Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold347
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: 466911
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 10870 characters in sequence are not A, C, G, or T
File 1 of 2
Found at i:734 original size:122 final size:122
Alignment explanation
Indices: 517--746 Score: 399
Period size: 122 Copynumber: 1.9 Consensus size: 122
507 AGGATCATAT
* *
517 TCAAATTCTTGACACTAAGACATTAAACAATCAATTCGGTACCAATTTTGGGCGTTACTAGGGTG
1 TCAAATTCTAGACACTAAGACATTAAACAATCAATTCGGTACCAATTTTGGGCGTTACAAGGGTG
*
582 CTAACCCTTCCTTGTCCGTAACTGACTCCCGAACCTATTTTCTCAAAGGAAGGATCG
66 CTAACCCTTCCTTGTCCGTAACAGACTCCCGAACCTATTTTCTCAAAGGAAGGATCG
639 TCAAATTCTAGACACTAAGACATTAAACAATCAATTCGGTACCAATTTTGGGCGTTACAAGGGTG
1 TCAAATTCTAGACACTAAGACATTAAACAATCAATTCGGTACCAATTTTGGGCGTTACAAGGGTG
* *
704 CTAACCCTT-CTTCGTGCGTAACAGACTCCCGAACCTTTTTTCT
66 CTAACCCTTCCTT-GTCCGTAACAGACTCCCGAACCTATTTTCT
747 TAAAATTCGT
Statistics
Matches: 102, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
121 3 0.03
122 99 0.97
ACGTcount: A:0.29, C:0.25, G:0.17, T:0.30
Consensus pattern (122 bp):
TCAAATTCTAGACACTAAGACATTAAACAATCAATTCGGTACCAATTTTGGGCGTTACAAGGGTG
CTAACCCTTCCTTGTCCGTAACAGACTCCCGAACCTATTTTCTCAAAGGAAGGATCG
Found at i:1808 original size:2 final size:2
Alignment explanation
Indices: 1801--1831 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
1791 ACAGTTCTCC
1801 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1832 TTTAAACCAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:4130 original size:25 final size:25
Alignment explanation
Indices: 4102--4158 Score: 66
Period size: 24 Copynumber: 2.4 Consensus size: 25
4092 ATCATTTTTT
4102 TATTTTTTGAATAT-TTGGAACTTTG
1 TATTTTTT-AATATATTGGAACTTTG
* *
4127 TA-TTTTTAATATATTTGAATTTTG
1 TATTTTTTAATATATTGGAACTTTG
4151 -ATTTTTTA
1 TATTTTTTA
4159 TAAAAAATTA
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 6 0.21
24 20 0.71
25 2 0.07
ACGTcount: A:0.26, C:0.02, G:0.11, T:0.61
Consensus pattern (25 bp):
TATTTTTTAATATATTGGAACTTTG
Found at i:11847 original size:12 final size:12
Alignment explanation
Indices: 11832--11861 Score: 60
Period size: 12 Copynumber: 2.5 Consensus size: 12
11822 AATAATTAAA
11832 TAAATTGGAAAT
1 TAAATTGGAAAT
11844 TAAATTGGAAAT
1 TAAATTGGAAAT
11856 TAAATT
1 TAAATT
11862 TGGATTTTGT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.13, T:0.37
Consensus pattern (12 bp):
TAAATTGGAAAT
Found at i:16781 original size:12 final size:12
Alignment explanation
Indices: 16761--16794 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
16751 CAACATAAAT
*
16761 AAATAAAATTAG
1 AAATTAAATTAG
*
16773 AAATTAAATTGG
1 AAATTAAATTAG
16785 AAATTAAATT
1 AAATTAAATT
16795 CAGATTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.59, C:0.00, G:0.09, T:0.32
Consensus pattern (12 bp):
AAATTAAATTAG
Found at i:21936 original size:40 final size:40
Alignment explanation
Indices: 21780--21948 Score: 176
Period size: 40 Copynumber: 4.2 Consensus size: 40
21770 TTTCTGAAAC
* * * * ** **
21780 AAACGTCGCTATAGGTTGAGCATTAGCCACGTTTTTTTAA
1 AAACGCCGCTATAGATCGAGCATTAGCGACACTTTTCAAA
* * **
21820 AAACGCCGCTATAGATTGATCATTAGCGACACTTTTTGAA
1 AAACGCCGCTATAGATCGAGCATTAGCGACACTTTTCAAA
* * *
21860 AAACGCCGCTATAGATCAAGCATTAGTGGCACTTTTCAAA
1 AAACGCCGCTATAGATCGAGCATTAGCGACACTTTTCAAA
* *
21900 AAACGCCGCTATAGATCGAGCATTAGCGACGCTTTTCAGA
1 AAACGCCGCTATAGATCGAGCATTAGCGACACTTTTCAAA
*
21940 AAATGCCGC
1 AAACGCCGC
21949 AAAACACGTT
Statistics
Matches: 109, Mismatches: 20, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
40 109 1.00
ACGTcount: A:0.31, C:0.22, G:0.20, T:0.27
Consensus pattern (40 bp):
AAACGCCGCTATAGATCGAGCATTAGCGACACTTTTCAAA
Found at i:24734 original size:80 final size:80
Alignment explanation
Indices: 24601--24807 Score: 229
Period size: 80 Copynumber: 2.6 Consensus size: 80
24591 AGCTTTAGTG
* * * *
24601 GCATTAGTAGCGCTTTTTAAAAAACGCCGTAATAGATCGAGAATTAGAGGCGCTTGTTGA-AAAA
1 GCATTAGCAGCGCTTTTCAAAAAACGCCGCAATAGATCGAGAATTAGAGGCGCTT-TTCAGAAAA
* *
24665 CACCGCTATAGATCGA
65 CACCACAATAGATCGA
* ** *
24681 GCATTAGCAGCGCTTTTCAGAAAACGTTGCAATAGATCGAGAATTAGCGGCGCTTTTCAGAAAAC
1 GCATTAGCAGCGCTTTTCAAAAAACGCCGCAATAGATCGAGAATTAGAGGCGCTTTTCAGAAAAC
*
24746 GCCACAATAGATCGA
66 ACCACAATAGATCGA
* * * * * *
24761 GAATTAGCGGCGCTTGTT-GAAAAACGCCACTATAGATCGAGCATTAG
1 GCATTAGCAGCGCTT-TTCAAAAAACGCCGCAATAGATCGAGAATTAG
24808 CTGCACTTTT
Statistics
Matches: 105, Mismatches: 20, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
79 3 0.03
80 100 0.95
81 2 0.02
ACGTcount: A:0.34, C:0.19, G:0.23, T:0.24
Consensus pattern (80 bp):
GCATTAGCAGCGCTTTTCAAAAAACGCCGCAATAGATCGAGAATTAGAGGCGCTTTTCAGAAAAC
ACCACAATAGATCGA
Found at i:24808 original size:40 final size:39
Alignment explanation
Indices: 24610--24817 Score: 202
Period size: 40 Copynumber: 5.2 Consensus size: 39
24600 GGCATTAGTA
* * *
24610 GCGCTTTTTAAAAAACGCC-GTAATAGATCGAGAATTAGAG
1 GCGC-TTTTCAAAAACGCCACT-ATAGATCGAGAATTAGCG
* * * * *
24650 GCGCTTGTTGAAAAACACCGCTATAGATCGAGCATTAGCA
1 GCGCTT-TTCAAAAACGCCACTATAGATCGAGAATTAGCG
*** *
24690 GCGCTTTTCAGAAAACGTTGCAATAGATCGAGAATTAGCG
1 GCGCTTTTCA-AAAACGCCACTATAGATCGAGAATTAGCG
*
24730 GCGCTTTTCAGAAAACGCCACAATAGATCGAGAATTAGCG
1 GCGCTTTTCA-AAAACGCCACTATAGATCGAGAATTAGCG
* * *
24770 GCGCTTGTTGAAAAACGCCACTATAGATCGAGCATTAGCT
1 GCGCTT-TTCAAAAACGCCACTATAGATCGAGAATTAGCG
*
24810 GCACTTTT
1 GCGCTTTT
24818 AGCAAAATGC
Statistics
Matches: 143, Mismatches: 21, Indels: 9
0.83 0.12 0.05
Matches are distributed among these distances:
39 7 0.05
40 132 0.92
41 4 0.03
ACGTcount: A:0.33, C:0.20, G:0.23, T:0.25
Consensus pattern (39 bp):
GCGCTTTTCAAAAACGCCACTATAGATCGAGAATTAGCG
Found at i:25364 original size:29 final size:28
Alignment explanation
Indices: 25292--25387 Score: 88
Period size: 29 Copynumber: 3.4 Consensus size: 28
25282 ATGCTTACGA
* * *
25292 TTTAGGGTATAAGTTTATGGTTTA-GTG
1 TTTAGGGTTTAAGTTTAAGGTTTAGGGG
* *
25319 TTTAGGATTTAATGTTTAAGGGTTAGGGG
1 TTTAGGGTTTAA-GTTTAAGGTTTAGGGG
25348 TTTAGGGTTTATAGTTTATA-GTTTAGGGG
1 TTTAGGGTTTA-AGTTTA-AGGTTTAGGGG
* *
25377 CTTAAGGTTTA
1 TTTAGGGTTTA
25388 TGGTTTAGTG
Statistics
Matches: 56, Mismatches: 9, Indels: 6
0.79 0.13 0.08
Matches are distributed among these distances:
27 10 0.18
28 10 0.18
29 34 0.61
30 2 0.04
ACGTcount: A:0.23, C:0.01, G:0.30, T:0.46
Consensus pattern (28 bp):
TTTAGGGTTTAAGTTTAAGGTTTAGGGG
Found at i:25904 original size:19 final size:19
Alignment explanation
Indices: 25874--25922 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
25864 AATTATATAA
* *
25874 AAATTTTAAAAT-TTATTT
1 AAATTTTCAAATATTACTT
*
25892 AATTCTTTCAAATATTACTT
1 AAAT-TTTCAAATATTACTT
25912 AAATTTTCAAA
1 AAATTTTCAAA
25923 AAGTATTTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
18 3 0.12
19 14 0.56
20 8 0.32
ACGTcount: A:0.43, C:0.08, G:0.00, T:0.49
Consensus pattern (19 bp):
AAATTTTCAAATATTACTT
Found at i:26467 original size:17 final size:17
Alignment explanation
Indices: 26423--26478 Score: 51
Period size: 18 Copynumber: 3.3 Consensus size: 17
26413 TTATATTTAT
* *
26423 TTAAAATAATTTGATAA
1 TTAAAAAAATTTAATAA
* *
26440 ATAATATAAATTTAATAA
1 TTAA-AAAAATTTAATAA
*
26458 TTAAAAAAATATAA-AA
1 TTAAAAAAATTTAATAA
26474 TTAAA
1 TTAAA
26479 TGAATGATCA
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
16 7 0.23
17 11 0.35
18 13 0.42
ACGTcount: A:0.62, C:0.00, G:0.02, T:0.36
Consensus pattern (17 bp):
TTAAAAAAATTTAATAA
Found at i:38233 original size:50 final size:50
Alignment explanation
Indices: 38124--38238 Score: 140
Period size: 50 Copynumber: 2.3 Consensus size: 50
38114 TGAGAGGTCT
* * * **
38124 CATGGAAGACCATATTTGGGACATGGCGTTGGCACCGAGATGAGAGGTCC
1 CATGAAAGACCATATTTGGGACATGGCATGGGCACCGAGATGAGAACTCC
** * *
38174 CCCGAAAGACCATGTTTGGGACATGGCATGGGCACCGATATGAGAACTCC
1 CATGAAAGACCATATTTGGGACATGGCATGGGCACCGAGATGAGAACTCC
*
38224 CATGTAAGACCATAT
1 CATGAAAGACCATAT
38239 CTNNNNNNNN
Statistics
Matches: 52, Mismatches: 13, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 52 1.00
ACGTcount: A:0.29, C:0.23, G:0.29, T:0.20
Consensus pattern (50 bp):
CATGAAAGACCATATTTGGGACATGGCATGGGCACCGAGATGAGAACTCC
Found at i:41538 original size:14 final size:14
Alignment explanation
Indices: 41519--41545 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
41509 ACCAAAAAAT
41519 AAAAATAAATAAAC
1 AAAAATAAATAAAC
41533 AAAAATAAATAAA
1 AAAAATAAATAAA
41546 AAGGTCTATT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.04, G:0.00, T:0.15
Consensus pattern (14 bp):
AAAAATAAATAAAC
Found at i:53193 original size:94 final size:94
Alignment explanation
Indices: 53001--53223 Score: 277
Period size: 94 Copynumber: 2.4 Consensus size: 94
52991 TACAGTAGCG
* *
53001 AATCTTATCTCCTTGAAGGTGTAGTGGAGCAAGATGAAGCTACAAATCCTACATCCCTGAAGTTG
1 AATCTTATCTCCTTGAAGATGCAGTGGAGCAAGATGAAGCTACAAATCCTACATCCCTGAAGTTG
* * * * *
53066 TAGTGGATCGGATTGAAATTATAACAACG
66 TAGTGGATCGAATCGAAACTACAACAACA
* * * *
53095 AATCTTATCTCCTTGAAGTTGCAGTGGAGCAAGATTAAGCTACAAATCCTATATCCTTGAAGTTG
1 AATCTTATCTCCTTGAAGATGCAGTGGAGCAAGATGAAGCTACAAATCCTACATCCCTGAAGTTG
**
53160 TAGTGGGAT-GAATCGAAACTACAATGACA
66 TAGT-GGATCGAATCGAAACTACAACAACA
* * * *
53189 AATCTCATCTCCCTGAAGATACAGTGGAGTAAGAT
1 AATCTTATCTCCTTGAAGATGCAGTGGAGCAAGAT
53224 AAAGTTATAA
Statistics
Matches: 111, Mismatches: 17, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
94 107 0.96
95 4 0.04
ACGTcount: A:0.34, C:0.17, G:0.21, T:0.28
Consensus pattern (94 bp):
AATCTTATCTCCTTGAAGATGCAGTGGAGCAAGATGAAGCTACAAATCCTACATCCCTGAAGTTG
TAGTGGATCGAATCGAAACTACAACAACA
Found at i:55942 original size:24 final size:24
Alignment explanation
Indices: 55894--55940 Score: 67
Period size: 24 Copynumber: 1.9 Consensus size: 24
55884 ACTGGTCATA
*
55894 GAGAGAATTGAGGAGGGATATTTG
1 GAGAGAATTGAGGAGGAATATTTG
*
55918 GAGAGATTTGAGGAGAGAATATT
1 GAGAGAATTGAGGAG-GAATATT
55941 GGGATTTGGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
24 14 0.70
25 6 0.30
ACGTcount: A:0.36, C:0.00, G:0.38, T:0.26
