Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015286.1 Kokia drynarioides strain JFW-HI SEQ_130331, 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: 659172
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Warning! 555 characters in sequence are not A, C, G, or T
File 2 of 2
Found at i:321578 original size:14 final size:14
Alignment explanation
Indices: 321559--321585 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
321549 TGACGTTCTA
321559 ATATATATATAATT
1 ATATATATATAATT
321573 ATATATATATAAT
1 ATATATATATAAT
321586 AAATGCGGTC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (14 bp):
ATATATATATAATT
Found at i:322358 original size:27 final size:26
Alignment explanation
Indices: 322282--322358 Score: 73
Period size: 27 Copynumber: 2.9 Consensus size: 26
322272 AATGAAAACA
* *
322282 TAAACCTAAACTTTAATTCTAAAATT
1 TAAACCTAAACTTAAATACTAAAATT
* * *
322308 TAAATCTTAACCTTAAATATTAAAATT
1 TAAA-CCTAAACTTAAATACTAAAATT
* *
322335 TCAAACCTAAACTTCAATGCTAAA
1 T-AAACCTAAACTTAAATACTAAA
322359 TCTTAAAAAA
Statistics
Matches: 39, Mismatches: 10, Indels: 3
0.75 0.19 0.06
Matches are distributed among these distances:
26 4 0.10
27 32 0.82
28 3 0.08
ACGTcount: A:0.47, C:0.17, G:0.01, T:0.35
Consensus pattern (26 bp):
TAAACCTAAACTTAAATACTAAAATT
Found at i:327318 original size:3 final size:3
Alignment explanation
Indices: 327310--327338 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
327300 GGGAAACACA
327310 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
327339 AAAATGGTGG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:328129 original size:2 final size:2
Alignment explanation
Indices: 328122--328153 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
328112 AACTGAAATA
328122 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
328154 TAATATGGAT
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:329502 original size:16 final size:16
Alignment explanation
Indices: 329481--329522 Score: 50
Period size: 16 Copynumber: 2.6 Consensus size: 16
329471 TAATTTGTAT
* *
329481 AAATTAATTAAGATTA
1 AAATTAATTAAAATCA
329497 AAATTACA-TAAAATCA
1 AAATTA-ATTAAAATCA
329513 AAATTAATTA
1 AAATTAATTA
329523 TAAAATTGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
15 1 0.05
16 20 0.91
17 1 0.05
ACGTcount: A:0.60, C:0.05, G:0.02, T:0.33
Consensus pattern (16 bp):
AAATTAATTAAAATCA
Found at i:331177 original size:18 final size:18
Alignment explanation
Indices: 331154--331196 Score: 52
Period size: 18 Copynumber: 2.4 Consensus size: 18
331144 AAATAATTTT
331154 TTAATTAAATAAATTT-AA
1 TTAATTAAAT-AATTTAAA
* *
331172 TTAATTGAATATTTTAAA
1 TTAATTAAATAATTTAAA
331190 TTAATTA
1 TTAATTA
331197 CAACTGAAAA
Statistics
Matches: 21, Mismatches: 3, Indels: 2
0.81 0.12 0.08
Matches are distributed among these distances:
17 4 0.19
18 17 0.81
ACGTcount: A:0.49, C:0.00, G:0.02, T:0.49
Consensus pattern (18 bp):
TTAATTAAATAATTTAAA
Found at i:334744 original size:21 final size:22
Alignment explanation
Indices: 334706--334752 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 22
334696 TTTATGGGGT
*
334706 TTTTAAAAAAAATATTCCTGGG
1 TTTTAAAAAAAATATTCCTGGC
* *
334728 TTTTAAAAGAAA-GTTCCTGGC
1 TTTTAAAAAAAATATTCCTGGC
334749 TTTT
1 TTTT
334753 CTTCTTTATG
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
21 11 0.50
22 11 0.50
ACGTcount: A:0.34, C:0.11, G:0.15, T:0.40
Consensus pattern (22 bp):
TTTTAAAAAAAATATTCCTGGC
Found at i:342964 original size:20 final size:23
Alignment explanation
Indices: 342914--342964 Score: 56
Period size: 20 Copynumber: 2.3 Consensus size: 23
342904 TTAATACTAC
342914 TTAAGTAATTTAATCCATGTTTAT
1 TTAA-TAATTTAATCCATGTTTAT
*
342938 TT-TTAATTT-AT-CATGTTT-T
1 TTAATAATTTAATCCATGTTTAT
342957 TTAATAAT
1 TTAATAAT
342965 ATTTTTTGTA
Statistics
Matches: 24, Mismatches: 2, Indels: 6
0.75 0.06 0.19
Matches are distributed among these distances:
19 3 0.12
20 11 0.46
21 2 0.08
22 6 0.25
24 2 0.08
ACGTcount: A:0.31, C:0.06, G:0.06, T:0.57
Consensus pattern (23 bp):
TTAATAATTTAATCCATGTTTAT
Found at i:345370 original size:50 final size:50
Alignment explanation
Indices: 345308--345407 Score: 191
Period size: 50 Copynumber: 2.0 Consensus size: 50
345298 GAATGTCCAT
*
345308 AAATGAGTTTAAGATCTATTATATTTGGGTCTTGTCCAATGTACTTTTAG
1 AAATGAGTTTAAGATCTATTATATTTGGATCTTGTCCAATGTACTTTTAG
345358 AAATGAGTTTAAGATCTATTATATTTGGATCTTGTCCAATGTACTTTTAG
1 AAATGAGTTTAAGATCTATTATATTTGGATCTTGTCCAATGTACTTTTAG
345408 TTCAGTCAGT
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
50 49 1.00
ACGTcount: A:0.29, C:0.10, G:0.17, T:0.44
Consensus pattern (50 bp):
AAATGAGTTTAAGATCTATTATATTTGGATCTTGTCCAATGTACTTTTAG
Found at i:346435 original size:3 final size:3
Alignment explanation
Indices: 346427--346464 Score: 76
Period size: 3 Copynumber: 12.7 Consensus size: 3
346417 AACCAATTTC
346427 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
346465 GTGATGCACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 35 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:358927 original size:20 final size:20
Alignment explanation
Indices: 358902--358962 Score: 59
Period size: 23 Copynumber: 2.9 Consensus size: 20
358892 ATTATATTAG
358902 TTTTGGTGTTTTTTTTACTA
1 TTTTGGTGTTTTTTTTACTA
*
358922 TTTTGGTTGATTTTTTTTTGCTA
1 TTTTGG-TG--TTTTTTTTACTA
* *
358945 TTTTTGAGTTGTTTTTTA
1 TTTTGGTGTT-TTTTTTA
358963 TTGTTTTGAT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
20 8 0.24
21 8 0.24
22 1 0.03
23 16 0.48
ACGTcount: A:0.10, C:0.03, G:0.16, T:0.70
Consensus pattern (20 bp):
TTTTGGTGTTTTTTTTACTA
Found at i:358940 original size:23 final size:24
Alignment explanation
Indices: 358910--358961 Score: 72
Period size: 23 Copynumber: 2.2 Consensus size: 24
358900 AGTTTTGGTG
358910 TTTTTTTTACTA-TTTTG-GTTGAT
1 TTTTTTTTACTATTTTTGAGTTG-T
*
358933 TTTTTTTTGCTATTTTTGAGTTGT
1 TTTTTTTTACTATTTTTGAGTTGT
358957 TTTTT
1 TTTTT
358962 ATTGTTTTGA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
23 11 0.42
24 11 0.42
25 4 0.15
ACGTcount: A:0.10, C:0.04, G:0.13, T:0.73
Consensus pattern (24 bp):
TTTTTTTTACTATTTTTGAGTTGT
Found at i:359022 original size:55 final size:56
Alignment explanation
Indices: 358940--359079 Score: 144
Period size: 55 Copynumber: 2.5 Consensus size: 56
358930 GATTTTTTTT
* *
358940 TGCTATTTTTGAGTTG-T-TTTTTATTGTTTTGATTGCTATTTT-CGTGTTATTTTTAC
1 TGCTA-TTTTG-GTTGCTATTTTTGTTGTTTTGAATGCTATTTTAC-TGTTATTTTTAC
* * * * *
358996 TGTTATTTT-GTTGCTATTTTTGTTGTTTTTAATGTTGTTTTACTGTTATTTTTGC
1 TGCTATTTTGGTTGCTATTTTTGTTGTTTTGAATGCTATTTTACTGTTATTTTTAC
* *
359051 TGCTGTTTTGGTTGTTATTTTTGTTGTTT
1 TGCTATTTTGGTTGCTATTTTTGTTGTTT
359080 GGATGTTATT
Statistics
Matches: 70, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
53 4 0.06
54 1 0.01
55 42 0.60
56 23 0.33
ACGTcount: A:0.10, C:0.06, G:0.18, T:0.66
Consensus pattern (56 bp):
TGCTATTTTGGTTGCTATTTTTGTTGTTTTGAATGCTATTTTACTGTTATTTTTAC
Found at i:359025 original size:32 final size:31
Alignment explanation
Indices: 358934--359036 Score: 100
Period size: 32 Copynumber: 3.1 Consensus size: 31
358924 TTGGTTGATT
* *
358934 TTTTTTTGCTATTTTTGAGTTGTTTTT-TATTG
1 TTTTGTTGCTATTTTT--GTTGTTTTTATGTTG
* *
358966 TTTTGATTGCTATTTTCGTGTTATTTTTACTGTTA
1 TTTTG-TTGCTATTTT--TGTTGTTTTTA-TGTTG
359001 TTTTGTTGCTATTTTTGTTGTTTTTAATGTTG
1 TTTTGTTGCTATTTTTGTTGTTTTT-ATGTTG
359033 TTTT
1 TTTT
359037 ACTGTTATTT
Statistics
Matches: 59, Mismatches: 6, Indels: 12
0.77 0.08 0.16
Matches are distributed among these distances:
32 21 0.36
33 19 0.32
34 10 0.17
35 9 0.15
ACGTcount: A:0.11, C:0.05, G:0.16, T:0.69
Consensus pattern (31 bp):
TTTTGTTGCTATTTTTGTTGTTTTTATGTTG
Found at i:359076 original size:44 final size:44
Alignment explanation
Indices: 358990--359092 Score: 122
