Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold337
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: 2178121
ACGTcount: A:0.32, C:0.15, G:0.15, T:0.32
Warning! 137747 characters in sequence are not A, C, G, or T
File 2 of 7
Found at i:342643 original size:20 final size:20
Alignment explanation
Indices: 342461--342655 Score: 83
Period size: 20 Copynumber: 9.8 Consensus size: 20
342451 CCCTGTTTGT
*
342461 ACTTTGGTACCCCTGATTAC
1 ACTTCGGTACCCCTGATTAC
* **
342481 ACTTAC-GTGCCCCT-ATTTGT
1 ACTT-CGGTACCCCTGA-TTAC
* * *
342501 ACTTCGGTACTCCTAATTGC
1 ACTTCGGTACCCCTGATTAC
** * * **
342521 ACTTATGTGCCCCTGTTTGT
1 ACTTCGGTACCCCTGATTAC
*
342541 ACTTCGGTACCCCTGATTGC
1 ACTTCGGTACCCCTGATTAC
** * * **
342561 ACTTATGTGCCCAT-ATTTGT
1 ACTTCGGTACCCCTGA-TTAC
*
342581 ACTTCGGTACCCCTGGTTAC
1 ACTTCGGTACCCCTGATTAC
* * *
342601 ACTTAC-GTACCCTTGTTTGC
1 ACTT-CGGTACCCCTGATTAC
*
342621 ACTTCGGTACCCCTGATCAC
1 ACTTCGGTACCCCTGATTAC
* *
342641 ACTTTGGTTCCCCTG
1 ACTTCGGTACCCCTG
342656 TTATGCATCT
Statistics
Matches: 127, Mismatches: 40, Indels: 16
0.69 0.22 0.09
Matches are distributed among these distances:
19 4 0.03
20 121 0.95
21 2 0.02
ACGTcount: A:0.16, C:0.31, G:0.17, T:0.36
Consensus pattern (20 bp):
ACTTCGGTACCCCTGATTAC
Found at i:347983 original size:23 final size:23
Alignment explanation
Indices: 347956--348031 Score: 116
Period size: 23 Copynumber: 3.3 Consensus size: 23
347946 AGTGTTATTG
347956 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* * *
347979 TTCAGTGGTAGCTACGGCTACGT
1 ATCAGTGGTAGCTTCGGCTACAT
*
348002 ATCAGTGCTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
348025 ATCAGTG
1 ATCAGTG
348032 TGGCACTTAT
Statistics
Matches: 46, Mismatches: 7, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 46 1.00
ACGTcount: A:0.21, C:0.22, G:0.26, T:0.30
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:354513 original size:18 final size:18
Alignment explanation
Indices: 354490--354524 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
354480 TGCTTCGGCG
354490 ACGTAATGTAATATCATT
1 ACGTAATGTAATATCATT
354508 ACGTAATGTAATATCAT
1 ACGTAATGTAATATCAT
354525 ACACTCAAAT
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:0.40, C:0.11, G:0.11, T:0.37
Consensus pattern (18 bp):
ACGTAATGTAATATCATT
Found at i:359203 original size:6 final size:6
Alignment explanation
Indices: 359192--359249 Score: 80
Period size: 6 Copynumber: 9.3 Consensus size: 6
359182 AGAGGAGACG
* *
359192 GATTTA GATTTA GATCTTT GGATTTT GATTTT GATTTT GATTTT GATTTT
1 GATTTT GATTTT GAT-TTT -GATTTT GATTTT GATTTT GATTTT GATTTT
359242 GATTTT GA
1 GATTTT GA
359250 AATTGGAGAT
Statistics
Matches: 49, Mismatches: 1, Indels: 4
0.91 0.02 0.07
Matches are distributed among these distances:
6 41 0.84
7 5 0.10
8 3 0.06
ACGTcount: A:0.21, C:0.02, G:0.19, T:0.59
Consensus pattern (6 bp):
GATTTT
Found at i:367617 original size:31 final size:31
Alignment explanation
Indices: 367576--367636 Score: 88
Period size: 31 Copynumber: 2.0 Consensus size: 31
367566 TGTATTTTTT
367576 TAATTAAGTGACTAA-AATGAAAATTTACCCA
1 TAATTAAGTGACTAATAATG-AAATTTACCCA
* *
367607 TAATTTAGTGACTAATAATGTAATTTACCC
1 TAATTAAGTGACTAATAATGAAATTTACCC
367637 TCACATCTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
31 23 0.85
32 4 0.15
ACGTcount: A:0.43, C:0.13, G:0.10, T:0.34
Consensus pattern (31 bp):
TAATTAAGTGACTAATAATGAAATTTACCCA
Found at i:368237 original size:18 final size:18
Alignment explanation
Indices: 368190--368237 Score: 51
Period size: 18 Copynumber: 2.6 Consensus size: 18
368180 AAAAAGAGCT
*
368190 AAAACAAAACACAAAGTTCA
1 AAAAC-AAA-ACAAACTTCA
* *
368210 AAACCCAAACAAACTTCA
1 AAAACAAAACAAACTTCA
368228 AAAACAAAAC
1 AAAACAAAAC
368238 CCAACCTATA
Statistics
Matches: 23, Mismatches: 5, Indels: 2
0.77 0.17 0.07
Matches are distributed among these distances:
18 17 0.74
19 2 0.09
20 4 0.17
ACGTcount: A:0.65, C:0.25, G:0.02, T:0.08
Consensus pattern (18 bp):
AAAACAAAACAAACTTCA
Found at i:369567 original size:34 final size:34
Alignment explanation
Indices: 369524--369593 Score: 122
Period size: 34 Copynumber: 2.1 Consensus size: 34
369514 AAATGATTAT
*
369524 ACCGGTAACAAGCCATGAGGCAATCAAGAATCAA
1 ACCGGTAACAAGCCACGAGGCAATCAAGAATCAA
*
369558 ACCGGTAACAAGGCACGAGGCAATCAAGAATCAA
1 ACCGGTAACAAGCCACGAGGCAATCAAGAATCAA
369592 AC
1 AC
369594 TCTTCCAACA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
34 34 1.00
ACGTcount: A:0.44, C:0.24, G:0.21, T:0.10
Consensus pattern (34 bp):
ACCGGTAACAAGCCACGAGGCAATCAAGAATCAA
Found at i:381157 original size:16 final size:16
Alignment explanation
Indices: 381133--381163 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
381123 TGTTTAGTTT
381133 ACTGGAATGAAATAAG
1 ACTGGAATGAAATAAG
*
381149 ACTGTAATGAAATAA
1 ACTGGAATGAAATAA
381164 CTATTTTGTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.52, C:0.06, G:0.19, T:0.23
Consensus pattern (16 bp):
ACTGGAATGAAATAAG
Found at i:382455 original size:69 final size:69
Alignment explanation
Indices: 382307--382496 Score: 253
Period size: 67 Copynumber: 2.8 Consensus size: 69
382297 CATAAATAAA
* * * *
382307 AAAAAGTTATATTACTCCACCACCGCACCCAATTATACATACAAAAAGTG--AACCTACAATGAC
1 AAAAAGTTATATTAGTCCACCACCACACCCATTTACACATACAAAAAGTGACAACCTACAATGAC
382370 ATAC
66 ATAC
* * * *
382374 AAAAAGTGATATTAGTCCACTACCACACCTATTTACACATACAAAAAGTGACAACCTACAATTAC
1 AAAAAGTTATATTAGTCCACCACCACACCCATTTACACATACAAAAAGTGACAACCTACAATGAC
*
382439 ATAT
66 ATAC
* *
382443 GAAAAGTTATATTAGTTCACCACCACACCCATTTACAC--ACAAAAAGTGACAACC
1 AAAAAGTTATATTAGTCCACCACCACACCCATTTACACATACAAAAAGTGACAACC
382497 CTCTATGGTA
Statistics
Matches: 107, Mismatches: 14, Indels: 4
0.86 0.11 0.03
Matches are distributed among these distances:
67 59 0.55
69 48 0.45
ACGTcount: A:0.44, C:0.26, G:0.08, T:0.22
Consensus pattern (69 bp):
AAAAAGTTATATTAGTCCACCACCACACCCATTTACACATACAAAAAGTGACAACCTACAATGAC
ATAC
Found at i:383072 original size:30 final size:29
Alignment explanation
Indices: 383034--383092 Score: 73
Period size: 30 Copynumber: 2.0 Consensus size: 29
383024 GAGGTGGGAT
*
383034 GTGAAGGGAATAAAAGTTTTAGGGAAAAA
1 GTGAAGGGAATAAAAATTTTAGGGAAAAA
* * *
383063 GTGAGAGGGAGTAAAAATTTTGGGGGAAAA
1 GTGA-AGGGAATAAAAATTTTAGGGAAAAA
383093 TAAAAGGTTT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
29 4 0.16
30 21 0.84
ACGTcount: A:0.44, C:0.00, G:0.36, T:0.20
Consensus pattern (29 bp):
GTGAAGGGAATAAAAATTTTAGGGAAAAA
Found at i:383374 original size:9 final size:9
Alignment explanation
Indices: 383357--383387 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
383347 TCGAGTTGAT
383357 TCGAATAAC
1 TCGAATAAC
*
383366 TCGATTAAC
1 TCGAATAAC
383375 TCGAATAAC
1 TCGAATAAC
383384 TCGA
1 TCGA
383388 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:394565 original size:18 final size:17
Alignment explanation
Indices: 394544--394591 Score: 60
Period size: 18 Copynumber: 2.7 Consensus size: 17
394534 TAAATAAATA
394544 AATGTTTTGAAATTGAAT
1 AATGTTTTGAAA-TGAAT
*
394562 AATGATTTGTAAATGAAT
1 AATGTTTTG-AAATGAAT
*
394580 AATATTTTGAAA
1 AATGTTTTGAAA
394592 ACGAACGACA
Statistics
Matches: 26, Mismatches: 3, Indels: 3
0.81 0.09 0.09
Matches are distributed among these distances:
17 3 0.12
18 20 0.77
19 3 0.12
ACGTcount: A:0.44, C:0.00, G:0.15, T:0.42
Consensus pattern (17 bp):
AATGTTTTGAAATGAAT
Found at i:394970 original size:25 final size:25
Alignment explanation
Indices: 394907--394987 Score: 67
Period size: 25 Copynumber: 3.2 Consensus size: 25
394897 TTAAACTGAA
* *
394907 ACTGAAACTATCT-TTGATAGTATAT
1 ACTGAAACTA-CTATAGGTAGTATAT
* *
394932 CCTGAAACTGCTATAGGTAGTATAT
1 ACTGAAACTACTATAGGTAGTATAT
* * *
394957 ATTGAGACTACTATAGATAG-ACTAT
1 ACTGAAACTACTATAGGTAGTA-TAT
394982 ACTGAA
1 ACTGAA
394988 TACACTTAAA
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
24 3 0.07
25 40 0.93
ACGTcount: A:0.37, C:0.14, G:0.16, T:0.33
Consensus pattern (25 bp):
ACTGAAACTACTATAGGTAGTATAT
Found at i:398344 original size:17 final size:18
Alignment explanation
Indices: 398319--398354 Score: 56
Period size: 17 Copynumber: 2.1 Consensus size: 18
398309 TTTAAAACAC
398319 ATTTGAAACATGA-CTTT
1 ATTTGAAACATGACCTTT
*
398336 ATTTTAAACATGACCTTT
1 ATTTGAAACATGACCTTT
398354 A
1 A
398355 GTAATTTGCA
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:0.36, C:0.14, G:0.08, T:0.42
Consensus pattern (18 bp):
ATTTGAAACATGACCTTT
Found at i:399080 original size:87 final size:88
Alignment explanation
Indices: 398947--399127 Score: 346
Period size: 87 Copynumber: 2.1 Consensus size: 88
398937 TCGTTTTGAG
398947 CAATTTAATTCTTTTCTTTTATGTTCTTTTAAATTTTTTTCTTTATTTCCCATTCACTTTTGCTT
1 CAATTTAATTCTTTTCTTTTATGTTCTTTTAAATTTTTTTCTTTATTTCCCATTCACTTTTGCTT
399012 CTCCCTCTGTTTTCCTCCCTTCT
66 CTCCCTCTGTTTTCCTCCCTTCT
399035 CAATTTAA-TCTTTTCTTTTATGTTCTTTTAAATTTTTTTCTTTATTTCCCATTCACTTTTGCTT
1 CAATTTAATTCTTTTCTTTTATGTTCTTTTAAATTTTTTTCTTTATTTCCCATTCACTTTTGCTT
399099 CTCCCTCTGTTTTCCTCCCTTCT
66 CTCCCTCTGTTTTCCTCCCTTCT
*
399122 CTATTT
1 CAATTT
399128 CTTTTAACTT
Statistics
Matches: 92, Mismatches: 1, Indels: 1
0.98 0.01 0.01
Matches are distributed among these distances:
87 84 0.91
88 8 0.09
ACGTcount: A:0.13, C:0.25, G:0.03, T:0.59
Consensus pattern (88 bp):
CAATTTAATTCTTTTCTTTTATGTTCTTTTAAATTTTTTTCTTTATTTCCCATTCACTTTTGCTT
CTCCCTCTGTTTTCCTCCCTTCT
Found at i:402498 original size:40 final size:38
Alignment explanation
Indices: 402400--402498 Score: 126
Period size: 39 Copynumber: 2.5 Consensus size: 38
402390 CCCAGCCCAA
**
402400 ACCCAATTACCCAACCCAATAAAACTAAAACTAAAGTTT
1 ACCCAATTA-CCAACCCAATAAAACTAAAACTAAAGACT
*
402439 ACCCAATTACTCAATCCAATAAAACTAAAACTAAAAGACT
1 ACCCAATTAC-CAACCCAATAAAACTAAAACT-AAAGACT
*
402479 ATCCAATTTACCAACCCAAT
1 ACCCAA-TTACCAACCCAAT
402499 TTACTAAAGT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
38 1 0.02
39 29 0.56
40 18 0.35
41 4 0.08
ACGTcount: A:0.48, C:0.28, G:0.02, T:0.21
Consensus pattern (38 bp):
ACCCAATTACCAACCCAATAAAACTAAAACTAAAGACT
Found at i:402583 original size:9 final size:9
Alignment explanation
Indices: 402571--402647 Score: 84
Period size: 9 Copynumber: 8.4 Consensus size: 9
402561 AAAAATAAAA
402571 AATTCGGGT
1 AATTCGGGT
402580 AATTCGGGT
1 AATTCGGGT
*
402589 ATTTTTC-GGT
1 A--ATTCGGGT
*
402599 AATTCGGTT
1 AATTCGGGT
* *
402608 AATTTGGTT
1 AATTCGGGT
402617 AATTCGGGT
1 AATTCGGGT
