Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: CP032254.1 Gossypioides kirkii chromosome KI_12
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: 43711324
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 1700 characters in sequence are not A, C, G, or T
File 28 of 135
Found at i:11154342 original size:32 final size:32
Alignment explanation
Indices: 11154306--11154368 Score: 92
Period size: 32 Copynumber: 2.0 Consensus size: 32
11154296 GTCATCGGAC
*
11154306 CTCATAA-TCTGAAAAGGATTCATATGCTCACT
1 CTCATAATTC-GAAAAGGATTCATATACTCACT
*
11154338 CTCATAATTCGTAAAGGATTCATATACTCAC
1 CTCATAATTCGAAAAGGATTCATATACTCAC
11154369 GATGACACAT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 26 0.93
33 2 0.07
ACGTcount: A:0.35, C:0.22, G:0.11, T:0.32
Consensus pattern (32 bp):
CTCATAATTCGAAAAGGATTCATATACTCACT
Found at i:11154404 original size:52 final size:52
Alignment explanation
Indices: 11154338--11154547 Score: 348
Period size: 52 Copynumber: 4.0 Consensus size: 52
11154328 TATGCTCACT
* *
11154338 CTCATAATTCGTAAAGGATTCATATACTCACGATGACACATAGTCATCGGAC
1 CTCATAATCCGTAAAGGATTCATATACTCACGATGAGACATAGTCATCGGAC
* *
11154390 CTTATAATCCGTAAAGGATTCATATACTCACGATTAGACATAGTCATCGGAC
1 CTCATAATCCGTAAAGGATTCATATACTCACGATGAGACATAGTCATCGGAC
*
11154442 CTCATAATCTGTAAAGGATTCATATACTCACGATGAGACATAGTCATCGGAC
1 CTCATAATCCGTAAAGGATTCATATACTCACGATGAGACATAGTCATCGGAC
* * *
11154494 CTCATAATCCGTAAAGGATTCATATACTCACGATGATACATAGTAATCAGAC
1 CTCATAATCCGTAAAGGATTCATATACTCACGATGAGACATAGTCATCGGAC
11154546 CT
1 CT
11154548 TTTGCATTTA
Statistics
Matches: 147, Mismatches: 11, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
52 147 1.00
ACGTcount: A:0.35, C:0.22, G:0.15, T:0.28
Consensus pattern (52 bp):
CTCATAATCCGTAAAGGATTCATATACTCACGATGAGACATAGTCATCGGAC
Found at i:11156634 original size:69 final size:66
Alignment explanation
Indices: 11156552--11156688 Score: 186
Period size: 69 Copynumber: 2.0 Consensus size: 66
11156542 CTATTATTAG
* *
11156552 CACTGTGTGTGCTCTCTGATT-AGCACTTTGTGTGCTCTCTGATTAGTACTTTGTGTACTCTCTG
1 CACTGTATGTGCTCTCTG-TTCAGCAC-TTATGTGCTCTCTG-TTAGTACTTTG-GTACTCTCTG
11156616 TTTAA
62 TTTAA
11156621 CACTGTATGTGCTCTCTGTTGCCCAGCACTTATGTGCTCTCTGTTAGTACTTTGGTACTCTCTGT
1 CACTGTATGTGCTCTCTGTT---CAGCACTTATGTGCTCTCTGTTAGTACTTTGGTACTCTCTGT
11156686 TTA
63 TTA
11156689 TTCCGTATAT
Statistics
Matches: 62, Mismatches: 2, Indels: 8
0.86 0.03 0.11
Matches are distributed among these distances:
68 2 0.03
69 31 0.50
70 11 0.18
71 13 0.21
72 5 0.08
ACGTcount: A:0.14, C:0.23, G:0.20, T:0.44
Consensus pattern (66 bp):
CACTGTATGTGCTCTCTGTTCAGCACTTATGTGCTCTCTGTTAGTACTTTGGTACTCTCTGTTTA
A
Found at i:11156639 original size:23 final size:23
Alignment explanation
Indices: 11156515--11156688 Score: 131
Period size: 23 Copynumber: 7.5 Consensus size: 23
11156505 CACAAGCGCA
*
11156515 CTCTCTGTTTAGCAC-GTCTCGTG
1 CTCTCTGTTTAGCACTGTGT-GTG
*
11156538 CTCTCTATTATTAGCACTGTGTGTG
1 CTCTCT-GT-TTAGCACTGTGTGTG
* *
11156563 CTCTCTGATTAGCACTTTGTGTG
1 CTCTCTGTTTAGCACTGTGTGTG
* * * *
11156586 CTCTCTGATTAGTACTTTGTGTA
1 CTCTCTGTTTAGCACTGTGTGTG
* *
11156609 CTCTCTGTTTAACACTGTATGTG
1 CTCTCTGTTTAGCACTGTGTGTG
* *
11156632 CTCTCTGTTGCCCAGCACT-TATGTG
1 CTCTCTGTT---TAGCACTGTGTGTG
* * *
11156657 CTCTCTG-TTAGTACTTTG-GTA
1 CTCTCTGTTTAGCACTGTGTGTG
11156678 CTCTCTGTTTA
1 CTCTCTGTTTA
11156689 TTCCGTATAT
Statistics
Matches: 124, Mismatches: 19, Indels: 17
0.77 0.12 0.11
Matches are distributed among these distances:
21 14 0.11
22 4 0.03
23 67 0.54
24 2 0.02
25 29 0.23
26 8 0.06
ACGTcount: A:0.14, C:0.24, G:0.19, T:0.44
Consensus pattern (23 bp):
CTCTCTGTTTAGCACTGTGTGTG
Found at i:11157412 original size:18 final size:16
Alignment explanation
Indices: 11157381--11157416 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 16
11157371 CCTCAATACC
11157381 ATTTCATTTCAATTTA
1 ATTTCATTTCAATTTA
11157397 ATTTCATTCATCAATTTA
1 ATTTCATT--TCAATTTA
11157415 AT
1 AT
11157417 ATTTACTAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 8 0.44
18 10 0.56
ACGTcount: A:0.33, C:0.14, G:0.00, T:0.53
Consensus pattern (16 bp):
ATTTCATTTCAATTTA
Found at i:11166419 original size:27 final size:28
Alignment explanation
Indices: 11166382--11166434 Score: 83
Period size: 29 Copynumber: 1.9 Consensus size: 28
11166372 TAATAATATG
11166382 TTTGAAC-A-ATACTTCCTAACATTTTT
1 TTTGAACAATATACTTCCTAACATTTTT
11166408 TTTGAAACAATATACTTCCTAACATTT
1 TTTG-AACAATATACTTCCTAACATTT
11166435 AATGTTACTA
Statistics
Matches: 24, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
26 4 0.17
27 3 0.12
28 1 0.04
29 16 0.67
ACGTcount: A:0.34, C:0.19, G:0.04, T:0.43
Consensus pattern (28 bp):
TTTGAACAATATACTTCCTAACATTTTT
Found at i:11170190 original size:30 final size:28
Alignment explanation
Indices: 11169979--11170255 Score: 109
Period size: 29 Copynumber: 9.4 Consensus size: 28
11169969 TTGTGAAATC
*
11169979 GGGGTTAAAAATGGGATTTTGGAAAGTTCA
1 GGGGTTAAAAAT-GGATTTTGGAAAGTT-T
*
11170009 GGGG-T-AAAATGGTAATTTTTGGGGAAA--TC
1 GGGGTTAAAAATGG--A-TTTT--GGAAAGTTT
*
11170038 GGGGTTAAAAATGGGATCTTGGAAAGTTT
1 GGGGTTAAAAAT-GGATTTTGGAAAGTTT
* *
11170067 GAGGG-T-AAAGTGGTAATTTTTAGTGAAA--TC
1 G-GGGTTAAAAATGG--A-TTTT-G-GAAAGTTT
11170097 GGGGTTAAAAATGGGATTTTGGAAAGTTT
1 GGGGTTAAAAAT-GGATTTTGGAAAGTTT
*
11170126 AGGGG-T-AAAATGGCAATTTTTGGTGAAA--TC
1 -GGGGTTAAAAATGG--A-TTTT-G-GAAAGTTT
11170156 GGGGTTAAAAATAGGATTTTGGAAAGTTT
1 GGGGTTAAAAAT-GGATTTTGGAAAGTTT
11170185 AGGGG-T-AAAATGGTAATTTGTGGTGAAA--TT
1 -GGGGTTAAAAATGG--ATTT-T-G-GAAAGTTT
*
11170215 GGGGTTAAAAATGAGATTTTAGAAAGTTT
1 GGGGTTAAAAATG-GATTTTGGAAAGTTT
*
11170244 GGGGGTAAAAAT
1 GGGGTTAAAAAT
11170256 ATAATTTTTG
Statistics
Matches: 192, Mismatches: 12, Indels: 87
0.66 0.04 0.30
Matches are distributed among these distances:
27 25 0.13
28 21 0.11
29 55 0.29
30 44 0.23
31 23 0.12
32 24 0.12
ACGTcount: A:0.34, C:0.02, G:0.32, T:0.32
Consensus pattern (28 bp):
GGGGTTAAAAATGGATTTTGGAAAGTTT
Found at i:11170262 original size:59 final size:59
Alignment explanation
Indices: 11169949--11170253 Score: 477
Period size: 59 Copynumber: 5.2 Consensus size: 59
11169939 TTTGACTTTC
* *
11169949 AGGGGTAAAATGGTAATTTTTTGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTC
1 AGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTT
* *
11170008 AGGGGTAAAATGGTAATTTTTGGGGAAATCGGGGTTAAAAATGGGATCTTGGAAAGTTT
1 AGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTT
* *
11170067 -GAGGGTAAAGTGGTAATTTTTAGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTT
1 AG-GGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTT
* *
11170126 AGGGGTAAAATGGCAATTTTTGGTGAAATCGGGGTTAAAAATAGGATTTTGGAAAGTTT
1 AGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTT
* * * *
11170185 AGGGGTAAAATGGTAATTTGTGGTGAAATTGGGGTTAAAAATGAGATTTTAGAAAGTTT
1 AGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTT
*
11170244 GGGGGTAAAA
1 AGGGGTAAAA
11170254 ATATAATTTT
Statistics
Matches: 225, Mismatches: 19, Indels: 4
0.91 0.08 0.02
Matches are distributed among these distances:
58 1 0.00
59 223 0.99
60 1 0.00
ACGTcount: A:0.33, C:0.02, G:0.32, T:0.32
Consensus pattern (59 bp):
AGGGGTAAAATGGTAATTTTTGGTGAAATCGGGGTTAAAAATGGGATTTTGGAAAGTTT
Found at i:11172141 original size:11 final size:11
Alignment explanation
Indices: 11172125--11172183 Score: 57
Period size: 11 Copynumber: 5.3 Consensus size: 11
11172115 TTACCATAAT
11172125 ATTAAATTTAA
1 ATTAAATTTAA
*
11172136 ATTAAATTCAA
1 ATTAAATTTAA
11172147 ACTTAAA-TTAA
1 A-TTAAATTTAA
**
11172158 ACTTAAATAAAA
1 A-TTAAATTTAA
*
11172170 AATAAATTTAA
1 ATTAAATTTAA
11172181 ATT
1 ATT
11172184 TAAAATAAAT
Statistics
Matches: 38, Mismatches: 8, Indels: 4
0.76 0.16 0.08
Matches are distributed among these distances:
11 30 0.79
12 8 0.21
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (11 bp):
ATTAAATTTAA
Found at i:11172189 original size:7 final size:6
Alignment explanation
Indices: 11172126--11172203 Score: 56
Period size: 6 Copynumber: 13.7 Consensus size: 6
11172116 TACCATAATA
* * * * *
11172126 TTAAAT TTAAA- TTAAAT TCAAAC TTAAA- TTAAAC TTAAA- TAAAAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT
* * *
11172171 ATAAAT TTAAAT TTAAA- ATAAAT TTGAAT TTAA
1 TTAAAT TTAAAT TTAAAT TTAAAT TTAAAT TTAA
11172204 CATAAACTTA
Statistics
Matches: 56, Mismatches: 12, Indels: 8
0.74 0.16 0.11
Matches are distributed among these distances:
5 18 0.32
6 38 0.68
ACGTcount: A:0.56, C:0.04, G:0.01, T:0.38
Consensus pattern (6 bp):
TTAAAT
Found at i:11172193 original size:17 final size:17
Alignment explanation
Indices: 11172126--11172232 Score: 90
Period size: 17 Copynumber: 6.3 Consensus size: 17
11172116 TACCATAATA
*
11172126 TTAAATTTAAATTAAAT
1 TTAAATTTAAAATAAAT
* * * *
11172143 TCAAACTTAAATTAAAC
1 TTAAATTTAAAATAAAT
**
11172160 TTAAATAAAAAATAAAT
1 TTAAATTTAAAATAAAT
11172177 TTAAATTTAAAATAAAT
1 TTAAATTTAAAATAAAT
* * *
11172194 TTGAATTTAACATAAAC
1 TTAAATTTAAAATAAAT
**
11172211 TT-AATTTCAAAGCAAAT
1 TTAAATTT-AAAATAAAT
11172228 TTAAA
1 TTAAA
11172233 ATGGTTTGGG
Statistics
Matches: 70, Mismatches: 18, Indels: 3
0.77 0.20 0.03
Matches are distributed among these distances:
16 5 0.07
17 63 0.90
18 2 0.03
ACGTcount: A:0.55, C:0.07, G:0.02, T:0.36
Consensus pattern (17 bp):
TTAAATTTAAAATAAAT
Found at i:11177109 original size:2 final size:2
Alignment explanation
Indices: 11177104--11177133 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
11177094 GACTACATAC
11177104 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
11177134 TGAGTATTTT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:11178533 original size:43 final size:42
Alignment explanation
Indices: 11178435--11178573 Score: 179
Period size: 42 Copynumber: 3.3 Consensus size: 42
11178425 TTATGAGGAA
* * * * *
11178435 AAACGTCGCTATAGAACATGATCTTTAGCGGCGCTTTCTCAT
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCCCAC
* * *
11178477 AAACGCCGCTAAAGAACATGGTCTTTAACGGTGTTTTTCCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCG-TTTTCCCAC
*
11178520 AAACGCCGCTAAAGAACATGATCTTTAGTGGCGTTTTCCCAC
1 AAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCCCAC
*
11178562 AAGCGCCGCTAA
1 AAACGCCGCTAA
11178574 TATTAACAGA
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
42 48 0.58
43 35 0.42
ACGTcount: A:0.28, C:0.26, G:0.19, T:0.27
Consensus pattern (42 bp):
AAACGCCGCTAAAGAACATGATCTTTAGCGGCGTTTTCCCAC
Found at i:11180532 original size:23 final size:22