Period size: 44 Copynumber: 2.4 Consensus size: 44
358980 TTCGTGTTAT
* *
358990 TTTTACTGTTA-TTTTGTTGCTATTTTTGTTGTTTTTAATGTTG
1 TTTTACTGTTATTTTTGCTGCTATTTTGGTTGTTTTTAATGTTG
* *
359033 TTTTACTGTTATTTTTGCTGCTGTTTTGGTTGTTATTT-TTGTTG
1 TTTTACTGTTATTTTTGCTGCTATTTTGGTTGTT-TTTAATGTTG
*
359077 TTTGGA-TGTTATTTTT
1 TTT-TACTGTTATTTTT
359093 TATGCTTTTT
Statistics
Matches: 52, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
43 11 0.21
44 37 0.71
45 4 0.08
ACGTcount: A:0.10, C:0.05, G:0.18, T:0.67
Consensus pattern (44 bp):
TTTTACTGTTATTTTTGCTGCTATTTTGGTTGTTTTTAATGTTG
Found at i:364632 original size:76 final size:76
Alignment explanation
Indices: 364506--364666 Score: 286
Period size: 76 Copynumber: 2.1 Consensus size: 76
364496 TCAAAAATTG
* *
364506 TAAAGTTTGCAAGCTGATAAAATAGTAAAATTAGTTTTTGGTCCTTCAAAACTTCACAATTCAAT
1 TAAAGTTTGCAAGCTAATAAAATAGTAAAATTAGTTTTTGGTCCTTCAAAACTTCACAAATCAAT
364571 CTTGACCCATA
66 CTTGACCCATA
*
364582 TAAAGTTTGTAAGCTAATAAAATAGTAAAATTAGTTTTTGGTCCTTCAAAACTTCACAAATCAAT
1 TAAAGTTTGCAAGCTAATAAAATAGTAAAATTAGTTTTTGGTCCTTCAAAACTTCACAAATCAAT
364647 CTTGACCCATA
66 CTTGACCCATA
*
364658 TAAAATTTG
1 TAAAGTTTG
364667 GCTTCACTAT
Statistics
Matches: 81, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
76 81 1.00
ACGTcount: A:0.39, C:0.16, G:0.11, T:0.35
Consensus pattern (76 bp):
TAAAGTTTGCAAGCTAATAAAATAGTAAAATTAGTTTTTGGTCCTTCAAAACTTCACAAATCAAT
CTTGACCCATA
Found at i:369701 original size:6 final size:6
Alignment explanation
Indices: 369690--369716 Score: 54
Period size: 6 Copynumber: 4.5 Consensus size: 6
369680 AAAATCATAT
369690 AAATTA AAATTA AAATTA AAATTA AAA
1 AAATTA AAATTA AAATTA AAATTA AAA
369717 AGTCTTCTGT
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:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (6 bp):
AAATTA
Found at i:374211 original size:6 final size:6
Alignment explanation
Indices: 374200--374239 Score: 80
Period size: 6 Copynumber: 6.7 Consensus size: 6
374190 TTTCTTTTTT
374200 GGTTAG GGTTAG GGTTAG GGTTAG GGTTAG GGTTAG GGTT
1 GGTTAG GGTTAG GGTTAG GGTTAG GGTTAG GGTTAG GGTT
374240 TTTGTTTTTG
Statistics
Matches: 34, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.15, C:0.00, G:0.50, T:0.35
Consensus pattern (6 bp):
GGTTAG
Found at i:386900 original size:23 final size:23
Alignment explanation
Indices: 386874--386919 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
386864 TAGGTTGAGT
* *
386874 TTTAA-ATTTTTGATTTATTTTGA
1 TTTAAGATTATTGATGT-TTTTGA
386897 TTTAAGATTATTGATGTTTTTGA
1 TTTAAGATTATTGATGTTTTTGA
386920 CCGATTTAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 11 0.55
24 9 0.45
ACGTcount: A:0.26, C:0.00, G:0.13, T:0.61
Consensus pattern (23 bp):
TTTAAGATTATTGATGTTTTTGA
Found at i:402623 original size:23 final size:23
Alignment explanation
Indices: 402597--402642 Score: 56
Period size: 23 Copynumber: 2.0 Consensus size: 23
402587 TTGAAACGCT
*
402597 AGACTAGAAATAACGTCACGATG
1 AGACAAGAAATAACGTCACGATG
* * *
402620 AGACAATAAATCATGTCACGATG
1 AGACAAGAAATAACGTCACGATG
402643 TGTTTTTTTA
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 19 1.00
ACGTcount: A:0.43, C:0.17, G:0.20, T:0.20
Consensus pattern (23 bp):
AGACAAGAAATAACGTCACGATG
Found at i:408547 original size:2 final size:2
Alignment explanation
Indices: 408540--408567 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
408530 GAAACTAGAC
408540 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
408568 AATTAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:409033 original size:22 final size:23
Alignment explanation
Indices: 409008--409069 Score: 65
Period size: 23 Copynumber: 2.7 Consensus size: 23
408998 TAAAAATGAT
*
409008 AAAATTATAATTTAATCT-T-TTA
1 AAAATTATAATTTAAT-TATAATA
* * *
409030 AAAATTACATTTTTATTATAATA
1 AAAATTATAATTTAATTATAATA
409053 AAAATTATAATTTAATT
1 AAAATTATAATTTAATT
409070 TCGCTCTCTT
Statistics
Matches: 31, Mismatches: 7, Indels: 3
0.76 0.17 0.07
Matches are distributed among these distances:
21 1 0.03
22 14 0.45
23 16 0.52
ACGTcount: A:0.48, C:0.03, G:0.00, T:0.48
Consensus pattern (23 bp):
AAAATTATAATTTAATTATAATA
Found at i:409113 original size:2 final size:2
Alignment explanation
Indices: 409106--409140 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
409096 TACTCATTTT
409106 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
409141 CAATACGATA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:410817 original size:31 final size:31
Alignment explanation
Indices: 410755--410818 Score: 85
Period size: 31 Copynumber: 2.1 Consensus size: 31
410745 TTACAATTTG
* *
410755 GTCACTGAACTATTAAAATTTTTTCACTTAA
1 GTCACTGAACTATCAAAAGTTTTTCACTTAA
*
410786 GTCACTGAACTACTCAAAAGTTTTT-ATTTAA
1 GTCACTGAACTA-TCAAAAGTTTTTCACTTAA
410817 GT
1 GT
410819 TACCGGATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
31 19 0.66
32 10 0.34
ACGTcount: A:0.34, C:0.16, G:0.09, T:0.41
Consensus pattern (31 bp):
GTCACTGAACTATCAAAAGTTTTTCACTTAA
Found at i:411981 original size:3 final size:3
Alignment explanation
Indices: 411973--412009 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
411963 AAGCTCTACT
*
411973 ATC ATC ATC ATC ATC ATC ATC AAC ATC ATC ATC ATC A
1 ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC ATC A
412010 CCATTATTCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.38, C:0.32, G:0.00, T:0.30
Consensus pattern (3 bp):
ATC
Found at i:416774 original size:25 final size:27
Alignment explanation
Indices: 416742--416802 Score: 83
Period size: 25 Copynumber: 2.4 Consensus size: 27
416732 CAGATTAAAT
*
416742 TCAAATAATTGA-TTTTTATAATGAAA
1 TCAAATAATTAATTTTTTATAATGAAA
*
416768 TC-AATAA-TAATTTTTTATAATGAAT
1 TCAAATAATTAATTTTTTATAATGAAA
416793 TCAAATAATT
1 TCAAATAATT
416803 TTGAGTTTGT
Statistics
Matches: 30, Mismatches: 2, Indels: 5
0.81 0.05 0.14
Matches are distributed among these distances:
24 2 0.07
25 20 0.67
26 7 0.23
27 1 0.03
ACGTcount: A:0.46, C:0.05, G:0.05, T:0.44
Consensus pattern (27 bp):
TCAAATAATTAATTTTTTATAATGAAA
Found at i:422056 original size:47 final size:48
Alignment explanation
Indices: 421956--422056 Score: 107
Period size: 47 Copynumber: 2.1 Consensus size: 48
421946 TAGCTTAAAA
* * * * * * *
421956 AAAAAAAGAAGCCCTTTTTTCAAAGCCATTTCTTCTTTTTTTATCCTT
1 AAAAAAAGAAACCCCTTTTCCAAAGCAATTTCATCTTTCTTTACCCTT
* *
422004 -TAAAAAGAAACCCCTTTTCCAAAGTAATTTCATC-TTCTTTACCCTT
1 AAAAAAAGAAACCCCTTTTCCAAAGCAATTTCATCTTTCTTTACCCTT
422050 AAAAAAA
1 AAAAAAA
422057 AAAAAATCCC
Statistics
Matches: 42, Mismatches: 10, Indels: 3
0.76 0.18 0.05
Matches are distributed among these distances:
46 10 0.24
47 32 0.76
ACGTcount: A:0.36, C:0.22, G:0.05, T:0.38
Consensus pattern (48 bp):
AAAAAAAGAAACCCCTTTTCCAAAGCAATTTCATCTTTCTTTACCCTT
Found at i:430978 original size:51 final size:52
Alignment explanation
Indices: 430902--431005 Score: 174
Period size: 51 Copynumber: 2.0 Consensus size: 52
430892 AATATTGCCA
430902 ATGGTATATGAAACTTCCTTCCAATCT-TTTTGTAATATTTTGGATTTGAAT
1 ATGGTATATGAAACTTCCTTCCAATCTCTTTTGTAATATTTTGGATTTGAAT
* * *
430953 ATGGTGTATGAAATTTCCTTCCAATCTCTTTTTTAATATTTTGGATTTGAAT
1 ATGGTATATGAAACTTCCTTCCAATCTCTTTTGTAATATTTTGGATTTGAAT
431005 A
1 A
431006 GGGAAATTTA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
51 25 0.51
52 24 0.49
ACGTcount: A:0.27, C:0.12, G:0.13, T:0.48
Consensus pattern (52 bp):
ATGGTATATGAAACTTCCTTCCAATCTCTTTTGTAATATTTTGGATTTGAAT
Found at i:448965 original size:14 final size:14
Alignment explanation
Indices: 448946--448972 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
448936 TTCATTGAAA
448946 TTTTAAAAAATAAT
1 TTTTAAAAAATAAT
448960 TTTTAAAAAATAA
1 TTTTAAAAAATAA
448973 AAATGTGTGA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (14 bp):