402626 AATTCGGGT
1 AATTCGGGT
*
402635 AATTCGAGT
1 AATTCGGGT
402644 AATT
1 AATT
402648 TTTAACCAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 6
0.82 0.10 0.08
Matches are distributed among these distances:
8 3 0.05
9 48 0.83
10 4 0.07
11 3 0.05
ACGTcount: A:0.23, C:0.09, G:0.26, T:0.42
Consensus pattern (9 bp):
AATTCGGGT
Found at i:402823 original size:12 final size:12
Alignment explanation
Indices: 402806--402830 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
402796 AGTAATTTCG
402806 GGTCGGTTAACC
1 GGTCGGTTAACC
402818 GGTCGGTTAACC
1 GGTCGGTTAACC
402830 G
1 G
402831 AATGAACACC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.24, G:0.36, T:0.24
Consensus pattern (12 bp):
GGTCGGTTAACC
Found at i:404929 original size:24 final size:24
Alignment explanation
Indices: 404875--405050 Score: 142
Period size: 24 Copynumber: 7.3 Consensus size: 24
404865 CATAACACCC
** *
404875 GCGAACCCCTATCATTAG-CTACCT
1 GCGAACCCCTATCACCAGAC-ACAT
* * **
404899 GCAAACCCCAATCACCAGACATTT
1 GCGAACCCCTATCACCAGACACAT
*
404923 GCGAACCCCTATCACTAGACACAT
1 GCGAACCCCTATCACCAGACACAT
* *
404947 GCGAACCCCTATCGCCAG-CTACCT
1 GCGAACCCCTATCACCAGAC-ACAT
* * **
404971 ACAAACCCCTATCATTAGACACAT
1 GCGAACCCCTATCACCAGACACAT
* *
404995 GTGAACCCCTATCACCAG-CTACTT
1 GCGAACCCCTATCACCAGAC-ACAT
* *
405019 GCGAACCCTTATCACCAAACACAT
1 GCGAACCCCTATCACCAGACACAT
405043 GCGAACCC
1 GCGAACCC
405051 TTTAATGTAT
Statistics
Matches: 117, Mismatches: 30, Indels: 10
0.75 0.19 0.06
Matches are distributed among these distances:
23 2 0.02
24 112 0.96
25 3 0.03
ACGTcount: A:0.31, C:0.39, G:0.11, T:0.19
Consensus pattern (24 bp):
GCGAACCCCTATCACCAGACACAT
Found at i:404954 original size:48 final size:48
Alignment explanation
Indices: 404875--405050 Score: 194
Period size: 48 Copynumber: 3.7 Consensus size: 48
404865 CATAACACCC
* * * * *
404875 GCGAACCCCTATCATTAG-CTACCTGCAAACCCCAATCACCAGAC-ATTT
1 GCGAACCCCTATCACTAGAC-ACATGCGAACCCCTATCACCAG-CTACTT
* *
404923 GCGAACCCCTATCACTAGACACATGCGAACCCCTATCGCCAGCTACCT
1 GCGAACCCCTATCACTAGACACATGCGAACCCCTATCACCAGCTACTT
* * * *
404971 ACAAACCCCTATCATTAGACACATGTGAACCCCTATCACCAGCTACTT
1 GCGAACCCCTATCACTAGACACATGCGAACCCCTATCACCAGCTACTT
* * *
405019 GCGAACCCTTATCACCAAACACATGCGAACCC
1 GCGAACCCCTATCACTAGACACATGCGAACCC
405051 TTTAATGTAT
Statistics
Matches: 106, Mismatches: 20, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
47 1 0.01
48 104 0.98
49 1 0.01
ACGTcount: A:0.31, C:0.39, G:0.11, T:0.19
Consensus pattern (48 bp):
GCGAACCCCTATCACTAGACACATGCGAACCCCTATCACCAGCTACTT
Found at i:405001 original size:72 final size:72
Alignment explanation
Indices: 404875--405035 Score: 189
Period size: 72 Copynumber: 2.2 Consensus size: 72
404865 CATAACACCC
** * ** *
404875 GCGAACCCCTATCATTAGCTACCTGCAAACCCCAATCACCAGACATTTGCGAACCCCTATCACTA
1 GCGAACCCCTATCACCAGCTACCTACAAACCCCAATCACCAGACACATGCGAACCCCTATCACCA
404940 GAC-ACAT
66 G-CTACAT
* * ** *
404947 GCGAACCCCTATCGCCAGCTACCTACAAACCCCTATCATTAGACACATGTGAACCCCTATCACCA
1 GCGAACCCCTATCACCAGCTACCTACAAACCCCAATCACCAGACACATGCGAACCCCTATCACCA
*
405012 GCTACTT
66 GCTACAT
*
405019 GCGAACCCTTATCACCA
1 GCGAACCCCTATCACCA
405036 AACACATGCG
Statistics
Matches: 74, Mismatches: 14, Indels: 2
0.82 0.16 0.02
Matches are distributed among these distances:
71 1 0.01
72 73 0.99
ACGTcount: A:0.30, C:0.39, G:0.11, T:0.20
Consensus pattern (72 bp):
GCGAACCCCTATCACCAGCTACCTACAAACCCCAATCACCAGACACATGCGAACCCCTATCACCA
GCTACAT
Found at i:406415 original size:39 final size:39
Alignment explanation
Indices: 406372--406457 Score: 147
Period size: 39 Copynumber: 2.2 Consensus size: 39
406362 CACCACTAAA
406372 ATTTCTTCTTTTCTTTCTTCT-TCAAATTCTACACTTCAT
1 ATTTCTTC-TTTCTTTCTTCTGTCAAATTCTACACTTCAT
406411 ATTTCTTCTTTCTTTCTTCTGTCAAATTCTACACTTCAT
1 ATTTCTTCTTTCTTTCTTCTGTCAAATTCTACACTTCAT
*
406450 CTTTCTTC
1 ATTTCTTC
406458 GGTTAAAAAC
Statistics
Matches: 45, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
38 12 0.27
39 33 0.73
ACGTcount: A:0.16, C:0.27, G:0.01, T:0.56
Consensus pattern (39 bp):
ATTTCTTCTTTCTTTCTTCTGTCAAATTCTACACTTCAT
Found at i:406517 original size:39 final size:39
Alignment explanation
Indices: 406434--406517 Score: 159
Period size: 39 Copynumber: 2.2 Consensus size: 39
406424 TTCTTCTGTC
*
406434 AAATTCTACACTTCATCTTTCTTCGGTTAAAAACCCCCA
1 AAATTTTACACTTCATCTTTCTTCGGTTAAAAACCCCCA
406473 AAATTTTACACTTCATCTTTCTTCGGTTAAAAACCCCCA
1 AAATTTTACACTTCATCTTTCTTCGGTTAAAAACCCCCA
406512 AAATTT
1 AAATTT
406518 GTCCTCACTT
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
39 44 1.00
ACGTcount: A:0.32, C:0.27, G:0.05, T:0.36
Consensus pattern (39 bp):
AAATTTTACACTTCATCTTTCTTCGGTTAAAAACCCCCA
Found at i:408702 original size:36 final size:36
Alignment explanation
Indices: 408655--408728 Score: 148
Period size: 36 Copynumber: 2.1 Consensus size: 36
408645 NNNTATATAT
408655 ATATATATATTTCTAAAACACAAAGCAGAGAACAAG
1 ATATATATATTTCTAAAACACAAAGCAGAGAACAAG
408691 ATATATATATTTCTAAAACACAAAGCAGAGAACAAG
1 ATATATATATTTCTAAAACACAAAGCAGAGAACAAG
408727 AT
1 AT
408729 TTGGGGGACT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
36 38 1.00
ACGTcount: A:0.53, C:0.14, G:0.11, T:0.23
Consensus pattern (36 bp):
ATATATATATTTCTAAAACACAAAGCAGAGAACAAG
Found at i:409132 original size:18 final size:18
Alignment explanation
Indices: 409108--409153 Score: 65
Period size: 18 Copynumber: 2.6 Consensus size: 18
409098 TTTTTTATTT
409108 TTCATATTCGTTTTACGA
1 TTCATATTCGTTTTACGA
* **
409126 TTTATATTTATTTTACGA
1 TTCATATTCGTTTTACGA
409144 TTCATATTCG
1 TTCATATTCG
409154 AGGTTCAGAG
Statistics
Matches: 22, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 22 1.00
ACGTcount: A:0.24, C:0.13, G:0.09, T:0.54
Consensus pattern (18 bp):
TTCATATTCGTTTTACGA
Found at i:409347 original size:15 final size:15
Alignment explanation
Indices: 409315--409347 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
409305 CGATTAAGGT
409315 CATAATTCATAACGC
1 CATAATTCATAACGC
409330 CATAAGTTCATAAC-C
1 CATAA-TTCATAACGC
409345 CAT
1 CAT
409348 TTACACACCA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 9 0.53
16 8 0.47
ACGTcount: A:0.39, C:0.27, G:0.06, T:0.27
Consensus pattern (15 bp):
CATAATTCATAACGC
Found at i:410743 original size:15 final size:15
Alignment explanation
Indices: 410706--410751 Score: 51
Period size: 15 Copynumber: 3.1 Consensus size: 15
410696 AATAAAAGAG
410706 AGAGAAG-AAAG-AA
1 AGAGAAGAAAAGAAA
410719 AGATGAAAGAAAAGAAA
1 AGA-G-AAGAAAAGAAA
*
410736 AGAGAAGAAAGGAAA
1 AGAGAAGAAAAGAAA
410751 A
1 A
410752 TTTCTCATGC
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
13 3 0.11
14 1 0.04
15 14 0.50
16 5 0.18
17 5 0.18
ACGTcount: A:0.70, C:0.00, G:0.28, T:0.02
Consensus pattern (15 bp):
AGAGAAGAAAAGAAA
Found at i:413205 original size:23 final size:23
Alignment explanation
Indices: 413179--413244 Score: 78
Period size: 24 Copynumber: 2.8 Consensus size: 23
413169 AACTTAATCG
*
413179 AACATGTTCACGAACAATAAACA
1 AACATGTTCACAAACAATAAACA
* **
413202 AACATGTTCATAAACATATAATTA
1 AACATGTTCACAAACA-ATAAACA
*
413226 AACATGTCCACAAACAATA
1 AACATGTTCACAAACAATA
413245 TTAATGAATA
Statistics
Matches: 36, Mismatches: 6, Indels: 2
0.82 0.14 0.05
Matches are distributed among these distances:
23 17 0.47
24 19 0.53
ACGTcount: A:0.52, C:0.20, G:0.06, T:0.23
Consensus pattern (23 bp):
AACATGTTCACAAACAATAAACA
Found at i:415433 original size:20 final size:21
Alignment explanation
Indices: 415408--415449 Score: 59
Period size: 20 Copynumber: 2.0 Consensus size: 21
415398 AAAAGTTTCC
* *
415408 ATATCATATCAT-TCCATTTT
1 ATATCACATCATATCAATTTT
415428 ATATCACATCATATCAATTTT
1 ATATCACATCATATCAATTTT
415449 A
1 A
415450 ACTTAAAACA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 11 0.58
21 8 0.42
ACGTcount: A:0.36, C:0.19, G:0.00, T:0.45
Consensus pattern (21 bp):
ATATCACATCATATCAATTTT
Found at i:424443 original size:10 final size:10
Alignment explanation
Indices: 424428--424460 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
424418 ACTTATAAAT
424428 ATTATAATAA
1 ATTATAATAA
424438 ATTATAATAA
1 ATTATAATAA
424448 A-TATAATAA
1 ATTATAATAA
424457 ATTA
1 ATTA
424461 AAAAGAATTT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 9 0.41
10 13 0.59
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (10 bp):
ATTATAATAA
Found at i:426083 original size:25 final size:24
Alignment explanation
Indices: 426024--426138 Score: 79
Period size: 25 Copynumber: 4.6 Consensus size: 24
426014 AAAGTACATA
* *
426024 AACGGAAAGCTCTTTTGAGCCATAT
1 AACGGAAAGCTCATGTGAGCCAT-T
*
426049 AAC-AAGAAGCTCATGTGAGCCATGT
1 AACGGA-AAGCTCATGTGAGCCAT-T
** *
426074 AACGGAAAGCTCCGGAGAGCCATT
1 AACGGAAAGCTCATGTGAGCCATT
* * *
426098 CACGGGAAGCTCATGCGAGCCAATT
1 AACGGAAAGCTCATGTGAGCC-ATT
* *
426123 AATTGGGAAGCTCATG
1 AA-CGGAAAGCTCATG
426139 AAAGAGCCTT
Statistics
Matches: 71, Mismatches: 15, Indels: 7
0.76 0.16 0.08
Matches are distributed among these distances:
24 18 0.25
25 40 0.56
26 13 0.18
ACGTcount: A:0.32, C:0.22, G:0.26, T:0.20
Consensus pattern (24 bp):
AACGGAAAGCTCATGTGAGCCATT
Found at i:426117 original size:24 final size:24
Alignment explanation
Indices: 426040--426189 Score: 86
Period size: 25 Copynumber: 5.9 Consensus size: 24
426030 AAGCTCTTTT
** *
426040 GAGCCATATAACAAGAAGCTCATGT
1 GAGCCAT-TAACGGGAAGCTCATGA
* **
426065 GAGCCATGTAACGGAAAGCTCCGGA
1 GAGCCAT-TAACGGGAAGCTCATGA
* *
426090 GAGCCATTCACGGGAAGCTCATGC
1 GAGCCATTAACGGGAAGCTCATGA
*
426114 GAGCCAATTAATTGGGAAGCTCATGAAA
1 GAGCC-ATTAA-CGGGAAGCTCATG--A
* * *
426142 GAGCCTTTAATCAGGAAGCTC-CGAA
1 GAGCCATTAA-CGGGAAGCTCATG-A
* *
426167 GAGCCATATATCGGGACGCTCAT
1 GAGCCAT-TAACGGGAAGCTCAT
426190 AAAAGTTGCG
Statistics
Matches: 95, Mismatches: 24, Indels: 11
0.73 0.18 0.08
Matches are distributed among these distances:
24 17 0.18
25 45 0.47
26 15 0.16
27 13 0.14
28 5 0.05
ACGTcount: A:0.33, C:0.23, G:0.26, T:0.19
Consensus pattern (24 bp):
GAGCCATTAACGGGAAGCTCATGA
Found at i:429348 original size:19 final size:20
Alignment explanation
Indices: 429310--429352 Score: 70
Period size: 20 Copynumber: 2.2 Consensus size: 20
429300 ATAATAATAA
429310 ACAAGCCCAAAAATAAAATT
1 ACAAGCCCAAAAATAAAATT
*
429330 ACAAGCCCAAATA-AAAATT
1 ACAAGCCCAAAAATAAAATT
429349 ACAA
1 ACAA
429353 ATCCAATTAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 10 0.45
20 12 0.55