Alignment explanation
Indices: 11180484--11180532 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
11180474 TTGAAACTAT
* *
11180484 TATAATTTTTTTGTTAAATTTT
1 TATAATTTTTTTGTTAAATGTA
**
11180506 TATAATTTTTTATGTTTTATGTA
1 TATAATTTTTT-TGTTAAATGTA
11180529 TATA
1 TATA
11180533 TTTATGATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (22 bp):
TATAATTTTTTTGTTAAATGTA
Found at i:11182584 original size:24 final size:24
Alignment explanation
Indices: 11182552--11182608 Score: 69
Period size: 24 Copynumber: 2.4 Consensus size: 24
11182542 CTTTCTCATA
* *
11182552 AGCGTCGCTAATGCTCTGATCTTT
1 AGCGGCGCTAATGCTCTGACCTTT
* * *
11182576 AGCGGCGCTTATGTTTTGACCTTT
1 AGCGGCGCTAATGCTCTGACCTTT
11182600 AGCGGCGCT
1 AGCGGCGCT
11182609 TTTTTATAAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
24 28 1.00
ACGTcount: A:0.14, C:0.25, G:0.26, T:0.35
Consensus pattern (24 bp):
AGCGGCGCTAATGCTCTGACCTTT
Found at i:11182634 original size:65 final size:65
Alignment explanation
Indices: 11182527--11182650 Score: 203
Period size: 65 Copynumber: 1.9 Consensus size: 65
11182517 GCTAATGCTC
* *
11182527 TGACCTTTAGCGGCGCTTTCTCATAAGCGTCGCTAATGCTCTGATCTTTAGCGGCGCTTATGTTT
1 TGACCTTTAGCGGCGCTTTCTCATAAGCGTCGCTAATACTCTGACCTTTAGCGGCGCTTATGTTT
* * *
11182592 TGACCTTTAGCGGCGCTTTTTTATAAGCGTCGCTAATACTCTGACCTTTAGTGGCGCTT
1 TGACCTTTAGCGGCGCTTTCTCATAAGCGTCGCTAATACTCTGACCTTTAGCGGCGCTT
11182651 TCTTATAAGT
Statistics
Matches: 54, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
65 54 1.00
ACGTcount: A:0.16, C:0.24, G:0.23, T:0.37
Consensus pattern (65 bp):
TGACCTTTAGCGGCGCTTTCTCATAAGCGTCGCTAATACTCTGACCTTTAGCGGCGCTTATGTTT
Found at i:11182649 original size:41 final size:41
Alignment explanation
Indices: 11182592--11182756 Score: 197
Period size: 41 Copynumber: 4.0 Consensus size: 41
11182582 GCTTATGTTT
* *
11182592 TGACCTTTAGCGGCGCTTTTTTATAAGCGTCGCTAATACTC
1 TGACCTTTAGCGGCGCTTTCTTATAAGTGTCGCTAATACTC
* * *
11182633 TGACCTTTAGTGGCGCTTTCTTATAAGTGCCGCTAATGCTC
1 TGACCTTTAGCGGCGCTTTCTTATAAGTGTCGCTAATACTC
* * * * *
11182674 TGATCTTTAGCGGCACTTTCTCATAAATGTCGCTAATATTC
1 TGACCTTTAGCGGCGCTTTCTTATAAGTGTCGCTAATACTC
* * *
11182715 TGACTTTTAGCGACGCTTTCTTATAAGTG-CTGCTAATGCTC
1 TGACCTTTAGCGGCGCTTTCTTATAAGTGTC-GCTAATACTC
11182756 T
1 T
11182757 TTCTCATATT
Statistics
Matches: 102, Mismatches: 21, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
40 1 0.01
41 101 0.99
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.38
Consensus pattern (41 bp):
TGACCTTTAGCGGCGCTTTCTTATAAGTGTCGCTAATACTC
Found at i:11182733 original size:82 final size:82
Alignment explanation
Indices: 11182596--11182756 Score: 232
Period size: 82 Copynumber: 2.0 Consensus size: 82
11182586 ATGTTTTGAC
* * * * * *
11182596 CTTTAGCGGCGCTTTTTTATAAGCGTCGCTAATACTCTGACCTTTAGTGGCGCTTTCTTATAAGT
1 CTTTAGCGGCACTTTCTCATAAACGTCGCTAATACTCTGACCTTTAGCGACGCTTTCTTATAAGT
11182661 GCCGCTAATGCTCTGAT
66 GCCGCTAATGCTCTGAT
* * *
11182678 CTTTAGCGGCACTTTCTCATAAATGTCGCTAATATTCTGACTTTTAGCGACGCTTTCTTATAAGT
1 CTTTAGCGGCACTTTCTCATAAACGTCGCTAATACTCTGACCTTTAGCGACGCTTTCTTATAAGT
*
11182743 GCTGCTAATGCTCT
66 GCCGCTAATGCTCT
11182757 TTCTCATATT
Statistics
Matches: 69, Mismatches: 10, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
82 69 1.00
ACGTcount: A:0.20, C:0.23, G:0.19, T:0.39
Consensus pattern (82 bp):
CTTTAGCGGCACTTTCTCATAAACGTCGCTAATACTCTGACCTTTAGCGACGCTTTCTTATAAGT
GCCGCTAATGCTCTGAT
Found at i:11184105 original size:56 final size:57
Alignment explanation
Indices: 11184024--11184154 Score: 142
Period size: 56 Copynumber: 2.3 Consensus size: 57
11184014 CTATTTAATA
* * * * * * *
11184024 ATTTGAGTGAATTACCTCTTGAATATTACATTTATATATA-TATTAGTATA-AGAGGAG
1 ATTTGAGTCAATTAACTATTAAATATT-CATTAATATACATTATTACTATATA-AGGAG
*
11184081 A-TTGAGTCAATTAACTATTAAATATTGATTAATATACATTATTACTATATAAGGAG
1 ATTTGAGTCAATTAACTATTAAATATTCATTAATATACATTATTACTATATAAGGAG
*
11184137 ATTTGAGTCAAATAACTA
1 ATTTGAGTCAATTAACTA
11184155 GTTCCATATG
Statistics
Matches: 62, Mismatches: 9, Indels: 6
0.81 0.12 0.08
Matches are distributed among these distances:
55 9 0.15
56 36 0.58
57 17 0.27
ACGTcount: A:0.40, C:0.08, G:0.13, T:0.39
Consensus pattern (57 bp):
ATTTGAGTCAATTAACTATTAAATATTCATTAATATACATTATTACTATATAAGGAG
Found at i:11185371 original size:41 final size:41
Alignment explanation
Indices: 11185320--11185473 Score: 218
Period size: 41 Copynumber: 3.7 Consensus size: 41
11185310 GGCGTTTATG
* *
11185320 AGAAAGCGCCGCTAATGCTCCGACCTTTAGTGGCGCTTTCAC
1 AGAAA-CGCCGCTAATGCTCCGACCTTTAGCGGCGCTTTCCC
* *
11185362 AGAAACGCCGCTAATGCTCCGACCTTTAACGACGCTTTCCC
1 AGAAACGCCGCTAATGCTCCGACCTTTAGCGGCGCTTTCCC
*
11185403 AGAAACGCCGCTAGTGCTCCGACCTTTAGCGGCGCTTTCCC
1 AGAAACGCCGCTAATGCTCCGACCTTTAGCGGCGCTTTCCC
* * * *
11185444 ATAAACGTCGCTAATGATCTGACCTTTAGC
1 AGAAACGCCGCTAATGCTCCGACCTTTAGC
11185474 AGTGTTTTTT
Statistics
Matches: 100, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
41 95 0.95
42 5 0.05
ACGTcount: A:0.23, C:0.32, G:0.21, T:0.24
Consensus pattern (41 bp):
AGAAACGCCGCTAATGCTCCGACCTTTAGCGGCGCTTTCCC
Found at i:11193920 original size:95 final size:95
Alignment explanation
Indices: 11193815--11194012 Score: 281
Period size: 95 Copynumber: 2.1 Consensus size: 95
11193805 ACCTCAATAA
* * * *
11193815 TAATAGTAATCATTCAATAAAATGGTATATTAGTCATTTCTTAATCGAGGTGATATTTAATTAA-
1 TAATAATAATCATTCAATAAAATGATAAATTAATCATTTCTTAATCGAGGTGATATTTAATTAAT
* *
11193879 CTCGTGACATAAATTCAATTAAGAATTTTAT
66 C-CATGACACAAATTCAATTAAGAATTTTAT
* * *
11193910 TAATAATAATCATTTAATAAAATGATAAATTAATCATTTCTTAATCGAGGTGATTTTTGATTAAT
1 TAATAATAATCATTCAATAAAATGATAAATTAATCATTTCTTAATCGAGGTGATATTTAATTAAT
* *
11193975 CCATGACACCAATTCAATTAAGAGTTTTAT
66 CCATGACACAAATTCAATTAAGAATTTTAT
11194005 TAATAATA
1 TAATAATA
11194013 TAGAAAAAAA
Statistics
Matches: 91, Mismatches: 11, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
95 90 0.99
96 1 0.01
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (95 bp):
TAATAATAATCATTCAATAAAATGATAAATTAATCATTTCTTAATCGAGGTGATATTTAATTAAT
CCATGACACAAATTCAATTAAGAATTTTAT
Found at i:11200226 original size:12 final size:12
Alignment explanation
Indices: 11200211--11200245 Score: 52
Period size: 12 Copynumber: 2.9 Consensus size: 12
11200201 TGTCATATGT
11200211 ATTTTTATGTAC
1 ATTTTTATGTAC
* *
11200223 ATTTTGATGGAC
1 ATTTTTATGTAC
11200235 ATTTTTATGTA
1 ATTTTTATGTA
11200246 TATATAATTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 19 1.00
ACGTcount: A:0.26, C:0.06, G:0.14, T:0.54
Consensus pattern (12 bp):
ATTTTTATGTAC
Found at i:11204290 original size:2 final size:2
Alignment explanation
Indices: 11204283--11204307 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
11204273 CAATTCCTTC
11204283 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
11204308 AGGCTCAACT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:11207606 original size:4 final size:4
Alignment explanation
Indices: 11207597--11207623 Score: 54
Period size: 4 Copynumber: 6.8 Consensus size: 4
11207587 CATAGCAAGA
11207597 AATT AATT AATT AATT AATT AATT AAT
1 AATT AATT AATT AATT AATT AATT AAT
11207624 ACTTGCTTAG
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (4 bp):
AATT
Found at i:11207945 original size:18 final size:17
Alignment explanation
Indices: 11207891--11207946 Score: 53
Period size: 18 Copynumber: 3.1 Consensus size: 17
11207881 CACCAATATA
11207891 TTAA-AAAAATTATTAAT
1 TTAATAAAAATTA-TAAT
11207908 ATTAATAACAAATT-TAAAT
1 -TTAATAA-AAATTAT-AAT
11207927 TTAATAAAATATTATAAT
1 TTAATAAAA-ATTATAAT
11207945 TT
1 TT
11207947 TCAATATATG
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
17 2 0.06
18 20 0.61
19 6 0.18
20 5 0.15
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAATAAAAATTATAAT
Found at i:11210822 original size:15 final size:15
Alignment explanation
Indices: 11210787--11210824 Score: 58
Period size: 15 Copynumber: 2.5 Consensus size: 15
11210777 TGCTGCTTTG
11210787 GGAGGAGGTGGTGCC
1 GGAGGAGGTGGTGCC
* *
11210802 GCAGGAGGTGGTGCT
1 GGAGGAGGTGGTGCC
11210817 GGAGGAGG
1 GGAGGAGG
11210825 AGGAGCTGGT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.16, C:0.11, G:0.61, T:0.13
Consensus pattern (15 bp):
GGAGGAGGTGGTGCC
Found at i:11210935 original size:6 final size:6
Alignment explanation
Indices: 11210924--11210955 Score: 64
Period size: 6 Copynumber: 5.3 Consensus size: 6
11210914 TCGTGGTCAA
11210924 ATTAGT ATTAGT ATTAGT ATTAGT ATTAGT AT
1 ATTAGT ATTAGT ATTAGT ATTAGT ATTAGT AT
11210956 CAGAATCGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 26 1.00
ACGTcount: A:0.34, C:0.00, G:0.16, T:0.50
Consensus pattern (6 bp):
ATTAGT
Found at i:11215446 original size:17 final size:18
Alignment explanation
Indices: 11215424--11215458 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
11215414 CATATGAGAA
11215424 AATTTTATA-AATTTTTT
1 AATTTTATATAATTTTTT
*
11215441 AATTTTCTATAATTTTTT
1 AATTTTATATAATTTTTT
11215459 TCATAATTAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.66
Consensus pattern (18 bp):
AATTTTATATAATTTTTT
Found at i:11218451 original size:25 final size:25
Alignment explanation
Indices: 11218423--11218489 Score: 64
Period size: 26 Copynumber: 2.6 Consensus size: 25
11218413 TTCTAACTTG
* * *
11218423 AATTTTTTTAATTTTTATAATTTAT
1 AATTTTTTTAATTTTAAAAATATAT
11218448 AATTTCTTTT-ATATTTAAAAATATAT
1 AATTT-TTTTAAT-TTTAAAAATATAT
*
11218474 AATTTTTATATATTTT
1 AATTTTTTTA-ATTTT
11218490 CTTTAAAACT
Statistics
Matches: 34, Mismatches: 4, Indels: 7
0.76 0.09 0.16
Matches are distributed among these distances:
25 10 0.29
26 22 0.65
27 2 0.06
ACGTcount: A:0.36, C:0.01, G:0.00, T:0.63
Consensus pattern (25 bp):
AATTTTTTTAATTTTAAAAATATAT
Found at i:11218519 original size:22 final size:22
Alignment explanation
Indices: 11218477--11218518 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
11218467 AATATATAAT
*
11218477 TTTTATATATTTTCTTTAAAAC
1 TTTTAAATATTTTCTTTAAAAC
11218499 TTTTAAATATTTT-TTTAAAA
1 TTTTAAATATTTTCTTTAAAA
11218519 AATAGATTAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.36, C:0.05, G:0.00, T:0.60
Consensus pattern (22 bp):
TTTTAAATATTTTCTTTAAAAC
Found at i:11219489 original size:8 final size:8
Alignment explanation
Indices: 11219476--11219516 Score: 57
Period size: 8 Copynumber: 5.1 Consensus size: 8
11219466 ATAATATAAA
11219476 TATAATTT
1 TATAATTT
11219484 TATAATTT
1 TATAATTT
11219492 TAATAA-TT
1 T-ATAATTT
11219500 TATAATTT
