Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NW_018397264.1 Herrania umbratica cultivar Fairchild unplaced genomic scaffold, ASM216827v2 scaffold_130.0, 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: 8132550
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 35170 characters in sequence are not A, C, G, or T
File 1 of 14
Found at i:1461 original size:23 final size:23
Alignment explanation
Indices: 1435--1507 Score: 58
Period size: 23 Copynumber: 3.2 Consensus size: 23
1425 ATTTAATCAC
1435 GTAATAACTTATTAATTAGTCAT
1 GTAATAACTTATTAATTAGTCAT
** * * *
1458 GTAATGCCTTACTAACTAGTTAT
1 GTAATAACTTATTAATTAGTCAT
* * * *
1481 ATAATATC-TATCAATTAGTCAC
1 GTAATAACTTATTAATTAGTCAT
1503 GTAAT
1 GTAAT
1508 GTTATATGAA
Statistics
Matches: 36, Mismatches: 14, Indels: 1
0.71 0.27 0.02
Matches are distributed among these distances:
22 13 0.36
23 23 0.64
ACGTcount: A:0.37, C:0.14, G:0.10, T:0.40
Consensus pattern (23 bp):
GTAATAACTTATTAATTAGTCAT
Found at i:12768 original size:8 final size:8
Alignment explanation
Indices: 12755--12784 Score: 51
Period size: 8 Copynumber: 3.8 Consensus size: 8
12745 AGGAATATTG
*
12755 CATACATA
1 CATACAAA
12763 CATACAAA
1 CATACAAA
12771 CATACAAA
1 CATACAAA
12779 CATACA
1 CATACA
12785 TGCATATATA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.57, C:0.27, G:0.00, T:0.17
Consensus pattern (8 bp):
CATACAAA
Found at i:19254 original size:15 final size:15
Alignment explanation
Indices: 19234--19270 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
19224 TTACACTCTT
*
19234 CCTTCTCTTCTCTGC
1 CCTTCTCTTCTCCGC
19249 CCTTCTCTTCTCCGC
1 CCTTCTCTTCTCCGC
19264 CTCTTCT
1 C-CTTCT
19271 ATTGCTGCTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 15 0.75
16 5 0.25
ACGTcount: A:0.00, C:0.49, G:0.05, T:0.46
Consensus pattern (15 bp):
CCTTCTCTTCTCCGC
Found at i:20747 original size:2 final size:2
Alignment explanation
Indices: 20740--20772 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
20730 ATTGTTTATC
*
20740 AT AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
20773 GTACAGAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.03, T:0.48
Consensus pattern (2 bp):
AT
Found at i:25131 original size:25 final size:24
Alignment explanation
Indices: 25097--25181 Score: 91
Period size: 25 Copynumber: 3.4 Consensus size: 24
25087 AAATAAAATT
*
25097 CCTACAATTATGATGATTTCCAATC
1 CCTATAATTATGATGA-TTCCAATC
*
25122 CCTATAATTAT-AGTGAATCCTAATC
1 CCTATAATTATGA-TGATTCC-AATC
*
25147 CCTATAATTATGGTGATTCTCAATC
1 CCTATAATTATGATGATTC-CAATC
*
25172 TCTATAATTA
1 CCTATAATTA
25182 CGTTTATTAA
Statistics
Matches: 51, Mismatches: 5, Indels: 8
0.80 0.08 0.12
Matches are distributed among these distances:
24 4 0.08
25 46 0.90
26 1 0.02
ACGTcount: A:0.33, C:0.20, G:0.08, T:0.39
Consensus pattern (24 bp):
CCTATAATTATGATGATTCCAATC
Found at i:27856 original size:5 final size:5
Alignment explanation
Indices: 27827--27869 Score: 54
Period size: 5 Copynumber: 8.8 Consensus size: 5
27817 NNNNNNNNNN
*
27827 AAAA- AAAA- AAAAA AAAAG AAGAAG AAAAG AAAAG AAAAG AAAA
1 AAAAG AAAAG AAAAG AAAAG AA-AAG AAAAG AAAAG AAAAG AAAA
27870 AGAATAATAA
Statistics
Matches: 36, Mismatches: 1, Indels: 3
0.90 0.03 0.08
Matches are distributed among these distances:
4 8 0.22
5 23 0.64
6 5 0.14
ACGTcount: A:0.86, C:0.00, G:0.14, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:27859 original size:21 final size:21
Alignment explanation
Indices: 27830--27873 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
27820 NNNNNNNAAA
*
27830 AAAAAAAAAAAAAAGAAGAAG
1 AAAAAAAAAAAAAAGAAAAAG
* *
27851 AAAAGAAAAGAAAAGAAAAAG
1 AAAAAAAAAAAAAAGAAAAAG
27872 AA
1 AA
27874 TAATAAGAAG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.84, C:0.00, G:0.16, T:0.00
Consensus pattern (21 bp):
AAAAAAAAAAAAAAGAAAAAG
Found at i:28368 original size:17 final size:17
Alignment explanation
Indices: 28346--28397 Score: 52
Period size: 17 Copynumber: 3.1 Consensus size: 17
28336 AGGCGCATTA
28346 AGTATTTTATTTTATTT
1 AGTATTTTATTTTATTT
* *
28363 AGTATTTT-TATTAGCTT
1 AGTATTTTATTTTA-TTT
* *
28380 AGGATTTTATTTTCTTT
1 AGTATTTTATTTTATTT
28397 A
1 A
28398 TTTTATTTAG
Statistics
Matches: 27, Mismatches: 6, Indels: 4
0.73 0.16 0.11
Matches are distributed among these distances:
16 4 0.15
17 20 0.74
18 3 0.11
ACGTcount: A:0.23, C:0.04, G:0.10, T:0.63
Consensus pattern (17 bp):
AGTATTTTATTTTATTT
Found at i:29566 original size:21 final size:21
Alignment explanation
Indices: 29507--29568 Score: 63
Period size: 21 Copynumber: 3.0 Consensus size: 21
29497 TAAATATTTT
29507 TAAAAATTTAATTAAATATAAA
1 TAAAAATTTAATTAAAT-TAAA
* ***
29529 GAAAAA-TTAAACCAATTAAA
1 TAAAAATTTAATTAAATTAAA
*
29549 TAAAAATTTAATTTAATTAA
1 TAAAAATTTAATTAAATTAA
29569 TTTAATTTTG
Statistics
Matches: 31, Mismatches: 8, Indels: 3
0.74 0.19 0.07
Matches are distributed among these distances:
20 9 0.29
21 17 0.55
22 5 0.16
ACGTcount: A:0.61, C:0.03, G:0.02, T:0.34
Consensus pattern (21 bp):
TAAAAATTTAATTAAATTAAA
Found at i:29629 original size:26 final size:25
Alignment explanation
Indices: 29583--29634 Score: 59
Period size: 26 Copynumber: 2.0 Consensus size: 25
29573 ATTTTGTATT
* ** *
29583 AAAAATTAAATTTTATTATTTTTAA
1 AAAAATTAAATATTAAAATTTATAA
29608 AAAAATTATAATATTAAAATTTATAA
1 AAAAATTA-AATATTAAAATTTATAA
29634 A
1 A
29635 CTTTATTTAT
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (25 bp):
AAAAATTAAATATTAAAATTTATAA
Found at i:29667 original size:19 final size:19
Alignment explanation
Indices: 29623--29671 Score: 55
Period size: 19 Copynumber: 2.6 Consensus size: 19
29613 TTATAATATT
* *
29623 AAAATTTATAAACTTTATT
1 AAAAATTATAAACTTTATA
* *
29642 TATAATTATAAACTTTATA
1 AAAAATTATAAACTTTATA
29661 AAAAATT-TAAA
1 AAAAATTATAAA
29672 AATAAAAAAA
Statistics
Matches: 24, Mismatches: 6, Indels: 1
0.77 0.19 0.03
Matches are distributed among these distances:
18 4 0.17
19 20 0.83
ACGTcount: A:0.53, C:0.04, G:0.00, T:0.43
Consensus pattern (19 bp):
AAAAATTATAAACTTTATA
Found at i:29934 original size:15 final size:16
Alignment explanation
Indices: 29907--29939 Score: 59
Period size: 15 Copynumber: 2.1 Consensus size: 16
29897 TTTTGATATT
29907 TTACAATGTAATGTGA
1 TTACAATGTAATGTGA
29923 TTACAA-GTAATGTGA
1 TTACAATGTAATGTGA
29938 TT
1 TT
29940 GTAAGTAATA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.65
16 6 0.35
ACGTcount: A:0.36, C:0.06, G:0.18, T:0.39
Consensus pattern (16 bp):
TTACAATGTAATGTGA
Found at i:30073 original size:33 final size:31
Alignment explanation
Indices: 30018--30124 Score: 110
Period size: 33 Copynumber: 3.3 Consensus size: 31
30008 TCTTTTATAT
*
30018 TTTATTTT-TAATGTTATATATTTTATTTTCA
1 TTTATTTTATAAT-TTATATATTTTATTTTAA
*
30049 TTTATTATTATAATCTTATATATTTTATTTTTA
1 TTTATT-TTATAAT-TTATATATTTTATTTTAA
* *
30082 TTT-TTAATATAATTTTTATATTATATATTTTAA
1 TTTATT-TTATAATTTATATATT-T-TATTTTAA
30115 TTTATTTTAT
1 TTTATTTTAT
30125 TTTACCTATA
Statistics
Matches: 65, Mismatches: 6, Indels: 8
0.82 0.08 0.10
Matches are distributed among these distances:
31 14 0.22
32 12 0.18
33 37 0.57
34 2 0.03
ACGTcount: A:0.30, C:0.02, G:0.01, T:0.67
Consensus pattern (31 bp):
TTTATTTTATAATTTATATATTTTATTTTAA
Found at i:30135 original size:33 final size:34
Alignment explanation
Indices: 30098--30162 Score: 98
Period size: 33 Copynumber: 1.9 Consensus size: 34
30088 ATATAATTTT
*
30098 TATATTATAT-A-TTTTAATTTATTTTATTTTACC
1 TATATTATATAATTTTTAATTT-TTATATTTTACC
30131 TATATTATATAATTTTTAATTTTTATATTTTA
1 TATATTATATAATTTTTAATTTTTATATTTTA
30163 TTTTATTTTA
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
33 10 0.34
34 10 0.34
35 9 0.31
ACGTcount: A:0.32, C:0.03, G:0.00, T:0.65
Consensus pattern (34 bp):
TATATTATATAATTTTTAATTTTTATATTTTACC
Found at i:30187 original size:24 final size:24
Alignment explanation
Indices: 30056--30192 Score: 72
Period size: 24 Copynumber: 5.7 Consensus size: 24
30046 TCATTTATTA
30056 TTATAATCTTATA-TATTTT-ATTT
1 TTAT-ATCTTATATTATTTTAATTT
* * *
30079 TTAT-TTTTAATATAATTTTTATATT
1 TTATATCTT-ATATTATTTTAAT-TT
* *
30104 ATATATTTTA-ATTTATTTT-A-TT
1 TTATATCTTATA-TTATTTTAATTT
* *
30126 TTACCTATATTATATAATTTTTAATTT
1 TTA--TATCTTATATTA-TTTTAATTT
* *
30153 TTATATTTTATTTTATTTTAATTT
1 TTATATCTTATATTATTTTAATTT
30177 TTGAT-TCTTATATTAT
1 TT-ATATCTTATATTAT
30193 ATGTTTTATT
Statistics
Matches: 89, Mismatches: 12, Indels: 25
0.71 0.10 0.20
Matches are distributed among these distances:
21 3 0.03
22 7 0.08
23 9 0.10
24 32 0.36
25 28 0.31
26 5 0.06
27 5 0.06
ACGTcount: A:0.30, C:0.03, G:0.01, T:0.66
Consensus pattern (24 bp):
TTATATCTTATATTATTTTAATTT
Found at i:30188 original size:49 final size:49
Alignment explanation
Indices: 30088--30223 Score: 129
Period size: 49 Copynumber: 2.8 Consensus size: 49
30078 TTTATTTTTA
* * *
30088 ATATAATTTTTATATTATATATTTTAATTTATTTT-ATTTTACCTATATT
1 ATATAATTTTTAT-TTTTATATTTTATTTTATTTTAATTTTACATATATT
** *
30137 ATATAATTTTTAATTTTTATATTTTATTTTATTTTAATTTTTGAT-TCTT