ACGTcount: A:0.60, C:0.21, G:0.05, T:0.14
Consensus pattern (20 bp):
ACAAGCCCAAAAATAAAATT
Found at i:429358 original size:19 final size:18
Alignment explanation
Indices: 429320--429358 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 18
429310 ACAAGCCCAA
*
429320 AAATAAAATTACAAGCCC
1 AAATAAAATTACAAACCC
*
429338 AAATAAAAATTACAAATCC
1 AAAT-AAAATTACAAACCC
429357 AA
1 AA
429359 TTACAAAAAA
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:0.62, C:0.18, G:0.03, T:0.18
Consensus pattern (18 bp):
AAATAAAATTACAAACCC
Found at i:430739 original size:20 final size:19
Alignment explanation
Indices: 430716--430753 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 19
430706 TAATTTCAAC
430716 TTTTCATTT-TTATTATTTTA
1 TTTT-ATTTATTATT-TTTTA
430736 TTTTATTTATTATTTTTT
1 TTTTATTTATTATTTTTT
430754 GCCCTTATTT
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
19 8 0.47
20 9 0.53
ACGTcount: A:0.18, C:0.03, G:0.00, T:0.79
Consensus pattern (19 bp):
TTTTATTTATTATTTTTTA
Found at i:435471 original size:21 final size:21
Alignment explanation
Indices: 435447--435487 Score: 55
Period size: 21 Copynumber: 2.0 Consensus size: 21
435437 GCTTCCCGTA
435447 CTTTTCATGCCGCTTCTCATT
1 CTTTTCATGCCGCTTCTCATT
* * *
435468 CTTTTCGTGTCGCTTTTCAT
1 CTTTTCATGCCGCTTCTCAT
435488 GCTTCTCGTG
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.07, C:0.29, G:0.12, T:0.51
Consensus pattern (21 bp):
CTTTTCATGCCGCTTCTCATT
Found at i:435496 original size:21 final size:21
Alignment explanation
Indices: 435457--435498 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
435447 CTTTTCATGC
* *
435457 CGCTTCTCATTCTTTTCGTGT
1 CGCTTCTCATGCTTCTCGTGT
*
435478 CGCTTTTCATGCTTCTCGTGT
1 CGCTTCTCATGCTTCTCGTGT
435499 TTGTTGTCAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.05, C:0.29, G:0.17, T:0.50
Consensus pattern (21 bp):
CGCTTCTCATGCTTCTCGTGT
Found at i:436353 original size:13 final size:14
Alignment explanation
Indices: 436335--436364 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
436325 TAGCACCAGT
436335 TTCTTTAT-AAATG
1 TTCTTTATAAAATG
436348 TTCTTTATAAAATG
1 TTCTTTATAAAATG
436362 TTC
1 TTC
436365 ATAATTGAGC
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 8 0.50
14 8 0.50
ACGTcount: A:0.30, C:0.10, G:0.07, T:0.53
Consensus pattern (14 bp):
TTCTTTATAAAATG
Found at i:444244 original size:20 final size:20
Alignment explanation
Indices: 444219--444260 Score: 75
Period size: 20 Copynumber: 2.1 Consensus size: 20
444209 TTTCTAACGA
*
444219 AATTTTAATATCATATTACT
1 AATTTTAATACCATATTACT
444239 AATTTTAATACCATATTACT
1 AATTTTAATACCATATTACT
444259 AA
1 AA
444261 CATTTCATAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (20 bp):
AATTTTAATACCATATTACT
Found at i:449831 original size:26 final size:25
Alignment explanation
Indices: 449802--449881 Score: 65
Period size: 26 Copynumber: 3.1 Consensus size: 25
449792 ATGTTCGGTT
449802 CACATAGTAGCCTGCACATAGTACTA
1 CACATAGTAGCCT-CACATAGTACTA
* * * *
449828 CACAT-GTAACCATTACCAT-CTAATA
1 CACATAGTAGCC-TCA-CATAGTACTA
*
449853 CACGTAGTAGCCTACACATAGTACTA
1 CACATAGTAGCCT-CACATAGTACTA
449879 CAC
1 CAC
449882 GCGTGATCGA
Statistics
Matches: 40, Mismatches: 9, Indels: 10
0.68 0.15 0.17
Matches are distributed among these distances:
25 18 0.45
26 22 0.55
ACGTcount: A:0.36, C:0.29, G:0.11, T:0.24
Consensus pattern (25 bp):
CACATAGTAGCCTCACATAGTACTA
Found at i:450012 original size:101 final size:99
Alignment explanation
Indices: 449803--449988 Score: 239
Period size: 101 Copynumber: 1.8 Consensus size: 99
449793 TGTTCGGTTC
* *
449803 ACATAGTAGCCTGCACATAGTACTACACATGTAACCATTACCATCTAATACACGTAGTAGCCTAC
1 ACATAGTAGCCTACACATAGTACTACACATGCAACCA-TACCATCTAATACACGTAGTAGCCTAC
* *
449868 ACATAGTACTACACGCGTGATCGAAACTATCCGGT
65 ACATAGTACTACACACGTGATCCAAACTATCCGGT
* * **
449903 ACGCATAGTAGTCTACACATAGTACTACACATGCAACC-TATCATTCTGGTACACGTAGTAGCCT
1 A--CATAGTAGCCTACACATAGTACTACACATGCAACCATACCA-TCTAATACACGTAGTAGCCT
* *
449967 GCACATAGTACTACACATGTGA
63 ACACATAGTACTACACACGTGA
449989 CCATCACTTT
Statistics
Matches: 74, Mismatches: 9, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
100 5 0.07
101 37 0.50
102 32 0.43
ACGTcount: A:0.33, C:0.26, G:0.16, T:0.25
Consensus pattern (99 bp):
ACATAGTAGCCTACACATAGTACTACACATGCAACCATACCATCTAATACACGTAGTAGCCTACA
CATAGTACTACACACGTGATCCAAACTATCCGGT
Found at i:452647 original size:25 final size:25
Alignment explanation
Indices: 452612--452680 Score: 93
Period size: 25 Copynumber: 2.8 Consensus size: 25
452602 ATTCATGTAT
452612 GCTCATGCGAGCTGAATAACGGAAA
1 GCTCATGCGAGCTGAATAACGGAAA
* * * *
452637 GCTCATACGAGCTGAGTATCGGGAA
1 GCTCATGCGAGCTGAATAACGGAAA
*
452662 GCTCATGTGAGCTGAATAA
1 GCTCATGCGAGCTGAATAA
452681 TGGGAAGTTC
Statistics
Matches: 36, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 36 1.00
ACGTcount: A:0.32, C:0.19, G:0.29, T:0.20
Consensus pattern (25 bp):
GCTCATGCGAGCTGAATAACGGAAA
Found at i:452685 original size:25 final size:25
Alignment explanation
Indices: 452612--452692 Score: 92
Period size: 25 Copynumber: 3.2 Consensus size: 25
452602 ATTCATGTAT
* *
452612 GCTCATGCGAGCTGAATAACGGAAA
1 GCTCATGCGAGCTGAATAATGGGAA
* *
452637 GCTCATACGAGCTGAGT-ATCGGGAA
1 GCTCATGCGAGCTGAATAAT-GGGAA
*
452662 GCTCATGTGAGCTGAATAATGGGAA
1 GCTCATGCGAGCTGAATAATGGGAA
*
452687 GTTCAT
1 GCTCAT
452693 TTCAGCTGTG
Statistics
Matches: 46, Mismatches: 8, Indels: 4
0.79 0.14 0.07
Matches are distributed among these distances:
24 1 0.02
25 43 0.93
26 2 0.04
ACGTcount: A:0.31, C:0.17, G:0.30, T:0.22
Consensus pattern (25 bp):
GCTCATGCGAGCTGAATAATGGGAA
Found at i:461673 original size:21 final size:21
Alignment explanation
Indices: 461649--461692 Score: 88
Period size: 21 Copynumber: 2.1 Consensus size: 21
461639 GATTTAATAC
461649 ACGAGTTAGCTAAATTAAGTT
1 ACGAGTTAGCTAAATTAAGTT
461670 ACGAGTTAGCTAAATTAAGTT
1 ACGAGTTAGCTAAATTAAGTT
461691 AC
1 AC
461693 AACGATCTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.39, C:0.11, G:0.18, T:0.32
Consensus pattern (21 bp):
ACGAGTTAGCTAAATTAAGTT
Found at i:464918 original size:24 final size:25
Alignment explanation
Indices: 464877--464928 Score: 63
Period size: 24 Copynumber: 2.1 Consensus size: 25
464867 ATGATTTATC
* *
464877 TTTGTTTTTTTTGGAAAAA-CGGAA
1 TTTGTTTTTTTTGAAAAAATCAGAA
464901 TTTGTTTTGTTTT-AAAAAATCAGAA
1 TTTGTTTT-TTTTGAAAAAATCAGAA
464926 TTT
1 TTT
464929 AAAAATGACA
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
24 13 0.54
25 11 0.46
ACGTcount: A:0.31, C:0.04, G:0.15, T:0.50
Consensus pattern (25 bp):
TTTGTTTTTTTTGAAAAAATCAGAA
Found at i:464919 original size:25 final size:24
Alignment explanation
Indices: 464877--464928 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
464867 ATGATTTATC
** *
464877 TTTGTTTTTTTTGGAAAAACGGAA
1 TTTGTTTTTTTTAAAAAAACAGAA
*
464901 TTTGTTTTGTTTTAAAAAATCAGAA
1 TTTGTTTT-TTTTAAAAAAACAGAA
464926 TTT
1 TTT
464929 AAAAATGACA
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
24 8 0.35
25 15 0.65
ACGTcount: A:0.31, C:0.04, G:0.15, T:0.50
Consensus pattern (24 bp):
TTTGTTTTTTTTAAAAAAACAGAA
Found at i:464994 original size:155 final size:153
Alignment explanation
Indices: 464660--465174 Score: 641
Period size: 154 Copynumber: 3.3 Consensus size: 153
464650 ATCAGCGGCT
* * *
464660 GTGCTAATAACGCGAAGGTCGCAGGTTCGAAACCTAG-ATGGGCCACTAAATGCAACTTCCTTT-
1 GTGCTAATAACGCGAAGGTCGCAGGTTCGAAACCT-GCATGGGCCATTAAATG--ATTTACTTTG
* * * *
464723 ATTTTTTTGGGAAAACGGCAACGTTT-TATATT-ATTTATTAAAACAGAATTT-AGAATGAAAAT
63 TTTTTTTTGGAAAAACGG-AA--TTTGT-T-TTGATTTA-AAAAACAGAATTTAAAAATGAAAA-
*
464785 CAACGGCCTATTAGCTCAGCTGGTTAGAGCGTC
121 CAAAGGCCTATTAGCTCAGCTGGTTAGAGCGTC
464818 GTGCTAATAACGCGAAGGTCGCAGGTTCGAAACCTGCATGGGCCATTAAATGATTTATCTTTGTT
1 GTGCTAATAACGCGAAGGTCGCAGGTTCGAAACCTGCATGGGCCATTAAATGATTTA-CTTTGTT
* *
464883 TTTTTTGGAAAAACGGAATTTGTTTTGTTTTAAAAAATCAGAATTTAAAAATGACAACAAAGGCC
65 TTTTTTGGAAAAACGGAATTTGTTTTGATTTAAAAAA-CAGAATTTAAAAATGAAAACAAAGGCC
464948 TATTAGCTCAGCTGGTTAGAGCGTC
129 TATTAGCTCAGCTGGTTAGAGCGTC
* * * * *
464973 GTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCATGGGCCATT-AGTAATTCA-TTTGTAG
1 GTGCTAATAACGCGAAGGTCGCAGGTTCGAAACCTGCATGGGCCATTAAATGATTTACTTTGT-T
* * * *
465036 TTTTTTGGAAAAACGGAAATTGTTTTGCTTTAAAAAACA-AATTTTTAAAAACTGATAAGAAAGG
65 TTTTTTGGAAAAACGGAATTTGTTTTGATTTAAAAAACAGAA--TTTAAAAA-TGAAAACAAAGG
*
465100 CCTATTAGCTCAGTTGGTTAGAGCGTC
127 CCTATTAGCTCAGCTGGTTAGAGCGTC
*
465127 GTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTGCATGGGCCATTA
1 GTGCTAATAACGCGAAGGTCGCAGGTTCGAAACCTGCATGGGCCATTA
465175 GTATTTCATT
Statistics
Matches: 325, Mismatches: 20, Indels: 27
0.87 0.05 0.07
Matches are distributed among these distances:
151 2 0.01
152 7 0.02
153 43 0.13
154 95 0.29
155 94 0.29
156 12 0.04
157 7 0.02
158 65 0.20
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (153 bp):
GTGCTAATAACGCGAAGGTCGCAGGTTCGAAACCTGCATGGGCCATTAAATGATTTACTTTGTTT
TTTTTGGAAAAACGGAATTTGTTTTGATTTAAAAAACAGAATTTAAAAATGAAAACAAAGGCCTA
TTAGCTCAGCTGGTTAGAGCGTC
Found at i:465157 original size:154 final size:151
Alignment explanation
Indices: 464789--465262 Score: 650
Period size: 154 Copynumber: 3.1 Consensus size: 151
464779 GAAAATCAAC
*
464789 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAAACCTG
1 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTG
* * * * *
464854 CATGGGCCATTAAATGATTTATCTTTGTTTTTTTTGGAAAAACGGAATTTGTTTTGTTTTAAAAA
66 CATGGGCCATT-AGTAATTCA--TTTGTTTTTTTTGGAAAAACGGAAATTGTTTTGCTTTAAAAA
* *
464919 ATCAGAATTTAAAAA-TGACAACAAA
128 A-CA-AATTTAAAAACTGATAAGAAA
464944 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTG
1 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTG
*
465009 CATGGGCCATTAGTAATTCATTTGTAGTTTTTTGGAAAAACGGAAATTGTTTTGCTTTAAAAAAC
66 CATGGGCCATTAGTAATTCATTTGT-TTTTTTTGGAAAAACGGAAATTGTTTTGCTTTAAAAAAC
465074 AAATTTTTAAAAACTGATAAGAAA
130 AAA--TTTAAAAACTGATAAGAAA
*
465098 GGCCTATTAGCTCAGTTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTG
1 GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTG
* * * *
465163 CATGGGCCATTAGTATTTCATTTTTTTTTACTTTTCGG-AAAACGGCAA-CGTTTTTGCTTTAGA
66 CATGGGCCATTAGTAATTCA-TTTGTTTT--TTTT-GGAAAAACGGAAATTG-TTTTGCTTT--A
*
465226 AAAAACGAATTTAAAAACTGATAAG-AA
124 AAAAACAAATTTAAAAACTGATAAGAAA
465253 GGCCTATTAG
1 GGCCTATTAG
465263 GTGCTAATAA
Statistics
Matches: 292, Mismatches: 16, Indels: 22