1 TATAATTT
*
11219508 TATTATTT
1 TATAATTT
11219516 T
1 T
11219517 TAAAAGGTTA
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
7 4 0.13
8 22 0.73
9 4 0.13
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (8 bp):
TATAATTT
Found at i:11219672 original size:17 final size:17
Alignment explanation
Indices: 11219650--11219690 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
11219640 GATCATAATC
11219650 TAAATTTACAAAAAAAT
1 TAAATTTACAAAAAAAT
*
11219667 TAAA-TT-GAAAAAAAT
1 TAAATTTACAAAAAAAT
11219682 TAAACTTTA
1 TAAA-TTTA
11219691 TAATAATCAT
Statistics
Matches: 20, Mismatches: 1, Indels: 5
0.77 0.04 0.19
Matches are distributed among these distances:
15 12 0.60
16 2 0.10
17 6 0.30
ACGTcount: A:0.61, C:0.05, G:0.02, T:0.32
Consensus pattern (17 bp):
TAAATTTACAAAAAAAT
Found at i:11227074 original size:25 final size:24
Alignment explanation
Indices: 11227017--11227075 Score: 59
Period size: 24 Copynumber: 2.5 Consensus size: 24
11227007 AAAAATAGGT
* *
11227017 TATA-TATTATTTTTCTAATATTA
1 TATATTATAATTTTTCTAATATCA
11227040 TATATTATAATTTTTACTAAT-TCA
1 TATATTATAATTTTT-CTAATATCA
*
11227064 TATTTTAATAAT
1 TATATT-ATAAT
11227076 AATTATATTA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
23 4 0.13
24 16 0.53
25 10 0.33
ACGTcount: A:0.37, C:0.05, G:0.00, T:0.58
Consensus pattern (24 bp):
TATATTATAATTTTTCTAATATCA
Found at i:11227136 original size:58 final size:58
Alignment explanation
Indices: 11227049--11227194 Score: 190
Period size: 58 Copynumber: 2.5 Consensus size: 58
11227039 ATATATTATA
* * *
11227049 ATTTTTACT-AATTCATATTTTAATAATAATTATATTAAAAATATTATTAAATT-ATATATT
1 ATTTTTATTAAATT-ATA-TTTAATAATAATTATATT-AAAATATAATTAAATTAAT-TAAT
* *
11227109 A-TTTTATTAAATTGTATTTAATAATAATTATGTTAAAATATAATTAAATTAATTAAT
1 ATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAATTAAT
11227166 ATTTTTATTAAATTATATTTAATAATAAT
1 ATTTTTATTAAATTATATTTAATAATAAT
11227195 CATTAAAATT
Statistics
Matches: 77, Mismatches: 6, Indels: 8
0.85 0.07 0.09
Matches are distributed among these distances:
57 19 0.25
58 45 0.58
59 8 0.10
60 5 0.06
ACGTcount: A:0.46, C:0.01, G:0.01, T:0.51
Consensus pattern (58 bp):
ATTTTTATTAAATTATATTTAATAATAATTATATTAAAATATAATTAAATTAATTAAT
Found at i:11227385 original size:16 final size:16
Alignment explanation
Indices: 11227364--11227419 Score: 87
Period size: 16 Copynumber: 3.5 Consensus size: 16
11227354 TGAATTACTG
11227364 ATTACAG-TCCTATTCC
1 ATTACAGCT-CTATTCC
*
11227380 ATTACAGCTCTACTCC
1 ATTACAGCTCTATTCC
11227396 ATTACAGCTCTATTCC
1 ATTACAGCTCTATTCC
11227412 ATTACAGC
1 ATTACAGC
11227420 GAACCAAACG
Statistics
Matches: 37, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
16 36 0.97
17 1 0.03
ACGTcount: A:0.27, C:0.32, G:0.07, T:0.34
Consensus pattern (16 bp):
ATTACAGCTCTATTCC
Found at i:11227540 original size:28 final size:28
Alignment explanation
Indices: 11227478--11227540 Score: 74
Period size: 28 Copynumber: 2.2 Consensus size: 28
11227468 GTACCAACTT
** *
11227478 GAAAAAAAATAGTTTAGGTGTCGCTTGT
1 GAAAAAAAATAGTTTAGGTGTCGAATGA
11227506 GACAAAAAAAT-GTTTAGGTGTCGAAATGA
1 GA-AAAAAAATAGTTTAGGTGTCG-AATGA
11227535 GAAAAA
1 GAAAAA
11227541 TGCATAGTTT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
28 18 0.60
29 12 0.40
ACGTcount: A:0.44, C:0.06, G:0.24, T:0.25
Consensus pattern (28 bp):
GAAAAAAAATAGTTTAGGTGTCGAATGA
Found at i:11231598 original size:30 final size:30
Alignment explanation
Indices: 11231562--11231637 Score: 107
Period size: 33 Copynumber: 2.4 Consensus size: 30
11231552 TTCCGGAGCC
*
11231562 GGAGATGCAGATGGTGGAGAGGAAGGAGAA
1 GGAGATGCAGATGGCGGAGAGGAAGGAGAA
11231592 GGAGATGCCGATGATGGCGGAGAGGAAGGAGAA
1 GGAGATG-C-A-GATGGCGGAGAGGAAGGAGAA
*
11231625 GGAGATGCCGATG
1 GGAGATGCAGATG
11231638 CTGGCGTAGA
Statistics
Matches: 41, Mismatches: 2, Indels: 6
0.84 0.04 0.12
Matches are distributed among these distances:
30 11 0.27
31 1 0.02
32 2 0.05
33 27 0.66
ACGTcount: A:0.33, C:0.08, G:0.49, T:0.11
Consensus pattern (30 bp):
GGAGATGCAGATGGCGGAGAGGAAGGAGAA
Found at i:11231608 original size:33 final size:33
Alignment explanation
Indices: 11231571--11231643 Score: 128
Period size: 33 Copynumber: 2.2 Consensus size: 33
11231561 CGGAGATGCA
*
11231571 GATGGTGGAGAGGAAGGAGAAGGAGATGCCGAT
1 GATGGCGGAGAGGAAGGAGAAGGAGATGCCGAT
11231604 GATGGCGGAGAGGAAGGAGAAGGAGATGCCGAT
1 GATGGCGGAGAGGAAGGAGAAGGAGATGCCGAT
*
11231637 GCTGGCG
1 GATGGCG
11231644 TAGACGTGGC
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
33 38 1.00
ACGTcount: A:0.30, C:0.10, G:0.49, T:0.11
Consensus pattern (33 bp):
GATGGCGGAGAGGAAGGAGAAGGAGATGCCGAT
Found at i:11237263 original size:25 final size:26
Alignment explanation
Indices: 11237225--11237276 Score: 63
Period size: 25 Copynumber: 2.0 Consensus size: 26
11237215 TATTTTTTTG
11237225 TATTTTAACAGAAA-A-TTAACATAAA
1 TATTTTAACAGAAATAGTTAACA-AAA
* *
11237250 TATTTTAGCTGAAATAGTTAACAAAA
1 TATTTTAACAGAAATAGTTAACAAAA
11237276 T
1 T
11237277 TAATTATTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 12 0.52
26 5 0.22
27 6 0.26
ACGTcount: A:0.50, C:0.08, G:0.08, T:0.35
Consensus pattern (26 bp):
TATTTTAACAGAAATAGTTAACAAAA
Found at i:11237597 original size:17 final size:17
Alignment explanation
Indices: 11237575--11237608 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
11237565 TATAAAAATA
*
11237575 TAAAAATTAAATTATAT
1 TAAAAATTAAAGTATAT
11237592 TAAAAATTAAAGTATAT
1 TAAAAATTAAAGTATAT
11237609 GGATTAAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (17 bp):
TAAAAATTAAAGTATAT
Found at i:11238514 original size:8 final size:8
Alignment explanation
Indices: 11238501--11238568 Score: 61
Period size: 8 Copynumber: 8.4 Consensus size: 8
11238491 TTTTAAAAAT
11238501 AAATTTTA
1 AAATTTTA
11238509 AAATTTTTTA
1 AAA--TTTTA
11238519 AAATTTTA
1 AAATTTTA
*
11238527 AAA--AT-
1 AAATTTTA
11238532 AAATTTTA
1 AAATTTTA
*
11238540 TAATTTTTTA
1 -AA-ATTTTA
11238550 AAATTTTA
1 AAATTTTA
11238558 AAATTTTA
1 AAATTTTA
11238566 AAA
1 AAA
11238569 ATTAATTATA
Statistics
Matches: 49, Mismatches: 4, Indels: 14
0.73 0.06 0.21
Matches are distributed among these distances:
5 3 0.06
6 1 0.02
7 1 0.02
8 27 0.55
9 4 0.08
10 13 0.27
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (8 bp):
AAATTTTA
Found at i:11238525 original size:9 final size:9
Alignment explanation
Indices: 11238504--11238571 Score: 57
Period size: 9 Copynumber: 7.1 Consensus size: 9
11238494 TAAAAATAAA
11238504 TTTTAAAATT
1 TTTTAAAA-T
11238514 TTTTAAAAT
1 TTTTAAAAT
*
11238523 TTTAAAAAT
1 TTTTAAAAT
*
11238532 AAATTTTATAATT
1 ---TTTTA-AAAT
11238545 TTTTAAAA-
1 TTTTAAAAT
11238553 TTTTAAAAT
1 TTTTAAAAT
*
11238562 TTTAAAAAT
1 TTTTAAAAT
11238571 T
1 T
11238572 AATTATATAT
Statistics
Matches: 48, Mismatches: 5, Indels: 11
0.75 0.08 0.17
Matches are distributed among these distances:
8 8 0.17
9 20 0.42
10 13 0.27
12 4 0.08
13 3 0.06
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (9 bp):
TTTTAAAAT
Found at i:11238528 original size:31 final size:31
Alignment explanation
Indices: 11238490--11238560 Score: 133
Period size: 31 Copynumber: 2.3 Consensus size: 31
11238480 AATAATTTTT
11238490 ATTTTAAAAATAAATTTTAAAATTTTTTAAA
1 ATTTTAAAAATAAATTTTAAAATTTTTTAAA
*
11238521 ATTTTAAAAATAAATTTTATAATTTTTTAAA
1 ATTTTAAAAATAAATTTTAAAATTTTTTAAA
11238552 ATTTTAAAA
1 ATTTTAAAA
11238561 TTTTAAAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
31 39 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (31 bp):
ATTTTAAAAATAAATTTTAAAATTTTTTAAA
Found at i:11238535 original size:23 final size:23
Alignment explanation
Indices: 11238509--11238552 Score: 61
Period size: 23 Copynumber: 1.9 Consensus size: 23
11238499 ATAAATTTTA
*
11238509 AAATTTTTTAAAATTTTAAAAAT
1 AAATTTTATAAAATTTTAAAAAT
**
11238532 AAATTTTATAATTTTTTAAAA
1 AAATTTTATAAAATTTTAAAA
11238553 TTTTAAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (23 bp):
AAATTTTATAAAATTTTAAAAAT
Found at i:11238557 original size:39 final size:40
Alignment explanation
Indices: 11238504--11238580 Score: 120
Period size: 39 Copynumber: 1.9 Consensus size: 40
11238494 TAAAAATAAA
*
11238504 TTTTAAAATTTTTTAAAATTTTAAAAATAAATTTTATAATT
1 TTTTAAAA-TTTTTAAAATTTTAAAAATAAATTATATAATT
*
11238545 TTTTAAAA-TTTTAAAATTTTAAAAATTAATTATATA
1 TTTTAAAATTTTTAAAATTTTAAAAATAAATTATATA
11238581 TTTATGTGAC
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
39 26 0.76
41 8 0.24
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (40 bp):
TTTTAAAATTTTTAAAATTTTAAAAATAAATTATATAATT
Found at i:11247846 original size:21 final size:21
Alignment explanation
Indices: 11247811--11247906 Score: 71
Period size: 21 Copynumber: 4.8 Consensus size: 21
11247801 TATATTATTA
*
11247811 TTTTGG-TGCTTTTTTTACTG
1 TTTTGGTTGCTATTTTTACTG
*
11247831 TTTTGGTTGCTATTTTTGCTG
1 TTTTGGTTGCTATTTTTACTG
* * *
11247852 CTTTGATACTG-TTTTTTTA-TGG
1 TTTTGGT--TGCTATTTTTACT-G
11247874 TTTTGG-T--T-TTTTTACTG
1 TTTTGGTTGCTATTTTTACTG
11247891 TTTTGGTTGCTATTTT
1 TTTTGGTTGCTATTTT
11247907 GGTGCTGTTT
Statistics
Matches: 59, Mismatches: 8, Indels: 17
0.70 0.10 0.20
Matches are distributed among these distances:
17 13 0.22
18 3 0.05
19 1 0.02
20 7 0.12
21 22 0.37
22 11 0.19
23 2 0.03
ACGTcount: A:0.07, C:0.08, G:0.20, T:0.65
Consensus pattern (21 bp):
TTTTGGTTGCTATTTTTACTG
Found at i:11247886 original size:18 final size:17
Alignment explanation
Indices: 11247862--11247898 Score: 58
Period size: 17 Copynumber: 2.2 Consensus size: 17
11247852 CTTTGATACT
11247862 GTTTTTTTA-TGGTTTTG
1 GTTTTTTTACT-GTTTTG
11247879 GTTTTTTTACTGTTTTG
1 GTTTTTTTACTGTTTTG
11247896 GTT
1 GTT
11247899 GCTATTTTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
17 18 0.95
18 1 0.05
ACGTcount: A:0.05, C:0.03, G:0.22, T:0.70
Consensus pattern (17 bp):
GTTTTTTTACTGTTTTG
Found at i:11247953 original size:12 final size:12
Alignment explanation
Indices: 11247933--11248040 Score: 80
Period size: 12 Copynumber: 9.3 Consensus size: 12
11247923 ATTTTAATGA
11247933 TGTTATTTTTGT
1 TGTTATTTTTGT
* *
11247945 TGCTATTTTTGC
1 TGTTATTTTTGT
*
11247957 TATTATTTTTGT
1 TGTTATTTTTGT
* *
11247969 TG--CTGTTT-T
1 TGTTATTTTTGT
11247978 TGTTATTTTTGT
1 TGTTATTTTTGT
**
11247990 TGTTA-TTTTAC
1 TGTTATTTTTGT
*
11248001 TGTTATTTTTGC
1 TGTTATTTTTGT
* * *
11248013 TGCTGTTTTGGT
1 TGTTATTTTTGT
*
11248025 TGTTATTTTGGT
1 TGTTATTTTTGT
11248037 TGTT
1 TGTT
11248041 TGGATGCTAT
Statistics
Matches: 73, Mismatches: 19, Indels: 8
0.73 0.19 0.08