Consensus pattern (24 bp):
GAGAGAATTGAGGAGGAATATTTG
Found at i:56649 original size:27 final size:27
Alignment explanation
Indices: 56609--56806 Score: 198
Period size: 27 Copynumber: 7.3 Consensus size: 27
56599 CGAGAGGTCA
**
56609 TAAAATGATTGAATTACCCCCACAGGG
1 TAAAATGACCGAATTACCCCCACAGGG
* * *
56636 TAAAATGACCGAATTACCTCTATAGGG
1 TAAAATGACCGAATTACCCCCACAGGG
** **
56663 TAAAATGACTAAATTACCCTTACAGGG
1 TAAAATGACCGAATTACCCCCACAGGG
* * *
56690 TAAAATGATCGAATTACCCCTAAAGGG
1 TAAAATGACCGAATTACCCCCACAGGG
* *
56717 TAAAATGATCGAATTACCCCCACAGGA
1 TAAAATGACCGAATTACCCCCACAGGG
* * *
56744 TAAAATGACCGAAATACCCTCATAGGG
1 TAAAATGACCGAATTACCCCCACAGGG
* * * * *
56771 TAATATGACTGAAATACCCCCATATGG
1 TAAAATGACCGAATTACCCCCACAGGG
56798 TAAAATGAC
1 TAAAATGAC
56807 TATTATACCC
Statistics
Matches: 143, Mismatches: 28, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
27 143 1.00
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.23
Consensus pattern (27 bp):
TAAAATGACCGAATTACCCCCACAGGG
Found at i:56678 original size:54 final size:54
Alignment explanation
Indices: 56620--56806 Score: 227
Period size: 54 Copynumber: 3.5 Consensus size: 54
56610 AAAATGATTG
56620 AATTACCCCCACAGGGTAAAATGACCGAATTACCTCTATAGGGTAAAATGACT-A
1 AATTACCCCCACAGGGTAAAATGACCGAATTACC-CTATAGGGTAAAATGACTCA
** * * *
56674 AATTACCCTTACAGGGTAAAATGATCGAATTACCCCTAAAGGGTAAAATGA-TCG
1 AATTACCCCCACAGGGTAAAATGACCGAATTA-CCCTATAGGGTAAAATGACTCA
* * * *
56728 AATTACCCCCACAGGATAAAATGACCGAAATACCCTCATAGGGTAATATGACTGA
1 AATTACCCCCACAGGGTAAAATGACCGAATTACCCT-ATAGGGTAAAATGACTCA
* *
56783 AA-TACCCCCATATGGTAAAATGAC
1 AATTACCCCCACAGGGTAAAATGAC
56807 TATTATACCC
Statistics
Matches: 112, Mismatches: 17, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
53 5 0.04
54 102 0.91
55 5 0.04
ACGTcount: A:0.40, C:0.22, G:0.17, T:0.22
Consensus pattern (54 bp):
AATTACCCCCACAGGGTAAAATGACCGAATTACCCTATAGGGTAAAATGACTCA
Found at i:56748 original size:81 final size:81
Alignment explanation
Indices: 56609--56806 Score: 229
Period size: 81 Copynumber: 2.4 Consensus size: 81
56599 CGAGAGGTCA
* * * * * * *
56609 TAAAATGATTGAATTACCCCCACAGGGTAAAATGACCGAATTACCTCTATAGGGTAAAATGA-CT
1 TAAAATGATCGAATTACCCCCAAAGGGTAAAATGACCGAATTACCCCCACAGGATAAAATGACCG
*
56673 AAATTACCCTTACAGGG
66 AAA-TACCCTCACAGGG
* *
56690 TAAAATGATCGAATTACCCCTAAAGGGTAAAATGATCGAATTACCCCCACAGGATAAAATGACCG
1 TAAAATGATCGAATTACCCCCAAAGGGTAAAATGACCGAATTACCCCCACAGGATAAAATGACCG
*
56755 AAATACCCTCATAGGG
66 AAATACCCTCACAGGG
* * * *
56771 TAATATGA-CTGAAATACCCCCATATGGTAAAATGAC
1 TAAAATGATC-GAATTACCCCCAAAGGGTAAAATGAC
56807 TATTATACCC
Statistics
Matches: 98, Mismatches: 17, Indels: 4
0.82 0.14 0.03
Matches are distributed among these distances:
80 1 0.01
81 93 0.95
82 4 0.04
ACGTcount: A:0.40, C:0.21, G:0.17, T:0.23
Consensus pattern (81 bp):
TAAAATGATCGAATTACCCCCAAAGGGTAAAATGACCGAATTACCCCCACAGGATAAAATGACCG
AAATACCCTCACAGGG
Found at i:57216 original size:28 final size:29
Alignment explanation
Indices: 57172--57255 Score: 138
Period size: 28 Copynumber: 3.0 Consensus size: 29
57162 GCTATACCGA
*
57172 TACT-GTATTGGGCTAAGGCCCATATTGT
1 TACTAGTATTGGGCTAAGGCCCACATTGT
57200 TAC-AGTATTGGGCTAAGGCCCACATTGT
1 TACTAGTATTGGGCTAAGGCCCACATTGT
57228 TACTA-TATTGGGCTAAGGCCCACATTGT
1 TACTAGTATTGGGCTAAGGCCCACATTGT
57256 ACTGTTACTA
Statistics
Matches: 53, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
28 52 0.98
29 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.24, T:0.32
Consensus pattern (29 bp):
TACTAGTATTGGGCTAAGGCCCACATTGT
Found at i:57900 original size:111 final size:111
Alignment explanation
Indices: 57706--57927 Score: 417
Period size: 111 Copynumber: 2.0 Consensus size: 111
57696 GATTTGTTAA
57706 ACGAGTCCCATTTGGCTTACCAATCACATAAAAATGGCTCTATACTCTACAATTTGAACGTCAAT
1 ACGAGTCCCATTTGGCTTACCAATCACATAAAAATGGCTCTATACTCTACAATTTGAACGTCAAT
57771 TCTCACACTCTCAACTCTAAAACACTAAAGTAATGTCCACCTCCGG
66 TCTCACACTCTCAACTCTAAAACACTAAAGTAATGTCCACCTCCGG
* *
57817 ACGAGTCCTATTTGGCTTACCAATCACATAAAAATGGCTCTATACTCTATAATTTGAACGTCAAT
1 ACGAGTCCCATTTGGCTTACCAATCACATAAAAATGGCTCTATACTCTACAATTTGAACGTCAAT
*
57882 TCTCATACTCTCAACTCTAAAACACTAAAGTAATGTCCACCTCCGG
66 TCTCACACTCTCAACTCTAAAACACTAAAGTAATGTCCACCTCCGG
57928 CTTACATATT
Statistics
Matches: 108, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
111 108 1.00
ACGTcount: A:0.33, C:0.27, G:0.11, T:0.28
Consensus pattern (111 bp):
ACGAGTCCCATTTGGCTTACCAATCACATAAAAATGGCTCTATACTCTACAATTTGAACGTCAAT
TCTCACACTCTCAACTCTAAAACACTAAAGTAATGTCCACCTCCGG
Found at i:65018 original size:20 final size:21
Alignment explanation
Indices: 64988--65057 Score: 63
Period size: 22 Copynumber: 3.3 Consensus size: 21
64978 GGGGTTAAAT
*
64988 ATTTCATTTATAAAAAAATAA
1 ATTTAATTTATAAAAAAATAA
*
65009 ATTT-ATTTATATTAAATAAT-A
1 ATTTAATTTATA--AAAAAATAA
* *
65030 ATTTAATATTTTAAATAAATAA
1 ATTTAAT-TTATAAAAAAATAA
65052 ATTTAA
1 ATTTAA
65058 AATTAATATT
Statistics
Matches: 40, Mismatches: 4, Indels: 9
0.75 0.08 0.17
Matches are distributed among these distances:
20 7 0.17
21 14 0.35
22 15 0.38
23 4 0.10
ACGTcount: A:0.53, C:0.01, G:0.00, T:0.46
Consensus pattern (21 bp):
ATTTAATTTATAAAAAAATAA
Found at i:65032 original size:21 final size:22
Alignment explanation
Indices: 64998--65057 Score: 70
Period size: 22 Copynumber: 2.8 Consensus size: 22
64988 ATTTCATTTA
* *
64998 TAAAAAAATAAATTTATTTATAT
1 TAAATAAATAAATTTA-ATATAT
*
65021 TAAAT-AAT-AATTTAATATTT
1 TAAATAAATAAATTTAATATAT
65041 TAAATAAATAAATTTAA
1 TAAATAAATAAATTTAA
65058 AATTAATATT
Statistics
Matches: 32, Mismatches: 3, Indels: 5
0.80 0.08 0.12
Matches are distributed among these distances:
20 9 0.28
21 9 0.28
22 10 0.31
23 4 0.12
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (22 bp):
TAAATAAATAAATTTAATATAT
Found at i:65063 original size:20 final size:20
Alignment explanation
Indices: 65016--65057 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 20
65006 TAAATTTATT
65016 TATATTAAATAATAATTTAA
1 TATATTAAATAATAATTTAA
*
65036 TATTTTAAATAAATAAATTTAA
1 TATATTAAAT-AAT-AATTTAA
65058 AATTAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 3 0.16
22 7 0.37
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (20 bp):
TATATTAAATAATAATTTAA
Found at i:65666 original size:27 final size:26
Alignment explanation
Indices: 65623--65675 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 26
65613 AATAAAGTAC
*
65623 ATTCTTTATTGCTTTCATATTTTCTTT
1 ATTCTTTATTGCTTTCAT-TTCTCTTT
65650 ATTCTTTATT-CTCTTCATTTCTCTTT
1 ATTCTTTATTGCT-TTCATTTCTCTTT
65676 GTTTTATAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
26 9 0.38
27 15 0.62
ACGTcount: A:0.13, C:0.19, G:0.02, T:0.66
Consensus pattern (26 bp):
ATTCTTTATTGCTTTCATTTCTCTTT
Found at i:66340 original size:100 final size:101
Alignment explanation
Indices: 66214--66414 Score: 395
Period size: 100 Copynumber: 2.0 Consensus size: 101
66204 TTTGATAGGA
66214 TCTATTTAGTCTTATTAACTTGCTAATATTGAATAATTGTATTGTATCTTTTAAATTAAATTTAT
1 TCTATTTAGTCTTATTAACTTGCTAATATTGAATAATTGTATTGTATCTTTTAAATTAAATTTAT
66279 AAATATTTTATTAAGATCAACATAAGATTTTATCAT
66 AAATATTTTATTAAGATCAACATAAGATTTTATCAT
66315 TCTATTTAGT-TTATTAACTTGCTAATATTGAATAATTGTATTGTATCTTTTAAATTAAATTTAT
1 TCTATTTAGTCTTATTAACTTGCTAATATTGAATAATTGTATTGTATCTTTTAAATTAAATTTAT
66379 AAATATTTTATTAAGATCAACATAAGATTTTATCAT
66 AAATATTTTATTAAGATCAACATAAGATTTTATCAT
66415 ATATATGTGG
Statistics
Matches: 100, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
100 90 0.90
101 10 0.10
ACGTcount: A:0.37, C:0.07, G:0.07, T:0.49
Consensus pattern (101 bp):
TCTATTTAGTCTTATTAACTTGCTAATATTGAATAATTGTATTGTATCTTTTAAATTAAATTTAT
AAATATTTTATTAAGATCAACATAAGATTTTATCAT
Found at i:67669 original size:9 final size:9
Alignment explanation
Indices: 67652--67688 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
67642 TGAGTTTTCG
67652 AATTCGAAT
1 AATTCGAAT
*
67661 AACTCGAAT
1 AATTCGAAT
*
67670 AATTTGAAT
1 AATTCGAAT
67679 AATTCGAAT
1 AATTCGAAT
67688 A
1 A
67689 TCAAACTATA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
9 24 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:68507 original size:5 final size:5
Alignment explanation
Indices: 68497--68522 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
68487 CTCGAAAATT
68497 TTCGA TTCGA TTCGA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA T
68523 CGAATGCTCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.19, C:0.19, G:0.19, T:0.42
Consensus pattern (5 bp):
TTCGA
Found at i:71088 original size:49 final size:49
Alignment explanation
Indices: 71034--71138 Score: 174
Period size: 49 Copynumber: 2.1 Consensus size: 49
71024 CCATATTCAA
*
71034 GAAGCTCATGCGAGCCTATAACAGGTAGCACCGAAGAGCCATTAATCGG
1 GAAGCTCATGCGAGCCTATAACAGGTAGCACCAAAGAGCCATTAATCGG
* * *
71083 GAAGCTCATGCGAGCTTATAATAGGTAGCTCCAAAGAGCCATTAATCGG
1 GAAGCTCATGCGAGCCTATAACAGGTAGCACCAAAGAGCCATTAATCGG
71132 GAAGCTC
1 GAAGCTC
71139 CGGATAGCCA
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
49 52 1.00
ACGTcount: A:0.32, C:0.23, G:0.26, T:0.19
Consensus pattern (49 bp):
GAAGCTCATGCGAGCCTATAACAGGTAGCACCAAAGAGCCATTAATCGG
Found at i:71170 original size:74 final size:75
Alignment explanation
Indices: 71065--71231 Score: 175
Period size: 74 Copynumber: 2.2 Consensus size: 75
71055 CAGGTAGCAC
* * *
71065 CGAAGAGCCAT-TAATCGGGAAGCTCATGCGAG-CTTATAAT-AGGTAGCTC-CAAAGAGCC-AT
1 CGAAGAGCCATAT-ATCGGAAAGCTCAAGCGAGAC--AT-ATCAGGAAGCTCACAAAGAGCCAAT
71125 TAATCGGGAAGCTC-
62 TAAT-GGGAAGCTCA
* * * *
71139 CGGATAGCCATATATCGGAAAGTTCAAGCGAGACATGTCAGGAAGCTCACAAAGAGCCAATTAAT
1 CGAAGAGCCATATATCGGAAAGCTCAAGCGAGACATATCAGGAAGCTCACAAAGAGCCAATTAAT
71204 GGGAAGCTCA
66 GGGAAGCTCA
*
71214 CGAAGAGTCATATATCGG
1 CGAAGAGCCATATATCGG
71232 GATGCTCATA
Statistics
Matches: 77, Mismatches: 10, Indels: 11
0.79 0.10 0.11
Matches are distributed among these distances:
72 1 0.01
73 10 0.13
74 43 0.56
75 23 0.30
ACGTcount: A:0.35, C:0.20, G:0.26, T:0.19
Consensus pattern (75 bp):
CGAAGAGCCATATATCGGAAAGCTCAAGCGAGACATATCAGGAAGCTCACAAAGAGCCAATTAAT
GGGAAGCTCA
