAA-AGGGATATGTTCTGTTGCTTCTTAAGGGA
*
31867 AAAAC
128 AAATC
* *
31872 AGATCTGGAAATATTAATTCATTCCATTGTTCTTCAGGGAAGATTGAATC
1 AGATCTGGAAATATTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATC
31922 AAGTTCAATT
Statistics
Matches: 272, Mismatches: 41, Indels: 7
0.85 0.13 0.02
Matches are distributed among these distances:
132 78 0.29
133 119 0.44
134 3 0.01
135 72 0.26
ACGTcount: A:0.32, C:0.15, G:0.21, T:0.33
Consensus pattern (132 bp):
AGATCTGGAAATATTGATTCATTCCACTGTTCTTCAGGGAAGATTGAATCGAGGCAGACTTGTTC
CACTATTCCTCAGGGAAGATCAAATTTGAAAAAAGGGATATGTTCTGTTGCTTCTTAAGGGAAAA
TC
Found at i:33604 original size:2 final size:2
Alignment explanation
Indices: 33597--33653 Score: 114
Period size: 2 Copynumber: 28.5 Consensus size: 2
33587 GCTTTATTGC
33597 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33639 AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT A
33654 ATCGCCTTTA
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 55 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:37438 original size:6 final size:6
Alignment explanation
Indices: 37427--37453 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
37417 GCAAAATAAG
37427 AATGCA AATGCA AATGCA AATGCA AAT
1 AATGCA AATGCA AATGCA AATGCA AAT
37454 AAACAAGGTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.52, C:0.15, G:0.15, T:0.19
Consensus pattern (6 bp):
AATGCA
Found at i:38956 original size:131 final size:130
Alignment explanation
Indices: 38725--39071 Score: 403
Period size: 131 Copynumber: 2.7 Consensus size: 130
38715 AGAAAATGAT
* * * *
38725 AATATCTAATTATTTCCAATCGAGAATAAAATGAGCTCTCATGCCTTAAAGCAGTCATTTATTAC
1 AATATCTAATTATTTCCAATCGAGAAT-AAATGACCTCTCATGCCTTAAAACAATAATTTATTAC
** * * *
38790 TCCAACCGAAATGAGGAGATATCACTCTTTAGTCTTA-AAATTCAATATTGATTTGAAAGAAAAC
65 TCCAACCGAAATGAAAAGATATCACTATTCAGTCTTACAAA-TCAATATTGATTCGAAAGAAAAC
38854 AAA
129 -AA
* *
38857 AATATCTAATTATTTCCAATCGAAAATAAATGACCTCTCAT-CCGTTAAAACAATAATTTATTAT
1 AATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCC-TTAAAACAATAATTTATTAC
* ** * * *
38921 TCTAATTGAAATGAAAAGATATCACTATTCCGTCTTACAAATCAATATTGATTCGAGAGAAAACG
65 TCCAACCGAAATGAAAAGATATCACTATTCAGTCTTACAAATCAATATTGATTCGAAAGAAAACA
*
38986 T
130 A
* * * * * *
38987 TATATCTAGTTATTTCCAATCGAGAATAAATGACCTCTCCTGCCTT-AAGCAGTTATTTATTACT
1 AATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAACAATAATTTATTACT
* *
39051 CCAACCAAAATGAAGAGATAT
66 CCAACCGAAATGAAAAGATAT
39072 TATTATTTTC
Statistics
Matches: 181, Mismatches: 31, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
129 30 0.17
130 41 0.23
131 81 0.45
132 29 0.16
ACGTcount: A:0.39, C:0.17, G:0.11, T:0.32
Consensus pattern (130 bp):
AATATCTAATTATTTCCAATCGAGAATAAATGACCTCTCATGCCTTAAAACAATAATTTATTACT
CCAACCGAAATGAAAAGATATCACTATTCAGTCTTACAAATCAATATTGATTCGAAAGAAAACAA
Found at i:40901 original size:31 final size:31
Alignment explanation
Indices: 40834--40904 Score: 81
Period size: 31 Copynumber: 2.3 Consensus size: 31
40824 GCCTGAGAGA
* * *
40834 CTACCCAAGATAATTTTCGGGCCATAGAGGC
1 CTACCCAAGATAAATCTCGGGCCACAGAGGC
* *
40865 TTACCCAAGATAAATCTCGAGGCCACATA-GC
1 CTACCCAAGATAAATCTCG-GGCCACAGAGGC
40896 CTACCCAAG
1 CTACCCAAG
40905 GCTCGCCTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 2
0.80 0.15 0.05
Matches are distributed among these distances:
31 26 0.79
32 7 0.21
ACGTcount: A:0.32, C:0.30, G:0.18, T:0.20
Consensus pattern (31 bp):
CTACCCAAGATAAATCTCGGGCCACAGAGGC
Found at i:41652 original size:17 final size:17
Alignment explanation
Indices: 41626--41659 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
41616 TTGAAAATAT
41626 AAAATATGACTTTTCAG
1 AAAATATGACTTTTCAG
*
41643 AAAATTTGACTTTTCAG
1 AAAATATGACTTTTCAG
41660 TTCAAAGTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.38, C:0.12, G:0.12, T:0.38
Consensus pattern (17 bp):
AAAATATGACTTTTCAG
Found at i:41685 original size:16 final size:16
Alignment explanation
Indices: 41661--41703 Score: 59
Period size: 16 Copynumber: 2.7 Consensus size: 16
41651 ACTTTTCAGT
*
41661 TCAAAGTCAACTCTAG
1 TCAAAGTCAACTATAG
* *
41677 TCAAGGTCAACTATGG
1 TCAAAGTCAACTATAG
41693 TCAAAGTCAAC
1 TCAAAGTCAAC
41704 GGGTCAGGTC
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.37, C:0.23, G:0.16, T:0.23
Consensus pattern (16 bp):
TCAAAGTCAACTATAG
Found at i:45899 original size:16 final size:16
Alignment explanation
Indices: 45886--45916 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
45876 GCCAAAGTTA
45886 ACTCTGGTCAAAGTCT
1 ACTCTGGTCAAAGTCT
*
45902 ACTCTGGTTAAAGTC
1 ACTCTGGTCAAAGTC
45917 AACGGGTCAG
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:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (16 bp):
ACTCTGGTCAAAGTCT
Found at i:59779 original size:2 final size:2
Alignment explanation
Indices: 59772--59798 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
59762 TACTTGTATC
59772 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 T
59799 TTCAAGGCCT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:64749 original size:93 final size:95
Alignment explanation
Indices: 64615--64808 Score: 232
Period size: 93 Copynumber: 2.1 Consensus size: 95
64605 GTTGAGGTGG
* * * * * **
64615 GTATCGATAC-AATGAGGAAGGTATTGATTCCATTGATTCCAGAATGCATAAATGGTATCGATAC
1 GTATCGGTACTAA-GAGAAAGGTATTGATACCAATGATTCCAGAATGCAAAAATGAAATCGATAC
* * * *
64679 TGTAATAGAGTATCGATACCATAGTATAGAA
65 TGAAAGAGAATATCGATACCAGAGTATAGAA
*
64710 -TATCGGTACTAAGAGAAAGGTATTGATACCAATGA-TCCAGAATGCAAAAATGAAATCGATATT
1 GTATCGGTACTAAGAGAAAGGTATTGATACCAATGATTCCAGAATGCAAAAATGAAATCGATACT
* *
64773 GAAAGGGAATATCGGTACCAGAGTATAGAA
66 GAAAGAGAATATCGATACCAGAGTATAGAA
64803 GTATCG
1 GTATCG
64809 ATACCATGGT
Statistics
Matches: 83, Mismatches: 14, Indels: 5
0.81 0.14 0.05
Matches are distributed among these distances:
93 48 0.58
94 33 0.40
95 2 0.02
ACGTcount: A:0.39, C:0.12, G:0.22, T:0.26
Consensus pattern (95 bp):
GTATCGGTACTAAGAGAAAGGTATTGATACCAATGATTCCAGAATGCAAAAATGAAATCGATACT
GAAAGAGAATATCGATACCAGAGTATAGAA
Found at i:65216 original size:54 final size:54
Alignment explanation
Indices: 65152--65654 Score: 679
Period size: 54 Copynumber: 9.3 Consensus size: 54
65142 GATTACCGAA
* * * **
65152 TGGCACTATGTATGCAACCTAAGAAATTTATAATGAGTTTATGAATTTCTATAT
1 TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
65206 TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
1 TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
* * **
65260 TGGCACTATGTGCGCAACCTAAGAAATTAATAATAAGTTTATGAATTTTTGTAT
1 TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
* * * * *
65314 CGGCATTATGTGTGCAACATAAGAAATTTATAATAAGTTTATGAATTTCCATAT
1 TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
* * *
65368 TGGCACTATGTGAGCAACCTAAGAAATTCATAATGAGTTTATGAATTTCCATAT
1 TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
* * *
65422 TGGCACTATGTGTGCAACCTAAGAAATTCATAATGAGTTTAT-TATTTTCGTAT
1 TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
* *
65475 TGGCACTATGTGTGCAGCCTAAGAAATTCATAATAAGTTTATAAATGTT-CGTAT
1 TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAAT-TTCCGTAT
65529 TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
1 TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
* * * * * * * *
65583 TGGTACTGTGTGTGCAACCCCACGTAATTCATGATAAGTTTGTGAATTAT-CATAT
1 TGGCACTATGTGTGCAA-CCTAAGAAATTCATAATAAGTTTATGAATT-TCCGTAT
*
65638 TGGCACTACGTGTGCAA
1 TGGCACTATGTGTGCAA
65655 ACAATAGAGG
Statistics
Matches: 401, Mismatches: 43, Indels: 9
0.89 0.09 0.02
Matches are distributed among these distances:
53 50 0.12
54 305 0.76
55 45 0.11
56 1 0.00
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Consensus pattern (54 bp):
TGGCACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTAT
Found at i:72748 original size:10 final size:10
Alignment explanation
Indices: 72730--72787 Score: 64
Period size: 10 Copynumber: 5.5 Consensus size: 10
72720 GCTATTTTTT
72730 AAAAAAAAAC
1 AAAAAAAAAC
72740 AAAACAAAAAGGC
1 AAAA-AAAAA--C
72753 AAAAAAAAAAC
1 -AAAAAAAAAC
72764 AAAAAAAAA-
1 AAAAAAAAAC
*
72773 ACAAAAAAAC
1 AAAAAAAAAC
72783 AAAAA
1 AAAAA
72788 TTTCAAAAAA
Statistics
Matches: 41, Mismatches: 2, Indels: 10
0.77 0.04 0.19
Matches are distributed among these distances:
9 8 0.20
10 17 0.41
11 6 0.15
13 6 0.15
14 4 0.10
ACGTcount: A:0.86, C:0.10, G:0.03, T:0.00
Consensus pattern (10 bp):
AAAAAAAAAC
Found at i:72759 original size:11 final size:11
Alignment explanation
Indices: 72730--72781 Score: 77
Period size: 11 Copynumber: 4.5 Consensus size: 11
72720 GCTATTTTTT
72730 AAAAAAAAACA
1 AAAAAAAAACA
*
72741 AAACAAAAAGGCA
1 AAA-AAAAA-ACA
72754 AAAAAAAAACA
1 AAAAAAAAACA
72765 AAAAAAAAACA
1 AAAAAAAAACA
72776 AAAAAA
1 AAAAAA
72782 CAAAAATTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 4
0.86 0.05 0.09
Matches are distributed among these distances:
11 22 0.59
12 10 0.27
13 5 0.14
ACGTcount: A:0.87, C:0.10, G:0.04, T:0.00
Consensus pattern (11 bp):
AAAAAAAAACA
Found at i:72762 original size:19 final size:18
Alignment explanation
Indices: 72730--72787 Score: 71
Period size: 19 Copynumber: 3.1 Consensus size: 18
72720 GCTATTTTTT
*
72730 AAAAAAAAACAAAACAAA
1 AAAAAAAAAAAAAACAAA
**
72748 AAGGCAAAAAAAAAACAAA
1 AA-AAAAAAAAAAAACAAA
72767 AAAAAAACAAAAAAACAAA
1 AAAAAAA-AAAAAAACAAA
72786 AA
1 AA
72788 TTTCAAAAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 3
0.80 0.12 0.07
Matches are distributed among these distances:
18 5 0.15
19 28 0.85
ACGTcount: A:0.86, C:0.10, G:0.03, T:0.00
Consensus pattern (18 bp):
AAAAAAAAAAAAAACAAA
Found at i:72786 original size:24 final size:24
Alignment explanation
Indices: 72730--72781 Score: 81
Period size: 24 Copynumber: 2.2 Consensus size: 24
72720 GCTATTTTTT
*
72730 AAAAAAAAACAAAACAAAAAGGCA
1 AAAAAAAAACAAAACAAAAAGACA
72754 AAAAAAAAACAAAA-AAAAA-ACA
1 AAAAAAAAACAAAACAAAAAGACA
72776 AAAAAA
1 AAAAAA
72782 CAAAAATTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
22 8 0.30
23 5 0.19
24 14 0.52
ACGTcount: A:0.87, C:0.10, G:0.04, T:0.00
Consensus pattern (24 bp):
AAAAAAAAACAAAACAAAAAGACA
Found at i:77760 original size:22 final size:21
Alignment explanation
Indices: 77735--77775 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
77725 TGAGAAATTG
*
77735 TTTTTAAAATATAAAAATGATA
1 TTTTGAAAATA-AAAAATGATA
*
77757 TTTTGAAATTAAAAAATGA
1 TTTTGAAAATAAAAAATGA
77776 AAATAATCTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.54, C:0.00, G:0.07, T:0.39
Consensus pattern (21 bp):
TTTTGAAAATAAAAAATGATA
Found at i:83419 original size:21 final size:22
Alignment explanation
Indices: 83371--83420 Score: 57
Period size: 24 Copynumber: 2.2 Consensus size: 22
83361 AACAAAAAGG
* *
83371 GGGAGAAGTGTTAAGGTATTAAGG
1 GGGAGAAGTGTTAA-G-AGTAAGA
83395 GGGAGAAGTGTTAA-AGTAAGA
1 GGGAGAAGTGTTAAGAGTAAGA
83416 GGGAG
1 GGGAG
83421 TAATTTCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 10 0.42
24 14 0.58
ACGTcount: A:0.36, C:0.00, G:0.44, T:0.20
Consensus pattern (22 bp):
GGGAGAAGTGTTAAGAGTAAGA
Found at i:86852 original size:54 final size:54
Alignment explanation
Indices: 86770--87407 Score: 900
Period size: 54 Copynumber: 11.8 Consensus size: 54
86760 ACCGAATGAT
* *