Matches are distributed among these distances:
9 3 0.04
10 4 0.05
11 13 0.18
12 53 0.73
ACGTcount: A:0.08, C:0.06, G:0.19, T:0.68
Consensus pattern (12 bp):
TGTTATTTTTGT
Found at i:11248028 original size:24 final size:23
Alignment explanation
Indices: 11247933--11248038 Score: 108
Period size: 24 Copynumber: 4.6 Consensus size: 23
11247923 ATTTTAATGA
11247933 TGTTATTTTTGTTGCTATTTTTGC
1 TGTTATTTTTGTTGCTA-TTTTGC
* *
11247957 TATTATTTTTGTTGCTGTTTT--
1 TGTTATTTTTGTTGCTATTTTGC
* *
11247978 TGTTATTTTTGTTGTTATTTTAC
1 TGTTATTTTTGTTGCTATTTTGC
* * *
11248001 TGTTATTTTTGCTGCTGTTTTGGT
1 TGTTATTTTTGTTGCTATTTT-GC
*
11248025 TGTTATTTTGGTTG
1 TGTTATTTTTGTTG
11248039 TTTGGATGCT
Statistics
Matches: 67, Mismatches: 12, Indels: 6
0.79 0.14 0.07
Matches are distributed among these distances:
21 18 0.27
23 22 0.33
24 27 0.40
ACGTcount: A:0.08, C:0.06, G:0.19, T:0.67
Consensus pattern (23 bp):
TGTTATTTTTGTTGCTATTTTGC
Found at i:11250649 original size:28 final size:28
Alignment explanation
Indices: 11250592--11250646 Score: 67
Period size: 29 Copynumber: 1.9 Consensus size: 28
11250582 TTTCTTAGTA
*
11250592 TTTATTTAATTTCCATGCCCTAATCCCT
1 TTTATTTAATTTCCAGGCCCTAATCCCT
*
11250620 TTTATTCTAATTTTCAGGTCCC-AATCC
1 TTTATT-TAATTTCCAGG-CCCTAATCC
11250647 TTTGGTATAC
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
28 6 0.26
29 14 0.61
30 3 0.13
ACGTcount: A:0.22, C:0.27, G:0.05, T:0.45
Consensus pattern (28 bp):
TTTATTTAATTTCCAGGCCCTAATCCCT
Found at i:11253938 original size:15 final size:17
Alignment explanation
Indices: 11253918--11253955 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
11253908 AGAACAATTG
11253918 TATTTTTC-A-TCTTTC
1 TATTTTTCTACTCTTTC
11253933 TATTTTTCTACTCTTTC
1 TATTTTTCTACTCTTTC
*
11253950 AATTTT
1 TATTTT
11253956 CTTTTCATTC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 8 0.40
16 1 0.05
17 11 0.55
ACGTcount: A:0.16, C:0.18, G:0.00, T:0.66
Consensus pattern (17 bp):
TATTTTTCTACTCTTTC
Found at i:11257899 original size:28 final size:29
Alignment explanation
Indices: 11257867--11257922 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
11257857 ATAATGTAAT
11257867 GTTT-GTGTAATGACACAAAACATTACGA
1 GTTTGGTGTAATGACACAAAACATTACGA
* ** *
11257895 GTTTGGTGTTATTTCACAAAATATTACG
1 GTTTGGTGTAATGACACAAAACATTACG
11257923 TTAGTTGTAA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
28 4 0.17
29 19 0.83
ACGTcount: A:0.34, C:0.12, G:0.18, T:0.36
Consensus pattern (29 bp):
GTTTGGTGTAATGACACAAAACATTACGA
Found at i:11259941 original size:11 final size:10
Alignment explanation
Indices: 11259907--11259971 Score: 57
Period size: 10 Copynumber: 6.8 Consensus size: 10
11259897 TGACATGTGG
*
11259907 TAAAAAATTA
1 TAAAAAATAA
11259917 TAAAAAA-AA
1 TAAAAAATAA
11259926 T-AAAAATCAA
1 TAAAAAAT-AA
*
11259936 TAAAAAATAT
1 TAAAAAATAA
**
11259946 TAAAATTTAA
1 TAAAAAATAA
11259956 T-AAAAAT-A
1 TAAAAAATAA
11259964 TAAAAAAT
1 TAAAAAAT
11259972 TAAAATTAGA
Statistics
Matches: 44, Mismatches: 7, Indels: 9
0.73 0.12 0.15
Matches are distributed among these distances:
8 7 0.16
9 12 0.27
10 19 0.43
11 6 0.14
ACGTcount: A:0.72, C:0.02, G:0.00, T:0.26
Consensus pattern (10 bp):
TAAAAAATAA
Found at i:11259970 original size:20 final size:19
Alignment explanation
Indices: 11259907--11259972 Score: 66
Period size: 20 Copynumber: 3.5 Consensus size: 19
11259897 TGACATGTGG
11259907 TAAAAAATTATAA-AAAAAA
1 TAAAAAATT-TAATAAAAAA
*
11259926 T-AAAAA-TCAATAAAAAA
1 TAAAAAATTTAATAAAAAA
*
11259943 TATTAAAATTTAATAAAAATA
1 TA-AAAAATTTAATAAAAA-A
11259964 TAAAAAATT
1 TAAAAAATT
11259973 AAAATTAGAA
Statistics
Matches: 38, Mismatches: 4, Indels: 9
0.75 0.08 0.18
Matches are distributed among these distances:
16 2 0.05
17 8 0.21
18 5 0.13
19 5 0.13
20 15 0.39
21 3 0.08
ACGTcount: A:0.71, C:0.02, G:0.00, T:0.27
Consensus pattern (19 bp):
TAAAAAATTTAATAAAAAA
Found at i:11259974 original size:19 final size:19
Alignment explanation
Indices: 11259907--11259974 Score: 68
Period size: 19 Copynumber: 3.6 Consensus size: 19
11259897 TGACATGTGG
11259907 TAAAAAATT-ATAAAAA-A
1 TAAAAAATTAATAAAAATA
* *
11259924 AATAAAAATCAATAAAAAATA
1 TA-AAAAATTAAT-AAAAATA
* *
11259945 TTAAAATTTAATAAAAATA
1 TAAAAAATTAATAAAAATA
11259964 TAAAAAATTAA
1 TAAAAAATTAA
11259975 AATTAGAAAA
Statistics
Matches: 39, Mismatches: 8, Indels: 6
0.74 0.15 0.11
Matches are distributed among these distances:
17 1 0.03
18 6 0.15
19 18 0.46
20 13 0.33
21 1 0.03
ACGTcount: A:0.72, C:0.01, G:0.00, T:0.26
Consensus pattern (19 bp):
TAAAAAATTAATAAAAATA
Found at i:11259986 original size:26 final size:27
Alignment explanation
Indices: 11259934--11259996 Score: 78
Period size: 26 Copynumber: 2.4 Consensus size: 27
11259924 AATAAAAATC
*
11259934 AATA-AAAAATATTAAAATTTAATAAA
1 AATATAAAAATATTAAAATTTAAAAAA
*
11259960 AATATAAAAA-ATTAAAA-TTAGAAAA
1 AATATAAAAATATTAAAATTTAAAAAA
11259985 AATATATAAAAT
1 AATATA-AAAAT
11259997 GCATCAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
25 12 0.38
26 15 0.47
27 5 0.16
ACGTcount: A:0.70, C:0.00, G:0.02, T:0.29
Consensus pattern (27 bp):
AATATAAAAATATTAAAATTTAAAAAA
Found at i:11259995 original size:25 final size:26
Alignment explanation
Indices: 11259924--11259996 Score: 78
Period size: 25 Copynumber: 2.7 Consensus size: 26
11259914 TTATAAAAAA
11259924 AATAAAAATCAATAAAAAATATTAAAATTT
1 AATAAAAAT--AT-AAAAA-ATTAAAATTT
11259954 AATAAAAATATAAAAAATTAAAA-TT
1 AATAAAAATATAAAAAATTAAAATTT
*
11259979 AGA-AAAAATATATAAAAT
1 A-ATAAAAATATAAAAAAT
11259997 GCATCAAAAA
Statistics
Matches: 41, Mismatches: 1, Indels: 7
0.84 0.02 0.14
Matches are distributed among these distances:
25 17 0.41
26 8 0.20
27 5 0.12
28 2 0.05
30 9 0.22
ACGTcount: A:0.70, C:0.01, G:0.01, T:0.27
Consensus pattern (26 bp):
AATAAAAATATAAAAAATTAAAATTT
Found at i:11260252 original size:90 final size:91
Alignment explanation
Indices: 11260088--11260331 Score: 295
Period size: 90 Copynumber: 2.7 Consensus size: 91
11260078 ATTAAGGGCG
* * ** *
11260088 GTTCAAGTATCCAATTGAGTG-TAAA-AAAATTAGGGGCTTAATTGC-TTTTTTGAAAAAGTTTG
1 GTTCAAGTATCCAATTGAATGCAAAATAAAAGCAAGGGCTTAATTGCTTTTTTTGAAAAAGTTTG
* *
11260150 A-GAGCTTCTTTGATGCATTTTGAAA
66 AGGACCTTCTTTGATGCATTTTAAAA
* * *
11260175 GTTTAAGTA-CACAATTGAATGCAAAATAAAAGTAATGGCTTAATTGCTTTTTTTGAAAAAGTTT
1 GTTCAAGTATC-CAATTGAATGCAAAATAAAAGCAAGGGCTTAATTGCTTTTTTTGAAAAAGTTT
11260239 GAGGACCTT-TTTGATGCATTTTAAAA
65 GAGGACCTTCTTTGATGCATTTTAAAA
* * * **
11260265 GTTCAAGTATCCAATTGAGTGCAAAATAAATGCAAGGGCTT-TTTTTTTTTTTTGAAAAAGTTTG
1 GTTCAAGTATCCAATTGAATGCAAAATAAAAGCAAGGGCTTAATTGCTTTTTTTGAAAAAGTTTG
11260329 AGG
66 AGG
11260332 GCTTTTTACA
Statistics
Matches: 135, Mismatches: 16, Indels: 10
0.84 0.10 0.06
Matches are distributed among these distances:
86 1 0.01
87 17 0.13
88 3 0.02
89 40 0.30
90 68 0.50
91 6 0.04
ACGTcount: A:0.34, C:0.09, G:0.19, T:0.38
Consensus pattern (91 bp):
GTTCAAGTATCCAATTGAATGCAAAATAAAAGCAAGGGCTTAATTGCTTTTTTTGAAAAAGTTTG
AGGACCTTCTTTGATGCATTTTAAAA
Found at i:11261534 original size:27 final size:28
Alignment explanation
Indices: 11261482--11261536 Score: 69
Period size: 28 Copynumber: 2.0 Consensus size: 28
11261472 CGAATATTAC
**
11261482 ATTTTCTAAGAAAATTTTATTCCTCTTT
1 ATTTTCTAAGAAAATTGAATTCCTCTTT
11261510 ATTTT-TAAGAAAAATTGAATT-CTCTTT
1 ATTTTCTAAG-AAAATTGAATTCCTCTTT
11261537 CATATCTCTA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
27 10 0.42
28 14 0.58
ACGTcount: A:0.33, C:0.11, G:0.05, T:0.51
Consensus pattern (28 bp):
ATTTTCTAAGAAAATTGAATTCCTCTTT
Found at i:11261671 original size:68 final size:68
Alignment explanation
Indices: 11261546--11261672 Score: 154
Period size: 68 Copynumber: 1.9 Consensus size: 68
11261536 TCATATCTCT
* * *
11261546 ATTTTTCATTTGTGTTACTTTCTTTTTCTTTCTCATATTTGATTTTCTCATATATCTCTTAAACC
1 ATTTTTCATTTGTGTTACTTTCTTTTTCTTTCTCATATTTGACTTTCCCATAAATCTCTTAAACC
11261611 TTA
66 TTA
*
11261614 ATTTTTCATATT-TGTTA--TTCTCTTTTCTTTTCTTATATTCT-ACTTTCCCATAAATCTCT
1 ATTTTTCAT-TTGTGTTACTTTCT-TTTTC-TTTCTCATATT-TGACTTTCCCATAAATCTCT
11261673 CAAATTTTAA
Statistics
Matches: 51, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
66 4 0.08
67 5 0.10
68 39 0.76
69 3 0.06
ACGTcount: A:0.19, C:0.19, G:0.03, T:0.59
Consensus pattern (68 bp):
ATTTTTCATTTGTGTTACTTTCTTTTTCTTTCTCATATTTGACTTTCCCATAAATCTCTTAAACC
TTA
Found at i:11261828 original size:14 final size:15
Alignment explanation
Indices: 11261804--11261833 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
11261794 AGTTGTTTCT
11261804 TTTCAAATTTTTTTA
1 TTTCAAATTTTTTTA
*
11261819 TTTCAATTTTTTTTA
1 TTTCAAATTTTTTTA
11261834 AAATTCACAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.23, C:0.07, G:0.00, T:0.70
Consensus pattern (15 bp):
TTTCAAATTTTTTTA
Found at i:11267801 original size:21 final size:20
Alignment explanation
Indices: 11267775--11267829 Score: 56
Period size: 21 Copynumber: 2.7 Consensus size: 20
11267765 TGTTCACCCG
11267775 ATCTCGATATTTGGAGTACAA
1 ATCTCGATATTTGGAGT-CAA
* *
11267796 ATCTCGAAATTTAGAGTCAA
1 ATCTCGATATTTGGAGTCAA
* * *
11267816 GTCTTGATACTTGG
1 ATCTCGATATTTGG
11267830 TGATTAAGTA
Statistics
Matches: 27, Mismatches: 7, Indels: 1
0.77 0.20 0.03
Matches are distributed among these distances:
20 12 0.44
21 15 0.56
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.35
Consensus pattern (20 bp):
ATCTCGATATTTGGAGTCAA
Found at i:11268892 original size:29 final size:27
Alignment explanation
Indices: 11268861--11269140 Score: 87
Period size: 29 Copynumber: 9.7 Consensus size: 27
11268851 CTTTTGGGCA
11268861 AAAATGGAATTTTGGAAAGTTTGGGGGT
1 AAAATGGAATTTTGGAAA-TTTGGGGGT
* **
11268889 AAAATGGTAATTTTTGGTAAA-ATCAGGGT
1 AAAATGG-AA-TTTTGG-AAATTTGGGGGT
* * *
11268918 CAAAATGGAATTTTAGAAAAGTTTAGAGGT
1 -AAAATGGAATTTT-GGAAA-TTTGGGGGT
* * * * *
11268948 AAAAGGGTAATTTTGGTAAAATCGAGGTT
1 AAAATGG-AATTTTGG-AAATTTGGGGGT
* * ** * *
11268977 AAAATAGACTTTTAAAAGATTCGAGGGT
1 AAAATGGAATTTTGGAA-ATTTGGGGGT
* * *
11269005 AAAATGGTAATTTTTGGTAAAATCGGGGTT
1 AAAATGG-AA-TTTTGG-AAATTTGGGGGT
* **
11269035 AAAAATGGAATTTTAGAAAATTTAAGGGT
1 -AAAATGGAATTTT-GGAAATTTGGGGGT
* * * *
11269064 AAAATAGTATTTTTGATGAAA-TCGAGGGT
1 AAAAT-GGAATTTTG--GAAATTTGGGGGT
* *
11269093 AAAAATGGAATTTTGGAAAACTTAGGGGT
1 -AAAATGGAATTTTGG-AAATTTGGGGGT
*
11269122 AAAAATGGAATTTTAGAAA
1 -AAAATGGAATTTTGGAAA
11269141 GTTTAAGGTA
Statistics
Matches: 184, Mismatches: 47, Indels: 42
0.67 0.17 0.15
Matches are distributed among these distances:
