Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold209
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: 944012
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 59703 characters in sequence are not A, C, G, or T
File 1 of 4
Found at i:1713 original size:42 final size:42
Alignment explanation
Indices: 1649--1809 Score: 169
Period size: 42 Copynumber: 3.8 Consensus size: 42
1639 GTTTACAACC
* * * *
1649 AAAAACGTCGTTAAAGATCATGTTCTTTAGCGGCGCTTAGAG
1 AAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTAGAG
* * *
1691 AAAAACGCCGCTAAAGAACATGTTTTTTGGCGGCGCTTAGAG
1 AAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTAGAG
* * * * ** *
1733 AAAAACGTCACTGAAGAACATGGTCTTTAGCGGCGTTTTTAT
1 AAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTAGAG
** *
1775 CTAAGCGCCGCTAAAGAACATGGTCTTTAGCGGCG
1 AAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCG
1810 TTTTTTTCTA
Statistics
Matches: 98, Mismatches: 21, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
42 98 1.00
ACGTcount: A:0.30, C:0.19, G:0.25, T:0.26
Consensus pattern (42 bp):
AAAAACGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTAGAG
Found at i:1790 original size:84 final size:84
Alignment explanation
Indices: 1696--1880 Score: 210
Period size: 84 Copynumber: 2.2 Consensus size: 84
1686 TAGAGAAAAA
* * * *
1696 CGCCGCTAAAGAACATGTTTTTTGGCGGCGCTTAGAGAAAAACGTCACTGAAGAACATGGTCTTT
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTAGAGAAAAACGCCACTGAAGAACATGGTCTTT
1761 AGCGGCGTTTTTATC-TAAG
66 AGCGGCGTTTTT-TCATAAG
* ****** * * * *
1780 CGCCGCTAAAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTGAATAACATGTTCTTT
1 CGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTAGAGAAAAACGCCACTGAAGAACATGGTCTTT
*
1845 AGCGGTGTTTTTTCATAAG
66 AGCGGCGTTTTTTCATAAG
1864 CGCCGCTAAAGAACATG
1 CGCCGCTAAAGAACATG
1881 ATCTCTAGTT
Statistics
Matches: 84, Mismatches: 16, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
83 2 0.02
84 82 0.98
ACGTcount: A:0.25, C:0.21, G:0.24, T:0.30
Consensus pattern (84 bp):
CGCCGCTAAAGAACATGGTCTTTAGCGGCGCTTAGAGAAAAACGCCACTGAAGAACATGGTCTTT
AGCGGCGTTTTTTCATAAG
Found at i:1810 original size:42 final size:42
Alignment explanation
Indices: 1746--2026 Score: 244
Period size: 42 Copynumber: 6.6 Consensus size: 42
1736 AACGTCACTG
1746 AAGAACATGGTCTTTAGCGGCGTTTTTATCTAAGCGCCGCTA
1 AAGAACATGGTCTTTAGCGGCGTTTTTATCTAAGCGCCGCTA
* *
1788 AAGAACATGGTCTTTAGCGGCGTTTTTTTCTAAGCGCCGCTG
1 AAGAACATGGTCTTTAGCGGCGTTTTTATCTAAGCGCCGCTA
* * *
1830 AATAACATGTTCTTTAGCGGTGTTTTT-TCATAAGCGCCGCTA
1 AAGAACATGGTCTTTAGCGGCGTTTTTATC-TAAGCGCCGCTA
* * ** *
1872 AAGAACATGATCTCTAGTTGCGTTTTTTAT-TAAGCGTCGCTA
1 AAGAACATGGTCTTTAGCGGCG-TTTTTATCTAAGCGCCGCTA
* * * * * ** *
1914 AAGAGCATGTTCTTTAACAGCGCTTTGTATAAAAACGCCGCTA
1 AAGAACATGGTCTTTAGCGGCG-TTTTTATCTAAGCGCCGCTA
* * ** * * **
1957 GAGATCATAATCTTTAGCGGCGCTTTTTTTAC-AAACATCGCTA
1 AAGAACATGGTCTTTAGCGGCG-TTTTTAT-CTAAGCGCCGCTA
* *
2000 CAGAACATGGTCTTTAGCGGCGCTTTT
1 AAGAACATGGTCTTTAGCGGCGTTTTT
2027 GTACAAAAAC
Statistics
Matches: 194, Mismatches: 40, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
41 2 0.01
42 128 0.66
43 63 0.32
44 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.21, T:0.34
Consensus pattern (42 bp):
AAGAACATGGTCTTTAGCGGCGTTTTTATCTAAGCGCCGCTA
Found at i:2525 original size:115 final size:114
Alignment explanation
Indices: 2313--2870 Score: 445
Period size: 115 Copynumber: 4.9 Consensus size: 114
2303 ATGCATGGTT
* * *
2313 AAGACCAAAAC-TCTGCGTTTTGGTTAAGATATTTTTCGGCGCTTCTCAAAAAGCGCCGCTAATA
1 AAGA-CAAAACGTCTGCGTTTTGGTTAACATATTTTGCGGCGCTTCTCAGAAAGCGCCGCTAATA
* * * * *
2377 CGATGCTTTAGCGGCGATTTCTCGT-GGATGCCACTAATTCCAGTATACATC
65 CTATGCTTTAGCGGCG-TTTCCCATAAG-CGCCACTAATTCCAGTATACATC
* * * *
2428 AAGACTTAAACGT-TGCGTTTTTGTTAATATATTTTGCGGCGCTTCTCAGAAAGCGCCGCAAATA
1 AAGAC-AAAACGTCTGCGTTTTGGTTAACATATTTTGCGGCGCTTCTCAGAAAGCGCCGCTAATA
* * * * * *
2492 ATATGCTTTAGCGGCGTTCCCCCATAAGCGCCACTAAGTCTAATATACCTC
65 CTATGCTTTAGCGGCGTT-TCCCATAAGCGCCACTAATTCCAGTATACATC
* ** ** *
2543 ACGA-AAAAATTCTGCGTTTTGG-TAAGCATATTTTGCGGCGCTT-TTTGCCAAGCGCCGCTAAT
1 AAGACAAAACGTCTGCGTTTTGGTTAA-CATATTTTGCGGCGCTTCTCAG-AAAGCGCCGCTAAT
* *** * ** *
2605 ACTATGATTTAGCGGCGTTTTTTGATATGCGCCACTAATAACTGTATACATC
64 ACTATGCTTTAGCGGCG-TTTCCCATAAGCGCCACTAATTCCAGTATACATC
* * * ** * *
2657 AAGACAAAAACGT-TGCGTTTTGGTTACCAAATGTTGTTGCGCTTCTCTGAAAACGCCGCTAATA
1 AAGAC-AAAACGTCTGCGTTTTGGTTAACATATTTTGCGGCGCTTCTCAGAAAGCGCCGCTAATA
* * * * ** * *
2721 GTATGCCTTAGTGGCGTGTACCC-TTTGCGCCACTAATTCTAGTATACCTC
65 CTATGCTTTAGCGGCGT-TTCCCATAAGCGCCACTAATTCCAGTATACATC
* *
2771 AAGACCAAAC-TCTGCGTTTTGGTTAAGATATTTTGCGGCGCTTTCCTCA-AAA-CGCCGCTAAT
1 AAGACAAAACGTCTGCGTTTTGGTTAACATATTTTGCGGCGC-TT-CTCAGAAAGCGCCGCTAAT
* * * *
2833 ATTATGCTTTAGCGGTGTTTTCCCTTAAACGCCACTAA
64 ACTATGCTTTAGCGGCG-TTTCCCATAAGCGCCACTAA
2871 CTGTAACATA
Statistics
Matches: 343, Mismatches: 82, Indels: 37
0.74 0.18 0.08
Matches are distributed among these distances:
112 1 0.00
113 63 0.18
114 121 0.35
115 146 0.43
116 12 0.03
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (114 bp):
AAGACAAAACGTCTGCGTTTTGGTTAACATATTTTGCGGCGCTTCTCAGAAAGCGCCGCTAATAC
TATGCTTTAGCGGCGTTTCCCATAAGCGCCACTAATTCCAGTATACATC
Found at i:3155 original size:115 final size:114
Alignment explanation
Indices: 3015--3231 Score: 337
Period size: 115 Copynumber: 1.9 Consensus size: 114
3005 TTCGTAAGCG
* * *
3015 CCGCAAATACTTTCTTTAGCGGCGTTTTAT-ATTAATCGCCACTAATTCTAGTATACATCCAGAC
1 CCGCAAATACTTCCTTTAGCGGCGTTTT-TCA-TAAACGCCACTAATTCTAGTATACATCAAGAC
* * *
3079 CAAAACGATGCGTTTTGGTCTTGAGATTTTGCGGCGCGCTTGGTGCATGCC
64 CAAAACGATGCGTTTTGATCTTCAGATCTTGCGGCGCGCTTGGTGCATGCC
*
3130 CCGCTAATACTTCCTTTAGCGGCGTTTTTCCATAAACGCCACTAATTCTAGTATACATCAAGACC
1 CCGCAAATACTTCCTTTAGCGGCGTTTTT-CATAAACGCCACTAATTCTAGTATACATCAAGACC
3195 AAAACGATGCGTTTTGATCTTCAGATCTTGCGGCGCG
65 AAAACGATGCGTTTTGATCTTCAGATCTTGCGGCGCG
3232 TGATGGTAAA
Statistics
Matches: 93, Mismatches: 7, Indels: 4
0.89 0.07 0.04
Matches are distributed among these distances:
114 1 0.01
115 91 0.98
116 1 0.01
ACGTcount: A:0.24, C:0.25, G:0.19, T:0.32
Consensus pattern (114 bp):
CCGCAAATACTTCCTTTAGCGGCGTTTTTCATAAACGCCACTAATTCTAGTATACATCAAGACCA
AAACGATGCGTTTTGATCTTCAGATCTTGCGGCGCGCTTGGTGCATGCC
Found at i:11271 original size:20 final size:21
Alignment explanation
Indices: 11246--11286 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
11236 TTATATAAAT
*
11246 TTATATATTAATA-ATGAATG
1 TTATATATTAAAACATGAATG
*
11266 TTATATTTTAAAACATGAATG
1 TTATATATTAAAACATGAATG
11287 GGTTGTCTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 11 0.61
21 7 0.39
ACGTcount: A:0.44, C:0.02, G:0.10, T:0.44
Consensus pattern (21 bp):
TTATATATTAAAACATGAATG
Found at i:12666 original size:84 final size:84
Alignment explanation
Indices: 12525--12705 Score: 249
Period size: 84 Copynumber: 2.2 Consensus size: 84
12515 AATTAAATTC
* * ** *
12525 TCTATTTTTCATAAAATATTCAATTCCCTTTCATATCTCTATTTTACATTGTTGTTATTCTTTTT
1 TCTATTTTCCATAAAATATTAAATTCCCTTTCATATCTCTATTTTACATTGACGTTATTC-TCTT
*
12590 TC-TTTCCCATATTTGATTA
65 TCATTTCCCACATTTGATTA
* *
12609 TCTATTTTCCATAAAATATTAAATTTCCTTTCATATCTCTATTTTTCATAT-ACGTTATTCTCTT
1 TCTATTTTCCATAAAATATTAAATTCCCTTTCATATCTCTATTTTACAT-TGACGTTATTCTCTT
*
12673 TCATTTCCCACATTTGATTC
65 TCATTTCCCACATTTGATTA
12693 TCTATTTTCCATA
1 TCTATTTTCCATA
12706 TGCTCTTTTT
Statistics
Matches: 86, Mismatches: 9, Indels: 4
0.87 0.09 0.04
Matches are distributed among these distances:
83 5 0.06
84 80 0.93
85 1 0.01
ACGTcount: A:0.24, C:0.20, G:0.03, T:0.54
Consensus pattern (84 bp):
TCTATTTTCCATAAAATATTAAATTCCCTTTCATATCTCTATTTTACATTGACGTTATTCTCTTT
CATTTCCCACATTTGATTA
Found at i:13876 original size:15 final size:15
Alignment explanation
Indices: 13853--13883 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
13843 CAATTTTCCC
13853 TAATCAAAATTACAT
1 TAATCAAAATTACAT
*
13868 TAATTAAAATTACAT
1 TAATCAAAATTACAT
13883 T
1 T
13884 TTTGTTACTC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.52, C:0.10, G:0.00, T:0.39
Consensus pattern (15 bp):
TAATCAAAATTACAT
Found at i:15278 original size:42 final size:42
Alignment explanation
Indices: 15168--15478 Score: 446
Period size: 42 Copynumber: 7.4 Consensus size: 42
15158 CGCTTACACA
*
15168 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTAAGG
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
* *
15210 AAATAAACGCCGCTAAAGATCATGTTCTTTAGCGGCACTTATG
1 AAA-AAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
* *
15253 AAAAAACACCGCTAAAGATCATGTTCTTTAGCGACGCTTAGG
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
* *
15295 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCACTTATG
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
*
15337 AAAAAACGCCGCTAAAGATCACGTTCTTTAGCGGCGCTTAGG
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
*
15379 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTTGGG
1 AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGC-TTAGG
* * * *
15422 AGAAAACGCCGCTAAA-AGTAATGTTCTATAGCGGCGCTT-GTT
1 AAAAAACGCCGCTAAAGA-TCATGTTCTTTAGCGGCGCTTAG-G
*
15464 CAAAAACGCCGCTAA
1 AAAAAACGCCGCTAA
15479 NNNNNNNNNN
Statistics
Matches: 243, Mismatches: 22, Indels: 8
0.89 0.08 0.03
Matches are distributed among these distances:
41 1 0.00
42 167 0.69
43 75 0.31
ACGTcount: A:0.33, C:0.22, G:0.22, T:0.24
Consensus pattern (42 bp):
AAAAAACGCCGCTAAAGATCATGTTCTTTAGCGGCGCTTAGG
Found at i:22583 original size:9 final size:9
Alignment explanation
Indices: 22548--23617 Score: 284
Period size: 9 Copynumber: 121.0 Consensus size: 9
22538 TTAGACAATA
22548 ATGTAAGTT
1 ATGTAAGTT
*
22557 A-GGAAGGTT
1 ATGTAA-GTT
22566 ATGT-A-TT
1 ATGTAAGTT
22573 ATGTAAGTT
1 ATGTAAGTT
22582 ATGTAAGTT
1 ATGTAAGTT
22591 ATGTAAGTT
1 ATGTAAGTT
*
22600 ATGTAATTT
1 ATGTAAGTT
*
22609 ATGTAAGTA
1 ATGTAAGTT
22618 ATGTAAGTT
1 ATGTAAGTT
* *
22627 ATTTAATTT
1 ATGTAAGTT
22636 ATGTAAGTT
1 ATGTAAGTT
22645 ATGTAAGTT
1 ATGTAAGTT
*
22654 ATTTAAGTT
1 ATGTAAGTT
* *
22663 ATTTAATTT
1 ATGTAAGTT
22672 ATGTAAGTT
1 ATGTAAGTT
22681 ATGTAAGTT
1 ATGTAAGTT
* *
22690 ATTTAATTT
1 ATGTAAGTT
22699 ATGTAAGCAATT
1 ATGTAAG---TT
*
22711 AGTAGAAAGATGGT
1 A-T-GTAAG-T--T
22725 ATGTAAGTT
1 ATGTAAGTT
22734 ATGTACTAAGTT
1 ATG---TAAGTT
22746 ATGT-A-TT
1 ATGTAAGTT
*
22753 ATGTAAATT
1 ATGTAAGTT
22762 ATGTACTAAGTT
1 ATG---TAAGTT
22774 ATGT-A-TT
1 ATGTAAGTT
* *
22781 ATGTAAATA
1 ATGTAAGTT
*
22790 ATTTAAGTT
1 ATGTAAGTT
* *
22799 AGGTAGGTT
1 ATGTAAGTT
22808 ATGT-A-TT
1 ATGTAAGTT
22815 ATGTAAGTT
1 ATGTAAGTT
*
22824 ATGTAAATT
1 ATGTAAGTT
*
22833 ATGTAATTT
1 ATGTAAGTT
*
22842 ATGTAAGTA
1 ATGTAAGTT
*
22851 ACGTAAGTT
1 ATGTAAGTT
* *
22860 ATTTAATTT
1 ATGTAAGTT
22869 ATGTAAGCAAGTT
1 ATGT----AAGTT
22882 ATGTAAGTT
1 ATGTAAGTT
* *
22891 ATATAATTT
1 ATGTAAGTT
*
22900 ATATAAGTT
1 ATGTAAGTT
* *
22909 ATATAATTT
1 ATGTAAGTT
**
22918 A-AAAATTGTT
1 ATGTAA--GTT
*
22928 ATGCAAGTTTAT
1 ATGTAAG--T-T
22940 ATGTAAGTTT
1 ATGTAAG-TT
22950 ATGT-A--T
1 ATGTAAGTT
* *
22956 -TGTATGGT
1 ATGTAAGTT
* *
22964 ATTTAAGAT
1 ATGTAAGTT
22973 ATGT-A-TT
1 ATGTAAGTT
*
22980 ATATAAGTT
1 ATGTAAGTT
* *
22989 ATGATATGAT
1 ATG-TAAGTT
*
22999 -TGATAAATT
1 ATG-TAAGTT
23008 -TG--AGTT
1 ATGTAAGTT
23014 ATGTAAGTTT
1 ATGTAAG-TT
23024 ATGT-A--T
1 ATGTAAGTT
*
23030 -TGTATGTT
1 ATGTAAGTT
* *
23038 ATTTAAGAT
1 ATGTAAGTT
23047 ATGT-A-TT
1 ATGTAAGTT
23054 ATGTAAGTTTAT
1 ATGTAAG--T-T
*
23066 ATATAAGTT
1 ATGTAAGTT
* *
23075 ATGATATGAT
1 ATG-TAAGTT
*
23085 -TGATAAATT
1 ATG-TAAGTT
23094 -TG--AGTT
1 ATGTAAGTT
23100 ATGTAAGTT
1 ATGTAAGTT
*
23109 ATGATATGATT
1 ATG-TAAG-TT
*
23120 -TATAAGTT
1 ATGTAAGTT
*
23128 ATGAAAGTT
1 ATGTAAGTT
23137 ATGT-A-TT
1 ATGTAAGTT
*
23144 ATGTAATTT
1 ATGTAAGTT
23153 ATGTAAGTT
1 ATGTAAGTT
*
23162 GTGT-A-TT
1 ATGTAAGTT
* *
23169 ATGCAAGTC
1 ATGTAAGTT
* * *
23178 ATATAGGCT
1 ATGTAAGTT
23187 ATGT-A-TT
1 ATGTAAGTT
23194 ATGTAAGTT
1 ATGTAAGTT
*
23203 AT-TATGTTATT
1 ATGTAAG---TT
23214 ATGTAAGTT
1 ATGTAAGTT
*
23223 ATGAAAGTTAT
1 ATGTAAG-T-T
*
23234 ATATAAGTT
1 ATGTAAGTT
**
23243 AT-TAA-AA
1 ATGTAAGTT
23250 ATGT-A-TT
1 ATGTAAGTT
*
23257 ATGTAATTT
1 ATGTAAGTT
*
23266 ATGCAAGTT
1 ATGTAAGTT
* *
23275 GTGT-A-TC
1 ATGTAAGTT
* *
23282 ATGCAAGTC
1 ATGTAAGTT
* * * *
23291 GTGCAGGCT
1 ATGTAAGTT
23300 ATGT-A-TT
1 ATGTAAGTT
23307 ATGTAAGTT
1 ATGTAAGTT
*
23316 ATGAAAGTTTT
1 ATGTAAG--TT
** *
23327 ATACAAGTG
1 ATGTAAGTT
**
23336 AT-TAA-AA
1 ATGTAAGTT
23343 ATGT-A-TT
1 ATGTAAGTT
*
23350 ATGTAATTT
1 ATGTAAGTT
*
23359 ATTTAAGTTATT
1 ATGTAAG---TT
23371 ATGTAAGTT
1 ATGTAAGTT
*
23380 ATGAAAGTT
1 ATGTAAGTT
23389 ATGT-A-TT
1 ATGTAAGTT
*
23396 ATGTAATTT
1 ATGTAAGTT
*
23405 AT-T---TA
1 ATGTAAGTT
23410 AT-TAAGTT
1 ATGTAAGTT
23418 ATGTAAGTT
1 ATGTAAGTT
*
23427 GTGT-A-TT
1 ATGTAAGTT
23434 AT-TAAAGTT
1 ATGT-AAGTT
*
23443 AAGT-A-TT
1 ATGTAAGTT
23450 ATGTAAGTT
1 ATGTAAGTT
*
23459 ATTTAAGTT
1 ATGTAAGTT
*
23468 ATGTAAGTG
1 ATGTAAGTT
*
23477 GTGT-A-TT
1 ATGTAAGTT
*
23484 ATGCAAGTT
1 ATGTAAGTT
*
23493 AAGTAAGTT
1 ATGTAAGTT
* *
23502 ATGTAGGCT
1 ATGTAAGTT
23511 ATGT-A-TT
1 ATGTAAGTT
*
23518 ATGCAAGTTTTT
1 ATGTAAG---TT
*