1 ATATAATTTTT-ATTTTTATATTTTATTTTATTTTAATTTTACATATATT
*
30186 ATATTATATGTTTTA-TTTTA-ATATT-TTTTATTTTAATT
1 ATA-TA-AT-TTTTATTTTTATATTTTATTTTATTTTAATT
30224 ATAATATCAT
Statistics
Matches: 75, Mismatches: 7, Indels: 11
0.81 0.08 0.12
Matches are distributed among these distances:
48 13 0.17
49 40 0.53
50 15 0.20
51 3 0.04
52 4 0.05
ACGTcount: A:0.29, C:0.02, G:0.01, T:0.67
Consensus pattern (49 bp):
ATATAATTTTTATTTTTATATTTTATTTTATTTTAATTTTACATATATT
Found at i:30220 original size:15 final size:15
Alignment explanation
Indices: 30191--30222 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
30181 TTCTTATATT
30191 ATATGTTTTATTTTA
1 ATATGTTTTATTTTA
*
30206 ATATTTTTTATTTTA
1 ATATGTTTTATTTTA
30221 AT
1 AT
30223 TATAATATCA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.28, C:0.00, G:0.03, T:0.69
Consensus pattern (15 bp):
ATATGTTTTATTTTA
Found at i:30226 original size:33 final size:33
Alignment explanation
Indices: 30140--30212 Score: 96
Period size: 31 Copynumber: 2.2 Consensus size: 33
30130 CTATATTATA
* * *
30140 TAATTTTTAATTTTTATATT-T-TATTTTATTT
1 TAATTTTTGATTCTTATATTATATGTTTTATTT
30171 TAATTTTTGATTCTTATATTATATGTTTTATTT
1 TAATTTTTGATTCTTATATTATATGTTTTATTT
30204 TAATATTTT
1 TAAT-TTTT
30213 TTATTTTAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
31 18 0.50
32 1 0.03
33 13 0.36
34 4 0.11
ACGTcount: A:0.26, C:0.01, G:0.03, T:0.70
Consensus pattern (33 bp):
TAATTTTTGATTCTTATATTATATGTTTTATTT
Found at i:31607 original size:216 final size:215
Alignment explanation
Indices: 31028--31671 Score: 713
Period size: 216 Copynumber: 3.0 Consensus size: 215
31018 TTATAAAGTA
* * *
31028 TATATT-TATATATATTACTTTATTATATATATATAAAATTAA--ATACGCAACTTATATATTGT
1 TATATTATA-ATATATTACTTTATTATATATATATGAAATTAATGATA--CAATTTATATATTAT
* * **
31090 AATGTTTTATATCAAAATTTGTATAAATAACAACTAATTATAAATAATGCGTTAT-AAAA--AAA
63 AATGTTTTATATCAAAGTTTGTATAAATAATAACTAATTATAAATAATATGTTATAAAAACTAAA
* * *
31152 G-AATAACTAATAAAATTATTAAGTATAATCACATAAATAAAGTTTATTA-AAGTTACAGTAATG
128 GTAATAACTAATAAAATTATTAAGTATAATCATATAAATAAAGTCTATTATAAGTTATAGTAATG
*
31215 TTTATGCATAAATT-AATAATATG
193 TTTATGTATAAATTAAAT-ATATG
* * * * * *
31238 CATA-TATAACT-TACTATTTTA-T-TATATATATGAAATTAATGACACAATTCATATGTTATAA
1 TATATTATAA-TATATTACTTTATTATATATATATGAAATTAATGATACAATTTATATATTATAA
*
31299 TGTTTAAATTCTTATAACAAAGTTTGTATAAATAATAACTAATTATAAATAATATGTTATAAAAA
65 TG------TT-TTATATCAAAGTTTGTATAAATAATAACTAATTATAAATAATATGTTATAAAAA
* ** * * * *
31364 CTAACGTAATAGTTATTAAAGTTATTAAGTATAATCATATAAATAAAGTCTAATATAAGTTATAA
123 CTAAAGTAATAACTAATAAAATTATTAAGTATAATCATATAAATAAAGTCTATTATAAGTTATAG
*
31429 TAATGCTTATGTATAAATTAAATATATG
188 TAATGTTTATGTATAAATTAAATATATG
31457 TATATGTATAATATATTACTTTATTATATATATATGAAATTAATGATACAATTTATATATTATAA
1 TATAT-TATAATATATTACTTTATTATATATATATGAAATTAATGATACAATTTATATATTATAA
* * * * * *
31522 TGTTTTATATCAAAGTTTATGTAAATAGTAACTAATGATAAACAATATGCTATAAAAACTAAAGT
65 TGTTTTATATCAAAGTTTGTATAAATAATAACTAATTATAAATAATATGTTATAAAAACTAAAGT
* * * * * * *
31587 AATAACGAATAAAATTATTAAATGTAATCATATAAATAAAG-CATATTATAAATTGTAGCAATAT
130 AATAACTAATAAAATTATTAAGTATAATCATATAAATAAAGTC-TATTATAAGTTATAGTAATGT
31651 TTATGTATAAATTAAATATAT
194 TTATGTATAAATTAAATATAT
31672 AATATATTTA
Statistics
Matches: 357, Mismatches: 54, Indels: 40
0.79 0.12 0.09
Matches are distributed among these distances:
207 31 0.09
208 1 0.00
209 12 0.03
210 6 0.02
213 2 0.01
214 44 0.12
215 5 0.01
216 122 0.34
217 5 0.01
218 41 0.11
219 32 0.09
220 4 0.01
221 13 0.04
222 1 0.00
223 38 0.11
ACGTcount: A:0.47, C:0.06, G:0.07, T:0.40
Consensus pattern (215 bp):
TATATTATAATATATTACTTTATTATATATATATGAAATTAATGATACAATTTATATATTATAAT
GTTTTATATCAAAGTTTGTATAAATAATAACTAATTATAAATAATATGTTATAAAAACTAAAGTA
ATAACTAATAAAATTATTAAGTATAATCATATAAATAAAGTCTATTATAAGTTATAGTAATGTTT
ATGTATAAATTAAATATATG
Found at i:31694 original size:16 final size:17
Alignment explanation
Indices: 31662--31694 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
31652 TATGTATAAA
31662 TTAAATATATAATATAT
1 TTAAATATATAATATAT
*
31679 TTAAATA-ATTATATAT
1 TTAAATATATAATATAT
31695 ATTCATAACA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (17 bp):
TTAAATATATAATATAT
Found at i:37961 original size:3 final size:3
Alignment explanation
Indices: 37953--37984 Score: 64
Period size: 3 Copynumber: 10.7 Consensus size: 3
37943 CCTATACCAA
37953 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AA
37985 AAGCAATAAT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 29 1.00
ACGTcount: A:0.69, C:0.00, G:0.00, T:0.31
Consensus pattern (3 bp):
AAT
Found at i:43881 original size:31 final size:31
Alignment explanation
Indices: 43843--43956 Score: 93
Period size: 31 Copynumber: 3.5 Consensus size: 31
43833 GTACAGTATA
43843 AACAAGATCTACAACACTTATTCGGGTCATT
1 AACAAGATCTACAACACTTATTCGGGTCATT
* *** * *
43874 AACAAGATCTATAACGAAGAACTTTGTGGATTAATAT
1 AACAAGATCTACAAC-ACTTA-TTCG-GG--TCAT-T
43911 AAACAAGATCTACAACACTTATTCGGGTCATT
1 -AACAAGATCTACAACACTTATTCGGGTCATT
* *
43943 TACAAGTTCTACAA
1 AACAAGATCTACAA
43957 AGAACTTTAT
Statistics
Matches: 62, Mismatches: 14, Indels: 14
0.69 0.16 0.16
Matches are distributed among these distances:
31 26 0.42
32 3 0.05
33 6 0.10
34 2 0.03
35 2 0.03
36 6 0.10
37 3 0.05
38 14 0.23
ACGTcount: A:0.39, C:0.18, G:0.13, T:0.29
Consensus pattern (31 bp):
AACAAGATCTACAACACTTATTCGGGTCATT
Found at i:60868 original size:2 final size:2
Alignment explanation
Indices: 60861--60885 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
60851 TAACATGTTC
60861 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
60886 ATTTAAATTA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:63540 original size:30 final size:30
Alignment explanation
Indices: 63506--63565 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 30
63496 GACGTATAAT
* *
63506 TAAATTTGTGTAATTTTATTTTGAATCAAA
1 TAAATTTGTATAATTTTATTTTAAATCAAA
*
63536 TAAATTTTTATAATTTTATTTTAAATCAAA
1 TAAATTTGTATAATTTTATTTTAAATCAAA
63566 NNNNNNNNNN
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
30 27 1.00
ACGTcount: A:0.40, C:0.03, G:0.05, T:0.52
Consensus pattern (30 bp):
TAAATTTGTATAATTTTATTTTAAATCAAA
Found at i:67657 original size:2 final size:2
Alignment explanation
Indices: 67652--67677 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
67642 ATGTGCACAC
67652 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
67678 TTGTATGTAT
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:70770 original size:21 final size:21
Alignment explanation
Indices: 70731--70770 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
70721 TATTTTCGTA
*
70731 TATACATTATTTTTAATTTTT
1 TATACATTATTATTAATTTTT
* *
70752 TATATATTATTATTGATTT
1 TATACATTATTATTAATTT
70771 ACTTGTGGAG
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (21 bp):
TATACATTATTATTAATTTTT
Found at i:72892 original size:21 final size:21
Alignment explanation
Indices: 72866--72920 Score: 74
Period size: 21 Copynumber: 2.6 Consensus size: 21
72856 CCATTTTCTG
*
72866 TTCATCAAACTTTTAAACCAA
1 TTCATCAAACTTTAAAACCAA
*
72887 TTCATCAAACTCTAAAACCAA
1 TTCATCAAACTTTAAAACCAA
* *
72908 TTTATAAAACTTT
1 TTCATCAAACTTT
72921 GATTCAGTTT
Statistics
Matches: 29, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.44, C:0.22, G:0.00, T:0.35
Consensus pattern (21 bp):
TTCATCAAACTTTAAAACCAA
Found at i:77107 original size:15 final size:17
Alignment explanation
Indices: 77087--77137 Score: 63
Period size: 15 Copynumber: 3.1 Consensus size: 17
77077 GAGAAATGTT
77087 ATAATTAAAATA-AT-A
1 ATAATTAAAATATATAA
77102 ATAATTAAAA-ATATAA
1 ATAATTAAAATATATAA
*
77118 ATATATTAAAATTTATAA
1 ATA-ATTAAAATATATAA
77136 AT
1 AT
77138 TAGAAATTTT
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
14 1 0.03
15 12 0.39
16 4 0.13
17 7 0.23
18 7 0.23
ACGTcount: A:0.63, C:0.00, G:0.00, T:0.37
Consensus pattern (17 bp):
ATAATTAAAATATATAA
Found at i:77137 original size:18 final size:16
Alignment explanation
Indices: 77087--77128 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 16
77077 GAGAAATGTT
77087 ATAATT-AAAATA-ATA
1 ATAATTAAAAATATA-A
77102 ATAATTAAAAATATAA
1 ATAATTAAAAATATAA
77118 ATATATTAAAA
1 ATA-ATTAAAA
77129 TTTATAAATT
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
15 6 0.25
16 10 0.42
17 8 0.33
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
ATAATTAAAAATATAA
Found at i:84850 original size:54 final size:53
Alignment explanation
Indices: 84792--84924 Score: 142
Period size: 54 Copynumber: 2.5 Consensus size: 53
84782 TTAATCACCA
*
84792 AAAGTGGATAGATATATTTAACCACCAAAAGTTAATGA-ATATATTTAACTATCG
1 AAAGTGGAT-GATACATTTAACCACCAAAAGTTAA-GAGATATATTTAACTATCG
* *** * *
84846 AAAGTGGATGAATACATTTAATCATTGAAAGTTGAGAGATATATTTAACTATTG
1 AAAGTGGATG-ATACATTTAACCACCAAAAGTTAAGAGATATATTTAACTATCG
**
84900 AAAGTAAATGGATACATTTAACCAC
1 AAAGTGGAT-GATACATTTAACCAC
84925 TAGAAATGAA
Statistics
Matches: 65, Mismatches: 11, Indels: 6
0.79 0.13 0.07
Matches are distributed among these distances:
