Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: NTFQ01015325.1 Kokia drynarioides strain JFW-HI SEQ_130371, 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: 591955
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Warning! 531 characters in sequence are not A, C, G, or T
File 2 of 3
Found at i:255540 original size:13 final size:14
Alignment explanation
Indices: 255522--255551 Score: 53
Period size: 13 Copynumber: 2.2 Consensus size: 14
255512 AAAATTTAAG
255522 GTTTAAAGTTCA-A
1 GTTTAAAGTTCAGA
255535 GTTTAAAGTTCAGA
1 GTTTAAAGTTCAGA
255549 GTT
1 GTT
255552 CAGGATAAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 12 0.75
14 4 0.25
ACGTcount: A:0.33, C:0.07, G:0.20, T:0.40
Consensus pattern (14 bp):
GTTTAAAGTTCAGA
Found at i:261265 original size:23 final size:22
Alignment explanation
Indices: 261233--261277 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 22
261223 CAAATGTCTA
*
261233 TTTTGTAATTAATTTTTTTATT
1 TTTTGTAATTAATTTTTATATT
261255 TTTTCGTAATTAATTTTTATATT
1 TTTT-GTAATTAATTTTTATATT
261278 GTTTAAGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.24, C:0.02, G:0.04, T:0.69
Consensus pattern (22 bp):
TTTTGTAATTAATTTTTATATT
Found at i:272195 original size:41 final size:38
Alignment explanation
Indices: 272124--272202 Score: 104
Period size: 41 Copynumber: 2.0 Consensus size: 38
272114 CAATTTAATG
*
272124 ACACTAATTCAATTAAAAAATTACACAAAAACTAATTTA
1 ACACTAAATCAATTAAAAAATTACACAAAAAC-AATTTA
* *
272163 ACACTAAATCAATTAAAAAAAATTGCATAAAAACAATTTA
1 ACACTAAATCAATT--AAAAAATTACACAAAAACAATTTA
272203 TGTATTAAAT
Statistics
Matches: 35, Mismatches: 3, Indels: 3
0.85 0.07 0.07
Matches are distributed among these distances:
39 13 0.37
40 6 0.17
41 16 0.46
ACGTcount: A:0.58, C:0.14, G:0.01, T:0.27
Consensus pattern (38 bp):
ACACTAAATCAATTAAAAAATTACACAAAAACAATTTA
Found at i:272627 original size:17 final size:16
Alignment explanation
Indices: 272607--272644 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
272597 ATAAAAAAAA
272607 TAAAAAACCTAAACTTG
1 TAAAAAA-CTAAACTTG
*
272624 TAAAAAACTGAACTTG
1 TAAAAAACTAAACTTG
272640 -AAAAA
1 TAAAAA
272645 TTTTGAATTT
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
15 5 0.25
16 8 0.40
17 7 0.35
ACGTcount: A:0.58, C:0.13, G:0.08, T:0.21
Consensus pattern (16 bp):
TAAAAAACTAAACTTG
Found at i:277910 original size:19 final size:20
Alignment explanation
Indices: 277873--277910 Score: 51
Period size: 19 Copynumber: 1.9 Consensus size: 20
277863 AATTGAATTG
*
277873 TAAACTTAATTTTTTATGTC
1 TAAACTTAATTTTTAATGTC
*
277893 TAAACTTTA-TTTTAATGT
1 TAAACTTAATTTTTAATGT
277911 GCTTATATGA
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 8 0.50
20 8 0.50
ACGTcount: A:0.32, C:0.08, G:0.05, T:0.55
Consensus pattern (20 bp):
TAAACTTAATTTTTAATGTC
Found at i:278295 original size:17 final size:18
Alignment explanation
Indices: 278255--278299 Score: 56
Period size: 17 Copynumber: 2.6 Consensus size: 18
278245 TATTTGAATA
* *
278255 TGTATTTACAATTTATTT
1 TGTATTTATAATTTATAT
*
278273 TCTATTTATAA-TTATAT
1 TGTATTTATAATTTATAT
278290 TGTATTTATA
1 TGTATTTATA
278300 TATATAAACT
Statistics
Matches: 23, Mismatches: 4, Indels: 1
0.82 0.14 0.04
Matches are distributed among these distances:
17 14 0.61
18 9 0.39
ACGTcount: A:0.31, C:0.04, G:0.04, T:0.60
Consensus pattern (18 bp):
TGTATTTATAATTTATAT
Found at i:278940 original size:31 final size:31
Alignment explanation
Indices: 278865--278942 Score: 97
Period size: 29 Copynumber: 2.5 Consensus size: 31
278855 TAAGAATTGG
*
278865 ATTAAATCAAAATTTCATGCATAAAATTACAC
1 ATTAAATCAAAA-TTCATACATAAAATTACAC
* *
278897 A--AAATCAAAATTCATATATATAATTACAC
1 ATTAAATCAAAATTCATACATAAAATTACAC
*
278926 ATTAAATCATAATTCAT
1 ATTAAATCAAAATTCAT
278943 GTACAAACTT
Statistics
Matches: 40, Mismatches: 4, Indels: 5
0.82 0.08 0.10
Matches are distributed among these distances:
29 17 0.43
30 9 0.22
31 13 0.32
32 1 0.03
ACGTcount: A:0.51, C:0.14, G:0.01, T:0.33
Consensus pattern (31 bp):
ATTAAATCAAAATTCATACATAAAATTACAC
Found at i:279551 original size:2 final size:2
Alignment explanation
Indices: 279542--279579 Score: 69
Period size: 2 Copynumber: 19.5 Consensus size: 2
279532 AAAAAATAAT
279542 TA TA -A 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 TA TA T
279580 CAATTATATT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 34 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:282378 original size:2 final size:2
Alignment explanation
Indices: 282371--282398 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
282361 CCAATGCCCT
282371 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC
282399 CCTTTTTAGT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.00, C:0.50, G:0.00, T:0.50
Consensus pattern (2 bp):
TC
Found at i:282729 original size:14 final size:14
Alignment explanation
Indices: 282688--282732 Score: 54
Period size: 14 Copynumber: 3.2 Consensus size: 14
282678 AAGATCCACG
* *
282688 ATTTAGAGTTTAAG
1 ATTTAGGGTTTAAA
* *
282702 ATTTATGGTCTAAA
1 ATTTAGGGTTTAAA
282716 ATTTAGGGTTTAAA
1 ATTTAGGGTTTAAA
282730 ATT
1 ATT
282733 CAAAATATAA
Statistics
Matches: 25, Mismatches: 6, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.36, C:0.02, G:0.18, T:0.44
Consensus pattern (14 bp):
ATTTAGGGTTTAAA
Found at i:283344 original size:29 final size:30
Alignment explanation
Indices: 283302--283359 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 30
283292 GGTTAACTTG
283302 CAATTGTATACAT-AAACTTTGATTTGATA
1 CAATTGTATACATAAAACTTTGATTTGATA
* *
283331 CAATTTTATACATAAAATTTTGATTTGAT
1 CAATTGTATACATAAAACTTTGATTTGAT
283360 CTAATTATTG
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
29 12 0.46
30 14 0.54
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.45
Consensus pattern (30 bp):
CAATTGTATACATAAAACTTTGATTTGATA
Found at i:295246 original size:75 final size:75
Alignment explanation
Indices: 295007--295247 Score: 308
Period size: 75 Copynumber: 3.3 Consensus size: 75
294997 TGAACCATGA
* * * *
295007 CTCCATTTTGAGAAGCTTGCTG---ATTTCTAAGATCTTCTTGGAGCCAACTGTTGGTAAAAGAG
1 CTCCATTTTGAGAAGCTTGCTGATCATTTCTATGATATTCTTGAAACCAACTGTTGGTAAAAGAG
295069 ACACCATTGG
66 ACACCATTGG
* * * * * * *
295079 CTCCATTTGGAGAAGCTAGGTGATCATTTCGATGATTTTCTTGAAACCAACTATTGGTAAAATAG
1 CTCCATTTTGAGAAGCTTGCTGATCATTTCTATGATATTCTTGAAACCAACTGTTGGTAAAAGAG
*
295144 GCACCATTGG
66 ACACCATTGG
* * *
295154 CTCCATTTCGAGAAGCTTGCTGATCATTTCTATGATATTCTTGAAACCAATTGTTGGGAAAAGAG
1 CTCCATTTTGAGAAGCTTGCTGATCATTTCTATGATATTCTTGAAACCAACTGTTGGTAAAAGAG
*
295219 ACACCATTAG
66 ACACCATTGG
*
295229 CTTCATTTTGAGAAGCTTG
1 CTCCATTTTGAGAAGCTTG
295248 GTCTTGCTGA
Statistics
Matches: 142, Mismatches: 24, Indels: 3
0.84 0.14 0.02
Matches are distributed among these distances:
72 19 0.13
75 123 0.87
ACGTcount: A:0.28, C:0.18, G:0.21, T:0.33
Consensus pattern (75 bp):
CTCCATTTTGAGAAGCTTGCTGATCATTTCTATGATATTCTTGAAACCAACTGTTGGTAAAAGAG
ACACCATTGG
Found at i:312536 original size:11 final size:11
Alignment explanation
Indices: 312520--312547 Score: 56
Period size: 11 Copynumber: 2.5 Consensus size: 11
312510 TTACTACTAG
312520 AACATTTAGCT
1 AACATTTAGCT
312531 AACATTTAGCT
1 AACATTTAGCT
312542 AACATT
1 AACATT
312548 ATATACTACT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.39, C:0.18, G:0.07, T:0.36
Consensus pattern (11 bp):
AACATTTAGCT
Found at i:314093 original size:2 final size:2
Alignment explanation
Indices: 314088--314130 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
314078 CACCCCTGAA
314088 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC TC
314130 T
1 T
314131 TCATTTCCTT
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.00, C:0.49, G:0.00, T:0.51
Consensus pattern (2 bp):
TC
Found at i:315450 original size:21 final size:21
Alignment explanation
Indices: 315426--315474 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
315416 TATTGTGCAC
*
315426 TCATTTTAAT-AGTTCATTTTA
1 TCATTTTAATCA-CTCATTTTA
315447 TCATTTTAATCACTCATTTTA
1 TCATTTTAATCACTCATTTTA
*
315468 TCTTTTT
1 TCATTTT
315475 TTTAATTTAT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.24, C:0.14, G:0.02, T:0.59
Consensus pattern (21 bp):
TCATTTTAATCACTCATTTTA
Found at i:315574 original size:22 final size:22
Alignment explanation
Indices: 315563--315606 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
315553 AAGAAAATTT
315563 TGGATTTTTACAAGAAAAAATC
1 TGGATTTTTACAAGAAAAAATC
**
315585 TGGATTTTTACGTGAAAAAATC
1 TGGATTTTTACAAGAAAAAATC
315607 ATTTTTTTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.41, C:0.09, G:0.16, T:0.34
Consensus pattern (22 bp):
TGGATTTTTACAAGAAAAAATC
Found at i:315577 original size:21 final size:23
Alignment explanation
Indices: 315548--315595 Score: 64
Period size: 22 Copynumber: 2.2 Consensus size: 23
315538 AGCATGGGTG
* *
315548 TTACAAAG-AAAATTTTGGATTT
1 TTACAAAGAAAAAATCTGGATTT
315570 TTAC-AAGAAAAAATCTGGATTT
1 TTACAAAGAAAAAATCTGGATTT
315592 TTAC
1 TTAC
315596 GTGAAAAAAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 3 0.13
22 20 0.87
ACGTcount: A:0.42, C:0.08, G:0.12, T:0.38
Consensus pattern (23 bp):
TTACAAAGAAAAAATCTGGATTT
Found at i:315624 original size:11 final size:11
Alignment explanation
Indices: 315608--315633 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
315598 GAAAAAATCA
315608 TTTTTTTTCTT
1 TTTTTTTTCTT
315619 TTTTTTTTCTT
1 TTTTTTTTCTT
315630 TTTT
1 TTTT
315634 AGAGTTAAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTTTTTCTT
Found at i:316531 original size:3 final size:3
Alignment explanation
Indices: 316523--316572 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
316513 TTAAACACAA
316523 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
316571 AA
1 AA
316573 AGGAAACAGC
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (3 bp):
AAT
Found at i:317801 original size:17 final size:17
Alignment explanation