23530 ATGTAAGTG
1 ATGTAAGTT
*
23539 GTGT-A-TT
1 ATGTAAGTT
23546 ATGTAAGTT
1 ATGTAAGTT
23555 ATGTAAGTT
1 ATGTAAGTT
* *
23564 ATGTAGGCT
1 ATGTAAGTT
23573 ATGT-A-TT
1 ATGTAAGTT
*
23580 ATCTAAGTTTTT
1 ATGTAAG---TT
*
23592 ATGTTA-TT
1 ATGTAAGTT
23600 ATGTAAGTT
1 ATGTAAGTT
*
23609 ATGCAAGTT
1 ATGTAAGTT
23618 TCTATATAAG
Statistics
Matches: 777, Mismatches: 170, Indels: 228
0.66 0.14 0.19
Matches are distributed among these distances:
5 10 0.01
6 9 0.01
7 103 0.13
8 63 0.08
9 454 0.58
10 31 0.04
11 26 0.03
12 65 0.08
13 10 0.01
14 6 0.01
ACGTcount: A:0.34, C:0.02, G:0.18, T:0.46
Consensus pattern (9 bp):
ATGTAAGTT
Found at i:22763 original size:28 final size:28
Alignment explanation
Indices: 22724--22788 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
22714 AGAAAGATGG
*
22724 TATGTAAGTTATGTACTAAGTTATGTAT
1 TATGTAAATTATGTACTAAGTTATGTAT
22752 TATGTAAATTATGTACTAAGTTATGTAT
1 TATGTAAATTATGTACTAAGTTATGTAT
22780 TATGTAAAT
1 TATGTAAAT
22789 AATTTAAGTT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.35, C:0.03, G:0.15, T:0.46
Consensus pattern (28 bp):
TATGTAAATTATGTACTAAGTTATGTAT
Found at i:22987 original size:40 final size:40
Alignment explanation
Indices: 22939--23065 Score: 144
Period size: 40 Copynumber: 3.3 Consensus size: 40
22929 TGCAAGTTTA
22939 TATGTAAGTTTATGTATTGTATGGTATTTAAGATATGTAT
1 TATGTAAGTTTATGTATTGTATGGTATTTAAGATATGTAT
* * *
22979 TATATAAG-TTATG-ATATG-ATTG-A--TAA-ATTTG-AGT
1 TATGTAAGTTTATGTAT-TGTATGGTATTTAAGATATGTA-T
*
23013 TATGTAAGTTTATGTATTGTATGTTATTTAAGATATGTAT
1 TATGTAAGTTTATGTATTGTATGGTATTTAAGATATGTAT
23053 TATGTAAGTTTAT
1 TATGTAAGTTTAT
23066 ATATAAGTTA
Statistics
Matches: 70, Mismatches: 7, Indels: 20
0.72 0.07 0.21
Matches are distributed among these distances:
33 1 0.01
34 12 0.17
35 10 0.14
36 4 0.06
37 2 0.03
38 5 0.07
39 10 0.14
40 25 0.36
41 1 0.01
ACGTcount: A:0.32, C:0.00, G:0.18, T:0.50
Consensus pattern (40 bp):
TATGTAAGTTTATGTATTGTATGGTATTTAAGATATGTAT
Found at i:23215 original size:20 final size:20
Alignment explanation
Indices: 23186--23246 Score: 72
Period size: 20 Copynumber: 3.1 Consensus size: 20
23176 TCATATAGGC
23186 TATG-TATTATGTAAGTTAT
1 TATGTTATTATGTAAGTTAT
23205 TATGTTATTATGTAAGTTAT
1 TATGTTATTATGTAAGTTAT
* * *
23225 GAAAGTTA-TATATAAGTTAT
1 -TATGTTATTATGTAAGTTAT
23245 TA
1 TA
23247 AAAATGTATT
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
19 5 0.14
20 26 0.72
21 5 0.14
ACGTcount: A:0.36, C:0.00, G:0.15, T:0.49
Consensus pattern (20 bp):
TATGTTATTATGTAAGTTAT
Found at i:23262 original size:43 final size:43
Alignment explanation
Indices: 23210--23406 Score: 142
Period size: 43 Copynumber: 4.3 Consensus size: 43
23200 GTTATTATGT
*
23210 TATTATGTAAGTTATGAAAGTTATATATAAGTTATTAAAAATG
1 TATTATGTAATTTATGAAAGTTATATATAAGTTATTAAAAATG
* * ** * ***
23253 TATTATGTAATTTATGCAAGTTGTGTATCATGCAAGTCGTGCAGGCTATG
1 TATTATGTAATTTATGAAAG-T-TATAT-AT--AAGTTAT-TA-AAAATG
* * * *
23303 TATTATGTAAGTTATGAAAGTTTTATACAAGTGATTAAAAATG
1 TATTATGTAATTTATGAAAGTTATATATAAGTTATTAAAAATG
** * * *
23346 TATTATGTAATTTATTTAAGTTATTATGTAAGTTATGAAAGTTATG
1 TATTATGTAATTTATGAAAGTTA-TATATAAGTTATTAAA--AATG
23392 TATTATGTAATTTAT
1 TATTATGTAATTTAT
23407 TTAATTAAGT
Statistics
Matches: 116, Mismatches: 28, Indels: 17
0.72 0.17 0.11
Matches are distributed among these distances:
43 40 0.34
44 14 0.12
45 9 0.08
46 20 0.17
47 1 0.01
48 9 0.08
49 2 0.02
50 21 0.18
ACGTcount: A:0.36, C:0.04, G:0.17, T:0.44
Consensus pattern (43 bp):
TATTATGTAATTTATGAAAGTTATATATAAGTTATTAAAAATG
Found at i:23274 original size:113 final size:113
Alignment explanation
Indices: 23098--23317 Score: 325
Period size: 113 Copynumber: 1.9 Consensus size: 113
23088 TAAATTTGAG
* * * *
23098 TTATGTAAGTTATGATATGATTTATAAGTTATGAAAGTTATGTATTATGTAATTTATGTAAGTTG
1 TTATGTAAGTTATGAAATGATATATAAGTTATGAAAG-AATGTATTATGTAATTTATGCAAGTTG
* *
23163 TGTATTATGCAAGTCATATAGGCTATGTATTATGTAAGTTATTATGTTA
65 TGTATCATGCAAGTCATACAGGCTATGTATTATGTAAGTTATTATGTTA
* *
23212 TTATGTAAGTTATGAAAGTTATATATAAGTTATTAAA-AATGTATTATGTAATTTATGCAAGTTG
1 TTATGTAAGTTATGAAA-TGATATATAAGTTATGAAAGAATGTATTATGTAATTTATGCAAGTTG
* *
23276 TGTATCATGCAAGTCGTGCAGGCTATGTATTATGTAAGTTAT
65 TGTATCATGCAAGTCATACAGGCTATGTATTATGTAAGTTAT
23318 GAAAGTTTTA
Statistics
Matches: 95, Mismatches: 10, Indels: 3
0.88 0.09 0.03
Matches are distributed among these distances:
113 63 0.66
114 16 0.17
115 16 0.17
ACGTcount: A:0.33, C:0.04, G:0.19, T:0.44
Consensus pattern (113 bp):
TTATGTAAGTTATGAAATGATATATAAGTTATGAAAGAATGTATTATGTAATTTATGCAAGTTGT
GTATCATGCAAGTCATACAGGCTATGTATTATGTAAGTTATTATGTTA
Found at i:23370 original size:21 final size:21
Alignment explanation
Indices: 23346--23423 Score: 68
Period size: 21 Copynumber: 3.5 Consensus size: 21
23336 ATTAAAAATG
23346 TATTATGTAATTTATTTAAGT
1 TATTATGTAATTTATTTAAGT
* **
23367 TATTATGTAAGTTATGAAAGTTAT
1 TATTATGTAATTTATTTAAG---T
23391 GTATTATGTAATTTATTTAA-T
1 -TATTATGTAATTTATTTAAGT
23412 TAAGTTATGTAA
1 T-A-TTATGTAA
23424 GTTGTGTATT
Statistics
Matches: 45, Mismatches: 6, Indels: 11
0.73 0.10 0.18
Matches are distributed among these distances:
20 1 0.02
21 19 0.42
22 8 0.18
24 1 0.02
25 16 0.36
ACGTcount: A:0.36, C:0.00, G:0.13, T:0.51
Consensus pattern (21 bp):
TATTATGTAATTTATTTAAGT
Found at i:23396 original size:25 final size:25
Alignment explanation
Indices: 23122--23472 Score: 135
Period size: 25 Copynumber: 14.8 Consensus size: 25
23112 ATATGATTTA
*
23122 TAAGTTATGAAAGTTATGTATTATG
1 TAAGTTATTAAAGTTATGTATTATG
* *
23147 TAATTTATGT-AAGTTGTGTATTATG
1 TAAGTTAT-TAAAGTTATGTATTATG
* * * *
23172 CAAGTCA-TATAGGCTATGTATTATG
1 TAAGTTATTA-AAGTTATGTATTATG
*
23197 TAAGTTATT--A--TGT-TATTATG
1 TAAGTTATTAAAGTTATGTATTATG
*
23217 TAAGTTATGAAAGTTA--TA-TA--
1 TAAGTTATTAAAGTTATGTATTATG
*
23237 TAAGTTATTAAA--AATGTATTATG
1 TAAGTTATTAAAGTTATGTATTATG
* ** * *
23260 TAATTTATGCAAGTTGTGTATCATG
1 TAAGTTATTAAAGTTATGTATTATG
* ** ** * *
23285 CAAGTCGTGCAGGCTATGTATTATG
1 TAAGTTATTAAAGTTATGTATTATG
*
23310 TAAGTTATGAAAGTT-T-TA-TA--
1 TAAGTTATTAAAGTTATGTATTATG
* * *
23330 CAAGTGATTAAA--AATGTATTATG
1 TAAGTTATTAAAGTTATGTATTATG
* *
23353 TAATTTATTTAAG---T-TATTATG
1 TAAGTTATTAAAGTTATGTATTATG
*
23374 TAAGTTATGAAAGTTATGTATTATG
1 TAAGTTATTAAAGTTATGTATTATG
* *
23399 TAATTTATTTAATTAAGTTATGTAAGT-TG
1 TAAGTTA-TT-A--AAGTTATGT-ATTATG
* *
23428 TGTA-TTATTAAAGTTAAGTATTATG
1 T-AAGTTATTAAAGTTATGTATTATG
*
23453 TAAGTTATTTAAGTTATGTA
1 TAAGTTATTAAAGTTATGTA
23473 AGTGGTGTAT
Statistics
Matches: 236, Mismatches: 57, Indels: 66
0.66 0.16 0.18
Matches are distributed among these distances:
18 1 0.00
19 1 0.00
20 39 0.17
21 23 0.10
22 6 0.03
23 22 0.09
24 6 0.03
25 114 0.48
26 2 0.01
27 2 0.01
28 2 0.01
29 15 0.06
30 3 0.01
ACGTcount: A:0.35, C:0.03, G:0.17, T:0.45
Consensus pattern (25 bp):
TAAGTTATTAAAGTTATGTATTATG
Found at i:23492 original size:34 final size:34
Alignment explanation
Indices: 23445--23568 Score: 136
Period size: 34 Copynumber: 3.8 Consensus size: 34
23435 TTAAAGTTAA
* *
23445 GTATTATGTAAGTTATTTAAGTTATGTAAGTGGT
1 GTATTATGCAAGTTATGTAAGTTATGTAAGTGGT
* * *
23479 GTATTATGCAAGTTAAGTAAGTTATGTAGGCT-AT
1 GTATTATGCAAGTTATGTAAGTTATGTAAG-TGGT
23513 GTATTATGCAAG-T-T-T---TTATGTAAGTGGT
1 GTATTATGCAAGTTATGTAAGTTATGTAAGTGGT
*
23541 GTATTATGTAAGTTATGTAAGTTATGTA
1 GTATTATGCAAGTTATGTAAGTTATGTA
23569 GGCTATGTAT
Statistics
Matches: 73, Mismatches: 9, Indels: 16
0.74 0.09 0.16
Matches are distributed among these distances:
27 1 0.01
28 20 0.27
29 1 0.01
30 1 0.01
31 2 0.03
33 1 0.01
34 46 0.63
35 1 0.01
ACGTcount: A:0.30, C:0.02, G:0.23, T:0.44
Consensus pattern (34 bp):
GTATTATGCAAGTTATGTAAGTTATGTAAGTGGT
Found at i:23520 original size:50 final size:50
Alignment explanation
Indices: 23412--23568 Score: 146
Period size: 50 Copynumber: 3.2 Consensus size: 50
23402 TTTATTTAAT
* * * *
23412 TAAGTTATGTAAGTTGTGTATTATTAAAGTTAAGTATTATGTAAGTTATT
1 TAAGTTATGTAAGTGGTGTATTATGAAAGTTAAGTATTATGTAAGCTATG
* *
23462 TAAGTTATGTAAGTGGTGTATTATGCAAGTTAAGTAAGTTATGTAGGCTATG
1 TAAGTTATGTAAGTGGTGTATTATGAAAGTTAAGT-A-TTATGTAAGCTATG
* * *** *
23514 T-A-TTATGCAAGT--T-T-TTATGTAAGTGGTGTATTATGTAAGTTATG
1 TAAGTTATGTAAGTGGTGTATTATGAAAGTTAAGTATTATGTAAGCTATG
23558 TAAGTTATGTA
1 TAAGTTATGTA
23569 GGCTATGTAT
Statistics
Matches: 89, Mismatches: 14, Indels: 12
0.77 0.12 0.10
Matches are distributed among these distances:
44 13 0.15
45 2 0.02
46 17 0.19
47 1 0.01
48 1 0.01
50 41 0.46
51 2 0.02
52 12 0.13
ACGTcount: A:0.31, C:0.02, G:0.22, T:0.45
Consensus pattern (50 bp):
TAAGTTATGTAAGTGGTGTATTATGAAAGTTAAGTATTATGTAAGCTATG
Found at i:23532 original size:28 final size:28
Alignment explanation
Indices: 23500--23595 Score: 79
Period size: 28 Copynumber: 3.2 Consensus size: 28
23490 GTTAAGTAAG
23500 TTATGTAGGCTATGTATTATGCAAGTTT
1 TTATGTAGGCTATGTATTATGCAAGTTT
* * *
23528 TTATGTAAG-TGGTGTATTATGTAAGTTATGT
1 TTATGTAGGCT-ATGTATTATGCAAG-T-T-T
23559 AAGTTATGTAGGCTATGTATTAT-CTAAGTTT
1 ---TTATGTAGGCTATGTATTATGC-AAGTTT
23590 TTATGT
1 TTATGT
23596 TATTATGTAA
Statistics
Matches: 53, Mismatches: 6, Indels: 18
0.69 0.08 0.23
Matches are distributed among these distances:
27 1 0.02
28 26 0.49
29 1 0.02
30 1 0.02
31 2 0.04
32 1 0.02
33 1 0.02
34 19 0.36
35 1 0.02
ACGTcount: A:0.26, C:0.04, G:0.22, T:0.48
Consensus pattern (28 bp):
TTATGTAGGCTATGTATTATGCAAGTTT
Found at i:23538 original size:62 final size:62
Alignment explanation
Indices: 23466--23595 Score: 226
Period size: 62 Copynumber: 2.1 Consensus size: 62
23456 GTTATTTAAG
23466 TTATGTAAGTGGTGTATTATGCAAGTTAAGTAAGTTATGTAGGCTATGTATTATGC-AAGTTT
1 TTATGTAAGTGGTGTATTATGCAAGTTAAGTAAGTTATGTAGGCTATGTATTAT-CTAAGTTT
* *
23528 TTATGTAAGTGGTGTATTATGTAAGTTATGTAAGTTATGTAGGCTATGTATTATCTAAGTTT
1 TTATGTAAGTGGTGTATTATGCAAGTTAAGTAAGTTATGTAGGCTATGTATTATCTAAGTTT
23590 TTATGT
1 TTATGT
23596 TATTATGTAA
Statistics
Matches: 65, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
61 1 0.02
62 64 0.98
ACGTcount: A:0.28, C:0.04, G:0.23, T:0.45
Consensus pattern (62 bp):
TTATGTAAGTGGTGTATTATGCAAGTTAAGTAAGTTATGTAGGCTATGTATTATCTAAGTTT
Found at i:23568 original size:25 final size:25
Alignment explanation
Indices: 23343--23617 Score: 105
Period size: 25 Copynumber: 11.0 Consensus size: 25
23333 GTGATTAAAA
* *
23343 ATGTATTATGTAATTTATTTAAG--
1 ATGTATTATGTAAGTTATGTAAGTT
*
23366 -T-TATTATGTAAGTTATGAAAGTT
1 ATGTATTATGTAAGTTATGTAAGTT
* *
23389 ATGTATTATGTAATTTATTTAA-TT
1 ATGTATTATGTAAGTTATGTAAGTT
* *
23413 AAG--TTATGTAAGTTGTGT-A-TT
1 ATGTATTATGTAAGTTATGTAAGTT
*
23434 AT-TA--AAGTTAAGTATTATGTAAGTT
1 ATGTATTATG-TAAG--TTATGTAAGTT
* **
23459 ATTTAAGTTATGTAAGTGGTGT-A-TT
1 ATGT-A-TTATGTAAGTTATGTAAGTT
* * * *
23484 ATGCAAGTTAAGTAAGTTATGTAGGCT
1 ATG-TA-TTATGTAAGTTATGTAAGTT
* *
23511 ATGTATTATGCAAGTTTTTATGTAAGTG
1 ATGTATTATGTAAG---TTATGTAAGTT
*
23539 GTGTATTATGTAAGTTATGTAAGTT
1 ATGTATTATGTAAGTTATGTAAGTT
* *
23564 ATGTAGGCTATGT-A-TTATCTAAGTTTTT
1 ATGTA--TTATGTAAGTTATGTAAG---TT
*
23592 ATGTTATTATGTAAGTTATGCAAGTT
1 ATG-TATTATGTAAGTTATGTAAGTT
23618 TCTATATAAG
Statistics
Matches: 184, Mismatches: 38, Indels: 57
0.66 0.14 0.20
Matches are distributed among these distances:
20 2 0.01
21 25 0.14
22 13 0.07
23 5 0.03
24 6 0.03
25 67 0.36
26 6 0.03
27 19 0.10
28 26 0.14
29 13 0.07
30 2 0.01
ACGTcount: A:0.31, C:0.02, G:0.19, T:0.47
Consensus pattern (25 bp):
ATGTATTATGTAAGTTATGTAAGTT
Found at i:25641 original size:124 final size:124
Alignment explanation
Indices: 25287--25659 Score: 298
Period size: 127 Copynumber: 3.0 Consensus size: 124
25277 GAACTGTTCC
* * * *
25287 TCAACCGAAACGGCGACGTTCTGAACATTTTGTAATACACATTTGTGGCGTTTTCATACTAAACG
1 TCAA-CGAAACGGTGACGTTCTGAACATTTTGTAATGCACATTTGTGGCGTTTCCATACAAAACG
*
25352 CCGCTAAAGCTTACAG-TTGCGGCGTTTTAAATACAAACGCCACTAAAGAGTTCAAATCAT
65 CCGCTAAAG-ATACAGTTTGCGGCGTTTTAAATACAAACGCCACTAAAGAGTTCAAATCAT
** ** * *** * * * *
25412 TCAA-GAAAATGACGCCGTTTTCGTTCACAAAAACATAT-ATG--GATTTGCGGCGTTTCTATA-
1 TCAACG--AA--ACG--G-TGACGTTCTGAACATTTTGTAATGCACATTTGTGGCGTTTCCATAC
* ** * * **
25472 AAAACGCCACTACTGTATAC-CTTCTGTGGCGTTTTTCATACAAACGCCACTAAA-A-TTCAAAT
59 AAAACGCCGCTAAAG-ATACAGTT-TGCGGCGTTTTAAATACAAACGCCACTAAAGAGTTCAAA-
25534 TCAT
121 TCAT
*
25538 GT-AACGAAACGGTGACGTTCTGAACATTTTGTAATGCACATTTGTGGCGTTTCCATACCAAACG
1 -TCAACGAAACGGTGACGTTCTGAACATTTTGTAATGCACATTTGTGGCGTTTCCATACAAAACG
* * *
25602 CCGCTAAAGATCACAGTTTGCGGCGTTTTAAATAAAAACGCCAGTAAGGAGTTCAAAT
65 CCGCTAAAGAT-ACAGTTTGCGGCGTTTTAAATACAAACGCCACTAAAGAGTTCAAAT
25660 AATTTAAGAA
Statistics
Matches: 180, Mismatches: 48, Indels: 40
0.67 0.18 0.15
Matches are distributed among these distances:
120 11 0.06
121 4 0.02
123 22 0.12
124 37 0.21
125 18 0.10
126 28 0.16
127 47 0.26
129 3 0.02
130 10 0.06
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (124 bp):
TCAACGAAACGGTGACGTTCTGAACATTTTGTAATGCACATTTGTGGCGTTTCCATACAAAACGC
CGCTAAAGATACAGTTTGCGGCGTTTTAAATACAAACGCCACTAAAGAGTTCAAATCAT
Found at i:26106 original size:21 final size:21
Alignment explanation
Indices: 26082--26132 Score: 93
Period size: 21 Copynumber: 2.4 Consensus size: 21
26072 ATAACCTAGA
26082 CCCTAAACCACAACCCTTATC
1 CCCTAAACCACAACCCTTATC
*