53 3 0.05
54 61 0.94
55 1 0.02
ACGTcount: A:0.44, C:0.10, G:0.15, T:0.32
Consensus pattern (53 bp):
AAAGTGGATGATACATTTAACCACCAAAAGTTAAGAGATATATTTAACTATCG
Found at i:84875 original size:27 final size:27
Alignment explanation
Indices: 84754--84920 Score: 92
Period size: 27 Copynumber: 6.2 Consensus size: 27
84744 ATAAAAAAAC
* * *
84754 TTTAATCATTGAAAATGAATGGATACA
1 TTTAATCATCGAAAGTGAATGAATACA
* * * *
84781 TTTAATCACCAAAAGTGGAT-AGATATA
1 TTTAATCATCGAAAGTGAATGA-ATACA
* * * * *
84808 TTTAACCACCAAAAGTTAATGAATATA
1 TTTAATCATCGAAAGTGAATGAATACA
*
84835 TTTAA-CTATCGAAAGTGGATGAATACA
1 TTTAATC-ATCGAAAGTGAATGAATACA
* *
84862 TTTAATCATTGAAAGTTG-A-GAGATATA
1 TTTAATCATCGAAAG-TGAATGA-ATACA
* * *
84889 TTTAA-CTATTGAAAGTAAATGGATACA
1 TTTAATC-ATCGAAAGTGAATGAATACA
84916 TTTAA
1 TTTAA
84921 CCACTAGAAA
Statistics
Matches: 111, Mismatches: 20, Indels: 18
0.74 0.13 0.12
Matches are distributed among these distances:
26 5 0.05
27 101 0.91
28 5 0.05
ACGTcount: A:0.44, C:0.09, G:0.14, T:0.33
Consensus pattern (27 bp):
TTTAATCATCGAAAGTGAATGAATACA
Found at i:84921 original size:27 final size:27
Alignment explanation
Indices: 84819--84921 Score: 102
Period size: 27 Copynumber: 3.8 Consensus size: 27
84809 TTAACCACCA
* *
84819 AAAGTTAATGAATATATTTAACTATCG
1 AAAGTTAATGAATACATTTAACTATTG
**
84846 AAAGTGGATGAATACATTTAA-TCATTG
1 AAAGTTAATGAATACATTTAACT-ATTG
* *
84873 AAAGTTGA-GAGATATATTTAACTATTG
1 AAAGTTAATGA-ATACATTTAACTATTG
* *
84900 AAAGTAAATGGATACATTTAAC
1 AAAGTTAATGAATACATTTAAC
84922 CACTAGAAAT
Statistics
Matches: 62, Mismatches: 10, Indels: 8
0.77 0.12 0.10
Matches are distributed among these distances:
26 3 0.05
27 57 0.92
28 2 0.03
ACGTcount: A:0.44, C:0.07, G:0.16, T:0.34
Consensus pattern (27 bp):
AAAGTTAATGAATACATTTAACTATTG
Found at i:97495 original size:2 final size:2
Alignment explanation
Indices: 97488--97512 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
97478 AGCAAAGGAC
97488 AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT A
97513 CAGTAATATA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:98772 original size:23 final size:24
Alignment explanation
Indices: 98737--98784 Score: 62
Period size: 23 Copynumber: 2.0 Consensus size: 24
98727 AGAAAGAAAT
*
98737 AGAAAGAGAGGAGA-AAAAAACAA
1 AGAAAAAGAGGAGATAAAAAACAA
* *
98760 AGAAAAAGCGGAGATAAAATACAA
1 AGAAAAAGAGGAGATAAAAAACAA
98784 A
1 A
98785 AATTGGTCAT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.67, C:0.06, G:0.23, T:0.04
Consensus pattern (24 bp):
AGAAAAAGAGGAGATAAAAAACAA
Found at i:120366 original size:21 final size:21
Alignment explanation
Indices: 120336--120384 Score: 89
Period size: 21 Copynumber: 2.3 Consensus size: 21
120326 GAAAAAGGCC
*
120336 TCTGCATGCTGCAGAGATGCA
1 TCTGCTTGCTGCAGAGATGCA
120357 TCTGCTTGCTGCAGAGATGCA
1 TCTGCTTGCTGCAGAGATGCA
120378 TCTGCTT
1 TCTGCTT
120385 TAATGATGTT
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 27 1.00
ACGTcount: A:0.18, C:0.24, G:0.27, T:0.31
Consensus pattern (21 bp):
TCTGCTTGCTGCAGAGATGCA
Found at i:131132 original size:2 final size:2
Alignment explanation
Indices: 131125--131155 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
131115 ACCATTCATT
131125 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
131156 TTCTTTTTCA
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:136676 original size:15 final size:16
Alignment explanation
Indices: 136645--136679 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
136635 ATAATTTTTT
*
136645 AATTTTTAAAAATTAA
1 AATTATTAAAAATTAA
136661 AATTATTAAAAA-TAA
1 AATTATTAAAAATTAA
136676 AATT
1 AATT
136680 CACATAACAG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
15 7 0.39
16 11 0.61
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
AATTATTAAAAATTAA
Found at i:140068 original size:12 final size:12
Alignment explanation
Indices: 140051--140089 Score: 53
Period size: 12 Copynumber: 3.2 Consensus size: 12
140041 ATTTATTTGA
140051 TTTCATTTTTAT
1 TTTCATTTTTAT
140063 TTTCATTTTTCAT
1 TTTCATTTTT-AT
*
140076 TCT-ATTTTTAT
1 TTTCATTTTTAT
140087 TTT
1 TTT
140090 ATAAATAATG
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 4 0.17
12 16 0.67
13 4 0.17
ACGTcount: A:0.15, C:0.10, G:0.00, T:0.74
Consensus pattern (12 bp):
TTTCATTTTTAT
Found at i:149516 original size:15 final size:16
Alignment explanation
Indices: 149496--149534 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
149486 AAATTAAAGA
149496 TAAAA-TATTAATATT
1 TAAAATTATTAATATT
*
149511 TAAAATTGTTAATATT
1 TAAAATTATTAATATT
149527 T-AAATTAT
1 TAAAATTAT
149535 CAATTATTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
15 11 0.52
16 10 0.48
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (16 bp):
TAAAATTATTAATATT
Found at i:149557 original size:27 final size:27
Alignment explanation
Indices: 149527--149580 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
149517 TGTTAATATT
* *
149527 TAAATTATCAATTATTATTATTTTAAA
1 TAAATTATAAATTATTAATATTTTAAA
149554 TAAATTATAAATTATTAATATTTTAAA
1 TAAATTATAAATTATTAATATTTTAAA
149581 AATAAAATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (27 bp):
TAAATTATAAATTATTAATATTTTAAA
Found at i:149775 original size:42 final size:43
Alignment explanation
Indices: 149674--149786 Score: 122
Period size: 42 Copynumber: 2.7 Consensus size: 43
149664 TATTTTAAAT
* **
149674 TTAAATT-TAATTAAAATTATTAATATTTTAATAATAATAATTT
1 TTAAATTATAAATAAAA-TATTAATATTTTAATAATAATAATGA
* * * **
149717 TTCAATTATAAGTAAAATACTAATATTTTAA-AATGTTAATGA
1 TTAAATTATAAATAAAATATTAATATTTTAATAATAATAATGA
*
149759 TTAAATTATAAATAAAATGTTAATATTT
1 TTAAATTATAAATAAAATATTAATATTT
149787 AAATGATCAA
Statistics
Matches: 58, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
42 31 0.53
43 19 0.33
44 8 0.14
ACGTcount: A:0.49, C:0.02, G:0.04, T:0.46
Consensus pattern (43 bp):
TTAAATTATAAATAAAATATTAATATTTTAATAATAATAATGA
Found at i:149850 original size:28 final size:29
Alignment explanation
Indices: 149795--149852 Score: 75
Period size: 28 Copynumber: 2.0 Consensus size: 29
149785 TTAAATGATC
**
149795 AATTATTAATATTTTAAAGAAATTATAAA
1 AATTATTAATATTTTAAAGAAAAAATAAA
149824 AATTATTAATA-TTTAAA-AATAAAATAAA
1 AATTATTAATATTTTAAAGAA-AAAATAAA
149852 A
1 A
149853 TAAAATAAAA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
27 2 0.08
28 13 0.50
29 11 0.42
ACGTcount: A:0.60, C:0.00, G:0.02, T:0.38
Consensus pattern (29 bp):
AATTATTAATATTTTAAAGAAAAAATAAA
Found at i:150031 original size:23 final size:23
Alignment explanation
Indices: 149992--150083 Score: 80
Period size: 23 Copynumber: 3.8 Consensus size: 23
149982 ATTAATATTT
*
149992 AAAATATTATTGA-TTAAATTATA
1 AAAATATTAAT-ATTTAAATTATA
*
150015 AAAATATTAATATTTAAATAAT-
1 AAAATATTAATATTTAAATTATA
*
150037 AAATTATTAATATTTTAAAGAAATTATA
1 AAAATATTAATA-TTT----AAATTATA
150065 AAAATTATTAATATTTAAA
1 AAAA-TATTAATATTTAAA
150084 AAATAAAATA
Statistics
Matches: 56, Mismatches: 5, Indels: 15
0.74 0.07 0.20
Matches are distributed among these distances:
22 12 0.21
23 21 0.38
24 3 0.05
27 6 0.11
28 6 0.11
29 8 0.14
ACGTcount: A:0.55, C:0.00, G:0.02, T:0.42
Consensus pattern (23 bp):
AAAATATTAATATTTAAATTATA
Found at i:150046 original size:38 final size:39
Alignment explanation
Indices: 149977--150055 Score: 101
Period size: 38 Copynumber: 2.1 Consensus size: 39
149967 AGATTTAAAT
*
149977 AAAATATTAATATTTAAAATATTATTGATTAA-ATTATA
1 AAAATATTAATATTTAAAATATAATTGATTAATATTATA
*
150015 AAAATATTAATATTT-AAATAATAAATT-ATTAATATTTTA
1 AAAATATTAATATTTAAAAT-AT-AATTGATTAATATTATA
150054 AA
1 AA
150056 GAAATTATAA
Statistics
Matches: 36, Mismatches: 2, Indels: 5
0.84 0.05 0.12
Matches are distributed among these distances:
37 4 0.11
38 22 0.61
39 10 0.28
ACGTcount: A:0.54, C:0.00, G:0.01, T:0.44
Consensus pattern (39 bp):
AAAATATTAATATTTAAAATATAATTGATTAATATTATA
Found at i:150065 original size:27 final size:26
Alignment explanation
Indices: 150007--150089 Score: 84
Period size: 29 Copynumber: 3.2 Consensus size: 26
149997 ATTATTGATT
* *
150007 AAATTATAAAAATATTAATATTT---
1 AAATAATAAAATTATTAATATTTAAA
150030 AAATAAT-AAATTATTAATATTTTAAA
1 AAATAATAAAATTATTAATA-TTTAAA
*
150056 GAAATTATAAAAATTATTAATATTTAAA
1 -AAATAAT-AAAATTATTAATATTTAAA
150084 AAATAA
1 AAATAA
150090 AATAAGGGAT
Statistics
Matches: 49, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
22 11 0.22
23 9 0.18
27 11 0.22
28 6 0.12
29 12 0.24
ACGTcount: A:0.59, C:0.00, G:0.01, T:0.40
Consensus pattern (26 bp):
AAATAATAAAATTATTAATATTTAAA
Found at i:150074 original size:29 final size:28
Alignment explanation
Indices: 150032--150087 Score: 87
Period size: 29 Copynumber: 2.0 Consensus size: 28
150022 TAATATTTAA
150032 ATAATAAATTATTAATATTTTAAAGAAATT
1 ATAATAAATTATTAATA-TTTAAA-AAATT
150062 ATAA-AAATTATTAATATTTAAAAAAT
1 ATAATAAATTATTAATATTTAAAAAAT
150088 AAAATAAGGG
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
27 4 0.15
28 6 0.23
29 12 0.46
30 4 0.15
ACGTcount: A:0.57, C:0.00, G:0.02, T:0.41
Consensus pattern (28 bp):
