Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Scaffold49
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: 1668912
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 42860 characters in sequence are not A, C, G, or T
File 3 of 9
Found at i:331225 original size:19 final size:21
Alignment explanation
Indices: 331177--331231 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
331167 AATTCCAATA
*
331177 ATTTGTATCGATACATTCAGT
1 ATTTGTATCGATACATTAAGT
**
331198 AAATGTATCGATACA-TAAGT
1 ATTTGTATCGATACATTAAGT
331218 -TTTGTATCGATACA
1 ATTTGTATCGATACA
331232 ATGTATCGCT
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
19 12 0.41
20 4 0.14
21 13 0.45
ACGTcount: A:0.35, C:0.13, G:0.15, T:0.38
Consensus pattern (21 bp):
ATTTGTATCGATACATTAAGT
Found at i:333783 original size:52 final size:51
Alignment explanation
Indices: 333664--333797 Score: 169
Period size: 52 Copynumber: 2.6 Consensus size: 51
333654 TTAAGTTTCT
* * *
333664 CAATTGTTCATAATCGGAGATACTCCAACCCCGATTTTATTTTCAAAACAC
1 CAATTTTTCATAATCGGGGATACTCCAACCCCGATTTTATATTCAAAACAC
* * *
333715 CAATTTTCCTTTAATCGGGGATACTCCAACTCCGATTTTATATTCAAAAACAC
1 CAATTTTTC-ATAATCGGGGATACTCCAACCCCGATTTTATATTC-AAAACAC
* * *
333768 CAATTTTTCACAATCGAGGATACTTCAACC
1 CAATTTTTCATAATCGGGGATACTCCAACC
333798 TCGTTATTTC
Statistics
Matches: 69, Mismatches: 12, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
51 7 0.10
52 47 0.68
53 15 0.22
ACGTcount: A:0.33, C:0.25, G:0.10, T:0.32
Consensus pattern (51 bp):
CAATTTTTCATAATCGGGGATACTCCAACCCCGATTTTATATTCAAAACAC
Found at i:333942 original size:79 final size:78
Alignment explanation
Indices: 333810--334044 Score: 238
Period size: 79 Copynumber: 3.0 Consensus size: 78
333800 GTTATTTCGT
** * *
333810 CGGGGATACTCCAACCCCGTTACCTCCGAGGGGATACTCAAACCCCGGCTTTATTTCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCC-GTTTTATTTCCAAAATAT
* *
333875 TGATTTCTCGTAAT
65 TGATTTCTCATAAC
* * * **
333889 TGGGGATACTCCAACCCTGTTATTTCCGAGGGGATACTCCAATCCCGATTTTATTT-CTTAATCA
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCG-TTTTATTTCCAAAAT-A
* *
333953 TCGATTTTTCATAAC
64 TTGATTTCTCATAAC
* *** * *
333968 CGGAGATACTCCAACCCCGTTATTTTTAAGGAGATACTCCAACCCCGTTATTATCTCCAAAATAT
1 CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGTT-TTATTTCCAAAATAT
*
334033 TAAATTTCTCAT
65 T-GATTTCTCAT
334045 CGGGACATAT
Statistics
Matches: 124, Mismatches: 27, Indels: 9
0.77 0.17 0.06
Matches are distributed among these distances:
78 7 0.06
79 105 0.85
80 12 0.10
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.32
Consensus pattern (78 bp):
CGGGGATACTCCAACCCCGTTATTTCCGAGGGGATACTCCAACCCCGTTTTATTTCCAAAATATT
GATTTCTCATAAC
Found at i:342666 original size:27 final size:28
Alignment explanation
Indices: 342636--342694 Score: 66
Period size: 28 Copynumber: 2.1 Consensus size: 28
342626 AAATATCAAG
* *
342636 AAAAAAAATATTAAAA-TAAACAATTCA
1 AAAAAAAATATAAAAACTAAAAAATTCA
***
342663 AAAAATTTTATAAAAACTAAAAAATTCA
1 AAAAAAAATATAAAAACTAAAAAATTCA
342691 AAAA
1 AAAA
342695 TAAACATCTA
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
27 12 0.46
28 14 0.54
ACGTcount: A:0.69, C:0.07, G:0.00, T:0.24
Consensus pattern (28 bp):
AAAAAAAATATAAAAACTAAAAAATTCA
Found at i:343053 original size:23 final size:24
Alignment explanation
Indices: 343007--343058 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
342997 AGGGAAGCGG
* *
343007 GAGAGAAAGAAGGAAAAATTGGGA
1 GAGAAAAAGAAGGAAAAATGGGGA
343031 GAGAAAAAGAAGGAAAAA-GGGGA
1 GAGAAAAAGAAGGAAAAATGGGGA
343054 GAGAA
1 GAGAA
343059 GGGGAGGGGG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
23 9 0.35
24 17 0.65
ACGTcount: A:0.58, C:0.00, G:0.38, T:0.04
Consensus pattern (24 bp):
GAGAAAAAGAAGGAAAAATGGGGA
Found at i:343279 original size:8 final size:8
Alignment explanation
Indices: 343261--343290 Score: 53
Period size: 8 Copynumber: 3.9 Consensus size: 8
343251 TTTAAAAAAT
343261 ATTTT-AA
1 ATTTTAAA
343268 ATTTTAAA
1 ATTTTAAA
343276 ATTTTAAA
1 ATTTTAAA
343284 ATTTTAA
1 ATTTTAA
343291 TTTTTATTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 5 0.23
8 17 0.77
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (8 bp):
ATTTTAAA
Found at i:343354 original size:19 final size:19
Alignment explanation
Indices: 343268--343368 Score: 70
Period size: 20 Copynumber: 5.4 Consensus size: 19
343258 AATATTTTAA
*
343268 ATTTTAAAA-TT-TTA-AA
1 ATTTTAAAATTTATTATAT
**
343284 ATTTTAATTTTTATTATAT
1 ATTTTAAAATTTATTATAT
343303 ATTTT-AAATTT-TTGA-AT
1 ATTTTAAAATTTATT-ATAT
* *
343320 ATTTTTAAAAAATTATTTTAT
1 A-TTTT-AAAATTTATTATAT
343341 ATTTTAAAATTTATCTATAT
1 ATTTTAAAATTTAT-TATAT
*
343361 TTTTTAAA
1 ATTTTAAA
343369 TTCTTTAAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 16
0.71 0.11 0.18
Matches are distributed among these distances:
16 7 0.11
17 7 0.11
18 12 0.18
19 14 0.22
20 20 0.31
21 5 0.08
ACGTcount: A:0.40, C:0.01, G:0.01, T:0.58
Consensus pattern (19 bp):
ATTTTAAAATTTATTATAT
Found at i:343369 original size:19 final size:18
Alignment explanation
Indices: 343293--343370 Score: 61
Period size: 19 Copynumber: 4.1 Consensus size: 18
343283 AATTTTAATT
343293 TTTATTATATATTTT-AAA
1 TTTATTATAT-TTTTAAAA
343311 TTT-TTGAATATTTTTAAAAA
1 TTTATT--ATATTTTT-AAAA
* *
343331 ATTATTTTATATTTTAAAA
1 TTTATTATAT-TTTTAAAA
*
343350 TTTATCTATATTTTTTAAA
1 TTTAT-TATATTTTTAAAA
343369 TT
1 TT
343371 CTTTAAAAAT
Statistics
Matches: 48, Mismatches: 5, Indels: 13
0.73 0.08 0.20
Matches are distributed among these distances:
17 2 0.04
18 7 0.15
19 24 0.50
20 13 0.27
21 2 0.04
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (18 bp):
TTTATTATATTTTTAAAA
Found at i:343527 original size:10 final size:10
Alignment explanation
Indices: 343469--343578 Score: 52
Period size: 10 Copynumber: 10.9 Consensus size: 10
343459 ATTATTTGTA
343469 ATAAA-ATAT
1 ATAAATATAT
*
343478 ATATATATAT
1 ATAAATATAT
* *
343488 ATATATATGAG
1 ATAAATAT-AT
343499 AT-AATCATCAT
1 ATAAAT-AT-AT
343510 -TAAAATATAT
1 AT-AAATATAT
343520 ATAAATATAT
1 ATAAATATAT
* *
343530 A-ATAT-TTT
1 ATAAATATAT
*
343538 AAAAATAATTAT
1 ATAAAT-A-TAT
*
343550 AATAAATAAAT
1 -ATAAATATAT
343561 ATAAATATAT
1 ATAAATATAT
343571 AT-AATATA
1 ATAAATATA
343579 AAAATATTAA
Statistics
Matches: 78, Mismatches: 12, Indels: 22
0.70 0.11 0.20
Matches are distributed among these distances:
8 3 0.04
9 16 0.21
10 37 0.47
11 11 0.14
12 6 0.08
13 5 0.06
ACGTcount: A:0.57, C:0.02, G:0.02, T:0.39
Consensus pattern (10 bp):
ATAAATATAT
Found at i:343566 original size:23 final size:22
Alignment explanation
Indices: 343540--343594 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 22
343530 AATATTTTAA
343540 AAATAATTATAATA-AATAAATAT
1 AAAT-ATTATAATATAA-AAATAT
343563 AAATATATATAATATAAAAATATT
1 AAATAT-TATAATATAAAAATA-T
*
343587 AATTATTA
1 AAATATTA
343595 AATCTCAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
22 2 0.07
23 18 0.64
24 8 0.29
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (22 bp):
AAATATTATAATATAAAAATAT
Found at i:343590 original size:43 final size:41
Alignment explanation
Indices: 343512--343592 Score: 101
Period size: 41 Copynumber: 1.9 Consensus size: 41
343502 ATCATCATTA
* * *
343512 AAATATATATAAATATATAATATTTTAAAAATAATTATAAT
1 AAATAAATATAAATATATAATATATAAAAAATAATTATAAT
343553 AAATAAATATAAATATAT-ATAATATAAAAATATTAATTAT
1 AAATAAATATAAATATATAAT-ATATAAAAA-A-TAATTAT
343593 TAAATCTCAA
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
40 2 0.06
41 24 0.71
42 1 0.03
43 7 0.21
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (41 bp):
AAATAAATATAAATATATAATATATAAAAAATAATTATAAT
Found at i:343649 original size:14 final size:14
Alignment explanation
Indices: 343630--343663 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
343620 TAAAAAAATT
*
343630 AAATAAAATATTAA
1 AAATAAAATATAAA
343644 AAAT-AAATATAAA
1 AAATAAAATATAAA
343657 AAATAAA
1 AAATAAA
343664 GTGTTTTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
13 12 0.67
14 6 0.33
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (14 bp):
AAATAAAATATAAA
Found at i:343721 original size:19 final size:20
Alignment explanation
Indices: 343697--343736 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
343687 TAATTATTTT
343697 TTATTT-TTTATTTAAAAAA
1 TTATTTATTTATTTAAAAAA
*
343716 TTATTTATTTTTTTAAAAAA
1 TTATTTATTTATTTAAAAAA
343736 T
1 T
343737 AACCTTTTAC
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 6 0.32
20 13 0.68
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (20 bp):
TTATTTATTTATTTAAAAAA
Found at i:343924 original size:25 final size:25
Alignment explanation
Indices: 343896--343944 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
343886 ATTAGATATC
**
343896 AATTTAATTATTA-AAATTATTTAAA
1 AATTTAAAAATTATAAATT-TTTAAA
343921 AATTTAAAAATTATAAATTTTTAA
1 AATTTAAAAATTATAAATTTTTAA
343945 TATAAGTTGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 16 0.76
26 5 0.24
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (25 bp):
AATTTAAAAATTATAAATTTTTAAA
Found at i:347876 original size:2 final size:2
Alignment explanation
Indices: 347869--347894 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
347859 TGTCTCTTGT
347869 TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC
347895 CCCTGCTTCA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:352793 original size:28 final size:25
Alignment explanation
Indices: 352761--352812 Score: 68
Period size: 27 Copynumber: 2.0 Consensus size: 25
352751 TATTTGTTAA
352761 CATATTGAAACATTTTTATAATAAAATT
1 CATATT-AAACATTTTT-TAA-AAAATT
*
352789 CATATTATACATTTTTTAAAAAAT
1 CATATTAAACATTTTTTAAAAAAT
352813 ACTAATGAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
25 5 0.22
26 3 0.13
27 9 0.39