86770 ACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTACGAATTTCCATATTGGC
1 ACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGC
* ** *
86824 ACTATGTGTGCAACCTAAGAAAATCATAATAAGTTTATGAATTTATGCATTGGC
1 ACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGC
* *
86878 ACTACGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCATATTGGC
1 ACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGC
* * * *
86932 ACTATGTGTGCAACCTAATAAATTCATAATAAGTTTATGATTTTACGTATTGTC
1 ACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGC
* * *
86986 ACTACGTGTACAACCTAAGAAATTCATAATGAA-TTTATGAATTTCCATATTGGC
1 ACTATGTGTGCAACCTAAGAAATTCATAAT-AAGTTTATGAATTTCCGTATTGGC
** * * *
87040 ACTATGTGTATAACCTAATAAATTCATAATGAGTTTATGAATTTCCGTATTGGA
1 ACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGC
* **
87094 ACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTAAGAATTTATGTATTGGC
1 ACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGC
* * *
87148 ACTATGTTTTCAACCTAAGAAATTCATAATAAGCTTATGAATTTCCGTATTGGC
1 ACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGC
** *
87202 ACTATGTACGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGC
1 ACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGC
* * * *
87256 ACTACGTGTGCAACCTAAGAAATTCATAATTAGTTTATGAATTTTCGTATTGGT
1 ACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGC
* *
87310 ATTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTTCGTATTGGC
1 ACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGC
* * * *
87364 ACTGTGTGTGCAACCCCACGTAATTCATAATAAGTTTATGAATT
1 ACTATGTGTGCAA-CCTAAGAAATTCATAATAAGTTTATGAATT
87408 GCTATATTGG
Statistics
Matches: 517, Mismatches: 64, Indels: 5
0.88 0.11 0.01
Matches are distributed among these distances:
53 1 0.00
54 487 0.94
55 29 0.06
ACGTcount: A:0.35, C:0.14, G:0.15, T:0.36
Consensus pattern (54 bp):
ACTATGTGTGCAACCTAAGAAATTCATAATAAGTTTATGAATTTCCGTATTGGC
Found at i:96463 original size:36 final size:36
Alignment explanation
Indices: 96409--96547 Score: 199
Period size: 36 Copynumber: 3.9 Consensus size: 36
96399 ACGAAAGAAA
96409 GCATC-ACACTTCCAATTCAAATCGAACGGAATGAG
1 GCATCGACACTTCCAATTCAAATCGAACGGAATGAG
*
96444 GCATCGACACTTCCGATTCAAATCGAACGGAATGAG
1 GCATCGACACTTCCAATTCAAATCGAACGGAATGAG
** * * *
96480 GCATCGGTACTTCCGATTCAAATCGAACGGAAGGAA
1 GCATCGACACTTCCAATTCAAATCGAACGGAATGAG
* *
96516 GCATCGGCACTTCCAATTCAAATCAAACGGAA
1 GCATCGACACTTCCAATTCAAATCGAACGGAA
96548 AGATGTATTG
Statistics
Matches: 95, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
35 5 0.05
36 90 0.95
ACGTcount: A:0.35, C:0.25, G:0.20, T:0.19
Consensus pattern (36 bp):
GCATCGACACTTCCAATTCAAATCGAACGGAATGAG
Found at i:99846 original size:7 final size:7
Alignment explanation
Indices: 99834--99870 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
99824 AGAAGATAGT
99834 TGAGTGA
1 TGAGTGA
99841 TGAGTGA
1 TGAGTGA
99848 TGAGTGA
1 TGAGTGA
99855 TGAGTGA
1 TGAGTGA
*
99862 TGAATGA
1 TGAGTGA
99869 TG
1 TG
99871 TAATTTACCC
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.30, C:0.00, G:0.41, T:0.30
Consensus pattern (7 bp):
TGAGTGA
Found at i:105197 original size:5 final size:5
Alignment explanation
Indices: 105187--105211 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
105177 AATAGTGACA
105187 AAAAT AAAAT AAAAT AAAAT AAAAT
1 AAAAT AAAAT AAAAT AAAAT AAAAT
105212 GATAAAAGTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.00, T:0.20
Consensus pattern (5 bp):
AAAAT
Found at i:107051 original size:91 final size:91
Alignment explanation
Indices: 106508--107047 Score: 807
Period size: 91 Copynumber: 6.0 Consensus size: 91
106498 GCGATGAAGC
* * * * *** *
106508 GAGCTAAGGTTAAACAAGTTC-TCTCATTATGAACTTATTCTCCCTCATCAAATGAGTTATTTTC
1 GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTATTCTC
*
106572 ATTATGAACTCTCCA-TCGAAAATGTT
66 ATTATGAACTCTCCACTAG-AAATGTT
* * * * * *
106598 GAGCCAAGGTTGAAGAAGTTCTTGTCATTAAGAACTTCTTCTCCCTCATCGGATGAGTTCTTCTC
1 GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTATTCTC
*
106663 ATTATGAATTCTCCACTAGAAATGTT
66 ATTATGAACTCTCCACTAGAAATGTT
* * *
106689 GAGCCAACGTTGAACAAGTTCTTCTCATTATGAACTTTTTCTCCCTCGTTGGATGAGTTCTTCTC
1 GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTATTCTC
106754 ATTATGAACTCTCCACTAGAAATGTT
66 ATTATGAACTCTCCACTAGAAATGTT
* * *
106780 GAGCCAAGGTTAAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAATTGTTCTC
1 GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTATTCTC
*
106845 ATTATAAACTCTCCACTAGAAATGTT
66 ATTATGAACTCTCCACTAGAAATGTT
106871 GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTATTCTC
1 GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTATTCTC
* *
106936 ATTATGAACTCCCCACTGGAAATGTT
66 ATTATGAACTCTCCACTAGAAATGTT
*
106962 GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTATTCTCCCTCGTTGGATGAGTTATTCTC
1 GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTATTCTC
*
107027 ATTATGAACTCTCTA-TAGAAA
66 ATTATGAACTCTCCACTAGAAA
107048 ATGTCAATCC
Statistics
Matches: 412, Mismatches: 36, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
90 23 0.06
91 387 0.94
92 2 0.00
ACGTcount: A:0.27, C:0.21, G:0.16, T:0.36
Consensus pattern (91 bp):
GAGCCAAGGTTGAACAAGTTCTTCTCATTATGAACTTCTTCTCCCTCGTTGGATGAGTTATTCTC
ATTATGAACTCTCCACTAGAAATGTT
Found at i:107991 original size:58 final size:54
Alignment explanation
Indices: 107921--108076 Score: 161
Period size: 58 Copynumber: 2.7 Consensus size: 54
107911 CATTTAAAAA
**
107921 CATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTAAAAATCTTTCGTTCTCAG-TTGT
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTAAAAATCTTT-G----CAGATAAT
* * * * *
107979 CATCAAGAAACCCCTAAAAATTAGGCTTTGCTTCCTTTAAAAAATCTTTGGAGATAAT
1 CATCAAGAAACCCCTGAAAATCAGGCTTAG-TT--TCT-AAAAATCTTTGCAGATAAT
108037 CATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTAAAAA
1 CATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTAAAAA
108077 CTCATTTGAA
Statistics
Matches: 82, Mismatches: 11, Indels: 14
0.77 0.10 0.13
Matches are distributed among these distances:
54 5 0.06
55 2 0.02
57 4 0.05
58 56 0.68
59 2 0.02
61 3 0.04
62 10 0.12
ACGTcount: A:0.37, C:0.21, G:0.13, T:0.29
Consensus pattern (54 bp):
CATCAAGAAACCCCTGAAAATCAGGCTTAGTTTCTAAAAATCTTTGCAGATAAT
Found at i:108068 original size:116 final size:111
Alignment explanation
Indices: 107869--108076 Score: 310
Period size: 116 Copynumber: 1.8 Consensus size: 111
107859 ATTTAAATTT
* *
107869 ATCAAGAAACTCCTAAAATTAGGCATAGCTTCTTTTAAAAATCATTTAAAAACATCAAGAAACCC
1 ATCAAGAAACCCCTAAAATTAGGCATAGCTTCTTTAAAAAATCATTTAAAAACATCAAGAAACCC
107934 CTGAAAATCAGGCTTAGTTTCTAAAAATCTTTCGTTCTCAGTTGTC
66 CTGAAAATCAGGCTTAGTTTCTAAAAATCTTTCGTTCTCAGTTGTC
* * *
107980 ATCAAGAAACCCCTAAAAATTAGGCTTTGCTTCCTTTAAAAAATC-TTTGGAGATAATCATCAAG
1 ATCAAGAAACCCCT-AAAATTAGGCATAGCTT-CTTTAAAAAATCATTT--A-A-AAACATCAAG
108044 AAACCCCTGAAAATCAGGCTTAGTTTCTAAAAA
60 AAACCCCTGAAAATCAGGCTTAGTTTCTAAAAA
108077 CTCATTTGAA
Statistics
Matches: 86, Mismatches: 5, Indels: 7
0.88 0.05 0.07
Matches are distributed among these distances:
111 13 0.15
112 18 0.21
113 11 0.13
114 1 0.01
115 1 0.01
116 42 0.49
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.30
Consensus pattern (111 bp):
ATCAAGAAACCCCTAAAATTAGGCATAGCTTCTTTAAAAAATCATTTAAAAACATCAAGAAACCC
CTGAAAATCAGGCTTAGTTTCTAAAAATCTTTCGTTCTCAGTTGTC
Found at i:110396 original size:7 final size:7
Alignment explanation
Indices: 110390--110445 Score: 76
Period size: 7 Copynumber: 7.4 Consensus size: 7
110380 TCTTCATTCT
110390 TTTTTCTC
1 TTTTT-TC
110398 TTTTTTC
1 TTTTTTC
110405 TTTTTTC
1 TTTTTTC
110412 TTTTTTC
1 TTTTTTC
110419 TTTTTTCTC
1 -TTTTT-TC
110428 TCTTTTTC
1 T-TTTTTC
110436 TTTTTTC
1 TTTTTTC
110443 TTT
1 TTT
110446 CTTTTCTATA
Statistics
Matches: 45, Mismatches: 0, Indels: 7
0.87 0.00 0.13
Matches are distributed among these distances:
7 25 0.56
8 14 0.31
9 6 0.13
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (7 bp):
TTTTTTC
Found at i:110397 original size:16 final size:16
Alignment explanation
Indices: 110386--110452 Score: 95
Period size: 17 Copynumber: 4.2 Consensus size: 16
110376 TCTCTCTTCA
110386 TTCTTTTTTCTCTTTT
1 TTCTTTTTTCTCTTTT
110402 TTC-TTTTT-TCTTTT
1 TTCTTTTTTCTCTTTT
110416 TTCTTTTTTCTCTCTTT
1 TTCTTTTTTCTCT-TTT
110433 TTCTTTTTTCT-TTCTT
1 TTCTTTTTTCTCTT-TT
110449 TTCT
1 TTCT
110453 ATATTTTTTC
Statistics
Matches: 47, Mismatches: 0, Indels: 8
0.85 0.00 0.15
Matches are distributed among these distances:
14 9 0.19
15 11 0.23
16 13 0.28
17 14 0.30
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (16 bp):
TTCTTTTTTCTCTTTT
Found at i:110421 original size:30 final size:31
Alignment explanation
Indices: 110386--110445 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
110376 TCTCTCTTCA
110386 TTCTTTTTTCTCT-TTTTTCTTTTTTCTTTT
1 TTCTTTTTTCTCTCTTTTTCTTTTTTCTTTT
110416 TTCTTTTTTCTCTCTTTTTCTTTTTTCTTT
1 TTCTTTTTTCTCTCTTTTTCTTTTTTCTTT
110446 CTTTTCTATA
Statistics
Matches: 29, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
30 13 0.45
31 16 0.55
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (31 bp):
TTCTTTTTTCTCTCTTTTTCTTTTTTCTTTT
Found at i:110489 original size:16 final size:16
Alignment explanation
Indices: 110386--110491 Score: 96
Period size: 16 Copynumber: 6.6 Consensus size: 16
110376 TCTCTCTTCA
110386 TTCTTTTTTC-TCTTTT
1 TTCTTTTTTCTTC-TTT
110402 TTCTTTTTTC-T-TTT
1 TTCTTTTTTCTTCTTT
110416 TTCTTTTTTCTCTCTTT
1 TTCTTTTTTCT-TCTTT
110433 TTCTTTTTTCTT-TCTT
1 TTCTTTTTTCTTCT-TT
*
110449 TTCTATATTTT-TTCTGTG
1 TTCT-T-TTTTCTTCT-TT
**
110467 TGATTTTTTCTTCTTT
1 TTCTTTTTTCTTCTTT
110483 TTCTTTTTT
1 TTCTTTTTT
110492 GGTATACCTC
Statistics
Matches: 75, Mismatches: 7, Indels: 16
0.77 0.07 0.16
Matches are distributed among these distances:
14 13 0.17
15 1 0.01
16 31 0.41
17 22 0.29
18 8 0.11
ACGTcount: A:0.03, C:0.16, G:0.03, T:0.78
Consensus pattern (16 bp):
TTCTTTTTTCTTCTTT
Found at i:119136 original size:18 final size:18
Alignment explanation
Indices: 119110--119144 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
119100 TCGAAAGGAC
*
119110 TGAAGTAAATGATAAGAT
1 TGAAGTAAATAATAAGAT
*
119128 TGAATTAAATAATAAGA
1 TGAAGTAAATAATAAGA
119145 CCGGATGGAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.54, C:0.00, G:0.17, T:0.29
Consensus pattern (18 bp):
TGAAGTAAATAATAAGAT
Found at i:126069 original size:18 final size:18
Alignment explanation
Indices: 126046--126083 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
126036 TTCCATCCTG
*
126046 TCTTATTATTTAATTCAA
1 TCTTATCATTTAATTCAA
*
126064 TCTTATCATTTATTTCAA
1 TCTTATCATTTAATTCAA
126082 TC
1 TC
126084 ACATGTTCCA
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:0.29, C:0.16, G:0.00, T:0.55
Consensus pattern (18 bp):
TCTTATCATTTAATTCAA
Found at i:129259 original size:16 final size:16
Alignment explanation
Indices: 129238--129270 Score: 50
Period size: 16 Copynumber: 2.1 Consensus size: 16
129228 AAAAAACAAT
129238 AATAAA-ATAAATATAA
1 AATAAACATAAAT-TAA
129254 AATAAACATAAATTAA
1 AATAAACATAAATTAA
129270 A
1 A
129271 GGACCTAATT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 10 0.62
17 6 0.38
ACGTcount: A:0.73, C:0.03, G:0.00, T:0.24
Consensus pattern (16 bp):
