Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397255.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_44.0, 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: 14367614
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Warning! 51264 characters in sequence are not A, C, G, or T
File 28 of 31
Found at i:13070731 original size:31 final size:31
Alignment explanation
Indices: 13070691--13070854 Score: 195
Period size: 31 Copynumber: 5.3 Consensus size: 31
13070681 AGAAACAAAT
* * *
13070691 AAATGTTGTTACATGCCATGCATATCAACTG
1 AAATGTTGTTACACGCCATGCATATCAAGTA
* *
13070722 AAATATTGTTACACGCCATGCATATCAAATA
1 AAATGTTGTTACACGCCATGCATATCAAGTA
* **
13070753 AAATGTTATTACACGCCATGTGTATCAAGTA
1 AAATGTTGTTACACGCCATGCATATCAAGTA
*
13070784 AAATGTTGTTACACGCCATGCGTATCAAGT-
1 AAATGTTGTTACACGCCATGCATATCAAGTA
* * * * *
13070814 CAATGTTGTTGCATGCCATGCATATTAAGTC
1 AAATGTTGTTACACGCCATGCATATCAAGTA
13070845 AAATGTTGTT
1 AAATGTTGTT
13070855 TTACGCCAAC
Statistics
Matches: 115, Mismatches: 17, Indels: 2
0.86 0.13 0.01
Matches are distributed among these distances:
30 25 0.22
31 90 0.78
ACGTcount: A:0.33, C:0.18, G:0.16, T:0.33
Consensus pattern (31 bp):
AAATGTTGTTACACGCCATGCATATCAAGTA
Found at i:13071595 original size:23 final size:23
Alignment explanation
Indices: 13071565--13071617 Score: 81
Period size: 23 Copynumber: 2.3 Consensus size: 23
13071555 TAAACCCTGA
13071565 CATGTCATAGATTCCCTT-CATGG
1 CATGTCATAGATT-CCTTCCATGG
13071588 CATGTCATAGATTCCTTCCATGG
1 CATGTCATAGATTCCTTCCATGG
*
13071611 CGTGTCA
1 CATGTCA
13071618 CAAACTCTGA
Statistics
Matches: 28, Mismatches: 1, Indels: 2
0.90 0.03 0.06
Matches are distributed among these distances:
22 4 0.14
23 24 0.86
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (23 bp):
CATGTCATAGATTCCTTCCATGG
Found at i:13071688 original size:47 final size:47
Alignment explanation
Indices: 13071588--13071691 Score: 127
Period size: 47 Copynumber: 2.2 Consensus size: 47
13071578 CCCTTCATGG
* * * * * *
13071588 CATGTCATAGATTCCTTCCATGGCGTGTCACAAACTCTGAACCCTCT
1 CATGTCACAGATTCCCTCCATGACATGTCACAAACTCTGAACACTAT
* *
13071635 TATGTCACAGATTCCCTCCATGACATGTCACAAATTCTGAACACTAT
1 CATGTCACAGATTCCCTCCATGACATGTCACAAACTCTGAACACTAT
*
13071682 CGTGTCACAG
1 CATGTCACAG
13071692 CTGTGTCACA
Statistics
Matches: 47, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
47 47 1.00
ACGTcount: A:0.27, C:0.30, G:0.14, T:0.29
Consensus pattern (47 bp):
CATGTCACAGATTCCCTCCATGACATGTCACAAACTCTGAACACTAT
Found at i:13071790 original size:23 final size:23
Alignment explanation
Indices: 13071697--13071791 Score: 63
Period size: 23 Copynumber: 4.2 Consensus size: 23
13071687 CACAGCTGTG
*
13071697 TCACATATGCTCACCATGT-TGTC
1 TCACATATTCTCACCATGTCT-TC
* *
13071720 TCACATATTCTCACCATG-GTAC
1 TCACATATTCTCACCATGTCTTC
* * * * * *
13071742 GC-CACATTCTCA-TACTGACGTG
1 TCACATATTCTCACCA-TGTCTTC
13071764 TCACATATTCTCACCATGTCTTC
1 TCACATATTCTCACCATGTCTTC
13071787 TCACA
1 TCACA
13071792 CATTTCTTCC
Statistics
Matches: 52, Mismatches: 15, Indels: 10
0.68 0.19 0.13
Matches are distributed among these distances:
20 1 0.02
21 11 0.21
22 3 0.06
23 36 0.69
24 1 0.02
ACGTcount: A:0.24, C:0.33, G:0.11, T:0.33
Consensus pattern (23 bp):
TCACATATTCTCACCATGTCTTC
Found at i:13071942 original size:165 final size:165
Alignment explanation
Indices: 13071742--13072038 Score: 380
Period size: 165 Copynumber: 1.8 Consensus size: 165
13071732 ACCATGGTAC
* * * * * *
13071742 GCCACATTCTCATACTGACGTGTCACATATTCTCACCATGTCTTCTCACACATTTCTTCCGAGTC
1 GCCACATTCTCACACTGACGTGTCACATATTCTCACCAGGTCATCTCACACATTCCCTCCAAGTC
* * * *
13071807 ATGTCACATATTCTCACCCTACCGTGTCACATATTCCCTCCATGGCGTATTAGAAACTCTAAACC
66 ATGTCACATATTCTCACCCTACCATGCCACATATTCCCTCCATAGCGTATCAGAAACTCTAAACC
13071872 CTATCGTGTCACACATTCCCAACATGCCATTTCAA
131 CTATCGTGTCACACATTCCCAACATGCCATTTCAA
* *
13071907 GCCACATTCTCACACT-AGTGTGTCACATATTCTCACCAGGTCATCTCACATATTCCCTCCAAGT
1 GCCACATTCTCACACTGA-CGTGTCACATATTCTCACCAGGTCATCTCACACATTCCCTCCAAGT
** * * * * * * * *
13071971 TGTGTCACATGTTCTTACCTTGCTATGCCACATATTCCCTCGATAGCGTGTCATAAACTCTAAAC
65 CATGTCACATATTCTCACCCTACCATGCCACATATTCCCTCCATAGCGTATCAGAAACTCTAAAC
13072036 CCT
130 CCT
13072039 GCTGTTTCAC
Statistics
Matches: 109, Mismatches: 22, Indels: 2
0.82 0.17 0.02
Matches are distributed among these distances:
164 1 0.01
165 108 0.99
ACGTcount: A:0.25, C:0.33, G:0.11, T:0.31
Consensus pattern (165 bp):
GCCACATTCTCACACTGACGTGTCACATATTCTCACCAGGTCATCTCACACATTCCCTCCAAGTC
ATGTCACATATTCTCACCCTACCATGCCACATATTCCCTCCATAGCGTATCAGAAACTCTAAACC
CTATCGTGTCACACATTCCCAACATGCCATTTCAA
Found at i:13071978 original size:23 final size:23
Alignment explanation
Indices: 13071925--13071980 Score: 58
Period size: 23 Copynumber: 2.4 Consensus size: 23
13071915 CTCACACTAG
* *
13071925 TGTGTCACATATTCTCACCAGGT
1 TGTGTCACATATTCCCACCAAGT
** * *
13071948 CATCTCACATATTCCCTCCAAGT
1 TGTGTCACATATTCCCACCAAGT
13071971 TGTGTCACAT
1 TGTGTCACAT
13071981 GTTCTTACCT
Statistics
Matches: 24, Mismatches: 9, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
23 24 1.00
ACGTcount: A:0.23, C:0.30, G:0.12, T:0.34
Consensus pattern (23 bp):
TGTGTCACATATTCCCACCAAGT
Found at i:13072778 original size:16 final size:17
Alignment explanation
Indices: 13072740--13072778 Score: 53
Period size: 17 Copynumber: 2.4 Consensus size: 17
13072730 TTCTTCTCAA
*
13072740 TTTTCCTTCCCTAATTC
1 TTTTCTTTCCCTAATTC
*
13072757 TTTTCTTTCCCT-ATTT
1 TTTTCTTTCCCTAATTC
13072773 TTTTCT
1 TTTTCT
13072779 CTCTCTCTCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
16 9 0.45
17 11 0.55
ACGTcount: A:0.08, C:0.28, G:0.00, T:0.64
Consensus pattern (17 bp):
TTTTCTTTCCCTAATTC
Found at i:13073390 original size:43 final size:43
Alignment explanation
Indices: 13073274--13073397 Score: 113
Period size: 43 Copynumber: 2.8 Consensus size: 43
13073264 AAGATAAAGG
* * * * * *
13073274 TCCTTATCTAAAATGAGGTTACATAAATTTAATGAAGGAATAAAC
1 TCCTCATCTAGAATGAGGCTACATAACTTTAA--AAAGAATAAAA
* * * **
13073319 TCCTCATATTAGAGTTAGGCTATGTAACTTTAAAAAGAATAAAA
1 TCCTCAT-CTAGAATGAGGCTACATAACTTTAAAAAGAATAAAA
*
13073363 TCTTCATCTAGAATGAGGCTACATAACTTTAAAAA
1 TCCTCATCTAGAATGAGGCTACATAACTTTAAAAA
13073398 TTTAAACAAA
Statistics
Matches: 61, Mismatches: 17, Indels: 4
0.74 0.21 0.05
Matches are distributed among these distances:
43 23 0.38
44 15 0.25
45 6 0.10
46 17 0.28
ACGTcount: A:0.43, C:0.13, G:0.13, T:0.31
Consensus pattern (43 bp):
TCCTCATCTAGAATGAGGCTACATAACTTTAAAAAGAATAAAA
Found at i:13073795 original size:18 final size:19
Alignment explanation
Indices: 13073762--13073802 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
13073752 AAATCTCCTC
13073762 AATTCATGGTAAAATGGGA
1 AATTCATGGTAAAATGGGA
* *
13073781 AATTTATGG-AAAATGGGT
1 AATTCATGGTAAAATGGGA
13073799 AATT
1 AATT
13073803 GGGAAACAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 12 0.60
19 8 0.40
ACGTcount: A:0.41, C:0.02, G:0.24, T:0.32
Consensus pattern (19 bp):
AATTCATGGTAAAATGGGA
Found at i:13077857 original size:62 final size:62
Alignment explanation
Indices: 13077791--13077915 Score: 241
Period size: 62 Copynumber: 2.0 Consensus size: 62
13077781 TAAATAAATA
*
13077791 AATAAATTTAAATTACAATGAATTAAAAGGCTTAAGATAACAAATAACTAGTTATAGGCTCG
1 AATAAATTTAAATTACAATGAATTAAAAGGCTTAAGATAACAAATAACTAGTTATAGACTCG
13077853 AATAAATTTAAATTACAATGAATTAAAAGGCTTAAGATAACAAATAACTAGTTATAGACTCG
1 AATAAATTTAAATTACAATGAATTAAAAGGCTTAAGATAACAAATAACTAGTTATAGACTCG
13077915 A
1 A
13077916 CTCTCTTGCT
Statistics
Matches: 62, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
62 62 1.00
ACGTcount: A:0.50, C:0.10, G:0.12, T:0.29
Consensus pattern (62 bp):
AATAAATTTAAATTACAATGAATTAAAAGGCTTAAGATAACAAATAACTAGTTATAGACTCG
Found at i:13078788 original size:171 final size:173
Alignment explanation
Indices: 13078596--13078936 Score: 553
Period size: 171 Copynumber: 2.0 Consensus size: 173
13078586 TTTCCCCCTC
*
13078596 TAATCAAAATAGTTCCTTTAGAAATTAAATTGATTC-TCTTAGATCTAAAAGAAATTGAAACCCA
1 TAATCAAAATAGTTCCTTTAGAAACTAAATTGATTCTTC-TAGATCTAAAAGAAATTGAAACCCA
* * * * *
13078660 AGAACCTAAGAATTCATGAACTATTTTCTCTCCTCTACCAATTATCTCTTCTTAGTTTTCCTTCC
65 AGAACCTAAGAACTCAAGAACCATTTTCTCTCCTCTACCAATTATATCTTCTCAGTTTTCCTTCC
*
13078725 CTAATTGTTTTCTCTCCCTATTCTTTTTTTT-TC-CTCTATCTT
130 CTAATTCTTTTCTCTCCCTATTCTTTTTTTTCTCTCTCTATCTT
* *
13078767 TAATCAAAATAGTTTCTTTAGAAACTAAATTGATTCTTCTAGATCTAAAAGAAATTGAAACCTAA
1 TAATCAAAATAGTTCCTTTAGAAACTAAATTGATTCTTCTAGATCTAAAAGAAATTGAAACCCAA
* *
13078832 GAACCTAAGAACTCAAGAACCATTTTCTCTCTTCTACCAATTGTATCTTCTCAGTTTTCCTTCCC
66 GAACCTAAGAACTCAAGAACCATTTTCTCTCCTCTACCAATTATATCTTCTCAGTTTTCCTTCCC
13078897 TAATTCTTTTCTCTCCCTATTCTTTTTTTTCTCTCTCTAT
131 TAATTCTTTTCTCTCCCTATTCTTTTTTTTCTCTCTCTAT
13078937 GTGCTCTTTA
Statistics
Matches: 156, Mismatches: 11, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
171 146 0.94
172 4 0.03
173 6 0.04
ACGTcount: A:0.28, C:0.23, G:0.06, T:0.43
Consensus pattern (173 bp):
TAATCAAAATAGTTCCTTTAGAAACTAAATTGATTCTTCTAGATCTAAAAGAAATTGAAACCCAA
GAACCTAAGAACTCAAGAACCATTTTCTCTCCTCTACCAATTATATCTTCTCAGTTTTCCTTCCC
TAATTCTTTTCTCTCCCTATTCTTTTTTTTCTCTCTCTATCTT
Found at i:13085625 original size:16 final size:16
Alignment explanation
Indices: 13085604--13085634 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
13085594 TTCTTATCGT
13085604 CTTCTTTTTTTTTTTC
1 CTTCTTTTTTTTTTTC
13085620 CTTCTTTTTTTTTTT
1 CTTCTTTTTTTTTTT
13085635 TGCTTTTCCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (16 bp):
CTTCTTTTTTTTTTTC
Found at i:13085659 original size:47 final size:44
Alignment explanation
Indices: 13085554--13085662 Score: 105
Period size: 47 Copynumber: 2.3 Consensus size: 44
13085544 TATGAAATAC
*
13085554 TGTGTTGTTTTTTTTTTTCTCTGTTGTTTTTTTATGTTTCTTCT
1 TGTGTTTTTTTTTTTTTTCTCTGTTGTTTTTTTATGTTTCTTCT
* *
13085598 TATCGTCTTCTTTTTTTTTTTCCTTCT-TT-TTTTTTTTTGCTTTTCCTTCT
1 TGT-GT-TT-TTTTTTTTTTT-C-TCTGTTGTTTTTTTATG--TTT-CTTCT
13085648 TGTGTTTTTTTTTTT
1 TGTGTTTTTTTTTTT
13085663 GTGTCAACTT
Statistics
Matches: 53, Mismatches: 4, Indels: 13
0.76 0.06 0.19
Matches are distributed among these distances:
44 2 0.04
45 2 0.04
46 1 0.02
47 28 0.53
48 5 0.09
49 8 0.15
50 7 0.13
ACGTcount: A:0.02, C:0.13, G:0.09, T:0.76
Consensus pattern (44 bp):
TGTGTTTTTTTTTTTTTTCTCTGTTGTTTTTTTATGTTTCTTCT
Found at i:13088183 original size:5 final size:5
Alignment explanation
Indices: 13088149--13088180 Score: 57
Period size: 5 Copynumber: 6.6 Consensus size: 5
13088139 CAGCAGTATC
13088149 TTTCT TTTCT TTTCT TTTCT TTTCT TTT-T TTT
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT TTT
13088181 TTTCGATTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
4 4 0.15
5 23 0.85
ACGTcount: A:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (5 bp):
TTTCT
Found at i:13089710 original size:2 final size:2
Alignment explanation
Indices: 13089698--13089737 Score: 55
Period size: 2 Copynumber: 20.0 Consensus size: 2
13089688 AGTAGGACCA
*
13089698 AT AT GAT AT AT AT AT AT AT AT AT AT AT A- AT AT AC AT AT AT
1 AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13089738 TTTTTCTCTT
Statistics
Matches: 34, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
1 1 0.03
2 31 0.91
3 2 0.06