28 6 0.26
ACGTcount: A:0.46, C:0.08, G:0.02, T:0.44
Consensus pattern (25 bp):
CATATTAAACATTTTTTAAAAAATT
Found at i:352849 original size:18 final size:18
Alignment explanation
Indices: 352826--352861 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
352816 AATGAAAAAT
352826 TTATTAAAAAAAAATTAA
1 TTATTAAAAAAAAATTAA
*
352844 TTATTAAAAATAAATTAA
1 TTATTAAAAAAAAATTAA
352862 AAACGTATTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.64, C:0.00, G:0.00, T:0.36
Consensus pattern (18 bp):
TTATTAAAAAAAAATTAA
Found at i:357851 original size:15 final size:15
Alignment explanation
Indices: 357833--357872 Score: 71
Period size: 15 Copynumber: 2.7 Consensus size: 15
357823 TCAAAATGTC
357833 ACAATTTGTATCGGT
1 ACAATTTGTATCGGT
357848 ACAATTTGTATCGGT
1 ACAATTTGTATCGGT
*
357863 ACAATGTGTA
1 ACAATTTGTA
357873 AATGTATCGG
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
15 24 1.00
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (15 bp):
ACAATTTGTATCGGT
Found at i:361789 original size:32 final size:32
Alignment explanation
Indices: 361737--361805 Score: 102
Period size: 32 Copynumber: 2.2 Consensus size: 32
361727 ACAGAAAATG
*
361737 TATCAATACATAAGGGTTGTATCGATACAATA
1 TATCGATACATAAGGGTTGTATCGATACAATA
** *
361769 TATCGATACATAAGTTTTGTATCGATACAATG
1 TATCGATACATAAGGGTTGTATCGATACAATA
361801 TATCG
1 TATCG
361806 CTACGAAGCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
32 33 1.00
ACGTcount: A:0.36, C:0.13, G:0.16, T:0.35
Consensus pattern (32 bp):
TATCGATACATAAGGGTTGTATCGATACAATA
Found at i:361851 original size:21 final size:21
Alignment explanation
Indices: 361822--361862 Score: 64
Period size: 21 Copynumber: 2.0 Consensus size: 21
361812 AGCTACTGCC
*
361822 AAGGAAATGTATTGATACATT
1 AAGGAAATGTATCGATACATT
*
361843 AAGGTAATGTATCGATACAT
1 AAGGAAATGTATCGATACAT
361863 CGATCTTTGT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.41, C:0.07, G:0.20, T:0.32
Consensus pattern (21 bp):
AAGGAAATGTATCGATACATT
Found at i:364341 original size:52 final size:51
Alignment explanation
Indices: 364229--364350 Score: 167
Period size: 52 Copynumber: 2.4 Consensus size: 51
364219 CAATTCTCCG
* * *
364229 CAATCGGGGATATTCCAACTCCGATTTTATTTTCAAAACACTAATTTTCTA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCTA
*
364280 TAATCGGGGATACTCCAACTCCGA-TTTATTTCCAAAAAACACCAATTTT-TCA
1 CAATCGGGGATACTCCAACTCCGATTTTATTTCC--AAAACACCAATTTTCT-A
364332 CAATCGGGGATACTCCAAC
1 CAATCGGGGATACTCCAAC
364351 CCCGTTAATC
Statistics
Matches: 63, Mismatches: 5, Indels: 5
0.86 0.07 0.07
Matches are distributed among these distances:
50 8 0.13
51 23 0.37
52 32 0.51
ACGTcount: A:0.33, C:0.25, G:0.11, T:0.31
Consensus pattern (51 bp):
CAATCGGGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTTCTA
Found at i:364364 original size:27 final size:28
Alignment explanation
Indices: 364334--364408 Score: 100
Period size: 27 Copynumber: 2.7 Consensus size: 28
364324 ATTTTTCACA
364334 ATCGGGGATACTCCAACCCCGTTA-ATC
1 ATCGGGGATACTCCAACCCCGTTATATC
* *
364361 ATCGGGGATACTCCAACCTCGTTATTTTC
1 ATCGGGGATACTCCAACCCCGTTA-TATC
*
364390 A-AGGGGATACTCCAACCCC
1 ATCGGGGATACTCCAACCCC
364409 TACTTTATTC
Statistics
Matches: 42, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
27 23 0.55
28 16 0.38
29 3 0.07
ACGTcount: A:0.25, C:0.32, G:0.19, T:0.24
Consensus pattern (28 bp):
ATCGGGGATACTCCAACCCCGTTATATC
Found at i:364513 original size:79 final size:79
Alignment explanation
Indices: 364361--364534 Score: 187
Period size: 79 Copynumber: 2.2 Consensus size: 79
364351 CCCGTTAATC
* * * *
364361 ATCGGGGATACTCCAACCTCGTTATTTTCAAGGGGATACTCCAACCCCTACTTTATTCTTAAAAT
1 ATCGGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCTACTTTATTCTCAAAAC
**
364426 ATTGATTTCT-TATA
66 ATCAATTTCTCT-TA
* ** *
364440 ATCGGGGATACTCCAACCCCGTTATTTCCGAA-GGGATACTCCAATCCC-GGTTTCATT-TCCAG
1 ATCGGGGATACTCCAACCCCGTTATTTCC-AAGGGGATACTCCAACCCCTACTTT-ATTCT-CAA
364502 AACATCAATTTCTCTTA
63 AACATCAATTTCTCTTA
364519 ATC-GGGATACTCCAAC
1 ATCGGGGATACTCCAAC
364535 TCCGATTTTA
Statistics
Matches: 81, Mismatches: 10, Indels: 9
0.81 0.10 0.09
Matches are distributed among these distances:
78 17 0.21
79 61 0.75
80 3 0.04
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.32
Consensus pattern (79 bp):
ATCGGGGATACTCCAACCCCGTTATTTCCAAGGGGATACTCCAACCCCTACTTTATTCTCAAAAC
ATCAATTTCTCTTA
Found at i:364548 original size:50 final size:51
Alignment explanation
Indices: 364472--364634 Score: 161
Period size: 51 Copynumber: 3.2 Consensus size: 51
364462 TATTTCCGAA
* * * * *
364472 GGGATACTCCAA-TCCCGGTTTCATTTCCAGAACATCAATTTCTCTTAATC-
1 GGGATACTCCAACT-CCGATTTTATTTCCAAAACACCAATTTCTCATAATCG
* * *
364522 GGGATACTCCAACTCCGATTTTATTTCTAAAACACCCATTTTTCATAATCG
1 GGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTCTCATAATCG
* * * * *
364573 GGGACACTCCAACTCTGATTTTATTTCCAAAGCACCGACTTT-TCACAATCG
1 GGGATACTCCAACTCCGATTTTATTTCCAAAACACC-AATTTCTCATAATCG
*
364624 GGGATATTCCA
1 GGGATACTCCA
364635 GCCCCGTTAT
Statistics
Matches: 93, Mismatches: 17, Indels: 5
0.81 0.15 0.04
Matches are distributed among these distances:
50 40 0.43
51 50 0.54
52 3 0.03
ACGTcount: A:0.28, C:0.27, G:0.13, T:0.33
Consensus pattern (51 bp):
GGGATACTCCAACTCCGATTTTATTTCCAAAACACCAATTTCTCATAATCG
Found at i:364732 original size:27 final size:27
Alignment explanation
Indices: 364694--364746 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
364684 CATCAATTTT
*
364694 TCATTGGGGATACTCCAACCCCGTTAA
1 TCATCGGGGATACTCCAACCCCGTTAA
*
364721 TCATCGGGGATACTCCAACCTCGTTA
1 TCATCGGGGATACTCCAACCCCGTTA
364747 CCTTCGAGGG
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.26
Consensus pattern (27 bp):
TCATCGGGGATACTCCAACCCCGTTAA
Found at i:364819 original size:51 final size:51
Alignment explanation
Indices: 364754--364974 Score: 237
Period size: 51 Copynumber: 4.3 Consensus size: 51
364744 TTACCTTCGA
* * * * * * *
364754 GGGGATACTTCAACCCCGGCTTTATTTCCAAAATATTGA-TTTCTCATAATT
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTC-CACAATC
* *
364805 GGGGATACTCCAACCCCGATTTTATTTCTAAAACACTAATTTTCCACAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTCCACAATC
* * **
364856 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTCC-ACAATC
* * * * *
364908 GGGGATACTCCAACTCCGATTTTATTTCTAAAAACACAAATTTTTCACAATC
1 GGGGATACTCCAACCCCGGTTTTATTTC-CAAAACACTAATTTTCCACAATC
*
364960 GAGGATACTCCAACC
1 GGGGATACTCCAACC
364975 TCATTATTTC
Statistics
Matches: 142, Mismatches: 25, Indels: 5
0.83 0.15 0.03
Matches are distributed among these distances:
51 78 0.55
52 50 0.35
53 14 0.10
ACGTcount: A:0.30, C:0.25, G:0.12, T:0.33
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGGTTTTATTTCCAAAACACTAATTTTCCACAATC
Found at i:364931 original size:52 final size:51
Alignment explanation
Indices: 364805--364974 Score: 225
Period size: 52 Copynumber: 3.3 Consensus size: 51
364795 TCTCATAATT
*
364805 GGGGATACTCCAACCCCGATTTTA-TTTCTAAAACACTAATTTTCCACAATC
1 GGGGATACTCCAACCCCGATTTTATTTTC-AAAACACAAATTTTCCACAATC
* * **
364856 GGGGATACTCCAACCCCGGTTTTATTTTCAAAACACCAATTTTCCTTTAATC
1 GGGGATACTCCAACCCCGATTTTATTTTCAAAACACAAATTTTCC-ACAATC
* * *
364908 GGGGATACTCCAACTCCGATTTTATTTCTAAAAACACAAATTTTTCACAATC
1 GGGGATACTCCAACCCCGATTTTATTT-TCAAAACACAAATTTTCCACAATC
*
364960 GAGGATACTCCAACC
1 GGGGATACTCCAACC
364975 TCATTATTTC
Statistics
Matches: 103, Mismatches: 13, Indels: 5
0.85 0.11 0.04
Matches are distributed among these distances:
51 38 0.37
52 50 0.49
53 15 0.15
ACGTcount: A:0.31, C:0.26, G:0.11, T:0.31
Consensus pattern (51 bp):
GGGGATACTCCAACCCCGATTTTATTTTCAAAACACAAATTTTCCACAATC
Found at i:364993 original size:28 final size:29
Alignment explanation
Indices: 364957--365038 Score: 89
Period size: 28 Copynumber: 2.9 Consensus size: 29
364947 ATTTTTCACA
* *
364957 ATCGAGGATACTCCAACCTCATTATTTC-
1 ATCGGGGATACTCCAACCCCATTATTTCG
* *
364985 ATCGGGGATACTCCAACCCCGTTACCTTCG
1 ATCGGGGATACTCCAACCCCATTA-TTTCG
*
365015 A--GGGGATACTCCAACCGCATTATT
1 ATCGGGGATACTCCAACCCCATTATT
365039 ATCTCCAAAA
Statistics
Matches: 45, Mismatches: 7, Indels: 5
0.79 0.12 0.09
Matches are distributed among these distances:
27 1 0.02
28 40 0.89
29 3 0.07
30 1 0.02
ACGTcount: A:0.26, C:0.30, G:0.17, T:0.27
Consensus pattern (29 bp):
ATCGGGGATACTCCAACCCCATTATTTCG
Found at i:371425 original size:52 final size:52
Alignment explanation
Indices: 371347--371475 Score: 240
Period size: 52 Copynumber: 2.5 Consensus size: 52
371337 CGAAATATGA
371347 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
371399 AAATTTGCCTGTATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
1 AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
*
371451 AAATTTCCCTGCATGTATCGATACA
1 AAATTTGCCTGCATGTATCGATACA
371476 ATGTATCGAT
Statistics
Matches: 74, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
52 74 1.00
ACGTcount: A:0.28, C:0.19, G:0.18, T:0.35
Consensus pattern (52 bp):
AAATTTGCCTGCATGTATCGATACATTTCATAGTGTATCGATACATCTGGGC
Found at i:371481 original size:13 final size:13
Alignment explanation
Indices: 371463--371488 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
371453 ATTTCCCTGC
371463 ATGTATCGATACA
1 ATGTATCGATACA
371476 ATGTATCGATACA
1 ATGTATCGATACA
371489 TTTGAGTAAT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:371575 original size:32 final size:32
Alignment explanation
Indices: 371533--371681 Score: 255
Period size: 32 Copynumber: 4.7 Consensus size: 32
371523 AGCTTCGTAG
* *
371533 CGATACATTGTATCGATATAA-ATCTTATGCAT
1 CGATACATTGTATCGATACAACA-CTTATGAAT
*
371565 TGATACATTGTATCGATACAACACTTATGAAT
1 CGATACATTGTATCGATACAACACTTATGAAT
371597 CGATACATTGTATCGATACAACACTTATGAAT
1 CGATACATTGTATCGATACAACACTTATGAAT
371629 CGATACATTGTATCGATACAACACTTATGAAT