TTTTAAAAAATAAT
Found at i:452482 original size:19 final size:19
Alignment explanation
Indices: 452446--452484 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
452436 TATTATTATT
**
452446 ATATTTATAATTGTAATAA
1 ATATTTATAATTAAAATAA
*
452465 ATATTTATTATTAAAATAA
1 ATATTTATAATTAAAATAA
452484 A
1 A
452485 ATTGAAATAT
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:0.51, C:0.00, G:0.03, T:0.46
Consensus pattern (19 bp):
ATATTTATAATTAAAATAA
Found at i:463552 original size:11 final size:11
Alignment explanation
Indices: 463524--463562 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
463514 TAATAACAGT
*
463524 AAAATAATAAC
1 AAAATAATAGC
* *
463535 AACATAATAGT
1 AAAATAATAGC
463546 AAAATAATAGC
1 AAAATAATAGC
463557 AAAATA
1 AAAATA
463563 GTGAGGCAAT
Statistics
Matches: 23, Mismatches: 5, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.67, C:0.08, G:0.05, T:0.21
Consensus pattern (11 bp):
AAAATAATAGC
Found at i:470594 original size:7 final size:7
Alignment explanation
Indices: 470582--470610 Score: 58
Period size: 7 Copynumber: 4.1 Consensus size: 7
470572 AGAATTTAAG
470582 ATTAAAT
1 ATTAAAT
470589 ATTAAAT
1 ATTAAAT
470596 ATTAAAT
1 ATTAAAT
470603 ATTAAAT
1 ATTAAAT
470610 A
1 A
470611 AAGATGTTTA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 22 1.00
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (7 bp):
ATTAAAT
Found at i:482328 original size:6 final size:6
Alignment explanation
Indices: 482317--482370 Score: 58
Period size: 6 Copynumber: 9.2 Consensus size: 6
482307 TTAGGGTTTA
* * *
482317 TTTGAT TTTGAT TTTGAT TTTGATT TTTGAT TTAGA- GTT-AT TTCGAT
1 TTTGAT TTTGAT TTTGAT TTTGA-T TTTGAT TTTGAT TTTGAT TTTGAT
482364 TTTGAT T
1 TTTGAT T
482371 GTATTCTGAT
Statistics
Matches: 39, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
4 1 0.03
5 2 0.05
6 30 0.77
7 6 0.15
ACGTcount: A:0.19, C:0.02, G:0.17, T:0.63
Consensus pattern (6 bp):
TTTGAT
Found at i:482365 original size:41 final size:41
Alignment explanation
Indices: 482275--482370 Score: 122
Period size: 41 Copynumber: 2.3 Consensus size: 41
482265 GATTATTCGA
* * * * *
482275 ATTTGATGTCGATATTGATTGTGATTTTTTATTTAGGGTTT
1 ATTTGATTTTGATTTTGATTGTGATTTTTGATTTAGAGTTT
*
482316 ATTTGATTTTGATTTTGATTTTGATTTTTGATTTAGAG-TT
1 ATTTGATTTTGATTTTGATTGTGATTTTTGATTTAGAGTTT
482356 ATTTCGATTTTGATT
1 ATTT-GATTTTGATT
482371 GTATTCTGAT
Statistics
Matches: 48, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
40 6 0.12
41 42 0.88
ACGTcount: A:0.20, C:0.02, G:0.19, T:0.59
Consensus pattern (41 bp):
ATTTGATTTTGATTTTGATTGTGATTTTTGATTTAGAGTTT
Found at i:484118 original size:12 final size:13
Alignment explanation
Indices: 484101--484130 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
484091 TTTTTCGACC
484101 CTTTTTTCAATTT
1 CTTTTTTCAATTT
*
484114 CTTTTTTCATTTT
1 CTTTTTTCAATTT
484127 CTTT
1 CTTT
484131 GATTAATTTA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.10, C:0.17, G:0.00, T:0.73
Consensus pattern (13 bp):
CTTTTTTCAATTT
Found at i:489367 original size:19 final size:21
Alignment explanation
Indices: 489323--489368 Score: 60
Period size: 19 Copynumber: 2.3 Consensus size: 21
489313 GCATTCTTTA
489323 TTTTTAATGTTGTAATTTATG
1 TTTTTAATGTTGTAATTTATG
* *
489344 CTTTTAAT-TT-TAATTTATT
1 TTTTTAATGTTGTAATTTATG
489363 TTTTTA
1 TTTTTA
489369 CAAACATTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
19 13 0.59
20 2 0.09
21 7 0.32
ACGTcount: A:0.24, C:0.02, G:0.07, T:0.67
Consensus pattern (21 bp):
TTTTTAATGTTGTAATTTATG
Found at i:490484 original size:23 final size:22
Alignment explanation
Indices: 490449--490511 Score: 56
Period size: 23 Copynumber: 2.8 Consensus size: 22
490439 GATTAAAATT
* *
490449 TTTAAATTGAAAAAATATGAAAA
1 TTTAATTTTAAAAAATAT-AAAA
* *
490472 TTTAATTTTAAAAAA-CTAAAT
1 TTTAATTTTAAAAAATATAAAA
490493 TTTAAATTTTATAAAAATA
1 TTT-AATTTTA-AAAAATA
490512 CAGATTTTAA
Statistics
Matches: 32, Mismatches: 5, Indels: 5
0.76 0.12 0.12
Matches are distributed among these distances:
21 6 0.19
22 8 0.25
23 18 0.56
ACGTcount: A:0.56, C:0.02, G:0.03, T:0.40
Consensus pattern (22 bp):
TTTAATTTTAAAAAATATAAAA
Found at i:490663 original size:15 final size:16
Alignment explanation
Indices: 490643--490679 Score: 58
Period size: 16 Copynumber: 2.4 Consensus size: 16
490633 TATACGTTTG
*
490643 ATTAATTAA-AATATT
1 ATTAATTAAGAATATA
490658 ATTAATTAAGAATATA
1 ATTAATTAAGAATATA
490674 ATTAAT
1 ATTAAT
490680 ATTATTTTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 9 0.45
16 11 0.55
ACGTcount: A:0.54, C:0.00, G:0.03, T:0.43
Consensus pattern (16 bp):
ATTAATTAAGAATATA
Found at i:493954 original size:20 final size:20
Alignment explanation
Indices: 493929--493969 Score: 59
Period size: 18 Copynumber: 2.1 Consensus size: 20
493919 AAAAAAAAAG
*
493929 TTTTTTTTTC--TTTTATCT
1 TTTTTTTTTCTTTTTTATAT
493947 TTTTTTTTTCTTTTTTATAT
1 TTTTTTTTTCTTTTTTATAT
493967 TTT
1 TTT
493970 AAATTTACGT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 10 0.50
20 10 0.50
ACGTcount: A:0.07, C:0.07, G:0.00, T:0.85
Consensus pattern (20 bp):
TTTTTTTTTCTTTTTTATAT
Found at i:494358 original size:22 final size:23
Alignment explanation
Indices: 494318--494363 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
494308 TAAATATTTT
* *
494318 TAATGATTTTTATTTTTTAAAAA
1 TAATGATTTATATTCTTTAAAAA
494341 TAATG-TTTATATTCTTTAAAAA
1 TAATGATTTATATTCTTTAAAAA
494363 T
1 T
494364 TTTAAAAATT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 16 0.76
23 5 0.24
ACGTcount: A:0.39, C:0.02, G:0.04, T:0.54
Consensus pattern (23 bp):
TAATGATTTATATTCTTTAAAAA
Found at i:494995 original size:19 final size:19
Alignment explanation
Indices: 494973--495017 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
494963 TTATATTAGG
494973 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
494992 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
495011 ATTTAAT
1 ATTTAAT
495018 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:495839 original size:15 final size:16
Alignment explanation
Indices: 495821--495850 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
495811 CTTCCCTATT
495821 TTCTA-TTTCTTTTAA
1 TTCTATTTTCTTTTAA
495836 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
495851 TTTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAA
Found at i:495843 original size:22 final size:22
Alignment explanation
Indices: 495816--495876 Score: 72
Period size: 22 Copynumber: 2.8 Consensus size: 22
495806 TTCGACTTCC
495816 CTATTTTCTATTT-CTTTTAATT
1 CTATTTTCT-TTTACTTTTAATT
*
495838 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTACTTTTAATT
* *
495860 CT-GTTTCTTTTATTTTT
1 CTATTTTCTTTTACTTTT
495877 CCTTAGATCA
Statistics
Matches: 36, Mismatches: 2, Indels: 3
0.88 0.05 0.07
Matches are distributed among these distances:
21 17 0.47
22 19 0.53
ACGTcount: A:0.15, C:0.11, G:0.02, T:0.72
Consensus pattern (22 bp):
CTATTTTCTTTTACTTTTAATT
Found at i:495866 original size:21 final size:22
Alignment explanation
Indices: 495830--495876 Score: 78
Period size: 21 Copynumber: 2.2 Consensus size: 22
495820 TTTCTATTTC
*
495830 TTTTAATTCTATTTTCTTTTAT
1 TTTTAATTCTAGTTTCTTTTAT
495852 TTTTAATTCT-GTTTCTTTTAT
1 TTTTAATTCTAGTTTCTTTTAT
495873 TTTT
1 TTTT
495877 CCTTAGATCA
Statistics
Matches: 24, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
21 14 0.58
22 10 0.42
ACGTcount: A:0.15, C:0.09, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTAATTCTAGTTTCTTTTAT
Found at i:499623 original size:105 final size:105
Alignment explanation
Indices: 499432--499624 Score: 257
Period size: 105 Copynumber: 1.8 Consensus size: 105
499422 ATGTGTTAGA
* *
499432 CTGAGTAACCGAGGTGGAGTGCTTGGTTGTCATTTCACTTCGCGTCAAAAGGGCTAACGCATTCT