Indices: 317779--317811 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
317769 ACTTTGTTTT
*
317779 TTATTTTTATTTATTTA
1 TTATTTCTATTTATTTA
317796 TTATTTCTATTTATTT
1 TTATTTCTATTTATTT
317812 TTTGTTCTCA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.21, C:0.03, G:0.00, T:0.76
Consensus pattern (17 bp):
TTATTTCTATTTATTTA
Found at i:320020 original size:104 final size:103
Alignment explanation
Indices: 319881--320086 Score: 276
Period size: 104 Copynumber: 2.0 Consensus size: 103
319871 AATTGGTTCC
*
319881 GAATAGGATATTCAATTACTTAGGTTCAAAGAAAAATCATACCCAA-CACG-TT-AGGACATAAT
1 GAATAGGATATTCAATTACTTAGGTTCAAAGAAAAATCATA-CCAAGCACGTTTGAGCACA-AAT
319943 TCCACGACTTCCCTACAATAAA-AGAACATTGCCTCGATTTTT
64 TCC-CGACTTCCCTA-AATAAAGA-AACATTGCCTCGATTTTT
* * * * *
319985 GAATAGGATATTCAATTACTTATGTTCGAAGAAAAATCGTACCAAGTACGTTTGAGCACAATTTC
1 GAATAGGATATTCAATTACTTAGGTTCAAAGAAAAATCATACCAAGCACGTTTGAGCACAAATTC
*
320050 CCGAGTTCCCTAAATAAAGAAACATTGCCTCGATTTT
66 CCGACTTCCCTAAATAAAGAAACATTGCCTCGATTTT
320087 GAAAATATTT
Statistics
Matches: 91, Mismatches: 7, Indels: 9
0.85 0.07 0.08
Matches are distributed among these distances:
103 27 0.30
104 52 0.57
105 7 0.08
106 5 0.05
ACGTcount: A:0.37, C:0.20, G:0.14, T:0.29
Consensus pattern (103 bp):
GAATAGGATATTCAATTACTTAGGTTCAAAGAAAAATCATACCAAGCACGTTTGAGCACAAATTC
CCGACTTCCCTAAATAAAGAAACATTGCCTCGATTTTT
Found at i:320497 original size:30 final size:30
Alignment explanation
Indices: 320443--320499 Score: 87
Period size: 30 Copynumber: 1.9 Consensus size: 30
320433 GTCAAAGACA
* **
320443 AAATTTTGGAAAGTTTGGTTGTCAAAAATG
1 AAATTTTGGAAAGTTAGGGAGTCAAAAATG
320473 AAATTTTGGAAAGTTAGGGAGTCAAAA
1 AAATTTTGGAAAGTTAGGGAGTCAAAA
320500 TATCATTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.40, C:0.04, G:0.25, T:0.32
Consensus pattern (30 bp):
AAATTTTGGAAAGTTAGGGAGTCAAAAATG
Found at i:325648 original size:21 final size:21
Alignment explanation
Indices: 325607--325654 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
325597 CTAACTCTAC
* *
325607 CGATACAAGTATGGATTCTAT
1 CGATACAAGTATGCATACTAT
325628 CGATACAAGTCATGCA-ACTAT
1 CGATACAAGT-ATGCATACTAT
325649 CGATAC
1 CGATAC
325655 CAAAAACTCC
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.35, C:0.21, G:0.17, T:0.27
Consensus pattern (21 bp):
CGATACAAGTATGCATACTAT
Found at i:334518 original size:12 final size:12
Alignment explanation
Indices: 334503--334530 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
334493 TTTTGACACC
334503 TTTTTTTTTAAT
1 TTTTTTTTTAAT
334515 TTTTTTTTTAAT
1 TTTTTTTTTAAT
334527 TTTT
1 TTTT
334531 ATATATTTAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (12 bp):
TTTTTTTTTAAT
Found at i:334905 original size:21 final size:22
Alignment explanation
Indices: 334881--334924 Score: 63
Period size: 21 Copynumber: 2.0 Consensus size: 22
334871 CGAAAAATGA
*
334881 AGGAAAAAAGAAATAAA-AAAG
1 AGGAAAAAAGAAAGAAAGAAAG
*
334902 AGGAAGAAAGAAAGAAAGAAAG
1 AGGAAAAAAGAAAGAAAGAAAG
334924 A
1 A
334925 AGAAGGAAGA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
21 15 0.75
22 5 0.25
ACGTcount: A:0.73, C:0.00, G:0.25, T:0.02
Consensus pattern (22 bp):
AGGAAAAAAGAAAGAAAGAAAG
Found at i:334922 original size:12 final size:11
Alignment explanation
Indices: 334872--334928 Score: 51
Period size: 11 Copynumber: 4.9 Consensus size: 11
334862 GGGGACCAAC
* *
334872 GAAAAATGAAG
1 GAAAAAAGAAA
334883 GAAAAAAGAAA
1 GAAAAAAGAAA
*
334894 TAAAAAAGAGGAA
1 GAAAAAAGA--AA
334907 GAAAGAAAGAAA
1 GAAA-AAAGAAA
*
334919 GAAAGAAGAA
1 GAAAAAAGAA
334929 GGAAGAAGGA
Statistics
Matches: 38, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
11 22 0.58
12 6 0.16
13 5 0.13
14 5 0.13
ACGTcount: A:0.72, C:0.00, G:0.25, T:0.04
Consensus pattern (11 bp):
GAAAAAAGAAA
Found at i:334929 original size:22 final size:22
Alignment explanation
Indices: 334887--334944 Score: 64
Period size: 22 Copynumber: 2.6 Consensus size: 22
334877 ATGAAGGAAA
* *
334887 AAAGAAATAAA-AAAGAGGAAG
1 AAAGAAAGAAAGAAAGAAGAAG
334908 AAAGAAAGAAAGAAAGAAGAAG
1 AAAGAAAGAAAGAAAGAAGAAG
* *
334930 GAAGAAGGAGAAGAA
1 AAAGAAAGA-AAGAA
334945 GGGGAAGAAG
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
21 10 0.32
22 16 0.52
23 5 0.16
ACGTcount: A:0.69, C:0.00, G:0.29, T:0.02
Consensus pattern (22 bp):
AAAGAAAGAAAGAAAGAAGAAG
Found at i:335349 original size:20 final size:21
Alignment explanation
Indices: 335308--335350 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
335298 TAATTTACTT
335308 TAATTTAATTTTGCTAGTTAG
1 TAATTTAATTTTGCTAGTTAG
*
335329 TAATTTAATTTTG-TTGTTAG
1 TAATTTAATTTTGCTAGTTAG
335349 TA
1 TA
335351 GTAGTAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.28, C:0.02, G:0.14, T:0.56
Consensus pattern (21 bp):
TAATTTAATTTTGCTAGTTAG
Found at i:335407 original size:111 final size:101
Alignment explanation
Indices: 335282--335493 Score: 334
Period size: 111 Copynumber: 2.0 Consensus size: 101
335272 TGTAAGTTTG
335282 GTTATTATGTTATTATTAATTTACTTTAATTTAATTTTGCTAGTTAGTAATTTAATTTTGTTGTT
1 GTTATTATGTTATTATTAATTTACTTTAATTTAATTTTGCTAGTTAGTAATTTAATTTTGTTGTT
335347 AGTAGTAGTAAGTAAAAAATATTGTTCATATTTATT
66 AGTAGTAGTAAGTAAAAAATATTGTTCATATTTATT
335383 NNNNNNNNNNGTTATTATGTTATTATTAATTTACTTTAATTTAATTTTGCTAGTTAGTAATTTAA
1 ----------GTTATTATGTTATTATTAATTTACTTTAATTTAATTTTGCTAGTTAGTAATTTAA
335448 TTTTGTTGTTAGTAGTAGTAAGTAAAAAATATTGTTCATATTTATT
56 TTTTGTTGTTAGTAGTAGTAAGTAAAAAATATTGTTCATATTTATT
335494 AATTTAAAAT
Statistics
Matches: 101, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
111 101 1.00
ACGTcount: A:0.30, C:0.03, G:0.11, T:0.51
Consensus pattern (101 bp):
GTTATTATGTTATTATTAATTTACTTTAATTTAATTTTGCTAGTTAGTAATTTAATTTTGTTGTT
AGTAGTAGTAAGTAAAAAATATTGTTCATATTTATT
Found at i:335460 original size:20 final size:21
Alignment explanation
Indices: 335419--335461 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
335409 TAATTTACTT
335419 TAATTTAATTTTGCTAGTTAG
1 TAATTTAATTTTGCTAGTTAG
*
335440 TAATTTAATTTTG-TTGTTAG
1 TAATTTAATTTTGCTAGTTAG
335460 TA
1 TA
335462 GTAGTAAGTA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.28, C:0.02, G:0.14, T:0.56
Consensus pattern (21 bp):
TAATTTAATTTTGCTAGTTAG
Found at i:336327 original size:22 final size:23
Alignment explanation
Indices: 336302--336345 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
336292 TAAGGAACGA
*
336302 AGAGCACCA-AGGTGCTAAATAG
1 AGAGCACCATACGTGCTAAATAG
*
336324 AGAGCACTATACGTGCTAAATA
1 AGAGCACCATACGTGCTAAATA
336346 ACGAAGAGTG
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 8 0.42
23 11 0.58
ACGTcount: A:0.41, C:0.18, G:0.23, T:0.18
Consensus pattern (23 bp):
AGAGCACCATACGTGCTAAATAG
Found at i:345148 original size:24 final size:24
Alignment explanation
Indices: 345121--345168 Score: 96
Period size: 24 Copynumber: 2.0 Consensus size: 24
345111 TCGGCATTAG
345121 AATTGCACCCACATTGAATGTCTC
1 AATTGCACCCACATTGAATGTCTC
345145 AATTGCACCCACATTGAATGTCTC
1 AATTGCACCCACATTGAATGTCTC
345169 TAACATTAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.29, C:0.29, G:0.12, T:0.29
Consensus pattern (24 bp):
AATTGCACCCACATTGAATGTCTC
Found at i:349579 original size:28 final size:26
Alignment explanation
Indices: 349546--349609 Score: 80
Period size: 23 Copynumber: 2.5 Consensus size: 26
349536 AACGTATACG
349546 TAAATCACATTTAAATATCTTTTAAGCA
1 TAAATCACA-TTAAATA-CTTTTAAGCA
349574 TAAATCAC---AAATACTTTTAAGCA
1 TAAATCACATTAAATACTTTTAAGCA
*
349597 AAAATCACATTAA
1 TAAATCACATTAA
349610 CTTTTAACAC
Statistics
Matches: 32, Mismatches: 1, Indels: 8
0.78 0.02 0.20
Matches are distributed among these distances:
23 17 0.53
24 5 0.16
26 2 0.06
28 8 0.25
ACGTcount: A:0.48, C:0.16, G:0.03, T:0.33
Consensus pattern (26 bp):
TAAATCACATTAAATACTTTTAAGCA
Found at i:350061 original size:36 final size:36
Alignment explanation
Indices: 350008--350119 Score: 170
Period size: 36 Copynumber: 3.1 Consensus size: 36
349998 TTAGCACAAT
* * *
350008 ATATTCACTATCACATGACATGAATAACAAACCCAC
1 ATATTTACTATCACATGACATGAATAACATACTCAC
* * *
350044 ATATTTACTGTCTCATGACATGAATAACATACTCAT
1 ATATTTACTATCACATGACATGAATAACATACTCAC
350080 ATATTTACTATCACATGACATGAATAACATACTCAC
1 ATATTTACTATCACATGACATGAATAACATACTCAC
350116 ATAT
1 ATAT
350120 CCACTTTCAC
Statistics
Matches: 67, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
36 67 1.00
ACGTcount: A:0.41, C:0.22, G:0.06, T:0.30
Consensus pattern (36 bp):
ATATTTACTATCACATGACATGAATAACATACTCAC
Found at i:351567 original size:30 final size:30
Alignment explanation
Indices: 351533--351739 Score: 215
Period size: 30 Copynumber: 6.9 Consensus size: 30
351523 TTAACCTCCA
351533 AACTTTTCAAAAATTCAAATTTGACCCTCG
1 AACTTTTCAAAAATTCAAATTTGACCCTCG
* *
351563 AACTTTCCAAAAATTCAAAATTGACTCCT--
1 AACTTTTCAAAAATTCAAATTTGAC-CCTCG
* **
351592 AAATTTTCCAAAAATTTGAATTTGACCCTCG
1 AACTTTT-CAAAAATTCAAATTTGACCCTCG
* *
351623 AA-TTTTCCAAAAATTCAAATTTAACCCTAG
1 AACTTTT-CAAAAATTCAAATTTGACCCTCG
* * *
351653 AACCTTCCAAAAATTCAAATTTGACTCTC-
1 AACTTTTCAAAAATTCAAATTTGACCCTCG
* * * *
351682 AAATTTTCCAAAAATTCCAATTTGACCCCCA
1 AACTTTT-CAAAAATTCAAATTTGACCCTCG
*
351713 AACTTTCCAAAAATTCAAATTTGACCC
1 AACTTTTCAAAAATTCAAATTTGACCC
351740 GTTTTAATGT
Statistics
Matches: 145, Mismatches: 25, Indels: 14
0.79 0.14 0.08
Matches are distributed among these distances:
29 12 0.08
30 121 0.83
31 12 0.08
ACGTcount: A:0.39, C:0.24, G:0.05, T:0.32
Consensus pattern (30 bp):
AACTTTTCAAAAATTCAAATTTGACCCTCG
Found at i:351604 original size:60 final size:60
Alignment explanation
Indices: 351528--351739 Score: 284
Period size: 60 Copynumber: 3.5 Consensus size: 60
351518 ATGCTTTAAC
* * *
351528 CTCC-AAACTTTTCAAAAATTCAAATTTGACCCTCGAACTTTCCAAAAATTCAAAATTGA
1 CTCCTAAACTTTCCAAAAATTCAAATTTGACCCTCGAATTTTCCAAAAATTCAAATTTGA
* ** *
351587 CTCCTAAATTTTCCAAAAATTTGAATTTGACCCTCGAATTTTCCAAAAATTCAAATTTAA
1 CTCCTAAACTTTCCAAAAATTCAAATTTGACCCTCGAATTTTCCAAAAATTCAAATTTGA