1 CGATACATTGTATCGATACAACACTTATGAAT
371661 CGATACATTGTATCGATACAA
1 CGATACATTGTATCGATACAA
371682 ATCGTTGAAA
Statistics
Matches: 112, Mismatches: 4, Indels: 2
0.95 0.03 0.02
Matches are distributed among these distances:
32 111 0.99
33 1 0.01
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (32 bp):
CGATACATTGTATCGATACAACACTTATGAAT
Found at i:371600 original size:19 final size:19
Alignment explanation
Indices: 371576--371667 Score: 82
Period size: 19 Copynumber: 5.5 Consensus size: 19
371566 GATACATTGT
371576 ATCGATACAACACTTATGA
1 ATCGATACAACACTTATGA
*
371595 ATCGAT---ACA--T-TGT
1 ATCGATACAACACTTATGA
371608 ATCGATACAACACTTATGA
1 ATCGATACAACACTTATGA
*
371627 ATCGAT---ACA--T-TGT
1 ATCGATACAACACTTATGA
371640 ATCGATACAACACTTATGA
1 ATCGATACAACACTTATGA
371659 ATCGATACA
1 ATCGATACA
371668 TTGTATCGAT
Statistics
Matches: 57, Mismatches: 4, Indels: 24
0.67 0.05 0.28
Matches are distributed among these distances:
13 16 0.28
14 2 0.04
16 12 0.21
18 2 0.04
19 25 0.44
ACGTcount: A:0.39, C:0.20, G:0.12, T:0.29
Consensus pattern (19 bp):
ATCGATACAACACTTATGA
Found at i:373866 original size:51 final size:51
Alignment explanation
Indices: 373807--373927 Score: 172
Period size: 50 Copynumber: 2.4 Consensus size: 51
373797 ATTTGATGTT
* * *
373807 TCGATACATCTAGGTAAAAAGGCAGAATGTATCGATACATTGAAGAACGTA
1 TCGATACATCTGGGTAAAAAGACAGAATGTATCGATACATTGAAAAACGTA
* *
373858 TCGATACATCTGGGT-AAAAGATAGAATGTATCGATACATTGAAAAATGTA
1 TCGATACATCTGGGTAAAAAGACAGAATGTATCGATACATTGAAAAACGTA
* *
373908 TTGATACATTTGGGTAAAAA
1 TCGATACATCTGGGTAAAAA
373928 ATGTGACTTT
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
50 44 0.71
51 18 0.29
ACGTcount: A:0.41, C:0.11, G:0.21, T:0.27
Consensus pattern (51 bp):
TCGATACATCTGGGTAAAAAGACAGAATGTATCGATACATTGAAAAACGTA
Found at i:375136 original size:31 final size:32
Alignment explanation
Indices: 375092--375168 Score: 86
Period size: 31 Copynumber: 2.5 Consensus size: 32
375082 AAGTCAAAGG
* * * * *
375092 TTCAAATTTGAAAAAATT-GAATTCGAAAAAT
1 TTCAAACTCGAAAAAATTCGAATCCAAAAAAA
*
375123 TTCAAACT-GGAAAAATTCGAATCCAAAAAAA
1 TTCAAACTCGAAAAAATTCGAATCCAAAAAAA
375154 TTCAAACTCGAAAAA
1 TTCAAACTCGAAAAA
375169 CCTTGAAATC
Statistics
Matches: 38, Mismatches: 6, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
30 8 0.21
31 25 0.66
32 5 0.13
ACGTcount: A:0.53, C:0.13, G:0.09, T:0.25
Consensus pattern (32 bp):
TTCAAACTCGAAAAAATTCGAATCCAAAAAAA
Found at i:375167 original size:16 final size:16
Alignment explanation
Indices: 375101--375168 Score: 52
Period size: 16 Copynumber: 4.4 Consensus size: 16
375091 GTTCAAATTT
* *
375101 GAAAAAATT-GAATTC
1 GAAAAAATTCAAACTC
*
375116 GAAAAATTTCAAACT-
1 GAAAAAATTCAAACTC
* *
375131 GGAAAAATTCGAA-TCC
1 GAAAAAATTCAAACT-C
*
375147 AAAAAAATTCAAACTC
1 GAAAAAATTCAAACTC
375163 GAAAAA
1 GAAAAA
375169 CCTTGAAATC
Statistics
Matches: 39, Mismatches: 10, Indels: 7
0.70 0.18 0.12
Matches are distributed among these distances:
14 1 0.03
15 18 0.46
16 19 0.49
17 1 0.03
ACGTcount: A:0.56, C:0.13, G:0.10, T:0.21
Consensus pattern (16 bp):
GAAAAAATTCAAACTC
Found at i:378324 original size:21 final size:21
Alignment explanation
Indices: 378285--378325 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
378275 TTGGACATGT
*
378285 TAAAATGCATGGAACATGGCA
1 TAAAATGCATGAAACATGGCA
378306 TAAAATGCAT-AAACAATGGC
1 TAAAATGCATGAAAC-ATGGC
378326 TGTAAAAATA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 3 0.17
21 15 0.83
ACGTcount: A:0.46, C:0.15, G:0.20, T:0.20
Consensus pattern (21 bp):
TAAAATGCATGAAACATGGCA
Found at i:379371 original size:20 final size:21
Alignment explanation
Indices: 379327--379375 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
379317 TATGGTCCGG
*
379327 TATCGATACATTTCAAGTATG
1 TATCGATACATTTCAAGTATA
**
379348 TATCGATACA-TTCACTTATA
1 TATCGATACATTTCAAGTATA
379368 TATCGATA
1 TATCGATA
379376 TATTAGCTTA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
20 15 0.60
21 10 0.40
ACGTcount: A:0.35, C:0.16, G:0.10, T:0.39
Consensus pattern (21 bp):
TATCGATACATTTCAAGTATA
Found at i:379818 original size:15 final size:15
Alignment explanation
Indices: 379788--379828 Score: 50
Period size: 15 Copynumber: 2.9 Consensus size: 15
379778 AAATTGTAAT
*
379788 AAATAAACT-AAA-A
1 AAATAAAATAAAACA
*
379801 AAATATAATAAAACA
1 AAATAAAATAAAACA
379816 AAATAAAATAAAA
1 AAATAAAATAAAA
379829 AAATAAGATT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
13 7 0.30
14 3 0.13
15 13 0.57
ACGTcount: A:0.78, C:0.05, G:0.00, T:0.17
Consensus pattern (15 bp):
AAATAAAATAAAACA
Found at i:380038 original size:63 final size:63
Alignment explanation
Indices: 379966--380092 Score: 209
Period size: 63 Copynumber: 2.0 Consensus size: 63
379956 ATTACTTTGC
** * *
379966 TTAGTGTTATTTTATATTTATTTTTGCTTCCTTATAAAATAAAAAATTTTCTTATATAATCAT
1 TTAGTGTTATTTTATATTTATTTTCACTTCCCTATAAAATAAAAAAATTTCTTATATAATCAT
*
380029 TTAGTGTTATTTTATATTTATTTTCACTTCCCTATAAAATAAAAAAATTTCTTGTATAATCAT
1 TTAGTGTTATTTTATATTTATTTTCACTTCCCTATAAAATAAAAAAATTTCTTATATAATCAT
380092 T
1 T
380093 AATTATATCA
Statistics
Matches: 59, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.34, C:0.09, G:0.05, T:0.52
Consensus pattern (63 bp):
TTAGTGTTATTTTATATTTATTTTCACTTCCCTATAAAATAAAAAAATTTCTTATATAATCAT
Found at i:380290 original size:15 final size:15
Alignment explanation
Indices: 380265--380297 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
380255 TACTAAAAAT
380265 TATAGATAATATTCAA
1 TATAGATAATATT-AA
380281 TATA-ATAATATTAA
1 TATAGATAATATTAA
380295 TAT
1 TAT
380298 TCAATAAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 5 0.29
15 8 0.47
16 4 0.24
ACGTcount: A:0.52, C:0.03, G:0.03, T:0.42
Consensus pattern (15 bp):
TATAGATAATATTAA
Found at i:380317 original size:24 final size:21
Alignment explanation
Indices: 380271--380309 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
380261 AAATTATAGA
*
380271 TAATATTCAATATAATAATAT
1 TAATATTCAATATAATAAAAT
380292 TAATATTCAATA-AATAAA
1 TAATATTCAATATAATAAA
380310 TAAAATTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.56, C:0.05, G:0.00, T:0.38
Consensus pattern (21 bp):
TAATATTCAATATAATAAAAT
Found at i:382319 original size:31 final size:31
Alignment explanation
Indices: 382281--382340 Score: 111
Period size: 31 Copynumber: 1.9 Consensus size: 31
382271 AAGTATGACA
*
382281 TATAGAAATTTGAATTTTATCTCATAGGCTT
1 TATAGAAATTTGAACTTTATCTCATAGGCTT
382312 TATAGAAATTTGAACTTTATCTCATAGGC
1 TATAGAAATTTGAACTTTATCTCATAGGC
382341 CATCACTTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 28 1.00
ACGTcount: A:0.33, C:0.12, G:0.13, T:0.42
Consensus pattern (31 bp):
TATAGAAATTTGAACTTTATCTCATAGGCTT
Found at i:390254 original size:29 final size:28
Alignment explanation
Indices: 390217--390297 Score: 94
Period size: 29 Copynumber: 2.9 Consensus size: 28
390207 TAATAAAATA
*
390217 TTAATTTATATGTAAATAAATAATTTATT
1 TTAATTTATATATAAATAAATAATTTA-T
**
390246 TTAATTTATATATAAATAAATTAAAATAT
1 TTAATTTATATATAAATAAA-TAATTTAT
*
390275 TTAATTTATATTTAAA-AAA-AATT
1 TTAATTTATATATAAATAAATAATT
390298 ATATGATATA
Statistics
Matches: 45, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
26 2 0.04
28 3 0.07
29 35 0.78
30 5 0.11
ACGTcount: A:0.51, C:0.00, G:0.01, T:0.48
Consensus pattern (28 bp):
TTAATTTATATATAAATAAATAATTTAT
Found at i:391093 original size:203 final size:203
Alignment explanation
Indices: 390740--391349 Score: 1067
Period size: 203 Copynumber: 3.0 Consensus size: 203
390730 TGGTCTTCAG
* * * *
390740 TTCCTATTTTCCTTGCATCTTTCTGTTTGGGTTTCTTGAGGAAAAATTTAGTAAGTGTTTTATCA
1 TTCCTATTTTCCTTGTATCTTTCTGTCTGGGTTTCTTGGGGAAAAATTTAGTAATTGTTTTATCA
* *
390805 TACATTTAACTTGACTCTTTAAGCGTGAAAATATCTACTTCTTTATGTAGATCTTTTCTTTTTAT
66 TACATTTAACTTGACTCTTTAAGCGTGAAAATATCTACTTGTTTATGTAGATCTTTTCTTTTTAG
*
390870 TCTGTTTTTAGTAAAAGAAAATAGGATGGGAATGTGCTTTTTCCCATTGATTTGGGCTGTCAATT
131 TCTATTTTTAGTAAAAGAAAATAGGATGGGAATGTGCTTTTTCCCATTGATTTGGGCTGTCAATT
390935 TGGTTCCT
196 TGGTTCCT
390943 TTCCTATTTTCCTTGTATCTTTCTGTCTGGGTTTCTTGGGGAAAAATTTAGTAATTGTTTTATCA
1 TTCCTATTTTCCTTGTATCTTTCTGTCTGGGTTTCTTGGGGAAAAATTTAGTAATTGTTTTATCA
*
391008 TACATTTAACTTGACTCTTTAAGCTTGAAAATATCTACTTGTTTATGTAGATCTTTTCTTTTTAG
66 TACATTTAACTTGACTCTTTAAGCGTGAAAATATCTACTTGTTTATGTAGATCTTTTCTTTTTAG
* * * *
391073 TCTATTTTTAGTATAAGAAAATATGATGGGAATGTGCTTTTTCCTATTGATTTGGGCTGTCAATC
131 TCTATTTTTAGTAAAAGAAAATAGGATGGGAATGTGCTTTTTCCCATTGATTTGGGCTGTCAATT
391138 TGGTTCCT
196 TGGTTCCT
* *
391146 TTCCTATTTTCCTTGTATCTTTCTGTCTGGGTTTCTCGGGGAAGAATTTAGTAATTGTTTTATCA
1 TTCCTATTTTCCTTGTATCTTTCTGTCTGGGTTTCTTGGGGAAAAATTTAGTAATTGTTTTATCA
391211 TACATTTAACTTGACTCTTTAAGCGTGAAAATATCTACTTGTTTATGTAGATCTTTTCTTTTTAG
66 TACATTTAACTTGACTCTTTAAGCGTGAAAATATCTACTTGTTTATGTAGATCTTTTCTTTTTAG
**
391276 TCTATTTTTAGTGGAAGAAAATAGGATGGGAATGTGCTTTTTCCCATTGATTTGGGCTGTCAATT
131 TCTATTTTTAGTAAAAGAAAATAGGATGGGAATGTGCTTTTTCCCATTGATTTGGGCTGTCAATT
*
391341 TGCTTCCT
196 TGGTTCCT
391349 T
1 T
391350 ATTGTCTTAT
Statistics
Matches: 386, Mismatches: 21, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
203 386 1.00
ACGTcount: A:0.22, C:0.14, G:0.17, T:0.47
Consensus pattern (203 bp):
TTCCTATTTTCCTTGTATCTTTCTGTCTGGGTTTCTTGGGGAAAAATTTAGTAATTGTTTTATCA
TACATTTAACTTGACTCTTTAAGCGTGAAAATATCTACTTGTTTATGTAGATCTTTTCTTTTTAG
TCTATTTTTAGTAAAAGAAAATAGGATGGGAATGTGCTTTTTCCCATTGATTTGGGCTGTCAATT
TGGTTCCT
Found at i:391583 original size:2 final size:2
Alignment explanation
Indices: 391576--391614 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
391566 ATTGAAAATT
391576 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
391615 TAATCTTTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:398582 original size:2 final size:2