26103 CCCTAAACCATAACCCTTATC
1 CCCTAAACCACAACCCTTATC
26124 CCCTAAACC
1 CCCTAAACC
26133 CTAAACCATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.33, C:0.47, G:0.00, T:0.20
Consensus pattern (21 bp):
CCCTAAACCACAACCCTTATC
Found at i:29277 original size:17 final size:18
Alignment explanation
Indices: 29238--29304 Score: 59
Period size: 17 Copynumber: 3.9 Consensus size: 18
29228 TTTTAGAATT
*
29238 TTTATAATTTTTGTAAAA
1 TTTATAAATTTTGTAAAA
*
29256 -ATATAAATTTTG-AAAA
1 TTTATAAATTTTGTAAAA
* **
29272 TTTATATATTTT-TTGAA
1 TTTATAAATTTTGTAAAA
*
29289 TTTTTAAATTTTGTAA
1 TTTATAAATTTTGTAA
29305 TTTTTGTTGT
Statistics
Matches: 36, Mismatches: 10, Indels: 6
0.69 0.19 0.12
Matches are distributed among these distances:
16 4 0.11
17 31 0.86
18 1 0.03
ACGTcount: A:0.39, C:0.00, G:0.06, T:0.55
Consensus pattern (18 bp):
TTTATAAATTTTGTAAAA
Found at i:30835 original size:3 final size:3
Alignment explanation
Indices: 30827--30859 Score: 66
Period size: 3 Copynumber: 11.0 Consensus size: 3
30817 TAAATAAATA
30827 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
30860 GTCTTTTAGC
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:44024 original size:27 final size:27
Alignment explanation
Indices: 43994--44045 Score: 86
Period size: 27 Copynumber: 1.9 Consensus size: 27
43984 TCGCCTTGCT
* *
43994 CTACGCTCAGAGGTCCCTTTGGAGCCA
1 CTACCCTCAGACGTCCCTTTGGAGCCA
44021 CTACCCTCAGACGTCCCTTTGGAGC
1 CTACCCTCAGACGTCCCTTTGGAGC
44046 GACCACGTAC
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 23 1.00
ACGTcount: A:0.17, C:0.37, G:0.23, T:0.23
Consensus pattern (27 bp):
CTACCCTCAGACGTCCCTTTGGAGCCA
Found at i:50322 original size:29 final size:31
Alignment explanation
Indices: 50282--50350 Score: 97
Period size: 30 Copynumber: 2.3 Consensus size: 31
50272 AATTTGATTA
* **
50282 AAAAAATATTTCGTATTTTA-CAACTCGGTT
1 AAAAAATATTTCATATTTTATCAACTCAATT
50312 AAAAAAT-TTTCATATTTTATCAACTCAATT
1 AAAAAATATTTCATATTTTATCAACTCAATT
50342 AAAAAATAT
1 AAAAAATAT
50351 ATGAAAATGG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
29 11 0.32
30 22 0.65
31 1 0.03
ACGTcount: A:0.45, C:0.12, G:0.04, T:0.39
Consensus pattern (31 bp):
AAAAAATATTTCATATTTTATCAACTCAATT
Found at i:52268 original size:30 final size:30
Alignment explanation
Indices: 52234--52296 Score: 108
Period size: 30 Copynumber: 2.1 Consensus size: 30
52224 ACTTATTTTA
*
52234 TTGTTAATTTTGTTATTATTTTAAAGACAT
1 TTGTTAATTTTGTTATGATTTTAAAGACAT
*
52264 TTGTTAATTTTGTTATGATTTTAGAGACAT
1 TTGTTAATTTTGTTATGATTTTAAAGACAT
52294 TTG
1 TTG
52297 CTTATTAAGT
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.27, C:0.03, G:0.14, T:0.56
Consensus pattern (30 bp):
TTGTTAATTTTGTTATGATTTTAAAGACAT
Found at i:69659 original size:124 final size:125
Alignment explanation
Indices: 69358--69689 Score: 471
Period size: 124 Copynumber: 2.7 Consensus size: 125
69348 GTTTCTAATA
*
69358 AAATAGTATAAAATCTCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAA-TCGCGTCCTCA
1 AAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATTCGCGTCCTCA
*
69422 TGGACGCGCTTTTGCTACAGTAGGTCACGGAAGAAATAATTATTTTTTTGACGTTTCTGAGC
66 -GGACGCGCTTTTGCTACAGTAAGTCACGGAAGAAATAA-TATTTTTTTGACGTTTCTGAGC
69484 AAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATTACG-GTCTCG
1 AAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATT-CGCGTC-C-
* * *
69548 TCA-G-CGCGCTTTTGCTACAGTAAGTCATGTAAGAAATAA-GTTTTTTTGACGTTTCTGAGC
63 TCAGGACGCGCTTTTGCTACAGTAAGTCACGGAAGAAATAATATTTTTTTGACGTTTCTGAGC
* *
69608 AAATAATATAAAATCGCTTCTAGTAGGATGCTATTTGAGAAGAATTTGTGAAA-TCGCG-CCATC
1 AAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATTCGCGTCC-TC
* *
69671 GTGGACGCTCTTTTGCTAC
65 -AGGACGCGCTTTTGCTAC
69690 TGTAGCATGT
Statistics
Matches: 188, Mismatches: 10, Indels: 18
0.87 0.05 0.08
Matches are distributed among these distances:
121 3 0.02
122 3 0.02
123 3 0.02
124 84 0.45
126 84 0.45
127 5 0.03
128 3 0.02
129 3 0.02
ACGTcount: A:0.30, C:0.16, G:0.21, T:0.33
Consensus pattern (125 bp):
AAATAGTATAAAATCGCTTCTAGCAGGATGCTATTTGAGAAGAATTTGTGAAATTCGCGTCCTCA
GGACGCGCTTTTGCTACAGTAAGTCACGGAAGAAATAATATTTTTTTGACGTTTCTGAGC
Found at i:72748 original size:18 final size:21
Alignment explanation
Indices: 72681--73149 Score: 151
Period size: 22 Copynumber: 19.4 Consensus size: 21
72671 TTAGGTTAAG
**
72681 GTTAGGGTTTTTAAGTT-AAGG
1 GTTAGGGTTTTTAA-TTAAATA
72702 GTTTAGGGTTTTTAATTAAATTA
1 G-TTAGGGTTTTTAATTAAA-TA
72725 GGTTAGGGTTTTTAATTAAATTAGGTTAA
1 -GTTAGGGTTTTTAATT-AA--A---T-A
**
72754 GGTTAGGGTTTTTAAGTT-AAGG
1 -GTTAGGGTTTTTAA-TTAAATA
72776 GTTTAGGGTTTTTAATTAAATTA
1 G-TTAGGGTTTTTAATTAAA-TA
72799 GGTTAGGGTTTTTAATTAAATTAGGTTAA
1 -GTTAGGGTTTTTAATT-AA--A---T-A
**
72828 GGTTAGGGTTTTTAAGTT-AAGG
1 -GTTAGGGTTTTTAA-TTAAATA
72850 GTTTAGGGTTTTTAATTAAATTA
1 G-TTAGGGTTTTTAATTAAA-TA
72873 GGTTAGGGTTTTTAATTAAATTAGGTTAA
1 -GTTAGGGTTTTTAATT-AA--A---T-A
**
72902 GGTTAGGGTTTTTAAGTT-AAGG
1 -GTTAGGGTTTTTAA-TTAAATA
72924 GTTTAGGGTTTTTAATTAAATTA
1 G-TTAGGGTTTTTAATTAAA-TA
72947 GGTTAGGGTTTTTAATTAAATTAGGTTAA
1 -GTTAGGGTTTTTAATT-AA--A---T-A
**
72976 GGTTAGGGTTTTTAAGTT-AAGG
1 -GTTAGGGTTTTTAA-TTAAATA
72998 GTTTAGGGTTTTTAATTAAATTA
1 G-TTAGGGTTTTTAATTAAA-TA
73021 GGTTAGGGTTTTTAATTAAATTAGGTTAA
1 -GTTAGGGTTTTTAATT-AA--A---T-A
**
73050 GGTTAGGGTTTTTAAGTT-AAGG
1 -GTTAGGGTTTTTAA-TTAAATA
73072 GTTTAGGGTTTTTAATTAAATTA
1 G-TTAGGGTTTTTAATTAAA-TA
73095 GGTTAGGGTTTTTAATTAAATTA
1 -GTTAGGGTTTTTAATTAAA-TA
* *
73118 GGTTAAGG-TTTTAATTAATTTA
1 -GTTAGGGTTTTTAATTAA-ATA
73140 GGTTAGGGTT
1 -GTTAGGGTT
73150 AGGGTTTTTA
Statistics
Matches: 362, Mismatches: 25, Indels: 120
0.71 0.05 0.24
Matches are distributed among these distances:
21 18 0.05
22 109 0.30
23 104 0.29
24 16 0.04
26 10 0.03
28 15 0.04
29 80 0.22
30 10 0.03
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.46
Consensus pattern (21 bp):
GTTAGGGTTTTTAATTAAATA
Found at i:72792 original size:74 final size:74
Alignment explanation
Indices: 72671--73258 Score: 1027
Period size: 74 Copynumber: 7.9 Consensus size: 74
72661 ATCGCAATAG
72671 TTAGGTTAAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTT
1 TTAGGTTAAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTT
72736 TTAATTAAA
66 TTAATTAAA
72745 TTAGGTTAAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTT
1 TTAGGTTAAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTT
72810 TTAATTAAA
66 TTAATTAAA
72819 TTAGGTTAAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTT
1 TTAGGTTAAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTT
72884 TTAATTAAA
66 TTAATTAAA
72893 TTAGGTTAAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTT
1 TTAGGTTAAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTT
72958 TTAATTAAA
66 TTAATTAAA
72967 TTAGGTTAAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTT
1 TTAGGTTAAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTT
73032 TTAATTAAA
66 TTAATTAAA
73041 TTAGGTTAAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTT
1 TTAGGTTAAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTT
73106 TTAATTAAA
66 TTAATTAAA
**** *
73115 TTAGGTTAAGGTTTTAATTAATTTAGGTT-AGGG-TTAGGGTTTTTAATTAAATTAGGTTAGGGT
1 TTAGGTTAAGGTTAGGGTT--TTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTA--G-
*
73178 TAAGGTTTTTAATTAAT
61 ---GGTTTTTAATTAAA
*
73195 TTAGGTTAAGGTTAGGGTTTTTAAGCTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTT
1 TTAGGTTAAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTT
73259 AGGAGTTAAG
Statistics
Matches: 492, Mismatches: 12, Indels: 20
0.94 0.02 0.04
Matches are distributed among these distances:
74 415 0.84
75 4 0.01
76 8 0.02
78 7 0.01
79 4 0.01
80 54 0.11
ACGTcount: A:0.28, C:0.00, G:0.26, T:0.46
Consensus pattern (74 bp):
TTAGGTTAAGGTTAGGGTTTTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTT
TTAATTAAA
Found at i:73127 original size:29 final size:29
Alignment explanation
Indices: 73094--73218 Score: 156
Period size: 29 Copynumber: 4.6 Consensus size: 29
73084 TAATTAAATT
73094 AGGTTAGGGTTTTTAATTAAATTAGGTT-
1 AGGTTAGGGTTTTTAATTAAATTAGGTTA
*
73122 A----A-GG-TTTTAATTAATTTAGGTTA
1 AGGTTAGGGTTTTTAATTAAATTAGGTTA
*
73145 GGGTTAGGGTTTTTAATTAAATTAGGTTA
1 AGGTTAGGGTTTTTAATTAAATTAGGTTA
* * *
73174 GGGTTAAGGTTTTTAATTAATTTAGGTTA
1 AGGTTAGGGTTTTTAATTAAATTAGGTTA
73203 AGGTTAGGGTTTTTAA
1 AGGTTAGGGTTTTTAA
73219 GCTAAGGGTT
Statistics
Matches: 83, Mismatches: 7, Indels: 13
0.81 0.07 0.13
Matches are distributed among these distances:
22 17 0.20
23 2 0.02
24 1 0.01
27 1 0.01
28 3 0.04
29 59 0.71
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.46
Consensus pattern (29 bp):
AGGTTAGGGTTTTTAATTAAATTAGGTTA
Found at i:73198 original size:58 final size:51
Alignment explanation
Indices: 72690--73218 Score: 415
Period size: 51 Copynumber: 10.5 Consensus size: 51
72680 GGTTAGGGTT
* *
72690 TTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAA
1 TTTAGGTTAA-GG-TTAGGGTTTTTAATTAAATTAGGTTAAGG-TTTTAATTAA
* * * *
72744 ATTAGGTTAAGGTTAGGGTTTTTAAGTT-AA--GGGTTTAGGGTTT--TTAA
1 TTTAGGTTAAGGTTAGGGTTTTTAA-TTAAATTAGGTTAAGGTTTTAATTAA
** ****
72791 -TTAAATT-AGGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTT--
1 TTTAGGTTAAGGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTTTAATTAA
* *
72838 TTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAA
1 TTTAGGTTAA-GG-TTAGGGTTTTTAATTAAATTAGGTTAAGG-TTTTAATTAA
* * * *
72892 ATTAGGTTAAGGTTAGGGTTTTTAAGTT-AA--GGGTTTAGGGTTT--TTAA
1 TTTAGGTTAAGGTTAGGGTTTTTAA-TTAAATTAGGTTAAGGTTTTAATTAA
** ****
72939 -TTAAATT-AGGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTAGGGTT--
1 TTTAGGTTAAGGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTTTAATTAA
* *
72986 TTTAAGTTAAGGGTTTAGGGTTTTTAATTAAATTAGGTTAGGGTTTTTAATTAA
1 TTTAGGTTAA-GG-TTAGGGTTTTTAATTAAATTAGGTTAAGG-TTTTAATTAA
* * * *
73040 ATTAGGTTAAGGTTAGGGTTTTTAAGTT-AA--GGGTTTAGGGTTT--TTAA
1 TTTAGGTTAAGGTTAGGGTTTTTAA-TTAAATTAGGTTAAGGTTTTAATTAA
**
73087 -TTAAATT-AGGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTTTAATTAA
1 TTTAGGTTAAGGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTTTAATTAA
*
73136 TTTAGGTTAGGGTTAGGGTTTTTAATTAAATTAGGTTAGGGTTAAGGTTTTTAATTAA
1 TTTAGGTTAAGGTTAGGGTTTTTAATT-AA--A--TTA-GGTTAAGG-TTTTAATTAA
73194 TTTAGGTTAAGGTTAGGGTTTTTAA
1 TTTAGGTTAAGGTTAGGGTTTTTAA
73219 GCTAAGGGTT
Statistics
Matches: 381, Mismatches: 53, Indels: 78
0.74 0.10 0.15
Matches are distributed among these distances:
44 6 0.02
45 54 0.14
46 15 0.04
47 38 0.10
48 12 0.03
49 19 0.05
50 27 0.07
51 73 0.19
52 55 0.14
53 12 0.03
54 25 0.07
56 3 0.01
57 8 0.02
58 34 0.09
ACGTcount: A:0.29, C:0.00, G:0.25, T:0.46
Consensus pattern (51 bp):
TTTAGGTTAAGGTTAGGGTTTTTAATTAAATTAGGTTAAGGTTTTAATTAA
Found at i:73277 original size:13 final size:13
Alignment explanation
Indices: 73253--73321 Score: 51
Period size: 14 Copynumber: 5.6 Consensus size: 13
73243 AAATTAGGTT
73253 AGGGTTAGGAGTTA
1 AGGGTTA-GAGTTA
*
73267 AGGGTTAGAGTTT
1 AGGGTTAGAGTTA
73280 AGGG-T----TTA
1 AGGGTTAGAGTTA
*
73288 A-GGTTAGGGTTA
1 AGGGTTAGAGTTA
73300 AGGGTTTAGAGTTA
1 AGGG-TTAGAGTTA
*
73314 GGGGTTAG
1 AGGGTTAG
73322 GGTTTTTAAT
Statistics
Matches: 44, Mismatches: 4, Indels: 15
0.70 0.06 0.24
Matches are distributed among these distances:
7 2 0.05
8 4 0.09
12 5 0.11
13 15 0.34
14 18 0.41
ACGTcount: A:0.25, C:0.00, G:0.42, T:0.33
Consensus pattern (13 bp):
AGGGTTAGAGTTA
Found at i:73281 original size:27 final size:26
Alignment explanation
Indices: 73251--73325 Score: 80
Period size: 27 Copynumber: 2.8 Consensus size: 26
73241 TTAAATTAGG
73251 TTAGGGTTAGGAGTTAAGGGTT-AGAGT
1 TTAGGGTTAGG-GTT-AGGGTTAAGAGT
* *
73278 TTAGGGTTTAAGGTTAGGGTTAAGGGT
1 TTAGGG-TTAGGGTTAGGGTTAAGAGT
*
73305 TTAGAGTTAGGGGTTAGGGTT
1 TTAGGGTTA-GGGTTAGGGTT
73326 TTTAATTAAA
Statistics
Matches: 41, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
26 9 0.22
27 28 0.68
28 4 0.10
ACGTcount: A:0.23, C:0.00, G:0.41, T:0.36
Consensus pattern (26 bp):
TTAGGGTTAGGGTTAGGGTTAAGAGT
Found at i:73326 original size:20 final size:19
Alignment explanation
Indices: 73246--73326 Score: 76
Period size: 20 Copynumber: 4.1 Consensus size: 19
73236 TTTAATTAAA
73246 TTAG-GTTAGGGTTAGGAGT
1 TTAGAGTTAGGGTTAGG-GT
* * *
73265 TAAGGGTTAGAGTTTAGGGT
1 TTAGAGTTAG-GGTTAGGGT
73285 TTA-AGGTTAGGGTTAAGGGT
1 TTAGA-GTTAGGGTT-AGGGT
73305 TTAGAGTTAGGGGTTAGGGT
1 TTAGAGTTA-GGGTTAGGGT
73325 TT
1 TT
73327 TTAATTAAAT
Statistics
Matches: 51, Mismatches: 5, Indels: 11
0.76 0.07 0.16
Matches are distributed among these distances:
19 6 0.12
20 33 0.65
21 12 0.24
ACGTcount: A:0.22, C:0.00, G:0.41, T:0.37
Consensus pattern (19 bp):
TTAGAGTTAGGGTTAGGGT
Found at i:73502 original size:7 final size:7
Alignment explanation
Indices: 73492--73516 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
73482 TTATATACAT
73492 AATACTA
1 AATACTA
73499 AATACTA
1 AATACTA
73506 AATACTA
1 AATACTA
73513 AATA
1 AATA
73517 TCAATCGACT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.12, G:0.00, T:0.28
Consensus pattern (7 bp):
AATACTA
Found at i:74385 original size:22 final size:22
Alignment explanation
Indices: 74354--74408 Score: 94
