Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold6
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: 4312818
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 226954 characters in sequence are not A, C, G, or T
File 8 of 14
Found at i:2580195 original size:25 final size:25
Alignment explanation
Indices: 2580167--2580216 Score: 73
Period size: 25 Copynumber: 2.0 Consensus size: 25
2580157 GGAAGAGAAG
**
2580167 ATGAAGAATGGAAGAAGGAAAAGGA
1 ATGAAGAACAGAAGAAGGAAAAGGA
*
2580192 ATGAAGAACAGAAGAAGGAGAAGGA
1 ATGAAGAACAGAAGAAGGAAAAGGA
2580217 GCCTTACCTG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.56, C:0.02, G:0.36, T:0.06
Consensus pattern (25 bp):
ATGAAGAACAGAAGAAGGAAAAGGA
Found at i:2580369 original size:18 final size:18
Alignment explanation
Indices: 2580346--2580392 Score: 85
Period size: 18 Copynumber: 2.6 Consensus size: 18
2580336 CGTTTATTGA
2580346 AAAATATTTTCCAAATGT
1 AAAATATTTTCCAAATGT
2580364 AAAATATTTTCCAAATGT
1 AAAATATTTTCCAAATGT
*
2580382 AAAATGTTTTC
1 AAAATATTTTC
2580393 AGTTAAACAA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.43, C:0.11, G:0.06, T:0.40
Consensus pattern (18 bp):
AAAATATTTTCCAAATGT
Found at i:2580456 original size:20 final size:20
Alignment explanation
Indices: 2580431--2580470 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2580421 CGTGAAATGA
*
2580431 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
2580451 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
2580471 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:2580463 original size:34 final size:35
Alignment explanation
Indices: 2580416--2580482 Score: 100
Period size: 34 Copynumber: 1.9 Consensus size: 35
2580406 CTGGAAAATG
* *
2580416 TTTTCCGTGAAATGATTT-CTGGAAAATGTTTTAC
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
*
2580450 TTTTCTGTAAAATGATTTACTGGAAAATATTTT
1 TTTTCCGTAAAATGATTTACTGGAAAATATTTT
2580483 CTGGTGTTTG
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 16 0.55
35 13 0.45
ACGTcount: A:0.30, C:0.09, G:0.15, T:0.46
Consensus pattern (35 bp):
TTTTCCGTAAAATGATTTACTGGAAAATATTTTAC
Found at i:2580486 original size:14 final size:15
Alignment explanation
Indices: 2580406--2580486 Score: 53
Period size: 14 Copynumber: 5.3 Consensus size: 15
2580396 TAAACAAACA
2580406 CTGGAAAATG-TTTT
1 CTGGAAAATGATTTT
*
2580420 CCGTG-AAATGA-TTT
1 CTG-GAAAATGATTTT
2580434 CTGGAAAATGTTTTACTTTT
1 CTGGAAAATG----A-TTTT
* *
2580454 CTGTAAAATGATTTA
1 CTGGAAAATGATTTT
2580469 CTGGAAAAT-ATTTT
1 CTGGAAAATGATTTT
2580483 CTGG
1 CTGG
2580487 TGTTTGATTG
Statistics
Matches: 52, Mismatches: 6, Indels: 18
0.68 0.08 0.24
Matches are distributed among these distances:
13 1 0.02
14 25 0.48
15 12 0.23
16 1 0.02
18 1 0.02
20 12 0.23
ACGTcount: A:0.30, C:0.10, G:0.19, T:0.42
Consensus pattern (15 bp):
CTGGAAAATGATTTT
Found at i:2583296 original size:18 final size:18
Alignment explanation
Indices: 2583275--2583325 Score: 66
Period size: 18 Copynumber: 2.8 Consensus size: 18
2583265 AGGAATGAAG
2583275 GAAGGGAGAAGAATGGAT
1 GAAGGGAGAAGAATGGAT
*** *
2583293 GAAGGGAGCTTACTGGAT
1 GAAGGGAGAAGAATGGAT
2583311 GAAGGGAGAAGAATG
1 GAAGGGAGAAGAATG
2583326 CCTGAGAGCT
Statistics
Matches: 25, Mismatches: 8, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.39, C:0.04, G:0.43, T:0.14
Consensus pattern (18 bp):
GAAGGGAGAAGAATGGAT
Found at i:2590782 original size:129 final size:129
Alignment explanation
Indices: 2590622--2590879 Score: 489
Period size: 129 Copynumber: 2.0 Consensus size: 129
2590612 CTCTCACTAC
*
2590622 TCCTGAAGTTATCATAGTCATAATGAATTTCTTTGTATTGCTGGCATTAGGCATCTATGAGGGTG
1 TCCTGAAGTTATCATAGTCATAATGAATTTCTTTATATTGCTGGCATTAGGCATCTATGAGGGTG
**
2590687 ACAAATATGTTTCTGCAGTTACTGTTTTCACGTATCTTTTGATAGTATCACTCTCTCGCCTTTT
66 ACAAATATGTTTCTGCAGTTACTGTTTTCAAATATCTTTTGATAGTATCACTCTCTCGCCTTTT
2590751 TCCTGAAGTTATCATAGTCATAATGAATTTCTTTATATTGCTGGCATTAGGCATCTATGAGGGTG
1 TCCTGAAGTTATCATAGTCATAATGAATTTCTTTATATTGCTGGCATTAGGCATCTATGAGGGTG
2590816 ACAAATATGTTTCTGCAGTTACTGTTTTCAAATATCTTTTGATAGTATCACTCTCTCGCCTTTT
66 ACAAATATGTTTCTGCAGTTACTGTTTTCAAATATCTTTTGATAGTATCACTCTCTCGCCTTTT
2590880 GGTTTTGTAG
Statistics
Matches: 126, Mismatches: 3, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
129 126 1.00
ACGTcount: A:0.24, C:0.17, G:0.17, T:0.42
Consensus pattern (129 bp):
TCCTGAAGTTATCATAGTCATAATGAATTTCTTTATATTGCTGGCATTAGGCATCTATGAGGGTG
ACAAATATGTTTCTGCAGTTACTGTTTTCAAATATCTTTTGATAGTATCACTCTCTCGCCTTTT
Found at i:2595219 original size:27 final size:28
Alignment explanation
Indices: 2595178--2595230 Score: 81
Period size: 27 Copynumber: 1.9 Consensus size: 28
2595168 GAGAAAATAA
*
2595178 TTTAATTAAAATAATTGATTAAATTTAT
1 TTTAATTAAAATAATTAATTAAATTTAT
*
2595206 TTTAATT-AATTAATTAATTAAATTT
1 TTTAATTAAAATAATTAATTAAATTT
2595231 TGGAATAGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 16 0.70
28 7 0.30
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (28 bp):
TTTAATTAAAATAATTAATTAAATTTAT
Found at i:2603266 original size:42 final size:42
Alignment explanation
Indices: 2603166--2603448 Score: 229
Period size: 43 Copynumber: 6.7 Consensus size: 42
2603156 TACATTCACC
* * *
2603166 TCAGCACATAGCAACCCCTTTCACAGTCA-AAGATACGGTGGAA
1 TCAGCACATAGCAACCCCTTT-ATATTCAGTA-ATACGGTGGAA
*
2603209 TCAGCACTTAGCAACCACCTTTATATTCAGTAATTACGG-GGAA
1 TCAGCACATAGCAACC-CCTTTATATTCAGTAA-TACGGTGGAA
* * *
2603252 T-AGCACATAGCAACCCCTTTCACAGTCA-AAGATACGGTGGAA
1 TCAGCACATAGCAACCCCTTT-ATATTCAGTA-ATACGGTGGAA
*
2603294 TCAGCACTTAGCAACCACCTTTATATTCAGTAATACGG-GGAA
1 TCAGCACATAGCAACC-CCTTTATATTCAGTAATACGGTGGAA
* * * *
2603336 TCAGCACATAGCAACCCCTTTAACAATCA-AAGATACAGTGGAA
1 TCAGCACATAGCAACCCCTTT-ATATTCAGTA-ATACGGTGGAA
* * * * * *
2603379 TCGGCACTTAGCAACCACCTTTAAAGTCAATAATTCGG-GGAA
1 TCAGCACATAGCAACC-CCTTTATATTCAGTAATACGGTGGAA
** * *
2603421 TCATAACTTAGCAACCCCTTTTTATTCA
1 TCAGCACATAGCAACCCCTTTATATTCA
2603449 ATGTTTTCCG
Statistics
Matches: 196, Mismatches: 30, Indels: 30
0.77 0.12 0.12
Matches are distributed among these distances:
41 26 0.13
42 70 0.36
43 77 0.39
44 23 0.12
ACGTcount: A:0.35, C:0.25, G:0.16, T:0.24
Consensus pattern (42 bp):
TCAGCACATAGCAACCCCTTTATATTCAGTAATACGGTGGAA
Found at i:2603311 original size:85 final size:86
Alignment explanation
Indices: 2603166--2603441 Score: 441
Period size: 85 Copynumber: 3.2 Consensus size: 86
2603156 TACATTCACC
2603166 TCAGCACATAGCAACCCCTTTCACAGTCAAAGATACGGTGGAATCAGCACTTAGCAACCACCTTT
1 TCAGCACATAGCAACCCCTTTCACAGTCAAAGATACGGTGGAATCAGCACTTAGCAACCACCTTT
2603231 ATATTCAGTAATTACGGGGAA
66 ATATTCAGTAATTACGGGGAA
2603252 T-AGCACATAGCAACCCCTTTCACAGTCAAAGATACGGTGGAATCAGCACTTAGCAACCACCTTT
1 TCAGCACATAGCAACCCCTTTCACAGTCAAAGATACGGTGGAATCAGCACTTAGCAACCACCTTT
2603316 ATATTCAGTAA-TACGGGGAA
66 ATATTCAGTAATTACGGGGAA
* * * *
2603336 TCAGCACATAGCAACCCCTTTAACAATCAAAGATACAGTGGAATCGGCACTTAGCAACCACCTTT
1 TCAGCACATAGCAACCCCTTTCACAGTCAAAGATACGGTGGAATCAGCACTTAGCAACCACCTTT
* * *
2603401 AAAGTCAATAATT-CGGGGAA
66 ATATTCAGTAATTACGGGGAA
** *
2603421 TCATAACTTAGCAACCCCTTT
1 TCAGCACATAGCAACCCCTTT
2603442 TTATTCAATG
Statistics
Matches: 178, Mismatches: 10, Indels: 5
0.92 0.05 0.03
Matches are distributed among these distances:
84 10 0.06
85 166 0.93
86 2 0.01
ACGTcount: A:0.35, C:0.26, G:0.16, T:0.23
Consensus pattern (86 bp):
TCAGCACATAGCAACCCCTTTCACAGTCAAAGATACGGTGGAATCAGCACTTAGCAACCACCTTT
ATATTCAGTAATTACGGGGAA
Found at i:2608547 original size:18 final size:18
Alignment explanation
Indices: 2608524--2608558 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
2608514 AAAACAAGCA
2608524 TTCTAT-TTTTTTCTTTTC
1 TTCTATCTTTTTT-TTTTC
2608542 TTCTATCTTTTTTTTTT
1 TTCTATCTTTTTTTTTT
2608559 TTTTTGCTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 10 0.62
19 6 0.38
ACGTcount: A:0.06, C:0.14, G:0.00, T:0.80
Consensus pattern (18 bp):
TTCTATCTTTTTTTTTTC
Found at i:2612081 original size:16 final size:17
Alignment explanation
Indices: 2612051--2612089 Score: 71
Period size: 16 Copynumber: 2.4 Consensus size: 17
2612041 TTCCAGATTA
2612051 ATTATTCCAAAAATAAT
1 ATTATTCCAAAAATAAT
2612068 ATTATTCC-AAAATAAT
1 ATTATTCCAAAAATAAT
2612084 ATTATT
1 ATTATT
2612090 TTAATAAGAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
16 14 0.64
17 8 0.36
ACGTcount: A:0.49, C:0.10, G:0.00, T:0.41
Consensus pattern (17 bp):
ATTATTCCAAAAATAAT
Found at i:2612166 original size:20 final size:19
Alignment explanation
Indices: 2612141--2612193 Score: 67
Period size: 20 Copynumber: 2.8 Consensus size: 19
2612131 GATAGTATTT
2612141 TTATTAATTTAATATTAAA
1 TTATTAATTTAATATTAAA
2612160 GTTATT-ATCTTAATATTAAA
1 -TTATTAAT-TTAATATTAAA
2612180 TTA--AATTTAATATT
1 TTATTAATTTAATATT
2612194 TATCTTATAG
Statistics
Matches: 31, Mismatches: 0, Indels: 7
0.82 0.00 0.18
Matches are distributed among these distances:
17 8 0.26
18 2 0.06
19 5 0.16
20 16 0.52
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (19 bp):
TTATTAATTTAATATTAAA
Found at i:2612296 original size:61 final size:61
Alignment explanation
Indices: 2612169--2612284 Score: 157
Period size: 61 Copynumber: 2.0 Consensus size: 61
2612159 AGTTATTATC
* * *
2612169 TTAATATTAAATTAAATTTAATATTTATCTTATAGATAAATATTCTATTAATTTAATAGGT
1 TTAATATTAAATTAAATATAATATTTATCTTATAGATAAATATTATATTAATTTAATAAGT
* * *
2612230 TTAATATTAAATTTAATATAATATTTATC-T-T-GATAAGTATTATATTAACTTAATA
1 TTAATATTAAATTAAATATAATATTTATCTTATAGATAAATATTATATTAATTTAATA
2612285 TTAAGTTTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
58 21 0.42
59 1 0.02
60 1 0.02
61 27 0.54
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.49
Consensus pattern (61 bp):
TTAATATTAAATTAAATATAATATTTATCTTATAGATAAATATTATATTAATTTAATAAGT
Found at i:2617323 original size:25 final size:25
Alignment explanation
Indices: 2617294--2617344 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 25
2617284 TTATTTTGAT
*
2617294 AGTATTTTTATTAAT-TTAATATTAA
1 AGTATTTATATTAATATTAA-ATTAA
*
2617319 AGTATTTATCTTAATATTAAATTAA
1 AGTATTTATATTAATATTAAATTAA
2617344 A
1 A
2617345 TTTAATATTT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 19 0.83
26 4 0.17
ACGTcount: A:0.43, C:0.02, G:0.04, T:0.51
Consensus pattern (25 bp):
AGTATTTATATTAATATTAAATTAA
Found at i:2617398 original size:61 final size:58
Alignment explanation
Indices: 2617329--2617444 Score: 160
Period size: 61 Copynumber: 1.9 Consensus size: 58
2617319 AGTATTTATC
* * *
2617329 TTAATATTAAATTAAATTTAATATTTATCTTATAGATAAATATTCTATTAATTTAATAGGT
1 TTAATATTAAATTAAATATAATATTTATC-T-T-GATAAATATTATATTAACTTAATAGGT
* *
2617390 TTAATATTAAATTTAATATAATATTTATCTTGATAAGTATTATATTAACTTAATA
1 TTAATATTAAATTAAATATAATATTTATCTTGATAAATATTATATTAACTTAATA
2617445 TTAAGTTTAA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
58 21 0.42
59 1 0.02
60 1 0.02
61 27 0.54
ACGTcount: A:0.43, C:0.03, G:0.04, T:0.49
Consensus pattern (58 bp):
TTAATATTAAATTAAATATAATATTTATCTTGATAAATATTATATTAACTTAATAGGT
Found at i:2626209 original size:19 final size:19
Alignment explanation
Indices: 2626181--2626234 Score: 99
Period size: 19 Copynumber: 2.8 Consensus size: 19
2626171 ATTGCACAAC