* * * *
351647 C-CCTAGAACCTTCCAAAAATTCAAATTTGACTCTCAAATTTTCCAAAAATTCCAATTTGA
1 CTCCTA-AACTTTCCAAAAATTCAAATTTGACCCTCGAATTTTCCAAAAATTCAAATTTGA
* *
351707 CCCCCAAACTTTCCAAAAATTCAAATTTGACCC
1 CTCCTAAACTTTCCAAAAATTCAAATTTGACCC
351740 GTTTTAATGT
Statistics
Matches: 132, Mismatches: 18, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
59 8 0.06
60 121 0.92
61 3 0.02
ACGTcount: A:0.39, C:0.25, G:0.05, T:0.32
Consensus pattern (60 bp):
CTCCTAAACTTTCCAAAAATTCAAATTTGACCCTCGAATTTTCCAAAAATTCAAATTTGA
Found at i:351666 original size:90 final size:90
Alignment explanation
Indices: 351530--351739 Score: 307
Period size: 90 Copynumber: 2.3 Consensus size: 90
351520 GCTTTAACCT
* *
351530 CCAAACTTTT-CAAAAATTCAAATTTGACCCTCGAACTTTCCAAAAATTCAAAATTGACTC-CTA
1 CCAAA-TTTTCCAAAAATTCAAATTTGACCCTAGAACCTTCCAAAAATTCAAAATTGACTCTC-A
**
351593 AATTTTCCAAAAATTTGAATTTGACCC
64 AATTTTCCAAAAATTCCAATTTGACCC
* * * *
351620 TCGAATTTTCCAAAAATTCAAATTTAACCCTAGAACCTTCCAAAAATTCAAATTTGACTCTCAAA
1 CCAAATTTTCCAAAAATTCAAATTTGACCCTAGAACCTTCCAAAAATTCAAAATTGACTCTCAAA
351685 TTTTCCAAAAATTCCAATTTGACCC
66 TTTTCCAAAAATTCCAATTTGACCC
*
351710 CCAAACTTTCCAAAAATTCAAATTTGACCC
1 CCAAATTTTCCAAAAATTCAAATTTGACCC
351740 GTTTTAATGT
Statistics
Matches: 106, Mismatches: 12, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
89 4 0.04
90 101 0.95
91 1 0.01
ACGTcount: A:0.39, C:0.25, G:0.05, T:0.31
Consensus pattern (90 bp):
CCAAATTTTCCAAAAATTCAAATTTGACCCTAGAACCTTCCAAAAATTCAAAATTGACTCTCAAA
TTTTCCAAAAATTCCAATTTGACCC
Found at i:351789 original size:3 final size:3
Alignment explanation
Indices: 351775--351811 Score: 65
Period size: 3 Copynumber: 12.3 Consensus size: 3
351765 TATATGTATA
*
351775 TAT TAA TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
351812 TAATCCCTTT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
3 32 1.00
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (3 bp):
TAT
Found at i:357327 original size:158 final size:158
Alignment explanation
Indices: 357039--357355 Score: 616
Period size: 158 Copynumber: 2.0 Consensus size: 158
357029 AGAGGAGCAA
357039 GAGGATTAAGAATGATGTGGGGGAGGTTAAGTCTCCATTAAAATGGGTTTGGTAATAGATGGTCG
1 GAGGATTAAGAATGATGTGGGGGAGGTTAAGTCTCCATTAAAATGGGTTTGGTAATAGATGGTCG
357104 ACAGGGGTTTGATCACGCAAGAGAGAGAGGACATGGTGACAACAACTTAAAATTACTACGAGTTT
66 ACAGGGGTTTGATCACGCAAGAGAGAGAGGACATGGTGACAACAACTTAAAATTACTACGAGTTT
357169 CACGTCGTAGAGGGGTACAAAATCCAAG
131 CACGTCGTAGAGGGGTACAAAATCCAAG
357197 GAGGATTAAGAATGATGTGGGGGAGGTTAAGTCTCCATTAAAATGGGTTTGGTAATAGATGGTCG
1 GAGGATTAAGAATGATGTGGGGGAGGTTAAGTCTCCATTAAAATGGGTTTGGTAATAGATGGTCG
* *
357262 ACAGGGGTTTGATCGCGTAAGAGAGAGAGGACATGGTGACAACAACTTAAAATTACTACGAGTTT
66 ACAGGGGTTTGATCACGCAAGAGAGAGAGGACATGGTGACAACAACTTAAAATTACTACGAGTTT
357327 CACGTCGTAGAGGGGTACAAAATCCAAG
131 CACGTCGTAGAGGGGTACAAAATCCAAG
357355 G
1 G
357356 GTATGTCAAA
Statistics
Matches: 157, Mismatches: 2, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
158 157 1.00
ACGTcount: A:0.33, C:0.12, G:0.31, T:0.24
Consensus pattern (158 bp):
GAGGATTAAGAATGATGTGGGGGAGGTTAAGTCTCCATTAAAATGGGTTTGGTAATAGATGGTCG
ACAGGGGTTTGATCACGCAAGAGAGAGAGGACATGGTGACAACAACTTAAAATTACTACGAGTTT
CACGTCGTAGAGGGGTACAAAATCCAAG
Found at i:363507 original size:12 final size:12
Alignment explanation
Indices: 363490--363523 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
363480 GCAATATATT
363490 TCTTTTCTTTTC
1 TCTTTTCTTTTC
363502 TCTTTTCTTTT-
1 TCTTTTCTTTTC
363513 TC-TTTCTTTTC
1 TCTTTTCTTTTC
363524 GTGATTTTTT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
10 8 0.38
11 2 0.10
12 11 0.52
ACGTcount: A:0.00, C:0.24, G:0.00, T:0.76
Consensus pattern (12 bp):
TCTTTTCTTTTC
Found at i:364280 original size:21 final size:21
Alignment explanation
Indices: 364255--364301 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
364245 CTTTCCTTCC
* *
364255 TCCTTGTGTTTCTTC-TTCTTG
1 TCCTTGTGCTTCCTCTTTC-TG
364276 TCCTTGTGCTTCCTCTTTCTG
1 TCCTTGTGCTTCCTCTTTCTG
364297 TCCTT
1 TCCTT
364302 CATACCAACC
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
21 20 0.87
22 3 0.13
ACGTcount: A:0.00, C:0.30, G:0.13, T:0.57
Consensus pattern (21 bp):
TCCTTGTGCTTCCTCTTTCTG
Found at i:370918 original size:15 final size:14
Alignment explanation
Indices: 370894--370924 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
370884 CTGTTGATGA
370894 TTGTTATAACTCCC
1 TTGTTATAACTCCC
370908 TTGTCTATAACTCCC
1 TTGT-TATAACTCCC
370923 TT
1 TT
370925 AGGTTGAGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.19, C:0.29, G:0.06, T:0.45
Consensus pattern (14 bp):
TTGTTATAACTCCC
Found at i:374831 original size:50 final size:50
Alignment explanation
Indices: 374776--374884 Score: 182
Period size: 50 Copynumber: 2.2 Consensus size: 50
374766 TAGCGAAACG
374776 GATTGAAGCCGCAATGGCAAATCTCATACACCTAAAGTTGTAGAGGGGCA
1 GATTGAAGCCGCAATGGCAAATCTCATACACCTAAAGTTGTAGAGGGGCA
* * *
374826 GATTGAAGCCGTAATGGCGAATCTCATTCACCTAAAGTTGTAGAGGGGCA
1 GATTGAAGCCGCAATGGCAAATCTCATACACCTAAAGTTGTAGAGGGGCA
*
374876 AATTGAAGC
1 GATTGAAGC
374885 TATAAGAGCG
Statistics
Matches: 55, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
50 55 1.00
ACGTcount: A:0.33, C:0.18, G:0.27, T:0.22
Consensus pattern (50 bp):
GATTGAAGCCGCAATGGCAAATCTCATACACCTAAAGTTGTAGAGGGGCA
Found at i:374896 original size:50 final size:50
Alignment explanation
Indices: 374795--374973 Score: 184
Period size: 50 Copynumber: 3.6 Consensus size: 50
374785 CGCAATGGCA
* **
374795 AATCTCATACACCTAAAGTTGTAGAGGGGCAGATTGAAGCCGTAATG-GCG
1 AATCTCATACACCTAAAGTTGTAGAGGGGCAAATTGAAGCTATAA-GAGCG
*
374845 AATCTCATTCACCTAAAGTTGTAGAGGGGCAAATTGAAGCTATAAGAGCG
1 AATCTCATACACCTAAAGTTGTAGAGGGGCAAATTGAAGCTATAAGAGCG
* * * * * * * *
374895 AATCTTATA-ATCCTAAAGCTGAAAAAGGGTAAATTGAAGCTACAAGAGCA
1 AATCTCATACA-CCTAAAGTTGTAGAGGGGCAAATTGAAGCTATAAGAGCG
* *
374945 AATCTTATAC-CCTTAAAGTTATAGAGGGG
1 AATCTCATACACC-TAAAGTTGTAGAGGGG
374974 TGGATTAAAA
Statistics
Matches: 107, Mismatches: 18, Indels: 8
0.80 0.14 0.06
Matches are distributed among these distances:
49 4 0.04
50 103 0.96
ACGTcount: A:0.37, C:0.16, G:0.23, T:0.24
Consensus pattern (50 bp):
AATCTCATACACCTAAAGTTGTAGAGGGGCAAATTGAAGCTATAAGAGCG
Found at i:375144 original size:39 final size:38
Alignment explanation
Indices: 375085--375257 Score: 177
Period size: 39 Copynumber: 4.4 Consensus size: 38
375075 AAGTCACCAC
375085 ATCCAATCTTTTACCTCGACCATGAGGCAGATTGAAGCA
1 ATCCAATCTTTTACC-CGACCATGAGGCAGATTGAAGCA
* * * * *
375124 ATCCAGTCTTTTGTCCCGACCATGGGGCAAATTGAAGTA
1 ATCCAATCTTTT-ACCCGACCATGAGGCAGATTGAAGCA
* * * *
375163 ATCCAATCTTTTACCCTAACCA-AAGGGTAGATTGAAGACC
1 ATCCAATCTTTTACCC-GACCATGA-GGCAGATTGAAG-CA
* * *
375203 ATCCGATCTCTTACCCCGACCATGAGGCAGATTGAAGTA
1 ATCCAATCTTTTA-CCCGACCATGAGGCAGATTGAAGCA
375242 ATCCAATCTTTTACCC
1 ATCCAATCTTTTACCC
375258 CTAAAGCTAT
Statistics
Matches: 105, Mismatches: 23, Indels: 13
0.74 0.16 0.09
Matches are distributed among these distances:
38 6 0.06
39 67 0.64
40 28 0.27
41 4 0.04
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.27
Consensus pattern (38 bp):
ATCCAATCTTTTACCCGACCATGAGGCAGATTGAAGCA
Found at i:376302 original size:30 final size:30
Alignment explanation
Indices: 376261--376379 Score: 132
Period size: 30 Copynumber: 4.0 Consensus size: 30
376251 TTATACTTTA
* * * *
376261 ACCCTCGAACTTTCTAAACATTTGAATTTT
1 ACCCCCGAACTTTCTAAAAATTTAAATTTG
376291 ACCCCCGAACTTT-TCAAAAATTTAAATTTG
1 ACCCCCGAACTTTCT-AAAAATTTAAATTTG
* *
376321 ACTCCCGAACTTTCCAAAAATTTAAATTTG
1 ACCCCCGAACTTTCTAAAAATTTAAATTTG
** * *
376351 ACCCTTGAACTTTCCAAAAATTCAAATTT
1 ACCCCCGAACTTTCTAAAAATTTAAATTT
376380 AACTCGGTTT
Statistics
Matches: 77, Mismatches: 10, Indels: 4
0.85 0.11 0.04
Matches are distributed among these distances:
29 1 0.01
30 76 0.99
ACGTcount: A:0.35, C:0.24, G:0.06, T:0.35
Consensus pattern (30 bp):
ACCCCCGAACTTTCTAAAAATTTAAATTTG
Found at i:376349 original size:60 final size:60
Alignment explanation
Indices: 376257--376384 Score: 159
Period size: 60 Copynumber: 2.1 Consensus size: 60
376247 GAAATTATAC
* * * * * *
376257 TTTAAC-CCTCGAACTTTCTAAACATTTGAATTTTACCCCCGAACTTTTCAAAAATTTAAA
1 TTTAACTCC-CGAACTTTCCAAAAATTTAAATTTGACCCCCGAACTTTCCAAAAATTCAAA
* **
376317 TTTGACTCCCGAACTTTCCAAAAATTTAAATTTGACCCTTGAACTTTCCAAAAATTCAAA
1 TTTAACTCCCGAACTTTCCAAAAATTTAAATTTGACCCCCGAACTTTCCAAAAATTCAAA
376377 TTTAACTC
1 TTTAACTC
376385 GGTTTTAATG
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
60 55 0.96
61 2 0.04
ACGTcount: A:0.35, C:0.23, G:0.05, T:0.36
Consensus pattern (60 bp):
TTTAACTCCCGAACTTTCCAAAAATTTAAATTTGACCCCCGAACTTTCCAAAAATTCAAA
Found at i:381315 original size:9 final size:9
Alignment explanation
Indices: 381301--381325 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
381291 ACTGTATGAT
381301 GCTAAAAGA
1 GCTAAAAGA
381310 GCTAAAAGA
1 GCTAAAAGA
381319 GCTAAAA
1 GCTAAAA
381326 AATTCAATTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.56, C:0.12, G:0.20, T:0.12
Consensus pattern (9 bp):
GCTAAAAGA
Found at i:383037 original size:17 final size:17
Alignment explanation
Indices: 383017--383050 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
383007 ATCACTCGTT
*
383017 ATTTCAATAGCATTTTC
1 ATTTCAATAACATTTTC
383034 ATTTCAATAACATTTTC
1 ATTTCAATAACATTTTC
383051 CATATCAACC
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.32, C:0.18, G:0.03, T:0.47
Consensus pattern (17 bp):
ATTTCAATAACATTTTC
Found at i:384192 original size:13 final size:13
Alignment explanation
Indices: 384174--384217 Score: 61
Period size: 13 Copynumber: 3.2 Consensus size: 13
384164 TCTTTATTTT
384174 TTATTATAATATA
1 TTATTATAATATA
384187 TTATTATAATACTA
1 TTATTATAATA-TA
*
384201 TTATTTATCATATA
1 TTA-TTATAATATA
384215 TTA
1 TTA
384218 ACACCAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 11 0.39
14 10 0.36
15 7 0.25
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (13 bp):