Period size: 22 Copynumber: 2.5 Consensus size: 22
74344 AAATAATGGT
74354 TTGAG-GAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
74375 TTGAGAGAATTTTGGAAGGAAA
1 TTGAGAGAATTTTGGAAGGAAA
74397 TTGAGAGGAATT
1 TTGAGA-GAATT
74409 GAGAGGAAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
21 5 0.16
22 22 0.69
23 5 0.16
ACGTcount: A:0.38, C:0.00, G:0.33, T:0.29
Consensus pattern (22 bp):
TTGAGAGAATTTTGGAAGGAAA
Found at i:74425 original size:12 final size:11
Alignment explanation
Indices: 74369--74425 Score: 57
Period size: 10 Copynumber: 5.2 Consensus size: 11
74359 GAATTTTGGA
74369 AGGAAATTGAG
1 AGGAAATTGAG
*
74380 A-GAATTTTG-G
1 AGGAA-ATTGAG
74390 AAGGAAATTGAG
1 -AGGAAATTGAG
74402 AGG-AATTGAG
1 AGGAAATTGAG
74412 AGGAAATATGAG
1 AGGAAAT-TGAG
74424 AG
1 AG
74426 AGGATTTGTT
Statistics
Matches: 38, Mismatches: 2, Indels: 11
0.75 0.04 0.22
Matches are distributed among these distances:
10 14 0.37
11 14 0.37
12 10 0.26
ACGTcount: A:0.44, C:0.00, G:0.35, T:0.21
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:74651 original size:28 final size:29
Alignment explanation
Indices: 74586--74651 Score: 73
Period size: 28 Copynumber: 2.3 Consensus size: 29
74576 GATTTCGCGG
74586 AAAAAAGGA-CCATTCCGGTAAATAATTA
1 AAAAAAGGACCCATTCCGGTAAATAATTA
* * * **
74614 AATAATGGACCCATTTCGGT-AATTTTTA
1 AAAAAAGGACCCATTCCGGTAAATAATTA
74642 AAAAAAGGAC
1 AAAAAAGGAC
74652 TTTTATTGGT
Statistics
Matches: 30, Mismatches: 7, Indels: 2
0.77 0.18 0.05
Matches are distributed among these distances:
28 21 0.70
29 9 0.30
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (29 bp):
AAAAAAGGACCCATTCCGGTAAATAATTA
Found at i:80688 original size:31 final size:31
Alignment explanation
Indices: 80650--80710 Score: 122
Period size: 31 Copynumber: 2.0 Consensus size: 31
80640 AGACTTTGTA
80650 ACACATCAATGTTCTTTTCCTATGGGATATT
1 ACACATCAATGTTCTTTTCCTATGGGATATT
80681 ACACATCAATGTTCTTTTCCTATGGGATAT
1 ACACATCAATGTTCTTTTCCTATGGGATAT
80711 CCTTTGGGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.26, C:0.20, G:0.13, T:0.41
Consensus pattern (31 bp):
ACACATCAATGTTCTTTTCCTATGGGATATT
Found at i:84313 original size:15 final size:15
Alignment explanation
Indices: 84290--84342 Score: 56
Period size: 15 Copynumber: 3.6 Consensus size: 15
84280 GTGTACTTAA
*
84290 TTCTTGATTTGATAT
1 TTCTAGATTTGATAT
*
84305 TTCTAGA-TT-ATTAA
1 TTCTAGATTTGA-TAT
*
84319 TTCTTGATTTGATAT
1 TTCTAGATTTGATAT
84334 TTCTAGATT
1 TTCTAGATT
84343 ATTAATCCAT
Statistics
Matches: 30, Mismatches: 5, Indels: 6
0.73 0.12 0.15
Matches are distributed among these distances:
13 1 0.03
14 10 0.33
15 18 0.60
16 1 0.03
ACGTcount: A:0.25, C:0.08, G:0.11, T:0.57
Consensus pattern (15 bp):
TTCTAGATTTGATAT
Found at i:84318 original size:29 final size:29
Alignment explanation
Indices: 84286--84348 Score: 126
Period size: 29 Copynumber: 2.2 Consensus size: 29
84276 TTATGTGTAC
84286 TTAATTCTTGATTTGATATTTCTAGATTA
1 TTAATTCTTGATTTGATATTTCTAGATTA
84315 TTAATTCTTGATTTGATATTTCTAGATTA
1 TTAATTCTTGATTTGATATTTCTAGATTA
84344 TTAAT
1 TTAAT
84349 CCATGTTTGA
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 34 1.00
ACGTcount: A:0.29, C:0.06, G:0.10, T:0.56
Consensus pattern (29 bp):
TTAATTCTTGATTTGATATTTCTAGATTA
Found at i:90426 original size:25 final size:25
Alignment explanation
Indices: 90332--90429 Score: 108
Period size: 25 Copynumber: 3.8 Consensus size: 25
90322 AGGTTCAAGT
* *
90332 GAGCCAAT-ATCGAGAAGCTCCGGA
1 GAGCCATTAATCGGGAAGCTCCGGA
* *
90356 GAGCCATTAATCGGGAAGCTCATGAAA
1 GAGCCATTAATCGGGAAGCTC-CG-GA
* *
90383 GAGCCTTTAAATCAGGAAGCTCCGGA
1 GAGCCATT-AATCGGGAAGCTCCGGA
90409 GAGCCATTAATCGGGAAGCTC
1 GAGCCATTAATCGGGAAGCTC
90430 ATAAGAGCTA
Statistics
Matches: 60, Mismatches: 10, Indels: 7
0.78 0.13 0.09
Matches are distributed among these distances:
24 7 0.12
25 23 0.38
26 9 0.15
27 9 0.15
28 12 0.20
ACGTcount: A:0.33, C:0.22, G:0.28, T:0.17
Consensus pattern (25 bp):
GAGCCATTAATCGGGAAGCTCCGGA
Found at i:90436 original size:25 final size:25
Alignment explanation
Indices: 90257--90437 Score: 95
Period size: 25 Copynumber: 7.2 Consensus size: 25
90247 GCTTTCTTTC
*
90257 GAGCCATATAA-CGGGAAGCTCCA-GA
1 GAGCCAT-TAATCGGGAAGCT-CATAA
* *
90282 GAGCCATGTAAT-GGGAAGCTTATAC
1 GAGCCAT-TAATCGGGAAGCTCATAA
* * * *
90307 GAGCCAAT-ATCGAGAAGGTTCA-AGT
1 GAGCCATTAATCGGGAA-GCTCATA-A
* * ***
90332 GAGCCAAT-ATCGAGAAGCTCCGGA
1 GAGCCATTAATCGGGAAGCTCATAA
90356 GAGCCATTAATCGGGAAGCTCATGAAA
1 GAGCCATTAATCGGGAAGCTCAT--AA
* * ***
90383 GAGCCTTTAAATCAGGAAGCTCCGGA
1 GAGCCATT-AATCGGGAAGCTCATAA
90409 GAGCCATTAATCGGGAAGCTCATAA
1 GAGCCATTAATCGGGAAGCTCATAA
90434 GAGC
1 GAGC
90438 TACGATGTGT
Statistics
Matches: 118, Mismatches: 28, Indels: 20
0.71 0.17 0.12
Matches are distributed among these distances:
23 2 0.02
24 17 0.14
25 71 0.60
26 8 0.07
27 8 0.07
28 12 0.10
ACGTcount: A:0.34, C:0.20, G:0.28, T:0.18
Consensus pattern (25 bp):
GAGCCATTAATCGGGAAGCTCATAA
Found at i:90529 original size:25 final size:25
Alignment explanation
Indices: 90497--90559 Score: 117
Period size: 25 Copynumber: 2.5 Consensus size: 25
90487 GAAGAGCTAT
90497 TAACGGGAAGCTCGCAAGAACCATA
1 TAACGGGAAGCTCGCAAGAACCATA
*
90522 TAACGGGAAGCTCGTAAGAACCATA
1 TAACGGGAAGCTCGCAAGAACCATA
90547 TAACGGGAAGCTC
1 TAACGGGAAGCTC
90560 ATGAGAGCTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.38, C:0.22, G:0.25, T:0.14
Consensus pattern (25 bp):
TAACGGGAAGCTCGCAAGAACCATA
Found at i:100456 original size:14 final size:17
Alignment explanation
Indices: 100424--100461 Score: 55
Period size: 14 Copynumber: 2.4 Consensus size: 17
100414 AATTATAAAG
100424 TATATTATTAAATTAAT
1 TATATTATTAAATTAAT
100441 TATATTA-TAAA-T-AT
1 TATATTATTAAATTAAT
100455 TATATTA
1 TATATTA
100462 AAAAATAAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
14 9 0.43
15 1 0.05
16 4 0.19
17 7 0.33
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (17 bp):
TATATTATTAAATTAAT
Found at i:100616 original size:4 final size:4
Alignment explanation
Indices: 100607--100669 Score: 55
Period size: 4 Copynumber: 16.8 Consensus size: 4
100597 TTAGTGAACA
* * *
100607 AAAG AAAG AAA- ACA- AAAG AAAG AAA- CAA- AAAG AAAG AAAG GAA-
1 AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG AAAG
100650 AAAG AAAG AAAG AAAAG AAA
1 AAAG AAAG AAAG -AAAG AAA
100670 AAGGAAAAAC
Statistics
Matches: 49, Mismatches: 6, Indels: 8
0.78 0.10 0.13
Matches are distributed among these distances:
3 10 0.20
4 35 0.71
5 4 0.08
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (4 bp):
AAAG
Found at i:100622 original size:14 final size:13
Alignment explanation
Indices: 100603--100669 Score: 80
Period size: 14 Copynumber: 4.8 Consensus size: 13
100593 TAAATTAGTG
100603 AACAAAAGAAAGAA
1 AACAAAAGAAAG-A
100617 AACAAAAGAAAGA
1 AACAAAAGAAAGA
100630 AACAAAAAGAAAGA
1 AAC-AAAAGAAAGA
*
100644 AAGGAAAAAGAAAGA
1 AA--CAAAAGAAAGA
*
100659 AAGAAAAGAAA
1 AACAAAAGAAA
100670 AAGGAAAAAC
Statistics
Matches: 48, Mismatches: 2, Indels: 7
0.84 0.04 0.12
Matches are distributed among these distances:
13 12 0.25
14 24 0.50
15 12 0.25
ACGTcount: A:0.78, C:0.04, G:0.18, T:0.00
Consensus pattern (13 bp):
AACAAAAGAAAGA
Found at i:100642 original size:28 final size:27
Alignment explanation
Indices: 100606--100678 Score: 87
Period size: 28 Copynumber: 2.7 Consensus size: 27
100596 ATTAGTGAAC
100606 AAAAGAAAGAAA-ACAAAAGAAAGAAACA
1 AAAAGAAAGAAAGA-AAAAGAAAGAAA-A
*
100634 AAAAGAAAGAAAGGAAAAAGAAAGAAAG
1 AAAAGAAAGAAA-GAAAAAGAAAGAAAA
*
100662 AAAAGAAA-AAGGAAAAA
1 AAAAGAAAGAAAGAAAAA
100679 CTAAAGGTTT
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
26 6 0.15
27 2 0.05
28 20 0.49
29 12 0.29
30 1 0.02
ACGTcount: A:0.78, C:0.03, G:0.19, T:0.00
Consensus pattern (27 bp):
AAAAGAAAGAAAGAAAAAGAAAGAAAA
Found at i:100650 original size:19 final size:18
Alignment explanation
Indices: 100607--100672 Score: 77
Period size: 18 Copynumber: 3.8 Consensus size: 18
100597 TTAGTGAACA
100607 AAAGAAAGAAAACA-AAAG
1 AAAGAAAGAAAA-AGAAAG
*
100625 AAAGAAACAAAAAGAAAG
1 AAAGAAAGAAAAAGAAAG
100643 AAAG---GAAAAAGAAAG
1 AAAGAAAGAAAAAGAAAG
100658 AAAGAAAAGAAAAAG
1 AAAG-AAAGAAAAAG
100673 GAAAAACTAA
Statistics
Matches: 41, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
15 14 0.34
17 1 0.02
18 19 0.46
19 7 0.17
ACGTcount: A:0.77, C:0.03, G:0.20, T:0.00
Consensus pattern (18 bp):
AAAGAAAGAAAAAGAAAG
Found at i:101659 original size:23 final size:23
Alignment explanation
Indices: 101632--101719 Score: 121
Period size: 23 Copynumber: 4.0 Consensus size: 23
101622 GGCTTTGCCG
*
101632 ATCAGACACTTTATGTGTCGTAC
1 ATCAGGCACTTTATGTGTCGTAC
101655 ATCAGGCACTTTATGTGTCGTATC
1 ATCAGGCACTTTATGTGTCGTA-C
*
101679 -TCAGGTACTTTATGTGTCGT--
1 ATCAGGCACTTTATGTGTCGTAC
101699 ATCAGGCAC-TTATGTGTCGTA
1 ATCAGGCACTTTATGTGTCGTA
101720 TACTAATCAG
Statistics
Matches: 59, Mismatches: 3, Indels: 8
0.84 0.04 0.11
Matches are distributed among these distances:
20 11 0.19
21 7 0.12
23 40 0.68
24 1 0.02
ACGTcount: A:0.22, C:0.19, G:0.22, T:0.38
Consensus pattern (23 bp):
ATCAGGCACTTTATGTGTCGTAC
Found at i:123149 original size:6 final size:6
Alignment explanation
Indices: 123140--123176 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
123130 AAATTACACA
123140 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT T
1 TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT TTTTAT T
123177 CCTTCTATTC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 31 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTAT
Found at i:124591 original size:12 final size:12
Alignment explanation
Indices: 124563--124603 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
124553 TCAAGTCATA
*
124563 AATCAAGTCTTC
1 AATCAAGTTTTC
124575 AATCAAGTTTTC
1 AATCAAGTTTTC
* *
124587 CATCAAGTTTTT
1 AATCAAGTTTTC
124599 AATCA
1 AATCA
124604 TAAAGTTTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
12 25 1.00
ACGTcount: A:0.34, C:0.20, G:0.07, T:0.39
Consensus pattern (12 bp):
AATCAAGTTTTC
Found at i:134039 original size:16 final size:17
Alignment explanation
Indices: 134011--134044 Score: 61
Period size: 16 Copynumber: 2.1 Consensus size: 17
134001 AGACAGGACA
134011 AATCAATAATGATTCTT
1 AATCAATAATGATTCTT
134028 AATCAA-AATGATTCTT
1 AATCAATAATGATTCTT
134044 A
1 A
134045 CATGATAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.65
17 6 0.35
ACGTcount: A:0.44, C:0.12, G:0.06, T:0.38
Consensus pattern (17 bp):
AATCAATAATGATTCTT
Found at i:137939 original size:13 final size:15
Alignment explanation
Indices: 137916--137948 Score: 52
Period size: 14 Copynumber: 2.3 Consensus size: 15
137906 ATTTTAACAA
137916 ATTTTCTTAAAA-TT
1 ATTTTCTTAAAAGTT
137930 ATTTTC-TAAAAGTT
1 ATTTTCTTAAAAGTT
137944 ATTTT
1 ATTTT
137949 TAATTAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 5 0.28
14 13 0.72
ACGTcount: A:0.33, C:0.06, G:0.03, T:0.58
Consensus pattern (15 bp):
ATTTTCTTAAAAGTT
Found at i:138310 original size:17 final size:17
Alignment explanation
Indices: 138288--138323 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
138278 GTTATTATTA
138288 AAATAAAATATTAAATT
1 AAATAAAATATTAAATT
**
138305 AAATAATTTATTAAATT
1 AAATAAAATATTAAATT
138322 AA
1 AA
138324 TAATTATTTA
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:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (17 bp):
AAATAAAATATTAAATT
Found at i:138328 original size:24 final size:26
Alignment explanation
Indices: 138301--138359 Score: 77
Period size: 24 Copynumber: 2.3 Consensus size: 26
138291 TAAAATATTA
138301 AATTAAATAATTTATTAAAT-T-AAT
1 AATTAAATAATTTATTAAATATAAAT
** *
138325 AATTATTTATTTTATTAAATATAAAT
1 AATTAAATAATTTATTAAATATAAAT
138351 AATTAAATA
1 AATTAAATA
138360 TGTATGTTTA
Statistics
Matches: 28, Mismatches: 5, Indels: 2
0.80 0.14 0.06
Matches are distributed among these distances:
24 17 0.61
25 1 0.04
26 10 0.36
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (26 bp):
AATTAAATAATTTATTAAATATAAAT
Found at i:139082 original size:25 final size:24
Alignment explanation
Indices: 139054--139101 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
139044 TTTTTGTATT
139054 CTCAATAAAA-TGTAAAAAATAAAAA
1 CTCAATAAAACT-T-AAAAATAAAAA
*
139079 CTCATTAAAACTTAAAAATAAAA
1 CTCAATAAAACTTAAAAATAAAA
139102 TATATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 10 0.48
25 10 0.48
26 1 0.05
ACGTcount: A:0.65, C:0.10, G:0.02, T:0.23
Consensus pattern (24 bp):
CTCAATAAAACTTAAAAATAAAAA
Found at i:140212 original size:25 final size:24
Alignment explanation
Indices: 140184--140231 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 24
140174 TTTTTGTATT
140184 CTCAATAAAA-TGTAAAAAATAAAAA
1 CTCAATAAAACT-T-AAAAATAAAAA
*
140209 CTCATTAAAACTTAAAAATAAAA
1 CTCAATAAAACTTAAAAATAAAA
140232 TATATAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
24 10 0.48
25 10 0.48
26 1 0.05
ACGTcount: A:0.65, C:0.10, G:0.02, T:0.23
Consensus pattern (24 bp):
CTCAATAAAACTTAAAAATAAAAA
Found at i:145256 original size:32 final size:32
Alignment explanation
Indices: 145215--145279 Score: 121
Period size: 32 Copynumber: 2.0 Consensus size: 32
145205 ACATTTTGCA
*