ATAATAAATTATTAATATTTAAAAAATT
Found at i:161683 original size:44 final size:45
Alignment explanation
Indices: 161609--161695 Score: 140
Period size: 44 Copynumber: 2.0 Consensus size: 45
161599 TTTAATACTT
* *
161609 TTATGTTGAATACCTTTAGTAGGCAAAGAATGTGATTAGTATAAC
1 TTATGTTGAATACCTTTAGTAGGCAAAGAATGTAATTAATATAAC
*
161654 TTATGTTGAATA-CTTTTGTAGGCAAAGAATGTAATTAATATA
1 TTATGTTGAATACCTTTAGTAGGCAAAGAATGTAATTAATATA
161696 GCAAGGGAAT
Statistics
Matches: 39, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
44 27 0.69
45 12 0.31
ACGTcount: A:0.37, C:0.07, G:0.18, T:0.38
Consensus pattern (45 bp):
TTATGTTGAATACCTTTAGTAGGCAAAGAATGTAATTAATATAAC
Found at i:166625 original size:2 final size:2
Alignment explanation
Indices: 166618--166651 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
166608 GAAGAGTATC
166618 AT 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 AT
166652 GCAAATTTTG
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:168602 original size:24 final size:24
Alignment explanation
Indices: 168548--168607 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
168538 CTCATTTAAT
168548 TATTATTTTATTATTAAAAATAAA
1 TATTATTTTATTATTAAAAATAAA
* *
168572 TAATATTTTATT-TTAAATATAATA
1 TATTATTTTATTATTAAAAATAA-A
*
168596 TGTTA-TTTATTA
1 TATTATTTTATTA
168608 GTTATAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
23 15 0.50
24 15 0.50
ACGTcount: A:0.43, C:0.00, G:0.02, T:0.55
Consensus pattern (24 bp):
TATTATTTTATTATTAAAAATAAA
Found at i:174631 original size:3 final size:3
Alignment explanation
Indices: 174623--174648 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
174613 CAAAACTCGA
174623 AAG AAG AAG AAG AAG AAG AAG AAG AA
1 AAG AAG AAG AAG AAG AAG AAG AAG AA
174649 AAAGCTTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (3 bp):
AAG
Found at i:184766 original size:2 final size:2
Alignment explanation
Indices: 184759--184789 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
184749 TTATCTCCTA
184759 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG TG TG TG T
184790 TATCTCCCAC
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:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:189229 original size:80 final size:80
Alignment explanation
Indices: 189085--189235 Score: 203
Period size: 80 Copynumber: 1.9 Consensus size: 80
189075 CAAGGTTATA
* * *
189085 TTTAAATCCGATGTTTGCCTTTTCTAATTCCACAGACATTGATTTAATATAAATTGCTTATGGTT
1 TTTAAATCCGATGTTTGCCTTTTCTAATTCCACAGACATTGATTCAATACAAATTGCCTATGGTT
189150 GTGATAATCTGCATG
66 GTGATAATCTGCATG
* * ** * * * *
189165 TTTAAATCTGATGTTTGCGTTTTCTAATTCTGCAGACATTGGTTCGATACAAGTTGCCTGTGGTT
1 TTTAAATCCGATGTTTGCCTTTTCTAATTCCACAGACATTGATTCAATACAAATTGCCTATGGTT
189230 GTGATA
66 GTGATA
189236 GTCTTTAACA
Statistics
Matches: 60, Mismatches: 11, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
80 60 1.00
ACGTcount: A:0.25, C:0.15, G:0.19, T:0.42
Consensus pattern (80 bp):
TTTAAATCCGATGTTTGCCTTTTCTAATTCCACAGACATTGATTCAATACAAATTGCCTATGGTT
GTGATAATCTGCATG
Found at i:191043 original size:34 final size:33
Alignment explanation
Indices: 190995--191061 Score: 107
Period size: 34 Copynumber: 2.0 Consensus size: 33
190985 ATCAAAATTA
*
190995 ATTCATATGGACACATTGAAGGTTATATTCATAT
1 ATTCATACGGACACATTGAAGGTTATATT-ATAT
*
191029 ATTCATACGTACACATTGAAGGTTATATTATAT
1 ATTCATACGGACACATTGAAGGTTATATTATAT
191062 CAAAATTAAT
Statistics
Matches: 31, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 4 0.13
34 27 0.87
ACGTcount: A:0.36, C:0.12, G:0.13, T:0.39
Consensus pattern (33 bp):
ATTCATACGGACACATTGAAGGTTATATTATAT
Found at i:191829 original size:23 final size:22
Alignment explanation
Indices: 191779--191830 Score: 59
Period size: 23 Copynumber: 2.3 Consensus size: 22
191769 TCTTATTTTT
* *
191779 TATTTTTTAAAAAATATAATAA
1 TATTTTTTAAAAAATAAAAAAA
*
191801 TAATTTTTTAAATTAATAAAAAAA
1 T-ATTTTTTAAA-AAATAAAAAAA
191825 TATTTT
1 TATTTT
191831 AATCATTTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
22 1 0.04
23 15 0.60
24 9 0.36
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (22 bp):
TATTTTTTAAAAAATAAAAAAA
Found at i:192026 original size:20 final size:21
Alignment explanation
Indices: 191980--192026 Score: 62
Period size: 20 Copynumber: 2.3 Consensus size: 21
191970 TATGTTTTCA
191980 TAATT-AAATTAACTTATTAT
1 TAATTAAAATTAACTTATTAT
* *
192000 TATTTAAAATTAA-TTATTTT
1 TAATTAAAATTAACTTATTAT
192020 TAATTAA
1 TAATTAA
192027 TAAATGATTA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
20 16 0.70
21 7 0.30
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (21 bp):
TAATTAAAATTAACTTATTAT
Found at i:192182 original size:21 final size:19
Alignment explanation
Indices: 192158--192203 Score: 58
Period size: 18 Copynumber: 2.4 Consensus size: 19
192148 AGTATACTGT
192158 TTTTTAAAAATTGAAAATTTA
1 TTTTTAAAAA-T-AAAATTTA
*
192179 TTTTT-AAAATAAAATTTG
1 TTTTTAAAAATAAAATTTA
192197 TTTTTAA
1 TTTTTAA
192204 TAGTTTTATG
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
18 12 0.52
19 2 0.09
20 4 0.17
21 5 0.22
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.52
Consensus pattern (19 bp):
TTTTTAAAAATAAAATTTA
Found at i:202091 original size:13 final size:13
Alignment explanation
Indices: 202073--202099 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
202063 TCAGCAGAGC
202073 AAGAAAAGAGCAG
1 AAGAAAAGAGCAG
202086 AAGAAAAGAGCAG
1 AAGAAAAGAGCAG
202099 A
1 A
202100 CACATTGCTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.63, C:0.07, G:0.30, T:0.00
Consensus pattern (13 bp):
AAGAAAAGAGCAG
Found at i:203674 original size:17 final size:17
Alignment explanation
Indices: 203652--203690 Score: 78
Period size: 17 Copynumber: 2.3 Consensus size: 17
203642 AAGCATATGT
203652 AGCATTAGTAGCAATGA
1 AGCATTAGTAGCAATGA
203669 AGCATTAGTAGCAATGA
1 AGCATTAGTAGCAATGA
203686 AGCAT
1 AGCAT
203691 CCAATCGTAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.41, C:0.13, G:0.23, T:0.23
Consensus pattern (17 bp):
AGCATTAGTAGCAATGA
Found at i:211354 original size:17 final size:18
Alignment explanation
Indices: 211332--211365 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
211322 TTGCATAAGT
211332 ATTCCCCAACTC-ATTTA
1 ATTCCCCAACTCGATTTA
*
211349 ATTCCCCCACTCGATTT
1 ATTCCCCAACTCGATTT
211366 TGCAGCACTG
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 11 0.73
18 4 0.27
ACGTcount: A:0.24, C:0.38, G:0.03, T:0.35
Consensus pattern (18 bp):
ATTCCCCAACTCGATTTA
Found at i:213315 original size:23 final size:23
Alignment explanation
Indices: 213271--213315 Score: 56
Period size: 24 Copynumber: 1.9 Consensus size: 23
213261 GCAACAATAT
*
213271 ATTTTTTTTAATATGGCATGTAAC
1 ATTTTTTCTAATATGG-ATGTAAC
213295 ATTTTTTCTAATTATGG-TGTA
1 ATTTTTTCTAA-TATGGATGTA
213316 TAACATATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 3
0.83 0.04 0.13
Matches are distributed among these distances:
23 4 0.21
24 10 0.53
25 5 0.26
ACGTcount: A:0.27, C:0.07, G:0.13, T:0.53
Consensus pattern (23 bp):
ATTTTTTCTAATATGGATGTAAC
Found at i:216163 original size:52 final size:52
Alignment explanation
Indices: 216107--216208 Score: 143
Period size: 53 Copynumber: 1.9 Consensus size: 52
216097 AATATTGAAT
* *
216107 ATGATGATCT-TTTTTTTTTTCAACTTAGTCCCTCAAACTTTAAACCTATTTG
1 ATGAT-ATCTATTTTTTTTTTCAACTTAATCCCACAAACTTTAAACCTATTTG
* *
216159 ATGATATTTAATTTTTTTTTTCAACTTAATCCCACGAACTTTAAACCTAT
1 ATGATATCT-ATTTTTTTTTTCAACTTAATCCCACAAACTTTAAACCTAT
216209 CATTCTCATT
Statistics
Matches: 44, Mismatches: 4, Indels: 3
0.86 0.08 0.06
Matches are distributed among these distances:
51 3 0.07
52 5 0.11
53 36 0.82
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (52 bp):
ATGATATCTATTTTTTTTTTCAACTTAATCCCACAAACTTTAAACCTATTTG
Found at i:219566 original size:3 final size:3
Alignment explanation
Indices: 219558--219587 Score: 60
Period size: 3 Copynumber: 10.0 Consensus size: 3
219548 GATAAAAACC
219558 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
219588 CTTGTTAGAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 27 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:223278 original size:16 final size:15
Alignment explanation
Indices: 223247--223280 Score: 50
Period size: 16 Copynumber: 2.2 Consensus size: 15
223237 ACTTGCAGGG
*
223247 TTATTTTATTATTTA
1 TTATTTTATTAATTA
223262 TTATTTATATTAATTA
1 TTATTT-TATTAATTA
223278 TTA
1 TTA
223281 AATAAAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
15 6 0.35
16 11 0.65
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (15 bp):
TTATTTTATTAATTA
Found at i:226822 original size:14 final size:14
Alignment explanation
Indices: 226789--226822 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
226779 AAAAAGAGAA
*
226789 TAAAAAAATATTTT
1 TAAAAAAATATTCT
*
226803 TTAAAAAATATTCT
1 TAAAAAAATATTCT
226817 TAAAAA
1 TAAAAA
226823 TTAATAATTA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 17 1.00
ACGTcount: A:0.59, C:0.03, G:0.00, T:0.38
Consensus pattern (14 bp):
