Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015276.1 Kokia drynarioides strain JFW-HI SEQ_130321, whole genome shotgun sequence
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: 629240
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.34
Warning! 408 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:343530 original size:43 final size:43
Alignment explanation
Indices: 343482--343571 Score: 128
Period size: 43 Copynumber: 2.1 Consensus size: 43
343472 TTATGAGGAA
* * *
343482 AAACACCGCTATAGAACATGGTCTTTAGCGGCGCTTATTCC-AC
1 AAACACCGCTAAAAAACATGGTCTTTAACGGCGCTT-TTCCTAC
*
343525 AAACACCGCTAAAAAACATGGTTTTTAACGGCGCTTTTCCTAC
1 AAACACCGCTAAAAAACATGGTCTTTAACGGCGCTTTTCCTAC
343568 AAAC
1 AAAC
343572 GCCACTAATA
Statistics
Matches: 42, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
42 4 0.10
43 38 0.90
ACGTcount: A:0.32, C:0.27, G:0.16, T:0.26
Consensus pattern (43 bp):
AAACACCGCTAAAAAACATGGTCTTTAACGGCGCTTTTCCTAC
Found at i:343725 original size:67 final size:68
Alignment explanation
Indices: 343651--343781 Score: 246
Period size: 67 Copynumber: 1.9 Consensus size: 68
343641 TTGTAAATTC
343651 ATATTCATTTTCAATTAAATTTTTACTCAAACCTTCATAAATTTCTTGAAAGATAGA-CCTTTTT
1 ATATTCATTTTCAATTAAATTTTTACTCAAACCTTCATAAATTTCTTGAAAGATAGATCCTTTTT
343715 AAG
66 AAG
*
343718 ATATTCATTTTCAATTAAATTTTTACTCAAATCTTCATAAATTTCTTGAAAGATAGATCCTTTT
1 ATATTCATTTTCAATTAAATTTTTACTCAAACCTTCATAAATTTCTTGAAAGATAGATCCTTTT
343782 AAGTGTTAGC
Statistics
Matches: 62, Mismatches: 1, Indels: 1
0.97 0.02 0.02
Matches are distributed among these distances:
67 56 0.90
68 6 0.10
ACGTcount: A:0.35, C:0.15, G:0.05, T:0.45
Consensus pattern (68 bp):
ATATTCATTTTCAATTAAATTTTTACTCAAACCTTCATAAATTTCTTGAAAGATAGATCCTTTTT
AAG
Found at i:348158 original size:29 final size:29
Alignment explanation
Indices: 348108--348316 Score: 233
Period size: 30 Copynumber: 7.1 Consensus size: 29
348098 CCCTAAAGGT
*
348108 CCCTAAACTATTCAAAAATTCCATTTTTAC
1 CCCTAAACT-TCCAAAAATTCCATTTTTAC
*
348138 CCCTAAACTTCAAAAAATTCCATTTTTAC
1 CCCTAAACTTCCAAAAATTCCATTTTTAC
** *
348167 CCC-AAACTTCCAAAAATTTTATTTTCGAC
1 CCCTAAACTTCCAAAAATTCCATTTT-TAC
* ** *
348196 CCCCAAACTTCCAAAAATTATATTTTCGA-
1 CCCTAAACTTCCAAAAATTCCATTTT-TAC
* *
348225 CCCTAAAACTTCTAAAAATTCCATTTTTAA
1 CCCT-AAACTTCCAAAAATTCCATTTTTAC
* *
348255 CCTTAAAACTTCAAAAAATTCCATTTTTAC
1 CCCT-AAACTTCCAAAAATTCCATTTTTAC
348285 CCCTAAAACTTCCAAAAATTCCATTTTTAC
1 CCCT-AAACTTCCAAAAATTCCATTTTTAC
348315 CC
1 CC
348317 TCGAATGTCT
Statistics
Matches: 158, Mismatches: 17, Indels: 8
0.86 0.09 0.04
Matches are distributed among these distances:
28 19 0.12
29 30 0.19
30 109 0.69
ACGTcount: A:0.37, C:0.27, G:0.01, T:0.34
Consensus pattern (29 bp):
CCCTAAACTTCCAAAAATTCCATTTTTAC
Found at i:348330 original size:29 final size:29
Alignment explanation
Indices: 348121--348341 Score: 207
Period size: 30 Copynumber: 7.6 Consensus size: 29
348111 TAAACTATTC
*
348121 AAAAATTCCATTTTTACCCCT-AAACTTCA
1 AAAAATTCCATTTTTA-CCCTAAAACTTCT
* *
348150 AAAAATTCCATTTTTACCC-CAAACTTCC
1 AAAAATTCCATTTTTACCCTAAAACTTCT
** * ** *
348178 AAAAATTTTATTTTCGACCCCCAAACTTCC
1 AAAAATTCCATTTT-TACCCTAAAACTTCT
** *
348208 AAAAATTATATTTTCGACCCTAAAACTTCT
1 AAAAATTCCATTTT-TACCCTAAAACTTCT
* *
348238 AAAAATTCCATTTTTAACCTTAAAACTTCA
1 AAAAATTCCATTTTT-ACCCTAAAACTTCT
*
348268 AAAAATTCCATTTTTACCCCTAAAACTTCC
1 AAAAATTCCATTTTTA-CCCTAAAACTTCT
**
348298 AAAAATTCCATTTTTACCCTCGAA-TGTCT
1 AAAAATTCCATTTTTACCCTAAAACT-TCT
348327 -AAAATTCCATTTTTA
1 AAAAATTCCATTTTTA
348342 ACCTCGAATT
Statistics
Matches: 168, Mismatches: 18, Indels: 13
0.84 0.09 0.07
Matches are distributed among these distances:
28 38 0.23
29 29 0.17
30 101 0.60
ACGTcount: A:0.37, C:0.25, G:0.02, T:0.36
Consensus pattern (29 bp):
AAAAATTCCATTTTTACCCTAAAACTTCT
Found at i:348723 original size:96 final size:96
Alignment explanation
Indices: 348606--348797 Score: 248
Period size: 96 Copynumber: 2.0 Consensus size: 96
348596 AAAACTTTAA
* **
348606 AATCGAGGCAATATTCTTTTAT-TTCGAGTTTTGAAA-ATTTGTGCCTTAACTTACTAGGTGCAA
1 AATCGAGGCAATATTCTTTTATCTTCGA-TTCTGAAATA-TTGCACCTTAACTTACTAGGTGCAA
**
348669 TTTTTCTTCAAATCGAA-ATAATCGAATACCCTT
64 CCTTTCTTCAAATC-AAGATAATCGAATACCCTT
* *
348702 AATCGAGGCAATGTT-TCTTTATCTTTGATTCTGAAATATTGCACCTTAACTTACTAGGTGCAAC
1 AATCGAGGCAATATTCT-TTTATCTTCGATTCTGAAATATTGCACCTTAACTTACTAGGTGCAAC
*
348766 CTTTCTTCAAATCAAGATAATCGAATATCCTT
65 CTTTCTTCAAATCAAGATAATCGAATACCCTT
348798 TTCCCAAAAA
Statistics
Matches: 84, Mismatches: 8, Indels: 8
0.84 0.08 0.08
Matches are distributed among these distances:
95 3 0.04
96 76 0.90
97 5 0.06
ACGTcount: A:0.30, C:0.18, G:0.13, T:0.39
Consensus pattern (96 bp):
AATCGAGGCAATATTCTTTTATCTTCGATTCTGAAATATTGCACCTTAACTTACTAGGTGCAACC
TTTCTTCAAATCAAGATAATCGAATACCCTT
Found at i:349936 original size:17 final size:17
Alignment explanation
Indices: 349910--349944 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
349900 GACTGGTTGT
349910 AGAATTTATTT-TTTTA
1 AGAATTTATTTCTTTTA
349926 AGAAGTTTATTTCTTTTA
1 AGAA-TTTATTTCTTTTA
349944 A
1 A
349945 TATTTTCATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 4 0.24
17 7 0.41
18 6 0.35
ACGTcount: A:0.31, C:0.03, G:0.09, T:0.57
Consensus pattern (17 bp):
AGAATTTATTTCTTTTA
Found at i:356020 original size:15 final size:16
Alignment explanation
Indices: 355991--356029 Score: 51
Period size: 17 Copynumber: 2.4 Consensus size: 16
355981 AGATTCGATT
* *
355991 TTTTTTATATTTTATAA
1 TTTTTTATGTTATAT-A
356008 TTTTTTATGTTATATA
1 TTTTTTATGTTATATA
356024 TTTTTT
1 TTTTTT
356030 GAAAATATTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 7 0.35
17 13 0.65
ACGTcount: A:0.23, C:0.00, G:0.03, T:0.74
Consensus pattern (16 bp):
TTTTTTATGTTATATA
Found at i:361084 original size:39 final size:37
Alignment explanation
Indices: 361032--361122 Score: 107
Period size: 37 Copynumber: 2.5 Consensus size: 37
361022 CATTCATTTA
361032 CAGCCTT--TTGTTGAAACCTTAG-TCTAAGAAAACTTAT
1 CAGCCTTCATTGTTGAAACCTTAGTTC-AA-AAAAC-TAT
361069 CAGCCTTCATTGTTGAAACCTTAGTTCAAAAAACTAT
1 CAGCCTTCATTGTTGAAACCTTAGTTCAAAAAACTAT
** *
361106 CTTCCTTCATTGCTGAA
1 CAGCCTTCATTGTTGAA
361123 TATCACCTTG
Statistics
Matches: 48, Mismatches: 3, Indels: 6
0.84 0.05 0.11
Matches are distributed among these distances:
37 24 0.50
38 5 0.10
39 17 0.35
40 2 0.04
ACGTcount: A:0.31, C:0.22, G:0.12, T:0.35
Consensus pattern (37 bp):
CAGCCTTCATTGTTGAAACCTTAGTTCAAAAAACTAT
Found at i:361602 original size:18 final size:18
Alignment explanation
Indices: 361573--361623 Score: 57
Period size: 18 Copynumber: 2.8 Consensus size: 18
361563 AATTCTTCTA
*
361573 GATTTGTAGGGATAGACT
1 GATTTCTAGGGATAGACT
* *
361591 GGTTTCTAGGGATAAACT
1 GATTTCTAGGGATAGACT
* *
361609 GATTTTTTGGGATAG
1 GATTTCTAGGGATAG
361624 GATCCTGATT
Statistics
Matches: 26, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
18 26 1.00
ACGTcount: A:0.25, C:0.06, G:0.31, T:0.37
Consensus pattern (18 bp):
GATTTCTAGGGATAGACT
Found at i:374409 original size:17 final size:18
Alignment explanation
Indices: 374389--374422 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
374379 ACACTTTATT
374389 AATTTG-GTTTTTATTTA
1 AATTTGAGTTTTTATTTA
*
374406 AATTTGATTTTTTATTT
1 AATTTGAGTTTTTATTT
374423 TTTTAAAAGA
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:0.24, C:0.00, G:0.09, T:0.68
Consensus pattern (18 bp):
AATTTGAGTTTTTATTTA
Found at i:374911 original size:19 final size:19
Alignment explanation
Indices: 374874--374912 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
374864 TAAATCGAAG
*
374874 ACAAAAAAGAAAATTTGGA
1 ACAAAAAAGAAAATGTGGA
**
374893 ACAAAAAAGTGAATGTGGA
1 ACAAAAAAGAAAATGTGGA
374912 A
1 A
374913 GAGTTAGGAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.59, C:0.05, G:0.21, T:0.15
Consensus pattern (19 bp):
ACAAAAAAGAAAATGTGGA
Found at i:381801 original size:11 final size:11
Alignment explanation
Indices: 381770--381810 Score: 55
Period size: 11 Copynumber: 3.5 Consensus size: 11
381760 TTAGAGTGGG
*
381770 TAAAAATTTTA
1 TAAAAAATTTA
381781 TATAATAAATTTA
1 TA-AA-AAATTTA
381794 TAAAAAATTTA
1 TAAAAAATTTA
381805 TAAAAA
1 TAAAAA
381811 CTAATTAAAA
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
11 15 0.56
12 4 0.15
13 8 0.30
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (11 bp):
TAAAAAATTTA
Found at i:389206 original size:16 final size:16