1 CTGAGTAACCGAGGTGGAGTGCTTGGGTGTCATTTCACTTCGCGTCAAAAGGGCCAACGCATTCT
*
499497 ACAAAAAAAAGAGAAGAAAAAAAATTGAGAGCATGTTGGG
66 ACAAAAAAAAGAAAAGAAAAAAAATTGAGAGCATGTTGGG
* * * * *
499537 CTGAGTAACCG-GGATGGAGTGCTTGGGTGTTATTTCATTTCGCGTCAAAAGGTCCAATGTATTC
1 CTGAGTAACCGAGG-TGGAGTGCTTGGGTGTCATTTCACTTCGCGTCAAAAGGGCCAACGCATTC
*
499601 TTA-AAGAAAAAA-AAAAGGAAAAAA
65 -TACAA-AAAAAAGAAAAGAAAAAAA
499625 TTTCACAAAA
Statistics
Matches: 76, Mismatches: 9, Indels: 6
0.84 0.10 0.07
Matches are distributed among these distances:
104 2 0.03
105 66 0.87
106 8 0.11
ACGTcount: A:0.36, C:0.14, G:0.25, T:0.24
Consensus pattern (105 bp):
CTGAGTAACCGAGGTGGAGTGCTTGGGTGTCATTTCACTTCGCGTCAAAAGGGCCAACGCATTCT
ACAAAAAAAAGAAAAGAAAAAAAATTGAGAGCATGTTGGG
Found at i:500211 original size:19 final size:19
Alignment explanation
Indices: 500189--500233 Score: 56
Period size: 19 Copynumber: 2.4 Consensus size: 19
500179 TTATATTAGG
500189 ATTTAATATTTAAGATAT-T
1 ATTTAATATTTAA-ATATGT
* *
500208 ATTTATTATTTAAATTTGT
1 ATTTAATATTTAAATATGT
500227 ATTTAAT
1 ATTTAAT
500234 TTATGTTTAT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
18 3 0.14
19 19 0.86
ACGTcount: A:0.38, C:0.00, G:0.04, T:0.58
Consensus pattern (19 bp):
ATTTAATATTTAAATATGT
Found at i:501049 original size:15 final size:16
Alignment explanation
Indices: 501031--501060 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
501021 CTTCCCTATT
501031 TTCTA-TTTCTTTTAA
1 TTCTATTTTCTTTTAA
501046 TTCTATTTTCTTTTA
1 TTCTATTTTCTTTTA
501061 TTTTTAATTC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (16 bp):
TTCTATTTTCTTTTAA
Found at i:501053 original size:22 final size:22
Alignment explanation
Indices: 501026--501071 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
501016 TTCGACTTCC
501026 CTATTTTCTATTT-CTTTTAATT
1 CTATTTTCT-TTTACTTTTAATT
*
501048 CTATTTTCTTTTATTTTTAATT
1 CTATTTTCTTTTACTTTTAATT
501070 CT
1 CT
501072 GTTTATTTTA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 3 0.14
22 19 0.86
ACGTcount: A:0.17, C:0.13, G:0.00, T:0.70
Consensus pattern (22 bp):
CTATTTTCTTTTACTTTTAATT
Found at i:501086 original size:22 final size:22
Alignment explanation
Indices: 501040--501086 Score: 69
Period size: 21 Copynumber: 2.2 Consensus size: 22
501030 TTTCTATTTC
* *
501040 TTTTAATTCTATTTTCTTTTAT
1 TTTTAATTCTAGTTTATTTTAT
501062 TTTTAATTCT-GTTTATTTTAT
1 TTTTAATTCTAGTTTATTTTAT
501083 TTTT
1 TTTT
501087 CCTTAGATCG
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.57
22 10 0.43
ACGTcount: A:0.17, C:0.06, G:0.02, T:0.74
Consensus pattern (22 bp):
TTTTAATTCTAGTTTATTTTAT
Found at i:502953 original size:6 final size:6
Alignment explanation
Indices: 502942--502970 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
502932 ACACTTGTCT
502942 TCTTCA TCTTCA TCTTCA TCTTCA TCTTC
1 TCTTCA TCTTCA TCTTCA TCTTCA TCTTC
502971 TTTCCTTTTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.14, C:0.34, G:0.00, T:0.52
Consensus pattern (6 bp):
TCTTCA
Found at i:503269 original size:18 final size:16
Alignment explanation
Indices: 503246--503281 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 16
503236 GTTTAAAAAT
503246 TTTAATTAATTATATTTA
1 TTTAATTAA--ATATTTA
503264 TTTAATTAAATATTTA
1 TTTAATTAAATATTTA
503280 TT
1 TT
503282 CTCATTTCAT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
16 9 0.50
18 9 0.50
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (16 bp):
TTTAATTAAATATTTA
Found at i:512547 original size:26 final size:26
Alignment explanation
Indices: 512518--512569 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
512508 GAATTCTGAA
512518 GAACCTTTATGTTCCCATCCACTCAC
1 GAACCTTTATGTTCCCATCCACTCAC
512544 GAACCTTTATGTTCCCATCCACTCAC
1 GAACCTTTATGTTCCCATCCACTCAC
512570 TTCTCAATGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.38, G:0.08, T:0.31
Consensus pattern (26 bp):
GAACCTTTATGTTCCCATCCACTCAC
Found at i:515217 original size:59 final size:59
Alignment explanation
Indices: 515154--515269 Score: 232
Period size: 59 Copynumber: 2.0 Consensus size: 59
515144 CTAAGTTTTG
515154 GTTGAAATGATAAAATTAAATATTTAAATTTTGTTGTGTCATTAGTTTAAATCTCATTA
1 GTTGAAATGATAAAATTAAATATTTAAATTTTGTTGTGTCATTAGTTTAAATCTCATTA
515213 GTTGAAATGATAAAATTAAATATTTAAATTTTGTTGTGTCATTAGTTTAAATCTCAT
1 GTTGAAATGATAAAATTAAATATTTAAATTTTGTTGTGTCATTAGTTTAAATCTCAT
515270 CATAATTAAC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 57 1.00
ACGTcount: A:0.37, C:0.05, G:0.12, T:0.46
Consensus pattern (59 bp):
GTTGAAATGATAAAATTAAATATTTAAATTTTGTTGTGTCATTAGTTTAAATCTCATTA
Found at i:516834 original size:13 final size:13
Alignment explanation
Indices: 516812--516844 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
516802 TACTTTTTTA
516812 ACACACACTTTGC
1 ACACACACTTTGC
*
516825 ACACATACTTTGC
1 ACACACACTTTGC
516838 ACACACA
1 ACACACA
516845 GGTGCTCGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.36, C:0.36, G:0.06, T:0.21
Consensus pattern (13 bp):
ACACACACTTTGC
Found at i:518725 original size:97 final size:97
Alignment explanation
Indices: 518559--518757 Score: 398
Period size: 97 Copynumber: 2.1 Consensus size: 97
518549 CTTTTGGGGG
518559 ATTTTTATTCCAATTTTGGACTTTTTTGGATTATTTTTCAAAATAAGGCACTTTCTACATTATTT
1 ATTTTTATTCCAATTTTGGACTTTTTTGGATTATTTTTCAAAATAAGGCACTTTCTACATTATTT
518624 TCAAAATATATCTTTTTCTAGGGCTACTATTT
66 TCAAAATATATCTTTTTCTAGGGCTACTATTT
518656 ATTTTTATTCCAATTTTGGACTTTTTTGGATTATTTTTCAAAATAAGGCACTTTCTACATTATTT
1 ATTTTTATTCCAATTTTGGACTTTTTTGGATTATTTTTCAAAATAAGGCACTTTCTACATTATTT
518721 TCAAAATATATCTTTTTCTAGGGCTACTATTT
66 TCAAAATATATCTTTTTCTAGGGCTACTATTT
518753 ATTTT
1 ATTTT
518758 GGTCAAGGCT
Statistics
Matches: 102, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
97 102 1.00
ACGTcount: A:0.27, C:0.13, G:0.09, T:0.51
Consensus pattern (97 bp):
ATTTTTATTCCAATTTTGGACTTTTTTGGATTATTTTTCAAAATAAGGCACTTTCTACATTATTT
TCAAAATATATCTTTTTCTAGGGCTACTATTT
Found at i:520446 original size:22 final size:22
Alignment explanation
Indices: 520421--520462 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
520411 TTTATAATTT
520421 AAATATATAAAAAAAATAAAAA
1 AAATATATAAAAAAAATAAAAA
* *
520443 AAATATATAACAAATATAAA
1 AAATATATAAAAAAAATAAA
520463 TAGTGATGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.21
Consensus pattern (22 bp):
AAATATATAAAAAAAATAAAAA
Found at i:520457 original size:11 final size:11
Alignment explanation
Indices: 520421--520460 Score: 53
Period size: 11 Copynumber: 3.6 Consensus size: 11
520411 TTTATAATTT
520421 AAATATATAAA
1 AAATATATAAA
* *
520432 AAAAATAAAAA
1 AAATATATAAA
*
520443 AAATATATAAC
1 AAATATATAAA
520454 AAATATA
1 AAATATA
520461 AATAGTGATG
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
11 24 1.00
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.23
Consensus pattern (11 bp):
AAATATATAAA
Found at i:520715 original size:59 final size:57
Alignment explanation
Indices: 520651--521002 Score: 259
Period size: 59 Copynumber: 6.0 Consensus size: 57
520641 TTTTTTTTTT
* * *
520651 TGTTGGCCATACAATGATCGACACCCTTATTTATCTAATAAAAAAATTGCATTTTTGGG
1 TGTTGGCCATGCAATGATCGACACCCTT-TTT-TCTAATAAAAAAATTACATTTTTTGG
* ** * * *
520710 TGTTGGTCATGCAATGGCCGACACTCTTTTTT-TGAGA-AAAAAAATTTCAAAATTTTTTTG
1 TGTTGGCCATGCAATGATCGACACCCTTTTTTCT-A-ATAAAAAAA-TT--ACATTTTTTGG
* *
520770 TGTTGACCATGCAATGATCGACACTTCC-TTTTTC-AGAT-AAAAAATTCAAAATTTTTTGG
1 TGTTGGCCATGCAATGATCGACAC--CCTTTTTTCTA-ATAAAAAAATT--ACATTTTTTGG
* * ** * *
520829 TGTTGGCCATGCAATGGTCGACTCTCCCTTTTTTCGGATAAAAAATTTACATTTTTGGG
1 TGTTGGCCATGCAATGATCGA--CACCCTTTTTTCTAATAAAAAAATTACATTTTTTGG
* * * * * *
520888 TGTTGACCATGCAATG-GCTGACACCCCTTTTTC-AAAAAAAAAATCAAAATTTTTTGG
1 TGTTGGCCATGCAATGATC-GACACCCTTTTTTCTAATAAAAAAAT-TACATTTTTTGG
* * *
520945 TGTTGGTCATGCAATGATCGACACCCGCTTTTCTCTAATAAAAAAATTGCATTTTTTG