Alignment explanation
Indices: 398575--398605 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
398565 GAGAAGGCCT
398575 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 T
398606 GCTAGGTTCA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:405759 original size:6 final size:6
Alignment explanation
Indices: 405750--405799 Score: 82
Period size: 6 Copynumber: 8.3 Consensus size: 6
405740 GCAAAGGCAA
* *
405750 AGATAG AGATAG AGATAG AGATAG AGACAG AGATAG AGAGAG AGATAG
1 AGATAG AGATAG AGATAG AGATAG AGATAG AGATAG AGATAG AGATAG
405798 AG
1 AG
405800 CTATATGTTA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
6 40 1.00
ACGTcount: A:0.50, C:0.02, G:0.36, T:0.12
Consensus pattern (6 bp):
AGATAG
Found at i:406962 original size:10 final size:10
Alignment explanation
Indices: 406940--406974 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
406930 AAATATAAAT
406940 TTTAAATTTTA
1 TTTAAA-TTTA
406951 TTTAAATTTA
1 TTTAAATTTA
*
406961 TTTAAGTTTA
1 TTTAAATTTA
406971 TTTA
1 TTTA
406975 TAGTATTTTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
10 17 0.74
11 6 0.26
ACGTcount: A:0.34, C:0.00, G:0.03, T:0.63
Consensus pattern (10 bp):
TTTAAATTTA
Found at i:409697 original size:12 final size:12
Alignment explanation
Indices: 409667--409697 Score: 53
Period size: 12 Copynumber: 2.6 Consensus size: 12
409657 AGTATCCCAC
409667 TTTTTTTCTTTT
1 TTTTTTTCTTTT
*
409679 TCTTTTTCTTTT
1 TTTTTTTCTTTT
409691 TTTTTTT
1 TTTTTTT
409698 ATTACCAAGG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
12 17 1.00
ACGTcount: A:0.00, C:0.10, G:0.00, T:0.90
Consensus pattern (12 bp):
TTTTTTTCTTTT
Found at i:413167 original size:16 final size:16
Alignment explanation
Indices: 413111--413167 Score: 51
Period size: 16 Copynumber: 3.6 Consensus size: 16
413101 ACCAGGTCTA
* * *
413111 TTCGGGTTCAAGCCTT
1 TTCGAGTTCAGGCTTT
* *
413127 TTCAAGTTCGGGCTTT
1 TTCGAGTTCAGGCTTT
*
413143 TTTGAGTTCAGGCTTT
1 TTCGAGTTCAGGCTTT
*
413159 TTCGGGTTC
1 TTCGAGTTC
413168 GGGTTCAAGT
Statistics
Matches: 31, Mismatches: 10, Indels: 0
0.76 0.24 0.00
Matches are distributed among these distances:
16 31 1.00
ACGTcount: A:0.11, C:0.19, G:0.26, T:0.44
Consensus pattern (16 bp):
TTCGAGTTCAGGCTTT
Found at i:413334 original size:16 final size:16
Alignment explanation
Indices: 413313--413345 Score: 52
Period size: 15 Copynumber: 2.2 Consensus size: 16
413303 ATTTGTGTTA
413313 TAATAT-TTTATTT-T
1 TAATATATTTATTTAT
413327 TAATATATTTATTTAT
1 TAATATATTTATTTAT
413343 TAA
1 TAA
413346 AATCTATATT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 6 0.35
15 7 0.41
16 4 0.24
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (16 bp):
TAATATATTTATTTAT
Found at i:413353 original size:20 final size:19
Alignment explanation
Indices: 413330--413367 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
413320 TTATTTTTAA
*
413330 TATATTTATTTATTAAAATC
1 TATATTTATATA-TAAAATC
413350 TATATTTATATATAAAAT
1 TATATTTATATATAAAAT
413368 TAATTTTTAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 6 0.35
20 11 0.65
ACGTcount: A:0.45, C:0.03, G:0.00, T:0.53
Consensus pattern (19 bp):
TATATTTATATATAAAATC
Found at i:414381 original size:4 final size:4
Alignment explanation
Indices: 414372--414400 Score: 58
Period size: 4 Copynumber: 7.2 Consensus size: 4
414362 ATTTTTAAAT
414372 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA T
414401 GAGATGTGAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 25 1.00
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (4 bp):
TTTA
Found at i:416009 original size:29 final size:29
Alignment explanation
Indices: 415967--416022 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
415957 TAAATGAGTT
* *
415967 ATTTTTTAACAAACCAAGAAGCTTTCTGA
1 ATTTTTGAACAAACCAAGAAGCATTCTGA
415996 ATTTTTGAACAAACCAAGAAGCATTCT
1 ATTTTTGAACAAACCAAGAAGCATTCT
416023 AAAGAGTATC
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.39, C:0.18, G:0.11, T:0.32
Consensus pattern (29 bp):
ATTTTTGAACAAACCAAGAAGCATTCTGA
Found at i:417151 original size:21 final size:22
Alignment explanation
Indices: 417125--417167 Score: 79
Period size: 21 Copynumber: 2.0 Consensus size: 22
417115 CAAAGCTCAT
417125 GATATAATTTAC-TTTTGATAA
1 GATATAATTTACTTTTTGATAA
417146 GATATAATTTACTTTTTGATAA
1 GATATAATTTACTTTTTGATAA
417168 ATTATTATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 12 0.57
22 9 0.43
ACGTcount: A:0.37, C:0.05, G:0.09, T:0.49
Consensus pattern (22 bp):
GATATAATTTACTTTTTGATAA
Found at i:418654 original size:17 final size:16
Alignment explanation
Indices: 418632--418738 Score: 63
Period size: 17 Copynumber: 6.3 Consensus size: 16
418622 TCTATCCGTT
418632 AATTTACTTAAAATTTA
1 AATTTA-TTAAAATTTA
**
418649 AATTTATTTATTATTTA
1 AATTTA-TTAAAATTTA
* * *
418666 ATTATTATTTATATTTA
1 AAT-TTATTAAAATTTA
* *
418683 TATTTAATTTAAAA-ATA
1 AATTT-A-TTAAAATTTA
*
418700 TATTTATTAAATATTTA
1 AATTTATTAAA-ATTTA
*
418717 AATTTATTAAGCATTTA
1 AATTTATTAA-AATTTA
418734 AATTT
1 AATTT
418739 TTTTTAAAAA
Statistics
Matches: 70, Mismatches: 14, Indels: 12
0.73 0.15 0.12
Matches are distributed among these distances:
15 5 0.07
16 4 0.06
17 54 0.77
18 7 0.10
ACGTcount: A:0.42, C:0.02, G:0.01, T:0.55
Consensus pattern (16 bp):
AATTTATTAAAATTTA
Found at i:418692 original size:11 final size:12
Alignment explanation
Indices: 418650--418693 Score: 58
Period size: 11 Copynumber: 3.8 Consensus size: 12
418640 TAAAATTTAA
418650 ATTT-ATTTATT
1 ATTTAATTTATT
418661 ATTTAA-TTATT
1 ATTTAATTTATT
418672 ATTTATATTTA-T
1 ATTTA-ATTTATT
418684 ATTTAATTTA
1 ATTTAATTTA
418694 AAAATATATT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
11 19 0.63
12 8 0.27
13 3 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (12 bp):
ATTTAATTTATT
Found at i:418692 original size:28 final size:27
Alignment explanation
Indices: 418630--418694 Score: 67
Period size: 28 Copynumber: 2.3 Consensus size: 27
418620 TATCTATCCG
*
418630 TTAATTTACTTAAAATTTAAATTTATT
1 TTAATTTAATTAAAATTTAAATTTATT
* ** *
418657 TATTATTTAATTATTATTTATATTTATAT
1 T-TAATTTAATTAAAATTTAAATTTAT-T
418686 TTAATTTAA
1 TTAATTTAA
418695 AAATATATTT
Statistics
Matches: 30, Mismatches: 6, Indels: 3
0.77 0.15 0.08
Matches are distributed among these distances:
27 1 0.03
28 27 0.90
29 2 0.07
ACGTcount: A:0.38, C:0.02, G:0.00, T:0.60
Consensus pattern (27 bp):
TTAATTTAATTAAAATTTAAATTTATT
Found at i:418766 original size:21 final size:22
Alignment explanation
Indices: 418742--418790 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 22
418732 TAAATTTTTT
*
418742 TTAAAAAAACAAAATATA-AAA
1 TTAAAAAAACAAAATACATAAA
**
418763 TTAAAAAAATTAAATACATAAA
1 TTAAAAAAACAAAATACATAAA
418785 TTAAAA
1 TTAAAA
418791 TCATTTTAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 15 0.62
22 9 0.38
ACGTcount: A:0.71, C:0.04, G:0.00, T:0.24
Consensus pattern (22 bp):
TTAAAAAAACAAAATACATAAA
Found at i:419195 original size:14 final size:14
Alignment explanation
Indices: 419178--419207 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
419168 AATTATAAAA
419178 TAAAAAAATATTTT
1 TAAAAAAATATTTT
*
419192 TAAAAATATATTTT
1 TAAAAAAATATTTT
419206 TA
1 TA
419208 TTTAAAAATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (14 bp):
TAAAAAAATATTTT
Found at i:419253 original size:31 final size:29
Alignment explanation
Indices: 419181--419253 Score: 85
Period size: 31 Copynumber: 2.4 Consensus size: 29
419171 TATAAAATAA
*
419181 AAAAATATTTTTAAAAATATATTTTTATTT
1 AAAAATA-TTATAAAAATATATTTTTATTT
*
419211 AAAAATTTTATAAAAATATTTATTTTTATATT
1 AAAAATATTATAAAAATA--TATTTTTAT-TT
419243 AAAAA-ATTATA
1 AAAAATATTATA
419254 TGTTTCTTTA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
29 10 0.27
30 6 0.16
31 14 0.38
32 7 0.19
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (29 bp):
AAAAATATTATAAAAATATATTTTTATTT
Found at i:420542 original size:21 final size:23
Alignment explanation
Indices: 420521--420570 Score: 63
Period size: 22 Copynumber: 2.3 Consensus size: 23
420511 CATGAGTTTA
420521 AAAT-TAAT-AAT-TTTAATATT
1 AAATATAATAAATATTTAATATT
*
420541 AAATATAATAAATATTTAATA-A
1 AAATATAATAAATATTTAATATT
420563 AAATATAA
1 AAATATAA
420571 ATTTAATTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 4
0.84 0.03 0.13
Matches are distributed among these distances:
20 4 0.15
21 4 0.15
22 11 0.42
23 7 0.27
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (23 bp):
AAATATAATAAATATTTAATATT
Found at i:421097 original size:29 final size:29
Alignment explanation
Indices: 421065--421147 Score: 84
Period size: 29 Copynumber: 2.8 Consensus size: 29
421055 AAATAAATAA
421065 TTTATATATTTAATTAATATTTATTTT-AT
1 TTTA-ATATTTAATTAATATTTATTTTAAT
*
421094 TTTAAAATATTTAAAT-ATATTTATTTTAAT
1 TTT--AATATTTAATTAATATTTATTTTAAT
421124 TTTAATAATTT--TTAATTATTTATT
1 TTTAAT-ATTTAATTAA-TATTTATT
421148 AACTTTTCAA
Statistics
Matches: 46, Mismatches: 2, Indels: 12
0.77 0.03 0.20
Matches are distributed among these distances:
27 1 0.02
28 4 0.09
29 26 0.57
30 14 0.30
31 1 0.02
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (29 bp):
TTTAATATTTAATTAATATTTATTTTAAT
Found at i:421104 original size:30 final size:32
Alignment explanation
Indices: 421070--421141 Score: 105
Period size: 30 Copynumber: 2.3 Consensus size: 32
421060 AATAATTTAT
421070 ATATTTAATTAATATTTATTTT-ATTTTAA-A
1 ATATTTAATTAATATTTATTTTAATTTTAATA
*
421100 ATATTTAAAT-ATATTTATTTTAATTTTAATA
1 ATATTTAATTAATATTTATTTTAATTTTAATA
*
421131 ATTTTTAATTA
1 ATATTTAATTA
421142 TTTATTAACT
Statistics
Matches: 36, Mismatches: 3, Indels: 4
0.84 0.07 0.09
Matches are distributed among these distances:
29 11 0.31
30 16 0.44
31 9 0.25
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (32 bp):