145215 ACAAAGATGGATAGCTCCAAAGGGCCAAAACT
1 ACAAAGATGGATAGCTCCAAAGGACCAAAACT
145247 ACAAAGATGGATAGCTCCAAAGGACCAAAACT
1 ACAAAGATGGATAGCTCCAAAGGACCAAAACT
145279 A
1 A
145280 GTGACTAAGC
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 32 1.00
ACGTcount: A:0.46, C:0.22, G:0.20, T:0.12
Consensus pattern (32 bp):
ACAAAGATGGATAGCTCCAAAGGACCAAAACT
Found at i:149114 original size:22 final size:22
Alignment explanation
Indices: 149086--149146 Score: 79
Period size: 22 Copynumber: 2.8 Consensus size: 22
149076 GATTTTTACA
*
149086 ATAAAGAATTGATTCAAACAAC
1 ATAAAGAATCGATTCAAACAAC
* *
149108 ATAAAGAATCGAGTCAATCAAC
1 ATAAAGAATCGATTCAAACAAC
*
149130 A-AAATAATCGATTCAAA
1 ATAAAGAATCGATTCAAA
149147 TAAGCAAATA
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
21 13 0.39
22 20 0.61
ACGTcount: A:0.54, C:0.15, G:0.10, T:0.21
Consensus pattern (22 bp):
ATAAAGAATCGATTCAAACAAC
Found at i:153987 original size:32 final size:31
Alignment explanation
Indices: 153951--154012 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
153941 ATATTACAAA
*
153951 ATTAAAAGTATATAAAAAACTAAA-AAAAATAG
1 ATTAAAA-T-TATAAAAAAATAAATAAAAATAG
*
153983 ATTAAAATTGTAAAAAAATAAATAAAAATA
1 ATTAAAATTATAAAAAAATAAATAAAAATA
154013 AAAAATTCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
30 12 0.44
31 8 0.30
32 7 0.26
ACGTcount: A:0.69, C:0.02, G:0.05, T:0.24
Consensus pattern (31 bp):
ATTAAAATTATAAAAAAATAAATAAAAATAG
Found at i:154476 original size:20 final size:20
Alignment explanation
Indices: 154434--154476 Score: 50
Period size: 20 Copynumber: 2.1 Consensus size: 20
154424 GCTTTTTATT
* * *
154434 TTTATTTTTATTTTTTTAAA
1 TTTATTTTTAATATTCTAAA
*
154454 TTTATTTTTAATATTCTAGA
1 TTTATTTTTAATATTCTAAA
154474 TTT
1 TTT
154477 TTAAGAATTG
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.26, C:0.02, G:0.02, T:0.70
Consensus pattern (20 bp):
TTTATTTTTAATATTCTAAA
Found at i:157331 original size:21 final size:20
Alignment explanation
Indices: 157299--157339 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
157289 CATCATCAAA
157299 CCTTTTTCAATT-TCACATTT
1 CCTTTTTCAATTAT-ACATTT
157319 CCTTTTCTCAATTATACATTT
1 CCTTTT-TCAATTATACATTT
157340 AATTTTCAAT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
20 6 0.32
21 12 0.63
22 1 0.05
ACGTcount: A:0.22, C:0.24, G:0.00, T:0.54
Consensus pattern (20 bp):
CCTTTTTCAATTATACATTT
Found at i:158267 original size:25 final size:26
Alignment explanation
Indices: 158239--158289 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
158229 GTCATCTCTG
*
158239 TTTTTCAATTAGTA-TTTATATAATA
1 TTTTTAAATTAGTAGTTTATATAATA
* *
158264 TTTTTAAATTATTAGTTTATTTAATA
1 TTTTTAAATTAGTAGTTTATATAATA
158290 ATTCCAATAT
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.35, C:0.02, G:0.04, T:0.59
Consensus pattern (26 bp):
TTTTTAAATTAGTAGTTTATATAATA
Found at i:160284 original size:34 final size:33
Alignment explanation
Indices: 160246--160330 Score: 89
Period size: 34 Copynumber: 2.5 Consensus size: 33
160236 AATAATACAA
* * *
160246 TAGCAAACAATATGCTTATAACAGTTCGATTCAG
1 TAGCAAA-AATATGCTTATAACAGATCAACTCAG
* * *
160280 TAGCAATTAATATGCTTATGATAGATCAACTCAG
1 TAGCAA-AAATATGCTTATAACAGATCAACTCAG
160314 TAGCAAAAATAATGCTT
1 TAGCAAAAAT-ATGCTT
160331 TTTATGTATT
Statistics
Matches: 42, Mismatches: 7, Indels: 4
0.79 0.13 0.08
Matches are distributed among these distances:
33 3 0.07
34 39 0.93
ACGTcount: A:0.40, C:0.15, G:0.14, T:0.31
Consensus pattern (33 bp):
TAGCAAAAATATGCTTATAACAGATCAACTCAG
Found at i:161217 original size:9 final size:9
Alignment explanation
Indices: 161190--161241 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
161180 ATTTTGATGT
161190 AAAAGAGAG
1 AAAAGAGAG
*
161199 GAAAGAAGAG
1 AAAAG-AGAG
161209 AAAAGAGAG
1 AAAAGAGAG
*
161218 AAGAAATAGAG
1 -A-AAAGAGAG
*
161229 AAAAGAAAG
1 AAAAGAGAG
161238 AAAA
1 AAAA
161242 TCCTATTTGA
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
9 18 0.51
10 10 0.29
11 7 0.20
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (9 bp):
AAAAGAGAG
Found at i:161283 original size:29 final size:28
Alignment explanation
Indices: 161228--161283 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
161218 AAGAAATAGA
* * *
161228 GAAAAGAAAGAAAATCCTATTTGAATTT
1 GAAAAGAAACAAAATCCTAGTTCAATTT
161256 GAAAAGAAAACAAAATCCTAGTTCAATT
1 GAAAAG-AAACAAAATCCTAGTTCAATT
161284 GGGGAAAGTT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 6 0.25
29 18 0.75
ACGTcount: A:0.52, C:0.11, G:0.12, T:0.25
Consensus pattern (28 bp):
GAAAAGAAACAAAATCCTAGTTCAATTT
Found at i:161378 original size:13 final size:13
Alignment explanation
Indices: 161360--161389 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
161350 TTTTGGGTCG
161360 AAATTTAAAAGAA
1 AAATTTAAAAGAA
*
161373 AAATTTAAGAGAA
1 AAATTTAAAAGAA
161386 AAAT
1 AAAT
161390 AAAAGGAACA
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:0.67, C:0.00, G:0.10, T:0.23
Consensus pattern (13 bp):
AAATTTAAAAGAA
Found at i:162171 original size:23 final size:24
Alignment explanation
Indices: 162122--162173 Score: 70
Period size: 24 Copynumber: 2.2 Consensus size: 24
162112 AAAAATTATT
* *
162122 TAAAAAATCATAAAGACAATATTA
1 TAAAAAATCATAAAGAAAATATAA
*
162146 TAAAAAATCATAAA-AAAATCTAA
1 TAAAAAATCATAAAGAAAATATAA
162169 TAAAA
1 TAAAA
162174 TTTGAAGTTT
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
23 11 0.44
24 14 0.56
ACGTcount: A:0.67, C:0.08, G:0.02, T:0.23
Consensus pattern (24 bp):
TAAAAAATCATAAAGAAAATATAA
Found at i:165415 original size:43 final size:43
Alignment explanation
Indices: 165367--165452 Score: 120
Period size: 43 Copynumber: 2.0 Consensus size: 43
165357 TCATATTTCA
*
165367 TTTCTCATCTCATAATCATTTCTCATC-TTTGCCATTTCAATAT
1 TTTCTCATCTCATAATCATTTCTCACCATTT-CCATTTCAATAT
** *
165410 TTTCTCATCTCATTTTCATTTCTCGCCATTTCCATTTCAATAT
1 TTTCTCATCTCATAATCATTTCTCACCATTTCCATTTCAATAT
165453 CAATCACATA
Statistics
Matches: 38, Mismatches: 4, Indels: 2
0.86 0.09 0.05
Matches are distributed among these distances:
43 35 0.92
44 3 0.08
ACGTcount: A:0.21, C:0.27, G:0.02, T:0.50
Consensus pattern (43 bp):
TTTCTCATCTCATAATCATTTCTCACCATTTCCATTTCAATAT
Found at i:168523 original size:12 final size:12
Alignment explanation
Indices: 168506--168561 Score: 51
Period size: 12 Copynumber: 4.8 Consensus size: 12
168496 AATTGAGACT
168506 GAAATGAGAATG
1 GAAATGAGAATG
* *
168518 GAAATGAGAGTA
1 GAAATGAGAATG
*
168530 GAAATGA-AATT
1 GAAATGAGAATG
* *
168541 GATATGAGAAAG
1 GAAATGAGAATG
*
168553 AAAATGAGA
1 GAAATGAGA
168562 TTGATTATGA
Statistics
Matches: 34, Mismatches: 9, Indels: 2
0.76 0.20 0.04
Matches are distributed among these distances:
11 8 0.24
12 26 0.76
ACGTcount: A:0.54, C:0.00, G:0.29, T:0.18
Consensus pattern (12 bp):
GAAATGAGAATG
Found at i:168525 original size:23 final size:23
Alignment explanation
Indices: 168499--168549 Score: 59
Period size: 23 Copynumber: 2.2 Consensus size: 23
168489 GAATATGAAT
168499 TGAGACT-GAAATGAGAATGGAAA
1 TGAGACTAGAAATGA-AATGGAAA
* * *
168522 TGAGAGTAGAAATGAAATTGATA
1 TGAGACTAGAAATGAAATGGAAA
168545 TGAGA
1 TGAGA
168550 AAGAAAATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
23 17 0.71
24 7 0.29
ACGTcount: A:0.47, C:0.02, G:0.29, T:0.22
Consensus pattern (23 bp):
TGAGACTAGAAATGAAATGGAAA
Found at i:171550 original size:83 final size:84
Alignment explanation
Indices: 171458--171624 Score: 257
Period size: 86 Copynumber: 2.0 Consensus size: 84
171448 GAGAGAGAAA
* *
171458 ATCAAGTTAAAGTCTGAAA-CTAATAGGACAAGGT-AACATCAAGATTTCAATATATTTTTAAGT
1 ATCAAGTTAAAGTCTGAAATC-AATAGGACAAGGTAAACATCAAAATTTCAATATATTTTTAAGC
171521 TTGATATTATTGAAAAAGCT
65 TTGATATTATTGAAAAAGCT
*
171541 ATCAAGTTAAAGTTTGAAATCAATAGGACAAGGTAAGAACATCAAAATTTCAATATATTTTTAAG
1 ATCAAGTTAAAGTCTGAAATCAATAGGACAAGGT-A-AACATCAAAATTTCAATATATTTTTAAG
*
171606 CTTGATATTATTTAAAAAG
64 CTTGATATTATTGAAAAAG
171625 AATGAAATTG
Statistics
Matches: 76, Mismatches: 4, Indels: 5
0.89 0.05 0.06
Matches are distributed among these distances:
83 31 0.41
84 1 0.01
86 44 0.58
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.34
Consensus pattern (84 bp):
ATCAAGTTAAAGTCTGAAATCAATAGGACAAGGTAAACATCAAAATTTCAATATATTTTTAAGCT
TGATATTATTGAAAAAGCT
Found at i:174107 original size:146 final size:146
Alignment explanation
Indices: 173860--174126 Score: 367
Period size: 146 Copynumber: 1.8 Consensus size: 146
173850 TCCATGCTAA
* * * * *
173860 TTGTATATATTATAATCTACTATAAAGTTAATTACACGTTTAGAGTTTAATGTTGCGTATCATTA
1 TTGTATATATTATAATATACCATAAAGTTAATTACACATTTAGAGTTTAATGTTACATATCATTA
* * *
173925 ATATAAAAATATACATTATAATATCATAATTTTATATAGGAT-TACATATTATTAATAATGTATC
66 ATATAAAAATATACATTATAATAGCATAACTATATATA-GATCTACATATTATTAATAATGTATC
173989 TTAATTATATATGTTTG
130 TTAATTATATATGTTTG
* * * * *
174006 TTGTATATATTATAATATACCATACAGTTAGTTATACATTTAGGGTTTAA-GCTTACATCTCATT
1 TTGTATATATTATAATATACCATAAAGTTAATTACACATTTAGAGTTTAATG-TTACATATCATT
* *
174070 AATGTAAAAATATACATTATAATAGCATACCTATATATAGATCTACATATTATTAAT
65 AATATAAAAATATACATTATAATAGCATAACTATATATAGATCTACATATTATTAAT
174127 CTACCTGAAT
Statistics
Matches: 104, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
145 4 0.04
146 100 0.96
ACGTcount: A:0.39, C:0.09, G:0.09, T:0.43
Consensus pattern (146 bp):
TTGTATATATTATAATATACCATAAAGTTAATTACACATTTAGAGTTTAATGTTACATATCATTA
ATATAAAAATATACATTATAATAGCATAACTATATATAGATCTACATATTATTAATAATGTATCT
TAATTATATATGTTTG
Found at i:175995 original size:21 final size:21
Alignment explanation
Indices: 175962--176026 Score: 84
Period size: 21 Copynumber: 3.3 Consensus size: 21
175952 ATTACAAAAT
*
175962 CATATC-T-TCTAAGATTGCG
1 CATATCATATCTAAGATTGCA
175981 CATATCATATCTAAGATTGCA
1 CATATCATATCTAAGATTGCA
*
176002 TATATCATATCTAAGATT--A
1 CATATCATATCTAAGATTGCA
176021 CATATC
1 CATATC
176027 CTTGAAGATT
Statistics
Matches: 41, Mismatches: 3, Indels: 4
0.85 0.06 0.08
Matches are distributed among these distances:
19 12 0.29
20 1 0.02
21 28 0.68
ACGTcount: A:0.35, C:0.18, G:0.09, T:0.37
Consensus pattern (21 bp):
CATATCATATCTAAGATTGCA
Found at i:176524 original size:44 final size:44
Alignment explanation
Indices: 176469--176798 Score: 139
Period size: 44 Copynumber: 7.6 Consensus size: 44
176459 GATCTACTCT
* *
176469 ACTGCAACTTCAGAGAGATAAGATCT-GTGGTTTTAATCCGCTCC
1 ACTGCAACTTCAGAGAGATAAGAT-TAGTGGCTTTAATCCGCTCA
* * * * *
176513 ACTGCAGCTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCA
1 ACTGCAACTTCAGAGAGATAAGATTAGTGGCTTTAATCCGCTCA
* *** * *
176557 ACTGCAACTTCA-AGGAGATAAGATTCGCCATCTTCAGT-CGACCTC-
1 ACTGCAACTTCAGA-GAGATAAGATTAG-TGGCTTTAATCCG--CTCA
** * * *
176602 ACTGCAACTTCAG-GAGGATAAGACTT-GATTAC-TTAGTCTGCTCC
1 ACTGCAACTTCAGAGA-GATAAGA-TTAG-TGGCTTTAATCCGCTCA
* * * *
176646 ACTGGAACTTCA-AGGAGATAAGACTAGAT-GC---GATCTGCTC-
1 ACTGCAACTTCAGA-GAGATAAGATTAG-TGGCTTTAATCCGCTCA
* *** * *
176686 TCTGCAACTTCAGAGAGATAAGATCT-GTTATTTTAATCCGTTCC
1 ACTGCAACTTCAGAGAGATAAGAT-TAGTGGCTTTAATCCGCTCA
* * * * * *
176730 ACTGTAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCC
1 ACTGCAACTTCAGAGAGATAAGATTAGTGGCTTTAATCCGCTCA
* *
176774 ACTGTAACTTCAGGGAGATAAGATT
1 ACTGCAACTTCAGAGAGATAAGATT
176799 CTCTATCTTC
Statistics
Matches: 217, Mismatches: 48, Indels: 42
0.71 0.16 0.14
Matches are distributed among these distances:
39 1 0.00
40 20 0.09
41 9 0.04
43 13 0.06
44 140 0.65
45 29 0.13
46 5 0.02
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.30
Consensus pattern (44 bp):
ACTGCAACTTCAGAGAGATAAGATTAGTGGCTTTAATCCGCTCA
Found at i:176704 original size:217 final size:219
Alignment explanation
Indices: 176373--176812 Score: 643
Period size: 217 Copynumber: 2.0 Consensus size: 219
176363 TTGTTTTTTT
* * * * * *
176373 AGTCTACCCCACTGCAATTTTAGGGGGATAAGACTTGCTTTCTTGAGTCTACTCCACTGCAACTT
1 AGTCGACCCCACTGCAACTTCAGGAGGATAAGACTTGATTACTTGAGTCTACTCCACTGCAACTT
* * *
176438 CAGGGAGATAAGACCCAATGTGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTGGTTTT
66 CAAGGAGATAAGACCCAATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTT
*
176503 AATCCGCTCCACTGCAGCTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCAACTGCAACTTC
131 AATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCAACTGCAACTTC
176568 AAGGAGATAAGATTCGCCATCTTC
196 AAGGAGATAAGATTCGCCATCTTC
* * *
176592 AGTCGACCTCACTGCAACTTCAGGAGGATAAGACTTGATTACTT-AGTCTGCTCCACTGGAACTT
1 AGTCGACCCCACTGCAACTTCAGGAGGATAAGACTTGATTACTTGAGTCTACTCCACTGCAACTT
* * *
176656 CAAGGAGATAAGA-CTAGATGCGATCTGCTCT-CTGCAACTTCAGAGAGATAAGATCTGTTATTT
66 CAAGGAGATAAGACCCA-ATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTT
* * * *
176719 TAATCCGTTCCACTGTAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCCACTGTAACTT
130 TAATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCAACTGCAACTT
* * *
176784 CAGGGAGATAAGATTCTCTATCTTC
195 CAAGGAGATAAGATTCGCCATCTTC
176809 AGTC
1 AGTC
176813 TTTTAAATTG
Statistics
Matches: 197, Mismatches: 23, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
217 118 0.60
218 42 0.21
219 37 0.19
ACGTcount: A:0.27, C:0.22, G:0.20, T:0.30
Consensus pattern (219 bp):
AGTCGACCCCACTGCAACTTCAGGAGGATAAGACTTGATTACTTGAGTCTACTCCACTGCAACTT
CAAGGAGATAAGACCCAATGCGATCTACTCTACTGCAACTTCAGAGAGATAAGATCTGTGATTTT