Alignment explanation
Indices: 389185--389225 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
389175 TACATGTAGA
389185 AAATAATAAAATAAAT
1 AAATAATAAAATAAAT
* *
389201 AAATAATATATTAAAT
1 AAATAATAAAATAAAT
*
389217 AAAAAATAA
1 AAATAATAA
389226 CTCTTAATTT
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.73, C:0.00, G:0.00, T:0.27
Consensus pattern (16 bp):
AAATAATAAAATAAAT
Found at i:389948 original size:23 final size:24
Alignment explanation
Indices: 389917--389986 Score: 70
Period size: 24 Copynumber: 3.0 Consensus size: 24
389907 AACATCCAAA
* *
389917 CAACAAAAACAATAACCAAAATAG
1 CAACAAAAACAACAACAAAAATAG
*
389941 CAAC-AAAATAACAACAAAAATAG
1 CAACAAAAACAACAACAAAAATAG
* ** *
389964 TAGTAAAAACAACCACAAAAATA
1 CAACAAAAACAACAACAAAAATA
389987 ATAGCAAAAG
Statistics
Matches: 37, Mismatches: 8, Indels: 2
0.79 0.17 0.04
Matches are distributed among these distances:
23 17 0.46
24 20 0.54
ACGTcount: A:0.67, C:0.19, G:0.04, T:0.10
Consensus pattern (24 bp):
CAACAAAAACAACAACAAAAATAG
Found at i:389962 original size:12 final size:12
Alignment explanation
Indices: 389915--389962 Score: 53
Period size: 12 Copynumber: 4.1 Consensus size: 12
389905 ATAACATCCA
*
389915 AACAACAAAAAC
1 AACAACAAAAAT
* *
389927 AATAACCAAAAT
1 AACAACAAAAAT
*
389939 AGCAAC-AAAAT
1 AACAACAAAAAT
389950 AACAACAAAAAT
1 AACAACAAAAAT
389962 A
1 A
389963 GTAGTAAAAA
Statistics
Matches: 29, Mismatches: 6, Indels: 2
0.78 0.16 0.05
Matches are distributed among these distances:
11 10 0.34
12 19 0.66
ACGTcount: A:0.71, C:0.19, G:0.02, T:0.08
Consensus pattern (12 bp):
AACAACAAAAAT
Found at i:389981 original size:24 final size:24
Alignment explanation
Indices: 389936--390007 Score: 72
Period size: 24 Copynumber: 2.9 Consensus size: 24
389926 CAATAACCAA
*
389936 AATAGCAACAAAATAACAACAAAAAT
1 AATAGC-A-AAAACAACAACAAAAAT
* * *
389962 AGTAGTAAAAACAACCACAAAAAT
1 AATAGCAAAAACAACAACAAAAAT
* *
389986 AATAGCAAAAGCAACACCAAAA
1 AATAGCAAAAACAACAACAAAA
390008 CAATAAAAAA
Statistics
Matches: 37, Mismatches: 9, Indels: 2
0.77 0.19 0.04
Matches are distributed among these distances:
24 32 0.86
25 1 0.03
26 4 0.11
ACGTcount: A:0.65, C:0.18, G:0.07, T:0.10
Consensus pattern (24 bp):
AATAGCAAAAACAACAACAAAAAT
Found at i:390024 original size:21 final size:21
Alignment explanation
Indices: 390000--390055 Score: 76
Period size: 21 Copynumber: 2.7 Consensus size: 21
389990 GCAAAAGCAA
* *
390000 CACCAAAACAATAAAAAATAG
1 CACCAAAACAACAAAAAACAG
*
390021 CACCAAAACAACAAAAGACAG
1 CACCAAAACAACAAAAAACAG
*
390042 CACCAAAATAACAA
1 CACCAAAACAACAA
390056 CACTTACAGA
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.64, C:0.25, G:0.05, T:0.05
Consensus pattern (21 bp):
CACCAAAACAACAAAAAACAG
Found at i:398684 original size:6 final size:6
Alignment explanation
Indices: 398673--398698 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
398663 GGAAGGGTTG
398673 GGGAGA GGGAGA GGGAGA GGGAGA GG
1 GGGAGA GGGAGA GGGAGA GGGAGA GG
398699 AAATAGGATG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.31, C:0.00, G:0.69, T:0.00
Consensus pattern (6 bp):
GGGAGA
Found at i:415075 original size:68 final size:74
Alignment explanation
Indices: 414941--415079 Score: 182
Period size: 68 Copynumber: 2.0 Consensus size: 74
414931 AGATCAAACT
* * * *
414941 TAATTACTTTAATATTAAATTAATATAATATAATATTTATCAATATAAGTATTAGATTAAATTTA
1 TAATTACTTTAATATTAAATTAATATAATATAATATCTATCAAGATAAATATTAAATTAAATTTA
415006 ATATTAAGA
66 ATATTAAGA
* *
415015 TAATTATTTTAATATTAAATT-A-AT-A-A-AATA-CTATCAAGATAAATATTAAATTTAATTTA
1 TAATTACTTTAATATTAAATTAATATAATATAATATCTATCAAGATAAATATTAAATTAAATTTA
415074 ATATTA
66 ATATTA
415080 CAAATTTTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
68 30 0.51
69 4 0.07
70 1 0.02
71 1 0.02
72 2 0.03
73 1 0.02
74 20 0.34
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (74 bp):
TAATTACTTTAATATTAAATTAATATAATATAATATCTATCAAGATAAATATTAAATTAAATTTA
ATATTAAGA
Found at i:419735 original size:20 final size:21
Alignment explanation
Indices: 419698--419739 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
419688 TTCACAAAAT
* *
419698 ATTTTTTATATATACATTTTA
1 ATTTTTTACAAATACATTTTA
419719 ATTTTTTACAAAT-CATTTTA
1 ATTTTTTACAAATACATTTTA
419739 A
1 A
419740 AAATTTTCGA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 8 0.42
21 11 0.58
ACGTcount: A:0.36, C:0.07, G:0.00, T:0.57
Consensus pattern (21 bp):
ATTTTTTACAAATACATTTTA
Found at i:422297 original size:6 final size:6
Alignment explanation
Indices: 422286--422316 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
422276 GGAAAATGGG
422286 AAGGGA AAGGGA AAGGGA AAGGGA AAGGGA A
1 AAGGGA AAGGGA AAGGGA AAGGGA AAGGGA A
422317 GGAGAGGATT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (6 bp):
AAGGGA
Found at i:425396 original size:45 final size:45
Alignment explanation
Indices: 425346--425436 Score: 182
Period size: 45 Copynumber: 2.0 Consensus size: 45
425336 TTAGTTGAAG
425346 AATGCCTTACTCCATTTAGACCATGTAATTTAAAGAATTTCTCAA
1 AATGCCTTACTCCATTTAGACCATGTAATTTAAAGAATTTCTCAA
425391 AATGCCTTACTCCATTTAGACCATGTAATTTAAAGAATTTCTCAA
1 AATGCCTTACTCCATTTAGACCATGTAATTTAAAGAATTTCTCAA
425436 A
1 A
425437 GGCTCCAAGC
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
45 46 1.00
ACGTcount: A:0.36, C:0.20, G:0.09, T:0.35
Consensus pattern (45 bp):
AATGCCTTACTCCATTTAGACCATGTAATTTAAAGAATTTCTCAA
Found at i:436085 original size:22 final size:21
Alignment explanation
Indices: 436034--436087 Score: 54
Period size: 22 Copynumber: 2.4 Consensus size: 21
436024 CCTCTTCAAA
**
436034 AATTTTAATTATATATAATTCT
1 AATTTT-ATTATATATAATTAG
*
436056 AATATTTATTATATTATATTTAG
1 AAT-TTTATTATA-TATAATTAG
436079 AATTTTATT
1 AATTTTATT
436088 CAAATTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
22 15 0.56
23 12 0.44
ACGTcount: A:0.39, C:0.02, G:0.02, T:0.57
Consensus pattern (21 bp):
AATTTTATTATATATAATTAG
Found at i:437010 original size:28 final size:29
Alignment explanation
Indices: 436978--437063 Score: 77
Period size: 33 Copynumber: 2.9 Consensus size: 29
436968 ATATCATTTA
* *
436978 TATTAAATTATTTAAATATTTTATGTATCATTA
1 TATTAAATTATTCAAATATTTTA--TAT-A-TC
437011 TATTAAATTATTCAAATATTTTATATATC
1 TATTAAATTATTCAAATATTTTATATATC
* * *
437040 -ATCAAATT-TACAAATAATTTATAT
1 TATTAAATTATTCAAATATTTTATAT
437064 TAATCACTTA
Statistics
Matches: 48, Mismatches: 5, Indels: 6
0.81 0.08 0.10
Matches are distributed among these distances:
27 14 0.29
28 7 0.15
29 1 0.02
30 1 0.02
31 3 0.06
33 22 0.46
ACGTcount: A:0.43, C:0.06, G:0.01, T:0.50
Consensus pattern (29 bp):
TATTAAATTATTCAAATATTTTATATATC
Found at i:437012 original size:33 final size:33
Alignment explanation
Indices: 436959--437041 Score: 130
Period size: 33 Copynumber: 2.5 Consensus size: 33
436949 AAATTAATTT
* *
436959 ATATTTTGTATATCATTTATATTAAATTATTTAA
1 ATATTTTATATATCA-TTATATTAAATTATTCAA
*
436993 ATATTTTATGTATCATTATATTAAATTATTCAA
1 ATATTTTATATATCATTATATTAAATTATTCAA
437026 ATATTTTATATATCAT
1 ATATTTTATATATCAT
437042 CAAATTTACA
Statistics
Matches: 45, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
33 32 0.71
34 13 0.29
ACGTcount: A:0.39, C:0.05, G:0.02, T:0.54
Consensus pattern (33 bp):
ATATTTTATATATCATTATATTAAATTATTCAA
Found at i:437910 original size:20 final size:21
Alignment explanation
Indices: 437876--437923 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
437866 AAATTTTCTT
* *
437876 TAATTTTTTTGTATTCTTTCA
1 TAATTTTTATGTATTCTCTCA
437897 TAATTTTTAT-TATTCTCTCA
1 TAATTTTTATGTATTCTCTCA
*
437917 TGATTTT
1 TAATTTT
437924 GAGTACGTTC
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
20 15 0.62
21 9 0.38
ACGTcount: A:0.21, C:0.10, G:0.04, T:0.65
Consensus pattern (21 bp):
TAATTTTTATGTATTCTCTCA
Found at i:441907 original size:74 final size:74
Alignment explanation
Indices: 441824--441972 Score: 280
Period size: 74 Copynumber: 2.0 Consensus size: 74
441814 GGAAAGACGC
441824 AATTCAAGCAGAATTAAATTCACTTTCTAAACGTGAGGTTTTTGGACCTATAGTCCAAACACCTA
1 AATTCAAGCAGAATTAAATTCACTTTCTAAACGTGAGGTTTTTGGACCTATAGTCCAAACACCTA
441889 AATATGTAA
66 AATATGTAA
* *
441898 AATTCAAGCAGAATTAAATTCACTTTCTAGACGTGAGGTTTTTGGACCTATAGTCCAAACATCTA
1 AATTCAAGCAGAATTAAATTCACTTTCTAAACGTGAGGTTTTTGGACCTATAGTCCAAACACCTA
441963 AATATGTAA
66 AATATGTAA
441972 A
1 A
441973 GCCGATAGGA
Statistics