27 3 0.02
28 45 0.24
29 76 0.41
30 48 0.26
31 12 0.07
ACGTcount: A:0.41, C:0.03, G:0.25, T:0.31
Consensus pattern (27 bp):
AAAATGGAATTTTGGAAATTTGGGGGT
Found at i:11268962 original size:58 final size:58
Alignment explanation
Indices: 11268860--11269135 Score: 271
Period size: 58 Copynumber: 4.7 Consensus size: 58
11268850 TCTTTTGGGC
* * *
11268860 AAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTTGGTAAAATCAGGGT
1 AAAAATGGAATTTTGAAAAGTTTAGAGGTAAAATGGTAATTTTTGGTAAAATCAGGGT
* *
11268918 CAAAATGGAATTTTAGAAAAGTTTAGAGGTAAAAGGGTAA-TTTTGGTAAAATC-GAGGT
1 AAAAATGGAATTTT-GAAAAGTTTAGAGGTAAAATGGTAATTTTTGGTAAAATCAG-GGT
* * * * * *
11268976 TAAAATAGACTTTT-AAAAGATTCGAGGGTAAAATGGTAATTTTTGGTAAAATCGGGGTT
1 AAAAATGGAATTTTGAAAAGTTTAGA-GGTAAAATGGTAATTTTTGGTAAAATCAGGG-T
* * *
11269035 AAAAATGGAATTTTAGAAAA-TTTA-AGGGTAAAATAGT-ATTTTTGATGAAATCGAGGGT
1 AAAAATGGAATTTT-GAAAAGTTTAGA-GGTAAAATGGTAATTTTTGGTAAAATC-AGGGT
* *
11269093 AAAAATGGAATTTTGGAAAA-CTTAGGGGTAAAAATGG-AATTTT
1 AAAAATGGAATTTT-GAAAAGTTTAGAGGT-AAAATGGTAATTTT
11269136 AGAAAGTTTA
Statistics
Matches: 182, Mismatches: 24, Indels: 23
0.79 0.10 0.10
Matches are distributed among these distances:
56 9 0.05
57 13 0.07
58 94 0.52
59 60 0.33
60 2 0.01
61 4 0.02
ACGTcount: A:0.40, C:0.03, G:0.25, T:0.32
Consensus pattern (58 bp):
AAAAATGGAATTTTGAAAAGTTTAGAGGTAAAATGGTAATTTTTGGTAAAATCAGGGT
Found at i:11269065 original size:116 final size:116
Alignment explanation
Indices: 11268885--11269096 Score: 320
Period size: 116 Copynumber: 1.8 Consensus size: 116
11268875 GAAAGTTTGG
*
11268885 GGGTAAAATGGTAATTTTTGGTAAAATCAGGGTCAAAATGGAATTTTAGAAAAGTTTAGAGGTAA
1 GGGTAAAATGGTAATTTTTGGTAAAATCAGGGTAAAAATGGAATTTTAGAAAAGTTTAGAGGTAA
* * *
11268950 AAGGGTAATTTTGGTAAAATCGAGGTTAAAATAGACTTTTAAAAGATTCGA
66 AAGAGTAATTTTGATAAAATCGAGGGTAAAATAGACTTTTAAAAGATTCGA
*
11269001 GGGTAAAATGGTAATTTTTGGTAAAATCGGGGTTAAAAATGGAATTTTAGAAAA-TTTA-AGGGT
1 GGGTAAAATGGTAATTTTTGGTAAAATCAGGG-TAAAAATGGAATTTTAGAAAAGTTTAGA-GGT
* * *
11269064 AAAATAGTATTTTTGATGAAATCGAGGGTAAAA
64 AAAAGAGTAATTTTGATAAAATCGAGGGTAAAA
11269097 ATGGAATTTT
Statistics
Matches: 86, Mismatches: 8, Indels: 4
0.88 0.08 0.04
Matches are distributed among these distances:
115 1 0.01
116 65 0.76
117 20 0.23
ACGTcount: A:0.41, C:0.03, G:0.25, T:0.32
Consensus pattern (116 bp):
GGGTAAAATGGTAATTTTTGGTAAAATCAGGGTAAAAATGGAATTTTAGAAAAGTTTAGAGGTAA
AAGAGTAATTTTGATAAAATCGAGGGTAAAATAGACTTTTAAAAGATTCGA
Found at i:11269151 original size:28 final size:28
Alignment explanation
Indices: 11269034--11269153 Score: 107
Period size: 29 Copynumber: 4.2 Consensus size: 28
11269024 AAATCGGGGT
11269034 TAAAAATGGAATTTTAGAAAATTTAAGGG
1 TAAAAATGGAATTTTAGAAAATTTAA-GG
* * * ** *
11269063 T-AAAATAGTATTTTTGATGAAATCGAGGG
1 TAAAAATGGAATTTTAGA--AAATTTAAGG
* * *
11269092 TAAAAATGGAATTTTGGAAAACTTAGGGG
1 TAAAAATGGAATTTTAGAAAATTTA-AGG
*
11269121 TAAAAATGGAATTTTAGAAAGTTTAAGG
1 TAAAAATGGAATTTTAGAAAATTTAAGG
11269149 TAAAA
1 TAAAA
11269154 TAGTAATTTT
Statistics
Matches: 71, Mismatches: 16, Indels: 9
0.74 0.17 0.09
Matches are distributed among these distances:
28 24 0.34
29 29 0.41
30 18 0.25
ACGTcount: A:0.45, C:0.02, G:0.23, T:0.31
Consensus pattern (28 bp):
TAAAAATGGAATTTTAGAAAATTTAAGG
Found at i:11269164 original size:87 final size:85
Alignment explanation
Indices: 11268860--11269164 Score: 255
Period size: 87 Copynumber: 3.5 Consensus size: 85
11268850 TCTTTTGGGC
* ** * * *
11268860 AAAAATGGAATTTTGGAAAGTTTGGGGGTAAAATGGTAATTTTTGGTAAAATC-AGGGTCAAAAT
1 AAAAATGGAATTTTAGAAAGTTT-AAGGTAAAATAGTAATTTTTGATGAAATCGAGGGT-AAAAT
* *
11268924 GGAATTTTAGAAAAGTTTAGAGGT
64 GGAATTTTGGAAAA--TTAGGGGT
* * * ** * ** * *
11268948 -AAAAGGGTAATTTTGGTAAA-ATCGAGGTTAAAATAG-ACTTTTAAAAG-ATTCGAGGGTAAAA
1 AAAAATGG-AATTTTAG-AAAGTTTAAGG-TAAAATAGTAATTTTTGATGAAATCGAGGGTAAAA
*
11269009 TGGTAATTTTTGGTAAAA-TCGGGGTT
63 TGG-AA-TTTTGG-AAAATTAGGGG-T
*
11269035 AAAAATGGAATTTTAGAAAATTTAAGGGTAAAATAGT-ATTTTTGATGAAATCGAGGGTAAAAAT
1 AAAAATGGAATTTTAGAAAGTTTAA-GGTAAAATAGTAATTTTTGATGAAATCGAGGGT-AAAAT
11269099 GGAATTTTGGAAAACTTAGGGGT
64 GGAATTTTGGAAAA-TTAGGGGT
11269122 AAAAATGGAATTTTAGAAAGTTTAAGGTAAAATAGTAATTTTT
1 AAAAATGGAATTTTAGAAAGTTTAAGGTAAAATAGTAATTTTT
11269165 AGAAAGTTTT
Statistics
Matches: 173, Mismatches: 27, Indels: 35
0.74 0.11 0.15
Matches are distributed among these distances:
86 32 0.18
87 82 0.47
88 45 0.26
89 14 0.08
ACGTcount: A:0.41, C:0.03, G:0.24, T:0.32
Consensus pattern (85 bp):
AAAAATGGAATTTTAGAAAGTTTAAGGTAAAATAGTAATTTTTGATGAAATCGAGGGTAAAATGG
AATTTTGGAAAATTAGGGGT
Found at i:11269293 original size:30 final size:30
Alignment explanation
Indices: 11269132--11269293 Score: 145
Period size: 30 Copynumber: 5.4 Consensus size: 30
11269122 AAAAATGGAA
*
11269132 TTTTAGAAAG-TTTAAGGT-AAAATAGTAAT
1 TTTTAGAAAGTTTTGAGGTCAAAATA-TAAT
11269161 TTTTAGAAAGTTTTGAGGTCAAAATATAA-
1 TTTTAGAAAGTTTTGAGGTCAAAATATAAT
* * * *
11269190 ATTTGGAAAAG-TTTAAGGGTCAAAATGTAAT
1 TTTTAG-AAAGTTTTGA-GGTCAAAATATAAT
** *
11269221 TTACAAAAAGTTTTGAGGTCAAAATATAA-
1 TTTTAGAAAGTTTTGAGGTCAAAATATAAT
* * *
11269250 TTCTAGAAAAGTTTGGGGGTCAAAATATAAT
1 TTTTAG-AAAGTTTTGAGGTCAAAATATAAT
*
11269281 TTTTAGATAGTTT
1 TTTTAGAAAGTTT
11269294 AGGAACCTCT
Statistics
Matches: 106, Mismatches: 19, Indels: 15
0.76 0.14 0.11
Matches are distributed among these distances:
29 21 0.20
30 69 0.65
31 16 0.15
ACGTcount: A:0.41, C:0.04, G:0.19, T:0.36
Consensus pattern (30 bp):
TTTTAGAAAGTTTTGAGGTCAAAATATAAT
Found at i:11269293 original size:60 final size:60
Alignment explanation
Indices: 11269133--11269293 Score: 204
Period size: 60 Copynumber: 2.7 Consensus size: 60
11269123 AAAATGGAAT
11269133 TTTAG-AAAGTTTAA-GGT-AAAATAGTAATTTTTAGAAAGTTTTGAGGTCAAAATATAAA
1 TTTAGAAAAGTTTAAGGGTCAAAATA-TAATTTTTAGAAAGTTTTGAGGTCAAAATATAAA
* * ** *
11269191 TTTGGAAAAGTTTAAGGGTCAAAATGTAATTTACAAAAAGTTTTGAGGTCAAAATAT-AA
1 TTTAGAAAAGTTTAAGGGTCAAAATATAATTTTTAGAAAGTTTTGAGGTCAAAATATAAA
** *
11269250 TTCTAGAAAAGTTTGGGGGTCAAAATATAATTTTTAGATAGTTT
1 TT-TAGAAAAGTTTAAGGGTCAAAATATAATTTTTAGAAAGTTT
11269294 AGGAACCTCT
Statistics
Matches: 86, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
58 4 0.05
59 13 0.15
60 64 0.74
61 5 0.06
ACGTcount: A:0.42, C:0.04, G:0.19, T:0.36
Consensus pattern (60 bp):
TTTAGAAAAGTTTAAGGGTCAAAATATAATTTTTAGAAAGTTTTGAGGTCAAAATATAAA
Found at i:11270039 original size:31 final size:32
Alignment explanation
Indices: 11270004--11270065 Score: 108
Period size: 32 Copynumber: 2.0 Consensus size: 32
11269994 TTTATTCCAT
11270004 CTTTTCATTTTCT-TTCTTTTAAAACTAAACC
1 CTTTTCATTTTCTCTTCTTTTAAAACTAAACC
*
11270035 CTTTTCATTTTCTCTTTTTTTAAAACTAAAC
1 CTTTTCATTTTCTCTTCTTTTAAAACTAAAC
11270066 AAAGAATGTC
Statistics
Matches: 29, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
31 13 0.45
32 16 0.55
ACGTcount: A:0.26, C:0.21, G:0.00, T:0.53
Consensus pattern (32 bp):
CTTTTCATTTTCTCTTCTTTTAAAACTAAACC
Found at i:11278543 original size:29 final size:28
Alignment explanation
Indices: 11278511--11278732 Score: 111
Period size: 28 Copynumber: 7.7 Consensus size: 28
11278501 GGAAGGTTTG
11278511 GGGGTAAAATGGTAATCTTTGGTAAAATC
1 GGGGTAAAATGGTAAT-TTTGGTAAAATC
*
11278540 GGGGTCAAAAATGG-AATTTTGG-AAAAGTTTA
1 GGGGT--AAAATGGTAATTTTGGTAAAA---TC
*
11278571 AGGGTAAAATGGTAATTTTGGTAAAATC
1 GGGGTAAAATGGTAATTTTGGTAAAATC
* * * * * *
11278599 AAGGTTAAAATGG-ACTTTTAG-AATATTT
1 -GGGGTAAAATGGTAATTTTGGTAA-AATC
11278627 GAGGGTAAAATGGTAATTTTTGGTAAAATC
1 G-GGGTAAAATGGTAA-TTTTGGTAAAATC
* * * *
11278657 GAGGTTAAAAATGG-AATTTTAG-AAATTT
1 G-GGGT-AAAATGGTAATTTTGGTAAAATC
*
11278685 GAGGGTAAAAATGG-AATTTTGG-AAAACTTG
1 G-GGGT-AAAATGGTAATTTTGGTAAAA--TC
*
11278715 GGGGTAAAA-AGTAATTTT
1 GGGGTAAAATGGTAATTTT
11278733 TGGAAAGTTT
Statistics
Matches: 153, Mismatches: 23, Indels: 35
0.73 0.11 0.17
Matches are distributed among these distances:
27 3 0.02
28 60 0.39
29 38 0.25
30 27 0.18
31 25 0.16
ACGTcount: A:0.39, C:0.03, G:0.26, T:0.32
Consensus pattern (28 bp):
GGGGTAAAATGGTAATTTTGGTAAAATC
Found at i:11278557 original size:59 final size:56
Alignment explanation
Indices: 11278486--11278710 Score: 265
Period size: 59 Copynumber: 3.9 Consensus size: 56
11278476 CTTCTTAGGA
* * * * *
11278486 TAAAAATAGAATTTTGGAAGGTTTGGGGGTAAAATGGTAATCTTTGGTAAAATCGGGG
1 TAAAAATGGAATTTTAGAA-ATTTGAGGGTAAAATGGTAAT-TTTGGTAAAATCGAGG
* * *
11278544 TCAAAAATGGAATTTTGGAAAAGTTTAAGGGTAAAATGGTAATTTTGGTAAAATCAAGG
1 T-AAAAATGGAATTTTAG-AAA-TTTGAGGGTAAAATGGTAATTTTGGTAAAATCGAGG
* *
11278603 TTAAAATGGACTTTTAGAATATTTGAGGGTAAAATGGTAATTTTTGGTAAAATCGAGG
1 TAAAAATGGAATTTTAGAA-ATTTGAGGGTAAAATGGTAA-TTTTGGTAAAATCGAGG
11278661 TTAAAAATGGAATTTTAGAAATTTGAGGGTAAAAATGG-AATTTTGG-AAAA
1 -TAAAAATGGAATTTTAGAAATTTGAGGGT-AAAATGGTAATTTTGGTAAAA
11278711 CTTGGGGGTA
Statistics
Matches: 147, Mismatches: 13, Indels: 16
0.84 0.07 0.09
Matches are distributed among these distances:
56 4 0.03
57 26 0.18
58 43 0.29
59 54 0.37
60 20 0.14
ACGTcount: A:0.40, C:0.03, G:0.25, T:0.32
Consensus pattern (56 bp):
TAAAAATGGAATTTTAGAAATTTGAGGGTAAAATGGTAATTTTGGTAAAATCGAGG
Found at i:11278590 original size:30 final size:30
Alignment explanation
Indices: 11278541--11278972 Score: 213
Period size: 30 Copynumber: 14.6 Consensus size: 30
11278531 GGTAAAATCG
*
11278541 GGGTCAAAAATGGAATTTTGGAAAAGTTTAA
1 GGGTC-AAAATGTAATTTTGGAAAAGTTTAA
*
11278572 GGGT-AAAATGGTAATTTTGGTAAAA--TCAA
1 GGGTCAAAAT-GTAATTTTGG-AAAAGTTTAA
* * * * * *
11278601 -GGTTAAAATGGACTTTTAGAATA-TTTGA
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAA
**
11278629 GGGT-AAAATGGTAATTTTTGGTAAAA--TCGA
1 GGGTCAAAAT-GTAA-TTTTGG-AAAAGTTTAA
* * * * *
11278659 GGTTAAAAATGGAATTTTAG-AAA-TTTGA
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAA
* * * **
11278687 GGGTAAAAATGGAATTTTGGAAAA-CTTGG
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAA
* *
11278716 GGGT-AAAAAGTAATTTTTGG-AAAGTTTTA
1 GGGTCAAAATGTAA-TTTTGGAAAAGTTTAA
* *
11278745 GGGTCAAAATATAATTTTAG-AAAGTTTAA
1 GGGTCAAAATGTAATTTTGGAAAAGTTTAA
* * **
11278774 GGGT-AAAGTAGTAATTTT-TAGAAAGTTTTG
1 GGGTCAAAAT-GTAATTTTGGA-AAAGTTTAA
* * *
11278804 GGGTTAAAAATATAATTTTGGAAAAGTTTAG
1 GGG-TCAAAATGTAATTTTGGAAAAGTTTAA
* *
11278835 GGGTCAAAATGTAATTTATAG-AAAGTTTTA
1 GGGTCAAAATGTAATTT-TGGAAAAGTTTAA
* *
11278865 GGGTCAAAATATAATTTT-GAAGAAGTTT-G
1 GGGTCAAAATGTAATTTTGGAA-AAGTTTAA
* *
11278894 GGTGTCAAAATGTAATTTATAG-AAAGTTT-T
1 GG-GTCAAAATGTAATTT-TGGAAAAGTTTAA
* *
11278924 GTGATCAAAATATAATTTTGGAAAAGTTTAA