AATCCGCTCCACTGCAACTTCAGGGAGATAGGATTATTGGCTTTAATCTGCTCAACTGCAACTTC
AAGGAGATAAGATTCGCCATCTTC
Found at i:177237 original size:44 final size:43
Alignment explanation
Indices: 177163--177280 Score: 157
Period size: 44 Copynumber: 2.7 Consensus size: 43
177153 ATATGCTATT
* * *
177163 TTCAACCTACTCCATTGTTGCTCAGGGAGATAGGA-TTCACAATC
1 TTCAACCTATTCCACTGCTGC-CAGGGAGATAGGACTT-ACAATC
*
177207 TTCAACCTATTCCACTGCTGACCAGAGAGATAGGACTTACAATC
1 TTCAACCTATTCCACTGCTG-CCAGGGAGATAGGACTTACAATC
177251 TTCAACCTATTCCACTGCTGTCCAGGGAGA
1 TTCAACCTATTCCACTGCTG-CCAGGGAGA
177281 AAGGGCTGGG
Statistics
Matches: 66, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
44 63 0.95
45 3 0.05
ACGTcount: A:0.28, C:0.27, G:0.18, T:0.27
Consensus pattern (43 bp):
TTCAACCTATTCCACTGCTGCCAGGGAGATAGGACTTACAATC
Found at i:177372 original size:44 final size:43
Alignment explanation
Indices: 177322--177548 Score: 134
Period size: 44 Copynumber: 5.2 Consensus size: 43
177312 CGGTGTAGGA
177322 AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCAGAG
1 AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCAG-G
* * * * * * * * *****
177366 AGGCAAG-GCTGGTGTCTTCAATCTGCTTCACTGTCGGTGTAGG
1 AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTG-CAACCCAGG
*
177409 AAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAACCCAGGG
1 -AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA-GG
* * * * * * * * ****
177454 AGGCAAGGT-TGGTGTCTTCAATCTGCTTCACTGTCGGTGCAGG
1 AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTG-CAACCCAGG
*
177497 AAGGCAAGATCTGCTATTTTTAACCTGCTCCGCTACAACCCAGGG
1 -AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCA-GG
177542 AGGCAAG
1 AGGCAAG
177549 GCTGGTGTCT
Statistics
Matches: 122, Mismatches: 53, Indels: 16
0.64 0.28 0.08
Matches are distributed among these distances:
43 37 0.30
44 48 0.39
45 37 0.30
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.26
Consensus pattern (43 bp):
AGGCAAGATCTGCTATTTTTAACCTGCTCCGCTGCAACCCAGG
Found at i:177404 original size:88 final size:88
Alignment explanation
Indices: 177284--177689 Score: 616
Period size: 88 Copynumber: 4.6 Consensus size: 88
177274 AGGGAGAAAG
* * *
177284 GGCTGGGGTCATCAATCTGCTTCACTGTCGGTGTAGGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCAATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
*
177349 TCCGCTGCAACCCAGAGAGGCAA
66 TCCGCTACAACCCAGAGAGGCAA
*
177372 GGCTGGTGTCTTCAATCTGCTTCACTGTCGGTGTAGGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCAATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
*
177437 TCCGCTACAACCCAGGGAGGCAA
66 TCCGCTACAACCCAGAGAGGCAA
*
177460 GGTTGGTGTCTTCAATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
1 GGCTGGTGTCTTCAATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
*
177525 TCCGCTACAACCCAGGGAGGCAA
66 TCCGCTACAACCCAGAGAGGCAA
* * * * ** * *
177548 GGCTGGTGTCTTCGATATGCTTCGCTGTCGGTGCAAGAAAACAATATCTG-TAATTTTTAACCTA
1 GGCTGGTGTCTTCAATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCT-ATTTTTAACCTG
* *
177612 CTCCGCTGCAACCTAGAGAGGCAA
65 CTCCGCTACAACCCAGAGAGGCAA
* *
177636 GGCTGGTGTCTTCAATCTGCTTCACTGTCGGTGCAAGAAGGCAAGATTTGCTAT
1 GGCTGGTGTCTTCAATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTAT
177690 CTTCACTGAT
Statistics
Matches: 291, Mismatches: 25, Indels: 4
0.91 0.08 0.01
Matches are distributed among these distances:
87 1 0.00
88 289 0.99
89 1 0.00
ACGTcount: A:0.23, C:0.24, G:0.26, T:0.28
Consensus pattern (88 bp):
GGCTGGTGTCTTCAATCTGCTTCACTGTCGGTGCAGGAAGGCAAGATCTGCTATTTTTAACCTGC
TCCGCTACAACCCAGAGAGGCAA
Found at i:179837 original size:25 final size:26
Alignment explanation
Indices: 179786--179846 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
179776 AAGAAAATCC
* **
179786 AAAAGAATGAAAGAATAATTATTTCA
1 AAAAGAATGAAAAAATAATTAGCTCA
*
179812 AAAAGAATGAAAAAAT-ATTGGCTCA
1 AAAAGAATGAAAAAATAATTAGCTCA
179837 AAAATGAATG
1 AAAA-GAATG
179847 CAAAGATGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 10 0.33
26 20 0.67
ACGTcount: A:0.57, C:0.05, G:0.15, T:0.23
Consensus pattern (26 bp):
AAAAGAATGAAAAAATAATTAGCTCA
Found at i:181019 original size:176 final size:176
Alignment explanation
Indices: 180725--184269 Score: 7081
Period size: 176 Copynumber: 20.1 Consensus size: 176
180715 GACCCCCCCC
180725 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
1 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
180790 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
66 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
180855 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
131 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
180901 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
1 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
180966 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
66 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
181031 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
131 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
181077 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
1 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
181142 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
66 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
181207 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
131 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
181253 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
1 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
181318 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
66 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
181383 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
131 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
181429 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
1 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
181494 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
66 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
181559 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
131 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
181605 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
1 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
181670 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
66 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
181735 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
131 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
181781 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
1 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
181846 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
66 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
181911 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
131 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
181957 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
1 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
182022 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
66 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
182087 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
131 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
182133 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
1 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
182198 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
66 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
182263 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
131 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
182309 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
1 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
182374 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
66 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
182439 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
131 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
182485 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
1 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
182550 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
66 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
182615 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
131 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
182661 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
1 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
182726 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
66 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
182791 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
131 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
182837 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
1 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
182902 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
66 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
182967 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
131 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
183013 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
1 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
183078 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
66 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
183143 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
131 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
183189 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
1 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
183254 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
66 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
183319 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
131 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
183365 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
1 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
183430 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
66 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
183495 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
131 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
183541 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
1 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
183606 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
66 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
183671 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
131 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
183717 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
1 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
183782 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
66 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
183847 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
131 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
183893 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
1 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
183958 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
66 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
184023 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
131 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
184069 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
1 CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
184134 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
66 GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
184199 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
131 CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
*
184245 CTGTCGGTGCAGAAAGGCAAGATCT
1 CTGTCGGTGCAGGAAGGCAAGATCT
184270 ATTATCTTCA
Statistics
Matches: 3368, Mismatches: 1, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
176 3368 1.00
ACGTcount: A:0.22, C:0.24, G:0.26, T:0.27
Consensus pattern (176 bp):
CTGTCGGTGCAGGAAGGCAAGATCTTCTATTTTTAACCTGCTCCGCTGCAACCCAGGGAGGCAAG
GCTAGTGTCTTCGATCTGCTTCGCTATCGGTGCAAGAAGGCAAGATCTGCAATTTTTAACTTGCT
CCGCTACAACTCAGGGAAGCAAGGTTGGTGACTTCGATCTGCTTCG
Found at i:186416 original size:25 final size:26
Alignment explanation
Indices: 186365--186425 Score: 70
Period size: 26 Copynumber: 2.3 Consensus size: 26
186355 AAGAAAATCC
* **
186365 AAAAGAATGAAAGAATAATTATTTCA
1 AAAAGAATGAAAAAATAATTAGCTCA
*
186391 AAAAGAATGAAAAAAT-ATTGGCTCA
1 AAAAGAATGAAAAAATAATTAGCTCA
186416 AAAATGAATG
1 AAAA-GAATG
186426 CAAAGATGTA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
25 10 0.33
26 20 0.67
ACGTcount: A:0.57, C:0.05, G:0.15, T:0.23
Consensus pattern (26 bp):
AAAAGAATGAAAAAATAATTAGCTCA
Found at i:192316 original size:23 final size:23
Alignment explanation
Indices: 192290--192334 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
192280 AAGAGATTTG
* *
192290 AAATCAACAATATACAAATCAAT
1 AAATAAACAATACACAAATCAAT
**
192313 AAATAAATTATACACAAATCAA
1 AAATAAACAATACACAAATCAA
192335 CAAAATAAGA
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.62, C:0.16, G:0.00, T:0.22
Consensus pattern (23 bp):
AAATAAACAATACACAAATCAAT
Found at i:192565 original size:19 final size:19