Matches: 73, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.38, C:0.17, G:0.14, T:0.32
Consensus pattern (74 bp):
AATTCAAGCAGAATTAAATTCACTTTCTAAACGTGAGGTTTTTGGACCTATAGTCCAAACACCTA
AATATGTAA
Found at i:442133 original size:16 final size:16
Alignment explanation
Indices: 442112--442148 Score: 74
Period size: 16 Copynumber: 2.3 Consensus size: 16
442102 TCCTATGGTG
442112 GATGCAATCATGTTTA
1 GATGCAATCATGTTTA
442128 GATGCAATCATGTTTA
1 GATGCAATCATGTTTA
442144 GATGC
1 GATGC
442149 CTTATTAGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.30, C:0.14, G:0.22, T:0.35
Consensus pattern (16 bp):
GATGCAATCATGTTTA
Found at i:444773 original size:20 final size:20
Alignment explanation
Indices: 444715--444803 Score: 81
Period size: 20 Copynumber: 4.5 Consensus size: 20
444705 TTCCAATACT
*
444715 AAAAATTATGAAAGAA-TATC
1 AAAAATTATG-AGGAAGTATC
* **
444735 AAGAATTATGACAAAGTATC
1 AAAAATTATGAGGAAGTATC
* * *
444755 AAAATTTATGAGGATGTATA
1 AAAAATTATGAGGAAGTATC
*
444775 AAAAATTATGAGGAAGTACC
1 AAAAATTATGAGGAAGTATC
*
444795 AAAACTTAT
1 AAAAATTAT
444804 ATGTATAAAA
Statistics
Matches: 54, Mismatches: 14, Indels: 2
0.77 0.20 0.03
Matches are distributed among these distances:
19 3 0.06
20 51 0.94
ACGTcount: A:0.52, C:0.07, G:0.15, T:0.27
Consensus pattern (20 bp):
AAAAATTATGAGGAAGTATC
Found at i:444862 original size:20 final size:20
Alignment explanation
Indices: 444837--444884 Score: 64
Period size: 19 Copynumber: 2.5 Consensus size: 20
444827 TATAAAAAAC
444837 AAAAATTATGAGGGAT-AACA
1 AAAAATTATGA-GGATGAACA
*
444857 AAAAA-TATGAGGATGCACA
1 AAAAATTATGAGGATGAACA
444876 AAAAATTAT
1 AAAAATTAT
444885 AAAGATGTAT
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
18 4 0.16
19 13 0.52
20 8 0.32
ACGTcount: A:0.56, C:0.06, G:0.17, T:0.21
Consensus pattern (20 bp):
AAAAATTATGAGGATGAACA
Found at i:444876 original size:19 final size:19
Alignment explanation
Indices: 444835--444999 Score: 70
Period size: 20 Copynumber: 8.4 Consensus size: 19
444825 AATATAAAAA
* *
444835 ACAAAAATTATGAGGGAT-A
1 ACAAAAAATATGA-GGATGC
444854 ACAAAAAATATGAGGATGC
1 ACAAAAAATATGAGGATGC
* * *
444873 ACAAAAAATTATAAAGATGT
1 ACAAAAAA-TATGAGGATGC
* * *
444893 ATAAAAAAGTTACGAGGGAAT-A
1 ACAAAAAA--TATGA-GG-ATGC
*
444915 AAAAAAAATATGAAGGAT--
1 ACAAAAAATATG-AGGATGC
* *
444933 ACCAAAAATA-CATGGATGC
1 ACAAAAAATATGA-GGATGC
**
444952 ACGAAAAAATACAAGGATGC
1 AC-AAAAAATATGAGGATGC
* *
444972 ACCAAAAAATATGAAGATGT
1 A-CAAAAAATATGAGGATGC
444992 ACAAAAAA
1 ACAAAAAA
445000 AAATGACAGA
Statistics
Matches: 113, Mismatches: 21, Indels: 24
0.72 0.13 0.15
Matches are distributed among these distances:
16 1 0.01
17 4 0.04
18 12 0.11
19 31 0.27
20 48 0.42
21 7 0.06
22 8 0.07
23 2 0.02
ACGTcount: A:0.57, C:0.09, G:0.17, T:0.17
Consensus pattern (19 bp):
ACAAAAAATATGAGGATGC
Found at i:444959 original size:20 final size:20
Alignment explanation
Indices: 444936--444982 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
444926 GAAGGATACC
* *
444936 AAAAATACATGGATGCACGA
1 AAAAATACAAGGATGCACCA
444956 AAAAATACAAGGATGCACCA
1 AAAAATACAAGGATGCACCA
444976 AAAAATA
1 AAAAATA
444983 TGAAGATGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.57, C:0.15, G:0.15, T:0.13
Consensus pattern (20 bp):
AAAAATACAAGGATGCACCA
Found at i:444990 original size:20 final size:21
Alignment explanation
Indices: 444917--445005 Score: 73
Period size: 20 Copynumber: 4.5 Consensus size: 21
444907 AGGGAATAAA
444917 AAAAAATATGAAGGAT--ACC
1 AAAAAATATGAAGGATGCACC
* * *
444936 -AAAAATA-CATGGATGCACG
1 AAAAAATATGAAGGATGCACC
*
444955 AAAAAATA-CAAGGATGCACC
1 AAAAAATATGAAGGATGCACC
* *
444975 AAAAAATATGAA-GATGTACA
1 AAAAAATATGAAGGATGCACC
*
444995 AAAAAAAATGA
1 AAAAAATATGA
445006 CAGAATACAA
Statistics
Matches: 57, Mismatches: 9, Indels: 7
0.78 0.12 0.10
Matches are distributed among these distances:
17 5 0.09
18 7 0.12
19 2 0.04
20 41 0.72
21 2 0.04
ACGTcount: A:0.58, C:0.11, G:0.16, T:0.15
Consensus pattern (21 bp):
AAAAAATATGAAGGATGCACC
Found at i:444999 original size:21 final size:20
Alignment explanation
Indices: 444975--445059 Score: 68
Period size: 21 Copynumber: 4.2 Consensus size: 20
444965 AGGATGCACC
444975 AAAAAATATGAAGATGTACAA
1 AAAAAATATGAAGA-GTACAA
*
444996 AAAAAA-ATGACAGAATACAA
1 AAAAAATATGA-AGAGTACAA
* **
445016 AAAATATAATGAA-A-TATTA
1 AAAAAAT-ATGAAGAGTACAA
*
445035 AAAAAATATGAGGAAGTACAA
1 AAAAAATATGAAG-AGTACAA
445056 AAAA
1 AAAA
445060 TAATGAGAGA
Statistics
Matches: 50, Mismatches: 8, Indels: 12
0.71 0.11 0.17
Matches are distributed among these distances:
18 4 0.08
19 9 0.18
20 16 0.32
21 17 0.34
22 4 0.08
ACGTcount: A:0.66, C:0.05, G:0.12, T:0.18
Consensus pattern (20 bp):
AAAAAATATGAAGAGTACAA
Found at i:445057 original size:20 final size:20
Alignment explanation
Indices: 444975--445059 Score: 77
Period size: 20 Copynumber: 4.2 Consensus size: 20
444965 AGGATGCACC
*
444975 AAAAAATATGAAGATGTACA
1 AAAAAATATGAAGAAGTACA
*
444995 AAAAAAAATGACAGAA-TAC-
1 AAAAAATATGA-AGAAGTACA
* *
445014 AAAAAATAT-AATGAAATATTA
1 AAAAAATATGAA-GAAGTA-CA
*
445035 AAAAAATATGAGGAAGTACA
1 AAAAAATATGAAGAAGTACA
445055 AAAAA
1 AAAAA
445060 TAATGAGAGA
Statistics
Matches: 52, Mismatches: 7, Indels: 12
0.73 0.10 0.17
Matches are distributed among these distances:
17 1 0.02
18 4 0.08
19 10 0.19
20 19 0.37
21 17 0.33
22 1 0.02
ACGTcount: A:0.66, C:0.05, G:0.12, T:0.18
Consensus pattern (20 bp):
AAAAAATATGAAGAAGTACA
Found at i:445065 original size:20 final size:20
Alignment explanation
Indices: 444974--445070 Score: 78
Period size: 19 Copynumber: 4.8 Consensus size: 20
444964 AAGGATGCAC
*
444974 CAAAAAAT-ATGAAGATGTA
1 CAAAAAATAATGAAGAAGTA
*
444993 CAAAAAAAAATGACAGAA-TA
1 CAAAAAATAATGA-AGAAGTA
*
445013 CAAAAAATATAATGAA-ATATTA
1 C-AAAAA-ATAATGAAGA-AGTA
*
445035 -AAAAAAT-ATGAGGAAGTA
1 CAAAAAATAATGAAGAAGTA
445053 CAAAAAATAATGAGAGAA
1 CAAAAAATAATGA-AGAA
445071 TACCATAAAA
Statistics
Matches: 62, Mismatches: 6, Indels: 18
0.72 0.07 0.21
Matches are distributed among these distances:
18 7 0.11
19 17 0.27
20 17 0.27
21 13 0.21
22 8 0.13
ACGTcount: A:0.64, C:0.05, G:0.13, T:0.18
Consensus pattern (20 bp):
CAAAAAATAATGAAGAAGTA
Found at i:445097 original size:60 final size:60
Alignment explanation
Indices: 444975--445101 Score: 150
Period size: 60 Copynumber: 2.1 Consensus size: 60
444965 AGGATGCACC
* * *
444975 AAAAAATATGAAGATGTACAAAAAAAAATGACAGAATACAAAAAATATAATGAAATATTA
1 AAAAAATATGAAGAAGTACAAAAAAAAATGACAGAATACAAAAAACAGAATGAAATATTA
* * * * *
445035 AAAAAATATGAGGAAGTACAAAAAATAATGAGAGAATACCATAAAACCCGAA-GAAATA-TA
1 AAAAAATATGAAGAAGTACAAAAAAAAATGACAGAATA-CA-AAAAACAGAATGAAATATTA
445095 AAAAAAT
1 AAAAAAT
445102 GAGGACGTAC
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
60 43 0.75
61 8 0.14
62 6 0.11
ACGTcount: A:0.64, C:0.07, G:0.12, T:0.17
Consensus pattern (60 bp):
AAAAAATATGAAGAAGTACAAAAAAAAATGACAGAATACAAAAAACAGAATGAAATATTA
Found at i:445270 original size:20 final size:19
Alignment explanation
Indices: 445221--445403 Score: 94
Period size: 20 Copynumber: 9.3 Consensus size: 19
445211 ATGATGTATA
445221 AAAAATTATCGAGAGAA-TAC
1 AAAAATTAT-GAG-GAAGTAC
445241 TAAAAA-TATGAGGAAGTATC
1 -AAAAATTATGAGGAAGTA-C
445261 AAAAATTATGAGAGAA-TAC
1 AAAAATTATGAG-GAAGTAC
* * *
445280 TATAAAACT-TGAGAAAATACC
1 -A-AAAATTATGAGGAAGTA-C
445301 AAATAA--AT-AGGAAGTAC
1 AAA-AATTATGAGGAAGTAC
*
445318 AAAAAATTATGAGGATGTAC
1 -AAAAATTATGAGGAAGTAC
* *
445338 AGAAAATTATGATGAAATAC
1 A-AAAATTATGAGGAAGTAC
*
445358 TAAGAAA-TATGAGAAAGTACC
1 -AA-AAATTATGAGGAAGTA-C
* *
445379 AAATATTATGAGGAAATACC
1 AAAAATTATGAGGAAGTA-C
445399 AAAAA
1 AAAAA
445404 AATTGAAAAA
Statistics
Matches: 128, Mismatches: 15, Indels: 39
0.70 0.08 0.21
Matches are distributed among these distances:
17 3 0.02
18 12 0.09
19 21 0.16
20 73 0.57
21 19 0.15
ACGTcount: A:0.55, C:0.08, G:0.16, T:0.22
Consensus pattern (19 bp):
AAAAATTATGAGGAAGTAC
Found at i:445387 original size:40 final size:40
Alignment explanation
Indices: 445221--445403 Score: 141
Period size: 40 Copynumber: 4.6 Consensus size: 40
445211 ATGATGTATA
* *
445221 AAAAATTATCGA-GAGAATACTAAAAA-TATGAGGAAGTATC
1 AAAAATTAT-GAGGA-AATACTAAAAACTATGAGAAAGTACC
*
445261 AAAAATTATGA-GAGAATACTATAAAACT-TGAGAAAATACC
1 AAAAATTATGAGGA-AATACTA-AAAACTATGAGAAAGTACC
* * * * *
445301 AAATAA--AT-AGGAAGTACAAAAAATTATGAGGATGTA-C
1 AAA-AATTATGAGGAAATACTAAAAACTATGAGAAAGTACC