ACGTcount: A:0.50, C:0.03, G:0.03, T:0.45
Consensus pattern (2 bp):
AT
Found at i:13103998 original size:15 final size:16
Alignment explanation
Indices: 13103973--13104005 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
13103963 CCTATGGATG
13103973 ATGCAATTTGCTTTTA
1 ATGCAATTTGCTTTTA
13103989 ATGC-ATTTGCTTTTA
1 ATGCAATTTGCTTTTA
13104004 AT
1 AT
13104006 TTAAGGAGGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 13 0.76
16 4 0.24
ACGTcount: A:0.24, C:0.12, G:0.12, T:0.52
Consensus pattern (16 bp):
ATGCAATTTGCTTTTA
Found at i:13108305 original size:22 final size:21
Alignment explanation
Indices: 13108257--13108301 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
13108247 GAACATTTGT
*
13108257 ACACAAATTTTAAAAAAAATA
1 ACACAAATTTTAAAAAAAACA
* *
13108278 ACACAAATTTTGAAAATAACA
1 ACACAAATTTTAAAAAAAACA
13108299 ACA
1 ACA
13108302 ACAACACAAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.62, C:0.13, G:0.02, T:0.22
Consensus pattern (21 bp):
ACACAAATTTTAAAAAAAACA
Found at i:13109880 original size:20 final size:21
Alignment explanation
Indices: 13109841--13109881 Score: 57
Period size: 20 Copynumber: 2.0 Consensus size: 21
13109831 GTGCAATCTA
*
13109841 GGCAAGATGTATCGGCACATT
1 GGCAAGATGTATCGACACATT
*
13109862 GGCAA-ATGTATCGATACATT
1 GGCAAGATGTATCGACACATT
13109882 CTTGATAGGA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
20 13 0.72
21 5 0.28
ACGTcount: A:0.32, C:0.17, G:0.24, T:0.27
Consensus pattern (21 bp):
GGCAAGATGTATCGACACATT
Found at i:13110670 original size:2 final size:2
Alignment explanation
Indices: 13110663--13110703 Score: 55
Period size: 2 Copynumber: 20.5 Consensus size: 2
13110653 AGAGTTAAGA
* * *
13110663 TG TG TG TG TG TG TG TG TG TG TG TG TG TT TA TA TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
13110704 ATGTATATGA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.05, C:0.00, G:0.41, T:0.54
Consensus pattern (2 bp):
TG
Found at i:13113236 original size:20 final size:20
Alignment explanation
Indices: 13113211--13113252 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
13113201 TATATTTAAA
13113211 AAAATTGTAATTAACCCGGT
1 AAAATTGTAATTAACCCGGT
13113231 AAAATTGTAATTAACCCGGT
1 AAAATTGTAATTAACCCGGT
13113251 AA
1 AA
13113253 CCACCAGTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.43, C:0.14, G:0.14, T:0.29
Consensus pattern (20 bp):
AAAATTGTAATTAACCCGGT
Found at i:13113319 original size:2 final size:2
Alignment explanation
Indices: 13113314--13113348 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
13113304 TGTGTGTGTG
13113314 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
13113349 GGAAAGAGAA
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:13118150 original size:52 final size:52
Alignment explanation
Indices: 13118088--13118192 Score: 210
Period size: 52 Copynumber: 2.0 Consensus size: 52
13118078 TATAAGATAG
13118088 AGAAAACTATTTTTCTTTTCTTTTTCTTTTATGAAATGGTTGAAGGCTTAGA
1 AGAAAACTATTTTTCTTTTCTTTTTCTTTTATGAAATGGTTGAAGGCTTAGA
13118140 AGAAAACTATTTTTCTTTTCTTTTTCTTTTATGAAATGGTTGAAGGCTTAGA
1 AGAAAACTATTTTTCTTTTCTTTTTCTTTTATGAAATGGTTGAAGGCTTAGA
13118192 A
1 A
13118193 TTTTAGTTGA
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
52 53 1.00
ACGTcount: A:0.28, C:0.10, G:0.15, T:0.48
Consensus pattern (52 bp):
AGAAAACTATTTTTCTTTTCTTTTTCTTTTATGAAATGGTTGAAGGCTTAGA
Found at i:13124787 original size:3 final size:3
Alignment explanation
Indices: 13124779--13124813 Score: 61
Period size: 3 Copynumber: 11.7 Consensus size: 3
13124769 TTGCTTTACT
*
13124779 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTG TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
13124814 TATGTATTTG
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 30 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:13125903 original size:18 final size:17
Alignment explanation
Indices: 13125880--13125913 Score: 59
Period size: 18 Copynumber: 1.9 Consensus size: 17
13125870 ATTTTTTATA
13125880 TTTTAAAAATTATAAATT
1 TTTTAAAAA-TATAAATT
13125898 TTTTAAAAATATAAAT
1 TTTTAAAAATATAAAT
13125914 ATTAATTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 7 0.44
18 9 0.56
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTTAAAAATATAAATT
Found at i:13125905 original size:17 final size:17
Alignment explanation
Indices: 13125880--13125913 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
13125870 ATTTTTTATA
*
13125880 TTTTAAAAATTATAAAT
1 TTTTAAAAAATATAAAT
*
13125897 TTTTTAAAAATATAAAT
1 TTTTAAAAAATATAAAT
13125914 ATTAATTTGT
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
TTTTAAAAAATATAAAT
Found at i:13126058 original size:34 final size:35
Alignment explanation
Indices: 13126020--13126087 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 35
13126010 TTTTTATAAT
*
13126020 TTTTTACTTTTGAAT-ATTT-TAAAATAATTTTTTA
1 TTTTTAATTTT-AATAATTTATAAAATAATTTTTTA
13126054 TTTTTAATTTTAATAAATTTATAAAATAATTTTT
1 TTTTTAATTTTAAT-AATTTATAAAATAATTTTT
13126088 AACAAAATCT
Statistics
Matches: 30, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
33 3 0.10
34 10 0.33
35 4 0.13
36 13 0.43
ACGTcount: A:0.37, C:0.01, G:0.01, T:0.60
Consensus pattern (35 bp):
TTTTTAATTTTAATAATTTATAAAATAATTTTTTA
Found at i:13126071 original size:27 final size:28
Alignment explanation
Indices: 13126015--13126071 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 28
13126005 TAAAATTTTT
*
13126015 ATAATTTTTTACTTTTGAATATTTTAAA
1 ATAATTTTTTACTTTTGAATATTTAAAA
*
13126043 ATAATTTTTTA-TTTTTAAT-TTTAATAA
1 ATAATTTTTTACTTTTGAATATTTAA-AA
13126070 AT
1 AT
13126072 TTATAAAATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
26 4 0.15
27 11 0.42
28 11 0.42
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.60
Consensus pattern (28 bp):
ATAATTTTTTACTTTTGAATATTTAAAA
Found at i:13128233 original size:15 final size:15
Alignment explanation
Indices: 13128213--13128251 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
13128203 TTTATTTACT
13128213 TTTTTATTTTTAATA
1 TTTTTATTTTTAATA
** *
13128228 TTTTTAACTTTAATT
1 TTTTTATTTTTAATA
13128243 TTTTTATTT
1 TTTTTATTT
13128252 AATAATTTTG
Statistics
Matches: 19, Mismatches: 5, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.23, C:0.03, G:0.00, T:0.74
Consensus pattern (15 bp):
TTTTTATTTTTAATA
Found at i:13130202 original size:27 final size:27
Alignment explanation
Indices: 13130164--13130216 Score: 72
Period size: 27 Copynumber: 2.0 Consensus size: 27
13130154 TTGATTATAT
*
13130164 TTAAGTTGTTTTATTTTAGTT-TTATG
1 TTAAGTTGTTTTAGTTTAGTTATTATG
*
13130190 TTAATTTGCTTTTAGTTTAGTTATTAT
1 TTAAGTTG-TTTTAGTTTAGTTATTAT
13130217 TGAGAAGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 7 0.30
27 12 0.52
28 4 0.17
ACGTcount: A:0.21, C:0.02, G:0.13, T:0.64
Consensus pattern (27 bp):
TTAAGTTGTTTTAGTTTAGTTATTATG
Found at i:13132808 original size:15 final size:15
Alignment explanation
Indices: 13132788--13132832 Score: 63
Period size: 15 Copynumber: 2.9 Consensus size: 15
13132778 TTGAAATAAA
*
13132788 ACTTTCCATTTTAAG
1 ACTTTCCATTTTAAC
13132803 ACTTTCCATTTTAAC
1 ACTTTCCATTTTAAC
*
13132818 TCTTTCCATTATTAA
1 ACTTTCCATT-TTAA
13132833 AACTCCTTTT
Statistics
Matches: 27, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
15 23 0.85
16 4 0.15
ACGTcount: A:0.27, C:0.22, G:0.02, T:0.49
Consensus pattern (15 bp):
ACTTTCCATTTTAAC
Found at i:13132843 original size:28 final size:29
Alignment explanation
Indices: 13132789--13132844 Score: 71
Period size: 30 Copynumber: 1.9 Consensus size: 29
13132779 TGAAATAAAA
*
13132789 CTTTCCATTTTAAGACTTTCCATTTTAACT
1 CTTTCCATTTTAAAAC-TTCCATTTTAACT
13132819 CTTTCCATTATTAAAAC-TCC-TTTTAA
1 CTTTCCATT-TTAAAACTTCCATTTTAA
13132845 TTTCGGAAAC
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
28 6 0.25
29 3 0.12
30 9 0.38
31 6 0.25
ACGTcount: A:0.27, C:0.23, G:0.02, T:0.48
Consensus pattern (29 bp):
CTTTCCATTTTAAAACTTCCATTTTAACT
Found at i:13133185 original size:77 final size:78
Alignment explanation
Indices: 13133085--13133250 Score: 235
Period size: 77 Copynumber: 2.1 Consensus size: 78
13133075 TGAATTTTTC
* *
13133085 AAATTAAAATACTATCCTTAATTTTAAGAATTTCTATTAAAATAGGAATCAATTTCATATTC-TT
1 AAATTAAAATACTATCCTTAATTTTAAGAATTACTATTAAAATAGGAAACAATTTCATATTCTTT
13133149 TATAAATCACCCA
66 TATAAATCACCCA
* ** * * * *
13133162 AAATTAAAATTCTATTTTTAATTTTAGGAATTACTTTTAAAGTAGGAAACAATTTCCTATTCTTT
1 AAATTAAAATACTATCCTTAATTTTAAGAATTACTATTAAAATAGGAAACAATTTCATATTCTTT
*
13133227 TATGAATCACCCA
66 TATAAATCACCCA
13133240 AAATTAAAATA
1 AAATTAAAATA
13133251 GAGCGCCTAT
Statistics
Matches: 77, Mismatches: 11, Indels: 1
0.87 0.12 0.01
Matches are distributed among these distances:
77 53 0.69
78 24 0.31
ACGTcount: A:0.42, C:0.13, G:0.05, T:0.40
Consensus pattern (78 bp):
AAATTAAAATACTATCCTTAATTTTAAGAATTACTATTAAAATAGGAAACAATTTCATATTCTTT
TATAAATCACCCA
Found at i:13133806 original size:25 final size:25
Alignment explanation
Indices: 13133750--13133831 Score: 69
Period size: 25 Copynumber: 3.1 Consensus size: 25
13133740 TATTAGCCAT
13133750 AAGGACTTATTTGACTCAAAATAAAAGTAA
1 AAGGACTTATTTGACTCAAAAT---A--AA
13133780 AAGGACTTATTTGACTCAAAATAAA
1 AAGGACTTATTTGACTCAAAATAAA
* *
13133805 AA-TA-TAGTATTTGACACAAAATAAA
1 AAGGACT--TATTTGACTCAAAATAAA
13133830 AA
1 AA
13133832 TATAAGAACT
Statistics
Matches: 48, Mismatches: 2, Indels: 9
0.81 0.03 0.15
Matches are distributed among these distances:
23 1 0.02
24 1 0.02
25 23 0.48
27 1 0.02
30 22 0.46
ACGTcount: A:0.52, C:0.10, G:0.11, T:0.27
Consensus pattern (25 bp):
AAGGACTTATTTGACTCAAAATAAA
Found at i:13133832 original size:25 final size:25
Alignment explanation
Indices: 13133787--13133835 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 25
13133777 TAAAAGGACT
*
13133787 TATTTGACTCAAAATAAAAATATAG
1 TATTTGACACAAAATAAAAATATAG
13133812 TATTTGACACAAAATAAAAATATA
1 TATTTGACACAAAATAAAAATATA
13133836 AGAACTTACT
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.55, C:0.08, G:0.06, T:0.31
Consensus pattern (25 bp):
TATTTGACACAAAATAAAAATATAG
Found at i:13134024 original size:23 final size:23
Alignment explanation
Indices: 13133997--13134043 Score: 76
Period size: 23 Copynumber: 2.0 Consensus size: 23
13133987 TTATGAAAAT
13133997 ATAACTTAAAAGAACAAATAAAG
1 ATAACTTAAAAGAACAAATAAAG
* *
13134020 ATAACTTCAAAGAACAATTAAAG
1 ATAACTTAAAAGAACAAATAAAG
13134043 A
1 A
13134044 GAAGAAAGAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.62, C:0.11, G:0.09, T:0.19
Consensus pattern (23 bp):
ATAACTTAAAAGAACAAATAAAG
Found at i:13136935 original size:28 final size:28
Alignment explanation
Indices: 13136876--13136947 Score: 74
Period size: 28 Copynumber: 2.6 Consensus size: 28
13136866 GTCTTTTCAT
*** *
13136876 TATTCATCCACTTTTGGTGGGTTGAAAG
1 TATTCATCCACTTTTGGAAAGTTGAAAA
13136904 TATTCATCCACTTTTGGAAAGTT-ACAAA
1 TATTCATCCACTTTTGGAAAGTTGA-AAA
**
13136932 TATTCATTTACTTTTG
1 TATTCATCCACTTTTG
13136948 ATGGGTGATC
Statistics
Matches: 37, Mismatches: 6, Indels: 2
0.82 0.13 0.04
Matches are distributed among these distances:
27 1 0.03
28 36 0.97
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.43
Consensus pattern (28 bp):
TATTCATCCACTTTTGGAAAGTTGAAAA
Found at i:13138111 original size:16 final size:17