ATATTTAATTAATATTTATTTTAATTTTAATA
Found at i:421211 original size:21 final size:22
Alignment explanation
Indices: 421187--421232 Score: 58
Period size: 21 Copynumber: 2.1 Consensus size: 22
421177 ATATATATAT
421187 ATTAATTTAATATCTG-TAAAA
1 ATTAATTTAATATCTGATAAAA
* * *
421208 ATTATTTTACTATCTGATCAAA
1 ATTAATTTAATATCTGATAAAA
421230 ATT
1 ATT
421233 CACTTTATGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
21 14 0.67
22 7 0.33
ACGTcount: A:0.41, C:0.09, G:0.04, T:0.46
Consensus pattern (22 bp):
ATTAATTTAATATCTGATAAAA
Found at i:421239 original size:23 final size:21
Alignment explanation
Indices: 421187--421239 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
421177 ATATATATAT
*
421187 ATTAATTTAATATCTGTAAAA
1 ATTACTTTAATATCTGTAAAA
* * *
421208 ATTATTTTACTATCTGATCAAA
1 ATTACTTTAATATCTG-TAAAA
421230 ATTCACTTTA
1 ATT-ACTTTA
421240 TGTTACGATT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 14 0.54
22 7 0.27
23 5 0.19
ACGTcount: A:0.40, C:0.11, G:0.04, T:0.45
Consensus pattern (21 bp):
ATTACTTTAATATCTGTAAAA
Found at i:421327 original size:21 final size:21
Alignment explanation
Indices: 421270--421335 Score: 77
Period size: 20 Copynumber: 3.3 Consensus size: 21
421260 CTAAACATAT
*
421270 ATTTTATTA-T-TAAT-TTTA
1 ATTTTATTATTATAATAATTA
* *
421288 ATTTTATTGTTA-CATAATTA
1 ATTTTATTATTATAATAATTA
421308 ATTTTATTATTATAATAATTA
1 ATTTTATTATTATAATAATTA
421329 ATTTTAT
1 ATTTTAT
421336 AATCATCGAT
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
18 8 0.21
19 3 0.08
20 14 0.36
21 14 0.36
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.61
Consensus pattern (21 bp):
ATTTTATTATTATAATAATTA
Found at i:422568 original size:12 final size:11
Alignment explanation
Indices: 422503--422583 Score: 55
Period size: 10 Copynumber: 7.5 Consensus size: 11
422493 AATTAAAAAA
*
422503 TAAATATAAA-
1 TAAATTTAAAT
*
422513 TAAACTTAAA-
1 TAAATTTAAAT
422523 TAAATTTAAAT
1 TAAATTTAAAT
422534 TAATTATTT--A-
1 TAA--ATTTAAAT
422544 TAAATTTAAAT
1 TAAATTTAAAT
422555 TAAATTTAAAAT
1 TAAATTT-AAAT
*
422567 TATATTTTAAAT
1 TA-AATTTAAAT
*
422579 AAAAT
1 TAAAT
422584 AAAACTTAAA
Statistics
Matches: 57, Mismatches: 6, Indels: 15
0.73 0.08 0.19
Matches are distributed among these distances:
8 4 0.07
10 21 0.37
11 13 0.23
12 11 0.19
13 8 0.14
ACGTcount: A:0.56, C:0.01, G:0.00, T:0.43
Consensus pattern (11 bp):
TAAATTTAAAT
Found at i:422594 original size:16 final size:17
Alignment explanation
Indices: 422573--422604 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
422563 AAATTATATT
422573 TTAAATAAA-ATAAAAC
1 TTAAATAAATATAAAAC
422589 TTAAATAAATATAAAA
1 TTAAATAAATATAAAA
422605 TATTAATATT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (17 bp):
TTAAATAAATATAAAAC
Found at i:423138 original size:17 final size:17
Alignment explanation
Indices: 423102--423138 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
423092 CTTTTTTAAT
* *
423102 AAATTTAAATTCAAAAA
1 AAATTGAAATTAAAAAA
423119 AAATTGAAATTAAAAAA
1 AAATTGAAATTAAAAAA
423136 AAA
1 AAA
423139 GGTTTAAATC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.70, C:0.03, G:0.03, T:0.24
Consensus pattern (17 bp):
AAATTGAAATTAAAAAA
Found at i:423562 original size:11 final size:11
Alignment explanation
Indices: 423546--423585 Score: 55
Period size: 10 Copynumber: 3.6 Consensus size: 11
423536 TTTAATTTAA
423546 TAAATTTAAAT
1 TAAATTTAAAT
*
423557 TAAA-TTAAAA
1 TAAATTTAAAT
423567 TAAATTTAAAT
1 TAAATTTAAAT
423578 ATAAATTT
1 -TAAATTT
423586 TTATTATTTG
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
10 9 0.36
11 9 0.36
12 7 0.28
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.42
Consensus pattern (11 bp):
TAAATTTAAAT
Found at i:423570 original size:10 final size:11
Alignment explanation
Indices: 423544--423585 Score: 59
Period size: 11 Copynumber: 3.8 Consensus size: 11
423534 TATTTAATTT
423544 AATAAATTTAA
1 AATAAATTTAA
*
423555 ATTAAA-TTAA
1 AATAAATTTAA
423565 AATAAATTTAA
1 AATAAATTTAA
423576 ATATAAATTT
1 A-ATAAATTT
423586 TTATTATTTG
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
10 9 0.33
11 10 0.37
12 8 0.30
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (11 bp):
AATAAATTTAA
Found at i:423570 original size:21 final size:22
Alignment explanation
Indices: 423544--423584 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
423534 TATTTAATTT
423544 AATAAATTTAAAT-TAAATTAA
1 AATAAATTTAAATATAAATTAA
423565 AATAAATTTAAATATAAATT
1 AATAAATTTAAATATAAATT
423585 TTTATTATTT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.61, C:0.00, G:0.00, T:0.39
Consensus pattern (22 bp):
AATAAATTTAAATATAAATTAA
Found at i:423749 original size:20 final size:20
Alignment explanation
Indices: 423693--423762 Score: 72
Period size: 18 Copynumber: 3.4 Consensus size: 20
423683 AATTTTTAAA
423693 ATTTAAATTATAAATATTATTAT
1 ATTTAAATT-T-AATA-TATTAT
423716 ATTT--ATTTAATATATTAT
1 ATTTAAATTTAATATATTAT
*
423734 ATTTAAATTTATTATAATATAT
1 ATTTAAATTTAATAT-AT-TAT
423756 ATTTAAA
1 ATTTAAA
423763 AAAAATTTAA
Statistics
Matches: 42, Mismatches: 1, Indels: 9
0.81 0.02 0.17
Matches are distributed among these distances:
18 10 0.24
19 4 0.10
20 9 0.21
21 5 0.12
22 10 0.24
23 4 0.10
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (20 bp):
ATTTAAATTTAATATATTAT
Found at i:427965 original size:22 final size:22
Alignment explanation
Indices: 427937--428011 Score: 71
Period size: 22 Copynumber: 3.3 Consensus size: 22
427927 TGAGAAGTTA
427937 AATAAAAAATTATATTTAAAAT
1 AATAAAAAATTATATTTAAAAT
** * *
427959 AATAAAAGTTTAGAGATATAAAGAT
1 AATAAAAAATT--ATATTTAAA-AT
*
427984 AGTAAAAAA-TATATTTAAAAT
1 AATAAAAAATTATATTTAAAAT
428005 AATAAAA
1 AATAAAA
428012 GTTTAGAGAT
Statistics
Matches: 40, Mismatches: 10, Indels: 7
0.70 0.18 0.12
Matches are distributed among these distances:
21 8 0.20
22 16 0.40
24 8 0.20
25 8 0.20
ACGTcount: A:0.63, C:0.00, G:0.07, T:0.31
Consensus pattern (22 bp):
AATAAAAAATTATATTTAAAAT
Found at i:428000 original size:46 final size:47
Alignment explanation
Indices: 427939--428036 Score: 189
Period size: 46 Copynumber: 2.1 Consensus size: 47
427929 AGAAGTTAAA
427939 TAAAAAATTATATTTAAAATAATAAAAGTTTAGAGATATAAAGATAG
1 TAAAAAATTATATTTAAAATAATAAAAGTTTAGAGATATAAAGATAG
427986 TAAAAAA-TATATTTAAAATAATAAAAGTTTAGAGATATAAAGATAG
1 TAAAAAATTATATTTAAAATAATAAAAGTTTAGAGATATAAAGATAG
428032 TAAAA
1 TAAAA
428037 TTTTTTCATC
Statistics
Matches: 51, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
46 44 0.86
47 7 0.14
ACGTcount: A:0.59, C:0.00, G:0.10, T:0.31
Consensus pattern (47 bp):
TAAAAAATTATATTTAAAATAATAAAAGTTTAGAGATATAAAGATAG
Found at i:428591 original size:21 final size:21
Alignment explanation
Indices: 428550--428594 Score: 56
Period size: 21 Copynumber: 2.1 Consensus size: 21
428540 TGAATATAGT
* *
428550 TTACATTTTGATCGTACTCAA
1 TTACATTTGGATCATACTCAA
428571 TTACATTTGGATCAT-CTTCAA
1 TTACATTTGGATCATAC-TCAA
428592 TTA
1 TTA
428595 AAATTATGTT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 1 0.05
21 20 0.95
ACGTcount: A:0.29, C:0.18, G:0.09, T:0.44
Consensus pattern (21 bp):
TTACATTTGGATCATACTCAA
Found at i:430025 original size:12 final size:12
Alignment explanation
Indices: 430008--430032 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
429998 AAAAGAGAAA
430008 TTTTGACAAAAT
1 TTTTGACAAAAT
430020 TTTTGACAAAAT
1 TTTTGACAAAAT
430032 T
1 T
430033 CCTTCATAAA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.08, G:0.08, T:0.44
Consensus pattern (12 bp):
TTTTGACAAAAT
Found at i:433237 original size:155 final size:154
Alignment explanation
Indices: 432930--433212 Score: 331
Period size: 155 Copynumber: 1.8 Consensus size: 154
432920 TAAAAATACT
* * *
432930 CGATACCCCTAAAGGACTTAAAAAGGGTTATAGAAAGGATGGACTTATCCTAAATACCCACATCA
1 CGATACCCCTAAAGGACTTAAAAAGGATTAGAGAAAGGATGAACTTATCCTAAATACCCACATCA
* * * * * *
432995 GCATAAAAGCGAACTTGGTGACAATCTAAGACTCGGTTTTAAAAAAAAAACTAAAATGCCCTTAA
66 GCATAAAAGCAAACTCGGTGACAACCTAAGACTAGGTTTT-AAAAAAAAACGAAAATGCCCCTAA
* *
433060 GAGATATCTTCGACGTAGAAGTACC
130 GAGATACCTTCGACATAGAAGTACC
** * * *
433085 CGATACCCCTAAAGGACTTAAAAA-GATTAGAGATGGGATGAAGTTATCCTAAATGCCCACTTTC
1 CGATACCCCTAAAGGACTTAAAAAGGATTAGAGAAAGGATGAACTTATCCTAAATACCCAC-ATC
* *
433149 -GACATGAAAA-CAAACTCGGTGACAACCTAGGACTAGGTTCTT-AAAAAATACGAAAATGCCCC
65 AG-CAT-AAAAGCAAACTCGGTGACAACCTAAGACTAGGTT-TTAAAAAAAAACGAAAATGCCCC
433211 TA
127 TA
433213 TTGGTATACC
Statistics
Matches: 108, Mismatches: 16, Indels: 9
0.81 0.12 0.07
Matches are distributed among these distances:
154 49 0.45
155 53 0.49
156 6 0.06
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (154 bp):
CGATACCCCTAAAGGACTTAAAAAGGATTAGAGAAAGGATGAACTTATCCTAAATACCCACATCA
GCATAAAAGCAAACTCGGTGACAACCTAAGACTAGGTTTTAAAAAAAAACGAAAATGCCCCTAAG
AGATACCTTCGACATAGAAGTACC
Found at i:435604 original size:166 final size:164
Alignment explanation
Indices: 435300--435681 Score: 452
Period size: 166 Copynumber: 2.3 Consensus size: 164
435290 AATCCCTCCG
* * * * * * * * *
435300 AAAATATTTATGGAATAGAAAACTCGATTTTTTGAGAAA-ATGGGGATTTCAAAGAAAAAATCCA
1 AAAAAATTTACGGAGTAGAAAACTCTATTTTTCGA-AAACAAGAGAATTTC-AAGAAAAAATCAA
435364 AAACATATGAAAATGAATGAATTTTTAAAAACAGATTTAATATAAAATAAATAATAATATTTGAT
64 AAACATATGAAAATGAATGAATTTTTAAAAACAGATTTAATATAAAATAAATAATAATATTTGAT
* * *
435429 AGATTTTAAAAATT-AAAAGTCAAGAAAAAGGC-CCTCG
129 AAATTTTAAAAATTAAAAACT-AAGAAAAA-GCTCC-CA
** *
435466 AAAAAATTTATTTGAGTAGAAAACTCTGTATTTT-GAAAACAAGAGAATTTCAAGAAAAAATTCA
1 AAAAAATTTA-CGGAGTAGAAAACTCTAT-TTTTCGAAAACAAGAGAATTTCAAGAAAAAA-TCA
* * * *
435530 AAAAC-TCATGAAAATGAATG-ATTTTTTAAAACTGATTTATTATGAAATAAATAATAATATTTG
63 AAAACAT-ATGAAAATGAATGAATTTTTAAAAACAGATTTAATATAAAATAAATAATAATATTTG
*
435593 ATAAATTTTAAAAATTAAAAACTAAGAAAAATCTCCCA