Found at i:77045 original size:27 final size:26
Alignment explanation
Indices: 77002--77057 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
76992 AATAAAGTAC
*
77002 ATTCTCTATTGCTTTCATATTTTCTTT
1 ATTCTCTATTGCTTTCAT-TTCTCTTT
*
77029 ATTCTTTATT-CTCTTCATTTCTCTTT
1 ATTCTCTATTGCT-TTCATTTCTCTTT
77055 ATT
1 ATT
77058 TTATAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 12 0.46
27 14 0.54
ACGTcount: A:0.14, C:0.20, G:0.02, T:0.64
Consensus pattern (26 bp):
ATTCTCTATTGCTTTCATTTCTCTTT
Found at i:77476 original size:17 final size:17
Alignment explanation
Indices: 77454--77489 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
77444 AAAATATAAA
77454 AAAAATTTAAAAATCAT
1 AAAAATTTAAAAATCAT
* *
77471 AAAAATTTTAAAATTAT
1 AAAAATTTAAAAATCAT
77488 AA
1 AA
77490 TTTTTTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAAATTTAAAAATCAT
Found at i:78919 original size:27 final size:26
Alignment explanation
Indices: 78876--78931 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 26
78866 AATAAAGTAC
*
78876 ATTCTCTATTGCTTTCATATTTTCTTT
1 ATTCTCTATTGCTTTCAT-TTCTCTTT
*
78903 ATTCTTTATT-CTCTTCATTTCTCTTT
1 ATTCTCTATTGCT-TTCATTTCTCTTT
78929 ATT
1 ATT
78932 TTATAACAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 12 0.46
27 14 0.54
ACGTcount: A:0.14, C:0.20, G:0.02, T:0.64
Consensus pattern (26 bp):
ATTCTCTATTGCTTTCATTTCTCTTT
Found at i:79350 original size:17 final size:17
Alignment explanation
Indices: 79328--79363 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
79318 AAAATATAAA
79328 AAAAATTTAAAAATCAT
1 AAAAATTTAAAAATCAT
* *
79345 AAAAATTTTAAAATTAT
1 AAAAATTTAAAAATCAT
79362 AA
1 AA
79364 TTTTTTAATT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.64, C:0.03, G:0.00, T:0.33
Consensus pattern (17 bp):
AAAAATTTAAAAATCAT
Found at i:81216 original size:23 final size:23
Alignment explanation
Indices: 81186--81234 Score: 89
Period size: 23 Copynumber: 2.1 Consensus size: 23
81176 TTTAAATGAA
81186 ATAAACACAACATAACCATTTTC
1 ATAAACACAACATAACCATTTTC
*
81209 ATAAACACAACATAAGCATTTTC
1 ATAAACACAACATAACCATTTTC
81232 ATA
1 ATA
81235 TAAAAAACAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.49, C:0.22, G:0.02, T:0.27
Consensus pattern (23 bp):
ATAAACACAACATAACCATTTTC
Found at i:81243 original size:23 final size:23
Alignment explanation
Indices: 81186--81243 Score: 73
Period size: 23 Copynumber: 2.5 Consensus size: 23
81176 TTTAAATGAA
*
81186 ATAAACACAACATAACCATTTTC
1 ATAAACAAAACATAACCATTTTC
* *
81209 ATAAACACAACATAAGCATTTTC
1 ATAAACAAAACATAACCATTTTC
81232 ATATAA-AAAACA
1 ATA-AACAAAACA
81244 ATTCTTTTCG
Statistics
Matches: 32, Mismatches: 2, Indels: 2
0.89 0.06 0.06
Matches are distributed among these distances:
23 30 0.94
24 2 0.06
ACGTcount: A:0.53, C:0.21, G:0.02, T:0.24
Consensus pattern (23 bp):
ATAAACAAAACATAACCATTTTC
Found at i:81479 original size:3 final size:3
Alignment explanation
Indices: 81473--81519 Score: 94
Period size: 3 Copynumber: 15.7 Consensus size: 3
81463 AGAAACAAAT
81473 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CAC CA
81520 AACAACCATA
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 44 1.00
ACGTcount: A:0.34, C:0.66, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:87739 original size:98 final size:98
Alignment explanation
Indices: 87570--87904 Score: 598
Period size: 98 Copynumber: 3.4 Consensus size: 98
87560 GTGCAATAAA
87570 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
87635 CCACTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCACTAAAATCCCAAACTCGGAATATTTCCTTT
* *
87668 ACTTTAAAAGAACATCCACTTATCAAAGATTTAAGGAATCACACCCAATACGTTAGGGCACGATT
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
87733 CCACTAAAATCCCAAACTCGGAATATTTCCTTT
66 CCACTAAAATCCCAAACTCGGAATATTTCCTTT
* * *
87766 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACGCCCAATACGTTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
** *
87831 CCTTTAGAATCCCAAACTCGGAATATTTCCTTT
66 CCACTAAAATCCCAAACTCGGAATATTTCCTTT
87864 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCA
1 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCA
87905 ATTTTCAAAA
Statistics
Matches: 226, Mismatches: 11, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
98 226 1.00
ACGTcount: A:0.38, C:0.25, G:0.11, T:0.27
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATT
CCACTAAAATCCCAAACTCGGAATATTTCCTTT
Found at i:89781 original size:44 final size:43
Alignment explanation
Indices: 89724--90524 Score: 395
Period size: 44 Copynumber: 18.8 Consensus size: 43
89714 CTAGTGCTTC
* * *
89724 AATCTACTTCACTGCAACTTCAGGGAGATAAGATTTGCTTCCTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTT-CTT
* * * * * *
89768 AGTCTGCTCCACTGCAACTTCAGGAAAATAAGACTAGATAC--
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTCTT
* * * * * *
89809 GATCTGCT-CTCTGTAACTTCAGAGAGATAAGATCTGAGATT-TT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-TGCTTCTT
* * * *
89852 AATCCGCTCTACTGCAACTTTAGGGAGATAGGA-TTG-TTGGCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTT--C-TT
* * *
89896 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGC--
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTCTT
* ** * *
89937 AATCTGCT-CTCTGCAACTTCAGAAAGATAAGATCTGAGATT-TT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-TGCTTCTT
** * * * **
89980 AATCCACTCCACTACAACTTTAGGGAGATAGGA-TTGTCGGCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-CTTC-TT
*
90024 AATCTGCT---C--C-AC-T---GGAGATAAGACTTGCCATCTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-CTTCTT
* *
90058 CAGTCTGCCCCACTGCAACTTCAGGGAGGATAAGACTTGCTTACTT
1 -AATCTGCTCCACTGCAACTTCAGGGA-GATAAGACTTGCTT-CTT
* * * *
90104 AGTCTGCTCCACTGCAACTTCAGGGAGATACGATTTGCCATCTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-CTTCTT
*
90148 CAGTCTGC-CTCACTGCAACTTC-GGGAGGATAAGACTTGCTTACTT
1 -AATCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGCTT-CTT
* * * * * *
90193 ATTCTGCTCCACTACAACTTGAGGGAGATAAGACTAGATGC--
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTCTT
* * ** * *
90234 GATCTGCT-CTCTGCAACTTCAGAAAGATAAGATCTGAGATT-TT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGA-CT-TGCTTCTT
** * * * **
90277 AATCCACTCCACTACAACTTTAGGGAGATAGGA-TTGTCGGCTTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-CTTC-TT
* *
90321 AATCTGCT----T-CCAC-T---GGAG-TAAGACTTGCCATCTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-CTTCTT
* *
90355 CAGTCTGCCCCACTGCAACTTCAGGGAGGATAAGACTTGCTTACTT
1 -AATCTGCTCCACTGCAACTTCAGGGA-GATAAGACTTGCTT-CTT
* * * *
90401 AGTCTGCTCCACTGCAACTTCAGGGAGATACGATTTGCCATCTT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTG-CTTCTT
*
90445 CAGTCTGC-CTCACTGCAACTTC-GGGAGGATAAGACTTGCTTACTT
1 -AATCTGCTC-CACTGCAACTTCAGGGA-GATAAGACTTGCTT-CTT
*
90490 ATTCTGCTCCACTGCAACTTCAGGGAGATAAGACT
1 AATCTGCTCCACTGCAACTTCAGGGAGATAAGACT
90525 AGATGTGATA
Statistics
Matches: 578, Mismatches: 110, Indels: 138
0.70 0.13 0.17
Matches are distributed among these distances:
34 17 0.03
35 26 0.04
37 1 0.00
38 4 0.01
39 5 0.01
40 66 0.11
41 33 0.06
42 16 0.03
43 19 0.03
44 228 0.39
45 136 0.24
46 27 0.05
ACGTcount: A:0.27, C:0.24, G:0.20, T:0.29
Consensus pattern (43 bp):
AATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGCTTCTT
Found at i:89927 original size:128 final size:128
Alignment explanation
Indices: 89724--90037 Score: 452
Period size: 128 Copynumber: 2.5 Consensus size: 128
89714 CTAGTGCTTC
* * * * * *
89724 AATCTACTTCACTGCAACTTCAGGGAGATAAGATTTGCTT--CCTTAGTCTGCTCCACTGCAACT
1 AATCCACTCCACTGCAACTTTAGGGAGATAGGA-TTG-TTGGCTTTAATCTGCTCCACTGCAACT
* * *
89787 TCAGGAAAATAAGACTAGATACGATCTGCTCTCTGTAACTTCAGAGAGATAAGATCTGAGATTTT
64 TCAGGAAAATAAGACTAGATACAATCTGCTCTCTGCAACTTCAGAAAGATAAGATCTGAGATTTT
* *
89852 AATCCGCTCTACTGCAACTTTAGGGAGATAGGATTGTTGGCTTTAATCTGCTCCACTGCAACTTC
1 AATCCACTCCACTGCAACTTTAGGGAGATAGGATTGTTGGCTTTAATCTGCTCCACTGCAACTTC
* * *
89917 AGGGAGATAAGACTAGATGCAATCTGCTCTCTGCAACTTCAGAAAGATAAGATCTGAGATTTT
66 AGGAAAATAAGACTAGATACAATCTGCTCTCTGCAACTTCAGAAAGATAAGATCTGAGATTTT
* *
89980 AATCCACTCCACTACAACTTTAGGGAGATAGGATTGTCGGCTTTAATCTGCTCCACTG
1 AATCCACTCCACTGCAACTTTAGGGAGATAGGATTGTTGGCTTTAATCTGCTCCACTG
90038 GAGATAAGAC
Statistics
Matches: 166, Mismatches: 18, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
126 2 0.01
127 3 0.02
128 161 0.97
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.30
Consensus pattern (128 bp):
AATCCACTCCACTGCAACTTTAGGGAGATAGGATTGTTGGCTTTAATCTGCTCCACTGCAACTTC
AGGAAAATAAGACTAGATACAATCTGCTCTCTGCAACTTCAGAAAGATAAGATCTGAGATTTT
Found at i:90116 original size:45 final size:44
Alignment explanation
Indices: 90037--90524 Score: 335
Period size: 45 Copynumber: 11.3 Consensus size: 44
90027 CTGCTCCACT
* *
90037 GGAGATAAGACTTGC-CATCTTCAGTCTGCCCCACTGCAACTTCAG
1 GGAGATAAGACTTGCTTA-CTT-AGTCTGCTCCACTGCAACTTCAG
90082 GGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAG
1 GGA-GATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAG
* * *
90127 GGAGATACGATTTGC-CATCTTCAGTCTGC-CTCACTGCAACTTC-G
1 GGAGATAAGACTTGCTTA-CTT-AGTCTGCTC-CACTGCAACTTCAG
* * *
90171 GGAGGATAAGACTTGCTTACTTATTCTGCTCCACTACAACTTGAG
1 GGA-GATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAG
* * * * *
90216 GGAGATAAGACTAG-ATGC-GA-TCTGCT-CTCTGCAACTTCAG
1 GGAGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAG
** * * * ** * *
90256 AAAGATAAGATCTGAGATT--TTAATCCACTCCACTACAACTTTAG
1 GGAGATAAGA-CT-TGCTTACTTAGTCTGCTCCACTGCAACTTCAG
* ** * *
90300 GGAGATAGGA-TTG-TCGGCTTTAATCTGCT----T-CCAC-T---
1 GGAGATAAGACTTGCT-TAC-TTAGTCTGCTCCACTGCAACTTCAG
* *
90335 GGAG-TAAGACTTGC-CATCTTCAGTCTGCCCCACTGCAACTTCAG
1 GGAGATAAGACTTGCTTA-CTT-AGTCTGCTCCACTGCAACTTCAG
90379 GGAGGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAG
1 GGA-GATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAG
* * *
90424 GGAGATACGATTTGC-CATCTTCAGTCTGC-CTCACTGCAACTTC-G
1 GGAGATAAGACTTGCTTA-CTT-AGTCTGCTC-CACTGCAACTTCAG
*
90468 GGAGGATAAGACTTGCTTACTTATTCTGCTCCACTGCAACTTCAG