TAAAAAAATATTCT
Found at i:240202 original size:14 final size:15
Alignment explanation
Indices: 240183--240213 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
240173 TGGATTTGAC
240183 TTTTC-TTTTTTCTT
1 TTTTCTTTTTTTCTT
240197 TTTTCTTTTTTTCTT
1 TTTTCTTTTTTTCTT
240212 TT
1 TT
240214 ATTTCCTATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 5 0.31
15 11 0.69
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (15 bp):
TTTTCTTTTTTTCTT
Found at i:240206 original size:8 final size:7
Alignment explanation
Indices: 240183--240213 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
240173 TGGATTTGAC
240183 TTTTCTT
1 TTTTCTT
240190 TTTTCTT
1 TTTTCTT
240197 TTTTCTTT
1 TTTTC-TT
240205 TTTTCTT
1 TTTTCTT
240212 TT
1 TT
240214 ATTTCCTATA
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.00, C:0.13, G:0.00, T:0.87
Consensus pattern (7 bp):
TTTTCTT
Found at i:241662 original size:37 final size:38
Alignment explanation
Indices: 241601--241673 Score: 96
Period size: 37 Copynumber: 1.9 Consensus size: 38
241591 AAAAAATATC
* * *
241601 TTATATTTTATATATAATTATTTAT-TTTTATTTTATT
1 TTATATTTTAAATATAATAATTTATAATTTATTTTATT
241638 TTAT-TTTTAAATATTAATAATTTATAATTTATTTTA
1 TTATATTTTAAATA-TAATAATTTATAATTTATTTTA
241674 AATACTAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
36 8 0.26
37 14 0.45
38 9 0.29
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (38 bp):
TTATATTTTAAATATAATAATTTATAATTTATTTTATT
Found at i:241836 original size:27 final size:26
Alignment explanation
Indices: 241794--241851 Score: 82
Period size: 27 Copynumber: 2.2 Consensus size: 26
241784 AACTTAATTT
*
241794 AATTT-TTTAAATATTAATAATTTAC
1 AATTTATTTAAATATTAATAATTAAC
*
241819 AATTTATTTAAAATATTAATAATTAAT
1 AATTTATTT-AAATATTAATAATTAAC
241846 AATTTA
1 AATTTA
241852 CGTATTAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
25 5 0.17
26 3 0.10
27 21 0.72
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (26 bp):
AATTTATTTAAATATTAATAATTAAC
Found at i:241955 original size:146 final size:151
Alignment explanation
Indices: 241628--242005 Score: 493
Period size: 146 Copynumber: 2.5 Consensus size: 151
241618 TTATTTATTT
* * *
241628 TTAT-TTTATTTTA-TTTTTAAATATTAATAATTTATAATTTATTTTAAATACTAATAATTATTA
1 TTATATTTATTTTATTTTTTAAATATTAATAATTTATAATTTATTTAAAATATTAATAATTAATA
* * *
241691 CTTTTAAATATTAATGTTTTATTTATAATTTATTCATTAATATTATAAAATATTTATACTTTATT
66 -TTTTAAATATTAATATTTTATTTATAATTTAATCATCAATATTATAAAATATTTATACTTTATT
*
241756 TATAATTTAGATATTATTATGA
130 TATAATTTAAATATTATTATGA
* *
241778 TTATATAACTTAATTTAATTTTTTAAATATTAATAATTTACAATTTATTTAAAATATTAATAATT
1 TTATAT---TT-ATTTTATTTTTTAAATATTAATAATTTATAATTTATTTAAAATATTAATAATT
* ** *
241843 AATAATTTACGTATTAATATTTTATTTATAATTTAATCATCAATATTTTAAAATA-TTATTA-TT
62 AATATTTTAAATATTAATATTTTATTTATAATTTAATCATCAATATTATAAAATATTTA-TACTT
*
241906 T-TTTAT-ATTTAAATATTATTGTGA
126 TATTTATAATTTAAATATTATTATGA
* * *
241930 -T-TATTTATTTTATTTTTTAAATATTAATAATTTATAATTTATTAAAAATATTAGTAATTGATA
1 TTATATTTATTTTATTTTTTAAATATTAATAATTTATAATTTATTTAAAATATTAATAATTAATA
241993 TTTTAAATATTAA
66 TTTTAAATATTAA
242006 AGATTTAATT
Statistics
Matches: 199, Mismatches: 22, Indels: 18
0.83 0.09 0.08
Matches are distributed among these distances:
146 62 0.31
147 2 0.01
150 7 0.04
151 2 0.01
152 16 0.08
153 5 0.03
154 8 0.04
155 51 0.26
156 46 0.23
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.55
Consensus pattern (151 bp):
TTATATTTATTTTATTTTTTAAATATTAATAATTTATAATTTATTTAAAATATTAATAATTAATA
TTTTAAATATTAATATTTTATTTATAATTTAATCATCAATATTATAAAATATTTATACTTTATTT
ATAATTTAAATATTATTATGA
Found at i:242224 original size:14 final size:14
Alignment explanation
Indices: 242194--242223 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
242184 GGAATTGCTA
242194 TTTCTCTTTTTTCT
1 TTTCTCTTTTTTCT
242208 TTTCTCTTTTTT-T
1 TTTCTCTTTTTTCT
242221 TTT
1 TTT
242224 TTTGGCTTTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 4 0.25
14 12 0.75
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (14 bp):
TTTCTCTTTTTTCT
Found at i:251509 original size:96 final size:96
Alignment explanation
Indices: 251345--251535 Score: 303
Period size: 96 Copynumber: 2.0 Consensus size: 96
251335 AGACAAAGCT
* * *
251345 CGAACATGGCTTATAATCTATTTGTCACGGGGTTATTACTCTCTTCCTCATAAACGTGTTTATAG
1 CGAACATGGCTTATAATCCACTTGTCACGGGGTTATTACTCTCTTCCTCATAAACGCGTTTATAG
251410 GAGTGTGCAGCACACCCGCTTATAAGGAGCC
66 GAGTGTGCAGCACACCCGCTTATAAGGAGCC
* * *
251441 CGAACATGGCTTATAGTCCACTTGTCACGGGGTTATTACTCT-TTCTTCCGTAAACGCGTTTATA
1 CGAACATGGCTTATAATCCACTTGTCACGGGGTTATTACTCTCTTCCT-CATAAACGCGTTTATA
*
251505 GGAGTGTGCAGTACACCCGCTTATAAGGAGC
65 GGAGTGTGCAGCACACCCGCTTATAAGGAGC
251536 TCAGGACTTT
Statistics
Matches: 87, Mismatches: 7, Indels: 2
0.91 0.07 0.02
Matches are distributed among these distances:
95 4 0.05
96 83 0.95
ACGTcount: A:0.24, C:0.23, G:0.22, T:0.31
Consensus pattern (96 bp):
CGAACATGGCTTATAATCCACTTGTCACGGGGTTATTACTCTCTTCCTCATAAACGCGTTTATAG
GAGTGTGCAGCACACCCGCTTATAAGGAGCC
Found at i:252367 original size:134 final size:134
Alignment explanation
Indices: 252173--252437 Score: 370
Period size: 134 Copynumber: 2.0 Consensus size: 134
252163 CTCTGATACC
* * *
252173 ACTTGTCACGGGGTCATTACCCTCTCTCCCATAAATGAGCTTATAGGGGTGTGCAGCACACCTGC
1 ACTTGTCACGGGGTCATTACCCTCTCTCCCATAAACGAGCTTATAGGGGTGTGCAACACACCCGC
** * *
252238 TTATAAAGAACCCAGGACCTCCCGTTTTTGTTCGATGTGGAATAGAGGCACTTTCCTCGTGACAC
66 TTATAAAGAACCCAGGACCTCCCGTTCCTGTCCGATGTGGAATAGAAGCACTTTCCTCGTGACAC
252303 TCTA
131 TCTA
* * * *
252307 ACTTGTCACGGGGTCATTACTCT-TTTCCCCATAAACGCGTTTATAGGGGTGTGCAACACACCCG
1 ACTTGTCACGGGGTCATTACCCTCTCT-CCCATAAACGAGCTTATAGGGGTGTGCAACACACCCG
* ** * *
252371 CTTATAATGGGCCCAGGACCTCCCGTTCCTGTCCGATGTGGGATAGAAGTACTTTCCTCGTGACA
65 CTTATAAAGAACCCAGGACCTCCCGTTCCTGTCCGATGTGGAATAGAAGCACTTTCCTCGTGACA
252436 CT
130 CT
252438 TTCTCCCACT
Statistics
Matches: 114, Mismatches: 16, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
133 2 0.02
134 112 0.98
ACGTcount: A:0.22, C:0.28, G:0.22, T:0.28
Consensus pattern (134 bp):
ACTTGTCACGGGGTCATTACCCTCTCTCCCATAAACGAGCTTATAGGGGTGTGCAACACACCCGC
TTATAAAGAACCCAGGACCTCCCGTTCCTGTCCGATGTGGAATAGAAGCACTTTCCTCGTGACAC
TCTA
Found at i:253228 original size:194 final size:188
Alignment explanation
Indices: 253019--253395 Score: 551
Period size: 187 Copynumber: 2.0 Consensus size: 188
253009 TATTATATAT
* *
253019 ATAAAATTAATGACACAACTTATATTTTATAATATTTTAATTTTTATATCAAAGTTTGTATAAAT
1 ATAAAATTAATGACACAACTTATATGTTATAATATTTT-A----TAT-T-AAAGTTCGTATAAAT
*
253084 AATAACCAATTATAAATAATATATTATAAAAATTAAAATGATAACTAATAAAATTATTAAGTGTA
59 AATAACCAATTATAAATAATATATTATAAAAACTAAAATGATAACTAATAAAATTATTAAGTGTA
*
253149 A-ACATATAAATAAAGTCTATTATAAGTTACAGT-ATGTTTATATATAAATTAACTATATAAAAA
124 ATA-ATATAAATAAAGTCTATTATAAGTTACAGTAATGTTTATATATAAATTAAATATATAAAAA
253212 A
188 A
* * *
253213 ATAAAATTAATGACACAATTTATATGTTATAATGTTTTATATTAAAGTTCGTATAAATAATAACT
1 ATAAAATTAATGACACAACTTATATGTTATAATATTTTATATTAAAGTTCGTATAAATAATAACC
* * *
253278 AATTATAAATAATATGTTATAAAAACTAAGATGATAATTAATAAAATTATTAAGTGTAATAATAT
66 AATTATAAATAATATATTATAAAAACTAAAATGATAACTAATAAAATTATTAAGTGTAATAATAT
* * *
253343 AAATTAAGTTTATTATAAGTTATAGTAATGTTTATATATAAATTAAATATATA
131 AAATAAAGTCTATTATAAGTTACAGTAATGTTTATATATAAATTAAATATATA
253396 TATAATTTTA
Statistics
Matches: 168, Mismatches: 13, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
187 102 0.61
188 27 0.16
189 3 0.02
193 1 0.01
194 35 0.21
ACGTcount: A:0.50, C:0.04, G:0.06, T:0.40
Consensus pattern (188 bp):
ATAAAATTAATGACACAACTTATATGTTATAATATTTTATATTAAAGTTCGTATAAATAATAACC
AATTATAAATAATATATTATAAAAACTAAAATGATAACTAATAAAATTATTAAGTGTAATAATAT
AAATAAAGTCTATTATAAGTTACAGTAATGTTTATATATAAATTAAATATATAAAAAA
Found at i:255249 original size:14 final size:14
Alignment explanation
Indices: 255230--255259 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
255220 ACTACATAAA
255230 TATAAAAATTAATT
1 TATAAAAATTAATT
*
255244 TATAAAAATTTATT
1 TATAAAAATTAATT
255258 TA
1 TA
255260 ATCCAAAATA
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):
TATAAAAATTAATT
Found at i:260923 original size:33 final size:34
Alignment explanation
Indices: 260881--260949 Score: 113
Period size: 33 Copynumber: 2.1 Consensus size: 34
260871 TAGTTTATTT
* *
260881 AAGGAAAATAAATTAGCATGGCTA-TTGGTCGAA
1 AAGGAAAATAAATTAGCATGCCTATTTGGTCAAA
260914 AAGGAAAATAAATTAGCATGCCTATTTGGTCAAA
1 AAGGAAAATAAATTAGCATGCCTATTTGGTCAAA
260948 AA
1 AA
260950 TATAAAGATG
Statistics
Matches: 33, Mismatches: 2, Indels: 1
0.92 0.06 0.03
Matches are distributed among these distances:
33 23 0.70
34 10 0.30
ACGTcount: A:0.45, C:0.10, G:0.20, T:0.25
Consensus pattern (34 bp):
AAGGAAAATAAATTAGCATGCCTATTTGGTCAAA
Found at i:263814 original size:26 final size:24
Alignment explanation
Indices: 263785--263842 Score: 66
Period size: 26 Copynumber: 2.4 Consensus size: 24
263775 TTAAATTTTT
263785 AATTATATATTATAAAAATTAATTAA
1 AATTATATATTATAAAAA-T-ATTAA
*
263811 AATTAT-TAATTATAATAATATTAA