0.88 0.05 0.07
Matches are distributed among these distances:
151 2 0.01
152 7 0.02
153 43 0.15
154 99 0.34
155 92 0.32
156 38 0.13
157 2 0.01
158 9 0.03
ACGTcount: A:0.31, C:0.16, G:0.22, T:0.31
Consensus pattern (151 bp):
GGCCTATTAGCTCAGCTGGTTAGAGCGTCGTGCTAATAACGCGAAGGTCGCAGGTTCGAGACCTG
CATGGGCCATTAGTAATTCATTTGTTTTTTTTGGAAAAACGGAAATTGTTTTGCTTTAAAAAACA
AATTTAAAAACTGATAAGAAA
Found at i:466889 original size:11 final size:11
Alignment explanation
Indices: 466873--466903 Score: 62
Period size: 11 Copynumber: 2.8 Consensus size: 11
466863 TATAGACAAC
466873 GCCGCTAAATT
1 GCCGCTAAATT
466884 GCCGCTAAATT
1 GCCGCTAAATT
466895 GCCGCTAAA
1 GCCGCTAAA
466904 AATCATGACC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.29, C:0.29, G:0.19, T:0.23
Consensus pattern (11 bp):
GCCGCTAAATT
Found at i:466956 original size:43 final size:43
Alignment explanation
Indices: 466895--467035 Score: 155
Period size: 43 Copynumber: 3.3 Consensus size: 43
466885 CCGCTAAATT
* *
466895 GCCGCTAAA-AATCATGACCTATAGCGGTGCTTTTATCACAAAC
1 GCCGCTAAAGAA-CATGACCTTTAGCGGCGCTTTTATCACAAAC
* * *
466938 GCCGCTAAAGACCATGACCTTTAGCGACACTTTTATCACAAAC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAAC
* * * **
466981 GCCGCTATAGAACA-AACCTTTAGCGGCGCTTCTCGCA-AAAC
1 GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAAC
467022 GCCGCTAAA-AACAT
1 GCCGCTAAAGAACAT
467036 AACATTTAAA
Statistics
Matches: 82, Mismatches: 14, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
40 4 0.05
41 12 0.15
42 17 0.21
43 48 0.59
44 1 0.01
ACGTcount: A:0.33, C:0.29, G:0.16, T:0.22
Consensus pattern (43 bp):
GCCGCTAAAGAACATGACCTTTAGCGGCGCTTTTATCACAAAC
Found at i:470790 original size:24 final size:24
Alignment explanation
Indices: 470758--470804 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
470748 CTAAATTTAG
*
470758 AACACTTTCCTTTC-CTTTCTCTTC
1 AACACTTTCC-ATCACTTTCTCTTC
*
470782 AACATTTTCCATCACTTTCTCTT
1 AACACTTTCCATCACTTTCTCTT
470805 ATTTCCCTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 2 0.10
24 18 0.90
ACGTcount: A:0.17, C:0.34, G:0.00, T:0.49
Consensus pattern (24 bp):
AACACTTTCCATCACTTTCTCTTC
Found at i:472349 original size:16 final size:16
Alignment explanation
Indices: 472328--472366 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
472318 AGCTTTCGTT
472328 TGACATTACAATTAGC
1 TGACATTACAATTAGC
472344 TGACATTACAATTAGC
1 TGACATTACAATTAGC
*
472360 TAACATT
1 TGACATT
472367 CTCATAACAT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.38, C:0.18, G:0.10, T:0.33
Consensus pattern (16 bp):
TGACATTACAATTAGC
Found at i:472517 original size:53 final size:53
Alignment explanation
Indices: 472444--472708 Score: 530
Period size: 53 Copynumber: 5.0 Consensus size: 53
472434 ATATATAGAA
472444 TATCCAGAAAAAAAATCATCGTGTTCATTTTGATTGTAATCGTCACATATAGG
1 TATCCAGAAAAAAAATCATCGTGTTCATTTTGATTGTAATCGTCACATATAGG
472497 TATCCAGAAAAAAAATCATCGTGTTCATTTTGATTGTAATCGTCACATATAGG
1 TATCCAGAAAAAAAATCATCGTGTTCATTTTGATTGTAATCGTCACATATAGG
472550 TATCCAGAAAAAAAATCATCGTGTTCATTTTGATTGTAATCGTCACATATAGG
1 TATCCAGAAAAAAAATCATCGTGTTCATTTTGATTGTAATCGTCACATATAGG
472603 TATCCAGAAAAAAAATCATCGTGTTCATTTTGATTGTAATCGTCACATATAGG
1 TATCCAGAAAAAAAATCATCGTGTTCATTTTGATTGTAATCGTCACATATAGG
472656 TATCCAGAAAAAAAATCATCGTGTTCATTTTGATTGTAATCGTCACATATAGG
1 TATCCAGAAAAAAAATCATCGTGTTCATTTTGATTGTAATCGTCACATATAGG
472709 CATCTTTACC
Statistics
Matches: 212, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
53 212 1.00
ACGTcount: A:0.36, C:0.15, G:0.15, T:0.34
Consensus pattern (53 bp):
TATCCAGAAAAAAAATCATCGTGTTCATTTTGATTGTAATCGTCACATATAGG
Found at i:472969 original size:49 final size:49
Alignment explanation
Indices: 472914--473014 Score: 132
Period size: 49 Copynumber: 2.1 Consensus size: 49
472904 CTCATTTTCT
* * * *
472914 CGATGCCATAGTCCAACTATGGTCTTACATGTAATCACATATCA-TATAC
1 CGATGCCATAGACCAACTATGGTCCTACACGGAATCACATATCACT-TAC
* *
472963 CGATGCCATAGACCAGCTATGGTCCTATACGGAATCACATATCACTTAC
1 CGATGCCATAGACCAACTATGGTCCTACACGGAATCACATATCACTTAC
473012 CGA
1 CGA
473015 AAGTACTCAT
Statistics
Matches: 45, Mismatches: 6, Indels: 2
0.85 0.11 0.04
Matches are distributed among these distances:
49 44 0.98
50 1 0.02
ACGTcount: A:0.32, C:0.27, G:0.15, T:0.27
Consensus pattern (49 bp):
CGATGCCATAGACCAACTATGGTCCTACACGGAATCACATATCACTTAC
Found at i:473881 original size:43 final size:39
Alignment explanation
Indices: 473817--473957 Score: 141
Period size: 33 Copynumber: 3.6 Consensus size: 39
473807 CACCGTGATT
473817 CGGGGAATCAGCACTTAGCAACCCCTTTCATATTCAATGATA
1 CGGGGAATCAGCACTTAGCAACCCCTTTCA-ATT-AA-GATA
* *
473859 CGGTGGAATCAGCACTTAGCAACCAC---CAA-TGA-AT-
1 CGG-GGAATCAGCACTTAGCAACCCCTTTCAATTAAGATA
473893 CGGGGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATA
1 CGGGGAATCAGCACTTAGCAACCCCTTTCA-A-TTAAGATA
* *
473934 CGGTGGGATTAGCACTTAGCAACC
1 CGG-GGAATCAGCACTTAGCAACC
473958 ACCAATGAAT
Statistics
Matches: 83, Mismatches: 6, Indels: 20
0.76 0.06 0.18
Matches are distributed among these distances:
33 21 0.25
34 3 0.04
35 2 0.02
36 2 0.02
37 2 0.02
38 1 0.01
39 3 0.04
40 4 0.05
41 3 0.04
42 21 0.25
43 21 0.25
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.23
Consensus pattern (39 bp):
CGGGGAATCAGCACTTAGCAACCCCTTTCAATTAAGATA
Found at i:473901 original size:33 final size:33
Alignment explanation
Indices: 473863--473990 Score: 114
Period size: 33 Copynumber: 3.6 Consensus size: 33
473853 ATGATACGGT
473863 GGAATCAGCACTTAGCAACCACCAATGAATCGG
1 GGAATCAGCACTTAGCAACCACCAATGAATCGG
* *
473896 GGAATCAGCACTTAGCAACCCCTTTCACATTTAAGATACGG
1 GGAATCAGCACTTAGCAACCAC---CA-A--TGA-AT-CGG
* * *
473937 TGGGATTAGCACTTAGCAACCACCAATGAATCGA
1 -GGAATCAGCACTTAGCAACCACCAATGAATCGG
473971 GGAATC-GACACTTAGCAACC
1 GGAATCAG-CACTTAGCAACC
473991 CTTTGGGGGA
Statistics
Matches: 76, Mismatches: 9, Indels: 20
0.72 0.09 0.19
Matches are distributed among these distances:
32 1 0.01
33 37 0.49
34 2 0.03
35 2 0.03
36 4 0.05
37 1 0.01
38 1 0.01
39 4 0.05
40 2 0.03
41 3 0.04
42 19 0.25
ACGTcount: A:0.34, C:0.27, G:0.20, T:0.20
Consensus pattern (33 bp):
GGAATCAGCACTTAGCAACCACCAATGAATCGG
Found at i:473909 original size:76 final size:75
Alignment explanation
Indices: 473783--473991 Score: 305
Period size: 75 Copynumber: 2.8 Consensus size: 75
473773 TATCCGTTAT
* * *
473783 CGGTGGATTCAGCACTTAAGCAACCACC-GTGATTCGGGGAATCAGCACTTAGCAACCCCTTTCA
1 CGGTGGAATCAGCACTT-AGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTTCA
*
473847 TATTCAATGATA
65 CATTCAA-GATA
473859 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTTCAC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTTCAC
*
473924 ATTTAAGATA
66 ATTCAAGATA
* * *
473934 CGGTGGGATTAGCACTTAGCAACCACCAATGAATCGAGGAATC-GACACTTAGCAACCC
1 CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAG-CACTTAGCAACCC
473992 TTTGGGGGAA
Statistics
Matches: 123, Mismatches: 8, Indels: 5
0.90 0.06 0.04
Matches are distributed among these distances:
74 1 0.01
75 67 0.54
76 55 0.45
ACGTcount: A:0.32, C:0.27, G:0.20, T:0.22
Consensus pattern (75 bp):
CGGTGGAATCAGCACTTAGCAACCACCAATGAATCGGGGAATCAGCACTTAGCAACCCCTTTCAC
ATTCAAGATA
Found at i:474121 original size:51 final size:50
Alignment explanation
Indices: 474043--474181 Score: 172
Period size: 50 Copynumber: 2.8 Consensus size: 50
474033 GATATCGGTT
*
474043 CACATAGTAGCCTGCACATAGTACTACACACGTGATCGAAGC-TATCCAGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGA-CCAAGCAT-TCCAGTA
* * * * * **
474094 CGCATAGTAGCCTGCACATAGTACTACACATGCGACCTATCATTCTGGTA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCAAGCATTCCAGTA
*
474144 CACGTAGTAGCCTGCACATAGTACTACACACGTGACCA
1 CACATAGTAGCCTGCACATAGTACTACACACGTGACCA
474182 TCACTTTCAC
Statistics
Matches: 74, Mismatches: 13, Indels: 3
0.82 0.14 0.03
Matches are distributed among these distances:
50 41 0.55
51 33 0.45
ACGTcount: A:0.31, C:0.29, G:0.18, T:0.22
Consensus pattern (50 bp):
CACATAGTAGCCTGCACATAGTACTACACACGTGACCAAGCATTCCAGTA
Found at i:476115 original size:26 final size:26
Alignment explanation
Indices: 476079--476129 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
476069 CATAATTTAC
476079 AATTACATTGCTTACACCGTTTCTTA
1 AATTACATTGCTTACACCGTTTCTTA
*
476105 AATTCCATTGCTTACACCGTTTCTT
1 AATTACATTGCTTACACCGTTTCTT
476130 CTATGAGAAA
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.24, C:0.25, G:0.08, T:0.43
Consensus pattern (26 bp):
AATTACATTGCTTACACCGTTTCTTA
Found at i:477760 original size:29 final size:29
Alignment explanation
Indices: 477723--477779 Score: 105
Period size: 29 Copynumber: 2.0 Consensus size: 29
477713 AACATGAAAC
477723 AACTAATCTATTAAGCAAGTCAGAAAATT
1 AACTAATCTATTAAGCAAGTCAGAAAATT
*
477752 AACTCATCTATTAAGCAAGTCAGAAAAT
1 AACTAATCTATTAAGCAAGTCAGAAAAT
477780 CAAAAGTTTC
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.47, C:0.16, G:0.11, T:0.26
Consensus pattern (29 bp):
AACTAATCTATTAAGCAAGTCAGAAAATT
Found at i:478422 original size:26 final size:26
Alignment explanation
Indices: 478386--478438 Score: 106
Period size: 26 Copynumber: 2.0 Consensus size: 26
478376 AAAACCACCC
478386 TTCACTTGTCCTTCTATAAATTAGAT
1 TTCACTTGTCCTTCTATAAATTAGAT
478412 TTCACTTGTCCTTCTATAAATTAGAT
1 TTCACTTGTCCTTCTATAAATTAGAT
478438 T
1 T
478439 ATCCAAAGCA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 27 1.00
ACGTcount: A:0.26, C:0.19, G:0.08, T:0.47
Consensus pattern (26 bp):
TTCACTTGTCCTTCTATAAATTAGAT
Found at i:479105 original size:15 final size:15
Alignment explanation
Indices: 479085--479119 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
479075 ATGACGAACC
479085 GCTCGTCTCAAGTTT
1 GCTCGTCTCAAGTTT
479100 GCTCGTCTCAAGTTT
1 GCTCGTCTCAAGTTT
479115 GCTCG
1 GCTCG
479120 AAAAGCCTCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.11, C:0.29, G:0.23, T:0.37
Consensus pattern (15 bp):
GCTCGTCTCAAGTTT
Found at i:479719 original size:41 final size:41
Alignment explanation
Indices: 479674--479792 Score: 157
Period size: 41 Copynumber: 2.9 Consensus size: 41
479664 TGCTCGACTT
* *
479674 TTAGCGACCCTTCTTCAAAAACGCCGCTAAAGCCCTGAGCA
1 TTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCTGAGCA
* **
479715 TTAGCGGCGATTCTTTTAAAACGCCGCTAAAGCCCTGAGCA
1 TTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCTGAGCA
* *
479756 TTAGCGGCGCTTTTTCAAAAAAACGCCACTAAAGCCC
1 TTAGCGGCGCTTCTTC--AAAAACGCCGCTAAAGCCC