1 GGA-GATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAG
90513 GGAGATAAGACT
1 GGAGATAAGACT
90525 AGATGTGATA
Statistics
Matches: 351, Mismatches: 50, Indels: 85
0.72 0.10 0.17
Matches are distributed among these distances:
34 6 0.02
35 14 0.04
38 1 0.00
39 4 0.01
40 24 0.07
41 10 0.03
42 5 0.01
43 9 0.03
44 118 0.34
45 128 0.36
46 30 0.09
47 2 0.01
ACGTcount: A:0.25, C:0.25, G:0.21, T:0.28
Consensus pattern (44 bp):
GGAGATAAGACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAG
Found at i:90211 original size:89 final size:90
Alignment explanation
Indices: 90037--90227 Score: 321
Period size: 89 Copynumber: 2.1 Consensus size: 90
90027 CTGCTCCACT
90037 GGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGGAGGATAAGACTTGCTTAC
1 GGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGGAGGATAAGACTTGCTTAC
*
90102 TTAGTCTGCTCCACTGCAACTTCAG
66 TTAGTCTGCTCCACTACAACTTCAG
* * *
90127 GGAGATACGATTTGCCATCTTCAGTCTGCCTCACTGCAACTTC-GGGAGGATAAGACTTGCTTAC
1 GGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGGAGGATAAGACTTGCTTAC
* *
90191 TTATTCTGCTCCACTACAACTTGAG
66 TTAGTCTGCTCCACTACAACTTCAG
90216 GGAGATAAGACT
1 GGAGATAAGACT
90228 AGATGCGATC
Statistics
Matches: 93, Mismatches: 8, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
89 53 0.57
90 40 0.43
ACGTcount: A:0.25, C:0.26, G:0.21, T:0.28
Consensus pattern (90 bp):
GGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGGAGGATAAGACTTGCTTAC
TTAGTCTGCTCCACTACAACTTCAG
Found at i:90498 original size:89 final size:90
Alignment explanation
Indices: 90345--90519 Score: 325
Period size: 89 Copynumber: 2.0 Consensus size: 90
90335 GGAGTAAGAC
90345 TTGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGGAGGATAAGACTTGCTTACTTAGTCTGCTC
1 TTGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGGAGGATAAGACTTGCTTACTTAGTCTGCTC
90410 CACTGCAACTTCAGGGAGATACGAT
66 CACTGCAACTTCAGGGAGATACGAT
* *
90435 TTGCCATCTTCAGTCTGCCTCACTGCAACTTC-GGGAGGATAAGACTTGCTTACTTATTCTGCTC
1 TTGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGGAGGATAAGACTTGCTTACTTAGTCTGCTC
90499 CACTGCAACTTCAGGGAGATA
66 CACTGCAACTTCAGGGAGATA
90520 AGACTAGATG
Statistics
Matches: 83, Mismatches: 2, Indels: 1
0.97 0.02 0.01
Matches are distributed among these distances:
89 52 0.63
90 31 0.37
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (90 bp):
TTGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGGAGGATAAGACTTGCTTACTTAGTCTGCTC
CACTGCAACTTCAGGGAGATACGAT
Found at i:90623 original size:297 final size:298
Alignment explanation
Indices: 89898--90608 Score: 1293
Period size: 297 Copynumber: 2.4 Consensus size: 298
89888 TTGGCTTTAA
*
89898 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCAATCTGCTCTCTGCAACTTCAGAAAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAAAG
89963 ATAAGATCTGAGATTTTAATCCACTCCACTACAACTTTAGGGAGATAGGATTGTCGGCTTTAATC
66 ATAAGATCTGAGATTTTAATCCACTCCACTACAACTTTAGGGAGATAGGATTGTCGGCTTTAATC
90028 TGC-TCCACTGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGGAGGATAAG
131 TGCTTCCACTGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGGAGGATAAG
90092 ACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATACGATTTGCCATCTTCAGTCTGCC
196 ACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATACGATTTGCCATCTTCAGTCTGCC
90157 TCACTGCAACTTCGGGAGGATAAGACTTGCTTACTTAT
261 TCACTGCAACTTCGGGAGGATAAGACTTGCTTACTTAT
* *
90195 TCTGCTCCACTACAACTTGAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAAAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAAAG
90260 ATAAGATCTGAGATTTTAATCCACTCCACTACAACTTTAGGGAGATAGGATTGTCGGCTTTAATC
66 ATAAGATCTGAGATTTTAATCCACTCCACTACAACTTTAGGGAGATAGGATTGTCGGCTTTAATC
90325 TGCTTCCACTGGAG-TAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGGAGGATAAG
131 TGCTTCCACTGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGGAGGATAAG
90389 ACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATACGATTTGCCATCTTCAGTCTGCC
196 ACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATACGATTTGCCATCTTCAGTCTGCC
90454 TCACTGCAACTTCGGGAGGATAAGACTTGCTTACTTAT
261 TCACTGCAACTTCGGGAGGATAAGACTTGCTTACTTAT
* * * **
90492 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGTGATATGTTCTCTGCAACTTCAGAGGG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAAAG
* * * *
90557 ATAAGATCTGAGGTTTTAATCCGC-CCACTACAACTTCAGTGAGATAGGATTG
66 ATAAGATCTGAGATTTTAATCCACTCCACTACAACTTTAGGGAGATAGGATTG
90609 CCAGCCACTA
Statistics
Matches: 399, Mismatches: 14, Indels: 3
0.96 0.03 0.01
Matches are distributed among these distances:
296 26 0.07
297 363 0.91
298 10 0.03
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (298 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTGCTCTCTGCAACTTCAGAAAG
ATAAGATCTGAGATTTTAATCCACTCCACTACAACTTTAGGGAGATAGGATTGTCGGCTTTAATC
TGCTTCCACTGGAGATAAGACTTGCCATCTTCAGTCTGCCCCACTGCAACTTCAGGGAGGATAAG
ACTTGCTTACTTAGTCTGCTCCACTGCAACTTCAGGGAGATACGATTTGCCATCTTCAGTCTGCC
TCACTGCAACTTCGGGAGGATAAGACTTGCTTACTTAT
Found at i:102365 original size:98 final size:98
Alignment explanation
Indices: 102196--102488 Score: 514
Period size: 98 Copynumber: 3.0 Consensus size: 98
102186 GCAATAAAAT
102196 TTTAAAAGAACATCCACCTATCCAAGATTTGAGAAATCACACCCAATACGTTAGGGCACGATTCC
1 TTTAAAAGAACATCCACCTATCCAAGATTTGAGAAATCACACCCAATACGTTAGGGCACGATTCC
*
102261 ACTAAAATCCCAAACTCGGAATATTTCCTTTAC
66 TCTAAAATCCCAAACTCGGAATATTTCCTTTAC
* * * *
102294 TTTAAAAGAACATCCACTTATCAAAGATTTAAGGAATCACACCCAATACGTTAGGGCACGATTCC
1 TTTAAAAGAACATCCACCTATCCAAGATTTGAGAAATCACACCCAATACGTTAGGGCACGATTCC
*
102359 TCTAAAATCCCAAACTCGAAATATTTCCTTTAC
66 TCTAAAATCCCAAACTCGGAATATTTCCTTTAC
*
102392 TTTAAAAGAACATCCACCTATCCAAGATTTGAGAAATCACACCCAATACGTTAGGGCACAATTCC
1 TTTAAAAGAACATCCACCTATCCAAGATTTGAGAAATCACACCCAATACGTTAGGGCACGATTCC
*
102457 TCCAAAATCCCAAACTCGGAATATTTCCTTTA
66 TCTAAAATCCCAAACTCGGAATATTTCCTTTA
102489 TTATTTTTAG
Statistics
Matches: 182, Mismatches: 13, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 182 1.00
ACGTcount: A:0.37, C:0.26, G:0.11, T:0.26
Consensus pattern (98 bp):
TTTAAAAGAACATCCACCTATCCAAGATTTGAGAAATCACACCCAATACGTTAGGGCACGATTCC
TCTAAAATCCCAAACTCGGAATATTTCCTTTAC
Found at i:103078 original size:21 final size:20
Alignment explanation
Indices: 103036--103078 Score: 50
Period size: 21 Copynumber: 2.1 Consensus size: 20
103026 AAATATTAGT
*
103036 TACAAAAAAAAATAAATGTA
1 TACAAAAAAAAATAAATATA
* *
103056 TACATAAAAAATATACATATA
1 TACA-AAAAAAAATAAATATA
103077 TA
1 TA
103079 TAGGTTTTTT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
20 4 0.21
21 15 0.79
ACGTcount: A:0.65, C:0.07, G:0.02, T:0.26
Consensus pattern (20 bp):
TACAAAAAAAAATAAATATA
Found at i:113077 original size:25 final size:25
Alignment explanation
Indices: 113039--113128 Score: 85
Period size: 25 Copynumber: 3.6 Consensus size: 25
113029 GGTCACCGAT
*
113039 TTCAGCTCTTATGAGCTTCCTGTTA
1 TTCAGCTCGTATGAGCTTCCTGTTA
* * **
113064 TTCAGCTCGCATGAGGTTCCCATTA
1 TTCAGCTCGTATGAGCTTCCTGTTA
* * *
113089 TTCAGCTCGAAAGAGCTTACTGTT-
1 TTCAGCTCGTATGAGCTTCCTGTTA
113113 TAT-AGCTCGTATGAGC
1 T-TCAGCTCGTATGAGC
113129 ATACATGTAT
Statistics
Matches: 51, Mismatches: 13, Indels: 3
0.76 0.19 0.04
Matches are distributed among these distances:
24 12 0.24
25 39 0.76
ACGTcount: A:0.21, C:0.23, G:0.20, T:0.36
Consensus pattern (25 bp):
TTCAGCTCGTATGAGCTTCCTGTTA
Found at i:118035 original size:14 final size:14
Alignment explanation
Indices: 118016--118042 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
118006 ACCATTCACC
118016 ATTTGTTTGTTACT
1 ATTTGTTTGTTACT
118030 ATTTGTTTGTTAC
1 ATTTGTTTGTTAC
118043 AAAATATTTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.07, G:0.15, T:0.63
Consensus pattern (14 bp):
ATTTGTTTGTTACT
Found at i:119405 original size:26 final size:26
Alignment explanation
Indices: 119357--119406 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
119347 TTTAGTTATT
*
119357 TTATTAGATATTTGATAATTTTACTA
1 TTATTAGATATTTAATAATTTTACTA
*
119383 TTATTTGAT-TTTAATAATGTTTAC
1 TTATTAGATATTTAATAAT-TTTAC
119407 ATAATTGTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 8 0.38
26 13 0.62
ACGTcount: A:0.32, C:0.04, G:0.08, T:0.56
Consensus pattern (26 bp):
TTATTAGATATTTAATAATTTTACTA
Found at i:122942 original size:19 final size:19
Alignment explanation
Indices: 122918--122955 Score: 76
Period size: 19 Copynumber: 2.0 Consensus size: 19
122908 TGAAATATGG
122918 GAACAGAAGGAGAGAAAGT
1 GAACAGAAGGAGAGAAAGT
122937 GAACAGAAGGAGAGAAAGT
1 GAACAGAAGGAGAGAAAGT
122956 TACAGATCTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.53, C:0.05, G:0.37, T:0.05
Consensus pattern (19 bp):
GAACAGAAGGAGAGAAAGT
Found at i:124228 original size:16 final size:18
Alignment explanation
Indices: 124189--124230 Score: 70
Period size: 17 Copynumber: 2.4 Consensus size: 18
124179 AGAAGTTGTG
124189 ATAATTATACATTTAAAA
1 ATAATTATACATTTAAAA
124207 ATAATTATA-ATTTAAAA
1 ATAATTATACATTTAAAA
124224 A-AATTAT
1 ATAATTAT
124231 GATAATTACA
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
16 6 0.25
17 9 0.38
18 9 0.38
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.40
Consensus pattern (18 bp):
ATAATTATACATTTAAAA
Found at i:124237 original size:25 final size:27
Alignment explanation
Indices: 124207--124257 Score: 79
Period size: 26 Copynumber: 2.0 Consensus size: 27
124197 ACATTTAAAA
*
124207 ATAATTATA-ATTTAAAAA-AATTATG
1 ATAATTACACATTTAAAAATAATTATG
124232 ATAATTACACATTTAAAAATAATTAT
1 ATAATTACACATTTAAAAATAATTAT
124258 AATTTAGTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 8 0.35
26 9 0.39
27 6 0.26
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.39
Consensus pattern (27 bp):
ATAATTACACATTTAAAAATAATTATG
Found at i:125627 original size:24 final size:24
Alignment explanation
Indices: 125600--125645 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
125590 AAGATTTAAT
125600 ATTTATTAGTATAATATATTTGGC
1 ATTTATTAGTATAATATATTTGGC
* *
125624 ATTTATTAGTATAGTTTATTTG
1 ATTTATTAGTATAATATATTTG
125646 ACTTACTAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 20 1.00