TTATTATAATATA
Found at i:390442 original size:17 final size:18
Alignment explanation
Indices: 390420--390459 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
390410 ACTCGCTATG
* *
390420 TCAATAGCA-TTTTCATT
1 TCAATAACATTTTTCATA
390437 TCAATAACATTTTTCATA
1 TCAATAACATTTTTCATA
390455 TCAAT
1 TCAAT
390460 CAAATAGTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.35, C:0.17, G:0.03, T:0.45
Consensus pattern (18 bp):
TCAATAACATTTTTCATA
Found at i:391574 original size:13 final size:13
Alignment explanation
Indices: 391556--391599 Score: 61
Period size: 13 Copynumber: 3.2 Consensus size: 13
391546 TTTATTTTTT
391556 TTATTATAATATA
1 TTATTATAATATA
391569 TTATTATAATACTA
1 TTATTATAATA-TA
*
391583 TTATTTATCATATA
1 TTA-TTATAATATA
391597 TTA
1 TTA
391600 ACACCAATAT
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
13 11 0.39
14 10 0.36
15 7 0.25
ACGTcount: A:0.41, C:0.05, G:0.00, T:0.55
Consensus pattern (13 bp):
TTATTATAATATA
Found at i:399297 original size:51 final size:52
Alignment explanation
Indices: 399241--399349 Score: 159
Period size: 51 Copynumber: 2.1 Consensus size: 52
399231 TTCTTTTTCT
*
399241 TTTTCATTTTGGAGAAAACCACGTTCATTTCCAAATGTTT-T-AGTTTCTCCA
1 TTTTCATTTTGGAGAAAACCACATTCATTTCCAAATGTTTCTCA-TTTCTCCA
* **
399292 TTTTCATTTTGGATAAAACCACATTTGTTTCCAAATGTTTCTCATTTCTCCA
1 TTTTCATTTTGGAGAAAACCACATTCATTTCCAAATGTTTCTCATTTCTCCA
399344 TTTTCA
1 TTTTCA
399350 CCATTTCTAT
Statistics
Matches: 52, Mismatches: 4, Indels: 3
0.88 0.07 0.05
Matches are distributed among these distances:
51 36 0.69
52 15 0.29
53 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.09, T:0.46
Consensus pattern (52 bp):
TTTTCATTTTGGAGAAAACCACATTCATTTCCAAATGTTTCTCATTTCTCCA
Found at i:401979 original size:44 final size:44
Alignment explanation
Indices: 401916--402004 Score: 178
Period size: 44 Copynumber: 2.0 Consensus size: 44
401906 GATATTGCAC
401916 CCATTATGTAGGAGGGGCAAATCCTATATTGATCAACCATATCT
1 CCATTATGTAGGAGGGGCAAATCCTATATTGATCAACCATATCT
401960 CCATTATGTAGGAGGGGCAAATCCTATATTGATCAACCATATCT
1 CCATTATGTAGGAGGGGCAAATCCTATATTGATCAACCATATCT
402004 C
1 C
402005 ACTACATAGA
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
44 45 1.00
ACGTcount: A:0.31, C:0.21, G:0.18, T:0.29
Consensus pattern (44 bp):
CCATTATGTAGGAGGGGCAAATCCTATATTGATCAACCATATCT
Found at i:414256 original size:7 final size:7
Alignment explanation
Indices: 414244--414269 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
414234 CCTCATTTCA
414244 TCATCCC
1 TCATCCC
414251 TCATCCC
1 TCATCCC
414258 TCATCCC
1 TCATCCC
414265 TCATC
1 TCATC
414270 TTTCTTTCCT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.15, C:0.54, G:0.00, T:0.31
Consensus pattern (7 bp):
TCATCCC
Found at i:415565 original size:15 final size:15
Alignment explanation
Indices: 415545--415577 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
415535 GAATCTCCCA
415545 ATCTTCATA-ATACTC
1 ATCTTCATAGATA-TC
415560 ATCTTCATAGATATC
1 ATCTTCATAGATATC
415575 ATC
1 ATC
415578 GTGAGAGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.82
16 3 0.18
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.39
Consensus pattern (15 bp):
ATCTTCATAGATATC
Found at i:425313 original size:18 final size:18
Alignment explanation
Indices: 425290--425327 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
425280 TTGAAACTTA
425290 GCATAAAATTCTAAAAAT
1 GCATAAAATTCTAAAAAT
425308 GCATAAAATTCTAAAAAT
1 GCATAAAATTCTAAAAAT
425326 GC
1 GC
425328 TTGCATATGA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.53, C:0.13, G:0.08, T:0.26
Consensus pattern (18 bp):
GCATAAAATTCTAAAAAT
Found at i:426609 original size:15 final size:15
Alignment explanation
Indices: 426589--426621 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
426579 GAATCTCCCA
426589 ATCTTCATA-ATACTC
1 ATCTTCATAGATA-TC
426604 ATCTTCATAGATATC
1 ATCTTCATAGATATC
426619 ATC
1 ATC
426622 GTGAGAGATG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 14 0.82
16 3 0.18
ACGTcount: A:0.33, C:0.24, G:0.03, T:0.39
Consensus pattern (15 bp):
ATCTTCATAGATATC
Found at i:428100 original size:22 final size:21
Alignment explanation
Indices: 428061--428101 Score: 55
Period size: 22 Copynumber: 1.9 Consensus size: 21
428051 TATTTAAAAG
**
428061 ATAAAAACTAAGTTAAAATCT
1 ATAAAAACTAAGGAAAAATCT
428082 ATAAAAACATAAGGAAAAAT
1 ATAAAAAC-TAAGGAAAAAT
428102 ACATGATTTC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 8 0.47
22 9 0.53
ACGTcount: A:0.63, C:0.07, G:0.07, T:0.22
Consensus pattern (21 bp):
ATAAAAACTAAGGAAAAATCT
Found at i:429352 original size:15 final size:15
Alignment explanation
Indices: 429334--429366 Score: 50
Period size: 15 Copynumber: 2.2 Consensus size: 15
429324 TCATGAAAGC
429334 AAAT-AACAACAAAAT
1 AAATAAACAA-AAAAT
429349 AAATAAACAAAAAAT
1 AAATAAACAAAAAAT
429364 AAA
1 AAA
429367 AAAATTAAAT
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 12 0.71
16 5 0.29
ACGTcount: A:0.79, C:0.09, G:0.00, T:0.12
Consensus pattern (15 bp):
AAATAAACAAAAAAT
Found at i:429409 original size:100 final size:99
Alignment explanation
Indices: 429303--429506 Score: 225
Period size: 100 Copynumber: 2.1 Consensus size: 99
429293 ATACAAATTA
* * *
429303 AATAAAAATAATAATGA-AATGTCATGAAAGCAAATAACAACA-AAATAAATAAACAAAAAATAA
1 AATAAAAATAATAAGGATAAGGT-ATGAAAACAAATAACAA-ATAAATAAATAAACAAAAAA-AA
* *
429366 AAAAATTAAATGCTAAAATAAACAAAC-AAATATAAAC
63 AAAAATTAAAAGCCAAAATAAAC-AACTAAATATAAAC
** * * * * * *
429403 AATAAAAATAATTGGGATGAGGTGTGAAAATAAATGACAAATAAATAAATAAACAAAAAACAATA
1 AATAAAAATAATAAGGATAAGGTATGAAAACAAATAACAAATAAATAAATAAACAAAAAAAAAAA
*
429468 AATTAAAAGCCAAAATAAACAACTAAATATAAAT
66 AATTAAAAGCCAAAATAAACAACTAAATATAAAC
429502 AATAA
1 AATAA
429507 TAAAAAAGAA
Statistics
Matches: 87, Mismatches: 14, Indels: 7
0.81 0.13 0.06
Matches are distributed among these distances:
98 3 0.03
99 36 0.41
100 45 0.52
101 3 0.03
ACGTcount: A:0.66, C:0.08, G:0.07, T:0.19
Consensus pattern (99 bp):
AATAAAAATAATAAGGATAAGGTATGAAAACAAATAACAAATAAATAAATAAACAAAAAAAAAAA
AATTAAAAGCCAAAATAAACAACTAAATATAAAC
Found at i:429750 original size:27 final size:25
Alignment explanation
Indices: 429714--429771 Score: 71
Period size: 25 Copynumber: 2.2 Consensus size: 25
429704 GCTTTGAATT
* *
429714 TTCTTTGAATGTATGTTTCAAAAAAAA
1 TTCTCTGAATGT-TGTAT-AAAAAAAA
429741 TTCTCTGAATGTTGTATAAAAAAAA
1 TTCTCTGAATGTTGTATAAAAAAAA
*
429766 ATCTCT
1 TTCTCT
429772 AAATCTTATT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
25 13 0.46
26 4 0.14
27 11 0.39
ACGTcount: A:0.40, C:0.10, G:0.10, T:0.40
Consensus pattern (25 bp):
TTCTCTGAATGTTGTATAAAAAAAA
Found at i:429954 original size:24 final size:24
Alignment explanation
Indices: 429910--429955 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
429900 AAGGGCAACT
*
429910 TTTAGGTTTTTTTCCATTTTTTAG
1 TTTAGGTTTTTTTCCAATTTTTAG
*
429934 TTTAGGGTTTTTTT-TAATTTTT
1 TTTA-GGTTTTTTTCCAATTTTT
429956 GGGCTTTGTA
Statistics
Matches: 19, Mismatches: 2, Indels: 2
0.83 0.09 0.09
Matches are distributed among these distances:
24 10 0.53
25 9 0.47
ACGTcount: A:0.13, C:0.04, G:0.13, T:0.70
Consensus pattern (24 bp):
TTTAGGTTTTTTTCCAATTTTTAG
Found at i:445667 original size:53 final size:51
Alignment explanation
Indices: 445596--445772 Score: 239
Period size: 51 Copynumber: 3.4 Consensus size: 51
445586 AAGGGGTTCA
* *
445596 ATGACTAAGTGTCATCGTGAGCAAATGAATCATTTATGGATTACAAAGGTCCG
1 ATGACTAAGTGTCATCGTGAGTAAATGAATCATTTATAGATT--AAAGGTCCG
* * * *
445649 ATGACTAATTGTCATCGTGAGTAAATGAATCCTTTACAGATTAAAGGTCTG
1 ATGACTAAGTGTCATCGTGAGTAAATGAATCATTTATAGATTAAAGGTCCG
* *
445700 ATGACTAAGTGTCATCGTGAGTAAATGAATTCA-TGATTGATTAAAGGTCCG
1 ATGACTAAGTGTCATCGTGAGTAAATGAA-TCATTTATAGATTAAAGGTCCG
*
445751 ATGACTTAGTGTCATCGTGAGT
1 ATGACTAAGTGTCATCGTGAGT
445773 GTATTAATTC
Statistics
Matches: 110, Mismatches: 13, Indels: 4
0.87 0.10 0.03
Matches are distributed among these distances:
51 71 0.65
52 2 0.02
53 37 0.34
ACGTcount: A:0.32, C:0.14, G:0.23, T:0.32
Consensus pattern (51 bp):
ATGACTAAGTGTCATCGTGAGTAAATGAATCATTTATAGATTAAAGGTCCG
Found at i:445807 original size:104 final size:103
Alignment explanation
Indices: 445596--445826 Score: 252
Period size: 104 Copynumber: 2.2 Consensus size: 103
445586 AAGGGGTTCA
* * *
445596 ATGACTAAGTGTCATCGTGAGCAAATGAATCATTTATGGATTACAAAGGTCCGATGACTAATTGT
1 ATGACTAAGTGTCATCGTGAGTAAATGAATCATTGATGGATTA-AAAGGTCCGATGACTAAGTGT
** * *
445661 CATCGTGAGTAAATGAATCCTTTACAGATTAAAGGTCTG
65 CATCGTGAGTAAATGAATCCTTTACAGAACAAAGATCCG
* *
445700 ATGACTAAGTGTCATCGTGAGTAAATGAATTCA-TGATTGATT-AAAGGTCCGATGACTTAGTGT
1 ATGACTAAGTGTCATCGTGAGTAAATGAA-TCATTGATGGATTAAAAGGTCCGATGACTAAGTGT
** * * *
445763 CATCGTGAGTGTATTAATTCTTATACGGAACAAGAGATCCG
65 CATCGTGAGTAAATGAATCCTT-TACAGAACAA-AGATCCG
* *
445804 ATGACTGTA-TGTCATCGTAAGTA
1 ATGACT-AAGTGTCATCGTGAGTA
445827 TTAAATGAAA
Statistics
Matches: 107, Mismatches: 16, Indels: 8
0.82 0.12 0.06
Matches are distributed among these distances:
102 37 0.35
103 7 0.07
104 59 0.55
105 4 0.04
ACGTcount: A:0.32, C:0.14, G:0.22, T:0.32
Consensus pattern (103 bp):
ATGACTAAGTGTCATCGTGAGTAAATGAATCATTGATGGATTAAAAGGTCCGATGACTAAGTGTC
ATCGTGAGTAAATGAATCCTTTACAGAACAAAGATCCG
Found at i:449640 original size:17 final size:18
Alignment explanation
Indices: 449620--449666 Score: 51
Period size: 18 Copynumber: 2.7 Consensus size: 18
449610 GCTTGATCAT
*
449620 ATGCAATCAGAT-ACCAG
1 ATGCAATCACATAACCAG
* *
449637 ATGCAGTCACATAATCAG
1 ATGCAATCACATAACCAG
*
449655 ATGCAACCACAT
1 ATGCAATCACAT
449667 GTTCGAATGC
Statistics
Matches: 24, Mismatches: 5, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
17 10 0.42
18 14 0.58
ACGTcount: A:0.40, C:0.26, G:0.15, T:0.19
Consensus pattern (18 bp):
ATGCAATCACATAACCAG
Found at i:456964 original size:10 final size:10
Alignment explanation
Indices: 456940--456990 Score: 50
Period size: 10 Copynumber: 4.9 Consensus size: 10