Alignment explanation
Indices: 192518--192632 Score: 131
Period size: 19 Copynumber: 5.8 Consensus size: 19
192508 AAATTAAATC
*
192518 TCTAAGATTACAAAATCATA
1 TCTAAGATTAC-ATATCATA
*
192538 TCTTCTAAGATTGCATATCATA
1 ---TCTAAGATTACATATCATA
*
192560 TCTAAGATTACACATCATA
1 TCTAAGATTACATATCATA
*
192579 TCTAAGATTGCATATCATA
1 TCTAAGATTACATATCATA
**
192598 TCTAAGATTACATATTGTA
1 TCTAAGATTACATATCATA
*
192617 TCTAAGATTCCATATC
1 TCTAAGATTACATATC
192633 CTTGAAGATT
Statistics
Matches: 81, Mismatches: 11, Indels: 4
0.84 0.11 0.04
Matches are distributed among these distances:
19 64 0.79
22 7 0.09
23 10 0.12
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (19 bp):
TCTAAGATTACATATCATA
Found at i:192590 original size:38 final size:38
Alignment explanation
Indices: 192518--192632 Score: 149
Period size: 38 Copynumber: 2.9 Consensus size: 38
192508 AAATTAAATC
192518 TCTAAGATTACAAAATCATATCTTCTAAGATTGCATATCATA
1 TCTAAGATTAC-AAATCATA---TCTAAGATTGCATATCATA
*
192560 TCTAAGATTACACATCATATCTAAGATTGCATATCATA
1 TCTAAGATTACAAATCATATCTAAGATTGCATATCATA
* ** *
192598 TCTAAGATTACATATTGTATCTAAGATTCCATATC
1 TCTAAGATTACAAATCATATCTAAGATTGCATATC
192633 CTTGAAGATT
Statistics
Matches: 68, Mismatches: 5, Indels: 4
0.88 0.06 0.05
Matches are distributed among these distances:
38 50 0.74
41 7 0.10
42 11 0.16
ACGTcount: A:0.38, C:0.17, G:0.08, T:0.37
Consensus pattern (38 bp):
TCTAAGATTACAAATCATATCTAAGATTGCATATCATA
Found at i:198168 original size:21 final size:21
Alignment explanation
Indices: 198137--198194 Score: 59
Period size: 21 Copynumber: 2.8 Consensus size: 21
198127 TAAAAAGTAA
198137 TAAAATAAATAATACATTAAAT
1 TAAAA-AAATAATACATTAAAT
*
198159 TAAAAAAATAACT-C-TTAATT
1 TAAAAAAATAA-TACATTAAAT
198179 TAAAGAAAATAA-ACAT
1 TAAA-AAAATAATACAT
198195 AATTATCTAA
Statistics
Matches: 31, Mismatches: 1, Indels: 9
0.76 0.02 0.22
Matches are distributed among these distances:
20 10 0.32
21 15 0.48
22 6 0.19
ACGTcount: A:0.62, C:0.07, G:0.02, T:0.29
Consensus pattern (21 bp):
TAAAAAAATAATACATTAAAT
Found at i:198197 original size:20 final size:20
Alignment explanation
Indices: 198137--198198 Score: 54
Period size: 20 Copynumber: 3.0 Consensus size: 20
198127 TAAAAAGTAA
* *
198137 TAAAATAAATAATACATTAAAT
1 TAAAA-AAATAACACA-TAATT
* *
198159 TAAAAAAATAACTCTTAATT
1 TAAAAAAATAACACATAATT
198179 TAAAGAAAATAA-ACATAATT
1 TAAA-AAAATAACACATAATT
198199 ATCTAAAAAA
Statistics
Matches: 33, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
20 14 0.42
21 14 0.42
22 5 0.15
ACGTcount: A:0.61, C:0.06, G:0.02, T:0.31
Consensus pattern (20 bp):
TAAAAAAATAACACATAATT
Found at i:202308 original size:1 final size:1
Alignment explanation
Indices: 202302--202332 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
202292 GACCATTCCC
202302 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
202333 CGTTTAGCGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:202445 original size:103 final size:104
Alignment explanation
Indices: 202265--202472 Score: 364
Period size: 103 Copynumber: 2.0 Consensus size: 104
202255 GCGTTTGGTG
* * * *
202265 TGGGGAGTTGACTTCAACAAGACTTGAGACCATTCCCTTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TGGGGAGTTGACTTCAACAAGACTTGAGACCATTCCCTTTTTTTTTTTTTTTTCTTCTTCTTCTT
*
202330 TTTCGTTTAGCGATAAATAGTTTAATCCCATGTTGTCTC
66 CTTCGTTTAGCGATAAATAGTTTAATCCCATGTTGTCTC
202369 TGGGGAGTTGA-TTCAACAAGACTTGAGACCATTCCCTTTTTTTTTTTTTTTTCTTCTTCTTCTT
1 TGGGGAGTTGACTTCAACAAGACTTGAGACCATTCCCTTTTTTTTTTTTTTTTCTTCTTCTTCTT
202433 CTTCGTTTAGCGATAAATAGTTTAATCCCATGTTGTCTC
66 CTTCGTTTAGCGATAAATAGTTTAATCCCATGTTGTCTC
202472 T
1 T
202473 CCATTTTCTA
Statistics
Matches: 99, Mismatches: 5, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
103 88 0.89
104 11 0.11
ACGTcount: A:0.18, C:0.17, G:0.14, T:0.50
Consensus pattern (104 bp):
TGGGGAGTTGACTTCAACAAGACTTGAGACCATTCCCTTTTTTTTTTTTTTTTCTTCTTCTTCTT
CTTCGTTTAGCGATAAATAGTTTAATCCCATGTTGTCTC
Found at i:210716 original size:24 final size:24
Alignment explanation
Indices: 210687--210733 Score: 60
Period size: 24 Copynumber: 1.9 Consensus size: 24
210677 CTATTTACAC
*
210687 AAAAAATTATAATTATA-ATTATAAT
1 AAAAAA-TAAAATTA-ACATTATAAT
210712 AAAAAATAAAATTAACATTATA
1 AAAAAATAAAATTAACATTATA
210734 GAAATTAACA
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 1 0.05
24 13 0.65
25 6 0.30
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (24 bp):
AAAAAATAAAATTAACATTATAAT
Found at i:210945 original size:19 final size:18
Alignment explanation
Indices: 210907--210959 Score: 61
Period size: 19 Copynumber: 2.9 Consensus size: 18
210897 TATTAAAAAC
* * *
210907 GAGAGACTTGAGAGACTT
1 GAGAGAGTTAAGAGAATT
*
210925 GAGAGGGTTTAAGAGAATT
1 GAGAGAG-TTAAGAGAATT
210944 GAGAGAGTTAAGAGAA
1 GAGAGAGTTAAGAGAA
210960 AGATGTAAAT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
18 14 0.48
19 15 0.52
ACGTcount: A:0.40, C:0.04, G:0.36, T:0.21
Consensus pattern (18 bp):
GAGAGAGTTAAGAGAATT
Found at i:222743 original size:11 final size:11
Alignment explanation
Indices: 222727--222754 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
222717 GTCGCGTCTT
222727 CCTTCGTTCTA
1 CCTTCGTTCTA
222738 CCTTCGTTCTA
1 CCTTCGTTCTA
222749 CCTTCG
1 CCTTCG
222755 CCTCCCGATT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.07, C:0.39, G:0.11, T:0.43
Consensus pattern (11 bp):
CCTTCGTTCTA
Found at i:223948 original size:63 final size:63
Alignment explanation
Indices: 223829--223949 Score: 165
Period size: 63 Copynumber: 1.9 Consensus size: 63
223819 GCACTTCTTC
* ** *
223829 CATGTCCTGCTTGTTGAATGCATTTGAAAGGGAGTGCACTTGGTCCTGTCTCTATAATGTTGT
1 CATGTCCTGCTTGTTGAATGCATTTGAAAGGGAGTGCACTTGGTACTGAATATATAATGTTGT
*
223892 CATGTCCTGCTTGTTGAATGCATTTGAAAGGGAGTG-AC-TGGTTAGTGAAATATATAAT
1 CATGTCCTGCTTGTTGAATGCATTTGAAAGGGAGTGCACTTGG-TACTG-AATATATAAT
223950 TTCAACCTCT
Statistics
Matches: 51, Mismatches: 5, Indels: 4
0.85 0.08 0.07
Matches are distributed among these distances:
61 3 0.06
62 5 0.10
63 43 0.84
ACGTcount: A:0.24, C:0.14, G:0.26, T:0.36
Consensus pattern (63 bp):
CATGTCCTGCTTGTTGAATGCATTTGAAAGGGAGTGCACTTGGTACTGAATATATAATGTTGT
Found at i:229837 original size:18 final size:17
Alignment explanation
Indices: 229809--229843 Score: 52
Period size: 18 Copynumber: 2.0 Consensus size: 17
229799 ATTATTAAGA
*
229809 ATTTTATTAAATTATAT
1 ATTTTATTAAAATATAT
229826 ATTTTAATTAAAATATAT
1 ATTTT-ATTAAAATATAT
229844 TTAATAATAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (17 bp):
ATTTTATTAAAATATAT
Found at i:230035 original size:39 final size:40
Alignment explanation
Indices: 229986--230094 Score: 112
Period size: 44 Copynumber: 2.6 Consensus size: 40
229976 AGTTTTTTCC
229986 ATTATGCTATTACACCTCTATTCCATTCAACCAAACACAAG
1 ATTA-GCTATTACACCTCTATTCCATTCAACCAAACACAAG
* ***
230027 ATTA-CTATTACGCCTCTATTACATTACATTCAACCAAACAGTGG
1 ATTAGCTATTACACCTCTATT-C----CATTCAACCAAACACAAG
*
230071 ATTAGCTATTACACCTCTAATCCA
1 ATTAGCTATTACACCTCTATTCCA
230095 ATACATCTCT
Statistics
Matches: 56, Mismatches: 6, Indels: 13
0.75 0.08 0.17
Matches are distributed among these distances:
39 15 0.27
40 3 0.05
41 4 0.07
44 20 0.36
45 14 0.25
ACGTcount: A:0.35, C:0.28, G:0.06, T:0.31
Consensus pattern (40 bp):
ATTAGCTATTACACCTCTATTCCATTCAACCAAACACAAG
Found at i:230100 original size:45 final size:44
Alignment explanation
Indices: 230009--230100 Score: 112
Period size: 45 Copynumber: 2.1 Consensus size: 44
229999 ACCTCTATTC
* * *
230009 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTACATTA
1 CATTCAACCAAACACAAGATTACTATTACACCTCTAATACAATA
*** *
230053 CATTCAACCAAACAGTGGATTAGCTATTACACCTCTAATCCAATA
1 CATTCAACCAAACACAAGATTA-CTATTACACCTCTAATACAATA
230098 CAT
1 CAT
230101 CTCTAATCCA
Statistics
Matches: 40, Mismatches: 7, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
44 19 0.47
45 21 0.52
ACGTcount: A:0.38, C:0.27, G:0.07, T:0.28
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACACCTCTAATACAATA
Found at i:230104 original size:16 final size:16
Alignment explanation
Indices: 230080--230131 Score: 95
Period size: 16 Copynumber: 3.2 Consensus size: 16
230070 GATTAGCTAT
230080 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
*
230096 TACATCTCTAATCCAA
1 TACACCTCTAATCCAA
230112 TACACCTCTAATCCAA
1 TACACCTCTAATCCAA
230128 TACA
1 TACA
230132 GCGAACCAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 34 1.00
ACGTcount: A:0.38, C:0.35, G:0.00, T:0.27
Consensus pattern (16 bp):
TACACCTCTAATCCAA
Found at i:235384 original size:18 final size:19
Alignment explanation
Indices: 235358--235397 Score: 55
Period size: 18 Copynumber: 2.2 Consensus size: 19
235348 TTGCTATTGC
*
235358 AGCAAGCATACGAGCTG-A
1 AGCAAGCATACAAGCTGCA
*
235376 AGCATGCATACAAGCTGCA
1 AGCAAGCATACAAGCTGCA
235395 AGC
1 AGC
235398 TCTTCAACAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
18 15 0.79
19 4 0.21
ACGTcount: A:0.38, C:0.25, G:0.25, T:0.12
Consensus pattern (19 bp):
AGCAAGCATACAAGCTGCA
Found at i:243401 original size:3 final size:3
Alignment explanation
Indices: 243393--243418 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
243383 TATTTTCTCC
243393 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
243419 GTTGTTGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:243423 original size:3 final size:3
Alignment explanation
Indices: 243417--243470 Score: 108
Period size: 3 Copynumber: 18.0 Consensus size: 3
243407 ATTATTATTA
243417 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
243465 TTG TTG
1 TTG TTG
243471 ATATTGTAAT
Statistics
Matches: 51, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 51 1.00
ACGTcount: A:0.00, C:0.00, G:0.33, T:0.67
Consensus pattern (3 bp):
TTG
Found at i:246425 original size:3 final size:3
Alignment explanation
Indices: 246417--246442 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
246407 TATTTTCTCC
246417 TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TT
246443 GTTGTTGTTG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:246447 original size:3 final size:3
Alignment explanation
Indices: 246441--246493 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
246431 ATTATTATTA
246441 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
246489 TTG TT
1 TTG TT
246494 NNNNNNNNNN
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:251981 original size:133 final size:133
Alignment explanation
Indices: 251806--253918 Score: 2975
Period size: 133 Copynumber: 16.0 Consensus size: 133
251796 GCGGAGCAGG
** * ** *
251806 TTGAAGATAGCAGATCTTGCCTTCTTGCATAGACAGTGAAGCAGATCGAAGATGGCAGATTTTAC
1 TTGAAGATTTCAGATCTTGCCTTCCTGCATAGACAGCAAAGCAGGTCGAAGATGGCAGATTTTAC
251871 CTCCTCGTGGTTACAGTGGAGTACATTGAAGCCGGTAATTCTACTTCCCTAGGCAGCAGTGGAAT
66 CTCCTCGTGGTTACAGTGGAGTACATTGAAGCCGGTAATTCTACTTCCCTAGGCAGCAGTGGAAT
251936 AGT
131 AGT
251939 TTGAAGATTTCAGATCTTGCCTTCCTGCATAGACAGCAAAGCAGGTCGAAGATGGCAGATTTTAC
1 TTGAAGATTTCAGATCTTGCCTTCCTGCATAGACAGCAAAGCAGGTCGAAGATGGCAGATTTTAC
252004 CTCCTCGTGGTTACAGTGGAGTACATTGAAGCCGGTAATTCTACTTCCCTAGGCAGCAGTGGAAT
66 CTCCTCGTGGTTACAGTGGAGTACATTGAAGCCGGTAATTCTACTTCCCTAGGCAGCAGTGGAAT
252069 AGT
131 AGT
252072 TTGAAGATTTCAGATCTTGCCTTCCTGCATAGACAGCAAAGCAGGTCGAAGATGGCAGATTTTAC
1 TTGAAGATTTCAGATCTTGCCTTCCTGCATAGACAGCAAAGCAGGTCGAAGATGGCAGATTTTAC
252137 CTCCTCGTGGTTACAGTGGAGTACATTGAAGCCGGTAATTCTACTTCCCTAGGCAGCAGTGGAAT
66 CTCCTCGTGGTTACAGTGGAGTACATTGAAGCCGGTAATTCTACTTCCCTAGGCAGCAGTGGAAT
252202 AGT
131 AGT
252205 TTGAAGATTTCAGATCTTGCCTTCCTGCATAGACAGCAAAGCAGGTCGAAGATGGCAGATTTTAC
1 TTGAAGATTTCAGATCTTGCCTTCCTGCATAGACAGCAAAGCAGGTCGAAGATGGCAGATTTTAC
252270 CTCCTCGTGGTTACAGTGGAGTACATTGAAGCCGGTAATTCTACTTCCCTAGGCAGCAGTGGAAT
66 CTCCTCGTGGTTACAGTGGAGTACATTGAAGCCGGTAATTCTACTTCCCTAGGCAGCAGTGGAAT
252335 AGT
131 AGT
252338 TTGAAGATTTCAGATCTTGCCTTCCTGCATAGACAGCAAAGCAGGTCGAAGATGGCAGATTTTAC
1 TTGAAGATTTCAGATCTTGCCTTCCTGCATAGACAGCAAAGCAGGTCGAAGATGGCAGATTTTAC
252403 CTCCTCGTGGTTACAGTGGAGTACATTGAAGCCGGTAATTCTACTTCCCTAGGCAGCAGTGGAAT
66 CTCCTCGTGGTTACAGTGGAGTACATTGAAGCCGGTAATTCTACTTCCCTAGGCAGCAGTGGAAT
252468 AGT
131 AGT
252471 TTGAAGATTTCAGATCTTGCCTTCCTGCATAGACAGCAAAGCAGGTCGAAGATGGCAGATTTTAC
1 TTGAAGATTTCAGATCTTGCCTTCCTGCATAGACAGCAAAGCAGGTCGAAGATGGCAGATTTTAC
252536 CTCCTCGTGGTTACAGTGGAGTACATTGAAGCCGGTAATTCTACTTCCCTAGGCAGCAGTGGAAT
66 CTCCTCGTGGTTACAGTGGAGTACATTGAAGCCGGTAATTCTACTTCCCTAGGCAGCAGTGGAAT
252601 AGT
131 AGT
252604 TTGAAGATTTCAGATCTTGCCTTCCTGCATAGACAGCAAAGCAGGTCGAAGATGGCAGATTTTAC
1 TTGAAGATTTCAGATCTTGCCTTCCTGCATAGACAGCAAAGCAGGTCGAAGATGGCAGATTTTAC
252669 CTCCTCGTGGTTACAGTGGAGTACATTGAAGCCGGTAATTCTACTTCCCTAGGCAGCAGTGGAAT
66 CTCCTCGTGGTTACAGTGGAGTACATTGAAGCCGGTAATTCTACTTCCCTAGGCAGCAGTGGAAT
252734 AGT
131 AGT
252737 TTGAAGATTTCAGATCTTGCCTTCCTGCATAGACAGCAAAGCAGGTCGAAGATGGCAGATTTTAC
1 TTGAAGATTTCAGATCTTGCCTTCCTGCATAGACAGCAAAGCAGGTCGAAGATGGCAGATTTTAC
252802 CTCCTCGTGGTTACAGTGGAGTACATTGAAGCCGGTAATTCTACTTCCCTAGGCAGCAGTGGAAT
66 CTCCTCGTGGTTACAGTGGAGTACATTGAAGCCGGTAATTCTACTTCCCTAGGCAGCAGTGGAAT
252867 AGT
131 AGT
252870 TTGAAGATTTCAGATCTTGCCTTCCTGCATAGACAGCAAAGCAGGTCGAAGATGGCAGATTTTAC
1 TTGAAGATTTCAGATCTTGCCTTCCTGCATAGACAGCAAAGCAGGTCGAAGATGGCAGATTTTAC