Alignment explanation
Indices: 13138081--13138118 Score: 53
Period size: 16 Copynumber: 2.3 Consensus size: 17
13138071 ATTTTTATAA
13138081 TTCTATGTAATAAATT-
1 TTCTATGTAATAAATTG
13138097 TTCTAT-TAATAAAATTG
1 TTCTATGTAAT-AAATTG
13138114 TTCTA
1 TTCTA
13138119 AGATTTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
15 4 0.20
16 11 0.55
17 5 0.25
ACGTcount: A:0.37, C:0.08, G:0.05, T:0.50
Consensus pattern (17 bp):
TTCTATGTAATAAATTG
Found at i:13141233 original size:32 final size:32
Alignment explanation
Indices: 13141192--13141260 Score: 129
Period size: 32 Copynumber: 2.2 Consensus size: 32
13141182 AATTAAAAAT
13141192 TATATATATATACATACGTGCATATAAATATA
1 TATATATATATACATACGTGCATATAAATATA
*
13141224 TATATATATATACATACGTGTATATAAATATA
1 TATATATATATACATACGTGCATATAAATATA
13141256 TATAT
1 TATAT
13141261 GTATGTAAAT
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 36 1.00
ACGTcount: A:0.46, C:0.07, G:0.06, T:0.41
Consensus pattern (32 bp):
TATATATATATACATACGTGCATATAAATATA
Found at i:13141234 original size:18 final size:18
Alignment explanation
Indices: 13141213--13141278 Score: 69
Period size: 18 Copynumber: 3.6 Consensus size: 18
13141203 ACATACGTGC
* *
13141213 ATATAAATATATATATAT
1 ATATAAATATGTATATAA
*
13141231 ATATACATACGTGTATATAA
1 ATATAAATA--TGTATATAA
* *
13141251 ATATATATATGTATGTAA
1 ATATAAATATGTATATAA
13141269 ATATAAATAT
1 ATATAAATAT
13141279 TATTTCAGTT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
18 25 0.62
20 15 0.38
ACGTcount: A:0.50, C:0.03, G:0.06, T:0.41
Consensus pattern (18 bp):
ATATAAATATGTATATAA
Found at i:13144192 original size:21 final size:20
Alignment explanation
Indices: 13144166--13144226 Score: 59
Period size: 21 Copynumber: 2.9 Consensus size: 20
13144156 TCAAAATTGC
13144166 TTGAATGATCTTTGAACTTGT
1 TTGAATGAT-TTTGAACTTGT
* * *
13144187 TTGAATGGTTTTTGCAGTTGT
1 TTGAAT-GATTTTGAACTTGT
*
13144208 TTCAATGAGTTTTGAACTT
1 TTGAATGA-TTTTGAACTT
13144227 AATTTATTAA
Statistics
Matches: 31, Mismatches: 7, Indels: 4
0.74 0.17 0.10
Matches are distributed among these distances:
20 1 0.03
21 28 0.90
22 2 0.06
ACGTcount: A:0.21, C:0.08, G:0.21, T:0.49
Consensus pattern (20 bp):
TTGAATGATTTTGAACTTGT
Found at i:13144334 original size:21 final size:21
Alignment explanation
Indices: 13144310--13144386 Score: 100
Period size: 21 Copynumber: 3.6 Consensus size: 21
13144300 AAATTGCTTG
*
13144310 AATGATCTTTGAACTTGTTTC
1 AATGATTTTTGAACTTGTTTC
*
13144331 AATGATTTTTGAAGTTGTTTC
1 AATGATTTTTGAACTTGTTTC
*
13144352 AATGAGTTTTTGAACTTGTTTA
1 AATGA-TTTTTGAACTTGTTTC
* *
13144374 AATTAGTTTTGAA
1 AATGATTTTTGAA
13144387 GTGCCTAAGT
Statistics
Matches: 49, Mismatches: 6, Indels: 2
0.86 0.11 0.04
Matches are distributed among these distances:
21 31 0.63
22 18 0.37
ACGTcount: A:0.27, C:0.06, G:0.17, T:0.49
Consensus pattern (21 bp):
AATGATTTTTGAACTTGTTTC
Found at i:13144364 original size:22 final size:22
Alignment explanation
Indices: 13144317--13144383 Score: 100
Period size: 22 Copynumber: 3.1 Consensus size: 22
13144307 TTGAATGATC
13144317 TTTGAACTTGTTTCAATGA-TT
1 TTTGAACTTGTTTCAATGAGTT
*
13144338 TTTGAAGTTGTTTCAATGAGTT
1 TTTGAACTTGTTTCAATGAGTT
* *
13144360 TTTGAACTTGTTTAAATTAGTT
1 TTTGAACTTGTTTCAATGAGTT
13144382 TT
1 TT
13144384 GAAGTGCCTA
Statistics
Matches: 41, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
21 18 0.44
22 23 0.56
ACGTcount: A:0.24, C:0.06, G:0.16, T:0.54
Consensus pattern (22 bp):
TTTGAACTTGTTTCAATGAGTT
Found at i:13144459 original size:118 final size:118
Alignment explanation
Indices: 13144261--13144492 Score: 281
Period size: 118 Copynumber: 2.0 Consensus size: 118
13144251 ATACATTTGC
* * *
13144261 TTTTGAACTACCTAAGTGTTTCTATGTAAAAAAGGATCAAAATTGCTTGAATGATCTTTGAACTT
1 TTTTGAACTACCTAAGTGTTTCCATGTAAAAAAGGATCAAAATTGCTTAAATGATCTTTGAAATT
* * * * *
13144326 GTTTCAATGATTTTTGAAGTTGTTT-CAATGAGTTTTTGAACTTGTTTAAATTAG
66 GATTCAATAAGTTTTGAACTTGTTTGCAA--AGTTTTTAAACTTGTTTAAATTAG
* * ** *
13144380 TTTTGAAGTGCCTAAGTGTTTCCATGT-AAAAAGTTTGAAAATTGCTTAAATGAGT-TTTGAAAT
1 TTTTGAACTACCTAAGTGTTTCCATGTAAAAAAGGATCAAAATTGCTTAAATGA-TCTTTGAAAT
* *
13144443 TGATTGAATAAGTTTTGAACTTGTTTGTAAAGTTTTTAAACTTGTTTAAA
65 TGATTCAATAAGTTTTGAACTTGTTTGCAAAGTTTTTAAACTTGTTTAAA
13144493 GAAGTTTTAA
Statistics
Matches: 96, Mismatches: 15, Indels: 6
0.82 0.13 0.05
Matches are distributed among these distances:
117 19 0.20
118 50 0.52
119 27 0.28
ACGTcount: A:0.31, C:0.08, G:0.17, T:0.44
Consensus pattern (118 bp):
TTTTGAACTACCTAAGTGTTTCCATGTAAAAAAGGATCAAAATTGCTTAAATGATCTTTGAAATT
GATTCAATAAGTTTTGAACTTGTTTGCAAAGTTTTTAAACTTGTTTAAATTAG
Found at i:13144477 original size:20 final size:21
Alignment explanation
Indices: 13144432--13144500 Score: 68
Period size: 21 Copynumber: 3.3 Consensus size: 21
13144422 TGCTTAAATG
* *
13144432 AGTTTTGAAATTGATTGAATA
1 AGTTTTGAACTTGTTTGAATA
*
13144453 AGTTTTGAACTTGTTTGTA-A
1 AGTTTTGAACTTGTTTGAATA
* * *
13144473 AGTTTTTAAACTTGTTTAAAGA
1 AG-TTTTGAACTTGTTTGAATA
13144495 AGTTTT
1 AGTTTT
13144501 AAACCTTACT
Statistics
Matches: 40, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
20 3 0.08
21 34 0.85
22 3 0.08
ACGTcount: A:0.32, C:0.03, G:0.17, T:0.48
Consensus pattern (21 bp):
AGTTTTGAACTTGTTTGAATA
Found at i:13144500 original size:21 final size:20
Alignment explanation
Indices: 13144406--13144504 Score: 65
Period size: 21 Copynumber: 4.8 Consensus size: 20
13144396 TGTTTCCATG
* * *
13144406 TAAAAAGTTTGAAAATTGCT
1 TAAAAAGTTTTAAACTTGTT
*
13144426 TAAATGAGTTTTGAAA-TTGATT
1 TAAA-AAGTTTT-AAACTTG-TT
* * *
13144448 GAATAAGTTTTGAACTTGTT
1 TAAAAAGTTTTAAACTTGTT
**
13144468 TGTAAAGTTTTTAAACTTGTT
1 TAAAAAG-TTTTAAACTTGTT
13144489 TAAAGAAGTTTTAAAC
1 TAAA-AAGTTTTAAAC
13144505 CTTACTTGCA
Statistics
Matches: 59, Mismatches: 14, Indels: 11
0.70 0.17 0.13
Matches are distributed among these distances:
20 11 0.19
21 39 0.66
22 9 0.15
ACGTcount: A:0.37, C:0.04, G:0.16, T:0.42
Consensus pattern (20 bp):
TAAAAAGTTTTAAACTTGTT
Found at i:13146120 original size:19 final size:19
Alignment explanation
Indices: 13146096--13146146 Score: 54
Period size: 18 Copynumber: 2.8 Consensus size: 19
13146086 ATTTCATTCA
13146096 AAAATATAAAAAAATAAAT
1 AAAATATAAAAAAATAAAT
*
13146115 AAAATA-AAAAATAA-CAAT
1 AAAATATAAAAA-AATAAAT
*
13146133 -AAATATTAAAAAAT
1 AAAATATAAAAAAAT
13146147 GAAGAAAAAG
Statistics
Matches: 27, Mismatches: 2, Indels: 7
0.75 0.06 0.19
Matches are distributed among these distances:
17 7 0.26
18 12 0.44
19 8 0.30
ACGTcount: A:0.76, C:0.02, G:0.00, T:0.22
Consensus pattern (19 bp):
AAAATATAAAAAAATAAAT
Found at i:13149910 original size:3 final size:3
Alignment explanation
Indices: 13149902--13149936 Score: 70
Period size: 3 Copynumber: 11.7 Consensus size: 3
13149892 TTTTATACAT
13149902 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA AT
13149937 TGACTGCCAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
ATA
Found at i:13152448 original size:65 final size:66
Alignment explanation
Indices: 13152365--13152494 Score: 172
Period size: 66 Copynumber: 2.0 Consensus size: 66
13152355 TTTTTAGTTG
* * **
13152365 ATTTTTTGTTAAGATTTTTGAGTTTAAGGACTCTATTACCCTAATGCCTTT-TGAAAGGTTTAAA
1 ATTTTTTGGTAAGATTTTTGAGTTCAAGGAAGCTATTACCCTAATG-CTTTCTGAAAGGTTTAAA
13152429 TT
65 TT
* * * *
13152431 ATTTTTTGGTGAGTTTTTTGAGTTCAAGGAAGCTATTACCTTAATGCTTTCTGAAGGGTTTAAA
1 ATTTTTTGGTAAGATTTTTGAGTTCAAGGAAGCTATTACCCTAATGCTTTCTGAAAGGTTTAAA
13152495 AGGCAACTTG
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
65 4 0.07
66 51 0.93
ACGTcount: A:0.26, C:0.10, G:0.18, T:0.45
Consensus pattern (66 bp):
ATTTTTTGGTAAGATTTTTGAGTTCAAGGAAGCTATTACCCTAATGCTTTCTGAAAGGTTTAAAT
T
Found at i:13169083 original size:36 final size:36
Alignment explanation
Indices: 13169043--13169133 Score: 101
Period size: 36 Copynumber: 2.5 Consensus size: 36
13169033 AGGTTATGCC
* * *
13169043 TGATCTTGTGAAAAGGCATGTTATGAAGGTTACACT
1 TGATCTTATGAAAAGGCATGTTATAAAAGTTACACT
* * *
13169079 TGATCTTATTAAAAGGCTTGTTGTAAAAGTTACACT
1 TGATCTTATGAAAAGGCATGTTATAAAAGTTACACT
* *
13169115 TGACCATATTGAAAAGGCA
1 TGATCTTA-TGAAAAGGCA
13169134 AGTTGATAGT
Statistics
Matches: 44, Mismatches: 10, Indels: 1
0.80 0.18 0.02
Matches are distributed among these distances:
36 36 0.82
37 8 0.18
ACGTcount: A:0.34, C:0.12, G:0.21, T:0.33
Consensus pattern (36 bp):
TGATCTTATGAAAAGGCATGTTATAAAAGTTACACT
Found at i:13174704 original size:20 final size:20
Alignment explanation
Indices: 13174679--13174721 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
13174669 ACATGTATCA
*
13174679 ATACATTTGTCCAATTATTG
1 ATACATTTGTCCAAGTATTG
*
13174699 ATACATTTGTCTAAGTATTG
1 ATACATTTGTCCAAGTATTG
13174719 ATA
1 ATA
13174722 AAAATGGAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.33, C:0.12, G:0.12, T:0.44
Consensus pattern (20 bp):
ATACATTTGTCCAAGTATTG
Found at i:13177164 original size:2 final size:2
Alignment explanation
Indices: 13177157--13177197 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
13177147 GTGTAAACCC
13177157 TA TA TA TA TA TA TA TA TA TA TA TA TA TA T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
13177198 AAGAGGGATC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:13179957 original size:1 final size:1
Alignment explanation
Indices: 13179951--13180006 Score: 103
Period size: 1 Copynumber: 56.0 Consensus size: 1
13179941 AATAAGAAGA
*
13179951 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGTGGGGGGGGGG
1 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG
13180007 TTTGGGTTCT
Statistics
Matches: 53, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
1 53 1.00
ACGTcount: A:0.00, C:0.00, G:0.98, T:0.02
Consensus pattern (1 bp):
G
Found at i:13182708 original size:31 final size:31
Alignment explanation
Indices: 13182670--13182904 Score: 163
Period size: 31 Copynumber: 7.6 Consensus size: 31
13182660 AGGCTTCAAA
* *
13182670 ATCTTAAGAATTCCTCCACCGAGAATCTTAT
1 ATCTTAAGAATTCCTCCACCGAGGATCTAAT
* ** *
13182701 ATCTTAAGAATTCCTCGACTAAGGTTCTAAT
1 ATCTTAAGAATTCCTCCACCGAGGATCTAAT
* * * *
13182732 ATTTTAAGAACTCCTTCACC-AAGATTCTAAT
1 ATCTTAAGAATTCCTCCACCGAGGA-TCTAAT
* ** * *
13182763 AGCTTAAGAATTCCAT-CATTGAGAATTTAAT
1 ATCTTAAGAATTCC-TCCACCGAGGATCTAAT
* * * *
13182794 ATCTTAAGAA-TCCTTTCATCGAGGGTCCAAT
1 ATCTTAAGAATTCC-TCCACCGAGGATCTAAT
* * * ** *
13182825 ATCTTAAGTATCCCTCTACTAAGGATCCAAT
1 ATCTTAAGAATTCCTCCACCGAGGATCTAAT
* *
13182856 GTCTTAAGAATTACTCC-CTCGAGGATCTAAT
1 ATCTTAAGAATTCCTCCAC-CGAGGATCTAAT
13182887 ATCTTAAGAATTCCTCCA
1 ATCTTAAGAATTCCTCCA
13182905 TCGGGCTTTC
Statistics
Matches: 151, Mismatches: 46, Indels: 13
0.72 0.22 0.06
Matches are distributed among these distances:
30 7 0.05
31 139 0.92
32 5 0.03
ACGTcount: A:0.33, C:0.22, G:0.11, T:0.34
Consensus pattern (31 bp):
ATCTTAAGAATTCCTCCACCGAGGATCTAAT
Found at i:13182919 original size:31 final size:32
Alignment explanation
Indices: 13182665--13182935 Score: 136
Period size: 31 Copynumber: 8.7 Consensus size: 32
13182655 GGAGGAGGCT
* * *
13182665 TCAAAATCTTAAGAATTCCTCCACCGAGAATC
1 TCAATATCTTAAGAATTCCTCCATCGAGGATC
* * * *
13182697 T-TATATCTTAAGAATTCCTCGA-CTAAGGTTC
1 TCAATATCTTAAGAATTCCTCCATC-GAGGATC
* * * * *
13182728 T-AATATTTTAAGAACTCCTTCA-CCAAGAT-