*
2626181 ATACTGATAACAATTTAGG
1 ATACTCATAACAATTTAGG
2626200 ATACTCATAACAATTTAGG
1 ATACTCATAACAATTTAGG
2626219 ATACTCATAACAATTT
1 ATACTCATAACAATTT
2626235 TATAGGTTGT
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 34 1.00
ACGTcount: A:0.43, C:0.15, G:0.09, T:0.33
Consensus pattern (19 bp):
ATACTCATAACAATTTAGG
Found at i:2626876 original size:22 final size:20
Alignment explanation
Indices: 2626833--2626871 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
2626823 TAATTTAAAA
2626833 TATAAAAATTTATTAATATG
1 TATAAAAATTTATTAATATG
*
2626853 TATATAAATTTATTAATAT
1 TATAAAAATTTATTAATAT
2626872 ATGTAAAAAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (20 bp):
TATAAAAATTTATTAATATG
Found at i:2626995 original size:20 final size:20
Alignment explanation
Indices: 2626970--2627009 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
2626960 AATATTTTCC
*
2626970 AGTAAATCATTTTATAGAAA
1 AGTAAAACATTTTATAGAAA
*
2626990 AGTAAAACATTTTCTAGAAA
1 AGTAAAACATTTTATAGAAA
2627010 TCATTTTACG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.50, C:0.07, G:0.10, T:0.33
Consensus pattern (20 bp):
AGTAAAACATTTTATAGAAA
Found at i:2627024 original size:34 final size:35
Alignment explanation
Indices: 2626958--2627024 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
2626948 CAAACACCAG
* *
2626958 AAAATATTTTCCAGTAAATCATTTTATAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
2626993 AAAACATTTTCTAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
2627025 CATTTTACTG
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
34 16 0.57
35 12 0.43
ACGTcount: A:0.46, C:0.10, G:0.09, T:0.34
Consensus pattern (35 bp):
AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
Found at i:2627491 original size:29 final size:29
Alignment explanation
Indices: 2627458--2627514 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
2627448 AAAAGCTCTT
*
2627458 TTTTTTCAA-AATTTACTGAAATGGGCCAC
1 TTTTTT-AATAATTTACCGAAATGGGCCAC
* *
2627487 TTTTTTAATTATTTACCGGAATGGGCCA
1 TTTTTTAATAATTTACCGAAATGGGCCA
2627515 TTTCTGCGAA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
28 2 0.08
29 22 0.92
ACGTcount: A:0.28, C:0.16, G:0.16, T:0.40
Consensus pattern (29 bp):
TTTTTTAATAATTTACCGAAATGGGCCAC
Found at i:2628023 original size:124 final size:125
Alignment explanation
Indices: 2627797--2628077 Score: 426
Period size: 124 Copynumber: 2.3 Consensus size: 125
2627787 TTATTTTGAG
**
2627797 TTGACGTTTCTG-GTCAAATAGTATAAAATCGCTTCTACCAGGATGCTATTAGAGAAGAAATTGT
1 TTGACGTTTCTGAG-CAAATAGTATAAAATCGCTGATACCAGGATGCTATTAGAGAAGAAATTGT
* * *
2627861 AAAATCGTGCCTTCGTGGACGCGATTTCGGTACAGTTGGTCATGTAAGAAAT-AA-TTTTT
65 AAAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAAATTTTTT
2627920 TTGACGTTTTCTGAGCAAATAGTATAAAATCGCTGATACCAGGATGCTA-TATGAGAAGAAATTG
1 TTGACG-TTTCTGAGCAAATAGTATAAAATCGCTGATACCAGGATGCTATTA-GAGAAGAAATTG
* *
2627984 TGAAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAGGAAATAAATTTTTT
64 TAAAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAAATTTTTT
* *
2628046 TTGACGTTTCTGAGCAAATAGTGTCAAATCGC
1 TTGACGTTTCTGAGCAAATAGTATAAAATCGC
2628078 GCCCTCATGG
Statistics
Matches: 144, Mismatches: 9, Indels: 8
0.89 0.06 0.05
Matches are distributed among these distances:
123 8 0.06
124 98 0.68
125 27 0.19
126 11 0.08
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (125 bp):
TTGACGTTTCTGAGCAAATAGTATAAAATCGCTGATACCAGGATGCTATTAGAGAAGAAATTGTA
AAATCGCGCCCTCGTGGACGCGATTTCGCTACAGTTGGTCATGTAAGAAATAAATTTTTT
Found at i:2629976 original size:24 final size:24
Alignment explanation
Indices: 2629944--2629999 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
2629934 TGTATGTGGA
2629944 GGTGTTTGCATCATGAACGGCGAC
1 GGTGTTTGCATCATGAACGGCGAC
2629968 GGTGTTTGCATCATGAACGGCGAC
1 GGTGTTTGCATCATGAACGGCGAC
*
2629992 GGAGTTTG
1 GGTGTTTG
2630000 AAAGCCATGC
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.20, C:0.18, G:0.36, T:0.27
Consensus pattern (24 bp):
GGTGTTTGCATCATGAACGGCGAC
Found at i:2631512 original size:14 final size:15
Alignment explanation
Indices: 2631495--2631528 Score: 52
Period size: 15 Copynumber: 2.3 Consensus size: 15
2631485 AATAATTATC
2631495 TAAAAATA-CATAAA
1 TAAAAATATCATAAA
*
2631509 TAAAAATATCTTAAA
1 TAAAAATATCATAAA
2631524 TAAAA
1 TAAAA
2631529 TTTAAAATTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 8 0.44
15 10 0.56
ACGTcount: A:0.68, C:0.06, G:0.00, T:0.26
Consensus pattern (15 bp):
TAAAAATATCATAAA
Found at i:2631659 original size:28 final size:29
Alignment explanation
Indices: 2631626--2631683 Score: 93
Period size: 29 Copynumber: 2.0 Consensus size: 29
2631616 TTGAAAATAT
2631626 TAAAAAT-TTTAAAATTATT-TTAAAAAAA
1 TAAAAATATTTAAAATT-TTCTTAAAAAAA
2631654 TAAAAATATTTAAAATTTTCTTAAAAAAA
1 TAAAAATATTTAAAATTTTCTTAAAAAAA
2631683 T
1 T
2631684 GAAATTGAAT
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 9 0.32
29 19 0.68
ACGTcount: A:0.59, C:0.02, G:0.00, T:0.40
Consensus pattern (29 bp):
TAAAAATATTTAAAATTTTCTTAAAAAAA
Found at i:2631742 original size:22 final size:21
Alignment explanation
Indices: 2631717--2631767 Score: 66
Period size: 22 Copynumber: 2.3 Consensus size: 21
2631707 TAATATGGAG
*
2631717 TTGAGAGATTTTTTGAAGGAAA
1 TTGAGAGA-TTTTGGAAGGAAA
*
2631739 TTGAGAGGATTTTGGAAGGAAT
1 TTGAGA-GATTTTGGAAGGAAA
2631761 TTGAGAG
1 TTGAGAG
2631768 TTTAAGAGAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
21 1 0.04
22 23 0.88
23 2 0.08
ACGTcount: A:0.33, C:0.00, G:0.33, T:0.33
Consensus pattern (21 bp):
TTGAGAGATTTTGGAAGGAAA
Found at i:2645725 original size:15 final size:15
Alignment explanation
Indices: 2645705--2645734 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
2645695 TAAAGATGTT
2645705 GATGGGGAAGGAATA
1 GATGGGGAAGGAATA
2645720 GATGGGGAAGGAATA
1 GATGGGGAAGGAATA
2645735 AATTTATGTT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.00, G:0.47, T:0.13
Consensus pattern (15 bp):
GATGGGGAAGGAATA
Found at i:2646351 original size:14 final size:14
Alignment explanation
Indices: 2646332--2646358 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
2646322 AAAGAGAAAA
2646332 AAAAAAGAAAAAGG
1 AAAAAAGAAAAAGG
2646346 AAAAAAGAAAAAG
1 AAAAAAGAAAAAG
2646359 AGTTTAATAT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.81, C:0.00, G:0.19, T:0.00
Consensus pattern (14 bp):
AAAAAAGAAAAAGG
Found at i:2648869 original size:3 final size:3
Alignment explanation
Indices: 2648861--2648892 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
2648851 AAACAAATAC
2648861 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AA
2648893 AAGCTAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:2654285 original size:34 final size:34
Alignment explanation
Indices: 2654247--2654318 Score: 135
Period size: 34 Copynumber: 2.1 Consensus size: 34
2654237 TCCCTCAGAC
*
2654247 TTGACCTTGCCCAATTTCTCTTTTGAATTTGTAA
1 TTGACCTTGCCCAATTTCTCTTCTGAATTTGTAA
2654281 TTGACCTTGCCCAATTTCTCTTCTGAATTTGTAA
1 TTGACCTTGCCCAATTTCTCTTCTGAATTTGTAA
2654315 TTGA
1 TTGA
2654319 GAGAGATGTA
Statistics
Matches: 37, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 37 1.00
ACGTcount: A:0.21, C:0.21, G:0.12, T:0.46
Consensus pattern (34 bp):
TTGACCTTGCCCAATTTCTCTTCTGAATTTGTAA
Found at i:2661395 original size:6 final size:6
Alignment explanation
Indices: 2661384--2661410 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
2661374 GCCCCTATAC
2661384 AAAAAG AAAAAG AAAAAG AAAAAG AAA
1 AAAAAG AAAAAG AAAAAG AAAAAG AAA
2661411 GAGTAAATTA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 21 1.00
ACGTcount: A:0.85, C:0.00, G:0.15, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:2662986 original size:125 final size:126
Alignment explanation
Indices: 2662762--2663072 Score: 396
Period size: 125 Copynumber: 2.4 Consensus size: 126
2662752 GATAAAATCA
* * * * * * * *
2662762 AAGCAGGATGCTTTATCAGAAGGATTTTTGAAGTTGCGTCCACGTGTACGCGCTTTTGCTATAGT
1 AAGCAGGATGCTTTATGAGAA-GAATTTTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGT
* *
2662827 AGGTCCTGAAAAAATAATTTTGACTTGACTTTTCTGAGCAAATAG-T-ATAAAAAATGCTTC
65 AGGTCCTGAAAAAATAATTTCGACTTGACTTTTCTGAGCAAATAGTTAAAAAAAAATGCTTC
2662887 AAGCAGGATGCTTTATGAGAAGAATTTTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTA
1 AAGCAGGATGCTTTATGAGAAGAATTTTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTA
* * *
2662952 GGTCCTGGAAGAAATAATTTCGAGTTGA-TGTTTCTGAGCAAATAGTTTTAAAAAAAAATGCTTG
66 GGTCCT-GAAAAAATAATTTCGACTTGACT-TTTCTGAGCAAATAG--TTAAAAAAAAATGCTTC
* *
2663016 AAGCAGGATGCTATT-TGAGAAGAATTTGTGAAATCGCGCCCTCATGGATGCGCTTTT
1 AAGCAGGATGCT-TTATGAGAAGAATTT-TGAAATCGCGCCCTCGTGGACGCGCTTTT
2663073 AAGTTAAGGG
Statistics
Matches: 163, Mismatches: 15, Indels: 11
0.86 0.08 0.06
Matches are distributed among these distances:
124 44 0.27
125 53 0.33
128 1 0.01
129 36 0.22
130 29 0.18
ACGTcount: A:0.30, C:0.15, G:0.23, T:0.32
Consensus pattern (126 bp):
AAGCAGGATGCTTTATGAGAAGAATTTTGAAATCGCGCCCTCGTGGACGCGCTTTTGCTACAGTA
GGTCCTGAAAAAATAATTTCGACTTGACTTTTCTGAGCAAATAGTTAAAAAAAAATGCTTC
Found at i:2663099 original size:21 final size:21
Alignment explanation
Indices: 2663069--2663574 Score: 398
Period size: 21 Copynumber: 23.1 Consensus size: 21
2663059 ATGGATGCGC
2663069 TTTT-AAGTTAAGGGTTAGGG
1 TTTTAAAGTTAAGGGTTAGGG
2663089 TTTTAAAGTTAAGGGTTAGGG
1 TTTTAAAGTTAAGGGTTAGGG
* *
2663110 TTTTAAGGTTTTAAAGTTAAGGGTTAGGG
1 TTTTAAAG--TT-AAG----GGT-TAGGG
*
2663139 TTTTAAAGTTAAGGGGTTGGGG
1 TTTTAAAGTTAA-GGGTTAGGG
* *
2663161 TTTT-TAGCTTAAGGGTTTATGG
1 TTTTAAAG-TTAAGGG-TTAGGG
*
2663183 TTTTAAAGTCAAGGGTTAGGG
1 TTTTAAAGTTAAGGGTTAGGG
2663204 TTTTAAAGTTAAGGGTTTAGGG
1 TTTTAAAGTTAAGGG-TTAGGG
* *
2663226 TTTTTAGGTTAAGGGTTTAGGG
1 TTTTAAAGTTAAGGG-TTAGGG
* *
2663248 TTTT-AGGTTAAAGGTTTAGGG
1 TTTTAAAGTT-AAGGGTTAGGG
* *
2663269 TTTTAAAGTTAAAGGTTAAGG
1 TTTTAAAGTTAAGGGTTAGGG
* *
2663290 TTTTTAAGTTAAGGGTTAGGA
1 TTTTAAAGTTAAGGGTTAGGG
*
2663311 TTTTTAAGTTAAGGGTTTAGGG
1 TTTTAAAGTTAAGGG-TTAGGG
* *
2663333 TTTTTAAGTTAAAGGTTTAGGG
1 TTTTAAAGTT-AAGGGTTAGGG
* *
2663355 GTTTAAAATTAAGGGTTAGGG
1 TTTTAAAGTTAAGGGTTAGGG
* *
2663376 TTTTTAAGTTAAGGGTTAGTG
1 TTTTAAAGTTAAGGGTTAGGG
* *
2663397 TTTT---TTTAAGTGTTAGGGG
1 TTTTAAAGTTAAGGGTTA-GGG
2663416 TTTT-AAGTTAAGGGTTTAGGG
1 TTTTAAAGTTAAGGG-TTAGGG
* * *
2663437 TTTTAAAGTCAAGAGTTAGTGT
1 TTTTAAAGTTAAGGGTTAG-GG
2663459 TTTTAAA-TTAAGGGTTTAGGG
1 TTTTAAAGTTAAGGG-TTAGGG
*
2663480 TTTATGGGTTTTAAGTTAAGGGTTTAGGG
1 ----T---TTTAAAGTTAAGGG-TTAGGG
* * * *
2663509 TTTTTAATTTAAAGATTAGGG
1 TTTTAAAGTTAAGGGTTAGGG
*
2663530 TTTTTAAGTTAAGGGTTAGGG
1 TTTTAAAGTTAAGGGTTAGGG
* *
2663551 TTTTTAAGTTAAGGTTTAGGG
1 TTTTAAAGTTAAGGGTTAGGG
2663572 TTT
1 TTT
2663575 GTCAATTAAA
Statistics
Matches: 401, Mismatches: 52, Indels: 65
0.77 0.10 0.13
Matches are distributed among these distances:
18 9 0.02
19 6 0.01
20 4 0.01
21 203 0.51
22 126 0.31
23 10 0.02
24 3 0.01
25 2 0.00
26 2 0.00
27 3 0.01
28 7 0.02
29 26 0.06
ACGTcount: A:0.26, C:0.01, G:0.31, T:0.43
Consensus pattern (21 bp):
TTTTAAAGTTAAGGGTTAGGG
Found at i:2663121 original size:29 final size:29
Alignment explanation