*
445338 AGAAAATTATGATGAAATACTAAGAAA-TATGAGAAAGTACC
1 A-AAAATTATGAGGAAATACTAA-AAACTATGAGAAAGTACC
* *
445379 AAATATTATGAGGAAATACCAAAAA
1 AAAAATTATGAGGAAATACTAAAAA
445404 AATTGAAAAA
Statistics
Matches: 115, Mismatches: 17, Indels: 23
0.74 0.11 0.15
Matches are distributed among these distances:
37 9 0.08
38 15 0.13
39 21 0.18
40 62 0.54
41 8 0.07
ACGTcount: A:0.55, C:0.08, G:0.16, T:0.22
Consensus pattern (40 bp):
AAAAATTATGAGGAAATACTAAAAACTATGAGAAAGTACC
Found at i:445580 original size:9 final size:9
Alignment explanation
Indices: 445566--445592 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
445556 GTGTTTATAT
445566 TTTTTTTTC
1 TTTTTTTTC
445575 TTTTTTTTC
1 TTTTTTTTC
445584 TTTTTTTTC
1 TTTTTTTTC
445593 ACCGAAACTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.00, C:0.11, G:0.00, T:0.89
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:451697 original size:15 final size:16
Alignment explanation
Indices: 451671--451700 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
451661 AGATAACTTT
451671 ATAAATTTTATAAACA
1 ATAAATTTTATAAACA
451687 ATAAA-TTTATAAAC
1 ATAAATTTTATAAAC
451701 CCAAAATAAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 9 0.64
16 5 0.36
ACGTcount: A:0.57, C:0.07, G:0.00, T:0.37
Consensus pattern (16 bp):
ATAAATTTTATAAACA
Found at i:460983 original size:2 final size:2
Alignment explanation
Indices: 460976--461002 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
460966 CGATTTAGTA
460976 AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT A
461003 GTACAATAAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:468272 original size:25 final size:25
Alignment explanation
Indices: 468225--468274 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
468215 GTAATTAGAG
*
468225 ATTATATTTTATTTTTAAAAAAATA
1 ATTATATTTTATTTTGAAAAAAATA
468250 ATTATA-TTTATTATTGAATAAAAAT
1 ATTATATTTTATT-TTGAA-AAAAAT
468275 CTTTACTAGT
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
24 6 0.27
25 10 0.45
26 6 0.27
ACGTcount: A:0.48, C:0.00, G:0.02, T:0.50
Consensus pattern (25 bp):
ATTATATTTTATTTTGAAAAAAATA
Found at i:472575 original size:2 final size:2
Alignment explanation
Indices: 472568--472597 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
472558 AAACCTCAGC
472568 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
472598 AAACCAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:476615 original size:25 final size:26
Alignment explanation
Indices: 476587--476642 Score: 71
Period size: 26 Copynumber: 2.2 Consensus size: 26
476577 TAAATTATTA
476587 TAAATA-TATTTTTAATT-TCTATAAT
1 TAAATATTATTTTTAATTATCTA-AAT
* *
476612 TAAATATTATTTTTTATTATTTAAAT
1 TAAATATTATTTTTAATTATCTAAAT
476638 TAAAT
1 TAAAT
476643 TCAAGTACAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
25 6 0.22
26 18 0.67
27 3 0.11
ACGTcount: A:0.41, C:0.02, G:0.00, T:0.57
Consensus pattern (26 bp):
TAAATATTATTTTTAATTATCTAAAT
Found at i:477558 original size:58 final size:57
Alignment explanation
Indices: 477449--477578 Score: 138
Period size: 58 Copynumber: 2.2 Consensus size: 57
477439 TTCAACTATT
* * * * * *
477449 ATTAAACTTAATCACTCTAATATTAAATTAATATAATACTTATCAAGATAAATATTAG
1 ATTAAATTTAATAACTCT-ATATTAAATTAATAGAATACTTATCAAAATAAACATTAA
477507 ATTAAATTTAATAACTCT-TATTAAATTAATAGAATA-TTATCTACAAAATAAACATTAA
1 ATTAAATTTAATAACTCTATATTAAATTAATAGAATACTTA--T-CAAAATAAACATTAA
* *
477565 ATTAGATTTCATAA
1 ATTAAATTTAATAA
477579 TAAGGTAATC
Statistics
Matches: 61, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
55 3 0.05
56 17 0.28
57 1 0.02
58 40 0.66
ACGTcount: A:0.49, C:0.09, G:0.03, T:0.38
Consensus pattern (57 bp):
ATTAAATTTAATAACTCTATATTAAATTAATAGAATACTTATCAAAATAAACATTAA
Found at i:480618 original size:18 final size:17
Alignment explanation
Indices: 480595--480632 Score: 58
Period size: 18 Copynumber: 2.2 Consensus size: 17
480585 AATGATTTTC
*
480595 TTAGATAGATATTAATAT
1 TTAGATAAATATTAA-AT
480613 TTAGATAAATATTAAAT
1 TTAGATAAATATTAAAT
480630 TTA
1 TTA
480633 TTAAAATAAT
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 5 0.26
18 14 0.74
ACGTcount: A:0.47, C:0.00, G:0.08, T:0.45
Consensus pattern (17 bp):
TTAGATAAATATTAAAT
Found at i:481286 original size:18 final size:18
Alignment explanation
Indices: 481263--481298 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
481253 CAAGAACTCT
481263 TTCTTGAAAAGGAGATTA
1 TTCTTGAAAAGGAGATTA
**
481281 TTCTTGGCAAGGAGATTA
1 TTCTTGAAAAGGAGATTA
481299 GAATCAATTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.33, C:0.08, G:0.25, T:0.33
Consensus pattern (18 bp):
TTCTTGAAAAGGAGATTA
Found at i:482347 original size:34 final size:34
Alignment explanation
Indices: 482304--482408 Score: 131
Period size: 34 Copynumber: 3.0 Consensus size: 34
482294 TCTCGTAATG
482304 TAAATATTTAATTGACTCTTCAAAAAATTTATTC
1 TAAATATTTAATTGACTCTTCAAAAAATTTATTC
*
482338 TAAATATTTAATTGACTCTCTCAAATACATAATTTTTTC
1 TAAATATTTAATTGACTCT-TC-AA-A-A-AATTTATTC
* *
482377 TAAATA-TTAATTGACTCTTCAACAATTTTATT
1 TAAATATTTAATTGACTCTTCAAAAAATTTATT
482409 AGATAAAATC
Statistics
Matches: 62, Mismatches: 4, Indels: 11
0.81 0.05 0.14
Matches are distributed among these distances:
33 6 0.10
34 20 0.32
35 2 0.03
36 4 0.06
37 3 0.05
38 13 0.21
39 14 0.23
ACGTcount: A:0.38, C:0.13, G:0.03, T:0.46
Consensus pattern (34 bp):
TAAATATTTAATTGACTCTTCAAAAAATTTATTC
Found at i:487842 original size:24 final size:27
Alignment explanation
Indices: 487799--487851 Score: 76
Period size: 25 Copynumber: 2.1 Consensus size: 27
487789 AGTATTTCCT
*
487799 CTCTTCTCTTCCTCCT-C-CACTCTCC
1 CTCTTCTCCTCCTCCTCCACACTCTCC
487824 CTCTTCTCCT-CTCCTCCACACTCTCC
1 CTCTTCTCCTCCTCCTCCACACTCTCC
487850 CT
1 CT
487852 TGGATTCACA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
24 5 0.20
25 10 0.40
26 10 0.40
ACGTcount: A:0.06, C:0.57, G:0.00, T:0.38
Consensus pattern (27 bp):
CTCTTCTCCTCCTCCTCCACACTCTCC
Found at i:494345 original size:5 final size:5
Alignment explanation
Indices: 494335--494379 Score: 90
Period size: 5 Copynumber: 9.0 Consensus size: 5
494325 ATCTTTATCT
494335 CATCC CATCC CATCC CATCC CATCC CATCC CATCC CATCC CATCC
1 CATCC CATCC CATCC CATCC CATCC CATCC CATCC CATCC CATCC
494380 TACTCCATCC
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 40 1.00
ACGTcount: A:0.20, C:0.60, G:0.00, T:0.20
Consensus pattern (5 bp):
CATCC
Found at i:499562 original size:26 final size:26
Alignment explanation
Indices: 499506--499555 Score: 73
Period size: 26 Copynumber: 1.9 Consensus size: 26
499496 ACACATTTGA
499506 AATTTAATCTTTTCTTATTTTTTTAG
1 AATTTAATCTTTTCTTATTTTTTTAG
* * *
499532 AATTTAGTCTTTTTTTTTTTTTTT
1 AATTTAATCTTTTCTTATTTTTTT
499556 TTAATTTCAA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
26 21 1.00
ACGTcount: A:0.18, C:0.06, G:0.04, T:0.72
Consensus pattern (26 bp):
AATTTAATCTTTTCTTATTTTTTTAG
Found at i:503122 original size:41 final size:41
Alignment explanation
Indices: 503065--503179 Score: 212
Period size: 41 Copynumber: 2.8 Consensus size: 41
503055 ACCCACAAAT
*
503065 AAGAATAAATGAAAAAGAAGCCCAGTCACTTATATTAGTGA
1 AAGAATAAAAGAAAAAGAAGCCCAGTCACTTATATTAGTGA
*
503106 AAGAATAAAAGAAAAAGAAGCGCAGTCACTTATATTAGTGA
1 AAGAATAAAAGAAAAAGAAGCCCAGTCACTTATATTAGTGA
503147 AAGAATAAAAGAAAAAGAAGCCCAGTCACTTAT
1 AAGAATAAAAGAAAAAGAAGCCCAGTCACTTAT
503180 GGTGCGTATA
Statistics
Matches: 71, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
41 71 1.00
ACGTcount: A:0.51, C:0.12, G:0.17, T:0.19
Consensus pattern (41 bp):
AAGAATAAAAGAAAAAGAAGCCCAGTCACTTATATTAGTGA
Found at i:503917 original size:3 final size:3
Alignment explanation
Indices: 503909--503934 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
503899 GATCTTTGCA
503909 GCT GCT GCT GCT GCT GCT GCT GCT GC
1 GCT GCT GCT GCT GCT GCT GCT GCT GC
503935 CGCTTGCTCT
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:0.35, G:0.35, T:0.31
Consensus pattern (3 bp):
GCT
Found at i:518587 original size:46 final size:45
Alignment explanation
Indices: 518451--518666 Score: 213
Period size: 46 Copynumber: 4.7 Consensus size: 45
518441 ACGCTAGAGC
* * * *
518451 GCTTACTGTTTCGCACTTCGTGCGCTTATTGTTTCGCACTTCGTGT
1 GCTTACTGTTTTGCACTTTGTGTGCTTACTGTTTCGCACTT-GTGT
* * * *
518497 ACTTACTGTTTCGCACTTCGTGTACTTACTGTTTCGCACTTTGTGT
1 GCTTACTGTTTTGCACTTTGTGTGCTTACTGTTTCGCAC-TTGTGT