1 TCAATATCTTAAGAATTCCTCCATCGAGGATC
* * *
13182757 TCTAATAGCTTAAGAATTCCAT-CATTGAGAAT-
1 TC-AATATCTTAAGAATTCC-TCCATCGAGGATC
* * *
13182789 TTAATATCTTAAGAA-TCCTTTCATCGAGGGTC
1 TCAATATCTTAAGAATTCC-TCCATCGAGGATC
* * * *
13182821 -CAATATCTTAAGTATCCCTCTA-CTAAGGATC
1 TCAATATCTTAAGAATTCCTCCATC-GAGGATC
* * *
13182852 -CAATGTCTTAAGAATTACTCCCTCGAGGATC
1 TCAATATCTTAAGAATTCCTCCATCGAGGATC
* *
13182883 T-AATATCTTAAGAATTCCTCCATCG-GGCTT
1 TCAATATCTTAAGAATTCCTCCATCGAGGATC
* * *
13182913 TCAATATCTAAAGGATTCTTCCA
1 TCAATATCTTAAGAATTCCTCCA
13182936 CCCAGGTTCC
Statistics
Matches: 178, Mismatches: 49, Indels: 25
0.71 0.19 0.10
Matches are distributed among these distances:
29 1 0.01
30 13 0.07
31 155 0.87
32 9 0.05
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (32 bp):
TCAATATCTTAAGAATTCCTCCATCGAGGATC
Found at i:13182975 original size:32 final size:33
Alignment explanation
Indices: 13182932--13183000 Score: 104
Period size: 32 Copynumber: 2.1 Consensus size: 33
13182922 AAAGGATTCT
* *
13182932 TCCACCCAGGTTCCAAACTTCAAA-AGAACTCC
1 TCCACCAAGGTTCCAAACTTCAAATAAAACTCC
*
13182964 TCCACCAAGGTTCCAAACTTTAAATAAAACTCC
1 TCCACCAAGGTTCCAAACTTCAAATAAAACTCC
13182997 TCCA
1 TCCA
13183001 TCGAGGCCTC
Statistics
Matches: 33, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
32 22 0.67
33 11 0.33
ACGTcount: A:0.36, C:0.35, G:0.07, T:0.22
Consensus pattern (33 bp):
TCCACCAAGGTTCCAAACTTCAAATAAAACTCC
Found at i:13186007 original size:20 final size:20
Alignment explanation
Indices: 13185984--13186041 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
13185974 TCATCTATGG
*
13185984 ATAGATGGACAAGTCTATCC
1 ATAGATGGACAAATCTATCC
* *
13186004 ATAGATGGCCAAATCTATCG
1 ATAGATGGACAAATCTATCC
* * *
13186024 ATAAATGGTCACATCTAT
1 ATAGATGGACAAATCTAT
13186042 TAATAGATAG
Statistics
Matches: 32, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 32 1.00
ACGTcount: A:0.36, C:0.19, G:0.17, T:0.28
Consensus pattern (20 bp):
ATAGATGGACAAATCTATCC
Found at i:13193522 original size:16 final size:15
Alignment explanation
Indices: 13193483--13193522 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 15
13193473 TTATAAAACC
13193483 TTAATTAAAACTAAA
1 TTAATTAAAACTAAA
*
13193498 TTATCTTAAACACTAAA
1 TTA-ATTAAA-ACTAAA
13193515 TTAATTAA
1 TTAATTAA
13193523 CAAAAACTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 3
0.81 0.08 0.12
Matches are distributed among these distances:
15 3 0.14
16 9 0.43
17 9 0.43
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.38
Consensus pattern (15 bp):
TTAATTAAAACTAAA
Found at i:13196325 original size:17 final size:17
Alignment explanation
Indices: 13196305--13196337 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
13196295 ACTAACTTAA
13196305 AAATTA-AAAACATAAAG
1 AAATTAGAAAAC-TAAAG
13196322 AAATTAGAAAACTAAA
1 AAATTAGAAAACTAAA
13196338 AATCACCCCC
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.70, C:0.06, G:0.06, T:0.18
Consensus pattern (17 bp):
AAATTAGAAAACTAAAG
Found at i:13198252 original size:20 final size:21
Alignment explanation
Indices: 13198229--13198277 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
13198219 ATAAAACATC
*
13198229 AAATGAAAAAT-AAAAATTTT
1 AAATGAAAAATCAAAAATTCT
* *
13198249 AAATAAAAAATCAAATATTCT
1 AAATGAAAAATCAAAAATTCT
13198270 AAATGAAA
1 AAATGAAA
13198278 TAAACACAAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 10 0.42
21 14 0.58
ACGTcount: A:0.65, C:0.04, G:0.04, T:0.27
Consensus pattern (21 bp):
AAATGAAAAATCAAAAATTCT
Found at i:13214862 original size:65 final size:63
Alignment explanation
Indices: 13214785--13214917 Score: 149
Period size: 63 Copynumber: 2.1 Consensus size: 63
13214775 TAGTGAGCTT
* * * * * * *
13214785 TTAACTGGTTAACTATTGATTTTAGTTGATTAAGTCTTCTTTGTCTTGCAATCTACTTCATTGTG
1 TTAACTAGTTAACTATGGATTTTACTCGA-T-AGCCTTCATTGTCTTGCAATCTACTTCACTGTG
* * * *
13214850 TTAACTAGTTAACTATGGGTTTTACTCGATAGCCTTCATTGTCTTGTAGTCTGCTTCACTGTG
1 TTAACTAGTTAACTATGGATTTTACTCGATAGCCTTCATTGTCTTGCAATCTACTTCACTGTG
13214913 TTAAC
1 TTAAC
13214918 CGACTAAGAA
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
63 32 0.56
64 1 0.02
65 24 0.42
ACGTcount: A:0.21, C:0.17, G:0.17, T:0.46
Consensus pattern (63 bp):
TTAACTAGTTAACTATGGATTTTACTCGATAGCCTTCATTGTCTTGCAATCTACTTCACTGTG
Found at i:13216358 original size:29 final size:29
Alignment explanation
Indices: 13216325--13216384 Score: 120
Period size: 29 Copynumber: 2.1 Consensus size: 29
13216315 AATAGATTGA
13216325 TTAAGTTATTAGAAGAATTGATTTAAAGT
1 TTAAGTTATTAGAAGAATTGATTTAAAGT
13216354 TTAAGTTATTAGAAGAATTGATTTAAAGT
1 TTAAGTTATTAGAAGAATTGATTTAAAGT
13216383 TT
1 TT
13216385 GATGTATATG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 31 1.00
ACGTcount: A:0.40, C:0.00, G:0.17, T:0.43
Consensus pattern (29 bp):
TTAAGTTATTAGAAGAATTGATTTAAAGT
Found at i:13221522 original size:8 final size:8
Alignment explanation
Indices: 13221509--13221538 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
13221499 TGATAATGCA
13221509 ATATATAC
1 ATATATAC
*
13221517 ATATATAT
1 ATATATAC
13221525 ATATATAC
1 ATATATAC
13221533 ATATAT
1 ATATAT
13221539 CTATATGTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
8 20 1.00
ACGTcount: A:0.50, C:0.07, G:0.00, T:0.43
Consensus pattern (8 bp):
ATATATAC
Found at i:13221530 original size:16 final size:16
Alignment explanation
Indices: 13221509--13221544 Score: 63
Period size: 16 Copynumber: 2.2 Consensus size: 16
13221499 TGATAATGCA
13221509 ATATATACATATATAT
1 ATATATACATATATAT
*
13221525 ATATATACATATATCT
1 ATATATACATATATAT
13221541 ATAT
1 ATAT
13221545 GTTTATGGGC
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 19 1.00
ACGTcount: A:0.47, C:0.08, G:0.00, T:0.44
Consensus pattern (16 bp):
ATATATACATATATAT
Found at i:13224239 original size:30 final size:30
Alignment explanation
Indices: 13224151--13224315 Score: 130
Period size: 30 Copynumber: 5.6 Consensus size: 30
13224141 TTAAGACAAC
*
13224151 TCTTGTCTTTAATTAAGAC-AAAAATATTTT
1 TCTTGTC-TAAATTAAGACAAAAAATATTTT
* *
13224181 ATTTTGTCTAAATTGAGAC-----ATATGTTT
1 -TCTTGTCTAAATTAAGACAAAAAATAT-TTT
* *
13224208 TCTTTTCTAGATTAAGACAAAAAATATTTT
1 TCTTGTCTAAATTAAGACAAAAAATATTTT
** *
13224238 TCTTGTCTTAAATTAAG-GTAAACATATTTT
1 TCTTGTC-TAAATTAAGACAAAAAATATTTT
* ** *
13224268 TCTTGTCTAAATTAAGACTAATCAT-TATT
1 TCTTGTCTAAATTAAGACAAAAAATATTTT
13224297 TCTTGTCTAAATTAAGACA
1 TCTTGTCTAAATTAAGACA
13224316 TACTTGTCTT
Statistics
Matches: 110, Mismatches: 16, Indels: 18
0.76 0.11 0.12
Matches are distributed among these distances:
26 18 0.16
27 3 0.03
29 30 0.27
30 41 0.37
31 18 0.16
ACGTcount: A:0.35, C:0.11, G:0.09, T:0.45
Consensus pattern (30 bp):
TCTTGTCTAAATTAAGACAAAAAATATTTT
Found at i:13224279 original size:29 final size:30
Alignment explanation
Indices: 13224198--13224340 Score: 141
Period size: 29 Copynumber: 4.8 Consensus size: 30
13224188 CTAAATTGAG
* * *
13224198 ACATATGTTTTCTTTTCTAGATTAAGACAAA
1 ACATAT-TTTTCTTGTCTAAATTAAGACTAA
* *
13224229 AAATATTTTTCTTGTCTTAAATTAAG-GTAA
1 ACATATTTTTCTTGTC-TAAATTAAGACTAA
13224259 ACATATTTTTCTTGTCTAAATTAAGACTAA
1 ACATATTTTTCTTGTCTAAATTAAGACTAA
* * *
13224289 TCAT-TATTTCTTGTCTAAATTAAGAC-AT
1 ACATATTTTTCTTGTCTAAATTAAGACTAA
* * *
13224317 ACTTGTCTTT-TTGTCTAAATTAAG
1 ACATATTTTTCTTGTCTAAATTAAG
13224341 GCATAGCATG
Statistics
Matches: 96, Mismatches: 13, Indels: 9
0.81 0.11 0.08
Matches are distributed among these distances:
28 17 0.18
29 34 0.35
30 32 0.33
31 13 0.14
ACGTcount: A:0.34, C:0.12, G:0.09, T:0.45
Consensus pattern (30 bp):
ACATATTTTTCTTGTCTAAATTAAGACTAA
Found at i:13224361 original size:28 final size:27
Alignment explanation
Indices: 13224266--13224379 Score: 106
Period size: 28 Copynumber: 4.1 Consensus size: 27
13224256 TAAACATATT
*
13224266 TTTCTTGTCTAAATTAAGAC-TAATCATTA
1 TTTCTTGTCTAAATTAAGACAT-A-CA-TG
*
13224295 TTTCTTGTCTAAATTAAGACATACTTG
1 TTTCTTGTCTAAATTAAGACATACATG
* *
13224322 TCTTTTTGTCTAAATTAAGGCATAGCATG
1 T-TTCTTGTCTAAATTAAGACATA-CATG
* *
13224351 TTTCTTATCTAACA-TAAGACAAACATG
1 TTTCTTGTCTAA-ATTAAGACATACATG
13224378 TT
1 TT
13224380 AAAGCTATTA
Statistics
Matches: 72, Mismatches: 9, Indels: 10
0.79 0.10 0.11
Matches are distributed among these distances:
27 8 0.11
28 37 0.51
29 26 0.36
30 1 0.01
ACGTcount: A:0.32, C:0.15, G:0.11, T:0.42
Consensus pattern (27 bp):
TTTCTTGTCTAAATTAAGACATACATG
Found at i:13231711 original size:25 final size:25
Alignment explanation
Indices: 13231683--13231734 Score: 68
Period size: 25 Copynumber: 2.1 Consensus size: 25
13231673 TAATGCATAT
* * *
13231683 CAACTCGTGGCCTTGCCACGTATAA
1 CAACCCGTAGCCTAGCCACGTATAA
*
13231708 CAACCCGTAGCCTAGCCACGTCTAA
1 CAACCCGTAGCCTAGCCACGTATAA
13231733 CA
1 CA
13231735 GTCTATTGGT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.27, C:0.37, G:0.17, T:0.19
Consensus pattern (25 bp):
CAACCCGTAGCCTAGCCACGTATAA
Found at i:13233821 original size:35 final size:34
Alignment explanation
Indices: 13233782--13233890 Score: 107
Period size: 35 Copynumber: 3.2 Consensus size: 34
13233772 TTACAATAGC
*
13233782 TTTTCACAAGCTCAGCCACAACCTTTAACAATGGT
1 TTTTCA-AAGCTCAACCACAACCTTTAACAATGGT
* * * * *
13233817 TTTTCATGAGATCAACCAAAAAC--TAA-AATAGT
1 TTTTCA-AAGCTCAACCACAACCTTTAACAATGGT
*
13233849 TTTTTAAAGGCTCAACCACAACCTTTAACAATGGT
1 TTTTCAAA-GCTCAACCACAACCTTTAACAATGGT
13233884 TTTTCAA
1 TTTTCAA
13233891 GGGATCAACC
Statistics
Matches: 56, Mismatches: 14, Indels: 8
0.72 0.18 0.10
Matches are distributed among these distances:
31 1 0.02
32 21 0.38
33 3 0.05
34 3 0.05
35 28 0.50
ACGTcount: A:0.37, C:0.22, G:0.10, T:0.31
Consensus pattern (34 bp):
TTTTCAAAGCTCAACCACAACCTTTAACAATGGT
Found at i:13233899 original size:35 final size:35
Alignment explanation
Indices: 13233801--13233906 Score: 119
Period size: 35 Copynumber: 3.1 Consensus size: 35
13233791 GCTCAGCCAC
* *
13233801 AACCTTTAACAATGGTTTTTCATGAGATCAACCAA
1 AACCTTTAACAATGGTTTTTCAAGGGATCAACCAA
* * * * * *
13233836 AAAC--TAA-AATAGTTTTTTAAAGGCTCAACCAC
1 AACCTTTAACAATGGTTTTTCAAGGGATCAACCAA
13233868 AACCTTTAACAATGGTTTTTCAAGGGATCAACCAA
1 AACCTTTAACAATGGTTTTTCAAGGGATCAACCAA
13233903 AACC
1 AACC
13233907 CAAAATCTAA
Statistics
Matches: 54, Mismatches: 14, Indels: 6
0.73 0.19 0.08
Matches are distributed among these distances:
32 21 0.39
33 3 0.06
34 3 0.06
35 27 0.50
ACGTcount: A:0.40, C:0.21, G:0.11, T:0.28
Consensus pattern (35 bp):
AACCTTTAACAATGGTTTTTCAAGGGATCAACCAA
Found at i:13234415 original size:73 final size:73
Alignment explanation
Indices: 13234322--13234513 Score: 228
Period size: 73 Copynumber: 2.6 Consensus size: 73
13234312 GACAGAGTGC
* * ** ** *
13234322 TCTTAGTTGCCTAACATGCTTCTTAGTCG-TGTAAGTTGTCTCTGTCTTGTAAT-TGAAGTTTTT
1 TCTTAGTTGACTAATATGCTTCTTAGTCGAT-TAAGTTGTCTCTGTCTTAAAATCCCAA-TTTCT
*
13234385 GGCAGTAAGT
64 GGCAGTAAGG
* *
13234395 TCTTAGTTAACTAATATGCTTCTTAGTCGATTAAGTTGTCTTTGTCTTAAAATCCCAATTTCTGG
1 TCTTAGTTGACTAATATGCTTCTTAGTCGATTAAGTTGTCTCTGTCTTAAAATCCCAATTTCTGG
*
13234460 CAGTGAGG
66 CAGTAAGG
13234468 TCTTAGTTGACTAATCATGCTTCTTAGTCGATTAAGTCT-TCTCTGT
1 TCTTAGTTGACTAAT-ATGCTTCTTAGTCGATTAAGT-TGTCTCTGT
13234514 TTTTGAACCG
Statistics
Matches: 102, Mismatches: 13, Indels: 7
0.84 0.11 0.06
Matches are distributed among these distances:
73 71 0.70
74 30 0.29
75 1 0.01
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.43
Consensus pattern (73 bp):
TCTTAGTTGACTAATATGCTTCTTAGTCGATTAAGTTGTCTCTGTCTTAAAATCCCAATTTCTGG
CAGTAAGG
Found at i:13239599 original size:57 final size:57
Alignment explanation
Indices: 13239511--13239624 Score: 183
Period size: 57 Copynumber: 2.0 Consensus size: 57
13239501 CATGAAAGAA
* *
13239511 AACCTCTATCACATATATTTATATGATTAAATATGCATTAAATAACAATATATATTC
1 AACCTCTATCACATATAGTTATACGATTAAATATGCATTAAATAACAATATATATTC
* * *
13239568 AACCTCTATCACATATAGTTATGCGATTAAATATGTATTAAGTAACAATATATATTC
1 AACCTCTATCACATATAGTTATACGATTAAATATGCATTAAATAACAATATATATTC
13239625 CTTGACCAAT
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
57 52 1.00
ACGTcount: A:0.42, C:0.14, G:0.06, T:0.38
Consensus pattern (57 bp):
AACCTCTATCACATATAGTTATACGATTAAATATGCATTAAATAACAATATATATTC
Found at i:13240485 original size:54 final size:55
Alignment explanation
Indices: 13240414--13240611 Score: 225
Period size: 54 Copynumber: 3.7 Consensus size: 55
13240404 ATTTTGGTGA
*
13240414 AAATTTCCAAC-GAAATTCCAT-GAGAAATG-TTTTTCCAATGAAAACTTCCGTTAG
1 AAATTTGCAACTG-AATTCCATGGA-AAATGCTTTTTCCAATGAAAACTTCCGTTAG
* *
13240468 AAATTTGCAACTGAATTCCATGGAAAATGCTTTTTCAACAA--AAAAATT--GTTGG
1 AAATTTGCAACTGAATTCCATGGAAAATGCTTTTTC--CAATGAAAACTTCCGTTAG
* **
13240521 AAATTTCTCAACAAAATTCCATTGG-AAATGC-TTTTCCAATGAAAACTTCCGTTAG
1 AAATTT-GCAACTGAATTCCA-TGGAAAATGCTTTTTCCAATGAAAACTTCCGTTAG
13240576 AAATTTGCAACTGAATTCCATGGAAAATGCTTTTTC
1 AAATTTGCAACTGAATTCCATGGAAAATGCTTTTTC
13240612 AACAAAAAAA
Statistics
Matches: 120, Mismatches: 11, Indels: 25
0.77 0.07 0.16
Matches are distributed among these distances:
51 3 0.03
53 24 0.20
54 57 0.47
55 33 0.28
57 3 0.03
ACGTcount: A:0.37, C:0.17, G:0.13, T:0.33
Consensus pattern (55 bp):
AAATTTGCAACTGAATTCCATGGAAAATGCTTTTTCCAATGAAAACTTCCGTTAG
Found at i:13240615 original size:108 final size:108
Alignment explanation
Indices: 13240414--13240645 Score: 423
Period size: 108 Copynumber: 2.2 Consensus size: 108
13240404 ATTTTGGTGA
* *
13240414 AAATTTC-CAACGAAATTCCATGAGAAATGTTTTTCCAATGAAAACTTCCGTTAGAAATTTGCAA
1 AAATTTCTCAACAAAATTCCATGAGAAATGCTTTTCCAATGAAAACTTCCGTTAGAAATTTGCAA
13240478 CTGAATTCCATGGAAAATGCTTTTTCAACAAAAAAATTGTTGG
66 CTGAATTCCATGGAAAATGCTTTTTCAACAAAAAAATTGTTGG
13240521 AAATTTCTCAACAAAATTCCATTG-GAAATGCTTTTCCAATGAAAACTTCCGTTAGAAATTTGCA
1 AAATTTCTCAACAAAATTCCA-TGAGAAATGCTTTTCCAATGAAAACTTCCGTTAGAAATTTGCA
13240585 ACTGAATTCCATGGAAAATGCTTTTTCAACAAAAAAATTGTTGG
65 ACTGAATTCCATGGAAAATGCTTTTTCAACAAAAAAATTGTTGG
13240629 AAATTTCTCAACAAAAT
1 AAATTTCTCAACAAAAT
13240646 GCTTTTCCAA
Statistics
Matches: 121, Mismatches: 2, Indels: 3
0.96 0.02 0.02
Matches are distributed among these distances:
107 7 0.06
108 112 0.93
109 2 0.02
ACGTcount: A:0.39, C:0.16, G:0.12, T:0.32
Consensus pattern (108 bp):
AAATTTCTCAACAAAATTCCATGAGAAATGCTTTTCCAATGAAAACTTCCGTTAGAAATTTGCAA
CTGAATTCCATGGAAAATGCTTTTTCAACAAAAAAATTGTTGG
Found at i:13242746 original size:75 final size:75
Alignment explanation
Indices: 13242598--13242746 Score: 199
Period size: 75 Copynumber: 2.0 Consensus size: 75
13242588 TCTACCCTTT
* * * * *
13242598 GGTGGAGTTGGGGGGATGGGTGGGATTACTCCCATCGGTGGTGGAGGTGGTTTAGGTGGTCTAGG
1 GGTGGAGTTGGGGGGATGGGTGGGATTACTCCCATAGGTGGCGGAGATGGTCTAGGTGGACTAGG
*
13242663 TGGACTTGGA
66 AGGACTTGGA
* ** *
13242673 GGTGGAGTTGGGGGGATTGGTGGGATTACTCCTTTAGGTGGCGGAGATGGTCTAGGTGGACTCGG
1 GGTGGAGTTGGGGGGATGGGTGGGATTACTCCCATAGGTGGCGGAGATGGTCTAGGTGGACTAGG
*
13242738 AGGGCTTGG
66 AGGACTTGG
13242747 GGGATTTGGT
Statistics
Matches: 63, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
75 63 1.00
ACGTcount: A:0.13, C:0.10, G:0.49, T:0.28
Consensus pattern (75 bp):
GGTGGAGTTGGGGGGATGGGTGGGATTACTCCCATAGGTGGCGGAGATGGTCTAGGTGGACTAGG
AGGACTTGGA
Found at i:13242793 original size:12 final size:12
Alignment explanation
Indices: 13242778--13242832 Score: 65
Period size: 12 Copynumber: 4.6 Consensus size: 12
13242768 TGGTACTGGT
13242778 GGTGGAGTTGGA
1 GGTGGAGTTGGA
** *
13242790 GGTGCCGTTGGT
1 GGTGGAGTTGGA
13242802 GGTGGAGTTGGA
1 GGTGGAGTTGGA
* *
13242814 GTTGGAGGTGGA
1 GGTGGAGTTGGA
13242826 GGTGGAG
1 GGTGGAG
13242833 CTGGTGCTGG
Statistics
Matches: 34, Mismatches: 9, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
12 34 1.00
ACGTcount: A:0.13, C:0.04, G:0.58, T:0.25
Consensus pattern (12 bp):
GGTGGAGTTGGA
Found at i:13242817 original size:18 final size:18
Alignment explanation
Indices: 13242796--13242848 Score: 61
Period size: 18 Copynumber: 2.9 Consensus size: 18
13242786 TGGAGGTGCC
13242796 GTTGGTGGTGGAGTTGGA
1 GTTGGTGGTGGAGTTGGA
* *
13242814 GTTGGAGGTGGAGGTGGA
1 GTTGGTGGTGGAGTTGGA
* * *
13242832 GCTGGTGCTGGTGTTGG
1 GTTGGTGGTGGAGTTGG
13242849 CGGTACTGGT
Statistics
Matches: 28, Mismatches: 7, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
18 28 1.00
ACGTcount: A:0.09, C:0.04, G:0.57, T:0.30
Consensus pattern (18 bp):
GTTGGTGGTGGAGTTGGA
Found at i:13246173 original size:28 final size:28
Alignment explanation
Indices: 13246141--13246194 Score: 90
Period size: 28 Copynumber: 1.9 Consensus size: 28
13246131 ATAGAAGTAA
*
13246141 ATATTCCTCCACCAATTGAACTAATGTG
1 ATATTCCTACACCAATTGAACTAATGTG
*
13246169 ATATTTCTACACCAATTGAACTAATG
1 ATATTCCTACACCAATTGAACTAATG
13246195 GAGGAGCAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 24 1.00
ACGTcount: A:0.35, C:0.22, G:0.09, T:0.33
Consensus pattern (28 bp):
ATATTCCTACACCAATTGAACTAATGTG
Found at i:13247267 original size:39 final size:39
Alignment explanation
Indices: 13247182--13247384 Score: 196
Period size: 39 Copynumber: 5.2 Consensus size: 39
13247172 TAAATACAAG
* * * *
13247182 TGTTCATAATCGAATTTGAGTACTTT-AATTGAAAATGAA
1 TGTTTATAATCAAATCTGAGTA-TTTCAAATGAAAATGAA
* *
13247221 T-TATTATAATCAAATTTGAGTATTTCAAATGAAGATGAA
1 TGT-TTATAATCAAATCTGAGTATTTCAAATGAAAATGAA
* * * *
13247260 GGTTTATAATCAAATCCGAGTATTTCATATAAAAATGAA
1 TGTTTATAATCAAATCTGAGTATTTCAAATGAAAATGAA
* * **
13247299 TGTTTATAATCAAATCCGAGTATGTCAAAT-AAAAACAA
1 TGTTTATAATCAAATCTGAGTATTTCAAATGAAAATGAA
* * * * *
13247337 TGTGTATAATCAAATATGAGTATTTCAATTAAAAACGAA
1 TGTTTATAATCAAATCTGAGTATTTCAAATGAAAATGAA
13247376 TGTTTATAA
1 TGTTTATAA
13247385 AGCTTAGTAG
Statistics
Matches: 137, Mismatches: 23, Indels: 8
0.82 0.14 0.05
Matches are distributed among these distances:
38 35 0.26
39 101 0.74
40 1 0.01
ACGTcount: A:0.43, C:0.08, G:0.13, T:0.35
Consensus pattern (39 bp):
TGTTTATAATCAAATCTGAGTATTTCAAATGAAAATGAA
Found at i:13247348 original size:38 final size:38
Alignment explanation
Indices: 13247149--13247384 Score: 179
Period size: 39 Copynumber: 6.1 Consensus size: 38
13247139 TCGTGAAATC
* * * * *
13247149 TAATCATATCCAAGTATTCCAAATAAATACAAGTGTTCA
1 TAATCAAATCCGAGTATTTCAAATAAAAACAA-TGTTTA
* ** * **
13247188 TAATCGAATTTGAGTACTTT-AATTGAAAATGAAT-TATTA
1 TAATCAAATCCGAGTA-TTTCAAAT-AAAAACAATGT-TTA
** * ** *
13247227 TAATCAAATTTGAGTATTTCAAATGAAGATGAAGGTTTA
1 TAATCAAATCCGAGTATTTCAAAT-AAAAACAATGTTTA
* *
13247266 TAATCAAATCCGAGTATTTCATATAAAAATGAATGTTTA
1 TAATCAAATCCGAGTATTTCAAATAAAAA-CAATGTTTA
* *
13247305 TAATCAAATCCGAGTATGTCAAATAAAAACAATGTGTA
1 TAATCAAATCCGAGTATTTCAAATAAAAACAATGTTTA
** *
13247343 TAATCAAATATGAGTATTTCAATTAAAAACGAATGTTTA
1 TAATCAAATCCGAGTATTTCAAATAAAAAC-AATGTTTA
13247382 TAA
1 TAA
13247385 AGCTTAGTAG
Statistics
Matches: 160, Mismatches: 30, Indels: 14
0.78 0.15 0.07
Matches are distributed among these distances:
38 40 0.25
39 112 0.70
40 8 0.05
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (38 bp):
TAATCAAATCCGAGTATTTCAAATAAAAACAATGTTTA
Found at i:13247377 original size:77 final size:75
Alignment explanation
Indices: 13247149--13247384 Score: 217
Period size: 78 Copynumber: 3.0 Consensus size: 75
13247139 TCGTGAAATC
* * * * * *
13247149 TAATCATATCCAAGTATTCCAAATAAATACAAGTGTTCATAATCGAATTTGAGTACTTT-AATTG
1 TAATCAAATCCGAGTATT-CAAATAAAAACAAGTG-T-ATAATCAAATATGAGTA-TTTCAATTA
13247213 AAAATGAAT-TATTA
62 AAAATGAATGT-TTA
** * ** * **
13247227 TAATCAAATTTGAGTATTTCAAATGAAGATGAAGGTTTATAATCAAATCCGAGTATTTC-ATATA
1 TAATCAAATCCGAGTA-TTCAAAT-AAAAACAA-GTGTATAATCAAATATGAGTATTTCAAT-TA
13247291 AAAATGAATGTTTA
62 AAAATGAATGTTTA
13247305 TAATCAAATCCGAGTATGTCAAATAAAAACAATGTGTATAATCAAATATGAGTATTTCAATTAAA
1 TAATCAAATCCGAGTAT-TCAAATAAAAACAA-GTGTATAATCAAATATGAGTATTTCAATTAAA
*
13247370 AACGAATGTTTA
64 AATGAATGTTTA
13247382 TAA
1 TAA
13247385 AGCTTAGTAG
Statistics
Matches: 127, Mismatches: 23, Indels: 17
0.76 0.14 0.10
Matches are distributed among these distances:
77 51 0.40
78 66 0.52
79 8 0.06
80 2 0.02
ACGTcount: A:0.44, C:0.10, G:0.12, T:0.34
Consensus pattern (75 bp):
TAATCAAATCCGAGTATTCAAATAAAAACAAGTGTATAATCAAATATGAGTATTTCAATTAAAAA
TGAATGTTTA
Found at i:13247611 original size:21 final size:21
Alignment explanation
Indices: 13247585--13247635 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
13247575 AAGCTTTAAA
*
13247585 TATCGATGCTTTTATTCAAAG
1 TATCGATACTTTTATTCAAAG
* *
13247606 TATCGATACTTTTGTTTAAAG
1 TATCGATACTTTTATTCAAAG
13247627 TATCGATAC
1 TATCGATAC
13247636 GTTTCAACCA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.29, C:0.14, G:0.14, T:0.43
Consensus pattern (21 bp):
TATCGATACTTTTATTCAAAG
Found at i:13250668 original size:64 final size:62
Alignment explanation
Indices: 13250599--13250833 Score: 242
Period size: 64 Copynumber: 3.7 Consensus size: 62
13250589 GTAACCTCGC
* * * *
13250599 CACATAATCATCATCATTGTTGATGGCCTCTCCACATATTCATAATCAACACTAGTGGCTACA
1 CACATAATCAT-ATCAATATTGATGGCCTCACCACATAATCATAATCAACACTAGTGGCTACA
* * *
13250662 CTACATAATCATAGTCAATA-TCAGTGGCCTCACCACATACTCATAATCAACACTAGTGGCAGTG
1 C-ACATAATCATA-TCAATATTGA-TGGCCTCACCACATAATCATAATCAACACTAGTGGC--TA
13250726 C-
61 CA
* * *
13250727 CACATAATCATAACCAATATTGGTGGCCTCACCACATAATCATAATCTACACTAGTGG-TAACA
1 CACATAATCAT-ATCAATATTGATGGCCTCACCACATAATCATAATCAACACTAGTGGCT-ACA
* * *
13250790 CCACATAATCATTATCAATATTGGTGACCTCGCCACATAATCAT
1 -CACATAATCA-TATCAATATTGATGGCCTCACCACATAATCAT
13250834 TGAAGTTATA
Statistics
Matches: 146, Mismatches: 15, Indels: 21
0.80 0.08 0.12
Matches are distributed among these distances:
61 1 0.01
62 1 0.01
63 4 0.03
64 134 0.92
65 4 0.03
66 2 0.01
ACGTcount: A:0.34, C:0.27, G:0.11, T:0.27
Consensus pattern (62 bp):
CACATAATCATATCAATATTGATGGCCTCACCACATAATCATAATCAACACTAGTGGCTACA
Found at i:13250698 original size:128 final size:128
Alignment explanation
Indices: 13250523--13250833 Score: 353
Period size: 128 Copynumber: 2.4 Consensus size: 128
13250513 TCATTAATGT
* * * *
13250523 TAGTGGCAATACCACATAATCCTTATCACTATCAGTGGCCT-AGCCACATAATCATAATCAACA-
1 TAGTGGTAACACCACATAATCATTATCAATATCAGTGGCCTCA-CCACATAATCATAATCAACAC
* * * * * *
13250586 TCAGTAAC-CTCGCCACATAATCATCATCATTGTTGATGGCCTCTCCACATATTCATAATCAACA
65 T-AGTAACACT-GCCACATAATCATAACCAATATTGATGGCCTCACCACATAATCATAATCAACA
13250650 C
128 C
* *
13250651 TAGTGGCT-ACACTACATAATCA-TAGTCAATATCAGTGGCCTCACCACATACTCATAATCAACA
1 TAGTGG-TAACACCACATAATCATTA-TCAATATCAGTGGCCTCACCACATAATCATAATCAACA
** * * *
13250714 CTAGTGGCAGTGCCACATAATCATAACCAATATTGGTGGCCTCACCACATAATCATAATCTACAC
64 CTAGTAACACTGCCACATAATCATAACCAATATTGATGGCCTCACCACATAATCATAATCAACAC
** * *
13250779 TAGTGGTAACACCACATAATCATTATCAATATTGGTGACCTCGCCACATAATCAT