Indices: 2663087--2663144 Score: 116
Period size: 29 Copynumber: 2.0 Consensus size: 29
2663077 TAAGGGTTAG
2663087 GGTTTTAAAGTTAAGGGTTAGGGTTTTAA
1 GGTTTTAAAGTTAAGGGTTAGGGTTTTAA
2663116 GGTTTTAAAGTTAAGGGTTAGGGTTTTAA
1 GGTTTTAAAGTTAAGGGTTAGGGTTTTAA
2663145 AGTTAAGGGG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 29 1.00
ACGTcount: A:0.28, C:0.00, G:0.31, T:0.41
Consensus pattern (29 bp):
GGTTTTAAAGTTAAGGGTTAGGGTTTTAA
Found at i:2663164 original size:43 final size:42
Alignment explanation
Indices: 2663069--2663574 Score: 482
Period size: 43 Copynumber: 11.5 Consensus size: 42
2663059 ATGGATGCGC
2663069 TTTTAAGTTAAGGGTTAGGGTTTTAAAGTTAAGGGTTAGGGTTTT
1 TTTTAAGTTAAGGGTTAGGGTTTTAAAGTTAAGGGTTAGGG---T
*
2663114 AAGGTTTTAAAGTTAAGGGTTAGGGTTTTAAAGTTAAGGGGTTGGGGT
1 ----TTTT-AAGTTAAGGGTTAGGGTTTTAAAGTTAA-GGGTTAGGGT
* *
2663162 TTTT-AGCTTAAGGGTTTATGGTTTTAAAGTCAAGGGTTAGGGT
1 TTTTAAG-TTAAGGG-TTAGGGTTTTAAAGTTAAGGGTTAGGGT
* * *
2663205 TTTAAAGTTAAGGGTTTAGGGTTTTTAGGTTAAGGGTTTAGGG-
1 TTTTAAGTTAAGGG-TTAGGGTTTTAAAGTTAAGGG-TTAGGGT
* * * *
2663248 TTTTAGGTTAAAGGTTTAGGGTTTTAAAGTTAAAGGTTAAGGT
1 TTTTAAGTT-AAGGGTTAGGGTTTTAAAGTTAAGGGTTAGGGT
* *
2663291 TTTTAAGTTAAGGGTTAGGATTTTTAAGTTAAGGGTTTAGGGT
1 TTTTAAGTTAAGGGTTAGGGTTTTAAAGTTAAGGG-TTAGGGT
* * *
2663334 TTTTAAGTTAAAGGTTTAGGGGTTTAAAATTAAGGGTTAGGGT
1 TTTTAAGTT-AAGGGTTAGGGTTTTAAAGTTAAGGGTTAGGGT
* * * *
2663377 TTTTAAGTTAAGGGTTAGTGTTTT---TTTAAGTGTTAGGGG
1 TTTTAAGTTAAGGGTTAGGGTTTTAAAGTTAAGGGTTAGGGT
* * *
2663416 TTTTAAGTTAAGGGTTTAGGGTTTTAAAGTCAAGAGTTAGTGT
1 TTTTAAGTTAAGGG-TTAGGGTTTTAAAGTTAAGGGTTAGGGT
* *
2663459 TTTTAAATTAAGGGTTTAGGGTTTATGGGTTTTAAGTTAAGGGTTTAGGGT
1 TTTTAAGTTAAGGG-TTAGGG----T---TTTAAAGTTAAGGG-TTAGGGT
* * * *
2663510 TTTTAATTTAAAGATTAGGGTTTTTAAGTTAAGGGTTAGGGT
1 TTTTAAGTTAAGGGTTAGGGTTTTAAAGTTAAGGGTTAGGGT
*
2663552 TTTTAAGTTAAGGTTTAGGGTTT
1 TTTTAAGTTAAGGGTTAGGGTTT
2663575 GTCAATTAAA
Statistics
Matches: 385, Mismatches: 50, Indels: 51
0.79 0.10 0.10
Matches are distributed among these distances:
39 26 0.07
40 9 0.02
42 68 0.18
43 152 0.39
44 53 0.14
46 1 0.00
47 1 0.00
48 1 0.00
49 4 0.01
50 45 0.12
51 25 0.06
ACGTcount: A:0.26, C:0.01, G:0.31, T:0.43
Consensus pattern (42 bp):
TTTTAAGTTAAGGGTTAGGGTTTTAAAGTTAAGGGTTAGGGT
Found at i:2663530 original size:50 final size:49
Alignment explanation
Indices: 2663418--2663574 Score: 152
Period size: 50 Copynumber: 3.3 Consensus size: 49
2663408 GTTAGGGGTT
* * * *
2663418 TTAA-GTTAAGGGTTTA-GGGTTTTAAAGTCAAGAGTTAGTGTTTTTAAA
1 TTAAGGTTTAGGGTTTATGGGTTTT-AAGTTAAGGGTTAGGGTTTTTAAA
*
2663466 TTAAGGGTTTAGGGTTTATGGGTTTTAAGTTAAGGGTTTAGGGTTTTTAAT
1 TTAA-GGTTTAGGGTTTATGGGTTTTAAGTTAAGGG-TTAGGGTTTTTAAA
* * *
2663517 TTAAAGATTAGGG----T---TTTTAAGTTAAGGGTTAGGGTTTTTAAG
1 TTAAGGTTTAGGGTTTATGGGTTTTAAGTTAAGGGTTAGGGTTTTTAAA
2663559 TTAAGGTTTAGGGTTT
1 TTAAGGTTTAGGGTTT
2663575 GTCAATTAAA
Statistics
Matches: 92, Mismatches: 10, Indels: 17
0.77 0.08 0.14
Matches are distributed among these distances:
42 24 0.26
43 14 0.15
46 1 0.01
48 4 0.04
50 26 0.28
51 23 0.25
ACGTcount: A:0.26, C:0.01, G:0.29, T:0.45
Consensus pattern (49 bp):
TTAAGGTTTAGGGTTTATGGGTTTTAAGTTAAGGGTTAGGGTTTTTAAA
Found at i:2664140 original size:18 final size:18
Alignment explanation
Indices: 2664114--2664156 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
2664104 GACTCGAAAA
*
2664114 AGGAAACATATAAGGGTT
1 AGGAAACATAAAAGGGTT
*
2664132 AGGATACATAAAAGGGTT
1 AGGAAACATAAAAGGGTT
2664150 AGGAAAC
1 AGGAAAC
2664157 GCACCTGGCG
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.47, C:0.07, G:0.28, T:0.19
Consensus pattern (18 bp):
AGGAAACATAAAAGGGTT
Found at i:2664814 original size:7 final size:7
Alignment explanation
Indices: 2664804--2664829 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2664794 TTATATACAT
2664804 AATACTA
1 AATACTA
2664811 AATACTA
1 AATACTA
2664818 AATACTA
1 AATACTA
2664825 AATAC
1 AATAC
2664830 CAATCGACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.58, C:0.15, G:0.00, T:0.27
Consensus pattern (7 bp):
AATACTA
Found at i:2665906 original size:11 final size:11
Alignment explanation
Indices: 2665892--2665947 Score: 53
Period size: 11 Copynumber: 5.0 Consensus size: 11
2665882 TAAAAATAGG
2665892 AATTTAAGAGA
1 AATTTAAGAGA
2665903 AATTTAAGAGGA
1 AATTTAAGA-GA
*
2665915 AA-TTGAGAGCA
1 AATTTAAGAG-A
2665926 AA-TTAAGAGGA
1 AATTTAAGA-GA
*
2665937 AATTTGAGAGA
1 AATTTAAGAGA
2665948 GGATTAGTTT
Statistics
Matches: 38, Mismatches: 3, Indels: 8
0.78 0.06 0.16
Matches are distributed among these distances:
10 1 0.03
11 27 0.71
12 10 0.26
ACGTcount: A:0.50, C:0.02, G:0.25, T:0.23
Consensus pattern (11 bp):
AATTTAAGAGA
Found at i:2665953 original size:23 final size:22
Alignment explanation
Indices: 2665889--2665946 Score: 73
Period size: 22 Copynumber: 2.6 Consensus size: 22
2665879 AGTTAAAAAT
* *
2665889 AGGAATTTAAGAG-AAATTTAAG
1 AGGAAATTGAGAGCAAA-TTAAG
2665911 AGGAAATTGAGAGCAAATTAAG
1 AGGAAATTGAGAGCAAATTAAG
2665933 AGGAAATTTGAGAG
1 AGGAAA-TTGAGAG
2665947 AGGATTAGTT
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
22 22 0.69
23 10 0.31
ACGTcount: A:0.48, C:0.02, G:0.28, T:0.22
Consensus pattern (22 bp):
AGGAAATTGAGAGCAAATTAAG
Found at i:2667579 original size:102 final size:103
Alignment explanation
Indices: 2667451--2667659 Score: 411
Period size: 102 Copynumber: 2.0 Consensus size: 103
2667441 TTTTTAAAAT
2667451 TTAAAGAGATATATATTTCATAATTTTCTTTTTTTTTTCTTTCACCTTAGTGTGACACTATCTAA
1 TTAAAGAGATATATATTTCATAATTTTCTTTTTTTTTTCTTTCACCTTAGTGTGACACTATCTAA
2667516 TTATCTTTAAATCATTTTTTATTTAATTTAGTTAACAA
66 TTATCTTTAAATCATTTTTTATTTAATTTAGTTAACAA
2667554 TTAAAGAGATA-ATATTTCATAATTTTCTTTTTTTTTTCTTTCACCTTAGTGTGACACTATCTAA
1 TTAAAGAGATATATATTTCATAATTTTCTTTTTTTTTTCTTTCACCTTAGTGTGACACTATCTAA
2667618 TTATCTTTAAATCATTTTTTATTTAATTTAGTTAACAA
66 TTATCTTTAAATCATTTTTTATTTAATTTAGTTAACAA
2667656 TTAA
1 TTAA
2667660 CTTTTTAAAT
Statistics
Matches: 106, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
102 95 0.90
103 11 0.10
ACGTcount: A:0.31, C:0.11, G:0.06, T:0.52
Consensus pattern (103 bp):
TTAAAGAGATATATATTTCATAATTTTCTTTTTTTTTTCTTTCACCTTAGTGTGACACTATCTAA
TTATCTTTAAATCATTTTTTATTTAATTTAGTTAACAA
Found at i:2680218 original size:146 final size:148
Alignment explanation
Indices: 2679920--2680218 Score: 487
Period size: 146 Copynumber: 2.0 Consensus size: 148
2679910 GGAATCATAT
2679920 CTTGT-ATAGATTATATTAGATTTGATATGGCATATCTTGTAAATCCCTAAAATAAAGGGATATG
1 CTTGTAATAGATTATATTAGATTTGATATGGCATATCTTGTAAATCCCTAAAATAAAGGGATATG
* * *
2679984 GTTAAATCTCATCCGTCGATGTAAATGTATCTTGACCGTCGATTTTGGGGGAGCTCAACTATAAA
66 GTTAAATCTCACCCATCGATGTAAATGTATATTGACCGTCGATTTTGGGGGAGCTCAACTATAAA
*
2680049 TAGAAAACATCCCTCTCA
131 TAGAAAACATCCCCCTCA
2680067 CTTGTAATAGATTATA-TAGATTTGATATGGCATATCTTGTAAATCCCTAAAATAAAGGGATATG
1 CTTGTAATAGATTATATTAGATTTGATATGGCATATCTTGTAAATCCCTAAAATAAAGGGATATG
* *
2680131 GTT-AATCTCGCCCATCGATGTAAATGTATATTGACCGTCGGTTTTGGGGGAGCTCAACTATAAA
66 GTTAAATCTCACCCATCGATGTAAATGTATATTGACCGTCGATTTTGGGGGAGCTCAACTATAAA
* * *
2680195 TAGAGAGCCTCCCCCTCA
131 TAGAAAACATCCCCCTCA
*
2680213 TTTGTA
1 CTTGTA
2680219 CTCATTCCAT
Statistics
Matches: 141, Mismatches: 10, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
146 75 0.53
147 56 0.40
148 10 0.07
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Consensus pattern (148 bp):
CTTGTAATAGATTATATTAGATTTGATATGGCATATCTTGTAAATCCCTAAAATAAAGGGATATG
GTTAAATCTCACCCATCGATGTAAATGTATATTGACCGTCGATTTTGGGGGAGCTCAACTATAAA
TAGAAAACATCCCCCTCA
Found at i:2686295 original size:4 final size:4
Alignment explanation
Indices: 2686286--2686367 Score: 53
Period size: 4 Copynumber: 20.8 Consensus size: 4
2686276 TTTTCACTTG
* ** * *
2686286 TTTA TTTA TTCA -TTA TTCC TTTTA TTTTA TTCA TTTA TTTA TTCA TTTA
1 TTTA TTTA TTTA TTTA TTTA TT-TA TT-TA TTTA TTTA TTTA TTTA TTTA
* * *
2686335 CTTA TTTA TATA -TTA TTTA TTCA TTTA -TTA TTT
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTTA TTT
2686368 TAATCTTTCT
Statistics
Matches: 58, Mismatches: 16, Indels: 8
0.71 0.20 0.10
Matches are distributed among these distances:
3 7 0.12
4 44 0.76
5 7 0.12
ACGTcount: A:0.24, C:0.09, G:0.00, T:0.67
Consensus pattern (4 bp):
TTTA
Found at i:2686328 original size:12 final size:12
Alignment explanation
Indices: 2686306--2686363 Score: 62
Period size: 12 Copynumber: 4.5 Consensus size: 12
2686296 CATTATTCCT
2686306 TTTATTTTATTCA
1 TTTA-TTTATTCA
2686319 TTTATTTATTCA
1 TTTATTTATTCA
* *
2686331 TTTACTTATTTATA
1 TTTATTTA-TT-CA
2686345 TATTATTTATTCA
1 T-TTATTTATTCA
2686358 TTTATT
1 TTTATT
2686364 ATTTTAATCT
Statistics
Matches: 38, Mismatches: 4, Indels: 7
0.78 0.08 0.14
Matches are distributed among these distances:
12 20 0.53
13 8 0.21
14 4 0.11
15 6 0.16
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (12 bp):
TTTATTTATTCA
Found at i:2691425 original size:14 final size:15
Alignment explanation
Indices: 2691399--2691431 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
2691389 TGCAAAATTG
*
2691399 GGAAGGACCTTATGT
1 GGAAGGACCTTATCT
2691414 GGAAGG-CCTTATCT
1 GGAAGGACCTTATCT
2691428 GGAA
1 GGAA
2691432 AAACGTTGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 11 0.65
15 6 0.35
ACGTcount: A:0.27, C:0.15, G:0.33, T:0.24
Consensus pattern (15 bp):
GGAAGGACCTTATCT
Found at i:2691541 original size:26 final size:26
Alignment explanation
Indices: 2691512--2691570 Score: 75
Period size: 26 Copynumber: 2.3 Consensus size: 26
2691502 ATATTTCATA
* *
2691512 AAAAAATATATAAA-AAAAGAGAAAAG
1 AAAAAATAGAAAAAGAAAAGA-AAAAG
*
2691538 AAAAAAAAGAAAAAGAAAAGAAAAAG
1 AAAAAATAGAAAAAGAAAAGAAAAAG
2691564 AAAAAAT
1 AAAAAAT
2691571 GGGAGGCCAA
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
26 22 0.79
27 6 0.21
ACGTcount: A:0.81, C:0.00, G:0.12, T:0.07
Consensus pattern (26 bp):
AAAAAATAGAAAAAGAAAAGAAAAAG
Found at i:2691544 original size:16 final size:16
Alignment explanation
Indices: 2691523--2691567 Score: 67
Period size: 16 Copynumber: 2.9 Consensus size: 16
2691513 AAAAATATAT
2691523 AAAAAAAGAGAAAAGA
1 AAAAAAAGAGAAAAGA
2691539 AAAAAAAGA-AAAAGA
1 AAAAAAAGAGAAAAGA
2691554 AAAGAAAA-AGAAAA
1 AAA-AAAAGAGAAAA
2691568 AATGGGAGGC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 10 0.37
16 17 0.63
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (16 bp):
AAAAAAAGAGAAAAGA
Found at i:2691550 original size:6 final size:6
Alignment explanation
Indices: 2691525--2691568 Score: 51
Period size: 6 Copynumber: 7.8 Consensus size: 6
2691515 AAATATATAA
2691525 AAAAAG AGAAAAG --AAA- AAAAAG AAAAAG -AAAAG AAAAAG AAAAA
1 AAAAAG A-AAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAAG AAAAA
2691569 ATGGGAGGCC
Statistics
Matches: 33, Mismatches: 0, Indels: 10
0.77 0.00 0.23
Matches are distributed among these distances:
4 3 0.09
5 8 0.24
6 17 0.52
7 5 0.15
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (6 bp):
AAAAAG
Found at i:2691558 original size:11 final size:11
Alignment explanation
Indices: 2691526--2691567 Score: 61
Period size: 11 Copynumber: 3.9 Consensus size: 11
2691516 AATATATAAA