456930 ATTGAAGTAA
456940 AAGAAGAAGAG
1 AAGAAGAA-AG
*
456951 AAGAGGAAAG
1 AAGAAGAAAG
456961 AAGAAGAAA-
1 AAGAAGAAAG
*
456970 AAGAACAGAAGG
1 AAG-A-AGAAAG
456982 AAGAAGAAA
1 AAGAAGAAA
456991 ATGTTGCCCA
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
9 3 0.09
10 15 0.45
11 12 0.36
12 3 0.09
ACGTcount: A:0.67, C:0.02, G:0.31, T:0.00
Consensus pattern (10 bp):
AAGAAGAAAG
Found at i:457411 original size:17 final size:17
Alignment explanation
Indices: 457386--457428 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
457376 ATATATTTTC
* *
457386 TCTAGTTGTCATTACAT
1 TCTAATTGTCACTACAT
*
457403 TCTAATTGTCACTGCAT
1 TCTAATTGTCACTACAT
*
457420 TGTAATTGT
1 TCTAATTGT
457429 TTTCACATTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 22 1.00
ACGTcount: A:0.23, C:0.16, G:0.14, T:0.47
Consensus pattern (17 bp):
TCTAATTGTCACTACAT
Found at i:458891 original size:147 final size:147
Alignment explanation
Indices: 458624--458907 Score: 496
Period size: 147 Copynumber: 1.9 Consensus size: 147
458614 CAAAGATGTC
*
458624 ACCACATAAATGTTTCTACATTTTATCAAGGATTTTACGCTGATAACACATTAAGAAGCACCAAT
1 ACCACATAAATGTTTCTACATTTTATCAAGGATTTTACACTGATAACACATTAAGAAGCACCAAT
* *
458689 GCAAGAGAATGCAAGTTGTCGCAACAAATTTAAATCATAATTTACGTCCAGAGATGTCACGACAA
66 GCAAGAGAACGCAAGTTGTCGCAACAAATTTAAATCATAATTTACATCCAGAGATGTCACGACAA
458754 TCTGCAACTGCCTTGTT
131 TCTGCAACTGCCTTGTT
* * *
458771 ACCACATAAATGTTTCTACATTTTATCAAGGATTTTACACTGCTAACACATTCAGAAGCACCAGT
1 ACCACATAAATGTTTCTACATTTTATCAAGGATTTTACACTGATAACACATTAAGAAGCACCAAT
* *
458836 GCAAGAGAACGCAAGTTGTCGCAGCAAATTTAAATCATAATTTGCATCCAGAGATGTCACGACAA
66 GCAAGAGAACGCAAGTTGTCGCAACAAATTTAAATCATAATTTACATCCAGAGATGTCACGACAA
458901 TCTGCAA
131 TCTGCAA
458908 TTACCTAATG
Statistics
Matches: 129, Mismatches: 8, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
147 129 1.00
ACGTcount: A:0.36, C:0.21, G:0.15, T:0.27
Consensus pattern (147 bp):
ACCACATAAATGTTTCTACATTTTATCAAGGATTTTACACTGATAACACATTAAGAAGCACCAAT
GCAAGAGAACGCAAGTTGTCGCAACAAATTTAAATCATAATTTACATCCAGAGATGTCACGACAA
TCTGCAACTGCCTTGTT
Found at i:467280 original size:28 final size:28
Alignment explanation
Indices: 467249--467350 Score: 105
Period size: 28 Copynumber: 3.6 Consensus size: 28
467239 CTTTTAATGA
* *
467249 AAATCTCTATTATGAATGCCTTTGTGGC
1 AAATCTCTATTAAGAACGCCTTTGTGGC
* *
467277 AAATCTTTGTTAAGAACGCCTTTGTGGC
1 AAATCTCTATTAAGAACGCCTTTGTGGC
* * * * * *
467305 GAATCTATGTTAAAAACACCTTCGTGGC
1 AAATCTCTATTAAGAACGCCTTTGTGGC
*
467333 TAATCTCTATTAAGAACG
1 AAATCTCTATTAAGAACG
467351 TATTTATGAA
Statistics
Matches: 60, Mismatches: 14, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
28 60 1.00
ACGTcount: A:0.29, C:0.19, G:0.18, T:0.34
Consensus pattern (28 bp):
AAATCTCTATTAAGAACGCCTTTGTGGC
Found at i:469823 original size:15 final size:15
Alignment explanation
Indices: 469803--469834 Score: 64
Period size: 15 Copynumber: 2.1 Consensus size: 15
469793 CTTTATGTTT
469803 CATAACCTCAAGAGC
1 CATAACCTCAAGAGC
469818 CATAACCTCAAGAGC
1 CATAACCTCAAGAGC
469833 CA
1 CA
469835 AACTATCATA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.41, C:0.34, G:0.12, T:0.12
Consensus pattern (15 bp):
CATAACCTCAAGAGC
Found at i:470111 original size:23 final size:23
Alignment explanation
Indices: 469952--470104 Score: 225
Period size: 23 Copynumber: 6.7 Consensus size: 23
469942 AAGTGATATG
469952 TTAATGTGATTTATGCTTAAATA
1 TTAATGTGATTTATGCTTAAATA
* *
469975 TTAATGTGATTTGTGTTTAAATA
1 TTAATGTGATTTATGCTTAAATA
* *
469998 TTAATGTGATCTGTGCTTAAATA
1 TTAATGTGATTTATGCTTAAATA
* *
470021 TTTATGTAATTTATGCTTAAATA
1 TTAATGTGATTTATGCTTAAATA
* * *
470044 TTAATGTAATTTGTGCTTAAACA
1 TTAATGTGATTTATGCTTAAATA
470067 TTAATGTGATTTATGCTTAAATA
1 TTAATGTGATTTATGCTTAAATA
470090 TTAATGTGATTTATG
1 TTAATGTGATTTATG
470105 TGTAAATGGA
Statistics
Matches: 116, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 116 1.00
ACGTcount: A:0.33, C:0.05, G:0.14, T:0.48
Consensus pattern (23 bp):
TTAATGTGATTTATGCTTAAATA
Found at i:472122 original size:21 final size:21
Alignment explanation
Indices: 472096--472161 Score: 96
Period size: 21 Copynumber: 3.1 Consensus size: 21
472086 CCTGTAGCTT
472096 CTACCAATACAAGTATTTGGA
1 CTACCAATACAAGTATTTGGA
* *
472117 CTACCAATACAAGTATTCGAA
1 CTACCAATACAAGTATTTGGA
* *
472138 CTACCGATACAAGTATTTAGA
1 CTACCAATACAAGTATTTGGA
472159 CTA
1 CTA
472162 TCGATTCTAC
Statistics
Matches: 39, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 39 1.00
ACGTcount: A:0.39, C:0.21, G:0.12, T:0.27
Consensus pattern (21 bp):
CTACCAATACAAGTATTTGGA
Found at i:484353 original size:12 final size:13
Alignment explanation
Indices: 484336--484386 Score: 52
Period size: 14 Copynumber: 3.8 Consensus size: 13
484326 TTGAGGAAGG
484336 GAAAGA-AGAAAA
1 GAAAGAGAGAAAA
484348 GAAAGAGGAGAAAA
1 GAAAGA-GAGAAAA
*
484362 AAGAAGA-AGGAAAA
1 GA-AAGAGA-GAAAA
484376 GAAAGAGAGAA
1 GAAAGAGAGAA
484387 GGAAAAAATT
Statistics
Matches: 32, Mismatches: 2, Indels: 9
0.74 0.05 0.21
Matches are distributed among these distances:
12 6 0.19
13 8 0.25
14 14 0.44
15 4 0.12
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (13 bp):
GAAAGAGAGAAAA
Found at i:484372 original size:16 final size:15
Alignment explanation
Indices: 484344--484394 Score: 59
Period size: 16 Copynumber: 3.2 Consensus size: 15
484334 GGGAAAGAAG
484344 AAAAGAA-AGAGGAGAA
1 AAAAGAAGA-AGGA-AA
484360 AAAAGAAGAAGGAAA
1 AAAAGAAGAAGGAAA
484375 AGAAAGAGAGAAGGAAA
1 A-AAAGA-AGAAGGAAA
484392 AAA
1 AAA
484395 TTTTTATCAC
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
15 3 0.09
16 18 0.56
17 11 0.34
ACGTcount: A:0.71, C:0.00, G:0.29, T:0.00
Consensus pattern (15 bp):
AAAAGAAGAAGGAAA
Found at i:484388 original size:17 final size:16
Alignment explanation
Indices: 484339--484392 Score: 55
Period size: 17 Copynumber: 3.6 Consensus size: 16
484329 AGGAAGGGAA
484339 AGAAGAAAAGAAAGAG
1 AGAAGAAAAGAAAGAG
484355 -G-AG-AAA-AAAGA-
1 AGAAGAAAAGAAAGAG
484366 AGAAGGAAAAGAAAGAG
1 AGAA-GAAAAGAAAGAG
484383 AGAAGGAAAA
1 AGAA-GAAAA
484393 AATTTTTATC
Statistics
Matches: 32, Mismatches: 0, Indels: 11
0.74 0.00 0.26
Matches are distributed among these distances:
12 6 0.19
13 4 0.12
14 3 0.09
15 4 0.12
16 5 0.16
17 10 0.31
ACGTcount: A:0.69, C:0.00, G:0.31, T:0.00
Consensus pattern (16 bp):
AGAAGAAAAGAAAGAG
Found at i:492396 original size:26 final size:26
Alignment explanation
Indices: 492367--492424 Score: 98
Period size: 26 Copynumber: 2.2 Consensus size: 26
492357 TACATTAACA
492367 TTTTTCTCTTTTCTTCTCACTTTATT
1 TTTTTCTCTTTTCTTCTCACTTTATT
*
492393 TTTTTCTCTTTTCTTTTCACTTTATT
1 TTTTTCTCTTTTCTTCTCACTTTATT
492419 TATTTT
1 T-TTTT
492425 TTCTCTTATG
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
26 26 0.87
27 4 0.13
ACGTcount: A:0.09, C:0.19, G:0.00, T:0.72
Consensus pattern (26 bp):
TTTTTCTCTTTTCTTCTCACTTTATT
Found at i:497247 original size:69 final size:69
Alignment explanation
Indices: 497155--497597 Score: 462
Period size: 69 Copynumber: 6.4 Consensus size: 69
497145 AAGTCCATTG
* * * *
497155 TTTGCAGATTCTGTTCCAAGCACCCCTGCCTACGCAGGTGACATGTTCCAA-GGGAAGAGCTCAT
1 TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTT-CAAGGGGAAGAGCTCAT
*
497219 CTGTT
65 CTATT
** * * * * *
497224 TTTGGGGAATCTGTTCCAAGCACCCCCGCTTATGCAGATAACATGTTCAAGGGGAAGGGCTCATC
1 TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGCTCATC
*
497289 TGTT
66 TATT
* * * * *
497293 TTTGCAGATTCTGTTCCAAGCACTCCGGCCTATGCAGATAGCATGTTTAAGGGGAAGAGTTCGTC
1 TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGCTCAT-
*
497358 CT-TG
65 CTATT
* * ** * * *
497362 TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACTTGTTTAAGGGTCAGGGTTCGTC
1 TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGCTCATC
* *
497427 CATA
66 TATT
* * * * * * *
497431 TTTGGAGATTCTGTTCCAAGCACTTCTGCCTATGAAGATAACTTGTTCAAGGGGAAGGGTTCGTC
1 TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGCTCATC
* *
497496 CATA
66 TATT
*
497500 TTTGCAGATTCTGTTCCAAGCACTCCTGCCTACTTG--GATAACATGTTCAAGGGGACGAGCTCA
1 TTTGCAGATTCTGTTCCAAGCACTCCTGCCTA--TGCAGATAACATGTTCAAGGGGAAGAGCTCA
497563 TCTATT
64 TCTATT
* *
497569 TTTGCAGAATCTGTTCCAAGCACCCCTGC
1 TTTGCAGATTCTGTTCCAAGCACTCCTGC
497598 TTATCATTAT
Statistics
Matches: 323, Mismatches: 46, Indels: 10
0.85 0.12 0.03
Matches are distributed among these distances:
68 4 0.01
69 315 0.98
70 2 0.01
71 2 0.01
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (69 bp):
TTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACATGTTCAAGGGGAAGAGCTCATC
TATT
Found at i:497507 original size:207 final size:206
Alignment explanation
Indices: 497147--497597 Score: 521
Period size: 207 Copynumber: 2.2 Consensus size: 206
497137 CCAGGGAAAA
* *
497147 GTCCATTGTTTGCAGATTCTGTTCCAAGCACCCCTGCCTACGCAGGTGACATGTTCCAAGGGAAG
1 GTCC-TTGTTTGCAGATTCTGTTCCAAGCACCCCTGCCTACGCAGATAACATGTTCCAAGGGAAG
** * * * *
497212 AGCTCATCTGTTTTTGGGGAATCTGTTCCAAGCACCCCCGCTTATGCAGATAACATGTTCAAGGG
65 AGCTCATCCATATTTGGAGAATCTGTTCCAAGCACCCCCGCCTATGAAGATAACATGTTCAAGGG
** * * *
497277 GAAGGGCTCATCTGTTTTTGCAGATTCTGTTCCAAGCACTCCGGCCTA-TGCAGATAGCATGTTT
130 GAAGGGCTCATCCATATTTGCAGATTCTGTTCCAAGCACTCCGGCCTACTG--GATAACATGTTC
*
497341 AAGGGGAAGAGTTC
193 AAGGGGAAGAGCTC
* * * * *
497355 GTCCTTGTTTGCAGATTCTGTTCCAAGCACTCCTGCCTATGCAGATAACTTGTT-TAAGGGTCAG
1 GTCCTTGTTTGCAGATTCTGTTCCAAGCACCCCTGCCTACGCAGATAACATGTTCCAAGGG-AAG
* * * * ** * *
497419 GGTTCGTCCATATTTGGAGATTCTGTTCCAAGCACTTCTGCCTATGAAGATAACTTGTTCAAGGG
65 AGCTCATCCATATTTGGAGAATCTGTTCCAAGCACCCCCGCCTATGAAGATAACATGTTCAAGGG
* * *
497484 GAAGGGTTCGTCCATATTTGCAGATTCTGTTCCAAGCACTCCTGCCTACTTGGATAACATGTTCA
130 GAAGGGCTCATCCATATTTGCAGATTCTGTTCCAAGCACTCCGGCCTAC-TGGATAACATGTTCA
*
497549 AGGGGACGAGCTC
194 AGGGGAAGAGCTC
* * *
497562 AT-CTATTTTTGCAGAATCTGTTCCAAGCACCCCTGC
1 GTCCT-TGTTTGCAGATTCTGTTCCAAGCACCCCTGC
497598 TTATCATTAT
Statistics
Matches: 204, Mismatches: 35, Indels: 9