1 TAGTGGTAACACCACATAATCATTATCAATATCAGTGGCCTCACCACATAATCAT
13250834 TGAAGTTATA
Statistics
Matches: 153, Mismatches: 23, Indels: 14
0.81 0.12 0.07
Matches are distributed among these distances:
127 3 0.02
128 145 0.95
129 5 0.03
ACGTcount: A:0.34, C:0.27, G:0.12, T:0.27
Consensus pattern (128 bp):
TAGTGGTAACACCACATAATCATTATCAATATCAGTGGCCTCACCACATAATCATAATCAACACT
AGTAACACTGCCACATAATCATAACCAATATTGATGGCCTCACCACATAATCATAATCAACAC
Found at i:13250834 original size:32 final size:32
Alignment explanation
Indices: 13250533--13250833 Score: 214
Period size: 32 Copynumber: 9.4 Consensus size: 32
13250523 TAGTGGCAAT
* * * *
13250533 ACCACATAATCCTTATCACTATCAGTGGCCT-
1 ACCACATAATCATAATCAATATTAGTGGCCTC
* * **
13250564 AGCCACATAATCATAATCAACATCAGTAACCTC
1 A-CCACATAATCATAATCAATATTAGTGGCCTC
* * * *
13250597 GCCACATAATCATCATCATTGTT-GATGGCCTC
1 ACCACATAATCATAATCAATATTAG-TGGCCTC
* * * *
13250629 TCCACATATTCATAATCAACACTAGTGG-CTAC
1 ACCACATAATCATAATCAATATTAGTGGCCT-C
* * *
13250661 ACTACATAATCATAGTCAATATCAGTGGCCTC
1 ACCACATAATCATAATCAATATTAGTGGCCTC
* * * *
13250693 ACCACATACTCATAATCAACACTAGTGGCAGT-
1 ACCACATAATCATAATCAATATTAGTGGC-CTC
* * *
13250725 GCCACATAATCATAACCAATATTGGTGGCCTC
1 ACCACATAATCATAATCAATATTAGTGGCCTC
* * * ***
13250757 ACCACATAATCATAATCTACACTAGTGGTAAC
1 ACCACATAATCATAATCAATATTAGTGGCCTC
* * *
13250789 ACCACATAATCATTATCAATATTGGTGACCTC
1 ACCACATAATCATAATCAATATTAGTGGCCTC
*
13250821 GCCACATAATCAT
1 ACCACATAATCAT
13250834 TGAAGTTATA
Statistics
Matches: 201, Mismatches: 61, Indels: 15
0.73 0.22 0.05
Matches are distributed among these distances:
31 5 0.02
32 192 0.96
33 4 0.02
ACGTcount: A:0.35, C:0.28, G:0.11, T:0.27
Consensus pattern (32 bp):
ACCACATAATCATAATCAATATTAGTGGCCTC
Found at i:13255822 original size:49 final size:49
Alignment explanation
Indices: 13255767--13255863 Score: 126
Period size: 50 Copynumber: 2.0 Consensus size: 49
13255757 ATCATAGGTT
* *
13255767 ACATGTC-CTTAACATG-TTTGTTACGTGCTTCATCACGTTTTGATGCATC
1 ACATGTCTC-TAACATGTTTTGTTACGTGCCTCACCACGTTTTG-TGCATC
* *
13255816 ACATGTCTCTAACATGTTTTGTTATGTGCCTCACCATGTTTTGTGCAT
1 ACATGTCTCTAACATGTTTTGTTACGTGCCTCACCACGTTTTGTGCAT
13255864 GCCTCCACAT
Statistics
Matches: 42, Mismatches: 4, Indels: 4
0.84 0.08 0.08
Matches are distributed among these distances:
49 19 0.45
50 23 0.55
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.42
Consensus pattern (49 bp):
ACATGTCTCTAACATGTTTTGTTACGTGCCTCACCACGTTTTGTGCATC
Found at i:13262376 original size:35 final size:35
Alignment explanation
Indices: 13262316--13262432 Score: 164
Period size: 36 Copynumber: 3.3 Consensus size: 35
13262306 TAGTTGATTA
13262316 AAATTGTTTAATTAAGTTGTT-GGCTTAATTAATT
1 AAATTGTTTAATTAAGTTGTTAGGCTTAATTAATT
* ** *
13262350 AAATTTTTTAATTAAGTCATTAGGCTTAATTGATT
1 AAATTGTTTAATTAAGTTGTTAGGCTTAATTAATT
* *
13262385 AAAATTGTTTAATTTAGTTGTTAGGCTTAATTAATA
1 -AAATTGTTTAATTAAGTTGTTAGGCTTAATTAATT
13262421 AAATTGTTTAAT
1 AAATTGTTTAAT
13262433 CAAATTATTA
Statistics
Matches: 71, Mismatches: 10, Indels: 3
0.85 0.12 0.04
Matches are distributed among these distances:
34 18 0.25
35 24 0.34
36 29 0.41
ACGTcount: A:0.35, C:0.03, G:0.13, T:0.49
Consensus pattern (35 bp):
AAATTGTTTAATTAAGTTGTTAGGCTTAATTAATT
Found at i:13262449 original size:70 final size:70
Alignment explanation
Indices: 13262309--13262451 Score: 207
Period size: 70 Copynumber: 2.0 Consensus size: 70
13262299 TCTTAAGTAG
* * * *
13262309 TTGATTAAAATTGTTTAATTAAGTTGTTGGCTTAATTAATTAAATTTTTTAATTAAGTCATTAGG
1 TTGATTAAAATTGTTTAATTAAGTTGTTGGCTTAATTAATAAAATTGTTTAATCAAATCATTAGG
*
13262374 CTTAA
66 ATTAA
* *
13262379 TTGATTAAAATTGTTTAATTTAGTTGTTAGGCTTAATTAATAAAATTGTTTAATCAAATTATTA-
1 TTGATTAAAATTGTTTAATTAAGTTGTT-GGCTTAATTAATAAAATTGTTTAATCAAATCATTAG
13262443 GATTAA
65 GATTAA
13262449 TTG
1 TTG
13262452 GCAATTACAT
Statistics
Matches: 65, Mismatches: 7, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
70 35 0.54
71 30 0.46
ACGTcount: A:0.36, C:0.03, G:0.13, T:0.48
Consensus pattern (70 bp):
TTGATTAAAATTGTTTAATTAAGTTGTTGGCTTAATTAATAAAATTGTTTAATCAAATCATTAGG
ATTAA
Found at i:13264074 original size:29 final size:30
Alignment explanation
Indices: 13264032--13264093 Score: 90
Period size: 29 Copynumber: 2.1 Consensus size: 30
13264022 GAGACTTTAC
* *
13264032 CTTAACCTTAAAAAGGTAGAAAGGTTCTAA
1 CTTAACATTAAAAAGGTACAAAGGTTCTAA
*
13264062 CTTAACATT-AAAAGGTACAGAGGTTCTAA
1 CTTAACATTAAAAAGGTACAAAGGTTCTAA
13264091 CTT
1 CTT
13264094 GGCCTTGAAA
Statistics
Matches: 29, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
29 21 0.72
30 8 0.28
ACGTcount: A:0.40, C:0.15, G:0.16, T:0.29
Consensus pattern (30 bp):
CTTAACATTAAAAAGGTACAAAGGTTCTAA
Found at i:13265769 original size:27 final size:28
Alignment explanation
Indices: 13265725--13265785 Score: 81
Period size: 27 Copynumber: 2.2 Consensus size: 28
13265715 CCTCCTTATA
*
13265725 TTTAAATGCACATGTTGAAAA-AAATGTT
1 TTTACATGCACATGTTGAAAACAAA-GTT
13265753 TTTACATGC-CATGTTGAAAACAAAGTT
1 TTTACATGCACATGTTGAAAACAAAGTT
*
13265780 GTTACA
1 TTTACA
13265786 AACTTTGTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
27 19 0.63
28 11 0.37
ACGTcount: A:0.39, C:0.11, G:0.15, T:0.34
Consensus pattern (28 bp):
TTTACATGCACATGTTGAAAACAAAGTT
Found at i:13265879 original size:29 final size:28
Alignment explanation
Indices: 13265844--13265927 Score: 82
Period size: 27 Copynumber: 3.0 Consensus size: 28
13265834 ATTATTACGA
13265844 GTCATGTTTAAAAAATGTTCTTGTTACAC
1 GTCATGTTTAAAAAATGTT-TTGTTACAC
* * *
13265873 G-CTATGTTGAAAAAA-ATTTTATTACAC
1 GTC-ATGTTTAAAAAATGTTTTGTTACAC
* *
13265900 GTCATATTTAAAAAATGTAGTTGTTACA
1 GTCATGTTTAAAAAATGT-TTTGTTACA
13265928 TACCATATTA
Statistics
Matches: 43, Mismatches: 8, Indels: 8
0.73 0.14 0.14
Matches are distributed among these distances:
27 19 0.44
28 5 0.12
29 19 0.44
ACGTcount: A:0.37, C:0.11, G:0.13, T:0.39
Consensus pattern (28 bp):
GTCATGTTTAAAAAATGTTTTGTTACAC
Found at i:13265912 original size:27 final size:27
Alignment explanation
Indices: 13265826--13265914 Score: 67
Period size: 27 Copynumber: 3.2 Consensus size: 27
13265816 ACCCTATTCA
** *
13265826 AAAAAAAAATTATTACGA-GTCATGTTT
1 AAAAAAATTTTATTAC-ACGTCATATTT
* *
13265853 AAAAAATGTTCTTGTTACACG-C-TATGTT
1 AAAAAA-ATT-TTATTACACGTCATAT-TT
13265881 GAAAAAAATTTTATTACACGTCATATTT
1 -AAAAAAATTTTATTACACGTCATATTT
13265909 AAAAAA
1 AAAAAA
13265915 TGTAGTTGTT
Statistics
Matches: 48, Mismatches: 7, Indels: 14
0.70 0.10 0.20
Matches are distributed among these distances:
27 23 0.48
28 9 0.19
29 16 0.33
ACGTcount: A:0.45, C:0.10, G:0.10, T:0.35
Consensus pattern (27 bp):
AAAAAAATTTTATTACACGTCATATTT
Found at i:13265942 original size:56 final size:56
Alignment explanation
Indices: 13265807--13265943 Score: 150
Period size: 56 Copynumber: 2.4 Consensus size: 56
13265797 AAAACTATTT
* * *
13265807 TTGTTACACACCCTATTCAAAAAAAAAATTATTACGAGTCATGTTTAAAAAATGTTC
1 TTGTTACACACCATATT-AAAAAAAAAATTATTACGAGTCATATTTAAAAAATGTAC
* * * * ** *
13265864 TTGTTACACGCTATGTTGAAAAAAATTTTATTAC-ACGTCATATTTAAAAAATGTAG
1 TTGTTACACACCATATTAAAAAAAAAATTATTACGA-GTCATATTTAAAAAATGTAC
*
13265920 TTGTTACATACCATATTAAAAAAA
1 TTGTTACACACCATATTAAAAAAA
13265944 TTTGTTACAC
Statistics
Matches: 64, Mismatches: 15, Indels: 3
0.78 0.18 0.04
Matches are distributed among these distances:
55 1 0.02
56 50 0.78
57 13 0.20
ACGTcount: A:0.42, C:0.13, G:0.09, T:0.35
Consensus pattern (56 bp):
TTGTTACACACCATATTAAAAAAAAAATTATTACGAGTCATATTTAAAAAATGTAC
Found at i:13272306 original size:27 final size:28
Alignment explanation
Indices: 13272276--13272353 Score: 81
Period size: 27 Copynumber: 2.9 Consensus size: 28
13272266 ATCATATTTG
13272276 AAAAGATTTTGCTACATGCCAT-TTAAA
1 AAAAGATTTTGCTACATGCCATGTTAAA
* * * *
13272303 AAAA-ATATTGTTACACGCCATGTTTAA
1 AAAAGATTTTGCTACATGCCATGTTAAA
* *
13272330 AATAGGTTTT-CTACATGCCATGTT
1 AAAAGATTTTGCTACATGCCATGTT
13272354 TACTATGTTA
Statistics
Matches: 40, Mismatches: 9, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
26 14 0.35
27 23 0.57
28 3 0.08
ACGTcount: A:0.36, C:0.15, G:0.13, T:0.36
Consensus pattern (28 bp):
AAAAGATTTTGCTACATGCCATGTTAAA
Found at i:13279533 original size:23 final size:23
Alignment explanation
Indices: 13279506--13279550 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
13279496 TCCTTTGTTG
*
13279506 CCTTCAGCATTTCCTCCTCTTTT
1 CCTTCACCATTTCCTCCTCTTTT
*
13279529 CCTTCACCATTTCTTCCTCTTT
1 CCTTCACCATTTCCTCCTCTTT
13279551 CCTGTATCAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.09, C:0.40, G:0.02, T:0.49
Consensus pattern (23 bp):
CCTTCACCATTTCCTCCTCTTTT
Found at i:13281197 original size:22 final size:21
Alignment explanation
Indices: 13281172--13281225 Score: 56
Period size: 21 Copynumber: 2.6 Consensus size: 21
13281162 GAAAAAATTG
* *
13281172 AGTGGAATGCACATGAAATGTA
1 AGTGAAATGCA-AGGAAATGTA
*
13281194 AGTGAAATGCAAGGAAATGCA
1 AGTGAAATGCAAGGAAATGTA
*
13281215 TGTG-AATGCAA
1 AGTGAAATGCAA
13281226 ATTAGAGAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
20 7 0.25
21 11 0.39
22 10 0.36
ACGTcount: A:0.43, C:0.09, G:0.28, T:0.20
Consensus pattern (21 bp):
AGTGAAATGCAAGGAAATGTA
Found at i:13281212 original size:10 final size:11
Alignment explanation
Indices: 13281172--13281225 Score: 51
Period size: 11 Copynumber: 5.1 Consensus size: 11
13281162 GAAAAAATTG
*
13281172 AGTGGAATGCA
1 AGTGAAATGCA
*
13281183 CA-TGAAATGTA
1 -AGTGAAATGCA
13281194 AGTGAAATGCA
1 AGTGAAATGCA
13281205 AG-GAAATGCA
1 AGTGAAATGCA
*
13281215 TGTG-AATGCA
1 AGTGAAATGCA
13281225 A
1 A
13281226 ATTAGAGAGT
Statistics
Matches: 35, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
10 16 0.46
11 18 0.51
12 1 0.03
ACGTcount: A:0.43, C:0.09, G:0.28, T:0.20
Consensus pattern (11 bp):
AGTGAAATGCA
Found at i:13282449 original size:22 final size:22
Alignment explanation
Indices: 13282414--13282467 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
13282404 ATTTCTATAA
13282414 TTATTTT-ATTTTTTTAGTGAG
1 TTATTTTAATTTTTTTAGTGAG
13282435 TTATTTTAATTTTTTTAGTGAG
1 TTATTTTAATTTTTTTAGTGAG
13282457 TTATTTTAATT
1 TTATTTTAATT
13282468 ATATCTTATT
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 7 0.22
22 25 0.78
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.67
Consensus pattern (22 bp):
TTATTTTAATTTTTTTAGTGAG
Found at i:13282858 original size:121 final size:121
Alignment explanation
Indices: 13282638--13282864 Score: 418
Period size: 121 Copynumber: 1.9 Consensus size: 121
13282628 TAAGTGATGC
13282638 AATTCTTAGACCATTAGAAAGTTAAGAGAGAGAGCTACAACTTTCATGAAGATCACTTTACCTAG
1 AATTCTTAGACCATTAGAAAGTTAAGAGAGAGAGCTACAACTTTCATGAAGATCACTTTACCTAG
* *
13282703 TTCTGTCTCCATGATAAAGAAAATGATGTCAGAAAATGACTGATCGTACTATCTCT
66 TTCTGTCTCCATGATAAAGAAAATCACGTCAGAAAATGACTGATCGTACTATCTCT
13282759 AATTCTTAGACCATTAGAAAGTTAAGAGAGAGAGCTACAACTTTCATGAAGATCACTTTACCTAG
1 AATTCTTAGACCATTAGAAAGTTAAGAGAGAGAGCTACAACTTTCATGAAGATCACTTTACCTAG
* *
13282824 TTCTGTCTCCATGATAGAGAAAATCACGTTAGAAAATGACT
66 TTCTGTCTCCATGATAAAGAAAATCACGTCAGAAAATGACT
13282865 AGACATACTA
Statistics
Matches: 102, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
121 102 1.00
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (121 bp):