1 TGTTGGCCATGCAATGATCGACA-CC-CTTTTTTCTAATAAAAAAATTACATTTTTTG
521003 ATGTCTCAAA
Statistics
Matches: 232, Mismatches: 41, Indels: 40
0.74 0.13 0.13
Matches are distributed among these distances:
56 9 0.04
57 46 0.20
58 10 0.04
59 98 0.42
60 54 0.23
61 14 0.06
62 1 0.00
ACGTcount: A:0.30, C:0.17, G:0.16, T:0.37
Consensus pattern (57 bp):
TGTTGGCCATGCAATGATCGACACCCTTTTTTCTAATAAAAAAATTACATTTTTTGG
Found at i:520785 original size:119 final size:112
Alignment explanation
Indices: 520643--520960 Score: 302
Period size: 119 Copynumber: 2.7 Consensus size: 112
520633 AAATTTTTTT
* * * *
520643 TTTTTTTTTGTTGGCCATACAATGATCGACACCCTTATTTATCTAATAAAAAAATTGCATTTTTG
1 TTTTTTTGTGTTGACCATGCAATGATCGACACCC-T-TTT-TC-AATAAAAAAATT-CATTTTTT
*
520708 GGTGTTGGTCATGCAATGGCCGACACT-CTTTTTTTGAGAAAAAAAATTTCAAAA
61 GGTGTTGGTCATGCAATGGCCGACACTCCTTTTTTCG-GAAAAAAAATTT--AAA
520762 TTTTTTTGTGTTGACCATGCAATGATCGACACTTCCTTTTTCAGAT-AAAAAATTCAAAATTTTT
1 TTTTTTTGTGTTGACCATGCAATGATCGACAC--CCTTTTTCA-ATAAAAAAATTC---ATTTTT
* * * * *
520826 TGGTGTTGGCCATGCAATGGTCGACTCTCCCTTTTTTCGGATAAAAAATTTACA
60 TGGTGTTGGTCATGCAATGGCCGACACT-CCTTTTTTCGGAAAAAAAATTTAAA
** * *
520880 TTTTTGGGTGTTGACCATGCAATG-GCTGACACCCCTTTTTCAA-AAAAAAAATCAAAATTTTTT
1 TTTTTTTGTGTTGACCATGCAATGATC-GACA-CCCTTTTTCAATAAAAAAATTC---ATTTTTT
520943 GGTGTTGGTCATGCAATG
61 GGTGTTGGTCATGCAATG
520961 ATCGACACCC
Statistics
Matches: 173, Mismatches: 15, Indels: 25
0.81 0.07 0.12
Matches are distributed among these distances:
116 37 0.21
117 19 0.11
118 32 0.18
119 63 0.36
120 12 0.07
121 10 0.06
ACGTcount: A:0.29, C:0.16, G:0.16, T:0.38
Consensus pattern (112 bp):
TTTTTTTGTGTTGACCATGCAATGATCGACACCCTTTTTCAATAAAAAAATTCATTTTTTGGTGT
TGGTCATGCAATGGCCGACACTCCTTTTTTCGGAAAAAAAATTTAAA
Found at i:520976 original size:116 final size:117
Alignment explanation
Indices: 520701--521000 Score: 338
Period size: 116 Copynumber: 2.5 Consensus size: 117
520691 AAAAAATTGC
* * * * * *
520701 ATTTTTGGGTGTTGGTCATGCAATGGCCGACA-CTCTTTTTTTGAGAAAAAAAATTTCAAAATTT
1 ATTTTTTGGTGTTGGTCATGCAATGGTCGACACCCCTTTTTTCG-GATAAAAAATTT--ACATTT
** * * *
520765 TTTTGTGTTGACCATGCAATGATCGACACTTCCTTTTTCAGATAAAAAATTCAAA
63 TTGGGTGTTGACCATGCAATGATCGACACTCCCTTTTTCAGAAAAAAAAATCAAA
* *
520820 ATTTTTTGGTGTTGGCCATGCAATGGTCGACTCTCCCTTTTTTCGGATAAAAAATTTACATTTTT
1 ATTTTTTGGTGTTGGTCATGCAATGGTCGACAC-CCCTTTTTTCGGATAAAAAATTTACATTTTT
*
520885 GGGTGTTGACCATGCAATG-GCTGACAC-CCCTTTTTCA-AAAAAAAAATCAAA
65 GGGTGTTGACCATGCAATGATC-GACACTCCCTTTTTCAGAAAAAAAAATCAAA
* * ** * *
520936 ATTTTTTGGTGTTGGTCATGCAATGATCGACACCCGCTTTTCTCTAATAAAAAAATTGCATTTTT
1 ATTTTTTGGTGTTGGTCATGCAATGGTCGACACCC-CTTTTTTCGGATAAAAAATTTACATTTTT
521001 TGATGTCTCA
Statistics
Matches: 155, Mismatches: 22, Indels: 11
0.82 0.12 0.06
Matches are distributed among these distances:
115 2 0.01
116 66 0.43
117 10 0.06
118 29 0.19
119 28 0.18
120 11 0.07
121 9 0.06
ACGTcount: A:0.29, C:0.17, G:0.16, T:0.38
Consensus pattern (117 bp):
ATTTTTTGGTGTTGGTCATGCAATGGTCGACACCCCTTTTTTCGGATAAAAAATTTACATTTTTG
GGTGTTGACCATGCAATGATCGACACTCCCTTTTTCAGAAAAAAAAATCAAA
Found at i:521238 original size:37 final size:37
Alignment explanation
Indices: 521188--521261 Score: 148
Period size: 37 Copynumber: 2.0 Consensus size: 37
521178 TGTTGACCAT
521188 GTAATGGCCGACACCAACTTCCCCTCATTCTCTATAA
1 GTAATGGCCGACACCAACTTCCCCTCATTCTCTATAA
521225 GTAATGGCCGACACCAACTTCCCCTCATTCTCTATAA
1 GTAATGGCCGACACCAACTTCCCCTCATTCTCTATAA
521262 ATAGAATTTA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 37 1.00
ACGTcount: A:0.27, C:0.35, G:0.11, T:0.27
Consensus pattern (37 bp):
GTAATGGCCGACACCAACTTCCCCTCATTCTCTATAA
Found at i:522038 original size:17 final size:16
Alignment explanation
Indices: 522016--522069 Score: 53
Period size: 17 Copynumber: 3.5 Consensus size: 16
522006 AAAAAATAAT
522016 AATTAGAATATATAGGA
1 AATTAGAATATA-AGGA
522033 AATTAGAA-A-AA--A
1 AATTAGAATATAAGGA
*
522045 AATTAAAATATACAGGA
1 AATTAGAATATA-AGGA
522062 AATTAGAA
1 AATTAGAA
522070 ATTAAATTTA
Statistics
Matches: 30, Mismatches: 2, Indels: 10
0.71 0.05 0.24
Matches are distributed among these distances:
12 8 0.27
13 1 0.03
14 2 0.07
15 2 0.07
16 1 0.03
17 16 0.53
ACGTcount: A:0.61, C:0.02, G:0.13, T:0.24
Consensus pattern (16 bp):
AATTAGAATATAAGGA
Found at i:522055 original size:29 final size:30
Alignment explanation
Indices: 522009--522112 Score: 102
Period size: 30 Copynumber: 3.5 Consensus size: 30
521999 ATTTTAAAAA
* * *
522009 AAATAATAATTAGAATATATAGGAAATTAG
1 AAATAAAAATTAAAATATACAGGAAATTAG
522039 AAA-AAAAATTAAAATATACAGGAAATTAG
1 AAATAAAAATTAAAATATACAGGAAATTAG
* * * * * *
522068 AAATTAAATTTAAAATAAAAACGAAATTAC
1 AAATAAAAATTAAAATATACAGGAAATTAG
* *
522098 AAATTAAATTTAAAA
1 AAATAAAAATTAAAA
522113 AGTAAACGAA
Statistics
Matches: 64, Mismatches: 9, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
29 26 0.41
30 38 0.59
ACGTcount: A:0.62, C:0.03, G:0.08, T:0.27
Consensus pattern (30 bp):
AAATAAAAATTAAAATATACAGGAAATTAG
Found at i:522083 original size:30 final size:30
Alignment explanation
Indices: 522022--522112 Score: 112
Period size: 30 Copynumber: 3.1 Consensus size: 30
522012 TAATAATTAG
* * *
522022 AATATATAGGAAATTAGAAA-AAAAATTAA
1 AATATAAAGGAAATTAGAAATTAAATTTAA
*
522051 AATATACAGGAAATTAGAAATTAAATTTAA
1 AATATAAAGGAAATTAGAAATTAAATTTAA
* * *
522081 AATAAAAACGAAATTACAAATTAAATTTAA
1 AATATAAAGGAAATTAGAAATTAAATTTAA
522111 AA
1 AA
522113 AGTAAACGAA
Statistics
Matches: 54, Mismatches: 7, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
29 19 0.35
30 35 0.65
ACGTcount: A:0.63, C:0.03, G:0.08, T:0.26
Consensus pattern (30 bp):
AATATAAAGGAAATTAGAAATTAAATTTAA
Found at i:522289 original size:24 final size:24
Alignment explanation
Indices: 522262--522321 Score: 102
Period size: 24 Copynumber: 2.5 Consensus size: 24
522252 TCAGCTCATC
*
522262 CTCGATGGTGTCAACATTGGGTGT
1 CTCGATGGTGTCAACATTGGCTGT
522286 CTCGATGGTGTCAACATTGGCTGT
1 CTCGATGGTGTCAACATTGGCTGT
522310 CTCGATTGGTGT
1 CTCGA-TGGTGT
522322 ACGTAGAAAG
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 28 0.82
25 6 0.18
ACGTcount: A:0.15, C:0.18, G:0.32, T:0.35
Consensus pattern (24 bp):
CTCGATGGTGTCAACATTGGCTGT
Found at i:524913 original size:86 final size:86
Alignment explanation
Indices: 524763--525256 Score: 789
Period size: 86 Copynumber: 5.7 Consensus size: 86
524753 TGCAACCGCT
*
524763 CATTATTTGATAAAAATTGTAATATAACAATAATAATAATATTTATTTAAATATATAAAATTAAT
1 CATTATTTGATAAAAATTGTAATAT---AATAATAATAATTTTTATTTAAATATATAAAATTAAT
524828 AAATAATGTATTGTCAAATCAACA
63 AAATAATGTATTGTCAAATCAACA
* *
524852 CATTATTTAATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATTTAAAATTAATAAA
1 CATTATTTGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATATAAAATTAATAAA
*
524917 TAATGTATTGTCAAATCAATA
66 TAATGTATTGTCAAATCAACA
524938 CATTATTTGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATATAAAATTAATAAA
1 CATTATTTGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATATAAAATTAATAAA
525003 TAATGTATTGTCAAATCAACA
66 TAATGTATTGTCAAATCAACA
525024 CATTATTTGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATATAAAATTAATAAA
1 CATTATTTGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATATAAAATTAATAAA
525089 TAATGTATTGTCAAATCAACA
66 TAATGTATTGTCAAATCAACA
* * *
525110 CATTATTTGATAAAAATTGT-A-AT-ATAATAATAATTTGTACTTTAAATATGA-AAATTTGATA
1 CATTATTTGATAAAAATTGTAATATAATAATAATAATTTTTA-TTTAAATAT-ATAAAATTAATA
*
525171 AATAATGTATTGTCAAATTAACA
64 AATAATGTATTGTCAAATCAACA
* * * * *
525194 CAATATTTTACATAAATTGTAATATAATAATAATAATTTTTATTTAAATAATATTAAATTAAT
1 CATTATTTGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAAT-ATATAAAATTAAT
525257 TTTAAATGTA
Statistics
Matches: 379, Mismatches: 19, Indels: 16
0.92 0.05 0.04