1 G-GGTCAAAATGTAATTTTGGAAAAGTTTAA
* *
11278955 GGGTTAAAATATAATTTT
1 GGGTCAAAATGTAATTTT
11278973 TAGACAGTTT
Statistics
Matches: 318, Mismatches: 54, Indels: 59
0.74 0.13 0.14
Matches are distributed among these distances:
27 6 0.02
28 53 0.17
29 75 0.24
30 137 0.43
31 41 0.13
32 6 0.02
ACGTcount: A:0.40, C:0.02, G:0.23, T:0.35
Consensus pattern (30 bp):
GGGTCAAAATGTAATTTTGGAAAAGTTTAA
Found at i:11278635 original size:28 final size:27
Alignment explanation
Indices: 11278547--11278780 Score: 135
Period size: 29 Copynumber: 8.1 Consensus size: 27
11278537 ATCGGGGTCA
* *
11278547 AAAATGGAATTTTGGAAAAGTTTAAGGGT
1 AAAATGGAATTTTAG-AAA-TTTGAGGGT
* * ** *
11278576 AAAATGGTAATTTTGGTAAAATCAAGGTT
1 AAAATGG-AATTTTAG-AAATTTGAGGGT
*
11278605 AAAATGGACTTTTAGAATATTTGAGGGT
1 AAAATGGAATTTTAGAA-ATTTGAGGGT
* * * *
11278633 AAAATGGTAATTTTTGGTAAAATCGAGGTT
1 AAAATGG-AA-TTTTAG-AAATTTGAGGGT
11278663 AAAAATGGAATTTTAGAAATTTGAGGGT
1 -AAAATGGAATTTTAGAAATTTGAGGGT
* * *
11278691 AAAAATGGAATTTTGGAAAACTTGGGGGT
1 -AAAATGGAATTTTAG-AAATTTGAGGGT
* * * *
11278720 AAAAAGTAATTTTTGGAAAGTTTTAGGGT
1 AAAATGGAA-TTTTAGAAA-TTTGAGGGT
** *
11278749 CAAAATATAATTTTAGAAAGTTTAAGGGT
1 -AAAATGGAATTTTAGAAA-TTTGAGGGT
11278778 AAA
1 AAA
11278781 GTAGTAATTT
Statistics
Matches: 164, Mismatches: 31, Indels: 21
0.76 0.14 0.10
Matches are distributed among these distances:
27 2 0.01
28 56 0.34
29 65 0.40
30 32 0.20
31 9 0.05
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.33
Consensus pattern (27 bp):
AAAATGGAATTTTAGAAATTTGAGGGT
Found at i:11278754 original size:117 final size:117
Alignment explanation
Indices: 11278488--11278762 Score: 294
Period size: 117 Copynumber: 2.4 Consensus size: 117
11278478 TCTTAGGATA
* * * *
11278488 AAAATAGAA-TTTTGGAAGGTTTGGGGGTAAAATGGTAATCTTTGGTAAAATCGGGGTCAAAAAT
1 AAAA-AGAACTTTTGGAAAGTTTGAGGGTAAAATGGTAATTTTTGGTAAAATCGAGGTCAAAAAT
* *
11278552 GGAATTTTGGAAAAGTTTAAGGGTAAAATGGTAATTTTGGTAAAATCAAGGTT
65 GGAATTTTAGAAAAGTTTAAGGGTAAAATGGTAATTTTGGTAAAATCAAGGGT
* * * *
11278605 AAAATGGACTTTTAGAATA-TTTGAGGGTAAAATGGTAATTTTTGGTAAAATCGAGGTTAAAAAT
1 AAAAAGAACTTTTGGAA-AGTTTGAGGGTAAAATGGTAATTTTTGGTAAAATCGAGGTCAAAAAT
* ***
11278669 GGAATTTTAG-AAA-TTTGAGGGTAAAAATGG-AATTTTGG-AAAACTTGGGGGT
65 GGAATTTTAGAAAAGTTTAAGGGT-AAAATGGTAATTTTGGTAAAA-TCAAGGGT
* * *
11278720 AAAAAGTAATTTTTGGAAAGTTTTAGGGTCAAAAT-ATAATTTT
1 AAAAAG-AACTTTTGGAAAGTTTGAGGGT-AAAATGGTAATTTT
11278763 AGAAAGTTTA
Statistics
Matches: 131, Mismatches: 20, Indels: 15
0.79 0.12 0.09
Matches are distributed among these distances:
114 4 0.03
115 26 0.20
116 35 0.27
117 66 0.50
ACGTcount: A:0.39, C:0.03, G:0.25, T:0.33
Consensus pattern (117 bp):
AAAAAGAACTTTTGGAAAGTTTGAGGGTAAAATGGTAATTTTTGGTAAAATCGAGGTCAAAAATG
GAATTTTAGAAAAGTTTAAGGGTAAAATGGTAATTTTGGTAAAATCAAGGGT
Found at i:11278850 original size:90 final size:88
Alignment explanation
Indices: 11278671--11278982 Score: 282
Period size: 90 Copynumber: 3.5 Consensus size: 88
11278661 TTAAAAATGG
* * ** * *
11278671 AATTTTAGAAA-TTTGAGGGTAAAA-ATGGAA-TTTTGGAAA-ACTTGGGGGTAAAAAGTA-ATT
1 AATTTTAGAAAGTTTAAGGGTAAAATAT--AATTTTTAGAAAGTTTTGGGGTTAAAAA-TATAAT
11278731 TTTGGAAAGTTTTA-GGGTCAAAATAT
63 TTTGGAAAG-TTTAGGGGTCAAAATAT
*
11278757 AATTTTAGAAAGTTTAAGGGTAAAGTAGTAATTTTTAGAAAGTTTTGGGGTTAAAAATATAATTT
1 AATTTTAGAAAGTTTAAGGGTAAAATA-TAATTTTTAGAAAGTTTTGGGGTTAAAAATATAATTT
*
11278822 TGGAAAAGTTTAGGGGTCAAAATGT
65 TGG-AAAGTTTAGGGGTCAAAATAT
* * * *
11278847 AATTTATAGAAAGTTTTAGGGTCAAAATATAATTTTGA-AGAAG-TTT-GGGTGTCAAAATGTAA
1 AATTT-TAGAAAGTTTAAGGGT-AAAATATAATTTTTAGA-AAGTTTTGGGGT-TAAAAATATAA
* * * *
11278909 TTTATAGAAAGTTTTGTGATCAAAATAT
62 TTT-TGGAAAGTTTAGGGGTCAAAATAT
* *
11278937 AATTTTGGAAAAGTTTAAGGGTTAAAATATAATTTTTAGACAGTTT
1 AATTTTAG-AAAGTTTAAGGG-TAAAATATAATTTTTAGAAAGTTT
11278983 AGGAACCTTT
Statistics
Matches: 187, Mismatches: 22, Indels: 29
0.79 0.09 0.12
Matches are distributed among these distances:
86 11 0.06
87 13 0.07
88 11 0.06
89 30 0.16
90 85 0.45
91 32 0.17
92 5 0.03
ACGTcount: A:0.39, C:0.02, G:0.21, T:0.37
Consensus pattern (88 bp):
AATTTTAGAAAGTTTAAGGGTAAAATATAATTTTTAGAAAGTTTTGGGGTTAAAAATATAATTTT
GGAAAGTTTAGGGGTCAAAATAT
Found at i:11278875 original size:60 final size:59
Alignment explanation
Indices: 11278664--11278982 Score: 337
Period size: 60 Copynumber: 5.4 Consensus size: 59
11278654 ATCGAGGTTA
* * * ** * *
11278664 AAAATGGAA-TTTTAGAAA-TTTGAGGGTAAAAATGGAATTTTGGAAAA-CTTGGGGGT
1 AAAATGTAATTTTTAGAAAGTTTTAGGGTCAAAATATAATTTTGGAAAAGTTTAGGGGT
* * * *
11278720 AAAAAGTAATTTTTGGAAAGTTTTAGGGTCAAAATATAATTTTAG-AAAGTTTAAGGGT
1 AAAATGTAATTTTTAGAAAGTTTTAGGGTCAAAATATAATTTTGGAAAAGTTTAGGGGT
* * *
11278778 AAAGTAGTAATTTTTAGAAAGTTTTGGGGTTAAAAATATAATTTTGGAAAAGTTTAGGGGT
1 AAAAT-GTAATTTTTAGAAAGTTTTAGGG-TCAAAATATAATTTTGGAAAAGTTTAGGGGT
*
11278839 CAAAATGTAATTTATAGAAAGTTTTAGGGTCAAAATATAATTTT-GAAGAAGTTT-GGGTGT
1 -AAAATGTAATTTTTAGAAAGTTTTAGGGTCAAAATATAATTTTGGAA-AAGTTTAGGG-GT
* * *
11278899 CAAAATGTAATTTATAGAAAGTTTT-GTGATCAAAATATAATTTTGGAAAAGTTTAAGGGTT
1 -AAAATGTAATTTTTAGAAAGTTTTAG-GGTCAAAATATAATTTTGGAAAAGTTT-AGGGGT
* *
11278960 AAAATATAATTTTTAGACAGTTT
1 AAAATGTAATTTTTAGAAAGTTT
11278983 AGGAACCTTT
Statistics
Matches: 223, Mismatches: 27, Indels: 22
0.82 0.10 0.08
Matches are distributed among these distances:
56 7 0.03
57 11 0.05
58 29 0.13
59 28 0.13
60 104 0.47
61 37 0.17
62 7 0.03
ACGTcount: A:0.40, C:0.02, G:0.22, T:0.36
Consensus pattern (59 bp):
AAAATGTAATTTTTAGAAAGTTTTAGGGTCAAAATATAATTTTGGAAAAGTTTAGGGGT
Found at i:11278982 original size:30 final size:30
Alignment explanation
Indices: 11278726--11278983 Score: 224
Period size: 30 Copynumber: 8.6 Consensus size: 30
11278716 GGGTAAAAAG
* *
11278726 TAATTTTTGGAAAGTTTTAGGGTCAAAATA
1 TAATTTTTAGAAAGTTTAAGGGTCAAAATA
*
11278756 TAA-TTTTAGAAAGTTTAAGGGT-AAAGTA
1 TAATTTTTAGAAAGTTTAAGGGTCAAAATA
** *
11278784 GTAATTTTTAGAAAGTTTTGGGGTTAAAAATA
1 -TAATTTTTAGAAAGTTTAAGGG-TCAAAATA
* * *
11278816 TAA-TTTTGGAAAAGTTTAGGGGTCAAAATG
1 TAATTTTTAG-AAAGTTTAAGGGTCAAAATA
* *
11278846 TAATTTATAGAAAGTTTTAGGGTCAAAATA
1 TAATTTTTAGAAAGTTTAAGGGTCAAAATA
* * *
11278876 TAATTTTGA-AGAAGTTT-GGGTGTCAAAATG
1 TAATTTTTAGA-AAGTTTAAGG-GTCAAAATA
* * *
11278906 TAATTTATAGAAAGTTT-TGTGATCAAAATA
1 TAATTTTTAGAAAGTTTAAG-GGTCAAAATA
* *
11278936 TAA-TTTTGGAAAAGTTTAAGGGTTAAAATA
1 TAATTTTTAG-AAAGTTTAAGGGTCAAAATA
*
11278966 TAATTTTTAGACAGTTTA
1 TAATTTTTAGAAAGTTTA
11278984 GGAACCTTTA
Statistics
Matches: 184, Mismatches: 31, Indels: 26
0.76 0.13 0.11
Matches are distributed among these distances:
28 5 0.03
29 27 0.15
30 120 0.65
31 27 0.15
32 5 0.03
ACGTcount: A:0.39, C:0.02, G:0.20, T:0.38
Consensus pattern (30 bp):
TAATTTTTAGAAAGTTTAAGGGTCAAAATA
Found at i:11279727 original size:31 final size:32
Alignment explanation
Indices: 11279692--11279755 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
11279682 TTTATTCCAT
*
11279692 CTTTTCATTTTCT-TTCTTTTAAAACTAAACC
1 CTTTTCATTTTCTCTTCTTTTAAAACCAAACC
* *
11279723 CTTTTCATTTTCTCTTTTTTTTAAACCAAACC
1 CTTTTCATTTTCTCTTCTTTTAAAACCAAACC
11279755 C
1 C
11279756 AGATCTGGAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
31 13 0.45
32 16 0.55
ACGTcount: A:0.23, C:0.25, G:0.00, T:0.52
Consensus pattern (32 bp):
CTTTTCATTTTCTCTTCTTTTAAAACCAAACC
Found at i:11280738 original size:16 final size:17
Alignment explanation
Indices: 11280717--11280754 Score: 69
Period size: 17 Copynumber: 2.3 Consensus size: 17
11280707 TTTGGACATT
11280717 AATTTAATTT-AAAATA
1 AATTTAATTTAAAAATA
11280733 AATTTAATTTAAAAATA
1 AATTTAATTTAAAAATA
11280750 AATTT
1 AATTT
11280755 TTATCCCATT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
16 10 0.48
17 11 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (17 bp):
AATTTAATTTAAAAATA
Found at i:11292253 original size:51 final size:51
Alignment explanation
Indices: 11292177--11292280 Score: 208
Period size: 51 Copynumber: 2.0 Consensus size: 51
11292167 TACTTCCTCC
11292177 TTTCTTTACAGCTTTTACTGGAGTAGGATCCTAGCTTGAAATGGCCTGTTA
1 TTTCTTTACAGCTTTTACTGGAGTAGGATCCTAGCTTGAAATGGCCTGTTA
11292228 TTTCTTTACAGCTTTTACTGGAGTAGGATCCTAGCTTGAAATGGCCTGTTA
1 TTTCTTTACAGCTTTTACTGGAGTAGGATCCTAGCTTGAAATGGCCTGTTA
11292279 TT
1 TT
11292281 GTTAATTTTT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
51 53 1.00
ACGTcount: A:0.21, C:0.17, G:0.21, T:0.40
Consensus pattern (51 bp):
TTTCTTTACAGCTTTTACTGGAGTAGGATCCTAGCTTGAAATGGCCTGTTA
Found at i:11295092 original size:8 final size:8
Alignment explanation
Indices: 11295079--11295120 Score: 61
Period size: 7 Copynumber: 5.4 Consensus size: 8
11295069 ACAATTAATT
11295079 AAATTTAA
1 AAATTTAA
11295087 AAATTTAA
1 AAATTTAA
11295095 AAA-TTAA
1 AAATTTAA
11295102 AAA-TTAA
1 AAATTTAA
11295109 AAATTTCAA
1 AAATTT-AA
11295118 AAA
1 AAA
11295121 ATTATTTAAG
Statistics
Matches: 32, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
7 14 0.44
8 13 0.41
9 5 0.16
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (8 bp):
AAATTTAA
Found at i:11298189 original size:36 final size:35
Alignment explanation
Indices: 11298115--11298191 Score: 93
Period size: 36 Copynumber: 2.2 Consensus size: 35
11298105 GTAATAAAAT
*
11298115 TAACAATAAATAAGAGTTATACAATATGCAAATAA
1 TAACAATAAATAAGAGTAATACAATATGCAAATAA
* * *
11298150 TAACAATAAAATAATAGTAATATAATAGTG-AAATGA
1 TAACAAT-AAATAAGAGTAATACAATA-TGCAAATAA
11298186 TAACAA
1 TAACAA
11298192 AACAGTAAGA
Statistics
Matches: 36, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
35 7 0.19
36 27 0.75
37 2 0.06
ACGTcount: A:0.58, C:0.06, G:0.09, T:0.26
Consensus pattern (35 bp):
TAACAATAAATAAGAGTAATACAATATGCAAATAA
Found at i:11302033 original size:39 final size:40
Alignment explanation
Indices: 11301990--11302080 Score: 139
Period size: 40 Copynumber: 2.3 Consensus size: 40
11301980 CAATGGATAA
*
11301990 CTTTTGAAGAGCCACAA-CCTTTTCATATTGGATGGACAC
1 CTTTTGAAGAGCCACAACCCTTTTCATATTGGATCGACAC
* *
11302029 CTTTTGAAAAGTCACAACCCTTTTCATATTGGATCGACAC
1 CTTTTGAAGAGCCACAACCCTTTTCATATTGGATCGACAC
11302069 CTTTTGGAAGAG
1 CTTTT-GAAGAG
11302081 ACTTGCCCAT
Statistics
Matches: 46, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
39 15 0.33
40 26 0.57
41 5 0.11
ACGTcount: A:0.29, C:0.22, G:0.18, T:0.32
Consensus pattern (40 bp):
CTTTTGAAGAGCCACAACCCTTTTCATATTGGATCGACAC
Found at i:11302073 original size:21 final size:21
Alignment explanation
Indices: 11302006--11302073 Score: 54
Period size: 21 Copynumber: 3.3 Consensus size: 21
11301996 AAGAGCCACA