518543 GCTTACTGTTTTGCACTTTGTGTGCTTACTGTTTCGCACCTTGTGT
1 GCTTACTGTTTTGCACTTTGTGTGCTTACTGTTTCGCA-CTTGTGT
* * * * *
518589 GGC-TACTGATTTGCGCTATGTGTGCCTACTGATT-GCACTGTGTGT
1 -GCTTACTGTTTTGCACTTTGTGTGCTTACTGTTTCGCACT-TGTGT
** *
518634 G-TCTACTGGATTGCACTGTGTGTGCTTACTGTT
1 GCT-TACTGTTTTGCACTTTGTGTGCTTACTGTT
518667 AAGTATTTCG
Statistics
Matches: 145, Mismatches: 19, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
44 3 0.02
45 32 0.22
46 105 0.72
47 5 0.03
ACGTcount: A:0.11, C:0.22, G:0.23, T:0.44
Consensus pattern (45 bp):
GCTTACTGTTTTGCACTTTGTGTGCTTACTGTTTCGCACTTGTGT
Found at i:518596 original size:23 final size:23
Alignment explanation
Indices: 518451--518589 Score: 199
Period size: 23 Copynumber: 6.0 Consensus size: 23
518441 ACGCTAGAGC
*
518451 GCTTACTGTTTCGCACTTCGTGC
1 GCTTACTGTTTCGCACTTCGTGT
*
518474 GCTTATTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACTTCGTGT
*
518497 ACTTACTGTTTCGCACTTCGTGT
1 GCTTACTGTTTCGCACTTCGTGT
* *
518520 ACTTACTGTTTCGCACTTTGTGT
1 GCTTACTGTTTCGCACTTCGTGT
* *
518543 GCTTACTGTTTTGCACTTTGTGT
1 GCTTACTGTTTCGCACTTCGTGT
518566 GCTTACTGTTTCGCACCTT-GTGT
1 GCTTACTGTTTCGCA-CTTCGTGT
518589 G
1 G
518590 GCTACTGATT
Statistics
Matches: 107, Mismatches: 8, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
23 104 0.97
24 3 0.03
ACGTcount: A:0.10, C:0.24, G:0.21, T:0.45
Consensus pattern (23 bp):
GCTTACTGTTTCGCACTTCGTGT
Found at i:518610 original size:23 final size:22
Alignment explanation
Indices: 518523--518664 Score: 106
Period size: 23 Copynumber: 6.2 Consensus size: 22
518513 TTCGTGTACT
* * *
518523 TACTGTTTCGCACTTTGTGTGCT
1 TACTGATT-GCACTATGTGTGCC
* * *
518546 TACTGTTTTGCACTTTGTGTGCT
1 TACTG-ATTGCACTATGTGTGCC
* *
518569 TACTGTTTCGCACCT-TGTGTGGC
1 TACTGATT-GCA-CTATGTGTGCC
*
518592 TACTGATTTGCGCTATGTGTGCC
1 TACTGA-TTGCACTATGTGTGCC
* *
518615 TACTGATTGCACTGTGTGTGTC
1 TACTGATTGCACTATGTGTGCC
* *
518637 TACTGGATTGCACTGTGTGTGCT
1 TACT-GATTGCACTATGTGTGCC
518660 TACTG
1 TACTG
518665 TTAAGTATTT
Statistics
Matches: 103, Mismatches: 10, Indels: 13
0.82 0.08 0.10
Matches are distributed among these distances:
22 23 0.22
23 73 0.71
24 7 0.07
ACGTcount: A:0.11, C:0.20, G:0.25, T:0.43
Consensus pattern (22 bp):
TACTGATTGCACTATGTGTGCC
Found at i:518611 original size:69 final size:69
Alignment explanation
Indices: 518452--518634 Score: 196
Period size: 69 Copynumber: 2.7 Consensus size: 69
518442 CGCTAGAGCG
* * * * *
518452 CTTACTGTTTCGCACT-TCGTGCGCTTATTGTTTCGCACTTCGTGTACTTACTGTTTCGCACTTC
1 CTTACTGTTTCGCACTAT-GTGTGCTTACTGTTTTGCACTTTGTGTGCTTACTGTTTCGCACTTC
518516 GTGTA
65 GTGTA
*
518521 CTTACTGTTTCGCACTTTGTGTGCTTACTGTTTTGCACTTTGTGTGCTTACTGTTTCGCACCTT-
1 CTTACTGTTTCGCACTATGTGTGCTTACTGTTTTGCACTTTGTGTGCTTACTGTTTCGCA-CTTC
*
518585 GTGTGG
65 GTGT-A
* * * *
518591 C-TACTGATTT-GCGCTATGTGTGCCTACTG-ATTGCACTGTGTGTG
1 CTTACTG-TTTCGCACTATGTGTGCTTACTGTTTTGCACTTTGTGTG
518635 TCTACTGGAT
Statistics
Matches: 99, Mismatches: 11, Indels: 9
0.83 0.09 0.08
Matches are distributed among these distances:
68 13 0.13
69 78 0.79
70 8 0.08
ACGTcount: A:0.11, C:0.23, G:0.22, T:0.44
Consensus pattern (69 bp):
CTTACTGTTTCGCACTATGTGTGCTTACTGTTTTGCACTTTGTGTGCTTACTGTTTCGCACTTCG
TGTA
Found at i:519364 original size:19 final size:19
Alignment explanation
Indices: 519340--519380 Score: 82
Period size: 19 Copynumber: 2.2 Consensus size: 19
519330 TCATGTCAAT
519340 TATCACGTCATCAACTTTC
1 TATCACGTCATCAACTTTC
519359 TATCACGTCATCAACTTTC
1 TATCACGTCATCAACTTTC
519378 TAT
1 TAT
519381 GTCAATCGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 22 1.00
ACGTcount: A:0.27, C:0.29, G:0.05, T:0.39
Consensus pattern (19 bp):
TATCACGTCATCAACTTTC
Found at i:524365 original size:6 final size:6
Alignment explanation
Indices: 524354--524380 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
524344 TGATCAGCTT
524354 CCCCCA CCCCCA CCCCCA CCCCCA CCC
1 CCCCCA CCCCCA CCCCCA CCCCCA CCC
524381 AGTAAAAAGT
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:0.15, C:0.85, G:0.00, T:0.00
Consensus pattern (6 bp):
CCCCCA
Found at i:527077 original size:34 final size:35
Alignment explanation
Indices: 527013--527078 Score: 91
Period size: 34 Copynumber: 1.9 Consensus size: 35
527003 TTTTTTTCTT
* *
527013 TTTATTTCTTTATTTTCCTTCTCTTCTTCTTCCCC
1 TTTATTTCTTTATTTTCCTTCTCGTATTCTTCCCC
527048 TTTATTT-TTT-TTTTCTCTTCTCGTATTCTTC
1 TTTATTTCTTTATTTTC-CTTCTCGTATTCTTC
527079 ATTGTAGAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
33 5 0.18
34 16 0.57
35 7 0.25
ACGTcount: A:0.06, C:0.26, G:0.02, T:0.67
Consensus pattern (35 bp):
TTTATTTCTTTATTTTCCTTCTCGTATTCTTCCCC
Found at i:528011 original size:24 final size:24
Alignment explanation
Indices: 527971--528037 Score: 66
Period size: 24 Copynumber: 2.7 Consensus size: 24
527961 GAACGAAAAA
*
527971 AAAAGAAGAAAAGTTAAAAGCACAT-
1 AAAAGAA-AAAAATTAAAAGCAC-TC
*
527996 AAAAGAAAAAAATT-AAATCACTC
1 AAAAGAAAAAAATTAAAAGCACTC
528019 AAAATGAAAAAAATATAAA
1 AAAA-GAAAAAAAT-TAAA
528038 GACCAATTGT
Statistics
Matches: 36, Mismatches: 2, Indels: 7
0.80 0.04 0.16
Matches are distributed among these distances:
22 1 0.03
23 10 0.28
24 15 0.42
25 8 0.22
26 2 0.06
ACGTcount: A:0.69, C:0.07, G:0.09, T:0.15
Consensus pattern (24 bp):
AAAAGAAAAAAATTAAAAGCACTC
Found at i:528887 original size:3 final size:3
Alignment explanation
Indices: 528879--528910 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
528869 TATCTATTTG
528879 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
528911 AACTCATCAG
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:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:532864 original size:219 final size:219
Alignment explanation
Indices: 532485--532922 Score: 876
Period size: 219 Copynumber: 2.0 Consensus size: 219
532475 ACTGTCATAG
532485 AAAGAAGCTTGAATTCTATACATGAAACTATACCTGGAAAGTTGGGATCAACTCATGCATAACAC
1 AAAGAAGCTTGAATTCTATACATGAAACTATACCTGGAAAGTTGGGATCAACTCATGCATAACAC
532550 ACAATATAAGGTGCTGCACTAGGAACCTAGGAGCCTAGGGAAACCAGGAAACTAACGGTTTAGAG
66 ACAATATAAGGTGCTGCACTAGGAACCTAGGAGCCTAGGGAAACCAGGAAACTAACGGTTTAGAG
532615 TTGGGCAATAGACATGGTCAGTTAAGAATTAGGAAAATGCGGTGCAGGGGAATAAACCAGATATG
131 TTGGGCAATAGACATGGTCAGTTAAGAATTAGGAAAATGCGGTGCAGGGGAATAAACCAGATATG
532680 GCAAGATATTCTGTGGTTGAGTGT
196 GCAAGATATTCTGTGGTTGAGTGT
532704 AAAGAAGCTTGAATTCTATACATGAAACTATACCTGGAAAGTTGGGATCAACTCATGCATAACAC
1 AAAGAAGCTTGAATTCTATACATGAAACTATACCTGGAAAGTTGGGATCAACTCATGCATAACAC
532769 ACAATATAAGGTGCTGCACTAGGAACCTAGGAGCCTAGGGAAACCAGGAAACTAACGGTTTAGAG
66 ACAATATAAGGTGCTGCACTAGGAACCTAGGAGCCTAGGGAAACCAGGAAACTAACGGTTTAGAG
532834 TTGGGCAATAGACATGGTCAGTTAAGAATTAGGAAAATGCGGTGCAGGGGAATAAACCAGATATG
131 TTGGGCAATAGACATGGTCAGTTAAGAATTAGGAAAATGCGGTGCAGGGGAATAAACCAGATATG
532899 GCAAGATATTCTGTGGTTGAGTGT
196 GCAAGATATTCTGTGGTTGAGTGT
532923 GGGCATAGGG
Statistics
Matches: 219, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
219 219 1.00
ACGTcount: A:0.36, C:0.15, G:0.26, T:0.23
Consensus pattern (219 bp):
AAAGAAGCTTGAATTCTATACATGAAACTATACCTGGAAAGTTGGGATCAACTCATGCATAACAC
ACAATATAAGGTGCTGCACTAGGAACCTAGGAGCCTAGGGAAACCAGGAAACTAACGGTTTAGAG
TTGGGCAATAGACATGGTCAGTTAAGAATTAGGAAAATGCGGTGCAGGGGAATAAACCAGATATG
GCAAGATATTCTGTGGTTGAGTGT
Found at i:538094 original size:25 final size:26
Alignment explanation
Indices: 538043--538097 Score: 69
Period size: 26 Copynumber: 2.2 Consensus size: 26
538033 TTTGTCTAAA
* *
538043 TTTATTTTTTAGTAAATTTATATATT
1 TTTATTTTTTAATAAATATATATATT
538069 TTTATTTTTTAATAAA-ATATCA-ATT
1 TTTATTTTTTAATAAATATAT-ATATT
538094 TTTA
1 TTTA
538098 GGTTATTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
25 10 0.38
26 16 0.62
ACGTcount: A:0.35, C:0.02, G:0.02, T:0.62
Consensus pattern (26 bp):
TTTATTTTTTAATAAATATATATATT
Found at i:541550 original size:90 final size:91
Alignment explanation
Indices: 541395--541578 Score: 284
Period size: 90 Copynumber: 2.0 Consensus size: 91
541385 GGATGTAAAA
* *
541395 ATGTATGATGTTATAGTCAAATGATTAGGCAGATAATGATCATCTAATACGACTATATTCTTAAA
1 ATGTATGATGTTATAGTCAAATGATTAGGCACATAATGATCATCTAATACGACTATATTCCTAAA
*
541460 ATATATG-AAAAACCCTTA-ATTGTGT
66 ATAAATGAAAAAACCCTTATA-TGTGT
* *
541485 ATGTATGATGTTATAGTCAAATGATTAGGCACATAATGTTCATCTGATACTG-CTATATTCCTAA
1 ATGTATGATGTTATAGTCAAATGATTAGGCACATAATGATCATCTAATAC-GACTATATTCCTAA
541549 AATAAATGAAAAAACCCTTATATGTGT