0.82 0.14 0.04
Matches are distributed among these distances:
206 7 0.03
207 191 0.94
208 4 0.02
209 2 0.01
ACGTcount: A:0.22, C:0.24, G:0.23, T:0.30
Consensus pattern (206 bp):
GTCCTTGTTTGCAGATTCTGTTCCAAGCACCCCTGCCTACGCAGATAACATGTTCCAAGGGAAGA
GCTCATCCATATTTGGAGAATCTGTTCCAAGCACCCCCGCCTATGAAGATAACATGTTCAAGGGG
AAGGGCTCATCCATATTTGCAGATTCTGTTCCAAGCACTCCGGCCTACTGGATAACATGTTCAAG
GGGAAGAGCTC
Found at i:500845 original size:8 final size:8
Alignment explanation
Indices: 500832--500913 Score: 50
Period size: 8 Copynumber: 10.5 Consensus size: 8
500822 CACTGTTATA
500832 ATTTAAAT
1 ATTTAAAT
*
500840 ATTTAATT
1 ATTTAAAT
500848 ATTTAAA-
1 ATTTAAAT
*
500855 ATTGT--TT
1 ATT-TAAAT
*
500862 ATTCAAAT
1 ATTTAAAT
500870 ATTTAAA-
1 ATTTAAAT
500877 A-TTATAAT
1 ATTTA-AAT
500885 AATTTAAAT
1 -ATTTAAAT
500894 ATTT-AAT
1 ATTTAAAT
*
500901 AATTAAAT
1 ATTTAAAT
500909 CATTT
1 -ATTT
500914 CTTTTCAATT
Statistics
Matches: 56, Mismatches: 8, Indels: 19
0.67 0.10 0.23
Matches are distributed among these distances:
6 3 0.05
7 15 0.27
8 28 0.50
9 7 0.12
10 3 0.05
ACGTcount: A:0.46, C:0.02, G:0.01, T:0.50
Consensus pattern (8 bp):
ATTTAAAT
Found at i:500891 original size:16 final size:16
Alignment explanation
Indices: 500870--500913 Score: 56
Period size: 16 Copynumber: 2.8 Consensus size: 16
500860 TTATTCAAAT
500870 ATTTAAA-ATTATAATA
1 ATTTAAATATT-TAATA
500886 ATTTAAATATTTAATA
1 ATTTAAATATTTAATA
500902 A-TTAAATCATTT
1 ATTTAAAT-ATTT
500914 CTTTTCAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
15 6 0.23
16 17 0.65
17 3 0.12
ACGTcount: A:0.50, C:0.02, G:0.00, T:0.48
Consensus pattern (16 bp):
ATTTAAATATTTAATA
Found at i:501121 original size:13 final size:13
Alignment explanation
Indices: 501106--501165 Score: 70
Period size: 13 Copynumber: 4.6 Consensus size: 13
501096 AATTAATAGA
501106 ATTAATTGATT-T
1 ATTAATTGATTCT
*
501118 AATTAATTGGTTCT
1 -ATTAATTGATTCT
501132 ATTAATTGATT-T
1 ATTAATTGATTCT
*
501144 GATCAATTGATTCT
1 -ATTAATTGATTCT
501158 ATTAATTG
1 ATTAATTG
501166 TCTATTTATA
Statistics
Matches: 40, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
12 1 0.03
13 37 0.93
14 2 0.05
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.52
Consensus pattern (13 bp):
ATTAATTGATTCT
Found at i:501135 original size:26 final size:26
Alignment explanation
Indices: 501106--501165 Score: 93
Period size: 26 Copynumber: 2.3 Consensus size: 26
501096 AATTAATAGA
* *
501106 ATTAATTGATTTAATTAATTGGTTCT
1 ATTAATTGATTTAATCAATTGATTCT
*
501132 ATTAATTGATTTGATCAATTGATTCT
1 ATTAATTGATTTAATCAATTGATTCT
501158 ATTAATTG
1 ATTAATTG
501166 TCTATTTATA
Statistics
Matches: 31, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
26 31 1.00
ACGTcount: A:0.32, C:0.05, G:0.12, T:0.52
Consensus pattern (26 bp):
ATTAATTGATTTAATCAATTGATTCT
Found at i:503629 original size:23 final size:22
Alignment explanation
Indices: 503553--503630 Score: 72
Period size: 23 Copynumber: 3.4 Consensus size: 22
503543 TTAAAAAATG
503553 ATTTTTTTCAAGTTTTTATTTT
1 ATTTTTTTCAAGTTTTTATTTT
503575 ATTTCTTTTCGAA-TTTATTATTTT
1 ATTT-TTTTC-AAGTTT-TTATTTT
503599 -TCCCTTTTTT-AAGTTTTTATTTAT
1 AT---TTTTTTCAAGTTTTTATTT-T
503623 ATTTTTTT
1 ATTTTTTT
503631 GTTTTTCGAA
Statistics
Matches: 47, Mismatches: 0, Indels: 18
0.72 0.00 0.28
Matches are distributed among these distances:
22 10 0.21
23 17 0.36
24 13 0.28
25 5 0.11
26 2 0.04
ACGTcount: A:0.18, C:0.08, G:0.04, T:0.71
Consensus pattern (22 bp):
ATTTTTTTCAAGTTTTTATTTT
Found at i:503725 original size:11 final size:10
Alignment explanation
Indices: 503706--503751 Score: 58
Period size: 10 Copynumber: 4.4 Consensus size: 10
503696 CTGATTTATC
503706 TTTTTGTATT
1 TTTTTGTATT
503716 TTTCTTGTA-T
1 TTT-TTGTATT
503726 TTTTTGTAATTT
1 TTTTTGT-A-TT
503738 TTTTTGTATT
1 TTTTTGTATT
503748 TTTT
1 TTTT
503752 CTATTGATTG
Statistics
Matches: 32, Mismatches: 0, Indels: 8
0.80 0.00 0.20
Matches are distributed among these distances:
9 4 0.12
10 14 0.44
11 6 0.19
12 8 0.25
ACGTcount: A:0.11, C:0.02, G:0.09, T:0.78
Consensus pattern (10 bp):
TTTTTGTATT
Found at i:503737 original size:21 final size:20
Alignment explanation
Indices: 503706--503756 Score: 75
Period size: 21 Copynumber: 2.5 Consensus size: 20
503696 CTGATTTATC
503706 TTTTTGTATTTTTCTTGTAT
1 TTTTTGTATTTTTCTTGTAT
*
503726 TTTTTGTAATTTTTTTTGTAT
1 TTTTTGT-ATTTTTCTTGTAT
*
503747 TTTTTCTATT
1 TTTTTGTATT
503757 GATTGAATCT
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
20 10 0.36
21 18 0.64
ACGTcount: A:0.12, C:0.04, G:0.08, T:0.76
Consensus pattern (20 bp):
TTTTTGTATTTTTCTTGTAT
Found at i:504642 original size:42 final size:42
Alignment explanation
Indices: 504583--504746 Score: 224
Period size: 42 Copynumber: 3.9 Consensus size: 42
504573 ATATGGTAGC
* * *
504583 TTCAATCTGCCCCATGATGGTGGTAAAAGATTGGATGAGGTT
1 TTCAATCTGCCCCATGATCGAGGTAAGAGATTGGATGAGGTT
504625 TTCAATCTGCCCCATGATCGAGGTAAGAGATTGGAT--GGTAT
1 TTCAATCTGCCCCATGATCGAGGTAAGAGATTGGATGAGGT-T
* * *
504666 CTTCAATCTGCCCCATGATTGGGGTAAGACATTGGATGAGGTT
1 -TTCAATCTGCCCCATGATCGAGGTAAGAGATTGGATGAGGTT
* *
504709 TTCAATTTGCCCCATGATCAAGGTAAGAGATTGGATGA
1 TTCAATCTGCCCCATGATCGAGGTAAGAGATTGGATGA
504747 CTTCATCCTG
Statistics
Matches: 107, Mismatches: 11, Indels: 8
0.85 0.09 0.06
Matches are distributed among these distances:
40 3 0.03
41 1 0.01
42 99 0.93
43 1 0.01
44 3 0.03
ACGTcount: A:0.27, C:0.16, G:0.27, T:0.30
Consensus pattern (42 bp):
TTCAATCTGCCCCATGATCGAGGTAAGAGATTGGATGAGGTT
Found at i:504720 original size:84 final size:84
Alignment explanation
Indices: 504575--504745 Score: 281
Period size: 84 Copynumber: 2.0 Consensus size: 84
504565 CTTCTTTAAT
*
504575 ATGGTAGCTTCAATCTGCCCCATGATGGTGGTAAAAGATTGGATGAGGTTTTCAATCTGCCCCAT
1 ATGGTAGCTTCAATCTGCCCCATGATGGTGGTAAAACATTGGATGAGGTTTTCAATCTGCCCCAT
*
504640 GATCGAGGTAAGAGATTGG
66 GATCAAGGTAAGAGATTGG
* * *
504659 ATGGTATCTTCAATCTGCCCCATGATTGG-GGTAAGACATTGGATGAGGTTTTCAATTTGCCCCA
1 ATGGTAGCTTCAATCTGCCCCATGA-TGGTGGTAAAACATTGGATGAGGTTTTCAATCTGCCCCA
504723 TGATCAAGGTAAGAGATTGG
65 TGATCAAGGTAAGAGATTGG
504743 ATG
1 ATG
504746 ACTTCATCCT
Statistics
Matches: 81, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
84 78 0.96
85 3 0.04
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.30
Consensus pattern (84 bp):
ATGGTAGCTTCAATCTGCCCCATGATGGTGGTAAAACATTGGATGAGGTTTTCAATCTGCCCCAT
GATCAAGGTAAGAGATTGG
Found at i:504952 original size:78 final size:77
Alignment explanation
Indices: 504581--505404 Score: 848
Period size: 78 Copynumber: 10.5 Consensus size: 77
504571 TAATATGGTA
* * * *
504581 GCTTCAATCTGCCCCATGAT-GGTGGTAAAAGATTGGATGAGGTTTTCAATCTGCCC-CATGA-T
1 GCTTCAATCTG-CCCATGATCGG-GGTAAGAGATTGG-TG-TGTCTTCAATCTGCCCTC-TAATT
* *
504643 CGAGGTAAGAGATTGGAT
61 AG-GGTAAAAGATTGGAT
* * * * * *
504661 GGTATCTTCAATCTGCCCCATGATTGGGGTAAGACATTGGATGAGGTTTTCAATTTGCCC-CATG
1 -G---CTTCAATCTG-CCCATGATCGGGGTAAGAGATTGG-TG-TGTCTTCAATCTGCCCTC-TA
* * *
504725 ATCAAGGTAAGAGATTGGAT
58 ATTAGGGTAAAAGATTGGAT
* * * ** * * * *
504745 GACTTC-ATCCTGCCCTGTGGTCGGGGTAAAAGATCAGTGTGTCTTTAATCTGCCTTTTGATTAG
1 G-CTTCAAT-CTGCCC-ATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTGCCCTCTAATTAG
504809 GGTAAAAGATTGGAT
63 GGTAAAAGATTGGAT
* * *
504824 GCTTCAATCTGTCCATGATCGAGGTAAGAGATCGGTGTGTCTTCAATCTGCCCTCTAATTAGGGT
1 GCTTCAATCTGCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTGCCCTCTAATTAGGGT
*
504889 AAAAGATTAGAT
66 AAAAGATTGGAT
* * * *
504901 GCTTCAATATGCCTCATGATCGGGGAAAGAGATTTGTGTGTCTTCAGTCTGCCCTCTAATTAGGG
1 GCTTCAATCTGCC-CATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTGCCCTCTAATTAGGG
*
504966 TAAAAGATTGAAT
65 TAAAAGATTGGAT
* * * ** * * *
504979 GCTTCAATCTGCCTCATGATTGAGGTAAAAGATCAGTGTGTCTTCAATTTACCCTCTGATTAGGG
1 GCTTCAATCTGCC-CATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTGCCCTCTAATTAGGG
505044 TAAAAGATTGGAT
65 TAAAAGATTGGAT
* * *
505057 GCTTCACTCTGCCCCATGATCGGGGTAAGAGATTGGTATGTCTTCAATCTGCCCTCTGATTAGGG
1 GCTTCAATCTG-CCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTGCCCTCTAATTAGGG
*
505122 TAAAATATTGGAT
65 TAAAAGATTGGAT
* * * * * *
505135 GCTTCAATCTGCCCTATTAACGAGGTAAGAGATTGGTGTGTATTCAATCTACTCTCTAATTAGGG
1 GCTTCAATCTGCCC-ATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTGCCCTCTAATTAGGG
*
505200 TAAAAGATTGAAT
65 TAAAAGATTGGAT
* * *
505213 GCTTCATTCTGCCCCATGATCGGGGTAAGAGATTGGTGTGTCTTTAATTTGCCCTCTAATTAGGG
1 GCTTCAATCTG-CCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTGCCCTCTAATTAGGG
505278 TAAAAGATTGGAT
65 TAAAAGATTGGAT
* *
505291 GTTTCAATTTGCCCTATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTGCCCTCTAATTAGGG
1 GCTTCAATCTGCCC-ATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTGCCCTCTAATTAGGG
* *
505356 TAAAAGATCGAAT
65 TAAAAGATTGGAT
* *
505369 GCTTCGATCTGCCTCATGATCGGGGTATGAGATTGG
1 GCTTCAATCTGCC-CATGATCGGGGTAAGAGATTGG
505405 ATGGTAGCTT
Statistics
Matches: 631, Mismatches: 97, Indels: 33
0.83 0.13 0.04
Matches are distributed among these distances:
77 70 0.11
78 421 0.67
79 39 0.06
80 7 0.01
81 22 0.03
83 1 0.00
84 69 0.11
85 2 0.00
ACGTcount: A:0.26, C:0.17, G:0.25, T:0.32
Consensus pattern (77 bp):
GCTTCAATCTGCCCATGATCGGGGTAAGAGATTGGTGTGTCTTCAATCTGCCCTCTAATTAGGGT
AAAAGATTGGAT
Found at i:505659 original size:42 final size:42
Alignment explanation
Indices: 505547--505662 Score: 119
Period size: 42 Copynumber: 2.8 Consensus size: 42
505537 TAGAGATGTA
* * **
505547 AGATTTGCCTTTGCAGCTTCAATGTAGCCCTT-TACAACTTTG
1 AGATTCGCCTTTGCAGCTTCAATCTA-CTTTTCTACAACTTTG
* * * *
505589 AGATTCGCCTTTACGGCTTTAATCTACTTTTCTA-AAGTCTTG
1 AGATTCGCCTTTGCAGCTTCAATCTACTTTTCTACAACT-TTG
*
505631 AGATTCGCCTTTGCAGCTTCAATTTACTTTTC
1 AGATTCGCCTTTGCAGCTTCAATCTACTTTTC
505663 CTCATCTCCA
Statistics
Matches: 60, Mismatches: 12, Indels: 4
0.79 0.16 0.05
Matches are distributed among these distances:
41 6 0.10
42 54 0.90
ACGTcount: A:0.21, C:0.23, G:0.15, T:0.41
Consensus pattern (42 bp):