252935 CTCCTCGTGGTTACAGTGGAGTACATTGAAGCCGGTAATTCTACTTCCCTAGGCAGCAGTGGAAT
66 CTCCTCGTGGTTACAGTGGAGTACATTGAAGCCGGTAATTCTACTTCCCTAGGCAGCAGTGGAAT
253000 AGT
131 AGT
253003 TTGAAGATTTCAGATCTTGCCTTCCTGCATAGACAGCAAAGCAGGTCGAAGATGGCAGATTTTAC
1 TTGAAGATTTCAGATCTTGCCTTCCTGCATAGACAGCAAAGCAGGTCGAAGATGGCAGATTTTAC
253068 CTCCTCGTGGTTACAGTGGAGTACATTGAAGCCGGTAATTCTACTTCCCTAGGCAGCAGTGGAAT
66 CTCCTCGTGGTTACAGTGGAGTACATTGAAGCCGGTAATTCTACTTCCCTAGGCAGCAGTGGAAT
253133 AGT
131 AGT
253136 TTGAAGATTTCAGATCTTGCCTTCCTGCATAGACAGCAAAGCAGGTCGAAGATGGCAGATTTTAC
1 TTGAAGATTTCAGATCTTGCCTTCCTGCATAGACAGCAAAGCAGGTCGAAGATGGCAGATTTTAC
253201 CTCCTCGTGGTTACAGTGGAGTACATTGAAGCCGGTAATTCTACTTCCCT----AG-AGTGGAAT
66 CTCCTCGTGGTTACAGTGGAGTACATTGAAGCCGGTAATTCTACTTCCCTAGGCAGCAGTGGAAT
*
253261 AGA
131 AGT
* * * * * * *
253264 TTGAAGATTTCAGATCTTGTCTCCCT--A-AG-CAGTAGTGGAGCAGATCAAAGATGG-TGAATT
1 TTGAAGATTTCAGATCTTGCCTTCCTGCATAGACAGCA---AAGCAGGTCGAAGATGGCAG-ATT
* *
253324 TTACCTCC-CTGTGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTACTTCCCTGGGCAGCAGT
62 TTACCTCCTC-GTGGTTACAGTGGAGTACATTGAAGCCGGTAATTCTACTTCCCTAGGCAGCAGT
*
253388 GGAATAGA
126 GGAATAGT
* * * * * *
253396 TTGAAGATTTCAGATCTTGTCTCCCT--A-AG-CAGTAGTGGAGCAGATCAAAGATTGTG-A-AT
1 TTGAAGATTTCAGATCTTGCCTTCCTGCATAGACAGCA---AAGCAGGTCGAAGA-TG-GCAGAT
* * * * * **
253455 TTTACCTCC-CTGAGGTTATAGTGGAGTACATTGAAGCCAGTAATTCT-TTCTCCCT-GAGTAAT
61 TTTACCTCCTC-GTGGTTACAGTGGAGTACATTGAAGCCGGTAATTCTACT-TCCCTAG-GCAGC
*
253517 AGTGGAATAGA
123 AGTGGAATAGT
* ** * * * * *
253528 TTGAAGATTACAGATCTTATC-TCTCTAGGCAATAG--TG--GAGTAGATCGAAGATGGCGGA-T
1 TTGAAGATTTCAGATCTTGCCTTC-CT--GC-ATAGACAGCAAAGCAGGTCGAAGATGGCAGATT
* * **
253587 TTACCTCC-CTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA-TCTCCCT-GAGCAATA
62 TTACCTCCTC-GTGGTTACAGTGGAGTACATTGAAGCCGGTAATTCTACT-TCCCTAG-GCAGCA
*
253649 GTGGAATAGA
124 GTGGAATAGT
* ** * * * * *
253659 TTGAAGATTACAGATCTTATC-TCTCTAGGCAATAG--TG--GAGTAGATCGAAGATGGCGGA-T
1 TTGAAGATTTCAGATCTTGCCTTC-CT--GC-ATAGACAGCAAAGCAGGTCGAAGATGGCAGATT
* * * *
253718 TTACCTCC-CTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTA--TCTCCTTGAGCAACA
62 TTACCTCCTC-GTGGTTACAGTGGAGTACATTGAAGCCGGTAATTCTACTTC-CCTAG-GCAGCA
* **
253780 GTTGAATAAA
124 GTGGAATAGT
* ** * * * * *
253790 TTGAAGATTACAGATCTTATC-TCC--C-TAGACAGTAGTGGAGTAGATCGAAGATGGTAGATTT
1 TTGAAGATTTCAGATCTTGCCTTCCTGCATAGACAGCA---AAGCAGGTCGAAGATGGCAGATTT
* * * *
253851 TACCT-CTCTGAGGTTACAGTGGAGTATATTGAAGCCAGTAATTCTAAC-TCCCT-GGTCGGCAG
63 TACCTCCTC-GTGGTTACAGTGGAGTACATTGAAGCCGGTAATTCT-ACTTCCCTAGG-CAGCAG
253913 TGGAAT
125 TGGAAT
253919 CGATCGAAGA
Statistics
Matches: 1901, Mismatches: 41, Indels: 77
0.94 0.02 0.04
Matches are distributed among these distances:
124 7 0.00
125 2 0.00
126 5 0.00
127 68 0.04
128 34 0.02
129 4 0.00
130 5 0.00
131 242 0.13
132 215 0.11
133 1312 0.69
134 3 0.00
137 2 0.00
138 2 0.00
ACGTcount: A:0.27, C:0.20, G:0.25, T:0.28
Consensus pattern (133 bp):
TTGAAGATTTCAGATCTTGCCTTCCTGCATAGACAGCAAAGCAGGTCGAAGATGGCAGATTTTAC
CTCCTCGTGGTTACAGTGGAGTACATTGAAGCCGGTAATTCTACTTCCCTAGGCAGCAGTGGAAT
AGT
Found at i:253508 original size:44 final size:44
Alignment explanation
Indices: 253460--253904 Score: 180
Period size: 44 Copynumber: 10.2 Consensus size: 44
253450 TGAATTTTAC
* * *
253460 CTCCCTGAGGTTATAGTGGAGTACATTGAAGCCAGTAATTCTTT
1 CTCCCTGAGGTAATAGTGGAGTAGATTGAAGCCAGTAATTCTAT
* * *
253504 CTCCCTGA-GTAATAGTGGAATAGATTGAAG--ATTACAGATCTTAT
1 CTCCCTGAGGTAATAGTGGAGTAGATTGAAGCCAGTA-A-TTC-TAT
* * * *** ** *
253548 CTCTCT-AGGCAATAGTGGAGTAGATCGAAGATGGCGGATT-TAC
1 CTCCCTGAGGTAATAGTGGAGTAGATTGAAGCCAG-TAATTCTAT
* * *
253591 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTAT
1 CTCCCTGAGGTAATAGTGGAGTAGATTGAAGCCAGTAATTCTAT
* * * *
253635 CTCCCTGA-GCAATAGTGGAATAGATTGAAG--ATTACAGATCTTAT
1 CTCCCTGAGGTAATAGTGGAGTAGATTGAAGCCAGTA-A-TTC-TAT
* * * *** ** *
253679 CTCTCT-AGGCAATAGTGGAGTAGATCGAAGATGGCGGATT-TAC
1 CTCCCTGAGGTAATAGTGGAGTAGATTGAAGCCAG-TAATTCTAT
* * *
253722 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTAT
1 CTCCCTGAGGTAATAGTGGAGTAGATTGAAGCCAGTAATTCTAT
* * * * * * * *
253766 CTCCTTGA-GCAACAGTTGAATAAATTGAAG--ATTACAGATCTTAT
1 CTCCCTGAGGTAATAGTGGAGTAGATTGAAGCCAGTA-A-TTC-TAT
** * * *** * *
253810 CTCCCT-AGACAGTAGTGGAGTAGATCGAAGATGGTAGATTTTAC
1 CTCCCTGAGGTAATAGTGGAGTAGATTGAAGCCAGTA-ATTCTAT
* * * * *
253854 CTCTCTGAGGTTACAGTGGAGTATATTGAAGCCAGTAATTCTAA
1 CTCCCTGAGGTAATAGTGGAGTAGATTGAAGCCAGTAATTCTAT
253898 CTCCCTG
1 CTCCCTG
253905 GTCGGCAGTG
Statistics
Matches: 284, Mismatches: 92, Indels: 50
0.67 0.22 0.12
Matches are distributed among these distances:
41 9 0.03
42 3 0.01
43 82 0.29
44 162 0.57
45 23 0.08
46 5 0.02
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (44 bp):
CTCCCTGAGGTAATAGTGGAGTAGATTGAAGCCAGTAATTCTAT
Found at i:253598 original size:87 final size:87
Alignment explanation
Indices: 253504--253862 Score: 228
Period size: 87 Copynumber: 4.1 Consensus size: 87
253494 GTAATTCTTT
* * *
253504 CTCCCTGAGTAATAGTGGAATAGATTGAAGATTACAGATCTTATCTCTCTAGGCAATAGTGGAGT
1 CTCCCTGAGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAGGCAATAGTGGAGT
*
253569 AGATCGAAGATGGCGGATTTAC
66 AGATCGAAGATGGCAGATTTAC
** * * * *
253591 CTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTA-A-TTC-TATCTCCCT-GAGCAATAGTG
1 CTCCCTGA-GCAACAGTGGAATAGATTGAAG--ATTACAGATCTTATCTCCCTAG-GCAATAGTG
* * ** *
253652 GAATAGATTGAAGATTACAGATCTTAT
62 GAGTAGATCGAAGATGGCAGAT-TTAC
* * * * ** * * ** *
253679 CTCTCT-AGGCAATAGTGGAGTAGATCGAAGATGGCGGAT-TTACCTCCCTGAGGTTACAGTGGA
1 CTCCCTGA-GCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCT-AGGCAATAGTGGA
* * *** * *
253742 GTACATTGAAGCCAGTA-ATTCTAT
64 GTAGATCGAAGATGGCAGATT-TAC
* * * * *
253766 CTCCTTGAGCAACAGTTGAATAAATTGAAGATTACAGATCTTATCTCCCTAGACAGTAGTGGAGT
1 CTCCCTGAGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAGGCAATAGTGGAGT
*
253831 AGATCGAAGATGGTAGATTTTAC
66 AGATCGAAGATGGCAGA-TTTAC
*
253854 CTCTCTGAG
1 CTCCCTGAG
253863 GTTACAGTGG
Statistics
Matches: 198, Mismatches: 59, Indels: 29
0.69 0.21 0.10
Matches are distributed among these distances:
85 1 0.01
86 2 0.01
87 122 0.62
88 66 0.33
89 4 0.02
90 3 0.02
ACGTcount: A:0.30, C:0.17, G:0.24, T:0.29
Consensus pattern (87 bp):
CTCCCTGAGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAGGCAATAGTGGAGT
AGATCGAAGATGGCAGATTTAC
Found at i:254710 original size:11 final size:11
Alignment explanation
Indices: 254683--254721 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
254673 TAAAATATAC
*
254683 GAAATAGAGGG
1 GAAATAGAGAG
254694 GAAAATAGAGAG
1 G-AAATAGAGAG
*
254706 GAAATACAGAG
1 GAAATAGAGAG
254717 GAAAT
1 GAAAT
254722 TTGTTTTTCG
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
11 15 0.60
12 10 0.40
ACGTcount: A:0.54, C:0.03, G:0.33, T:0.10
Consensus pattern (11 bp):
GAAATAGAGAG
Found at i:261971 original size:47 final size:47
Alignment explanation
Indices: 261796--261971 Score: 158
Period size: 47 Copynumber: 3.7 Consensus size: 47
261786 AAAAGCTGCT
* * * * *
261796 AATACGTTGTGGATGAACCACTAGTCAAACATATGAACTGCCAACTAA
1 AATACGTTGTGGATAAACCACTGGTCGAACAGATG-ACTGCGAACTAA
* * * *
261844 AATACTTTGTGGATAAAACACTGG-CTGAGCAGATGACTGGGAACTAA
1 AATACGTTGTGGATAAACCACTGGTC-GAACAGATGACTGCGAACTAA
* * * * * * *
261891 AATATGTTGTGAATGAACCATTGGTTGAGCAGATGATTGCTGAA-TAA
1 AATACGTTGTGGATAAACCACTGGTCGAACAGATGACTGC-GAACTAA
*
261938 AATACATTGTGGATAAACCACTGGTCGAACAGAT
1 AATACGTTGTGGATAAACCACTGGTCGAACAGAT
261972 AAACTGCCAA
Statistics
Matches: 100, Mismatches: 25, Indels: 7
0.76 0.19 0.05
Matches are distributed among these distances:
47 71 0.71
48 29 0.29
ACGTcount: A:0.37, C:0.15, G:0.22, T:0.26
Consensus pattern (47 bp):
AATACGTTGTGGATAAACCACTGGTCGAACAGATGACTGCGAACTAA
Found at i:263100 original size:21 final size:21
Alignment explanation
Indices: 263076--263115 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
263066 TCCTAAGATG
*
263076 TGAATTGGATTGAATTGAGTA
1 TGAATTGGATTAAATTGAGTA
*
263097 TGAATTGTATTAAATTGAG
1 TGAATTGGATTAAATTGAG
263116 CTAAATTTAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.35, C:0.00, G:0.25, T:0.40
Consensus pattern (21 bp):
TGAATTGGATTAAATTGAGTA
Found at i:263648 original size:25 final size:24
Alignment explanation
Indices: 263613--263720 Score: 87
Period size: 25 Copynumber: 4.4 Consensus size: 24
263603 AGTTTTTTGT
*
263613 GAGCTTTCCGATTAATGGCTCTTCG
1 GAGCTTCCCGA-TAATGGCTCTTCG
*
263638 GAGCTTCCCGAT-ATGGTTCGCTT--
1 GAGCTTCCCGATAATGG--CTCTTCG
* * *
263661 GAACTTCCCGATATATGGCTATCCG
1 GAGCTTCCCGATA-ATGGCTCTTCG
*
263686 GAGCTTCCTGATTAATGGCTCTTCG
1 GAGCTTCCCGA-TAATGGCTCTTCG
*
263711 GAGCTACCCG
1 GAGCTTCCCG
263721 TTATACAGCC
Statistics
Matches: 64, Mismatches: 12, Indels: 14
0.71 0.13 0.16
Matches are distributed among these distances:
23 17 0.27
24 1 0.02
25 44 0.69
26 2 0.03
ACGTcount: A:0.18, C:0.27, G:0.24, T:0.31
Consensus pattern (24 bp):
GAGCTTCCCGATAATGGCTCTTCG
Found at i:264386 original size:30 final size:32
Alignment explanation
Indices: 264327--264386 Score: 79
Period size: 30 Copynumber: 1.9 Consensus size: 32
264317 ATATATTATA
* * *
264327 ATATTATATCTTAATTATTAAGTATATATATT
1 ATATTATATATTAATTAATAAGTAAATATATT
264359 ATATTATATATT-A-TAATAAGTAAATATA
1 ATATTATATATTAATTAATAAGTAAATATA
264387 ATAAATAAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
30 13 0.52
31 1 0.04
32 11 0.44
ACGTcount: A:0.47, C:0.02, G:0.03, T:0.48
Consensus pattern (32 bp):
ATATTATATATTAATTAATAAGTAAATATATT
Found at i:264386 original size:32 final size:33
Alignment explanation
Indices: 264313--264386 Score: 80
Period size: 35 Copynumber: 2.2 Consensus size: 33
264303 CTTAAAGTTA
* *
264313 AAATATATATTATAATATTATATCTTAATTATT
1 AAATATATATTATAATATTATATCTTAATAAGT
*
264346 AAGTATATATATTATATTA-TATAT-TATAATAAGT
1 AA--ATATATATTATAATATTATATCT-TAATAAGT
264380 AAATATA
1 AAATATA
264387 ATAAATAAAA
Statistics
Matches: 35, Mismatches: 3, Indels: 7
0.78 0.07 0.16
Matches are distributed among these distances:
32 5 0.14
33 3 0.09
34 13 0.37
35 14 0.40
ACGTcount: A:0.49, C:0.01, G:0.03, T:0.47
Consensus pattern (33 bp):
AAATATATATTATAATATTATATCTTAATAAGT
Found at i:265179 original size:15 final size:15
Alignment explanation
Indices: 265159--265213 Score: 55
Period size: 15 Copynumber: 3.7 Consensus size: 15
265149 GAATTTATTA
265159 AATTGATATTGATTG
1 AATTGATATTGATTG
265174 AATTGATATAT-ATTG
1 AATTGATAT-TGATTG
265189 -ATT-AT-TTGAATTG
1 AATTGATATTG-ATTG
265202 AATTGAATATTG
1 AATTG-ATATTG
265214 GTTGTATTTG
Statistics
Matches: 33, Mismatches: 0, Indels: 12
0.73 0.00 0.27
Matches are distributed among these distances:
11 1 0.03
12 1 0.03
13 6 0.18
14 6 0.18
15 13 0.39
16 3 0.09
17 3 0.09
ACGTcount: A:0.36, C:0.00, G:0.16, T:0.47
Consensus pattern (15 bp):
AATTGATATTGATTG
Found at i:274664 original size:15 final size:16
Alignment explanation
Indices: 274630--274661 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
274620 TATAGGTACC
274630 ACATTGAAAAAAAATA
1 ACATTGAAAAAAAATA
274646 ACATTGAAAAAAAATA
1 ACATTGAAAAAAAATA
274662 CATGTACCAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.19
Consensus pattern (16 bp):
ACATTGAAAAAAAATA
Found at i:275296 original size:18 final size:18
Alignment explanation
Indices: 275273--275315 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
275263 TTATAGGTTG
275273 TTAATTAAATAAATTT-AA
1 TTAATTAAA-AAATTTAAA
* *
275291 TTAATTGAAAATTTTAAA
1 TTAATTAAAAAATTTAAA
275309 TTAATTA
1 TTAATTA
275316 CACCTTGAAT
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.51, C:0.00, G:0.02, T:0.47
Consensus pattern (18 bp):
TTAATTAAAAAATTTAAA
Found at i:276675 original size:21 final size:21
Alignment explanation
Indices: 276649--276689 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
276639 TTAGAGTCAT
276649 AAATAAT-TAATTAAAGTATTA
1 AAATAATATAA-TAAAGTATTA
*
276670 AAATAATATAATCAAGTATT
1 AAATAATATAATAAAGTATT
276690 CTTATATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 15 0.83
22 3 0.17
ACGTcount: A:0.56, C:0.02, G:0.05, T:0.37
Consensus pattern (21 bp):
AAATAATATAATAAAGTATTA
Found at i:278291 original size:87 final size:86
Alignment explanation
Indices: 278163--278356 Score: 257
Period size: 87 Copynumber: 2.3 Consensus size: 86
278153 AGTCTTTAAA
* *
278163 TTTTAAAAAAAACAATTAAG-CCGTTTTTTTTTGCACTCAATTGAGCACTTAAACTTTAAAAATG
1 TTTTCAAAAAAACAATTAAGCCCCTTTTTTTTTGCACTCAATTGAGCACTTAAACTTTAAAAATG
*
278227 CATCAAAAAGGCCCTC-AAAT
66 CATCAAAAAGACCCTCAAAAT
* * * * * * *
278247 TTCTTCAAAAAAAGTAATTAAGCCCCTTTTTTTTTTCACTCAATTGGGTACTTGAATTTTCAAAA
1 TT-TTCAAAAAAA-CAATTAAGCCCCTTTTTTTTTGCACTCAATTGAGCACTTAAACTTTAAAAA
*
278312 TGTATCAAAAAGACCCTCAAAAT
64 TGCATCAAAAAGACCCTCAAAAT
278335 TTTTCAAAAAAACAATTAAGCC
1 TTTTCAAAAAAACAATTAAGCC
278357 TCTGGCNNNN
Statistics
Matches: 94, Mismatches: 12, Indels: 6
0.84 0.11 0.05
Matches are distributed among these distances:
84 2 0.02
85 9 0.10
86 16 0.17
87 61 0.65
88 6 0.06
ACGTcount: A:0.40, C:0.18, G:0.09, T:0.34
Consensus pattern (86 bp):
TTTTCAAAAAAACAATTAAGCCCCTTTTTTTTTGCACTCAATTGAGCACTTAAACTTTAAAAATG
CATCAAAAAGACCCTCAAAAT
Done.