65 AATAAATGAAAAAACCCTTATATGTGT
541576 ATG
1 ATG
541579 ATTTGTTGAG
Statistics
Matches: 86, Mismatches: 5, Indels: 5
0.90 0.05 0.05
Matches are distributed among these distances:
90 65 0.76
91 20 0.23
92 1 0.01
ACGTcount: A:0.38, C:0.12, G:0.15, T:0.35
Consensus pattern (91 bp):
ATGTATGATGTTATAGTCAAATGATTAGGCACATAATGATCATCTAATACGACTATATTCCTAAA
ATAAATGAAAAAACCCTTATATGTGT
Found at i:546122 original size:2 final size:2
Alignment explanation
Indices: 546115--546152 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
546105 AAGATTTAAT
546115 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
546153 GGAAAATGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:548714 original size:20 final size:20
Alignment explanation
Indices: 548685--548821 Score: 159
Period size: 20 Copynumber: 7.3 Consensus size: 20
548675 CATTTAAAAT
548685 TTGCTTTGCTTTGCTTTATA
1 TTGCTTTGCTTTGCTTTATA
548705 TTG---T--TTTGCTTTATA
1 TTGCTTTGCTTTGCTTTATA
*
548720 TTACTTTGCTTTGCTTTATA
1 TTGCTTTGCTTTGCTTTATA
*
548740 TTGCTTTGCTTTGCTTTGTA
1 TTGCTTTGCTTTGCTTTATA
*
548760 -----TTACTTTGCTTTATA
1 TTGCTTTGCTTTGCTTTATA
*
548775 TTGCTTTGCTTTGCTTTATC
1 TTGCTTTGCTTTGCTTTATA
*
548795 TTACTTTGCTTTGCTTTATA
1 TTGCTTTGCTTTGCTTTATA
548815 TTGCTTT
1 TTGCTTT
548822 ATATCAAAGC
Statistics
Matches: 97, Mismatches: 10, Indels: 20
0.76 0.08 0.16
Matches are distributed among these distances:
15 26 0.27
17 1 0.01
18 1 0.01
20 69 0.71
ACGTcount: A:0.11, C:0.15, G:0.13, T:0.61
Consensus pattern (20 bp):
TTGCTTTGCTTTGCTTTATA
Found at i:548819 original size:35 final size:35
Alignment explanation
Indices: 548688--548821 Score: 153
Period size: 35 Copynumber: 3.7 Consensus size: 35
548678 TTAAAATTTG
* *
548688 CTTTGCTTTGCTTTATATTGTTTTGCTTTATATTA
1 CTTTGCTTTGCTTTATATTGCTTTGCTTTATCTTA
* *
548723 CTTTGCTTTGCTTTATATTGCTTTGCTTT-GCTTT
1 CTTTGCTTTGCTTTATATTGCTTTGCTTTATCTTA
* *
548757 GTATTACTTTGCTTTATATTGCTTTGCTTTGCTTTATCTTA
1 CT-TTGCTTTGCTTTATA-----TTGCTTTGCTTTATCTTA
548798 CTTTGCTTTGCTTTATATTGCTTT
1 CTTTGCTTTGCTTTATATTGCTTT
548822 ATATCAAAGC
Statistics
Matches: 82, Mismatches: 10, Indels: 14
0.77 0.09 0.13
Matches are distributed among these distances:
34 3 0.04
35 49 0.60
40 26 0.32
41 4 0.05
ACGTcount: A:0.11, C:0.15, G:0.13, T:0.61
Consensus pattern (35 bp):
CTTTGCTTTGCTTTATATTGCTTTGCTTTATCTTA
Found at i:548821 original size:15 final size:15
Alignment explanation
Indices: 548690--548786 Score: 77
Period size: 15 Copynumber: 5.8 Consensus size: 15
548680 AAAATTTGCT
548690 TTGCTTTGCTTTATA
1 TTGCTTTGCTTTATA
*
548705 TTGTTTTGCTTTATATTA
1 TTGCTTTGC-TT-TA-TA
548723 CTTTGCTTTGCTTTATA
1 --TTGCTTTGCTTTATA
*
548740 TTGCTTTGCTTTGCTTTGTA
1 -----TTGCTTTGCTTTATA
*
548760 TTACTTTGCTTTATA
1 TTGCTTTGCTTTATA
548775 TTGCTTTGCTTT
1 TTGCTTTGCTTT
548787 GCTTTATCTT
Statistics
Matches: 68, Mismatches: 6, Indels: 16
0.76 0.07 0.18
Matches are distributed among these distances:
15 32 0.47
16 2 0.03
17 4 0.06
18 4 0.06
19 2 0.03
20 24 0.35
ACGTcount: A:0.11, C:0.13, G:0.13, T:0.62
Consensus pattern (15 bp):
TTGCTTTGCTTTATA
Found at i:548861 original size:25 final size:25
Alignment explanation
Indices: 548827--549075 Score: 139
Period size: 25 Copynumber: 9.6 Consensus size: 25
548817 GCTTTATATC
*
548827 AAAGCAAAGCAAAGCAAAGGAAAAT
1 AAAGCAAAGCAAAGCAAAGTAAAAT
* *
548852 AAAGCAAAGCAAAGCAAAGCAATAT
1 AAAGCAAAGCAAAGCAAAGTAAAAT
548877 AAAGCAAAGCAAAG-AGAAGTAATATAATAT
1 AAAGCAAAGCAAAGCA-AAG---TA-AA-AT
*
548907 AAAGCAAAGCAAAGCAAAGTAATAT
1 AAAGCAAAGCAAAGCAAAGTAAAAT
* *
548932 AAAG-AAGAGCAACGTAATGCAAAGCAAAGT
1 AAAGCAA-AGC-A---AA-GCAAAGTAAAAT
* * **
548962 AAAGTAAAGAAAAGCAAAGTAATCT
1 AAAGCAAAGCAAAGCAAAGTAAAAT
* * * ***
548987 AAAGCAATGTAAAGCAAAGCAATGC
1 AAAGCAAAGCAAAGCAAAGTAAAAT
* *
549012 AAAGCAATGCAAAG-AAA-TATAAAGC
1 AAAGCAAAGCAAAGCAAAGTA-AAA-T
* *
549037 AATA-TAAAGCAAAGCAAAGTAATAT
1 AA-AGCAAAGCAAAGCAAAGTAAAAT
*
549062 AAACCAAAGCAAAG
1 AAAGCAAAGCAAAG
549076 AAATATAAAC
Statistics
Matches: 177, Mismatches: 27, Indels: 40
0.73 0.11 0.16
Matches are distributed among these distances:
23 1 0.01
24 8 0.05
25 112 0.63
26 10 0.06
27 4 0.02
28 1 0.01
29 4 0.02
30 34 0.19
31 3 0.02
ACGTcount: A:0.59, C:0.12, G:0.17, T:0.12
Consensus pattern (25 bp):
AAAGCAAAGCAAAGCAAAGTAAAAT
Found at i:548862 original size:30 final size:29
Alignment explanation
Indices: 548826--549075 Score: 145
Period size: 30 Copynumber: 8.3 Consensus size: 29
548816 TGCTTTATAT
*
548826 CAAAGCAAAGCAAAGCAAAGGAAAATAAAG
1 CAAAGCAAAGCAAAGCAAA-TAAAATAAAG
548856 CAAAGCAAAGCAAAGC-AAT---ATAAAG
1 CAAAGCAAAGCAAAGCAAATAAAATAAAG
* *
548881 CAAAGCAAAG-AGAAGTAATATAATATAAAG
1 CAAAGCAAAGCA-AAGCAA-ATAAAATAAAG
* *
548911 CAAAGCAAAGCAAAGTAATATAAAGA-AGAG
1 CAAAGCAAAGCAAAGCAA-ATAAA-ATAAAG
* * * *
548941 CAACGTAATGCAAAGCAAAGTAAAGTAAAG
1 CAAAGCAAAGCAAAGCAAA-TAAAATAAAG
* * **
548971 AAAAGCAAAGTAATCTAAAGCAATGTAAAGCAAAG
1 CAAAGCAAAG----C-AAAGCAA-ATAAAATAAAG
* * *
549006 CAATGCAAAGCAATGCAAAGAAATATAAAG
1 CAAAGCAAAGCAAAGCAAATAAA-ATAAAG
* * *
549036 CAATA-TAAAGCAAAGCAAAGTAATATAAAC
1 CAA-AGCAAAGCAAAGCAAA-TAAAATAAAG
549066 CAAAGCAAAG
1 CAAAGCAAAG
549076 AAATATAAAC
Statistics
Matches: 170, Mismatches: 30, Indels: 40
0.71 0.12 0.17
Matches are distributed among these distances:
24 1 0.01
25 19 0.11
26 1 0.01
27 2 0.01
29 7 0.04
30 110 0.65
31 5 0.03
34 1 0.01
35 24 0.14
ACGTcount: A:0.59, C:0.12, G:0.17, T:0.12
Consensus pattern (29 bp):
CAAAGCAAAGCAAAGCAAATAAAATAAAG
Found at i:548880 original size:20 final size:20
Alignment explanation
Indices: 548857--549089 Score: 81
Period size: 20 Copynumber: 11.4 Consensus size: 20
548847 AAAATAAAGC
548857 AAAGCAAAGCAAAGCAATAT
1 AAAGCAAAGCAAAGCAATAT
*
548877 AAAGCAAAGCAAAGAGAAGTAATATAAT
1 AAAGCAAAGC----A-AAG-CA-AT-AT
548905 ATAAAGCAAAGCAAAGCAA-AGT
1 --AAAGCAAAGCAAAGCAATA-T
* **
548927 AATA-TAAAG-AAGAGCAACGT
1 AA-AGCAAAGCAA-AGCAATAT
* *
548947 AATGCAAAGCAAAGTAA-AGT
1 AAAGCAAAGCAAAGCAATA-T
* * *
548967 AAAGAAAAGCAAAGTAATCT
1 AAAGCAAAGCAAAGCAATAT
* *
548987 AAAGCAATGTAAAGC-----
1 AAAGCAAAGCAAAGCAATAT
* **
549002 AAAGCAATGCAAAGCAATGC
1 AAAGCAAAGCAAAGCAATAT
**
549022 AAAG-AAATATAAAGCAATAT
1 AAAGCAAA-GCAAAGCAATAT
*
549042 AAAGCAAAGCAAAGTAATAT
1 AAAGCAAAGCAAAGCAATAT
* *
549062 AAACCAAAGCAAAGAAATAT
1 AAAGCAAAGCAAAGCAATAT
*
549082 AAACCAAA
1 AAAGCAAA
549090 CTTCTTTGAT
Statistics
Matches: 162, Mismatches: 26, Indels: 50
0.68 0.11 0.21
Matches are distributed among these distances:
15 14 0.09
19 4 0.02
20 111 0.69
21 7 0.04
22 1 0.01
23 1 0.01
24 2 0.01
25 6 0.04
26 2 0.01
27 2 0.01
28 2 0.01
30 10 0.06
ACGTcount: A:0.59, C:0.12, G:0.16, T:0.13
Consensus pattern (20 bp):
AAAGCAAAGCAAAGCAATAT
Found at i:548954 original size:35 final size:35
Alignment explanation
Indices: 548915--549025 Score: 127
Period size: 35 Copynumber: 3.2 Consensus size: 35
548905 ATAAAGCAAA
* *
548915 GCAAAGCAAAGTAATA-TAAAGAAGAGCAACGTAAT
1 GCAAAGCAAAGTAA-AGTAAAGAAAAGCAAAGTAAT
548950 GCAAAGCAAAGTAAAGTAAAGAAAAGCAAAGTAAT
1 GCAAAGCAAAGTAAAGTAAAGAAAAGCAAAGTAAT
* * * * *
548985 -CTAAAGCAATGTAAAGCAAAGCAATGCAAAGCAAT
1 GC-AAAGCAAAGTAAAGTAAAGAAAAGCAAAGTAAT
549020 GCAAAG
1 GCAAAG
549026 AAATATAAAG
Statistics
Matches: 66, Mismatches: 7, Indels: 6
0.84 0.09 0.08
Matches are distributed among these distances:
34 2 0.03
35 63 0.95
36 1 0.02
ACGTcount: A:0.55, C:0.13, G:0.20, T:0.13
Consensus pattern (35 bp):
GCAAAGCAAAGTAAAGTAAAGAAAAGCAAAGTAAT
Found at i:549074 original size:5 final size:5
Alignment explanation
Indices: 548826--549055 Score: 100
Period size: 5 Copynumber: 46.0 Consensus size: 5
548816 TGCTTTATAT
* * *
548826 CAAAG CAAAG CAAAG CAAAG GAAAA TAAAG CAAAG CAAAG CAAAG CAATA-
1 CAAAG CAAAG CAAAG CAAAG CAAAG CAAAG CAAAG CAAAG CAAAG CAA-AG
* * * *
548876 TAAAG CAAAG CAAAG -AGAAG TAATA- TAATA- TAAAG CAAAG CAAAG
1 CAAAG CAAAG CAAAG CA-AAG CAA-AG CAA-AG CAAAG CAAAG CAAAG
* * * * * * *
548921 CAAAG TAATA- TAAAG -AAGAG CAACG TAATG CAAAG CAAAG TAAAG TAAAG
1 CAAAG CAA-AG CAAAG CAA-AG CAAAG CAAAG CAAAG CAAAG CAAAG CAAAG
* * * * * * *
548971 AAAAG CAAAG -TAAT CTAAAG CAATG TAAAG CAAAG CAATG CAAAG CAATG
1 CAAAG CAAAG CAAAG C-AAAG CAAAG CAAAG CAAAG CAAAG CAAAG CAAAG
* * *
549021 CAAAG -AAATA TAAAG CAATA- TAAAG CAAAG CAAAG
1 CAAAG CAAA-G CAAAG CAA-AG CAAAG CAAAG CAAAG
549056 TAATATAAAC
Statistics
Matches: 175, Mismatches: 34, Indels: 32