2691526 AAAAGAGAAAAG
1 AAAA-AGAAAAG
2691538 -AAAA-AAAAG
1 AAAAAGAAAAG
2691547 AAAAAGAAAAG
1 AAAAAGAAAAG
2691558 AAAAAGAAAA
1 AAAAAGAAAA
2691568 AATGGGAGGC
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
9 5 0.18
10 5 0.18
11 18 0.64
ACGTcount: A:0.83, C:0.00, G:0.17, T:0.00
Consensus pattern (11 bp):
AAAAAGAAAAG
Found at i:2692522 original size:44 final size:43
Alignment explanation
Indices: 2692456--2693015 Score: 165
Period size: 44 Copynumber: 12.7 Consensus size: 43
2692446 CATTATGACG
*
2692456 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGCCACT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGACA-T
* * * * * *
2692500 AATCTTATC-CCTCTAAATTTGCAGTGGGGCAGATTGAAGATAT
1 AATCTTATCTCC-CTGAAGTTGCAGTGGAGCAGACTAAAGACAT
* * *
2692543 AAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAGATAGCG
1 AA-TCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGACA--T
* * * * * * *
2692589 AACCTTATTTCCCTGAAGTTGCAGTAGAACAGATTGAAGCTATAAATT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AA---AGACA-T
* * * * * **
2692637 GCAGATCTTATCTCTCTGAAGCTGTAGTAGAGCAGATTCTAG-CA-
1 --A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGACAT
* *
2692681 AACCTTATCTCCCCGAAGTTGCAGT-G-G-AG-C----G----
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGACAT
* * *
2692712 AATCTTATTTCCCTGAAGTTGCAGTTGAGCAG-CTTGAAGTTACA-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGAC-TAAAG--ACAT
* * * * * * *
2692756 AGTCTTCTCTCTCTAAAGTTGCAGTGGAGCAGACTGAAGATAGC
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGACA-T
* * ** * *
2692800 AATCTTATTTCCCTGAAGTTGCAGCGGAATAGATTAAAGCTATATATT
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAG----ACA-T
* * * * *
2692848 ACAGATCTTATCTCTCTGAAGTTGCAGTAGAGAAGA-TCATA-TCA-
1 --A-ATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT-AAAGACAT
* * *
2692892 AACCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGATAGGCTACA-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACT--A-A-A-G--ACAT
* * *
2692941 AACCTTATCTCCCTGAAGTTGTAGTGGAGCAGATTAAAGCCACA-
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAG--ACAT
*
2692985 AACCTTATCTCCCTGAAGTTGCAGTGGAGCA
1 AATCTTATCTCCCTGAAGTTGCAGTGGAGCA
2693016 AATTGAAGAT
Statistics
Matches: 391, Mismatches: 81, Indels: 88
0.70 0.14 0.16
Matches are distributed among these distances:
31 22 0.06
32 1 0.00
33 2 0.01
34 3 0.01
38 2 0.01
39 2 0.01
40 1 0.00
41 46 0.12
42 5 0.01
43 6 0.02
44 160 0.41
45 33 0.08
46 6 0.02
47 2 0.01
48 3 0.01
49 38 0.10
50 3 0.01
51 56 0.14
ACGTcount: A:0.30, C:0.20, G:0.22, T:0.29
Consensus pattern (43 bp):
AATCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTAAAGACAT
Found at i:2692879 original size:211 final size:212
Alignment explanation
Indices: 2692518--2692921 Score: 596
Period size: 211 Copynumber: 1.9 Consensus size: 212
2692508 CCCTCTAAAT
* * *
2692518 TTGCAGTGGGGCAGATTGAAGATATAAGTCTTATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAG
1 TTGCAGTGGAGCAGATTGAAGATACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAG
* * *
2692583 ATAGCGAACCTTATTTCCCTGAAGTTGCAGTAGAACAGATTGAAGCTATAAATTGCAGATCTTAT
66 ATAGCGAACCTTATTTCCCTGAAGTTGCAGCAGAACAGATTAAAGCTATAAATTACAGATCTTAT
* *
2692648 CTCTCTGAAGCTGTAGTAGAGCAGATTC-TAGCAAACCTTATCTCCCCGAAGTTGCAGTGGAGCG
131 CTCTCTGAAGCTGCAGTAGAGAAGA-TCATAGCAAACCTTATCTCCCCGAAGTTGCAGTGGAGCG
2692712 AATCTTATTTCCCTGAAG
195 AATCTTATTTCCCTGAAG
* * * * *
2692730 TTGCAGTTGAGCAGCTTGAAGTTACAAGTCTTCTCTCTCTAAAGTTGCAGTGGAGCAGACTGAAG
1 TTGCAGTGGAGCAGATTGAAGATACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAG
* * * *
2692795 ATAGC-AATCTTATTTCCCTGAAGTTGCAGCGGAATAGATTAAAGCTATATATTACAGATCTTAT
66 ATAGCGAACCTTATTTCCCTGAAGTTGCAGCAGAACAGATTAAAGCTATAAATTACAGATCTTAT
* * **
2692859 CTCTCTGAAGTTGCAGTAGAGAAGATCATATCAAACCTTATCTCCTTGAAGTTGCAGTGGAGC
131 CTCTCTGAAGCTGCAGTAGAGAAGATCATAGCAAACCTTATCTCCCCGAAGTTGCAGTGGAGC
2692922 AGATTGAAGA
Statistics
Matches: 170, Mismatches: 21, Indels: 3
0.88 0.11 0.02
Matches are distributed among these distances:
210 2 0.01
211 106 0.62
212 62 0.36
ACGTcount: A:0.29, C:0.19, G:0.23, T:0.29
Consensus pattern (212 bp):
TTGCAGTGGAGCAGATTGAAGATACAAGTCTTATCTCCCTAAAGTTGCAGTGGAGCAGACTGAAG
ATAGCGAACCTTATTTCCCTGAAGTTGCAGCAGAACAGATTAAAGCTATAAATTACAGATCTTAT
CTCTCTGAAGCTGCAGTAGAGAAGATCATAGCAAACCTTATCTCCCCGAAGTTGCAGTGGAGCGA
ATCTTATTTCCCTGAAG
Found at i:2692950 original size:49 final size:49
Alignment explanation
Indices: 2692890--2693027 Score: 205
Period size: 44 Copynumber: 2.9 Consensus size: 49
2692880 AAGATCATAT
* *
2692890 CAAACCTTATCTCCTTGAAGTTGCAGTGGAGCAGATTGAAGATAGGCTA
1 CAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGGCCA
*
2692939 CAAACCTTATCTCCCTGAAGTTGTAGTGGAGCAGATT--A-A-A-GCCA
1 CAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGGCCA
*
2692983 CAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAAATTGAAGATAG
1 CAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAG
2693028 CGAATCTCAT
Statistics
Matches: 79, Mismatches: 5, Indels: 10
0.84 0.05 0.11
Matches are distributed among these distances:
44 38 0.48
45 1 0.01
46 2 0.03
47 2 0.03
48 1 0.01
49 35 0.44
ACGTcount: A:0.32, C:0.20, G:0.22, T:0.25
Consensus pattern (49 bp):
CAAACCTTATCTCCCTGAAGTTGCAGTGGAGCAGATTGAAGATAGGCCA
Found at i:2693788 original size:18 final size:17
Alignment explanation
Indices: 2693746--2693789 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 17
2693736 TTGGTTTTGA
*
2693746 TCTTTTCCTTGTTTCTTT
1 TCTTTT-CTCGTTTCTTT
2693764 TCGTTTTCTCGTTTCATTT
1 TC-TTTTCTCGTTTC-TTT
2693783 TCTTTTC
1 TCTTTTC
2693790 ATTTTTTACA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 14 0.61
19 9 0.39
ACGTcount: A:0.02, C:0.23, G:0.07, T:0.68
Consensus pattern (17 bp):
TCTTTTCTCGTTTCTTT
Found at i:2694675 original size:20 final size:20
Alignment explanation
Indices: 2694650--2694733 Score: 86
Period size: 20 Copynumber: 4.2 Consensus size: 20
2694640 TTTTCACTTG
2694650 TTTATTTATTCA-TTATTCAT
1 TTTATTTATTCATTTATT-AT
2694670 TTTATTTTATTCATTTATTCAT
1 TTTA-TTTATTCATTTATT-AT
*
2694692 TAT-TTTACTT-ATTTA-TAT
1 TTTATTTA-TTCATTTATTAT
*
2694710 ATTATTTATTCATTTATTAT
1 TTTATTTATTCATTTATTAT
2694730 TTTA
1 TTTA
2694734 ATCCTTCTTT
Statistics
Matches: 54, Mismatches: 4, Indels: 12
0.77 0.06 0.17
Matches are distributed among these distances:
18 5 0.09
19 10 0.19
20 19 0.35
21 10 0.19
22 10 0.19
ACGTcount: A:0.26, C:0.07, G:0.00, T:0.67
Consensus pattern (20 bp):
TTTATTTATTCATTTATTAT
Found at i:2694688 original size:8 final size:8
Alignment explanation
Indices: 2694653--2694731 Score: 55
Period size: 8 Copynumber: 10.5 Consensus size: 8
2694643 TCACTTGTTT
2694653 ATTTATTC
1 ATTTATTC
2694661 A-TTATTC
1 ATTTATTC
2694668 A-TT-TT-
1 ATTTATTC
2694673 ATTTTATTC
1 A-TTTATTC
2694682 ATTTATTC
1 ATTTATTC
*
2694690 A-TTATTTT
1 ATTTA-TTC
* *
2694698 ACTTATTT
1 ATTTATTC
*
2694706 ATATATT-
1 ATTTATTC
2694713 ATTTATTC
1 ATTTATTC
2694721 ATTTATT-
1 ATTTATTC
2694728 ATTT
1 ATTT
2694732 TAATCCTTCT
Statistics
Matches: 60, Mismatches: 4, Indels: 15
0.76 0.05 0.19
Matches are distributed among these distances:
5 1 0.02
6 2 0.03
7 24 0.40
8 29 0.48
9 4 0.07
ACGTcount: A:0.27, C:0.08, G:0.00, T:0.66
Consensus pattern (8 bp):
ATTTATTC
Found at i:2694729 original size:35 final size:34
Alignment explanation
Indices: 2694668--2694733 Score: 87
Period size: 35 Copynumber: 1.9 Consensus size: 34
2694658 TTCATTATTC
* *
2694668 ATTTTATTTTATTCATTTATTCATTATTTTACTT
1 ATTTTATATTATTCATTCATTCATTATTTTACTT
* *
2694702 ATTTATATATTATTTATTCATTTATTATTTTA
1 ATTT-TATATTATTCATTCATTCATTATTTTA
2694734 ATCCTTCTTT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
34 4 0.15
35 23 0.85
ACGTcount: A:0.27, C:0.06, G:0.00, T:0.67
Consensus pattern (34 bp):
ATTTTATATTATTCATTCATTCATTATTTTACTT
Found at i:2697548 original size:31 final size:31
Alignment explanation
Indices: 2697507--2697567 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
2697497 AAATAGCTCC
* * *
2697507 ACATGGCCCAACTGGCCAGCTCGTGTGGCCT
1 ACATGACCCAACTGGCCAACCCGTGTGGCCT
2697538 ACATGACCCAACTGGCCAACCCGTGTGGCC
1 ACATGACCCAACTGGCCAACCCGTGTGGCC
2697568 CAGACGACCT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.20, C:0.38, G:0.26, T:0.16
Consensus pattern (31 bp):
ACATGACCCAACTGGCCAACCCGTGTGGCCT
Found at i:2697611 original size:17 final size:18
Alignment explanation
Indices: 2697589--2697624 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
2697579 ACAGGTACCT
2697589 ATGTGGCCCACAC-GCCC
1 ATGTGGCCCACACAGCCC
*
2697606 ATGTGGCCGACACAGCCC
1 ATGTGGCCCACACAGCCC
2697624 A
1 A
2697625 AATAGCCCAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 12 0.71
18 5 0.29
ACGTcount: A:0.22, C:0.42, G:0.25, T:0.11
Consensus pattern (18 bp):
ATGTGGCCCACACAGCCC
Found at i:2700512 original size:6 final size:6
Alignment explanation
Indices: 2700503--2700537 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
2700493 GATTCAGATA
2700503 CAAATG CAAATG CAAATG CAAATG CAAATG CAAAT
1 CAAATG CAAATG CAAATG CAAATG CAAATG CAAAT
2700538 TTTAATACAG
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.51, C:0.17, G:0.14, T:0.17
Consensus pattern (6 bp):
CAAATG
Found at i:2710342 original size:14 final size:14
Alignment explanation
Indices: 2710323--2710355 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
2710313 GCACTTCACT
2710323 AGTTCGCAGC-TCTC
1 AGTTCG-AGCATCTC
2710337 AGTTCGAGCATCTC
1 AGTTCGAGCATCTC
2710351 AGTTC
1 AGTTC
2710356 ACAAGCTTTC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 3 0.17
14 15 0.83
ACGTcount: A:0.18, C:0.30, G:0.21, T:0.30
Consensus pattern (14 bp):
AGTTCGAGCATCTC
Found at i:2710465 original size:117 final size:118
Alignment explanation
Indices: 2710250--2710472 Score: 331
Period size: 117 Copynumber: 1.9 Consensus size: 118
2710240 TAGCTCGCAC
* * * *
2710250 TTCTCTAGCTCACATGCATGGCTCACACTTTACTAGCTCGCATGCATTGCTTGGAGATAGCTCGC
1 TTCTCTAGCTCACATGCATAGCTCACACTTTACCAGCTCGCATGCATTACTTGGAGACAGCTCGC
* **
2710315 ACTTCACTAGTTCGCAGCTCTCAGTTCGAGCATCTCAGTTCACAAGCTTTCTA
66 ACTTCACCAGTTCGCAGCTCTCAGTTAAAGCATCTCAGTTCACAAGCTTTCTA
* ** * *
2710368 TTCTC-AGTTCACATGCATAGCTCGTACTTTACCAGCTCGCATGCATTACTTGGAGACAGTTCGT
1 TTCTCTAGCTCACATGCATAGCTCACACTTTACCAGCTCGCATGCATTACTTGGAGACAGCTCGC
2710432 ACTTCACCAGTTCGCAGCTCTCAGTTAAAGCATCTCAGTTC
66 ACTTCACCAGTTCGCAGCTCTCAGTTAAAGCATCTCAGTTC
2710473 GTATGCATAG
Statistics
Matches: 93, Mismatches: 12, Indels: 1
0.88 0.11 0.01
Matches are distributed among these distances:
117 88 0.95
118 5 0.05
ACGTcount: A:0.22, C:0.29, G:0.17, T:0.31
Consensus pattern (118 bp):
TTCTCTAGCTCACATGCATAGCTCACACTTTACCAGCTCGCATGCATTACTTGGAGACAGCTCGC
ACTTCACCAGTTCGCAGCTCTCAGTTAAAGCATCTCAGTTCACAAGCTTTCTA
Found at i:2711989 original size:35 final size:35
Alignment explanation
Indices: 2711950--2712147 Score: 107
Period size: 35 Copynumber: 5.9 Consensus size: 35
2711940 ATTGAATGTA
* **
2711950 TATAACCAAATGTATGTATACACTCATCAAATACT
1 TATAACCAAATGCATAAATACACTCATCAAATACT
* * * *
2711985 TATAACCGAATGCATAAATATACTTATCAACTACT
1 TATAACCAAATGCATAAATACACTCATCAAATACT