AATTCTTAGACCATTAGAAAGTTAAGAGAGAGAGCTACAACTTTCATGAAGATCACTTTACCTAG
TTCTGTCTCCATGATAAAGAAAATCACGTCAGAAAATGACTGATCGTACTATCTCT
Found at i:13284194 original size:32 final size:32
Alignment explanation
Indices: 13284046--13284194 Score: 83
Period size: 32 Copynumber: 4.7 Consensus size: 32
13284036 TATAAGGTTG
* * * *
13284046 ATGATTACGTGGTGAGGCCA-TGGATATTGATT
1 ATGATTATGTGGCGAGGCCACTAG-TGTTGATT
* * *
13284078 ATGATTATGTGGAGCGGCCATTAGTGTTGACTT
1 ATGATTATGTGGCGAGGCCACTAGTGTTGA-TT
* * * * *
13284111 -TGATTACGT-GCAAGGCCA-TCAATATTGACT
1 ATGATTATGTGGCGAGGCCACT-AGTGTTGATT
** *
13284141 ATGATTATACGGC-ATGACCACTAGTGTTGATT
1 ATGATTATGTGGCGA-GGCCACTAGTGTTGATT
*
13284173 ATGATTATGTAGCGAGGCCACT
1 ATGATTATGTGGCGAGGCCACT
13284195 GGCAGTGATG
Statistics
Matches: 86, Mismatches: 23, Indels: 16
0.69 0.18 0.13
Matches are distributed among these distances:
30 2 0.02
31 19 0.22
32 59 0.69
33 6 0.07
ACGTcount: A:0.26, C:0.15, G:0.26, T:0.33
Consensus pattern (32 bp):
ATGATTATGTGGCGAGGCCACTAGTGTTGATT
Found at i:13285862 original size:22 final size:22
Alignment explanation
Indices: 13285821--13285864 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
13285811 TGCCCAGTTG
*
13285821 TAGAAGAATCGACACTTCAAAA
1 TAGAAGAATCGACACCTCAAAA
**
13285843 TAGAAGAATCGATTCCTCAAAA
1 TAGAAGAATCGACACCTCAAAA
13285865 ACAGAAAACT
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.48, C:0.18, G:0.14, T:0.20
Consensus pattern (22 bp):
TAGAAGAATCGACACCTCAAAA
Found at i:13285870 original size:23 final size:22
Alignment explanation
Indices: 13285822--13285870 Score: 53
Period size: 22 Copynumber: 2.2 Consensus size: 22
13285812 GCCCAGTTGT
* *
13285822 AGAAGAATCGACACTTCAAAAT
1 AGAAGAATCGACACCTCAAAAC
**
13285844 AGAAGAATCGATTCCTCAAAAAC
1 AGAAGAATCGACACCTC-AAAAC
13285867 AGAA
1 AGAA
13285871 AACTATAAAC
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
22 14 0.64
23 8 0.36
ACGTcount: A:0.51, C:0.18, G:0.14, T:0.16
Consensus pattern (22 bp):
AGAAGAATCGACACCTCAAAAC
Found at i:13286487 original size:35 final size:36
Alignment explanation
Indices: 13286419--13286487 Score: 95
Period size: 36 Copynumber: 1.9 Consensus size: 36
13286409 GTCTTGGTAG
* * *
13286419 AGGTTATTCTTGATCTTGCAAAAAGGCAAGTTGTGA
1 AGGTTATGCCTGATCTTACAAAAAGGCAAGTTGTGA
*
13286455 AGGTTATGCCTGATCTTAC-AAAAGGCATGTTGT
1 AGGTTATGCCTGATCTTACAAAAAGGCAAGTTGT
13286488 AAAAGTTAGC
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
35 13 0.45
36 16 0.55
ACGTcount: A:0.29, C:0.13, G:0.25, T:0.33
Consensus pattern (36 bp):
AGGTTATGCCTGATCTTACAAAAAGGCAAGTTGTGA
Found at i:13287813 original size:19 final size:21
Alignment explanation
Indices: 13287789--13287836 Score: 68
Period size: 20 Copynumber: 2.5 Consensus size: 21
13287779 TTAGTTTATG
13287789 AAATTGAATTA-G-TTAATTT
1 AAATTGAATTAGGATTAATTT
13287808 AAATTGAA-TAGGATTAATTT
1 AAATTGAATTAGGATTAATTT
13287828 AAATT-AATT
1 AAATTGAATT
13287837 TATTAATAAA
Statistics
Matches: 26, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
18 2 0.08
19 11 0.42
20 13 0.50
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (21 bp):
AAATTGAATTAGGATTAATTT
Found at i:13288914 original size:73 final size:74
Alignment explanation
Indices: 13288791--13288951 Score: 182
Period size: 73 Copynumber: 2.2 Consensus size: 74
13288781 GACAGAGAAC
* * * * * * *
13288791 ACTTAATCGACTAAGAAGCATTATTAGTCGACTAAGAGCTTAGTGTCAAAAATTGGGT-TTAG-A
1 ACTTAATCGACTAAGAAGCAATATTAGTAGACTAAGAACTCACTGCCAAAAATT-GGTATCAGAA
13288854 GATAAAAATG
65 GATAAAAATG
* * * * *
13288864 ACTTAATCAACTAAGAGGCAATGTTAGTAGGCTAAGAACTCACTGCCAAAAGTTGGTATCAGAAG
1 ACTTAATCGACTAAGAAGCAATATTAGTAGACTAAGAACTCACTGCCAAAAATTGGTATCAGAAG
*
13288929 ATAGAAATG
66 ATAAAAATG
13288938 ACTTAATCGACTAA
1 ACTTAATCGACTAA
13288952 AAAACATGTT
Statistics
Matches: 72, Mismatches: 14, Indels: 3
0.81 0.16 0.03
Matches are distributed among these distances:
72 3 0.04
73 46 0.64
74 23 0.32
ACGTcount: A:0.40, C:0.14, G:0.20, T:0.26
Consensus pattern (74 bp):
ACTTAATCGACTAAGAAGCAATATTAGTAGACTAAGAACTCACTGCCAAAAATTGGTATCAGAAG
ATAAAAATG
Found at i:13296781 original size:16 final size:15
Alignment explanation
Indices: 13296748--13296781 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
13296738 CATGACATAA
*
13296748 TATTTAAATACTAAT
1 TATTTAAATACAAAT
13296763 TATTTAAATATCAAAT
1 TATTTAAATA-CAAAT
13296779 TAT
1 TAT
13296782 GTGAAGTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 10 0.59
16 7 0.41
ACGTcount: A:0.47, C:0.06, G:0.00, T:0.47
Consensus pattern (15 bp):
TATTTAAATACAAAT
Found at i:13297570 original size:30 final size:30
Alignment explanation
Indices: 13297536--13297639 Score: 97
Period size: 30 Copynumber: 3.5 Consensus size: 30
13297526 AATCATTAAT
* *
13297536 TATAAGAGTTTATTTAAATCAAAATAAAAA
1 TATAAAAGCTTATTTAAATCAAAATAAAAA
* * * *
13297566 TATAAAAGCTTATTTGACTTAAAATAAAAG
1 TATAAAAGCTTATTTAAATCAAAATAAAAA
*
13297596 TAAAAAAGCTTGA-TTAAATGC--AATAAAAA
1 TATAAAAGCTT-ATTTAAAT-CAAAATAAAAA
*
13297625 TATAAAAACTTATTT
1 TATAAAAGCTTATTT
13297640 GAATTTTTCT
Statistics
Matches: 58, Mismatches: 13, Indels: 7
0.74 0.17 0.09
Matches are distributed among these distances:
28 1 0.02
29 18 0.31
30 38 0.66
31 1 0.02
ACGTcount: A:0.54, C:0.06, G:0.08, T:0.33
Consensus pattern (30 bp):
TATAAAAGCTTATTTAAATCAAAATAAAAA
Found at i:13298536 original size:21 final size:21
Alignment explanation
Indices: 13298512--13298557 Score: 74
Period size: 21 Copynumber: 2.2 Consensus size: 21
13298502 TTTCTAGGTT
*
13298512 TCAAGTATCGGTACTTGTTCA
1 TCAAGTATCGATACTTGTTCA
*
13298533 TCAAGTATCGATACTTGTTCT
1 TCAAGTATCGATACTTGTTCA
13298554 TCAA
1 TCAA
13298558 AAGGCTTTTG
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.26, C:0.20, G:0.15, T:0.39
Consensus pattern (21 bp):
TCAAGTATCGATACTTGTTCA
Found at i:13300843 original size:29 final size:28
Alignment explanation
Indices: 13300722--13300843 Score: 111
Period size: 28 Copynumber: 4.2 Consensus size: 28
13300712 ATGTTTGGTT
13300722 TTAATTTAGATAAGAAAATATATTTATC
1 TTAATTTAGATAAGAAAATATATTTATC
* * * * *
13300750 TTAATTAAAGAGAACAAAAATATTTTTTGTC
1 TTAATT-TAGATAA-GAAAATA-TATTTATC
* *
13300781 TTAATCTAAATAAGAAAATATATTTATC
1 TTAATTTAGATAAGAAAATATATTTATC
* *
13300809 TCAATTTAGACAAGATAAA-ATATTCTATC
1 TTAATTTAGATAAGA-AAATATATT-TATC
13300838 TTAATT
1 TTAATT
13300844 AAAGAGAAGA
Statistics
Matches: 72, Mismatches: 17, Indels: 9
0.73 0.17 0.09
Matches are distributed among these distances:
28 28 0.39
29 23 0.32
30 10 0.14
31 11 0.15
ACGTcount: A:0.46, C:0.07, G:0.07, T:0.40
Consensus pattern (28 bp):
TTAATTTAGATAAGAAAATATATTTATC
Found at i:13309416 original size:14 final size:13
Alignment explanation
Indices: 13309401--13309458 Score: 57
Period size: 14 Copynumber: 4.5 Consensus size: 13
13309391 ATATTATAAT
13309401 TAAAATAAAAATA
1 TAAAATAAAAATA
*
13309414 TTAAAATAAATATA
1 -TAAAATAAAAATA
* *
13309428 TAATATAAGAATA
1 TAAAATAAAAATA
13309441 -AAAAT-AAAATA
1 TAAAATAAAAATA
*
13309452 AAAAATA
1 TAAAATA
13309459 TATAAAAAAT
Statistics
Matches: 36, Mismatches: 6, Indels: 5
0.77 0.13 0.11
Matches are distributed among these distances:
11 5 0.14
12 9 0.25
13 10 0.28
14 12 0.33
ACGTcount: A:0.72, C:0.00, G:0.02, T:0.26
Consensus pattern (13 bp):
TAAAATAAAAATA
Found at i:13309444 original size:33 final size:31
Alignment explanation
Indices: 13309390--13309463 Score: 87
Period size: 33 Copynumber: 2.3 Consensus size: 31
13309380 AAATATTTTT
* *
13309390 AATATTATAATTAAAATAAAAATATTAA-AATA
1 AATA-TATAATTAAAATAAAAATA-AAATAAAA
13309422 AATATATAATATAAGAATAAAAATAAAATAAAA
1 AATATATAAT-TAA-AATAAAAATAAAATAAAA
13309455 AATATATAA
1 AATATATAA
13309464 AAAATTAACA
Statistics
Matches: 37, Mismatches: 2, Indels: 5
0.84 0.05 0.11
Matches are distributed among these distances:
31 6 0.16
32 9 0.24
33 22 0.59
ACGTcount: A:0.69, C:0.00, G:0.01, T:0.30
Consensus pattern (31 bp):
AATATATAATTAAAATAAAAATAAAATAAAA
Found at i:13309451 original size:19 final size:19
Alignment explanation
Indices: 13309390--13309451 Score: 63
Period size: 19 Copynumber: 3.2 Consensus size: 19
13309380 AAATATTTTT
* *
13309390 AATATTATAATTAAAATAAA
1 AATATTAAAATAAAAAT-AA
* *
13309410 AATATTAAAATAAATATAT
1 AATATTAAAATAAAAATAA
13309429 AATA-TAAGAATAAAAATAA
1 AATATTAA-AATAAAAATAA
13309448 AATA
1 AATA
13309452 AAAAATATAT
Statistics
Matches: 35, Mismatches: 6, Indels: 3
0.80 0.14 0.07
Matches are distributed among these distances:
18 3 0.09
19 18 0.51
20 14 0.40
ACGTcount: A:0.68, C:0.00, G:0.02, T:0.31
Consensus pattern (19 bp):
AATATTAAAATAAAAATAA
Found at i:13309481 original size:54 final size:57
Alignment explanation
Indices: 13309405--13309524 Score: 126
Period size: 52 Copynumber: 2.1 Consensus size: 57
13309395 TATAATTAAA
13309405 ATAAAAATATTAAAATAAATATATAATATAAG-AATAA-AAA-TAAAATAAAA-A-AT-AT
1 ATAAAAA-ATT-AAA-AAATATATAATATAAGTAA-AACAAATTAAAATAAAATATATAAT
* ** *
13309460 ATAAAAAATTAACATTTATATAATATAGGTAAAACAAATTAAAATAAAATATATAAT
1 ATAAAAAATTAAAAAATATATAATATAAGTAAAACAAATTAAAATAAAATATATAAT
13309517 ATAAAAAA
1 ATAAAAAA
13309525 ATATTAAAGA
Statistics
Matches: 55, Mismatches: 4, Indels: 10
0.80 0.06 0.14
Matches are distributed among these distances:
52 15 0.27
53 7 0.13
54 13 0.24
55 8 0.15
56 2 0.04
57 10 0.18
ACGTcount: A:0.68, C:0.02, G:0.03, T:0.28
Consensus pattern (57 bp):
ATAAAAAATTAAAAAATATATAATATAAGTAAAACAAATTAAAATAAAATATATAAT
Found at i:13309523 original size:15 final size:15
Alignment explanation
Indices: 13309505--13310007 Score: 122
Period size: 15 Copynumber: 34.1 Consensus size: 15
13309495 AAATTAAAAT
13309505 AAAATATATAATATA
1 AAAATATATAATATA
* *
13309520 AAAAAATATTAA-AGA
1 AAAATATA-TAATATA
* *
13309535 AATGAAAATAAAATATA
1 AA--AATATATAATATA
13309552 TAAAATTATATAATAAATA
1 -AAAA-TATATAAT--ATA
13309571 AAAATA-A-AATATA
1 AAAATATATAATATA
* * *
13309584 TGACAT-TAAAATATA
1 -AAAATATATAATATA
*
13309599 TTCAAAATATTATTATATA
1 ---AAAATA-TATAATATA
13309618 AAAAT-TAATAATATAA
1 AAAATAT-ATAATAT-A
*
13309634 ATAAATATATAAAAT-
1 A-AAATATATAATATA
13309649 AAAATATA-AATATTA
1 AAAATATATAATA-TA
* * *
13309664 ATAATAAATAAAAT-
1 AAAATATATAATATA
* * *
13309678 AAAATATATGACATT
1 AAAATATATAATATA
13309693 AAAATATAT--T-TA
1 AAAATATATAATATA
*
13309705 AGAAATGATATTATAT-
1 A-AAAT-ATATAATATA
13309721 AAAATA-ATAATAT-
1 AAAATATATAATATA
*
13309734 AAAATATAAATATATTA
1 AAAATATATA-ATA-TA
*
13309751 AAAATA-AAAATAT-
1 AAAATATATAATATA
*
13309764 AAAATATTTAATA-A
1 AAAATATATAATATA
*
13309778 TAAATA-A-AA-AT-
1 AAAATATATAATATA
13309789 AAAATATATGACAT-TA
1 AAAATATAT-A-ATATA
13309805 AAAATATAT--T-TA
1 AAAATATATAATATA
*
13309817 AGAAATGATATTATAT-
1 A-AAAT-ATATAATATA
13309833 AAAA-AT-TAATAATA
1 AAAATATATAAT-ATA
13309847 AAAATATA-AATATA
1 AAAATATATAATATA
*
13309861 TTAAAA-ATAAAATAT-
1 --AAAATATATAATATA
13309876 AAAATATTATAATA-A
1 AAAATA-TATAATATA
*
13309891 TAAATA-A-AA-AT-
1 AAAATATATAATATA
* * *
13309902 AAAATATATGACATT
1 AAAATATATAATATA
*
13309917 AAAA-ATAT-AT-TC
1 AAAATATATAATATA
*
13309929 AAAATATGATATTATA
1 AAAATAT-ATAATATA
13309945 TAAAA-AT-TAATAATA
1 -AAAATATATAAT-ATA
13309960 AAAATATA-AATATA
1 AAAATATATAATATA
*
13309974 TTAAAA-ATAAAATAT-
1 --AAAATATATAATATA
13309989 AAAATACTATAATAATA
1 AAAATA-TATAAT-ATA
13310006 AA
1 AA