*
11302006 ACCTTTTCATATTGGATGGAC
1 ACCTTTTCATATTGGATCGAC
* **
11302027 ACCTTTTGA-A-AAG-TC-AC
1 ACCTTTTCATATTGGATCGAC
11302044 AACCCTTTTCATATTGGATCGAC
1 -A-CCTTTTCATATTGGATCGAC
11302067 ACCTTTT
1 ACCTTTT
11302074 GGAAGAGACT
Statistics
Matches: 34, Mismatches: 7, Indels: 12
0.64 0.13 0.23
Matches are distributed among these distances:
17 2 0.06
18 2 0.06
19 8 0.24
20 2 0.06
21 15 0.44
22 3 0.09
23 2 0.06
ACGTcount: A:0.26, C:0.24, G:0.13, T:0.37
Consensus pattern (21 bp):
ACCTTTTCATATTGGATCGAC
Found at i:11306984 original size:39 final size:39
Alignment explanation
Indices: 11306925--11307016 Score: 141
Period size: 40 Copynumber: 2.3 Consensus size: 39
11306915 ATGCACTCAG
*
11306925 TGGACACATTTTGAAGAGTCACAACCC-TTTCATATTGGA
1 TGGACAC-TTTTGAAAAGTCACAACCCTTTTCATATTGGA
11306964 TGGACATCTTTTGAAAAGTCACAACCCTTTTCATATTGGA
1 TGGACA-CTTTTGAAAAGTCACAACCCTTTTCATATTGGA
11307004 TGGACACCTTTTG
1 TGGACA-CTTTTG
11307017 GAAGAGACTT
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
39 24 0.49
40 25 0.51
ACGTcount: A:0.28, C:0.21, G:0.17, T:0.34
Consensus pattern (39 bp):
TGGACACTTTTGAAAAGTCACAACCCTTTTCATATTGGA
Found at i:11308429 original size:27 final size:27
Alignment explanation
Indices: 11308397--11308457 Score: 79
Period size: 27 Copynumber: 2.2 Consensus size: 27
11308387 TTTATAAATT
* *
11308397 TTTTAAAAATTAAAT-TAAATTTTATTA
1 TTTTAAAAATAAAATAT-AATTTTATCA
11308424 TTTTAAAAATAAAATATAATTTTATCA
1 TTTTAAAAATAAAATATAATTTTATCA
11308451 TTATTAA
1 TT-TTAA
11308458 TTATAAAGAA
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 25 0.83
28 5 0.17
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (27 bp):
TTTTAAAAATAAAATATAATTTTATCA
Found at i:11312692 original size:4 final size:4
Alignment explanation
Indices: 11312683--11312716 Score: 68
Period size: 4 Copynumber: 8.5 Consensus size: 4
11312673 CAATCAAAAT
11312683 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
1 ATAC ATAC ATAC ATAC ATAC ATAC ATAC ATAC AT
11312717 CCAGGGAAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 30 1.00
ACGTcount: A:0.50, C:0.24, G:0.00, T:0.26
Consensus pattern (4 bp):
ATAC
Found at i:11313104 original size:118 final size:119
Alignment explanation
Indices: 11312950--11313188 Score: 435
Period size: 118 Copynumber: 2.0 Consensus size: 119
11312940 TTAAATTTTA
11312950 CAATTTCAATCACACCACCTATTCACGACACCCCTCTTAAACAGTCATTGACCAACATAAATATG
1 CAATTTCAAT-ACACCACCTATTCACGACACCCCTCTTAAACAGTCATTGACCAACATAAATATG
11313015 AACCCAACTTAACTCTAATAAGCAACTGCTAAAAATAGCTACCAAATGAAACATT
65 AACCCAACTTAACTCTAATAAGCAACTGCTAAAAATAGCTACCAAATGAAACATT
* *
11313070 CAATTTCAAT-CACCACCTATTGACGACACCCCTCTTAAACCGTCATTGACCAACATAAATATGA
1 CAATTTCAATACACCACCTATTCACGACACCCCTCTTAAACAGTCATTGACCAACATAAATATGA
*
11313134 ACCCAACTTAACTCTAATAAGCAACTGCTAAAAATAGCTACCAACTGAAACATT
66 ACCCAACTTAACTCTAATAAGCAACTGCTAAAAATAGCTACCAAATGAAACATT
11313188 C
1 C
11313189 GAGCTATACA
Statistics
Matches: 116, Mismatches: 3, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
118 106 0.91
120 10 0.09
ACGTcount: A:0.41, C:0.29, G:0.07, T:0.23
Consensus pattern (119 bp):
CAATTTCAATACACCACCTATTCACGACACCCCTCTTAAACAGTCATTGACCAACATAAATATGA
ACCCAACTTAACTCTAATAAGCAACTGCTAAAAATAGCTACCAAATGAAACATT
Found at i:11313211 original size:2 final size:2
Alignment explanation
Indices: 11313204--11313244 Score: 82
Period size: 2 Copynumber: 20.5 Consensus size: 2
11313194 ATACATCTAT
11313204 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
11313245 ACATTTAGAA
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 39 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:11326358 original size:3 final size:3
Alignment explanation
Indices: 11326350--11326377 Score: 56
Period size: 3 Copynumber: 9.3 Consensus size: 3
11326340 AAATAATCCT
11326350 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA A
11326378 ATGCTCCATC
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 25 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AGA
Found at i:11331330 original size:20 final size:20
Alignment explanation
Indices: 11331307--11331366 Score: 59
Period size: 20 Copynumber: 2.9 Consensus size: 20
11331297 ATTTTTTAGA
11331307 TTTTAAAATTTAAATTTAAT
1 TTTTAAAATTTAAATTTAAT
* *
11331327 TTTTAATATTAATAAAATT-AT
1 TTTTAAAATT--TAAATTTAAT
*
11331348 TTTATTAAATTTAAATTTA
1 TTT-TAAAATTTAAATTTA
11331367 TTATATCTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 7
0.72 0.12 0.16
Matches are distributed among these distances:
20 15 0.48
21 5 0.16
22 11 0.35
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (20 bp):
TTTTAAAATTTAAATTTAAT
Found at i:11346551 original size:26 final size:26
Alignment explanation
Indices: 11346520--11346582 Score: 76
Period size: 26 Copynumber: 2.4 Consensus size: 26
11346510 TCATGGGAGC
11346520 TATTAAAATAAAAACATTAA-ATTTAAA
1 TATTAAAATAAAAACA-TAATA-TTAAA
*
11346547 T-TTAAAAATAAAAATATAATATTAAA
1 TATT-AAAATAAAAACATAATATTAAA
11346573 TATTAAAATA
1 TATTAAAATA
11346583 TTAAAAAATA
Statistics
Matches: 32, Mismatches: 1, Indels: 7
0.80 0.03 0.17
Matches are distributed among these distances:
26 17 0.53
27 15 0.47
ACGTcount: A:0.63, C:0.02, G:0.00, T:0.35
Consensus pattern (26 bp):
TATTAAAATAAAAACATAATATTAAA
Found at i:11348287 original size:22 final size:21
Alignment explanation
Indices: 11348262--11348304 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
11348252 TTACAAGTTT
11348262 AGGAGTATGAGATTAGGGGTTA
1 AGGAGTATGA-ATTAGGGGTTA
* *
11348284 AGGATTATGATTTAGGGGTTA
1 AGGAGTATGAATTAGGGGTTA
11348305 TAGTTTAGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.30, C:0.00, G:0.37, T:0.33
Consensus pattern (21 bp):
AGGAGTATGAATTAGGGGTTA
Found at i:11364811 original size:20 final size:20
Alignment explanation
Indices: 11364783--11364858 Score: 59
Period size: 21 Copynumber: 3.9 Consensus size: 20
11364773 CGAATTTTAT
*
11364783 ATTTCTTTATATTTTATATA
1 ATTTCTATATATTTTATATA
* * * * *
11364803 ATTTTTTTACAACTTTATAAA
1 ATTTCTATA-TATTTTATATA
*
11364824 ATTT-TATA-ATTTTTTAT-
1 ATTTCTATATATTTTATATA
11364841 ATTTCTATATATTTTATA
1 ATTTCTATATATTTTATA
11364859 ATTTTTACGA
Statistics
Matches: 44, Mismatches: 9, Indels: 7
0.73 0.15 0.12
Matches are distributed among these distances:
17 4 0.09
18 10 0.23
19 7 0.16
20 11 0.25
21 12 0.27
ACGTcount: A:0.33, C:0.05, G:0.00, T:0.62
Consensus pattern (20 bp):
ATTTCTATATATTTTATATA
Found at i:11364845 original size:58 final size:59
Alignment explanation
Indices: 11364777--11364924 Score: 173
Period size: 58 Copynumber: 2.5 Consensus size: 59
11364767 TTTTTACGAA
*
11364777 TTTTATATTTCTTTATATTTTATATAATTTTTTTAC-AACTTTATAAAATTTTATAA-TT
1 TTTTATATTTCTTTATATTTT-TATAATTTTTTTACGAACTTTATAAAATTTTACAATTT
* **
11364835 TTTTATATTTCTATATA-TTTTATAA--TTTTTACGATTTTTATAAAATTTTACAATTT
1 TTTTATATTTCTTTATATTTTTATAATTTTTTTACGAACTTTATAAAATTTTACAATTT
*
11364891 TTTTATATATT-TTTAAGATTTTTATATATTTTTT
1 TTTTATAT-TTCTTT-ATATTTTTATA-ATTTTTT
11364925 CTAATTTTTA
Statistics
Matches: 76, Mismatches: 6, Indels: 13
0.80 0.06 0.14
Matches are distributed among these distances:
54 7 0.09
55 17 0.22
56 17 0.22
57 7 0.09
58 23 0.30
59 1 0.01
61 4 0.05
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (59 bp):
TTTTATATTTCTTTATATTTTTATAATTTTTTTACGAACTTTATAAAATTTTACAATTT
Found at i:11364861 original size:56 final size:58
Alignment explanation
Indices: 11364777--11364898 Score: 162
Period size: 55 Copynumber: 2.1 Consensus size: 58
11364767 TTTTTACGAA
* *
11364777 TTTTATATTTCTTTATATTTTATATAATTTTTTTAC-AACTTTATAAAATTTTATAA-TT
1 TTTTATATTTCTATATATTTTATATAA--TTTTTACGAACTTTATAAAATTTTACAATTT
**
11364835 TTTTATATTTCTATATA-TTT-TATAATTTTTACGATTTTTATAAAATTTTACAATTT
1 TTTTATATTTCTATATATTTTATATAATTTTTACGAACTTTATAAAATTTTACAATTT
11364891 TTTTATAT
1 TTTTATAT
11364899 ATTTTTAAGA
Statistics
Matches: 58, Mismatches: 4, Indels: 6
0.85 0.06 0.09
Matches are distributed among these distances:
54 7 0.12
55 17 0.29
56 15 0.26
57 3 0.05
58 16 0.28
ACGTcount: A:0.32, C:0.05, G:0.01, T:0.62
Consensus pattern (58 bp):
TTTTATATTTCTATATATTTTATATAATTTTTACGAACTTTATAAAATTTTACAATTT
Found at i:11364885 original size:19 final size:19
Alignment explanation
Indices: 11364852--11364923 Score: 74
Period size: 19 Copynumber: 3.7 Consensus size: 19
11364842 TTTCTATATA
11364852 TTTTAT-AATTTTTACGAT
1 TTTTATAAATTTTTACGAT
* *
11364870 TTTTATAAAATTTTACAATTT
1 TTTTATAAATTTTTACGA--T
* *
11364891 TTTTATATATTTTTAAGAT
1 TTTTATAAATTTTTACGAT
*
11364910 TTTTATATATTTTT
1 TTTTATAAATTTTT
11364924 TCTAATTTTT
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
18 6 0.13
19 24 0.53
21 15 0.33
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (19 bp):
TTTTATAAATTTTTACGAT
Found at i:11364903 original size:10 final size:10
Alignment explanation
Indices: 11364780--11364923 Score: 79
Period size: 10 Copynumber: 14.9 Consensus size: 10
11364770 TTACGAATTT
11364780 TATATTTCTT-
1 TATATTT-TTA
11364790 TATA-TTTTA
1 TATATTTTTA
*
11364799 TATAATTTTTT
1 TAT-ATTTTTA
* **
11364810 TACAACTTTA
1 TATATTTTTA
* *
11364820 TAAAATTTTA
1 TATATTTTTA
11364830 TA-ATTTTT-
1 TATATTTTTA
*
11364838 TATATTTCTA
1 TATATTTTTA
11364848 TATA-TTTTA
1 TATATTTTTA
11364857 TA-ATTTTTA
1 TATATTTTTA
**
11364866 -CGATTTTTA
1 TATATTTTTA
* *
11364875 TAAAATTTTA
1 TATATTTTTA
* *
11364885 CAATTTTTTTA
1 -TATATTTTTA
11364896 TATATTTTTA
1 TATATTTTTA
*
11364906 -AGATTTTTA
1 TATATTTTTA
11364915 TATATTTTT
1 TATATTTTT
11364924 TCTAATTTTT
Statistics
Matches: 102, Mismatches: 22, Indels: 20
0.71 0.15 0.14
Matches are distributed among these distances:
8 5 0.05
9 41 0.40
10 44 0.43
11 12 0.12
ACGTcount: A:0.32, C:0.04, G:0.01, T:0.62
Consensus pattern (10 bp):
TATATTTTTA
Found at i:11364931 original size:10 final size:10
Alignment explanation
Indices: 11364777--11364946 Score: 76
Period size: 10 Copynumber: 17.6 Consensus size: 10
11364767 TTTTTACGAA
11364777 TTTTAT-ATT
1 TTTTATAATT
11364786 TCTTTAT-ATT
1 T-TTTATAATT
*
11364796 TTATATAATT
1 TTTTATAATT
*
11364806 TTTT-TACA-A
1 TTTTATA-ATT
* **
11364815 CTTTATAAAA
1 TTTTATAATT
11364825 TTTTATAATT
1 TTTTATAATT
11364835 TTTTAT-A-T
1 TTTTATAATT
* *
11364843 TTCTAT-ATA
1 TTTTATAATT
11364852 TTTTATAA-T
1 TTTTATAATT
**
11364861 TTTTACGA-T
1 TTTTATAATT
**
11364870 TTTTATAAAA
1 TTTTATAATT
*
11364880 TTTTACAATT
1 TTTTATAATT
11364890 TTTT-TATATAT
1 TTTTATA-AT-T
11364901 TTTTA-AGA-T
1 TTTTATA-ATT
11364910 TTTTATATATT
1 TTTTATA-ATT
*