ACGTcount: A:0.30, C:0.02, G:0.13, T:0.54
Consensus pattern (24 bp):
ATTTATTAGTATAATATATTTGGC
Found at i:130560 original size:15 final size:16
Alignment explanation
Indices: 130531--130560 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
130521 GAAATATATA
130531 TATATATGTGTATAAT
1 TATATATGTGTATAAT
130547 TATATATG-GTATAA
1 TATATATGTGTATAA
130561 ATGTGAATTT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.40, C:0.00, G:0.13, T:0.47
Consensus pattern (16 bp):
TATATATGTGTATAAT
Found at i:142937 original size:21 final size:21
Alignment explanation
Indices: 142911--142952 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
142901 AAACAATACA
142911 TATAACCCACTATGGAGAAAT
1 TATAACCCACTATGGAGAAAT
142932 TATAACCCACTATGGAGAAAT
1 TATAACCCACTATGGAGAAAT
142953 CATCCAACCT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.43, C:0.19, G:0.14, T:0.24
Consensus pattern (21 bp):
TATAACCCACTATGGAGAAAT
Found at i:146966 original size:45 final size:45
Alignment explanation
Indices: 146902--146995 Score: 188
Period size: 45 Copynumber: 2.1 Consensus size: 45
146892 TGCCTCAAGC
146902 TTTCACTATCTCTAGACATTCATCCTAATTCAGGGCTATTTTAGT
1 TTTCACTATCTCTAGACATTCATCCTAATTCAGGGCTATTTTAGT
146947 TTTCACTATCTCTAGACATTCATCCTAATTCAGGGCTATTTTAGT
1 TTTCACTATCTCTAGACATTCATCCTAATTCAGGGCTATTTTAGT
146992 TTTC
1 TTTC
146996 TCCTCATTTT
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 49 1.00
ACGTcount: A:0.23, C:0.22, G:0.11, T:0.44
Consensus pattern (45 bp):
TTTCACTATCTCTAGACATTCATCCTAATTCAGGGCTATTTTAGT
Found at i:148189 original size:24 final size:24
Alignment explanation
Indices: 148162--148239 Score: 63
Period size: 24 Copynumber: 3.2 Consensus size: 24
148152 TCACTTCAGG
148162 GTTTGTAACTAACTTCATATTAGA
1 GTTTGTAACTAACTTCATATTAGA
* * *
148186 GTTT-TAGAGTGGATAC-TCACT-TCAGG
1 GTTTGTA-ACT--A-ACTTCA-TATTAGA
148212 GTTTGTAACTAACTTCATATTAGA
1 GTTTGTAACTAACTTCATATTAGA
148236 GTTT
1 GTTT
148240 TAGAGTGGAT
Statistics
Matches: 40, Mismatches: 6, Indels: 16
0.65 0.10 0.26
Matches are distributed among these distances:
23 5 0.12
24 17 0.43
26 13 0.32
27 5 0.12
ACGTcount: A:0.28, C:0.13, G:0.18, T:0.41
Consensus pattern (24 bp):
GTTTGTAACTAACTTCATATTAGA
Found at i:148227 original size:50 final size:50
Alignment explanation
Indices: 148152--148249 Score: 196
Period size: 50 Copynumber: 2.0 Consensus size: 50
148142 GAAGATTAAT
148152 TCACTTCAGGGTTTGTAACTAACTTCATATTAGAGTTTTAGAGTGGATAC
1 TCACTTCAGGGTTTGTAACTAACTTCATATTAGAGTTTTAGAGTGGATAC
148202 TCACTTCAGGGTTTGTAACTAACTTCATATTAGAGTTTTAGAGTGGAT
1 TCACTTCAGGGTTTGTAACTAACTTCATATTAGAGTTTTAGAGTGGAT
148250 TAGTAATTGA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.28, C:0.13, G:0.20, T:0.39
Consensus pattern (50 bp):
TCACTTCAGGGTTTGTAACTAACTTCATATTAGAGTTTTAGAGTGGATAC
Found at i:150248 original size:27 final size:27
Alignment explanation
Indices: 150210--150264 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
150200 TCATATGTGC
150210 TAATAACTGAAAGTTATGATTTTTAGG
1 TAATAACTGAAAGTTATGATTTTTAGG
150237 TAATAACTGAAAGTTATGATTTTTAGG
1 TAATAACTGAAAGTTATGATTTTTAGG
150264 T
1 T
150265 TTTTTGGCAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.36, C:0.04, G:0.18, T:0.42
Consensus pattern (27 bp):
TAATAACTGAAAGTTATGATTTTTAGG
Found at i:156762 original size:39 final size:39
Alignment explanation
Indices: 156708--156866 Score: 318
Period size: 39 Copynumber: 4.1 Consensus size: 39
156698 ATGCCCCCTT
156708 TTTTTCGTTTTAACTGTTGGTGAATATAATTTCCCAATG
1 TTTTTCGTTTTAACTGTTGGTGAATATAATTTCCCAATG
156747 TTTTTCGTTTTAACTGTTGGTGAATATAATTTCCCAATG
1 TTTTTCGTTTTAACTGTTGGTGAATATAATTTCCCAATG
156786 TTTTTCGTTTTAACTGTTGGTGAATATAATTTCCCAATG
1 TTTTTCGTTTTAACTGTTGGTGAATATAATTTCCCAATG
156825 TTTTTCGTTTTAACTGTTGGTGAATATAATTTCCCAATG
1 TTTTTCGTTTTAACTGTTGGTGAATATAATTTCCCAATG
156864 TTT
1 TTT
156867 CTAACAACGT
Statistics
Matches: 120, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 120 1.00
ACGTcount: A:0.23, C:0.13, G:0.15, T:0.50
Consensus pattern (39 bp):
TTTTTCGTTTTAACTGTTGGTGAATATAATTTCCCAATG
Found at i:161750 original size:43 final size:42
Alignment explanation
Indices: 161687--161955 Score: 299
Period size: 43 Copynumber: 6.3 Consensus size: 42
161677 AACAAGCGCC
*
161687 AACGTCGCTAAAGATCGTGACCTTTAGCGGCGCTTCTCTCACA
1 AACGCCGCTAAAGATCGTGACCTTTAGCGGCGCTTCTC-CACA
* *
161730 AACGCCGCTAAAGATTGTGACCTTTAGCGGCACTTC-CCACA
1 AACGCCGCTAAAGATCGTGACCTTTAGCGGCGCTTCTCCACA
*
161771 CAATCGCCGCTAAAGATCGTGACCTTTAGCGGCGCTTCCCCCACA
1 -AA-CGCCGCTAAAGATCGTGACCTTTAGCGGCGCTT-CTCCACA
* * *
161816 AACGCTGCTAAAGCTCGTGACCTTTAGCGACGCTTCTCCAACA
1 AACGCCGCTAAAGATCGTGACCTTTAGCGGCGCTTCTCC-ACA
* * *
161859 AACGCCGCTAAAGATCTTGGCCTTTAGCGACGCTTCTACCACA
1 AACGCCGCTAAAGATCGTGACCTTTAGCGGCGCTTCT-CCACA
* * * * * *
161902 AACACCACTAAA-ACTCATGACCCTTAGCGGCGCTTTTTCACA
1 AACGCCGCTAAAGA-TCGTGACCTTTAGCGGCGCTTCTCCACA
* *
161944 AATGCCACTAAA
1 AACGCCGCTAAA
161956 AACATGACTT
Statistics
Matches: 196, Mismatches: 23, Indels: 15
0.84 0.10 0.06
Matches are distributed among these distances:
41 4 0.02
42 21 0.11
43 161 0.82
44 5 0.03
45 5 0.03
ACGTcount: A:0.27, C:0.33, G:0.18, T:0.23
Consensus pattern (42 bp):
AACGCCGCTAAAGATCGTGACCTTTAGCGGCGCTTCTCCACA
Found at i:163150 original size:17 final size:18
Alignment explanation
Indices: 163123--163156 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
163113 TTAACCTATA
163123 AAATAAAAAAAGTTTTTT
1 AAATAAAAAAAGTTTTTT
163141 AAAT-AAAAAAGTTTTT
1 AAATAAAAAAAGTTTTT
163157 CTTTACTCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 12 0.75
18 4 0.25
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (18 bp):
AAATAAAAAAAGTTTTTT
Found at i:165910 original size:39 final size:39
Alignment explanation
Indices: 165867--165974 Score: 117
Period size: 40 Copynumber: 2.7 Consensus size: 39
165857 TTGGAAAACC
*
165867 CCGCTAATGCTCATTTTTAGCGGCATTTTCCAAAAAGCG
1 CCGCTAATGCTCATTTTTAGCGGCGTTTTCCAAAAAGCG
* * * *** *
165906 CCGCTAATACTTGATCTTTAGCGGCGTTTTTTTAATAGCG
1 CCGCTAATGC-TCATTTTTAGCGGCGTTTTCCAAAAAGCG
* *
165946 TCGCTAATGCTTATTTTTAGCGGCGTTTT
1 CCGCTAATGCTCATTTTTAGCGGCGTTTT
165975 TTATCCAAAC
Statistics
Matches: 56, Mismatches: 12, Indels: 2
0.80 0.17 0.03
Matches are distributed among these distances:
39 26 0.46
40 30 0.54
ACGTcount: A:0.20, C:0.21, G:0.19, T:0.39
Consensus pattern (39 bp):
CCGCTAATGCTCATTTTTAGCGGCGTTTTCCAAAAAGCG
Found at i:165975 original size:39 final size:39
Alignment explanation
Indices: 165842--165977 Score: 132
Period size: 39 Copynumber: 3.5 Consensus size: 39
165832 GGGCTTAGGG
** * *
165842 TTTTT-GCGGCGCTTTTTGGAAAA-CCCCGCTAATGCTCA
1 TTTTTAGCGGCG-TTTTTTAAAAAGCGCCGCTAATGCTTA
* ** *
165880 TTTTTAGCGGCATTTTCCAAAAAGCGCCGCTAATACTTGA
1 TTTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCTT-A
* * * *
165920 TCTTTAGCGGCGTTTTTTTAATAGCGTCGCTAATGCTTA
1 TTTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCTTA
165959 TTTTTAGCGGCGTTTTTTA
1 TTTTTAGCGGCGTTTTTTA
165978 TCCAAACGCC
Statistics
Matches: 78, Mismatches: 17, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
38 13 0.17
39 34 0.44
40 31 0.40
ACGTcount: A:0.20, C:0.21, G:0.20, T:0.40
Consensus pattern (39 bp):
TTTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCTTA
Found at i:169990 original size:33 final size:35
Alignment explanation
Indices: 169952--170026 Score: 93
Period size: 32 Copynumber: 2.2 Consensus size: 35
169942 AGGAATTTCG
*
169952 TATTTTTTAAGATTTTTTTG-AGAATTTTCGGA-T
1 TATTTTTTAAGATTTTTTCGAAGAATTTTCGGAGT
**
169985 TA-TTTTTGGGATTTTTTCGAAGAATTTTCGGAGT
1 TATTTTTTAAGATTTTTTCGAAGAATTTTCGGAGT
*
170019 TTTTTTTT
1 TATTTTTT
170027 GGAGTGAGGA
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
32 14 0.40
33 14 0.40
34 2 0.06
35 5 0.14
ACGTcount: A:0.20, C:0.04, G:0.17, T:0.59
Consensus pattern (35 bp):
TATTTTTTAAGATTTTTTCGAAGAATTTTCGGAGT
Found at i:170754 original size:25 final size:25
Alignment explanation
Indices: 170726--170773 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
170716 TCAAGAAAAT
170726 TTCTATTTTATTACATCAAATAAAC
1 TTCTATTTTATTACATCAAATAAAC
170751 TTCTATTTTATTACATCAAATAA
1 TTCTATTTTATTACATCAAATAA
170774 TATCAAAATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.40, C:0.15, G:0.00, T:0.46
Consensus pattern (25 bp):
TTCTATTTTATTACATCAAATAAAC
Found at i:170805 original size:45 final size:45
Alignment explanation
Indices: 170741--170828 Score: 140
Period size: 45 Copynumber: 2.0 Consensus size: 45
170731 TTTTATTACA
* *
170741 TCAAATAAACTTCTATTTTATTACATCAAATAATATCAAAATAAC
1 TCAAAAAAACTTCTATTTTATTACATAAAATAATATCAAAATAAC
* *
170786 TCAAAAAAATTTCTATTTTATTATATAAAATAATATCAAAATA
1 TCAAAAAAACTTCTATTTTATTACATAAAATAATATCAAAATA
170829 TTCAAAATAT
Statistics
Matches: 39, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 39 1.00
ACGTcount: A:0.51, C:0.11, G:0.00, T:0.38
Consensus pattern (45 bp):
TCAAAAAAACTTCTATTTTATTACATAAAATAATATCAAAATAAC
Found at i:171258 original size:18 final size:18
Alignment explanation
Indices: 171235--171273 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
171225 ACTGGGAAAG
*
171235 GGATACATATAAGGGTTA
1 GGATACATATAAGGGCTA
171253 GGATACATATAAGGGCTA
1 GGATACATATAAGGGCTA
171271 GGA
1 GGA
171274 AACGCACCTG
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.38, C:0.08, G:0.31, T:0.23
Consensus pattern (18 bp):
GGATACATATAAGGGCTA
Found at i:172121 original size:20 final size:20
Alignment explanation
Indices: 172084--172121 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
172074 TTTATTTTTA
*
172084 AAAATCTACATAATAATTGT
1 AAAATCTACATAAAAATTGT
172104 AAAATCTA-ATATAAAATT
1 AAAATCTACATA-AAAATT
172122 TACCTCGTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 2
0.84 0.05 0.11
Matches are distributed among these distances:
19 3 0.19
20 13 0.81
ACGTcount: A:0.55, C:0.08, G:0.03, T:0.34
Consensus pattern (20 bp):
AAAATCTACATAAAAATTGT
Found at i:172821 original size:11 final size:11
Alignment explanation
Indices: 172801--172838 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