* * *
2712020 TATAATCGAATGCAT--ATACA--CATCAAAT-GT
1 TATAACCAAATGCATAAATACACTCATCAAATACT
* * *
2712050 ATACAACCGAATGCATATATAC-CT-ATCAAATACT
1 -TATAACCAAATGCATAAATACACTCATCAAATACT
* *
2712084 TATAATCGAATGCAT--ATACA--CATCAAAGGTA--
1 TATAACCAAATGCATAAATACACTCATCAAA--TACT
* * * *
2712115 TATAACCGAATGCATATATATACTTATCAAATA
1 TATAACCAAATGCATAAATACACTCATCAAATA
2712148 AGATATAAAT
Statistics
Matches: 129, Mismatches: 20, Indels: 30
0.72 0.11 0.17
Matches are distributed among these distances:
30 1 0.01
31 43 0.33
33 36 0.28
34 1 0.01
35 48 0.37
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.30
Consensus pattern (35 bp):
TATAACCAAATGCATAAATACACTCATCAAATACT
Found at i:2712045 original size:31 final size:31
Alignment explanation
Indices: 2711974--2712132 Score: 153
Period size: 31 Copynumber: 4.9 Consensus size: 31
2711964 TGTATACACT
*
2711974 CATCAAATACTTATAACCGAATGCATAAATATA
1 CATCAAATACTTATAACCGAATGCAT--ATACA
* *
2712007 CTTATCAACTACTTATAATCGAATGCATATACA
1 C--ATCAAATACTTATAACCGAATGCATATACA
* * *
2712040 CATCAAAT-GTATACAACCGAATGCATATATA
1 CATCAAATACT-TATAACCGAATGCATATACA
*
2712071 CCTATCAAATACTTATAATCGAATGCATATACA
1 -C-ATCAAATACTTATAACCGAATGCATATACA
2712104 CATCAAAGGTA--TATAACCGAATGCATATA
1 CATCAAA--TACTTATAACCGAATGCATATA
2712133 TATACTTATC
Statistics
Matches: 105, Mismatches: 13, Indels: 18
0.77 0.10 0.13
Matches are distributed among these distances:
30 1 0.01
31 46 0.44
32 2 0.02
33 32 0.30
34 1 0.01
35 23 0.22
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.28
Consensus pattern (31 bp):
CATCAAATACTTATAACCGAATGCATATACA
Found at i:2712060 original size:66 final size:65
Alignment explanation
Indices: 2711988--2712147 Score: 259
Period size: 64 Copynumber: 2.4 Consensus size: 65
2711978 AAATACTTAT
* *
2711988 AACCGAATGCATAAATATACTTATCAACTACTTATAATCGAATGCATATACACATCAAATGTATA
1 AACCGAATGCAT-AATATACTTATCAAATACTTATAATCGAATGCATATACACATCAAAGGTATA
2712053 C
65 C
* *
2712054 AACCGAATGCAT-ATATACCTATCAAATACTTATAATCGAATGCATATACACATCAAAGGTATAT
1 AACCGAATGCATAATATACTTATCAAATACTTATAATCGAATGCATATACACATCAAAGGTATAC
2712118 AACCGAATGCATATATATACTTATCAAATA
1 AACCGAATGCATA-ATATACTTATCAAATA
2712148 AGATATAAAT
Statistics
Matches: 87, Mismatches: 5, Indels: 4
0.91 0.05 0.04
Matches are distributed among these distances:
64 60 0.69
66 27 0.31
ACGTcount: A:0.44, C:0.19, G:0.08, T:0.29
Consensus pattern (65 bp):
AACCGAATGCATAATATACTTATCAAATACTTATAATCGAATGCATATACACATCAAAGGTATAC
Found at i:2712666 original size:78 final size:78
Alignment explanation
Indices: 2712493--2712746 Score: 377
Period size: 78 Copynumber: 3.3 Consensus size: 78
2712483 AAGTATTTAC
* * * * * * *
2712493 AATTCATACTTTTAATTCAATTCAAGTACTTGTATATGTATATACATCTAT-TT-GAATCACACA
1 AATTCATACCTTTAATTCAATTCAAGAACTTATACATGTATATACATATATATTCGAACCTCACA
* *
2712556 CATACATATGTAA
66 TATACATATATAA
* * *
2712569 AATTCATACCTTTAATTCAATTAAAAAACTTATACATGTATATACATATATATTCAAACCTCACA
1 AATTCATACCTTTAATTCAATTCAAGAACTTATACATGTATATACATATATATTCGAACCTCACA
*
2712634 TATACATATATAT
66 TATACATATATAA
2712647 AATTCATACCTTTAATTCAATTCAAGAACTTATACATGTATATACATATATATTCGAACCTCACA
1 AATTCATACCTTTAATTCAATTCAAGAACTTATACATGTATATACATATATATTCGAACCTCACA
2712712 TATACATATATAA
66 TATACATATATAA
2712725 AATTCATACCTTTAATTCAATT
1 AATTCATACCTTTAATTCAATT
2712747 TATATACTTT
Statistics
Matches: 159, Mismatches: 17, Indels: 2
0.89 0.10 0.01
Matches are distributed among these distances:
76 44 0.28
77 2 0.01
78 113 0.71
ACGTcount: A:0.41, C:0.17, G:0.04, T:0.38
Consensus pattern (78 bp):
AATTCATACCTTTAATTCAATTCAAGAACTTATACATGTATATACATATATATTCGAACCTCACA
TATACATATATAA
Found at i:2716010 original size:15 final size:14
Alignment explanation
Indices: 2715986--2716027 Score: 66
Period size: 15 Copynumber: 2.9 Consensus size: 14
2715976 CTGAACCCTC
2715986 TTTTTTTCTTCTCT
1 TTTTTTTCTTCTCT
2716000 TTTTTTCTCTTCTCT
1 TTTTTT-TCTTCTCT
2716015 TTTCTTTTCTTCT
1 TTT-TTTTCTTCT
2716028 ACCCCTCTTC
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
14 6 0.23
15 17 0.65
16 3 0.12
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (14 bp):
TTTTTTTCTTCTCT
Found at i:2716786 original size:54 final size:54
Alignment explanation
Indices: 2716720--2716995 Score: 228
Period size: 54 Copynumber: 5.1 Consensus size: 54
2716710 ATTCGTGGGC
* * * * * *
2716720 AAATGACTGAAATACCCTCGGAGTGTAAAATGAACGAAGTACCCC-TGAAGGATA
1 AAATGACCGAAATACCCCCAGAGGGTAAAATGAACGAAGTACCCCAAG-AGGGTA
* * *
2716774 AAATGACCGAAATACCCCCAGAGGGTAAAATGACCAAAGTACCCCAATAGGGTA
1 AAATGACCGAAATACCCCCAGAGGGTAAAATGAACGAAGTACCCCAAGAGGGTA
* * * *
2716828 AAATGGCTGAAATACCCCCAGAGGG-AAAAT-AACCGAAATACCCCCAGAGGGTA
1 AAATGACCGAAATACCCCCAGAGGGTAAAATGAA-CGAAGTACCCCAAGAGGGTA
* * * **
2716881 AAATGACCAAAATACCCTC-GAAGGGTAAAAT-AACTTAAAAACCCTC-AGAGGGTA
1 AAATGACCGAAATACCCCCAG-AGGGTAAAATGAAC-GAAGTACCC-CAAGAGGGTA
* * *
2716935 AAACGACCGAAATACCCCC-GAAGGGTAAAATG-ACTGAAATACCCTC-ATAGGGTA
1 AAATGACCGAAATACCCCCAG-AGGGTAAAATGAAC-GAAGTACCC-CAAGAGGGTA
2716989 AAATGAC
1 AAATGAC
2716996 TATTATACCC
Statistics
Matches: 186, Mismatches: 29, Indels: 14
0.81 0.13 0.06
Matches are distributed among these distances:
52 2 0.01
53 41 0.22
54 142 0.76
55 1 0.01
ACGTcount: A:0.43, C:0.22, G:0.20, T:0.15
Consensus pattern (54 bp):
AAATGACCGAAATACCCCCAGAGGGTAAAATGAACGAAGTACCCCAAGAGGGTA
Found at i:2716879 original size:80 final size:80
Alignment explanation
Indices: 2716772--2716996 Score: 296
Period size: 80 Copynumber: 2.8 Consensus size: 80
2716762 CCCTGAAGGA
*
2716772 TAAAATGACCGAAATACCCCCAGAGGGTAAAATGACCAAAGTACCC-CAATAGGGTAAAATGGCT
1 TAAAATGACCGAAATACCCCCAGAGGGTAAAATGACCAAA-TACCCTC-ATAGGGTAAAATGACT
*
2716836 GAAATACCCCCAGAGGG
64 GAAAAACCCCCAGAGGG
* *
2716853 -AAAATAACCGAAATACCCCCAGAGGGTAAAATGACCAAAATACCCTCGA-AGGGTAAAATAACT
1 TAAAATGACCGAAATACCCCCAGAGGGTAAAATGACC-AAATACCCTC-ATAGGGTAAAATGACT
* *
2716916 TAAAAACCCTCAGAGGG
64 GAAAAACCCCCAGAGGG
* *
2716933 TAAAACGACCGAAATACCCCC-GAAGGGTAAAATGACTGAAATACCCTCATAGGGTAAAATGACT
1 TAAAATGACCGAAATACCCCCAG-AGGGTAAAATGAC-CAAATACCCTCATAGGGTAAAATGACT
2716997 ATTATACCCT
Statistics
Matches: 127, Mismatches: 11, Indels: 12
0.85 0.07 0.08
Matches are distributed among these distances:
80 68 0.54
81 59 0.46
ACGTcount: A:0.43, C:0.23, G:0.20, T:0.15
Consensus pattern (80 bp):
TAAAATGACCGAAATACCCCCAGAGGGTAAAATGACCAAATACCCTCATAGGGTAAAATGACTGA
AAAACCCCCAGAGGG
Found at i:2716924 original size:27 final size:27
Alignment explanation
Indices: 2716720--2716996 Score: 174
Period size: 27 Copynumber: 10.3 Consensus size: 27
2716710 ATTCGTGGGC
* * *
2716720 AAATGACTGAAATACCCTCGGAGTGTA
1 AAATGACTGAAAAACCCTCAGAGGGTA
** * *
2716747 AAATGAAC-GAAGTACCC-CTGAAGGATA
1 AAATG-ACTGAAAAACCCTCAG-AGGGTA
* * *
2716774 AAATGACCGAAATACCCCCAGAGGGTA
1 AAATGACTGAAAAACCCTCAGAGGGTA
* * *
2716801 AAATGAC-CAAAGTACCC-CAATAGGGTA
1 AAATGACTGAAA-AACCCTC-AGAGGGTA
* * *
2716828 AAATGGCTGAAATACCCCCAGAGGG-A
1 AAATGACTGAAAAACCCTCAGAGGGTA
* * * *
2716854 AAATAACCGAAATACCCCCAGAGGGTA
1 AAATGACTGAAAAACCCTCAGAGGGTA
*
2716881 AAATGAC-CAAAATACCCTC-GAAGGGTA
1 AAATGACTGAAAA-ACCCTCAG-AGGGTA
* *
2716908 AAATAACTTAAAAACCCTCAGAGGGTA
1 AAATGACTGAAAAACCCTCAGAGGGTA
* * * *
2716935 AAACGACCGAAATACCC-CCGAAGGGTA
1 AAATGACTGAAAAACCCTCAG-AGGGTA
* *
2716962 AAATGACTGAAATACCCTCATAGGGTA
1 AAATGACTGAAAAACCCTCAGAGGGTA
2716989 AAATGACT
1 AAATGACT
2716997 ATTATACCCT
Statistics
Matches: 204, Mismatches: 31, Indels: 30
0.77 0.12 0.11
Matches are distributed among these distances:
26 37 0.18
27 153 0.75
28 14 0.07
ACGTcount: A:0.43, C:0.22, G:0.20, T:0.15
Consensus pattern (27 bp):
AAATGACTGAAAAACCCTCAGAGGGTA
Found at i:2716972 original size:134 final size:135
Alignment explanation
Indices: 2716728--2716992 Score: 322
Period size: 134 Copynumber: 2.0 Consensus size: 135
2716718 GCAAATGACT
* * * * * * *
2716728 GAAATACCCTCGGAGTGTAAAATGAACGAAGTACCCCTGAAGGATAAAATGACCGAAATACCCCC
1 GAAATACCCCCAGAGGGTAAAATGAACAAAATACCCCTGAAGGATAAAATAACCGAAAAACCCCC
* *
2716793 AGAGGGTAAAATGACCAAAGTACCCCAATAGGGTAAAATGGCTGAAATACCCCCAGAGGG-AAAA
66 AGAGGGTAAAACGACCAAAGTACCCCAATAGGGTAAAATGACTGAAATACCCCCAGAGGGTAAAA
2716857 TAACC
131 TAACC
* * ** *
2716862 GAAATACCCCCAGAGGGTAAAATGACCAAAATA-CCCTCGAAGGGTAAAATAACTTAAAAACCCT
1 GAAATACCCCCAGAGGGTAAAATGAACAAAATACCCCT-GAAGGATAAAATAACCGAAAAACCCC
* * *
2716926 CAGAGGGTAAAACGACCGAAA-TACCCCCGA-AGGGTAAAATGACTGAAATACCCTCATAGGGTA
65 CAGAGGGTAAAACGACC-AAAGTA-CCCCAATAGGGTAAAATGACTGAAATACCCCCAGAGGGTA
2716989 AAAT
128 AAAT
2716993 GACTATTATA
Statistics
Matches: 110, Mismatches: 17, Indels: 7
0.82 0.13 0.05
Matches are distributed among these distances:
133 4 0.04
134 93 0.85
135 13 0.12
ACGTcount: A:0.43, C:0.22, G:0.20, T:0.15
Consensus pattern (135 bp):
GAAATACCCCCAGAGGGTAAAATGAACAAAATACCCCTGAAGGATAAAATAACCGAAAAACCCCC
AGAGGGTAAAACGACCAAAGTACCCCAATAGGGTAAAATGACTGAAATACCCCCAGAGGGTAAAA
TAACC
Found at i:2717006 original size:81 final size:81
Alignment explanation
Indices: 2716720--2717024 Score: 295
Period size: 81 Copynumber: 3.8 Consensus size: 81
2716710 ATTCGTGGGC
** * * * * *
2716720 AAATGACTGAAATACCCTC-GGAGTGTAAAATGAACGAAGTACCC-CTGAAGGATAAAATGACCG
1 AAATGACTGAAATACCCTCAATAGGGTAAAATG-ACTAAATACCCTCAG-AGGGTAAAATGACCG
2716783 AAATACCCCCAGAGGGTA
64 AAATACCCCCAGAGGGTA
* * * *
2716801 AAATGAC-CAAAGTACCC-CAATAGGGTAAAATGGCTGAAATACCCCCAGAGGG-AAAATAACCG
1 AAATGACTGAAA-TACCCTCAATAGGGTAAAATGACT-AAATACCCTCAGAGGGTAAAATGACCG
2716863 AAATACCCCCAGAGGGTA
64 AAATACCCCCAGAGGGTA
** * * * *
2716881 AAATGACCAAAATACCCTCGA-AGGGTAAAATAACTTAAAAACCCTCAGAGGGTAAAACGACCGA
1 AAATGACTGAAATACCCTCAATAGGGTAAAATGAC-TAAATACCCTCAGAGGGTAAAATGACCGA
2716945 AATACCCCC-GAAGGGTA
65 AATACCCCCAG-AGGGTA
* * *
2716962 AAATGACTGAAATACCCTC-ATAGGGTAAAATGACTATTATACCCTTAG-GAGATAAAATGACCG
1 AAATGACTGAAATACCCTCAATAGGGTAAAATGACTA-AATACCCTCAGAG-GGTAAAATGACCG
2717025 TTATAGCCTT
Statistics
Matches: 186, Mismatches: 26, Indels: 24
0.79 0.11 0.10
Matches are distributed among these distances:
80 74 0.40
81 110 0.59
82 2 0.01
ACGTcount: A:0.42, C:0.22, G:0.20, T:0.16
Consensus pattern (81 bp):
AAATGACTGAAATACCCTCAATAGGGTAAAATGACTAAATACCCTCAGAGGGTAAAATGACCGAA
ATACCCCCAGAGGGTA
Found at i:2717148 original size:19 final size:19
Alignment explanation
Indices: 2717124--2717160 Score: 74
Period size: 19 Copynumber: 1.9 Consensus size: 19
2717114 ATGACATGAC
2717124 ATGGGGGAAGTATACTGAT
1 ATGGGGGAAGTATACTGAT
2717143 ATGGGGGAAGTATACTGA
1 ATGGGGGAAGTATACTGA
2717161 CTGGTGGCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.05, G:0.38, T:0.24
Consensus pattern (19 bp):
ATGGGGGAAGTATACTGAT
Found at i:2717381 original size:28 final size:28
Alignment explanation
Indices: 2717341--2717457 Score: 173
Period size: 28 Copynumber: 4.2 Consensus size: 28
2717331 ACTGTACTGG
* *
2717341 TTACTATATTGGGCTAAGGCTCACACTA
1 TTACTGTATTGGGCTAAGGCCCACACTA
*
2717369 TTACTGTACTGGGCTAAGGCCCACACTA
1 TTACTGTATTGGGCTAAGGCCCACACTA
* *
2717397 TTACTGTATTGGGCTAAGGCCCACATTG
1 TTACTGTATTGGGCTAAGGCCCACACTA
*
2717425 TTACTGTTTTGGGCTAAGGCCCACACTA
1 TTACTGTATTGGGCTAAGGCCCACACTA
2717453 -TACTG
1 TTACTG