Matches are distributed among these distances:
83 15 0.04
84 57 0.15
85 3 0.01
86 257 0.68
87 23 0.06
89 24 0.06
ACGTcount: A:0.50, C:0.04, G:0.05, T:0.41
Consensus pattern (86 bp):
CATTATTTGATAAAAATTGTAATATAATAATAATAATTTTTATTTAAATATATAAAATTAATAAA
TAATGTATTGTCAAATCAACA
Found at i:525374 original size:12 final size:12
Alignment explanation
Indices: 525357--525404 Score: 51
Period size: 12 Copynumber: 3.7 Consensus size: 12
525347 AAACATGTTC
525357 ATTAATTTCCAA
1 ATTAATTTCCAA
525369 ATTAATTTCAACTTAA
1 ATTAATTTC--C--AA
*
525385 ATTAATTTTCAA
1 ATTAATTTCCAA
525397 ATTAATTT
1 ATTAATTT
525405 TTACACAAAT
Statistics
Matches: 31, Mismatches: 1, Indels: 8
0.77 0.03 0.20
Matches are distributed among these distances:
12 19 0.61
14 2 0.06
16 10 0.32
ACGTcount: A:0.42, C:0.10, G:0.00, T:0.48
Consensus pattern (12 bp):
ATTAATTTCCAA
Found at i:525403 original size:16 final size:16
Alignment explanation
Indices: 525367--525401 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
525357 ATTAATTTCC
*
525367 AAATTAATTTCAACTT
1 AAATTAATTTCAAATT
525383 AAATTAATTTTCAAATT
1 AAATTAA-TTTCAAATT
525400 AA
1 AA
525402 TTTTTACACA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 7 0.41
17 10 0.59
ACGTcount: A:0.49, C:0.09, G:0.00, T:0.43
Consensus pattern (16 bp):
AAATTAATTTCAAATT
Found at i:525414 original size:28 final size:28
Alignment explanation
Indices: 525357--525414 Score: 71
Period size: 28 Copynumber: 2.1 Consensus size: 28
525347 AAACATGTTC
**
525357 ATTAATTTCCAAATTAATTTCAACTTAA
1 ATTAATTTCCAAATTAATTTCAACACAA
* **
525385 ATTAATTTTCAAATTAATTTTTACACAA
1 ATTAATTTCCAAATTAATTTCAACACAA
525413 AT
1 AT
525415 ATTCTTCGTG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
28 25 1.00
ACGTcount: A:0.43, C:0.12, G:0.00, T:0.45
Consensus pattern (28 bp):
ATTAATTTCCAAATTAATTTCAACACAA
Found at i:529355 original size:59 final size:59
Alignment explanation
Indices: 529232--529625 Score: 363
Period size: 60 Copynumber: 6.6 Consensus size: 59
529222 TGTCGATCAT
* *
529232 GGCCATTGCATGGCCAACACCCAAAAATGTAATTTTTTTATCCGAGAAAAGAGGG-TGTC
1 GGCCATTGCATGGCCAACACCAAAAAATGTAATTTTTTTATCTGAGAAAAG-GGGATGTC
* *
529291 AGCCATTG-ATGGCCAACACCAAAAAATTTTGAATTTTTTTATCTGA-AAAAGGGGATGTC
1 GGCCATTGCATGGCCAACACCAAAAAA-TGT-AATTTTTTTATCTGAGAAAAGGGGATGTC
* * *
529350 GGCCATTGCATGGCCTACACCCAAAAATGTAATTTTTTTTATCTAAGAAAA-GGGAGTGTC
1 GGCCATTGCATGGCCAACACCAAAAAATGTAA-TTTTTTTATCTGAGAAAAGGGGA-TGTC
* * * * * *
529410 AGCCATTGCATGACCAACACCCAAAAATGCAATTTTTTTATTTGAGAAAAGGGGGTGTC
1 GGCCATTGCATGGCCAACACCAAAAAATGTAATTTTTTTATCTGAGAAAAGGGGATGTC
* * * * *
529469 GACCATTGAATGGCCAACACCAAAAAAATTTGAAATTTTTTT-TCTCA-AAAAGGGAATGTC
1 GGCCATTGCATGGCCAACACC-AAAAAA--TGTAATTTTTTTATCTGAGAAAAGGGGATGTC
** * * * * * *
529529 GGCCATTTAATGACCAACATCC-AAAAATATAATTTTTTTATCAGATAAATAGGGG-CGTT
1 GGCCATTGCATGGCCAACA-CCAAAAAATGTAATTTTTTTATCTGAGAAA-AGGGGATGTC
* * * *
529588 GACCATTGTATGGCCAACACAAAAAAATTGTACTTTTT
1 GGCCATTGCATGGCCAACACCAAAAAA-TGTAATTTTT
529626 ATCTGACAAA
Statistics
Matches: 275, Mismatches: 43, Indels: 33
0.78 0.12 0.09
Matches are distributed among these distances:
57 10 0.04
58 26 0.09
59 110 0.40
60 113 0.41
61 5 0.02
62 11 0.04
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (59 bp):
GGCCATTGCATGGCCAACACCAAAAAATGTAATTTTTTTATCTGAGAAAAGGGGATGTC
Found at i:529469 original size:119 final size:117
Alignment explanation
Indices: 529191--529625 Score: 407
Period size: 119 Copynumber: 3.6 Consensus size: 117
529181 TTTTTTACTG
* *
529191 AAATGCAATTTTTTTATCCGAGAAAATAGGGTGTCGATCATGGCCATTGCATGGCCAACACCCAA
1 AAATGCAATTTTTTTATCTGAG-AAA-AGGGGGT-G-TC--GGCCATTGCATGGCCAACACCCAA
** * *
529256 AAATGTAATTTTTTTATCCGAGAAAAGAGG-GTGTCAGCCATTGATGGCCAACACCAAA
60 AAATGTAATTTTTTTATCTAAGAAAAG-GGAGTGTCAGCCATTGATGACCAACACCCAA
* *
529314 AAATTTTG-AATTTTTTTATCTGA-AAAAGGGGATGTCGGCCATTGCATGGCCTACACCCAAAAA
1 AAA---TGCAATTTTTTTATCTGAGAAAAGGGGGTGTCGGCCATTGCATGGCCAACACCCAAAAA
529377 TGTAATTTTTTTTATCTAAGAAAAGGGAGTGTCAGCCATTGCATGACCAACACCCAA
63 TGTAA-TTTTTTTATCTAAGAAAAGGGAGTGTCAGCCATTG-ATGACCAACACCCAA
* * * *
529434 AAATGCAATTTTTTTATTTGAGAAAAGGGGGTGTCGACCATTGAATGGCCAACACCAAAAAAATT
1 AAATGCAATTTTTTTATCTGAGAAAAGGGGGTGTCGGCCATTGCATGGCCAACACC-CAAAAA--
* * * * * *
529499 TGAAATTTTTTT-TCTCA-AAAAGGGAATGTCGGCCATTTAATGACCAACATCCAA
63 TGTAATTTTTTTATCTAAGAAAAGGGAGTGTCAGCCA-TTGATGACCAACACCCAA
** * * * * **
529553 AAATATAATTTTTTTATCAGATAAATAGGGGCGT-T-GACCATTGTATGGCCAACACAAAAAAAT
1 AAATGCAATTTTTTTATCTGAGAAA-AGGGG-GTGTCGGCCATTGCATGGCCAACACCCAAAAA-
*
529616 TGTACTTTTT
63 TGTAATTTTT
529626 ATCTGACAAA
Statistics
Matches: 269, Mismatches: 29, Indels: 34
0.81 0.09 0.10
Matches are distributed among these distances:
117 11 0.04
118 53 0.20
119 129 0.48
120 35 0.13
121 10 0.04
122 9 0.03
123 6 0.02
125 14 0.05
126 2 0.01
ACGTcount: A:0.35, C:0.17, G:0.18, T:0.30
Consensus pattern (117 bp):
AAATGCAATTTTTTTATCTGAGAAAAGGGGGTGTCGGCCATTGCATGGCCAACACCCAAAAATGT
AATTTTTTTATCTAAGAAAAGGGAGTGTCAGCCATTGATGACCAACACCCAA
Found at i:534756 original size:13 final size:13
Alignment explanation
Indices: 534738--534763 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
534728 GACTTCAAAA
534738 ATTATTTATTTAG
1 ATTATTTATTTAG
534751 ATTATTTATTTAG
1 ATTATTTATTTAG
534764 TATTTGTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.31, C:0.00, G:0.08, T:0.62
Consensus pattern (13 bp):
ATTATTTATTTAG
Found at i:541220 original size:17 final size:18
Alignment explanation
Indices: 541183--541223 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
541173 TATATAATTT
* *
541183 TTAAATATATATAATACA
1 TTAAAAATATATAAAACA
541201 TTAAAAATAT-TAAAACA
1 TTAAAAATATATAAAACA
541218 TTAAAA
1 TTAAAA
541224 TAAATATTTC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
17 12 0.57
18 9 0.43
ACGTcount: A:0.61, C:0.05, G:0.00, T:0.34
Consensus pattern (18 bp):
TTAAAAATATATAAAACA
Found at i:541336 original size:30 final size:30
Alignment explanation
Indices: 541302--541366 Score: 103
Period size: 30 Copynumber: 2.2 Consensus size: 30
541292 CAACTTAATA
* * *
541302 AACAAATGTCTCTAAAATAATAACAGAATT
1 AACAAATGCCTCTAAAAAAATAACAAAATT
541332 AACAAATGCCTCTAAAAAAATAACAAAATT
1 AACAAATGCCTCTAAAAAAATAACAAAATT
541362 AACAA
1 AACAA
541367 TAAAATAAGT
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.58, C:0.15, G:0.05, T:0.22
Consensus pattern (30 bp):
AACAAATGCCTCTAAAAAAATAACAAAATT
Found at i:545510 original size:3 final size:3
Alignment explanation
Indices: 545504--545547 Score: 79
Period size: 3 Copynumber: 14.3 Consensus size: 3
545494 CTTCTTACAT
545504 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T-AA TAA T
545548 TAAATTTTAG
Statistics
Matches: 40, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
3 37 0.93
4 3 0.08
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Found at i:546304 original size:31 final size:29
Alignment explanation
Indices: 546269--546358 Score: 90
Period size: 31 Copynumber: 3.0 Consensus size: 29
546259 AATTTATGAG
546269 AATTGAAACAAATTCAAAATTTCATGTATAA
1 AATTG-AACAAATTCAAAATTT-ATGTATAA
* * *
546300 AATTGCACAAATTTAAAGTTTATGTATAA
1 AATTGAACAAATTCAAAATTTATGTATAA
* **
546329 AATTGCACATAAAACCAAAATTTATGTATA
1 AATTG-A-ACAAATTCAAAATTTATGTATA
546359 GTTTTGAGAT
Statistics
Matches: 48, Mismatches: 9, Indels: 4
0.79 0.15 0.07
Matches are distributed among these distances:
29 13 0.27
30 13 0.27
31 22 0.46
ACGTcount: A:0.49, C:0.10, G:0.08, T:0.33
Consensus pattern (29 bp):
AATTGAACAAATTCAAAATTTATGTATAA
Found at i:546310 original size:30 final size:29
Alignment explanation
Indices: 546276--546358 Score: 103
Period size: 29 Copynumber: 2.8 Consensus size: 29
546266 GAGAATTGAA
546276 ACAAATTCAAAATTTCATGTATAAAATTGC
1 ACAAATTCAAAATTT-ATGTATAAAATTGC
* *