AATAAACATAAATTAA
Found at i:130427 original size:2 final size:2
Alignment explanation
Indices: 130420--130453 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
130410 AACTACTACA
130420 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
130454 TACATACATA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:130565 original size:22 final size:22
Alignment explanation
Indices: 130540--130582 Score: 86
Period size: 22 Copynumber: 2.0 Consensus size: 22
130530 CAATTATTCA
130540 CAATTCAAACAACTCAAAAACT
1 CAATTCAAACAACTCAAAAACT
130562 CAATTCAAACAACTCAAAAAC
1 CAATTCAAACAACTCAAAAAC
130583 AAATGAAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.56, C:0.28, G:0.00, T:0.16
Consensus pattern (22 bp):
CAATTCAAACAACTCAAAAACT
Found at i:131686 original size:45 final size:45
Alignment explanation
Indices: 131635--131930 Score: 269
Period size: 45 Copynumber: 6.6 Consensus size: 45
131625 TAATCCAAGG
* * *
131635 CTTTTGATTATTGGGTTTCCAAAAGTAAAATCAAATGATTAGTTC
1 CTTTTGATTATTGGGTTGCCAAAATTAAAATCAAAGGATTAGTTC
** * *
131680 CTTTTGATTATTGTATTAG-CAAAAGTAAATTCAAAGGATTAGCTT-
1 CTTTTGATTATTGGGTT-GCCAAAATTAAAATCAAAGGATTAG-TTC
* *
131725 CTTTTGATTATTGGGTTGCCGATATTAAAATCAAAGGATTAGTTTC
1 CTTTTGATTATTGGGTTGCCAAAATTAAAATCAAAGGATTAG-TTC
* * *** *
131771 C-TTTGGTTACTGGG-TGAGGAAATTAAAATCAAAAGATTAGTTC
1 CTTTTGATTATTGGGTTGCCAAAATTAAAATCAAAGGATTAGTTC
* * * *
131814 ATTTTGATTACTAGGTTGCAAAAAATTAAAATCAAAGGATTAGTTC
1 CTTTTGATTATTGGGTTGC-CAAAATTAAAATCAAAGGATTAGTTC
* * * * * *
131860 CTTTTGATTATTGGGTTTG-GAAAATTAAAATATAAATGATCAATTT
1 CTTTTGATTATTGGG-TTGCCAAAATTAAAAT-CAAAGGATTAGTTC
*
131906 CTTTTGATTATTGGGTTGCTAAAAT
1 CTTTTGATTATTGGGTTGCCAAAAT
131931 CAAATGATTA
Statistics
Matches: 206, Mismatches: 35, Indels: 19
0.79 0.13 0.07
Matches are distributed among these distances:
43 3 0.01
44 34 0.17
45 99 0.48
46 67 0.33
47 3 0.01
ACGTcount: A:0.34, C:0.09, G:0.18, T:0.40
Consensus pattern (45 bp):
CTTTTGATTATTGGGTTGCCAAAATTAAAATCAAAGGATTAGTTC
Found at i:132153 original size:58 final size:58
Alignment explanation
Indices: 132037--132154 Score: 141
Period size: 58 Copynumber: 2.0 Consensus size: 58
132027 GTGTTGATTC
* * *
132037 TAACTTTGTAAAGAAAATAAATTGGTGAATTTATTTTATTGAAAATCTTTAATGATTA
1 TAACTTTGTAAAGAAAATAAATCGGTGAATTTATTTTATTGAAAATCTTGAATAATTA
* * * *
132095 TAACTTTGT-AAGTAAAATAAATCGTTGAATTTATTTTCTTGAGAAT-TGTGGATAATTA
1 TAACTTTGTAAAG-AAAATAAATCGGTGAATTTATTTTATTGAAAATCT-TGAATAATTA
132153 TA
1 TA
132155 TTTTATTAAA
Statistics
Matches: 51, Mismatches: 7, Indels: 4
0.82 0.11 0.06
Matches are distributed among these distances:
57 4 0.08
58 47 0.92
ACGTcount: A:0.39, C:0.04, G:0.14, T:0.43
Consensus pattern (58 bp):
TAACTTTGTAAAGAAAATAAATCGGTGAATTTATTTTATTGAAAATCTTGAATAATTA
Found at i:138881 original size:39 final size:39
Alignment explanation
Indices: 138838--138916 Score: 131
Period size: 39 Copynumber: 2.0 Consensus size: 39
138828 TTTATTTAAA
138838 TACAATAATATTTTCTTTTTCGCCTTTTAATATGATTTT
1 TACAATAATATTTTCTTTTTCGCCTTTTAATATGATTTT
** *
138877 TACAATTTTATTTTCTTTTTCGCCTTTTAATCTGATTTT
1 TACAATAATATTTTCTTTTTCGCCTTTTAATATGATTTT
138916 T
1 T
138917 TTATTTGTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
39 37 1.00
ACGTcount: A:0.22, C:0.14, G:0.05, T:0.59
Consensus pattern (39 bp):
TACAATAATATTTTCTTTTTCGCCTTTTAATATGATTTT
Found at i:138904 original size:19 final size:19
Alignment explanation
Indices: 138846--138905 Score: 50
Period size: 19 Copynumber: 3.1 Consensus size: 19
138836 AATACAATAA
138846 TATTTTCTTTTTCGCCTTT
1 TATTTTCTTTTTCGCCTTT
* ** **
138865 TAATATGATTTTTAC-AATTT
1 T-ATTTTCTTTTT-CGCCTTT
138885 TATTTTCTTTTTCGCCTTT
1 TATTTTCTTTTTCGCCTTT
138904 TA
1 TA
138906 ATCTGATTTT
Statistics
Matches: 28, Mismatches: 10, Indels: 6
0.64 0.23 0.14
Matches are distributed among these distances:
18 1 0.04
19 14 0.50
20 12 0.43
21 1 0.04
ACGTcount: A:0.17, C:0.15, G:0.05, T:0.63
Consensus pattern (19 bp):
TATTTTCTTTTTCGCCTTT
Found at i:139448 original size:16 final size:16
Alignment explanation
Indices: 139427--139463 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
139417 TTTTGTATAT
*
139427 TATATAATTTTTAAAA
1 TATATAAGTTTTAAAA
139443 TATAT-AGTTTTAAAA
1 TATATAAGTTTTAAAA
139458 TATATA
1 TATATA
139464 TAGTAAGGGT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
15 14 0.74
16 5 0.26
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (16 bp):
TATATAAGTTTTAAAA
Found at i:139464 original size:17 final size:16
Alignment explanation
Indices: 139427--139467 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
139417 TTTTGTATAT
* *
139427 TATATAATTTTTAAAA
1 TATATAGTTTTAAAAA
139443 TATATAGTTTTAAAATA
1 TATATAGTTTTAAAA-A
139460 TATATAGT
1 TATATAGT
139468 AAGGGTTCCC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 13 0.59
17 9 0.41
ACGTcount: A:0.46, C:0.00, G:0.05, T:0.49
Consensus pattern (16 bp):
TATATAGTTTTAAAAA
Found at i:140610 original size:13 final size:13
Alignment explanation
Indices: 140592--140616 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
140582 TGGAAGTTTT
140592 AATTTTAAATTTA
1 AATTTTAAATTTA
140605 AATTTTAAATTT
1 AATTTTAAATTT
140617 TGCAATTAAG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (13 bp):
AATTTTAAATTTA
Found at i:151232 original size:21 final size:20
Alignment explanation
Indices: 151207--151246 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 20
151197 GTTTTGAAAA
* *
151207 TTTAATATATATTATATAATT
1 TTTAAAATATAATAT-TAATT
151228 TTTAAAATATAATATTAAT
1 TTTAAAATATAATATTAAT
151247 ATATATATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 4 0.24
21 13 0.76
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (20 bp):
TTTAAAATATAATATTAATT
Found at i:151234 original size:28 final size:27
Alignment explanation
Indices: 151198--151251 Score: 72
Period size: 28 Copynumber: 2.0 Consensus size: 27
151188 ATCATACGAG
* *
151198 TTTTGAAAATTTAATATATATTATATAA
1 TTTTGAAAATATAATAT-TAATATATAA
*
151226 TTTTTAAAATATAATATTAATATATA
1 TTTTGAAAATATAATATTAATATATA
151252 TATATTATCC
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
27 8 0.35
28 15 0.65
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (27 bp):
TTTTGAAAATATAATATTAATATATAA
Found at i:151256 original size:14 final size:14
Alignment explanation
Indices: 151211--151258 Score: 50
Period size: 13 Copynumber: 3.7 Consensus size: 14
151201 TGAAAATTTA
151211 ATATATATT-ATAT
1 ATATATATTAATAT
* *
151224 A-AT-TTTTAAAAT
1 ATATATATTAATAT
151236 ATA-ATATTAATAT
1 ATATATATTAATAT
151249 ATATATATTA
1 ATATATATTA
151259 TCCTCTTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 7
0.71 0.11 0.18
Matches are distributed among these distances:
11 3 0.11
12 6 0.22
13 12 0.44
14 6 0.22
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (14 bp):
ATATATATTAATAT
Found at i:161496 original size:31 final size:29
Alignment explanation
Indices: 161461--161537 Score: 100
Period size: 31 Copynumber: 2.6 Consensus size: 29
161451 AGAGTTTATA
*
161461 TTTTTTTTGGGATTTTTAAGAATTTAGGAGT
1 TTTTTTTTGGGATTTTTAA-AATTTAAG-GT
*
161492 TTTTTTTTGAGATTTTTTAAAATTTAAGGT
1 TTTTTTTTGGGA-TTTTTAAAATTTAAGGT
*
161522 TTTTTTTTGGAATTTT
1 TTTTTTTTGGGATTTT
161538 AGCAATTTTA
Statistics
Matches: 41, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
29 4 0.10
30 12 0.29
31 18 0.44
32 7 0.17
ACGTcount: A:0.22, C:0.00, G:0.17, T:0.61
Consensus pattern (29 bp):
TTTTTTTTGGGATTTTTAAAATTTAAGGT
Found at i:161556 original size:31 final size:29
Alignment explanation
Indices: 161460--161557 Score: 101
Period size: 30 Copynumber: 3.2 Consensus size: 29
161450 TAGAGTTTAT
*
161460 ATTTTTTTTGGGATTTTTAAGAATTT-AGG
1 ATTTTTTTTTGGATTTTT-AGAATTTAAGG
*
161489 AGTTTTTTTTTGAGATTTTTTAAAATTTAAGG
1 A-TTTTTTTTTG-GA-TTTTTAGAATTTAAGG
*
161521 -TTTTTTTTTGGAATTTTAGCAATTTTAAGG
1 ATTTTTTTTTGGATTTTTAG-AA-TTTAAGG
161551 ATTTTTT
1 ATTTTTT
161558 AGAAAATAAC
Statistics
Matches: 58, Mismatches: 4, Indels: 12
0.78 0.05 0.16
Matches are distributed among these distances:
28 5 0.09
29 5 0.09
30 26 0.45
31 14 0.24
32 8 0.14
ACGTcount: A:0.24, C:0.01, G:0.16, T:0.58
Consensus pattern (29 bp):
ATTTTTTTTTGGATTTTTAGAATTTAAGG
Found at i:162542 original size:22 final size:21
Alignment explanation
Indices: 162516--162556 Score: 73
Period size: 22 Copynumber: 1.9 Consensus size: 21
162506 GCTGTGGAAT
162516 TGATGGTCTTGATGGATGAAGC
1 TGATGGTCTTGAT-GATGAAGC
162538 TGATGGTCTTGATGATGAA
1 TGATGGTCTTGATGATGAA
162557 ATGGAGATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.24, C:0.07, G:0.34, T:0.34
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGC
Found at i:164797 original size:17 final size:17
Alignment explanation
Indices: 164777--164809 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
164767 TCATTTCTGA
*
164777 TTTTTTTTCTTTTTGTC
1 TTTTCTTTCTTTTTGTC
164794 TTTTCTTTCTTTTTGT
1 TTTTCTTTCTTTTTGT
164810 ACTCTAATTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.00, C:0.12, G:0.06, T:0.82
Consensus pattern (17 bp):
TTTTCTTTCTTTTTGTC
Found at i:165153 original size:22 final size:21
Alignment explanation
Indices: 165127--165168 Score: 66
Period size: 22 Copynumber: 2.0 Consensus size: 21
165117 GGTTGTAGAA
165127 TTGATGGTCTTGATGGATGAAG
1 TTGATGGTCTTGAT-GATGAAG
*
165149 TTGATGGTGTTGATGATGAA
1 TTGATGGTCTTGATGATGAA
165169 ATGGAGATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.32
22 13 0.68
ACGTcount: A:0.24, C:0.02, G:0.36, T:0.38
Consensus pattern (21 bp):
TTGATGGTCTTGATGATGAAG
Found at i:172230 original size:54 final size:54
Alignment explanation
Indices: 172164--172347 Score: 253
Period size: 54 Copynumber: 3.4 Consensus size: 54
172154 TTTATTAAGA
* * *
172164 TGCACACGTAGTGCCTATACGGTCGTTCATCAACCTATGATGAATTCTGTGGGT
1 TGCACACATAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCTGTGGGT
* * *
172218 TGCACACATAGTGCATATACGATTGTTCATCAATATATGATGAATTAC-GTGGGT
1 TGCACACATAGTGCCTATACGGTTGTTCATCAACATATGATGAATT-CTGTGGGT
* * * *
172272 TGCACACATAGTGCCTGTATGGTTGTTCATCAACATATGATGGATTATGTGGGT
1 TGCACACATAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCTGTGGGT
*
172326 TGCACACATAGTGCCCATACGG
1 TGCACACATAGTGCCTATACGG
172348 AAATTCATAA
Statistics
Matches: 112, Mismatches: 16, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
54 111 0.99
55 1 0.01
ACGTcount: A:0.26, C:0.19, G:0.23, T:0.32
Consensus pattern (54 bp):
TGCACACATAGTGCCTATACGGTTGTTCATCAACATATGATGAATTCTGTGGGT
Found at i:172355 original size:54 final size:54
Alignment explanation
Indices: 172164--172371 Score: 240
Period size: 54 Copynumber: 3.9 Consensus size: 54
172154 TTTATTAAGA
* * *
172164 TGCACACGTAGTGCCTATACGG-TCGTTCATCAACCTATGATGAATTCTGTGGGT
1 TGCACACATAGTGCCTATACGGAT-GTTCATCAACATATGATGAATTATGTGGGT
* * *
172218 TGCACACATAGTGCATATAC-GATTGTTCATCAATATATGATGAATTACGTGGGT
1 TGCACACATAGTGCCTATACGGA-TGTTCATCAACATATGATGAATTATGTGGGT
* * * *
172272 TGCACACATAGTGCCTGTATGGTTGTTCATCAACATATGATGGATTATGTGGGT
1 TGCACACATAGTGCCTATACGGATGTTCATCAACATATGATGAATTATGTGGGT
* ** * * *
172326 TGCACACATAGTGCCCATACGGAAATTCATAAACTTATTATGAATT
1 TGCACACATAGTGCCTATACGGATGTTCATCAACATATGATGAATT
172372 TCTTAGTTTT
Statistics
Matches: 128, Mismatches: 23, Indels: 6
0.82 0.15 0.04