172791 TTACGGTTTA
*
172801 AAAAAAATTTT
1 AAAAATATTTT
172812 AAAAATATTTT
1 AAAAATATTTT
172823 AAAAAT-TATTT
1 AAAAATAT-TTT
172834 AAAAA
1 AAAAA
172839 AAAGGAGTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
10 1 0.04
11 24 0.96
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:176007 original size:18 final size:19
Alignment explanation
Indices: 175984--176021 Score: 69
Period size: 18 Copynumber: 2.1 Consensus size: 19
175974 TTAAAAAAGT
175984 ATTTTAAAAA-TATTTTAA
1 ATTTTAAAAAGTATTTTAA
176002 ATTTTAAAAAGTATTTTAA
1 ATTTTAAAAAGTATTTTAA
176021 A
1 A
176022 AAAAGTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 10 0.53
19 9 0.47
ACGTcount: A:0.50, C:0.00, G:0.03, T:0.47
Consensus pattern (19 bp):
ATTTTAAAAAGTATTTTAA
Found at i:176037 original size:11 final size:11
Alignment explanation
Indices: 176023--176047 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
176013 TATTTTAAAA
176023 AAAGTATTTTT
1 AAAGTATTTTT
176034 AAAGTATTTTT
1 AAAGTATTTTT
176045 AAA
1 AAA
176048 TTAAAAAAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.44, C:0.00, G:0.08, T:0.48
Consensus pattern (11 bp):
AAAGTATTTTT
Found at i:176644 original size:23 final size:20
Alignment explanation
Indices: 176612--176659 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 20
176602 TCACAATGCT
176612 ATTTTTGTTTATAAGATTGACA
1 ATTTTTGTTTA-AA-ATTGACA
*
176634 ATTTTATGTTTAAATTTGACA
1 ATTTT-TGTTTAAAATTGACA
176655 ATTTT
1 ATTTT
176660 GTATTCTCAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
21 11 0.46
22 7 0.29
23 6 0.25
ACGTcount: A:0.31, C:0.04, G:0.10, T:0.54
Consensus pattern (20 bp):
ATTTTTGTTTAAAATTGACA
Found at i:178019 original size:4 final size:4
Alignment explanation
Indices: 178010--178034 Score: 50
Period size: 4 Copynumber: 6.2 Consensus size: 4
178000 ATAATAAAAA
178010 TATT TATT TATT TATT TATT TATT T
1 TATT TATT TATT TATT TATT TATT T
178035 TTAATCTTAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 21 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TATT
Found at i:184293 original size:17 final size:18
Alignment explanation
Indices: 184260--184303 Score: 56
Period size: 17 Copynumber: 2.5 Consensus size: 18
184250 AATATTACTG
184260 TATTATTATCAGTTTAT-
1 TATTATTATCAGTTTATA
184277 TATTATTATCA-TATTATA
1 TATTATTATCAGT-TTATA
*
184295 TAGTATTAT
1 TATTATTAT
184304 TATGTTTATT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
16 1 0.04
17 15 0.62
18 8 0.33
ACGTcount: A:0.34, C:0.05, G:0.05, T:0.57
Consensus pattern (18 bp):
TATTATTATCAGTTTATA
Found at i:186647 original size:25 final size:25
Alignment explanation
Indices: 186618--186666 Score: 98
Period size: 25 Copynumber: 2.0 Consensus size: 25
186608 TAATAATAAA
186618 AATAATATTAATTAAATTTTAACTT
1 AATAATATTAATTAAATTTTAACTT
186643 AATAATATTAATTAAATTTTAACT
1 AATAATATTAATTAAATTTTAACT
186667 CAATTAGTAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.49, C:0.04, G:0.00, T:0.47
Consensus pattern (25 bp):
AATAATATTAATTAAATTTTAACTT
Found at i:189574 original size:9 final size:9
Alignment explanation
Indices: 189557--189593 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
189547 TGAGTTTTCG
189557 AATTCGAAT
1 AATTCGAAT
*
189566 AACTCGAAT
1 AATTCGAAT
189575 AATTCGAAT
1 AATTCGAAT
189584 AATTCGAAT
1 AATTCGAAT
189593 A
1 A
189594 TCAAACTATA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.46, C:0.14, G:0.11, T:0.30
Consensus pattern (9 bp):
AATTCGAAT
Found at i:190474 original size:5 final size:5
Alignment explanation
Indices: 190464--190494 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
190454 CTCGAAAATT
*
190464 TTCGA TTCGA TTCGA TTCTA TTCGA TTCGA T
1 TTCGA TTCGA TTCGA TTCGA TTCGA TTCGA T
190495 CGAATGCTCA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.19, C:0.19, G:0.16, T:0.45
Consensus pattern (5 bp):
TTCGA
Found at i:190726 original size:17 final size:16
Alignment explanation
Indices: 190693--190732 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 16
190683 ATTCGCATTC
*
190693 GTATATATTTAAATAT
1 GTATATATGTAAATAT
190709 GTATATATGTACAATAT
1 GTATATATGTA-AATAT
190726 GTATATA
1 GTATATA
190733 AAATAATAGA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
16 10 0.45
17 12 0.55
ACGTcount: A:0.42, C:0.03, G:0.10, T:0.45
Consensus pattern (16 bp):
GTATATATGTAAATAT
Found at i:191025 original size:6 final size:6
Alignment explanation
Indices: 191016--191047 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
191006 GAAATATGCG
191016 TATGTA TATGTA TATGTA TATGTA TATGTA TA
1 TATGTA TATGTA TATGTA TATGTA TATGTA TA
191048 GTAAATACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (6 bp):
TATGTA
Found at i:191097 original size:17 final size:17
Alignment explanation
Indices: 191075--191112 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
191065 AATGATAGCA
191075 AATAAT-GTAATAATAAT
1 AATAATGGT-ATAATAAT
*
191092 AATAATGGTATAATGAT
1 AATAATGGTATAATAAT
191109 AATA
1 AATA
191113 TCATAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
17 17 0.89
18 2 0.11
ACGTcount: A:0.55, C:0.00, G:0.11, T:0.34
Consensus pattern (17 bp):
AATAATGGTATAATAAT
Found at i:192983 original size:21 final size:20
Alignment explanation
Indices: 192950--192988 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
192940 CAAAACAACG
192950 TAGTTTTTCCTTTTAACTTAA
1 TAGTTTTTCC-TTTAACTTAA
192971 TAGTTTTGT-CTTTAACTT
1 TAGTTTT-TCCTTTAACTT
192989 TAGAAAAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
20 8 0.47
21 8 0.47
22 1 0.06
ACGTcount: A:0.21, C:0.13, G:0.08, T:0.59
Consensus pattern (20 bp):
TAGTTTTTCCTTTAACTTAA
Found at i:198458 original size:16 final size:15
Alignment explanation
Indices: 198430--198462 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 15
198420 TGCATATATG
198430 TAAATAAATAAATAA
1 TAAATAAATAAATAA
198445 TAAATAAGATAAATAA
1 TAAATAA-ATAAATAA
198461 TA
1 TA
198463 GTGTAAGTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 7 0.41
16 10 0.59
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (15 bp):
TAAATAAATAAATAA
Found at i:201659 original size:13 final size:13
Alignment explanation
Indices: 201641--201686 Score: 56
Period size: 13 Copynumber: 3.5 Consensus size: 13
201631 CTTTTTGTTG
201641 TTCTTTATGGTTC
1 TTCTTTATGGTTC
* * *
201654 TTCTTTTTTTGTTG
1 TTC-TTTATGGTTC
201668 TTCTTTATGGTTC
1 TTCTTTATGGTTC
201681 TTCTTT
1 TTCTTT
201687 TGGCATAAAA
Statistics
Matches: 26, Mismatches: 6, Indels: 2
0.76 0.18 0.06
Matches are distributed among these distances:
13 16 0.62
14 10 0.38
ACGTcount: A:0.04, C:0.13, G:0.13, T:0.70
Consensus pattern (13 bp):
TTCTTTATGGTTC
Found at i:201669 original size:27 final size:27
Alignment explanation
Indices: 201632--201687 Score: 112
Period size: 27 Copynumber: 2.1 Consensus size: 27
201622 GTGTGCGCTC
201632 TTTTTGTTGTTCTTTATGGTTCTTCTT
1 TTTTTGTTGTTCTTTATGGTTCTTCTT
201659 TTTTTGTTGTTCTTTATGGTTCTTCTT
1 TTTTTGTTGTTCTTTATGGTTCTTCTT
201686 TT
1 TT
201688 GGCATAAAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 29 1.00
ACGTcount: A:0.04, C:0.11, G:0.14, T:0.71
Consensus pattern (27 bp):
TTTTTGTTGTTCTTTATGGTTCTTCTT
Found at i:208961 original size:20 final size:19
Alignment explanation
Indices: 208912--208962 Score: 61
Period size: 20 Copynumber: 2.7 Consensus size: 19
208902 TTCATGTATA
*
208912 TTTTAAGTT-TTTTTAAAT
1 TTTTAAATTATTTTTAAAT
208930 TTTTATAA-TATTTTTATAAT
1 TTTTA-AATTATTTTTA-AAT
208950 TTTTAAATTATTT
1 TTTTAAATTATTT
208963 GTAGATATGA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 6 0.21
19 9 0.32
20 13 0.46
ACGTcount: A:0.31, C:0.00, G:0.02, T:0.67
Consensus pattern (19 bp):
TTTTAAATTATTTTTAAAT
Found at i:209754 original size:17 final size:18
Alignment explanation
Indices: 209699--209758 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
209689 TAGACTTCCT
*
209699 AAAAACAAAATAATTAATTA
1 AAAAATAAAAT-A-TAATTA
* *
209719 TAAAATAAATTATAATTA
1 AAAAATAAAATATAATTA
*
209737 AAAAATAAAATAT-TTTA
1 AAAAATAAAATATAATTA
209754 AAAAA
1 AAAAA
209759 AAACCTTTTT
Statistics
Matches: 34, Mismatches: 6, Indels: 3
0.79 0.14 0.07
Matches are distributed among these distances:
17 8 0.24
18 17 0.50
19 1 0.03
20 8 0.24
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (18 bp):
AAAAATAAAATATAATTA
Found at i:213180 original size:18 final size:18
Alignment explanation
Indices: 213154--213191 Score: 51
Period size: 18 Copynumber: 2.1 Consensus size: 18
213144 GTTTTAAATC
*
213154 ATATGTTTT-ATTATTTAT
1 ATATATTTTGATT-TTTAT
213172 ATATATTTTGATTTTTAT
1 ATATATTTTGATTTTTAT
213190 AT
1 AT
213192 GAACTTGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
18 15 0.83
19 3 0.17
ACGTcount: A:0.29, C:0.00, G:0.05, T:0.66
Consensus pattern (18 bp):
ATATATTTTGATTTTTAT
Found at i:214051 original size:31 final size:29
Alignment explanation
Indices: 213982--214055 Score: 94
Period size: 29 Copynumber: 2.5 Consensus size: 29
213972 ACAACGTGAT
**
213982 AACATAAGTGACTAAAACGTAACATTTCA
1 AACATAAGTGACTAAAACGTAACATGCCA
*
214011 AACATAAGTGACTAAAACGTAATATGAGCCA
1 AACATAAGTGACTAAAACGTAACAT--GCCA
*
214042 AACAAAAGTGACTA
1 AACATAAGTGACTA
214056 TTTTAGTAGT
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
29 24 0.62
31 15 0.38
ACGTcount: A:0.50, C:0.16, G:0.14, T:0.20
Consensus pattern (29 bp):
AACATAAGTGACTAAAACGTAACATGCCA
Found at i:225149 original size:86 final size:87
Alignment explanation
Indices: 225046--225220 Score: 343
Period size: 86 Copynumber: 2.0 Consensus size: 87
225036 TGCAATATAT
225046 AAACATAAAATGATGCTAAATCAATAATTGTGTTAATAATTTGTGAGAATTGTATCAAATCAAAT
1 AAACATAAAATGATGCTAAATCAATAATTGTGTTAATAATTTGTGAGAATTGTATCAAATCAAAT
225111 TTTCATGTATAAAATTGCACAA
66 TTTCATGTATAAAATTGCACAA
225133 AAACATAAAAT-ATGCTAAATCAATAATTGTGTTAATAATTTGTGAGAATTGTATCAAATCAAAT
1 AAACATAAAATGATGCTAAATCAATAATTGTGTTAATAATTTGTGAGAATTGTATCAAATCAAAT
225197 TTTCATGTATAAAATTGCACAA
66 TTTCATGTATAAAATTGCACAA
225219 AA
1 AA
225221 TCAAAGTCTA
Statistics
Matches: 88, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