0.73 0.14 0.13
Matches are distributed among these distances:
4 12 0.07
5 150 0.86
6 13 0.07
ACGTcount: A:0.59, C:0.12, G:0.18, T:0.11
Consensus pattern (5 bp):
CAAAG
Found at i:549708 original size:111 final size:107
Alignment explanation
Indices: 549491--549814 Score: 492
Period size: 106 Copynumber: 3.0 Consensus size: 107
549481 TGGAAATATG
*
549491 CCTTATTTTTTAGAAAATCCTAATTAATCAGAAAAATATTAGAAATCCTTCTAACAGAAAAAAAA
1 CCTTATTTTTTAGAAAATCCTAATTAATCAGAAAAATATTAGAAATCCTTCTAACAG----ACAA
* * *
549556 AAAATATTAAGCTATTAAGCATCATCTTGATGAACCATTTTCTTTT
62 AAAATATGAAGTTATTAAGCATCATCTTGATGAACCCTTTTCTTTT
549602 CCTTATTTTTTAGAAAATCCTAATTAATCAGAAAAATATTAGAAATCCTTCTAACAGACAAAAAA
1 CCTTATTTTTTAGAAAATCCTAATTAATCAGAAAAATATTAGAAATCCTTCTAACAGACAAAAAA
* *
549667 TATGAAGTTATTAAGCATCATCCTGCTGAACCC-TTTCTTTT
66 TATGAAGTTATTAAGCATCATCTTGATGAACCCTTTTCTTTT
* * * *
549708 CCATATTTTTTAGAAAATCCTAATTAATAAGAAAAATATTAGAAATCCTTCTCACAAACAAAAAA
1 CCTTATTTTTTAGAAAATCCTAATTAATCAGAAAAATATTAGAAATCCTTCTAACAGACAAAAAA
549773 TATGAA-TCTATTAAGCATCATCTTGATGAA-CCTTTTCTTTT
66 TATGAAGT-TATTAAGCATCATCTTGATGAACCCTTTTCTTTT
549814 C
1 C
549815 TAAACTATCA
Statistics
Matches: 199, Mismatches: 12, Indels: 9
0.90 0.05 0.04
Matches are distributed among these distances:
105 3 0.02
106 104 0.52
107 35 0.18
111 57 0.29
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.35
Consensus pattern (107 bp):
CCTTATTTTTTAGAAAATCCTAATTAATCAGAAAAATATTAGAAATCCTTCTAACAGACAAAAAA
TATGAAGTTATTAAGCATCATCTTGATGAACCCTTTTCTTTT
Found at i:550323 original size:116 final size:106
Alignment explanation
Indices: 550158--550528 Score: 478
Period size: 116 Copynumber: 3.4 Consensus size: 106
550148 TGGAGATATG
* *
550158 CCTTATTTTTTTAGAAAATCCTAATTAATCAAAAAAAT-ATAAGAAATCCTTCAAACAGACAAAA
1 CCTTA-TTTTTTAGAAAATCCTAATTAATCAGAAAAATAAT-AGAAATCCTTCTAACAGACAAAA
*
550222 AATATGAAGCTATTAAGCATCATCCTGATTAACCATTTTCTTTT
64 AATATGAAGCTATTAAGCATCATCCTGATGAACCATTTT-TTTT
* *
550266 CTTTGCTTTGCTCATTTTTTAGAAAATCCTAATTAATTAGAAAATTAATAGAAATCCTTCTAACA
1 C----C--T--T-ATTTTTTAGAAAATCCTAATTAATCAGAAAAATAATAGAAATCCTTCTAACA
* * * *
550331 AACAAAAAATATGAAACTATTAAGCATCATCTTGATGAACCCTTTTTTTT
57 GACAAAAAATATGAAGCTATTAAGCATCATCCTGATGAACCATTTTTTTT
*
550381 CCTTATTTTTTAGAAAATCCTAATTAATCAGAAAAATATTAGAAATCCTTCTAACAGACAAAAAA
1 CCTTATTTTTTAGAAAATCCTAATTAATCAGAAAAATAATAGAAATCCTTCTAACAGAC-AAAAA
* *
550446 ATATGAAGCTATTAAGCATCAACCTGATGAACTC-TTTCTTTT
65 ATATGAAGCTATTAAGCATCATCCTGATGAAC-CATTTTTTTT
550488 CCTTATTTTTTAGAAAATCCTAATTAATCAGACAAAA-AATA
1 CCTTATTTTTTAGAAAATCCTAATTAATCAGA-AAAATAATA
550529 TGAAGCTATT
Statistics
Matches: 232, Mismatches: 18, Indels: 27
0.84 0.06 0.10
Matches are distributed among these distances:
106 51 0.22
107 77 0.33
108 6 0.03
109 1 0.00
111 1 0.00
112 1 0.00
114 1 0.00
115 5 0.02
116 86 0.37
117 3 0.01
ACGTcount: A:0.41, C:0.16, G:0.07, T:0.35
Consensus pattern (106 bp):
CCTTATTTTTTAGAAAATCCTAATTAATCAGAAAAATAATAGAAATCCTTCTAACAGACAAAAAA
TATGAAGCTATTAAGCATCATCCTGATGAACCATTTTTTTT
Found at i:550401 original size:106 final size:107
Alignment explanation
Indices: 550279--550528 Score: 396
Period size: 107 Copynumber: 2.3 Consensus size: 107
550269 TGCTTTGCTC
* *
550279 ATTTTTTAGAAAATCCTAATTAATTAGAAAATTAATAGAAATCCTTCTAACAAAC-AAAAAATAT
1 ATTTTTTAGAAAATCCTAATTAATCAGAAAAATAATAGAAATCCTTCTAACAAACAAAAAAATAT
* * *
550343 GAAACTATTAAGCATCATCTTGATGAACCCTTTTTTTTCCTT
66 GAAACTATTAAGCATCAACCTGATGAACCCTTTCTTTTCCTT
* *
550385 ATTTTTTAGAAAATCCTAATTAATCAGAAAAATATTAGAAATCCTTCTAACAGACAAAAAAATAT
1 ATTTTTTAGAAAATCCTAATTAATCAGAAAAATAATAGAAATCCTTCTAACAAACAAAAAAATAT
* *
550450 GAAGCTATTAAGCATCAACCTGATGAACTCTTTCTTTTCCTT
66 GAAACTATTAAGCATCAACCTGATGAACCCTTTCTTTTCCTT
550492 ATTTTTTAGAAAATCCTAATTAATCAGACAAAA-AATA
1 ATTTTTTAGAAAATCCTAATTAATCAGA-AAAATAATA
550529 TGAAGCTATT
Statistics
Matches: 132, Mismatches: 10, Indels: 3
0.91 0.07 0.02
Matches are distributed among these distances:
106 51 0.39
107 77 0.58
108 4 0.03
ACGTcount: A:0.43, C:0.15, G:0.07, T:0.35
Consensus pattern (107 bp):
ATTTTTTAGAAAATCCTAATTAATCAGAAAAATAATAGAAATCCTTCTAACAAACAAAAAAATAT
GAAACTATTAAGCATCAACCTGATGAACCCTTTCTTTTCCTT
Found at i:554442 original size:27 final size:27
Alignment explanation
Indices: 554408--554532 Score: 106
Period size: 27 Copynumber: 4.3 Consensus size: 27
554398 TTACTATGCT
*
554408 TTGCTTTGTTTTGCTGTGCTTTTTATG
1 TTGCTTTGTTTTGCTGTGCTTTTTATA
* *
554435 TTGCTTTGCTTTGCTGTGCTTTTTGTA
1 TTGCTTTGTTTTGCTGTGCTTTTTATA
* * *
554462 TTGCTTTTCTTGTTTCGCTTTGCTCTTTGTATTGC
1 TTGC---T-TTGTTTTGCTGTGCT-TTT-TA-T-A
*
554497 TTTGCTTTGTTTTGCTGTGCTTTTTACA
1 T-TGCTTTGTTTTGCTGTGCTTTTTATA
554525 TTGCTTTG
1 TTGCTTTG
554533 CTGTGCTTTT
Statistics
Matches: 77, Mismatches: 12, Indels: 18
0.72 0.11 0.17
Matches are distributed among these distances:
27 35 0.45
28 1 0.01
30 3 0.04
31 15 0.19
32 16 0.21
33 2 0.03
34 1 0.01
35 1 0.01
36 3 0.04
ACGTcount: A:0.04, C:0.15, G:0.20, T:0.61
Consensus pattern (27 bp):
TTGCTTTGTTTTGCTGTGCTTTTTATA
Found at i:554444 original size:17 final size:15
Alignment explanation
Indices: 554404--554519 Score: 87
Period size: 15 Copynumber: 7.7 Consensus size: 15
554394 CATATTACTA
554404 TGCTTTGCTTTGTTT
1 TGCTTTGCTTTGTTT
* *
554419 TGCTGTGCTTT-TTA
1 TGCTTTGCTTTGTTT
*
554433 TG--TTGCTTTGCTT
1 TGCTTTGCTTTGTTT
* *
554446 TGCTGTGCTTTTTGTAT
1 TGCTTTGC--TTTGTTT
*
554463 TGCTTTTC-TTGTTT
1 TGCTTTGCTTTGTTT
* *
554477 CGCTTTGCTCTTTGTAT
1 TGCTTTG--CTTTGTTT
554494 TGCTTTGCTTTGTTT
1 TGCTTTGCTTTGTTT
*
554509 TGCTGTGCTTT
1 TGCTTTGCTTT
554520 TTACATTGCT
Statistics
Matches: 76, Mismatches: 17, Indels: 16
0.70 0.16 0.15
Matches are distributed among these distances:
12 6 0.08
13 3 0.04
14 14 0.18
15 30 0.39
16 1 0.01
17 22 0.29
ACGTcount: A:0.03, C:0.16, G:0.21, T:0.61
Consensus pattern (15 bp):
TGCTTTGCTTTGTTT
Found at i:554493 original size:31 final size:32
Alignment explanation
Indices: 554404--554534 Score: 141
Period size: 32 Copynumber: 4.3 Consensus size: 32
554394 CATATTACTA
*
554404 TGCTTTGCTTTGTTTTGCTGTGC-TTTT-TA-
1 TGCTTTGCTTTGTTTCGCTGTGCTTTTTGTAT
554433 TG--TTGCTTTGCTTT-GCTGTGCTTTTTGTAT
1 TGCTTTGCTTTG-TTTCGCTGTGCTTTTTGTAT
* * *
554463 TGCTTTTC-TTGTTTCGCTTTGCTCTTTGTAT
1 TGCTTTGCTTTGTTTCGCTGTGCTTTTTGTAT
* **
554494 TGCTTTGCTTTGTTTTGCTGTGCTTTTTACAT
1 TGCTTTGCTTTGTTTCGCTGTGCTTTTTGTAT
554526 TGCTTTGCT
1 TGCTTTGCT
554535 GTGCTTTTTA
Statistics
Matches: 85, Mismatches: 9, Indels: 13
0.79 0.08 0.12
Matches are distributed among these distances:
27 15 0.18
28 7 0.08
29 4 0.05
30 5 0.06
31 24 0.28
32 30 0.35
ACGTcount: A:0.04, C:0.16, G:0.20, T:0.60
Consensus pattern (32 bp):
TGCTTTGCTTTGTTTCGCTGTGCTTTTTGTAT
Found at i:554534 original size:5 final size:5
Alignment explanation
Indices: 554324--554519 Score: 75
Period size: 5 Copynumber: 38.4 Consensus size: 5
554314 TTGCTCGATA
* * **
554324 TTGCT TTGCT TTGCT TTGCT TTGCT TT-TT ATTACT TTGCT TTGCT TT-AA
1 TTGCT TTGCT TTGCT TTGCT TTGCT TTGCT -TTGCT TTGCT TTGCT TTGCT
* * * * * *
554373 TTGAT TTGCT TTTCT TGGC- TT-CAT ATTACT ATGCT TTGCT TTGTT TTGCT
1 TTGCT TTGCT TTGCT TTGCT TTGC-T -TTGCT TTGCT TTGCT TTGCT TTGCT
* ** * *
554423 GTGCTT TTTAT GTTGCT TTGCT TTGCT GTGCTTT TTG-T ATTGCT TTTC-
1 TTGC-T TTGCT -TTGCT TTGCT TTGCT TTGC--T TTGCT -TTGCT TTGCT
* *
554471 TTG-T TTCGCT TTGCTCT TTG-T ATTGCT TTGCT TTGTT TTGCT GTGCT
1 TTGCT TT-GCT TTG--CT TTGCT -TTGCT TTGCT TTGCT TTGCT TTGCT
554518 TT
1 TT
554520 TTACATTGCT
Statistics
Matches: 141, Mismatches: 30, Indels: 40
0.67 0.14 0.19
Matches are distributed among these distances:
3 1 0.01
4 10 0.07
5 107 0.76
6 14 0.10
7 9 0.06
ACGTcount: A:0.06, C:0.16, G:0.18, T:0.60
Consensus pattern (5 bp):
TTGCT
Found at i:554534 original size:17 final size:15
Alignment explanation
Indices: 554308--554534 Score: 80
Period size: 15 Copynumber: 14.7 Consensus size: 15
554298 CAGTACTTGA
***
554308 ATTGCTTTGCTCGAT
1 ATTGCTTTGCTTTTT
*
554323 ATTGCTTTGCTTTGCT
1 ATTGCTTTGCTTT-TT
554339 -TTGCTTTGCTTTTT
1 ATTGCTTTGCTTTTT
*
554353 ATTACTTTGCTTTGCTTT
1 ATTGCTTTGC-TT--TTT
*
554371 AATTGATTTGCTTTTCT
1 -ATTGCTTTGCTTTT-T
* * *
554388 -TGGC-TT-CATATT
1 ATTGCTTTGCTTTTT
554400 ACTATGCTTTGCTTTGTT
1 A-T-TGCTTTGCTTT-TT
*
554418 -TTGCTGTGCTTTTT
1 ATTGCTTTGCTTTTT
*
554432 A-TG--TTGCTTTGCT
1 ATTGCTTTGCTTT-TT
*
554445 -TTGCTGTGCTTTTTGT
1 ATTGCTTTGC-TTTT-T
* *