Matches are distributed among these distances:
53 1 0.01
54 125 0.98
55 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (54 bp):
TGCACACATAGTGCCTATACGGATGTTCATCAACATATGATGAATTATGTGGGT
Found at i:172369 original size:108 final size:108
Alignment explanation
Indices: 172164--172371 Score: 267
Period size: 108 Copynumber: 1.9 Consensus size: 108
172154 TTTATTAAGA
* * *
172164 TGCACACGTAGTGCCTATACGGTCGTTCATCAACCTATGATGAATTCTGTGGGTTGCACACATAG
1 TGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTGGGTTGCACACATAG
* ** *
172229 TGCATATACGATTGTTCATCAATATATGATGAATTACGTGGGT
66 TGCACATACGATAATTCATAAATATATGATGAATTACGTGGGT
* * * *
172272 TGCACACATAGTGCCTGTATGGTTGTTCATCAACATATGATGGATTATGTGGGTTGCACACATAG
1 TGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTGGGTTGCACACATAG
* *
172337 TGCCCATACGGA-AATTCATAAACT-TATTATGAATT
66 TGCACATAC-GATAATTCATAAA-TATATGATGAATT
172372 TCTTAGTTTT
Statistics
Matches: 85, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
108 82 0.96
109 3 0.04
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (108 bp):
TGCACACATAGTGCCTATACGGTCGTTCATCAACATATGATGAATTATGTGGGTTGCACACATAG
TGCACATACGATAATTCATAAATATATGATGAATTACGTGGGT
Found at i:172769 original size:19 final size:21
Alignment explanation
Indices: 172729--172784 Score: 71
Period size: 19 Copynumber: 2.7 Consensus size: 21
172719 TACCCCTACC
172729 ATGGTATCGATACTACTATATT
1 ATGGTATCGATACTAC-ATATT
172751 ATGGTATCGATACT-C-TATT
1 ATGGTATCGATACTACATATT
* *
172770 ACGGTACCGATACTA
1 ATGGTATCGATACTA
172785 TTTCTGCATT
Statistics
Matches: 31, Mismatches: 2, Indels: 4
0.84 0.05 0.11
Matches are distributed among these distances:
19 16 0.52
21 1 0.03
22 14 0.45
ACGTcount: A:0.30, C:0.18, G:0.16, T:0.36
Consensus pattern (21 bp):
ATGGTATCGATACTACATATT
Found at i:175311 original size:24 final size:24
Alignment explanation
Indices: 175284--175349 Score: 98
Period size: 24 Copynumber: 2.8 Consensus size: 24
175274 TCTATGCGAT
175284 ACTTTATGTGCAATTCTACGTGGC
1 ACTTTATGTGCAATTCTACGTGGC
*
175308 ACTTTATGTGCAATTCTATGTGGC
1 ACTTTATGTGCAATTCTACGTGGC
*
175332 A-TTACATGTGCAATTCTA
1 ACTT-TATGTGCAATTCTA
175350 TGCGACACTA
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
23 2 0.05
24 37 0.95
ACGTcount: A:0.24, C:0.18, G:0.18, T:0.39
Consensus pattern (24 bp):
ACTTTATGTGCAATTCTACGTGGC
Found at i:175329 original size:12 final size:12
Alignment explanation
Indices: 175288--175351 Score: 62
Period size: 12 Copynumber: 5.3 Consensus size: 12
175278 TGCGATACTT
175288 TATGTGCAATTC
1 TATGTGCAATTC
* *
175300 TACGTGGCACTT-
1 TATGT-GCAATTC
175312 TATGTGCAATTC
1 TATGTGCAATTC
175324 TATGTGGC-ATTAC
1 TATGT-GCAATT-C
175337 -ATGTGCAATTC
1 TATGTGCAATTC
175348 TATG
1 TATG
175352 CGACACTATT
Statistics
Matches: 42, Mismatches: 4, Indels: 12
0.72 0.07 0.21
Matches are distributed among these distances:
11 8 0.19
12 26 0.62
13 8 0.19
ACGTcount: A:0.23, C:0.17, G:0.20, T:0.39
Consensus pattern (12 bp):
TATGTGCAATTC
Found at i:179422 original size:23 final size:23
Alignment explanation
Indices: 179370--179446 Score: 100
Period size: 23 Copynumber: 3.2 Consensus size: 23
179360 AAATATTAAA
*
179370 TAATTAAATTAATTTTAATCATTAAT
1 TAATT-AATTAATTTTGAT-A-TAAT
179396 TAATTAATTAATTTTGATATAAT
1 TAATTAATTAATTTTGATATAAT
* *
179419 TAATTAATTAATTTTGGTAAAAT
1 TAATTAATTAATTTTGATATAAT
179442 TAATT
1 TAATT
179447 TTTCTATAAT
Statistics
Matches: 48, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
23 30 0.62
24 1 0.02
25 12 0.25
26 5 0.10
ACGTcount: A:0.44, C:0.01, G:0.04, T:0.51
Consensus pattern (23 bp):
TAATTAATTAATTTTGATATAAT
Found at i:179446 original size:4 final size:4
Alignment explanation
Indices: 179354--179431 Score: 60
Period size: 4 Copynumber: 20.5 Consensus size: 4
179344 ATTCATATAC
* * *
179354 TTAA TTAA AT-A TTAA ATAA TTAAA TTAA TT-- TTAA -TCA TTAA TTAA
1 TTAA TTAA TTAA TTAA TTAA TT-AA TTAA TTAA TTAA TTAA TTAA TTAA
*
179399 TTAA TTAA TT-- TTGA TATAA TTAA TTAA TTAA TT
1 TTAA TTAA TTAA TTAA T-TAA TTAA TTAA TTAA TT
179432 TTGGTAAAAT
Statistics
Matches: 59, Mismatches: 7, Indels: 16
0.72 0.09 0.20
Matches are distributed among these distances:
2 4 0.07
3 4 0.07
4 44 0.75
5 7 0.12
ACGTcount: A:0.47, C:0.01, G:0.01, T:0.50
Consensus pattern (4 bp):
TTAA
Found at i:180767 original size:26 final size:24
Alignment explanation
Indices: 180738--180809 Score: 67
Period size: 24 Copynumber: 3.0 Consensus size: 24
180728 TTTATGTTTA
180738 GTATTATATATAATTTTATATTATGT
1 GTATTATATAT-ATTTTATATTAT-T
*
180764 GTATT-TATAT-TATATATATTATT
1 GTATTATATATAT-TTTATATTATT
* * *
180787 ATAGTATTTATATTTTATATTAT
1 GTATTATATATATTTTATATTAT
180810 ATAGTATATT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
23 5 0.13
24 22 0.58
25 6 0.16
26 5 0.13
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.60
Consensus pattern (24 bp):
GTATTATATATATTTTATATTATT
Found at i:180776 original size:32 final size:33
Alignment explanation
Indices: 180734--180853 Score: 109
Period size: 32 Copynumber: 3.5 Consensus size: 33
180724 GATTTTTATG
* *
180734 TTTAGTATTATATATAATT-TTATATTATGTGTA-
1 TTTA-TATTATATAT-ATTATTATAGTATGTATAT
*
180767 TTTATATTATATATATTATTATAGTATTTATAT
1 TTTATATTATATATATTATTATAGTATGTATAT
* *
180800 TTTATATTATATAGTATATTATTAAATAATATTTATAT
1 TTTATA-T-TATA-TATATTATT--ATAGTATGTATAT
180838 TTTATATTTATATATA
1 TTTATA-TTATATATA
180854 GTATATATTA
Statistics
Matches: 76, Mismatches: 4, Indels: 11
0.84 0.04 0.12
Matches are distributed among these distances:
31 3 0.04
32 21 0.28
33 10 0.13
34 1 0.01
35 4 0.05
36 13 0.17
37 4 0.05
38 20 0.26
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (33 bp):
TTTATATTATATATATTATTATAGTATGTATAT
Found at i:180783 original size:24 final size:23
Alignment explanation
Indices: 180750--180821 Score: 92
Period size: 24 Copynumber: 3.0 Consensus size: 23
180740 ATTATATATA
*
180750 ATTTTATATTATGT-GTATTTAT
1 ATTTTATATTATATAGTATTTAT
180772 ATTATATATATTATTATAGTATTTAT
1 ATT-T-TATATTA-TATAGTATTTAT
180798 ATTTTATATTATATAGTATATTAT
1 ATTTTATATTATATAGTAT-TTAT
180822 TAAATAATAT
Statistics
Matches: 44, Mismatches: 1, Indels: 8
0.83 0.02 0.15
Matches are distributed among these distances:
22 3 0.07
23 9 0.20
24 18 0.41
25 3 0.07
26 11 0.25
ACGTcount: A:0.35, C:0.00, G:0.06, T:0.60
Consensus pattern (23 bp):
ATTTTATATTATATAGTATTTAT
Found at i:180835 original size:31 final size:31
Alignment explanation
Indices: 180765--180862 Score: 87
Period size: 33 Copynumber: 3.1 Consensus size: 31
180755 ATATTATGTG
* *
180765 TATTTATATTATATATATTATTATAGTATTTA
1 TATTTATATTATATATATTATTATAG-AATAA
180797 TATTTTATATTATATAGTA-TATTATTA-AATAA
1 TA-TTTATATTATATA-TATTATTA-TAGAATAA
* *
180829 TATTTATATTTTATAT-TTATATATAGTAT-A
1 TATTTATATTATATATATTAT-TATAGAATAA
180859 TATT
1 TATT
180863 ACATTATTAT
Statistics
Matches: 56, Mismatches: 4, Indels: 14
0.76 0.05 0.19
Matches are distributed among these distances:
30 11 0.20
31 16 0.29
32 7 0.12
33 18 0.32
34 4 0.07
ACGTcount: A:0.39, C:0.00, G:0.03, T:0.58
Consensus pattern (31 bp):
TATTTATATTATATATATTATTATAGAATAA
Found at i:180882 original size:64 final size:63
Alignment explanation
Indices: 180765--180919 Score: 151
Period size: 64 Copynumber: 2.5 Consensus size: 63
180755 ATATTATGTG
**
180765 TATTTATATTATATATATTATTATAGTATTTATATTTTATATTATATAGTATATTATTAAATAA
1 TATTTATATTATATATATTATTATAGTA-TTATATTACATATTATATAGTATATTATTAAATAA
* * *
180829 TATTTATATTTTATAT-TTATATATAGTA-TATATTACATTATTAT-TAGTTTA-TATTATAT-A
1 TATTTATATTATATATATTAT-TATAGTATTATATTACA-TATTATATAGTATATTATTAAATAA
* *
180889 TATATCATA-TATATAATATATGTTATAGTAT
1 TAT-TTATATTATAT-ATAT-TATTATAGTAT
180920 ACGATATATA
Statistics
Matches: 76, Mismatches: 8, Indels: 15
0.77 0.08 0.15
Matches are distributed among these distances:
60 8 0.11
61 13 0.17
62 21 0.28
63 12 0.16
64 22 0.29
ACGTcount: A:0.39, C:0.01, G:0.04, T:0.55
Consensus pattern (63 bp):
TATTTATATTATATATATTATTATAGTATTATATTACATATTATATAGTATATTATTAAATAA
Found at i:180928 original size:2 final size:2
Alignment explanation
Indices: 180769--180909 Score: 60
Period size: 2 Copynumber: 75.5 Consensus size: 2
180759 TATGTGTATT
* *
180769 TA TA T- TA TA TA TA T- TA T- TA TA GTA TT TA TA T- TT TA TA T-
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA
* * * *
180807 TA TA TA GTA TA T- TA T- TA AA TA -A TA TT TA TA T- TT TA TA TT
1 TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
180846 TA TA TA TA GTA TA TA T- TA CA T- TA T- TA T- TA GTT TA TA T- TA
1 TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA
180885 TA TA TA TA TCA TA TA TA TA -A TA TA T
1 TA TA TA TA T-A TA TA TA TA TA TA TA T
180910 GTTATAGTAT
Statistics
Matches: 105, Mismatches: 14, Indels: 40
0.66 0.09 0.25
Matches are distributed among these distances:
1 15 0.14
2 81 0.77
3 9 0.09
ACGTcount: A:0.40, C:0.01, G:0.03, T:0.55
Consensus pattern (2 bp):
TA
Found at i:180944 original size:7 final size:7
Alignment explanation
Indices: 180765--180944 Score: 91
Period size: 7 Copynumber: 26.3 Consensus size: 7
180755 ATATTATGTG
180765 TATT-TA
1 TATTATA
180771 TATTATA
1 TATTATA
180778 TA-TAT-
1 TATTATA
180783 TATTATA
1 TATTATA
180790 GTATT-TA
1 -TATTATA
*
180797 TATTTTA
1 TATTATA
180804 TATTATA
1 TATTATA
*
180811 TAGTATA
1 TATTATA
180818 TTATTA-A
1 -TATTATA
*
180825 -ATAATA
1 TATTATA
180831 T-TTATA
1 TATTATA
*
180837 TTTTATA
1 TATTATA
180844 T-TTATA
1 TATTATA
180850 TATAGTATA
1 TAT--TATA
*
180859 TATTACA
1 TATTATA
180866 TTATTAT-
1 -TATTATA
180873 TAGTT-TA
1 TA-TTATA
180880 TATTATA
1 TATTATA
180887 TA-TATA
1 TATTATA
180893 TCA-TATA
1 T-ATTATA
*
180900 TATAATA
1 TATTATA
180907 TATGT-TA
1 TAT-TATA
*
180914 TAGTATA
1 TATTATA
*
180921 CGA-TATA
1 -TATTATA
*
180928 TAGTTTTA
1 TA-TTATA
180936 TATTATA
1 TATTATA
180943 TA
1 TA
180945 ATACAATATT
Statistics
Matches: 137, Mismatches: 14, Indels: 45
0.70 0.07 0.23
Matches are distributed among these distances:
5 5 0.04
6 39 0.28
7 67 0.49
8 19 0.14
9 7 0.05
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.54
Consensus pattern (7 bp):
TATTATA
Found at i:198195 original size:16 final size:16
Alignment explanation
Indices: 198174--198206 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
198164 CCCATTTATC
198174 ATTTTAAAACACACTT
1 ATTTTAAAACACACTT
198190 ATTTTAAAACACACTT
1 ATTTTAAAACACACTT
198206 A
1 A
198207 AAACACACAC
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.45, C:0.18, G:0.00, T:0.36
Consensus pattern (16 bp):
ATTTTAAAACACACTT
Found at i:218004 original size:216 final size:215
Alignment explanation
Indices: 217621--218055 Score: 559
Period size: 216 Copynumber: 2.0 Consensus size: 215
217611 TCGATGAGCT
* * * * * *
217621 ATTTTCCATCCAAGGTTTTCAAGTCGAATTTCAACTTCACGACGAAGTATATTAGACTAGAAGAA
1 ATTTTCAAACCAAGGTTTTCAAGTCAAATTTCAACTTCACCACAAAGGATATTAGACTAGAAGAA
* * * * * *
217686 GATCGAAAATCAACTGTGATTTAGCTTAACTCAACAACGAGGAGCTACTTCCCAATCTAGATTTC
66 GACCAAAAATCAACTGCGATTTAACTTAACACAACAACGAGGAACTACTTCCCAATCTAGATTTC
* * * * ***
217751 GATATAGATTTCAACTTCATGATGAAGGATATCATGCTCCAGTCATTTGAGATCGAATT-AACTT
131 GAGATAGATTTCAACTTCATAAAGAAGGATATCATGCTCAAGTC-TCCAAGATCG-ATTCAACTT
* * *
217815 CATGAAGAAGTATTCATCCATA