13310008 TAAAAATAAA
Statistics
Matches: 369, Mismatches: 43, Indels: 150
0.66 0.08 0.27
Matches are distributed among these distances:
11 12 0.03
12 20 0.05
13 49 0.13
14 72 0.20
15 98 0.27
16 58 0.16
17 43 0.12
18 7 0.02
19 10 0.03
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.32
Consensus pattern (15 bp):
AAAATATATAATATA
Found at i:13309527 original size:17 final size:17
Alignment explanation
Indices: 13309505--13309652 Score: 57
Period size: 17 Copynumber: 9.1 Consensus size: 17
13309495 AAATTAAAAT
13309505 AAAATATATAATATAAA
1 AAAATATATAATATAAA
*
13309522 AAAATAT-TAA-AGAAA
1 AAAATATATAATATAAA
*
13309537 TGAAAATA-A-AATATATA
1 --AAAATATATAATATAAA
*
13309554 AAATTATATAATA-AATA
1 AAAATATATAATATAA-A
*
13309571 AAAATA-A-AATAT-AT
1 AAAATATATAATATAAA
* * * **
13309585 GACAT-TAAAATATATTC
1 AAAATATATAATATA-AA
* *
13309602 AAAATAT-TATTATATA
1 AAAATATATAATATAAA
13309618 AAAAT-TAATAATATAAA
1 AAAATAT-ATAATATAAA
* *
13309635 TAAATATATAAAATAAA
1 AAAATATATAATATAAA
13309652 A
1 A
13309653 TATAAATATT
Statistics
Matches: 94, Mismatches: 21, Indels: 32
0.64 0.14 0.22
Matches are distributed among these distances:
14 4 0.04
15 20 0.21
16 14 0.15
17 54 0.57
18 2 0.02
ACGTcount: A:0.66, C:0.01, G:0.02, T:0.31
Consensus pattern (17 bp):
AAAATATATAATATAAA
Found at i:13309563 original size:10 final size:9
Alignment explanation
Indices: 13309542--13310012 Score: 61
Period size: 9 Copynumber: 52.7 Consensus size: 9
13309532 AGAAATGAAA
13309542 ATAAAATAT
1 ATAAAATAT
13309551 ATAAAAT-T
1 ATAAAATAT
* *
13309559 ATATAATAA
1 ATAAAATAT
13309568 ATAAAA-AT
1 ATAAAATAT
13309576 A-AAATATAT
1 ATAAA-ATAT
13309585 GACATTAAAATAT
1 ---A-TAAAATAT
13309598 ATTCAAAATAT
1 A-T-AAAATAT
*
13309609 -T--ATTAT
1 ATAAAATAT
13309615 ATAAAA-AT
1 ATAAAATAT
13309623 -TAATAATAT
1 ATAA-AATAT
*
13309632 AAATAAATAT
1 ATA-AAATAT
*
13309642 ATAAAATAAA
1 ATAAAAT-AT
13309652 ATATAAATAT
1 ATA-AAATAT
*
13309662 -TAATAATAA
1 ATAA-AATAT
13309671 ATAAAATA-
1 ATAAAATAT
*
13309679 A-AATATATGAC
1 ATAA-A-AT-AT
13309690 ATTAAAATAT
1 A-TAAAATAT
** * *
13309700 ATTTAAGAA
1 ATAAAATAT
* *
13309709 ATGATATTAT
1 AT-AAAATAT
13309719 ATAAAATAAT
1 ATAAAAT-AT
13309729 AATATAAA-AT
1 -ATA-AAATAT
13309739 AT-AAATAT
1 ATAAAATAT
*
13309747 ATTAAA-A-
1 ATAAAATAT
13309754 ATAAAA-AT
1 ATAAAATAT
13309762 ATAAAATAT
1 ATAAAATAT
* *
13309771 TTAATAATAA
1 ATAA-AATAT
13309781 AT-AAA-A-
1 ATAAAATAT
13309787 ATAAAATAT
1 ATAAAATAT
* *
13309796 ATGACAT-T
1 ATAAAATAT
13309804 A-AAAATAT
1 ATAAAATAT
13309812 ATTTAAGAA-AT
1 A--TAA-AATAT
**
13309823 GATATTATAT
1 -ATAAAATAT
13309833 A-AAAATTAAT
1 ATAAAA-T-AT
13309843 AATAAAA-AT
1 -ATAAAATAT
13309852 AT-AAATAT
1 ATAAAATAT
*
13309860 ATTAAA-A-
1 ATAAAATAT
13309867 AT-AAA-AT
1 ATAAAATAT
13309874 ATAAAATATT
1 ATAAAATA-T
*
13309884 ATAATAATAA
1 ATAA-AATAT
13309894 AT-AAA-A-
1 ATAAAATAT
13309900 ATAAAATAT
1 ATAAAATAT
* *
13309909 ATGACAT-T
1 ATAAAATAT
13309917 A-AAAATAT
1 ATAAAATAT
13309925 ATTCAAAATAT
1 A-T-AAAATAT
**
13309936 GATATTATAT
1 -ATAAAATAT
13309946 A-AAAATTAAT
1 ATAAAA-T-AT
13309956 AATAAAA-AT
1 -ATAAAATAT
13309965 AT-AAATAT
1 ATAAAATAT
*
13309973 ATTAAA-A-
1 ATAAAATAT
13309980 AT-AAA-AT
1 ATAAAATAT
13309987 ATAAAATACT
1 ATAAAATA-T
*
13309997 ATAATAATAA
1 ATAA-AATAT
13310007 ATAAAA
1 ATAAAA
13310013 ATAAATATAT
Statistics
Matches: 343, Mismatches: 44, Indels: 150
0.64 0.08 0.28
Matches are distributed among these distances:
6 16 0.05
7 46 0.13
8 66 0.19
9 84 0.24
10 65 0.19
11 40 0.12
12 17 0.05
13 6 0.02
14 3 0.01
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (9 bp):
ATAAAATAT
Found at i:13309575 original size:32 final size:32
Alignment explanation
Indices: 13309501--13309584 Score: 98
Period size: 32 Copynumber: 2.6 Consensus size: 32
13309491 AAACAAATTA
* *
13309501 AAATAAAATATATAATATAAAAAAATATTAAAG
1 AAATAAAA-ATAAAATATATAAAAATATTAAAG
* * *
13309534 AAATGAAAATAAAATATATAAAATTA-TATAAT
1 AAATAAAAATAAAATATATAAAAATATTA-AAG
13309566 AAATAAAAATAAAATATAT
1 AAATAAAAATAAAATATAT
13309585 GACATTAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 3
0.83 0.11 0.06
Matches are distributed among these distances:
31 2 0.05
32 35 0.80
33 7 0.16
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (32 bp):
AAATAAAAATAAAATATATAAAAATATTAAAG
Found at i:13309597 original size:112 final size:109
Alignment explanation
Indices: 13309503--13310195 Score: 806
Period size: 113 Copynumber: 6.3 Consensus size: 109
13309493 ACAAATTAAA
* * *
13309503 ATAAAATATATAATATAAAAAAATATTAAAGA-AATGAAAATAAAATATATAAAATTAT-ATAAT
1 ATAAAA-AT-TAATATAAAAAAATA-TAAATATATTAAAAATAAAATATA-AAAATTATAATAAT
* *
13309566 AAATAAAAATAAAATATATGACATTAAAATATATTCAAAATATTATTAT
62 AAATAAAAATAAAATATATGACATTAAAATATATTAAAAAGA-TATTAT
* * *
13309615 ATAAAAATT-A-ATAATATAA-ATAAATATA-T-AAAATAAAATATAAATA-T-TAATAATAAAT
1 ATAAAAATTAATATAAAAAAATATAAATATATTAAAAATAAAATATAAAAATTATAATAATAAAT
13309673 -AAAATAAAATATATGACATTAAAATATATTTAAGAAATGATATTAT
66 AAAAATAAAATATATGACATTAAAATATA-TTAA-AAA-GATATTAT
*
13309719 AT-AAAA-TAATA-ATATAAAATATAAATATATTAAAAATAAAAATATAAAATATT-TAATAATA
1 ATAAAAATTAATATA-AAAAAATATAAATATATTAAAAAT-AAAATATAAAA-ATTATAATAATA
13309780 AATAAAAATAAAATATATGACATTAAAAATATATTTAAGAAATGATATTAT
63 AATAAAAATAAAATATATGACATT-AAAATATA-TTAA-AAA-GATATTAT
*
13309831 ATAAAAATTAATA-ATAAAAATATAAATATATTAAAAATAAAATATAAAATATTATAATAATAAA
1 ATAAAAATTAATATAAAAAAATATAAATATATTAAAAATAAAATATAAAA-ATTATAATAATAAA
13309895 TAAAAATAAAATATATGACATTAAAAATATATTCAAAATATGATATTAT
65 TAAAAATAAAATATATGACATT-AAAATATATT-AAAA-A-GATATTAT
* *
13309944 ATAAAAATTAATA-ATAAAAATATAAATATATTAAAAATAAAATATAAAATACTATAATAATAAA
1 ATAAAAATTAATATAAAAAAATATAAATATATTAAAAATAAAATATAAAA-ATTATAATAATAAA
13310008 TAAAAAT-AAATATATGACATTAAAATATATTTAAGAAATGATATTAT
65 TAAAAATAAAATATATGACATTAAAATATA-TTAA-AAA-GATATTAT
*
13310055 AT-AAAATTAATA-ATAAAAATATAAATATATTAAAAATAAAA-A-AAAATATTATAATAATAAA
1 ATAAAAATTAATATAAAAAAATATAAATATATTAAAAATAAAATATAAAA-ATTATAATAATAAA
* *
13310116 TAAAAAT-AAATATATGATATTAAAA-ATTATTTAAGAATGATATTAT
65 TAAAAATAAAATATATGACATTAAAATA-TA-TTAA-AAAGATATTAT
* *
13310162 ATAGAAATTAATA-ATAAAAATATAAA-ATATTAAA
1 ATAAAAATTAATATAAAAAAATATAAATATATTAAA
13310196 CTTATATTTT
Statistics
Matches: 541, Mismatches: 15, Indels: 55
0.89 0.02 0.09
Matches are distributed among these distances:
102 30 0.06
103 19 0.04
104 20 0.04
105 23 0.04
106 7 0.01
107 26 0.05
108 91 0.17
109 3 0.01
110 52 0.10
111 44 0.08
112 71 0.13
113 149 0.28
114 6 0.01
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (109 bp):
ATAAAAATTAATATAAAAAAATATAAATATATTAAAAATAAAATATAAAAATTATAATAATAAAT
AAAAATAAAATATATGACATTAAAATATATTAAAAAGATATTAT
Found at i:13309640 original size:13 final size:13
Alignment explanation
Indices: 13309619--13309675 Score: 50
Period size: 12 Copynumber: 4.5 Consensus size: 13
13309609 TATTATATAA
*
13309619 AAATTAATAATAT
1 AAATAAATAATAT
13309632 AAATAAAT-ATAT
1 AAATAAATAATAT
13309644 AAA-ATAA-AATAT
1 AAATA-AATAATAT
*
13309656 AAAT-ATTAATAAT
1 AAATAAATAAT-AT
13309669 AAATAAA
1 AAATAAA
13309676 ATAAAATATA
Statistics
Matches: 35, Mismatches: 3, Indels: 11
0.71 0.06 0.22
Matches are distributed among these distances:
11 2 0.06
12 19 0.54
13 13 0.37
14 1 0.03
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (13 bp):
AAATAAATAATAT
Found at i:13309641 original size:113 final size:113
Alignment explanation
Indices: 13309603--13310195 Score: 834
Period size: 113 Copynumber: 5.4 Consensus size: 113
13309593 AATATATTCA
13309603 AAATATTATTATATAAAAATTAATAATAT---AA-ATAAATATA-T-AAAATAAAATAT-AAATA
1 AAATA-TATTATATAAAAATTAATAATATAAAAATATAAATATATTAAAAATAAAATATAAAATA
13309661 -T-TAATAATAAAT-AAAATAAAATATATGACATTAAAATATATTTAAG
65 TTATAATAATAAATAAAAATAAAATATATGACATTAAAATATATTTAAG
13309707 AAATGATATTATAT-AAAA-TAATAATAT-AAAATATAAATATATTAAAAATAAAAATATAAAAT
1 AAAT-ATATTATATAAAAATTAATAATATAAAAATATAAATATATTAAAAAT-AAAATATAAAAT
13309769 ATT-TAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTTAAG
64 ATTATAATAATAAATAAAAATAAAATATATGACATT-AAAATATATTTAAG
13309819 AAATGATATTATATAAAAATTAAT-A-ATAAAAATATAAATATATTAAAAATAAAATATAAAATA
1 AAAT-ATATTATATAAAAATTAATAATATAAAAATATAAATATATTAAAAATAAAATATAAAATA
*
13309882 TTATAATAATAAATAAAAATAAAATATATGACATTAAAAATATATTCAA-
65 TTATAATAATAAATAAAAATAAAATATATGACATT-AAAATATATTTAAG
13309931 AATATGATATTATATAAAAATTAAT-A-ATAAAAATATAAATATATTAAAAATAAAATATAAAAT
1 AA-AT-ATATTATATAAAAATTAATAATATAAAAATATAAATATATTAAAAATAAAATATAAAAT
*
13309994 ACTATAATAATAAATAAAAAT-AAATATATGACATTAAAATATATTTAAG
64 ATTATAATAATAAATAAAAATAAAATATATGACATTAAAATATATTTAAG
13310043 AAATGATATTATAT-AAAATTAAT-A-ATAAAAATATAAATATATTAAAAATAAAA-A-AAAATA
1 AAAT-ATATTATATAAAAATTAATAATATAAAAATATAAATATATTAAAAATAAAATATAAAATA
*
13310103 TTATAATAATAAATAAAAAT-AAATATATGATATTAAAA-ATTATTTAAG
65 TTATAATAATAAATAAAAATAAAATATATGACATTAAAATA-TATTTAAG
*
13310151 -AATGATATTATATAGAAATTAAT-A-ATAAAAATATAAA-ATATTAAA
1 AAAT-ATATTATATAAAAATTAATAATATAAAAATATAAATATATTAAA
13310196 CTTATATTTT
Statistics
Matches: 464, Mismatches: 6, Indels: 35
0.92 0.01 0.07
Matches are distributed among these distances:
102 9 0.02
103 4 0.01
104 14 0.03
105 10 0.02
106 1 0.00
107 27 0.06
108 79 0.17
109 6 0.01
110 51 0.11
111 44 0.09
112 63 0.14
113 152 0.33
114 4 0.01
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (113 bp):
AAATATATTATATAAAAATTAATAATATAAAAATATAAATATATTAAAAATAAAATATAAAATAT
TATAATAATAAATAAAAATAAAATATATGACATTAAAATATATTTAAG
Found at i:13309642 original size:27 final size:24
Alignment explanation
Indices: 13309612--13310036 Score: 82
Period size: 24 Copynumber: 17.8 Consensus size: 24
13309602 AAAATATTAT
13309612 TATATAAAAATTAATAATATAAATAAA
1 TATAT-AAAA-TAA-AATATAAATAAA
13309639 TATATAAAATAAAATATAAATATTAA
1 TATATAAAATAAAATATAAATA--AA
*
13309665 TA-AT-AAATAAAATA-AAATATA
1 TATATAAAATAAAATATAAATAAA
* * * *
13309686 TGACATTAAAAT-ATAT-TTAAGAAA
1 T-ATA-TAAAATAAAATATAAATAAA
* *
13309710 TGATATTATATAAAATAATAATATAAA
1 T-ATATAAAATAAAAT-ATAA-ATAAA
* * *
13309737 -ATAT-AAATATATTAAAAATAAA
1 TATATAAAATAAAATATAAATAAA
* *
13309759 AATATAAAATATTTAATAATAAATAAA
1 TATATAAAATA--AAAT-ATAAATAAA
* * *
13309786 -A-ATAAAATATATGACATTAA-AAA
1 TATATAAAATA-A-AATATAAATAAA
** * *
13309809 TATATTTAAGAAATGATATTATATAAA
1 TATATAAAATAAA--ATA-TAAATAAA
* *
13309836 AAT-TAATAATAAAAATATAAATATA
1 TATATAA-AAT-AAAATATAAATAAA
*
13309861 T-TA-AAAATAAAATATAAA-ATA
1 TATATAAAATAAAATATAAATAAA
*
13309882 T-TATAATAAT-AAATAAAAATAAA
1 TATATAA-AATAAAATATAAATAAA
* *
13309905 -ATAT---ATGACAT-TAAA-AATA
1 TATATAAAATAAAATATAAATAA-A
** *
13309924 TAT-TCAAAATATGATATTATATAAA
1 TATAT-AAAATAAAATA-TAAATAAA
* *
13309949 AAT-TAATAATAAAAATATAAATATA
1 TATATAA-AAT-AAAATATAAATAAA
13309974 T-TA-AAAATAAAATAT--A-AAA
1 TATATAAAATAAAATATAAATAAA
*
13309993 TACTATAATAAT-AAATAAAAATAAA
1 TA-TATAA-AATAAAATATAAATAAA
* *
13310018 TATATGACATTAAAATATA
1 TATAT-AAAATAAAATATA
13310037 TTTAAGAAAT
Statistics
Matches: 292, Mismatches: 54, Indels: 106
0.65 0.12 0.23
Matches are distributed among these distances:
18 2 0.01
19 10 0.03
20 6 0.02
21 10 0.03
22 40 0.14
23 41 0.14
24 67 0.23
25 63 0.22
26 26 0.09
27 24 0.08
28 3 0.01
ACGTcount: A:0.64, C:0.01, G:0.02, T:0.33
Consensus pattern (24 bp):
TATATAAAATAAAATATAAATAAA
Done.