1 AATTATAT-ATTATAAAAATATTAA
263835 AATT-TATA
1 AATTATATA
263843 AATAAAGTAT
Statistics
Matches: 29, Mismatches: 1, Indels: 7
0.78 0.03 0.19
Matches are distributed among these distances:
23 2 0.07
24 10 0.34
25 2 0.07
26 15 0.52
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (24 bp):
AATTATATATTATAAAAATATTAA
Found at i:263885 original size:41 final size:44
Alignment explanation
Indices: 263838--263948 Score: 133
Period size: 41 Copynumber: 2.6 Consensus size: 44
263828 ATATTAAAAT
*
263838 TTATAAATAAAGTATTAATATTTTAAAATT-T-AATGATTAA-A
1 TTATAAATAAAATATTAATATTTTAAAATTATCAATGATTAATA
* *
263879 TTATAAAGAAAATATTAATA-TTT-AAATTATCAATTATTAATA
1 TTATAAATAAAATATTAATATTTTAAAATTATCAATGATTAATA
* * *
263921 TTTTAAATAAATTATAAATATTTTAAAA
1 TTATAAATAAAATATTAATATTTTAAAA
263949 ACAAAATAAA
Statistics
Matches: 58, Mismatches: 7, Indels: 7
0.81 0.10 0.10
Matches are distributed among these distances:
39 5 0.09
40 4 0.07
41 26 0.45
42 17 0.29
43 3 0.05
44 3 0.05
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (44 bp):
TTATAAATAAAATATTAATATTTTAAAATTATCAATGATTAATA
Found at i:263919 original size:22 final size:19
Alignment explanation
Indices: 263841--263943 Score: 73
Period size: 20 Copynumber: 5.1 Consensus size: 19
263831 TTAAAATTTA
*
263841 TAAATAAAGTATTAATATTT
1 TAAATAAATTATTAATA-TT
* *
263861 TAAAATTTAATGATTAA-ATT
1 T-AAA-TAAATTATTAATATT
* *
263881 ATAAAGAAAATATTAATATT
1 -TAAATAAATTATTAATATT
263901 TAAATTATCAATTATTAATATTT
1 TAAA-TA--AATTATTAATA-TT
*
263924 TAAATAAATTATAAATATT
1 TAAATAAATTATTAATATT
263943 T
1 T
263944 TAAAAACAAA
Statistics
Matches: 65, Mismatches: 10, Indels: 17
0.71 0.11 0.18
Matches are distributed among these distances:
19 14 0.22
20 20 0.31
21 5 0.08
22 20 0.31
23 6 0.09
ACGTcount: A:0.51, C:0.01, G:0.03, T:0.45
Consensus pattern (19 bp):
TAAATAAATTATTAATATT
Found at i:264095 original size:42 final size:42
Alignment explanation
Indices: 264049--264199 Score: 125
Period size: 42 Copynumber: 3.6 Consensus size: 42
264039 TTTAATCACA
264049 ATAATTTTTAAATTATAAATAAAATATTAATATTTTAAAATG
1 ATAATTTTTAAATTATAAATAAAATATTAATATTTTAAAATG
* * * *
264091 ATAATTGTTACAGTATAAATAAAATATAAATA-TTTAAATATG
1 ATAATTTTTAAATTATAAATAAAATATTAATATTTTAAA-ATG
* * * * *
264133 TTAATATTTAAA--AT--ATCAATTATTAATATTTTAATAAATT
1 ATAATTTTTAAATTATAAATAAAATATTAATATTTT-A-AAATG
*
264173 ATAAATTATTAATATT-TAAATAAAATA
1 AT-AATTTTTAA-ATTATAAATAAAATA
264200 AAATAAATAA
Statistics
Matches: 82, Mismatches: 17, Indels: 17
0.71 0.15 0.15
Matches are distributed among these distances:
38 11 0.13
39 3 0.04
40 6 0.07
41 15 0.18
42 40 0.49
43 1 0.01
45 6 0.07
ACGTcount: A:0.52, C:0.01, G:0.03, T:0.44
Consensus pattern (42 bp):
ATAATTTTTAAATTATAAATAAAATATTAATATTTTAAAATG
Found at i:264179 original size:26 final size:26
Alignment explanation
Indices: 264106--264203 Score: 101
Period size: 26 Copynumber: 3.6 Consensus size: 26
264096 TGTTACAGTA
264106 TAAATAAAATATAAA-TATTTAAATATGT
1 TAAATAAAATATAAATTA-TT-AATAT-T
*
264134 TAATATTTAAAATATCAATTATTAATATT
1 TAA-A--TAAAATATAAATTATTAATATT
* *
264163 TTAATAAATTATAAATTATTAATATT
1 TAAATAAAATATAAATTATTAATATT
264189 TAAATAAAATA-AAAT
1 TAAATAAAATATAAAT
264204 AAATAATCAT
Statistics
Matches: 60, Mismatches: 6, Indels: 11
0.78 0.08 0.14
Matches are distributed among these distances:
25 4 0.07
26 29 0.48
28 4 0.07
29 4 0.07
30 5 0.08
31 12 0.20
32 2 0.03
ACGTcount: A:0.55, C:0.01, G:0.01, T:0.43
Consensus pattern (26 bp):
TAAATAAAATATAAATTATTAATATT
Found at i:274909 original size:19 final size:20
Alignment explanation
Indices: 274881--274928 Score: 71
Period size: 20 Copynumber: 2.4 Consensus size: 20
274871 TAAAAATATG
274881 TATTTAATTATAAAAA-AACA
1 TATTT-ATTATAAAAAGAACA
*
274901 TATTTATTATAAAAAGAATA
1 TATTTATTATAAAAAGAACA
274921 TATTTATT
1 TATTTATT
274929 TTCATTTTAA
Statistics
Matches: 26, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
19 10 0.38
20 16 0.62
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.44
Consensus pattern (20 bp):
TATTTATTATAAAAAGAACA
Found at i:285936 original size:31 final size:31
Alignment explanation
Indices: 285896--285975 Score: 89
Period size: 29 Copynumber: 2.7 Consensus size: 31
285886 TTAAATTAAA
*
285896 AAATATATAATTAAATATAATT-TTAATATTC
1 AAATATATAATTAAATATAATTATAAATA-TC
*
285927 AAATTTATAA-TAAA-A-AATTATAAATATC
1 AAATATATAATTAAATATAATTATAAATATC
285955 ATAATATAT-ATTAAATATAAT
1 A-AATATATAATTAAATATAAT
285976 AAAAGTTAAC
Statistics
Matches: 41, Mismatches: 3, Indels: 10
0.76 0.06 0.19
Matches are distributed among these distances:
28 8 0.20
29 16 0.39
30 5 0.12
31 12 0.29
ACGTcount: A:0.56, C:0.03, G:0.00, T:0.41
Consensus pattern (31 bp):
AAATATATAATTAAATATAATTATAAATATC
Found at i:293840 original size:87 final size:89
Alignment explanation
Indices: 293722--293894 Score: 235
Period size: 92 Copynumber: 1.9 Consensus size: 89
293712 AACACTAGGA
* * *
293722 TTGAATAGTAATCATCTCCCATTAAATAAAAT-AAAAT-TTATGATAACATTAAACTTATGAGAT
1 TTGAAAAGTAATCATCTCCCATTAAATAAAATAAAAATATTATGATAACATTAAACTTATAAAAT
293785 TTAATTTGGATAAAAATATTAAAT
66 TTAATTTGGATAAAAATATTAAAT
* *
293809 TTGAAAAGTAATTC-TCTCCCATTATATAAAATAAAAAATAAATTATGATAATATTAAACTTATA
1 TTGAAAAGTAA-TCATCTCCCATTAAATAAAAT-AAAAAT--ATTATGATAACATTAAACTTATA
*
293873 AAATTTGATTTGGATAAAAATA
62 AAATTTAATTTGGATAAAAATA
293895 AAGTAATCTT
Statistics
Matches: 74, Mismatches: 6, Indels: 7
0.85 0.07 0.08
Matches are distributed among these distances:
87 27 0.36
88 2 0.03
89 5 0.07
92 40 0.54
ACGTcount: A:0.49, C:0.08, G:0.08, T:0.36
Consensus pattern (89 bp):
TTGAAAAGTAATCATCTCCCATTAAATAAAATAAAAATATTATGATAACATTAAACTTATAAAAT
TTAATTTGGATAAAAATATTAAAT
Found at i:313869 original size:12 final size:12
Alignment explanation
Indices: 313852--313876 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
313842 CATGAATGAC
313852 TAATTTCTCTGT
1 TAATTTCTCTGT
313864 TAATTTCTCTGT
1 TAATTTCTCTGT
313876 T
1 T
313877 TCAGCTTTCA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.16, C:0.16, G:0.08, T:0.60
Consensus pattern (12 bp):
TAATTTCTCTGT
Found at i:321040 original size:6 final size:6
Alignment explanation
Indices: 321025--321056 Score: 55
Period size: 6 Copynumber: 5.3 Consensus size: 6
321015 TACAATCACA
*
321025 CCTTCG CCTTCC CCTTCC CCTTCC CCTTCC CC
1 CCTTCC CCTTCC CCTTCC CCTTCC CCTTCC CC
321057 CACTCACTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.00, C:0.66, G:0.03, T:0.31
Consensus pattern (6 bp):
CCTTCC
Found at i:325788 original size:2 final size:2
Alignment explanation
Indices: 325781--325817 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
325771 CTTCAACAAA
325781 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
1 AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG AG A
325818 AGTTTAAACT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.49, T:0.00
Consensus pattern (2 bp):
AG
Found at i:328334 original size:23 final size:21
Alignment explanation
Indices: 328300--328347 Score: 62
Period size: 23 Copynumber: 2.2 Consensus size: 21
328290 AAATTATAAA
328300 TAATATTTAATAA-TAATTAAG
1 TAATATTTAATAATTAATT-AG
328321 TAATATTATAAATAATTAATTAG
1 TAATATT-T-AATAATTAATTAG
328344 TAAT
1 TAAT
328348 TAATCTTTTA
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
21 7 0.29
22 1 0.04
23 11 0.46
24 5 0.21
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.44
Consensus pattern (21 bp):
TAATATTTAATAATTAATTAG
Found at i:328384 original size:21 final size:22
Alignment explanation
Indices: 328358--328399 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
328348 TAATCTTTTA
*
328358 ATTAAAAAA-GAAAATTAAAAT
1 ATTAAAAAAGGAAAAATAAAAT
328379 ATTAAAAAAGGAAAAATAAAA
1 ATTAAAAAAGGAAAAATAAAA
328400 ATAGAAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 9 0.47
22 10 0.53
ACGTcount: A:0.74, C:0.00, G:0.07, T:0.19
Consensus pattern (22 bp):
ATTAAAAAAGGAAAAATAAAAT
Found at i:328394 original size:23 final size:21
Alignment explanation
Indices: 328358--328402 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 21
328348 TAATCTTTTA
*
328358 ATTAAAAAAGAAAATTAAAAT
1 ATTAAAAAAGAAAATAAAAAT
328379 ATTAAAAAAGGAAAAATAAAAAT
1 ATTAAAAAA-G-AAAATAAAAAT
328402 A
1 A
328403 GAAAAAAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 9 0.43
22 1 0.05
23 11 0.52
ACGTcount: A:0.73, C:0.00, G:0.07, T:0.20
Consensus pattern (21 bp):
ATTAAAAAAGAAAATAAAAAT
Found at i:328407 original size:22 final size:21
Alignment explanation
Indices: 328361--328409 Score: 55
Period size: 23 Copynumber: 2.3 Consensus size: 21
328351 TCTTTTAATT
* *
328361 AAAAAAGAAAATTAAAATATT
1 AAAAAAGAAAATAAAAATATG
328382 AAAAAAGGAAAAATAAAAATA-G
1 AAAAAA-G-AAAATAAAAATATG
328404 AAAAAA
1 AAAAAA
328410 AAATCGTATC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 6 0.25
22 7 0.29
23 11 0.46
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (21 bp):
AAAAAAGAAAATAAAAATATG
Found at i:328408 original size:23 final size:21
Alignment explanation