546306 ACAAATTTAAAGTTTATGTATAAAATTGC
1 ACAAATTCAAAATTTATGTATAAAATTGC
**
546335 ACATAAAACCAAAATTTATGTATA
1 AC--AAATTCAAAATTTATGTATA
546359 GTTTTGAGAT
Statistics
Matches: 45, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
29 16 0.36
30 13 0.29
31 16 0.36
ACGTcount: A:0.48, C:0.11, G:0.07, T:0.34
Consensus pattern (29 bp):
ACAAATTCAAAATTTATGTATAAAATTGC
Found at i:558913 original size:14 final size:14
Alignment explanation
Indices: 558894--558924 Score: 62
Period size: 14 Copynumber: 2.2 Consensus size: 14
558884 CCTCAAAATA
558894 AAATTACATCAATC
1 AAATTACATCAATC
558908 AAATTACATCAATC
1 AAATTACATCAATC
558922 AAA
1 AAA
558925 AGCTTTAACA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.55, C:0.19, G:0.00, T:0.26
Consensus pattern (14 bp):
AAATTACATCAATC
Found at i:559695 original size:23 final size:21
Alignment explanation
Indices: 559667--559708 Score: 57
Period size: 23 Copynumber: 1.9 Consensus size: 21
559657 TTTTTGTTTA
*
559667 ATTTAATTTTTATTTGATTTGTT
1 ATTTAAATTTT-TTT-ATTTGTT
559690 ATTTAAATTTTTTTATTTG
1 ATTTAAATTTTTTTATTTG
559709 GTAGAGTAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 5 0.28
22 3 0.17
23 10 0.56
ACGTcount: A:0.24, C:0.00, G:0.07, T:0.69
Consensus pattern (21 bp):
ATTTAAATTTTTTTATTTGTT
Found at i:571469 original size:2 final size:2
Alignment explanation
Indices: 571462--571493 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
571452 TTATTGAATC
571462 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
571494 TAATTTTTAA
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:572642 original size:59 final size:58
Alignment explanation
Indices: 572517--572653 Score: 150
Period size: 59 Copynumber: 2.3 Consensus size: 58
572507 AAAGCTTAGG
* * * **
572517 TACCAAATTAGAAAAAAATGTCAAGTTCAGGTAACAAATTGGGTAAAAAAATAGATATG
1 TACCAAATTA-AAAAAAATATCAAGTTCAAGTAACAAATTAGGTAAAAAAATAGATAAA
* * *
572576 TACCAAATTAAAAAAAAGTATCAAGTTCAAGTATCAAATTAGGTCAAAAAA-AGTTTAAA
1 TACCAAATTAAAAAAAA-TATCAAGTTCAAGTAACAAATTAGGTAAAAAAATAG-ATAAA
*
572635 TATCAAATTAAGAAAAAAT
1 TACCAAATTAA-AAAAAAT
572654 GTGAAATTTA
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
58 9 0.14
59 51 0.77
60 6 0.09
ACGTcount: A:0.54, C:0.09, G:0.12, T:0.25
Consensus pattern (58 bp):
TACCAAATTAAAAAAAATATCAAGTTCAAGTAACAAATTAGGTAAAAAAATAGATAAA
Found at i:572652 original size:28 final size:28
Alignment explanation
Indices: 572598--572652 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
572588 AAAAAGTATC
* * **
572598 AAGTTCAAGTATCAAATTAGGTCAAAAA
1 AAGTTCAAATATCAAATTAAGAAAAAAA
*
572626 AAGTTTAAATATCAAATTAAGAAAAAA
1 AAGTTCAAATATCAAATTAAGAAAAAA
572653 TGTGAAATTT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.56, C:0.07, G:0.11, T:0.25
Consensus pattern (28 bp):
AAGTTCAAATATCAAATTAAGAAAAAAA
Found at i:573541 original size:11 final size:11
Alignment explanation
Indices: 573516--573547 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
573506 TAGCAAATGG
573516 TTTTAAAATTA
1 TTTTAAAATTA
573527 --TTAAAATTA
1 TTTTAAAATTA
573536 TTTTAAAATTA
1 TTTTAAAATTA
573547 T
1 T
573548 AATCATCATC
Statistics
Matches: 19, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
9 9 0.47
11 10 0.53
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (11 bp):
TTTTAAAATTA
Found at i:574134 original size:15 final size:16
Alignment explanation
Indices: 574107--574154 Score: 50
Period size: 15 Copynumber: 3.2 Consensus size: 16
574097 GCACTAACCC
574107 AAAATCTCC-AAAATCA
1 AAAATC-CCTAAAATCA
*
574123 AAAA-CCCTAAAA-AA
1 AAAATCCCTAAAATCA
574137 AAAATCCCT-AAATCA
1 AAAATCCCTAAAATCA
574152 AAA
1 AAA
574155 CTCTTACCCA
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
14 10 0.37
15 13 0.48
16 4 0.15
ACGTcount: A:0.62, C:0.23, G:0.00, T:0.15
Consensus pattern (16 bp):
AAAATCCCTAAAATCA
Found at i:574220 original size:23 final size:23
Alignment explanation
Indices: 574189--574244 Score: 69
Period size: 23 Copynumber: 2.4 Consensus size: 23
574179 GATCACCCAA
* *
574189 AACCCAAAATTTCCAAATT-GAAC
1 AACCTAAAATCTCCAAATTCG-AC
574212 AACCTAAAATCTCCAAATTCGAC
1 AACCTAAAATCTCCAAATTCGAC
574235 AACCATAAAA
1 AACC-TAAAA
574245 AATTCATGGT
Statistics
Matches: 29, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 23 0.79
24 6 0.21
ACGTcount: A:0.50, C:0.27, G:0.04, T:0.20
Consensus pattern (23 bp):
AACCTAAAATCTCCAAATTCGAC
Found at i:577322 original size:49 final size:49
Alignment explanation
Indices: 577251--577349 Score: 198
Period size: 49 Copynumber: 2.0 Consensus size: 49
577241 ACTAAATATG
577251 ACCAAACCATAAATCATGGGAGTGTTAAAGGTAGATAGAATCAAATTGA
1 ACCAAACCATAAATCATGGGAGTGTTAAAGGTAGATAGAATCAAATTGA
577300 ACCAAACCATAAATCATGGGAGTGTTAAAGGTAGATAGAATCAAATTGA
1 ACCAAACCATAAATCATGGGAGTGTTAAAGGTAGATAGAATCAAATTGA
577349 A
1 A
577350 AAGAAAAAGA
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 50 1.00
ACGTcount: A:0.45, C:0.12, G:0.20, T:0.22
Consensus pattern (49 bp):
ACCAAACCATAAATCATGGGAGTGTTAAAGGTAGATAGAATCAAATTGA
Found at i:585665 original size:15 final size:13
Alignment explanation
Indices: 585642--585676 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 13
585632 AAATTCTCCC
585642 AAAAATAAATAAAT
1 AAAAATAAAT-AAT
585656 AAATAATAAATAAT
1 AAA-AATAAATAAT
585670 AAAAATA
1 AAAAATA
585677 TTTTGTTGAA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.20
14 9 0.45
15 7 0.35
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (13 bp):
AAAAATAAATAAT
Found at i:586670 original size:23 final size:23
Alignment explanation
Indices: 586626--586671 Score: 58
Period size: 23 Copynumber: 2.0 Consensus size: 23
586616 ACATTGTTCG
* *
586626 TGAACATGTTCGATTAAGTTAAA
1 TGAACATGTTCGATGAAATTAAA
586649 TGAACATGTTCG-TGAATATTAAA
1 TGAACATGTTCGATGAA-ATTAAA
586672 CAAACGAACA
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
22 3 0.15
23 17 0.85
ACGTcount: A:0.39, C:0.09, G:0.17, T:0.35
Consensus pattern (23 bp):
TGAACATGTTCGATGAAATTAAA
Found at i:593018 original size:20 final size:21
Alignment explanation
Indices: 592993--593031 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
592983 TCAATTTGAT
*
592993 AATTAATTATATT-TCAAAAA
1 AATTAATCATATTATCAAAAA
593013 AATTAATCATATTATCAAA
1 AATTAATCATATTATCAAA
593032 TATTGACAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 12 0.71
21 5 0.29
ACGTcount: A:0.54, C:0.08, G:0.00, T:0.38
Consensus pattern (21 bp):
AATTAATCATATTATCAAAAA
Found at i:593733 original size:30 final size:29
Alignment explanation
Indices: 593699--593762 Score: 74
Period size: 29 Copynumber: 2.2 Consensus size: 29
593689 TTAAATTTTA
*
593699 AAAAATTAAAAAATTATAGTTTAAAAAAAT
1 AAAAATCAAAAAATT-TAGTTTAAAAAAAT
** * *
593729 AAAAATCATTAAATTTATTTTAAAAATAT
1 AAAAATCAAAAAATTTAGTTTAAAAAAAT
593758 AAAAA
1 AAAAA
593763 ATATTTTTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
29 17 0.59
30 12 0.41
ACGTcount: A:0.64, C:0.02, G:0.02, T:0.33
Consensus pattern (29 bp):
AAAAATCAAAAAATTTAGTTTAAAAAAAT
Found at i:606414 original size:18 final size:17
Alignment explanation
Indices: 606390--606433 Score: 52
Period size: 18 Copynumber: 2.5 Consensus size: 17
606380 CAAAACCTCA
*
606390 CTTACAAATATTCAATCT
1 CTTACAAA-ATTAAATCT
*
606408 TTTACAACAATTAAATCT
1 CTTACAA-AATTAAATCT
606426 CTTACAAA
1 CTTACAAA
606434 GAAGGTCTAC
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 1 0.05
18 20 0.91
19 1 0.05
ACGTcount: A:0.43, C:0.20, G:0.00, T:0.36
Consensus pattern (17 bp):
CTTACAAAATTAAATCT
Found at i:609429 original size:26 final size:26
Alignment explanation
Indices: 609394--609445 Score: 86
Period size: 26 Copynumber: 2.0 Consensus size: 26
609384 ATAGCATTAA
* *
609394 TAACTTCCAAGCTATTCGATTGGATT
1 TAACTTCCAAGCTATCCAATTGGATT
609420 TAACTTCCAAGCTATCCAATTGGATT
1 TAACTTCCAAGCTATCCAATTGGATT