AGATTCGCCTTTGCAGCTTCAATCTACTTTTCTACAACTTTG
Found at i:505758 original size:49 final size:49
Alignment explanation
Indices: 505705--505873 Score: 169
Period size: 49 Copynumber: 3.4 Consensus size: 49
505695 GAATTAATCC
* * * *
505705 TTCCCTTCACATCTCTAAGGTATAAGGTTCATCATTGTGGCTTCAACCT
1 TTCCCTCCACATCTCTAAGGTACAAGGTTTATCATTGCGGCTTCAACCT
* * * * * * *
505754 TTCCCTCCATATCTCCATGGTACAAGATTTACCATTGCGACTTCAATCT
1 TTCCCTCCACATCTCTAAGGTACAAGGTTTATCATTGCGGCTTCAACCT
* * * *
505803 TTCTCAT-CACATCTCTAAGGTACAAGGTTTGTTATTGGGGCTTCAACCT
1 TTC-CCTCCACATCTCTAAGGTACAAGGTTTATCATTGCGGCTTCAACCT
* *
505852 TTCCCTCCATATCTCTAGGGTA
1 TTCCCTCCACATCTCTAAGGTA
505874 TTAGATTTGC
Statistics
Matches: 93, Mismatches: 25, Indels: 4
0.76 0.20 0.03
Matches are distributed among these distances:
48 2 0.02
49 89 0.96
50 2 0.02
ACGTcount: A:0.22, C:0.27, G:0.14, T:0.36
Consensus pattern (49 bp):
TTCCCTCCACATCTCTAAGGTACAAGGTTTATCATTGCGGCTTCAACCT
Found at i:505900 original size:98 final size:98
Alignment explanation
Indices: 505666--505905 Score: 284
Period size: 98 Copynumber: 2.4 Consensus size: 98
505656 ACTTTTCCTC
* * * * * * *
505666 ATCTCCAGGGTATGAGATTCACCGTTGTGGAATTAATCCTTCCCTTCACATCTCTAAGGTATAAG
1 ATCTCCAGGGTATAAGATTTACCGTTGCGGATTTAATCTTTCCCATCACATCTCTAAGGTACAAG
*
505731 GTTCATCATTGTGGCTTCAACCTTTCCCTCCAT
66 GTTCATCATTGGGGCTTCAACCTTTCCCTCCAT
* * * * *
505764 ATCTCCATGGTACAAGATTTACCATTGC-GACTTCAATCTTTCTCATCACATCTCTAAGGTACAA
1 ATCTCCAGGGTATAAGATTTACCGTTGCGGA-TTTAATCTTTCCCATCACATCTCTAAGGTACAA
** *
505828 GGTTTGTTATTGGGGCTTCAACCTTTCCCTCCAT
65 GGTTCATCATTGGGGCTTCAACCTTTCCCTCCAT
* * * *
505862 ATCTCTAGGGTATTAGATTTGCCGTTGCGGTTTTAATCTTTCCC
1 ATCTCCAGGGTATAAGATTTACCGTTGCGGATTTAATCTTTCCC
505906 TTCAAACCTG
Statistics
Matches: 115, Mismatches: 25, Indels: 4
0.80 0.17 0.03
Matches are distributed among these distances:
97 2 0.02
98 112 0.97
99 1 0.01
ACGTcount: A:0.22, C:0.25, G:0.16, T:0.37
Consensus pattern (98 bp):
ATCTCCAGGGTATAAGATTTACCGTTGCGGATTTAATCTTTCCCATCACATCTCTAAGGTACAAG
GTTCATCATTGGGGCTTCAACCTTTCCCTCCAT
Found at i:506640 original size:11 final size:10
Alignment explanation
Indices: 506619--506657 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
506609 TCGCCCTCTC
506619 CTTTTTTTTT
1 CTTTTTTTTT
506629 CTTTTCTTTTT
1 CTTTT-TTTTT
* *
506640 CTTTTTCTCT
1 CTTTTTTTTT
506650 CTTTTTTT
1 CTTTTTTT
506658 GGGTGAAATA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
10 15 0.60
11 10 0.40
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (10 bp):
CTTTTTTTTT
Found at i:506652 original size:16 final size:15
Alignment explanation
Indices: 506614--506657 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
506604 TCACCTCGCC
*
506614 CTCTCCTTTTTTTTT
1 CTCTCTTTTTTTTTT
*
506629 CTTTTCTTTTTCTTTTT
1 C-TCTCTTTTT-TTTTT
506646 CTCTCTTTTTTT
1 CTCTCTTTTTTT
506658 GGGTGAAATA
Statistics
Matches: 24, Mismatches: 3, Indels: 4
0.77 0.10 0.13
Matches are distributed among these distances:
15 3 0.12
16 15 0.62
17 6 0.25
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (15 bp):
CTCTCTTTTTTTTTT
Found at i:510544 original size:7 final size:7
Alignment explanation
Indices: 510532--510567 Score: 58
Period size: 7 Copynumber: 5.4 Consensus size: 7
510522 ATACAGGCAA
510532 AAAAAGC
1 AAAAAGC
510539 AAAAAGC
1 AAAAAGC
510546 AAAAAGC
1 AAAAAGC
510553 -AAAAGC
1 AAAAAGC
510559 -AAAAGC
1 AAAAAGC
510565 AAA
1 AAA
510568 GGAAACAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 12 0.43
7 16 0.57
ACGTcount: A:0.72, C:0.14, G:0.14, T:0.00
Consensus pattern (7 bp):
AAAAAGC
Found at i:510549 original size:6 final size:6
Alignment explanation
Indices: 510533--510567 Score: 52
Period size: 6 Copynumber: 5.5 Consensus size: 6
510523 TACAGGCAAA
510533 AAAAGC AAAAAGC AAAAAGC AAAAGC AAAAGC AAA
1 AAAAGC -AAAAGC -AAAAGC AAAAGC AAAAGC AAA
510568 GGAAACAAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
6 15 0.54
7 13 0.46
ACGTcount: A:0.71, C:0.14, G:0.14, T:0.00
Consensus pattern (6 bp):
AAAAGC
Found at i:511661 original size:104 final size:107
Alignment explanation
Indices: 511420--511661 Score: 285
Period size: 109 Copynumber: 2.3 Consensus size: 107
511410 TTTAAACGAA
* * ** *
511420 ATATTTGATTACTTAGGTTCAAGAAAAACTCATACCCAACACGTTAGGGCACAATTTTTCGAGTC
1 ATATTTAATTACTTAGGTTCAAGAAAAACTCACACCCAACACGTTAGGGCACAATTCCTCGACTC
** * *
511485 CCCTAAAATACCAGAATATTGAGCATTAATTGGTTCCAAATAGG
66 CCCTAAAATAAAAGAACACT-AGCATTAATT-GTTCCAAATAGG
*
511529 ATATTTAATTATTTAGGTTCAAAGAAAAA-TCACACCCAACACGTTAGGGCACAATTCCTCGACT
1 ATATTTAATTACTTAGGTTC-AAGAAAAACTCACACCCAACACGTTAGGGCACAATTCCTCGACT
* * * **
511593 TCCCTAAAATAAAATAACACT-GCCTTAATT-TT-TGAATAGG
65 CCCCTAAAATAAAAGAACACTAGCATTAATTGTTCCAAATAGG
511633 ATATTTAATTACTTAGGTTCGAAGAAAAA
1 ATATTTAATTACTTAGGTTC-AAGAAAAA
511662 ATTGTACCCA
Statistics
Matches: 115, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
104 33 0.29
105 2 0.02
107 8 0.07
109 64 0.56
110 8 0.07
ACGTcount: A:0.38, C:0.18, G:0.14, T:0.30
Consensus pattern (107 bp):
ATATTTAATTACTTAGGTTCAAGAAAAACTCACACCCAACACGTTAGGGCACAATTCCTCGACTC
CCCTAAAATAAAAGAACACTAGCATTAATTGTTCCAAATAGG
Found at i:511707 original size:104 final size:104
Alignment explanation
Indices: 511420--511728 Score: 266
Period size: 109 Copynumber: 2.9 Consensus size: 104
511410 TTTAAACGAA
* * * ** *
511420 ATATTTGATTACTTAGGTTC-AAGAAAAACTCATACCCAACACGTTAGGGCACAATTTTTCGAGT
1 ATATTTAATTACTTAGGTTCAAAGAAAAA-TCACACCCAACACGTTAGAGCACAATTCCTCGACT
* * * * * **
511484 CCCCTAAAATACCAG-AATATTGAGCATTAATTGGTTCCAAATAGG
65 CCCCTAAAATA-AAGAAACACT--GCCTCAATT--TT-TGAATAGG
* * *
511529 ATATTTAATTATTTAGGTTCAAAGAAAAATCACACCCAACACGTTAGGGCACAATTCCTCGACTT
1 ATATTTAATTACTTAGGTTCAAAGAAAAATCACACCCAACACGTTAGAGCACAATTCCTCGACTC
*
511594 CCCTAAAATAAA-ATAACACTGCCTTAATTTTTGAATAGG
66 CCCTAAAATAAAGA-AACACTGCCTCAATTTTTGAATAGG
* *** ** * * *
511633 ATATTTAATTACTTAGGTTCGAAGAAAAAATTGTACCCAGTACGTTTGAGCACAATTTCTCGAGT
1 ATATTTAATTACTTAGGTTCAAAG-AAAAATCACACCCAACACGTTAGAGCACAATTCCTCGACT
*
511698 CCCCT-AAATAAAGAAACATTGCCTCAATTTT
65 CCCCTAAAATAAAGAAACACTGCCTCAATTTT
511729 GAAAATATTT
Statistics
Matches: 168, Mismatches: 27, Indels: 15
0.80 0.13 0.07
Matches are distributed among these distances:
104 50 0.30
105 38 0.23
107 8 0.05
108 1 0.01
109 63 0.38
110 8 0.05
ACGTcount: A:0.37, C:0.19, G:0.14, T:0.30
Consensus pattern (104 bp):
ATATTTAATTACTTAGGTTCAAAGAAAAATCACACCCAACACGTTAGAGCACAATTCCTCGACTC
CCCTAAAATAAAGAAACACTGCCTCAATTTTTGAATAGG
Found at i:511795 original size:7 final size:7
Alignment explanation
Indices: 511783--511812 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
511773 TTGATTAAAA
511783 TTATTTT
1 TTATTTT
511790 TTATTTT
1 TTATTTT
511797 TTA-TTT
1 TTATTTT
511803 TTATTTT
1 TTATTTT
511810 TTA
1 TTA
511813 AATGAGCATG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (7 bp):
TTATTTT
Found at i:511805 original size:13 final size:13
Alignment explanation
Indices: 511787--511812 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
511777 TTAAAATTAT
511787 TTTTTATTTTTTA
1 TTTTTATTTTTTA
511800 TTTTTATTTTTTA
1 TTTTTATTTTTTA
511813 AATGAGCATG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (13 bp):
TTTTTATTTTTTA
Found at i:512116 original size:30 final size:31
Alignment explanation
Indices: 512078--512193 Score: 123
Period size: 30 Copynumber: 3.8 Consensus size: 31
512068 GGAAAAACGA
512078 GGTCAAAAATAAAATTTTGGAAAG-TTTAGG
1 GGTCAAAAATAAAATTTTGGAAAGTTTTAGG
* * * *
512108 GGTTAAAAACAAAACTTTGGAAAGTTTTA-A
1 GGTCAAAAATAAAATTTTGGAAAGTTTTAGG
* *
512138 GGTCAAAAATAAATTTTTGTAAAGTTTTA-G
1 GGTCAAAAATAAAATTTTGGAAAGTTTTAGG
* *
512168 GGTC-AAATTCAAATTTTTGGAAAGTT
1 GGTCAAAAAT-AAAATTTTGGAAAGTT
512194 CGAGGTTTAA
Statistics
Matches: 72, Mismatches: 12, Indels: 4
0.82 0.14 0.05
Matches are distributed among these distances:
29 4 0.06
30 64 0.89
31 4 0.06
ACGTcount: A:0.41, C:0.05, G:0.19, T:0.34
Consensus pattern (31 bp):
GGTCAAAAATAAAATTTTGGAAAGTTTTAGG
Found at i:512187 original size:60 final size:60
Alignment explanation
Indices: 512077--512193 Score: 155
Period size: 60 Copynumber: 1.9 Consensus size: 60
512067 AGGAAAAACG
*
512077 AGGTCAAAAATAAAATTTTGGAAAGTTTAGGGGTTAAAAACAAAACTTTGGAAAGTTTTA
1 AGGTCAAAAATAAAATTTTGGAAAGTTTAGGGGTCAAAAACAAAACTTTGGAAAGTTTTA
* * ** **
512137 AGGTCAAAAATAAATTTTTGTAAAGTTTTA-GGGTCAAATTCAAATTTTTGGAAAGTT
1 AGGTCAAAAATAAAATTTTGGAAAG-TTTAGGGGTCAAAAACAAAACTTTGGAAAGTT
512194 CGAGGTTTAA
Statistics
Matches: 49, Mismatches: 7, Indels: 2
0.84 0.12 0.03
Matches are distributed among these distances:
60 45 0.92
61 4 0.08
ACGTcount: A:0.42, C:0.05, G:0.19, T:0.34
Consensus pattern (60 bp):
AGGTCAAAAATAAAATTTTGGAAAGTTTAGGGGTCAAAAACAAAACTTTGGAAAGTTTTA
Found at i:514706 original size:15 final size:16
Alignment explanation
Indices: 514686--514717 Score: 57
Period size: 15 Copynumber: 2.1 Consensus size: 16
514676 TAGGATTCAG
514686 TTATGCATGAT-GATA
1 TTATGCATGATAGATA
514701 TTATGCATGATAGATA
1 TTATGCATGATAGATA
514717 T
1 T
514718 GGAATGTATT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 11 0.69
16 5 0.31
ACGTcount: A:0.34, C:0.06, G:0.19, T:0.41
Consensus pattern (16 bp):
TTATGCATGATAGATA
Found at i:528578 original size:3 final size:3
Alignment explanation
Indices: 528570--528594 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
528560 TCCGAGGACA
528570 CCT CCT CCT CCT CCT CCT CCT CCT C
1 CCT CCT CCT CCT CCT CCT CCT CCT C
528595 TGCTTCTGCC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.00, C:0.68, G:0.00, T:0.32
Consensus pattern (3 bp):
CCT
Found at i:531768 original size:75 final size:75
Alignment explanation
Indices: 531645--531795 Score: 302
Period size: 75 Copynumber: 2.0 Consensus size: 75
531635 ATGTCTTGCT
531645 ACAAAGCATGAATGTAGATTTAGAAGTTCCTACAGCAGAAATCTCATAGCTCTAGTTATATCTTG
1 ACAAAGCATGAATGTAGATTTAGAAGTTCCTACAGCAGAAATCTCATAGCTCTAGTTATATCTTG
531710 TTTGTTTCAA