194 CACGAAGAAGGAGTCATCCATA
* *
217837 ATTTTCAAACCAAGGTTTTCATGTCAAATTTCAACTTCACCACAAAGGATATTGGACTAGAAGAA
1 ATTTTCAAACCAAGGTTTTCAAGTCAAATTTCAACTTCACCACAAAGGATATTAGACTAGAAGAA
* * *
217902 GACCAAAAATCAATTGCGATTTAACTTAACACAACAACGAGGAACTATTTCCCAATCTAGATTTT
66 GACCAAAAATCAACTGCGATTTAACTTAACACAACAACGAGGAACTACTTCCCAATCTAGATTTC
* *
217967 GAGCTAGCTTTCAACTTCA-AACAGAAGGATATCATGCTCAAGTCTCCAAGATCGATTCAACTTC
131 GAGATAGATTTCAACTTCATAA-AGAAGGATATCATGCTCAAGTCTCCAAGATCGATTCAACTTC
*
218031 ACGACGAAGGAGTCATCCATA
195 ACGAAGAAGGAGTCATCCATA
218052 ATTT
1 ATTT
218056 AGCTTAACTA
Statistics
Matches: 187, Mismatches: 30, Indels: 5
0.84 0.14 0.02
Matches are distributed among these distances:
214 3 0.02
215 35 0.19
216 149 0.80
ACGTcount: A:0.36, C:0.20, G:0.15, T:0.29
Consensus pattern (215 bp):
ATTTTCAAACCAAGGTTTTCAAGTCAAATTTCAACTTCACCACAAAGGATATTAGACTAGAAGAA
GACCAAAAATCAACTGCGATTTAACTTAACACAACAACGAGGAACTACTTCCCAATCTAGATTTC
GAGATAGATTTCAACTTCATAAAGAAGGATATCATGCTCAAGTCTCCAAGATCGATTCAACTTCA
CGAAGAAGGAGTCATCCATA
Found at i:218778 original size:19 final size:20
Alignment explanation
Indices: 218751--218907 Score: 80
Period size: 21 Copynumber: 7.8 Consensus size: 20
218741 TATTGTTTTG
218751 TTTAGTATTAT-GTATATAGT
1 TTTA-TATTATAGTATATAGT
218771 TTTATATTATGTAGTATATAGT
1 TTTATATTA--TAGTATATAGT
* *
218793 ATTTGTATTATAGTATTTATGT
1 -TTTATATTATAGTATATA-GT
218815 TTTATAATATATAGTATAT--T
1 TTTAT-AT-TATAGTATATAGT
* * * *
218835 ATTATATAATA-TTTATA-A
1 TTTATATTATAGTATATAGT
*
218853 TCTATATTTATA-TATATAGT
1 TTTATA-TTATAGTATATAGT
* *
218873 ATATATATATATATTAT-TAG-
1 -TTTATAT-TATAGTATATAGT
218893 TTTATATTATA-TATA
1 TTTATATTATAGTATA
218908 GAATACGTAT
Statistics
Matches: 108, Mismatches: 15, Indels: 30
0.71 0.10 0.20
Matches are distributed among these distances:
17 7 0.06
18 11 0.10
19 22 0.20
20 10 0.09
21 25 0.23
22 16 0.15
23 17 0.16
ACGTcount: A:0.37, C:0.01, G:0.08, T:0.55
Consensus pattern (20 bp):
TTTATATTATAGTATATAGT
Found at i:218841 original size:17 final size:17
Alignment explanation
Indices: 218816--218908 Score: 60
Period size: 17 Copynumber: 5.8 Consensus size: 17
218806 TATTTATGTT
*
218816 TTATAATATATAGTATA
1 TTATTATATATAGTATA
218833 TTATTATATA-A-TAT-
1 TTATTATATATAGTATA
*
218847 TTA-TA-ATCTA-TAT-
1 TTATTATATATAGTATA
218860 TTA-TATATATAGTATA
1 TTATTATATATAGTATA
*
218876 TATATATATATTATTAGTTTA
1 T-TAT-TATA-TA-TAGTATA
218897 -TATTATATATAG
1 TTATTATATATAG
218909 AATACGTATA
Statistics
Matches: 63, Mismatches: 4, Indels: 19
0.73 0.05 0.22
Matches are distributed among these distances:
12 2 0.03
13 11 0.17
14 7 0.11
15 6 0.10
16 5 0.08
17 13 0.21
18 4 0.06
19 7 0.11
20 2 0.03
21 6 0.10
ACGTcount: A:0.42, C:0.01, G:0.04, T:0.53
Consensus pattern (17 bp):
TTATTATATATAGTATA
Found at i:218842 original size:2 final size:2
Alignment explanation
Indices: 218817--218972 Score: 72
Period size: 2 Copynumber: 82.5 Consensus size: 2
218807 ATTTATGTTT
* *
218817 TA TA -A TA TA TA GTA TA T- TA T- TA TA TA -A TA TT TA TA -A TC
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
* *
218855 TA TA TT TA TA TA TA TA GTA TA TA TA TA TA TA T- TA T- TA GTT TA
1 TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA -TA TA
* **
218897 TA T- TA TA TA TA GA -A TA CG TA TA GTA TA TA TA TA T- TA TA GTA
1 TA TA TA TA TA TA TA TA TA TA TA TA -TA TA TA TA TA TA TA TA -TA
* *
218938 TA -A AA TA TA TA GT- TT TA TA T- TA TA TA -A TA TA -A TA T
1 TA TA TA TA TA TA -TA TA TA TA TA TA TA TA TA TA TA TA TA T
218973 TCAATATAAT
Statistics
Matches: 118, Mismatches: 15, Indels: 42
0.67 0.09 0.24
Matches are distributed among these distances:
1 15 0.13
2 93 0.79
3 10 0.08
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.49
Consensus pattern (2 bp):
TA
Found at i:218846 original size:13 final size:14
Alignment explanation
Indices: 218822--218907 Score: 62
Period size: 15 Copynumber: 6.4 Consensus size: 14
218812 TGTTTTATAA
218822 TATATAGTATATTAT
1 TATATA-TATATTAT
218837 TATATA-ATA-T-T
1 TATATATATATTAT
*
218848 TATA-ATCTA-TATT
1 TATATATATATTA-T
*
218861 TATATATATAGTAT
1 TATATATATATTAT
218875 ATATATATATATTAT
1 -TATATATATATTAT
218890 TAGT-T-TATATTA-
1 TA-TATATATATTAT
218902 TATATA
1 TATATA
218908 GAATACGTAT
Statistics
Matches: 59, Mismatches: 3, Indels: 20
0.72 0.04 0.24
Matches are distributed among these distances:
10 1 0.02
11 9 0.15
12 4 0.07
13 15 0.25
14 8 0.14
15 22 0.37
ACGTcount: A:0.42, C:0.01, G:0.03, T:0.53
Consensus pattern (14 bp):
TATATATATATTAT
Found at i:218877 original size:11 final size:11
Alignment explanation
Indices: 218861--218939 Score: 62
Period size: 11 Copynumber: 7.4 Consensus size: 11
218851 AATCTATATT
218861 TATATATATAG
1 TATATATATAG
218872 TATATATATA-
1 TATATATATAG
218882 TATAT-TATTAG
1 TATATATA-TAG
*
218893 TTTATAT-TA-
1 TATATATATAG
*
218902 TATATAGAATACG
1 TATATA-TATA-G
218915 TATAGTATATA-
1 TATA-TATATAG
218926 TATAT-TATAG
1 TATATATATAG
218936 TATA
1 TATA
218940 AAATATATAG
Statistics
Matches: 55, Mismatches: 4, Indels: 19
0.71 0.05 0.24
Matches are distributed among these distances:
9 11 0.20
10 14 0.25
11 20 0.36
12 1 0.02
13 7 0.13
14 2 0.04
ACGTcount: A:0.43, C:0.01, G:0.08, T:0.48
Consensus pattern (11 bp):
TATATATATAG
Found at i:218971 original size:27 final size:26
Alignment explanation
Indices: 218816--218972 Score: 88
Period size: 27 Copynumber: 5.6 Consensus size: 26
218806 TATTTATGTT
218816 TTATA-ATAT-ATAGTATA-TTATTATA
1 TTATATATATAATA-TATAGTT-TTATA
* * *
218841 TAATATTTATAATCTATA-TTTATATA
1 TTATATATATAATATATAGTTT-TATA
*
218867 TATAGTATATATATATATATTATTAGTTTATA
1 T-TA-TATATATA-ATATA-TAGT--TTTATA
*
218899 TTATATATAGAATACGTATAGTATATATATA
1 TTATATATATAATA--TATAGT-T-T-TATA
*
218930 TTATAGTATAAAATATATAGTTTTATA
1 TTATA-TATATAATATATAGTTTTATA
218957 TTATATAATATAATAT
1 TTATAT-ATATAATAT
218973 TCAATATAAT
Statistics
Matches: 105, Mismatches: 11, Indels: 30
0.72 0.08 0.21
Matches are distributed among these distances:
25 5 0.05
26 15 0.14
27 20 0.19
28 8 0.08
29 9 0.09
30 19 0.18
31 14 0.13
32 13 0.12
33 2 0.02
ACGTcount: A:0.44, C:0.01, G:0.05, T:0.50
Consensus pattern (26 bp):
TTATATATATAATATATAGTTTTATA
Found at i:239522 original size:17 final size:20
Alignment explanation
Indices: 239477--239528 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 20
239467 CATCATGAGG
239477 AGAAAGAAGAGAAATGTAGAA
1 AGAAAGAAGA-AAATGTAGAA
239498 AGAGAAGAAGAAAA-G-A-AA
1 AGA-AAGAAGAAAATGTAGAA
239516 AGAAAGAA-AAAAT
1 AGAAAGAAGAAAAT
239529 TGAAAATGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 4 0.14
17 5 0.17
18 5 0.17
19 1 0.03
20 1 0.03
21 6 0.21
22 7 0.24
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.06
Consensus pattern (20 bp):
AGAAAGAAGAAAATGTAGAA
Found at i:241777 original size:34 final size:35
Alignment explanation
Indices: 241700--242075 Score: 433
Period size: 34 Copynumber: 10.9 Consensus size: 35
241690 AGCAAAGTCA
* * *
241700 ATCTTAAGTCTTCATC-GGAGAGTAGTGAAGCAATC
1 ATCTTAAGCCTTCA-CAGAAGAGTAGTGAAGCAACC
*
241735 ATCTTAAGCCTTCACAGAAGTGTAGTGAAGC-ACC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAACC
* *
241769 ATCTTAAGCCTTCATAGAGGAGTAGTGAAGCAAACC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGC-AACC
* * * *
241805 ATCTT-AGCCTTCACCGGAGAGTAGTGAGGCAATC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAACC
*
241839 ATCTTAAGCCTTCACAGAAGAGTAGTAAAGC-ACC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAACC
* *
241873 ATCTTAAGCCTTCACGGAGGAGTAGTGAAGCAAACC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGC-AACC
* * * * *
241909 ATCTTAATCCTTCACCGGAGAGTAGTGAAACAATC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAACC
*
241944 ATCTTAAACCTTCACAGAAGAGTAGTGAAGC-ACC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAACC
** * *
241978 ATCTTAAGCCTTCACAGGGGAGTAATAAAGC-ACC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAACC
* * *
242012 ATCTGAAGCCTTCACAGAGGAGTAATGAAGC-ACC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAACC
*
242046 ATCTTAAGCCTTCACCGAAGAGTAGTGAAG
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAG
242076 TAAATCCATC
Statistics
Matches: 291, Mismatches: 44, Indels: 13
0.84 0.13 0.04
Matches are distributed among these distances:
34 157 0.54
35 97 0.33
36 37 0.13
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (35 bp):
ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAACC
Found at i:241968 original size:105 final size:105
Alignment explanation
Indices: 241700--242075 Score: 539
Period size: 104 Copynumber: 3.6 Consensus size: 105
241690 AGCAAAGTCA
* * *
241700 ATCTTAAGTCTTCATCGGAGAGTAGTGAAGCAATCATCTTAAGCCTTCACAGAAGTGTAGTGAAG
1 ATCTTAAGCCTTCACCGGAGAGTAGTGAAGCAATCATCTTAAGCCTTCACAGAAGAGTAGTGAAG
**
241765 CACCATCTTAAGCCTTCATAGAGGAGTAGTGAAGCAAACC
66 CACCATCTTAAGCCTTCACGGAGGAGTAGTGAAGCAAACC
* *
241805 ATCTT-AGCCTTCACCGGAGAGTAGTGAGGCAATCATCTTAAGCCTTCACAGAAGAGTAGTAAAG
1 ATCTTAAGCCTTCACCGGAGAGTAGTGAAGCAATCATCTTAAGCCTTCACAGAAGAGTAGTGAAG
241869 CACCATCTTAAGCCTTCACGGAGGAGTAGTGAAGCAAACC
66 CACCATCTTAAGCCTTCACGGAGGAGTAGTGAAGCAAACC
* * *
241909 ATCTTAATCCTTCACCGGAGAGTAGTGAAACAATCATCTTAAACCTTCACAGAAGAGTAGTGAAG
1 ATCTTAAGCCTTCACCGGAGAGTAGTGAAGCAATCATCTTAAGCCTTCACAGAAGAGTAGTGAAG
* *
241974 CACCATCTTAAGCCTTCACAGG-GGAGTAATAAAGC--ACC
66 CACCATCTTAAGCCTTCAC-GGAGGAGTAGTGAAGCAAACC
* * * * *
242012 ATCTGAAGCCTTCA-CAGAGGAGTAATGAAGC-ACCATCTTAAGCCTTCACCGAAGAGTAGTGAA
1 ATCTTAAGCCTTCACCGGA-GAGTAGTGAAGCAATCATCTTAAGCCTTCACAGAAGAGTAGTGAA
242075 G
65 G
242076 TAAATCCATC
Statistics
Matches: 246, Mismatches: 22, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
102 33 0.13
103 25 0.10
104 97 0.39
105 89 0.36
106 2 0.01
ACGTcount: A:0.34, C:0.22, G:0.22, T:0.22
Consensus pattern (105 bp):
ATCTTAAGCCTTCACCGGAGAGTAGTGAAGCAATCATCTTAAGCCTTCACAGAAGAGTAGTGAAG
CACCATCTTAAGCCTTCACGGAGGAGTAGTGAAGCAAACC
Found at i:242936 original size:215 final size:213
Alignment explanation
Indices: 242081--243171 Score: 1532
Period size: 215 Copynumber: 5.1 Consensus size: 213
242071 TGAAGTAAAT
*
242081 CCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAATGATGTTTTAA
1 CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAATGATGTTTTAA
* * * * * *
242146 GAAGATGAAACTTTTGAAAATGAAGAATGCGATTTTTAAAATTTCATAATTTATAAGTCCTTTGG
66 GAAGATG-AATTTTTGAAAACGAAGAATGTGATTTTCAAAATTTCACAATTTATAAGTCC-TTCG
242211 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
129 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
* *
242276 AAGATGATAAGTCTTTCAGG
194 AAGATGATAAGTCCTTCGGG
* *
242296 CCATCCATGAA-ACCTTCGGGTAGGATGTTTTCACATGAAATTGAAAATGAAAAA--ATG----A
1 CCATCCAT-AAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAATGATGTTTTA
* * * *
242354 TGATG--GAATTTTTGAAAACAAAGAATGTGATTTACAAAATTTTCACAATTTATAAGTCCTTCG
65 AGAAGATGAATTTTTGAAAACGAAGAATGTGATTTTCAAAA-TTTCACAATTTATAAGTCCTTCG
* * * * *
242417 GGGCATCTGTAAGTCTTTTGATCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAGC
129 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
*
242482 AAGATGATAAGTCCTTTGGG
194 AAGATGATAAGTCCTTCGGG
* *
242502 CCAACCATAAGACTTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAATGATGTTTTA
1 CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATG-AAAAATGATGTTTTA