554461 ATTGCTTTTCTTGTT
1 ATTGCTTTGCTTTTT
*
554476 -TCGCTTTGCTCTTTGT
1 ATTGCTTTGCT-TTT-T
554492 ATTGCTTTGCTTTGTT
1 ATTGCTTTGCTTT-TT
*
554508 -TTGCTGTGCTTTTT
1 ATTGCTTTGCTTTTT
554522 ACATTGCTTTGCT
1 --ATTGCTTTGCT
554535 GTGCTTTTTA
Statistics
Matches: 156, Mismatches: 28, Indels: 54
0.66 0.12 0.23
Matches are distributed among these distances:
12 7 0.04
13 6 0.04
14 18 0.12
15 62 0.40
16 19 0.12
17 29 0.19
18 7 0.04
19 8 0.05
ACGTcount: A:0.07, C:0.16, G:0.18, T:0.59
Consensus pattern (15 bp):
ATTGCTTTGCTTTTT
Found at i:575504 original size:35 final size:35
Alignment explanation
Indices: 575458--575527 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 35
575448 ATATTAAAAT
* **
575458 TGATCATGGATTAGGTTATTTGCTCGGATCCGAAA
1 TGATCATGGATTAGGTTATTCGCTCAAATCCGAAA
*
575493 TGATCATGGATTTGGTTATTCGCTCAAATCCGAAA
1 TGATCATGGATTAGGTTATTCGCTCAAATCCGAAA
575528 GCTCGTTAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 31 1.00
ACGTcount: A:0.27, C:0.16, G:0.23, T:0.34
Consensus pattern (35 bp):
TGATCATGGATTAGGTTATTCGCTCAAATCCGAAA
Found at i:575719 original size:11 final size:11
Alignment explanation
Indices: 575679--575726 Score: 51
Period size: 11 Copynumber: 4.4 Consensus size: 11
575669 AGCTTCTTTT
*
575679 TTTTGCTGTTA
1 TTTTGTTGTTA
* *
575690 TTTTGTTATCA
1 TTTTGTTGTTA
* *
575701 TTTCGTTGTTG
1 TTTTGTTGTTA
575712 TTTTGTTGTTA
1 TTTTGTTGTTA
575723 TTTT
1 TTTT
575727 ATGCTACTAT
Statistics
Matches: 28, Mismatches: 9, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
11 28 1.00
ACGTcount: A:0.08, C:0.06, G:0.17, T:0.69
Consensus pattern (11 bp):
TTTTGTTGTTA
Found at i:576825 original size:2 final size:2
Alignment explanation
Indices: 576818--576842 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
576808 AACATTGTTA
576818 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
576843 ACTTCTTTTT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:585020 original size:6 final size:6
Alignment explanation
Indices: 585009--585047 Score: 51
Period size: 6 Copynumber: 6.5 Consensus size: 6
584999 TGATCAAAAT
* * *
585009 TGAAAG TGAAAG TGAAAG TGAAAT TGGAAT TGAAAG TGA
1 TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGAAAG TGA
585048 TATGAATTGT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.46, C:0.00, G:0.31, T:0.23
Consensus pattern (6 bp):
TGAAAG
Found at i:588497 original size:5 final size:5
Alignment explanation
Indices: 588487--588515 Score: 58
Period size: 5 Copynumber: 5.8 Consensus size: 5
588477 AACCCTCTAA
588487 ACCCC ACCCC ACCCC ACCCC ACCCC ACCC
1 ACCCC ACCCC ACCCC ACCCC ACCCC ACCC
588516 ATCAAGATTA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 24 1.00
ACGTcount: A:0.21, C:0.79, G:0.00, T:0.00
Consensus pattern (5 bp):
ACCCC
Found at i:590071 original size:72 final size:72
Alignment explanation
Indices: 589985--590129 Score: 290
Period size: 72 Copynumber: 2.0 Consensus size: 72
589975 CATAAAATTG
589985 AATGAAATGCAGGAAAACCTAGCCATATTTCAGTATTTCCTTTATCACTATACTCTAGGATTCAA
1 AATGAAATGCAGGAAAACCTAGCCATATTTCAGTATTTCCTTTATCACTATACTCTAGGATTCAA
590050 ATCAATA
66 ATCAATA
590057 AATGAAATGCAGGAAAACCTAGCCATATTTCAGTATTTCCTTTATCACTATACTCTAGGATTCAA
1 AATGAAATGCAGGAAAACCTAGCCATATTTCAGTATTTCCTTTATCACTATACTCTAGGATTCAA
590122 ATCAATA
66 ATCAATA
590129 A
1 A
590130 CGAGGCACCT
Statistics
Matches: 73, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
72 73 1.00
ACGTcount: A:0.38, C:0.19, G:0.11, T:0.32
Consensus pattern (72 bp):
AATGAAATGCAGGAAAACCTAGCCATATTTCAGTATTTCCTTTATCACTATACTCTAGGATTCAA
ATCAATA
Found at i:593368 original size:21 final size:22
Alignment explanation
Indices: 593342--593385 Score: 63
Period size: 22 Copynumber: 2.0 Consensus size: 22
593332 TATTTTTTTA
593342 TAATTC-ATAAAAATAAAAAAT
1 TAATTCAATAAAAATAAAAAAT
* *
593363 TAATTCAATTAAATTAAAAAAT
1 TAATTCAATAAAAATAAAAAAT
593385 T
1 T
593386 TTAAAAGTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 6 0.30
22 14 0.70
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (22 bp):
TAATTCAATAAAAATAAAAAAT
Found at i:594268 original size:27 final size:25
Alignment explanation
Indices: 594223--594275 Score: 61
Period size: 27 Copynumber: 2.0 Consensus size: 25
594213 TTCCTTTTAC
* *
594223 TAAAAAAATAAAATTAATTCTAAAAAA
1 TAAAAAAATAAAA-GAAAT-TAAAAAA
*
594250 TAAAAAAATAAAGGAAATTAAAAAA
1 TAAAAAAATAAAAGAAATTAAAAAA
594275 T
1 T
594276 GAAATGTTTT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
25 8 0.35
26 3 0.13
27 12 0.52
ACGTcount: A:0.72, C:0.02, G:0.04, T:0.23
Consensus pattern (25 bp):
TAAAAAAATAAAAGAAATTAAAAAA
Found at i:599608 original size:2 final size:2
Alignment explanation
Indices: 599601--599644 Score: 79
Period size: 2 Copynumber: 22.0 Consensus size: 2
599591 GGAAGGGGAC
*
599601 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA AA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
599643 GA
1 GA
599645 TACAGGAAGA
Statistics
Matches: 40, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.52, C:0.00, G:0.48, T:0.00
Consensus pattern (2 bp):
GA
Found at i:602631 original size:13 final size:13
Alignment explanation
Indices: 602610--602643 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
602600 ATAATATAAT
602610 AATAATAATCCTA
1 AATAATAATCCTA
*
602623 AATATTAATCCTA
1 AATAATAATCCTA
*
602636 AAAAATAA
1 AATAATAA
602644 AATTTAAATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.59, C:0.12, G:0.00, T:0.29
Consensus pattern (13 bp):
AATAATAATCCTA
Found at i:611589 original size:21 final size:23
Alignment explanation
Indices: 611563--611607 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
611553 TAACTCAACT
*
611563 AATTA-TTTTATAT-ATAATATA
1 AATTATTTTTACATAATAATATA
611584 AATTATTTTTACATAATAATATA
1 AATTATTTTTACATAATAATATA
611607 A
1 A
611608 GTCTAGAAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 5 0.24
22 7 0.33
23 9 0.43
ACGTcount: A:0.49, C:0.02, G:0.00, T:0.49
Consensus pattern (23 bp):
AATTATTTTTACATAATAATATA
Found at i:611601 original size:20 final size:21
Alignment explanation
Indices: 611563--611601 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
611553 TAACTCAACT
*
611563 AATTATTTTATATATAATATA
1 AATTATTTTATACATAATATA
611584 AATTATTTT-TACATAATA
1 AATTATTTTATACATAATA
611602 ATATAAGTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 8 0.47
21 9 0.53
ACGTcount: A:0.46, C:0.03, G:0.00, T:0.51
Consensus pattern (21 bp):
AATTATTTTATACATAATATA
Found at i:624787 original size:21 final size:21
Alignment explanation
Indices: 624763--624812 Score: 57
Period size: 21 Copynumber: 2.4 Consensus size: 21
624753 ATATTATTTT
*
624763 AATAAATAATTT-AATTATAAA
1 AATAAA-AATTTAAAATATAAA
*
624784 AATAAAATTTTAAAATATAAA
1 AATAAAAATTTAAAATATAAA
*
624805 AAAAAAAA
1 AATAAAAA
624813 ATATCTTTGT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
20 4 0.17
21 20 0.83
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (21 bp):
AATAAAAATTTAAAATATAAA
Found at i:625877 original size:28 final size:27
Alignment explanation
Indices: 625810--625864 Score: 74
Period size: 28 Copynumber: 2.0 Consensus size: 27
625800 AATTTATCTT
* *
625810 ATTATTAATAATTTTCTAATATTAATTA
1 ATTATT-ATAATTTCCTAATATTAACTA
625838 ATTATTATTAATTTCCTAATATTAACT
1 ATTATTA-TAATTTCCTAATATTAACT
625865 GGTTAATTAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
27 1 0.04
28 23 0.96
ACGTcount: A:0.40, C:0.07, G:0.00, T:0.53
Consensus pattern (27 bp):
ATTATTATAATTTCCTAATATTAACTA
Found at i:626225 original size:2 final size:2
Alignment explanation
Indices: 626218--626249 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
626208 TTTGAATTCA
626218 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
626250 GGCTCATTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:629030 original size:15 final size:17
Alignment explanation
Indices: 628988--629039 Score: 65
Period size: 17 Copynumber: 3.2 Consensus size: 17
628978 TCTAAATGTA
628988 AAATAATTTTTATAATT
1 AAATAATTTTTATAATT
*
629005 ATATAATTTTTA-AA-T
1 AAATAATTTTTATAATT
629020 AAATAAATTTTT-TAATT
1 AAAT-AATTTTTATAATT
629037 AAA
1 AAA
629040 ACTTATCACA
Statistics
Matches: 30, Mismatches: 2, Indels: 6
0.79 0.05 0.16
Matches are distributed among these distances:
15 4 0.13
16 11 0.37
17 15 0.50
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (17 bp):
AAATAATTTTTATAATT
Done.