479793 AAAAAACTCA
Statistics
Matches: 66, Mismatches: 10, Indels: 2
0.85 0.13 0.03
Matches are distributed among these distances:
41 49 0.74
43 17 0.26
ACGTcount: A:0.29, C:0.30, G:0.18, T:0.22
Consensus pattern (41 bp):
TTAGCGGCGCTTCTTCAAAAACGCCGCTAAAGCCCTGAGCA
Found at i:480402 original size:56 final size:58
Alignment explanation
Indices: 480323--480430 Score: 139
Period size: 56 Copynumber: 1.9 Consensus size: 58
480313 AATCAAATGA
* *
480323 AGAAATAGAAAACATTTGGAAATGATTAAGCTTTTCTCC-AAATAAAAATGAACATGG
1 AGAAATAGAAAACATTTGAAAATGAATAAGCTTTTCTCCAAAATAAAAATGAACATGG
* ** * *
480380 AGAAAT-GAAAATATTTGAAAATGAATGTGGTTTTCTCCAAAATGAAAATGA
1 AGAAATAGAAAACATTTGAAAATGAATAAGCTTTTCTCCAAAATAAAAATGA
480431 CAATGAAAAA
Statistics
Matches: 43, Mismatches: 7, Indels: 2
0.83 0.13 0.04
Matches are distributed among these distances:
56 26 0.60
57 17 0.40
ACGTcount: A:0.47, C:0.08, G:0.17, T:0.28
Consensus pattern (58 bp):
AGAAATAGAAAACATTTGAAAATGAATAAGCTTTTCTCCAAAATAAAAATGAACATGG
Found at i:480442 original size:56 final size:54
Alignment explanation
Indices: 480307--480444 Score: 132
Period size: 56 Copynumber: 2.4 Consensus size: 54
480297 AATGAATCGC
* * *
480307 ATAATAAATCAAATGAAGAAATAGAAAACATTTGGAAATGATTAAGCTTTTCTCCAA
1 ATAA-AAATGAAATGAA-AAAT-GAAAACATTTGAAAATGAATAAGCTTTTCTCCAA
* * ** *
480364 ATAAAAATGAACATGGAGAAATGAAAATATTTGAAAATGAATGTGGTTTTCTCCAAA
1 ATAAAAATGAA-AT-GAAAAATGAAAACATTTGAAAATGAATAAGCTTTTCTCC-AA
*
480421 ATGAAAATGACAATGAAAAATGAA
1 ATAAAAATGA-AATGAAAAATGAA
480445 TTTATATTTT
Statistics
Matches: 67, Mismatches: 10, Indels: 9
0.78 0.12 0.10
Matches are distributed among these distances:
56 41 0.61
57 23 0.34
58 3 0.04
ACGTcount: A:0.51, C:0.08, G:0.15, T:0.26
Consensus pattern (54 bp):
ATAAAAATGAAATGAAAAATGAAAACATTTGAAAATGAATAAGCTTTTCTCCAA
Found at i:481878 original size:10 final size:11
Alignment explanation
Indices: 481852--481877 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
481842 TTAAAAATAA
481852 AAAAATATTTT
1 AAAAATATTTT
481863 AAAAATATTTT
1 AAAAATATTTT
481874 AAAA
1 AAAA
481878 TTAAAAAATT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:481891 original size:7 final size:8
Alignment explanation
Indices: 481874--481902 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
481864 AAAATATTTT
481874 AAAATTAA
1 AAAATTAA
481882 AAAATTAA
1 AAAATTAA
481890 AAAATTAA
1 AAAATTAA
481898 AAAAT
1 AAAAT
481903 ATTTATTATA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAATTAA
Found at i:485503 original size:22 final size:22
Alignment explanation
Indices: 485478--485520 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
485468 TATCCAAACA
485478 ATAACAATAAAATAGTAGCAAC
1 ATAACAATAAAATAGTAGCAAC
* * *
485500 ATAATAGTGAAATAGTAGCAA
1 ATAACAATAAAATAGTAGCAA
485521 AACAGTGAGA
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.56, C:0.09, G:0.14, T:0.21
Consensus pattern (22 bp):
ATAACAATAAAATAGTAGCAAC
Found at i:488423 original size:10 final size:10
Alignment explanation
Indices: 488418--488474 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
488408 TTAAAAATTC
488418 AAAAAATTTA
1 AAAAAATTTA
* *
488428 TAAAATTTATA
1 AAAAAATT-TA
488439 AAAAAATTTA
1 AAAAAATTTA
*
488449 AAAAAACATTA
1 AAAAAA-TTTA
**
488460 AAATGATTTA
1 AAAAAATTTA
488470 AAAAA
1 AAAAA
488475 TATAAACAAA
Statistics
Matches: 35, Mismatches: 10, Indels: 4
0.71 0.20 0.08
Matches are distributed among these distances:
10 20 0.57
11 15 0.43
ACGTcount: A:0.67, C:0.02, G:0.02, T:0.30
Consensus pattern (10 bp):
AAAAAATTTA
Found at i:488432 original size:9 final size:9
Alignment explanation
Indices: 488402--488441 Score: 55
Period size: 9 Copynumber: 4.6 Consensus size: 9
488392 ATTAATTTTT
488402 TAAAATTTA
1 TAAAATTTA
*
488411 -AAAATTCA
1 TAAAATTTA
*
488419 AAAAATTTA
1 TAAAATTTA
488428 TAAAATTTA
1 TAAAATTTA
488437 TAAAA
1 TAAAA
488442 AAATTTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
8 7 0.26
9 20 0.74
ACGTcount: A:0.62, C:0.03, G:0.00, T:0.35
Consensus pattern (9 bp):
TAAAATTTA
Found at i:488451 original size:9 final size:9
Alignment explanation
Indices: 488403--488453 Score: 50
Period size: 9 Copynumber: 5.4 Consensus size: 9
488393 TTAATTTTTT
488403 AAAATTT-A
1 AAAATTTAA
*
488411 AAAATTCAA
1 AAAATTTAA
488420 AAAATTTATA
1 AAAATTTA-A
*
488430 AAATTTATAAA
1 AAAATT-T-AA
488441 AAAATTTAA
1 AAAATTTAA
488450 AAAA
1 AAAA
488454 ACATTAAAAT
Statistics
Matches: 35, Mismatches: 4, Indels: 7
0.76 0.09 0.15
Matches are distributed among these distances:
8 6 0.17
9 14 0.40
10 7 0.20
11 7 0.20
12 1 0.03
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (9 bp):
AAAATTTAA
Found at i:490010 original size:23 final size:24
Alignment explanation
Indices: 489959--490011 Score: 60
Period size: 23 Copynumber: 2.3 Consensus size: 24
489949 TAAATTTTAT
489959 TTGATAAATGTTTTGATATAATAAA
1 TTGAT-AATGTTTTGATATAATAAA
489984 --GATAATGTTTTTGA-ATAA-AAA
1 TTGATAATG-TTTTGATATAATAAA
490005 TTGATAA
1 TTGATAA
490012 ATTTCAAGTG
Statistics
Matches: 25, Mismatches: 0, Indels: 8
0.76 0.00 0.24
Matches are distributed among these distances:
21 3 0.12
22 8 0.32
23 14 0.56
ACGTcount: A:0.45, C:0.00, G:0.13, T:0.42
Consensus pattern (24 bp):
TTGATAATGTTTTGATATAATAAA
Found at i:491770 original size:8 final size:8
Alignment explanation
Indices: 491757--491791 Score: 52
Period size: 8 Copynumber: 4.1 Consensus size: 8
491747 AAAAAATCGT
491757 AATAATAA
1 AATAATAA
491765 AATAATAA
1 AATAATAA
491773 AATAATAA
1 AATAATAA
491781 GAGATAATAA
1 -A-ATAATAA
491791 A
1 A
491792 CACAATATTA
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
8 16 0.64
9 2 0.08
10 7 0.28
ACGTcount: A:0.71, C:0.00, G:0.06, T:0.23
Consensus pattern (8 bp):
AATAATAA
Found at i:500659 original size:14 final size:14
Alignment explanation
Indices: 500636--500675 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
500626 ACAGAAAAGT
*
500636 AAAACATTTTTCAG
1 AAAACATTTTACAG
* *
500650 AAATCATTTTACGG
1 AAAACATTTTACAG
500664 AAAACATTTTAC
1 AAAACATTTTAC
500676 TGGCAATCAA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.42, C:0.15, G:0.07, T:0.35
Consensus pattern (14 bp):
AAAACATTTTACAG
Found at i:500659 original size:34 final size:35
Alignment explanation
Indices: 500601--500667 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
500591 CAAACACCAG
* *
500601 AAAATATTTTCCAGTAAATTATTTTACAGAAAAGT
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAAGT
* *
500636 AAAACATTTTTCAG-AAATCATTTTACGGAAAA
1 AAAACATTTTCCAGTAAATCATTTTACAGAAAA
500668 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:504585 original size:24 final size:24
Alignment explanation
Indices: 504535--504585 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
504525 TTTAAATATG
*
504535 AAAGGATGTTTTAGTAATTTTATT
1 AAAGGATGTTTTAGTAATTTTACT
*
504559 AAAGGATGTTTTAGTAATTTTCCT
1 AAAGGATGTTTTAGTAATTTTACT
504583 AAA
1 AAA
504586 TAAGTTTAAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.35, C:0.04, G:0.16, T:0.45
Consensus pattern (24 bp):
AAAGGATGTTTTAGTAATTTTACT
Found at i:506763 original size:45 final size:45
Alignment explanation
Indices: 506712--506799 Score: 167
Period size: 45 Copynumber: 2.0 Consensus size: 45
506702 GACTTTGTCT
506712 CTTTGACCTTTTATGACTCAAAATTATCACTGAAAACATATTGTA
1 CTTTGACCTTTTATGACTCAAAATTATCACTGAAAACATATTGTA
*
506757 CTTTGACCTTTTGTGACTCAAAATTATCACTGAAAACATATTG
1 CTTTGACCTTTTATGACTCAAAATTATCACTGAAAACATATTG
506800 CATTAGAGGT
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 42 1.00
ACGTcount: A:0.34, C:0.18, G:0.10, T:0.38
Consensus pattern (45 bp):
CTTTGACCTTTTATGACTCAAAATTATCACTGAAAACATATTGTA
Found at i:510575 original size:41 final size:42
Alignment explanation
Indices: 510491--510576 Score: 102
Period size: 41 Copynumber: 2.1 Consensus size: 42
510481 TTTCATAATT
* * * * * *
510491 AAAACAGAGCCCAAAAAATTGAAGAGACCCAACGCACACGGA
1 AAAACAGAGCCCAAAAAACTAAACAGACCCAAAGAACAAGGA
*
510533 AAAACAGAGCCC-AAAAACTAAACAGGCCCAAAGAACAAGGA
1 AAAACAGAGCCCAAAAAACTAAACAGACCCAAAGAACAAGGA
510574 AAA
1 AAA
510577 GTCCAAACAA
Statistics
Matches: 37, Mismatches: 7, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
41 25 0.68
42 12 0.32
ACGTcount: A:0.55, C:0.24, G:0.17, T:0.03
Consensus pattern (42 bp):
AAAACAGAGCCCAAAAAACTAAACAGACCCAAAGAACAAGGA
Found at i:516795 original size:12 final size:12
Alignment explanation
Indices: 516771--516808 Score: 51
Period size: 12 Copynumber: 3.2 Consensus size: 12
516761 ATTAAAATGG
516771 AAGAAAAAGTTAA
1 AAGAAAAA-TTAA
*
516784 ATGAAAAATTAA
1 AAGAAAAATTAA
516796 AAGAAAAA-TAA
1 AAGAAAAATTAA
516807 AA
1 AA
516809 CGTCGTCGTA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
11 5 0.22
12 11 0.48
13 7 0.30
ACGTcount: A:0.74, C:0.00, G:0.11, T:0.16
Consensus pattern (12 bp):
AAGAAAAATTAA
Found at i:524640 original size:3 final size:3
Alignment explanation
Indices: 524632--524665 Score: 68
Period size: 3 Copynumber: 11.3 Consensus size: 3
524622 ATCCATCACA
524632 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT A
524666 CAATTTCCTT
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:525709 original size:15 final size:15
Alignment explanation
Indices: 525689--525740 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 15
525679 ACTACAAGAC
525689 ATTTATTATTAATAT
1 ATTTATTATTAATAT
*
525704 ATTTATAATTGTAATAAAT
1 ATTTATTA-T-TAAT--AT
*
525723 ATTTATTATTAAAAT
1 ATTTATTATTAATAT
525738 ATT
1 ATT
525741 AATATTGAAT
Statistics
Matches: 30, Mismatches: 3, Indels: 8
0.73 0.07 0.20
Matches are distributed among these distances:
15 12 0.40
16 1 0.03
17 7 0.23
18 1 0.03
19 9 0.30
ACGTcount: A:0.44, C:0.00, G:0.02, T:0.54
Consensus pattern (15 bp):
ATTTATTATTAATAT
Found at i:535447 original size:171 final size:166
Alignment explanation
Indices: 534672--535581 Score: 1389
Period size: 167 Copynumber: 5.5 Consensus size: 166
534662 CGTTACGATT
534672 TGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGACGCTCTAACCAGCTGAGC
1 TGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGACGCTCTAACCAGCTGAGC
* *** * * * ** * * *
534737 TAATAGGCCGTTGATATTCTAACCTAAATTCTGTTCTGCTAAATAC--TAACATGTTGCGGTGTT
66 TAATAGGCCGTTGATACTCCCGCTTAAATTTTGTTTTAATAAATACTGTAACAGGTTGCCGTTTT
* *
534800 CCAAAAAACAAAAAATAAAG--GAAAAAGCCACTAA
131 CCAAAAAACAAAAAATAAAGAAAAAAAAGCCATTAA