86 77 0.88
87 11 0.12
ACGTcount: A:0.46, C:0.09, G:0.11, T:0.34
Consensus pattern (87 bp):
AAACATAAAATGATGCTAAATCAATAATTGTGTTAATAATTTGTGAGAATTGTATCAAATCAAAT
TTTCATGTATAAAATTGCACAA
Found at i:225265 original size:31 final size:29
Alignment explanation
Indices: 225198--225268 Score: 90
Period size: 29 Copynumber: 2.4 Consensus size: 29
225188 AAATCAAATT
*
225198 TTCATGTATAAAATTGCACAAAATCAAAG
1 TTCATGTATAAAATTGCACAAAACCAAAG
*
225227 -TCTATGTATAAAATTGCACATTAGACCAAAG
1 TTC-ATGTATAAAATTGCACA--AAACCAAAG
225258 TTCATGTATAA
1 TTCATGTATAA
225269 TTTTGAGATT
Statistics
Matches: 36, Mismatches: 2, Indels: 6
0.82 0.05 0.14
Matches are distributed among these distances:
28 2 0.06
29 17 0.47
31 15 0.42
32 2 0.06
ACGTcount: A:0.44, C:0.14, G:0.11, T:0.31
Consensus pattern (29 bp):
TTCATGTATAAAATTGCACAAAACCAAAG
Found at i:225824 original size:22 final size:22
Alignment explanation
Indices: 225793--225834 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
225783 CCTTTTTTAC
*
225793 TTTGTTATATATAG-ATTATTA
1 TTTGTTATATAGAGTATTATTA
225814 TTTGTTTATATAGAGTATTAT
1 TTTG-TTATATAGAGTATTAT
225835 GACCAATTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 9 0.50
23 5 0.28
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.57
Consensus pattern (22 bp):
TTTGTTATATAGAGTATTATTA
Found at i:225825 original size:20 final size:21
Alignment explanation
Indices: 225793--225834 Score: 68
Period size: 20 Copynumber: 2.0 Consensus size: 21
225783 CCTTTTTTAC
*
225793 TTTGTTATATATAGATTATTA
1 TTTGTTATATATAGAGTATTA
225814 TTTGTT-TATATAGAGTATTA
1 TTTGTTATATATAGAGTATTA
225834 T
1 T
225835 GACCAATTGA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
20 14 0.70
21 6 0.30
ACGTcount: A:0.31, C:0.00, G:0.12, T:0.57
Consensus pattern (21 bp):
TTTGTTATATATAGAGTATTA
Found at i:226061 original size:29 final size:29
Alignment explanation
Indices: 226006--226061 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 29
225996 CTCTGACCTG
* *
226006 TAAAACGCATCTAGGTCAGCGCGTTTTGT
1 TAAAACGCATCTAAGTCAGCACGTTTTGT
* * *
226035 TAAAGCGCTTCTAAGTCAGCACTTTTT
1 TAAAACGCATCTAAGTCAGCACGTTTT
226062 TGCCCGTGTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
29 22 1.00
ACGTcount: A:0.25, C:0.21, G:0.20, T:0.34
Consensus pattern (29 bp):
TAAAACGCATCTAAGTCAGCACGTTTTGT
Found at i:228401 original size:23 final size:20
Alignment explanation
Indices: 228355--228394 Score: 53
Period size: 20 Copynumber: 1.9 Consensus size: 20
228345 AAAAACTTTA
* *
228355 TTTTAATATTATTTATACAT
1 TTTTAATATTATTCATAAAT
228375 TTTTAATATTATTACATAAA
1 TTTTAATATTATT-CATAAA
228395 CTGTTTTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.40, C:0.05, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTAATATTATTCATAAAT
Found at i:231191 original size:26 final size:26
Alignment explanation
Indices: 231155--231218 Score: 69
Period size: 28 Copynumber: 2.4 Consensus size: 26
231145 AAAATAAAGT
*
231155 AAGAAACAAAAGAGAATAG-AAA-ATAA
1 AAGAAA-AAAAAAGAA-AGTAAATATAA
231181 AAGAAAAAAAAAGAAAGTTAAAATATAA
1 AAGAAAAAAAAAGAAAG-T-AAATATAA
231209 AAGAAAAAAA
1 AAGAAAAAAA
231219 TACTCAAAAC
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
24 2 0.06
25 8 0.24
26 6 0.18
27 3 0.09
28 14 0.42
ACGTcount: A:0.77, C:0.02, G:0.12, T:0.09
Consensus pattern (26 bp):
AAGAAAAAAAAAGAAAGTAAATATAA
Found at i:237682 original size:27 final size:27
Alignment explanation
Indices: 237652--237705 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
237642 AAGATTCCAG
237652 AAATCATCAAAACTTATATAAGGCTTT
1 AAATCATCAAAACTTATATAAGGCTTT
* *
237679 AAATCATCAAAGCTTATATCAGGCTTT
1 AAATCATCAAAACTTATATAAGGCTTT
237706 CTGATGGTAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.41, C:0.17, G:0.09, T:0.33
Consensus pattern (27 bp):
AAATCATCAAAACTTATATAAGGCTTT
Found at i:238211 original size:2 final size:2
Alignment explanation
Indices: 238204--238229 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
238194 TTAAATGTAC
238204 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
238230 TAAGTCCGCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:239044 original size:6 final size:6
Alignment explanation
Indices: 239033--239062 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
239023 GTCACATTTT
239033 AAAATA AAAATA AAAATA AAAATA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA
239063 CAATGGACAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:242958 original size:21 final size:21
Alignment explanation
Indices: 242932--242975 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
242922 ATTATAAGAA
*
242932 AATATTAATTAAAAG-TTAATT
1 AATATTAACT-AAAGCTTAATT
242953 AATATTAACTAAAGCTTAATT
1 AATATTAACTAAAGCTTAATT
242974 AA
1 AA
242976 ACATATATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 4 0.19
21 17 0.81
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.39
Consensus pattern (21 bp):
AATATTAACTAAAGCTTAATT
Found at i:245883 original size:21 final size:21
Alignment explanation
Indices: 245857--245898 Score: 75
Period size: 21 Copynumber: 2.0 Consensus size: 21
245847 AGAGAGGGAC
*
245857 GATAAACCCTAGTTTTTTTAA
1 GATAAACCCTAGTTTGTTTAA
245878 GATAAACCCTAGTTTGTTTAA
1 GATAAACCCTAGTTTGTTTAA
245899 CTAGGGTTGC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.33, C:0.14, G:0.12, T:0.40
Consensus pattern (21 bp):
GATAAACCCTAGTTTGTTTAA
Found at i:247454 original size:169 final size:170
Alignment explanation
Indices: 247151--247479 Score: 464
Period size: 169 Copynumber: 1.9 Consensus size: 170
247141 GTCACATTGT
* * ** *
247151 GACGTTGAGTGTAAATCGTCGCGACGAGATCAGGCCACCATGCCACAATGCGATGTCAAGCATGG
1 GACGTCGAGTGTAAATCATCGCGACGAGATCAGGCCACCATGCCACAACACGATGTCAAGCATAG
* * * * *
247216 GTTGTTTAGATGAGACCTAGTTAGTATGTTGTGTCACGACGAGGAGCCTCATAACTTCGCGACGT
66 GTTGTTGAGATGAGACCTAGTTACTATATTGTGTCACGACAAGGACCCTCATAACTTCGCGACGT
*
247281 CAACCTAAAATTTTGTAAACATTACAGTTTGTCATATCGC
131 CAACCTAAAATTTTATAAACATTACAGTTTGTCATATCGC
* * * *
247321 GACGTCGA-TGTAGATCATCGCGACGAGATCAGGCCACTATGCCACGACACTATGTCAAGCATAG
1 GACGTCGAGTGTAAATCATCGCGACGAGATCAGGCCACCATGCCACAACACGATGTCAAGCATAG
* *
247385 GTTGTTGAGATGAGACCTAGTTACTATATTGTGTCGCGACAAGGAACCCT-ATAACTTCGCGATG
66 GTTGTTGAGATGAGACCTAGTTACTATATTGTGTCACGACAAGG-ACCCTCATAACTTCGCGACG
* *
247449 TCAACCTAGAATTTTATAAACATTACGGTTT
130 TCAACCTAAAATTTTATAAACATTACAGTTT
247480 AGTCCTAATT
Statistics
Matches: 139, Mismatches: 19, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
169 128 0.92
170 11 0.08
ACGTcount: A:0.29, C:0.21, G:0.23, T:0.27
Consensus pattern (170 bp):
GACGTCGAGTGTAAATCATCGCGACGAGATCAGGCCACCATGCCACAACACGATGTCAAGCATAG
GTTGTTGAGATGAGACCTAGTTACTATATTGTGTCACGACAAGGACCCTCATAACTTCGCGACGT
CAACCTAAAATTTTATAAACATTACAGTTTGTCATATCGC
Found at i:248379 original size:53 final size:53
Alignment explanation
Indices: 248321--248425 Score: 176
Period size: 53 Copynumber: 2.0 Consensus size: 53
248311 GGATGATTAA
248321 TTATGTAAATTAGTGAAGTTGATGCTCCTAATGC-TTTAAATTCATGTTTCTAG
1 TTATGTAAATTAGTGAAGTTGATGCTCCTAAT-CTTTTAAATTCATGTTTCTAG
* *
248374 TTATGTAAATTAGTGAATTTTATGCTCCTAATCTTTTAAATTCATGTTTCTA
1 TTATGTAAATTAGTGAAGTTGATGCTCCTAATCTTTTAAATTCATGTTTCTA
248426 TACTTAGGAG
Statistics
Matches: 49, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
52 1 0.02
53 48 0.98
ACGTcount: A:0.29, C:0.11, G:0.13, T:0.47
Consensus pattern (53 bp):
TTATGTAAATTAGTGAAGTTGATGCTCCTAATCTTTTAAATTCATGTTTCTAG
Found at i:253287 original size:22 final size:22
Alignment explanation
Indices: 253261--253312 Score: 104
Period size: 22 Copynumber: 2.4 Consensus size: 22
253251 CGTCCCTTCT
253261 CCTCTCCCCTTTCCTTATCTCC
1 CCTCTCCCCTTTCCTTATCTCC
253283 CCTCTCCCCTTTCCTTATCTCC
1 CCTCTCCCCTTTCCTTATCTCC
253305 CCTCTCCC
1 CCTCTCCC
253313 TTCGCTTTCT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.04, C:0.58, G:0.00, T:0.38
Consensus pattern (22 bp):
CCTCTCCCCTTTCCTTATCTCC
Found at i:253567 original size:26 final size:25
Alignment explanation
Indices: 253536--253659 Score: 85
Period size: 26 Copynumber: 4.7 Consensus size: 25
253526 GTTTTACTAA
253536 TTTTATTTATTTCTTTAATTATTCT
1 TTTTATTTATTTCTTTAATTATTCT
* *
253561 TGTTTATTTAGTTTCTTTATTTCTATCT
1 T-TTTATTTA-TTTCTTTAATTAT-TCT
* *
253589 TATTA-TTATTAT-TATTAGTT-TTACT
1 TTTTATTTATT-TCT-TTAATTATT-CT
253614 AATTTTATTTAATTTCTTT-ATTATTCT
1 --TTTTATTT-ATTTCTTTAATTATTCT
253641 TGTTTATTTAGTTTCTTTA
1 T-TTTATTTA-TTTCTTTA
253660 CTGTTGATTT
Statistics
Matches: 78, Mismatches: 6, Indels: 28
0.70 0.05 0.25
Matches are distributed among these distances:
24 1 0.01
25 9 0.12
26 31 0.40
27 22 0.28
28 11 0.14
29 4 0.05
ACGTcount: A:0.21, C:0.07, G:0.04, T:0.68
Consensus pattern (25 bp):
TTTTATTTATTTCTTTAATTATTCT
Found at i:253597 original size:40 final size:39
Alignment explanation
Indices: 253537--253659 Score: 101
Period size: 39 Copynumber: 3.1 Consensus size: 39
253527 TTTTACTAAT
*
253537 TTTATTT-ATTTCTTTAATTATTCTTGTTTATTTAGTTTC
1 TTTATTTAATTTCATT-ATTATTCTTGTTTATTTAGTTTC
* * * * *
253576 TTTATTTCTATCTT-ATTATTATTATT-ATTAGTTTTACTAAT-
1 TTTATTT-AAT-TTCATTATTATTCTTGTTTA--TTTAGT-TTC
*
253617 TTTATTTAATTTCTTTATTATTCTTGTTTATTTAGTTTC
1 TTTATTTAATTTCATTATTATTCTTGTTTATTTAGTTTC
253656 TTTA
1 TTTA
253660 CTGTTGATTT
Statistics
Matches: 64, Mismatches: 11, Indels: 18
0.69 0.12 0.19
Matches are distributed among these distances:
38 1 0.02
39 21 0.33
40 20 0.31
41 19 0.30
42 3 0.05
ACGTcount: A:0.21, C:0.07, G:0.04, T:0.67
Consensus pattern (39 bp):
TTTATTTAATTTCATTATTATTCTTGTTTATTTAGTTTC
Found at i:253610 original size:80 final size:81
Alignment explanation
Indices: 253491--253659 Score: 315
Period size: 80 Copynumber: 2.1 Consensus size: 81
253481 ATTATTGTTA
253491 TTTCTTTATTTCTATCTTTATTATTATTATTATTAGTTTTACTAATTTTATTT-ATTTCTTTAAT
1 TTTCTTTATTTCTATCTTTATTATTATTATTATTAGTTTTACTAATTTTATTTAATTTCTTT-AT
253555 TATTCTTGTTTATTTAG
65 TATTCTTGTTTATTTAG
253572 TTTCTTTATTTCTATC-TTATTATTATTATTATTAGTTTTACTAATTTTATTTAATTTCTTTATT
1 TTTCTTTATTTCTATCTTTATTATTATTATTATTAGTTTTACTAATTTTATTTAATTTCTTTATT