11364921 TTTTCTAATT
1 TTTTATAATT
*
11364931 TTTAATAATT
1 TTTTATAATT
11364941 TTTTAT
1 TTTTAT
11364947 TAAAATTTAA
Statistics
Matches: 122, Mismatches: 26, Indels: 25
0.71 0.15 0.14
Matches are distributed among these distances:
8 7 0.06
9 37 0.30
10 64 0.52
11 14 0.11
ACGTcount: A:0.31, C:0.04, G:0.01, T:0.64
Consensus pattern (10 bp):
TTTTATAATT
Found at i:11364944 original size:40 final size:39
Alignment explanation
Indices: 11364842--11364945 Score: 104
Period size: 40 Copynumber: 2.6 Consensus size: 39
11364832 ATTTTTTATA
*
11364842 TTTCTATATATTTTATAA-TTTTTACGATTTTTATAAAATT
1 TTTCTA-AT-TTTTATAATTTTTTAAGATTTTTATAAAATT
* * * *
11364882 TTAC-AATTTTTTTATATATTTTTAAGATTTTTATATATTT
1 TTTCTAATTTTTATA-AT-TTTTTAAGATTTTTATAAAATT
11364922 TTTCTAATTTTTAATAATTTTTTA
1 TTTCTAATTTTT-ATAATTTTTTA
11364946 TTAAAATTTA
Statistics
Matches: 52, Mismatches: 7, Indels: 10
0.75 0.10 0.14
Matches are distributed among these distances:
37 6 0.12
38 3 0.06
39 1 0.02
40 31 0.60
41 9 0.17
42 2 0.04
ACGTcount: A:0.31, C:0.04, G:0.02, T:0.63
Consensus pattern (39 bp):
TTTCTAATTTTTATAATTTTTTAAGATTTTTATAAAATT
Found at i:11364999 original size:13 final size:13
Alignment explanation
Indices: 11364960--11364998 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
11364950 AATTTAATCA
*
11364960 TATTTA-TTGTTT
1 TATTTATTTATTT
11364972 TATTTATTTATTT
1 TATTTATTTATTT
11364985 TATTTATATTATTT
1 TATTTAT-TTATTT
11364999 AATAAAAGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
12 6 0.25
13 12 0.50
14 6 0.25
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (13 bp):
TATTTATTTATTT
Found at i:11366651 original size:22 final size:22
Alignment explanation
Indices: 11366607--11366652 Score: 56
Period size: 22 Copynumber: 2.1 Consensus size: 22
11366597 TGGGATGGGC
* * *
11366607 AATAAGATGAAAAGCAAAGAAG
1 AATAAGAAGAAAAGAAAAAAAG
*
11366629 AATAAGAAGAAAGGAAAAAAAG
1 AATAAGAAGAAAAGAAAAAAAG
11366651 AA
1 AA
11366653 AACAATAAAT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.70, C:0.02, G:0.22, T:0.07
Consensus pattern (22 bp):
AATAAGAAGAAAAGAAAAAAAG
Found at i:11378453 original size:39 final size:39
Alignment explanation
Indices: 11378378--11378454 Score: 127
Period size: 39 Copynumber: 2.0 Consensus size: 39
11378368 ATGAATCTAA
* *
11378378 CTCTTAATTTTTCTAAGTTTGTTGTTGAATGCGTGATAC
1 CTCTTAATTTTTCTAAGTTTATTGTTGAATACGTGATAC
*
11378417 CTCTTAATTTTTCTAAGTTTATTGTTGAATATGTGATA
1 CTCTTAATTTTTCTAAGTTTATTGTTGAATACGTGATA
11378455 TGGGACTTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.23, C:0.10, G:0.16, T:0.51
Consensus pattern (39 bp):
CTCTTAATTTTTCTAAGTTTATTGTTGAATACGTGATAC
Found at i:11388898 original size:13 final size:13
Alignment explanation
Indices: 11388876--11388906 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
11388866 TTCATGTATT
*
11388876 TTAATTTTTTTAA
1 TTAATGTTTTTAA
11388889 TTAATGTTTTTAA
1 TTAATGTTTTTAA
11388902 TTAAT
1 TTAAT
11388907 AAATATTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.32, C:0.00, G:0.03, T:0.65
Consensus pattern (13 bp):
TTAATGTTTTTAA
Found at i:11388924 original size:26 final size:26
Alignment explanation
Indices: 11388895--11388947 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 26
11388885 TTAATTAATG
11388895 TTTTTAATTAATAAATATTTTT-TTTA
1 TTTTTAATTAATAAAT-TTTTTATTTA
11388921 TTTTTAATTAATAAATTTTTTATTTA
1 TTTTTAATTAATAAATTTTTTATTTA
11388947 T
1 T
11388948 ATAATAATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 5 0.19
26 21 0.81
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (26 bp):
TTTTTAATTAATAAATTTTTTATTTA
Found at i:11388933 original size:22 final size:22
Alignment explanation
Indices: 11388902--11388954 Score: 61
Period size: 22 Copynumber: 2.3 Consensus size: 22
11388892 ATGTTTTTAA
**
11388902 TTAATAAATATTTTTTTTATTT
1 TTAATAAATAAATTTTTTATTT
*
11388924 TTAATTAATAAATTTTTTATTT
1 TTAATAAATAAATTTTTTATTT
11388946 ATATAATAA
1 -T-TAATAA
11388955 TTATGTAATT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
22 19 0.76
23 1 0.04
24 5 0.20
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (22 bp):
TTAATAAATAAATTTTTTATTT
Found at i:11391558 original size:18 final size:18
Alignment explanation
Indices: 11391524--11391562 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
11391514 TAAAATTGGG
11391524 TTGATGAACTAATTTAAT
1 TTGATGAACTAATTTAAT
* *
11391542 TTGAGTGAATTAATTAAAT
1 TTGA-TGAACTAATTTAAT
11391561 TT
1 TT
11391563 ATTTTAATTA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.38, C:0.03, G:0.13, T:0.46
Consensus pattern (18 bp):
TTGATGAACTAATTTAAT
Found at i:11392740 original size:3 final size:3
Alignment explanation
Indices: 11392732--11392757 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
11392722 TTGTAAACCA
11392732 TAT TAT TAT TAT TAT TAT TAT TAT TA
1 TAT TAT TAT TAT TAT TAT TAT TAT TA
11392758 AAGAAAGAAA
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:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:11404527 original size:27 final size:27
Alignment explanation
Indices: 11404489--11404546 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
11404479 ATGATCAGAA
11404489 TTACAAAATGAGTTAACTAAACACTCC
1 TTACAAAATGAGTTAACTAAACACTCC
11404516 TTACAAAATGAGTTAACTAAACACTCC
1 TTACAAAATGAGTTAACTAAACACTCC
11404543 TTAC
1 TTAC
11404547 TAACTAGTAC
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.43, C:0.22, G:0.07, T:0.28
Consensus pattern (27 bp):
TTACAAAATGAGTTAACTAAACACTCC
Found at i:11412391 original size:3 final size:3
Alignment explanation
Indices: 11412383--11412409 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
11412373 GTGCTTTCAA
11412383 CAC CAC CAC CAC CAC CAC CAC CAC CAC
1 CAC CAC CAC CAC CAC CAC CAC CAC CAC
11412410 TACTACTTCC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.33, C:0.67, G:0.00, T:0.00
Consensus pattern (3 bp):
CAC
Found at i:11424516 original size:25 final size:25
Alignment explanation
Indices: 11424458--11424517 Score: 61
Period size: 24 Copynumber: 2.4 Consensus size: 25
11424448 AAAAAATAGG
* *
11424458 TTTTATATTATTTTTCTAATATTATA
1 TTTTA-ATAATTTTTCTAATATCATA
*
11424484 TGTT-ATAATTTTTACTAAT-TCATA
1 TTTTAATAATTTTT-CTAATATCATA
11424508 TTTTAATAAT
1 TTTTAATAAT
11424518 AATTATATTA
Statistics
Matches: 28, Mismatches: 4, Indels: 5
0.76 0.11 0.14
Matches are distributed among these distances:
24 15 0.54
25 10 0.36
26 3 0.11
ACGTcount: A:0.33, C:0.05, G:0.02, T:0.60
Consensus pattern (25 bp):
TTTTAATAATTTTTCTAATATCATA
Found at i:11424553 original size:38 final size:37
Alignment explanation
Indices: 11424500--11424588 Score: 110
Period size: 37 Copynumber: 2.4 Consensus size: 37
11424490 AATTTTTACT
* *
11424500 AATTCATATTTTAATAATAATTATATTAAAAATATTATTA
1 AATT-ATA-TTTAATAATAATCATATT-AAAATATAATTA
*
11424540 AATTATATTTAATAATAATCATGTTAAAATATAATTA
1 AATTATATTTAATAATAATCATATTAAAATATAATTA
11424577 AATTA-A-TTAATA
1 AATTATATTTAATA
11424589 TTTTTATTAA
Statistics
Matches: 46, Mismatches: 3, Indels: 5
0.85 0.06 0.09
Matches are distributed among these distances:
35 6 0.13
36 1 0.02
37 16 0.35
38 16 0.35
39 3 0.07
40 4 0.09
ACGTcount: A:0.52, C:0.02, G:0.01, T:0.45
Consensus pattern (37 bp):
AATTATATTTAATAATAATCATATTAAAATATAATTA
Found at i:11425274 original size:6 final size:6
Alignment explanation
Indices: 11425265--11425309 Score: 90
Period size: 6 Copynumber: 7.5 Consensus size: 6
11425255 ATATATATAA
11425265 ACTTCT ACTTCT ACTTCT ACTTCT ACTTCT ACTTCT ACTTCT ACT
1 ACTTCT ACTTCT ACTTCT ACTTCT ACTTCT ACTTCT ACTTCT ACT
11425310 GTACTACTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 39 1.00
ACGTcount: A:0.18, C:0.33, G:0.00, T:0.49
Consensus pattern (6 bp):
ACTTCT
Found at i:11438360 original size:6 final size:6
Alignment explanation
Indices: 11438351--11438387 Score: 74
Period size: 6 Copynumber: 6.2 Consensus size: 6
11438341 ATAGGATTGG
11438351 GGGAGA GGGAGA GGGAGA GGGAGA GGGAGA GGGAGA G
1 GGGAGA GGGAGA GGGAGA GGGAGA GGGAGA GGGAGA G
11438388 TTTTTCTCCT
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:0.32, C:0.00, G:0.68, T:0.00
Consensus pattern (6 bp):
GGGAGA
Found at i:11441059 original size:15 final size:14
Alignment explanation
Indices: 11441023--11441074 Score: 59
Period size: 14 Copynumber: 3.4 Consensus size: 14
11441013 AAATATAAAA
11441023 ATAAAATATTTAAT
1 ATAAAATATTTAAT
11441037 ATAAAATATTTAAT
1 ATAAAATATTTAAT
*
11441051 TTCAAAATATAATTTAAT
1 AT--AAA-AT-ATTTAAT
11441069 ATAAAA
1 ATAAAA
11441075 AAATTATATT
Statistics
Matches: 32, Mismatches: 2, Indels: 7
0.78 0.05 0.17
Matches are distributed among these distances:
14 15 0.47
15 1 0.03
16 6 0.19
17 2 0.06
18 8 0.25
ACGTcount: A:0.58, C:0.02, G:0.00, T:0.40
Consensus pattern (14 bp):
ATAAAATATTTAAT
Found at i:11442665 original size:23 final size:22
Alignment explanation
Indices: 11442638--11442683 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 22
11442628 ACTGATAGTG
*
11442638 TATTAAATATTTTCCTTTAATTT
1 TATTAAATATTTT-CATTAATTT
**
11442661 TATTAGTTATTTTCATTAATTT
1 TATTAAATATTTTCATTAATTT
11442683 T
1 T
11442684 TATTTTTTAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
22 9 0.45
23 11 0.55
ACGTcount: A:0.28, C:0.07, G:0.02, T:0.63
Consensus pattern (22 bp):
TATTAAATATTTTCATTAATTT
Found at i:11443761 original size:18 final size:19
Alignment explanation
Indices: 11443728--11443766 Score: 62
Period size: 18 Copynumber: 2.1 Consensus size: 19
11443718 CTCAATTTTA
11443728 ATTAAAATAATAAAAAATT
1 ATTAAAATAATAAAAAATT
*
11443747 ATTAAAAT-TTAAAAAATT
1 ATTAAAATAATAAAAAATT
11443765 AT
1 AT
11443767 AATTTAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
18 11 0.58
19 8 0.42
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (19 bp):
ATTAAAATAATAAAAAATT
Found at i:11449363 original size:3 final size:3
Alignment explanation
Indices: 11449355--11449398 Score: 88
Period size: 3 Copynumber: 14.7 Consensus size: 3
11449345 TTTAACACTT
11449355 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
11449399 TTATTATTTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 41 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:11457607 original size:2 final size:2
Alignment explanation
Indices: 11457600--11457634 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
11457590 TGGATTGATG
11457600 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
11457635 GCCTTCAGTG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Done.