2717458 CTACTGTATA
Statistics
Matches: 80, Mismatches: 9, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
27 5 0.06
28 75 0.94
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.31
Consensus pattern (28 bp):
TTACTGTATTGGGCTAAGGCCCACACTA
Found at i:2717491 original size:61 final size:56
Alignment explanation
Indices: 2717341--2717491 Score: 151
Period size: 56 Copynumber: 2.6 Consensus size: 56
2717331 ACTGTACTGG
* * * **
2717341 TTACTATATTGGGCTAAGGCTCACACT-ATTACTGTACTGGGCTAAGGCCCACACTA
1 TTACTGTATAGGGCTAAGGCCCACACTGA-TACTGTTTTGGGCTAAGGCCCACACTA
* * *
2717397 TTACTGTATTGGGCTAAGGCCCACATTGTTACTGTTTTGGGCTAAGGCCCACACTATA
1 TTACTGTATAGGGCTAAGGCCCACACTGATACTGTTTTGGGCTAAGGCCCACAC--TA
* *
2717455 CTGCTACTGTATAGGGCTCAGGCCCAGACTGATACTG
1 -T--TACTGTATAGGGCTAAGGCCCACACTGATACTG
2717492 CATGACTACT
Statistics
Matches: 78, Mismatches: 11, Indels: 7
0.81 0.11 0.07
Matches are distributed among these distances:
56 47 0.60
58 2 0.03
59 1 0.01
61 28 0.36
ACGTcount: A:0.24, C:0.25, G:0.23, T:0.29
Consensus pattern (56 bp):
TTACTGTATAGGGCTAAGGCCCACACTGATACTGTTTTGGGCTAAGGCCCACACTA
Found at i:2724431 original size:27 final size:27
Alignment explanation
Indices: 2724393--2724747 Score: 359
Period size: 27 Copynumber: 13.3 Consensus size: 27
2724383 GATTCATGGG
2724393 AAAATGATCGAAATACCCCCGGAGGGT
1 AAAATGATCGAAATACCCCCGGAGGGT
*
2724420 AAAATGATCGAAATACCTCCGGAGGGT
1 AAAATGATCGAAATACCCCCGGAGGGT
*
2724447 AAAGTGA-CTGAAATACCCCCGGAGGGT
1 AAAATGATC-GAAATACCCCCGGAGGGT
*
2724474 AAAATGA-CTGAAATACCCCCAGAGGGT
1 AAAATGATC-GAAATACCCCCGGAGGGT
* * *
2724501 AAAATGATCGAAGTATCCTCGGAGGGT
1 AAAATGATCGAAATACCCCCGGAGGGT
*
2724528 AAAATGA-CTGAAATACCCCTGGAGGGT
1 AAAATGATC-GAAATACCCCCGGAGGGT
*
2724555 AAAATGATCGAAATA-CCCCTGAGGGT
1 AAAATGATCGAAATACCCCCGGAGGGT
**
2724581 AAAATGAGT-GAAATACCCCTAGAGGGT
1 AAAATGA-TCGAAATACCCCCGGAGGGT
* * *
2724608 AAAATAATTGAAATACCCCCGGAGAG-
1 AAAATGATCGAAATACCCCCGGAGGGT
* *
2724634 -AAATGACCGAAATACCCCCGAAGGGT
1 AAAATGATCGAAATACCCCCGGAGGGT
* * *
2724660 AAAATGATTGAAATACCCCCGAAAGGT
1 AAAATGATCGAAATACCCCCGGAGGGT
* * * * *
2724687 AAAATCA-CTAAAATGCCCTCGAAGGGT
1 AAAATGATC-GAAATACCCCCGGAGGGT
***
2724714 AAAATGA-CTGAAATACCCCAATAGGGT
1 AAAATGATC-GAAATACCCCCGGAGGGT
2724741 AAAATGA
1 AAAATGA
2724748 CTGTTATACC
Statistics
Matches: 276, Mismatches: 42, Indels: 20
0.82 0.12 0.06
Matches are distributed among these distances:
25 20 0.07
26 25 0.09
27 229 0.83
28 2 0.01
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.17
Consensus pattern (27 bp):
AAAATGATCGAAATACCCCCGGAGGGT
Found at i:2724528 original size:81 final size:80
Alignment explanation
Indices: 2724393--2724747 Score: 400
Period size: 81 Copynumber: 4.4 Consensus size: 80
2724383 GATTCATGGG
* *
2724393 AAAATGA-TCGAAATACCCCCGGAGGGTAAAATGATCGAAATACCTCCGGAGGGTAAAGTGACTG
1 AAAATGACT-GAAATACCCCCAGAGGGTAAAATGATCGAAATACC-CCGGAGGGTAAAATGACTG
2724457 AAATACCCCCGGAGGGT
64 AAATACCCCCGGAGGGT
* *
2724474 AAAATGACTGAAATACCCCCAGAGGGTAAAATGATCGAAGTATCCTCGGAGGGTAAAATGACTGA
1 AAAATGACTGAAATACCCCCAGAGGGTAAAATGATCGAAATA-CCCCGGAGGGTAAAATGACTGA
*
2724539 AATACCCCTGGAGGGT
65 AATACCCCCGGAGGGT
* * * *
2724555 AAAATGA-TCGAAATA-CCCCTGAGGGTAAAATGAGT-GAAATACCCCTAGAGGGTAAAATAATT
1 AAAATGACT-GAAATACCCCCAGAGGGTAAAATGA-TCGAAATACCCC-GGAGGGTAAAATGACT
*
2724617 GAAATACCCCCGGAGAG-
63 GAAATACCCCCGGAGGGT
* * * * * *
2724634 -AAATGACCGAAATACCCCC-GAAGGGTAAAATGATTGAAATACCCCCGAAAGGTAAAATCACTA
1 AAAATGACTGAAATACCCCCAG-AGGGTAAAATGATCGAAATA-CCCCGGAGGGTAAAATGACTG
* * *
2724697 AAATGCCCTCGAAGGGT
64 AAATACCCCCGGAGGGT
* *
2724714 AAAATGACTGAAATACCCCAATAGGGTAAAATGA
1 AAAATGACTGAAATACCCCCAGAGGGTAAAATGA
2724748 CTGTTATACC
Statistics
Matches: 234, Mismatches: 27, Indels: 26
0.82 0.09 0.09
Matches are distributed among these distances:
78 14 0.06
79 48 0.21
80 55 0.24
81 114 0.49
82 3 0.01
ACGTcount: A:0.40, C:0.19, G:0.23, T:0.17
Consensus pattern (80 bp):
AAAATGACTGAAATACCCCCAGAGGGTAAAATGATCGAAATACCCCGGAGGGTAAAATGACTGAA
ATACCCCCGGAGGGT
Found at i:2724770 original size:27 final size:26
Alignment explanation
Indices: 2724709--2724782 Score: 87
Period size: 27 Copynumber: 2.8 Consensus size: 26
2724699 ATGCCCTCGA
**
2724709 AGGGTAAAATGACTGAAATACCCCAAT
1 AGGGTAAAATGACTGTTATACCCC-AT
2724736 AGGGTAAAATGACTGTTATACCCC-T
1 AGGGTAAAATGACTGTTATACCCCAT
*
2724761 AGGAGATAAAATGACCGTTATA
1 AGG-G-TAAAATGACTGTTATA
2724783 GCCTTATGAT
Statistics
Matches: 42, Mismatches: 3, Indels: 4
0.86 0.06 0.08
Matches are distributed among these distances:
25 4 0.10
26 1 0.02
27 37 0.88
ACGTcount: A:0.41, C:0.16, G:0.20, T:0.23
Consensus pattern (26 bp):
AGGGTAAAATGACTGTTATACCCCAT
Found at i:2725142 original size:28 final size:28
Alignment explanation
Indices: 2725102--2725212 Score: 143
Period size: 28 Copynumber: 4.0 Consensus size: 28
2725092 ACTGTACTGG
*
2725102 TTACTGTATTGGGCTAAGGCCCACACTA
1 TTACTATATTGGGCTAAGGCCCACACTA
* *
2725130 TTACTATACTGGGCTACGGCCCACACTA
1 TTACTATATTGGGCTAAGGCCCACACTA
* * *
2725158 TTACTATATTGGGCTAAGGCCTACATTG
1 TTACTATATTGGGCTAAGGCCCACACTA
*
2725186 TTACTGCT-TTGGGCTAAGGCCCACACT
1 TTACT-ATATTGGGCTAAGGCCCACACT
2725213 GTACTGCTAC
Statistics
Matches: 71, Mismatches: 11, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
28 70 0.99
29 1 0.01
ACGTcount: A:0.23, C:0.26, G:0.21, T:0.30
Consensus pattern (28 bp):
TTACTATATTGGGCTAAGGCCCACACTA
Found at i:2727733 original size:213 final size:212
Alignment explanation
Indices: 2727344--2727737 Score: 550
Period size: 213 Copynumber: 1.9 Consensus size: 212
2727334 CTTTTGAGCA
*
2727344 AATTTTTTCTACAACAATCTCTTAAAAGAATTTAATTTGCAAAAAAGAATAAGTTTCTGTTTTAA
1 AATTTTTTCTACAACAATCTCTTAAAAGAATTTAATATGCAAAAAAGAATAAGTTTCTGTTTTAA
* *
2727409 AATTTTAAGTTTTTATTTACATTAATCCTCGTAACCATTCAAAAAATTGTAATGATGTATGAGAA
66 AATTTTAAGTTTTTATTTACATCAATCCTCGAAACCATTCAAAAAATTGTAATGATGTATGAGAA
*
2727474 TAGATTCCCTAATAATATCGATGTAAAATATGGAAAAACTCTCTATAAGAGAGGTCTCAATTTTC
131 TAGATTCCCTAATAATATCGATGTAAAATATGGAAAAACCCTCTATAAGAGAGGTCTCAATTTTC
2727539 CCAAAATTCTCTTGAGT
196 CCAAAATTCTCTTGAGT
* * * *
2727556 AATTTTTCTCTCCAACAATCTCTTCAAAATAATTTAGTATGC-AAAAA-ATTAAGTTT-TCGTTT
1 AATTTTT-TCTACAACAATCTCTT-AAAAGAATTTAATATGCAAAAAAGAATAAGTTTCT-GTTT
* *
2727618 TAAAATTTTGAAGTTTTTATTTACATCCATCTTC-AAATCCATT-AAAAAATTTGTAATGATGTA
63 TAAAATTTT-AAGTTTTTATTTACATCAATCCTCGAAA-CCATTCAAAAAA-TTGTAATGATGTA
* * *
2727681 TGAGAATAGATT-CCTCAATAATATCGTTGTAAAATA-GGCAAGAGCCCTCTATAAGAG
125 TGAGAATAGATTCCCT-AATAATATCGATGTAAAATATGG-AAAAACCCTCTATAAGAG
2727738 GCTATTAGTT
Statistics
Matches: 161, Mismatches: 13, Indels: 15
0.85 0.07 0.08
Matches are distributed among these distances:
211 1 0.01
212 41 0.25
213 105 0.65
214 14 0.09
ACGTcount: A:0.38, C:0.14, G:0.11, T:0.37
Consensus pattern (212 bp):
AATTTTTTCTACAACAATCTCTTAAAAGAATTTAATATGCAAAAAAGAATAAGTTTCTGTTTTAA
AATTTTAAGTTTTTATTTACATCAATCCTCGAAACCATTCAAAAAATTGTAATGATGTATGAGAA
TAGATTCCCTAATAATATCGATGTAAAATATGGAAAAACCCTCTATAAGAGAGGTCTCAATTTTC
CCAAAATTCTCTTGAGT
Found at i:2730023 original size:50 final size:50
Alignment explanation
Indices: 2729894--2730135 Score: 229
Period size: 50 Copynumber: 4.9 Consensus size: 50
2729884 TGATAATAAC
* ** *
2729894 ATGCCAATGCCATTTCCCAGACATGGTCTTACATGGGA--T-TTTTCTTG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
* * * ** * *
2729941 TACTGCCAATGCCATATCCTAGATATGGTCTTACATGGGAGTTCTTATATCG
1 -A-TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
* * ** *
2729993 ATGCCCATGCCATGTCCCAGGCATGGTCTTACGGGGGACCTCTCATCTTG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
* * * *
2730043 GTGCCAACGCCATGTCCCAGATATAGTCTTACATGGGACCTCTCATCTCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
* ** *
2730093 GTGCCAACACCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
2730136 TTACCCAAAT
Statistics
Matches: 159, Mismatches: 31, Indels: 6
0.81 0.16 0.03
Matches are distributed among these distances:
48 1 0.01
49 34 0.21
50 117 0.74
51 2 0.01
52 5 0.03
ACGTcount: A:0.21, C:0.28, G:0.21, T:0.30
Consensus pattern (50 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCG
Found at i:2733540 original size:20 final size:21
Alignment explanation
Indices: 2733500--2733555 Score: 69
Period size: 20 Copynumber: 2.7 Consensus size: 21
2733490 GTATGTTGCT
*
2733500 TTTATGGCATAGTTTGTTAGCC
1 TTTATGGCATA-TTTGCTAGCC
2733522 TTTATGGCAT-TTTGCTAGCC
1 TTTATGGCATATTTGCTAGCC
* *
2733542 TTTTTGGTATATTT
1 TTTATGGCATATTT
2733556 TGTAAGTCGC
Statistics
Matches: 30, Mismatches: 3, Indels: 3
0.83 0.08 0.08
Matches are distributed among these distances:
20 17 0.57
21 3 0.10
22 10 0.33
ACGTcount: A:0.16, C:0.12, G:0.20, T:0.52
Consensus pattern (21 bp):
TTTATGGCATATTTGCTAGCC
Found at i:2738561 original size:11 final size:11
Alignment explanation
Indices: 2738545--2738573 Score: 58
Period size: 11 Copynumber: 2.6 Consensus size: 11
2738535 TGAGACATGG
2738545 TTAGAATAACT
1 TTAGAATAACT
2738556 TTAGAATAACT
1 TTAGAATAACT
2738567 TTAGAAT
1 TTAGAAT
2738574 CCCCTGTCCT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.45, C:0.07, G:0.10, T:0.38
Consensus pattern (11 bp):
TTAGAATAACT
Found at i:2741718 original size:60 final size:60
Alignment explanation
Indices: 2741634--2741861 Score: 262
Period size: 60 Copynumber: 3.8 Consensus size: 60
2741624 TGTTCTTAAA
** * *
2741634 CAGAGG-TTTCCACAAAGGTGTCCTTTTCATTCAGTAGTCGCCACAAAGGCTTTCCTGTC
1 CAGAGGTTTTCCACAAAGGCATCCTTTACATTCAGTACTCGCCACAAAGGCTTTCCTGTC
* * * * *
2741693 CAGAGGTTTTCCACAAAGCCATCCTTTGCATTCAGTTCTCACCACAAAGGCTTTCTTGTC
1 CAGAGGTTTTCCACAAAGGCATCCTTTACATTCAGTACTCGCCACAAAGGCTTTCCTGTC
** ** *
2741753 CAGATTTTTTCCACAAATACATCCTTTACATTCAGTACTCGCTACAAAGGCTTTCCTGTC
1 CAGAGGTTTTCCACAAAGGCATCCTTTACATTCAGTACTCGCCACAAAGGCTTTCCTGTC
* * * **
2741813 CAGA-TTTTTGCCACAAAGGTATCCTTTACATTCAATACTTACCACAAAG
1 CAGAGGTTTT-CCACAAAGGCATCCTTTACATTCAGTACTCGCCACAAAG
2741862 CATGTCCTTT
Statistics
Matches: 143, Mismatches: 24, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
59 11 0.08
60 132 0.92
ACGTcount: A:0.26, C:0.28, G:0.14, T:0.32
Consensus pattern (60 bp):
CAGAGGTTTTCCACAAAGGCATCCTTTACATTCAGTACTCGCCACAAAGGCTTTCCTGTC
Found at i:2742795 original size:22 final size:22
Alignment explanation
Indices: 2742769--2742822 Score: 74
Period size: 22 Copynumber: 2.5 Consensus size: 22
2742759 TAACTCTCCC
2742769 TTAACTTAACAA-ATGTGTCCTT
1 TTAACTTAACAAGA-GTGTCCTT
*
2742791 TTAACTTAACAAGAGTTTCCTT
1 TTAACTTAACAAGAGTGTCCTT
*
2742813 TAAACTTAAC
1 TTAACTTAAC
2742823 TCAAGTCTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
22 28 0.97
23 1 0.03
ACGTcount: A:0.35, C:0.19, G:0.07, T:0.39
Consensus pattern (22 bp):
TTAACTTAACAAGAGTGTCCTT
Found at i:2746562 original size:22 final size:22
Alignment explanation
Indices: 2746519--2746563 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
2746509 TGTAACAAGA
* **
2746519 TTTTAATTTGACATGTTTAATT
1 TTTTAATTTAACATGTACAATT
*
2746541 TTTTAATTTAACTTGTACAATT
1 TTTTAATTTAACATGTACAATT
2746563 T
1 T
2746564 CACTCGATTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.29, C:0.07, G:0.07, T:0.58
Consensus pattern (22 bp):