534834 TGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGACGCTCTAACCAGCTGAGC
1 TGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGACGCTCTAACCAGCTGAGC
* * * * * *
534899 TAATAGGCCGCTGATATTCCCGCTAAAATTCTATTTTAATAAATACTGTAACAGGTTGACGTTTT
66 TAATAGGCCGTTGATACTCCCGCTTAAATTTTGTTTTAATAAATACTGTAACAGGTTGCCGTTTT
534964 CCAAAAAACAAAAAATAAAGCAAAAAAAAGCCATTAA
131 CCAAAAAACAAAAAATAAAG-AAAAAAAAGCCATTAA
535001 TGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGACGCTCTAACCAGCTGAGC
1 TGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGACGCTCTAACCAGCTGAGC
* * * * * *
535066 TAATAGGCCGTCGATACTGCTGTTTAAATTTTGTTTAAATAAATACTGTAACAGGTTGACGTTTT
66 TAATAGGCCGTTGATACTCCCGCTTAAATTTTGTTTTAATAAATACTGTAACAGGTTGCCGTTTT
535131 CCAAAAAACAAAAAATAAAGACAAAAAAAGCCATTAA
131 CCAAAAAACAAAAAATAAAGA-AAAAAAAGCCATTAA
*
535168 TGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACAACGCTCTAACCAGCTGAGC
1 TGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGACGCTCTAACCAGCTGAGC
* * * **
535233 TAATAGGCCGTCGATACTGCTGCTTAAATTTTGTTGAAATAAATACTGTAACAGGTTGCCGTTTT
66 TAATAGGCCGTTGATACTCCCGCTTAAATTTTGTTTTAATAAATACTGTAACAGGTTGCCGTTTT
535298 CCAAAAAACAAAAAATAAAGAAAAAAAAGCCATTAAA
131 CCAAAAAACAAAAAATAAAGAAAAAAAAGCCATT-AA
535335 TGGCCCATGCAGGTCTCGAACCGACCTGCGACCTTCGCGTTATTAGCACGACGCTCTAACCAGCT
1 TGGCCCATGCAGGTCTCG-A---ACCTGCGACCTTCGCGTTATTAGCACGACGCTCTAACCAGCT
* *
535400 GAGCTAATAGGCCGTTGATACTCCCGCTTAAATTTTGTTTTAATAAATACTATAACAGGTTTCCG
62 GAGCTAATAGGCCGTTGATACTCCCGCTTAAATTTTGTTTTAATAAATACTGTAACAGGTTGCCG
*
535465 TTTTCCAAAAAACAAAAAATAAAGAAAAAATA-CCATTAA
127 TTTTCCAAAAAACAAAAAATAAAGAAAAAAAAGCCATTAA
* *
535504 TGGCCCATGCAGGTTTCGAACCTGTGACCTTCGCGTTATTAGCACGACGCTCTAACCAGCTGAGC
1 TGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGACGCTCTAACCAGCTGAGC
535569 TAATAGGCCGTTG
66 TAATAGGCCGTTG
535582 TGTACCCTTG
Statistics
Matches: 696, Mismatches: 41, Indels: 19
0.92 0.05 0.03
Matches are distributed among these distances:
162 101 0.15
164 33 0.05
165 58 0.08
166 14 0.02
167 334 0.48
168 2 0.00
169 19 0.03
170 5 0.01
171 130 0.19
ACGTcount: A:0.33, C:0.23, G:0.18, T:0.25
Consensus pattern (166 bp):
TGGCCCATGCAGGTCTCGAACCTGCGACCTTCGCGTTATTAGCACGACGCTCTAACCAGCTGAGC
TAATAGGCCGTTGATACTCCCGCTTAAATTTTGTTTTAATAAATACTGTAACAGGTTGCCGTTTT
CCAAAAAACAAAAAATAAAGAAAAAAAAGCCATTAA
Found at i:540908 original size:2 final size:2
Alignment explanation
Indices: 540903--540932 Score: 51
Period size: 2 Copynumber: 15.0 Consensus size: 2
540893 ATATATATAT
*
540903 AG AG AG AG AG AG AG AG AG TG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG
540933 TAAAATTAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.47, C:0.00, G:0.50, T:0.03
Consensus pattern (2 bp):
AG
Found at i:541219 original size:31 final size:29
Alignment explanation
Indices: 541184--541248 Score: 76
Period size: 29 Copynumber: 2.2 Consensus size: 29
541174 CTTAAAATTT
* * *
541184 TACATAAATTTTAGTTTAATGTGTAATTGTA
1 TACATAAATTTTAATTT--GGTGTAATTATA
*
541215 TACATGAATTTTAATTTGGTGTAATTATA
1 TACATAAATTTTAATTTGGTGTAATTATA
541244 TACAT
1 TACAT
541249 GAAACTTTGA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
29 15 0.50
31 15 0.50
ACGTcount: A:0.35, C:0.05, G:0.12, T:0.48
Consensus pattern (29 bp):
TACATAAATTTTAATTTGGTGTAATTATA
Found at i:546132 original size:48 final size:50
Alignment explanation
Indices: 546072--546176 Score: 151
Period size: 50 Copynumber: 2.1 Consensus size: 50
546062 TTATATCGTA
** **
546072 ATAAATTTAAATTTAAC-AAAATTTTTTTATATATA-ACAAAAAAATTAC
1 ATAAATTTAAATTTAACAAAAAAATTTAAATATATATACAAAAAAATTAC
*
546120 ATAAATTTAAATTTAACAAAAAAATTTAAATATATATATAAAAAAATTAC
1 ATAAATTTAAATTTAACAAAAAAATTTAAATATATATACAAAAAAATTAC
546170 ATAAATT
1 ATAAATT
546177 ATATGTTCAA
Statistics
Matches: 50, Mismatches: 5, Indels: 2
0.88 0.09 0.04
Matches are distributed among these distances:
48 17 0.34
49 14 0.28
50 19 0.38
ACGTcount: A:0.58, C:0.05, G:0.00, T:0.37
Consensus pattern (50 bp):
ATAAATTTAAATTTAACAAAAAAATTTAAATATATATACAAAAAAATTAC
Found at i:546179 original size:22 final size:22
Alignment explanation
Indices: 546137--546180 Score: 54
Period size: 22 Copynumber: 2.0 Consensus size: 22
546127 TAAATTTAAC
*
546137 AAAAAAATTTAAATATATATAT
1 AAAAAAATTTAAATAAATATAT
*
546159 AAAAAAA-TTACATAAATTATAT
1 AAAAAAATTTAAATAAA-TATAT
546181 GTTCAAAGTC
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
21 7 0.37
22 12 0.63
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (22 bp):
AAAAAAATTTAAATAAATATAT
Found at i:546312 original size:21 final size:21
Alignment explanation
Indices: 546288--546330 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
546278 TCGTAATAAA
*
546288 TTTAAATTTAACAAAAAAAAT
1 TTTAAATATAACAAAAAAAAT
*
546309 TTTATATATAACAAAAAAAAT
1 TTTAAATATAACAAAAAAAAT
546330 T
1 T
546331 ACATAAATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.60, C:0.05, G:0.00, T:0.35
Consensus pattern (21 bp):
TTTAAATATAACAAAAAAAAT
Found at i:546534 original size:22 final size:22
Alignment explanation
Indices: 546506--546559 Score: 58
Period size: 22 Copynumber: 2.4 Consensus size: 22
546496 ATATACATAG
*
546506 GAAAAATATG-GAATAAAATTTT
1 GAAAAATATGTGAA-AAAATATT
546528 GAAAAATTATGTTGAAAAAATATT
1 GAAAAA-TATG-TGAAAAAATATT
546552 -AAAAATAT
1 GAAAAATAT
546560 ATATAATAGT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
22 9 0.32
23 9 0.32
24 7 0.25
25 3 0.11
ACGTcount: A:0.57, C:0.00, G:0.11, T:0.31
Consensus pattern (22 bp):
GAAAAATATGTGAAAAAATATT
Found at i:546655 original size:19 final size:19
Alignment explanation
Indices: 546616--546656 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 19
546606 TTGAAATATC
*
546616 TTTATTATAAAAACATCAT
1 TTTATTATAAAAACATAAT
* *
546635 TTTATTATAAATACCTAAT
1 TTTATTATAAAAACATAAT
546654 TTT
1 TTT
546657 TTTAAATGTA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.41, C:0.10, G:0.00, T:0.49
Consensus pattern (19 bp):
TTTATTATAAAAACATAAT
Found at i:574062 original size:161 final size:161
Alignment explanation
Indices: 573797--574118 Score: 644
Period size: 161 Copynumber: 2.0 Consensus size: 161
573787 GTCGAATTTT
573797 TCAACCTTACCTAGATAGATTTGTGGTTGTATTTATTGATGATATACTAATCTATTCCAAGATAG
1 TCAACCTTACCTAGATAGATTTGTGGTTGTATTTATTGATGATATACTAATCTATTCCAAGATAG
573862 AAACCGAGCATGTACAGCACTTGAGAATTGTGCTACAAATCTTGAGGGAGAAACAGTTGTATGCA
66 AAACCGAGCATGTACAGCACTTGAGAATTGTGCTACAAATCTTGAGGGAGAAACAGTTGTATGCA
573927 AAGTTTAGTAAATGTGAATTCTGGCTTCATG
131 AAGTTTAGTAAATGTGAATTCTGGCTTCATG
573958 TCAACCTTACCTAGATAGATTTGTGGTTGTATTTATTGATGATATACTAATCTATTCCAAGATAG
1 TCAACCTTACCTAGATAGATTTGTGGTTGTATTTATTGATGATATACTAATCTATTCCAAGATAG
574023 AAACCGAGCATGTACAGCACTTGAGAATTGTGCTACAAATCTTGAGGGAGAAACAGTTGTATGCA
66 AAACCGAGCATGTACAGCACTTGAGAATTGTGCTACAAATCTTGAGGGAGAAACAGTTGTATGCA
574088 AAGTTTAGTAAATGTGAATTCTGGCTTCATG
131 AAGTTTAGTAAATGTGAATTCTGGCTTCATG
574119 AGGTCAAATT
Statistics
Matches: 161, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
161 161 1.00
ACGTcount: A:0.32, C:0.14, G:0.20, T:0.33
Consensus pattern (161 bp):
TCAACCTTACCTAGATAGATTTGTGGTTGTATTTATTGATGATATACTAATCTATTCCAAGATAG
AAACCGAGCATGTACAGCACTTGAGAATTGTGCTACAAATCTTGAGGGAGAAACAGTTGTATGCA
AAGTTTAGTAAATGTGAATTCTGGCTTCATG
Found at i:574642 original size:12 final size:12
Alignment explanation
Indices: 574625--574649 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
574615 TTTACAAATC
574625 ACAAAAGTTTGA
1 ACAAAAGTTTGA
574637 ACAAAAGTTTGA
1 ACAAAAGTTTGA
574649 A
1 A
574650 ATACTTGATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.52, C:0.08, G:0.16, T:0.24
Consensus pattern (12 bp):
ACAAAAGTTTGA
Found at i:577524 original size:25 final size:25
Alignment explanation
Indices: 577496--577545 Score: 82
Period size: 25 Copynumber: 2.0 Consensus size: 25
577486 GGAGAAAATG
577496 TATGATTTATTTACAATTAAATTTA
1 TATGATTTATTTACAATTAAATTTA
* *
577521 TATGATTTATTTATAATTTAATTTA
1 TATGATTTATTTACAATTAAATTTA
577546 ATTTATTATA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.38, C:0.02, G:0.04, T:0.56
Consensus pattern (25 bp):
TATGATTTATTTACAATTAAATTTA
Found at i:594397 original size:29 final size:29
Alignment explanation
Indices: 594353--594972 Score: 896
Period size: 29 Copynumber: 21.9 Consensus size: 29
594343 GTAAAAAAAT
*
594353 CCTAATTTAATTAAAAACCCTAAACACTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
*
594383 CCTAATTTAATAAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
* *
594412 CCTAATTTAATAAAAAACTCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
* *
594441 CTTAATTTAATTAAAAACCATAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
594470 CCTAATTTAATTAAAAACCCTAACCTTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
* *
594499 CTTAATTTAATTAAAAACCCTAATCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
594528 CATAATTTAATT--AAA----AACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
594551 CCTAATTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
594580 CCTAACTTAATTAAAAACCCTAACCCT-A
1 CCTAATTTAATTAAAAACCCTAACCCTAA
594608 --T--TTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
594633 CCTATTTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
594662 CCTATTTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
594691 CCTATTTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
594720 CCTATTTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
594749 CCTATTTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
594778 CCTATTTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
594807 CCTATTTTAATTAAAAACCCTAACCCTAA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
594836 CCTAATTTAATTAAAAACCATAAACCCTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
*
594866 CTTAATTTAATTAAAAACCCTAA--C-AA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
594892 CCTAATTTAATTAAAAACCCTAA--C-AA
1 CCTAATTTAATTAAAAACCCTAACCCTAA
*
594918 CTTAATTTAATTAAAAACCCTAAACCCTAA
1 CCTAATTTAATTAAAAACCCT-AACCCTAA
*
594948 CTTAATTTAATTAAAAACCCTAACC
1 CCTAATTTAATTAAAAACCCTAACC
594973 ATTAACAAAA
Statistics
Matches: 550, Mismatches: 24, Indels: 33
0.91 0.04 0.05
Matches are distributed among these distances:
23 18 0.03
24 21 0.04
25 4 0.01
26 48 0.09
27 7 0.01
28 1 0.00
29 381 0.69
30 70 0.13
ACGTcount: A:0.45, C:0.25, G:0.00, T:0.30
Consensus pattern (29 bp):
CCTAATTTAATTAAAAACCCTAACCCTAA
Found at i:594897 original size:26 final size:26