* *
242567 AGAAGATGGAATTTTTGAAAACGAAGAATGTGATTTTCAAAATTTCATAA--TAT-A-TCCCTCG
65 AGAAGAT-GAATTTTTGAAAACGAAGAATGTGATTTTCAAAATTTCACAATTTATAAGTCCTTCG
* * * *
242628 GGCCATCAATAAGTCTTTCGAGCATGATGTTTAAATCCTTCGAGTCATCTGTAAGTCTTTAGAGC
129 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
242693 AAGATGATAAGTCCTTCGGG
194 AAGATGATAAGTCCTTCGGG
242713 CCATCCATAAGACCTTCGGG-AGGGATGTTTTCAAATGAATTTGAAAATGAAAAAGTGATGTTTT
1 CCATCCATAAGACCTTCGGGTA-GGATGTTTTCAAATGAATTTGAAAATGAAAAA-TGATGTTTT
** *
242777 AAGAAGATGAATTTTTTGAAAACGAAGAATGCAATTTTCAAAATTTCACAATTTATAAGAACC-T
64 AAGAAGATGAA-TTTTTGAAAACGAAGAATGTGATTTTCAAAATTTCACAATTTATAAG-TCCTT
* * *
242841 CAGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGCTCATCTGTAAGCCTTTAGA
127 CGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGA
242906 GCAAGA-GTATAAGTCCTTCGGG
192 GCAAGATG-ATAAGTCCTTCGGG
* * *
242928 TCATCCATAAAACCTTCGGG-AGGGATGTTTTCAAATGAATTTGAAAATGAAAAGTGATGTTTTA
1 CCATCCATAAGACCTTCGGGTA-GGATGTTTTCAAATGAATTTGAAAATGAAAAATGATGTTTTA
* * *
242992 AGAATATGGAAGTTTTGAAAACGAAGAATGTGATTTTCAAAATTTCACAGTTTATAAGTCCTTCG
65 AGAAGAT-GAATTTTTGAAAACGAAGAATGTGATTTTCAAAATTTCACAATTTATAAGTCCTTCG
* *
243057 GGCCATCAGTAAGCCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATTTGTAAGCCTTTAGAGC
129 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
243122 AAGATGATAAGTCCTTCGGG
194 AAGATGATAAGTCCTTCGGG
* * *
243142 CAATCCATAAAACCTTCGGGTATGATGTTT
1 CCATCCATAAGACCTTCGGGTAGGATGTTT
243172 AAAAAGATTA
Statistics
Matches: 785, Mismatches: 65, Indels: 53
0.87 0.07 0.06
Matches are distributed among these distances:
205 2 0.00
206 149 0.19
207 24 0.03
209 7 0.01
210 9 0.01
211 181 0.23
212 1 0.00
213 15 0.02
214 167 0.21
215 194 0.25
216 36 0.05
ACGTcount: A:0.33, C:0.15, G:0.20, T:0.32
Consensus pattern (213 bp):
CCATCCATAAGACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAATGATGTTTTAA
GAAGATGAATTTTTGAAAACGAAGAATGTGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGG
CCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCAA
GATGATAAGTCCTTCGGG
Found at i:243111 original size:42 final size:41
Alignment explanation
Indices: 243045--243142 Score: 115
Period size: 42 Copynumber: 2.4 Consensus size: 41
243035 TTCACAGTTT
* * *
243045 ATAAGTCCTTCGGGCCATCAGTAAGCCTTTCGAGCATGATG
1 ATAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
* * **
243086 CTTAAATCCTTCGGGTCATTTGTAAGCCTTTAGAGCAAGATG
1 -ATAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
*
243128 ATAAGTCCTTCGGGC
1 ATAAATCCTTCGGGC
243143 AATCCATAAA
Statistics
Matches: 46, Mismatches: 10, Indels: 1
0.81 0.18 0.02
Matches are distributed among these distances:
41 12 0.26
42 34 0.74
ACGTcount: A:0.24, C:0.22, G:0.23, T:0.30
Consensus pattern (41 bp):
ATAAATCCTTCGGGCCATCAGTAAGCCTTTAGAGCAAGATG
Found at i:243210 original size:181 final size:181
Alignment explanation
Indices: 243004--243352 Score: 592
Period size: 181 Copynumber: 1.9 Consensus size: 181
242994 AATATGGAAG
* * *
243004 TTTTGAAAACGAAGAATGTGATTTTCAAAATTTCACAGTTTATAAGTCCTTCGGGCCATCAGTAA
1 TTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCAGGCCATCAGTAA
* *
243069 GCCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATTTGTAAGCCTTTAGAGCAAGATGATAAGT
66 GCCTTTCGAGCATGATGCTTAAATCATTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAAGT
243134 CCTTCGGGCAATCCATAAAACCTTCGGGTATG-ATGTTTAAAAAGATTAAAT
131 CCTTCGGGCAATCCATAAAACCTTCGGGTA-GAATGTTTAAAAAGATTAAAT
* *
243185 TTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCAGGCTATTAGTAA
1 TTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCAGGCCATCAGTAA
*
243250 GTCTTTCGAGCATGATGCTTAAATCATTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAAGT
66 GCCTTTCGAGCATGATGCTTAAATCATTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAAGT
* *
243315 CTTTCGGGCTATCCATAAAACCTTCGGGTAGAATGTTT
131 CCTTCGGGCAATCCATAAAACCTTCGGGTAGAATGTTT
243353 TCACATGAAT
Statistics
Matches: 157, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
180 1 0.01
181 156 0.99
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (181 bp):
TTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCAGGCCATCAGTAA
GCCTTTCGAGCATGATGCTTAAATCATTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGATAAGT
CCTTCGGGCAATCCATAAAACCTTCGGGTAGAATGTTTAAAAAGATTAAAT
Found at i:243511 original size:43 final size:41
Alignment explanation
Indices: 243441--243543 Score: 98
Period size: 43 Copynumber: 2.5 Consensus size: 41
243431 TTCACAATTT
* * * * **
243441 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCACTATG
1 ATAAATCCTTCGGGTCATCAGTAAGTCTCTCGAGAAAGATG
* ** *
243482 CTTAAAATCCTTCGGGTCATTTGTGAGTCTCTCGAGAAAGATG
1 -AT-AAATCCTTCGGGTCATCAGTAAGTCTCTCGAGAAAGATG
243525 ATAAATCCTTCGGGTCATC
1 ATAAATCCTTCGGGTCATC
243544 CATAAGACCT
Statistics
Matches: 48, Mismatches: 12, Indels: 3
0.76 0.19 0.05
Matches are distributed among these distances:
41 16 0.33
42 2 0.04
43 30 0.62
ACGTcount: A:0.25, C:0.22, G:0.21, T:0.31
Consensus pattern (41 bp):
ATAAATCCTTCGGGTCATCAGTAAGTCTCTCGAGAAAGATG
Found at i:243608 original size:56 final size:56
Alignment explanation
Indices: 243519--243625 Score: 160
Period size: 56 Copynumber: 1.9 Consensus size: 56
243509 TCTCTCGAGA
*
243519 AAGATGATAAATCCTTCGGGTCATCCATAAGACCTTAGGGCAAGATGTTTTGCACC
1 AAGATGATAAATCCTTCGGGCCATCCATAAGACCTTAGGGCAAGATGTTTTGCACC
* * * * *
243575 AAGATGATAAGTCCTTCGGGCCATCCATGAGACCTTCGGGTAGGATGTTTT
1 AAGATGATAAATCCTTCGGGCCATCCATAAGACCTTAGGGCAAGATGTTTT
243626 CACATGATTT
Statistics
Matches: 45, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 45 1.00
ACGTcount: A:0.27, C:0.21, G:0.24, T:0.28
Consensus pattern (56 bp):
AAGATGATAAATCCTTCGGGCCATCCATAAGACCTTAGGGCAAGATGTTTTGCACC
Found at i:248486 original size:6 final size:6
Alignment explanation
Indices: 248475--248499 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
248465 TAACACCTCG
248475 TGCATT TGCATT TGCATT TGCATT T
1 TGCATT TGCATT TGCATT TGCATT T
248500 TTCATTGCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.16, G:0.16, T:0.52
Consensus pattern (6 bp):
TGCATT
Found at i:250818 original size:17 final size:20
Alignment explanation
Indices: 250773--250824 Score: 58
Period size: 22 Copynumber: 2.7 Consensus size: 20
250763 CATCATGAGG
250773 AGAAAGAAGAGAAATGTAGAA
1 AGAAAGAAGA-AAATGTAGAA
250794 AGAGAAGAAGAAAA-G-A-AA
1 AGA-AAGAAGAAAATGTAGAA
250812 AGAAAGAA-AAAAT
1 AGAAAGAAGAAAAT
250825 TGAAAATGAG
Statistics
Matches: 29, Mismatches: 0, Indels: 8
0.78 0.00 0.22
Matches are distributed among these distances:
16 4 0.14
17 5 0.17
18 5 0.17
19 1 0.03
20 1 0.03
21 6 0.21
22 7 0.24
ACGTcount: A:0.69, C:0.00, G:0.25, T:0.06
Consensus pattern (20 bp):
AGAAAGAAGAAAATGTAGAA
Found at i:253075 original size:34 final size:35
Alignment explanation
Indices: 252998--253373 Score: 442
Period size: 34 Copynumber: 10.9 Consensus size: 35
252988 AGCAAAGTCA
* * *
252998 ATCTTAATCCTTCATC-GGAGAGTAGTGAAGCAATC
1 ATCTTAAGCCTTCA-CAGAAGAGTAGTGAAGCAACC
*
253033 ATCTTAAGCCTTCACAGAAGTGTAGTGAAGC-ACC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAACC
*
253067 ATCTTAAGCCTTCACAGAGGAGTAGTGAAGCAAACC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGC-AACC
* * * *
253103 ATCTT-AGCCTTCACCGGAGAGTAGTGAGGCAATC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAACC
* *
253137 ATCTTGAGCCTTCACAGAAGAGTAGTAAAGC-ACC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAACC
* *
253171 ATCTTAAGCCTTCACGGAGGAGTAGTGAAGCAAACC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGC-AACC
* * * * *
253207 ATCTTAATCCTTCACCGGAGAGTAGTGAAACAATC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAACC
253242 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGC-ACC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAACC
** * *
253276 ATCTTAAGCCTTCACAGGGGAGTAATAAAGC-ACC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAACC
* * *
253310 ATCTGAAGCCTTCACAGAGGAGTAATGAAGC-ACC
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAACC
*
253344 ATCTTAAGCCTTCACCGAAGAGTAGTGAAG
1 ATCTTAAGCCTTCACAGAAGAGTAGTGAAG
253374 TAAATCCATC
Statistics
Matches: 293, Mismatches: 42, Indels: 13
0.84 0.12 0.04
Matches are distributed among these distances:
34 158 0.54
35 98 0.33
36 37 0.13
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.22
Consensus pattern (35 bp):
ATCTTAAGCCTTCACAGAAGAGTAGTGAAGCAACC
Found at i:253266 original size:105 final size:105
Alignment explanation
Indices: 252998--253373 Score: 548
Period size: 104 Copynumber: 3.6 Consensus size: 105
252988 AGCAAAGTCA
* * *
252998 ATCTTAATCCTTCATCGGAGAGTAGTGAAGCAATCATCTTAAGCCTTCACAGAAGTGTAGTGAAG
1 ATCTTAAGCCTTCACCGGAGAGTAGTGAAGCAATCATCTTAAGCCTTCACAGAAGAGTAGTGAAG
*
253063 CACCATCTTAAGCCTTCACAGAGGAGTAGTGAAGCAAACC
66 CACCATCTTAAGCCTTCACGGAGGAGTAGTGAAGCAAACC
* * *
253103 ATCTT-AGCCTTCACCGGAGAGTAGTGAGGCAATCATCTTGAGCCTTCACAGAAGAGTAGTAAAG
1 ATCTTAAGCCTTCACCGGAGAGTAGTGAAGCAATCATCTTAAGCCTTCACAGAAGAGTAGTGAAG
253167 CACCATCTTAAGCCTTCACGGAGGAGTAGTGAAGCAAACC
66 CACCATCTTAAGCCTTCACGGAGGAGTAGTGAAGCAAACC
* *
253207 ATCTTAATCCTTCACCGGAGAGTAGTGAAACAATCATCTTAAGCCTTCACAGAAGAGTAGTGAAG
1 ATCTTAAGCCTTCACCGGAGAGTAGTGAAGCAATCATCTTAAGCCTTCACAGAAGAGTAGTGAAG
* *
253272 CACCATCTTAAGCCTTCACAGG-GGAGTAATAAAGC--ACC
66 CACCATCTTAAGCCTTCAC-GGAGGAGTAGTGAAGCAAACC
* * * * *
253310 ATCTGAAGCCTTCA-CAGAGGAGTAATGAAGC-ACCATCTTAAGCCTTCACCGAAGAGTAGTGAA
1 ATCTTAAGCCTTCACCGGA-GAGTAGTGAAGCAATCATCTTAAGCCTTCACAGAAGAGTAGTGAA
253373 G
65 G
253374 TAAATCCATC
Statistics
Matches: 247, Mismatches: 21, Indels: 9
0.89 0.08 0.03
Matches are distributed among these distances:
102 34 0.14
103 25 0.10
104 97 0.39
105 89 0.36
106 2 0.01
ACGTcount: A:0.34, C:0.23, G:0.22, T:0.22
Consensus pattern (105 bp):
ATCTTAAGCCTTCACCGGAGAGTAGTGAAGCAATCATCTTAAGCCTTCACAGAAGAGTAGTGAAG
CACCATCTTAAGCCTTCACGGAGGAGTAGTGAAGCAAACC
Found at i:254411 original size:214 final size:214
Alignment explanation
Indices: 253379--254470 Score: 1523
Period size: 215 Copynumber: 5.1 Consensus size: 214
253369 TGAAGTAAAT
* *
253379 CCATCCATAAGACCTTCGGGTAGGATGTTTTCACATGAATTTGAAAATGAAAAATGATGTTTTAA
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAATGATGTTTTAA
* * * * * *
253444 GAAGATGAAACTTTTGAAAATGAAGAATGCGATTTTTAAAATTTCATAATTTATAAGTCCTTTGG
66 GAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCC-TTCG
* *
253509 GGTCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTTATCTGTAAGCCTTTAGAGC
130 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
*
253574 AAGATGATAAGTCTTTCGGG
195 AAGATGATAAGTCCTTCGGG
* * * *
253594 CCATCCATGAAACCTTCGGGTAGGATGTTTTCACATGAAATTGAAAATGAAAAA--ATG-ATT--
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAATGATGTTTTAA
*
253654 ----ATGGAATTTTTGAAAACAAAGAATGCGATTTTCAAAATTTTCACAATTTATAAGTCCTTCG
66 GAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAA-TTTCACAATTTATAAGTCCTTCG
* * * * *
253715 GGCCATCTGTAAGTCTTTTGATCATGATGCTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGACC
130 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
253780 AAGATGATAAGTCCTTCGGG
195 AAGATGATAAGTCCTTCGGG
* *
253800 CCATCCATAAGACTTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAAAATGATGTTTT
1 CCATCCATAAAACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATG--AAAAATGATGTTTT
* * *
253865 AAGAAGATGGAATTTTTGAAAACGAAGAATGTGATTTTCAAAATTTCATAA--TAT-A-TCCCTC
64 AAGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTC
* * ** *
253926 GGGCCATCAATAAGTCTTTTGAGCATGATATTTAAATCCTTCGGGTCATCTGTAAGTCTTTAGAG
129 GGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAG
* *
253991 CAAGATGATAAGTCATTCGGA
194 CAAGATGATAAGTCCTTCGGG
* *
254012 CCATCCATAAGACCTTTGGG-AGGGATGTTTTCAAATGAATTTGAAAATGAAAAAGTGATGTTTT
1 CCATCCATAAAACCTTCGGGTA-GGATGTTTTCAAATGAATTTGAAAATGAAAAA-TGATGTTTT
* * *
254076 AAGAAGAT-GAATTTTTTAAAAACGAAGAATGCAATTTTCAAAATTTCACAATTTATAAGTCCCT
64 AAGAAGATGGAA-TTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTT
* * *
254140 CAGGCCATCAATAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGCTCATCTGTAAGCCTTTAGA
128 CGGGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGA
254205 GCAAGATGATAAGTCCTTCGGG
193 GCAAGATGATAAGTCCTTCGGG
* * *
254227 TCATCCATAAAACCTTCGGG-AGGGATGTTTTCAAATGAATTTGAAAATGAAAAGTAATGTTTTA
1 CCATCCATAAAACCTTCGGGTA-GGATGTTTTCAAATGAATTTGAAAATGAAAAATGATGTTTTA
* * * * *
254291 AGAATATGGAAGTTTTGAAAATGAAGAATGTGATTTTCAAAATTTCACAGTTTATAAGTCCTTCG
65 AGAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCG
* *
254356 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATTTGTAAGCCTTTAGAGC
130 GGCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGC
254421 AAGATGATAAGTCCTTCGGG
195 AAGATGATAAGTCCTTCGGG
* *
254441 CAATCCATAAAACCTTCGGGTATGATGTTT
1 CCATCCATAAAACCTTCGGGTAGGATGTTT
254471 AAAAAGATGA
Statistics
Matches: 784, Mismatches: 72, Indels: 43
0.87 0.08 0.05
Matches are distributed among these distances:
206 156 0.20
207 18 0.02
208 5 0.01
210 11 0.01
211 55 0.07
212 130 0.17
213 7 0.01
214 171 0.22
215 189 0.24
216 7 0.01
217 35 0.04
ACGTcount: A:0.33, C:0.15, G:0.19, T:0.33
Consensus pattern (214 bp):
CCATCCATAAAACCTTCGGGTAGGATGTTTTCAAATGAATTTGAAAATGAAAAATGATGTTTTAA
GAAGATGGAATTTTTGAAAACGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGG
GCCATCAGTAAGTCTTTCGAGCATGATGCTTAAATCCTTCGGGTCATCTGTAAGCCTTTAGAGCA
AGATGATAAGTCCTTCGGG
Found at i:254607 original size:181 final size:181
Alignment explanation
Indices: 254303--254651 Score: 592
Period size: 181 Copynumber: 1.9 Consensus size: 181
254293 AATATGGAAG
* *
254303 TTTTGAAAATGAAGAATGTGATTTTCAAAATTTCACAGTTTATAAGTCCTTCGGGCCATCAGTAA
1 TTTTGAAAATGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAA
* * *
254368 GTCTTTCGAGCATGATGCTTAAATCCTTCAGGTCATTTGTAAGCCTTTAGAGCAAGATGATAAGT
66 GTCTTTCGAGCATGATGCTTAAATCATTCAGGTCATCTGTAAGCCTTTAGAGCAAGATGACAAGT
254433 CCTTCGGGCAATCCATAAAACCTTCGGGTATG-ATGTTTAAAAAGATGAAAT
131 CCTTCGGGCAATCCATAAAACCTTCGGGTA-GAATGTTTAAAAAGATGAAAT
* *
254484 TTTTGAAAATGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCTATTAGTAA
1 TTTTGAAAATGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAA
*
254549 GTCTTTCGAGCATGATGCTTAAATCATTCGGGTCATCTGTAAGCCTTTAGAGCAAGATGACAAGT
66 GTCTTTCGAGCATGATGCTTAAATCATTCAGGTCATCTGTAAGCCTTTAGAGCAAGATGACAAGT
* *
254614 CTTTCGGGCTATCCATAAAACCTTCGGGTAGAATGTTT
131 CCTTCGGGCAATCCATAAAACCTTCGGGTAGAATGTTT
254652 TCACATGAAT
Statistics
Matches: 157, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
180 1 0.01
181 156 0.99
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.33
Consensus pattern (181 bp):
TTTTGAAAATGAAGAATGCGATTTTCAAAATTTCACAATTTATAAGTCCTTCGGGCCATCAGTAA
GTCTTTCGAGCATGATGCTTAAATCATTCAGGTCATCTGTAAGCCTTTAGAGCAAGATGACAAGT
CCTTCGGGCAATCCATAAAACCTTCGGGTAGAATGTTTAAAAAGATGAAAT
Found at i:254810 original size:43 final size:41
Alignment explanation
Indices: 254740--254842 Score: 107
Period size: 43 Copynumber: 2.5 Consensus size: 41
254730 TTTACAATTT
* * * **
254740 ATAAGTCCTTCGGGCCATCAGTAAGTCTTTCGAGCACTATG
1 ATAAATCCTTCGGGTCATCAGTAAGTCTCTCGAGCAAGATG
* ** *
254781 CTTAAAATCCTTCGGGTCATTTGTGAGTCTCTCGAGCAAGATG
1 -AT-AAATCCTTCGGGTCATCAGTAAGTCTCTCGAGCAAGATG
254824 ATAAATCCTTCGGGTCATC
1 ATAAATCCTTCGGGTCATC
254843 CATAAGACCT
Statistics
Matches: 49, Mismatches: 11, Indels: 3
0.78 0.17 0.05
Matches are distributed among these distances:
41 16 0.33
42 2 0.04
43 31 0.63
ACGTcount: A:0.24, C:0.23, G:0.21, T:0.31
Consensus pattern (41 bp):
ATAAATCCTTCGGGTCATCAGTAAGTCTCTCGAGCAAGATG
Found at i:254907 original size:56 final size:56
Alignment explanation
Indices: 254817--254924 Score: 162
Period size: 56 Copynumber: 1.9 Consensus size: 56
254807 GTCTCTCGAG
*
254817 CAAGATGATAAATCCTTCGGGTCATCCATAAGACCTTAGGGCAGGATGTTTTGCAC
1 CAAGATGATAAATCCTTCGGGCCATCCATAAGACCTTAGGGCAGGATGTTTTGCAC
* * * * *
254873 CAAGATGATAAGTCCTTCGGGCCATCCATGAGACCTTCGGGTATGATGTTTT
1 CAAGATGATAAATCCTTCGGGCCATCCATAAGACCTTAGGGCAGGATGTTTT
254925 CACATGAATT
Statistics
Matches: 46, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
56 46 1.00
ACGTcount: A:0.26, C:0.21, G:0.24, T:0.29
Consensus pattern (56 bp):
CAAGATGATAAATCCTTCGGGCCATCCATAAGACCTTAGGGCAGGATGTTTTGCAC
Found at i:257678 original size:16 final size:16
Alignment explanation
Indices: 257648--257677 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
257638 AAAAAGTGGG
257648 AAAATAAAGATAAAAC
1 AAAATAAAGATAAAAC
257664 AAAAT-AAGATAAAA
1 AAAATAAAGATAAAA
257678 AAAGGAAATA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.77, C:0.03, G:0.07, T:0.13
Consensus pattern (16 bp):
AAAATAAAGATAAAAC
Found at i:257767 original size:18 final size:18
Alignment explanation
Indices: 257746--257788 Score: 59
Period size: 18 Copynumber: 2.4 Consensus size: 18
257736 GTTGTTTTTA
*
257746 AAATAAAAGATAAGAATT
1 AAATAAAAGAAAAGAATT
* *
257764 AAATAAAGGAAAATAATT
1 AAATAAAAGAAAAGAATT
257782 AAATAAA
1 AAATAAA
257789 TAATCTAAAG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.70, C:0.00, G:0.09, T:0.21
Consensus pattern (18 bp):
AAATAAAAGAAAAGAATT
Found at i:259023 original size:201 final size:202
Alignment explanation
Indices: 258660--259026 Score: 456
Period size: 201 Copynumber: 1.8 Consensus size: 202
258650 TTTTGTTGCC
* * * * *
258660 AAATCGTAGTCAACCTTGGTCTTCTTCTTAGGTTAAAGACCTCGGTTTGAAAATTCAACCAGAAA
1 AAATCGCAGCCAACCTAGGTCTTCTTCTTAGCTTAAAGACCTCAGTTTGAAAATTCAACCAGAAA
* * * * *
258725 GTAGTTCCTTGATTCTAACATATGGTTGATATGCCCTCGAGCTAAATGGAATCGAACTCGAAGGT
66 GTAGTTCCTCGATTCTAACATACGGTTGATATACCCTCGAGCTAAATGGAATCGAACTCAAAAGT
***
258790 TTTTGTTGAAAGATAGCCCTTATCGCCTTGAGCTATGTTGTAAATTCGACTGGGAGATAGTTCCT
131 TTCCATTGAAAGATAGCCCTTATCGCCTTGAGCTATGTTGTAAATTCGACTGGGAGATAGTTCCT
258855 TGTTGTT
196 TGTTGTT
* *
258862 AAATCGCAGCCAACCTAGGTCTTCTT-TTTGACTTAAAGACCTCAGTTT-AAACTTCAACC-GAA
1 AAATCGCAGCCAACCTAGGTCTTCTTCTTAG-CTTAAAGACCTCAGTTTGAAAATTCAACCAG-A
* * * * *
258924 AAGTAGTTTCTCG-TTGCTACCATGCGGTTGATGTACCCTCGAGCTGAATGGAATCGAACTCAAA
64 AAGTAGTTCCTCGATT-CTAACATACGGTTGATATACCCTCGAGCTAAATGGAATCGAACTCAAA
* * *
258988 AGTTTCCATTGACAA-TTAGCTCTTCTCGCCTTGAGCTAT
128 AGTTTCCATTGA-AAGATAGCCCTTATCGCCTTGAGCTAT
259027 ACTATAATAG
Statistics
Matches: 138, Mismatches: 23, Indels: 9
0.81 0.14 0.05
Matches are distributed among these distances:
200 3 0.02
201 95 0.69
202 40 0.29
ACGTcount: A:0.27, C:0.21, G:0.20, T:0.33
Consensus pattern (202 bp):
AAATCGCAGCCAACCTAGGTCTTCTTCTTAGCTTAAAGACCTCAGTTTGAAAATTCAACCAGAAA
GTAGTTCCTCGATTCTAACATACGGTTGATATACCCTCGAGCTAAATGGAATCGAACTCAAAAGT
TTCCATTGAAAGATAGCCCTTATCGCCTTGAGCTATGTTGTAAATTCGACTGGGAGATAGTTCCT
TGTTGTT
Found at i:259864 original size:32 final size:32
Alignment explanation
Indices: 259778--259866 Score: 97
Period size: 32 Copynumber: 2.8 Consensus size: 32
259768 TTCATATCAG
* ** *
259778 GATGTTGAATCCCCAAAGATGCAACAATATTC
1 GATGTTGAATCTCCAAAGATGCCCCAACATTC
* * *
259810 GATGTTGAATATCCAAAAATGCCCCAACATTT
1 GATGTTGAATCTCCAAAGATGCCCCAACATTC
* *
259842 GATTTTGAATCTTCAAAGATGCCCC
1 GATGTTGAATCTCCAAAGATGCCCC
259867 CACTCTTCCT
Statistics
Matches: 46, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
32 46 1.00
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (32 bp):
GATGTTGAATCTCCAAAGATGCCCCAACATTC
Found at i:260907 original size:13 final size:14
Alignment explanation
Indices: 260890--260935 Score: 60
Period size: 15 Copynumber: 3.4 Consensus size: 14
260880 TTCTTGACCC
260890 TTTTTCTTTGTTTA
1 TTTTTCTTTGTTTA
260904 TTTTCTCTTTGTTTA
1 TTTT-TCTTTGTTTA
*
260919 -TTTTCTTT-TTGA
1 TTTTTCTTTGTTTA
260931 TTTTT
1 TTTTT
260936 GTTCTTGGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
12 3 0.10
13 9 0.31
14 7 0.24
15 10 0.34
ACGTcount: A:0.07, C:0.09, G:0.07, T:0.78
Consensus pattern (14 bp):
TTTTTCTTTGTTTA
Found at i:260914 original size:15 final size:15
Alignment explanation
Indices: 260890--260929 Score: 64
Period size: 15 Copynumber: 2.7 Consensus size: 15
260880 TTCTTGACCC
260890 TTTT-TCTTTGTTTA
1 TTTTCTCTTTGTTTA
260904 TTTTCTCTTTGTTTA
1 TTTTCTCTTTGTTTA
*
260919 TTTTCTTTTTG
1 TTTTCTCTTTG
260930 ATTTTTGTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
14 4 0.17
15 20 0.83
ACGTcount: A:0.05, C:0.10, G:0.07, T:0.78
Consensus pattern (15 bp):
TTTTCTCTTTGTTTA
Found at i:263971 original size:561 final size:560
Alignment explanation
Indices: 263066--264194 Score: 1945
Period size: 561 Copynumber: 2.0 Consensus size: 560
263056 AGTTTCCTGG
* *
263066 TTTAAGTTTTAAAGAAGGGTACCCGAGTTCTCCTCACTGGTGCCCCCTTGGGCTCGCCAGACCCT
1 TTTAGGTTTTAAAGAAGGGTACCCGAGTTCTCCTCACTAGTGCCCCCTTGGGCTCGCCAGACCCT
* *
263131 TAGTCCTAAGCCCATTACAAGCTTATATGGACTAAGTTAAACTCGAGAGGATACATTCCCTTATG
66 TAGTCCTAAGCCCATTACAAGCTTATACGGACTAAGTTAAACTCGAGAGGATACAATCCCTTATG
* *
263196 CCTATACGGAGAATAAATTCACACGAAGACATAAGGTACATGAATCCCGAAGGTTACTTTCAAGG
131 CCCATACGGAGAATAAATTCACACGAAGACATAAGGTACATGAATCCCGAAGGTTACTTGCAAGG
* *
263261 CCCGCATGAAGAATAAATTCTCACGAAGGCGTCGCTTTCACCCCCACTTAAAAAGGCTTCAGAGC
196 CCCACACGAAGAATAAATTCTCACGAAGGCGTCGCTTTCACCCCCACTTAAAAAGGCTTCAGAGC
*
263326 TCGAATATAGAGGCAGAGATGAAAACTTTTTCAATAATCTGAAATCATTGAAAAAACGTCAGTAT
261 TCGAATATAGAGCCAGAGATGAAAACTTTTTCAATAATCTGAAATCATTGAAAAAACGTCAGTAT
263391 AACTATTTATTTGAAAAATAATCAAAGATAAATAACAAGAATCGAAAAGTTAAATTAAAATTTAA
326 AACTATTTATTTGAAAAATAATCAAAGATAAATAACAAGAATCGAAAAGTTAAATTAAAATTTAA
263456 ACTTACAATTTTCGCTTTAAAAAAGACAACCAAAAATTAATTCTAGCTTAACTCACTTACCTGTC
391 ACTTACAATTTTCGCTTTAAAAAAGACAACC-AAAATTAATTCTAGCTTAACTCACTTACCTGTC
263521 CCCAGCAGACCCGCAAAGCTATTGCGATCGTCTTTCGGGTTGGGCCTGGAATTGGGCTTCGACTT
455 CCCAGCAGACCCGCAAAGCTATTGCGATCGTCTTTCGGGTTGGGCCTGGAATTGGGCTTCGACTT
263586 AAATAAGCTGGTTAGAGTCACCACCGATCATTTAAAAAATA
520 AAATAAGCTGGTTAGAGTCACCACCGATCATTTAAAAAATA
* * * * *
263627 TTTAGGTTTTAAAGAAGGGTATCTGAGTTCTCCTCACTAGTGCCCCCTTGGTCTTGCCAGACTCT
1 TTTAGGTTTTAAAGAAGGGTACCCGAGTTCTCCTCACTAGTGCCCCCTTGGGCTCGCCAGACCCT
*
263692 TAGTCCTAAGCCCATTACAAGCTTATGCGGACTAAGTTAAACTCGAGAGGATACAATCCCTTATG
66 TAGTCCTAAGCCCATTACAAGCTTATACGGACTAAGTTAAACTCGAGAGGATACAATCCCTTATG
* *
263757 CCCATACGGAGAATAAATTCACACGAAGACATAAGGTACATGAATCCTGAAGGTTACTTGCTAGG
131 CCCATACGGAGAATAAATTCACACGAAGACATAAGGTACATGAATCCCGAAGGTTACTTGCAAGG
* *
263822 CCCACACGAAGAATAAATTCTCACGAAGGCGTCGCTTTCACCCCTACTTAAAAAGGGTTCAGAGC
196 CCCACACGAAGAATAAATTCTCACGAAGGCGTCGCTTTCACCCCCACTTAAAAAGGCTTCAGAGC
**
263887 TCGGGTATAGAGCCAGAGATGAAAACTTTTTCAATAATCTGAAATCATT-AAAAAACGTCAGTAT