TTTTAATTTAACATGTACAATT
Found at i:2760322 original size:17 final size:18
Alignment explanation
Indices: 2760300--2760333 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
2760290 AAAAAGTTGT
2760300 TATAAG-GTTAGATAAAC
1 TATAAGTGTTAGATAAAC
*
2760317 TATAAGTGTTGGATAAA
1 TATAAGTGTTAGATAAA
2760334 AGTCTAAATA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 6 0.40
18 9 0.60
ACGTcount: A:0.44, C:0.03, G:0.21, T:0.32
Consensus pattern (18 bp):
TATAAGTGTTAGATAAAC
Found at i:2763232 original size:2 final size:2
Alignment explanation
Indices: 2763225--2763255 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
2763215 TCTCATTCTC
2763225 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
2763256 CGTATATATT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
AG
Found at i:2768450 original size:9 final size:9
Alignment explanation
Indices: 2768438--2768486 Score: 62
Period size: 9 Copynumber: 5.4 Consensus size: 9
2768428 TTGAATTTTT
*
2768438 ATAATTTGA
1 ATAATTCGA
*
2768447 ATAACTCGA
1 ATAATTCGA
2768456 ATAATTCGA
1 ATAATTCGA
*
2768465 ATAACTCGA
1 ATAATTCGA
*
2768474 ATAATTTGA
1 ATAATTCGA
2768483 ATAA
1 ATAA
2768487 CAGATGAGTA
Statistics
Matches: 34, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
9 34 1.00
ACGTcount: A:0.47, C:0.10, G:0.10, T:0.33
Consensus pattern (9 bp):
ATAATTCGA
Found at i:2768461 original size:18 final size:18
Alignment explanation
Indices: 2768438--2768487 Score: 91
Period size: 18 Copynumber: 2.8 Consensus size: 18
2768428 TTGAATTTTT
2768438 ATAATTTGAATAACTCGA
1 ATAATTTGAATAACTCGA
*
2768456 ATAATTCGAATAACTCGA
1 ATAATTTGAATAACTCGA
2768474 ATAATTTGAATAAC
1 ATAATTTGAATAAC
2768488 AGATGAGTAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 30 1.00
ACGTcount: A:0.46, C:0.12, G:0.10, T:0.32
Consensus pattern (18 bp):
ATAATTTGAATAACTCGA
Found at i:2768589 original size:20 final size:20
Alignment explanation
Indices: 2768566--2768628 Score: 85
Period size: 20 Copynumber: 3.2 Consensus size: 20
2768556 AAATTACAAA
*
2768566 AAAAAAATCAAAATAATTTT
1 AAAAAATTCAAAATAATTTT
2768586 AAAAAATTCAAAATAATTTT
1 AAAAAATTCAAAATAATTTT
*
2768606 -TAAAATTCAAAAT-ATTTAT
1 AAAAAATTCAAAATAATTT-T
2768625 AAAA
1 AAAA
2768629 GTTCTAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 4 0.11
19 13 0.34
20 21 0.55
ACGTcount: A:0.62, C:0.05, G:0.00, T:0.33
Consensus pattern (20 bp):
AAAAAATTCAAAATAATTTT
Found at i:2768591 original size:19 final size:19
Alignment explanation
Indices: 2768567--2768628 Score: 81
Period size: 19 Copynumber: 3.2 Consensus size: 19
2768557 AATTACAAAA
2768567 AAAAAATCAAAATAATTTT
1 AAAAAATCAAAATAATTTT
2768586 AAAAAATTCAAAATAATTTT
1 AAAAAA-TCAAAATAATTTT
* *
2768606 TAAAATTCAAAAT-ATTTAT
1 AAAAAATCAAAATAATTT-T
2768625 AAAA
1 AAAA
2768629 GTTCTAAAAT
Statistics
Matches: 38, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
18 4 0.11
19 17 0.45
20 17 0.45
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (19 bp):
AAAAAATCAAAATAATTTT
Found at i:2768640 original size:18 final size:17
Alignment explanation
Indices: 2768583--2768640 Score: 53
Period size: 18 Copynumber: 3.2 Consensus size: 17
2768573 TCAAAATAAT
*
2768583 TTTAAAAAATTCAAAATAA
1 TTTATAAAATTC-AAA-AA
*
2768602 TTTTTAAAATTCAAAATA
1 TTTATAAAATTCAAAA-A
*
2768620 TTTATAAAAGTTCTAAAA
1 TTTATAAAA-TTCAAAAA
2768638 TTT
1 TTT
2768641 GCATTTTTAA
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
17 1 0.03
18 16 0.48
19 16 0.48
ACGTcount: A:0.52, C:0.05, G:0.02, T:0.41
Consensus pattern (17 bp):
TTTATAAAATTCAAAAA
Found at i:2769047 original size:21 final size:21
Alignment explanation
Indices: 2769021--2769060 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
2769011 ACCTTATCTA
*
2769021 AAGTTAAAAGTCAAAACTATC
1 AAGTTAAAAGGCAAAACTATC
2769042 AAGTTAAAAGGCAAAACTA
1 AAGTTAAAAGGCAAAACTA
2769061 CGTTGTTTGA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.55, C:0.12, G:0.12, T:0.20
Consensus pattern (21 bp):
AAGTTAAAAGGCAAAACTATC
Found at i:2784569 original size:16 final size:16
Alignment explanation
Indices: 2784538--2784582 Score: 58
Period size: 14 Copynumber: 2.9 Consensus size: 16
2784528 AAACATCATA
2784538 AATTAATTT-T-AATT
1 AATTAATTTCTCAATT
2784552 AATTAATTTCTCAATT
1 AATTAATTTCTCAATT
*
2784568 AAATAATTTTCTCAA
1 AATTAA-TTTCTCAA
2784583 CTCGATTCTA
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
14 9 0.33
15 1 0.04
16 9 0.33
17 8 0.30
ACGTcount: A:0.42, C:0.09, G:0.00, T:0.49
Consensus pattern (16 bp):
AATTAATTTCTCAATT
Found at i:2784580 original size:17 final size:16
Alignment explanation
Indices: 2784536--2784582 Score: 53
Period size: 16 Copynumber: 2.9 Consensus size: 16
2784526 ATAAACATCA
2784536 TAAATTAATTT-T-AAT
1 TAAA-TAATTTCTCAAT
*
2784551 TAATTAATTTCTCAAT
1 TAAATAATTTCTCAAT
2784567 TAAATAATTTTCTCAA
1 TAAATAA-TTTCTCAA
2784583 CTCGATTCTA
Statistics
Matches: 27, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
14 6 0.22
15 4 0.15
16 9 0.33
17 8 0.30
ACGTcount: A:0.43, C:0.09, G:0.00, T:0.49
Consensus pattern (16 bp):
TAAATAATTTCTCAAT
Found at i:2786697 original size:27 final size:27
Alignment explanation
Indices: 2786667--2786724 Score: 89
Period size: 27 Copynumber: 2.1 Consensus size: 27
2786657 TTCAGAGCTT
2786667 GCCATACGTACTATTCCTTCAAAGTTC
1 GCCATACGTACTATTCCTTCAAAGTTC
* * *
2786694 GCCATACGTACTATTCTTTCAATGTTT
1 GCCATACGTACTATTCCTTCAAAGTTC
2786721 GCCA
1 GCCA
2786725 CACATATCAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.24, C:0.28, G:0.12, T:0.36
Consensus pattern (27 bp):
GCCATACGTACTATTCCTTCAAAGTTC
Found at i:2786845 original size:27 final size:27
Alignment explanation
Indices: 2786815--2786890 Score: 109
Period size: 27 Copynumber: 2.8 Consensus size: 27
2786805 TTCAGAGCTT
2786815 GCCATACGTACTATTCCTTCAAAGTTC
1 GCCATACGTACTATTCCTTCAAAGTTC
*
2786842 GCCATACGTACTATTCCTTCAATGTTC
1 GCCATACGTACTATTCCTTCAAAGTTC
* *
2786869 GCCACACATA-TCATTCCTTCAA
1 GCCATACGTACT-ATTCCTTCAA
2786891 GGTTTATCAC
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
26 1 0.02
27 44 0.98
ACGTcount: A:0.26, C:0.32, G:0.09, T:0.33
Consensus pattern (27 bp):
GCCATACGTACTATTCCTTCAAAGTTC
Found at i:2786939 original size:148 final size:148
Alignment explanation
Indices: 2786635--2786936 Score: 532
Period size: 148 Copynumber: 2.0 Consensus size: 148
2786625 ATACGCCACG
* * *
2786635 ACATTTCTTACAGAACATTTTCTTCAGAGCTTGCCATACGTACTATTCCTTCAAAGTTCGCCATA
1 ACATTTCTTGCGGAACAGTTTCTTCAGAGCTTGCCATACGTACTATTCCTTCAAAGTTCGCCATA
* * * *
2786700 CGTACTATTCTTTCAATGTTTGCCACACATATCATTCCTTCGAGGTTTGTCACACTTACAATTCT
66 CGTACTATTCCTTCAATGTTCGCCACACATATCATTCCTTCAAGGTTTATCACACTTACAATTCT
2786765 TCAGAGTTAGCCATACAT
131 TCAGAGTTAGCCATACAT
2786783 ACATTTCTTGCGGAACAGTTTCTTCAGAGCTTGCCATACGTACTATTCCTTCAAAGTTCGCCATA
1 ACATTTCTTGCGGAACAGTTTCTTCAGAGCTTGCCATACGTACTATTCCTTCAAAGTTCGCCATA
2786848 CGTACTATTCCTTCAATGTTCGCCACACATATCATTCCTTCAAGGTTTATCACACTTACAATTCT
66 CGTACTATTCCTTCAATGTTCGCCACACATATCATTCCTTCAAGGTTTATCACACTTACAATTCT
2786913 TCAGAGTTAGCCATACAT
131 TCAGAGTTAGCCATACAT
2786931 ATCATT
1 A-CATT
2786937 CTTCTAGGGT
Statistics
Matches: 146, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
148 142 0.97
149 4 0.03
ACGTcount: A:0.26, C:0.26, G:0.12, T:0.36
Consensus pattern (148 bp):
ACATTTCTTGCGGAACAGTTTCTTCAGAGCTTGCCATACGTACTATTCCTTCAAAGTTCGCCATA
CGTACTATTCCTTCAATGTTCGCCACACATATCATTCCTTCAAGGTTTATCACACTTACAATTCT
TCAGAGTTAGCCATACAT
Found at i:2786963 original size:27 final size:27
Alignment explanation
Indices: 2786901--2786968 Score: 75
Period size: 27 Copynumber: 2.6 Consensus size: 27
2786891 GGTTTATCAC
*
2786901 ACTTACAATTCTTC-AGAGTTAGCCAT
1 ACTTACCATTCTTCTAGAGTTAGCCAT
* * * * *
2786927 ACATATCATTCTTCTAGGGTTGGTCAT
1 ACTTACCATTCTTCTAGAGTTAGCCAT
2786954 ACTTACCATTCTTCT
1 ACTTACCATTCTTCT
2786969 CCTTCAAGGT
Statistics
Matches: 33, Mismatches: 8, Indels: 1
0.79 0.19 0.02
Matches are distributed among these distances:
26 11 0.33
27 22 0.67
ACGTcount: A:0.25, C:0.24, G:0.12, T:0.40
Consensus pattern (27 bp):
ACTTACCATTCTTCTAGAGTTAGCCAT
Found at i:2787094 original size:27 final size:27
Alignment explanation
Indices: 2787063--2787232 Score: 181
Period size: 27 Copynumber: 6.3 Consensus size: 27
2787053 TCCATATATC
2787063 GCCACAAAGGCTTTAATTTCATAGATT
1 GCCACAAAGGCTTTAATTTCATAGATT
* *
2787090 TCCACAAAGGCTTTAATATCATAGATT
1 GCCACAAAGGCTTTAATTTCATAGATT
* * *
2787117 TCCACAAAGG-TTTCCATTTCAGAGATT
1 GCCACAAAGGCTTT-AATTTCATAGATT
* *
2787144 GTCACAAAGTC-TTACATTTCATA-ATT
1 GCCACAAAGGCTTTA-ATTTCATAGATT
*
2787170 GCCACAAAGGCTTCT-ACTTCATAGATT
1 GCCACAAAGGCTT-TAATTTCATAGATT
2787197 GCCACAAAGGCTTCT-ATATT-ATAGATT
1 GCCACAAAGGCTT-TAAT-TTCATAGATT
2787224 GCCACAAAG
1 GCCACAAAG
2787233 ACTTCCAGTT
Statistics
Matches: 122, Mismatches: 14, Indels: 14
0.81 0.09 0.09
Matches are distributed among these distances:
26 22 0.18
27 97 0.80
28 3 0.02
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.32
Consensus pattern (27 bp):
GCCACAAAGGCTTTAATTTCATAGATT
Found at i:2787192 original size:80 final size:81
Alignment explanation
Indices: 2787063--2787232 Score: 213
Period size: 80 Copynumber: 2.1 Consensus size: 81
2787053 TCCATATATC
* * *
2787063 GCCACAAAGGCTTTAATTTCATAGATTTCCACAAAGGCTTTAATATCATAGATTTCCACAAAGGT
1 GCCACAAAGGCTTTAATTTCATAGATTGCCACAAAGGCTTTAATATCATAGATTGCCACAAAGGC
2787128 TTCCAT-TTCAGAGATT
66 TTCCATATT-AGAGATT
* * *
2787144 GTCACAAAGTC-TTACATTTCATA-ATTGCCACAAAGGCTTCTACT-TCATAGATTGCCACAAAG
1 GCCACAAAGGCTTTA-ATTTCATAGATTGCCACAAAGGCTT-TAATATCATAGATTGCCACAAAG
* *
2787206 GCTTCTATATTATAGATT
64 GCTTCCATATTAGAGATT
2787224 GCCACAAAG
1 GCCACAAAG
2787233 ACTTCCAGTT
Statistics
Matches: 77, Mismatches: 9, Indels: 7
0.83 0.10 0.08
Matches are distributed among these distances:
80 55 0.71
81 22 0.29
ACGTcount: A:0.34, C:0.21, G:0.14, T:0.32
Consensus pattern (81 bp):
GCCACAAAGGCTTTAATTTCATAGATTGCCACAAAGGCTTTAATATCATAGATTGCCACAAAGGC
TTCCATATTAGAGATT
Found at i:2787978 original size:13 final size:13
Alignment explanation
Indices: 2787960--2787984 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2787950 TAAGTTGTAT
2787960 GTGTGAAAATTTC
1 GTGTGAAAATTTC
2787973 GTGTGAAAATTT
1 GTGTGAAAATTT
2787985 AATCGTTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:2789052 original size:41 final size:41
Alignment explanation
Indices: 2788952--2789057 Score: 142
Period size: 41 Copynumber: 2.6 Consensus size: 41
2788942 CTATTGTATA
* ** *
2788952 TCTAGCAGGCTTAAGGCCGGTGATGTAATTCAGACTTTATG
1 TCTAGCAGGCTTAATGCCGGTGAAATAATTCAGACTTTAAG
* *
2788993 TCCAGCTGGCTTAATGCCGGTGAAATAATTCAGACTTTAAG
1 TCTAGCAGGCTTAATGCCGGTGAAATAATTCAGACTTTAAG
2789034 TCTAGCAGGC-TAATTGCCGGTGAA
1 TCTAGCAGGCTTAA-TGCCGGTGAA
2789058 TTGAATCAGG
Statistics
Matches: 56, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
40 3 0.05
41 53 0.95
ACGTcount: A:0.26, C:0.19, G:0.25, T:0.29
Consensus pattern (41 bp):
TCTAGCAGGCTTAATGCCGGTGAAATAATTCAGACTTTAAG
Found at i:2795256 original size:13 final size:13
Alignment explanation
Indices: 2795238--2795262 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