609446 GTGACTTGAT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.29, C:0.21, G:0.13, T:0.37
Consensus pattern (26 bp):
TAACTTCCAAGCTATCCAATTGGATT
Found at i:610368 original size:22 final size:21
Alignment explanation
Indices: 610326--610375 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
610316 AAGCTCAGAC
* *
610326 AATTTTTTTTTTACTACTTTT
1 AATTTTTTTTTAACTAATTTT
*
610347 AATTTTTTATTTAATTAATTTT
1 AATTTTTT-TTTAACTAATTTT
610369 AGATTTT
1 A-ATTTT
610376 AAAGGAATCA
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 8 0.33
22 11 0.46
23 5 0.21
ACGTcount: A:0.26, C:0.04, G:0.02, T:0.68
Consensus pattern (21 bp):
AATTTTTTTTTAACTAATTTT
Found at i:618461 original size:17 final size:16
Alignment explanation
Indices: 618439--618482 Score: 52
Period size: 17 Copynumber: 2.6 Consensus size: 16
618429 GAAATATATT
*
618439 TTAAAAAATATAAATGA
1 TTAAAAAATATAAA-AA
*
618456 TTAAAAAGTATAAAAA
1 TTAAAAAATATAAAAA
618472 TATAAAAAATA
1 T-TAAAAAATA
618483 GTTTTTTAAC
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
16 2 0.09
17 21 0.91
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (16 bp):
TTAAAAAATATAAAAA
Found at i:621941 original size:131 final size:133
Alignment explanation
Indices: 621700--621943 Score: 350
Period size: 131 Copynumber: 1.8 Consensus size: 133
621690 TCAGCATGAA
* *
621700 TATGTATGTATGTTCTGCATTCATGTTCGTTTGCATATTTGAACATGAGTATGGTGATATGACCT
1 TATGTATGTATGTTCGGCATCCATGTTCGTTTGCATATTTGAACATGAGTATGGTGATATGACCT
* * *
621765 TCTAAAGATTACATGGCAATTCAATAATTATGCAATTTTCTTCATCATCATCATGACACATGAAT
66 TCTAAAGATTACATGGCAATACAATAATTATGCAACTTTCATCATCATCATCATGACACATGAAT
621830 CTT
131 CTT
* *
621833 TATGTATGTATGTAT-GGCATCCATGTTTG-TTGCATATTTGGACATGA-TATGGTGATATGACC
1 TATGTATGTATGT-TCGGCATCCATGTTCGTTTGCATATTTGAACATGAGTATGGTGATATGACC
* * * * *
621895 TTTTAAAGATTACATGGCAATACAATCATTCTGTAGCTTTCATCATCAT
65 TTCTAAAGATTACATGGCAATACAATAATTATGCAACTTTCATCATCAT
621944 GACATTATCA
Statistics
Matches: 98, Mismatches: 12, Indels: 4
0.86 0.11 0.04
Matches are distributed among these distances:
131 56 0.57
132 17 0.17
133 24 0.24
134 1 0.01
ACGTcount: A:0.29, C:0.15, G:0.16, T:0.40
Consensus pattern (133 bp):
TATGTATGTATGTTCGGCATCCATGTTCGTTTGCATATTTGAACATGAGTATGGTGATATGACCT
TCTAAAGATTACATGGCAATACAATAATTATGCAACTTTCATCATCATCATCATGACACATGAAT
CTT
Found at i:622202 original size:163 final size:156
Alignment explanation
Indices: 621833--622243 Score: 414
Period size: 163 Copynumber: 2.6 Consensus size: 156
621823 CATGAATCTT
* * * * *
621833 TATGTATGTATGTATGGCATCCATGTTTGTTGCATATTTGGACATGA-TATGGTGATATGACCTT
1 TATGTATGTATGAATGACATCCATGTTTATTGTATATTTGGACATGAGTATGGAGATATGACCTT
* * *
621897 TTAAAGATTACATGGCAATACAATCATTCTGTAGCTTTCATCATCATGACATTATCATTAACCAA
66 CTAAAGATTACATGGCAATACAATCATTCTGCAGCTTTCATCATCATCACATTATCATTAACCAA
** *
621962 TTAGATTATCAGCATATGTATGTATG
131 ACAGATTATCAGCATATGTATGTAAG
* * * * * * *
621988 TATGTTTGAATCAATGACATCCATGTTTGTTTCATATTTGGAGTTTGGACATGAGTTTGGAGGTA
1 TATGTATGTATGAATGACATCCATGTTT-ATT-GTA--T--A-TTTGGACATGAGTATGGAGATA
* *
622053 TGAACTTCTAAAGATTACATGGCAATACCATCATTCTGCAG-TTTCATCATCATCATCATCATCA
59 TGACCTTCTAAAGATTACATGGCAATACAATCATTCTGCAGCTTTCATCATCATCA-CAT--T-A
* *
622117 TCTTTAACCAAACAGATTATCAGCATAAATCTTTATGTAAG
120 TCATTAACCAAACAGATTATCAGCAT--A--TGTATGTAAG
* * * *
622158 TATGTATGTATGAATGATATCCATGCTTATTGTATATCTGGACATGAGTAT-AACGATATGACCT
1 TATGTATGTATGAATGACATCCATGTTTATTGTATATTTGGACATGAGTATGGA-GATATGACCT
*
622222 TCTAAAGATTACATGGCGATAC
65 TCTAAAGATTACATGGCAATAC
622244 GAACATTTTC
Statistics
Matches: 205, Mismatches: 34, Indels: 26
0.77 0.13 0.10
Matches are distributed among these distances:
155 23 0.11
156 2 0.01
157 1 0.00
159 1 0.00
161 1 0.00
162 25 0.12
163 89 0.43
164 1 0.00
165 1 0.00
166 25 0.12
168 3 0.01
169 2 0.01
170 31 0.15
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (156 bp):
TATGTATGTATGAATGACATCCATGTTTATTGTATATTTGGACATGAGTATGGAGATATGACCTT
CTAAAGATTACATGGCAATACAATCATTCTGCAGCTTTCATCATCATCACATTATCATTAACCAA
ACAGATTATCAGCATATGTATGTAAG
Found at i:629273 original size:126 final size:128
Alignment explanation
Indices: 629061--629311 Score: 380
Period size: 126 Copynumber: 1.9 Consensus size: 128
629051 TAGCCAACCA
* *
629061 GTGTCTTGTCTAATGTTCATGTTAAATGGTTGAACTTCAAGCTGTTCATATTGATCATAAACAGC
1 GTGTCTTGTCTAATGTTCATGTTAAACGGTTGAACTTCAAGCTGTTCATATTGATCACAAACAGC
*
629126 TGGTGCAACCATATTAA-TG-GGTTCACTAACATGTGCAGCCATTTCGTGAGGTACCCATCTT
66 TGGTGCAACCATATTAAGTGAGGTTCACTAACAGGTGCAGCCATTTCGTGAGGTACCCATCTT
* * * *
629187 GTGTCTTGTCTAATTTTCATGTTAAACGGTTGAACTTCAAGCTGTTCATATTGATCACGAGCAGT
1 GTGTCTTGTCTAATGTTCATGTTAAACGGTTGAACTTCAAGCTGTTCATATTGATCACAAACAGC
*
629252 TGGTGCAACCATATTAATGGGTTGAGGTTGACTAACAGGTGCAGCCATTTCGTGAGGTAC
66 TGGTGCAACCATATTAA---G-TGAGGTTCACTAACAGGTGCAGCCATTTCGTGAGGTAC
629312 GATTGCACCT
Statistics
Matches: 111, Mismatches: 8, Indels: 6
0.89 0.06 0.05
Matches are distributed among these distances:
126 76 0.68
131 2 0.02
132 33 0.30
ACGTcount: A:0.25, C:0.18, G:0.22, T:0.34
Consensus pattern (128 bp):
GTGTCTTGTCTAATGTTCATGTTAAACGGTTGAACTTCAAGCTGTTCATATTGATCACAAACAGC
TGGTGCAACCATATTAAGTGAGGTTCACTAACAGGTGCAGCCATTTCGTGAGGTACCCATCTT
Found at i:642428 original size:27 final size:27
Alignment explanation
Indices: 642390--642444 Score: 110
Period size: 27 Copynumber: 2.0 Consensus size: 27
642380 TTTTCTTTTT
642390 TAAAATTTAAATATTCTAAAAGAACTA
1 TAAAATTTAAATATTCTAAAAGAACTA
642417 TAAAATTTAAATATTCTAAAAGAACTA
1 TAAAATTTAAATATTCTAAAAGAACTA
642444 T
1 T
642445 GTTAACCCAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.55, C:0.07, G:0.04, T:0.35
Consensus pattern (27 bp):
TAAAATTTAAATATTCTAAAAGAACTA
Found at i:644245 original size:30 final size:30
Alignment explanation
Indices: 644210--644283 Score: 148
Period size: 30 Copynumber: 2.5 Consensus size: 30
644200 GTGAAGATAA
644210 TAATGATTCATTTTATTACCAAAAAAAAAG
1 TAATGATTCATTTTATTACCAAAAAAAAAG
644240 TAATGATTCATTTTATTACCAAAAAAAAAG
1 TAATGATTCATTTTATTACCAAAAAAAAAG
644270 TAATGATTCATTTT
1 TAATGATTCATTTT
644284 TAAATTATAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 44 1.00
ACGTcount: A:0.46, C:0.09, G:0.07, T:0.38
Consensus pattern (30 bp):
TAATGATTCATTTTATTACCAAAAAAAAAG
Found at i:649486 original size:51 final size:51
Alignment explanation
Indices: 649428--649542 Score: 203
Period size: 51 Copynumber: 2.3 Consensus size: 51
649418 AAAGAATTTA
* *
649428 ATAAAAAAATTAATAGTATTAATTATTGAAATTAAATTTGAAATTTAAAAG
1 ATAAAAAAATTAATAGTATTAACTATTGAAATTAAATTTAAAATTTAAAAG
*
649479 GTAAAAAAATTAATAGTATTAACTATTGAAATTAAATTTAAAATTTAAAAG
1 ATAAAAAAATTAATAGTATTAACTATTGAAATTAAATTTAAAATTTAAAAG
649530 ATAAAAAAATTAA
1 ATAAAAAAATTAA
649543 AATTTAAAAA
Statistics
Matches: 60, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
51 60 1.00
ACGTcount: A:0.57, C:0.01, G:0.07, T:0.35
Consensus pattern (51 bp):
ATAAAAAAATTAATAGTATTAACTATTGAAATTAAATTTAAAATTTAAAAG
Found at i:650130 original size:20 final size:21
Alignment explanation
Indices: 650102--650145 Score: 54
Period size: 20 Copynumber: 2.1 Consensus size: 21
650092 TTATAGAAAA
* *
650102 TTATGTATAATTTTCACATTT
1 TTATGTATAATTTTAAAATTT
*
650123 TTAT-TATATTTTTAAAATTT
1 TTATGTATAATTTTAAAATTT
650143 TTA
1 TTA
650146 GCAACATGAC
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
20 16 0.80
21 4 0.20
ACGTcount: A:0.32, C:0.05, G:0.02, T:0.61
Consensus pattern (21 bp):
TTATGTATAATTTTAAAATTT
Found at i:652633 original size:3 final size:3
Alignment explanation
Indices: 652625--652660 Score: 72
Period size: 3 Copynumber: 12.0 Consensus size: 3
652615 AATTGTGTAA
652625 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT
652661 TTGGTAGCTA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
ATT
Done.