Indices: 328361--328410 Score: 55
Period size: 22 Copynumber: 2.3 Consensus size: 21
328351 TCTTTTAATT
* *
328361 AAAAAAGAAAATTAAAATATTA
1 AAAAAAGAAAATAAAAATA-GA
*
328383 AAAAAGGAAAAATAAAAATAGA
1 AAAAAAG-AAAATAAAAATAGA
328405 AAAAAA
1 AAAAAA
328411 AATCGTATCA
Statistics
Matches: 23, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
22 12 0.52
23 11 0.48
ACGTcount: A:0.78, C:0.00, G:0.08, T:0.14
Consensus pattern (21 bp):
AAAAAAGAAAATAAAAATAGA
Found at i:343472 original size:20 final size:20
Alignment explanation
Indices: 343447--343489 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
343437 TGCAGGAGTG
* *
343447 ATTTTATTTTTTTTTTCAAA
1 ATTTTATTTTTTATTTAAAA
343467 ATTTTATTTTTTATTTAAAA
1 ATTTTATTTTTTATTTAAAA
343487 ATT
1 ATT
343490 AATTATGAAT
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:0.30, C:0.02, G:0.00, T:0.67
Consensus pattern (20 bp):
ATTTTATTTTTTATTTAAAA
Found at i:348098 original size:28 final size:29
Alignment explanation
Indices: 348067--348123 Score: 89
Period size: 28 Copynumber: 2.0 Consensus size: 29
348057 CTATTTTAAA
*
348067 ATATTTAAATAAATTTTTAT-TTTTTATT
1 ATATTCAAATAAATTTTTATATTTTTATT
*
348095 ATATTCAATTAAATTTTTATATTTTTATT
1 ATATTCAAATAAATTTTTATATTTTTATT
348124 TTATATCTTA
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
28 18 0.69
29 8 0.31
ACGTcount: A:0.35, C:0.02, G:0.00, T:0.63
Consensus pattern (29 bp):
ATATTCAAATAAATTTTTATATTTTTATT
Found at i:368306 original size:128 final size:133
Alignment explanation
Indices: 368035--368430 Score: 662
Period size: 128 Copynumber: 3.0 Consensus size: 133
368025 TGGCATGTGG
368035 TTGCAGATAGACCACAGCTAAAAACGAAGGATAGAAGTATATGATATAATAAAGTAAAACTCAAT
1 TTGCAGATAGACCACAGCTAAAAACGAAGGATAGAAGTATATGATATAATAAAGTAAAACT-AAT
368100 TTGGTGAAATATTGCTTCCATTGGTTAAGCAACTGGTACAACAATCATGGTTTTGATTGAATCTG
65 TTGGTGAAAT-TTGCTTCCATTGGTT-AGCAACTGGTACAACAATCATGGTTTTGATTGAATCTG
368165 AAAAGT
128 AAAAGT
* * *
368171 TTGCAGATAGACCACAGCTAAAGACGAAGGATAGAAGTGTCTGATATAAT-AAG-AAAACTAATT
1 TTGCAGATAGACCACAGCTAAAAACGAAGGATAGAAGTATATGATATAATAAAGTAAAACTAATT
368234 TGGTGAAATTTGCTTCCATTGG-T-GC-ACTGGTACAACAATCATGGTTTTGATTGAATCTGAAA
66 TGGTGAAATTTGCTTCCATTGGTTAGCAACTGGTACAACAATCATGGTTTTGATTGAATCTGAAA
368296 AGT
131 AGT
*
368299 TTGCAGATAGACCACAGCTAAAAACGAAGGATAGAAGTATATGATATAATAAAGTAAAACTCATT
1 TTGCAGATAGACCACAGCTAAAAACGAAGGATAGAAGTATATGATATAATAAAGTAAAACTAATT
*
368364 T-GTGAAATATGCTT-CATTGGTTAAGCAACTGGTACAACAATCATGGTTTTGATTGAATCTGAA
66 TGGTGAAATTTGCTTCCATTGGTT-AGCAACTGGTACAACAATCATGGTTTTGATTGAATCTGAA
368427 AAGT
130 AAGT
368431 GAAAGGCCAT
Statistics
Matches: 246, Mismatches: 8, Indels: 16
0.91 0.03 0.06
Matches are distributed among these distances:
128 93 0.38
129 18 0.07
130 10 0.04
131 3 0.01
132 53 0.22
133 13 0.05
134 6 0.02
135 3 0.01
136 47 0.19
ACGTcount: A:0.39, C:0.13, G:0.20, T:0.29
Consensus pattern (133 bp):
TTGCAGATAGACCACAGCTAAAAACGAAGGATAGAAGTATATGATATAATAAAGTAAAACTAATT
TGGTGAAATTTGCTTCCATTGGTTAGCAACTGGTACAACAATCATGGTTTTGATTGAATCTGAAA
AGT
Found at i:386356 original size:16 final size:16
Alignment explanation
Indices: 386332--386365 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 16
386322 TAAATTAAAT
386332 ATTTAAGTG-TAAAAA
1 ATTTAAGTGTTAAAAA
386347 ATTTATAGTGTTAAAAA
1 ATTTA-AGTGTTAAAAA
386364 AT
1 AT
386366 ATTTATAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 5 0.29
16 4 0.24
17 8 0.47
ACGTcount: A:0.50, C:0.00, G:0.12, T:0.38
Consensus pattern (16 bp):
ATTTAAGTGTTAAAAA
Found at i:386369 original size:19 final size:17
Alignment explanation
Indices: 386328--386372 Score: 58
Period size: 16 Copynumber: 2.6 Consensus size: 17
386318 TTAATAAATT
386328 AAATATTTA-AGTGTAA
1 AAATATTTATAGTGTAA
386344 AAA-ATTTATAGTGTTAAA
1 AAATATTTATAGTG-T-AA
386362 AAATATTTATA
1 AAATATTTATA
386373 AATATTTTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
15 5 0.20
16 7 0.28
17 1 0.04
18 5 0.20
19 7 0.28
ACGTcount: A:0.51, C:0.00, G:0.09, T:0.40
Consensus pattern (17 bp):
AAATATTTATAGTGTAA
Found at i:387296 original size:29 final size:30
Alignment explanation
Indices: 387244--387339 Score: 115
Period size: 29 Copynumber: 3.2 Consensus size: 30
387234 TATATTATTA
* *
387244 AAAAATTAAATTAAAATGATTTTTAAAATA-
1 AAAAATTAAATT-AAATTAATTTTAAAATAT
**
387274 AAAAATTAAATTACTTTAATTTT-AAATAT
1 AAAAATTAAATTAAATTAATTTTAAAATAT
* *
387303 AAAAATTAAATTAAATTAAATATAAAATAT
1 AAAAATTAAATTAAATTAATTTTAAAATAT
387333 AAAAATT
1 AAAAATT
387340 TGATAAATAC
Statistics
Matches: 56, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
28 5 0.09
29 26 0.46
30 25 0.45
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (30 bp):
AAAAATTAAATTAAATTAATTTTAAAATAT
Found at i:387331 original size:30 final size:30
Alignment explanation
Indices: 387244--387339 Score: 106
Period size: 30 Copynumber: 3.2 Consensus size: 30
387234 TATATTATTA
* **
387244 AAAAATTAAATTAAAATGATTTTTAAAATA-
1 AAAAATTAAATT-AAATTAAATTTAAAATAT
* * *
387274 AAAAATTAAATT-ACTTTAATTTTAAATAT
1 AAAAATTAAATTAAATTAAATTTAAAATAT
*
387303 AAAAATTAAATTAAATTAAATATAAAATAT
1 AAAAATTAAATTAAATTAAATTTAAAATAT
387333 AAAAATT
1 AAAAATT
387340 TGATAAATAC
Statistics
Matches: 54, Mismatches: 10, Indels: 4
0.79 0.15 0.06
Matches are distributed among these distances:
28 10 0.19
29 12 0.22
30 32 0.59
ACGTcount: A:0.60, C:0.01, G:0.01, T:0.38
Consensus pattern (30 bp):
AAAAATTAAATTAAATTAAATTTAAAATAT
Found at i:388503 original size:27 final size:27
Alignment explanation
Indices: 388473--388526 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
388463 TAAACTTAAG
* *
388473 TATATAATATTTATTTAATTTTATTCT
1 TATAAAATAATTATTTAATTTTATTCT
*
388500 TATAAAATAATTATTTTATTTTATTCT
1 TATAAAATAATTATTTAATTTTATTCT
388527 CTGAATCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.35, C:0.04, G:0.00, T:0.61
Consensus pattern (27 bp):
TATAAAATAATTATTTAATTTTATTCT
Found at i:394973 original size:2 final size:2
Alignment explanation
Indices: 394968--394993 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
394958 TACATATGCA
394968 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
394994 GTATTAAGCA
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:401566 original size:21 final size:19
Alignment explanation
Indices: 401521--401561 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
401511 AAAATTGTAG
*
401521 AAAAAGAAAAAACAACATA
1 AAAAATAAAAAACAACATA
401540 AAAAATAAAAAA-AACATTA
1 AAAAATAAAAAACAACA-TA
401559 AAA
1 AAA
401562 CAAATTATAA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
18 4 0.20
19 16 0.80
ACGTcount: A:0.80, C:0.07, G:0.02, T:0.10
Consensus pattern (19 bp):
AAAAATAAAAAACAACATA
Found at i:413276 original size:89 final size:88
Alignment explanation
Indices: 413098--413279 Score: 269
Period size: 89 Copynumber: 2.1 Consensus size: 88
413088 GGTCCCCGTT
* *
413098 TGTTTGGGGTAAACACTAAGTAATTTATTCTTCCAGTTTACTCCCTAGTTTATTAAAGGTTTCCA
1 TGTTTGGGGTAAACACTAAGCAATTTATTCTTCCAGTTTACTCCCTAGTTTATAAAAGGTTTCCA
413163 CTTTCTGAACATTCTCTCCTGTA
66 CTTTCTGAACATTCTCTCCTGTA
* *
413186 TGTTT-GGGTAAACTA-TAAGCAATTTGTTCTTCCTGTTTACTCCCTAGTATATATAAAAGGTTT
1 TGTTTGGGGTAAAC-ACTAAGCAATTTATTCTTCCAGTTTACTCCCTAGT-T-TATAAAAGGTTT
**
413249 CCTGTTTCTGAACATTCTCTCCTGTA
63 CCACTTTCTGAACATTCTCTCCTGTA
413275 TGTTT
1 TGTTT
413280 ACTAAAGTCA
Statistics
Matches: 85, Mismatches: 6, Indels: 5
0.89 0.06 0.05
Matches are distributed among these distances:
87 38 0.45
88 7 0.08
89 40 0.47
ACGTcount: A:0.23, C:0.19, G:0.14, T:0.43
Consensus pattern (88 bp):
TGTTTGGGGTAAACACTAAGCAATTTATTCTTCCAGTTTACTCCCTAGTTTATAAAAGGTTTCCA
CTTTCTGAACATTCTCTCCTGTA
Found at i:421213 original size:15 final size:16
Alignment explanation
Indices: 421182--421229 Score: 55
Period size: 16 Copynumber: 3.1 Consensus size: 16
421172 TTTTATTAGT
*
421182 ACCCTTTCTTTAATCA
1 ACCCTTTCTTGAATCA
421198 ACCCTTT-TTGAATCA
1 ACCCTTTCTTGAATCA
*
421213 ATACCTTTCTT-AATCA
1 A-CCCTTTCTTGAATCA
421229 A
1 A
421230 ATATATTTTT
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
15 8 0.29
16 18 0.64
17 2 0.07
ACGTcount: A:0.29, C:0.27, G:0.02, T:0.42
Consensus pattern (16 bp):
ACCCTTTCTTGAATCA
Found at i:421264 original size:4 final size:4
Alignment explanation
Indices: 421255--421284 Score: 60
Period size: 4 Copynumber: 7.5 Consensus size: 4
421245 TTTTAATACT
421255 TTGG TTGG TTGG TTGG TTGG TTGG TTGG TT
1 TTGG TTGG TTGG TTGG TTGG TTGG TTGG TT
421285 TTGGACCTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.47, T:0.53
Consensus pattern (4 bp):
TTGG
Found at i:422987 original size:34 final size:35
Alignment explanation
Indices: 422892--423004 Score: 106
Period size: 34 Copynumber: 3.3 Consensus size: 35
422882 CTTCAACAAT
* ** * *
422892 AGATGTTATATGTC-AAGG-TAAAATATTTATCACT
1 AGATGTTACATGTCAAAGGCT-AAAGCTTTAACACC
*
422926 AGATGTTAAATGTCAAAGGCTAAAGCTTTAACACC
1 AGATGTTACATGTCAAAGGCTAAAGCTTTAACACC
* * *
422961 AGATGTTACATG-CTAAGGTTAAAGCTTCAACACC
1 AGATGTTACATGTCAAAGGCTAAAGCTTTAACACC
*
422995 AGATATTACA
1 AGATGTTACA