Alignment explanation
Indices: 594864--594971 Score: 171
Period size: 26 Copynumber: 4.0 Consensus size: 26
594854 CATAAACCCT
594864 AACTTAATTTAATTAAAAACCCTAAC
1 AACTTAATTTAATTAAAAACCCTAAC
*
594890 AACCTAATTTAATTAAAAACCCTAAC
1 AACTTAATTTAATTAAAAACCCTAAC
594916 AACTTAATTTAATTAAAAACCCTAAACCC
1 AACTTAATTTAATTAAAAACCCT-AA--C
594945 TAACTTAATTTAATTAAAAACCCTAAC
1 -AACTTAATTTAATTAAAAACCCTAAC
594972 CATTAACAAA
Statistics
Matches: 76, Mismatches: 2, Indels: 7
0.89 0.02 0.08
Matches are distributed among these distances:
26 47 0.62
27 3 0.04
29 3 0.04
30 23 0.30
ACGTcount: A:0.49, C:0.21, G:0.00, T:0.30
Consensus pattern (26 bp):
AACTTAATTTAATTAAAAACCCTAAC
Found at i:598375 original size:124 final size:124
Alignment explanation
Indices: 598169--598448 Score: 508
Period size: 124 Copynumber: 2.3 Consensus size: 124
598159 CCACGAGGGC
*
598169 GCGATTTTATACTATTTGCTCAAAAACGTCAAAAAAAATTATTTCTTACATGACCAACTATAGCG
1 GCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCAACTATAGCG
*
598234 AAATTGCGTCCACGAGGGCACGATTTCACTATTCCTTCTCAAATAGCATCCTGGTAGAA
66 AAATCGCGTCCACGAGGGCACGATTTCACTATTCCTTCTCAAATAGCATCCTGGTAGAA
*
598293 GCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCAACTGTAGCG
1 GCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCAACTATAGCG
598358 AAATCGCGTCCACGAGGGCACGATTTCACTATTCCTTCTCAAATAGCATCCTGGTAGAA
66 AAATCGCGTCCACGAGGGCACGATTTCACTATTCCTTCTCAAATAGCATCCTGGTAGAA
*
598417 GCGATTTTATACTATTTGAC-CAGAAACATCAA
1 GCGATTTTATACTATTTG-CTCAGAAACGTCAA
598449 CTCGAAATAA
Statistics
Matches: 151, Mismatches: 4, Indels: 2
0.96 0.03 0.01
Matches are distributed among these distances:
124 150 0.99
125 1 0.01
ACGTcount: A:0.34, C:0.22, G:0.15, T:0.30
Consensus pattern (124 bp):
GCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTACATGACCAACTATAGCG
AAATCGCGTCCACGAGGGCACGATTTCACTATTCCTTCTCAAATAGCATCCTGGTAGAA
Found at i:599039 original size:14 final size:14
Alignment explanation
Indices: 598997--599046 Score: 50
Period size: 14 Copynumber: 3.6 Consensus size: 14
598987 CTAAACTTCA
598997 ATTATAATAA-ATTT
1 ATTA-AATAATATTT
*
599011 ATTAAA-ACTACTTT
1 ATTAAATAATA-TTT
599025 ATTAAATAATATTT
1 ATTAAATAATATTT
*
599039 AATAAATA
1 ATTAAATA
599047 TTATGATATA
Statistics
Matches: 30, Mismatches: 3, Indels: 6
0.77 0.08 0.15
Matches are distributed among these distances:
12 1 0.03
13 3 0.10
14 23 0.77
15 3 0.10
ACGTcount: A:0.52, C:0.04, G:0.00, T:0.44
Consensus pattern (14 bp):
ATTAAATAATATTT
Found at i:602837 original size:24 final size:24
Alignment explanation
Indices: 602806--602918 Score: 79
Period size: 24 Copynumber: 4.6 Consensus size: 24
602796 CAATTGTCAA
* * *
602806 GAAGCTCATACGAGCCGTAAACGG
1 GAAGCTCATAAGAGCCATAAACAG
*
602830 GAAGCTCA-AGAGAGCCATTAACAG
1 GAAGCTCATA-AGAGCCATAAACAG
602854 GAAGCTCATAAGAGCCA-AATATC-G
1 GAAGCTCATAAGAGCCATAA-A-CAG
* * *
602878 AGAAGCTCGTGAGAACCATATAACAG
1 -GAAGCTCATAAGAGCCATA-AACAG
* *
602904 GATGCTTATAAGAGC
1 GAAGCTCATAAGAGC
602919 TAAATAACAG
Statistics
Matches: 68, Mismatches: 13, Indels: 15
0.71 0.14 0.16
Matches are distributed among these distances:
23 2 0.03
24 35 0.51
25 27 0.40
26 3 0.04
27 1 0.01
ACGTcount: A:0.39, C:0.20, G:0.25, T:0.16
Consensus pattern (24 bp):
GAAGCTCATAAGAGCCATAAACAG
Found at i:602883 original size:49 final size:50
Alignment explanation
Indices: 602830--602924 Score: 129
Period size: 50 Copynumber: 1.9 Consensus size: 50
602820 CCGTAAACGG
*
602830 GAAGCTCAAGAGAGCCAT-TAACAGGAAGCTCATAAGAGCCAAATATCGA
1 GAAGCTCAAGAGAACCATATAACAGGAAGCTCATAAGAGCCAAATATCGA
** * * *
602879 GAAGCTCGTGAGAACCATATAACAGGATGCTTATAAGAGCTAAATA
1 GAAGCTCAAGAGAACCATATAACAGGAAGCTCATAAGAGCCAAATA
602925 ACAGGACACT
Statistics
Matches: 39, Mismatches: 6, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
49 15 0.38
50 24 0.62
ACGTcount: A:0.42, C:0.18, G:0.22, T:0.18
Consensus pattern (50 bp):
GAAGCTCAAGAGAACCATATAACAGGAAGCTCATAAGAGCCAAATATCGA
Found at i:607361 original size:20 final size:19
Alignment explanation
Indices: 607311--607361 Score: 57
Period size: 21 Copynumber: 2.5 Consensus size: 19
607301 AATGTTTGTT
*
607311 CTTTCTTCTTCTTCTTTTTG
1 CTTTCTT-TTCTTCTTTTAG
*
607331 CTTCTCCTTTCTTTCTTTTAG
1 CTT-TCTTTTC-TTCTTTTAG
607352 CTTTCTTTTC
1 CTTTCTTTTC
607362 CTTTAATCTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
20 12 0.46
21 14 0.54
ACGTcount: A:0.02, C:0.27, G:0.04, T:0.67
Consensus pattern (19 bp):
CTTTCTTTTCTTCTTTTAG
Found at i:608195 original size:90 final size:91
Alignment explanation
Indices: 608067--608247 Score: 355
Period size: 90 Copynumber: 2.0 Consensus size: 91
608057 AAGATAGTTT
608067 TGGTGGTGTATGTTTTTTTTTATATATTGTAATAATAATTTGTATATTTTAATAATAAGATATAA
1 TGGTGGTGTATGTTTTTTTTTATATATTGTAATAATAATTTGTATATTTTAATAATAAGATATAA
608132 TTTATATTTTTCAAAAAAATATATAA
66 TTTATATTTTTCAAAAAAATATATAA
608158 TGGTGGTGTA-GTTTTTTTTTATATATTGTAATAATAATTTGTATATTTTAATAATAAGATATAA
1 TGGTGGTGTATGTTTTTTTTTATATATTGTAATAATAATTTGTATATTTTAATAATAAGATATAA
608222 TTTATATTTTTCAAAAAAATATATAA
66 TTTATATTTTTCAAAAAAATATATAA
608248 AAAGTTAATT
Statistics
Matches: 90, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
90 80 0.89
91 10 0.11
ACGTcount: A:0.39, C:0.01, G:0.10, T:0.50
Consensus pattern (91 bp):
TGGTGGTGTATGTTTTTTTTTATATATTGTAATAATAATTTGTATATTTTAATAATAAGATATAA
TTTATATTTTTCAAAAAAATATATAA
Found at i:610573 original size:3 final size:3
Alignment explanation
Indices: 610567--610592 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
610557 CCTCCTCCTA
610567 TTG TTG TTG TTG TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TTG TTG TTG TTG TT
610593 ATAACCAATG
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:0.00, C:0.00, G:0.31, T:0.69
Consensus pattern (3 bp):
TTG
Found at i:611179 original size:19 final size:19
Alignment explanation
Indices: 611138--611177 Score: 53
Period size: 20 Copynumber: 2.1 Consensus size: 19
611128 TATATATATG
* *
611138 TTATGTGTTGTTTGTAATT
1 TTATGTGTTATTTATAATT
611157 TTATGTGTTTATTTATAATT
1 TTATGTG-TTATTTATAATT
611177 T
1 T
611178 ATTAAATAAT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 7 0.39
20 11 0.61
ACGTcount: A:0.20, C:0.00, G:0.15, T:0.65
Consensus pattern (19 bp):
TTATGTGTTATTTATAATT
Found at i:612867 original size:6 final size:6
Alignment explanation
Indices: 612856--612885 Score: 60
Period size: 6 Copynumber: 5.0 Consensus size: 6
612846 ATATTTTTTG
612856 AAAATA AAAATA AAAATA AAAATA AAAATA
1 AAAATA AAAATA AAAATA AAAATA AAAATA
612886 TTTACATTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 24 1.00
ACGTcount: A:0.83, C:0.00, G:0.00, T:0.17
Consensus pattern (6 bp):
AAAATA
Found at i:613694 original size:19 final size:19
Alignment explanation
Indices: 613662--613699 Score: 51
Period size: 18 Copynumber: 2.0 Consensus size: 19
613652 ATTATAATAG
*
613662 TTTTTTTAATATGT-TTAA
1 TTTTTTTAAAATGTATTAA
613680 TTTTTTTAAAAATGTATTAA
1 TTTTTTT-AAAATGTATTAA
613700 CGTCACACCT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
18 7 0.41
19 6 0.35
20 4 0.24
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (19 bp):
TTTTTTTAAAATGTATTAA
Found at i:618718 original size:17 final size:17
Alignment explanation
Indices: 618696--618777 Score: 53
Period size: 17 Copynumber: 4.6 Consensus size: 17
618686 CTAAAATTAA
*
618696 TATAAACTTACTAAA-AT
1 TATAAAATTA-TAAATAT
618713 TATAAAAATTATAAATAT
1 TAT-AAAATTATAAATAT
618731 TATAAAA-TATGAAA-AT
1 TATAAAATTAT-AAATAT
*
618747 ATATAATAAGTTATAAGAAAT
1 -TATAA-AA-TTATAA-ATAT
*
618768 TAAAAAATTA
1 TATAAAATTA
618778 AAAAATTTAT
Statistics
Matches: 54, Mismatches: 2, Indels: 17
0.74 0.03 0.23
Matches are distributed among these distances:
16 5 0.09
17 19 0.35
18 16 0.30
19 4 0.07
20 8 0.15
21 2 0.04
ACGTcount: A:0.60, C:0.02, G:0.04, T:0.34
Consensus pattern (17 bp):
TATAAAATTATAAATAT
Found at i:618777 original size:8 final size:9
Alignment explanation
Indices: 618708--618876 Score: 78
Period size: 9 Copynumber: 18.4 Consensus size: 9
618698 TAAACTTACT
618708 AAAATTATA
1 AAAATTATA
618717 AAAATTATA
1 AAAATTATA
*
618726 AATATTAT-
1 AAAATTATA
*
618734 AAAA-TATG
1 AAAATTATA
618742 AAAATATATA
1 AAAAT-TATA
*
618752 ATAAGTTATA
1 A-AAATTATA
618762 AGAAATTA-A
1 A-AAATTATA
618771 AAAATTA-A
1 AAAATTATA
*
618779 AAAATTTATT
1 AAAA-TTATA
* * *
618789 AGAATTCTTG
1 AAAATT-ATA
* * *
618799 AAAGTAACCA
1 AAAATTA-TA
*
618809 AAAAGTA-A
1 AAAATTATA
** *
618817 AAAAAAATT
1 AAAATTATA
*
618826 AAAATTATT
1 AAAATTATA
618835 AAAATTATA
1 AAAATTATA
*
618844 TAAACTTATA
1 -AAAATTATA
618854 AAAATTATAA
1 AAAATTAT-A
*
618864 AAAATCATA
1 AAAATTATA
618873 AAAA
1 AAAA
618877 CTTGAGCTAG
Statistics
Matches: 121, Mismatches: 28, Indels: 22
0.71 0.16 0.13
Matches are distributed among these distances:
7 3 0.02
8 24 0.20
9 50 0.41
10 41 0.34
11 3 0.02
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (9 bp):
AAAATTATA
Found at i:618847 original size:19 final size:19
Alignment explanation
Indices: 618825--618876 Score: 68
Period size: 19 Copynumber: 2.7 Consensus size: 19
618815 AAAAAAAAAT
*
618825 TAAAATTATTAAAATTATA
1 TAAAATTATAAAAATTATA
*
618844 TAAACTTATAAAAATTATA
1 TAAAATTATAAAAATTATA
* *
618863 AAAAATCATAAAAA
1 TAAAATTATAAAAA
618877 CTTGAGCTAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.63, C:0.04, G:0.00, T:0.33
Consensus pattern (19 bp):
TAAAATTATAAAAATTATA
Found at i:627910 original size:16 final size:16
Alignment explanation
Indices: 627891--627941 Score: 52
Period size: 15 Copynumber: 3.3 Consensus size: 16
627881 TTCATATTGG
627891 TAATTTTTTATTTGAA
1 TAATTTTTTATTTGAA
* *
627907 TAA-TTTTAATTTG-G
1 TAATTTTTTATTTGAA
**
627921 TTGTTTTTTATTTGAA
1 TAATTTTTTATTTGAA
627937 TAATT
1 TAATT
627942 CTCCTTTTAT
Statistics
Matches: 25, Mismatches: 8, Indels: 4
0.68 0.22 0.11
Matches are distributed among these distances:
14 1 0.04
15 18 0.72
16 6 0.24
ACGTcount: A:0.27, C:0.00, G:0.10, T:0.63
Consensus pattern (16 bp):
TAATTTTTTATTTGAA
Found at i:633038 original size:45 final size:44
Alignment explanation
Indices: 632957--633047 Score: 128
Period size: 45 Copynumber: 2.0 Consensus size: 44
632947 ACCTCTATTC
*
632957 CATTCAACCAAACACAAGATTACTATTACGCCTCTATTCCATTA
1 CATTCAACCAAACACAAGATTACTATTACACCTCTATTCCATTA
*** *
633001 CATTCAACCAAACAGTTGATTTGCTATTACACCTCTATTCCATTA
1 CATTCAACCAAACACAAGA-TTACTATTACACCTCTATTCCATTA
633046 CA