127 ATAAATTTTAAAAATTAAAAACTAAGAAAAAGCTCCCA
*
435631 AAAAAATTTACGGAGTAGAAAACTCTATTTTTCGAAAACAGGAGAATTTCA
1 AAAAAATTTACGGAGTAGAAAACTCTATTTTTCGAAAACAAGAGAATTTCA
435682 TTTAAAAATC
Statistics
Matches: 187, Mismatches: 21, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
163 4 0.02
164 32 0.17
165 12 0.06
166 86 0.46
167 49 0.26
168 4 0.02
ACGTcount: A:0.50, C:0.08, G:0.12, T:0.30
Consensus pattern (164 bp):
AAAAAATTTACGGAGTAGAAAACTCTATTTTTCGAAAACAAGAGAATTTCAAGAAAAAATCAAAA
ACATATGAAAATGAATGAATTTTTAAAAACAGATTTAATATAAAATAAATAATAATATTTGATAA
ATTTTAAAAATTAAAAACTAAGAAAAAGCTCCCA
Found at i:435786 original size:164 final size:164
Alignment explanation
Indices: 435300--435786 Score: 429
Period size: 166 Copynumber: 2.9 Consensus size: 164
435290 AATCCCTCCG
* * * * * * *
435300 AAAATATTTAT-GGAATAGAAAACTCGATTTTTTGAGAAA-ATGGGGATTTCAAAGAAAAAA-TC
1 AAAAAATTTATCGGAGTAGAAAACTCTATATTTTGA-AAACAAGAGAATTTC-AAGAAAAAATTC
* * * * * *
435362 CAAAACAT-ATGAAAATGAATGAATTTTTAAAAACAGATTTAATATA-AAATAAATAATAATATT
64 AAAAAC-TCATAAAAATAAAAGAA-TTTTCAAAACTGATTTAATA-AGAAATAAATAATAATATT
*
435425 TGATAGATTTTAAAAATTAAAAGTCAAGAAAAAGGCCCTCG
126 TGATA-ATTTTAAAAATTAAAA-TCAAGAAAAAGGCCCTCA
** *
435466 AAAAAATTTATTTGAGTAGAAAACTCTGTATTTTGAAAACAAGAGAATTTCAAGAAAAAATTCAA
1 AAAAAATTTATCGGAGTAGAAAACTCTATATTTTGAAAACAAGAGAATTTCAAGAAAAAATTCAA
* * * * * * *
435531 AAACTCATGAAAATGAATGATTTTTTAAAACTGATTTATTATGAAATAAATAATAATATTTGATA
66 AAACTCATAAAAATAAAAGAATTTTCAAAACTGATTTAATAAGAAATAAATAATAATATTTGAT-
* *
435596 AATTTTAAAAATTAAAAACTAAGAAAAA-TCTCC-CA
130 AATTTTAAAAATTAAAATC-AAGAAAAAGGC-CCTCA
* ***
435631 AAAAAATTTA-CGGAGTAGAAAACTCTAT-TTTTCGAAAACAGGAGAATTTCATTTAAAAA-TCA
1 AAAAAATTTATCGGAGTAGAAAACTCTATATTTT-GAAAACAAGAGAATTTCAAGAAAAAATTCA
* * **
435693 ATAACTCA-AAAAATAAAAGAAAATTTTCAAAATTGATTTAATAAGATTTAAATAATAATATTTG
65 AAAACTCATAAAAATAAAAG--AATTTTCAAAACTGATTTAATAAGAAATAAATAATAATATTTG
* **
435757 AATAATTTTGATACTTTAAAATCAAGAAAA
128 -ATAATTTT-AAAAATTAAAATCAAGAAAA
435787 TTTTATCAAA
Statistics
Matches: 268, Mismatches: 40, Indels: 28
0.80 0.12 0.08
Matches are distributed among these distances:
162 8 0.03
163 14 0.05
164 86 0.32
165 24 0.09
166 87 0.32
167 49 0.18
ACGTcount: A:0.51, C:0.08, G:0.10, T:0.31
Consensus pattern (164 bp):
AAAAAATTTATCGGAGTAGAAAACTCTATATTTTGAAAACAAGAGAATTTCAAGAAAAAATTCAA
AAACTCATAAAAATAAAAGAATTTTCAAAACTGATTTAATAAGAAATAAATAATAATATTTGATA
ATTTTAAAAATTAAAATCAAGAAAAAGGCCCTCA
Found at i:441694 original size:155 final size:156
Alignment explanation
Indices: 441449--442295 Score: 556
Period size: 155 Copynumber: 5.5 Consensus size: 156
441439 CTAAGTTCAA
* * * * *
441449 GAAAAATTACGAAAAT-CTCTCT-AGGAGATGCCTTCGACGTAAAAGTA-CCCGATACCCCTAAA
1 GAAAAATTATGAAAATGCTC-CTAAAG-GATACCTTCGACGTGAAAGTATCCCGGTACCCCTAAA
* *
441511 AGACTTAAGAAGGATTATAGAAAT-GTGATGAACCTATCCTAAATACCTACCTTCGGCATAAAGC
64 AGACTTAAAAAGGA--CTAGAAATGGTGATGAACCTATCCTAAATACCTACCTTCGGCATAAAGC
*
441575 AAACCTGGTGATAA-CTAGGACTCAGTTTT
127 GAACCTGGTGATAACCTAGGACTCAGTTTT
*
441604 GAAAAATTATGAAAATGCTCCTAAAGGATACCTTCGACGTGAAAGTATCTCGGTACCCCTAAAAG
1 GAAAAATTATGAAAATGCTCCTAAAGGATACCTTCGACGTGAAAGTATCCCGGTACCCCTAAAAG
* * *
441669 ACTTAAAAAGGACTGGAAATGGTGATAAACCTATCCT--A-A---A--------A-AAAGCGGAC
66 ACTTAAAAAGGACTAGAAATGGTGATGAACCTATCCTAAATACCTACCTTCGGCATAAAGCGAAC
* *
441719 CCGGTGATAACCTAGGACTTAGTTTT
131 CTGGTGATAACCTAGGACTCAGTTTT
* * * ** * * * *
441745 GAAAAAGTATGAAAATACCCCTAGGGGATACCTTCGACGTGAAAGTATCCCAGTAACACTAAAGG
1 GAAAAATTATGAAAATGCTCCTAAAGGATACCTTCGACGTGAAAGTATCCCGGTACCCCTAAAAG
* * * *
441810 ACTTTAAAA-GACTAGAGATGG-GATGAACATATCCTAAATGCCTACCTTCGGCATAAAAGCGAA
66 ACTTAAAAAGGACTAGAAATGGTGATGAACCTATCCTAAATACCTACCTTCGGCAT-AAAGCGAA
*
441873 CCTGGTGACAACCTAGGACTCAGTTTT
130 CCTGGTGATAACCTAGGACTCAGTTTT
* * * * * *
441900 -AGAAAATTATGAAAAATTAAATGC-CCATAGAGGATACATTTGACGTCAAAGTATCCAGGTATC
1 GA-AAAATTATG----A--AAATGCTCC-TAAAGGATACCTTCGACGTGAAAGTATCCCGGTACC
* * * * *
441963 TCTAAAAGACTTAAAAAGGACTAGAAATGGTGATGAACCTATACTAAAT-GCTCACATTTGGCAT
58 CCTAAAAGACTTAAAAAGGACTAGAAATGGTGATGAACCTATCCTAAATACCT-ACCTTCGGCAT
* * * ** *
442027 AAAAGTGGA-TTCGGTGATAACCTAGGACTTGGTTCT
122 -AAAGCGAACCT-GGTGATAACCTAGGACTCAGTTTT
* ** * ** * * * * *
442063 -AGGAAATTACAAAAATAC-CCTTATGGGTATACTTTCAACGTAAAAGTATTCCGGTGA-CTCTA
1 GA-AAAATTATGAAAATGCTCC-TAAAGG-ATACCTTCGACGTGAAAGTATCCCGGT-ACCCCTA
* * * * * *
442125 AAGGACTTAAGAAGGATTATAGAAATGG-GATGAACCTATTCTAAATACCCATCTTCGGCATAAA
62 AAAGACTTAAAAAGGA--CTAGAAATGGTGATGAACCTATCCTAAATACCTACCTTCGGCAT-AA
* *
442189 AGCTGATCC-GGTGATAACCTATGACTCA-TTTT
124 AGC-GAACCTGGTGATAACCTAGGACTCAGTTTT
* *** * * * ** * *
442221 GAAAAATTATAAAAATGC-CCTTGGGGGATACTTTCAACGTAAAAGTA-CTTGATACCCCTAAAG
1 GAAAAATTATGAAAATGCTCC-TAAAGGATACCTTCGACGTGAAAGTATCCCGGTACCCCTAAAA
442284 GACTTAAAAAGG
65 GACTTAAAAAGG
442296 GTTATAGAAG
Statistics
Matches: 550, Mismatches: 100, Indels: 83
0.75 0.14 0.11
Matches are distributed among these distances:
139 12 0.02
140 26 0.05
141 79 0.14
145 1 0.00
149 1 0.00
152 1 0.00
153 2 0.00
154 7 0.01
155 91 0.17
156 51 0.09
157 31 0.06
158 63 0.11
159 50 0.09
160 13 0.02
161 48 0.09
162 14 0.03
163 60 0.11
ACGTcount: A:0.38, C:0.18, G:0.19, T:0.25
Consensus pattern (156 bp):
GAAAAATTATGAAAATGCTCCTAAAGGATACCTTCGACGTGAAAGTATCCCGGTACCCCTAAAAG
ACTTAAAAAGGACTAGAAATGGTGATGAACCTATCCTAAATACCTACCTTCGGCATAAAGCGAAC
CTGGTGATAACCTAGGACTCAGTTTT
Found at i:442242 original size:158 final size:154
Alignment explanation
Indices: 441709--442292 Score: 499
Period size: 158 Copynumber: 3.7 Consensus size: 154
441699 CTATCCTAAA
* * * * * *
441709 AAAAGCGGACCCGGTGATAACCTAGGACTTAGTTTT-GAAAAAGTATGAAAATACCCCTAGGGGA
1 AAAAGCTGATCCGGTGATAACCTAGGACTCAGTTTTAG-AAAATTATAAAAATACCCTTAGGGGA
* * * * * * *
441773 TACCTTCGACGTGAAAGTATCCCAGTAACACTAAAGGACTTTAAAA-GACTAGAGATGGGATGAA
65 TACTTTCAACGTAAAAGTATTCCGGT-ACTCTAAAGGAC-TTAAAAGGACTAGAAATGGGATGAA
* * * *
441837 CATATCCTAAATGCCTACCTTCGGCAT
128 CCTATACTAAATGCCCATCTTCGGCAT
* * *
441864 AAAAGC-GAACCTGGTGACAACCTAGGACTCAGTTTTAGAAAATTATGAAAAATTAAATGCCCAT
1 AAAAGCTGATCC-GGTGATAACCTAGGACTCAGTTTTAGAAAATTAT-AAAAA-T--A--CCCTT
* * * *
441928 AGAGGATACATTT-GACGTCAAAGTA-TCCAGGTATCTCTAAAAGACTTAAAAAGGACTAGAAAT
59 AGGGGATAC-TTTCAACGTAAAAGTATTCC-GGTA-CTCTAAAGGACTT-AAAAGGACTAGAAAT
441991 GGTGATGAACCTATACTAAATGCTCACAT-TT-GGCAT
120 GG-GATGAACCTATACTAAATGC-C-CATCTTCGGCAT
* ** * * * *
442027 AAAAG-TGGATTCGGTGATAACCTAGGACTTGGTTCTAGGAAATTACAAAAATACCCTTATGGGT
1 AAAAGCT-GATCCGGTGATAACCTAGGACTCAGTTTTAGAAAATTATAAAAATACCCTTA-GGGG
*
442091 ATACTTTCAACGTAAAAGTATTCCGGTGACTCTAAAGGACTTAAGAAGGATTATAGAAATGGGAT
64 ATACTTTCAACGTAAAAGTATTCCGGT-ACTCTAAAGGACTTAA-AAGGA--CTAGAAATGGGAT
* *
442156 GAACCTATTCTAAATACCCATCTTCGGCAT
125 GAACCTATACTAAATGCCCATCTTCGGCAT
* * *
442186 AAAAGCTGATCCGGTGATAACCTATGACTCA-TTTT-GAAAAATTATAAAAATGCCCTTGGGGGA
1 AAAAGCTGATCCGGTGATAACCTAGGACTCAGTTTTAG-AAAATTATAAAAATACCCTTAGGGGA
* *
442249 TACTTTCAACGTAAAAGTACTT--GATACCCCTAAAGGACTTAAAA
65 TACTTTCAACGTAAAAGTA-TTCCGGTA-CTCTAAAGGACTTAAAA
442293 AGGGTTATAG
Statistics
Matches: 351, Mismatches: 47, Indels: 62
0.76 0.10 0.13
Matches are distributed among these distances:
154 4 0.01
155 38 0.11
156 21 0.06
157 38 0.11
158 61 0.17
159 54 0.15
160 15 0.04
161 39 0.11
162 18 0.05
163 56 0.16
164 6 0.02
165 1 0.00
ACGTcount: A:0.37, C:0.18, G:0.19, T:0.26
Consensus pattern (154 bp):
AAAAGCTGATCCGGTGATAACCTAGGACTCAGTTTTAGAAAATTATAAAAATACCCTTAGGGGAT
ACTTTCAACGTAAAAGTATTCCGGTACTCTAAAGGACTTAAAAGGACTAGAAATGGGATGAACCT
ATACTAAATGCCCATCTTCGGCAT
Found at i:444042 original size:22 final size:22
Alignment explanation
Indices: 444011--444064 Score: 56
Period size: 23 Copynumber: 2.4 Consensus size: 22
444001 TTTTCTTGCA
* *
444011 GCTGGTGCTA-GTTTCATTGGTT
1 GCTGGAGCTACGTTTCA-TGCTT
444033 GCTGGAGCTACTGTTTCATGCTT
1 GCTGGAGCTAC-GTTTCATGCTT
*
444056 GCTGAAGCT
1 GCTGGAGCT
444065 GCTGCAAGCT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 9 0.33
23 12 0.44
24 6 0.22
ACGTcount: A:0.13, C:0.19, G:0.30, T:0.39
Consensus pattern (22 bp):
GCTGGAGCTACGTTTCATGCTT
Found at i:444320 original size:24 final size:25
Alignment explanation
Indices: 444296--444346 Score: 66
Period size: 28 Copynumber: 1.9 Consensus size: 25
444286 ATTTTAATTG
*
444296 CTTCTCCTTTTTCTTTGCTGTTTGCTTT
1 CTTCTCCTTTTTCTTGGCTGTTTG---T
444324 CTTCTCCTTTTTCTTGGCTGTTT
1 CTTCTCCTTTTTCTTGGCTGTTT
444347 TCTAATTGTT
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
28 22 1.00
ACGTcount: A:0.00, C:0.25, G:0.12, T:0.63
Consensus pattern (25 bp):
CTTCTCCTTTTTCTTGGCTGTTTGT
Found at i:444803 original size:15 final size:14
Alignment explanation
Indices: 444783--444816 Score: 50
Period size: 15 Copynumber: 2.4 Consensus size: 14
444773 AAATTAATAA
*
444783 AAAAAATCAAATTGT
1 AAAAAATAAAATT-T
444798 AAAAAATAAAATTT
1 AAAAAATAAAATTT
444812 AAAAA
1 AAAAA
444817 TTAAGATAAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 6 0.33
15 12 0.67
ACGTcount: A:0.71, C:0.03, G:0.03, T:0.24
Consensus pattern (14 bp):
AAAAAATAAAATTT
Found at i:445236 original size:165 final size:166
Alignment explanation
Indices: 445003--445360 Score: 415
Period size: 165 Copynumber: 2.2 Consensus size: 166
444993 TTTATTGGTA
* * * ** * * * *
445003 ATTT-AATAACAATATTAGATAAATTTTAAAAATTTTAAACTGAGAAAAATGCTTCTAAAAATAT
1 ATTTAAATAAAAATATTTGATGAATTTTAAAAATTAAAAACTGAGAAAAATCCTCCCAAAAAAAT
* * *
445067 TTACGAAGAAGAAAACTTGGT-TTTTCGAAAAAAGAGAA-TTTCAAGGAAAAATTCAAAAACTCA
66 TTACGAAGAAGAAAACTTCGTATTTTCGAAAAAAGAGAATTTTAAAGAAAAAATTC-AAAACTCA
* * **
445130 TGAACATGAATTAATTTTTCAAAAA-T-ATTCTAATGTG
130 TGAAAATGAATGAATTTTT-AAAAACTGATT-TAATAAG
445167 ATTTAAATAAAAATATTTGATGAATTTTAAAAATTAAAAA-TCGATG-AAAATCCTCCCAAAAAA