423005 CATCAAGGTC
Statistics
Matches: 67, Mismatches: 10, Indels: 4
0.83 0.12 0.05
Matches are distributed among these distances:
34 41 0.61
35 25 0.37
36 1 0.01
ACGTcount: A:0.39, C:0.15, G:0.16, T:0.30
Consensus pattern (35 bp):
AGATGTTACATGTCAAAGGCTAAAGCTTTAACACC
Found at i:440743 original size:62 final size:62
Alignment explanation
Indices: 440635--440762 Score: 193
Period size: 62 Copynumber: 2.1 Consensus size: 62
440625 ACATAATTAT
* * * *
440635 TCTACAAGGCAGCTAATGCATACTCAATTCCACCTCAGTAATGAATATGAACATGCTATTTC
1 TCTACAAGGCAGCTAATGCATACTCAATTCCACCTCAGGAACGAATATGAACATGCCAATTC
* * *
440697 TCTACTAGGCAGCTAATGCATACTCAATTCCACTTCAGGAACGAATATGAGCATGCCAATTC
1 TCTACAAGGCAGCTAATGCATACTCAATTCCACCTCAGGAACGAATATGAACATGCCAATTC
440759 TCTA
1 TCTA
440763 ATAAAGGCAA
Statistics
Matches: 59, Mismatches: 7, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
62 59 1.00
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.28
Consensus pattern (62 bp):
TCTACAAGGCAGCTAATGCATACTCAATTCCACCTCAGGAACGAATATGAACATGCCAATTC
Found at i:442325 original size:16 final size:16
Alignment explanation
Indices: 442304--442345 Score: 50
Period size: 16 Copynumber: 2.7 Consensus size: 16
442294 TTTTAGATAC
* *
442304 AATTATTTAATCATGT
1 AATTATATAATCATAT
*
442320 AATTATATATTCATAT
1 AATTATATAATCATAT
442336 AATT-TATAAT
1 AATTATATAAT
442346 ACATTATTTA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
15 5 0.23
16 17 0.77
ACGTcount: A:0.43, C:0.05, G:0.02, T:0.50
Consensus pattern (16 bp):
AATTATATAATCATAT
Found at i:442471 original size:15 final size:14
Alignment explanation
Indices: 442444--442470 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
442434 TGACAATTAA
442444 AAGTTATTTTTTTG
1 AAGTTATTTTTTTG
442458 AAGTTATTTTTTT
1 AAGTTATTTTTTT
442471 TTGACTATGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.22, C:0.00, G:0.11, T:0.67
Consensus pattern (14 bp):
AAGTTATTTTTTTG
Found at i:446661 original size:19 final size:19
Alignment explanation
Indices: 446637--446673 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
446627 AAGCATAATG
446637 ATAATACTAACACTCTTAA
1 ATAATACTAACACTCTTAA
* *
446656 ATAATATTGACACTCTTA
1 ATAATACTAACACTCTTA
446674 CAAACTTTAA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.43, C:0.19, G:0.03, T:0.35
Consensus pattern (19 bp):
ATAATACTAACACTCTTAA
Found at i:465125 original size:33 final size:34
Alignment explanation
Indices: 465088--465152 Score: 87
Period size: 33 Copynumber: 1.9 Consensus size: 34
465078 CTACTTTAGC
* * *
465088 ATTTTTGTTAGAATTT-CATTGAAAAAAAAAGGT
1 ATTTTTGATAAAATTTGAATTGAAAAAAAAAGGT
*
465121 ATTTTTGATAAAATTTGAATTTAAAAAAAAAG
1 ATTTTTGATAAAATTTGAATTGAAAAAAAAAG
465153 TCAAAAAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
33 14 0.52
34 13 0.48
ACGTcount: A:0.48, C:0.02, G:0.12, T:0.38
Consensus pattern (34 bp):
ATTTTTGATAAAATTTGAATTGAAAAAAAAAGGT
Found at i:466058 original size:22 final size:21
Alignment explanation
Indices: 466024--466077 Score: 63
Period size: 21 Copynumber: 2.5 Consensus size: 21
466014 TATAAAAAAA
* * *
466024 TTAAAATATTATTTTTATTAAT
1 TTAAAAAAATATTATTA-TAAT
*
466046 TTAAAAAAATATTATTATATT
1 TTAAAAAAATATTATTATAAT
466067 TTAAAAAAATA
1 TTAAAAAAATA
466078 AAAAAATAAA
Statistics
Matches: 28, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
21 14 0.50
22 14 0.50
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (21 bp):
TTAAAAAAATATTATTATAAT
Found at i:466062 original size:19 final size:21
Alignment explanation
Indices: 466038--466077 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
466028 AATATTATTT
466038 TTATTA-A-TTTAAAAAAATA
1 TTATTATATTTTAAAAAAATA
466057 TTATTATATTTTAAAAAAATA
1 TTATTATATTTTAAAAAAATA
466078 AAAAAATAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 6 0.32
20 1 0.05
21 12 0.63
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
TTATTATATTTTAAAAAAATA
Found at i:479459 original size:2 final size:2
Alignment explanation
Indices: 479452--479477 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
479442 TAGCAAAACC
479452 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
479478 GTATTAATTC
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:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:482944 original size:2 final size:2
Alignment explanation
Indices: 482937--482966 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
482927 ATTAAAAATT
482937 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
482967 GTTGTTGAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:498429 original size:46 final size:46
Alignment explanation
Indices: 498376--498465 Score: 153
Period size: 46 Copynumber: 2.0 Consensus size: 46
498366 TTTAAGATGA
* *
498376 AGGTGAACTTTCTCGGGTATAGTCGATATGTGCCCTTTGGTCAAGC
1 AGGTGAACTTTCTCAGGTATAGTCAATATGTGCCCTTTGGTCAAGC
*
498422 AGGTGAACTTTCTCAGGTATAGTCAATATGTGCCTTTTGGTCAA
1 AGGTGAACTTTCTCAGGTATAGTCAATATGTGCCCTTTGGTCAA
498466 ACAATCCCCT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
46 41 1.00
ACGTcount: A:0.22, C:0.18, G:0.26, T:0.34
Consensus pattern (46 bp):
AGGTGAACTTTCTCAGGTATAGTCAATATGTGCCCTTTGGTCAAGC
Found at i:501678 original size:17 final size:17
Alignment explanation
Indices: 501658--501705 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
501648 AAAAAAATAC
*
501658 AAATAAAATAAAATGAA
1 AAATAAAATCAAATGAA
* * *
501675 AAATAACATCCAGTGAA
1 AAATAAAATCAAATGAA
501692 AAATAAAATCAAAT
1 AAATAAAATCAAAT
501706 TATGATAATA
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
17 24 1.00
ACGTcount: A:0.67, C:0.08, G:0.06, T:0.19
Consensus pattern (17 bp):
AAATAAAATCAAATGAA
Found at i:508751 original size:63 final size:62
Alignment explanation
Indices: 508672--508872 Score: 210
Period size: 63 Copynumber: 3.4 Consensus size: 62
508662 TACAAGTTTA
508672 ATATATTTATATTTTTTATTATTAATTTTTATATAGTATCATTTCTTAAATATATTTTTAATGTC
1 ATATATTT-TA-TTTTTATTATTAATTTTTATATA-TATCATTTCTTAAATATATTTTTAATGTC
* * *
508737 ATATATTTTATTTTTA-T-TT-ATTTTTATA-ATAT--TTT-AT-ATTTTATTTTTAA--T-
1 ATATATTTTATTTTTATTATTAATTTTTATATATATCATTTCTTAAATATATTTTTAATGTC
* * *
508788 ATAT-TTATATTTATATTATTAATTTTTATATAATATCATATCTTAAATATATTTTTAATGTC
1 ATATATTTTATTTTTATTATTAATTTTTATAT-ATATCATTTCTTAAATATATTTTTAATGTC
*
508850 ATATATTTTATTTTCATTTATTA
1 ATATATTTTATTTTTA-TTATTA
508873 TTATAATCTT
Statistics
Matches: 110, Mismatches: 12, Indels: 29
0.73 0.08 0.19
Matches are distributed among these distances:
50 9 0.08
51 5 0.05
52 3 0.03
53 9 0.08
54 11 0.10
55 5 0.05
56 3 0.03
57 2 0.02
58 4 0.04
59 12 0.11
60 9 0.08
61 3 0.03
62 5 0.05
63 14 0.13
64 8 0.07
65 8 0.07
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.62
Consensus pattern (62 bp):
ATATATTTTATTTTTATTATTAATTTTTATATATATCATTTCTTAAATATATTTTTAATGTC
Found at i:508758 original size:15 final size:15
Alignment explanation
Indices: 508737--508896 Score: 65
Period size: 15 Copynumber: 9.9 Consensus size: 15
508727 TTTTAATGTC
508737 ATATATTTTATTTTT
1 ATATATTTTATTTTT
*
508752 ATTTATTTTTATAATATTT
1 ATATA-TTTTAT--T-TTT
508771 -TATATTTTATTTTT
1 ATATATTTTATTTTT
*
508785 A-ATATATTTATATTT
1 ATATAT-TTTATTTTT
*
508800 ATAT-TATTAATTTTT
1 ATATAT-TTTATTTTT
* **
508815 ATATAATATCATATCTTAA
1 ATAT-AT-T-TTAT-TTTT
* * *
508834 ATATATTTTTAATGTC
1 ATATA-TTTTATTTTT
*
508850 ATATATTTTATTTTC
1 ATATATTTTATTTTT
* *
508865 ATTTATTATTATAATCTT
1 ATATATT-TTAT--TTTT
508883 ATATATTTTATTTT
1 ATATATTTTATTTT
508897 CATTTCTTTA
Statistics
Matches: 109, Mismatches: 21, Indels: 30
0.68 0.13 0.19
Matches are distributed among these distances:
14 7 0.06
15 43 0.39
16 18 0.17
17 15 0.14
18 16 0.15
19 10 0.09
ACGTcount: A:0.33, C:0.03, G:0.01, T:0.64
Consensus pattern (15 bp):
ATATATTTTATTTTT
Found at i:508769 original size:21 final size:21
Alignment explanation
Indices: 508745--508810 Score: 71
Period size: 23 Copynumber: 3.0 Consensus size: 21
508735 TCATATATTT
508745 TATTTTTATTTATTTTT-ATAA
1 TATTTTTATTTATTTTTAAT-A
508766 TATTTTATATTTTATTTTTAATA
1 TATTTT-TA-TTTATTTTTAATA
*
508789 TATTTATATTTATATTATTAAT
1 TATTTTTATTTAT-TT-TTAAT
508811 TTTTATATAA
Statistics
Matches: 39, Mismatches: 1, Indels: 8
0.81 0.02 0.17
Matches are distributed among these distances:
21 11 0.28
22 6 0.15
23 20 0.51
24 2 0.05
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (21 bp):
TATTTTTATTTATTTTTAATA
Found at i:508815 original size:21 final size:22
Alignment explanation
Indices: 508745--508818 Score: 93
Period size: 21 Copynumber: 3.5 Consensus size: 22
508735 TCATATATTT
508745 TATTTT-TATTTAT-TTTTATAA
1 TATTTTATATTTATATTTT-TAA
508766 TATTTTATATTT-TATTTTTAA
1 TATTTTATATTTATATTTTTAA
*
508787 TATATTTATATTTATATTATTAA
1 TAT-TTTATATTTATATTTTTAA
508810 T-TTTTATAT
1 TATTTTATAT
508819 AATATCATAT
Statistics
Matches: 48, Mismatches: 1, Indels: 8
0.84 0.02 0.14
Matches are distributed among these distances:
21 20 0.42
22 19 0.40
23 9 0.19
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (22 bp):
TATTTTATATTTATATTTTTAA
Done.