1 CA
633048 CCTCTAATCC
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
44 16 0.39
45 25 0.61
ACGTcount: A:0.34, C:0.29, G:0.05, T:0.32
Consensus pattern (44 bp):
CATTCAACCAAACACAAGATTACTATTACACCTCTATTCCATTA
Found at i:633047 original size:16 final size:16
Alignment explanation
Indices: 633026--633063 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
633016 TTGATTTGCT
*
633026 ATTACACCTCTATTCC
1 ATTACACCTCTAATCC
633042 ATTACACCTCTAATCC
1 ATTACACCTCTAATCC
*
633058 AATACA
1 ATTACA
633064 GCGAACCAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.34, C:0.34, G:0.00, T:0.32
Consensus pattern (16 bp):
ATTACACCTCTAATCC
Found at i:634446 original size:154 final size:154
Alignment explanation
Indices: 634161--634449 Score: 377
Period size: 154 Copynumber: 1.9 Consensus size: 154
634151 TTTATTTTAT
** * * * *
634161 ATTCTTTCACTTGATTAATTATAAAGTTCATAAATCTAACAAGCTCAATTAATTAGTATGAGTCA
1 ATTCTTTCACACGATTAATTATAAAGTTCATAAATATAACAACCTCAATTAATCAGTACGAGTCA
* * * * *
634226 TCAAATTTAATTAATTAATTTATCATGCGTTATTAAATTCAAGTAATCAATTTATAAGTTTTTGA
66 TCAAATTAAATTAATTAATCTATAATGAGTTATTAAATTCAAGTAATCAATTTATAAGTTTATGA
634291 TGTTCTAAATTCACAATAGAATAC
131 TGTTCTAAATTCACAATAGAATAC
* * *
634315 ATTCTTTCACACGATTAATTATAAAGTTCATAAATATAACAACCTTAATTAATCGGTACGAGTTA
1 ATTCTTTCACACGATTAATTATAAAGTTCATAAATATAACAACCTCAATTAATCAGTACGAGTCA
* * *
634380 -CAAAATTAAATTAA-TATATCTATAATGAGTTATTCAGTTTAAGTAATTC-ATTTATAAGTTTA
66 TC-AAATTAAATTAATTA-ATCTATAATGAGTTATTAAATTCAAGTAA-TCAATTTATAAGTTTA
634442 TGATGTTC
128 TGATGTTC
634450 CAAACTCATA
Statistics
Matches: 115, Mismatches: 17, Indels: 6
0.83 0.12 0.04
Matches are distributed among these distances:
153 3 0.03
154 110 0.96
155 2 0.02
ACGTcount: A:0.39, C:0.11, G:0.09, T:0.40
Consensus pattern (154 bp):
ATTCTTTCACACGATTAATTATAAAGTTCATAAATATAACAACCTCAATTAATCAGTACGAGTCA
TCAAATTAAATTAATTAATCTATAATGAGTTATTAAATTCAAGTAATCAATTTATAAGTTTATGA
TGTTCTAAATTCACAATAGAATAC
Found at i:642407 original size:57 final size:58
Alignment explanation
Indices: 642329--642451 Score: 176
Period size: 57 Copynumber: 2.1 Consensus size: 58
642319 ATTTCTAGGT
* * * *
642329 CATTTTCATTTGCATTTTGGAGAAAACCACATTCATTTTCAAATGATT-CTATTTCTC
1 CATTTTCATTTGCATTATGGAGAAAACCACAATCATTTCCAAATGATTCCCATTTCTC
* * *
642386 CATTTTCATTTTCATTATGGAGAAAACCATAATCATTTCCAAATGTTTCCCATTTCTC
1 CATTTTCATTTGCATTATGGAGAAAACCACAATCATTTCCAAATGATTCCCATTTCTC
642444 CATTTTCA
1 CATTTTCA
642452 CAATTTCTAT
Statistics
Matches: 58, Mismatches: 7, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
57 42 0.72
58 16 0.28
ACGTcount: A:0.28, C:0.21, G:0.07, T:0.43
Consensus pattern (58 bp):
CATTTTCATTTGCATTATGGAGAAAACCACAATCATTTCCAAATGATTCCCATTTCTC
Found at i:647822 original size:78 final size:79
Alignment explanation
Indices: 647722--647880 Score: 311
Period size: 78 Copynumber: 2.0 Consensus size: 79
647712 TAGTAAATGT
647722 AAAATTATATTTTTGTACATTTTAAAGTTATAAAAATTTTATTTAATCTTTAAAAATTATAAAAA
1 AAAATTATATTTTTGTACATTTTAAAGTTATAAAAATTTTATTTAATCTTTAAAAATTATAAAAA
647787 TATAGGATATAAAA
66 TATAGGATATAAAA
647801 AAAATTATA-TTTTGTACATTTTAAAGTTATAAAAATTTTATTTAATCTTTAAAAATTATAAAAA
1 AAAATTATATTTTTGTACATTTTAAAGTTATAAAAATTTTATTTAATCTTTAAAAATTATAAAAA
647865 TATAGGATATAAAA
66 TATAGGATATAAAA
647879 AA
1 AA
647881 TTAAAATTTC
Statistics
Matches: 80, Mismatches: 0, Indels: 1
0.99 0.00 0.01
Matches are distributed among these distances:
78 71 0.89
79 9 0.11
ACGTcount: A:0.50, C:0.03, G:0.05, T:0.42
Consensus pattern (79 bp):
AAAATTATATTTTTGTACATTTTAAAGTTATAAAAATTTTATTTAATCTTTAAAAATTATAAAAA
TATAGGATATAAAA
Found at i:650500 original size:27 final size:27
Alignment explanation
Indices: 650469--650530 Score: 74
Period size: 27 Copynumber: 2.4 Consensus size: 27
650459 ATATTTTGAA
*
650469 AATATAT-AAA-AAATTAAAATATATG
1 AATATATAAAAGAAATAAAAATATATG
* * *
650494 AATATATAAAAGAACTAAAAATTTATA
1 AATATATAAAAGAAATAAAAATATATG
650521 AATATATAAA
1 AATATATAAA
650531 TATATAAAGG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
25 7 0.23
26 3 0.10
27 21 0.68
ACGTcount: A:0.65, C:0.02, G:0.03, T:0.31
Consensus pattern (27 bp):
AATATATAAAAGAAATAAAAATATATG
Found at i:650526 original size:35 final size:34
Alignment explanation
Indices: 650475--650548 Score: 112
Period size: 35 Copynumber: 2.1 Consensus size: 34
650465 TGAAAATATA
*
650475 TAAAAAATTAAAATATATGAATATATAAAAGAAC
1 TAAAAAATTAAAATATATAAATATATAAAAGAAC
* *
650509 TAAAAATTTATAAATATATAAATATATAAAGGAAC
1 TAAAAAATTA-AAATATATAAATATATAAAAGAAC
650544 TAAAA
1 TAAAA
650549 TAACACATGG
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
34 9 0.25
35 27 0.75
ACGTcount: A:0.64, C:0.03, G:0.05, T:0.28
Consensus pattern (34 bp):
TAAAAAATTAAAATATATAAATATATAAAAGAAC
Found at i:652635 original size:400 final size:401
Alignment explanation
Indices: 651885--652686 Score: 1597
Period size: 400 Copynumber: 2.0 Consensus size: 401
651875 ATTAAGTTTT
651885 TAAAAGATATTATATAAAATATAAAAATAAAAATATTTGTTTATTTAAAAAAAGTTTTAGGATTT
1 TAAAAGATATTATATAAAATATAAAAATAAAAATATTTGTTTATTTAAAAAAAGTTTTAGGATTT
651950 TATATAGTATAGATTTATAGAGTTTTTTTTTAGAAATTTTTATAAAAATGAAATATAGAGCAAGG
66 TATATAGTATAGATTTATAGAGTTTTTTTTTAGAAATTTTTATAAAAATGAAATATAGAGCAAGG
652015 AAGAAAAGCAAATAAAAAAGGTGGAAAAGAACAGGGCATAGGACGTCATTCAAGTCACAACCATG
131 AAGAAAAGCAAATAAAAAAGGTGGAAAAGAACAGGGCATAGGACGTCATTCAAGTCACAACCATG
652080 CTTTGAAAGCAATGGCTCAGGCGCGTGGCCGCTTAAAAGGTGAGAGCAACAACGCAACATTATTT
196 CTTTGAAAGCAATGGCTCAGGCGCGTGGCCGCTTAAAAGGTGAGAGCAACAACGCAACATTATTT
652145 ACAGGCAGAGGCAGATGGGGTAGGGGCCAAGCCCCCAACACCATCCTTTATCCCATCCAAAAATT
261 ACAGGCAGAGGCAGATGGGGTAGGGGCCAAGCCCCCAACACCATCCTTTATCCCATCCAAAAATT
652210 CACTAGCCAGGTTTTTGATTAATAATAAATTTGGGTACCTTTAAAACAAAACCAGACTTCTCAGC
326 CACTAGCCAGGTTTTTGATTAATAATAAATTTGGGTACCTTTAAAACAAAACCAGACTTCTCAGC
652275 AGGTAAAATAC
391 AGGTAAAATAC
652286 TAAAAGATA-TATATAAAATATAAAAATAAAAATATTTGTTTATTTAAAAAAAGTTTTAGGATTT
1 TAAAAGATATTATATAAAATATAAAAATAAAAATATTTGTTTATTTAAAAAAAGTTTTAGGATTT
652350 TATATAGTATAGATTTATAGAGTTTTTTTTTAGAAATTTTTATAAAAATGAAATATAGAGCAAGG
66 TATATAGTATAGATTTATAGAGTTTTTTTTTAGAAATTTTTATAAAAATGAAATATAGAGCAAGG
652415 AAGAAAAGCAAATAAAAAAGGTGGAAAAGAACAGGGCATAGGACGTCATTCAAGTCACAACCATG
131 AAGAAAAGCAAATAAAAAAGGTGGAAAAGAACAGGGCATAGGACGTCATTCAAGTCACAACCATG
652480 CTTTGAAAGCAATGGCTCAGGCGCGTGGCCGCTTAAAAGGTGAGAGCAACAACGCAACATTATTT
196 CTTTGAAAGCAATGGCTCAGGCGCGTGGCCGCTTAAAAGGTGAGAGCAACAACGCAACATTATTT
652545 ACAGGCAGAGGCAGATGGGGTAGGGGCCAAGCCCCCAACACCATCCTTTATCCCATCCAAAAATT
261 ACAGGCAGAGGCAGATGGGGTAGGGGCCAAGCCCCCAACACCATCCTTTATCCCATCCAAAAATT
652610 CACTAGCCAGGTTTTTGATTAATAATAAATTTGGGTACCTTTAAAACAAAACCAGACTTCTCAGC
326 CACTAGCCAGGTTTTTGATTAATAATAAATTTGGGTACCTTTAAAACAAAACCAGACTTCTCAGC
652675 AGGTAAAATAC
391 AGGTAAAATAC
652686 T
1 T
652687 GCTTATTTTC
Statistics
Matches: 401, Mismatches: 0, Indels: 1
1.00 0.00 0.00
Matches are distributed among these distances:
400 392 0.98
401 9 0.02
ACGTcount: A:0.40, C:0.15, G:0.18, T:0.27
Consensus pattern (401 bp):
TAAAAGATATTATATAAAATATAAAAATAAAAATATTTGTTTATTTAAAAAAAGTTTTAGGATTT
TATATAGTATAGATTTATAGAGTTTTTTTTTAGAAATTTTTATAAAAATGAAATATAGAGCAAGG
AAGAAAAGCAAATAAAAAAGGTGGAAAAGAACAGGGCATAGGACGTCATTCAAGTCACAACCATG
CTTTGAAAGCAATGGCTCAGGCGCGTGGCCGCTTAAAAGGTGAGAGCAACAACGCAACATTATTT
ACAGGCAGAGGCAGATGGGGTAGGGGCCAAGCCCCCAACACCATCCTTTATCCCATCCAAAAATT
CACTAGCCAGGTTTTTGATTAATAATAAATTTGGGTACCTTTAAAACAAAACCAGACTTCTCAGC
AGGTAAAATAC
Found at i:656716 original size:28 final size:28
Alignment explanation
Indices: 656658--656717 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 28
656648 AAAGCCGTTT
656658 TTTTTTTAAATTTACCGAAATGGACCGA
1 TTTTTTTAAATTTACCGAAATGGACCGA
* * *
656686 TTTTTTTATTATTTACCGGAATGGTCC-A
1 TTTTTTTA-AATTTACCGAAATGGACCGA
656714 TTTT
1 TTTT
656718 CCGGGAAATC
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
28 13 0.46
29 15 0.54
ACGTcount: A:0.25, C:0.13, G:0.13, T:0.48
Consensus pattern (28 bp):
TTTTTTTAAATTTACCGAAATGGACCGA
Found at i:660286 original size:56 final size:57
Alignment explanation
Indices: 660197--660319 Score: 169
Period size: 56 Copynumber: 2.2 Consensus size: 57
660187 TATGTAAAAC
* ** *
660197 TATGTAAAATGATTAAGCCCAATAACTTTTGTTAATGGTTAGTAA-ATTTATCAAA-T
1 TATGTAAAATGATTAAGCCCAAAAAAGTGTGTTAATGGTTAGTAAGA-TTATCAAATT
*
660253 TATGTAAAATTATTAAGCCCAAAAAAGTGTGTTAATGGTTAGTAAGATTATCAAATT
1 TATGTAAAATGATTAAGCCCAAAAAAGTGTGTTAATGGTTAGTAAGATTATCAAATT
*
660310 TAGGTAAAAT
1 TATGTAAAAT
660320 ATGTTATGGT
Statistics
Matches: 59, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
56 48 0.81
57 11 0.19
ACGTcount: A:0.41, C:0.07, G:0.15, T:0.37
Consensus pattern (57 bp):
TATGTAAAATGATTAAGCCCAAAAAAGTGTGTTAATGGTTAGTAAGATTATCAAATT
Found at i:660340 original size:23 final size:23
Alignment explanation
Indices: 660322--660414 Score: 143
Period size: 23 Copynumber: 4.0 Consensus size: 23
660312 GGTAAAATAT
660322 GTTATGGTTTTTAAATAAATTAG
1 GTTATGGTTTTTAAATAAATTAG
*
660345 ATTA-GAGTTTTTAAATAAATTAG
1 GTTATG-GTTTTTAAATAAATTAG
*
660368 GTTAGGGTTTTTAAATAAATTAG
1 GTTATGGTTTTTAAATAAATTAG
*
660391 GTTATGGTTTTTAATTAAATTAG
1 GTTATGGTTTTTAAATAAATTAG
660414 G
1 G
660415 GTAGGGTTAG
Statistics
Matches: 64, Mismatches: 4, Indels: 4
0.89 0.06 0.06
Matches are distributed among these distances:
22 1 0.02
23 62 0.97
24 1 0.02
ACGTcount: A:0.35, C:0.00, G:0.18, T:0.46
Consensus pattern (23 bp):
GTTATGGTTTTTAAATAAATTAG
Found at i:660422 original size:23 final size:23
Alignment explanation
Indices: 660327--660508 Score: 121
Period size: 23 Copynumber: 7.2 Consensus size: 23
660317 AATATGTTAT
* **
660327 GGTTTTTAAATAAATTAGATTAG
1 GGTTTTTAATTAAATTAGGGTAG
* * *
660350 AGTTTTTAAATAAATTAGGTTAG
1 GGTTTTTAATTAAATTAGGGTAG
* * *
660373 GGTTTTTAAATAAATTAGGTTAT
1 GGTTTTTAATTAAATTAGGGTAG
660396 GGTTTTTAATTAAATTAGGGTAGGGTTAG
1 GGTTTTTAATTAAA-T----TAGGG-TAG
660425 GGTTTTTAATTAAATTAGGTTAAGGTTAG
1 GGTTTTTAATTAAATTA-G----GG-TAG
*
660454 GGTTTTTGATTAAATTAGGGTAG
1 GGTTTTTAATTAAATTAGGGTAG
660477 GGTTAGGGTTTTAATTAAATTAGGGTAG
1 GG-T----TTTTAATTAAATTAGGGTAG
660505 GGTT
1 GGTT
660509 AGGGTTAATG
Statistics
Matches: 134, Mismatches: 9, Indels: 32
0.77 0.05 0.18
Matches are distributed among these distances:
23 61 0.46
24 6 0.04
25 1 0.01
27 1 0.01
28 27 0.20
29 38 0.28
ACGTcount: A:0.31, C:0.00, G:0.25, T:0.43
Consensus pattern (23 bp):
GGTTTTTAATTAAATTAGGGTAG
Done.