2795228 TAAGTTATAT
2795238 GTGTGAAAATTTC
1 GTGTGAAAATTTC
2795251 GTGTGAAAATTT
1 GTGTGAAAATTT
2795263 GATCGTTTGA
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.04, G:0.24, T:0.40
Consensus pattern (13 bp):
GTGTGAAAATTTC
Found at i:2796714 original size:34 final size:34
Alignment explanation
Indices: 2796657--2796725 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
2796647 TCTATATGGG
* *
2796657 TAGTATTGAATACGTATAAATATACATGTATAGT
1 TAGTATTGAATAAGTATAAATATACATGTAAAGT
* * * *
2796691 TAGTTTTGAATAAGTGTATATATATATGTAAAGT
1 TAGTATTGAATAAGTATAAATATACATGTAAAGT
2796725 T
1 T
2796726 CTTGTATTGA
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
34 29 1.00
ACGTcount: A:0.39, C:0.03, G:0.16, T:0.42
Consensus pattern (34 bp):
TAGTATTGAATAAGTATAAATATACATGTAAAGT
Found at i:2797034 original size:41 final size:41
Alignment explanation
Indices: 2796916--2797034 Score: 132
Period size: 41 Copynumber: 2.9 Consensus size: 41
2796906 AATGGAAATT
* * * **
2796916 TTCAGGCTTAAAGTCTAGCAGGCTTAAGGCCGGTGATGTAA
1 TTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGAAATAA
* * *
2796957 TTCAGACTTTATGTCCAGCTGGCTTAATGCCGGTGAAATAA
1 TTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGAAATAA
* *
2796998 TTTAGACTTTAAGTCTAGCAGGC-TAATTGCCAGTGAA
1 TTCAGACTTTAAGTCTAGCAGGCTTAA-TGCCGGTGAA
2797035 TTGAATCAGG
Statistics
Matches: 64, Mismatches: 13, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
40 3 0.05
41 61 0.95
ACGTcount: A:0.28, C:0.18, G:0.24, T:0.30
Consensus pattern (41 bp):
TTCAGACTTTAAGTCTAGCAGGCTTAATGCCGGTGAAATAA
Found at i:2798075 original size:2 final size:2
Alignment explanation
Indices: 2798064--2798097 Score: 52
Period size: 2 Copynumber: 17.5 Consensus size: 2
2798054 TGTAAGTGAT
*
2798064 TA TA -A TA TA TA TA TA TA TA TA TA AA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
2798098 GAAAATGGTT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
1 1 0.03
2 28 0.97
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (2 bp):
TA
Found at i:2807526 original size:58 final size:57
Alignment explanation
Indices: 2807400--2807526 Score: 134
Period size: 58 Copynumber: 2.2 Consensus size: 57
2807390 ATAGCCACGA
** * *
2807400 AAGC-TTCCTTT-ACAGAGATTTCCACAAAGGATTTCCTTTCTAGAGTTTGCCACAG
1 AAGCGTTCCTTTGACAGAGATCGCAACAAAGGATTTCCTTTCTAGAGTTTGCCACAC
* * * *
2807455 AAGCTTTCTTTTGACAGAGATCGCAACAAAGGCTTTTCCTTT-TAGCGATTTGCCACAC
1 AAGCGTTCCTTTGACAGAGATCGCAACAAAGG-ATTTCCTTTCTAGAG-TTTGCCACAC
*
2807513 AGGCGTTCCTTTGA
1 AAGCGTTCCTTTGA
2807527 GAGTTTTGCC
Statistics
Matches: 58, Mismatches: 10, Indels: 5
0.79 0.14 0.07
Matches are distributed among these distances:
55 4 0.07
56 6 0.10
57 20 0.34
58 28 0.48
ACGTcount: A:0.25, C:0.24, G:0.18, T:0.33
Consensus pattern (57 bp):
AAGCGTTCCTTTGACAGAGATCGCAACAAAGGATTTCCTTTCTAGAGTTTGCCACAC
Found at i:2807628 original size:29 final size:29
Alignment explanation
Indices: 2807393--2807629 Score: 95
Period size: 28 Copynumber: 8.3 Consensus size: 29
2807383 TTCAGATATA
*
2807393 GCCACGAAA-GCTT-CCTTTAC-AGAGATTT
1 GCCAC-AAAGGCTTACCTTT-CTAGAGTTTT
* *
2807421 -CCACAAAGGATTTCCTTTCTAGAG-TTT
1 GCCACAAAGGCTTACCTTTCTAGAGTTTT
* * * *
2807448 GCCACAGAA-GCTTTCTTTTGAC-AGAG-ATC
1 GCCACA-AAGGCTTACCTTT--CTAGAGTTTT
* * * *
2807477 GCAACAAAGGCTTTTCCTTT-TAGCGATTT
1 GCCACAAAGGC-TTACCTTTCTAGAGTTTT
* *
2807506 GCCACACAGGCGTT-CCTTT-GAGAGTTTT
1 GCCACAAAGGC-TTACCTTTCTAGAGTTTT
* * *
2807534 GCCATAAGGGCTTACCTTTCTAGGGTTTT
1 GCCACAAAGGCTTACCTTTCTAGAGTTTT
* * * *
2807563 GCCACAAAGGC-TATCTTT-TAACAGATTC
1 GCCACAAAGGCTTACCTTTCT-AGAGTTTT
** * *
2807591 AACTCAAAGACTTACCTTTCTAGAGTTTT
1 GCCACAAAGGCTTACCTTTCTAGAGTTTT
2807620 GCCACAAAGG
1 GCCACAAAGG
2807630 TTGTCCTCTT
Statistics
Matches: 153, Mismatches: 40, Indels: 31
0.68 0.18 0.14
Matches are distributed among these distances:
26 3 0.02
27 14 0.09
28 68 0.44
29 59 0.39
30 9 0.06
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (29 bp):
GCCACAAAGGCTTACCTTTCTAGAGTTTT
Found at i:2807909 original size:53 final size:52
Alignment explanation
Indices: 2807842--2807993 Score: 198
Period size: 53 Copynumber: 2.9 Consensus size: 52
2807832 TAATTTTTTC
*
2807842 CCATATGATACCATAACCCACCAGTTATAGTCTTACATGATATGGTCTTA-TTT
1 CCATATGATACCATAACCCACCAGTTACAGTCTTACA-GATATGGTC-TACTTT
* * *
2807895 CGATATGATGCCATAACCCACCAATTACAGTCTTACACGATATGGTCTACTTT
1 CCATATGATACCATAACCCACCAGTTACAGTCTTACA-GATATGGTCTACTTT
* * * *
2807948 CCATATGATCCCACAACCCATCAGTTACAGTCTTACAGGTATGGTC
1 CCATATGATACCATAACCCACCAGTTACAGTCTTACAGATATGGTC
2807994 CTTTAGCGCC
Statistics
Matches: 87, Mismatches: 11, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
52 10 0.11
53 77 0.89
ACGTcount: A:0.30, C:0.26, G:0.13, T:0.31
Consensus pattern (52 bp):
CCATATGATACCATAACCCACCAGTTACAGTCTTACAGATATGGTCTACTTT
Found at i:2814135 original size:33 final size:33
Alignment explanation
Indices: 2814091--2814170 Score: 108
Period size: 33 Copynumber: 2.4 Consensus size: 33
2814081 TATTTGATTA
*
2814091 CTTTCTTCACTCGTTTC-TCATGCAAGCTCTCTTT
1 CTTT-TTCACTCGTTTCAT-ATGCAAGCACTCTTT
* *
2814125 CTTTTTCACTCGTTTCATTTTCAAGCACTCTTT
1 CTTTTTCACTCGTTTCATATGCAAGCACTCTTT
2814158 CTTTTTCACTCGT
1 CTTTTTCACTCGT
2814171 GTCTTTTTCA
Statistics
Matches: 42, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
33 37 0.88
34 5 0.12
ACGTcount: A:0.12, C:0.30, G:0.07, T:0.50
Consensus pattern (33 bp):
CTTTTTCACTCGTTTCATATGCAAGCACTCTTT
Found at i:2814179 original size:33 final size:33
Alignment explanation
Indices: 2814113--2814181 Score: 111
Period size: 33 Copynumber: 2.1 Consensus size: 33
2814103 GTTTCTCATG
* *
2814113 CAAGCTCTCTTTCTTTTTCACTCGTTTCATTTT
1 CAAGCACTCTTTCTTTTTCACTCGTGTCATTTT
*
2814146 CAAGCACTCTTTCTTTTTCACTCGTGTCTTTTT
1 CAAGCACTCTTTCTTTTTCACTCGTGTCATTTT
2814179 CAA
1 CAA
2814182 CAACAACACT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.14, C:0.28, G:0.07, T:0.51
Consensus pattern (33 bp):
CAAGCACTCTTTCTTTTTCACTCGTGTCATTTT
Found at i:2815313 original size:16 final size:17
Alignment explanation
Indices: 2815279--2815320 Score: 59
Period size: 16 Copynumber: 2.5 Consensus size: 17
2815269 TTTGCACACT
*
2815279 TTTTTTTATATTCGAAAC
1 TTTTTTT-TACTCGAAAC
2815297 TTTTTTTTACTCG-AAC
1 TTTTTTTTACTCGAAAC
2815313 TTTTTTTT
1 TTTTTTTT
2815321 GCTTCTTTTC
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
16 11 0.48
17 5 0.22
18 7 0.30
ACGTcount: A:0.19, C:0.12, G:0.05, T:0.64
Consensus pattern (17 bp):
TTTTTTTTACTCGAAAC
Found at i:2815319 original size:17 final size:19
Alignment explanation
Indices: 2815276--2815320 Score: 60
Period size: 17 Copynumber: 2.5 Consensus size: 19
2815266 TATTTTGCAC
*
2815276 ACTTTTTTTTATATTCGAA
1 ACTTTTTTTTATACTCGAA
2815295 AC-TTTTTTT-TACTCG-A
1 ACTTTTTTTTATACTCGAA
2815311 ACTTTTTTTT
1 ACTTTTTTTT
2815321 GCTTCTTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
16 3 0.12
17 12 0.50
18 7 0.29
19 2 0.08
ACGTcount: A:0.20, C:0.13, G:0.04, T:0.62
Consensus pattern (19 bp):
ACTTTTTTTTATACTCGAA
Found at i:2819249 original size:22 final size:21
Alignment explanation
Indices: 2819184--2819253 Score: 70
Period size: 22 Copynumber: 3.3 Consensus size: 21
2819174 AAAAAATTTT
*
2819184 AAAAAAGAACAAAAT-TTTGA
1 AAAAAAGAAGAAAATATTTGA
* * **
2819204 AAAACAAAAAGAAAAAATAGGA
1 AAAA-AAGAAGAAAATATTTGA
2819226 AAAAAAGAATGAAAATATTTGA
1 AAAAAAGAA-GAAAATATTTGA
2819248 AAAAAA
1 AAAAAA
2819254 AAAGTGGCCT
Statistics
Matches: 38, Mismatches: 9, Indels: 4
0.75 0.18 0.08
Matches are distributed among these distances:
20 4 0.11
21 12 0.32
22 22 0.58
ACGTcount: A:0.71, C:0.03, G:0.11, T:0.14
Consensus pattern (21 bp):
AAAAAAGAAGAAAATATTTGA
Found at i:2820553 original size:1 final size:1
Alignment explanation
Indices: 2820547--2820663 Score: 63
Period size: 1 Copynumber: 117.0 Consensus size: 1
2820537 TAGTTTTATA
* * * * * * * * *
2820547 TTTTTTTTATTTTTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTTTGTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
** * * * * * * * *
2820612 TGCTTTTATTTTTATTTTTATTTTTATTTTTATTTTTATTTTATTTTATTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
2820664 ATTATGCACT
Statistics
Matches: 79, Mismatches: 37, Indels: 0
0.68 0.32 0.00
Matches are distributed among these distances:
1 79 1.00
ACGTcount: A:0.08, C:0.01, G:0.08, T:0.84
Consensus pattern (1 bp):
T
Found at i:2820666 original size:5 final size:6
Alignment explanation
Indices: 2820535--2820663 Score: 115
Period size: 6 Copynumber: 22.3 Consensus size: 6
2820525 AGTGGTTTCA
* * * * *
2820535 TTTAGT TTTATA TTT-TT TTTA-T TTT-TT TTTGTT TTTGTT TTTGTT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
* * * * * **
2820580 TTTGTT TTTGTT TTTGTT TTTGTT TTTGTT TTTGCT TTTATT TTTATT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT
2820628 TTTATT TTTATT TTTATT TTTA-T TTTA-T TTTATT TT
1 TTTATT TTTATT TTTATT TTTATT TTTATT TTTATT TT
2820664 ATTATGCACT
Statistics
Matches: 113, Mismatches: 6, Indels: 8
0.89 0.05 0.06
Matches are distributed among these distances:
5 22 0.19
6 91 0.81
ACGTcount: A:0.09, C:0.01, G:0.08, T:0.82
Consensus pattern (6 bp):
TTTATT
Found at i:2825218 original size:18 final size:18
Alignment explanation
Indices: 2825195--2825229 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
2825185 GACTGCTTCA
2825195 TCCACATGCCCCAAGGCC
1 TCCACATGCCCCAAGGCC
2825213 TCCACATGCCCCAAGGC
1 TCCACATGCCCCAAGGC
2825230 TTTAAGGAAG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.23, C:0.49, G:0.17, T:0.11
Consensus pattern (18 bp):
TCCACATGCCCCAAGGCC
Found at i:2838051 original size:68 final size:70
Alignment explanation
Indices: 2837971--2838112 Score: 252
Period size: 70 Copynumber: 2.1 Consensus size: 70
2837961 TGATGATATG
* *
2837971 GAATTTTATATATACATATCTATAATACT-TG-AAAAAGAAAGCATATAAATGACTACATGAACC
1 GAATTTTATATATACATATCTATAATACTCGGAAAAAAAAAAGCATATAAATGACTACATGAACC
2838034 TATTA
66 TATTA
2838039 GAATTTTATATATACATATCTATAATACTCGGAAAAAAAAAAGCATATAAATGACTACATGAACC
1 GAATTTTATATATACATATCTATAATACTCGGAAAAAAAAAAGCATATAAATGACTACATGAACC
2838104 TATTA
66 TATTA
2838109 GAAT
1 GAAT
2838113 CGAGGCCTGA
Statistics
Matches: 70, Mismatches: 2, Indels: 2
0.95 0.03 0.03
Matches are distributed among these distances:
68 29 0.41
69 1 0.01
70 40 0.57
ACGTcount: A:0.48, C:0.12, G:0.09, T:0.31
Consensus pattern (70 bp):
GAATTTTATATATACATATCTATAATACTCGGAAAAAAAAAAGCATATAAATGACTACATGAACC
TATTA
Found at i:2841683 original size:17 final size:17
Alignment explanation
Indices: 2841661--2841731 Score: 80
Period size: 17 Copynumber: 4.5 Consensus size: 17
2841651 ATTAGAACAT
2841661 TCTTTCTTAATCATTAA
1 TCTTTCTTAATCATTAA
2841678 TCTTTCTTAATCATTAA
1 TCTTTCTTAATCATTAA
* **
2841695 TCATT-AGAA-CATT-A
1 TCTTTCTTAATCATTAA
2841709 --TTTCTTAATCATTAA
1 TCTTTCTTAATCATTAA
2841724 TCTTTCTT
1 TCTTTCTT
2841732 TTCATCTCAA
Statistics
Matches: 43, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
12 2 0.05
13 2 0.05
14 5 0.12
15 5 0.12
16 2 0.05
17 27 0.63
ACGTcount: A:0.30, C:0.17, G:0.01, T:0.52
Consensus pattern (17 bp):
TCTTTCTTAATCATTAA
Done.