261 TCGAATATAGAGCCAGAGATGAAAACTTTTTCAATAATCTGAAATCATTGAAAAAACGTCAGTAT
263951 AACTATTTATTTGAAAAAATAATCAAAGATAAATAACAAGAATCGAAAAGTTAAATTAAAATTTA
326 AACTATTTATTTG-AAAAATAATCAAAGATAAATAACAAGAATCGAAAAGTTAAATTAAAATTTA
* * * *
264016 AACTTACAATTTTCGCTTTAAAAAATACAACCGAAATTATTTCTGGCTTAACTCACTTACCTGTC
390 AACTTACAATTTTCGCTTTAAAAAAGACAACCAAAATTAATTCTAGCTTAACTCACTTACCTGTC
* * * * *
264081 CCCAGCAGACTCGCAAAGCTGTTGCGGTTGTCTTTCGGGTTGGGCTTGGAATTGGGCTTCGACTT
455 CCCAGCAGACCCGCAAAGCTATTGCGATCGTCTTTCGGGTTGGGCCTGGAATTGGGCTTCGACTT
* *
264146 AAATAAGTTGGTTAGAGTCGCCACCGATCATTTAAAAAATA
520 AAATAAGCTGGTTAGAGTCACCACCGATCATTTAAAAAATA
264187 TTTAGGTT
1 TTTAGGTT
264195 GATCGAACAC
Statistics
Matches: 535, Mismatches: 32, Indels: 3
0.94 0.06 0.01
Matches are distributed among these distances:
560 165 0.31
561 370 0.69
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (560 bp):
TTTAGGTTTTAAAGAAGGGTACCCGAGTTCTCCTCACTAGTGCCCCCTTGGGCTCGCCAGACCCT
TAGTCCTAAGCCCATTACAAGCTTATACGGACTAAGTTAAACTCGAGAGGATACAATCCCTTATG
CCCATACGGAGAATAAATTCACACGAAGACATAAGGTACATGAATCCCGAAGGTTACTTGCAAGG
CCCACACGAAGAATAAATTCTCACGAAGGCGTCGCTTTCACCCCCACTTAAAAAGGCTTCAGAGC
TCGAATATAGAGCCAGAGATGAAAACTTTTTCAATAATCTGAAATCATTGAAAAAACGTCAGTAT
AACTATTTATTTGAAAAATAATCAAAGATAAATAACAAGAATCGAAAAGTTAAATTAAAATTTAA
ACTTACAATTTTCGCTTTAAAAAAGACAACCAAAATTAATTCTAGCTTAACTCACTTACCTGTCC
CCAGCAGACCCGCAAAGCTATTGCGATCGTCTTTCGGGTTGGGCCTGGAATTGGGCTTCGACTTA
AATAAGCTGGTTAGAGTCACCACCGATCATTTAAAAAATA
Found at i:264761 original size:18 final size:18
Alignment explanation
Indices: 264740--264786 Score: 62
Period size: 18 Copynumber: 2.7 Consensus size: 18
264730 GTTGTTTTTA
264740 AAATAAAAGATAAGAATT
1 AAATAAAAGATAAGAATT
* *
264758 AAATAAAAGAAAATAATT
1 AAATAAAAGATAAGAATT
264776 AAA-AAAA-ATAA
1 AAATAAAAGATAA
264787 TCTAAAGAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
16 3 0.12
17 4 0.15
18 19 0.73
ACGTcount: A:0.74, C:0.00, G:0.06, T:0.19
Consensus pattern (18 bp):
AAATAAAAGATAAGAATT
Found at i:264783 original size:13 final size:15
Alignment explanation
Indices: 264761--264797 Score: 51
Period size: 14 Copynumber: 2.5 Consensus size: 15
264751 AAGAATTAAA
264761 TAAAAGAAAATAAT-
1 TAAAAGAAAATAATC
264775 TAAAA-AAAATAATC
1 TAAAAGAAAATAATC
264789 TAAAGAGAA
1 TAAA-AGAA
264798 TGAGATAAAG
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
13 8 0.40
14 9 0.45
15 1 0.05
16 2 0.10
ACGTcount: A:0.70, C:0.03, G:0.08, T:0.19
Consensus pattern (15 bp):
TAAAAGAAAATAATC
Found at i:265323 original size:24 final size:24
Alignment explanation
Indices: 265295--265342 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
265285 ATAATATCAT
* * *
265295 TATTTTAATTAAAACACTTAAAAC
1 TATTTAAACTAAAACACCTAAAAC
*
265319 TATTTAAACTAAAATACCTAAAAC
1 TATTTAAACTAAAACACCTAAAAC
265343 AAAGATAAAA
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.52, C:0.15, G:0.00, T:0.33
Consensus pattern (24 bp):
TATTTAAACTAAAACACCTAAAAC
Found at i:272773 original size:40 final size:40
Alignment explanation
Indices: 272716--272797 Score: 155
Period size: 40 Copynumber: 2.0 Consensus size: 40
272706 TACAGGTTTA
272716 TAATACACTTCGATGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGATGTATATGGTGGGCACGACCTTATGTG
*
272756 TAATACACTTCGGTGTATATGGTGGGCACGACCTTATGTG
1 TAATACACTTCGATGTATATGGTGGGCACGACCTTATGTG
272796 TA
1 TA
272798 GCACTACGGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
40 41 1.00
ACGTcount: A:0.24, C:0.17, G:0.26, T:0.33
Consensus pattern (40 bp):
TAATACACTTCGATGTATATGGTGGGCACGACCTTATGTG
Found at i:273483 original size:20 final size:20
Alignment explanation
Indices: 273458--273496 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
273448 ATTCCCCTGT
*
273458 TGTTCACGGGTATTGTTCAC
1 TGTTCACGGGTACTGTTCAC
273478 TGTTCACGGGTACTGTTCA
1 TGTTCACGGGTACTGTTCA
273497 TTATTCATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.15, C:0.21, G:0.26, T:0.38
Consensus pattern (20 bp):
TGTTCACGGGTACTGTTCAC
Found at i:273503 original size:20 final size:20
Alignment explanation
Indices: 273460--273503 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
273450 TCCCCTGTTG
* *
273460 TTCACGGGTATTGTTCACTG
1 TTCACGGGTACTGTTCACTA
*
273480 TTCACGGGTACTGTTCATTA
1 TTCACGGGTACTGTTCACTA
273500 TTCA
1 TTCA
273504 TAAAAAAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.18, C:0.20, G:0.20, T:0.41
Consensus pattern (20 bp):
TTCACGGGTACTGTTCACTA
Found at i:279668 original size:40 final size:40
Alignment explanation
Indices: 279613--279753 Score: 255
Period size: 40 Copynumber: 3.5 Consensus size: 40
279603 GATGATATAC
279613 GTGGGCACGACCTTATGTGTAATACACTTCGGTGTATATG
1 GTGGGCACGACCTTATGTGTAATACACTTCGGTGTATATG
* *
279653 GTGGGCACGACCTTATGTGTAATATACTTCGGTGTACATG
1 GTGGGCACGACCTTATGTGTAATACACTTCGGTGTATATG
*
279693 GTAGGCACGACCTTATGTGTAATACACTTCGGTGTATATG
1 GTGGGCACGACCTTATGTGTAATACACTTCGGTGTATATG
279733 GTGGGCACGACCTTATGTGTA
1 GTGGGCACGACCTTATGTGTA
279754 GCACTACGGT
Statistics
Matches: 95, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 95 1.00
ACGTcount: A:0.23, C:0.18, G:0.28, T:0.32
Consensus pattern (40 bp):
GTGGGCACGACCTTATGTGTAATACACTTCGGTGTATATG
Found at i:279979 original size:46 final size:46
Alignment explanation
Indices: 279857--279982 Score: 157
Period size: 45 Copynumber: 2.8 Consensus size: 46
279847 GGTAAGCATG
* *
279857 AAAATAAGCTTACGAGCTTATGGAAT-ATTGGCAAGTATATGGGTA
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATGGGTA
*** * * *
279902 AAAATAAGCTTACGAGCTTATGGGGCAAATGGTAATTATTTTGGT-
1 AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATGGGTA
279947 AAAATAAGCTTACGAGCTTATGGAAATAAATGGTAA
1 AAAATAAGCTTACGAGCTTATGG-AATAAATGGTAA
279983 AATATTGGAT
Statistics
Matches: 68, Mismatches: 11, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
45 46 0.68
46 22 0.32
ACGTcount: A:0.39, C:0.09, G:0.23, T:0.29
Consensus pattern (46 bp):
AAAATAAGCTTACGAGCTTATGGAATAAATGGTAAGTATATGGGTA
Found at i:289182 original size:14 final size:14
Alignment explanation
Indices: 289158--289202 Score: 56
Period size: 14 Copynumber: 3.2 Consensus size: 14
289148 AATGATATTG
*
289158 TTTAGACTTTAAAT
1 TTTAGAGTTTAAAT
*
289172 TTTAGGGTTT-AAT
1 TTTAGAGTTTAAAT
289185 ATTTAGAGTTTAAAT
1 -TTTAGAGTTTAAAT
289200 TTT
1 TTT
289203 TAGGATTAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
13 3 0.12
14 20 0.77
15 3 0.12
ACGTcount: A:0.31, C:0.02, G:0.13, T:0.53
Consensus pattern (14 bp):
TTTAGAGTTTAAAT
Found at i:289304 original size:18 final size:17
Alignment explanation
Indices: 289283--289318 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
289273 AAAAGTAGTA
*
289283 AGTAGATAAAAAATTAAC
1 AGTAAATAAAAAA-TAAC
289301 AGTAAATAAAAAATAAC
1 AGTAAATAAAAAATAAC
289318 A
1 A
289319 AATACATTGT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.67, C:0.06, G:0.08, T:0.19
Consensus pattern (17 bp):
AGTAAATAAAAAATAAC
Found at i:291228 original size:24 final size:23
Alignment explanation
Indices: 291201--291258 Score: 71
Period size: 23 Copynumber: 2.5 Consensus size: 23
291191 ACGTTGAACG
*
291201 AACATGTTCGCGAACATCTAAACA
1 AACATGTTCACGAACAT-TAAACA
* *
291225 AACATATTCATGAACATTAAACA
1 AACATGTTCACGAACATTAAACA
*
291248 AACACGTTCAC
1 AACATGTTCAC
291259 AAATGTTAAA
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
23 14 0.50
24 14 0.50
ACGTcount: A:0.45, C:0.24, G:0.09, T:0.22
Consensus pattern (23 bp):
AACATGTTCACGAACATTAAACA
Found at i:297762 original size:19 final size:19
Alignment explanation
Indices: 297697--297762 Score: 53
Period size: 19 Copynumber: 3.4 Consensus size: 19
297687 ATCTAGTCAC
*
297697 TTAAATCCAACGATTCATA
1 TTAAATCCAATGATTCATA
* * * *
297716 TTTGACAT-GAATGACTCATC
1 -TT-AAATCCAATGATTCATA
*
297736 TTAGATCCAATGATTCATA
1 TTAAATCCAATGATTCATA
297755 TTAAATCC
1 TTAAATCC
297763 TTCCAAATTA
Statistics
Matches: 34, Mismatches: 10, Indels: 5
0.69 0.20 0.10
Matches are distributed among these distances:
18 3 0.09
19 18 0.53
20 10 0.29
21 3 0.09
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (19 bp):
TTAAATCCAATGATTCATA
Found at i:303165 original size:29 final size:29
Alignment explanation
Indices: 303101--303198 Score: 108
Period size: 29 Copynumber: 3.3 Consensus size: 29
303091 GAAAATTACA
* * * *
303101 AAAATATCACCTTTATTAAAAATAATTACC
1 AAAATGTCACATTT-TTTAAAATAATTCCC
* *
303131 ATAATGTCAC-TATTTTTAAAAGAATTCCC
1 AAAATGTCACAT-TTTTTAAAATAATTCCC
*
303160 AAAATGCCACATTTTTTAAAATAATTCCC
1 AAAATGTCACATTTTTTAAAATAATTCCC
303189 AAAATGTCAC
1 AAAATGTCAC
303199 CGAGTCGGGT
Statistics
Matches: 57, Mismatches: 9, Indels: 5
0.80 0.13 0.07
Matches are distributed among these distances:
29 46 0.81
30 11 0.19
ACGTcount: A:0.44, C:0.18, G:0.04, T:0.34
Consensus pattern (29 bp):
AAAATGTCACATTTTTTAAAATAATTCCC
Found at i:306113 original size:24 final size:24
Alignment explanation
Indices: 306079--306133 Score: 83
Period size: 24 Copynumber: 2.3 Consensus size: 24
306069 GCCGGACGTG
*
306079 CCACCGTCTGGGCATGGAGAAGTC
1 CCACCGCCTGGGCATGGAGAAGTC
* *
306103 CCACCGCCTGGGCGTGGGGAAGTC
1 CCACCGCCTGGGCATGGAGAAGTC
306127 CCACCGC
1 CCACCGC
306134 GTGGTGGTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.16, C:0.36, G:0.35, T:0.13
Consensus pattern (24 bp):
CCACCGCCTGGGCATGGAGAAGTC
Found at i:307033 original size:16 final size:16
Alignment explanation
Indices: 307012--307048 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
307002 CCCGATGTGG
307012 AGGGTGATCCTTGGTT
1 AGGGTGATCCTTGGTT
307028 AGGGTGATCCTTGGTT
1 AGGGTGATCCTTGGTT
307044 AGGGT
1 AGGGT
307049 TGAATCAGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.14, C:0.11, G:0.41, T:0.35
Consensus pattern (16 bp):
AGGGTGATCCTTGGTT
Found at i:309858 original size:13 final size:13
Alignment explanation
Indices: 309855--309884 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
309845 CCGTTGACCA
*
309855 GACCTGACCCGTT
1 GACCCGACCCGTT
309868 GACCCGACCCGTT
1 GACCCGACCCGTT
309881 GACC
1 GACC
309885 GGCGTTGACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.17, C:0.43, G:0.23, T:0.17
Consensus pattern (13 bp):
GACCCGACCCGTT
Found at i:309860 original size:18 final size:18
Alignment explanation
Indices: 309837--309876 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
309827 GTTATAACCT
309837 GACCTGACCCGTTGACCA
1 GACCTGACCCGTTGACCA
*
309855 GACCTGACCCGTTGACCC
1 GACCTGACCCGTTGACCA
309873 GACC
1 GACC
309877 CGTTGACCGG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 21 1.00
ACGTcount: A:0.20, C:0.42, G:0.23, T:0.15
Consensus pattern (18 bp):
GACCTGACCCGTTGACCA
Found at i:309894 original size:31 final size:33
Alignment explanation
Indices: 309836--309904 Score: 81
Period size: 31 Copynumber: 2.2 Consensus size: 33
309826 GGTTATAACC
*
309836 TGACCTGACCCGTTGACCAGACCTGACC-C-GT
1 TGACCCGACCCGTTGACCAGACCTGACCACTGT
* *
309867 TGACCCGACCCGTTGACC-GGCGTTGACCACTGT
1 TGACCCGACCCGTTGACCAGAC-CTGACCACTGT
309900 TGACC
1 TGACC
309905 AAAACTTTGA
Statistics
Matches: 32, Mismatches: 3, Indels: 4
0.82 0.08 0.10
Matches are distributed among these distances:
30 2 0.06
31 22 0.69
32 1 0.03
33 7 0.22
ACGTcount: A:0.17, C:0.38, G:0.25, T:0.20
Consensus pattern (33 bp):
TGACCCGACCCGTTGACCAGACCTGACCACTGT
Done.