1 ATTTAAATAAAAATATTTGATGAATTTTAAAAATTAAAAACT-GA-GAAAAATCCTCCCAAAAAA
* * *
445230 ATTTACGAAGAAGAAAACTTCGTATTTTGGAAATAGGAGAATTTTAAAGAAAAAATTCAAAACTC
64 ATTTACGAAGAAGAAAACTTCGTATTTTCGAAAAAAGAGAATTTTAAAGAAAAAATTCAAAACTC
445295 ATGAAAATGAATGAATTTTTAAAAACTGATTTAATAAG
129 ATGAAAATGAATGAATTTTTAAAAACTGATTTAATAAG
* * * *
445333 AATTAAATGATAATATTTGAAGAATTTT
1 ATTTAAATAAAAATATTTGATGAATTTT
445361 GATACTTGAA
Statistics
Matches: 164, Mismatches: 23, Indels: 12
0.82 0.12 0.06
Matches are distributed among these distances:
164 5 0.03
165 72 0.44
166 70 0.43
167 17 0.10
ACGTcount: A:0.49, C:0.08, G:0.11, T:0.32
Consensus pattern (166 bp):
ATTTAAATAAAAATATTTGATGAATTTTAAAAATTAAAAACTGAGAAAAATCCTCCCAAAAAAAT
TTACGAAGAAGAAAACTTCGTATTTTCGAAAAAAGAGAATTTTAAAGAAAAAATTCAAAACTCAT
GAAAATGAATGAATTTTTAAAAACTGATTTAATAAG
Found at i:445350 original size:166 final size:165
Alignment explanation
Indices: 445059--445360 Score: 412
Period size: 166 Copynumber: 1.8 Consensus size: 165
445049 AAATGCTTCT
* * * *
445059 AAAAATATTTACGAAGAAGAAAACTTGGTTTTTCGAAAAAAGAGAATTTCAAGGAAAAATTCAAA
1 AAAAAAATTTACGAAGAAGAAAACTTCGTTTTTCGAAAAAAGAGAATTTAAAGAAAAAATTCAAA
* * ** * *
445124 AACTCATGAACATGAATTAATTTTTCAAAAATATTCTAATGTGATTTAAATAAAAATATTTGATG
66 AACTCATGAAAATGAATGAATTTTTCAAAAATATTCTAATAAGAATTAAATAAAAATATTTGAAG
445189 AATTTTAAAAATTAAAAATCGATGAAAATCCTCCC
131 AATTTTAAAAATTAAAAATCGATGAAAATCCTCCC
* * *
445224 AAAAAAATTTACGAAGAAGAAAACTTCGTATTTTGGAAATAGGAGAATTTTAAAGAAAAAATTC-
1 AAAAAAATTTACGAAGAAGAAAACTTCGT-TTTTCGAAAAAAGAGAA-TTTAAAGAAAAAATTCA
* *
445288 AAAACTCATGAAAATGAATGAATTTTT-AAAAACTGATT-TAATAAGAATTAAATGATAATATTT
64 AAAACTCATGAAAATGAATGAATTTTTCAAAAA-T-ATTCTAATAAGAATTAAATAAAAATATTT
445351 GAAGAATTTT
127 GAAGAATTTT
445361 GATACTTGAA
Statistics
Matches: 118, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
165 32 0.27
166 69 0.58
167 17 0.14
ACGTcount: A:0.49, C:0.08, G:0.12, T:0.31
Consensus pattern (165 bp):
AAAAAAATTTACGAAGAAGAAAACTTCGTTTTTCGAAAAAAGAGAATTTAAAGAAAAAATTCAAA
AACTCATGAAAATGAATGAATTTTTCAAAAATATTCTAATAAGAATTAAATAAAAATATTTGAAG
AATTTTAAAAATTAAAAATCGATGAAAATCCTCCC
Found at i:446972 original size:77 final size:77
Alignment explanation
Indices: 446886--447031 Score: 292
Period size: 77 Copynumber: 1.9 Consensus size: 77
446876 TTCATTTTGA
446886 AAATAAAATGAATCTCAGTTTAGTAAATAATTCGAGTCATCTTAGCTTTAGTTCAGTATAGGTTA
1 AAATAAAATGAATCTCAGTTTAGTAAATAATTCGAGTCATCTTAGCTTTAGTTCAGTATAGGTTA
446951 TCTCAGTTTAGT
66 TCTCAGTTTAGT
446963 AAATAAAATGAATCTCAGTTTAGTAAATAATTCGAGTCATCTTAGCTTTAGTTCAGTATAGGTTA
1 AAATAAAATGAATCTCAGTTTAGTAAATAATTCGAGTCATCTTAGCTTTAGTTCAGTATAGGTTA
447028 TCTC
66 TCTC
447032 TTAGTGAACT
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 69 1.00
ACGTcount: A:0.34, C:0.12, G:0.15, T:0.38
Consensus pattern (77 bp):
AAATAAAATGAATCTCAGTTTAGTAAATAATTCGAGTCATCTTAGCTTTAGTTCAGTATAGGTTA
TCTCAGTTTAGT
Found at i:449712 original size:2 final size:2
Alignment explanation
Indices: 449705--449736 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
449695 GTAGATTTAC
449705 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
449737 CATGGCAGGT
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:455419 original size:20 final size:20
Alignment explanation
Indices: 455396--455445 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 20
455386 TATTTCAAAC
455396 ATGTATCAACACATTCACTT
1 ATGTATCAACACATTCACTT
* * *
455416 ATGTATCGATATATTCACTT
1 ATGTATCAACACATTCACTT
455436 ATTGTATCAA
1 A-TGTATCAA
455446 TACAAATTAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
20 18 0.72
21 7 0.28
ACGTcount: A:0.34, C:0.18, G:0.08, T:0.40
Consensus pattern (20 bp):
ATGTATCAACACATTCACTT
Found at i:457462 original size:26 final size:26
Alignment explanation
Indices: 457431--457482 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 26
457421 ATTTAAGTTT
*
457431 AATTTAATTTAAA-ATATAAATATTA
1 AATTTTATTTAAATATATAAATATTA
**
457456 AATTTTATTTAAATATATTTATATTA
1 AATTTTATTTAAATATATAAATATTA
457482 A
1 A
457483 TAAATAAATA
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
25 12 0.52
26 11 0.48
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (26 bp):
AATTTTATTTAAATATATAAATATTA
Found at i:457835 original size:32 final size:32
Alignment explanation
Indices: 457793--457894 Score: 89
Period size: 32 Copynumber: 3.1 Consensus size: 32
457783 TTAAGTTCTT
*
457793 TTTTATTTATTAAATAAATATAATTTTAATTA
1 TTTTAATTATTAAATAAATATAATTTTAATTA
** * *
457825 TTTTAATTATTATTTAATATAAATATTATTTATATA
1 TTTTAATTATTAAATAA-ATATA-ATT-TTAAT-TA
* *
457861 TTTTTATT-TTTAATAAATATAATTTTTAATTA
1 TTTTAATTATTAAATAAATATAA-TTTTAATTA
457893 TT
1 TT
457895 ATTTAACATA
Statistics
Matches: 54, Mismatches: 11, Indels: 10
0.72 0.15 0.13
Matches are distributed among these distances:
32 18 0.33
33 9 0.17
34 9 0.17
35 9 0.17
36 9 0.17
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (32 bp):
TTTTAATTATTAAATAAATATAATTTTAATTA
Found at i:457835 original size:36 final size:34
Alignment explanation
Indices: 457781--457899 Score: 106
Period size: 34 Copynumber: 3.5 Consensus size: 34
457771 TTTGTTTAAT
*
457781 TTTTAAGTTCTTTTTTATTTATTAAATAAATATAA
1 TTTTAA-TTATTTTTTATTTATTAAATAAATATAA
*
457816 TTTTAATTATTTTAATTA-TTATTTAATATAAATATTA
1 TTTTAATTATTTT--TTATTTA-TTAA-ATAAATATAA
457853 -TTT-A-TATATTTTTATTT-TT-AATAAATATAA
1 TTTTAATTAT-TTTTTATTTATTAAATAAATATAA
*
457883 TTTTTAATTATTATTTA
1 -TTTTAATTATTTTTTA
457900 ACATAAAAAT
Statistics
Matches: 70, Mismatches: 4, Indels: 22
0.73 0.04 0.23
Matches are distributed among these distances:
30 9 0.13
31 1 0.01
32 5 0.07
33 9 0.13
34 14 0.20
35 13 0.19
36 10 0.14
37 9 0.13
ACGTcount: A:0.38, C:0.01, G:0.01, T:0.61
Consensus pattern (34 bp):
TTTTAATTATTTTTTATTTATTAAATAAATATAA
Found at i:457877 original size:30 final size:29
Alignment explanation
Indices: 457824--457898 Score: 82
Period size: 30 Copynumber: 2.6 Consensus size: 29
457814 AATTTTAATT
* *
457824 ATTT-TAATTATTA-TTTAATATAAATATT
1 ATTTATAATTATTATTTTTA-ATAAATATA
*
457852 ATTTATATATTTTTATTTTTAATAAATATA
1 ATTTATA-ATTATTATTTTTAATAAATATA
*
457882 ATTTTTAATTATTATTT
1 ATTTATAATTATTATTT
457899 AACATAAAAA
Statistics
Matches: 39, Mismatches: 5, Indels: 5
0.80 0.10 0.10
Matches are distributed among these distances:
28 4 0.10
29 11 0.28
30 20 0.51
31 4 0.10
ACGTcount: A:0.39, C:0.00, G:0.00, T:0.61
Consensus pattern (29 bp):
ATTTATAATTATTATTTTTAATAAATATA
Found at i:457891 original size:59 final size:61
Alignment explanation
Indices: 457819--457973 Score: 181
Period size: 59 Copynumber: 2.5 Consensus size: 61
457809 AATATAATTT
* *
457819 TAATTATTTTAATTATTATTTAATATAAATATTATTTATATATTTTTATTTT-TAATAAATA
1 TAATT-TTTTAATTATTATTTAATATAAATATTATTTATATACTTATATTTTGTAATAAATA
* * * * *
457880 TAA-TTTTTAATTATTATTTAACATAAA-AATATTTTTTTACTTATATTTTGTTATAAATA
1 TAATTTTTTAATTATTATTTAATATAAATATTATTTATATACTTATATTTTGTAATAAATA
457939 TAATTTTATTTAAAATTATTATTTAATATAAATAT
1 TAA-TTT-TTT--AATTATTATTTAATATAAATAT
457974 AAAATTAATT
Statistics
Matches: 78, Mismatches: 9, Indels: 10
0.80 0.09 0.10
Matches are distributed among these distances:
58 17 0.22
59 33 0.42
60 1 0.01
61 5 0.06
62 3 0.04
64 18 0.23
65 1 0.01
ACGTcount: A:0.41, C:0.01, G:0.01, T:0.57
Consensus pattern (61 bp):
TAATTTTTTAATTATTATTTAATATAAATATTATTTATATACTTATATTTTGTAATAAATA
Found at i:458027 original size:19 final size:19
Alignment explanation
Indices: 457969--458028 Score: 50
Period size: 21 Copynumber: 3.0 Consensus size: 19
457959 ATTTAATATA
*
457969 AATATAAAATTAATTATTTAT
1 AATATAATA-TAATTATTT-T
* *
457990 TATATACATATACA-CATTTT
1 AATATA-ATATA-ATTATTTT
458010 AATATAATATAATTATTTT
1 AATATAATATAATTATTTT
458029 TTATTATCAT
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
18 1 0.03
19 10 0.32
20 6 0.19
21 11 0.35
22 3 0.10
ACGTcount: A:0.47, C:0.05, G:0.00, T:0.48
Consensus pattern (19 bp):
AATATAATATAATTATTTT
Found at i:458263 original size:16 final size:16
Alignment explanation
Indices: 458238--458284 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
458228 TTTAAAAAAA
*
458238 TCAAATTAATTCAAAT
1 TCAAAATAATTCAAAT
*
458254 TCAAAATAATTTAAAAT
1 TCAAAATAA-TTCAAAT
*
458271 T-AAAATAACTCAAA
1 TCAAAATAATTCAAA
458285 CTTAAATATA
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
15 4 0.15
16 15 0.58
17 7 0.27
ACGTcount: A:0.57, C:0.11, G:0.00, T:0.32
Consensus pattern (16 bp):
TCAAAATAATTCAAAT
Found at i:458289 original size:16 final size:16
Alignment explanation
Indices: 458250--458297 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
458240 AAATTAATTC
* *
458250 AAATTCAAAATAATTTA
1 AAATT-AAAATAACTCA
458267 AAATTAAAATAACTCA
1 AAATTAAAATAACTCA
*
458283 AACTTAAATATAACT
1 AAATTAAA-ATAACT
458298 TTAAATTTTA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
16 16 0.59
17 11 0.41
ACGTcount: A:0.58, C:0.10, G:0.00, T:0.31
Consensus pattern (16 bp):
AAATTAAAATAACTCA
Found at i:458426 original size:40 final size:39
Alignment explanation
Indices: 458370--458460 Score: 130
Period size: 40 Copynumber: 2.3 Consensus size: 39
458360 TCTATTTAAA
*
458370 AATAATTACCAAAATTTGGAGAAATATTTTGAAAACTTG-G
1 AATAATTA-CAAAATTTGGAG-AATACTTTGAAAACTTGAG
*
458410 AATAATTACAACAATTTGTAGAATACTTTGAAAACTTGAG
1 AATAATTACAA-AATTTGGAGAATACTTTGAAAACTTGAG
458450 AATAATTACAA
1 AATAATTACAA
458461 TCTTGCCAAA
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
39 19 0.40
40 28 0.60
ACGTcount: A:0.47, C:0.09, G:0.12, T:0.32
Consensus pattern (39 bp):
AATAATTACAAAATTTGGAGAATACTTTGAAAACTTGAG
Found at i:458453 original size:19 final size:19
Alignment explanation
Indices: 458392--458456 Score: 60
Period size: 19 Copynumber: 3.4 Consensus size: 19
458382 AATTTGGAGA
*
458392 AATATTTTGAAAACTTG-G
1 AATAATTTGAAAACTTGAG