66 TTTGTTTCAA
531720 ACAAAGCATGAATGTAGATTTAGAAGTTCCTACAGCAGAAATCTCATAGCTCTAGTTATATCTTG
1 ACAAAGCATGAATGTAGATTTAGAAGTTCCTACAGCAGAAATCTCATAGCTCTAGTTATATCTTG
531785 TTTGTTTCAA
66 TTTGTTTCAA
531795 A
1 A
531796 TCAATATTTT
Statistics
Matches: 76, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
75 76 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (75 bp):
ACAAAGCATGAATGTAGATTTAGAAGTTCCTACAGCAGAAATCTCATAGCTCTAGTTATATCTTG
TTTGTTTCAA
Found at i:534134 original size:20 final size:22
Alignment explanation
Indices: 534099--534140 Score: 61
Period size: 20 Copynumber: 2.0 Consensus size: 22
534089 ATCCATGTTG
*
534099 ATATATTTATTTAAATT-TTTA
1 ATATATTTATTCAAATTATTTA
534120 ATATA-TTATTCAAATTATTTA
1 ATATATTTATTCAAATTATTTA
534141 TTTAAATATT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 10 0.53
21 9 0.47
ACGTcount: A:0.40, C:0.02, G:0.00, T:0.57
Consensus pattern (22 bp):
ATATATTTATTCAAATTATTTA
Found at i:540069 original size:36 final size:36
Alignment explanation
Indices: 540022--540183 Score: 218
Period size: 36 Copynumber: 4.5 Consensus size: 36
540012 AGCCTTATGA
* *
540022 TCTAATCGAGACATAAGCTCTTCCTTAGCATTACGC
1 TCTAATCGAGACGTAAGCACTTCCTTAGCATTACGC
* * *
540058 TCTAACCGAGACGTAAGCACTTTCATAGCATTACGC
1 TCTAATCGAGACGTAAGCACTTCCTTAGCATTACGC
*
540094 TCTAATCGAGATGTAAGCACTTCCTTAGCATTACGC
1 TCTAATCGAGACGTAAGCACTTCCTTAGCATTACGC
* * * *
540130 TCTAATCGAGACGTATGCA-ATCACTTAACATTATGC
1 TCTAATCGAGACGTAAGCACTTC-CTTAGCATTACGC
540166 TCTAATCGAGACGTAAGC
1 TCTAATCGAGACGTAAGC
540184 TCTTTCATTG
Statistics
Matches: 110, Mismatches: 15, Indels: 2
0.87 0.12 0.02
Matches are distributed among these distances:
35 2 0.02
36 108 0.98
ACGTcount: A:0.30, C:0.25, G:0.16, T:0.28
Consensus pattern (36 bp):
TCTAATCGAGACGTAAGCACTTCCTTAGCATTACGC
Found at i:542196 original size:56 final size:56
Alignment explanation
Indices: 542116--542231 Score: 232
Period size: 56 Copynumber: 2.1 Consensus size: 56
542106 TTTTATTTTT
542116 AATAGCAATTAACTGTTACATTTTTTTTGCAATTTACTCCTTTTCCTTAATTAATG
1 AATAGCAATTAACTGTTACATTTTTTTTGCAATTTACTCCTTTTCCTTAATTAATG
542172 AATAGCAATTAACTGTTACATTTTTTTTGCAATTTACTCCTTTTCCTTAATTAATG
1 AATAGCAATTAACTGTTACATTTTTTTTGCAATTTACTCCTTTTCCTTAATTAATG
542228 AATA
1 AATA
542232 AATCATCAAA
Statistics
Matches: 60, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
56 60 1.00
ACGTcount: A:0.30, C:0.16, G:0.07, T:0.47
Consensus pattern (56 bp):
AATAGCAATTAACTGTTACATTTTTTTTGCAATTTACTCCTTTTCCTTAATTAATG
Found at i:543158 original size:94 final size:94
Alignment explanation
Indices: 543041--543227 Score: 320
Period size: 94 Copynumber: 2.0 Consensus size: 94
543031 TATTAAAGGG
543041 TTTGATAAATATTTTTATGTTTGAGATTATTTAGGAATATAAAAAATTGAGTTATTTTAACGTTA
1 TTTGATAAATATTTTTATGTTTGAGATTATTTAGGAATATAAAAAATTGAGTTATTTTAACGTTA
543106 TTTATTTAATTACAAAGTATATATATATA
66 TTTATTTAATTACAAAGTATATATATATA
* *** * *
543135 TTTGATAAATATTTTTATTTTTGAGATTATTTAGGAATATTGGAAATTGGGTTGTTTTAACGTTA
1 TTTGATAAATATTTTTATGTTTGAGATTATTTAGGAATATAAAAAATTGAGTTATTTTAACGTTA
543200 TTTATTTAATTACAAAGTATATATATAT
66 TTTATTTAATTACAAAGTATATATATAT
543228 TAATATATGT
Statistics
Matches: 87, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
94 87 1.00
ACGTcount: A:0.36, C:0.02, G:0.12, T:0.49
Consensus pattern (94 bp):
TTTGATAAATATTTTTATGTTTGAGATTATTTAGGAATATAAAAAATTGAGTTATTTTAACGTTA
TTTATTTAATTACAAAGTATATATATATA
Found at i:546968 original size:29 final size:28
Alignment explanation
Indices: 546930--546994 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 28
546920 GTTATTTATG
*
546930 TGATGATTTTG-AGTTGTGATATCAGTATGA
1 TGAT-ATTTTGCA-TTGTGATATC-GCATGA
* *
546960 TGTTATTTTGCATTGTGTTATCGCATGA
1 TGATATTTTGCATTGTGATATCGCATGA
546988 TGATATT
1 TGATATT
546995 GCATCATATA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
28 11 0.37
29 15 0.50
30 4 0.13
ACGTcount: A:0.23, C:0.06, G:0.23, T:0.48
Consensus pattern (28 bp):
TGATATTTTGCATTGTGATATCGCATGA
Found at i:548405 original size:36 final size:36
Alignment explanation
Indices: 548340--548513 Score: 186
Period size: 36 Copynumber: 4.8 Consensus size: 36
548330 TTGAGCTGAA
* * * *
548340 ATAGCCTTATGCTCTAACCTAGACATAAGCTCTTCC
1 ATAGCATTATGCTCTAACCGAGACGTAAGCACTTCC
* * *
548376 TTAGCATTACGCTCTAACCGAGACGTAAGCACTTTC
1 ATAGCATTATGCTCTAACCGAGACGTAAGCACTTCC
* * * * * *
548412 ACAGCATTACGCTCTAAGCAAGACGTATGCACTTTC
1 ATAGCATTATGCTCTAACCGAGACGTAAGCACTTCC
* *
548448 ACAGCATTGTGCTCTAACCGAGACGTAAGCACTTCC
1 ATAGCATTATGCTCTAACCGAGACGTAAGCACTTCC
* * *
548484 TTAGCATTATGCTCTAATCGAGATGTAAGC
1 ATAGCATTATGCTCTAACCGAGACGTAAGC
548514 TCTTTCATTG
Statistics
Matches: 115, Mismatches: 23, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
36 115 1.00
ACGTcount: A:0.29, C:0.27, G:0.17, T:0.28
Consensus pattern (36 bp):
ATAGCATTATGCTCTAACCGAGACGTAAGCACTTCC
Found at i:556511 original size:7 final size:7
Alignment explanation
Indices: 556499--556524 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
556489 AGGAAAGAAA
556499 GATGAGG
1 GATGAGG
556506 GATGAGG
1 GATGAGG
556513 GATGAGG
1 GATGAGG
556520 GATGA
1 GATGA
556525 TTAGGAATGG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.31, C:0.00, G:0.54, T:0.15
Consensus pattern (7 bp):
GATGAGG
Found at i:565489 original size:20 final size:18
Alignment explanation
Indices: 565465--565516 Score: 70
Period size: 20 Copynumber: 2.8 Consensus size: 18
565455 AGCAGTATTT
565465 TATTAATTTAATATTAAA
1 TATTAATTTAATATTAAA
*
565483 GTGATTATTTTAATATTAAA
1 -T-ATTAATTTAATATTAAA
565503 T-TTAATTTAATATT
1 TATTAATTTAATATT
565517 TGTCTTGTAG
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 12 0.40
19 2 0.07
20 16 0.53
ACGTcount: A:0.42, C:0.00, G:0.04, T:0.54
Consensus pattern (18 bp):
TATTAATTTAATATTAAA
Found at i:579892 original size:15 final size:15
Alignment explanation
Indices: 579874--579973 Score: 61
Period size: 15 Copynumber: 7.1 Consensus size: 15
579864 CCAATGAAAA
* *
579874 AGCATGAGATGAAGG
1 AGCAAGAGAAGAAGG
579889 AGCAAGAGAAGAA-G
1 AGCAAGAGAAGAAGG
**
579903 AG-AA-AGAAGAAAAA
1 AGCAAGAGAAG-AAGG
* * *
579917 ACCATGAGATGAAGG
1 AGCAAGAGAAGAAGG
579932 AGCAAGAGAAGAA-G
1 AGCAAGAGAAGAAGG
*
579946 AG-AA-AGAAGAA-A
1 AGCAAGAGAAGAAGG
*
579958 AGGAAGAGAAGAAGG
1 AGCAAGAGAAGAAGG
579973 A
1 A
579974 AGAAGAAGAA
Statistics
Matches: 65, Mismatches: 13, Indels: 14
0.71 0.14 0.15
Matches are distributed among these distances:
12 14 0.22
13 8 0.12
14 14 0.22
15 25 0.38
16 4 0.06
ACGTcount: A:0.57, C:0.05, G:0.34, T:0.04
Consensus pattern (15 bp):
AGCAAGAGAAGAAGG
Found at i:579929 original size:43 final size:43
Alignment explanation
Indices: 579870--579958 Score: 169
Period size: 43 Copynumber: 2.1 Consensus size: 43
579860 GGAGCCAATG
*
579870 AAAAAGCATGAGATGAAGGAGCAAGAGAAGAAGAGAAAGAAGA
1 AAAAACCATGAGATGAAGGAGCAAGAGAAGAAGAGAAAGAAGA
579913 AAAAACCATGAGATGAAGGAGCAAGAGAAGAAGAGAAAGAAGA
1 AAAAACCATGAGATGAAGGAGCAAGAGAAGAAGAGAAAGAAGA
579956 AAA
1 AAA
579959 GGAAGAGAAG
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 45 1.00
ACGTcount: A:0.60, C:0.06, G:0.30, T:0.04
Consensus pattern (43 bp):
AAAAACCATGAGATGAAGGAGCAAGAGAAGAAGAGAAAGAAGA
Found at i:580403 original size:17 final size:17
Alignment explanation
Indices: 580378--580421 Score: 61
Period size: 17 Copynumber: 2.6 Consensus size: 17
580368 CATGCATTTC
580378 TTTTAATTGTCATTGCA
1 TTTTAATTGTCATTGCA
* *
580395 TTTTTATTGTCTTTGCA
1 TTTTAATTGTCATTGCA
*
580412 TTTTACTTGT
1 TTTTAATTGT
580422 TTTAGCATTT
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.16, C:0.11, G:0.11, T:0.61
Consensus pattern (17 bp):
TTTTAATTGTCATTGCA
Found at i:580429 original size:17 final size:16
Alignment explanation
Indices: 580378--580431 Score: 56
Period size: 17 Copynumber: 3.2 Consensus size: 16
580368 CATGCATTTC
*
580378 TTTTAATTGTCATTGCA
1 TTTT-ATTGTCTTTGCA
580395 TTTTTATTGTCTTTGCA
1 -TTTTATTGTCTTTGCA
580412 TTTTACTTGT-TTTAGCA
1 TTTTA-TTGTCTTT-GCA
580429 TTT
1 TTT
580432 GCATTGTAGT
Statistics
Matches: 33, Mismatches: 1, Indels: 5
0.85 0.03 0.13
Matches are distributed among these distances:
16 8 0.24
17 21 0.64
18 4 0.12
ACGTcount: A:0.17, C:0.11, G:0.11, T:0.61
Consensus pattern (16 bp):
TTTTATTGTCTTTGCA
Found at i:589443 original size:18 final size:18
Alignment explanation
Indices: 589420--589478 Score: 77
Period size: 18 Copynumber: 3.3 Consensus size: 18
589410 TAATCATTTT
589420 AATATTGAATTAACATAA
1 AATATTGAATTAACATAA
**
589438 AATATT-AGATTAA-ATTT
1 AATATTGA-ATTAACATAA
589455 AATATTGAATTAACATAA
1 AATATTGAATTAACATAA
589473 AATATT
1 AATATT
589479 AGATTAAATT
Statistics
Matches: 34, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
17 14 0.41
18 20 0.59
ACGTcount: A:0.53, C:0.03, G:0.05, T:0.39
Consensus pattern (18 bp):
AATATTGAATTAACATAA
Found at i:589460 original size:17 final size:17
Alignment explanation
Indices: 589438--589496 Score: 75
Period size: 17 Copynumber: 3.4 Consensus size: 17
589428 ATTAACATAA
589438 AATATTAGATTAAATTT
1 AATATTAGATTAAATTT
**
589455 AATATT-GAATTAACATAA
1 AATATTAG-ATTAA-ATTT
589473 AATATTAGATTAAATTT
1 AATATTAGATTAAATTT
589490 AATATTA
1 AATATTA
589497 AATCTTATTA
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
16 1 0.03
17 20 0.57
18 13 0.37
19 1 0.03
ACGTcount: A:0.51, C:0.02, G:0.05, T:0.42
Consensus pattern (17 bp):
AATATTAGATTAAATTT
Found at i:589463 original size:35 final size:35
Alignment explanation
Indices: 589417--589495 Score: 158
Period size: 35 Copynumber: 2.3 Consensus size: 35
589407 ACTTAATCAT
589417 TTTAATATTGAATTAACATAAAATATTAGATTAAA
1 TTTAATATTGAATTAACATAAAATATTAGATTAAA
589452 TTTAATATTGAATTAACATAAAATATTAGATTAAA
1 TTTAATATTGAATTAACATAAAATATTAGATTAAA
589487 TTTAATATT
1 TTTAATATT
589496 AAATCTTATT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 44 1.00
ACGTcount: A:0.49, C:0.03, G:0.05, T:0.43
Consensus pattern (35 bp):
TTTAATATTGAATTAACATAAAATATTAGATTAAA
Done.