253636 ATTCTTGTTTATTTAG
66 ATTCTTGTTTATTTAG
253652 TTTCTTTA
1 TTTCTTTA
253660 CTGTTGATTT
Statistics
Matches: 87, Mismatches: 0, Indels: 3
0.97 0.00 0.03
Matches are distributed among these distances:
80 63 0.72
81 24 0.28
ACGTcount: A:0.22, C:0.08, G:0.04, T:0.67
Consensus pattern (81 bp):
TTTCTTTATTTCTATCTTTATTATTATTATTATTAGTTTTACTAATTTTATTTAATTTCTTTATT
ATTCTTGTTTATTTAG
Found at i:259580 original size:40 final size:41
Alignment explanation
Indices: 259474--259580 Score: 128
Period size: 41 Copynumber: 2.6 Consensus size: 41
259464 AATCAGTAGT
* *
259474 GGCGTTTATGAGAAAAACGCTGCAAAAGGTCAAGCATTAAC
1 GGCGTCTATGAGAAAAACGCCGCAAAAGGTCAAGCATTAAC
* * * *
259515 GGTGTTTATGAGAAAAACACCGCAAAAGGTCAAGCATTAGC
1 GGCGTCTATGAGAAAAACGCCGCAAAAGGTCAAGCATTAAC
*
259556 GGCG-CTA-GAAGAAAAATGCCGCAAA
1 GGCGTCTATG-AGAAAAACGCCGCAAA
259581 GTATAATTTT
Statistics
Matches: 57, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
39 1 0.02
40 16 0.28
41 40 0.70
ACGTcount: A:0.40, C:0.18, G:0.25, T:0.17
Consensus pattern (41 bp):
GGCGTCTATGAGAAAAACGCCGCAAAAGGTCAAGCATTAAC
Found at i:260020 original size:22 final size:21
Alignment explanation
Indices: 259992--260040 Score: 61
Period size: 17 Copynumber: 2.5 Consensus size: 21
259982 CATCTATTGT
259992 TCGGATTTAATTTTGGCATGCA
1 TCGGATTTAATTTT-GCATGCA
260014 TCGGA--T--TTTTGCATGCA
1 TCGGATTTAATTTTGCATGCA
260031 TCGGATTTAA
1 TCGGATTTAA
260041 CTTGTAAAAG
Statistics
Matches: 23, Mismatches: 0, Indels: 9
0.72 0.00 0.28
Matches are distributed among these distances:
17 12 0.52
18 4 0.17
19 1 0.04
20 1 0.04
22 5 0.22
ACGTcount: A:0.22, C:0.14, G:0.22, T:0.41
Consensus pattern (21 bp):
TCGGATTTAATTTTGCATGCA
Found at i:260027 original size:17 final size:17
Alignment explanation
Indices: 260001--260038 Score: 67
Period size: 17 Copynumber: 2.2 Consensus size: 17
259991 TTCGGATTTA
260001 ATTTTGGCATGCATCGG
1 ATTTTGGCATGCATCGG
*
260018 ATTTTTGCATGCATCGG
1 ATTTTGGCATGCATCGG
260035 ATTT
1 ATTT
260039 AACTTGTAAA
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 20 1.00
ACGTcount: A:0.18, C:0.16, G:0.24, T:0.42
Consensus pattern (17 bp):
ATTTTGGCATGCATCGG
Found at i:272461 original size:18 final size:20
Alignment explanation
Indices: 272433--272469 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
272423 TGCTTCAAAT
272433 ATTTATCAGAA-GTTTCAGG
1 ATTTATCAGAAGGTTTCAGG
272452 ATTT-TCAGAAGGTTTCAG
1 ATTTATCAGAAGGTTTCAG
272470 TCTTAAACTA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 6 0.35
19 11 0.65
ACGTcount: A:0.30, C:0.11, G:0.22, T:0.38
Consensus pattern (20 bp):
ATTTATCAGAAGGTTTCAGG
Found at i:274482 original size:15 final size:16
Alignment explanation
Indices: 274462--274497 Score: 56
Period size: 15 Copynumber: 2.2 Consensus size: 16
274452 CTTTTTTGGG
274462 AAAAAAATTAA-AATT
1 AAAAAAATTAATAATT
274477 AAAAAAATTAATTAATT
1 AAAAAAATTAA-TAATT
274494 AAAA
1 AAAA
274498 TAAAAAAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 11 0.58
17 8 0.42
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (16 bp):
AAAAAAATTAATAATT
Found at i:277881 original size:17 final size:18
Alignment explanation
Indices: 277850--277887 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 18
277840 TTAATATACT
277850 ATTTAAAAATATATTTAC
1 ATTTAAAAATATATTTAC
* *
277868 ATTTAATAAT-TATTTTC
1 ATTTAAAAATATATTTAC
277885 ATT
1 ATT
277888 AAATTTAAGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
17 9 0.50
18 9 0.50
ACGTcount: A:0.42, C:0.05, G:0.00, T:0.53
Consensus pattern (18 bp):
ATTTAAAAATATATTTAC
Found at i:279404 original size:22 final size:21
Alignment explanation
Indices: 279371--279412 Score: 50
Period size: 21 Copynumber: 2.0 Consensus size: 21
279361 ATTTATATAA
*
279371 TCCTTATGTGATATGTTTTTTC
1 TCCTTATGTGAT-TGATTTTTC
279393 TCCTT-TGTTGATTGATTTTT
1 TCCTTATG-TGATTGATTTTT
279413 GGTAAAATTA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
21 9 0.50
22 9 0.50
ACGTcount: A:0.12, C:0.12, G:0.14, T:0.62
Consensus pattern (21 bp):
TCCTTATGTGATTGATTTTTC
Found at i:279561 original size:22 final size:24
Alignment explanation
Indices: 279509--279562 Score: 60
Period size: 22 Copynumber: 2.3 Consensus size: 24
279499 ATTTGGACGA
279509 TTAAATTATTGTTATTAAATATGCT
1 TTAAATTATTGTTATT-AATATGCT
*
279534 TGAAATTATTG-TATT-ATAT-CTT
1 TTAAATTATTGTTATTAATATGC-T
279556 TTAAATT
1 TTAAATT
279563 GAATTTATAA
Statistics
Matches: 26, Mismatches: 2, Indels: 5
0.79 0.06 0.15
Matches are distributed among these distances:
21 1 0.04
22 11 0.42
24 4 0.15
25 10 0.38
ACGTcount: A:0.35, C:0.04, G:0.07, T:0.54
Consensus pattern (24 bp):
TTAAATTATTGTTATTAATATGCT
Found at i:283427 original size:201 final size:202
Alignment explanation
Indices: 283068--283462 Score: 666
Period size: 201 Copynumber: 2.0 Consensus size: 202
283058 AAATTCAACC
*
283068 ATATCATTATCATTTACCTAATCAAAATTTGATATAATTCAAATTCTTAAAACATTTCCAAACCT
1 ATATCAATATCATTTACCTAATCAAAATTTGATATAATTCAAATTCTTAAAACATTTCCAAACCT
* * *
283133 ATAAGATTATATATCATAAATCAAGTATGTATCCAAACATTTATTTGTACACATTTATTTCATTT
66 ATAAGATTATATATCATAAATCAAGCATATATCCAAACATTTACTTGTACACATTTATTTCATTT
* *
283198 CAATTTATTAACTATACTACATATTATAATATAGGTAATCTACCTTGTTTGGACAACTCTTATAT
131 CAATTTACTAACTATACTACATATTATAATATAGATAATCTACCTTGTTTGGACAACTCTTATAT
283263 ACAACAA
196 ACAACAA
283270 ATATCAATATCATTTACCTAATCAAAATTTGATATAATTCAAATTCTTAAAACATTTCCAAACCT
1 ATATCAATATCATTTACCTAATCAAAATTTGATATAATTCAAATTCTTAAAACATTTCCAAACCT
** * *
283335 ATATTATT-TATATCATAATTCAAGCATATATCCAAACATTTACTTGTACGCATTTATTTCATTT
66 ATAAGATTATATATCATAAATCAAGCATATATCCAAACATTTACTTGTACACATTTATTTCATTT
* * *
283399 CATTTTACTAACTATACTACATATTATAATTTAGATAATCTACCTTGTTTGGACAGCTCTTATA
131 CAATTTACTAACTATACTACATATTATAATATAGATAATCTACCTTGTTTGGACAACTCTTATA
283463 CATTAATTTG
Statistics
Matches: 180, Mismatches: 13, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
201 110 0.61
202 70 0.39
ACGTcount: A:0.38, C:0.16, G:0.05, T:0.41
Consensus pattern (202 bp):
ATATCAATATCATTTACCTAATCAAAATTTGATATAATTCAAATTCTTAAAACATTTCCAAACCT
ATAAGATTATATATCATAAATCAAGCATATATCCAAACATTTACTTGTACACATTTATTTCATTT
CAATTTACTAACTATACTACATATTATAATATAGATAATCTACCTTGTTTGGACAACTCTTATAT
ACAACAA
Found at i:283583 original size:70 final size:70
Alignment explanation
Indices: 283485--283765 Score: 327
Period size: 70 Copynumber: 4.0 Consensus size: 70
283475 TAGCAATTAT
* * * *
283485 ATACCAAATTAAACAGCA-TTTATACACCAAAATTTGGACAGCT-TATATACAACAAATGGGCAG
1 ATACCAAATTTAACAGCACTTT-TACACCAAAATTT-AACAGCTATATATACAACAAATAGGCAA
283548 CATATAC
64 CATATAC
* * *
283555 ATACCAAATTTAATAGCACTTTTACACCAAAATTTAACAGC-ATATATACAGCAAATAGACAACA
1 ATACCAAATTTAACAGCACTTTTACACCAAAATTTAACAGCTATATATACAACAAATAGGCAACA
*
283619 TATAT
66 TATAC
* *
283624 ATACCAAATTTAACAGCAC-TTTACACCAAAATTTAACAGCATAGATATACAACAATTAGGCAAC
1 ATACCAAATTTAACAGCACTTTTACACCAAAATTTAACAGC-TATATATACAACAAATAGGCAAC
283688 ATATAC
65 ATATAC
* * * * * * * * *
283694 ATACCAAATTGAGCAGTATTTTTACACCAAGATTGAACAGTATATATATATAACAAATGGGCAAC
1 ATACCAAATTTAACAGCACTTTTACACCAAAATTTAACAG-CTATATATACAACAAATAGGCAAC
283759 ATATAC
65 ATATAC
283765 A
1 A
283766 CAATACATCA
Statistics
Matches: 180, Mismatches: 25, Indels: 11
0.83 0.12 0.05
Matches are distributed among these distances:
68 21 0.12
69 45 0.25
70 67 0.37
71 47 0.26
ACGTcount: A:0.46, C:0.19, G:0.09, T:0.26
Consensus pattern (70 bp):
ATACCAAATTTAACAGCACTTTTACACCAAAATTTAACAGCTATATATACAACAAATAGGCAACA
TATAC
Found at i:283631 original size:139 final size:139
Alignment explanation
Indices: 283482--283741 Score: 353
Period size: 139 Copynumber: 1.9 Consensus size: 139
283472 GAATAGCAAT
* * * *
283482 TATATACCAAATTAAACAGCATTTATACACCAAAATTTGGACAGC-T-TATATACAACAAATGGG
1 TATATACCAAATTAAACAGCACTT-TACACCAAAATTT-AACAGCATAGATATACAACAAATAGG
* * * *
283545 CAGCATATACATACCAAATTTAATAGCACTTTTACACCAAAATTTAACAGCATATATACAGCAAA
64 CAACATATACATACCAAATTGAACAGCACTTTTACACCAAAATTGAACAGCATATATACAGCAAA
283610 TAGACAACATA
129 TAGACAACATA
* *
283621 TATATACCAAATTTAACAGCACTTTACACCAAAATTTAACAGCATAGATATACAACAATTAGGCA
1 TATATACCAAATTAAACAGCACTTTACACCAAAATTTAACAGCATAGATATACAACAAATAGGCA
* * * * *
283686 ACATATACATACCAAATTGAGCAGTATTTTTACACCAAGATTGAACAGTATATATA
66 ACATATACATACCAAATTGAACAGCACTTTTACACCAAAATTGAACAGCATATATA
283742 TATAACAAAT
Statistics
Matches: 104, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
137 5 0.05
138 14 0.13
139 85 0.82
ACGTcount: A:0.45, C:0.19, G:0.09, T:0.27
Consensus pattern (139 bp):
TATATACCAAATTAAACAGCACTTTACACCAAAATTTAACAGCATAGATATACAACAAATAGGCA
ACATATACATACCAAATTGAACAGCACTTTTACACCAAAATTGAACAGCATATATACAGCAAATA
GACAACATA
Found at i:283912 original size:2 final size:2
Alignment explanation
Indices: 283905--283935 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
283895 CTTAAACATC
283905 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
283936 CCAAATAGAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:284633 original size:41 final size:41
Alignment explanation
Indices: 284588--284701 Score: 140
Period size: 41 Copynumber: 2.8 Consensus size: 41
284578 TTGTATAAAA
* *
284588 CACCGGCATAAAGCCTGCTAGGCACAAAGCCTGATACATTT
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGATACAATT
* * * * *
284629 CACCGGCACAAAGCCTGCTAGACATAAGGTCTGATATAATT
1 CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGATACAATT
*
284670 CACCGGCACT-GAGCCTGCTAGGCATAAAGCCT
1 CACCGGCA-TAAAGCCTGCTAGGCATAAAGCCT
284702 AAACTTAAAA
Statistics
Matches: 60, Mismatches: 12, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
41 60 1.00
ACGTcount: A:0.31, C:0.29, G:0.21, T:0.19
Consensus pattern (41 bp):
CACCGGCATAAAGCCTGCTAGGCATAAAGCCTGATACAATT
Found at i:284839 original size:2 final size:2
Alignment explanation
Indices: 284832--284871 Score: 71
Period size: 2 Copynumber: 20.0 Consensus size: 2
284822 AGCATAACAA
*
284832 AT AT AT AT AT AT AT AT AT AT AT AT AT AA 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
284872 CATAGTTAGT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Done.