** *
458410 AATAATTACAACAATTTGTAG
1 AATAATTTGAA-AACTTG-AG
*
458431 AATACTTTGAAAACTTGAG
1 AATAATTTGAAAACTTGAG
458450 AATAATT
1 AATAATT
458457 ACAATCTTGC
Statistics
Matches: 35, Mismatches: 9, Indels: 5
0.71 0.18 0.10
Matches are distributed among these distances:
18 8 0.23
19 13 0.37
20 5 0.14
21 9 0.26
ACGTcount: A:0.45, C:0.08, G:0.12, T:0.35
Consensus pattern (19 bp):
AATAATTTGAAAACTTGAG
Found at i:460005 original size:2 final size:2
Alignment explanation
Indices: 459998--460023 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
459988 ACCGACAAAC
459998 AG AG AG AG AG AG AG AG AG AG AG AG AG
1 AG AG AG AG AG AG AG AG AG AG AG AG AG
460024 CGCATTGGAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
AG
Found at i:460425 original size:20 final size:19
Alignment explanation
Indices: 460412--460449 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
460402 AAATTAATTT
460412 TTAAAAATAAAAATATAAAA
1 TTAAAAATAAAAAT-TAAAA
*
460432 TTAATAATAAAAATTAAA
1 TTAAAAATAAAAATTAAA
460450 TATATAAATA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 4 0.24
20 13 0.76
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (19 bp):
TTAAAAATAAAAATTAAAA
Found at i:460430 original size:14 final size:14
Alignment explanation
Indices: 460413--460457 Score: 56
Period size: 14 Copynumber: 3.3 Consensus size: 14
460403 AATTAATTTT
*
460413 TAAAAATAAAAATA
1 TAAAATTAAAAATA
*
460427 TAAAATTAATAATA
1 TAAAATTAAAAATA
*
460441 -AAAATTAAATATA
1 TAAAATTAAAAATA
460454 TAAA
1 TAAA
460458 TAAATGTTAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
13 11 0.42
14 15 0.58
ACGTcount: A:0.71, C:0.00, G:0.00, T:0.29
Consensus pattern (14 bp):
TAAAATTAAAAATA
Found at i:460451 original size:11 final size:13
Alignment explanation
Indices: 460415--460457 Score: 52
Period size: 13 Copynumber: 3.2 Consensus size: 13
460405 TTAATTTTTA
*
460415 AAAATAAAAATAT
1 AAAATTAAAATAT
460428 AAAATTAATAATA-
1 AAAATTAA-AATAT
460441 AAAATTAAATATAT
1 AAAATTAAA-ATAT
460455 AAA
1 AAA
460458 TAAATGTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 5
0.81 0.03 0.16
Matches are distributed among these distances:
12 1 0.04
13 18 0.69
14 7 0.27
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (13 bp):
AAAATTAAAATAT
Found at i:466518 original size:13 final size:13
Alignment explanation
Indices: 466500--466525 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
466490 TACACAAAGT
466500 ATGTATCGATACA
1 ATGTATCGATACA
466513 ATGTATCGATACA
1 ATGTATCGATACA
466526 CAAAAAAATT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:466544 original size:34 final size:32
Alignment explanation
Indices: 466482--466546 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
466472 TAGCCAAACT
**
466482 TGTATCGATACACAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAATGTATCGATACAA
466514 TGTATCGATACACAAAAAAATTGTATCGATACA
1 TGTATCGATACAC-AAAAAA-TGTATCGATACA
466547 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 13 0.45
33 4 0.14
34 12 0.41
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACAAAAAATGTATCGATACAA
Found at i:467692 original size:21 final size:21
Alignment explanation
Indices: 467659--467708 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
467649 TTGCAAGTTG
*
467659 AAATAAAGAAGTTGGCTAATGA
1 AAATAAAGAAGTTAGCTAA-GA
*
467681 AAATAATG-AGTTAGCTAAGAA
1 AAATAAAGAAGTTAGCTAAG-A
467702 AAATAAA
1 AAATAAA
467709 ATTTGCATAA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 16 0.67
22 7 0.29
ACGTcount: A:0.56, C:0.04, G:0.18, T:0.22
Consensus pattern (21 bp):
AAATAAAGAAGTTAGCTAAGA
Found at i:471575 original size:13 final size:13
Alignment explanation
Indices: 471557--471594 Score: 58
Period size: 13 Copynumber: 2.9 Consensus size: 13
471547 CATTTTTCTT
471557 TGTATCGATACAA
1 TGTATCGATACAA
*
471570 TGTATCGATACAC
1 TGTATCGATACAA
*
471583 TATATCGATACA
1 TGTATCGATACA
471595 GGGGGATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
13 23 1.00
ACGTcount: A:0.37, C:0.18, G:0.13, T:0.32
Consensus pattern (13 bp):
TGTATCGATACAA
Found at i:471749 original size:20 final size:20
Alignment explanation
Indices: 471706--471751 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
471696 AAATCTTTTG
471706 CAAAATACTTGTTTTTCACTT
1 CAAAATACTTGTTTTTCAC-T
*
471727 CAAATTACTTCGTTTTTCA-T
1 CAAAATACTT-GTTTTTCACT
471747 CAAAA
1 CAAAA
471752 CCAGCATCAA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
20 5 0.23
21 9 0.41
22 8 0.36
ACGTcount: A:0.33, C:0.20, G:0.04, T:0.43
Consensus pattern (20 bp):
CAAAATACTTGTTTTTCACT
Found at i:473486 original size:39 final size:40
Alignment explanation
Indices: 473432--473522 Score: 105
Period size: 39 Copynumber: 2.3 Consensus size: 40
473422 GAGATTTTTT
* * *
473432 TTTAGTAAAAGGGGAGAATGCATAAATTTGCTAAAATTA-
1 TTTAGTTAAGGGGGAGAATGCACAAATTTGCTAAAATTAC
* * *
473471 TCTTA-TTAAGGGGGAGAATGTACGAATTTGTTAAAATTAC
1 T-TTAGTTAAGGGGGAGAATGCACAAATTTGCTAAAATTAC
473511 TTTAGTTAAGGG
1 TTTAGTTAAGGG
473523 TGAAAGAAAA
Statistics
Matches: 43, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
39 32 0.74
40 11 0.26
ACGTcount: A:0.37, C:0.05, G:0.23, T:0.34
Consensus pattern (40 bp):
TTTAGTTAAGGGGGAGAATGCACAAATTTGCTAAAATTAC
Found at i:474185 original size:13 final size:13
Alignment explanation
Indices: 474167--474192 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
474157 TACACAAAGT
474167 ATGTATCGATACA
1 ATGTATCGATACA
474180 ATGTATCGATACA
1 ATGTATCGATACA
474193 CAAAAAAATT
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:0.38, C:0.15, G:0.15, T:0.31
Consensus pattern (13 bp):
ATGTATCGATACA
Found at i:474211 original size:34 final size:32
Alignment explanation
Indices: 474149--474213 Score: 94
Period size: 32 Copynumber: 2.0 Consensus size: 32
474139 TAGCCAAACT
**
474149 TGTATCGATACACAAAGTATGTATCGATACAA
1 TGTATCGATACACAAAAAATGTATCGATACAA
474181 TGTATCGATACACAAAAAAATTGTATCGATACA
1 TGTATCGATACAC-AAAAAA-TGTATCGATACA
474214 TTGGCTTGTA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
32 13 0.45
33 4 0.14
34 12 0.41
ACGTcount: A:0.43, C:0.15, G:0.14, T:0.28
Consensus pattern (32 bp):
TGTATCGATACACAAAAAATGTATCGATACAA
Found at i:475142 original size:29 final size:31
Alignment explanation
Indices: 475092--475149 Score: 84
Period size: 29 Copynumber: 1.9 Consensus size: 31
475082 CTATCTTTAA
*
475092 TAATATATAATATAATATAATACTATTTATT
1 TAATATATAATATAATAGAATACTATTTATT
*
475123 TAATA-ATAAT-TAATAGAATATTATTTA
1 TAATATATAATATAATAGAATACTATTTA
475150 ATATTACAAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 15 0.60
30 5 0.20
31 5 0.20
ACGTcount: A:0.50, C:0.02, G:0.02, T:0.47
Consensus pattern (31 bp):
TAATATATAATATAATAGAATACTATTTATT
Found at i:475339 original size:15 final size:14
Alignment explanation
Indices: 475302--475338 Score: 56
Period size: 15 Copynumber: 2.6 Consensus size: 14
475292 GAAATGTTAT
*
475302 TATTAAAATATTAC
1 TATTAAAATATTAA
475316 TATTTAAAATATTAA
1 TA-TTAAAATATTAA
475331 TATTAAAA
1 TATTAAAA
475339 ACTAATAGTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
14 8 0.38
15 13 0.62
ACGTcount: A:0.54, C:0.03, G:0.00, T:0.43
Consensus pattern (14 bp):
TATTAAAATATTAA
Found at i:475389 original size:22 final size:22
Alignment explanation
Indices: 475354--475395 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
475344 TAGTTTAACG
* * *
475354 ATAAATAGTTTTTATTATTTTA
1 ATAAATAATATTTAATATTTTA
475376 ATAAATAATATTTAATATTT
1 ATAAATAATATTTAATATTT
475396 ATATCAATAT
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (22 bp):
ATAAATAATATTTAATATTTTA
Found at i:475415 original size:39 final size:37
Alignment explanation
Indices: 475365--475470 Score: 94
Period size: 39 Copynumber: 2.8 Consensus size: 37
475355 TAAATAGTTT
475365 TTATTAT-TTTAATAAATAATATTTAATATTTATATCAA
1 TTATTATATTTAATAAATAATATTTAATATTTA-AT-AA
* *
475403 -TATTACTATTTAA-AGAAT-ATAAGTTAATTTTTAATAA
1 TTATTA-TATTTAATA-AATAAT-ATTTAATATTTAATAA
*
475440 TTATTATATTAATATAAATAATATTTTAATA
1 TTATTATATTTA-ATAAATAATA-TTTAATA
475471 ATAAATATCA
Statistics
Matches: 54, Mismatches: 5, Indels: 17
0.71 0.07 0.22
Matches are distributed among these distances:
37 12 0.22
38 16 0.30
39 26 0.48
ACGTcount: A:0.46, C:0.02, G:0.02, T:0.50
Consensus pattern (37 bp):
TTATTATATTTAATAAATAATATTTAATATTTAATAA
Found at i:475456 original size:17 final size:17
Alignment explanation
Indices: 475444--475477 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
475434 TAATAATTAT
475444 TATATTAATATAAATAA
1 TATATTAATATAAATAA
*
475461 TATTTTAATAATAAATA
1 TATATTAAT-ATAAATA
475478 TCATTATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (17 bp):
TATATTAATATAAATAA
Found at i:475540 original size:14 final size:14
Alignment explanation
Indices: 475517--475562 Score: 51
Period size: 14 Copynumber: 3.3 Consensus size: 14
475507 AATATGTTAG
475517 TATT-AAATATTAT
1 TATTAAAATATTAT
475530 TATTAAAATATT-T
1 TATTAAAATATTAT
*
475543 CTATTATAAATATTAA
1 -TATTA-AAATATTAT
475559 TATT
1 TATT
475563 TAATATTAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
13 5 0.18
14 12 0.43
15 11 0.39
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (14 bp):
TATTAAAATATTAT
Found at i:475540 original size:29 final size:29
Alignment explanation
Indices: 475498--475562 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 29
475488 AAGTATTTAA
* *
475498 TATTAGTATAATATGT-TAGTATTAAATAT
1 TATTATTAAAATATGTCTAGTA-TAAATAT
* *
475527 TATTATTAAAATATTTCTATTATAAATAT
1 TATTATTAAAATATGTCTAGTATAAATAT
*
475556 TAATATT
1 TATTATT
475563 TAATATTAAA
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
29 26 0.87
30 4 0.13
ACGTcount: A:0.43, C:0.02, G:0.05, T:0.51
Consensus pattern (29 bp):
TATTATTAAAATATGTCTAGTATAAATAT
Done.